Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold211
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1275876
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 151255 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:7357 original size:164 final size:164
Alignment explanation
Indices: 7086--7577 Score: 876
Period size: 164 Copynumber: 3.0 Consensus size: 164
7076 CAGATTTTGC
7086 AGCAAGGCCCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTT
1 AGCAAGGCCCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTT
7151 GTGTGATCCCCATTCAAGGGAACTGCTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTG
66 GTGTGATCCCCATTCAAGGGAACTGCTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTG
7216 TTCAGACAGTGTGTCACATTTTCAACAGGCACAG
131 TTCAGACAGTGTGTCACATTTTCAACAGGCACAG
* *
7250 AGCAAGGCCCAGTTCTTAGAGCCGCCTTTAGTGGGACACATGAAAGACATCTTTAGCTCAAATTT
1 AGCAAGGCCCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTT
*
7315 GTGTGATCCCCATTCAAGGGAACTGCTCTTTACCAAGTTTTATTCCTTGGGGGTATCCATATGTG
66 GTGTGATCCCCATTCAAGGGAACTGCTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTG
*
7380 TTCAGACAGTGTGTCACATGTTCAACAGGCACAG
131 TTCAGACAGTGTGTCACATTTTCAACAGGCACAG
* *
7414 AGCAAAGCCCAGTTCTTAGAGTCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTT
1 AGCAAGGCCCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTT
* * * *
7479 GTGTGATCACCATTCAAGGGAACTGTTCTTTACCAAGTGTTATTCCTTGAGGCTATCCATATGTG
66 GTGTGATCCCCATTCAAGGGAACTGCTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTG
* *
7544 TTCATACAGTGTGTCACATTTTCAACAGGTACAG
131 TTCAGACAGTGTGTCACATTTTCAACAGGCACAG
7578 TTTCAGTTGG
Statistics
Matches: 312, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
164 312 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (164 bp):
AGCAAGGCCCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTT
GTGTGATCCCCATTCAAGGGAACTGCTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTG
TTCAGACAGTGTGTCACATTTTCAACAGGCACAG
Found at i:12686 original size:187 final size:187
Alignment explanation
Indices: 12370--12735 Score: 637
Period size: 187 Copynumber: 2.0 Consensus size: 187
12360 GCTAACAAAA
** *
12370 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAG
1 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAAAAAGTTGTCCTTTTGCAG
* *
12435 ATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCAGATAGTTTATGAAA
66 ATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCAGATAATCTATGAAA
12500 AA-ATTACCAGCTTTTGAACTTAGTCATTTTTAT-GGCAAAATATTGCAAACTAGTTTG
131 AACA-TACCAGCTTTTGAACTTAGTCATTTTT-TGGGCAAAATATTGCAAACTAGTTTG
12557 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAAAAAGTTGTCCTTTTGCAG
1 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAAAAAGTTGTCCTTTTGCAG
* *
12622 ATCAATTGTACATATATCAGTGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATCTATGAAA
66 ATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCAGATAATCTATGAAA
12687 AACATACCAGCTTTTGAACTTAGTCATTTTTTGGGCAAAATATTGCAAA
131 AACATACCAGCTTTTGAACTTAGTCATTTTTTGGGCAAAATATTGCAAA
12736 TACGCCATAT
Statistics
Matches: 170, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
186 1 0.01
187 168 0.99
188 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (187 bp):
GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAAAAAGTTGTCCTTTTGCAG
ATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCAGATAATCTATGAAA
AACATACCAGCTTTTGAACTTAGTCATTTTTTGGGCAAAATATTGCAAACTAGTTTG
Found at i:17642 original size:2 final size:2
Alignment explanation
Indices: 17635--17679 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
17625 CACATAAAAT
17635 GA GA GA GA -A G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17675 GA GA G
1 GA GA G
17680 CGCTCAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21150 original size:4 final size:4
Alignment explanation
Indices: 21141--21213 Score: 146
Period size: 4 Copynumber: 18.2 Consensus size: 4
21131 GATTCGATAG
21141 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
21189 TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC T
21214 TCCAAACCTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:27656 original size:12 final size:12
Alignment explanation
Indices: 27635--27666 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
27625 TGAAAAGTTT
*
27635 ACAACAACGACG
1 ACAACGACGACG
27647 ACAACGACGACG
1 ACAACGACGACG
27659 ACAACGAC
1 ACAACGAC
27667 AGAAAACGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.34, G:0.19, T:0.00
Consensus pattern (12 bp):
ACAACGACGACG
Found at i:28233 original size:126 final size:126
Alignment explanation
Indices: 28005--28235 Score: 275
Period size: 126 Copynumber: 1.8 Consensus size: 126
27995 ACCAGACTCG
* * * * * *
28005 AATCGACCTATATTTGGACGCAATAACACCAGAGTACAATGAAATTGGAATGATCAGACGTTCAA
1 AATCGACCTACATATGGACGCAAGAACACCAGAGTACAATGAAATTGGAATGATAAAAAGTTCAA
** * * *
28070 GTTATAGTGATCATCTTTTACACAAAACAACTGAATCTGTTCGCCCTGCTGATGAAAATCA
66 GCAATAGTGATCAGCTCTTACACAAAACAACTAAATCTGTTCGCCCTGCTGATGAAAATCA
* * * *
28131 AATCGACCTACATATGGACGCAAGATCATCAGAGTACTATGAAATTGGAATGATAAAAAGTTCCA
1 AATCGACCTACATATGGACGCAAGAACACCAGAGTACAATGAAATTGGAATGATAAAAAGTTCAA
* * * *
28196 GCAACTTG-GATCAGCTCTTATATAAAACAATTAAATCTGT
66 GCAA-TAGTGATCAGCTCTTACACAAAACAACTAAATCTGT
28236 CCACTTTGCT
Statistics
Matches: 85, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
126 83 0.98
127 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (126 bp):
AATCGACCTACATATGGACGCAAGAACACCAGAGTACAATGAAATTGGAATGATAAAAAGTTCAA
GCAATAGTGATCAGCTCTTACACAAAACAACTAAATCTGTTCGCCCTGCTGATGAAAATCA
Found at i:66363 original size:2 final size:2
Alignment explanation
Indices: 66356--66407 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
66346 GTAAGTCATT
66356 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
66398 TC TC TC TC TC
1 TC TC TC TC TC
66408 CTGTGCAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:78179 original size:31 final size:32
Alignment explanation
Indices: 78087--78180 Score: 129
Period size: 32 Copynumber: 3.0 Consensus size: 32
78077 TAATTTTTAT
* * *
78087 ATCAGCAGTTTAGTGTCTATAGTTTCATCTTT
1 ATCATCAGTTTAGTGTCTATAGTTTTATCTTC
78119 ATCATCAGTTTAGTGTCTATAGTTTTATCTTC
1 ATCATCAGTTTAGTGTCTATAGTTTTATCTTC
*
78151 ATCATCAGTTT-G-GTGTATAGTTTTTATCTT
1 ATCATCAGTTTAGTGTCTATAG-TTTTATCTT
78181 TGGTATCACT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
30 7 0.12
31 10 0.18
32 40 0.70
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (32 bp):
ATCATCAGTTTAGTGTCTATAGTTTTATCTTC
Found at i:100490 original size:20 final size:20
Alignment explanation
Indices: 100465--100514 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
100455 TAAAAAGTTT
100465 ACAGACGGACAGACAGACGG
1 ACAGACGGACAGACAGACGG
*
100485 ACAGACGGACAGACGGACGG
1 ACAGACGGACAGACAGACGG
100505 ACAGACGGAC
1 ACAGACGGAC
100515 GACGGACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (20 bp):
ACAGACGGACAGACAGACGG
Found at i:100515 original size:4 final size:4
Alignment explanation
Indices: 100468--100521 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
100458 AAAGTTTACA
* * * * *
100468 GACG GACA GACA GACG GACA GACG GACA GACG GACG GACA GACG GAC-
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
100515 GACG GAC
1 GACG GAC
100522 AAAAAGTGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.35, C:0.26, G:0.39, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:111874 original size:21 final size:22
Alignment explanation
Indices: 111844--111889 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
111834 ATTTGGGTCC
*
111844 ACTCGGGGTTTAC-TTGCGTTT
1 ACTCGAGGTTTACTTTGCGTTT
*
111865 ACTCGAGGTTTACTTTGGGTTT
1 ACTCGAGGTTTACTTTGCGTTT
111887 ACT
1 ACT
111890 TTGAAATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.43
Consensus pattern (22 bp):
ACTCGAGGTTTACTTTGCGTTT
Found at i:112083 original size:11 final size:11
Alignment explanation
Indices: 112054--112095 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
112044 CTCTGTGTCC
112054 ACTCTGGGTTT
1 ACTCTGGGTTT
*
112065 GA-TTTGGGTTT
1 -ACTCTGGGTTT
112076 ACTCTGGGTTT
1 ACTCTGGGTTT
*
112087 GCTCTGGGT
1 ACTCTGGGT
112096 CCACTCTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 1 0.04
11 24 0.92
12 1 0.04
ACGTcount: A:0.07, C:0.14, G:0.33, T:0.45
Consensus pattern (11 bp):
ACTCTGGGTTT
Found at i:112101 original size:22 final size:22
Alignment explanation
Indices: 112044--112102 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
112034 TGGGTTTACT
*
112044 CTCTGTGTCCACTCTGGGTTTG
1 CTCTGGGTCCACTCTGGGTTTG
* * **
112066 ATTTGGGTTTACTCTGGGTTTG
1 CTCTGGGTCCACTCTGGGTTTG
112088 CTCTGGGTCCACTCT
1 CTCTGGGTCCACTCT
112103 AGTAAACCCG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.07, C:0.24, G:0.27, T:0.42
Consensus pattern (22 bp):
CTCTGGGTCCACTCTGGGTTTG
Found at i:112117 original size:11 final size:11
Alignment explanation
Indices: 112103--112146 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
112093 GGTCCACTCT
112103 AGTAAACCCGA
1 AGTAAACCCGA
112114 AGTAAACCC-A
1 AGTAAACCCGA
112124 GAGTAAACCCAGAA
1 -AGTAAACCC-G-A
112138 AGTAAACCC
1 AGTAAACCC
112147 AGGGTTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 18 0.62
13 9 0.31
14 1 0.03
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (11 bp):
AGTAAACCCGA
Found at i:112145 original size:24 final size:22
Alignment explanation
Indices: 112103--112148 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
112093 GGTCCACTCT
112103 AGTAAACCCGAAGTAAACCCAG
1 AGTAAACCCGAAGTAAACCCAG
112125 AGTAAACCCAGAAAGTAAACCCAG
1 AGTAAACCC-G-AAGTAAACCCAG
112149 GGTTTAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (22 bp):
AGTAAACCCGAAGTAAACCCAG
Found at i:126116 original size:53 final size:53
Alignment explanation
Indices: 126036--126142 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
126026 CTCGAAGTAG
*
126036 TAAACCATAAACTACTTATGAGAGATATTTACATACCTAATAGTGCACTTTTT
1 TAAACCATAAACTACTTATGAGAGATATTTACATACCTAATAGTGCACTATTT
126089 TAAACCATAAACTACTTATGAGAGATATTTACATACCTAATAGTGCACTATTT
1 TAAACCATAAACTACTTATGAGAGATATTTACATACCTAATAGTGCACTATTT
126142 T
1 T
126143 GAGAAAGTGC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (53 bp):
TAAACCATAAACTACTTATGAGAGATATTTACATACCTAATAGTGCACTATTT
