Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 127 of 221
Found at i:39063588 original size:21 final size:21
Alignment explanation
Indices: 39063538--39063593 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
39063528 AATAACTAAC
39063538 TAATCTTAATTAA-C-TAAAT
1 TAATCTTAATTAATCATAAAT
39063557 TAA-CTTTAATTAATCATATAA-
1 TAATC-TTAATTAATCATA-AAT
39063578 TAATCTTAATTAATCA
1 TAATCTTAATTAATCA
39063594 AAGATAGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.03
19 11 0.34
20 1 0.03
21 16 0.50
22 3 0.09
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATCTTAATTAATCATAAAT
Found at i:39089484 original size:50 final size:50
Alignment explanation
Indices: 39089404--39089696 Score: 451
Period size: 50 Copynumber: 5.8 Consensus size: 50
39089394 ATTTGGGTAA
*
39089404 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
39089454 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
*
39089504 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
* * *
39089554 AGAAGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
* * * * * *
39089604 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
** *
39089654 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
39089697 TGTTATTATC
Statistics
Matches: 223, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
50 189 0.85
51 34 0.15
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
Found at i:39092754 original size:10 final size:10
Alignment explanation
Indices: 39092739--39092763 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39092729 GTTTCAATCC
39092739 AATTTTCTTT
1 AATTTTCTTT
39092749 AATTTTCTTT
1 AATTTTCTTT
39092759 AATTT
1 AATTT
39092764 ATACCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (10 bp):
AATTTTCTTT
Found at i:39099205 original size:15 final size:15
Alignment explanation
Indices: 39099196--39099230 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39099186 AAAAATCAAA
39099196 AAAATCAAAAAAATC
1 AAAATCAAAAAAATC
* *
39099211 AAAATCGAAAAAATG
1 AAAATCAAAAAAATC
39099226 AAAAT
1 AAAAT
39099231 GATGAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.14
Consensus pattern (15 bp):
AAAATCAAAAAAATC
Found at i:39099224 original size:9 final size:9
Alignment explanation
Indices: 39099185--39099214 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
39099175 ACCAAAGAAT
39099185 AAAAAATCA
1 AAAAAATCA
39099194 AAAAAATCA
1 AAAAAATCA
39099203 AAAAAATCA
1 AAAAAATCA
39099212 AAA
1 AAA
39099215 TCGAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATCA
Found at i:39102701 original size:71 final size:71
Alignment explanation
Indices: 39102615--39102789 Score: 226
Period size: 71 Copynumber: 2.5 Consensus size: 71
39102605 ATCTAGTACG
* * *
39102615 TGTCGCGACACAGGTACCCCTTTATT-TCTACACGCAACTTTGAAGTATTAAAATTTGAAAATAA
1 TGTCGCGACATAGGTACCCCTGTATTGT-GACACGCAACTTTGAAGTATTAAAATTTGAAAATAA
39102679 CAGGCCA
65 CAGGCCA
* * *
39102686 TGTCGTGACATAGGTACCCCTGTGTTGTGACACGCAACTTTGAAGTATTAAAATTTGAAAATACC
1 TGTCGCGACATAGGTACCCCTGTATTGTGACACGCAACTTTGAAGTATTAAAATTTGAAAATAAC
*
39102751 AGGCCG
66 AGGCCA
* * * * *
39102757 TGTTGCGACATAGGTTCCCTTGTGTTGCGACAC
1 TGTCGCGACATAGGTACCCCTGTATTGTGACAC
39102790 ATTACTTCGA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
71 90 0.99
72 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (71 bp):
TGTCGCGACATAGGTACCCCTGTATTGTGACACGCAACTTTGAAGTATTAAAATTTGAAAATAAC
AGGCCA
Found at i:39110898 original size:16 final size:17
Alignment explanation
Indices: 39110879--39110923 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
39110869 TTTTAATTAG
39110879 TTTAATTTAATTAATT-
1 TTTAATTTAATTAATTC
39110895 TTTAATCTTAA-TAATTC
1 TTTAAT-TTAATTAATTC
39110912 TTT-A-TTAATTAA
1 TTTAATTTAATTAA
39110924 ACTAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 3 0.12
16 12 0.46
17 7 0.27
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATTTAATTAATTC
Found at i:39113245 original size:22 final size:24
Alignment explanation
Indices: 39113202--39113245 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
39113192 TGATAATATG
39113202 TTTTGATATAACAAATTAAAGTAT
1 TTTTGATATAACAAATTAAAGTAT
*
39113226 TTTTGA-ATAA-AATTTAAAGT
1 TTTTGATATAACAAATTAAAGT
39113246 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTAT
Found at i:39113371 original size:20 final size:20
Alignment explanation
Indices: 39113346--39113387 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39113336 CAAACTTTAA
39113346 AATCAAGTTAAAA-TTATTTT
1 AATCAAG-TAAAAGTTATTTT
*
39113366 AATCAAGTAAAAGTTCTTTT
1 AATCAAGTAAAAGTTATTTT
39113386 AA
1 AA
39113388 CTAGTCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
AATCAAGTAAAAGTTATTTT
Found at i:39113638 original size:13 final size:13
Alignment explanation
Indices: 39113617--39113680 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
39113607 AGTTCTTTAT
*
39113617 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
39113630 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
39113643 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
39113656 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
39113669 TGCTTTTGAAAA
1 TGCTTTTGAAAA
39113681 TTTTGAGCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:39129302 original size:18 final size:19
Alignment explanation
Indices: 39129281--39129321 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
39129271 AGTTAACCTT
*
39129281 TATTATTTAA-AGAATTAA
1 TATTATTTAATAAAATTAA
39129299 TATTATTTAATAAAATTAA
1 TATTATTTAATAAAATTAA
39129318 TATT
1 TATT
39129322 TTGGACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATTATTTAATAAAATTAA
Found at i:39136855 original size:15 final size:15
Alignment explanation
Indices: 39136831--39136867 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
39136821 TGAATTTAGA
39136831 TTAA-TTCAAA-ATT
1 TTAATTTCAAATATT
39136844 TTGAATTTCAAATATT
1 TT-AATTTCAAATATT
39136860 TTAATTTC
1 TTAATTTC
39136868 CAAACAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 2 0.10
15 12 0.57
16 5 0.24
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAATTTCAAATATT
Found at i:39141611 original size:50 final size:50
Alignment explanation
Indices: 39141556--39141679 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
39141546 TATCCTAGAT
* * *
39141556 ATGGTCTTACATGGGA-GTCCTCATATCGGTGCCCATGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCT-CTCATATCGGTGCCAACGCCATGTCCCAAAC
** * * ** *
39141606 ATGGTCTTACGGGGGACCTCTCGTCTCGGTGCCAACGGGATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAAC
39141656 ATGGTCTTACATGGGACCTCTCAT
1 ATGGTCTTACATGGGACCTCTCAT
39141680 GATCTCAAGG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAAC
Found at i:39147525 original size:13 final size:13
Alignment explanation
Indices: 39147507--39147531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39147497 TTTCAGCAGA
39147507 AATCCACTATTAC
1 AATCCACTATTAC
39147520 AATCCACTATTA
1 AATCCACTATTA
39147532 TAATGGGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (13 bp):
AATCCACTATTAC
Found at i:39149399 original size:21 final size:21
Alignment explanation
Indices: 39149347--39149399 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
39149337 TAAGGTAGTA
* *
39149347 TTAAAGTTTCATTGAAAAATT
1 TTAACGTTTCGTTGAAAAATT
39149368 TTAACGTTTCGTTGAAAAATT
1 TTAACGTTTCGTTGAAAAATT
39149389 TTAACGTTTCG
1 TTAACGTTTCG
39149400 ATAGTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.43
Consensus pattern (21 bp):
TTAACGTTTCGTTGAAAAATT
Found at i:39159313 original size:13 final size:13
Alignment explanation
Indices: 39159276--39159339 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
39159266 TTCTTCATTA
39159276 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
39159289 CTGTGGAAAAGTG
1 CTTTTGAAAAGTG
*
39159302 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
39159315 CTTTT-AAGAAGTG
1 CTTTTGAA-AAGTG
39159328 CTTTTGAAAAGT
1 CTTTTGAAAAGT
39159340 TTGGTTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.93
14 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:39169897 original size:15 final size:18
Alignment explanation
Indices: 39169859--39169899 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
39169849 AGCAAATACT
39169859 AATAATAAGAACAGTAAC
1 AATAATAAGAACAGTAAC
*
39169877 AGTAATAA-AA-A-TAAC
1 AATAATAAGAACAGTAAC
39169892 AATAATAA
1 AATAATAA
39169900 TACTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 2 0.10
18 7 0.33
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (18 bp):
AATAATAAGAACAGTAAC
Found at i:39172443 original size:14 final size:14
Alignment explanation
Indices: 39172424--39172453 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39172414 AGTGAGAGAG
*
39172424 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
39172438 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
39172452 GA
1 GA
39172454 ATGAGGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:39175296 original size:29 final size:28
Alignment explanation
Indices: 39175256--39175322 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 28
39175246 TACCAGAAGC
39175256 AAAAA-AACAAAAA-ATTAGAATATAAAAAT
1 AAAAATAA-AAAAATATTA-AA-ATAAAAAT
* *
39175285 TAAATTAAAAAAATTATTAAAATAAAAAT
1 AAAAATAAAAAAA-TATTAAAATAAAAAT
39175314 AAAAATAAA
1 AAAAATAAA
39175323 TAATGACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 23 0.74
30 4 0.13
31 4 0.13
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (28 bp):
AAAAATAAAAAAATATTAAAATAAAAAT
Found at i:39175785 original size:54 final size:54
Alignment explanation
Indices: 39175703--39175811 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
39175693 ATTTCTTCAC
* *
39175703 TTAGTATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATCTCTTTCAAGAG
1 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
39175757 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
1 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
39175811 T
1 T
39175812 AAGAGCAACT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (54 bp):
TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
Found at i:39177620 original size:12 final size:12
Alignment explanation
Indices: 39177603--39177649 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
39177593 TTATTGCAAT
39177603 TGATTTTTTATA
1 TGATTTTTTATA
39177615 TGATTTTTTAT-
1 TGATTTTTTATA
*
39177626 TTATTTTTATATA
1 TGATTTTT-TATA
39177639 T-ATTTTTTATA
1 TGATTTTTTATA
39177650 ATTGTTGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 11 0.34
12 20 0.62
13 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (12 bp):
TGATTTTTTATA
Found at i:39177643 original size:23 final size:23
Alignment explanation
Indices: 39177605--39177648 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
39177595 ATTGCAATTG
39177605 ATTTTTTATATGATTTTTTATTT
1 ATTTTTTATATGATTTTTTATTT
39177628 ATTTTTATATAT-ATTTTTTAT
1 ATTTTT-TATATGATTTTTTAT
39177649 AATTGTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTTTTATATGATTTTTTATTT
Found at i:39178364 original size:39 final size:39
Alignment explanation
Indices: 39178236--39178366 Score: 113
Period size: 40 Copynumber: 3.3 Consensus size: 39
39178226 GGCGTTTGGA
* * * *
39178236 ACAAAAGCGCCACAAAAAAATCGAGCATTAGCGGCGATTT
1 ACAAAAGCGCCGC-TAAAAATAGAGAATTAGCGGCGATTT
* ** *
39178276 AGCCAAAGCGCCGCTAAAGGTAGAGAATCT-GCGACGATTT
1 A-CAAAAGCGCCGCTAAAAATAGAGAAT-TAGCGGCGATTT
*
39178316 CCAAGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGATTT
1 ACAA-AAGCGCCGCTAAAAATAGAGAATTAGCGGCGATTT
*
39178355 ATATAAAGCGCC
1 ACA-AAAGCGCC
39178367 ACAAGAAACC
Statistics
Matches: 71, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
38 1 0.01
39 23 0.32
40 36 0.51
41 11 0.15
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (39 bp):
ACAAAAGCGCCGCTAAAAATAGAGAATTAGCGGCGATTT
Found at i:39178469 original size:41 final size:41
Alignment explanation
Indices: 39178412--39178731 Score: 263
Period size: 41 Copynumber: 7.8 Consensus size: 41
39178402 ATTTTTAAAC
* * *
39178412 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTCGGAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * *
39178453 CTTTAGTGGCGTTTTTACCTTG-GCGCCGCTAATGCCCCGAT
1 CTTTAGTGGCGTTTTTATC-TGAGCGCCGCTAATGCTCGGAT
* * * * * *
39178494 CTTTAGCGGCATTTTTATATGAGCGCCACTAAAGCTCTGG-C
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGAT
* * * * *
39178535 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAGGCTCGGAG
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * *
39178576 CTATAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGG-C
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGAT
* * *
39178617 CTTTAGTGACGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * * *
39178658 CTTTAGTGACGTTTTTATCTGAGTGCCACTAATTCTCCTG-C
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCT-CGGAT
* *
39178699 CTTTAGCGGCGTTTGTT-TCTAAGCGCCGCTAAT
1 CTTTAGTGGCGTTT-TTATCTGAGCGCCGCTAAT
39178732 AGTAACAAAA
Statistics
Matches: 223, Mismatches: 48, Indels: 16
0.78 0.17 0.06
Matches are distributed among these distances:
40 6 0.03
41 208 0.93
42 9 0.04
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (41 bp):
CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
Found at i:39178549 original size:82 final size:82
Alignment explanation
Indices: 39178412--39178731 Score: 358
Period size: 82 Copynumber: 3.9 Consensus size: 82
39178402 ATTTTTAAAC
* * * * * ** **
39178412 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTC-GGATCTTTAGTGGCGTTTTTACCTTGG
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGG-CCTTTAGCGGCGTTTTTGTCTAAG
* *
39178476 CGCCGCTAATGCCCCGAT
65 CGCCGCTAATGCTCGGAT
* * *
39178494 CTTTAGCGGCATTTTTATATGAGCGCCACTAAAGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
* *
39178559 GCCGCTAAGGCTCGGAG
66 GCCGCTAATGCTCGGAT
* * * * * *
39178576 CTATAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGGCCTTTAGTGACGTTTTTGTCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
39178641 GCCGCTAATGCTCGGAT
66 GCCGCTAATGCTCGGAT
* * * *
39178658 CTTTAGTGACGTTTTTATCTGAGTGCCACTAATTCTCCT-GCCTTTAGCGGCGTTTGTT-TCTAA
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCT-CTGGCCTTTAGCGGCGTTT-TTGTCTAA
39178721 GCGCCGCTAAT
64 GCGCCGCTAAT
39178732 AGTAACAAAA
Statistics
Matches: 202, Mismatches: 33, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
82 196 0.97
83 6 0.03
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
GCCGCTAATGCTCGGAT
Found at i:39179224 original size:15 final size:15
Alignment explanation
Indices: 39179203--39179240 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
39179193 TTTAAGGTTA
39179203 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
39179218 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
39179233 ATTTAGGG
1 ATTTAGGG
39179241 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:39179243 original size:14 final size:14
Alignment explanation
Indices: 39179176--39179243 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
39179166 TACGGGGTAT
*
39179176 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
39179190 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
39179202 A-ATTTAGGGGTTAG
1 AGATTTA-GGGTTTG
*
39179216 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
39179231 AGATTTAGGGTTT
1 AGATTTAGGGTTT
39179244 CAACGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:39182062 original size:27 final size:26
Alignment explanation
Indices: 39182029--39182206 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
39182019 TAAATTGTAC
39182029 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * * *
39182056 TGTACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
*
39182082 ATGCACTAAGTGTGCGAATTGACCATGT
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
39182110 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
39182138 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
39182165 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
39182192 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39182207 GGCTCAATAT
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 26 0.20
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:39182147 original size:82 final size:81
Alignment explanation
Indices: 39182030--39182185 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
39182020 AAATTGTACA
* * * *
39182030 GCACTAAGTGTGCGATTCGACTATGTTGTACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39182094 TGCGAATTGACCATGTG
65 TGCGAATTGACCATGTG
** *
39182111 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39182176 TGCGAGTTGA
65 TGCGAATTGA
39182186 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 47 0.72
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGTG
Found at i:39182197 original size:82 final size:81
Alignment explanation
Indices: 39182029--39182206 Score: 214
Period size: 82 Copynumber: 2.2 Consensus size: 81
39182019 TAAATTGTAC
* * * *
39182029 AGCACTAAGTGTGCGATTCGACTATGTTGTACTAAGTGTGCGAAATGAATATGATGCACTAAGTG
1 AGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
*
39182094 TGCGAATTGACCATGT
66 TGCGAATTGACCATAT
* ** *
39182110 GGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAG
1 AGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAG
* **
39182174 TGTGCGAGTTGATTATAT
64 TGTGCGAATTGACCATAT
*
39182192 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39182207 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.22
82 63 0.78
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
AGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
TGCGAATTGACCATAT
Found at i:39182217 original size:27 final size:27
Alignment explanation
Indices: 39182111--39182217 Score: 79
Period size: 27 Copynumber: 3.9 Consensus size: 27
39182101 TGACCATGTG
* * *
39182111 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
39182139 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
39182166 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
39182193 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
39182218 CATTCGTGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 52 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:39198227 original size:27 final size:27
Alignment explanation
Indices: 39198197--39198248 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39198187 AATAAACAAA
* *
39198197 TAAATAAGTAAGTAATTATTTATTTGT
1 TAAATAAATAAGTAATTAATTATTTGT
**
39198224 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATAAGTAATTAATTATTT
39198249 AAATGTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (27 bp):
TAAATAAATAAGTAATTAATTATTTGT
Found at i:39199145 original size:11 final size:11
Alignment explanation
Indices: 39199129--39199155 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
39199119 TTCGTTTAAT
39199129 TTACTTTCATA
1 TTACTTTCATA
39199140 TTACTTTCATA
1 TTACTTTCATA
39199151 TTACT
1 TTACT
39199156 GGTTGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.56
Consensus pattern (11 bp):
TTACTTTCATA
Found at i:39201105 original size:21 final size:21
Alignment explanation
Indices: 39201076--39201128 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
39201066 ACATCTTTGA
*
39201076 TATATATATTTATATACAATTT
1 TATATATATTTAT-TAAAATTT
39201098 TA-ATATATTTATTAAAATTT
1 TATATATATTTATTAAAATTT
39201118 TATATATATTT
1 TATATATATTT
39201129 GAAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.31
21 18 0.62
22 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATATATTTATTAAAATTT
Found at i:39201134 original size:20 final size:19
Alignment explanation
Indices: 39201079--39201137 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
39201069 TCTTTGATAT
39201079 ATATATTTATATACAATTTTA
1 ATATATTTATA-A-AATTTTA
39201100 ATATATTTATTAAAATTTTA
1 ATATATTTA-TAAAATTTTA
39201120 TATATATTTGA-AAAATTT
1 -ATATATTT-ATAAAATTT
39201138 ATCAATCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 14 0.40
21 18 0.51
22 3 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATATTTATAAAATTTTA
Found at i:39201246 original size:13 final size:13
