Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001050.1 Hibiscus syriacus cultivar Beakdansim tig00002080_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: 54253
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2304 original size:12 final size:12
Alignment explanation
Indices: 2289--2313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2279 ATATTTTTAG
2289 TAAAAATTTATT
1 TAAAAATTTATT
2301 TAAAAATTTATT
1 TAAAAATTTATT
2313 T
1 T
2314 TTTTATCTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAAATTTATT
Found at i:4470 original size:3 final size:3
Alignment explanation
Indices: 4462--4487 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4452 AAAGAGATAA
4462 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
4488 AAATATACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:8922 original size:13 final size:13
Alignment explanation
Indices: 8893--8933 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
8883 AGTTTTCGGT
8893 TTTAAGATTTAAAA
1 TTTAAGA-TTAAAA
* *
8907 TTTAAGGTTAAGA
1 TTTAAGATTAAAA
8920 TTTAAGATTAAAA
1 TTTAAGATTAAAA
8933 T
1 T
8934 AAATTATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.41
Consensus pattern (13 bp):
TTTAAGATTAAAA
Found at i:10756 original size:138 final size:138
Alignment explanation
Indices: 10495--11791 Score: 1429
Period size: 138 Copynumber: 9.4 Consensus size: 138
10485 CAACATCCAG
* * *
10495 AAAGTTGAAGGGT-TTCAAGAGATGTCAAATGA-TCA-ATGCAAGGTAGTTCAACCAAACTTTCA
1 AAAGTTGAA-GCTATTCAAGAGATGTCAAATGACTGAGA--CAAGGAAGTTCAACCAAACTTTCA
* * * * * *
10557 CACCACCTACAGTCGAGGGTTTTGAGTTTGATGGCTCCTA-ATAGATTAGAGATTTTCTTTAAAT
63 CACCACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCC-AGATAGATTAGGGATCTTCCTTAAAT
10621 TCTTGCAAGCAC
127 TCTTGCAAGCAC
* * * * * * *
10633 AAAATTTAAGCTGTTCAAGAGATGCCAAGTCACTTAGACAAGGAAGTTCAACCAAACTTTCACAC
1 AAAGTTGAAGCTATTCAAGAGATGTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACAC
* * ** **
10698 CACCTACAGTCAAGGATTTTAAGGTGGATGGCTCCAGATAGGCTAGGGATCTTTTTTAAATTCTT
66 CACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCCAGATAGATTAGGGATCTTCCTTAAATTCTT
10763 GCAAGCAC
131 GCAAGCAC
* * * * * * ** *
10771 AAAGCTGTAGCCATTCAAGAGATGCCAAATCACTGAGACAAGAAAGTTCTTCCAAACTTCCACAC
1 AAAGTTGAAGCTATTCAAGAGATGTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACAC
* * * * * * *
10836 CACCTACAATCGAGGGTTTTAAGGCTGATGGCTCCTGTTAAATTAGGGAGCTTCCTTAAATTCTT
66 CACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCCAGATAGATTAGGGATCTTCCTTAAATTCTT
10901 GCAAGCAC
131 GCAAGCAC
* * * *
10909 AAAGGTTAAATCT-TTCAAGAGATGTCAAATGACTCA-AGTAAGGAAGTTCAACCAAACTTTCAC
1 AAA-GTTGAAGCTATTCAAGAGATGTCAAATGACTGAGA-CAAGGAAGTTCAACCAAACTTTCAC
* * * *
10972 ACCACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCCTGATAGATCAGGGATCTTCCTTAAACTA
64 ACCACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCCAGATAGATTAGGGATCTTCCTTAAATTC
11037 TTGCAAGCAC
129 TTGCAAGCAC
* * * * *
11047 AAAGTTTAAGCTTTTCAAGAGATGTCAAATTACTAAGGCAAGGAAGTTCAACCAAACTTTCACAC
1 AAAGTTGAAGCTATTCAAGAGATGTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACAC
* *
11112 CACCTACAATCAAGGGTTTTAAGGTTGATGG-T-AATTGATAGATTAGGGATCTTCCTTAAATTC
66 CACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCCA--GATAGATTAGGGATCTTCCTTAAATTC
11175 TTGCAAGCAC
129 TTGCAAGCAC
* * * *
11185 GAAGTTGAAGGC-ATTCCAGAGATTTCAAATGACTGAGGCAAGGAAGTTCAACCAAACTTTCACA
