Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008213.1 Hibiscus syriacus cultivar Beakdansim tig00110839_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: 2348840
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1827374 original size:2 final size:2
Alignment explanation
Indices: 1827367--1827411 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1827357 CCTTATTTTG
1827367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1827409 TA T
1 TA T
1827412 CATTTTGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1827599 original size:5 final size:5
Alignment explanation
Indices: 1827586--1827621 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1827576 TTTCATCGTT
* *
1827586 TTTTA TTTTG TTTTA TTTTA TTGTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1827622 CTTGGAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1832360 original size:29 final size:30
Alignment explanation
Indices: 1832318--1832385 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
1832308 GAAACAAAAT
* * *
1832318 TTTGTCTCTCTTGAGACAATA-TCTTTGAG
1 TTTGTTTCTCTTGAAACAAAAGTCTTTGAG
1832347 TTTGTTTCTCTTGAAACAAAAGTCTTTGAG
1 TTTGTTTCTCTTGAAACAAAAGTCTTTGAG
*
1832377 TCTGTTTCT
1 TTTGTTTCT
1832386 ATTAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (30 bp):
TTTGTTTCTCTTGAAACAAAAGTCTTTGAG
Found at i:1832844 original size:134 final size:131
Alignment explanation
Indices: 1832521--1832852 Score: 377
Period size: 131 Copynumber: 2.5 Consensus size: 131
1832511 ATTGTCCTCG
* *
1832521 TCACGTAGGAACCGTGTCATCCCCCGACCAGATCTCCTCATCA-AGTAGGAGCCGTGTCAACCTT
1 TCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACA-TAGGAGCCGTGTCACCCTT
* * *
1832585 AGATAACATGTCATCCTCATCACGTAGGAACCATGTTATCATCTCTAAAGATGGTCTGCCATTCT
65 AGATAACATGTCATCCTCATCACGTAGGAACCATGTTATCATCTCTAAAGATGGACTGCAACTCT
1832650 CA
130 CA
* * * * * *
1832652 TCACATAGGAACCATGTCAT-CTCTCGACCAGATCTCCTCATCACGTAAGAGCTGTGTCACCCTT
1 TCACGTAGGAACCGTGTCATCCCCT-GACCAGATCTCCTCATCACATAGGAGCCGTGTCACCCTT
* ** *
1832716 AGATAACCA-GTCGTCCTCATCGTGTTGGAACCATGTTATCACTCTCCCTAAAGAT-GACTAG-A
65 AGATAA-CATGTCATCCTCATCACGTAGGAACCATGTTATCA-TCT--CTAAAGATGGACT-GCA
1832778 ACTCTTCA
125 ACTC-TCA
* * ** *
1832786 TCACGTATGAGCCGTGTCATCCCCTGATTAGATCTCCTCATCACATAGGAGCCATGTCACCCTTA
1 TCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACATAGGAGCCGTGTCACCCTTA
1832851 GA
66 GA
1832853 CGACCAGACC
Statistics
Matches: 166, Mismatches: 26, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
130 2 0.01
131 86 0.52
132 5 0.03
133 6 0.04
134 64 0.39
135 3 0.02
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (131 bp):
TCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCATCACATAGGAGCCGTGTCACCCTTA
GATAACATGTCATCCTCATCACGTAGGAACCATGTTATCATCTCTAAAGATGGACTGCAACTCTC
A
Found at i:1833048 original size:3 final size:3
Alignment explanation
Indices: 1833042--1833099 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
1833032 TGCAAAAAAA
*
1833042 ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT AATT ATT ATT ATT CTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
1833087 ATT ATT AATT ATT
1 ATT ATT -ATT ATT
1833100 TTACAATTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1833077 original size:30 final size:32
Alignment explanation
Indices: 1833041--1833099 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
1833031 CTGCAAAAAA
1833041 AATTATTATTATTATTA-TATT-ATTATTATT
1 AATTATTATTATTATTATTATTAATTATTATT
*
1833071 AATTATTATTATTCTTATTATTAATTATT
1 AATTATTATTATTATTATTATTAATTATT
1833100 TTACAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 16 0.62
31 4 0.15
32 6 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (32 bp):
AATTATTATTATTATTATTATTAATTATTATT
Found at i:1833088 original size:22 final size:21
Alignment explanation
Indices: 1833042--1833099 Score: 91
Period size: 22 Copynumber: 2.8 Consensus size: 21
1833032 TGCAAAAAAA
1833042 ATTATTATT-ATTATTATATT
1 ATTATTATTAATTATTATATT
1833062 ATTATTATTAATTATTATTATT
1 ATTATTATTAATTATTA-TATT
*
1833084 CTTATTATTAATTATT
1 ATTATTATTAATTATT
1833100 TTACAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 9 0.26
21 7 0.20
22 19 0.54
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTATTAATTATTATATT
Found at i:1834547 original size:30 final size:31
Alignment explanation
Indices: 1834513--1834611 Score: 118
Period size: 30 Copynumber: 3.3 Consensus size: 31
1834503 ACAGTTTAGC
*
1834513 CCTTTAAATTTATATTTTT-TCTATTTAAGT
1 CCTTTAAATTTCTATTTTTGTCTATTTAAGT
* *
1834543 CCTTTAACTTTCTATTTTTGT-TATTTTAGT
1 CCTTTAAATTTCTATTTTTGTCTATTTAAGT
1834573 CCTTT-AATTGTCTATTTTTGT-TATCTTAA-T
1 CCTTTAAATT-TCTATTTTTGTCTAT-TTAAGT
1834603 CCTTTAAAT
1 CCTTTAAAT
1834612 GTTTGTATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.05
30 50 0.83
31 7 0.12
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (31 bp):
CCTTTAAATTTCTATTTTTGTCTATTTAAGT
Found at i:1834723 original size:2 final size:2
Alignment explanation
Indices: 1834716--1834776 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1834706 CCTTATTTTG
1834716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1834758 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1834777 TTTGTTTTCT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1834964 original size:5 final size:5
Alignment explanation
Indices: 1834951--1834991 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
1834941 CGTTTTTCAT
* *
1834951 TTTTA TTTTG TTTTA TTTTA TTTTA TTGTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1834992 CTTGGCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1836593 original size:17 final size:19
Alignment explanation
Indices: 1836571--1836610 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1836561 AAATCTAATG
1836571 AATTAAT-T-AAAGAAAAA
1 AATTAATCTAAAAGAAAAA
1836588 AATTAATCTCAAAAGAAAAA
1 AATTAATCT-AAAAGAAAAA
1836608 AAT
1 AAT
1836611 ATTAGAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
20 12 0.60
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (19 bp):
AATTAATCTAAAAGAAAAA
Found at i:1838538 original size:3 final size:3
Alignment explanation
Indices: 1838530--1838558 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1838520 TATTTGTCAT
1838530 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1838559 TCTTTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1838997 original size:73 final size:74
Alignment explanation
Indices: 1838872--1839064 Score: 280
Period size: 74 Copynumber: 2.6 Consensus size: 74
1838862 TCGGAGGATT
** * ** **
1838872 TAATCATCAAGAAACCTTTGAAAATCAAACTTGGTTTATTTAAAAATTCATTT-GGAATATCATA
1 TAATCATCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTAAAAATAGAATA
1838936 TCAATCAGG
66 TCAATCAGG
**
1838945 TAATTTTCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTAAAAATAGAATA
1 TAATCATCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTAAAAATAGAATA
* *
1839010 TCAGTCTGG
66 TCAATCAGG
1839019 TAATCATCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAA
1 TAATCATCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAA
1839065 AAATCATTTG
Statistics
Matches: 106, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 48 0.45
74 58 0.55
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (74 bp):
TAATCATCAAGAAACCTTTGAAAATCAAACTTGACTTCTTTAAAAATTCATTTAAAAATAGAATA
TCAATCAGG
Found at i:1844496 original size:21 final size:22
Alignment explanation
Indices: 1844461--1844520 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
1844451 AGAACCCATT
* *
1844461 GGGGGTATCGATTCCC-TC-AA
1 GGGGGAATCGGTTCCCATCAAA
1844481 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGGTTCCCA-TCAAA
1844505 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
1844521 CTTCAAGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 2 0.06
21 12 0.35
23 16 0.47
24 4 0.12
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCATCAAA
Found at i:1844510 original size:23 final size:24
Alignment explanation
Indices: 1844479--1844526 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
1844469 CGATTCCCTC
1844479 AAGGAGGGAATCGGTTCCCATTCA
1 AAGGAGGGAATCGGTTCCCATTCA
*
1844503 AAGG-GGGAATCGGTTCCCCTTCA
1 AAGGAGGGAATCGGTTCCCATTCA
1844526 A
1 A
1844527 GGGTATCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (24 bp):
AAGGAGGGAATCGGTTCCCATTCA
Found at i:1851466 original size:29 final size:29
Alignment explanation
Indices: 1851444--1851514 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
1851434 AATCAATAAC
*
1851444 CCTAATTTTTTATATTAATAATCAGAACT
1 CCTAATATTTTATATTAATAATCAGAACT
* * * *
1851473 CCTTATATTTTATATTTATAATTAGGACT
1 CCTAATATTTTATATTAATAATCAGAACT
1851502 CCTAAT-TTTTATA
1 CCTAATATTTTATA
1851515 ATTTCATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 7 0.19
29 29 0.81
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (29 bp):
CCTAATATTTTATATTAATAATCAGAACT
Found at i:1851518 original size:29 final size:29
Alignment explanation
Indices: 1851444--1851523 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
1851434 AATCAATAAC
*
1851444 CCTAATTTTT-TATATTAATAATCAGAACT
1 CCTAATTTTTATA-ATTTATAATCAGAACT
* * *
1851473 CCTTATATTTTAT-ATTTATAATTAGGACT
1 CCTAAT-TTTTATAATTTATAATCAGAACT
1851502 CCTAATTTTTATAATTTCATAA
1 CCTAATTTTTATAATTT-ATAA
1851524 AATATTTGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 6 0.14
29 27 0.64
30 8 0.19
31 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.49
Consensus pattern (29 bp):
CCTAATTTTTATAATTTATAATCAGAACT
Found at i:1855015 original size:13 final size:13
Alignment explanation
Indices: 1854997--1855031 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1854987 AATGGGCAAT
*
1854997 TTTGAAAATTATG
1 TTTGAAAATAATG
*
1855010 TTTGAAAACAATG
1 TTTGAAAATAATG
1855023 TTTGAAAAT
1 TTTGAAAAT
1855032 CAATATGTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (13 bp):
TTTGAAAATAATG
