Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold393
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: 1263635
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 115792 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1067240 original size:16 final size:16
Alignment explanation
Indices: 1067216--1067247 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1067206 AAATCTATCT
*
1067216 GTCATAGTATATCTAC
1 GTCACAGTATATCTAC
1067232 GTCACAGTATATCTAC
1 GTCACAGTATATCTAC
1067248 CTGTTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (16 bp):
GTCACAGTATATCTAC
Found at i:1067999 original size:114 final size:114
Alignment explanation
Indices: 1067861--1068067 Score: 283
Period size: 114 Copynumber: 1.8 Consensus size: 114
1067851 CCTGTCAAAA
* * *
1067861 TATATTTACCTGTCATTATATATCTATC-TGTCATAATATATCTACCTGTAATCGTATATCTACA
1 TATATCTACCTGTCATCATATATCTA-CATGTCACAATATATCTACCTGTAATCGTATATCTACA
* *
1067925 TGTCCTAGTACATTTACCTGTTGTAGTATATACTAGTATACCCGTCATAG
65 TATCCTAGTACATTTACCTGTTGAAGTATATACTAGTATACCCGTCATAG
* * * *
1067975 TATATCTACCTGTCA-CAGTATATCTACATGTCACAGTATATCTACCTGTCATGGTATATCTGCA
1 TATATCTACCTGTCATCA-TATATCTACATGTCACAATATATCTACCTGTAATCGTATATCTACA
* *
1068039 TATCCTATTACATTTACTTGTTGAAGTAT
65 TATCCTAGTACATTTACCTGTTGAAGTAT
1068068 TTAACTCTCT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 2 0.03
114 78 0.98
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (114 bp):
TATATCTACCTGTCATCATATATCTACATGTCACAATATATCTACCTGTAATCGTATATCTACAT
ATCCTAGTACATTTACCTGTTGAAGTATATACTAGTATACCCGTCATAG
Found at i:1079960 original size:33 final size:32
Alignment explanation
Indices: 1079869--1079947 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
1079859 CCTAGCCATC
1079869 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
*
1079901 CTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
1079933 TTTCCCCCACGGAAA
1 TTTCCCCC-CGGAAA
1079948 GCTGACTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 38 0.86
33 6 0.14
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (32 bp):
TTTCCCCCCGGAAAAATGGCTATATAGCAGTT
Found at i:1082611 original size:36 final size:36
Alignment explanation
Indices: 1082565--1082667 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
1082555 ACCCTACTAT
1082565 GGGGGAAAAGCTACTATATAGTAGCTTTTCCCCCCG
1 GGGGGAAAAGCTACTATATAGTAGCTTTTCCCCCCG
1082601 GGGGGAAAAGCTACTATATAGTAGCTTTTCCCCCCG
1 GGGGGAAAAGCTACTATATAGTAGCTTTTCCCCCCG
* *
1082637 GGGGGAAAGGCTACTATATAGTAGGTTTTCC
1 GGGGGAAAAGCTACTATATAGTAGCTTTTCC
1082668 GGGGGGAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (36 bp):
GGGGGAAAAGCTACTATATAGTAGCTTTTCCCCCCG
Found at i:1100355 original size:2 final size:2
Alignment explanation
Indices: 1100350--1100376 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1100340 GTGCTAAAAT
1100350 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 G
1100377 CATTTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1112332 original size:20 final size:20
Alignment explanation
Indices: 1112302--1112349 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1112292 GGTTGATAAA
1112302 TATAGATTCACATATGTTAAC
1 TATA-ATTCACATATGTTAAC
* *
1112323 TTTAATTCACATCTGTTAAC
1 TATAATTCACATATGTTAAC
1112343 TATAATT
1 TATAATT
1112350 AAGAGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (20 bp):
