Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008312.1 Hibiscus syriacus cultivar Beakdansim tig00111005_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: 1258310
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:396435 original size:183 final size:183
Alignment explanation
Indices: 395722--396893 Score: 2145
Period size: 183 Copynumber: 6.4 Consensus size: 183
395712 CTTTCAACAT
** * * * * * *
395722 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
395787 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
395852 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTT--ACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
395903 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATGCCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
395968 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
396033 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
396086 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTAT-AA-ATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
396149 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
396214 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
396267 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
396332 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
396397 AATGTGTCGATACGATTTAAAAAAGGGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
396450 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
*
396515 GGTCTACAACCTATATCGACACTTTTTAATAATGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
396580 AATGTGTCGATACGATTCAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
396633 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
*
396698 GGTCTAAAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
396763 AATGTGTCGAAACGATTTAAAAAAGTGTCGACATTTACATATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
396816 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
*
396881 TGTCTACAACCTA
66 GGTCTACAACCTA
396894 AAATGTGTCG
Statistics
Matches: 963, Mismatches: 24, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
181 335 0.35
182 4 0.00
183 624 0.65
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACAGGTATAAATATACCGGTTGTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:399434 original size:28 final size:23
Alignment explanation
Indices: 399378--399431 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
399368 TAACTACAAG
*
399378 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTAGCGTT
*
399401 TATATAATGTAATAGGTAGCGCT
1 TATATAATGTAATAGGTAGCGTT
399424 TATATAAT
1 TATATAAT
399432 ATATTGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGCGTT
Found at i:399884 original size:18 final size:18
Alignment explanation
Indices: 399863--399899 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
399853 GTAATTGGAG
399863 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
399881 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
399899 T
1 T
399900 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:399907 original size:24 final size:24
Alignment explanation
Indices: 399855--399901 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
399845 TTTCATATGT
* *
399855 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
399879 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
399902 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:400199 original size:39 final size:39
Alignment explanation
Indices: 400156--400242 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
400146 TCCGATGCTC
*
400156 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
400195 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
400234 ATCAAAATC
1 ATCAAAATC
400243 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:400694 original size:23 final size:23
Alignment explanation
Indices: 400663--400735 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
400653 ATAGGTAAAA
*
400663 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
400686 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
400709 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
400732 ATAT
1 ATAT
400736 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:401125 original size:23 final size:23
Alignment explanation
Indices: 401094--401166 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
401084 ATAGGTAAAA
*
401094 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
401117 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
401140 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
401163 ATAT
1 ATAT
401167 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:401255 original size:431 final size:432
Alignment explanation
Indices: 400452--401515 Score: 2028
Period size: 431 Copynumber: 2.5 Consensus size: 432
400442 TTATCTTTGG
400452 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
*
400517 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTT
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
*
400582 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAGGTATGGACACTTTC
131 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
400647 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
196 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
400712 TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCCATCCTTTTTATAAAAGTGTCCATACTTTT
261 TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCCATCCTTTTTATAAAAGTGTCCATACTTTT
400777 TTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAA
326 TTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAA
400842 TTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATAT-
391 TTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
400883 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
400948 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
401013 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
131 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
401078 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
196 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
*
401143 TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTT
261 TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCCATCCTTTTTATAAAAGTGTCCATACTTTT
*
401208 TTCACTGTTGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAA
326 TTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAA
401273 TTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
391 TTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
* *
401315 TT-A--TTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTT
1 TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
*
401377 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTCAAAAAATT
66 TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
*
401442 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTC
131 GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
401507 AATATAATA
196 AATATAATA
401516 TAATGTAATA
Statistics
Matches: 624, Mismatches: 8, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
429 194 0.31
431 428 0.69
432 2 0.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (432 bp):
TTAATGTTGTTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTT
TTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
GAAACATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTC
AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATA
TAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCCATCCTTTTTATAAAAGTGTCCATACTTTT
TTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATTTTAATTTAGTAA
TTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATA
Found at i:403115 original size:32 final size:33
Alignment explanation
Indices: 403074--403166 Score: 116
Period size: 32 Copynumber: 2.8 Consensus size: 33
403064 GGGTCGAGTT
*
403074 TTTTTTAAGTTTAATATTCGGGTCGGGTC-GGG
1 TTTTTTAAGTGTAATATTCGGGTCGGGTCAGGG
* * *
403106 TTTTTTAAGTGTAATATTCGGGTAGGATCAGGT
1 TTTTTTAAGTGTAATATTCGGGTCGGGTCAGGG
* * *
403139 TTTTTTAAATGTAACATTCAGGTCGGGT
1 TTTTTTAAGTGTAATATTCGGGTCGGGT
403167 TTAGGGTGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
32 26 0.51
33 25 0.49
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.43
Consensus pattern (33 bp):
TTTTTTAAGTGTAATATTCGGGTCGGGTCAGGG
Found at i:403630 original size:258 final size:260
Alignment explanation
Indices: 403165--403644 Score: 732
Period size: 260 Copynumber: 1.9 Consensus size: 260
403155 TTCAGGTCGG
*** * *
403165 GTTTAGGGTGAAAAATACCCGACCCAACATGGAAAAAAAATAATTGTACCTTATATATTTATGAA
1 GTTTAGGGTGAAAAATACCCGACCCAACACCCAAAAAAAATAATTGTACATTATATATTTAGGAA
* * * *
403230 TAATTATAATAATACACTTCTATATATAATTTTTTTTAATTAAATCACTGTTTTTATTGAATAAA
66 TAATTACAATAATACACCTCTATATATAATTTTTTTCAATTAAATCACTATTTTTATTGAATAAA
* * *
403295 AATAATTTTTATTATTATTTAGGGTCGGGTCGAGTTTTTAATTCATATATTCGGGTCGGGTTGGG
131 AATAATTTTTATTATTATTTAGGGTCGGGTCGAGTTTCTAATTCATATATTCGGGTCAGGTCGGG