Found at i:1855565 original size:44 final size:44
Alignment explanation
Indices: 1855510--1855612 Score: 145
Period size: 44 Copynumber: 2.3 Consensus size: 44
1855500 CGATGCACTG
*
1855510 CATAGTGTATCGATGCACATTCAAG-GAATGCATCGGTGCACCTT
1 CATAGTGTATCGATGCACATTCAAGAG-ATGCATCGGTACACCTT
* * *
1855554 CATAGTGTATCGATGCATATTCAAGAGATGCATTGGTACACTTT
1 CATAGTGTATCGATGCACATTCAAGAGATGCATCGGTACACCTT
*
1855598 TATAGTGTATCGATG
1 CATAGTGTATCGATG
1855613 TATAGTACAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
44 52 0.98
45 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGAGATGCATCGGTACACCTT
Found at i:1855576 original size:21 final size:21
Alignment explanation
Indices: 1855497--1855576 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
1855487 CCGACGAGTA
*
1855497 TATCGATGCAC-TGCATAGTG
1 TATCGATGCACATTCATAGTG
1855517 TATCGATGCACATTCA-AGGAATG
1 TATCGATGCACATTCATA-G--TG
* * *
1855540 CATCGGTGCACCTTCATAGTG
1 TATCGATGCACATTCATAGTG
*
1855561 TATCGATGCATATTCA
1 TATCGATGCACATTCA
1855577 AGAGATGCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
20 12 0.26
21 18 0.38
23 16 0.34
24 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
TATCGATGCACATTCATAGTG
Found at i:1872993 original size:65 final size:65
Alignment explanation
Indices: 1872921--1873076 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 65
1872911 TACACTTGGG
* * *
1872921 GTGCATCGATACACT-AATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGG-
1872984 CT
64 CT
* * * * *
1872986 GTGCATCGGTACA-TAAAATGCATTTGATGTTTCAATAAAATCAGGAGTGTATTGATGCATGGCT
1 GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCT
*
1873050 GTGCATCGGTACAC-AAAATGCATTCGA
1 GTGCATCGGTACACTAAAATACATTCGA
1873077 ATTAGGGTGT
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
64 28 0.35
65 49 0.62
66 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACTAAAATACATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCT
Found at i:1875428 original size:28 final size:28
Alignment explanation
Indices: 1875388--1875441 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1875378 AACTAATTTG
*
1875388 TTACAAATCGATAATATGAATGACCATT
1 TTACAAATCGATAACATGAATGACCATT
*
1875416 TTACAAATCGATAACATTAATGACCA
1 TTACAAATCGATAACATGAATGACCA
1875442 ATTTGTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (28 bp):
TTACAAATCGATAACATGAATGACCATT
Found at i:1875583 original size:7 final size:7
Alignment explanation
Indices: 1875573--1875628 Score: 85
Period size: 7 Copynumber: 7.7 Consensus size: 7
1875563 TATTTTATTT
1875573 TTTTTAC
1 TTTTTAC
1875580 TTTTTTAC
1 -TTTTTAC
*
1875588 TTGTTAC
1 TTTTTAC
1875595 TTTTTAC
1 TTTTTAC
1875602 TTTTTAC
1 TTTTTAC
1875609 TCTTTTAC
1 T-TTTTAC
1875617 TTTTTAC
1 TTTTTAC
1875624 TTTTT
1 TTTTT
1875629 TTTATGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
7 31 0.69
8 14 0.31
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.71
Consensus pattern (7 bp):
TTTTTAC
Found at i:1875594 original size:15 final size:15
Alignment explanation
Indices: 1875573--1875629 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
1875563 TATTTTATTT
1875573 TTTTTACTTTTTTAC
1 TTTTTACTTTTTTAC
*
1875588 TTGTTAC-TTTTTAC
1 TTTTTACTTTTTTAC
*
1875602 TTTTTACTCTTTTAC
1 TTTTTACTTTTTTAC
1875617 TTTTTACTTTTTT
1 TTTTTACTTTTTT
1875630 TTATGTTGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 13 0.35
15 24 0.65
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTTACTTTTTTAC
Found at i:1875598 original size:22 final size:23
Alignment explanation
Indices: 1875573--1875629 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 23
1875563 TATTTTATTT
1875573 TTTTTACTTTTTTACT-TGTTAC
1 TTTTTACTTTTTTACTCTGTTAC
*
1875595 TTTTTAC-TTTTTACTCTTTTAC
1 TTTTTACTTTTTTACTCTGTTAC
1875617 TTTTTACTTTTTT
1 TTTTTACTTTTTT
1875630 TTATGTTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 8 0.25
22 19 0.59
23 5 0.16
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTTACTTTTTTACTCTGTTAC
Found at i:1875614 original size:29 final size:29
Alignment explanation
Indices: 1875573--1875628 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1875563 TATTTTATTT
*
1875573 TTTTTACTTTTTTACTTGTTACTTTTTAC
1 TTTTTACTCTTTTACTTGTTACTTTTTAC
*
1875602 TTTTTACTCTTTTACTTTTTACTTTTT
1 TTTTTACTCTTTTACTTGTTACTTTTT
1875629 TTTATGTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTTTACTCTTTTACTTGTTACTTTTTAC
Found at i:1875782 original size:3 final size:3
Alignment explanation
Indices: 1875768--1875848 Score: 137
Period size: 3 Copynumber: 27.0 Consensus size: 3
1875758 TTGTTTTCGT
*
1875768 TTA TTC TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1875814 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1875849 ATAATATGTA
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1878045 original size:3 final size:3
Alignment explanation
Indices: 1878037--1878071 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1878027 CGTTATGTCA
1878037 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1878072 GTTTGAGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1881570 original size:26 final size:27
Alignment explanation
Indices: 1881536--1881589 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
1881526 TCATAAAATC
*
1881536 ATTTATCAGTATTCAGAAAT-AAAACAA
1 ATTTATCAG-AATCAGAAATAAAAACAA
*
1881563 ATTT-TCAGAATCAGATATAAAAACAA
1 ATTTATCAGAATCAGAAATAAAAACAA
1881589 A
1 A
1881590 ATACAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 12 0.50
27 4 0.17
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (27 bp):
ATTTATCAGAATCAGAAATAAAAACAA
Found at i:1882416 original size:43 final size:43
Alignment explanation
Indices: 1882036--1882416 Score: 360
Period size: 43 Copynumber: 8.8 Consensus size: 43
1882026 GCAAAAACGT
* * *** *
1882036 TAAGGTCTTACCCTTGCACATAGCAAAAGAGTATGAGGAAACGG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGAGGAAACTG
* * * *
1882080 TAAGGTCTTACCCTTGCACATAGAAAAGGAGCCT-AGGAAACGG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGAGGAAACTG
** *
1882123 TAAGGTCTTATGCTTGCACACAGCAAA-GAAGCCT-AGGAAACTA
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAA-CCTGAGGAAACTG
* * *
1882166 TAAGGTCTTACCCGTGCACACAGCAAAGGAACCTG-GGAAAAATTA
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGAGG--AAACTG
* * * *
1882211 TAAGGCTTACCATTTCACATAGCAAAGGAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAGGAAACTG
* *
1882254 TAAGGCTTACCCTTGCACACATCAAAGGAACCTAGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GAGGAAACTG
* * * * *
1882298 TAA-GCCTACCATTACACACAGCAAAGGAACCTG-GAAAAAATG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAG-GAAACTG
* *
1882340 TAAGGCTTACCCTTGCACACAGTAAAGGAACCTGAGAAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAGGAAACTG
* *
1882383 TAAGGCTTACCCTTGTACAGAGCAAAGGAACCTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTG
1882417 CCAGTGAAAA
Statistics
Matches: 288, Mismatches: 39, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
41 1 0.00
42 11 0.04
43 192 0.67
44 72 0.25
45 12 0.04
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAGGAAACTG
Found at i:1884748 original size:16 final size:16
Alignment explanation
Indices: 1884716--1884749 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1884706 GACTTTTCGG
1884716 TCAAAGTCAACACCGA
1 TCAAAGTCAACACCGA
1884732 TCAACAGTCAACA-CGA
1 TCAA-AGTCAACACCGA
1884748 TC
1 TC
1884750 GGCTCGGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.41, C:0.32, G:0.12, T:0.15
Consensus pattern (16 bp):
TCAAAGTCAACACCGA
Found at i:1885488 original size:386 final size:386
Alignment explanation
Indices: 1884775--1885547 Score: 1393
Period size: 386 Copynumber: 2.0 Consensus size: 386
1884765 AGCTTGGCTT
*
1884775 GGCTCCCCTGGAGGACAAACGATGCCCATTCATAGGAGCGGCGCGTGCGGCGGCCTAGGAGGTCG
1 GGCTCCCCTGGAGGACAAACGATGCACATTCATAGGAGCGGCGCGTGCGGCGGCCTAGGAGGTCG
* * *
1884840 AAAAAATTTCATAAAATTTTGTAAAATTATTTCAAGGCATTTTGAGACACTTACCAAGCCCGGTT
66 AAAAAATTCCATAAAATTTTCTAAAATTATTTCAAGGCATTTTGAGACACTTACCAAGCCCGATT
* *
1884905 CACAATTTTGAACGACAGAGAGCTCGATTCCGAAATGTCGTAAACTTTGACTTCCTCACCTCCCT
131 CACAATTTTGAACGACAGAGAGCTCAATTCCGAAATGTCATAAACTTTGACTTCCTCACCTCCCT
* *
1884970 CACGCGCTGGTGGCGACGGAGACAAGAAGGGAACCGGTGAACTTAGAACTATGCAAGGAACACGA
196 CACGCGCCGGTGGCGACGGAGACAAGAAGGGAACCGGTGAACTTAGAACGATGCAAGGAACACGA
* * *
1885035 TGGTGCGGGAGGTGTAAAAACGGGTGGTTGGATCGACCAGAATCGACGGAAAACTAATAGCGATT
261 TGGTGCGGGAGGTGTAAAAACGGGTGGTCGGATCGACCAGAATCGACGGAAAACCAATAGAGATT
* * *
1885100 GAGTTAAAACCGATAAAGATTTCGGTTGAGTTTTACGGTGAACGTTGTTGATTCAGGACGG
326 GAGTTAAAACCAAAAAAGATTTCGGTTGAGTTTTACGGTGAACGTTGCTGATTCAGGACGG
* *
1885161 GGCTCCCCTGGAGGACAAACGATGCACATTCATAGGGGCGGCGCGTGCGGCGGCCTTGGAGGTCG
1 GGCTCCCCTGGAGGACAAACGATGCACATTCATAGGAGCGGCGCGTGCGGCGGCCTAGGAGGTCG
1885226 AAAAAATTCCATAAAATTTTCTAAAATTATTTCAAGGCATTTTGAGACACTTACCAAGCCCGATT
66 AAAAAATTCCATAAAATTTTCTAAAATTATTTCAAGGCATTTTGAGACACTTACCAAGCCCGATT
1885291 CACAATTTTGAACGACAGAGAGCTCAATTCCGAAATGTCATAAACTTTGACTTCCTCACCTCCCT
131 CACAATTTTGAACGACAGAGAGCTCAATTCCGAAATGTCATAAACTTTGACTTCCTCACCTCCCT
*
1885356 CACGCGCCGGTGGCGACGGAGACAAGAAGGGCACCGGTGAACTTAGAACGATGCAAGGAACACGA
196 CACGCGCCGGTGGCGACGGAGACAAGAAGGGAACCGGTGAACTTAGAACGATGCAAGGAACACGA
1885421 TGGTGCGGGAGGTGTAAAAACGGGTGGTCGGATCGACCAGAATCGACGGAAAACCAATAGAGATT
261 TGGTGCGGGAGGTGTAAAAACGGGTGGTCGGATCGACCAGAATCGACGGAAAACCAATAGAGATT
1885486 GAGTTAAAACCAAAAAAGATTTCGGTTGAGTTTTACGGTGAACGTTGCTGATTCAGGACGG
326 GAGTTAAAACCAAAAAAGATTTCGGTTGAGTTTTACGGTGAACGTTGCTGATTCAGGACGG
1885547 G
1 G
1885548 ATAAAGGTTG
Statistics
Matches: 370, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
386 370 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (386 bp):
GGCTCCCCTGGAGGACAAACGATGCACATTCATAGGAGCGGCGCGTGCGGCGGCCTAGGAGGTCG
AAAAAATTCCATAAAATTTTCTAAAATTATTTCAAGGCATTTTGAGACACTTACCAAGCCCGATT
CACAATTTTGAACGACAGAGAGCTCAATTCCGAAATGTCATAAACTTTGACTTCCTCACCTCCCT
