Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 134 of 145
Found at i:44023265 original size:30 final size:28
Alignment explanation
Indices: 44023231--44023299 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 28
44023221 AAAAGTTTAG
* * *
44023231 AGACTAAATTTGACCAATTTGAGAAGTACA
1 AGACTAAATCTAACCAAATT-AG-AGTACA
*
44023261 AGACTAAAACTAACCAAATTAGAGTACA
1 AGACTAAATCTAACCAAATTAGAGTACA
44023289 ATGACTAAATC
1 A-GACTAAATC
44023300 CATAATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 7 0.21
29 10 0.30
30 16 0.48
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (28 bp):
AGACTAAATCTAACCAAATTAGAGTACA
Found at i:44025578 original size:15 final size:14
Alignment explanation
Indices: 44025562--44025617 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
44025552 ATTTAAAATA
44025562 AAAATATTAAATTT
1 AAAATATTAAATTT
*
44025576 -AAAT-TTAAAAAGTT
1 AAAATATT--AAATTT
*
44025590 ATAATATTAAATATT
1 AAAATATTAAAT-TT
44025605 AAAATATTAAATT
1 AAAATATTAAATT
44025618 CATTATCGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
12 2 0.06
13 4 0.12
14 9 0.27
15 16 0.48
16 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
AAAATATTAAATTT
Found at i:44025604 original size:7 final size:7
Alignment explanation
Indices: 44025563--44025616 Score: 58
Period size: 7 Copynumber: 7.6 Consensus size: 7
44025553 TTTAAAATAA
44025563 AAATATT
1 AAATATT
44025570 AAAT-TT
1 AAATATT
44025576 AAAT-TT
1 AAATATT
*
44025582 AAAAAGTT
1 AAATA-TT
44025590 ATAATATT
1 A-AATATT
44025598 AAATATT
1 AAATATT
44025605 AAAATATT
1 -AAATATT
44025613 AAAT
1 AAAT
44025617 TCATTATCGG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 11 0.27
7 14 0.34
8 13 0.32
9 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:44025611 original size:8 final size:8
Alignment explanation
Indices: 44025554--44025615 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
44025544 TTTAATTTAT
44025554 TTAAAATA
1 TTAAAATA
44025562 --AAAATA
1 TTAAAATA
44025568 TT-AAAT-
1 TTAAAATA
44025574 TT-AAAT-
1 TTAAAATA
44025580 TTAAAA-A
1 TTAAAATA
*
44025587 GTTATAATA
1 -TTAAAATA
44025596 TT-AAATA
1 TTAAAATA
44025603 TTAAAATA
1 TTAAAATA
44025611 TTAAA
1 TTAAA
44025616 TTCATTATCG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
6 14 0.31
7 13 0.29
8 17 0.38
9 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
TTAAAATA
Found at i:44025887 original size:16 final size:15
Alignment explanation
Indices: 44025857--44025896 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
44025847 AAGATACATC
*
44025857 AAAATTAAAATTTTA
1 AAAATTAAAAATTTA
44025872 AAAATATAAAAATTTAA
1 AAAAT-TAAAAATTT-A
44025889 AAAATTAA
1 AAAATTAA
44025897 CATAGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTAAAAATTTA
Found at i:44027741 original size:8 final size:8
Alignment explanation
Indices: 44027711--44027743 Score: 52
Period size: 7 Copynumber: 4.4 Consensus size: 8
44027701 ATGTTTTAAA
44027711 AAAATATT
1 AAAATATT
44027719 AAAAT-TT
1 AAAATATT
44027726 AAAA-ATT
1 AAAATATT
44027733 AAAATATT
1 AAAATATT
44027741 AAA
1 AAA
44027744 GTAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 12 0.52
8 11 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATATT
Found at i:44028195 original size:17 final size:18
Alignment explanation
Indices: 44028175--44028217 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
44028165 TTTTTAATAA
44028175 TTATTAAGTA-TTTTAAG
1 TTATTAAGTAGTTTTAAG
* *
44028192 TTATTTAGTAGTTTTATG
1 TTATTAAGTAGTTTTAAG
*
44028210 TTAATAAG
1 TTATTAAG
44028218 AAAATTTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (18 bp):
TTATTAAGTAGTTTTAAG
Found at i:44037295 original size:21 final size:21
Alignment explanation
Indices: 44037250--44037295 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
44037240 ATTAAATAGT
*
44037250 TAATAGATAAAAATAATAAAA
1 TAATAGATAAAAATAAGAAAA
44037271 TAATA-ATAGAAAA-AAGAAAA
1 TAATAGATA-AAAATAAGAAAA
44037291 CTAAT
1 -TAAT
44037296 CTCCCTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (21 bp):
TAATAGATAAAAATAAGAAAA
Found at i:44039134 original size:28 final size:29
Alignment explanation
Indices: 44039085--44039141 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
44039075 TCCTTCATTC
44039085 GGTCACTACCAATGCTTCATAAGCTTGTT
1 GGTCACTACCAATGCTTCATAAGCTTGTT
44039114 GGTCACTACC-ATGCTTCATAAGCTTGTT
1 GGTCACTACCAATGCTTCATAAGCTTGTT
44039142 ATAGACAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (29 bp):
GGTCACTACCAATGCTTCATAAGCTTGTT
Found at i:44042572 original size:24 final size:24
Alignment explanation
Indices: 44042545--44042596 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
44042535 TTAGTAAGTC
*
44042545 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
44042569 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
44042593 AAAT
1 AAAT
44042597 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:44043860 original size:20 final size:21
Alignment explanation
Indices: 44043837--44043875 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
44043827 TTTATATCCA
44043837 ATTTATAATTC-TTATTTGGG
1 ATTTATAATTCATTATTTGGG
* *
44043857 ATTTTTATTTCATTATTTG
1 ATTTATAATTCATTATTTG
44043876 TTGTCTATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (21 bp):
ATTTATAATTCATTATTTGGG
Found at i:44044137 original size:51 final size:51
Alignment explanation
Indices: 44044082--44044201 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
44044072 GCCCTCAAAG
*
44044082 TTTACACATTCTATCAATTTG-TTATTGATTTAACAAATTTAACCCACAACA
1 TTTACACATTCTATCAATTTGATCA-TGATTTAACAAATTTAACCCACAACA
* * * * *
44044133 TTTACACATTTTGTCAATTTGATCATGATTTAACATATTTAACCCATAATA
1 TTTACACATTCTATCAATTTGATCATGATTTAACAAATTTAACCCACAACA
*
44044184 ATTACACATTCTATCAAT
1 TTTACACATTCTATCAAT
44044202 ATTTACGCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 57 0.97
52 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (51 bp):
TTTACACATTCTATCAATTTGATCATGATTTAACAAATTTAACCCACAACA
Found at i:44049556 original size:18 final size:18
Alignment explanation
Indices: 44049534--44049579 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
44049524 AATTAAGAAA
*
44049534 AATTTTTTATTTTTTAAT
1 AATTTTTTATTATTTAAT
* *
44049552 TATTTTTAATTATTTAAT
1 AATTTTTTATTATTTAAT
44049570 AATTTATTTA
1 AATTT-TTTA
44049580 ATCAAAGTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
AATTTTTTATTATTTAAT
Found at i:44055115 original size:23 final size:21
Alignment explanation
Indices: 44055071--44055124 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
44055061 AATTCATTTT
*
44055071 TTTAAAATATTTATGAAAAATAA
1 TTTAAAA-ATTTATCAAAAAT-A
*
44055094 TTTAAAAATTTGTCAAATAATA
1 TTTAAAAATTTATCAAA-AATA
*
44055116 TTCAAAAAT
1 TTTAAAAAT
44055125 CGTAAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (21 bp):
TTTAAAAATTTATCAAAAATA
Found at i:44055976 original size:16 final size:18
Alignment explanation
Indices: 44055950--44055983 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
44055940 GTCTATATTA
44055950 TTTATAAATTTTA-ATTT
1 TTTATAAATTTTAGATTT
44055967 TTTA-AAATTTTAGATTT
1 TTTATAAATTTTAGATTT
44055984 AAACTCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATAAATTTTAGATTT
Found at i:44059791 original size:21 final size:21
Alignment explanation
Indices: 44059762--44059801 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
44059752 TAAATATTGT
*
44059762 CACTGTTCAT-GGACTTGACCC
1 CACTATTCATAGGA-TTGACCC
44059783 CACTATTCATAGGATTGAC
1 CACTATTCATAGGATTGAC
44059802 ATTCTGAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (21 bp):
CACTATTCATAGGATTGACCC
Found at i:44064203 original size:3 final size:3
Alignment explanation
Indices: 44064190--44064222 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
44064180 TTTCAAGAAA
44064190 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
44064223 GGAACAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:44065356 original size:45 final size:45
