Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008025.1 Hibiscus syriacus cultivar Beakdansim tig00110500_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: 2744542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1407317 original size:39 final size:39
Alignment explanation
Indices: 1407241--1407534 Score: 393
Period size: 39 Copynumber: 7.7 Consensus size: 39
1407231 AGGTTGAATA
*
1407241 AGTTCTTCAGACTATGAA---CTTCTTCCTCTTCAAATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * *
1407277 AGTTCTTCAGATTATGAACTCCTTCTTTCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * *
1407316 AGTTCTTCAAACTATGAACTTCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
1407355 AGTTCTTCAGACTATGAACT-C--CTTCCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
*
1407391 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * *
1407430 AGTCCTTCATACTATGAACTCCTTCTTTCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * * **
1407469 AGTTCTTCAGATTGTGAACTTCTTCTTCCTCTTCAGGCG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
*
1407508 AGTTCTTCAGATTATGAACTCCTTCTT
1 AGTTCTTCAGACTATGAACTCCTTCTT
1407535 GAAATGTTTT
Statistics
Matches: 226, Mismatches: 26, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
36 51 0.23
37 1 0.00
38 1 0.00
39 173 0.77
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (39 bp):
AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
Found at i:1407371 original size:78 final size:78
Alignment explanation
Indices: 1407241--1407534 Score: 438
Period size: 78 Copynumber: 3.8 Consensus size: 78
1407231 AGGTTGAATA
* * *
1407241 AGTTCTTCAGACTATGAA---CTTCTTCCTCTTCAAATGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
*
1407303 TTCTCTTCATATG
66 TTCTCTTCAGATG
*
1407316 AGTTCTTCAAACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTC-
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
1407380 --CTCTTCAGATG
66 TTCTCTTCAGATG
* * *
1407391 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGTCCTTCATACTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
1407456 TTCTCTTCAGATG
66 TTCTCTTCAGATG
* * * *
1407469 AGTTCTTCAGATTGTGAACTTCTTCTTCCTCTTCAGGCGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
1407534 T
66 T
1407535 GAAATGTTTT
Statistics
Matches: 197, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
75 87 0.44
78 110 0.56
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (78 bp):
AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
TTCTCTTCAGATG
Found at i:1407373 original size:114 final size:114
Alignment explanation
Indices: 1407241--1407534 Score: 426
Period size: 114 Copynumber: 2.6 Consensus size: 114
1407231 AGGTTGAATA
* *
1407241 AGTTCTTCAGACTATGAACTTCTTCCTCTTCAAATGAGTTCTTCAGATTATGAACTCCTTCTTTC
1 AGTTCTTCAGACTATGAACTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTCC
* * * *
1407306 TCTTCATATGAGTTCTTCAAACTATGAACTTCTTCTTCCTCTTCAGACG
66 TCTTCAGACGAGTCCTTCAAACTATGAACTCCTTCTTCCTCTTCAGACG
* *
1407355 AGTTCTTCAGACTATGAACTCCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCTTCC
1 AGTTCTTCAGACTATGAACTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTCC
* * *
1407420 TCTTCAGACGAGTCCTTCATACTATGAACTCCTTCTTTCTCTTCAGATG
66 TCTTCAGACGAGTCCTTCAAACTATGAACTCCTTCTTCCTCTTCAGACG
* * **
1407469 AGTTCTTCAGATTGTGAACTTCTTCTTCCTCTTCAGGCGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAA---CTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
1407534 T
63 T
1407535 GAAATGTTTT
Statistics
Matches: 160, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
114 119 0.74
117 41 0.26
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (114 bp):
AGTTCTTCAGACTATGAACTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTCC
TCTTCAGACGAGTCCTTCAAACTATGAACTCCTTCTTCCTCTTCAGACG
Found at i:1407656 original size:72 final size:72
Alignment explanation
Indices: 1407539--1407798 Score: 396
Period size: 73 Copynumber: 3.6 Consensus size: 72
1407529 CTTCTTGAAA
* * *
1407539 TGTTTTAAGAAAAATAATCTCAATTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCCAGCGGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGGA
*
1407604 AACATTT
66 AACAATT
** * *
1407611 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTATTATTTCGAGTGAAATTTTCTCAAGCAAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGC-GG
1407676 AAA-AAGTT
65 AAACAA-TT
*
1407684 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCG-G
1407749 AAACAATT
65 AAACAATT
*
1407757 TGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1407799 GAAAACATCC
Statistics
Matches: 170, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
72 57 0.34
73 111 0.65
74 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (72 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGGA
AACAATT
Found at i:1407707 original size:36 final size:35
Alignment explanation
Indices: 1407609--1407791 Score: 118
Period size: 37 Copynumber: 5.1 Consensus size: 35
1407599 GCGGAAACAT
* *
1407609 TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 TTTGTTTTAAGAAAAACAATCTCAAGCGAGAAAAA
* ** *** *
1407644 TTAT-TATTTCGAGTGAAATTTTCTCAAGCAAGAAAAA
1 TT-TGT-TTT-AAGAAAAACAATCTCAAGCGAGAAAAA
* *
1407681 GTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 -TTTGTTTTAAGAAAAACAATCTCAAGCGAGAAAAA
** **
1407717 -TTGCTATTTCAAGTGAAACTTTCTCAAGCGAGAAACAA
1 TTTG-T-TTT-AAGAAAAACAATCTCAAGCGAGAAA-AA
* * *
1407755 TTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAA
1 TTTGTTTTAAGAAAAACAATCTCAAGCGAGAAAAA
1407790 TT
1 TT
1407792 GCTATTTGAA
Statistics
Matches: 107, Mismatches: 31, Indels: 20
0.68 0.20 0.13
Matches are distributed among these distances:
34 3 0.03
35 8 0.07
36 43 0.40
37 44 0.41
38 6 0.06
39 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (35 bp):
TTTGTTTTAAGAAAAACAATCTCAAGCGAGAAAAA
Found at i:1411883 original size:2 final size:2
Alignment explanation
Indices: 1411876--1411936 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1411866 ACAACAAAGG
1411876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1411918 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1411937 AAAGGATAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1413564 original size:18 final size:16
Alignment explanation
Indices: 1413533--1413569 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
1413523 ATGAAGAAAA
1413533 AAATAAAAAAAAATGC
1 AAATAAAAAAAAATGC
1413549 AAATAAATATAAAAATGC
1 AAATAAA-A-AAAAATGC
1413567 AAA
1 AAA
1413570 CACAAACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (16 bp):
AAATAAAAAAAAATGC
Found at i:1416002 original size:6 final size:6
Alignment explanation
Indices: 1415993--1416021 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1415983 ATAAAAATAA
1415993 AATTAT AATTAT AATTAT AATTAT AATTA
1 AATTAT AATTAT AATTAT AATTAT AATTA
1416022 AATGACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:1417079 original size:45 final size:45
Alignment explanation
Indices: 1417021--1417115 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
1417011 AACGGGGACA
* *
1417021 TGGAGGGATTGCTGGCAGTGCTGGAAGCTACTAGAATTTGCAACG
1 TGGAGGAACTGCTGGCAGTGCTGGAAGCTACTAGAATTTGCAACG
* * *
1417066 TGGAGGAACTGCTGGCAGTGCTGGAAGCTATTGGAATTTGTAACG
1 TGGAGGAACTGCTGGCAGTGCTGGAAGCTACTAGAATTTGCAACG
1417111 TGGAG
1 TGGAG
1417116 CTGCTGGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.14, G:0.37, T:0.25
Consensus pattern (45 bp):
TGGAGGAACTGCTGGCAGTGCTGGAAGCTACTAGAATTTGCAACG
Found at i:1422363 original size:23 final size:23
Alignment explanation
Indices: 1422337--1422403 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
1422327 CCACAGCTCT
1422337 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* *
1422360 TATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
* *
1422383 TAGAATTGCACCGTAGTGCCA
1 TATAATTGCACCGAAGTGCCA
1422404 TATAATAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:1423440 original size:2 final size:2
Alignment explanation
Indices: 1423435--1423474 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1423425 TCATATATTC
1423435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1423475 GTCAATGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1427506 original size:23 final size:23
Alignment explanation
Indices: 1427480--1427548 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
1427470 CACCACAGCT
1427480 CGTATAATTGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
*
1427503 CGTATAATTGCACCGAAGTGCCG
1 CGTATAATTGCACCGAAGTGCCA
* *
1427526 CGTAGAATTGCACCGCAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
1427549 TATAATAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:1428803 original size:18 final size:18
Alignment explanation
Indices: 1428761--1428803 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1428751 TTAGTCATGC
* *
1428761 ATACATATAATTAATGTA
1 ATACATATAATCAATATA
1428779 ATACATATAATCACATATA
1 ATACATATAATCA-ATATA
1428798 AT-CATA
1 ATACATA
1428804 ACAAACACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (18 bp):
ATACATATAATCAATATA
Found at i:1430240 original size:22 final size:22
Alignment explanation
Indices: 1430197--1430240 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1430187 ACCTTCTCCT
* *
1430197 TCTTGTTCTTCTTTCTTCATCA
1 TCTTCTTCTTCCTTCTTCATCA
1430219 TCTTCTTCTTCCTT-TTCGATCA
1 TCTTCTTCTTCCTTCTTC-ATCA
1430241 ACTCATGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.09, C:0.30, G:0.05, T:0.57
Consensus pattern (22 bp):
TCTTCTTCTTCCTTCTTCATCA
Found at i:1434695 original size:20 final size:20
Alignment explanation
Indices: 1434643--1434695 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1434633 GATTCAAGTG
* * *
1434643 GTATCGATAGCAAGAGGGGA
1 GTATCGATACCATGAGGAGA
*
1434663 GTATCGATACCATGAGGATA
1 GTATCGATACCATGAGGAGA
1434683 GTATCGATACCAT
1 GTATCGATACCAT
1434696 TGAGCACTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (20 bp):
