Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015091.1 Kokia drynarioides strain JFW-HI SEQ_130135, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 803680
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 595 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:619066 original size:29 final size:29
Alignment explanation
Indices: 619024--619084 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
619014 TATATCCTCA
619024 TTGTGTAATGTTATATAAG-AATTTTGATT
1 TTGTGTAATGTTATATAAGAAATTTT-ATT
* *
619053 TTGTGTAATTTTATATATGAAATTTTATT
1 TTGTGTAATGTTATATAAGAAATTTTATT
619082 TTG
1 TTG
619085 ATTCAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (29 bp):
TTGTGTAATGTTATATAAGAAATTTTATT
Found at i:624651 original size:20 final size:22
Alignment explanation
Indices: 624604--624652 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
624594 ACGTCTTTAA
*
624604 AATTTTTAAAAAAATTTATAAT
1 AATTTTTAAAAAAATTTAAAAT
* *
624626 -TTTTTTTAAAAAA-TTAAAAT
1 AATTTTTAAAAAAATTTAAAAT
624646 AATTTTT
1 AATTTTT
624653 GGTATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTTTAAAAAAATTTAAAAT
Found at i:627932 original size:9 final size:9
Alignment explanation
Indices: 627918--627950 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
627908 ACAGATAAAA
627918 AATAATTTT
1 AATAATTTT
627927 AATAA-TTT
1 AATAATTTT
627935 AATTAATTTT
1 AA-TAATTTT
627945 AATAAT
1 AATAAT
627951 ATTGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.23
9 12 0.55
10 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AATAATTTT
Found at i:630001 original size:30 final size:31
Alignment explanation
Indices: 629929--630001 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
629919 ATCCAATTTA
* *
629929 ATACTCAAACTTGACACTTTTTCCTAATTTG
1 ATACTTAAACTTGACACTTTTTCCTAAGTTG
* * *
629960 GTACCTAAACTTGACACTTTTT-TTAAGTTG
1 ATACTTAAACTTGACACTTTTTCCTAAGTTG
629990 ATACTTAAACTT
1 ATACTTAAACTT
630002 TTTGGGGTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.42
Consensus pattern (31 bp):
ATACTTAAACTTGACACTTTTTCCTAAGTTG
Found at i:630297 original size:28 final size:27
Alignment explanation
Indices: 630208--630311 Score: 91
Period size: 28 Copynumber: 3.5 Consensus size: 27
630198 TTTAATAAAT
*
630208 TTAGGTACCAAATTGAATCTAAAAAAAAG
1 TTAGGTACCAAATTGGA--TAAAAAAAAG
* *
630237 CTTAGGTATCAAATTAGGAAAAAAATGCAAAG
1 -TTAGGTACCAAATT-GGATAAAAA---AAAG
*
630269 TTCAAGTACCAAATTGGATAAAAAAAAG
1 TT-AGGTACCAAATTGGATAAAAAAAAG
630297 TTTAGGTACCAAATT
1 -TTAGGTACCAAATT
630312 AAGAAAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
28 15 0.25
29 7 0.11
30 13 0.21
31 12 0.20
32 14 0.23
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (27 bp):
TTAGGTACCAAATTGGATAAAAAAAAG
Found at i:636330 original size:21 final size:21
Alignment explanation
Indices: 636306--636346 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
636296 TGGACGAATG
*
636306 GTAT-ATCTAACCAACTACAAT
1 GTATAATCCAACCAA-TACAAT
636327 GTATAATCCAACCAATACAA
1 GTATAATCCAACCAATACAA
636347 AACAGAGCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (21 bp):
GTATAATCCAACCAATACAAT
Found at i:638232 original size:21 final size:24
Alignment explanation
Indices: 638183--638233 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
638173 TCAATCACAC
*
638183 TAATTTTTTATAGTAAAAATAGAT
1 TAATTTTTTATAGCAAAAATAGAT
*
638207 GAATTTTTTA-A-CAAAAAT-GAT
1 TAATTTTTTATAGCAAAAATAGAT
638228 TAATTT
1 TAATTT
638234 GCTCTTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 1 0.04
24 9 0.38
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (24 bp):
TAATTTTTTATAGCAAAAATAGAT
Found at i:645703 original size:30 final size:29
Alignment explanation
Indices: 645651--645711 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
645641 TATTTATAAT
* *
645651 TTTTAAAAAATTAAATTAAATTATTATTA
1 TTTTAAAAAATCAAAATAAATTATTATTA
*
645680 TTTTAAAAGATCAAAATATAATTATTATTA
1 TTTTAAAAAATCAAAATA-AATTATTATTA
645710 TT
1 TT
645712 AATTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TTTTAAAAAATCAAAATAAATTATTATTA
Found at i:650485 original size:18 final size:19
Alignment explanation
Indices: 650462--650514 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
650452 TTAAAAAATA
650462 ATTTTTATATTTTTAATG-
1 ATTTTTATATTTTTAATGT
* *
650480 ATTTTTA-ATTCTTAAAAGT
1 ATTTTTATATT-TTTAATGT
650499 ATTTTTAT-TTTTTAAT
1 ATTTTTATATTTTTAAT
650515 TTTAAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 3 0.11
18 16 0.57
19 9 0.32
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTTTTATATTTTTAATGT
Found at i:650513 original size:19 final size:18
Alignment explanation
Indices: 650462--650513 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
650452 TTAAAAAATA
*
650462 ATTTTTATATTTTT-AATG
1 ATTTTTAT-TTTTTAAAAG
* *
650480 ATTTTTAATTCTTAAAAG
1 ATTTTTATTTTTTAAAAG
650498 TATTTTTATTTTTTAA
1 -ATTTTTATTTTTTAA
650514 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 4 0.15
18 10 0.37
19 13 0.48
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (18 bp):
ATTTTTATTTTTTAAAAG
Found at i:651149 original size:22 final size:21
Alignment explanation
Indices: 651105--651151 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
651095 TATTGTGTAG
**
651105 ATTAATATAAACTAATTTTTT
1 ATTAATATAAACTAATTCATT
*
651126 ATTAATATAAGATTAATTCATT
1 ATTAATATAA-ACTAATTCATT
651148 ATTA
1 ATTA
651152 TAATATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTAATATAAACTAATTCATT
Found at i:663336 original size:14 final size:13
Alignment explanation
Indices: 663317--663345 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
663307 TTTTAATAAT
663317 ATTA-AAAAGTTA
1 ATTATAAAAGTTA
663329 ATTATAAAAGTTA
1 ATTATAAAAGTTA
663342 ATTA
1 ATTA
663346 CTTTACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
ATTATAAAAGTTA
Found at i:666535 original size:148 final size:147
Alignment explanation
Indices: 666267--666623 Score: 601
Period size: 148 Copynumber: 2.4 Consensus size: 147
666257 GGTAACTTAT
*
666267 CTGTTTATTTTTCTAGTCTATATTTGATTTAAAATGTTAAGGCGCATGGCTAAATGGTGATCACA
1 CTGTTTATTTTTCTAGTCTATATTTGGTTTAAAATGTTAAGG-GCATGGCTAAATGGTGATCACA
*
666332 TGAAGGGTTAATAAGTTAAAATCTTTAGGTTTCATATTCGGGTGGATGAGTGGAGGCATGATGAA
65 TGAAGGGTTAATAAGTTAAAATCTTTAGGTTTCATATTCGGGTCGATGAGTGGAGGCATGATGAA
*