CACGCGCCGGTGGCGACGGAGACAAGAAGGGAACCGGTGAACTTAGAACGATGCAAGGAACACGA
TGGTGCGGGAGGTGTAAAAACGGGTGGTCGGATCGACCAGAATCGACGGAAAACCAATAGAGATT
GAGTTAAAACCAAAAAAGATTTCGGTTGAGTTTTACGGTGAACGTTGCTGATTCAGGACGG
Found at i:1887138 original size:44 final size:44
Alignment explanation
Indices: 1887089--1887416 Score: 246
Period size: 43 Copynumber: 7.5 Consensus size: 44
1887079 TGTTAAGGTC
* * ** *
1887089 GTCTTACCCTTGCACATAGGAAAAGAGTATGAGGAAACGATAAT
1 GTCTTACCCTTGCACATAGCAAAGGAGCCTGAGGAAACGATAAG
*
1887133 GTCTTACCCTTGCACATAGCAAAGGAGCCT-AGGAAACGGTAAG
1 GTCTTACCCTTGCACATAGCAAAGGAGCCTGAGGAAACGATAAG
* * * *
1887176 GTCTTACCCTTGCATACAACAAAGGAGCCTG-GGAAACTATAAG
1 GTCTTACCCTTGCACATAGCAAAGGAGCCTGAGGAAACGATAAG
* * * *
1887219 GTCTTACCCTTGCACACAGCAAAGGAACTTGGGGAAAACTG-TAAG
1 GTCTTACCCTTGCACATAGCAAAGGAGCCTGAGG-AAAC-GATAAG
* * * *
1887264 G-CTCACCCTTGCACATAGTAAAGGAACCTGGGGAAACTG-TAAG
1 GTCTTACCCTTGCACATAGCAAAGGAGCCTGAGGAAAC-GATAAG
* * * *
1887307 G-CTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTG-TAAG
1 GTCTTACCCTTGCACATAGCAAAGGAGCCT-GAGGAAAC-GATAAG
* * * * * *
1887351 G-CTTACCCTTACACACAACAAAGAAACATG-GGAAAACTG-TAAG
1 GTCTTACCCTTGCACATAGCAAAGGAGCCTGAGG-AAAC-GATAAG
* *
1887394 G-CTTAACCTTGCACACAGCAAAG
1 GTCTTACCCTTGCACATAGCAAAG
1887417 AAACCTGTCA
Statistics
Matches: 248, Mismatches: 30, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
42 2 0.01
43 141 0.57
44 96 0.39
45 9 0.04
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19
Consensus pattern (44 bp):
GTCTTACCCTTGCACATAGCAAAGGAGCCTGAGGAAACGATAAG
Found at i:1887181 original size:43 final size:43
Alignment explanation
Indices: 1887135--1887423 Score: 348
Period size: 43 Copynumber: 6.7 Consensus size: 43
1887125 ACGATAATGT
* * * *
1887135 CTTACCCTTGCACATAGCAAAGGAGCCT-AGGAAACGGTAAGG
1 CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGG
* * * *
1887177 TCTTACCCTTGCATACAACAAAGGAGCCT-GGGAAACTATAAGG
1 -CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGG
*
1887220 TCTTACCCTTGCACACAGCAAAGGAACTTGGGGAAAACTGTAAGG
1 -CTTACCCTTGCACACAGCAAAGGAACCTGGGG-AAACTGTAAGG
* * *
1887265 CTCACCCTTGCACATAGTAAAGGAACCTGGGGAAACTGTAAGG
1 CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGG
*
1887308 CTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTGTAAGG
1 CTTACCCTTGCACACAGCAAAGGAACCT-GGGGAAACTGTAAGG
* * * * *
1887352 CTTACCCTTACACACAACAAAGAAACATGGGAAAACTGTAAGG
1 CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGG
* *
1887395 CTTAACCTTGCACACAGCAAAGAAACCTG
1 CTTACCCTTGCACACAGCAAAGGAACCTG
1887424 TCAGTGAAAA
Statistics
Matches: 216, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
43 135 0.62
44 71 0.33
45 10 0.05
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (43 bp):
CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGG
Found at i:1887312 original size:87 final size:86
Alignment explanation
Indices: 1887135--1887423 Score: 357
Period size: 87 Copynumber: 3.3 Consensus size: 86
1887125 ACGATAATGT
* * * * *
1887135 CTTACCCTTGCACATAGCAAAGGAGCCT-AGGAAACGGTAAGGTCTTACCCTTGCATACAACAAA
1 CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGG-CTTACCCTTGCACACAACAAA
* *
1887199 GGAGCCT-GGGAAACTATAAGG
65 GGAACCTGGGGAAACTGTAAGG
* * * **
1887220 TCTTACCCTTGCACACAGCAAAGGAACTTGGGGAAAACTGTAAGGCTCACCCTTGCACATAGTAA
1 -CTTACCCTTGCACACAGCAAAGGAACCTGGGG-AAACTGTAAGGCTTACCCTTGCACACAACAA
1887285 AGGAACCTGGGGAAACTGTAAGG
64 AGGAACCTGGGGAAACTGTAAGG
* *
1887308 CTTACCCTTGCACACAACAAAGGAACCTGGGGGAAACTGTAAGGCTTACCCTTACACACAACAAA
1 CTTACCCTTGCACACAGCAAAGGAACCT-GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAA
* * *
1887373 GAAACATGGGAAAACTGTAAGG
65 GGAACCTGGGGAAACTGTAAGG
* *
1887395 CTTAACCTTGCACACAGCAAAGAAACCTG
1 CTTACCCTTGCACACAGCAAAGGAACCTG
1887424 TCAGTGAAAA
Statistics
Matches: 174, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
86 26 0.15
87 121 0.70
88 27 0.16
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (86 bp):
CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAG
GAACCTGGGGAAACTGTAAGG
Found at i:1887325 original size:130 final size:130
Alignment explanation
Indices: 1887138--1887423 Score: 389
Period size: 130 Copynumber: 2.2 Consensus size: 130
1887128 ATAATGTCTT
* *
1887138 ACCCTTGCACATAGCAAAGGAGCCT-AGGAAACGGTAAGGTCTTACCCTTGCATACAACAAAGGA
1 ACCCTTGCACATAGCAAAGGAACCTGAGGAAACGGTAAGGTCTTACCCTTGCACACAACAAAGGA
* * * * *
1887202 GCCT-GGGAAACTATAAGGTCTTACCCTTGCACACAGCAAAGGAACTTGGGGAAAACTGTAAGGC
66 ACCTGGGGAAACTATAAGG-CTTACCCTTACACACAACAAAGAAACAT-GGGAAAACTGTAAGGC
1887266 TC
129 TC
* * *
1887268 ACCCTTGCACATAGTAAAGGAACCTGGGGAAACTGTAAGG-CTTACCCTTGCACACAACAAAGGA
1 ACCCTTGCACATAGCAAAGGAACCTGAGGAAACGGTAAGGTCTTACCCTTGCACACAACAAAGGA
*
1887332 ACCTGGGGGAAACTGTAAGGCTTACCCTTACACACAACAAAGAAACATGGGAAAACTGTAAGGCT
66 ACCT-GGGGAAACTATAAGGCTTACCCTTACACACAACAAAGAAACATGGGAAAACTGTAAGGCT
*
1887397 T
130 C
* * *
1887398 AACCTTGCACACAGCAAAGAAACCTG
1 ACCCTTGCACATAGCAAAGGAACCTG
1887424 TCAGTGAAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
130 88 0.64
131 36 0.26
132 13 0.09
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.17
Consensus pattern (130 bp):
ACCCTTGCACATAGCAAAGGAACCTGAGGAAACGGTAAGGTCTTACCCTTGCACACAACAAAGGA
ACCTGGGGAAACTATAAGGCTTACCCTTACACACAACAAAGAAACATGGGAAAACTGTAAGGCTC
Found at i:1889661 original size:13 final size:13
Alignment explanation
Indices: 1889643--1889669 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1889633 TTGACTTTTT
1889643 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
1889656 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
1889669 G
1 G
1889670 TCGTTCAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:1891764 original size:6 final size:6
Alignment explanation
Indices: 1891753--1891814 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
1891743 TTTTCTCTCA
1891753 CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT
1 CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT
1891801 CTCACT CTCACT CT
1 CTCACT CTCACT CT
1891815 TTCTTCCTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCACT
Found at i:1895328 original size:14 final size:14
Alignment explanation
Indices: 1895309--1895342 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1895299 TGGCAGCTTT
1895309 GACCCGTTTAACCC
1 GACCCGTTTAACCC
*
1895323 GACCCGTTTGACCC
1 GACCCGTTTAACCC
1895337 GACCCG
1 GACCCG
1895343 GTCCGACCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.44, G:0.21, T:0.18
Consensus pattern (14 bp):
GACCCGTTTAACCC
Found at i:1895403 original size:10 final size:11
Alignment explanation
Indices: 1895377--1895419 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
1895367 ACTGCCTAAC
*
1895377 CCGTTGATCGA
1 CCGTTGACCGA
1895388 CCGTTGACCG-
1 CCGTTGACCGA
1895398 CCGTTGACCGAA
1 CCGTTGACCG-A
*
1895410 CCTTTGACCG
1 CCGTTGACCG
1895420 GTGTTGACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 10 0.36
11 9 0.32
12 9 0.32
ACGTcount: A:0.16, C:0.35, G:0.26, T:0.23
Consensus pattern (11 bp):
CCGTTGACCGA
Found at i:1895419 original size:22 final size:22
Alignment explanation
Indices: 1895377--1895432 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1895367 ACTGCCTAAC
*
1895377 CCGTTGATCG-ACCGTTGACCG
1 CCGTTGACCGAACCGTTGACCG
*
1895398 CCGTTGACCGAACCTTTGACCG
1 CCGTTGACCGAACCGTTGACCG
**
1895420 GTGTTGACCGAAC
1 CCGTTGACCGAAC
1895433 GTTAACTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.18, C:0.32, G:0.27, T:0.23
Consensus pattern (22 bp):
CCGTTGACCGAACCGTTGACCG
Found at i:1897573 original size:44 final size:44
Alignment explanation
Indices: 1897504--1897667 Score: 222
Period size: 44 Copynumber: 3.8 Consensus size: 44
1897494 AGATTTCCTT
* * *
1897504 GTTTTCATCAGGCTCCTTCGCTGTGTGCAAGGGTAAGCCTTACA
1 GTTTTCCTCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACA
* * *
1897548 GTTTTCCTCAGGTTCCTTTGATGTGTGCAAGGGCAAGCCATACA
1 GTTTTCCTCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACA
** * *
1897592 GTTCCCCCCAGGTTCCTTTGCTGTGTGCAAAGGTAAGCCTTACA
1 GTTTTCCTCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACA
*
1897636 GTTTTCC-CAAGTTCCTTTGCTGTGTGCAAGGG
1 GTTTTCCTCAGGTTCCTTTGCTGTGTGCAAGGG
1897668 GAAGTGATGT
Statistics
Matches: 103, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 23 0.22
44 80 0.78
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (44 bp):
GTTTTCCTCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACA
Found at i:1897983 original size:17 final size:17
Alignment explanation
Indices: 1897963--1898021 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1897953 TTTGAGGAAG
1897963 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
1897980 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
1897996 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
1898013 TAGTTCATT
1 TAGTTCATT
1898022 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:1898035 original size:18 final size:18
Alignment explanation
Indices: 1898012--1898050 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1898002 ATTCATGCAT
1898012 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
1898030 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
1898048 TTA
1 TTA
1898051 TTTAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:1899823 original size:18 final size:17
Alignment explanation
Indices: 1899769--1899817 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1899759 TTGGACCCTT
* *
1899769 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1899787 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1899805 AGTGCATTCGATG
1 AGTGCA-TCGATG
1899818 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1899850 original size:45 final size:46
Alignment explanation
Indices: 1899786--1899893 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 46
1899776 CGGTGCACTA
*
1899786 AGAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
*
1899831 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCC
**
1899877 TCAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
1899894 GGTATGTGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
45 31 0.54
46 23 0.40
47 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (46 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCC
Found at i:1900617 original size:25 final size:24
Alignment explanation
Indices: 1900585--1900634 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 24
1900575 TTAAGCTCAA
1900585 AATAATAAAGTTAAAATCAAACCAAAT
1 AATAAT-AAGTT-AAATC-AACCAAAT
1900612 ATATAATAAGTTAAATCAACCAA
1 A-ATAATAAGTTAAATCAACCAA
1900635 GCATCCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 5 0.23
27 6 0.27
28 5 0.23
ACGTcount: A:0.60, C:0.12, G:0.04, T:0.24
Consensus pattern (24 bp):
AATAATAAGTTAAATCAACCAAAT
Found at i:1902665 original size:23 final size:22
Alignment explanation
Indices: 1902635--1902712 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 22
1902625 GCATGACCTT
1902635 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1902657 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1902679 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
1902702 GATGCATCGAT
1 G-TGCATCGAT
1902713 ACACTGTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 15 0.34
22 2 0.05
23 19 0.43
24 8 0.18
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1902691 original size:21 final size:22
Alignment explanation
Indices: 1902635--1902697 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
1902625 GCATGACCTT
1902635 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTC-AGGC
* * *
1902658 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGC
*
1902679 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
1902698 AAGGGATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGC
Found at i:1910839 original size:17 final size:17
Alignment explanation
Indices: 1910819--1910877 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1910809 TTTAGGGAAG
1910819 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
1910836 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
1910852 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
1910869 TAGTTCATT
1 TAGTTCATT
1910878 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:1910891 original size:18 final size:18
Alignment explanation
Indices: 1910868--1910912 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1910858 ATTCATGCAT
1910868 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
* * *
1910886 TTAGTTTATTGATTAATG
1 TTAGTTCATTGAATAAAG
1910904 TTA-TTCATT
1 TTAGTTCATT
1910913 AATTAATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:1913033 original size:44 final size:44
Alignment explanation
Indices: 1912943--1913138 Score: 218
Period size: 44 Copynumber: 4.5 Consensus size: 44
1912933 AAAAAAATAG
* * * **
1912943 TAAGGACTTACTCTTGCACATAGCAAAGGAGTCT-A-GGAAACTA
1 TAAGG-CTTACCCTTGCACACAGCAAAAGAACCTGAGGGAAACTA
* *
1912986 TAAGGTCTTCCCCTTGCGCACAGCAAAAGAACCTG-GGGAAACTA
1 TAAGG-CTTACCCTTGCACACAGCAAAAGAACCTGAGGGAAACTA
* *
1913030 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGAGGGAAACTA
* * * * *
1913074 TAAGGCTTACCCTTGCACATAGGAAATGAACATGAGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGAGGGAAACTA
*
1913118 TAAAGCTTACCCTTGCACACA
1 TAAGGCTTACCCTTGCACACA
1913139 ACAGAGGAGC
Statistics
Matches: 132, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
43 52 0.39
44 80 0.61
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (44 bp):
TAAGGCTTACCCTTGCACACAGCAAAAGAACCTGAGGGAAACTA
Found at i:1913126 original size:88 final size:87
Alignment explanation
Indices: 1912949--1913157 Score: 242
Period size: 88 Copynumber: 2.4 Consensus size: 87
1912939 ATAGTAAGGA
* * * * *
1912949 CTTACTCTTGCACATAGCAAAGGAGTCT-AGGAAACTATAAGGTCTTCCCCTTGCGCACAGCAAA
1 CTTACCCTTGCACACAGCAAAGGAGCCTGAGGAAACTATAAGGTCTTACCCTTGCACACAGCAAA
* *
1913013 AGAACCTGGGGAAACTATAAGG
66 AGAACATGGGGAAACTATAAAG
* * * *
1913035 CTTACCCTTGCACACAGCAAAGGAACCTGAGGGAAACTGTAAGG-CTTACCCTTGCACATAGGAA
1 CTTACCCTTGCACACAGCAAAGGAGCCTGA-GGAAACTATAAGGTCTTACCCTTGCACACAGCAA
* *
1913099 ATGAACATGAGGGAAACTGTAAAG
65 AAGAACATG-GGGAAACTATAAAG
* * *
1913123 CTTACCCTTGCACACAACAGAGGAGCCTGATGAAA
1 CTTACCCTTGCACACAGCAAAGGAGCCTGAGGAAA
1913158 ACAGGGAAAC
Statistics
Matches: 103, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
86 24 0.23
87 28 0.27
88 51 0.50
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.19
Consensus pattern (87 bp):
CTTACCCTTGCACACAGCAAAGGAGCCTGAGGAAACTATAAGGTCTTACCCTTGCACACAGCAAA
AGAACATGGGGAAACTATAAAG
Found at i:1915788 original size:20 final size:20
Alignment explanation
Indices: 1915763--1915803 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1915753 TAGGGAGAGG
*
1915763 ATTGAAAGGTTAAGACCTTT
1 ATTGAAAGGTTAAGAACTTT
1915783 ATTGAAAGGTTAAGAACTTT
1 ATTGAAAGGTTAAGAACTTT
1915803 A
1 A
1915804 AATGAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTGAAAGGTTAAGAACTTT
Found at i:1918729 original size:24 final size:24
Alignment explanation
Indices: 1918702--1918753 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1918692 AACGGATATA
*
1918702 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1918726 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1918750 TCAA
1 TCAA
1918754 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1918813 original size:12 final size:11
Alignment explanation
Indices: 1918758--1918830 Score: 60
Period size: 12 Copynumber: 6.2 Consensus size: 11
1918748 GGTCAAGTAA
1918758 CAGATCAGAAT
1 CAGATCAGAAT
*
1918769 CCA-AGTCAAGTAT
1 -CAGA-TC-AGAAT
1918782 CAGATCAGAAT
1 CAGATCAGAAT
1918793 CCATG-TCAGATAT
1 -CA-GATCAGA-AT
1918806 CAGATCAGAAT
1 CAGATCAGAAT
1918817 CCAGATCAGAAT
1 -CAGATCAGAAT
1918829 CA
1 CA
1918831 AAATAGAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
11 10 0.20
12 33 0.65
13 8 0.16
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (11 bp):
CAGATCAGAAT
Found at i:1918816 original size:24 final size:24
Alignment explanation
Indices: 1918725--1918819 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
1918715 CATAAATCAG
* *
1918725 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAA
*
1918749 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
1918773 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
1918797 GTC-AGATATCAGATCAGAATCCA
1 GTCAAG-TATCAGATCAGAATCCA
1918820 GATCAGAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 5 0.08
24 59 0.92
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:1918825 original size:24 final size:24
Alignment explanation
Indices: 1918758--1918830 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 24
1918748 GGTCAAGTAA
1918758 CAGATCAGAATCCA-AGTCA-AGTAT
1 CAGATCAGAATCCAGA-TCAGA-TAT
1918782 CAGATCAGAATCCATG-TCAGATAT
1 CAGATCAGAATCCA-GATCAGATAT
1918806 CAGATCAGAATCCAGATCAGA-AT
1 CAGATCAGAATCCAGATCAGATAT
1918829 CA
1 CA
1918831 AAATAGAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.11
24 39 0.87
25 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (24 bp):
CAGATCAGAATCCAGATCAGATAT
Found at i:1923513 original size:24 final size:24
Alignment explanation
Indices: 1923486--1923537 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1923476 AACGGATATA
*
1923486 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1923510 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1923534 TCAA
1 TCAA
1923538 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1923576 original size:24 final size:24
Alignment explanation
Indices: 1923509--1923603 Score: 113
Period size: 24 Copynumber: 4.0 Consensus size: 24
1923499 CATAAATCAG
* *
1923509 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAA
*
1923533 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
1923557 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
1923581 GTC-AGATATCAGATCAGAATCCA
1 GTCAAG-TATCAGATCAGAATCCA
1923604 GATCAGAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
23 5 0.08
24 57 0.92
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:1923594 original size:48 final size:48
Alignment explanation
Indices: 1923509--1923603 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
1923499 CATAAATCAG
1923509 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
* *
1923557 GTCAAGTATCATATCAG-AATCCATGTC-AGATATCAGATCAGAATCCA
1 GTCAAGTATCATATCAGAAAT-CAGGTCAAG-TAACAGATCAGAATCCA
1923604 GATCAGAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 5 0.12
48 38 0.88
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
Found at i:1923597 original size:12 final size:11
Alignment explanation
Indices: 1923542--1923616 Score: 55
Period size: 12 Copynumber: 6.4 Consensus size: 11
1923532 GGTCAAGTAA
1923542 CAGATCAGAAT
1 CAGATCAGAAT
*
1923553 CCA-AGTCAAGTAT
1 -CAGA-TC-AGAAT
*
1923566 CATATCAGAAT
1 CAGATCAGAAT
1923577 CCATG-TCAGATAT
1 -CA-GATCAGA-AT
1923590 CAGATCAGAAT
1 CAGATCAGAAT
1923601 CCAGATCAGAAT
1 -CAGATCAGAAT
1923613 CAGA
1 CAGA
1923617 ACAAAATTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
11 12 0.23
12 33 0.63
13 7 0.13
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (11 bp):
CAGATCAGAAT
Found at i:1923609 original size:24 final size:24
Alignment explanation
Indices: 1923542--1923616 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
1923532 GGTCAAGTAA
1923542 CAGATCAGAATCCA-AGTCA-AGTAT
1 CAGATCAGAATCCAGA-TCAGA-TAT
*
1923566 CATATCAGAATCCATG-TCAGATAT
1 CAGATCAGAATCCA-GATCAGATAT
1923590 CAGATCAGAATCCAGATCAGA-AT
1 CAGATCAGAATCCAGATCAGATAT
1923613 CAGA
1 CAGA
1923617 ACAAAATTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
23 7 0.16
24 37 0.82
25 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (24 bp):
CAGATCAGAATCCAGATCAGATAT
Found at i:1928860 original size:17 final size:17
Alignment explanation
Indices: 1928840--1928882 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1928830 CAAATGCATC