GTATCGATACCATGAGGAGA
Found at i:1435200 original size:55 final size:57
Alignment explanation
Indices: 1435110--1435223 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 57
1435100 ATTACCAAAT
* *
1435110 GGCACTGAGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTGAGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTAAGAATTTCCATATG
1435167 GGCACT-ATGTGTGC-AAAA-CTAAGAAATTCATACTAAGTGTAAGAATTTCCATATG
1 GGCACTGA-GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTAAGAATTTCCATATG
1435222 GG
1 GG
1435224 AAATATATGT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 37 0.69
56 5 0.09
57 12 0.22
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (57 bp):
GGCACTGAGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTAAGAATTTCCATATG
Found at i:1435245 original size:55 final size:55
Alignment explanation
Indices: 1435125--1435253 Score: 170
Period size: 55 Copynumber: 2.3 Consensus size: 55
1435115 TGAGTGTGCA
* * * * * *
1435125 AAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGC
1 AAAA-CTAAGAAATTCATACTAAGTGTAAGAATTTCCATATGGGAAATATATGTAC
1435181 AAAACTAAGAAATTCATACTAAGTGTAAGAATTTCCATATGGGAAATATATGTAC
1 AAAACTAAGAAATTCATACTAAGTGTAAGAATTTCCATATGGGAAATATATGTAC
*
1435236 AAATA-TAAGAAGTTCATA
1 AAA-ACTAAGAAATTCATA
1435254 ATAATTAGGT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 60 0.92
56 5 0.08
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (55 bp):
AAAACTAAGAAATTCATACTAAGTGTAAGAATTTCCATATGGGAAATATATGTAC
Found at i:1435553 original size:68 final size:68
Alignment explanation
Indices: 1435437--1435632 Score: 322
Period size: 68 Copynumber: 2.9 Consensus size: 68
1435427 AAGATTAAAT
* *
1435437 GCCTAACTGTGCATTTGACAA-AAATTTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GCCTAACTGTGCATTTGA-AAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTT
1435501 TGAG
65 TGAG
*
1435505 GCCTAACTGTGCATTTGAAAGAAATGTGTCAATCATGCTAGTTGGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGAAAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTT
1435570 GAG
66 GAG
* * *
1435573 GCCTAACTGTGCATTTGACAGAAATGTGTCAACCATGCTAGTTAGATGAAAGACTAAGTG
1 GCCTAACTGTGCATTTGAAAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTG
1435633 TGATGTAGGG
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
67 2 0.02
68 118 0.98
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGAAAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:1440714 original size:14 final size:14
Alignment explanation
Indices: 1440695--1440741 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1440685 AGTGCTTCAA
1440695 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
1440709 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
1440723 CTTTT-TGTTTTCTT
1 CTTTTCT-TTTTCTT
1440737 CTTTT
1 CTTTT
1440742 GAGTGCTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.10
14 28 0.90
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:1442621 original size:18 final size:18
Alignment explanation
Indices: 1442598--1442633 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1442588 TTGACAGAAA
1442598 GGTGTCAATCATGCCAGT
1 GGTGTCAATCATGCCAGT
1442616 GGTGTCAATCATGCCAGT
1 GGTGTCAATCATGCCAGT
1442634 TAGATGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (18 bp):
GGTGTCAATCATGCCAGT
Found at i:1442675 original size:86 final size:86
Alignment explanation
Indices: 1442530--1442701 Score: 326
Period size: 86 Copynumber: 2.0 Consensus size: 86
1442520 TTGACAGAAA
*
1442530 GGTGTCAATAATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1 GGTGTCAATAATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1442595 AAAGGTGTCAATCATGCCAGT
66 AAAGGTGTCAATCATGCCAGT
*
1442616 GGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1 GGTGTCAATAATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1442681 AAAGGTGTCAATCATGCCAGT
66 AAAGGTGTCAATCATGCCAGT
1442702 TAGATGAAAG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (86 bp):
GGTGTCAATAATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
AAAGGTGTCAATCATGCCAGT
Found at i:1442725 original size:68 final size:68
Alignment explanation
Indices: 1442616--1442919 Score: 536
Period size: 68 Copynumber: 4.5 Consensus size: 68
1442606 TCATGCCAGT
1442616 GGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1 GGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1442681 AAA
66 AAA
*
1442684 GGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTATGCATTTGACAG
1 GGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1442749 AAA
66 AAA
* * * *
1442752 GGTGTCAATCATGCCAGCTAGATGAATGGCTAAGTGCCTTTGAGGCCTAGCTGTGCATTTGACAT
1 GGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1442817 AAA
66 AAA
* * *
1442820 GGTGTCAATTATGCCAGTTAGATGAATGGCTAAGTGCCTTTGAGGCCTAGCTGTGCATTTGACAG
1 GGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
1442885 AAA
66 AAA
1442888 GGTGTCAATCATGCCAGTTAGATGAAAGGCTA
1 GGTGTCAATCATGCCAGTTAGATGAAAGGCTA
1442920 TATATATATA
Statistics
Matches: 225, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 225 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (68 bp):
GGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAG
AAA
Found at i:1447260 original size:16 final size:17
Alignment explanation
Indices: 1447236--1447288 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 17
1447226 GATACCCCTA
1447236 TGAGTGTATCCATACAC
1 TGAGTGTATCCATACAC
**
1447253 TG-GTGTATAGATACACCC
1 TGAGTGTATCCATACA--C
1447271 TGCAGTGTATCCATACAC
1 TG-AGTGTATCCATACAC
1447289 CCCTGGCTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 11 0.39
17 2 0.07
18 4 0.14
20 11 0.39
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (17 bp):
TGAGTGTATCCATACAC
Found at i:1449218 original size:90 final size:89
Alignment explanation
Indices: 1449102--1449274 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
1449092 TAATCCTGAA
* *
1449102 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
*
1449167 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGGAAACTTGGATATAAGAGGAT
1449192 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
*
1449257 AGGGAAACTTGGCTATAA
66 AGGGAAACTTGGATATAA
1449275 AATGGTGTGA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGAAACTTGGATATAAGAGGAT
Found at i:1450672 original size:11 final size:10
Alignment explanation
Indices: 1450639--1450673 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1450629 TATGATGAAC
1450639 TTTTTAA-AA
1 TTTTTAATAA
1450648 TTTTTAATAA
1 TTTTTAATAA
*
1450658 TTTTTCATAA
1 TTTTTAATAA
1450668 TTTTTA
1 TTTTTA
1450674 GTTCATCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:1451253 original size:18 final size:19
Alignment explanation
Indices: 1451230--1451286 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 19
1451220 TATATTTTCC
1451230 AACAATTGGTATCTTTTT-
1 AACAATTGGTATCTTTTTA
1451248 AACAATTGGTATCCTTTTGTA
1 AACAATTGGTAT-CTTTT-TA
*
1451269 AACAATTGGTATATTTTT
1 AACAATTGGTATCTTTTT
1451287 CATTAGATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 12 0.34
19 6 0.17
20 5 0.14
21 12 0.34
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (19 bp):
AACAATTGGTATCTTTTTA
Found at i:1451752 original size:21 final size:21
Alignment explanation
Indices: 1451714--1451754 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1451704 TTTGAATTTA
* **
1451714 ATGAAGGTGTACTGATACCCT
1 ATGAAGGGGTACCAATACCCT
1451735 ATGAAGGGGTACCAATACCC
1 ATGAAGGGGTACCAATACCC
1451755 CCTGTTATAG
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:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (21 bp):
ATGAAGGGGTACCAATACCCT
Found at i:1452911 original size:17 final size:17
Alignment explanation
Indices: 1452891--1452929 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1452881 TAAACCAATT
1452891 GACCCGTTAACCGAACC
1 GACCCGTTAACCGAACC
* * *
1452908 GACCCGTTGATCGACCC
1 GACCCGTTAACCGAACC
1452925 GACCC
1 GACCC
1452930 ATTGACCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.44, G:0.21, T:0.13
Consensus pattern (17 bp):
GACCCGTTAACCGAACC
Found at i:1453630 original size:29 final size:29
Alignment explanation
Indices: 1453586--1453665 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
1453576 ATATCTGAAT
1453586 GGGATTTA-TCCCCGTCCTGATTCTGCAG
1 GGGATTTATTCCCCGTCCTGATTCTGCAG
* * *
1453614 GGGATTTATTCCTCGTCCTGATTCTTCAT
1 GGGATTTATTCCCCGTCCTGATTCTGCAG
* *
1453643 GGGATATATTCCCCGTTCTGATT
1 GGGATTTATTCCCCGTCCTGATT
1453666 ATGTATGAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
28 8 0.18
29 37 0.82
ACGTcount: A:0.15, C:0.25, G:0.21, T:0.39
Consensus pattern (29 bp):
GGGATTTATTCCCCGTCCTGATTCTGCAG
Found at i:1457157 original size:138 final size:137
Alignment explanation
Indices: 1456996--1457470 Score: 508
Period size: 138 Copynumber: 3.4 Consensus size: 137
1456986 AAGTGATTTA
* ** * * * * * * * **
1456996 AGGTTGATGGCTACAAATGGATTAGGAATCTTACTTAAATTCCTGCAACAATAAAGGTCAAGGAT
1 AGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAAC-AGAAAGGTCAAGTTT
* * * * *
1457061 TTCAAGAGATACCAATTGGTTGAGGGAATGTATTTCAACCAAATTTTCACACCCATTGCAGCAAA
65 TTCAAGAGATGCCAAATGGTTGAGGCAAGGTACTTCAACCAAATTTTCACACCCATTGCAGCAAA
*
1457126 GGCTTTGG
130 AGCTTTGG
* * ** *
1457134 AGTTTGATGACTCCTGATAGATTAGGGATC-TCCATTAGACTCTTGCGGTCAGAAAGGCCAAGTT
1 AGGTTGATGGCTCCTGATAGATTAGGGATCTTCC-TTAGACTCTTGC-AACAGAAAGGTCAAGTT
* * *
1457198 TTTCAAGAGATGCCAAGTGGTTGAGGCAAGGTAGTTCAATCAAATTTTCACACCCATTGCAG-AA
64 TTTCAAGAGATGCCAAATGGTTGAGGCAAGGTACTTCAACCAAATTTTCACACCCATTGCAGCAA
*
1457262 AATGCTTTGA
129 AA-GCTTTGG
* * *
1457272 AGGTTGATGGCTCTTGATAGACTAAGGATCTTCCTTAGACTCTTGCAACCAGAAAGGTCAAGTTT
1 AGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAA-CAGAAAGGTCAAGTTT
* *
1457337 TTCAAGAGATGCCAAATGGTTAAGGCAAGGCAGCTT-AACCAAATTTTCACACCCATTGCAGCAA
65 TTCAAGAGATGCCAAATGGTTGAGGCAAGGTA-CTTCAACCAAATTTTCACACCCATTGCAGCAA
1457401 AAGCTTT-G
129 AAGCTTTGG