Found at i:155603 original size:397 final size:397
Alignment explanation
Indices: 154870--155667 Score: 1587
Period size: 397 Copynumber: 2.0 Consensus size: 397
154860 AGAGTGTTAA
154870 AAAAGAGGATGATGAGAAAGTAGCTAAAGATAACAATGGTACAGAGTCAAGTGAAATGAAAAATG
1 AAAAGAGGATGATGAGAAAGTAGCTAAAGATAACAATGGTACAGAGTCAAGTGAAATGAAAAATG
154935 TGCCAAATTTCCTAGATGATGTAGATTCTTTGAATGAGAAAAAGTCTTCAAAAAATGAATCTCAG
66 TGCCAAATTTCCTAGATGATGTAGATTCTTTGAATGAGAAAAAGTCTTCAAAAAATGAATCTCAG
155000 GTGAAGTCAAAGAAAAATTATACTCAGAAGGAAGAGAAGAAAGAAAAACCAATGGAACAAGAAGA
131 GTGAAGTCAAAGAAAAATTATACTCAGAAGGAAGAGAAGAAAGAAAAACCAATGGAACAAGAAGA
155065 AAGCAAGGATTTGCTGCCCCTCACAGTGCATAATCTAGAGGATGATGTGAAGAAGGAATCTGAAA
196 AAGCAAGGATTTGCTGCCCCTCACAGTGCATAATCTAGAGGATGATGTGAAGAAGGAATCTGAAA
155130 AAAAGAACGAAGTAAAAGCAAGTGAAAAGATTGATTCCCATCCAACAGAAAAAGAAAATTCTTCT
261 AAAAGAACGAAGTAAAAGCAAGTGAAAAGATTGATTCCCATCCAACAGAAAAAGAAAATTCTTCT
155195 CATGAAATTAAAAAGGAATCGAAAAGCAAGGAAAGTGAAAATTCAGTAGACAATGGCTCCTTAGA
326 CATGAAATTAAAAAGGAATCGAAAAGCAAGGAAAGTGAAAATTCAGTAGACAATGGCTCCTTAGA
*
155260 GGAGAAN
391 GGAGAAG
155267 AAAAGAGGATGATGAGAAAGTAGCTAAAGATAACAATGGTACAGAGTCAAGTGAAATGAAAAATG
1 AAAAGAGGATGATGAGAAAGTAGCTAAAGATAACAATGGTACAGAGTCAAGTGAAATGAAAAATG
155332 TGCCAAATTTCCTAGATGATGTAGATTCTTTGAATGAGAAAAAGTCTTCAAAAAATGAATCTCAG
66 TGCCAAATTTCCTAGATGATGTAGATTCTTTGAATGAGAAAAAGTCTTCAAAAAATGAATCTCAG
155397 GTGAAGTCAAAGAAAAATTATACTCAGAAGGAAGAGAAGAAAGAAAAACCAATGGAACAAGAAGA
131 GTGAAGTCAAAGAAAAATTATACTCAGAAGGAAGAGAAGAAAGAAAAACCAATGGAACAAGAAGA
155462 AAGCAAGGATTTGCTGCCCCTCACAGTGCATAATCTAGAGGATGATGTGAAGAAGGAATCTGAAA
196 AAGCAAGGATTTGCTGCCCCTCACAGTGCATAATCTAGAGGATGATGTGAAGAAGGAATCTGAAA
155527 AAAAGAACGAAGTAAAAGCAAGTGAAAAGATTGATTCCCATCCAACAGAAAAAGAAAATTCTTCT
261 AAAAGAACGAAGTAAAAGCAAGTGAAAAGATTGATTCCCATCCAACAGAAAAAGAAAATTCTTCT
155592 CATGAAATTAAAAAGGAATCGAAAAGCAAGGAAAGTGAAAATTCAGTAGACAATGGCTCCTTAGA
326 CATGAAATTAAAAAGGAATCGAAAAGCAAGGAAAGTGAAAATTCAGTAGACAATGGCTCCTTAGA
155657 GGAGAAG
391 GGAGAAG
155664 AAAA
1 AAAA
155668 ATCCAGAGGG
Statistics
Matches: 400, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
397 400 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (397 bp):
AAAAGAGGATGATGAGAAAGTAGCTAAAGATAACAATGGTACAGAGTCAAGTGAAATGAAAAATG
TGCCAAATTTCCTAGATGATGTAGATTCTTTGAATGAGAAAAAGTCTTCAAAAAATGAATCTCAG
GTGAAGTCAAAGAAAAATTATACTCAGAAGGAAGAGAAGAAAGAAAAACCAATGGAACAAGAAGA
AAGCAAGGATTTGCTGCCCCTCACAGTGCATAATCTAGAGGATGATGTGAAGAAGGAATCTGAAA
AAAAGAACGAAGTAAAAGCAAGTGAAAAGATTGATTCCCATCCAACAGAAAAAGAAAATTCTTCT
CATGAAATTAAAAAGGAATCGAAAAGCAAGGAAAGTGAAAATTCAGTAGACAATGGCTCCTTAGA
GGAGAAG
Found at i:159274 original size:14 final size:14
Alignment explanation
Indices: 159255--159283 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
159245 CTTCTGCATT
159255 CAATAATATTGTAG
1 CAATAATATTGTAG
159269 CAATAATATTGTAG
1 CAATAATATTGTAG
159283 C
1 C
159284 TTTTGTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (14 bp):
CAATAATATTGTAG
Found at i:167908 original size:21 final size:21
Alignment explanation
Indices: 167884--167950 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
167874 AAAAACAATG
167884 TCGTAATAACGAGGTATTTTC
1 TCGTAATAACGAGGTATTTTC
* *
167905 TCGTAATAACGGGGTCTTTTC
1 TCGTAATAACGAGGTATTTTC
**
167926 TCGTAATAACGACATATTTTC
1 TCGTAATAACGAGGTATTTTC
167947 TCGT
1 TCGT
167951 GATTTCTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGTAATAACGAGGTATTTTC
Found at i:168366 original size:43 final size:43
Alignment explanation
Indices: 168305--168414 Score: 139
Period size: 43 Copynumber: 2.5 Consensus size: 43
168295 CATAACTCAG
* * * * *
168305 CCCCCCCCCCCCAAAAAAAATATATAAATAATATATATAACCC
1 CCCCCCCCCCCCAAAAAAAAAAAATAAAAAAAATATATAAACC
*
168348 CCCCCCCCCCCCCAAAAAAAAAAATAAAAAAAATATATAAACC
1 CCCCCCCCCCCCAAAAAAAAAAAATAAAAAAAATATATAAACC
*
168391 CCCCCCCCCCTCTCGAAAAAAAAA
1 CCCCCCCCCC-C-CAAAAAAAAAA
168415 GAAGAACAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 47 0.81
44 1 0.02
45 10 0.17
ACGTcount: A:0.48, C:0.38, G:0.01, T:0.13
Consensus pattern (43 bp):
CCCCCCCCCCCCAAAAAAAAAAAATAAAAAAAATATATAAACC
Found at i:173359 original size:27 final size:28
Alignment explanation
Indices: 173329--173381 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
173319 AACCCAGGTT
173329 TTCTACA-TTGATATCATAACCTAGGCC
1 TTCTACATTTGATATCATAACCTAGGCC
*
173356 TTCTACATTTTATATCATAACCTAGG
1 TTCTACATTTGATATCATAACCTAGG
173382 TTTTTGACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (28 bp):
TTCTACATTTGATATCATAACCTAGGCC
Found at i:173534 original size:27 final size:27
Alignment explanation
Indices: 173504--173573 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
173494 AGTCTCCTGC
*
173504 ATTGATAATAAAACCTACCAATTTTGT
1 ATTGATAATGAAACCTACCAATTTTGT
** * * *
173531 ATTGATTTTGAAACCAATCTATTTTGT
1 ATTGATAATGAAACCTACCAATTTTGT
173558 ATTGATAATGAAACCT
1 ATTGATAATGAAACCT
173574 GTGAACTGGT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (27 bp):
ATTGATAATGAAACCTACCAATTTTGT
Found at i:177554 original size:26 final size:26
Alignment explanation
Indices: 177250--177538 Score: 375
Period size: 26 Copynumber: 11.2 Consensus size: 26
177240 AGGTATTATA
* *
177250 AAATTACATGTAACACAGAACCAGGT
1 AAATTACAGGTCACACAGAACCAGGT
* ** *
177276 AAATAATGGGT-A-ACAGAACCAGTT
1 AAATTACAGGTCACACAGAACCAGGT
* *
177300 GAATTATAGGTCACACAGAACCAGGT
1 AAATTACAGGTCACACAGAACCAGGT
* *
177326 AAATTACAGGTCACACAAAATCAGGT
1 AAATTACAGGTCACACAGAACCAGGT
** *
177352 AAATTACAGGTCACATGGAATCAGGT
1 AAATTACAGGTCACACAGAACCAGGT
** *
177378 AAATTACAGGTCACATGGAACCAAGT
1 AAATTACAGGTCACACAGAACCAGGT
*
177404 AAATTACAGGTCACACAGAAACAGGT
1 AAATTACAGGTCACACAGAACCAGGT
* *
177430 AAATTACAGGTCACACAAAACCAAGT
1 AAATTACAGGTCACACAGAACCAGGT
* *
177456 AAATTACAGTTTACACAGAACCAGGT
1 AAATTACAGGTCACACAGAACCAGGT
177482 AAATTACAGGTCACACAGAACCAGGT
1 AAATTACAGGTCACACAGAACCAGGT
177508 AAATTACAGGTCACACAGAACCAGGT
1 AAATTACAGGTCACACAGAACCAGGT
177534 AAATT
1 AAATT
177539 GCTGGTATCA
Statistics
Matches: 230, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
24 19 0.08
25 2 0.01
26 209 0.91
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (26 bp):
AAATTACAGGTCACACAGAACCAGGT
Found at i:180232 original size:71 final size:71
Alignment explanation
Indices: 180116--180252 Score: 256
Period size: 71 Copynumber: 1.9 Consensus size: 71
180106 CTTGGATAGC
* *
180116 CTAGTCGAATTATTGGGGGCCTTAAAGGAGCGATAGTGAGGACTCATTGATTTAAAATTGCATGT
1 CTAGTCGAATTATTGGGGGCCTTAAAGGAGCGAAAGTGAGGACTCATTAATTTAAAATTGCATGT
180181 CCTAGT
66 CCTAGT
180187 CTAGTCGAATTATTGGGGGCCTTAAAGGAGCGAAAGTGAGGACTCATTAATTTAAAATTGCATGT
1 CTAGTCGAATTATTGGGGGCCTTAAAGGAGCGAAAGTGAGGACTCATTAATTTAAAATTGCATGT
180252 C
66 C
180253 TTATTCAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (71 bp):
CTAGTCGAATTATTGGGGGCCTTAAAGGAGCGAAAGTGAGGACTCATTAATTTAAAATTGCATGT
CCTAGT
Found at i:181012 original size:43 final size:44
Alignment explanation
Indices: 180959--181044 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
180949 GACAGTTGAA
* * *
180959 ACTTTTCATAATAT-ATCTAGTGTCGACCAGGGGACAGGTCGAC
1 ACTTTCCATAACATAATCTACTGTCGACCAGGGGACAGGTCGAC
181002 ACTTTCCATAACATAATCTACTGTCGACCAGGGGACAGGTCGA
1 ACTTTCCATAACATAATCTACTGTCGACCAGGGGACAGGTCGA
181045 TAGTTGACAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 12 0.31
44 27 0.69
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (44 bp):
ACTTTCCATAACATAATCTACTGTCGACCAGGGGACAGGTCGAC
Found at i:181092 original size:58 final size:58
Alignment explanation
Indices: 180999--181111 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
180989 GGGACAGGTC
* *
180999 GACACTTTCCATAACATAATCTACTGTCGACCAGGGGACAGGTCGATAGTTGACAGTT
1 GACACTTCCCATAACATAATCTACTGTCGACCAGGGGACAGGTCGACAGTTGACAGTT
* * * *
181057 GACACTTCCCATAATATACTCTACTGTCGATCAGGGGACAGGTTGACAGTTGACA
1 GACACTTCCCATAACATAATCTACTGTCGACCAGGGGACAGGTCGACAGTTGACA
181112 CTTTTGGGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (58 bp):
GACACTTCCCATAACATAATCTACTGTCGACCAGGGGACAGGTCGACAGTTGACAGTT
Found at i:183354 original size:18 final size:18
Alignment explanation
Indices: 183331--183366 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
183321 ACCTTGAAAG
*
183331 ATAAAGAGAACATATCAA
1 ATAAAGAGAACACATCAA
*
183349 ATAAAGAGTACACATCAA
1 ATAAAGAGAACACATCAA
183367 TTAATTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.14, G:0.11, T:0.17
Consensus pattern (18 bp):
ATAAAGAGAACACATCAA
Found at i:185599 original size:17 final size:17
Alignment explanation
Indices: 185574--185660 Score: 156
Period size: 17 Copynumber: 5.1 Consensus size: 17
185564 CCACGCGTAT
*
185574 TGTCTGACCATAGAAAA
1 TGTCCGACCATAGAAAA
185591 TGTCCGACCATAGAAAA
1 TGTCCGACCATAGAAAA
*
185608 TGTCTGACCATAGAAAA
1 TGTCCGACCATAGAAAA
185625 TGTCCGACCATAGAAAA
1 TGTCCGACCATAGAAAA
185642 TGTCCGACCATAGAAAA
1 TGTCCGACCATAGAAAA
185659 TG
1 TG
185661 CGTACTTAAC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 67 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (17 bp):
TGTCCGACCATAGAAAA
Found at i:192210 original size:33 final size:33
Alignment explanation
Indices: 192151--192221 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
192141 CCCTTCACCT
*
192151 TCCTCTCCCTCCTCCTCCTCCCCTTCCTTCTTC
1 TCCTCTCCCTCCTCCTCCTCCCCTTCCTCCTTC
* * * *
192184 TCCTCTTCCTCTTCCTTCTCCTCTTCCTCCTTC
1 TCCTCTCCCTCCTCCTCCTCCCCTTCCTCCTTC
192217 TCCTC
1 TCCTC
192222 AACTTCTGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (33 bp):
TCCTCTCCCTCCTCCTCCTCCCCTTCCTCCTTC
Found at i:192214 original size:21 final size:21
Alignment explanation
Indices: 192159--192214 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
192149 CTTCCTCTCC
*
192159 CTCCTCCTCCTCCCCTTCCTT
1 CTCCTCCTCCTCCTCTTCCTT
* *
192180 CTTCTCCTCTTCCTCTTCCTT
1 CTCCTCCTCCTCCTCTTCCTT
*
192201 CTCCTCTTCCTCCT
1 CTCCTCCTCCTCCT
192215 TCTCCTCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCTCCTCCTCCTCTTCCTT
Found at i:192220 original size:15 final size:15
Alignment explanation
Indices: 192160--192221 Score: 70
Period size: 15 Copynumber: 3.9 Consensus size: 15
192150 TTCCTCTCCC
* *
192160 TCCTCCTCCTCCCCT
1 TCCTCCTTCTCCTCT
*
192175 TCCTTCTTCTCCTCT
1 TCCTCCTTCTCCTCT
192190 TCCTCTTCCTTCTCCTCT
1 T-C-C-TCCTTCTCCTCT
192208 TCCTCCTTCTCCTC
