Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002259.1 Hibiscus syriacus cultivar Beakdansim tig00004592_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: 132567
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4964 original size:12 final size:13
Alignment explanation
Indices: 4937--4966 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4927 AGATTTTCTA
4937 TGAAAATAATTTT
1 TGAAAATAATTTT
4950 TGAAAATAA-TTT
1 TGAAAATAATTTT
4962 TGAAA
1 TGAAA
4967 TTACTCCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (13 bp):
TGAAAATAATTTT
Found at i:9335 original size:22 final size:21
Alignment explanation
Indices: 9293--9332 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9283 AAGACTATTT
9293 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
9314 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
9333 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:11300 original size:65 final size:64
Alignment explanation
Indices: 11223--11371 Score: 165
Period size: 65 Copynumber: 2.3 Consensus size: 64
11213 TACACTAGGG
*** * *
11223 TGTGCATCGGTGCACAAATTTGCTTCGATGTTTCAA-AAATAGCCGGGGTGCATCGATGCATGAC
1 TGTGCATCGGTGCACAAATTCAATTCGATGTTTCAATAAA-AGCCAGAGTGCATCGATGCATGAC
* * * *
11287 TTGTGCATCGGTGCACAAAATCAATTCGATGTTTTAATAAAATCCAGAGTGCATCGATGCATGGC
1 -TGTGCATCGGTGCACAAATTCAATTCGATGTTTCAATAAAAGCCAGAGTGCATCGATGCATGAC
* * *
11352 TGTGTATCAGTGCATAAATT
1 TGTGCATCGGTGCACAAATT
11372 GTATTTGAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
64 16 0.23
65 51 0.73
66 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
TGTGCATCGGTGCACAAATTCAATTCGATGTTTCAATAAAAGCCAGAGTGCATCGATGCATGAC
Found at i:12244 original size:84 final size:84
Alignment explanation
Indices: 12123--12588 Score: 600
Period size: 84 Copynumber: 5.6 Consensus size: 84
12113 AAAACACCTT
* * *
12123 CAACAAAAGACCTTCGAGTTCGATTCCACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAA
* *
12188 GGCGAGAGGGGCTATCTGC
66 GGCGAGAAGGGTTATCTGC
* * * * * *
12207 CAACAAAAGTCCTTCGAGTTTGATTACACTCAACTCAAAAGCATATCATTTACAGCATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAA
* *
12272 GGCAAGAAGGGTTATCTGT
66 GGCGAGAAGGGTTATCTGC
* * ** *
12291 CAATC--AAGACCTTCGAGTTTGATTACACT-ATGCTCAAATGTGCATCATTTGCAGTATAACTC
1 CAA-CAAAAGACCTTCGAGTTCGATTACACTCA-GCTCAAAGGCACATCATTTGCAGCATAACTC
12353 AAGGCGAGAAGGGTTATCTGC
64 AAGGCGAGAAGGGTTATCTGC
* *
12374 CAACAAAAGACCTTCGAGTTCGATCACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAA
* *
12439 GGCGAGAAGGGTTATATGT
66 GGCGAGAAGGGTTATCTGC
* * * * * *
12458 CAAC-CAAGACATTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCGTAGCTTAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAA
*
12522 GGCGAGAAGGGTTATCTTC
66 GGCGAGAAGGGTTATCTGC
*
12541 CAACAAAAGACCTTCG-GATTCAATTACACTCAGCTCAAAGGCACATCA
1 CAACAAAAGACCTTCGAG-TTCGATTACACTCAGCTCAAAGGCACATCA
12589 AAGTTATCTG
Statistics
Matches: 328, Mismatches: 47, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
82 2 0.01
83 142 0.43
84 182 0.55
85 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (84 bp):
CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAA
GGCGAGAAGGGTTATCTGC
Found at i:12405 original size:167 final size:167
Alignment explanation
Indices: 12129--12588 Score: 672
Period size: 167 Copynumber: 2.8 Consensus size: 167
12119 CCTTCAACAA
*
12129 AAGACCTTCGAGTTCGATTCCACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTCAAGGCGAG
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTCAAGGCGAG
* * * * * * *
12194 AGGGGCTATCTGCCAACAAAAGTCCTTCGAGTTTGATTACACTCAACTCAAAAGCATATCATTTA
