Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4824.1
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: 43311
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1362 original size:83 final size:83
Alignment explanation
Indices: 1223--1389 Score: 298
Period size: 83 Copynumber: 2.0 Consensus size: 83
1213 CCTAAATTCG
1223 ATCGGGAACATAATACGACTCATCACATCATCCAAATCGAGCTCGTATCAGTTGGTATCAGAGCT
1 ATCGGGAACATAATACGACTCATCACATCATCCAAATCGAGCTCGTATCAGTTGGTATCAGAGCT
*
1288 GGTTAATTTAGGTACGTA
66 GGTTAAATTAGGTACGTA
* * *
1306 ATCGGGAATATAATACGACTCGTCACATCATCCGAATCGAGCTCGTATCAGTTGGTATCAGAGCT
1 ATCGGGAACATAATACGACTCATCACATCATCCAAATCGAGCTCGTATCAGTTGGTATCAGAGCT
1371 GGTTAAATTAGGTACGTA
66 GGTTAAATTAGGTACGTA
1389 A
1 A
1390 ATTGTAGATT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (83 bp):
ATCGGGAACATAATACGACTCATCACATCATCCAAATCGAGCTCGTATCAGTTGGTATCAGAGCT
GGTTAAATTAGGTACGTA
Found at i:1420 original size:14 final size:13
Alignment explanation
Indices: 1401--1461 Score: 95
Period size: 13 Copynumber: 4.6 Consensus size: 13
1391 TTGTAGATTC
1401 AAAAAAAAATCGA
1 AAAAAAAAATCGA
1414 AAAAAAAAATCGA
1 AAAAAAAAATCGA
*
1427 AAAAAAAAATTGAA
1 AAAAAAAAATCG-A
*
1441 AAAAAAAAATTGA
1 AAAAAAAAATCGA
1454 AAAAAAAA
1 AAAAAAAA
1462 TTGCATACGG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
13 33 0.72
14 13 0.28
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAAAAAAATCGA
Found at i:1436 original size:26 final size:27
Alignment explanation
Indices: 1401--1461 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
1391 TTGTAGATTC
1401 AAAAAAAAATCG-AAAAAAAAAATCGA
1 AAAAAAAAATCGAAAAAAAAAAATCGA
* *
1427 AAAAAAAAATTGAAAAAAAAAAATTGA
1 AAAAAAAAATCGAAAAAAAAAAATCGA
1454 AAAAAAAA
1 AAAAAAAA
1462 TTGCATACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (27 bp):
AAAAAAAAATCGAAAAAAAAAAATCGA
Found at i:2851 original size:30 final size:30
Alignment explanation
Indices: 2815--2875 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2805 TACGTTCCGT
*
2815 TCTTTCCCTAATACTTCTTCTATGACTAAG
1 TCTTTCCCTAATACTTCTTCTACGACTAAG
2845 TCTTTCCCTAATACTTCTTCTACGACTAAG
1 TCTTTCCCTAATACTTCTTCTACGACTAAG
2875 T
1 T
2876 GGGGGCAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.43
Consensus pattern (30 bp):
TCTTTCCCTAATACTTCTTCTACGACTAAG
Found at i:4349 original size:30 final size:30
Alignment explanation
Indices: 4313--4374 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
4303 ATCGACCTTA
*
4313 AGAGCGGTTATCACCAAATACGGATGCGTG
1 AGAGCGGTTATCACCAAATACGGATGCATG
4343 AGAGCGGTTATCACCAAATACGGATGCATG
1 AGAGCGGTTATCACCAAATACGGATGCATG
4373 AG
1 AG
4375 GGAGATGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (30 bp):
AGAGCGGTTATCACCAAATACGGATGCATG
Found at i:8534 original size:42 final size:42
Alignment explanation
Indices: 8487--8569 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
8477 TTTCCAAGGC
*
8487 ACTTATTCGGCCAAGAAGTAGCTGCTAACTAATTCTATGTTA
1 ACTTATTCAGCCAAGAAGTAGCTGCTAACTAATTCTATGTTA
*
8529 ACTTATTCAGCGAAGAAGTAGCTGCTAACTAATTCTATGTT
1 ACTTATTCAGCCAAGAAGTAGCTGCTAACTAATTCTATGTT
8570 GACCATAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (42 bp):
ACTTATTCAGCCAAGAAGTAGCTGCTAACTAATTCTATGTTA
