Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 118 of 198
Found at i:37853540 original size:83 final size:82
Alignment explanation
Indices: 37853401--37853657 Score: 336
Period size: 83 Copynumber: 3.1 Consensus size: 82
37853391 AAAGCCCCTA
*
37853401 CTAAAGCCCCAGCGCACCAGCAGCGCTTATTGGAAAACGCCGCTAAAGCCTAGAGCATTAGTGGC
1 CTAAAG-CCCAGCGCATCAGCAGCGCTTATTGGAAAACGCCGCTAAAGCCTAGAGCATTAGTGGC
37853466 GCTTTTTCAAAAATGCCG
65 GCTTTTTCAAAAATGCCG
*
37853484 CTAAAGCCGCAGCGCATCAGCGGCGCTTATTGGAAAACGCCGCTAAAGCCTAGAGCATTAGTGGC
1 CTAAAGCC-CAGCGCATCAGCAGCGCTTATTGGAAAACGCCGCTAAAGCCTAGAGCATTAGTGGC
*
37853549 GCTTTTTCAGAAATGCCG
65 GCTTTTTCAAAAATGCCG
* * * * * ** * * * * *
37853567 CTAAATCCCAGAGCATTAGCAACGCTTTTTCAAAAATGCCACTAAA-TCTCAGAGCATTAGCGAC
1 CTAAAGCCCAGCGCATCAGCAGCGCTTATTGGAAAACGCCGCTAAAGCCT-AGAGCATTAGTGGC
*
37853631 GCTTTTTCAAAAACGCCG
65 GCTTTTTCAAAAATGCCG
37853649 CTAAAGCCC
1 CTAAAGCCC
37853658 CGAAAAGCTC
Statistics
Matches: 153, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
81 2 0.01
82 67 0.44
83 84 0.55
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (82 bp):
CTAAAGCCCAGCGCATCAGCAGCGCTTATTGGAAAACGCCGCTAAAGCCTAGAGCATTAGTGGCG
CTTTTTCAAAAATGCCG
Found at i:37853766 original size:40 final size:40
Alignment explanation
Indices: 37853719--37853827 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 40
37853709 CTAGAAAACT
*
37853719 CCGCTAATTCTCTATTTTTAGCGGCGATTTTC-AAAAAGCG
1 CCGCTAATACTCTATTTTTAGCGGCG-TTTTCTAAAAAGCG
* * *
37853759 CCTCTAATACTCTA-TTTTAGCGGCGTTTCCTTAAAAGCG
1 CCGCTAATACTCTATTTTTAGCGGCGTTTTCTAAAAAGCG
* *
37853798 CCGCTAATGCTCGATTTTTAGCGGCGTTTT
1 CCGCTAATACTCTATTTTTAGCGGCGTTTT
37853828 TTGTCCAAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 4 0.07
39 29 0.49
40 26 0.44
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (40 bp):
CCGCTAATACTCTATTTTTAGCGGCGTTTTCTAAAAAGCG
Found at i:37862001 original size:12 final size:11
Alignment explanation
Indices: 37861963--37862006 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
37861953 TATTTATAAC
37861963 TAAAAATAAAA
1 TAAAAATAAAA
** *
37861974 TGTAATTAAAA
1 TAAAAATAAAA
37861985 TAAAAATAAACA
1 TAAAAATAAA-A
37861997 TAAAAATAAA
1 TAAAAATAAA
37862007 TTTTATTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:37865198 original size:96 final size:96
Alignment explanation
Indices: 37865075--37865359 Score: 502
Period size: 96 Copynumber: 3.0 Consensus size: 96
37865065 TGGCCAAATG
*
37865075 AAATA-AG-GAATACAATTGAGGTATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
1 AAATAGAGAGAATACAATTGAGATATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
37865138 ATAAGGGTTTCCAATGTCCAATTAAATATCC
66 ATAAGGGTTTCCAATGTCCAATTAAATATCC
37865169 AAATAGAGAGAATACAATTGAGATATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
1 AAATAGAGAGAATACAATTGAGATATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
*
37865234 ATAAGGGTTTCCAATGTCAAATTAAATATCC
66 ATAAGGGTTTCCAATGTCCAATTAAATATCC
* *
37865265 AAATAGTGAGAATACAATTGAGATATCACTTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
1 AAATAGAGAGAATACAATTGAGATATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
* *
37865330 ATAAGGGTTTCTAGTGTCCAATTAAATATC
66 ATAAGGGTTTCCAATGTCCAATTAAATATC
37865360 TAACTAGAAA
Statistics
Matches: 182, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
94 5 0.03
95 2 0.01
96 175 0.96
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (96 bp):
AAATAGAGAGAATACAATTGAGATATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
ATAAGGGTTTCCAATGTCCAATTAAATATCC
Found at i:37865982 original size:43 final size:43
Alignment explanation
Indices: 37865934--37866019 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
37865924 GATGTGAGTC
*
37865934 TCGAAGCCCAATTTTAGACCCATGAATCTGATGGGGTCACATT
1 TCGAAGCCCAATTTTAGACCCATGAATCTAATGGGGTCACATT
37865977 TCGAAGCCCAATTTTAGACCCATGAATCTAATGGGGTCACATT
1 TCGAAGCCCAATTTTAGACCCATGAATCTAATGGGGTCACATT
37866020 ACCTCAAGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (43 bp):
TCGAAGCCCAATTTTAGACCCATGAATCTAATGGGGTCACATT
Found at i:37866960 original size:12 final size:12
Alignment explanation
Indices: 37866943--37866967 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37866933 CTTTTCCATC
37866943 TATCTTCTTTAT
1 TATCTTCTTTAT
37866955 TATCTTCTTTAT
1 TATCTTCTTTAT
37866967 T
1 T
37866968 GTTCCAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TATCTTCTTTAT
Found at i:37868847 original size:226 final size:225
Alignment explanation
Indices: 37868424--37868876 Score: 818
Period size: 226 Copynumber: 2.0 Consensus size: 225
37868414 CCAATTGCCT
*
37868424 TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTCAACTGAAATA
1 TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTCAACTAAAATA
* *
37868489 ATCACAGGTAAAGTAGAAGAGTTACCCAAAAAAAACATATTTAAGGTTAAATGGTAGTACCTTTA
66 ATCACAAGTAAAGTAGAAGAGTTACCCAAAAAAAACATATTTAAGGTGAAATGGTAGTACCTTTA
* *
37868554 ACTCTAACTTGGGTGGTTCTTCTGTTGAGGCTTTCAACTGCTTGTACTTATGGTATTCTAAATCT
131 ACTCTAACTTGGGTGGTTCTTCAGTTGAGGCTTTCAACTGCTTATACTTATGGTATTCTAAATCT
37868619 AAAGACTTGGAATGGGATTTGTGAAGTGAA
196 AAAGACTTGGAATGGGATTTGTGAAGTGAA
*
37868649 TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTGAACTAAAATA
1 TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTCAACTAAAATA
37868714 ATCACAAGTAAAGTAGAAGAGTTACCCAAAAAAAAACATATTTAAGGTGAAATGGTAGTACCTTT
66 ATCACAAGTAAAGTAGAAGAGTTACCC-AAAAAAAACATATTTAAGGTGAAATGGTAGTACCTTT
*
37868779 AACTCTAACTTGGGTGGTTCTTCAGTTGAGTCTTTCAACTGCTTATACTTATAGG-ATTCTAAAT
130 AACTCTAACTTGGGTGGTTCTTCAGTTGAGGCTTTCAACTGCTTATACTTAT-GGTATTCTAAAT
37868843 CTAAAGACTTGGAATGGGATTTGTGAAGTGAA
194 CTAAAGACTTGGAATGGGATTTGTGAAGTGAA
37868875 TC
1 TC
37868877 CCTTCAATTC
Statistics
Matches: 219, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
225 89 0.41
226 128 0.58
227 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (225 bp):
TCTTGAATTTCTTCAAGACATCAATCAGCTTCTATTCTTGATTCTCGGTTAATTCAACTAAAATA
ATCACAAGTAAAGTAGAAGAGTTACCCAAAAAAAACATATTTAAGGTGAAATGGTAGTACCTTTA
ACTCTAACTTGGGTGGTTCTTCAGTTGAGGCTTTCAACTGCTTATACTTATGGTATTCTAAATCT
AAAGACTTGGAATGGGATTTGTGAAGTGAA
Found at i:37880742 original size:12 final size:12
Alignment explanation
Indices: 37880725--37880764 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
37880715 TTATATGCCT
37880725 GTGTGCCAGGCC
1 GTGTGCCAGGCC
37880737 GTGTGCCAGGCC
1 GTGTGCCAGGCC
* *
37880749 ATGTGCTAGGCC
1 GTGTGCCAGGCC
37880761 GTGT
1 GTGT
37880765 AACAGCCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.28, G:0.40, T:0.23
Consensus pattern (12 bp):
GTGTGCCAGGCC
Found at i:37889462 original size:16 final size:16
Alignment explanation
Indices: 37889441--37889472 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37889431 AATAGAATTA
37889441 AATGGGAAAAAGATGG
1 AATGGGAAAAAGATGG
37889457 AATGGGAAAAAGATGG
1 AATGGGAAAAAGATGG
37889473 CAAAATATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (16 bp):
AATGGGAAAAAGATGG
Found at i:37898481 original size:24 final size:24
Alignment explanation
Indices: 37898449--37898510 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
37898439 GTGCTTCCCT
37898449 TTAAGTGCT-TTTCGGAGCTACCCG
1 TTAAGTGCTCTTT-GGAGCTACCCG
37898473 TTAAGTGCTCTTTGGAGCTACCCG
1 TTAAGTGCTCTTTGGAGCTACCCG
37898497 TTATAG-GCTCTTTG
1 TTA-AGTGCTCTTTG
37898511 TAAGCTTCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (24 bp):
TTAAGTGCTCTTTGGAGCTACCCG
Found at i:37898525 original size:25 final size:24
Alignment explanation
Indices: 37898464--37898526 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
37898454 TGCTTTTCGG
*
37898464 AGCTACCCGTTA-AGTGCTCTTTGG
1 AGCTACCCGTTATAG-GCTCTTTGA
37898488 AGCTACCCGTTATAGGCTCTTTGTA
1 AGCTACCCGTTATAGGCTCTTTG-A
* *
37898513 AGCTTCCCTTTATA
1 AGCTACCCGTTATA
37898527 TTTCCCGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.59
25 14 0.41
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (24 bp):
AGCTACCCGTTATAGGCTCTTTGA
Found at i:37904497 original size:24 final size:24
Alignment explanation
Indices: 37904470--37904517 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37904460 AAATTAGTAA
37904470 GTCAAATAAACTACACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
* * *
37904494 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
37904518 ACTAAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
GTCAAATAAACTACACTAATAAAT
Found at i:37906441 original size:24 final size:24
Alignment explanation
Indices: 37906414--37906461 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37906404 AAATTAGTAA
37906414 GTCAAATAAACTACACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
* * *
37906438 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
37906462 ACTAAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
GTCAAATAAACTACACTAATAAAT
Found at i:37908385 original size:24 final size:24
Alignment explanation
Indices: 37908358--37908405 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37908348 AAATTAGTAA
37908358 GTCAAATAAACTACACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
* * *
37908382 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTACACTAATAAAT
37908406 ACTAAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
GTCAAATAAACTACACTAATAAAT
Found at i:37909565 original size:20 final size:20
Alignment explanation
Indices: 37909506--37909588 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
