Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009235.1 Hibiscus syriacus cultivar Beakdansim tig00112857_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: 1478786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1399800 original size:20 final size:20
Alignment explanation
Indices: 1399777--1399845 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
1399767 GATTTCAACT
1399777 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
1399797 ATCGCAACTCGATCTCCAACT
1 ATCGCAACGCGAAATGGAA-A
*
1399818 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1399838 AACGCAAC
1 ATCGCAAC
1399846 ACGATTTTCA
Statistics
Matches: 33, Mismatches: 15, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1399817 original size:41 final size:41
Alignment explanation
Indices: 1399772--1399874 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
1399762 GTTGCGATTT
* * *
1399772 CAACTATCGCAACGCGAAATGGAAAATCGCAACTCGATCTC
1 CAACTATCGCAATGCGAAATGGAAAAACGCAACACGATCTC
* *
1399813 CAACTATCGCAATGCGAAATGGAAAAACGCAACACGATTTT
1 CAACTATCGCAATGCGAAATGGAAAAACGCAACACGATCTC
1399854 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAATGCGAAATG
1399875 CAACGTGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (41 bp):
CAACTATCGCAATGCGAAATGGAAAAACGCAACACGATCTC
Found at i:1399888 original size:142 final size:142
Alignment explanation
Indices: 1399632--1399903 Score: 429
Period size: 142 Copynumber: 1.9 Consensus size: 142
1399622 ACAATTGTAG
* *
1399632 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCAAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCAAAATGGAAAA
* * *
1399697 CCACAACGCGATTTTCAACTATCGTAACGCGAAATGCAACGCGAATTTGCGAT-GATGGAGATCG
66 ACACAACACGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAG-TGGAGATCG
1399761 CGTTGCGATTTCA
130 CGTTGCGATTTCA
* * *
1399774 ACTATCGCAACGCGAAATGGAAAATCGCAACTCGATCTCCAACTATCGCAATGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCAAAATGGAAAA
* * *
1399839 ACGCAACACGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAGTGGAGATCGC
66 ACACAACACGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
1399904 AATGCAAATT
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
142 117 0.99
143 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (142 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCAAAATGGAAAA
ACACAACACGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
GTTGCGATTTCA
Found at i:1400513 original size:16 final size:16
Alignment explanation
Indices: 1400487--1400525 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1400477 TCGGGTTACT
1400487 ATTTACGTGAATAGTGA
1 ATTT-CGTGAATAGTGA
1400504 ATTTCGTGAATAGTGA
1 ATTTCGTGAATAGTGA
*
1400520 AATTCG
1 ATTTCG
1400526 GTCGGTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (16 bp):
ATTTCGTGAATAGTGA
Found at i:1400523 original size:17 final size:17
Alignment explanation
Indices: 1400487--1400520 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1400477 TCGGGTTACT
1400487 ATTTACGTGAATAGTGA
1 ATTTACGTGAATAGTGA
1400504 ATTT-CGTGAATAGTGA
1 ATTTACGTGAATAGTGA
1400520 A
1 A
1400521 ATTCGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTGA
Found at i:1411753 original size:15 final size:17
Alignment explanation
Indices: 1411720--1411753 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1411710 CGTATCCAAT
1411720 AGTTCCAGATTATTAGA
1 AGTTCCAGATTATTAGA
1411737 AGTTCCA-ATTA-TAGA
1 AGTTCCAGATTATTAGA
1411752 AG
1 AG
1411754 CTTCTTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (17 bp):
AGTTCCAGATTATTAGA
Found at i:1422950 original size:31 final size:31
Alignment explanation
Indices: 1422890--1423015 Score: 191
Period size: 31 Copynumber: 4.0 Consensus size: 31
1422880 ATGGTCGAGG
* *
1422890 GTTTACCTATGTTCTTCAGGGGCATATGGATT
1 GTTTACCTATGTTCTTC-GGGACATATGGACT
1422922 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1422953 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1422984 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1423015 G
1 G
1423016 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
31 71 0.80
32 18 0.20
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1428513 original size:14 final size:15
Alignment explanation
Indices: 1428494--1428528 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1428484 AAATCGAAAC
1428494 CGGTTTTTT-CGGTT
1 CGGTTTTTTACGGTT
1428508 CGGTTTTTTGACGGTT
1 CGGTTTTTT-ACGGTT
1428524 CGGTT
1 CGGTT
1428529 CGATTTATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
16 10 0.53
ACGTcount: A:0.03, C:0.14, G:0.31, T:0.51
