Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003198.1 Hibiscus syriacus cultivar Beakdansim tig00006731_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: 627338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:536043 original size:61 final size:61
Alignment explanation
Indices: 535948--536070 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
535938 AAAAAAACTT
535948 TAAATTAATTACTTTGAATAATTGTTTTTTCCCCTTCTATACATGCTGCCATGCGTATCCA
1 TAAATTAATTACTTTGAATAATTGTTTTTTCCCCTTCTATACATGCTGCCATGCGTATCCA
536009 TAAATTAATTACTTTGAATAATTGTTTTTTCCCCTTCTATACATGCTGCCATGCGTATCCA
1 TAAATTAATTACTTTGAATAATTGTTTTTTCCCCTTCTATACATGCTGCCATGCGTATCCA
536070 T
1 T
536071 TTGAGTCGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (61 bp):
TAAATTAATTACTTTGAATAATTGTTTTTTCCCCTTCTATACATGCTGCCATGCGTATCCA
Found at i:537719 original size:24 final size:23
Alignment explanation
Indices: 537692--537739 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
537682 TTTTTGGGTG
537692 AAATGAATTAACTATTTTTCATGA
1 AAAT-AATTAACTATTTTTCATGA
*
537716 AAATACTTAACTATTTTTCATGA
1 AAATAATTAACTATTTTTCATGA
537739 A
1 A
537740 TAGAGATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATAATTAACTATTTTTCATGA
Found at i:550483 original size:24 final size:24
Alignment explanation
Indices: 550470--550606 Score: 168
Period size: 24 Copynumber: 5.7 Consensus size: 24
550460 AAACATAATT
* *
550470 CATGTCAAGTATCATATCAAAATT
1 CATGTCAAGTATCATATCAGAATC
* *
550494 CAGGTCAAGTATCATATCACAATC
1 CATGTCAAGTATCATATCAGAATC
*
550518 CAAGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
550542 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
* *
550566 CATGTCAAGTATCAGATCAGAATT
1 CATGTCAAGTATCATATCAGAATC
* *
550590 CAAGTCGAGTATCATAT
1 CATGTCAAGTATCATAT
550607 AAAATATTCA
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
23 2 0.02
24 96 0.96
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:550594 original size:72 final size:72
Alignment explanation
Indices: 550470--550606 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 72
550460 AAACATAATT
* * *
550470 CATGTCAAGTATCATATCAAAATTCAGGTCAAGTATCATATCACAATCCAAGTCAAGTATCATAT
1 CATGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCACAATCCAAGTCAAGTATCATAT
550535 CAGAATC
66 CAGAATC
* * * * *
550542 CATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAGTCGAGTATCATA
1 CATGTCAAG-TATCAGATCAAAATCCAGGTCAAGTATCAGATCACAATCCAAGTCAAGTATCATA
550606 T
65 T
550607 AAAATATTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 2 0.04
72 54 0.96
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (72 bp):
CATGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCACAATCCAAGTCAAGTATCATAT
CAGAATC
Found at i:554967 original size:2 final size:2
Alignment explanation
Indices: 554960--554988 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
554950 TTTTTAAAAC
554960 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 A
554989 CCCTCATCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:555212 original size:24 final size:24
Alignment explanation
Indices: 555199--555317 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
555189 AAACATAATT
*
555199 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
555223 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
555247 TAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
555271 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
555295 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
555318 TCAAGTCGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:555333 original size:48 final size:47
Alignment explanation
Indices: 555199--555335 Score: 175
Period size: 48 Copynumber: 2.9 Consensus size: 47
555189 AAACATAATT
* * *
555199 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCAGATCAGAATCCAAGTCAA-TATCATATCAGAATC
* * *
555247 TAAGTCAAGTATCAGATCAGAATCCATGTCAGATATCATATCAGAATC
1 CATGTCAAGTATCAGATCAGAATCCAAGTCA-ATATCATATCAGAATC
