Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 100 of 187
Found at i:29599523 original size:30 final size:30
Alignment explanation
Indices: 29599487--29599571 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
29599477 ACAATATAAT
29599487 ATTAAAGACTATACTTAATTTTTAATTTAG
1 ATTAAAGACTATACTTAATTTTTAATTTAG
* *
29599517 ATTAAAGGCTATAATTAATTTTTAATTTAG
1 ATTAAAGACTATACTTAATTTTTAATTTAG
29599547 ATTAAAGACTATACTTAATTTTTAA
1 ATTAAAGACTATACTTAATTTTTAA
29599572 AAATTAAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (30 bp):
ATTAAAGACTATACTTAATTTTTAATTTAG
Found at i:29615348 original size:9 final size:9
Alignment explanation
Indices: 29615336--29615368 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
29615326 GAATTATTTG
29615336 AATCGAGTT
1 AATCGAGTT
*
29615345 AATCGAATT
1 AATCGAGTT
29615354 AATCGAGTT
1 AATCGAGTT
29615363 AATCGA
1 AATCGA
29615369 ATCAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (9 bp):
AATCGAGTT
Found at i:29615359 original size:18 final size:18
Alignment explanation
Indices: 29615336--29615370 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29615326 GAATTATTTG
29615336 AATCGAGTTAATCGAATT
1 AATCGAGTTAATCGAATT
29615354 AATCGAGTTAATCGAAT
1 AATCGAGTTAATCGAAT
29615371 CAATTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (18 bp):
AATCGAGTTAATCGAATT
Found at i:29615435 original size:9 final size:9
Alignment explanation
Indices: 29615421--29615449 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
29615411 TAAATTTTTA
29615421 AATTCGAAT
1 AATTCGAAT
29615430 AATTCGAAT
1 AATTCGAAT
29615439 AATTCGAAT
1 AATTCGAAT
29615448 AA
1 AA
29615450 AAACTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29616372 original size:14 final size:14
Alignment explanation
Indices: 29616353--29616379 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29616343 TTAAAAAAAT
29616353 TTAAGTTTGATTTA
1 TTAAGTTTGATTTA
29616367 TTAAGTTTGATTT
1 TTAAGTTTGATTT
29616380 TAAACCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (14 bp):
TTAAGTTTGATTTA
Found at i:29627434 original size:29 final size:29
Alignment explanation
Indices: 29627376--29627438 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
29627366 CAATAAATAA
29627376 AAAATATATAAAATTATTAAATATTAAATT
1 AAAATATATAAAATTATTAAATA-TAAATT
*
29627406 AAAATATTATAAATATTTTTAAA-A-AAATT
1 AAAATA-TATAAA-ATTATTAAATATAAATT
29627435 AAAA
1 AAAA
29627439 ATAATATGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 9 0.30
30 6 0.20
31 7 0.23
32 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAATATATAAAATTATTAAATATAAATT
Found at i:29627440 original size:30 final size:30
Alignment explanation
Indices: 29627368--29627441 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
29627358 AAAAATTTCA
*
29627368 ATAAATAAAAAATATATAAAATTATTAAAT
1 ATAAATTAAAAATATATAAAATTATTAAAT
*
29627398 ATTAAATT-AAAATATTATAAATATTTTTAAA-
1 A-TAAATTAAAAATA-TATAAA-ATTATTAAAT
29627429 A-AAATTAAAAATA
1 ATAAATTAAAAATA
29627442 ATATGGGCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 5 0.13
30 13 0.34
31 12 0.32
32 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
ATAAATTAAAAATATATAAAATTATTAAAT
Found at i:29628708 original size:16 final size:16
Alignment explanation
Indices: 29628687--29628721 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
29628677 GAGACCGAAA
*
29628687 GGTATTCTTAGCTAAG
1 GGTATTCTTAACTAAG
29628703 GGTATTCTTAACTAAG
1 GGTATTCTTAACTAAG
29628719 GGT
1 GGT
29628722 GGTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (16 bp):
GGTATTCTTAACTAAG
Found at i:29628776 original size:19 final size:19
Alignment explanation
Indices: 29628741--29628777 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29628731 CTTAGTTGAG
*
29628741 GATAATTAGCGACTTAATT
1 GATAATTAGAGACTTAATT
*
29628760 GATAATTAGAGATTTAAT
1 GATAATTAGAGACTTAAT
29628778 CAATCATAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (19 bp):
GATAATTAGAGACTTAATT
Found at i:29630623 original size:12 final size:11
Alignment explanation
Indices: 29630591--29630626 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
29630581 TGACTTCTTG
*
29630591 TTTAAATTTAT
1 TTTAAATTTAA
29630602 TTTAAATTTAA
1 TTTAAATTTAA
29630613 TTTAAATTTTAA
1 TTTAAA-TTTAA
29630625 TT
1 TT
29630627 GTAGTTGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:29635640 original size:27 final size:27
Alignment explanation
Indices: 29635610--29635683 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 27
29635600 ATATTGTTAT
29635610 ATTTTAATAAAAAAT-AAAATATTAAAA
1 ATTTTAATAAAAAATAAAAATA-TAAAA
* *
29635637 A-TTTATTAAAAATTAGAAAATATAAAA
1 ATTTTAATAAAAAATA-AAAATATAAAA
**
29635664 ATCGTAA-AAAAATATAAAAA
1 ATTTTAATAAAAA-ATAAAAA
29635684 AATTTGTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
26 11 0.30
27 16 0.43
28 10 0.27
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATTTTAATAAAAAATAAAAATATAAAA
Found at i:29635648 original size:26 final size:27
Alignment explanation
Indices: 29635612--29635665 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
29635602 ATTGTTATAT
29635612 TTTAATAAAAAAT--AAAATATTAAAAA
1 TTTAATAAAAAATAGAAAATA-TAAAAA
* *
29635638 TTTATTAAAAATTAGAAAATATAAAAA
1 TTTAATAAAAAATAGAAAATATAAAAA
29635665 T
1 T
29635666 CGTAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.46
27 7 0.29
28 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTAATAAAAAATAGAAAATATAAAAA
Found at i:29635681 original size:10 final size:10
Alignment explanation
Indices: 29635668--29635783 Score: 62
Period size: 10 Copynumber: 11.8 Consensus size: 10
29635658 ATAAAAATCG
*
29635668 TAAAAAAATA
1 TAAAAAATTA
29635678 TAAAAAAATT-
1 T-AAAAAATTA
** *
29635688 TGTAAAATTT
1 TAAAAAATTA
29635698 TATAAAAATTA
1 TA-AAAAATTA
29635709 TAAAAAATTA
1 TAAAAAATTA
*
29635719 TAAAATATT-
1 TAAAAAATTA
**
29635728 T-TGAAA-TA
1 TAAAAAATTA
29635736 TAAAAAATT-
1 TAAAAAATTA
* *
29635745 TATAAAATTT
1 TAAAAAATTA
* *
29635755 TATAAAATCA
1 TAAAAAATTA
29635765 TAAGAAAATTA
1 TAA-AAAATTA
*
29635776 TACAAAAT
1 TAAAAAAT
29635784 GTAAAGAAAT
Statistics
Matches: 80, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
7 1 0.01
8 3 0.04
9 18 0.22
10 35 0.44
11 23 0.29
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:29635704 original size:57 final size:57
Alignment explanation
Indices: 29635632--29635798 Score: 167
Period size: 57 Copynumber: 2.9 Consensus size: 57
29635622 AATAAAATAT
* * *
29635632 TAAAAATTTATTAAAAATTAGAAAATATA-AAAATCGTAAAAAAATATAAAAAAATTTG
1 TAAAATTTTA-TAAAAATTAGAAAATATACAAAAT-GTAAAGAAATATAAAAAAATTTA
* * * * ***
29635690 TAAAATTTTATAAAAATTATAAAAAATTATAAAATATTTTGAAATAT-AAAAAATTTA
1 TAAAATTTTATAAAAATTAGAAAATA-TACAAAATGTAAAGAAATATAAAAAAATTTA
*
29635747 TAAAATTTTATAAAATCATAAGAAAATTATACAAAATGTAAAGAAATATAAA
1 TAAAATTTTATAAAA--ATTAGAAAA-TATACAAAATGTAAAGAAATATAAA
29635799 TTTCGTAAAT
Statistics
Matches: 86, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
57 38 0.44
58 18 0.21
59 27 0.31
60 3 0.03
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (57 bp):
TAAAATTTTATAAAAATTAGAAAATATACAAAATGTAAAGAAATATAAAAAAATTTA
Found at i:29635967 original size:9 final size:9
Alignment explanation
Indices: 29635953--29636048 Score: 54
Period size: 9 Copynumber: 10.6 Consensus size: 9
29635943 GGTCTTTATT
*
29635953 TTTTTATGA
1 TTTTTATAA
29635962 TTTTTAATAA
1 TTTTT-ATAA
* *
29635972 ATTTTAAAA
1 TTTTTATAA
29635981 TTTTTAT-A
1 TTTTTATAA
29635989 TTTTTATTAAA
1 TTTTTA-T-AA
*
29636000 ATTTTATAA
1 TTTTTATAA
*
29636009 TTTTTCTAA
1 TTTTTATAA
** *
29636018 AGTTTATTA
1 TTTTTATAA
29636027 TTTATTAT--
1 TTT-TTATAA
*
29636035 TATTTATAA
1 TTTTTATAA
29636044 TTTTT
1 TTTTT
29636049 TTCTAATCTT
Statistics
Matches: 64, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
7 4 0.06
8 9 0.14
9 33 0.52
10 12 0.19
11 6 0.09
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29635993 original size:28 final size:29
Alignment explanation
Indices: 29635953--29636013 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
29635943 GGTCTTTATT
29635953 TTTTTATGATTTTTAAT-AAATTTTAAAA
1 TTTTTATGATTTTTAATAAAATTTTAAAA
* *
29635981 TTTTTAT-ATTTTTATTAAAATTTTATAA
1 TTTTTATGATTTTTAATAAAATTTTAAAA
29636009 TTTTT
1 TTTTT
29636014 CTAAAGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTTTATGATTTTTAATAAAATTTTAAAA
Found at i:29636004 original size:19 final size:21
Alignment explanation
Indices: 29635975--29636013 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
29635965 TTAATAAATT
29635975 TTAAAATTTTTAT-ATTTTTA
1 TTAAAATTTTTATAATTTTTA
29635995 TTAAAA-TTTTATAATTTTT
1 TTAAAATTTTTATAATTTTT
29636014 CTAAAGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTAAAATTTTTATAATTTTTA
Found at i:29636018 original size:19 final size:20
Alignment explanation
Indices: 29635976--29636018 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29635966 TAATAAATTT
*
29635976 TAAAATTTTTATATTTTTAT
1 TAAAATTTTTATATTTTTAC
29635996 TAAAA-TTTTATAATTTTT-C
1 TAAAATTTTTAT-ATTTTTAC
29636015 TAAA
1 TAAA
29636019 GTTTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAAATTTTTATATTTTTAC
