Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001983.1 Hibiscus syriacus cultivar Beakdansim tig00004041_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: 530088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:324270 original size:97 final size:95
Alignment explanation
Indices: 324155--324336 Score: 301
Period size: 97 Copynumber: 1.9 Consensus size: 95
324145 CATGAATCTC
* *
324155 ATAAGAAATGAAGGCAATAAGATGTACATCAAGCAAATAGACTACGGATGAATCCATGAATGACA
1 ATAAGAAATGAAGGCAATAAGATGAACATCAAGCAAATAGAC-ACGGATGAATCCATGAATCACA
*
324220 GGCAAATGGATTATGGATGAACAAGACACCTG
65 GGCAAATGGA-CATGGATGAACAAGACACCTG
* *
324252 ATAAGAAATGAAGGCAATAAGATGAACATCAAGCAAATGGACATGGATGAATCCATGAATCACAG
1 ATAAGAAATGAAGGCAATAAGATGAACATCAAGCAAATAGACACGGATGAATCCATGAATCACAG
324317 GCAAATGGACATGGATGAAC
66 GCAAATGGACATGGATGAAC
324337 CCATGAATCA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 10 0.12
96 30 0.38
97 40 0.50
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (95 bp):
ATAAGAAATGAAGGCAATAAGATGAACATCAAGCAAATAGACACGGATGAATCCATGAATCACAG
GCAAATGGACATGGATGAACAAGACACCTG
Found at i:324321 original size:33 final size:33
Alignment explanation
Indices: 324284--324370 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
324274 TGAACATCAA
*
324284 GCAAATGGACATGGATGAATCCATGAATCACAG
1 GCAAATGGACATGGATGAACCCATGAATCACAG
324317 GCAAATGGACATGGATGAACCCATGAATCACAG
1 GCAAATGGACATGGATGAACCCATGAATCACAG
* *
324350 ACAAATGGACTATGAATGAAC
1 GCAAATGGAC-ATGGATGAAC
324371 AAGACACCTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
33 41 0.82
34 9 0.18
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
GCAAATGGACATGGATGAACCCATGAATCACAG
Found at i:324357 original size:129 final size:130
Alignment explanation
Indices: 324187--324466 Score: 413
Period size: 129 Copynumber: 2.2 Consensus size: 130
324177 TGTACATCAA
* * * * * * *
324187 GCAAATAGACTACGGATGAATCCATGAATGACAGGCAAATGGATTATGGATGAACAAGACACCTG
1 GCAAATGGACTATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTG
* * *
324252 ATAAGAAATGAAGGCAATAAGATGAA-CATCAAGCAAATGGAC-ATGGATGAATCCATGAATCAC
66 ATAAGAAATGAAGGC-ATAAGAT-AAGCATCAAGCAAAAGGACTATGGACGAATCCATGAATAAC
324315 AG
129 AG
324317 GCAAATGGAC-ATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTG
1 GCAAATGGACTATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTG
*
324381 ATAAGAAATGAAGGCATAAGATAAGCATCAAGCAAAAGGGCTATGGACGAATCCATGAATAACAG
66 ATAAGAAATGAAGGCATAAGATAAGCATCAAGCAAAAGGACTATGGACGAATCCATGAATAACAG
*
324446 GCAAATGGACTATGAATGAAC
1 GCAAATGGACTATGGATGAAC
324467 AAGACATCTG
Statistics
Matches: 135, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
127 2 0.01
128 21 0.16
129 94 0.70
130 18 0.13
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (130 bp):
GCAAATGGACTATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTG
ATAAGAAATGAAGGCATAAGATAAGCATCAAGCAAAAGGACTATGGACGAATCCATGAATAACAG
Found at i:324552 original size:97 final size:97
Alignment explanation
Indices: 324327--324604 Score: 416
Period size: 97 Copynumber: 2.9 Consensus size: 97
324317 GCAAATGGAC
* * *
324327 ATGGATGAACCCATGAATCACAGACAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
1 ATGGATGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
* ***
324392 AGGC-ATAAGAT-AAGCATCAAGCAAAAGGGCT
66 AGGCAATAACATGAA-CATCAAGCAAAAGAAAT
* * *
324423 ATGGACGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACATCTGATAAGAGATGA
1 ATGGATGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
*
324488 AGGCAATAACATGAACATCAAGCAAATGAAAT
66 AGGCAATAACATGAACATCAAGCAAAAGAAAT
*
324520 ATGGATGAATCCATGAATAACAGGCAAATGGACTATGGATGAACAAGACACCTGATAAGAAATGA
1 ATGGATGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
*
324585 AGACAATAACATGAACATCA
66 AGGCAATAACATGAACATCA
324605 GACCAGGTTC
Statistics
Matches: 164, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
96 63 0.38
97 99 0.60
98 2 0.01
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (97 bp):
ATGGATGAATCCATGAATAACAGGCAAATGGACTATGAATGAACAAGACACCTGATAAGAAATGA
AGGCAATAACATGAACATCAAGCAAAAGAAAT
Found at i:327702 original size:21 final size:21
Alignment explanation
Indices: 327676--327725 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
327666 CACTCTCGTT
327676 CTCTTCCTTCGGTGGTTCTGA
1 CTCTTCCTTCGGTGGTTCTGA
*
327697 CTCTTCCTTTGGTGGTTCTGA
1 CTCTTCCTTCGGTGGTTCTGA
327718 CTCTTCCT
1 CTCTTCCT
327726 CATTGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.04, C:0.30, G:0.20, T:0.46
Consensus pattern (21 bp):
CTCTTCCTTCGGTGGTTCTGA
Found at i:342777 original size:25 final size:25
Alignment explanation
Indices: 342743--342790 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
342733 AATGATATCC
342743 CGACTTTAGCGTACTACTTTATTCT
1 CGACTTTAGCGTACTACTTTATTCT
342768 CGACTTTAGCGTACTACTTTATT
1 CGACTTTAGCGTACTACTTTATT
342791 AAGTCATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (25 bp):
CGACTTTAGCGTACTACTTTATTCT
Found at i:343884 original size:42 final size:42
Alignment explanation
Indices: 343835--343914 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
343825 ATTCATCTAT
* *
343835 AAGATCCGGGTGTTCGATGAAAGCACATAACATCATCTGTAG
1 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTGTAG
343877 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCT
1 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCT
343915 ACAAAAGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (42 bp):
AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTGTAG
Found at i:343923 original size:42 final size:42
Alignment explanation
Indices: 343835--343938 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
343825 ATTCATCTAT
* * ** *
343835 AAGATCCGGGTGTTCGATGAAAGCACATAACATCATCTGTAG
1 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTACAA
343877 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTACAA
1 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTACAA
*
343919 AAGATAC-GG-GTACGACGAAA
1 AAGATCCGGGTGTACGACGAAA
343939 AGAACATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 11 0.20
41 2 0.04
42 43 0.77
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.18
Consensus pattern (42 bp):
AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTACAA
Found at i:352362 original size:60 final size:60
Alignment explanation
Indices: 352263--352377 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
352253 AATAAGACCT
* *** ** *
352263 TCATTTTAAATTAATCCCTAAACTTTTGAGTGTTCCAATTTTGTCCCTAAACTATAACTA
1 TCATTCTAAATTAATCCCTAAACTTTTGAACCTTCCAATTTCATCCCCAAACTATAACTA
* *
352323 TCATTCTAAATTAGT-CCTCAAACTTTTGAACCTTTCAATTTCATCCCCAAACTAT
1 TCATTCTAAATTAATCCCT-AAACTTTTGAACCTTCCAATTTCATCCCCAAACTAT
352378 GACCTTGAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
59 3 0.07
60 42 0.93
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (60 bp):
TCATTCTAAATTAATCCCTAAACTTTTGAACCTTCCAATTTCATCCCCAAACTATAACTA
Found at i:353816 original size:15 final size:16
Alignment explanation
Indices: 353790--353828 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
353780 AAATATTATT
353790 TATTAT-TTATTTT-A
1 TATTATATTATTTTCA
353804 TATTATATTATTTTCA
1 TATTATATTATTTTCA
353820 TATT-TATTA
1 TATTATATTA
353829 ATAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 12 0.52
16 5 0.22
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATATTATTTTCA
Found at i:354707 original size:23 final size:22
Alignment explanation
Indices: 354681--354747 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 22
354671 AAAATAATTT
*
354681 CAGAATCGAAAAACACTGTTTAC
1 CAGAA-CGAAAAACTCTGTTTAC
* *
354704 CAGAACTGAAAAACTTTATTTAC
1 CAGAAC-GAAAAACTCTGTTTAC
354727 CAGAACCGAAAAACTCTGTTT
1 CAGAA-CGAAAAACTCTGTTT
354748 CTATATGGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (22 bp):
CAGAACGAAAAACTCTGTTTAC
Found at i:357638 original size:27 final size:27
Alignment explanation
Indices: 357583--357638 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
357573 TTCGTGCCCA
*
357583 AAATCATATATAAAAAAATCTTTTAAT
1 AAATCATATATAAAAAAATATTTTAAT
* *
357610 AAATCA-ATATAAAAATATATATTTCAT
1 AAATCATATATAAAAAAATAT-TTTAAT
357637 AA
1 AA