66 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTA
* *
12259 CAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAATC
131 CAGCATAACTCAAGGCAAGAAGGGTTATATGTCAACC
* * * * *
12296 AAGACCTTCGAGTTTGATTACACT-ATGCTCAAATGTGCATCATTTGCAGTATAACTCAAGGCGA
1 AAGACCTTCGAGTTCGATTACACTCA-GCTCAAAGGCGCATCATTTGCAGCATAGCTCAAGGCGA
*
12360 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATCACACTCAGCTCAAAGGCACATCATTT
65 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
*
12425 ACAGCATAACTCAAGGCGAGAAGGGTTATATGTCAACC
130 ACAGCATAACTCAAGGCAAGAAGGGTTATATGTCAACC
* * * * *
12463 AAGACATTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCGTAGCTTAAGGCGAG
1 AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTCAAGGCGAG
* *
12528 AAGGGTTATCTTCCAACAAAAGACCTTCG-GATTCAATTACACTCAGCTCAAAGGCACATCA
66 AAGGGTTATCTGCCAACAAAAGACCTTCGAG-TTCGATTACACTCAGCTCAAAGGCACATCA
12589 AAGTTATCTG
Statistics
Matches: 260, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
166 2 0.01
167 257 0.99
168 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (167 bp):
AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTCAAGGCGAG
AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTA
CAGCATAACTCAAGGCAAGAAGGGTTATATGTCAACC
Found at i:12706 original size:87 final size:86
Alignment explanation
Indices: 12593--12893 Score: 336
Period size: 86 Copynumber: 3.5 Consensus size: 86
12583 ACATCAAAGT
* * *
12593 TATCTGTCAACAAAATACCTTCGAGTTCGATTACACTCAGCTCAAACGCATATCCAATTTACAGC
1 TATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGC
* *
12658 ATAGCACAAGGCGAGAATGGC
66 ATAGCTCAAGGCGAGAAAGGC
* ** * *
12679 TATCTGTCAACAAAAAGACCTTCGAGTTCGATTAAACTCAGCTCCGAGGCACATCAAATTTATAG
1 TATCTGTCAAC-AAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAG
* * *
12744 CATAGCTCAAGGAGAGAAGGGA
65 CATAGCTCAAGGCGAGAAAGGC
* * * * * * *
12766 TATATGTCATCAAAAGACCTTCTAGTTCGAATACACTCAGCTCAAGGGCATGTCAAATTTGCAGC
1 TATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGC
* * * *
12831 ATAACTTAAGTCGAGAAAAGC
66 ATAGCTCAAGGCGAGAAAGGC
* *
12852 TATCTGTCAACAAAA-A-CTGTCGAGTTCGATTCCATTCAGCTC
1 TATCTGTCAACAAAAGACCT-TCGAGTTCGATTACACTCAGCTC
12894 GATGATAGAT
Statistics
Matches: 176, Mismatches: 37, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
84 2 0.01
85 20 0.11
86 82 0.47
87 72 0.41
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (86 bp):
TATCTGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGC
ATAGCTCAAGGCGAGAAAGGC
Found at i:12729 original size:146 final size:143
Alignment explanation
Indices: 12469--12741 Score: 361
Period size: 146 Copynumber: 1.9 Consensus size: 143
12459 AACCAAGACA
* * * ** *
12469 TTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCGTAGCTTAAGGCGAGAAGGGT
1 TTCGAGTTCGACTACACTCAGCTCAAACGCACATCATTTACAGCATAGCACAAGGCGAGAAGGGC
*
12534 TATCTTCCAACAAAAGACCTTCGGATTCAATTACACTCAGCTCAAAGGCACATCAAAGTTATCTG
66 TATCTTCCAACAAAAGACCTTCGGATTCAATTAAACTCAGCTCAAAGGCACATCAAAGTTATCTG
12599 TCAACAAAATACC
131 TCAACAAAATACC
* * *
12612 TTCGAGTTCGATTACACTCAGCTCAAACGCATATCCAATTTACAGCATAGCACAAGGCGAGAATG
1 TTCGAGTTCGACTACACTCAGCTCAAACGCACAT-C-ATTTACAGCATAGCACAAGGCGAGAAGG
* ** *
12677 GCTATCTGT-CAACAAAAAGACCTTC-GAGTTCGATTAAACTCAGCTCCGAGGCACATCAAATTT
64 GCTATCT-TCCAAC-AAAAGACCTTCGGA-TTCAATTAAACTCAGCTCAAAGGCACATCAAAGTT
12740 AT
126 AT
12742 AGCATAGCTC
Statistics
Matches: 111, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
143 31 0.28
144 1 0.01
145 35 0.32
146 44 0.40
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (143 bp):
TTCGAGTTCGACTACACTCAGCTCAAACGCACATCATTTACAGCATAGCACAAGGCGAGAAGGGC