Alignment explanation
Indices: 39201228--39201252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39201218 TTACATAATA
39201228 CATAACTTACATT
1 CATAACTTACATT
39201241 CATAACTTACAT
1 CATAACTTACAT
39201253 AAACTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAACTTACATT
Found at i:39201285 original size:38 final size:38
Alignment explanation
Indices: 39201241--39201412 Score: 104
Period size: 39 Copynumber: 4.5 Consensus size: 38
39201231 AACTTACATT
* * *
39201241 CATAACTTACATAAACTTATATGTTACCTTACATAATA
1 CATAACTTACATAAACTTATATATAAACTTACATAATA
* * *
39201279 CATAACTTATATAAAATTTTTATATAAACTTACATAATA
1 CATAACTTACAT-AAACTTATATATAAACTTACATAATA
* * * *
39201318 CATAGCATACAT-AACTCACATAATACAAAACTTACATAACTTA
1 CATAACTTACATAAACT--TAT-ATA-TAAACTTACATAA--TA
* * * * *
39201361 AATATCTTACA-ACAC-T-TACAT-AACCTACATAATA
1 CATAACTTACATAAACTTATATATAAACTTACATAATA
39201395 CATAACTTACAT-AACTTA
1 CATAACTTACATAAACTTA
39201413 CATAATACAT
Statistics
Matches: 99, Mismatches: 24, Indels: 24
0.67 0.16 0.16
Matches are distributed among these distances:
34 13 0.13
35 1 0.01
36 10 0.10
37 3 0.03
38 13 0.13
39 32 0.32
40 3 0.03
41 12 0.12
43 12 0.12
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (38 bp):
CATAACTTACATAAACTTATATATAAACTTACATAATA
Found at i:39201338 original size:9 final size:9
Alignment explanation
Indices: 39201305--39201676 Score: 233
Period size: 9 Copynumber: 43.8 Consensus size: 9
39201295 TTTTTATATA
39201305 AACTTACAT
1 AACTTACAT
39201314 AA--TACAT
1 AACTTACAT
* *
39201321 AGCATACAT
1 AACTTACAT
*
39201330 AACTCACAT
1 AACTTACAT
*
39201339 AA--TACAA
1 AACTTACAT
39201346 AACTTACAT
1 AACTTACAT
*
39201355 AACTTAAAT
1 AACTTACAT
*
39201364 ATCTTACA-
1 AACTTACAT
39201372 ACACTTACAT
1 A-ACTTACAT
*
39201382 AACCTACAT
1 AACTTACAT
39201391 AA--TACAT
1 AACTTACAT
39201398 AACTTACAT
1 AACTTACAT
39201407 AACTTACAT
1 AACTTACAT
*
39201416 AATACATA-AT
1 -A-ACTTACAT
39201426 AACTTAC--
1 AACTTACAT
39201433 AACTTAC--
1 AACTTACAT
39201440 AACTTACAT
1 AACTTACAT
*
39201449 AACATACATT
1 AACTTACA-T
**
39201459 AA-TTTGAT
1 AACTTACAT
39201467 AACTTACAT
1 AACTTACAT
*
39201476 AAGTTACAT
1 AACTTACAT
39201485 AA--TACAT
1 AACTTACAT
39201492 AACTTAC--
1 AACTTACAT
39201499 AACTTACAT
1 AACTTACAT
*
39201508 AACATACATT
1 AACTTACA-T
***
39201518 AA-TTTGGT
1 AACTTACAT
39201526 AACTTACAT
1 AACTTACAT
* *
39201535 AAGTTACAC
1 AACTTACAT
39201544 AA--TACAT
1 AACTTACAT
39201551 AACTTAC--
1 AACTTACAT
39201558 AACTTACAT
1 AACTTACAT
*
39201567 AACATACAT
1 AACTTACAT
* **
39201576 TACTTTGAT
1 AACTTACAT
39201585 AACTTACAT
1 AACTTACAT
*
39201594 AAGTTACAT
1 AACTTACAT
*
39201603 AA--TACAC
1 AACTTACAT
39201610 AACTTACAT
1 AACTTACAT
* *
39201619 AGCTTACTT
1 AACTTACAT
39201628 AA--TACAT
1 AACTTACAT
*
39201635 GACTTACAT
1 AACTTACAT
39201644 AACTT--AT
1 AACTTACAT
*
39201651 ACACGTACAT
1 A-ACTTACAT
39201661 AACTTACAT
1 AACTTACAT
*
39201670 AATTTAC
1 AACTTAC
39201677 TTAATACATA
Statistics
Matches: 279, Mismatches: 52, Indels: 64
0.71 0.13 0.16
Matches are distributed among these distances:
7 73 0.26
8 14 0.05
9 175 0.63
10 13 0.05
11 4 0.01
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:39201422 original size:25 final size:25
Alignment explanation
Indices: 39201305--39201672 Score: 183
Period size: 25 Copynumber: 14.5 Consensus size: 25
39201295 TTTTTATATA
* *
39201305 AACTTACATAATACATAGCATACAT
1 AACTTACATAATACATAACTTACAT
* *
39201330 AACTCACATAATACAAAACTTACAT
1 AACTTACATAATACATAACTTACAT
* *
39201355 AACTTAAATATCTTACA-ACACTTACAT
1 AACTTACATA--ATACATA-ACTTACAT
*
39201382 AACCTACATAATACATAACTTACAT
1 AACTTACATAATACATAACTTACAT
39201407 AACTTACATAATACATAATAACTTAC--
1 AACTTACATAATAC---ATAACTTACAT
* *
39201433 AACTTACA-ACTTACATAACATACATT
1 AACTTACATA-ATACATAACTTACA-T
** *
39201459 AA-TTTGATAACTTACATAAGTTACAT
1 AACTTACATAA--TACATAACTTACAT
39201485 AA--TACATAACTTAC--AACTTACAT
1 AACTTACATAA--TACATAACTTACAT
* ***
39201508 AACATACATTAATTTGGTAACTTACAT
1 AACTTACA-TAA-TACATAACTTACAT
* *
39201535 AAGTTACACAATACATAACTTAC--
1 AACTTACATAATACATAACTTACAT
* **
39201558 AACTTACATAACATACATTACTTTGAT
1 AACTTACAT-A-ATACATAACTTACAT
*
39201585 AACTTACATAAGTTACATAA--TACAC
1 AACTTACATAA--TACATAACTTACAT
* *
39201610 AACTTACATAGCTTACTTAA--TACAT
1 AACTTACATA--ATACATAACTTACAT
* * *
39201635 GACTTACATAACT-TATACACGTACAT
1 AACTTACATAA-TACATA-ACTTACAT
39201661 AACTTACATAAT
1 AACTTACATAAT
39201673 TTACTTAATA
Statistics
Matches: 266, Mismatches: 46, Indels: 62
0.71 0.12 0.17
Matches are distributed among these distances:
23 27 0.10
24 3 0.01
25 126 0.47
26 40 0.15
27 61 0.23
28 9 0.03
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:39201510 original size:59 final size:59
Alignment explanation
Indices: 39201405--39201617 Score: 340
Period size: 59 Copynumber: 3.6 Consensus size: 59
39201395 CATAACTTAC
39201405 ATAACTTACATAA--TACATAATAACTTACAACTTACAACTTACATAACATACATTAATTTG
1 ATAACTTACATAAGTTACATAAT-AC--ACAACTTACAACTTACATAACATACATTAATTTG
*
39201465 ATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAACATACATTAATTTG
1 ATAACTTACATAAGTTACATAATACACAACTTACAACTTACATAACATACATTAATTTG
* * * *
39201524 GTAACTTACATAAGTTACACAATACATAACTTACAACTTACATAACATACATTACTTTG
1 ATAACTTACATAAGTTACATAATACACAACTTACAACTTACATAACATACATTAATTTG
39201583 ATAACTTACATAAGTTACATAATACACAACTTACA
1 ATAACTTACATAAGTTACATAATACACAACTTACA
39201618 TAGCTTACTT
Statistics
Matches: 144, Mismatches: 7, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
59 121 0.84
60 13 0.09
61 2 0.01
62 8 0.06
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (59 bp):
ATAACTTACATAAGTTACATAATACACAACTTACAACTTACATAACATACATTAATTTG
Found at i:39201647 original size:118 final size:117
Alignment explanation
Indices: 39201374--39201649 Score: 353
Period size: 118 Copynumber: 2.3 Consensus size: 117
39201364 ATCTTACAAC
* * *
39201374 ACTTACATAACCTACATAATACATAACTTACATAACTTACATAATACATAATAACTTACAACTTA
1 ACTTACAT-ACTTACTTAATACATAACTTACATAACTTACATAATACACAATAAC-TACAACTTA
*
39201439 CAACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACATA
64 CAACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACACA
* *** *
39201493 ACTTACA-ACTTACATAACATACATTAA-TTTGGTAACTTACATAAGTTACACAAT-AC-ATAAC
1 ACTTACATACTTAC-TTA-ATACA-TAACTTACATAACTTACATAA--TACACAATAACTACAAC
*
39201554 TTACAACTTACATAACATACATTACTTTGATAACTTACATAAGTTACATAATACACA
61 TTACAACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACACA
*
39201611 ACTTACATAGCTTACTTAATACATGACTTACATAACTTA
1 ACTTACATA-CTTACTTAATACATAACTTACATAACTTA
39201650 TACACGTACA
Statistics
Matches: 134, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
117 7 0.05
118 81 0.60
119 29 0.22
120 10 0.07
121 7 0.05
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.33
Consensus pattern (117 bp):
ACTTACATACTTACTTAATACATAACTTACATAACTTACATAATACACAATAACTACAACTTACA
ACTTACATAACATACATTAATTTGATAACTTACATAAGTTACATAATACACA
Found at i:39203903 original size:21 final size:22
Alignment explanation
Indices: 39203877--39203923 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
39203867 CTCTGCTCAA
*
39203877 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
39203898 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
39203920 ACTC
1 ACTC
39203924 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:39214645 original size:18 final size:19
Alignment explanation
Indices: 39214624--39214673 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
39214614 AGCAACCGAT
39214624 GGAGGAACATGCTCGA-GA
1 GGAGGAACATGCTCGAGGA
*
39214642 GGAGGAACATGCT-TAGGA
1 GGAGGAACATGCTCGAGGA
*
39214660 AGAGGAACATGCTC
1 GGAGGAACATGCTC
39214674 TGGTGTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.34, C:0.16, G:0.36, T:0.14
Consensus pattern (19 bp):
GGAGGAACATGCTCGAGGA
Found at i:39215581 original size:29 final size:31
Alignment explanation
Indices: 39215524--39215590 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
39215514 GATATCAGTC
* *
39215524 ATGCAGTGAACAGTATGTAATATCATTAATCG
1 ATGCAGTGAACAGTA-GTAAAATCATTAATCA
39215556 ATGCAGT-AACAGTA-TAAAATCATTAATCA
1 ATGCAGTGAACAGTAGTAAAATCATTAATCA
39215585 ATGCAG
1 ATGCAG
39215591 ATATGCAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 19 0.58
31 7 0.21
32 7 0.21
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (31 bp):
ATGCAGTGAACAGTAGTAAAATCATTAATCA
Found at i:39216003 original size:27 final size:27
Alignment explanation
Indices: 39215973--39216167 Score: 203
Period size: 27 Copynumber: 7.2 Consensus size: 27
39215963 TCATCTCCTA
** *
39215973 GGGGTATAACAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
39216000 GGGGTATTTCAATCATTTTATCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
39216027 GGGCTATTTCGGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
**
39216054 GGGGTATTTCAGTCATTTTACTTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
39216081 GAGGTATTT-TGTTCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* * *
39216108 GGGGTATTTCGGTCATTCTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
**
39216135 GGGGTATTTTGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
39216162 GAGGTA
1 GGGGTA
39216168 GTTTGGTCAT
Statistics
Matches: 139, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 137 0.99
28 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:39216047 original size:54 final size:52
Alignment explanation
Indices: 39215984--39216167 Score: 233
Period size: 54 Copynumber: 3.4 Consensus size: 52
39215974 GGGTATAACA
* * *
39215984 GTCATTTTACCTTATGGGGGTATTTCAATCATTTTATCTTATGGGGCTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTA-CTTATGGGG-TATTTTG
*
39216038 GTCATTTTACCCTATAGGGGTATTTCAGTCATTTTACTTTATGGAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTAC-TTATGG-GGTATTTTG
* * * *
39216092 TTCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTA-CTTAT-GGGGTATTTTG
*
39216146 GTCATTTTACCCTATGGAGGTA
1 GTCATTTTACCCTATGGGGGTA
39216168 GTTTGGTCAT
Statistics
Matches: 115, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
