Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009279.1 Hibiscus syriacus cultivar Beakdansim tig00112962_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: 57994
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1327 original size:64 final size:66
Alignment explanation
Indices: 1248--1426 Score: 256
Period size: 64 Copynumber: 2.8 Consensus size: 66
1238 CTTAGGCTAC
* *
1248 TCTCAAGCGATACAAAATTTGTTTCAAGAGAAACAATCTC-AAGGTTTATGTTTCAAGAGAAA-T
1 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACT
1311 G
66 G
1312 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGG-TTATGTTTCAAAAGAAACT
1 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACT
1376 G
66 G
* **** **
1377 TCTCAAGCGAGATAAAAAAAATTTCGGGAGAAACAATCTCAAAGGTTTAT
1 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
1427 CAATTTTGTT
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
64 55 0.53
65 44 0.43
66 4 0.04
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (66 bp):
TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAAAGAAACT
G
Found at i:1408 original size:65 final size:64
Alignment explanation
Indices: 1269--1423 Score: 213
Period size: 65 Copynumber: 2.4 Consensus size: 64
1259 ACAAAATTTG
* ****
1269 TTTCAAGAGAAACAATCTC-AAGGTTTATGTTTCAAGAGAAATGTCTCAAGCGAGACAAAATTTG
1 TTTCAAGAGAAACAATCTCAAAGG-TTATGTTTCAAAAGAAATGTCTCAAGCGAGACAAAAAAAA
*
1333 TTTCAAGAGAAACAATCTCAAAGGTTATGTTTCAAAAGAAACTGTCTCAAGCGAGATAAAAAAAA
1 TTTCAAGAGAAACAATCTCAAAGGTTATGTTTCAAAAGAAA-TGTCTCAAGCGAGACAAAAAAAA
**
1398 TTTCGGGAGAAACAATCTCAAAGGTT
1 TTTCAAGAGAAACAATCTCAAAGGTT
1424 TATCAATTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 35 0.43
65 46 0.57
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (64 bp):
TTTCAAGAGAAACAATCTCAAAGGTTATGTTTCAAAAGAAATGTCTCAAGCGAGACAAAAAAAA
Found at i:1693 original size:36 final size:36
Alignment explanation
Indices: 1637--1721 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
1627 GAGGAAGACT
* * * *
1637 ATCTTAAGTGAGACACAATTTGTTTTTATGAAAA-A
1 ATCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
*
1672 TGTCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
1 -ATCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
1709 ATCTCAAGTGAGA
1 ATCTCAAGTGAGA
1722 TCAATTTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 41 0.98
37 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (36 bp):
ATCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
Found at i:1728 original size:35 final size:34
Alignment explanation
Indices: 1636--1743 Score: 94
Period size: 36 Copynumber: 3.0 Consensus size: 34
1626 TGAGGAAGAC
* * *
1636 TATCTTAAGTGAGACACAATTTGTTTTTATGAAAAA
1 TATCTCAAGTGAG--ACAATTTGTTTTAAAGAAAAA
*
1672 TGTCTCAAGTGAGACAAAATTTGTTTTAAAGAAAACA
1 TATCTCAAGTGAGAC--AATTTGTTTTAAAGAAAA-A
*
1709 -ATCTCAAGTGAGATCAATTT-TTGTTCAAGAAAAA
1 TATCTCAAGTGAGA-CAATTTGTT-TTAAAGAAAAA
1743 T
1 T
1744 TTTCTCTAGC
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
34 5 0.08
35 14 0.23
36 39 0.65
37 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (34 bp):
TATCTCAAGTGAGACAATTTGTTTTAAAGAAAAA
Found at i:6766 original size:21 final size:21
Alignment explanation
Indices: 6717--6774 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
6707 AACATGACAG
*
6717 ATGAACTGCCATGTCAGAACC
1 ATGAACTACCATGTCAGAACC
* *
6738 AT-AGACTACCATGTCAGCATC
1 ATGA-ACTACCATGTCAGAACC
*
6759 ATGAACTACCACGTCA
1 ATGAACTACCATGTCA
6775 CACCATAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (21 bp):
