Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007964.1 Hibiscus syriacus cultivar Beakdansim tig00110393_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: 1737572
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 6
Found at i:5258 original size:36 final size:36
Alignment explanation
Indices: 5209--5485 Score: 491
Period size: 36 Copynumber: 7.7 Consensus size: 36
5199 CAAAAGTTTG
* * *
5209 TTCCGATTCAAGTCAAACGGAGGGAAGCATCTGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
* *
5245 TTCCGATTTAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
* *
5281 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGTAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
5317 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
5353 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
5389 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
5425 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
5461 TTCCGATTCAAGTCGAACGGAAGGA
1 TTCCGATTCAAGTCGAACGGAAGGA
5486 TGTGTCTTAC
Statistics
Matches: 234, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 234 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
Found at i:15272 original size:16 final size:18
Alignment explanation
Indices: 15237--15284 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
15227 TAACAATATT
*
15237 TATATTTCTTTATTTGTA
1 TATATTTCATTATTTGTA
15255 TATATTTCATT-TTT-TA
1 TATATTTCATTATTTGTA
*
15271 TATATGTCA-TATTT
1 TATATTTCATTATTT
15285 ATTAATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 13 0.48
17 3 0.11
18 10 0.37
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (18 bp):
TATATTTCATTATTTGTA
Found at i:18097 original size:20 final size:20
Alignment explanation
Indices: 18063--18116 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
18053 GTAAAGAAAA
18063 TTACAA-TTA-AACTAATAC
1 TTACAAGTTACAACTAATAC
18081 TTACAAGTTACAACTAATAC
1 TTACAAGTTACAACTAATAC
*
18101 TAACAAGTTACAACTA
1 TTACAAGTTACAACTA
18117 TAAAATAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 6 0.18
19 3 0.09
20 24 0.73
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.30
Consensus pattern (20 bp):
TTACAAGTTACAACTAATAC
Found at i:18197 original size:8 final size:8
Alignment explanation
Indices: 18184--18222 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
18174 TTATGACTTT
18184 AAAATTAC
1 AAAATTAC
18192 AAAATTAC
1 AAAATTAC
18200 AAAATTA-
1 AAAATTAC
18207 ATAAATTAC
1 A-AAATTAC
18216 AAAATTA
1 AAAATTA
18223 ATAAATTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 27 0.93
9 1 0.03
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATTAC
Found at i:18238 original size:24 final size:24
Alignment explanation
Indices: 18185--18230 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
18175 TATGACTTTA
18185 AAATTACAAAATTACAAAATTAAT
1 AAATTACAAAATTACAAAATTAAT
18209 AAATTACAAAATTA-ATAAATTA
1 AAATTACAAAATTACA-AAATTA
18231 TGATATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATTACAAAATTACAAAATTAAT
Found at i:18243 original size:16 final size:16
Alignment explanation
Indices: 18184--18230 Score: 78
Period size: 16 Copynumber: 2.9 Consensus size: 16
18174 TTATGACTTT
18184 AAAATTACA-AAATTAC
1 AAAATTA-ATAAATTAC
18200 AAAATTAATAAATTAC
1 AAAATTAATAAATTAC
18216 AAAATTAATAAATTA
1 AAAATTAATAAATTA
18231 TGATATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 1 0.03
16 29 0.97
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTAATAAATTAC
Found at i:22484 original size:33 final size:33
Alignment explanation
Indices: 22442--22505 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
22432 TGTGTATGTC
22442 ATATATATATATATGATTTTTTATTAAAATTAT
1 ATATATATATATATGATTTTTTATTAAAATTAT
22475 ATATATATATATATGATTTTTTATTAAAATT
1 ATATATATATATATGATTTTTTATTAAAATT
22506 GCATATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (33 bp):
ATATATATATATATGATTTTTTATTAAAATTAT
Found at i:22521 original size:23 final size:23
Alignment explanation
Indices: 22495--22538 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
22485 ATATGATTTT
*
22495 TTATTAAAATTGCATATTTCCCG
1 TTATTAAAATTGCATACTTCCCG
**
22518 TTATTTGAATTGCATACTTCC
1 TTATTAAAATTGCATACTTCC
22539 AGTTTGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (23 bp):
TTATTAAAATTGCATACTTCCCG
Found at i:33382 original size:29 final size:29
Alignment explanation
Indices: 33349--33436 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
33339 CTCGAATGAC
33349 CTATCCAGAGGTCATAAAGATCCTCGGTA
1 CTATCCAGAGGTCATAAAGATCCTCGGTA
33378 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-A
*
33408 CTATCCAGAGATCATAAAGATCCTCGGTA
1 CTATCCAGAGGTCATAAAGATCCTCGGTA
33437 AACTGTTCAT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 29 0.51
30 28 0.49
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (29 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTA
Found at i:33413 original size:30 final size:30
Alignment explanation
Indices: 33349--33437 Score: 162
Period size: 30 Copynumber: 3.0 Consensus size: 30
33339 CTCGAATGAC
33349 CTATCCAGAGGTCATAAAGATCCTCGGT-A
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
33378 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
33408 CTATCCAGAGATCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
33438 ACTGTTCATA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
29 28 0.48
30 30 0.52
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:34268 original size:19 final size:19
Alignment explanation
Indices: 34244--34295 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
34234 TACATGTAGG
34244 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
34263 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
34282 TGCATCGATGCACT
1 TGCATCGATGCACT
34296 AATTGCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:37384 original size:33 final size:33
Alignment explanation
Indices: 37339--37403 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
37329 AAATTCACTT
* *
37339 AATTGATACATATATAATTAACCTTATATTCAG
1 AATTGATACATATACAATTAACATTATATTCAG
* *
37372 AATTCGAT-CATATCCGATTAACATTATATTCA
1 AATT-GATACATATACAATTAACATTATATTCA
37404 ATCTTCCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (33 bp):
AATTGATACATATACAATTAACATTATATTCAG
Found at i:40694 original size:50 final size:49
Alignment explanation
Indices: 40640--40757 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 49
40630 AAAGCGCGCG
* * *
40640 CCCTGAATCGCGCTATACGCTGATTTGGCGCCACGTGGGTATAGCTCGCC
1 CCCTG-ATCGCGCTATACGCTGATCTGGCGCCACGTGGGAATAGCACGCC
** * * *
40690 CCCTGCCCCGCGATATATGGTGATCTGGCGCCACGTGGGAATAGCACGCC
1 CCCTG-ATCGCGCTATACGCTGATCTGGCGCCACGTGGGAATAGCACGCC
40740 CCCTGATCCGCGCTATAC
1 CCCTGAT-CGCGCTATAC
40758 CTGGGTATCT
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (49 bp):
CCCTGATCGCGCTATACGCTGATCTGGCGCCACGTGGGAATAGCACGCC
Found at i:41232 original size:111 final size:111
Alignment explanation
Indices: 41046--41257 Score: 406
Period size: 111 Copynumber: 1.9 Consensus size: 111
41036 ATATCTCTAT
* *
41046 ACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGTTG
1 ACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTG
41111 ATTTATTTAATGCATGATTATTAGATTAAGAATTAAACATCTCGAC
66 ATTTATTTAATGCATGATTATTAGATTAAGAATTAAACATCTCGAC
41157 ACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTG
1 ACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTG
41222 ATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 ATTTATTTAATGCATGATTATTAGATTAAGAATTAA
41258 TTTTTGTAAT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 99 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGTTG
ATTTATTTAATGCATGATTATTAGATTAAGAATTAAACATCTCGAC
Found at i:43120 original size:15 final size:15
Alignment explanation
Indices: 43100--43135 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
43090 ACCTTCTCAG
43100 GATGACGACGACGAC
1 GATGACGACGACGAC
43115 GATGACGACGACGAC
1 GATGACGACGACGAC
43130 GATGAC
1 GATGAC
43136 AGCGAGGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.25, G:0.33, T:0.08
Consensus pattern (15 bp):
GATGACGACGACGAC
Found at i:45239 original size:12 final size:12
Alignment explanation
Indices: 45222--45246 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45212 TGCTCTTAAC
45222 AAGGTACAAAAT
1 AAGGTACAAAAT
45234 AAGGTACAAAAT
1 AAGGTACAAAAT
45246 A
1 A
45247 CAAGGCTAAG
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:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (12 bp):
AAGGTACAAAAT
Found at i:47141 original size:21 final size:21
Alignment explanation
Indices: 47115--47157 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
47105 GCATGGGCAT
47115 CACATCATTACTTTTGAACCC
1 CACATCATTACTTTTGAACCC
* *
47136 CACATCATTTCTTTTGAGCCC
1 CACATCATTACTTTTGAACCC
47157 C
1 C
47158 GTGATAGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.35
Consensus pattern (21 bp):
CACATCATTACTTTTGAACCC
Found at i:53850 original size:179 final size:179
Alignment explanation
Indices: 53550--53909 Score: 720
Period size: 179 Copynumber: 2.0 Consensus size: 179
53540 TAAAAGGCTT
53550 ACATAAATGGATAAAGGCTTGCATAACAACATAGGCTTAATCCTGGCAATAAAAGGCCCAACAAT
1 ACATAAATGGATAAAGGCTTGCATAACAACATAGGCTTAATCCTGGCAATAAAAGGCCCAACAAT
53615 TGAGATCCAACACAAAAGAAACTAGTAACCCTAAAGCCTATGATGAAGAGTACAAAAAAGTATCC
66 TGAGATCCAACACAAAAGAAACTAGTAACCCTAAAGCCTATGATGAAGAGTACAAAAAAGTATCC
53680 AATTTTCTACAGCGAAAATGCATTAGAATTGGAAAAATAGCTACCCCAA
131 AATTTTCTACAGCGAAAATGCATTAGAATTGGAAAAATAGCTACCCCAA
53729 ACATAAATGGATAAAGGCTTGCATAACAACATAGGCTTAATCCTGGCAATAAAAGGCCCAACAAT
1 ACATAAATGGATAAAGGCTTGCATAACAACATAGGCTTAATCCTGGCAATAAAAGGCCCAACAAT
53794 TGAGATCCAACACAAAAGAAACTAGTAACCCTAAAGCCTATGATGAAGAGTACAAAAAAGTATCC
66 TGAGATCCAACACAAAAGAAACTAGTAACCCTAAAGCCTATGATGAAGAGTACAAAAAAGTATCC
53859 AATTTTCTACAGCGAAAATGCATTAGAATTGGAAAAATAGCTACCCCAA
131 AATTTTCTACAGCGAAAATGCATTAGAATTGGAAAAATAGCTACCCCAA
53908 AC
1 AC
53910 CTATGTTCGT
Statistics
Matches: 181, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
179 181 1.00
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (179 bp):
ACATAAATGGATAAAGGCTTGCATAACAACATAGGCTTAATCCTGGCAATAAAAGGCCCAACAAT
TGAGATCCAACACAAAAGAAACTAGTAACCCTAAAGCCTATGATGAAGAGTACAAAAAAGTATCC
AATTTTCTACAGCGAAAATGCATTAGAATTGGAAAAATAGCTACCCCAA
Found at i:54556 original size:13 final size:13
Alignment explanation