*
403360 TAAAATTTTATTTTGGTCGGGTCGGGTTGGGTTTTTTTTAAGTGTGATATTCAGGTCGAGTTCGA
196 TAAAACTTTATTTTGGTCGGGTCGGGTTGGGTTTTTTTTAAGTGTGATATTCAGGTCGAGTTCGA
* * *
403425 GTTTAGGGTGAAAAATACTCGACCCGAC-CCCAAAAAAATATAATTTTACATTATATATTTAGGA
1 GTTTAGGGTGAAAAATACCCGACCCAACACCCAAAAAAA-ATAATTGTACATTATATATTTAGGA
* *
403489 ATAATTACAATATTACACCTCTATATATAA-TTTTTTCAATTAAGTCACTATTTTTATTGAATAA
65 ATAATTACAATAATACACCTCTATATATAATTTTTTTCAATTAAATCACTATTTTTATTGAATAA
* *
403553 AAATAATTTTT-TTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCAGGTCGG
130 AAATAATTTTTATTATTATTTAGGGTCGGGTCGAGTTTCTAATTCATATATTCGGGTCAGGTCGG
* *
403617 GTGAAACTTTATTTTGGTCGGTTCGGGT
195 GTAAAACTTTATTTTGGTCGGGTCGGGT
403645 CGAGTCTCGG
Statistics
Matches: 197, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
258 73 0.37
259 49 0.25
260 75 0.38
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (260 bp):
GTTTAGGGTGAAAAATACCCGACCCAACACCCAAAAAAAATAATTGTACATTATATATTTAGGAA
TAATTACAATAATACACCTCTATATATAATTTTTTTCAATTAAATCACTATTTTTATTGAATAAA
AATAATTTTTATTATTATTTAGGGTCGGGTCGAGTTTCTAATTCATATATTCGGGTCAGGTCGGG
TAAAACTTTATTTTGGTCGGGTCGGGTTGGGTTTTTTTTAAGTGTGATATTCAGGTCGAGTTCGA
Found at i:404023 original size:16 final size:16
Alignment explanation
Indices: 404002--404050 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
403992 ATGTTTCAGA
404002 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
404018 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
*
404034 TTAACAGATTCTAATTC
1 TT--CAGATTCCAATTC
404051 ACTCATTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.39
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:404736 original size:22 final size:22
Alignment explanation
Indices: 404710--404785 Score: 95
Period size: 21 Copynumber: 3.5 Consensus size: 22
404700 TTTATTTTAT
404710 TTTATTTTAATATAGGGTTAAC
1 TTTATTTTAATATAGGGTTAAC
* **
404732 TTTA-TTTAATTTA-AATTCAA-
1 TTTATTTTAATATAGGGTT-AAC
404752 TTTATTTTAATATAGGGTTAAC
1 TTTATTTTAATATAGGGTTAAC
404774 TTTATTTTAATA
1 TTTATTTTAATA
404786 AATTAAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 6 0.14
21 20 0.45
22 18 0.41
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (22 bp):
TTTATTTTAATATAGGGTTAAC
Found at i:405485 original size:15 final size:16
Alignment explanation
Indices: 405447--405487 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
405437 ACAGAGCCTC
*
405447 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
405463 TGAATCATTCAACGCT
1 TGAATCATTCAACACT
405479 T-AATCATTC
1 TGAATCATTC
405488 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:405680 original size:22 final size:22
Alignment explanation
Indices: 405632--405672 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
405622 ATTAAATGAA
405632 ATTATGAGTTTGTTTATTATTT
1 ATTATGAGTTTGTTTATTATTT
405654 ATTATGAGTTTG-TTATTAT
1 ATTATGAGTTTGTTTATTAT
405673 CTGTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (22 bp):
ATTATGAGTTTGTTTATTATTT
Found at i:405849 original size:13 final size:13
Alignment explanation
Indices: 405831--405859 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
405821 TCCCTTTAGA
405831 TTTTTATTTGTAT
1 TTTTTATTTGTAT
405844 TTTTTATTTGTAT
1 TTTTTATTTGTAT
405857 TTT
1 TTT
405860 CATATATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTATTTGTAT
Found at i:411464 original size:29 final size:29
Alignment explanation
Indices: 411419--411476 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
411409 GTGTTGGCCG
*
411419 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
411448 TAGGTCGCCATGTCTTCCCGGCGATCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
411477 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.26, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:411538 original size:14 final size:14
Alignment explanation
Indices: 411519--411565 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
411509 CGTTGGGCAT
411519 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
411533 CCGAGGTCATCCGA
1 CCGAGGCCATCCGA
*
411547 CTGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
411561 ACGAG
1 CCGAG
411566 CTATGCGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.23, C:0.36, G:0.30, T:0.11
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:411584 original size:33 final size:33
Alignment explanation
Indices: 411547--411609 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
411537 GGTCATCCGA
*
411547 CTGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CTGAGGCCAACCGAACGAGCTATGCGAGGGCAT
* *
411580 CTGAGGGCAACCGAGCGAGCTATGCGAGGG
1 CTGAGGCCAACCGAACGAGCTATGCGAGGG
411610 AATCCTATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.24, C:0.25, G:0.38, T:0.13
Consensus pattern (33 bp):
CTGAGGCCAACCGAACGAGCTATGCGAGGGCAT
Found at i:411619 original size:15 final size:15
Alignment explanation
Indices: 411599--411629 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
411589 ACCGAGCGAG
411599 CTATGCGAGGGAATC
1 CTATGCGAGGGAATC
411614 CTATGCGAGGGAATC
1 CTATGCGAGGGAATC
411629 C
1 C
411630 GCTACAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.19
Consensus pattern (15 bp):
CTATGCGAGGGAATC
Found at i:411703 original size:31 final size:33
Alignment explanation
Indices: 411665--411737 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
411655 GCGACCTACC
*
411665 CTCGCTCGGTTG-CC-CGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
411696 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
*
411729 CTCGGTCGG
1 CTCGCTCGG
411738 AGGGCCTCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 12 0.32
32 2 0.05
33 24 0.63
ACGTcount: A:0.08, C:0.38, G:0.29, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:411746 original size:33 final size:33
Alignment explanation
Indices: 411679--411750 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
411669 CTCGGTTGCC
* **
411679 CGGATTCCCTCGCATAGCTCGCTCGGTTGCCCT
1 CGGATGCCCTCGCATAGCTCGCTCGGAGGCCCT
* *
411712 CGGATGCCCTCGCATAGCTCGGTCGGAGGGCCT
1 CGGATGCCCTCGCATAGCTCGCTCGGAGGCCCT
411745 CGGATG
1 CGGATG
411751 TTCTCGGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.35, G:0.32, T:0.22
Consensus pattern (33 bp):
CGGATGCCCTCGCATAGCTCGCTCGGAGGCCCT
Found at i:411783 original size:14 final size:14
Alignment explanation
Indices: 411764--411791 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
411754 TCGGATGCTT
411764 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
411778 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
411792 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:411791 original size:24 final size:23
Alignment explanation
Indices: 411711--411794 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 23
411701 TCGGTTGCCC
* * *
411711 TCGGATGCCCTCGCATAGCTCGG
1 TCGGATGGCCTCGGATGGCTCGG
* *
411734 TCGGAGGGCCTCGGAT-GTTC--
1 TCGGATGGCCTCGGATGGCTCGG
*
411754 TCGGAT-GCTTTCGGATGGCCTCGG
1 TCGGATGGC-CTCGGATGG-CTCGG
411778 TCGGATGGCCTCGGATG
1 TCGGATGGCCTCGGATG
411795 CCCAGCGTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
19 2 0.04
20 11 0.23
21 1 0.02
22 5 0.11
23 13 0.28
24 13 0.28
25 2 0.04
ACGTcount: A:0.11, C:0.27, G:0.37, T:0.25
Consensus pattern (23 bp):
TCGGATGGCCTCGGATGGCTCGG
Found at i:416575 original size:35 final size:37
Alignment explanation
Indices: 416507--416576 Score: 92
Period size: 35 Copynumber: 1.9 Consensus size: 37
416497 GGAAAATATT
*
416507 TATATATTTTCTTTAAAAAAATTAAATTCATAAAATG
1 TATATATTTTCTTTAAAAAAATTAAAATCATAAAATG
*
416544 TATATATTTT-TTT-ATAAAATTAAAAAT-ATAAAA
1 TATATATTTTCTTTAAAAAAATT-AAAATCATAAAA
416577 AGGTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 13 0.43
36 7 0.23
37 10 0.33
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (37 bp):
TATATATTTTCTTTAAAAAAATTAAAATCATAAAATG
Found at i:416977 original size:30 final size:30
Alignment explanation
Indices: 416941--417000 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
416931 AAACACACCC
*
416941 TAAGAAGTGGTGAATGTACGTAGAATTAAG
1 TAAGAAGTGATGAATGTACGTAGAATTAAG
*
416971 TAAGAAGTGATGGATGTACGTAGAATTAAG
1 TAAGAAGTGATGAATGTACGTAGAATTAAG
417001 AGTGAGTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.27
Consensus pattern (30 bp):
TAAGAAGTGATGAATGTACGTAGAATTAAG
Found at i:417898 original size:21 final size:20
Alignment explanation
Indices: 417812--417968 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
417802 AAATGACCAA
**
417812 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
417831 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
417851 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
417871 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
417892 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
417912 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
417932 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
417953 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