1 AAAGTTGAA-GCTATTCAAGAGATGTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACA
* ** *
11249 CCACCTACAATCAAGGGTTTTAAGGTTGATGGCTCTTGATAGATCAGGGATCTTCCTTAAATTCT
65 CCACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCCAGATAGATTAGGGATCTTCCTTAAATTCT
11314 TGCAAGCAC
130 TGCAAGCAC
* * * *
11323 AAAGTTGAAGCCT-TTCAAGAGATGTCAAATGACTGAGGCAAGGAAGTTCTATCAAACTTCCACA
1 AAAGTTGAAG-CTATTCAAGAGATGTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACA
* * * *
11387 CCACCTACAGTCAAGGGTTTTAAGGTTGATGGTTTCTA-CTAGATTAGGAATCTTCCTTAAATTC
65 CCACCTACAGTCAAGGGTTTTAAGGTTGATGG-CTCCAGATAGATTAGGGATCTTCCTTAAATTC
11451 TTGCAAGCAC
129 TTGCAAGCAC
* *
11461 AAAGTAGAAGGC-ATTCAAGAGATTTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACA
1 AAAGTTGAA-GCTATTCAAGAGATGTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACA
* * * * * *
11525 CCACCTACAATCAAGGGTTTTAAGGCTGACGGCTCCTA-ATAGATCAGTGATATTCCTTAAATTC
65 CCACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCC-AGATAGATTAGGGATCTTCCTTAAATTC
*
11589 TTGCAAGCAG
129 TTGCAAGCAC
* * * * * **
11599 AAAGTTTAAGCTTTTCAAGGGATGTCAAATGACTGAGGCTAGGAAGTTCAACCAAACTTTTGCAC
1 AAAGTTGAAGCTATTCAAGAGATGTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACAC
* * * * * * * * *
11664 GAAGC-ACAGTCAAGGGTTTTAAGTTTGATGACACCTGATAGATTGGGGATCCTCTTTAAATTCT
66 -CACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCCAGATAGATTAGGGATCTTCCTTAAATTCT
* *
11728 TGCAAACAG
130 TGCAAGCAC
* * * * *
11737 AAACTTGAAGGGT-TTCAAGAGATGCCAAATGA-TCGAGGCAGGGAAGTTCAACCAA
1 AAAGTTGAA-GCTATTCAAGAGATGTCAAATGACT-GAGACAAGGAAGTTCAACCAA
11792 CTTAGTGCAA
Statistics
Matches: 987, Mismatches: 148, Indels: 48
0.83 0.13 0.04
Matches are distributed among these distances:
137 18 0.02
138 951 0.96
139 17 0.02
140 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (138 bp):
AAAGTTGAAGCTATTCAAGAGATGTCAAATGACTGAGACAAGGAAGTTCAACCAAACTTTCACAC
CACCTACAGTCAAGGGTTTTAAGGTTGATGGCTCCAGATAGATTAGGGATCTTCCTTAAATTCTT
GCAAGCAC
Found at i:16682 original size:14 final size:14
Alignment explanation
Indices: 16663--16690 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16653 AAGTGAAAGA
16663 ATAGTTATATAATT
1 ATAGTTATATAATT
16677 ATAGTTATATAATT
1 ATAGTTATATAATT
16691 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:21891 original size:41 final size:41
Alignment explanation
Indices: 21846--22004 Score: 257
Period size: 41 Copynumber: 3.9 Consensus size: 41
21836 GATTCTGACT
** * *
21846 ATCGCAACGAGTATCCGTAAAATTGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
21887 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
21928 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
21968 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCC
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCC
22005 TTCCATATCT
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 38 0.35
41 71 0.65
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:21893 original size:20 final size:20
Alignment explanation
Indices: 21846--22004 Score: 169
Period size: 20 Copynumber: 7.8 Consensus size: 20
21836 GATTCTGACT
*
21846 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
21867 ATTGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
21887 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
21908 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