53 1 0.01
54 109 0.95
55 5 0.04
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (52 bp):
GTCATTTTACCCTATGGGGGTATTTCAGTCATTTTACTTATGGGGTATTTTG
Found at i:39216097 original size:81 final size:81
Alignment explanation
Indices: 39215971--39216177 Score: 270
Period size: 81 Copynumber: 2.6 Consensus size: 81
39215961 TTTCATCTCC
** * ** * *
39215971 TAGGGGTATAACAGTCATTTTACCTTATGGGGGTATTTCAATCATTTTATCTTATGGGGCTATTT
1 TAGGGGTATTTCAGTCATTTTACCTTATGGAGGTATTTTGATCATTTTACCCTATGGGGCTATTT
*
39216036 CGGTCATTTTACCCTA
66 CGGTCATTCTACCCTA
* * *
39216052 TAGGGGTATTTCAGTCATTTTACTTTATGGAGGTATTTTGTTCATTTTACCCTATGGGGGTATTT
1 TAGGGGTATTTCAGTCATTTTACCTTATGGAGGTATTTTGATCATTTTACCCTATGGGGCTATTT
39216117 CGGTCATTCTACCCTA
66 CGGTCATTCTACCCTA
** * * *
39216133 TAGGGGTATTTTGGTCATTTTACCCTATGGAGGTAGTTTGGTCAT
1 TAGGGGTATTTCAGTCATTTTACCTTATGGAGGTATTTTGATCAT
39216178 AATAGTGTAA
Statistics
Matches: 109, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 109 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (81 bp):
TAGGGGTATTTCAGTCATTTTACCTTATGGAGGTATTTTGATCATTTTACCCTATGGGGCTATTT
CGGTCATTCTACCCTA
Found at i:39224976 original size:20 final size:19
Alignment explanation
Indices: 39224913--39224977 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
39224903 AACCCAATAA
* * *
39224913 GTATCGATATTTTTAAGAGG
1 GTATCAATAATTTTAA-AAG
*
39224933 GTATCAATAATTTTATAAAA
1 GTATCAATAATTTTA-AAAG
39224953 GTATCAATAATTTTAAAATG
1 GTATCAATAATTTTAAAA-G
39224973 GTATC
1 GTATC
39224978 GATACCAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 3 0.08
20 34 0.89
21 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (19 bp):
GTATCAATAATTTTAAAAG
Found at i:39225220 original size:19 final size:19
Alignment explanation
Indices: 39225174--39225221 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
39225164 GTATATATTT
39225174 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
* *
39225192 TAAATCTTATTTAGGTATA
1 TAAATTTTATTTAGGTAGA
*
39225211 TAAGTTTTATT
1 TAAATTTTATT
39225222 CATATTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:39229837 original size:19 final size:18
Alignment explanation
Indices: 39229808--39229847 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
39229798 GTATATATTT
39229808 TAAATTTATTTAGGTAGA
1 TAAATTTATTTAGGTAGA
39229826 TAAATCTTATTTAGGTAGA
1 TAAAT-TTATTTAGGTAGA
39229845 TAA
1 TAA
39229848 GTTTTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (18 bp):
TAAATTTATTTAGGTAGA
Found at i:39236643 original size:33 final size:33
Alignment explanation
Indices: 39236606--39236670 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
39236596 CAATACAACC
39236606 AATGTCTCAATTTCATATATATTATCAACTTGA
1 AATGTCTCAATTTCATATATATTATCAACTTGA
39236639 AATGTCTCAATTTCATATATATTATCAACTTG
1 AATGTCTCAATTTCATATATATTATCAACTTG
39236671 TATGCATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (33 bp):
AATGTCTCAATTTCATATATATTATCAACTTGA
Found at i:39247634 original size:14 final size:14
Alignment explanation
Indices: 39247615--39247644 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39247605 CATTCCGAAG
*
39247615 TATATATATATACA
1 TATATACATATACA
39247629 TATATACATATACA
1 TATATACATATACA
39247643 TA
1 TA
39247645 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATACATATACA
Found at i:39248185 original size:56 final size:56
Alignment explanation
Indices: 39248094--39248216 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
39248084 GAGATTGGTG
* * *
39248094 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
39248151 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
39248206 CTGAGTGTGCG
1 CTAAGTGTGCG
39248217 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:39248203 original size:27 final size:28
Alignment explanation
Indices: 39248094--39248216 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
39248084 GAGATTGGTG
* * * *
39248094 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
39248123 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
39248151 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
39248179 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
39248206 CTGAGTGTGCG
1 CTAAGTGTGCG
39248217 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:39248227 original size:27 final size:27
Alignment explanation
Indices: 39248119--39248229 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
39248109 TAAATTGTAC
* * *
39248119 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
39248147 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
39248175 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
39248202 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
39248229 A
1 A
39248230 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:39255953 original size:8 final size:8
Alignment explanation
Indices: 39255937--39255970 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
39255927 CATTCCGAAG
*
39255937 TATATATA
1 TATACATA
39255945 TATACATA
1 TATACATA
39255953 TATACATA
1 TATACATA
39255961 TATACATA
1 TATACATA
39255969 TA
1 TA
39255971 CATAAGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (8 bp):
TATACATA
Found at i:39255971 original size:14 final size:15
Alignment explanation
Indices: 39255937--39255974 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
39255927 CATTCCGAAG
*
39255937 TATATATATATACATA
1 TATACATATATACA-A
39255953 TATACATATATAC-A
1 TATACATATATACAA
39255967 TATACATA
1 TATACATA
39255975 AGTATGCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
16 12 0.57
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (15 bp):
TATACATATATACAA
Found at i:39256533 original size:27 final size:28
Alignment explanation
Indices: 39256424--39256547 Score: 178
Period size: 28 Copynumber: 4.4 Consensus size: 28
39256414 GAGATTGGCG
* * * *
39256424 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
39256453 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
39256481 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
39256509 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
39256536 CTGAGTGTGCGA
1 CTAAGTGTGCGA
39256548 ACTTAATATA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 25 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:39264705 original size:30 final size:31
Alignment explanation
Indices: 39264659--39264722 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
39264649 ATTTCTTATG
39264659 CCAATATTTCGATACCCATATCTTTGAATTT
1 CCAATATTTCGATACCCATATCTTTGAATTT
* *
39264690 CCAATATTT-GATACCCTTATCTTTGACTTT
1 CCAATATTTCGATACCCATATCTTTGAATTT
39264720 CCA
1 CCA
39264723 TAATATGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (31 bp):
CCAATATTTCGATACCCATATCTTTGAATTT
Found at i:39269880 original size:50 final size:51
Alignment explanation
Indices: 39269773--39269901 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 51
39269763 AAAGAGATCC
* * * * **
39269773 CATGTAAGACCATGTCTGGAACATGGCGTTGGTACCAAGATGAGAGGTCCT
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAACTCCT
* * * *
39269824 C-CGTAAGACCATGTTTGGGACATGGCATGGGCACCTATATGAGAACT-CT
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAACTCCT
* *
39269873 CATGTAAGACCATATCTGGGATATGGCAT
1 CATGTAAGACCATGTCTGGGACATGGCAT
39269902 TAGCAGTACA
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
49 3 0.05
50 59 0.94
51 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (51 bp):
CATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAACTCCT
Found at i:39281662 original size:27 final size:27
Alignment explanation
Indices: 39281132--39281651 Score: 628
Period size: 27 Copynumber: 19.3 Consensus size: 27
39281122 AGAGGCCAAT
* *
39281132 AAATGACCAAAATAACCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39281159 AAATGACCAAAATACTCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
39281186 AAATGACCAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
39281213 GAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39281240 GAATGACCAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39281267 AAAT-AGCCAAAATAACCCCATAGGGTA
1 AAATGA-CCGAAATACCCCCATAGGGTA
* *
39281294 AAATAATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39281321 GAACGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39281348 AAAGGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39281375 AAATGACCAAAATACTCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
**
39281402 AAATGACTAAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39281429 AAATAACCAAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39281456 GAATGACAGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
***
39281483 AAATGACCGAAATACCCCCATAAAATA
1 AAATGACCGAAATACCCCCATAGGGTA
** * *
39281510 AAATGACTAAAATACCCCCATAAGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39281537 AAATGACCGAAATACCCCTATAGTGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39281564 AAATGATCGAAATAACCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
39281591 GAATGATCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
39281618 AAATAATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
39281645 AAATGAC
1 AAATGAC
39281652 TGTTATACCC
Statistics
Matches: 431, Mismatches: 60, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.00
27 429 1.00
28 1 0.00
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:39290531 original size:17 final size:16
Alignment explanation
Indices: 39290488--39290557 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
39290478 TTTTTGGTAC
* * *
39290488 TTTAGGGTTTATGTTT
1 TTTAGAGTTTAAGGTT
*
39290504 TTTAGATTTTAAGGTT
1 TTTAGAGTTTAAGGTT
*
39290520 TTTACGAGTTT-AGGACT
1 TTTA-GAGTTTAAGG-TT
*
39290537 TTTATGGGTTTAAGGTT
1 TTTA-GAGTTTAAGGTT
39290554 TTTA
1 TTTA
39290558 ACTGTTCTGG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
16 19 0.45
17 20 0.48
18 3 0.07
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTAGAGTTTAAGGTT
Found at i:39295222 original size:23 final size:23
Alignment explanation