357639 CATAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATCATATATAAAAAAATATTTTAAT
Found at i:358254 original size:2 final size:2
Alignment explanation
Indices: 358247--358284 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
358237 CAATCGTGCA
358247 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
358285 TCCAACTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360525 original size:17 final size:17
Alignment explanation
Indices: 360505--360538 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
360495 TTTATTAAAA
360505 TTTTAAGTTTAATTTAG
1 TTTTAAGTTTAATTTAG
* *
360522 TTTTTATTTTAATTTAG
1 TTTTAAGTTTAATTTAG
360539 AGTGAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
TTTTAAGTTTAATTTAG
Found at i:363273 original size:21 final size:23
Alignment explanation
Indices: 363249--363290 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
363239 GCACCTAAAC
363249 TATC-ATTTTTATT-TTTTTTAA
1 TATCTATTTTTATTATTTTTTAA
*
363270 TATCTATTTTTTTTATTTTTT
1 TATCTATTTTTATTATTTTTT
363291 TCACAACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (23 bp):
TATCTATTTTTATTATTTTTTAA
Found at i:365465 original size:14 final size:15
Alignment explanation
Indices: 365428--365467 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
365418 TAACAAAAAG
365428 AATA-ATTTTA-ATA
1 AATATATTTTATATA
365441 AATATATTTTTATATA
1 AATATA-TTTTATATA
365457 AA-ATATTTTAT
1 AATATATTTTAT
365468 TTTCTTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 8 0.33
16 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATATTTTATATA
Found at i:366568 original size:21 final size:21
Alignment explanation
Indices: 366520--366608 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
366510 GTTTCCAGAT
* *
366520 TCGCAACGAGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
366541 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
366562 TTGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
366582 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
366603 TCGCAA
1 TCGCAA
366609 CACGATTTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
20 16 0.28
21 41 0.72
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:366627 original size:41 final size:41
Alignment explanation
Indices: 366598--366679 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
366588 TGCGAACTTG
366598 GACTATCGCAACACGATTTACATATTCGCATTGCGATAGTC
1 GACTATCGCAACACGATTTACATATTCGCATTGCGATAGTC
***
366639 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTATCGCAACACGATTTACATATTCGCATTGCGATAGTC
366680 CAAGTTCGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (41 bp):
GACTATCGCAACACGATTTACATATTCGCATTGCGATAGTC
Found at i:366634 original size:20 final size:20
Alignment explanation
Indices: 366611--366675 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
366601 TATCGCAACA
366611 CGATTTACATATTCGCATTG
1 CGATTTACATATTCGCATTG
*
366631 CGATAGT-CGACTA-TCGCATTG
1 CGAT-TTAC-A-TATTCGCATTG
366652 CGATTTACATATTCGCATTG
1 CGATTTACATATTCGCATTG
366672 CGAT
1 CGAT
366676 AGTCCAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 2 0.05
20 19 0.50
21 15 0.39
22 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (20 bp):
CGATTTACATATTCGCATTG
Found at i:366647 original size:21 final size:23
Alignment explanation
Indices: 366617--366717 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 23
366607 AACACGATTT
366617 ACATATTCGCATTGCGATAGTCG
1 ACATATTCGCATTGCGATAGTCG
*
366640 AC-TA-TCGCATTGCGAT--T-T
1 ACATATTCGCATTGCGATAGTCG
366658 ACATATTCGCATTGCGATAGTC-
1 ACATATTCGCATTGCGATAGTCG
**
366680 -CA-AGTTCGCAAGGCGATAGTCG
1 ACATA-TTCGCATTGCGATAGTCG
*
366702 A-A-ATTCGCGTTGCGAT
1 ACATATTCGCATTGCGAT
366718 TTATTCCAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 13 0.20
21 39 0.61
22 5 0.08
23 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
ACATATTCGCATTGCGATAGTCG
Found at i:366696 original size:41 final size:41
Alignment explanation
Indices: 366599--366696 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
366589 GCGAACTTGG
** *
366599 ACTATCGCAACACGATTTACATATTCGCATTGCGATAGTCG
1 ACTATCGCAAGGCGATTTACATATTCGCATTGCGATAGTCA
**
366640 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCA
1 ACTATCGCAAGGCGATTTACATATTCGCATTGCGATAGT-CA
*
366682 AGT-TCGCAAGGCGAT
1 ACTATCGCAAGGCGAT
366697 AGTCGAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
41 46 0.94
42 3 0.06
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (41 bp):
ACTATCGCAAGGCGATTTACATATTCGCATTGCGATAGTCA
Found at i:367423 original size:12 final size:12
Alignment explanation
Indices: 367406--367430 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
367396 ATACCACAAG
367406 TCGTTGCGATTT
1 TCGTTGCGATTT
367418 TCGTTGCGATTT
1 TCGTTGCGATTT
367430 T
1 T
367431 GGACTATCGC
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:0.08, C:0.16, G:0.24, T:0.52
Consensus pattern (12 bp):
TCGTTGCGATTT
Found at i:367534 original size:41 final size:41
Alignment explanation
Indices: 367477--367558 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
367467 GAACTTGGAC
* *
367477 TTACATATTCGCATTGCTATAGTC-GACTATCGCATTGCGAT
1 TTACATATTCGCATTGCGATAGTCTAACT-TCGCATTGCGAT
*
367518 TTACATATTCGCATTGCGATAGTCTAAGTTCGCATTGCGAT
1 TTACATATTCGCATTGCGATAGTCTAACTTCGCATTGCGAT
367559 AGTCGAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.95
42 2 0.05
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (41 bp):
TTACATATTCGCATTGCGATAGTCTAACTTCGCATTGCGAT
Found at i:367551 original size:21 final size:21
Alignment explanation
Indices: 367484--367578 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
367474 GACTTACATA
* *
367484 TTCGCATTGCTATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
367504 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
*
367525 TTCGCATTGCGATAGTCTAAG
1 TTCGCATTGCGATAGTCGAAG
367546 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
367567 TTCGCGTTGCGA
1 TTCGCATTGCGA
367579 ATCTGGAAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
20 16 0.25
21 46 0.73
22 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:368792 original size:16 final size:16
Alignment explanation
Indices: 368773--368804 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
368763 AATTTAATAT
368773 CAATTGACTTTACTAA
1 CAATTGACTTTACTAA
368789 CAATTGACTTTACTAA
1 CAATTGACTTTACTAA
368805 ATAAAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
CAATTGACTTTACTAA
Found at i:370018 original size:26 final size:26
Alignment explanation
Indices: 369988--370038 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
369978 TCCAATCAAT
369988 TTGCATATTAACAAAATTTGAGTATA
1 TTGCATATTAACAAAATTTGAGTATA
370014 TTGCATATTAACAAAATTTGAGTAT
1 TTGCATATTAACAAAATTTGAGTAT
370039 CAATTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (26 bp):
TTGCATATTAACAAAATTTGAGTATA
Found at i:371115 original size:107 final size:107
Alignment explanation
Indices: 370929--371140 Score: 415
Period size: 107 Copynumber: 2.0 Consensus size: 107
370919 GAAAGTATTC
*
370929 AACGTTCACATAACGGCTAATACAAATTGGTTCATCTAACGGCTAGTAAATTAAACGTTCCCAAA
1 AACGTGCACATAACGGCTAATACAAATTGGTTCATCTAACGGCTAGTAAATTAAACGTTCCCAAA
370994 ACATTCATAAATTTATATTATTATTTGCAACTTTGTCGTCAT
66 ACATTCATAAATTTATATTATTATTTGCAACTTTGTCGTCAT
371036 AACGTGCACATAACGGCTAATACAAATTGGTTCATCTAACGGCTAGTAAATTAAACGTTCCCAAA
1 AACGTGCACATAACGGCTAATACAAATTGGTTCATCTAACGGCTAGTAAATTAAACGTTCCCAAA
371101 ACATTCATAAATTTATATTATTATTTGCAACTTTGTCGTC
66 ACATTCATAAATTTATATTATTATTTGCAACTTTGTCGTC
371141 TCCGTTAAAT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (107 bp):
AACGTGCACATAACGGCTAATACAAATTGGTTCATCTAACGGCTAGTAAATTAAACGTTCCCAAA
ACATTCATAAATTTATATTATTATTTGCAACTTTGTCGTCAT
Found at i:371163 original size:17 final size:16
Alignment explanation
Indices: 371141--371173 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
371131 CTTTGTCGTC
371141 TCCGTTAAATGACAATG
1 TCCGTTAAATGA-AATG
371158 TCCGTTAAATGAAATG
1 TCCGTTAAATGAAATG
371174 CCCCCAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (16 bp):
TCCGTTAAATGAAATG
Found at i:371268 original size:18 final size:20
Alignment explanation
