Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 146 of 335
Found at i:42894292 original size:64 final size:64
Alignment explanation
Indices: 42894211--42894394 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
42894201 AGACATTATG
* *
42894211 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
42894275 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
42894340 AA
63 AA
* * * *
42894342 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
42894395 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:42898930 original size:2 final size:2
Alignment explanation
Indices: 42898925--42898951 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42898915 AAAGCCTTTG
42898925 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 A
42898952 GTTTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42901688 original size:5 final size:5
Alignment explanation
Indices: 42901678--42901709 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
42901668 TAAACATGTG
42901678 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
42901710 GAACACACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:42901891 original size:24 final size:24
Alignment explanation
Indices: 42901859--42901910 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42901849 CATCAAAGTC
* *
42901859 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
42901883 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
42901907 AAAT
1 AAAT
42901911 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:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:42914778 original size:15 final size:15
Alignment explanation
Indices: 42914745--42914789 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
42914735 TTTAACTTGG
* *
42914745 TCTTAATT-ATGTGT
1 TCTTAATTCTTGTTT
42914759 TCTTAATTCTTGTTT
1 TCTTAATTCTTGTTT
42914774 TCTTAATTCTTGTTT
1 TCTTAATTCTTGTTT
42914789 T
1 T
42914790 GATATCCCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 8 0.29
15 20 0.71
ACGTcount: A:0.16, C:0.11, G:0.09, T:0.64
Consensus pattern (15 bp):
TCTTAATTCTTGTTT
Found at i:42923213 original size:5 final size:5
Alignment explanation
Indices: 42923203--42923235 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
42923193 AAAATTTGTG
*
42923203 AAAAT AAAAT AAAAT AATAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
42923236 GAACAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:42923400 original size:24 final size:25
Alignment explanation
Indices: 42923385--42923437 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
42923375 AATCAAAGTC
42923385 AAATATATTATGCTAATAAAATGCT
1 AAATATATTATGCTAATAAAATGCT
* * *
42923410 AAATATATTATACTCAT-AAATACT
1 AAATATATTATGCTAATAAAATGCT
42923434 AAAT
1 AAAT
42923438 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (25 bp):
AAATATATTATGCTAATAAAATGCT
Found at i:42926625 original size:23 final size:23
Alignment explanation
Indices: 42926595--42926638 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
42926585 TTTTTGCAAT
42926595 GAAAATTATTTTCTATACATAAC
1 GAAAATTATTTTCTATACATAAC
42926618 GAAAATTATTTTCTATACATA
1 GAAAATTATTTTCTATACATA
42926639 CATTAAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (23 bp):
GAAAATTATTTTCTATACATAAC
Found at i:42931233 original size:23 final size:23
Alignment explanation
Indices: 42931207--42931252 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
42931197 TCCCAGAATC
42931207 AAATCAAATTCATTGAAGGGTAA
1 AAATCAAATTCATTGAAGGGTAA
42931230 AAATCAAATTCATTGAAGGGTAA
1 AAATCAAATTCATTGAAGGGTAA
42931253 CTCCATAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (23 bp):
AAATCAAATTCATTGAAGGGTAA
Found at i:42935350 original size:195 final size:193
Alignment explanation
Indices: 42935010--42935398 Score: 643
Period size: 195 Copynumber: 2.0 Consensus size: 193
42935000 GGTCGTGTGA
* * *
42935010 CCCAAGTCAGTATGTATGCTCTGCTTTTACACGACCTAAGACACGGGTGTGTTTGGAGCCGTTTG
1 CCCAAGTCAGTATGTATGCTCTGCTTTTACACAACCTAAGACACGGGCGTGTTTGGAGCCGTGTG
* * *
42935075 AGGTATACGGCCTGTTCACTCGGGCATGGGGTTCCTGTATGTTTGAAATTTTCCTAAGTTTTCAA
66 AGGCATACGGCCTGTTCACTCAGGCATGGGGTCCCTGTATGTTTGAAATTTTCCTAAGTTTTCAA
* *
42935140 AACTTTCACATGTTATCGGTTTAGTCCCGAACCACTTTTAAAGCATGTTTAAGGCATCGTAGG
131 AACTTTCACATGTTATCGGTTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCATCATAGG
* *
42935203 CCCAAGTCAGTATGTATGCTCTGTTTTTTTATACAACCTAAGACACGGGCGTGTTTGGAGCCGTG
1 CCCAAGTCAGTATGTATGCTCTG--CTTTTACACAACCTAAGACACGGGCGTGTTTGGAGCCGTG
*
42935268 TGAGGCATACGGCCTGTTCACTCAGGCGTGGGGTCCCTGTATGTTTGAAATTTTCCTAAGTTTTC
64 TGAGGCATACGGCCTGTTCACTCAGGCATGGGGTCCCTGTATGTTTGAAATTTTCCTAAGTTTTC
* *
42935333 AAAATTTTCATATGTTATCGGTTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCATCATAGG
129 AAAACTTTCACATGTTATCGGTTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCATCATAGG
42935398 C
1 C
42935399 TATTATAAGG
Statistics
Matches: 181, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
193 23 0.13
195 158 0.87
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (193 bp):
CCCAAGTCAGTATGTATGCTCTGCTTTTACACAACCTAAGACACGGGCGTGTTTGGAGCCGTGTG
AGGCATACGGCCTGTTCACTCAGGCATGGGGTCCCTGTATGTTTGAAATTTTCCTAAGTTTTCAA
AACTTTCACATGTTATCGGTTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCATCATAGG
Found at i:42942567 original size:55 final size:55
Alignment explanation
Indices: 42942502--42942631 Score: 138
Period size: 55 Copynumber: 2.4 Consensus size: 55
42942492 CTCGTGTTCA
* * *
42942502 TTTAATAGGTTCGACCACGAG-TGTTAGACACGGACGTATCGCACGCCCGTGCTGT
1 TTTAACAGGTTCGACCACG-GTTCTTACACACGGACGTATCGCACGCCCGTGCTGT
* * * *
42942557 TTTAACAGGTTC-ATCCACGGTTCTTCCACACGGGCGTGTCGCACGCCCGTGGTGT
1 TTTAACAGGTTCGA-CCACGGTTCTTACACACGGACGTATCGCACGCCCGTGCTGT
** *
42942612 TTTGGCAGGCTCGACCACGG
1 TTTAACAGGTTCGACCACGG
42942632 CCATATCGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
54 2 0.03
55 59 0.95
56 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (55 bp):
TTTAACAGGTTCGACCACGGTTCTTACACACGGACGTATCGCACGCCCGTGCTGT
Found at i:42945672 original size:55 final size:55
Alignment explanation
Indices: 42945607--42945733 Score: 141
Period size: 55 Copynumber: 2.3 Consensus size: 55
42945597 CCCGTGTTCA
* *
42945607 TTTAATAGGTTCGACCACAGG-TATTAGACACGGGCATGTCGCACGCTCGT-GCTGT
1 TTTAACAGGTTCGACCAC-GGTTATTACACACGGGCATGTCGCACGCTCGTAG-TGT
* * * *
42945662 TTTAACAGGTTTGTCCACGGTTCTTCCACACGGGCATGTCGCACGCTCGTAGTGT
1 TTTAACAGGTTCGACCACGGTTATTACACACGGGCATGTCGCACGCTCGTAGTGT
** *
42945717 TTTGGCAGGCTCGACCA
1 TTTAACAGGTTCGACCA
42945734 TGGCCATGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
54 2 0.03
55 56 0.95
56 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.28
Consensus pattern (55 bp):
TTTAACAGGTTCGACCACGGTTATTACACACGGGCATGTCGCACGCTCGTAGTGT
Found at i:42948691 original size:26 final size:26
Alignment explanation
Indices: 42948662--42948714 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
42948652 TTTACAGTTT
42948662 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
42948688 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
42948714 T
1 T
42948715 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:42949078 original size:32 final size:34
Alignment explanation
Indices: 42949023--42949087 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
42949013 CTATGGGCCA
* *
42949023 TATTGTTATCTGAATAAGGGGCTAAGGCCCAGTT
1 TATTGTAATCTGAATAAAGGGCTAAGGCCCAGTT
*
42949057 TATTGTAATCT-AA-AAAGGGCTATGGCCCAGT
1 TATTGTAATCTGAATAAAGGGCTAAGGCCCAGT
42949088 ACCACTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 16 0.57
33 2 0.07
34 10 0.36
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (34 bp):
TATTGTAATCTGAATAAAGGGCTAAGGCCCAGTT
Found at i:42953429 original size:28 final size:28
Alignment explanation
Indices: 42953325--42953482 Score: 96
Period size: 28 Copynumber: 5.7 Consensus size: 28
42953315 CTGCACAATC
* *
42953325 GATGTCTT-GCACGCTAAGTG-CTATACCG
1 GATGT-TTCGCACACTAAGTGTC-ATATCG
* *
42953353 GATGTTTCGCACACTAAGTGCCATCCTC-
1 GATGTTTCGCACACTAAGTGTCAT-ATCG
** *
42953381 GATACTTCGCACACTAAGTGTCATTTCG
1 GATGTTTCGCACACTAAGTGTCATATCG
*
42953409 GATGTTTTGCACACTAAGTGTCATCATC-
1 GATGTTTCGCACACTAAGTGTCAT-ATCG
* ** ** *
42953437 AATACTTCATACACT--GTGTCATTTCG
1 GATGTTTCGCACACTAAGTGTCATATCG
42953463 GATGTCTT-GCACACTAAGTG
1 GATGT-TTCGCACACTAAGTG
42953483 CCATCCTCAA
Statistics
Matches: 98, Mismatches: 23, Indels: 18
0.71 0.17 0.13
Matches are distributed among these distances:
25 2 0.02
26 14 0.14
27 6 0.06
28 72 0.73
29 4 0.04
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (28 bp):
GATGTTTCGCACACTAAGTGTCATATCG
Found at i:42953476 original size:54 final size:54
Alignment explanation
Indices: 42953351--42953506 Score: 215
Period size: 54 Copynumber: 2.8 Consensus size: 54
42953341 AGTGCTATAC
* *
42953351 CGGATGTTTCGCACACTAAGTGCCATCCTCGATACTTCGCACACTAAGTGTCATTT
1 CGGATGTTT-GCACACTAAGTGCCATCCTCAATACTTCACACACT-AGTGTCATTT
* * *
42953407 CGGATGTTTTGCACACTAAGTGTCATCATCAATACTTCATACACT-GTGTCATTT
1 CGGATG-TTTGCACACTAAGTGCCATCCTCAATACTTCACACACTAGTGTCATTT
*
42953461 CGGATGTCTTGCACACTAAGTGCCATCCTCAATACTTCGCACACTA
1 CGGATGT-TTGCACACTAAGTGCCATCCTCAATACTTCACACACTA