666397 TGTAACTTATAATATATG
130 TGTAACTTATAATATATA
*
666415 CTGTTTATTTTTCTAGTCTATATTTGGTTTAAAATGTTAAGGTGTATGGCTAAATGGTGATCACA
1 CTGTTTATTTTTCTAGTCTATATTTGGTTTAAAATGTTAAGG-GCATGGCTAAATGGTGATCACA
* *
666480 TGAAGGGTTAATAAGTTACAATCTTTAGGTTTCATATTCGGGTCGATGAGTGGAGGCATGATGAC
65 TGAAGGGTTAATAAGTTAAAATCTTTAGGTTTCATATTCGGGTCGATGAGTGGAGGCATGATGAA
* *
666545 TGTAACTTATAGTGTATA
130 TGTAACTTATAATATATA
*
666563 CTGTTTATTTTTCTAGTCTATA-TTGGTTTAAAATGTTAA-GGCATGGATAAATGGTGATCAC
1 CTGTTTATTTTTCTAGTCTATATTTGGTTTAAAATGTTAAGGGCATGGCTAAATGGTGATCAC
666624 TTAAAGGACT
Statistics
Matches: 198, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
145 19 0.10
146 1 0.01
147 17 0.09
148 161 0.81
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (147 bp):
CTGTTTATTTTTCTAGTCTATATTTGGTTTAAAATGTTAAGGGCATGGCTAAATGGTGATCACAT
GAAGGGTTAATAAGTTAAAATCTTTAGGTTTCATATTCGGGTCGATGAGTGGAGGCATGATGAAT
GTAACTTATAATATATA
Found at i:668573 original size:142 final size:140
Alignment explanation
Indices: 668295--668582 Score: 472
Period size: 142 Copynumber: 2.0 Consensus size: 140
668285 TTTCTGCACG
*
668295 TTTTGGCACTTATCGGAAACTTATCTGATTAAGAGAGTCACATGCTAAGAACTATTGAAATATTG
1 TTTTGTCACTTATCGGAAACTTATCTGATTAAGAGAGTCACATGCTAAGAACTATTGAAATATTG
*
668360 AACTGAAATCGGTAGAAAGTTGAAGGGACTGTTATTGGCAGGCAGAAAGGTGATAGTAAACGTTT
66 AACTGAAATCGGTAGAAAGTTGAAGAGACTGTTATTGGCAGGCAGAAAGGTGATAGTAAACGTTT
668425 AGAATCTTTA
131 AGAATCTTTA
* * *
668435 TTTTGTCACTTATTGGGAACTTATCTGATT-A-AGAGTCACATGCTAAGAACTTTTGAAATATTG
1 TTTTGTCACTTATCGGAAACTTATCTGATTAAGAGAGTCACATGCTAAGAACTATTGAAATATTG
*
668498 AACTTAAATCGGTAGAAAGTAAGTTGAAGAGACTGTTATTGGCAGGCAGAAAGGTGATAGTAAAC
66 AACTGAAATCGGTAG--A--AAGTTGAAGAGACTGTTATTGGCAGGCAGAAAGGTGATAGTAAAC
668563 GTTTAGAATCTTTA
127 GTTTAGAATCTTTA
668577 TTTTGT
1 TTTTGT
668583 TTACTTTTTC
Statistics
Matches: 138, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
138 45 0.33
139 1 0.01
140 28 0.20
142 64 0.46
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (140 bp):
TTTTGTCACTTATCGGAAACTTATCTGATTAAGAGAGTCACATGCTAAGAACTATTGAAATATTG
AACTGAAATCGGTAGAAAGTTGAAGAGACTGTTATTGGCAGGCAGAAAGGTGATAGTAAACGTTT
AGAATCTTTA
Found at i:673265 original size:2 final size:2
Alignment explanation
Indices: 673258--673282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
673248 TTATACAATC
673258 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
673283 CATACATTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:678706 original size:11 final size:11
Alignment explanation
Indices: 678653--678712 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
678643 TCACGTCAGC
*
678653 AAATGATTTTA
1 AAATTATTTTA
678664 AAATTA--TTA
1 AAATTATTTTA
678673 AAATTATTTTTA
1 AAATTA-TTTTA
678685 AAA-TA---TA
1 AAATTATTTTA
678692 AAATTATTTTA
1 AAATTATTTTA
678703 AAATTATTTT
1 AAATTATTTT
678713 TTAAAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
7 5 0.12
8 2 0.05
9 9 0.22
11 19 0.46
12 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:678706 original size:30 final size:31
Alignment explanation
Indices: 678662--678730 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
678652 CAAATGATTT
678662 TAAAATTA--TTAAAATTA-TTTTTAAAATA
1 TAAAATTATTTTAAAATTATTTTTTAAAATA
678690 TAAAATTATTTTAAAATTATTTTTTAAAATA
1 TAAAATTATTTTAAAATTATTTTTTAAAATA
678721 TAAAATTATT
1 TAAAATTATT
678731 AAAACCATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 8 0.21
30 9 0.24
31 21 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAAAATTATTTTAAAATTATTTTTTAAAATA
Found at i:678882 original size:9 final size:9
Alignment explanation
Indices: 678865--678939 Score: 65
Period size: 9 Copynumber: 8.9 Consensus size: 9
678855 TTAAGGATGA
*
678865 TAATGATTT
1 TAATAATTT
678874 TAATAATTT
1 TAATAATTT
678883 TAAATTAATTT
1 T-AA-TAATTT
678894 TAATAATTT
1 TAATAATTT
*
678903 T-ATATTTT
1 TAATAATTT
678911 TAA-AA---
1 TAATAATTT
678916 -AATAATTT
1 TAATAATTT
678924 TAATAATTT
1 TAATAATTT
678933 TAA-AATT
1 TAATAATT
678940 ATTTATATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
8 12 0.22
9 28 0.51
10 4 0.07
11 7 0.13
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (9 bp):
TAATAATTT
Found at i:678921 original size:21 final size:22
Alignment explanation
Indices: 678895--678937 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
678885 AATTAATTTT
*
678895 AATAATTTT-ATATTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
678916 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
678938 TTATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:681711 original size:11 final size:10
Alignment explanation
Indices: 681686--681716 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
681676 CGATTGAGCT
681686 AAATTTTTTA
1 AAATTTTTTA
681696 AAATTTTTTA
1 AAATTTTTTA
681706 ATAATTTTTTA
1 A-AATTTTTTA
681717 TCACCGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
AAATTTTTTA
Found at i:682415 original size:101 final size:101
Alignment explanation
Indices: 682240--682446 Score: 387
Period size: 101 Copynumber: 2.0 Consensus size: 101
682230 TTGAGGTTTG
* *
682240 AATTTTGTAAATGAAAAACAAAATTTAAAGAATTTTTCCTTTATTCAAAGATATTGACCTAATGT
1 AATTTTGTAAATAAAAAACAAAATTTAAAGAATTTTTCCTTTATTCAAAGACATTGACCTAATGT
*
682305 AGGGTAAACTCCACGTAAGGTTATTAAATTATTAAT
66 AGGGTAAACTCCACGTAAGATTATTAAATTATTAAT
682341 AATTTTGTAAATAAAAAACAAAATTTAAAGAATTTTTCCTTTATTCAAAGACATTGACCTAATGT
1 AATTTTGTAAATAAAAAACAAAATTTAAAGAATTTTTCCTTTATTCAAAGACATTGACCTAATGT
682406 AGGGTAAACTCCACGTAAGATTATTAAATTATTAAT
66 AGGGTAAACTCCACGTAAGATTATTAAATTATTAAT
682442 AATTT
1 AATTT
682447 ACGTATTGAT
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 103 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37
Consensus pattern (101 bp):
AATTTTGTAAATAAAAAACAAAATTTAAAGAATTTTTCCTTTATTCAAAGACATTGACCTAATGT
AGGGTAAACTCCACGTAAGATTATTAAATTATTAAT
Found at i:692463 original size:23 final size:22
Alignment explanation
Indices: 692421--692470 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
692411 CATTTATCTA
*
692421 ATAATTTTAAAATATTAAATCC
1 ATAATTTTAAAATATGAAATCC
692443 ATAATATTTAAAAT-TCGAAATCC
1 ATAAT-TTTAAAATAT-GAAATCC
692466 A-AATT
1 ATAATT
692471 GCGTGCTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 9 0.36
23 15 0.60
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAATTTTAAAATATGAAATCC
