Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008103.1 Hibiscus syriacus cultivar Beakdansim tig00110633_pilon, whole genome shotgun sequence
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: 1996589
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1265937 original size:21 final size:21
Alignment explanation
Indices: 1265886--1265937 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1265876 CTGACCATAA
*
1265886 TCCCCCTACTACCTTCTCTTCT
1 TCCCCCT-CTACCTTCTCATCT
**
1265908 TCCTTCTCT-CCTTCCTCATCT
1 TCCCCCTCTACCTT-CTCATCT
1265929 TCCCCCTCT
1 TCCCCCTCT
1265938 TCCATCTCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.06, C:0.52, G:0.00, T:0.42
Consensus pattern (21 bp):
TCCCCCTCTACCTTCTCATCT
Found at i:1265993 original size:21 final size:21
Alignment explanation
Indices: 1265969--1266011 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1265959 ATAACCATCA
1265969 AAATTAAATTATAATATTAAT
1 AAATTAAATTATAATATTAAT
** *
1265990 AAATTGGATTATATTATTAAT
1 AAATTAAATTATAATATTAAT
1266011 A
1 A
1266012 TTAAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
AAATTAAATTATAATATTAAT
Found at i:1267072 original size:42 final size:42
Alignment explanation
Indices: 1267020--1267125 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 42
1267010 GATTCACCTG
*
1267020 TCATCGTTCAAGAGGCCTCC-CTTA-TCATTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCC-CCTCCTACT-ATTCAAGAGGCCCCTA
* * *
1267062 TCATCCTTCAAGAGGCCCCTCCTACTGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTCCTACTATTCAAGAGGCCCCTA
*
1267104 TCATCGTTCAAGAGGTCCCTCC
1 TCATCGTTCAAGAGGCCCCTCC
1267126 CACCGTTCGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 2 0.04
42 53 0.95
43 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCTACTATTCAAGAGGCCCCTA
Found at i:1267123 original size:21 final size:21
Alignment explanation
Indices: 1267016--1267123 Score: 107
Period size: 21 Copynumber: 5.1 Consensus size: 21
1267006 GCCCGATTCA
1267016 CCTGTCATCGTTCAAGAGGCCTC
1 CCTGTCATCGTTCAAGAGG-C-C
*
1267039 CCT-T-ATCATTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
1267058 CCTATCATCCTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
*
1267079 CC--TCCTACTGTTCAAGAGGCC
1 CCTGTCAT-C-GTTCAAGAGGCC
*
1267100 CCTGTCATCGTTCAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
1267121 CCT
1 CCT
1267124 CCCACCGTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
19 7 0.10
20 3 0.04
21 55 0.75
22 2 0.03
23 6 0.08
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.26
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:1267132 original size:21 final size:21
Alignment explanation
Indices: 1267047--1267138 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
1267037 TCCCTTATCA
**
1267047 TTCAAGAGGCCCCTATCATCC-
1 TTCAAGAGGCCCCTCCCA-CCG
* *
1267068 TTCAAGAGGCCCCTCCTACTG
1 TTCAAGAGGCCCCTCCCACCG
** *
1267089 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCCCACCG
*
1267110 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
*
1267131 TTCGAGAG
1 TTCAAGAG
1267139 CCGATTCACA
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:1268502 original size:13 final size:14
Alignment explanation
Indices: 1268477--1268509 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1268467 AAATTGATGT
1268477 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
1268491 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
1268504 ATTTGT
1 ATTTGT
1268510 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:1268570 original size:14 final size:14
Alignment explanation
Indices: 1268551--1268587 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1268541 GCTTGTTTAA
1268551 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1268565 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1268579 TTGATTTGT
1 TTGATTTGT
1268588 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1268597 original size:78 final size:77
Alignment explanation
Indices: 1268477--1268651 Score: 287
Period size: 78 Copynumber: 2.3 Consensus size: 77
1268467 AAATTGATGT
1268477 ATTTGTAAAAGTTGATTTGTAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTG
1 ATTTGTAAAAGTTGATTTGTAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTG
1268542 CTTGTTTAATTG
66 CTTGTTTAATTG
* * * ***
1268554 ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATTATTCTTATTTTTT
1 ATTTGTAAAAGTTGATTTGT-AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT
1268619 GCTTGTTTAATTG
65 GCTTGTTTAATTG
1268632 ATTTGTAAAAGTTGATTTGT
1 ATTTGTAAAAGTTGATTTGT
1268652 TGTTTTAAAT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
77 20 0.22
78 71 0.78
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (77 bp):
ATTTGTAAAAGTTGATTTGTAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTG
CTTGTTTAATTG
Found at i:1268639 original size:37 final size:38
Alignment explanation
Indices: 1268532--1268649 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 38
1268522 GAAATAAGAA
1268532 TTATTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATT
1 TTATTTTTTGCTTGTTTAATTGATTTGT-AAAGTTGATT
**** * *
1268571 TGTAAAAGTTGATTTGTTTAATTGATGTGTAAA-TT-ATT
1 T-TATTTTTTG-CTTGTTTAATTGATTTGTAAAGTTGATT
1268609 CTTATTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATT
1 -TTATTTTTTGCTTGTTTAATTGATTTGT-AAAGTTGATT
1268649 T
1 T
1268650 GTTGTTTTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
37 16 0.26
38 11 0.18
39 7 0.11
40 11 0.18
41 16 0.26
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (38 bp):
TTATTTTTTGCTTGTTTAATTGATTTGTAAAGTTGATT
Found at i:1268736 original size:20 final size:20
Alignment explanation
Indices: 1268711--1268772 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
1268701 AAGGTACACT
*
1268711 TTCGCAATGCGAAAGTTAAA
1 TTCGCAATGCGAAAGTCAAA
*
1268731 TTCGCAATGTGAAAGTCAAA
1 TTCGCAATGCGAAAGTCAAA
* *
1268751 ATCGCAACGCGAAAGTCAAA
1 TTCGCAATGCGAAAGTCAAA
1268771 TT
1 TT
1268773 AGCGTTGCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (20 bp):
TTCGCAATGCGAAAGTCAAA
Found at i:1268837 original size:20 final size:20
Alignment explanation
Indices: 1268814--1268852 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1268804 CAACCCGAAT
**
1268814 GTCAAATTCGTGTTGCGATA
1 GTCAAATTCACGTTGCGATA
1268834 GTCAAATTCACGTTGCGAT
1 GTCAAATTCACGTTGCGAT
1268853 TTCGCATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
GTCAAATTCACGTTGCGATA
Found at i:1269117 original size:12 final size:12
Alignment explanation
Indices: 1269102--1269135 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1269092 AGGTGAAGCC
*
1269102 GATTGTGATTGA
1 GATTTTGATTGA
*
1269114 GATTTTGATTGC
1 GATTTTGATTGA
1269126 GATTTTGATT
1 GATTTTGATT
1269136 TTCTTTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.50
Consensus pattern (12 bp):
GATTTTGATTGA
Found at i:1271427 original size:24 final size:24
Alignment explanation
Indices: 1271393--1271446 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1271383 CTGAAACATC
*
1271393 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGGATTGACCAAG
* *
1271417 ATCAAAGTCCGGGGATTGACCAAG
1 ATCAAAATCCGAGGATTGACCAAG
1271441 ATCAAA
1 ATCAAA
1271447 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (24 bp):
ATCAAAATCCGAGGATTGACCAAG
Found at i:1272200 original size:15 final size:16
Alignment explanation
Indices: 1272163--1272193 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1272153 AAATCATTGA
1272163 AAAATTATATAAAAAT
1 AAAATTATATAAAAAT
*
1272179 AAAATTATGTAAAAA
1 AAAATTATATAAAAA
1272194 ATAATTAAAG
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:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:1272384 original size:20 final size:20
Alignment explanation
Indices: 1272359--1272424 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1272349 TAAAACCTGA
*
1272359 TGCGAAATTAAAATTCGTGT
1 TGCGAAATTAAAATTCGAGT
1272379 TGCG-AATTCGAAAA-TCGAGT
1 TGCGAAATT--AAAATTCGAGT
** * *
1272399 TGCGAAAACAAAATTTGCGT
1 TGCGAAATTAAAATTCGAGT
1272419 TGCGAA
1 TGCGAA
1272425 TTCAGAAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 8 0.22
20 23 0.62
21 6 0.16
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGAAATTAAAATTCGAGT
Found at i:1272404 original size:40 final size:40
Alignment explanation
Indices: 1272359--1272466 Score: 103
Period size: 40 Copynumber: 2.7 Consensus size: 40
1272349 TAAAACCTGA
* *
1272359 TGCGAAATTAAAATTCGTGTTGCGAATTC-GAAAATCGAGT
1 TGCGAAATTAAAATTCGAGTTGCGAATTCAG-AAATCAAGT
** * *
1272399 TGCGAAAACAAAATTTGCGTTGCGAATTCAGAAATCAAGT
1 TGCGAAATTAAAATTCGAGTTGCGAATTCAGAAATCAAGT
* * *
1272439 TACGAATTTGGAAA-TCGAGTTGCGAATT
1 TGCGAAATT-AAAATTCGAGTTGCGAATT
1272467 TGACTTCTGT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
40 50 0.93
41 4 0.07
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (40 bp):
TGCGAAATTAAAATTCGAGTTGCGAATTCAGAAATCAAGT
Found at i:1272467 original size:20 final size:21
Alignment explanation
Indices: 1272417--1272548 Score: 96
Period size: 20 Copynumber: 6.6 Consensus size: 21
1272407 CAAAATTTGC
** *
1272417 GTTGCGAATTCAGAAATC-AA
1 GTTGCGAATTTGGAAATCTGA
*
1272437 GTTACGAATTTGGAAATC-GA
1 GTTGCGAATTTGGAAATCTGA
** *
1272457 GTTGCGAATTT-GACTTCTGT
1 GTTGCGAATTTGGAAATCTGA
** *
1272477 GTTGCGAATTT-GACTTCTGT
1 GTTGCGAATTTGGAAATCTGA
1272497 GTTGCGAATTTGGAAA-CTGA
1 GTTGCGAATTTGGAAATCTGA
* ** *
1272517 GTTGCGAAATTGGAGTTC-GC
1 GTTGCGAATTTGGAAATCTGA
1272537 GTTGCGAATTTG
1 GTTGCGAATTTG
1272549 TTGGTCATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 4 0.04
20 86 0.92
21 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (21 bp):
GTTGCGAATTTGGAAATCTGA
Found at i:1274460 original size:16 final size:16
Alignment explanation
Indices: 1274436--1274482 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
1274426 GAATGTTCCC
1274436 AGAACTACTCTCTATT
1 AGAACTACTCTCTATT
*
1274452 AGAAATA--CTCTATT
1 AGAACTACTCTCTATT
1274466 AGAACTACTCTCTATT
1 AGAACTACTCTCTATT
1274482 A
1 A
1274483 ACACCATCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.48
16 14 0.52
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (16 bp):
