Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006248.1 Hibiscus syriacus cultivar Beakdansim tig00014891_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: 137724
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9005 original size:24 final size:23
Alignment explanation
Indices: 8948--9005 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
8938 AAAAAAATAA
*
8948 ATTTATAAAATACAAAATAAATT
1 ATTTATAAAATACAAAATAAAAT
* * *
8971 ATTAATCAAATATATAAATAAAAT
1 ATTTATAAAATACA-AAATAAAAT
*
8995 ATTTATGAAAT
1 ATTTATAAAAT
9006 TATGGTGGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (23 bp):
ATTTATAAAATACAAAATAAAAT
Found at i:13700 original size:21 final size:23
Alignment explanation
Indices: 13665--13712 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
13655 TAAAATATTA
*
13665 TAAATTTATATAATA-TTTAAGC
1 TAAATATATATAATATTTTAAGC
*
13687 TAAATATA-ATAATATTTTAAGT
1 TAAATATATATAATATTTTAAGC
13709 TAAA
1 TAAA
13713 ACCGTCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
TAAATATATATAATATTTTAAGC
Found at i:18528 original size:20 final size:20
Alignment explanation
Indices: 18503--18550 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
18493 TCATTTAAAT
18503 ATTATAAAAATCTAGGATAA
1 ATTATAAAAATCTAGGATAA
*
18523 ATTATAAAAATTTAGGATAA
1 ATTATAAAAATCTAGGATAA
18543 ATTATAAA
1 ATTATAAA
18551 TTTGATAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (20 bp):
ATTATAAAAATCTAGGATAA
Found at i:21857 original size:16 final size:16
Alignment explanation
Indices: 21838--21928 Score: 53
Period size: 16 Copynumber: 5.6 Consensus size: 16
21828 TGACCCGAAT
21838 CGAAAATAACCCAAAC
1 CGAAAATAACCCAAAC
*
21854 CGAAATTAA-CCAGAAC
1 CGAAAATAACCCA-AAC
*
21870 C-AAAATTAACCCGAAC
1 CGAAAA-TAACCCAAAC
* * *
21886 C-AAAAGCAACCAAAAT
1 CGAAAA-TAACCCAAAC
* *
21902 CGAAAGTAAACCAAAC
1 CGAAAATAACCCAAAC
*
21918 TGAAAAATAAC
1 CG-AAAATAAC
21929 TTGAATTGAA
Statistics
Matches: 54, Mismatches: 16, Indels: 9
0.68 0.20 0.11
Matches are distributed among these distances:
15 6 0.11
16 37 0.69
17 11 0.20
ACGTcount: A:0.56, C:0.25, G:0.09, T:0.10
Consensus pattern (16 bp):
CGAAAATAACCCAAAC
Found at i:22254 original size:30 final size:31
Alignment explanation
Indices: 22218--22280 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
22208 GTCTAAATGA
* *
22218 TAAGATTATCAAACAAGAAGACATATTT-TT
1 TAAGATTAACAAACAAGAAAACATATTTATT
22248 TAAGATTAACAAACAAGAAAACATATTTATT
1 TAAGATTAACAAACAAGAAAACATATTTATT
22279 TA
1 TA
22281 TAAGAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.32
Consensus pattern (31 bp):
TAAGATTAACAAACAAGAAAACATATTTATT
Found at i:25127 original size:15 final size:15
Alignment explanation
Indices: 25107--25201 Score: 154
Period size: 15 Copynumber: 6.3 Consensus size: 15
25097 GCTTTGATCT
25107 TCTTCAGAATTTTCA
1 TCTTCAGAATTTTCA
25122 TCTTCAGAATTTTCA
1 TCTTCAGAATTTTCA
*
25137 TCTTCAGGATTTTCA
1 TCTTCAGAATTTTCA
25152 TCTTCAGAATTTTCA
1 TCTTCAGAATTTTCA
*
25167 TCTTCAGGATTTTCA
1 TCTTCAGAATTTTCA
*
25182 TCTTCAGGATTTTCA
1 TCTTCAGAATTTTCA
*
25197 CCTTC
1 TCTTC
25202 CTCGATCATT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 76 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.46
Consensus pattern (15 bp):
TCTTCAGAATTTTCA
Found at i:25170 original size:45 final size:45
Alignment explanation
Indices: 25107--25201 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
25097 GCTTTGATCT
25107 TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTCAGGATTTTCA
1 TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTCAGGATTTTCA
*
25152 TCTTCAGAATTTTCATCTTCAGGATTTTCATCTTCAGGATTTTCA
1 TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTCAGGATTTTCA
*
25197 CCTTC
1 TCTTC
25202 CTCGATCATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.46
Consensus pattern (45 bp):
TCTTCAGAATTTTCATCTTCAGAATTTTCATCTTCAGGATTTTCA
Found at i:32877 original size:16 final size:16
Alignment explanation
Indices: 32858--32947 Score: 51
Period size: 16 Copynumber: 5.6 Consensus size: 16
32848 TGACCCGAAT
32858 CGAAAATAACCCAAAC
1 CGAAAATAACCCAAAC
*
32874 CGAAATTAA-CCAGAAC
1 CGAAAATAACCCA-AAC
*
32890 C-AAAATTAACCCGAAC
1 CGAAAA-TAACCCAAAC
* * *
32906 C-AAAAGCAACCAAAAT
1 CGAAAA-TAACCCAAAC
* * *
32922 CGAAAGTAAACCGAAC
1 CGAAAATAACCCAAAC
*
32938 TGAAAATAAC
1 CGAAAATAAC
32948 TTGAATTGAA
Statistics
Matches: 53, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
15 6 0.11
16 42 0.79
17 5 0.09
ACGTcount: A:0.54, C:0.26, G:0.10, T:0.10
Consensus pattern (16 bp):
CGAAAATAACCCAAAC
Found at i:32959 original size:32 final size:32
Alignment explanation
Indices: 32919--33001 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
32909 AAGCAACCAA
**
32919 AATC-GAAAGTAAACCGAACTGAAA-ATAACTTG
1 AATCTGAAAGTAAACCGAACT-AAATATAAC-CC
* *
32951 AAT-TGAAAGTAACCCGAACTAAATTTAACCC
1 AATCTGAAAGTAAACCGAACTAAATATAACCC
32982 AATCTGAAAGTAAACCGAAC
1 AATCTGAAAGTAAACCGAAC
33002 AAGATCACTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 6 0.14
32 37 0.86
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (32 bp):
AATCTGAAAGTAAACCGAACTAAATATAACCC
Found at i:33273 original size:30 final size:32
Alignment explanation
Indices: 33236--33303 Score: 113
Period size: 30 Copynumber: 2.2 Consensus size: 32
33226 AGTCTAAATG