1 TCCTCCTTCTCCTC
192222 AACTTCTGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 24 0.60
16 2 0.05
17 2 0.05
18 12 0.30
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (15 bp):
TCCTCCTTCTCCTCT
Found at i:192220 original size:21 final size:21
Alignment explanation
Indices: 192162--192220 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 21
192152 CCTCTCCCTC
* *
192162 CTCCTCCTCC-CCTTCCTTCTT
1 CTCCTCTTCCTCCTT-CTCCTT
192183 CTCCTCTTCCT-C-T-TCCTT
1 CTCCTCTTCCTCCTTCTCCTT
192201 CTCCTCTTCCTCCTTCTCCT
1 CTCCTCTTCCTCCTTCTCCT
192221 CAACTTCTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
20 2 0.06
21 14 0.44
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (21 bp):
CTCCTCTTCCTCCTTCTCCTT
Found at i:194482 original size:4 final size:4
Alignment explanation
Indices: 194473--194499 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
194463 TCTAGACCCA
194473 GGAG GGAG GGAG GGAG GGAG GGAG GGA
1 GGAG GGAG GGAG GGAG GGAG GGAG GGA
194500 TTGAACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:206220 original size:2 final size:2
Alignment explanation
Indices: 206213--206252 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
206203 AAAATTACAT
206213 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
206253 ATTATACTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:207557 original size:15 final size:13
Alignment explanation
Indices: 207537--207585 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 13
207527 ATCGTGGTTA
207537 TTTTTTGTTGTTGTT
1 TTTTTTGTT-TT-TT
207552 TTTTTTGTTCTTCTT
1 TTTTTTGTT-TT-TT
207567 TTTTTTCGTTTTTT
1 TTTTTT-GTTTTTT
207581 TTTTT
1 TTTTT
207586 GGGGGGGGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 7 0.23
15 21 0.68
16 3 0.10
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:216624 original size:7 final size:7
Alignment explanation
Indices: 216609--216675 Score: 80
Period size: 7 Copynumber: 9.6 Consensus size: 7
216599 TTTAGATATT
216609 GAATCTC
1 GAATCTC
*
216616 GAATTTC
1 GAATCTC
216623 GAATCTC
1 GAATCTC
216630 GAATCTC
1 GAATCTC
* *
216637 GTATTTC
1 GAATCTC
*
216644 GAATGTC
1 GAATCTC
* *
216651 GTATTTC
1 GAATCTC
216658 GAATCTC
1 GAATCTC
216665 GAATCTC
1 GAATCTC
216672 GAAT
1 GAAT
216676 GATCCTTCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (7 bp):
GAATCTC
Found at i:216634 original size:21 final size:21
Alignment explanation
Indices: 216609--216675 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
216599 TTTAGATATT
216609 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
* *
216630 GAATCTCGTATTTCGAATGTC
1 GAATCTCGAATTTCGAATCTC
* * *
216651 GTATTTCGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
216672 GAAT
1 GAAT
216676 GATCCTTCTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:216659 original size:28 final size:28
Alignment explanation
Indices: 216609--216676 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
216599 TTTAGATATT
*
216609 GAATCTCGAATTTCGAATCTCGAATCTC
1 GAATCTCGAATGTCGAATCTCGAATCTC
* * * *
216637 GTATTTCGAATGTCGTATTTCGAATCTC
1 GAATCTCGAATGTCGAATCTCGAATCTC
216665 GAATCTCGAATG
1 GAATCTCGAATG
216677 ATCCTTCTCG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (28 bp):
GAATCTCGAATGTCGAATCTCGAATCTC
Found at i:221545 original size:11 final size:11
Alignment explanation
Indices: 221495--221545 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
221485 AACCCCCACC
221495 AAAAA-AAAAA
1 AAAAATAAAAA
*
221505 AATAATAAAAA
1 AAAAATAAAAA
*
221516 CCAAAAAAAAAAA
1 --AAAAATAAAAA
*
221529 AAAAATAAATA
1 AAAAATAAAAA
221540 AAAAAT
1 AAAAAT
221546 TCATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 4 0.12
11 20 0.61
13 9 0.27
ACGTcount: A:0.86, C:0.04, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:232163 original size:10 final size:10
Alignment explanation
Indices: 232148--232175 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
232138 TAAATGGTAC
232148 TACTAATGTG
1 TACTAATGTG
232158 TACTAATGTG
1 TACTAATGTG
232168 TACTAATG
1 TACTAATG
232176 CACTGTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (10 bp):
TACTAATGTG
Found at i:245457 original size:3 final size:3
Alignment explanation
Indices: 245449--245496 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
245439 CGTATCCAGT
*
245449 CAA CAA CAA CAA CAA CAA CATTT CAA CAA CAA -AA TCAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CA--A CAA CAA CAA CAA -CAA CAA CAA CAA
245496 C
1 C
245497 TAAAGTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 2 0.05
3 33 0.85
4 2 0.05
5 2 0.05
ACGTcount: A:0.60, C:0.31, G:0.00, T:0.08
Consensus pattern (3 bp):
CAA
Found at i:245474 original size:23 final size:23
Alignment explanation
Indices: 245448--245491 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
245438 GCGTATCCAG
245448 TCAACAACAACAA-CAACAACATT
1 TCAACAACAA-AATCAACAACATT
245471 TCAACAACAAAATCAACAACA
1 TCAACAACAAAATCAACAACA
245492 ACAACTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.59, C:0.30, G:0.00, T:0.11
Consensus pattern (23 bp):
TCAACAACAAAATCAACAACATT
Found at i:246432 original size:13 final size:13
Alignment explanation
Indices: 246414--246438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
246404 GTGTATTTTT
246414 CAAAAAAAAAAAC
1 CAAAAAAAAAAAC
246427 CAAAAAAAAAAA
1 CAAAAAAAAAAA
246439 AAAACCAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAC
Found at i:259715 original size:5 final size:5
Alignment explanation
Indices: 259705--259768 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
259695 TATTTTTTAA
*
259705 TTTGT TTTG- TTTG- TTTGT TTGATGT TATTGT TGTTGG TTT-T TTTGT
1 TTTGT TTTGT TTTGT TTTGT TT--TGT T-TTGT T-TTGT TTTGT TTTGT
*
259751 TTTGT TTGGT TTTGT TTT
1 TTTGT TTTGT TTTGT TTT
259769 CGGTTTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
4 11 0.22
5 25 0.51
6 8 0.16
7 4 0.08
8 1 0.02
ACGTcount: A:0.03, C:0.00, G:0.23, T:0.73
Consensus pattern (5 bp):
TTTGT
Found at i:260520 original size:16 final size:16
Alignment explanation
Indices: 260499--260531 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
260489 AACACTATTT
*
260499 GAAAGAAAAGCGTCGG
1 GAAAGAAAAGAGTCGG
260515 GAAAGAAAAGAGTCGG
1 GAAAGAAAAGAGTCGG
260531 G
1 G
260532 TTGTTTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.09, G:0.39, T:0.06
Consensus pattern (16 bp):
GAAAGAAAAGAGTCGG
Found at i:261635 original size:130 final size:130
Alignment explanation
Indices: 261397--261657 Score: 486
Period size: 130 Copynumber: 2.0 Consensus size: 130
261387 TACTGGATAT
261397 ATGATTTTTTAAATGTTAAAAATACATTTAACTGAATTGTAAAACGCAGTTTAATTGGTCTGATT
1 ATGATTTTTTAAATGTTAAAAATACATTTAACTGAATTGTAAAACGCAGTTTAATTGGTCTGATT
* *
261462 AATAATGATATAATATGATTATATCAAGTTACGCAACACCATTAAGCGCAGAACGCTACAAAAAA
66 AATAATGATATAATATGATTATATCAAATTACGCAACAACATTAAGCGCAGAACGCTACAAAAAA
* *
261527 ATGATTTTTTAAATGTTAAAAATACATTTAACTGAATTGTAAAGCGTAGTTTAATTGGTCTGATT
1 ATGATTTTTTAAATGTTAAAAATACATTTAACTGAATTGTAAAACGCAGTTTAATTGGTCTGATT
261592 AATAATGATATAATATGATTATATCAAATTACGCAACAACATTAAGCGCAGAACGCTACAAAAAA
66 AATAATGATATAATATGATTATATCAAATTACGCAACAACATTAAGCGCAGAACGCTACAAAAAA
261657 A
1 A
261658 AATCATTACG
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (130 bp):
ATGATTTTTTAAATGTTAAAAATACATTTAACTGAATTGTAAAACGCAGTTTAATTGGTCTGATT
AATAATGATATAATATGATTATATCAAATTACGCAACAACATTAAGCGCAGAACGCTACAAAAAA
Found at i:262357 original size:2 final size:2
Alignment explanation
Indices: 262350--262389 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
262340 ACTGGATATG
262350 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
262390 AACGTAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:264391 original size:33 final size:33
Alignment explanation
Indices: 264318--264393 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
264308 TAACATTAAA
* * *
264318 ATGTATT-TAATATTTACAGCCGTTACATTTGC
1 ATGTATTATACTATTTACAGTCGTTACATTTAC
* *
264350 ATGTATTATACTATTTACAGTCATTAAATTTAC
1 ATGTATTATACTATTTACAGTCGTTACATTTAC
*
264383 ATGGATTATAC
1 ATGTATTATAC
264394 AACTGTACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 7 0.19
33 30 0.81
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (33 bp):
ATGTATTATACTATTTACAGTCGTTACATTTAC
Found at i:264484 original size:33 final size:33
Alignment explanation
Indices: 264422--265141 Score: 531
Period size: 33 Copynumber: 22.0 Consensus size: 33
264412 TAAAGTCATG
* * *
264422 CATTTACATATATAATACTATTTAGAGTCGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * *
264455 CATTTACACGTATTAAACTAATTACAGTCGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
*
264488 CATTTACATATATTATACTATTTACAGTCGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * *
264521 AATTTATATGTATTATACTATTTGCAGTCGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * * *
264554 CATTTACATATTTTATTCTTTTTACAGTCGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * *
264587 CATTTACATGCATTATACTATTTATAGTCTTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * * * * *
264620 CATTTACATGTTTTATAATATTTAAATTCATTT
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * *
264653 CATTTACATGCAATATACTATTTTA-AGTCATTA
1 CATTTACATGTATTATACTA-TTTACAGTCGTTA
* * *
264686 GATTTACATTTATTATACTATTTACAGTCATTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
** * * * *
264719 CATTTATTTGTTTTATACTTTTTACAGTGGTAA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * *
264752 CATTTACATATATTATACTATTTACATTCATTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * * *
264785 CATTTACATTTTTTTTTAAAAATACTTTTTACAGTCGTAA
1 CATTTACA---TGTATT----ATACTATTTACAGTCGTTA
** *
264825 CATTTACATACATCATACTATTTACAGTCGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * *
264858 CATTTACATGAATCATACTATTTACAGCCGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * *
264891 CATTTACA--TA--ATTCTTTTTACACTCGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* *
264920 C-TTTACATGCATTATACTA-TTACAGTCTTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * * *
264951 CATTTACATATATTATTCTTTTTACAGTTGTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * *
264984 C-TTTACATGCATTATACTA-TTAAAGTCTTTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * * * *
265015 CAAGTTT---TATACTACTAGTATTTAAAGTCATTA
1 C-A-TTTACATGTATTA-TACTATTTACAGTCGTTA
