Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007850.1 Hibiscus syriacus cultivar Beakdansim tig00110209_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: 1775394
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1563822 original size:87 final size:87
Alignment explanation
Indices: 1563731--1563909 Score: 313
Period size: 87 Copynumber: 2.1 Consensus size: 87
1563721 AGAAACTGTC
* *
1563731 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
1563796 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * *
1563818 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
1563883 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
1563905 TCAAG
1 TCAAG
1563910 AGAAACTGTC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:1564009 original size:189 final size:189
Alignment explanation
Indices: 1563629--1564014 Score: 508
Period size: 189 Copynumber: 2.0 Consensus size: 189
1563619 AGAAACTATC
* *
1563629 TCAAGGGAGACAAAATTTTGTTTCAATGGAAACTATCTCAAGAGAGACAAAATTAATTTCTAAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCTAAGG
* * **
1563694 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
66 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
* * **** *
1563759 GAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTT
131 GAAAATACCCCAAGCGAGATAAAATTTATTTCAAGGAAAACAAATTCAATATTTATGTT
** * *
1563818 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTC-AAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCTAA-G
1563882 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAA
65 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAA
** * * ** *
1563947 AGAAAATGTCTCAAGGGAGATGGAA-TTAGTTTCAATGAAAACAAATTCAAATATTT-TGTT
130 AGAAAATACCCCAAGCGAGATAAAATTTA-TTTCAAGGAAAACAAATTC-AATATTTATGTT
1564007 TCAAGGGA
1 TCAAGGGA
1564015 AACTTGGAAA
Statistics
Matches: 170, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
188 5 0.03
189 159 0.94
190 6 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (189 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCTAAGG
AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
GAAAATACCCCAAGCGAGATAAAATTTATTTCAAGGAAAACAAATTCAATATTTATGTT
Found at i:1564350 original size:106 final size:106
Alignment explanation
Indices: 1564155--1564488 Score: 449
Period size: 106 Copynumber: 3.2 Consensus size: 106
1564145 TCCAAGTAAG
* * * * **
1564155 TTGTATTGT-TCTGAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAA
1 TTGTATTGTCTC-GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
** * * *
1564218 TTGTTTGTTGAC-AGCCAACCGCCCCTTCGCTGTGAAGTTGAGC
64 TTGTTTGTTGACAAG-CAGTCGTCCCTTCGTTGTGAAGTTGAAC
* *
1564261 TTGTACTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATT
1 TTGTATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
1564326 GTTTGTTGACAAGCAGTCGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAAGCAGTCGTCCCTTCGTTGTGAAGTTGAAC
* *
1564367 TTGTATTGTCTTGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
1 TTGTATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* * *
1564432 GTTTGTTGACAATCAGTCGTCCCTTCATTGTGGAGTTGAAC
66 GTTTGTTGACAAGCAGTCGTCCCTTCGTTGTGAAGTTGAAC
*
1564473 TTGTGTTGTCTCGAGT
1 TTGTATTGTCTCGAGT
1564489 GGCACGATAT
Statistics
Matches: 203, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
106 198 0.98
107 5 0.02
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
TTGTATTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
GTTTGTTGACAAGCAGTCGTCCCTTCGTTGTGAAGTTGAAC
Found at i:1565107 original size:32 final size:32
Alignment explanation
Indices: 1565066--1565177 Score: 93
Period size: 32 Copynumber: 3.5 Consensus size: 32
1565056 TTTGCATCAG
* * *
1565066 GATGTTGAAT-TCCCAAAGATGCCCTAATATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAATATTC
*
1565098 GATGTTGAATCTCAAAAAATGCCCCAATATTT
1 GATGTTGAATCTCAAAAAATGCCCCAATATTC
* ** * * *
1565130 GATGTTAAAT-AAAAAAAATACCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAATATTC
*
1565161 AATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
1565178 GATGCCCTCA
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
31 25 0.39
32 35 0.55
33 4 0.06
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAATATTC
Found at i:1566224 original size:69 final size:69
Alignment explanation
Indices: 1566108--1566245 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 69
1566098 TGTCTCTCTC
**
1566108 TTGATGCTTCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTTCATGATCTTCGAGTAAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1566173 TCAT
66 TCAT
* * *
1566177 TTGATGC-TCTATGATCTTTGAGTAAAGTGGTTCAGTGATTC-GAAAATGATTGTGCTTGATCAA
1 TTGATGCTTC-ATGATCTTCGAGTAAAGTGATTCAGTAATTCAG-AAATGATTGTGCTTGATCAA
*
1566240 TTTCAT
64 TCTCAT
1566246 AGTTTGAATC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 3 0.05
69 58 0.95
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (69 bp):
TTGATGCTTCATGATCTTCGAGTAAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:1569366 original size:15 final size:15
Alignment explanation
Indices: 1569348--1569382 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1569338 AAAAACAAAT
*
1569348 TAAAAAAAGATAAGA
1 TAAAAAAAGAAAAGA
*
1569363 TAAAGAAAGAAAAGA
1 TAAAAAAAGAAAAGA
1569378 TAAAA
1 TAAAA
1569383 TAGTAAGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (15 bp):
TAAAAAAAGAAAAGA
Found at i:1569450 original size:46 final size:46
Alignment explanation
Indices: 1569362--1569454 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 46
1569352 AAAAGATAAG
*
1569362 ATAAAGAAAGAAAAGATAAAATAGTAAGTAAAATAAATATAAAAAA
1 ATAAAGAAAGAAAAGATAAAATAGTAAATAAAATAAATATAAAAAA
1569408 ATAAAGAAA-AAGAAGA-AAATATA-TAAAT-AAATGAAATAATAAAAAA
1 ATAAAGAAAGAA-AAGATAAA-ATAGTAAATAAAAT-AAAT-ATAAAAAA
1569454 A
1 A
1569455 AAATATATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
44 4 0.10
45 13 0.31
46 25 0.60
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (46 bp):
ATAAAGAAAGAAAAGATAAAATAGTAAATAAAATAAATATAAAAAA
Found at i:1569471 original size:22 final size:26
Alignment explanation
Indices: 1569442--1569503 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
1569432 AAATAAATGA
1569442 AATAATAAA-AAA-A-AAATATATAT
1 AATAATAAATAAATAGAAATATATAT
1569465 -ATAATAAATAAATAGTAAATATATAT
1 AATAATAAATAAATAG-AAATATATAT
*
1569491 AATAATTAATAAA
1 AATAATAAATAAA
1569504 ACTAATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.24
23 3 0.09
24 1 0.03
26 10 0.30
27 11 0.33
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (26 bp):
AATAATAAATAAATAGAAATATATAT
Found at i:1569474 original size:26 final size:27
Alignment explanation
Indices: 1569445--1569504 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
1569435 TAAATGAAAT
1569445 AATAAAAAAAAAATATATAT-ATAATA
1 AATAAAAAAAAAATATATATAATAATA
* ** *
1569471 AATAAATAGTAAATATATATAATAATT
1 AATAAAAAAAAAATATATATAATAATA
1569498 AATAAAA
1 AATAAAA
1569505 CTAATAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
AATAAAAAAAAAATATATATAATAATA
Found at i:1569517 original size:13 final size:13
Alignment explanation
Indices: 1569441--1569545 Score: 61
Period size: 12 Copynumber: 7.5 Consensus size: 13
1569431 TAAATAAATG
*
1569441 AAATAATAAAAAAA
1 AAATAAT-AATAAA
*
1569455 AAATATATATATAAT
1 AAATA-ATA-ATAAA
*
1569470 AAATAAATAGTAAA
1 AAAT-AATAATAAA
1569484 TATATATAATAATTAATA
1 -A-A-ATAATAA-TAA-A
1569502 AAACTAATAATAAA
1 AAA-TAATAATAAA
*
1569516 AAATAAT-ATATA
1 AAATAATAATAAA
*
1569528 AAATAAT-CTAAA
1 AAATAATAATAAA
1569540 AAATAA
1 AAATAA
1569546 AAAATATATA
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
12 20 0.27
13 4 0.05
14 13 0.18
15 17 0.23
16 13 0.18
17 6 0.08
18 1 0.01