TATCTTCCAACAAAAGACCTTCGGATTCAATTAAACTCAGCTCAAAGGCACATCAAAGTTATCTG
TCAACAAAATACC
Found at i:12824 original size:86 final size:86
Alignment explanation
Indices: 12597--12833 Score: 287
Period size: 87 Copynumber: 2.7 Consensus size: 86
12587 CAAAGTTATC
* ** *
12597 TGTCAACAAAATACCTTCGAGTTCGATTACACTCAGCTCAAACGCATATCCAATTTACAGCATAG
1 TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAGGGCATATCAAATTTACAGCATAG
* * * *
12662 CACAAGGCGAGAATGGCTATC
66 CACAAGGAGAGAAGGGATATA
* * * *
12683 TGTCAACAAAAAGACCTTCGAGTTCGATTAAACTCAGCTC-CGAGGCACATCAAATTTATAGCAT
1 TGTCAAC-AAAAGACCTTCGAGTTCGATTACACTCAGCTCAAG-GGCATATCAAATTTACAGCAT
*
12747 AGCTCAAGGAGAGAAGGGATATA
64 AGCACAAGGAGAGAAGGGATATA
* * * * *
12770 TGTCATCAAAAGACCTTCTAGTTCGAATACACTCAGCTCAAGGGCATGTCAAATTTGCAGCATA
1 TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAGGGCATATCAAATTTACAGCATA
12834 ACTTAAGTCG
Statistics
Matches: 126, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
86 54 0.43
87 72 0.57
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (86 bp):
TGTCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAGGGCATATCAAATTTACAGCATAG
CACAAGGAGAGAAGGGATATA
Found at i:13175 original size:169 final size:169
Alignment explanation
Indices: 12865--13192 Score: 460
Period size: 169 Copynumber: 1.9 Consensus size: 169
12855 CTGTCAACAA
* * * * *
12865 AAACTGTCGAGTTCGATTCCATTCAGCTCGATGATAGATCCACCACATGGTAGCAATAAGAAACC
1 AAACTATCGAGTTCGATTCCATTCAGCTCGATGACACATCCACCACATGGTAGCAACAAAAAACC
* ** * * * * *
12930 ACTTTCTGGTTGAAGTTGAGGTCTTCAAGTCAAGAAGAAGATCTGGGGTAATCTCTCATCTCATT
66 ACTTTCTGGTTAAAGCCGAGGTCTTCAAGTCAAGAAAAAGATCTGGGGCAATCTCCCACCTCAGT
*
12995 ACAACATAACTCAAGGCAAGAAGGGTTATCAGTCAATGT
131 ACAACATAACTCAAGACAAGAAGGGTTATCAGTCAATGT
* *
13034 AAACTATCGAGTTCGATTCCATTCAGTTCGATGACACATCCACCATATGGTAGCAACAAAAAACC
1 AAACTATCGAGTTCGATTCCATTCAGCTCGATGACACATCCACCACATGGTAGCAACAAAAAACC
*
13099 ACTTTCTGGTTAAAGCCGAGGTCTTTAAGTCAAGAAAAAGATCTGGGGCAATCTCCCAGCCT-AG
66 ACTTTCTGGTTAAAGCCGAGGTCTTCAAGTCAAGAAAAAGATCTGGGGCAATCTCCCA-CCTCAG
* * *
13163 TACAATATAACTCAAGACGAGAAGTGTTAT
130 TACAACATAACTCAAGACAAGAAGGGTTAT
13193 TTGTCAACGA
Statistics
Matches: 138, Mismatches: 20, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
169 136 0.99
170 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (169 bp):
AAACTATCGAGTTCGATTCCATTCAGCTCGATGACACATCCACCACATGGTAGCAACAAAAAACC
ACTTTCTGGTTAAAGCCGAGGTCTTCAAGTCAAGAAAAAGATCTGGGGCAATCTCCCACCTCAGT
ACAACATAACTCAAGACAAGAAGGGTTATCAGTCAATGT
Found at i:13754 original size:37 final size:36
Alignment explanation
Indices: 13711--14150 Score: 394
Period size: 39 Copynumber: 11.8 Consensus size: 36
13701 AGAAAATGAT
*
13711 TTTTGAAAATGTATATATTATATAGTTTTTGAAAACA
1 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACA
13748 TTTTGAAAATATATAATATAATATATAGTTTTTGAAAACA
1 TTTTG-AAA-AT-T-ATATAATATATAGTTTTTGAAAACA
13788 TTTTGAAAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTG--AAAAT-TATATAATATATAGTTTTTGAAAACA
* *
13827 TTTTGAATATATATGTAATATATAGTTTTTGAAAACA
1 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACA
* *
13864 TTTTGAATATATATATATATAATATAATTTTTGAAAACA
1 TTTTGAAAAT-TATATA-AT-ATATAGTTTTTGAAAACA
* *
13903 TTTTAAAAACTTATATAATATATAG-TTTTGAAATCA
1 TTTTGAAAA-TTATATAATATATAGTTTTTGAAAACA
**
13939 TTTTGAAAAACTTATATAATATATAGTTTTAAAAAACA
1 TTTTG-AAAA-TTATATAATATATAGTTTTTGAAAACA
* *
13977 TTTTTTTGAAAA-CATATAATATATAG-TTTTAAAAACA
1 ---TTTTGAAAATTATATAATATATAGTTTTTGAAAACA
* *
14014 TTTTTTTTTGAAAA-CATATAATATATAG-TTTT-AAAATA
1 -----TTTTGAAAATTATATAATATATAGTTTTTGAAAACA
* * * *