Alignment explanation
Indices: 44065292--44065391 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
44065282 TTTTTGGCCA
* * * * *
44065292 AGTATAAATAATTAATAATAAATATTATGTAATTTAGTTAAAATT
1 AGTATAAATAACTAATAATAAATAGTATGCAACTTAGTCAAAATT
*
44065337 AGTATAAATCACTAATAATAAATAGTATGCAACTTAGTCAAAATT
1 AGTATAAATAACTAATAATAAATAGTATGCAACTTAGTCAAAATT
**
44065382 AAAATAAATA
1 AGTATAAATA
44065392 GTTTTTAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (45 bp):
AGTATAAATAACTAATAATAAATAGTATGCAACTTAGTCAAAATT
Found at i:44069712 original size:16 final size:17
Alignment explanation
Indices: 44069686--44069731 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
44069676 TTTCGACTGT
44069686 TAATT-TAATTATATT-
1 TAATTATAATTATATTC
*
44069701 TTATTATAATTA-ATTC
1 TAATTATAATTATATTC
44069717 TAATTATAATT-TATT
1 TAATTATAATTATATT
44069732 GATCCAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTATAATTATATTC
Found at i:44090783 original size:4 final size:4
Alignment explanation
Indices: 44090761--44090802 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
44090751 TCATGAATAT
* * *
44090761 ATAC ATGC ATGC ATGC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
44090803 TGTATCAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:44095064 original size:4 final size:4
Alignment explanation
Indices: 44095055--44095087 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
44095045 AAAATGATGG
44095055 TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA T
44095088 CAAATGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:44097352 original size:6 final size:7
Alignment explanation
Indices: 44097330--44097354 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44097320 TATGTATCTC
44097330 AAATGAA
1 AAATGAA
44097337 AAATGAA
1 AAATGAA
44097344 AAATGAA
1 AAATGAA
44097351 AAAT
1 AAAT
44097355 TAGGGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (7 bp):
AAATGAA
Found at i:44107546 original size:3 final size:3
Alignment explanation
Indices: 44107538--44107587 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
44107528 TCCCTTTTGT
44107538 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44107586 TT
1 TT
44107588 TACATTAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44111055 original size:15 final size:16
Alignment explanation
Indices: 44111035--44111064 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44111025 TTTTAGGGTT
44111035 CTTTTT-TGATTGAGC
1 CTTTTTATGATTGAGC
44111050 CTTTTTATGATTGAG
1 CTTTTTATGATTGAG
44111065 AATCCTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (16 bp):
CTTTTTATGATTGAGC
Found at i:44113454 original size:15 final size:17
Alignment explanation
Indices: 44113403--44113453 Score: 70
Period size: 16 Copynumber: 3.1 Consensus size: 17
44113393 AAAATTGTAA
*
44113403 TTTCTAT-CTTTCTATT
1 TTTCTATCCTTTCAATT
44113419 TTTCTATCCTTTCAATT
1 TTTCTATCCTTTCAATT
*
44113436 TTTC-ATCTTTTCAATT
1 TTTCTATCCTTTCAATT
44113452 TT
1 TT
44113454 CTTTCCATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTATCCTTTCAATT
Found at i:44117822 original size:50 final size:50
Alignment explanation
Indices: 44117767--44117905 Score: 174
Period size: 50 Copynumber: 2.8 Consensus size: 50
44117757 CATTAAGATT
*
44117767 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** ** * *
44117817 ATGAGAGGTCCCCCGTAAGACCATGTCTAAGACATGGCATTGGCACTGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * *
44117867 ATGAGA--ACCCATGTAAGACCATTTCTGGGATATGGCATT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATT
44117906 AACAATATAA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
48 26 0.35
50 49 0.65
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:44130336 original size:29 final size:30
Alignment explanation
Indices: 44130304--44130362 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
44130294 TCACGTGTAT
*
44130304 AATTACAC-CAAATTAAAGTTCATGTATAC
1 AATTACACGCAAATTAAAGTTCATATATAC
* *
44130333 AATTGCACGTTAAATTAAAGTTCATATATA
1 AATTACACG-CAAATTAAAGTTCATATATA
44130363 ATTTTGAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
31 18 0.72
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (30 bp):
AATTACACGCAAATTAAAGTTCATATATAC
Found at i:44131838 original size:30 final size:29
Alignment explanation
Indices: 44131797--44131879 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 29
44131787 AAGTTTAAAA
44131797 TTTAGGTAATAGTTATATACGTATTAATATT
1 TTTAGGTAATAGTTATATAC-TA-TAATATT
44131828 TTTA-GTAATAGTTATATACTATAATATTAT
1 TTTAGGTAATAGTTATATACTATAATA-T-T
* * *
44131858 TTTATGTATTAGTAATATACTA
1 TTTAGGTAATAGTTATATACTA
44131880 ATTTAATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 5 0.11
29 3 0.06
30 20 0.43
31 19 0.40
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTAGGTAATAGTTATATACTATAATATT
Found at i:44131859 original size:31 final size:29
Alignment explanation
Indices: 44131797--44131879 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
44131787 AAGTTTAAAA
44131797 TTTAGGTAATAGTTATATACGTATTAATATT
1 TTTAGGTAATAGTTATATAC-TATTAATA-T
*
44131828 TTTA-GTAATAGTTATATACTATAATATTAT
1 TTTAGGTAATAGTTATATACTAT--TAATAT
* * *
44131858 TTTATGTATTAGTAATATACTA
1 TTTAGGTAATAGTTATATACTA
44131880 ATTTAATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 3 0.07
30 20 0.43
31 23 0.50
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTAGGTAATAGTTATATACTATTAATAT
Found at i:44132947 original size:18 final size:17
Alignment explanation
Indices: 44132926--44132968 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
44132916 TTTTTTATTT
* *
44132926 TATTTTTACATTTTTCTA
1 TATTTTTA-ACTTTTATA
44132944 TATTTTCTAACTTTTATA
1 TATTTT-TAACTTTTATA
44132962 TATTTTT
1 TATTTTT
44132969 TCCATTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 19 0.86
19 2 0.09
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTTAACTTTTATA
Found at i:44133326 original size:24 final size:25
Alignment explanation
Indices: 44133299--44133357 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
44133289 TCAAATTCGT
*
44133299 CATCATTCATGATCAAAACCACC-C
1 CATCATTCATCATCAAAACCACCAC
* *
44133323 CATCA-TCATCATCAACATCACCAC
1 CATCATTCATCATCAAAACCACCAC
44133347 CATCA-TCATCA
1 CATCATTCATCA
44133358 AAAACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.37, C:0.39, G:0.02, T:0.22
Consensus pattern (25 bp):
CATCATTCATCATCAAAACCACCAC
Found at i:44133363 original size:24 final size:23
Alignment explanation
Indices: 44133318--44133363 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
44133308 TGATCAAAAC
**
44133318 CACCCCATCATCATCATCAACAT
1 CACCCCATCATCATCAAAAACAT
44133341 CACCACCATCATCATCAAAAACA
1 CACC-CCATCATCATCAAAAACA
44133364 AAAAGATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (23 bp):
CACCCCATCATCATCAAAAACAT
Found at i:44135236 original size:21 final size:21
Alignment explanation
Indices: 44135210--44135256 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
44135200 AAGGTCCATG
*
44135210 GTCCAAGATCTAGGATCTAGA
1 GTCCAAGATCAAGGATCTAGA
* * *
44135231 GTCCAAGGTCAAGGGTCTAGG
1 GTCCAAGATCAAGGATCTAGA
44135252 GTCCA
1 GTCCA
44135257 TAGTTTATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (21 bp):
GTCCAAGATCAAGGATCTAGA
Found at i:44149367 original size:27 final size:26
Alignment explanation
Indices: 44149314--44149371 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
44149304 AGTACTGTTT
** *
44149314 TAACAAAGAAAAATATCAGAAGCAAC
1 TAACAAAGAAAAATAAAAGAAGAAAC
*
44149340 TAACCAAGAAAAATAAAAGAGAGAAAC
1 TAACAAAGAAAAATAAAAGA-AGAAAC
44149367 TAACA
1 TAACA
44149372 TGAACACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (26 bp):
TAACAAAGAAAAATAAAAGAAGAAAC
Found at i:44151016 original size:17 final size:17
Alignment explanation
Indices: 44150994--44151027 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44150984 ATATATTTTT
*