Found at i:692834 original size:18 final size:19
Alignment explanation
Indices: 692801--692845 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
692791 TCGGTTTAAA
692801 TTAAATAAAATATTAAAAAT
1 TTAAA-AAAATATTAAAAAT
*
692821 TTAAAAAAAT-TTAAATAT
1 TTAAAAAAATATTAAAAAT
692839 TATAAAA
1 T-TAAAA
692846 TTTTGTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAAAATATTAAAAAT
Found at i:694063 original size:15 final size:15
Alignment explanation
Indices: 694043--694102 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
694033 ATTTAAAGCC
694043 AATACTTAAATTTTA
1 AATACTTAAATTTTA
* *
694058 AATACTTAATTTTTCT
1 AATACTTAAATTTT-A
*
694074 AACACTTTAAATTTTA
1 AATAC-TTAAATTTTA
*
694090 AAGACTT-AATTTT
1 AATACTTAAATTTT
694103 TCTAAAACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
14 6 0.16
15 15 0.41
16 8 0.22
17 8 0.22
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (15 bp):
AATACTTAAATTTTA
Found at i:694085 original size:32 final size:32
Alignment explanation
Indices: 694048--694112 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
694038 AAGCCAATAC
* *
694048 TTAAATTTTAAATACTTAATTTTTCTAACACT
1 TTAAATTTTAAAGACTTAATTTTTCTAAAACT
694080 TTAAATTTTAAAGACTTAATTTTTCTAAAACT
1 TTAAATTTTAAAGACTTAATTTTTCTAAAACT
694112 T
1 T
694113 ATTTTTTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (32 bp):
TTAAATTTTAAAGACTTAATTTTTCTAAAACT
Found at i:694103 original size:15 final size:15
Alignment explanation
Indices: 694046--694133 Score: 56
Period size: 15 Copynumber: 5.7 Consensus size: 15
694036 TAAAGCCAAT
* *
694046 ACTTAAATTTTAAAT
1 ACTTAATTTTTAAAG
* *
694061 ACTTAATTTTTCTAAC
1 ACTTAATTTTT-AAAG
*
694077 ACTTTAAATTTTAAAG
1 AC-TTAATTTTTAAAG
694093 ACTTAATTTTTCTAAA-
1 ACTTAA-TTTT-TAAAG
*
694109 ACTT-ATTTTT-TAG
1 ACTTAATTTTTAAAG
694122 CACTTAATTTTT
1 -ACTTAATTTTT
694134 CAACTTATCA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
12 1 0.02
13 1 0.02
14 8 0.14
15 21 0.36
16 15 0.26
17 12 0.21
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.51
Consensus pattern (15 bp):
ACTTAATTTTTAAAG
Found at i:694112 original size:16 final size:16
Alignment explanation
Indices: 694056--694134 Score: 67
Period size: 15 Copynumber: 5.0 Consensus size: 16
694046 ACTTAAATTT
694056 TAAATACTTAATTTTTC
1 TAAA-ACTTAATTTTTC
* *
694073 TAACACTTTAA-ATTT-
1 TAAAAC-TTAATTTTTC
694088 TAAAGACTTAATTTTTC
1 TAAA-ACTTAATTTTTC
694105 TAAAACTT-ATTTTT-
1 TAAAACTTAATTTTTC
**
694119 TAGCACTTAATTTTTC
1 TAAAACTTAATTTTTC
694135 AACTTATCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
14 6 0.12
15 19 0.38
16 14 0.28
17 11 0.22
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.51
Consensus pattern (16 bp):
TAAAACTTAATTTTTC
Found at i:694404 original size:30 final size:28
Alignment explanation
Indices: 694355--694435 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 28
694345 CCAATTAAAT
***
694355 TTAAATTTTTAATTTTAAAAAATAGAGAAA
1 TTAAATTTTTAAAAATAAAAAATA-A-AAA
694385 TTAAATTTTTAAAAATAAAAATATAAAAA
1 TTAAATTTTTAAAAATAAAAA-ATAAAAA
* *
694414 CTAAA-TTTCAAAAATACAAAAA
1 TTAAATTTTTAAAAATA-AAAAA
694436 ATATAGCAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 11 0.25
29 11 0.25
30 19 0.43
31 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (28 bp):
TTAAATTTTTAAAAATAAAAAATAAAAA
Found at i:694405 original size:29 final size:28
Alignment explanation
Indices: 694372--694434 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
694362 TTTAATTTTA
* * *
694372 AAAAATAGAGAAATTAAATTTTTAAAAAT
1 AAAAATAGAAAAACTAAA-TTTCAAAAAT
*
694401 AAAAATATAAAAACTAAATTTCAAAAAT
1 AAAAATAGAAAAACTAAATTTCAAAAAT
694429 ACAAAA
1 A-AAAA
694435 AATATAGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAAATAGAAAAACTAAATTTCAAAAAT
Found at i:695148 original size:31 final size:31
Alignment explanation
Indices: 695074--695141 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
695064 AAAAAAAATT
* * * *
695074 AATAGCCTAGTGATTTAAATAAAAACTTTCG
1 AATAGTCTAATGACTTAAATAAAAACTTTCA
* *
695105 AATAGTCTAATGACTTAAATGAAAATTTTCA
1 AATAGTCTAATGACTTAAATAAAAACTTTCA
695136 AATAGT
1 AATAGT
695142 TCAATGATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (31 bp):
AATAGTCTAATGACTTAAATAAAAACTTTCA
Found at i:699820 original size:16 final size:17
Alignment explanation
Indices: 699793--699824 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
699783 AAAAGAGTAA
699793 ATCTATTTTTTAATAGT
1 ATCTATTTTTTAATAGT
699810 ATCTA-TTTTTAATAG
1 ATCTATTTTTTAATAG
699825 AAATGACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
ATCTATTTTTTAATAGT
Found at i:704452 original size:23 final size:23
Alignment explanation
Indices: 704424--704469 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
704414 TTAAGGTTAA
*
704424 CTTCTACTCTTAGTCTCTATATT
1 CTTCTACTATTAGTCTCTATATT
704447 CTTCTACTATTAGTCTCTATATT
1 CTTCTACTATTAGTCTCTATATT
704470 TAGTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (23 bp):
CTTCTACTATTAGTCTCTATATT
Found at i:708763 original size:29 final size:30
Alignment explanation
Indices: 708729--708787 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
708719 GTTAAATAAA
**
708729 CTTCAAAAAT-AAAAATTCTAAAGTCAAAT
1 CTTCAAAAATAAAAAAAACTAAAGTCAAAT
708758 CTTCAAAAATAAAAAAAACTAAAGTCAAAT
1 CTTCAAAAATAAAAAAAACTAAAGTCAAAT
708788 AACACTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (30 bp):
CTTCAAAAATAAAAAAAACTAAAGTCAAAT
Found at i:714479 original size:18 final size:17
Alignment explanation
Indices: 714423--714486 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
714413 TTGTTTTAGA
*
714423 AATTTTTTAAA-ATTTT
1 AATTTTTTAAATATTAT
* * *
714439 AACTTTATATAATCATTAG
1 AATTTTTTA-AAT-ATTAT
714458 AATTTTTTAAATTATTAT
1 AATTTTTTAAA-TATTAT
714476 AATTTTTTAAA
1 AATTTTTTAAA
714487 CAATATAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
16 7 0.19
17 2 0.05
18 17 0.46
19 11 0.30
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTTTTAAATATTAT
Found at i:714493 original size:17 final size:19
Alignment explanation
Indices: 714458--714499 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
714448 TAATCATTAG
* *
714458 AATTTTTTAAATTATTAT-
1 AATTTTTTAAATCAATATA
714476 AATTTTTTAAA-CAATATA
1 AATTTTTTAAATCAATATA
714494 AATTTT
1 AATTTT