14052 TTTTGAAAACTATATGATATATA-ATTTTGAAAATA
1 TTTTGAAAATTATATAATATATAGTTTTTGAAAACA
* * *
14087 TTTTTTAAAA-TATATAATACATAGTTTTT-AAAATA
1 -TTTTGAAAATTATATAATATATAGTTTTTGAAAACA
* * *
14122 TTTTTAAAAATATATATTATATAGTTTTT
1 TTTTGAAAATTATATAATATATAGTTTTT
14151 TGGAAATATT
Statistics
Matches: 358, Mismatches: 25, Indels: 42
0.84 0.06 0.10
Matches are distributed among these distances:
33 9 0.03
34 24 0.07
35 40 0.11
36 26 0.07
37 86 0.24
38 33 0.09
39 93 0.26
40 38 0.11
41 9 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATTATATAATATATAGTTTTTGAAAACA
Found at i:14151 original size:25 final size:25
Alignment explanation
Indices: 14122--14169 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
14112 TTTTAAAATA
14122 TTTTTAAAAATATATATTATATAGT
1 TTTTTAAAAATATATATTATATAGT
** * *
14147 TTTTTGGAAATATTTTTTATATA
1 TTTTTAAAAATATATATTATATA
14170 TAATATATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (25 bp):
TTTTTAAAAATATATATTATATAGT
Found at i:14158 original size:37 final size:36
Alignment explanation
Indices: 13702--14163 Score: 344
Period size: 37 Copynumber: 12.3 Consensus size: 36
13692 TTTTTCTTTA
* *
13702 GAAAATGATTTTTGAAAATGTATATATTATATAGTTTTT
1 GAAAAT-ATTTTT-AAAA-ATATATAATATATAGTTTTT
* *
13741 GAAAACATTTTGAAAATATATAATATAATATATAGTTTTT
1 GAAAATATTTT-TAAA-A-AT-ATATAATATATAGTTTTT
* *
13781 GAAAACATTTTGAAAAAATATATATAATATATAGTTTTT
1 GAAAATATTTT--TAAAA-ATATATAATATATAGTTTTT
* * * *
13820 GAAAACATTTTGAATATATATGTAATATATAGTTTTT
1 GAAAATATTTTTAA-AAATATATAATATATAGTTTTT
* * * *
13857 GAAAACATTTTGAATATATATATATATAATATAATTTTT
1 GAAAATATTTTTAA-AAATATATA-AT-ATATAGTTTTT
*
13896 GAAAACA-TTTTAAAAACTTATATAATATATAG-TTTT
1 GAAAATATTTTTAAAAA--TATATAATATATAGTTTTT
* *
13932 G-AAATCATTTTGAAAAACTTATATAATATATAGTTTTAA
1 GAAAAT-ATTTTTAAAAA--TATATAATATATAGTTTT-T
* * * * *
13971 AAAACATTTTTTTGAAAACATATAATATATAGTTTTA
1 GAAA-ATATTTTTAAAAATATATAATATATAGTTTTT
* * * *
14008 AAAACATTTTTTTTTGAAAACATATAATATATAG-TTTT
1 GAAA-A--TATTTTTAAAAATATATAATATATAGTTTTT
* * * *
14046 -AAAATATTTTGAAAACTATATGATATATA-ATTTT
1 GAAAATATTTTTAAAAATATATAATATATAGTTTTT
* *
14080 GAAAATATTTTTTAAAATATATAATACATAGTTTTT
1 GAAAATATTTTTAAAAATATATAATATATAGTTTTT
*
14116 -AAAATATTTTTAAAAATATATATTATATAGTTTTTT
1 GAAAATATTTTTAAAAATATATAATATATAG-TTTTT
*
14152 GGAAATATTTTT
1 GAAAATATTTTT
14164 TATATATAAT
Statistics
Matches: 363, Mismatches: 38, Indels: 46
0.81 0.09 0.10
Matches are distributed among these distances:
34 23 0.06
35 54 0.15
36 16 0.04
37 95 0.26
38 41 0.11
39 86 0.24
40 42 0.12
41 6 0.02
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
GAAAATATTTTTAAAAATATATAATATATAGTTTTT
Found at i:20568 original size:3 final size:3
Alignment explanation
Indices: 20562--20587 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20552 TTTGTTGTTG
20562 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
20588 CCCTTTTTTA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20631 original size:19 final size:19
Alignment explanation
Indices: 20595--20631 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20585 ATTCCCTTTT
*
20595 TTATTTTTTGTATTTTATC
1 TTATTTTTTGTATCTTATC
*
20614 TTATTTTTTTTATCTTAT
1 TTATTTTTTGTATCTTAT
20632 TTCCCTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (19 bp):
TTATTTTTTGTATCTTATC
Found at i:20676 original size:31 final size:32
Alignment explanation
Indices: 20641--20717 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 32
20631 TTTCCCTTAA
* * *
20641 ATTTATTCTATTTTTT-ACTTTTGTTTTATTT
1 ATTTATTATATTTTTTCACTTTTCTTTGATTT
* *
20672 ATTTAATAT-TTTTTTCATTTTTCTTTGATTT
