Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 136 of 189
Found at i:39559379 original size:21 final size:23
Alignment explanation
Indices: 39559334--39559380 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39559324 TCACCTGCAA
* *
39559334 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
39559357 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
39559378 TAA
1 TAA
39559381 TAAATGAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:39567861 original size:44 final size:44
Alignment explanation
Indices: 39567798--39567886 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
39567788 TCAGAATATG
39567798 TAAGGAATGATAAGAACCCTAGAAATTGGGGATTTAAGGCCGAT
1 TAAGGAATGATAAGAACCCTAGAAATTGGGGATTTAAGGCCGAT
39567842 TAAGGAATGATAAGAACCCTAGAAATTGGGGATTTAAGGCCGAT
1 TAAGGAATGATAAGAACCCTAGAAATTGGGGATTTAAGGCCGAT
39567886 T
1 T
39567887 CCTTGCTGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (44 bp):
TAAGGAATGATAAGAACCCTAGAAATTGGGGATTTAAGGCCGAT
Found at i:39572325 original size:20 final size:20
Alignment explanation
Indices: 39572300--39572344 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
39572290 GTCTTAACCG
39572300 AATTAATTAG-GTTTTAG-TTT
1 AATTAATT-GTGTTTT-GTTTT
39572320 AATTAATTGTGTTTTGTTTT
1 AATTAATTGTGTTTTGTTTT
39572340 AATTA
1 AATTA
39572345 TAAGGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (20 bp):
AATTAATTGTGTTTTGTTTT
Found at i:39573287 original size:23 final size:23
Alignment explanation
Indices: 39573261--39573318 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
39573251 ATTTGGTTTG
39573261 TTTCGTACCAAAATCTC-ATACCA
1 TTTCGTACCAAAATC-CAATACCA
* *
39573284 TTTCGTACCAACATCCAATTCCA
1 TTTCGTACCAAAATCCAATACCA
*
39573307 TTTCTTACCAAA
1 TTTCGTACCAAA
39573319 CACCAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (23 bp):
TTTCGTACCAAAATCCAATACCA
Found at i:41151973 original size:11 final size:11
Alignment explanation
Indices: 41151957--41151997 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
41151947 TAGTTTCTTC
41151957 AAAAAAATTCAA
1 AAAAAAATTC-A
41151969 AAAAAAATTCA
1 AAAAAAATTCA
41151980 AAAAAAATTCA
1 AAAAAAATTCA
41151991 AAAAAAA
1 AAAAAAA
41151998 ATTTGGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:41151974 original size:12 final size:12
Alignment explanation
Indices: 41151957--41152000 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
41151947 TAGTTTCTTC
41151957 AAAAAAATTCAA
1 AAAAAAATTCAA
41151969 AAAAAAATTC-A
1 AAAAAAATTCAA
41151980 AAAAAAATTCAA
1 AAAAAAATTCAA
41151992 AAAAAAATT
1 AAAAAAATT
41152001 TGGTTTCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:41151987 original size:23 final size:23
Alignment explanation
Indices: 41151957--41152000 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
41151947 TAGTTTCTTC
41151957 AAAAAAATTCAAAAAAAAATTCA
1 AAAAAAATTCAAAAAAAAATTCA
41151980 AAAAAAATTCAAAAAAAAATT
1 AAAAAAATTCAAAAAAAAATT
41152001 TGGTTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAAAATTCAAAAAAAAATTCA
Found at i:41155705 original size:12 final size:12
Alignment explanation
Indices: 41155688--41155736 Score: 82
Period size: 12 Copynumber: 4.1 Consensus size: 12
41155678 TAGTAGTTTC
41155688 TCAAAAAAAAAT
1 TCAAAAAAAAAT
41155700 TCAAAAAAAAAAT
1 TC-AAAAAAAAAT
41155713 TC-AAAAAAAAT
1 TCAAAAAAAAAT
41155724 TCAAAAAAAAAT
1 TCAAAAAAAAAT
41155736 T
1 T
41155737 TGTTTCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.31
12 12 0.34
13 12 0.34
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.18
Consensus pattern (12 bp):
TCAAAAAAAAAT
Found at i:41155707 original size:11 final size:11
Alignment explanation
Indices: 41155691--41155733 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
41155681 TAGTTTCTCA
41155691 AAAAAAAATTC
1 AAAAAAAATTC
41155702 AAAAAAAAAATTC
1 --AAAAAAAATTC
41155715 AAAAAAAATTC
1 AAAAAAAATTC
41155726 AAAAAAAA
1 AAAAAAAA
41155734 ATTTGTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:41155708 original size:13 final size:13
Alignment explanation
Indices: 41155690--41155734 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
41155680 GTAGTTTCTC
41155690 AAAAAAAAATTCA
1 AAAAAAAAATTCA
41155703 AAAAAAAAATTC-
1 AAAAAAAAATTCA
41155715 -AAAAAAAATTCA
1 AAAAAAAAATTCA
41155727 AAAAAAAA
1 AAAAAAAA
41155735 TTTGTTTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.37
13 19 0.63
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:41155794 original size:13 final size:13
Alignment explanation
Indices: 41155776--41155822 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
41155766 ATCAAGTTGA
41155776 AAAAAAAATTGTG
1 AAAAAAAATTGTG
41155789 AAAAAAAATTGTG
1 AAAAAAAATTGTG
*
41155802 -AAAAAATTTCGTG
1 AAAAAAAATT-GTG
41155815 AAAAAAAA
1 AAAAAAAA
41155823 GAAAGAAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 8 0.27
13 16 0.53
14 6 0.20
ACGTcount: A:0.64, C:0.02, G:0.13, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTGTG
Found at i:41163645 original size:19 final size:18
Alignment explanation
Indices: 41163609--41163648 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41163599 TTTCCACTCG
*
41163609 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
41163627 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
41163646 TTT
1 TTT
41163649 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:41164720 original size:14 final size:14
Alignment explanation
Indices: 41164703--41164749 Score: 80
Period size: 13 Copynumber: 3.5 Consensus size: 14
41164693 CTAGCTTTTC
41164703 TTTTTTTT-ACAAT
1 TTTTTTTTCACAAT
41164716 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
41164730 TTTTTTTTCA-AAT
1 TTTTTTTTCACAAT
41164743 TTTTTTT
1 TTTTTTT
41164750 CAACTTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 18 0.55
14 15 0.45
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:41164750 original size:12 final size:12
Alignment explanation
Indices: 41164703--41164752 Score: 64
Period size: 12 Copynumber: 3.9 Consensus size: 12
41164693 CTAGCTTTTC
*
41164703 TTTTTTTTACAAT
1 TTTTTTTT-CAAA
41164716 TTTTTTTTCACAA
1 TTTTTTTTCA-AA
41164729 TTTTTTTTTCAAA
1 -TTTTTTTTCAAA
41164742 TTTTTTTTCAA
1 TTTTTTTTCAA
41164753 CTTGATATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
12 13 0.38
13 11 0.32
14 10 0.29
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:41164808 original size:12 final size:13
Alignment explanation
Indices: 41164788--41164823 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
41164778 AATGGAAACA
41164788 AATTTTTTTTTTG
1 AATTTTTTTTTTG
41164801 AATTTTTTTTTTG
1 AATTTTTTTTTTG
41164814 AATTTTTTTT
1 AATTTTTTTT
41164824 CGAGAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:41170899 original size:52 final size:52
Alignment explanation
Indices: 41170816--41170916 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
41170806 TAAGGCAACG
* * *
41170816 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
41170868 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAA
41170917 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCAGTTGAAGCTCAAACAA
Found at i:41175967 original size:37 final size:37
Alignment explanation
Indices: 41175917--41175995 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41175907 TTATTACGAA
* * * *
41175917 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAAGCCCCACACGAAGTCATCGG
*
41175954 GTCTTACCCGGACAAAAGCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAAGCCCCACACGAAGTCATCGG
41175991 GTCTT
1 GTCTT
41175996 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACAAAAGCCCCACACGAAGTCATCGG
Found at i:41176176 original size:47 final size:47
Alignment explanation
Indices: 41176114--41176387 Score: 467