*
33236 ATAAGATTATCAAACAAGAAAACATATT-TTT
1 ATAAGATTAACAAACAAGAAAACATATTATTT
33267 -TAAGATTAACAAACAAGAAAACATATTATTT
1 ATAAGATTAACAAACAAGAAAACATATTATTT
33298 ATAAGA
1 ATAAGA
33304 ATATATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 26 0.76
31 3 0.09
32 5 0.15
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.29
Consensus pattern (32 bp):
ATAAGATTAACAAACAAGAAAACATATTATTT
Found at i:34803 original size:60 final size:59
Alignment explanation
Indices: 34715--34883 Score: 173
Period size: 60 Copynumber: 2.8 Consensus size: 59
34705 ATGAAAGCGG
* * *
34715 AATATTCAAAAGTTT-GGTGACTTATTTAGAAAGAGGGTAATAGTTTAGGGATGAAATT-A
1 AATATTAAAAAGTTTAAG-GACTAATTTAGAAAGAGGGTAATAGTTT-GGGATGAAATTGA
* * * * * * *
34774 GAATGTTCAAAAGTTTAAGGTCTACTTTAGAATGAGAGTCATAGTTTGAGGATGAAATTGA
1 -AATATTAAAAAGTTTAAGGACTAATTTAGAAAGAGGGTAATAGTTTG-GGATGAAATTGA
*
34835 AATATTAAAAAGTTTAAGGACTAATTTAGAATA-AGGGTTATAGTTTGGG
1 AATATTAAAAAGTTTAAGGACTAATTTAGAA-AGAGGGTAATAGTTTGGG
34884 GACATATGAT
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
59 3 0.03
60 85 0.94
61 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (59 bp):
AATATTAAAAAGTTTAAGGACTAATTTAGAAAGAGGGTAATAGTTTGGGATGAAATTGA
Found at i:35076 original size:59 final size:58
Alignment explanation
Indices: 34965--35151 Score: 186
Period size: 60 Copynumber: 3.1 Consensus size: 58
34955 CACATGCCCT
* * *
34965 CAAATTATGATATTCATTCTAAATTAGTCCCTAAACTTTT-AATCATTCCAATTTCATCCT
1 CAAACTATGATA-TCATTCTAAATTAGTCCC-AAACTTTTGAA-CATTTCAATTTCATCCC
* * * *
35025 TATAA-TATGATATCATTCTAAATTAGTACGCAAACTTTTGAACTTTTCAA-TTCTTTCCC
1 CA-AACTATGATATCATTCTAAATTAGT-CCCAAACTTTTGAACATTTCAATTTC-ATCCC
35084 CAAACTATGACCT-TCATTCTAAATTAGTCCTCAAACTTTTTGAACATTTCAATTTCAT-CC
1 CAAACTATGA--TATCATTCTAAATTAGTCC-CAAAC-TTTTGAACATTTCAATTTCATCCC
35144 CAAACTAT
1 CAAACTAT
35152 ACGTATATAC
Statistics
Matches: 107, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
58 5 0.05
59 39 0.36
60 42 0.39
61 18 0.17
62 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (58 bp):
CAAACTATGATATCATTCTAAATTAGTCCCAAACTTTTGAACATTTCAATTTCATCCC
Found at i:35146 original size:60 final size:56
Alignment explanation
Indices: 34976--35151 Score: 178
Period size: 59 Copynumber: 3.0 Consensus size: 56
34966 AAATTATGAT
* *
34976 ATTCATTCTAAATTAGTCCCTAAACTTTT-AATCATTCCAATTTCATCCTTATAA-TATG
1 ATTCATTCTAAATTAGTCCC-AAACTTTTGAA-CATTTCAATTTCATCC-CA-AACTATG
* * *
35034 ATATCATTCTAAATTAGTACGCAAACTTTTGAACTTTTCAA-TTCTTTCCCCAAACTATG
1 AT-TCATTCTAAATTAGT-CCCAAACTTTTGAACATTTCAATTTC-AT-CCCAAACTATG
35093 ACCTTCATTCTAAATTAGTCCTCAAACTTTTTGAACATTTCAATTTCATCCCAAACTAT
1 A--TTCATTCTAAATTAGTCC-CAAAC-TTTTGAACATTTCAATTTCATCCCAAACTAT
35152 ACGTATATAC
Statistics
Matches: 99, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
58 7 0.07
59 37 0.37
60 36 0.36
61 16 0.16
62 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (56 bp):
ATTCATTCTAAATTAGTCCCAAACTTTTGAACATTTCAATTTCATCCCAAACTATG
Found at i:35351 original size:61 final size:61
Alignment explanation
Indices: 35279--35462 Score: 212
Period size: 61 Copynumber: 3.0 Consensus size: 61
35269 TGGATTCGAT
* ** *
35279 GATGAAATTGGAATATTTAAAAGTTTGGGGACCAATTTAAAATGAGGGCCATAGTTTAGGG
1 GATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAGTTTAGGG
* * * * *
35340 GGTGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTTATAGTTTCA--G
1 GATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAGTTT-AGGG
* * * *
35400 GATGAAATTGAAATATTCAAAAATTTAAGGATCAATTTAAAATG-GCGGTCATAGTTTTGGG
1 GATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAG-GGTCATAGTTTAGGG
35461 GA
1 GA
35463 CATATGATAT
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
59 1 0.01
60 48 0.48
61 51 0.50
62 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (61 bp):
GATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGGGTCATAGTTTAGGG
Found at i:35454 original size:60 final size:59
Alignment explanation
Indices: 35279--35456 Score: 198
Period size: 60 Copynumber: 2.9 Consensus size: 59
35269 TGGATTCGAT
* ** *
35279 GATGAAATTGGAATATTTAAAAGTTTGGGGACCAATTTAAAATGAGGGCCATAGTTTAGGG
1 GATGAAATTGGAATATTCAAAAGTTTAAGGA-CAATTTAAAATGAGGGTCATAGTTTA-GG
* * * *
35340 GGTGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTTATAGTTTCA-G
1 GATGAAATTGGAATATTCAAAAGTTTAAGGAC-AATTTAAAATGAGGGTCATAGTTT-AGG
* *
35400 GATGAAATTGAAATATTCAAAAATTTAAGGATCAATTTAAAATG-GCGGTCATAGTTT
1 GATGAAATTGGAATATTCAAAAGTTTAAGGA-CAATTTAAAATGAG-GGTCATAGTTT
35457 TGGGGACATA
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 49 0.49
61 48 0.48
62 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (59 bp):
GATGAAATTGGAATATTCAAAAGTTTAAGGACAATTTAAAATGAGGGTCATAGTTTAGG
Found at i:40287 original size:9 final size:9
Alignment explanation
Indices: 40255--40324 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 9
40245 CTGCTGGAAA
*
40255 ACCGGTTTA
1 ACCGGTTTG
*
40264 ACCAGTTTTG
1 ACC-GGTTTG
40274 AACCGGTTTG
1 -ACCGGTTTG
*
40284 ACCGGTCTG
1 ACCGGTTTG
*
40293 AATCGGTTTG
1 -ACCGGTTTG
*
40303 ACCGGTCTG
1 ACCGGTTTG
*
40312 AACCGGGTTG
1 -ACCGGTTTG
40322 ACC
1 ACC
40325 CGACCCGACT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
9 21 0.45
10 23 0.49
11 3 0.06
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:40299 original size:10 final size:10