417969 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:417921 original size:41 final size:41
Alignment explanation
Indices: 417812--417968 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
417802 AAATGACCAA
* **
417812 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
417851 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
417892 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
417933 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
417969 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:418028 original size:20 final size:20
Alignment explanation
Indices: 417935--418144 Score: 183
Period size: 20 Copynumber: 10.5 Consensus size: 20
417925 CGATTTTCCA
* ** *
417935 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
417955 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
417975 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
417995 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
418015 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTATCCGT
* *
418035 ATATCGCACCGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
418055 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
418075 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
418095 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
418115 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
418135 AAATCACAAC
1 AAATCGCAAC
418145 ACTGAAATTT
Statistics
Matches: 154, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 150 0.97
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:418866 original size:24 final size:24
Alignment explanation
Indices: 418827--418873 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
418817 AAATTTGGTC
418827 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
418851 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
418874 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:419065 original size:12 final size:12
Alignment explanation
Indices: 419048--419072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
419038 ATATAATCCT
419048 GAAGAAGAAAAA
1 GAAGAAGAAAAA
419060 GAAGAAGAAAAA
1 GAAGAAGAAAAA
419072 G
1 G
419073 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:424401 original size:12 final size:12
Alignment explanation
Indices: 424368--424420 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
424358 TAAGATTTAA
* *
424368 TTTATTTTTCTT
1 TTTAGTTTTATT
424380 TTTAAGTTTTCATT
1 TTT-AGTTTT-ATT
424394 TTTA-TTTTATT
1 TTTAGTTTTATT
*
424405 TTAAGTTTTATT
1 TTTAGTTTTATT
424417 TTTA
1 TTTA
424421 AACATGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 6 0.18
12 17 0.50
13 6 0.18
14 5 0.15
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTAGTTTTATT
Found at i:424421 original size:13 final size:13
Alignment explanation
Indices: 424373--424421 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
424363 TTTAATTTAT
*
424373 TTTTCTTTTTAAG
1 TTTTATTTTTAAG
424386 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
424398 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
424410 TTTTATTTTTAA
1 TTTTATTTTTAA
424422 ACATGTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 4 0.13
11 2 0.06
12 9 0.29
13 11 0.35
14 5 0.16
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:430437 original size:12 final size:13
Alignment explanation
Indices: 430406--430439 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
430396 AAATTAGATG
*
430406 CACTTAATTAAAT
1 CACTTAAATAAAT
430419 CACTTAAATAAAT
1 CACTTAAATAAAT
430432 -ACTTAAAT
1 CACTTAAAT
430440 TACATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (13 bp):
CACTTAAATAAAT
Found at i:445772 original size:59 final size:59
Alignment explanation
Indices: 445669--445787 Score: 175
Period size: 59 Copynumber: 2.0 Consensus size: 59
445659 CATGTCAAAA
* *
445669 TGACGAGTTCTATTAAAAATATACTTTAATGGACGTAGACGTTGGTTCTAATAATTTAT
1 TGACGAGTTCCATTAAAAATATACTTTAATGGACGTAGACGTTGGGTCTAATAATTTAT
* * * * *
445728 TGACGAGTTCCATTAAAAATATATTTTAATGGATGTTGATGTTGGGTCTAATATTTTAT
1 TGACGAGTTCCATTAAAAATATACTTTAATGGACGTAGACGTTGGGTCTAATAATTTAT
445787 T
1 T
445788 ATATTTCATG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (59 bp):
TGACGAGTTCCATTAAAAATATACTTTAATGGACGTAGACGTTGGGTCTAATAATTTAT
Found at i:445997 original size:31 final size:28
Alignment explanation
Indices: 445959--446037 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 28
445949 ACATTTGAAG
445959 CATTAACTCATACATTACATTATATCAGAAA
1 CATTAACTCATACATTACATTATAT---AAA
445990 CATTAACTCATACATTACA-T-TATAAA
1 CATTAACTCATACATTACATTATATAAA
*
446016 CATTAACTCCTACATTACATTA
1 CATTAACTCATACATTACATTA
446038 CATTACAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
26 21 0.47
27 1 0.02
29 3 0.07
30 1 0.02
31 19 0.42
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (28 bp):
CATTAACTCATACATTACATTATATAAA
Found at i:446011 original size:17 final size:17
Alignment explanation
Indices: 445959--446011 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
445949 ACATTTGAAG
445959 CATTAACTCATACATTA
1 CATTAACTCATACATTA
*
445976 CATTATA-TCAGA-A--A
1 CATTA-ACTCATACATTA
445990 CATTAACTCATACATTA
1 CATTAACTCATACATTA
446007 CATTA
1 CATTA
446012 TAAACATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 1 0.03
14 10 0.34
15 1 0.03
16 1 0.03
17 15 0.52
18 1 0.03
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (17 bp):
CATTAACTCATACATTA
Found at i:446038 original size:31 final size:31
Alignment explanation
Indices: 445947--446042 Score: 103
Period size: 31 Copynumber: 3.3 Consensus size: 31
445937 TACTTAATGT
* * *
445947 TTACATTTGAAGCATTAACTCATACATTACA
1 TTACATTAGAAACATTAACTCCTACATTACA
* *
445978 TTATATCAGAAACATTAA---CT-CA-TACA
1 TTACATTAGAAACATTAACTCCTACATTACA
*
446004 TTACATTATAAACATTAACTCCTACATTACA
1 TTACATTAGAAACATTAACTCCTACATTACA
446035 TTACATTA
1 TTACATTA
446043 CAATACAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
26 19 0.37
27 2 0.04
28 1 0.02
29 2 0.04
30 2 0.04
31 26 0.50
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (31 bp):
TTACATTAGAAACATTAACTCCTACATTACA
Found at i:452837 original size:2 final size:2
Alignment explanation
Indices: 452793--452818 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
452783 TATTGAAGAA
452793 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
452819 GGCGATTTTT
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:453083 original size:47 final size:48
Alignment explanation
Indices: 453008--453128 Score: 147
Period size: 51 Copynumber: 2.5 Consensus size: 48
452998 CACGTAGGGG
* *
453008 TATAGCGCGGATCAGGTACCACGCTATACCTTTA-CTG-CATAATTTTA
1 TATAGCGCGGA-CAGGTACCGCGATATACCTTTACCTGACATAATTTTA
*
453055 TATAGCGCGTGACAGGTACCGCGATATACTTTTACTCCTGACATAATTTTA
1 TATAGCGCG-GACAGGTACCGCGATATACCTTTA--CCTGACATAATTTTA
*
453106 TATAGCGCGGGGCAGGTACCGCG
1 TATAGCGC-GGACAGGTACCGCG
453129 TTTTGTATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
47 28 0.44
48 2 0.03
50 3 0.05
51 30 0.47
52 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
TATAGCGCGGACAGGTACCGCGATATACCTTTACCTGACATAATTTTA
Found at i:454629 original size:41 final size:40
Alignment explanation
Indices: 454572--454656 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 40
454562 AATGGTATTC
454572 AAATTGAATGAAATTTGTTTAAATTCAAATTGAATGAAAA
1 AAATTGAATGAAATTTGTTTAAATTCAAATTGAATGAAAA
*
454612 GAAATTGAATGAAATTTGTTTAAATTCAAGTTGAATGAAAA
1 -AAATTGAATGAAATTTGTTTAAATTCAAATTGAATGAAAA
454653 AAAT
1 AAAT
454657 CAATTTCGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.09
41 39 0.91
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.34
Consensus pattern (40 bp):
AAATTGAATGAAATTTGTTTAAATTCAAATTGAATGAAAA
Found at i:458468 original size:31 final size:30
Alignment explanation
Indices: 458395--458468 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
458385 TTGATCATTG
*
458395 AATTTTCAAA-AATTATAAAATAATCATAA
1 AATTTTCAAATTATTATAAAATAATCATAA
* *
458424 AATTTATCGAATTATTATAAAATAATTATTAA
1 AATTT-TCAAATTATTATAAAATAATCA-TAA
*
458456 AGTTTTCAAATTA
1 AATTTTCAAATTA
458469 GTAAATAGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.14
30 4 0.11
31 21 0.57
32 7 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (30 bp):
AATTTTCAAATTATTATAAAATAATCATAA
Found at i:459477 original size:3 final size:3
Alignment explanation
Indices: 459469--459495 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
459459 CCAAAACCAG
459469 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
459496 GAAGATGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:463403 original size:35 final size:36
Alignment explanation
Indices: 463340--463411 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 36
463330 AATTATTAAG
* *
463340 TATGAATGTTTGTATTTTGTTTGTCCCCATATGAAC
1 TATGAATGCTTGTATTTTGTTTGCCCCCATATGAAC
463376 TATGAATGCTTGTA-TTTGTTTGCCCCCATATGAAC
1 TATGAATGCTTGTATTTTGTTTGCCCCCATATGAAC