ATGAACTACCATGTCAGAACC
Found at i:7530 original size:30 final size:30
Alignment explanation
Indices: 7496--7711 Score: 120
Period size: 30 Copynumber: 7.2 Consensus size: 30
7486 TCCTCTTCTT
*
7496 TCAATTGAAGTATTCCTCCTTCCCTTCTCG
1 TCAATTGAAGTATTCTTCCTTCCCTTCTCG
* *
7526 TCAATTGAAGTGTT-TTCTCTGCCCTTCTCG
1 TCAATTGAAGTATTCTTC-CTTCCCTTCTCG
* * * * *
7556 TCGACTGAATTATTC-TCCATCCTTTTCTCG
1 TCAATTGAAGTATTCTTCCTTCC-CTTCTCG
* * * * *
7586 CCGATTGAAGTATTCTTCGC--CATCTTATCT
1 TCAATTGAAGTATTCTTC-CTTC-CCTTCTCG
* * *
7616 TCAATTGAAGTATTCTTTCTCCCCTCCTCG
1 TCAATTGAAGTATTCTTCCTTCCCTTCTCG
* * * *
7646 TCAAATGAAGTATTTTTCGC-CCCCTTCTTG
1 TCAATTGAAGTATTCTTC-CTTCCCTTCTCG
* * * *
7676 TCGATTGAAGGATTTTTCC-TCCTCTTCTTG
1 TCAATTGAAGTATTCTTCCTTCC-CTTCTCG
7706 TCAATT
1 TCAATT
7712 AGAGTATCAG
Statistics
Matches: 142, Mismatches: 34, Indels: 20
0.72 0.17 0.10
Matches are distributed among these distances:
29 9 0.06
30 128 0.90
31 4 0.03
32 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.12, T:0.42
Consensus pattern (30 bp):
TCAATTGAAGTATTCTTCCTTCCCTTCTCG
Found at i:13949 original size:138 final size:137
Alignment explanation
Indices: 13701--14123 Score: 537
Period size: 138 Copynumber: 3.1 Consensus size: 137
13691 TTAAGGTCAA
* * ** * *
13701 TTGACCTTTCTAATTGCAATAAACTATGGAAGATCCCT-GATCTATCAGGAGCCATCAACCATCA
1 TTGACCTTTCTGATTGCAAGAGTCTAAGGAAGATCCCTAG-TCTATCAGGAGCCATCAACCTTCA
* * *
13765 AAGCTTTTGCTGCAATGGGTGTGAAAATTTGGTT-AAGCTGCCTTGCCTTAACCATTTGGCATCT
65 AAGCTTTT-CTGCAATGGGTGTGAAAATTTGGTTGAA-CTACCTTGCCTCAACCAATTGGCATCT
13829 CTTGAAAAAC
128 CTTGAAAAAC
* * *
13839 TTGACCTTTCTGGTTGCAAGAGTCTAAGGAAGATCCTTAGTCTATCAAGAGCCATCAACCTTCAA
1 TTGACCTTTCTGATTGCAAGAGTCTAAGGAAGATCCCTAGTCTATCAGGAGCCATCAACCTTCAA
* *
13904 AGCATTTTCTGCAATGGGTGTGAAAATTTGATTGAACTACCTTGCCTCAACCACTTGGCATCTCT
66 AGC-TTTTCTGCAATGGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAACCAATTGGCATCTCT
13969 TGAAAAAC
130 TGAAAAAC
* * * * * *
13977 TTGGCCTTTCTGACTGCAAGAGTCTAATGG-AGATCCCTAATCTATCAGGAGTCATCAAACTCCA
1 TTGACCTTTCTGATTGCAAGAGTCTAA-GGAAGATCCCTAGTCTATCAGGAGCCATCAACCTTCA
* * * *
14041 AAGCCTTTGCTGCAATGGGTGTGAAAATTTGGTTGAAATACCTTCCCTCAACCAATTGGTATCTC
65 AAG-CTTTTCTGCAATGGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAACCAATTGGCATCTC
**
14106 TTGAAATCC
129 TTGAAAAAC
14115 TTGACCTTT
1 TTGACCTTT
14124 ATTGTTGCAG
Statistics
Matches: 249, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
138 239 0.96
139 10 0.04
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (137 bp):
TTGACCTTTCTGATTGCAAGAGTCTAAGGAAGATCCCTAGTCTATCAGGAGCCATCAACCTTCAA
AGCTTTTCTGCAATGGGTGTGAAAATTTGGTTGAACTACCTTGCCTCAACCAATTGGCATCTCTT
GAAAAAC
Found at i:14154 original size:138 final size:136
Alignment explanation
Indices: 13730--14244 Score: 525
Period size: 138 Copynumber: 3.7 Consensus size: 136
13720 TAAACTATGG
* *
13730 AAGATCCCTGATCTATCAGGAGCCATCAACCATCAAAGCTTTTGCTGCAATGGGTGTGAAAATTT
1 AAGATCCCTAATCTATCAGGAGCCATCAACC-TCAAAGCATTTGCTGCAATGGGTGTGAAAATTT
* * * *
13795 GGTT-AAGCTGCCTTGCCTTAACCATTTGGCATCTCTTGAAAAACTTGACCTTTCTGGTTGCAAG
65 GGTTGAA-CTACCTTGCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTT-TTGTTGCAAG
*
13859 AGTCTAAGG
128 AGTCTAAGT
* * * *
13868 AAGATCCTTAGTCTATCAAGAGCCATCAACCTTCAAAGCATTTTCTGCAATGGGTGTGAAAATTT
1 AAGATCCCTAATCTATCAGGAGCCATCAACC-TCAAAGCATTTGCTGCAATGGGTGTGAAAATTT
* * * * *
13933 GATTGAACTACCTTGCCTCAACCACTTGGCATCTCTTGAAAAACTTGGCCTTTCTGACTGCAAGA
65 GGTTGAACTACCTTGCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTTTG-TTGCAAGA
13998 GTCTAA-T
129 GTCTAAGT
* * * *
14005 GGAGATCCCTAATCTATCAGGAGTCATCAAACTCCAAAGCCTTTGCTGCAATGGGTGTGAAAATT
1 -AAGATCCCTAATCTATCAGGAGCCATCAACCT-CAAAGCATTTGCTGCAATGGGTGTGAAAATT
* * * ** *
14070 TGGTTGAAATACCTTCCCTCAACCAATTGGTATCTCTTGAAATCCTTGACCTTTATTGTTGCAGG
64 TGGTTGAACTACCTTGCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTT-TTGTTGCAAG
* *
14135 AATTTAAGT
128 AGTCTAAGT
* * ** * * * * *** *
14144 AAGATTCCTAATCCATTTGTAGCCATCAACCTTAAATCACTTAAG-TGCAATTACTGT-ACAAGT
1 AAGATCCCTAATCTATCAGGAGCCATCAACCTCAAAGCA-TT-TGCTGCAATGGGTGTGA-AAAT
* *
14207 TTGGTTGAACTACCTAGCCTCAATCAATTGGCATCTCT
63 TTGGTTGAACTACCTTGCCTCAACCAATTGGCATCTCT
14245 CAAAGAGCTT
Statistics
Matches: 310, Mismatches: 58, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
137 7 0.02
138 297 0.96
139 6 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (136 bp):
AAGATCCCTAATCTATCAGGAGCCATCAACCTCAAAGCATTTGCTGCAATGGGTGTGAAAATTTG
GTTGAACTACCTTGCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTTTGTTGCAAGAGT
CTAAGT
Found at i:14217 original size:276 final size:277
Alignment explanation
Indices: 13726--14244 Score: 629
Period size: 276 Copynumber: 1.9 Consensus size: 277
13716 GCAATAAACT
* * *
13726 ATGGAAGATCCCTGATCTATCAGGAGCCATCAACCATCAAAGCTTTTGCTGCAATGGGTGTGAAA
1 ATGGAAGATCCCTAATCTATCAGGAGCCATCAAACATCAAAGCCTTTGCTGCAATGGGTGTGAAA
* * * * * *
13791 ATTTGGTTAAGCTGCCTTGCCTTAACCATTTGGCATCTCTTGAAAAACTTGACCTTTCTGGTTGC
66 ATTTGGTTAAGATACCTTCCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTATGGTTGC
* * * ** *
13856 AAGAGTCTAAGGAAGATCCTTAGTCTATCAAGAGCCATCAACCTTCAAAGCATTTTCTGCAATGG
131 AAGAATCTAAGGAAGATCCTTAATCCATCAAGAGCCATCAACCTTCAAAGCATTAACTGCAATGA
* * *
13921 GTGTGAAAATTTGATTGAACTACCTTGCCTCAACCACTTGGCATCTCTTGAAAAACTTGGCCTTT
196 CTGTGAAAATTTGATTGAACTACCTAGCCTCAACCAATTGGCATCTCTTGAAAAACTTGGCCTTT
13986 CTGACTGCAAGAGTCTA
261 CTGACTGCAAGAGTCTA
*
14003 ATGG-AGATCCCTAATCTATCAGGAGTCATCAAAC-TCCAAAGCCTTTGCTGCAATGGGTGTGAA
1 ATGGAAGATCCCTAATCTATCAGGAGCCATCAAACAT-CAAAGCCTTTGCTGCAATGGGTGTGAA
* ** *
14066 AATTTGGTTGAA-ATACCTTCCCTCAACCAATTGGTATCTCTTGAAATCCTTGACCTTTATTGTT
65 AATTTGGTT-AAGATACCTTCCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTATGGTT
* * * ** * *
14130 GCAGGAATTTAAGTAAGATTCC-TAATCCAT-TTGTAGCCATCAACCTT-AAATCACTTAAGTGC
129 GCAAGAATCTAAGGAAGA-TCCTTAATCCATCAAG-AGCCATCAACCTTCAAAGCA-TTAACTGC
* * * *
14192 AATTACTGT-ACAAGTTTGGTTGAACTACCTAGCCTCAATCAATTGGCATCTCT
191 AATGACTGTGA-AAATTTGATTGAACTACCTAGCCTCAACCAATTGGCATCTCT
14245 CAAAGAGCTT
Statistics
Matches: 202, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
275 8 0.04
276 185 0.92
277 9 0.04
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (277 bp):
ATGGAAGATCCCTAATCTATCAGGAGCCATCAAACATCAAAGCCTTTGCTGCAATGGGTGTGAAA
ATTTGGTTAAGATACCTTCCCTCAACCAATTGGCATCTCTTGAAAAACTTGACCTTTATGGTTGC
AAGAATCTAAGGAAGATCCTTAATCCATCAAGAGCCATCAACCTTCAAAGCATTAACTGCAATGA
CTGTGAAAATTTGATTGAACTACCTAGCCTCAACCAATTGGCATCTCTTGAAAAACTTGGCCTTT
CTGACTGCAAGAGTCTA
Found at i:17507 original size:29 final size:29
Alignment explanation
Indices: 17474--17555 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 29
17464 TCTCATACAT
* *
17474 AATCAGAACGGGGAATATATCCCATGAAG
1 AATCAGGACGGGGAATAAATCCCATGAAG
* * *
17503 AATCAGGACGAGGAATAAATCCCCTGCAG
1 AATCAGGACGGGGAATAAATCCCATGAAG
17532 AATCAGGACGGGG-ATAAATCCCAT
1 AATCAGGACGGGGAATAAATCCCAT