Indices: 39295192--39295236 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39295182 TTTCTTAGTG
* *
39295192 TAGTAATTTTCGGGGTATTACAA
1 TAGTAATTTTCAGGATATTACAA
39295215 TAGTAATTTTCAGGATATTACA
1 TAGTAATTTTCAGGATATTACA
39295237 GAGCCATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCAGGATATTACAA
Found at i:39306435 original size:61 final size:59
Alignment explanation
Indices: 39306314--39306438 Score: 135
Period size: 61 Copynumber: 2.1 Consensus size: 59
39306304 TTTATAAAAA
* * * *
39306314 AATATAATATTTATCAAAATAAAATATTAGATTAAATTTAATATTAAATCTATTAAATT
1 AATATAATACTTATCAAAATAAAATATTAAATTAAATTTAATATTAAATCAATCAAATT
* * * * *
39306373 AATATAATACTTATCTACAATATAACTATTAAATTTAATTTAATATTAAGGT-AATCACATT
1 AATATAATACTTATC-AAAATA-AAATATTAAATTAAATTTAATATTAA-ATCAATCAAATT
39306434 AATAT
1 AATAT
39306439 TAAATTAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 14 0.26
60 5 0.09
61 34 0.63
62 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (59 bp):
AATATAATACTTATCAAAATAAAATATTAAATTAAATTTAATATTAAATCAATCAAATT
Found at i:39307010 original size:27 final size:25
Alignment explanation
Indices: 39306955--39307022 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
39306945 CTTCCCTAAG
* *
39306955 CCCCCAAAACTTTTTTCCTTTTGCTTT
1 CCCCCAAAAC--TTTTACTTTTCCTTT
39306982 CCCCCAAAACTTTTACTTTCTCCTGTT
1 CCCCCAAAACTTTTACTTT-TCCT-TT
*
39307009 CCCTCAAAACTTTT
1 CCCCCAAAACTTTT
39307023 TTTCAAACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 8 0.22
26 3 0.08
27 25 0.69
ACGTcount: A:0.19, C:0.35, G:0.03, T:0.43
Consensus pattern (25 bp):
CCCCCAAAACTTTTACTTTTCCTTT
Found at i:39307066 original size:39 final size:36
Alignment explanation
Indices: 39307023--39307094 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
39307013 CAAAACTTTT
39307023 TTTCAAACTTATGTCTACTATTTATATTATTAAATTAAA
1 TTTCAAA-TTATG-C-ACTATTTATATTATTAAATTAAA
* *
39307062 TTTCACATTTTGCACTATTTATATTATTAAATT
1 TTTCAAATTATGCACTATTTATATTATTAAATT
39307095 GTTTAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 20 0.65
37 1 0.03
38 4 0.13
39 6 0.19
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (36 bp):
TTTCAAATTATGCACTATTTATATTATTAAATTAAA
Found at i:39307398 original size:19 final size:19
Alignment explanation
Indices: 39307374--39307411 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39307364 AAGTTAATAC
*
39307374 AAATTTGATTACGATGGGT
1 AAATTTGATGACGATGGGT
*
39307393 AAATTTGATGACGGTGGGT
1 AAATTTGATGACGATGGGT
39307412 GGCAGAGGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (19 bp):
AAATTTGATGACGATGGGT
Found at i:39308684 original size:16 final size:16
Alignment explanation
Indices: 39308663--39308693 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39308653 ACCATGAATG
*
39308663 TCACAAGTGAATTAAT
1 TCACAAATGAATTAAT
39308679 TCACAAATGAATTAA
1 TCACAAATGAATTAA
39308694 GAATTAATTC
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:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (16 bp):
TCACAAATGAATTAAT
Found at i:39309715 original size:24 final size:24
Alignment explanation
Indices: 39309683--39309731 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
39309673 CCTAAGAGTT
39309683 TGATTTTCTCCCTTTTACATAGTC
1 TGATTTTCTCCCTTTTACATAGTC
39309707 TGATTTTCTCCCTTTTACATAGTC
1 TGATTTTCTCCCTTTTACATAGTC
39309731 T
1 T
39309732 TCAATCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.51
Consensus pattern (24 bp):
TGATTTTCTCCCTTTTACATAGTC
Found at i:39309800 original size:25 final size:25
Alignment explanation
Indices: 39309757--39309824 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
39309747 AAGAAAGAAA
*
39309757 TAAAACAGCAAAA-AGAAAATCTACTC
1 TAAAA-AG-AAAAGAGAAAATCTAATC
39309783 TAAAAAGAAAAGAGAAAATCTAATC
1 TAAAAAGAAAAGAGAAAATCTAATC
*
39309808 TACAAATGAAAAG-GAAA
1 TA-AAAAGAAAAGAGAAA
39309825 GGAAAGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
24 4 0.11
25 20 0.53
26 14 0.37
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (25 bp):
TAAAAAGAAAAGAGAAAATCTAATC
Found at i:39316271 original size:21 final size:23
Alignment explanation
Indices: 39316229--39316274 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
39316219 TAATTAATCA
*
39316229 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
39316252 TAAA-AGAAG-AAATAT-TTTT-
1 TAAACAGAAGCAAATATCTTTTC
39316271 TAAA
1 TAAA
39316275 AAAAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 5 0.23
22 5 0.23
23 4 0.18
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:39319553 original size:15 final size:16
Alignment explanation
Indices: 39319514--39319554 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
39319504 AAAGTTTCTC
*
39319514 CAAATTTTTAAGTTTT
1 CAAAATTTTAAGTTTT
39319530 CAAAA-TTTAAGTTTT
1 CAAAATTTTAAGTTTT
39319545 -AAAATTTTAA
1 CAAAATTTTAA
39319555 TTACAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 15 0.65
16 4 0.17
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (16 bp):
CAAAATTTTAAGTTTT
Found at i:39321081 original size:26 final size:26
Alignment explanation
Indices: 39321036--39321099 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
39321026 CGACCCATGG
*
39321036 CTCATGTGAGCAGGCCCATTTCACAA
1 CTCATGTGAGCAGACCCATTTCACAA
* *
39321062 CTCGTGTGAGCAGACTCATTTCACAA
1 CTCATGTGAGCAGACCCATTTCACAA
39321088 CTCATGTGAGCA
1 CTCATGTGAGCA
39321100 ACGATGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (26 bp):
CTCATGTGAGCAGACCCATTTCACAA
Found at i:39323057 original size:35 final size:35
Alignment explanation
Indices: 39323006--39323076 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
39322996 CACACAGCCG
*
39323006 TGTGACCCCTGCAGTATGAAATTTTCTATCTTTTT
1 TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
* *
39323041 TGTGATCCCTGTAGTATAAAATTTTCTATCTTTTT
1 TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
39323076 T
1 T
39323077 CTTAATGCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (35 bp):
TGTGACCCCTGCAGTATAAAATTTTCTATCTTTTT
Found at i:39324273 original size:42 final size:42
Alignment explanation
Indices: 39324223--39324347 Score: 241
Period size: 42 Copynumber: 3.0 Consensus size: 42
39324213 ATTCATATGT
39324223 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAAA
1 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAAA
39324265 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAAA
1 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAAA
*
39324307 TTGGTTTAGTGGAATAGAGACTGTAATAGCATAAGGAAAAA
1 TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAA
39324348 TGCTCAAATG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (42 bp):
TTGGTTTAGTGGAATAGAGACTGAAATAGCATAAGGAAAAAA
Found at i:39326067 original size:66 final size:66
Alignment explanation
Indices: 39325889--39326067 Score: 198
Period size: 66 Copynumber: 2.7 Consensus size: 66
39325879 CTAGTGAGCT
* * **
39325889 TACTGACTTGGGTCACACGGCCAAGCCACACGTCCATGTGCTAGGCTGTGTGAAAAATGATGGGC
1 TACTGACTTGTGTCACACGGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAATGATGGGC
39325954 A
66 A
* ** * *
39325955 TACTGACTTGTGACACACGGCCAAGCCACACACCCGTGAGCTAGGCCATGTGAAAACTGGA-GGG
1 TACTGACTTGTGTCACACGGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAAT-GATGGG
*
39326019 TA
65 CA
* ** * * *
39326021 TACTGACTTATGTCACACGGTTAAGTCACACGTCTGTGTGCCAGGCC
1 TACTGACTTGTGTCACACGGCCAAGCCACACGTCCGTGTGCTAGGCC
39326068 GTCTGACACT
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
66 90 0.98
67 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (66 bp):
TACTGACTTGTGTCACACGGCCAAGCCACACGTCCGTGTGCTAGGCCATGTGAAAAATGATGGGC
A
Found at i:39327390 original size:36 final size:35
Alignment explanation
Indices: 39327340--39327411 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
39327330 ACATTTAATA
39327340 CATATCTCGGAAGATCA-TCTTCCATATTTGCCAAG
1 CATATCTCGGAAGATCACT-TTCCATATTTGCCAAG
* * *
39327375 CATATCTTTGGAAGATCACTTTTCTTATTTGCCAAG
1 CATATC-TCGGAAGATCACTTTCCATATTTGCCAAG
39327411 C
1 C
39327412 TCCAGAGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 6 0.19
36 25 0.78
37 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (35 bp):
CATATCTCGGAAGATCACTTTCCATATTTGCCAAG
Found at i:39329926 original size:3 final size:3
Alignment explanation
Indices: 39329918--39329958 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
39329908 ATGACTCACC
* *
39329918 TAT TAT TAT TAT TAT T-T TTT TTT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
39329959 CTTTAACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (3 bp):
TAT
Found at i:39329945 original size:14 final size:14
Alignment explanation
Indices: 39329918--39329958 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
39329908 ATGACTCACC
39329918 TATTATTATTATTAT
1 TATTATT-TTATTAT
* *
39329933 TTTTTTTTTATTAT
1 TATTATTTTATTAT
39329947 TATTATTTTATT
1 TATTATTTTATT
39329959 CTTTAACTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:39332451 original size:41 final size:40
Alignment explanation
Indices: 39332406--39332520 Score: 131
Period size: 40 Copynumber: 2.8 Consensus size: 40
39332396 AGCGGCACTT
* *
39332406 TTAGCGGCGTTTGTACAAAAAACGCCGCTAAAAATCGAGCA
1 TTAGCGGCGTTT-TAGAAAAAACGCCACTAAAAATCGAGCA
** ** *
39332447 TTAGCGGCGCATTAGTTAAAACGCCACTAAAGATCGAGCA
1 TTAGCGGCGTTTTAGAAAAAACGCCACTAAAAATCGAGCA
* *
39332487 TTAGCGGCGTTTTTTGAAAAAACGCCACAAAAAA
1 TTAGCGGCG-TTTTAGAAAAAACGCCACTAAAAA
39332521 CCTAAGCCCA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
40 32 0.54
41 27 0.46
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGTTTTAGAAAAAACGCCACTAAAAATCGAGCA
Found at i:39332636 original size:41 final size:41
Alignment explanation
Indices: 39332557--39332676 Score: 168
Period size: 41 Copynumber: 2.9 Consensus size: 41
39332547 CCTTTCGGGG
* * * * *
39332557 CTTTAGCGACGTTTTTAAAAAAATCGCCGCTAAAGCTCAGAT
1 CTTTAGCGGCGTTTCT-AGAAAAGCGCCGCTAATGCTCAGAT
39332599 CTTTAGCGGCGTTTCTAGAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTCTAGAAAAGCGCCGCTAATGCTCAGAT
* *
39332640 CTTTAGCGGCGATTCTAGAAATGCGCCGCTAATGCTC