Found at i:9283 original size:56 final size:56
Alignment explanation
Indices: 9197--9307 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
9187 TTAAAATGGT
**
9197 GATTCCTGGTTTTCAAGGAAGGTCGGATCCCGAGGCCTATCTTGAATGGGAGAAGC
1 GATTCCTACTTTTCAAGGAAGGTCGGATCCCGAGGCCTATCTTGAATGGGAGAAGC
9253 GATTCCTACTTTTCAAGGAAGGTCGGATCCCGAGGCCTATCTTGAATGGGAGAAG
1 GATTCCTACTTTTCAAGGAAGGTCGGATCCCGAGGCCTATCTTGAATGGGAGAAG
9308 AAGGTGGAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (56 bp):
GATTCCTACTTTTCAAGGAAGGTCGGATCCCGAGGCCTATCTTGAATGGGAGAAGC
Found at i:9629 original size:24 final size:24
Alignment explanation
Indices: 9602--9648 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
9592 GATCCGCGCC
9602 GATGTGGAGGAAGATCGAGAAGCT
1 GATGTGGAGGAAGATCGAGAAGCT
*
9626 GATGTGTAGGAAGATCGAGAAGC
1 GATGTGGAGGAAGATCGAGAAGC
9649 CACCATGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.40, T:0.17
Consensus pattern (24 bp):
GATGTGGAGGAAGATCGAGAAGCT
Found at i:10566 original size:231 final size:231
Alignment explanation
Indices: 10163--10611 Score: 889
Period size: 231 Copynumber: 1.9 Consensus size: 231
10153 CGAGAATGGA
10163 GAAATCTTGGTTGTGAAAAGAAGTCTCACTTTGCAAGGTGCCGAAAATGATCAACAACGCGAAAA
1 GAAATCTTGGTTGTGAAAAGAAGTCTCACTTTGCAAGGTGCCGAAAATGATCAACAACGCGAAAA
10228 CATCTTCCATACGCGATGTCAAGTGCAAGGTAAGATTTGTTGCATGATAATCGATGGGGGAAGTT
66 CATCTTCCATACGCGATGTCAAGTGCAAGGTAAGATTTGTTGCATGATAATCGATGGGGGAAGTT
10293 GTACAAATGTGGCTAGTACGTTGATGGTGGAGAAACTCGGATTGGCCACCACCAAACATCCCCAT
131 GTACAAATGTGGCTAGTACGTTGATGGTGGAGAAACTCGGATTGGCCACCACCAAACATCCCCAT
10358 CCGTATAAACTCCAATGGCTTAAGAAACAACTTCAT
196 CCGTATAAACTCCAATGGCTTAAGAAACAACTTCAT
*
10394 GAAATCTTGGTTGTGAAAAGAAGTCTCACTTTGCAAGGTGCCGAAAATGATCAACAATGCGAAAA
1 GAAATCTTGGTTGTGAAAAGAAGTCTCACTTTGCAAGGTGCCGAAAATGATCAACAACGCGAAAA
10459 CATCTTCCATACGCGATGTCAAGTGCAAGGTAAGATTTGTTGCATGATAATCGATGGGGGAAGTT
66 CATCTTCCATACGCGATGTCAAGTGCAAGGTAAGATTTGTTGCATGATAATCGATGGGGGAAGTT
10524 GTACAAATGTGGCTAGTACGTTGATGGTGGAGAAACTCGGATTGGCCACCACCAAACATCCCCAT
131 GTACAAATGTGGCTAGTACGTTGATGGTGGAGAAACTCGGATTGGCCACCACCAAACATCCCCAT
10589 CCGTATAAACTCCAATGGCTTAA
196 CCGTATAAACTCCAATGGCTTAA
10612 CGATGGTGGA
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 217 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (231 bp):
GAAATCTTGGTTGTGAAAAGAAGTCTCACTTTGCAAGGTGCCGAAAATGATCAACAACGCGAAAA
CATCTTCCATACGCGATGTCAAGTGCAAGGTAAGATTTGTTGCATGATAATCGATGGGGGAAGTT
GTACAAATGTGGCTAGTACGTTGATGGTGGAGAAACTCGGATTGGCCACCACCAAACATCCCCAT
CCGTATAAACTCCAATGGCTTAAGAAACAACTTCAT
Found at i:11392 original size:80 final size:80
Alignment explanation
Indices: 11259--11419 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
11249 CCGCAATTCC
11259 AAACCGACCTACTTACCGGAGCAATCCTGAAGAGACGAAAGAATTACAAAAGCAAGTAAATGAAC
1 AAACCGACCTACTTACCGGAGCAATCCTGAAGAGACGAAAGAATTACAAAAGCAAGTAAATGAAC
11324 TCCTTGAAAAGGGCT
66 TCCTTGAAAAGGGCT
* *
11339 AAACCGACCTGCTTACTGGAGCAATCCTGAAGAGACGAAAGAATTACAAAAGCAAGTAAATGAAC
1 AAACCGACCTACTTACCGGAGCAATCCTGAAGAGACGAAAGAATTACAAAAGCAAGTAAATGAAC
11404 TCCTTGAAAAGGGCT
66 TCCTTGAAAAGGGCT
11419 A
1 A
11420 TGTGCGTGAA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (80 bp):
AAACCGACCTACTTACCGGAGCAATCCTGAAGAGACGAAAGAATTACAAAAGCAAGTAAATGAAC
