Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1190296 original size:18 final size:17
Alignment explanation
Indices: 1190269--1190302 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1190259 ATTTTATAAA
1190269 TTTAAAATTAATTTAAT
1 TTTAAAATTAATTTAAT
1190286 TTTATAAATTAATTTAA
1 TTTA-AAATTAATTTAA
1190303 ATTAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATTAATTTAAT
Found at i:1190311 original size:24 final size:25
Alignment explanation
Indices: 1190258--1190312 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1190248 AAATTATTTA
*
1190258 AATTTTATAAATTTAAAATTAATTT
1 AATTTTATAAATTTAAAATTAAATT
*
1190283 AATTTTATAAA-TT-AATTTAAATT
1 AATTTTATAAATTTAAAATTAAATT
1190306 AGATTTT
1 A-ATTTT
1190313 GTGAAGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
24 7 0.26
25 11 0.41
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTTTATAAATTTAAAATTAAATT
Found at i:1190531 original size:2 final size:2
Alignment explanation
Indices: 1190520--1190604 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
1190510 TGAGGTTAAA
1190520 AT AT -T 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
1190561 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
1190603 AT
1 AT
1190605 GTGTGTGTGT
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1194500 original size:21 final size:20
Alignment explanation
Indices: 1194476--1194678 Score: 128
Period size: 21 Copynumber: 9.8 Consensus size: 20
1194466 CATATTCGCA
1194476 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTAGTCCAAGTT--CG
* *
1194497 TTGCGA-TAGTCGACGTTCGTG
1 TTGCGATTAGTCCAAGTTC--G
* * * *
1194518 TTGCAATTTATTTCAAATTCG
1 TTGCGA-TTAGTCCAAGTTCG
*
1194539 TTGCGA-TAGTCGAAGTTCGTG
1 TTGCGATTAGTCCAAGTTC--G
*
1194560 TTGCGATTTATTCCAAGTTCG
1 TTGCGA-TTAGTCCAAGTTCG
*
1194581 TTGCGATTTATTCCAAGTTCG
1 TTGCGA-TTAGTCCAAGTTCG
* *
1194602 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTAGTCCAAGTTCG
*
1194623 TTGCGA-TAGTCAAAGTTCGCG
1 TTGCGATTAGTCCAAGTT--CG
* *
1194644 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTAGTCCAAGTTCG
1194665 TTGCGA-TAGTCCAA
1 TTGCGATTAGTCCAA
1194679 AATCGCAACG
Statistics
Matches: 147, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
19 24 0.16
21 98 0.67
23 25 0.17
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTAGTCCAAGTTCG
Found at i:1194543 original size:42 final size:42
Alignment explanation
Indices: 1194495--1194675 Score: 258
Period size: 42 Copynumber: 4.3 Consensus size: 42
1194485 TCCAAGTTCG
* * *
1194495 CGTTGCGATAGTCGACGTTCGTGTTGCAATTTATTTCAAATT
1 CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATT
*
1194537 CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATT
* *
1194579 CGTTGCGATTTATTCCAAGTTC--GTTGCGATTTATTCCAAATT
1 CGTTGCGA--TAGTCGAAGTTCGTGTTGCGATTTATTCCAAATT
* *
1194621 CGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATT
1194663 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1194676 CAAAATCGCA
Statistics
Matches: 126, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
40 10 0.08
42 106 0.84
44 10 0.08
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATT
Found at i:1194548 original size:63 final size:62
Alignment explanation
Indices: 1194476--1194678 Score: 232
Period size: 63 Copynumber: 3.2 Consensus size: 62
1194466 CATATTCGCA
* * * *
1194476 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGACGTTCGTGTTGCAATTTATTTCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCAAAGTTCG-GTTGCGATTTATTCCAAATTCG
* * * * *
1194539 TTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAGTTC-GTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCAAAGTTCGGTTGCGATTTATTCCAAATTCG
* *
1194602 TTGCGATTTATTCCAAATT--CGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCAAAGTTCG-GTTGCGATTTATTCCAAATTCG
1194665 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1194679 AATCGCAACG
Statistics
Matches: 118, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
61 17 0.14
63 84 0.71
65 17 0.14
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (62 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCAAAGTTCGGTTGCGATTTATTCCAAATTCG
Found at i:1195578 original size:21 final size:20
Alignment explanation
Indices: 1195545--1195809 Score: 171
Period size: 21 Copynumber: 12.7 Consensus size: 20
1195535 CGTTACGATT
*
1195545 TTGGACTATCGCAA-CGAAC
1 TTGGAATATCGCAACCGAAC
1195564 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAAC-CGAAC
* *
1195587 TTCGACTATCGCAA-CGAAC
1 TTGGAATATCGCAACCGAAC
1195606 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAAC-CGAAC
* *
1195629 TTCGACTATCGCAACGCGAAC
1 TTGGAATATCGCAAC-CGAAC
1195650 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAAC-CGAAC
* *
1195673 TTCGACTATCGCAA-CGAAC
1 TTGGAATATCGCAACCGAAC
*
1195692 TTGGAAAAAATCGCAACGCGAAC
1 TTGG--AATATCGCAAC-CGAAC
* *
1195715 TTTGACTATCGCAA-CGAAC
1 TTGGAATATCGCAACCGAAC
* * * *
1195734 TTCGACTATCGGAACGCGAAT
1 TTGGAATATCGCAAC-CGAAC
*
1195755 TTGAAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAAC-CGAAC
* * *
1195778 TTGGACTATCACAA-CGAAT
1 TTGGAATATCGCAACCGAAC
*
1195797 TTGGAAAATCGCA
1 TTGGAATATCGCA
1195810 TTGCGATAGC
Statistics
Matches: 196, Mismatches: 32, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
19 55 0.28
21 77 0.39
23 64 0.33
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
TTGGAATATCGCAACCGAAC
Found at i:1195607 original size:42 final size:42
Alignment explanation
Indices: 1195548--1195735 Score: 340
Period size: 42 Copynumber: 4.4 Consensus size: 42
1195538 TACGATTTTG
1195548 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1195590 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1195632 GACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1195676 GACTATCGCAACGAACTTGGAAAAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1195718 GACTATCGCAACGAACTT
1 GACTATCGCAACGAACTT
1195736 CGACTATCGG
Statistics
Matches: 142, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
42 100 0.70
44 42 0.30
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1195691 original size:86 final size:86
Alignment explanation
Indices: 1195548--1195730 Score: 334
Period size: 86 Copynumber: 2.2 Consensus size: 86
1195538 TACGATTTTG
1195548 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 GACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
*
1195611 ATAAATCGCAACGCGAACTTC
66 AAAAATCGCAACGCGAACTTC
1195632 GACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 GACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
*
1195697 AAAAATCGCAACGCGAACTTT
66 AAAAATCGCAACGCGAACTTC
1195718 GACTATCGCAACG
1 GACTATCGCAACG
1195731 AACTTCGACT
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
84 11 0.12
86 84 0.88
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (86 bp):
GACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
AAAAATCGCAACGCGAACTTC
Found at i:1195776 original size:128 final size:127
Alignment explanation
Indices: 1195548--1195782 Score: 357
Period size: 128 Copynumber: 1.8 Consensus size: 127
1195538 TACGATTTTG
* *
1195548 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCGCAACGAACTTGGAAAAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTCGAAT
*
1195613 AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTC
66 -AATCGCAACGCGAACTTCGAATATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1195676 GACTATCGCAACGAACTTGGAAAAAATCGCAACGCGAACTTTGACTATCGCAACGAACTTCGACT
1 GACTATCGCAACGAACTTGGAAAAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTCGAAT
* *
1195741 -ATCGGAACGCGAA-TTTGAAATAAATCGCAACGCGAACTTGGA
66 AATCGCAACGCGAACTTCG-AAT--ATCGCAACGCGAACTTGGA
1195783 CTATCACAAC
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
125 3 0.03
126 14 0.14
128 80 0.82
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (127 bp):
GACTATCGCAACGAACTTGGAAAAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTCGAAT
AATCGCAACGCGAACTTCGAATATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1195782 original size:86 final size:84
Alignment explanation
Indices: 1195548--1195753 Score: 292
Period size: 86 Copynumber: 2.5 Consensus size: 84
1195538 TACGATTTTG
* *
1195548 GACTATCGCAA-CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAA
1 GACTATCGCAACCGAACTTCGAAT-AATCGCAACGCGAACTTCGAATATCGCAACGAACTTGGAA
*
1195612 TAAATCGCAACGCGAACTTC
65 AAAATCGCAACGCGAACTTC
* *
1195632 GACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 GACTATCGCAAC-CGAACTTCGAAT-AATCGCAACGCGAACTTCGAATATCGCAACGAACTTGGA
*
1195697 AAAAATCGCAACGCGAACTTT
64 AAAAATCGCAACGCGAACTTC
* *
1195718 GACTATCGCAA-CGAACTTCGACT-ATCGGAACGCGAA
1 GACTATCGCAACCGAACTTCGAATAATCGCAACGCGAA
1195754 TTTGAAATAA
Statistics
Matches: 115, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
82 12 0.10
84 21 0.18
86 82 0.71
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.18
Consensus pattern (84 bp):
GACTATCGCAACCGAACTTCGAATAATCGCAACGCGAACTTCGAATATCGCAACGAACTTGGAAA
AAATCGCAACGCGAACTTC
Found at i:1195834 original size:21 final size:21
Alignment explanation
Indices: 1195805--1195857 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1195795 ATTTGGAAAA
*
1195805 TCGCATTGCGATAGCCGAAGT