AGAACTACTCTCTATT
Found at i:1274464 original size:14 final size:14
Alignment explanation
Indices: 1274445--1274476 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1274435 CAGAACTACT
1274445 CTCTATTAGAAATA
1 CTCTATTAGAAATA
*
1274459 CTCTATTAGAACTA
1 CTCTATTAGAAATA
1274473 CTCT
1 CTCT
1274477 CTATTAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (14 bp):
CTCTATTAGAAATA
Found at i:1276566 original size:18 final size:18
Alignment explanation
Indices: 1276529--1276566 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1276519 TTCTGTTTTC
*
1276529 TTCTCCTTTTTTTTGTTG
1 TTCTCCTTTTTTTTGCTG
1276547 TTCTCCCTTTTTTTT-CTG
1 TTCT-CCTTTTTTTTGCTG
1276565 TT
1 TT
1276567 TTGCAGGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.71
Consensus pattern (18 bp):
TTCTCCTTTTTTTTGCTG
Found at i:1276566 original size:21 final size:21
Alignment explanation
Indices: 1276519--1276568 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
1276509 TTGCTGTGGG
1276519 TTCTGTTTTCTTCTCCTTTTT
1 TTCTGTTTTCTTCTCCTTTTT
1276540 TT-TGTTGTTC-TC-CCTTTTTT
1 TTCTGTT-TTCTTCTCC-TTTTT
1276560 TTCTGTTTT
1 TTCTGTTTT
1276569 GCAGGTGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.08
20 15 0.58
21 9 0.35
ACGTcount: A:0.00, C:0.20, G:0.08, T:0.72
Consensus pattern (21 bp):
TTCTGTTTTCTTCTCCTTTTT
Found at i:1277019 original size:3 final size:3
Alignment explanation
Indices: 1277013--1277051 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
1277003 TTTTTTTATT
1277013 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA
1277052 TGATGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1279724 original size:75 final size:75
Alignment explanation
Indices: 1279635--1279829 Score: 338
Period size: 75 Copynumber: 2.6 Consensus size: 75
1279625 CGTTAAACAG
* *
1279635 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCATTCTATTTTTCTCGGAGCC
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCATTATATTTTTCTCGAAGCC
1279700 AAACCATTCA
66 AAACCATTCA
*
1279710 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCATTATGTTTTTCTCGAAGCC
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCATTATATTTTTCTCGAAGCC
1279775 AAACCATTCA
66 AAACCATTCA
* *
1279785 GGGGGAATCGGTACCCCCTT-GGGGGAAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCA
1279830 ATCTGGAATT
Statistics
Matches: 115, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 23 0.20
75 92 0.80
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (75 bp):
GGGGGAATCGGTACCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCATTATATTTTTCTCGAAGCC
AAACCATTCA
Found at i:1282487 original size:22 final size:23
Alignment explanation
Indices: 1282424--1282486 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1282414 GAACCCCTAC
*
1282424 AGGGGGAATCGGTTCCCCTTGAA
1 AGGGGGAATCGGTTCCCCTTCAA
1282447 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
* * *
1282470 GGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
1282487 TCTGCACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:1284833 original size:17 final size:17
Alignment explanation
Indices: 1284811--1284846 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1284801 TACTTGATTA
1284811 ATAACATAACAAGCGGT
1 ATAACATAACAAGCGGT
1284828 ATAACATAACAAGCGGT
1 ATAACATAACAAGCGGT
1284845 AT
1 AT
1284847 TTGTGGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (17 bp):
ATAACATAACAAGCGGT
Found at i:1294045 original size:18 final size:19
Alignment explanation
Indices: 1294022--1294078 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
1294012 CTCAGTAATC
*
1294022 TATTCC-CTGGTAATCTTT
1 TATTCCACTGATAATCTTT
1294040 TATTCCTACTGATAATCTTT
1 TATTCC-ACTGATAATCTTT
1294060 TATTCCTACTGATAATCTT
1 TATTCC-ACTGATAATCTT
1294079 ACATTCTGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 6 0.17
20 30 0.83
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.49
Consensus pattern (19 bp):
TATTCCACTGATAATCTTT
Found at i:1294057 original size:20 final size:20
Alignment explanation
Indices: 1294032--1294078 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1294022 TATTCCCTGG
1294032 TAATCTTTTATTCCTACTGA
1 TAATCTTTTATTCCTACTGA
1294052 TAATCTTTTATTCCTACTGA
1 TAATCTTTTATTCCTACTGA
1294072 TAATCTT
1 TAATCTT
1294079 ACATTCTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (20 bp):
TAATCTTTTATTCCTACTGA
Found at i:1294084 original size:20 final size:20
Alignment explanation
Indices: 1294041--1294084 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1294031 GTAATCTTTT
**
1294041 ATTCCTACTGATAATCTTTT
1 ATTCCTACTGATAATCTTAC
1294061 ATTCCTACTGATAATCTTAC
1 ATTCCTACTGATAATCTTAC
1294081 ATTC
1 ATTC
1294085 TGTGAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTCCTACTGATAATCTTAC
Found at i:1300059 original size:4 final size:4
Alignment explanation
Indices: 1300042--1300147 Score: 68
Period size: 4 Copynumber: 26.5 Consensus size: 4
1300032 CTGAATAATT
* * * * * * * **
1300042 TACA TGCA TGCA TACA TACC TACC TAAA TTCA TACA TGCA TGGA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * *
1300090 TACA TACA TACA TGCA TACC TAAA TTCA TACA TGCA TGCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1300138 TATA TACA TA
1 TACA TACA TA
1300148 TATTAAGATT
Statistics
Matches: 78, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
4 78 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:1300108 original size:32 final size:32
Alignment explanation
Indices: 1300042--1300108 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1300032 CTGAATAATT
* * *
1300042 TACATGCATGCATACATACCTACCTAAATTCA
1 TACATGCATGCATACATACATACATAAATGCA
* *
1300074 TACATGCATGGATACATACATACATACATGCA
1 TACATGCATGCATACATACATACATAAATGCA
1300106 TAC
1 TAC
1300109 CTAAATTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
TACATGCATGCATACATACATACATAAATGCA
Found at i:1300110 original size:44 final size:44
Alignment explanation
Indices: 1300042--1300147 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 44
1300032 CTGAATAATT
* * * *
1300042 TACATGCATGCATACATACCTACCTAAATTCATACATGCATGGA
1 TACATACATACATACATACATACCTAAATTCATACATGCATGCA
*
1300086 TACATACATACATACATGCATACCTAAATTCATACATGCATGCA
1 TACATACATACATACATACATACCTAAATTCATACATGCATGCA
*
1300130 TACATACATATATACATA
1 TACATACATACATACATA
1300148 TATTAAGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.28
Consensus pattern (44 bp):
TACATACATACATACATACATACCTAAATTCATACATGCATGCA
Found at i:1300234 original size:4 final size:4
Alignment explanation
Indices: 1300220--1300252 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1300210 ATAATGAAAG
*
1300220 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1300253 TCTTGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.03, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1300478 original size:24 final size:24
Alignment explanation
Indices: 1300451--1300523 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
1300441 CGTTCATTTA
1300451 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
1300475 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * *
1300499 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
1300523 C
1 C
1300524 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.10, C:0.15, G:0.26, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:1300480 original size:14 final size:14
Alignment explanation
Indices: 1300461--1300516 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
1300451 CGTTCGTGAA
1300461 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1300475 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1300489 CG-T---TTATGTT
1 CGTTCGGTTATGTT
1300499 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1300513 CGTT
1 CGTT
1300517 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1300533 original size:24 final size:24
Alignment explanation
Indices: 1300462--1300523 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
1300452 GTTCGTGAAC
*
1300462 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1300486 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1300510 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1300524 ATTCATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:1301586 original size:16 final size:16
Alignment explanation
Indices: 1301565--1301631 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
1301555 TTTATATTCG
1301565 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1301581 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
1301597 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
1301613 CTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1301627 TTTAT
1 TTTAT
1301632 TAAATGTACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 4 0.09
15 2 0.04
16 41 0.87
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1301602 original size:32 final size:32
Alignment explanation
Indices: 1301561--1301623 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1301551 AACGTTTATA
*
1301561 TTCGTTTATGTTCGTGTTCATTTATGTTCGTG
1 TTCGTTTATGTTCGTGTTCACTTATGTTCGTG
*
1301593 TTCGTTTATGTTCGTGTTCGCTTATGTTCGT
1 TTCGTTTATGTTCGTGTTCACTTATGTTCGT
1301624 TTATTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.08, C:0.14, G:0.22, T:0.56
Consensus pattern (32 bp):
TTCGTTTATGTTCGTGTTCACTTATGTTCGTG
Found at i:1301715 original size:16 final size:16
Alignment explanation
Indices: 1301694--1301726 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1301684 AAAAAAAATT
1301694 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1301710 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1301726 T
1 T
1301727 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1304132 original size:108 final size:107
Alignment explanation
Indices: 1304013--1304213 Score: 262
Period size: 108 Copynumber: 1.9 Consensus size: 107
1304003 AAATAATCCT
*
1304013 AAAAATATATAACATGCATAAAAG-TGGGTAAATTACAAAAACATTC-CATACAAGTGATCATTT
1 AAAAATATATAACATGCATAAAAGATGGGTAAATTA-AAAAACAGTCTC-TACAAGTGATCA-TT
* *
1304076 TGCAAAAACACGCATAACTTAGTGGGACTAAACAGAAATTAAATC
63 TACAAAAACACGCATAACTTAGGGGGACTAAACAGAAATTAAATC