1 ATTTATTATATTTTTTCACTTTTCTTTGATTT
*
20703 ATATTATTTTATTTT
1 AT-TTATTATATTTT
20718 ATTTATATTC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
30 6 0.17
31 21 0.58
32 5 0.14
33 4 0.11
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (32 bp):
ATTTATTATATTTTTTCACTTTTCTTTGATTT
Found at i:20706 original size:26 final size:25
Alignment explanation
Indices: 20664--20723 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
20654 TTTACTTTTG
*
20664 TTTTATTTATTTAATATTTTTTTCAT
1 TTTTATTTATTTAATATTATTTT-AT
*
20690 TTTTCTTTGATTT-ATATTATTTTA-
1 TTTTATTT-ATTTAATATTATTTTAT
20714 TTTTATTTAT
1 TTTTATTTAT
20724 ATTCTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 2 0.07
24 7 0.23
25 1 0.03
26 16 0.53
27 4 0.13
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTATTTATTTAATATTATTTTAT
Found at i:20721 original size:19 final size:18
Alignment explanation
Indices: 20688--20735 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 18
20678 TATTTTTTTC
20688 ATTTTTCTTTGATTTATATT
1 ATTTTT-TTT-ATTTATATT
20708 ATTTTATTTTATTTATATT
1 ATTTT-TTTTATTTATATT
*
20727 CTTTTTTTT
1 ATTTTTTTT
20736 CATCCTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 8 0.31
21 1 0.04
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (18 bp):
ATTTTTTTTATTTATATT
Found at i:20723 original size:14 final size:14
Alignment explanation
Indices: 20593--20726 Score: 55
Period size: 14 Copynumber: 9.1 Consensus size: 14
20583 TTATTCCCTT
20593 TTTTATTT-TTTGTA
1 TTTTATTTATTT-TA
20607 TTTTATCTTATTTT-
1 TTTTAT-TTATTTTA
**
20621 TTTTATCTTATTTCCC
1 TTTTAT-TTATTT-TA
** *
20637 TTAAATTTATTCTA
1 TTTTATTTATTTTA
*
20651 -TTT-TTTACTTTTG
1 TTTTATTTA-TTTTA
20664 TTTTATTTATTTAATA
1 TTTTATTTATTT--TA
20680 TTTT-TTTCATTTT-
1 TTTTATTT-ATTTTA
*
20693 TCTTTGATTTATATTA
1 T-TTT-ATTTATTTTA
20709 TTTTATTTTATTTATA
1 TTTTA-TTTATTT-TA
20725 TT
1 TT
20727 CTTTTTTTTC
Statistics
Matches: 91, Mismatches: 13, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
12 4 0.04
13 5 0.05
14 30 0.33
15 28 0.31
16 24 0.26
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:20767 original size:10 final size:10
Alignment explanation
Indices: 20752--20776 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20742 TTGATTTGTT
20752 ATTTTAGTTA
1 ATTTTAGTTA
20762 ATTTTAGTTA
1 ATTTTAGTTA
20772 ATTTT
1 ATTTT
20777 TTTATGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (10 bp):
ATTTTAGTTA
Found at i:25705 original size:22 final size:22
Alignment explanation
Indices: 25675--25728 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
25665 TGAATAATTA
* *
25675 AAATTGACACCCCT-TTAAAAT
1 AAATTGACACCACTCTAAAAAT
25696 AATATTGACACCACTCTAAAAAT
1 AA-ATTGACACCACTCTAAAAAT
25719 AAA-TGACACC
1 AAATTGACACC
25729 GTACTATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.31
22 12 0.41
23 8 0.28
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (22 bp):
AAATTGACACCACTCTAAAAAT
Found at i:29610 original size:21 final size:21
Alignment explanation
Indices: 29586--29636 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
29576 CAAGTACTTG
29586 TACTCTCC-GTTTGAGTATCCA
1 TACTCTCCAGTTT-AGTATCCA
*
29607 TACTC-CCTAGTTTATTATCCA
1 TACTCTCC-AGTTTAGTATCCA
29628 TACTCTCCA
1 TACTCTCCA
29637 ACATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 18 0.69
22 6 0.23
ACGTcount: A:0.22, C:0.31, G:0.08, T:0.39
Consensus pattern (21 bp):
TACTCTCCAGTTTAGTATCCA
Found at i:35432 original size:40 final size:39
Alignment explanation
Indices: 35388--35485 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 39
35378 AATCCTCGTG