* * * * *
265048 CATTTACATGCAATATACTATTTAAAATCATTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
*
265081 CATTTAC------TATACTATTTACAGTCATTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
* * * * *
265108 TATTTACATGAATTATACTGTTTAAAGTCATTA
1 CATTTACATGTATTATACTATTTACAGTCGTTA
265141 C
1 C
265142 GGCAGGTAAA
Statistics
Matches: 541, Mismatches: 117, Indels: 58
0.76 0.16 0.08
Matches are distributed among these distances:
27 24 0.04
28 6 0.01
29 16 0.03
30 1 0.00
31 29 0.05
32 41 0.08
33 384 0.71
34 11 0.02
36 4 0.01
37 2 0.00
40 23 0.04
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (33 bp):
CATTTACATGTATTATACTATTTACAGTCGTTA
Found at i:264499 original size:66 final size:66
Alignment explanation
Indices: 264422--265141 Score: 603
Period size: 66 Copynumber: 11.0 Consensus size: 66
264412 TAAAGTCATG
* * * * * *
264422 CATTTACATATATAATACTATTTAGAGTCGTTACATTTACACGTATTAAACTAATTACAGTCGTT
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
264487 A
66 A
* * * *
264488 CATTTACATATATTATACTATTTACAGTCGTTAAATTTATATGTATTATACTATTTGCAGTCGTT
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
264553 A
66 A
* * * * *
264554 CATTTACATATTTTATTCTTTTTACAGTCGTTACATTTACATGCATTATACTATTTATAGTCTTT
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
264619 A
66 A
* * * * * * * * *
264620 CATTTACATGTTTTATAATATTTAAATTCATTTCATTTACATGCAATATACTATTTTA-AGTCAT
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTA-TTTACAGTCGT
264684 TA
65 TA
* * * ** ** * * *
264686 GATTTACATTTATTATACTATTTACAGTCATTACATTTATTTGTTTTATACTTTTTACAGTGGTA
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
264751 A
66 A
* * *** *
264752 CATTTACATATATTATACTATTTACATTCATTACATTTACATTTTTTTTTAAAAATACTTTTTAC
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACA---TGCATT----ATACTATTTAC
*
264817 AGTCGTAA
59 AGTCGTTA
* * * * *
264825 CATTTACATACATCATACTATTTACAGTCGTTACATTTACATGAATCATACTATTTACAGCCGTT
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
264890 A
66 A
* * *
264891 CATTTACATA-A-T-T-CTTTTTACACTCGTTAC-TTTACATGCATTATACTA-TTACAGTCTTT
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
264950 A
66 A
* * * * *
264951 CATTTACATATATTATTCTTTTTACAGTTGTTAC-TTTACATGCATTATACTA-TTAAAGTCTTT
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
265014 A
66 A
* * * * * * *
265015 CAAGTTT---TATACTACTAGTATTTAAAGTCATTACATTTACATGCAATATACTATTTAAAATC
1 C-A-TTTACATATATTA-TACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTC
*
265077 ATTA
63 GTTA
* * * * * *
265081 CATTTAC------TATACTATTTACAGTCATTATATTTACATGAATTATACTGTTTAAAGTCATT
1 CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
265140 A
66 A
265141 C
1 C
265142 GGCAGGTAAA
Statistics
Matches: 546, Mismatches: 88, Indels: 46
0.80 0.13 0.07
Matches are distributed among these distances:
60 65 0.12
61 19 0.03
62 16 0.03
63 8 0.01
64 61 0.11
65 24 0.04
66 287 0.53
67 4 0.01
69 5 0.01
70 2 0.00
73 55 0.10
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (66 bp):
CATTTACATATATTATACTATTTACAGTCGTTACATTTACATGCATTATACTATTTACAGTCGTT
A
Found at i:264849 original size:18 final size:18
Alignment explanation
Indices: 264826--264883 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
264816 CAGTCGTAAC
264826 ATTTACATACATCATACT
1 ATTTACATACATCATACT
*
264844 ATTTACAGT-CGT--TAC-
1 ATTTACA-TACATCATACT
264859 ATTTACATGA-ATCATACT
1 ATTTACAT-ACATCATACT
264877 ATTTACA
1 ATTTACA
264884 GCCGTTACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 1 0.03
15 8 0.25
16 3 0.09
17 3 0.09
18 16 0.50
19 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (18 bp):
ATTTACATACATCATACT
Found at i:264975 original size:93 final size:94
Alignment explanation
Indices: 264809--264991 Score: 237
Period size: 93 Copynumber: 2.0 Consensus size: 94
264799 TTTAAAAATA
*
264809 CTTTTTACAGTCGTAACATTTACATACATCATACTATTTACAGTCGTTACATTTACATGAATCAT
1 CTTTTTACACTCGTAACATTTACATACATCATACTATTTACAGTCGTTACATTTACATGAATCAT
264874 ACTATTTACAGCCGTTACATTTACATAATT
66 ACTATTTACAGCCGTTAC-TTTACATAATT
* * * * *
264904 CTTTTTACACTCGTTAC-TTTACATGCATTATACTA-TTACAGTCTTTACATTTACAT-ATATTA
1 CTTTTTACACTCGTAACATTTACATACATCATACTATTTACAGTCGTTACATTTACATGA-ATCA
* * **
264966 TTCTTTTTACAGTTGTTACTTTACAT
65 TACTATTTACAGCCGTTACTTTACAT
264992 GCATTATACT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
92 8 0.10
93 38 0.49
94 16 0.21
95 15 0.19
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.45
Consensus pattern (94 bp):
CTTTTTACACTCGTAACATTTACATACATCATACTATTTACAGTCGTTACATTTACATGAATCAT
ACTATTTACAGCCGTTACTTTACATAATT
Found at i:265091 original size:27 final size:27
Alignment explanation
Indices: 265061--265114 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
265051 TTACATGCAA
265061 TATACTATTTAAAATCATTACATTTAC
1 TATACTATTTAAAATCATTACATTTAC
* * *
265088 TATACTATTTACAGTCATTATATTTAC
1 TATACTATTTAAAATCATTACATTTAC
265115 ATGAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (27 bp):
TATACTATTTAAAATCATTACATTTAC
Found at i:265892 original size:13 final size:13
Alignment explanation
Indices: 265874--266002 Score: 249
Period size: 13 Copynumber: 9.9 Consensus size: 13
265864 CCCTCATCTG
265874 CTTATAGTGGTAC
1 CTTATAGTGGTAC
265887 CTTATAGTGGTAC
1 CTTATAGTGGTAC
*
265900 CTTATAGTGGTAT
1 CTTATAGTGGTAC
265913 CTTATAGTGGTAC
1 CTTATAGTGGTAC
265926 CTTATAGTGGTAC
1 CTTATAGTGGTAC
265939 CTTATAGTGGTAC
1 CTTATAGTGGTAC
265952 CTTATAGTGGTAC
1 CTTATAGTGGTAC
265965 CTTATAGTGGTAC
1 CTTATAGTGGTAC
265978 CTTATAGTGGTAC
1 CTTATAGTGGTAC
265991 CTTATAGTGGTA
1 CTTATAGTGGTA
266003 TCTATATCTT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
13 114 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (13 bp):
CTTATAGTGGTAC
Found at i:268372 original size:20 final size:20
Alignment explanation
Indices: 268347--268386 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
268337 AAGACCTACT
268347 GGTTTCTAGTGAACCCACTA
1 GGTTTCTAGTGAACCCACTA
*
268367 GGTTTCTAGTGATCCCACTA
1 GGTTTCTAGTGAACCCACTA
268387 ACCCACTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (20 bp):
GGTTTCTAGTGAACCCACTA
Found at i:268735 original size:2 final size:2
Alignment explanation
Indices: 268728--268763 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
268718 AAAATGAATT
268728 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
268764 ATTTGAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:271373 original size:2 final size:2
Alignment explanation
Indices: 271366--271403 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
271356 TAATCAGTGA
271366 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
271404 AAACCATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:273560 original size:56 final size:56
Alignment explanation
Indices: 273474--273899 Score: 556
Period size: 56 Copynumber: 7.8 Consensus size: 56
273464 NNNNNNNNNN
273474 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
1 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
*
273530 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATC
1 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
*
273586 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATC
1 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
* * * **
273642 ATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGTATCCTGAAAGGACTGTAAC
1 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
* * *
273698 ATGCTTC-GTTTCCTGACAGGGCTGTATCATGCTCAGTACCCTGACAGGGCCGTATT
1 ATGC-TCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
* * * * *
273754 TTGCTCAGTATCCTGACATGTCTGTATCATGCTCAGTATCCTGACA--GCT-CAGT
1 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
* * * *
273807 AT--TCAG-AT-ATG--A---CTGTATTATGCTCAGTATCCTGACATGACTGTATT
1 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
* *
273854 -TGCTCAGTATCCTGACAGCGCTGTATCATGCTCAGTGTCCTGACAG
1 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAG
273900 CTCAGTATTC
Statistics
Matches: 325, Mismatches: 31, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
44 24 0.07
46 3 0.01
47 3 0.01
48 4 0.01
49 4 0.01
50 4 0.01
51 4 0.01
52 1 0.00
53 3 0.01
54 2 0.01
55 25 0.08
56 246 0.76
57 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (56 bp):
ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATT
Found at i:273618 original size:84 final size:84
Alignment explanation
Indices: 273474--273899 Score: 558
Period size: 84 Copynumber: 5.2 Consensus size: 84
273464 NNNNNNNNNN
* * *
273474 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGT
1 ATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGTATCCTGACAGGACTGTATCATGCTCAGT
273539 ATCCTGACAGGGCTGTATC
66 ATCCTGACAGGGCTGTATC
* *
273558 ATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGTATCCTGACAGGGCTGTATCATGCTCAGT
1 ATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGTATCCTGACAGGACTGTATCATGCTCAGT
273623 ATCCTGACAGGGCTGTATC
66 ATCCTGACAGGGCTGTATC
* *
273642 ATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGTATCCTGAAAGGACTGTAACATGCTTC-G
1 ATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGTATCCTGACAGGACTGTATCATGC-TCAG
*
273706 TTTCCTGACAGGGCTGTATC
65 TATCCTGACAGGGCTGTATC
* * * * *
273726 ATGCTCAGTACCCTGACAGGGCCGTATTTTGCTCAGTATCCTGACATGTCTGTATCATGCTCAGT
1 ATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGTATCCTGACAGGACTGTATCATGCTCAGT
*
273791 ATCCTGACA--GCT-CAGT-
66 ATCCTGACAGGGCTGTA-TC
* * *
273807 AT--TCAG-AT-ATG--A---CTGTATTATGCTCAGTATCCTGACATGACTGTAT-TTGCTCAGT
1 ATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGTATCCTGACAGGACTGTATCATGCTCAGT
*
273862 ATCCTGACAGCGCTGTATC
66 ATCCTGACAGGGCTGTATC
*
273881 ATGCTCAGTGTCCTGACAG
1 ATGCTCAGTATCCTGACAG
273900 CTCAGTATTC
Statistics
Matches: 304, Mismatches: 24, Indels: 31
0.85 0.07 0.09
Matches are distributed among these distances:
71 17 0.06
72 31 0.10
73 4 0.01
74 3 0.01
75 1 0.00
76 4 0.01
77 3 0.01
78 3 0.01
79 4 0.01
80 1 0.00
81 3 0.01
82 4 0.01
83 2 0.01
84 222 0.73
85 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (84 bp):
ATGCTCAGTATCCTGACAGGGCTGTATTATGCTCAGTATCCTGACAGGACTGTATCATGCTCAGT
ATCCTGACAGGGCTGTATC
Found at i:273808 original size:28 final size:28
Alignment explanation
Indices: 273474--273800 Score: 530
Period size: 28 Copynumber: 11.7 Consensus size: 28