TCCTTGAAAAGGGCT
Found at i:11686 original size:62 final size:62
Alignment explanation
Indices: 11589--11712 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
11579 GAGTTTATTT
*
11589 TCAAAAATCGCCCTTAAGAGTGGTTATCACCAAATACGGAGGCGTGAGGGAGATGAGTGGAA
1 TCAAAAATCGACCTTAAGAGTGGTTATCACCAAATACGGAGGCGTGAGGGAGATGAGTGGAA
* *
11651 TCAAAAATTGACCTTAAGAGTGGTTATCACCAAATACGGATGCGTGAGGGAGATGAGTGGAA
1 TCAAAAATCGACCTTAAGAGTGGTTATCACCAAATACGGAGGCGTGAGGGAGATGAGTGGAA
11713 GACTGCGTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.21
Consensus pattern (62 bp):
TCAAAAATCGACCTTAAGAGTGGTTATCACCAAATACGGAGGCGTGAGGGAGATGAGTGGAA
Found at i:20113 original size:30 final size:31
Alignment explanation
Indices: 20087--20153 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
20077 CAAGCTCGTT
20087 TCCAGCTCCACGAGCTCTATCC-AGCTCAAA
1 TCCAGCTCCACGAGCTCTATCCAAGCTCAAA
* ** *
20117 TCTAGCTCCACGAGCTCCGT-CTAGCTCAAA
1 TCCAGCTCCACGAGCTCTATCCAAGCTCAAA
20147 TCCAGCT
1 TCCAGCT
20154 TATTCGAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (31 bp):
TCCAGCTCCACGAGCTCTATCCAAGCTCAAA
Found at i:21716 original size:27 final size:27
Alignment explanation
Indices: 21687--22026 Score: 384
Period size: 27 Copynumber: 12.7 Consensus size: 27
21677 TAATAAAAAG
* * *
21687 AAATTACCGAAATACCCTCGATTTATG
1 AAATTATCGAAATACCCTCGATTTGTA
*
21714 AAATTATCGAAACACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
* *
21741 AAATTATCGAAATACCCCCGATTTATA
1 AAATTATCGAAATACCCTCGATTTGTA
* * * *
21768 AAATTATCAAAAAACCCTC-AATTGTG
1 AAATTATCGAAATACCCTCGATTTGTA
* * *
21794 AAATTA-CTAAAATACCCTCAATTTATA
1 AAATTATC-GAAATACCCTCGATTTGTA
* *
21821 AAATTACCAAAATACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
*
21848 AAATTA-CTGAAATACCCTCGA-TTGTG
1 AAATTATC-GAAATACCCTCGATTTGTA
*
21874 AAATTATTGAAATACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
*
21901 AAATTATCGAAATACCCTCAATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
*
21928 AAATTATTGAAATACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
* *
21955 AAATTACCGAAACACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
* * * * *
21982 AAATTATTGAAATATCCTTG-TAGTATA
1 AAATTATCGAAATACCCTCGAT-TTGTA
22009 AAATTATCGAAATACCCT
1 AAATTATCGAAATACCCT
22027 TGTAGTGTAA
Statistics
Matches: 267, Mismatches: 39, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
25 1 0.00
26 45 0.17
27 220 0.82
28 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTATCGAAATACCCTCGATTTGTA
Found at i:21823 original size:80 final size:80
Alignment explanation
Indices: 21687--22026 Score: 380
Period size: 80 Copynumber: 4.2 Consensus size: 80
21677 TAATAAAAAG
* * * *
21687 AAATTACCGAAATACCCTCGATTTATGAAATTA-TCGAAACACCCTCGATTTGTAAAATTATCGA
1 AAATTATCGAAATACCCTC-AATTGTGAAATTACT-GAAATACCCTCGATTTGTAAAATTATCGA
* *
21751 AATACCCCCGATTTATA
64 AATACCCTCGATTTGTA
* * * * * * *
21768 AAATTATCAAAAAACCCTCAATTGTGAAATTACTAAAATACCCTCAATTTATAAAATTACCAAAA
1 AAATTATCGAAATACCCTCAATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTATCGAAA
21833 TACCCTCGATTTGTA
66 TACCCTCGATTTGTA
* *
21848 AAATTA-CTGAAATACCCTCGATTGTGAAATTATTGAAATACCCTCGATTTGTAAAATTATCGAA
1 AAATTATC-GAAATACCCTCAATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTATCGAA
*
21912 ATACCCTCAATTTGTA
65 ATACCCTCGATTTGTA
* * * * * *
21928 AAATTATTGAAATACCCTCGATTTGTAAAATTACCGAAACACCCTCGATTTGTAAAATTATTGAA
1 AAATTATCGAAATACCCTC-AATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTATCGAA
* * * *
21993 ATATCCTTG-TAGTATA
65 ATACCCTCGAT-TTGTA
22009 AAATTATCGAAATACCCT
1 AAATTATCGAAATACCCT
22027 TGTAGTGTAA
Statistics
Matches: 217, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
79 1 0.00
80 135 0.62
81 81 0.37
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (80 bp):
AAATTATCGAAATACCCTCAATTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTATCGAAA
TACCCTCGATTTGTA
Found at i:21905 original size:107 final size:107
Alignment explanation
Indices: 21687--21995 Score: 399
Period size: 107 Copynumber: 2.9 Consensus size: 107
21677 TAATAAAAAG
* * * *
21687 AAATTACCGAAATACCCTCGATTTATGAAATTATCGAAACACCCTCGATTTGTAAAATTA-TCGA
1 AAATTACTGAAATACCCTCAATTTATAAAATTATCGAAATACCCTCGATTTGTAAAATTACT-GA
* * ** * *
21751 AATACCCCCGATTTATAAAATTATCAAAAAACCCTCAATTGTG
65 AATACCCTCGATTTGTAAAATTATTGAAATACCCTCAATTGTA
* * *
21794 AAATTACTAAAATACCCTCAATTTATAAAATTACCAAAATACCCTCGATTTGTAAAATTACTGAA
1 AAATTACTGAAATACCCTCAATTTATAAAATTATCGAAATACCCTCGATTTGTAAAATTACTGAA
* *
21859 ATACCCTCGA-TTGTGAAATTATTGAAATACCCTCGATTTGTA
66 ATACCCTCGATTTGTAAAATTATTGAAATACCCTC-AATTGTA
* * *
21901 AAATTA-TCGAAATACCCTCAATTTGTAAAATTATTGAAATACCCTCGATTTGTAAAATTACCGA
1 AAATTACT-GAAATACCCTCAATTTATAAAATTATCGAAATACCCTCGATTTGTAAAATTACTGA
*
21965 AACACCCTCGATTTGTAAAATTATTGAAATA
65 AATACCCTCGATTTGTAAAATTATTGAAATA
21996 TCCTTGTAGT
Statistics
Matches: 175, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
106 20 0.11
107 136 0.78
108 19 0.11
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (107 bp):
AAATTACTGAAATACCCTCAATTTATAAAATTATCGAAATACCCTCGATTTGTAAAATTACTGAA
ATACCCTCGATTTGTAAAATTATTGAAATACCCTCAATTGTA
Found at i:22050 original size:27 final size:27
Alignment explanation
Indices: 21844--22070 Score: 137
Period size: 27 Copynumber: 8.5 Consensus size: 27
21834 ACCCTCGATT
* *
21844 TGTAAAATTACTGAAATACCCTCG-AT
1 TGTAAAATTACTGAAATACCCTTGTAG
* * * *
21870 TGTGAAATTATTGAAATACCCTCG-ATT
1 TGTAAAATTACTGAAATACCCTTGTA-G
** *
21897 TGTAAAATTA-TCGAAATACCC-TCAATT
1 TGTAAAATTACT-GAAATACCCTTGTA-G
* * *
21924 TGTAAAATTATTGAAATACCCTCG-ATT
1 TGTAAAATTACTGAAATACCCTTGTA-G
* * * *
21951 TGTAAAATTACCGAAACACCCTCG-ATT
1 TGTAAAATTACTGAAATACCCTTGTA-G
* *
21978 TGTAAAATTATTGAAATATCCTTGTAG
1 TGTAAAATTACTGAAATACCCTTGTAG
*
22005 TATAAAATTA-TCGAAATACCCTTGTAG
1 TGTAAAATTACT-GAAATACCCTTGTAG
* * *
22032 TGTAAAATGACTGACATACCCCTGTAG
1 TGTAAAATTACTGAAATACCCTTGTAG
*
22059 GGTAAAA-TACTG
1 TGTAAAATTACTG
22071 TTTTGCCCTT
Statistics
Matches: 169, Mismatches: 24, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
26 29 0.17
27 137 0.81
28 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (27 bp):
TGTAAAATTACTGAAATACCCTTGTAG
Found at i:23528 original size:54 final size:54
Alignment explanation
Indices: 23468--23578 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 54
23458 CAGCCTACTA
* *
23468 GCATTAATCACGTTTCTTGCTCCTAGGCTATTCATGCACCAGCAGCTCTTTAAT
1 GCATTAATCACATTTCATGCTCCTAGGCTATTCATGCACCAGCAGCTCTTTAAT