Indices: 54538--54563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54528 TGCATATTAA
54538 CATTGGGCTTCTC
1 CATTGGGCTTCTC
54551 CATTGGGCTTCTC
1 CATTGGGCTTCTC
54564 TACTGCTGGA
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:0.08, C:0.31, G:0.23, T:0.38
Consensus pattern (13 bp):
CATTGGGCTTCTC
Found at i:56679 original size:162 final size:164
Alignment explanation
Indices: 56412--56737 Score: 593
Period size: 162 Copynumber: 2.0 Consensus size: 164
56402 AATGTCTCCA
* * *
56412 CTTAGAGGCTGCTAATAGAATAGCAATGTATTCTCTCTCATAAATAGATAAAGCAACATGTTTAG
1 CTTAGAGACTGCTAATAGAATAACAATGTATTCTCTCTCATAAATAGATAAAGCAACATGTCTAG
56477 GACTGAGAGCTTTACTTAAAAATGCTATAGGTCTGCCATCTTGAGATAAAACAACCCCTATGCCT
66 GACTGAGAGCTTTACTTAAAAATGCTATAGGTCTGCCATCTTGAGATAAAACAACCCCTATGCCT
56542 TCAGAG-T-GCATCAATTTCCAATTAAATTTTTT
131 TCAGAGCTGGCATCAATTTCCAATTAAATTTTTT
*
56574 CTTAGAGACTGCTAATAGAATAACAATGTATTCTCTCTCATAAATAGATAAAGCAGCATGTCTAG
1 CTTAGAGACTGCTAATAGAATAACAATGTATTCTCTCTCATAAATAGATAAAGCAACATGTCTAG
56639 GACTGAGAGCTTTACTTAAAAATGCTATAGGTCTGCCATCTTGAGATAAAACAACCCCTATGCCT
66 GACTGAGAGCTTTACTTAAAAATGCTATAGGTCTGCCATCTTGAGATAAAACAACCCCTATGCCT
*
56704 TCAGAGCTGGCATCAGTTTCCAATTAAATTTTTT
131 TCAGAGCTGGCATCAATTTCCAATTAAATTTTTT
56738 TAGTAAAGTC
Statistics
Matches: 157, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
162 132 0.84
163 1 0.01
164 24 0.15
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (164 bp):
CTTAGAGACTGCTAATAGAATAACAATGTATTCTCTCTCATAAATAGATAAAGCAACATGTCTAG
GACTGAGAGCTTTACTTAAAAATGCTATAGGTCTGCCATCTTGAGATAAAACAACCCCTATGCCT
TCAGAGCTGGCATCAATTTCCAATTAAATTTTTT
Found at i:59542 original size:13 final size:13
Alignment explanation
Indices: 59521--59558 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
59511 TGCATATTAA
* *
59521 ATTGAGCTTGTCC
1 ATTGGGCTTCTCC
59534 ATTGGGCTTCTCC
1 ATTGGGCTTCTCC
59547 ATTGGGCTTCTC
1 ATTGGGCTTCTC
59559 TGCTGGATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.11, C:0.26, G:0.24, T:0.39
Consensus pattern (13 bp):
ATTGGGCTTCTCC
Found at i:65828 original size:42 final size:42
Alignment explanation
Indices: 65734--65817 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
65724 AAAGAGTCAA
*
65734 AAGGAGATAGACAAATTAAAGGCTCAGTTGAATCAAGAGTTT
1 AAGGAGAAAGACAAATTAAAGGCTCAGTTGAATCAAGAGTTT
65776 AAGGAGAAAGACAAATTAAAGGCTCAGTTGAATCAAGAGTTT
1 AAGGAGAAAGACAAATTAAAGGCTCAGTTGAATCAAGAGTTT
65818 GAGATGAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.23
Consensus pattern (42 bp):
AAGGAGAAAGACAAATTAAAGGCTCAGTTGAATCAAGAGTTT
Found at i:82429 original size:18 final size:19
Alignment explanation
Indices: 82406--82446 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
82396 CCGCTACTAG
82406 TGAACCGGAAG-GAACCGT
1 TGAACCGGAAGTGAACCGT
**
82424 TGAACCGGCTGTGAACCGT
1 TGAACCGGAAGTGAACCGT
82443 TGAA
1 TGAA
82447 TCAGACCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.17
Consensus pattern (19 bp):
TGAACCGGAAGTGAACCGT
Found at i:86998 original size:3 final size:3
Alignment explanation
Indices: 86992--87033 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
86982 TTTTTTTATT
86992 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
87034 AACGAAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:87291 original size:76 final size:76
Alignment explanation
Indices: 87160--88029 Score: 1606
Period size: 76 Copynumber: 11.5 Consensus size: 76
87150 GATGGAAATG
* * * *
87160 TTTGAAAACATCATGCACTGAAGGGCTTACATATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87225 CCCGAAGGCTT
66 CCCGAAGGCTT
87236 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87301 CCCGAAGGCTT
66 CCCGAAGGCTT
87312 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87377 CCCGAAGGCTT
66 CCCGAAGGCTT
87388 TTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
87453 TCCCGAAGGCTT
65 TCCCGAAGGCTT
87465 TTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
87530 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
87542 TTTGG-AACATCATGCACTGAAGGACTTACAGATGACCATAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87605 CCCGAAGGCTT
66 CCCGAAGGCTT
87616 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87680 CCCGAAGGCTT
66 CCCGAAGGCTT
87691 TTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTGAAAACATCAAAAAGC
1 TTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
*
87755 TCCCGAAGGTTT
65 TCCCGAAGGCTT
87767 TTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG-AAACATCAAAAAGC
1 TTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
87831 TCCCGAAGGCTT
65 TCCCGAAGGCTT
87843 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87908 CCCGAAGGCTT
66 CCCGAAGGCTT
*
87919 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87984 CCCGAAGGCTT
66 CCCGAAGGCTT
87995 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
88030 TGGGAAATAG
Statistics
Matches: 779, Mismatches: 9, Indels: 12
0.97 0.01 0.01
Matches are distributed among these distances:
74 23 0.03
75 178 0.23
76 422 0.54
77 156 0.20
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:87783 original size:227 final size:228
Alignment explanation
Indices: 87160--88029 Score: 1606
Period size: 227 Copynumber: 3.8 Consensus size: 228
87150 GATGGAAATG
* * * *
87160 TTTGAAAACATCATGCACTGAAGGGCTTACATATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87225 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
87290 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAG
87355 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
87388 TTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
1 TTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
87453 TCCCGAAGGCTTTTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAA
65 TCCCGAAGGCTTTTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAA
*
87518 ACATCAAAAAGCTCCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGATGACCATA
129 ACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTA
87582 AGGCTTTGAAAACATC-AAAAGCTCCCGAAGGCTT
194 AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
87616 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
87680 CCCGAAGGCTTTTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTGAAAA
66 CCCGAAGGCTTTTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAA
*
87744 CATCAAAAAGCTCCCGAAGGTTTTTTGGAAAACATCATGCACTGAAGGACTTACAGATGACCCTA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTA
87809 AGGCTTTG-AAACATCAAAAAGCTCCCGAAGGCTT
194 AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
87843 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
87908 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
87973 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
88030 TGGGAAATAG
Statistics
Matches: 626, Mismatches: 9, Indels: 15
0.96 0.01 0.02
Matches are distributed among these distances:
225 34 0.05
226 71 0.11
227 238 0.38
228 84 0.13
229 123 0.20
230 76 0.12
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (228 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:93718 original size:17 final size:16
Alignment explanation
Indices: 93692--93723 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
93682 TCAATTTTCC
93692 TTTTTTTTCTTCTTTT
1 TTTTTTTTCTTCTTTT
93708 TTTTCTTTTCTTCTTT
1 TTTT-TTTTCTTCTTT
93724 CTTTGCTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCTTCTTTT
Found at i:100563 original size:3 final size:3
Alignment explanation
Indices: 100557--100613 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
100547 TTTTTTTATT
*
100557 TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
100605 TAA TAA TAA
1 TAA TAA TAA
100614 AACGAAATGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:105442 original size:24 final size:24
Alignment explanation
Indices: 105415--105498 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
105405 TGAATTATGT
* *
105415 TATGATACCTGACCTAGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
*
105439 TATGATA-TTGACATGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
*
105462 TATGATACATGACCTGGATTCTGA
1 TATGATACTTGACCTGGATTCTGA
105486 TATGATACTTGAC
1 TATGATACTTGAC
105499 TTGAATTATG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 20 0.38
24 33 0.62
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTGA
Found at i:105625 original size:35 final size:35
Alignment explanation
Indices: 105576--105720 Score: 245
Period size: 35 Copynumber: 4.1 Consensus size: 35
105566 TGGAGGAAGA
* * * * *
105576 TTACTTGGAGGCTCCTCGGCTTTGTTCTCAGTGCC
1 TTACTTGCATGCTCCACGGCTTTGTGCTCAGGGCC
105611 TTACTTGCATGCTCCACGGCTTTGTGCTCAGGGCC
1 TTACTTGCATGCTCCACGGCTTTGTGCTCAGGGCC
105646 TTACTTGCATGCTCCACGGCTTTGTGCTCAGGGCC
1 TTACTTGCATGCTCCACGGCTTTGTGCTCAGGGCC
105681 TTACTTGCATGCTCCACGGCTTTGTGCTCAGGGCC
1 TTACTTGCATGCTCCACGGCTTTGTGCTCAGGGCC
105716 TTACT
1 TTACT
105721 GTTCGTGACA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 105 1.00
ACGTcount: A:0.11, C:0.30, G:0.25, T:0.34
Consensus pattern (35 bp):
TTACTTGCATGCTCCACGGCTTTGTGCTCAGGGCC
Found at i:105789 original size:2 final size:2
Alignment explanation
Indices: 105782--105830 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
105772 TGAATTGGGG
105782 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
105824 TA TA TA T
1 TA TA TA T
105831 GTTTTAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:109164 original size:21 final size:20
Alignment explanation
Indices: 109124--109165 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
109114 CCAACTTACA
*
109124 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
109144 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
109165 A
1 A
109166 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:111286 original size:139 final size:139
Alignment explanation
Indices: 111032--111301 Score: 477
Period size: 139 Copynumber: 1.9 Consensus size: 139
111022 AGTATCTGTG
*
111032 TAGTCTCTGACTTTTCAGCACTATCATCGTCTTCTTTTCTTTGTAGCTTATCTTCTACAAAGATA
1 TAGTCTCTGACTTTTCAGCACTATCATCGTCTTATTTTCTTTGTAGCTTATCTTCTACAAAGATA
* * *
111097 ACATCTCTGCTAATGATCACTTTGCGGGCAGTGGTATCCTACAAGCGATACCCCTTTACTCCATC
66 ACATCCCTGCTAATGATCACTTTGCGGGCAGTGGGATCCCACAAGCGATACCCCTTTACTCCATC
111162 AACATCTTA
131 AACATCTTA
* *
111171 TAGTCTCTGACTTTTCAGCACTATCATCGTCTTATTTTCTTTGTATCTTTTCTTCTACAAAGATA
1 TAGTCTCTGACTTTTCAGCACTATCATCGTCTTATTTTCTTTGTAGCTTATCTTCTACAAAGATA