Found at i:29636487 original size:19 final size:17
Alignment explanation
Indices: 29636459--29636510 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
29636449 ATTATAGTCA
*
29636459 TAAAATTTGATTAAATT
1 TAAATTTTGATTAAATT
*
29636476 ATAAATTATTGATAAAAATT
1 -TAAATT-TTGAT-TAAATT
29636496 TAAATTTTGAGTTAA
1 TAAATTTTGA-TTAA
29636511 TCGAATTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 11 0.39
19 12 0.43
20 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (17 bp):
TAAATTTTGATTAAATT
Found at i:29644575 original size:15 final size:15
Alignment explanation
Indices: 29644549--29644592 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
29644539 TAACATTTTC
29644549 AAAAAATA-AAAATA
1 AAAAAATAGAAAATA
29644563 AAAAAATAGAAAATTA
1 AAAAAATAGAAAA-TA
*
29644579 TAAAAAT-GAAAATA
1 AAAAAATAGAAAATA
29644593 TTAAGAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 10 0.37
15 9 0.33
16 8 0.30
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
AAAAAATAGAAAATA
Found at i:29644575 original size:16 final size:15
Alignment explanation
Indices: 29644549--29644590 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
29644539 TAACATTTTC
29644549 AAAAAAT-AAAAATA
1 AAAAAATGAAAAATA
*
29644563 AAAAAATAGAAAATTA
1 AAAAAAT-GAAAAATA
*
29644579 TAAAAATGAAAA
1 AAAAAATGAAAA
29644591 TATTAAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 5 0.21
16 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (15 bp):
AAAAAATGAAAAATA
Found at i:29647610 original size:30 final size:31
Alignment explanation
Indices: 29647575--29647632 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
29647565 TTTCCAAGCC
29647575 TAGGGGC-AAAATCATAATTTTGT-GAAACTT
1 TAGGGGCAAAAAT-ATAATTTTGTAGAAACTT
*
29647605 TAGGGGCAAAAATGTAATTTTGTAGAAA
1 TAGGGGCAAAAATATAATTTTGTAGAAA
29647633 TGTGATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (31 bp):
TAGGGGCAAAAATATAATTTTGTAGAAACTT
Found at i:29647931 original size:51 final size:51
Alignment explanation
Indices: 29647801--29648094 Score: 276
Period size: 51 Copynumber: 5.8 Consensus size: 51
29647791 AGTTGCTAGG
* ** *
29647801 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-ATGATAGGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATA-GATTCGA
* ** *
29647852 TGCA--TTTGTAGTACTATGTGCAGGCTACTATACGTACCGGATAGCTTCGA
1 T-CACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGATTCGA
* * * * *
29647902 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT-AGATTCGA
* * * * * *
29647953 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGAATCGGA-ATGA-TAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATA-GATTCGA
* * * * * *
29648003 TCGCATGTGTAGTACTATGTGTAGGCTTCTATGTGTACCGGATAGCTTCAA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGATTCGA
*
29648054 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
29648095 GTATCATTTA
Statistics
Matches: 199, Mismatches: 35, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
49 4 0.02
50 77 0.39
51 114 0.57
52 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGATTCGA
Found at i:29648012 original size:101 final size:102
Alignment explanation
Indices: 29647797--29648094 Score: 304
Period size: 101 Copynumber: 2.9 Consensus size: 102
29647787 GTGAAGTTGC
* ** * *
29647797 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATA-GGTTGCATTTG
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGAAAATGGTCACGTGTG
*
29647860 TAGTACTATGTGCAGGCTACTATACGT--ACCGGATAGCT
65 TAGTACTATGTGCAGGCTAC--TACGTGAACCGGATAGCA
* * *
29647898 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACGTGTGT
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAATGGTCACGTGTGT
* *
29647963 AGTACTATGTGTAGGCTACTACGTGAATCGGA-ATG-A
66 AGTACTATGTGCAGGCTACTACGTGAACCGGATA-GCA
* * * * * *** **
29647999 TAGGTCGCATGTGTAGTACTATGTGTAGGCTTCTATGTGTACCGGAT-AGCTTCAATCACGTGTG
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAAT-GGTCACGTGTG
*
29648063 TAGTACTATGTGCAGGCTACTATGTGAACCGG
65 TAGTACTATGTGCAGGCTACTACGTGAACCGG
29648095 GTATCATTTA
Statistics
Matches: 164, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
100 10 0.06
101 122 0.74
102 32 0.20
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (102 bp):
TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAATGGTCACGTGTGT
AGTACTATGTGCAGGCTACTACGTGAACCGGATAGCA
Found at i:29648075 original size:152 final size:152
Alignment explanation
Indices: 29647799--29648084 Score: 482
Period size: 152 Copynumber: 1.9 Consensus size: 152
29647789 GAAGTTGCTA
* * *
29647799 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTTGCATTTGTAGT
1 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAATGATAGGTCGCATGTGTAGT
*
29647864 ACTATGTGCAGGCTACTATACGTACCGGATAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCT
66 ACTATGTGCAGGCTACTATACGTACCGGATAGCTTCAATCACGTGTGTAGTACTATGTGCAGGCT
29647929 ACTACGTGTATCGGATGAAAAT
131 ACTACGTGTATCGGATGAAAAT
* *
29647951 GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGAATCGGAATGATAGGTCGCATGTGTAGT
1 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAATGATAGGTCGCATGTGTAGT
* * **
29648016 ACTATGTGTAGGCTTCTATGTGTACCGGATAGCTTCAATCACGTGTGTAGTACTATGTGCAGGCT
66 ACTATGTGCAGGCTACTATACGTACCGGATAGCTTCAATCACGTGTGTAGTACTATGTGCAGGCT
29648081 ACTA
131 ACTA
29648085 TGTGAACCGG
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
152 124 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (152 bp):
GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAATGATAGGTCGCATGTGTAGT
ACTATGTGCAGGCTACTATACGTACCGGATAGCTTCAATCACGTGTGTAGTACTATGTGCAGGCT
ACTACGTGTATCGGATGAAAAT
Found at i:29653140 original size:10 final size:10
Alignment explanation
Indices: 29653125--29653156 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
29653115 ATATTTAGTA
29653125 AAAGATTGAG
1 AAAGATTGAG
29653135 AAAGATTGAG
1 AAAGATTGAG
29653145 AAAGATTG-G
1 AAAGATTGAG
29653154 AAA
1 AAA
29653157 ATTTAGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (10 bp):
AAAGATTGAG
Found at i:29655443 original size:16 final size:18
Alignment explanation
Indices: 29655422--29655463 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
29655412 CATCACCACA
29655422 AAACAACTCT-TA-TTTG
1 AAACAACTCTCTACTTTG
29655438 AAACAAC-CTCTACTTTG
1 AAACAACTCTCTACTTTG
29655455 AGAACAACT
1 A-AACAACT
29655464 ATGTCGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 9 0.41
17 5 0.23
18 6 0.27
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (18 bp):
AAACAACTCTCTACTTTG
Found at i:29656133 original size:79 final size:79
Alignment explanation
Indices: 29656042--29656200 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 79
29656032 CACATTTTCC
* *
29656042 ATTCTTCCTCTTCGCCTTCTTCTGGTACATCTTGTTCACTTGTTTACAACACTTCCTTTTTCCAT
1 ATTCTTCCTCTTCGCCTTCTTCTGGTACATCCTGTTCACTTGTTTACAACACTTCCTCTTTCCAT
29656107 CAAAAGAACCCTCT
66 CAAAAGAACCCTCT
*
29656121 ATTCTTCCTCTTCGCCTTCTTCTGGTACATCCTGTTCACTTGTTTGCAACACTTCCTCTTTCCAT
1 ATTCTTCCTCTTCGCCTTCTTCTGGTACATCCTGTTCACTTGTTTACAACACTTCCTCTTTCCAT
29656186 CAAAAGAACCCTCT
66 CAAAAGAACCCTCT
29656200 A
1 A
29656201 CGGATCATAA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.19, C:0.33, G:0.08, T:0.40
Consensus pattern (79 bp):
ATTCTTCCTCTTCGCCTTCTTCTGGTACATCCTGTTCACTTGTTTACAACACTTCCTCTTTCCAT
CAAAAGAACCCTCT
Found at i:29660799 original size:38 final size:38
Alignment explanation
Indices: 29660757--29660836 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
29660747 AGATTGTTAG
* *
29660757 AAGTTCTGTGACTCAAATTCCTATTAAACATAAAATAC
1 AAGTTCTGTAACCCAAATTCCTATTAAACATAAAATAC
* *
29660795 AAGTTGTTTAACCCAAATTCCTATTAAACATAAAATAC
1 AAGTTCTGTAACCCAAATTCCTATTAAACATAAAATAC
29660833 AAGT
1 AAGT
29660837 CAAGCTGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.31
Consensus pattern (38 bp):
AAGTTCTGTAACCCAAATTCCTATTAAACATAAAATAC
Found at i:29661307 original size:9 final size:9
Alignment explanation
Indices: 29661295--29661342 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
29661285 GACTTTTAGC
29661295 ATTTTTATA
1 ATTTTTATA
29661304 ATTTTTATA
1 ATTTTTATA
29661313 ATTTTTGA-A
1 ATTTTT-ATA
*
29661322 A-ATTT-TA
1 ATTTTTATA
29661329 ATTTTTATA
1 ATTTTTATA
29661338 ATTTT
1 ATTTT
29661343 AAAAATTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 2 0.06
8 6 0.18
9 24 0.73
10 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:29661332 original size:16 final size:15
Alignment explanation
Indices: 29661311--29661344 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29661301 ATAATTTTTA
29661311 TAATTTTTGAAAATTT
1 TAATTTTT-AAAATTT
*
29661327 TAATTTTTATAATTT
1 TAATTTTTAAAATTT
29661342 TAA
1 TAA
29661345 AAATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TAATTTTTAAAATTT
Found at i:29661336 original size:25 final size:24
Alignment explanation
Indices: 29661302--29661358 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
29661292 AGCATTTTTA
* *
29661302 TAATTTTTATAATTTTTGAAAATTT
1 TAATTTTTATAA-TTTTAAAAATTC
29661327 TAATTTTTATAATTTTAAAAATTC
1 TAATTTTTATAATTTTAAAAATTC
29661351 T-ATTTTTA
1 TAATTTTTA
29661359 AAAAATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.23