273464 NNNNNNNNNN
273474 ATGCTCAGTATCCTGACAGGGCTGTATC
1 ATGCTCAGTATCCTGACAGGGCTGTATC
*
273502 ATGCTCAGTATCCTGACAGGGCTGTATT
1 ATGCTCAGTATCCTGACAGGGCTGTATC
273530 ATGCTCAGTATCCTGACAGGGCTGTATC
1 ATGCTCAGTATCCTGACAGGGCTGTATC
273558 ATGCTCAGTATCCTGACAGGGCTGTATC
1 ATGCTCAGTATCCTGACAGGGCTGTATC
273586 ATGCTCAGTATCCTGACAGGGCTGTATC
1 ATGCTCAGTATCCTGACAGGGCTGTATC
273614 ATGCTCAGTATCCTGACAGGGCTGTATC
1 ATGCTCAGTATCCTGACAGGGCTGTATC
*
273642 ATGCTCAGTATCCTGACAGGGCTGTATT
1 ATGCTCAGTATCCTGACAGGGCTGTATC
* * *
273670 ATGCTCAGTATCCTGAAAGGACTGTAAC
1 ATGCTCAGTATCCTGACAGGGCTGTATC
*
273698 ATGCTTC-GTTTCCTGACAGGGCTGTATC
1 ATGC-TCAGTATCCTGACAGGGCTGTATC
* * *
273726 ATGCTCAGTACCCTGACAGGGCCGTATT
1 ATGCTCAGTATCCTGACAGGGCTGTATC
* * *
273754 TTGCTCAGTATCCTGACATGTCTGTATC
1 ATGCTCAGTATCCTGACAGGGCTGTATC
273782 ATGCTCAGTATCCTGACAG
1 ATGCTCAGTATCCTGACAG
273801 CTCAGTATTC
Statistics
Matches: 274, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
27 2 0.01
28 270 0.99
29 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (28 bp):
ATGCTCAGTATCCTGACAGGGCTGTATC
Found at i:273823 original size:44 final size:44
Alignment explanation
Indices: 273756--273942 Score: 144
Period size: 44 Copynumber: 4.0 Consensus size: 44
273746 GCCGTATTTT
* * * *
273756 GCTCAGTATCCTGACATGTCTGTATCATGCTCAGTATCCTGACA
1 GCTCAGTATTCAGATATGACTGTATCATGCTCAGTATCCTGACA
*
273800 GCTCAGTATTCAGATATGACTGTATTATGCTCAGTATCCTGACA
1 GCTCAGTATTCAGATATGACTGTATCATGCTCAGTATCCTGACA
* *
273844 TGACT--GTATTTGCTCAGTATCCTGACAGCGCTGTATCATGCTCAGTGTCCTGACA
1 -G-CTCAGTA--T--TCAG-AT-ATG--A---CTGTATCATGCTCAGTATCCTGACA
* * * *
273899 GCTCAGTATTCAAATATGACTGTATTATGCTTAGTTTCCTGACA
1 GCTCAGTATTCAGATATGACTGTATCATGCTCAGTATCCTGACA
273943 TGGCTGTATC
Statistics
Matches: 115, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
44 64 0.56
45 1 0.01
46 3 0.03
47 1 0.01
48 4 0.03
49 4 0.03
50 4 0.03
51 3 0.03
52 1 0.01
53 3 0.03
54 1 0.01
55 26 0.23
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (44 bp):
GCTCAGTATTCAGATATGACTGTATCATGCTCAGTATCCTGACA
Found at i:273864 original size:27 final size:27
Alignment explanation
Indices: 273800--273898 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 27
273790 TATCCTGACA
* * *
273800 GCTCAGTATTCAGATATGACTGTATTAT
1 GCTCAGTATCCTGACATGACTGTATT-T
273828 GCTCAGTATCCTGACATGACTGTATTT
1 GCTCAGTATCCTGACATGACTGTATTT
* *
273855 GCTCAGTATCCTGACA-GCGCTGTATCAT
1 GCTCAGTATCCTGACATG-ACTGTAT-TT
*
273883 GCTCAGTGTCCTGACA
1 GCTCAGTATCCTGACA
273899 GCTCAGTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
26 1 0.02
27 23 0.37
28 39 0.62
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (27 bp):
GCTCAGTATCCTGACATGACTGTATTT
Found at i:273894 original size:28 final size:27
Alignment explanation
Indices: 273818--273900 Score: 105
Period size: 27 Copynumber: 3.0 Consensus size: 27
273808 TTCAGATATG
273818 ACTGTATTATGCTCAGTATCCTGACATG-
1 ACTGTA-TATGCTCAGTATCCTGACA-GC
*
273846 ACTGTATTTGCTCAGTATCCTGACAGC
1 ACTGTATATGCTCAGTATCCTGACAGC
* *
273873 GCTGTATCATGCTCAGTGTCCTGACAGC
1 ACTGTAT-ATGCTCAGTATCCTGACAGC
273901 TCAGTATTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.02
27 24 0.49
28 24 0.49
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (27 bp):
ACTGTATATGCTCAGTATCCTGACAGC
Found at i:273895 original size:99 final size:99
Alignment explanation
Indices: 273719--273972 Score: 366
Period size: 99 Copynumber: 2.5 Consensus size: 99
273709 CCTGACAGGG
* * * * *
273719 CTGTATCATGCTCAGTACCCTGACAGGGCCGTATTTTGCTCAGTATCCTGACATG-TCTGTATCA
1 CTGTATTATGCTCAGTATCCTGACATGGCTGTA-TTTGCTCAGTATCCTGACA-GCGCTGTATCA
*
273783 TGCTCAGTATCCTGACAGCTCAGTATTCAGATATGA
64 TGCTCAGTATCCTGACAGCTCAGTATTCAAATATGA
*
273819 CTGTATTATGCTCAGTATCCTGACATGACTGTATTTGCTCAGTATCCTGACAGCGCTGTATCATG
1 CTGTATTATGCTCAGTATCCTGACATGGCTGTATTTGCTCAGTATCCTGACAGCGCTGTATCATG
*
273884 CTCAGTGTCCTGACAGCTCAGTATTCAAATATGA
66 CTCAGTATCCTGACAGCTCAGTATTCAAATATGA
* * * *
273918 CTGTATTATGCTTAGTTTCCTGACATGGCTGTATCATGCTCAGTATCCTAACAGC
1 CTGTATTATGCTCAGTATCCTGACATGGCTGTAT-TTGCTCAGTATCCTGACAGC
273973 TCAGTATTCA
Statistics
Matches: 139, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
98 1 0.01
99 92 0.66
100 46 0.33
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (99 bp):
CTGTATTATGCTCAGTATCCTGACATGGCTGTATTTGCTCAGTATCCTGACAGCGCTGTATCATG
CTCAGTATCCTGACAGCTCAGTATTCAAATATGA
Found at i:273907 original size:28 final size:28
Alignment explanation
Indices: 273821--273907 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
273811 AGATATGACT
* * *
273821 GTATTATGCTCAGTATCCTGACATG-ACT
1 GTATCATGCTCAGTATCCTGACA-GCGCA
* *
273849 GTAT-TTGCTCAGTATCCTGACAGCGCT
1 GTATCATGCTCAGTATCCTGACAGCGCA
* *
273876 GTATCATGCTCAGTGTCCTGACAGCTCA
1 GTATCATGCTCAGTATCCTGACAGCGCA
273904 GTAT
1 GTAT
273908 TCAAATATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
26 1 0.02
27 23 0.45
28 27 0.53
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (28 bp):
GTATCATGCTCAGTATCCTGACAGCGCA
Found at i:273956 original size:72 final size:72
Alignment explanation
Indices: 273843--274039 Score: 301
Period size: 72 Copynumber: 2.8 Consensus size: 72
273833 GTATCCTGAC
*
273843 ATGACTGTATT-TGCTCAGTATCCTGACA-GCGCTGTATCATGCTCAGTGTCCTGACAGCTCAGT
1 ATGACTGTATTATGCTCAGTATCCTGACATG-GCTGTATCATGCTCAGTATCCTGACAGCTCAGT
273906 ATTCAAAT
65 ATTCAAAT
* * *
273914 ATGACTGTATTATGCTTAGTTTCCTGACATGGCTGTATCATGCTCAGTATCCTAACAGCTCAGTA
1 ATGACTGTATTATGCTCAGTATCCTGACATGGCTGTATCATGCTCAGTATCCTGACAGCTCAGTA
*
273979 TTCAGAT
66 TTCAAAT
* *
273986 ATGACTGTATTATGCTCAGTATCCTGACATGACTGTAT-TTGCTCAGTATCCTGA
1 ATGACTGTATTATGCTCAGTATCCTGACATGGCTGTATCATGCTCAGTATCCTGA
274040 TAGGGTTGTA
Statistics
Matches: 114, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
71 25 0.22
72 88 0.77
73 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (72 bp):
ATGACTGTATTATGCTCAGTATCCTGACATGGCTGTATCATGCTCAGTATCCTGACAGCTCAGTA
TTCAAAT
Found at i:274035 original size:27 final size:28
Alignment explanation
Indices: 273971--274039 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
273961 TATCCTAACA
* * *
273971 GCTCAGTATTCAGATATGACTGTATTAT
1 GCTCAGTATCCTGACATGACTGTATTAT
273999 GCTCAGTATCCTGACATGACTGTATT-T
1 GCTCAGTATCCTGACATGACTGTATTAT
274026 GCTCAGTATCCTGA
1 GCTCAGTATCCTGA
274040 TAGGGTTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 15 0.39
28 23 0.61
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (28 bp):
GCTCAGTATCCTGACATGACTGTATTAT
Found at i:277851 original size:441 final size:439
Alignment explanation
Indices: 277016--277895 Score: 1715
Period size: 441 Copynumber: 2.0 Consensus size: 439
277006 CAGTTTTTAG
277016 TGGTCTTGTTATGTTTTTTTTGTAGTTTGTGTTTAATACATTCATAAAACATTTTCTTTGCTCTA
1 TGGTCTTGTTATGTTTTTTTTGTAGTTTGTGTTTAATACATTCATAAAACATTTTCTTTGCTCTA
277081 TTTAATACAATAACATGTATATAGCCATGTTTAATAATAGGATATCTCTACATATCCATTAGACA
66 TTTAATACAATAACATGTATATAGCCATGTTTAATAATAGGATATCTCTACATATCCATTAGACA
*
277146 GGTTGGGTTTTTATTTATTCTTTCATCTTATATCTTTTTTTGTTTGATATATATGTACATGCTTT
131 GGTTGGGTTTTTATTTATTCTTTCATCTTATATCTTTTTTTGTTTGATATATATGTACATGCCTT
*
277211 TACTCAATATCTGTTTGATCAGCGAATGCATTCCTTAAATTTCTATAATCTGTAATTTTTCACAG
196 TACTCAATATCTGTTTCATCAGCGAATGCATTCCTTAAATTTCTATAATCTGTAATTTTTCACAG
277276 AATAATCTTTACTATGTTGGTTTATGTGTGGAATATTTTGTAAACACAATGGTTAGAATTTATAT
261 AATAATCTTTACTATGTTGGTTTATGTGTGGAATATTTTGTAAACACAATGGTTAGAATTTATAT
277341 GTGATTGAGGAGGAGGGGGATTGATCAGTAAATAAATAGTGCATGCTTTTCTTTTCTAGCTGCCT
326 GTGATTGAGGAGGAGGGGGATTGATCAGTAAATAAATAGTGCATGCTTTTCTTTTCTAGCTGCCT
277406 GATAACTCTCCAGACTATAGTGGTATTCTACAAGAACATTGACTTTTGT
391 GATAACTCTCCAGACTATAGTGGTATTCTACAAGAACATTGACTTTTGT
277455 NTGGTCTTGTTATGTTTTTTTTTGTAGTTTGTGTTTAATACATTCATAAAACATTTTCTTTGCTC
1 -TGGTCTTGTTATG-TTTTTTTTGTAGTTTGTGTTTAATACATTCATAAAACATTTTCTTTGCTC
277520 TATTTAATACAATAACATGTATATAGCCATGTTTAATAATAGGATATCTCTACATATCCATTAGA
64 TATTTAATACAATAACATGTATATAGCCATGTTTAATAATAGGATATCTCTACATATCCATTAGA
*
277585 CAGTTTGGGTTTTTATTTATTCTTTCATCTTATATCTTTTTTTGTTTGATATATATGTACATGCC
129 CAGGTTGGGTTTTTATTTATTCTTTCATCTTATATCTTTTTTTGTTTGATATATATGTACATGCC
277650 TTTACTCAATATCTGTTTCATCAGCGAATGCATTCCTTAAATTTCTATAATCTGTAATTTTTCAC
194 TTTACTCAATATCTGTTTCATCAGCGAATGCATTCCTTAAATTTCTATAATCTGTAATTTTTCAC
277715 AGAATAATCTTTACTATGTTGGTTTATGTGTGGAATATTTTGTAAACACAATGGTTAGAATTTAT
259 AGAATAATCTTTACTATGTTGGTTTATGTGTGGAATATTTTGTAAACACAATGGTTAGAATTTAT
277780 ATGTGATTGAGGAGGAGGGGGATTGATCAGTAAATAAATAGTGCATGCTTTTCTTTTCTAGCTGC
324 ATGTGATTGAGGAGGAGGGGGATTGATCAGTAAATAAATAGTGCATGCTTTTCTTTTCTAGCTGC
277845 CTGATAACTCTCCAGACTATAGTGGTATTCTACAAGAACATTGACTTTTGT
389 CTGATAACTCTCCAGACTATAGTGGTATTCTACAAGAACATTGACTTTTGT
277896 CAATAAAAAT
Statistics
Matches: 436, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
440 13 0.03
441 423 0.97
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (439 bp):
TGGTCTTGTTATGTTTTTTTTGTAGTTTGTGTTTAATACATTCATAAAACATTTTCTTTGCTCTA
TTTAATACAATAACATGTATATAGCCATGTTTAATAATAGGATATCTCTACATATCCATTAGACA
GGTTGGGTTTTTATTTATTCTTTCATCTTATATCTTTTTTTGTTTGATATATATGTACATGCCTT
TACTCAATATCTGTTTCATCAGCGAATGCATTCCTTAAATTTCTATAATCTGTAATTTTTCACAG
AATAATCTTTACTATGTTGGTTTATGTGTGGAATATTTTGTAAACACAATGGTTAGAATTTATAT
GTGATTGAGGAGGAGGGGGATTGATCAGTAAATAAATAGTGCATGCTTTTCTTTTCTAGCTGCCT
GATAACTCTCCAGACTATAGTGGTATTCTACAAGAACATTGACTTTTGT
Found at i:283904 original size:17 final size:17
Alignment explanation
Indices: 283882--283914 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
283872 AGTGTGAGCA
283882 AATATCTACATCTACAT
1 AATATCTACATCTACAT
283899 AATATCTACATCTACA
1 AATATCTACATCTACA
283915 CACGAGTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATCTACATCTACAT
Found at i:291626 original size:15 final size:16
Alignment explanation
Indices: 291606--291635 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
291596 ATCATGTAAT
291606 GTATAGATGA-GATAC
1 GTATAGATGATGATAC
291621 GTATAGATGATGATA
1 GTATAGATGATGATA
291636 TAAAGACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.30
Consensus pattern (16 bp):
GTATAGATGATGATAC
Found at i:298072 original size:15 final size:16
Alignment explanation
Indices: 298049--298083 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
298039 GATAGTAGTA
*
298049 TCGCTCCTTTGC-CTT
1 TCGCACCTTTGCACTT
298064 TCGCACCTTTGCACTT