Indices: 371216--371261 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
371206 TTTGATTCAC
371216 GAAATATAATATTATTTTTT
1 GAAATATAATATTATTTTTT
371236 GAAATATAATATTATTTTTT
1 GAAATATAATATTATTTTTT
371256 GAAATA
1 GAAATA
371262 ATATTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
GAAATATAATATTATTTTTT
Found at i:371283 original size:16 final size:17
Alignment explanation
Indices: 371262--371296 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
371252 TTTTGAAATA
371262 ATATTA-TCAAAATATT
1 ATATTATTCAAAATATT
*
371278 ATATTATTTAAAATATT
1 ATATTATTCAAAATATT
371295 AT
1 AT
371297 TGGTAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTATTCAAAATATT
Found at i:371599 original size:50 final size:49
Alignment explanation
Indices: 371537--371673 Score: 150
Period size: 50 Copynumber: 2.8 Consensus size: 49
371527 ATATTTTATG
* * *
371537 GGAGATGTACATACTTACAATGATATAAGTATGTGTTTATTTTTAGGTT
1 GGAGATGTACATACTTACAACGATATAAATATGTGTTTATTTTTAAGTT
* * * * *
371586 GAGAGATTTACATACTTACACCGGTGTAAATGTGTGTTTATTTTTAAGTT
1 G-GAGATGTACATACTTACAACGATATAAATATGTGTTTATTTTTAAGTT
* *
371636 GGAAGATGTGCATACTTAC-ACCAGTATAAATATGTGTT
1 GG-AGATGTACATACTTACAACGA-TATAAATATGTGTT
371674 AATTGTTATA
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
49 3 0.04
50 67 0.96
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (49 bp):
GGAGATGTACATACTTACAACGATATAAATATGTGTTTATTTTTAAGTT
Found at i:373415 original size:21 final size:21
Alignment explanation
Indices: 373389--373444 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
373379 GTCATATCAG
373389 CACTGTGAACTATCACTTCAA
1 CACTGTGAACTATCACTTCAA
373410 CACTGTGAA-T-TGCTACTTCAA
1 CACTGTGAACTAT-C-ACTTCAA
*
373431 CACCGT-AACTATCA
1 CACTGTGAACTATCA
373445 ATTACGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 1 0.03
20 5 0.17
21 23 0.77
22 1 0.03
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (21 bp):
CACTGTGAACTATCACTTCAA
Found at i:374819 original size:20 final size:20
Alignment explanation
Indices: 374794--374886 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
374784 TTTTCCCAAT
374794 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
374814 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
374834 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
374855 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
374876 TCGCAATGCGA
1 TCGCAATGCGA
374887 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:374836 original size:41 final size:41
Alignment explanation
Indices: 374791--374886 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
374781 CGATTTTCCC
*
374791 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
374832 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
374873 AAATCGCAATGCGA
1 AATTCGCAATGCGA
374887 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:374899 original size:41 final size:41
Alignment explanation
Indices: 374813--374947 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
374803 GAATAAGTAA
* * * *
374813 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
374854 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
374895 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
374936 TTCGCAACGCGA
1 ATCGCAACGCGA
374948 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:374900 original size:20 final size:20
Alignment explanation
Indices: 374875--374969 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
374865 AATTGAGAAA
*
374875 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
374895 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
374916 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
374936 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
374956 TTCGCAACGCGATA
1 ATCGCAACGCGATA
374970 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:375487 original size:20 final size:20
Alignment explanation
Indices: 375462--375499 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
375452 CGATTCTCTC
375462 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
375482 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
375500 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:376821 original size:18 final size:18
Alignment explanation
Indices: 376800--376844 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
376790 TCCACTTCGG
*
376800 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
376818 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
376836 GAGCCATCA
1 GAGCCATCA
376845 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:377368 original size:19 final size:20
Alignment explanation
Indices: 377314--377380 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
377304 TAGTTTACTT
* *
377314 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
377334 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
377354 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
377373 TCGCAACG
1 TCGCAACG
377381 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:377388 original size:14 final size:14
Alignment explanation
Indices: 377369--377425 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
377359 ATGCGAAATG
377369 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
377383 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
377399 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
377415 AAAATCGCAAC
1 AAAATCGCAAC
377426 ACGAAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:377411 original size:32 final size:32
Alignment explanation
Indices: 377353--377442 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
377343 GGAAATGGCT
*
377353 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
377386 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
*
377418 ATCGCAACACGAAATGAAATCGCAA
1 ATCGCAACGCGAAATGAAATCGCAA
377443 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 40 0.73
33 15 0.27
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:377478 original size:14 final size:14
Alignment explanation
Indices: 377459--377581 Score: 102
Period size: 14 Copynumber: 7.9 Consensus size: 14
377449 TTGTGTTTCG
*
377459 CGTTGCGATTTTAT
1 CGTTGCGATTTTGT
377473 CGTTGCGATTTGTGTTT
1 CGTTGCGATTT-TG--T
377490 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
377506 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
377522 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
377538 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
377554 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
377570 CGTTGCGATTTT
1 CGTTGCGATTTT
377582 CATTTCGCAT
Statistics
Matches: 91, Mismatches: 5, Indels: 26
0.75 0.04 0.21
Matches are distributed among these distances:
14 45 0.49
15 1 0.01
16 9 0.10
17 1 0.01
18 24 0.26
19 11 0.12
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:377528 original size:32 final size:32
Alignment explanation
Indices: 377454--377597 Score: 234
Period size: 32 Copynumber: 4.4 Consensus size: 32
377444 GCGATTTGTG
* **
377454 TTTCGCGTTGCGATTTTATCGTTGCGATTTGTG
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTT-CA
377487 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
377519 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
377551 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
377584 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
377598 AGCCATTTCC
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
32 59 0.56
33 47 0.44
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:377548 original size:65 final size:65
Alignment explanation
Indices: 377454--377597 Score: 236
Period size: 65 Copynumber: 2.2 Consensus size: 65
377444 GCGATTTGTG
**
377454 TTTCGCGTTGCGATTTTATCGTTGCGATTTGTGTTTCGCGTTGCGATTTTGTCGTTGCGA-TTTC
1 TTTCGCGTTGCGATTTTATCGTTGCGATTT-CATTTCGCGTTGCGATTTTGTCGTTGCGATTTTC
377518 A
65 A
*
377519 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCATTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTCATTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
377584 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
377598 AGCCATTTCC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
64 27 0.36
