Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002447.1 Hibiscus syriacus cultivar Beakdansim tig00005017_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: 62355
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1931 original size:54 final size:54
Alignment explanation
Indices: 1874--2199 Score: 361
Period size: 54 Copynumber: 5.9 Consensus size: 54
1864 TAGTTCCTAT
* * * * * * * * * *
1874 ACGGTAGTTCATCAACCTATAATAAATTCCATGAGTTGCACACATAGTGCTTG-T
1 ACGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTG-TCGAA
*
1928 ACGGTTGTTCATTAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCGAA
1 ACGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCGAA
1982 ACGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCGAA
1 ACGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCGAA
* * *
2036 ACGGTTATTCATCAACATATGATTAATTCCGTGGGTTGCACACTTAGTG-CTGAA
1 ACGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTC-GAA
* *
2090 ACGGTTGTTCATCAACATATGATGAATTTCATGGGTTGCACACTTGGTGGT-GAA
1 ACGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGT-GTCGAA
* * * *
2144 ATGATTATTCATATGTTATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTG
1 ACGGTTGTTC-------ATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTG
2200 CCTGTACGGA
Statistics
Matches: 235, Mismatches: 26, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
53 3 0.01
54 195 0.83
55 1 0.00
60 1 0.00
61 35 0.15
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (54 bp):
ACGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCGAA
Found at i:2127 original size:162 final size:163
Alignment explanation
Indices: 1881--2199 Score: 419
Period size: 162 Copynumber: 1.9 Consensus size: 163
1871 TATACGGTAG
* * *
1881 TTCATCAACCTATAATAAATTCCATGAGTTGCACACATAGTGCTTGTACGGTTGTTCATTAACAT
1 TTCATCAACATATAATAAATTCCATGAGTTGCACACATAGTGCTTGAACGGTTGTTCATCAACAT
* * *
1946 ATGATGAATTTCGTGGGTTGCACACTTAGT-GTCGAAACGGTTGTTC-ATCAACATATGATGAAT
66 ATGATGAATTTCATGGGTTGCACACTTAGTGGT-GAAACGATTATTCTATCAACATATGATGAAT
*
2009 TTCGTGGGTTGCACACTTAGTGTCGAAACGGTTA
130 TCCGTGGGTTGCACACTTAGTGTCGAAACGGTTA
* * * * *
2043 TTCATCAACATATGATTAATTCCGTGGGTTGCACACTTAGTGC-TGAAACGGTTGTTCATCAACA
1 TTCATCAACATATAATAAATTCCATGAGTTGCACACATAGTGCTTG-AACGGTTGTTCATCAACA
* *
2107 TATGATGAATTTCATGGGTTGCACACTTGGTGGTGAAATGATTATTCATATGTTATCAACATATG
65 TATGATGAATTTCATGGGTTGCACACTTAGTGGTGAAACGATTATTC------TATCAACATATG
2172 ATGAATTCCGTGGGTTGCACACTTAGTG
124 ATGAATTCCGTGGGTTGCACACTTAGTG
2200 CCTGTACGGA
Statistics
Matches: 134, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
161 2 0.01
162 92 0.69
163 2 0.01
169 38 0.28
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (163 bp):
TTCATCAACATATAATAAATTCCATGAGTTGCACACATAGTGCTTGAACGGTTGTTCATCAACAT
ATGATGAATTTCATGGGTTGCACACTTAGTGGTGAAACGATTATTCTATCAACATATGATGAATT
CCGTGGGTTGCACACTTAGTGTCGAAACGGTTA
Found at i:2215 original size:61 final size:62
Alignment explanation
Indices: 2095--2217 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 62
2085 CTGAAACGGT
* * * * *
2095 TGTTCATCAACATATGATGAATTTCATGGGTTGCACACTTGGTGGTGAAATGATTATTCATA
1 TGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTGCTGAAAGGATAATTCATA
* * *
2157 TGTT-ATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTGTACGGA-AATTCATA
1 TGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTG-CTGAAAGGATAATTCATA
2218 AACTTATTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
61 43 0.83
62 9 0.17
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (62 bp):
TGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTGCTGAAAGGATAATTCATA
Found at i:2594 original size:22 final size:22
Alignment explanation
Indices: 2569--2623 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
2559 TGGCTCATTA
2569 GTATCGATACTACCATACCATG
1 GTATCGATACTACCATACCATG
* *
2591 GTATCGATACTACTATACTATG
1 GTATCGATACTACCATACCATG
2613 GTA-CTGATACT
1 GTATC-GATACT
2624 CTATTACGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (22 bp):
GTATCGATACTACCATACCATG
Found at i:2690 original size:20 final size:20
Alignment explanation
Indices: 2665--2714 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2655 GTGATCAATG
2665 GTATCGATACCTTCCTCAT-A
1 GTATCGATACCTTCCTC-TCA
*
2685 GTATCGATACCTTTCTCTCA
1 GTATCGATACCTTCCTCTCA
2705 GTATCGATAC
1 GTATCGATAC
2715 TGATTGCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (20 bp):
GTATCGATACCTTCCTCTCA
Found at i:10719 original size:23 final size:23
Alignment explanation
Indices: 10692--10735 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
10682 CTACTAGTAG
*
10692 AAATAGAGTTTTCCGGTTCTGGT
1 AAATAGAGTTTTCCGATTCTGGT
* *
10715 AAATAGGGTTTTTCGATTCTG
1 AAATAGAGTTTTCCGATTCTG
10736 AAATTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (23 bp):
AAATAGAGTTTTCCGATTCTGGT
Found at i:20369 original size:12 final size:12
Alignment explanation