* * ** * *
1457409 ATGGTTGATGGCTCCTGATAGATCAGGGATCTTCCATAGTTTATTGCAATTAGAAAGGTCAA
1 A-GGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAA-CAGAAAGGTCAA
1457471 TTGACCTTAA
Statistics
Matches: 280, Mismatches: 49, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
137 6 0.02
138 264 0.94
139 10 0.04
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (137 bp):
AGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAACAGAAAGGTCAAGTTTT
TCAAGAGATGCCAAATGGTTGAGGCAAGGTACTTCAACCAAATTTTCACACCCATTGCAGCAAAA
GCTTTGG
Found at i:1465313 original size:30 final size:30
Alignment explanation
Indices: 1465104--1465320 Score: 113
Period size: 30 Copynumber: 7.2 Consensus size: 30
1465094 CTGATACTCT
* * *
1465104 AATTGACAAGAAGAGG-AGGAAAAATCCTTC
1 AATTGACGAGAAG-GGAAGGAAGAATACTTC
* * * *
1465134 AATCGACAAGAAGGG-GGCGAAAAATACTTC
1 AATTGACGAGAAGGGAAG-GAAGAATACTTC
* * * *
1465164 ATTTGACGAGGAGGGGAGAAAGAATACTTC
1 AATTGACGAGAAGGGAAGGAAGAATACTTC
* * *
1465194 AATTGAAGATAAGATGG--CGAAGAATACTTC
1 AATTGACGAGAAG--GGAAGGAAGAATACTTC
* * * * *
1465224 AATCGGCGAGAAAAGGATGG-AGAATAATTC
1 AATTGACGAG-AAGGGAAGGAAGAATACTTC
* * * *
1465254 AGTCGACGAGAAGGGCAGAGAA-AACACTTC
1 AATTGACGAGAAGGGAAG-GAAGAATACTTC
*
1465284 AATTGACGAGAAGGGAAGGAGGAATACTTC
1 AATTGACGAGAAGGGAAGGAAGAATACTTC
1465314 AAATTGA
1 -AATTGA
1465321 AAGAAGAGGA
Statistics
Matches: 141, Mismatches: 35, Indels: 21
0.72 0.18 0.11
Matches are distributed among these distances:
29 12 0.09
30 116 0.82
31 11 0.08
32 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.17
Consensus pattern (30 bp):
AATTGACGAGAAGGGAAGGAAGAATACTTC
Found at i:1466081 original size:21 final size:21
Alignment explanation
Indices: 1466052--1466109 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1466042 GTTATGGTGT
*
1466052 TGACGTGGTAGTTCATGATGC
1 TGACATGGTAGTTCATGATGC
* *
1466073 TGACATGGTAG-TCTATGGTTC
1 TGACATGGTAGTTC-ATGATGC
*
1466094 TGACATGGCAGTTCAT
1 TGACATGGTAGTTCAT
1466110 CTGTCATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (21 bp):
TGACATGGTAGTTCATGATGC
Found at i:1466206 original size:21 final size:21
Alignment explanation
Indices: 1466164--1466212 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1466154 CGCTATGTTA
* *
1466164 TCAACCACCGTAAACTGTCATG
1 TCAA-CACCGTAAACCGCCATG
*
1466186 TCAACACCGTGAACCGCCATG
1 TCAACACCGTAAACCGCCATG
*
1466207 TTAACA
1 TCAACA
1466213 ACGTCAACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (21 bp):
TCAACACCGTAAACCGCCATG
Found at i:1471225 original size:35 final size:32
Alignment explanation
Indices: 1471172--1471277 Score: 86
Period size: 36 Copynumber: 3.0 Consensus size: 32
1471162 CTAGAGACAA
*
1471172 TTTTTCTTGAAACAAAATTGATCTCACTTGAGAT
1 TTTTTCTTAAAAC-AAATTG-TCTCACTTGAGAT
*
1471206 TGTTTTCTTTAAAACAAATTTTGTCTCACTTGAGACA
1 T-TTTTC-TTAAAACAAA--TTGTCTCACTTGAGA-T
* *
1471243 TTTTTCATAAAAACAAATTGTGTCTCACTTAAGAT
1 TTTTTC-TTAAAACAAA-T-TGTCTCACTTGAGAT
1471278 AGTCTTCCTC
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
34 1 0.02
35 10 0.17
36 45 0.75
37 4 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (32 bp):
TTTTTCTTAAAACAAATTGTCTCACTTGAGAT
Found at i:1471233 original size:36 final size:35
Alignment explanation
Indices: 1471193--1471277 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 35
1471183 ACAAAATTGA
* * *
1471193 TCTCACTTGAGATTGTTTTCTTTAAAACAAATTTTG
1 TCTCACTTGAGATT-TTTTCATAAAAACAAATTGTG
*
1471229 TCTCACTTGAGACATTTTTCATAAAAACAAATTGTG
1 TCTCACTTGAGA-TTTTTTCATAAAAACAAATTGTG
*
1471265 TCTCACTTAAGAT
1 TCTCACTTGAGAT
1471278 AGTCTTCCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 41 0.98
37 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (35 bp):
TCTCACTTGAGATTTTTTCATAAAAACAAATTGTG
Found at i:1471269 original size:72 final size:73
Alignment explanation
Indices: 1471126--1471277 Score: 177
Period size: 72 Copynumber: 2.1 Consensus size: 73
1471116 TCTGTCGCCT
* * **
1471126 TTGAGATTGTTTCTCTTGAAACAAAGTTTCGTCTCGCTAGAGACAATTTTTCTTGAAACAAAATT
1 TTGAGATTGTTTCTCTTAAAACAAAGTTTCGTCTCACTAGAGACAATTTTTCTAAAAACAAAATT
1471191 GATCTCAC
66 GATCTCAC
* *
1471199 TTGAGATTGTTT-TCTTTAAAACAAA-TTTTGTCTCACTTGAGAC-ATTTTTCATAAAAAC-AAA
1 TTGAGATTGTTTCTC-TTAAAACAAAGTTTCGTCTCACTAGAGACAATTTTTC-TAAAAACAAAA
*
1471260 TTGTGTCTCAC
64 TTG-ATCTCAC
*
1471271 TTAAGAT
1 TTGAGAT
1471278 AGTCTTCCTC
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
71 13 0.19
72 34 0.50
73 21 0.31
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (73 bp):
TTGAGATTGTTTCTCTTAAAACAAAGTTTCGTCTCACTAGAGACAATTTTTCTAAAAACAAAATT
GATCTCAC
Found at i:1471544 original size:104 final size:104
Alignment explanation
Indices: 1471358--1471551 Score: 255
Period size: 104 Copynumber: 1.9 Consensus size: 104
1471348 CTAGAAATAC
* * * * **
1471358 AAATTTTGAAATTGTTTCACTTGAAACAAAATTGATAACATTTGATATTGTTTTTCTTAAAAACA
1 AAATTTAGAAATTATTTCACTTGAAACAAAATTGATAACATTTGAGATTGTTTCTCCCAAAAACA
* *
1471423 AATCTTGTCTCATTTGAGACAGTTTTCCATCAAAACACA
66 AATCTTATCTCACTTGAGACAGTTTTCCATCAAAACACA
* *
1471462 AAATTTAGAAATTATTTCACTTGAAACAAAATTGATAAACCTTTGAGATTGTTTCTCCCGAAAA-
1 AAATTTAGAAATTATTTCACTTGAAACAAAATTGAT-AACATTTGAGATTGTTTCTCCCAAAAAC
* * *
1471526 AATTTTTATCTCGCTTGAGACAGTTT
65 AAATCTTATCTCACTTGAGACAGTTT
1471552 CTTTTGAAAC
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 55 0.72
105 21 0.28
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (104 bp):
AAATTTAGAAATTATTTCACTTGAAACAAAATTGATAACATTTGAGATTGTTTCTCCCAAAAACA
AATCTTATCTCACTTGAGACAGTTTTCCATCAAAACACA
Found at i:1471649 original size:30 final size:30
Alignment explanation
Indices: 1471548--1471657 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 30
1471538 GCTTGAGACA
*
1471548 GTTTCTTTTGAAACATAAACCTTTGAGATT
1 GTTTCTCTTGAAACATAAACCTTTGAGATT
* * *
1471578 GTTTCTCTTGAAACA-AATTTTGTCTCGCTTGAGA-C
1 GTTTCTCTTGAAACATAA-----AC-C-TTTGAGATT
*
1471613 ATTTCTCTTGAAACATAAACCTTTGAGATT
1 GTTTCTCTTGAAACATAAACCTTTGAGATT
1471643 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
1471658 AATTTTGTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
29 8 0.13
30 29 0.47
31 1 0.02
34 1 0.02
35 15 0.24
36 8 0.13
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (30 bp):
GTTTCTCTTGAAACATAAACCTTTGAGATT
Found at i:1471650 original size:65 final size:66
Alignment explanation
Indices: 1471496--1471676 Score: 294
Period size: 65 Copynumber: 2.8 Consensus size: 66
1471486 AACAAAATTG
** * *
1471496 ATAAACCTTTGAGATTGTTTCTCCCGAAA-AAATTTTTATCTCGCTTGAGACAGTTTCTTTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAA-TTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
1471560 AC
65 AC
1471562 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACA-TTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1471626 C
66 C
*
1471627 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTATCGCTTGAGA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGA
1471677 GTAGCCTAAG
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
65 61 0.56
66 45 0.41
67 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (66 bp):
ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
C
Found at i:1474623 original size:139 final size:139
Alignment explanation
Indices: 1474403--1474836 Score: 564
Period size: 139 Copynumber: 3.1 Consensus size: 139
1474393 GTAGGAATTG
* ** * *
1474403 TGTTATCTCTAAATTATCCCTAAAGATGGCTAGATGTCCTCATCATATAAGAACAATGTCGTCCA
1 TGTTATCTCCAAATTATCCCTAAAGATGGCTAGATGTCCTCATCACGTAGGAACAATGTCATCCA
** * * * *
1474468 CCAACCAAATCTCCTCAACGCATAGGAGCAGCGTCATCCTCAAACAATCAGACTTCCTCATCACG
66 CTGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACG
*
1474533 TAGGAACCA
131 TAAGAACCA
* *
1474542 TGTTGTCTCCAAATTATCCCTAAAGATGGCTAGATGTCCTCATCACGTAGGAACAATATCATCCA
1 TGTTATCTCCAAATTATCCCTAAAGATGGCTAGATGTCCTCATCACGTAGGAACAATGTCATCCA
* * * * * * * *
1474607 CTGACCAGACCACCTCAACGCGTAGGACCAGTGTCATCCTCTGATAACCAGACTTCATCACCACG
66 CTGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACG
*
1474672 TAAGAA-CG
131 TAAGAACCA
* *
1474680 TGTTATCTCCAATTTATCCCTAAAGATGGCTAGAAGTCCTCATCACGTAGGAACAATGTCATCCA
1 TGTTATCTCCAAATTATCCCTAAAGATGGCTAGATGTCCTCATCACGTAGGAACAATGTCATCCA
* * * * * *
1474745 CTGACCAGATGTCCTCAACGTGTAGAAGCAGTGTCATCCTCAGACAATCAAACTTCCTCATAATG
66 CTGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACG
*
1474810 TAAGAACCC
131 TAAGAACCA
*
1474819 TGTTATCACCAAATTATC
1 TGTTATCTCCAAATTATC
1474837 TCCATATTGA
Statistics
Matches: 250, Mismatches: 44, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
138 119 0.48
139 131 0.52
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (139 bp):
TGTTATCTCCAAATTATCCCTAAAGATGGCTAGATGTCCTCATCACGTAGGAACAATGTCATCCA
CTGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAATCAGACTTCCTCATCACG
TAAGAACCA
Found at i:1474898 original size:15 final size:15
Alignment explanation
Indices: 1474878--1474928 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1474868 GAACAATTTC
1474878 ATTTTTAAATCCTCT
1 ATTTTTAAATCCTCT
* * *
1474893 ATTTTT-CATACTGT
1 ATTTTTAAATCCTCT
*
1474907 CATTTTTAAATCCTTT
1 -ATTTTTAAATCCTCT
1474923 ATTTTT
1 ATTTTT
1474929 CAGACAAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 5 0.18
ACGTcount: A:0.24, C:0.16, G:0.02, T:0.59
Consensus pattern (15 bp):
ATTTTTAAATCCTCT
Found at i:1475170 original size:55 final size:56
Alignment explanation
Indices: 1475067--1475173 Score: 137
Period size: 55 Copynumber: 1.9 Consensus size: 56
1475057 ATTGTGTCCT
* * *
1475067 AAAATTAAAGAGGGAACAAAATGTAAATACCAAACTTGTAATTGTACCATTTTCTG
1 AAAATTAAAGAGGGAACAAAATGTAAACACCAAACATGTAATTATACCATTTTCTG
* * *
1475123 AAAATTAAAGAGGGAA-AAAATGTAAGCACCAAGCAATG-ATTTATACCATTT
1 AAAATTAAAGAGGGAACAAAATGTAAACACCAAAC-ATGTAATTATACCATTT
1475174 GTAATTTATG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 26 0.59
56 18 0.41
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (56 bp):