463411 T
1 T
463412 GCCCTTGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 21 0.62
36 13 0.38
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (36 bp):
TATGAATGCTTGTATTTTGTTTGCCCCCATATGAAC
Found at i:467598 original size:59 final size:60
Alignment explanation
Indices: 467522--467636 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 60
467512 TGGTCCCGAC
*
467522 TATAGAGTATTGATTTATTAAGTCTATCGACTATTAA-AAGTTATAAAATA-TCATTTGAT
1 TATAGAGTATTGATTTATTAAGTCCATCGACTA-TAATAAGTTATAAAATAGTCATTTGAT
* *
467581 TATAGGGTATT-ACTTTATTGAGTCCATCGACTATAATAAGTTATAAAATAGTCATT
1 TATAGAGTATTGA-TTTATTAAGTCCATCGACTATAATAAGTTATAAAATAGTCATT
467637 AGACTATTCG
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 4 0.08
59 41 0.82
60 5 0.10
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (60 bp):
TATAGAGTATTGATTTATTAAGTCCATCGACTATAATAAGTTATAAAATAGTCATTTGAT
Found at i:468155 original size:29 final size:29
Alignment explanation
Indices: 468112--468171 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
468102 TCCCAAACTA
468112 ACAATATTGTATGTTTGTATAATTGGTAG
1 ACAATATTGTATGTTTGTATAATTGGTAG
*
468141 ACAATATTGTTTGTTTGTATAATTGGTAG
1 ACAATATTGTATGTTTGTATAATTGGTAG
468170 AC
1 AC
468172 CAAACTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (29 bp):
ACAATATTGTATGTTTGTATAATTGGTAG
Found at i:468343 original size:59 final size:60
Alignment explanation
Indices: 468265--468381 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 60
468255 ATTGGAAGAC
* *
468265 TCAAAAGTTTGGAGACTAATTTAGAA-TGAGGGTCACAGTTT-GGGGTGAAATTAGAATGT
1 TCAAAAGTTTAGAGACTAATTTAGAAGT-AGAGTCACAGTTTAGGGGTGAAATTAGAATGT
* * *
468324 TCAAAAGTTTA-AGGACTAATTTATAAGTAGATTCATAGTTTAGGGGTGAAATTAGAAT
1 TCAAAAGTTTAGA-GACTAATTTAGAAGTAGAGTCACAGTTTAGGGGTGAAATTAGAAT
468382 ATTTGAAGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
58 1 0.02
59 32 0.64
60 17 0.34
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (60 bp):
TCAAAAGTTTAGAGACTAATTTAGAAGTAGAGTCACAGTTTAGGGGTGAAATTAGAATGT
Found at i:473637 original size:39 final size:38
Alignment explanation
Indices: 473567--473651 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 38
473557 GTACTTCTAG
** *
473567 GGTCTTCTTCATTTGCCTGAAGACGTTATGCAGTCGTGA
1 GGTCTTCTTCATTTGCCTGAAGACGCCATGCAATCGT-A
* *
473606 GGTCTTTTTCATTTGTCTGAAGACGCCATGCAATCGTA
1 GGTCTTCTTCATTTGCCTGAAGACGCCATGCAATCGTA
473644 GAGTCTTC
1 G-GTCTTC
473652 ATATTTGGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 2 0.05
39 37 0.95
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (38 bp):
GGTCTTCTTCATTTGCCTGAAGACGCCATGCAATCGTA
Found at i:475263 original size:35 final size:35
Alignment explanation
Indices: 475202--475269 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
475192 ACATTTATGA
* *
475202 GGTATCGATACTTGAAGAACAGTATCGATACCAAG
1 GGTACCGATACTTGAAGAACAATATCGATACCAAG
*
475237 GGTACCGATACCTT-AAGGACAATATCGATACCA
1 GGTACCGATA-CTTGAAGAACAATATCGATACCA
475270 TCTTTGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 26 0.90
36 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (35 bp):
GGTACCGATACTTGAAGAACAATATCGATACCAAG
Found at i:476690 original size:22 final size:21
Alignment explanation
Indices: 476659--476699 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
476649 ATTGTAATAG
*
476659 GGGAACCGATTCCCCTGCTATA
1 GGGAACCGA-TACCCTGCTATA
*
476681 GGGAATCGATACCCTGCTA
1 GGGAACCGATACCCTGCTA
476700 CAGTGCTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTATA
Found at i:481489 original size:19 final size:19
Alignment explanation
Indices: 481465--481512 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
481455 ATAACTACAT
481465 CAGAAATGGAGCTTAAATG
1 CAGAAATGGAGCTTAAATG
481484 CAGAAATGGAGCTTAAATG
1 CAGAAATGGAGCTTAAATG
481503 CAGAAATGGA
1 CAGAAATGGA
481513 CTCAGAACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (19 bp):
CAGAAATGGAGCTTAAATG
Found at i:487336 original size:2 final size:2
Alignment explanation
Indices: 487329--487395 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
487319 CGATGAGGTG
487329 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
487371 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
487396 GGTTATTACT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:487990 original size:2 final size:2
Alignment explanation
Indices: 487983--488042 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
487973 TTATGTATGA
487983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
488025 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
488043 GTTTATGTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:492090 original size:23 final size:23
Alignment explanation
Indices: 492064--492144 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
492054 GATCATATTC
* *
492064 ATTTAATGTTCGCGAACGTGTTT
1 ATTTAATGTTCGCAAACATGTTT
* *
492087 ATTTAATGTCCGCAAACATGTTC
1 ATTTAATGTTCGCAAACATGTTT
*
492110 GTTTAATGTTCGCAAACATGTTT
1 ATTTAATGTTCGCAAACATGTTT
*
492133 GTTTATATGTTC
1 ATTTA-ATGTTC
492145 ACGAATGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 44 0.88
24 6 0.12
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (23 bp):
ATTTAATGTTCGCAAACATGTTT
Found at i:510847 original size:34 final size:34
Alignment explanation
Indices: 510808--510941 Score: 178
Period size: 34 Copynumber: 3.7 Consensus size: 34
510798 CAACCGAATC
510808 ATTAGGTGAATCATTGGAATTTCTTATTAGAAGT
1 ATTAGGTGAATCATTGGAATTTCTTATTAGAAGT
*
510842 ATTAGGTGAATCATTGGAATTTCTTATTAGAAAT
1 ATTAGGTGAATCATTGGAATTTCTTATTAGAAGT
*
510876 ATTAGGTGAATCATTGAAATTTCTAATAGGATTATTAGAAGT
1 ATTAGGTGAATCATTGGAATTTC--------TTATTAGAAGT
510918 ATTAGGTGAATCATTGGAATTTCT
1 ATTAGGTGAATCATTGGAATTTCT
510942 AATCGGATTA
Statistics
Matches: 88, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
34 56 0.64
42 32 0.36
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (34 bp):
ATTAGGTGAATCATTGGAATTTCTTATTAGAAGT
Found at i:510958 original size:42 final size:42
Alignment explanation
Indices: 510865--510958 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
510855 TTGGAATTTC
*
510865 TTATTAGAAATATTAGGTGAATCATTGAAATTTCTAATAGGA
1 TTATTAGAAGTATTAGGTGAATCATTGAAATTTCTAATAGGA
* *
510907 TTATTAGAAGTATTAGGTGAATCATTGGAATTTCTAATCGGA
1 TTATTAGAAGTATTAGGTGAATCATTGAAATTTCTAATAGGA
510949 TTATTAGAAG
1 TTATTAGAAG
510959 GTTTAACCGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (42 bp):
TTATTAGAAGTATTAGGTGAATCATTGAAATTTCTAATAGGA
Found at i:512960 original size:21 final size:21
Alignment explanation
Indices: 512934--512973 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
512924 CTAGTTTAAC
512934 ATCATGGACTGTTATGTCAAT
1 ATCATGGACTGTTATGTCAAT
512955 ATCATGGACTGTTATGTCA
1 ATCATGGACTGTTATGTCA
512974 GCACCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (21 bp):
ATCATGGACTGTTATGTCAAT
Found at i:518057 original size:17 final size:17
Alignment explanation
Indices: 518035--518067 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
518025 TTTAGTGTAA
*
518035 TTTTGTTAAACTTTAAC
1 TTTTGTTAAACATTAAC
518052 TTTTGTTAAACATTAA
1 TTTTGTTAAACATTAA
518068 TTTATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52
Consensus pattern (17 bp):
TTTTGTTAAACATTAAC
Found at i:518193 original size:19 final size:19
Alignment explanation
Indices: 518169--518214 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
518159 TAGGATGAAT
518169 TATTAAT-TTTTTTAAATAA
1 TATTAATATTTTTTAAA-AA
518188 TATTAATATTTTTTAAAAA
1 TATTAATATTTTTTAAAAA
518207 T-TTAATAT
1 TATTAATAT
518215 CAAGATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTAATATTTTTTAAAAA
Found at i:518200 original size:21 final size:19
Alignment explanation
Indices: 518174--518214 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
518164 TGAATTATTA
518174 ATTTTTTTAAATAATATTAAT
1 ATTTTTTTAAA-AAT-TTAAT
518195 A-TTTTTTAAAAATTTAAT
1 ATTTTTTTAAAAATTTAAT
518213 AT
1 AT
518215 CAAGATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 9 0.47
21 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTTTAAAAATTTAAT
Found at i:518462 original size:24 final size:24
Alignment explanation
Indices: 518435--518511 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
518425 AAATTAAATT
518435 AGTTTATTCCCAAATCATGAATAA
1 AGTTTATTCCCAAATCATGAATAA
* * * *
518459 AGTTTGA-TACC-AATGCTTCAA-ATT
1 AGTTT-ATTCCCAAAT-CATGAATA-A
518483 AGTTTATTCCCAAATCATGAATAA
1 AGTTTATTCCCAAATCATGAATAA
518507 AGTTT
1 AGTTT
518512 GATACCAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
23 5 0.13
24 29 0.74
25 5 0.13
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (24 bp):
AGTTTATTCCCAAATCATGAATAA
Found at i:518501 original size:48 final size:48
Alignment explanation
Indices: 518430--518525 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
518420 AGATAAAATT
518430 AAATTAGTTTATTCCCAAATCATGAATAAAGTTTGATACCAATGCTTC
1 AAATTAGTTTATTCCCAAATCATGAATAAAGTTTGATACCAATGCTTC