TATAATTCACATATGTTAAC
Found at i:1113993 original size:173 final size:172
Alignment explanation
Indices: 1113061--1114029 Score: 1656
Period size: 172 Copynumber: 5.6 Consensus size: 172
1113051 TATCGAGTCC
*
1113061 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATTT
1 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTAATAGTGGTATAAACATTTGGTATAAATTT
*
1113126 AATGAAAATCTGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACGG
66 AATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACGG
* *
1113191 AGTCATTATTGCGGTCAAAGTACCATAACTCCAACAAAAAGT
131 AGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAGT
* *
1113233 ATCTACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATTT
1 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTAATAGTGGTATAAACATTTGGTATAAATTT
* * *
1113298 AATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTAACAAGGCCAATTTTCGGAT-AAACTG
66 AATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAAC-G
*
1113362 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAGG
130 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAGT
*
1113405 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGT-ATAAGTGGTGTAAACATTTGGTATAAATT
1 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTAAT-AGTGGTATAAACATTTGGTATAAATT
*
1113469 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAACTTTTGGATAAAACG
65 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
*
1113534 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAGG
130 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAGT
*
1113577 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGT-ATAAGTGGTGTAAACATTTGGTATAAATT
1 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTAAT-AGTGGTATAAACATTTGGTATAAATT
* * *
1113641 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCGACTTTTGGAAAAAACG
65 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
1113706 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAGT
130 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAGT
* * *
1113749 ATCGACCAATGCTGACTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATTT
1 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTAATAGTGGTATAAACATTTGGTATAAATTT
* * *
1113814 AATGAAAATCCGTCCAAATTTGTAGGCATGAGAGCGCTTACAAGGTCGATTTTTGGATAAAACAG
66 AATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACGG
1113879 AGTCATTATTGTGGTCAAAAGTCCCATAACTCCAACAAAAAGT
131 AGTCATTATTGTGGTC-AAAGTCCCATAACTCCAACAAAAAGT
* *
1113922 ATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTCGTATAAATTT
1 ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTAATAGTGGTATAAACATTTGGTATAAATTT
1113987 AATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
66 AATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
1114030 AAAAGCGTGA
Statistics
Matches: 760, Mismatches: 32, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
171 6 0.01
172 619 0.81
173 135 0.18
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (172 bp):
ATCGACCAATGCTGATTTTCGAACTTGACCAAAGTAATAGTGGTATAAACATTTGGTATAAATTT
AATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACGG
AGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAGT
Found at i:1114054 original size:8 final size:8
Alignment explanation
Indices: 1114043--1114112 Score: 86