1 TCGCGTTGCGATAGCCGAAGT
* *
1195826 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGCCGAAGT
*
1195847 TCACGTTGCGA
1 TCGCGTTGCGA
1195858 ATCTGGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGCCGAAGT
Found at i:1208228 original size:12 final size:12
Alignment explanation
Indices: 1208211--1208240 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1208201 AATAAGAAGG
1208211 ATAGAAGCAGAA
1 ATAGAAGCAGAA
1208223 ATAGAAGCAGAA
1 ATAGAAGCAGAA
*
1208235 ACAGAA
1 ATAGAA
1208241 CGGCTAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.10, G:0.23, T:0.07
Consensus pattern (12 bp):
ATAGAAGCAGAA
Found at i:1212748 original size:22 final size:22
Alignment explanation
Indices: 1212720--1212766 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1212710 ACAATAAAAT
1212720 TTTTACACATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
*
1212742 TTTTACATATAAACGTAAATAA
1 TTTTACACATAAACGTAAATAA
1212764 TTT
1 TTT
1212767 AAATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (22 bp):
TTTTACACATAAACGTAAATAA
Found at i:1213230 original size:32 final size:32
Alignment explanation
Indices: 1213194--1213258 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
1213184 ACTACGTGGC
*
1213194 ATAAGGCGCGC-AGCACGCCTTATCCAGTGTGT
1 ATAAGGCGCGCGA-CACGCCTTATCAAGTGTGT
*
1213226 ATAAGGCGCGCGACACGTCTTATCAAGTGTGT
1 ATAAGGCGCGCGACACGCCTTATCAAGTGTGT
1213258 A
1 A
1213259 ACCATGTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (32 bp):
ATAAGGCGCGCGACACGCCTTATCAAGTGTGT
Found at i:1217194 original size:2 final size:2
Alignment explanation
Indices: 1217020--1217175 Score: 135
Period size: 2 Copynumber: 79.5 Consensus size: 2
1217010 AATGGAAATA
1217020 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
* * * *
1217062 AT AT AT AT AT AT A- AT AG A- AT ACT AA AA AT GGT A- AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT AT -AT AT
* * * * * * * *
1217102 -T AA AG A- AA AC AC AA AG A- AT GT 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
1217141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1217176 AAAAAGTAAA
Statistics
Matches: 133, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
1 6 0.05
2 122 0.92
3 5 0.04
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1217203 original size:17 final size:17
Alignment explanation
Indices: 1217183--1217228 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1217173 ATAAAAAAGT
1217183 AAATAATATATACAATA
1 AAATAATATATACAATA
*
1217200 AAATAATATA-ATAATA
1 AAATAATATATACAATA
1217216 AATATAGATATAT
1 AA-ATA-ATATAT
1217229 GCGTATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 7 0.28
17 13 0.52
18 5 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATAATATATACAATA
Found at i:1219141 original size:106 final size:104
Alignment explanation
Indices: 1218950--1219205 Score: 399
Period size: 106 Copynumber: 2.5 Consensus size: 104
1218940 GTTGTTTAGG
* * *
1218950 CCAATATCCTTCG-TCGTGAAGTTGAAATTGACTCTGAAACT-GGAAAGTGTATTGACAGTCAGC
1 CCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAAGTATATTGACAGTCAGC
*
1219013 CGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGT
65 CGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCTTGAGT
* * *
1219053 CCAATATCCTTCGCTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTCGACAGTCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAGTATAT-T-GACAGTCAG
1219118 CCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCTTGAGT
64 CCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCTTGAGT
*
1219159 CCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
1219206 CCCCTTTGTC
Statistics
Matches: 140, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 36 0.26
104 9 0.06
105 1 0.01
106 94 0.67
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (104 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAGTATATTGACAGTCAGCC
GCCCCTTCGCTGTGAAGTTGAGCTTGTGCTATCTTGAGT
Found at i:1220329 original size:17 final size:16
Alignment explanation
Indices: 1220307--1220362 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
1220297 ACCCACCTTA
1220307 TTTTTCTTTTCTTTTT
1 TTTTTCTTTTCTTTTT
*
1220323 CTTTTTCTTTTGTTTTT
1 -TTTTTCTTTTCTTTTT
*
1220340 TTGTTCTTTT-TTCCTTT
1 TTTTTCTTTTCTT--TTT
1220357 TTTTTC
1 TTTTTC
1220363 AATTTAGGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.06
16 9 0.26
17 23 0.68
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTT
Found at i:1220338 original size:22 final size:22
Alignment explanation
Indices: 1220308--1220350 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1220298 CCCACCTTAT
1220308 TTTTCTTTTCTTT-TTCTTTTTC
1 TTTTCTTTT-TTTGTTCTTTTTC
*
1220330 TTTTGTTTTTTTGTTCTTTTT
1 TTTTCTTTTTTTGTTCTTTTT
1220351 TCCTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.84
Consensus pattern (22 bp):
TTTTCTTTTTTTGTTCTTTTTC
Found at i:1220361 original size:11 final size:11
Alignment explanation
Indices: 1220307--1220351 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
1220297 ACCCACCTTA
*
1220307 TTTTTCTTTTC
1 TTTTTCTTTTT
1220318 TTTTTCTTTTT
1 TTTTTCTTTTT
* *
1220329 CTTTTGTTTTT
1 TTTTTCTTTTT
*
1220340 TTGTTCTTTTT
1 TTTTTCTTTTT
1220351 T
1 T
1220352 CCTTTTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1220476 original size:68 final size:66
Alignment explanation
Indices: 1220346--1220477 Score: 167
Period size: 68 Copynumber: 2.0 Consensus size: 66
1220336 TTTTTTGTTC
* *** *
1220346 TTTTTTCCTTTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGTTTTTCTTTTTT
1 TTTTTTCCTTTTTTTTCAACTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGAAATACTTTTTT
1220411 G
66 G
* *
1220412 TTTTTTCCTTTTTTTTTCCAACTT-GGGACGCCCTTTCGGGTTTTCATCCTAAGCGAAATACTTT
1 TTTTTTCC-TTTTTTTT-CAACTTAGGG-CGCCCTTTCGGGTTTTCACCCTAAACGAAATACTTT
1220476 TT
63 TT
1220478 GACTGTATCT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 8 0.14
67 11 0.20
68 37 0.66
ACGTcount: A:0.13, C:0.22, G:0.14, T:0.52
Consensus pattern (66 bp):
TTTTTTCCTTTTTTTTCAACTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGAAATACTTTTTT
G
Found at i:1226202 original size:15 final size:15
Alignment explanation
Indices: 1226165--1226217 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1226155 TTGAGACATT
*
1226165 ACCCGCCCCACATTC
1 ACCCGCCCCACATCC
** * *
1226180 GTCTGCCCCGCATCC
1 ACCCGCCCCACATCC
1226195 ACCCGCCCCACATCC
1 ACCCGCCCCACATCC
*
1226210 GCCCGCCC
1 ACCCGCCC
1226218 AGCTAAATAT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.13, C:0.62, G:0.13, T:0.11
Consensus pattern (15 bp):
ACCCGCCCCACATCC
Found at i:1234889 original size:18 final size:16
Alignment explanation
Indices: 1234868--1234911 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1234858 AATAAGATTA
1234868 ATAATAATAATAATATAT
1 ATAATAA-AATAATA-AT
*
1234886 ATAATAAAATACTAAT
1 ATAATAAAATAATAAT
1234902 ATAATTAAAA
1 ATAA-TAAAA
1234912 ACGTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 11 0.46
18 7 0.29
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATAAAATAATAAT
Found at i:1235416 original size:129 final size:130
Alignment explanation
Indices: 1235068--1235433 Score: 350
Period size: 134 Copynumber: 2.8 Consensus size: 130
1235058 TTGGGAGACG
* * * * * *
1235068 ACACTGCTCATACATGCTGAAGAGTTCTGGTCATCTAAGGGTGACAAGACTCCTACATAATGAGA
1 ACACGGCTCATACGTGATGAAGAGTTCTGGTTATC-AAGGTTGACAAG-CTCCTACATAATGAGG
* * * *
1235133 AGATTTAGTCATGG-GATGACACTGATCATACGTGATGAAGAGTTCTTTGCCATCTTTAGGAAGG
64 AGA-TCAGTC-GGGTGATGACACGGATCATACGTGATGAAGAGTTCTTGGCCATC-TTA-GAAGG
1235197 GTGATA
125 GTGATA
* ** * * * *
1235203 ACTCAGTTTC-TACGTGATGAGGATGAT-TGGTTATCTAGGTTGACATAGCTCCTACATAATAAG
1 ACAC-GGCTCATACGTGATGAAGA-GTTCTGGTTATCAAGGTTGACA-AGCTCCTACATAATGAG
* * *
1235266 GAAATCTAGTCGAGTGATGACACGGCTCATACGTGATGAAGAGTT-TTGGCCATC-TA-AA-GGT
63 GAGATC-AGTCGGGTGATGACACGGATCATACGTGATGAAGAGTTCTTGGCCATCTTAGAAGGGT
1235327 GATA
127 GATA
*
1235331 ACACGGCTCATACGTGATGAAGAGTTCTGGTTATCAAGGATTGACACGTCTCCTACATAATGAGG
1 ACACGGCTCATACGTGATGAAGAGTTCTGGTTATCAAGG-TTGACAAG-CTCCTACATAATGAGG
* * *
1235396 AGATCAGGTCGGGTGATGACACGGTTCCTATGTGATGA
64 AGATCA-GTCGGGTGATGACACGGATCATACGTGATGA
1235434 GGACAACAAG
Statistics
Matches: 188, Mismatches: 33, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
127 5 0.03
128 35 0.19
129 54 0.29
131 2 0.01
133 10 0.05
134 56 0.30
135 22 0.12
136 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (130 bp):
ACACGGCTCATACGTGATGAAGAGTTCTGGTTATCAAGGTTGACAAGCTCCTACATAATGAGGAG
ATCAGTCGGGTGATGACACGGATCATACGTGATGAAGAGTTCTTGGCCATCTTAGAAGGGTGATA
Found at i:1235827 original size:91 final size:91
Alignment explanation
Indices: 1235672--1235841 Score: 288
Period size: 91 Copynumber: 1.9 Consensus size: 91
1235662 AAGTGTTGAA
*
1235672 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTAGATGAGTTCTTCTCATTATGAAC
1235737 TCTCCACTGGAAATGTTAATGCAAGG
66 TCTCCACTGGAAATGTTAATGCAAGG
* *
1235763 TTGAACGAGTTCTTGTCATTATGAACTTCTTCT-TCCTTGTTAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCT-CTTGTTAGATGAGTTCTTCTCATTATGAA
*
1235827 CTCTTCACTGGAAAT
65 CTCTCCACTGGAAAT
1235842 ATTGATCCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
90 1 0.01
91 73 0.99