AAAATTAAAGAGGGAACAAAATGTAAACACCAAACATGTAATTATACCATTTTCTG
Found at i:1476120 original size:4 final size:4
Alignment explanation
Indices: 1476111--1476135 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1476101 ACTTTAACCA
1476111 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
1476136 CTAATATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1476226 original size:131 final size:135
Alignment explanation
Indices: 1476075--1476363 Score: 435
Period size: 135 Copynumber: 2.2 Consensus size: 135
1476065 TTATTTCAAA
**
1476075 CTAACTACTAACTTTTATTTTATTGCACTTTAACCATTATTTATTTATTTATTT-A-T-TTA-TT
1 CTAACTACTAACTTTTATTTTATTGCACTCAAACCATTATTTATTTATTTATTTAATTATTATTT
* * *
1476136 CTAATATTTGATTCGACCTTATGGTGACCCGATATGGGGTATGATCGGCATTATTATGGTTCGGA
66 CTAATATTCGATTCGACCTTATGGTGACCCGATACGGGGTATGATCCGCATTATTATGGTTCGGA
1476201 CTCTG
131 CTCTG
* * *
1476206 CTAATTACTAACTTTTATTTTATTGCTCTCAAACCATTGTTTATTTATTTATTTAATTATTATTT
1 CTAACTACTAACTTTTATTTTATTGCACTCAAACCATTATTTATTTATTTATTTAATTATTATTT
* * * *
1476271 CTAATATTCGATTCGACCTTGTGGTGACCTGATCCGGGTTATGATCCGCATTATTATGGTTCGGA
66 CTAATATTCGATTCGACCTTATGGTGACCCGATACGGGGTATGATCCGCATTATTATGGTTCGGA
1476336 CTCTG
131 CTCTG
1476341 CTAACTACTAACTTTT-TTTTATT
1 CTAACTACTAACTTTTATTTTATT
1476364 TATTTTATTT
Statistics
Matches: 141, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
131 49 0.35
132 1 0.01
133 1 0.01
134 10 0.07
135 80 0.57
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (135 bp):
CTAACTACTAACTTTTATTTTATTGCACTCAAACCATTATTTATTTATTTATTTAATTATTATTT
CTAATATTCGATTCGACCTTATGGTGACCCGATACGGGGTATGATCCGCATTATTATGGTTCGGA
CTCTG
Found at i:1478158 original size:28 final size:28
Alignment explanation
Indices: 1478126--1478180 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1478116 TTATAACAAT
*
1478126 AATTAATTATTAAAATAT-AAAATAATAA
1 AATTAATTATCAAAAT-TCAAAATAATAA
* *
1478154 AATTATTTATCATAATTCAAAATAATA
1 AATTAATTATCAAAATTCAAAATAATA
1478181 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (28 bp):
AATTAATTATCAAAATTCAAAATAATAA
Found at i:1479340 original size:15 final size:15
Alignment explanation
Indices: 1479309--1479355 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
1479299 GAGCTTTGTA
1479309 AATA-ATAATATTAAT
1 AATATATAATA-TAAT
1479324 AATATTATTATATATAAT
1 AATA-TA-TA-ATATAAT
1479342 AATATATAATATAA
1 AATATATAATATAA
1479356 ATGTCACTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.36
16 2 0.07
17 3 0.11
18 10 0.36
19 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATAATATAAT
Found at i:1479582 original size:45 final size:45
Alignment explanation
Indices: 1479528--1479681 Score: 141
Period size: 45 Copynumber: 3.3 Consensus size: 45
1479518 GTTGATTTGA
*
1479528 TTCCACTACTCTTTCGTGAGACTTCATACTTTACTGAAAAATCTG
1 TTCCACTACTCTTCCGTGAGACTTCATACTTTACTGAAAAATCTG
* *****
1479573 TTCCACTACTCTTCCGTGAAGA--TCATATTTTGATCTTGCTCCTGCTTCTG
1 TTCCACTACTCTTCCGTG-AGACTTCATACTTT-A-C-TG---AAAAATCTG
* * *
1479623 TTTCACTACTCTTCCGTGAGACTTCATACTTTGCTAAAAAATCTG
1 TTCCACTACTCTTCCGTGAGACTTCATACTTTACTGAAAAATCTG
1479668 TTCCACTACTCTTC
1 TTCCACTACTCTTC
1479682 TATGGAGAGT
Statistics
Matches: 83, Mismatches: 17, Indels: 18
0.70 0.14 0.15
Matches are distributed among these distances:
44 8 0.10
45 35 0.42
46 4 0.05
47 2 0.02
48 1 0.01
49 4 0.05
50 21 0.25
51 8 0.10
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (45 bp):
TTCCACTACTCTTCCGTGAGACTTCATACTTTACTGAAAAATCTG
Found at i:1479646 original size:95 final size:95
Alignment explanation
Indices: 1479531--1479827 Score: 418
Period size: 95 Copynumber: 3.1 Consensus size: 95
1479521 GATTTGATTC
* * *
1479531 CACTACTCTTTCGTGAGACTTCATACTTTACTGAAAAATCTGTTCCACTACTCTTCCGTGAAGAT
1 CACTACTCTTCCGTGAGACTTCATACTTTGCTGAAAAATCTGTTCCACTACTCTTCCGTGGAGAT
*
1479596 CATATTTTGATCTTGCTCCTGCTTCTGTTT
66 CAAATTTTGATCTTGCTCCTGCTTCTGTTT
* **
1479626 CACTACTCTTCCGTGAGACTTCATACTTTGCTAAAAAATCTGTTCCACTACTCTTCTATGGAGAG
1 CACTACTCTTCCGTGAGACTTCATACTTTGCTGAAAAATCTGTTCCACTACTCTTCCGTGGAGA-
1479691 T-AAATTTTGATCTTGCTCCTGCTTCTGTTT
65 TCAAATTTTGATCTTGCTCCTGCTTCTGTTT
* ** * * **
1479721 CAGTACTCTTCTTTGAGACTTCATACTTTGTTGAAACATCCATTCCACTACTCTTCCGTGGAGAT
1 CACTACTCTTCCGTGAGACTTCATACTTTGCTGAAAAATCTGTTCCACTACTCTTCCGTGGAGAT
* *
1479786 CAAATTTTGATATTGCTCCTACTTCT-TCTT
66 CAAATTTTGATCTTGCTCCTGCTTCTGT-TT
1479816 CACTACTCTTCC
1 CACTACTCTTCC
1479828 TCTGAGGATA
Statistics
Matches: 178, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
94 2 0.01
95 175 0.98
96 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (95 bp):
CACTACTCTTCCGTGAGACTTCATACTTTGCTGAAAAATCTGTTCCACTACTCTTCCGTGGAGAT
CAAATTTTGATCTTGCTCCTGCTTCTGTTT
Found at i:1480110 original size:95 final size:95
Alignment explanation
Indices: 1479903--1480110 Score: 308
Period size: 95 Copynumber: 2.2 Consensus size: 95
1479893 TGGAATACTT
* * * * *
1479903 CACTACTCTTTCGTGAAGGTTGAAAATAATTGACTTGAGAATAATCTAATTTCACTACTCTTCCG
1 CACTACTCTTTCGTGGAGGCTGAAAATAATAGACTTGAGAAGAATCTAATTTCACTACTCTTCCA
* *
1479968 TGAAGATTAGATTCGAAGTTGATTTGATTC
66 TGAAGATCAGATTCGAAGTTAATTTGATTC
* * *
1479998 CACAACTCTTCCGTGGAGGCTGAAAATGATAGACTTGAGAAGAATCTAATTTCACTACTCTTCCA
1 CACTACTCTTTCGTGGAGGCTGAAAATAATAGACTTGAGAAGAATCTAATTTCACTACTCTTCCA
*
1480063 TGAAGATCATATTCGAAGTTAATTTGATTC
66 TGAAGATCAGATTCGAAGTTAATTTGATTC
*
1480093 CACTACTCTTTCATGGAG
1 CACTACTCTTTCGTGGAG
1480111 ATCTTACGAA
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 99 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (95 bp):
CACTACTCTTTCGTGGAGGCTGAAAATAATAGACTTGAGAAGAATCTAATTTCACTACTCTTCCA
TGAAGATCAGATTCGAAGTTAATTTGATTC
Found at i:1480197 original size:20 final size:20
Alignment explanation
Indices: 1480174--1480841 Score: 847
Period size: 20 Copynumber: 33.5 Consensus size: 20
1480164 ACCCAAAGGA
* * *
1480174 TTTACAAATTACCCAGAGGT
1 TTTACAAATGACCCGGAGGC
**
1480194 TTTACAAATGACCATGAGGC
1 TTTACAAATGACCCGGAGGC
1480214 TTTACAAATGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* *
1480234 TTTTCAAATGACCCGGAGTC
1 TTTACAAATGACCCGGAGGC
*
1480254 TTTACAAATGA-CTGGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480273 TTTACAAATGACTCGGAGGC
1 TTTACAAATGACCCGGAGGC
**
1480293 TTTACAAATGACTTGGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480313 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480333 TTTACAATTGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* * *
1480353 GTTAAAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480373 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480393 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480413 TTTACAATTGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* * *
1480433 GTTAAAAATGACCTGGAGGC
1 TTTACAAATGACCCGGAGGC
* *
1480453 TTTACAATTGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
* * *
1480473 TTTATAAATGACCCGAAAGC
1 TTTACAAATGACCCGGAGGC
* **
1480493 TTTACAAATGAACCAAAGGC
1 TTTACAAATGACCCGGAGGC
*
1480513 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480533 TTTACAAGTGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* *
1480553 TTTATAATTGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
1480573 TTTACAAATGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480593 TTTACAAATGACCTGGAGGC
1 TTTACAAATGACCCGGAGGC
* *
1480613 TTTATAAATGACCCGAAGGC
1 TTTACAAATGACCCGGAGGC
*
1480633 TTTACAAATGACCC-AAGGGC
1 TTTACAAATGACCCGGA-GGC
*
1480653 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
* *
1480673 TATACAAACGACCC-GAGCGC
1 TTTACAAATGACCCGGAG-GC
1480693 TTTACAAATGACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
* **
1480713 TTTACAAAGGACCTAGAGGC
1 TTTACAAATGACCCGGAGGC
* *
1480733 TTTACAATTGACTCGGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480753 TTTACAAATGACCCGAAGGC
1 TTTACAAATGACCCGGAGGC
*
1480773 TTTACAAATAACCCGGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480793 TTTACAAATGGCCCGGAGGC
1 TTTACAAATGACCCGGAGGC
*
1480813 TTTACAAATGACCCAGAGGC
1 TTTACAAATGACCCGGAGGC
1480833 TTTACAAAT
1 TTTACAAAT
1480842 TTATGGGAAA
Statistics
Matches: 563, Mismatches: 80, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
19 22 0.04
20 537 0.95
21 4 0.01
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (20 bp):
TTTACAAATGACCCGGAGGC
Found at i:1488039 original size:18 final size:17
Alignment explanation
Indices: 1487995--1488056 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 17
1487985 ATAAAGACAA
**
1487995 AAAATATAATTAATCCT
1 AAAATATAATTAATATT
*
1488012 ATAATAATAATTAATGATT
1 AAAAT-ATAATTAAT-ATT
1488031 AAAATATAA--AATATT
1 AAAATATAATTAATATT
1488046 AAAAT-TAATTA
1 AAAATATAATTA
1488057 TCACAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 3 0.08
15 8 0.22
16 4 0.11
17 4 0.11
18 13 0.35
19 5 0.14
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAATATAATTAATATT
Found at i:1489292 original size:15 final size:15
Alignment explanation
Indices: 1489261--1489307 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
1489251 GTGCTTTGTA
1489261 AATA-ATAATATTAAT
1 AATATATAATA-TAAT
1489276 AATATTATTATATATAAT
1 AATA-TA-TA-ATATAAT
1489294 AATATATAATATAA
1 AATATATAATATAA
1489308 ACGTCACTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.36
16 2 0.07
17 3 0.11
18 10 0.36
19 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATATAATATAAT
Found at i:1498433 original size:60 final size:60
Alignment explanation
Indices: 1498294--1498433 Score: 142
Period size: 60 Copynumber: 2.3 Consensus size: 60
1498284 AGCATGTGCA
* * * * * *
1498294 AAAAGTTT-GAGGACTAATTTATAATGAATATCATAGTTTGGGGATGAAATTTAAATATTC
1 AAAAGTTTAG-GGACTAATTTAGAATGAATACCATAGTTTAGGAATAAAATTGAAATATTC
* * *
1498354 AAATGTTAAAGGACTAATTTAGAATG-ATAACCATAGTTTAGGAATAAAATTGAAATACTT-
1 AAAAGTTTAGGGACTAATTTAGAATGAAT-ACCATAGTTTAGGAATAAAATTGAAATA-TTC
*
1498414 AAAAGTTTAGGGACCAATTT
1 AAAAGTTTAGGGACTAATTT
1498434 GATATAAGGA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