* *
23522 GCATTAATCACATTTCATGCTCCTAGGCTGTTCATGCACTAGCAGCTCTTTAAT
1 GCATTAATCACATTTCATGCTCCTAGGCTATTCATGCACCAGCAGCTCTTTAAT
23576 GCA
1 GCA
23579 CCAGCAGCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.34
Consensus pattern (54 bp):
GCATTAATCACATTTCATGCTCCTAGGCTATTCATGCACCAGCAGCTCTTTAAT
Found at i:23579 original size:19 final size:20
Alignment explanation
Indices: 23555--23593 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
23545 TAGGCTGTTC
*
23555 ATGCACTAGCAGCT-CTTTA
1 ATGCACCAGCAGCTCCTTTA
23574 ATGCACCAGCAGCTCCTTTA
1 ATGCACCAGCAGCTCCTTTA
23594 TTACTGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (20 bp):
ATGCACCAGCAGCTCCTTTA
Found at i:27331 original size:20 final size:20
Alignment explanation
Indices: 27272--27332 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
27262 CCAATAAAAT
*
27272 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
* *
27292 AAATTGAGCTCGATTAAGCTG
1 AAA-TGAGCTCAATTGAGCTG
27313 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
27333 GTCGGAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:28187 original size:200 final size:200
Alignment explanation
Indices: 27844--28244 Score: 784
Period size: 200 Copynumber: 2.0 Consensus size: 200
27834 GTAAAAAGGC
27844 AAACTTAAAACATCATTCTTACAATCAAATGGACAAAACTCCTTCCATATCCATAACTCATCAAA
1 AAACTTAAAACATCATTCTTACAATCAAATGGACAAAACTCCTTCCATATCCATAACTCATCAAA
27909 TGGTCGAGACAAAGACAAATATGTTTTTAAGCATTCAAACCTTTCAATTTGCTTCCACAAGTCAT
66 TGGTCGAGACAAAGACAAATATGTTTTTAAGCATTCAAACCTTTCAATTTGCTTCCACAAGTCAT
27974 TGTTCAAGTAAATGGAATGCGAGTAATGGAACAAGAAATTTAAATCTTCATCACAAACACACAAA
131 TGTTCAAGTAAATGGAATGCGAGTAATGGAACAAGAAATTTAAATCTTCATCACAAACACACAAA
28039 TGAAA
196 TGAAA
*
28044 AAACTTAAAACATCATTCTTACAATCATATGGACAAAACTCCTTCCATATCCATAACTCATCAAA
1 AAACTTAAAACATCATTCTTACAATCAAATGGACAAAACTCCTTCCATATCCATAACTCATCAAA
*
28109 TTGTCGAGACAAAGACAAATATGTTTTTAAGCATTCAAACCTTTCAATTTGCTTCCACAAGTCAT
66 TGGTCGAGACAAAGACAAATATGTTTTTAAGCATTCAAACCTTTCAATTTGCTTCCACAAGTCAT
28174 TGTTCAAGTAAATGGAATGCGAGTAATGGAACAAGAAATTTAAATCTTCATCACAAACACACAAA
131 TGTTCAAGTAAATGGAATGCGAGTAATGGAACAAGAAATTTAAATCTTCATCACAAACACACAAA
28239 TGAAA
196 TGAAA
28244 A
1 A
28245 GTTTCATATG
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 199 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (200 bp):
AAACTTAAAACATCATTCTTACAATCAAATGGACAAAACTCCTTCCATATCCATAACTCATCAAA
TGGTCGAGACAAAGACAAATATGTTTTTAAGCATTCAAACCTTTCAATTTGCTTCCACAAGTCAT
TGTTCAAGTAAATGGAATGCGAGTAATGGAACAAGAAATTTAAATCTTCATCACAAACACACAAA
TGAAA
Found at i:29625 original size:18 final size:18
Alignment explanation
Indices: 29604--29638 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29594 TTTTTCTTTT
29604 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
29622 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
29639 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:30566 original size:15 final size:15
Alignment explanation
Indices: 30533--30571 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
30523 TTTAACTTGA
30533 TTTTTTTTGCTCACCT
1 TTTTTTTTGCTCA-CT
30549 TTTTTTTTGCTCGA-T
1 TTTTTTTTGCTC-ACT
30564 TTTTTTTT
1 TTTTTTTT
30572 CATTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 12 0.55