44150994 AATTAAATTTTTTTAAA
1 AATTAAATATTTTTAAA
*
44151011 AATTAACTATTTTTAAA
1 AATTAAATATTTTTAAA
44151028 CAAGAAAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTAAATATTTTTAAA
Found at i:44154377 original size:18 final size:18
Alignment explanation
Indices: 44154332--44154377 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
44154322 TAAACCGACA
*
44154332 ATTAATTTTAAATTATTT
1 ATTAATTTTAAATAATTT
* *
44154350 ATGAATTTTTAATAATTT
1 ATTAATTTTAAATAATTT
44154368 ATTTAATTTT
1 A-TTAATTTT
44154378 GACTAGATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTAATTTTAAATAATTT
Found at i:44159973 original size:16 final size:16
Alignment explanation
Indices: 44159939--44159990 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
44159929 ATAGCATTAG
44159939 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
44159955 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* * *
44159971 TCATACCATATTCAAT
1 TCATGCAATACTCAAT
44159987 TCAT
1 TCAT
44159991 AAGTATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 5 0.17
16 21 0.72
17 3 0.10
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:44161228 original size:16 final size:15
Alignment explanation
Indices: 44161207--44161248 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
44161197 TTTGGTTTTT
44161207 TATTTCTTTTTATTTC
1 TATTTC-TTTTATTTC
44161223 TATTTCTTTTA-TT-
1 TATTTCTTTTATTTC
*
44161236 TATTTGTTTTATT
1 TATTTCTTTTATT
44161249 ATTATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.42
14 3 0.12
15 5 0.21
16 6 0.25
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.76
Consensus pattern (15 bp):
TATTTCTTTTATTTC
Found at i:44161942 original size:20 final size:20
Alignment explanation
Indices: 44161904--44161942 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44161894 GGTCTTTGTA
* *
44161904 TTATCAAATTAGTCCATTTG
1 TTATCAAATGAGTCAATTTG
*
44161924 TTATCAAATGGGTCAATTT
1 TTATCAAATGAGTCAATTT
44161943 AGCCTCTACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
TTATCAAATGAGTCAATTTG
Found at i:44164296 original size:3 final size:3
Alignment explanation
Indices: 44164288--44164325 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
44164278 CTTGAAGCTC
44164288 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
44164326 GCCTAAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:44172239 original size:25 final size:25
Alignment explanation
Indices: 44172205--44172255 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
44172195 ATCGATTCAA
*
44172205 TCGATTTTTAACTCGGTTCAATCGT
1 TCGATTTTTAACTCGGTTAAATCGT
*
44172230 TCGATTTTTAACTTGGTTAAATCGT
1 TCGATTTTTAACTCGGTTAAATCGT
44172255 T
1 T
44172256 TTCAAGTAAT
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:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (25 bp):
TCGATTTTTAACTCGGTTAAATCGT
Found at i:44174203 original size:47 final size:45
Alignment explanation
Indices: 44174144--44174256 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 45
44174134 TAAGAAAAAG
** * *
44174144 CCTTTCTTCAAAGCCATTTCTTTTTTTTTTATCCTTTAAAAAGAAA-C
1 CCTTT-TTCAAAGCCATTTC-TTCCTCTTTACCCTTTAAAAA-AAACC
*
44174191 CCTTTTTCCAAAGTCATTTCTTCCTCTTTACCCTTTAAAAAAAATCC
1 CCTTTTT-CAAAGCCATTTCTTCCTCTTTACCCTTTAAAAAAAA-CC
44174238 CCTTTTTTCAAAGCCATTT
1 CC-TTTTTCAAAGCCATTT
44174257 TTTGCTTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
45 3 0.05
46 19 0.34
47 29 0.52
48 5 0.09
ACGTcount: A:0.27, C:0.26, G:0.04, T:0.44
Consensus pattern (45 bp):
CCTTTTTCAAAGCCATTTCTTCCTCTTTACCCTTTAAAAAAAACC
Found at i:44176736 original size:20 final size:21
Alignment explanation
Indices: 44176713--44176754 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
44176703 TTTTTTAGAT
*
44176713 AATTATGT-TTATTTTCTTTA
1 AATTAAGTGTTATTTTCTTTA
*
44176733 AATTAAGTGTTATTTTTTTTA
1 AATTAAGTGTTATTTTCTTTA
44176754 A
1 A
44176755 CTTCATGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (21 bp):
AATTAAGTGTTATTTTCTTTA
Found at i:44178698 original size:25 final size:25
Alignment explanation
Indices: 44178645--44178691 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
44178635 ATAATTGTAG
44178645 TGTATTTA-G-TATTATTTAT-ATGA
1 TGTATTTATGTTATTATTT-TCATGA
44178668 TGTATTTATGTTATTATTTTCATG
1 TGTATTTATGTTATTATTTTCATG
44178692 TGTTATTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 8 0.38
24 2 0.10
25 11 0.52
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.60
Consensus pattern (25 bp):
TGTATTTATGTTATTATTTTCATGA
Found at i:44179419 original size:16 final size:16
Alignment explanation
Indices: 44179394--44179432 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
44179384 ACGAATTTTC
44179394 TGTTTGGGCT-ATGGG
1 TGTTTGGGCTCATGGG
*
44179409 TTGTTTTGGCTCATGGG
1 -TGTTTGGGCTCATGGG
44179426 TGTTTGG
1 TGTTTGG
44179433 CATTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.05, C:0.08, G:0.41, T:0.46
Consensus pattern (16 bp):
TGTTTGGGCTCATGGG
Found at i:44183665 original size:16 final size:16
Alignment explanation
Indices: 44183644--44183679 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
44183634 ATCCTTTATC
*
44183644 ACTTGGTGTCAATACA
1 ACTTGGTGCCAATACA
*
44183660 ACTTGGTGCCAATATA
1 ACTTGGTGCCAATACA
44183676 ACTT
1 ACTT
44183680 TGTGAGACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (16 bp):
ACTTGGTGCCAATACA
Found at i:44184058 original size:15 final size:15
Alignment explanation
Indices: 44184038--44184076 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
44184028 GAATTATTTA
44184038 AAAATATTAAAAGA-T
1 AAAATATTAAAA-ATT
*
44184053 AAAATACTAAAAATT
1 AAAATATTAAAAATT
44184068 AAAATATTA
1 AAAATATTA
44184077 TTTTTACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATATTAAAAATT
Found at i:44189060 original size:248 final size:248
Alignment explanation
Indices: 44188622--44189117 Score: 983
Period size: 248 Copynumber: 2.0 Consensus size: 248
44188612 GTGTCTTCTC
44188622 CATTTTGGGGGTATTGTCACCCTCCACTATTGCCGCACGCCATTTATCTTTTTCTTTTTTTCGTC
1 CATTTTGGGGGTATTGTCACCCTCCACTATTGCCGCACGCCATTTATCTTTTTCTTTTTTTCGTC
44188687 AATAAAGTAATAAATTCAGGTTGATAATACTGGTTTATTTATCAATTTAGTCGATTTTGAGAGAA
66 AATAAAGTAATAAATTCAGGTTGATAATACTGGTTTATTTATCAATTTAGTCGATTTTGAGAGAA
44188752 CCGTCTAAGAAAAAAATTTTGAAAATAAAAATAAAAATTTGACAGTTGAATTGAGCTTACAATTT
131 CCGTCTAAGAAAAAAATTTTGAAAATAAAAATAAAAATTTGACAGTTGAATTGAGCTTACAATTT
44188817 AGAAAAAAAAATATTTTAGATTTTTAAGATTAATTAAATAATTAATTAATTAA
196 AGAAAAAAAAATATTTTAGATTTTTAAGATTAATTAAATAATTAATTAATTAA
44188870 CATTTTGGGGGTATTGTCACCCTCCACTATTGCCGCACGCCATTTATCTTTTTCTTTTTTTCGTC
1 CATTTTGGGGGTATTGTCACCCTCCACTATTGCCGCACGCCATTTATCTTTTTCTTTTTTTCGTC
44188935 AATAAAGTAATAAATTCAGGTTGATAATACTGGTTTATTTATCAATTTAGTCGATTTTGAGAGAA
66 AATAAAGTAATAAATTCAGGTTGATAATACTGGTTTATTTATCAATTTAGTCGATTTTGAGAGAA
44189000 CCGTCTAAGAAAAAAATTTTGAAAATAAAAATAAAAATTTGACAGTTGAATTGAGCTTACAATTT
131 CCGTCTAAGAAAAAAATTTTGAAAATAAAAATAAAAATTTGACAGTTGAATTGAGCTTACAATTT
*
44189065 AGAAAAAAAAATATTTTAGATTTTTAAGATTAATTAATTAATTAATTAATTAA
196 AGAAAAAAAAATATTTTAGATTTTTAAGATTAATTAAATAATTAATTAATTAA
44189118 TTATTAAATT
Statistics
Matches: 247, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
248 247 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (248 bp):
CATTTTGGGGGTATTGTCACCCTCCACTATTGCCGCACGCCATTTATCTTTTTCTTTTTTTCGTC
AATAAAGTAATAAATTCAGGTTGATAATACTGGTTTATTTATCAATTTAGTCGATTTTGAGAGAA
CCGTCTAAGAAAAAAATTTTGAAAATAAAAATAAAAATTTGACAGTTGAATTGAGCTTACAATTT
AGAAAAAAAAATATTTTAGATTTTTAAGATTAATTAAATAATTAATTAATTAA
Found at i:44189102 original size:4 final size:4
Alignment explanation
Indices: 44189093--44189124 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
44189083 GATTTTTAAG
44189093 ATTA ATTA ATTA ATTA ATTA ATTA ATT- ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
44189125 ATTGACGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:44189811 original size:9 final size:9
Alignment explanation