59 2 0.03
60 60 0.94
61 2 0.03
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (60 bp):
AAAAGTTTAGGGACTAATTTAGAATGAATACCATAGTTTAGGAATAAAATTGAAATATTC
Found at i:1498754 original size:21 final size:21
Alignment explanation
Indices: 1498728--1498795 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
1498718 TTTATCCATT
** *
1498728 TTTTATTTTTTATTCTTATTA
1 TTTTATTACTTATTATTATTA
1498749 TTTTATTACTTATTATTATTA
1 TTTTATTACTTATTATTATTA
1498770 TTATTATTA-TTAATTAAATTATTA
1 TT-TTATTACTT-ATT--ATTATTA
1498794 TT
1 TT
1498796 ACAGGCCCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 22 0.55
22 9 0.22
24 9 0.22
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATTACTTATTATTATTA
Found at i:1498760 original size:15 final size:15
Alignment explanation
Indices: 1498730--1498780 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
1498720 TATCCATTTT
1498730 TTATT-TTTTATT-C
1 TTATTATTTTATTAC
1498743 TTATTATTTTATTAC
1 TTATTATTTTATTAC
1498758 TTATTATTATTATTA-
1 TTATTATT-TTATTAC
1498773 TTATTATT
1 TTATTATT
1498781 AATTAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.14
14 7 0.20
15 17 0.49
16 6 0.17
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTATTTTATTAC
Found at i:1498764 original size:3 final size:3
Alignment explanation
Indices: 1498737--1498796 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
1498727 TTTTTATTTT
*
1498737 TTA TTC TTA TTA TT- TTA TTA CTTA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A
*
1498783 TTA -AA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1498797 CAGGCCCACA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.06
3 40 0.82
4 6 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1500078 original size:17 final size:18
Alignment explanation
Indices: 1500047--1500080 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1500037 TTTTCAATAC
1500047 TTTTACATTAGTATTTTA
1 TTTTACATTAGTATTTTA
*
1500065 TTTT-CATTATTATTTT
1 TTTTACATTAGTATTTT
1500081 TTTATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTACATTAGTATTTTA
Found at i:1500761 original size:16 final size:17
Alignment explanation
Indices: 1500740--1500772 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1500730 TGGCGACTCC
*
1500740 CAAAAT-ATTTTTTTAT
1 CAAAATCATTTATTTAT
1500756 CAAAATCATTTATTTAT
1 CAAAATCATTTATTTAT
1500773 TCATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
CAAAATCATTTATTTAT
Found at i:1504022 original size:42 final size:42
Alignment explanation
Indices: 1503965--1504049 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
1503955 ACTCTTTCAC
1503965 ATATAACACAGTTTCTATTTGTATGGAAGA-TGTATTACCTAT
1 ATATAACACAGTTTCTATTTGTATGGAAGAGT-TATTACCTAT
*
1504007 ATATAACACATTTTCTATTTGTATGGAAGAGTTATTACCTAT
1 ATATAACACAGTTTCTATTTGTATGGAAGAGTTATTACCTAT
1504049 A
1 A
1504050 GTACCTATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (42 bp):
ATATAACACAGTTTCTATTTGTATGGAAGAGTTATTACCTAT
Found at i:1506933 original size:18 final size:18
Alignment explanation
Indices: 1506907--1506944 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1506897 GTAATATTCG
1506907 AATAATTAAATAGAATAT
1 AATAATTAAATAGAATAT
* *
1506925 AATATTTAAATCGAATAT
1 AATAATTAAATAGAATAT
1506943 AA
1 AA
1506945 AATCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAATTAAATAGAATAT
Found at i:1507332 original size:28 final size:28
Alignment explanation
Indices: 1507301--1507355 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1507291 ATATCATATA
* *
1507301 CCAGTGATCAAAAACCATATATCAGAAT
1 CCAGAGATCAAAAACCATAAATCAGAAT
1507329 CCAGAGATCAAAAACCATAAATCAGAA
1 CCAGAGATCAAAAACCATAAATCAGAA
1507356 ACTATGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.51, C:0.22, G:0.11, T:0.16
Consensus pattern (28 bp):
CCAGAGATCAAAAACCATAAATCAGAAT
Found at i:1510571 original size:22 final size:19
Alignment explanation
Indices: 1510543--1510584 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
1510533 ATATATTTTT
1510543 TAAAATATTCTAAAGTGATAAA
1 TAAAATATT-TAAA-T-ATAAA
1510565 TAAAATATTTAAATATAAA
1 TAAAATATTTAAATATAAA
1510584 T
1 T
1510585 TAATATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 1 0.05
21 4 0.20
22 9 0.45
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
TAAAATATTTAAATATAAA
Found at i:1511986 original size:2 final size:2
Alignment explanation
Indices: 1511981--1512005 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1511971 TATATATATA
1511981 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1512006 TTAAGATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1513599 original size:28 final size:28
Alignment explanation
Indices: 1513545--1513606 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1513535 GTTATTATGG
* *
1513545 TTTAATATTTATTATCATGAGCTTATTT
1 TTTAATATTTATTATCAGGAGCCTATTT
*
1513573 TTTAATATTTATTATTAGG-GACCTATTT
1 TTTAATATTTATTATCAGGAG-CCTATTT
*
1513601 TATAAT
1 TTTAAT
1513607 TTATTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (28 bp):
TTTAATATTTATTATCAGGAGCCTATTT
Found at i:1516444 original size:49 final size:49
Alignment explanation
Indices: 1516387--1516508 Score: 181
Period size: 49 Copynumber: 2.5 Consensus size: 49
1516377 TTATTTACTT
* *
1516387 GGTTTCTGCTTCGATGTTCTATTGGTAAATTTAAATGTTTCGTTTAATC
1 GGTTTCTGCTTCGCTGTTCTATTGGTAAATTTAAATGTTTCATTTAATC
** *
1516436 GGTTTCTGCTTCGCTGTTCTATAAGTAAATTTAAATGTTTCATTTACTC
1 GGTTTCTGCTTCGCTGTTCTATTGGTAAATTTAAATGTTTCATTTAATC
* *
1516485 TGTTTCTGCTTTGCTGTTCTATTG
1 GGTTTCTGCTTCGCTGTTCTATTG
1516509 ATAATGTTCT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (49 bp):
GGTTTCTGCTTCGCTGTTCTATTGGTAAATTTAAATGTTTCATTTAATC
Found at i:1520482 original size:16 final size:17
Alignment explanation
Indices: 1520447--1520483 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1520437 ATGAGACGAA
1520447 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
1520464 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
1520480 AAAA
1 AAAA
1520484 TAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:1521563 original size:20 final size:21
Alignment explanation
Indices: 1521517--1521604 Score: 124
Period size: 21 Copynumber: 4.2 Consensus size: 21
1521507 GCCGTAAAAG
*
1521517 GCGACGAAATGGATACTTTTG
1 GCGACGAAATGGATACTTTTA
* *
1521538 GCGACGAAACGAATAC-TTTA
1 GCGACGAAATGGATACTTTTA
*
1521558 GCGACGAAATGGACACTTTTA
1 GCGACGAAATGGATACTTTTA
*
1521579 GCGACGAAATGGGTACTTTTA
1 GCGACGAAATGGATACTTTTA
1521600 GCGAC
1 GCGAC
1521605 TGAACTCGTC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.28
21 42 0.72
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (21 bp):
GCGACGAAATGGATACTTTTA
Found at i:1521596 original size:41 final size:42
Alignment explanation
Indices: 1521517--1521604 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
1521507 GCCGTAAAAG
* *
1521517 GCGACGAAATGGATACTTTTGGCGACGAAACGAATAC-TTTA
1 GCGACGAAATGGACACTTTTAGCGACGAAACGAATACTTTTA
* **
1521558 GCGACGAAATGGACACTTTTAGCGACGAAATGGGTACTTTTA
1 GCGACGAAATGGACACTTTTAGCGACGAAACGAATACTTTTA
1521600 GCGAC
1 GCGAC
1521605 TGAACTCGTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 32 0.78
42 9 0.22
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (42 bp):
GCGACGAAATGGACACTTTTAGCGACGAAACGAATACTTTTA
Found at i:1526151 original size:30 final size:29
Alignment explanation
Indices: 1526102--1526227 Score: 123
Period size: 29 Copynumber: 4.4 Consensus size: 29
1526092 TAAACATATT
* **
1526102 AAATACATTTTATT-TTATTTTATTTTAA
1 AAATATATTTTATTCTTATTTTAACTTAA
*
1526130 AATATATATTTTAGTCTTA-TTTAACTTAA
1 AA-ATATATTTTATTCTTATTTTAACTTAA
* * * *
1526159 AAAAATATTTTATTTTTATCTTAACTTATG
1 AAATATATTTTATTCTTATTTTAACTTA-A
*
1526189 AAATATATTTTATTCTTATTTTAA-TTTA
1 AAATATATTTTATTCTTATTTTAACTTAA
*
1526217 AGATATATTTT
1 AAATATATTTT
1526228 TAAAATTTAA
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
28 25 0.32
29 30 0.38
30 24 0.30
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAACTTAA
Found at i:1526162 original size:73 final size:73
Alignment explanation
Indices: 1526016--1526161 Score: 172
Period size: 73 Copynumber: 2.0 Consensus size: 73
1526006 TTTTATTTTT
* * * * *
1526016 ATATTAACTTATTAAGTAATTTTATTTTTGTTTTAATTTGAAAAATATATTATAATCTTGTTTTA
1 ATATAAACATATTAAATAATTTTATTTTTATTTTAATTTGAAAAATATATTATAATCTTGATTTA
*
1526081 AGTTAAAA
66 ACTTAAAA
* * *
1526089 ATATAAACATATTAAATACATTTTA-TTTTATTTT-ATTTTAAAATATATATTTTAGTCTT-ATT
1 ATATAAACATATTAAATA-ATTTTATTTTTATTTTAATTTGAAAA-ATATATTATAATCTTGATT
1526151 TAACTTAAAA
64 TAACTTAAAA
1526161 A
1 A
1526162 AATATTTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
72 20 0.32
73 36 0.58
74 6 0.10
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (73 bp):
ATATAAACATATTAAATAATTTTATTTTTATTTTAATTTGAAAAATATATTATAATCTTGATTTA
ACTTAAAA
Found at i:1526284 original size:30 final size:31
Alignment explanation
Indices: 1526214--1526302 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 31
1526204 TTATTTTAAT
* *
1526214 TTAAGATATATTTTTAAAATTTAATATAAGA
1 TTAAGATATATTTTTAAAAGTTAAAATAAGA
* *
1526245 ATAAGATATATTTTT-GAAGTTAAAATAAGA
1 TTAAGATATATTTTTAAAAGTTAAAATAAGA
* * *
1526275 TTAAAATATATTTTTCAAA-TAAAAATAA
1 TTAAGATATATTTTTAAAAGTTAAAATAA
1526303 AATATATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 33 0.67
31 16 0.33
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (31 bp):
TTAAGATATATTTTTAAAAGTTAAAATAAGA
Found at i:1526308 original size:54 final size:54
Alignment explanation
Indices: 1526239--1526343 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
1526229 AAAATTTAAT
* * * * *
1526239 ATAAGAATAAGATATATTT-TTGAAGTTAAAATAAGATTAAAATATATTTTTCAA
1 ATAAAAATAAAATATATTTAAT-AAGTTAAAATAAAAATAAAATATATTTTTCAA
*
1526293 ATAAAAATAAAATATATTTAATAAGTTAAGATAAAAATAAAATATATTTTT
1 ATAAAAATAAAATATATTTAATAAGTTAAAATAAAAATAAAATATATTTTT
1526344 TAATTTTAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