37909496 CAAGCAATTC
*
37909506 TAACTTGTTTGAAAATCATTT
1 TAACTTGGTT-AAAATCATTT
* *
37909527 TGA--TGTGTTAAAATGATTT
1 TAACTTG-GTTAAAATCATTT
*
37909546 TAACTTGGTTGAAATCATTT
1 TAACTTGGTTAAAATCATTT
* *
37909566 TGACTAGGTTAAAATCATTT
1 TAACTTGGTTAAAATCATTT
37909586 TAA
1 TAA
37909589 ATTGATTTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.27
20 32 0.65
21 4 0.08
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (20 bp):
TAACTTGGTTAAAATCATTT
Found at i:37909577 original size:40 final size:40
Alignment explanation
Indices: 37909506--37909588 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
37909496 CAAGCAATTC
* *
37909506 TAACTTGTTTGAAAATCATTTTGATGTGTTAAAATGATTT
1 TAACTTGGTTGAAAATCATTTTGATGTGTTAAAATCATTT
37909546 TAACTTGGTTG-AAATCATTTTGACTAG-GTTAAAATCATTT
1 TAACTTGGTTGAAAATCATTTTGA-T-GTGTTAAAATCATTT
37909586 TAA
1 TAA
37909589 ATTGATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 12 0.31
40 26 0.67
41 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (40 bp):
TAACTTGGTTGAAAATCATTTTGATGTGTTAAAATCATTT
Found at i:37912782 original size:14 final size:14
Alignment explanation
Indices: 37912763--37912805 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
37912753 AATATTAATT
37912763 ATTTAAATAATTAA
1 ATTTAAATAATTAA
*
37912777 ATTTAATTAATT-A
1 ATTTAAATAATTAA
**
37912790 ATTTAACCAATTAA
1 ATTTAAATAATTAA
37912804 AT
1 AT
37912806 AATTTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTAAATAATTAA
Found at i:37919099 original size:21 final size:19
Alignment explanation
Indices: 37919052--37919094 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
37919042 TTTTATTTTT
*
37919052 TTCTTA-TTTTTAATATTTA
1 TTCTTAGTTTTTAA-ATTTC
37919071 TTCTTAGTTTTTAAATTTC
1 TTCTTAGTTTTTAAATTTC
37919090 TTCTT
1 TTCTT
37919095 TTAGTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
TTCTTAGTTTTTAAATTTC
Found at i:37920265 original size:63 final size:62
Alignment explanation
Indices: 37920194--37920397 Score: 169
Period size: 63 Copynumber: 3.2 Consensus size: 62
37920184 ATTGTTCATT
*
37920194 ATCGTAAATCAATGAACTTAGGTTGTGATCATAAATCAGCGAACCTTATTAATAACAGTTGTG
1 ATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTTA-TAATAACAGTTGTG
* * * * * * * * *
37920257 ATCATAAATTAACGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAA-CTTAGAA-AAGATTGTT
1 ATCGTAAATCAATGA---ACTTAG-GTTGTGATCGTAAATCAGCGAACCTTATAATAACA--G-T
37920320 TGTG
59 TGTG
* * * * **
37920324 ATCGTAAATCAATGAACTTAGGCTGTGATCGTAAATCAGGGAGCCTTAATAATATCAAATGTG
1 ATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTT-ATAATAACAGTTGTG
37920387 ATCGTAAATCA
1 ATCGTAAATCA
37920398 GCAAGTTGTT
Statistics
Matches: 106, Mismatches: 25, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
63 44 0.42
64 10 0.09
65 5 0.05
66 11 0.10
67 36 0.34
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (62 bp):
ATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTTATAATAACAGTTGTG
Found at i:37920328 original size:130 final size:130
Alignment explanation
Indices: 37920111--37920493 Score: 496
Period size: 130 Copynumber: 2.9 Consensus size: 130
37920101 CAGTGTTACA
* * *
37920111 AATAATATCAGTTGTGATTGTAAATCAGCGAGCTATTTGGAATTGCGATTGTAAATCAGCTAACT
1 AATAATATCAGTTGTGATCGTAAATCAGCGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
* * * *
37920176 CAAAAAAAATTGTTCATTATCGTAAATCAATGAACTTAGGTTGTGATCATAAATCAGCGAACCTT
66 CAGAAAAGATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTT
* * * * *
37920241 ATTAATAACAGTTGTGATCATAAATTAACGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
1 AATAATATCAGTTGTGATCGTAAATCAGCGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
* ** * * *
37920306 TAGAAAAGATTGTTTGTGATCGTAAATCAATGAACTTAGGCTGTGATCGTAAATCAGGGAGCCTT
66 CAGAAAAGATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTT
** * * * **
37920371 AATAATATCAAATGTGATCGTAAATCAGCAAGTTGTTTGGAGTTATGATCGTAAATCAGCTAACT
1 AATAATATCAGTTGTGATCGTAAATCAGCGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
* * * * *
37920436 CAGAGAAGATTGTTCCTGATCGTTAATCAATGAACTTAGCTTGTGAACGTAAATCAGC
66 CAGAAAAGATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGC
37920494 AAGCTGTTTG
Statistics
Matches: 214, Mismatches: 39, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
130 214 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (130 bp):
AATAATATCAGTTGTGATCGTAAATCAGCGAGCTATTTGGAGTTGCGATCGTAAATCAGCTAACT
CAGAAAAGATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAACCTT
Found at i:37920586 original size:94 final size:94
Alignment explanation
Indices: 37920383--37920566 Score: 260
Period size: 94 Copynumber: 2.0 Consensus size: 94
37920373 TAATATCAAA
* * ** * *
37920383 TGTGATCGTAAATCAGCAAGTTGTTTGGAGTTATGATCGTAAATCAGCTAACTCAGAGAAGATTG
1 TGTGAACGTAAATCAGCAAGCTGTTTGGAGTTACAATCATAAATAAGCTAACTCAGAGAAGATTG
* *
37920448 TTCCTGATCGTTAATCAATGAACTTAGCT
66 TTCCTGATCATAAATCAATGAACTTAGCT
* *
37920477 TGTGAACGTAAATCAGCAAGCTGTTTGGAGTTGCAATCATAAATAAGCTAACTTAGAGAAGATTG
1 TGTGAACGTAAATCAGCAAGCTGTTTGGAGTTACAATCATAAATAAGCTAACTCAGAGAAGATTG
**
37920542 TTTGTGATCATAAATCAATGAACTT
66 TTCCTGATCATAAATCAATGAACTT
37920567 GGGCTGTAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (94 bp):
TGTGAACGTAAATCAGCAAGCTGTTTGGAGTTACAATCATAAATAAGCTAACTCAGAGAAGATTG
TTCCTGATCATAAATCAATGAACTTAGCT
Found at i:37924086 original size:27 final size:25
Alignment explanation
Indices: 37924028--37924090 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 25
37924018 GGCGGCTAGG
37924028 GAAAAGAAAAAGAAGAAAAGAAAAA
1 GAAAAGAAAAAGAAGAAAAGAAAAA
** *
37924053 GGGAAGAAAATGAAGGAAAATGAAAAA
1 GAAAAGAAAAAGAA-GAAAA-GAAAAA
37924080 GAAAAGAAAAA
1 GAAAAGAAAAA
37924091 AGAAAAAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 11 0.37
26 5 0.17
27 14 0.47
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (25 bp):
GAAAAGAAAAAGAAGAAAAGAAAAA
Found at i:37928276 original size:23 final size:23
Alignment explanation
Indices: 37928246--37928291 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
37928236 TTTAACAGAG
37928246 TGTAAGCTTCAAATTGCCCATGA
1 TGTAAGCTTCAAATTGCCCATGA
37928269 TGTAAGCTTCAAATTGCCCATGA
1 TGTAAGCTTCAAATTGCCCATGA
37928292 AGAACATACC
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:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (23 bp):
TGTAAGCTTCAAATTGCCCATGA
Found at i:37932542 original size:28 final size:28
Alignment explanation
Indices: 37932510--37932563 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
37932500 GACATTACCG
*
37932510 TAAATGTAAAAGTCTGTCAAGACTATCA
1 TAAATGTAAAAGTCTATCAAGACTATCA
** *
37932538 TAAATGTGGAAGTCTATCAGGACTAT
1 TAAATGTAAAAGTCTATCAAGACTAT
37932564 TGTATATCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (28 bp):
TAAATGTAAAAGTCTATCAAGACTATCA
Found at i:37932619 original size:24 final size:24
Alignment explanation
Indices: 37932554--37932620 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
37932544 TGGAAGTCTA
* * *
37932554 TCAGGACTATTGTATATCTGGAAG
1 TCAGAACTATCGTATATGTGGAAG
*
37932578 TCAGAACTATCATATATGTGGAAG
1 TCAGAACTATCGTATATGTGGAAG
* *
37932602 TTAGTACTATCGTATATGT
1 TCAGAACTATCGTATATGT
37932621 CGAGGTCCGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (24 bp):
TCAGAACTATCGTATATGTGGAAG
Found at i:37932638 original size:28 final size:28
Alignment explanation
Indices: 37932601--37932667 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
37932591 ATATGTGGAA
* * *
37932601 GTTAGTACTATCGTATATGTCGAGGTCC
1 GTTAGGACTATCGTAAATGTCGAAGTCC
* * * *
37932629 GTTATGACTATCTTAAATGTGGAAGTTC
1 GTTAGGACTATCGTAAATGTCGAAGTCC
37932657 GTTAGGACTAT
1 GTTAGGACTAT
37932668 ATTTTAAGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (28 bp):
GTTAGGACTATCGTAAATGTCGAAGTCC
Found at i:37935101 original size:51 final size:51
Alignment explanation
Indices: 37934983--37935167 Score: 212
Period size: 51 Copynumber: 3.6 Consensus size: 51
37934973 TTATCATTCA
* * * * *
37934983 ATACACGTAGTAGTCTTCACATAGTACTACACACGTGA-TAAAACTTTCCG
1 ATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCG
* *
37935033 ATTCACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAGCCTTCCG
1 ATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCG
* * ** * *
37935084 GTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCTAT-TG
1 ATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCT-TCCG
* *
37935135 ACACACGTAGTAGCCTGCACTTAGTACTACACA
1 ATACACGTAGTAGCCTGCACATAGTACTACACA
37935168 CGTGTTTATA
Statistics
Matches: 114, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
50 34 0.30
51 79 0.69
52 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (51 bp):
ATACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAAAACCTTCCG
Found at i:37938577 original size:16 final size:16
Alignment explanation
Indices: 37938556--37938600 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
37938546 TTTAGGGGCA
37938556 AAAATGTAATTTTGCC
1 AAAATGTAATTTTGCC
37938572 AAAATGTAATTTTGCC
1 AAAATGTAATTTTGCC
*
37938588 AAAATGTGATTTT
1 AAAATGTAATTTT
37938601 TGGACTGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (16 bp):
AAAATGTAATTTTGCC
Found at i:37938988 original size:51 final size:51
Alignment explanation
Indices: 37938823--37939018 Score: 193
Period size: 51 Copynumber: 3.9 Consensus size: 51
37938813 AGTGAAAGTG
* * *
37938823 ATGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-ATGA