Alignment explanation
Indices: 40272--40317 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
40262 TAACCAGTTT
*
40272 TGAACCGGTT
1 TGAACCGGTC
40282 TG-ACCGGTC
1 TGAACCGGTC
* *
40291 TGAATCGGTT
1 TGAACCGGTC
40301 TG-ACCGGTC
1 TGAACCGGTC
40310 TGAACCGG
1 TGAACCGG
40318 GTTGACCCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (10 bp):
TGAACCGGTC
Found at i:40299 original size:19 final size:19
Alignment explanation
Indices: 40272--40324 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
40262 TAACCAGTTT
40272 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTC
*
40291 TGAATCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTC
*
40310 TGAACCGGGTTGACC
1 TGAACCGGTTTGACC
40325 CGACCCGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.32, T:0.26
Consensus pattern (19 bp):
TGAACCGGTTTGACCGGTC
Found at i:40340 original size:17 final size:17
Alignment explanation
Indices: 40318--40375 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
40308 TCTGAACCGG
*
40318 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
40335 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
40352 GTTGACCCAACCCGACC
1 GTTGACCCGACCCGACC
40369 GTTGACC
1 GTTGACC
40376 GTGACCGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.19, C:0.43, G:0.22, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:40375 original size:7 final size:7
Alignment explanation
Indices: 40365--40407 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
40355 GACCCAACCC
40365 GACCGTT
1 GACCGTT
40372 GACCG-T
1 GACCGTT
40378 GACCGTT
1 GACCGTT
40385 GACCG-T
1 GACCGTT
40391 GACCGTT
1 GACCGTT
40398 GACCGTT
1 GACCGTT
40405 GAC
1 GAC
40408 TTTGTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:40383 original size:13 final size:13
Alignment explanation
Indices: 40365--40403 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
40355 GACCCAACCC
40365 GACCGTTGACCGT
1 GACCGTTGACCGT
40378 GACCGTTGACCGT
1 GACCGTTGACCGT
40391 GACCGTTGACCGT
1 GACCGTTGACCGT
40404 TGACTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:40390 original size:20 final size:20
Alignment explanation
Indices: 40365--40407 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
40355 GACCCAACCC
40365 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
40385 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
40405 GAC
1 GAC
40408 TTTGTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:41344 original size:63 final size:63
Alignment explanation
Indices: 41276--41399 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
41266 CTAATGTGAC
* ** * *
41276 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
41339 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
41400 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:47633 original size:10 final size:10
Alignment explanation
Indices: 47602--47696 Score: 97
Period size: 10 Copynumber: 9.6 Consensus size: 10
47592 GCTGCTGGAA
47602 AACCGGTTT-
1 AACCGGTTTG
*
47611 AACCAGTTTTG
1 AACC-GGTTTG
47622 AACCGGTTTG
1 AACCGGTTTG
47632 AACCGGTTTG
1 AACCGGTTTG
* * *
47642 ATCGGGTCTG
1 AACCGGTTTG
47652 AACCGGTTTG
1 AACCGGTTTG
*
47662 -ACCGGTCTG
1 AACCGGTTTG
47671 AACCGGGTTTG
1 AACC-GGTTTG
*
47682 -ACCGGTCTG
1 AACCGGTTTG
47691 AACCGG
1 AACCGG
47697 GTTAACCCGA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
9 17 0.24
10 44 0.63
11 9 0.13
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:47673 original size:39 final size:40
Alignment explanation
Indices: 47618--47696 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
47608 TTTAACCAGT
* *
47618 TTTGAACCGGTTTGAACC-GGTTTGATCGGGTCTGAACCGG
1 TTTGAACCGGTCTGAACCGGGTTTGA-CCGGTCTGAACCGG
47658 TTTG-ACCGGTCTGAACCGGGTTTGACCGGTCTGAACCGG
1 TTTGAACCGGTCTGAACCGGGTTTGACCGGTCTGAACCGG
47697 GTTAACCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 25 0.69
40 11 0.31
ACGTcount: A:0.16, C:0.23, G:0.33, T:0.28
Consensus pattern (40 bp):
TTTGAACCGGTCTGAACCGGGTTTGACCGGTCTGAACCGG
Found at i:47699 original size:20 final size:19
Alignment explanation
Indices: 47618--47696 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 19
47608 TTTAACCAGT
*
47618 TTTGAACCGGTTTGAACCGG
1 TTTG-ACCGGTCTGAACCGG
*
47638 TTTGATCGGGTCTGAACCGG
1 TTTGA-CCGGTCTGAACCGG
47658 TTTGACCGGTCTGAACCGGG
1 TTTGACCGGTCTGAACC-GG
47678 TTTGACCGGTCTGAACCGG
1 TTTGACCGGTCTGAACCGG
47697 GTTAACCCGA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
19 14 0.26
20 40 0.74
ACGTcount: A:0.16, C:0.23, G:0.33, T:0.28
Consensus pattern (19 bp):
TTTGACCGGTCTGAACCGG
Found at i:47723 original size:17 final size:17
Alignment explanation
Indices: 47701--47754 Score: 108
Period size: 17 Copynumber: 3.2 Consensus size: 17
47691 AACCGGGTTA
47701 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
47718 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
47735 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
47752 ACC
1 ACC
47755 GTGACCGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.48, G:0.22, T:0.11
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:47761 original size:6 final size:7
Alignment explanation
Indices: 47744--47773 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
47734 GACCCGACCC