** * * * *
1304121 AAAAATATATAACATGCATATGAGATGGGTAAATTATAAATCGGTCTCTACATGTGATCATTTAC
1 AAAAATATATAACATGCATAAAAGATGGGTAAATTAAAAAACAGTCTCTACAAGTGATCATTTAC
* *
1304186 AAAAACATGCATAACTTAGGGGGCCTAA
66 AAAAACACGCATAACTTAGGGGGACTAA
1304214 GTGCAATTTC
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
107 29 0.36
108 39 0.49
109 12 0.15
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (107 bp):
AAAAATATATAACATGCATAAAAGATGGGTAAATTAAAAAACAGTCTCTACAAGTGATCATTTAC
AAAAACACGCATAACTTAGGGGGACTAAACAGAAATTAAATC
Found at i:1305633 original size:134 final size:134
Alignment explanation
Indices: 1305422--1306132 Score: 870
Period size: 134 Copynumber: 5.3 Consensus size: 134
1305412 ATCGAGAAAC
* * ** * * *** *
1305422 GTTGACTCATTCCTCTGTTCTTCATTGAAGGTTGAATCTAGGTAGACTTGTTCCACTAACACTCG
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCA
* * ** * *
1305487 GGGAATACCAAATCTTGAAAGAGATTGATATGTTCCGCTTTTTCTTGAGGGAAAATCAGATCTGG
66 GGTAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGG
1305552 GGAT
131 GGAT
** * * ** *
1305556 GTTGATTCATTCCACTGTTCTTCAAAGAAGATTGAATCGAGGCAGGCTTGTTCCTTTATTACTCA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCA
* * *
1305621 GGTAATATCAAATCTTGAAAGAGATGGATATGTTTCGCTTCTTCTTGAGGGAAAATCATATTTGG
66 GGTAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGG
*
1305686 GGAC
131 GGAT
* * * *
1305690 GTTGACTCGTTCCACTATTCTTCAAGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCA
* * ***
1305755 GGCAATATCAAATCTTGAAAGAGAGGGATATGTTTCACTTCTTCTTGAGGGAAAATCAGATCCAT
66 GGTAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGG
1305820 GGAT
131 GGAT
* * * * * *
1305824 GTTGATTCGTTCCACTATTCTTTAGGGAAGATTGGATCGAGATAGAATTGTTCCACTGTTACTCA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCA
* * * * *
1305889 TGTAATATCAAATCTTGAAAGAGAAGGATATGTTCCACTTCTTCTTGA-GGAAAATTTAGATCTG
66 GGTAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAA-TCAGATCTG
*
1305953 GGGAC
130 GGGAT
* **
1305958 GTTGATTCATTCCAATGTTCTTCAGGGAAGATTGAATATAGGTAGACTTGTTCCACTGTTACTCA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCA
* * * *
1306023 GGAAATATCAAATCTTGAAAGAAGAGGGATATGTTTCGCCTCTTCTTGA-GGAAAATCATATATG
66 GGTAATATCAAATCTTGAAAG-AGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTG
1306087 GGGAT
130 GGGAT
*
1306092 GTTGATTCATTCCACTGTTAC-TCAGGGAAGATCGAATCGAG
1 GTTGATTCATTCCACTGTT-CTTCAGGGAAGATTGAATCGAG
1306133 TTCTATCTCC
Statistics
Matches: 497, Mismatches: 77, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
133 6 0.01
134 461 0.93
135 30 0.06
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (134 bp):
GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCA
GGTAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGG
GGAT
Found at i:1309242 original size:5 final size:6
Alignment explanation
Indices: 1309228--1309341 Score: 70
Period size: 6 Copynumber: 17.7 Consensus size: 6
1309218 ACTTGATTTA
* * ***
1309228 TTTTCT TTTTCT TTTACCTCT TTTTCT TTTTTT CTTTTGT TTTTCT TCAACT
1 TTTTCT TTTTCT TTT---TCT TTTTCT TTTTCT -TTTTCT TTTTCT TTTTCT
*
1309280 TTTTCTAT ATTTTCT CTTTTCT TTTT-T TTTTTT TTTTCT ATTATT-T
1 TTTTC--T -TTTTCT -TTTTCT TTTTCT TTTTCT TTTTCT -TT-TTCT
1309326 TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTT
1309342 TCTATATTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 22
0.72 0.09 0.18
Matches are distributed among these distances:
5 7 0.08
6 50 0.58
7 15 0.17
8 3 0.03
9 11 0.13
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:1309312 original size:13 final size:13
Alignment explanation
Indices: 1309296--1309344 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1309286 ATATTTTCTC
*
1309296 TTTTCTTTT-TTT
1 TTTTTTTTTCTTT
*
1309308 TTTTTTTTTCTAT
1 TTTTTTTTTCTTT
*
1309321 TATTTTTTTCTTT
1 TTTTTTTTTCTTT
*
1309334 TTCTTTTTTCT
1 TTTTTTTTTCT
1309345 ATATTTTCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 8 0.27
13 22 0.73
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:1309326 original size:19 final size:17
Alignment explanation
Indices: 1309289--1309342 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 17
1309279 TTTTTCTATA
1309289 TTTTCTCTTTTCTTTTTT
1 TTTTCT-TTTTCTTTTTT
*
1309307 TTTTTTTTTTCTATTATTT
1 TTTTCTTTTTCT-TT-TTT
1309326 TTTTCTTTTTCTTTTTT
1 TTTTCTTTTTCTTTTTT
1309343 CTATATTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 9 0.28
18 9 0.28
19 14 0.44
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTCTTTTTCTTTTTT
Found at i:1309334 original size:26 final size:25
Alignment explanation
Indices: 1309301--1309362 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
1309291 TTCTCTTTTC
1309301 TTTT-TTTTTTTTTTTTCTATTATTT
1 TTTTCTTTTTTTTTTTTCTA-TATTT
*
1309326 TTTTCTTTTTCTTTTTTCTATATTT
1 TTTTCTTTTTTTTTTTTCTATATTT
*
1309351 TCTCTCTTTTTT
1 T-TTTCTTTTTT
1309363 ATGACTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.31
26 22 0.69
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTCTTTTTTTTTTTTCTATATTT
Found at i:1314175 original size:21 final size:21
Alignment explanation
Indices: 1314130--1314177 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1314120 TGAGGGTTTT
* * **
1314130 ATGTAGTCCTCCGGGATAATT
1 ATGTGGTCCTCCGGGACAAAA
1314151 ATGTGGTCCTCCGGGACAAAA
1 ATGTGGTCCTCCGGGACAAAA
1314172 ATGTGG
1 ATGTGG
1314178 CACTTTGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (21 bp):
ATGTGGTCCTCCGGGACAAAA
Found at i:1314224 original size:23 final size:23
Alignment explanation
Indices: 1314172--1314224 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1314162 CGGGACAAAA
*
1314172 ATGTGGCACTTTGGTGCAAACCT
1 ATGTGGTACTTTGGTGCAAACCT
1314195 ATGTGGTACTTTGGTGCAAACCT
1 ATGTGGTACTTTGGTGCAAACCT
1314218 ATGTGGT
1 ATGTGGT
1314225 CATTCGGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (23 bp):
ATGTGGTACTTTGGTGCAAACCT
Found at i:1327247 original size:61 final size:60
Alignment explanation
Indices: 1327106--1327290 Score: 178
Period size: 61 Copynumber: 3.1 Consensus size: 60
1327096 GCATCATATG
* * * * *
1327106 TCCC-AAAACTATAACCCTCATTTTATATTGGTCCTTAAACTTTTGAATATTCCAATTTCA
1 TCCCTAAAA-TATGACCCTCATTATAAATTGATCCTTAAACTTTTGAACATTCCAATTTCA
** ** * *
1327166 TCCCTAAACCATGATTCTCATTATAAATTAATCCTTAAAACTTTTGAACATTCTAATTTCA
1 TCCCTAAAATATGACCCTCATTATAAATTGATCCTT-AAACTTTTGAACATTCCAATTTCA
* ** *
1327227 -CCCATAAAATATGACCCTCATTGTAAATTGATCCCCAAACTTTT-AAGTATTCCAATTTCA
1 TCCC-TAAAATATGACCCTCATTATAAATTGATCCTTAAACTTTTGAA-CATTCCAATTTCA
1327287 TCCC
1 TCCC
1327291 CAAATTCATC
Statistics
Matches: 99, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
59 2 0.02
60 45 0.45
61 52 0.53
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (60 bp):
TCCCTAAAATATGACCCTCATTATAAATTGATCCTTAAACTTTTGAACATTCCAATTTCA
Found at i:1327566 original size:60 final size:60
Alignment explanation
Indices: 1327408--1327576 Score: 184
Period size: 60 Copynumber: 2.8 Consensus size: 60
1327398 CATATAGCTT
* * * * * *
1327408 GGGATGAAATTGGAATATTAAAAAGTTTGGGGACCAATTTAGAATGAAGGTTATAGTTTG
1 GGGATGAAATTTGAATATTAAAAAGTTTAGAGACTAATTTAGAATGAAGGTCATAGTTTA
* *
1327468 GGGATGAAA-TTGAAATATTCAAAAGTTTA-AGGATTAATTTAGAATGATA-GTCATAGTTTA
1 GGGATGAAATTTG-AATATTAAAAAGTTTAGA-GACTAATTTAGAATGA-AGGTCATAGTTTA
* * *
1327528 GTGATGAAATTTGAATATTTAAAAGTTTAGAGACTAATTTAAAAT-AAGG
1 GGGATGAAATTTGAATATTAAAAAGTTTAGAGACTAATTTAGAATGAAGG
1327577 GTCCTACTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
58 1 0.01
59 4 0.04
60 81 0.89
61 5 0.05
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (60 bp):
GGGATGAAATTTGAATATTAAAAAGTTTAGAGACTAATTTAGAATGAAGGTCATAGTTTA
Found at i:1328024 original size:74 final size:74
Alignment explanation
Indices: 1327880--1328020 Score: 266
Period size: 74 Copynumber: 1.9 Consensus size: 74
1327870 TTTAGACACA
1327880 TTCAGTCATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATT
1 TTCAGTCATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATT
1327945 TTTACCACG
66 TTTACCACG
*
1327954 TTCAGTCGTTCATTATCAATATTAATTTATTTATTATTATTATCTATACTC-TTTTCAATTAATT
1 TTCAGTCATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATT
1328018 TTT
66 TTT
1328021 TACCTCAACA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 16 0.24
74 50 0.76
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (74 bp):
TTCAGTCATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATT
TTTACCACG
Found at i:1328043 original size:74 final size:74
Alignment explanation
Indices: 1327886--1328050 Score: 221
Period size: 74 Copynumber: 2.3 Consensus size: 74
1327876 CACATTCAGT
*
1327886 CATTCATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATTTTTACC
1 CATTAATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATTTTTACC
** *
1327951 ACGTTCAGT
66 ACGAACAGG
* *
1327960 CGTTCATTATCAATATTAATTTATTTATTATTATTATCTATACTC-TTTTCAATTAATTTTTTAC
1 CATTAATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAA-TTTTTAC
*
1328024 CTC-AACAGG
65 CACGAACAGG
1328033 CATCTAATTAT--ATATTAA
1 CAT-TAATTATCAATATTAA
1328051 ATTGAATTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
72 7 0.09
73 16 0.20
74 59 0.72
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.50
Consensus pattern (74 bp):
CATTAATTATCAATATTAATTTATTTATTATTATTATCTATACTCGTTTTCAATTAATTTTTACC
ACGAACAGG
Found at i:1330498 original size:37 final size:36
Alignment explanation
Indices: 1330439--1330670 Score: 272
Period size: 35 Copynumber: 6.7 Consensus size: 36
1330429 AAACAATCGT
1330439 TTTTGAAAAATATATATA-ATATAATTTTTAAAACA
1 TTTTGAAAAATATATATATATATAATTTTTAAAACA
*
1330474 TTTTGAAAAATATATATAATATATAATTTTTAAATCA
1 TTTTGAAAAATATATAT-ATATATAATTTTTAAAACA
* *
1330511 TTTTGAAAAAT-TATATATATAGT--TTTTAAAAACTT
1 TTTTGAAAAATATATATATATA-TAATTTTTAAAAC-A
* *
1330546 TTTTGAAAACT-TATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATAT-ATATATAATTTTTAAAACA
*
1330582 TTTTG-AAAATATATATATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATATATATAATTTTTAAAACA
*
1330617 TTTT---AAA-A-ATATATATAT-AGTTTTAAAACA
1 TTTTGAAAAATATATATATATATAATTTTTAAAACA
*
1330647 TTTTGAAATATATATATATATATA
1 TTTTGAAAAATATATATATATATA
1330671 TATTATAGTT