Consensus pattern (15 bp):
CGGTTTTTTACGGTT
Found at i:1428819 original size:18 final size:17
Alignment explanation
Indices: 1428774--1428807 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1428764 TTTTCAGGTA
1428774 TCACAAATTTTTTTAAC
1 TCACAAATTTTTTTAAC
1428791 GTCACAAATTTTTTTAA
1 -TCACAAATTTTTTTAA
1428808 TCAAACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (17 bp):
TCACAAATTTTTTTAAC
Found at i:1434710 original size:29 final size:29
Alignment explanation
Indices: 1434667--1434749 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
1434657 CTCACCTAAC
* *
1434667 TAAATTGATGTAAGCCATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1434697 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
1434726 TAAATGATGTAAGTAATGATATCA
1 TAAATGATGTAAGCAATGACATCA
1434750 ATTTAGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 43 0.91
30 4 0.09
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1439464 original size:29 final size:29
Alignment explanation
Indices: 1439421--1439503 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
1439411 CTTACCTAAC
*
1439421 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
1439451 TAAATGATATAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
1439480 TAAATGATGTAAGTAATGATATCA
1 TAAATGATGTAAGCAATGACATCA
1439504 ATTTAGTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 42 0.91
30 4 0.09
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1440655 original size:40 final size:40
Alignment explanation
Indices: 1440595--1440674 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
1440585 TTTTTATAGA
* * *
1440595 ATAAGATGGATAAACTTTGTTATGAGCCTCGTTAAAAACT
1 ATAAAATGGATAAACTTTGTTACGAGCCTCGTCAAAAACT
*
1440635 ATAAAATGGATAAATTTTGTTACGAGCCTCGTCAAAAACT
1 ATAAAATGGATAAACTTTGTTACGAGCCTCGTCAAAAACT
1440675 TTCCTAAGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (40 bp):
ATAAAATGGATAAACTTTGTTACGAGCCTCGTCAAAAACT
Found at i:1441832 original size:28 final size:28
Alignment explanation
Indices: 1441771--1441835 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
1441761 TATGATTTTG
*
1441771 AAGAAACAATAAAAAATTAAGTATTAAA
1 AAGAACCAATAAAAAATTAAGTATTAAA
1441799 AAGAACCAATAAAAAATTAAGTATTAAA
1 AAGAACCAATAAAAAATTAAGTATTAAA
1441827 AAGAACCAA
1 AAGAACCAA
1441836 AGCTAATAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.66, C:0.08, G:0.08, T:0.18
Consensus pattern (28 bp):
AAGAACCAATAAAAAATTAAGTATTAAA
Found at i:1442090 original size:34 final size:32
Alignment explanation
Indices: 1442029--1442092 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
1442019 CTCTTTTCTG
* * *
1442029 TATTATATTTTTATTTATTTAATAAAAATATT
1 TATTATATTTTTATTAAATTAAAAAAAATATT
1442061 TATTAATATTATTTATTAAATTAAAAAAAATA
1 TATT-ATATT-TTTATTAAATTAAAAAAAATA
1442093 AGTTGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 4 0.15
33 5 0.19
34 18 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTATATTTTTATTAAATTAAAAAAAATATT
Found at i:1443419 original size:13 final size:12
Alignment explanation
Indices: 1443401--1443447 Score: 67
Period size: 13 Copynumber: 3.8 Consensus size: 12
1443391 TCATTAGCAA
*
1443401 AAATAAAGTAAGT
1 AAATAAA-TAAAT
1443414 AAATAAATAAAT
1 AAATAAATAAAT
1443426 AAATAAAATAAAT
1 AAAT-AAATAAAT
1443439 AAATAAATA
1 AAATAAATA
1443448 TTATCAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 13 0.41
13 19 0.59
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:1443420 original size:4 final size:4
Alignment explanation
Indices: 1443401--1443447 Score: 67
Period size: 4 Copynumber: 11.2 Consensus size: 4
1443391 TCATTAGCAA
*
1443401 AAAT AAAGT AAGT AAAT AAAT AAAT AAAT AAAAT AAAT AAAT AAAT A
1 AAAT AAA-T AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT A
1443448 TTATCAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1443423 original size:17 final size:17
Alignment explanation
Indices: 1443401--1443447 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1443391 TCATTAGCAA
*
1443401 AAATAAAGTAAGT-AAAT
1 AAATAAA-TAAATAAAAT
1443418 AAATAAATAAATAAAAT
1 AAATAAATAAATAAAAT
1443435 AAATAAATAAATA
1 AAATAAATAAATA
1443448 TTATCAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAATAAATAAATAAAAT
Found at i:1447553 original size:21 final size:21
Alignment explanation
Indices: 1447505--1447603 Score: 101
Period size: 21 Copynumber: 4.6 Consensus size: 21
1447495 TCAAAATGGA
*
1447505 GTGCATGGATGCACTAGTGCCA-G
1 GTGCATGGATG--C-AGTGCAAGG
*
1447528 GTGCATGGATGCAGTGCAACG
1 GTGCATGGATGCAGTGCAAGG
* *
1447549 GTGCATGGATACAGTGCAGGG
1 GTGCATGGATGCAGTGCAAGG