*
111236 ACATCCCTGCTAATGATCACTTTGCGGGCAGTGGGATCCCACAAGTGATACCCCTTTACTCCATC
66 ACATCCCTGCTAATGATCACTTTGCGGGCAGTGGGATCCCACAAGCGATACCCCTTTACTCCATC
111301 A
131 A
111302 GCATACCCCA
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 124 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (139 bp):
TAGTCTCTGACTTTTCAGCACTATCATCGTCTTATTTTCTTTGTAGCTTATCTTCTACAAAGATA
ACATCCCTGCTAATGATCACTTTGCGGGCAGTGGGATCCCACAAGCGATACCCCTTTACTCCATC
AACATCTTA
Found at i:120560 original size:20 final size:19
Alignment explanation
Indices: 120509--120575 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
120499 CAATCCGACT
120509 TAAAATAATATATTTATT-A
1 TAAAATAATA-ATTTATTAA
**
120528 -AAAAT-ATTTTTTATTCAA
1 TAAAATAATAATTTATT-AA
120546 TAAAATAATAATTTAATTAA
1 TAAAATAATAATTT-ATTAA
*
120566 AAAAATAATA
1 TAAAATAATA
120576 TATGGGGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
16 6 0.16
17 2 0.05
18 6 0.16
19 5 0.13
20 16 0.42
21 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATAATAATTTATTAA
Found at i:130666 original size:29 final size:29
Alignment explanation
Indices: 130632--130690 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
130622 CCTAAATTAA
130632 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
130661 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
130690 T
1 T
130691 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:135359 original size:29 final size:29
Alignment explanation
Indices: 135322--135380 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
135312 CCTAAATTAA
135322 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
* *
135351 TTTGGTGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
135380 T
1 T
135381 AGGTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:140053 original size:29 final size:29
Alignment explanation
Indices: 140019--140077 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
140009 CCTAAATTAA
*
140019 TTTGATGTTATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
140048 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
140077 T
1 T
140078 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:143436 original size:21 final size:21
Alignment explanation
Indices: 143406--143504 Score: 89
Period size: 23 Copynumber: 4.6 Consensus size: 21
143396 GATTTACATA
*
143406 TTCGCATTGCGATA-GTCGAAG
1 TTCGCGTTGCGATATGTC-AAG
*
143427 TTCGCGTTGCGATTTATTTCAAG
1 TTCGCGTTGCGA--TATGTCAAG
*
143450 TTCGCGTTGCGATTTATTTCAAG
1 TTCGCGTTGCGA--TATGTCAAG
143473 TT--CGTTGCGATA-GTCGAAG
1 TTCGCGTTGCGATATGTC-AAG
143492 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
143505 TTATTCTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.03
19 7 0.10
21 28 0.41
23 30 0.43
24 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATATGTCAAG
Found at i:143453 original size:23 final size:23
Alignment explanation
Indices: 143424--143509 Score: 119
Period size: 23 Copynumber: 3.9 Consensus size: 23
143414 GCGATAGTCG
143424 AAGTTCGCGTTGCGATTTATTTC
1 AAGTTCGCGTTGCGATTTATTTC
143447 AAGTTCGCGTTGCGATTTATTTC
1 AAGTTCGCGTTGCGATTTATTTC
*
143470 AAGTT--CGTTGCGA--TA-GTC
1 AAGTTCGCGTTGCGATTTATTTC
143488 GAAGTTCGCGTTGCGATTTATT
1 -AAGTTCGCGTTGCGATTTATT
143510 CTAAATTCGT
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.04
19 7 0.13
21 16 0.29
23 30 0.55
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (23 bp):
AAGTTCGCGTTGCGATTTATTTC
Found at i:143504 original size:42 final size:42
Alignment explanation
Indices: 143446--143543 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
143436 CGATTTATTT
*
143446 CAAGTTCGCGTTGCGATTTATT-TCAAGTTCGTTGCGATAGTC
1 CAAGTTCGCGTTGCGATTTATTCT-AAATTCGTTGCGATAGTC
* *
143488 GAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGTGATAGTC
1 CAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTC
* *
143530 CAAGCTAGCGTTGC
1 CAAGTTCGCGTTGC
143544 AATTCTATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
CAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATAGTC
Found at i:143568 original size:6 final size:6
Alignment explanation
Indices: 143552--143583 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
143542 GCAATTCTAT
*
143552 GACCAC AACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GACCAC GA
143584 TGTGATTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.38, C:0.47, G:0.16, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:144802 original size:25 final size:24
Alignment explanation
Indices: 144774--144821 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
144764 GCTTAATTTA
144774 AAACTCATAAAATTTTAGAGAAAAT
1 AAACTCA-AAAATTTTAGAGAAAAT
* *
144799 AAACTTAAAAATTTTATAGAAAA
1 AAACTCAAAAATTTTAGAGAAAA
144822 AGAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (24 bp):
AAACTCAAAAATTTTAGAGAAAAT
Found at i:144831 original size:24 final size:24
Alignment explanation
Indices: 144782--144831 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
144772 TAAAACTCAT
**
144782 AAAATTTTAGAGAAAATAAACTTA
1 AAAATTTTAGAGAAAATAAAAATA
*
144806 AAAATTTTATAGAAAA-AGAAAATA
1 AAAATTTTAGAGAAAATA-AAAATA
144830 AA
1 AA
144832 TTACCTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.26
Consensus pattern (24 bp):
AAAATTTTAGAGAAAATAAAAATA
Found at i:145536 original size:2 final size:2
Alignment explanation
Indices: 145529--145564 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
145519 TATATCATTC
145529 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
145565 ATGATTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:150142 original size:14 final size:14
Alignment explanation
Indices: 150123--150150 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
150113 TATAACTAGC
150123 GAACCAAATTATAT
1 GAACCAAATTATAT
150137 GAACCAAATTATAT
1 GAACCAAATTATAT
150151 AAATCATCAG
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:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
GAACCAAATTATAT
Found at i:152664 original size:18 final size:19
Alignment explanation
Indices: 152635--152672 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
152625 TACTTCTGCT
152635 GTTGATGAAGATGAAAAGA
1 GTTGATGAAGATGAAAAGA
*
152654 GTTGA-GAAGATGAGAAGA
1 GTTGATGAAGATGAAAAGA
152672 G
1 G
152673 AATGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.37, T:0.18
Consensus pattern (19 bp):
GTTGATGAAGATGAAAAGA
Found at i:160211 original size:28 final size:29
Alignment explanation
Indices: 160150--160209 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
160140 TACGCAAGAC
* *
160150 ATTTTAAGGATATTTTAAAATTATTTGAT
1 ATTTTAAAGATATTTAAAAATTATTTGAT
160179 ATTTTAAAGATA-TTAAAAATTA-TTGA-
1 ATTTTAAAGATATTTAAAAATTATTTGAT
160205 ATTTT
1 ATTTT
160210 TTTAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
27 4 0.14
28 9 0.31
29 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (29 bp):
ATTTTAAAGATATTTAAAAATTATTTGAT
Found at i:160510 original size:196 final size:187
Alignment explanation
Indices: 160168--160560 Score: 644
Period size: 196 Copynumber: 2.0 Consensus size: 187
160158 GATATTTTAA
*
160168 AATTATTTGATATTTTAAAGATATTAAAAATTATTGAATTTTTTTAATAATTTAGAGTGAATATA
1 AATTATTTGATATTTTAAAGATATTAAAAATTATTGAATTTTTTCAATAATTTAGAGTGAATATA
160233 AAGTAGTATTTGTGTTTCTTATTTTATAAAAGAAGAAAGATATCCTTGAGAATCTTCTTATAATA
66 AAGTAGTATTTGTGTTTCTTATTTTATAAAAGAAGAAAGATATCCTTGAGAATCTTCTTATAATA
160298 TTGGTCAATATCAAAATAATTAATAAAATGTTAAAATAATAAATAAAATTACTTTTTT
131 TTGGTCAATATCAAAATAATTAATAAAATGTTAAAATAATAAATAAAATTA-TTTTTT
*
160356 -ATTATTTGATATTTTAAAGATATTAAAAATTATTTAATTTTTTCAATAATTTAGAGTGAATATA
1 AATTATTTGATATTTTAAAGATATTAAAAATTATTGAATTTTTTCAATAATTTAGAGTGAATATA
* *
160420 AAGTAGTATAAGTTAGAATTGTGTTTCTTATTTTATAAAGGAAGAAAGGTATCCTTGAGAATCTT
66 AAGTAG--T-A--T----TTGTGTTTCTTATTTTATAAAAGAAGAAAGATATCCTTGAGAATCTT
160485 CTTATAATATTGGTCAATATCAAAATAATTAATAAAATGTTAAAATAATAAATAAAATTATTTTT
122 CTTATAATATTGGTCAATATCAAAATAATTAATAAAATGTTAAAATAATAAATAAAATTATTTTT
160550 T
187 T
160551 AATTAATTTG
1 AATT-ATTTG
160561 TGGTAAGTAC
Statistics
Matches: 190, Mismatches: 4, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
187 68 0.36
189 1 0.01
190 1 0.01
192 1 0.01
195 6 0.03
196 108 0.57
197 5 0.03
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (187 bp):
AATTATTTGATATTTTAAAGATATTAAAAATTATTGAATTTTTTCAATAATTTAGAGTGAATATA
AAGTAGTATTTGTGTTTCTTATTTTATAAAAGAAGAAAGATATCCTTGAGAATCTTCTTATAATA
TTGGTCAATATCAAAATAATTAATAAAATGTTAAAATAATAAATAAAATTATTTTTT
Found at i:174535 original size:33 final size:35
Alignment explanation
Indices: 174483--174558 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 35
174473 ATTTATGATT
* *
174483 AAATAAAATACTAATAATAAT-AATTAAAATATATTG
1 AAATAAAATA-TAATAATAATAAATT-AAATAAATTA
174519 AAATAAAAT-TAA-AATAATAAATTAAATAAATTA
1 AAATAAAATATAATAATAATAAATTAAATAAATTA
174552 AAATAAA
1 AAATAAA
174559 TAAACAGTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 21 0.57
34 7 0.19
36 9 0.24
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (35 bp):
AAATAAAATATAATAATAATAAATTAAATAAATTA
Found at i:174548 original size:9 final size:10
Alignment explanation
Indices: 174504--174559 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
174494 TAATAATAAT
174504 AATTAAAATA
1 AATTAAAATA
* *
174514 TATTGAAATAA
1 AATTAAAAT-A
174525 AATTAAAATAATA
1 AATT--AA-AATA
174538 AATT-AAATA
1 AATTAAAATA
174547 AATTAAAATA
1 AATTAAAATA
174557 AAT
1 AAT
174560 AAACAGTGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
9 8 0.22
10 16 0.43
11 4 0.11
13 6 0.16
14 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AATTAAAATA
Found at i:174552 original size:22 final size:25
Alignment explanation
Indices: 174509--174562 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 25
174499 ATAATAATTA
*
174509 AAATATATTGAAATAAAATTAAAAT
1 AAATAAATTGAAATAAAATTAAAAT
174534 -AATAAATT-AAAT-AAATTAAAAT
1 AAATAAATTGAAATAAAATTAAAAT
174556 AAATAAA
1 AAATAAA
174563 CAGTGACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (25 bp):
AAATAAATTGAAATAAAATTAAAAT
Found at i:174562 original size:9 final size:9
Alignment explanation
Indices: 174519--174584 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
174509 AAATATATTG
174519 AAATAAAATT
1 AAATAAAA-T
*
174529 AAA-ATAAT
1 AAATAAAAT
*
174537 AAATTAAAT
1 AAATAAAAT
174546 AAATTAAAAT
1 AAA-TAAAAT
174556 AAATAAACAGT
1 AAATAAA-A-T