* *
1928840 AATGAACTACCTAATTA
1 AATGAACTACATAACTA
* *
1928857 AATGAAGTGCATAACTA
1 AATGAACTACATAACTA
1928874 AATGAACTA
1 AATGAACTA
1928883 TATGTATTAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (17 bp):
AATGAACTACATAACTA
Found at i:1928894 original size:17 final size:17
Alignment explanation
Indices: 1928872--1928913 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1928862 AGTGCATAAC
*
1928872 TAAATGAACTATATGTA
1 TAAATGAACTATATGCA
* *
1928889 TTAATGAAGTATATGCA
1 TAAATGAACTATATGCA
1928906 TAAATGAA
1 TAAATGAA
1928914 ATGCATGCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (17 bp):
TAAATGAACTATATGCA
Found at i:1930243 original size:54 final size:54
Alignment explanation
Indices: 1929842--1930247 Score: 544
Period size: 54 Copynumber: 7.5 Consensus size: 54
1929832 TAACTATTAC
* * * * *
1929842 AACTCACTAT-AATTTCCTTGGTTTGTACACATAGTGCCGATATGGTAATTCACA
1 AACTCATTATGAA-TTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * * *
1929896 AACTCATTATGAATTTCGTTGGTTGCACACATAGTGTCGATACGGTAATTCATA
1 AACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
*
1929950 AACTCGTTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
1 AACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * * *
1930004 AACTCATTATAAATTCCGTGGGTTGCGCACATAGTGCCGATACGATAATTCATA
1 AACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* ** * *
1930058 AACTCATTATGAGTTCTTTGGGTTGCATACATAGTGCCGATATGGTAATTCACA
1 AACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * *
1930112 AACTCATTATGAATTTCGTTGGTTGCACACATAGAGCCGATACGGTAATTCACA
1 AACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* * * *
1930166 AACTCATTATGAATTACGTGGGTTGCACATATAGTGTCGATACGGTAATTCATA
1 AACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
* *
1930220 AACTTATTATGAATTCCGCGGGTTGCAC
1 AACTCATTATGAATTCCGTGGGTTGCAC
1930248 TGATAGCCGT
Statistics
Matches: 306, Mismatches: 45, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
54 304 0.99
55 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
AACTCATTATGAATTCCGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
Found at i:1932879 original size:5 final size:5
Alignment explanation
Indices: 1932869--1932925 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
1932859 TGTTCAGAGA
* **
1932869 AAAAT AAAAT AAAATT AAGCAT ATGAT AAAAT AAAAT -AAAT AAAAT GAAAAT
1 AAAAT AAAAT AAAA-T AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
1932921 AAAAT
1 AAAAT
1932926 GAAAGGGGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 4 0.09
5 28 0.65
6 10 0.23
7 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:1932911 original size:9 final size:10
Alignment explanation
Indices: 1932869--1932925 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
1932859 TGTTCAGAGA
1932869 AAAATAAAAT
1 AAAATAAAAT
*
1932879 AAAATTAAGCAT
1 AAAA-TAA-AAT
**
1932891 ATGATAAAAT
1 AAAATAAAAT
1932901 AAAAT-AAAT
1 AAAATAAAAT
1932910 AAAATGAAAAT
1 AAAAT-AAAAT
1932921 AAAAT
1 AAAAT
1932926 GAAAGGGGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
9 9 0.24
10 9 0.24
11 15 0.41
12 4 0.11
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:1932916 original size:22 final size:22
Alignment explanation
Indices: 1932872--1932930 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
1932862 TCAGAGAAAA
* * *
1932872 ATAAAATAAAATTAAGCATATG
1 ATAAAATAAAATAAAGAAAATG
*
1932894 ATAAAATAAAATAAATAAAATG
1 ATAAAATAAAATAAAGAAAATG
1932916 --AAAATAAAATGAAAG
1 ATAAAATAAAAT-AAAG
1932931 GGGTTGCCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 10 0.32
21 3 0.10
22 18 0.58
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (22 bp):
ATAAAATAAAATAAAGAAAATG
Found at i:1932922 original size:11 final size:11
Alignment explanation
Indices: 1932896--1932929 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1932886 AGCATATGAT
1932896 AAAATAAAAT-
1 AAAATAAAATG
1932906 -AAATAAAATG
1 AAAATAAAATG
1932916 AAAATAAAATG
1 AAAATAAAATG
1932927 AAA
1 AAA
1932930 GGGGTTGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:1939440 original size:54 final size:53
Alignment explanation
Indices: 1939358--1939752 Score: 488
Period size: 54 Copynumber: 7.4 Consensus size: 53
1939348 GAACATATCA
*
1939358 TGCACACATAGTGCCGATACGGTAATTCACAAACGCATTATGAATTCAGTGGGT
1 TGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTC-GTGGGT
**
1939412 TGCACACATAGTGCCGATACGGCGATTCACAAACTCATTATGAATTCTGTGGGT
1 TGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTC-GTGGGT
* * ** * * * *
1939466 TTCACACATAGTGCTGATACAATAATTCATAAACTTATTATGAATTATGCGGGT
1 TGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATT-CGTGGGT
* *
1939520 TGCACAC--AGTGTCGATACGGTAATTCACAAACTCATTATGAATTTCGTTGGT
1 TGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAA-TTCGTGGGT
* * *
1939572 TGCACACATAGTGCCAACACGGTAACTCACAAACTCATTATGAATTTCGTGGGT
1 TGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAA-TTCGTGGGT
** * * *
1939626 TGCACACATAGTGTTGATACTGTAATTCACAAACCCATTATGAATTTCGAGGGT
1 TGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAA-TTCGTGGGT
* * * *
1939680 TGCATACATAATGCCAATACGGTAATTCATAAACTCATTATGAATTACGTGGGT
1 TGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATT-CGTGGGT
1939734 TGCACACATAGTGCCGATA
1 TGCACACATAGTGCCGATA
1939753 GTACACATAG
Statistics
Matches: 287, Mismatches: 49, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
52 40 0.14
53 4 0.01
54 243 0.85
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (53 bp):
TGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTCGTGGGT
Found at i:1939636 original size:160 final size:160
Alignment explanation
Indices: 1939362--1939748 Score: 519
Period size: 160 Copynumber: 2.4 Consensus size: 160
1939352 ATATCATGCA
*
1939362 CACATAGTGCCGATACGGTAATTCACAAACGCATTATGAA-TTCAGTGGGTTGCACACATAGTGC
1 CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTTC-GTGGGTTGCACACATAGTGC
* * * * *
1939426 CGATACGGCGATTCACAAACTCATTATGAATTCTGTGGGTTTCACACATAGTGCTGATACAATAA
65 CAACACGGCAACTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACAATAA
* ** *
1939491 TTCATAAACTTATTATGAATTAT-GCGGGTTG
130 TTCACAAACCCATTATGAATT-TCGAGGGTTG
* * *
1939522 CACACAGTGTCGATACGGTAATTCACAAACTCATTATGAATTTCGTTGGTTGCACACATAGTGCC
1 CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCC
* * **
1939587 AACACGGTAACTCACAAACTCATTATGAATT-TCGTGGGTTGCACACATAGTGTTGATACTGTAA
66 AACACGGCAACTCACAAACTCATTATGAATTCT-GTGGGTTGCACACATAGTGCTGATACAATAA
1939651 TTCACAAACCCATTATGAATTTCGAGGGTTG
130 TTCACAAACCCATTATGAATTTCGAGGGTTG
* * * *
1939682 CATACATAATGCCAATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTGCACACATAGTG
1 C--ACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTTCGTGGGTTGCACACATAGTG
1939747 CC
64 CC
1939749 GATAGTACAC
Statistics
Matches: 198, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
159 2 0.01
160 136 0.69
161 3 0.02
162 57 0.29
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (160 bp):
CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTTCGTGGGTTGCACACATAGTGCC
AACACGGCAACTCACAAACTCATTATGAATTCTGTGGGTTGCACACATAGTGCTGATACAATAAT
TCACAAACCCATTATGAATTTCGAGGGTTG
Found at i:1946006 original size:54 final size:54
Alignment explanation
Indices: 1945920--1946391 Score: 547
Period size: 54 Copynumber: 8.8 Consensus size: 54
1945910 TTAACTATTA
* * * * *
1945920 AAACTCATTAT-AATTTCCTTGGTTTGCTCACATAGTGTCGATATGGTAATTTAC
1 AAACTCATTATGAA-TTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
* * * * * *
1945974 AAACTCATTATGATTTTCGTGGGTTGCACACATAGTGCCGATACGATAATTAAT
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
* * * * *
1946028 AAAATCAATATGAATTCCATGGGTTGCACACATAGTGCCGATACGATAATTCAC
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
** * * ** *
1946082 AAACTCATTATGAATTTTGTGGGCTACACACATAGTACCGATACGGTAATTCAT
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
* * * * *
1946136 AAACTC---ATGAATTCCTTGGTTTGCACACATAGTGTCAATATGGTAATTTAC
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
* * * *
1946187 TAACTCAATATGAATTACGTGGGTTGCACACATAGTGTCGATATGGTAATTCAC
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
* * * *
1946241 AAAATCATTATGAATTCCTTGGGTTGCACACATAGTGTTGATACAGTAATTCAC
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
* * *
1946295 AAACTCATTATGAATTTCGTGGGTTGCACACATTGTGTCGATACGGTAATTCAT
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
*
1946349 AAACACATTATGAATTCCGTGGGTTGCACACATAGTGTCGATA
1 AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATA
1946392 GTACACATAG
Statistics
Matches: 351, Mismatches: 63, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
51 38 0.11
54 312 0.89
55 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
AAACTCATTATGAATTCCGTGGGTTGCACACATAGTGTCGATACGGTAATTCAC
Found at i:1946301 original size:213 final size:216
Alignment explanation
Indices: 1945934--1946387 Score: 655
Period size: 213 Copynumber: 2.1 Consensus size: 216
1945924 TCATTATAAT
* * * * *
1945934 TTCCTTGGTTTGCTCACATAGTGTCGATATGGTAATTTACAAACTCATTATGATTTTCGTGGGTT
1 TTCCTTGGTTTGCACACATAGTGTCAATATGGTAATTTACAAACTCAATATGAATTACGTGGGTT
*
1945999 GCACACATAGTGCCGATACGATAATTAATAAAATCAATATGAATTCCATGGGTTGCACACATAGT
66 GCACACATAGTGCCGATACGATAATTAACAAAATCAATATGAATTCCATGGGTTGCACACATAGT
*
1946064 GCCGATACGATAATTCACAAACTCATTATGAATTTTGTGGGCTACACACATAGTACCGATACGGT
131 GCCGATACGATAATTCACAAACTCATTATGAATTTCGTGGGCTACACACATAGTACCGATACGGT
1946129 AATTCAT-AA-AC-TCATGAA
196 AATTCATAAACACATCATGAA
*
1946147 TTCCTTGGTTTGCACACATAGTGTCAATATGGTAATTTACTAACTCAATATGAATTACGTGGGTT
1 TTCCTTGGTTTGCACACATAGTGTCAATATGGTAATTTACAAACTCAATATGAATTACGTGGGTT
* * * * * *
1946212 GCACACATAGTGTCGATATGGTAATTCACAAAATCATTATGAATTCCTTGGGTTGCACACATAGT
66 GCACACATAGTGCCGATACGATAATTAACAAAATCAATATGAATTCCATGGGTTGCACACATAGT
** * * * **
1946277 GTTGATAC-AGTAATTCACAAACTCATTATGAATTTCGTGGGTTGCACACATTGTGTCGATACGG