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAA
Found at i:1569528 original size:26 final size:24
Alignment explanation
Indices: 1569482--1569545 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 24
1569472 ATAAATAGTA
* *
1569482 AATATATATAATAATTAATAAAACT
1 AATATAAAAAATAATTAATAAAA-T
1569507 AATAATAAAAAATAA-TATATAAAAT
1 AAT-ATAAAAAATAATTA-ATAAAAT
*
1569532 AATCTAAAAAATAA
1 AATATAAAAAATAA
1569546 AAAATATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 10 0.29
25 9 0.26
26 15 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (24 bp):
AATATAAAAAATAATTAATAAAAT
Found at i:1569533 original size:31 final size:32
Alignment explanation
Indices: 1569498--1569566 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
1569488 TATAATAATT
*
1569498 AATAAAACT-AATAATAAAAAATA-ATATATAA
1 AATAAAACTAAAAAATAAAAAATATATAT-TAA
*
1569529 AAT-AATCTAAAAAATAAAAAATATATATTAA
1 AATAAAACTAAAAAATAAAAAATATATATTAA
*
1569560 AGTAAAA
1 AATAAAA
1569567 AAGAAAATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
30 4 0.13
31 21 0.68
32 6 0.19
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (32 bp):
AATAAAACTAAAAAATAAAAAATATATATTAA
Found at i:1570060 original size:2 final size:2
Alignment explanation
Indices: 1570055--1570080 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1570045 ACTCGATTGA
1570055 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
1570081 TTAATATCAA
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:1576707 original size:170 final size:173
Alignment explanation
Indices: 1576425--1576768 Score: 658
Period size: 170 Copynumber: 2.0 Consensus size: 173
1576415 TTTTTTTATC
1576425 TTCCTTAAACGTGTCAGTTGATGTTTACTTGGTTTATACTTCATGATCACACCCGTTTGTTGCAT
1 TTCCTTAAACGTGTCAGTTGATGTTTACTTGGTTTATACTTCATGATCACACCCGTTTGTTGCAT
1576490 TTTCTCTATAGAAAATCGATATTATACCCGGGGTTTTGATGTTAACCTGCAAAGTAAGCCC-TTT
66 TTTCTCTATAGAAAATCGATATTATACCCGGGGTTTTGATGTTAACCTGCAAAGTAAGCCCTTTT
1576554 ACTTGATTG-TTAGA-TCAGCTTGGGAGAATTCTATGTAGGTT
131 ACTTGATTGTTTAGATTCAGCTTGGGAGAATTCTATGTAGGTT
1576595 TTCCTTAAACGTGTCAGTTGATGTTTACTTGGTTTATACTTCATGATCACACCCGTTTGTTGCAT
1 TTCCTTAAACGTGTCAGTTGATGTTTACTTGGTTTATACTTCATGATCACACCCGTTTGTTGCAT
1576660 TTTCTCTATAGAAAATCGATATTATACCCGGGGTTTTGATGTTAACCTGCAAAGTAAGCCCTTTT
66 TTTCTCTATAGAAAATCGATATTATACCCGGGGTTTTGATGTTAACCTGCAAAGTAAGCCC-TTT
1576725 TACTTGATTGTTTAGATTCAGCTTGGGAGAATTCTATGTAGGTT
130 TACTTGATTGTTTAGATTCAGCTTGGGAGAATTCTATGTAGGTT
1576769 CTGTTGTAGG
Statistics
Matches: 170, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
170 126 0.74
172 12 0.07
173 5 0.03
174 27 0.16
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (173 bp):
TTCCTTAAACGTGTCAGTTGATGTTTACTTGGTTTATACTTCATGATCACACCCGTTTGTTGCAT
TTTCTCTATAGAAAATCGATATTATACCCGGGGTTTTGATGTTAACCTGCAAAGTAAGCCCTTTT
ACTTGATTGTTTAGATTCAGCTTGGGAGAATTCTATGTAGGTT
Found at i:1578128 original size:16 final size:17
Alignment explanation
Indices: 1578097--1578179 Score: 57
Period size: 17 Copynumber: 4.9 Consensus size: 17
1578087 ATATATTAAC
1578097 TTATTAAATATATTTTA
1 TTATTAAATATATTTTA
*
1578114 TTATTAACT-TATTTTA
1 TTATTAAATATATTTTA
* **
1578130 -AAAAAAAT-TATTTTTA
1 TTATTAAATATA-TTTTA
*
1578146 TTTTTAAAAATATATTTTA
1 TTATT--AAATATATTTTA
1578165 -TATTAAAATATATTT
1 TTATT-AAATATATTT
1578180 AAATATATGA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
15 6 0.12
16 12 0.24
17 19 0.37
18 3 0.06
19 9 0.18
20 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTAAATATATTTTA
Found at i:1578148 original size:21 final size:19
Alignment explanation
Indices: 1578122--1578172 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
1578112 TATTATTAAC
1578122 TTATTTTAAAAAAAATTATTT
1 TTATTTTAAAAAAAA-TA-TT
* *
1578143 TTATTTTTAAAAATATATT
1 TTATTTTAAAAAAAATATT
*
1578162 TTATATTAAAA
1 TTATTTTAAAA
1578173 TATATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 11 0.42
20 2 0.08
21 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTTTAAAAAAAATATT
Found at i:1583721 original size:39 final size:39
Alignment explanation
Indices: 1583651--1583738 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
1583641 TGTGCGCCCC
* *
1583651 TGGAGTATTC-TCAATTTGCCTGAAGACGTCATGTAGTTG
1 TGGAGTCTTCTTC-ATTTGCCTGAAGACGTCATGCAGTTG
* * *
1583690 TGGGGTCTTCTTCATTTGTCTGAAGATGTCATGCAGTTG
1 TGGAGTCTTCTTCATTTGCCTGAAGACGTCATGCAGTTG
1583729 TGGAGTCTTC
1 TGGAGTCTTC
1583739 ATATTTAGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 40 0.95
40 2 0.05
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (39 bp):
TGGAGTCTTCTTCATTTGCCTGAAGACGTCATGCAGTTG
Found at i:1584375 original size:21 final size:19
Alignment explanation
Indices: 1584351--1584658 Score: 184
Period size: 21 Copynumber: 14.7 Consensus size: 19
1584341 CATATTCGCA
1584351 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
1584372 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
1584393 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
1584414 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
*
1584435 TTGCGATAATCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
1584456 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
1584477 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* * *
1584498 TTGCGATTTATTCTAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* * *
1584519 TTGTGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
*
1584540 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
1584561 TTGCGATAGTCGGACCAAATTCG
1 TTGCGATAGT----CCAAGTTCG
1584584 TTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
*
1584603 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* * *
1584624 TTGCAATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
1584645 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1584659 AATCGCAACG
Statistics
Matches: 243, Mismatches: 26, Indels: 38
0.79 0.08 0.12
Matches are distributed among these distances:
19 52 0.21
21 139 0.57
23 52 0.21
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:1584397 original size:42 final size:41
Alignment explanation
Indices: 1584351--1584658 Score: 272
Period size: 42 Copynumber: 7.3 Consensus size: 41
1584341 CATATTCGCA
* *
1584351 TTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTT--CG
* * *
1584393 TTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
*
1584435 TTGCGATAATCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
* * *
1584477 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
* * *
1584519 TTGTGATTTATTCCAAATT--CGTTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
* *
1584561 TTGCGATAGTCGGACCAAATT--CGTTGCGA-TAGTCCAAGTTCG
1 TTGCGATAGT----CCAAGTTCGCGTTGCGATTATTCCAAGTTCG
* * *
1584603 TTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
1584645 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1584659 AATCGCAACG
Statistics
Matches: 223, Mismatches: 27, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
38 5 0.02
40 19 0.09
42 159 0.71
44 40 0.18
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTTCG
Found at i:1584437 original size:63 final size:63
Alignment explanation
Indices: 1584360--1584572 Score: 254
Period size: 63 Copynumber: 3.3 Consensus size: 63
1584350 ATTGCGATAG
1584360 TCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
* * * * *
1584425 TCCAAATTCGTTGCGATAATCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
* * * * *
1584486 TCGAAGTTCGCGTTGCGATTTATTCTAAATT--CGTTGTGATTTATTCCAAATTCGTTGCGATTT
1 TCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTT
1584549 AT
62 AT
1584551 TCCAAGTTCGTTGCGATAGTCG
1 TCCAAGTTCGTTGCGATAGTCG
1584573 GACCAAATTC
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