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATATTA
* * * * * * * *
37938873 AAGGTCGCATGTCTCGTACTATATGCAGGCTACTATGCGTA-CTGGATAGCTT-
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATC-GGATA--TTA
* * *
37938925 -CGATCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGATATTA
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATATTA
* *
37938975 ATGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCG
37939019 AATGATAATA
Statistics
Matches: 114, Mismatches: 25, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
49 3 0.03
50 35 0.31
51 74 0.65
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATATTA
Found at i:37945915 original size:51 final size:50
Alignment explanation
Indices: 37945789--37945973 Score: 176
Period size: 51 Copynumber: 3.7 Consensus size: 50
37945779 TATCATTCGA
* * * *
37945789 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTTCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACATGATCAAACCTTCCGG
* * *
37945839 TTCACGTAGTAGCATGCCCATAGTACTACACACATGA-CGAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACATGATC-AAA-CCTTCCGG
* ** * * * *
37945890 TACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACATGATCA-AACCT-TCCGG
* *
37945941 TACACGTAGTAGTCTGCACTTAGTACTACACAC
1 TACACGTAGTAGCCTGCACATAGTACTACACAC
37945974 GTGTTTATAG
Statistics
Matches: 110, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
49 1 0.01
50 35 0.32
51 71 0.65
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACATGATCAAACCTTCCGG
Found at i:37956357 original size:19 final size:18
Alignment explanation
Indices: 37956321--37956360 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
37956311 ATGTATATGC
37956321 ATATATTAAAATACGTAT
1 ATATATTAAAATACGTAT
* *
37956339 ATATATGTATAATATGTAT
1 ATATAT-TAAAATACGTAT
37956358 ATA
1 ATA
37956361 AAAAATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (18 bp):
ATATATTAAAATACGTAT
Found at i:37958376 original size:44 final size:44
Alignment explanation
Indices: 37958319--37958472 Score: 145
Period size: 44 Copynumber: 3.6 Consensus size: 44
37958309 TATGCGATCT
* *
37958319 GCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
* * *** *
37958363 GCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATACGATCT
1 GCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
** * *
37958404 ATTCTAC-GACAACTTCAGAGAGATGAGATCTGTGGTTTTAATCC
1 GCTCCACTG-CAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
* *
37958448 GCTCCACTGTAGCTTCAGAGAGATA
1 GCTCCACTGCAACTTCAGAGAGATA
37958473 GGATTGGTAC
Statistics
Matches: 81, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
40 1 0.01
41 28 0.35
42 1 0.01
43 1 0.01
44 49 0.60
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
Found at i:37958392 original size:85 final size:85
Alignment explanation
Indices: 37958287--37958472 Score: 257
Period size: 85 Copynumber: 2.2 Consensus size: 85
37958277 TACTCTACTA
* ** * * *
37958287 CAACTTCATGGAGATAAGACTTTATGCGATCTGCTCTACTG-CAACTTTAGAGAGATAAGATCTG
1 CAACTTCAGGGAGATAAGACTGGATACGATCTACTCTAC-GACAACTTCAGAGAGATAAGATCTG
37958351 TGGTTTTAATCCGCTCCACTG
65 TGGTTTTAATCCGCTCCACTG
* *
37958372 CAACTTCAGGGAGATAAGACTGGATACGATCTATTCTACGACAACTTCAGAGAGATGAGATCTGT
1 CAACTTCAGGGAGATAAGACTGGATACGATCTACTCTACGACAACTTCAGAGAGATAAGATCTGT
37958437 GGTTTTAATCCGCTCCACTG
66 GGTTTTAATCCGCTCCACTG
* * *
37958457 TAGCTTCAGAGAGATA
1 CAACTTCAGGGAGATA
37958473 GGATTGGTAC
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 1 0.01
85 88 0.99
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (85 bp):
CAACTTCAGGGAGATAAGACTGGATACGATCTACTCTACGACAACTTCAGAGAGATAAGATCTGT
GGTTTTAATCCGCTCCACTG
Found at i:37958543 original size:50 final size:50
Alignment explanation
Indices: 37958484--37958641 Score: 201
Period size: 50 Copynumber: 3.2 Consensus size: 50
37958474 GATTGGTACA
37958484 TTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
1 TTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
** * ** * * * *
37958534 TTCAATCTGTTCCACTGCACA-GCCGGGGAAGTAAAATTCACCGTTGTGGC
1 TTCAATCTGTTTAACTGCA-ATGTCGGGGAAACAAGATTCGCCGTCGTAGC
* *
37958584 TTCAATCTATTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
1 TTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
37958634 TTCAATCT
1 TTCAATCT
37958642 ATTCCACTAC
Statistics
Matches: 86, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
49 1 0.01
50 84 0.98
51 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (50 bp):
TTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
Found at i:37958642 original size:50 final size:50
Alignment explanation
Indices: 37958484--37958694 Score: 199
Period size: 50 Copynumber: 4.2 Consensus size: 50
37958474 GATTGGTACA
*
37958484 TTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
1 TTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
* ** * ** * * * *
37958534 TTCAATCTGTTCCACTGCACA-GCCGGGGAAGTAAAATTCACCGTTGTGGC
1 TTCAATCTATTTAACTGCA-ATGTCGGGGAAACAAGATTCGCCGTCGTAGC
*
37958584 TTCAATCTATTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
1 TTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
** * * ** * ** * *
37958634 TTCAATCTATTCCACTACACTACCAGGGAAGTAAGATTCGCCGTTGTGGC
1 TTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
37958684 TTCAATCTATT
1 TTCAATCTATT
37958695 CCACTGTAAT
Statistics
Matches: 127, Mismatches: 32, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
49 1 0.01
50 125 0.98
51 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (50 bp):
TTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGC
Found at i:37958663 original size:100 final size:100
Alignment explanation
Indices: 37958484--37958694 Score: 343
Period size: 100 Copynumber: 2.1 Consensus size: 100
37958474 GATTGGTACA
* *
37958484 TTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCAC
* *
37958549 TGCACAGCCGGGGAAGTAAAATTCACCGTTGTGGC
66 TACACAGCCAGGGAAGTAAAATTCACCGTTGTGGC
*
37958584 TTCAATCTATTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCAC
1 TTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCAC
* *
37958649 TACACTA-CCAGGGAAGTAAGATTCGCCGTTGTGGC
66 TACAC-AGCCAGGGAAGTAAAATTCACCGTTGTGGC
37958684 TTCAATCTATT
1 TTCAATCTATT
37958695 CCACTGTAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 102 0.99
101 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (100 bp):
TTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCAC
TACACAGCCAGGGAAGTAAAATTCACCGTTGTGGC
Found at i:37958695 original size:50 final size:50
Alignment explanation
Indices: 37958507--37958700 Score: 201
Period size: 50 Copynumber: 3.9 Consensus size: 50
37958497 ACTGCAATGT
** *
37958507 CGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCAC-AGC
1 CGGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACTA-C
* * * * ** * * **
37958557 CGGGGAAGTAAAATTCACCGTTGTGGCTTCAATCTATTTAATTGCAATGT
1 CGGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACTAC
** *
37958607 CGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACTAC
1 CGGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACTAC
* * *
37958657 CAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTG
1 CGGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTG
37958701 TAATGCCAAA
Statistics
Matches: 111, Mismatches: 32, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
50 111 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (50 bp):
CGGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACTAC
Found at i:37958996 original size:88 final size:88
Alignment explanation
Indices: 37958884--37959068 Score: 280
Period size: 88 Copynumber: 2.1 Consensus size: 88
37958874 CATTACAACG
* * * * * * *
37958884 TCAAGGCGAGAAGACTGGTGTCTTCGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTA
1 TCAAGGAGACAAGACTGGTATCTTCGATCTACTTCACTGCCAATACAAGAAGACAAGATCTGCTA
*
37958949 TTTTCAACCTACTCCACTGCTGC
66 TTTTCAACCTACTCCACTACTGC
* *
37958972 TCAGGGAGACAAGACTGGTATCTTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTA
1 TCAAGGAGACAAGACTGGTATCTTCGATCTACTTCACTGCCAATACAAGAAGACAAGATCTGCTA
37959037 TTTTCAACCTACTCCACTACTGC
66 TTTTCAACCTACTCCACTACTGC
37959060 TCAAGGAGA
1 TCAAGGAGA
37959069 TAAGGCTGAA
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (88 bp):
TCAAGGAGACAAGACTGGTATCTTCGATCTACTTCACTGCCAATACAAGAAGACAAGATCTGCTA
TTTTCAACCTACTCCACTACTGC
Found at i:37963619 original size:8 final size:8
Alignment explanation
Indices: 37963606--37963631 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
37963596 ATGATGTGGA
37963606 AAAAGAAT
1 AAAAGAAT
37963614 AAAAGAAT
1 AAAAGAAT
37963622 AAAAGAAT
1 AAAAGAAT
37963630 AA
1 AA
37963632 TTACTCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAGAAT
Found at i:37970980 original size:15 final size:14
Alignment explanation
Indices: 37970956--37970987 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
37970946 CAAAATAAGT
37970956 GTATATATATATAA
1 GTATATATATATAA
37970970 GTATGATATATATAA
1 GTAT-ATATATATAA
37970985 GTA
1 GTA
37970988 AAACTTGAAA
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:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (14 bp):
GTATATATATATAA
Found at i:37971043 original size:35 final size:35
Alignment explanation
Indices: 37971004--37971077 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
37970994 GAAAATATGT
** ** * *
37971004 ATATGCATATATTAAAATACGTATATATATGTATA
1 ATATGCATATAAAAAAATAAATATATATATATAAA
*