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (91 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTAGATGAGTTCTTCTCATTATGAAC
TCTCCACTGGAAATGTTAATGCAAGG
Found at i:1235964 original size:117 final size:116
Alignment explanation
Indices: 1235758--1236322 Score: 703
Period size: 117 Copynumber: 4.9 Consensus size: 116
1235748 AATGTTAATG
* * ** *
1235758 CAAGGTTGAACGAGTTCTTGTCATTATGAACTTCTTCTTCCTTGTTAGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* *
1235823 TGAACTCTTCACTGGAAATATTGATCCACCTCCTTCTGTGATGGATTCGAAC
66 TGAACTCTT-ACTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTCAAAC
*
1235875 CAAGGTTGAACAAGTTCTTCTCGTTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* * * * *
1235940 TGAACT-TTCCACTGAAAATGTTGATCCACATCTTTCTTTGATGGAATCAAAC
66 TGAACTCTT--ACTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTCAAAC
* *
1235992 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* * * * *
1236057 TGAACTCTCAACTGAAAATGTTGATCCATCTCTTTCTGTGATGGAATCAAAC
66 TGAACTCT-TACTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTCAAAC
*
1236109 CAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* * * *
1236174 TGAACTCTTA-TGGAAATGTTGGTTCACCTCCTTCTGTGGTGGACTT--GA-
66 TGAACTCTTACTGGAAATGTTGATCCACCTCCTTCTGTGATGGA-TTCAAAC
1236222 -AA-G--GAACAAGTTCTTCTCATTATGAACTT-TCTCATT--T-A-T-GATGAGTTCTTCTCAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT-TC-TTCCTCATTGGATGAGTTCTTCTCAT
* * *
1236277 TATGAACTCTT-CTGGAAATGTTGGTTCACCTCCTTCTGTGGTGGAT
64 TATGAACTCTTACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAT
1236323 CATGATCTTT
Statistics
Matches: 408, Mismatches: 33, Indels: 27
0.87 0.07 0.06
Matches are distributed among these distances:
104 1 0.00
105 60 0.15
106 1 0.00
107 1 0.00
108 2 0.00
109 27 0.07
110 2 0.00
111 1 0.00
112 2 0.00
114 1 0.00
115 27 0.07
116 4 0.01
117 278 0.68
118 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (116 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
TGAACTCTTACTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTCAAAC
Found at i:1236029 original size:20 final size:21
Alignment explanation
Indices: 1236004--1236062 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
1235994 AGGTTGAACA
*
1236004 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTG
*
1236025 A-TTCTTCCTC-TT-TGGA-TG
1 AGTTCTT-CTCATTATGAACTG
1236043 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
1236063 CTCAACTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 10 0.33
21 5 0.17
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.47
Consensus pattern (21 bp):
AGTTCTTCTCATTATGAACTG
Found at i:1236287 original size:16 final size:16
Alignment explanation
Indices: 1236233--1236289 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
1236223 AGGAACAAGT
1236233 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
*
1236249 T-TTCTCATTTATGATGAGT
1 TCTTCTCA-TTATGA--A-C
1236268 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
1236284 TCTTCT
1 TCTTCT
1236290 GGAAATGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 6 0.18
16 13 0.38
17 1 0.03
18 1 0.03
19 7 0.21
20 6 0.18
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:1239221 original size:13 final size:14
Alignment explanation
Indices: 1239199--1239237 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1239189 TCTTGATTCA
1239199 ATTTCTTTTTTTTC
1 ATTTCTTTTTTTTC
1239213 ATTTCTTTTTTTTC
1 ATTTCTTTTTTTTC
*
1239227 -TTTATTTTTTT
1 ATTTCTTTTTTT
1239238 CCTTTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (14 bp):
ATTTCTTTTTTTTC
Found at i:1239226 original size:9 final size:9
Alignment explanation
Indices: 1239214--1239256 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
1239204 TTTTTTTTCA
1239214 TTTCTTTTT
1 TTTCTTTTT
1239223 TTTCTTTATT
1 TTTCTTT-TT
1239233 TTT-TTCCTTT
1 TTTCTT--TTT
1239243 TTTCTTTTT
1 TTTCTTTTT
1239252 TTTCT
1 TTTCT
1239257 CTGATGGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 17 0.57
10 10 0.33
11 3 0.10
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1239730 original size:9 final size:9
Alignment explanation
Indices: 1239716--1239745 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1239706 TCAATCCCTC
1239716 TTTTTTCTT
1 TTTTTTCTT
1239725 TTTTTTCTT
1 TTTTTTCTT
1239734 TTTTTTCTT
1 TTTTTTCTT
1239743 TTT
1 TTT
1239746 ACTTCGAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1246280 original size:20 final size:21
Alignment explanation
Indices: 1246227--1246282 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
1246217 AATTAATTAG
1246227 TAATA-AGATTAATAAAAATAA
1 TAATATAGATTAAT-AAAATAA
*
1246248 TAATATAGA-TAATAAAATAC
1 TAATATAGATTAATAAAATAA
1246268 TAATATA-ATTAATAA
1 TAATATAGATTAATAA
1246283 TGTTTTTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 1 0.03
20 19 0.59
21 9 0.28
22 3 0.09
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (21 bp):
TAATATAGATTAATAAAATAA
Found at i:1257343 original size:11 final size:11
Alignment explanation
Indices: 1257303--1257367 Score: 62
Period size: 11 Copynumber: 6.0 Consensus size: 11
1257293 AGTTTTAGAA
* *
1257303 ATTATAAAATG
1 ATTATTAAATT
1257314 ATTATT-AATT
1 ATTATTAAATT
*
1257324 -TTTTTAAATT
1 ATTATTAAATT
1257334 ATTATTAAATT
1 ATTATTAAATT
*
1257345 ATTATTAAAATA
1 ATTATT-AAATT
*
1257357 ATTATCAAATT
1 ATTATTAAATT
1257368 TATTGAATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
9 4 0.09
10 7 0.16
11 24 0.55
12 9 0.20
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:1257355 original size:23 final size:23
Alignment explanation
Indices: 1257303--1257367 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
1257293 AGTTTTAGAA
*
1257303 ATTA-TAAAATGATTATT-AATT
1 ATTATTAAAATAATTATTAAATT
* *
1257324 -TT-TTTAAATTATTATTAAATT
1 ATTATTAAAATAATTATTAAATT
*
1257345 ATTATTAAAATAATTATCAAATT
1 ATTATTAAAATAATTATTAAATT
1257368 TATTGAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 13 0.37
21 4 0.11
22 2 0.06
23 16 0.46
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTATTAAAATAATTATTAAATT
Found at i:1261967 original size:16 final size:16
Alignment explanation
Indices: 1261946--1262044 Score: 171
Period size: 16 Copynumber: 6.2 Consensus size: 16
1261936 AGTATTACCC
1261946 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
1261962 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1261978 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1261994 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1262010 GACATGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1262026 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1262042 GAC
1 GAC
1262045 TTATAAATGA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 78 1.00
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:1262002 original size:48 final size:48
Alignment explanation
Indices: 1261946--1262044 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
1261936 AGTATTACCC
*
1261946 GACCTGTTTTCAACCTGACCTGTTTTCAACCTGACCTGTTTTTAACCT
1 GACCTGTTTTCAACCTGACATGTTTTCAACCTGACCTGTTTTTAACCT
1261994 GACCTGTTTTCAACCTGACATGTTTTCAACCTGACCTGTTTTTAACCT
1 GACCTGTTTTCAACCTGACATGTTTTCAACCTGACCTGTTTTTAACCT
1262042 GAC
1 GAC
1262045 TTATAAATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.38
Consensus pattern (48 bp):
GACCTGTTTTCAACCTGACATGTTTTCAACCTGACCTGTTTTTAACCT
Found at i:1262339 original size:14 final size:14
Alignment explanation
Indices: 1262317--1262363 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1262307 TGCAAAGGAA
*
1262317 AATTAATATAGTTT
1 AATTTATATAGTTT
1262331 AATTTATATA----
1 AATTTATATAGTTT
1262341 AA-TTATATAGTTT
1 AATTTATATAGTTT
1262354 AATTTATATA
1 AATTTATATA
1262364 AAGACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:1262350 original size:23 final size:24
Alignment explanation
Indices: 1262316--1262365 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1262306 ATGCAAAGGA
1262316 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1262340 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1262363 AAA
1 AAA
1262366 GACAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1262550 original size:14 final size:14
Alignment explanation
Indices: 1262528--1262558 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1262518 TCCATTTAAA
1262528 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
1262542 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
1262556 TTA
1 TTA
1262559 AAGTTTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:1262684 original size:20 final size:20
Alignment explanation
Indices: 1262661--1262713 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
1262651 ATAAGTAATT
*
1262661 TACTTTATATAGTTTATATA
1 TACTTTATATAGTTTATACA
* * *
1262681 TACTATACATGGTTTATACA
1 TACTTTATATAGTTTATACA
1262701 TACATATTATATA
1 TAC-T-TTATATA
1262714 AAATTATTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 19 0.79
21 1 0.04
22 4 0.17
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (20 bp):
TACTTTATATAGTTTATACA
Found at i:1263083 original size:21 final size:20
Alignment explanation
Indices: 1263058--1263118 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1263048 TTTACATTAG
**
1263058 GGTTTATGATTTAGTGTTTA
1 GGTTTATGATTTAAAGTTTA