24 11 0.37
25 12 0.40
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TAATTTTTATAATTTTAAAAATTC
Found at i:29661389 original size:20 final size:18
Alignment explanation
Indices: 29661364--29661402 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
29661354 TTTTAAAAAA
29661364 TATTTTAAATGATTTTCTAT
1 TATTTTAAATG-TTTT-TAT
29661384 TATTTTAAATGTTTTTAT
1 TATTTTAAATGTTTTTAT
29661402 T
1 T
29661403 TTTATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (18 bp):
TATTTTAAATGTTTTTAT
Found at i:29667413 original size:3 final size:3
Alignment explanation
Indices: 29667407--29667435 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29667397 AAAAAATGTC
29667407 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29667436 GATCCAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29669156 original size:2 final size:2
Alignment explanation
Indices: 29669149--29669179 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29669139 GACAGATCAG
29669149 AT AT AT 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 AT AT AT A
29669180 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29669184 original size:2 final size:2
Alignment explanation
Indices: 29669179--29669219 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29669169 ATATATATAT
29669179 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29669220 TTACTGTAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29692301 original size:18 final size:19
Alignment explanation
Indices: 29692278--29692313 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29692268 ACAAACTCTC
*
29692278 AAATAAATCCA-TAATTTA
1 AAATAAAACCATTAATTTA
29692296 AAATAAAACCATTAATTT
1 AAATAAAACCATTAATTT
29692314 CTAAGTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAAAACCATTAATTTA
Found at i:29711537 original size:21 final size:21
Alignment explanation
Indices: 29711499--29711547 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29711489 CCTAAGTTTA
*
29711499 GAGACTTAAGGCTTAAGTATC
1 GAGACTTAAGGCTCAAGTATC
* *
29711520 GAGACTTACAGGC-CAAGTCTT
1 GAGACTTA-AGGCTCAAGTATC
29711541 GAGACTT
1 GAGACTT
29711548 GCAACCCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (21 bp):
GAGACTTAAGGCTCAAGTATC
Found at i:29714226 original size:21 final size:21
Alignment explanation
Indices: 29714200--29714241 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29714190 TGATGAAGGA
29714200 GAAGAGCGCCGCTGGATTATG
1 GAAGAGCGCCGCTGGATTATG
29714221 GAAGAGCGCCGCTGGATTATG
1 GAAGAGCGCCGCTGGATTATG
29714242 TCGAAAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.38, T:0.19
Consensus pattern (21 bp):
GAAGAGCGCCGCTGGATTATG
Found at i:29719452 original size:27 final size:27
Alignment explanation
Indices: 29719411--29719686 Score: 302
Period size: 27 Copynumber: 10.2 Consensus size: 27
29719401 ATTCATGGGC
** *
29719411 AAATGACTAAAATACCCTTGACGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * * *
29719438 AAATGACCGAGATACCCTTAAAAGGCA
1 AAATGACCGAAATACCCTTGAAGGGTA
*
29719465 AAATAACCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
29719492 AAATGATCGAAATGCCCTTGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
*
29719519 AAATGATCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* **
29719546 AAATGACTGAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
29719573 AAATGACCGAAATACCCCTGAAAGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * * * *
29719600 AAATAATCGAAATGCCCTCGAATGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
29719627 AAATGACCGAAATACCCCTAAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * *
29719654 AAATAACAGAAATACCC-TCATAGGGTA
1 AAATGACCGAAATACCCTTGA-AGGGTA
29719681 AAATGA
1 AAATGA
29719687 TTGTTATACC
Statistics
Matches: 206, Mismatches: 42, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
26 2 0.01
27 204 0.99
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCTTGAAGGGTA
Found at i:29720058 original size:28 final size:29
Alignment explanation
Indices: 29720017--29720119 Score: 131
Period size: 28 Copynumber: 3.6 Consensus size: 29
29720007 TACTGTATTG
29720017 CACTGATTACTGTATTGGGCTAAGGCCAC-
1 CACTG-TTACTGTATTGGGCTAAGGCCACA
29720046 CACTGTTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGG-CCACA
* * *
29720076 AACTGTTACTATAATGGGCTAAGGCC-CA
1 CACTGTTACTGTATTGGGCTAAGGCCACA
29720104 CACTG-TACTGATATTG
1 CACTGTTACTG-TATTG
29720120 TATATGGCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
27 4 0.06
28 29 0.45
29 11 0.17
30 21 0.32
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (29 bp):
CACTGTTACTGTATTGGGCTAAGGCCACA
Found at i:29720083 original size:30 final size:30
Alignment explanation
Indices: 29720018--29720105 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
29720008 ACTGTATTGC
*
29720018 ACTGATTACTGTATTGGGCTAAGG-CCAC-C
1 ACTG-TTACTGTATTGGGCTAAGGCCCACAA
29720047 ACTGTTACTGTATTGGGCTAAGGCCCACAA
1 ACTGTTACTGTATTGGGCTAAGGCCCACAA
* *
29720077 ACTGTTACTATAATGGGCTAAGGCCCACA
1 ACTGTTACTGTATTGGGCTAAGGCCCACA
29720106 CTGTACTGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
28 19 0.35
29 8 0.15
30 27 0.50
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (30 bp):
ACTGTTACTGTATTGGGCTAAGGCCCACAA
Found at i:29726778 original size:50 final size:50
Alignment explanation
Indices: 29726711--29726886 Score: 183
Period size: 50 Copynumber: 3.5 Consensus size: 50
29726701 ACTGCCAATT
* * * * **
29726711 CCATATCCCAGATATGGTCTTACATGAGA-GTCCTCATATAGGTGCCCATT
1 CCATGTCCCAGACATGGTCTTACATGAGACCT-CTCATATAGGTGCCAACG
* ** * * *
29726761 TCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACG
* * *
29726811 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACG
* *
29726861 CCATGTCCTAAACATGGTCTTACATG
1 CCATGTCCCAGACATGGTCTTACATG
29726887 GGATCTCTTT
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
50 107 0.99
51 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACG
Found at i:29726887 original size:50 final size:50
Alignment explanation
Indices: 29726762--29726894 Score: 221
Period size: 50 Copynumber: 2.7 Consensus size: 50
29726752 GTGCCCATTT
**
29726762 CATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC
29726812 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC
* * *
29726862 CATGTCCTAAACATGGTCTTACATGGGATCTCT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCT
29726895 TTACCCAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.26
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC
Found at i:29729791 original size:27 final size:27
Alignment explanation
Indices: 29729754--29730042 Score: 362
Period size: 27 Copynumber: 10.7 Consensus size: 27
29729744 ATTCATGGGC
*
29729754 AAATGACCGAAATACCCTTGATGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * *
29729781 AAATAATCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
*
29729808 AAATAACCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
29729835 AAATGGCCGAAATGCCCTTGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * * *
29729862 AAATGACTGAAATACCCTTAAAAGGCA
1 AAATGACCGAAATACCCTTGAAGGGTA
* *
29729889 AAATGACCGAAATACCCCTAAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
*
29729916 AAATGATCGAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * *
29729943 AAATGACTGAAATACCCCTAAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
* * *
29729970 AAATAACCGAAATGCCCTCGAAGGGTA
1 AAATGACCGAAATACCCTTGAAGGGTA
*
29729997 AAATGACCGAAATACCCCTGAATGGGTA
1 AAATGACCGAAATACCCTTGAA-GGGTA
* *
29730025 AAATAACCAAAATACCCT
1 AAATGACCGAAATACCCT
29730043 CACATGGTAA
Statistics
Matches: 222, Mismatches: 39, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
27 202 0.91
28 20 0.09
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCTTGAAGGGTA
Found at i:29730454 original size:30 final size:30
Alignment explanation
Indices: 29730388--29730477 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 30
29730378 TACTACATTG
29730388 CACTGATTACTGTATTGGGCTAAGGCCC-C-
1 CACTG-TTACTGTATTGGGCTAAGGCCCACA
*
29730417 TACTGTTACTGTATTGGGCTAAGGCCCACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
* *
29730447 CACTGTTACTGTAATGGGCTAAGGCCTACA
1 CACTGTTACTGTATTGGGCTAAGGCCCACA
29730477 C
1 C
29730478 TGTACTGATA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
28 22 0.40
29 5 0.09
30 28 0.51
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (30 bp):
CACTGTTACTGTATTGGGCTAAGGCCCACA
Found at i:29732268 original size:24 final size:24
Alignment explanation
Indices: 29732222--29732270 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
29732212 ACTTTTTCTA
* *
29732222 TAAATATAATAAATTATATTTATT
1 TAAATATAATAAAGTATAGTTATT
29732246 TAAATATTAATAAAGTA-AGTTATT
1 TAAATA-TAATAAAGTATAGTTATT
29732270 T
1 T
29732271 TCACATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
TAAATATAATAAAGTATAGTTATT
Found at i:29741480 original size:6 final size:6
Alignment explanation
Indices: 29741469--29741533 Score: 130
Period size: 6 Copynumber: 10.8 Consensus size: 6
29741459 TTATATAATT
29741469 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
29741517 TATTTA TATTTA TATTT