Period size: 8 Copynumber: 8.8 Consensus size: 8
1114033 AGCGTGACGG
*
1114043 ACGGACGC
1 ACGGACCC
1114051 ACGGACCC
1 ACGGACCC
* *
1114059 ACAGACAC
1 ACGGACCC
1114067 ACGGACCC
1 ACGGACCC
* *
1114075 ACAGACAC
1 ACGGACCC
1114083 ACGGACCC
1 ACGGACCC
*
1114091 ACGGACAC
1 ACGGACCC
1114099 ACGGACCC
1 ACGGACCC
1114107 ACGGAC
1 ACGGAC
1114113 GGACGCCCGG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 51 1.00
ACGTcount: A:0.33, C:0.43, G:0.24, T:0.00
Consensus pattern (8 bp):
ACGGACCC
Found at i:1114109 original size:16 final size:16
Alignment explanation
Indices: 1114043--1114112 Score: 113
Period size: 16 Copynumber: 4.4 Consensus size: 16
1114033 AGCGTGACGG
*
1114043 ACGGACGCACGGACCC
1 ACGGACACACGGACCC
*
1114059 ACAGACACACGGACCC
1 ACGGACACACGGACCC
*
1114075 ACAGACACACGGACCC
1 ACGGACACACGGACCC
1114091 ACGGACACACGGACCC
1 ACGGACACACGGACCC
1114107 ACGGAC
1 ACGGAC
1114113 GGACGCCCGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.33, C:0.43, G:0.24, T:0.00
Consensus pattern (16 bp):
ACGGACACACGGACCC
Found at i:1115696 original size:2 final size:2
Alignment explanation
Indices: 1115689--1115739 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1115679 AACACATATA
1115689 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
1115731 AG AG AG AG A
1 AG AG AG AG A
1115740 TTTACCTGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1120974 original size:19 final size:18
Alignment explanation
Indices: 1120950--1120986 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1120940 GGGGGGGGGG
1120950 GTGATGAAGAGTCCTAGA
1 GTGATGAAGAGTCCTAGA
1120968 NGTGATGAAGAGTCCTAGA
1 -GTGATGAAGAGTCCTAGA
1120987 ATATTGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.22
Consensus pattern (18 bp):
GTGATGAAGAGTCCTAGA
Found at i:1133021 original size:42 final size:42
Alignment explanation
Indices: 1132962--1133171 Score: 384
Period size: 42 Copynumber: 5.0 Consensus size: 42
1132952 CACAAAAATA
1132962 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAGTAGT
1 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAGTAGT
*
1133004 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAATAGT
1 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAGTAGT
*
1133046 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAATAGT
1 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAGTAGT
*
1133088 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAGTGGT
1 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAGTAGT
*
1133130 CTTTAGTCAGCTTATGATAAATTGTAGATAATTGACAGTAGT
1 CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAGTAGT
1133172 GTTATTAAAC
Statistics
Matches: 163, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 163 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (42 bp):
CTTTAGTCAGCTTATGATAAATTGTAGCTAATTGACAGTAGT
Found at i:1133057 original size:25 final size:25
Alignment explanation
Indices: 1133029--1133099 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
1133019 GATAAATTGT
1133029 AGCTAATTGACAATAGTCTTTAGTC
1 AGCTAATTGACAATAGTCTTTAGTC
* *
1133054 AGCTTA-TGATAA-A----TT-GT-
1 AGCTAATTGACAATAGTCTTTAGTC
1133071 AGCTAATTGACAATAGTCTTTAGTC
1 AGCTAATTGACAATAGTCTTTAGTC
1133096 AGCT
1 AGCT
1133100 TATGATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 5 0.15
18 7 0.21