17556 TCAGATATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 10 0.22
29 36 0.78
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (29 bp):
AATCAGGACGGGGAATAAATCCCATGAAG
Found at i:17565 original size:29 final size:28
Alignment explanation
Indices: 17474--17566 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
17464 TCTCATACAT
* * *
17474 AATCAGAACGGGGAATATATCCCATGAAG
1 AATCAGGACGGGG-ATAAATCCCATGCAG
* *
17503 AATCAGGACGAGGAATAAATCCCCTGCAG
1 AATCAGGACG-GGGATAAATCCCATGCAG
*
17532 AATCAGGACGGGGATAAATCCCATTCAG
1 AATCAGGACGGGGATAAATCCCATGCAG
17560 ATATCAG
1 A-ATCAG
17567 AAATGCATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.30
29 36 0.67
30 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (28 bp):
AATCAGGACGGGGATAAATCCCATGCAG
Found at i:17638 original size:2 final size:2
Alignment explanation
Indices: 17631--17669 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17621 TGTCACGTAA
17631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17670 ATCAATTCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18218 original size:13 final size:14
Alignment explanation
Indices: 18168--18225 Score: 57
Period size: 13 Copynumber: 4.3 Consensus size: 14
18158 TTAGAAAATT
*
18168 TCAACGATCAACGG
1 TCAACAATCAACGG
*
18182 TCAACAGTCAA-GG
1 TCAACAATCAACGG
**
18195 TCAACTTTCAACGG
1 TCAACAATCAACGG
*
18209 TCAA-AATCAATGG
1 TCAACAATCAACGG
18222 TCAA
1 TCAA
18226 TGGGTCGGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
13 21 0.58
14 15 0.42
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (14 bp):
TCAACAATCAACGG
Found at i:18247 original size:17 final size:17
Alignment explanation
Indices: 18222--18265 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
18212 AAATCAATGG
*
18222 TCAATGGGTCGGGTCGA
1 TCAACGGGTCGGGTCGA
* *
18239 TCAACGGGTCGGTTCGG
1 TCAACGGGTCGGGTCGA
*
18256 TTAACGGGTC
1 TCAACGGGTC
18266 AATTGGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.39, T:0.25
Consensus pattern (17 bp):
TCAACGGGTCGGGTCGA
Found at i:19427 original size:21 final size:21
Alignment explanation
Indices: 19402--19463 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
19392 CTATAACAGG
19402 GGGTATTGGTACCCCTTCATA
1 GGGTATTGGTACCCCTTCATA
19423 GGGTATTGGTACCCCTTCATA
1 GGGTATTGGTACCCCTTCATA
* *
19444 GGGTATTAGTACACCTTCAT
1 GGGTATTGGTACCCCTTCAT
19464 TAAATTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (21 bp):
GGGTATTGGTACCCCTTCATA
Found at i:20412 original size:32 final size:31
Alignment explanation
Indices: 20376--20451 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
20366 GGGGCCGTGA
*
20376 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
20408 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
20439 AGCCTACCTAAGA
1 GGCCTACCTAAGA
20452 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:20434 original size:63 final size:63
Alignment explanation
Indices: 20328--20451 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
20318 CCCTAAGGGA
* * *
20328 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
20391 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
20452 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:21267 original size:13 final size:14
Alignment explanation
Indices: 21245--21281 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
21235 GTCAAAGAAA
21245 GTCAACGGTCAACG
1 GTCAACGGTCAACG
21259 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
21272 GTCAACGGTC
1 GTCAACGGTC