42953507 AGTGCCGTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
53 1 0.01
54 48 0.55
56 36 0.41
57 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (54 bp):
CGGATGTTTGCACACTAAGTGCCATCCTCAATACTTCACACACTAGTGTCATTT
Found at i:42953511 original size:28 final size:28
Alignment explanation
Indices: 42953358--42953512 Score: 122
Period size: 28 Copynumber: 5.6 Consensus size: 28
42953348 TACCGGATGT
42953358 TTCGCACACTAAGTGCCATCCTCGATAC
1 TTCGCACACTAAGTGCCATCCTCGATAC
* * **
42953386 TTCGCACACTAAGTGTCAT-TTCGGATGT
1 TTCGCACACTAAGTGCCATCCTC-GATAC
* * * *
42953414 TTTGCACACTAAGTGTCATCATCAATAC
1 TTCGCACACTAAGTGCCATCCTCGATAC
** * * *
42953442 TTCATACACT--GTGTCAT-TTCGGATGTC
1 TTCGCACACTAAGTGCCATCCTC-GAT-AC
*
42953469 TT-GCACACTAAGTGCCATCCTCAATAC
1 TTCGCACACTAAGTGCCATCCTCGATAC
42953496 TTCGCACACTAAGTGCC
1 TTCGCACACTAAGTGCC
42953513 GTTCGTTTGG
Statistics
Matches: 98, Mismatches: 21, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
25 2 0.02
26 14 0.14
27 8 0.08
28 70 0.71
29 4 0.04
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.31
Consensus pattern (28 bp):
TTCGCACACTAAGTGCCATCCTCGATAC
Found at i:42953954 original size:68 final size:63
Alignment explanation
Indices: 42953807--42953954 Score: 181
Period size: 63 Copynumber: 2.3 Consensus size: 63
42953797 ATATAGTTCG
* *
42953807 GCTCTCTTGTACACATGGTGAACACTTAGTACCACCCATGTGACCTAGCCAGTTTATCTCGTA
1 GCTCTCTTGTACACATGGTGAACACATAGTACCACCCATGCGACCTAGCCAGTTTATCTCGTA
* * *
42953870 GCTCTCTTGT-CTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATTATAATATCT
1 GCTCTCTTGTAC-ACATGGTGAACACATAGTACCACCCATGCGACCTAGC--CAGT-T--TATCT
42953934 CGTA
60 CGTA
*
42953938 GCTTTCTTGTACACATG
1 GCTCTCTTGTACACATG
42953955 ATGTGCACTC
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
62 1 0.01
63 43 0.60
65 3 0.04
66 1 0.01
68 23 0.32
69 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (63 bp):
GCTCTCTTGTACACATGGTGAACACATAGTACCACCCATGCGACCTAGCCAGTTTATCTCGTA
Found at i:42962704 original size:43 final size:42
Alignment explanation
Indices: 42962592--42962704 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
42962582 GAAATTTACG
*
42962592 TGTAAGACCATGTCTGGGACATCT-GCATCGTATCTATTCTCG
1 TGTAAGACCATGTCTGGGACAT-TGGCATCGTATCTATTCTCA
* * *
42962634 TATAAGACCCTGTCTGGGACATCGGCATCG-ATACTGAATT-TCA
1 TGTAAGACCATGTCTGGGACATTGGCATCGTAT-CT--ATTCTCA
*
42962677 TGTAAGACCATGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
42962705 TGTACTTATC
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 2 0.03
42 28 0.47
43 26 0.44
44 3 0.05
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTATCTATTCTCA
Found at i:42970561 original size:17 final size:19
Alignment explanation
Indices: 42970539--42970581 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
42970529 ATAGAAATAT
42970539 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
42970556 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
42970575 AATCTTA
1 AATCTTA
42970582 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:42970571 original size:19 final size:19
Alignment explanation
Indices: 42970547--42970583 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
42970537 ATAATCTTCA
42970547 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
42970566 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
42970584 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:42970609 original size:22 final size:22
Alignment explanation
Indices: 42970547--42970606 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 22
42970537 ATAATCTTCA
42970547 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
42970566 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
42970588 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
42970607 GATTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:42970896 original size:17 final size:17
Alignment explanation
Indices: 42970872--42970906 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42970862 TGTTTCCCTG
*
42970872 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
42970890 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
42970907 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:42976984 original size:40 final size:40
Alignment explanation
Indices: 42976925--42977142 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
42976915 CGGATGATAA
*
42976925 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
42976965 CCGGGCTAAGTCCCTAAGGCATTTGTGCGAGTAACTATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
42977005 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
42977045 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
* **
42977086 -CGGGCTAAGTCCCGAAGGCAGTTAAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
42977125 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
42977143 TACTTGGTTT
Statistics
Matches: 158, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 18 0.11
40 139 0.88
41 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42978668 original size:28 final size:28
Alignment explanation
Indices: 42978607--42978704 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
42978597 TCACAAATTG
** * *
42978607 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
42978636 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
42978664 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
42978692 GCACTAAGTGTGC
1 GCACTAAGTGTGC
42978705 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:42986344 original size:28 final size:28
Alignment explanation
Indices: 42986283--42986380 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
42986273 TCACAAATTG
** * *
42986283 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
42986312 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
42986340 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
42986368 GCACTAAGTGTGC
1 GCACTAAGTGTGC
42986381 GGGCNGAAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:42987662 original size:38 final size:40
Alignment explanation
Indices: 42987605--42987703 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 40
42987595 AAATTGAATG
* *
42987605 ATATCC-GGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
42987643 ATATCCGGGTTAAGA-CCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
42987682 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
42987704 GCATTCGTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 21 0.42
39 23 0.46
40 6 0.12
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:42987696 original size:39 final size:40
Alignment explanation
Indices: 42987642--42987755 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
42987632 ATGCTGAAAT
* *
42987642 TATATCCGGGTTAAGA-CCGAAGGCAATTGTGCTAGTAGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAGC
* *
42987681 TATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTAGC
* *
42987721 TAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAA
42987756 ATCGTGATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
39 18 0.27
40 46 0.70
41 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAGC
Found at i:42987768 original size:40 final size:38
Alignment explanation
Indices: 42987601--42987785 Score: 146
Period size: 40 Copynumber: 4.8 Consensus size: 38
42987591 TGAGAAATTG
* *
42987601 AATG-ATATCC-GGCTAAGCCCCGAAGACAATTATGCTG-A
1 AATGTATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCA
* * *
42987639 AAT-TATATCCGGGTTAAGA-CCGAAGGCAATTGTGCT
1 AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
42987675 AGTAGCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA
1 AAT-G-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
42987715 AGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCA
1 A-ATG-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* * *
42987755 AATCGTGATATCCGGGTTAAGTCCCGTAGGC
1 AAT-GT-ATATCCGGGCTAAGACCCGAAGGC
42987786 CTTGGTGCGG
Statistics
Matches: 118, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
35 2 0.02
36 4 0.03
37 2 0.02
38 16 0.14
39 23 0.19
40 70 0.59
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.24
Consensus pattern (38 bp):
AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
Found at i:42995786 original size:40 final size:40
Alignment explanation
Indices: 42995742--42995856 Score: 160
Period size: 40 Copynumber: 2.9 Consensus size: 40
42995732 CGCTGAAAAT
* *
42995742 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAGC
* *
42995782 TATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTAGC
* *
42995822 TAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAA
42995857 ATTGATATCC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.04
40 62 0.93
41 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTAGC
Found at i:42997783 original size:26 final size:26
Alignment explanation
Indices: 42997754--42997806 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
42997744 TTTACAGTTT
42997754 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
42997780 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
42997806 T
1 T
42997807 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:42998299 original size:136 final size:137