1 CTTTAGCGGCGTTTCTAGAAAAGCGCCGCTAATGCTC
39332677 GAGGCTTTAG
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 57 0.80
42 14 0.20
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTCTAGAAAAGCGCCGCTAATGCTCAGAT
Found at i:39333190 original size:14 final size:14
Alignment explanation
Indices: 39333160--39333211 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
39333150 GGGTTGTGAT
* *
39333160 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
*
39333174 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
* *
39333188 TTAATGGTTAGAGG
1 TTAAGGGTTAGGGG
*
39333202 TTAAGAGTTA
1 TTAAGGGTTA
39333212 AGGATTTAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.37
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:39333211 original size:21 final size:21
Alignment explanation
Indices: 39333172--39333212 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39333162 AAGGTTTATG
* * *
39333172 GGTTAGGGGTTAGGGGTTAAT
1 GGTTAGAGGTTAAGAGTTAAT
39333193 GGTTAGAGGTTAAGAGTTAA
1 GGTTAGAGGTTAAGAGTTAA
39333213 GGATTTAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.41, T:0.32
Consensus pattern (21 bp):
GGTTAGAGGTTAAGAGTTAAT
Found at i:39334600 original size:148 final size:150
Alignment explanation
Indices: 39334331--39334648 Score: 475
Period size: 148 Copynumber: 2.1 Consensus size: 150
39334321 ATAATTTTTT
* * *
39334331 GCGGCGTTTTTAT-GAAAAACGCCACAAAAAATAATTTTACTTCAAAAAAATAGCGCCATTTTAG
1 GCGGCGTTTTTATAAAAAAACACCACAAAAAATAATTTTACTTCAAAAAAATAGCGCCATTTTAA
* *
39334395 CATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTTGCGGCATTTTTATGAAAAA-
66 CATAACAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTTGCGGCATTTTTAT-AAAAAG
* *
39334459 CGCCGTAAAATG-TAAGCAATA
130 CGCCGCAAAA-GATAAGCAAAA
* * *
39334480 GCGGCGTTTTTATAAAAAAACACCAC-AAAATTAATTTTACTT-TAAAAAATAGCGTCATTTTAA
1 GCGGCGTTTTTATAAAAAAACACCACAAAAAATAATTTTACTTCAAAAAAATAGCGCCATTTTAA
*
39334543 CATAACAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTTGCGGCATTTTTATAAAAAGT
66 CATAACAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTTGCGGCATTTTTATAAAAAGC
39334608 GCCGCAAAAGATAAGCAAAA
131 GCCGCAAAAGATAAGCAAAA
*
39334628 GGGGCGTTTTTATAAAAAAAC
1 GCGGCGTTTTTATAAAAAAAC
39334649 CCAAAAGCTT
Statistics
Matches: 154, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
147 6 0.04
148 110 0.71
149 28 0.18
150 10 0.06
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (150 bp):
GCGGCGTTTTTATAAAAAAACACCACAAAAAATAATTTTACTTCAAAAAAATAGCGCCATTTTAA
CATAACAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTTGCGGCATTTTTATAAAAAGC
GCCGCAAAAGATAAGCAAAA
Found at i:39339118 original size:43 final size:42
Alignment explanation
Indices: 39339068--39339336 Score: 313
Period size: 43 Copynumber: 6.3 Consensus size: 42
39339058 ATTATGTTTT
*
39339068 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAGTCTA
1 TAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCATGGTCTA
* * * * *
39339111 TGGCGGCGTTTGAGGAAAAAGTGCCACTAAAGGTCATGGTCAA
1 TAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
39339154 TAGCGGCGTTTGTTGGAAAAGTGCCACTAATGGTCATGGTCTA
1 TAGCGGCGTTTG-TGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
39339197 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAATGGTCATGGTCTT
1 TAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
39339240 TAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGGTTATGGTCTT
1 TAGCGGCGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGGTCTA
* * * *
39339283 TGGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGGTCTT
1 TAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTA
39339326 TAGCGGCGTTT
1 TAGCGGCGTTT
39339337 ATTTTTAAAA
Statistics
Matches: 199, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
42 4 0.02
43 191 0.96
44 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGTCTA
Found at i:39339173 original size:86 final size:86
Alignment explanation
Indices: 39339066--39339336 Score: 357
Period size: 86 Copynumber: 3.2 Consensus size: 86
39339056 AGATTATGTT
* * *
39339066 TTTAGCGGCGTTTG-TGAGAAAAGCGCCGCTAAAGGTCATAGTCTATGGCGGCGTTTGAGGAAAA
1 TTTAGCGGCGTTTGTTG-GAAAAGCGCCGCTAAAGGTCATGGTCTATGGCGGCGTTTGTGGGAAA
* *
39339130 AGTGCCACTAAAGGTCATGGTC
65 AGCGCCGCTAAAGGTCATGGTC
** * * * * *
39339152 AATAGCGGCGTTTGTTGGAAAAGTGCCACTAATGGTCATGGTCTATAGCGGCGTTTTTGGGAAAA
1 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTCTATGGCGGCGTTTGTGGGAAAA
*
39339217 GCGCCGCTAATGGTCATGGTC
66 GCGCCGCTAAAGGTCATGGTC
* *
39339238 TTTAGCGGCGTTT-TTGGAAAAAGCGCCGCTAAAGGTTATGGTCTTTGGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTGTTGG-AAAAGCGCCGCTAAAGGTCATGGTCTATGGCGGCGTTTGTGGGAAA
* *
39339302 AGCACCGCTAAAGGTCTTGGTC
65 AGCGCCGCTAAAGGTCATGGTC
39339324 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
39339337 ATTTTTAAAA
Statistics
Matches: 158, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
85 4 0.03
86 152 0.96
87 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTCTATGGCGGCGTTTGTGGGAAAA
GCGCCGCTAAAGGTCATGGTC
Found at i:39339301 original size:129 final size:129
Alignment explanation
Indices: 39339068--39339336 Score: 349
Period size: 129 Copynumber: 2.1 Consensus size: 129
39339058 ATTATGTTTT
* *
39339068 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAGTCTATGGCGGCGTTTGAGGAAAAAGT
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAGTCTATAGCGGCGTTTGAGGAAAAAGC
* ** *
39339133 GCCACTAAAGGTCATGGTCAATAGCGGCGTTTGTTGGAAAAGTGCCACTAATGGTCATGGTCTA
66 GCCACTAAAGGTCATGGTCAATAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGTCATGGTCTA
* * * * * **
39339197 TAGCGGCGTTTTTGGGAAAAGCGCCGCTAATGGTCATGGTCTTTAGCGGCGTTTTTGGAAAAAGC
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAGTCTATAGCGGCGTTTGAGGAAAAAGC
* * ** * * * *
39339262 GCCGCTAAAGGTTATGGTCTTTGGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGGTCTT
66 GCCACTAAAGGTCATGGTCAATAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGTCATGGTCTA
39339326 TAGCGGCGTTT
1 TAGCGGCGTTT
39339337 ATTTTTAAAA
Statistics
Matches: 119, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
129 119 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (129 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATAGTCTATAGCGGCGTTTGAGGAAAAAGC
GCCACTAAAGGTCATGGTCAATAGCGGCGTTTGTGGGAAAAGCACCACTAAAGGTCATGGTCTA
Found at i:39341386 original size:202 final size:202
Alignment explanation
Indices: 39341034--39341442 Score: 705
Period size: 202 Copynumber: 2.0 Consensus size: 202
39341024 AAATTTTATC
** * *
39341034 AAAATAATTTATGATTCGTGAATAGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTACTTA
1 AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
*
39341099 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTCAATTGTGAAAAATCTATTTGGTTGGAA
66 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCTATTTGGTTGGAA
*
39341164 TATTTATTTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
131 TATTTAATTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
39341229 ATGATGA
196 ATGATGA
*
39341236 AAAATAAAGTATGATTCATGAATGGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
1 AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
*
39341301 AATTAGATAATTATGAAAAGCTTAATGATTAAGGGCTAAATTGTGAAAAATCTAATTT-GTTGGA
66 AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCT-ATTTGGTTGGA
*
39341365 ATATTTAATTATT-TGTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTATAGAA
130 ATATTTAATTATTAT-TTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAA
39341429 AGATGATGA
194 AGATGATGA
39341438 AAAAT
1 AAAAT
39341443 CATCCATGTC
Statistics
Matches: 196, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
201 1 0.01
202 191 0.97
203 4 0.02
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (202 bp):
AAAATAAAGTATGATTCATGAATAGCATTATAGGGAAAGTTGAAGGACTAATTAATAGTTAATTA
AATTAGATAATTATGAAAAGCTTAATGATTAAGGACTAAATTGTGAAAAATCTATTTGGTTGGAA
TATTTAATTATTATTTATTTTAATTAATAAATTAAGTATATATTTTTATAGAATATTACAGAAAG
ATGATGA
Found at i:39350312 original size:2 final size:2
Alignment explanation
Indices: 39350305--39350335 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
39350295 GTCTGCTATT
*
39350305 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39350336 TGAAGCTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:39352849 original size:9 final size:9
Alignment explanation
Indices: 39352835--39352874 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
39352825 GTAGTGATTC
39352835 AATTCGGTT
1 AATTCGGTT
*
39352844 AATTCGGAT
1 AATTCGGTT
39352853 AATTCGGTT
1 AATTCGGTT
*
39352862 AATTCGGGT
1 AATTCGGTT
39352871 AATT
1 AATT
39352875 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39352858 original size:18 final size:18
Alignment explanation
Indices: 39352835--39352874 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
39352825 GTAGTGATTC
39352835 AATTCGGTTAATTCGGAT
1 AATTCGGTTAATTCGGAT
*
39352853 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGAT
39352871 AATT
1 AATT
39352875 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (18 bp):
AATTCGGTTAATTCGGAT
Found at i:39367631 original size:6 final size:6
Alignment explanation
Indices: 39367620--39367646 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39367610 ACCCCTTTCT
39367620 TCCATC TCCATC TCCATC TCCATC TCC
1 TCCATC TCCATC TCCATC TCCATC TCC
39367647 TTTCTGCAAT
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:0.15, C:0.52, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCATC
Found at i:39371380 original size:12 final size:12
Alignment explanation
Indices: 39371363--39371387 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39371353 AGGTGCTGCA
39371363 AAAGAAACAAAG
1 AAAGAAACAAAG
39371375 AAAGAAACAAAG
1 AAAGAAACAAAG
39371387 A
1 A
39371388 GCAGAAGAAG
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:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAACAAAG
Found at i:39374972 original size:17 final size:17
Alignment explanation
Indices: 39374941--39374989 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 17