65 47 0.64
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (65 bp):
TTTCGCGTTGCGATTTTATCGTTGCGATTTCATTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:377616 original size:20 final size:19
Alignment explanation
Indices: 377582--377635 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
377572 TTGCGATTTT
*
377582 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
377601 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
377621 CA-TTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
377636 TTTAAGTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 11 0.34
19 7 0.22
20 14 0.44
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:379622 original size:14 final size:15
Alignment explanation
Indices: 379603--379679 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
379593 CGAAATGGCT
379603 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
379617 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
379635 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
379654 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
379668 ATCGCAATGCGA
1 ATCGCAA-GCGA
379680 TTTTCATTCG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:379635 original size:19 final size:19
Alignment explanation
Indices: 379613--379679 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
379603 ATCGCAACGA
379613 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
379632 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
379650 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
379664 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
379680 TTTTCATTCG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:380118 original size:14 final size:14
Alignment explanation
Indices: 380099--380134 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
380089 ATTGTTTAAT
380099 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
380113 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
380127 TGATTTGT
1 TGATTTGT
380135 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:380701 original size:14 final size:14
Alignment explanation
Indices: 380682--380717 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
380672 ATTGTTTAAT
380682 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
380696 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
380710 TGATTTGT
1 TGATTTGT
380718 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:381278 original size:14 final size:14
Alignment explanation
Indices: 381259--381294 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
381249 ATTGTTTAAT
381259 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
381273 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
381287 TGATTTGT
1 TGATTTGT
381295 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:381864 original size:14 final size:14
Alignment explanation
Indices: 381845--381880 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
381835 ATTGTTTAAT
381845 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
381859 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
381873 TGATTTGT
1 TGATTTGT
381881 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:381937 original size:586 final size:590
Alignment explanation
Indices: 379635--382251 Score: 4779
Period size: 586 Copynumber: 4.5 Consensus size: 590
379625 GCGAAATGAA
* *** *
379635 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGATTTTC-ATTCGCATTGCGAT
1 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
379699 TTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAA
66 TTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAA
379764 CTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTG-AAATGTTAAAA
131 CTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAA
379828 GTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAAT
196 GTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAAT
379893 GTTTGGTTAAGTACCTAGAATTCAATAAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
261 GTTTGGTTAAGTACCTAGAATTCAAT-AATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
*
379958 TG-TTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGTTGTGTGAAATGGATGTACG
325 TGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACG
380022 GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTA-TATTTT
390 GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTT
380086 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACA
455 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACA
380151 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGC-AAA
520 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
380215 CAGACT
585 CAGACT
380221 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
1 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
*
380286 TTTCTCGTTGCGATAACCATTTTCGCA-TGCGATAGTCAAATGAATGGCTAATAAGTGATGACAA
66 TTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAA
380350 CTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAA
131 CTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAA
380415 GTGCACACAT-AAATACACATAATGCAAGTTTTGTTAAC--ATATACTCCTTTTGGTTTGAAAAT
196 GTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAAT
380477 GTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGTAGGTTTTAGATGTGTAGG-AGT
261 GTTTGGTTAAGTACCTAGAATTCAATAATTTGCTG-TT-T-GTAGGTTTTAGATGTGTAGGAAGT
380541 CTTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTA
323 CTTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTA
380606 CGGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAAT-A-AA--ATTATTATT
388 CGGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATT
380667 TTTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTA
453 TTTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTA
380732 CATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGC-TT-TGTTGAAGGCAA
518 CATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAA
380795 AACA-ACT
583 AACAGACT
380802 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTT-GCATTGCGAT
1 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
*
380866 TTTCGCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAAATGAATGTCTAATAAGTGATGACA
66 TTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTC-AAATGAATGTCTAATAAGTGATGACA
380931 ACTGAACAGATCATAGCAATGTTC-AACTCAAGTTACT-ATAC-TG-CTAACTGAAAATGTTAAA
130 ACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAA
380992 AGTGCACACA-AAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTG-AAA
195 AGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAA
381055 TGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
260 TGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCT
381120 TGTTTGAGCAAATG-TTGGTTTCTGCAGGTT-ATCCTTAAGTGAGCTGTGTGAAATGGATGTACG
325 TGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACG
381183 GGGTCACAAAGTTGTTGATTCATTGATTC-ATAATTGATGAAGAAATAAGAATTATTATTA-TTT
390 GGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTT
381246 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACA
455 TTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACA
381311 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
520 TAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAA
381376 CAGACT
585 CAGACT
381382 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
1 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
*
381447 TTTCTCGTTGCGATAACCA-TTTCGCATTGCGATAGTCAAA-G-ATGTCCAATAAGTGATGACAA
66 TTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAA
381509 CTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAA
131 CTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAA
381574 GTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAAT
196 GTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAAT
381639 GTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTT
261 GTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTT
*
381704 ATTTGAGCAAATGTTTGGTTTCTGCAGG-TAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGG
326 GTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGG
*
381768 GATCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTT
391 GGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTT
381833 TGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACAT
456 TGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACAT
381898 AATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAAC
521 AATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAAC
381963 AGACT
586 AGACT
381968 ATCGCAACGCGAAATGGCTATCGC-ACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
1 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
*
382032 TTTCCTCGTTGCGATAGCCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAA-TGATGACA
66 TTT-CTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACA
*
382096 ACTGAACAGATCATAGCAATGTTTAAACTCAAGTTACTAATACATGCCTAACT-AAAATGTTAAA
130 ACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAA
*
382160 AGTG--CACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGTTTTG-AAA
195 AGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAA
*
382222 TATTTGGTTAAGTACCTAGAATTCAATAAT
260 TGTTTGGTTAAGTACCTAGAATTCAATAAT
382252 AATTGTTAAA
Statistics
Matches: 1977, Mismatches: 18, Indels: 74
0.96 0.01 0.04
Matches are distributed among these distances:
574 17 0.01
575 63 0.03
576 38 0.02
577 178 0.09
578 81 0.04
579 64 0.03
580 136 0.07
581 146 0.07
582 110 0.06
583 209 0.11
584 161 0.08
585 137 0.07
586 469 0.24
587 97 0.05
588 61 0.03
589 10 0.01
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (590 bp):
ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGATTTTCGTTTCGCATTGCGAT
TTTCTCGTTGCGATAACCATTTTCGCATTGCGATAGTCAAATGAATGTCTAATAAGTGATGACAA
CTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAA
GTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAAT
GTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTT
GTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGTGTGAAATGGATGTACGG
GGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTT
TGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACAT
AATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAAC
AGACT
Found at i:383359 original size:12 final size:12
Alignment explanation
Indices: 383342--383366 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
383332 ATATAATCCT
383342 GAAGAAGAAAAA
1 GAAGAAGAAAAA
383354 GAAGAAGAAAAA
1 GAAGAAGAAAAA
383366 G
1 G
383367 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:385655 original size:22 final size:19
Alignment explanation
Indices: 385630--385749 Score: 62
Period size: 19 Copynumber: 6.7 Consensus size: 19
385620 CTTAATGTCC
385630 ATCGCAACGCGGAAACGACAAA
1 ATCGCAACGC-GAAACG--AAA
* *
385652 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
*
385671 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAACGAAA
* *
385685 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
**
385704 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAACGAAA
* *
385718 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAA
385737 ATCGCAACGCGAA
1 ATCGCAACGCGAA
385750 TTTAATTTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.24
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 34 0.43
21 5 0.06
22 9 0.11
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAACGAAA
Found at i:385673 original size:19 final size:19
Alignment explanation
Indices: 385649--385749 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 19
385639 CGGAAACGAC
385649 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
385668 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
*
385682 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
385701 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
**
385715 GGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
385734 AAAATCGCAACGCGAA
1 AAAATCGCAATGCGAA
385750 TTTAATTTCG
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
14 19 0.29
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 34 0.52
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:385688 original size:33 final size:33
Alignment explanation
Indices: 385651--385745 Score: 181
Period size: 33 Copynumber: 2.9 Consensus size: 33
385641 GAAACGACAA
385651 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
385684 AATCGCAATGCGAAATGAAAATCGCAACGAGGG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
385717 AATCGCAATGCGAAATGAAAATCGCAACG
1 AATCGCAATGCGAAATGAAAATCGCAACG
385746 CGAATTTAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:385925 original size:14 final size:14
Alignment explanation
Indices: 385906--385942 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
385896 CATCAATTAA
385906 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
385920 ACAAATCACCTTTT
1 ACAAATCAACTTTT
385934 ACAAATCAA
1 ACAAATCAA
385943 TTAAACAATC
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:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:387365 original size:21 final size:21
Alignment explanation
Indices: 387299--387365 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
387289 GTGAATCGGG
*
387299 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
387319 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
387341 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
387362 CTCT
1 CTCT
387366 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:387384 original size:42 final size:41
Alignment explanation
Indices: 387299--387421 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
387289 GTGAATCGGG
* * * * *
387299 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
387341 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
387383 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
387422 CGAGTCGGCT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:389450 original size:20 final size:19
Alignment explanation
Indices: 389419--389615 Score: 130
Period size: 20 Copynumber: 10.8 Consensus size: 19
389409 TCTTTTGGTT
389419 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
389438 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
389459 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
389478 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
389492 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
389508 -CTA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
389525 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
389545 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
389564 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
389583 GAAATG-AAATCGCAATGC
1 GAAATGAAAATCGCAACGA
389601 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
389616 TGCGATTTTG
Statistics
Matches: 146, Mismatches: 19, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
14 17 0.12
15 1 0.01
16 4 0.03
17 4 0.03
18 27 0.18
19 44 0.30
20 47 0.32
21 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:389536 original size:19 final size:19
Alignment explanation
Indices: 389514--389620 Score: 164
Period size: 19 Copynumber: 5.7 Consensus size: 19
389504 GCGACTAGAC
389514 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
389533 AATCGCAACCGCGAAATTAA
1 AATCGCAA-CGCGAAATGAA
389553 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
389572 AATCGCAACGCGAAATG-A
1 AATCGCAACGCGAAATGAA
*
389590 AATCGCAATGCGAAATG-A
1 AATCGCAACGCGAAATGAA
*
389608 AATCGCAATGCGA
1 AATCGCAACGCGA
389621 TTTTGGTTTC
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
18 31 0.37
19 35 0.42
20 18 0.21
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:389546 original size:39 final size:36
Alignment explanation
Indices: 389419--389621 Score: 163
Period size: 33 Copynumber: 5.6 Consensus size: 36
389409 TCTTTTGGTT
*
389419 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAT-A-GA-AATCGCAACGC
** *
389458 GGAAATGACTATCGCAA--CGAGAG-AATCGCAACGC
1 -GAAATGAAAATCGCAACGCGATAGAAATCGCAACGC
** *
389492 GAAATGACTATCGCGA--C--TAGACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGATAGA-AATCGCAACGC
389525 GAAATGAAAATCGCAACCGCGAAATTA-AAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCG--A-TAGAAATCGCAACGC
* *
389564 GAAATGAAAATCGCAACGCGAAATGAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGATA-GAAATCGCAACGC