Alignment explanation
Indices: 42998054--42998339 Score: 502
Period size: 136 Copynumber: 2.1 Consensus size: 137
42998044 GAGTAGTCTC
42998054 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* * *
42998119 TGTTATCTGAATAAGGGGCTAAGGCCTAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
42998184 ACTGTTA
131 ACTGTTA
*
42998191 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
42998255 TGTTATCTGAATAAGGGGTTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
42998320 ACTGTTA
131 ACTGTTA
**
42998327 CCTGAATGGGCTT
1 CCCAAATGGGCTT
42998340 AGGCCCAATA
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
136 122 0.86
137 20 0.14
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:43003437 original size:26 final size:26
Alignment explanation
Indices: 43003400--43003534 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
43003390 TGATACAAAT
* *
43003400 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
43003426 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
43003452 TGATAATAGGTTAGGTAAAT-TTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
43003477 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
43003503 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
43003529 TGATAA
1 TGATAA
43003535 GAATTCATGT
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 23 0.23
26 79 0.77
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:43003491 original size:51 final size:52
Alignment explanation
Indices: 43003400--43003534 Score: 245
Period size: 51 Copynumber: 2.6 Consensus size: 52
43003390 TGATACAAAT
43003400 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
43003452 TGATAATAGGTTAGGTAAAT-TTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
* *
43003503 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAA
43003535 GAATTCATGT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
51 50 0.62
52 30 0.38
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
Found at i:43005043 original size:26 final size:26
Alignment explanation
Indices: 43005014--43005066 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
43005004 TTTACAGTTT
43005014 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
43005040 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
43005066 T
1 T
43005067 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:43005570 original size:134 final size:137
Alignment explanation
Indices: 43005318--43005597 Score: 503
Period size: 134 Copynumber: 2.1 Consensus size: 137
43005308 AGTCTCCCCA
43005318 AATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
1 AATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
* *
43005383 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATCACTG
66 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTG
43005448 TTACC-C
131 TTACCTC
*
43005454 AATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
1 AATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
43005518 ATCT-AATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTG
66 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTG
*
43005582 TTACCTG
131 TTACCTC
43005589 AATGGGCTT
1 AATGGGCTT
43005598 AGGCCCAATA
Statistics
Matches: 139, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
134 63 0.45
135 60 0.43
136 16 0.12
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (137 bp):
AATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTG
TTACCTC
Found at i:43006468 original size:23 final size:22
Alignment explanation
Indices: 43006432--43006553 Score: 68
Period size: 23 Copynumber: 5.4 Consensus size: 22
43006422 AGATTGCGCA
* *
43006432 ATAATAGTTCCTATAGGCTTCAC
1 ATAATATTTTCTATAGG-TTCAC
* *
43006455 ATGATATTTTCTATAGGGTTCGC
1 ATAATATTTTCTATA-GGTTCAC
* * * *
43006478 ATAACATTTACTATGGGATTCGC
1 ATAATATTTTCTATAGG-TTCAC
* *
43006501 ATAACA-GTTCTTATACGGTTCAC
1 ATAATATTTTC-TATA-GGTTCAC
* *
43006524 ATGATATTTCCTATAAGGTTCAC
1 ATAATATTTTCTAT-AGGTTCAC
43006547 AT-ATATT
1 ATAATATT
43006554 CACTAAAGGC
Statistics
Matches: 77, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
22 9 0.12
23 61 0.79
24 7 0.09
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (22 bp):
ATAATATTTTCTATAGGTTCAC
Found at i:43006567 original size:21 final size:23
Alignment explanation
Indices: 43006520--43006568 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
43006510 CTTATACGGT
*
43006520 TCACATGATATTTCCTATAAGGT
1 TCACATGATATTTCCTATAAGGC
43006543 TCACAT-ATA-TTCACTA-AAGGC
1 TCACATGATATTTC-CTATAAGGC
43006564 TCACA
1 TCACA
43006569 CAAAAATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 12 0.50
22 6 0.25
23 6 0.25
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (23 bp):
TCACATGATATTTCCTATAAGGC
Found at i:43006835 original size:23 final size:23
Alignment explanation
Indices: 43006804--43006898 Score: 102
Period size: 23 Copynumber: 4.1 Consensus size: 23
43006794 GGTTTACACA
* *
43006804 ATAACAGTTCCTATAGGGTTCGC
1 ATAATAGTTCCTATAGGGTTTGC
* *
43006827 ATAATAGTTACTATAAGGTTTGC
1 ATAATAGTTCCTATAGGGTTTGC
*
43006850 ATAATAATTCCTATA-GGTTTGGC
1 ATAATAGTTCCTATAGGGTTT-GC
* * *
43006873 ATGATATTTCTTATAGGGTTTGC
1 ATAATAGTTCCTATAGGGTTTGC
43006896 ATA
1 ATA
43006899 TACTCATTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
22 5 0.08
23 50 0.83
24 5 0.08
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (23 bp):
ATAATAGTTCCTATAGGGTTTGC
Found at i:43006893 original size:46 final size:46
Alignment explanation
Indices: 43006811--43006898 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
43006801 ACAATAACAG
43006811 TTCCTATAGGGTTCGCATAATAGTTACTATAAGGTTTGCATAATAA
1 TTCCTATAGGGTTCGCATAATAGTTACTATAAGGTTTGCATAATAA
* * * * *
43006857 TTCCTATAGGTTTGGCATGATA-TTTCTTATAGGGTTTGCATA
1 TTCCTATAGGGTTCGCATAATAGTTAC-TATAAGGTTTGCATA
43006899 TACTCATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 3 0.08
46 33 0.92
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.41
Consensus pattern (46 bp):
TTCCTATAGGGTTCGCATAATAGTTACTATAAGGTTTGCATAATAA
Found at i:43010398 original size:44 final size:43
Alignment explanation
Indices: 43010339--43010674 Score: 250
Period size: 44 Copynumber: 7.6 Consensus size: 43
43010329 ATCTTGCTTT
* *
43010339 ACTGCAATTTTAGAGAGATAAGGATTGTGACTTTGATCTGCTCC
1 ACTGCAACTTCAGAGAGATAA-GATTGTGACTTTGATCTGCTCC
* *
43010383 ACTGCACCTTCAGAGAGATAAGATCTGCTAACTTT-AGTCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGAT-TG-TGACTTTGA-TCTGCTCC
* * * * * *
43010428 ACTGCAACTTCAGGGAGATAAGACTTGGGTAATTTTATCCTGCACT
1 ACTGCAACTTCAGAGAGATAAGA-TTGTG-ACTTTGAT-CTGCTCC
* * *
43010474 ACTGCAACTTCAGAGAGATAAGGATTGGGGCTTCGATCTGCTCC
1 ACTGCAACTTCAGAGAGATAA-GATTGTGACTTTGATCTGCTCC
* * * * *
43010518 ACTACAACTTTAGGGAGATAAGATCT-TCTA-TCTTCAGTCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGAT-TGT-GACT-TTGA-TCTGCTCC
* * * *
43010563 ACTACAACTTCAGGGAGATAAGACTTGCT-A-TTTCAATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGA-TTG-TGACTTT-GATCTGCTCC
* * *
43010607 ACTACAACTTCAGAGAGATAAGGTTTGTGACTTCGATCTGCTCC
1 ACTGCAACTTCAGAGAGATAA-GATTGTGACTTTGATCTGCTCC
* *
43010651 ACTGTAACTTCAGGGAGATAAGAT
1 ACTGCAACTTCAGAGAGATAAGAT
43010675 CTTCAATCTT
Statistics
Matches: 235, Mismatches: 38, Indels: 39
0.75 0.12 0.12
Matches are distributed among these distances:
43 10 0.04
44 106 0.45
45 83 0.35
46 33 0.14
47 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (43 bp):
ACTGCAACTTCAGAGAGATAAGATTGTGACTTTGATCTGCTCC
Found at i:43010502 original size:46 final size:44
Alignment explanation
Indices: 43010284--43010674 Score: 208
Period size: 44 Copynumber: 8.7 Consensus size: 44
43010274 TCTACTGTAA
* *
43010284 CTGCTCCACTGCAACTTCA-AGGAGATACAG-TTCGTGTATTTTTTTAT
1 CTGCTCCACTGCAACTTCAGA-GAGATA-AGATT-GGGTA--ATTTTAT
** * * * * *
43010331 CTTGCTTTACTGCAATTTTAGAGAGATAAGGATTGTG-ACTTTGAT
1 C-TGCTCCACTGCAACTTCAGAGAGATAA-GATTGGGTAATTTTAT
* * *
43010376 CTGCTCCACTGCACCTTCAGAGAGATAAGATCT-GCTAACTTTAGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGGGTAATTTTA-T
*
43010421 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATTTTAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGGGTAATTTTAT
* * ** **
43010466 CCTGCACTACTGCAACTTCAGAGAGATAAGGATTGGG-GCTTCGAT
1 -CTGCTCCACTGCAACTTCAGAGAGATAA-GATTGGGTAATTTTAT
* * * ** *
43010511 CTGCTCCACTACAACTTTAGGGAGATAAGATCT-TCT-ATCTTCAGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGGGTAAT-TTTA-T
* * * *
43010556 CTGCTCCACTACAACTTCAGGGAGATAAGACTT-GCT-ATTTCAAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGGGTAATTT-TAT
* * * * * **
43010600 CCGCTCCACTACAACTTCAGAGAGATAAGGTT-TGTGACTTCGAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATTGGGT-AATTTTAT
* *
43010644 CTGCTCCACTGTAACTTCAGGGAGATAAGAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGAT
43010675 CTTCAATCTT
Statistics
Matches: 272, Mismatches: 53, Indels: 41
0.74 0.14 0.11
Matches are distributed among these distances:
43 10 0.04
44 111 0.41
45 79 0.29
46 40 0.15
47 5 0.02
48 24 0.09
49 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGATTGGGTAATTTTAT
Found at i:43010536 original size:135 final size:135
Alignment explanation