* *
1263078 GTGTTTGTGGTTTAAAGTTTAA
1 G-GTTTATGATTTAAAGTTT-A
*
1263100 GGTTTATGATTTAAGGTTT
1 GGTTTATGATTTAAAGTTT
1263119 CTATAAACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.91
22 2 0.06
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.52
Consensus pattern (20 bp):
GGTTTATGATTTAAAGTTTA
Found at i:1263232 original size:20 final size:20
Alignment explanation
Indices: 1263193--1263240 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1263183 TAATTTATTA
*
1263193 TATATATA-TATATATAGTT
1 TATATATACTATACATAGTT
*
1263212 TATATATACTATACATGGTT
1 TATATATACTATACATAGTT
*
1263232 TATAAATAC
1 TATATATAC
1263241 ATATTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (20 bp):
TATATATACTATACATAGTT
Found at i:1263453 original size:537 final size:537
Alignment explanation
Indices: 1262450--1263915 Score: 2261
Period size: 537 Copynumber: 2.8 Consensus size: 537
1262440 TTTTGGCAAT
* * *
1262450 ACATTAGTTTACAAAGG-CCAATACATAAGCCCACTATTTTATTACAAATATATATGCATTAGTG
1 ACATTAGTTTACATAGGCCCAATGC--AAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
* ** *
1262514 CTAGTCCATTTAAATTAGGGTTTATGGTTTAGTGTTTA-TGGTTTAAAGTTTAGAA--TTAGGGT
64 CTAGTCCATTTAAATTAGGGTTTATGATTTAGTGTTTAGT-GTTTATGGTTTA-AAGTTTAAGGT
* *
1262576 TTAGGATTT-AGGATTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTT
127 TTATGATTTAAGG-TTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGTATAGTGTTT
*
1262640 CTATAAACTATATAAGT-A---A-T-T-TA-CT-T-TATATAGTTTATATATACTATACATGGTT
191 CTATAAACTATATAAGTAATTTATTATATATATATATATATAGTTTATATATACTATACATGGTT
1262695 TATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATAT
256 TATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATAT
* *
1262760 AAAATATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAAT
321 AAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATATGGTTCATAAAT
*
1262825 AGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTC
386 AGTAGTACATGTCATATTAATTTAAATTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTC
* * *
1262890 ACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGTTCAT
451 ACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCAT
**
1262955 TTGCAATAGTGCTAATTTATTA
516 TTGCAATAGTGCTAATCCATTA
*
1262977 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAATGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* *
1263042 AGTCCATTTACATTAGGGTTTATGATTTAGTGTTTAGTGTTTGTGGTTTAAAGTTTAAGGTTTAT
66 AGTCCATTTAAATTAGGGTTTATGATTTAGTGTTTAGTGTTTATGGTTTAAAGTTTAAGGTTTAT
*
1263107 GATTTAAGGTTTCTATAAACTATATATTTTACTACTTTATATAGTTTATGTATAGTGTTTCTATA
131 GATTTAAGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGTATAGTGTTTCTATA
*
1263172 AACTATATAAGTAATTTATTATATATATATATATATAGTTTATATATACTATACATGGTTTATAA
196 AACTATATAAGTAATTTATTATATATATATATATATAGTTTATATATACTATACATGGTTTATAC
1263237 ATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAAC
261 ATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAAC
1263302 ATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATATGGTTCATAAATAGTAG
326 ATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATATGGTTCATAAATAGTAG
* *
1263367 TACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATT
391 TACATGTCATATTAATTTAAATTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATT
*
1263432 AATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCA
456 AATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCA
*
1263497 ATAGTGCTAGTCCATTA
521 ATAGTGCTAATCCATTA
* * *
1263514 ACATTAATTTAGATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGAT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* *
1263579 AGTCCATTTATATTAGGGTTTATGATTTAGTGTTTAGTGTTTATGATTTAAAGTTTAGGGTTTAG
66 AGTCCATTTAAATTAGGGTTTATGATTTAGTGTTTAGTGTTTATGGTTTAAAGTTTA------A-
* * *
1263644 GGTTTATTATTTAGGGTTTTTATAAACTATATATTTTATTACTTTATATAGTTTATGTATAGTGT
124 GGTTTATGATTTAAGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGTATAGTGT
1263709 TTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATAG-TT-TATATA-TATA
189 TTCTATAAACTATATAAGTAATTTA--TTATATA---TATATATATATAGTTTATATATACTATA
1263771 CATGGTTTATACATACATA-T-TAT-AAA--A-TT-AT----TTAATAAAATTATTTAAATGTAA
249 CATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAA
1263825 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATATGGTT
314 ATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATATGGTT
1263890 CATAAATAGTAGTACATGTCATATTA
379 CATAAATAGTAGTACATGTCATATTA
1263916 GTGTTTGTCA
Statistics
Matches: 873, Mismatches: 39, Indels: 46
0.91 0.04 0.05
Matches are distributed among these distances:
525 2 0.00
526 81 0.09
527 97 0.11
528 10 0.01
531 1 0.00
532 1 0.00
533 1 0.00
534 2 0.00
535 115 0.13
536 1 0.00
537 413 0.47
539 2 0.00
540 2 0.00
541 1 0.00
543 4 0.00
544 89 0.10
545 1 0.00
546 29 0.03
547 6 0.01
548 2 0.00
549 13 0.01
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (537 bp):
ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
AGTCCATTTAAATTAGGGTTTATGATTTAGTGTTTAGTGTTTATGGTTTAAAGTTTAAGGTTTAT
GATTTAAGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGTATAGTGTTTCTATA
AACTATATAAGTAATTTATTATATATATATATATATAGTTTATATATACTATACATGGTTTATAC
ATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAAC
ATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTCCATATTATATGGTTCATAAATAGTAG
TACATGTCATATTAATTTAAATTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATT
AATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCA
ATAGTGCTAATCCATTA
Found at i:1263613 original size:14 final size:14
Alignment explanation
Indices: 1263611--1263662 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1263601 TGATTTAGTG
*
1263611 TTTAGTGTTTATGA
1 TTTAGGGTTTATGA
** * *
1263625 TTTAAAGTTTAGGG
1 TTTAGGGTTTATGA
*
1263639 TTTAGGGTTTATTA
1 TTTAGGGTTTATGA
1263653 TTTAGGGTTT
1 TTTAGGGTTT
1263663 TTATAAACTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:1263649 original size:21 final size:21
Alignment explanation
Indices: 1263591--1263642 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1263581 TCCATTTATA
**
1263591 TTAGGGTTTATGATTTAGTGT
1 TTAGGGTTTATGATTTAAAGT
*
1263612 TTAGTGTTTATGATTTAAAGT
1 TTAGGGTTTATGATTTAAAGT
1263633 TTAGGGTTTA
1 TTAGGGTTTA
1263643 GGGTTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (21 bp):
TTAGGGTTTATGATTTAAAGT
Found at i:1263698 original size:49 final size:49
Alignment explanation
Indices: 1263655--1263753 Score: 137
Period size: 48 Copynumber: 2.0 Consensus size: 49
1263645 GTTTATTATT
* ** *
1263655 TAGGGTTTTTATAAACTATATATTTTA-TTACTTTATATAGTTTATGTA
1 TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGTA
* *
1263703 TAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATA
1 TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGTA
1263752 TA
1 TA
1263754 TATAGTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 22 0.50
49 22 0.50
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (49 bp):
TAGGGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATGTA
Found at i:1263719 original size:48 final size:49
Alignment explanation
Indices: 1263645--1263753 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 49
1263635 AGGGTTTAGG
* * * ** *
1263645 GTTTATTATTTAGGGTTTTTATAAACTATATATTTTA-TTACTTTATATA
1 GTTTA-TATATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA
*
1263694 GTTTATGTATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA
1 GTTTATATATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA
1263743 GTTTATATATA
1 GTTTATATATA
1263754 TATAGTTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 24 0.47
49 27 0.53
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (49 bp):
GTTTATATATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA
Found at i:1263757 original size:15 final size:15
Alignment explanation
Indices: 1263737--1263770 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1263727 TAATTTACTT
1263737 TATATAGTTTATATA
1 TATATAGTTTATATA
1263752 TATATAGTTTATATA
1 TATATAGTTTATATA
1263767 TATA
1 TATA
1263771 CATGGTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:1263766 original size:17 final size:17
Alignment explanation
Indices: 1263737--1263781 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1263727 TAATTTACTT
1263737 TATATAG-TT-TATATA
1 TATATAGTTTATATATA
1263752 TATATAGTTTATATATA
1 TATATAGTTTATATATA
* *
1263769 TACATGGTTTATA
1 TATATAGTTTATA
1263782 CATACATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 7 0.27
16 2 0.08
17 17 0.65
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:1263781 original size:15 final size:16
Alignment explanation
Indices: 1263743--1263789 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1263733 ACTTTATATA
*
1263743 GTTTATATATATATAG
1 GTTTATATATACATAG
*
1263759 TTTATATATATACAT-G
1 GTT-TATATATACATAG
*
1263775 GTTTATACATACATA
1 GTTTATATATACATA
1263790 TTATAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.40
16 5 0.20
17 10 0.40
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (16 bp):
GTTTATATATACATAG
Found at i:1263808 original size:13 final size:13
Alignment explanation
Indices: 1263792--1263818 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1263782 CATACATATT