**
35388 ATATTATTATTATTATTATTTATTACTTTTATATACATAT
1 ATATTATT-TTATTATTATTTATTACTAATATATACATAT
** *
35428 ATATT-TTTTATTTATATACCTATTACTAATATATATATAT
1 ATATTATTTTA-TTAT-TATTTATTACTAATATATACATAT
35468 ATA-TATTTTATT-TTATTT
1 ATATTATTTTATTATTATTT
35486 GATCATTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
37 3 0.06
38 4 0.08
39 9 0.19
40 32 0.67
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (39 bp):
ATATTATTTTATTATTATTTATTACTAATATATACATAT
Found at i:35641 original size:7 final size:6
Alignment explanation
Indices: 35623--35672 Score: 57
Period size: 7 Copynumber: 7.8 Consensus size: 6
35613 ATTTTTTTCC
35623 TTTTTA -TTTTA TTTATTA TTTATTA TTTTTA TTCTTTA TTTTTA TGTTTT
1 TTTTTA TTTTTA TTT-TTA TTT-TTA TTTTTA TT-TTTA TTTTTA T-TTTT
35673 TCCTTTTAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.12
6 12 0.30
7 23 0.57
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:35641 original size:27 final size:27
Alignment explanation
Indices: 35601--35679 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 27
35591 TCTTTACTCT
35601 TTTTTATTGTTTATTTTTTTCCTTTTTA
1 TTTTTATT-TTTATTTTTTTCCTTTTTA
* *
35629 -TTTTATTTATTA-TTTATT-ATTTTTA
1 TTTTTATTT-TTATTTTTTTCCTTTTTA
*
35654 TTCTTTATTTTTATGTTTTTCCTTTT
1 TT-TTTATTTTTATTTTTTTCCTTTT
35680 AGCTCCTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
25 6 0.15
26 10 0.24
27 21 0.51
28 4 0.10
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (27 bp):
TTTTTATTTTTATTTTTTTCCTTTTTA
Found at i:35652 original size:20 final size:20
Alignment explanation
Indices: 35629--35672 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
35619 TTCCTTTTTA
35629 TTTTATT-TATTATTTATTAT-
1 TTTTATTCT-TTATTT-TTATG
35649 TTTTATTCTTTATTTTTATG
1 TTTTATTCTTTATTTTTATG
35669 TTTT
1 TTTT
35673 TCCTTTTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 17 0.77
21 1 0.05
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTATTCTTTATTTTTATG
Found at i:35661 original size:13 final size:12
Alignment explanation
Indices: 35623--35672 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 12
35613 ATTTTTTTCC
35623 TTTTTA-TTTTA
1 TTTTTATTTTTA
35634 TTTATTATTTATTA
1 TTT-TTATTT-TTA
35648 TTTTTATTCTTTA
1 TTTTTATT-TTTA
35661 TTTTTATGTTTT
1 TTTTTAT-TTTT
35673 TCCTTTTAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.09
12 3 0.09
13 20 0.59
14 8 0.24
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:49875 original size:7 final size:8
Alignment explanation
Indices: 49862--49920 Score: 54
Period size: 7 Copynumber: 7.8 Consensus size: 8
49852 ATGCCACTTG
49862 TATTATAA
1 TATTATAA
49870 -ATTATAA
1 TATTATAA
*
49877 TATTATTA
1 TATTATAA
* *
49885 TATAATAT
1 TATTATAA
49893 TA-TATACA
1 TATTATA-A
49901 TATTATAA
1 TATTATAA
49909 T-TTATAA
1 TATTATAA
49916 T-TTAT
1 TATTAT
49921 GCGGTCGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 21 0.50
8 17 0.40
9 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (8 bp):
TATTATAA
Found at i:54054 original size:7 final size:7
Alignment explanation
Indices: 54042--54067 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54032 CGAGCACTTT
54042 CGCTTAG
1 CGCTTAG
54049 CGCTTAG
1 CGCTTAG
54056 CGCTTAG
1 CGCTTAG
54063 CGCTT
1 CGCTT
54068 CGGCGTCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.31, G:0.27, T:0.31
Consensus pattern (7 bp):
CGCTTAG
Found at i:57266 original size:112 final size:111
Alignment explanation
Indices: 57056--57280 Score: 441
Period size: 112 Copynumber: 2.0 Consensus size: 111
57046 GGTTATTATC
57056 TAACAGAACTTGAAATACACAAGAACAGTTTCACTTGGTCTTCACATCAGAAATGAAAGCAAAAT