21928 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
21948 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
21968 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
21989 ATCGCAACGCGTATCC
1 ATCGCAACGCGTATCC
22005 TTCCATATCT
Statistics
Matches: 113, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
20 65 0.58
21 48 0.42
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:21974 original size:81 final size:82
Alignment explanation
Indices: 21846--22004 Score: 275
Period size: 81 Copynumber: 2.0 Consensus size: 82
21836 GATTCTGACT
* * *
21846 ATCGCAACGAGTATCCGTAAAATTGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
21911 GCAACGCGTATCCGTAA
66 GCAACGCGTATCCGTAA
*
21928 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
21992 GCAACGCGTATCC
66 GCAACGCGTATCC
22005 TTCCATATCT
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 57 0.78
82 16 0.22
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (82 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATC
GCAACGCGTATCCGTAA
Found at i:22050 original size:27 final size:27
Alignment explanation
Indices: 22020--22094 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
22010 TATCTCCGGC
22020 GAAATACCTCACAACCATTCACGGTCA
1 GAAATACCTCACAACCATTCACGGTCA
22047 GAAATACCTCACAACCATTCACGGTCA
1 GAAATACCTCACAACCATTCACGGTCA
* *
22074 GAAATCCCTCACAATCATTCA
1 GAAATACCTCACAACCATTCA
22095 TATATGGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.37, C:0.33, G:0.09, T:0.20
Consensus pattern (27 bp):
GAAATACCTCACAACCATTCACGGTCA
Found at i:22450 original size:21 final size:21
Alignment explanation
Indices: 22390--22468 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 21
22380 TTCTAAATTT
22390 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
*
22410 AAAATTGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
** *
22430 ACTATCGTAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
22451 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
22469 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
20 27 0.56
21 21 0.44
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.14
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:22487 original size:33 final size:33
Alignment explanation
Indices: 22445--22525 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
22435 CGTAACGAGA
22445 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
22478 GAAATGAAAATCGTAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
22511 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
22526 TTACGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:23106 original size:20 final size:20
Alignment explanation
Indices: 23083--23192 Score: 159
Period size: 20 Copynumber: 5.4 Consensus size: 20
23073 TTCCTGATGA
23083 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
23103 GTTGCGAGTTTACGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
23124 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
23144 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
23164 GTTGCGATTTCACGGATACTC
1 GTTGCGATTT-ACGGATACGC
23185 GTTGCGAT
1 GTTGCGAT
23193 AGTCAGAATC
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.02
20 45 0.56
21 32 0.40
22 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:23140 original size:41 final size:40
Alignment explanation
Indices: 23083--23192 Score: 159
Period size: 41 Copynumber: 2.7 Consensus size: 40