* *
174567 GACTAAAAT
1 AAATAAAAT
174576 AAATAAAAT
1 AAATAAAAT
174585 TAAAACTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
8 4 0.09
9 21 0.48
10 13 0.30
11 6 0.14
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (9 bp):
AAATAAAAT
Found at i:176113 original size:3 final size:3
Alignment explanation
Indices: 176105--176155 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
176095 AATATTTATT
* * *
176105 TAA TAA TAAA TAA TAA TAA TAA TAA TTA TGTA TAA TAA TGA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
176152 TAA T
1 TAA T
176156 TTTAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:176423 original size:23 final size:23
Alignment explanation
Indices: 176393--176438 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
176383 ACAGATGACC
176393 CTAAGGCTTTGAAAACATCAAAA
1 CTAAGGCTTTGAAAACATCAAAA
176416 CTAAGGCTTTGAAAACATCAAAA
1 CTAAGGCTTTGAAAACATCAAAA
176439 ATCCCGAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (23 bp):
CTAAGGCTTTGAAAACATCAAAA
Found at i:176500 original size:94 final size:93
Alignment explanation
Indices: 176321--176509 Score: 258
Period size: 94 Copynumber: 2.0 Consensus size: 93
176311 ACAGATGACC
* * *
176321 CTAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTGGAAACATCATGCACTGTACTTACA
1 CTAAGGCTTTGAAAACATCAAAAA-CTCCCGAAGGCTTTTAGAAACATCATG-ACTGTACTTACA
*
176386 GATGACCCTAAGGCTTTGAAAACATCAAAA
64 GATAACCCTAAGGCTTTGAAAACATCAAAA
176416 CTAAGGCTTTGAAAACATCAAAAA-TCCCG-AGGCTTTTTAGAAACATCATG-CTGTAAGACTTA
1 CTAAGGCTTTGAAAACATCAAAAACTCCCGAAGGC-TTTTAGAAACATCATGACTGT---ACTTA
*
176478 CGGATAACCCTAAGGCTTTGAAAACATCAAAA
62 CAGATAACCCTAAGGCTTTGAAAACATCAAAA
176510 GCTCCCGAAG
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
91 4 0.05
92 4 0.05
93 19 0.22
94 35 0.41
95 23 0.27
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (93 bp):
CTAAGGCTTTGAAAACATCAAAAACTCCCGAAGGCTTTTAGAAACATCATGACTGTACTTACAGA
TAACCCTAAGGCTTTGAAAACATCAAAA
Found at i:176568 original size:74 final size:76
Alignment explanation
Indices: 176416--176686 Score: 418
Period size: 74 Copynumber: 3.7 Consensus size: 76
176406 AACATCAAAA
* *
176416 CTAAGGCTTTGAAAACATCAAAAA--TCCCG-AGGCTTTTTAGAAACATCATG--CTGTAAGACT
1 CTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACT
* *
176476 TACGGATAACC
66 TACAGATGACC
*
176487 CTAAGGCTTTGAAAACATC-AAAAGCTCCCGAA-GATTTTTGGAAACATCATGCACTGTAGGACT
1 CTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACT
176550 TACAGATGACC
66 TACAGATGACC
*
176561 CTAAGGCTTTG-AAACATCAAAAATCTCCCGAAGGCTTTTTGG-AACATCATGCACTGTAGGACT
1 CTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACT
176624 TACAGATGACC
66 TACAGATGACC
176635 CT-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
1 CTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
176687 TTTGAAAACA
Statistics
Matches: 183, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
70 4 0.02
71 19 0.10
72 22 0.12
73 16 0.09
74 105 0.57
75 17 0.09
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (76 bp):
CTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACT
TACAGATGACC
Found at i:176693 original size:46 final size:46
Alignment explanation
Indices: 176641--176732 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
176631 GACCCTAGGC
176641 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
176687 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
176733 CACTGTAGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (46 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
Found at i:176723 original size:195 final size:196
Alignment explanation
Indices: 176494--176883 Score: 714
Period size: 195 Copynumber: 2.0 Consensus size: 196
176484 ACCCTAAGGC
176494 TTTGAAAACATCAAAAGCTCCCGAAGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATGA
1 TTTGAAAACATCAAAAGCTCCCGAAGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATGA
*
176559 CCCTAAGGCTTTG-AAACATCAAAAATCTCCCGAAGGCTTTTTGG-AACATCATGCACTGTAGGA
66 CCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGA
176622 CTTACAGATGACCCT-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
131 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
176686 G
196 G
*
176687 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATC-AAAAGCTCCCGAA-GATTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
*
176752 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGTAG
64 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
176817 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
129 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
176882 AT
194 AT
176884 ACACTGTAGG
Statistics
Matches: 189, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
193 12 0.06
194 13 0.07
195 52 0.28
196 29 0.15
197 34 0.18
198 49 0.26
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (196 bp):
TTTGAAAACATCAAAAGCTCCCGAAGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATGA
CCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGA
CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
G
Found at i:176774 original size:76 final size:76
Alignment explanation
Indices: 176687--177133 Score: 849
Period size: 76 Copynumber: 5.9 Consensus size: 76
176677 AAACATCATG
176687 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
176752 GACCCTAAGGC
66 GACCCTAAGGC
*
176763 TTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
176828 GACCCTAAGGC
66 GACCCTAAGGC
*
176839 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATACACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
176904 GACCCTAAGGC
66 GACCCTAAGGC
176915 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGTAGGACTTACAGA
*
176980 TGACCCTAAGGT
65 TGACCCTAAGGC
*
176992 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTATGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
177057 GACCCTAAGGC
66 GACCCTAAGGC
177068 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
177133 G
66 G
177134 TGGGAAATAG
Statistics
Matches: 362, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
76 288 0.80
77 74 0.20
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (76 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
GACCCTAAGGC
Found at i:176794 original size:122 final size:119
Alignment explanation
Indices: 176568--176808 Score: 437
Period size: 122 Copynumber: 2.0 Consensus size: 119
176558 ACCCTAAGGC
*
176568 TTTGAAACATCAAAAATCTCCCGAAGGCTTTTTGGAACATCATGCACTGTAGGACTTACAGATGA
1 TTTGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAACATCATGCACTGTAGGACTTACAGATGA
176633 CCCTAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
66 CCCTAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
176687 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTG-AAACATCAAAAAGCTCCCGAAGGCTTTTTGG-AACATCATGCACTGTAGGACTTACAGAT
*
176752 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATG
64 GACCCT-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
176809 CACTGTAGGA
Statistics
Matches: 117, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
119 4 0.03
120 30 0.26
121 34 0.29
122 49 0.42
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (119 bp):
TTTGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAACATCATGCACTGTAGGACTTACAGATGA
CCCTAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATG
Found at i:176970 original size:229 final size:228
Alignment explanation
Indices: 176687--177133 Score: 849
Period size: 229 Copynumber: 2.0 Consensus size: 228
176677 AAACATCATG
176687 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
*
176752 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGTAG
66 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
176817 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
131 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
176882 ATACACTGTAGGACTTACAGATGACCCTAAGGC
196 ATACACTGTAGGACTTACAGATGACCCTAAGGC
176915 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGTAGGACTTACAGA
*
176980 TGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTA
65 TGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTA
*
177045 TGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAT
130 GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAT
*
177110 CATGCACTGTAGGACTTACAGATG
195 CATACACTGTAGGACTTACAGATG
177134 TGGGAAATAG
Statistics
Matches: 214, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
228 29 0.14
229 185 0.86
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (228 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
ATACACTGTAGGACTTACAGATGACCCTAAGGC
Found at i:177035 original size:153 final size:152
Alignment explanation
Indices: 176687--177133 Score: 849
Period size: 153 Copynumber: 2.9 Consensus size: 152
176677 AAACATCATG
176687 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
*
176752 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGTAG
66 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
176817 GACTTACAGATGACCCTAAGGC
131 GACTTACAGATGACCCTAAGGC
*
176839 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATACACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
176904 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGTA
66 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGTA
*
176969 GGACTTACAGATGACCCTAAGGT
130 GGACTTACAGATGACCCTAAGGC
*
176992 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTATGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
177057 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
66 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
177122 GACTTACAGATG
131 GACTTACAGATG
177134 TGGGAAATAG
Statistics
Matches: 289, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
152 140 0.48
153 149 0.52
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (152 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
GACTTACAGATGACCCTAAGGC
Found at i:177864 original size:22 final size:22
Alignment explanation
Indices: 177786--177862 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
177776 AATAAAGCTT
177786 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
177808 TCATCTTTAAAAAGAAAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
177830 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
177852 TCACCTTTGAA
1 TCATCTTTGAA
177863 GAATGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:178329 original size:54 final size:54