54 43 0.98
55 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (54 bp):
ATAAAAATAAAATATATTTAATAAGTTAAAATAAAAATAAAATATATTTTTCAA
Found at i:1530155 original size:22 final size:21
Alignment explanation
Indices: 1530121--1530161 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1530111 ATAATTATTT
1530121 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
1530142 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
1530162 TTTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:1543159 original size:46 final size:46
Alignment explanation
Indices: 1543104--1543197 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1543094 ATGATCACGC
1543104 AATATTTTATCAATCAAATAAATTGTGATATGTTATATTTAAGGGT
1 AATATTTTATCAATCAAATAAATTGTGATATGTTATATTTAAGGGT
1543150 AATATTTTATCAATCAAATAAATTGTGATATGTTATATTTAAGGGT
1 AATATTTTATCAATCAAATAAATTGTGATATGTTATATTTAAGGGT
1543196 AA
1 AA
1543198 ACAATACAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (46 bp):
AATATTTTATCAATCAAATAAATTGTGATATGTTATATTTAAGGGT
Found at i:1543746 original size:206 final size:205
Alignment explanation
Indices: 1543364--1543748 Score: 531
Period size: 206 Copynumber: 1.9 Consensus size: 205
1543354 CGTTATTCTG
* * * *
1543364 CGTTGGATGAACTTATTAAAAACATCATAATGCCACGTAAAAAAACTTGCTTATGGTTTTTTATA
1 CGTTGGATGAACTTATTAAAAACATCATAATGCCACATAAAAAAACTTGCATAAGGTTTTCTATA
* * * * ** *
1543429 TAAAGGAATATAAACCCACTGTTGGGAAATGATATTTATTTTTAAACCCTAAAAAAGCTGTTGCA
66 TAAAGGAATATAAACCAACTGTTAGGAAAGGATATTTATTTTTAAACCCTAAAAAAGATACTACA
*
1543494 AAAAAGAAGAATACAAACAATCAAGTGAAGGAAGAAGAAGAGAAGACTAAAATAAAAAAATAGAT
131 AAAAAGAAGAATACAAACAATCAAGTGAAGGAAGAAGAAAAGAAGACTAAAATAAAAAAATAGAT
1543559 GCAGAAAACT
196 GCAGAAAACT
* *
1543569 CGTTGGATGAACTTATTGAACACATCATAATGCCACAT-AAAAAACTTGCATAAGGTTTTCTATA
1 CGTTGGATGAACTTATTAAAAACATCATAATGCCACATAAAAAAACTTGCATAAGGTTTTCTATA
* * *
1543633 TAAAGGAATATAAACCAACTTTTAGGAAAGGATCTTCT-TCTTTCTAAACCCTAAAGAAGATACT
66 TAAAGGAATATAAACCAACTGTTAGGAAAGGATATT-TAT-TTT-TAAACCCTAAAAAAGATACT
* * * * *
1543697 ATAAAAAAGAATAATACAAACAGTCACGTGAAGTAAGAAGAAAAGAAGACTA
128 ACAAAAAAGAAGAATACAAACAATCAAGTGAAGGAAGAAGAAAAGAAGACTA
1543749 CAATCAAAGA
Statistics
Matches: 155, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
204 55 0.35
205 39 0.25
206 61 0.39
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (205 bp):
CGTTGGATGAACTTATTAAAAACATCATAATGCCACATAAAAAAACTTGCATAAGGTTTTCTATA
TAAAGGAATATAAACCAACTGTTAGGAAAGGATATTTATTTTTAAACCCTAAAAAAGATACTACA
AAAAAGAAGAATACAAACAATCAAGTGAAGGAAGAAGAAAAGAAGACTAAAATAAAAAAATAGAT
GCAGAAAACT
Found at i:1555297 original size:18 final size:18
Alignment explanation
Indices: 1555274--1555308 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1555264 ATAATGTCAA
*
1555274 ATGATTCCTTAACCTCAT
1 ATGATTCCCTAACCTCAT
1555292 ATGATTCCCTAACCTCA
1 ATGATTCCCTAACCTCA
1555309 GACAACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (18 bp):
ATGATTCCCTAACCTCAT
Found at i:1569862 original size:21 final size:21
Alignment explanation
Indices: 1569836--1569882 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1569826 TGAAGGGCAT
1569836 AATAACTCCAGAATGCCAACA
1 AATAACTCCAGAATGCCAACA
1569857 AATAACTCCAGAATGCCAACA
1 AATAACTCCAGAATGCCAACA
1569878 AATAA
1 AATAA
1569883 ACAAGTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.51, C:0.26, G:0.09, T:0.15
Consensus pattern (21 bp):
AATAACTCCAGAATGCCAACA
Found at i:1570822 original size:2 final size:2
Alignment explanation
Indices: 1570817--1570849 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1570807 TATATAATGT
1570817 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 T
1570850 GCATATCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1576038 original size:13 final size:13
Alignment explanation
Indices: 1576017--1576054 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1576007 CTCCCCTTTT
1576017 TAATAATTAATAA
1 TAATAATTAATAA
*
1576030 TACTAATTAATAA
1 TAATAATTAATAA
1576043 TAATAA-TAATAA
1 TAATAATTAATAA
1576055 ATTAAAACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATAATTAATAA
Found at i:1579025 original size:20 final size:20
Alignment explanation
Indices: 1578992--1579034 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1578982 CCAATTTCGT
*
1578992 AACGCGAATCTGTAAATCGC
1 AACGCAAATCTGTAAATCGC
*
1579012 AACGCAAATTTGTAAATCGC
1 AACGCAAATCTGTAAATCGC
1579032 AAC
1 AAC
1579035 ACAGAAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
AACGCAAATCTGTAAATCGC
Found at i:1579056 original size:60 final size:59
Alignment explanation
Indices: 1579008--1579199 Score: 269
Period size: 60 Copynumber: 3.2 Consensus size: 59
1578998 AATCTGTAAA
* *
1579008 TCGCAACGCAAATTTGTAAATCGCAACACAGAAGTCAAATTCACAACGCGATAGTCAAAT
1 TCGCAACGCAAA-TTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* *
1579068 TCGCAACACAAA-AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACGCAAATTGT-AAA-TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* * *
1579128 TTGCAACGCGAATCTGTAAATCGCAACACAAAAGTCAATTTCGCAACGCGATAGTCAAAT
1 TCGCAACGCAAAT-TGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
*
1579188 TCGCAACACAAA
1 TCGCAACGCAAA
1579200 AGTCAAATTC
Statistics
Matches: 116, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.02
59 3 0.03
60 106 0.91
61 3 0.03
62 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (59 bp):
TCGCAACGCAAATTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:1579063 original size:20 final size:20
Alignment explanation
Indices: 1579028--1579235 Score: 197
Period size: 20 Copynumber: 10.3 Consensus size: 20
1579018 AATTTGTAAA
*
1579028 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * * *
1579048 TCACAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
1579068 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
1579088 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
1579108 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * **
1579128 TTGCAACGCGAATCTGT-AAA-
1 TCGCAACAC-AA-AAGTCAAAT
*
1579148 TCGCAACACAAAAGTCAATT
1 TCGCAACACAAAAGTCAAAT
* * *
1579168 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
1579188 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
1579208 TCGCAA-AGAGAAATTTCAAAT
1 TCGCAACACA-AAA-GTCAAAT
1579229 TCGCAAC
1 TCGCAAC
1579236 TGAATTTCAA
Statistics
Matches: 151, Mismatches: 30, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 125 0.83
21 16 0.11
22 2 0.01
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:1579072 original size:40 final size:40
Alignment explanation
Indices: 1579028--1579213 Score: 241
Period size: 40 Copynumber: 4.7 Consensus size: 40
1579018 AATTTGTAAA
* *
1579028 TCGCAACACAGAAGTCAAATTCACAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* * *
1579068 TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* * * * *
1579108 TCGCAACGCGATAGTCAAATTTGCAACGCGAATCTGT-AAA-
1 TCGCAACACAAAAGTCAAATTCGCAACGCG-AT-AGTCAAAT
*
1579148 TCGCAACACAAAAGTCAATTTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
1579188 TCGCAACACAAAAGTCAAATTCGCAA
1 TCGCAACACAAAAGTCAAATTCGCAA
1579214 AGAGAAATTT
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
38 2 0.02
39 5 0.04
40 109 0.89
41 4 0.03
42 2 0.02
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.18
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:1579212 original size:60 final size:60
Alignment explanation
Indices: 1579028--1579235 Score: 278
Period size: 60 Copynumber: 3.5 Consensus size: 60
1579018 AATTTGTAAA
* *
1579028 TCGCAACACAGAAGTCAAATTCACAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
* * **
1579088 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTTGCAACGCGAATCTGT-AAA-
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACAC-AA-AAGTCAAAT
*
1579148 TCGCAACACAAAAGTCAATTTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
* *
1579208 TCGCAA-AGAGAAATTTCAAATTCGCAAC
1 TCGCAACACA-AAA-GTCAAATTCGCAAC
1579236 TGAATTTCAA
Statistics
Matches: 128, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
58 2 0.02
59 7 0.05
60 100 0.78
61 17 0.13
62 2 0.02
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (60 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:1579269 original size:38 final size:40
Alignment explanation
Indices: 1579202--1579312 Score: 122
Period size: 39 Copynumber: 2.8 Consensus size: 40
1579192 AACACAAAAG
*
1579202 TCAAATTCGCAA-AGAGAAATTTCAAATTCGCAACT-GAATT
1 TCAAATTCGCAACA-CG-AATTTCAAATTCGCAACTAGAATT
* *
1579242 TCAAATTCGCAAC-TGAATTTCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACTAGAATT
* * *
1579281 TCGAATTCGTAACACGAATTT-AATTTCGCAAC
1 TCAAATTCGCAACACGAATTTCAAATTCGCAAC
1579313 AGGTTTTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
38 18 0.29
39 26 0.42
40 18 0.29
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.31
Consensus pattern (40 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACTAGAATT
Found at i:1579287 original size:20 final size:19
Alignment explanation
Indices: 1579219--1579312 Score: 118
Period size: 19 Copynumber: 4.9 Consensus size: 19
1579209 CGCAAAGAGA
1579219 AATTTCAAATTCGCAACTG
1 AATTTCAAATTCGCAACTG
1579238 AATTTCAAATTCGCAACTG
1 AATTTCAAATTCGCAACTG
1579257 AATTTCAAATTCGCAACTAG
1 AATTTCAAATTCGCAACT-G
* * * *
1579277 ATTTTCGAATTCGTAACACG
1 AATTTCAAATTCGCAAC-TG
*
1579297 AATTT-AATTTCGCAAC
1 AATTTCAAATTCGCAAC
1579313 AGGTTTTAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
19 45 0.69
20 20 0.31
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (19 bp):
AATTTCAAATTCGCAACTG
Found at i:1579488 original size:14 final size:15
Alignment explanation
Indices: 1579469--1579506 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1579459 TTCCCATCTC
1579469 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1579483 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1579499 TAATTTTT
1 TAATTTTT