17 1 0.05
ACGTcount: A:0.05, C:0.15, G:0.08, T:0.72
Consensus pattern (15 bp):
TTTTTTTTGCTCACT
Found at i:30576 original size:11 final size:11
Alignment explanation
Indices: 30562--30631 Score: 59
Period size: 11 Copynumber: 5.8 Consensus size: 11
30552 TTTTTGCTCG
30562 ATTTTTTTTTC
1 ATTTTTTTTTC
**
30573 ATTTTTTTTGA
1 ATTTTTTTTTC
30584 ATTTTTTTTTTC
1 A-TTTTTTTTTC
30596 AATCAATTTTTTTTC
1 -AT---TTTTTTTTC
*
30611 GATTTTTTTTTT
1 -ATTTTTTTTTC
30623 ATTTTTTTT
1 ATTTTTTTT
30632 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
11 19 0.40
12 17 0.35
13 1 0.02
15 11 0.23
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTTC
Found at i:32148 original size:20 final size:20
Alignment explanation
Indices: 32125--32171 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
32115 GGGTTAAGAT
*
32125 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
32145 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
32165 TGAGCTG
1 TGAGCTG
32172 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:33564 original size:20 final size:20
Alignment explanation
Indices: 33541--33594 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33531 AGTTTTTCCC
*
33541 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33561 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33581 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33595 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33576 original size:30 final size:30
Alignment explanation
Indices: 33541--33614 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33531 AGTTTTTCCC
33541 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33571 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33601 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33615 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33604 original size:20 final size:20
Alignment explanation
Indices: 33541--33605 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33531 AGTTTTTCCC
* * * *
33541 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33561 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33580 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33601 AGCTC
1 AGCTC
33606 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:35619 original size:48 final size:48
Alignment explanation
Indices: 35567--35672 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
35557 TTGTCTTTTC
*
35567 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
35615 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
35663 TTTCTTTTTC
1 TTTCTTTTTC
35673 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:35715 original size:18 final size:18
Alignment explanation
Indices: 35648--35715 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
35638 TTTTCACATC
* *
35648 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTCACTCT
* **
35666 CTTTTTCCATGACACTCGTTT
1 CTTTTTCAATCTCACTC---T
35687 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCACTCT
35706 CTTTTTCAAT
1 CTTTTTCAAT
35716 TTCTTGTTCC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 18 0.47
19 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.18, C:0.28, G:0.03, T:0.51