131 GCCGATACGA-TAATTCACAAACTCATTATGAATTTCGTGGGCTACACACATAGTACCGATACGG
*
1946341 TAATTCATAAACACATTATGAA
195 TAATTCATAAACACATCATGAA
* *
1946363 TTCCGTGGGTTGCACACATAGTGTC
1 TTCCTTGGTTTGCACACATAGTGTC
1946388 GATAGTACAC
Statistics
Matches: 213, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
212 1 0.00
213 179 0.84
214 2 0.01
215 2 0.01
216 29 0.14
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (216 bp):
TTCCTTGGTTTGCACACATAGTGTCAATATGGTAATTTACAAACTCAATATGAATTACGTGGGTT
GCACACATAGTGCCGATACGATAATTAACAAAATCAATATGAATTCCATGGGTTGCACACATAGT
GCCGATACGATAATTCACAAACTCATTATGAATTTCGTGGGCTACACACATAGTACCGATACGGT
AATTCATAAACACATCATGAA
Found at i:1947212 original size:20 final size:21
Alignment explanation
Indices: 1947169--1947212 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1947159 AAACTAACTT
** *
1947169 ACATCCATAAATCTCTGAATA
1 ACATCCATAAATCTCCAAAGA
1947190 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
1947210 ACA
1 ACA
1947213 CTTAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.48, C:0.27, G:0.05, T:0.20
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:1963280 original size:24 final size:24
Alignment explanation
Indices: 1963221--1963285 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
1963211 GATACATTAC
* *
1963221 CTGAATTCTGTTCTGATTTTTAAT
1 CTGAATTCTGTTATGATATTTAAT
* * *
1963245 CTGGATTTTGTTATGATATTTGAT
1 CTGAATTCTGTTATGATATTTAAT
* *
1963269 TTGAATTCTGTTTTGAT
1 CTGAATTCTGTTATGAT
1963286 TTATGATATC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.20, C:0.08, G:0.17, T:0.55
Consensus pattern (24 bp):
CTGAATTCTGTTATGATATTTAAT
Found at i:1969576 original size:25 final size:26
Alignment explanation
Indices: 1969524--1969576 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1969514 ACCGAAGTAC
*
1969524 TAATACACAAAAGGTCGTTCCCACCA
1 TAATACACAAAAGGTCGATCCCACCA
*
1969550 TAATACACATAAGGTC-ATCCCACCA
1 TAATACACAAAAGGTCGATCCCACCA
1969575 TA
1 TA
1969577 TGCACTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (26 bp):
TAATACACAAAAGGTCGATCCCACCA
Found at i:1974344 original size:20 final size:20
Alignment explanation
Indices: 1974321--1974359 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1974311 CATACTTTGC
1974321 TTTTTTATTTTCCATGTTTA
1 TTTTTTATTTTCCATGTTTA
1974341 TTTTTTATTTTCCATGTTT
1 TTTTTTATTTTCCATGTTT
1974360 TTACATTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTATTTTCCATGTTTA
Found at i:1999709 original size:18 final size:18
Alignment explanation
Indices: 1999686--1999743 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
1999676 CAACAATTGG
1999686 TAACAATTGGTATCTTTT
1 TAACAATTGGTATCTTTT
*
1999704 TAACAATTGATATCCTTTT
1 TAACAATTGGTAT-CTTTT
1999723 GTAAACAATTGGTATCTTTT
1 -T-AACAATTGGTATCTTTT
1999743 T
1 T
1999744 CATTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.34
19 6 0.17
20 6 0.17
21 11 0.31
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.48
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:2000324 original size:13 final size:13
Alignment explanation
Indices: 2000282--2000316 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2000272 CTATGACGCG
2000282 CATTTATGACACA
1 CATTTATGACACA
*
2000295 CATTTATGACTCA
1 CATTTATGACACA
2000308 CATTTATGA
1 CATTTATGA
2000317 AACGCATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:2000324 original size:26 final size:26
Alignment explanation
Indices: 2000273--2000324 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2000263 GTCATAAATC
* *
2000273 TATGACGCGCATTTATGACACACATT
1 TATGACGCACATTTATGAAACACATT
* *
2000299 TATGACTCACATTTATGAAACGCATT
1 TATGACGCACATTTATGAAACACATT
2000325 GAGCGTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (26 bp):
TATGACGCACATTTATGAAACACATT
Found at i:2007060 original size:18 final size:19
Alignment explanation
Indices: 2007039--2007081 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2007029 TTAACAAAAG
2007039 AAAAAGAATTAATT-T-TTT
1 AAAAAGAATT-ATTATGTTT
*
2007057 AAAAAAAATTATTATGTTT
1 AAAAAGAATTATTATGTTT
2007076 AAAAAG
1 AAAAAG
2007082 GGCAACACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 10 0.48
19 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (19 bp):
AAAAAGAATTATTATGTTT
Found at i:2010549 original size:54 final size:55
Alignment explanation
Indices: 2010376--2010534 Score: 239
Period size: 55 Copynumber: 2.9 Consensus size: 55
2010366 CTATGTGTAC
* *
2010376 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCAAGAGCTGATGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
2010431 TACAAGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGAAGAATCACCG
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
** * *
2010486 TACAGGCACTTTGTGTGCA-ACCCACGAAATTCATCATGAGTTTATGAAT
1 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAAT
2010535 TTTCGTATAG
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
54 25 0.27
55 69 0.73
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (55 bp):
TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
Found at i:2011909 original size:196 final size:197
Alignment explanation
Indices: 2011575--2011967 Score: 770
Period size: 196 Copynumber: 2.0 Consensus size: 197
2011565 AAGGTGAAGG
2011575 TACTATGGATGTAGATTTATGGTTAAACGATGTGATGATGATGTTGGAAAGCCTTCAATCCTCCG
1 TACTATGGATGTAGATTTATGGTTAAACGATGTGATGATGATGTTGGAAAGCCTTCAATCCTCCG
2011640 ACCATGAGAAGTTGGGTGGAGCTATATCGGTACTCAAAGGATCGGCTAGGGTATGGTGGAGAAAC
66 ACCATGAGAAGTTGGGTGGAGCTATATCGGTACTCAAAGGATCGGCTAGGGTATGGTGGAGAAAC
2011705 ATGATAATGTATGCGTCACCCGAGAAAGTGAACTGGCAGTTCTTTCAAGA-GAGTTTAAAAACAA
131 ATGATAATGTATGCGTCACCCGAGAAAGTGAACTGGCAGTTCTTTCAAGAGGAGTTTAAAAACAA
2011769 GT
196 GT
2011771 TACTATGGATGTAGATTTATGGTTAAACGATGTGATGATGATGTTGGAAAGCCTTCAATCCTCCG
1 TACTATGGATGTAGATTTATGGTTAAACGATGTGATGATGATGTTGGAAAGCCTTCAATCCTCCG
*
2011836 ACCATGAGAAGTTGGGTGGAGCTATATCGTTACTCAAAGGATCGGCTAGGGTATGGTGGAGAAAC
66 ACCATGAGAAGTTGGGTGGAGCTATATCGGTACTCAAAGGATCGGCTAGGGTATGGTGGAGAAAC
2011901 ATGATAATGTATGCGTCACCCGAGAAAGTGAACTGGCAGTTCTTTCAAGAGGAGTTTAAAAACAA
131 ATGATAATGTATGCGTCACCCGAGAAAGTGAACTGGCAGTTCTTTCAAGAGGAGTTTAAAAACAA
2011966 GT
196 GT
2011968 ATATCGGGGA
Statistics
Matches: 195, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
196 179 0.92
197 16 0.08
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (197 bp):
TACTATGGATGTAGATTTATGGTTAAACGATGTGATGATGATGTTGGAAAGCCTTCAATCCTCCG
ACCATGAGAAGTTGGGTGGAGCTATATCGGTACTCAAAGGATCGGCTAGGGTATGGTGGAGAAAC
ATGATAATGTATGCGTCACCCGAGAAAGTGAACTGGCAGTTCTTTCAAGAGGAGTTTAAAAACAA
GT
Found at i:2017234 original size:55 final size:54
Alignment explanation
Indices: 2017166--2017348 Score: 260
Period size: 55 Copynumber: 3.4 Consensus size: 54
2017156 CATATTTTCG
* *
2017166 GAATTCATCATGAGTTGATGAATCACCGTACAGGGACTTTGTGTGCATATTCAC
1 GAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTTGTGTGCATATTCAC
* *
2017220 GAAATTCATTATGAGTTCATGAATCACCGTACAAGCACTTTGTGTGCATATTCAC
1 G-AATTCATCATGAGTTGATGAATCACCGTACAAGCACTTTGTGTGCATATTCAC
* * **
2017275 GGAATTCATCATGAGTTGATGAATCACCATACAAGCACTTTATGTGCA-ACCCAC
1 -GAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTTGTGTGCATATTCAC
2017329 TGAATTCATCATGAGTTGAT
1 -GAATTCATCATGAGTTGAT
2017349 AAATTTTTGT
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
54 24 0.21
55 91 0.78
56 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (54 bp):
GAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTTGTGTGCATATTCAC
Found at i:2023732 original size:80 final size:78
Alignment explanation
Indices: 2023636--2023975 Score: 324
Period size: 80 Copynumber: 4.3 Consensus size: 78
2023626 TATAGAAAAT
** *
2023636 AAGTTCATAAAAAGAAGAACTTGTTCAACCTTTACTCGATTCTATCACAAAATGAGTTGGATCAA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTACTCGATTCCATCACAAAA-GAGTTGGATCAA
*
2023701 CATTTCCTAGAGAAA
65 CATTTCC-AGAGAAG
* * * * * * *
2023716 AAGTTCATAATGAGAAGAACTTGTTCAGCCTTGACT-TA-TCCATCACAAAAAAAGGTAGATCAG
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTACTCGATTCCATCAC-AAAAGAGTTGGATCAA
* *
2023779 TATTTCCAAAGAAG
65 CATTTCCAGAGAAG
* * * * * * *
2023793 AATTTCATAATGAGAAGAACTCGCTCAACCTCTGCTTGATTCTATCACAGAAAGAGTTGGATCAA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTACTCGATTCCATCACA-AAAGAGTTGGATCAA
*
2023858 CATTTCAAAGAGAAG
65 CATTTC-CAGAGAAG
* ** * * * *
2023873 AAGTTCATAATGAGAAGCACTTGTTCAATATGTGCTCAATTCCATCACTAAAGGAGTTGGATCAA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTACTCGATTCCATCAC-AAAAGAGTTGGATCAA
* *
2023938 CATTTTCAAAGAAG
65 CATTTCCAGAGAAG
* *
2023952 AAGTTCATAATGAAAACAACTTGT
1 AAGTTCATAATGAGAAGAACTTGT
2023976 ATCTCAAGAA
Statistics
Matches: 208, Mismatches: 46, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
77 34 0.16
78 23 0.11
79 55 0.26
80 95 0.46
81 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (78 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTACTCGATTCCATCACAAAAGAGTTGGATCAAC
ATTTCCAGAGAAG
Found at i:2025847 original size:15 final size:15
Alignment explanation
Indices: 2025816--2025844 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2025806 ATATTGTTCA
2025816 ATTTAATTTTTATTT
1 ATTTAATTTTTATTT
2025831 ATTTAA-TTTTATTT
1 ATTTAATTTTTATTT
2025845 TATATTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTAATTTTTATTT
Found at i:2039906 original size:29 final size:29
Alignment explanation
Indices: 2039873--2039929 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2039863 ATTTATATAG
2039873 ATGTTTG-TCATCGTTTT-ATTTATATAATA
1 ATGTTTGCTCAT-GTTTTAATTTAT-TAATA
*
2039902 ATGTTTGCTTATGTTTTAATTTATTAAT
1 ATGTTTGCTCATGTTTTAATTTATTAAT
2039930 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (29 bp):
ATGTTTGCTCATGTTTTAATTTATTAATA
Found at i:2040518 original size:42 final size:41
Alignment explanation
Indices: 2040471--2040561 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 41
2040461 TTTGTGAACA
* * * *