714500 GAAGTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTTTTAAATCAATATA
Found at i:714497 original size:18 final size:18
Alignment explanation
Indices: 714453--714499 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
714443 TTATATAATC
* **
714453 ATTAGAATTTTTTAAATT
1 ATTATAATTTTTTAAACA
714471 ATTATAATTTTTTAAACA
1 ATTATAATTTTTTAAACA
714489 A-TATAAATTTT
1 ATTAT-AATTTT
714500 GAAGTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTATAATTTTTTAAACA
Found at i:714520 original size:20 final size:19
Alignment explanation
Indices: 714495--714567 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 19
714485 AACAATATAA
714495 ATTTTGAAGTTTTTATAAA-T
1 ATTTTGAA-TTTTTA-AAATT
714515 ATTTTGAA-TTTTAAAGATT
1 ATTTTGAATTTTTAAA-ATT
714534 ATTTTGAATTTTTAAAAATT
1 ATTTTGAATTTTT-AAAATT
714554 ATTTTGTAATTTTT
1 ATTTTG-AATTTTT
714568 GTCAAGAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
17 2 0.04
18 6 0.12
19 9 0.19
20 21 0.44
21 10 0.21
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:725114 original size:29 final size:28
Alignment explanation
Indices: 725072--725143 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 28
725062 TCGAGGTTTG
* * *
725072 AAAAT-GTGATTTTGGATACTCGGGGGT
1 AAAATGGTAATTTTGGACACTCGGGGGC
* *
725099 AAAATGGTAAATTTTGAACACTTGGGGGC
1 AAAATGGT-AATTTTGGACACTCGGGGGC
725128 AAAATGGTAATTTTGG
1 AAAATGGTAATTTTGG
725144 GAAAGTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 5 0.14
28 9 0.24
29 23 0.62
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (28 bp):
AAAATGGTAATTTTGGACACTCGGGGGC
Found at i:725271 original size:60 final size:59
Alignment explanation
Indices: 725177--725559 Score: 352
Period size: 60 Copynumber: 6.5 Consensus size: 59
725167 ATTTTAGACA
* *** * *
725177 TTCGAGAGTAAAATGGGGTTTTTTGGAAAGAATCGGGATCAAAAATGAAATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCGGG-TCAAAAATGAAATTTTTGGAAG
** * * *
725237 TTTAAGGGTAAAATGGTAATTTTTAGAAAAAATCGAGGTAAAAAATGGAATTATTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCG-GGTCAAAAATGAAATTTTTGGAAG
* * * * *
725297 TTCGGGGGTAAAATGGTAA-TTTTATAAAAATTAGGGTCAAAAAT-AGAATTTTTGGAAT
1 TTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCGGGTCAAAAATGA-AATTTTTGGAAG
* * * *
725355 TTCGGGGGTAAAATGGTAA-TTTT-GGAAAAATCGATGTCAAAAATCAAATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCG-GGTCAAAAATGAAATTTTTGGAAG
**
725413 TTCGAGGGTAAAATGGTAATTTTTAG--AAAA-CGGGTCAAAAATGGTATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCGGGTCAAAAATGAAATTTTTGGAAG
* * * * * * **
725469 TTC-AGGGGTAAAATGGTAA-TTATCGGAAAAATCGAGATTAAAAAATGGAATTTTTTTAAG
1 TTCGA-GGGTAAAATGGTAATTTTTAGAAAAAATCG-G-GTCAAAAATGAAATTTTTGGAAG
* *
725529 TTTGAGGGTAAAATGATAATTTTTAGAAAAA
1 TTCGAGGGTAAAATGGTAATTTTTAGAAAAA
725560 TTGAGATTAA
Statistics
Matches: 265, Mismatches: 44, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
55 5 0.02
56 37 0.14
57 12 0.05
58 86 0.32
59 18 0.07
60 96 0.36
61 11 0.04
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (59 bp):
TTCGAGGGTAAAATGGTAATTTTTAGAAAAAATCGGGTCAAAAATGAAATTTTTGGAAG
Found at i:725317 original size:29 final size:29
Alignment explanation
Indices: 725225--725489 Score: 123
Period size: 28 Copynumber: 9.1 Consensus size: 29
725215 TCAAAAATGA
***
725225 AATTTTTGGAAGTTTAAGGGTAAAATGGT
1 AATTTTTGGAAGTTCGGGGGTAAAATGGT
* ** *
725254 AATTTTTAGAAAAAATC-GAGGTAAAAAATGG-
1 AATTTTT-G-GAAGTTCGGGGGT--AAAATGGT
*
725285 AATTATTGGAAGTTCGGGGGTAAAATGGT
1 AATTTTTGGAAGTTCGGGGGTAAAATGGT
** * * *** *
725314 AATTTTATAAAAATTAGGGTCAAAAATAG-
1 AATTTT-TGGAAGTTCGGGGGTAAAATGGT
*
725343 AATTTTTGGAATTTCGGGGGTAAAATGGT
1 AATTTTTGGAAGTTCGGGGGTAAAATGGT
** ** **
725372 AA-TTTTGGAAAAATC-GATGTCAAAAAT-CA
1 AATTTTTGG-AAGTTCGGGGGT--AAAATGGT
*
725401 AATTTTTGGAAGTTCGAGGGTAAAATGGT
1 AATTTTTGGAAGTTCGGGGGTAAAATGGT
* ** ***
725430 AATTTTTAGAA-AACGGGTCAAAAATGGT
1 AATTTTTGGAAGTTCGGGGGTAAAATGGT
*
725458 -ATTTTTGGAAGTTCAGGGGTAAAATGGT
1 AATTTTTGGAAGTTCGGGGGTAAAATGGT
725486 AATT
1 AATT
725490 ATCGGAAAAA
Statistics
Matches: 165, Mismatches: 55, Indels: 32
0.65 0.22 0.13
Matches are distributed among these distances:
27 9 0.05
28 57 0.35
29 47 0.28
30 36 0.22
31 9 0.05
32 7 0.04
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGGGGGTAAAATGGT
Found at i:725359 original size:58 final size:58
Alignment explanation
Indices: 725197--725560 Score: 346
Period size: 58 Copynumber: 6.2 Consensus size: 58
725187 AAATGGGGTT
* ***
725197 TTTTGGAAAGAATCG-GGATCAAAAAT-GAAATTTTTGGAAGTTTAAGGGTAAAATGGTAA
1 TTTTAGAAA-AATCGAGG-TCAAAAATAG-AATTTTTGGAAGTTCGGGGGTAAAATGGTAA
* * *
725256 TTTTTAGAAAAAATCGAGGTAAAAAATGGAATTATTGGAAGTTCGGGGGTAAAATGGTAA
1 -TTTTAG-AAAAATCGAGGTCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAATGGTAA
* * *
725316 TTTTATAAAAAT-TAGGGTCAAAAATAGAATTTTTGGAATTTCGGGGGTAAAATGGTAA
1 TTTTAGAAAAATCGA-GGTCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAATGGTAA
* * *
725374 TTTTGGAAAAATCGATGTCAAAAATCA-AATTTTTGGAAGTTCGAGGGTAAAATGGTAA
1 TTTTAGAAAAATCGAGGTCAAAAAT-AGAATTTTTGGAAGTTCGGGGGTAAAATGGTAA
* * *
725432 TTTTTAG-AAAA-CG-GGTCAAAAATGGTATTTTTGGAAGTTCAGGGGTAAAATGGTAA
1 -TTTTAGAAAAATCGAGGTCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAATGGTAA
** * * * ** * * *
725488 TTATCGGAAAAATCGAGATTAAAAAATGGAATTTTTTTAAGTTTGAGGGTAAAATGATAA
1 TT-TTAGAAAAATCGAG-GTCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAATGGTAA
725548 TTTTTAGAAAAAT
1 -TTTTAGAAAAAT
725561 TGAGATTAAA
Statistics
Matches: 253, Mismatches: 37, Indels: 28
0.80 0.12 0.09
Matches are distributed among these distances:
55 2 0.01
56 39 0.15
57 7 0.03
58 99 0.39
59 13 0.05
60 85 0.34
61 8 0.03
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (58 bp):
TTTTAGAAAAATCGAGGTCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAATGGTAA
Found at i:725428 original size:116 final size:114
Alignment explanation
Indices: 725215--725561 Score: 396
Period size: 116 Copynumber: 3.0 Consensus size: 114
725205 AGAATCGGGA
* *
725215 TCAAAAATGAAATTTTTGGAAGTTT-AAGGGTAAAATGGTAATTTTTAGAAAAAATCGAGGTAAA
1 TCAAAAATG-AATTTTTGGAA-TTTCAGGGGTAAAATGGTAA-TTTT-GGAAAAATCGA-GTAAA
* *
725279 AAATGGAATTATTGGAAGTTCGGGGGTAAAATGGTAATTTTATAAAAATTAGGG
61 AAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTATAAAAATTAGGG
* *