61 12 0.10
63 90 0.71
65 24 0.19
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (63 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
Found at i:1584487 original size:126 final size:122
Alignment explanation
Indices: 1584351--1584651 Score: 381
Period size: 126 Copynumber: 2.4 Consensus size: 122
1584341 CATATTCGCA
* *
1584351 TTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTAGTCGAAATT--CGTTGCGATTTATTCCAAATTCGT
* *
1584415 TGCGATTTATTCCAAATTCGTTGCGATAAT-CCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
64 TGCGATTTATTCCAAATTCGTTGCGATAATGCCAAATT--CGTTGCGA--TAGTCCAAGTTCG
* * *
1584477 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGTGATTTATTCCAAATTCGTT
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TTAGTCGAAATTCGTTGCGATTTATTCCAAATTCGTT
* *
1584542 GCGATTTATTCCAAGTTCGTTGCGATAGTCGGACCAAATTCGTTGCGATAGTCCAAGTTCG
65 GCGATTTATTCCAAATTCGTTGCGATAAT--G-CCAAATTCGTTGCGATAGTCCAAGTTCG
* * *
1584603 TTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGCGAT
1 TTGCGATAGTCGAAGTTCGCGTTGCGA-TTAGTCGAAATTCGTTGCGAT
1584652 AGTCCAAAAT
Statistics
Matches: 157, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
126 135 0.86
128 16 0.10
130 6 0.04
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (122 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTAGTCGAAATTCGTTGCGATTTATTCCAAATTCGTTG
CGATTTATTCCAAATTCGTTGCGATAATGCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:1584583 original size:23 final size:21
Alignment explanation
Indices: 1584552--1584621 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 21
1584542 GCGATTTATT
1584552 CCAAGTTCGTTGCGATAGTCGG
1 CCAAGTTCGTTGCGATAGTC-G
*
1584574 ACCAAATTCGTTGCGATAGT--
1 -CCAAGTTCGTTGCGATAGTCG
1584594 CCAAGTTCGTTGCGATAGTCG
1 CCAAGTTCGTTGCGATAGTCG
1584615 --AAGTTCG
1 CCAAGTTCG
1584622 CGTTGCAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
19 25 0.58
23 18 0.42
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (21 bp):
CCAAGTTCGTTGCGATAGTCG
Found at i:1586148 original size:173 final size:174
Alignment explanation
Indices: 1585856--1586204 Score: 673
Period size: 173 Copynumber: 2.0 Consensus size: 174
1585846 CGCTCCCTTT
1585856 GTCAGCAACTTGGTCAGCCCGTCTGCCACCTGATGGCACTCTAGAACATAGTTCACCTGAAGTTG
1 GTCAGCAACTTGGTCAGCCCGTCTGCCACC--ATGGCACTCTAGAACATAGTTCACCTGAAGTTG
1585921 TTTAGCTTCAACCTTTTCACGAACGAAATGCACGTCCATGTCAACATGTTTTGACTGAGCATGGT
64 TTTAGCTTCAACCTTTTCACGAACGAAATGCACGTCCATGTCAACATGTTTTGACTGAGCATGGT
1585986 ACACTGGATTCGTACTCAATGCAACAGCGCTTGTATTATCACACCA
129 ACACTGGATTCGTACTCAATGCAACAGCGCTTGTATTATCACACCA
1586032 GTCAGCAACTTGGTCAGCCCGTCTGCCACC-TGGCACTCTAGAACATAGTTCACCTGAAGTTGTT
1 GTCAGCAACTTGGTCAGCCCGTCTGCCACCATGGCACTCTAGAACATAGTTCACCTGAAGTTGTT
1586096 TAGCTTCAACCTTTTCACGAACGAAATGCACGTCCATGTCAACATGTTTTGACTGAGCATGGTAC
66 TAGCTTCAACCTTTTCACGAACGAAATGCACGTCCATGTCAACATGTTTTGACTGAGCATGGTAC
1586161 ACTGGATTCGTACTCAATGCAACAGCGCTTGTATTATCACACCA
131 ACTGGATTCGTACTCAATGCAACAGCGCTTGTATTATCACACCA
1586205 AATGACAGAT
Statistics
Matches: 173, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
173 143 0.83
176 30 0.17
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (174 bp):
GTCAGCAACTTGGTCAGCCCGTCTGCCACCATGGCACTCTAGAACATAGTTCACCTGAAGTTGTT
TAGCTTCAACCTTTTCACGAACGAAATGCACGTCCATGTCAACATGTTTTGACTGAGCATGGTAC
ACTGGATTCGTACTCAATGCAACAGCGCTTGTATTATCACACCA
Found at i:1607494 original size:8 final size:8
Alignment explanation
Indices: 1607481--1607505 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1607471 CGGTGGAATA
1607481 GGTTTTGG
1 GGTTTTGG
1607489 GGTTTTGG
1 GGTTTTGG
1607497 GGTTTTGG
1 GGTTTTGG
1607505 G
1 G
1607506 TGTTCTTGCC
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (8 bp):
GGTTTTGG
Found at i:1607608 original size:20 final size:21
Alignment explanation
Indices: 1607554--1607616 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1607544 GATTCCCCTG
1607554 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1607578 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1607598 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1607617 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1611466 original size:22 final size:21
Alignment explanation
Indices: 1611424--1611463 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1611414 GAGTTTGTTT
*
1611424 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1611445 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1611464 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1617112 original size:18 final size:19
Alignment explanation
Indices: 1617089--1617125 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1617079 CCAGTAATCA
1617089 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
1617107 TATTCCTACTGGTAATCTT
1 TATTCC-ACTGGTAATCTT
1617126 ACATTCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:1617131 original size:20 final size:20
Alignment explanation
Indices: 1617095--1617132 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1617085 ATCATATTCC
**
1617095 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
1617115 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1617133 ATAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:1618457 original size:10 final size:10
Alignment explanation
Indices: 1618435--1618497 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
1618425 TTTAAATGAA
1618435 AAACGAACAT
1 AAACGAACAT
* *
1618445 AAATGAACGT
1 AAACGAACAT
*
1618455 AAACGAACAC
1 AAACGAACAT
1618465 AAACGAACGGACAT
1 AAACG-A---ACAT
1618479 AAACGAACAT
1 AAACGAACAT
*
1618489 AAACAAACA
1 AAACGAACA
1618498 CAATAAATGA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
10 32 0.76
11 1 0.02
13 1 0.02
14 8 0.19
ACGTcount: A:0.59, C:0.21, G:0.13, T:0.08
Consensus pattern (10 bp):
AAACGAACAT
Found at i:1618460 original size:20 final size:20
Alignment explanation
Indices: 1618435--1618473 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1618425 TTTAAATGAA
* *
1618435 AAACGAACATAAATGAACGT
1 AAACGAACACAAACGAACGT
1618455 AAACGAACACAAACGAACG
1 AAACGAACACAAACGAACG
1618474 GACATAAACG
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:0.56, C:0.21, G:0.15, T:0.08
Consensus pattern (20 bp):
AAACGAACACAAACGAACGT
Found at i:1618492 original size:34 final size:34
Alignment explanation
Indices: 1618436--1618500 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1618426 TTAAATGAAA
* * *
1618436 AACGAACATAAATGAACGTAAACGAACACAAACG
1 AACGAACATAAACGAACATAAACAAACACAAACG
*
1618470 AACGGACATAAACGAACATAAACAAACACAA
1 AACGAACATAAACGAACATAAACAAACACAA
1618501 TAAATGAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (34 bp):
AACGAACATAAACGAACATAAACAAACACAAACG
Found at i:1618519 original size:22 final size:23
Alignment explanation
Indices: 1618454--1618527 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
1618444 TAAATGAACG
* *
1618454 TAAACGAACACAAACGAACGGAC-A
1 TAAACGAACATAAACAAAC--ACAA
1618478 TAAACGAACATAAACAAACACAA
1 TAAACGAACATAAACAAACACAA
* *
1618501 TAAATGAACA-ACACAAACACAA
1 TAAACGAACATAAACAAACACAA
*
1618523 AAAAC
1 TAAAC
1618528 AAACTTATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
22 16 0.37
23 10 0.23
24 17 0.40
ACGTcount: A:0.62, C:0.23, G:0.08, T:0.07
Consensus pattern (23 bp):
TAAACGAACATAAACAAACACAA
Found at i:1622136 original size:78 final size:78
Alignment explanation
Indices: 1622007--1622161 Score: 274
Period size: 78 Copynumber: 2.0 Consensus size: 78
1621997 TCTAACTTTC
* * *
1622007 CTTGATTTTCATCAGGATTACAGTAGAATCCATCACCTTCCTGCTTCTCAATACTTGCCTCTGTC
1 CTTGATTTTCATCAGGATTACAGTAGAAGCCATCACCTTCCTGCTTCTCAATACGTGACTCTGTC