1 TCGCACCTTTGCACTT
298080 TCGC
1 TCGC
298084 CATCGCATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.06, C:0.40, G:0.14, T:0.40
Consensus pattern (16 bp):
TCGCACCTTTGCACTT
Found at i:298089 original size:22 final size:22
Alignment explanation
Indices: 298064--298105 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
298054 CCTTTGCCTT
*
298064 TCGCACCTTTGCACTTTCGCCA
1 TCGCACCTTCGCACTTTCGCCA
*
298086 TCGCATCTTCGCACTTTCGC
1 TCGCACCTTCGCACTTTCGC
298106 TCCTTCGCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.40, G:0.14, T:0.33
Consensus pattern (22 bp):
TCGCACCTTCGCACTTTCGCCA
Found at i:298099 original size:30 final size:30
Alignment explanation
Indices: 298063--298135 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
298053 TCCTTTGCCT
*
298063 TTCGCACCTTT-GCACTTTCGCCATCGCATC
1 TTCGCACCTTTCGCACCTTCGCCATCGCA-C
* *
298093 TTCGCA-CTTTCGCTCCTTCGCCGTCGCAC
1 TTCGCACCTTTCGCACCTTCGCCATCGCAC
298122 TCTCGCA-CTTTCGC
1 T-TCGCACCTTTCGC
298136 CTTCGCAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 6 0.16
30 32 0.84
ACGTcount: A:0.10, C:0.42, G:0.15, T:0.33
Consensus pattern (30 bp):
TTCGCACCTTTCGCACCTTCGCCATCGCAC
Found at i:298104 original size:8 final size:8
Alignment explanation
Indices: 298061--298158 Score: 52
Period size: 8 Copynumber: 13.0 Consensus size: 8
298051 GCTCCTTTGC
298061 CTTTCGCA
1 CTTTCGCA
298069 CCTTT-GCA
1 -CTTTCGCA
298077 CTTTCGC-
1 CTTTCGCA
*
298084 C-ATCGCA
1 CTTTCGCA
298091 -TCTTCGCA
1 CT-TTCGCA
*
298099 CTTTCGCT
1 CTTTCGCA
*
298107 CCTTCGC-
1 CTTTCGCA
*
298114 C-GTCGCA
1 CTTTCGCA
*
298121 CTCTCGCA
1 CTTTCGCA
298129 CTTTCGC-
1 CTTTCGCA
298136 C-TTCGCAA
1 CTTTCGC-A
298144 C-TTCGCA
1 CTTTCGCA
*
298151 CTCTCGCA
1 CTTTCGCA
298159 TCTTCGACCT
Statistics
Matches: 71, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
6 13 0.18
7 10 0.14
8 43 0.61
9 5 0.07
ACGTcount: A:0.11, C:0.43, G:0.14, T:0.32
Consensus pattern (8 bp):
CTTTCGCA
Found at i:298150 original size:30 final size:29
Alignment explanation
Indices: 298079--298158 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
298069 CCTTTGCACT
*
298079 TTCGCCATCGCA-TCTTCGCACTTTCGCTCC
1 TTCGCCGTCGCACTC-TCGCACTTTCGC-CC
298109 TTCGCCGTCGCACTCTCGCACTTTCG-CC
1 TTCGCCGTCGCACTCTCGCACTTTCGCCC
*
298137 TTCGCAACTTCGCACTCTCGCA
1 TTCGC--CGTCGCACTCTCGCA
298159 TCTTCGACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 7 0.16
30 36 0.80
31 2 0.04
ACGTcount: A:0.11, C:0.44, G:0.15, T:0.30
Consensus pattern (29 bp):
TTCGCCGTCGCACTCTCGCACTTTCGCCC
Found at i:298152 original size:22 final size:22
Alignment explanation
Indices: 298094--298157 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
298084 CATCGCATCT
* * *
298094 TCGCACTTTCGCTCCTTCGCCG
1 TCGCACTCTCGCACTTTCGCCG
*
298116 TCGCACTCTCGCACTTTCGCCT
1 TCGCACTCTCGCACTTTCGCCG
*
298138 TCGCAACT-TCGCACTCTCGC
1 TCGC-ACTCTCGCACTTTCGC
298158 ATCTTCGACC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.09, C:0.45, G:0.16, T:0.30
Consensus pattern (22 bp):
TCGCACTCTCGCACTTTCGCCG
Found at i:314848 original size:13 final size:13
Alignment explanation
Indices: 314830--314855 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
314820 TTCAAAAGAT
314830 TTGGAGAAATAAA
1 TTGGAGAAATAAA
314843 TTGGAGAAATAAA
1 TTGGAGAAATAAA
314856 ATGACAGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
TTGGAGAAATAAA
Found at i:316643 original size:16 final size:16
Alignment explanation
Indices: 316618--316651 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
316608 AATTGATTAT
*
316618 GAGTCTGTTTGGGTAC
1 GAGTCGGTTTGGGTAC
316634 GAGTCGGTTTGGGTAC
1 GAGTCGGTTTGGGTAC
316650 GA
1 GA
316652 CTACACTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.41, T:0.32
Consensus pattern (16 bp):
GAGTCGGTTTGGGTAC
Found at i:319060 original size:12 final size:12
Alignment explanation
Indices: 319029--319062 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
319019 GCTCATTTGA
* *
319029 AACAACAACAAT
1 AACAACAGCAAC
319041 AACAACAGCAAC
1 AACAACAGCAAC
319053 AACAACAGCA
1 AACAACAGCA
319063 GAGGAACAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.29, G:0.06, T:0.03
Consensus pattern (12 bp):
AACAACAGCAAC
Found at i:319679 original size:2 final size:2
Alignment explanation
Indices: 319674--319719 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
319664 TTTTTTTTCA
319674 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
319716 AG AG
1 AG AG
319720 TACCAGAGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:320327 original size:54 final size:54
Alignment explanation
Indices: 320245--320353 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
320235 ACAGTTTTAG
320245 AATGTGGCCATATTAGCAGCACCATATAGAGCCTGAACCCGTATACCAGGGACC
1 AATGTGGCCATATTAGCAGCACCATATAGAGCCTGAACCCGTATACCAGGGACC
320299 AATGTGGCCATATTAGCAGCACCATATAGAGCCTGAACCCGTATACCAGGGACC
1 AATGTGGCCATATTAGCAGCACCATATAGAGCCTGAACCCGTATACCAGGGACC
320353 A
1 A
320354 TCAATTGCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (54 bp):
AATGTGGCCATATTAGCAGCACCATATAGAGCCTGAACCCGTATACCAGGGACC
Found at i:320890 original size:12 final size:12
Alignment explanation
Indices: 320873--320898 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
320863 TTTTTAGCCG
320873 TGTATTAAAACC
1 TGTATTAAAACC
320885 TGTATTAAAACC
1 TGTATTAAAACC
320897 TG
1 TG
320899 ACAAGCTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (12 bp):
TGTATTAAAACC
Found at i:323866 original size:21 final size:21
Alignment explanation
Indices: 323840--323880 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
323830 GTTGTACATG
323840 TAATGAACATGCAAATATCTC
1 TAATGAACATGCAAATATCTC
323861 TAATGAACATGCAAATATCT
1 TAATGAACATGCAAATATCT
323881 TACATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (21 bp):
TAATGAACATGCAAATATCTC
Found at i:333921 original size:100 final size:100
Alignment explanation
Indices: 333809--333997 Score: 378
Period size: 100 Copynumber: 1.9 Consensus size: 100
333799 TTTATCTATT
333809 TATATATATATCGGATAAAAAGTTCTTTACAAACATCTTTATAACGCGCAAGAGGGTACCTACCT
1 TATATATATATCGGATAAAAAGTTCTTTACAAACATCTTTATAACGCGCAAGAGGGTACCTACCT
333874 GTGTCCCCCGAGGAGAGAATCGGGAAGCATTATGC
66 GTGTCCCCCGAGGAGAGAATCGGGAAGCATTATGC
333909 TATATATATATCGGATAAAAAGTTCTTTACAAACATCTTTATAACGCGCAAGAGGGTACCTACCT
1 TATATATATATCGGATAAAAAGTTCTTTACAAACATCTTTATAACGCGCAAGAGGGTACCTACCT
333974 GTGTCCCCCGAGGAGAGAATCGGG
66 GTGTCCCCCGAGGAGAGAATCGGG
333998 TAGATTTCTG
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (100 bp):
TATATATATATCGGATAAAAAGTTCTTTACAAACATCTTTATAACGCGCAAGAGGGTACCTACCT
GTGTCCCCCGAGGAGAGAATCGGGAAGCATTATGC
Found at i:342825 original size:21 final size:21
Alignment explanation
Indices: 342786--342825 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
342776 TAATGTTAAG
*
342786 AATGTTTGTGTTTTTACAATA
1 AATGTTTGTGTTTTAACAATA
342807 AATGTTT-TGTTCTTAACAA
1 AATGTTTGTGTT-TTAACAA
342826 CGATATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.50
Consensus pattern (21 bp):
AATGTTTGTGTTTTAACAATA
Found at i:346645 original size:2 final size:2
Alignment explanation
Indices: 346638--346674 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
346628 GAGAGGGAAC
346638 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
346675 GGGGTGTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:347431 original size:20 final size:22
Alignment explanation
Indices: 347398--347437 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
347388 TAGAAGAATC
*
347398 ATTTCTCCTTTGGGA-ATTATA
1 ATTTCTCCTATGGGATATTATA
347419 ATTT-TCCTATGGGATATTA
1 ATTTCTCCTATGGGATATTA
347438 ATTTTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (22 bp):
ATTTCTCCTATGGGATATTATA
Found at i:352618 original size:7 final size:7
Alignment explanation
Indices: 352602--352637 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
352592 AAAATTGTTA
352602 ACGCACG
1 ACGCACG
*
352609 ACGGACG
1 ACGCACG
352616 ACGCACG
1 ACGCACG
*
352623 TCGCACG
1 ACGCACG
352630 ACGCACG
1 ACGCACG
352637 A
1 A
352638 AAACGGATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.39, G:0.31, T:0.03
Consensus pattern (7 bp):
ACGCACG
Found at i:354692 original size:169 final size:169
Alignment explanation
Indices: 354403--354763 Score: 686
Period size: 169 Copynumber: 2.1 Consensus size: 169
354393 GTTCAGGGCC
*
354403 TAGTGAAAAATGTATTAAATCTTAGAAATTTTCTTTTATTTCTATATAATTGAGAATTACTAAAT
1 TAGTG-AAAATGTATTAAATCTTAGAAATTTTCTTTTATTTCTATATAATCGAGAATTACTAAAT
354468 GCATGGTTATGTCGTCCATGAAGCCCTGTACCAAACTTGTGAAATTCAAGTCTTTTGGGTCAGGT
65 GCATGGTTATGTCGTCCATGAAGCCCTGTACCAAACTTGTGAAATTCAAGTCTTTTGGGTCAGGT
354533 ATTCAGGACTATGGCCGGAACCAATAGGGCCTTATACAGG
130 ATTCAGGACTATGGCCGGAACCAATAGGGCCTTATACAGG
*
354573 TAGTGAAAATGTATTAAATCTTAGAAATTTTCTTTTATTTCTTTATAATCGAGAATTACTAAATG
1 TAGTGAAAATGTATTAAATCTTAGAAATTTTCTTTTATTTCTATATAATCGAGAATTACTAAATG
*
354638 CATGGTTATGTCGTCCATGAAGCCCTGTACCAAACTTGTGAAATTCATGTCTTTTGGGTCAGGTA
66 CATGGTTATGTCGTCCATGAAGCCCTGTACCAAACTTGTGAAATTCAAGTCTTTTGGGTCAGGTA
354703 TTCAGGACTATGGCCGGAACCAATAGGGCCTTATACAGG
131 TTCAGGACTATGGCCGGAACCAATAGGGCCTTATACAGG
354742 TAGTGAAAATGTATTAAATCTT
1 TAGTGAAAATGTATTAAATCTT
354764 TAAAAATCTA
Statistics
Matches: 188, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
169 183 0.97
170 5 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (169 bp):
TAGTGAAAATGTATTAAATCTTAGAAATTTTCTTTTATTTCTATATAATCGAGAATTACTAAATG
CATGGTTATGTCGTCCATGAAGCCCTGTACCAAACTTGTGAAATTCAAGTCTTTTGGGTCAGGTA
TTCAGGACTATGGCCGGAACCAATAGGGCCTTATACAGG
Found at i:360451 original size:71 final size:71
Alignment explanation
Indices: 360335--360484 Score: 273
Period size: 71 Copynumber: 2.1 Consensus size: 71
360325 TTAAACGTAT
* *
360335 TTACTTTTAGAAGAGACTCTTTGAGTAAGCTTGATAAATATTATACTTGATGTGACTCAATCTAT
1 TTACTTTTAGAAGAGACTCTTTGAGCAAGCTTGAAAAATATTATACTTGATGTGACTCAATCTAT
360400 ACCCAA
66 ACCCAA
360406 TTACTTTTAGAAGAGACTCTTTGAGCAAGCTTGAAAAATATTATACTTGATGTGACTCAATCTAT
1 TTACTTTTAGAAGAGACTCTTTGAGCAAGCTTGAAAAATATTATACTTGATGTGACTCAATCTAT
360471 ACCCAA
66 ACCCAA
360477 TTATCTTT
1 TTA-CTTT
360485 ACAGTCGTGT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 72 0.95
72 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (71 bp):
TTACTTTTAGAAGAGACTCTTTGAGCAAGCTTGAAAAATATTATACTTGATGTGACTCAATCTAT