1579507 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1582380 original size:18 final size:18
Alignment explanation
Indices: 1582357--1582392 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1582347 AAACAAAAGG
*
1582357 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1582375 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1582393 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1582777 original size:20 final size:20
Alignment explanation
Indices: 1582752--1582852 Score: 168
Period size: 20 Copynumber: 5.0 Consensus size: 20
1582742 AAATTGCAAC
1582752 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
*
1582772 GCGAATTTGACTTTCGTGTT
1 GCGAATTTGACTTTCGCGTT
*
1582792 GCGAATTTGACTTTCGTGTT
1 GCGAATTTGACTTTCGCGTT
1582812 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
1582832 GCGAATTT-ACCTTTCGCGTT
1 GCGAATTTGA-CTTTCGCGTT
1582852 G
1 G
1582853 TAAATTTACC
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
19 1 0.01
20 77 0.99
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.42
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:1582858 original size:20 final size:20
Alignment explanation
Indices: 1582762--1582871 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
1582752 GCGAATTTGA
*
1582762 CTTTCGCGTTGCGAATTTGA-
1 CTTTCGCGTTGCAAATTT-AC
* *
1582782 CTTTCGTGTTGCGAATTTGA-
1 CTTTCGCGTTGCAAATTT-AC
* *
1582802 CTTTCGTGTTGCGAATTTGA-
1 CTTTCGCGTTGCAAATTT-AC
*
1582822 CTTTCGCGTTGCGAATTTAC
1 CTTTCGCGTTGCAAATTTAC
*
1582842 CTTTCGCGTTGTAAATTTAC
1 CTTTCGCGTTGCAAATTTAC
*
1582862 CTTTTGCGTT
1 CTTTCGCGTT
1582872 ATGAATTTGT
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
19 1 0.01
20 83 0.99
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.45
Consensus pattern (20 bp):
CTTTCGCGTTGCAAATTTAC
Found at i:1582878 original size:20 final size:20
Alignment explanation
Indices: 1582822--1582879 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1582812 GCGAATTTGA
**
1582822 CTTTCGCGTTGCGAATTTAC
1 CTTTCGCGTTATGAATTTAC
* *
1582842 CTTTCGCGTTGTAAATTTAC
1 CTTTCGCGTTATGAATTTAC
*
1582862 CTTTTGCGTTATGAATTT
1 CTTTCGCGTTATGAATTT
1582880 GTACCTTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (20 bp):
CTTTCGCGTTATGAATTTAC
Found at i:1582878 original size:60 final size:60
Alignment explanation
Indices: 1582753--1582880 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 60
1582743 AATTGCAACG
* * * *
1582753 CGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGTGTTGCGAATTTGACTTTCGTGTTG
1 CGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCAAATTTGACTTTCGCGTTA
* *
1582813 CGAATTTGACTTTCGCGTTGCGAATTT-ACCTTTCGCGTTGTAAATTT-ACCTTTTGCGTTA
1 CGAATTTGACTTTCGCGTTGCGAATTTGA-CTTTCGCGTTGCAAATTTGA-CTTTCGCGTTA
*
1582873 TGAATTTG
1 CGAATTTG
1582881 TACCTTCAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 2 0.03
60 57 0.97
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (60 bp):
CGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCAAATTTGACTTTCGCGTTA
Found at i:1583053 original size:65 final size:67
Alignment explanation
Indices: 1582947--1583102 Score: 219
Period size: 69 Copynumber: 2.3 Consensus size: 67
1582937 AAATCAACTT
*
1582947 TTCAATTAAACAAGCAAAAAAATCATTCTTATTTACACATCAAATTAAACAAATCAAC-TT-T-T
1 TTCAATTAAACAAGC-AAAAAATAATTCTTATTTACACATC-AATTAAACAAATCAACTTTATGT
*
1583009 ACAA
64 AAAA
* *
1583013 TTCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTAAACAAATCAACTTTCAATGT
1 TTCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAACAAATCAACTTT--ATGT
1583078 AAAA
64 AAAA
1583082 TTCAATTAAACAAGCAAAAAA
1 TTCAATTAAACAAGCAAAAAA
1583103 AGTGTACCCC
Statistics
Matches: 81, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
64 16 0.20
65 24 0.30
66 15 0.19
68 1 0.01
69 25 0.31
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (67 bp):
TTCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAACAAATCAACTTTATGTAA
AA
Found at i:1584494 original size:21 final size:20
Alignment explanation
Indices: 1584451--1584509 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
1584441 CTTGAACGAC
* * *
1584451 AGGGGCCTCTTGAACGGTGGA
1 AGGGG-CTCTTGAATGATAGA
1584472 AGGGGTCTCTTGAATGATAGA
1 AGGGG-CTCTTGAATGATAGA
*
1584493 AGGCGCTCTTGAATGAT
1 AGGGGCTCTTGAATGAT
1584510 GATAGGTGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.25
Consensus pattern (20 bp):
AGGGGCTCTTGAATGATAGA
Found at i:1586704 original size:19 final size:18
Alignment explanation
Indices: 1586680--1586720 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
1586670 CGCAACGAGA
*
1586680 AAATCGCAATGCGAAAAT
1 AAATCGCAACGCGAAAAT
1586698 GAAATCGCAACGCGAAAAT
1 -AAATCGCAACGCGAAAAT
1586717 AAAT
1 AAAT
1586721 TGCGTTGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (18 bp):
AAATCGCAACGCGAAAAT
Found at i:1587145 original size:22 final size:22
Alignment explanation
Indices: 1587118--1587165 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1587108 GGAGATAGAA
*
1587118 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCGCCGAAGATGGGGAC
*
1587140 GGATTTCGTCGAAGATGGGGAC
1 GGATTTCGCCGAAGATGGGGAC
1587162 GGAT
1 GGAT
1587166 GTCGTCGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.44, T:0.21
Consensus pattern (22 bp):
GGATTTCGCCGAAGATGGGGAC
Found at i:1587170 original size:22 final size:22
Alignment explanation
Indices: 1587130--1587172 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1587120 ATTTCGCCGG
*
1587130 AGATGGGGACGGATTTCGTCGA
1 AGATGGGGACGGATGTCGTCGA
1587152 AGATGGGGACGGATGTCGTCG
1 AGATGGGGACGGATGTCGTCG
1587173 TAGAGAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.44, T:0.21
Consensus pattern (22 bp):
AGATGGGGACGGATGTCGTCGA
Found at i:1587304 original size:20 final size:20
Alignment explanation
Indices: 1587279--1587529 Score: 171
Period size: 20 Copynumber: 12.4 Consensus size: 20
1587269 ATTGTGTTTC
*
1587279 GCGTTGTGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTTT
*
1587299 GCGTTGCGCATTTGACTTTT
1 GCGTTGCGAATTTGACTTTT
* * * **
1587319 GTGTTGCGAATTTAAAATTCA
1 GCGTTGCGAATTT-GACTTTT
* * *
1587340 GTGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTTTT
* * *
1587360 GCGTTACGAATTTGACTATC
1 GCGTTGCGAATTTGACTTTT
1587380 GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTTT
* ** * **
1587400 GTGTTATGAATTTGAAATTCA
1 GCGTTGCGAATTTG-ACTTTT
* * *
1587421 GTGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTTTT
1587441 GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTTT
**
1587461 TTGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTTT
** * * *
1587481 TTGTTG-TAGATTTGACTATC
1 GCGTTGCGA-ATTTGACTTTT
* * *
1587501 ACGTTGCAAATTTGACTTCT
1 GCGTTGCGAATTTGACTTTT
*
1587521 GTGTTGCGA
1 GCGTTGCGA
1587530 TTTATATATT
Statistics
Matches: 180, Mismatches: 47, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
19 1 0.01
20 147 0.82
21 32 0.18
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTT
Found at i:1587431 original size:61 final size:60
Alignment explanation
Indices: 1587340--1587525 Score: 196
Period size: 60 Copynumber: 3.1 Consensus size: 60
1587330 TTAAAATTCA
* * * *
1587340 GTGTTGCGAATTTGACTATC-GCGTTACGAATTTGACTATCGCGTTGCGAATTTGACTTTT
1 GTGTTACGAATTTGAAT-TCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
*
1587400 GTGTTATGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
1 GTGTTACGAATTTG-AATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
* * * *** * * * *
1587461 TTGTTGCGAATTTGACTTTTTTGTTG-TAGATTTGACTATCACGTTGCAAATTTGACTTCT
1 GTGTTACGAATTTGAATTCAGTGTTGCGA-ATTTGACTATCGCGTTGCGAATTTGACTTTT
1587521 GTGTT
1 GTGTT
1587526 GCGATTTATA
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 54 0.51
61 51 0.48
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.44
Consensus pattern (60 bp):
GTGTTACGAATTTGAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTT
Found at i:1587494 original size:81 final size:81
Alignment explanation
Indices: 1587277--1587495 Score: 323
Period size: 81 Copynumber: 2.7 Consensus size: 81
1587267 ATATTGTGTT
* * * *
1587277 TCGCGTTGTGAATTTGACTTTTGCGTTGCGCATTTGACTTTTGTGTTGCGAATTTAAAATTCAGT
1 TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTTTTGTGTTGTGAATTTGAAATTCAGT
1587342 GTTGCGAATTTGACTA
66 GTTGCGAATTTGACTA
* * * *
1587358 TCGCGTTACGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTATGAATTTGAAATTCAGT
1 TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTTTTGTGTTGTGAATTTGAAATTCAGT
1587423 GTTGCGAATTTGACTA
66 GTTGCGAATTTGACTA
** *
1587439 TCGCGTTGCGAATTTGACTTTTTTGTTGCGAATTTGACTTTTTTGTTGT-AGATTTGA
1 TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTTTTGTGTTGTGA-ATTTGA
1587496 CTATCACGTT
Statistics
Matches: 122, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 1 0.01
81 121 0.99
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (81 bp):
TCGCGTTGCGAATTTGACTTTTGCGTTGCGAATTTGACTTTTGTGTTGTGAATTTGAAATTCAGT
GTTGCGAATTTGACTA
Found at i:1587546 original size:60 final size:62
Alignment explanation
Indices: 1587367--1587546 Score: 205
Period size: 61 Copynumber: 3.0 Consensus size: 62
1587357 ATCGCGTTAC
** * *
1587367 GAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTATGAATTTGA-A-ATTCAGTGTTGC
1 GAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGATATATT-TGTGTTGA
*
1587428 GAATTTGACTATCGCGTTGCGAATTTGACTTTTTTGTTGCGAATTTGACT-T-TTT-TGTTGTA
1 GAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGA-TATATTTGTGTTG-A
* * *
1587489 G-ATTTGACTATCACGTTGCAAATTTGACTTCTGTGTTGCG-ATTT-ATATATTTGTGTTG
1 GAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGATATATTTGTGTTG
1587547 CGATATTGGA
Statistics
Matches: 103, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
57 1 0.01
58 2 0.02
59 7 0.07
60 45 0.44
61 46 0.45
62 2 0.02
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.46
Consensus pattern (62 bp):
GAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGATATATTTGTGTTGA
Found at i:1587601 original size:19 final size:19
Alignment explanation
Indices: 1587564--1587610 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1587554 GGAAATTGGG
*
1587564 TTGCGAAATTAGAGTTCGCA
1 TTGCG-AATTAGAGATCGCA
* *
1587584 TTGCGAATTTGAGATCGCG
1 TTGCGAATTAGAGATCGCA
1587603 TTGCGAAT
1 TTGCGAAT
1587611 ATTTTGGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.32
Consensus pattern (19 bp):
TTGCGAATTAGAGATCGCA
Found at i:1590161 original size:63 final size:63
Alignment explanation
Indices: 1590094--1590232 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 63
1590084 ATCCCTTGAC
* *
1590094 GGGTGCATCGATGAACAATCTATG-CATCGGTACA-TAATACCATTCGATGTTTGTATTTTAAGG
1 GGGTGCATCGATGAACAA-CT-TGACATCGATACACTAATACCATTCGATGTTTGTATTTTAAAG
* * * *
1590157 GGGTGCATCGATGCACTACTTGTACATCGATACACTAATGCCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGAACAACTTG-ACATCGATACACTAATACCATTCGATGTTTGTATTTTAAAG
* *
1590221 GAGTACATCGAT
1 GGGTGCATCGAT
1590233 ACACCTCATG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
61 2 0.03
62 2 0.03
63 25 0.38
64 36 0.55
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (63 bp):
GGGTGCATCGATGAACAACTTGACATCGATACACTAATACCATTCGATGTTTGTATTTTAAAG
Found at i:1590249 original size:64 final size:63
Alignment explanation
Indices: 1590116--1590252 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 63
1590106 GAACAATCTA
* * * * * *
1590116 TGCATCGGTACATAATACCATTCGATGTTTGTATTTTAAGGGGGTGCATCGATGCACTACTTG
1 TGCATCGATACATAATACCATTCGATGTTTGTATTTTAAAGGAGTACATCGATACACTACATG
* * *
1590179 TACATCGATACACTAATGCCATTCGATGTTTTTATTTTAAAGGAGTACATCGATACACCT-CATG
1 TGCATCGATACA-TAATACCATTCGATGTTTGTATTTTAAAGGAGTACATCGATACA-CTACATG
1590243 TGCATCGATA
1 TGCATCGATA
1590253 TACCTTGAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
63 10 0.16
64 50 0.81
65 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (63 bp):
TGCATCGATACATAATACCATTCGATGTTTGTATTTTAAAGGAGTACATCGATACACTACATG
Found at i:1596746 original size:64 final size:63
Alignment explanation
Indices: 1596668--1596792 Score: 155
Period size: 64 Copynumber: 2.0 Consensus size: 63
1596658 ATCCCTTGAC
* * *
1596668 GGGTGCATCGATGCACAA-TCTATGCATCGGTACA-TAAATCCCATTCGATGTTTGTATTTTAAG
1 GGGTACATCGATGCACAACT-TATGCATCGATACACT-AATCACATTCGATGTTT-TATTTTAAG
1596731 G
63 G
* * *
1596732 GGGTACATCGATGCACTACTTGTGCATCGATACACTAATGACATTCGATGTTTTATTTTAA
1 GGGTACATCGATGCACAACTTATGCATCGATACACTAATCACATTCGATGTTTTATTTTAA
1596793 AGGAGGCATC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
63 8 0.15
64 43 0.81
65 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
GGGTACATCGATGCACAACTTATGCATCGATACACTAATCACATTCGATGTTTTATTTTAAGG
Found at i:1604082 original size:31 final size:32
Alignment explanation
Indices: 1604044--1604117 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
1604034 GGTTACGTCA
* *
1604044 GGGACCATATTGA-AAATAGACTAAATATTGG
1 GGGACCATATTGACAAACAGACTAAATATTAG
*
1604075 GGGACCATATT-ACAAACAGACTAAATGTTAG
1 GGGACCATATTGACAAACAGACTAAATATTAG
*
1604106 GGGACTATATTG
1 GGGACCATATTG
1604118 CAAGTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (32 bp):
GGGACCATATTGACAAACAGACTAAATATTAG
Found at i:1604155 original size:29 final size:29
Alignment explanation
Indices: 1604096--1604155 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
1604086 ACAAACAGAC
* * * *
1604096 TAAATGTTAGGGGACTATATTGCAAGTTT
1 TAAAAGTTAGGGGACTATAATGAAAGCTT
1604125 TAAAAGTTAGGGGACCTA-AATGAAAGCTT
1 TAAAAGTTAGGGGA-CTATAATGAAAGCTT
1604154 TA
1 TA
1604156 GAAAAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (29 bp):
TAAAAGTTAGGGGACTATAATGAAAGCTT
Found at i:1615799 original size:37 final size:37
Alignment explanation
Indices: 1615758--1615837 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
1615748 ATATTCTAAA
1615758 TAATTAAATTTTATAAAATACATATTTAAAAACTATT
1 TAATTAAATTTTATAAAATACATATTTAAAAACTATT
1615795 TAATTAAATTTTATAAAATACATATTTAAAAACTATT
1 TAATTAAATTTTATAAAATACATATTTAAAAACTATT
*
1615832 TGATTA
1 TAATTA
1615838 GACGTTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (37 bp):
TAATTAAATTTTATAAAATACATATTTAAAAACTATT
Found at i:1619167 original size:26 final size:26
Alignment explanation
Indices: 1619106--1619156 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1619096 TTTGAGTTTG
1619106 ATGTCGTTTGAATGGTATCAAAAAAA
1 ATGTCGTTTGAATGGTATCAAAAAAA
1619132 ATGTCGTTTGAATGGTAT-AAAAAAA
1 ATGTCGTTTGAATGGTATCAAAAAAA
1619157 GTCTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (26 bp):
ATGTCGTTTGAATGGTATCAAAAAAA
Found at i:1629450 original size:20 final size:20
Alignment explanation
Indices: 1629408--1629450 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1629398 TTTTGAAGTT
* * * *
1629408 TTAATAAGATATTTGATTTG
1 TTAATAAGATAATTAAATGG
1629428 TTAATAAGATAATTAAATGG
1 TTAATAAGATAATTAAATGG
1629448 TTA
1 TTA
1629451 GGAGTGTTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (20 bp):
TTAATAAGATAATTAAATGG
Found at i:1631510 original size:103 final size:103
Alignment explanation
Indices: 1631326--1631551 Score: 398
Period size: 103 Copynumber: 2.2 Consensus size: 103
1631316 GTCGAGGGTC
*
1631326 TATGTGGTTCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1631391 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
1631429 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1631494 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
1631532 TATGTGGTCCTTATGGACAT
1 TATGTGGTCCTTAGGGACAT
1631552 TATTATATGG
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 116 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1631597 original size:23 final size:23
Alignment explanation
Indices: 1631567--1631622 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1631557 TATGGAACTA
1631567 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
* *
1631590 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
1631613 CGGTGCAATT
1 CGGTGCAATT
1631623 ATATGAGCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.27
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:1633388 original size:23 final size:23
Alignment explanation
Indices: 1633309--1633390 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
1633299 TCGAGGGTTT
*
1633309 TATGTGGTCCTTCGAG-ACAAA--
1 TATGTGGTCCTTCG-GTGCAAACC
* * *
1633330 TATGAGGTACTTTGGTGCAAACC
1 TATGTGGTCCTTCGGTGCAAACC
*
1633353 TATGTTG-CACTTCGGTGCAAACC
1 TATGTGGTC-CTTCGGTGCAAACC
1633376 TATGTGGTCCTTCGG
1 TATGTGGTCCTTCGG
1633391 GACAATCATG
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
23 30 0.64
24 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGTCCTTCGGTGCAAACC
Found at i:1633693 original size:26 final size:26
Alignment explanation
Indices: 1633657--1633716 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
1633647 GACTGAGTTG
1633657 TGGAGGATAGCATGATATCATTCGAT
1 TGGAGGATAGCATGATATCATTCGAT
1633683 TGGAGGATAGCATGATATCATTCGAT
1 TGGAGGATAGCATGATATCATTCGAT
*
1633709 TGAAGGAT
1 TGGAGGAT
1633717 TAAATTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (26 bp):
TGGAGGATAGCATGATATCATTCGAT
Found at i:1637966 original size:20 final size:19
Alignment explanation
Indices: 1637926--1637966 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1637916 GTTGAAAATG
* *
1637926 ATTTGATTTTTAAAGCAAA
1 ATTTGATTTTGAAAACAAA
1637945 ATTTGATTTTGAAGAACAAA
1 ATTTGATTTTGAA-AACAAA
1637965 AT
1 AT
1637967 AAAATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (19 bp):
ATTTGATTTTGAAAACAAA
Found at i:1640151 original size:15 final size:15
Alignment explanation
Indices: 1640133--1640167 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1640123 ACAAGTTACA
*
1640133 TATAAAAAGATAAGG
1 TATAAAAAGATAAAG
*
1640148 TATAAAAATATAAAG
1 TATAAAAAGATAAAG
1640163 TATAA
1 TATAA
1640168 GGACTAAATA
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:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (15 bp):
TATAAAAAGATAAAG
Found at i:1640552 original size:16 final size:16
Alignment explanation
Indices: 1640531--1640572 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1640521 AAAAGTAAAA
1640531 GTTAGCAATTAATAGC
1 GTTAGCAATTAATAGC
1640547 GTTAGCAATTAATAGC
1 GTTAGCAATTAATAGC
* *
1640563 ATTAGAAATT
1 GTTAGCAATT
1640573 TAACCTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (16 bp):
GTTAGCAATTAATAGC
Found at i:1641688 original size:48 final size:48
Alignment explanation
Indices: 1641617--1641716 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
1641607 ATTCAGGTAC
1641617 TTAACGTTATAAATTTTATCTCTTTAAGTATCGGAGTCGTTAATAACG
1 TTAACGTTATAAATTTTATCTCTTTAAGTATCGGAGTCGTTAATAACG
1641665 TTAACGTTATAAATTTTATCTCTTTAAGTATCGGAGTCGTTAATAACG
1 TTAACGTTATAAATTTTATCTCTTTAAGTATCGGAGTCGTTAATAACG
1641713 TTAA
1 TTAA
1641717 GTAACACGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (48 bp):
TTAACGTTATAAATTTTATCTCTTTAAGTATCGGAGTCGTTAATAACG
Found at i:1641822 original size:19 final size:19
Alignment explanation
Indices: 1641758--1641828 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
1641748 ATTTTATATA
*
1641758 AAATTTTAAAAAAAATTAT
1 AAATTTTAAAAAAAATCAT
* *
1641777 ATATTTCTAAATAAGAAAACA-
1 AAATTT-TAAA-AA-AAATCAT
*
1641798 AAATTTTAAAATAAATCAT
1 AAATTTTAAAAAAAATCAT
1641817 AAATTTTAAAAA
1 AAATTTTAAAAA
1641829 TATTCATTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
18 5 0.12
19 17 0.41
20 8 0.20
21 7 0.17
22 4 0.10
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (19 bp):
AAATTTTAAAAAAAATCAT
Found at i:1644999 original size:16 final size:17
Alignment explanation
Indices: 1644980--1645016 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1644970 TAAAATATTA
1644980 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
1644996 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
1645013 TTTT
1 TTTT
1645017 TCATCCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Done.