19 3 0.09
23 3 0.09
24 7 0.21
25 9 0.26
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (25 bp):
AGCTAATTGACAATAGTCTTTAGTC
Found at i:1133319 original size:11 final size:11
Alignment explanation
Indices: 1133299--1133335 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1133289 AATATATTTT
*
1133299 AATAAGGATTA
1 AATAAAGATTA
1133310 AATAAAGATTA
1 AATAAAGATTA
1133321 AATAAAGATTA
1 AATAAAGATTA
1133332 AATA
1 AATA
1133336 TAGAGTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (11 bp):
AATAAAGATTA
Found at i:1134566 original size:22 final size:22
Alignment explanation
Indices: 1134540--1134583 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1134530 GGGAAAACTT
1134540 CTATTTTACATACATTAATAAA
1 CTATTTTACATACATTAATAAA
* *
1134562 CTATTTTTCATACATTGATAAA
1 CTATTTTACATACATTAATAAA
1134584 GAAGCAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (22 bp):
CTATTTTACATACATTAATAAA
Found at i:1138041 original size:19 final size:19
Alignment explanation
Indices: 1138017--1138056 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1138007 ATGTGTATAT
1138017 AACTTATGTGTAAGTTAAC
1 AACTTATGTGTAAGTTAAC
1138036 AACTTATGTGTAAGTTAAC
1 AACTTATGTGTAAGTTAAC
1138055 AA
1 AA
1138057 AGTTTAGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
AACTTATGTGTAAGTTAAC
Found at i:1139543 original size:4 final size:4
Alignment explanation
Indices: 1139519--1139565 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
1139509 GTTTACAGAT
* * *
1139519 GGAC GGAC AGAC AGAC AGAC GGAC GGAC GGAC GGAC GGAC -GAC GGAC
1 GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC
1139566 AACAGGTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 37 0.93
ACGTcount: A:0.32, C:0.26, G:0.43, T:0.00
Consensus pattern (4 bp):
GGAC
Found at i:1150614 original size:166 final size:160
Alignment explanation
Indices: 1150388--1151046 Score: 499
Period size: 166 Copynumber: 4.1 Consensus size: 160
1150378 GTATTTTTTC
* * * * * *
1150388 AAAAATCTTCTTCTCAAAAACTATTCGGCCTGAAAAGCTTAAACTTGTGTGGAGGCATCCTCATG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAA-TTGAGTGGAAGCATCCTCA-G
* * * *
1150453 TAGTGTAGATTCAAGTGTGTTCAAATCATGATCCTGGGGGCTAGGGAGGGGCCACAAGAGGGGGA
64 TAGTGTAGATTCAAGTTTGTTCAAATAATGATCC-AGGGG-TAGGGAGGGGCCACAA-TGGGGGA
1150518 TCAAATTTTACATAGGAATATATAGAGAAAATCTTT
126 T-AAATTTTACATAGGAATATATAGAGAAAATCTTT
* * *
1150554 AAAAATCTTCTTCTCAAAAACTATTAGGTCAGGAAAGCTCAAATTAAAGTGGAAGCATCCTTAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATT-GAGTGGAAGCATCCTCA-G
* * * *
1150619 TAGTGTAGATTCAAGTTTGTTCAAATTATGGTCCCCAGGGGTAGGGCGGGGCTACAATGGGGGAT
64 TAGTGTAGATTCAAGTTTGTTCAAATAATGAT--CCAGGGGTAGGGAGGGGCCACAATGGGGGAT
* *
1150684 AAATTTT---T----ATTTATTGAGAAAATCTTT
127 AAATTTTACATAGGAATATATAGAGAAAATCTTT
* * * * *
1150711 AAACATCTTTTTCTC-AAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAAGCACCCCCAGT
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAA-TTGAGTGGAAGCATCCTCAG-
* * * * * * *
1150775 TCGTATAGATTCAAGTTTGTTTAAATAAT-AGTACAGTGGTAGGGTGAGGCCACAATGGGGGATG
64 TAGTGTAGATTCAAGTTTGTTCAAATAATGA-TCCAGGGGTAGGGAGGGGCCACAATGGGGGAT-
*
1150839 AATTTTTACATAGGAATATATAGAGAAAAAATCTTT
127 AAATTTTACATAGGAATATATAGAG--AAAATCTTT
* * * * * * * **
1150875 AAAAAGCTT-TT-T-AAAGACTATTTA-GCCAGAAAAGCTTAAACTTGTGTAGAGGCATCCTTGG