* *
555295 CATGTCAAGTATCAGATCAGAATTCAAGTCGAAAATCATAT
1 CATGTCAAGTATCAGATCAGAATCCAAGTC-AATATCATAT
555336 AAAATATTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
48 75 0.97
49 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (47 bp):
CATGTCAAGTATCAGATCAGAATCCAAGTCAATATCATATCAGAATC
Found at i:557829 original size:23 final size:23
Alignment explanation
Indices: 557803--557848 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
557793 TCAACGAGTT
* *
557803 GGGTCAACGGGTCGGGTCGGGTC
1 GGGTCAACGGGTCAGATCGGGTC
*
557826 GGGTCAATGGGTCAGATCGGGTC
1 GGGTCAACGGGTCAGATCGGGTC
557849 AATGGGTCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.20
Consensus pattern (23 bp):
GGGTCAACGGGTCAGATCGGGTC
Found at i:557837 original size:18 final size:18
Alignment explanation
Indices: 557816--557865 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
557806 TCAACGGGTC
557816 GGGTCGGGTCGGGTCAAT
1 GGGTCGGGTCGGGTCAAT
* *
557834 GGGTCAGATCGGGTCAAT
1 GGGTCGGGTCGGGTCAAT
557852 GGGTCGGGTCGGGT
1 GGGTCGGGTCGGGT
557866 TGTAACCGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.12, C:0.16, G:0.50, T:0.22
Consensus pattern (18 bp):
GGGTCGGGTCGGGTCAAT
Found at i:559316 original size:31 final size:31
Alignment explanation
Indices: 559281--559351 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
559271 GTGACCCTTT
* * **
559281 GGTAGGCTCCGA-AGCCTCGTGATCTTTCTTG
1 GGTAGGC-CCGACAGCCCCGAGATCACTCTTG
*
559312 GGTAGGCCCTACAGCCCCGAGATCACTCTTG
1 GGTAGGCCCGACAGCCCCGAGATCACTCTTG
559343 GGTAGGCCC
1 GGTAGGCCC
559352 TATGGCTCCG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (31 bp):
GGTAGGCCCGACAGCCCCGAGATCACTCTTG
Found at i:562747 original size:159 final size:160
Alignment explanation
Indices: 562438--562749 Score: 547
Period size: 159 Copynumber: 2.0 Consensus size: 160
562428 CAGGCTCTAA
562438 TTAACCTAATTAATTATGTTAAATGAATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAAAG
1 TTAACCTAATTAATTATGTTAAATGAATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAAAG
* * * *
562503 TCTAAGGGTTAGGGCTTTAATTATTAATCCTAATTAATTATCCTTTTTATTGAATCGAATAATCG
66 TCTAAGGGTTAAGGCTCTAATTATTAACCCTAATTAATTATCCTTTTTATTGAATCAAATAATCG
562568 ATGAAAACCCTCGGGCATAAAGGCGATGGC
131 ATGAAAACCCTCGGGCATAAAGGCGATGGC
562598 TTAACCTAATTAATTATGTTAAAT-ACATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAAA
1 TTAACCTAATTAATTATGTTAAATGA-ATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAAA
*
562662 GTCTAA-GGTTAAGGCTCTAATTATTAACCCTAATTAATTCTCCTTTTTATTGAATCAAATAATC
65 GTCTAAGGGTTAAGGCTCTAATTATTAACCCTAATTAATTATCCTTTTTATTGAATCAAATAATC
*
562726 GATGAAAACCCTTGGGCATAAAGG
130 GATGAAAACCCTCGGGCATAAAGG
562750 TGAGGGCCAA
Statistics
Matches: 145, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
159 77 0.53
160 68 0.47
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (160 bp):
TTAACCTAATTAATTATGTTAAATGAATATCTAATTAAAAAGTTCAAGGACTAAAGTGTAAAAAG
TCTAAGGGTTAAGGCTCTAATTATTAACCCTAATTAATTATCCTTTTTATTGAATCAAATAATCG
ATGAAAACCCTCGGGCATAAAGGCGATGGC
Found at i:564822 original size:14 final size:15
Alignment explanation
Indices: 564803--564831 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
564793 ATTTTTGGTA
564803 ATAATAAT-AATATT
1 ATAATAATAAATATT
564817 ATAATAATAAATATT
1 ATAATAATAAATATT
564832 TTTGGGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAATAAATATT
Found at i:565192 original size:77 final size:78
Alignment explanation
Indices: 565050--565196 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 78
565040 AAAGGTGACA
* *
565050 CTGATCCAACTCCTTATGTGATGGATAAGCCAAGGTTTGAACAAGTTCTTCTCATTATGAACTTC
1 CTGATCCAACTCCTTATGTGATGGATAAGCAAAGGTTTGAACAAGCTCTTCTCATTATGAACTTC
565115 TTCTCTGGAAATG
66 TTCTCTGGAAATG
* * * **
565128 CTGATTCATCTCCTTCTGTGATGGATGAA-CAAAGG-TTGAACAAGCTCTTCTTGTTATGAACTT
1 CTGATCCAACTCCTTATGTGATGGAT-AAGCAAAGGTTTGAACAAGCTCTTCTCATTATGAACTT
565191 CTTCTC
65 CTTCTC