1622072 CCAGTTAATTTTA
66 CCAGTTAATTTTA
*
1622085 CTTGATTTTCATCAGGATTACAGTAGAAGCCATCGCCTTCCTGCTTCTCAATACGTGACTCTGTC
1 CTTGATTTTCATCAGGATTACAGTAGAAGCCATCACCTTCCTGCTTCTCAATACGTGACTCTGTC
1622150 CCAGTTAATTTT
66 CCAGTTAATTTT
1622162 CCTTCTATAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (78 bp):
CTTGATTTTCATCAGGATTACAGTAGAAGCCATCACCTTCCTGCTTCTCAATACGTGACTCTGTC
CCAGTTAATTTTA
Found at i:1628455 original size:14 final size:14
Alignment explanation
Indices: 1628436--1628467 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1628426 ATTATTTATT
1628436 AAATAAAAATATCA
1 AAATAAAAATATCA
*
1628450 AAATAAAAATATTA
1 AAATAAAAATATCA
1628464 AAAT
1 AAAT
1628468 TAATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATAAAAATATCA
Found at i:1634161 original size:12 final size:12
Alignment explanation
Indices: 1634144--1634168 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1634134 GTCAAATAAT
1634144 TTAGGCACCAAA
1 TTAGGCACCAAA
1634156 TTAGGCACCAAA
1 TTAGGCACCAAA
1634168 T
1 T
1634169 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:1643639 original size:9 final size:9
Alignment explanation
Indices: 1643625--1643651 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1643615 CTTCATTACT
1643625 CCAATCATC
1 CCAATCATC
1643634 CCAATCATC
1 CCAATCATC
1643643 CCAATCATC
1 CCAATCATC
1643652 TATCTCATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (9 bp):
CCAATCATC
Found at i:1646773 original size:16 final size:16
Alignment explanation
Indices: 1646754--1646795 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
1646744 ATGAGTCGAG
1646754 TTGAGCTCGAGTATTA
1 TTGAGCTCGAGTATTA
1646770 TTGAGCTCGAGTATTA
1 TTGAGCTCGAGTATTA
1646786 TTGAGCTCGA
1 TTGAGCTCGA
1646796 CTCGACTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (16 bp):
TTGAGCTCGAGTATTA
Found at i:1647535 original size:20 final size:20
Alignment explanation
Indices: 1647510--1647557 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
1647500 AAGCCTTCGA
1647510 TATGGAGACT-GATCC-TCTAG
1 TATGGAGACTAG-TCCTTC-AG
1647530 TATGGAGACTAGTCCTTCAG
1 TATGGAGACTAGTCCTTCAG
1647550 TATGGAGA
1 TATGGAGA
1647558 GCAGCGGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (20 bp):
TATGGAGACTAGTCCTTCAG
Found at i:1650292 original size:3 final size:3
Alignment explanation
Indices: 1650284--1650327 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
1650274 GTTTTACATT
1650284 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T
1650328 ATTTTGCAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1652933 original size:18 final size:19
Alignment explanation
Indices: 1652905--1652941 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1652895 GGTTTTTTAA
1652905 CGGTTCGGGTTTTTCGGTT
1 CGGTTCGGGTTTTTCGGTT
1652924 CGGTTC-GGTTTTTCGGTT
1 CGGTTCGGGTTTTTCGGTT
1652942 TTTCAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.00, C:0.16, G:0.35, T:0.49
Consensus pattern (19 bp):
CGGTTCGGGTTTTTCGGTT
Found at i:1657216 original size:14 final size:14
Alignment explanation
Indices: 1657197--1657235 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1657187 TAATGGGGAG
1657197 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
1657211 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
1657225 GAATCTCTGCA
1 TAATCCCTGCA
1657236 TATAGACAGA
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:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:1660583 original size:55 final size:54
Alignment explanation
Indices: 1660485--1660600 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 54
1660475 GTATTGTGTC
* * *
1660485 CAGATTGACCTGATTTCCTCATAGAGAATGAACAATGTTAACACCAAATTATCTT
1 CAGATTAACCTGATTTCCTCAAAGAGAATGAACAATGTCAACACCAAATTAT-TT
*
1660540 CAGATTAACCTGATTTCCTCAAAGAGAA-GAAACAGTGTCAACACCAAATTATTT
1 CAGATTAACCTGATTTCCTCAAAGAGAATG-AACAATGTCAACACCAAATTATTT
1660594 CTAGATT
1 C-AGATT
1660601 GACTCGACGT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
54 4 0.07
55 51 0.93
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (54 bp):
CAGATTAACCTGATTTCCTCAAAGAGAATGAACAATGTCAACACCAAATTATTT
Found at i:1661001 original size:55 final size:55
Alignment explanation
Indices: 1660771--1661002 Score: 295
Period size: 55 Copynumber: 4.2 Consensus size: 55
1660761 AGCAGTGTTG
* * *
1660771 TCTCTAGATTGACCCGATTTCCTCAGAGAGAAAT-AACATTATCAACACCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCATAGAG-AATGAACAGTATCAACACCAAATTA
* * *** *
1660826 TCTCTAGATTAACGTAATTTCCTCATAGAGAATGAACAGTGTCAACACCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCATAGAGAATGAACAGTATCAACACCAAATTA
* * * * *
1660881 TCTTCATATTAACCCGATTTTCTCATAGAGAATGAACAGTTTCAACACCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCATAGAGAATGAACAGTATCAACACCAAATTA
* * *
1660936 TCTTCAGATTGACCCGATTGCCTCATAGAGAATGAACAGTATCAATACCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCATAGAGAATGAACAGTATCAACACCAAATTA
1660991 TCTCCAGATTGA
1 TCTCCAGATTGA
1661003 TCCAACGTCC
Statistics
Matches: 154, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
54 3 0.02
55 151 0.98
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (55 bp):
TCTCCAGATTGACCCGATTTCCTCATAGAGAATGAACAGTATCAACACCAAATTA
Found at i:1661385 original size:3 final size:3
Alignment explanation
Indices: 1661377--1661434 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
1661367 GTTTTACGTT
1661377 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1661423 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1661435 GTACATTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1662871 original size:31 final size:31
Alignment explanation
Indices: 1662797--1662863 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1662787 ACAGTTATTC
*
1662797 GGGGACCATATTGCAAACAAACTAAATGTTG
1 GGGGACCATATTGAAAACAAACTAAATGTTG
1662828 GGGGACCATATTGAAAACAAACTAAATGTTG
1 GGGGACCATATTGAAAACAAACTAAATGTTG
1662859 GGGGA
1 GGGGA
1662864 TTGTATTGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.21
Consensus pattern (31 bp):
GGGGACCATATTGAAAACAAACTAAATGTTG
Found at i:1665467 original size:31 final size:31
Alignment explanation
Indices: 1665432--1665498 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1665422 TACAATGCAA
* *
1665432 TCCCCTAACATTTAGTCCGTTTTCAATATGG
1 TCCCCTAACATTTAGTCCGTTTGCAATACGG
* *
1665463 TCCCCCAACATTTAGTCTGTTTGCAATACGG
1 TCCCCTAACATTTAGTCCGTTTGCAATACGG
1665494 -CCCCT
1 TCCCCT
1665499 GACGTAACTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.34
Consensus pattern (31 bp):
TCCCCTAACATTTAGTCCGTTTGCAATACGG
Found at i:1673497 original size:20 final size:20
Alignment explanation
Indices: 1673474--1673516 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1673464 ATTTTAATTT
* *
1673474 TAAAATCAAATACTTAAATA
1 TAAAATAAAATAATTAAATA
*
1673494 TAAAATAAAATAATTCAATA
1 TAAAATAAAATAATTAAATA
1673514 TAA
1 TAA
1673517 TTATTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAATAAAATAATTAAATA
Found at i:1674807 original size:174 final size:174
Alignment explanation
Indices: 1674517--1674859 Score: 596
Period size: 174 Copynumber: 2.0 Consensus size: 174
1674507 TTCCAGTCTA
*
1674517 GTGAAATTACGAACATACATTGATGTTGCATGACTTTTATTTTTGGTCATTGCTTTCTCCAAATC
1 GTGAAATTACGAACATACATTGATGTTGCATGACTTTGATTTTTGGTCATTGCTTTCTCCAAATC
* *
1674582 TAGAGCCCAATTTCTACCTTCGTTGAGCATTGCCTCTAGCTAGGCACTTTTGTCTGCCCAAACTT
66 TAGAGCCCAATTTCTAACTTCGTTGAGCATTGCCTCTACCTAGGCACTTTTGTCTGCCCAAACTT
* *
1674647 TACCCAATTTGAAGTATGTCTCCCTAACAATACTTACCAGTTTG
131 TACCCAATTTGAAGTATGTCTCCCAAACAATAATTACCAGTTTG
* * * *
1674691 GTGAAATTATGAACATACATTGATGTTGGATGAGTTTGATTTTTGGTCATTGCTTTCTCCAGATC
1 GTGAAATTACGAACATACATTGATGTTGCATGACTTTGATTTTTGGTCATTGCTTTCTCCAAATC