Consensus pattern (18 bp):
CTTTTTCAATCTCACTCT
Found at i:37445 original size:9 final size:9
Alignment explanation
Indices: 37430--37464 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
37420 TGAATTTCGT
37430 CTTTTTTGA
1 CTTTTTTGA
*
37439 TTTTTTTGA
1 CTTTTTTGA
37448 CTTTTTTGA
1 CTTTTTTGA
37457 CTATTTTT
1 CT-TTTTT
37465 TTGCGGGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (9 bp):
CTTTTTTGA
Found at i:39287 original size:29 final size:29
Alignment explanation
Indices: 39254--39313 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
39244 ATAACCAAAC
* *
39254 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
39283 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
39312 CT
1 CT
39314 TTGAATCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:39306 original size:15 final size:15
Alignment explanation
Indices: 39260--39307 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39250 AAACCTACAA
*
39260 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
39275 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
39289 AAACTTCATATCCAT
1 AAACTTCATATCCAT
39304 AAAC
1 AAAC
39308 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:39553 original size:19 final size:19
Alignment explanation
Indices: 39529--39574 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
39519 AGTAAGTTTA
*
39529 AAAAAAACGAAAAAAATTC
1 AAAAAAACAAAAAAAATTC
39548 AAAAAAACAAAAAAAATTC
1 AAAAAAACAAAAAAAATTC
39567 AAACAAAA
1 AAA-AAAA
39575 ATTCTGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.78, C:0.11, G:0.02, T:0.09
Consensus pattern (19 bp):
AAAAAAACAAAAAAAATTC
Found at i:39587 original size:12 final size:11
Alignment explanation
Indices: 39538--39578 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
39528 AAAAAAAACG
39538 AAAAAAATTC-
1 AAAAAAATTCA
39548 AAAAAAA--CA
1 AAAAAAATTCA
39557 AAAAAAATTCA
1 AAAAAAATTCA
39568 AACAAAAATTC
1 AA-AAAAATTC
39579 TGAAAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.04
9 7 0.26
10 7 0.26
11 4 0.15
12 8 0.30
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:39598 original size:16 final size:18
Alignment explanation
Indices: 39567--39600 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
39557 AAAAAAATTC
39567 AAACAAAAATTCTGAAAA
1 AAACAAAAATTCTGAAAA
39585 AAAC-AAAA-TCTGAAAA
1 AAACAAAAATTCTGAAAA
39601 TTTGAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.68, C:0.12, G:0.06, T:0.15
Consensus pattern (18 bp):
AAACAAAAATTCTGAAAA
Found at i:40516 original size:12 final size:12
Alignment explanation
Indices: 40501--40534 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
40491 CTTGAAAGAG
*
40501 ATTGAGAAAGTC
1 ATTGAAAAAGTC
40513 ATTGAAAAAGTC
1 ATTGAAAAAGTC
40525 ATTGAAAAAG
1 ATTGAAAAAG
40535 AAAAAGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.24
Consensus pattern (12 bp):
ATTGAAAAAGTC
Found at i:40666 original size:30 final size:28
Alignment explanation
Indices: 40630--40685 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
40620 AAGCGAAAAA
* *
40630 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
40660 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
40686 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Done.