2040471 ACAAACACCGCTAAAGGTTATGTTTTTTAGCGACGTTGTTTT
1 ACAAACACCGCTAAAGGTAAAGATATTTAGCGACGTT-TTTT
* **
2040513 ACAAACACTGCTAAAGGTAAAGATATTTAGCGGTGTTTTTT
1 ACAAACACCGCTAAAGGTAAAGATATTTAGCGACGTTTTTT
2040554 ACAAACAC
1 ACAAACAC
2040562 ACCACTAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 12 0.29
42 30 0.71
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (41 bp):
ACAAACACCGCTAAAGGTAAAGATATTTAGCGACGTTTTTT
Found at i:2047106 original size:41 final size:41
Alignment explanation
Indices: 2046971--2047107 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 41
2046961 GTTTGTAAAC
* *
2046971 ACAAACGCCACTAAAGTATGAGTCTTTAGA-GGTGTTTGTAT
1 ACAAACGCCACTAAAATATGAGTCTTTA-ACGGCGTTTGTAT
* * * * *
2047012 A-ATAACTCTACTAAAATATGAATCTATAGCGGCGTTTGTAT
1 ACA-AACGCCACTAAAATATGAGTCTTTAACGGCGTTTGTAT
* * * * *
2047053 AAAAATGTCACTAAATTATGAGTCTTTAACGACGTTTGTAT
1 ACAAACGCCACTAAAATATGAGTCTTTAACGGCGTTTGTAT
2047094 ACAAACGCCACTAA
1 ACAAACGCCACTAA
2047108 TGTGCTGATA
Statistics
Matches: 74, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
40 1 0.01
41 72 0.97
42 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (41 bp):
ACAAACGCCACTAAAATATGAGTCTTTAACGGCGTTTGTAT
Found at i:2047254 original size:41 final size:41
Alignment explanation
Indices: 2047209--2047336 Score: 177
Period size: 41 Copynumber: 3.1 Consensus size: 41
2047199 CATATTACGA
* **
2047209 CATTTTTATAAAAAAGCCACTAAAGTACGAGTCAATAGCGG
1 CATTTGTATAAAAAAGCCACTAAAGTACGAGTCTTTAGCGG
*
2047250 CATTTGTATAAAAACA-CCACTAAAGTATGAGTCTTTAGCGG
1 CATTTGTATAAAAA-AGCCACTAAAGTACGAGTCTTTAGCGG
* * *
2047291 CGTTTGTATAAAAATGCCACTAAAATACGAGTCTTTAGCGG
1 CATTTGTATAAAAAAGCCACTAAAGTACGAGTCTTTAGCGG
2047332 CATTT
1 CATTT
2047337 TTTTCTTAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
41 75 0.99
42 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (41 bp):
CATTTGTATAAAAAAGCCACTAAAGTACGAGTCTTTAGCGG
Found at i:2062311 original size:2 final size:2
Alignment explanation
Indices: 2062304--2062349 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2062294 TACGAAAAGC
2062304 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
2062346 AT AT
1 AT AT
2062350 GACATGCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2065621 original size:13 final size:14
Alignment explanation
Indices: 2065585--2065622 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2065575 TTTGTGTAAA
*
2065585 ATCGTTGATCGTTG
1 ATCGTTGACCGTTG
2065599 ATCGTTGACCGTTG
1 ATCGTTGACCGTTG
*
2065613 A-CTTTGACCG
1 ATCGTTGACCG
2065623 AAAAGTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (14 bp):
ATCGTTGACCGTTG
Found at i:2079483 original size:84 final size:84
Alignment explanation
Indices: 2079376--2079541 Score: 242
Period size: 84 Copynumber: 2.0 Consensus size: 84
2079366 AATGTCCCTC
* *
2079376 CACGATAAAGCCGATAATAAAACCCAGGACATTGACCGACTTCTCACAACCCCAGGAACACAAAG
1 CACGATAAAGCCGATAATAAAACCCAGGACATCGACCGACTGCTCACAACCCCAGGAACACAAAG
*
2079441 GAGTCGACTATGAGACGTT
66 GAGCCGACTATGAGACGTT
* * * * *
2079460 CACGATAACGCCGATAATGAAACCCATGACATCGATCGACTGCTCACAACTCCAGGAACACAAAG
1 CACGATAAAGCCGATAATAAAACCCAGGACATCGACCGACTGCTCACAACCCCAGGAACACAAAG
* *
2079525 GTGCCGACTGTGAGACG
66 GAGCCGACTATGAGACG
2079542 AATGGAGCAC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.15
Consensus pattern (84 bp):
CACGATAAAGCCGATAATAAAACCCAGGACATCGACCGACTGCTCACAACCCCAGGAACACAAAG
GAGCCGACTATGAGACGTT
Found at i:2080663 original size:82 final size:80
Alignment explanation
Indices: 2080388--2080669 Score: 388
Period size: 80 Copynumber: 3.5 Consensus size: 80
2080378 CTTACATAAC
*
2080388 TAAAATAGTTCTCCATCTACATAACTAAAGAGATGAAAACAACAAACTTCGCACATAATCATAAA
1 TAAAATAGTTCTCCATCTACATAACTAAAGAGATGAAAACAAAAAACTTCGCACATAATCATAAA
2080453 CTTCTCACATTACAT
66 CTTCTCACATTACAT
*
2080468 TAAAATAGTTCTCCATCTACATAACTAAAGAGATGAAAACAAAAAACTTCGCACATAATCCTAAA
1 TAAAATAGTTCTCCATCTACATAACTAAAGAGATGAAAACAAAAAACTTCGCACATAATCATAAA
*
2080533 CTTCTCACATTATAT
66 CTTCTCACATTACAT
* * ** *
2080548 TAAAATAGTTCTCCATCTACATAACTAAAGAGATGAAAATAAAAAAATATTTCACATAATTATAA
1 TAAAATAGTTCTCCATCTACATAACTAAAGAGATGAAAACAAAAAACT-TCGCACATAATCAT-A
* * *
2080613 AACCTCTTACAGTACAT
64 AACTTCTCACATTACAT
* * *
2080630 T-AAATGAGTTCTCTATCTACAT-ACTTAAGGAGATTAAAAC
1 TAAAAT-AGTTCTCCATCTACATAAC-TAAAGAGATGAAAAC
2080670 GACAAACATT
Statistics
Matches: 181, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
80 123 0.68
81 16 0.09
82 42 0.23
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.28
Consensus pattern (80 bp):
TAAAATAGTTCTCCATCTACATAACTAAAGAGATGAAAACAAAAAACTTCGCACATAATCATAAA
CTTCTCACATTACAT
Found at i:2081085 original size:22 final size:22
Alignment explanation
Indices: 2081060--2081101 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2081050 GTTTATGAAA
* *
2081060 TTGAAAGAAAAGAAATCAAGAT
1 TTGAAAGAAAAAAAAACAAGAT
2081082 TTGAAAGAAAAAAAAACAAG
1 TTGAAAGAAAAAAAAACAAG
2081102 GTAAATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.05, G:0.17, T:0.14
Consensus pattern (22 bp):
TTGAAAGAAAAAAAAACAAGAT
Found at i:2084485 original size:19 final size:19
Alignment explanation
Indices: 2084457--2084567 Score: 80
Period size: 19 Copynumber: 5.7 Consensus size: 19
2084447 ATAACCAACA
* *
2084457 AATTCACAACCCAGTTTCG
1 AATTCGCAACACAGTTTCG
** *
2084476 AATTCGCAACAC-GAACTCC
1 AATTCGCAACACAG-TTTCG
*
2084495 AATTTCGCAACATAGTTTCCG
1 AA-TTCGCAACACAGTTT-CG
* * *
2084516 AATTCGCAACTCGAATTTGG
1 AATTCGCAACAC-AGTTTCG
* *
2084536 AATTCGCAACACAATTTGG
1 AATTCGCAACACAGTTTCG
2084555 AATTCGCAACACA
1 AATTCGCAACACA
2084568 TAAGTCGAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
18 1 0.01
19 34 0.47
20 30 0.41
21 8 0.11
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (19 bp):
AATTCGCAACACAGTTTCG
Found at i:2084579 original size:20 final size:19
Alignment explanation
Indices: 2084535--2084580 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2084525 CTCGAATTTG
** *
2084535 GAATTCGCAACACAATTTG
1 GAATTCGCAACACAAAGTC
2084554 GAATTCGCAACACATAAGTC
1 GAATTCGCAACACA-AAGTC
2084574 GAATTCG
1 GAATTCG
2084581 TAACTCGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (19 bp):
GAATTCGCAACACAAAGTC
Found at i:2085672 original size:24 final size:24
Alignment explanation
Indices: 2085621--2085674 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2085611 GTATTCAAAA
* *
2085621 TTTGATCTTGGTCAATACTTGGAC
1 TTTGATCTTGGTCAATACTCGCAC
*
2085645 TTTGATCTTGGTCAATACTCGCAG
1 TTTGATCTTGGTCAATACTCGCAC
2085669 TTTGAT
1 TTTGAT
2085675 GATATTTCAG
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:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGCAC
Found at i:2088537 original size:27 final size:27
Alignment explanation
Indices: 2088502--2088554 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2088492 TCACAACTCA
* * *
2088502 AATTCGTAACTCGAAAATTGAATTCGT
1 AATTCGTAACACAAAAATTAAATTCGT
*
2088529 AATTTGTAACACAAAAATTAAATTCG
1 AATTCGTAACACAAAAATTAAATTCG
2088555 CAACACGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (27 bp):
AATTCGTAACACAAAAATTAAATTCGT
Found at i:2088653 original size:20 final size:20
Alignment explanation
Indices: 2088628--2088696 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
2088618 AGTTCAATTT
2088628 TCGAGTTGCCAATTTTAATA
1 TCGAGTTGCCAATTTTAATA
2088648 TCGAGTTG-CAA--TT--T-
1 TCGAGTTGCCAATTTTAATA
* *
2088662 TCGTGTTGCGAATTTTAATA
1 TCGAGTTGCCAATTTTAATA
*
2088682 TCGAGTTGCGAATTT
1 TCGAGTTGCCAATTT
2088697 GATTTTTGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 7 0.17
15 3 0.08
17 4 0.10
19 4 0.10
20 22 0.55
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (20 bp):
TCGAGTTGCCAATTTTAATA
Found at i:2088660 original size:34 final size:34
Alignment explanation
Indices: 2088617--2088696 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
2088607 CGTAACTCGA
2088617 GAGTT-CAATTTTCGAGTTGCCAATTTTAATATC
1 GAGTTGCAATTTTCGAGTTGCCAATTTTAATATC
* *
2088650 GAGTTGCAATTTTCGTGTTGCGAATTTTAATATC
1 GAGTTGCAATTTTCGAGTTGCCAATTTTAATATC
2088684 GAGTTGCGAATTT
1 GAGTTGC-AATTT
2088697 GATTTTTGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 5 0.12
34 33 0.77
35 5 0.12
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (34 bp):
GAGTTGCAATTTTCGAGTTGCCAATTTTAATATC
Found at i:2088707 original size:20 final size:20
Alignment explanation
Indices: 2088684--2088722 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2088674 TTTTAATATC
*
2088684 GAGTTGCGAATTTGATTTTT
1 GAGTTACGAATTTGATTTTT
2088704 GAGTTACGAATTTGATTTT
1 GAGTTACGAATTTGATTTT
2088723 CTTAAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GAGTTACGAATTTGATTTTT
Found at i:2088959 original size:24 final size:24
Alignment explanation
Indices: 2088927--2088988 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
2088917 CCTTGAATAC
2088927 ATATTCAACTAGTTTAAATGATGG
1 ATATTCAACTAGTTTAAATGATGG
*
2088951 ATATTCAACTAGTTTAGATGATGG
1 ATATTCAACTAGTTTAAATGATGG
*
2088975 ATATTGAACTAGTT
1 ATATTCAACTAGTT
2088989 GAAAAATCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (24 bp):
ATATTCAACTAGTTTAAATGATGG
Found at i:2090904 original size:21 final size:21
Alignment explanation
Indices: 2090878--2090987 Score: 84
Period size: 21 Copynumber: 5.2 Consensus size: 21
2090868 AATGTGGATT
2090878 CTGAACGATGCAG-GGTAGATC
1 CTGAACGATG-AGAGGTAGATC
*
2090899 CTGAACGATGAGAGGTGGATC
1 CTGAACGATGAGAGGTAGATC
* *
2090920 TTGAACGATGGGA-GT-GACCTC
1 CTGAACGATGAGAGGTAGA--TC
* *
2090941 TTGAACGATGAGAGGTAAATC
1 CTGAACGATGAGAGGTAGATC
* * *
2090962 CTAAACAATG-GTAGGTGGATC
1 CTGAACGATGAG-AGGTAGATC
2090983 CTGAA
1 CTGAA
2090988 TAATGGTAGG
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
20 5 0.07
21 62 0.86
22 2 0.03
23 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (21 bp):
CTGAACGATGAGAGGTAGATC
Found at i:2090992 original size:21 final size:21
Alignment explanation
Indices: 2090959--2091003 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2090949 TGAGAGGTAA