565197 CCTCATCGGA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 31 0.51
78 28 0.46
79 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (78 bp):
CTGATCCAACTCCTTATGTGATGGATAAGCAAAGGTTTGAACAAGCTCTTCTCATTATGAACTTC
TTCTCTGGAAATG
Found at i:565224 original size:116 final size:116
Alignment explanation
Indices: 565092--565338 Score: 277
Period size: 116 Copynumber: 2.1 Consensus size: 116
565082 AGGTTTGAAC
* * * *
565092 AAGTTCTTCTCATTATGAACTTCTTCT-CTGGAAATGCTGATTCATCTCCTTCTGTGATGG-AT-
1 AAGTTCTTCTCATTATGAAC-TC-TCTAATAGAAATGCTGATTCACCTCCTTCTATGATGGAATC
* ** *
565154 GAACAAAGGTTGAACAAGCTCTTCTTGTTATGAACTTCTTCTCCCTCATCGGA-
64 GAACAAAGGTT-AAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATCAGAT
* * ** *
565207 AATGTTCTTCTCATTATGAACTCTCTAATATAAATGTTGATTTGCCTTCTTCTATGATGGAATCG
1 AA-GTTCTTCTCATTATGAACTCTCTAATAGAAATGCTGATTCACCTCCTTCTATGATGGAATCG
* * *
565272 AACCAAGGTTAAAAAGTTTTTCTCATTATGAACTTCTTCTCCCTCATCAGAT
65 AACAAAGGTTAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATCAGAT
*
565324 GAGTTCTTCTCATTA
1 AAGTTCTTCTCATTA
565339 CAAACCCTTC
Statistics
Matches: 110, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
114 3 0.03
115 28 0.25
116 68 0.62
117 11 0.10
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (116 bp):
AAGTTCTTCTCATTATGAACTCTCTAATAGAAATGCTGATTCACCTCCTTCTATGATGGAATCGA
ACAAAGGTTAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCATCAGAT
Found at i:565798 original size:283 final size:282
Alignment explanation
Indices: 565259--565835 Score: 741
Period size: 283 Copynumber: 2.0 Consensus size: 282
565249 TGCCTTCTTC
*
565259 TATGATGGAATCGAACCAAGGTTAAAAAGTTTTTCTCATTATGAACTTCTTCTCCCTCATCAGAT
1 TATGATGGAATCGAACCAAGGTTAAAAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGAT
* *
565324 GAGTTCTTCTCATTACAAACCCTTCCATTGGAAATGTTGATCCATCCCCTTATGTGATATAATCG
66 GAGTTCTTCTCATTACAAACCCTTCCATTGGAAATGTTGATCCATCCCCTTATATGATAGAATCG
* * *
565389 AGTGAAATGTTGAACAAGTTATTCTAATTAGGAACTTCTTTAGTGGAAGTGTTGATCAACATCCT
131 AATGAAATGTTGAACAAGTTATTCTAATTAGGAACTTATTTAGTGGAAATGTTGATCAACATCCT
* ** *
565454 TCTGTGATGGATTTGAACAAAGTGATGATGCTGATCTAACTCCTTATACGATGAATGAGCCAAAT
196 TATGTGATGGATTCAAACAAAGTGATGATGCTGATCTAACTCCTTATACGATGAATGAGCCAAAG
565519 TCGATGTTGTTCCAACTCCTTA
261 TCGATGTTGTTCCAACTCCTTA
* * * * *
565541 TGTGATGGAATTGAGCTAAGGTTGAACAAA-TTCTTCTCATTATGAACTTCTTCTCCCTCATCGG
1 TATGATGGAATCGAACCAAGGTT-AA-AAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAG
* * ** * * *
565605 ATGAGTTCTTCTCATTGCAAAGCCTTTTATTTGAAATGTTGATCCA-CCTCCTTCTATGATGGAA
64 ATGAGTTCTTCTCATTACAAACCCTTCCATTGGAAATGTTGATCCATCC-CCTTATATGATAGAA
* * * * *
565669 TCGAATGAAATGTTGAACATGTTATTCTCATTAGGAACTTATTTATTGGAAAAT-TTTATCCAC-
128 TCGAATGAAATGTTGAACAAGTTATTCTAATTAGGAACTTATTTAGTGG-AAATGTTGATCAACA
* * * *
565732 TCCCTTATGTGATGGATTCAAACAAAGTGATGATGTTGAT-TCAGCTCCTTATGCGATGTATGAG
192 T-CCTTATGTGATGGATTCAAACAAAGTGATGATGCTGATCT-AACTCCTTATACGATGAATGAG
* * * *
565796 CCAAGGTCGGTGTTGTTCCACCTCTTTA
255 CCAAAGTCGATGTTGTTCCAACTCCTTA
*
565824 TATGATAGAATC
1 TATGATGGAATC
565836 AAGCAAATGT
Statistics
Matches: 251, Mismatches: 38, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
282 23 0.09
283 222 0.88
284 6 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (282 bp):
TATGATGGAATCGAACCAAGGTTAAAAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGAT
GAGTTCTTCTCATTACAAACCCTTCCATTGGAAATGTTGATCCATCCCCTTATATGATAGAATCG
AATGAAATGTTGAACAAGTTATTCTAATTAGGAACTTATTTAGTGGAAATGTTGATCAACATCCT
TATGTGATGGATTCAAACAAAGTGATGATGCTGATCTAACTCCTTATACGATGAATGAGCCAAAG
TCGATGTTGTTCCAACTCCTTA
Found at i:566458 original size:18 final size:18
Alignment explanation
Indices: 566432--566470 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
566422 TTGGGAATTG
*
566432 TTGCAAGAGCAGTCTTTA
1 TTGCAAGAGCAGTCTTCA
* *
566450 TTGCTAGAGTAGTCTTCA
1 TTGCAAGAGCAGTCTTCA
566468 TTG
1 TTG
566471 TTTTCTAGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (18 bp):