47744 GACCGTT
1 GACCGTT
47751 GACCG-T
1 GACCGTT
47757 GACCGTT
1 GACCGTT
47764 GACCGTT
1 GACCGTT
47771 GAC
1 GAC
47774 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:47762 original size:13 final size:13
Alignment explanation
Indices: 47744--47769 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47734 GACCCGACCC
47744 GACCGTTGACCGT
1 GACCGTTGACCGT
47757 GACCGTTGACCGT
1 GACCGTTGACCGT
47770 TGACTTTCTT
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:48718 original size:32 final size:31
Alignment explanation
Indices: 48642--48718 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
48632 CTAATGTGAC
** *
48642 TCTTAGGTAGGCTTTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
48673 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
48705 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
48719 CACGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:49594 original size:16 final size:18
Alignment explanation
Indices: 49573--49610 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
49563 CGCTTTAGCT
*
49573 TCTCAA-ACTAATCT-TC
1 TCTCAACACCAATCTCTC
49589 TCTCAACACCAATCTCTC
1 TCTCAACACCAATCTCTC
49607 TCTC
1 TCTC
49611 TCTCTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 7 0.37
18 6 0.32
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.34
Consensus pattern (18 bp):
TCTCAACACCAATCTCTC
Found at i:55063 original size:40 final size:40
Alignment explanation
Indices: 55019--55096 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
55009 CAAACAATAA
* *
55019 ATACCCTAAACCACAACAAAACTCACACAAATACCCATAC
1 ATACCCCAAACCACAACAAAACTCACACAAACACCCATAC
*
55059 ATACCCCAAACCACAACAAAACTCACACTAACACCCAT
1 ATACCCCAAACCACAACAAAACTCACACAAACACCCAT
55097 TGACAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.49, C:0.40, G:0.00, T:0.12
Consensus pattern (40 bp):
ATACCCCAAACCACAACAAAACTCACACAAACACCCATAC
Found at i:55808 original size:45 final size:42
Alignment explanation
Indices: 55748--55843 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 42
55738 TCTTAACCAT
*
55748 TAATCTTACAAATATTTAAAAATTTCTTATAGATAATTTC-AG-ATA
1 TAATATTACAAATATTT--AAA-TT-TTATAGAT-ATTTCTAGTATA
*
55793 TAATATTATAAATATTTAAATTTTATAGATATTTCTAGTTATA
1 TAATATTACAAATATTTAAATTTTATAGATATTTCTAG-TATA
55836 TAATATTA
1 TAATATTA
55844 ATATTATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
40 5 0.11
41 10 0.22
42 2 0.04
43 14 0.30
45 15 0.33
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (42 bp):
TAATATTACAAATATTTAAATTTTATAGATATTTCTAGTATA
Found at i:57359 original size:72 final size:72
Alignment explanation
Indices: 57271--57427 Score: 264
Period size: 72 Copynumber: 2.2 Consensus size: 72
57261 GTGACGTGAC
*
57271 GGATGCGAATTTGTTCTTACAAGGACAGCTTGGGAACAACACCAACGATCCTGCGTCCA-T-CCT
1 GGATGCGAATTTGTTCTTACAAGGACAGCTTGGGAACAACACCAACAATCCTGCGT-CAGTACC-
57334 TGCAAACAT
64 TGCAAACAT
57343 GGATGCGAATTTGTTCTTACAAGGACAGCTTGGGAACAACACCAACAATCCTGCGTCAGTACCTG
1 GGATGCGAATTTGTTCTTACAAGGACAGCTTGGGAACAACACCAACAATCCTGCGTCAGTACCTG
57408 CAAACAT
66 CAAACAT
*
57415 GGATGCGACTTTG
1 GGATGCGAATTTG
57428 CCACGAAGTG
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
71 2 0.02
72 77 0.95
73 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (72 bp):
GGATGCGAATTTGTTCTTACAAGGACAGCTTGGGAACAACACCAACAATCCTGCGTCAGTACCTG
CAAACAT
Found at i:57705 original size:72 final size:72
Alignment explanation
Indices: 57560--57765 Score: 310
Period size: 72 Copynumber: 2.9 Consensus size: 72
57550 GACGGATGCG
** * *
57560 GATTTGTTCTTACCAGGACAGCTT--G-AGAACACCAACGATCCTGCATCCGTCCCTGCAAACAT
1 GATTTGTTCTTAGAAGGACAGCTTGGGAACAACACCAACGATCCTGCGTCCGTCCCTGCAAACAT
**
57622 GGATGCG
66 GGATGAA
*
57629 GATTTGTTCTTAGAAGGACAGCTTGGGAACAACACCAACGATTCTGCGTCCGTCCCTGCAAACAT
1 GATTTGTTCTTAGAAGGACAGCTTGGGAACAACACCAACGATCCTGCGTCCGTCCCTGCAAACAT
57694 GGATGAA
66 GGATGAA
* *
57701 GATTTGTTCTTAGAAGGACAGCTTGGGAACAACACCAACGATCCTGAGTTCGTCCCTGCAAACAT
1 GATTTGTTCTTAGAAGGACAGCTTGGGAACAACACCAACGATCCTGCGTCCGTCCCTGCAAACAT
57766 TGTTGATAGT
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
69 22 0.18
71 1 0.01
72 101 0.81
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (72 bp):
GATTTGTTCTTAGAAGGACAGCTTGGGAACAACACCAACGATCCTGCGTCCGTCCCTGCAAACAT
GGATGAA
Found at i:58707 original size:10 final size:10
Alignment explanation
Indices: 58692--58766 Score: 68
Period size: 10 Copynumber: 7.8 Consensus size: 10
58682 TAAACGAACC
58692 GAACGAACAA
1 GAACGAACAA
58702 GAACGAATC--
1 GAACGAA-CAA
58711 GAACGAACAA
1 GAACGAACAA
* *
58721 GAACAAAC-C
1 GAACGAACAA
58730 GAACGAACAA
1 GAACGAACAA
* *
58740 GAACAAAC-T
1 GAACGAACAA
*
58749 GAACGAACAT
1 GAACGAACAA
58759 GAACGAAC
1 GAACGAAC
58767 CGAACGCATA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
8 1 0.02
9 21 0.40
10 30 0.57
11 1 0.02
ACGTcount: A:0.55, C:0.23, G:0.19, T:0.04
Consensus pattern (10 bp):
GAACGAACAA
Found at i:58708 original size:19 final size:19
Alignment explanation
Indices: 58684--58772 Score: 133
Period size: 19 Copynumber: 4.7 Consensus size: 19
58674 TAGGCATGTA
58684 AACGAACCGAACGAACAAG
1 AACGAACCGAACGAACAAG
*
58703 AACGAATCGAACGAACAAG
1 AACGAACCGAACGAACAAG
*
58722 AACAAACCGAACGAACAAG
1 AACGAACCGAACGAACAAG
* * *
58741 AACAAACTGAACGAACATG
1 AACGAACCGAACGAACAAG