Alignment explanation
Indices: 178237--178384 Score: 206
Period size: 54 Copynumber: 2.7 Consensus size: 54
178227 TGGTTCATAG
* * *
178237 AACATTTGACAACACATTCATCCTTTCCTATGGCTTCTGCTCAGATGTTTGTAA
1 AACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCTCAGATGTTTGTAA
* * *
178291 AACATGTGACAACACATTCATCATTTCTTGTGGTTTCTGCTCAGATTTTTGTAA
1 AACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCTCAGATGTTTGTAA
* * * *
178345 AGCATTTGACAATACATTCGTCATATCCTGTGGTTTCTGC
1 AACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGC
178385 ACAAATTTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (54 bp):
AACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCTCAGATGTTTGTAA
Found at i:182447 original size:134 final size:134
Alignment explanation
Indices: 182202--182610 Score: 746
Period size: 134 Copynumber: 3.1 Consensus size: 134
182192 CTAATTTCAG
* * *
182202 CTTTATTGACATTAGCCTTCATTGGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGACTT
1 CTTTTTTGACATTAGCCTTCATTGGACTAATAAAAGGATTCAACTCATCACAATGTCTTTGACTT
*
182267 GACAATCACAGTGGAGCGAACACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATAT
66 GACAATCACAGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATAT
182332 GACT
131 GACT
**
182336 CTTTTTTGACATTAGCCTTCATTGGACTAATAAAAATATTCAACTCATCACAATGTCTTTGACTT
1 CTTTTTTGACATTAGCCTTCATTGGACTAATAAAAGGATTCAACTCATCACAATGTCTTTGACTT
*
182401 GACAATCACAGTGGAGCAAACACCGAACTTCCAAATACCCGATCAAGGTCATGCTTTGAATATAT
66 GACAATCACAGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATAT
182466 GACT
131 GACT
*
182470 CTTTTTTGACATTAGCCTTCATTGGACTAATAAAAGGATTCAACTCATCATAATGTCTTTGACTT
1 CTTTTTTGACATTAGCCTTCATTGGACTAATAAAAGGATTCAACTCATCACAATGTCTTTGACTT
182535 GACAATCACAGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATAT
66 GACAATCACAGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATAT
182600 GACT
131 GACT
182604 CTTTTTT
1 CTTTTTT
182611 TAGGAGAACT
Statistics
Matches: 264, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 264 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (134 bp):
CTTTTTTGACATTAGCCTTCATTGGACTAATAAAAGGATTCAACTCATCACAATGTCTTTGACTT
GACAATCACAGTGGAGCAAACACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATAT
GACT
Found at i:187073 original size:19 final size:19
Alignment explanation
Indices: 187028--187074 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
187018 ATACCTGAAA
187028 ATAAAACATAAATAAATATT
1 ATAAAA-ATAAATAAATATT
* *
187048 ATGAAAAT-AATAAGTATAT
1 ATAAAAATAAATAAATAT-T
187067 ATAAAAAT
1 ATAAAAAT
187075 TTGAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
ATAAAAATAAATAAATATT
Found at i:187880 original size:18 final size:17
Alignment explanation
Indices: 187854--187896 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
187844 AATATATTGC
*
187854 AAATAAAATTAAAATAAT
1 AAATTAAATTAAAAT-AT
187872 AAATTAAATTAAAATAT
1 AAATTAAATTAAAATAT
187889 AAA-TAAAT
1 AAATTAAAT
187897 AGTGACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 5 0.21
18 14 0.58
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATTAAATTAAAATAT
Found at i:189087 original size:3 final size:3
Alignment explanation
Indices: 189079--189132 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
189069 AATATTTATT
* *
189079 TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TGTA TAA TAA TGA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
189126 TAA TAA T
1 TAA TAA T
189133 TTTAATGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 40 0.89
4 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:189107 original size:22 final size:23
Alignment explanation
Indices: 189079--189132 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
189069 AATATTTATT
189079 TAATAATAA-ATAATAATAATAA
1 TAATAATAATATAATAATAATAA
* *
189101 TAATAATAATGT-ATAATAATGA
1 TAATAATAATATAATAATAATAA
189123 TAATAATAAT
1 TAATAATAAT
189133 TTTAATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TAATAATAATATAATAATAATAA
Found at i:201780 original size:45 final size:45
Alignment explanation
Indices: 201729--201815 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
201719 TCCCGTAGAA
201729 AAAAGTTACTTCCTCCAAACTCATTTCCAGATTTGATTACCGATC
1 AAAAGTTACTTCCTCCAAACTCATTTCCAGATTTGATTACCGATC
*
201774 AAAAGTTACTTCCTCCAAACTCATTTTCAGATTTGATTACCG
1 AAAAGTTACTTCCTCCAAACTCATTTCCAGATTTGATTACCG
201816 CGACAACAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34
Consensus pattern (45 bp):
AAAAGTTACTTCCTCCAAACTCATTTCCAGATTTGATTACCGATC
Found at i:223350 original size:15 final size:15
Alignment explanation
Indices: 223326--223359 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
223316 AAAATGAGTG
*
223326 AAAATGAAAAAAGAA
1 AAAATAAAAAAAGAA
*
223341 AAAATAAAAAAATAA
1 AAAATAAAAAAAGAA
223356 AAAA
1 AAAA
223360 ATGAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAATAAAAAAAGAA
Found at i:223357 original size:7 final size:8
Alignment explanation
Indices: 223326--223369 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
223316 AAAATGAGTG
*
223326 AAAATGAA
1 AAAATAAA
*
223334 AAAA-GAA
1 AAAATAAA
223341 AAAATAAA
1 AAAATAAA
223349 AAAATAAA
1 AAAATAAA
*
223357 AAAATGAA
1 AAAATAAA
223365 AAAAT
1 AAAAT
223370 GGAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 7 0.21
8 26 0.79
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:224466 original size:55 final size:55
Alignment explanation
Indices: 224382--224916 Score: 641
Period size: 55 Copynumber: 9.7 Consensus size: 55
224372 AACGATAATC
* * *
224382 GAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * *
224437 GAAGATTGTTTGAGTCTTATACTCTCTGAAAAAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * * *
224492 GAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATATGGAGCAGACACGATGGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * *
224547 GAAGATTGTTCGAGTCTTGTACTCTCTGAAGGAAT-GAGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAG-GGAGCAGACACGATTGAT
** *
224602 GAAGATTGTTCGAGTCTTATACTCTCTGCGGAAATAGGGAGCAGACACAATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * *
224657 GAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGACACGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * * *
224712 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGATTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGAT
* * *
224768 GAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAGCAGACACGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
* * ** * * * * *
224823 GAAGATTCTTCAAGT-TCCTACTCCCT-AAGAAAGAGGGAAC-GAACCCG-TTGACA
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGA-T
* * *
224876 GAAGATTGTTCGAGT-TCTATACTCCCCGAAGAAAGAGGGAG
1 GAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAG
224917 TGAACTCGTT
Statistics
Matches: 415, Mismatches: 58, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
52 5 0.01
53 29 0.07
54 15 0.04
55 313 0.75
56 53 0.13
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGAT
Found at i:224880 original size:53 final size:54
Alignment explanation
Indices: 224823--224969 Score: 174
Period size: 55 Copynumber: 2.7 Consensus size: 54
224813 CACGATTGAT
* * *
224823 GAAGATTCTTCAAGTTC-CTACTCCCTAAGAAAGAGGGAACGAACCCGTT-GACA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAACGAACCCGTTCG-CA
* ** *
224876 GAAGATTGTTCGAGTTCTATACTCCCCGAAGAAAGAGGGAGTGAACTCGTTCGCA
1 GAAGATTGTTCGAGTTCTATACT-CCCTAAGAAAGAGGGAACGAACCCGTTCGCA
*
224931 GAAAATTGTTCGAGTTCTATACTCCCTAA-AAATGAGGGA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAA-GAGGGA
224970 GCGAGCTCGT
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
53 18 0.22
54 15 0.19
55 47 0.58
56 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAACGAACCCGTTCGCA
Found at i:228693 original size:23 final size:22
Alignment explanation
Indices: 228646--228696 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
228636 TGAGGTTGAT
*
228646 TTTATTATTTGATTTTCATATTC
1 TTTA-TATTTGATTTTCATAATC
228669 TTTATATTTG-TTTTCAGTAAATC
1 TTTATATTTGATTTTCA-T-AATC
228692 TTTAT
1 TTTAT
228697 TTTCTTTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 6 0.24
22 7 0.28
23 12 0.48
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.63
Consensus pattern (22 bp):
TTTATATTTGATTTTCATAATC
Found at i:229695 original size:16 final size:16
Alignment explanation
Indices: 229674--229741 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
229664 GCCTCTGAAA
*
229674 CATTCATCATTTAAAT
1 CATTCAACATTTAAAT
*
229690 CATTCAACATTTGAAT
1 CATTCAACATTTAAAT
* * *
229706 CATTTAATATTTGAAT
1 CATTCAACATTTAAAT
* * *
229722 CATTTAATATTTGAAT
1 CATTCAACATTTAAAT
229738 CATT
1 CATT
229742 TAAGACTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (16 bp):
CATTCAACATTTAAAT
Found at i:229742 original size:16 final size:16
Alignment explanation
Indices: 229682--229744 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
229672 AACATTCATC
* * *
229682 ATTTAAATCATTCAAC
1 ATTTGAATCATTTAAT
229698 ATTTGAATCATTTAAT
1 ATTTGAATCATTTAAT
229714 ATTTGAATCATTTAAT
1 ATTTGAATCATTTAAT
229730 ATTTGAATCATTTAA
1 ATTTGAATCATTTAA
229745 GACTTAATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTTGAATCATTTAAT
Found at i:234815 original size:4 final size:4
Alignment explanation
Indices: 234801--234843 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
234791 GTAATTATTA
*
234801 TTAT ATAT TTAT TTAT TT-T TTAT ATTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTA
234844 ATAACAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.80
5 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:234866 original size:12 final size:12
Alignment explanation
Indices: 234844--234902 Score: 75
Period size: 12 Copynumber: 4.9 Consensus size: 12
234834 TATTTATTTA
*
234844 ATAACAATAATGT
1 ATAATAATAAT-T
234857 AT-ATAATAATT
1 ATAATAATAATT
*
234868 ATAATAATAATC
1 ATAATAATAATT
*
234880 ATAATAATAATA
1 ATAATAATAATT
234892 ATAATAATAAT
1 ATAATAATAAT
234903 AATGGGTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
11 3 0.07
12 37 0.88
13 2 0.05
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:234874 original size:3 final size:3
Alignment explanation
Indices: 234859--234905 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
234849 AATAATGTAT
* *
234859 ATA ATA ATT ATA ATA ATA ATC ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