Statistics
Matches: 172, Mismatches: 11, Indels: 27
0.82 0.05 0.13
Matches are distributed among these distances:
30 14 0.08
31 10 0.06
32 1 0.01
33 5 0.03
34 9 0.05
35 75 0.44
36 22 0.13
37 36 0.21
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTTGAAAAATATATATATATATAATTTTTAAAACA
Found at i:1330526 original size:71 final size:72
Alignment explanation
Indices: 1330439--1330670 Score: 288
Period size: 71 Copynumber: 3.3 Consensus size: 72
1330429 AAACAATCGT
*
1330439 TTTTGAAAAATATATATAATATAATTTTTAAAACATTTTGAAAAATATATATAATATATAATTTT
1 TTTTGAAAAATATATATAATATAGTTTTTAAAACATTTTGAAAAATATATATAATATATAATTTT
*
1330504 TAAATCA
66 TAAAACA
* * *
1330511 TTTTGAAAAAT-TATAT-ATATAGTTTTTAAAAACTTTTTTGAAAACT-TATATAATATATAGTT
1 TTTTGAAAAATATATATAATATAGTTTTT-AAAAC-ATTTTGAAAAATATATATAATATATAATT
1330573 TTTAAAACA
64 TTTAAAACA
*
1330582 TTTTG-AAAATATATATATATATAGTTTTTAAAACATTTT---AAA-A-ATAT-ATATAT-AGTT
1 TTTTGAAAAATATATATA-ATATAGTTTTTAAAACATTTTGAAAAATATATATAATATATAATTT
1330639 TTAAAACA
65 TTAAAACA
*
1330647 TTTTGAAATATATATATATATATA
1 TTTTGAAAAATATATATA-ATATA
1330671 TATTATAGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 20
0.83 0.06 0.12
Matches are distributed among these distances:
65 15 0.10
66 23 0.16
67 4 0.03
68 2 0.01
70 15 0.10
71 47 0.33
72 26 0.18
73 11 0.08
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (72 bp):
TTTTGAAAAATATATATAATATAGTTTTTAAAACATTTTGAAAAATATATATAATATATAATTTT
TAAAACA
Found at i:1330669 original size:108 final size:106
Alignment explanation
Indices: 1330439--1330672 Score: 338
Period size: 106 Copynumber: 2.2 Consensus size: 106
1330429 AAACAATCGT
*
1330439 TTTTGAAAAATATATATAATATA-A-TTTTTAAAACATTTTGAAAAATATATATAATATATAATT
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTG-AAAATATATAT-ATATATAGTT
* *
1330502 TTTAAATCATTTTGAAAAATTATATATATAGTTTTTAAAAACTT
64 TTTAAAACATTTT-AAAAATTATATATATAGTTTTTAAAAACTA
*
1330546 TTTTGAAAACT-TATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATATATAGTTTT
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATATATAGTTTT
1330610 TAAAACATTTTAAAAA-TATATATATAG-TTTT-AAAAC-A
66 TAAAACATTTTAAAAATTATATATATAGTTTTTAAAAACTA
*
1330647 TTTTGAAATATATATATATATATATA
1 TTTTGAAAAATATATATA-ATATATA
1330673 TTATAGTTTT
Statistics
Matches: 117, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
101 9 0.08
102 11 0.09
103 11 0.09
104 11 0.09
105 5 0.04
106 32 0.27
107 22 0.19
108 16 0.14
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (106 bp):
TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATATATAGTTTT
TAAAACATTTTAAAAATTATATATATAGTTTTTAAAAACTA
Found at i:1330682 original size:108 final size:106
Alignment explanation
Indices: 1330439--1330672 Score: 329
Period size: 108 Copynumber: 2.2 Consensus size: 106
1330429 AAACAATCGT
* *
1330439 TTTTGAAAAA-TATATATA-ATATAATTTTTAAAACATTTTGAAAAATATATATAATATATAATT
1 TTTTGAAAAATTATATATATATATAGTTTTTAAAACATTTTG-AAAATATATAT-ATATATAGTT
* *
1330502 TTTAAATCATTTTGAAAAATTATATATATAGTTTTTAAAAACTT
64 TTTAAAACATTTT-AAAAATTATATATATAGTTTTTAAAAACTA
*
1330546 TTTTGAAAACTTATATA-ATATATAGTTTTTAAAACATTTTGAAAATATATATATATATAGTTTT
1 TTTTGAAAAATTATATATATATATAGTTTTTAAAACATTTTGAAAATATATATATATATAGTTTT
1330610 TAAAACATTTTAAAAA-TATATATATAG-TTTT-AAAAC-A
66 TAAAACATTTTAAAAATTATATATATAGTTTTTAAAAACTA
*
1330647 TTTTGAAATATATATATATATATATA
1 TTTTGAAAAAT-TATATATATATATA
1330673 TTATAGTTTT
Statistics
Matches: 116, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
101 9 0.08
102 11 0.09
103 11 0.09
104 11 0.09
105 5 0.04
106 21 0.18
107 21 0.18
108 27 0.23
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (106 bp):
TTTTGAAAAATTATATATATATATAGTTTTTAAAACATTTTGAAAATATATATATATATAGTTTT
TAAAACATTTTAAAAATTATATATATAGTTTTTAAAAACTA
Found at i:1330694 original size:108 final size:105
Alignment explanation
Indices: 1330439--1330734 Score: 311
Period size: 107 Copynumber: 2.8 Consensus size: 105
1330429 AAACAATCGT
* *
1330439 TTTTGAAAAA-TATATATA-ATATAATTTTTAAAACATTTTGAAAAATATATATAATATATAATT
1 TTTTGAAAAATTATATATATATAT-AGTTTTAAAACATTTTG-AAAATATATAT-ATATATAGTT
* *
1330502 TTTAAATCATTTTGAAAAATTATATATATAGTTTTTAAAAACTT
63 TTTAAAACATTTT-AAAAATTATATATATAGTTTTTAAAAACTA
*
1330546 TTTTGAAAACTTATATA-ATATATAGTTTTTAAAACATTTTGAAAATATATATATATATAGTTTT
1 TTTTGAAAAATTATATATATATATAG-TTTTAAAACATTTTGAAAATATATATATATATAGTTTT
1330610 TAAAACATTTTAAAAA-TATATATATAG-TTTT-AAAAC-A
65 TAAAACATTTTAAAAATTATATATATAGTTTTTAAAAACTA
** * *
1330647 TTTTGAAATATATATATATATATATATTATAGTTTTAAAATGTTTTTGAAAACATATAT-TCTAT
1 TTTTG-AA-A-A-AT-TATATATATA-TATAGTTTTAAAA-CATTTTGAAAATATATATATATAT
* *
1330711 GGTTTTGAAAACAATTTTTAAAAA
59 AGTTTTTAAAAC-A-TTTTAAAAA
1330735 AAAAGCATAT
Statistics
Matches: 164, Mismatches: 12, Indels: 24
0.82 0.06 0.12
Matches are distributed among these distances:
101 5 0.03
102 7 0.04
103 5 0.03
104 12 0.07
105 6 0.04
106 27 0.16
107 47 0.29
108 46 0.28
109 9 0.05
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (105 bp):
TTTTGAAAAATTATATATATATATAGTTTTAAAACATTTTGAAAATATATATATATATAGTTTTT
AAAACATTTTAAAAATTATATATATAGTTTTTAAAAACTA
Found at i:1330704 original size:42 final size:41
Alignment explanation
Indices: 1330625--1330705 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
1330615 CATTTTAAAA
*
1330625 ATATATATATAGTTTTAAAACATTTTGAAATATATATATAT
1 ATATATATATAGTTTTAAAACATTTTGAAATACATATATAT
**
1330666 ATATATATTATAGTTTTAAAATGTTTTTGAAA-ACATATAT
1 ATATATA-TATAGTTTTAAAA-CATTTTGAAATACATATAT
1330706 TCTATGGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 7 0.20
42 20 0.57
43 8 0.23
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.47
Consensus pattern (41 bp):
ATATATATATAGTTTTAAAACATTTTGAAATACATATATAT
Found at i:1330789 original size:15 final size:15
Alignment explanation
Indices: 1330769--1330820 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1330759 AAAATGTTTT
1330769 TTTATTATATTTATA
1 TTTATTATATTTATA
1330784 TTTATT-TATTTATTA
1 TTTATTATATTTA-TA
* *
1330799 TTTATTTTATTTTTA
1 TTTATTATATTTATA
1330814 TTTATTA
1 TTTATTA
1330821 CTTATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 6 0.18
15 22 0.67
16 5 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTATATTTATA
Found at i:1330791 original size:4 final size:4
Alignment explanation
Indices: 1330769--1330834 Score: 56
Period size: 4 Copynumber: 17.8 Consensus size: 4
1330759 AAAATGTTTT
1330769 TTTA TTATA TTTA --TA TTTA TTTA TTTA -TTA TTTA TTT- TATT- TTTA
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
*
1330814 TTTA -TTA CTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
1330835 TTATTTTTCA
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
2 2 0.04
3 12 0.22
4 36 0.67
5 4 0.07
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:1330807 original size:26 final size:28
Alignment explanation
Indices: 1330773--1330840 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
1330763 TGTTTTTTTA
1330773 TTATATTTATATTTATTTA-T-TTATTAT
1 TTAT-TTTATATTTATTTATTATTATTAT
*
1330800 TTATTTTATTTTTATTTATTACTTATTAT
1 TTATTTTATATTTATTTATTA-TTATTAT
1330829 TTATTTT-TATTT
1 TTATTTTATATTT
1330841 TTCAGGTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 13 0.36
27 5 0.14
28 4 0.11
29 14 0.39
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (28 bp):
TTATTTTATATTTATTTATTATTATTAT
Found at i:1330841 original size:30 final size:30
Alignment explanation
Indices: 1330769--1330842 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
1330759 AAAATGTTTT
* * *
1330769 TTTATTATATTTATATTTATTTATTTATTA
1 TTTATTTTATTTTTATTTATTTACTTATTA
1330799 TTTATTTTATTTTTATTTA-TTACTTATTA
1 TTTATTTTATTTTTATTTATTTACTTATTA
1330828 TTTATTTTTATTTTT
1 TTTA-TTTTATTTTT
1330843 CAGGTCCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.32
30 27 0.68
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTATTTTATTTTTATTTATTTACTTATTA
Found at i:1331854 original size:23 final size:23
Alignment explanation
Indices: 1331828--1331874 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1331818 TTTATGCATG
1331828 TTTTAATTTAGCCATTATTATTT
1 TTTTAATTTAGCCATTATTATTT
* *
1331851 TTTTGATTTAGCCATTGTTATTT
1 TTTTAATTTAGCCATTATTATTT
1331874 T
1 T
1331875 AATTTTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (23 bp):
TTTTAATTTAGCCATTATTATTT
Found at i:1333168 original size:15 final size:15
Alignment explanation
Indices: 1333145--1333174 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1333135 TAATTTAATC
1333145 AAAAATTAAAATGTT
1 AAAAATTAAAATGTT
*
1333160 AAAAGTTAAAATGTT
1 AAAAATTAAAATGTT
1333175 CTAAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
AAAAATTAAAATGTT
Found at i:1334203 original size:3 final size:3
Alignment explanation
Indices: 1334195--1334228 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1334185 TTGACGTTAC
*
1334195 GAA GAA GAA GAA GAA GAA GAA GAG GAA GAGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA
1334229 ATGAGACACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1337073 original size:37 final size:37
Alignment explanation
Indices: 1337018--1337090 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
1337008 GGGGTAAGTA
*
1337018 TCTCGTTGTTATTACTCTTAAACTAGCTTCGAGTGTC
1 TCTCCTTGTTATTACTCTTAAACTAGCTTCGAGTGTC
* *
1337055 TCTCCTTGTTATTACTCTTAAATTAGCTTTGAGTGT
1 TCTCCTTGTTATTACTCTTAAACTAGCTTCGAGTGT
1337091 ATTTCTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (37 bp):
TCTCCTTGTTATTACTCTTAAACTAGCTTCGAGTGTC
Found at i:1339622 original size:3 final size:3
Alignment explanation
Indices: 1339610--1339671 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
1339600 ATTGATTTAT
*
1339610 TTA TTA -TA TTA TTA TATA TTA TTA TTA TTA TAA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1339654 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
1339672 ATATATTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1339654 original size:23 final size:24
Alignment explanation
Indices: 1339610--1339679 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 24
1339600 ATTGATTTAT
1339610 TTATTA-TATTATTATATATTATTA
1 TTATTATTATTATTAT-TATTATTA