Period size: 47 Copynumber: 5.8 Consensus size: 47
41176104 CCCTTCGGGA
* * * * *
41176114 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCCTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41176161 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41176208 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41176255 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41176302 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41176349 CTTATCACATATATATACACTTTCACATTCATCACATCG
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCG
41176388 AATCCTAAAT
Statistics
Matches: 216, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
47 187 0.87
49 29 0.13
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41183016 original size:12 final size:12
Alignment explanation
Indices: 41183001--41183042 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
41182991 AATACAAAAT
41183001 TTTTTTTTTGAA
1 TTTTTTTTTGAA
41183013 TTTTTTTTTGAA
1 TTTTTTTTTGAA
41183025 -TTTTTTTTGAA
1 TTTTTTTTTGAA
41183036 TTTTTTT
1 TTTTTTT
41183043 GATTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:41183018 original size:11 final size:11
Alignment explanation
Indices: 41183002--41183052 Score: 79
Period size: 10 Copynumber: 4.7 Consensus size: 11
41182992 ATACAAAATT
41183002 TTTTTTTTGAA
1 TTTTTTTTGAA
41183013 TTTTTTTTTGAA
1 -TTTTTTTTGAA
41183025 TTTTTTTTGAA
1 TTTTTTTTGAA
41183036 -TTTTTTTG-A
1 TTTTTTTTGAA
41183045 TTTTTTTT
1 TTTTTTTT
41183053 ACAATACCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 1 0.03
10 15 0.39
11 11 0.29
12 11 0.29
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:41183051 original size:12 final size:11
Alignment explanation
Indices: 41183001--41183052 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
41182991 AATACAAAAT
41183001 TTTTTTTTTGAA
1 TTTTTTTTTG-A
41183013 TTTTTTTTTGA
1 TTTTTTTTTGA
*
41183024 ATTTTTTTTGA
1 TTTTTTTTTGA
*
41183035 -ATTTTTTTGA
1 TTTTTTTTTGA
41183045 TTTTTTTT
1 TTTTTTTT
41183053 ACAATACCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.25
11 17 0.47
12 10 0.28
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:41183052 original size:13 final size:12
Alignment explanation
Indices: 41182999--41183052 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
41182989 TGAATACAAA
41182999 ATTTTTTTTTTG
1 ATTTTTTTTTTG
*
41183011 AATTTTTTTTTG
1 ATTTTTTTTTTG
*
41183023 A-ATTTTTTTTG
1 ATTTTTTTTTTG
*
41183034 A--ATTTTTTTG
1 ATTTTTTTTTTG
41183044 ATTTTTTTT
1 ATTTTTTTT
41183053 ACAATACCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.25
11 10 0.28
12 17 0.47
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
ATTTTTTTTTTG
Found at i:41200594 original size:24 final size:24
Alignment explanation
Indices: 41200570--41200616 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
41200560 AAACTACTTC
41200570 TAAAAAAAACTCAAGAGAGAATTCT
1 TAAAAAAAACTCAA-AGAGAATTCT
** *
41200595 TGGAGAAAACTCAAAGAGAATT
1 TAAAAAAAACTCAAAGAGAATT
41200617 TTCACTCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAAAAAACTCAAAGAGAATTCT
Found at i:41217171 original size:23 final size:21
Alignment explanation
Indices: 41217136--41217179 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
41217126 GGCTGTTAAA
*
41217136 AAAAGGAGCTTAAAGATCATT
1 AAAAGGAGCTTAAAGAGCATT
41217157 AAAAGGAGTCTTTAAAGAGCATT
1 AAAAGGAG-C-TTAAAGAGCATT
41217180 TTATGCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (21 bp):
AAAAGGAGCTTAAAGAGCATT
Found at i:41219493 original size:19 final size:18
Alignment explanation
Indices: 41219457--41219496 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41219447 TTTCCACTCG
*
41219457 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
41219475 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
41219494 TTT
1 TTT
41219497 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:41220566 original size:15 final size:14
Alignment explanation
Indices: 41220546--41220582 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
41220536 ACTAGCTCTA
41220546 TTTTTTTTTCATAAT
1 TTTTTTTTTCA-AAT
41220561 TTTTTTTTTCAAAT
1 TTTTTTTTTCAAAT
41220575 TTTTTTTT
1 TTTTTTTT
41220583 CACAACTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTTTTCAAAT
Found at i:41220582 original size:13 final size:14
Alignment explanation
Indices: 41220545--41220584 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
41220535 AACTAGCTCT
41220545 ATTTTTTTTTCATA
1 ATTTTTTTTTCATA
41220559 ATTTTTTTTTTCA-A
1 A-TTTTTTTTTCATA
41220573 ATTTTTTTTTCA
1 ATTTTTTTTTCA
41220585 CAACTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.44
14 3 0.12
15 11 0.44
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTTTTTTCATA
Found at i:41227847 original size:15 final size:15
Alignment explanation
Indices: 41227827--41227857 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41227817 CCAACCTTCA
*
41227827 AATTTTAGGTCAATT
1 AATTTTACGTCAATT
41227842 AATTTTACGTCAATT
1 AATTTTACGTCAATT
41227857 A
1 A
41227858 TACATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (15 bp):
AATTTTACGTCAATT
Found at i:41228931 original size:11 final size:11
Alignment explanation
Indices: 41228915--41228941 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41228905 TAGAAATTAG
41228915 TTTGTGAAACT
1 TTTGTGAAACT
41228926 TTTGTGAAACT
1 TTTGTGAAACT
41228937 TTTGT
1 TTTGT
41228942 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:41230447 original size:91 final size:91
Alignment explanation
Indices: 41230325--41230531 Score: 299
Period size: 91 Copynumber: 2.3 Consensus size: 91
41230315 TTGATTTTAG
* * *
41230325 TAAATTCATATAATACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTATA
1 TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
* *
41230390 TTTAAT-ATTAATTATTTTAAATTGTA
66 TGTAATAATT-ATTATTTTAAATTATA
* * *
41230416 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
41230481 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * *
41230507 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAATAAAATTTATTA
41230532 GTTATAATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 100 0.97
92 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:41230706 original size:15 final size:15
Alignment explanation
Indices: 41230671--41230722 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41230661 TTAAGAATTT
*
41230671 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41230685 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41230699 TATTTAATAATAAT-
1 TATTTAATTATAATA
41230713 TATGTTAATT
1 TAT-TTAATT
41230723 TTATTTTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41230767 original size:119 final size:120
Alignment explanation
Indices: 41230546--41230838 Score: 481
Period size: 119 Copynumber: 2.5 Consensus size: 120
41230536 TAATATTTTA
* * *
41230546 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTTTATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTTTATTT
*
41230610 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41230666 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTTATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTTTATTTT
*
41230730 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41230785 AA---T-TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
41230839 ATGATTAAAT
Statistics
Matches: 165, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
115 44 0.27
116 3 0.02
117 3 0.02
119 66 0.40
120 47 0.28
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTTTATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:41230786 original size:16 final size:16
Alignment explanation
Indices: 41230755--41230796 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