1 AAAAATCTTCTTCTCAAAAACTA-TTAGGCCAGGAAAGCTCAAA-TTGAGTGGAAGCATCC-TCA
* * * ****
1150936 GTAGTGTAAATTCAAGTTTG--CAAAATCACA-G-TCCATTGTGGTAGGGCGGGGCTGTGAT-GG
63 GTAGTGTAGATTCAAGTTTGTTC-AAAT-A-ATGATCCA--GGGGTAGGGAGGGGCCACAATGGG
* *
1150996 CGATTGAATTTTTACATAGGAATATATAGAGAAAATCTTT
123 GGA-T-AAATTTTACATAGGAATATATAGAGAAAATCTTT
*
1151036 AAAAATATTCT
1 AAAAATCTTCT
1151047 GGGAAAGTTT
Statistics
Matches: 398, Mismatches: 68, Indels: 58
0.76 0.13 0.11
Matches are distributed among these distances:
154 26 0.07
155 7 0.02
156 64 0.16
157 32 0.08
158 1 0.00
161 24 0.06
162 62 0.16
163 49 0.12
164 23 0.06
165 9 0.02
166 95 0.24
167 4 0.01
168 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (160 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTGAGTGGAAGCATCCTCAGTA
GTGTAGATTCAAGTTTGTTCAAATAATGATCCAGGGGTAGGGAGGGGCCACAATGGGGGATAAAT
TTTACATAGGAATATATAGAGAAAATCTTT
Found at i:1152811 original size:2 final size:2
Alignment explanation
Indices: 1152804--1152850 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1152794 TTTCCAGGGA
1152804 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
1152846 AG AG A
1 AG AG A
1152851 TCAAACTGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1158052 original size:18 final size:18
Alignment explanation
Indices: 1158021--1158055 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1158011 GTAAAGTATG
*
1158021 TTTTTGCATGCAAATATT
1 TTTTTGCATACAAATATT
*
1158039 TTTTTTCATACAAATAT
1 TTTTTGCATACAAATAT
1158056 ATATACATCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTTTGCATACAAATATT
Found at i:1161864 original size:74 final size:74
Alignment explanation
Indices: 1161737--1161915 Score: 252
Period size: 74 Copynumber: 2.4 Consensus size: 74
1161727 AACCAAATCA
** *
1161737 ACGAAGTCTTCGACAGTATATCCTATAGCAAGGTATGGACCATTACACACAAATGTTGA-AGGTC
1 ACGAAGTCTTCGACAGTATATCCTATAGCAAGGTATAAACCATTACACACAAATGTTGATA-GCC
*
1161801 TGTTCAATAT
65 TGTACAATAT
* * *
1161811 ATGAAGTCTTCGACAGTATATCCTATAGCAAGGTATAAACCATTGCACCCAAATGTTGATAGCCT
1 ACGAAGTCTTCGACAGTATATCCTATAGCAAGGTATAAACCATTACACACAAATGTTGATAGCCT
1161876 GTACAATAT
66 GTACAATAT
* * *
1161885 ACGAAGTCTTCGACAGTTTATCATACAGCAA
1 ACGAAGTCTTCGACAGTATATCCTATAGCAA
1161916 CGTGGATCTT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 92 0.99
75 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (74 bp):
ACGAAGTCTTCGACAGTATATCCTATAGCAAGGTATAAACCATTACACACAAATGTTGATAGCCT
GTACAATAT
Found at i:1165259 original size:21 final size:21
Alignment explanation
Indices: 1165233--1165304 Score: 135
Period size: 21 Copynumber: 3.4 Consensus size: 21
1165223 AAATCATTTG
1165233 AAGATAGGTACAATTGAATTA
1 AAGATAGGTACAATTGAATTA
1165254 AAGATAGGTACAATTGAATTA
1 AAGATAGGTACAATTGAATTA
*
1165275 AAGATAGGTACAATTGAATTG
1 AAGATAGGTACAATTGAATTA
1165296 AAGATAGGT
1 AAGATAGGT
1165305 GTAAATAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.28
Consensus pattern (21 bp):
AAGATAGGTACAATTGAATTA
Found at i:1165358 original size:21 final size:21
Alignment explanation
Indices: 1165332--1165404 Score: 146
Period size: 21 Copynumber: 3.5 Consensus size: 21
1165322 TCTCTAAATT
1165332 ATTATACCTAGGTACAAATGA
1 ATTATACCTAGGTACAAATGA
1165353 ATTATACCTAGGTACAAATGA
1 ATTATACCTAGGTACAAATGA
1165374 ATTATACCTAGGTACAAATGA
1 ATTATACCTAGGTACAAATGA
1165395 ATTATACCTA