ACCCAA
Found at i:367023 original size:13 final size:13
Alignment explanation
Indices: 367005--367035 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
366995 AATGAGTGAA
367005 TGTAATAAAAATC
1 TGTAATAAAAATC
*
367018 TGTAATAAAAATT
1 TGTAATAAAAATC
367031 TGTAA
1 TGTAA
367036 GTTTTGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (13 bp):
TGTAATAAAAATC
Found at i:373759 original size:30 final size:29
Alignment explanation
Indices: 373724--373786 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
373714 TAAAAAAAGG
*
373724 AAACAATACAAAAAAATACAA-AAAATAAAA
1 AAACAAAACAAAAAAAT-CAACAAAA-AAAA
**
373754 AAACAAAACAATCAAATCAACAAAAAAAA
1 AAACAAAACAAAAAAATCAACAAAAAAAA
373783 AAAC
1 AAAC
373787 TCTCTGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.78, C:0.14, G:0.00, T:0.08
Consensus pattern (29 bp):
AAACAAAACAAAAAAATCAACAAAAAAAA
Found at i:374280 original size:16 final size:17
Alignment explanation
Indices: 374255--374289 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
374245 TTTTATCTAC
374255 TAGCTGTTTTTGTGAAT
1 TAGCTGTTTTTGTGAAT
374272 TAGCT-TTTTTGTGAAT
1 TAGCTGTTTTTGTGAAT
374288 TA
1 TA
374290 TTGTCGACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.54
Consensus pattern (17 bp):
TAGCTGTTTTTGTGAAT
Found at i:378237 original size:14 final size:14
Alignment explanation
Indices: 378197--378229 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
378187 GGATAGAACA
378197 ACTTTAGATAATTT
1 ACTTTAGATAATTT
378211 ACTTTAGATAATTT
1 ACTTTAGATAATTT
378225 ACTTT
1 ACTTT
378230 TATCAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (14 bp):
ACTTTAGATAATTT
Found at i:384237 original size:33 final size:33
Alignment explanation
Indices: 384192--384256 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
384182 GTTAAACGCA
384192 TATGTATAAATTTGATATAAACAATTCATTCAT
1 TATGTATAAATTTGATATAAACAATTCATTCAT
*
384225 TATGTATTAATTTGATATAAACAATTCATTCA
1 TATGTATAAATTTGATATAAACAATTCATTCA
384257 ACAACCTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (33 bp):
TATGTATAAATTTGATATAAACAATTCATTCAT
Found at i:387298 original size:21 final size:21
Alignment explanation
Indices: 387274--387327 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
387264 TCCACTTAAG
*
387274 TCTGTAAAATTTACTCAAAAA
1 TCTGTAAAATTCACTCAAAAA
* **
387295 TCTGTAAAATTCATTCAATGA
1 TCTGTAAAATTCACTCAAAAA
387316 TCTGTAAAATTC
1 TCTGTAAAATTC
387328 TCTGTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (21 bp):
TCTGTAAAATTCACTCAAAAA
Found at i:392041 original size:13 final size:13
Alignment explanation
Indices: 392023--392047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
392013 AAAGTGAATC
392023 ATTATGATTACAA
1 ATTATGATTACAA
392036 ATTATGATTACA
1 ATTATGATTACA
392048 TTTCACTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
ATTATGATTACAA
Found at i:394679 original size:18 final size:18
Alignment explanation
Indices: 394652--394687 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
394642 GATTTTTTGT
*
394652 CATTTCAGTAGAAAAGAA
1 CATTTCAGTAAAAAAGAA
*
394670 CATTTTAGTAAAAAAGAA
1 CATTTCAGTAAAAAAGAA
394688 TTCAACATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (18 bp):
CATTTCAGTAAAAAAGAA
Found at i:398206 original size:16 final size:14
Alignment explanation
Indices: 398187--398226 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
398177 TTTTTTGTTT
398187 GTTTGTTTTTTGGTGG
1 GTTT-TTTTTTGG-GG
*
398203 GTTTTTTTTTGGGT
1 GTTTTTTTTTGGGG
398217 GTTTTTTTTT
1 GTTTTTTTTT
398227 TTGCGTTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 8 0.35
16 4 0.17
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (14 bp):
GTTTTTTTTTGGGG
Found at i:406795 original size:57 final size:57
Alignment explanation
Indices: 406726--406841 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
406716 CATTTCATTG
406726 TCAAGAAAATACTTAAAGATATAAAAACCCTTAATAAAATTTAGTGATTCCAAGGAC
1 TCAAGAAAATACTTAAAGATATAAAAACCCTTAATAAAATTTAGTGATTCCAAGGAC
*
406783 TCAAGAAAATACTTAAAGATATAAAAACCCTTGATAAAATTTAGTGATTCCAAGGAC
1 TCAAGAAAATACTTAAAGATATAAAAACCCTTAATAAAATTTAGTGATTCCAAGGAC
406840 TC
1 TC
406842 TAGTTAATGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (57 bp):
TCAAGAAAATACTTAAAGATATAAAAACCCTTAATAAAATTTAGTGATTCCAAGGAC
Found at i:425753 original size:39 final size:38
Alignment explanation
Indices: 425652--425927 Score: 277
Period size: 39 Copynumber: 7.1 Consensus size: 38
425642 GTTATGCTAC
* *
425652 TGAACAGTTATAGGCTGTTTCCACTTTGCTT-AATGGTAT
1 TGAATAGTT-TAGGCTGTTTCCACTTTG-TTGTATGGTAT
* ** *
425691 TGAATTGTTTAGGCTG-TTCCACTTTGTTGTATTCTAC
1 TGAATAGTTTAGGCTGTTTCCACTTTGTTGTATGGTAT
* *
425728 TGAATAGTTATAAGCTGTTTCCACTTTGTTGTATGTTAT
1 TGAATAGTT-TAGGCTGTTTCCACTTTGTTGTATGGTAT
* * * *
425767 TGAATTGTTTCAGGCTATTTCCACTTTGTTTTAGGGTAT
1 TGAATAGTTT-AGGCTGTTTCCACTTTGTTGTATGGTAT
* * *
425806 TGAAGAGTTTTAGGCTGTTTCCACTTTGTTTTATGGAAT
1 TGAATAG-TTTAGGCTGTTTCCACTTTGTTGTATGGTAT
* * *
425845 TGAATTGTTTCAGGCTATTTCCACTTTGTTATATGGTAT
1 TGAATAGTTT-AGGCTGTTTCCACTTTGTTGTATGGTAT
* ** *
425884 TGAAAAGTTATAGGCTGTTTCCTTTTTGTTGTATGGTAC
1 TGAATAGTT-TAGGCTGTTTCCACTTTGTTGTATGGTAT
425923 TGAAT
1 TGAAT
425928 TGTTGTATGG
Statistics
Matches: 195, Mismatches: 35, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
36 2 0.01
37 22 0.11
38 17 0.09
39 150 0.77
40 4 0.02
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.47
Consensus pattern (38 bp):
TGAATAGTTTAGGCTGTTTCCACTTTGTTGTATGGTAT
Found at i:425831 original size:78 final size:78
Alignment explanation
Indices: 425652--425931 Score: 359
Period size: 78 Copynumber: 3.6 Consensus size: 78
425642 GTTATGCTAC
* * *
425652 TGAACAGTTATAGGCTGTTTCCACTTTGCTT-AATGGTATTGAATTGTTT-AGGCT-GTTCCACT
1 TGAAAAGTTATAGGCTGTTTCCACTTTG-TTGTATGGTATTGAATTGTTTCAGGCTATTTCCACT
* ** *
425714 TTGTTGTATTCTAC
65 TTGTTATATGGTAT
* * *
425728 TGAATAGTTATAAGCTGTTTCCACTTTGTTGTATGTTATTGAATTGTTTCAGGCTATTTCCACTT
1 TGAAAAGTTATAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTTCAGGCTATTTCCACTT
* *
425793 TGTTTTAGGGTAT
66 TGTTATATGGTAT
* * * *
425806 TGAAGAGTTTTAGGCTGTTTCCACTTTGTTTTATGGAATTGAATTGTTTCAGGCTATTTCCACTT
1 TGAAAAGTTATAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTTCAGGCTATTTCCACTT
425871 TGTTATATGGTAT
66 TGTTATATGGTAT
** *
425884 TGAAAAGTTATAGGCTGTTTCCTTTTTGTTGTATGGTACTGAATTGTT
1 TGAAAAGTTATAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTT
425932 GTATGGTATA
Statistics
Matches: 176, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
75 2 0.01
76 42 0.24
77 5 0.03
78 127 0.72
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (78 bp):
TGAAAAGTTATAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTTCAGGCTATTTCCACTT
TGTTATATGGTAT
Found at i:425940 original size:57 final size:57
Alignment explanation
Indices: 425870--425988 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 57
425860 TATTTCCACT
* **
425870 TTGTTATATGGTATTGAA-A-AGTTATAGGCTGTTTCCTTTTTGTTGTATGGTACTGAA
1 TTGTTATATGGTA-T-AAGATAGGTATAGGCTGTTTCCACTTTGTTGTATGGTACTGAA
* * *
425927 TTGTTGTATGGTATAAGATAGGTATAGGCTGTTTCCACTTTGTTTTATGGTATTGAA
1 TTGTTATATGGTATAAGATAGGTATAGGCTGTTTCCACTTTGTTGTATGGTACTGAA
425984 TTGTT
1 TTGTT
425989 TTAGGCTGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
55 2 0.04
56 2 0.04
57 50 0.93
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.48
Consensus pattern (57 bp):
TTGTTATATGGTATAAGATAGGTATAGGCTGTTTCCACTTTGTTGTATGGTACTGAA
Found at i:425982 original size:135 final size:135
Alignment explanation
Indices: 425816--426066 Score: 380
Period size: 135 Copynumber: 1.9 Consensus size: 135
425806 TGAAGAGTTT
425816 TAGGCTGTTTCCACTTTGTTTTATGGAATTGAATTGTTTCAGGCTATTTCC-ACTTTGTTATATG
1 TAGGCTGTTTCCACTTTGTTTTATGGAATTGAATTGTTTCAGGCTATTTCCTA-TTTGTTATATG
* * * * *
425880 GTATTGAAA-AGTTATAGGCTGTTTCCTTTTTGTTGTATGGTACTGAATTGTTGTATGGTATAAG
65 ATATTGAAATA-TTATAGACTGTTTCCATTTTGTTGAATGATACTGAATTGTTGTATGGTATAAG
425944 ATAGGTA
129 ATAGGTA
* * * *
425951 TAGGCTGTTTCCACTTTGTTTTATGGTATTGAATTGTTTTAGGCTGTTTCCTATTTGTTGTATGA
1 TAGGCTGTTTCCACTTTGTTTTATGGAATTGAATTGTTTCAGGCTATTTCCTATTTGTTATATGA
*
426016 TATTGAAATATTATAGACTGTTTCCATTTTGTTGAATGATATTGAATTGTT
66 TATTGAAATATTATAGACTGTTTCCATTTTGTTGAATGATACTGAATTGTT
426067 TAAAGCTGTT
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
135 102 0.98
136 2 0.02
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.48
Consensus pattern (135 bp):
TAGGCTGTTTCCACTTTGTTTTATGGAATTGAATTGTTTCAGGCTATTTCCTATTTGTTATATGA
TATTGAAATATTATAGACTGTTTCCATTTTGTTGAATGATACTGAATTGTTGTATGGTATAAGAT
AGGTA
Found at i:425994 original size:39 final size:39
Alignment explanation
Indices: 425951--426409 Score: 499
Period size: 39 Copynumber: 11.7 Consensus size: 39
425941 AAGATAGGTA
*
425951 TAGGCTGTTTCCACTTTGTTTTATGGTATTGAATTGTTT
1 TAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTT
* * * *
425990 TAGGCTGTTTCCTA-TTTGTTGTATGATATTGAAATATTA
1 TAGGCTGTTTCC-ACTTTGTTGTATGGTATTGAATTGTTT
* * * *
426029 TAGACTGTTTCCATTTTGTTGAATGATATTGAATTGTTT
1 TAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTT
* * * **
426068 AAAGCTGTTTCCACTTTGATGTATTATATTGAATTGTTT
1 TAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTT
* * * *
426107 TAGGCTGTTTCCACTTTGTTGTAT-ATGATTAAATAGTTA
1 TAGGCTGTTTCCACTTTGTTGTATGGT-ATTGAATTGTTT
* * * *
426146 TAGGCTGTATCCACTTTTTATGTATGGTATTGAATAGTTA
1 TAGGCTGTTTCCACTTTGT-TGTATGGTATTGAATTGTTT
* ** * * *
426186 TAGGCTGTTTCCTCTTTGTTGTATTTTATTAAATAGTTA
1 TAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTT
*
426225 TAGGCTGTTTCCACTTTTTATGTATGGTATTGAATTGTTT
1 TAGGCTGTTTCCACTTTGT-TGTATGGTATTGAATTGTTT
* * * * * *
426265 AAGACTGTTTCCTCTTTGTTGTATGATATTGAATAGTTA
1 TAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTT
**
426304 TAGGCTGTTTCCACTTTGTTGGGTGGTATTGAATTGTTT
1 TAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTT
* * * *
426343 AAAGCTATTTACACTTTGTTGTATGGTATTGAATTGTTT
1 TAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTT
426382 TAGGCTGTTTCCACTTTGTTGTATGGTA
1 TAGGCTGTTTCCACTTTGTTGTATGGTA
426410 CTGTAGATTC
Statistics
Matches: 349, Mismatches: 65, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
38 3 0.01
39 282 0.81
40 63 0.18
41 1 0.00
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (39 bp):