*
1674756 TAGAGCCCAATTTCTAACTTCGTTGAGCATTGCCTCTACCTGGGCACTTTTGTCTGCCCAAACTT
66 TAGAGCCCAATTTCTAACTTCGTTGAGCATTGCCTCTACCTAGGCACTTTTGTCTGCCCAAACTT
1674821 TACCCAATTTGAAGTATGTCTCCCAAACAATAATTACCA
131 TACCCAATTTGAAGTATGTCTCCCAAACAATAATTACCA
1674860 CAGAAAGATG
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
174 159 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (174 bp):
GTGAAATTACGAACATACATTGATGTTGCATGACTTTGATTTTTGGTCATTGCTTTCTCCAAATC
TAGAGCCCAATTTCTAACTTCGTTGAGCATTGCCTCTACCTAGGCACTTTTGTCTGCCCAAACTT
TACCCAATTTGAAGTATGTCTCCCAAACAATAATTACCAGTTTG
Found at i:1680616 original size:19 final size:19
Alignment explanation
Indices: 1680596--1680631 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1680586 CTTCAATTAT
1680596 TTTAAT-TTTATTTATTTA
1 TTTAATATTTATTTATTTA
1680614 TTTAATATTTATTTATTT
1 TTTAATATTTATTTATTT
1680632 TGGCCACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTAATATTTATTTATTTA
Found at i:1684748 original size:27 final size:27
Alignment explanation
Indices: 1684718--1684776 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 27
1684708 TATATTAATG
* *
1684718 AATATTATAGGGTTTTTCTCTCTACCC
1 AATATTATAGGGGTTTCCTCTCTACCC
1684745 AATA-T-TAGGGGTTTCCTCTCTACCC
1 AATATTATAGGGGTTTCCTCTCTACCC
1684770 AATATTA
1 AATATTA
1684777 GAGTTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 22 0.79
26 2 0.07
27 4 0.14
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (27 bp):
AATATTATAGGGGTTTCCTCTCTACCC
Found at i:1684753 original size:25 final size:25
Alignment explanation
Indices: 1684725--1684784 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1684715 ATGAATATTA
1684725 TAGGGTTTTTCTCTCTACCCAATAT
1 TAGGGTTTTTCTCTCTACCCAATAT
* *
1684750 TAGGGGTTTCCTCTCTACCCAATAT
1 TAGGGTTTTTCTCTCTACCCAATAT
*
1684775 TAGAGTTTTT
1 TAGGGTTTTT
1684785 GACCGTGTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (25 bp):
TAGGGTTTTTCTCTCTACCCAATAT
Found at i:1684923 original size:51 final size:52
Alignment explanation
Indices: 1684833--1684937 Score: 167
Period size: 51 Copynumber: 2.0 Consensus size: 52
1684823 TCTTGATTTA
1684833 TGTTTTAAGTGCAGTAGTAATTCTGGAGAGACGAATGATCTTGAAAATGAAC
1 TGTTTTAAGTGCAGTAGTAATTCTGGAGAGACGAATGATCTTGAAAATGAAC
* * * *
1684885 TGTTTTGAGTGCAG-AGTGATTCTGGAGAGATGAGTGATCTTGAAAATGAAC
1 TGTTTTAAGTGCAGTAGTAATTCTGGAGAGACGAATGATCTTGAAAATGAAC
1684936 TG
1 TG
1684938 ATAGGATTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 36 0.73
52 13 0.27
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (52 bp):
TGTTTTAAGTGCAGTAGTAATTCTGGAGAGACGAATGATCTTGAAAATGAAC
Found at i:1703381 original size:16 final size:16
Alignment explanation
Indices: 1703350--1703396 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
1703340 TGGTAATGAA
1703350 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
1703367 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
1703384 ATAAAAAAATGAA
1 ATAAAAAAATGAA
1703397 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:1711869 original size:26 final size:27
Alignment explanation
Indices: 1711834--1711885 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
1711824 AGATTTAAGG
1711834 TTTAAGGTTTATGATTTG-GGTTTGAA
1 TTTAAGGTTTATGATTTGTGGTTTGAA
*
1711860 TTTAGGGTTTATGATTTGTGGTTTGA
1 TTTAAGGTTTATGATTTGTGGTTTGA
1711886 GGTGGAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (27 bp):
TTTAAGGTTTATGATTTGTGGTTTGAA
Found at i:1712338 original size:13 final size:13
Alignment explanation
Indices: 1712300--1712339 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1712290 GGCCCATGAA
*
1712300 CCGCGCCTTACGA
1 CCGCGCCTTACGG
*
1712313 CCGTGCCTTACGG
1 CCGCGCCTTACGG
1712326 CCGCGCCTTACGG
1 CCGCGCCTTACGG
1712339 C
1 C
1712340 TCCTGTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.10, C:0.45, G:0.28, T:0.17
Consensus pattern (13 bp):
CCGCGCCTTACGG
Found at i:1713009 original size:31 final size:29
Alignment explanation
Indices: 1712953--1713037 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 29
1712943 TTTTTTTATC
*
1712953 TTTATATTCTTTTTTATTGAATTTTATTCACT
1 TTTA-ATTC-TTTTT-TTGTATTTTATTCACT
*
1712985 TTTAATTATCATTTTTTT-TATTTTATTCGCT
1 TTTAA-T-TC-TTTTTTTGTATTTTATTCACT
1713016 TTTAATTCTTTTTTTGTATTTT
1 TTTAATTCTTTTTTTGTATTTT
1713038 TATTAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 7 0.15
29 8 0.17
30 1 0.02
31 17 0.36
32 7 0.15
33 7 0.15
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (29 bp):
TTTAATTCTTTTTTTGTATTTTATTCACT
Found at i:1714292 original size:19 final size:20
Alignment explanation
Indices: 1714258--1714295 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1714248 TATAATTTAA
1714258 TTACATTTTAATTATATATC
1 TTACATTTTAATTATATATC
*
1714278 TTACGTTTT-ATTATATAT
1 TTACATTTTAATTATATAT
1714296 TTTATAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (20 bp):
TTACATTTTAATTATATATC
Found at i:1720317 original size:21 final size:21
Alignment explanation
Indices: 1720291--1720337 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1720281 ATAAAGAAAG
1720291 TCTTGGAGATTGTTTCAAGGA
1 TCTTGGAGATTGTTTCAAGGA
*
1720312 TCTTGGAGATTGTTTCAAGTA
1 TCTTGGAGATTGTTTCAAGGA
1720333 TCTTG
1 TCTTG
1720338 TCGGGAATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.43
Consensus pattern (21 bp):
TCTTGGAGATTGTTTCAAGGA
Found at i:1720942 original size:30 final size:30
Alignment explanation
Indices: 1720907--1720970 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
1720897 TGTTCTCTGA
1720907 ATTATCAGGTACTTCTATTTCAGATTATGT
1 ATTATCAGGTACTTCTATTTCAGATTATGT
*
1720937 ATTATCAGGTACTTCTATTTCAGATTCTGT
1 ATTATCAGGTACTTCTATTTCAGATTATGT
1720967 ATTA
1 ATTA
1720971 AAGAAAAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (30 bp):
ATTATCAGGTACTTCTATTTCAGATTATGT
Found at i:1721901 original size:30 final size:30
Alignment explanation
Indices: 1721865--1721921 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1721855 CCCGAAGGAC
1721865 CTATCCAGAGGCCATAAAGATCCTCGGTAA
1 CTATCCAGAGGCCATAAAGATCCTCGGTAA
*
1721895 CTATCCAGAGGTCATAAAGATCCTCGG
1 CTATCCAGAGGCCATAAAGATCCTCGG
1721922 CATCTGTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGCCATAAAGATCCTCGGTAA
Found at i:1721963 original size:31 final size:31
Alignment explanation
Indices: 1721923--1722048 Score: 139
Period size: 32 Copynumber: 4.0 Consensus size: 31
1721913 GATCCTCGGC
* *
1721923 ATCTGTCCATAGGTTCCGAAGAACCTAGGTA
1 ATCTGTCCATATGTTCCGAAGAACATAGGTA
* **
1721954 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 ATCTGTCCATATGTTCCGAAGAACATAGGTA
*
1721985 TATTTGTCCATATG-TCTCGAA-AGACATAGGTA
1 -ATCTGTCCATATGTTC-CGAAGA-ACATAGGTA
*
1722017 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-TCTGTCCATATGTTCCGAAGAACATAGGTA
1722049 TACCCTCGAC
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
31 30 0.38
32 45 0.58
33 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (31 bp):
ATCTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:1725697 original size:23 final size:25
Alignment explanation
Indices: 1725664--1725711 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
1725654 AAAATTTTAT
*
1725664 TAAAATTTTAG-GAG-ATAAAATTA
1 TAAAATCTTAGAGAGTATAAAATTA
*
1725687 TAAAATCTTAGAGAGTGTAAAATTA
1 TAAAATCTTAGAGAGTATAAAATTA
1725712 AATAATTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 3 0.14
25 8 0.38
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.33
Consensus pattern (25 bp):
TAAAATCTTAGAGAGTATAAAATTA
Found at i:1730612 original size:14 final size:14
Alignment explanation
Indices: 1730595--1730644 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1730585 ATTACTTTTA
1730595 TATTTTATTTTATT