1 ATTATACCTA
1165405 TCTTCAATTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (21 bp):
ATTATACCTAGGTACAAATGA
Found at i:1165418 original size:21 final size:21
Alignment explanation
Indices: 1165394--1165457 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
1165384 GGTACAAATG
1165394 AATTATACCTATCTTCAATTC
1 AATTATACCTATCTTCAATTC
* ** ** *
1165415 AATTAAAGATAGGTTCAATTG
1 AATTATACCTATCTTCAATTC
1165436 AATTATACCTATC-TCTAATTC
1 AATTATACCTATCTTC-AATTC
1165457 A
1 A
1165458 TTTGAAGATA
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (21 bp):
AATTATACCTATCTTCAATTC
Found at i:1165466 original size:42 final size:42
Alignment explanation
Indices: 1165243--1165475 Score: 161
Period size: 42 Copynumber: 5.6 Consensus size: 42
1165233 AAGATAGGTA
* * * ** ** *
1165243 CAATTGAATTAAAGATAGGTACAATTGAATTAAAGATAGGTA
1 CAATTCAATTAAAGATAGGTACAAATGAATTATACCTATCTT
* * **
1165285 CAATTGAATTGAAGATAGGTGTAAAT-AATTATACCTATCTCT
1 CAATTCAATTAAAGATAGGTACAAATGAATTATACCTATCT-T
* * ** ** *
1165327 AAATT--ATTATACCTAGGTACAAATGAATTATACCTAGGTA
1 CAATTCAATTAAAGATAGGTACAAATGAATTATACCTATCTT
* * * **
1165367 CAAATGAATTATACCTAGGTACAAATGAATTATACCTATCTT
1 CAATTCAATTAAAGATAGGTACAAATGAATTATACCTATCTT
* *
1165409 CAATTCAATTAAAGATAGGTTCAATTGAATTATACCTATC-T
1 CAATTCAATTAAAGATAGGTACAAATGAATTATACCTATCTT
* *
1165450 CTAATTCATTTGAAGATAGGTA-AAAT
1 C-AATTCAATTAAAGATAGGTACAAAT
1165476 TCATTTAAAG
Statistics
Matches: 150, Mismatches: 36, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
40 16 0.11
41 26 0.17
42 108 0.72
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (42 bp):
CAATTCAATTAAAGATAGGTACAAATGAATTATACCTATCTT
Found at i:1165517 original size:21 final size:21
Alignment explanation
Indices: 1165452--1165520 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
1165442 ACCTATCTCT
*
1165452 AATTCATTTGAAGATAGGTAA
1 AATTCATTTGAAGATAGGTAC
*
1165473 AATTCATTTAAAGATAGGTAC
1 AATTCATTTGAAGATAGGTAC
* *
1165494 AATTGATTTGAAGATAGGTTC
1 AATTCATTTGAAGATAGGTAC
1165515 AATTCA
1 AATTCA
1165521 GACATATCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (21 bp):
AATTCATTTGAAGATAGGTAC
Found at i:1166119 original size:21 final size:21
Alignment explanation
Indices: 1166092--1166185 Score: 125
Period size: 21 Copynumber: 4.2 Consensus size: 21
1166082 TGAAGATAGG
1166092 TTCAATTCAATTGTACCTATC
1 TTCAATTCAATTGTACCTATC
*
1166113 TTTAATTCAATTGTACCTATC
1 TTCAATTCAATTGTACCTATC
1166134 TTCAATTCATTGCATTTGTACCTATC
1 TTCAATTCA----A-TTGTACCTATC
*
1166160 TTCAAATCAATTGTACCTATC
1 TTCAATTCAATTGTACCTATC
1166181 TTCAA
1 TTCAA
1166186 ATGAATTAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
21 44 0.68
22 1 0.02
25 1 0.02
26 19 0.29
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAATTCAATTGTACCTATC
Found at i:1166252 original size:43 final size:42
Alignment explanation
Indices: 1166168--1166293 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 42
1166158 TCTTCAAATC
* *
1166168 AATTGTACCTATCTTCAAATGAATTAAAGATAGGTATAATTG
1 AATTGTACCTATCTTCAAATCAATTAAAGATAGGTACAATTG
* *
1166210 AATTGTACCTATC-TCTAATTCAATTTGAAGATAGGTACAATTG
1 AATTGTACCTATCTTC-AAATCAA-TTAAAGATAGGTACAATTG
* ** ** * * *
1166253 AATTGAAGATAGGTACAATTGAATTAAAGATAGGTACAATT
1 AATTGTACCTATCTTCAAATCAATTAAAGATAGGTACAATT
1166294 ATTTGAAGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 2 0.03