Indices: 43010284--43010676 Score: 481
Period size: 135 Copynumber: 2.9 Consensus size: 135
43010274 TCTACTGTAA
* * * * * *
43010284 CTGCTCCACTGCAACTTCAAGGAGATACAG--TTCGTGTATTTTTTTATCTTGCTTTACTGCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATA-AGACTT-GGGTA--ATTTTATCCTGCTCTACTGCAAC
* * * *
43010347 TTTAGAGAGATAAGGATTGTGACTTTGATCTGCTCCACTGCACCTTCAGAGAGATAAGATCTGCT
62 TTCAGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCT
*
43010412 AACTTTAGT
127 AACTTCAGT
*
43010421 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATTTTATCCTGCACTACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATTTTATCCTGCTCTACTGCAACTTCA
* * * * * *
43010486 GAGAGATAAGGATTGGGGCTTCGATCTGCTCCACTACAACTTTAGGGAGATAAGATCTTCTATCT
66 GAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACT
43010551 TCAGT
131 TCAGT
* * * * *
43010556 CTGCTCCACTACAACTTCAGGGAGATAAGACTT-GCT-ATTTCAATCC-GCTCCACTACAACTTC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATTT-TATCCTGCTCTACTGCAACTTC
* *
43010618 AGAGAGATAAGGTTTGTGACTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCT
65 AGAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT
43010677 TCAATCTTTA
Statistics
Matches: 223, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
133 70 0.31
134 6 0.03
135 113 0.51
136 2 0.01
137 30 0.13
138 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (135 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGGTAATTTTATCCTGCTCTACTGCAACTTCA
GAGAGATAAGGATTGTGACTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTAACT
TCAGT
Found at i:43013518 original size:46 final size:46
Alignment explanation
Indices: 43013451--43013543 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
43013441 AGAACGTGCC
43013451 CCTCAAGGTTATGAAAGGTAGTCTTTCCCATGTCCTCAGGATGCAT
1 CCTCAAGGTTATGAAAGGTAGTCTTTCCCATGTCCTCAGGATGCAT
*
43013497 CCTCAAGGTTATGAAAGGTAGTCTTTCCTATGTCCTCAGGATGCAT
1 CCTCAAGGTTATGAAAGGTAGTCTTTCCCATGTCCTCAGGATGCAT
43013543 C
1 C
43013544 TTTATCTGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (46 bp):
CCTCAAGGTTATGAAAGGTAGTCTTTCCCATGTCCTCAGGATGCAT
Found at i:43021556 original size:127 final size:127
Alignment explanation
Indices: 43021254--43021569 Score: 463
Period size: 127 Copynumber: 2.5 Consensus size: 127
43021244 GAAAAACCGT
* * * * * *
43021254 AACCCAGCACGATAGGGCACAATGCCTCGAATTTCCAAACATTGAACATTGCGTTGCTTTAGAAT
1 AACCCAGCACGATAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTTGTTTTAAAAT
* * *
43021319 TTATAAAACACGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAATCAGAAATCGA
66 TTAGAAAACACGAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAATCAGAAATCAA
*
43021381 AACCCAGCACGATAGGGCACGATTTCTCAAATTTCCAAACATTGAACATTGCCTTGTTTTAAAAT
1 AACCCAGCACGATAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTTGTTTTAAAAT
*
43021446 TTGGAAAACACGAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAA-CGAGAAATCAA
66 TTAGAAAACACGAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAATC-AGAAATCAA
* * ** *
43021508 AACCCAGCACGATAGGACACGATTCCCCAAATTTCCAAACATCAAACATTACCTTCGTTTTA
1 AACCCAGCACGATAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTT-GTTTTA
43021570 GGGAATTTTC
Statistics
Matches: 170, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
126 1 0.01
127 163 0.96
128 6 0.04
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (127 bp):
AACCCAGCACGATAGGGCACGATTCCTCAAATTTCCAAACATTGAACATTGCCTTGTTTTAAAAT
TTAGAAAACACGAGTGAAATTCTAAAGAAATATTCAATTATTTTGAACAAATCAGAAATCAA
Found at i:43025237 original size:2 final size:2
Alignment explanation
Indices: 43025230--43025268 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
43025220 CATATGTCAG
43025230 AT AT 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 A
43025269 GCAGCTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43027169 original size:35 final size:35
Alignment explanation
Indices: 43027123--43027198 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
43027113 GTCCAATAAC
*
43027123 GATCAAGGCAATAGCCCAAATGCATAATGCTATTG
1 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
43027158 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
1 GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
43027193 GATCAA
1 GATCAA
43027199 CTAGAATTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (35 bp):
GATCAAGGCAATAGCCCAAACGCATAATGCTATTG
Found at i:43033192 original size:18 final size:18
Alignment explanation
Indices: 43033169--43033205 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43033159 TAGGGAACTC
43033169 TAAATCCTTCT-GGGATTT
1 TAAATCCTT-TAGGGATTT
43033187 TAAATCCTTTAGGGATTT
1 TAAATCCTTTAGGGATTT
43033205 T
1 T
43033206 TATATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (18 bp):
TAAATCCTTTAGGGATTT
Found at i:43034550 original size:18 final size:18
Alignment explanation
Indices: 43034529--43034563 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43034519 GATGCAGTTC
43034529 TAGAGACAGATACAAATA
1 TAGAGACAGATACAAATA
**
43034547 TAGATTCAGATACAAAT
1 TAGAGACAGATACAAAT
43034564 GCAGACATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.23
Consensus pattern (18 bp):
TAGAGACAGATACAAATA
Found at i:43034568 original size:12 final size:12
Alignment explanation
Indices: 43034553--43034592 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
43034543 AATATAGATT
43034553 CAGATACAAATG
1 CAGATACAAATG
* *
43034565 CAGACATAAATG
1 CAGATACAAATG
*
43034577 CGGATACAAATG
1 CAGATACAAATG
43034589 CAGA
1 CAGA
43034593 CACAGATCTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (12 bp):
CAGATACAAATG
Found at i:43036338 original size:15 final size:14
Alignment explanation
Indices: 43036314--43036345 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
43036304 CCACTATTGG
43036314 TTTCACTAACCCAA
1 TTTCACTAACCCAA
43036328 TTTCTACTAACCCAA
1 TTTC-ACTAACCCAA
43036343 TTT
1 TTT
43036346 TTGGGGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTCACTAACCCAA
Found at i:43053750 original size:20 final size:20
Alignment explanation
Indices: 43053725--43053769 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
43053715 TTTTCACCTA
*
43053725 AATAGAGAAAATTAAAGCAG
1 AATAGAGAAAATGAAAGCAG
43053745 AATAGAGAAAATGAAAGCAG
1 AATAGAGAAAATGAAAGCAG
43053765 AATAG
1 AATAG
43053770 GGTAAGGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.22, T:0.13
Consensus pattern (20 bp):
AATAGAGAAAATGAAAGCAG
Found at i:43055316 original size:7 final size:7
Alignment explanation
Indices: 43055304--43055329 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43055294 TAAAAATTTA
43055304 AATATTC
1 AATATTC
43055311 AATATTC
1 AATATTC
43055318 AATATTC
1 AATATTC
43055325 AATAT
1 AATAT
43055330 GAAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:43056301 original size:42 final size:42
Alignment explanation
Indices: 43056254--43056333 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
43056244 AATATGTATT
43056254 AATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGTTATG
1 AATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGTTATG
43056296 AATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
1 AATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGT
43056334 CATTAATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (42 bp):
AATTCAAAAGGTTGACATATGATAGTTGTGATCTTAGTTATG
Found at i:43057947 original size:11 final size:11
Alignment explanation
Indices: 43057931--43057955 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43057921 TTGCAAGTTA
43057931 AATTTTATTTT
1 AATTTTATTTT
43057942 AATTTTATTTT
1 AATTTTATTTT
43057953 AAT
1 AAT
43057956 ATTACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
AATTTTATTTT
Found at i:43061954 original size:28 final size:29
Alignment explanation
Indices: 43061923--43062053 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 29
43061913 GTGACGAGAT
43061923 TGGCACTAAGTGTGCGTGCTGGAAA-ATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
43061951 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ****
43061980 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
43062009 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
43062038 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
43062054 AAATCGAGTA
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
28 26 0.30
29 61 0.70
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:43061990 original size:29 final size:28
Alignment explanation
Indices: 43061923--43061994 Score: 126
Period size: 28 Copynumber: 2.5 Consensus size: 28
43061913 GTGACGAGAT
*
43061923 TGGCACTAAGTGTGCGTGCTGGAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAATA
43061951 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAA-ATA
43061980 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
43061995 GAGCTCGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 24 0.57
29 18 0.43
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (28 bp):
TGGCACTAAGTGTGCATGCTGGAAAATA
Found at i:43069693 original size:29 final size:29
Alignment explanation
Indices: 43069660--43069733 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
43069650 GTGACGAGAT
43069660 TGGCACTAAGTGTGCGTGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
43069689 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
43069718 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
43069734 AGCTCGAAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:43069749 original size:29 final size:29
Alignment explanation
Indices: 43069717--43069792 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
43069707 CTGGAAATAT
* *
43069717 ATGGCACTAAGTGTGCGAGCTCGAAGGGC
1 ATGGCACTAAGTGTGCGAGCTCAAAGCGC
* * * *
43069746 ATGGCACTATGTGTGCGGGCTTAAATCGC
1 ATGGCACTAAGTGTGCGAGCTCAAAGCGC
43069775 ATGGCACTAAGTGTGCGA
1 ATGGCACTAAGTGTGCGA
43069793 AATCGAGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGCTCAAAGCGC
Found at i:43069750 original size:58 final size:58
Alignment explanation
Indices: 43069660--43069792 Score: 142
Period size: 58 Copynumber: 2.3 Consensus size: 58
43069650 GTGACGAGAT
* * * * *
43069660 TGGCACTAAGTGTGCGTGCTGGAAAAATATGGCACTAAGTGTGCATGCTGGAAAT-ATA
1 TGGCACTAAGTGTGCGAGCTCGAAAAACATGGCACTAAGTGTGCAGGCT-GAAATCACA
*** * * * *
43069718 TGGCACTAAGTGTGCGAGCTCGAAGGGCATGGCACTATGTGTGCGGGCTTAAATCGCA
1 TGGCACTAAGTGTGCGAGCTCGAAAAACATGGCACTAAGTGTGCAGGCTGAAATCACA
43069776 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
43069793 AATCGAGTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
57 4 0.06
58 58 0.94
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.24
Consensus pattern (58 bp):
TGGCACTAAGTGTGCGAGCTCGAAAAACATGGCACTAAGTGTGCAGGCTGAAATCACA
Found at i:43071662 original size:39 final size:39
Alignment explanation
Indices: 43071559--43071819 Score: 342
Period size: 39 Copynumber: 6.6 Consensus size: 39
43071549 CGTTCAAACA
* * * * * *
43071559 CCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCACAACTCGCACAATTG
* * * *
43071599 CCTTCAGGACTTAACCCGGATATCACAACTTGCACAATCG
1 CCTTC-GGGCTTAGCCCGGATATCACAACTCGCACAATTG
* * *
43071639 CCTTTGGGCTTAGCCCGGATATCATATCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTG
*
43071678 CCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATCG
1 CCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTG
* *
43071717 CCTTCGGGCTTAGCCCGGATATCATATCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTG
* *
43071756 CCTTCGGGCTTAGCCCGGATATCACAATTCGTACAATTG
1 CCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTG
43071795 CCTTCGGGCTTAGCCCGGATATCAC
1 CCTTCGGGCTTAGCCCGGATATCAC
43071820 TCGAACATTC
Statistics
Matches: 192, Mismatches: 28, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
39 159 0.83
40 31 0.16
41 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCACAACTCGCACAATTG
Found at i:43071713 original size:78 final size:78
Alignment explanation
Indices: 43071559--43071818 Score: 385
Period size: 78 Copynumber: 3.3 Consensus size: 78
43071549 CGTTCAAACA
* * * * * * * *
43071559 CCTTCGGGACATAGCCCGGTTATGATAACCCGCACAAATGCCTTCAGGACTTAACCCGGATATCA
1 CCTTCGGG-CTTAGCCCGGATATCATATCTCGCACAATTGCCTTC-GGGCTTAGCCCGGATATCA
*
43071624 CAACTTGCACAATCG
64 CAACTCGCACAATCG
*
43071639 CCTTTGGGCTTAGCCCGGATATCATATCTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCACA
1 CCTTCGGGCTTAGCCCGGATATCATATCTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCACA
43071704 ACTCGCACAATCG
66 ACTCGCACAATCG
43071717 CCTTCGGGCTTAGCCCGGATATCATATCTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCACA
1 CCTTCGGGCTTAGCCCGGATATCATATCTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCACA
* * *
43071782 ATTCGTACAATTG
66 ACTCGCACAATCG
43071795 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
43071819 CTCGAACATT
Statistics
Matches: 166, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
78 129 0.78
79 30 0.18
80 7 0.04
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (78 bp):
CCTTCGGGCTTAGCCCGGATATCATATCTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCACA
ACTCGCACAATCG
Found at i:43074631 original size:15 final size:15
Alignment explanation
Indices: 43074611--43074647 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
43074601 TAAGATAAAA
43074611 AATGAACTAAATTCC
1 AATGAACTAAATTCC
*
43074626 AATGAACTAATTTCC
1 AATGAACTAAATTCC
43074641 AATGAAC
1 AATGAAC
43074648 CCTTCCTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (15 bp):
AATGAACTAAATTCC
Found at i:43082607 original size:25 final size:25
Alignment explanation
Indices: 43082560--43082607 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
43082550 CAATACGGTT
*
43082560 TACTACCTATAGTAGTTTCAAATTA
1 TACTACCTATAGTAGTTGCAAATTA
*
43082585 TACTATCTATAGTA-TTGCGAAAT
1 TACTACCTATAGTAGTTGC-AAAT
43082608 AAACAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (25 bp):
TACTACCTATAGTAGTTGCAAATTA
Found at i:43088406 original size:43 final size:43
Alignment explanation
Indices: 43088366--43088513 Score: 190
Period size: 43 Copynumber: 3.4 Consensus size: 43
43088356 AATCCTAGAT
* * * * *
43088366 ATGGTCTTACATGTTATCAT-ATATCGATGCCACTGTCCTAGAG
1 ATGGTCTTACACGTAATCATAATAT-GATGCCAATGTCCCAGAC
* *
43088409 AGGGTCTTACACGAAATCATAATATGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCATAATATGATGCCAATGTCCCAGAC
* *
43088452 ATGGTCTTACACGTAATCTTAATATAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCATAATATGATGCCAATGTCCCAGAC
*
43088495 ATGGTCTTACATGTAATCA
1 ATGGTCTTACACGTAATCA
43088514 CATCTTGGTA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 87 0.96
44 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCATAATATGATGCCAATGTCCCAGAC
Found at i:43094695 original size:49 final size:49
Alignment explanation
Indices: 43094633--43094866 Score: 245
Period size: 49 Copynumber: 4.7 Consensus size: 49
43094623 CAAAGCTACT
* * *
43094633 TGGTACGCATAGTAGCCTGCACTTAGTACTACAGATGCAACCAATTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATC
* ** **
43094682 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCAACC-AATTATC
* * * * * *
43094732 TGATATACGTAGTAGCCTTCACTTAGAACTACACACGTG-ATCGAAGTTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACA--TGCAACCAA-TTATC
* * * * *
43094783 GGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATC
*
43094832 CGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACA
43094867 CGTGACCTCA
Statistics
Matches: 149, Mismatches: 31, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
49 75 0.50
50 41 0.28
51 32 0.21
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCAACCAATTATC
Found at i:43097277 original size:19 final size:19
Alignment explanation
Indices: 43097242--43097279 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
43097232 TTACAATTTA
*
43097242 AATTTTTATTTTCTTTTCT
1 AATTTTTATTTTATTTTCT
43097261 AATTTTTCA-TTTATTTTCT
1 AATTTTT-ATTTTATTTTCT
43097280 TCTGACAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTATTTTATTTTCT
Found at i:43105924 original size:48 final size:48
Alignment explanation
Indices: 43105853--43106277 Score: 414
Period size: 48 Copynumber: 8.9 Consensus size: 48
43105843 TAAATTGTCA
* * *
43105853 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * * * *
43105901 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * * *
43105949 ATTCCATGTCCCAGACATAGACTTACGCTAGCT-ATCATAAT-GAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCA-CAT-ATCGAGGCCG
* * * * * * *
43105997 ATGTCATGTCCCAGACATGGTCTTATACTAACACACATATCAACGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* *
43106045 ATGCCATGTCCCAGACATGGTCTTACACT-GACTCTCATAAT-GTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCACAT-ATCGAGGCCG
* * *
43106093 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * *
43106141 ATGCCATGTCCCAGACATGGTCTTACATTAGCACACATATCTACGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
* * * *
43106189 ATGCCATGTCCCATACATGGTCTTACACT-GAATCTCATAAT-GTGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCACAT-ATCGAGGCCG
* *
43106237 ATGCCATGTCCCA-AGCATGGTCTTACACTAGCACACCTATC
1 ATGCCATGTCCCAGA-CATGGTCTTACACTAGCTCACATATC
43106278 ACCCAAATGG
Statistics
Matches: 304, Mismatches: 60, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
47 8 0.03
48 288 0.95
49 8 0.03
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCG
Found at i:43106118 original size:144 final size:144
Alignment explanation
Indices: 43105853--43106278 Score: 524
Period size: 144 Copynumber: 3.0 Consensus size: 144
43105843 TAAATTGTCA
* * * * * *
43105853 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCAGACA
* * * * *
43105918 TGGTCTTACACT-AGCTCTCGTCTCAATGT---CGATTCCATGTCCCAGACATAGACTTACGCTA
66 TGGTCTTACACTGA-CTCTC--AT-AATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTA
* * *
43105979 GCTA-TCATAAT-GAGGCTG
127 GC-ACACAT-ATCAAGGCCG
* * * *
43105997 ATGTCATGTCCCAGACATGGTCTTATACTAACACACATATCAACGTCGATGCCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCAGACA
43106062 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
66 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
*
43106127 ACATATCAATGCCG
131 ACATATCAAGGCCG
* * *
43106141 ATGCCATGTCCCAGACATGGTCTTACATTAGCACACATATCTACGCCGATGCCATGTCCCATACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCAGACA
*
43106206 TGGTCTTACACTGAATCTCATAATGTGGCCGATGCCATGTCCCA-AGCATGGTCTTACACTAGCA