41230745 ATGGTTTGAG
41230755 TAAATTCATATAAGAATAT
1 TAAATT-AT-TAAGAAT-T
41230774 T-AATTATTAAGAATT
1 TAAATTATTAAGAATT
41230789 TAAATTAT
1 TAAATTAT
41230797 ATATTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 13 0.59
17 2 0.09
18 4 0.18
19 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (16 bp):
TAAATTATTAAGAATT
Found at i:41230814 original size:16 final size:16
Alignment explanation
Indices: 41230795--41230836 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41230785 AATTTAAATT
*
41230795 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41230811 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41230826 AT-TATGTTTAA
1 ATATAT-TTTAA
41230837 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41230821 original size:15 final size:15
Alignment explanation
Indices: 41230773--41230827 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
41230763 TATAAGAATA
*
41230773 TTAATTATTAAGA-AT
1 TTAATTA-TAATATAT
41230788 TTAAATTAT-ATAT-T
1 TT-AATTATAATATAT
41230802 TTAATTATAATATAT
1 TTAATTATAATATAT
*
41230817 TTAATAATAAT
1 TTAATTATAAT
41230828 TATGTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 6 0.18
14 9 0.26
15 14 0.41
16 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAATTATAATATAT
Found at i:41230950 original size:147 final size:143
Alignment explanation
Indices: 41230774--41231042 Score: 459
Period size: 147 Copynumber: 1.9 Consensus size: 143
41230764 ATAAGAATAT
* *
41230774 TAATTATTAAGAATTTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 TAATTATTAAGAATTTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAAT
*
41230839 ATGATTAAATTATTTATTATTGATATTAATAATCTTGTTAAAATTTAAATAA-AATAATTTACCA
66 ATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTT-AATAACAATAATTTACCA
41230903 AAACAAAATTCTGC
130 AAACAAAATTCTGC
41230917 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
1 TAATTATTAAGAA---T-TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
41230982 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAATAACAATAA
62 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAATAACAATAA
41231043 CAATAATCAT
Statistics
Matches: 118, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
143 13 0.11
146 6 0.05
147 99 0.84
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (143 bp):
TAATTATTAAGAATTTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAAT
ATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAATAACAATAATTTACCAA
AACAAAATTCTGC
Found at i:41230957 original size:18 final size:17
Alignment explanation
Indices: 41230929--41230963 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41230919 ATTATTAAGA
*
41230929 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41230946 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41230964 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41231212 original size:45 final size:44
Alignment explanation
Indices: 41231123--41231217 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
41231113 TTACACCTCT
*
41231123 ATTACATTCAACCAAACACAGGATTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
*** *
41231167 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC
*
41231212 AGTACA
1 ATTACA
41231218 CCTCTATTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 20 0.45
45 24 0.55
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
Found at i:41231219 original size:16 final size:16
Alignment explanation
Indices: 41231198--41231265 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
41231188 GATTTGCTAT
* *
41231198 TACACCTCTATTCCAG
1 TACACCTCTAATCCAA
* *
41231214 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
41231230 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
41231246 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
41231262 TACA
1 TACA
41231266 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.32, C:0.37, G:0.01, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:41235100 original size:11 final size:11
Alignment explanation
Indices: 41235067--41235100 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
41235057 CTTCTAAATT
41235067 TTTTTTTC-AA
1 TTTTTTTCGAA
41235077 TTTTTTTCG-A
1 TTTTTTTCGAA
41235087 TTTTTTTCGAA
1 TTTTTTTCGAA
41235098 TTT
1 TTT
41235101 CCTCTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.71
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:41248274 original size:39 final size:40
Alignment explanation
Indices: 41248109--41248333 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
41248099 GCTACTCGTT
* *
41248109 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
41248149 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41248189 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * * * *
41248229 CCAATGCCTTCAGG-CTTAGCCTGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * ** *
41248268 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCAGTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
41248309 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41248334 CATCATTCGA
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 115 0.72
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41249528 original size:56 final size:56
Alignment explanation
Indices: 41249461--41249580 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
41249451 TATTAGTTTA
41249461 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
41249517 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
41249573 TTTCCCAT
1 TTGCCCAT
41249581 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:41260977 original size:16 final size:16
Alignment explanation
Indices: 41260952--41260982 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41260942 TTAGGAGCTG
*
41260952 CTAATTAATTTGTCTC
1 CTAATAAATTTGTCTC
41260968 CTAATAAATTTGTCT
1 CTAATAAATTTGTCT
41260983 TAGCCGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (16 bp):
CTAATAAATTTGTCTC
Found at i:41264269 original size:14 final size:14
Alignment explanation
Indices: 41264250--41264304 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
41264240 TCCATTGAGC
41264250 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
**
41264264 GAGAAAACCAAAAA
1 GAGAAAAAGAAAAA
*
41264278 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
41264293 GAAAGAAAAGAA
1 GAGA-AAAAGAA
41264305 TGACGAAAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 15 0.47
15 17 0.53
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:41265526 original size:46 final size:46
Alignment explanation
Indices: 41265473--41265566 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
41265463 CAAAGAAAAG
*
41265473 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
41265519 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
41265565 AC
1 AC
41265567 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:41280982 original size:26 final size:25
Alignment explanation
Indices: 41280967--41281021 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
41280957 GAGAGAAAAC
41280967 GAAA-AAGAAAATAAAAATGAGAAA
1 GAAAGAAGAAAATAAAAATGAGAAA
* *
41280991 GAAAGAAGAAAAGAAAGATCGAGAGAA
1 GAAAGAAGAAAATAAAAAT-GAGA-AA
41281018 GAAA
1 GAAA
41281022 AATTGAGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 12 0.46
26 4 0.15
27 6 0.23
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.05
Consensus pattern (25 bp):
GAAAGAAGAAAATAAAAATGAGAAA
Found at i:41281007 original size:12 final size:12
Alignment explanation
Indices: 41280954--41281008 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
41280944 CTATGTAACA
41280954 AAAGAGAGAAAACG
1 AAAGA-AGAAAA-G
*
41280968 AAA-AAGAAAAT
1 AAAGAAGAAAAG
41280979 AAA-AATGAGAAAG
1 AAAGAA-GA-AAAG