518478 AAATTAGTTTATTCCCAAATCATGAATAAAGTTTGATACCAATGCTTC
1 AAATTAGTTTATTCCCAAATCATGAATAAAGTTTGATACCAATGCTTC
518526 TTATCCAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (48 bp):
AAATTAGTTTATTCCCAAATCATGAATAAAGTTTGATACCAATGCTTC
Found at i:518519 original size:24 final size:24
Alignment explanation
Indices: 518444--518519 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
518434 TAGTTTATTC
518444 CCAAATCATGAATAAAGTTTGATA
1 CCAAATCATGAATAAAGTTTGATA
* * * *
518468 CC-AATGCTTCAA-ATTAGTTT-ATTC
1 CCAAAT-CATGAATA-AAGTTTGA-TA
518492 CCAAATCATGAATAAAGTTTGATA
1 CCAAATCATGAATAAAGTTTGATA
518516 CCAA
1 CCAA
518520 TGCTTCTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
23 5 0.13
24 28 0.74
25 5 0.13
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (24 bp):
CCAAATCATGAATAAAGTTTGATA
Found at i:518751 original size:2 final size:2
Alignment explanation
Indices: 518744--518775 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
518734 TATCCGTCTG
518744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
518776 GTGTTAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:519237 original size:2 final size:2
Alignment explanation
Indices: 519230--519298 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
519220 AAGTGGATCT
519230 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
519272 TA 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 TA T
519299 TCATGGGAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:523581 original size:18 final size:18
Alignment explanation
Indices: 523555--523590 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
523545 TTAGGAATGG
*
523555 TTGCAAAAGTAGTCTTCA
1 TTGCAAAAGAAGTCTTCA
*
523573 TTGCTAAAGAAGTCTTCA
1 TTGCAAAAGAAGTCTTCA
523591 AGCTTTTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
TTGCAAAAGAAGTCTTCA
Found at i:524312 original size:41 final size:42
Alignment explanation
Indices: 524267--524358 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
524257 GGATAGCTCG
* * **
524267 AAGGACTTA-TCATCTTGCTCGAAAGGCTTA-TAGATGACCCA
1 AAGGACTTAGGCATCATGCTCGAAACACTTACT-GATGACCCA
* *
524308 AAGGATTTAGGCATCATGCTCGAAACACTTACTGATGGCCCA
1 AAGGACTTAGGCATCATGCTCGAAACACTTACTGATGACCCA
524350 AAGGACTTA
1 AAGGACTTA
524359 CTAAGTAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 8 0.19
42 33 0.79
43 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.25
Consensus pattern (42 bp):
AAGGACTTAGGCATCATGCTCGAAACACTTACTGATGACCCA
Found at i:524570 original size:42 final size:43
Alignment explanation
Indices: 524470--524570 Score: 109
Period size: 41 Copynumber: 2.4 Consensus size: 43
524460 AATCATGTGA
* * *
524470 AAACATCATGC-CCAAAGGTATCATGGATGGCCCGAAGGACTT
1 AAACATCATGCTCGAAAGGTATCATAGATGACCCGAAGGACTT
* * * * *
524512 -ATCATCTTGCTTGAAAGGT-TTATAGATGACCCGAAGGATTT
1 AAACATCATGCTCGAAAGGTATCATAGATGACCCGAAGGACTT
524553 AAACATCATGCTCGAAAG
1 AAACATCATGCTCGAAAG
524571 ACTTACTGAT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
41 26 0.57
42 20 0.43
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (43 bp):
AAACATCATGCTCGAAAGGTATCATAGATGACCCGAAGGACTT
Found at i:524577 original size:237 final size:238
Alignment explanation
Indices: 524097--524755 Score: 921
Period size: 237 Copynumber: 2.7 Consensus size: 238
524087 CAACTGTATA
* * *
524097 TTAC-GAT-GCCCGAAGGACTTACTAAGTAAAAAACTTTTGGAAATCGCTTTCTTATTTTTCAAA
1 TTACTGATGGCCCGAAGGACTTACTAAGTAAGAAAC-TTTGGAAATCG-TTTTTTACTTTT-AAA
* * *
524160 AAAATCAATTTTCAGAAAAGATTTAAATGAGAAGCTTTGGCAATAGCTTTCTCATTTTTCGAAAA
63 AAAATCAATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAA
* * *
524225 TCACATGAAAACATCATGCCCGAAGGTCTTATGGATAGCTCGAAGGACTTATCATCTTGCTCGAA
128 TCACGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAA
**
524290 AGGCTTATAGATGACCCAAAGGATTTAGGCATCATGCTCGAAACAC
193 AGGCTTATAGATGACCCAAAGGATTTAAACATCATGCTCGAAACAC
* *
524336 TTACTGATGGCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTTTACCTTT-AAAAA
1 TTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTTTACTTTTAAAAAA
* *
524400 ATCAATTTTCAGAAAAGATTTAAATGAGAAACTTTAGAAATCGCTTTCTCATTTTTTGAAAATCA
66 ATCAATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCA
* * * * *
524465 TGTGAAAACATCATGCCCAAAGGTATCATGGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGG
131 CGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGG
* * *
524530 TTTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGAC
196 CTTATAGATGACCCAAAGGATTTAAACATCATGCTCGAAACAC
* * *
524573 TTACTGATGGCTCGAGGGACTTACTAAGTAAGAAACTCTGGAAATCGTTTTCTTACTTTTCAAGA
1 TTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTT-TTACTTTT----A
* *
524638 AAAAAATCAATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGCTATCTCATTTTTCAAA
61 AAAAAATCAATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAA
* * * *
524703 AATCACGT-AAAGACATCTTTCCTGAAGGTCTTACGGATGGCCCGAAGGACTTA
126 AATCACGTGAAA-ACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTA
524756 CTAATCAAGA
Statistics
Matches: 371, Mismatches: 40, Indels: 14
0.87 0.09 0.03
Matches are distributed among these distances:
237 207 0.56
238 7 0.02
239 13 0.04
240 14 0.04
241 25 0.07
242 3 0.01
243 102 0.27
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (238 bp):
TTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTTTACTTTTAAAAAA
ATCAATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCA
CGTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGG
CTTATAGATGACCCAAAGGATTTAAACATCATGCTCGAAACAC
Found at i:526339 original size:28 final size:28
Alignment explanation
Indices: 526308--526438 Score: 138
Period size: 28 Copynumber: 4.7 Consensus size: 28
526298 TGACTTGGTA
* * * *
526308 AGGTAATATATTTTAGGTTAATTTGAGG
1 AGGTAATATGTTTCAAGTTAATTTGGGG
**
526336 AGGTAATGA-GTTTCTGGTTAATTTGGGG
1 AGGTAAT-ATGTTTCAAGTTAATTTGGGG
* * *
526364 ATGTAATATGTTTCAAGTTGATTTTGGG
1 AGGTAATATGTTTCAAGTTAATTTGGGG
* *
526392 AGGTAATGTGTTTCAAGTTGATTTGGGG
1 AGGTAATATGTTTCAAGTTAATTTGGGG
*
526420 AGGTAATGTGTTTCAAGTT
1 AGGTAATATGTTTCAAGTT
526439 GGCTTCTTCG
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.01
28 87 0.98
29 1 0.01
ACGTcount: A:0.25, C:0.03, G:0.30, T:0.42
Consensus pattern (28 bp):
AGGTAATATGTTTCAAGTTAATTTGGGG
Found at i:526439 original size:28 final size:28
Alignment explanation
Indices: 526328--526439 Score: 152
Period size: 28 Copynumber: 4.0 Consensus size: 28
526318 TTTTAGGTTA
* * ** *
526328 ATTTGAGGAGGTAATGAGTTTCTGGTTA
1 ATTTGGGGAGGTAATGTGTTTCAAGTTG
* *
526356 ATTTGGGGATGTAATATGTTTCAAGTTG
1 ATTTGGGGAGGTAATGTGTTTCAAGTTG
*
526384 ATTTTGGGAGGTAATGTGTTTCAAGTTG
1 ATTTGGGGAGGTAATGTGTTTCAAGTTG
526412 ATTTGGGGAGGTAATGTGTTTCAAGTTG
1 ATTTGGGGAGGTAATGTGTTTCAAGTTG
526440 GCTTCTTCGG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (28 bp):
ATTTGGGGAGGTAATGTGTTTCAAGTTG
Found at i:527088 original size:21 final size:21
Alignment explanation
Indices: 527063--527118 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
527053 CTTCTTGAAG
*
527063 TATTTGATCTGTTTT-CTTTCT
1 TATTT-ATCTCTTTTGCTTTCT
*
527084 TATTTTTCTCTTTTGCTTTCT
1 TATTTATCTCTTTTGCTTTCT
*
527105 T-TTCTCTCTCTTTT
1 TATT-TATCTCTTTT
527119 CTTATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.30
21 21 0.70
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.70
Consensus pattern (21 bp):
TATTTATCTCTTTTGCTTTCT
Found at i:527386 original size:2 final size:2
Alignment explanation
Indices: 527379--527429 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
527369 ACAACAAGGG
527379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
527421 AT AT AT AT A
1 AT AT AT AT A
527430 AGTATAAATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:533667 original size:131 final size:131
Alignment explanation
Indices: 533432--533797 Score: 511
Period size: 131 Copynumber: 2.8 Consensus size: 131
533422 ATTAATACTG
* * * * * * *
533432 AAAATAGTAATATATTTTCATTTCGGTTGGAGTAATAAATGATTGCTTAAAGGTATGAGAAG-TC
1 AAAATAGTGATATATCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGA-AAGATC
* * * * *
533496 ATTTATTCTTGGTTGGAAATAATTAGATATTGTGGTTTTCTTTCGAATCAATATTGAATTTTAAG
65 ATTTATTCTCGATTGGAAATAATTAGATATTATAGTTTTCTCTCGAATCAATATTGAATTTTAAG
*
533561 AC
130 AA
* *
533563 GAAATAGTGATATATCTTCCTTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAAAGATCA
1 AAAATAGTGATATATCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAAAGATCA
*
533628 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGA
66 TTTATTCTCGATTGGAAATAATTAGATATTATAGTTTTCTCTCGAATCAATATTGAATTTTAAGA
533693 A
131 A
* * * *
533694 AAAATAGTGATATCTCTTCATTTCGATCGCAA-TAATAAATGACTGCATTAAGGCATGAGAGATC
1 AAAATAGTGATATATCTTCATTTCGATTG-AAGTAATAAATGACTGCTTTAAGGCATGAAAGATC
*
533758 ATTTATTCTCAATTGGAAATAATTAGATATTATAGTTTTC
65 ATTTATTCTCGATTGGAAATAATTAGATATTATAGTTTTC
533798 GTTCTTAAAA
Statistics
Matches: 210, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
130 3 0.01
131 205 0.98