37971039 ATATGTATATAAAAAAATAAATATATATATATAAA
1 ATATGCATATAAAAAAATAAATATATATATATAAA
37971074 ATAT
1 ATAT
37971078 TTATAATAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (35 bp):
ATATGCATATAAAAAAATAAATATATATATATAAA
Found at i:37971046 original size:19 final size:18
Alignment explanation
Indices: 37971010--37971076 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
37971000 ATGTATATGC
37971010 ATATATTAAAATACGTAT
1 ATATATTAAAATACGTAT
* *
37971028 ATATATGTATAATATGTAT
1 ATATAT-TAAAATACGTAT
* **
37971047 ATA-A-AAAAATAAATAT
1 ATATATTAAAATACGTAT
37971063 ATATATATAAAATA
1 ATATAT-TAAAATA
37971077 TTTATAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 11 0.29
17 1 0.03
18 7 0.18
19 19 0.50
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (18 bp):
ATATATTAAAATACGTAT
Found at i:37971576 original size:3 final size:3
Alignment explanation
Indices: 37971568--37971600 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
37971558 ATGACAACAG
*
37971568 TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37971601 CAAACTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:37972953 original size:19 final size:19
Alignment explanation
Indices: 37972929--37972994 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
37972919 AAAAATTATA
37972929 AAAAATATTTTTAAAAATT
1 AAAAATATTTTTAAAAATT
* ** *
37972948 AAAAAT-TATTATAATTATA
1 AAAAATAT-TTTTAAAAATT
* *
37972967 AAAAATGTTTTTAAAATTT
1 AAAAATATTTTTAAAAATT
*
37972986 TAAAATATT
1 AAAAATATT
37972995 AATTAAATAC
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
18 1 0.03
19 32 0.94
20 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAAATATTTTTAAAAATT
Found at i:37972970 original size:37 final size:38
Alignment explanation
Indices: 37972898--37972996 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
37972888 ACATTTAGTT
* * *
37972898 TTTTTTAAAATTTATAATTATAAAAATTATAAAAAATA
1 TTTTTAAAAATTTAAAATTATTAAAATTATAAAAAATA
* * *
37972936 TTTTTAAAAATTAAAAATTATTATAATTATAAAAAATG
1 TTTTTAAAAATTTAAAATTATTAAAATTATAAAAAATA
*
37972974 TTTTTAAAATTTTAAAA-TATTAA
1 TTTTTAAAAATTTAAAATTATTAA
37972997 TTAAATACTA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
37 5 0.10
38 47 0.90
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
TTTTTAAAAATTTAAAATTATTAAAATTATAAAAAATA
Found at i:37974279 original size:9 final size:9
Alignment explanation
Indices: 37974262--37974298 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
37974252 TGAGTTTTCA
37974262 AATTCGAAT
1 AATTCGAAT
*
37974271 AACTCGAAT
1 AATTCGAAT
37974280 AATTCGAAT
1 AATTCGAAT
37974289 AATTCGAAT
1 AATTCGAAT
37974298 A
1 A
37974299 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:37986083 original size:27 final size:27
Alignment explanation
Indices: 37986045--37986130 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
37986035 TATTCTTGGC
37986045 GAACTCTGAAGGTGTAGTAAGTATGGT
1 GAACTCTGAAGGTGTAGTAAGTATGGT
** * *
37986072 GAACTCTGAAGGAATAATATA-TATGGC
1 GAACTCTGAAGGTGTAGTA-AGTATGGT
* * *
37986099 GAACTCTAAAGATGCAGTAAGTATGGT
1 GAACTCTGAAGGTGTAGTAAGTATGGT
37986126 GAACT
1 GAACT
37986131 TTATAGGAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 1 0.02
27 44 0.96
28 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (27 bp):
GAACTCTGAAGGTGTAGTAAGTATGGT
Found at i:37986118 original size:54 final size:54
Alignment explanation
Indices: 37986041--37986143 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
37986031 ATGGTATTCT
* * *
37986041 TGGCGAACTCTGAAGGTGTAGTAAGTATGGTGAACTCTGA-AGGAATAATATATA
1 TGGCGAACTCTAAAGATGCAGTAAGTATGGTGAACT-TGATAGGAATAATATATA
*
37986095 TGGCGAACTCTAAAGATGCAGTAAGTATGGTGAACTTTATAGGAATAAT
1 TGGCGAACTCTAAAGATGCAGTAAGTATGGTGAACTTGATAGGAATAAT
37986144 GTGTACAGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 2 0.05
54 42 0.95
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (54 bp):
TGGCGAACTCTAAAGATGCAGTAAGTATGGTGAACTTGATAGGAATAATATATA
Found at i:37986155 original size:54 final size:54
Alignment explanation
Indices: 37986043--37986165 Score: 149
Period size: 54 Copynumber: 2.3 Consensus size: 54
37986033 GGTATTCTTG
* * * **
37986043 GCGAACTCTGAAGGTGTAGTAAGTATGGTGAACTCTGAAGGAATAATATATATG
1 GCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGAAGGAATAATATATACA
* * *
37986097 GCGAACTCTAAAGATGCAGTAAGTATGGTGAACT-TTATAGGAATAATGTGTACA
1 GCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGA-AGGAATAATATATACA
37986151 GCGAACTCTGAAAGA
1 GCGAACTCT-AAAGA
37986166 AAGGCTTCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
53 2 0.03
54 52 0.88
55 5 0.08
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (54 bp):
GCGAACTCTAAAGATGCAGTAAGTATGGTGAACTCTGAAGGAATAATATATACA
Found at i:38004288 original size:15 final size:16
Alignment explanation
Indices: 38004268--38004304 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
38004258 ATCGTTAAAA
38004268 TTATTATC-ATTGTAT
1 TTATTATCTATTGTAT
38004283 TTATTA-CTATTGTAT
1 TTATTATCTATTGTAT
*
38004298 TTGTTAT
1 TTATTAT
38004305 TACGATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (16 bp):
TTATTATCTATTGTAT
Found at i:38016262 original size:44 final size:43
Alignment explanation
Indices: 38016210--38016764 Score: 260
Period size: 44 Copynumber: 12.8 Consensus size: 43
38016200 TATCGCATCT
* *
38016210 AGTCTTATCTCCCTGAAGTTGTAGTGGAGTAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
** * * *
38016254 AGTCTTATC-CTTTTGAAGTTGCAGT-GAGGCAGAATGAAGATGGAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * * *
38016299 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAG-GTTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * *
38016342 TAATCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAGGAA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
*
38016387 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGATTGAAGATAGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * *
38016432 AATCTTATCTCCCTGAAGTTGCAGAGGAGCAG-GTTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * ** * * *
38016475 TAATCCTATCTTCCTGAAGTTGCAGTAGAGTGGATTAA-AACCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * * * * *
38016519 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
38016560 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * * * ** * * *
38016604 AATCCTATCTTCATGAAGTTGCAGTGGAGTGGATTAA-AACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* ** * * * * * *
38016647 GGATCTTATCTTTCTGAAGTTGCAG-AGAGTAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* *
38016688 AGTCTTATCTCCCTGAAGTTGAAGTGGAGCAGACTAAGTAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* **
38016732 AGTCTTATCTCTCTGAAGTTGCAGCAGAGCAGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
38016765 TCACATCAAA
Statistics
Matches: 382, Mismatches: 94, Indels: 70
0.70 0.17 0.13
Matches are distributed among these distances:
40 40 0.10
41 20 0.05
42 14 0.04
43 24 0.06
44 212 0.55
45 64 0.17
46 6 0.02
47 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:38016360 original size:89 final size:89
Alignment explanation
Indices: 38016267--38016463 Score: 208
Period size: 89 Copynumber: 2.2 Consensus size: 89
38016257 CTTATCCTTT
*
38016267 TGAAGTTGCAGT-GAGGCAGAATGAAG-ATGGAAAATCTTAT-CTCCCTAAAGTTGTAGTG-GAG
1 TGAAGTTGCAGTGGA-GCAGAAT-AAGTA-GGAAAATCTTATCCT-CCTAAAGTTGCAGTGAG-G
* *
38016328 CAGGTTAAAG-CCG-ATAATCTTATCTCCC
61 CAGATTAAAGACAGCA-AATCTTATCTCCC
* * * *
38016356 TGAAGTTGCAATGGAGCAGACTAAGTAGGAAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGAT
1 TGAAGTTGCAGTGGAGCAGAATAAGTAGGAAAATCTTATCCTCCTAAAGTTGCAGTGAGGCAGAT
* *
38016421 TGAAGATAGCAAATCTTATCTCCC
66 TAAAGACAGCAAATCTTATCTCCC
*
38016445 TGAAGTTGCAGAGGAGCAG
1 TGAAGTTGCAGTGGAGCAG
38016464 GTTAAAGCCG
Statistics
Matches: 91, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
88 36 0.40
89 52 0.57
90 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (89 bp):
TGAAGTTGCAGTGGAGCAGAATAAGTAGGAAAATCTTATCCTCCTAAAGTTGCAGTGAGGCAGAT
TAAAGACAGCAAATCTTATCTCCC
Found at i:38016371 original size:133 final size:133
Alignment explanation
Indices: 38016212--38016498 Score: 439
Period size: 133 Copynumber: 2.2 Consensus size: 133
38016202 TCGCATCTAG
* * * * **
38016212 TCTTATCTCCCTGAAGTTGTAGTGGAGTAGACTAAGTAAGCAAGTCTTATCCTTTTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGAAAGTCTTATCCTCCTGAAGTTGCA
* * *
38016277 GTGAGGCAGAATGAAGATGGAAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGGTTAAAGCCGA
66 GTGAGGCAGAATGAAGATAGAAAATCTTATCTCCCTAAAGTTGCAGAGGAGCAGGTTAAAGCCGA
38016342 TAA
131 TAA
*
38016345 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAGGAAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGAAAGTCTTATCCTCCTGAAGTTGCA
* * *
38016410 GTGAGGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGAGGAGCAGGTTAAAGCCGA
66 GTGAGGCAGAATGAAGATAGAAAATCTTATCTCCCTAAAGTTGCAGAGGAGCAGGTTAAAGCCGA
38016475 TAA
131 TAA
* *
38016478 TCCTATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCA
38016499 GTAGAGTGGA
Statistics
Matches: 139, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 139 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (133 bp):
TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGAAAGTCTTATCCTCCTGAAGTTGCA
GTGAGGCAGAATGAAGATAGAAAATCTTATCTCCCTAAAGTTGCAGAGGAGCAGGTTAAAGCCGA
TAA
Found at i:38016526 original size:133 final size:132
Alignment explanation
Indices: 38016256--38016719 Score: 445