58760 AACGAACCGAACG
1 AACGAACCGAACG
58773 CATACAAATG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.53, C:0.25, G:0.19, T:0.03
Consensus pattern (19 bp):
AACGAACCGAACGAACAAG
Found at i:58713 original size:5 final size:4
Alignment explanation
Indices: 58684--58772 Score: 55
Period size: 4 Copynumber: 22.0 Consensus size: 4
58674 TAGGCATGTA
*
58684 AACG AACCG AACG AAC- AA-G AACG AATCG AACG AAC- AA-G AACA AACCG
1 AACG AA-CG AACG AACG AACG AACG AA-CG AACG AACG AACG AACG AA-CG
*
58731 AACG AAC- AA-G AACA AACTG AACG AACATG AACG AACCG AACG
1 AACG AACG AACG AACG AAC-G AACG AAC--G AACG AA-CG AACG
58773 CATACAAATG
Statistics
Matches: 68, Mismatches: 4, Indels: 26
0.69 0.04 0.27
Matches are distributed among these distances:
3 12 0.18
4 34 0.50
5 18 0.26
6 4 0.06
ACGTcount: A:0.53, C:0.25, G:0.19, T:0.03
Consensus pattern (4 bp):
AACG
Found at i:58913 original size:10 final size:10
Alignment explanation
Indices: 58898--59005 Score: 99
Period size: 10 Copynumber: 10.1 Consensus size: 10
58888 CATTTAAATG
*
58898 ATAAACGAAT
1 ATAAACGAAC
58908 ATAAACGAAC
1 ATAAACGAAC
*
58918 ATAAACGAAT
1 ATAAACGAAC
58928 ATAAACGAAC
1 ATAAACGAAC
58938 ATAAACGAACAC
1 ATAAACG-A-AC
*
58950 AAACGAACGAAC
1 ATA--AACGAAC
58962 ATAAACGAAC
1 ATAAACGAAC
*
58972 ATAATAAATGAAC
1 ---ATAAACGAAC
*
58985 ATAAACAAAC
1 ATAAACGAAC
*
58995 TTAAACGAAC
1 ATAAACGAAC
59005 A
1 A
59006 ACACAAACAC
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
10 57 0.71
11 1 0.01
12 8 0.10
13 10 0.12
14 4 0.05
ACGTcount: A:0.60, C:0.18, G:0.09, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:58960 original size:14 final size:14
Alignment explanation
Indices: 58941--58971 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58931 AACGAACATA
58941 AACGAACACAAACG
1 AACGAACACAAACG
*
58955 AACGAACATAAACG
1 AACGAACACAAACG
58969 AAC
1 AAC
58972 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:59294 original size:14 final size:14
Alignment explanation
Indices: 59275--59319 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
59265 CCATCTGTTT
59275 GAACATAAATGAAC
1 GAACATAAATGAAC
59289 GAACATAAATGAAC
1 GAACATAAATGAAC
59303 GAACATATAATCGAAC
1 GAACATA-AAT-GAAC
59319 G
1 G
59320 TTCACGAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 21 0.72
15 3 0.10
16 5 0.17
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:59401 original size:40 final size:41
Alignment explanation
Indices: 59350--59429 Score: 126
Period size: 40 Copynumber: 1.9 Consensus size: 41
59340 AACGAGCCAT
*
59350 TTGTTCGTGTTCGTTCATTTAAT-TAAACGAACATAAAATC
1 TTGTTCATGTTCGTTCATTTAATATAAACGAACATAAAATC
59390 TTGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAA
1 TTGTTCATGTTCGTTCATTTAAT--ATAAACGAACATAAA
59430 CGAACTTCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 22 0.61
43 14 0.39
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (41 bp):
TTGTTCATGTTCGTTCATTTAATATAAACGAACATAAAATC
Found at i:78538 original size:26 final size:25
Alignment explanation
Indices: 78492--78544 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
78482 TTTTAAATTT
*
78492 ATATTTTAGTAAATTTATATTATTA
1 ATATTTTAGTAAATTTATATTAATA
*
78517 ATATGTTTAG-AAATTATGTATTAATA
1 ATAT-TTTAGTAAATT-TATATTAATA
78543 AT
1 AT
78545 GTAGTTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (25 bp):
ATATTTTAGTAAATTTATATTAATA
Found at i:82523 original size:12 final size:13
Alignment explanation
Indices: 82498--82524 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
82488 CTTAAAATAA
82498 TTTTAGGAATTTT
1 TTTTAGGAATTTT
82511 TTTTAGGAATTTT
1 TTTTAGGAATTTT
82524 T
1 T
82525 GGAGACCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (13 bp):
TTTTAGGAATTTT
Found at i:84288 original size:17 final size:18
Alignment explanation
Indices: 84252--84332 Score: 96
Period size: 17 Copynumber: 4.6 Consensus size: 18
84242 TCTACGTCTA
*
84252 ATAACTGTAAAACATCTG
1 ATAACTGTAAATCATCTG
*
84270 ATAACT-TAAATCATTTG
1 ATAACTGTAAATCATCTG
84287 ATAACTGTAAAT-ATCTG
1 ATAACTGTAAATCATCTG
*
84304 ATAACTGTGAAAT-GTCTG
1 ATAACTGT-AAATCATCTG
*
84322 ATAACTATAAA
1 ATAACTGTAAA
84333 CATTTAGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
17 30 0.54
18 26 0.46
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (18 bp):
ATAACTGTAAATCATCTG
Found at i:85794 original size:13 final size:13
Alignment explanation
Indices: 85776--85800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85766 TGAACCGGTT
85776 TGACCCGACCCGC
1 TGACCCGACCCGC
85789 TGACCCGACCCG
1 TGACCCGACCCG
85801 GGTGCTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.52, G:0.24, T:0.08
Consensus pattern (13 bp):
TGACCCGACCCGC
Found at i:85891 original size:30 final size:28
Alignment explanation
Indices: 85800--85903 Score: 136
Period size: 28 Copynumber: 3.6 Consensus size: 28
85790 GACCCGACCC
*
85800 GGGTGCTATTTTCGTAATTAACTTTAAAA
1 GGGTGCTATTTTCGTAATT-ATTTTAAAA
* * * *
85829 GGGTACTGTTTTTGTAATTATTTTAGAA
1 GGGTGCTATTTTCGTAATTATTTTAAAA
85857 GGGTGCTATTTTCGTAATTATTTTTAAAAA
1 GGGTGCTATTTTCGTAATTA-TTTT-AAAA
85887 GGGTGCTATTTTCGTAA
1 GGGTGCTATTTTCGTAA
85904 AAGTTGACTG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 24 0.38
29 20 0.31
30 20 0.31
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (28 bp):