2090959 ATCCTAAACAATGGTAGGTGG
1 ATCCTAAACAATGGTAGGTGG
* *
2090980 ATCCTGAATAATGGTAGGTGG
1 ATCCTAAACAATGGTAGGTGG
2091001 ATC
1 ATC
2091004 AAGCTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (21 bp):
ATCCTAAACAATGGTAGGTGG
Found at i:2091363 original size:21 final size:21
Alignment explanation
Indices: 2091339--2091550 Score: 216
Period size: 21 Copynumber: 10.1 Consensus size: 21
2091329 TGAAACAATC
*
2091339 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* **
2091360 TCACATAAAGCACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
*
2091381 TCACGTAAAGCACATACCTCA
1 TCACGTAAAGCACCTACCTCA
**
2091402 TCACGTAAAGCA-CTATTATCA
1 TCACGTAAAGCACCTA-CCTCA
*
2091423 TCACGTAAAGTACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* * *
2091444 CCACGTAAAGTAACTACCTCA
1 TCACGTAAAGCACCTACCTCA
**
2091465 TCACGTAAAGCACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
*
2091486 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
*
2091507 TCACGTAAAGTA-CTGACCTCA
1 TCACGTAAAGCACCT-ACCTCA
*
2091528 TCACGTAAAGCACCTAACTCA
1 TCACGTAAAGCACCTACCTCA
2091549 TC
1 TC
2091551 CCGTGGAGGT
Statistics
Matches: 156, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.03
21 144 0.92
22 7 0.04
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:2091712 original size:21 final size:21
Alignment explanation
Indices: 2091649--2091790 Score: 70
Period size: 21 Copynumber: 7.0 Consensus size: 21
2091639 GTGATGAAAT
* *
2091649 AGGTGATGGATCTCGATGTCG
1 AGGTGATAGATCTCGGTGTCG
** * *
2091670 AGGTG-TA-AAGTCGG-CTAG
1 AGGTGATAGATCTCGGTGTCG
*
2091688 AGGTGATTGATCTCGGTGTCG
1 AGGTGATAGATCTCGGTGTCG
*
2091709 AGGTG-TAGA-GTCGGCTG--G
1 AGGTGATAGATCTCGG-TGTCG
*
2091727 AGGTGATGGATCTCGGTGTCG
1 AGGTGATAGATCTCGGTGTCG
* *
2091748 AGGTG-TAGA-ATCGG-CTCAATG
1 AGGTGATAGATCTCGGTGTC---G
*
2091769 AGGTGATGGATCTCGGTGTCG
1 AGGTGATAGATCTCGGTGTCG
2091790 A
1 A
2091791 AGTGGAGAAT
Statistics
Matches: 86, Mismatches: 21, Indels: 28
0.64 0.16 0.21
Matches are distributed among these distances:
18 15 0.17
19 18 0.21
20 18 0.21
21 26 0.30
22 3 0.03
23 4 0.05
24 2 0.02
ACGTcount: A:0.20, C:0.13, G:0.40, T:0.27
Consensus pattern (21 bp):
AGGTGATAGATCTCGGTGTCG
Found at i:2091785 original size:42 final size:42
Alignment explanation
Indices: 2091649--2091937 Score: 367
Period size: 42 Copynumber: 7.0 Consensus size: 42
2091639 GTGATGAAAT
* * *
2091649 AGGTGATGGATCTCGATGTCGAGGTGTA-AAGTCGGCT--A-G
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAA-TCGGCTCGATG
* * * *
2091688 AGGTGATTGATCTCGGTGTCGAGGTGTAGAGTCGGCT-G--G
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
* * *
2091727 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCAATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
*
2091769 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
* *
2091811 AGGTGATGGATCTCGGTGTCGAAGTAGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
* **
2091853 ATGTGATGGATCTCATTGTCGAAGTGGAGAATCGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
*
2091895 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
2091937 A
1 A
2091938 AAAAGTGGGG
Statistics
Matches: 225, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 68 0.30
40 1 0.00
42 156 0.69
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGGCTCGATG
Found at i:2093412 original size:20 final size:20
Alignment explanation
Indices: 2093389--2093451 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
2093379 TTTATTTCAA
*
2093389 GAAAATCAAATTCGTAACTC
1 GAAAATCAAATTCGCAACTC
*
2093409 GAAAATGAAATTCGCAACTC
1 GAAAATCAAATTCGCAACTC
** **
2093429 GAATTTTGAATTCGCAACTC
1 GAAAATCAAATTCGCAACTC
2093449 GAA
1 GAA
2093452 TTTCATTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACTC
Found at i:2093452 original size:20 final size:20
Alignment explanation
Indices: 2093417--2093454 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2093407 TCGAAAATGA
2093417 AATTCGCAACTCGAATTTTG
1 AATTCGCAACTCGAATTTTG
2093437 AATTCGCAACTCGAATTT
1 AATTCGCAACTCGAATTT
2093455 CATTTTCGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
AATTCGCAACTCGAATTTTG
Found at i:2094125 original size:20 final size:20
Alignment explanation
Indices: 2094102--2094146 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2094092 CGAAAATCGA
*
2094102 GTTGCGAAAATGAAATTCGC
1 GTTGCGAAAATGAAACTCGC
*
2094122 GTTGCGAAATTGAAACTCGC
1 GTTGCGAAAATGAAACTCGC
*
2094142 TTTGC
1 GTTGC
2094147 AAATTCGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
GTTGCGAAAATGAAACTCGC
Found at i:2094480 original size:15 final size:14
Alignment explanation
Indices: 2094462--2094491 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2094452 ATAAAATGAA
2094462 ATAATATAATATAAT
1 ATAATATAA-ATAAT
2094477 ATAATATAAATAAT
1 ATAATATAAATAAT
2094491 A
1 A
2094492 GAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATATAAATAAT
Found at i:2095192 original size:179 final size:179
Alignment explanation
Indices: 2094892--2095249 Score: 716
Period size: 179 Copynumber: 2.0 Consensus size: 179
2094882 TAAGAGCAAA
2094892 TCTGAATCAACAAATGAAATATTTTTCAAATCCGTTGATTTCTTGTCTTCATCCTCTAGTTCCCT
1 TCTGAATCAACAAATGAAATATTTTTCAAATCCGTTGATTTCTTGTCTTCATCCTCTAGTTCCCT
2094957 ATACAAATCATCAAAAAAATTAGTTTCCATAAATCTATCCACAAAAGGTTCATAAATATCAATGA
66 ATACAAATCATCAAAAAAATTAGTTTCCATAAATCTATCCACAAAAGGTTCATAAATATCAATGA
2095022 AGCTAATGTTTTCCATAGAACTAGGATATTTCATTTCTTTGTAAACAAC
131 AGCTAATGTTTTCCATAGAACTAGGATATTTCATTTCTTTGTAAACAAC
2095071 TCTGAATCAACAAATGAAATATTTTTCAAATCCGTTGATTTCTTGTCTTCATCCTCTAGTTCCCT
1 TCTGAATCAACAAATGAAATATTTTTCAAATCCGTTGATTTCTTGTCTTCATCCTCTAGTTCCCT
2095136 ATACAAATCATCAAAAAAATTAGTTTCCATAAATCTATCCACAAAAGGTTCATAAATATCAATGA
66 ATACAAATCATCAAAAAAATTAGTTTCCATAAATCTATCCACAAAAGGTTCATAAATATCAATGA
2095201 AGCTAATGTTTTCCATAGAACTAGGATATTTCATTTCTTTGTAAACAAC
131 AGCTAATGTTTTCCATAGAACTAGGATATTTCATTTCTTTGTAAACAAC
2095250 AAATTTAACA
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
179 179 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (179 bp):
TCTGAATCAACAAATGAAATATTTTTCAAATCCGTTGATTTCTTGTCTTCATCCTCTAGTTCCCT
ATACAAATCATCAAAAAAATTAGTTTCCATAAATCTATCCACAAAAGGTTCATAAATATCAATGA
AGCTAATGTTTTCCATAGAACTAGGATATTTCATTTCTTTGTAAACAAC
Found at i:2100267 original size:57 final size:57
Alignment explanation
Indices: 2100182--2100338 Score: 226
Period size: 57 Copynumber: 2.8 Consensus size: 57
2100172 TACATTCAAA
*
2100182 AATTCCCAAAATATCACCTTTTTCAAAATAATTCCCAGAATGTAACATTTTTCAAAAT
1 AATTCCCAAAATATCACCTTTTTCAAAATATTTCCCAGAATGTAAC-TTTTTCAAAAT
** * *
2100240 AATTCCCAAAATGCCA-CTTTTTCAAAATATTTCCCAGAATATCACTTTTTCAAAAT
1 AATTCCCAAAATATCACCTTTTTCAAAATATTTCCCAGAATGTAACTTTTTCAAAAT
* * *
2100296 ATTTCCCAAAATATCACCTTTTTTAAAATATTTCCCATAATGT
1 AATTCCCAAAATATCACCTTTTTCAAAATATTTCCCAGAATGT
2100339 CACCAGGTCG
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
56 24 0.28
57 49 0.56
58 14 0.16
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (57 bp):
AATTCCCAAAATATCACCTTTTTCAAAATATTTCCCAGAATGTAACTTTTTCAAAAT
Found at i:2100342 original size:29 final size:29
Alignment explanation
Indices: 2100176--2100342 Score: 198
Period size: 29 Copynumber: 5.9 Consensus size: 29
2100166 ATAGTCTACA
2100176 TTCAAAA-A-TTCCCAAAATATCACCTTT
1 TTCAAAATATTTCCCAAAATATCACCTTT
* * * * *
2100203 TTCAAAATAATTCCCAGAATGTAACATTT
1 TTCAAAATATTTCCCAAAATATCACCTTT
* **
2100232 TTCAAAATAATTCCCAAAATGCCA-CTTT
1 TTCAAAATATTTCCCAAAATATCACCTTT
*
2100260 TTCAAAATATTTCCCAGAATATCA-CTTT
1 TTCAAAATATTTCCCAAAATATCACCTTT
2100288 TTCAAAATATTTCCCAAAATATCACCTTT
1 TTCAAAATATTTCCCAAAATATCACCTTT
* * *
2100317 TTTAAAATATTTCCCATAATGTCACC
1 TTCAAAATATTTCCCAAAATATCACC
2100343 AGGTCGGGTC
Statistics
Matches: 121, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 7 0.06
28 51 0.42
29 63 0.52
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (29 bp):
TTCAAAATATTTCCCAAAATATCACCTTT
Found at i:2100408 original size:27 final size:22
Alignment explanation
Indices: 2100344--2100396 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
2100334 AATGTCACCA
*
2100344 GGTCGGGTCTGTCAACGGGACG
1 GGTCGGGTCGGTCAACGGGACG
*
2100366 GGTCGGGTCGGTCAACGGGTCG
1 GGTCGGGTCGGTCAACGGGACG
2100388 GGTCGGGTC
1 GGTCGGGTC
2100397 AGACCGATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCGGTCAACGGGACG
Found at i:2104250 original size:18 final size:17
Alignment explanation
Indices: 2104196--2104244 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2104186 TTGGACTCCT
* *
2104196 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
2104214 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
2104232 AGTGCATTCGATG
1 AGTGCA-TCGATG
2104245 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:2104348 original size:64 final size:62
Alignment explanation
Indices: 2104196--2104358 Score: 159
Period size: 64 Copynumber: 2.5 Consensus size: 62
2104186 TTGGACTCCT
* * * *
2104196 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCC
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAG-C
* * ** *
2104259 TGGTGCATCGATGAATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAG
1 -AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAA--AAAT-AG
2104324 -
62 C
*
2104324 AGTGCATCGATGCATGGAGAGTGCATGGAATGCAT
1 AGTGCATCGATGCATGGAGAGTGCATCG-ATGCAT
2104359 TCGATGTTTC
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
63 1 0.01
64 67 0.84
65 6 0.08
66 4 0.05
67 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (62 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGC
Found at i:2104402 original size:21 final size:21
Alignment explanation
Indices: 2104378--2104417 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2104368 CAATTTATTC
2104378 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
2104399 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
2104418 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Done.