Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1174
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: 1120009
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 47637 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:912870 original size:20 final size:20
Alignment explanation
Indices: 912843--912894 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
912833 TACTCCGCCA
912843 GTTT-TTTTTT-TTT-GTTT
1 GTTTGTTTTTTGTTTGGTTT
*
912860 TTTTGTTTTTTGTTTGGTTT
1 GTTTGTTTTTTGTTTGGTTT
912880 GTTTGTTTGTTTGTT
1 GTTTGTTT-TTTGTT
912895 CAAAACCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 6 0.21
19 3 0.10
20 11 0.38
21 6 0.21
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (20 bp):
GTTTGTTTTTTGTTTGGTTT
Found at i:912883 original size:4 final size:4
Alignment explanation
Indices: 912853--912894 Score: 59
Period size: 4 Copynumber: 10.5 Consensus size: 4
912843 GTTTTTTTTT
*
912853 TTTG TTTT TTTG TTT- TTTG TTTGG TTTG TTTG TTTG TTTG TT
1 TTTG TTTG TTTG TTTG TTTG TTT-G TTTG TTTG TTTG TTTG TT
912895 CAAAACCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 4 0.12
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (4 bp):
TTTG
Found at i:912892 original size:17 final size:16
Alignment explanation
Indices: 912850--912892 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
912840 CCAGTTTTTT
*
912850 TTTTTTGTTT-TTTTG
1 TTTTTTGTTTGGTTTG
912865 TTTTTTGTTTGGTTTG
1 TTTTTTGTTTGGTTTG
912881 TTTGTTTGTTTG
1 TTT-TTTGTTTG
912893 TTCAAAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.40
16 7 0.28
17 8 0.32
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (16 bp):
TTTTTTGTTTGGTTTG
Found at i:916380 original size:2 final size:2
Alignment explanation
Indices: 916373--916417 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
916363 ACTGATAATA
916373 CT 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 CT
916415 CT C
1 CT C
916418 CACACACACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:928627 original size:46 final size:46
Alignment explanation
Indices: 928574--928895 Score: 635
Period size: 46 Copynumber: 7.0 Consensus size: 46
928564 TTCCTATTAT
*
928574 CACTCTTGGGTTAGAAATGTGTGCATAAAGGGATAAACCGCATACA
1 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
928620 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
1 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
928666 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
1 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
928712 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
1 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
928758 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
1 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
928804 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
1 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
928850 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
1 CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
928896 TACCCAAACC
Statistics
Matches: 275, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 275 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (46 bp):
CACTCTTGGGTTAGAAATGTGTGCACAAAGGGATAAACCGCATACA
Found at i:932134 original size:26 final size:25
Alignment explanation
Indices: 932070--932134 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 25
932060 ATCTTTTACA
* *
932070 ATTTTATGCTATGCTATGGTATGCG
1 ATTTTATGCTATGCTATGCTATGAG
*
932095 ATTTTA----ATGATATGCTATGAG
1 ATTTTATGCTATGCTATGCTATGAG
932116 ATTTGTATGCTATGCTATG
1 ATTT-TATGCTATGCTATG
932135 AGAAATTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
21 16 0.52
22 2 0.06
25 6 0.19
26 7 0.23
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.45
Consensus pattern (25 bp):
ATTTTATGCTATGCTATGCTATGAG
Found at i:932181 original size:15 final size:15
Alignment explanation
Indices: 932161--932189 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
932151 GGGTTAATGA
932161 TATGGTATGCTATGC
1 TATGGTATGCTATGC
932176 TATGGTATGCTATG
1 TATGGTATGCTATG
932190 AGATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (15 bp):
TATGGTATGCTATGC
Found at i:932411 original size:21 final size:21
Alignment explanation
Indices: 932373--932460 Score: 126
Period size: 21 Copynumber: 4.2 Consensus size: 21
932363 GAATGCGATT
932373 CTATGAGATTGT--ATGCTATG
1 CTATGAGATT-TCAATGCTATG
* *
932393 GTATGAGATTCCAATGCTATG
1 CTATGAGATTTCAATGCTATG
932414 CTATGAGATTTCAATGCTATG
1 CTATGAGATTTCAATGCTATG
*
932435 CTATGGGATTTCAATGCTATG
1 CTATGAGATTTCAATGCTATG
932456 CTATG
1 CTATG
932461 CTATCGTGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
20 9 0.15
21 52 0.85
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (21 bp):
CTATGAGATTTCAATGCTATG
Found at i:932431 original size:42 final size:41
Alignment explanation
Indices: 932342--932460 Score: 132
Period size: 42 Copynumber: 2.9 Consensus size: 41
932332 TGTTGTATGC
* * * * *