*
1339634 TTATTATAATTATTA-TATTATTA
1 TTATTATTATTATTATTATTATTA
*
1339657 TTATTATTATTATTAATA-TATTA
1 TTATTATTATTATTATTATTATTA
1339680 AATATATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 27 0.64
24 8 0.19
25 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTATTATTATTATTATTATTA
Found at i:1339694 original size:11 final size:10
Alignment explanation
Indices: 1339614--1339694 Score: 71
Period size: 9 Copynumber: 8.2 Consensus size: 10
1339604 ATTTATTTAT
*
1339614 TATATTATTA
1 TATATTATAA
*
1339624 TATATTATTA
1 TATATTATAA
1339634 T-TATTATAA
1 TATATTATAA
*
1339643 T-TATTATAT
1 TATATTATAA
*
1339652 TATTATTATTA
1 TA-TATTATAA
1339663 T-TATTATTAA
1 TATATTA-TAA
1339673 TATATTA-AA
1 TATATTATAA
1339682 TATATATATAA
1 TATAT-TATAA
1339693 TA
1 TA
1339695 ATAATAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
9 28 0.47
10 16 0.27
11 16 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATTATAA
Found at i:1341682 original size:109 final size:109
Alignment explanation
Indices: 1341547--1341766 Score: 431
Period size: 109 Copynumber: 2.0 Consensus size: 109
1341537 TATCATTTTG
*
1341547 AAAATATTATCAAATTTTAAGGCTAATTTGAAAAAAATAATAATGAAAACTTGTCAAATTGTCAA
1 AAAATATTATCAAATTTTAAGGCTAATTTGAAAAAAAAAATAATGAAAACTTGTCAAATTGTCAA
1341612 GTTAGGGGGAAATTAAATTAGATCCTTTTATTAGCTTGCTACCC
66 GTTAGGGGGAAATTAAATTAGATCCTTTTATTAGCTTGCTACCC
1341656 AAAATATTATCAAATTTTAAGGCTAATTTGAAAAAAAAAATAATGAAAACTTGTCAAATTGTCAA
1 AAAATATTATCAAATTTTAAGGCTAATTTGAAAAAAAAAATAATGAAAACTTGTCAAATTGTCAA
1341721 GTTAGGGGGAAATTAAATTAGATCCTTTTATTAGCTTGCTACCC
66 GTTAGGGGGAAATTAAATTAGATCCTTTTATTAGCTTGCTACCC
1341765 AA
1 AA
1341767 GCTTGCTAAT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (109 bp):
AAAATATTATCAAATTTTAAGGCTAATTTGAAAAAAAAAATAATGAAAACTTGTCAAATTGTCAA
GTTAGGGGGAAATTAAATTAGATCCTTTTATTAGCTTGCTACCC
Found at i:1345084 original size:47 final size:47
Alignment explanation
Indices: 1345015--1345109 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1345005 ACTAAAATTC
1345015 TGGTCACTGTCTTATAAATCACAGAGCATCATGAGATAGGCCTGAAG
1 TGGTCACTGTCTTATAAATCACAGAGCATCATGAGATAGGCCTGAAG
1345062 TGGTCACTGTCTTATAAATCACAGAGCATCATGAGATAGGCCTGAAG
1 TGGTCACTGTCTTATAAATCACAGAGCATCATGAGATAGGCCTGAAG
1345109 T
1 T
1345110 CCTTGACTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (47 bp):
TGGTCACTGTCTTATAAATCACAGAGCATCATGAGATAGGCCTGAAG
Found at i:1346379 original size:2 final size:2
Alignment explanation
Indices: 1346335--1346369 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1346325 ATTAAATAAT
1346335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1346370 GTTAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1346630 original size:34 final size:34
Alignment explanation
Indices: 1346591--1346693 Score: 94
Period size: 34 Copynumber: 3.2 Consensus size: 34
1346581 AATATTTTTA
1346591 ATTATTGAGAACATTTATAAATTTTGTAAAAACG
1 ATTATTGAGAACATTTATAAATTTTGTAAAAACG
* * * * *
1346625 ATTATTCA-AATGAATTAGAAATATTT-T---TA--
1 ATTATTGAGAA-CATTTATAAAT-TTTGTAAAAACG
1346654 ATTATTGAGAACATTTATAAATTTTGTAAAAACG
1 ATTATTGAGAACATTTATAAATTTTGTAAAAACG
1346688 ATTATT
1 ATTATT
1346694 CAAATGAATT
Statistics
Matches: 50, Mismatches: 10, Indels: 18
0.64 0.13 0.23
Matches are distributed among these distances:
28 3 0.06
29 16 0.32
30 2 0.04
31 1 0.02
32 1 0.02
33 2 0.04
34 22 0.44
35 3 0.06
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.42
Consensus pattern (34 bp):
ATTATTGAGAACATTTATAAATTTTGTAAAAACG
Found at i:1346680 original size:63 final size:63
Alignment explanation
Indices: 1346581--1346713 Score: 257
Period size: 63 Copynumber: 2.1 Consensus size: 63
1346571 TATTTATCAC
1346581 AATATTTTTAATTATTGAGAACATTTATAAATTTTGTAAAAACGATTATTCAAATGAATTAGA
1 AATATTTTTAATTATTGAGAACATTTATAAATTTTGTAAAAACGATTATTCAAATGAATTAGA
1346644 AATATTTTTAATTATTGAGAACATTTATAAATTTTGTAAAAACGATTATTCAAATGAATTAGA
1 AATATTTTTAATTATTGAGAACATTTATAAATTTTGTAAAAACGATTATTCAAATGAATTAGA
1346707 ATATATT
1 A-ATATT
1346714 AAAAGTTAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
63 64 0.93
64 5 0.07
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (63 bp):
AATATTTTTAATTATTGAGAACATTTATAAATTTTGTAAAAACGATTATTCAAATGAATTAGA
Found at i:1356974 original size:21 final size:21
Alignment explanation
Indices: 1356903--1356985 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
1356893 CAGAACCCCA
*
1356903 GGGGGGTATCGATTCTCCT-AT
1 GGGGGGAATCGATTC-CCTCAT
* *
1356924 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATT-CCC-TCAT
* *
1356947 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGAATCGATTCCCTCAT
1356968 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
1356986 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
20 11 0.21
21 22 0.42
22 5 0.10
23 14 0.27
ACGTcount: A:0.16, C:0.24, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAT
Found at i:1365155 original size:19 final size:19
Alignment explanation
Indices: 1365131--1365182 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1365121 GCGATTTTGA
*
1365131 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATACTT
1365150 AAAATGTGTTGCGATACTT
1 AAAATGTGTTGCGATACTT
1365169 AAAATGTGTTGCGA
1 AAAATGTGTTGCGA
1365183 GGGTTTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (19 bp):
AAAATGTGTTGCGATACTT
Found at i:1365224 original size:19 final size:19
Alignment explanation
Indices: 1365128--1365236 Score: 92
Period size: 19 Copynumber: 5.4 Consensus size: 19
1365118 AACGCGATTT
1365128 TGAAAAATGTGTTGCGATAG
1 TGAAAAA-GTGTTGCGATAG
* * *
1365148 TTAAAATGTGTTGCGATAC
1 TGAAAAAGTGTTGCGATAG
* * **
1365167 TTAAAATGTGTTGCGAGGG
1 TGAAAAAGTGTTGCGATAG
1365186 TTTGAAAAACGATTTGTTGCGATAG
1 --TGAAAAA-G---TGTTGCGATAG
1365211 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
1365230 TGAAAAA
1 TGAAAAA
1365237 TCCAAAATAA
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
19 45 0.62
20 5 0.07
21 5 0.07
22 2 0.03
23 7 0.10
25 9 0.12
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
TGAAAAAGTGTTGCGATAG
Found at i:1365396 original size:17 final size:17
Alignment explanation
Indices: 1365374--1365412 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1365364 GTGTTGCGAT
*
1365374 AGTGTAAAAGATTCTCA
1 AGTGTAAAAGATTCCCA
1365391 AGTGTAAAAGATTCCCA
1 AGTGTAAAAGATTCCCA
1365408 AGTGT
1 AGTGT
1365413 TTGCAATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (17 bp):
AGTGTAAAAGATTCCCA
Found at i:1365525 original size:19 final size:20
Alignment explanation
Indices: 1365486--1365525 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1365476 TGGTTCACGG
*
1365486 AATGTAAAATTATCAGTGGA
1 AATGTAAAATTACCAGTGGA
*
1365506 AATGTAAGATTACCAG-GGA
1 AATGTAAAATTACCAGTGGA
1365525 A
1 A
1365526 TAAGATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (20 bp):
AATGTAAAATTACCAGTGGA
Found at i:1366352 original size:21 final size:21
Alignment explanation
Indices: 1366326--1366395 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1366316 ATTTTGGAAA
*
1366326 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* **
1366347 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
1366366 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
1366387 ATCGCAACG
1 ATCGCAACG
1366396 AATTTGGACT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.38
21 24 0.62
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:1366369 original size:19 final size:19
Alignment explanation
Indices: 1366318--1366403 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 19
1366308 TCGTTGCAAT
1366318 TTTGGAAAATCGCAACGCGAA
1 TTTGGAAAATCGCAA--CGAA
* * **
1366339 CTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGAA
1366358 TTTGGAAAATCGCAACGTGAA
1 TTTGGAAAATCGCAAC--GAA
* **
1366379 CTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGAA
1366398 TTTGGA
1 TTTGGA
1366404 CTAACGTAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
19 24 0.47
21 27 0.53
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (19 bp):
TTTGGAAAATCGCAACGAA
Found at i:1366371 original size:40 final size:40
Alignment explanation
Indices: 1366318--1366403 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
1366308 TCGTTGCAAT
1366318 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
* *
1366358 TTTGGAAAATCGCAACGTGAACTTGGACTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
1366398 TTTGGA
1 TTTGGA
1366404 CTAACGTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAA
Found at i:1366404 original size:19 final size:19
Alignment explanation
Indices: 1366343--1366406 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
1366333 CGCGAACTTC
1366343 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
** *
1366362 GAAAATCGCAACGTGAACTTG
1 GACTATCGCAAC--GAATTTG
1366383 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAATTTG
1366402 GACTA
1 GACTA
1366407 ACGTAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 21 0.57
21 16 0.43
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.23
Consensus pattern (19 bp):
GACTATCGCAACGAATTTG
Found at i:1366616 original size:19 final size:19
Alignment explanation
Indices: 1366574--1366621 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1366564 GGAAACTGAT
* * *
1366574 TTGCGATATTGGAGATTGCG
1 TTGCGAT-TTAGAGATCGCA
1366594 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
1366613 TTGCGATTT
1 TTGCGATTT
1366622 TGTTGGTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Found at i:1367414 original size:17 final size:17
Alignment explanation
Indices: 1367392--1367447 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1367382 TATTTTTTAT
*
1367392 TATTATATTTGTATAAA
1 TATTATATTTATATAAA
*
1367409 TATTAT-TTTTTATTAAA
1 TATTATATTTATA-TAAA
* *
1367426 -ATAATATTTATATAAT
1 TATTATATTTATATAAA
1367442 TATTAT
1 TATTAT
1367448 TTATTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTATATTTATATAAA
Found at i:1367444 original size:30 final size:28
Alignment explanation
Indices: 1367410--1367477 Score: 82
Period size: 30 Copynumber: 2.4 Consensus size: 28
1367400 TTGTATAAAT
*
1367410 ATTATTTTTTATTAAAATAATATTTATATA