Indices: 20352--20376 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20342 TGCATGAGAT
20352 ACCATTTTTATG
1 ACCATTTTTATG
20364 ACCATTTTTATG
1 ACCATTTTTATG
20376 A
1 A
20377 AATGTGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
ACCATTTTTATG
Found at i:23332 original size:20 final size:20
Alignment explanation
Indices: 23307--23353 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
23297 AGTGAAAATT
23307 CAAAACACCATATTTAAAAG
1 CAAAACACCATATTTAAAAG
23327 CAAAACACCATATTTAAAAG
1 CAAAACACCATATTTAAAAG
23347 CAAAACA
1 CAAAACA
23354 TAGCTTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.57, C:0.21, G:0.04, T:0.17
Consensus pattern (20 bp):
CAAAACACCATATTTAAAAG
Found at i:29962 original size:13 final size:13
Alignment explanation
Indices: 29944--29972 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29934 CCACCGTACT
29944 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
29957 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
29970 CCG
1 CCG
29973 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:30704 original size:3 final size:3
Alignment explanation
Indices: 30696--30845 Score: 210
Period size: 3 Copynumber: 49.0 Consensus size: 3
30686 ATTATTTATT
*
30696 TAA TAA TAA TAA TATA TAA TAA TAA TATA TAA TAT TAA TAA TAA TAAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA
* **
30744 TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
30792 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAT TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30840 TAA TAA
1 TAA TAA
30846 AATGGATAAA
Statistics
Matches: 132, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
3 123 0.93
4 9 0.07
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:31444 original size:114 final size:114
Alignment explanation
Indices: 31097--31772 Score: 1000
Period size: 114 Copynumber: 5.8 Consensus size: 114
31087 TTGATGAGTC
* * *
31097 CTTCTCATTATGAACTTTTTCTTCCTTCTTCCGAT-GAGTTCTTCTCATTATGAACTTTAC-CTG
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACCTT-CTCTG
* * * *
31160 GCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATT
65 GAAATGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTT
31210 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCT
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAAC-CTT-CT
* *
31275 CTGGAAATGATTATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTT
62 CTGGAAATGATGATCCATCAA-GTGATGAATTCAAGCAAAAGGTTGAACAAGTT
31329 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACCTTCTCTGG
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACCTTCTCTGG
* * *
31393 AAAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTT
66 AAATG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTT
*
31443 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACTT
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAAC-CTTC-T
* * *
31508 CTGGAAATGATTACCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTT
62 CTGGAAATGATGATCCATCAA-GTGATGAATTCAAGCAAAAGGTTGAACAAGTT
31562 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACCTTCTCTGG
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACCTTCTCTGG
* * *
31626 AAAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTT
66 AAATG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTT
*
31676 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTTCTCT
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACCTTCTCT
*
31741 GGAAATGTTGATCCATCAAGTGATGAATTCAA
64 GGAAATGATGATCCATCAAGTGATGAATTCAA
31773 ATCTTTGCTA
Statistics
Matches: 514, Mismatches: 32, Indels: 31
0.89 0.06 0.05
Matches are distributed among these distances:
113 33 0.06
114 147 0.29
115 27 0.05
116 83 0.16
117 55 0.11
118 31 0.06
119 138 0.27
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (114 bp):
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACCTTCTCTGG
AAATGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTT
Found at i:31503 original size:233 final size:233
Alignment explanation
Indices: 31097--31772 Score: 1166
Period size: 233 Copynumber: 2.9 Consensus size: 233
31087 TTGATGAGTC
* * *
31097 CTTCTCATTATGAACTTTTTCTTCCTTCTTCCGATGAGTTCTTCTCATTATGAACTTTAC-CTGG
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT-CTCTGG
* * * * * * *
31161 CAATG-TTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 AAAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
31225 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATTATC
130 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATTATC
31290 CATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTT
195 CATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTT
31329 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGA
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGA
31394 AAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