21282 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:21293 original size:17 final size:17
Alignment explanation
Indices: 21271--21328 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
21261 CACGGTCAAC
21271 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
21288 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* * *
21305 GGTCAACAGTCGAGTCA
1 GGTCAACGGTCGGGTCG
21322 GGTCAAC
1 GGTCAAC
21329 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:21298 original size:7 final size:7
Alignment explanation
Indices: 21245--21281 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
21235 GTCAAAGAAA
21245 GTCAACG
1 GTCAACG
21252 GTCAACG
1 GTCAACG
21259 GTC-ACG
1 GTCAACG
21265 GTCAACG
1 GTCAACG
21272 GTCAACG
1 GTCAACG
21279 GTC
1 GTC
21282 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:21346 original size:19 final size:19
Alignment explanation
Indices: 21322--21391 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
21312 AGTCGAGTCA
*
21322 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
21341 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
21360 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
21379 GGTCAAACCGGTT
1 GGTCAAACCGGTT
21392 TTCCAGCAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 1 0.02
19 48 0.98
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:21352 original size:9 final size:9
Alignment explanation
Indices: 21322--21390 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
21312 AGTCGAGTCA
*
21322 GGTCAACCC
1 GGTCAAACC
*
21331 GGTTCAGACC
1 GG-TCAAACC
21341 GGTCAAACC
1 GGTCAAACC
*
21350 GGTTCAGACC
1 GG-TCAAACC
21360 GGTCAAACC
1 GGTCAAACC
*
21369 GGTTCGAACC
1 GG-TCAAACC
21379 GGTCAAACC
1 GGTCAAACC
21388 GGT
1 GGT
21391 TTTCCAGCAG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 27 0.54
10 23 0.46
ACGTcount: A:0.25, C:0.32, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:27681 original size:32 final size:31
Alignment explanation
Indices: 27645--27720 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
27635 GGGGCCGTGA
*
27645 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
27677 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
27708 AGCCTACCTAAGA
1 GGCCTACCTAAGA
27721 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:27703 original size:63 final size:63
Alignment explanation
Indices: 27597--27720 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
27587 CCCTAAGGGA
* * *
27597 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
27660 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
27721 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:28536 original size:13 final size:14
Alignment explanation
Indices: 28514--28550 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
28504 GTCAAAGAAA
28514 GTCAACGGTCAACG
1 GTCAACGGTCAACG
28528 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
28541 GTCAACGGTC
1 GTCAACGGTC
28551 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:28562 original size:17 final size:17
Alignment explanation
Indices: 28540--28597 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
28530 CACGGTCAAC
28540 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
28557 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
28574 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
28591 GGTCAAC
1 GGTCAAC
28598 CCAGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:28567 original size:7 final size:7
Alignment explanation