Indices: 44189792--44189825 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
44189782 TTATTAATTA
44189792 TTAAGTTCGG
1 TTAA-TTCGG
44189802 TTAATTCGG
1 TTAATTCGG
44189811 TTAATTCGG
1 TTAATTCGG
44189820 TTAATT
1 TTAATT
44189826 ACCCGATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (9 bp):
TTAATTCGG
Found at i:44190269 original size:16 final size:16
Alignment explanation
Indices: 44190248--44190280 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44190238 TGCGACAATG
44190248 GGGTTTTAATTAGAAA
1 GGGTTTTAATTAGAAA
44190264 GGGTTTTAATTAGAAA
1 GGGTTTTAATTAGAAA
44190280 G
1 G
44190281 AGATTTCAAT
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:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (16 bp):
GGGTTTTAATTAGAAA
Found at i:44194365 original size:30 final size:30
Alignment explanation
Indices: 44194331--44194387 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
44194321 ATGTTACCAT
44194331 AAATACTTTTAATAACTAGAGCACAATAAC
1 AAATACTTTTAATAACTAGAGCACAATAAC
44194361 AAATACTTTTAATAACTAGAGCACAAT
1 AAATACTTTTAATAACTAGAGCACAAT
44194388 CAGTGTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (30 bp):
AAATACTTTTAATAACTAGAGCACAATAAC
Found at i:44196346 original size:12 final size:12
Alignment explanation
Indices: 44196329--44196371 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
44196319 AAATCACAAT
*
44196329 ATAATAATAACA
1 ATAATAACAACA
44196341 ATAATAACAACA
1 ATAATAACAACA
* *
44196353 ACAATAACCACA
1 ATAATAACAACA
44196365 ATAATAA
1 ATAATAA
44196372 TAAGTCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAATAACAACA
Found at i:44197807 original size:13 final size:14
Alignment explanation
Indices: 44197789--44197819 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
44197779 ACTTGGACTC
44197789 TTTTATTT-TTTAG
1 TTTTATTTATTTAG
44197802 TTTTATTTATTTAG
1 TTTTATTTATTTAG
44197816 TTTT
1 TTTT
44197820 GGGCCTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (14 bp):
TTTTATTTATTTAG
Found at i:44198727 original size:11 final size:11
Alignment explanation
Indices: 44198711--44198741 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
44198701 GAAGATCATG
44198711 CAAAGTGAGTT
1 CAAAGTGAGTT
44198722 CAAAGTGAGTT
1 CAAAGTGAGTT
*
44198733 CAAAATGAG
1 CAAAGTGAG
44198742 CATGGTAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (11 bp):
CAAAGTGAGTT
Found at i:44201273 original size:17 final size:17
Alignment explanation
Indices: 44201251--44201283 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
44201241 ATATTTTTTA
44201251 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
44201268 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
44201284 TATATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:44202517 original size:33 final size:33
Alignment explanation
Indices: 44202475--44202567 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
44202465 ATATAAACTT
44202475 AATTCCACAAATCATCCTTACAAATTATTCAAC
1 AATTCCACAAATCATCCTTACAAATTATTCAAC
*
44202508 AATTCCACAAATCATCCTCACAAATTATTCAAC
1 AATTCCACAAATCATCCTTACAAATTATTCAAC
*
44202541 AATTCCACAAATAATCCTTACAAATTA
1 AATTCCACAAATCATCCTTACAAATTA
44202568 ACAACCCGGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (33 bp):
AATTCCACAAATCATCCTTACAAATTATTCAAC
Found at i:44204864 original size:107 final size:107
Alignment explanation
Indices: 44204727--44204921 Score: 327
Period size: 107 Copynumber: 1.8 Consensus size: 107
44204717 CTTTTTTTTC
* * *
44204727 TTTTTTGCTTAAGAATATATTAAACCTTTTGATGGGAAGAGAGATGACAGCCAAGTACCCCACCC
1 TTTTTTGCTTAAGAATATATTAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
*
44204792 CGGTTACTCAGCCCAACATATTCCTAATTTATTATATTTATA
66 CAGTTACTCAGCCCAACATATTCCTAATTTATTATATTTATA
* *
44204834 TTTTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
1 TTTTTTGCTTAAGAATATATTAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
*
44204899 CAGTTACTCAGCCTAACATATTC
66 CAGTTACTCAGCCCAACATATTC
44204922 TTAAAAATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 81 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (107 bp):
TTTTTTGCTTAAGAATATATTAAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
CAGTTACTCAGCCCAACATATTCCTAATTTATTATATTTATA
Found at i:44207297 original size:3 final size:3
Alignment explanation
Indices: 44207289--44207340 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
44207279 TAAAGTGATA
44207289 AAT AAT AAT -AT AAT AAT -AT AAT AAT -AT AAT -AT AAT AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
44207330 AAT AAA AAT AA
1 AAT AAT AAT AA
44207341 AAATTGGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
2 9 0.22
3 31 0.76
4 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44207303 original size:5 final size:5
Alignment explanation
Indices: 44207293--44207333 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
44207283 GTGATAAATA
44207293 ATAAT ATAAT A-ATAT AATAAT ATAAT ATAAT A-AAT ATAAT A
1 ATAAT ATAAT ATA-AT -ATAAT ATAAT ATAAT ATAAT ATAAT A
44207334 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 5 0.16
5 23 0.72
6 3 0.09
7 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:44207311 original size:16 final size:15
Alignment explanation
Indices: 44207286--44207340 Score: 71
Period size: 16 Copynumber: 3.7 Consensus size: 15
44207276 AATTAAAGTG
44207286 ATAAATAATAATATA
1 ATAAATAATAATATA
44207301 ATAATATAATAATATA
1 ATAA-ATAATAATATA
44207317 AT--ATAATAAATATA
1 ATAAATAAT-AATATA
44207331 ATAAA-AATAA
1 ATAAATAATAA
44207341 AAATTGGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.14
14 10 0.28
15 7 0.19
16 14 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAATAATAATATA
Found at i:44207325 original size:8 final size:8
Alignment explanation
Indices: 44207286--44207319 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
44207276 AATTAAAGTG
44207286 ATAA-ATA
1 ATAATATA
44207293 ATAATATA
1 ATAATATA
44207301 ATAATATA
1 ATAATATA
44207309 ATAATATA
1 ATAATATA
44207317 ATA
1 ATA
44207320 TAATAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 22 0.85
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAATATA
Found at i:44209320 original size:12 final size:12
Alignment explanation
Indices: 44209303--44209330 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
44209293 AGGACTAAAT
44209303 TGAGGGCTGTTA
1 TGAGGGCTGTTA
44209315 TGAGGGCTGTTA
1 TGAGGGCTGTTA
44209327 TGAG
1 TGAG
44209331 CATGAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.07, G:0.43, T:0.32
Consensus pattern (12 bp):
TGAGGGCTGTTA
Found at i:44209701 original size:23 final size:23
Alignment explanation
Indices: 44209668--44209765 Score: 117
Period size: 23 Copynumber: 4.3 Consensus size: 23
44209658 NNNNNNNNNN
* *
44209668 TCAGTGTTAGCTACAGCTAAATA
1 TCAGTGGTAGCTACAGCTACATA
* * *
44209691 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTACAGCTACATA
*
44209714 TCAGTGGTAGCTACGGCTACATA
1 TCAGTGGTAGCTACAGCTACATA
*
44209737 TTAGTGGTAGCTTA-AGCTACATA
1 TCAGTGGTAGC-TACAGCTACATA
44209760 TCAGTG
1 TCAGTG
44209766 TGACACTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 62 0.97
24 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTACAGCTACATA
Found at i:44209743 original size:46 final size:46
Alignment explanation
Indices: 44209668--44209765 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
44209658 NNNNNNNNNN
* ** *
44209668 TCAGTGTTAGCTACAGCTAAATATCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTACAGCTAAATATCAGTGGTAGCTTAAGCTACATA
* * *
44209714 TCAGTGGTAGCTACGGCTACATATTAGTGGTAGCTTAAGCTACATA
1 TCAGTGGTAGCTACAGCTAAATATCAGTGGTAGCTTAAGCTACATA
44209760 TCAGTG
1 TCAGTG
44209766 TGACACTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (46 bp):
TCAGTGGTAGCTACAGCTAAATATCAGTGGTAGCTTAAGCTACATA
Found at i:44212664 original size:45 final size:45
Alignment explanation
Indices: 44212612--44212702 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