932342 TATGCTATGGTATGATATGACGAATGCGATTCTATGAGATTG
1 TATGCTATGGTATGAGAT-TCCAATGCTATGCTATGAGATTG
932384 TATGCTATGGTATGAGATTCCAATGCTATGCTATGAGATT-
1 TATGCTATGGTATGAGATTCCAATGCTATGCTATGAGATTG
* * *
932424 TCAATGCTATGCTATGGGATTTCAATGCTATGCTATG
1 T--ATGCTATGGTATGAGATTCCAATGCTATGCTATG
932461 CTATCGTGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
40 1 0.01
41 18 0.27
42 48 0.72
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (41 bp):
TATGCTATGGTATGAGATTCCAATGCTATGCTATGAGATTG
Found at i:943723 original size:174 final size:173
Alignment explanation
Indices: 943390--943802 Score: 614
Period size: 174 Copynumber: 2.3 Consensus size: 173
943380 TATTGCATAT
* *
943390 TCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATA
1 TCTTTTGCAGATCAACTGTACATATATTAGAGGTGTGCATATTGCTAGGATTTTGA--T-T--T-
* *
943455 ATTTATGAAAAAATACAAGCTTTTGAACTAAGTCATGTTTTGGCAAAATATTGCATATAGGGTAC
60 -TTTATGAAAAAATACAAGCTTTCGAACTAAGTAATGTTTTGGCAAAATATTGCATATAGGGTAC
* *
943520 CCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGGTTGC
124 CCTCATTGTACAGATAACCCCTCCTACAGTTTTCAAGATAGGAAGGTTGC
943570 TCTTTTGCAGATCAACTGTACATATATTAGAGGTGTGCATATTGCTAGGATTTTGATTTTTTATG
1 TCTTTTGCAGATCAACTGTACATATATTAGAGGTGTGCATATTGCTAGGATTTTGATTTTTTATG
* * *
943635 AAAAAAATGCCAGCTTTCGAACTTAA-TAATTTTTTGGCAAAATATTGCATATAGGGTACCCTCA
66 -AAAAAATACAAGCTTTCGAAC-TAAGTAATGTTTTGGCAAAATATTGCATATAGGGTACCCTCA
*
943699 TTGTACAGATAGCCCCTCCTACAGTTTTCAAGATAGGAAGGTTGC
129 TTGTACAGATAACCCCTCCTACAGTTTTCAAGATAGGAAGGTTGC
* * *
943744 TCTTTTGCAGATCAACTGTACATACATTTGAGGTGTGCATATTGCTAGGTTTTTG-TTTT
1 TCTTTTGCAGATCAACTGTACATATATTAGAGGTGTGCATATTGCTAGGATTTTGATTTT
943803 CTGGTATTTT
Statistics
Matches: 218, Mismatches: 13, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
173 10 0.05
174 148 0.68
175 4 0.02
177 1 0.00
178 1 0.00
180 54 0.25
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (173 bp):
TCTTTTGCAGATCAACTGTACATATATTAGAGGTGTGCATATTGCTAGGATTTTGATTTTTTATG
AAAAAATACAAGCTTTCGAACTAAGTAATGTTTTGGCAAAATATTGCATATAGGGTACCCTCATT
GTACAGATAACCCCTCCTACAGTTTTCAAGATAGGAAGGTTGC
Found at i:945698 original size:2 final size:2
Alignment explanation
Indices: 945691--945728 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
945681 CTAATTTTTG
945691 TA TA TA TA TA TA TA 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
945729 NNNNNNNNNN
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:945815 original size:2 final size:2
Alignment explanation
Indices: 945808--945832 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
945798 NNNNNNNNNN
945808 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
945833 CAGAGAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:950596 original size:12 final size:12
Alignment explanation
Indices: 950579--950604 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
950569 AGAACGGAAT
950579 GTGAAGCCCCCA
1 GTGAAGCCCCCA
950591 GTGAAGCCCCCA
1 GTGAAGCCCCCA
950603 GT
1 GT
950605 TGGTAAATTA
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:0.23, C:0.38, G:0.27, T:0.12
Consensus pattern (12 bp):
GTGAAGCCCCCA
Found at i:953056 original size:3 final size:3
Alignment explanation
Indices: 953048--953077 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
953038 TTTAAGGGCA
*
953048 ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
953078 GAAAGTGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:965308 original size:35 final size:35
Alignment explanation
Indices: 965269--965353 Score: 134
Period size: 35 Copynumber: 2.4 Consensus size: 35
965259 CTCATCAAAT
*
965269 CAATATAAATATTTGAACATCTCAGCAACTCCTTC
1 CAATATAAATATATGAACATCTCAGCAACTCCTTC
*
965304 CAATATAAATATATGAACATCTCCGCAACTCCTTC
1 CAATATAAATATATGAACATCTCAGCAACTCCTTC
* *
965339 TAATATAAATGTATG
1 CAATATAAATATATG
965354 CACTAGTCTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (35 bp):
CAATATAAATATATGAACATCTCAGCAACTCCTTC
Found at i:965643 original size:2 final size:2
Alignment explanation
Indices: 965638--965673 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
965628 TAGAATTATT
965638 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
965674 ATACAAGTAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:966354 original size:2 final size:2
Alignment explanation
Indices: 966347--966390 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
966337 GGAAAATCTT
* * *
966347 TC TC TC TC TC TC TC TC TC TC CC CC CC 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
966389 TC
1 TC
966391 ATCAATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (2 bp):
TC
Found at i:966633 original size:17 final size:17
Alignment explanation
Indices: 966611--966644 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
966601 TGCTAAAATG
*
966611 CGGAACGGAAAGCGGAA
1 CGGAACGGAAAACGGAA
966628 CGGAACGGAAAACGGAA
1 CGGAACGGAAAACGGAA
966645 AATCTTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.38, T:0.00
Consensus pattern (17 bp):