132 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (131 bp):
AAAATAGTGATATATCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAAAGATCA
TTTATTCTCGATTGGAAATAATTAGATATTATAGTTTTCTCTCGAATCAATATTGAATTTTAAGA
A
Found at i:539042 original size:97 final size:97
Alignment explanation
Indices: 538911--539087 Score: 318
Period size: 97 Copynumber: 1.8 Consensus size: 97
538901 CCATTATTTT
538911 TTACAATTAAAATAATAATTAAAGTAGTAAATAAAATTTTATTGAGAATATTGCTTCTTCAAAAT
1 TTACAATTAAAATAATAATTAAAGTAGTAAATAAAATTTTATTGAGAATATTGCTTCTTCAAAAT
538976 TTGAGTAAATTATATGTTGTATCTTACACTAG
66 TTGAGTAAATTATATGTTGTATCTTACACTAG
* * * *
539008 TTACAATTAAATTAATAATTTAATTAGTAAATAAAATTTTATTTAGAATATTGCTTCTTCAAAAT
1 TTACAATTAAAATAATAATTAAAGTAGTAAATAAAATTTTATTGAGAATATTGCTTCTTCAAAAT
539073 TTGAGTAAATTATAT
66 TTGAGTAAATTATAT
539088 ATATATATTG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 76 1.00
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.42
Consensus pattern (97 bp):
TTACAATTAAAATAATAATTAAAGTAGTAAATAAAATTTTATTGAGAATATTGCTTCTTCAAAAT
TTGAGTAAATTATATGTTGTATCTTACACTAG
Found at i:542699 original size:24 final size:24
Alignment explanation
Indices: 542667--542772 Score: 117
Period size: 24 Copynumber: 4.5 Consensus size: 24
542657 CATTTAAATG
*
542667 ATAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAAATAAACGAAC
** **
542691 ATAAACGAACGGATGTAAAC-AGAC
1 ATAAACGAACACAAATAAACGA-AC
542715 ATAAACGAACAC-AATAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
* *
542738 ATAAATGAACACAAATGAACGAAC
1 ATAAACGAACACAAATAAACGAAC
*
542762 GTAAACGAACA
1 ATAAACGAACA
542773 TAAAAGAAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 19 0.29
24 47 0.71
ACGTcount: A:0.57, C:0.19, G:0.14, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAC
Found at i:542966 original size:14 final size:13
Alignment explanation
Indices: 542948--543013 Score: 66
Period size: 14 Copynumber: 5.1 Consensus size: 13
542938 GATTGGACTA
542948 AACATAAATGAAC
1 AACATAAATGAAC
*
542961 ACACATAAACGAAC
1 A-ACATAAATGAAC
542975 GAACATAAATG---
1 -AACATAAATGAAC
542986 AACATAAATGAAC
1 AACATAAATGAAC
*
542999 AAACATAAACGAAC
1 -AACATAAATGAAC
543013 A
1 A
543014 TATTACCGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
10 10 0.23
13 2 0.05
14 31 0.70
15 1 0.02
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.12
Consensus pattern (13 bp):
AACATAAATGAAC
Found at i:542998 original size:24 final size:24
Alignment explanation
Indices: 542963--543015 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
542953 AAATGAACAC
* *
542963 ACATAAACGAACGAACATAAATGA
1 ACATAAACGAACAAACATAAACGA
*
542987 ACATAAATGAACAAACATAAACGA
1 ACATAAACGAACAAACATAAACGA
543011 ACATA
1 ACATA
543016 TTACCGAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.17, G:0.09, T:0.13
Consensus pattern (24 bp):
ACATAAACGAACAAACATAAACGA
Found at i:543015 original size:10 final size:10
Alignment explanation
Indices: 542975--542999 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
542965 ATAAACGAAC
542975 GAACATAAAT
1 GAACATAAAT
542985 GAACATAAAT
1 GAACATAAAT
542995 GAACA
1 GAACA
543000 AACATAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (10 bp):
GAACATAAAT
Found at i:562222 original size:12 final size:14
Alignment explanation
Indices: 562192--562223 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
562182 TCTTCTTCCT
562192 TTCTCCATCTTTTC
1 TTCTCCATCTTTTC
562206 TTCTCCAT-TTTTC
1 TTCTCCATCTTTTC
562219 -TCTCC
1 TTCTCC
562224 TAGTCCCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 5 0.28
14 8 0.44
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (14 bp):
TTCTCCATCTTTTC
Found at i:566658 original size:77 final size:77
Alignment explanation
Indices: 566569--566820 Score: 315
Period size: 77 Copynumber: 3.2 Consensus size: 77
566559 TATATATAAG
**
566569 AAATACGGTTGCGCATAAAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAAT
1 AAATA-GGTTGCGCCCAAAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAAT
566634 ATTTTTATTAATA
65 ATTTTTATTAATA
* * * * * *
566647 AAATAGGTTGCGCCCAAGAATATCATGGTTCACTCAGAAATAGGTTGCGATCTGGAATGTTAATA
1 AAATAGGTTGCGCCCAAAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAATA
*
566712 TTTTTTACTAATA
66 -TTTTTATTAATA
* * * * * * *
566725 AAATGGGTTGCACCCGAAAATGTCATGGTTGACTAAGAAATAGGTTGTGATATGAAATCTGAATA
1 AAATAGGTTGCGCCCAAAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAATA
566790 TTTTTATTAATA
66 TTTTTATTAATA
* * *
566802 AAATGGGTTGTGCCTAAAA
1 AAATAGGTTGCGCCCAAAA
566821 TGTTATCAGA
Statistics
Matches: 147, Mismatches: 26, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
77 78 0.53
78 69 0.47
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (77 bp):
AAATAGGTTGCGCCCAAAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAATA
TTTTTATTAATA
Found at i:566764 original size:78 final size:76
Alignment explanation
Indices: 566586--566811 Score: 317
Period size: 77 Copynumber: 2.9 Consensus size: 76
566576 GTTGCGCATA
566586 AAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAATATTTTTATTAATAAAAT
1 AAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAATATTTTTATTAATAAAAT
* *
566651 AGGTTGCGCCC
66 GGGTTGCACCC
* * * * * *
566662 AAGAATATCATGGTTCACTCAGAAATAGGTTGCGATCTGGAATGTTAATATTTTTTACTAATAAA
1 AA-AATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAATA-TTTTTATTAATAAA
566727 ATGGGTTGCACCC
64 ATGGGTTGCACCC
* * * *
566740 GAAAATGTCATGGTTGACTAAGAAATAGGTTGTGATATGAAATCTGAATATTTTTATTAATAAAA
1 -AAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAATATTTTTATTAATAAAA
566805 TGGGTTG
65 TGGGTTG
566812 TGCCTAAAAT
Statistics
Matches: 130, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
76 2 0.02
77 63 0.48
78 63 0.48
79 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (76 bp):
AAAATGTCATGGTTCACTAAGAAATAGGTTGCGATATGAAATATTAATATTTTTATTAATAAAAT
GGGTTGCACCC
Found at i:567234 original size:22 final size:22
Alignment explanation
Indices: 567206--567249 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
567196 ATTATGTTAC
*
567206 TCCAACTGATAATTTTTTAGGT
1 TCCAACTGATAATATTTTAGGT
*
567228 TCCAACTTATAATATTTTAGGT
1 TCCAACTGATAATATTTTAGGT
567250 ATCGCTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (22 bp):
TCCAACTGATAATATTTTAGGT
Found at i:568357 original size:3 final size:3
Alignment explanation
Indices: 568349--568398 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
568339 CGTCCTCGTC
568349 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
568397 AT
1 AT
568399 GAAACGAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:571676 original size:2 final size:2
Alignment explanation
Indices: 571669--571693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
571659 GCAGTGGTGC
571669 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 A
571694 AGGAAACGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:582768 original size:6 final size:6
Alignment explanation
Indices: 582757--582803 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
582747 ATAGGAAACC
* *
582757 AAAGTG AAAGTG AAAGCG AAAGCG AAAGCG AAAGCG AAAGCG AAAGC
1 AAAGCG AAAGCG AAAGCG AAAGCG AAAGCG AAAGCG AAAGCG AAAGC
582804 TCAAAGACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.51, C:0.13, G:0.32, T:0.04
Consensus pattern (6 bp):
AAAGCG
Found at i:584334 original size:2 final size:2
Alignment explanation
Indices: 584327--584361 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
584317 ACTATTACTC
584327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
584362 CAAATTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:584455 original size:30 final size:29
Alignment explanation
Indices: 584414--584496 Score: 102
Period size: 25 Copynumber: 2.9 Consensus size: 29
584404 AGCAATAATG
* *
584414 ATATGTTAGAACATTAAATATAAATTTTAA
1 ATATTTTAGAACATTAAATAT-AATTTAAA
584444 ATATTTTAGAACATT-AA-AT--TTTAAA
1 ATATTTTAGAACATTAAATATAATTTAAA
584469 ATATTTTAGAACATTAAATATATATTTA
1 ATATTTTAGAACATTAAATATA-ATTTA
584497 TGAGATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
25 20 0.43
26 2 0.04
27 2 0.04
28 2 0.04
29 2 0.04
30 18 0.39
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (29 bp):
ATATTTTAGAACATTAAATATAATTTAAA
Found at i:587551 original size:3 final size:3
Alignment explanation
Indices: 587543--587604 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
587533 TTTTTATCCA
* *
587543 TAT TAT TAT TAT TAT TAT TTT TAT CCA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
*
587588 TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
587605 AATATATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 49 0.96
4 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:587570 original size:27 final size:27
Alignment explanation
Indices: 587533--587588 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
587523 AGATACTAAT
587533 TTTTTATCCATATTATTATTATTATTA
1 TTTTTATCCATATTATTATTATTATTA