1263792 ATAAAATTATTTA
1 ATAAAATTATTTA
1263805 ATAAAATTATTTA
1 ATAAAATTATTTA
1263818 A
1 A
1263819 ATGTAAATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:1263828 original size:15 final size:14
Alignment explanation
Indices: 1263792--1263834 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1263782 CATACATATT
1263792 ATAAAATTATTT-A
1 ATAAAATTATTTAA
1263805 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
1263819 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
1263834 A
1 A
1263835 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:1264179 original size:23 final size:23
Alignment explanation
Indices: 1264149--1264227 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
1264139 ATGCATATTA
1264149 CATTAATATACATATCATACATG
1 CATTAATATACATATCATACATG
*
1264172 CATTAATA-A-ATTATACATATATG
1 CATTAATATACA-TAT-CATACATG
* *
1264195 CATACATATTATACATA-CATGCATG
1 CAT---TAATATACATATCATACATG
1264220 CATTAATA
1 CATTAATA
1264228 AATTATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
21 1 0.02
22 8 0.18
23 18 0.41
25 9 0.20
26 4 0.09
27 3 0.07
28 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.35
Consensus pattern (23 bp):
CATTAATATACATATCATACATG
Found at i:1270512 original size:2 final size:2
Alignment explanation
Indices: 1270505--1270529 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1270495 GTTAAATCCA
1270505 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1270530 CTTGTTGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1270932 original size:18 final size:18
Alignment explanation
Indices: 1270909--1270947 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1270899 TACGTACAAA
*
1270909 TATTAAA-AAATATTTATT
1 TATTAAAGAAA-ATATATT
1270927 TATTAAAGAAAATATATT
1 TATTAAAGAAAATATATT
1270945 TAT
1 TAT
1270948 ATTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTAAAGAAAATATATT
Found at i:1271978 original size:30 final size:32
Alignment explanation
Indices: 1271944--1272011 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 32
1271934 ATAGGTTTTA
1271944 TATTTTATAGT-AAT-ATAATTATATAAATAT
1 TATTTTATAGTAAATAATAATTATATAAATAT
* * * *
1271974 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATAGT-AAATAATAATTATATAAATAT
1272007 TATTT
1 TATTT
1272012 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 9 0.29
32 3 0.10
33 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATTTTATAGTAAATAATAATTATATAAATAT
Found at i:1272013 original size:30 final size:28
Alignment explanation
Indices: 1271972--1272035 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
1271962 TTATATAAAT
* *
1271972 ATTATTTTTTATTAAAATAATATTTATATA
1 ATTATTATTTATTAAAAT-ATATTAAT-TA
* *
1272002 ATTATTATTTATTTAAATTTATTAATTA
1 ATTATTATTTATTAAAATATATTAATTA
1272030 ATTATT
1 ATTATT
1272036 TTTTTTGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 8 0.27
29 6 0.20
30 16 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTATTATTTATTAAAATATATTAATTA
Found at i:1273844 original size:21 final size:20
Alignment explanation
Indices: 1273818--1273887 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 20
1273808 GCCATCTCCG
1273818 CAGGGTTACATTCCTAGCCC
1 CAGGGTTACATTCCTAGCCC
1273838 TCAGGGTTACATTCCTAGTCCGC
1 -CAGGGTTACATTCCTAG-CC-C
* *
1273861 CA-GGTTACATGCATAGCCC
1 CAGGGTTACATTCCTAGCCC
1273880 GCAGGGTT
1 -CAGGGTT
1273888 TTATTACACC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 1 0.02
20 4 0.09
21 33 0.77
22 4 0.09
23 1 0.02
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (20 bp):
CAGGGTTACATTCCTAGCCC
Found at i:1274762 original size:63 final size:63
Alignment explanation
Indices: 1274661--1274785 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 63
1274651 CAATGTCACG
* * *
1274661 ACCAACTTATCACTTCACATTTATTTAATTTATCCATAACATTTTATCCAATATATTCAAACA
1 ACCAACTTATCACTTAACATTTATTCAATTTATCCATAACATTTTATACAATATATTCAAACA
* * *
1274724 ACCAA-TTGATCACTTAACATTTATTCAATTTATTCATAACATTTTATATAATTTATTCAAAC
1 ACCAACTT-ATCACTTAACATTTATTCAATTTATCCATAACATTTTATACAATATATTCAAAC
1274786 TTCACATAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 2 0.04
63 53 0.96
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.42
Consensus pattern (63 bp):
ACCAACTTATCACTTAACATTTATTCAATTTATCCATAACATTTTATACAATATATTCAAACA
Found at i:1274769 original size:23 final size:22
Alignment explanation
Indices: 1274738--1274782 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1274728 ATTGATCACT
1274738 TAACATTTAT-TCAATTTATTCA
1 TAACATTTATAT-AATTTATTCA
1274760 TAACATTTTATATAATTTATTCA
1 TAACA-TTTATATAATTTATTCA
1274783 AACTTCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 15 0.71
24 1 0.05
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (22 bp):
TAACATTTATATAATTTATTCA
Found at i:1275166 original size:138 final size:138
Alignment explanation
Indices: 1274918--1275267 Score: 619
Period size: 138 Copynumber: 2.5 Consensus size: 138
1274908 CCATCCATCT
*
1274918 ATAGTTCCCCGGGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
1274983 CGAAGGCGCGCCCCCGGGAACACGCTTTCACCATTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 CGAAGGCGCGCCCCCGGAAACACGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
1275048 TGACATGA
131 TGACATGA
*
1275056 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
****
1275121 CGAAGGCGCGCCCCCGGAAATTTTCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
66 CGAAGGCGCGCCCCCGGAAACACGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
1275186 TGACATGA
131 TGACATGA
1275194 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1275259 CAAAGGCGC
66 CGAAGGCGC
1275268 CCCTCGGGAA
Statistics
Matches: 202, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
138 202 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (138 bp):
ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
CGAAGGCGCGCCCCCGGAAACACGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTAC
TGACATGA
Found at i:1278441 original size:21 final size:21
Alignment explanation
Indices: 1278415--1278455 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1278405 CCTAAATAAT
*
1278415 TTTTTAAAATTTTTATTTAAA
1 TTTTTAAAATATTTATTTAAA
**
1278436 TTTTTATGATATTTATTTAA
1 TTTTTAAAATATTTATTTAA
1278456 TATAATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTAAAATATTTATTTAAA
Found at i:1278495 original size:21 final size:21
Alignment explanation
Indices: 1278469--1278510 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1278459 AATAATTAAT
*
1278469 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
1278490 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
1278511 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:1281625 original size:59 final size:59
Alignment explanation
Indices: 1281533--1281646 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
1281523 AATAAATAGA
* * * *
1281533 TAAGTGTCCTATCGAACCTTCCTAGTCGCAATGAAGAGGCAAACTCGATAATATGACTC
1 TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGACAAACTCGATAATATGACTC
* *
1281592 TAAGTGTCATATTGAACCCTCCTAGTTGCAATGAAAAGACAAACTCGATAATATG
1 TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGACAAACTCGATAATATG
1281647 GCTCAAACCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (59 bp):
TAAGTGTCATATCGAACCCTCCTAGTCGCAATGAAAAGACAAACTCGATAATATGACTC
Found at i:1282850 original size:26 final size:26
Alignment explanation
Indices: 1282821--1282872 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1282811 AGTTTTCAAG
*
1282821 ACTTCATTCAGACTAATCCATAGCTA
1 ACTTCATTCAGACTAATCAATAGCTA
*
1282847 ACTTCATTCTGACTAATCAATAGCTA
1 ACTTCATTCAGACTAATCAATAGCTA
1282873 CCCGGGTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.33
Consensus pattern (26 bp):
ACTTCATTCAGACTAATCAATAGCTA
Found at i:1285345 original size:18 final size:18
Alignment explanation
Indices: 1285313--1285348 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1285303 TCGAAGCCTG
**
1285313 TAAAATAATTGTAATATA
1 TAAAATAATAATAATATA
1285331 TAAAATAATAATAATATA
1 TAAAATAATAATAATATA
1285349 ATGATTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAATAATAATAATATA
Found at i:1286233 original size:83 final size:84
Alignment explanation
Indices: 1286091--1286331 Score: 297
Period size: 83 Copynumber: 2.8 Consensus size: 84
1286081 TGATATGTCA
* * * * * *
1286091 TTGAGCTGAATGGAATCGAACTCGACAGTTTTTTGTTGACAGATAGCCTTTCTCACCTTGAGTTA
1 TTGAGCTGAATGTAATCAAACTCGA-AGGTCTTTGTTGACAGATAACC-CTCTCACCTTGAGTTA
*
1286156 TGCTGTAAATTTGTTATACCC
64 TGCTGTAAATTTGGTATACCC
*
1286177 TTGAGCTGAATGTAATCAAACTCG-AGG-GTTTGTTGACAGATAACTCCTCTCACCTTGAGTTAT
1 TTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAAC-CCTCTCACCTTGAGTTAT
* ** *
1286240 GCTATAAATTTGGTATGTCT
65 GCTGTAAATTTGGTATACCC
* * *
1286260 TTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
1 TTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCC-TCTCACCTTGAGTTAT
1286325 GCTGTAA
65 GCTGTAA
1286332 TAGGCTAGGA
Statistics
Matches: 135, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
83 69 0.51
84 8 0.06
85 36 0.27
86 22 0.16
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (84 bp):
TTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTCTCACCTTGAGTTATG
CTGTAAATTTGGTATACCC