725333 TCAAAAATAGAATTTTTGGAATTTCGGGGGTAAAATGGTAATTTTGGAAAAATCGATGTCAAAAA
1 TCAAAAAT-GAATTTTTGGAATTTCAGGGGTAAAATGGTAATTTTGGAAAAATCGA-GTAAAAAA
** *
725398 TCAAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTT-TAGAAAA--CGGG
64 TGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTATA-AAAATTAGGG
* * *
725447 TCAAAAATGGTATTTTTGGAAGTTCAGGGGTAAAATGGTAATTATCGGAAAAATCGAGATTAAAA
1 TCAAAAAT-GAATTTTTGGAATTTCAGGGGTAAAATGGTAATT-TTGGAAAAATCGAG--TAAAA
** * * *
725512 AATGGAATTTTTTTAAGTTTGAGGGTAAAATGATAATTTTTAGAAAAATT
62 AATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAA-TTTTATAAAAATT
725562 GAGATTAAAA
Statistics
Matches: 196, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
114 43 0.22
115 14 0.07
116 89 0.45
117 15 0.08
118 34 0.17
119 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.33
Consensus pattern (114 bp):
TCAAAAATGAATTTTTGGAATTTCAGGGGTAAAATGGTAATTTTGGAAAAATCGAGTAAAAAATG
GAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTATAAAAATTAGGG
Found at i:725564 original size:30 final size:29
Alignment explanation
Indices: 725530--725616 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 29
725520 TTTTTTAAGT
725530 TTGAGGGTAAAATGATAATTTTTAGAAAAA
1 TTGAGGGTAAAATGATAATTTTTA-AAAAA
** * * *
725560 TTGAGATTAAAATG-GAATTGTTAAAAAG
1 TTGAGGGTAAAATGATAATTTTTAAAAAA
*
725588 TTTAGGGGTAAAAAT-ATAATTTTTAAAAA
1 TTGA-GGGT-AAAATGATAATTTTTAAAAA
725617 GTTTGGGGTC
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
28 7 0.16
29 9 0.20
30 28 0.64
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (29 bp):
TTGAGGGTAAAATGATAATTTTTAAAAAA
Found at i:725599 original size:29 final size:29
Alignment explanation
Indices: 725568--725633 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
725558 AATTGAGATT
*
725568 AAAATGGAATTGTTAAAAAGTTTAGGGGTA
1 AAAATAGAATTGTTAAAAAGTTT-GGGGTA
* *
725598 AAAATATAATTTTTAAAAAGTTTGGGGTCA
1 AAAATAGAATTGTTAAAAAGTTTGGGGT-A
725628 AAAATA
1 AAAATA
725634 TGATTTTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.32
Consensus pattern (29 bp):
AAAATAGAATTGTTAAAAAGTTTGGGGTA
Found at i:725610 original size:59 final size:59
Alignment explanation
Indices: 725196--725616 Score: 195
Period size: 58 Copynumber: 7.2 Consensus size: 59
725186 AAAATGGGGT
* * * * *** * *
725196 TTTTTGGAAAGAATCGGGATCAAAAATGAAATTTTTGGAAGTTTAAGGGTAAAATGGTAA
1 TTTTTAGAAA-AATCGAGATTAAAAATGGAATTTTAAAAAGTTTGAGGGTAAAATGATAA
* * ** * * *
725256 TTTTTAGAAAAAATCGAGGTAAAAAATGGAATTATT-GGAAGTTCGGGGGTAAAATGGTAA
1 TTTTTAG-AAAAATCGAGATTAAAAATGGAATT-TTAAAAAGTTTGAGGGTAAAATGATAA
* * * * * *** * *
725316 -TTTTATAAAAAT-TAGGGTCAAAAATAGAATTTTTGGAA-TTTCGGGGGTAAAATGGTAA
1 TTTTTAGAAAAATCGA-GATTAAAAATGGAATTTTAAAAAGTTT-GAGGGTAAAATGATAA
* * ** *** * *
725374 -TTTTGGAAAAATCGATG-TCAAAAATCAAATTTTTGGAAGTTCGAGGGTAAAATGGTAA
1 TTTTTAGAAAAATCGA-GATTAAAAATGGAATTTTAAAAAGTTTGAGGGTAAAATGATAA
* * * *** * *
725432 TTTTTAG-AAAA-CG-GGTCAAAAATGGTATTTTTGGAAG-TTCAGGGGTAAAATGGTAA
1 TTTTTAGAAAAATCGAGATTAAAAATGGAATTTTAAAAAGTTTGA-GGGTAAAATGATAA
* ** ***
725488 TTATCGGAAAAATCGAGATTAAAAAATGGAATTTTTTTAAGTTTGAGGGTAAAATGATAA
1 TTTTTAGAAAAATCGAGATT-AAAAATGGAATTTTAAAAAGTTTGAGGGTAAAATGATAA
*
725548 TTTTTAGAAAAATTGAGATT-AAAATGGAATTGTTAAAAAGTTT-AGGGGTAAAAAT-ATAA
1 TTTTTAGAAAAATCGAGATTAAAAATGGAATT-TTAAAAAGTTTGA-GGGT-AAAATGATAA
725607 TTTTTA-AAAA
1 TTTTTAGAAAA
725617 GTTTGGGGTC
Statistics
Matches: 299, Mismatches: 44, Indels: 38
0.78 0.12 0.10
Matches are distributed among these distances:
55 3 0.01
56 37 0.12
57 11 0.04
58 106 0.35
59 38 0.13
60 96 0.32
61 8 0.03
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.33
Consensus pattern (59 bp):
TTTTTAGAAAAATCGAGATTAAAAATGGAATTTTAAAAAGTTTGAGGGTAAAATGATAA
Found at i:725650 original size:30 final size:30
Alignment explanation
Indices: 725575--725641 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
725565 ATTAAAATGG
*
725575 AATTGTTAAAAAGTTTAGGGGTAAAAATAT
1 AATTTTTAAAAAGTTTAGGGGTAAAAATAT
725605 AATTTTTAAAAAGTTT-GGGGTCAAAAATAT
1 AATTTTTAAAAAGTTTAGGGGT-AAAAATAT
*
725635 GATTTTT
1 AATTTTT
725642 GGATAGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.42, C:0.01, G:0.18, T:0.39
Consensus pattern (30 bp):
AATTTTTAAAAAGTTTAGGGGTAAAAATAT
Found at i:727494 original size:17 final size:17
Alignment explanation
Indices: 727468--727568 Score: 62
Period size: 17 Copynumber: 5.9 Consensus size: 17
727458 CTTTTGATTT
*
727468 AATTTTAATTTACAA-TA
1 AATTTAAATTTA-AAGTA
727485 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAGTA
* *** * *
727502 AATTCAAACCCAAAAATG
1 AATTTAAA-TTTAAAGTA
727520 AATTTAAATTTAGAA-TA
1 AATTTAAATTTA-AAGTA
* *
727537 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAGTA
* *
727554 AATTAAAAATTAAAG
1 AATTTAAATTTAAAG
727569 ATTGGACTCA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
16 4 0.06
17 47 0.73
18 13 0.20
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:731376 original size:13 final size:13
Alignment explanation
Indices: 731358--731382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
731348 AATGTTTTAA
731358 ATGATTTAATTAC
1 ATGATTTAATTAC
731371 ATGATTTAATTA
1 ATGATTTAATTA
731383 GAAAAATTGA
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:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATGATTTAATTAC
Found at i:731802 original size:52 final size:52
Alignment explanation
Indices: 731635--731926 Score: 286
Period size: 52 Copynumber: 5.6 Consensus size: 52
731625 TAAATGTAAA
* * * *
731635 AGGTCTGAT-ATCTATGCGTCATCATGAGTATATGAATTCTTTATGAATTATG
1 AGGTCTGATGAT-TATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* * * * *
731687 AGATTTTATGATTACGTGTTATCGTGAGTATATGAAT-CTTTATGGATTATG
1 AGGTCTGATGATTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* *
731738 A-GTTTCGATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCT-GATGATTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* * * * * * * *
731790 AGGTCTAATGATTACGTGTTATCATGAGTATATGAATCCCTTACGGATTTTA
1 AGGTCTGATGATTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* * * * * *
731842 AAGTCCGATGACTATATGTCATCGTGAGTATATGAATCATTTATGGATTTTG
1 AGGTCTGATGATTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* *
731894 AGGTCTGATGACTACT-TGTCATTGTGAGTATAT
1 AGGTCTGATGATTA-TGTGTCATCGTGAGTATAT
731927 TGTCGAAACC
Statistics