TAGGCTGTTTCCACTTTGTTGTATGGTATTGAATTGTTT
Found at i:426103 original size:174 final size:174
Alignment explanation
Indices: 425778--426105 Score: 396
Period size: 174 Copynumber: 1.9 Consensus size: 174
425768 GAATTGTTTC
*
425778 AGGCTATTTCCACTTTGTTTTAGGGTATTGAAGAGTTTTAGGCTGTTTCCACTTTGTTTTATGGA
1 AGGCTATTTCCACTTTGTTTTAGGGTATTGAAGAGTTTTAGGCTGTTTCCACTTTGTTGTATGGA
* * * * * **
425843 ATTGAATTGTTTCAGGCTATTTCCACTTTGTTATATGGTATTGAAAAGTTATAGGCTGTTTCCTT
66 ATTGAAATATTTCAGACTATTTCCACTTTGTTATATGATATTGAAAAGTTATAAGCTGTTTCCAC
* *
425908 TTTGTTGTATGGTACTGAATTGTTGTATGGTATAAGATAGGTAT
131 TTTGATGTATGATACTGAATTGTTGTATGGTATAAGATAGGTAT
* * **
425952 AGGCTGTTTCCACTTTGTTTTATGGTATTGAATTGTTTTAGGCTGTTTCCTA-TTTGTTGTAT-G
1 AGGCTATTTCCACTTTGTTTTAGGGTATTGAAGAGTTTTAGGCTGTTTCC-ACTTTGTTGTATGG
* * **
426015 ATATTGAAATATTAT-AGACTGTTTCCATTTTGTTGA-ATGATATTGAATTGTT-TAAAGCTGTT
65 A-ATTGAAATATT-TCAGACTATTTCCACTTTGTT-ATATGATATTGAAAAGTTAT-AAGCTGTT
* *
426077 TCCACTTTGATGTATTATATTGAATTGTT
126 TCCACTTTGATGTATGATACTGAATTGTT
426106 TTAGGCTGTT
Statistics
Matches: 129, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
173 3 0.02
174 123 0.95
175 3 0.02
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.48
Consensus pattern (174 bp):
AGGCTATTTCCACTTTGTTTTAGGGTATTGAAGAGTTTTAGGCTGTTTCCACTTTGTTGTATGGA
ATTGAAATATTTCAGACTATTTCCACTTTGTTATATGATATTGAAAAGTTATAAGCTGTTTCCAC
TTTGATGTATGATACTGAATTGTTGTATGGTATAAGATAGGTAT
Found at i:426372 original size:21 final size:21
Alignment explanation
Indices: 426348--426409 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
426338 TGTTTAAAGC
426348 TATTTACACTTTGTTGTATGG
1 TATTTACACTTTGTTGTATGG
* *
426369 TATTGA-A--TTGTTTTA-GG
1 TATTTACACTTTGTTGTATGG
* *
426386 CTGTTTCCACTTTGTTGTATGG
1 -TATTTACACTTTGTTGTATGG
426408 TA
1 TA
426410 CTGTAGATTC
Statistics
Matches: 29, Mismatches: 7, Indels: 10
0.63 0.15 0.22
Matches are distributed among these distances:
17 2 0.07
18 10 0.34
19 1 0.03
20 1 0.03
21 13 0.45
22 2 0.07
ACGTcount: A:0.18, C:0.10, G:0.21, T:0.52
Consensus pattern (21 bp):
TATTTACACTTTGTTGTATGG
Found at i:426685 original size:39 final size:39
Alignment explanation
Indices: 426631--427259 Score: 907
Period size: 39 Copynumber: 15.6 Consensus size: 39
426621 GGAATTTACA
426631 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
* * *
426670 GTATTGAATTGTTTCAGACTATTTTCACTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
* * *
426709 GTATTGAATTGTTTCAGACTATTTCCACTTTGTTGTCTG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
*
426748 GTATTGGATTGTTTCAGGCTGTTTCCACTTTGTTGTATGGTATTCAATG
1 GTATTGAATTGTTTCAGGCTGTTTCCAC--T-TTGT-T-G---T--ATG
*
426797 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTCTG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
*
426836 GTATTGAATTGTTTCAGGCTGTTTCCTCTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
* *
426875 GTATTGAATGGTATTGGATTGTTTAAGGCTGTTTCCACTTTGTTGTCTG
1 GTA-T---T-G-A----ATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
426924 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
426963 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
* * *
427002 GTATTGAATTGTTTAAGGCCGTTTCCTCTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
*
427041 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTCTG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
427080 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
* * *
427119 GTATTGAATTGTTTCAGACTATTTCCACTTTGTTGTCTG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
*
427158 GTATTGGATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
427197 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
1 GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
427236 GTATTGAATTGTTTCAGGCTGTTT
1 GTATTGAATTGTTTCAGGCTGTTT
427260 GCTCTGAGCC
Statistics
Matches: 536, Mismatches: 34, Indels: 40
0.88 0.06 0.07
Matches are distributed among these distances:
39 451 0.84
40 1 0.00
41 2 0.00
42 4 0.01
43 3 0.01
44 4 0.01
45 3 0.01
46 4 0.01
47 2 0.00
48 1 0.00
49 61 0.11
ACGTcount: A:0.16, C:0.13, G:0.23, T:0.49
Consensus pattern (39 bp):
GTATTGAATTGTTTCAGGCTGTTTCCACTTTGTTGTATG
Found at i:428640 original size:10 final size:10
Alignment explanation
Indices: 428625--428650 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
428615 ATACACATAC
428625 AAAATAGACG
1 AAAATAGACG
428635 AAAATAGACG
1 AAAATAGACG
428645 AAAATA
1 AAAATA
428651 TTTAAACTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.15, T:0.12
Consensus pattern (10 bp):
AAAATAGACG
Found at i:429442 original size:5 final size:5
Alignment explanation
Indices: 429428--429491 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
429418 TAGTACATTA
* * * *
429428 TATAT AATAT TATAT TAATAT AATAT TATAT AATAAT ATGTAT TATAT
1 TATAT TATAT TATAT T-ATAT TATAT TATAT TAT-AT -TATAT TATAT
429476 TAATAT TATAT TATAT
1 T-ATAT TATAT TATAT
429492 AATAATATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
5 33 0.70
6 13 0.28
7 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (5 bp):
TATAT
Found at i:429447 original size:28 final size:28
Alignment explanation
Indices: 429424--429499 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 28
429414 AAAATAGTAC
429424 ATTATAT-ATAATATTATATTAATATAAT
1 ATTATATAATAATATTATATTAATAT-AT
429452 ATTATATAATAATATGTATTATATTAATATTAT
1 ATTATATAAT-A-A--TATTATATTAATA-TAT
429485 ATTATATAATAATAT
1 ATTATATAATAATAT
429500 GTATCACATG
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
28 7 0.17
29 5 0.12
30 1 0.02
31 2 0.05
32 1 0.02
33 25 0.60
34 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
ATTATATAATAATATTATATTAATATAT
Found at i:429474 original size:33 final size:33
Alignment explanation
Indices: 429435--429503 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
429425 TTATATATAA
429435 TATTATATTAATATAATATTATATAATAATATG
1 TATTATATTAATATAATATTATATAATAATATG
*
429468 TATTATATTAATATTATATTATATAATAATATG
1 TATTATATTAATATAATATTATATAATAATATG
429501 TAT
1 TAT
429504 CACATGTACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (33 bp):
TATTATATTAATATAATATTATATAATAATATG
Found at i:429499 original size:18 final size:16
Alignment explanation
Indices: 429424--429495 Score: 85
Period size: 16 Copynumber: 4.4 Consensus size: 16
429414 AAAATAGTAC
429424 ATTATATATAATATTAT
1 ATTA-ATATAATATTAT
429441 ATTAATATAATATTAT
1 ATTAATATAATATTAT
*
429457 A-TAATAATATGTATTAT
1 ATTAAT-ATA-ATATTAT
*
429474 ATTAATATTATATTAT
1 ATTAATATAATATTAT
429490 A-TAATA
1 ATTAATA
429496 ATATGTATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
15 9 0.18
16 23 0.47
17 13 0.27
18 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (16 bp):
ATTAATATAATATTAT
Found at i:438444 original size:59 final size:59
Alignment explanation
Indices: 438379--438500 Score: 217
Period size: 59 Copynumber: 2.1 Consensus size: 59
438369 GTTACATACC
*
438379 ATTGTGTGTGTAGAATGTATTACTGGTATAAACAGTACATGTATAAAGTACAGCACCAA
1 ATTGTGTGTGTAGAATGTATTACCGGTATAAACAGTACATGTATAAAGTACAGCACCAA
* *
438438 ATTGTGTGTGTAGAATGTATTACCGGTATATACAGTACATGTATATAGTACAGCACCAA
1 ATTGTGTGTGTAGAATGTATTACCGGTATAAACAGTACATGTATAAAGTACAGCACCAA
438497 ATTG
1 ATTG
438501 ATTTGATGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (59 bp):
ATTGTGTGTGTAGAATGTATTACCGGTATAAACAGTACATGTATAAAGTACAGCACCAA
Found at i:440384 original size:14 final size:15
Alignment explanation
Indices: 440357--440385 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
440347 TATCTGTTAT
440357 TTTCAAGATCTTGTC
1 TTTCAAGATCTTGTC
440372 TTTCAAG-TCTTGTC
1 TTTCAAGATCTTGTC
440386 AGCGGTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (15 bp):
TTTCAAGATCTTGTC
Found at i:442785 original size:23 final size:23
Alignment explanation
Indices: 442753--442895 Score: 250
Period size: 23 Copynumber: 6.2 Consensus size: 23
442743 AGAGACTGGT
*
442753 TACAACCCAAGTTCCAGGTAGAC
1 TACAATCCAAGTTCCAGGTAGAC
442776 TACAATCCAAGTTCCAGGTAGAC
1 TACAATCCAAGTTCCAGGTAGAC
442799 TACAATCCAAGTTCCAGGTAGAC
1 TACAATCCAAGTTCCAGGTAGAC
*
442822 TACAATCCAAGTTCCAGGTAGAA
1 TACAATCCAAGTTCCAGGTAGAC
*
442845 TACAATCCAAGTTCCAGGTAGAA
1 TACAATCCAAGTTCCAGGTAGAC
442868 TACAATCCAAGTTCCAGGTAGAC
1 TACAATCCAAGTTCCAGGTAGAC
*
442891 AACAA
1 TACAA
442896 GGTTTGTTGC
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 116 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (23 bp):
TACAATCCAAGTTCCAGGTAGAC
Found at i:453297 original size:21 final size:22
Alignment explanation
Indices: 453271--453320 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
453261 TTGAATCTCC
*
453271 TATTTTCATGAATATTTATTT-
1 TATTTTAATGAATATTTATTTG
* *
453292 TATTTTAATTATTATTTATTTG
1 TATTTTAATGAATATTTATTTG
453314 TATTTTA
1 TATTTTA
453321 TTTATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (22 bp):
TATTTTAATGAATATTTATTTG
Found at i:453320 original size:22 final size:21
Alignment explanation
Indices: 453283--453329 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
453273 TTTTCATGAA
453283 TATTTATTTTATTTTAATTAT
1 TATTTATTTTATTTTAATTAT
*
453304 TATTTATTTGTATTTTATTTAT
1 TATTTATTT-TATTTTAATTAT
453326 TATT
1 TATT
453330 AGATCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TATTTATTTTATTTTAATTAT
Found at i:459808 original size:15 final size:15
Alignment explanation
Indices: 459788--459818 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
459778 CCAAATAAAC
*
459788 ATCTTATCTTATCAT
1 ATCTTATCTTACCAT
459803 ATCTTATCTTACCAT
1 ATCTTATCTTACCAT
459818 A
1 A
459819 CAGAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCTTATCTTACCAT
Found at i:460343 original size:22 final size:22
Alignment explanation
Indices: 460319--460449 Score: 226
Period size: 22 Copynumber: 6.0 Consensus size: 22
460309 TGATAAATTG
*
460319 GAACAACATTAAACGATACTCG
1 GAACAACATTAAACGATACTCA
* *
460341 GAATAACATTAAACGATACTCG
1 GAACAACATTAAACGATACTCA
*
460363 GTACAACATTAAACGATACTCA
1 GAACAACATTAAACGATACTCA
460385 GAACAACATTAAACGATACTCA
1 GAACAACATTAAACGATACTCA
460407 GAACAACATTAAACGATACTCA
1 GAACAACATTAAACGATACTCA
460429 GAACAACATTAAACGATACTC
1 GAACAACATTAAACGATACTC
460450 CTGGTTAGTT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 104 1.00
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (22 bp):
GAACAACATTAAACGATACTCA
Done.