Found at i:1286724 original size:65 final size:63
Alignment explanation
Indices: 1286586--1286758 Score: 219
Period size: 60 Copynumber: 2.7 Consensus size: 63
1286576 GAAGTTGAGA
* * * * * *
1286586 TTTGAATTGGATATCATTCATTGTGAAGTTGAAATCCAA---GGGT-TGTTTCACCAAATTGGT
1 TTTGAGTTGGATATCATTC-GTGTGAAGTTGAAATCCAATCTGAGTAAGTTTCACCAAATTAGC
1286646 TTTGAGTTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTAGC
1 TTTGAGTTGGATATCATTCGT-GTGAAGTTGAAATCCAATC-TGAGTAAGTTTCACCAAATTAGC
*
1286711 TTTGAGTTGGATATCCTTCGTGTGAAGTTGAAATCCAATCTCGAGTAA
1 TTTGAGTTGGATATCATTCGTGTGAAGTTGAAATCCAATCT-GAGTAA
1286759 ATTGTGTCGC
Statistics
Matches: 99, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
59 1 0.01
60 35 0.35
63 1 0.01
64 28 0.28
65 34 0.34
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (63 bp):
TTTGAGTTGGATATCATTCGTGTGAAGTTGAAATCCAATCTGAGTAAGTTTCACCAAATTAGC
Found at i:1286858 original size:64 final size:64
Alignment explanation
Indices: 1286772--1286892 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
1286762 GTGTCGCTTC
** *
1286772 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTATT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGAATCTGAATGAAACTGAAAAGTTATTTATT
* * *
1286836 GAGTCCAATATTCTTCACTGTGAAGTTGAAATTGAATCTGAATGAAATTGGAAAGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGAATCTGAATGAAACTGAAAAGTT
1286893 GTTTGCTGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGAATCTGAATGAAACTGAAAAGTTATTTATT
Found at i:1288693 original size:19 final size:18
Alignment explanation
Indices: 1288636--1288706 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 18
1288626 TTTTCTTCAC
* *
1288636 TTTTTCCTTTGTT-TTTG
1 TTTTTCTTTTTTTCTTTG
* ** *
1288653 TTTCTCTTTTTTAATTTC
1 TTTTTCTTTTTTTCTTTG
1288671 TTTTTGCTTTTTTTCTTTG
1 TTTTT-CTTTTTTTCTTTG
1288690 TTTTTCTCTTTTTTCTT
1 TTTTTCT-TTTTTTCTT
1288707 CTTCTCACAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
17 9 0.21
18 9 0.21
19 24 0.57
ACGTcount: A:0.03, C:0.14, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTTCTTTTTTTCTTTG
Found at i:1291713 original size:12 final size:13
Alignment explanation
Indices: 1291696--1291724 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1291686 TTAATTACGA
1291696 AAAATTAAAA-TT
1 AAAATTAAAATTT
1291708 AAAATTAAAATTT
1 AAAATTAAAATTT
1291721 AAAA
1 AAAA
1291725 ATTCAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:1293949 original size:21 final size:21
Alignment explanation
Indices: 1293876--1293950 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
1293866 CAGTTTCCAG
* * * *
1293876 ATTCGCAACGCGATTATGACT
1 ATTCGCAATGCGATTTTCACA
1293897 A-TCGCAATGCGATTTTC-CA
1 ATTCGCAATGCGATTTTCACA
**
1293916 ATTTCGCGTTGCGATTTTCACA
1 A-TTCGCAATGCGATTTTCACA
1293938 ATTCGCAATGCGA
1 ATTCGCAATGCGA
1293951 ATAAGTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 25 0.58
22 3 0.07
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCACA
Found at i:1293965 original size:20 final size:21
Alignment explanation
Indices: 1293940--1293987 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1293930 TTTTCACAAT
*
1293940 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
*
1293960 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTAAGAAAA
1293981 TCGCAAT
1 TCGCAAT
1293988 ACGATACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1294005 original size:20 final size:20
Alignment explanation
Indices: 1293989--1294053 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
1293979 AATCGCAATA
1293989 CGATACTGACTATCGCAACG
1 CGATACTGACTATCGCAACG
* *
1294009 CGATACTTACTTTCGCAACG
1 CGATACTGACTATCGCAACG
*
1294029 CGATACTGACTTTCGCAACG
1 CGATACTGACTATCGCAACG
*
1294049 AGATA
1 CGATA
1294054 ATACATAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (20 bp):
CGATACTGACTATCGCAACG
Found at i:1294268 original size:22 final size:22
Alignment explanation
Indices: 1294240--1294283 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1294230 CACTCTCTCA
1294240 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1294262 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1294284 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1294574 original size:20 final size:20
Alignment explanation
Indices: 1294546--1294594 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1294536 TTTATTCTCT
*
1294546 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
1294566 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
1294586 TGTTGCGAT
1 CGTTGCGAT
1294595 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1294595 original size:20 final size:20
Alignment explanation
Indices: 1294562--1294604 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1294552 GATAGTCAAA
1294562 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
* *
1294582 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTGTCATT
1294602 TTC
1 TTC
1294605 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:1295944 original size:18 final size:18
Alignment explanation
Indices: 1295923--1295971 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
1295913 CTCTACTTTG
1295923 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
*
1295941 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
1295959 AGAGCCATCACCT
1 AGAGCCATCACCT
1295972 GATCAACCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.45, G:0.12, T:0.14
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:1296530 original size:20 final size:20
Alignment explanation
Indices: 1296505--1296550 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1296495 TAGTTTACTT
1296505 TCGCAACAC-GAAAATGACTA
1 TCGCAACACAG-AAATGACTA
* *
1296525 TCGCAACGCAGAAATGGCTA
1 TCGCAACACAGAAATGACTA
1296545 TCGCAA
1 TCGCAA
1296551 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAATGACTA
Found at i:1296559 original size:19 final size:20
Alignment explanation
Indices: 1296516--1296560 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1296506 CGCAACACGA
1296516 AAATGACTATCGCAACGCAG
1 AAATGACTATCGCAACGCAG
* *
1296536 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCAG
1296555 AAATGA
1 AAATGA
1296561 AAATCGCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCAG
Found at i:1296566 original size:19 final size:19
Alignment explanation
Indices: 1296544--1296640 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
1296534 AGAAATGGCT
1296544 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1296563 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
1296577 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1296596 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1296610 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1296629 ATCGCAATGCGA
1 ATCGCAATGCGA
1296641 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 21 0.33
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.51
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1296586 original size:33 final size:33
Alignment explanation
Indices: 1296544--1296637 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1296534 AGAAATGGCT
1296544 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
1296577 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
1296610 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
1296638 CGATTTGTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:1296612 original size:14 final size:14
Alignment explanation
Indices: 1296560--1296618 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1296550 ATGCGAAATG
*
1296560 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
1296574 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1296593 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1296607 AAAATCGCAACG
1 AAAATCGCAACG
1296619 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 1 0.03
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1296671 original size:14 final size:14
Alignment explanation
Indices: 1296652--1296710 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1296642 TTGTGTTTCG
1296652 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1296666 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1296683 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1296699 CATTGCGATTTT
1 CGTTGCGATTTT
1296711 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 18 0.49
15 3 0.08
16 3 0.08
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1296684 original size:33 final size:33
Alignment explanation
Indices: 1296647--1296726 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1296637 GCGATTTGTG
* *
1296647 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1296680 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1296713 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1296727 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
Found at i:1296692 original size:19 final size:19
Alignment explanation
Indices: 1296668--1296726 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1296658 GATTTTGTCG
1296668 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1296687 TTGCGA-TTT--TGT--CA
1 TTGCGATTTTCATTTCGCA
1296701 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1296720 TTGCGAT