23073 TTCCTGATGA
* *
23083 GTTGCGATTTACGGATACGCGTTGCGAGTTTACGTATTA-TC
1 GTTGCGATTTACGGATACGCGTTGCGA-TTTACGGA-TACGC
23124 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
*
23164 GTTGCGATTTCACGGATACTCGTTGCGAT
1 GTTGCGATTT-ACGGATACGCGTTGCGAT
23193 AGTCAGAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
39 2 0.03
40 18 0.28
41 44 0.69
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (40 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
Found at i:23206 original size:41 final size:40
Alignment explanation
Indices: 23083--23215 Score: 146
Period size: 41 Copynumber: 3.3 Consensus size: 40
23073 TTCCTGATGA
* * *
23083 GTTGCGATTTACGGATACGCGTTGCGAGTTTACGTATTA-TC
1 GTTGCGATTTACGGATACGCGTTGCGA-TTCACG-AATACGC
* *
23124 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGCGTTGCGATTCACGAATACGC
*
23164 GTTGCGATTTCACGGATACTCGTTGCGATAGTCA-GAAT-CGC
1 GTTGCGATTT-ACGGATACGCGTTGCGAT--TCACGAATACGC
23205 GTTGCGATTTA
1 GTTGCGATTTA
23216 TATGTTCGCG
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
39 2 0.02
40 18 0.22
41 57 0.70
42 3 0.04
43 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (40 bp):
GTTGCGATTTACGGATACGCGTTGCGATTCACGAATACGC
Found at i:23206 original size:61 final size:61
Alignment explanation
Indices: 23083--23215 Score: 175
Period size: 61 Copynumber: 2.2 Consensus size: 61
23073 TTCCTGATGA
* * *
23083 GTTGCGATTTACGGATACGCGTTGCGAGTTTACGTATTATCGTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGCGTTGCGAGTTTACGGATTATCGTTGCGATTCACGAATACGC
23144 GTTGCGATTTACGGATACGCGTTGCGA-TTTCACGGA-TACTCGTTGCGATAGTCA-GAAT-CGC
1 GTTGCGATTTACGGATACGCGTTGCGAGTTT-ACGGATTA-TCGTTGCGAT--TCACGAATACGC
23205 GTTGCGATTTA
1 GTTGCGATTTA
23216 TATGTTCGCG
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
60 5 0.08
61 55 0.85
62 3 0.05
63 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (61 bp):
GTTGCGATTTACGGATACGCGTTGCGAGTTTACGGATTATCGTTGCGATTCACGAATACGC
Found at i:23990 original size:31 final size:30
Alignment explanation
Indices: 23955--24043 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 30
23945 AAGTTAATTT
* *
23955 TTAATTTGATCCATAAATTTTAGATAAAACG
1 TTAATTTGATCCTTAAA-TTTAGATAAAACA
* * *
23986 TTAATTTAACCCTTAAATTTAGATAAAATA
1 TTAATTTGATCCTTAAATTTAGATAAAACA
*
24016 TTAATTTGATCCTTAAAATTTAAATAAA
1 TTAATTTGATCCTT-AAATTTAGATAAA
24044 TATCAATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 23 0.47
31 26 0.53
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (30 bp):
TTAATTTGATCCTTAAATTTAGATAAAACA
Found at i:24045 original size:30 final size:30
Alignment explanation
Indices: 23955--24052 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 30
23945 AAGTTAATTT
* *
23955 TTAATTTGATCCATAAATTTTAGATAAA-A
1 TTAATTTGATCCTTAAAATTTAGATAAATA
* *
23984 CGTTAATTTAACCCTT-AAATTTAGATAAAATA
1 --TTAATTTGATCCTTAAAATTTAGAT-AAATA
*
24016 TTAATTTGATCCTTAAAATTTAAATAAATA
1 TTAATTTGATCCTTAAAATTTAGATAAATA
*
24046 TCAATTT
1 TTAATTT
24053 AACTTATGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
30 32 0.57
31 23 0.41
32 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (30 bp):
TTAATTTGATCCTTAAAATTTAGATAAATA
Found at i:24473 original size:31 final size:31
Alignment explanation
Indices: 24438--24535 Score: 87
Period size: 30 Copynumber: 3.2 Consensus size: 31
24428 AAGTTAATTT
* *
24438 TTAATTTGATCCATAAATTTTAGATAAAATA