234906 GGGTAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:235259 original size:124 final size:122
Alignment explanation
Indices: 235038--235333 Score: 371
Period size: 124 Copynumber: 2.4 Consensus size: 122
235028 GTTGAATAAA
* * * *
235038 TTCTTCTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCGCT-GGGGATGATGTTGACC
1 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCTGGGGGATGATGCTAACC
* * * * * *
235101 TATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAACTCTTCTTATTTTGAAC
65 TATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAACTCTTCTCATTGTGAAC
* * *
235159 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGGAAGGTTTATGCTAAT
1 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGG--GGATGATGCTAAC
* * *
235224 CTATCTGCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC
64 CTATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAACTCTTCTCATTGTGAAC
* *
235283 TTCTTCTTCTTCTTCTTCAGATAAGTTCTTCTTATTATGAACTTTCTCTGG
1 TTCTTC-T-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
235334 AAATGTTGAT
Statistics
Matches: 151, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
121 14 0.09
122 32 0.21
124 64 0.42
125 1 0.01
126 40 0.26
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.44
Consensus pattern (122 bp):
TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGGGGATGATGCTAACCT
ATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAACTCTTCTCATTGTGAAC
Found at i:235459 original size:113 final size:113
Alignment explanation
Indices: 235250--235822 Score: 666
Period size: 113 Copynumber: 5.0 Consensus size: 113
235240 TAGAATTATG
** *
235250 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCTTCTTCAGAT-AAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-T-TTCTTCTTCAGATGAA-TTCTTC
* * * * *
235314 TTATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
63 TCATTATGAACTCTATCTGGAAATGCTGATCCATCAAATGATGAATTTGAA
* * *
235365 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAATTCTTCCCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAATTCTTCTCA
* * * * * *
235430 TTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCTATCTGGAAATGCTGATCCATCAAATGATGAATTTGAA
* * *
235478 CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCTT
1 CAAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTC--A-GATGAATTCTT
* ** * * **
235543 CTCATTATGAACTCTACCTGGAAATTTTAATCCATCAAAAGATGAATTCAAA
62 CTCATTATGAACTCTATCTGGAAATGCTGATCCATCAAATGATGAATTTGAA
* * *
235595 CAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAATTCTTCTCA
* * * *
235660 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAA-TTCAA
66 TTATGAACTCTATCTGGAAATGCTGATCCATCAAATGATGAATTTGAA
* * *
235707 GCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTT-TTCTTTAGATGATGAGTTCTT
1 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGA--A-TTCTT
* * *
235771 CTCATTATGAACTCTATCTGGTAATGCTGATCCATCAATTGATGGATTTGAA
62 CTCATTATGAACTCTATCTGGAAATGCTGATCCATCAAATGATGAATTTGAA
235823 TCTTTGCTAA
Statistics
Matches: 392, Mismatches: 56, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
112 14 0.04
113 154 0.39
114 42 0.11
115 81 0.21
116 45 0.11
117 56 0.14
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAATTCTTCTCA
TTATGAACTCTATCTGGAAATGCTGATCCATCAAATGATGAATTTGAA
Found at i:235599 original size:230 final size:228
Alignment explanation
Indices: 235249--235808 Score: 750
Period size: 230 Copynumber: 2.4 Consensus size: 228
235239 ATAGAATTAT
** * * *
235249 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCTTCTTCTTC-A-GATAAGTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC--CTTCTTCAATGATGAGTTCT
* * * ** **
235312 TCTTATTATGAACT-TTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAA
64 TCTCATTATGAACTCTAC-CTGGAAATGTTAATCCATCAAAAGATGAATTCAAACAAAAGGTTAA
* *
235376 ACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAATTCTTCCCATTATGAACTCG
128 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCCCATTATGAACTCG
* * **
235441 AACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
193 AACTGGAAAAGCTGATCCATCAAATGATGAATTCAA
235477 GCAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGATGAGTTCT
1 GCAAAAGG-TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC-AATGATGAGTTCT
*
235542 TCTCATTATGAACTCTACCTGGAAATTTTAATCCATCAAAAGATGAATTCAAACAAAAGGTTAAA
64 TCTCATTATGAACTCTACCTGGAAATGTTAATCCATCAAAAGATGAATTCAAACAAAAGGTTAAA
* * ***
235607 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC
129 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCCCATTATGAACTCGA
*
235672 TCTGGAAAAGCTGATCCATCAAATGATGAATTCAA
194 ACTGGAAAAGCTGATCCATCAAATGATGAATTCAA
* * *
235707 GCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-TTTCTTTAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA-ATGATGAGTTCTT
* * * *
235771 CTCATTATGAACTCTATCTGGTAATGCTGATCCATCAA
65 CTCATTATGAACTCTACCTGGAAATGTTAATCCATCAA
235809 TTGATGGATT
Statistics
Matches: 293, Mismatches: 33, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
227 8 0.03
228 59 0.20
229 66 0.23
230 158 0.54
231 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (228 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAATGATGAGTTCTTC
TCATTATGAACTCTACCTGGAAATGTTAATCCATCAAAAGATGAATTCAAACAAAAGGTTAAACA
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCCCATTATGAACTCGAAC
TGGAAAAGCTGATCCATCAAATGATGAATTCAA
Found at i:236683 original size:101 final size:98
Alignment explanation
Indices: 236509--237022 Score: 611
Period size: 101 Copynumber: 5.3 Consensus size: 98
236499 GATCATGTAG
* *
236509 TTCATCTTT-TAATTCCAATGATTGGTTCTGT--GGTTCCTACCAAACCAGATCAGATAACTCAA
1 TTCATCTTTCAAATT-CAATGATTGGTT-TGTAGGGTTCATACCAAACCAGATCAGATAACTCAA
*
236571 AGAACACTTCCAGAAGATGGTATTGGGTCTCGAGCAAA
64 AGAACACTTCCAGAAGATGCTA-TGGG--TCGAGCAAA
* *
236609 TTCATCTTTCAAATCCAATGATTGGTTCTGT-GGTTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATTCAATGATTGGTT-TGTAGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
236673 GAACACTTCCAGAAGATGGTATTGGGTCTCGAGCAAA
65 GAACACTTCCAGAAGATGCTA-TGGG--TCGAGCAAA
*
236710 TTCATCTTTCAAATTCAATGATTGGTTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATTCAATGATTGG-TTTGTAGGGTTCATACCAAACCAGATCAGATAACTCAAA
* *
236775 GAACACTTTCAGAAGATGCTA----T-GAGCACA
65 GAACACTTCCAGAAGATGCTATGGGTCGAGCAAA
*
236804 TTCATCTTCCAAATTCAATGATTGGTTT-TAGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATTCAATGATTGGTTTGTAGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* ***
236868 AACACTTCCAGAAGATGCTATGAG-C-A-CTTG
66 AACACTTCCAGAAGATGCTATGGGTCGAGCAAA
*
236898 TTC-TAC-TTCTAAATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAA
1 TTCAT-CTTTC-AAATTCAATGATTGGTTTGTAGGGTTCATACCAAACCAGATCAGATAACTCAA
*
236961 AGAACACTTCCAGAAGATGCTA----T-GAGCACA
64 AGAACACTTCCAGAAGATGCTATGGGTCGAGCAAA
236991 TTCAT-TTTCCAAATTCAATGATTGGTTCTGTA
1 TTCATCTTT-CAAATTCAATGATTGGTT-TGTA
237023 TAGAAACATG
Statistics
Matches: 375, Mismatches: 20, Indels: 44
0.85 0.05 0.10
Matches are distributed among these distances:
92 56 0.15
93 29 0.08
94 58 0.15
95 58 0.15
100 25 0.07
101 96 0.26
102 53 0.14
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (98 bp):
TTCATCTTTCAAATTCAATGATTGGTTTGTAGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATGGGTCGAGCAAA
Found at i:236966 original size:95 final size:93
Alignment explanation
Indices: 236703--237017 Score: 526
Period size: 95 Copynumber: 3.4 Consensus size: 93
236693 ATTGGGTCTC
* *
236703 GAGCAAATTCATCTTTCAAATTCAATGATTGGTTTTTTAGGGTTCATACCAAACCAGATCAGATA
1 GAGCACATTCATCTTCCAAATTCAATGATTGG-TTTTTAGGGTTCATACCAAACCAGATCAGATA
*
236768 ACTCAAAGAACACTTTCAGAAGATGCTAT
65 ACTCAAAGAACACTTCCAGAAGATGCTAT
236797 GAGCACATTCATCTTCCAAATTCAATGATTGG-TTTTAGGGTTCATACCAAACCAGATCAGATAA
1 GAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAA
236861 CTCAAAGAACACTTCCAGAAGATGCTAT
66 CTCAAAGAACACTTCCAGAAGATGCTAT
* *
236889 GAGCACTTGTTC-TACTTCTAAATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGA
1 GAGCAC--ATTCAT-CTTCCAAATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGA
236953 TAACTCAAAGAACACTTCCAGAAGATGCTAT
63 TAACTCAAAGAACACTTCCAGAAGATGCTAT
*
236984 GAGCACATTCATTTTCCAAATTCAATGATTGGTT
1 GAGCACATTCATCTTCCAAATTCAATGATTGGTT
237018 CTGTATAGAA
Statistics
Matches: 208, Mismatches: 8, Indels: 11
0.92 0.04 0.05
Matches are distributed among these distances:
92 65 0.31
93 24 0.12
94 53 0.25
95 66 0.32
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (93 bp):
GAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAA
CTCAAAGAACACTTCCAGAAGATGCTAT
Found at i:236977 original size:187 final size:192
Alignment explanation
Indices: 236509--237021 Score: 670
Period size: 187 Copynumber: 2.6 Consensus size: 192
236499 GATCATGTAG
* * *
236509 TTCATCTTT-TAATTCCAATGATTGG-TTCT-GTGGTTCCTACCAAACCAGATCAGATAACTCAA
1 TTCATCTTTCAAATT-CAATGATTGGTTTTTAG-GGTTCATACCAAACCAGATCAGATAACTCAA
* * * *
236571 AGAACACTTCCAGAAGATGGTATTGGGTCTCGAGCAAATTCATCTTTCAAATCCAATGATTGGTT
64 AGAACACTTCCAGAAGATGCTA-------T-GAGCACATTCATCTTCCAAATTCAATGATTGGTT
* * *
236636 CTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGGTATTGGGTC
121 CTGTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAG--
236701 TCGAGCAAA
184 TCGAGCAAA
236710 TTCATCTTTCAAATTCAATGATTGGTTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATTCAATGATTGG-TTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
236775 GAACACTTTCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTT-T-TAGGGT
65 GAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGT-GGGT
***
236838 TCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-C-A-CTTG
129 TCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCGAGCAAA
236898 TTC-TAC-TTCTAAATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAA
1 TTCAT-CTTTC-AAATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAA
*
236961 AGAACACTTCCAGAAGATGCTATGAGCACATTCATTTTCCAAATTCAATGATTGGTTCTGT
64 AGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGT
237022 ATAGAAACAT
Statistics
Matches: 287, Mismatches: 16, Indels: 30
0.86 0.05 0.09
Matches are distributed among these distances:
187 97 0.34
188 21 0.07
189 2 0.01
190 1 0.00
193 4 0.01
194 53 0.18
195 31 0.11
196 1 0.00
201 19 0.07
202 4 0.01
203 53 0.18
204 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (192 bp):
TTCATCTTTCAAATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTGGGTTC
ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCGAGCAAA
Found at i:237806 original size:1 final size:1
Alignment explanation
Indices: 237802--237868 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
237792 TTTGACCCCC
* * * * * * * * *
237802 TTTTTTTCTTTTCTCTTTTTTTTTCTTTTTTTTTCTTTTTTTTTCTTTTTTTCTTTCTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
237867 TT
1 TT
237869 CTCTTCAAGC
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:237822 original size:17 final size:16
Alignment explanation
Indices: 237802--237868 Score: 93
Period size: 17 Copynumber: 4.1 Consensus size: 16
237792 TTTGACCCCC
237802 TTTTTTTCTTTTCTCTT
1 TTTTTTTCTTTTCT-TT
237819 TTTTTTTCTTTT-TTT
1 TTTTTTTCTTTTCTTT
237834 TTCTTTTT-TTTTCTTT
1 TT-TTTTTCTTTTCTTT
237850 TTTTCTTTCTTTTCTTT
1 TTTT-TTTCTTTTCTTT
237867 TT
1 TT
237869 CTCTTCAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.22
16 14 0.30
17 22 0.48
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTCTTTTCTTT
Found at i:237823 original size:10 final size:10
Alignment explanation
Indices: 237810--237868 Score: 68
Period size: 10 Copynumber: 6.1 Consensus size: 10
237800 CCTTTTTTTC
237810 TTTTCTCTTT
1 TTTTCTCTTT
*
237820 TTTTTTCTTT
1 TTTTCTCTTT
*
237830 TTTTTTCTTT
1 TTTTCTCTTT
*
237840 TTTTTTCTTT
1 TTTTCTCTTT
*
237850 TTTTCT-TTC
1 TTTTCTCTTT
237859 TTTTCT-TTT
1 TTTTCTCTTT
237868 T
1 T
237869 CTCTTCAAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
9 11 0.24
10 34 0.76
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:237840 original size:27 final size:27
Alignment explanation
Indices: 237802--237874 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
237792 TTTGACCCCC
237802 TTTTTTTCTTTTCTCTT-TTTTTTTCTT
1 TTTTTTTCTTTTCTCTTCTTTTTTTC-T
* *
237829 TTTTTTTCTTTTTTTTTCTTTTTTTCT
1 TTTTTTTCTTTTCTCTTCTTTTTTTCT
*
237856 TTCTTTTCTTTTTCTCTTC
1 TTTTTTTC-TTTTCTCTTC
237875 AAGCATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTTTCTTTTCTCTTCTTTTTTTCT
Found at i:245172 original size:15 final size:16
Alignment explanation
Indices: 245149--245181 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
245139 AATAATGAAT
245149 AATGAATGTATG-CAA
1 AATGAATGTATGCCAA
*
245164 AATGCATGTATGCCAA
1 AATGAATGTATGCCAA
245180 AA
1 AA
245182 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGAATGTATGCCAA
Found at i:248512 original size:18 final size:18
Alignment explanation
Indices: 248481--248521 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
248471 ATATTAATAA
248481 GAAAATATATAAATACTAT
1 GAAAATATATAAATA-TAT
248500 GAAAATA-ATAAATATAT
1 GAAAATATATAAATATAT
248517 -AAAAT
1 GAAAAT
248522 TTTGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 3 0.14
18 7 0.32
19 7 0.32
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
GAAAATATATAAATATAT
Found at i:250657 original size:9 final size:9
Alignment explanation
Indices: 250645--250708 Score: 76
Period size: 9 Copynumber: 7.1 Consensus size: 9
250635 ATTATTTATT
*
250645 TAATAACAA
1 TAATAATAA
*
250654 TAATGTATA-
1 TAAT-AATAA
*
250663 TAATAATTA
1 TAATAATAA
250672 TAATAATAA
1 TAATAATAA
*
250681 TCATAATAA
1 TAATAATAA
250690 TAATAATAA
1 TAATAATAA
250699 TAATAATAA
1 TAATAATAA
250708 T
1 T
250709 GGGTAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
8 2 0.04
9 42 0.91
10 2 0.04
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
TAATAATAA
Found at i:250669 original size:12 final size:12
Alignment explanation
Indices: 250647--250705 Score: 75
Period size: 12 Copynumber: 4.9 Consensus size: 12
250637 TATTTATTTA
*
250647 ATAACAATAATGT
1 ATAATAATAAT-T
250660 AT-ATAATAATT
1 ATAATAATAATT
*
250671 ATAATAATAATC
1 ATAATAATAATT
*
250683 ATAATAATAATA
1 ATAATAATAATT
250695 ATAATAATAAT
1 ATAATAATAAT
250706 AATGGGTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
11 3 0.07
12 37 0.88
13 2 0.05
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:250677 original size:3 final size:3
Alignment explanation
Indices: 250662--250708 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
250652 AATAATGTAT
* *
250662 ATA ATA ATT ATA ATA ATA ATC ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
250709 GGGTAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:261336 original size:24 final size:23
Alignment explanation
Indices: 261309--261360 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
261299 AGGAGGAGAT
*
261309 CAAGCAAAGAAAAACAACCACTAG
1 CAAGCAAAGAAAAACAAACA-TAG
*
261333 CAAG---AGAAAAACAAACATAT
1 CAAGCAAAGAAAAACAAACATAG
261353 CAAGCAAA
1 CAAGCAAA
261361 AGGAACAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
20 6 0.26
21 12 0.52
23 1 0.04
24 4 0.17
ACGTcount: A:0.62, C:0.21, G:0.12, T:0.06
Consensus pattern (23 bp):
CAAGCAAAGAAAAACAAACATAG
Found at i:261356 original size:20 final size:21
Alignment explanation
Indices: 261311--261349 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
261301 GAGGAGATCA
*
261311 AGCAA-AGAAAAACAACCACT
1 AGCAAGAGAAAAACAAACACT
261331 AGCAAGAGAAAAACAAACA
1 AGCAAGAGAAAAACAAACA
261350 TATCAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.64, C:0.21, G:0.13, T:0.03
Consensus pattern (21 bp):
AGCAAGAGAAAAACAAACACT
Found at i:262933 original size:3 final size:3
Alignment explanation
Indices: 262909--262995 Score: 56
Period size: 3 Copynumber: 29.3 Consensus size: 3
262899 GCTTAAAAAA
* * * * *
262909 TAT TA- TAT TGT TAT TTT TAT TAT TAT AAT AAT TACT TAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* *
262954 TAG TAT TAT TAT TAT T-T T-T TATT TAT TAA T-T TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT T
262996 TTGTAGGTCC
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
2 7 0.11
3 50 0.76
4 9 0.14
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:262975 original size:25 final size:26
Alignment explanation
Indices: 262908--262997 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 26
262898 GGCTTAAAAA
* *
262908 ATATTATATTGTTATTTTTATTATTAT
1 ATATTAT-TTTTTATTTTTAATATTAT
* * *
262935 AATAATTACTTATTATTTTTAGTATTAT
1 -AT-ATTATTTTTTATTTTTAATATTAT
262963 -TATTATTTTTTATTTATTAAT-TTAT
1 ATATTATTTTTTATTT-TTAATATTAT
262988 ATATTATTTT
1 ATATTATTTT
262998 GTAGGTCCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 16 0.30
26 14 0.26
28 19 0.36
29 4 0.08
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (26 bp):
ATATTATTTTTTATTTTTAATATTAT
Found at i:267236 original size:23 final size:23
Alignment explanation
Indices: 267206--267265 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
267196 CATTTTATAT
*
267206 GGCACTTCGGTGTAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
267229 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
* *
267252 GGTACTTCAGTGCA
1 GGCACTTCGGTGCA
267266 TTTATTCGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:271702 original size:19 final size:19
Alignment explanation
Indices: 271678--271747 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
271668 TCTTTTGGTT
271678 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
271697 GAAATGAAATTCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
271714 --TA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
271730 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
271748 ACAGAATCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 9 0.22
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 27 0.68
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:271723 original size:33 final size:33
Alignment explanation
Indices: 271686--271772 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
271676 TTGAAATGAA
* *
271686 AATCGCAACGCGAAATGAAATTCGCAACTAGAG
1 AATCGCAACGCGAAATGAAATTCGCAACGACAG
*
271719 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAATTCGCAACGACAG
*
271752 AATCGTAACGCGAAATGAAAT
1 AATCGCAACGCGAAATGAAAT
271773 CTAAGTGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAATTCGCAACGACAG
Found at i:272005 original size:22 final size:22
Alignment explanation
Indices: 271953--272007 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
271943 TGGTTGTGAG
**
271953 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
271975 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
271997 GGATTTCTTCG
1 GGATTTCTTCG
272008 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:272200 original size:20 final size:20
Alignment explanation
Indices: 272177--272287 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
272167 TATGTATTAT
272177 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
272197 CGTTGCGATATACGGATACA
1 CGTTGCGATTTACGGATACG
272217 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
272237 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
272257 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
272277 CGTTGCGATTT
1 CGTTGCGATTT
272288 TGGAAAATCG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
20 78 0.99
21 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:272261 original size:40 final size:40
Alignment explanation
Indices: 272154--272287 Score: 146
Period size: 40 Copynumber: 3.3 Consensus size: 40
272144 CTTTAAATAT
*
272154 CGCGTTGCGATTTTATGTATT-ATCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTATGTGTTCA-CGTTGCGATTTACGGATA
* * *
272195 CGCGTTGCGATATACG-GATACACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATGTG-TTCACGTTGCGATTTACGGATA
* * ** *
272235 CGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTATGTGTTCACGTTGCGATTTACGGATA
272275 CGCGTTGCGATTT
1 CGCGTTGCGATTT
272288 TGGAAAATCG
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
40 66 0.85
41 12 0.15
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (40 bp):
CGCGTTGCGATTTATGTGTTCACGTTGCGATTTACGGATA
Found at i:272304 original size:21 final size:21
Alignment explanation
Indices: 272274--272391 Score: 91
Period size: 21 Copynumber: 5.7 Consensus size: 21
272264 ATTTTCATAT
*
272274 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * **
272295 TCGCAATGCGATTTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
272316 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
* *
272337 TCGCGTTGCGATTTTGGAAAC
1 TCGCATTGCGATTTTGGAAAA
* **
272358 T-G-ATTTGCGATTCTGG-GGA
1 TCGCA-TTGCGATTTTGGAAAA
272377 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