1 TATTTA TATTTA TATTT
29741534 GTTCGCTAAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:29742002 original size:22 final size:22
Alignment explanation
Indices: 29741969--29742029 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
29741959 ACCCAGTCCG
* *
29741969 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
29741992 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
29742014 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
29742030 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:29742042 original size:16 final size:16
Alignment explanation
Indices: 29742005--29742044 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29741995 TTAATAAAAT
* *
29742005 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
29742021 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
29742037 TAAAATTA
1 TAAAATTA
29742045 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:29742103 original size:66 final size:67
Alignment explanation
Indices: 29742033--29742175 Score: 252
Period size: 68 Copynumber: 2.1 Consensus size: 67
29742023 AAATTAATTG
*
29742033 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
29742097 GA
66 GA
*
29742099 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
29742164 TGA
65 TGA
29742167 TTAGTAAAA
1 TTAGTAAAA
29742176 CAAACTTGAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
66 26 0.36
68 46 0.64
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:29742129 original size:9 final size:9
Alignment explanation
Indices: 29742117--29742144 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29742107 TTTATCAAAT
29742117 TATTAATTG
1 TATTAATTG
29742126 TATTAATTG
1 TATTAATTG
29742135 TATTAATTG
1 TATTAATTG
29742144 T
1 T
29742145 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:29750528 original size:10 final size:10
Alignment explanation
Indices: 29750504--29750580 Score: 57
Period size: 10 Copynumber: 7.2 Consensus size: 10
29750494 GTTCAGATTC
*
29750504 AAAAATGAAA
1 AAAAAAGAAA
29750514 TAAAAAAGAAA
1 -AAAAAAGAAA
29750525 AAAAAAGAAA
1 AAAAAAGAAA
* *
29750535 AAAGATGAAA
1 AAAAAAGAAA
29750545 AAAGAAA-ATTAA
1 AAA-AAAGA--AA
29750557 TGAAAAAAGAAA
1 --AAAAAAGAAA
*
29750569 AGAAAAGAAA
1 AAAAAAGAAA
29750579 AA
1 AA
29750581 TGAGTGAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
10 32 0.60
11 10 0.19
12 4 0.08
13 3 0.06
14 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:29750535 original size:17 final size:17
Alignment explanation
Indices: 29750504--29750580 Score: 64
Period size: 17 Copynumber: 4.3 Consensus size: 17
29750494 GTTCAGATTC
*
29750504 AAAAATGAAATAAAAAAG
1 AAAAAAGAAA-AAAAAAG
*
29750522 AAAAAAAAAGAAAAAAGATG
1 AAAAAAGAA-AAAAAA-A-G
** *
29750542 AAAAAAGAAAATTAATG
1 AAAAAAGAAAAAAAAAG
*
29750559 AAAAAAGAAAAGAAAAG
1 AAAAAAGAAAAAAAAAG
29750576 AAAAA
1 AAAAA
29750581 TGAGTGAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
17 20 0.43
18 12 0.26
19 6 0.13
20 9 0.19
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAG
Found at i:29750545 original size:27 final size:26
Alignment explanation
Indices: 29750515--29750580 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
29750505 AAAATGAAAT
*
29750515 AAAAAAGAAAAAAAAAGAAAAAAGATG
1 AAAAAAGAAAAAAAAAGAAAAAAGA-A
** *
29750542 AAAAAAGAAAATTAATGAAAAAAGAA
1 AAAAAAGAAAAAAAAAGAAAAAAGAA
29750568 AAGAAAAGAAAAA
1 AA-AAAAGAAAAA
29750581 TGAGTGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (26 bp):
AAAAAAGAAAAAAAAAGAAAAAAGAA
Found at i:29754077 original size:27 final size:27
Alignment explanation
Indices: 29754024--29754077 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
29754014 ATGAATGGGT
*
29754024 GTAATTAATCAAAAGATAAATCTTTTG
1 GTAATTAATCAAAAGATAAATCATTTG
* * *
29754051 GTAATTGATCAAAAGTTATATCATTTG
1 GTAATTAATCAAAAGATAAATCATTTG
29754078 ATTATTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (27 bp):
GTAATTAATCAAAAGATAAATCATTTG
Found at i:29754738 original size:36 final size:35
Alignment explanation
Indices: 29754647--29754741 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 35
29754637 ACTTTGACGT
*
29754647 GCTCGCAACTTAAGTGGAGCTCGCGTATTTGGGTGA
1 GCTCACAACTTAAGT-GAGCTCGCGTATTTGGGTGA
** ** *
29754683 GCTCACAACTTTTGATGAGCTCGCAG-ATTTGTTTTA
1 GCTCACAACTTAAG-TGAGCTCGC-GTATTTGGGTGA
29754719 GCTCACAACTTCAAGTGAGCTCG
1 GCTCACAACTT-AAGTGAGCTCG
29754742 TGGGTTTGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
36 45 0.94
37 3 0.06
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (35 bp):
GCTCACAACTTAAGTGAGCTCGCGTATTTGGGTGA
Found at i:29766002 original size:15 final size:15
Alignment explanation
Indices: 29765969--29766018 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
29765959 ATTTGATAAG
* *
29765969 TTGAAAAATTAAGTG
1 TTGAAAAGTTAAGTA
*
29765984 TTGAAAAGTTAAGCA
1 TTGAAAAGTTAAGTA
*
29765999 TTGAAAAGCTAAGTA
1 TTGAAAAGTTAAGTA
29766014 TTGAA
1 TTGAA
29766019 TTTAAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (15 bp):
TTGAAAAGTTAAGTA
Found at i:29767298 original size:31 final size:31
Alignment explanation
Indices: 29767258--29767349 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 31
29767248 TAAACTTTCT
*
29767258 AAAAGTTTTGAAAATTTCAATTAGATCCT-TC
1 AAAACTTTTGAAAATTTCAATTA-ATCCTCTC
* * *
29767289 AAAACTTTTGGAAA-TTCTTATTAATTCTCTC
1 AAAACTTTTGAAAATTTC-AATTAATCCTCTC
* * * *
29767320 AAAATTTTTAAAAATTTCAAGTAAACCTCT
1 AAAACTTTTGAAAATTTCAATTAATCCTCT
29767350 TTTTTTAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
30 7 0.15
31 37 0.79
32 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (31 bp):
AAAACTTTTGAAAATTTCAATTAATCCTCTC
Found at i:29774653 original size:12 final size:12
Alignment explanation
Indices: 29774636--29774660 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29774626 AACTCATTGC
29774636 TTGGATCTCGAT
1 TTGGATCTCGAT
29774648 TTGGATCTCGAT
1 TTGGATCTCGAT
29774660 T
1 T
29774661 AAAATGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (12 bp):
TTGGATCTCGAT
Found at i:29776689 original size:26 final size:26
Alignment explanation
Indices: 29776649--29776721 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 26
29776639 CGTGTATTTC
29776649 TTTTATATATATACATACATATAAT-
1 TTTTATATATATACATACATATAATA
* *
29776674 TTTCTATATATTTACATACATA-CATA
1 TTT-TATATATATACATACATATAATA
* *
29776700 TTTTATATATGTACATGCATAT
1 TTTTATATATATACATACATAT
29776722 TTTTTTTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 21 0.51
26 20 0.49
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (26 bp):
TTTTATATATATACATACATATAATA
Found at i:29789079 original size:44 final size:44
Alignment explanation
Indices: 29788967--29789468 Score: 375
Period size: 44 Copynumber: 11.6 Consensus size: 44
29788957 ATTATACAGG
* *
29788967 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGA-AGTGCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGT--A-A
*
29789013 TCTTATCTCCCTGAGATTACAGCGGAGCAAATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
* *
29789057 TCCTATCTCCCTGAGATTACAGCGGAGCAAATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
* * * *
29789101 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG---G--A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
* * * ** *
29789140 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGATC-GCG-TCAG--G
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAT-AGTAA
* * * *
29789181 TCTTATTTCCCTGAGATTACAGTGGAGCAGACCGAAGA-AGTGCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGT--A-A
29789227 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
* * * * * *
29789271 TCCTATTTCCCTGAGATTACAGTGGAGCGGAT---TGA-AG-GA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
* * * ** *
29789310 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGATC-GCG-TCAG--G
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAT-AGTAA
* * * * *
29789351 TCTTATTTCCCTGAGGTTACAGTGGAGCAGACCGAAGA-AGTGCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGT--A-A
29789397 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
* * *
29789441 TTTTATTTCCCTGAGATTACAGTGGAGC
1 TCTTATCTCCCTGAGATTACAGCGGAGC
29789469 GGATTGAAGG
Statistics
Matches: 364, Mismatches: 64, Indels: 58
0.75 0.13 0.12
Matches are distributed among these distances:
38 3 0.01
39 49 0.13
40 2 0.01
41 59 0.16
42 5 0.01
44 132 0.36
45 3 0.01
46 102 0.28
47 9 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAA
Found at i:29789203 original size:80 final size:80
Alignment explanation
Indices: 29789108--29789546 Score: 409
Period size: 80 Copynumber: 5.2 Consensus size: 80
29789098 TAATCCTATC
29789108 TCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
1 TCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
29789173 GCGTCAGGTCTTATT
66 GCGTCAGGTCTTATT
** * * *
29789188 TCCCTGAGATTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTG-AGATTACAGCGG
1 TCCCTGAGATTACAGTGGAGC-G---GATTAA-AG--GATCTTATCTCTCTGAAG-TTACAGCAG
* ** * *
29789252 AGCAGATCAAAGAT-AGTAATCCTATT
58 AGTAGATC-GCG-TCAG--GTCTTATT
*
29789278 TCCCTGAGATTACAGTGGAGCGGATTGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