39374931 TAGAATTGTG
*
39374941 TTGAGAAAATTATTTAAT
1 TTGA-AAAATAATTTAAT
39374959 TTGAAAAATAATTT-AT
1 TTGAAAAATAATTTAAT
*
39374975 TT--AAATTAATTTAAT
1 TTGAAAAATAATTTAAT
39374990 AAATAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 4 0.14
17 9 0.32
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TTGAAAAATAATTTAAT
Found at i:39377551 original size:19 final size:19
Alignment explanation
Indices: 39377504--39377554 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
39377494 GTAATATATA
39377504 TAATTGATAT-TTTATGAT
1 TAATTGATATATTTATGAT
39377522 TGAATTG-TATATTTATG-T
1 T-AATTGATATATTTATGAT
39377540 TAATTGAATATATTT
1 TAATTG-ATATATTT
39377555 TGAATTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.17
18 6 0.21
19 18 0.62
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTGATATATTTATGAT
Found at i:39379613 original size:25 final size:23
Alignment explanation
Indices: 39379569--39379614 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
39379559 ATGTTAATTG
39379569 ATTTAATTTTAAATAAAATAATA
1 ATTTAATTTTAAATAAAATAATA
* *
39379592 ATTTACATATTTAGATAGAATAA
1 ATTTA-AT-TTTAAATAAAATAA
39379615 ATATGTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 2 0.11
25 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTTAATTTTAAATAAAATAATA
Found at i:39384542 original size:26 final size:25
Alignment explanation
Indices: 39384513--39384569 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
39384503 CTTGTTATCT
39384513 TTTTTTCAAATTTCAG-CTTCTCATAC
1 TTTTTTCAAATTTCAGCCTT-TC-TAC
** *
39384539 TTTTCCCAAATTTCGGCCTTTCTAC
1 TTTTTTCAAATTTCAGCCTTTCTAC
39384564 TTTTTT
1 TTTTTT
39384570 TTTTGACATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 7 0.28
26 15 0.60
27 3 0.12
ACGTcount: A:0.18, C:0.25, G:0.05, T:0.53
Consensus pattern (25 bp):
TTTTTTCAAATTTCAGCCTTTCTAC
Found at i:39391078 original size:45 final size:45
Alignment explanation
Indices: 39391002--39391108 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
39390992 GTAATGGTAG
*
39391002 CAGTAACAGTAACAGTAACAGAATTCAACACACAAAGTG-CTGAAT
1 CAGTAATAGTAACAGTAACAGAATTCAACACACAAAGTGTC-GAAT
* * * *
39391047 CTGTCATAGTAAC-GATAACAGTATTCGACACACAAAGTGTCGAAT
1 CAGTAATAGTAACAG-TAACAGAATTCAACACACAAAGTGTCGAAT
39391092 CAGTAATAGTAACAGTA
1 CAGTAATAGTAACAGTA
39391109 GTAAGCATCT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.02
45 49 0.94
46 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (45 bp):
CAGTAATAGTAACAGTAACAGAATTCAACACACAAAGTGTCGAAT
Found at i:39391368 original size:40 final size:40
Alignment explanation
Indices: 39391308--39391394 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
39391298 AATTCATTAC
* * *
39391308 TTCAGTAATTTCACAGTTCAATGCAATACACATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
* * * *
39391348 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAAGAATA
1 TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
39391388 TTCAGTA
1 TTCAGTA
39391395 TTCCATAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAATACACAAAACAATA
Found at i:39392186 original size:5 final size:5
Alignment explanation
Indices: 39392176--39392202 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39392166 TTACCTATTT
39392176 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
39392203 CTTATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:39393927 original size:34 final size:34
Alignment explanation
Indices: 39393884--39393954 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
39393874 GATTTCGAAA
39393884 TCTCAAACAATCATGATCATCAACACTAAAATTT
1 TCTCAAACAATCATGATCATCAACACTAAAATTT
39393918 TCTCAAACAATCATGATCATCAACACTAAAATTT
1 TCTCAAACAATCATGATCATCAACACTAAAATTT
39393952 TCT
1 TCT
39393955 ACTGGGCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.31
Consensus pattern (34 bp):
TCTCAAACAATCATGATCATCAACACTAAAATTT
Found at i:39398337 original size:45 final size:45
Alignment explanation
Indices: 39398242--39398341 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
39398232 TAACGGTAGT
* * **
39398242 AGTAACAGTAACAGTATTCAACGCAAAAAGTGTTGAATCTGTAAC
1 AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
* * *
39398287 AGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCAATAAC
1 AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
*
39398332 TGTAACAGTA
1 AGTAACAGTA
39398342 GTCGGCATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCAACACAAAAAGTGTCGAATCAATAAC
Found at i:39399425 original size:5 final size:5
Alignment explanation
Indices: 39399415--39399510 Score: 192
Period size: 5 Copynumber: 19.2 Consensus size: 5
39399405 TTTCTTTACC
39399415 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
39399465 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA T
39399511 CTTATTTATT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 91 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:39402307 original size:20 final size:20
Alignment explanation
Indices: 39402284--39402338 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
39402274 GTGACAAGGC
*
39402284 ACACGCCCGTGTGACTGAGG
1 ACACGCCCATGTGACTGAGG
**
39402304 ACACTTCCATGTGACTGAAGG
1 ACACGCCCATGTGACTG-AGG
* *
39402325 TCACACCCATGTGA
1 ACACGCCCATGTGA
39402339 GTAGGCCGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (20 bp):
ACACGCCCATGTGACTGAGG
Found at i:39402336 original size:21 final size:20
Alignment explanation
Indices: 39402293--39402338 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
39402283 CACACGCCCG
**
39402293 TGTGACTGAGGACACTTCCA
1 TGTGACTGAGGACACACCCA
*
39402313 TGTGACTGAAGGTCACACCCA
1 TGTGACTG-AGGACACACCCA
39402334 TGTGA
1 TGTGA
39402339 GTAGGCCGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (20 bp):
TGTGACTGAGGACACACCCA
Found at i:39403230 original size:15 final size:16
Alignment explanation
Indices: 39403210--39403239 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39403200 GAAATTTCCT
39403210 ACTAACTCG-ACAATC
1 ACTAACTCGCACAATC
39403225 ACTAACTCGCACAAT
1 ACTAACTCGCACAAT
39403240 TTGCTACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (16 bp):
ACTAACTCGCACAATC
Found at i:39416007 original size:41 final size:41
Alignment explanation
Indices: 39415948--39416161 Score: 288
Period size: 41 Copynumber: 5.2 Consensus size: 41
39415938 AGAATATCCT
*
39415948 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * *
39415989 TGAATTGCACATATGTGCCTCTGTTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* * * *
39416030 TGAATTGCACATACGTGCCCTTTTTTTTTAGTTTGGTACCCC
1 TGAATTGCACATACGTGCCC-CTGTTTGTACTTTGGTACCCC
* **
39416072 CGAATTGCACATATATGCCCCTGTTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
* *
39416113 TGAATTGCACATACGTGCCCCT-TTTGTACTATAGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
39416153 TGAA-TGCAC
1 TGAATTGCAC
39416162 TTTTGTACCC
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 5 0.03
40 20 0.13
41 91 0.61
42 33 0.22
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.36
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
Found at i:39416096 original size:83 final size:82
Alignment explanation
Indices: 39415948--39416142 Score: 284
Period size: 83 Copynumber: 2.4 Consensus size: 82
39415938 AGAATATCCT
* * * * *
39415948 TGAATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCCTGAATTGCACATATGTGCCTCTGT
1 TGAATTGCACATACGTGCCCTTTTTTGTACTTTGATACCCCCGAATTGCACATATATGCCCCTGT
39416013 TTGTACTTCGGTACCCC
66 TTGTACTTCGGTACCCC
* * *
39416030 TGAATTGCACATACGTGCCCTTTTTTTTTAGTTTGGTACCCCCGAATTGCACATATATGCCCCTG
1 TGAATTGCACATACGTGCCC-TTTTTTGTACTTTGATACCCCCGAATTGCACATATATGCCCCTG
*
39416095 TTTGTACTTTGGTACCCC
65 TTTGTACTTCGGTACCCC
*
39416113 TGAATTGCACATACGTGCCC-CTTTTGTACT
1 TGAATTGCACATACGTGCCCTTTTTTGTACT
39416143 ATAGTACCCC
Statistics
Matches: 100, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
81 7 0.07
82 20 0.20
83 73 0.73
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.37
Consensus pattern (82 bp):
TGAATTGCACATACGTGCCCTTTTTTGTACTTTGATACCCCCGAATTGCACATATATGCCCCTGT
TTGTACTTCGGTACCCC
Found at i:39416901 original size:15 final size:15
Alignment explanation
Indices: 39416883--39416917 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
39416873 AGTCGTGTGT
39416883 GACATACAGCCTGGC
1 GACATACAGCCTGGC
39416898 GACATACAGCCTGGC
1 GACATACAGCCTGGC
39416913 GACAT
1 GACAT
39416918 GGCCGTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (15 bp):
GACATACAGCCTGGC
Found at i:39419657 original size:165 final size:165
Alignment explanation
Indices: 39419385--39419710 Score: 598
Period size: 165 Copynumber: 2.0 Consensus size: 165
39419375 AGTATAGACA
*
39419385 AAAACTTAAGTTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCCACTCAAACT
1 AAAACTTAAGCTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCCACTCAAACT
* *
39419450 AATTTATACATGCATAGACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
66 AATTTACACATGCATACACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
**
39419515 TCTGAATTGAAATTCTCCTCTATTATAGTTGTCCT
131 TCTGAATTGAAACCCTCCTCTATTATAGTTGTCCT
*
39419550 AAAACTTAAGCTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCTACTCAAACT
1 AAAACTTAAGCTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCCACTCAAACT
39419615 AATTTACACATGCATACACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
66 AATTTACACATGCATACACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
39419680 TCTGAATTGAAACCCTCCTCTATTATAGTTG
131 TCTGAATTGAAACCCTCCTCTATTATAGTTG
39419711 CCCCAAAATT
Statistics
Matches: 155, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 155 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (165 bp):
AAAACTTAAGCTACTTATACAATTTACAATTAATTATAACTTTACTACACATTCCCACTCAAACT
AATTTACACATGCATACACAATAGGTAAATACAATTGCAGTACATGGTAATTTAATTAGAAGAAA
TCTGAATTGAAACCCTCCTCTATTATAGTTGTCCT
Found at i:39422511 original size:31 final size:31
Alignment explanation
Indices: 39422462--39422975 Score: 664
Period size: 31 Copynumber: 16.7 Consensus size: 31
39422452 GTATATGTTT
* * *