CGGAACGGAAAACGGAA
Found at i:968755 original size:95 final size:95
Alignment explanation
Indices: 968643--968849 Score: 344
Period size: 95 Copynumber: 2.2 Consensus size: 95
968633 TCTTTCAAAC
968643 GTTTTGTAAACATTTCTTAGAAATGTTTTAAGAAAATGTTATCATAACGTAACAAAAACCACACA
1 GTTTTGTAAACATTTCTTAGAAATGTTTTAAGAAAATGTTATCATAACGTAACAAAAACCACACA
* *
968708 GATTTACGTTGTAATAGCGTTTTCAAAAAT
66 GATTCACGTTGTAATAACGTTTTCAAAAAT
* * *
968738 GTTTTGTAAACATTTCTTAGAAATGTTTTTAGAAAATGTTATTATAACGTAAGAAAAACCACACA
1 GTTTTGTAAACATTTCTTAGAAATGTTTTAAGAAAATGTTATCATAACGTAACAAAAACCACACA
*
968803 GATTCACGTTGTAATAACGTTTTTAAAAAT
66 GATTCACGTTGTAATAACGTTTTCAAAAAT
968833 GTTTTGGT-AACATTTCT
1 GTTTT-GTAAACATTTCT
968850 ACAACGTTTT
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
95 103 0.98
96 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (95 bp):
GTTTTGTAAACATTTCTTAGAAATGTTTTAAGAAAATGTTATCATAACGTAACAAAAACCACACA
GATTCACGTTGTAATAACGTTTTCAAAAAT
Found at i:968876 original size:11 final size:12
Alignment explanation
Indices: 968852--968880 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
968842 ACATTTCTAC
968852 AACGTTTTTAAA
1 AACGTTTTTAAA
968864 AACGTTTTT-AA
1 AACGTTTTTAAA
968875 AACGTT
1 AACGTT
968881 GTTGTGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (12 bp):
AACGTTTTTAAA
Found at i:971402 original size:14 final size:14
Alignment explanation
Indices: 971383--971438 Score: 94
Period size: 14 Copynumber: 4.0 Consensus size: 14
971373 TAGTATAGAA
971383 GTTTGTATCTATAT
1 GTTTGTATCTATAT
*
971397 GTTTGTATCTATAA
1 GTTTGTATCTATAT
*
971411 GTTAGTATCTATAT
1 GTTTGTATCTATAT
971425 GTTTGTATCTATAT
1 GTTTGTATCTATAT
971439 CAGTTGACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (14 bp):
GTTTGTATCTATAT
Found at i:971418 original size:28 final size:28
Alignment explanation
Indices: 971381--971437 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
971371 TGTAGTATAG
*
971381 AAGTTTGTATCTATATGTTTGTATCTAT
1 AAGTTAGTATCTATATGTTTGTATCTAT
971409 AAGTTAGTATCTATATGTTTGTATCTAT
1 AAGTTAGTATCTATATGTTTGTATCTAT
971437 A
1 A
971438 TCAGTTGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (28 bp):
AAGTTAGTATCTATATGTTTGTATCTAT
Found at i:976669 original size:2 final size:2
Alignment explanation
Indices: 976662--976711 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
976652 CTGAGTCGTT
976662 GA GA GA 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 GA GA GA
976704 GA GA GA GA
1 GA GA GA GA
976712 ATCGGCGTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:990484 original size:17 final size:17
Alignment explanation
Indices: 990464--990522 Score: 118
Period size: 17 Copynumber: 3.5 Consensus size: 17
990454 ACAGATTCCT
990464 TTACATTGCTCAGTATA
1 TTACATTGCTCAGTATA
990481 TTACATTGCTCAGTATA
1 TTACATTGCTCAGTATA
990498 TTACATTGCTCAGTATA
1 TTACATTGCTCAGTATA
990515 TTACATTG
1 TTACATTG
990523 AGTTTGTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (17 bp):
TTACATTGCTCAGTATA
Found at i:1005665 original size:2 final size:2
Alignment explanation
Indices: 1005658--1005714 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1005648 TGCACTTTTT
1005658 GA GA GA 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 GA GA GA
1005700 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
1005715 GGTTTACAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1009956 original size:14 final size:15
Alignment explanation
Indices: 1009939--1009967 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1009929 AACCCCCCCC
1009939 CCAAA-AAAAAAAAA
1 CCAAATAAAAAAAAA
1009953 CCAAATAAAAAAAAA
1 CCAAATAAAAAAAAA
1009968 AACCTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.03
Consensus pattern (15 bp):
CCAAATAAAAAAAAA
Found at i:1009979 original size:17 final size:16
Alignment explanation
Indices: 1009937--1009979 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1009927 CCAACCCCCC
1009937 CCCCAAAAAAAAAAAA
1 CCCCAAAAAAAAAAAA
**
1009953 CCAAATAAAAAAAAAAA
1 CCCCA-AAAAAAAAAAA
1009970 CCTCCAAAAA
1 CC-CCAAAAA
1009980 CAAATGCCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
16 3 0.14
17 17 0.81
18 1 0.05
ACGTcount: A:0.72, C:0.23, G:0.00, T:0.05
Consensus pattern (16 bp):
CCCCAAAAAAAAAAAA
Found at i:1016279 original size:4 final size:4
Alignment explanation
Indices: 1016270--1016331 Score: 108
Period size: 4 Copynumber: 15.8 Consensus size: 4
1016260 TGATACATAT
1016270 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
1016318 ATA- AAAG ATAG ATA
1 ATAG ATAG ATAG ATA
1016332 AATCAACACA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 2 0.04
4 53 0.96
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:1031486 original size:30 final size:29
Alignment explanation
Indices: 1031446--1031520 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
1031436 AATACGTTGC
* *
1031446 CGGTCCAATAGATCACAGTCTATTGACTGG
1 CGGT-CAATAGATCACAGTCTATTGACCGA
*
1031476 CGGTCTAATAGATCGCAGTCTATTGACCGA