1 TTAATTTGATCCATAAAGTTTAAATAAAATA
* * *
24469 TTAATTT-AACCCTTAAGTTTAAATAAAATA
1 TTAATTTGATCCATAAAGTTTAAATAAAATA
*
24499 TTAGTTTGAT-CATTAGAA-TTTAAAT-AAATA
1 TTAATTTGATCCA-TA-AAGTTTAAATAAAATA
*
24529 TCAATTT
1 TTAATTT
24536 AACTTATGAA
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
30 35 0.66
31 16 0.30
32 2 0.04
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (31 bp):
TTAATTTGATCCATAAAGTTTAAATAAAATA
Found at i:24497 original size:30 final size:31
Alignment explanation
Indices: 24456--24538 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 31
24446 ATCCATAAAT
* * *
24456 TTTAGATAAAATATTAATTTAACCCTTA-AG
1 TTTAAATAAAATATTAATTTAACCATTAGAA
* * *
24486 TTTAAATAAAATATTAGTTTGATCATTAGAA
1 TTTAAATAAAATATTAATTTAACCATTAGAA
*
24517 TTTAAAT-AAATATCAATTTAAC
1 TTTAAATAAAATATTAATTTAAC
24539 TTATGAATCT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
30 34 0.81
31 8 0.19
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (31 bp):
TTTAAATAAAATATTAATTTAACCATTAGAA
Found at i:26180 original size:37 final size:37
Alignment explanation
Indices: 26107--26181 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
26097 GTTGAAAAAT
*
26107 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
26144 ATTTATATAATTTAT-TTTACAAAATTTAAAAT-ATAAA
1 ATTTATAT-ATTT-TCTTTAAAAAAATTAAAATCATAAA
26181 A
1 A
26182 AGTTTAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 18 0.55
39 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:27249 original size:14 final size:13
Alignment explanation
Indices: 27199--27286 Score: 56
Period size: 13 Copynumber: 6.7 Consensus size: 13
27189 AATTTAACCC
*
27199 TTTTTTATTATT-
1 TTTTTTATTTTTA
*
27211 TTTTTTATTTCTA
1 TTTTTTATTTTTA
**
27224 TTTCGT-TTTTTA
1 TTTTTTATTTTTA
27236 TTCTTTTATTTTTA
1 TT-TTTTATTTTTA
*
27250 TTTTTT-TTCTTAA
1 TTTTTTATT-TTTA
* *
27263 TTTCACTTATCTTTA
1 TTT--TTTATTTTTA
27278 TTTTTTATT
1 TTTTTTATT
27287 ATTGTTATTT
Statistics
Matches: 56, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
12 19 0.34
13 20 0.36
14 8 0.14
15 8 0.14
16 1 0.02
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:27353 original size:18 final size:18
Alignment explanation
Indices: 27313--27347 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27303 TCTTTTATTT
27313 ATTTTTTATATATTTTTA
1 ATTTTTTATATATTTTTA
27331 ATTTTTTA-ACTATTTTT
1 ATTTTTTATA-TATTTTT
27348 CTTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTTATATATTTTTA
Found at i:27370 original size:24 final size:23
Alignment explanation
Indices: 27343--27415 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
27333 TTTTTAACTA
*
27343 TTTTTCTTTTTATTTATTTTCCTT
1 TTTTTCTTTTTATTTATTTT-ATT
*
27367 TTTTTCTTTTGATTTATTTTATT
1 TTTTTCTTTTTATTTATTTTATT
* *
27390 TTTTACTTATTA-TTATTATTATT
1 TTTTTCTTTTTATTTATT-TTATT
27413 TTT
1 TTT
27416 CATTTTCCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 5 0.12
23 19 0.44
24 19 0.44
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (23 bp):
TTTTTCTTTTTATTTATTTTATT
Found at i:27391 original size:23 final size:22
Alignment explanation
Indices: 27230--27415 Score: 77
Period size: 23 Copynumber: 8.2 Consensus size: 22
27220 TCTATTTCGT
*
27230 TTTTTATTCTTTTATTT-TTAT-
1 TTTTT-TTCTTTTATTTATTTTA
* *
27251 TTTTTTTC-TTAATTTCA-CTTA
1 TTTTTTTCTTTTATTT-ATTTTA
*
27272 TCTTTATT-TTTTA-TTATTGTTA
1 T-TTTTTTCTTTTATTTATT-TTA
27294 TTTTAATATTCTTTTATTTATTTT-