44212602 CTATTTCGCA
*
44212612 TACTGGCCCATTTTATCTTTAAATTCACGCTTTTTTCCC-TAAATT
1 TACTGGCCCATTTTATCTTTAAATTCACAC-TTTTTCCCTTAAATT
44212657 TACTGGCCCATTTTATCTTTAAATTCACACTTTTTCCCTTAAATT
1 TACTGGCCCATTTTATCTTTAAATTCACACTTTTTCCCTTAAATT
44212702 T
1 T
44212703 CCTTTTACCT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 8 0.18
45 36 0.82
ACGTcount: A:0.23, C:0.24, G:0.05, T:0.47
Consensus pattern (45 bp):
TACTGGCCCATTTTATCTTTAAATTCACACTTTTTCCCTTAAATT
Found at i:44215957 original size:16 final size:17
Alignment explanation
Indices: 44215936--44215976 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
44215926 TAAAAGAATA
44215936 TTTTATTTA-T-ATAAAT
1 TTTTATTTATTAAT-AAT
*
44215952 TTTTATATATTAATAAT
1 TTTTATTTATTAATAAT
44215969 TTTTATTT
1 TTTTATTT
44215977 TCTAGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 8 0.38
17 11 0.52
18 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTTATTAATAAT
Found at i:44218043 original size:16 final size:17
Alignment explanation
Indices: 44218022--44218062 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
44218012 TAAAAGAATA
44218022 TTTTATTTA-T-ATAAAT
1 TTTTATTTATTAAT-AAT
*
44218038 TTTTATATATTAATAAT
1 TTTTATTTATTAATAAT
44218055 TTTTATTT
1 TTTTATTT
44218063 TCTAGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 8 0.38
17 11 0.52
18 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTTATTAATAAT
Found at i:44218993 original size:34 final size:34
Alignment explanation
Indices: 44218942--44219046 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
44218932 CTTAGTATAA
* * *
44218942 AAGGTGCCGCT-TATGCATTGAGAACCCTTAATTG
1 AAGGTGCCCCTAT-TGCATTGAAAATCCTTAATTG
* *
44218976 AAGGTGCCCCTATTGCATTGAAAATCCTTAACTA
1 AAGGTGCCCCTATTGCATTGAAAATCCTTAATTG
* *
44219010 AATGTGTCCCTGA-TGCATTGAAAATCCTTAATTG
1 AAGGTGCCCCT-ATTGCATTGAAAATCCTTAATTG
44219044 AAG
1 AAG
44219047 ATTGAAGAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 57 0.97
35 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (34 bp):
AAGGTGCCCCTATTGCATTGAAAATCCTTAATTG
Found at i:44219512 original size:10 final size:9
Alignment explanation
Indices: 44219481--44219540 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
44219471 TTTTTTTTTC
44219481 AAAAATCAA
1 AAAAATCAA
*
44219490 AGAAAATC-T
1 A-AAAATCAA
*
44219499 AAAAGTCAA
1 AAAAATCAA
44219508 AAAAATCATA
1 AAAAATCA-A
44219518 AAAAAT-AA
1 AAAAATCAA
*
44219526 AAAATGTCAA
1 AAAA-ATCAA
44219536 AAAAA
1 AAAAA
44219541 ACTTAAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
8 10 0.25
9 11 0.28
10 19 0.47
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (9 bp):
AAAAATCAA
Found at i:44219512 original size:17 final size:19
Alignment explanation
Indices: 44219481--44219521 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
44219471 TTTTTTTTTC
44219481 AAAAATCAAAGAAAATC-T
1 AAAAATCAAAGAAAATCAT
*
44219499 AAAAGTCAAA-AAAATCAT
1 AAAAATCAAAGAAAATCAT
44219517 AAAAA
1 AAAAA
44219522 ATAAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAATCAAAGAAAATCAT
Found at i:44219529 original size:27 final size:28
Alignment explanation
Indices: 44219481--44219540 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
44219471 TTTTTTTTTC
**
44219481 AAAAATCAAAGAAAATCTAAAA-GTCAA
1 AAAAATCAAAGAAAATAAAAAATGTCAA
44219508 AAAAATCATAA-AAAATAAAAAATGTCAA
1 AAAAATCA-AAGAAAATAAAAAATGTCAA
44219536 AAAAA
1 AAAAA
44219541 ACTTAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (28 bp):
AAAAATCAAAGAAAATAAAAAATGTCAA
Found at i:44219569 original size:3 final size:3
Alignment explanation
Indices: 44219561--44219602 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
44219551 TAAAAGTTAT
44219561 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44219603 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44220703 original size:14 final size:15
Alignment explanation
Indices: 44220675--44220724 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
44220665 GTTTTTATGG
44220675 TTTTGTAAATGAAATT
1 TTTTGTAAA-GAAATT
44220691 TTTTGTAAA-AAATT
1 TTTTGTAAAGAAATT
*
44220705 TAATTT-TCAAGAAATT
1 T--TTTGTAAAGAAATT
44220721 TTTT
1 TTTT
44220725 TACAACAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 9 0.30
15 3 0.10
16 18 0.60
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (15 bp):
TTTTGTAAAGAAATT
Found at i:44231849 original size:19 final size:19
Alignment explanation
Indices: 44231820--44231891 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
44231810 TTAAGTAATT
44231820 ATTTATATAATTTTTTTGTA
1 ATTT-TATAATTTTTTTGTA
*
44231840 ATTTTATAATTTTTTT-CA
1 ATTTTATAATTTTTTTGTA
**
44231858 ATTTT-TAATAATTTTGTA
1 ATTTTATAATTTTTTTGTA
*
44231876 ACTTCTTTTAATTTTT
1 A-TT-TTATAATTTTT
44231892 GTACTTTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.19
18 8 0.19
19 14 0.33
20 6 0.14
21 6 0.14
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTATAATTTTTTTGTA
Found at i:44231862 original size:28 final size:26
Alignment explanation
Indices: 44231831--44231907 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 26
44231821 TTTATATAAT
44231831 TTTTTTGTAATTTTATAATTTTTTTCAA
1 TTTTTTGTAATTTT-TAATTTTTTT-AA
** *
44231859 TTTTTAATAATTTTGTAACTTCTTTTAA
1 TTTTTTGTAATTTT-TAA-TTTTTTTAA
* *
44231887 -TTTTTGTACTTTTTCATTTTT
1 TTTTTTGTAATTTTTAATTTTT
44231908 AAAGATTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
25 4 0.10
26 2 0.05
27 10 0.26
28 17 0.44
29 6 0.15
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTTTGTAATTTTTAATTTTTTTAA
Found at i:44232379 original size:12 final size:12
Alignment explanation
Indices: 44232362--44232391 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44232352 AAATTAAAAT
*
44232362 ATTTTTTTTTTA
1 ATTTTTTTTATA
44232374 ATTTTTTTTATA
1 ATTTTTTTTATA
44232386 ATTTTT
1 ATTTTT
44232392 AAATTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTTTATA
Found at i:44239397 original size:16 final size:16
Alignment explanation
Indices: 44239365--44239394 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
44239355 AAAATACTAA
44239365 AAATAATTTAATAAAT
1 AAATAATTTAATAAAT
44239381 AAAT-ATTTAATAAA
1 AAATAATTTAATAAA
44239395 ATACTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAATTTAATAAAT
Found at i:44240222 original size:73 final size:73
Alignment explanation
Indices: 44240136--44240281 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
44240126 AATCAAATGT
*
44240136 TGACCAAAGCATGAAAAATAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
1 TGACCAAAGCATGAAAAACAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
44240201 TATTTTAA
66 TATTTTAA
44240209 TGACCAAAGCATGAAAAACAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
1 TGACCAAAGCATGAAAAACAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
44240274 TATTTTAA
66 TATTTTAA
44240282 CCATTACCTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (73 bp):
TGACCAAAGCATGAAAAACAATATAATTTTAGGTAAAAATTACATAACATAATCTAATGCCCTAT
TATTTTAA
Found at i:44246497 original size:30 final size:30
Alignment explanation
Indices: 44246463--44246524 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
44246453 TTAAATTATA
*
44246463 AACCTTCTAAAAATAGAAAATTTATAATTT
1 AACCTTCTAAAAATAGAAAATTTATAAGTT
* * * *
44246493 AACCTTTTAAAACTAGTAAATTTTTAAGTT
1 AACCTTCTAAAAATAGAAAATTTATAAGTT
44246523 AA
1 AA
44246525 TACAATAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39
Consensus pattern (30 bp):
AACCTTCTAAAAATAGAAAATTTATAAGTT
Found at i:44252251 original size:23 final size:23
Alignment explanation
Indices: 44252224--44252277 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
44252214 GTTGGGGTCA
44252224 TTGGGCCTTTAAGG-TTT-TCAATT
1 TTGGGCCTTT-AGGATTTGT-AATT
* *
44252247 TTGGGTCTTTTGGATTTGTAATT
1 TTGGGCCTTTAGGATTTGTAATT
44252270 TTGGGCCT
1 TTGGGCCT
44252278 GCAATTTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 23 0.88
24 1 0.04
ACGTcount: A:0.13, C:0.11, G:0.26, T:0.50