1 CGGTC-AATAGATCACAGTCTATTGACCGA
*
1031506 CAGTCAATAGATCAC
1 CGGTCAATAGATCAC
1031521 TTTCAAATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.26
30 29 0.74
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (29 bp):
CGGTCAATAGATCACAGTCTATTGACCGA
Found at i:1032218 original size:11 final size:11
Alignment explanation
Indices: 1032202--1032226 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1032192 GCAAAACAAG
1032202 TTTGTGTATTA
1 TTTGTGTATTA
1032213 TTTGTGTATTA
1 TTTGTGTATTA
1032224 TTT
1 TTT
1032227 AGCAAAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (11 bp):
TTTGTGTATTA
Found at i:1047992 original size:146 final size:146
Alignment explanation
Indices: 1047709--1047978 Score: 470
Period size: 146 Copynumber: 1.9 Consensus size: 146
1047699 GTCTGTGCAA
1047709 TCGTGTCCAGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCAGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * *
1047774 TGATGACCTAAGAGTGTGTCATGACCATGAACCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TGATGACCTAAGAGTGTGTCATGACCATGAACCAAGGTCAATTGAGAAAGGTCAAGGTCACTGGC
1047839 AGAAAAAGTGCAAAAT
131 AGAAAAAGTGCAAAAT
1047855 TCGTGTCCAGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCAGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
* * * *
1047920 TTATGACCTAAGGGTGTGTCATGACCTTG-ACCAAGGTCAATTGAGAAAGTTCAAGGTCA
66 TGATGACCTAAGAGTGTGTCATGACCATGAACCAAGGTCAATTGAGAAAGGTCAAGGTCA
1047979 TTGTTTCAAA
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
145 26 0.22
146 91 0.78
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (146 bp):
TCGTGTCCAGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
TGATGACCTAAGAGTGTGTCATGACCATGAACCAAGGTCAATTGAGAAAGGTCAAGGTCACTGGC
AGAAAAAGTGCAAAAT
Found at i:1062108 original size:10 final size:11
Alignment explanation
Indices: 1062084--1062271 Score: 155
Period size: 11 Copynumber: 17.9 Consensus size: 11
1062074 GCGTCTTTTA
1062084 ACCCCAATGAT
1 ACCCCAATGAT
*
1062095 ACCCAAATGA-
1 ACCCCAATGAT
1062105 ACCCCAATGAT
1 ACCCCAATGAT
1062116 ACCCCAATGAT
1 ACCCCAATGAT
*
1062127 A-CACAA--AT
1 ACCCCAATGAT
*
1062135 ACACCTAATGAT
1 AC-CCCAATGAT
*
1062147 ACCCCTATGAT
1 ACCCCAATGAT
*
1062158 A-CCAAATGAT
1 ACCCCAATGAT
*
1062168 ATCCCAATGA-
1 ACCCCAATGAT
*
1062178 ACCCCAATGTT
1 ACCCCAATGAT
*
1062189 ACCCCCATGAT
1 ACCCCAATGAT
1062200 A-CCCAA--AT
1 ACCCCAATGAT
*
1062208 ACACCGAATGAT
1 AC-CCCAATGAT
* *
1062220 ACCCCTATGGT
1 ACCCCAATGAT
*
1062231 A-CCAAATGAT
1 ACCCCAATGAT
*
1062241 ATCCCAATGA-
1 ACCCCAATGAT
1062251 ACCCCAATGAT
1 ACCCCAATGAT
*
1062262 ACCCTAATGA
1 ACCCCAATGA
1062272 ACTTTGAAAT
Statistics
Matches: 139, Mismatches: 25, Indels: 26
0.73 0.13 0.14
Matches are distributed among these distances:
8 6 0.04
10 56 0.40
11 69 0.50
12 8 0.06
ACGTcount: A:0.39, C:0.32, G:0.10, T:0.20
Consensus pattern (11 bp):
ACCCCAATGAT
Found at i:1062109 original size:21 final size:21
Alignment explanation
Indices: 1062083--1062273 Score: 121
Period size: 21 Copynumber: 9.1 Consensus size: 21
1062073 TGCGTCTTTT
1062083 AACCCCAATGATACCCAAATG
1 AACCCCAATGATACCCAAATG
*
1062104 AACCCCAATGATACCCCAATG
1 AACCCCAATGATACCCAAATG
* *
1062125 ATA-CACAA--ATACACCTAATG
1 A-ACCCCAATGATAC-CCAAATG
*
1062145 ATACCCCTATGATA-CCAAATG
1 A-ACCCCAATGATACCCAAATG
* *
1062166 ATATCCCAATGA-ACCCCAATG
1 A-ACCCCAATGATACCCAAATG
* *
1062187 TTACCCCCATGATACCCAAAT-
1 -AACCCCAATGATACCCAAATG
* **
1062208 -ACACCGAATGATACCCCTATGG
1 AAC-CCCAATGATACCCAAAT-G
* *
1062230 TA-CCAAATGATATCCC-AATG
1 AACCCCAATGATA-CCCAAATG
*
1062250 AACCCCAATGATACCCTAATG
1 AACCCCAATGATACCCAAATG
1062271 AAC
1 AAC
1062274 TTTGAAATAT
Statistics
Matches: 134, Mismatches: 21, Indels: 30
0.72 0.11 0.16
Matches are distributed among these distances:
19 6 0.04
20 28 0.21
21 85 0.63
22 11 0.08
23 4 0.03
ACGTcount: A:0.39, C:0.32, G:0.09, T:0.19
Consensus pattern (21 bp):
AACCCCAATGATACCCAAATG
Found at i:1062208 original size:73 final size:73
Alignment explanation
Indices: 1062089--1062271 Score: 296
Period size: 73 Copynumber: 2.5 Consensus size: 73
1062079 TTTTAACCCC
*
1062089 AATGATA-CCCAAATGAACCCCAATGATACCCCAATGATACACAAATACACCTAATGATACCCCT
1 AATGATATCCC-AATGAACCCCAATGATACCCCAATGATACACAAATACACCGAATGATACCCCT
1062153 ATGATACCA
65 ATGATACCA
* * *
1062162 AATGATATCCCAATGAACCCCAATGTTACCCCCATGATACCCAAATACACCGAATGATACCCCTA
1 AATGATATCCCAATGAACCCCAATGATACCCCAATGATACACAAATACACCGAATGATACCCCTA
*
1062227 TGGTACCA
66 TGATACCA
*
1062235 AATGATATCCCAATGAACCCCAATGATACCCTAATGA
1 AATGATATCCCAATGAACCCCAATGATACCCCAATGA
1062272 ACTTTGAAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
73 98 0.97
74 3 0.03
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.20
Consensus pattern (73 bp):
AATGATATCCCAATGAACCCCAATGATACCCCAATGATACACAAATACACCGAATGATACCCCTA
TGATACCA
Found at i:1063615 original size:147 final size:146
Alignment explanation
Indices: 1063282--1064139 Score: 1127
Period size: 146 Copynumber: 5.9 Consensus size: 146