GGGTGCTATTTTCGTAATTATTTTAAAA
Found at i:89984 original size:3 final size:3
Alignment explanation
Indices: 89976--90038 Score: 65
Period size: 3 Copynumber: 20.0 Consensus size: 3
89966 ATATTTATTA
* *
89976 AAT AAT AAT AAT -AT ATAT ATAT ATAT AAAT AAT AAT AAT AAT ATT TAT
1 AAT AAT AAT AAT AAT A-AT A-AT A-AT -AAT AAT AAT AAT AAT AAT AAT
90024 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
90039 TTAAGTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.72
4 12 0.23
5 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:90006 original size:24 final size:21
Alignment explanation
Indices: 89976--90038 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 21
89966 ATATTTATTA
89976 AATAATAATAATATATATATAT
1 AATAATAATAATA-ATATATAT
89998 ATATAAATAATAATAATAATATTTAT
1 A-AT-AATAATAATAAT-ATA--TAT
90024 AATAATAATAATAAT
1 AATAATAATAATAAT
90039 TTAAGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
22 1 0.03
23 4 0.11
24 25 0.69
25 2 0.06
26 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAATAATAATAATATATAT
Found at i:90322 original size:76 final size:76
Alignment explanation
Indices: 90166--90822 Score: 1197
Period size: 76 Copynumber: 8.6 Consensus size: 76
90156 TATGGAAATG
* *
90166 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
90231 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* * *
90243 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
90308 CCCGAAGGCTT
66 CCCGAAGGCTT
90319 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
90384 CCCGAAGGCTT
66 CCCGAAGGCTT
90395 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
90460 CCCGAAGGCTT
66 CCCGAAGGCTT
** *
90471 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGATTCGAAGGCTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
90536 CCCGAAGGCTT
66 CCCGAAGGCTT
90547 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
90612 CTCGAAGGCTT
66 CCCGAAGGCTT
90623 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
90688 CCCGAAGGCTT
66 CCCGAAGGCTT
90699 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
90764 CCCGAAGGTTT
66 CCCGAAGGCTT
**
90775 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGATTCGAAGGCTTT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT
90823 TTGGAAACAT
Statistics
Matches: 561, Mismatches: 19, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
76 520 0.93
77 41 0.07
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:90828 original size:199 final size:200
Alignment explanation
Indices: 90613--91009 Score: 760
Period size: 199 Copynumber: 2.0 Consensus size: 200
90603 CAAAAAGCTC
90613 TCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACA
1 TCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACA
90678 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
66 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
90743 CTTTGAAAACATCAAAAAGCTCCCGAAGG-TTTTTTGGAAACATCATGCACTGAAGGGCTTACAG
131 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAG
90807 ATGAT
196 ATGAT
90812 TCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACA
1 TCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACA
90877 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
66 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
90942 CTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTTGGAAACATCATGCACTGTAGGACTTACAG
131 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAG
91007 ATG
196 ATG
91010 TGAGAAATAG
Statistics
Matches: 194, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
199 158 0.81
200 36 0.19
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (200 bp):
TCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACA
TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAG
ATGAT
Found at i:90835 original size:47 final size:47
Alignment explanation
Indices: 90764--90869 Score: 185
Period size: 47 Copynumber: 2.3 Consensus size: 47
90754 TCAAAAAGCT
*
90764 CCCGAAGGTTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
**
90811 TTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
90858 CCCGAAGGCTTT
1 CCCGAAGGCTTT
90870 GAAAACATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (47 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:90839 original size:123 final size:123
Alignment explanation
Indices: 90688--90945 Score: 489
Period size: 123 Copynumber: 2.1 Consensus size: 123
90678 TCAAAAAGCT
90688 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
*
90753 ATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
**
90811 TTCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
90876 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
90934 CCCGAAGGCTTT
1 CCCGAAGGCTTT
90946 GAAAACATCA
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 130 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (123 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:90893 original size:76 final size:76
Alignment explanation
Indices: 90813--91009 Score: 358
Period size: 76 Copynumber: 2.6 Consensus size: 76
90803 ACAGATGATT
90813 CGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
90878 CAAAAAGCTCC
66 CAAAAAGCTCC
90889 CGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
90954 CAAAAAGCTCC
66 CAAAAAGCTCC