Matches: 199, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
50 3 0.02
51 42 0.21
52 148 0.74
53 6 0.03
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.40
Consensus pattern (52 bp):
AGGTCTGATGATTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
Found at i:731890 original size:104 final size:102
Alignment explanation
Indices: 731652--731904 Score: 310
Period size: 103 Copynumber: 2.4 Consensus size: 102
731642 ATATCTATGC
* * * * * *
731652 GTCATCATGAGTATATGAATTCTTTATGAATTATGAGATTTTATGATTACGTGTTATCGTGAGTA
1 GTCATCGTGAGTATATGAA-TCTTTATGGATTATGAGGTCTAATGATTACGTGTTATCATGAGTA
* * * * * *
731717 TATGAATCTTTATGGATTATGAGTTTCGATGATTATGT
65 TATGAATCCTTACGGATTATAAGTTCCGATGACTATAT
*
731755 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTAATGATTACGTGTTATCATGAGTA
1 GTCATCGTGAGTATATGAAT-CTTTATGGATTATGAGGTCTAATGATTACGTGTTATCATGAGTA
*
731820 TATGAATCCCTTACGGATTTTAAAG-TCCGATGACTATAT
65 TATGAAT-CCTTACGGATTAT-AAGTTCCGATGACTATAT
* *
731859 GTCATCGTGAGTATATGAATCATTTATGGATTTTGAGGTCTGATGA
1 GTCATCGTGAGTATATGAATC-TTTATGGATTATGAGGTCTAATGA
731905 CTACTTGTCA
Statistics
Matches: 129, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
102 1 0.01
103 64 0.50
104 62 0.48
105 2 0.02
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.40
Consensus pattern (102 bp):
GTCATCGTGAGTATATGAATCTTTATGGATTATGAGGTCTAATGATTACGTGTTATCATGAGTAT
ATGAATCCTTACGGATTATAAGTTCCGATGACTATAT
Found at i:731922 original size:104 final size:102
Alignment explanation
Indices: 731652--731926 Score: 318
Period size: 104 Copynumber: 2.7 Consensus size: 102
731642 ATATCTATGC
* * * * *
731652 GTCATCATGAGTATATGAATTCTTTATGAATTATGAGATTTTATGATTACGTGTTATCGTGAGTA
1 GTCATCGTGAGTATATGAA-TCTTTATGGATTATGAGGTCTAATGATTACGTGTTATCGTGAGTA
* * * * * *
731717 TATGAATCTTTATGGATTATGAGTTTCGATGATTATGT
65 TATGAATCCTTACGGATTATAAGTTCCGATGACTATAT
* *
731755 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTAATGATTACGTGTTATCATGAGTA
1 GTCATCGTGAGTATATGAAT-CTTTATGGATTATGAGGTCTAATGATTACGTGTTATCGTGAGTA
*
731820 TATGAATCCCTTACGGATTTTAAAG-TCCGATGACTATAT
65 TATGAAT-CCTTACGGATTAT-AAGTTCCGATGACTATAT
* * * * * *
731859 GTCATCGTGAGTATATGAATCATTTATGGATTTTGAGGTCTGATGACTACTTGTCATTGTGAGTA
1 GTCATCGTGAGTATATGAATC-TTTATGGATTATGAGGTCTAATGATTACGTGTTATCGTGAGTA
731924 TAT
65 TAT
731927 TGTCGAAACC
Statistics
Matches: 146, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
102 1 0.01
103 64 0.44
104 79 0.54
105 2 0.01
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.41
Consensus pattern (102 bp):
GTCATCGTGAGTATATGAATCTTTATGGATTATGAGGTCTAATGATTACGTGTTATCGTGAGTAT
ATGAATCCTTACGGATTATAAGTTCCGATGACTATAT
Found at i:732562 original size:96 final size:96
Alignment explanation
Indices: 732388--732572 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 96
732378 GAAAAGGATG
* ** * *
732388 TTCGATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATCGA
* *
732453 AGATAAGGAAATATTGCCTCGATTAAGAGTA
66 AGATAAAGAAATATTACCTCGATTAAGAGTA
*
732484 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATGCG
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAAT-CG
*
732549 AA-ATAAA-AGAATATTATCTCGATT
65 AAGATAAAGA-AATATTACCTCGATT
732573 TTAAAGTCTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
95 1 0.01
96 73 0.94
97 4 0.05
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAAAATCGA
AGATAAAGAAATATTACCTCGATTAAGAGTA
Found at i:732977 original size:59 final size:58
Alignment explanation
Indices: 732914--733096 Score: 258
Period size: 59 Copynumber: 3.1 Consensus size: 58
732904 TAATTTTGAG
* *
732914 AGTTTCGAGGTCAAAAACGGAATTTTTGGAAGGTCAAGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC-AGGGTAAAAATGGAATTTTTGGA
*
732973 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGATAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCAGGG-TAAAAATGGAATTTTTGGA
* * * * *
733032 AGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGAAAAAATGTAATTTTCGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC-AGGGTAAAAATGGAATTTTTGGA
733091 TAGTTT
1 -AGTTT
733097 AGGGACCTCC
Statistics
Matches: 112, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
58 3 0.03
59 101 0.90
60 8 0.07
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (58 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCAGGGTAAAAATGGAATTTTTGGA
Found at i:732991 original size:30 final size:29
Alignment explanation
Indices: 732914--733096 Score: 210
Period size: 29 Copynumber: 6.2 Consensus size: 29
732904 TAATTTTGAG
*
732914 AGTTTCGAGGTCAAAAACGGAATTTTTGGA
1 AGTTTCGAGGT-AAAAATGGAATTTTTGGA
* *
732944 AG-GTCAAGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGA-GGTAAAAATGGAATTTTTGGA
732973 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
1 AGTTTCGAGGT-AAAAATGGAATTTTTGGA
*
733003 AG-TTCGGGGATAAAAATGGAATTTTTGGA
1 AGTTTCGAGG-TAAAAATGGAATTTTTGGA
*
733032 AGTTTCGAGGTTAAAAATGGGATTTTTGGA
1 AGTTTCGAGG-TAAAAATGGAATTTTTGGA
* * *
733062 AG-TTCGAGGGAAAAAATGTAATTTTCGGA
1 AGTTTCGA-GGTAAAAATGGAATTTTTGGA
733091 TAGTTT
1 -AGTTT
733097 AGGGACCTCC
Statistics
Matches: 132, Mismatches: 13, Indels: 15
0.82 0.08 0.09
Matches are distributed among these distances:
29 71 0.54
30 59 0.45
31 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
AGTTTCGAGGTAAAAATGGAATTTTTGGA
Found at i:734824 original size:13 final size:13
Alignment explanation
Indices: 734806--734831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
734796 TTGGGCTTGA
734806 TTTGTAATTGGAC
1 TTTGTAATTGGAC
734819 TTTGTAATTGGAC
1 TTTGTAATTGGAC
734832 ATTATTTTAA
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:734861 original size:23 final size:25
Alignment explanation
Indices: 734835--734883 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
734825 ATTGGACATT
734835 ATTTTA-AATAAATTTAAATTT-AA
1 ATTTTATAATAAATTTAAATTTCAA
734858 A-TTTATAATAAATTTAAATTTCAA
1 ATTTTATAATAAATTTAAATTTCAA
734882 AT
1 AT
734884 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.17
23 16 0.70
24 3 0.13
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTTATAATAAATTTAAATTTCAA
Found at i:734869 original size:17 final size:17
Alignment explanation
Indices: 734849--734929 Score: 110
Period size: 17 Copynumber: 4.8 Consensus size: 17
734839 TAAATAAATT
734849 TAAATTTAAATTT-ATAA
1 TAAATTTAAATTTCA-AA