587560 TTTTTATCCATATTATTATTATTATTA
1 TTTTTATCCATATTATTATTATTATTA
587587 TT
1 TT
587589 ATCATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTATCCATATTATTATTATTATTA
Found at i:587616 original size:11 final size:11
Alignment explanation
Indices: 587600--587636 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
587590 TCATTATTAT
587600 TATTAAATATA
1 TATTAAATATA
587611 TATTAAATATA
1 TATTAAATATA
*
587622 TA-TAAAAATA
1 TATTAAATATA
587632 -ATTAA
1 TATTAA
587637 TTACAGGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
9 1 0.04
10 10 0.42
11 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATTAAATATA
Found at i:588075 original size:19 final size:20
Alignment explanation
Indices: 588051--588090 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
588041 CCCAACCTGG
588051 AAAAAAAAAC-AGAGACAGA
1 AAAAAAAAACGAGAGACAGA
588070 AAAAAAAAACGGAGAGACAGA
1 AAAAAAAAAC-GAGAGACAGA
588091 GAACACAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACGAGAGACAGA
Found at i:588126 original size:14 final size:14
Alignment explanation
Indices: 588107--588133 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
588097 AGAGAGACGG
588107 AGAGAAAAAAAAAC
1 AGAGAAAAAAAAAC
588121 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
588134 GATATACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAGAAAAAAAAAC
Found at i:589088 original size:13 final size:13
Alignment explanation
Indices: 589072--589111 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
589062 ATATAATAAA
589072 TAAATATTTATTT
1 TAAATATTTATTT
*
589085 TAAATAAATTATTT
1 TAAAT-ATTTATTT
589099 T-AATATTTATTT
1 TAAATATTTATTT
589111 T
1 T
589112 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:589815 original size:18 final size:18
Alignment explanation
Indices: 589768--589817 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
589758 TTTCAAAATT
589768 TTTTTA-TTTATTTATTA
1 TTTTTATTTTATTTATTA
**
589785 TTTTTATAATATTTA-TA
1 TTTTTATTTTATTTATTA
589802 TGTTTTATTTTATTTA
1 T-TTTTATTTTATTTA
589818 CAAGTATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTTATTTTATTTATTA
Found at i:596918 original size:10 final size:10
Alignment explanation
Indices: 596903--596935 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
596893 GCAATCATTC
596903 TTTACATTTT
1 TTTACATTTT
596913 TTTACA-TTT
1 TTTACATTTT
*
596922 TTTACATTTA
1 TTTACATTTT
596932 TTTA
1 TTTA
596936 TTTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTACATTTT
Found at i:596925 original size:19 final size:19
Alignment explanation
Indices: 596898--596935 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
596888 ATATGGCAAT
*
596898 CATTCTTTACATTTTTTTA
1 CATTCTTTACATTTATTTA
*
596917 CATTTTTTACATTTATTTA
1 CATTCTTTACATTTATTTA
596936 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:600476 original size:8 final size:8
Alignment explanation
Indices: 600454--600534 Score: 60
Period size: 9 Copynumber: 9.8 Consensus size: 8
600444 ATTATGCTTG
600454 AAGAAAAGA
1 AAGAAAA-A
600463 AA-AAAAA
1 AAGAAAAA
600470 AAGAAAAA
1 AAGAAAAA
600478 TAA-ATAAATA
1 -AAGA-AAA-A
*
600488 AATAAAAA
1 AAGAAAAA
*
600496 AATAGAAAA
1 AAGA-AAAA
600505 AAG-AAAA
1 AAGAAAAA
*
600512 AAGAGAAA
1 AAGAAAAA
600520 AAGAAGAAA
1 AAGAA-AAA
600529 AAGAAA
1 AAGAAA
600535 GGGGGTCAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
7 10 0.16
8 23 0.38
9 26 0.43
10 2 0.03
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (8 bp):
AAGAAAAA
Found at i:600520 original size:15 final size:14
Alignment explanation
Indices: 600465--600534 Score: 61
Period size: 15 Copynumber: 4.8 Consensus size: 14
600455 AGAAAAGAAA
*
600465 AAAAAAAGAAAAAT
1 AAAAAAAGAAAAAG
* *
600479 AAATAAATAAATAA-
1 AAAAAAAGAAA-AAG
*
600493 AAAAATAGAAAAAAG
1 AAAAAAAG-AAAAAG
600508 AAAAAAGAGAAAAAG
1 AAAAAA-AGAAAAAG
600523 AAGAAAAAGAAA
1 AA-AAAAAGAAA
600535 GGGGGTCAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 16 0.36
15 23 0.51
16 6 0.13
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.07
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:601835 original size:86 final size:84
Alignment explanation
Indices: 601687--601900 Score: 302
Period size: 86 Copynumber: 2.5 Consensus size: 84
601677 TGAATGTGCT
* ** * * *
601687 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAGTTATTGAAT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAAAACCAATCATTGAAT
601752 TTAGAAAGATGAAGGAGACC
66 TTAGAAAGATGAAGGAG-CC
*
601772 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
1 C-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAAAACCAATCATTGAA
* * * * *
601837 TTTTGGAAGATGAATGTGCT
65 TTTAGAAAGATGAAGGAGCC
601857 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
601901 TGGTAAGAAC
Statistics
Matches: 116, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
84 43 0.37
85 3 0.03
86 70 0.60
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (84 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAAAACCAATCATTGAAT
TTAGAAAGATGAAGGAGCC
Found at i:602757 original size:114 final size:113
Alignment explanation
Indices: 602552--603225 Score: 1003
Period size: 114 Copynumber: 5.9 Consensus size: 113
602542 ATTCATATCT
* * *
602552 ATCATTTGATGGATTGA-CATTTCAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCAATTGATGGATT-ATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
602616 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATTC
65 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTAAATTC
*
602665 ATCAAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-AATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*** *
602730 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
65 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTT-ACCTAAATTC
* * * * * *
602780 ATCATTTGAGGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
*
602844 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATTC
62 GGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTAAATTC
*
602896 ATCAAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-AATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*** *
602961 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGGTTTGAATTC
65 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTT-ACCTAAATTC
* *
603011 ATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
603076 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATTC
66 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTAAATTC
*
603124 ATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
603188 GAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTT
603226 GCATAATTCT
Statistics
Matches: 504, Mismatches: 47, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
112 70 0.14
113 39 0.08
114 276 0.55
115 19 0.04
116 10 0.02
117 87 0.17
118 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (113 bp):
ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACCTAAATTC
Found at i:602952 original size:231 final size:228
Alignment explanation
Indices: 602576--603226 Score: 1164
Period size: 231 Copynumber: 2.9 Consensus size: 228
602566 TGACATTTCA
602576 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
602641 TTGTTCAACCTTTTACCTAAATTCATCAAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAAT
66 TTGTTCAACCTTTTACCTAAATTCATCAAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAAT
602706 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGG
131 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGG
*
602771 TTTGAATTCATCATTTGAGGGATCAACATTGCC
196 TTTGAATTCATCAATTGAGGGATCAACATTGCC
602804 AG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
1 AGAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
602868 GAATTTGTTCAACCTTTTACCTAAATTCATCAAATTGATGGATTATTTTTTCCAGAGAAAGTTCA
62 GAATTTGTTCAACCTTTTACCTAAATTCATCAAATTGATGGATTATTTTTTCCAGAGAAAGTTCA
602933 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTT
127 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTT
* * * *
602998 TTGGTTTGAATTCATCAATTGATGGATCAGCTTTTCC
192 TTGGTTTGAATTCATCAATTGAGGGATCAACATTGCC
603035 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
*
603100 TTGTTCAACCTTTTACCTAAATTCATC-AATTGATGGATTATCTTTTCCAGAG-AAGTTCATAAT
66 TTGTTCAACCTTTTACCTAAATTCATCAAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAAT
* * *
603163 GAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTG
131 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTG
603227 CATAATTCTA
Statistics
Matches: 409, Mismatches: 9, Indels: 12
0.95 0.02 0.03
Matches are distributed among these distances:
226 72 0.18
227 27 0.07
228 87 0.21
229 1 0.00
230 1 0.00
231 218 0.53
232 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (228 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTACCTAAATTCATCAAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAAT
GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGG
TTTGAATTCATCAATTGAGGGATCAACATTGCC