1 TATTTTATTTTATT
1730609 TATTTTATTTT-TT
1 TATTTTATTTTATT
1730622 TATCATTTCCATTTTATT
1 TAT--TTT--ATTTTATT
1730640 TATTT
1 TATTT
1730645 AATATTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.16
14 11 0.35
15 3 0.10
16 2 0.06
17 5 0.16
18 5 0.16
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTATTTTATT
Found at i:1730651 original size:22 final size:22
Alignment explanation
Indices: 1730610--1730652 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1730600 TATTTTATTT
*
1730610 ATTTTATTTTTTTATCATTTCC
1 ATTTTATTTTTTAATCATTTCC
1730632 ATTTTATTTATTTAAT-ATTTC
1 ATTTTATTT-TTTAATCATTTC
1730653 TTATCTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTATTTTTTAATCATTTCC
Found at i:1730656 original size:14 final size:14
Alignment explanation
Indices: 1730639--1730672 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1730629 TCCATTTTAT
1730639 TTATTTAATATTTC
1 TTATTTAATATTTC
* *
1730653 TTATCTAATATTTT
1 TTATTTAATATTTC
1730667 TTATTT
1 TTATTT
1730673 TTAGGAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTTAATATTTC
Found at i:1731043 original size:23 final size:21
Alignment explanation
Indices: 1730997--1731043 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1730987 AATTAATCAT
1730997 TTAACCAGGATCTGACATATG
1 TTAACCAGGATCTGACATATG
* *
1731018 TTAACACATGATCATGATATATG
1 TTAAC-CAGGATC-TGACATATG
1731041 TTA
1 TTA
1731044 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATATG
Found at i:1731344 original size:15 final size:16
Alignment explanation
Indices: 1731320--1731356 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1731310 TTTAATTTCT
1731320 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
1731334 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
1731350 TGATTCA
1 T-ATTCA
1731357 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:1731889 original size:14 final size:15
Alignment explanation
Indices: 1731872--1731940 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 15
1731862 ATGGTATTAC
1731872 TTTTATATTT-TATT
1 TTTTATATTTATATT
*
1731886 TTTTTTATTT-TATTT
1 TTTTATATTTATA-TT
*
1731901 TTTTATTATTTCTATT
1 TTTTA-TATTTATATT
1731917 TTGTT-TATTTAATATT
1 TT-TTATATTT-ATATT
*
1731933 TCTTATAT
1 TTTTATAT
1731941 AACATTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 11 0.24
15 13 0.29
16 17 0.38
17 4 0.09
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.75
Consensus pattern (15 bp):
TTTTATATTTATATT
Found at i:1731891 original size:16 final size:15
Alignment explanation
Indices: 1731872--1731924 Score: 72
Period size: 14 Copynumber: 3.4 Consensus size: 15
1731862 ATGGTATTAC
1731872 TTTTATATTTTATTT
1 TTTTATATTTTATTT
1731887 TTTT-TATTTTATTT
1 TTTTATATTTTATTT
1731901 TTTTATTATTTCTATTT
1 TTTTA-TATTT-TATTT
1731918 TGTTTAT
1 T-TTTAT
1731925 TTAATATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.41
15 4 0.12
16 5 0.15
17 7 0.21
18 4 0.12
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTATATTTTATTT
Found at i:1731893 original size:30 final size:29
Alignment explanation
Indices: 1731841--1731924 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
1731831 ATGGGTTCCT
*
1731841 TTCTTTT-TA-TTTATGTTGTTTATGGTA
1 TTCTTTTATATTTTATTTTGTTTATGGTA
* **
1731868 TTACTTTTATATTTTATTTTTTTTATTTTA
1 TT-CTTTTATATTTTATTTTGTTTATGGTA
*
1731898 TTTTTTTATTATTTCTATTTTGTTTAT
1 TTCTTTTA-TATTT-TATTTTGTTTAT
1731925 TTAATATTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
27 2 0.04
28 5 0.11
29 7 0.15
30 21 0.46
31 11 0.24
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.74
Consensus pattern (29 bp):
TTCTTTTATATTTTATTTTGTTTATGGTA
Found at i:1731901 original size:13 final size:14
Alignment explanation
Indices: 1731872--1731926 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
1731862 ATGGTATTAC
*
1731872 TTTTATATTTTATT
1 TTTTTTATTTTATT
1731886 TTTTTTATTTTATTT
1 TTTTTTATTTTA-TT
1731901 TTTTATTATTTCTATT
1 TTTT-TTATTT-TATT
*
1731917 TTGTTTATTT
1 TTTTTTATTT
1731927 AATATTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 11 0.31
15 12 0.33
16 11 0.31
17 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (14 bp):
TTTTTTATTTTATT
Found at i:1731907 original size:22 final size:22
Alignment explanation
Indices: 1731879--1731935 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1731869 TACTTTTATA
* *
1731879 TTTTATTTTTTTTATTTTATTT
1 TTTTATTATTTCTATTTTATTT
*
1731901 TTTTATTATTTCTATTTTGTTT
1 TTTTATTATTTCTATTTTATTT
* *
1731923 ATTTAATATTTCT
1 TTTTATTATTTCT
1731936 TATATAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTATTATTTCTATTTTATTT
Found at i:1731932 original size:16 final size:15
Alignment explanation
Indices: 1731872--1731933 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
1731862 ATGGTATTAC
*
1731872 TTTTATATTT-TATT
1 TTTTTTATTTATATT
1731886 TTTTTTATTT-TATTT
1 TTTTTTATTTATA-TT
*
1731901 TTTTATTATTTCTATT
1 TTTT-TTATTTATATT
*
1731917 TTGTTTATTTAATATT
1 TTTTTTATTT-ATATT
1731933 T
1 T
1731934 CTTATATAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
14 11 0.27
15 12 0.29
16 16 0.39
17 2 0.05
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTTATTTATATT
Found at i:1732030 original size:20 final size:20
Alignment explanation
Indices: 1731990--1732027 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1731980 AAAGGTAAGC
*
1731990 AATTTGAATTTTGTAATTTA
1 AATTTAAATTTTGTAATTTA
1732010 AATTTAAATTTT-TAATTT
1 AATTTAAATTTTGTAATTT
1732028 TAATCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTAAATTTTGTAATTTA
Found at i:1735824 original size:43 final size:43
Alignment explanation
Indices: 1735771--1735892 Score: 226
Period size: 43 Copynumber: 2.8 Consensus size: 43
1735761 ACGAAGGGGC
* *
1735771 CATCCGCGATTTCAACTCCACGACGGAGGATATTGTACCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
1735814 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
1735857 CATCCACGATTTCAACTCCACGACGGAGGATATCGT
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGT
1735893 GTCATTCAGG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCCACA
Found at i:1736800 original size:3 final size:3
Alignment explanation
Indices: 1736783--1736851 Score: 50
Period size: 3 Copynumber: 21.3 Consensus size: 3
1736773 GTCTAAAAAA
* *
1736783 TAT TTT TAT TA- TAT TATT TATT TATT TAC TAT TAT TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TA-T
*
1736831 TAT TATT TAT TTT TAT ATAT T
1 TAT TA-T TAT TAT TAT -TAT T
1736852 TTTTGTAGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
2 2 0.04
3 33 0.60
4 20 0.36
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1736836 original size:29 final size:29
Alignment explanation
Indices: 1736783--1736839 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1736773 GTCTAAAAAA
*
1736783 TATTTTTATTATATTATTTATTTATTTAC
1 TATTATTATTATATTATTTATTTATTTAC
1736812 TATTATTATTATTATTATTTA-TTATTTA
1 TATTATTATTA-TATTATTTATTTATTTA
1736840 TTTTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTATTATTATATTATTTATTTATTTAC
Found at i:1736841 original size:26 final size:27
Alignment explanation
Indices: 1736783--1736851 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
1736773 GTCTAAAAAA
1736783 TATTT-TTATTA-TATTATTTATTTAT
1 TATTTATTATTATTATTATTTATTTAT
*
1736808 T-TACTATTATTATTATTA-TTATTTAT
1 TAT-TTATTATTATTATTATTTATTTAT
*
1736834 TATTTATTTTTATATATT
1 TATTTATTATTAT-TATT
1736852 TTTTGTAGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 1 0.03
25 2 0.06
26 23 0.64
27 10 0.28
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (27 bp):
TATTTATTATTATTATTATTTATTTAT
Found at i:1736851 original size:14 final size:14
Alignment explanation
Indices: 1736783--1736852 Score: 65