1 TAACAGAACTTGAAATACACAAGAACAGTTTCACTTGGTCTTCACATCAGAAATGAAAGCAAAAT
57121 GTTAAACAAAATGGATTATAGGAAAAAAGTGATGTTGCAAGACAGG
66 GTTAAACAAAATGGATTATAGGAAAAAAGTGATGTTGCAAGACAGG
57167 TAACAGAACTTGAAATACACAAGAACAGTTTCACTTGGTCTTCACATACAGAAATGAAAGCAAAA
1 TAACAGAACTTGAAATACACAAGAACAGTTTCACTTGGTCTTCACAT-CAGAAATGAAAGCAAAA
57232 TGTTAAACAAAATGGATTATAGGAAAAAAGTGATGTTGCAAGACAGG
65 TGTTAAACAAAATGGATTATAGGAAAAAAGTGATGTTGCAAGACAGG
57279 TA
1 TA
57281 GACACACCGT
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 47 0.42
112 66 0.58
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (111 bp):
TAACAGAACTTGAAATACACAAGAACAGTTTCACTTGGTCTTCACATCAGAAATGAAAGCAAAAT
GTTAAACAAAATGGATTATAGGAAAAAAGTGATGTTGCAAGACAGG
Found at i:61446 original size:3 final size:3
Alignment explanation
Indices: 61438--61503 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
61428 TCGTTTGACT
61438 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
61486 CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC
61504 GCAACAACTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:62791 original size:32 final size:32
Alignment explanation
Indices: 62755--62817 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
62745 CAACCTAAGG
* *
62755 GAGTATCTTGGGGCCTGAGAGCCTACCCAAGA
1 GAGTACCTTGGGGCCTCAGAGCCTACCCAAGA
62787 GAGTACCTTGGGGCCTCAGAGCCTACCCAAG
1 GAGTACCTTGGGGCCTCAGAGCCTACCCAAG
62818 TGTCACCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.30, T:0.17
Consensus pattern (32 bp):
GAGTACCTTGGGGCCTCAGAGCCTACCCAAGA
Found at i:63966 original size:27 final size:28
Alignment explanation
Indices: 63905--63967 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
63895 CAGGGCTTGG
*
63905 GGGTATTTTAGGTCATTTTACACTTCAT
1 GGGTATTTTAGGTCATTTTACACTTCAA
** *
63933 GATTATTTT-GGTCATTTTACAGTTCAA
1 GGGTATTTTAGGTCATTTTACACTTCAA
63960 GGGTATTT
1 GGGTATTT
63968 CAGTCCTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (28 bp):
GGGTATTTTAGGTCATTTTACACTTCAA
Found at i:67696 original size:27 final size:27
Alignment explanation
Indices: 67666--67802 Score: 256
Period size: 27 Copynumber: 5.1 Consensus size: 27
67656 CTTGTTTGCC
67666 TGTGGCTTTGATGATACTGGAGGCCTT
1 TGTGGCTTTGATGATACTGGAGGCCTT
67693 TGTGGCTTTGATGATACTGGAGGCCTT
1 TGTGGCTTTGATGATACTGGAGGCCTT
67720 TGTGGCTTTGATGATACTGGAGGCCTT
1 TGTGGCTTTGATGATACTGGAGGCCTT
67747 TGTGGCTTTGATGATACTGGAGGCCTT
1 TGTGGCTTTGATGATACTGGAGGCCTT
* *
67774 TGTGCCTGTGATGATACTGGAGGCCTT
1 TGTGGCTTTGATGATACTGGAGGCCTT
67801 TG
1 TG
67803 GGGCATCATT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 108 1.00
ACGTcount: A:0.15, C:0.15, G:0.34, T:0.36
Consensus pattern (27 bp):
TGTGGCTTTGATGATACTGGAGGCCTT
Found at i:72866 original size:21 final size:21
Alignment explanation
Indices: 72814--72860 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
72804 GTTTCCAGAT
72814 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
72835 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
72856 TCGCA
1 TCGCA
72861 TTGCGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:73105 original size:4 final size:5
Alignment explanation
Indices: 73077--73105 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
73067 CACGACCCGA
73077 GACGG GACGG GACGG GACGG GAC-G GACGG
1 GACGG GACGG GACGG GACGG GACGG GACGG
73106 CGGCGGCGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.21, G:0.59, T:0.00
Consensus pattern (5 bp):
GACGG
Found at i:75178 original size:38 final size:38
Alignment explanation
Indices: 75128--75205 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
75118 GGGTATTTTC
*