1063272 TTTTTAACAA
* * * * * * * *
1063282 TGACCTTGAACTT-CCTCAATTGACCTTTGGTCAAGGTCATGACATACTCTCAGGTTATAAGCAT
1 TGACCTTGACCTTGCC-CAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAA
* * * * * * *
1063346 TC-TAGATGTGAATTAAGAACTTCCAATATTTGTCCATTAGAAAGATATGGACTGGACACGAGTT
65 TCTTTG-TGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATT
** *
1063410 TTATAC-TTTTCTGCAAG
129 TTGCACTTTTTCTGCCAG
* * * *
1063427 TGACCTTGGCCTTGCCCAAATGACCTTGGGTCAAGGTCATGACAAACCCTTAGCTTATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * * * *
1063492 CTTTGTGTGAACTGAGAACTTCCAATGTTTCTCCAGAAGAAAGATATGGACCGAACAAGAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
* *
1063557 GCATTTTTTTCTGCCAT
131 GCA-CTTTTTCTGCCAG
* * *
1063574 TGACCTTGACCTTGTCCAAATGACCTTGGGTCAAGGTCATGACACATCCTT-GAGCCATAAGCAA
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAG-GTCATAAGCAA
1063638 TCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATTAA-AAAGATATGGACCGGACACGAATT
65 TCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCA-TAAGAAAGATATGGACCGGACACGAATT
*
1063702 TTGCAACTTTTTCTGTCAG
129 TTGC-ACTTTTTCTGCCAG
* * * *
1063721 AGACCTTGACCTTGCCCGAATGACCTTGGGTTAAGGTCATGACACACCCTTAGGTCATTAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* *
1063786 CTTTGTGTGAAGTTAA-AACTTCCAAAGTTTCTCCATAAGGAAGATATGGACCGGACACGAATTT
66 CTTTGTGTGAAG-TAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTT
***
1063850 TGCACTTTTTCTGTTGG
130 TGCACTTTTTCTGCCAG
* *
1063867 TGACCTTGACCTTG-CCAGAATGACCTTGGTTCAAGGTCATGACACACCTTTAGGTCATAAGCAA
1 TGACCTTGACCTTGCCCA-AATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAA
* * * *
1063931 TCTTTGTGTGGAGTAAAAACTTCTAATATTTCTCCATAAGAAAGATATGGACCGGACACGAATTT
65 TCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTT
1063996 TGCACTTTTTCTGCCAG
130 TGCACTTTTTCTGCCAG
* * *
1064013 TGACCTTGACCTTGCCCGAATGACCTTGGTTCAAGGTCATGACACACCCTTAGGTCATAAGCCAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
*
1064078 CTTTGTGTGAAGTAAGAACTTCTAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
1064140 CGAACAGACA
Statistics
Matches: 629, Mismatches: 71, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
145 110 0.17
146 263 0.42
147 249 0.40
148 7 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (146 bp):
TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTT
GCACTTTTTCTGCCAG
Found at i:1064163 original size:12 final size:12
Alignment explanation
Indices: 1064146--1064180 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1064136 GAATCGAACA
1064146 GACAGACGGACG
1 GACAGACGGACG
*
1064158 GACAGACAGACG
1 GACAGACGGACG
*
1064170 GACGGACGGAC
1 GACAGACGGAC
1064181 AAGGTGATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00
Consensus pattern (12 bp):
GACAGACGGACG
Found at i:1064164 original size:16 final size:16
Alignment explanation
Indices: 1064143--1064181 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1064133 CACGAATCGA
1064143 ACAGACAGACGGACGG
1 ACAGACAGACGGACGG
1064159 ACAGACAGACGGACGG
1 ACAGACAGACGGACGG
*
1064175 ACGGACA
1 ACAGACA
1064182 AGGTGATTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (16 bp):
ACAGACAGACGGACGG
Found at i:1064168 original size:20 final size:20
Alignment explanation
Indices: 1064143--1064181 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1064133 CACGAATCGA
1064143 ACAGACAGACGGACGGACAG
1 ACAGACAGACGGACGGACAG
*
1064163 ACAGACGGACGGACGGACA
1 ACAGACAGACGGACGGACA
1064182 AGGTGATTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (20 bp):
ACAGACAGACGGACGGACAG
Found at i:1069814 original size:21 final size:21
Alignment explanation
Indices: 1069788--1069832 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1069778 CTAAATACTG
1069788 TATACAGGATAATTTTTTACC
1 TATACAGGATAATTTTTTACC
1069809 TATACAGGATAATTTTTTACC
1 TATACAGGATAATTTTTTACC
1069830 TAT
1 TAT
1069833 GAGATTTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (21 bp):
TATACAGGATAATTTTTTACC
Found at i:1070899 original size:136 final size:136
Alignment explanation
Indices: 1070653--1070925 Score: 528
Period size: 136 Copynumber: 2.0 Consensus size: 136
1070643 TTCATGTAAA
1070653 TCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTTAATTTTGGGATAAAACGGAGTCATTA
1 TCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTTAATTTTGGGATAAAACGGAGTCATTA
*
1070718 TTGTGGTCAAAGTCCCATAACTCAAACAAAAAGTATCGACCAATGCTGATTTTCGAACTTGACCA
66 TTGTGGTCAAAGTCCCATAACTCAAACAAAAAGTATCGACAAATGCTGATTTTCGAACTTGACCA
1070783 AAGTAT
131 AAGTAT
1070789 TCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTTAATTTTGGGATAAAACGGAGTCATTA
1 TCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTTAATTTTGGGATAAAACGGAGTCATTA
*
1070854 TTGTGGTCAAAGTCCCATAACTCAAACAAAAAGTATCGACAAATGCTGATTTTCGAACTTGACCG
66 TTGTGGTCAAAGTCCCATAACTCAAACAAAAAGTATCGACAAATGCTGATTTTCGAACTTGACCA
1070919 AAGTAT
131 AAGTAT
1070925 T
1 T
1070926 AGTGATGTAA
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (136 bp):
TCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTTAATTTTGGGATAAAACGGAGTCATTA
TTGTGGTCAAAGTCCCATAACTCAAACAAAAAGTATCGACAAATGCTGATTTTCGAACTTGACCA
AAGTAT
Found at i:1072123 original size:31 final size:31
Alignment explanation
Indices: 1072085--1072149 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1072075 CCTGGTGGGC
1072085 TATATTGACTGA-CAGTGGTTTCGCCATCGAG
1 TATATTGACTGAGC-GTGGTTTCGCCATCGAG
1072116 TATATTGACTGAGCGTGGTTTCGCCATCGAG
1 TATATTGACTGAGCGTGGTTTCGCCATCGAG
1072147 TAT
1 TAT
1072150 TCAGAGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (31 bp):
TATATTGACTGAGCGTGGTTTCGCCATCGAG
Found at i:1073151 original size:26 final size:26
Alignment explanation
Indices: 1073122--1073177 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1073112 ATATACCCTT
1073122 AATTAATAATAAGATCGTAAGATTTG
1 AATTAATAATAAGATCGTAAGATTTG
1073148 AATTAATAATAAGATCGTAAGATTTG
1 AATTAATAATAAGATCGTAAGATTTG
1073174 AATT
1 AATT
1073178 CTTGTTCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (26 bp):
AATTAATAATAAGATCGTAAGATTTG
Found at i:1076439 original size:13 final size:13
Alignment explanation
Indices: 1076421--1076446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1076411 AAATTAAAAC
1076421 CATGAACATCAAT
1 CATGAACATCAAT
1076434 CATGAACATCAAT
1 CATGAACATCAAT
1076447 TATTTTTTTT
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:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
CATGAACATCAAT
Found at i:1083723 original size:399 final size:400
Alignment explanation
Indices: 1082974--1083733 Score: 1202
Period size: 399 Copynumber: 1.9 Consensus size: 400
1082964 CTTAATTACC
* * * *
1082974 CTCCAAACTGAACTTTTATTCTGCAGCCACGTCAACGTCTAACCAGACTGGCCATTGTGATAGAA
1 CTCCAAACTGAACTTTTATTCTGCAACCACATCAACGTCTAACCAGACCGGCCATAGTGATAGAA
* * **
1083039 AATGTTAAACTCAATTTCATTGGTTATTATTCCTGATGGTCCAATCAGAATTAGTCTTTCTCGAA
66 AATGTTAAACTCAATTTCATTGATTAATATTCCTGATGGTCCAATCAGAACCAGTCTTTCTCGAA
* * *
1083104 GACGTCAAAATGGCTGGCCCTGTCAGAAGTCAATGTGGCTGCAGAATAAAAATTCAGTTTGGAGA
131 GACGTCAAAATGGCTGGCCCTGTCAGAAATCAATGTGGCTGCAGAATAAAAATTCAGTATGAAGA
* * * *
1083169 GTTTTTAAGGAATGTTATCGGAATTTACAGATGTAAGTAGCGTGCGTTTGATGTGAGATTTTAAA
196 GTATTTAAGGAATGTTATCAGAATTTACAGATGTAAGTAGCGTGCATTTGATGTAAGATTTTAAA
*
1083234 AGATTAGTGCGAATGTTTCTCGACTTGTTGCAATACTGCTGTTGTCATAGGCAAAATCCCATCGT
261 AGATTAGTGCGAATGTTTCTCGACTTGTTGCAATACTGCTGTTGTCAGAGGCAAAATCCCATCGT
*
1083299 GAGCCCTGGACCTGTAAATGTCCGAGTAAAAATAAATCACCGTGTTGGGATATTTAATCCCACAG
326 GAGCCCTGGACCGGTAAATGTCCGAGTAAAAATAAATCACCGTGTTGGGATATTTAATCCCACAG
1083364 GAAAAAAAGT
391 GAAAAAAAGT
* * * **
1083374 CTCCAAACTGAACTTTTATTCTGCAACCACATCGACTTCTGACCAGACCGGCCATAGTGATAGCT
1 CTCCAAACTGAACTTTTATTCTGCAACCACATCAACGTCTAACCAGACCGGCCATAGTGATAGAA
1083439 AATGTTAAACTCAATTTCATTGATTAATATTCCTGATGGTCCAATCAGAACCAGTCTTTCTCGAA
66 AATGTTAAACTCAATTTCATTGATTAATATTCCTGATGGTCCAATCAGAACCAGTCTTTCTCGAA
* * *
1083504 GATGTCAAAATGGCTGGCCCTGTCAGAAATCAATGTGGTTGCAG-ATTAAAATTCAGTAT-AATG
131 GACGTCAAAATGGCTGGCCCTGTCAGAAATCAATGTGGCTGCAGAATAAAAATTCAGTATGAA-G
* * ** *
1083567 AGTATTTAAGGAATTTTATCAGAGTTT-TTGTATGTAAGTAGCGTGCATTTTATGTAAGATTTTA
195 AGTATTTAAGGAATGTTATCAGAATTTACAG-ATGTAAGTAGCGTGCATTTGATGTAAGATTTTA
*
1083631 AAAGATTGGTGCGAATGTTTCTCGACTTGTTGCAATACTGCTGTTGTCAGAGGCAAAATCCCATC
259 AAAGATTAGTGCGAATGTTTCTCGACTTGTTGCAATACTGCTGTTGTCAGAGGCAAAATCCCATC
1083696 GTGAGCCCTGGACCGGTAAATGTCCGAGTAAAAATAAA
324 GTGAGCCCTGGACCGGTAAATGTCCGAGTAAAAATAAA
1083734 CTGGCGTCTT
Statistics
Matches: 327, Mismatches: 31, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
398 2 0.01
399 167 0.51
400 158 0.48
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (400 bp):
CTCCAAACTGAACTTTTATTCTGCAACCACATCAACGTCTAACCAGACCGGCCATAGTGATAGAA
AATGTTAAACTCAATTTCATTGATTAATATTCCTGATGGTCCAATCAGAACCAGTCTTTCTCGAA
GACGTCAAAATGGCTGGCCCTGTCAGAAATCAATGTGGCTGCAGAATAAAAATTCAGTATGAAGA
GTATTTAAGGAATGTTATCAGAATTTACAGATGTAAGTAGCGTGCATTTGATGTAAGATTTTAAA
AGATTAGTGCGAATGTTTCTCGACTTGTTGCAATACTGCTGTTGTCAGAGGCAAAATCCCATCGT
GAGCCCTGGACCGGTAAATGTCCGAGTAAAAATAAATCACCGTGTTGGGATATTTAATCCCACAG
GAAAAAAAGT
Found at i:1097943 original size:161 final size:160
Alignment explanation
Indices: 1097599--1097969 Score: 496
Period size: 161 Copynumber: 2.3 Consensus size: 160
1097589 GGTCCACCAA
* * * *
1097599 CAGTTTCCGTTCATTTTCTTTGCAGACGATGAACATATCGAAATGAAATTTGGTATACATGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGACGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * * * *
1097664 TTAAGATAATATCTAGGTCGAGTTGATATTGGGTTCGATCGAGCAGTTTTCTACAGAGTTATGCC
66 TTAAGATAATATCAAGGTCAAGTTGATAGTGGGTACGATCGAGCAATTTTCTACAGAGTTATGCC
* * *
1097729 CCTTGGACGTAGAGAAATTCTAGTTATTTG
131 CCTTGGACGTAGACAAATTCCAATTATTTG
1097759 CAGTTTCCGCTCATTTTCTTCGCAGA-GATTGAACATATTGAAATGAAATTTGGTATACAGGTTT
1 CAGTTTCCGCTCATTTTCTTCGCAGACGA-TGAACATATTGAAATGAAATTTGGTATACAGGTTT
* *
1097823 ATTATGATAATATCAAGGTCAAGGTCT-ATAGTGTGTACGATCGAGCAATTTT-TGACAGAGTTA