1 TTTT--T-TTCTTTTATTTATTTTA
* * *
27318 TTATATATT-TTTAATTT-TTTAA
1 TT-T-TTTTCTTTTATTTATTTTA
* *
27340 CTATTTTTCTTTTTATTTATTTTCC
1 -TTTTTTTC-TTTTATTTATTTT-A
27365 TTTTTTTCTTTTGATTTATTTTA
1 TTTTTTTCTTTT-ATTTATTTTA
*
27388 TTTTTTACTTATTA-TTATTATTA
1 TTTTTTTCTT-TTATTTATT-TTA
27411 TTTTT
1 TTTTT
27416 CATTTTCCTT
Statistics
Matches: 124, Mismatches: 18, Indels: 44
0.67 0.10 0.24
Matches are distributed among these distances:
19 6 0.05
20 5 0.04
21 17 0.14
22 25 0.20
23 32 0.26
24 25 0.20
25 8 0.06
26 6 0.05
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (22 bp):
TTTTTTTCTTTTATTTATTTTA
Found at i:32844 original size:84 final size:80
Alignment explanation
Indices: 32591--33593 Score: 929
Period size: 84 Copynumber: 12.2 Consensus size: 80
32581 ATTTGTCAAT
* *
32591 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATATCTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
32656 AGAAGGGTTATCTGC
66 AGAAGGGTTATCTGC
* * * * * *** * * *
32671 CAAAGACCTCCAAGTTTGATTACACTCAGCTTCGGGGGCACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
32736 TAGAAGGGTTATATGTCAC
65 GAGAAGGGTTATCTG---C
* * * * * *
32755 CAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGTAGTACAACTTAAGTCT
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* *
32820 ATAAGGGTTGTCTGCC
66 AGAAGGGTTATCTG-C
* * * *
32836 AACAAAAGACATTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAACATAGCTTAA
1 --C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAA
* *
32900 GTCGAGAAGGGCTATATGC
62 GTCGAGAAGGGTTATCTGC
** * * * * * *
32919 CAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACACCATTTGCAGCATAACTTAAGTC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
32984 GAGAAGGGTTATCTGC
65 GAGAAGGGTTATCTGC
* * *
33000 CAATAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGACACATCATTTGCAGCATAGCTTA
1 C----AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTA
* *
33064 AGTCGAGAATGGCTATCTGC
61 AGTCGAGAAGGGTTATCTGC
* * * * * * * * *
33084 CAAAGACCTCCGAGTTCGATTACACTCAGCTTCGAGAGCACATTATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTTGCAGCATAACTTAAGTC
*
33149 TAGAAGGGTTATCTATGAC
65 GAGAAGGGTTATC--TG-C
* * * * *
33168 CAAAAGACCTTTGAGTTCGACTACGTTCAGCTCTAAGGCACATCATTTACAGCATAGCTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
33233 GAGAAGGGTTATCTGC
65 GAGAAGGGTTATCTGC
** * * * *
33249 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
33314 AAGAAGGGTTATATGCCAAC
65 GAGAAGGGTTATCTG----C
* * *
33334 CAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * *
33399 AGAATGGCTATCTTC
66 AGAAGGGTTATCTGC
* * * * * * * * *
33414 CAAAGACC-CCTGAGTTCGATTACACTCAGCTTCGAGGGCACATAATTTACAGCATAACTCAAGG
1 CAAAGACCTTC-GAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
33478 CTAGAAGGGTTATCTGTCAC
64 CGAGAAGGGTTATCTG---C
* * *
33498 CAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTGG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
*
33563 AGAAGGGCTATCTGC
66 AGAAGGGTTATCTGC
33578 C--A-ACCTTCGAGTTCGA
1 CAAAGACCTTCGAGTTCGA
33594 TTATATTCAA
Statistics
Matches: 734, Mismatches: 157, Indels: 67
0.77 0.16 0.07
Matches are distributed among these distances:
77 13 0.02
78 1 0.00
80 124 0.17
81 201 0.27
82 3 0.00
83 84 0.11
84 232 0.32
85 76 0.10
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (80 bp):
CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
AGAAGGGTTATCTGC