42 35 0.51
43 31 0.45
44 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (42 bp):
AATTGTACCTATCTTCAAATCAATTAAAGATAGGTACAATTG
Found at i:1166260 original size:21 final size:21
Alignment explanation
Indices: 1166234--1166311 Score: 131
Period size: 21 Copynumber: 3.8 Consensus size: 21
1166224 CTAATTCAAT
1166234 TTGAAGATAGGTACAATTGAA
1 TTGAAGATAGGTACAATTGAA
1166255 TTGAAGATAGGTACAATTGAA
1 TTGAAGATAGGTACAATTGAA
* *
1166276 TTAAAGATAGGTACAATT-AT
1 TTGAAGATAGGTACAATTGAA
1166296 TTGAAGATAGGTACAA
1 TTGAAGATAGGTACAA
1166312 ATATTTGAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 16 0.30
21 38 0.70
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGAAGATAGGTACAATTGAA
Found at i:1166304 original size:20 final size:21
Alignment explanation
Indices: 1166232--1166320 Score: 128
Period size: 21 Copynumber: 4.3 Consensus size: 21
1166222 CTCTAATTCA
1166232 ATTTGAAGATAGGTACAATTG
1 ATTTGAAGATAGGTACAATTG
*
1166253 AATTGAAGATAGGTACAATTG
1 ATTTGAAGATAGGTACAATTG
* *
1166274 AATTAAAGATAGGTACAATT-
1 ATTTGAAGATAGGTACAATTG
*
1166294 ATTTGAAGATAGGTACAAAT-
1 ATTTGAAGATAGGTACAATTG
1166314 ATTTGAA
1 ATTTGAA
1166321 TATATGTTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
20 24 0.38
21 39 0.62
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (21 bp):
ATTTGAAGATAGGTACAATTG
Found at i:1185121 original size:34 final size:32
Alignment explanation
Indices: 1185038--1185160 Score: 124
Period size: 34 Copynumber: 3.8 Consensus size: 32
1185028 TTACATTGTA
1185038 AAGTAATGCATTACATTACCATTAC-TTCATG
1 AAGTAATGCATTACATTACCATTACATTCATG
* *** * *
1185069 AATTTGGGCATTAAATTACCATTACCATTTCTTG
1 AAGTAATGCATTACATTACCATTA-CA-TTCATG
* *
1185103 AAGTAATGCATTACATTACCATTACA-TGAGTA
1 AAGTAATGCATTACATTACCATTACATTCA-TG
1185135 AAGTAATGCATTACCATTACCATTAC
1 AAGTAATGCATTA-CATTACCATTAC
1185161 TTTTTTTTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
31 20 0.27
32 15 0.21
33 14 0.19
34 24 0.33
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (32 bp):
AAGTAATGCATTACATTACCATTACATTCATG
Found at i:1189439 original size:15 final size:12
Alignment explanation
Indices: 1189406--1189431 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1189396 ACGGACAGAC
1189406 TTCCAAATATTT
1 TTCCAAATATTT
1189418 TTCCAAATATTT
1 TTCCAAATATTT
1189430 TT
1 TT
1189432 TGTCCAAACT
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:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (12 bp):
TTCCAAATATTT
Found at i:1193459 original size:2 final size:2
Alignment explanation
Indices: 1193436--1193478 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
1193426 AAAACGTTTC
* *
1193436 TA TA TA CA TA -A TA TA CTG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
1193478 T
1 T
1193479 GCAAGAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1194000 original size:44 final size:44
Alignment explanation
Indices: 1193951--1194048 Score: 187
Period size: 45 Copynumber: 2.2 Consensus size: 44
1193941 ACGGGTTGTG
1193951 TCCTTTTCTACTGGTTGGGTTAATAAGGGTTCAGCTCTTGATGC
1 TCCTTTTCTACTGGTTGGGTTAATAAGGGTTCAGCTCTTGATGC
1193995 TCCTTTTTCTACTGGTTGGGTTAATAAGGGTTCAGCTCTTGATGC
1 TCC-TTTTCTACTGGTTGGGTTAATAAGGGTTCAGCTCTTGATGC
1194040 TCCTTTTCT
1 TCCTTTTCT
1194049 TTGCTTAACA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 9 0.17