65 ATTAAGATAATATCAAGGTCAA-GT-TGATAGTGGGTACGATCGAGCAATTTTCT-ACAGAGTTA
* * *
1097886 TGGCTCTTGGACGTATACAAATTCCAATTATTTG
127 TGCCCCTTGGACGTAGACAAATTCCAATTATTTG
* * * *
1097920 CAGTTTCCGCTCATTTCCTTCGCAGACGGTGCACATATTGATATGAAATT
1 CAGTTTCCGCTCATTTTCTTCGCAGACGATGAACATATTGAAATGAAATT
1097970 AATTATAAAA
Statistics
Matches: 185, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
159 2 0.01
160 77 0.42
161 104 0.56
162 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (160 bp):
CAGTTTCCGCTCATTTTCTTCGCAGACGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
TTAAGATAATATCAAGGTCAAGTTGATAGTGGGTACGATCGAGCAATTTTCTACAGAGTTATGCC
CCTTGGACGTAGACAAATTCCAATTATTTG
Found at i:1107741 original size:164 final size:161
Alignment explanation
Indices: 1107328--1107993 Score: 965
Period size: 161 Copynumber: 4.1 Consensus size: 161
1107318 GGTCCACCAA
* * * * ** *
1107328 CAGTTTCCGTTCATTTTCTTCGTAGACGATGAACATATTGAAATGCAATTTAATATACAGATTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * * *
1107393 TCATGCTAATATCTAGGTCAAGTTCGATATTGGGTTCGATCGAGCACTTTTTGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
1107458 CCCTTGGACGTAGAAAAATTCCAGTTATTTG
131 CCCTTGGACGTAGAAAAATTCCAGTTATTTG
* * * * * *
1107489 TAGTTTCCGCTCATTTTCTACGCAGAGGATGAACATACTGGAATCAAATTTGGTATTCAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
*
1107554 GCATGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
*
1107619 CCCTTGGACGTAGAAAAATTCTAGTTAATATTTG
131 CCCTTGGACGTAGAAAAATTCCAG-T--TATTTG
*
1107653 CAGCTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* *
1107718 TCATGATAATATCTAAGTCAAGTTCGATATTGGGTACGATTGAGCAATTTTCGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
1107783 CCCTTGGACGTAGAAAAATTCCAGTTATTTG
131 CCCTTGGACGTAGAAAAATTCCAGTTATTTG
* * * * *
1107814 CCGTTTCCGTTCATTTTCTTCGCAGAGTATGAACATATTGGAATGAAATTTGGTATACTGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * * **
1107879 TTATGATAATATCTAGGTCAAGTTCGATATTGGGTATGATAGAGCAATTTTCGACAGAGTTATAC
66 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
* *
1107944 CCCTTGGACTTA-AAAAATTCCATTTATTTG
131 CCCTTGGACGTAGAAAAATTCCAGTTATTTG
* * *
1107974 CAGTGTCCGTTTATTTTCTT
1 CAGTTTCCGCTCATTTTCTT
1107994 GTGGATGTTT
Statistics
Matches: 455, Mismatches: 47, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
160 34 0.07
161 270 0.59
162 1 0.00
163 1 0.00
164 149 0.33
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (161 bp):
CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
CCCTTGGACGTAGAAAAATTCCAGTTATTTG
Found at i:1107928 original size:325 final size:324
Alignment explanation
Indices: 1107332--1107963 Score: 994
Period size: 325 Copynumber: 1.9 Consensus size: 324
1107322 CACCAACAGT
* * *
1107332 TTCCGTTCATTTTCTTCGTAGACGATGAACATATTGAAATGCAATTTAATATACAGATTTATCAT
1 TTCCGCTCATTTTCTTCGCAGACGATGAACATATTGAAATGAAATTTAATATACAGATTTATCAT
* * * * *
1107397 GCTAATATCTAGGTCAAGTTCGATATTGGGTTCGATCGAGCACTTTTTGACAGAGTTATGGCCCT
66 GATAATATCTAAGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
*
1107462 TGGACGTAGAAAAATTCCAGTTATTTGTAGTTTCCGCTCATTTTCTACGCAGAGGATGAACATAC
131 TGGACGTAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTCTACGCAGAGGATGAACATAC
*
1107527 TGGAATCAAATTTGGTATTCAGGTTTAGCATGATAATATCTAGGTCAAGTTCGATATTGGGTACG
196 TGGAATCAAATTTGGTATACAGGTTTAGCATGATAATATCTAGGTCAAGTTCGATATTGGGTACG
* **
1107592 ATCGAGCAATTTTCGACAGAGTTATGGCCCTTGGACGTAGAAAAATTCTAGTTAATATTTGCAGC
261 ATAGAGCAATTTTCGACAGAGTTATACCCCTTGGACGTA-AAAAATTCTAGTTAATATTTGCAGC
* ** *
1107657 TTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCAT
1 TTCCGCTCATTTTCTTCGCAGACGATGAACATATTGAAATGAAATTTAATATACAGATTTATCAT
*
1107722 GATAATATCTAAGTCAAGTTCGATATTGGGTACGATTGAGCAATTTTCGACAGAGTTATGGCCCT
66 GATAATATCTAAGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
* * * * *
1107787 TGGACGTAGAAAAATTCCAGTTATTTGCCGTTTCCGTTCATTTTCTTCGCAGAGTATGAACATAT
131 TGGACGTAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTCTACGCAGAGGATGAACATAC
* * ** *
1107852 TGGAATGAAATTTGGTATACTGGTTTATTATGATAATATCTAGGTCAAGTTCGATATTGGGTATG
196 TGGAATCAAATTTGGTATACAGGTTTAGCATGATAATATCTAGGTCAAGTTCGATATTGGGTACG
*
1107917 ATAGAGCAATTTTCGACAGAGTTATACCCCTTGGACTTAAAAAATTC
261 ATAGAGCAATTTTCGACAGAGTTATACCCCTTGGACGTAAAAAATTC
1107964 CATTTATTTG
Statistics
Matches: 278, Mismatches: 29, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
324 8 0.03
325 270 0.97
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (324 bp):
TTCCGCTCATTTTCTTCGCAGACGATGAACATATTGAAATGAAATTTAATATACAGATTTATCAT
GATAATATCTAAGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGGCCCT
TGGACGTAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATTTTCTACGCAGAGGATGAACATAC
TGGAATCAAATTTGGTATACAGGTTTAGCATGATAATATCTAGGTCAAGTTCGATATTGGGTACG
ATAGAGCAATTTTCGACAGAGTTATACCCCTTGGACGTAAAAAATTCTAGTTAATATTTGCAGC
Found at i:1110195 original size:363 final size:362
Alignment explanation
Indices: 1109530--1110255 Score: 1310
Period size: 363 Copynumber: 2.0 Consensus size: 362