1 TCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
29789343 GCGTCAGGTCTTATT
66 GCGTCAGGTCTTATT
* ** * * *
29789358 TCCCTGAGGTTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTG-AGATTACAGCGG
1 TCCCTGAGATTACAGTGGAGC-G---GATTAA-AG--GATCTTATCTCTCTGAAG-TTACAGCAG
* ** * *
29789422 AGCAGATCAAAGAT-AGTAATTTTATT
58 AGTAGATC-GCG-TCAG--GTCTTATT
*
29789448 TCCCTGAGATTACAGTGGAGCGGATTGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
1 TCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
*
29789513 GCGTCAAGTCTTATT
66 GCGTCAGGTCTTATT
*
29789528 TCCCTGAGGTTACAGTGGA
1 TCCCTGAGATTACAGTGGA
29789547 ACAGACCGAA
Statistics
Matches: 284, Mismatches: 47, Indels: 56
0.73 0.12 0.14
Matches are distributed among these distances:
80 71 0.25
81 4 0.01
82 5 0.02
83 58 0.20
84 11 0.04
85 4 0.01
86 10 0.04
87 58 0.20
88 6 0.02
89 4 0.01
90 53 0.19
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (80 bp):
TCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
GCGTCAGGTCTTATT
Found at i:29789252 original size:170 final size:170
Alignment explanation
Indices: 29789013--29789598 Score: 989
Period size: 170 Copynumber: 3.5 Consensus size: 170
29789003 GAAGTGCAGA
* * * * * *
29789013 TCTTATCTCCCTGAGATTACAGCGGAGCAAATCAAAGATAGT--A-ATCCTATCTCCCTGAGATT
1 TCTTATTTCCCTGAGATTACAGTGGAGCAGACCGAAGA-AGTGCAGATCTTATCTCCCTGAGATT
* * *
29789075 ACAGCGGAGCAAATCAAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGA
65 ACAGCGGAGCAGATCAAAGATAGTAATCCTATTTCCCTGAGATTACAGTGGAGCGGATTGAAGGA
29789140 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGG
130 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGG
29789181 TCTTATTTCCCTGAGATTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTGAGATTA
29789246 CAGCGGAGCAGATCAAAGATAGTAATCCTATTTCCCTGAGATTACAGTGGAGCGGATTGAAGGAT
66 CAGCGGAGCAGATCAAAGATAGTAATCCTATTTCCCTGAGATTACAGTGGAGCGGATTGAAGGAT
29789311 CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGG
131 CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGG
*
29789351 TCTTATTTCCCTGAGGTTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTGAGATTA
**
29789416 CAGCGGAGCAGATCAAAGATAGTAATTTTATTTCCCTGAGATTACAGTGGAGCGGATTGAAGGAT
66 CAGCGGAGCAGATCAAAGATAGTAATCCTATTTCCCTGAGATTACAGTGGAGCGGATTGAAGGAT
*
29789481 CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAAG
131 CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGG
* * * *
29789521 TCTTATTTCCCTGAGGTTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTA
1 TCTTATTTCCCTGAGATTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTGAGATTA
29789586 CAGCGGAGCAGAT
66 CAGCGGAGCAGAT
29789599 TGAAGCCAGT
Statistics
Matches: 399, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
167 3 0.01
168 33 0.08
169 1 0.00
170 362 0.91
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (170 bp):
TCTTATTTCCCTGAGATTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTGAGATTA
CAGCGGAGCAGATCAAAGATAGTAATCCTATTTCCCTGAGATTACAGTGGAGCGGATTGAAGGAT
CTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAGG
Found at i:29789454 original size:214 final size:211
Alignment explanation
Indices: 29788967--29789468 Score: 543
Period size: 214 Copynumber: 2.3 Consensus size: 211
29788957 ATTATACAGG
29788967 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAGTGCAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAGT-CAGATCTTATCTCCCTGAGATTA
29789032 CAGCGGAGCAAATCAAAGATAGTAATCCTATCTCCCTGAGATTACAGCGGAGCAAATCAAAGATA
65 CAGCGGAGCAAATCAAAGATAGTAATCCTATCTCCCTGAGATTACAGCGGAGCAAAT--AAGATA
** * *
29789097 GTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAG
128 GTAATCCTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGGATCTTATCTCCCTGAAGTTACAG
* * * *
29789162 CAGAGTAGATCGCGTCAGG
193 CAGAGCAGACCGAGTCAGA
* *
29789181 TCTTATTTCCCTGAGATTACAGTGGAGCAGACCGAAGAAGTGCAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAGT-CAGATCTTATCTCCCTGAGATTA
* * * ** *
29789246 CAGCGGAGCAGATCAAAGATAGTAATCCTATTTCCCTGAGATTACAGTGGAGCGGAT-TGA-AG-
65 CAGCGGAGCAAATCAAAGATAGTAATCCTATCTCCCTGAGATTACAGCGGAGCAAATAAGATAGT
* * * * * * *
29789308 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCGT-CAGG-TCTTATTTCCCTGAGGTTA
130 AATCCTATCTCCCTGAGA-TTACAGCAGAGCAGAT----TAAAGGATCTTATCTCCCTGAAGTTA
**
29789370 CAGTGGAGCAGACCGAAGAAGTGCAGA
190 CAGCAGAGCAGACC---G-AGT-CAGA
* * * *
29789397 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGT-A-ATTTTATTTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGA-AGTCAGATCTTATCTCCCTGAGATTA
*
29789460 CAGTGGAGC
65 CAGCGGAGC
29789469 GGATTGAAGG
Statistics
Matches: 245, Mismatches: 32, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
208 1 0.00
209 25 0.10
210 2 0.01
211 28 0.11
212 3 0.01
213 1 0.00
214 142 0.58
215 3 0.01
216 37 0.15
217 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (211 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAGTCAGATCTTATCTCCCTGAGATTAC
AGCGGAGCAAATCAAAGATAGTAATCCTATCTCCCTGAGATTACAGCGGAGCAAATAAGATAGTA
ATCCTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGGATCTTATCTCCCTGAAGTTACAGCAG
AGCAGACCGAGTCAGA
Found at i:29791276 original size:3 final size:3
Alignment explanation
Indices: 29791268--29791300 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
29791258 TTTATTTTTG
*
29791268 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29791301 AATTGCTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29791393 original size:25 final size:25
Alignment explanation
Indices: 29791357--29791407 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29791347 TATAATTTTC
*
29791357 TATATATTTACATACATACATATTT
1 TATATATGTACATACATACATATTT
*
29791382 TATATATGTACATACATATATATTT
1 TATATATGTACATACATACATATTT
29791407 T
1 T
29791408 TTTTACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (25 bp):
TATATATGTACATACATACATATTT
Found at i:29791414 original size:21 final size:23
Alignment explanation
Indices: 29791359--29791415 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 23
29791349 TAATTTTCTA
29791359 TATATTTACATACATACATATTT
1 TATATTTACATACATACATATTT
*
29791382 TATATATGTACATACATATATATTT
1 TATAT-T-TACATACATACATATTT
29791407 T-T-TTTACAT
1 TATATTTACAT
29791416 TTTTATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 5 0.16
22 1 0.03
23 6 0.19
24 2 0.06
25 17 0.55
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (23 bp):
TATATTTACATACATACATATTT
Found at i:29792975 original size:28 final size:30
Alignment explanation
Indices: 29792920--29792981 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
29792910 TAAAAACTTG
*
29792920 AAAATATATAAAATTTATTACAAAAAGACAT
1 AAAATATATAAAA-TTATTAAAAAAAGACAT
*
29792951 AAAA-ATATAAAA-TATTAAAAAAAGACTT
1 AAAATATATAAAATTATTAAAAAAAGACAT
29792979 AAA
1 AAA
29792982 TATGAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 17 0.59
30 8 0.28
31 4 0.14
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (30 bp):
AAAATATATAAAATTATTAAAAAAAGACAT
Found at i:29795245 original size:17 final size:17
Alignment explanation
Indices: 29795223--29795255 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29795213 TGATTGAATT
*
29795223 TTTTTTAATGTTTTATA
1 TTTTTTAATATTTTATA
29795240 TTTTTTAATATTTTAT
1 TTTTTTAATATTTTAT
29795256 TTATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTTTAATATTTTATA
Found at i:29796820 original size:116 final size:116
Alignment explanation
Indices: 29796659--29797000 Score: 486
Period size: 116 Copynumber: 2.9 Consensus size: 116
29796649 TTTTTGGTCC
* * * * * *
29796659 AAACGCCGTGAATATGTATTAAAAGATTGCAACACGGCGCCGTTTTTAGCTGTATTTTTAGTGGC
1 AAACGCCGCGAATATGTATTAAGAGTTTGCAAAACGGTGCCGTTTTTAGCTGCATTTTTAGTGGC
* * *
29796724 ATTTTGACTAAAACACCGCAAAAGGTTTTGCGTTAGTGGCATTTTCACCAA
66 GTTTTGACTAAAACACCGCAAAAGGTTATGCGTTAGTGGTATTTTCACCAA
* * *
29796775 AAACGCCGCGAATATGTATTAAGAGTTTGCAAAACGGTGCTGTTTTTAGCTACGTTTTTAGTGGC
1 AAACGCCGCGAATATGTATTAAGAGTTTGCAAAACGGTGCCGTTTTTAGCTGCATTTTTAGTGGC
* * * *
29796840 GTTTTGACTAAAACACCGCAAAAGGTTATACATTAGTGGTGTTTTCACGAA
66 GTTTTGACTAAAACACCGCAAAAGGTTATGCGTTAGTGGTATTTTCACCAA
* * * * *
29796891 AAATGCCGCGAATATTTATTAAGAGTTTGCAAAAAGGTGCCATTTTTAGTTGCATTTTTAGTGGC
1 AAACGCCGCGAATATGTATTAAGAGTTTGCAAAACGGTGCCGTTTTTAGCTGCATTTTTAGTGGC
*
29796956 GTTTTGACTAAAACGCCGCAAAAGGTTATGCGTTAGTGGTATTTT
66 GTTTTGACTAAAACACCGCAAAAGGTTATGCGTTAGTGGTATTTT
29797001 TTTATAAACG
Statistics
Matches: 198, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
116 198 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (116 bp):
AAACGCCGCGAATATGTATTAAGAGTTTGCAAAACGGTGCCGTTTTTAGCTGCATTTTTAGTGGC
GTTTTGACTAAAACACCGCAAAAGGTTATGCGTTAGTGGTATTTTCACCAA
Found at i:29797118 original size:23 final size:24
Alignment explanation
Indices: 29797092--29797143 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
29797082 CAAGTTAGAT
* *
29797092 TTCCCTGATTTCTTTT-CCCCAAC
1 TTCCCTAACTTCTTTTCCCCCAAC
*
29797115 TTCCC-AACTTCTTTTCCCCCAAT
1 TTCCCTAACTTCTTTTCCCCCAAC
29797138 TTCCCT
1 TTCCCT
29797144 CAAGTTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.13, C:0.42, G:0.02, T:0.42
Consensus pattern (24 bp):