Consensus pattern (23 bp):
TTGGGCCTTTAGGATTTGTAATT
Found at i:44255263 original size:44 final size:44
Alignment explanation
Indices: 44255213--44255389 Score: 354
Period size: 44 Copynumber: 4.0 Consensus size: 44
44255203 TGTCGGATAT
44255213 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
1 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
44255257 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
1 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
44255301 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
1 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
44255345 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
1 TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
44255389 T
1 T
44255390 AGAAACTCAT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 133 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (44 bp):
TGCATACTTTGCAAATATGCTCTCTTAGTTTATGCACTCTCTTA
Found at i:44256005 original size:29 final size:29
Alignment explanation
Indices: 44255972--44256030 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
44255962 ATTTATTTTG
* *
44255972 TTTTGTTATTTAAATCATTGTTGATATCC
1 TTTTGTTATTTAAATAATTATTGATATCC
* *
44256001 TTTTGTTATTTGAATAATTATTGTTATCC
1 TTTTGTTATTTAAATAATTATTGATATCC
44256030 T
1 T
44256031 ATTCAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (29 bp):
TTTTGTTATTTAAATAATTATTGATATCC
Found at i:44256286 original size:62 final size:62
Alignment explanation
Indices: 44256199--44256343 Score: 236
Period size: 62 Copynumber: 2.3 Consensus size: 62
44256189 TAATAATTAC
* *
44256199 ACTTTTTTTTTTTTTTTTTATTTTTTGCAGTCAATCATATTATCAAAACACACCCTTGAATT
1 ACTTTTTTTTTTTTTTTTTACTTTTTGCAGTCAATCATATTATCAAAACACACACTTGAATT
*
44256261 ACTTTTTTTTTTTTTTTTTACTTTTTGCAGTCAATCATATTATCCAAACACACACTTGAATT
1 ACTTTTTTTTTTTTTTTTTACTTTTTGCAGTCAATCATATTATCAAAACACACACTTGAATT
*
44256323 ACTTTTTCTTTCTTTGTTTTT
1 ACTTTTT-TTT-TTTTTTTTT
44256344 CAAGAAATTC
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 66 0.86
63 3 0.04
64 8 0.10
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.56
Consensus pattern (62 bp):
ACTTTTTTTTTTTTTTTTTACTTTTTGCAGTCAATCATATTATCAAAACACACACTTGAATT
Found at i:44259634 original size:12 final size:12
Alignment explanation
Indices: 44259617--44259653 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
44259607 ATTATATTTT
44259617 TATAAAAAATTA
1 TATAAAAAATTA
*
44259629 TATAAAAAATAA
1 TATAAAAAATTA
44259641 TATTAAAAAATTA
1 TA-TAAAAAATTA
44259654 ATTCGAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TATAAAAAATTA
Found at i:44260046 original size:41 final size:41
Alignment explanation
Indices: 44259989--44260156 Score: 336
Period size: 41 Copynumber: 4.1 Consensus size: 41
44259979 AAATAATAAA
44259989 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
1 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
44260030 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
1 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
44260071 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
1 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
44260112 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
1 ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
44260153 ATAA
1 ATAA
44260157 ATGCATTAAA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (41 bp):
ATAAGCATAATAATGGAGTAAGGAACACAGACCAAGCTTTG
Found at i:44266436 original size:21 final size:20
Alignment explanation
Indices: 44266408--44266463 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
44266398 CTTTGTTCAA
*
44266408 AATTTTAATAAATAATTATT
1 AATTTTAATAAATAATAATT
44266428 AATTATTAAATAAA-AATAATT
1 AATT-TT-AATAAATAATAATT
44266449 ATATTTTAA-AAATAA
1 A-ATTTTAATAAATAA
44266464 AATAATATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 3 0.10
20 8 0.26
21 11 0.35
22 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTTTAATAAATAATAATT
Found at i:44266468 original size:22 final size:24
Alignment explanation
Indices: 44266417--44266469 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
44266407 AAATTTTAAT
*
44266417 AAATAATTATTAATTATTAAATAA
1 AAATAATTATTAATTATTAAAAAA
44266441 AAATAATTA-T-ATT-TTAAAAATA
1 AAATAATTATTAATTATTAAAAA-A
44266463 AAATAAT
1 AAATAAT
44266470 ATGAAAGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
22 11 0.41
23 1 0.04
24 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATAATTATTAATTATTAAAAAA
Found at i:44266982 original size:24 final size:24
Alignment explanation
Indices: 44266950--44266998 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
44266940 AGAACATCCT
* *
44266950 AAAAGTTAAGTGATAAAATGAAAA
1 AAAAATTAAGTAATAAAATGAAAA
* *
44266974 AAAAATTAAGTAATCAAATTAAAA
1 AAAAATTAAGTAATAAAATGAAAA
44266998 A
1 A
44266999 CGTCCTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.22
Consensus pattern (24 bp):
AAAAATTAAGTAATAAAATGAAAA
Found at i:44267124 original size:34 final size:36
Alignment explanation
Indices: 44267058--44267128 Score: 119
Period size: 34 Copynumber: 2.0 Consensus size: 36
44267048 ACATCATTAG
44267058 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
1 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
*
44267094 TTTATCTAAATTGAT-A-ACTATTAATTATTTTCGT
1 TTTATCTAAATTGATAACACTACTAATTATTTTCGT
44267128 T
1 T
44267129 AAACTGATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 18 0.53
35 1 0.03
36 15 0.44
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (36 bp):
TTTATCTAAATTGATAACACTACTAATTATTTTCGT
Found at i:44273634 original size:17 final size:19
Alignment explanation
Indices: 44273614--44273658 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
44273604 TTTTCTTTCA
44273614 AAAATATTTA-TTT-AAAT
1 AAAATATTTATTTTAAAAT
*
44273631 AAAATACTTATTTTAAAAT
1 AAAATATTTATTTTAAAAT
*
44273650 AATATATTT
1 AAAATATTT
44273659 TAAGATACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 3 0.13
19 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTTATTTTAAAAT
Found at i:44273649 original size:14 final size:14
Alignment explanation
Indices: 44273630--44273669 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
44273620 TTTATTTAAA
44273630 TAAAATACTTATTT
1 TAAAATACTTATTT
*
44273644 TAAAATAATATATTT
1 TAAAATACT-TATTT
*
44273659 TAAGATACTTA
1 TAAAATACTTA
44273670 AATCTTGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TAAAATACTTATTT
Found at i:44275753 original size:17 final size:18
Alignment explanation
Indices: 44275714--44275760 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
44275704 ATAAAAAATT
44275714 AAAATTAA-AAAATATCAA
1 AAAATTAATAAAATA-CAA
44275732 AAAATTAATAAAATA-AA
1 AAAATTAATAAAATACAA
* *
44275749 TAAATAAATAAA
1 AAAATTAATAAA
44275761 TTATAGTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 12 0.46
18 8 0.31
19 6 0.23
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATTAATAAAATACAA
Found at i:44275754 original size:13 final size:13
Alignment explanation
Indices: 44275699--44275761 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
44275689 TAATAATATT
44275699 ATAAAATAAA-AA
1 ATAAAATAAATAA
44275711 ATTAAAATTAAA-AA
1 A-TAAAA-TAAATAA
*
44275725 ATATCAAA-AAATTA
1 ATA--AAATAAATAA
44275739 ATAAAATAAATAA
1 ATAAAATAAATAA
44275752 AT-AAATAAAT
1 ATAAAATAAAT
44275762 TATAGTAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
12 12 0.28
13 17 0.40
14 11 0.26
15 3 0.07
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAAATAAATAA
Found at i:44278614 original size:20 final size:19
Alignment explanation
Indices: 44278589--44278626 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
44278579 TAAGCTTTTT
44278589 TATTTTTAATATAATTAAAA
1 TATTTTT-ATATAATTAAAA
*
44278609 TATTTTTATATTATTAAA
1 TATTTTTATATAATTAAA
44278627 TTACTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTATATAATTAAAA
Found at i:44287241 original size:10 final size:9
Alignment explanation