41280992 AAAGAAGAAAAG
1 AAAGAAGAAAAG
41281004 AAAGA
1 AAAGA
41281009 TCGAGAGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 9 0.25
14 5 0.14
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:41281868 original size:50 final size:50
Alignment explanation
Indices: 41281793--41281892 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
41281783 CATTTCTTGA
41281793 GGACACCTTGCACCTTAGTGCAAACTGATTTGATAGAGGGTCACGCGCGG
1 GGACACCTTGCACCTTAGTGCAAACTGATTTGATAGAGGGTCACGCGCGG
41281843 GGACACCTTGCACCTTAGTGCAAACTGATTTGATAGAGGGTCACGCGCGG
1 GGACACCTTGCACCTTAGTGCAAACTGATTTGATAGAGGGTCACGCGCGG
41281893 ACCAAGATCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (50 bp):
GGACACCTTGCACCTTAGTGCAAACTGATTTGATAGAGGGTCACGCGCGG
Found at i:41285196 original size:18 final size:17
Alignment explanation
Indices: 41285173--41285211 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
41285163 CTCTTTGTGC
41285173 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
41285191 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
41285209 TCT
1 TCT
41285212 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:41298899 original size:18 final size:18
Alignment explanation
Indices: 41298878--41298916 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41298868 AAAGGAACAT
41298878 AGAAAAAGA-AATTGAAAA
1 AGAAAAAGAGAA-TGAAAA
41298896 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
41298914 AGA
1 AGA
41298917 GCAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:41300732 original size:33 final size:34
Alignment explanation
Indices: 41300668--41300742 Score: 134
Period size: 33 Copynumber: 2.2 Consensus size: 34
41300658 GAGTTAGTTT
*
41300668 ATTAAATTTAGTTCAGCTTAAATAAGTGTTAG-A
1 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
41300701 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
41300735 ATTAATTT
1 ATTAATTT
41300743 GTTTAAATCT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 31 0.77
34 9 0.22
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (34 bp):
ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
Found at i:41303503 original size:21 final size:23
Alignment explanation
Indices: 41303458--41303504 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41303448 TCACCTGCAA
* *
41303458 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
41303481 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
41303502 TAA
1 TAA
41303505 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:41311236 original size:32 final size:32
Alignment explanation
Indices: 41311200--41311265 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
41311190 TCTAGCATTT
* *
41311200 TCATAGGAGTTTTTCATGACTTGGAAACTCGA
1 TCATAGGAGTTTTCCATCACTTGGAAACTCGA
41311232 TCATAGGAGTTTTCCATCACTTGGAAACTCGA
1 TCATAGGAGTTTTCCATCACTTGGAAACTCGA
41311264 TC
1 TC
41311266 TTGGTCCGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (32 bp):
TCATAGGAGTTTTCCATCACTTGGAAACTCGA
Found at i:41314229 original size:32 final size:32
Alignment explanation
Indices: 41314193--41314258 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
41314183 TCTAGTGTTT
*
41314193 TCATAGGAGTTTTCCATGACTTGGAAACTCGA
1 TCATAGGAGTTTTCCATCACTTGGAAACTCGA
41314225 TCATAGGAGTTTTCCATCACTTGGAAACTCGA
1 TCATAGGAGTTTTCCATCACTTGGAAACTCGA
41314257 TC
1 TC
41314259 TTGGTCCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (32 bp):
TCATAGGAGTTTTCCATCACTTGGAAACTCGA
Found at i:41314402 original size:17 final size:16
Alignment explanation
Indices: 41314365--41314402 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41314355 ATTGTAATTG
*
41314365 AAAAAATTCGAAGTAA
1 AAAAAATACGAAGTAA
*
41314381 CAAAAATACGAAGTAA
1 AAAAAATACGAAGTAA
41314397 AAAAAA
1 AAAAAA
41314403 GTGAAGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.68, C:0.08, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAAAATACGAAGTAA
Found at i:41316807 original size:23 final size:22
Alignment explanation
Indices: 41316756--41316819 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 22
41316746 CCTCGTCTTT
*
41316756 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
41316778 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
41316801 TTCTTTTCAATTTCTTTTT
1 TTCTTTTC--TTTCTTTTT
41316820 GTTTCACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
21 2 0.06
22 5 0.14
23 16 0.46
24 11 0.31
25 1 0.03
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.66
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:41324983 original size:16 final size:19
Alignment explanation
Indices: 41324946--41324992 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 19
41324936 CAAGTGAGAG
41324946 AAAAAGAAAAGAGAGTGAA
1 AAAAAGAAAAGAGAGTGAA
41324965 AAAAAGAAAAGA-A-TG-A
1 AAAAAGAAAAGAGAGTGAA
41324981 AAAAAGAAAAGA
1 AAAAAGAAAAGA
41324993 CTGTGAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.46
17 2 0.07
18 1 0.04
19 12 0.43
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAGAGAGTGAA
Found at i:41335076 original size:12 final size:12
Alignment explanation
Indices: 41335059--41335093 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
41335049 TCGTGAATTG
*
41335059 AAAAAAAAGTTT
1 AAAAAAAAGTTC
41335071 AAAAAAAAGTTC
1 AAAAAAAAGTTC
41335083 AAAAAAAAGTT
1 AAAAAAAAGTT
41335094 GTATTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.69, C:0.03, G:0.09, T:0.20
Consensus pattern (12 bp):
AAAAAAAAGTTC
Found at i:41336135 original size:12 final size:12
Alignment explanation
Indices: 41336106--41336180 Score: 64
Period size: 12 Copynumber: 6.2 Consensus size: 12
41336096 AAACAGCATG
41336106 TGAAAAAGAAAA
1 TGAAAAAGAAAA
** *
41336118 ACAAAAAGAAAT
1 TGAAAAAGAAAA
41336130 TGAAAAAGAAAA
1 TGAAAAAGAAAA
* *
41336142 TGAACATG-AAA
1 TGAAAAAGAAAA
*
41336153 -GAAAACAAGAAAT
1 TG-AAA-AAGAAAA
41336166 TGAAAAAGAAAA
1 TGAAAAAGAAAA
41336178 TGA
1 TGA
41336181 GAATGAGAGT
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
10 1 0.02
11 5 0.11
12 35 0.74
13 5 0.11
14 1 0.02
ACGTcount: A:0.69, C:0.04, G:0.16, T:0.11
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:41336212 original size:25 final size:26
Alignment explanation
Indices: 41336167--41336221 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
41336157 ACAAGAAATT
*
41336167 GAAAAAGAAAATGAGAATGAGAGTGA
1 GAAAAAGAAAAAGAGAATGAGAGTGA
*
41336193 GAAAAA-AAAAAGA-AATTGAGATTGA
1 GAAAAAGAAAAAGAGAA-TGAGAGTGA
41336218 -AAAA
1 GAAAA
41336222 GGATGTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 6 0.23
25 14 0.54
26 6 0.23
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (26 bp):
GAAAAAGAAAAAGAGAATGAGAGTGA
Found at i:41342806 original size:52 final size:52
Alignment explanation
Indices: 41342749--41342849 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
41342739 CATGCACATA
* *
41342749 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
* *
41342801 TTTGAGCTTTAACCGAGCTAGAAATGAGATCTTAAGCTGTTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
41342850 CGTTGCCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:41343148 original size:79 final size:79
Alignment explanation
Indices: 41343053--41343211 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
41343043 CTTATTCATT
*
41343053 AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
1 AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAAAA
41343118 CCTAAATACGTCAC
66 CCTAAATACGTCAC
41343132 AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAAAA
1 AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAAAA
41343197 CCTAAATACGTCAC
66 CCTAAATACGTCAC
41343211 A
1 A
41343212 TATCAGCATG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (79 bp):
AAAACACAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAAAA
CCTAAATACGTCAC
Found at i:41349163 original size:52 final size:52
Alignment explanation
Indices: 41349106--41349206 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
41349096 CATGCACATA
* *
41349106 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
*
41349158 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGTTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
41349207 CGTTGCCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:41349505 original size:79 final size:79
Alignment explanation
Indices: 41349410--41349564 Score: 310
Period size: 79 Copynumber: 2.0 Consensus size: 79
41349400 CTTATTCATT
41349410 AAAACATAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
1 AAAACATAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
41349475 CCTAAATACGTTAC
66 CCTAAATACGTTAC
41349489 AAAACATAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
1 AAAACATAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
41349554 CCTAAATACGT
66 CCTAAATACGT
41349565 CACATATCAG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.55, C:0.21, G:0.04, T:0.20
Consensus pattern (79 bp):
AAAACATAAACAACATCAAATCAATACCAAAACATACTTAAATACACACATAATACATAGTAGAA
CCTAAATACGTTAC
Found at i:41351385 original size:13 final size:13
Alignment explanation
Indices: 41351363--41351401 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
41351353 ATAGTAGATT
41351363 CTCG-AAAAAAAA
1 CTCGAAAAAAAAA
41351375 CTCGAAAAAAAAA
1 CTCGAAAAAAAAA
*
41351388 TTC-AAAAAAAAA
1 CTCGAAAAAAAAA
41351400 CT
1 CT
41351402 AGTTTCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.67, C:0.15, G:0.05, T:0.13
Consensus pattern (13 bp):
CTCGAAAAAAAAA
Found at i:41351462 original size:15 final size:15
Alignment explanation
Indices: 41351442--41351491 Score: 86
Period size: 14 Copynumber: 3.5 Consensus size: 15
41351432 TCAAGTTGTG
41351442 AAAAAAAATT-TGAA
1 AAAAAAAATTGTGAA
41351456 AAAAAAAATTGTG-A
1 AAAAAAAATTGTGAA
41351470 AAAAAAAATTGTGAA
1 AAAAAAAATTGTGAA
41351485 AAAAAAA
1 AAAAAAA
41351492 GCTAGTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (15 bp):
AAAAAAAATTGTGAA
Found at i:41351467 original size:27 final size:29
Alignment explanation
Indices: 41351437--41351491 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
41351427 GGATATCAAG
41351437 TTGTG-AAAAAAAATT-TGAAAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAAAA
41351464 TTGTGAAAAAAAAATTGTGAAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAAA
41351492 GCTAGTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 5 0.19
28 10 0.38
29 11 0.42
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.22
Consensus pattern (29 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAAAA
Found at i:41390870 original size:15 final size:15
Alignment explanation
Indices: 41390850--41390904 Score: 85
Period size: 14 Copynumber: 3.6 Consensus size: 15
41390840 GATATCAAGT
41390850 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
41390865 TG-AAAAAAAATTCG
1 TGAAAAAAAAATTCG
41390879 TGAAAAAAAAATTTTCG
1 TGAAAAAAAAA--TTCG
41390896 TGAAAAAAA
1 TGAAAAAAA
41390905 GAAGAAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.38
15 10 0.27
17 13 0.35
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:41390874 original size:17 final size:17
Alignment explanation
Indices: 41390852--41390904 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
41390842 TATCAAGTTG
41390852 AAAAAAAAATTCGTG--
1 AAAAAAAAATTCGTGAA
41390867 -AAAAAAAATTCGTGAA
1 AAAAAAAAATTCGTGAA
**
41390883 AAAAAAATTTTCGTGAA
1 AAAAAAAAATTCGTGAA
41390900 AAAAA
1 AAAAA
41390905 GAAGAAGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 14 0.42
17 19 0.58
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (17 bp):
AAAAAAAAATTCGTGAA
Found at i:41407855 original size:104 final size:104
Alignment explanation
Indices: 41407675--41407898 Score: 387
Period size: 104 Copynumber: 2.2 Consensus size: 104
41407665 TGTATATAAA
** * *
41407675 AGGGGTTGCTGTGTGCTGATTCCCCGGTTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
41407740 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
41407779 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
41407843 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
41407883 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
41407899 GATATCCATT
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
104 113 0.99
105 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:41407950 original size:71 final size:72
Alignment explanation
Indices: 41407817--41407968 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
41407807 TCATTGGTGG
* *
41407817 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
41407882 GAGGGGT
66 GAGGGGT
***
41407889 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
41407953 GAGGGGT
66 GAGGGGT
41407960 TGCTAAGTG
1 TGCTAAGTG
41407969 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:41415920 original size:39 final size:40
Alignment explanation
Indices: 41415875--41416097 Score: 242
Period size: 39 Copynumber: 5.7 Consensus size: 40
41415865 GCTCCTCGTT
* * * *
41415875 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
41415915 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
41415954 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
41415993 CAAAGGCCTTCGGG-CTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
41416032 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
41416073 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41416098 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
38 14 0.09
39 76 0.48
40 56 0.36
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41416106 original size:41 final size:41
Alignment explanation
Indices: 41416029--41416106 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41416019 TTTGTATCTC
* * *
41416029 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41416070 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41416107 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41423904 original size:39 final size:40
Alignment explanation
Indices: 41423779--41424000 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
41423769 GCTCCTCGTT
* * *
41423779 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACT--CA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
41423817 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
41423856 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
41423895 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
41423935 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
41423976 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41424001 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
37 30 0.19
38 1 0.01
39 39 0.25
40 75 0.48
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41423934 original size:79 final size:79
Alignment explanation
Indices: 41423779--41424000 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 79
41423769 GCTCCTCGTT
* * *
41423779 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACT-CACAATGCCTTCGGGACTTAACCCGG-A
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTGCACAAAGCCTTCGGGACTTAACCCGGAA
41423842 TTTAATAACTCGCA
66 TTTAATAACTCGCA
* * *
41423856 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACT-GCACAAA-GCCTTCGGGACTTAACCCGG
* *
41423920 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
41423935 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-T-GCACAAAGCCTTCGGGACTTAACCCG
41423999 GA
63 GA
41424001 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
76 3 0.02
77 28 0.23
78 8 0.07
79 50 0.41
80 25 0.20