Found at i:33002 original size:165 final size:164
Alignment explanation
Indices: 32591--33580 Score: 1139
Period size: 165 Copynumber: 6.0 Consensus size: 164
32581 ATTTGTCAAT
** * * * * *
32591 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTGCAGCATATCTTAAGTC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
* *** * * * **
32655 GAGAAGGGTTATCTG-C--C-AAAGACCTCCAAGTTTGATTACACTCAGCTTCGGGGGCACATCA
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC-TC-AAGGCACATCA
* * * * * * *
32716 TTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCAC
129 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---C
** * * * * * * * * *
32755 CAAAGACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCATATCATTTGTAGTACAACTTAAGTC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
* * *
32819 TATAAGGGTTGTCTGCCAACAAAAGACATTTGAGTTCGACTACGCTCAGCTCAACGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCAT
* *
32884 TTGCAACATAGCTTAAGTCGAGAAGGGCTATATGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
* *
32919 CAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACACCATTTGCAGCATAACTTAAGTC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
* * *
32984 GAGAAGGGTTATCTGCCAATAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCAT
*
33049 TTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
* * * * * *
33084 CAAAGACCTCCGAGTTCGATTACACTCAGCTTCGAGAGCACATTATTTACAGCATAACTCAAGGC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
*** * *
33149 TAGAAGGGTTATCTATGACCAAAAGACCTTTGAGTTCGACTACGTTCAGCTCTAAGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTC-AAGGCACATCAT
* *
33214 TTACAGCATAGCTTAAGTCGAGAAGGGTTATCTGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
33249 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
* * * *
33314 AAGAAGGGTTATATGCCAACCAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCAT
* * * *
33379 TTGCAGCACAACTTAAGTCGAGAATGGCTATCTTC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
* * * * *
33414 CAAAGACCCCTGAGTTCGATTACACTCAGCTTCGAGGGCACATAATTTACAGCATAACTCAAGGC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
* * * * *
33479 TAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCAT
* *
33543 TTGCAGCATAACTTAAGTGGAGAAGGGCTATCTGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
33578 CAA
1 CAA
33581 CCTTCGAGTT
Statistics
Matches: 716, Mismatches: 102, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
164 173 0.24
165 478 0.67
166 3 0.00
167 40 0.06
168 22 0.03
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (164 bp):
CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCACATCATT
TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
Found at i:34942 original size:6 final size:6
Alignment explanation
Indices: 34926--34986 Score: 61
Period size: 6 Copynumber: 9.5 Consensus size: 6
34916 AAATTTAACA
*
34926 ATTTATT ATTTTT ATTTTT ATTTCT ATTTGATT -TTTTT ATTCTTTT ATTTTT
1 ATTT-TT ATTTTT ATTTTT ATTTTT ATTT--TT ATTTTT A-T-TTTT ATTTTT
34978 ATTTTT ATT
1 ATTTTT ATT
34987 CTTAATTTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
5 2 0.04
6 30 0.64
7 9 0.19
8 6 0.13
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:34975 original size:16 final size:16
Alignment explanation
Indices: 34935--35071 Score: 59
Period size: 16 Copynumber: 8.2 Consensus size: 16
34925 AATTTATTAT
*
34935 TTTTATTTTTAT-TTC