66 TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGA-CATGGTCTTACACTAGCA
*
43106270 CACCTATCA
130 CACATATCA
43106279 CCCAAATGGC
Statistics
Matches: 247, Mismatches: 28, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
141 5 0.02
142 1 0.00
143 4 0.02
144 236 0.96
145 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (144 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACGCCGATGCCATGTCCCAGACA
TGGTCTTACACTGACTCTCATAATGTGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCAC
ACATATCAAGGCCG
Found at i:43111818 original size:21 final size:20
Alignment explanation
Indices: 43111793--43111835 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
43111783 AAAGCCCTAA
43111793 CTTTTTCTCCTT-TTTC-TTT
1 CTTTTT-TCCTTCTTTCTTTT
43111812 CTCTTTTTCCTTCTTTCTTTT
1 CT-TTTTTCCTTCTTTCTTTT
43111833 CTT
1 CTT
43111836 AAGTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
CTTTTTTCCTTCTTTCTTTT
Found at i:43111935 original size:15 final size:14
Alignment explanation
Indices: 43111902--43111946 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
43111892 CTTATTCTTT
*
43111902 TATAAT-TATTATA
1 TATAATATAATATA
43111915 -ATAATATAATATGA
1 TATAATATAATAT-A
43111929 TATAATATAATATA
1 TATAATATAATATA
43111943 TATA
1 TATA
43111947 CTTAAGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 5 0.18
13 5 0.18
14 6 0.21
15 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TATAATATAATATA
Found at i:43112017 original size:18 final size:18
Alignment explanation
Indices: 43111967--43112014 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
43111957 AAGTATTACA
*
43111967 TATATTATTATATACATATG
1 TATATTATT-T-TACACATG
43111987 TATATTATTTTACACATG
1 TATATTATTTTACACATG
43112005 TA-ATTATTTT
1 TATATTATTTT
43112015 TACCATACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.30
18 9 0.33
19 1 0.04
20 9 0.33
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (18 bp):
TATATTATTTTACACATG
Found at i:43112454 original size:30 final size:29
Alignment explanation
Indices: 43112409--43112470 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
43112399 ACTTTTTTTA
*
43112409 TTGTTATTTTGTTATTATTTTAAAGACAT
1 TTGTTATTTTATTATTATTTTAAAGACAT
*
43112438 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTT-ATTTTATTATTATTTTAAAGACAT
43112468 TTG
1 TTG
43112471 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.58
Consensus pattern (29 bp):
TTGTTATTTTATTATTATTTTAAAGACAT
Found at i:43112569 original size:18 final size:18
Alignment explanation
Indices: 43112548--43112587 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
43112538 GAAATATTTA
*
43112548 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTAT-GTAT
43112566 TTTTGATGTATTATGTAT
1 TTTTGATGTATTATGTAT
43112584 TTTT
1 TTTT
43112588 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATGTAT
Found at i:43112610 original size:12 final size:12
Alignment explanation
Indices: 43112589--43112622 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43112579 TGTATTTTTT
*
43112589 AAAATTATATAA
1 AAAATAATATAA
43112601 AAAATAATATAA
1 AAAATAATATAA
*
43112613 AAATTAATAT
1 AAAATAATAT
43112623 GGGTGGGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:43117761 original size:13 final size:13
Alignment explanation
Indices: 43117726--43117767 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
43117716 AGTATGTATG
43117726 TATATGATTAG-T
1 TATATGATTAGAT
43117738 T-TATGATTAGAT
1 TATATGATTAGAT
*
43117750 TATATTATTAGAT
1 TATATGATTAGAT
*
43117763 GATAT
1 TATAT
43117768 TAAGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 9 0.35
12 3 0.12
13 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (13 bp):
TATATGATTAGAT
Found at i:43122449 original size:19 final size:19
Alignment explanation
Indices: 43122425--43122461 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
43122415 CTGGAAAACT
43122425 TTGCAATTCAAAGATAAAG
1 TTGCAATTCAAAGATAAAG
43122444 TTGCAATTCAAAGATAAA
1 TTGCAATTCAAAGATAAA
43122462 TTTAATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (19 bp):
TTGCAATTCAAAGATAAAG
Found at i:43130308 original size:45 final size:45
Alignment explanation
Indices: 43130256--43130385 Score: 136
Period size: 45 Copynumber: 2.8 Consensus size: 45
43130246 CCTGAGCTGA
* * * * *
43130256 TGAACAGTTAGCTCTAACGAGCTGAAATGGTAAGCTTTTTTCAGT
1 TGAACAGTAAGCTCTAACGAGCTGAAATGGTAAGCTCTATTAAGC
* *
43130301 TGAACAGTAAGCTC-ATACGAGTTGAAACGGTAAGCTCTATTAAGC
1 TGAACAGTAAGCTCTA-ACGAGCTGAAATGGTAAGCTCTATTAAGC
**
43130346 TGAACAGTAAGCTCTTTCGAGCTGATATATCGGTAAGCTC
1 TGAACAGTAAGCTCTAACGAGCTGA-A-AT-GGTAAGCTC
43130386 ATACGAGCTG
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
44 1 0.01
45 57 0.83
46 1 0.01
47 1 0.01
48 9 0.13
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (45 bp):
TGAACAGTAAGCTCTAACGAGCTGAAATGGTAAGCTCTATTAAGC
Found at i:43130368 original size:22 final size:22
Alignment explanation
Indices: 43130256--43130370 Score: 74
Period size: 22 Copynumber: 5.1 Consensus size: 22
43130246 CCTGAGCTGA
* **
43130256 TGAACAGTTAGCTCTAACGAGC
1 TGAACAGTAAGCTCTTTCGAGC
* *
43130278 TGAA-ATGGTAAGCTTTTTTC-AGT
1 TGAACA--GTAAGC-TCTTTCGAGC
* * *
43130301 TGAACAGTAAGCTCATACGAGT
1 TGAACAGTAAGCTCTTTCGAGC
* *
43130323 TGAAACGGTAAGCTCTATT-AAGC
1 TG-AACAGTAAGCTCT-TTCGAGC
43130346 TGAACAGTAAGCTCTTTCGAGC
1 TGAACAGTAAGCTCTTTCGAGC
43130368 TGA
1 TGA
43130371 TATATCGGTA
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
21 6 0.09
22 33 0.47
23 26 0.37
24 5 0.07
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (22 bp):
TGAACAGTAAGCTCTTTCGAGC
Found at i:43136898 original size:168 final size:167
Alignment explanation
Indices: 43136591--43136909 Score: 372
Period size: 168 Copynumber: 1.9 Consensus size: 167
43136581 ATCCAGTTTG
* ** ***
43136591 GGCTCTAGCAACCCTTTGTAACATTCTCAACATTGCATATGTTACAGTGTCATCATTGTTCTCAT
1 GGCTCTAGCAACCCTTTGTAACACTCTCAACATTG-ATATGTTACAGCATCATCACCATTCTCAT
* * * * * *
43136656 AGCCTCTACTATCATTGGCAGTGAAGTTCTCCATATAATTTTCCTCAGGGATTTGATCCCCTCCC
65 AGCCTCCACCAACATTGGCAGTGAAGTTCTCCATATAATTCTCCTCAAGGATTAGATCCCCTCCC
**
43136721 TGGACAGTGGGCGACTCTACAGGTGCAGCCCTATTTTA
130 TAAACAGTGGGCGACTCTACAGGTGCAGCCCTATTTTA
* *
43136759 GGCTCTAGCAACCCTTTGTAACACTCTCAATATTG-TCTGTATCACAGCATCATCACCATTCTCA
1 GGCTCTAGCAACCCTTTGTAACACTCTCAACATTGATATGT-T-ACAGCATCATCACCATTCTCA
* * * * * *
43136823 TAGCCTCCGCCAACATTGGC-GATGGAGTTCTTCATATAATTCTCCTCAAGGATTAGGTTCTCTC
64 TAGCCTCCACCAACATTGGCAG-TGAAGTTCTCCATATAATTCTCCTCAAGGATTAGATCCCCTC
* *
43136887 CCTAAACAGTGGGTGTCTCTACA
128 CCTAAACAGTGGGCGACTCTACA
43136910 AGTACAGCGC
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
166 4 0.03
167 2 0.02
168 118 0.95
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (167 bp):
GGCTCTAGCAACCCTTTGTAACACTCTCAACATTGATATGTTACAGCATCATCACCATTCTCATA
GCCTCCACCAACATTGGCAGTGAAGTTCTCCATATAATTCTCCTCAAGGATTAGATCCCCTCCCT
AAACAGTGGGCGACTCTACAGGTGCAGCCCTATTTTA
Found at i:43138057 original size:22 final size:22
Alignment explanation
Indices: 43138032--43138076 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
43138022 ACATATTAGA
*
43138032 TTGTAGTTTAACCACCAATGGT
1 TTGTAGATTAACCACCAATGGT
**
43138054 TTGTAGATTAACTGCCAATGGT
1 TTGTAGATTAACCACCAATGGT
43138076 T
1 T
43138077 GTGGACAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (22 bp):
TTGTAGATTAACCACCAATGGT
Found at i:43139279 original size:14 final size:13
Alignment explanation
Indices: 43139253--43139280 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43139243 CTTGGCAAGG
43139253 ATCATTTTTAAAA
1 ATCATTTTTAAAA
43139266 ATCATTTTTAAAA
1 ATCATTTTTAAAA
43139279 AT
1 AT
43139281 TCCAACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATCATTTTTAAAA
Found at i:43139418 original size:19 final size:19
Alignment explanation
Indices: 43139396--43139468 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 19
43139386 ATGAAAAAAT
43139396 AATTTCCAAATAAAAATTA
1 AATTTCCAAATAAAAATTA
* * *
43139415 AA-TTACAAGAAAATAAATAA
1 AATTTCCAA-ATAA-AAATTA
* *
43139435 AATTT-CACATACCAAATTA
1 AATTTCCAAATA-AAAATTA
43139454 AATTTCC-AATAAAAA
1 AATTTCCAAATAAAAA
43139469 AAAACTATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
18 8 0.20
19 20 0.50
20 10 0.25
21 2 0.05
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.27
Consensus pattern (19 bp):
AATTTCCAAATAAAAATTA
Found at i:43147871 original size:35 final size:35
Alignment explanation
Indices: 43147825--43147894 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
43147815 CTCCTCCTTT
**
43147825 AATGAGTCTAGTTGGACTAAAATTCATGTCCTATG
1 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
43147860 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
1 AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
43147895 TTAAACTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (35 bp):
AATGAGTCTAGTTAAACTAAAATTCATGTCCTATG
Found at i:43152174 original size:6 final size:6
Alignment explanation
Indices: 43152156--43152202 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
43152146 TCATTACTGC
*
43152156 AGATGT AGCTGT AGATGT AGATGT AGATGT AGATGT AGATGT AGATG
1 AGATGT AGATGT AGATGT AGATGT AGATGT AGATGT AGATGT AGATG
43152203 AATGTGATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (6 bp):