* * *
90965 TGAAGGCTTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 CGAAGGC-TTTTTGGAAACATCATGCACTGAAGGGCTTACAGATG
91010 TGAGAAATAG
Statistics
Matches: 117, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
76 82 0.70
77 35 0.30
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (76 bp):
CGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCTCC
Found at i:91709 original size:22 final size:22
Alignment explanation
Indices: 91684--91763 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
91674 CATAAAGCTT
*
91684 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* * *
91706 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTAAAAAGAGAATCTA
* * **
91728 TCATCTCTGAAGTGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
91750 TTATCTTTAAAAAG
1 TCATCTTTAAAAAG
91764 TGCAGATGTA
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:92085 original size:169 final size:169
Alignment explanation
Indices: 91806--92143 Score: 658
Period size: 169 Copynumber: 2.0 Consensus size: 169
91796 TTAATCAGGA
*
91806 GAATAGAGTCTGTTCTGATTTGACTCTTGAAACATATCACAAAGAAGATTTATTCCAATTCATTT
1 GAATAGAGTCTGTTCTGATTTGACTCTTGAAACACATCACAAAGAAGATTTATTCCAATTCATTT
*
91871 CATGTCTCCACATATAATCAGATCTCGAATAAGGCAACTTGGATCATATAATGTCGATATGCTTA
66 CATGTCTCCACATATAATCAGATCTCGAATAAGGCAACTTGGATCATATAATGTCGAGATGCTTA
91936 ACAACAACTTGTAGTTCAACCATAGTTGGCTCCACTAGT
131 ACAACAACTTGTAGTTCAACCATAGTTGGCTCCACTAGT
91975 GAATAGAGTCTGTTCTGATTTGACTCTTGAAACACATCACAAAGAAGATTTATTCCAATTCATTT
1 GAATAGAGTCTGTTCTGATTTGACTCTTGAAACACATCACAAAGAAGATTTATTCCAATTCATTT
92040 CATGTCTCCACATATAATCAGATCTCGAATAAGGCAACTTGGATCATATAATGTCGAGATGCTTA
66 CATGTCTCCACATATAATCAGATCTCGAATAAGGCAACTTGGATCATATAATGTCGAGATGCTTA
92105 ACAACAACTTGTAGTTCAACCATAGTTGGCTCCACTAGT
131 ACAACAACTTGTAGTTCAACCATAGTTGGCTCCACTAGT
92144 TTCTTATTGT
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 167 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (169 bp):
GAATAGAGTCTGTTCTGATTTGACTCTTGAAACACATCACAAAGAAGATTTATTCCAATTCATTT
CATGTCTCCACATATAATCAGATCTCGAATAAGGCAACTTGGATCATATAATGTCGAGATGCTTA
ACAACAACTTGTAGTTCAACCATAGTTGGCTCCACTAGT
Found at i:92366 original size:54 final size:54
Alignment explanation
Indices: 92284--92395 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 54
92274 CGAATAGCAG
***
92284 GTTCGTAAAACATTTAACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* **
92338 GTTCGTAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
92392 GTTC
1 GTTC
92396 TCAATCATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:94733 original size:114 final size:114
Alignment explanation
Indices: 94533--94963 Score: 729
Period size: 114 Copynumber: 3.8 Consensus size: 114
94523 GATCATGCAG
* * * * * *
94533 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
94598 ACACATCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
* * *
94647 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAATA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
94712 ACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
*
94761 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAATTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
94826 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAACAAA
66 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
*
94875 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAATTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
94940 ACACTTCCAGAAGATGCTA-TGAGC
66 ACACTTCCAGAAGATGCTATTGAGC
94964 ACATTCATCT
Statistics
Matches: 304, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
113 5 0.02
114 299 0.98
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
Found at i:95032 original size:93 final size:92
Alignment explanation
Indices: 94874--95052 Score: 270
Period size: 93 Copynumber: 1.9 Consensus size: 92
94864 CCATGAACAA
* * *
94874 ATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAATTCAAAG
1 ATTCATCTTCCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAAG
*
94939 AACACTTCCAGAAGATGCTATGAGCAC
66 AACACTTCCAGAAGATACTATGAGCAC
* * *
94966 ATTCATCTTCCAAATTCAATGATTGGTTCTGTGG-TTTCATACCAAACCAGATCAGATAACTCAA
1 ATTCATCTTCCAAATCCAATGATTGATT-T-TGGAGTTCATACCAAACCAGATCAGATAACTCAA
95030 AGAACACTTCCAGAAGATACTAT
64 AGAACACTTCCAGAAGATACTAT
95053 TGGGTCTTCT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
92 25 0.32
93 50 0.64
94 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (92 bp):
ATTCATCTTCCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATACTATGAGCAC
Found at i:97170 original size:16 final size:15
Alignment explanation
Indices: 97149--97180 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
97139 TCAATTATCC
97149 TTTTTCTTCTTCTCTT
1 TTTTTCTTCTT-TCTT
97165 TTTTTCTTCTTTCTT
1 TTTTTCTTCTTTCTT
97180 T
1 T
97181 GTTGGATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTCTTTCTT
Found at i:103791 original size:2 final size:2
Alignment explanation
Indices: 103784--103838 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
103774 TTATTAAATA
103784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
103826 A- AT A- AT AT TT AT A
1 AT AT AT AT AT AT AT A
103839 ATAATAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:103839 original size:12 final size:12