734866 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
734883 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
* * *
734900 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTCAAA
*
734917 TAAATTCAAATTT
1 TAAATTTAAATTT
734930 TCTTGGGCCC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
17 56 0.98
18 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:734892 original size:23 final size:23
Alignment explanation
Indices: 734841--734900 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
734831 CATTATTTTA
**
734841 AATAAATTTAAATTTAAATTTAT
1 AATAAATTTAAATTTAAATAAAT
734864 AATAAATTTAAATTTCAAATAAAT
1 AATAAATTTAAATTT-AAATAAAT
*
734888 -TTAAATTTCAAAT
1 AATAAATTT-AAAT
734901 AAACTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAATTTAAATAAAT
Found at i:734900 original size:7 final size:6
Alignment explanation
Indices: 734843--734929 Score: 62
Period size: 6 Copynumber: 15.2 Consensus size: 6
734833 TTATTTTAAA
734843 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* * * *
734889 TAAATT TCAAA-- TAAACT TAATTT TAAA-A TAAATT CAAATT T
1 TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT T
734930 TCTTGGGCCC
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
4 8 0.12
5 8 0.12
6 40 0.62
7 8 0.12
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:734903 original size:11 final size:10
Alignment explanation
Indices: 734837--734893 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
734827 TGGACATTAT
734837 TTTAAATAAA
1 TTTAAATAAA
734847 TTTAAATTTAAA
1 TTTAAA--TAAA
734859 TTTATAATAAA
1 TTTA-AATAAA
734870 TTTAAAT---
1 TTTAAATAAA
*
734877 TTCAAATAAA
1 TTTAAATAAA
734887 TTTAAAT
1 TTTAAAT
734894 TTCAAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 6 0.15
10 15 0.38
11 8 0.21
12 8 0.21
13 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:736597 original size:15 final size:16
Alignment explanation
Indices: 736564--736598 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
736554 AAATTATGAC
*
736564 TAAATAAAAAATTTAA
1 TAAATAAAAAATGTAA
736580 TAAATAAAAAATGT-A
1 TAAATAAAAAATGTAA
736595 TAAA
1 TAAA
736599 AATATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAATAAAAAATGTAA
Found at i:741327 original size:17 final size:17
Alignment explanation
Indices: 741292--741332 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
741282 GGAAAAAGTA
*
741292 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
741310 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
741327 GTTAAA
1 GTTAAA
741333 AGTCAAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.49, C:0.02, G:0.27, T:0.22
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:742166 original size:15 final size:15
Alignment explanation
Indices: 742127--742171 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
742117 TAACCCTAGA
742127 CAAAATCTTGTCTTTC
1 CAAAATCTT-TCTTTC
*
742143 CAAAGTCTTTCATTT-
1 CAAAATCTTTC-TTTC
742158 CAAAATCTTTCTTT
1 CAAAATCTTTCTTT
742172 GAGCACTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 3 0.12
15 12 0.46
16 11 0.42
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (15 bp):
CAAAATCTTTCTTTC
Found at i:750539 original size:68 final size:68
Alignment explanation
Indices: 750429--750566 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
750419 TTATATGTCA
*
750429 TAATAGAGTTGATATTTAGCGTCAAAGCTAATAGTTAAGTTAACAAAATGACATGAATGATACAA
1 TAATAGAGTTGATATTTAGCATCAAAGCTAATAGTTAAGTTAACAAAATGACATGAATGATACAA
750494 TAT
66 TAT
*
750497 TAATAGAGTTGATATTTAGCATCAAAGCTAATAGTTAGGTTAACAAAATGACATGAATGATACAA
1 TAATAGAGTTGATATTTAGCATCAAAGCTAATAGTTAAGTTAACAAAATGACATGAATGATACAA
750562 TAT
66 TAT
750565 TA
1 TA
750567 TGATTTTCAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (68 bp):
TAATAGAGTTGATATTTAGCATCAAAGCTAATAGTTAAGTTAACAAAATGACATGAATGATACAA
TAT
Found at i:753395 original size:28 final size:28
Alignment explanation
Indices: 753361--753430 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
753351 ATTTATTTTG
753361 TTTATTTTTTAATTCAAAAACCTTATTT
1 TTTATTTTTTAATTCAAAAACCTTATTT
753389 TTTATTTTTTAATTCAAAAACCTTATTT
1 TTTATTTTTTAATTCAAAAACCTTATTT
753417 TTTATTTTTTAATT
1 TTTATTTTTTAATT
753431 TTATAATTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTATTTTTTAATTCAAAAACCTTATTT
Found at i:756256 original size:13 final size:13
Alignment explanation
Indices: 756238--756262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
756228 AATTTCACAT
756238 TAATTTTTTATTA
1 TAATTTTTTATTA
756251 TAATTTTTTATT
1 TAATTTTTTATT
756263 TAGGTTAATA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TAATTTTTTATTA
Found at i:770659 original size:16 final size:16
Alignment explanation
Indices: 770638--770668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
770628 TTGCAATTAT
770638 ATGGTTGTTGCTGGTG
1 ATGGTTGTTGCTGGTG
*
770654 ATGGTTGTTGTTGGT
1 ATGGTTGTTGCTGGT
770669 AATCATCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.03, G:0.42, T:0.48
Consensus pattern (16 bp):
ATGGTTGTTGCTGGTG
Found at i:772548 original size:30 final size:29
Alignment explanation
Indices: 772513--772694 Score: 143
Period size: 30 Copynumber: 6.1 Consensus size: 29
772503 GGAGAATTTG
*
772513 GGGTCAAAATGCGATTATTGGAAAGTTCGA
1 GGGTCAAAATGTGATT-TTGGAAAGTTCGA
* ** *
772543 GGGTCAAAATGTGATTTTAAGAATTTTAG-
1 GGGTCAAAATGTGATTTT-GGAAAGTTCGA
* * * *
772572 GGGCCAAAATGTGATTTTTAGAAAGTTTGT
1 GGGTCAAAATGTGA-TTTTGGAAAGTTCGA
* * * *
772602 GGGTTAAAATGTGAGCTTTGAGAAA-TTTGG
1 GGGTCAAAATGTGA-TTTTG-GAAAGTTCGA
*
772632 GGGTCAAAATGTGATTTTTGGAAAGTTCGT
1 GGGTCAAAATGTGA-TTTTGGAAAGTTCGA
* *
772662 GGGTCAAAATGTGATTTTTGAGAAGTTCAA
1 GGGTCAAAATGTGATTTTGGA-AAGTTCGA
772692 GGG
1 GGG
772695 ACCTTCTGAG
Statistics
Matches: 123, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
29 32 0.26
30 87 0.71
31 4 0.03
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.34
Consensus pattern (29 bp):
GGGTCAAAATGTGATTTTGGAAAGTTCGA
Found at i:772656 original size:60 final size:58
Alignment explanation
Indices: 772507--772685 Score: 232
Period size: 60 Copynumber: 3.0 Consensus size: 58
772497 AATTTCGGAG
* * * *
772507 AATTTGGGGTCAAAATGCGATTATTGGAAAGTTCGAGGGTCAAAATGTGATTTTAAGA
1 AATTTGGGGTCAAAATGTGATTTTTGGAAAGTTCGTGGGTCAAAATGTGATTTTGAGA
* * * * * *