Period size: 128 Copynumber: 3.6 Consensus size: 132
38016246 AGTAAGCAAG
** * * * *
38016256 TCTTATCCTTTTGAAGTTGCAGTGAGGCAGAATGAAGATGGAAAATCTTATCTCCCTAAAGTTGT
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGAT-GCAAATCTTATCTCCCTGAAGTTGC
* * * ** * * *
38016321 AGTGGAGCAGGTTAAAGCCGATAATCTTATCTCCCTGAAGTTGCAATGGAGCAGACT--AA-GTA
65 AGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCTT
38016383 GGAAA
130 GG--A
38016388 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTG
1 -TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGAT-GCAAATCTTATCTCCCTGAAGTTG
* *
38016453 CAGAGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTAGAGTGGATTAAAACCT
64 CAGTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCT
38016518 TGGA
129 TGGA
* * * * *
38016522 TCTTAT-CTCTCTGAAGTTGCAGAGA-GCAGATCG--CAT-CTAGTCTTATCTCCCTGAAGTTGC
1 TCTTATCCTC-CTGAAGTTGCAGTGAGGCAGATTGAAGATGCAAATCTTATCTCCCTGAAGTTGC
* * *
38016582 AGTGGAGCAGACTAAGTAAG-C-A-AATCCTATCTTCATGAAGTTGCAGTGGAGTGGATTAAAAC
65 AGTGGAGCAG-GTTA--AAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAAC
38016644 CTTGGA
127 CTTGGA
* * * * * * * * *
38016650 TCTTATCTTTCTGAAGTTGCAGAGA-GTAGATCG--CAT-CTAGTCTTATCTCCCTGAAGTTGAA
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGATGCAAATCTTATCTCCCTGAAGTTGCA
38016711 GTGGAGCAG
66 GTGGAGCAG
38016720 ACTAAGTAGG
Statistics
Matches: 292, Mismatches: 31, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
128 139 0.48
129 4 0.01
130 3 0.01
131 3 0.01
132 10 0.03
133 127 0.43
134 1 0.00
135 2 0.01
136 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGATGCAAATCTTATCTCCCTGAAGTTGCA
GTGGAGCAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTG
GA
Found at i:38016612 original size:128 final size:128
Alignment explanation
Indices: 38016434--38016760 Score: 482
Period size: 128 Copynumber: 2.6 Consensus size: 128
38016424 AGATAGCAAA
* * *
38016434 TCTTATCTCCCTGAAGTTGCAGAGGAGCAG-GTTA--AAGCCGATAATCCTATCTTCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-C-A-AATCCTATCTTCCTGAAGTT
38016496 GCAGTAGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTA
63 GCAGTAGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTA
38016561 G
128 G
*
38016562 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCTTCATGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCTTCCTGAAGTTGCA
* * *
38016627 GTGGAGTGGATTAAAACCTTGGATCTTATCTTTCTGAAGTTGCAGAGAGTAGATCGCATCTAG
66 GTAGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * * *
38016690 TCTTATCTCCCTGAAGTTGAAGTGGAGCAGACTAAGTAGGCAAGTCTTATC-TCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCTTC-CTGAAGTTGC
*
38016754 AGCAGAG
65 AGTAGAG
38016761 CAGATCACAT
Statistics
Matches: 181, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
127 2 0.01
128 172 0.95
129 3 0.02
130 1 0.01
131 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (128 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCTTCCTGAAGTTGCA
GTAGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
Found at i:38018242 original size:16 final size:17
Alignment explanation
Indices: 38018221--38018253 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
38018211 TAAATCTATA
38018221 TACATA-TATATTTTTG
1 TACATATTATATTTTTG
38018237 TACATATTTATATTTTT
1 TACATA-TTATATTTTT
38018254 TTCAACTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (17 bp):
TACATATTATATTTTTG
Found at i:38018569 original size:15 final size:15
Alignment explanation
Indices: 38018551--38018589 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
38018541 ATCGTTAAAA
38018551 TTATTATCATTGTAT
1 TTATTATCATTGTAT
38018566 TTATTA-CTATTGTAT
1 TTATTATC-ATTGTAT
*
38018581 TTGTTATCA
1 TTATTATCA
38018590 CGATATTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (15 bp):
TTATTATCATTGTAT
Found at i:38029317 original size:40 final size:40
Alignment explanation
Indices: 38029262--38029340 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
38029252 GCAAGCTCAA
*
38029262 CTTTTCATCTGCTGTAGAAAGTGATAACAATTAGAACAAG
1 CTTTTAATCTGCTGTAGAAAGTGATAACAATTAGAACAAG
38029302 CTTTTAATCTGCTGTAGAAAGTGATAACAATTAGAACAA
1 CTTTTAATCTGCTGTAGAAAGTGATAACAATTAGAACAA
38029341 TCCTGGACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (40 bp):
CTTTTAATCTGCTGTAGAAAGTGATAACAATTAGAACAAG
Found at i:38031086 original size:20 final size:21
Alignment explanation
Indices: 38031055--38031093 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38031045 TTTATGGTTT
38031055 TAAATAATTTTTGGGTAAAAA
1 TAAATAATTTTTGGGTAAAAA
*
38031076 TAAAT-ATTTTTGGTTAAA
1 TAAATAATTTTTGGGTAAA
38031094 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (21 bp):
TAAATAATTTTTGGGTAAAAA
Found at i:38035837 original size:14 final size:14
Alignment explanation
Indices: 38035818--38035851 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
38035808 AACCCTAAAT
38035818 CCCTAAC-TCTTAAC
1 CCCTAACGTC-TAAC
38035832 CCCTAACGTCTAAC
1 CCCTAACGTCTAAC
38035846 CCCTAA
1 CCCTAA
38035852 ACCTTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.29, C:0.44, G:0.03, T:0.24
Consensus pattern (14 bp):
CCCTAACGTCTAAC
Found at i:38036340 original size:41 final size:41
Alignment explanation
Indices: 38036265--38036536 Score: 289
Period size: 41 Copynumber: 6.7 Consensus size: 41
38036255 TTTTTTGCGA
**
38036265 CGCTTTTTCAAAAACGCTGCTAAAGCCCCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
* * * * *
38036306 CGATTTTTCAAAAATGCCATTAAATCCCCTAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
* * *
38036347 CGCTTTTTCAAAAACGCCGCTAAATCCCCTAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
* * * *
38036388 TGCTTTTTTAAAAAC-ACAGCTAAAGCCCCGAGCATTAGCAG
1 CGCTTTTTCAAAAACGCCA-CTAAAGCCCCGAGCATTAGCGG
* * * **
38036429 CACTTTTTTAAAAACGCCTCTAAAGCCCCGAGCA-T-GCAA
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
* * * * *
38036468 TGCTTTTTCAAAAATGCCGCTAAAACCTCGAGCATTAGCGG
1 CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
*
38036509 CGCTTTTTCAAAAACGCCGCTAAAGCCC
1 CGCTTTTTCAAAAACGCCACTAAAGCCC
38036537 TAAAAGGTCA
Statistics
Matches: 191, Mismatches: 36, Indels: 8
0.81 0.15 0.03
Matches are distributed among these distances:
39 30 0.16
40 3 0.02
41 157 0.82
42 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (41 bp):
CGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCATTAGCGG
Found at i:38036401 original size:82 final size:82
Alignment explanation
Indices: 38036265--38036536 Score: 336
Period size: 82 Copynumber: 3.3 Consensus size: 82
38036255 TTTTTTGCGA
* * * *
38036265 CGCTTTTTCAAAAACGCTGCTAAAGCCCCGAGCATTAGCGGCGATTTTTCAAAAATGCCATTAAA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCACTAAA
* *
38036330 TCCCCTAGCATTAGCGG
66 ACCCCGAGCATTAGCGG
* * *
38036347 CGCTTTTTCAAAAACGCCGCTAAATCCCCTAGCATTAGCGGTGCTTTTTTAAAAA--CACAGCTA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAATGC-CA-CTA
* *
38036410 AAGCCCCGAGCATTAGCAG
64 AAACCCCGAGCATTAGCGG
* * * ** *
38036429 CACTTTTTTAAAAACGCCTCTAAAGCCCCGAGCA-T-GCAATGCTTTTTCAAAAATGCCGCTAAA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCACTAAA
*
38036492 ACCTCGAGCATTAGCGG
66 ACCCCGAGCATTAGCGG
38036509 CGCTTTTTCAAAAACGCCGCTAAAGCCC
1 CGCTTTTTCAAAAACGCCGCTAAAGCCC
38036537 TAAAAGGTCA
Statistics
Matches: 161, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
80 60 0.37
81 4 0.02
82 97 0.60
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (82 bp):
CGCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAATGCCACTAAA
ACCCCGAGCATTAGCGG
Found at i:38036626 original size:40 final size:40
Alignment explanation
Indices: 38036571--38036659 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
38036561 TGGGCTTAGG
* *
38036571 TTTTTTGCGGAGTTTTTTCGAAAAACG-TCGCTAATGCTC-A
1 TTTTTAGCGGAG-TTTTTCAAAAAACGCT-GCTAATGCTCGA
* *
38036611 TTTTTAGCGGCGTTTTTCAAAAAACGCTGTTAATGCTCGA
1 TTTTTAGCGGAGTTTTTCAAAAAACGCTGCTAATGCTCGA
*
38036651 TCTTTAGCG
1 TTTTTAGCG
38036660 AAAATTTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 22 0.52
40 20 0.48
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGAGTTTTTCAAAAAACGCTGCTAATGCTCGA
Found at i:38036627 original size:39 final size:40
Alignment explanation
Indices: 38036584--38036659 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
38036574 TTTGCGGAGT
* *
38036584 TTTTTCGAAAAACG-TCGCTAATGCTC-ATTTTTAGCGGCG
1 TTTTTCAAAAAACGCT-GCTAATGCTCGATCTTTAGCGGCG
*
38036623 TTTTTCAAAAAACGCTGTTAATGCTCGATCTTTAGCG
1 TTTTTCAAAAAACGCTGCTAATGCTCGATCTTTAGCG
38036660 AAAATTTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 22 0.69
40 10 0.31
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (40 bp):
TTTTTCAAAAAACGCTGCTAATGCTCGATCTTTAGCGGCG
Found at i:38042795 original size:52 final size:52
Alignment explanation
Indices: 38042738--38042841 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
38042728 ACTTTGATAG
*
38042738 TTAAAATAGGGTGACAAAGATTGAGGTGCAGATCAAATTGCTCTCTTGAGAC
1 TTAAAATAGGGTGACAAAGATTGAGGTGCAGATCAAATTACTCTCTTGAGAC
38042790 TTAAAATAGGGTGACAAAGATTGAGGTGCAGATCAAATTACTCTCTTGAGAC
1 TTAAAATAGGGTGACAAAGATTGAGGTGCAGATCAAATTACTCTCTTGAGAC
38042842 GATACTCGCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (52 bp):
TTAAAATAGGGTGACAAAGATTGAGGTGCAGATCAAATTACTCTCTTGAGAC
Found at i:38043159 original size:30 final size:27
Alignment explanation
Indices: 38043125--38043189 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
38043115 TAAAATACTC