272392 TATTTCGCGT
Statistics
Matches: 74, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.01
20 23 0.31
21 48 0.65
22 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:277603 original size:20 final size:21
Alignment explanation
Indices: 277580--277628 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
277570 TTTTTTTCCT
277580 TTTTAATTTA-TCATTTTTTA
1 TTTTAATTTATTCATTTTTTA
* *
277600 TTTTAA-TTATTTATTTTTTC
1 TTTTAATTTATTCATTTTTTA
277620 TTTTAATTT
1 TTTTAATTT
277629 TAGTGTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 20 0.80
21 2 0.08
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTAATTTATTCATTTTTTA
Found at i:277718 original size:17 final size:16
Alignment explanation
Indices: 277688--277806 Score: 68
Period size: 16 Copynumber: 7.2 Consensus size: 16
277678 AAATCTAACA
277688 TTTTTATTTTTATTAT
1 TTTTTATTTTTATTAT
277704 TTTTTATTTTATATTAT
1 TTTTTATTTT-TATTAT
* ***
277721 TATTTT-TTCTT-TCCC
1 T-TTTTATTTTTATTAT
* *
277736 TTTTGATTGATTTAATAT
1 TTTTTATT--TTTATTAT
277754 TTTTTATTTTCT-TTAT
1 TTTTTATTTT-TATTAT
277770 TTTCTT-TTTATT-TTAT
1 TTT-TTATTT-TTATTAT
*
277786 TTTATTATTATTATTAT
1 TTT-TTATTTTTATTAT
277803 TTTT
1 TTTT
277807 CCTTCCTTTC
Statistics
Matches: 78, Mismatches: 14, Indels: 22
0.68 0.12 0.19
Matches are distributed among these distances:
14 3 0.04
15 4 0.05
16 35 0.45
17 25 0.32
18 11 0.14
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTTATTTTTATTAT
Found at i:277777 original size:5 final size:5
Alignment explanation
Indices: 277755--277805 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
277745 ATTTAATATT
* *
277755 TTTTA TTTT- CTTTA TTTTCT TTTTA TTTTA TTTTA TTATTA TTATTA
1 TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TT-TTA TT-TTA
277802 TTTT
1 TTTT
277806 TCCTTCCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 21 0.54
6 15 0.38
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:277830 original size:76 final size:81
Alignment explanation
Indices: 277689--277837 Score: 202
Period size: 80 Copynumber: 1.9 Consensus size: 81
277679 AATCTAACAT
* * *
277689 TTTTATTTTTATTATTTTTTATTTTATATTATTATTTTTTCTTTCCCTTTTGATTGATTTAATAT
1 TTTTATTTTTATTATTTTTTATTATATATTATTATTTTTTCCTTCCCTTTTCATTGATTTAATAT
277754 TT-TTTATTTTCTTTA
66 TTATTTATTTTCTTTA
* *
277769 TTTTCTTTTTATT-TTATTTTATTAT-TATTATTA-TTTTTCCTT-CC-TTTCATTTATTTAATA
1 TTTTATTTTTATTATT-TTTTATTATATATTATTATTTTTTCCTTCCCTTTTCATTGATTTAATA
277829 TTTATTTAT
65 TTTATTTAT
277838 AATTTCTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
76 17 0.27
77 7 0.11
78 8 0.13
79 10 0.16
80 20 0.32
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.72
Consensus pattern (81 bp):
TTTTATTTTTATTATTTTTTATTATATATTATTATTTTTTCCTTCCCTTTTCATTGATTTAATAT
TTATTTATTTTCTTTA
Found at i:277863 original size:79 final size:74
Alignment explanation
Indices: 277703--277867 Score: 183
Period size: 76 Copynumber: 2.1 Consensus size: 74
277693 ATTTTTATTA
* *
277703 TTTTTTATTTTATATTATTATTTTTTCTTTCCCTTTTGATTGATTTAATATTTTTTATTTTCTTT
1 TTTTTTATTTTATATTATTATTTTTTCCTTCCCTTTTCATTGATTTAATATTTTTTATTTTCTTT
**
277768 ATTTTCTTT
66 ATTAACTTT
*
277777 TTATTTTATTTTATTATTATTATTATTTTTCCTT-CC-TTTCATTTATTTAATATTTATTTATAA
1 TT-TTTTATTTTA-TATTATTA-T-TTTTTCCTTCCCTTTTCATTGATTTAATATTT-TTTAT--
277840 TTTC-TTATCTAACATTT
59 TTTCTTTAT-TAAC-TTT
277857 TTTTTTATTTT
1 TTTTTTATTTT
277868 TTAGGGATAT
Statistics
Matches: 77, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
74 2 0.03
75 10 0.13
76 25 0.32
77 8 0.10
78 12 0.16
79 15 0.19
80 5 0.06
ACGTcount: A:0.20, C:0.08, G:0.01, T:0.70
Consensus pattern (74 bp):
TTTTTTATTTTATATTATTATTTTTTCCTTCCCTTTTCATTGATTTAATATTTTTTATTTTCTTT
ATTAACTTT
Found at i:283612 original size:42 final size:41
Alignment explanation
Indices: 283566--283679 Score: 106
Period size: 42 Copynumber: 2.7 Consensus size: 41
283556 GGTTAATCAA
** *
283566 TAGCGGCGTTTATAGTAAAAACGCCGTAATAGAGT-GTTAAT
1 TAGCGGCGTTTATA-TAAAAACGCCACAATAGAGTGGTAAAT
* * * *
283607 GTAGCGGTGTCTATACCACAAACGCCACAATAGAGTGGTAAAT
1 -TAGCGGCGTTTATA-TAAAAACGCCACAATAGAGTGGTAAAT
*
283650 TAGC-GCGTTTATATATAAAACGTCACAATA
1 TAGCGGCGTTTATATA-AAAACGCCACAATA
283680 TGGTTGTTTA
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
40 1 0.02
41 19 0.33
42 32 0.56
43 5 0.09
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (41 bp):
TAGCGGCGTTTATATAAAAACGCCACAATAGAGTGGTAAAT
Found at i:285104 original size:42 final size:42
Alignment explanation
Indices: 285033--285227 Score: 140
Period size: 42 Copynumber: 4.8 Consensus size: 42
285023 GAGTAGAACA
* * *
285033 ATAGCGGCGTTTTT-TTACAAACGCTGCAATAGGTGTAATAT
1 ATAGTGGCGTTTTTATAACAAACGCCGCAATAGGTGTAATAT
**
285074 ATAGTGGCGTTTTTATAACAAACGCCGCAATATATTTGT-AT-T
1 ATAGTGGCGTTTTTATAACAAACGCCGC-A-ATAGGTGTAATAT
* * * * **
285116 TTAGTGGTGTTTTTAAATAA-AAATGCCGCAAAAAAT-TAGATAT
1 ATAGTGGCGTTTTT--ATAACAAACGCCGCAATAGGTGTA-ATAT
* * *
285159 -TAATGGCG--TTTATAACAATCGCCGCAATAGGTGTACTAT
1 ATAGTGGCGTTTTTATAACAAACGCCGCAATAGGTGTAATAT
*
285198 ATAGTGGCGTTTTT-TACCAAAC-CCGCAATA
1 ATAGTGGCGTTTTTATAACAAACGCCGCAATA
285228 TATTTGAATT
Statistics
Matches: 119, Mismatches: 22, Indels: 27
0.71 0.13 0.16
Matches are distributed among these distances:
38 4 0.03
39 14 0.12
40 21 0.18
41 22 0.18
42 36 0.30
43 12 0.10
44 10 0.08
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (42 bp):
ATAGTGGCGTTTTTATAACAAACGCCGCAATAGGTGTAATAT
Found at i:285309 original size:124 final size:124
Alignment explanation
Indices: 285058--285312 Score: 284
Period size: 124 Copynumber: 2.1 Consensus size: 124
285048 TACAAACGCT
* *
285058 GCAATAGGTGTAATATATAGTGGCGTTTTTATAACAAACGCCGCAATATATTTGTATTTTAGTGG
1 GCAATAGGTGTAATATATAGTGGCGTTTTTATAACAAACGCCGCAATATATTTGAATTTTAGCGG
* * * * * * *
285123 TGTTTTTAAATAAAAATGCCGCAAAAAATTAGATATTAATGGCGTTTATAACAATCGCC
66 CGTTTCTAAACAAAAACGCCGCAAAAAATTAGACATTAATGGCGTTTATAAAAAGCGCC
* *
285182 GCAATAGGTGTACTATATAGTGGCGTTTTT-TACCAAAC-CCGCAATATATTTGAATTGTTA-CG
1 GCAATAGGTGTAATATATAGTGGCGTTTTTATAACAAACGCCGCAATATATTTGAATT-TTAGCG
* * * * * * *
285244 GCGTTTCTAGACACAAACGCCGCAATATATATGGACATTAGCT-GCGTTTATTAAAAAGCGTC
65 GCGTTTCTAAACAAAAACGCCGCAAAAAAT-TAGACATTA-ATGGCGTTTA-TAAAAAGCGCC
285306 GCAATAG
1 GCAATAG
285313 AGTATAACTG
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
122 40 0.37
123 24 0.22
124 45 0.41
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (124 bp):
GCAATAGGTGTAATATATAGTGGCGTTTTTATAACAAACGCCGCAATATATTTGAATTTTAGCGG
CGTTTCTAAACAAAAACGCCGCAAAAAATTAGACATTAATGGCGTTTATAAAAAGCGCC
Found at i:295439 original size:86 final size:86
Alignment explanation
Indices: 295305--295496 Score: 242
Period size: 86 Copynumber: 2.2 Consensus size: 86
295295 ACTAAATCTA
* * * * **
295305 AAAACCTACT-CGACGTTTGTAGGAAAAACGCCGCTAAAAATCATCACCTACTGCGGTGTTTGTA
1 AAAACCTACTACGGCGTTTTTAAGAAAAACGCCGCTAAAAATCAACACCTACTGCGACGTTTGTA
*
295369 GGAAAAACGCCGCAAAATATC
66 GGAAAAACGCCGCAAAACATC
* ** *
295390 AAAACCTACTACGGCGTTTTTAAGTAAAACGCCGCTAAATCTCAACACCTACTGCGACGTTTTTA
1 AAAACCTACTACGGCGTTTTTAAGAAAAACGCCGCTAAAAATCAACACCTACTGCGACGTTTGTA
* *
295455 GGAAACACGCCGCTAAACATC
66 GGAAAAACGCCGCAAAACATC
* *
295476 AACACCTATTACGGCGTTTTT
1 AAAACCTACTACGGCGTTTTT
295497 TAAAACTTTA
Statistics
Matches: 91, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 10 0.11
86 81 0.89
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (86 bp):
AAAACCTACTACGGCGTTTTTAAGAAAAACGCCGCTAAAAATCAACACCTACTGCGACGTTTGTA
GGAAAAACGCCGCAAAACATC
Found at i:295495 original size:43 final size:43
Alignment explanation
Indices: 295308--295496 Score: 211
Period size: 43 Copynumber: 4.4 Consensus size: 43
295298 AAATCTAAAA
* * * *
295308 ACCTACT-CGACGTTTGTAGGAAAAACGCCGCTAAAAATCATC
1 ACCTACTACGGCGTTTTTAGGAAAAACGCCGCTAAACATCAAC
* * * * * *
295350 ACCTACTGCGGTGTTTGTAGGAAAAACGCCGCAAAATATCAAA
1 ACCTACTACGGCGTTTTTAGGAAAAACGCCGCTAAACATCAAC
* *
295393 ACCTACTACGGCGTTTTTAAGTAAAACGCCGCTAAATC-TCAAC
1 ACCTACTACGGCGTTTTTAGGAAAAACGCCGCTAAA-CATCAAC
* * *
295436 ACCTACTGCGACGTTTTTAGGAAACACGCCGCTAAACATCAAC
1 ACCTACTACGGCGTTTTTAGGAAAAACGCCGCTAAACATCAAC
*
295479 ACCTATTACGGCGTTTTT
1 ACCTACTACGGCGTTTTT
295497 TAAAACTTTA
Statistics
Matches: 122, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
42 8 0.07
43 114 0.93
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
ACCTACTACGGCGTTTTTAGGAAAAACGCCGCTAAACATCAAC
Found at i:296144 original size:30 final size:30
Alignment explanation
Indices: 296110--296208 Score: 123
Period size: 30 Copynumber: 3.3 Consensus size: 30
296100 ATTTAAGTGT
296110 TTAAAGTATTTTTTTAATTAAAATAAGTAC
1 TTAAAGTATTTTTTTAATTAAAATAAGTAC
*
296140 TTAAAGTTATTTTTTT-ATTAAAATATGTAC
1 TTAAAG-TATTTTTTTAATTAAAATAAGTAC
* * *
296170 CTAAAGTA-TTTTTTAATCAAAATAGGTA-
1 TTAAAGTATTTTTTTAATTAAAATAAGTAC
296198 TCTAAAGTATT
1 T-TAAAGTATT
296209 CAACTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.10
29 20 0.33
30 25 0.42
31 9 0.15
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.46
Consensus pattern (30 bp):
TTAAAGTATTTTTTTAATTAAAATAAGTAC
Found at i:296179 original size:29 final size:29
Alignment explanation
Indices: 296111--296208 Score: 124
Period size: 29 Copynumber: 3.3 Consensus size: 29
296101 TTTAAGTGTT
*
296111 TAAAGTATTTTTTTAATTAAAATAAGTACT
1 TAAAGTATTTTTTT-ATTAAAATAAGTACC
*
296141 TAAAGTTATTTTTTTATTAAAATATGTACC
1 TAAAG-TATTTTTTTATTAAAATAAGTACC
* * * *
296171 TAAAGTATTTTTTAATCAAAATAGGTATC
1 TAAAGTATTTTTTTATTAAAATAAGTACC
296200 TAAAGTATT
1 TAAAGTATT
296209 CAACTTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
29 29 0.48
30 23 0.38
31 9 0.15
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (29 bp):
TAAAGTATTTTTTTATTAAAATAAGTACC
Found at i:297698 original size:2 final size:2
Alignment explanation
Indices: 297691--297722 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
297681 ATTATTTTAA
297691 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
297723 GCTTTTCATT
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):
AT
Found at i:298426 original size:18 final size:19
Alignment explanation
Indices: 298403--298438 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
298393 AAACGAATAT
*
298403 AAAACATGT-AAAATTAAG
1 AAAACATATAAAAATTAAG
298421 AAAACATATAAAAATTAA
1 AAAACATATAAAAATTAA
298439 ATACATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAAATTAAG
Done.