81 8 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:41424009 original size:41 final size:41
Alignment explanation
Indices: 41423932--41424009 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41423922 TTTGTATCTC
* * *
41423932 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41423973 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41424010 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41426678 original size:56 final size:56
Alignment explanation
Indices: 41426592--41426711 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
41426582 ACAAGGGATG
*
41426592 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAGGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
41426648 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
41426704 ATGGGCAA
1 ATGGGCAA
41426712 TAAACTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:41429760 original size:56 final size:56
Alignment explanation
Indices: 41429674--41429793 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41429664 ACAAGGGATG
41429674 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
41429730 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
41429786 ATGGGCAA
1 ATGGGCAA
41429794 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:41433371 original size:47 final size:47
Alignment explanation
Indices: 41433302--41434042 Score: 1212
Period size: 47 Copynumber: 15.6 Consensus size: 47
41433292 AGTATATGTG
* *
41433302 GAATGTGAAAGTATATATATATGTGATAAGGCCTAATGGCTGATGTGAT
1 GAATGTGAAAG--TGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41433351 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
41433398 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41433447 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41433494 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41433541 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
41433590 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41433639 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41433686 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
41433733 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
41433780 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
41433827 GAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
41433874 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* *
41433921 GAATGTGAAGGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * * * * *
41433968 GAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGAT
1 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
* * *
41434015 GGACGTGAAAGTGTATAAATGTGATAAG
1 GAATGTGAAAGTGTATATATGTGATAAG
41434043 TCCCGAAGGG
Statistics
Matches: 659, Mismatches: 29, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
47 507 0.77
49 152 0.23
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
Found at i:41442901 original size:20 final size:20
Alignment explanation
Indices: 41442876--41442943 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
41442866 TCCATGCGGT
41442876 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* *
41442896 TCAGCTCATTCGGGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* * *
41442916 TCAGTTCACACGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
41442936 TCAGCTCA
1 TCAGCTCA
41442944 TTGAGCTCGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:41450759 original size:11 final size:11
Alignment explanation
Indices: 41450728--41450761 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41450718 GCATAAAGAC
41450728 GTTCACACCAT
1 GTTCACACCAT
*
41450739 GTTCA-GCCAT
1 GTTCACACCAT
41450749 GTTCACACCAT
1 GTTCACACCAT
41450760 GT
1 GT
41450762 GTCTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (11 bp):
GTTCACACCAT
Found at i:41453815 original size:15 final size:16
Alignment explanation
Indices: 41453797--41453826 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41453787 AAGAAAAGCA
41453797 AAAAAAAT-GAGTGAT
1 AAAAAAATAGAGTGAT
41453812 AAAAAAATAGAGTGA
1 AAAAAAATAGAGTGA
41453827 AACAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (16 bp):
AAAAAAATAGAGTGAT
Found at i:41457263 original size:11 final size:11
Alignment explanation
Indices: 41457232--41457265 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41457222 GCATAAAGAC
41457232 GTTCACACCAT
1 GTTCACACCAT
*
41457243 GTTCA-GCCAT
1 GTTCACACCAT
41457253 GTTCACACCAT
1 GTTCACACCAT
41457264 GT
1 GT
41457266 GGATCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (11 bp):
GTTCACACCAT
Found at i:41458177 original size:14 final size:15
Alignment explanation
Indices: 41458153--41458181 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41458143 CAAAAGATAG
41458153 GTTTGTGAAAAAAAA
1 GTTTGTGAAAAAAAA
41458168 GTTT-TGAAAAAAAA
1 GTTTGTGAAAAAAAA
41458182 ATTCGTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (15 bp):
GTTTGTGAAAAAAAA
Found at i:41459288 original size:6 final size:6
Alignment explanation
Indices: 41459279--41459313 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
41459269 AAAAATAAAA
*
41459279 TGAGAG TGAGAG TGAGAG TGAGAG TGAGAG CGAGA
1 TGAGAG TGAGAG TGAGAG TGAGAG TGAGAG TGAGA
41459314 AAAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.49, T:0.14
Consensus pattern (6 bp):
TGAGAG
Found at i:41465773 original size:23 final size:22
Alignment explanation
Indices: 41465721--41465773 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
41465711 TCCTCGTCTT
*
41465721 TTTCTTTTGTTTCTTTCTCTAA
1 TTTCTTTTCTTTCTTTCTCTAA
* *
41465743 CTTATTTTCTCTTCTTTCT-TCAA
1 TTTCTTTTCT-TTCTTTCTCT-AA
41465766 TTTCTTTT
1 TTTCTTTT
41465774 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTCTCTAA
Found at i:41465848 original size:18 final size:18
Alignment explanation
Indices: 41465825--41465863 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41465815 CTCTTTTTGC
41465825 TCTTTTTC-ATTCTCTTTT
1 TCTTTTTCGATT-TCTTTT
41465843 TCTTTTTCGATTTCTTTT
1 TCTTTTTCGATTTCTTTT
41465861 TCT
1 TCT
41465864 GTCTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (18 bp):
TCTTTTTCGATTTCTTTT
Found at i:41471671 original size:11 final size:11
Alignment explanation
Indices: 41471655--41471687 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41471645 TTCAGCTTGT
41471655 TAGGAAACTTC
1 TAGGAAACTTC
41471666 TAGGAAA-TTAC
1 TAGGAAACTT-C
41471677 TAGGAAACTTC
1 TAGGAAACTTC
41471688 ATAAAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (11 bp):
TAGGAAACTTC
Found at i:41479316 original size:19 final size:19
Alignment explanation
Indices: 41479288--41479326 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41479278 AATAAATTAC
*
41479288 TCATCATAGTTAATTGAGT
1 TCATCATAGTTAATTAAGT
*
41479307 TCATCTTAGTTAATTAAGT
1 TCATCATAGTTAATTAAGT
41479326 T
1 T
41479327 GCTGGACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (19 bp):
TCATCATAGTTAATTAAGT
Found at i:41483165 original size:20 final size:20
Alignment explanation
Indices: 41483103--41483169 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
41483093 AGCTAATAAC
*
41483103 GAGCTGAATTGAGCTCGAAT
1 GAGCTGACTTGAGCTCGAAT
*
41483123 AAGCTGACTTGAGCTCGAAT
1 GAGCTGACTTGAGCTCGAAT
41483143 GAGCTGACTTGAGCTC-AAGT
1 GAGCTGACTTGAGCTCGAA-T
41483163 GAGCTGA
1 GAGCTGA
41483170 ACCACATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 2 0.05
20 41 0.95
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (20 bp):
GAGCTGACTTGAGCTCGAAT
Found at i:41485712 original size:20 final size:20
Alignment explanation
Indices: 41485684--41485747 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
41485674 GCTGATAGAA
* *
41485684 AGCTAAATTGAGCTCGAATG
1 AGCTGAATTGAGCTCAAATG
41485704 AGCTGAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