AGATGT
Found at i:43157150 original size:26 final size:26
Alignment explanation
Indices: 43157121--43157195 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 26
43157111 ATTCAACTGG
43157121 TCCATATCGGTTCTCAATCCAACCAA
1 TCCATATCGGTTCTCAATCCAACCAA
* * * ***
43157147 TCCATATTGGCTCTCAGTCCAATTGA
1 TCCATATCGGTTCTCAATCCAACCAA
* * *
43157173 TCCACATCTGTTCTCAACCCAAC
1 TCCATATCGGTTCTCAATCCAAC
43157196 TGGTCAATAA
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.35, G:0.09, T:0.29
Consensus pattern (26 bp):
TCCATATCGGTTCTCAATCCAACCAA
Found at i:43162916 original size:25 final size:25
Alignment explanation
Indices: 43162862--43162909 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
43162852 AAGCTCCTCT
* *
43162862 AAGCTGAATAATGGGAAGCTCATGA
1 AAGCTAAATAACGGGAAGCTCATGA
*
43162887 GAGCTAAATAACGGGAAGCTCAT
1 AAGCTAAATAACGGGAAGCTCAT
43162910 ACAAGCTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.19
Consensus pattern (25 bp):
AAGCTAAATAACGGGAAGCTCATGA
Found at i:43164950 original size:25 final size:27
Alignment explanation
Indices: 43164913--43164965 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
43164903 TCAAACATGC
43164913 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
43164939 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
43164965 A
1 A
43164966 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:43166486 original size:26 final size:26
Alignment explanation
Indices: 43166450--43166557 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
43166440 TGAAATGCCC
* *
43166450 ATCATGGAACATTTACCTAAACAATT
1 ATCATGGAACATTTACCTAACCCATT
43166476 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
43166502 ATCATGGAATATTCACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
43166528 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
43166554 ATCA
1 ATCA
43166558 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:43168535 original size:19 final size:20
Alignment explanation
Indices: 43168511--43168551 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
43168501 ATAATTAAAA
43168511 AAAATT-CTTCAATT-TTTTT
1 AAAATTACTT-AATTATTTTT
43168530 AAAATTACTTAATTATTTTT
1 AAAATTACTTAATTATTTTT
43168550 AA
1 AA
43168552 TTTTTGCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
AAAATTACTTAATTATTTTT
Found at i:43168676 original size:7 final size:7
Alignment explanation
Indices: 43168664--43168688 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43168654 TAAATATTTA
43168664 AAATTAT
1 AAATTAT
43168671 AAATTAT
1 AAATTAT
43168678 AAATTAT
1 AAATTAT
43168685 AAAT
1 AAAT
43168689 ATTTTTTCAC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTAT
Found at i:43170714 original size:12 final size:12
Alignment explanation
Indices: 43170697--43170721 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43170687 TTGTGTGTTC
43170697 TTTATTTTATTT
1 TTTATTTTATTT
43170709 TTTATTTTATTT
1 TTTATTTTATTT
43170721 T
1 T
43170722 ATTTTCACAA
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:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:43174765 original size:46 final size:46
Alignment explanation
Indices: 43174715--43174888 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
43174705 TGGTCGAGCA
* *
43174715 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* * * *
43174761 TCCGAACTCGTTAAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAA--A--CG
* *
43174808 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
*
43174854 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT
43174889 AGGCGGGTTA
Statistics
Matches: 107, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 60 0.56
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
Found at i:43174871 original size:93 final size:93
Alignment explanation
Indices: 43174712--43174882 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
43174702 GGATGGTCGA
* *
43174712 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTAAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTAAGT
43174777 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
** * *
43174805 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGTGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTC-CGAACTCGTTAAG
43174869 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
43174883 ACTTATAGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCGAACTCGTTAAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:43183465 original size:71 final size:69
Alignment explanation
Indices: 43183352--43183493 Score: 164
Period size: 71 Copynumber: 2.0 Consensus size: 69
43183342 GAAAGAAACG
*
43183352 TTTGAAAAATCAAAGAACGTTAGAAAAAGAAGTATTTGAGAAACCAAAGAAGAGCATTTGAAAGA
1 TTTGAAAAATCAAAGAACGTTAGAAAAAGAAGTATTTGAGAAACC---GAAGAGCATCTGAAAGA
43183417 AAAGCTT
63 AAAGCTT
* * * * *
43183424 TTTGAAAAA-CAGAGAGCGTTTA-AAAGAGAAGCT-TTTGAGAAACCGAAGAGTATCTGAAAGAC
1 TTTGAAAAATCAAAGAACG-TTAGAAAAAGAAG-TATTTGAGAAACCGAAGAGCATCTGAAAGAA
43183486 AAGCTT
64 AAGCTT
43183492 TT
1 TT
43183494 GAGAGAAGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
68 23 0.37
71 26 0.42
72 13 0.21
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (69 bp):
TTTGAAAAATCAAAGAACGTTAGAAAAAGAAGTATTTGAGAAACCGAAGAGCATCTGAAAGAAAA
GCTT
Found at i:43186078 original size:18 final size:18
Alignment explanation
Indices: 43186052--43186088 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
43186042 TTCAAATTCG
* *
43186052 AATTTGAATAACTTGAAT
1 AATTCGAATAAATTGAAT
43186070 AATTCGAATAAATTGAAT
1 AATTCGAATAAATTGAAT
43186088 A
1 A
43186089 TTAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (18 bp):
AATTCGAATAAATTGAAT
Found at i:43187029 original size:96 final size:96
Alignment explanation
Indices: 43186851--43187044 Score: 289
Period size: 96 Copynumber: 2.0 Consensus size: 96
43186841 TCGCTTCTTT
* *
43186851 TTGCTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCTTGGGCTCCTT
1 TTGCTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
* ** * * * *
43186916 GTCTGCTTTATCGTTCCCTTCGATGACAGAC
66 ATCTGCTCGATCATTCCCATCGATAACAAAC
* *
43186947 TTGCTCCTCTTTGCCCTCTTGGCTTCGGCTTTTCCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
1 TTGCTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
43187012 ATCTGCTCGATCATTCCCATCGATAACAAAC
66 ATCTGCTCGATCATTCCCATCGATAACAAAC
43187043 TT
1 TT
43187045 CCTCGGACAC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.13, C:0.34, G:0.17, T:0.36
Consensus pattern (96 bp):
TTGCTCCTCTTTGCCCTCTTGGCTTCGACTTTACCCTTGCTCGAACCAAGCTTCCTGGGCTCCGT
ATCTGCTCGATCATTCCCATCGATAACAAAC
Found at i:43191793 original size:26 final size:26
Alignment explanation
Indices: 43191742--43191793 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
43191732 AATAAACTAA
* * *
43191742 TAAATTTACCTTTAAAATACTTTTAT
1 TAAATTTACCTTTAAAAAAATATTAT
43191768 TAAATTTA-CTTTAAAAAAATAATTAT
1 TAAATTTACCTTTAAAAAAAT-ATTAT
43191794 ATCATTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATTTACCTTTAAAAAAATATTAT
Found at i:43191927 original size:25 final size:25
Alignment explanation
Indices: 43191899--43191949 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
43191889 TGCTTTCTTA
43191899 AAAACACTATTATCAAAAAGTATCC
1 AAAACACTATTATCAAAAAGTATCC
43191924 AAAACACTATTATCAAAAAGTATCC
1 AAAACACTATTATCAAAAAGTATCC
43191949 A
1 A
43191950 CTATCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.24
Consensus pattern (25 bp):
AAAACACTATTATCAAAAAGTATCC
Found at i:43193310 original size:14 final size:15
Alignment explanation
Indices: 43193284--43193313 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43193274 TTCTAATTCT
43193284 AAAAATTTAAAAAAA
1 AAAAATTTAAAAAAA
43193299 AAAAATTTAAAAAAA
1 AAAAATTTAAAAAAA
43193314 TTCATAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAATTTAAAAAAA
Found at i:43195082 original size:62 final size:60
Alignment explanation
Indices: 43194979--43195102 Score: 185
Period size: 62 Copynumber: 2.0 Consensus size: 60
43194969 AGCCGTATGA
* ** * *
43194979 GGTACACGGGCTAGCACACGGGCATGTGACCAGGCTGTGTGACTCATTGATTTGATAAATAG
1 GGTACAAGGGCTAGCACACGGGCATGTGACCAGGCCATGTGACAC-TAG-TTTGATAAATAG
43195041 GGTACAAGGGCTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
1 GGTACAAGGGCTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
43195101 GG
1 GG
43195103 CACATGGGTG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 14 0.25
61 2 0.04
62 41 0.72
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.22
Consensus pattern (60 bp):
GGTACAAGGGCTAGCACACGGGCATGTGACCAGGCCATGTGACACTAGTTTGATAAATAG
Found at i:43204131 original size:15 final size:15
Alignment explanation
Indices: 43204111--43204144 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
43204101 TTTATACACA
*
43204111 AAATGTGTGGTTAAT
1 AAATGTATGGTTAAT
43204126 AAATGTATGGTTAAT
1 AAATGTATGGTTAAT
43204141 AAAT
1 AAAT
43204145 ACTCAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (15 bp):
AAATGTATGGTTAAT
Found at i:43211660 original size:36 final size:36
Alignment explanation
Indices: 43211620--43211690 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
43211610 AGAGGTGAAA
* *