TTGCAAGAGCAGTCTTCA
Found at i:567350 original size:107 final size:105
Alignment explanation
Indices: 567223--567471 Score: 315
Period size: 107 Copynumber: 2.3 Consensus size: 105
567213 TGAAAATTTG
* * *
567223 GCTTAGCTTCTTTCAAAATCCATTTGTAAACATCAAGAAAC-CCTAAAAATCAAGCTTTGCTTTT
1 GCTTATCTTCTTT-AAAATCCATTTGTAAACATCAAGAAACTCCTAAAAATCAAGCTTAGCTTCT
* * *
567287 TTCAAAATTCATTTGAAGACATCAAAAAACACATGAATATCAT
65 TTAAAAATTCATTTGAAAACATCAAAAAAC-CATGAA-ATCAA
** *
567330 G-TTGATCTTCTTTGAAAATCCATTTGTAAACATCAAGAAACTCCTGCAAATCAGGCTTAGCTTC
1 GCTT-ATCTTCTTT-AAAATCCATTTGTAAACATCAAGAAACTCCTAAAAATCAAGCTTAGCTTC
*
567394 TTTAAAAATTCATTTGAAAACATCAAGAAACCATGAAATCAA
64 TTTAAAAATTCATTTGAAAACATCAAAAAACCATGAAATCAA
567436 GCTTATCTTCTTTATAAATCTCATTTG-ATAACATCA
1 GCTTATCTTCTTTA-AAATC-CATTTGTA-AACATCA
567472 TATTGTTTGG
Statistics
Matches: 125, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
105 1 0.01
106 22 0.18
107 57 0.46
108 45 0.36
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (105 bp):
GCTTATCTTCTTTAAAATCCATTTGTAAACATCAAGAAACTCCTAAAAATCAAGCTTAGCTTCTT
TAAAAATTCATTTGAAAACATCAAAAAACCATGAAATCAA
Found at i:567354 original size:54 final size:50
Alignment explanation
Indices: 567223--567471 Score: 223
Period size: 54 Copynumber: 4.7 Consensus size: 50
567213 TGAAAATTTG
* * *
567223 GCTTAGCTTCTTTCAAAATCCATTTGTAAACATCAAGAAACCCTAAAAATCAA
1 GCTTATCTTCTTT-AAAATCCATTTG-AAACATCAAGAAACCAT-GAAATCAA
* * * *
567276 GCTT-TGCTTTTTTCAAAATTCATTTGAAGACATCAAAAAACACATGAATATCAT
1 GCTTAT-CTTCTTT-AAAATCCATTTGAA-ACATCAAGAAAC-CATGAA-ATCAA
* *
567330 G-TTGATCTTCTTTGAAAATCCATTTGTAAACATCAAGAAACTCCTGCAAATCAG
1 GCTT-ATCTTCTTT-AAAATCCATTTG-AAACATCAAGAAAC-CATG-AAATCAA
* *
567384 GCTTAGCTTCTTTAAAAATTCATTTGAAAACATCAAGAAACCATGAAATCAA
1 GCTTATCTTCTTT-AAAATCCATTTG-AAACATCAAGAAACCATGAAATCAA
567436 GCTTATCTTCTTTATAAATCTCATTTGATAACATCA
1 GCTTATCTTCTTTA-AAATC-CATTTGA-AACATCA
567472 TATTGTTTGG
Statistics
Matches: 162, Mismatches: 22, Indels: 24
0.78 0.11 0.12
Matches are distributed among these distances:
51 1 0.01
52 25 0.15
53 53 0.33
54 76 0.47
55 7 0.04
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (50 bp):
GCTTATCTTCTTTAAAATCCATTTGAAACATCAAGAAACCATGAAATCAA
Found at i:569597 original size:20 final size:20
Alignment explanation
Indices: 569574--569650 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
569564 TTTTTGCTTT
569574 CTTT-TCTCTCATTTTTTTTA
1 CTTTATCTCTC-TTTTTTTTA
*
569594 CTTTATTTCTCTTTTTTTTA
1 CTTTATCTCTCTTTTTTTTA
* * *
569614 -TGTT-TTTTTCTTCTTTTTA
1 CT-TTATCTCTCTTTTTTTTA
*
569633 CTATATCTTCTCTTTTTT
1 CTTTATC-TCTCTTTTTT
569651 GTCTTTGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
19 15 0.33
20 17 0.38
21 13 0.29
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.73
Consensus pattern (20 bp):
CTTTATCTCTCTTTTTTTTA
Found at i:569604 original size:21 final size:20
Alignment explanation
Indices: 569580--569650 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 20
569570 CTTTCTTTTC
569580 TCTCATTTTTTTTACTTTATT
1 TCTC-TTTTTTTTACTTTATT
569601 TCTCTTTTTTTTA-TGTT-TT
1 TCTCTTTTTTTTACT-TTATT
* * *
569620 TTTCTTCTTTTTACTATATCT
1 TCTCTTTTTTTTACTTTAT-T
569641 TCTCTTTTTT
1 TCTCTTTTTT
569651 GTCTTTGTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 15 0.37
20 13 0.32
21 13 0.32
ACGTcount: A:0.10, C:0.15, G:0.01, T:0.73
Consensus pattern (20 bp):
TCTCTTTTTTTTACTTTATT
Found at i:569610 original size:19 final size:19
Alignment explanation
Indices: 569586--569650 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
569576 TTTCTCTCAT
569586 TTTTTTTACTTTATTTCTC
1 TTTTTTTACTTTATTTCTC
*
569605 TTTTTTTTA-TGTT-TTTTTC
1 -TTTTTTTACT-TTATTTCTC
*
569624 TTCTTTTTACTATATCTTCTC
1 TT-TTTTTACTTTAT-TTCTC
569645 TTTTTT
1 TTTTTT
569651 GTCTTTGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
18 2 0.05
19 13 0.35
20 16 0.43
21 6 0.16
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTTTACTTTATTTCTC
Found at i:572537 original size:204 final size:204
Alignment explanation
Indices: 572050--572663 Score: 1122
Period size: 204 Copynumber: 3.0 Consensus size: 204
572040 AATCATTAAT
572050 CAGAGAAAAAATCTTTTTTTCTTTCAAAATAACATAATTAACTGTAAATTAAATAAATTCAAACT
1 CAGAGAAAAAATCTTTTTTTCTTTCAAAATAACATAATTAACTGTAAATTAAATAAATTCAAACT
*
572115 CAAAATTTCTAAATTCCAAATGTAGGGTAATCAAATCGTGGCTTGACTCTCGATTTGTTTTAGAA
66 CAAAATTTCTAAATTCCAAATGTAGGGTAATCAACTCGTGGCTTGACTCTCGATTTGTTTTAGAA
* * *
572180 AACAAATTTTTCCCAGCAAAGTCACTAAGATGTCGTCATTATTTTTCGCCCATGTGGGTCAAAAA
131 AACAAATTTTCCCCAGCAGAGTCACTAAGATGTCGTCATTGTTTTTCGCCCATGTGGGTCAAAAA
572245 CTAGTATGA
196 CTAGTATGA
*
572254 CAGAGAAAAAATATTTTTTTTCTTTCAAAATAACATAATTAACTGTAAATTAAATAAATTCAAAC
1 CAGAGAAAAAAT-CTTTTTTTCTTTCAAAATAACATAATTAACTGTAAATTAAATAAATTCAAAC
572319 TCAAAATTTCTAAATTCCAAATGTAGGGTAATCAACTCGTGGCTTGACTCTCGATTTGTTTTAGA
65 TCAAAATTTCTAAATTCCAAATGTAGGGTAATCAACTCGTGGCTTGACTCTCGATTTGTTTTAGA
** *
572384 AAACAAATTTTCCCCATTAGAGTCACTAAGATGTCGTCATTGTCTTTCGCCCATGTGGGTCAAAA
130 AAACAAATTTTCCCCAGCAGAGTCACTAAGATGTCGTCATTGTTTTTCGCCCATGTGGGTCAAAA
572449 ACTAGTATGA
195 ACTAGTATGA
572459 CAGAGAAAAAATCTTTTTTTCTTTCAAAATAACATAATTAACTGTAAATTAAATAAATTCAAACT
1 CAGAGAAAAAATCTTTTTTTCTTTCAAAATAACATAATTAACTGTAAATTAAATAAATTCAAACT
*
572524 CAAAATTTCTAAATTCCAAATGTATGGTAATCAACTCGTGGCTTGACTCTCGATTTGTTTTAGAA
66 CAAAATTTCTAAATTCCAAATGTAGGGTAATCAACTCGTGGCTTGACTCTCGATTTGTTTTAGAA
572589 AA-AATATTTTCCCCAGCAGAGTCACTAAGATGTCGTCATTGTTTTTCGCCCATGTGGGTCAAAA
131 AACAA-ATTTTCCCCAGCAGAGTCACTAAGATGTCGTCATTGTTTTTCGCCCATGTGGGTCAAAA
572653 ACTAGTATGA
195 ACTAGTATGA
572663 C
1 C
572664 TTGGGTTTTT
Statistics
Matches: 395, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
203 2 0.01
204 197 0.50
205 196 0.50
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (204 bp):
CAGAGAAAAAATCTTTTTTTCTTTCAAAATAACATAATTAACTGTAAATTAAATAAATTCAAACT
CAAAATTTCTAAATTCCAAATGTAGGGTAATCAACTCGTGGCTTGACTCTCGATTTGTTTTAGAA
AACAAATTTTCCCCAGCAGAGTCACTAAGATGTCGTCATTGTTTTTCGCCCATGTGGGTCAAAAA
CTAGTATGA
Found at i:580787 original size:15 final size:15
Alignment explanation
Indices: 580759--580816 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
580749 AAGCTTTCTC
*
580759 CACCATCTCTCTGCTA
1 CACC-TCTCCCTGCTA
580775 CACCTCTCCCTGCTA
1 CACCTCTCCCTGCTA
*
580790 CACCTCTCCCTGTTA
1 CACCTCTCCCTGCTA
580805 CACCTCTCCCTG
1 CACCTCTCCCTG
580817 GTCTGCCCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 36 0.90
16 4 0.10
ACGTcount: A:0.14, C:0.50, G:0.07, T:0.29
Consensus pattern (15 bp):
CACCTCTCCCTGCTA
Found at i:580979 original size:87 final size:87
Alignment explanation
Indices: 580833--581008 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
580823 CCACTATTGA
* * **
580833 CACATATCTACGTGGGCCTAGATGACTCTATATTGGTTGGCTCACCACCCGCAAGATCTACAGTT
1 CACATATCTACGTAGGCCTAGATGACTCTACATTGGTTGGCTCACCACCCGCAAGATCTACAACT
*
580898 GTGGCCTCTGAAAGTCTCTGGG
66 GTGGCCTCTGAAAATCTCTGGG
* * *
580920 CACATCTCTACGTAGGCCTATATGACTCTACGTTGGTTGGCTCACCACCCGCAAGATCTACAACT
1 CACATATCTACGTAGGCCTAGATGACTCTACATTGGTTGGCTCACCACCCGCAAGATCTACAACT
580985 GTGGCCTCTGAAAATCTCTGGG
66 GTGGCCTCTGAAAATCTCTGGG
581007 CA
1 CA
581009 TTACCTTAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (87 bp):
CACATATCTACGTAGGCCTAGATGACTCTACATTGGTTGGCTCACCACCCGCAAGATCTACAACT
GTGGCCTCTGAAAATCTCTGGG
Found at i:587647 original size:14 final size:14
Alignment explanation
Indices: 587628--587662 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
587618 ATCTGAACCA
587628 AGTCAACTCGCCTG
1 AGTCAACTCGCCTG
*
587642 AGTCAACTCGTCTG
1 AGTCAACTCGCCTG
587656 AGTCAAC
1 AGTCAAC
587663 CCGTTGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (14 bp):
AGTCAACTCGCCTG
Found at i:589857 original size:32 final size:32
Alignment explanation
Indices: 589816--589888 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
589806 TAAGATGACC
* * *
589816 CTTGGGTAGGCTTCGAGGCCTCGAGAAACTTT
1 CTTGGGTAGGATCCGAGGCCCCGAGAAACTTT