39422462 TATACATTGTC-AAATTGATTTGTATAAAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
39422492 TATACATTGTCGAATTTGATTTGTTTATAGG
1 TATACATTGCCGAATTTGATTTGTATATAGA
** * * *
39422523 TATACATTGTTGAAATTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
39422554 TATACATTGTC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
39422584 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
39422615 TATACATTGCCGAATTTAATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
39422646 TATATATTGCCTAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
39422676 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
39422707 TATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
39422738 TATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
39422769 TATACATTCCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
39422799 TATACATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
39422829 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
39422860 TATACATTGCCAAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
39422891 TATTCATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
39422921 TATACATTGCTGAATTTGATTTGTATATGAATA
1 TATACATTGCCGAATTTGATTTGTATAT--AGA
*
39422954 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
39422976 AGCATTGAAT
Statistics
Matches: 431, Mismatches: 45, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
29 2 0.00
30 143 0.33
31 264 0.61
32 8 0.02
33 14 0.03
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:39422582 original size:61 final size:62
Alignment explanation
Indices: 39422462--39422975 Score: 664
Period size: 61 Copynumber: 8.4 Consensus size: 62
39422452 GTATATGTTT
* * * * *
39422462 TATACATTGTC-AAATTGATTTGTATAAAGATATACATTGTCGAATTTGATTTGTTTATAGG
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
** * * * *
39422523 TATACATTGTTGAAATTGAATTGTTTATAGATATACATTGTC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
39422584 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTAATTTGTATATGGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* *
39422646 TATATATTGCC-TAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * *
39422707 TATACATTGTCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* *
39422769 TATACATTCCCG-AATTGATTTGTATATAGATATACATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
39422829 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCAAATTTGATTTGTATATGGA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * *
39422891 TATTCATTGCC-AAATTGATTTGTATATAGATATACATTGCTGAATTTGATTTGTATATGAATA
1 TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATAT--AGA
*
39422954 TATATATTGCCG-AATTGATTTG
1 TATACATTGCCGAAATTGATTTG
39422976 AGCATTGAAT
Statistics
Matches: 392, Mismatches: 53, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
60 29 0.07
61 207 0.53
62 136 0.35
63 20 0.05
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (62 bp):
TATACATTGCCGAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
Found at i:39422598 original size:92 final size:91
Alignment explanation
Indices: 39422462--39422975 Score: 631
Period size: 92 Copynumber: 5.6 Consensus size: 91
39422452 GTATATGTTT
* * * *
39422462 TATACATTGTCAAATTGATTTGTATAAAGATATACATTGTCGAATTTGATTTGTTTATAGGTATA
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGGTATA
* * *
39422527 CATTGTTGAAATTGAATTGTTTATAGA
66 CATTG-CGAAATTGATTTGTATATAGA
*
39422554 TATACATTGTCAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATAT-GGTTAT
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGG-TAT
* * *
39422618 ACATTGCCGAATTTAATTTGTATATGGA
65 ACATTG-CGAAATTGATTTGTATATAGA
* * *
39422646 TATATATTGCCTAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGATATA
1 TATACATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGGTATA
* * *
39422711 CATTGTCGAATTTGATTTGTATATGGT
66 CATTG-CGAAATTGATTTGTATATAGA
* * *
39422738 TATACATTGCCGAATTTGATTTGTATATAGATATACATTCCCGAA-TTGATTTGTATATAGATAT
1 TATACATTGCC-AAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGGTAT
*
39422802 ACATTGCCAAATTGATTTGTATATAGA
65 ACATTGCGAAATTGATTTGTATATAGA
* * * *
39422829 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCAAATTTGATTTGTATAT-GGATA
1 TATACATTGCC-AAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGG-TA
* *
39422893 TTCATTGCCAAATTGATTTGTATATAGA
64 TACATTGCGAAATTGATTTGTATATAGA
* * * *
39422921 TATACATTGCTGAATTTGATTTGTATATGAATATATATATTGCCGAA-TTGATTTG
1 TATACATTGC-CAAATTGATTTGTATAT--AGATATACATTGCCGAATTTGATTTG
39422976 AGCATTGAAT
Statistics
Matches: 377, Mismatches: 37, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
91 61 0.16
92 265 0.70
93 39 0.10
94 12 0.03
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (91 bp):
TATACATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGGTATA
CATTGCGAAATTGATTTGTATATAGA
Found at i:39424731 original size:30 final size:31
Alignment explanation
Indices: 39424691--39424776 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
39424681 ATAGTACGAG
*
39424691 GTATGAATATG-TTAATATGAATG-TTACAAT
1 GTATGAATATGAAT-ATATGAATGATTACAAT
* *
39424721 GTATGCATATGAATATATGAATGATTAC-AG
1 GTATGAATATGAATATATGAATGATTACAAT
* * *
39424751 GTAAGAAAATGAAAATATGAATGATT
1 GTATGAATATGAATATATGAATGATT
39424777 GATGCCGATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 42 0.89
31 5 0.11
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (31 bp):
GTATGAATATGAATATATGAATGATTACAAT
Found at i:39432036 original size:16 final size:15
Alignment explanation
Indices: 39432015--39432044 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39432005 GAACAGATCA
39432015 AAAAATAAATAAAAAT
1 AAAAATAAA-AAAAAT
39432031 AAAAATAAAAAAAA
1 AAAAATAAAAAAAA
39432045 CTTTGAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:39433401 original size:169 final size:169
Alignment explanation
Indices: 39433114--39433753 Score: 933
Period size: 169 Copynumber: 3.8 Consensus size: 169
39433104 CGTCGTTGCG
* **
39433114 GCTTTAATCTATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTCGATCCGCTC
1 GCTTTAATCTATTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTC
* * * * * * *
39433179 CACCTCAGCTA-TTCTAAGTCTCAACGCCAGGGAGATAAGATCCGCTGCCCTCAGCTTTAATCTG
66 CACTTCAACTATTTC-AACTCTTAACACCAGGGAGATAAGATTCGCTACCCTCAGCTTTAATCTG
39433243 CTCCGCTGCAACACTAGGGAAACAAGATTCGCTACATTTA
130 CTCCGCTGCAACACTAGGGAAACAAGATTCGCTACATTTA
* * *
39433283 GCTTTAATCTGTTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCTGTTC
1 GCTTTAATCTATTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTC
* *
39433348 CACTTCAATTATTTCAACTCTTAACACCAGAGAGATAAGATTCGCTACCCTCAGCTTTAATCTGC
66 CACTTCAACTATTTCAACTCTTAACACCAGGGAGATAAGATTCGCTACCCTCAGCTTTAATCTGC
*
39433413 TCCGCTGCAACACTAGGGAAACAAGATTCGCTACTTTTA
131 TCCGCTGCAACACTAGGGAAACAAGATTCGCTACATTTA
* *
39433452 GCTTTAATCCATTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCTGCTC
1 GCTTTAATCTATTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTC
* * *
39433517 CACTTCAGCTATTTCAACTCTTAACACCAGGGAGATAAGATTCGCTGCCCTCAACTTTAATCTGC
66 CACTTCAACTATTTCAACTCTTAACACCAGGGAGATAAGATTCGCTACCCTCAGCTTTAATCTGC
** * * *
39433582 TCCATTGCAACGCTAGGGAAACAATATTCGCTACCTTTA
131 TCCGCTGCAACACTAGGGAAACAAGATTCGCTACATTTA
* * *
39433621 ACTTTAATCTGTTCCACTATAATTCCAAAGAGATAGGA-TCTGCTGCCCACAGCTTTAATCCGCT
1 GCTTTAATCTATTCCACTATAATGCCAAAGAGATAGGATTC-GCTGCCCACAGCTTTAATCCGCT
* * * * * *
39433685 CTACTTCATCTATTTCAAGTCTTAACGCCAGGGAGATAAGATTCGTTACCCTCAGCTTTAATCTT
65 CCACTTCAACTATTTCAACTCTTAACACCAGGGAGATAAGATTCGCTACCCTCAGCTTTAATCTG
39433750 CTCC
130 CTCC
39433754 ACTATAATGT
Statistics
Matches: 427, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
168 2 0.00
169 422 0.99
170 3 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (169 bp):
GCTTTAATCTATTCCACTATAATGCCAAAGAGATAGGATTCGCTGCCCACAGCTTTAATCCGCTC
CACTTCAACTATTTCAACTCTTAACACCAGGGAGATAAGATTCGCTACCCTCAGCTTTAATCTGC
TCCGCTGCAACACTAGGGAAACAAGATTCGCTACATTTA
Found at i:39433824 original size:44 final size:44
Alignment explanation
Indices: 39433775--39433861 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
39433765 AGGAAAGTAA
39433775 GATTCACAATCTTCAACCTATTCCACTGCTAACTAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTAACTAGGGAGATAG
* * *
39433819 GATTCACAATCTTTAACCTATTCCGCTGCTGACTAGGGAGATA
1 GATTCACAATCTTCAACCTATTCCACTGCTAACTAGGGAGATA
39433862 AGGCTAGGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (44 bp):
GATTCACAATCTTCAACCTATTCCACTGCTAACTAGGGAGATAG
Found at i:39436800 original size:9 final size:9
Alignment explanation
Indices: 39436786--39436870 Score: 116
Period size: 9 Copynumber: 9.4 Consensus size: 9
39436776 TTTGGTTAAA
39436786 AATTAACCG
1 AATTAACCG
*
39436795 AATTAACCA
1 AATTAACCG
39436804 AATTAACCG
1 AATTAACCG
*
39436813 AATTACCCG
1 AATTAACCG
39436822 AATTAACCG
1 AATTAACCG
*
39436831 AATTAATCG
1 AATTAACCG
*
39436840 AATTACCCG
1 AATTAACCG
*
39436849 AATTAACCA
1 AATTAACCG
*
39436858 AATTAACCA
1 AATTAACCG
39436867 AATT
1 AATT
39436871 GAATCACTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 67 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:39436822 original size:27 final size:27
Alignment explanation
Indices: 39436786--39436870 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
39436776 TTTGGTTAAA
*
39436786 AATTAACCGAATTAACCAAATTAACCG
1 AATTACCCGAATTAACCAAATTAACCG
* *
39436813 AATTACCCGAATTAACCGAATTAATCG
1 AATTACCCGAATTAACCAAATTAACCG
*
39436840 AATTACCCGAATTAACCAAATTAACCA
1 AATTACCCGAATTAACCAAATTAACCG
39436867 AATT
1 AATT
39436871 GAATCACTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (27 bp):
AATTACCCGAATTAACCAAATTAACCG
Found at i:39437017 original size:18 final size:18
Alignment explanation
Indices: 39436977--39437020 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39436967 TAATTTTATG
**
39436977 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
39436995 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
39437013 CTTGGGTT
1 ATTGGGTT
39437021 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Done.