38043125 TAATATATAATTAAATTAAAATTAATTAAT
1 TAATATATAATTAAA-TAAAATTAA--AAT
* * *
38043155 TAATAGATAATTATATCAAATTAAAAT
1 TAATATATAATTAAATAAAATTAAAAT
38043182 TAATATAT
1 TAATATAT
38043190 CATATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 10 0.32
29 8 0.26
30 13 0.42
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
TAATATATAATTAAATAAAATTAAAAT
Found at i:38053473 original size:36 final size:36
Alignment explanation
Indices: 38053426--38053499 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
38053416 GGAGGAGCGC
* * *
38053426 ATCAGTCAGAATAGATCTGAAAGGCTGCTCAACTGA
1 ATCAGTCAGAATAGACCCGAAAGGCTACTCAACTGA
* *
38053462 ATCAGTCAGAATTGACCCGAAAGGCTACTTAACTGA
1 ATCAGTCAGAATAGACCCGAAAGGCTACTCAACTGA
38053498 AT
1 AT
38053500 AGAGTTTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (36 bp):
ATCAGTCAGAATAGACCCGAAAGGCTACTCAACTGA
Found at i:38054525 original size:18 final size:17
Alignment explanation
Indices: 38054482--38054526 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
38054472 AATTTTTTTC
* *
38054482 TTTCACTTTATTATTAT
1 TTTCTCTTTATTATTAG
38054499 TTTCTTCTTTATTATTTAG
1 TTTC-TCTTTATTA-TTAG
38054518 TTTCTCTTT
1 TTTCTCTTT
38054527 TATTTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.16, C:0.13, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTCTCTTTATTATTAG
Found at i:38054530 original size:19 final size:18
Alignment explanation
Indices: 38054487--38054526 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
38054477 TTTTCTTTCA
*
38054487 CTTTATTATTATTTTCTT
1 CTTTATTATTAGTTTCTT
38054505 CTTTATTATTTAGTTTC-T
1 CTTTATTA-TTAGTTTCTT
38054523 CTTT
1 CTTT
38054527 TATTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.15, C:0.12, G:0.03, T:0.70
Consensus pattern (18 bp):
CTTTATTATTAGTTTCTT
Found at i:38062496 original size:18 final size:19
Alignment explanation
Indices: 38062464--38062500 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38062454 ATAAACGACC
38062464 TAAAAAGAAATTAAACAAA
1 TAAAAAGAAATTAAACAAA
*
38062483 TAAAAATAAA-TAAACAAA
1 TAAAAAGAAATTAAACAAA
38062501 AAATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (19 bp):
TAAAAAGAAATTAAACAAA
Found at i:38094256 original size:22 final size:22
Alignment explanation
Indices: 38094228--38094325 Score: 124
Period size: 22 Copynumber: 4.5 Consensus size: 22
38094218 ATACCACAGT
* *
38094228 AGTAGGCACCGAAGTGCTAAAC
1 AGTAGGCACCGAAGTGCGAATC
* *
38094250 AGTAGGCATCAAAGTGCGAATC
1 AGTAGGCACCGAAGTGCGAATC
* * *
38094272 AGTAGGCACCGTAGTGTGAAGC
1 AGTAGGCACCGAAGTGCGAATC
*
38094294 AATAGGCACCGAAGTGCGAATC
1 AGTAGGCACCGAAGTGCGAATC
38094316 AGTAGGCACC
1 AGTAGGCACC
38094326 ACAGTGCAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.34, C:0.21, G:0.30, T:0.15
Consensus pattern (22 bp):
AGTAGGCACCGAAGTGCGAATC
Found at i:38094331 original size:22 final size:21
Alignment explanation
Indices: 38094228--38094337 Score: 103
Period size: 22 Copynumber: 5.0 Consensus size: 21
38094218 ATACCACAGT
* *
38094228 AGTAGGCACCGAAGTGCTAAAC
1 AGTAGGCACC-AAGTGCGAATC
*
38094250 AGTAGGCATCAAAGTGCGAATC
1 AGTAGGCA-CCAAGTGCGAATC
* * *
38094272 AGTAGGCACCGTAGTGTGAAGC
1 AGTAGGCACC-AAGTGCGAATC
*
38094294 AATAGGCACCGAAGTGCGAATC
1 AGTAGGCACC-AAGTGCGAATC
*
38094316 AGTAGGCACCACAGTGCAAATC
1 AGTAGGCACCA-AGTGCGAATC
38094338 CTGTACAAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.03
22 69 0.96
23 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.28, T:0.15
Consensus pattern (21 bp):
AGTAGGCACCAAGTGCGAATC
Found at i:38102168 original size:17 final size:18
Alignment explanation
Indices: 38102146--38102181 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38102136 ACAATGTCAT
*
38102146 GTGCTT-AACCATTTTTA
1 GTGCTTAAACCAGTTTTA
38102163 GTGCTTAAACCAGTTTTA
1 GTGCTTAAACCAGTTTTA
38102181 G
1 G
38102182 GTGCCCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (18 bp):
GTGCTTAAACCAGTTTTA
Found at i:38110598 original size:16 final size:16
Alignment explanation
Indices: 38110577--38110607 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38110567 TTCACTATTA
*
38110577 TGTCTTTTTTATTTTC
1 TGTCTTTTATATTTTC
38110593 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
38110608 GCATGCATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:38112260 original size:37 final size:39
Alignment explanation
Indices: 38112210--38112287 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 39
38112200 TTTAATAGTT
38112210 TAGTATTAAATTAAATCAA-ATTAAA-T-ACTTATCTTAA
1 TAGTATTAAATTAAATCAATATTAAAGTGA-TTATCTTAA
** * *
38112247 TAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAA
1 TAGTATTAAATTAAATCAATATTAAAGTGATTATCTTAA
38112286 TA
1 TA
38112288 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 15 0.44
38 6 0.18
39 12 0.35
40 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (39 bp):
TAGTATTAAATTAAATCAATATTAAAGTGATTATCTTAA
Found at i:38112363 original size:16 final size:17
Alignment explanation
Indices: 38112345--38112401 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
38112335 AATAAGATTT
38112345 AATATTAAATTAATAT-
1 AATATTAAATTAATATA
* * *
38112361 AATATT-TATCAAGATA
1 AATATTAAATTAATATA
*
38112377 AATATTATATTAAT-TA
1 AATATTAAATTAATATA
38112393 AATATTAAA
1 AATATTAAA
38112402 GTGATTAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.18
16 22 0.67
17 5 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATATTAAATTAATATA
Found at i:38133093 original size:16 final size:16
Alignment explanation
Indices: 38133072--38133105 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38133062 GAAAGAAGCA
38133072 ATAACATTATATTGTG
1 ATAACATTATATTGTG
*
38133088 ATAACATTGTATTGTG
1 ATAACATTATATTGTG
38133104 AT
1 AT
38133106 TATGATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (16 bp):
ATAACATTATATTGTG
Found at i:38135159 original size:39 final size:37
Alignment explanation
Indices: 38135089--38135161 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
38135079 ATTGATTTAA
38135089 TATTAAATTAAATTAAATACTTATCTTAATATTATTT
1 TATTAAATTAAATTAAATACTTATCTTAATATTATTT
*
38135126 TATTAATTTAATATTAAAGTGAC-TATCTTAATATTA
1 TATTAAATTAA-ATTAAA-T-ACTTATCTTAATATTA
38135162 AATTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 10 0.31
38 6 0.19
39 14 0.44
40 2 0.06
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (37 bp):
TATTAAATTAAATTAAATACTTATCTTAATATTATTT
Found at i:38146881 original size:2 final size:2
Alignment explanation
Indices: 38146874--38146903 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38146864 AATTTATTCC
*
38146874 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38146904 TTCTCAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38148062 original size:40 final size:41
Alignment explanation
Indices: 38147923--38148077 Score: 204
Period size: 41 Copynumber: 3.8 Consensus size: 41
38147913 GGCGCTAATG
* * * *
38147923 GAAAAATGCCGCAATAGGTAAAGTAGTAGCGGCATTTATGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCATTTATGA
* *
38147964 GAAAAACGCCGCAAAAGGTCAAGCAGTAGTGGCGTTTATGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCATTTATGA
* *
38148005 GGAAAACGCCGCAAAAAGTCAAGCAGTAGCGGCATTTATGA
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCATTTATGA
* * *
38148046 GAAAAATGCTGCAAAAGGT-AAGCAATAGCGGC
1 GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGC
38148078 GTTTTAATCA
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 12 0.12
41 87 0.88
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.17
Consensus pattern (41 bp):
GAAAAACGCCGCAAAAGGTCAAGCAGTAGCGGCATTTATGA
Found at i:38148191 original size:34 final size:35
Alignment explanation
Indices: 38148152--38148241 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 35
38148142 CATATCCACG
* **
38148152 AAATCCCTTATGTTTTTCCCCTAA-AAATTTCCCC
1 AAATCCCTTATGTTTTTCCCCAAACAAAACTCCCC
*
38148186 GAATCCCTTAAT-TTTTTCCCCAAATCAAAACTCCCC
1 AAATCCCTT-ATGTTTTTCCCCAAA-CAAAACTCCCC
*
38148222 AAATCCCTTA-GATTTTCCCC
1 AAATCCCTTATGTTTTTCCCC
38148242 GACCGTCTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
34 19 0.41
35 11 0.24
36 16 0.35
ACGTcount: A:0.28, C:0.34, G:0.03, T:0.34
Consensus pattern (35 bp):
AAATCCCTTATGTTTTTCCCCAAACAAAACTCCCC
Found at i:38148314 original size:25 final size:25
Alignment explanation
Indices: 38148281--38148349 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
38148271 CCCTATACTG
**
38148281 CATCGCCGTTGACACTCCTCTGTCA
1 CATCGCCGTCAACACTCCTCTGTCA
*
38148306 CATCGCCGTCAACACTCCTCTGTCG
1 CATCGCCGTCAACACTCCTCTGTCA
*
38148331 CATTGCCGTCAACACTCCT
1 CATCGCCGTCAACACTCCT
38148350 TTGCCGCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.17, C:0.42, G:0.14, T:0.26
Consensus pattern (25 bp):
CATCGCCGTCAACACTCCTCTGTCA
Found at i:38148357 original size:25 final size:25
Alignment explanation
Indices: 38148292--38148383 Score: 96
Period size: 25 Copynumber: 3.7 Consensus size: 25
38148282 ATCGCCGTTG
* * *
38148292 ACACTCCTCTGTCACATCGCCGTCA
1 ACACTCCTCTGCCGCATTGCCGTCA
*
38148317 ACACTCCTCTGTCGCATTGCCGTCA
1 ACACTCCTCTGCCGCATTGCCGTCA
* *
38148342 ACACTCCTTTGCCGCA-TGACCGTCG
1 ACACTCCTCTGCCGCATTG-CCGTCA
* *
38148367 ACACTCCTTTGCTGCAT
1 ACACTCCTCTGCCGCAT
38148384 CGCTGTGTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
24 2 0.03
25 57 0.97
ACGTcount: A:0.17, C:0.40, G:0.15, T:0.27
Consensus pattern (25 bp):
ACACTCCTCTGCCGCATTGCCGTCA
Found at i:38150448 original size:29 final size:28