Indices: 44287213--44287246 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
44287203 CTATTTAAAT
44287213 TAAAAATTA
1 TAAAAATTA
44287222 TAAAAATTA
1 TAAAAATTA
*
44287231 TAAAATTTTA
1 TAAAA-ATTA
44287241 TAAAAA
1 TAAAAA
44287247 ATAGAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:44287414 original size:82 final size:83
Alignment explanation
Indices: 44287312--44287476 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 83
44287302 TAGATAACCC
44287312 ATTTTACCTAATCATATTTTTTTTCTAGATCCTAGTTTTTCGGATCTAAGATTTAAGTTTACTAT
1 ATTTTACCTAATCATATTTTTTTTCTAGATCCTAGTTTTTCGGATCTAAGATTTAAGTTTACTAT
44287377 GTAATTAAATACGTTTGA
66 GTAATTAAATACGTTTGA
44287395 ATTTTACCT-ATCATATTTTTTTTCTAGATCCTAGTTTTTCGGATCTAAGATTTAAGTTTACTAT
1 ATTTTACCTAATCATATTTTTTTTCTAGATCCTAGTTTTTCGGATCTAAGATTTAAGTTTACTAT
44287459 GTAATTAAATACGTTTGA
66 GTAATTAAATACGTTTGA
44287477 TTAAATAAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 73 0.89
83 9 0.11
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (83 bp):
ATTTTACCTAATCATATTTTTTTTCTAGATCCTAGTTTTTCGGATCTAAGATTTAAGTTTACTAT
GTAATTAAATACGTTTGA
Found at i:44288588 original size:116 final size:116
Alignment explanation
Indices: 44288436--44288667 Score: 457
Period size: 115 Copynumber: 2.0 Consensus size: 116
44288426 TAAAAAAAAA
44288436 AAACCCAAAAGTTTCTTTCTCAAATAAAATATAAAAAATATTTTTTGTAGCAATTATAATTTGCA
1 AAACCCAAAAGTTTCTTTCTCAAATAAAATATAAAAAATATTTTTTGTAGCAATTATAATTTGCA
44288501 TAATTGAGAAGTTTGAAAAATACATTAAATAAGGTGAAAAAAAAAGATAAT
66 TAATTGAGAAGTTTGAAAAATACATTAAATAAGGTGAAAAAAAAAGATAAT
44288552 AAACCCAAAAGTTTC-TTCTCAAATAAAATATAAAAAATATTTTTTGTAGCAATTATAATTTGCA
1 AAACCCAAAAGTTTCTTTCTCAAATAAAATATAAAAAATATTTTTTGTAGCAATTATAATTTGCA
44288616 TAATTGAGAAGTTTGAAAAATACATTAAATAAGGTGAAAAAAAAAGATAAT
66 TAATTGAGAAGTTTGAAAAATACATTAAATAAGGTGAAAAAAAAAGATAAT
44288667 A
1 A
44288668 GATAATATAT
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
115 101 0.87
116 15 0.13
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (116 bp):
AAACCCAAAAGTTTCTTTCTCAAATAAAATATAAAAAATATTTTTTGTAGCAATTATAATTTGCA
TAATTGAGAAGTTTGAAAAATACATTAAATAAGGTGAAAAAAAAAGATAAT
Found at i:44290502 original size:276 final size:277
Alignment explanation
Indices: 44290001--44290553 Score: 1099
Period size: 276 Copynumber: 2.0 Consensus size: 277
44289991 TGCCTCTTTA
44290001 TATTTATAAAAAAATTATTTTAATTTTTGATTTATTTTAGTTTTTAAATTTGCACCATTTGTCAA
1 TATTTATAAAAAAATTATTTTAATTTTTGATTTATTTTAGTTTTTAAATTTGCACCATTTGTCAA
44290066 AATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTGTCACCTAGAC
66 AATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTGTCACCTAGAC
44290131 CTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGACTCTTAGGCC
131 CTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGACTCTTAGGCC
44290196 CGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAAAAAGAGTAAG
196 CGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAAAAAGAGTAAG
44290261 CCCGAGCACGGCCCGGC
261 CCCGAGCACGGCCCGGC
44290278 TATTTAT-AAAAAATTATTTTAATTTTTGATTTATTTTAGTTTTTAAATTTGCACCATTTGTCAA
1 TATTTATAAAAAAATTATTTTAATTTTTGATTTATTTTAGTTTTTAAATTTGCACCATTTGTCAA
44290342 AATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTGTCACCTAGAC
66 AATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTGTCACCTAGAC
44290407 CTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGACTCTTAGGCC
131 CTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGACTCTTAGGCC
44290472 CGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAAAAAGAGTAAG
196 CGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAAAAAGAGTAAG
44290537 CCCGAGCACGGCCCGGC
261 CCCGAGCACGGCCCGGC
44290554 CTGGCCCAAT
Statistics
Matches: 276, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
276 269 0.97
277 7 0.03
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (277 bp):
TATTTATAAAAAAATTATTTTAATTTTTGATTTATTTTAGTTTTTAAATTTGCACCATTTGTCAA
AATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTGTCACCTAGAC
CTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGACTCTTAGGCC
CGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAAAAAGAGTAAG
CCCGAGCACGGCCCGGC
Found at i:44290638 original size:276 final size:275
Alignment explanation
Indices: 44290056--44290614 Score: 811
Period size: 276 Copynumber: 2.0 Consensus size: 275
44290046 AAATTTGCAC
44290056 CATTTGTCAAAATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTG
1 CATTTGTCAAAATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTG
44290121 TCACCTAGACCTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGA
66 TCACCTAGACCTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGA
44290186 CTCTTAGGCCCGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAA
131 CTCTTAGGCCCGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAA
* ** **** ***
44290251 AAAGAGTAAGCCCGAGCACGGCCCGGCTATTTATAAAAAATTATTTTAATTTTTGATTTATTTTA
196 AAAGAGTAAGCCCGAGCACGGCCCGGCTATTTATAAAAAATCA-TCAAAAAAATGATTTATAAAA
* **** **** *
44290316 GTTTTTAAATTTGCAC
260 ATAAAAAAATAAAAAA
44290332 CATTTGTCAAAATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTG
1 CATTTGTCAAAATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTG
44290397 TCACCTAGACCTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGA
66 TCACCTAGACCTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGA
44290462 CTCTTAGGCCCGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAA
131 CTCTTAGGCCCGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAA
* *
44290527 AAAGAGTAAGCCCGAGCACGGCCCGGCCTGGCCCAATTTTTAATAAA-CA-CAAAAAAAT-ATTT
196 AAAGAGTAAGCCCGAGCACGGCCCGG-CT------ATTTATAAAAAATCATCAAAAAAATGATTT
44290589 -TAAAAATAAAAAAATAAAAAA
254 ATAAAAATAAAAAAATAAAAAA
*
44290610 TATTT
1 CATTT
44290615 TAAAAGTATT
Statistics
Matches: 253, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
276 221 0.87
277 2 0.01
278 12 0.05
279 4 0.02
280 3 0.01
282 1 0.00
283 10 0.04
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (275 bp):
CATTTGTCAAAATACCTCAAAATGAAAAAAAAAGAGTTAACATTGTTAACTTTATTCCACATGTG
TCACCTAGACCTGTCCATGGGCCGGGTTCGGGCCGGGCTGGGCCCGGAAAAATTTTTCGGCCCGA
CTCTTAGGCCCGGGCCCATCCCAAAATATGGGCCTAAAATTTTTCCCGGGCCCGGCCCGGAAAAA
AAAGAGTAAGCCCGAGCACGGCCCGGCTATTTATAAAAAATCATCAAAAAAATGATTTATAAAAA
TAAAAAAATAAAAAA
Found at i:44291230 original size:28 final size:28
Alignment explanation
Indices: 44291191--44291256 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
44291181 ATAAAAATTA
44291191 ACCAAAATATTA-TAAGTTTTTT-TTATTT
1 ACCAAAATATTACT--GTTTTTTATTATTT
*
44291219 ACCAAAATATTACTTTTTTTTATTATTT
1 ACCAAAATATTACTGTTTTTTATTATTT
*
44291247 ACGAAAATAT
1 ACCAAAATAT
44291257 ACCAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 6 0.18
28 27 0.79
29 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (28 bp):
ACCAAAATATTACTGTTTTTTATTATTT
Found at i:44291752 original size:18 final size:19
Alignment explanation
Indices: 44291703--44291761 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
44291693 CTATTCTCAT
44291703 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
44291722 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
44291740 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
44291759 TTA
1 TTA
44291762 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:44292376 original size:30 final size:32
Alignment explanation
Indices: 44292342--44292402 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
44292332 CACTTTTTAA
44292342 ACAAT-TTTA-ATGATTTTCAATTTTTAAAAG
1 ACAATATTTATATGATTTTCAATTTTTAAAAG
** *
44292372 ACAATATTTATATTTTTTTGAATTTTTAAAA
1 ACAATATTTATATGATTTTCAATTTTTAAAA
44292403 ATTTAAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 4 0.15
32 17 0.65
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (32 bp):
ACAATATTTATATGATTTTCAATTTTTAAAAG
Found at i:44292617 original size:14 final size:14
Alignment explanation