TTCCCTAACTTCTTTTCCCCCAAC
Found at i:29802462 original size:42 final size:42
Alignment explanation
Indices: 29802359--29802559 Score: 206
Period size: 43 Copynumber: 4.7 Consensus size: 42
29802349 CGGCATTTAT
* * * **
29802359 GCTAAAGGTTATGTTCTTTAGTGACGTTTGTAGAGAAAAATGCC
1 GCTAAAGGTCATGTTCTATAGCGACGTTTGT-G-GAAAAGCGCC
* *
29802403 GCTAAAGGTCATATTCTATAGCGACGTTTGTGGGAAAGCGCC
1 GCTAAAGGTCATGTTCTATAGCGACGTTTGTGGAAAAGCGCC
* * *
29802445 GCTAAAGGCCATGTTCTATAGATG-CGTTTGTGGTAAAAGTGCC
1 GCTAAAGGTCATGTTCTATAG-CGACGTTTGTGG-AAAAGCGCC
* * * *
29802488 GTTAAAAGTCATGTTCTTTAACGACGTTTGTGGGAAAAGCGCC
1 GCTAAAGGTCATGTTCTATAGCGACGTTTGT-GGAAAAGCGCC
* *
29802531 GCTAAAGGTCATGTTTTATAGCGGCGTTT
1 GCTAAAGGTCATGTTCTATAGCGACGTTT
29802560 TTCGCATAAA
Statistics
Matches: 128, Mismatches: 25, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
42 36 0.28
43 63 0.49
44 29 0.23
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (42 bp):
GCTAAAGGTCATGTTCTATAGCGACGTTTGTGGAAAAGCGCC
Found at i:29802527 original size:86 final size:86
Alignment explanation
Indices: 29802359--29802551 Score: 248
Period size: 86 Copynumber: 2.2 Consensus size: 86
29802349 CGGCATTTAT
* * * *
29802359 GCTAAAGGTTATGTTCTTTAGTGACGTTTGTAGAGAAAAATGCCGCTAAAGGTCATATTCTATAG
1 GCTAAAGGTCATGTTCTATAGTGACGTTTGTAGAGAAAAATGCCGCTAAAAGTCATATTCTATAA
29802424 CGACGTTTGTGGGAAAGCGCC
66 CGACGTTTGTGGGAAAGCGCC
* * * * *
29802445 GCTAAAGGCCATGTTCTATAGATG-CGTTTGT-G-GTAAAAGTGCCGTTAAAAGTCATGTTCTTT
1 GCTAAAGGTCATGTTCTATAG-TGACGTTTGTAGAG-AAAAATGCCGCTAAAAGTCATATTCTAT
29802507 AACGACGTTTGTGGGAAAAGCGCC
64 AACGACGTTTGTGGG-AAAGCGCC
*
29802531 GCTAAAGGTCATGTTTTATAG
1 GCTAAAGGTCATGTTCTATAG
29802552 CGGCGTTTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 38 0.41
86 52 0.56
87 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (86 bp):
GCTAAAGGTCATGTTCTATAGTGACGTTTGTAGAGAAAAATGCCGCTAAAAGTCATATTCTATAA
CGACGTTTGTGGGAAAGCGCC
Found at i:29804285 original size:11 final size:11
Alignment explanation
Indices: 29804269--29804298 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29804259 ATATATAATA
29804269 TAAAAAATATT
1 TAAAAAATATT
*
29804280 TAAAAATTATT
1 TAAAAAATATT
29804291 TAAAAAAT
1 TAAAAAAT
29804299 TAATTAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAAAAATATT
Found at i:29804296 original size:12 final size:12
Alignment explanation
Indices: 29804269--29804306 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
29804259 ATATATAATA
29804269 TAAAAAA-TATT
1 TAAAAAATTATT
29804280 T-AAAAATTATT
1 TAAAAAATTATT
*
29804291 TAAAAAATTAAT
1 TAAAAAATTATT
29804303 TAAA
1 TAAA
29804307 TGCTGATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 5 0.21
11 6 0.25
12 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:29805097 original size:2 final size:2
Alignment explanation
Indices: 29805086--29805126 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
29805076 TTAGACACAC
*
29805086 AT AT AC AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
29805127 AATTAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:29805209 original size:18 final size:17
Alignment explanation
Indices: 29805187--29805227 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
29805177 AAAATAAATT
29805187 CAAAATTTCAAAAATCC
1 CAAAATTTCAAAAATCC
* *
29805204 CTAAAATTTTAAAATTCC
1 C-AAAATTTCAAAAATCC
29805222 CAAAAT
1 CAAAAT
29805228 CAATCGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (17 bp):
CAAAATTTCAAAAATCC
Found at i:29805570 original size:13 final size:13
Alignment explanation
Indices: 29805552--29805577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29805542 AACTTAGCTG
29805552 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
29805565 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
29805578 AGTTTAGCTG
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:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
TTCCTTCTGTTTC
Found at i:29808155 original size:27 final size:27
Alignment explanation
Indices: 29808118--29808170 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
29808108 GGTGATTAAA
29808118 ATTGAAGGAATAAATTAGTTTTATTTT
1 ATTGAAGGAATAAATTAGTTTTATTTT
*
29808145 ATTGAATGAATAAATTAGTTTTATTT
1 ATTGAAGGAATAAATTAGTTTTATTT
29808171 AATTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (27 bp):
ATTGAAGGAATAAATTAGTTTTATTTT
Found at i:29808416 original size:16 final size:16
Alignment explanation
Indices: 29808392--29808422 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29808382 GTTATTATGA
*
29808392 TTGATTAAAAAACAAC
1 TTGAGTAAAAAACAAC
29808408 TTGAGTAAAAAACAA
1 TTGAGTAAAAAACAA
29808423 GTATTTGGTA
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:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (16 bp):
TTGAGTAAAAAACAAC
Found at i:29808473 original size:6 final size:6
Alignment explanation
Indices: 29808462--29808490 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29808452 AAATATTCAT
29808462 TGTTAA TGTTAA TGTTAA TGTTAA TGTTA
1 TGTTAA TGTTAA TGTTAA TGTTAA TGTTA
29808491 TAGTTCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
TGTTAA
Found at i:29810132 original size:18 final size:18
Alignment explanation
Indices: 29810086--29810133 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
29810076 TATAAGAATA
*
29810086 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
29810102 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
29810119 TTAATTATAATATAT
1 TTAATTATAATATAT
29810134 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:29810138 original size:15 final size:15
Alignment explanation
Indices: 29810103--29810154 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29810093 TTAATAATTT
*
29810103 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29810117 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29810131 TATTTAATAATAAT-
1 TATTTAATTATAATA
29810145 TATGTTAATT
1 TAT-TTAATT
29810155 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29810212 original size:66 final size:66
Alignment explanation
Indices: 29810136--29810333 Score: 199
Period size: 66 Copynumber: 3.2 Consensus size: 66
29810126 TAATATATTT
29810136 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
29810201 G
66 G
* * * * *
29810202 AATATTAATTAT-TAAGAGTTT-TA--TTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT
1 AATAATAATTATGTTA-A-TTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAT
**
29810254 -TT
64 AAG
*
29810256 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATCATGATTTGAGTAAATTCATATAA
1 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
29810321 G
66 G
*
29810322 AATATTAATTAT
1 AATAATAATTAT
29810334 TAAGAATTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 32
0.68 0.11 0.22
Matches are distributed among these distances:
53 3 0.03
54 14 0.14
55 6 0.06
56 4 0.04
57 3 0.03
58 1 0.01
59 9 0.09
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 4 0.04
65 6 0.06
66 25 0.25
67 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (66 bp):
AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
G
Found at i:29810236 original size:61 final size:60
Alignment explanation
Indices: 29810171--29810358 Score: 172
Period size: 61 Copynumber: 3.1 Consensus size: 60
29810161 TTACAGTATC
29810171 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAGTTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGA-TTTTATTAAATT
* * * * * * * * * *
29810232 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTATATTTTA-CAGTATC
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGATTTTATTA-AATT
*
29810291 ATATATCATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG-ATTTTATTAAATT
29810352 ATATATT
1 ATATATT
29810359 TTAATTATAA
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
57 11 0.12
58 7 0.08
59 16 0.17
60 17 0.18
61 24 0.26
62 7 0.08
63 11 0.12
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (60 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGATTTTATTAAATT
Found at i:29810258 original size:15 final size:15
Alignment explanation
Indices: 29810223--29810274 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29810213 TTAAGAGTTT
*
29810223 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29810237 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29810251 TATTTAATAATAAT-
1 TATTTAATTATAATA
29810265 TATGTTAATT
1 TAT-TTAATT
29810275 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29810277 original size:120 final size:120
Alignment explanation
Indices: 29810064--29810390 Score: 627
Period size: 120 Copynumber: 2.7 Consensus size: 120
29810054 NNNNNNNNNN
*
29810064 TGAGTAAATTCATATAAGAATATTAATTATTAATAATTTTATTAAATTATATATTTTAATTATAA
1 TGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA
*
29810129 TATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATT
66 TATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATCATGATT
*
29810184 TGAGTAAATTCATATAAGAATATTAATTATTAAGAGTTTTATTAAATTATATATTTTAATTATAA
1 TGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA
29810249 TATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATCATGATT
66 TATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATCATGATT
29810304 TGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA
1 TGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA
29810369 TATATTTAATAATAATTATGTT
66 TATATTTAATAATAATTATGTT
29810391 TAAATATGAT
Statistics
Matches: 203, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 203 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
TGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAA
TATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATCATGATT
Found at i:29810373 original size:16 final size:16
Alignment explanation
Indices: 29810352--29810393 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29810342 TTATTAAATT
*
29810352 ATATATTTTAATTATA
1 ATATATTTTAATAATA
29810368 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
29810383 AT-TATGTTTAA
1 ATATAT-TTTAA
29810394 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:29810378 original size:15 final size:15
Alignment explanation
Indices: 29810343--29810384 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29810333 TTAAGAATTT
*
29810343 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29810357 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29810371 TATTTAATAATAAT
1 TATTTAATTATAAT
29810385 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29810508 original size:157 final size:157
Alignment explanation
Indices: 29810330--29810642 Score: 581
Period size: 157 Copynumber: 2.0 Consensus size: 157
29810320 AGAATATTAA
*
29810330 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
*
29810395 TATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATAA
66 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
*
29810460 TAATTTACCAAAACAAATTTCTGCTAT
131 TAATTTACCAAAACAAATTTATGCTAT
*
29810487 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
29810552 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
66 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
*
29810617 TCATTTACCAAAACAAATTTATGCTA
131 TAATTTACCAAAACAAATTTATGCTA
29810643 AGGGTATTCT
Statistics
Matches: 151, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 151 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (157 bp):
TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
TAATTTACCAAAACAAATTTATGCTAT
Found at i:29810524 original size:18 final size:17
Alignment explanation
Indices: 29810496--29810530 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29810486 TTTATTAAGA
*
29810496 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29810513 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29810531 TTAATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29810790 original size:16 final size:16
Alignment explanation
Indices: 29810769--29810801 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29810759 TTGCTATTAT
29810769 ACCTCTAATCCAATAC
1 ACCTCTAATCCAATAC
29810785 ACCTCTAATCCAATAC
1 ACCTCTAATCCAATAC
29810801 A
1 A
29810802 GCGAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.24
Consensus pattern (16 bp):
ACCTCTAATCCAATAC
Found at i:29811601 original size:48 final size:48
Alignment explanation
Indices: 29811548--29811657 Score: 186
Period size: 48 Copynumber: 2.3 Consensus size: 48
29811538 AAAAAAAATT
29811548 ATTATATTAAAAATTGCCTTATTTAAAACATTATTGTAAAGAATTTCG
1 ATTATATTAAAAATTGCCTTATTTAAAACATTATTGTAAAGAATTTCG
* *
29811596 ATTATA-AAAAAATTTGCCTTATTTAAAACGTTATTGTAAAGAATTTCG
1 ATTATATTAAAAA-TTGCCTTATTTAAAACATTATTGTAAAGAATTTCG
29811644 ATTATATTAAAAAT
1 ATTATATTAAAAAT
29811658 ATTAAAGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
47 5 0.09
48 47 0.82
49 5 0.09
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (48 bp):
ATTATATTAAAAATTGCCTTATTTAAAACATTATTGTAAAGAATTTCG
Found at i:29812250 original size:18 final size:18
Alignment explanation
Indices: 29812224--29812266 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29812214 GACTCGAAAA
* * *
29812224 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
29812242 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
29812260 AGGATAC
1 AGGATAC
29812267 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:29814120 original size:11 final size:12
Alignment explanation
Indices: 29814104--29814156 Score: 67
Period size: 11 Copynumber: 4.7 Consensus size: 12
29814094 TTAAATAGGG
29814104 ATTTGAGA-GAA
1 ATTTGAGAGGAA
29814115 ATTTGAGAGGAA
1 ATTTGAGAGGAA
29814127 A-TTGAGA-GAA
1 ATTTGAGAGGAA
*
29814137 AATTGAGAGGAA
1 ATTTGAGAGGAA
*
29814149 ATTAGAGA
1 ATTTGAGA
29814157 AAGGATTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 4 0.11
11 20 0.54
12 13 0.35
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:29814134 original size:22 final size:22
Alignment explanation
Indices: 29814106--29814158 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
29814096 AAATAGGGAT
*
29814106 TTGAGAGAAATTTGAGAGGAAA
1 TTGAGAGAAAATTGAGAGGAAA
29814128 TTGAGAGAAAATTGAGAGGAAA
1 TTGAGAGAAAATTGAGAGGAAA
29814150 TT-AGAGAAA
1 TTGAGAGAAA
29814159 GGATTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (22 bp):
TTGAGAGAAAATTGAGAGGAAA
Found at i:29817282 original size:16 final size:17
Alignment explanation
Indices: 29817251--29817295 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
29817241 CCGATATAAT
* * *
29817251 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
29817268 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
29817284 AAATATTTTTAA
1 AAATATTTTTAA
29817296 AATACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:29817592 original size:8 final size:8
Alignment explanation
Indices: 29817579--29817658 Score: 63
Period size: 8 Copynumber: 9.1 Consensus size: 8
29817569 ATATATTTAT
29817579 TTTTTAAA
1 TTTTTAAA
29817587 TTTTTAAA
1 TTTTTAAA
*
29817595 TTTTAAAATA
1 TTTT-TAA-A
29817605 TTTTTAAAATA
1 TTTTT--AA-A
29817616 CTTTTTAAA
1 -TTTTTAAA
*
29817625 TTTTTTAA
1 TTTTTAAA
29817633 -TTTTAAA
1 TTTTTAAA
29817640 TACTTTTAAA
1 T--TTTTAAA
29817650 TTTTTAAA
1 TTTTTAAA
29817658 T
1 T
29817659 AAATTTTTGG
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
7 6 0.10
8 27 0.45
9 3 0.05
10 15 0.25
11 4 0.07
12 5 0.08
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTTTAAA
Found at i:29817609 original size:18 final size:18
Alignment explanation
Indices: 29817577--29817659 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
29817567 AAATATATTT
*
29817577 ATTTTTTAA-ATTTTTAA
1 ATTTTTAAATATTTTTAA
*
29817594 ATTTTAAAATATTTTTAAAA
1 ATTTTTAAATATTTTT--AA
29817614 TACTTTTTAAAT-TTTTT-A
1 -A-TTTTTAAATATTTTTAA
*
29817632 A-TTTTAAATACTTTTAA
1 ATTTTTAAATATTTTTAA
29817649 ATTTTTAAATA
1 ATTTTTAAATA
29817660 AATTTTTGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
15 8 0.15
16 4 0.07
17 10 0.19
18 16 0.30
20 2 0.04
21 6 0.11
22 8 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTAAATATTTTTAA
Found at i:29817622 original size:12 final size:11
Alignment explanation
Indices: 29817595--29817632 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
29817585 AATTTTTAAA
29817595 TTTTAAAATAT
1 TTTTAAAATAT
29817606 TTTTAAAATACT
1 TTTTAAAATA-T
29817618 TTTT-AAAT-T
1 TTTTAAAATAT
29817627 TTTTAA
1 TTTTAA
29817633 TTTTAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.20
10 1 0.04
11 14 0.56
12 5 0.20
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:29817666 original size:37 final size:37
Alignment explanation
Indices: 29817579--29817649 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
29817569 ATATATTTAT
*
29817579 TTTTTAAATTTTTAAATTTTAAAATATTTTTAAAATA
1 TTTTTAAATTTTTAAATTTTAAAATACTTTTAAAATA
*
29817616 CTTTTTAAATTTTTTAATTTT-AAATACTTTTAAA
1 -TTTTTAAATTTTTAAATTTTAAAATACTTTTAAA
29817650 TTTTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 12 0.39
38 19 0.61
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (37 bp):
TTTTTAAATTTTTAAATTTTAAAATACTTTTAAAATA
Found at i:29818875 original size:113 final size:113
Alignment explanation
Indices: 29818706--29818932 Score: 454
Period size: 113 Copynumber: 2.0 Consensus size: 113
29818696 ATGGACTGAA
29818706 TCATAAAATATAAATTAAATGGAAAATATTGATAAATACATGATATCGAATGAATGTGACATTGT
1 TCATAAAATATAAATTAAATGGAAAATATTGATAAATACATGATATCGAATGAATGTGACATTGT
29818771 TATATGATTGGAGAGTATGTTTAGGATGATGTTATAAGGTTAAAATAG
66 TATATGATTGGAGAGTATGTTTAGGATGATGTTATAAGGTTAAAATAG
29818819 TCATAAAATATAAATTAAATGGAAAATATTGATAAATACATGATATCGAATGAATGTGACATTGT
1 TCATAAAATATAAATTAAATGGAAAATATTGATAAATACATGATATCGAATGAATGTGACATTGT
29818884 TATATGATTGGAGAGTATGTTTAGGATGATGTTATAAGGTTAAAATAG
66 TATATGATTGGAGAGTATGTTTAGGATGATGTTATAAGGTTAAAATAG
29818932 T
1 T
29818933 AAACGGATTT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (113 bp):
TCATAAAATATAAATTAAATGGAAAATATTGATAAATACATGATATCGAATGAATGTGACATTGT
TATATGATTGGAGAGTATGTTTAGGATGATGTTATAAGGTTAAAATAG
Found at i:29819081 original size:20 final size:18
Alignment explanation
Indices: 29819045--29819081 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29819035 AGGGTTATTG
29819045 TGTGTTGTACGGGATATA
1 TGTGTTGTACGGGATATA
29819063 TGTGTTGATAC-GGATATA