772565 ATTTTAGGGGCCAAAATGTGATTTTTAGAAAGTTTGTGGGTTAAAATGTGAGCTTTGAGA
1 AATTT-GGGGTCAAAATGTGATTTTTGGAAAGTTCGTGGGTCAAAATGTGA-TTTTGAGA
772625 AATTTGGGGGTCAAAATGTGATTTTTGGAAAGTTCGTGGGTCAAAATGTGATTTTTGAGA
1 AATTT-GGGGTCAAAATGTGATTTTTGGAAAGTTCGTGGGTCAAAATGTGA-TTTTGAGA
772685 A
1 A
772686 GTTCAAGGGA
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 4 0.04
59 38 0.38
60 59 0.58
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (58 bp):
AATTTGGGGTCAAAATGTGATTTTTGGAAAGTTCGTGGGTCAAAATGTGATTTTGAGA
Found at i:774307 original size:17 final size:17
Alignment explanation
Indices: 774285--774332 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
774275 GGACATTCTT
774285 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
774302 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
774319 TGTAAACTTAAAAT
1 TTTAAATTTAAAAT
774333 TGGGTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:775111 original size:209 final size:208
Alignment explanation
Indices: 774743--775242 Score: 748
Period size: 209 Copynumber: 2.4 Consensus size: 208
774733 ACTTCTCTAT
* * * *
774743 ATCTCATAAGGAAGATGACCGCTTCATTACTTCAACCCACTTCTCTGTATCTCATCAGGAAGATA
1 ATCTCATAAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGAT-
* *
774808 GGGGTTTGAAGTTTCACTCACATTAAGTTTCACTTCATTAAATTGGTCTACTTCTTTGTATCTCA
65 GGGGTTTGAAGTTTCACTCACATTAAGCTTCACTTCATTAAATTGGTATACTTCTTTGTATCTCA
* *
774873 TCAAGAAGATAACCGCTTTATTATTTTAATCCATTTCTCTGTATCTCATCAAGAAGACAGATTTG
130 TCAAGAAGATAACCGCTTCATTATTTTAATCCATTTATCTGTATCTCATCAAGAAGACAGATTTG
*
774938 GTTCACTTCTTTGC
195 GTTCACTTATTTGC
* * *
774952 ATCTCATCAGGAAGATGATCACTTTATTGCTTCGACTCACTTCTCTGTATCTCATCAGGAAGATG
1 ATCTCATAAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATG
* * *
775017 GGGTTTGAAAGTTTCACTCACATTAAGCTTCGCTTCATTGAATTGGTATACTTCTTTGTATCTCT
66 GGGTTTG-AAGTTTCACTCACATTAAGCTTCACTTCATTAAATTGGTATACTTCTTTGTATCTCA
* * * * * * *
775082 TTAGGAAGATGACCGCTTCATTGTTTTAATCCATTTATTTGTATCTCATCAGGAAGACGGATTTG
130 TCAAGAAGATAACCGCTTCATTATTTTAATCCATTTATCTGTATCTCATCAAGAAGACAGATTTG
775147 GTTCACTTATTTGC
195 GTTCACTTATTTGC
* * *
775161 ATCTCGTAAGGAAGATGACCACTTTATTGCTTCGACCCAGTTCTCTGTATCTCATCAAGAAGATG
1 ATCTCATAAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATG
*
775226 GGGTTTGAATTTTCACT
66 GGGTTTGAAGTTTCACT
775243 TTTCCTTATG
Statistics
Matches: 261, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
208 17 0.07
209 244 0.93
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (208 bp):
ATCTCATAAGGAAGATGACCACTTTATTGCTTCGACCCACTTCTCTGTATCTCATCAGGAAGATG
GGGTTTGAAGTTTCACTCACATTAAGCTTCACTTCATTAAATTGGTATACTTCTTTGTATCTCAT
CAAGAAGATAACCGCTTCATTATTTTAATCCATTTATCTGTATCTCATCAAGAAGACAGATTTGG
TTCACTTATTTGC
Found at i:783299 original size:24 final size:24
Alignment explanation
Indices: 783253--783305 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
783243 TCTTGTCATT
* * *
783253 ATTTGTTCCTGTAGCTGTTTTTGC
1 ATTTGTTCCTGCAGCTCTCTTTGC
* *
783277 ATTTGTTCCTGCATCTCTCTTTGG
1 ATTTGTTCCTGCAGCTCTCTTTGC
783301 ATTTG
1 ATTTG
783306 CTCTAGCCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (24 bp):
ATTTGTTCCTGCAGCTCTCTTTGC
Found at i:787182 original size:60 final size:60
Alignment explanation
Indices: 787116--787234 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
787106 AATTTGGGGT
* * *
787116 CAAAATGCGATTTTAGGAAAGTTCGAGAGTCAAAATGTGATTTTTGAGAATTTTAAGGGC
1 CAAAATGCGATTTTAGGAAAGTTCGAGAGTCAAAATGTGATTTTTAAGAAGTTCAAGGGC
* * * *
787176 CAAAATGTGATTTTTGGAAAGTTCGCGGGTCAAAATGTGATTTTTAAGAAGTTCAAGGG
1 CAAAATGCGATTTTAGGAAAGTTCGAGAGTCAAAATGTGATTTTTAAGAAGTTCAAGGG
787235 ACCTTCTGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (60 bp):
CAAAATGCGATTTTAGGAAAGTTCGAGAGTCAAAATGTGATTTTTAAGAAGTTCAAGGGC
Found at i:787220 original size:30 final size:30
Alignment explanation
Indices: 787112--787220 Score: 130
Period size: 30 Copynumber: 3.6 Consensus size: 30
787102 AAAGAATTTG
* *
787112 GGGTCAAAATGCGATTTTAGGAAAGTTCGA
1 GGGTCAAAATGTGATTTTTGGAAAGTTCGA
* * **
787142 GAGTCAAAATGTGATTTTT-GAGAATTTTAA
1 GGGTCAAAATGTGATTTTTGGA-AAGTTCGA
* *
787172 GGGCCAAAATGTGATTTTTGGAAAGTTCGC
1 GGGTCAAAATGTGATTTTTGGAAAGTTCGA
787202 GGGTCAAAATGTGATTTTT
1 GGGTCAAAATGTGATTTTT
787221 AAGAAGTTCA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
29 2 0.03
30 60 0.94
31 2 0.03
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATGTGATTTTTGGAAAGTTCGA
Found at i:787228 original size:30 final size:31
Alignment explanation
Indices: 787112--787234 Score: 119
Period size: 30 Copynumber: 4.1 Consensus size: 31
787102 AAAGAATTTG
* *
787112 GGGTCAAAATGCGA-TTTTAGGAAAGTTCGA
1 GGGTCAAAATGTGATTTTTAAGAAAGTTCGA
* * * **
787142 GAGTCAAAATGTGATTTTTGAG-AATTTTAA
1 GGGTCAAAATGTGATTTTTAAGAAAGTTCGA
* * *
787172 GGGCCAAAATGTGATTTTT-GGAAAGTTCGC
1 GGGTCAAAATGTGATTTTTAAGAAAGTTCGA
*
787202 GGGTCAAAATGTGATTTTTAAG-AAGTTCAA
1 GGGTCAAAATGTGATTTTTAAGAAAGTTCGA
787232 GGG
1 GGG
787235 ACCTTCTGAG
Statistics
Matches: 72, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
29 1 0.01
30 65 0.90
31 6 0.08
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.32
Consensus pattern (31 bp):
GGGTCAAAATGTGATTTTTAAGAAAGTTCGA
Found at i:801239 original size:4 final size:4
Alignment explanation
Indices: 801230--801260 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
801220 CTATTATATT
801230 ATTA ATTA ATTA ATTA ATTA ATT- ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
801261 TTTATAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:801245 original size:12 final size:11
Alignment explanation
Indices: 801222--801265 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
801212 CTTTTGAACT
801222 ATTATATTATTA
1 ATTA-ATTATTA
801234 ATTAATTAATTA
1 ATTAATT-ATTA
801246 ATTAATTATTA
1 ATTAATTATTA
*
801257 ATTATTTAT
1 ATTAATTAT
801266 AATCTACGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 15 0.50
12 15 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTAATTATTA
Found at i:801594 original size:12 final size:12
Alignment explanation
Indices: 801577--801603 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
801567 ACGATTTAAG
801577 TAAAATAATTTA
1 TAAAATAATTTA
801589 TAAAATAATTTA
1 TAAAATAATTTA
801601 TAA
1 TAA
801604 TATATAGCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATAATTTA
Done.