1 ATTATTTTTTATTAAAATAA-ATTAAT-TA
* * *
1367440 ATTATTATTTATTTAAATTAATTAATTA
1 ATTATTTTTTATTAAAATAAATTAATTA
1367468 ATTATTTTTT
1 ATTATTTTTT
1367478 GTACTAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 11 0.33
29 5 0.15
30 17 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTATTTTTTATTAAAATAAATTAATTA
Found at i:1369280 original size:21 final size:21
Alignment explanation
Indices: 1369254--1369319 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
1369244 TCTTCGCAGT
1369254 GTTACATTCCTAGCCCTCAGG
1 GTTACATTCCTAGCCCTCAGG
* *
1369275 GTTACATTCCTAGCCTGTCA-T
1 GTTACATTCCTAGCC-CTCAGG
* *
1369296 GTTACATGCCTAGCCCGCAGG
1 GTTACATTCCTAGCCCTCAGG
1369317 GTT
1 GTT
1369320 TTATGACACC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 2 0.05
21 32 0.86
22 3 0.08
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.30
Consensus pattern (21 bp):
GTTACATTCCTAGCCCTCAGG
Found at i:1369992 original size:14 final size:14
Alignment explanation
Indices: 1369973--1370003 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1369963 TTTTATCCTT
1369973 AACATATACATTAA
1 AACATATACATTAA
1369987 AACATATACATTAA
1 AACATATACATTAA
1370001 AAC
1 AAC
1370004 CAACTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:1370192 original size:63 final size:64
Alignment explanation
Indices: 1370069--1370198 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 64
1370059 TTTCATGCAC
* * *
1370069 ACAACCAACTTATCACTTCACATTTATTCAATTTGTCCATATCATTTTATCCAATATATTCA-A
1 ACAACCAAATGATCACTTCACATTTATTCAATTTATCCATATCATTTTATCCAATATATTCATA
** *
1370132 ACAACCAAATGATCACTTCACATTTATTCAATTTATCCATAAT-ATTTTATCTTATTTATTCATA
1 ACAACCAAATGATCACTTCACATTTATTCAATTTATCCAT-ATCATTTTATCCAATATATTCATA
1370196 ACA
1 ACA
1370199 TTTTATCCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
63 53 0.90
64 6 0.10
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.41
Consensus pattern (64 bp):
ACAACCAAATGATCACTTCACATTTATTCAATTTATCCATATCATTTTATCCAATATATTCATA
Found at i:1370211 original size:23 final size:23
Alignment explanation
Indices: 1370154--1370216 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
1370144 TCACTTCACA
* * *
1370154 TTTATTCAATTTATCCATAATAT
1 TTTATCCAATTTATTCATAACAT
**
1370177 TTTATCTTATTTATTCATAACAT
1 TTTATCCAATTTATTCATAACAT
1370200 TTTATCCAATTTATTCA
1 TTTATCCAATTTATTCA
1370217 AACTTCACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTATCCAATTTATTCATAACAT
Found at i:1370529 original size:116 final size:116
Alignment explanation
Indices: 1370261--1371155 Score: 1409
Period size: 116 Copynumber: 7.7 Consensus size: 116
1370251 ATCCAATTTC
*
1370261 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * *
1370326 GGACCGCGCTTTCACCACTTTGGGTACTGATATGAATAGTG-CCCCAAGGG
66 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
*
1370376 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCCCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * * *
1370441 AGAACGCTCCTTCACCACTTTGGGTACTAACATGAATAGTGCCCCCGAGGG
66 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
** * *
1370492 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATTAAATAATAGAAGGCACCCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGG---CGCCCC
* *
1370557 CCGGGAACGC-CCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCTGAGGG
63 CCGGGAACGCGCC-TTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
*
1370611 ACATGAGGGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
*
1370676 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCTGAGGG
66 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
*
1370727 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCTCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCC-CCC
* * *
1370792 GGGAACGTGCCTTCACCACTTTGGGCACTGACATGAATAGTGCCCCCGAGGG
65 GGGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
*
1370844 ACATGAGTTACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* *
1370909 GGAACGCGCCTTCACCACTTTGGGTTA-AGATATGAATAGTGCCCCCAAGGG
66 GGAACGCGCCTTCACCACTTTGGG-TACTGATATGAATAGTGCCCCCGAGGG
* * **
1370960 GCATGAGTGACGTAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGTACCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* *
1371025 GGAACGCGCCTTCGCCACTTTGGGTTCTGATATGAATAGTGCCCCCGAGGG
66 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
* * *
1371076 GCATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGATGGCGCCCCCGG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
*
1371141 GGAACGCACCTTCAC
66 GGAACGCGCCTTCAC
1371156 GTGAATAGTA
Statistics
Matches: 721, Mismatches: 50, Indels: 17
0.91 0.06 0.02
Matches are distributed among these distances:
115 99 0.14
116 401 0.56
117 113 0.16
118 2 0.00
119 106 0.15
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (116 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
Found at i:1370902 original size:233 final size:232
Alignment explanation
Indices: 1370261--1371155 Score: 1409
Period size: 233 Copynumber: 3.8 Consensus size: 232
1370251 ATCCAATTTC
*
1370261 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * * *
1370326 GGACCGCGCTTTCACCACTTTGGGTACTGATATGAATAGTG-CCCCAAGGGACATGAGTGACATA
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATA
* * *
1370390 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCCCCCCCCGAGAACGCTCCTTCA
131 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCA
* *
1370455 CCACTTTGGGTACTAACATGAATAGTGCCCCCGAGGG
196 CCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
** * *
1370492 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATTAAATAATAGAAGGCACCCCCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGG---CGCCCC
* *
1370557 CCGGGAACGC-CCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCTGAGGGACATGAGGGA
63 CCGGGAACGCGCC-TTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGA
1370621 CATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCC
127 CATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCC
*
1370686 TTCACCACTTTGGGTACTGATATGAATAGTGCCCCTGAGGG
192 TTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
*
1370727 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCTCCC
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCC-CCC
* * *
1370792 GGGAACGTGCCTTCACCACTTTGGGCACTGACATGAATAGTGCCCCCGAGGGACATGAGTTACAT
65 GGGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACAT
1370857 AATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTC
130 AATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTC
* *
1370922 ACCACTTTGGGTTA-AGATATGAATAGTGCCCCCAAGGG
195 ACCACTTTGGG-TACTGATATGAATAGTGCCCCCGAGGG
* * **
1370960 GCATGAGTGACGTAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGTACCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * * *
1371025 GGAACGCGCCTTCGCCACTTTGGGTTCTGATATGAATAGTGCCCCCGAGGGGCATGAGTGACATA
66 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATA
* * *
1371090 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGATGGCGCCCCCGGGGAACGCACCTTCA
131 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCA
1371155 C
196 C
1371156 GTGAATAGTA
Statistics
Matches: 611, Mismatches: 45, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
231 52 0.09
232 129 0.21
233 214 0.35
234 48 0.08
235 168 0.27
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (232 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATA
ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCA
CCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
Found at i:1371013 original size:349 final size:347
Alignment explanation
Indices: 1370261--1371155 Score: 1411
Period size: 349 Copynumber: 2.6 Consensus size: 347
1370251 ATCCAATTTC
*
1370261 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * *
1370326 GGACCGCGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCAAGGGACATGAGTGACATAA
66 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCGAGGGACATGAGTGACATAA
* * *
1370391 TAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCCCCCCCCGAGAACGCTCCTTCAC
131 TAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCCCCGGGAACG-TCCTTCAC
*
1370456 CACTTTGGGTACTAACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAA
195 CACTTTGGGCACTAACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAA
**
1370521 CATATTCTCTGATTAAATAATAGAAGGCACCCCCCCCCGGGAACGCCCTTTCACCACTTTGGGTA
260 CATATTCTCTGACAAAATAATAGAAGG--CCCCCCCCCGGGAACGCCCTTTCACCACTTTGGGTA
* **
1370586 CTGACATGAATAGTGCCCCTGAGGG
323 CAGACATGAATAGTGCCCCCAAGGG
*
1370611 ACATGAGGGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
1370676 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCTGAGGGACATGAGTGACATA
66 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCC-GAGGGACATGAGTGACATA
1370741 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCTCCCGGGAACGTGCCTTC
130 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCC-CCCGGGAACGT-CCTTC
* *
1370806 ACCACTTTGGGCACTGACATGAATAGTGCCCCCGAGGGACATGAGTTACATAATAGGGCAATGAT
193 ACCACTTTGGGCACTAACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGAT
* *
1370871 AACATATTCTCTGACAAAATAATGGAAGG-CGCCCCCCGGGAACGCGCC-TTCACCACTTTGGGT
258 AACATATTCTCTGACAAAATAATAGAAGGCCCCCCCCCGGGAACGC-CCTTTCACCACTTTGGG-
*
1370934 TA-AGATATGAATAGTGCCCCCAAGGG
321 TACAGACATGAATAGTGCCCCCAAGGG
* * **
1370960 GCATGAGTGACGTAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGTACCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
* * *
1371025 GGAACGCGCCTTCGCCACTTTGGGTTCTGATATGAATAGTGCCCCCGAGGGGCATGAGTGACATA
66 GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTG-CCCCGAGGGACATGAGTGACATA
* *
1371090 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGG-ATGGCGCCCCCGGGGAACGCACCTTC
130 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAT-GCGCCCCCCGGGAACG-TCCTTC
1371154 AC
193 AC
1371156 GTGAATAGTA
Statistics
Matches: 508, Mismatches: 29, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
348 18 0.04
349 210 0.41
350 114 0.22
351 64 0.13
352 102 0.20
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (347 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCG
GGAACGCGCCTTCACCACTTTGGGTACTGATATGAATAGTGCCCCGAGGGACATGAGTGACATAA
TAGGGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCCCCGGGAACGTCCTTCACC
ACTTTGGGCACTAACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAAC
ATATTCTCTGACAAAATAATAGAAGGCCCCCCCCCGGGAACGCCCTTTCACCACTTTGGGTACAG
ACATGAATAGTGCCCCCAAGGG
Found at i:1374364 original size:26 final size:26
Alignment explanation
Indices: 1374319--1374407 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
1374309 ATATTATATA
* *
1374319 AATTATTTATATTTTAATTTTATAAAAT
1 AATTAATTATA-TTT-ATTTAATAAAAT
* *
1374347 GATTAATTATATTTATTTAATATAAT
1 AATTAATTATATTTATTTAATAAAAT
*
1374373 AATTAA-TATTATTTATTATAAAAAAAT
1 AATTAATTA-TATTTATT-TAATAAAAT
*
1374400 TATTAATT
1 AATTAATT
1374408 TTAAAATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
25 2 0.04
26 23 0.46
27 15 0.30
28 10 0.20
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (26 bp):
AATTAATTATATTTATTTAATAAAAT
Found at i:1374375 original size:22 final size:22
Alignment explanation
Indices: 1374350--1374393 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1374340 ATAAAATGAT
1374350 TAATT-ATATTTATTTAATATAA
1 TAATTAATA-TTATTTAATATAA
*
1374372 TAATTAATATTATTTATTATAA
1 TAATTAATATTATTTAATATAA
1374394 AAAAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTAATATTATTTAATATAA
Found at i:1375098 original size:61 final size:60
Alignment explanation
Indices: 1374990--1375106 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 60
1374980 AAAATACCAG
* * * * *
1374990 CGTGGCATCTGACTCAGCAGAACCTAGGTAAAGCGTATCCCCGGGGATGCGCCTTTCATA
1 CGTGGCATCCGACTCAGCAAAACCCAGGAAAAGCGCATCCCCGGGGATGCGCCTTTCATA
1375050 CGTGGCATCCGACTCAGCAAAAACCCAGGAAAAGCGCATCCCCGGGGATGCGCCTTT
1 CGTGGCATCCGACTCAGC-AAAACCCAGGAAAAGCGCATCCCCGGGGATGCGCCTTT
1375107 GTGCCACCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 17 0.33
61 34 0.67
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.18
Consensus pattern (60 bp):
CGTGGCATCCGACTCAGCAAAACCCAGGAAAAGCGCATCCCCGGGGATGCGCCTTTCATA
Found at i:1376338 original size:22 final size:22
Alignment explanation
Indices: 1376307--1376359 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1376297 GATTTTTTTT
* *
1376307 ATGAATAGTGATGAACAATACC
1 ATGAACAGTGATAAACAATACC
* *
1376329 ATGAACAGTGATAAACAGTACT
1 ATGAACAGTGATAAACAATACC
*
1376351 GTGAACAGT
1 ATGAACAGT
1376360 ATATCGATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (22 bp):
ATGAACAGTGATAAACAATACC
Found at i:1376464 original size:21 final size:21
Alignment explanation
Indices: 1376427--1376466 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1376417 AAAAATTTGT
**
1376427 ATCGATGCACTGTTACAGTGC
1 ATCGATGCACTACTACAGTGC
1376448 ATCGATGCACTACTACAGT
1 ATCGATGCACTACTACAGT
1376467 AATTTTAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (21 bp):
ATCGATGCACTACTACAGTGC
Found at i:1377115 original size:57 final size:57
Alignment explanation
Indices: 1377023--1377140 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 57
1377013 TGCTAACCCG
* * **
1377023 TATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTATAGTCCC-A
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATA-TCCCAA
* *
1377080 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATCCCAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATATCCCAA
1377137 TATG
1 TATG
1377141 CAGCCTGCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 4 0.07
57 50 0.93
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (57 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATATCCCAA
Found at i:1380406 original size:14 final size:15
Alignment explanation
Indices: 1380381--1380410 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1380371 TATAAAATAT
1380381 AATAATTAAATTTAA
1 AATAATTAAATTTAA
1380396 AATAATT-AATTTAA
1 AATAATTAAATTTAA
1380410 A
1 A
1380411 GATTCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAATTAAATTTAA
Found at i:1381650 original size:23 final size:27
Alignment explanation
Indices: 1381596--1381651 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1381586 AAATGTGTTC
*
1381596 GATATATATATATATATAAAGACATAT
1 GATATATACATATATATAAAGACATAT
*
1381623 AATATATACATAT-TAT-AAGA-A-AT
1 GATATATACATATATATAAAGACATAT
1381646 GATATA
1 GATATA
1381652 GGATATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.27
24 1 0.04
25 4 0.15
26 3 0.12
27 11 0.42
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.36
Consensus pattern (27 bp):
GATATATACATATATATAAAGACATAT
Found at i:1395799 original size:3 final size:3
Alignment explanation
Indices: 1395793--1395940 Score: 88
Period size: 3 Copynumber: 48.3 Consensus size: 3
1395783 ATTATAATGT
* *
1395793 TAA TAA TAA TAG TAA TAA TAA TTAA TAA TAA TAAA TGA TAA CTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA -TAA TAA
* * * * * * *
1395841 CAA T-A TAG TAA CAA TATG TAA TATA TAA TTGA CAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TA-A TAA TA-A TAA -TAA TAA TAA TAA TAA TAA
* * * *
1395888 TAG TAA GTAA TAA TAA T-A TAA TAT TAA TAA TAG TAA T-A TAA -GA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1395931 TAA TAA TAA T
1 TAA TAA TAA T
1395941 GTTAATAGCA
Statistics
Matches: 108, Mismatches: 26, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
2 7 0.06
3 82 0.76
4 19 0.18
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1395838 original size:20 final size:19
Alignment explanation
Indices: 1395776--1395940 Score: 79
Period size: 20 Copynumber: 8.4 Consensus size: 19
1395766 ACAGTAATGG
* *
1395776 TAATAATATTATAATGTTAA
1 TAATAATAATA-AATGATAA
* *
1395796 TAATAATAGT-AATAATAA
1 TAATAATAATAAATGATAA
1395814 TTAATAATAATAAATGATAA
1 -TAATAATAATAAATGATAA
* * * *
1395834 CTAATAACAATATAGTAACAA
1 -TAATAATAATA-AATGATAA
* * *
1395855 TATGTAATATATAATTGACAA
1 TA-ATAATA-ATAAATGATAA
*
1395876 TAATAATACT-AAT-AGTAA
1 TAATAATAATAAATGA-TAA
1395894 GTAATAATAATATAAT-ATTAA
1 -TAATAATAATA-AATGA-TAA
*
1395915 TAATAGTAATATAA-GATAA
1 TAATAATAATA-AATGATAA
1395934 TAATAAT
1 TAATAAT
1395941 GTTAATAGCA
Statistics
Matches: 113, Mismatches: 22, Indels: 21
0.72 0.14 0.13
Matches are distributed among these distances:
17 1 0.01
18 10 0.09
19 28 0.25
20 47 0.42
21 24 0.21
22 3 0.03
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (19 bp):
TAATAATAATAAATGATAA
Found at i:1400161 original size:193 final size:191
Alignment explanation
Indices: 1399904--1400303 Score: 493
Period size: 193 Copynumber: 2.1 Consensus size: 191
1399894 ATATTTATCT
* * **
1399904 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTATGTCACTAAATTACGTAAAATTTC
1 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGTCAATAAATTAAATAAAATTTC
*** *
1399969 GTTATTGAT-GATTTATATCGCCATGGATAATACATTAAAATCAACCTATATGTGACGAAACAA-
66 GTTATTGATCG-TTTATATCGCCACAAACAATACATTAAAATCAACCTATATGTGACGAAA-AAG
*
1400032 ATATCGTCAAATTTTTAGTGACATAATATAAAT-GTTACCTAATAATATTATGAATGACGTTTAT
129 ATA--GTCAAATTTTTAGTGACA-AA-ATAAATCGTTACCTAATAATATTATGAATGACGATTAT
1400096 GC
190 GC
* * * ** **
1400098 ATAACGTCACTTTATAATTTATATTCTATGACAGTTGGTTACGTCAATAAATTAAAT-AAATTTC
1 ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGTCAATAAATTAAATAAAATTTC
* * * * *
1400162 GTTATTGATCGTTTATATTGTCACAAACAATGCATTAAAATCAACTTATATGTGATGAAAAAGAT
66 GTTATTGATCGTTTATATCGCCACAAACAATACATTAAAATCAACCTATATGTGACGAAAAAGAT
* * *
1400227 AGTCACATTTTTAGTGACAAAATATATCGTTACCTAATAATATTATGAATGATGATTATGC
131 AGTCAAATTTTTAGTGACAAAATAAATCGTTACCTAATAATATTATGAATGACGATTATGC
*
1400288 ATAACGTCACCATATA
1 ATAACGTCACTATATA
1400304 TAATGTCACC
Statistics
Matches: 177, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
189 5 0.03
190 47 0.27
191 17 0.10
192 2 0.01
193 59 0.33
194 47 0.27
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (191 bp):
ATAACGTCACTATATAATTAATATTCAATGACAACTAATTACGTCAATAAATTAAATAAAATTTC
GTTATTGATCGTTTATATCGCCACAAACAATACATTAAAATCAACCTATATGTGACGAAAAAGAT
AGTCAAATTTTTAGTGACAAAATAAATCGTTACCTAATAATATTATGAATGACGATTATGC
Found at i:1403662 original size:3 final size:3
Alignment explanation
Indices: 1403656--1403707 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
1403646 ATCTTCTTAA
*
1403656 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AGT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1403702 AAT AAT
1 AAT AAT
1403708 TAGAACATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1405782 original size:19 final size:20
Alignment explanation
Indices: 1405758--1405795 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1405748 TTCAACACAA
1405758 TAATAATAAAAT-ATAGTAC
1 TAATAATAAAATAATAGTAC
*
1405777 TAATAATAATATAATAGTA
1 TAATAATAAAATAATAGTA
1405796 AAACAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (20 bp):
TAATAATAAAATAATAGTAC
Found at i:1405803 original size:22 final size:21
Alignment explanation
Indices: 1405754--1405803 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1405744 ATAGTTCAAC
**
1405754 ACAATAATAATAAAATATAGT
1 ACAATAATAATAAAATATAAA
*
1405775 ACTAATAATAATATAATAGTAAA
1 AC-AATAATAATAAAATA-TAAA
1405798 ACAATA
1 ACAATA
1405804 CTTATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 18 0.75
23 4 0.17
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (21 bp):
ACAATAATAATAAAATATAAA
Found at i:1408013 original size:24 final size:24
Alignment explanation
Indices: 1407981--1408033 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1407971 GACTTTGAAC
1407981 GCTTGTACCATTAACATTCCTATT
1 GCTTGTACCATTAACATTCCTATT
**
1408005 GCTTGTACCATTGGCATTCCTATT
1 GCTTGTACCATTAACATTCCTATT
1408029 GCTTG
1 GCTTG
1408034 AACCCAGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.42
Consensus pattern (24 bp):
GCTTGTACCATTAACATTCCTATT
Found at i:1408155 original size:3 final size:3
Alignment explanation
Indices: 1408147--1408259 Score: 183
Period size: 3 Copynumber: 38.0 Consensus size: 3
1408137 AATATTTTCA
* * *
1408147 AAT AAT AAT AAT AAT GAT GAT GAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1408195 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1408242 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
1408260 GATCTAATGT