Indices: 28514--28550 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
28504 GTCAAAGAAA
28514 GTCAACG
1 GTCAACG
28521 GTCAACG
1 GTCAACG
28528 GTC-ACG
1 GTCAACG
28534 GTCAACG
1 GTCAACG
28541 GTCAACG
1 GTCAACG
28548 GTC
1 GTC
28551 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:28613 original size:19 final size:19
Alignment explanation
Indices: 28591--28680 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
28581 AGTCGGGTCG
* *
28591 GGTCAACCCAGTTCAGACC
1 GGTCAAACCGGTTCAGACC
28610 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
28629 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
28648 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
28668 GGTCAAACCGGTT
1 GGTCAAACCGGTT
28681 TTCCAGCAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.02
19 48 0.75
20 15 0.23
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:28621 original size:9 final size:9
Alignment explanation
Indices: 28607--28679 Score: 83
Period size: 9 Copynumber: 7.7 Consensus size: 9
28597 CCCAGTTCAG
28607 ACCGGTCAA
1 ACCGGTCAA
*
28616 ACCGGTTCAG
1 ACCGG-TCAA
28626 ACCGGTCAA
1 ACCGGTCAA
*
28635 ACCGGTTCGA
1 ACCGG-TCAA
28645 ACCGGTCAA
1 ACCGGTCAA
28654 ACCGGTTCAAA
1 ACCGG-TC-AA
*
28665 ACTGGTCAA
1 ACCGGTCAA
28674 ACCGGT
1 ACCGGT
28680 TTTCCAGCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 28 0.52
10 20 0.37
11 6 0.11
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:29560 original size:21 final size:19
Alignment explanation
Indices: 29536--29592 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 19
29526 ATATTTAATG
*
29536 AAAAATATACCAATTGTTT
1 AAAAAGATACCAATTGTTT
29555 ACAAAAGGATACCAATTG-TT
1 A-AAAA-GATACCAATTGTTT
29575 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
29593 GGAAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 11 0.32
19 6 0.18
20 7 0.21
21 10 0.29
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTT
Found at i:31695 original size:90 final size:89
Alignment explanation
Indices: 31543--31715 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
31533 TCACACCATT
*
31543 TTATAGCCAAGTTTCCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
31608 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
31632 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
31697 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
31716 TTCAGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:33559 original size:20 final size:19
Alignment explanation
Indices: 33534--33588 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 19
33524 TTGCAGCCAG
33534 GGGTGTATGGATACACTGCA
1 GGGTGTATGGATACACT-CA
*
33554 GGGTGTATCGATACAC-CA
1 GGGTGTATGGATACACTCA
33572 --GTGTATGGATACACTCA
1 GGGTGTATGGATACACTCA
33589 TAGGGGTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 13 0.41
17 2 0.06
18 2 0.06
20 15 0.47
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (19 bp):
GGGTGTATGGATACACTCA
Found at i:35057 original size:29 final size:28
Alignment explanation
Indices: 35019--35086 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 28
35009 AATGAGGTCT
*
35019 CATGGAGAATCAGGACGGGGAATAAATCC
1 CATGCAGAATCAGGA-GGGGAATAAATCC
* *
35048 CATGTAGAAT---TAGGGGAATAAATCC
1 CATGCAGAATCAGGAGGGGAATAAATCC
35073 CATGCAGATATCAG
1 CATGCAGA-ATCAG
35087 AAATACATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 20 0.62
26 3 0.09
29 9 0.28
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.19
Consensus pattern (28 bp):