* *
41485724 AGCTG-ATTGGAGCTAAAACG
1 AGCTGAATT-GAGCTCAAATG
41485744 AGCT
1 AGCT
41485748 AAAGGAGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:41488585 original size:40 final size:41
Alignment explanation
Indices: 41488541--41488624 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 41
41488531 TAAATAAAAG
41488541 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTA-AT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
* * * *
41488581 AAAGTCCAGCAACTCATTTATTAAGTAAGATGAGTTTATAT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
41488622 AAA
1 AAA
41488625 TTGCAAGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 34 0.87
41 5 0.13
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (41 bp):
AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTATAT
Found at i:41497478 original size:162 final size:162
Alignment explanation
Indices: 41497211--41497536 Score: 528
Period size: 162 Copynumber: 2.0 Consensus size: 162
41497201 TTGATTTTAT
* * * *
41497211 TTTTCCTTCGTATACGCATCTAAGGCCTTGCTAATAAATTCTTGAATGGTTCCATTTGGTTTTGA
1 TTTTCCTTCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
*
41497276 ACGCTTTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTCCTT
66 ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTCCTT
* *
41497341 GAGCTTGAATTGGGCCTTTGTGGCTCGTATCA
131 AAGCTTGAATTGGGCCTTTGTGACTCGTATCA
* *
41497373 TTTTCCTTTGTATACGCATCTAAGGCCTTGCTAATGAAGTCTTGAATGATTCCATTTAG-TTTCA
1 TTTTCCTTCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
* *
41497437 TACGCATTTGGCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATTACGTCCT
66 -ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTCCT
*
41497502 TAAGCTTGAATTGGGCCTTTTTGACTCGTATCA
130 TAAGCTTGAATTGGGCCTTTGTGACTCGTATCA
41497535 TT
1 TT
41497537 CCCCCATTCC
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
161 4 0.03
162 147 0.97
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (162 bp):
TTTTCCTTCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTCCTT
AAGCTTGAATTGGGCCTTTGTGACTCGTATCA
Found at i:41504327 original size:21 final size:21
Alignment explanation
Indices: 41504303--41504347 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
41504293 AAATTCACAT
41504303 ATTTAAAACAAGACAC-AATTA
1 ATTTAAAACAAGAC-CTAATTA
**
41504324 ATTTAAATTAAGACCTAATTA
1 ATTTAAAACAAGACCTAATTA
41504345 ATT
1 ATT
41504348 CGGTTAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (21 bp):
ATTTAAAACAAGACCTAATTA
Found at i:41510145 original size:162 final size:162
Alignment explanation
Indices: 41509869--41510192 Score: 506
Period size: 162 Copynumber: 2.0 Consensus size: 162
41509859 TTGATTTTCT
* * * * *
41509869 TTTTCCATCGTATACGCATCTAATGCCTTGCTAATAAATTCTTGAATGGTTCGATTTAGTTTTGA
1 TTTTCCATCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
* *
41509934 ATGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTCCTT
66 ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACATCCTT
41509999 GAGCTTGAATTGGGCCTGTGTGACTCATATCA
131 GAGCTTGAATTGGGCCTGTGTGACTCATATCA
* * * *
41510031 TTTTCCTTTGTATACGCATCTAAGGCGTTGCTAATGAAGTCTTGAATGATTCCATTTAG-TTTCA
1 TTTTCCATCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
*
41510095 TACGCATTTGCCTTGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACATCCT
66 -ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACATCCT
* *
41510160 TGAGCTTGAATTGGGCCTTTGTGACTCGTATCA
130 TGAGCTTGAATTGGGCCTGTGTGACTCATATCA
41510193 GTGAGGTATC
Statistics
Matches: 147, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
161 4 0.03
162 143 0.97
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (162 bp):
TTTTCCATCGTATACGCATCTAAGGCCTTGCTAATAAAGTCTTGAATGATTCCATTTAGTTTTCA
ACGCATTTGCCTGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACATCCTT
GAGCTTGAATTGGGCCTGTGTGACTCATATCA
Found at i:41510714 original size:18 final size:18
Alignment explanation
Indices: 41510687--41510735 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
41510677 ACGTTGTAAT
*
41510687 GAAAACGAAAAAGAAAAA
1 GAAATCGAAAAAGAAAAA
*
41510705 GAAATTGAAAAAGAAAAA
1 GAAATCGAAAAAGAAAAA
41510723 GAAATCGAAAAAG
1 GAAATCGAAAAAG
41510736 TGAGAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.06
Consensus pattern (18 bp):
GAAATCGAAAAAGAAAAA
Found at i:41510721 original size:5 final size:6
Alignment explanation
Indices: 41510687--41510765 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
41510677 ACGTTGTAAT
* ** **
41510687 GAAAAC GAAAAA GAAAAA GAAATT GAAAAA GAAAAA GAAATC GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** * *
41510735 GTGAGA GAAAAA GAAAAC GAAGAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA
41510766 TTGAAAAATA
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
6 48 0.89
7 2 0.04
8 4 0.07
ACGTcount: A:0.71, C:0.04, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:41510796 original size:18 final size:18
Alignment explanation
Indices: 41510765--41510799 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41510755 AGAAAAGAAA
41510765 ATTGAAAAATAAATTGAG
1 ATTGAAAAATAAATTGAG
41510783 ATTGAGAAAA-AAATTGA
1 ATTGA-AAAATAAATTGA
41510800 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (18 bp):
ATTGAAAAATAAATTGAG
Found at i:41516466 original size:30 final size:30
Alignment explanation
Indices: 41516432--41516503 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
41516422 TCTAGCATCC
* *
41516432 CCATTCAGCTCCCTAAATACATGCATGCCT
1 CCATTCAGCTCCCTAAACACATGCATGCAT
* * *
41516462 CCATTCATCTCCTTAAACACATTCATGCAT
1 CCATTCAGCTCCCTAAACACATGCATGCAT
**
41516492 TAATTCAGCTCC
1 CCATTCAGCTCC
41516504 ATATGCACAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.35, G:0.07, T:0.31
Consensus pattern (30 bp):
CCATTCAGCTCCCTAAACACATGCATGCAT
Found at i:41520926 original size:18 final size:18
Alignment explanation
Indices: 41520907--41520943 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
41520897 AGGAAGACAG
41520907 AAAGAGAAATCGAAAAAGAA
1 AAAGAG-AA-CGAAAAAGAA
41520927 AAAGAGAACGAAAAAGA
1 AAAGAGAACGAAAAAGA
41520944 GCAAAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.70, C:0.05, G:0.22, T:0.03
Consensus pattern (18 bp):
AAAGAGAACGAAAAAGAA
Found at i:41520949 original size:20 final size:20
Alignment explanation
Indices: 41520907--41520954 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
41520897 AGGAAGACAG
41520907 AAAGAGAAATCGAAAAAG-AA
1 AAAGAG-AATCGAAAAAGAAA
41520927 AAAGAGAA-CGAAAAAGAGCAA
1 AAAGAGAATCGAAAAAGA--AA
41520948 AAAGAGA
1 AAAGAGA
41520955 TTGAGAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.32
19 2 0.08
20 6 0.24
21 9 0.36
ACGTcount: A:0.69, C:0.06, G:0.23, T:0.02
Consensus pattern (20 bp):
AAAGAGAATCGAAAAAGAAA
Found at i:41521037 original size:18 final size:19
Alignment explanation
Indices: 41520993--41521038 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
41520983 CAAGAAAAGT
*
41520993 GAAAAAGAAATTGAAGATA
1 GAAAAAGAAAATGAAGATA
* *
41521012 G-AAGAGAAAATG-AGTTA
1 GAAAAAGAAAATGAAGATA
41521029 GAAAAAGAAA
1 GAAAAAGAAA
41521039 CAAAAGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.23
18 16 0.73
19 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAAAAGAAAATGAAGATA
Found at i:41522734 original size:33 final size:33
Alignment explanation
Indices: 41522697--41522760 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
41522687 GAGTTAGTTT
*
41522697 ATTAAATTTAGTTCAGCTCAAATAAGTGTTACA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTACA
* *
41522730 ATTAATTTTAGTTCAACTTAAATAAGTGTTA
1 ATTAAATTTAGTTCAACTCAAATAAGTGTTA
41522761 GTAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (33 bp):
ATTAAATTTAGTTCAACTCAAATAAGTGTTACA
Found at i:41536176 original size:46 final size:46