589848 CTTGGGTAGGATCCGAGGCCCCGAGAAACTTT
1 CTTGGGTAGGATCCGAGGCCCCGAGAAACTTT
589880 CTTGGGTAG
1 CTTGGGTAG
589889 ATCATGGGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.26
Consensus pattern (32 bp):
CTTGGGTAGGATCCGAGGCCCCGAGAAACTTT
Found at i:593186 original size:44 final size:44
Alignment explanation
Indices: 593136--593437 Score: 442
Period size: 44 Copynumber: 6.9 Consensus size: 44
593126 GTTTGACACA
*
593136 TTTCTGCCAATAATGCACCGTTATGCATTTTTATTTATGGCACC
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACC
* *
593180 TTTCTGCCAATAATGCACCATTATGTATTTTCATTTATGGCACC
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACC
* *
593224 TTTCTGCCAATAATGCACCATTATGCATTTTCATTTATGGCACA
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACC
* * * * * *
593268 TTTCTGCCAATAATACATCGTTATTCAATTTCATTTATGACATC
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACC
* * *
593312 TTTCTGTCAATAATGCACCGTTATGCATTTTCATTTATGGAACT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACC
* *
593356 TTTCTGCCAATAATGCACAGTTATGCATTTTCATTTATGGCACA
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACC
* *
593400 TGTATGCCAATAATGCACCGTTATGCATTTTCATTTAT
1 TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
593438 TTTGGTAACA
Statistics
Matches: 229, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 229 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
TTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACC
Found at i:593266 original size:25 final size:25
Alignment explanation
Indices: 593194--593266 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 25
593184 TGCCAATAAT
*
593194 GCACCATTATGTATTTTCATTTATG
1 GCACCATTATGCATTTTCATTTATG
** * *
593219 GCACC-TT-T-C--TGCCAATAAT-
1 GCACCATTATGCATTTTCATTTATG
593238 GCACCATTATGCATTTTCATTTATG
1 GCACCATTATGCATTTTCATTTATG
593263 GCAC
1 GCAC
593267 ATTTCTGCCA
Statistics
Matches: 33, Mismatches: 9, Indels: 12
0.61 0.17 0.22
Matches are distributed among these distances:
19 5 0.15
20 8 0.24
21 1 0.03
22 1 0.03
23 1 0.03
24 8 0.24
25 9 0.27
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (25 bp):
GCACCATTATGCATTTTCATTTATG
Found at i:599848 original size:44 final size:43
Alignment explanation
Indices: 599792--600048 Score: 334
Period size: 44 Copynumber: 5.9 Consensus size: 43
599782 AGTGGCACCA
* * *
599792 TTCTGTCAATAATCCACCGTTATGCATTTTTATTTATGGCATCT
1 TTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA-CT
* * *
599836 TTATGCCAATAATGCACCGTTATGCATTTTCATTTACGACACCT
1 TTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA-CT
* * * *
599880 TTCGGCCAATAATGCACCATTATGCATTTTCATTTACGACACAT
1 TTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCAC-T
* *
599924 TTCTGCCCATAATGCACCGTTATGCATTTTCATTTATAGCACAT
1 TTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCAC-T
*
599968 TTCTGCCAATAATGCACCATTATGCATTTTCATTTATGGCATCT
1 TTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCA-CT
* *
600012 TTCTACCAATAATACACCGTTATGCATTTTCATTTAT
1 TTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
600049 TTCAGTAACA
Statistics
Matches: 189, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
43 1 0.01
44 187 0.99
45 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (43 bp):
TTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCACT
Found at i:600035 original size:132 final size:132
Alignment explanation
Indices: 599800--600047 Score: 372
Period size: 132 Copynumber: 1.9 Consensus size: 132
599790 CATTCTGTCA
* * *
599800 ATAATCCACCGTTATGCATTTTTATTTATGGCATCTTTATGCCAATAATGCACCGTTATGCATTT
1 ATAATCCACCGTTATGCATTTTCATTTATAGCATCTTTATGCCAATAATGCACCATTATGCATTT
* *
599865 TCATTTACGACACCTTTCGGCCAATAATGCACCATTATGCATTTTCATTTACGACACATTTCTGC
66 TCATTTACGACACCTTTCGACCAATAATACACCATTATGCATTTTCATTTACGACACATTTCTGC
599930 CC
131 CC
* *
599932 ATAATGCACCGTTATGCATTTTCATTTATAGCA-CATTTCTGCCAATAATGCACCATTATGCATT
1 ATAATCCACCGTTATGCATTTTCATTTATAGCATC-TTTATGCCAATAATGCACCATTATGCATT