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 103 0.98
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1411836 original size:78 final size:78
Alignment explanation
Indices: 1411702--1411857 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
1411692 ATAAATGGTA
* *
1411702 AAATATGAGAAAATGATTTGGAATAGTGTTTTAGACTAATGTGTAACAACAGATGAATTAAGAGG
1 AAATATGAGAAAATGATTTGGAATAATGTTTTAGACTAATGTGTAACAACAAATGAATTAAGAGG
1411767 GCATTTTGGTCCT
66 GCATTTTGGTCCT
1411780 AAATATGAGAAAATGATTTGGAATAATGTTTTAGACTAATGTGTAACAACAAATGAATTAAGAGG
1 AAATATGAGAAAATGATTTGGAATAATGTTTTAGACTAATGTGTAACAACAAATGAATTAAGAGG
1411845 GCATTTTGGTCCT
66 GCATTTTGGTCCT
1411858 TTAAGGGGGA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (78 bp):
AAATATGAGAAAATGATTTGGAATAATGTTTTAGACTAATGTGTAACAACAAATGAATTAAGAGG
GCATTTTGGTCCT
Found at i:1412541 original size:20 final size:19
Alignment explanation
Indices: 1412497--1412546 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
1412487 TGATGCAATT
**
1412497 GGTATCGATACTAAGAGGG
1 GGTATCGATACTAAGAGAA
*
1412516 GGTATCGATACTATGGAGAA
1 GGTATCGATACTA-AGAGAA
1412536 GGTATCGATAC
1 GGTATCGATAC
1412547 CATTGATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (19 bp):
GGTATCGATACTAAGAGAA
Found at i:1423243 original size:43 final size:43
Alignment explanation
Indices: 1423158--1423243 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
1423148 GCAAAATGAA
* * * *
1423158 GACGCTGTTTTAAATCCTTCTGTGAAGAAACATGCACTAGATT
1 GACGCTGATTGAAATCCTTCTGTGAAGAAACAAGCACAAGATT
* *
1423201 GACGCTGATTGAACTCCTTCTGTGAAGAATCAAGCGA-AAGATT
1 GACGCTGATTGAAATCCTTCTGTGAAGAAACAAGC-ACAAGATT
1423244 TTCATTGATC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (43 bp):
GACGCTGATTGAAATCCTTCTGTGAAGAAACAAGCACAAGATT
Found at i:1423316 original size:20 final size:20
Alignment explanation
Indices: 1423286--1423350 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
1423276 AGTGAAAGGT
*
1423286 TGAACAAGTTCTTCTCATTA
1 TGAACTAGTTCTTCTCATTA
*
1423306 TGAACTTGTTCTTCCTCA-T-
1 TGAACTAGTTCTT-CTCATTA
* * *
1423325 CGGACGAGTTCTTCTCATTA
1 TGAACTAGTTCTTCTCATTA
1423345 TGAACT
1 TGAACT
1423351 CTCCATTGAA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 4 0.12
19 10 0.30
20 15 0.45
21 4 0.12
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (20 bp):
TGAACTAGTTCTTCTCATTA
Found at i:1423555 original size:124 final size:124
Alignment explanation
Indices: 1423398--1424148 Score: 993
Period size: 124 Copynumber: 6.1 Consensus size: 124
1423388 GAATCAAATA
* * * *
1423398 AAATGTTTATGCTAATCTATCTCCTTCTACGATAGAGTCGAGCAAAAAGTTGAACAAGTTCTTCT
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
* * * * * *
1423463 CATTATGAACTTTTTCTTCATCTTCAGATGAGTTCTTCTCATTAGGAACTCTCTATTGG
66 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * * *
1423522 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTTGAGTAAACGGTTGAACAAATTCTTCT
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
* * *
1423587 CATTATGAACTTTTTCTCCCTCATCGGATGAGTTATTCTCATTATGAACTCTCCATTGG
66 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * ** ** *
1423646 AAATTTTAATGCAAATCTATCTCCTTCTATGATAGAGTCGAACAAAAGGTTGAACAAGTTCTTCT
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
* * ** * *
1423711 CATTATGTACTTATTCTTTCTCTTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGG
66 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * * *
1423770 AAATATTGATGCTGATCTATCTCCTTTTGCGATAGAGTTGAGCAAAAGGTTGAA-AATGTTATTC
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAA-GTTCTTC
* * * *
1423834 TCATTATAAACTTCTTCTCTCTCATCAGATGATTTCTTCTCATTATGAACTCTCTATTGG
65 TCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * ** * *
1423894 AAATATTGATACTGATCTATCTTTTTTTGCGATAGAGTCGAGAAAAAGGTTGAACAAGTTCTTCT
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
*
1423959 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTTTCCATTGG
66 CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
* * * *
1424018 AAGTGTTGATGTTGATCTATCTCCTTTTGTGATAGAGTCGAGCGAAAAGGTTGAACAAGTTCTTC
1 AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGC-AAAAGGTTGAACAAGTTCTTC
* * * *
1424083 TCATTATGAACTTCTTCTCCCTTATCGGACGAGTTCTTCTCATTATGAACTCTCCA-TGA
65 TCATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
1424142 AAATGTT
1 AAATGTT
1424149 AATCCCTCGA
Statistics
Matches: 549, Mismatches: 75, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
123 2 0.00
124 472 0.86
125 75 0.14
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (124 bp):
AAATGTTGATGCTGATCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCT
CATTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
Found at i:1424353 original size:137 final size:138
Alignment explanation
Indices: 1424068--1424410 Score: 460
Period size: 137 Copynumber: 2.5 Consensus size: 138
1424058 AGCGAAAAGG
* * * *
1424068 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGACGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTCATCGGATGAGTTCTTCTCATTATGAAC
* *
1424133 TCTCCATGAAAATGTTAATCCCTCGAATGAGGTGTCACTGATTCAACTCCATATACGATGAATCG
66 TCTACATGAAAATGTTAATCCCTCGAATGAGGTGTCACTGATTCAACTCCATATAAGATGAATCG
*
1424198 AGCTAAGG
131 AGCTAAGA
* *
1424206 TTGAATAAGTTATTCTCATTATGAACTTCTTTTTCCTCATCGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTCATCGGATGAGTTCTTCTCATTATGAAC
* * * * *
1424271 TCTAC-TGGAAATGTTGA-CCTTTCGAGTGAGGTGTCGCTGATTCAACTCCATATAAGATGAATC
66 TCTACATGAAAATGTTAATCC-CTCGAATGAGGTGTCACTGATTCAACTCCATATAAGATGAATC
1424334 GAGCTAAGA
130 GAGCTAAGA
* * * * *
1424343 TTGAACAAGTTCTTTTTATTATAAAC--CTTTTCTCCCTCATCAGATGAGTTCTTCTCATTATTA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTTT-T-CCTCATCGGATGAGTTCTTCTCATTATGA
1424406 ACTCT
64 ACTCT
1424411 CCACTAGAAA
Statistics
Matches: 181, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
135 5 0.03
136 3 0.02
137 110 0.61
138 63 0.35
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (138 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTCATCGGATGAGTTCTTCTCATTATGAAC
TCTACATGAAAATGTTAATCCCTCGAATGAGGTGTCACTGATTCAACTCCATATAAGATGAATCG
AGCTAAGA
Found at i:1425927 original size:20 final size:22
Alignment explanation
Indices: 1425897--1425936 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1425887 TTTTAAGATG
1425897 CTTGTAAATAA-AAAATTGGGA
1 CTTGTAAATAAGAAAATTGGGA
1425918 CTTG-AAATAAGAAAATTGG
1 CTTGTAAATAAGAAAATTGG
1425937 AATTTTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (22 bp):
CTTGTAAATAAGAAAATTGGGA
Found at i:1429100 original size:45 final size:45
Alignment explanation
Indices: 1429046--1429372 Score: 519
Period size: 45 Copynumber: 7.2 Consensus size: 45
1429036 ATTATTCATT
*
1429046 ATTTCCATTTATGGCATCCTTTCATGCCTTTAACGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
1429092 ATTTCATTTATGACATCCTTTCATGCCTTTAATGAACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * *
1429137 ATTTCATTTATAGTATCATTTCATGCCTTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1429182 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1429227 ATTTCATTTATGGCATCCTTTCATACCTTTAATGAACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1429272 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1429317 ATTTCATTTATGGCATCATTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1429362 ATTTCATTTAT
1 ATTTCATTTAT
1429373 ATAATAAAAA
Statistics
Matches: 257, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
45 253 0.98
46 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.43
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:1429177 original size:21 final size:21
Alignment explanation
Indices: 1429153--1429218 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
1429143 TTTATAGTAT
1429153 CATTTCATGCCTTTAATGCAC
1 CATTTCATGCCTTTAATGCAC
* *
1429174 CATTATGCATTTCATTT-ATGGCATC
1 CATT-T-CA-TGCCTTTAAT-GCA-C
1429199 C-TTTCATGCCTTTAATGCAC
1 CATTTCATGCCTTTAATGCAC
1429219 TGTTATGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
22 5 0.14
23 5 0.14
24 10 0.29
25 2 0.06
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.41
Consensus pattern (21 bp):
CATTTCATGCCTTTAATGCAC
Found at i:1429841 original size:20 final size:20
Alignment explanation
Indices: 1429812--1429861 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1429802 GTAATCCATG
1429812 GTATCAATACTTTCCTTTTA
1 GTATCAATACTTTCCTTTTA
*
1429832 GTATCGATACTTTCCTTTTA
1 GTATCAATACTTTCCTTTTA
1429852 GTATCAATAC
1 GTATCAATAC
1429862 CCCATTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.46
Consensus pattern (20 bp):
GTATCAATACTTTCCTTTTA
Found at i:1433456 original size:15 final size:15
Alignment explanation
Indices: 1433433--1433470 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1433423 CAATTCAGTC
*
1433433 GGAGTCATCCGATAT
1 GGAGCCATCCGATAT
*
1433448 GGAGCCATCTGATAT
1 GGAGCCATCCGATAT
1433463 GGAGCCAT
1 GGAGCCAT
1433471 AGAAATAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (15 bp):
GGAGCCATCCGATAT
Found at i:1436102 original size:45 final size:45
Alignment explanation
Indices: 1436044--1436236 Score: 332
Period size: 45 Copynumber: 4.3 Consensus size: 45
1436034 GTTATTCATT
*
1436044 ATTTCCATTTATGGCATCCTTTCACGCCTTTAATGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1436090 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1436135 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGA
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
1436180 ATTTCATTTATGGCATCCTTTCATGCCTTTAAAGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1436225 ATTTCATTTATG
1 ATTTCATTTATG
1436237 TAATAAAAAC
Statistics
Matches: 139, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 135 0.97
46 4 0.03
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:1440484 original size:18 final size:18
Alignment explanation
Indices: 1440461--1440495 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1440451 GGAATAAAAC
1440461 ATTTAGTTATTTTAAGAT
1 ATTTAGTTATTTTAAGAT
1440479 ATTTAGTTATTTTAAGA
1 ATTTAGTTATTTTAAGA
1440496 CAGTCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
ATTTAGTTATTTTAAGAT
Done.