*
389601 GAAATG-AAATCGCAATGCGAT
1 GAAATGAAAATCGCAACGCGAT
389622 TTTGGTTTCG
Statistics
Matches: 138, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
31 2 0.01
33 40 0.29
34 11 0.08
35 1 0.01
36 16 0.12
37 18 0.13
38 6 0.04
39 27 0.20
40 15 0.11
41 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (36 bp):
GAAATGAAAATCGCAACGCGATAGAAATCGCAACGC
Found at i:389638 original size:19 final size:19
Alignment explanation
Indices: 389616--389680 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
389606 GAAATCGCAA
*
389616 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
389635 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
** *
389654 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTGATTT-CGCGT
389674 TGCGATT
1 TGCGATT
389681 CTCATTCTCG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.11, C:0.18, G:0.26, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:390295 original size:20 final size:20
Alignment explanation
Indices: 390202--390295 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
390192 CGCTAAGTAA
*
390202 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
390222 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
390242 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
390263 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
390283 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
390296 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:390314 original size:41 final size:41
Alignment explanation
Indices: 390223--390357 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
390213 AAAGTCAGTA
* * * ** *
390223 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
390263 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
390305 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
390346 TCGCGTTGCGAT
1 TCGCGTTGCGAT
390358 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:390328 original size:20 final size:20
Alignment explanation
Indices: 390284--390376 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
390274 ATAGTCAGTA
* **
390284 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
390305 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
390325 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
390346 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
390366 TCGCATTGCGA
1 TCGCATTGCGA
390377 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:390358 original size:41 final size:41
Alignment explanation
Indices: 390284--390379 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
390274 ATAGTCAGTA
*
390284 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
390325 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
390366 TCGCATTGCGAATT
1 TCGCATTGCGAATT
390380 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:393115 original size:4 final size:4
Alignment explanation
Indices: 393106--393149 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
393096 TAGACAACTC
* * * *
393106 TATG TATG TATG TAAG TATG TATG CATG CATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
393150 AATTTGTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (4 bp):
TATG
Found at i:399840 original size:2 final size:2
Alignment explanation
Indices: 399835--399861 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
399825 ATGCAAAAAA
399835 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 A
399862 ATTTCATGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:402128 original size:15 final size:15
Alignment explanation
Indices: 402108--402138 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
402098 TAGGAACACC
*
402108 AAAAGTGTCATTTTT
1 AAAAGTGTCATGTTT
402123 AAAAGTGTCATGTTT
1 AAAAGTGTCATGTTT
402138 A
1 A
402139 TCAGAGTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (15 bp):
AAAAGTGTCATGTTT
Found at i:404083 original size:22 final size:22
Alignment explanation
Indices: 404055--404098 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
404045 TCAATTATAA
*
404055 ATGTATTT-ATTTTTATAATTAT
1 ATGTATTTGATTATTAT-ATTAT
404077 ATGTATTTGATTATTATATTAT
1 ATGTATTTGATTATTATATTAT
404099 TAATTCAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATGTATTTGATTATTATATTAT
Found at i:405572 original size:2 final size:2
Alignment explanation
Indices: 405562--405606 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
405552 TTTTATTTTT
405562 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
405603 -A TA T
1 TA TA T
405607 TGTCGGAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 3 0.08
2 34 0.87
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:406077 original size:39 final size:37
Alignment explanation
Indices: 405881--406094 Score: 202
Period size: 39 Copynumber: 5.6 Consensus size: 37
405871 TAGTTTAAAA
405881 TATATATTATATA-TTTTTTAAAAGCATTTTGAAAACATT
1 TATATATTATATAGTTTTTTAAAA-CATTTTG-AAA-ATT
*
405920 TATATATTATATAGATTTTTAAAAATCATTTTGAAAATT
1 TATATATTATATAG-TTTTTTAAAA-CATTTTGAAAATT
* * *
405959 TATATAATATATAG-TTTTGAAAACGTTTTGAAAACATT
1 TATATATTATATAGTTTTTTAAAACATTTTG-AAA-ATT
* * * * *
405997 TATATATTATATGGTTTTTAAAAATATTTTGAAGATA
1 TATATATTATATAGTTTTTTAAAACATTTTGAAAATT
*
406034 TATATAATATATAGTTTTTTTAAAACATTTTTGAAAA--
1 TATATATTATATAG-TTTTTTAAAACA-TTTTGAAAATT
* * *
406071 TGTATATTGTATAGTTTTTAAAAA
1 TATATATTATATAGTTTTTTAAAA
406095 AAATCATTTT
Statistics
Matches: 147, Mismatches: 21, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
36 15 0.10
37 36 0.24
38 27 0.18
39 50 0.34
40 3 0.02
41 16 0.11
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.48
Consensus pattern (37 bp):
TATATATTATATAGTTTTTTAAAACATTTTGAAAATT
Found at i:406167 original size:22 final size:24
Alignment explanation
Indices: 406114--406161 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
406104 TGAAAACACG
* *
406114 TATAATATATAGTTTTGAAATTTA
1 TATATTATATAGTTTTGAAATATA
*
406138 TATATTATATATTTTTGAAA-ATA
1 TATATTATATAGTTTTGAAATATA
406161 T
1 T
406162 TTTTATAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TATATTATATAGTTTTGAAATATA
Found at i:406198 original size:18 final size:18
Alignment explanation
Indices: 406171--406208 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
406161 TTTTTATAAC
*
406171 ATATTGTTATTATTATTT
1 ATATTATTATTATTATTT
406189 ATATTATTATTATTATTT
1 ATATTATTATTATTATTT
406207 AT
1 AT
406209 TTCCCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATTATTATTATTATTT
Found at i:407386 original size:28 final size:27
Alignment explanation
Indices: 407324--407389 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
407314 TTTTTTTATA
* * * *
407324 TTATTTATTTTATTTCCTTTTTTATTT
1 TTATTTATTTCATTTCATTATTTACTT
407351 TTATTTTATTTCATTTCATTGATTTACTT
1 TTA-TTTATTTCATTTCATT-ATTTACTT
407380 TTATTTATTT
1 TTATTTATTT
407390 ACTTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 3 0.09
28 21 0.64
29 9 0.27
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (27 bp):
TTATTTATTTCATTTCATTATTTACTT
Found at i:407389 original size:14 final size:14
Alignment explanation
Indices: 407310--407399 Score: 55
Period size: 14 Copynumber: 6.6 Consensus size: 14
407300 TTTTTTTTGA
*
407310 TTTATTTTTTTA-T
1 TTTATTTATTTACT
*
407323 ATTATTTATTTTA-T
1 TTTATTTA-TTTACT
** *
407337 TTCCTTT-TTTATT
1 TTTATTTATTTACT
407350 TTTATTTTATTT-CAT
1 TTTA-TTTATTTAC-T
* *
407365 TTCATTGATTTACT
1 TTTATTTATTTACT
407379 TTTATTTATTTACT
1 TTTATTTATTTACT
407393 TTT-TTTA
1 TTTATTTA
407400 GTCTTTATTT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
12 4 0.07
13 13 0.22
14 34 0.58
15 8 0.14
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (14 bp):
TTTATTTATTTACT
Found at i:407497 original size:25 final size:24
Alignment explanation
Indices: 407453--407506 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
407443 ATTTTATATA
* *
407453 TTTTTTATTTTATG-TTTTTTGCCC
1 TTTTTTATCTAATGTTTTTTTG-CC
407477 TTTTTTATCTAATGTTTTTTTTGCC
1 TTTTTTATCTAATG-TTTTTTTGCC
407502 TTTTT
1 TTTTT
407507 CAGTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 12 0.46
25 7 0.27
26 7 0.27
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTTTTATCTAATGTTTTTTTGCC
Found at i:419759 original size:31 final size:31
Alignment explanation
Indices: 419721--419786 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
419711 TCGAGGGTTT
**
419721 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAACGA-ACATATGGACAGTA
* *
419752 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAACGAACATATGGACAGTA
419783 TACC
1 TACC
419787 GAGGATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGACAGTA
Found at i:419819 original size:30 final size:30
Alignment explanation
Indices: 419774--419927 Score: 247
Period size: 30 Copynumber: 5.1 Consensus size: 30
419764 AAGGAACATA
419774 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
419805 TGGACAGCTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
419835 TGGACAGCTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
419865 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
419895 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
419924 TGGA
1 TGGA
419928 TAGGTCCTTC
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 18 0.15
30 93 0.79
31 7 0.06
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:423993 original size:31 final size:31
Alignment explanation
Indices: 423955--424020 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
423945 TCGAGGGTTT
**
423955 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAACGA-ACATATGGACAGTA
* *
423986 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAACGAACATATGGACAGTA
424017 TACC
1 TACC
424021 GAGGATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGACAGTA
Found at i:424053 original size:30 final size:30
Alignment explanation
Indices: 424008--424161 Score: 238
Period size: 30 Copynumber: 5.1 Consensus size: 30
423998 AAGGAACATA
424008 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
424039 TGGACAGCTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
**
424069 TGGACAACTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
424099 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
424129 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
424158 TGGA
1 TGGA
424162 TAGGTCCTTC
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
29 18 0.16
30 91 0.78
31 7 0.06
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:428202 original size:31 final size:31
Alignment explanation
Indices: 428164--428229 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
428154 TCGAGGGTTT
**
428164 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAACGA-ACATATGGACAGTA
* *
428195 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAACGAACATATGGACAGTA
428226 TACC
1 TACC
428230 GAGGATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGACAGTA
Found at i:428372 original size:29 final size:30
Alignment explanation
Indices: 428217--428369 Score: 238
Period size: 30 Copynumber: 5.1 Consensus size: 30
428207 AAGGAACATA
428217 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
428248 TGGACAGCTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
428278 TGGACAGCTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
428308 TGGACAGTTA-CGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
428337 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
428366 TGGA
1 TGGA
428370 TAGGTCCTTC
Statistics
Matches: 116, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
29 46 0.40
30 63 0.54
31 7 0.06
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:428645 original size:2 final size:2
Alignment explanation
Indices: 428633--428728 Score: 169
Period size: 2 Copynumber: 49.0 Consensus size: 2
428623 ATGTATGTGG
*
428633 AT AT GT AT AT AT AT A- 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
428674 AT AT AT AT AT -T 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
428715 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
428729 GAAAGGTGCA
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 88 0.98
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:429686 original size:25 final size:25
Alignment explanation
Indices: 429639--429686 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
429629 TTGGTGCAAA
*
429639 GGGAACCGATCCCCCCATGAGGGAG
1 GGGAACCGATCCCCCCATCAGGGAG
429664 GGGAACCGATTCCCCCCA-CAGGG
1 GGGAACCGA-TCCCCCCATCAGGG
429687 GAATCGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.23, C:0.35, G:0.33, T:0.08
Consensus pattern (25 bp):
GGGAACCGATCCCCCCATCAGGGAG
Found at i:429688 original size:21 final size:21
Alignment explanation
Indices: 429662--429701 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
429652 CCCATGAGGG
*
429662 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
429683 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
429702 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:430857 original size:155 final size:151
Alignment explanation
Indices: 430600--430906 Score: 578
Period size: 155 Copynumber: 2.0 Consensus size: 151
430590 ACTTGAACCC
430600 GTTGCTATCATCAACTTGTTCGTATCTACTGTAATGCCGTTTGTATCAAAAATCGTGACAAAACA
1 GTTGCTATCATCAACTTGTTCGTATCTACTGTAATGCCGTTTGTATCAAAAATCGTGACAAAACA
430665 AAACCATAGGAGTACGTTCCTACCTCCTAGGTCAATATTTCCATCTTGATCCGGATTACATAGCC
66 AAACCATAGGAGTACGTTCCTACCTCCTAGGTCAATATTTCCATCTTGATCCGGATTACATAGCC
430730 AATGCCTTAGGCTTGGATAAT
131 AATGCCTTAGGCTTGGATAAT
430751 GTTGCTATCATCAACTTGTTCGTATCTTCTACTGTAATGCCGTTTGTATCAAAAATCGTGACAAA
1 GTTGCTATCATCAACTTGTTCGTA---TCTACTGTAATGCCGTTTGTATCAAAAATCGTGACAAA
430816 ACCAAAACCATAGGAGTACGTTCCTACCTCCTAGGTCAATATTTCCATCTTGATCCGGATTACAT
63 A-CAAAACCATAGGAGTACGTTCCTACCTCCTAGGTCAATATTTCCATCTTGATCCGGATTACAT
430881 AGCCAATGCCTTAGGCTTGGATAAT
127 AGCCAATGCCTTAGGCTTGGATAAT
430906 G
1 G
430907 AAGGTTTATC
Statistics
Matches: 152, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
151 24 0.16
154 39 0.26
155 89 0.59
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (151 bp):
GTTGCTATCATCAACTTGTTCGTATCTACTGTAATGCCGTTTGTATCAAAAATCGTGACAAAACA
AAACCATAGGAGTACGTTCCTACCTCCTAGGTCAATATTTCCATCTTGATCCGGATTACATAGCC
AATGCCTTAGGCTTGGATAAT
Found at i:440368 original size:15 final size:16
Alignment explanation
Indices: 440350--440389 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
440340 TATATATATT
440350 GAAAATATAA-TTTTC
1 GAAAATATAATTTTTC
440365 GAAAATATAATTTTTC
1 GAAAATATAATTTTTC
*
440381 AAAAATATA
1 GAAAATATA
440390 TATGGTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (16 bp):
GAAAATATAATTTTTC
Found at i:449490 original size:24 final size:24
Alignment explanation
Indices: 449458--449576 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
449448 TTCGATTTGA
*
449458 ATTCTGATCTGACACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
449482 ATTCTGATCTGATA-TCTGAAATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
449506 ATTTTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
449530 ATTCTGATCTGATACTTGACCTAG
1 ATTCTGATCTGATACTTGACATGG
* *
449554 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
449577 AATTATGTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:452287 original size:32 final size:32
Alignment explanation
Indices: 452246--452309 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
452236 GAGAGGAGTC
452246 AGCCCATCACTCATACCATCCCACACTCTAAG
1 AGCCCATCACTCATACCATCCCACACTCTAAG
*
452278 AGCCCATCACTCCTACCATCCCACACTCTAAG
1 AGCCCATCACTCATACCATCCCACACTCTAAG
452310 TGAAAAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.45, G:0.06, T:0.19
Consensus pattern (32 bp):
AGCCCATCACTCATACCATCCCACACTCTAAG
Found at i:452304 original size:16 final size:17
Alignment explanation
Indices: 452248--452305 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 17
452238 GAGGAGTCAG
*
452248 CCCATCACTCATACCAT
1 CCCATCACTCCTACCAT
** *
452265 CCCA-CACT-CTAAGAG
1 CCCATCACTCCTACCAT
452280 CCCATCACTCCTACCAT
1 CCCATCACTCCTACCAT
452297 CCCA-CACTC
1 CCCATCACTC
452306 TAAGTGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 7 0.22
16 13 0.41
17 12 0.38
ACGTcount: A:0.28, C:0.50, G:0.03, T:0.19
Consensus pattern (17 bp):
CCCATCACTCCTACCAT
Found at i:465613 original size:2 final size:2
Alignment explanation