* * * * *
599996 TTCATTTATGGCATCTTTCTACCAATAATACACCGTTATGCATTTTCATTTA
65 TTCATTTACGACACCTTTCGACCAATAATACACCATTATGCATTTTCATTTA
600048 TTTCAGTAAC
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
131 1 0.01
132 102 0.99
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.39
Consensus pattern (132 bp):
ATAATCCACCGTTATGCATTTTCATTTATAGCATCTTTATGCCAATAATGCACCATTATGCATTT
TCATTTACGACACCTTTCGACCAATAATACACCATTATGCATTTTCATTTACGACACATTTCTGC
CC
Found at i:601413 original size:13 final size:13
Alignment explanation
Indices: 601395--601420 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
601385 TTTAAATCCT
601395 TTCAAAATAGTCA
1 TTCAAAATAGTCA
601408 TTCAAAATAGTCA
1 TTCAAAATAGTCA
601421 CTGACCTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTCAAAATAGTCA
Found at i:604410 original size:490 final size:489
Alignment explanation
Indices: 603472--604459 Score: 1642
Period size: 490 Copynumber: 2.0 Consensus size: 489
603462 TCAAGAACCG
* *
603472 TTAGAAAGATAAAAGACAGACAGTCATATCTCCAAAAGACATGTCGACCAAATAATATCAGGATC
1 TTAGAAAGATAAAAGACAGACAATCATATCTCCAAAAGACATGTCGACAAAATAATATCAGGATC
* * *
603537 CTATTCAAAAAGTCTTCGCAAGTCTGCTACTATTATGGTCTTGTTTTCCAAGGTTTGGTTGTATG
66 CTATTCAAAAAGTCTTCACAAGTCTGCTACTATTATGGTCTTGTTTTCCAAGGCTTGGTCGTATG
* *
603602 GATCAATTGAAAAACGTTAGTCCATCTTCCTTTGTTGTGAGCCTTATGATGAATATATCATAAAT
131 GATCAATTG-AAAACGTTAGTCAATATTCCTTTGTTGTGAGCCTTATGATGAATATATCATAAAT
*
603667 GGTGCTATCAAAAAATGGAAACTTAGGTCTTTGATTGTTTCTGAATGACTCCATAAACATTCATT
195 GGTGCTATCAAAAAATGGAAACTTAGGTCTTTGATTATTTCTGAATGACTCCATAAACATTCATT
**
603732 TAATTTATAACTTTGTTAGACAAACCAAATTAAAAAAAATAATCAATATTTAACCAAAAATCAAG
260 TAATTTATAACTTCATTAGACAAACCAAATTAAAAAAAATAATCAATATTTAACCAAAAATCAAG
* *
603797 GTCAAAGTTCAAACCATGGGATTAAATTTTTAATCAAAATTGAATTGAATATATCAATGCCAATA
325 GTCAAAGTTCAAACCAGGGGATTAAATTTTTAATCAAAATTGAATCGAATATATCAATGCCAATA
*
603862 AATATTCTATAATCCATAATAGTCAAAAAACAAAACTGAATTTTCTAATCACGTCATGATTTTTG
390 AATATTCTATAATCCATAATAGTCAAAAAACAAAACTGAATTTTCTAATCACGTCATGATTTTCG
603927 AAGTAATTCGTAATAAGGTTGTCTAAATGACTTTA
455 AAGTAATTCGTAATAAGGTTGTCTAAATGACTTTA
* * *
603962 TTAGAAAGATAAGAGATAGACAATCATATCTCCAAAAGACATGTCGACAAAATATTATTATTAGG
1 TTAGAAAGATAAAAGACAGACAATCATATCTCCAAAAGACATGTCGACAAAATA--A-TATCAGG
* *
604027 ATCCTATTCAAAAAGTCTTCATAAGTCTGCTACTATTCTGGTCTTGTTTTCCAAGGCTTGGTCGT
63 ATCCTATTCAAAAAGTCTTCACAAGTCTGCTACTATTATGGTCTTGTTTTCCAAGGCTTGGTCGT
* *
604092 GTGGATCAATTG-AAACTGTTAGTCAATATTCCTTT-TATGTGAGCCTTGTGATGAATATATCAT
128 ATGGATCAATTGAAAAC-GTTAGTCAATATTCCTTTGT-TGTGAGCCTTATGATGAATATATCAT
* *
604155 AAATGGTGCTATCAAAAATTGGAAACTTAGGTCTTTGATTATTTCTGAATGATTCCATAAACATT
191 AAATGGTGCTATCAAAAAATGGAAACTTAGGTCTTTGATTATTTCTGAATGACTCCATAAACATT
* *
604220 CATTTAATTTATAACTTCATTAGACAAACCGAATT-TAAAAAATAATCAATATTTAACCAAAAAT
256 CATTTAATTTATAACTTCATTAGACAAACCAAATTAAAAAAAATAATCAATATTTAACCAAAAAT
* *
604284 CAAGGTCAAAGTTCAAACTAGGGGATTAATTTTTTAATC-AAATTGAATCGAATATATCAATGCC
321 CAAGGTCAAAGTTCAAACCAGGGGATTAAATTTTTAATCAAAATTGAATCGAATATATCAATGCC
* *
604348 AATAAATATTCTATAATTCATAATAGTCAAAAACCAAAACTGAATTTTCTAATCACGTCATGATT
386 AATAAATATTCTATAATCCATAATAGTCAAAAAACAAAACTGAATTTTCTAATCACGTCATGATT
604413 TTCGAAGTAATTCGTAATAAGGTTGTCTAAATGACTTTA
451 TTCGAAGTAATTCGTAATAAGGTTGTCTAAATGACTTTA
604452 TTAGAAAG
1 TTAGAAAG
604460 CGAAAACTTA
Statistics
Matches: 465, Mismatches: 28, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
490 183 0.39
491 69 0.15
492 136 0.29
493 77 0.17
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (489 bp):
TTAGAAAGATAAAAGACAGACAATCATATCTCCAAAAGACATGTCGACAAAATAATATCAGGATC
CTATTCAAAAAGTCTTCACAAGTCTGCTACTATTATGGTCTTGTTTTCCAAGGCTTGGTCGTATG
GATCAATTGAAAACGTTAGTCAATATTCCTTTGTTGTGAGCCTTATGATGAATATATCATAAATG
GTGCTATCAAAAAATGGAAACTTAGGTCTTTGATTATTTCTGAATGACTCCATAAACATTCATTT
AATTTATAACTTCATTAGACAAACCAAATTAAAAAAAATAATCAATATTTAACCAAAAATCAAGG
TCAAAGTTCAAACCAGGGGATTAAATTTTTAATCAAAATTGAATCGAATATATCAATGCCAATAA