CATGCAGAATCAGGAGGGGAATAAATCC
Found at i:38009 original size:68 final size:68
Alignment explanation
Indices: 37900--38203 Score: 536
Period size: 68 Copynumber: 4.5 Consensus size: 68
37890 TATATATATA
37900 TAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGC
1 TAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGC
37965 ACT
66 ACT
*
37968 TAGCCATTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGC
1 TAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGC
38033 ACT
66 ACT
* ** * * *
38036 TAGCCATTCATCTAGTTGGCATGATTGACACCTTTCTATCAAATGCATAGTTAGGCCTCAAAGGC
1 TAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGC
38101 ACT
66 ACT
*
38104 TAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGC
1 TAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGC
38169 ACT
66 ACT
38172 TAGCCTTTCATCTAACTGGCATGATTGACACC
1 TAGCCTTTCATCTAACTGGCATGATTGACACC
38204 ACTGGCATGA
Statistics
Matches: 225, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 225 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (68 bp):
TAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGC
ACT
Found at i:38209 original size:18 final size:18
Alignment explanation
Indices: 38186--38221 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
38176 CTTTCATCTA
38186 ACTGGCATGATTGACACC
1 ACTGGCATGATTGACACC
38204 ACTGGCATGATTGACACC
1 ACTGGCATGATTGACACC
38222 TTTCTGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (18 bp):
ACTGGCATGATTGACACC
Found at i:38263 original size:86 final size:86
Alignment explanation
Indices: 38118--38289 Score: 326
Period size: 86 Copynumber: 2.0 Consensus size: 86
38108 CTTTCATCTA
38118 ACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCAT
1 ACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCAT
*
38183 CTAACTGGCATGATTGACACC
66 CTAACTAGCATGATTGACACC
38204 ACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCAT
1 ACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCAT
*
38269 CTAACTAGCATTATTGACACC
66 CTAACTAGCATGATTGACACC
38290 TTTCTGTCAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (86 bp):
ACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCAT
CTAACTAGCATGATTGACACC
Found at i:40098 original size:14 final size:14
Alignment explanation
Indices: 40079--40125 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
40069 GCAAGCACTC
40079 AAAAGAAGAAAACA-
1 AAAAGAAGAAAA-AG
40093 AAAAGAAGAAAAAG
1 AAAAGAAGAAAAAG
40107 AAAAGAA-AAGAAAG
1 AAAAGAAGAA-AAAG
40121 AAAAG
1 AAAAG
40126 TTGAAGCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.10
14 28 0.90
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAAG
Found at i:40109 original size:20 final size:20
Alignment explanation
Indices: 40084--40124 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40074 CACTCAAAAG
40084 AAGAAAACAAAAAG-AAGAAA
1 AAGAAAA-AAAAAGAAAGAAA
*
40104 AAGAAAAGAAAAGAAAGAAA
1 AAGAAAAAAAAAGAAAGAAA
40124 A
1 A
40125 GTTGAAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAAAGAAAGAAA
Found at i:45239 original size:60 final size:63
Alignment explanation
Indices: 45140--45321 Score: 219
Period size: 60 Copynumber: 2.8 Consensus size: 63
45130 ATCACACTTA
* * *
45140 TCTTTCATATAACTAGCATGGTTGACACATTTCTGTCAAATGCACAGTTAGGCCTC-AGGCAC-
1 TCTTTCATCTAACTAGCAT-GATGACACATTTCTTTCAAATGCACAGTTAGGCCTCAAGGCACT
45202 T-TTTCATCTAACTAGCATGATGACACATTTCTTTCAAATGCACAGTTAGGCCTCAAAGGCACT
1 TCTTTCATCTAACTAGCATGATGACACATTTCTTTCAAATGCACAGTTAGGCCTC-AAGGCACT