43211620 TATGATGCCTTAGAGGTAAGTATGAAAGAATAATGT
1 TATGATGCCTTAGAGGCAAGTATGAAAGAACAATGT
* * *
43211656 TATGATGCCTTGGAGGCGAGTATGGAAGAACAATG
1 TATGATGCCTTAGAGGCAAGTATGAAAGAACAATG
43211691 CTAATAGCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.30, T:0.27
Consensus pattern (36 bp):
TATGATGCCTTAGAGGCAAGTATGAAAGAACAATGT
Found at i:43212023 original size:60 final size:59
Alignment explanation
Indices: 43211919--43212056 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
43211909 ACTCTACAAT
* * ** * * *
43211919 AGTAGATATATAATGAACTCTCCAATAATGTAGTTTACTTAAATGGGTGAACTCTAAAAG
1 AGTAGATATATAATGAACTCTCCAATAAAG-AGTTCACGCAAATGAGTGAACACCAAAAG
* * *
43211979 TGTAGATATATAATGAACTCTCCGATGAAA-AGGTTCACGCAAATGAGTGAACACCATAAG
1 AGTAGATATATAATGAACTCTCCAAT-AAAGA-GTTCACGCAAATGAGTGAACACCAAAAG
*
43212039 AGTAGACATATAATGAAC
1 AGTAGATATATAATGAAC
43212057 GGTTCGCCTG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.02
60 61 0.95
61 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (59 bp):
AGTAGATATATAATGAACTCTCCAATAAAGAGTTCACGCAAATGAGTGAACACCAAAAG
Found at i:43214022 original size:26 final size:26
Alignment explanation
Indices: 43213993--43214047 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
43213983 TGGAATCATT
*
43213993 CCACTAAAGTACAATGATTGGACATG
1 CCACTAAAGAACAATGATTGGACATG
43214019 CCACTAAAGAACAATGATTGGACATG
1 CCACTAAAGAACAATGATTGGACATG
43214045 CCA
1 CCA
43214048 TTGACTACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (26 bp):
CCACTAAAGAACAATGATTGGACATG
Found at i:43214072 original size:12 final size:12
Alignment explanation
Indices: 43214055--43214080 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43214045 CCATTGACTA
43214055 CAAATAGTGTTG
1 CAAATAGTGTTG
43214067 CAAATAGTGTTG
1 CAAATAGTGTTG
43214079 CA
1 CA
43214081 TGTGATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (12 bp):
CAAATAGTGTTG
Found at i:43228662 original size:20 final size:20
Alignment explanation
Indices: 43228637--43228694 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
43228627 TGCGTAACAA
43228637 AGGCACCAAAGTGAAAAT-AG
1 AGGCACCAAAGTG-AAATCAG
*
43228657 AGGCA-CAAATGTGCAATCAG
1 AGGCACCAAA-GTGAAATCAG
* *
43228677 AGGCACCGAAGTGCAATC
1 AGGCACCAAAGTGAAATC
43228695 CTGTACAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 7 0.21
20 23 0.70
21 3 0.09
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.12
Consensus pattern (20 bp):
AGGCACCAAAGTGAAATCAG
Found at i:43230407 original size:22 final size:22
Alignment explanation
Indices: 43230382--43230454 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
43230372 AAATGTCCAA
43230382 TAAAAAACCCAATTAAAAATTC
1 TAAAAAACCCAATTAAAAATTC
** ** *
43230404 TAAAAAATTCAA--AAATGTCC
1 TAAAAAACCCAATTAAAAATTC
43230424 AATAAAAAACCCAATTAAAAATTC
1 --TAAAAAACCCAATTAAAAATTC
43230448 TAAAAAA
1 TAAAAAA
43230455 TTATCAATAT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
20 5 0.14
22 27 0.73
24 5 0.14
ACGTcount: A:0.62, C:0.15, G:0.01, T:0.22
Consensus pattern (22 bp):
TAAAAAACCCAATTAAAAATTC
Found at i:43230419 original size:44 final size:44
Alignment explanation
Indices: 43230369--43230456 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
43230359 CTATTGGAGA
43230369 CAAAAATGTCCAATAAAAAACCCAATTAAAAATTCTAAAAAATT
1 CAAAAATGTCCAATAAAAAACCCAATTAAAAATTCTAAAAAATT
43230413 CAAAAATGTCCAATAAAAAACCCAATTAAAAATTCTAAAAAATT
1 CAAAAATGTCCAATAAAAAACCCAATTAAAAATTCTAAAAAATT
43230457 ATCAATATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.23
Consensus pattern (44 bp):
CAAAAATGTCCAATAAAAAACCCAATTAAAAATTCTAAAAAATT
Found at i:43234243 original size:23 final size:24
Alignment explanation
Indices: 43234216--43234272 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
43234206 AATATTTACG
*
43234216 AAGTTAAGTG-AGTG-ATTAATTTA
1 AAGTTAA-TGAAGTGAATTAACTTA
43234239 AAGTTTAATGAAGTGAATTAACTTA
1 AAG-TTAATGAAGTGAATTAACTTA
43234264 AA-TTAATGA
1 AAGTTAATGA
43234273 TAGTTAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 12 0.40
24 8 0.27
25 10 0.33
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.37
Consensus pattern (24 bp):
AAGTTAATGAAGTGAATTAACTTA
Found at i:43234258 original size:25 final size:22
Alignment explanation
Indices: 43234226--43234272 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 22
43234216 AAGTTAAGTG
*
43234226 AGTGATTAATTTAAAGTTTAATGA
1 AGTGATTAACTTAAA--TTAATGA
43234250 AGTGAATTAACTTAAATTAATGA
1 AGTG-ATTAACTTAAATTAATGA
43234273 TAGTTAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 4 0.19
25 10 0.48
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (22 bp):
AGTGATTAACTTAAATTAATGA
Found at i:43235364 original size:3 final size:3
Alignment explanation
Indices: 43235356--43235409 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
43235346 GAATGGTAAG
43235356 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43235404 TAT TAT
1 TAT TAT
43235410 GGTATTGAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:43236004 original size:18 final size:18
Alignment explanation
Indices: 43235961--43236007 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
43235951 GACTGTCTGC
** *
43235961 TACTGAATAATTGACTGT
1 TACTGAATAAACGACTGA
43235979 TA-TAGAATAAACGACTGA
1 TACT-GAATAAACGACTGA
43235997 TACTGAATAAA
1 TACTGAATAAA
43236008 TGAATATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (18 bp):
TACTGAATAAACGACTGA
Found at i:43236018 original size:18 final size:19
Alignment explanation
Indices: 43235997--43236037 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
43235987 AAACGACTGA
43235997 TACTGAA-TAAATGAATAT
1 TACTGAATTAAATGAATAT
* *
43236015 TACT-AATTAACTGATTAT
1 TACTGAATTAAATGAATAT
43236033 TACTG
1 TACTG
43236038 TTGACTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
TACTGAATTAAATGAATAT
Found at i:43237608 original size:12 final size:13
Alignment explanation
Indices: 43237574--43237609 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
43237564 TTTCTTCCAT
43237574 GGAGATACTTTCA
1 GGAGATACTTTCA
43237587 GGAGATACTTTCA
1 GGAGATACTTTCA
43237600 GGA-ATACTTT
1 GGAGATACTTT
43237610 ATCACCAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (13 bp):
GGAGATACTTTCA
Found at i:43249097 original size:17 final size:18
Alignment explanation
Indices: 43249069--43249104 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
43249059 GTAATAAATT
43249069 TTTTTTGAAATTTTTTTA
1 TTTTTTGAAATTTTTTTA
43249087 TTTTTTG-AATTTTTTTA
1 TTTTTTGAAATTTTTTTA
43249104 T
1 T
43249105 AATCTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTTTGAAATTTTTTTA
Found at i:43250461 original size:13 final size:13
Alignment explanation
Indices: 43250443--43250467 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43250433 TGACGTTATG
43250443 AATAAAAAAATAC
1 AATAAAAAAATAC
43250456 AATAAAAAAATA
1 AATAAAAAAATA
43250468 AAACATTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAAAAATAC
Found at i:43252502 original size:46 final size:46
Alignment explanation
Indices: 43252415--43252578 Score: 131
Period size: 46 Copynumber: 3.6 Consensus size: 46
43252405 CAACATAATG
* * * * *
43252415 CCATAGTGCCTTTTAACTATGGTCTTACTCACTTTCTGTCATGTTGT
1 CCATAATGTCTTTCAACTATGGTCTTATTCACTTTCCGTCATGTT-T
* * *
43252462 -CATAATGTCTTTCAACCATGGTCTTATTTATTTTCCGTCATGTTT
1 CCATAATGTCTTTCAACTATGGTCTTATTCACTTTCCGTCATGTTT
* * * * *
43252507 CCATAGTGTCTTGCAACTATGGCCTTA-T-ACGTTTTCGAT-ATAG-TG
1 CCATAATGTCTTTCAACTATGGTCTTATTCAC-TTTCCG-TCAT-GTTT
*
43252552 CCATAGTGTCTTTCAACTATGGTCTTA
1 CCATAATGTCTTTCAACTATGGTCTTA
43252579 CACGTTTTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
44 1 0.01
45 35 0.36
46 60 0.62
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.43
Consensus pattern (46 bp):
CCATAATGTCTTTCAACTATGGTCTTATTCACTTTCCGTCATGTTT
Found at i:43252569 original size:45 final size:45
Alignment explanation
Indices: 43252507--43252630 Score: 160
Period size: 45 Copynumber: 2.8 Consensus size: 45
43252497 CGTCATGTTT
* * * *
43252507 CCATAGTGTCTTGCAACTATGGCCTTATACGTTTTCGATATAGTG
1 CCATAGTGTCTTTCAACTATGGTCTTACACGTTTTCGATATAATG
**
43252552 CCATAGTGTCTTTCAACTATGGTCTTACACGTTTTTTATATAATG
1 CCATAGTGTCTTTCAACTATGGTCTTACACGTTTTCGATATAATG
* *
43252597 CCATAGCT-CCTTTCAACTATGGTCTTACATGTTT
1 CCATAG-TGTCTTTCAACTATGGTCTTACACGTTT
43252631 GAATCGTGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
45 69 0.99
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (45 bp):
CCATAGTGTCTTTCAACTATGGTCTTACACGTTTTCGATATAATG
Found at i:43252643 original size:45 final size:45
Alignment explanation
Indices: 43252520--43252648 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 45
43252510 TAGTGTCTTG
* * * *
43252520 CAACTATGGCCTTATACGTTTTCG-ATATAGTGCCATAG-TGTCTTT
1 CAACTATGGTCTTACACGTTTT-GAATATAATGCCATAGCT-CCTTT
**
43252565 CAACTATGGTCTTACACGTTTTTTATATAATGCCATAGCTCCTTT
1 CAACTATGGTCTTACACGTTTTGAATATAATGCCATAGCTCCTTT
* * *
43252610 CAACTATGGTCTTACATG-TTTGAATCGTGATGCCATAGC
1 CAACTATGGTCTTACACGTTTTGAAT-ATAATGCCATAGC
43252649 GTATTTTACC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
44 5 0.07
45 65 0.92
46 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (45 bp):
CAACTATGGTCTTACACGTTTTGAATATAATGCCATAGCTCCTTT
Done.