ATATTCTATAATCCATAATAGTCAAAAAACAAAACTGAATTTTCTAATCACGTCATGATTTTCGA
AGTAATTCGTAATAAGGTTGTCTAAATGACTTTA
Found at i:610123 original size:8 final size:8
Alignment explanation
Indices: 610110--610141 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
610100 TTGGATTCTA
610110 AAATTTTT
1 AAATTTTT
610118 AAATTTTT
1 AAATTTTT
610126 AAATTTTT
1 AAATTTTT
610134 AAATTTTT
1 AAATTTTT
610142 TTGTATGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
AAATTTTT
Found at i:612195 original size:33 final size:34
Alignment explanation
Indices: 612137--612221 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 34
612127 GATTATTGGT
* * *
612137 TTAC-AAAATGTAAGATTATCTTCAGAAAT-ACA
1 TTACTAAAACGTAACATTATCATCAGAAATAACA
*
612169 TTACTAAAACGTAATATTATCATCAGAAATAACA
1 TTACTAAAACGTAACATTATCATCAGAAATAACA
* *
612203 TTACTGAAACATAACATTA
1 TTACTAAAACGTAACATTA
612222 CTATGGAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 4 0.09
33 22 0.49
34 19 0.42
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (34 bp):
TTACTAAAACGTAACATTATCATCAGAAATAACA
Found at i:612410 original size:23 final size:20
Alignment explanation
Indices: 612373--612416 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 20
612363 TTTTAAAAGT
612373 TAAAATTTAATATTAAATTA
1 TAAAATTTAATATTAAATTA
*
612393 TAAATATTTCAATCATTATATTA
1 TAAA-ATTT-AAT-ATTAAATTA
612416 T
1 T
612417 CTTACTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 4 0.20
22 3 0.15
23 9 0.45
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATTTAATATTAAATTA
Found at i:614437 original size:21 final size:20
Alignment explanation
Indices: 614401--614441 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
614391 TTAATTATAT
* *
614401 TAAATTTATATTTAATATTAA
1 TAAATTTAAATATAAT-TTAA
614422 TAAATTTAAATATAATTTAA
1 TAAATTTAAATATAATTTAA
614442 ATTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATTTAAATATAATTTAA
Found at i:616524 original size:13 final size:13
Alignment explanation
Indices: 616508--616533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
616498 TTATACACAT
616508 ATACACTTTGAAA
1 ATACACTTTGAAA
616521 ATACACTTTGAAA
1 ATACACTTTGAAA
616534 CACTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
ATACACTTTGAAA
Found at i:618281 original size:17 final size:17
Alignment explanation
Indices: 618259--618344 Score: 93
Period size: 18 Copynumber: 4.9 Consensus size: 17
618249 GAAAATCCTT
*
618259 TGATAACTGTAAATATC
1 TGATAACTATAAATATC
618276 TGATAACT-TAAAATCATC
1 TGATAACTAT-AAAT-ATC
*
618294 TGATAATTATAAATATC
1 TGATAACTATAAATATC
** *
618311 TGATAACGGTGAAATGTC
1 TGATAACTAT-AAATATC
618329 TGATAACTATAAATAT
1 TGATAACTATAAATAT
618345 TTAGAATTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.02
17 27 0.47
18 28 0.49
19 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (17 bp):
TGATAACTATAAATATC
Found at i:618298 original size:35 final size:36
Alignment explanation
Indices: 618250--618344 Score: 113
Period size: 35 Copynumber: 2.7 Consensus size: 36
618240 TTGGTAATTG
* * * *
618250 AAAATCCTTTGATAACTGTAAATATCTGATAAC-TT
1 AAAATCATCTGATAACTATAAATATCTGATAACGGT
*
618285 AAAATCATCTGATAATTATAAATATCTGATAACGGT
1 AAAATCATCTGATAACTATAAATATCTGATAACGGT
* *
618321 GAAAT-GTCTGATAACTATAAATAT
1 AAAATCATCTGATAACTATAAATAT
618345 TTAGAATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 46 0.90
36 5 0.10
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35
Consensus pattern (36 bp):
AAAATCATCTGATAACTATAAATATCTGATAACGGT
Found at i:623979 original size:21 final size:22
Alignment explanation
Indices: 623955--623995 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
623945 AATTAAGAAG
*
623955 TTTGTTTAT-GCTTAATATTAT
1 TTTGTTCATCGCTTAATATTAT
*
623976 TTTGTTCATCGTTTAATATT
1 TTTGTTCATCGCTTAATATT
623996 TTACCTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.22, C:0.07, G:0.10, T:0.61
Consensus pattern (22 bp):
TTTGTTCATCGCTTAATATTAT
Done.