66 AAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
* * *
31459 TCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACTTCTGGAAATGATTACCC
131 TCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATTATCC
31524 ATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTT
196 ATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTT
31562 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGA
1 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGA
31627 AAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
66 AAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
31692 TCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACT-TT-CTCTGGAAATG-TTGATC
131 TCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATT-ATC
*
31754 CATCAA-GTGATGAATTCAA
195 CATCAATTTGATGAATTCAA
31773 ATCTTTGCTA
Statistics
Matches: 424, Mismatches: 17, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
230 14 0.03
231 19 0.04
232 63 0.15
233 328 0.77
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (233 bp):
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGA
AAAGAATGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATTATCC
ATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTT
Found at i:32638 original size:51 final size:51
Alignment explanation
Indices: 32412--33274 Score: 1627
Period size: 51 Copynumber: 16.8 Consensus size: 51
32402 TCTGTCCAAT
*
32412 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCT-AAC
*
32464 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
32516 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
32568 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
32619 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
32671 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
32723 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
32775 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
32826 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
32877 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
32928 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
32979 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
33030 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
33081 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
33132 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
* *
33183 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
33235 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
33275 TGAGCACATA
Statistics
Matches: 802, Mismatches: 6, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
51 458 0.57
52 342 0.43
53 2 0.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (51 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAC
Found at i:34224 original size:1 final size:1
Alignment explanation
Indices: 34220--34255 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
34210 GACCCCCCCC
* *
34220 TTTTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34256 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:44832 original size:13 final size:15
Alignment explanation
Indices: 44810--44846 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
44800 TTTGACATAA
44810 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
44822 AAATAAAATACTTGC
1 AAATAAAATACTTGC
44837 AAATAAAATA
1 AAATAAAATA
44847 AAACATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:46205 original size:13 final size:13
Alignment explanation
Indices: 46187--46215 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
46177 CCACCGTACT
46187 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
46200 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
46213 CCG
1 CCG
46216 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:46944 original size:3 final size:3
Alignment explanation
Indices: 46936--47091 Score: 231
Period size: 3 Copynumber: 51.0 Consensus size: 3
46926 ATTATTTATT
*
46936 TAA TAA TAA TAA TATA TAA TAA TAA TATA TAA TAT TAA TAA TAA TAAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA
* **
46984 TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
47032 TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47080 TAA TAA TAA TAA
1 TAA TAA TAA TAA
47092 AATGGATAAA
Statistics
Matches: 138, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
3 129 0.93
4 9 0.07
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52255 original size:17 final size:18
Alignment explanation
Indices: 52212--52252 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
52202 GAATTATATT
52212 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
52229 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
52247 ATTAAA
1 AGTAAA
52253 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:58570 original size:23 final size:24
Alignment explanation
Indices: 58526--58572 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
58516 ATACATTGAC
*