* *
45265 TAGCCTTTCATCTAACTGGCATGATTGACATC-TTTTTTGTCAAATGCACAGTTAGGC
1 T---CTTTCATCTAACTAGCATGA-TGACA-CATTTCTT-TCAAATGCACAGTTAGGC
45322 ATTTAATCTT
Statistics
Matches: 105, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
60 34 0.32
61 16 0.15
62 7 0.07
63 1 0.01
67 18 0.17
68 10 0.10
69 19 0.18
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (63 bp):
TCTTTCATCTAACTAGCATGATGACACATTTCTTTCAAATGCACAGTTAGGCCTCAAGGCACT
Found at i:45605 original size:54 final size:56
Alignment explanation
Indices: 45532--45643 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 56
45522 ACATATATTT
* *
45532 CCATATGGAAATTCTTACACTTAGTATGAATTTCTTAG-TTTTGCACACAT-AGTGC
1 CCATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTGCACAC-TCAGTGC
45587 CCATACGGAAA-TCATACACTTAGTATGAATTTCTTAGCTTTTTGCACACTCAGTGC
1 CCATACGGAAATTCATACACTTAGTATGAATTTCTTAGC-TTTTGCACACTCAGTGC
45643 C
1 C
45644 ATTTGGTAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
54 25 0.48
55 11 0.21
56 16 0.31
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (56 bp):
CCATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTTTTGCACACTCAGTGC
Found at i:46071 original size:20 final size:20
Alignment explanation
Indices: 46046--46098 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
46036 TCAGTGCTCA
*
46046 ATGGTATCGATACTATCCTC
1 ATGGTATCGATACTACCCTC
*
46066 ATGGTATCGATACTCCCCTC
1 ATGGTATCGATACTACCCTC
* *
46086 TTGCTATCGATAC
1 ATGGTATCGATAC
46099 CACTGAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (20 bp):
ATGGTATCGATACTACCCTC
Found at i:47635 original size:22 final size:21
Alignment explanation
Indices: 47605--47645 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
47595 ATTAATATAT
*
47605 TTGAATTGTATCTATAATAAG
1 TTGAATTGTATATATAATAAG
47626 TTGAACTTGTATATATAATA
1 TTGAA-TTGTATATATAATA
47646 TAATCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (21 bp):
TTGAATTGTATATATAATAAG
Found at i:53070 original size:23 final size:23
Alignment explanation
Indices: 53037--53104 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
53027 ATTATTATAT
* *
53037 GGCACTGCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTATACGC
*
53060 GGCACTTCGGTGCAATTATACGT
1 GGCACTTCGGTGCAATTATACGC
*
53083 GGCACTTTGGTGCAATTATACG
1 GGCACTTCGGTGCAATTATACG
53105 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:56435 original size:21 final size:21
Alignment explanation
Indices: 56393--56435 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56383 GATTCGGGCT
* * *
56393 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
56414 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
56435 A
1 A
56436 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:56507 original size:23 final size:22
Alignment explanation
Indices: 56463--56507 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
56453 AATGTCATGG
*
56463 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
56485 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
56508 AGAAAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:56989 original size:2 final size:2
Alignment explanation
Indices: 56982--57034 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
56972 AATCATTGAC
56982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57022 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
57035 AACCAAGTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
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
Done.