45 44 0.83
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.44
Consensus pattern (44 bp):
TCCTTTTCTACTGGTTGGGTTAATAAGGGTTCAGCTCTTGATGC
Found at i:1200407 original size:89 final size:89
Alignment explanation
Indices: 1200304--1200476 Score: 346
Period size: 89 Copynumber: 1.9 Consensus size: 89
1200294 TACAGAAAGA
1200304 TGATGCATAAAATAGTATTTGCAATTATAATATACTAAAGAATGACATTTTAACTCCTTCATATT
1 TGATGCATAAAATAGTATTTGCAATTATAATATACTAAAGAATGACATTTTAACTCCTTCATATT
1200369 TTCAATACATTGATTTTTTCTTTC
66 TTCAATACATTGATTTTTTCTTTC
1200393 TGATGCATAAAATAGTATTTGCAATTATAATATACTAAAGAATGACATTTTAACTCCTTCATATT
1 TGATGCATAAAATAGTATTTGCAATTATAATATACTAAAGAATGACATTTTAACTCCTTCATATT
1200458 TTCAATACATTGATTTTTT
66 TTCAATACATTGATTTTTT
1200477 TTATCAGGTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (89 bp):
TGATGCATAAAATAGTATTTGCAATTATAATATACTAAAGAATGACATTTTAACTCCTTCATATT
TTCAATACATTGATTTTTTCTTTC
Found at i:1216819 original size:2 final size:2
Alignment explanation
Indices: 1216814--1216860 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1216804 ATGTCTATAA
1216814 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
1216856 TC TC T
1 TC TC T
1216861 TCAAAACAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1218085 original size:21 final size:21
Alignment explanation
Indices: 1218060--1218102 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1218050 TAAAGCTTTC
1218060 ACCACAATACATGAA-GGTTTT
1 ACCACAATACAT-AATGGTTTT
*
1218081 ACCACCATACATAATGGTTTT
1 ACCACAATACATAATGGTTTT
1218102 A
1 A
1218103 ATACACCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (21 bp):
ACCACAATACATAATGGTTTT
Found at i:1218426 original size:21 final size:21
Alignment explanation
Indices: 1218342--1218512 Score: 162
Period size: 21 Copynumber: 8.1 Consensus size: 21
1218332 CGACATAACG
*
1218342 TAATGATGTTACCACTTCATA
1 TAATGATGTTACCACTGCATA
* * * *
1218363 TAAAGATTTTACCCCTGAATA
1 TAATGATGTTACCACTGCATA
* ** ** * *
1218384 TAATGGTGAAATAACAGTATA
1 TAATGATGTTACCACTGCATA
1218405 TAATGATGTTACCACTGCATA
1 TAATGATGTTACCACTGCATA
* *
1218426 TAATTATGTTAGCACTGCATA
1 TAATGATGTTACCACTGCATA
*
1218447 TAATGATGTTACCACTGCATG
1 TAATGATGTTACCACTGCATA
*
1218468 TAATGATATTACCACTGCATA
1 TAATGATGTTACCACTGCATA
* * * *
1218489 TGATGATATTACTATTGCATA
1 TAATGATGTTACCACTGCATA
1218510 TAA
1 TAA
1218513 ATGAAATACC
Statistics
Matches: 117, Mismatches: 33, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 117 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (21 bp):
TAATGATGTTACCACTGCATA
Found at i:1218523 original size:42 final size:42
Alignment explanation
Indices: 1218402--1218534 Score: 133
Period size: 42 Copynumber: 3.2 Consensus size: 42
1218392 AAATAACAGT
* * ** *
1218402 ATATAATGATGTTACCACTGCATATAATTATGTTAGCACTGC
1 ATATAATGATATTACCACTGCATATAATGATAATACCACTGC
* * *
1218444 ATATAATGATGTTACCACTGCATGTAATGATATTACCACTGC
1 ATATAATGATATTACCACTGCATATAATGATAATACCACTGC
* * * * *
1218486 ATATGATGATATTACTATTGCATATAAATGA-AATACCAGTTC
1 ATATAATGATATTACCACTGCATAT-AATGATAATACCACTGC
1218528 ATATAAT
1 ATATAAT
1218535 ATGAAATTGA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 72 0.94
43 5 0.06
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (42 bp):
ATATAATGATATTACCACTGCATATAATGATAATACCACTGC
Done.