1109520 ATGTTAAATG
1109530 GTAATTTCTTACGATTAGAGACGGAGAAAACTCCAGAAAATATTTTTTTTTTCAAAATTAAAGCC
1 GTAATTTCTTACGATTAGAGACGGAGAAAACTCCAGAAAATATTTTTTTTTTCAAAATTAAAGCC
1109595 TGATGAGGCATGAAATATCACCATAAACACGTATAGCACAGTTAAGTATTATATCTTACATATAC
66 TGATGAGGCATGAAATATCACCATAAACACGTATAGCACAGTTAAGTATTATATCTTACATATAC
1109660 ATCTTATTAGTCATTTAAAAATATTATGCAATGAAATATTAAACTGTAATTATGATACTATAATG
131 ATCTTATTAGTCATTTAAAAATATTATGCAATGAAATATTAAACTGTAATTATGATACTATAATG
*
1109725 TAATTATGATTATTCAAATTTCGACAAATAATACCTATACAAATAAAGTTCAGAAATTACATTGC
196 TAATTATCATTATTCAAATTTCGACAAATAATACCTATACAAATAAAGTTCAGAAATTACATTGC
* ******
1109790 CAATGCGTGCCTGTGTTGAATGAAATAGACATGATTTGAGAGAATTTTTTTATGTTGACTATAAA
261 CAATGCGTGCCTGGGTTGAATGAAATAGACATGATTTGAGAGAAAAAAAAT-TGTTGACTATAAA
1109855 TCAATAAC-ACGTGATATGCATGATTAATTAAGAAAAA
325 TCAATAACAACGTGATATGCATGATTAATTAAGAAAAA
1109892 NGTAATTTCTTACGATTAGAGACGGAGAAAACTCCAGAAAATATTTTTTTTTTCAAAATTAAAGC
1 -GTAATTTCTTACGATTAGAGACGGAGAAAACTCCAGAAAATATTTTTTTTTTCAAAATTAAAGC
1109957 CTGATGAGGCATGAAATATCACCATAAACACGTATAGCACAGTTAAGTATTATATCTTACATATA
65 CTGATGAGGCATGAAATATCACCATAAACACGTATAGCACAGTTAAGTATTATATCTTACATATA
*
1110022 CATCTTATTAGTCATTTAAAAATATTATGCAATGAAATATTGAACTGTAATTATGATACTATAAT
130 CATCTTATTAGTCATTTAAAAATATTATGCAATGAAATATTAAACTGTAATTATGATACTATAAT
* *
1110087 GTAATTATCATTATTCAAATTTTGATAAATAATACCTATACAAATAAAGTTCAGAAATTACATTG
195 GTAATTATCATTATTCAAATTTCGACAAATAATACCTATACAAATAAAGTTCAGAAATTACATTG
*
1110152 CCCATGCGTGCCTGGGTTGAATGAAATAGACATGATTTGAGAGAAAAAAAATTGTTGACTATAAA
260 CCAATGCGTGCCTGGGTTGAATGAAATAGACATGATTTGAGAGAAAAAAAATTGTTGACTATAAA
1110217 TCAATAACAGACGTGATATGCATGATTAATTAAGAAAAA
325 TCAATAACA-ACGTGATATGCATGATTAATTAAGAAAAA
1110256 AATCATAAGT
Statistics
Matches: 349, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
362 21 0.06
363 299 0.86
364 29 0.08
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (362 bp):
GTAATTTCTTACGATTAGAGACGGAGAAAACTCCAGAAAATATTTTTTTTTTCAAAATTAAAGCC
TGATGAGGCATGAAATATCACCATAAACACGTATAGCACAGTTAAGTATTATATCTTACATATAC
ATCTTATTAGTCATTTAAAAATATTATGCAATGAAATATTAAACTGTAATTATGATACTATAATG
TAATTATCATTATTCAAATTTCGACAAATAATACCTATACAAATAAAGTTCAGAAATTACATTGC
CAATGCGTGCCTGGGTTGAATGAAATAGACATGATTTGAGAGAAAAAAAATTGTTGACTATAAAT
CAATAACAACGTGATATGCATGATTAATTAAGAAAAA
Found at i:1112846 original size:16 final size:15
Alignment explanation
Indices: 1112827--1112877 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
1112817 ACTTCTCACT
1112827 TTCGCTCCTTCGCATC
1 TTCGCT-CTTCGCATC
*
1112843 TTCGCT-GTCGCATC
1 TTCGCTCTTCGCATC
* *
1112857 TTCGCACTTTCGCAAC
1 TTCGCTC-TTCGCATC
1112873 TTCGC
1 TTCGC
1112878 ACCTCGACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.41
16 17 0.59
ACGTcount: A:0.10, C:0.39, G:0.16, T:0.35
Consensus pattern (15 bp):
TTCGCTCTTCGCATC
Found at i:1112854 original size:38 final size:38
Alignment explanation
Indices: 1112798--1112878 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
1112788 GATAGTTGTA
* * **
1112798 TCGCTTCTTCGCCTTCGCAACTTCTCACTTTCGCTCCT
1 TCGCATCTTCGCCTTCGCAACTTCGCACTTTCGCAACT
*
1112836 TCGCATCTTCG-CTGTCGCATCTTCGCACTTTCGCAACT
1 TCGCATCTTCGCCT-TCGCAACTTCGCACTTTCGCAACT
1112874 TCGCA
1 TCGCA
1112879 CCTCGACCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.05
38 35 0.95
ACGTcount: A:0.11, C:0.40, G:0.14, T:0.36
Consensus pattern (38 bp):
TCGCATCTTCGCCTTCGCAACTTCGCACTTTCGCAACT
Found at i:1119830 original size:166 final size:164
Alignment explanation
Indices: 1119626--1120007 Score: 505
Period size: 166 Copynumber: 2.3 Consensus size: 164
1119616 CATNTTGGCT
* *
1119626 AAAATAAACAAAGT-ACTCATTTAACAGGAAGATGACGTCCGATTAGTACAAAATACATCCCACG
1 AAAATAAACAAAGTCA-TCATTTAACAGGAAGTTGACGTCCGATT-GTACAAAATACATCCCACA
**
1119690 ATATGGCATGCCTTAACAAACACTGTGTAAAAAATTTCAAGCATCTCCGATAAATAGCTGCTGAG
64 ATATGGCATGCCAAAACAAACACTGTGT-AAAAATTTCAAGCATCTCCGATAAATAGCTGCTGAG
* *
1119755 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCAA
128 AAATCTTTGACAAAAATTTGTTTGAAAATGTTGGCAA
* * * * * *
1119792 AAAATAAACAAAGTCATTATTTAACGGGAAGTTGACGTCTGATTGAAACAAAAATATATTCCACA
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTG-TAC-AAAATACATCCCACA
* * * *
1119857 ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
64 ATATGGCATGCCAAAACAAACACTGTGTAAAAATTTCAAGCATCTCCGATAAATAGCTGCTGAGA
* **
1119922 AATCTTTGACAAAAATTTGTTTGAACATGTTGGCTT
129 AATCTTTGACAAAAATTTGTTTGAAAATGTTGGCAA
* **
1119958 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACAACCGATTGGTACA
1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATT-GTACA
1120008 GA
Statistics
Matches: 186, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
165 2 0.01
166 146 0.78
167 38 0.20
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (164 bp):
AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGTACAAAATACATCCCACAAT
ATGGCATGCCAAAACAAACACTGTGTAAAAATTTCAAGCATCTCCGATAAATAGCTGCTGAGAAA
TCTTTGACAAAAATTTGTTTGAAAATGTTGGCAA
Done.