1 TTGCGAT
1296727 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 8 0.24
15 3 0.09
16 2 0.06
17 2 0.06
18 3 0.09
19 15 0.45
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1296745 original size:20 final size:19
Alignment explanation
Indices: 1296711--1296765 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1296701 TTGCGATTTT
1296711 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
1296730 CATTTCCGCGTTGCGATAGC
1 CATTT-CGCATTGCGATAGC
1296750 CATTTTCGCATTGCGA
1 CA-TTTCGCATTGCGA
1296766 AAGTAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:1296776 original size:20 final size:20
Alignment explanation
Indices: 1296753--1296791 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1296743 CGATAGCCAT
1296753 TTTCGCATTGCGAAAGTAAG
1 TTTCGCATTGCGAAAGTAAG
**
1296773 TTTCGTGTTGCGAAAGTAA
1 TTTCGCATTGCGAAAGTAA
1296792 ACTATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
TTTCGCATTGCGAAAGTAAG
Found at i:1298601 original size:14 final size:14
Alignment explanation
Indices: 1298567--1298605 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1298557 TTGATTGTTT
1298567 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1298581 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1298595 TGTTGATTTGT
1 AATTGATTTGT
1298606 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1298769 original size:19 final size:19
Alignment explanation
Indices: 1298745--1298828 Score: 133
Period size: 19 Copynumber: 4.7 Consensus size: 19
1298735 GCAACGAGAG
1298745 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1298764 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1298783 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1298802 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
1298816 AATCGCAATGCGA
1 AATCGCAATGCGA
1298829 TTCTGTATTA
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.18
15 1 0.02
16 2 0.03
17 2 0.03
19 46 0.74
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1298787 original size:38 final size:33
Alignment explanation
Indices: 1298732--1298828 Score: 140
Period size: 38 Copynumber: 2.8 Consensus size: 33
1298722 GAAACTGACT
*
1298732 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1298765 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAA
1298803 ATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAACGAGAAAATCGCAATGCGA
1298829 TTCTGTATTA
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
33 23 0.40
34 1 0.02
35 2 0.03
36 2 0.03
37 1 0.02
38 29 0.50
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:1298863 original size:20 final size:20
Alignment explanation
Indices: 1298838--1298890 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1298828 ATTCTGTATT
1298838 ATCTCGTTGCGATAGTCAGA
1 ATCTCGTTGCGATAGTCAGA
* * *
1298858 ATCTCGCTGCGAAAGTCAGT
1 ATCTCGTTGCGATAGTCAGA
* *
1298878 ATCGCATTGCGAT
1 ATCTCGTTGCGAT
1298891 TTTGTATTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (20 bp):
ATCTCGTTGCGATAGTCAGA
Found at i:1298930 original size:20 final size:20
Alignment explanation
Indices: 1298844--1298931 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
1298834 TATTATCTCG
* * *
1298844 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGTATCGCA
* *
1298864 CTGCGAAAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
* * *
1298884 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--TAGTCAGTATCGCA
*
1298905 TTGCGATAGTCAGTATTGCA
1 TTGCGATAGTCAGTATCGCA
1298925 TTGCGAT
1 TTGCGAT
1298932 TTTCCAAATT
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.06
20 33 0.65
21 13 0.25
22 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCA
Found at i:1298950 original size:41 final size:41
Alignment explanation
Indices: 1298865--1298994 Score: 138
Period size: 41 Copynumber: 3.1 Consensus size: 41
1298855 AGAATCTCGC
* * ** * *
1298865 TGCGAAAGTCAGTATCGCATTGCGATTTT-GTATTATCGCGT
1 TGCGATAGTCAGTATTGCATTGCGATTTTCCAAAT-TCGCAT
1298906 TGCGATAGTCAGTATTGCATTGCGATTTTCCAAATTCGCAT
1 TGCGATAGTCAGTATTGCATTGCGATTTTCCAAATTCGCAT
** *
1298947 TGCGATTTTCCA-AATTCGCATTGCGATTTTCCAAATTCGCAT
1 TGCGATAGT-CAGTATT-GCATTGCGATTTTCCAAATTCGCAT
1298989 TGCGAT
1 TGCGAT
1298995 TTACTTATTC
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
41 42 0.55
42 35 0.45
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (41 bp):
TGCGATAGTCAGTATTGCATTGCGATTTTCCAAATTCGCAT
Found at i:1299006 original size:20 final size:21
Alignment explanation
Indices: 1298922--1299013 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
1298912 AGTCAGTATT
1298922 GCATTGCGATTTTCCAAATTC
1 GCATTGCGATTTTCCAAATTC
1298943 GCATTGCGATTTTCCAAATTC
1 GCATTGCGATTTTCCAAATTC
1298964 GCATTGCGATTTTCCAAATTC
1 GCATTGCGATTTTCCAAATTC
* **
1298985 GCATTGCGA-TTTACTTATTC
1 GCATTGCGATTTTCCAAATTC
1299005 GCATTGCGA
1 GCATTGCGA
1299014 ATTGGGAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
20 17 0.25
21 51 0.75
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (21 bp):
GCATTGCGATTTTCCAAATTC
Found at i:1299028 original size:41 final size:42
Alignment explanation
Indices: 1298922--1299028 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 42
1298912 AGTCAGTATT
* * * *
1298922 GCATTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAATTC
1 GCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTC
* * * **
1298964 GCATTGCGATTTTCCAAATTCGCATTGCGA-TTTACTTATTC
1 GCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTC
**
1299005 GCATTGCGAATTGGGAAAATCGCA
1 GCATTGCGAATTGCCAAAATCGCA
1299029 ACGCGAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 27 0.47
42 30 0.53
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (42 bp):
GCATTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTC
Found at i:1299055 original size:21 final size:22
Alignment explanation
Indices: 1299003--1299055 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1298993 ATTTACTTAT
1299003 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1299024 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1299045 TCGCATTGCGA
1 TCGCATTGCGA
1299056 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1299253 original size:3 final size:3
Alignment explanation
Indices: 1299245--1299285 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1299235 ATATATAAAT
1299245 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1299286 GTTTTTGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1299430 original size:3 final size:3
Alignment explanation
Indices: 1299424--1299452 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1299414 GTTGTTGTTG
1299424 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1299453 TTGAAGATGG
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:1303242 original size:33 final size:32
Alignment explanation
Indices: 1303186--1303263 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 32
1303176 TCAATTGCAA
* *
1303186 CAAAGTTTACGATAATTGAAATACTTAAATACTT
1 CAAAG-TT-CGATAATTCAAATACTTAAAAACTT
*
1303220 CCAAGTTCGATAAATTCAAATACTTAAAAACTT
1 CAAAGTTCGAT-AATTCAAATACTTAAAAACTT
1303253 CAAAGTTCGAT
1 CAAAGTTCGAT
1303264 GTTTGAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
32 4 0.10
33 31 0.79
34 4 0.10
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (32 bp):
CAAAGTTCGATAATTCAAATACTTAAAAACTT
Found at i:1303358 original size:31 final size:32
Alignment explanation
Indices: 1303320--1303380 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1303310 ATCATCTTCT
1303320 CCTTCTTCGTTT-GGGGGATATTCCAAGTTTG
1 CCTTCTTCGTTTGGGGGGATATTCCAAGTTTG
1303351 CCTTCTTCGTTTGGGGGGATATTCCAAGTT
1 CCTTCTTCGTTTGGGGGGATATTCCAAGTT
1303381 CGACTTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (32 bp):
CCTTCTTCGTTTGGGGGGATATTCCAAGTTTG
Found at i:1307732 original size:13 final size:13
Alignment explanation
Indices: 1307716--1307740 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1307706 TCCTTTTCCT
1307716 TTTCCCTTTCCCC
1 TTTCCCTTTCCCC
1307729 TTTCCCTTTCCC
1 TTTCCCTTTCCC
1307741 TGGTTGTCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTCCCTTTCCCC
Found at i:1308164 original size:9 final size:8
Alignment explanation
Indices: 1308139--1308163 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1308129 TATTTTTATT
1308139 ATTAAAAA
1 ATTAAAAA
1308147 ATTAAAAA
1 ATTAAAAA
1308155 ATTAAAAA
1 ATTAAAAA
1308163 A
1 A
1308164 AATATAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATTAAAAA
Found at i:1317180 original size:2 final size:2
Alignment explanation
Indices: 1317173--1317198 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1317163 TTCGTGTTAA
1317173 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
1317199 GGGTGATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1317656 original size:14 final size:14
Alignment explanation
Indices: 1317637--1317673 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1317627 ATAAATAGTC
1317637 AATTAAATTGAATT
1 AATTAAATTGAATT
*
1317651 AATTAAATTGATTT
1 AATTAAATTGAATT
*
1317665 AATCAAATT
1 AATTAAATT
1317674 ATTTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (14 bp):
AATTAAATTGAATT
Found at i:1317679 original size:13 final size:14
Alignment explanation