Period size: 14 Copynumber: 4.9 Consensus size: 14
1736773 GTCTAAAAAA
1736783 TATTT-TTATTATAT
1 TATTTATTATT-TAT
*
1736797 TATTTATTTATTTAC
1 TATTTA-TTATTTAT
1736812 TA-TTATTATTATTAT
1 TATTTATTA-T-TTAT
1736827 TATTTATTATTTAT
1 TATTTATTATTTAT
1736841 T-TTTATATATTT
1 TATTTAT-TATTT
1736853 TTTGTAGGCT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
13 8 0.17
14 19 0.40
15 10 0.21
16 11 0.23
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTATTATTTAT
Found at i:1738090 original size:14 final size:13
Alignment explanation
Indices: 1738068--1738102 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1738058 ATGGTATTAC
*
1738068 TTTTATATTTTAT
1 TTTTTTATTTTAT
1738081 TTTATTTATTTTAT
1 TTT-TTTATTTTAT
1738095 TTTTTTAT
1 TTTTTTAT
1738103 CATTTCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTATTTTAT
Found at i:1749078 original size:482 final size:484
Alignment explanation
Indices: 1748130--1749096 Score: 1692
Period size: 482 Copynumber: 2.0 Consensus size: 484
1748120 GGATTGCTTT
1748130 TCACGTGAACCACAAGGGGGGAGAGAGAAAATATATTGTCTTCAGATTTCTCTTTTCACCATGGA
1 TCACGTGAACCACAAGGGGGGAGAGAGAAAATATATTGTCTTCAGATTTCTCTTTTCACCATGGA
* * * * * *
1748195 TGACTGTTCATCAAGAATTCAAACCTTTTGTTGAGTCGGTATTTTTCCTGTGAAAATAAGTGTCG
66 TGACTGATCATCAAGAATTCAAACCTTTTGTTCAGACGATATTTTTCCTGCGAAAACAAGTGTCG
** *
1748260 TTATTTTTAAAATTTCGTCTTTAAAAAGTAAGTGTTTTTCTTCTTATATAAGATAAAACACAATT
131 TTATTTTTAAAATTTCGTCTCCAAAAAGTAAGTGTTTTTCTTCTTACATAAGATAAAACACAATT
* * *
1748325 TGAGGAGTCGCCACCAATCATTTATCGAGGTATGATTGATCACCAGAAATGTTATGTTATTTTAA
196 TGAGGAGTCGCCACCAATCATATATCGAGGTATGATTGATCACCAAAAATGCTATGTTATTTTAA
1748390 TAAAATTTATAAAAATAGTATTAAAACAACCCAAAAAGAGTGTTCTTACCAGAAAATGAGTTCGA
261 TAAAATTTATAAAAATAGTATTAAAACAACCCAAAAAGAGTGTTCTTACCAGAAAATGAGTTCGA
*
1748455 GAGTCGGTTACGTGTGGGGAAGGGTTAGCATCCTCACAACGCCCAAAATTAGTACATTTTTTATT
326 GAGTCGGTTACGTGTGGGGAAGGGTTAACATCCTCACAACGCCCAAAATTAGTACATTTTTTATT
*
1748520 AATTAATTGTTTTTACAATAAAATTTATAAATTTGGATTTAATTTAATTTTTGATCCCTCCAACA
391 AATTAATTGTCTTTACAATAAAATTTATAAATTTGGATTTAATTTAATTTTTGATCCCTCCAACA
*
1748585 AATATCATAGTATTATTTTATACCGATAA
456 AATATCATAGTATTATTTTATACCAATAA
*
1748614 TCACGTGAACCACAAGGGGGGAGAGAGAGAAAATATATTGTCTTTAGATTTCTCTTTTCACCATG
1 TCACGTGAACCACAA-GGGGG-GAGAGAGAAAATATATTGTCTTCAGATTTCTCTTTTCACCATG
1748679 GATGACTGATCATCAAGAATTCAAACCTTTTG-TCAGACGATA-TTTTCCTGCGAAAACAAGTGT
64 GATGACTGATCATCAAGAATTCAAACCTTTTGTTCAGACGATATTTTTCCTGCGAAAACAAGTGT
1748742 CGTTATTTTCT-AAATTTCGTCTCCAAAAAGTAAGTGTTTTTCTTCTTACATAAGATAAAACACA
129 CGTTATTTT-TAAAATTTCGTCTCCAAAAAGTAAGTGTTTTTCTTCTTACATAAGATAAAACACA
* *
1748806 ATTTGAGGAGTCGCTACCAATCATATATCGAGGTATGATTGGTCACCAAAAATGCTATGTTATTT
193 ATTTGAGGAGTCGCCACCAATCATATATCGAGGTATGATTGATCACCAAAAATGCTATGTTATTT
1748871 TAATAAAATTTAT-AAAATAGTATTAAAACAACCC-AAAAGAGTGTTCTTACCAGAAAATGAGTT
258 TAATAAAATTTATAAAAATAGTATTAAAACAACCCAAAAAGAGTGTTCTTACCAGAAAATGAGTT
*
1748934 CGAGAGTCGGTTACGTGTGGGGAAGGGTTAACATCCTCACAACGCCCAAAATTGGTACATTTTTT
323 CGAGAGTCGGTTACGTGTGGGGAAGGGTTAACATCCTCACAACGCCCAAAATTAGTACATTTTTT
*
1748999 ATTAATTAATTGTCTTTGCAATAAAATTTATAAATTTGGATTTAATTTAATTTTTGATCCCTCCA
388 ATTAATTAATTGTCTTTACAATAAAATTTATAAATTTGGATTTAATTTAATTTTTGATCCCTCCA
1749064 ACAAATATCATAGTATTATTTTATACCAATAA
453 ACAAATATCATAGTATTATTTTATACCAATAA
1749096 T
1 T
1749097 AATTTAAAAT
Statistics
Matches: 460, Mismatches: 20, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
482 187 0.41
483 21 0.05
484 166 0.36
485 13 0.03
486 73 0.16
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (484 bp):
TCACGTGAACCACAAGGGGGGAGAGAGAAAATATATTGTCTTCAGATTTCTCTTTTCACCATGGA
TGACTGATCATCAAGAATTCAAACCTTTTGTTCAGACGATATTTTTCCTGCGAAAACAAGTGTCG
TTATTTTTAAAATTTCGTCTCCAAAAAGTAAGTGTTTTTCTTCTTACATAAGATAAAACACAATT
TGAGGAGTCGCCACCAATCATATATCGAGGTATGATTGATCACCAAAAATGCTATGTTATTTTAA
TAAAATTTATAAAAATAGTATTAAAACAACCCAAAAAGAGTGTTCTTACCAGAAAATGAGTTCGA
GAGTCGGTTACGTGTGGGGAAGGGTTAACATCCTCACAACGCCCAAAATTAGTACATTTTTTATT
AATTAATTGTCTTTACAATAAAATTTATAAATTTGGATTTAATTTAATTTTTGATCCCTCCAACA
AATATCATAGTATTATTTTATACCAATAA
Found at i:1750480 original size:3 final size:3
Alignment explanation
Indices: 1750472--1750539 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
1750462 TCAGGTTTTG
1750472 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1750520 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
1750540 TAAATACGTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1757466 original size:36 final size:36
Alignment explanation
Indices: 1757416--1757484 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1757406 CTATGCACAT
* *
1757416 AAAGATCCTGTTAGATTAATACCAAAAGTATTCCAC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTCCAC
*
1757452 AAAGATCCTATTAGATTGATACCAAAAGCATTC
1 AAAGATCCTATTAGATTAATACCAAAAGCATTC
1757485 TACGGTAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (36 bp):
AAAGATCCTATTAGATTAATACCAAAAGCATTCCAC
Found at i:1758012 original size:43 final size:43
Alignment explanation
Indices: 1757943--1758032 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
1757933 ATAAATTGTC
**
1757943 TTTGGAGAAGTTGGGAATGAAAGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
* *
1757986 TTTGGAGAAGTTAAGAGTGAAGGTTATCCCCTATATGTAAAGT
1 TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
1758029 TTTG
1 TTTG
1758033 TTTGATGTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (43 bp):
TTTGGAGAAGTTAAGAATGAAAGTTATCCCCTATATGTAAAGT
Found at i:1758812 original size:19 final size:19
Alignment explanation
Indices: 1758788--1758824 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1758778 AGATCAAGTT
*
1758788 GAAGCGAAGTATAGAAGAG
1 GAAGCGAAATATAGAAGAG
1758807 GAAGCGAAATATAGAAGA
1 GAAGCGAAATATAGAAGA
1758825 TGTTAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.32, T:0.11
Consensus pattern (19 bp):
GAAGCGAAATATAGAAGAG
Found at i:1762956 original size:41 final size:41
Alignment explanation
Indices: 1762892--1762969 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
1762882 CATCATCATG
* *
1762892 TTGGGACATTTTGAAGGTCCATTT-TGACCAGAAATGAAAAT
1 TTGGGACATTTGGAAGGTCCATTTCAGA-CAGAAATGAAAAT
*
1762933 TTGGTACATTTGGAAGG-CACATTTCAGACAGAAATGA
1 TTGGGACATTTGGAAGGTC-CATTTCAGACAGAAATGA
1762970 TCCATGAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 1 0.03
41 29 0.91
42 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (41 bp):
TTGGGACATTTGGAAGGTCCATTTCAGACAGAAATGAAAAT
Found at i:1764576 original size:137 final size:135
Alignment explanation
Indices: 1764322--1764593 Score: 332
Period size: 137 Copynumber: 2.0 Consensus size: 135
1764312 CAACAAACAA
* * * *
1764322 CTTTTCAGTTTCATTTAGAGTCAATTTCAACTTCACAACGAAAGATATTGAAGTCAAATCAATAC
1 CTTTCCAGTTTCATTTAAAGTCAATTTCAACTTCACAACGAAAGATATTGAACTCAAATCAACAC
* * *
1764387 AACCAAAGATTGGATTTCAACTTCACAATGAAGGATATCCTATTCAAAGCTCAACTTCAC-AGCG
66 AACCAAACATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACGA-CG
1764451 AAGGGG
130 AAGGGG
* ** * *
1764457 CTTTCCAGTTTCATTTAAAGTTAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAA-CAACA
1 CTTTCCAGTTTCATTTAAAGTCAATTTCAACTTCACAACGAAAGATATTGAACTC-AAATCAACA
* * * * * *
1764521 GCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCTAGGCTCAACTTCACGA
65 -CAA-CCAAACATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACGA
1764586 CGAAGGGG
128 CGAAGGGG
1764594 TCATTCATGA
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
135 51 0.44
136 6 0.05
137 57 0.50
138 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (135 bp):
CTTTCCAGTTTCATTTAAAGTCAATTTCAACTTCACAACGAAAGATATTGAACTCAAATCAACAC
AACCAAACATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACGACGA
AGGGG
Found at i:1764835 original size:40 final size:42
Alignment explanation
Indices: 1764768--1764869 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 42
1764758 ATGGCCAAAT
* *
1764768 GTCCTCATCACGAAGGAACAATGTCAT-C-TA-CCAATCAGAAC
1 GTCCTCATCACGAAGGAACAA-GTCATCCTTAGACAACCAG-AC
*
1764809 -TCCTCATCACGAAGGAGTCACA-TCATCCTTAGACAACCAGAC
1 GTCCTCATCACGAAGGA-ACA-AGTCATCCTTAGACAACCAGAC
1764851 GTCCTCATCACGAAGGAAC
1 GTCCTCATCACGAAGGAAC
1764870 TGTGTTATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
40 20 0.39
41 3 0.06
42 6 0.12
43 22 0.43
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (42 bp):
GTCCTCATCACGAAGGAACAAGTCATCCTTAGACAACCAGAC
Found at i:1764972 original size:97 final size:96
Alignment explanation
Indices: 1764806--1765030 Score: 272
Period size: 97 Copynumber: 2.3 Consensus size: 96
1764796 TACCAATCAG
* *
1764806 AACTCCTCATCACGAAGGAGTC-ACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAAC
1 AACTCCTCATCACGAAGGAG-CAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAAC
* * * *
1764870 TGTGTTATCTCCAATATCTTCAATGATGGTCA
65 AGTGTTATCTCAAATATCTTCAAAGATGGCCA
* * * * * *
1764902 TAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCATATGTCATCATCATGAAATAAC
1 -AACTCCTCATCACGAAGGAGCAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAAC
*
1764967 AGTGTTATCTCAAATATCTTTAAAGATGGCCA
65 AGTGTTATCTCAAATATCTTCAAAGATGGCCA
* * *
1764999 GACGTCCTCATCACGAAGGAACAATATCATCC
1 AAC-TCCTCATCACGAAGGAGCAACATCATCC
1765031 ACCGATAAGA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
96 3 0.03
97 106 0.97
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (96 bp):
AACTCCTCATCACGAAGGAGCAACATCATCCTTAGACAACCAGACGTCATCATCACGAAAGAACA
GTGTTATCTCAAATATCTTCAAAGATGGCCA
Found at i:1765077 original size:137 final size:137
Alignment explanation
Indices: 1764903--1765444 Score: 757
Period size: 137 Copynumber: 4.0 Consensus size: 137
1764893 TGATGGTCAT
* * *
1764903 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCATATGTCATCATCATGAAATAACA
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
*
1764968 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATATCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
*
1765033 CGATAAG
131 CGATCAG
*
1765040 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATATCCTCATCATGAAAGAACA
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
*
1765105 TTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
1765170 CGATCAG
131 CGATCAG
* * * * * * *
1765177 AACTCCTCATCATGAATGAGCAACATCATTCTTAGATAGCTAGATGTCCTCATCACGAATGAACC
1 AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
* * *
1765242 GTGTTATCTCAAATATATTTAAAGATGGCCAGACATCCTCATCACGAAGAAACAATGTCATCCAC
66 GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
1765307 CGATCAG
131 CGATCAG
* * * * * *
1765314 AACTACTCATCACGTAGGAGC--CGAGTCATCCTCAGATAACCAGACGTCCTCATCA-CAAAGGA
1 AACTCCTCATCACGAAGGAGCAAC-A-TCATTCTTAGATAACCAGATGTCCTCATCATGAAA-GA
** * * * * * *
1765376 ACCTTGTTATCTTAAATATCTTCAAAGGTGGTCAGACGTCCTCATCATGAAGGAACAATGTCATA
63 ACAGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATC
1765441 CACC
128 CACC
1765445 AGTTAGATCT
Statistics
Matches: 362, Mismatches: 40, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
135 1 0.00
136 3 0.01
137 358 0.99
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (137 bp):
AACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAACCAGATGTCCTCATCATGAAAGAACA
GTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
CGATCAG
Found at i:1765189 original size:234 final size:233
Alignment explanation
Indices: 1764735--1765169 Score: 554
Period size: 234 Copynumber: 1.9 Consensus size: 233
1764725 CGAAGGAACC
* * * *
1764735 GTGTTATCCTAAATGTCTTAAAGATGGCCAAATGTCCTCATCACGAAGGAACAATGTCATCTACC
1 GTGTTATCCTAAATATCTTAAAGATGGCCAAACGTCCTCATCACGAAGGAACAATATCATCCACC
* *
1764800 AATCAGAACTCCTCATCACGAAGGAGTCACATCATCCTTAGACAACCAGACGTCCTCATCACGAA
66 AATAAGAACTCCTCATCACGAAGGAGTCACATCATCCTTAGACAACCAGACATCCTCATCACGAA
* * * * *
1764865 GGAACTGTGTTATCTCCAATATCTTCAATGATGGTCATAACTCCTCATCACGAAGGAGCAACATC
131 AGAACTGTGTTATCTCAAATATCTTCAAAGATGGCCATAACTCCTCATCACGAAGGAACAACATC
* ** * **
1764930 ATTCTTAGATAACCATATGTCATCATCATGAAATAACA
196 ATCCACAGATAAACATACCTCATCATCATGAAATAACA
*
1764968 GTGTTAT-CTCAAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATATCATCCA
1 GTGTTATCCT-AAATATC-TTAAAGATGGCCAAACGTCCTCATCACGAAGGAACAATATCATCCA
* * * * *
1765032 CCGATAAGAACTCCTCATCACGAAGGAG-CAACATCATTCTTAGATAACCAGATATCCTCATCAT
64 CCAATAAGAACTCCTCATCACGAAGGAGTC-ACATCATCCTTAGACAACCAGACATCCTCATCAC
* *
1765096 GAAAGAACAT-TGTTATCTCAAATATCTTTAAAGATGGCCA-GACGTCCTCATCACGAAGGAACA
128 GAAAGAAC-TGTGTTATCTCAAATATCTTCAAAGATGGCCATAAC-TCCTCATCACGAAGGAACA
**
1765159 ATGTCATCCAC
191 ACATCATCCAC
1765170 CGATCAGAAC
Statistics
Matches: 173, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
232 2 0.01
233 16 0.09
234 154 0.89
235 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (233 bp):
GTGTTATCCTAAATATCTTAAAGATGGCCAAACGTCCTCATCACGAAGGAACAATATCATCCACC
AATAAGAACTCCTCATCACGAAGGAGTCACATCATCCTTAGACAACCAGACATCCTCATCACGAA
AGAACTGTGTTATCTCAAATATCTTCAAAGATGGCCATAACTCCTCATCACGAAGGAACAACATC
ATCCACAGATAAACATACCTCATCATCATGAAATAACA
Found at i:1766767 original size:112 final size:114
Alignment explanation
Indices: 1766633--1766850 Score: 257
Period size: 112 Copynumber: 1.9 Consensus size: 114
1766623 TATTAGTAAT
* * *
1766633 TATATTTTATAATATTTTGAATTTA-GACTATTAATTTAT-ATTTTTACAA-TTTAATCAC-TGA
1 TATATTTCATAATATTTAGAA-TTAGGACTATTAATTT-TGATATTTACAATTTTAATC-CTTGA
* ** *
1766694 GGTTTAATATTTTAATTTTAAATAATA-TTTTAGGATTATTTACACTAATAA
63 GGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTATTTACACTAATAA
* * * * *
1766745 TATATTTCATGATATTTAGAATTAGGATTTTTAATTTTGATATTTACAATTTTAATCCTTTAGTT
1 TATATTTCATAATATTTAGAATTAGGACTATTAATTTTGATATTTACAATTTTAATCCTTGAGGT
*
1766810 TTAAAATAATAATTTTAAATATTATTTTTAGAATTATTTAC
66 TTAAAATAATAATTTTAAATAATATTTTTAGAATTATTTAC
1766851 TATTATAGTA
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
111 4 0.05
112 38 0.43
113 31 0.35
114 15 0.17
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.52
Consensus pattern (114 bp):
TATATTTCATAATATTTAGAATTAGGACTATTAATTTTGATATTTACAATTTTAATCCTTGAGGT
TTAAAATAATAATTTTAAATAATATTTTTAGAATTATTTACACTAATAA
Found at i:1770094 original size:36 final size:36
Alignment explanation
Indices: 1770053--1770128 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
1770043 ATTTTCGGGA
*
1770053 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1770089 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1770125 TTTT
1 TTTT
1770129 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:1770568 original size:15 final size:15
Alignment explanation
Indices: 1770548--1770576 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1770538 TATCACAATC
1770548 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
1770563 GCGCAGGATTCCGG
1 GCGCAGGATTCCGG
1770577 AGCACCGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.45, T:0.14
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:1774920 original size:35 final size:36
Alignment explanation
Indices: 1774878--1774951 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
1774868 ATTTTCGGGA
*
1774878 TTTGCTA-TTTTGGCAAAATTCGAATAAATACGATT
1 TTTGCTATTTTTGGCAAAATTCGAATAAAGACGATT
1774913 TTTGCTATTTTTGGCAAAATTCGAATAAAGACGATT
1 TTTGCTATTTTTGGCAAAATTCGAATAAAGACGATT
1774949 TTT
1 TTT
1774952 TTAGCTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 7 0.19
36 30 0.81
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (36 bp):
TTTGCTATTTTTGGCAAAATTCGAATAAAGACGATT
Done.