1 TGTGTTG-TACGGGATATA
29819081 T
1 T
29819082 TAGTGATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.24, C:0.05, G:0.30, T:0.41
Consensus pattern (18 bp):
TGTGTTGTACGGGATATA
Found at i:29820500 original size:2 final size:2
Alignment explanation
Indices: 29820493--29820524 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29820483 ATAAGGATGA
29820493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29820525 TAAACTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29822953 original size:21 final size:20
Alignment explanation
Indices: 29822908--29822951 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
29822898 GAAAATAAAG
*
29822908 AAAATGAGGAGAGGAGAAAA
1 AAAATGAGGAGAAGAGAAAA
29822928 AAAATGAAGGAGAA-AGAAAA
1 AAAATG-AGGAGAAGAGAAAA
29822948 AAAA
1 AAAA
29822952 ATTGGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (20 bp):
AAAATGAGGAGAAGAGAAAA
Found at i:29825184 original size:22 final size:22
Alignment explanation
Indices: 29825156--29825199 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29825146 CCGAAATTCT
29825156 ACCCCATGCACATATTGTTATA
1 ACCCCATGCACATATTGTTATA
29825178 ACCCCATGCACATATTGTTATA
1 ACCCCATGCACATATTGTTATA
29825200 CATTTTGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (22 bp):
ACCCCATGCACATATTGTTATA
Found at i:29827706 original size:19 final size:19
Alignment explanation
Indices: 29827682--29827732 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
29827672 TTTTTTTGTA
*
29827682 AAAAAATAAAAAATTATAT
1 AAAAAAGAAAAAATTATAT
*
29827701 AAAAAAGAAAAAGTTATA-
1 AAAAAAGAAAAAATTATAT
29827719 AAATATAAGAAAAA
1 AAA-A-AAGAAAAA
29827733 CTATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 17 0.61
20 8 0.29
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (19 bp):
AAAAAAGAAAAAATTATAT
Found at i:29827728 original size:20 final size:18
Alignment explanation
Indices: 29827690--29827744 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
29827680 TAAAAAAATA
*
29827690 AAAAATTATATAAAA-AAG
1 AAAAACTATA-AAAATAAG
*
29827708 AAAAAGTTATAAAATATAAG
1 AAAAA-CTATAAAA-ATAAG
29827728 AAAAACTATAAAAATAA
1 AAAAACTATAAAAATAA
29827745 AATATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 12 0.36
19 13 0.39
20 8 0.24
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAAACTATAAAAATAAG
Found at i:29827790 original size:17 final size:17
Alignment explanation
Indices: 29827760--29827808 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
29827750 TAAAATTGAT
* *
29827760 ATAAACTTATTAAAATC
1 ATAAAATTAATAAAATC
*
29827777 ATAAAAATT-ATAAAATT
1 AT-AAAATTAATAAAATC
29827794 ATAAAATTAATAAAA
1 ATAAAATTAATAAAA
29827809 CTTATTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.22
17 16 0.59
18 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAATTAATAAAATC
Found at i:29827791 original size:8 final size:8
Alignment explanation
Indices: 29827729--29827813 Score: 59
Period size: 8 Copynumber: 10.0 Consensus size: 8
29827719 AAATATAAGA
*
29827729 AAAACTAT
1 AAAATTAT
29827737 AAAA--AT
1 AAAATTAT
29827743 AAAA-TATT
1 AAAATTA-T
29827751 AAAATTGAT
1 AAAATT-AT
29827760 ATAAACTTATT
1 A-AAA-TTA-T
*
29827771 AAAATCAT
1 AAAATTAT
29827779 AAAAATTAT
1 -AAAATTAT
29827788 AAAATTAT
1 AAAATTAT
29827796 AAAATTAAT
1 AAAATT-AT
29827805 AAAACTTAT
1 AAAA-TTAT
29827814 TTAAGAAACG
Statistics
Matches: 65, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
6 6 0.09
7 1 0.02
8 24 0.37
9 20 0.31
10 10 0.15
11 4 0.06
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (8 bp):
AAAATTAT
Found at i:29827806 original size:26 final size:27
Alignment explanation
Indices: 29827751--29827813 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
29827741 ATAAAATATT
*
29827751 AAAATTGATATAAACTTATTAAAA-TCATA
1 AAAATT-ATA-AAACTTA-TAAAATTAATA
29827780 AAAATTATAAAA-TTATAAAATTAATA
1 AAAATTATAAAACTTATAAAATTAATA
*
29827806 AAACTTAT
1 AAAATTAT
29827814 TTAAGAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 5 0.16
26 14 0.45
27 3 0.10
28 3 0.10
29 6 0.19
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (27 bp):
AAAATTATAAAACTTATAAAATTAATA
Found at i:29828421 original size:10 final size:10
Alignment explanation
Indices: 29828296--29828488 Score: 50
Period size: 10 Copynumber: 19.6 Consensus size: 10
29828286 TTATGATTTT
29828296 TTTTTTATAA
1 TTTTTTATAA
*
29828306 ATTTTT-TAA
1 TTTTTTATAA
* *
29828315 GTTTATATAA
1 TTTTTTATAA
* * *
29828325 ATTTTAATAC
1 TTTTTTATAA
* *
29828335 TTTTTTTTTA
1 TTTTTTATAA
29828345 TGGTTTTTATAGA
1 T--TTTTTATA-A
* *
29828358 ATTTTAATAA
1 TTTTTTATAA
**
29828368 GCTTTTATAA
1 TTTTTTATAA
* *
29828378 TGTTTTAAATA
1 TTTTTTATA-A
29828389 TGTTTTTATTAA
1 T-TTTTTA-TAA
29828401 --TTTTA-AGA
1 TTTTTTATA-A
29828409 TTTTTTATAA
1 TTTTTTATAA
* *
29828419 TTTATTAAAA
1 TTTTTTATAA
*
29828429 TTTATTAT-A
1 TTTTTTATAA
29828438 -TTTTTAT-A
1 TTTTTTATAA
29828446 TTTTTATATCAA
1 TTTTT-TAT-AA
*
29828458 -TTTTCAT-A
1 TTTTTTATAA
*
29828466 -TTTTTATGA
1 TTTTTTATAA
29828475 -TTTTTAT-A
1 TTTTTTATAA
29828483 TTTTTT
1 TTTTTT
29828489 TTATGAAAAA
Statistics
Matches: 136, Mismatches: 30, Indels: 35
0.68 0.15 0.17
Matches are distributed among these distances:
7 1 0.01
8 16 0.12
9 30 0.22
10 60 0.44
11 14 0.10
12 13 0.10
13 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:29828426 original size:20 final size:18
Alignment explanation
Indices: 29828370--29828488 Score: 62
Period size: 20 Copynumber: 6.2 Consensus size: 18
29828360 TTTAATAAGC
29828370 TTTTATAATGTTTTAAATATGT
1 TTTTATAA--TTTTAAA-AT-T
*
29828392 TTTTATTAATTTTAAGATT
1 TTTTA-TAATTTTAAAATT
29828411 TTTTATAATTTATTAAAATT
1 TTTTATAA-TT-TTAAAATT
* * *
29828431 TATTAT-ATTTTTATATT
1 TTTTATAATTTTAAAATT
* *
29828448 TTTATATCAATTTTCATA-T
1 TTT-TAT-AATTTTAAAATT
* * *
29828467 TTTTATGATTTTTATATT
1 TTTTATAATTTTAAAATT
29828485 TTTT
1 TTTT
29828489 TTATGAAAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
17 16 0.20
18 16 0.20
19 13 0.16
20 22 0.27
21 6 0.07
22 5 0.06
23 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTATAATTTTAAAATT
Found at i:29828446 original size:8 final size:8
Alignment explanation
Indices: 29828428--29828487 Score: 66
Period size: 8 Copynumber: 6.8 Consensus size: 8
29828418 ATTTATTAAA
29828428 ATTTATTAT
1 ATTT-TTAT
29828437 ATTTTTAT
1 ATTTTTAT
29828445 ATTTTTAT
1 ATTTTTAT
29828453 ATCAATTTTCAT
1 AT---TTTT-AT
29828465 ATTTTTAT
1 ATTTTTAT
29828473 GATTTTTAT
1 -ATTTTTAT
29828482 ATTTTT
1 ATTTTT
29828488 TTTATGAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
8 22 0.48
9 16 0.35
11 4 0.09
12 4 0.09
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (8 bp):
ATTTTTAT
Found at i:29828451 original size:29 final size:29
Alignment explanation
Indices: 29828410--29828481 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
29828400 ATTTTAAGAT
* *
29828410 TTTTTATA-ATTTATTA-AAATTTATTATA
1 TTTTTATATTTTTATTATAAATTT-TCATA
*
29828438 TTTTTATATTTTTA-TATCAATTTTCATA
1 TTTTTATATTTTTATTATAAATTTTCATA
29828466 TTTTTATGATTTTTAT
1 TTTTTAT-ATTTTTAT
29828482 ATTTTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 21 0.57
29 16 0.43
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (29 bp):
TTTTTATATTTTTATTATAAATTTTCATA
Found at i:29834145 original size:5 final size:5
Alignment explanation
Indices: 29834135--29834160 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29834125 CAAGCAATAA
29834135 TAGTG TAGTG TAGTG TAGTG TAGTG T
1 TAGTG TAGTG TAGTG TAGTG TAGTG T
29834161 GTTTGGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.42
Consensus pattern (5 bp):
TAGTG
Found at i:29848768 original size:20 final size:20
Alignment explanation
Indices: 29848740--29848794 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
29848730 AAGACTATGA
*
29848740 ACCACTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
29848760 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* *
29848780 TCCATTCTATTTACT
1 ACCATTCCATTTACT
29848795 AAGCATAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:29848866 original size:21 final size:21
Alignment explanation
Indices: 29848841--29848881 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29848831 TAGCGTGTTT
* *
29848841 ATCCATGACATAGGTAAATTC
1 ATCCATAACATAAGTAAATTC
29848862 ATCCATAACATAAGTAAATT
1 ATCCATAACATAAGTAAATT
29848882 TCTCACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (21 bp):
ATCCATAACATAAGTAAATTC
Found at i:29856192 original size:27 final size:25
Alignment explanation
Indices: 29856162--29856277 Score: 78
Period size: 27 Copynumber: 4.4 Consensus size: 25
29856152 TTAAATAACC
29856162 GAAATACCCATGTAAGGTAAAATGACT
1 GAAATACCCA-GTAAGGTAAAATGA-T
* *
29856189 GAAATACCCCCG-AAGGGTTAAATGAT
1 GAAATA-CCCAGTAA-GGTAAAATGAT
*
29856215 CGAAATACCCCA-TAAGGTAAAATAATT
1 -GAAATA-CCCAGTAAGGTAAAATGA-T
29856242 GAAATACCCCCA-T-AGGATAAAATGAT
1 GAAATA--CCCAGTAAGG-TAAAATGAT
29856268 CGAAATACCC
1 -GAAATACCC
29856278 CCGAAGGGTA
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
25 3 0.04
26 21 0.28
27 48 0.64
28 3 0.04
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (25 bp):
GAAATACCCAGTAAGGTAAAATGAT
Done.