Indices: 1317641--1317680 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1317631 ATAGTCAATT
* *
1317641 AAATTGAATTAATT
1 AAATTGATTTAATC
1317655 AAATTGATTTAATC
1 AAATTGATTTAATC
1317669 AAATT-ATTTAAT
1 AAATTGATTTAAT
1317681 TTTATTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (14 bp):
AAATTGATTTAATC
Found at i:1319539 original size:30 final size:30
Alignment explanation
Indices: 1319483--1319539 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1319473 GATTTATTTA
* *
1319483 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTTG
1319513 GTGACCAAAGTATAAACTTT-GAAAAGT
1 GTGACCAAAGTATAAA-TTTGGAAAAGT
1319540 ATAGGGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTTG
Found at i:1319549 original size:30 final size:30
Alignment explanation
Indices: 1319483--1319549 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
1319473 GATTTATTTA
* * *
1319483 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTAG
1319513 GTGACCAAAGTATAAACTTT-GAAAAGTATAG
1 GTGACCAAAGTATAAA-TTTGGAAAAGT-TAG
1319544 G-GACCA
1 GTGACCA
1319550 TAATGTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.28
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTAG
Found at i:1320771 original size:9 final size:9
Alignment explanation
Indices: 1320757--1320819 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
1320747 ATTCCATTAC
1320757 TGGAATTTA
1 TGGAATTTA
*
1320766 TGGAATTTC
1 TGGAATTTA
*
1320775 TCGAATTTA
1 TGGAATTTA
*
1320784 TGG-AGTTA
1 TGGAATTTA
*
1320792 CTGGAATTTC
1 -TGGAATTTA
*
1320802 TGGAATTTT
1 TGGAATTTA
*
1320811 TGGTATTTA
1 TGGAATTTA
1320820 AAATTTAAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
8 4 0.10
9 35 0.83
10 3 0.07
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.46
Consensus pattern (9 bp):
TGGAATTTA
Found at i:1320782 original size:18 final size:18
Alignment explanation
Indices: 1320759--1320809 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1320749 TCCATTACTG
1320759 GAATTTATGGAATTTCTC
1 GAATTTATGGAATTTCTC
* * *
1320777 GAATTTATGGAGTTACTG
1 GAATTTATGGAATTTCTC
*
1320795 GAATTTCTGGAATTT
1 GAATTTATGGAATTT
1320810 TTGGTATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (18 bp):
GAATTTATGGAATTTCTC
Found at i:1320787 original size:27 final size:27
Alignment explanation
Indices: 1320761--1320819 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1320751 CATTACTGGA
1320761 ATTTA-TGGAATTTCTCGAATTTATGG
1 ATTTACTGGAATTTCTCGAATTTATGG
* * *
1320787 AGTTACTGGAATTTCTGGAATTTTTGG
1 ATTTACTGGAATTTCTCGAATTTATGG
1320814 TATTTA
1 -ATTTA
1320820 AAATTTAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 19 0.70
28 4 0.15
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (27 bp):
ATTTACTGGAATTTCTCGAATTTATGG
Found at i:1321785 original size:38 final size:38
Alignment explanation
Indices: 1321734--1321883 Score: 176
Period size: 38 Copynumber: 3.9 Consensus size: 38
1321724 GAGTCGAGGG
* * *
1321734 TTACATCATTCGGGATGACAGGTCATCCGGGACACAGA
1 TTACATCCTTCGGGATGACAGGTCCTACGGGACACAGA
*
1321772 TTACATCCTTCGGGATGACAGGTCCTTCGGGACACAGA
1 TTACATCCTTCGGGATGACAGGTCCTACGGGACACAGA
* *
1321810 TTACATCTTTCGGGATGATC-GGTCCTACGGGACATAGA
1 TTACATCCTTCGGGATGA-CAGGTCCTACGGGACACAGA
* * * * **
1321848 TGACATCCTACAGGATGATAGGTCCTTTGGGACACA
1 TTACATCCTTCGGGATGACAGGTCCTACGGGACACA
1321884 ATTTATATGA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 95 0.99
39 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (38 bp):
TTACATCCTTCGGGATGACAGGTCCTACGGGACACAGA
Found at i:1321786 original size:21 final size:21
Alignment explanation
Indices: 1321761--1321824 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1321751 ACAGGTCATC
1321761 CGGGACACAGATTACATCCTT
1 CGGGACACAGATTACATCCTT
* *
1321782 CGGGATGACAG-----GTCCTT
1 CGGGA-CACAGATTACATCCTT
*
1321799 CGGGACACAGATTACATCTTT
1 CGGGACACAGATTACATCCTT
1321820 CGGGA
1 CGGGA
1321825 TGATCGGTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
16 4 0.12
17 10 0.31
21 14 0.44
22 4 0.12
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (21 bp):
CGGGACACAGATTACATCCTT
Found at i:1321864 original size:76 final size:76
Alignment explanation
Indices: 1321734--1321883 Score: 203
Period size: 76 Copynumber: 2.0 Consensus size: 76
1321724 GAGTCGAGGG
* * * *
1321734 TTACATCATTCGGGATGACAGGTCATCCGGGACACAGATTACATCCTTCGGGATGACAGGTCCTT
1 TTACATCATTCGGGATGACAGGTCATACGGGACACAGATGACATCCTACAGGATGACAGGTCCTT
1321799 CGGGACACAGA
66 CGGGACACAGA
* * * *
1321810 TTACATCTTTCGGGATGATC-GGTCCTACGGGACATAGATGACATCCTACAGGATGATAGGTCCT
1 TTACATCATTCGGGATGA-CAGGTCATACGGGACACAGATGACATCCTACAGGATGACAGGTCCT
*
1321874 TTGGGACACA
65 TCGGGACACA
1321884 ATTTATATGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 63 0.98
77 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (76 bp):
TTACATCATTCGGGATGACAGGTCATACGGGACACAGATGACATCCTACAGGATGACAGGTCCTT
CGGGACACAGA
Found at i:1321996 original size:12 final size:12
Alignment explanation
Indices: 1321959--1322059 Score: 107
Period size: 12 Copynumber: 8.6 Consensus size: 12
1321949 CTCAATACTG
1321959 TACATGGGCTAA
1 TACATGGGCTAA
* * *
1321971 TGCAT-AGATAA
1 TACATGGGCTAA
1321982 TACATGGGCTAA
1 TACATGGGCTAA
1321994 TACATGGGCTAA
1 TACATGGGCTAA
* * *
1322006 TGCAT-AGATAA
1 TACATGGGCTAA
1322017 TACATGGGCTAA
1 TACATGGGCTAA
* *
1322029 TACATTGACTAA
1 TACATGGGCTAA
*
1322041 TACATGGGTTAA
1 TACATGGGCTAA
1322053 TACATGG
1 TACATGG
1322060 TCTTATAAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
11 16 0.23
12 54 0.77
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (12 bp):
TACATGGGCTAA
Found at i:1321998 original size:35 final size:35
Alignment explanation
Indices: 1321959--1322033 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
1321949 CTCAATACTG
1321959 TACATGGGCTAATGCATAGATAATACATGGGCTAA
1 TACATGGGCTAATGCATAGATAATACATGGGCTAA
1321994 TACATGGGCTAATGCATAGATAATACATGGGCTAA
1 TACATGGGCTAATGCATAGATAATACATGGGCTAA
1322029 TACAT
1 TACAT
1322034 TGACTAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (35 bp):
TACATGGGCTAATGCATAGATAATACATGGGCTAA
Found at i:1322041 original size:35 final size:35
Alignment explanation
Indices: 1321959--1322059 Score: 139
Period size: 35 Copynumber: 2.9 Consensus size: 35
1321949 CTCAATACTG
*
1321959 TACATGGGCTAATGCATAGATAATACATGGGCTAA
1 TACATGGACTAATGCATAGATAATACATGGGCTAA
*
1321994 TACATGGGCTAATGCATAGATAATACATGGGCTAA
1 TACATGGACTAATGCATAGATAATACATGGGCTAA
* * * *
1322029 TACATTGACTAATACATGGGTTAATACATGG
1 TACATGGACTAATGCAT-AGATAATACATGG
1322060 TCTTATAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 49 0.82
36 11 0.18
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (35 bp):
TACATGGACTAATGCATAGATAATACATGGGCTAA
Found at i:1328866 original size:234 final size:232
Alignment explanation
Indices: 1328402--1328883 Score: 738
Period size: 234 Copynumber: 2.0 Consensus size: 232
1328392 TATATTCGGG
*
1328402 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGGTTTTTTTAAGTGTGATATTT
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGGTTTTTTTAAGTGTGATATTC
1328467 GGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAACACCCGACCCAACCCAAAAATATATATAATAA
66 GGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAACACCCGACCCAACCCAAAAATATATATAAT-A
** * *
1328532 TTTACCTTATATATTTAGGAATAATTATAATAATGCCCCTCTATATATAATTTTTTTCAATTAAG
130 TTTACCTTATATATTTAAAAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAG
1328597 TCATTGTTTTTATTGAATAAAAATATATTTTTTTTTATT
195 TCATTGTTTTTATTGAATAAAAATATA-TTTTTTTTATT
*
1328636 TCGGGTTGGGTCGGGTGAAACTTTATTTTGGTCGGGT-AGGGTCGGTTTTTTTAAGTGTGATATT
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCA-GGTCGGTTTTTTTAAGTGTGATATT
* *
1328700 CGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCGACCCAAAAA-ATATA
65 CGGGTCGGGTCGAGTTCGGGTTTAGGGTG-AAAA-A--C-ACCCGACCCAACCCAAAAATATATA
*
1328764 TAAT-TTTACCTTATATATTTAAAAATAATTACAATAATATCCCTCTATATATAATTTTTTTTCA
125 TAATATTTACCTTATATATTTAAAAATAATTACAATAATACCCCTCTATATATAA-TTTTTTTCA
* *
1328828 ATTAAGTCATTGTTTTTATTGAATACAAATA-ATTTTTTTATTACT
189 ATTAAGTCATTGTTTTTATTGAATAAAAATATA-TTTTTT-TTATT
1328873 TCGGGTCGGGT
1 TCGGGTCGGGT
1328884 TTCTAATTTA
Statistics
Matches: 228, Mismatches: 12, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
233 1 0.00
234 88 0.39
235 4 0.02
236 54 0.24
237 53 0.23
238 10 0.04
239 18 0.08
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (232 bp):
TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTCGGTTTTTTTAAGTGTGATATTC
GGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAACACCCGACCCAACCCAAAAATATATATAATAT
TTACCTTATATATTTAAAAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGT
CATTGTTTTTATTGAATAAAAATATATTTTTTTTATT
Found at i:1331787 original size:28 final size:28
Alignment explanation
Indices: 1331738--1331791 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1331728 AAATTAGTCT
*
1331738 TATTAATATATTAAATGATAAATATAACA
1 TATTAATACATTAAATGATAAA-ATAACA
*
1331767 TATTAA-ACATTAGATGATAAAATAA
1 TATTAATACATTAAATGATAAAATAA
1331792 TGCTCAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 13 0.57
29 6 0.26
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (28 bp):
TATTAATACATTAAATGATAAAATAACA
Done.