Alignment explanation
Indices: 41536123--41536212 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
41536113 CAAAGAAAAG
41536123 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGAATATGATAA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGAATATGATAA
* * *
41536169 ACCTCGACCCAGTATCAATGATGATAGGAGCCTTGGTATATGAT
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGAATATGAT
41536213 GAAGGCCACA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 39 0.98
47 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGAATATGATAA
Found at i:41538931 original size:19 final size:18
Alignment explanation
Indices: 41538895--41538934 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41538885 TTTCCACTCG
*
41538895 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
41538913 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
41538932 TTT
1 TTT
41538935 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:41540460 original size:46 final size:46
Alignment explanation
Indices: 41540407--41540500 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 46
41540397 CAAAGAAAAG
* *
41540407 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTTGTCTATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAGGAACCTTGGTATATGATGA
*
41540453 ACCTCGACCCAGTATCAATGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
41540499 AC
1 AC
41540501 GCCACACTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAGGAACCTTGGTATATGATGA
Found at i:41554923 original size:17 final size:17
Alignment explanation
Indices: 41554903--41554944 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
41554893 AACACTTCAC
41554903 TTTTTTTTAATACTCAA
1 TTTTTTTTAATACTCAA
** *
41554920 TTTTTTTTAATTTTTAA
1 TTTTTTTTAATACTCAA
41554937 TTTTTTTT
1 TTTTTTTT
41554945 CTTTAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTTAATACTCAA
Found at i:41559073 original size:40 final size:40
Alignment explanation
Indices: 41559007--41559084 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
41558997 TTAATTTAAA
* *
41559007 TAAACTCATCTTATTTAATAAATGAGTTGCTGGACTTTAT
1 TAAACTCATCTTAGTTAATAAATGAGTTGCTAGACTTTAT
* * * *
41559047 TAAACTCATGTTAGTTAGTAATTGAGTTGTTAGACTTT
1 TAAACTCATCTTAGTTAATAAATGAGTTGCTAGACTTT
41559085 CTTTTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (40 bp):
TAAACTCATCTTAGTTAATAAATGAGTTGCTAGACTTTAT
Found at i:41560416 original size:17 final size:18
Alignment explanation
Indices: 41560381--41560422 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
41560371 AGAAAATTGA
*
41560381 AAATGAGATTGCAAAAAG
1 AAATGAGAGTGCAAAAAG
41560399 AAATGAGAGTGC-AAAAG
1 AAATGAGAGTGCAAAAAG
41560416 AAATGAG
1 AAATGAG
41560423 TGATATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.55, C:0.05, G:0.26, T:0.14
Consensus pattern (18 bp):
AAATGAGAGTGCAAAAAG
Found at i:41571779 original size:6 final size:6
Alignment explanation
Indices: 41571768--41571810 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
41571758 TCACTCATCT
* * * *
41571768 TAATAA TAATAA TAATAC TATTAC TAATAC TAATAT TAATAC T
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC T
41571811 TACCTCACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (6 bp):
TAATAC
Found at i:41575415 original size:21 final size:21
Alignment explanation
Indices: 41575373--41575415 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
41575363 TTCAGTATGC
*
41575373 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
41575394 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
41575415 A
1 A
41575416 ATTTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:41576545 original size:37 final size:39
Alignment explanation
Indices: 41576459--41576554 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
41576449 CACACCAGAA
* *
41576459 TGGCACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGT
1 TGGCACCCAGTGCCTCATCGGAAAGTACGAAGCAATAGT
* *
41576498 TGACACCCAGTGTCTCATCGGCAAAG-ACGAAG-AA-AGT
1 TGGCACCCAGTGCCTCATCGG-AAAGTACGAAGCAATAGT
*
41576535 TGGCACCCAGTACCTCATCG
1 TGGCACCCAGTGCCTCATCG
41576555 AATCTATCCG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
37 20 0.41
38 2 0.04
39 24 0.49
40 3 0.06
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (39 bp):
TGGCACCCAGTGCCTCATCGGAAAGTACGAAGCAATAGT
Found at i:41576915 original size:6 final size:6
Alignment explanation
Indices: 41576904--41576946 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
41576894 CCACTCATCT
* * * *
41576904 TAATAA TAATAA TAATAC TATTAC TAATAC TAATAT TAATAC T
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC T
41576947 TACCTCACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (6 bp):
TAATAC
Found at i:41578289 original size:25 final size:23
Alignment explanation
Indices: 41578245--41578305 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
41578235 AATTTGATTT
*
41578245 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
41578269 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
41578293 ATATAAATTATAT
1 AT-TTAATTATAT
41578306 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:41578294 original size:35 final size:34
Alignment explanation
Indices: 41578253--41578332 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 34
41578243 TTATTTAATA
* *
41578253 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTAT-ATTTAAATATCATAAATT
*
41578287 CATATAATATAAATTATATTTAAATATCATTAATT
1 -ATATAATATAAATTATATTTAAATATCATAAATT
41578322 ATATAAT-TAAA
1 ATATAATATAAA
41578333 CAAATAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (34 bp):
ATATAATATAAATTATATTTAAATATCATAAATT
Found at i:41584989 original size:39 final size:39
Alignment explanation
Indices: 41584935--41585012 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
41584925 TGTTTCTATC
*
41584935 CTTAGCCGAGCCATCACCTATCCTATCCCTAAAACACTT
1 CTTAGCCGAACCATCACCTATCCTATCCCTAAAACACTT
* * *
41584974 CTTAGTCGAACCATCACCTATCCTATTCTTAAAACACTT
1 CTTAGCCGAACCATCACCTATCCTATCCCTAAAACACTT
41585013 TTGATAAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.29
Consensus pattern (39 bp):
CTTAGCCGAACCATCACCTATCCTATCCCTAAAACACTT
Found at i:41586280 original size:27 final size:28
Alignment explanation
Indices: 41586245--41586298 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
41586235 GCTGGACTTG
*
41586245 GACATCATTAAAAACATGTAATAAAATT
1 GACATCATTAAAAACATGCAATAAAATT
* *
41586273 GACA-CATTAATAACATGCATTAAAAT
1 GACATCATTAAAAACATGCAATAAAAT
41586299 AAAACACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (28 bp):
GACATCATTAAAAACATGCAATAAAATT
Found at i:41587518 original size:14 final size:14
Alignment explanation
Indices: 41587499--41587525 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41587489 TGCATCTCCC
41587499 CATGCATGAATCTA
1 CATGCATGAATCTA
41587513 CATGCATGAATCT
1 CATGCATGAATCT
41587526 GCCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:41589816 original size:12 final size:12
Alignment explanation
Indices: 41589783--41589827 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
41589773 TTTTCACTCG
41589783 ATTTC-TTTTCA
1 ATTTCTTTTTCA
* *
41589794 AGTTCTCTTTCA
1 ATTTCTTTTTCA
41589806 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
41589818 ATCTCTTTTT
1 ATTTCTTTTT
41589828 GTTTTTCACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:41589849 original size:16 final size:18
Alignment explanation
Indices: 41589811--41589850 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
41589801 TTTCAATTTC
41589811 TTTTTCAATCTCTTTTTG
1 TTTTTCAATCTCTTTTTG
*
41589829 TTTTTCACTCTC-TTTTG
1 TTTTTCAATCTCTTTTTG
41589846 TTTTT
1 TTTTT
41589851 GAAATCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTCAATCTCTTTTTG
Done.