Indices: 44292582--44292622 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
44292572 AAATAAGTCG
44292582 TTATACCTTTAAAA
1 TTATACCTTTAAAA
44292596 TTAT---TTTAAAA
1 TTATACCTTTAAAA
44292607 TTATACCTTTAAAA
1 TTATACCTTTAAAA
44292621 TT
1 TT
44292623 TAATCACAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 11 0.46
14 13 0.54
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (14 bp):
TTATACCTTTAAAA
Found at i:44296237 original size:6 final size:6
Alignment explanation
Indices: 44296226--44296257 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
44296216 CACTGGATGT
44296226 GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GC
1 GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GC
44296258 AGAAGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.34, G:0.19, T:0.00
Consensus pattern (6 bp):
GCCAAA
Found at i:44320167 original size:20 final size:20
Alignment explanation
Indices: 44320142--44320189 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
44320132 GTTTATTTTT
44320142 AAATAATT-TTCTAAAAAATA
1 AAATAATTATT-TAAAAAATA
44320162 AAATAATTATTTAAAAAATA
1 AAATAATTATTTAAAAAATA
44320182 ATAATAAT
1 A-AATAAT
44320190 AAACAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATAATTATTTAAAAAATA
Found at i:44322039 original size:95 final size:97
Alignment explanation
Indices: 44321928--44322119 Score: 345
Period size: 95 Copynumber: 2.0 Consensus size: 97
44321918 ACCGAATTGC
*
44321928 ATTGATAAATATTAGTTTGGTTG-ATCAGTTTTTTCAAAATTATTCTTATTAATTTAAATATAAG
1 ATTGATAAATATTAGTTTGGGTGAAT-AGTTTTTTCAAAATTATTCTTATTAATTTAAATATAAG
44321992 TTAAAATTAAATATAAAAATCCAGTTTTTTTCT
65 TTAAAATTAAATATAAAAATCCAGTTTTTTTCT
44322025 ATTGAT-AA-ATTAGTTTGGGTGAATAGTTTTTTCAAAATTATTCTTATTAATTTAAATATAAGT
1 ATTGATAAATATTAGTTTGGGTGAATAGTTTTTTCAAAATTATTCTTATTAATTTAAATATAAGT
44322088 TAAAATTAAATATAAAAATCCAGTTTTTTTCT
66 TAAAATTAAATATAAAAATCCAGTTTTTTTCT
44322120 CATATTAATT
Statistics
Matches: 93, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
95 83 0.89
96 4 0.04
97 6 0.06
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.47
Consensus pattern (97 bp):
ATTGATAAATATTAGTTTGGGTGAATAGTTTTTTCAAAATTATTCTTATTAATTTAAATATAAGT
TAAAATTAAATATAAAAATCCAGTTTTTTTCT
Found at i:44328494 original size:15 final size:15
Alignment explanation
Indices: 44328474--44328525 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
44328464 TATGTTTTAT
44328474 ATATTATTTTATATC
1 ATATTATTTTATATC
44328489 ATATTATTTTATATC
1 ATATTATTTTATATC
* * *
44328504 ATATTGTATTATATT
1 ATATTATTTTATATC
44328519 ATATTAT
1 ATATTAT
44328526 ATTAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (15 bp):
ATATTATTTTATATC
Found at i:44328513 original size:5 final size:5
Alignment explanation
Indices: 44328473--44328529 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
44328463 TTATGTTTTA
* * * * *
44328473 TATAT TATTT TATAT CATAT TATTT TATAT CATAT TGTAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
44328523 TATAT TA
1 TATAT TA
44328530 AATAAACTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:44329625 original size:21 final size:24
Alignment explanation
Indices: 44329563--44329631 Score: 110
Period size: 23 Copynumber: 3.0 Consensus size: 24
44329553 GGCTTTACTG
44329563 ATCAGGCACTTTATGTGTCGTA-C
1 ATCAGGCACTTTATGTGTCGTATC
44329586 ATCAGGCACTTTATGTGTCGTATC
1 ATCAGGCACTTTATGTGTCGTATC
44329610 -TCAGGCAC-TT-TGTGTCGTATC
1 ATCAGGCACTTTATGTGTCGTATC
44329631 A
1 A
44329632 GGCACCACGT
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.25
22 2 0.05
23 30 0.68
24 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (24 bp):
ATCAGGCACTTTATGTGTCGTATC
Found at i:44329830 original size:15 final size:14
Alignment explanation
Indices: 44329810--44329842 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
44329800 GAGAAAATTT
44329810 AAAATTTGCATATTG
1 AAAATTTG-ATATTG
44329825 AAAA-TTGATATTG
1 AAAATTTGATATTG
44329838 AAAAT
1 AAAAT
44329843 AAAAGGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.59
14 3 0.18
15 4 0.24
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (14 bp):
AAAATTTGATATTG
Found at i:44339117 original size:2 final size:2
Alignment explanation
Indices: 44339110--44339134 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44339100 GAAAAGTTGC
44339110 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
44339135 GTAGAATTAA
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:44343169 original size:55 final size:55
Alignment explanation
Indices: 44343085--44343194 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
44343075 GTATGAGGGA
44343085 CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
1 CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
44343140 CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
1 CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
44343195 ACACTACAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (55 bp):
CATTATAGAACCATACCTATCCATTGACGCAAGATATCCTATTAGAAAACTATGT
Found at i:44346247 original size:3 final size:3
Alignment explanation
Indices: 44346191--44346232 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
44346181 GGTTATTATT
44346191 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44346233 ACTGAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:44347238 original size:20 final size:21
Alignment explanation
Indices: 44347205--44347246 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
44347195 CTAATTCAAC
*
44347205 TCAAGAATTATCAAATTAAAT
1 TCAAGAATTATCAAATAAAAT
*
44347226 TCAA-AATTTTCAAATAAAAT
1 TCAAGAATTATCAAATAAAAT
44347246 T
1 T
44347247 GGAATAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (21 bp):
TCAAGAATTATCAAATAAAAT
Found at i:44348042 original size:34 final size:35
Alignment explanation
Indices: 44347987--44348053 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
44347977 CAAACACCAG
*
44347987 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
44348022 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
44348054 TATTTTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:44350118 original size:20 final size:19
Alignment explanation
Indices: 44350080--44350119 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
44350070 AAAATTCATA
*
44350080 AAAATAAAAAAATATATTT
1 AAAATAAAAAAATAGATTT
*
44350099 AAAATTAAAAAATAAGATTT
1 AAAATAAAAAAAT-AGATTT
44350119 A
1 A
44350120 GTCAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAATAAAAAAATAGATTT
Found at i:44356046 original size:33 final size:33
Alignment explanation
Indices: 44356009--44356075 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
44355999 GCTCTTTTAG
44356009 AGTTCACATCTTTTTAAGTAATTTTGAATCACT
1 AGTTCACATCTTTTTAAGTAATTTTGAATCACT
* **
44356042 AGTTCATATCTTTTTGGGTAATTTTGAATCACT
1 AGTTCACATCTTTTTAAGTAATTTTGAATCACT
44356075 A
1 A
44356076 AGTCGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (33 bp):
AGTTCACATCTTTTTAAGTAATTTTGAATCACT
Found at i:44356601 original size:21 final size:21
Alignment explanation
Indices: 44356575--44356630 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
44356565 AACAGCGGTG
*
44356575 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
44356596 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
44356617 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
44356631 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:44369177 original size:18 final size:17
Alignment explanation
Indices: 44369135--44369186 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
44369125 CGATTATGTC
44369135 AAATTTAAGTATCAAGA
1 AAATTTAAGTATCAAGA
*
44369152 AATGTTTAAGTATCAA-A
1 AA-ATTTAAGTATCAAGA
44369169 TTAAATTTAA-TATCAAGA
1 --AAATTTAAGTATCAAGA
44369187 TAAGGGGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 9 0.31
18 18 0.62
19 2 0.07
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.35
Consensus pattern (17 bp):
AAATTTAAGTATCAAGA
Done.