Alignment explanation
Indices: 38150416--38150499 Score: 65
Period size: 29 Copynumber: 3.1 Consensus size: 28
38150406 ACATTTAAAG
38150416 TTAATGATTATCATAACTTACATAAACAT
1 TTAATGATTATCA-AACTTACATAAACAT
** *
38150445 TTAAACATT-T-AAACATT---T-AA-AG
1 TTAATGATTATCAAAC-TTACATAAACAT
38150467 TTAATGATTATCAGAACTTACATAAACAT
1 TTAATGATTATCA-AACTTACATAAACAT
38150496 TTAA
1 TTAA
38150500 AGAATTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
22 8 0.20
23 3 0.08
24 4 0.10
25 3 0.08
26 3 0.08
27 4 0.10
28 3 0.08
29 12 0.30
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (28 bp):
TTAATGATTATCAAACTTACATAAACAT
Found at i:38150451 original size:8 final size:8
Alignment explanation
Indices: 38150438--38150465 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
38150428 ATAACTTACA
38150438 TAAACATT
1 TAAACATT
38150446 TAAACATT
1 TAAACATT
38150454 TAAACATT
1 TAAACATT
38150462 TAAA
1 TAAA
38150466 GTTAATGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAACATT
Found at i:38150508 original size:51 final size:51
Alignment explanation
Indices: 38150406--38150508 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
38150396 TTAACTCTTT
* *
38150406 ACATTTAAAGTTAATGATTATCATAACTTACATAAACATTTAAACATTTAA
1 ACATTTAAAGTTAATGATTATCAGAACTTACATAAACATTTAAACAATTAA
*
38150457 ACATTTAAAGTTAATGATTATCAGAACTTACATAAACATTTAAAGAATTAA
1 ACATTTAAAGTTAATGATTATCAGAACTTACATAAACATTTAAACAATTAA
38150508 A
1 A
38150509 AAATGTAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.35
Consensus pattern (51 bp):
ACATTTAAAGTTAATGATTATCAGAACTTACATAAACATTTAAACAATTAA
Found at i:38158012 original size:22 final size:22
Alignment explanation
Indices: 38157984--38158028 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38157974 TCCGCAGAGT
38157984 AGGATTATTTTCGAAATATGCA
1 AGGATTATTTTCGAAATATGCA
38158006 AGGATTATTTTCGAAATATGCA
1 AGGATTATTTTCGAAATATGCA
38158028 A
1 A
38158029 ACAAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
AGGATTATTTTCGAAATATGCA
Found at i:38159621 original size:8 final size:10
Alignment explanation
Indices: 38159584--38159619 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
38159574 TATTTCTACA
38159584 AAATATATTT
1 AAATATATTT
38159594 AAATATATTT
1 AAATATATTT
38159604 AAATATATTT
1 AAATATATTT
38159614 AAATAT
1 AAATAT
38159620 TTCAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAATATATTT
Found at i:38159627 original size:20 final size:20
Alignment explanation
Indices: 38159567--38159627 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 20
38159557 TATTAAACAA
38159567 ATTTAAATATTTCTACAAAATAT
1 ATTTAAATA-TT-T-CAAAATAT
*
38159590 ATTTAAATATATT-TAAATAT
1 ATTTAAATAT-TTCAAAATAT
38159610 ATTTAAATATTTCAAAAT
1 ATTTAAATATTTCAAAAT
38159628 GTTTATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.06
20 20 0.59
22 2 0.06
23 10 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTAAATATTTCAAAATAT
Found at i:38170987 original size:9 final size:9
Alignment explanation
Indices: 38170973--38170999 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38170963 AGCTACAGTG
38170973 TTAACTAAC
1 TTAACTAAC
38170982 TTAACTAAC
1 TTAACTAAC
38170991 TTAACTAAC
1 TTAACTAAC
38171000 ATCAAGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAACTAAC
Found at i:38174990 original size:9 final size:9
Alignment explanation
Indices: 38174976--38175022 Score: 76
Period size: 9 Copynumber: 5.2 Consensus size: 9
38174966 ATTCTATCTG
38174976 TTAACCGAA
1 TTAACCGAA
*
38174985 TTAACCAAA
1 TTAACCGAA
38174994 TTAACCGAA
1 TTAACCGAA
*
38175003 TTACCCGAA
1 TTAACCGAA
38175012 TTAACCGAA
1 TTAACCGAA
38175021 TT
1 TT
38175023 GAATCACTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (9 bp):
TTAACCGAA
Found at i:38186403 original size:72 final size:68
Alignment explanation
Indices: 38186318--38186454 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 68
38186308 TGATTTAACT
* *
38186318 TAATCACTTTAATATTAAATTAATATAATATTTATCTACAAGAGAAACATTAAATTAAATTTAAT
1 TAATCACTTTAATATTAAATTAATAAAATA-CTAT-TA-AA-AGAAACATTAAATTAAATTTAAT
38186383 ATTAGGA
62 ATTAGGA
* **
38186390 TAATCACTTTAATATTAAATTAATAAAATACTATTAAAATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATACTATTAAAAGAAACATTAAATTAAATTTAATATTA
38186455 AACTATTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 24 0.40
69 2 0.03
70 2 0.03
71 3 0.05
72 29 0.48
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATTAAAAGAAACATTAAATTAAATTTAATATTA
GGA
Found at i:38186412 original size:11 final size:11
Alignment explanation
Indices: 38186398--38186473 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
38186388 GATAATCACT
38186398 TTAATATTAAA
1 TTAATATTAAA
38186409 TTAATA--AAA
1 TTAATATTAAA
*
38186418 -TACTATTAAA
1 TTAATATTAAA
*
38186428 ATAAGTATTAAA
1 TTAA-TATTAAA
38186440 TTAA-ATTTAATA
1 TTAATA-TTAA-A
38186452 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
38186465 ATAATATTA
1 TTAATATTA
38186474 TTTTTCGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:38186413 original size:20 final size:18
Alignment explanation
Indices: 38186366--38186472 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
38186356 CAAGAGAAAC
38186366 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
*
38186383 ATTAGGA-TAATCACTTTAAT
1 ATTA-AATTAAT-A-TTTAAT
** *
38186403 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
38186422 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
38186439 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
38186459 ATTAAAATAATATT
1 ATTAAATTAATATT
38186473 ATTTTTCGAA
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
17 15 0.22
18 9 0.13
19 22 0.32
20 22 0.32
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:38186460 original size:37 final size:36
Alignment explanation
Indices: 38186398--38186473 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
38186388 GATAATCACT
38186398 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
38186435 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
38186471 TTA
1 TTA
38186474 TTTTTCGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:38203513 original size:22 final size:21
Alignment explanation
Indices: 38203488--38203531 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
38203478 TGATAAACTT
38203488 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
38203510 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
38203531 T
1 T
38203532 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:38209033 original size:17 final size:17
Alignment explanation
Indices: 38209003--38209038 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38208993 AGTGTGATAT
38209003 AACTCCAACAAGCTTCC
1 AACTCCAACAAGCTTCC
* *
38209020 AACTCGAACGAGCTTCC
1 AACTCCAACAAGCTTCC
38209037 AA
1 AA
38209039 ATCACTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.17
Consensus pattern (17 bp):
AACTCCAACAAGCTTCC
Found at i:38209547 original size:25 final size:25
Alignment explanation
Indices: 38209517--38209575 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
38209507 CTGTAATCAA
* *
38209517 TAAGCTCCTTCAAGCTTAATAACGG
1 TAAGCTCATTCAAGCTCAATAACGG
* * *
38209542 TAAGCTCATTCGAGCTCAGTATCGG
1 TAAGCTCATTCAAGCTCAATAACGG
38209567 TAAGCTCAT
1 TAAGCTCAT
38209576 ATAAGCTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (25 bp):
TAAGCTCATTCAAGCTCAATAACGG
Found at i:38213317 original size:12 final size:12
Alignment explanation
Indices: 38213300--38213326 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
38213290 ATATTAAGCT
38213300 AATGATTCCTAA
1 AATGATTCCTAA
38213312 AATGATTCCTAA
1 AATGATTCCTAA
38213324 AAT
1 AAT
38213327 TAAGATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (12 bp):
AATGATTCCTAA
Found at i:38213660 original size:44 final size:44
Alignment explanation
Indices: 38213597--38213702 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 44
38213587 TGTAGGCTTT
* * *
38213597 CAAAAAATGCTCAAATCACCTAAACTCAAAATACTGAGTCATCC
1 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
38213641 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
1 CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
38213685 CAAAACATGCTCAATATC
1 CAAAACATGCTC-ATATC
38213703 TCTACTTCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
44 53 0.91
45 5 0.09
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (44 bp):
CAAAACATGCTCATATCACCTAAACTCAAAATACCGAGTCATCC
Found at i:38214011 original size:14 final size:14
Alignment explanation
Indices: 38213973--38214012 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
38213963 GGTGCAGGAC
* *
38213973 TGGAGGTGGACCGG
1 TGGAGGTGGATCAG
*
38213987 TGGAAGTGGATCAG
1 TGGAGGTGGATCAG
38214001 TGGAGGTGGATC
1 TGGAGGTGGATC
38214013 GATGCTCGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.20, C:0.10, G:0.50, T:0.20
Consensus pattern (14 bp):
TGGAGGTGGATCAG
Found at i:38214312 original size:14 final size:14
Alignment explanation
Indices: 38214293--38214325 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
38214283 GAGGTAGACC
38214293 GGAGGTGGACCGGT
1 GGAGGTGGACCGGT
*
38214307 GGAGGTGGATCGGT
1 GGAGGTGGACCGGT
38214321 GGAGG
1 GGAGG
38214326 ACGGAGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.09, G:0.61, T:0.15
Consensus pattern (14 bp):
GGAGGTGGACCGGT
Found at i:38216796 original size:6 final size:6
Alignment explanation