58526 AAATTATATAAATACAATAACATT
1 AAATTATATAAATACAAAAACATT
58550 AAATTAT-TAGAA-ACAAAAACATT
1 AAATTATATA-AATACAAAAACATT
58573 CATTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATTATATAAATACAAAAACATT
Found at i:61464 original size:8 final size:8
Alignment explanation
Indices: 61451--61491 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
61441 CTCATTTTCA
61451 GAGAATTT
1 GAGAATTT
61459 GAGAATTT
1 GAGAATTT
*
61467 -AGAGTTT
1 GAGAATTT
*
61474 GGGAATTT
1 GAGAATTT
61482 GAGAATTT
1 GAGAATTT
61490 GA
1 GA
61492 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:61792 original size:128 final size:128
Alignment explanation
Indices: 61564--62355 Score: 1224
Period size: 128 Copynumber: 6.2 Consensus size: 128
61554 ATCGGAGTAT
* * * *
61564 TATTCACATGAAGGAGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAAAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
61629 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACTTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
61692 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
61757 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * *
61820 -AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
**
61884 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCAC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
61948 TATTCACATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATCATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
* *
62013 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTGTTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * *** *
62076 -AGGGGACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTTGCCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
**
62140 ATTGCCCTATTATGTCACTCATGT-CCTCGGGGACACCCG--ATATCAGTACCTATTATTTCAC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
62201 TATTCACATGAAGGCGCG-TCCCGGGGGCGCGCCTTCCATTA-TTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
62264 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATAT-AGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
***
62326 -AGGGACATGAAGGCGCGTTCCCGGGGGCGC
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGC
Statistics
Matches: 603, Mismatches: 53, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
123 41 0.07
124 49 0.08
125 61 0.10
126 5 0.01
127 15 0.02
128 431 0.71
129 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:62024 original size:256 final size:256
Alignment explanation
Indices: 61569--62351 Score: 1418
Period size: 256 Copynumber: 3.1 Consensus size: 256
61559 AGTATTATTC
* *
61569 ACATGAAGGAGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAAAGAATATGTTATCATTGCC
1 ACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCATAGAATATGTTATCATTGCC
** *
61634 CTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACTTATTATTTCACTATTCAC
66 CTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCAC
61699 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCT
131 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCT
61764 ATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGG
196 ATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGG
*
61825 ACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCATAGAATATGTTATCATTGCC
1 ACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCATAGAATATGTTATCATTGCC
61890 CTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCAC
66 CTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCAC
* *
61955 ATGAAGGCGCGTTCCCGGGGGCGCACCTTCCATCATTTCATCAGAGAATATGTTATCATTGCCCT
131 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCT
*
62020 ATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTGTTATTTCTCAGGGG
196 ATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGG
* *
62081 ACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTTGCCATAGAATATGTTATCATTGCC
1 ACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCATAGAATATGTTATCATTGCC
62146 CTATTATGTCACTCATGT-CCTCGGGGACACCCG--ATATCAGTACCTATTATTTCACTATTCAC
66 CTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCAC
62208 ATGAAGGCGCG-TCCCGGGGGCGCGCCTTCCATTA-TTCATCAGAGAATATGTTATCATTGCCCT
131 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCT
62271 ATTATGTCACTCATGTCCCTCGGGGACACTAGATATAT-AGTACCTATTATTTCTCA-GGG
196 ATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGG
62330 ACATGAAGGCGCGTTCCCGGGG
1 ACATGAAGGCGCGTTCCCGGGG
62352 GCGC
Statistics
Matches: 512, Mismatches: 15, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
249 25 0.05
250 17 0.03
251 67 0.13
252 21 0.04
253 40 0.08
255 15 0.03
256 327 0.64
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (256 bp):
ACATGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCATAGAATATGTTATCATTGCC
CTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCAC
ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGG
Done.