Indices: 465606--465630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
465596 ATTCTAGCTT
465606 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
465631 TTGTTCAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:471306 original size:39 final size:39
Alignment explanation
Indices: 471236--471349 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 39
471226 CTTGTCTCGA
* **
471236 AAAATTATATTAGATTTTTTTTTATCAAAACTAACAAATTT
1 AAAATTATATT--ATATTTTTTTATTGAAACTAACAAATTT
471277 AAAATTATATTATATTTTTTTATTGAAACTAACAAATTT
1 AAAATTATATTATATTTTTTTATTGAAACTAACAAATTT
** * *
471316 GCAATTATATTTTA-TATTTTATTGAAACTAACAA
1 AAAATTATATTATATTTTTTTATTGAAACTAACAA
471350 TTTTGCAACA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 19 0.29
39 36 0.55
41 11 0.17
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (39 bp):
AAAATTATATTATATTTTTTTATTGAAACTAACAAATTT
Found at i:471345 original size:38 final size:39
Alignment explanation
Indices: 471263--471357 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 39
471253 TTTTTTATCA
** *
471263 AAACTAACAAATTTAAAATTATATTATATTTTTTTATTG
1 AAACTAACAAATTTGCAATTATATTATATTATTTTATTG
*
471302 AAACTAACAAATTTGCAATTATATTTTA-TATTTTATTG
1 AAACTAACAAATTTGCAATTATATTATATTATTTTATTG
*
471340 AAACTAACAATTTTGCAA
1 AAACTAACAAATTTGCAA
471358 CAAAAATCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 26 0.51
39 25 0.49
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (39 bp):
AAACTAACAAATTTGCAATTATATTATATTATTTTATTG
Found at i:472319 original size:30 final size:28
Alignment explanation
Indices: 472285--472344 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
472275 CATTTTGAGT
* *
472285 AACGAAATGAAACGTTAGGCACTAAACTGG
1 AACGAAA--AAACATTAGACACTAAACTGG
*
472315 AACGAAAAAATATTAGACACTAAACTGG
1 AACGAAAAAACATTAGACACTAAACTGG
472343 AA
1 AA
472345 AAACGAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 20 0.74
30 7 0.26
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (28 bp):
AACGAAAAAACATTAGACACTAAACTGG
Found at i:475846 original size:19 final size:20
Alignment explanation
Indices: 475803--475846 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
475793 TAGTTCTTAT
475803 GTTTTCTCCATTATTATTCA
1 GTTTTCTCCATTATTATTCA
* * *
475823 CTTTTCTGCTTTATT-TTCA
1 GTTTTCTCCATTATTATTCA
475842 GTTTT
1 GTTTT
475847 GAAAAGGGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.14, C:0.18, G:0.07, T:0.61
Consensus pattern (20 bp):
GTTTTCTCCATTATTATTCA
Found at i:486525 original size:19 final size:19
Alignment explanation
Indices: 486495--486542 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
486485 GTAAAAAGAT
*
486495 ATTAAAAT-AATAAAAGCG
1 ATTAAAATAAATAAAAGCA
486513 ATTAAAATAAATAAAAGCA
1 ATTAAAATAAATAAAAGCA
*
486532 ATTAAAGTAAA
1 ATTAAAATAAA
486543 AATAAGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.23
Consensus pattern (19 bp):
ATTAAAATAAATAAAAGCA
Found at i:488014 original size:21 final size:21
Alignment explanation
Indices: 487967--488014 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
487957 AATGCATTTG
*
487967 ATTTTTTTTCTTTTTTTTCAC
1 ATTTTTGTTCTTTTTTTTCAC
* *
487988 ACTTTTGTTGTTTTATTTTC-C
1 ATTTTTGTTCTTTT-TTTTCAC
488009 ATTTTT
1 ATTTTT
488015 TCATGTCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.73
Consensus pattern (21 bp):
ATTTTTGTTCTTTTTTTTCAC
Found at i:494655 original size:18 final size:19
Alignment explanation
Indices: 494634--494680 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
494624 GTAAAAAGAT
*
494634 ATTAAAAT-AATAAAAGCG
1 ATTAAAATAAATAAAAGCA
494652 ATT-AAATAAATAAAAGCA
1 ATTAAAATAAATAAAAGCA
*
494670 ATTAAAGTAAA
1 ATTAAAATAAA
494681 AATAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (19 bp):
ATTAAAATAAATAAAAGCA
Found at i:496771 original size:26 final size:26
Alignment explanation
Indices: 496735--496791 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
496725 AAACAATCTT
*
496735 TTTTTCAAACTATTTTTTTCTTTTTC
1 TTTTTCAAACTATTTTTTCCTTTTTC
* *
496761 TTTTTCTAACTATTTTTTCCTTTTTT
1 TTTTTCAAACTATTTTTTCCTTTTTC
496787 TTTTT
1 TTTTT
496792 ATTTTTCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTTCAAACTATTTTTTCCTTTTTC
Found at i:497800 original size:22 final size:22
Alignment explanation
Indices: 497772--497816 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
497762 ATTGTTCATG
*
497772 TGGTATCGATACTGTAAGAACA
1 TGGTATCGATACTATAAGAACA
497794 TGGTATCGATACTATAAGAACA
1 TGGTATCGATACTATAAGAACA
497816 T
1 T
497817 TATTGGTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (22 bp):
TGGTATCGATACTATAAGAACA
Found at i:500669 original size:14 final size:13
Alignment explanation
Indices: 500635--500668 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
500625 AGCATTGTGA
*
500635 AAAGAAAATAATG
1 AAAGAAAATAAAG
500648 AAAGAAAATAAAG
1 AAAGAAAATAAAG
500661 AAAGAAAA
1 AAAGAAAA
500669 ATGAAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:502291 original size:19 final size:20
Alignment explanation
Indices: 502263--502307 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
502253 CATTAATTTT
*
502263 TTAAAATTAT-AAATTATTA
1 TTAAATTTATCAAATTATTA
*
502282 TTAAATTTATCATATTATTA
1 TTAAATTTATCAAATTATTA
*
502302 TAAAAT
1 TTAAAT
502308 AATTACTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATTTATCAAATTATTA
Found at i:503419 original size:41 final size:41
Alignment explanation
Indices: 503326--503493 Score: 157
Period size: 40 Copynumber: 4.1 Consensus size: 41
503316 GTGATCAAAG
* * * **
503326 AGTGCAAGATTATTGCAGC-TTTTATCAAAAATGCTGCT-A
1 AGTGCATGATTATTGCGGCGTTTTATCAAAAACGCCACTAA
* *
503365 GGTGCATGATTATTGCGGCGTTTTATCAAAAACGTCACTAA
1 AGTGCATGATTATTGCGGCGTTTTATCAAAAACGCCACTAA
* *
503406 AGTGCATAATTATTGCGGCG-TTTAT-AAAAACCGCCGCTAA
1 AGTGCATGATTATTGCGGCGTTTTATCAAAAA-CGCCACTAA
* * *
503446 GGTGCATGACTATTGCGGC-TTTTATTGCAAAAACGCCAGTAA
1 AGTGCATGATTATTGCGGCGTTTTA-T-CAAAAACGCCACTAA
*
503488 AATGCA
1 AGTGCA
503494 ACGCCACTAA
Statistics
Matches: 104, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
39 21 0.20
40 47 0.45
41 20 0.19
42 11 0.11
43 5 0.05
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (41 bp):
AGTGCATGATTATTGCGGCGTTTTATCAAAAACGCCACTAA
Found at i:503469 original size:80 final size:82
Alignment explanation
Indices: 503326--503494 Score: 204
Period size: 80 Copynumber: 2.1 Consensus size: 82
503316 GTGATCAAAG
* * * *
503326 AGTGCAAGATTATTGCAGCTTTTATCAAAAATGCTGCTAGGTGCATGATTATTGCGGCGTTTTA-
1 AGTGCAAGATTATTGCAGCGTTTATCAAAAACGCCGCTAGGTGCATGACTATTGCGGCGTTTTAT
503390 T-CAAAAACGTCACTAA
66 TGCAAAAACGTCACTAA
*
503406 AGTGCATA-ATTATTGCGGCGTTTAT-AAAAACCGCCGCTAAGGTGCATGACTATTGCGGC-TTT
1 AGTGCA-AGATTATTGCAGCGTTTATCAAAAA-CGCCGCT-AGGTGCATGACTATTGCGGCGTTT
* *
503468 TATTGCAAAAACGCCAGTAA
63 TATTGCAAAAACGTCACTAA
*
503488 AATGCAA
1 AGTGCAA
503495 CGCCACTAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
79 5 0.07
80 31 0.41
81 22 0.29
82 18 0.24
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (82 bp):
AGTGCAAGATTATTGCAGCGTTTATCAAAAACGCCGCTAGGTGCATGACTATTGCGGCGTTTTAT
TGCAAAAACGTCACTAA
Found at i:503582 original size:42 final size:41
Alignment explanation
Indices: 503535--503627 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
503525 TTTTATAAAC
** * * * *
503535 GCCGCTACTGTAAATTACTATTGCGGTCTTTATTACAAAAAT
1 GCCGCTAAGGTAAATGACTATTGC-GACGTTACTACAAAAAT
* *
503577 GCCGCTAAGGTACATGACTGTTGCGACGTTACTACAAAAAT
1 GCCGCTAAGGTAAATGACTATTGCGACGTTACTACAAAAAT
503618 GCCGCTAAGG
1 GCCGCTAAGG
503628 CTTTTTGTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 24 0.56
42 19 0.44
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (41 bp):
GCCGCTAAGGTAAATGACTATTGCGACGTTACTACAAAAAT
Found at i:509519 original size:21 final size:21
Alignment explanation
Indices: 509494--509541 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
509484 TTATCTTTGT
509494 AGAAGATAAACTACAAAGAAA
1 AGAAGATAAACTACAAAGAAA
*
509515 AGAAGATAAACTATAAAGAAA
1 AGAAGATAAACTACAAAGAAA
509536 AGAAGA
1 AGAAGA
509542 CGATGATAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.67, C:0.06, G:0.17, T:0.10
Consensus pattern (21 bp):
AGAAGATAAACTACAAAGAAA
Done.