Found at i:603552 original size:3 final size:3
Alignment explanation
Indices: 603544--603599 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
603534 TTTTTATCCA
*
603544 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
603592 TAT TAT TA
1 TAT TAT TA
603600 AATATATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:603611 original size:11 final size:11
Alignment explanation
Indices: 603595--603626 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
603585 TTATTATTAT
603595 TATTAAATATA
1 TATTAAATATA
603606 TATTAAATATA
1 TATTAAATATA
603617 TATATAAATA
1 TAT-TAAATA
603627 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:604060 original size:16 final size:16
Alignment explanation
Indices: 604039--604069 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
604029 CCCAACCTGA
604039 AAAAAAAAACAGAGAC
1 AAAAAAAAACAGAGAC
*
604055 AAAAAAAAACGGAGA
1 AAAAAAAAACAGAGA
604070 GACAGAGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAGAGAC
Found at i:605076 original size:13 final size:13
Alignment explanation
Indices: 605060--605099 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
605050 ATATAATAAA
605060 TAAATATTTATTT
1 TAAATATTTATTT
*
605073 TAAATAAATTATTT
1 TAAAT-ATTTATTT
605087 T-AATATTTATTT
1 TAAATATTTATTT
605099 T
1 T
605100 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:609121 original size:14 final size:14
Alignment explanation
Indices: 609102--609131 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
609092 TTTAGATTTT
*
609102 TTAAAATTACATTA
1 TTAAAAATACATTA
609116 TTAAAAATACATTA
1 TTAAAAATACATTA
609130 TT
1 TT
609132 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:609226 original size:14 final size:14
Alignment explanation
Indices: 609209--609273 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
609199 AATTATGTGA
609209 TAGTGTTTATGATT
1 TAGTGTTTATGATT
* *
609223 TAGTGTTTAGGGTT
1 TAGTGTTTATGATT
*
609237 TA-TGATTTA-AAGTT
1 TAGTG-TTTATGA-TT
* *
609251 TAGGGTTTATGGTT
1 TAGTGTTTATGATT
609265 TAGTGTTTA
1 TAGTGTTTA
609274 GGGTCTAGGG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
13 2 0.05
14 36 0.92
15 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (14 bp):
TAGTGTTTATGATT
Found at i:609237 original size:21 final size:21
Alignment explanation
Indices: 609213--609277 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
609203 ATGTGATAGT
609213 GTTTATGATTTAGTGTTTAGG
1 GTTTATGATTTAGTGTTTAGG
**
609234 GTTTATGATTTAAAGTTTAGG
1 GTTTATGATTTAGTGTTTAGG
*
609255 GTTTATGGTTTAGTGTTTAGG
1 GTTTATGATTTAGTGTTTAGG
609276 GT
1 GT
609278 CTAGGGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (21 bp):
GTTTATGATTTAGTGTTTAGG
Found at i:609285 original size:21 final size:21
Alignment explanation
Indices: 609213--609286 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
609203 ATGTGATAGT
*
609213 GTTTATGATTTAGTGTTTAGG
1 GTTTATGGTTTAGTGTTTAGG
* **
609234 GTTTATGATTTAAAGTTTAGG
1 GTTTATGGTTTAGTGTTTAGG
609255 GTTTATGGTTTAGTGTTTAGG
1 GTTTATGGTTTAGTGTTTAGG
* *
609276 GTCTAGGGTTT
1 GTTTATGGTTT
609287 TACAGATGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.19, C:0.01, G:0.30, T:0.50
Consensus pattern (21 bp):
GTTTATGGTTTAGTGTTTAGG
Found at i:610290 original size:21 final size:22
Alignment explanation
Indices: 610250--610295 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
610240 CATATATAGG
610250 AAGAAGAGAATTCAAAAAATTT
1 AAGAAGAGAATTCAAAAAATTT
*
610272 AAGAAGAGAATTCAAAAATTTT
1 AAGAAGAGAATTCAAAAAATTT
610294 AA
1 AA
610296 CTTTCGCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (22 bp):
AAGAAGAGAATTCAAAAAATTT
Found at i:618606 original size:23 final size:22
Alignment explanation
Indices: 618580--618622 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
618570 ATATAAACTG
*
618580 TTAAATTATAAAATTAAAAATGA
1 TTAAATTAGAAAA-TAAAAATGA
*
618603 TTAATTTAGAAAATAAAAAT
1 TTAAATTAGAAAATAAAAAT
618623 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (22 bp):
TTAAATTAGAAAATAAAAATGA
Found at i:620489 original size:18 final size:18
Alignment explanation
Indices: 620466--620503 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
620456 CTTGTTTTAC
620466 TTTTCCTTGTGGGGAATG
1 TTTTCCTTGTGGGGAATG
620484 TTTTCCTTGTGGGGAATG
1 TTTTCCTTGTGGGGAATG
620502 TT
1 TT
620504 AGGTCATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.32, T:0.47
Consensus pattern (18 bp):
TTTTCCTTGTGGGGAATG
Found at i:623561 original size:34 final size:34
Alignment explanation
Indices: 623523--623668 Score: 251
Period size: 34 Copynumber: 4.3 Consensus size: 34
623513 GCATTGAGGT
*
623523 TTTTGTTTTCATTTCGTTATGATAGCATAGAGAT
1 TTTTGTTTTCATTTCGTTATGATAGCATAGAGAA
623557 TTTTGTTTGT-ATTTCGTTATGATAGCATAGAGAA
1 TTTTGTTT-TCATTTCGTTATGATAGCATAGAGAA
*
623591 -TTTGTTTTCATTTTGTTATGATAGCATAGAGAA
1 TTTTGTTTTCATTTCGTTATGATAGCATAGAGAA
623624 TTTTGTTTTCATTTCGTTATGATAGCATAGAGAA
1 TTTTGTTTTCATTTCGTTATGATAGCATAGAGAA
623658 TTTTGTTTTCA
1 TTTTGTTTTCA
623669 ATATTTTTAT
Statistics
Matches: 106, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
32 1 0.01
33 30 0.28
34 74 0.70
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.50
Consensus pattern (34 bp):
TTTTGTTTTCATTTCGTTATGATAGCATAGAGAA
Found at i:623602 original size:67 final size:68
Alignment explanation
Indices: 623523--623668 Score: 251
Period size: 67 Copynumber: 2.2 Consensus size: 68
623513 GCATTGAGGT
*
623523 TTTTGTTTTCATTTCGTTATGATAGCATAGAGATTTTTGTTTGT-ATTTCGTTATGATAGCATAG
1 TTTTGTTTTCATTTCGTTATGATAGCATAGAGAATTTTGTTT-TCATTTCGTTATGATAGCATAG
623587 AGAA
65 AGAA
*
623591 -TTTGTTTTCATTTTGTTATGATAGCATAGAGAATTTTGTTTTCATTTCGTTATGATAGCATAGA
1 TTTTGTTTTCATTTCGTTATGATAGCATAGAGAATTTTGTTTTCATTTCGTTATGATAGCATAGA
623655 GAA
66 GAA
623658 TTTTGTTTTCA
1 TTTTGTTTTCA
623669 ATATTTTTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
66 1 0.01
67 63 0.85
68 10 0.14
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.50
Consensus pattern (68 bp):
TTTTGTTTTCATTTCGTTATGATAGCATAGAGAATTTTGTTTTCATTTCGTTATGATAGCATAGA
GAA
Found at i:640994 original size:34 final size:34
Alignment explanation
Indices: 640904--640995 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
640894 TTTATCCTCC
* * * *
640904 TCTTATTCTTCTTCTTCCCACTATATCTTTTTCT
1 TCTTATTCTTCTTCTTCACACTGTATATTCTTCT
* *
640938 TCTTATTCTTCTT-TCCCACACTGTTTATTCTTCT
1 TCTTATTCTTCTTCT-TCACACTGTATATTCTTCT
640972 TCTTCA-TCTTCTTCTTCACACTGT
1 TCTT-ATTCTTCTTCTTCACACTGT
640996 GAAATCTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
33 1 0.02
34 45 0.94
35 2 0.04
ACGTcount: A:0.12, C:0.30, G:0.02, T:0.55
Consensus pattern (34 bp):
TCTTATTCTTCTTCTTCACACTGTATATTCTTCT
Found at i:642913 original size:32 final size:32
Alignment explanation
Indices: 642869--642945 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
642859 GTTTGTGTGA
* * * *
642869 TGCATTCGGATAATGCATAGT-AGAGTTAGTTT
1 TGCATTCAGATAATGCATA-TCAGAGTCAATGT
642901 TGCATTCAGATAATGCATATCAGAGTCAATGT
1 TGCATTCAGATAATGCATATCAGAGTCAATGT
*
642933 TGCATTTAGATAA
1 TGCATTCAGATAA
642946 CACACATCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (32 bp):
TGCATTCAGATAATGCATATCAGAGTCAATGT
Found at i:644211 original size:23 final size:23
Alignment explanation
Indices: 644184--644232 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
644174 TGGTGGTTGG
644184 TTTAATGG-ATATTTTAACTTTAT
1 TTTAATGGTATA-TTTAACTTTAT
*
644207 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
644230 TTT
1 TTT
644233 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:648650 original size:11 final size:11
Alignment explanation
Indices: 648636--648663 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
648626 TGAAAAAGTG
648636 AAAAAAAAAGA
1 AAAAAAAAAGA
648647 AAAAAAAAAGA
1 AAAAAAAAAGA
648658 AAAAAA
1 AAAAAA
648664 TGTGTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:649732 original size:40 final size:40
Alignment explanation
Indices: 649678--649799 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
649668 ACCGTAGTGC
649678 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
649718 TACATATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
649758 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
649798 TA
1 TA
649800 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:653609 original size:19 final size:17
Alignment explanation
Indices: 653589--653677 Score: 69
Period size: 17 Copynumber: 5.2 Consensus size: 17
653579 TTTTTTCATC
*
653589 TCTCATTTTT-TTCTCTT
1 TCTC-TTTTTCTTTTCTT
653606 TCTCTTTTTCTTTTCTT
1 TCTCTTTTTCTTTTCTT
*
653623 TCTCATTTTCATTTT-TT
1 TCTCTTTTTC-TTTTCTT
*
653640 T-TCTTCTTCGTTTTCATT
1 TCTCTTTTTC-TTTTC-TT
*
653658 T-TCTTTTTCTATTTTTT
1 TCTCTTTTTCT-TTTCTT
653675 TCT
1 TCT
653678 TCTTCTGTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
16 15 0.25
17 26 0.44
18 18 0.31
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (17 bp):
TCTCTTTTTCTTTTCTT
Done.