1 TTTTATTTTTTTATTC
34950 TATTTGATTTTTTTATTC
1 T-TTT-ATTTTTTTATTC
* *
34968 TTTTATTTTTATTTTTA
1 TTTTATTTTT-TTATTC
**
34985 TTCTTAATTTCACTTA-TC
1 TT-TT-ATTT-TTTTATTC
*
35003 -TTTA-TTTTTTATTA
1 TTTTATTTTTTTATTC
**
35017 TTGTTATTTTAATATTC
1 TT-TTATTTTTTTATTC
*
35034 TTTTATTTATTTATT-
1 TTTTATTTTTTTATTC
*
35049 TATTTATTTAATTTTTTTC
1 T-TTTATTT--TTTTATTC
35068 TTTT
1 TTTT
35072 TGACCTATTT
Statistics
Matches: 89, Mismatches: 18, Indels: 27
0.66 0.13 0.20
Matches are distributed among these distances:
13 3 0.03
14 3 0.03
15 4 0.04
16 31 0.35
17 26 0.29
18 15 0.17
19 7 0.08
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTTATTTTTTTATTC
Found at i:35105 original size:16 final size:16
Alignment explanation
Indices: 35039--35105 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
35029 TATTCTTTTA
*
35039 TTTATTTATTTATT-TA
1 TTTATTTATTT-TTCTT
*
35055 TTTAATT-TTTTTCTT
1 TTTATTTATTTTTCTT
**
35070 TTTGACCTATTTTTCTT
1 TTT-ATTTATTTTTCTT
35087 TTTATTTATTTTTCTT
1 TTTATTTATTTTTCTT
35103 TTT
1 TTT
35106 TTTCTTTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.05
15 7 0.17
16 22 0.52
17 11 0.26
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (16 bp):
TTTATTTATTTTTCTT
Found at i:35122 original size:41 final size:43
Alignment explanation
Indices: 35034--35137 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 43
35024 TTTAATATTC
35034 TTTTATTTATTTATTTATTTATTTAATTTTTTTCTTTTTGACCTA
1 TTTTATTT-TTTATTTATTTATTT-ATTTTTTTCTTTTTGACCTA
**
35079 TTTT-TCTTTTTATTTATTT-TTCT-TTTTTTTC-TTTTGATTTA
1 TTTTAT-TTTTTATTTATTTATT-TATTTTTTTCTTTTTGACCTA
*
35120 TTTTATTTTTTACTTATT
1 TTTTATTTTTTATTTATT
35138 ATTATTATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
41 23 0.43
42 9 0.17
43 2 0.04
44 13 0.25
45 6 0.11
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (43 bp):
TTTTATTTTTTATTTATTTATTTATTTTTTTCTTTTTGACCTA
Found at i:35605 original size:23 final size:23
Alignment explanation
Indices: 35575--35629 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
35565 GCCAACCAAA
* *
35575 CATGAAAATATAGATTCTATTCT
1 CATGAAAATATAAATTATATTCT
35598 CATGAAAATATAAATTATATTCT
1 CATGAAAATATAAATTATATTCT
*
35621 CATAAAAAT
1 CATGAAAAT
35630 CTCATTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.36
Consensus pattern (23 bp):
CATGAAAATATAAATTATATTCT
Found at i:37257 original size:17 final size:17
Alignment explanation
Indices: 37235--37269 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
37225 TGCTAATCTG
37235 TGATTGGAATGGATTGC
1 TGATTGGAATGGATTGC
37252 TGATTGGAATGGATTGC
1 TGATTGGAATGGATTGC
37269 T
1 T
37270 TACTGTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.34, T:0.37
Consensus pattern (17 bp):
TGATTGGAATGGATTGC
Found at i:47542 original size:2 final size:2
Alignment explanation
Indices: 47535--47559 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47525 CCAACACCAA
47535 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 A
47560 ATTCGATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50523 original size:15 final size:16
Alignment explanation
Indices: 50485--50525 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
50475 ACAGAGCCTC
*
50485 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
50501 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
50517 T-AATCATTC
1 TGAATCATTC
50526 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Done.