Indices: 38216785--38216811 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38216775 TTAATAAATA
38216785 ATTAAT ATTAAT ATTAAT ATTAAT ATT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATT
38216812 GATACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTAAT
Found at i:38220582 original size:3 final size:3
Alignment explanation
Indices: 38220574--38220633 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
38220564 AGAGTTCATT
* * *
38220574 TTC TTC TTC TTC CTC TTC TTC TTC TTC TTC TTC CTC TTC CTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
38220622 TTC TTC TTC TTC
1 TTC TTC TTC TTC
38220634 GTCGTCGTCG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:38223150 original size:15 final size:17
Alignment explanation
Indices: 38223115--38223147 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38223105 TTCTAATACT
38223115 ATATAAAATATTCTAAA
1 ATATAAAATATTCTAAA
*
38223132 ATATGAAATATT-TAAA
1 ATATAAAATATTCTAAA
38223148 TATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATAAAATATTCTAAA
Found at i:38223240 original size:2 final size:2
Alignment explanation
Indices: 38223229--38223257 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38223219 AAATTCTTGC
38223229 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38223258 ACATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38224312 original size:12 final size:12
Alignment explanation
Indices: 38224295--38224322 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38224285 AAATTTTTTC
38224295 TTTTTTTCTTTA
1 TTTTTTTCTTTA
38224307 TTTTTTTCTTTA
1 TTTTTTTCTTTA
38224319 TTTT
1 TTTT
38224323 CCCTTTTTTT
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:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTCTTTA
Found at i:38224330 original size:20 final size:20
Alignment explanation
Indices: 38224288--38224333 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
38224278 AATTTTTAAA
**
38224288 TTTTTTCTTTTTTTCTTTAT
1 TTTTTTCTTTTTTTCCCTAT
38224308 TTTTTTCTTTATTTTCCCT-T
1 TTTTTTCTTT-TTTTCCCTAT
38224328 TTTTTT
1 TTTTTT
38224334 AAAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTCTTTTTTTCCCTAT
Found at i:38233597 original size:27 final size:27
Alignment explanation
Indices: 38233566--38233620 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
38233556 CCTAGACATG
38233566 TATATATCTATTGCCACACTTTGTACT
1 TATATATCTATTGCCACACTTTGTACT
*
38233593 TATATATCTATTGTCACACTTTGTACT
1 TATATATCTATTGCCACACTTTGTACT
38233620 T
1 T
38233621 TGCAACTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (27 bp):
TATATATCTATTGCCACACTTTGTACT
Found at i:38235094 original size:25 final size:26
Alignment explanation
Indices: 38235065--38235120 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
38235055 TTAATTAGTA
*
38235065 TAAAATATT-AATAATTCAAT-AAAT
1 TAAAATATTAAATAATTAAATAAAAT
38235089 TGAAAA-ATTAAATAATTAAATAAAAT
1 T-AAAATATTAAATAATTAAATAAAAT
38235115 TAAAAT
1 TAAAAT
38235121 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.15
25 18 0.67
26 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATATTAAATAATTAAATAAAAT
Found at i:38235839 original size:16 final size:15
Alignment explanation
Indices: 38235814--38235847 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
38235804 AAAGTTGATA
*
38235814 ATAATTAATATATATT
1 ATAATAAATATA-ATT
38235830 ATAATAAATATAATT
1 ATAATAAATATAATT
38235845 ATA
1 ATA
38235848 TACTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:38246246 original size:37 final size:37
Alignment explanation
Indices: 38246205--38246338 Score: 146
Period size: 37 Copynumber: 3.6 Consensus size: 37
38246195 ACAAGCACAG
* * *
38246205 TAATCCATCCGAAAATACGCCAAATGCTC-ATAAGAGT
1 TAATCCAACCGAAAACACGCCAAATGCTCTA-AAGAGC
* * * *
38246242 TAATCCAACC-AATACACGCCAATTGCTTTGAAGAGC
1 TAATCCAACCGAAAACACGCCAAATGCTCTAAAGAGC
* *
38246278 TAATCCAACCAAAAACACGCCAATTGCTCTAAAGAGC
1 TAATCCAACCGAAAACACGCCAAATGCTCTAAAGAGC
* *
38246315 TAGTCCAACCGAAAACACACCAAA
1 TAATCCAACCGAAAACACGCCAAA
38246339 ACAGGGAGTA
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
36 29 0.36
37 52 0.64
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (37 bp):
TAATCCAACCGAAAACACGCCAAATGCTCTAAAGAGC
Found at i:38246761 original size:23 final size:24
Alignment explanation
Indices: 38246733--38246787 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
38246723 AATTATTAGC
*
38246733 TTACATTTCATATTCCAATTT-AT
1 TTACATTTCATATTCCAATTTAAG
38246756 TTACATTTCATATTCCAATTTAAG
1 TTACATTTCATATTCCAATTTAAG
38246780 TTACATTT
1 TTACATTT
38246788 TATACCCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (24 bp):
TTACATTTCATATTCCAATTTAAG
Found at i:38246776 original size:13 final size:13
Alignment explanation
Indices: 38246737--38246776 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
38246727 ATTAGCTTAC
38246737 ATTTCATATTCCA
1 ATTTCATATTCCA
*
38246750 ATTT-AT-TTAC-
1 ATTTCATATTCCA
38246760 ATTTCATATTCCA
1 ATTTCATATTCCA
38246773 ATTT
1 ATTT
38246777 AAGTTACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 4 0.18
11 5 0.23
12 5 0.23
13 8 0.36
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTCATATTCCA
Found at i:38252689 original size:25 final size:25
Alignment explanation
Indices: 38252633--38252689 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
38252623 GACATATATC
* *
38252633 TTGATTTGATTTGATTTGGTTCCAA
1 TTGATTTGATTTGATTTGATTCAAA
** * *
38252658 TCAATTTGATTTTATTTTATTCAAA
1 TTGATTTGATTTGATTTGATTCAAA
38252683 TTGATTT
1 TTGATTT
38252690 AAAGGCTCAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.56
Consensus pattern (25 bp):
TTGATTTGATTTGATTTGATTCAAA
Found at i:38254101 original size:114 final size:114
Alignment explanation
Indices: 38253792--38254350 Score: 752
Period size: 114 Copynumber: 4.9 Consensus size: 114
38253782 AAAATAAGCA
* *
38253792 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGTCG-TTTCTCGAGCT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT-GAGCT
* * * * * *
38253855 TTCGAGGATTTAGAGGAGTTTATAAGAAAGCGTCGCTAATGATCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
38253905 TTAGCGGCGTTTTTGGG-AAGCGCCGCAAAAAAACCTAAGCCCAACGATGCCATTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
38253969 TCGGGGATTTAGCAGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGTT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * *
38254018 TTAGCGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCCTTTTTTAAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
38254083 TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGC-CTAAGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTC-AGGGCT
** * *
38254132 TTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAAACCTAAGCCCAACAATGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
38254197 TCAGGGATTTAGCGGCGTTTTT-GGTAAAGCGCCGCTAATACCCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAATGCTCAGGGCT
* * *
38254246 TTAGCGGAGTTTTTGGAAAAGCGCCGCAAAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGC
1 TTAGCGGCGTTTTTGGGAAAGCGCCGC--AAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
*
38254311 TTTCGGGGATTTAGCGGCGTTTTT-TGAAAAGCGCCGCTAA
64 TTTCGGGGATTTAGCGGCGTTTTTAAG-AAAGCGCCGCTAA
38254351 AAATATTTTA
Statistics
Matches: 395, Mismatches: 43, Indels: 13
0.88 0.10 0.03
Matches are distributed among these distances:
112 9 0.02
113 103 0.26
114 212 0.54
115 1 0.00
116 70 0.18
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:38254618 original size:15 final size:15
Alignment explanation
Indices: 38254598--38254628 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38254588 CATATTTTAA
38254598 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
38254613 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
38254628 G
1 G
38254629 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:38254949 original size:15 final size:16
Alignment explanation
Indices: 38254929--38254970 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
38254919 TGAGATTTAA
38254929 GGTTTAGGGGTTAG-T
1 GGTTTAGGGGTTAGAT
38254944 GGTTTAGGGGTTAGAT
1 GGTTTAGGGGTTAGAT
38254960 -G-TTAGGGGTTA
1 GGTTTAGGGGTTA
38254971 AGAGTTAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.38
15 15 0.58
16 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (16 bp):
GGTTTAGGGGTTAGAT
Found at i:38254966 original size:14 final size:14
Alignment explanation
Indices: 38254932--38254980 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
38254922 GATTTAAGGT
38254932 TTAGGGGTTAG-TGG
1 TTAGGGGTTAGAT-G
38254946 TTTAGGGGTTAGATG
1 -TTAGGGGTTAGATG
38254961 TTAGGGGTTAAGA-G
1 TTAGGGGTT-AGATG
38254975 TTAGGG
1 TTAGGG
38254981 ATTTAAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 16 0.50
15 15 0.47
16 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (14 bp):
TTAGGGGTTAGATG
Found at i:38254978 original size:36 final size:36
Alignment explanation
Indices: 38254907--38254988 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
38254897 TTAGGGATTA
* * *
38254907 TGGTTTAAGGGTTGAGATTTAAGGTTTAGGGGTTAG
1 TGGTTTAAGGGTTGAGATTTAAGGGTTAAGAGTTAG
* *
38254943 TGGTTTAGGGGTT-AGATGTTAGGGGTTAAGAGTTAG
1 TGGTTTAAGGGTTGAGAT-TTAAGGGTTAAGAGTTAG
38254979 -GGATTTAAGG
1 TGG-TTTAAGG
38254989 TTTAGGGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
35 6 0.16
36 32 0.84
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (36 bp):
TGGTTTAAGGGTTGAGATTTAAGGGTTAAGAGTTAG
Done.