* *
1447570 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCAGTGCAAGG
*
1447591 GTGTATGGATGCA
1 GTGCATGGATGCA
1447604 CTTTGACACC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.09
21 51 0.75
23 11 0.16
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.21
Consensus pattern (21 bp):
GTGCATGGATGCAGTGCAAGG
Found at i:1447604 original size:21 final size:21
Alignment explanation
Indices: 1447527--1447605 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
1447517 ACTAGTGCCA
* **
1447527 GGTGCATGGATGCAGTGCAAC
1 GGTGCATGGATGCACTGCAGG
* *
1447548 GGTGCATGGATACAGTGCAGG
1 GGTGCATGGATGCACTGCAGG
1447569 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
1447590 GGTGTATGGATGCACT
1 GGTGCATGGATGCACT
1447606 TTGACACCCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:1469759 original size:20 final size:20
Alignment explanation
Indices: 1469733--1469774 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 20
1469723 ATACAAGTTT
1469733 AAAAAAATATAGTTACAATAC
1 AAAAAAA-ATAGTTACAATAC
1469754 AAAAAAAATAGTTACAATAC
1 AAAAAAAATAGTTACAATAC
1469774 A
1 A
1469775 TAATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAAAAAATAGTTACAATAC
Found at i:1471363 original size:23 final size:23
Alignment explanation
Indices: 1471337--1471403 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
1471327 CCACAGCTCA
1471337 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* *
1471360 TATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
* *
1471383 TAGAATTGCACCGTAGTGCCA
1 TATAATTGCACCGAAGTGCCA
1471404 TATAATAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:1471590 original size:103 final size:103
Alignment explanation
Indices: 1471419--1471636 Score: 384
Period size: 103 Copynumber: 2.1 Consensus size: 103
1471409 TAATGTCCAT
* * *
1471419 AAGGACCACATATCATTCTTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGCGTCTCACCA
1471484 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1471522 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGCGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGAGATCAAGTATGCGTCTCACC
1471586 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1471625 AAGGACCACATA
1 AAGGACCACATA
1471637 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 107 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGCGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1472882 original size:32 final size:30
Alignment explanation
Indices: 1472846--1472909 Score: 101
Period size: 32 Copynumber: 2.1 Consensus size: 30
1472836 TTGGTTAGAA
*
1472846 GAAAGGAGTTTGTTGTGTAAGAGATTGAAGAT
1 GAAAGGAGTGTGTTGTGTAAGAGA-TGAA-AT
1472878 GAAAGGAGTGTGTTGTGTAAGAGATGAAAT
1 GAAAGGAGTGTGTTGTGTAAGAGATGAAAT
1472908 GA
1 GA
1472910 GTGTGTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 4 0.13
32 23 0.74
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (30 bp):
GAAAGGAGTGTGTTGTGTAAGAGATGAAAT
Found at i:1472902 original size:25 final size:25
Alignment explanation
Indices: 1472874--1472921 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1472864 AAGAGATTGA
*
1472874 AGATGAAAGGAGTGTGTTGTGTAAG
1 AGATGAAAGGAGTGTGTTATGTAAG
*
1472899 AGATGAAATGAGTGTGTTATGTA
1 AGATGAAAGGAGTGTGTTATGTA
1472922 CGAGTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTATGTAAG
Found at i:1475038 original size:6 final size:6
Alignment explanation
Indices: 1475022--1475051 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1475012 ATCAAATTAA
1475022 AAAACTT AAAATT AAAATT AAAATT AAAAT
1 AAAA-TT AAAATT AAAATT AAAATT AAAAT
1475052 AATAATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:1475405 original size:2 final size:2
Alignment explanation
Indices: 1475393--1475429 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1475383 GATTCAAATT
1475393 TA TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1475430 AACGTACCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1476196 original size:2 final size:2
Alignment explanation
Indices: 1476189--1476238 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1476179 GAAAATTATG
1476189 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
1476231 TA TA TA TA
1 TA TA TA TA
1476239 GAGAGAGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1476243 original size:2 final size:2
Alignment explanation
Indices: 1476238--1476281 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1476228 ATATATATAT
1476238 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1476280 AG
1 AG
1476282 CAGTATCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.