Alignment explanation
Indices: 103780--103844 Score: 75
Period size: 10 Copynumber: 5.6 Consensus size: 12
103770 ATATTTATTA
103780 AATAATATATAT
1 AATAATATATAT
103792 -AT-ATATATAT
1 AATAATATATAT
103802 -AT-ATATATAT
1 AATAATATATAT
103812 ATATATATATATAT
1 A-ATA-ATATATAT
*
103826 AATAATATTTAT
1 AATAATATATAT
103838 AATAATA
1 AATAATA
103845 ATAATAATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
10 18 0.38
11 2 0.04
12 16 0.33
13 3 0.06
14 9 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATAATATATAT
Found at i:103845 original size:18 final size:20
Alignment explanation
Indices: 103768--103855 Score: 87
Period size: 22 Copynumber: 4.5 Consensus size: 20
103758 TTTGGGTTTG
103768 TAATATTTAT-TA-A-ATAA
1 TAATATTTATATATATATAA
*
103785 TATATATATATATATATATATA
1 TA-ATATTTATATATATATA-A
*
103807 TATATATATATATATATATAA
1 TA-ATATTTATATATATATAA
103828 TAATATTTATA-ATA-ATAA
1 TAATATTTATATATATATAA
103846 TAATAATTTA
1 TAAT-ATTTA
103856 AGTAAAATAA
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
17 2 0.03
18 15 0.24
19 10 0.16
20 9 0.14
21 6 0.10
22 21 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTTATATATATATAA
Found at i:114732 original size:20 final size:20
Alignment explanation
Indices: 114691--114733 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
114681 CTTTTAAAAT
* *
114691 AATATTATTTTTTCAATTTA
1 AATAATATTTTTTCAATATA
114711 AATAATATTTTTT-AACTATA
1 AATAATATTTTTTCAA-TATA
114731 AAT
1 AAT
114734 TTTAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAATATTTTTTCAATATA
Found at i:115966 original size:26 final size:25
Alignment explanation
Indices: 115920--115972 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
115910 TTTTAAATTT
*
115920 ATATTTTAGTAAATTTATATTATTA
1 ATATTTTAGTAAATTTATATTAATA
*
115945 ATATGTTTAG-AAATTATGTATTAATA
1 ATAT-TTTAGTAAATT-TATATTAATA
115971 AT
1 AT
115973 GTAGTTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (25 bp):
ATATTTTAGTAAATTTATATTAATA
Found at i:117698 original size:4 final size:4
Alignment explanation
Indices: 117689--117714 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
117679 TGCTGTGCAA
117689 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
117715 GAGCAACACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:120063 original size:19 final size:19
Alignment explanation
Indices: 120019--120064 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
120009 GATGGGCATT
** *
120019 GTTTGACCGGTCTGAACCG
1 GTTTGACCAATCTGAACCA
*
120038 GTCTGACCAATCTGAACCA
1 GTTTGACCAATCTGAACCA
120057 GTTTGACC
1 GTTTGACC
120065 CGACCTGACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (19 bp):
GTTTGACCAATCTGAACCA
Found at i:120190 original size:30 final size:29
Alignment explanation
Indices: 120089--120193 Score: 140
Period size: 29 Copynumber: 3.6 Consensus size: 29
120079 GACCCGATCT
*
120089 GGGTGCTATTTTCGTAATTAATTTTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
* * *
120118 GGGTGTTATTTTTGTAATTATTTTTAGAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
120147 GGGTG-TCATTTTCGTAATTATTTTTAAAAA
1 GGGTGCT-ATTTTCGTAATTATTTTT-AAAA
*
120177 TGGTGCTATTTTCGTAA
1 GGGTGCTATTTTCGTAA
120194 AAGTTGATTG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.02
29 47 0.71
30 17 0.26
31 1 0.02
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.49
Consensus pattern (29 bp):
GGGTGCTATTTTCGTAATTATTTTTAAAA
Found at i:121803 original size:18 final size:18
Alignment explanation
Indices: 121780--121861 Score: 87
Period size: 18 Copynumber: 4.6 Consensus size: 18
121770 TCTACGTCTA
121780 ATAACTGTAAAACATCTG
1 ATAACTGTAAAACATCTG
*
121798 ATAACT-TAAAATCATTTG
1 ATAACTGTAAAA-CATCTG
*
121816 ATAACTGT-AAATATCTG
1 ATAACTGTAAAACATCTG
* **
121833 ATAACTGTGAAATGTCTG
1 ATAACTGTAAAACATCTG
*
121851 ATAACTATAAA
1 ATAACTGTAAA
121862 CATTTAGAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
17 17 0.31
18 37 0.67
19 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (18 bp):
ATAACTGTAAAACATCTG
Found at i:121853 original size:35 final size:35
Alignment explanation
Indices: 121774--121864 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
121764 AATTAATCTA
*
121774 CGTCTAATAACTGTAAAACATCTGATAACTTAAAAT
1 CGTCTGATAACTGT-AAACATCTGATAACTTAAAAT
* * * *
121810 CATTTGATAACTGTAAATATCTGATAACTGTGAAAT
1 CGTCTGATAACTGTAAACATCTGATAACT-TAAAAT
*
121846 -GTCTGATAACTATAAACAT
1 CGTCTGATAACTGTAAACAT
121865 TTAGAATTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
35 29 0.64
36 16 0.36
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (35 bp):
CGTCTGATAACTGTAAACATCTGATAACTTAAAAT
Found at i:123421 original size:28 final size:28
Alignment explanation
Indices: 123353--123456 Score: 127
Period size: 28 Copynumber: 3.6 Consensus size: 28
123343 GACCCGACCC
*
123353 GGGTGCTATTTTCGTAATTAACTTTAAAA
1 GGGTGCTATTTTCGTAATT-ATTTTAAAA
* * * *
123382 GGGTACTGTTTTTGTAATTATTTTAGAA
1 GGGTGCTATTTTCGTAATTATTTTAAAA
123410 GGGTGCTATTTTCGTAATTATTTTTAAAAA
1 GGGTGCTATTTTCGTAATTA-TTTT-AAAA
*
123440 GGGTGCTAATTTCGTAA
1 GGGTGCTATTTTCGTAA
123457 AAGTTGATTG
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
28 24 0.38
29 20 0.32
30 19 0.30
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (28 bp):
GGGTGCTATTTTCGTAATTATTTTAAAA
Done.