75128 ATTAATTATCACCTGTTAATGAATTATTAAAGATAACA
1 ATTAATTATCACCTGTTAATCAATTATTAAAGATAACA
75166 ATTAATTATCACCTGTTAATCAATTATTAAAGATAACA
1 ATTAATTATCACCTGTTAATCAATTATTAAAGATAACA
75204 AT
1 AT
75206 ATATCAAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (38 bp):
ATTAATTATCACCTGTTAATCAATTATTAAAGATAACA
Found at i:84209 original size:16 final size:16
Alignment explanation
Indices: 84184--84226 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
84174 TTAAACATTG
* **
84184 TTATTTTTATTATTTA
1 TTATTATTATTATAAA
84200 TTATTATTATTATAAA
1 TTATTATTATTATAAA
*
84216 ATATTATTATT
1 TTATTATTATT
84227 TACAAATTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATTATAAA
Found at i:84970 original size:34 final size:34
Alignment explanation
Indices: 84907--84976 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
84897 TGCATATTTA
**
84907 ATTTCTTATATTTTAATTTAAATGTTTTGTTTGTT
1 ATTTCTTATATTTTAATTTAAATAATTTGTTT-TT
**
84942 ATTTCTTA-ATTTTAATTTATTTAATTTGTTTTT
1 ATTTCTTATATTTTAATTTAAATAATTTGTTTTT
84975 AT
1 AT
84977 GACTAATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 4 0.13
34 19 0.61
35 8 0.26
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (34 bp):
ATTTCTTATATTTTAATTTAAATAATTTGTTTTT
Found at i:86975 original size:48 final size:49
Alignment explanation
Indices: 86923--87022 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 49
86913 TTTATGTTCG
* * **
86923 TAATTAGCATTTATTATTC-TTCAATTTTTTGAATTAATTTAACTTTAC
1 TAATTAGCATTCATTATTCTTTAAATCCTTTGAATTAATTTAACTTTAC
86971 TAATTAGCATTCATTATTCTTTAAATCCTTTGAATTAATTTAACTTTAC
1 TAATTAGCATTCATTATTCTTTAAATCCTTTGAATTAATTTAACTTTAC
87020 TAA
1 TAA
87023 CTTATCTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 18 0.38
49 29 0.62
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (49 bp):
TAATTAGCATTCATTATTCTTTAAATCCTTTGAATTAATTTAACTTTAC
Found at i:91503 original size:3 final size:3
Alignment explanation
Indices: 91495--91543 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
91485 CGTCCCATGA
*
91495 TAT TAT TAT TAT TAT TAT TAT TAT TA- AATT TAT TACT TAAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T T-AT TAT TAT
91542 TA
1 TA
91544 ATTACATTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 1 0.03
3 33 0.82
4 5 0.12
5 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:98682 original size:27 final size:27
Alignment explanation
Indices: 98644--98701 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
98634 ATACATACCA
98644 CTCCTCATCTGTTGCACGTGATGACAG
1 CTCCTCATCTGTTGCACGTGATGACAG
98671 CTCCTCATCTGTTGCACGTGATGACAG
1 CTCCTCATCTGTTGCACGTGATGACAG
98698 CTCC
1 CTCC
98702 GTTGACATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.33, G:0.21, T:0.29
Consensus pattern (27 bp):
CTCCTCATCTGTTGCACGTGATGACAG
Found at i:100782 original size:56 final size:56
Alignment explanation
Indices: 100678--100838 Score: 234
Period size: 56 Copynumber: 2.9 Consensus size: 56
100668 TGCTCAAATT
* * *
100678 TTTCTCAAAATCTGATCTCCCCTGAAAGAATAGTGGAGCAGACCCATCTTCCAAAGA
1 TTTCTC-AAGTCTAATCTCCCCTGAAAGAATAGTGGAGCAGACTCATCTTCCAAAGA
* * *
100735 TTTCTCAAGTCTAATCTCCCCTGAAAGAAGAGTGAAGCATACTCATCTTCCAAAGA
1 TTTCTCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCAGACTCATCTTCCAAAGA
* *
100791 TTTCTCAAGTCTTATCT-CCCTGAAAGAATAGTGGAGCAGACTCGTCTT
1 TTTCTCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCAGACTCATCTT
100839 TCAACGTTGA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 27 0.29
56 60 0.65
57 6 0.06
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (56 bp):
TTTCTCAAGTCTAATCTCCCCTGAAAGAATAGTGGAGCAGACTCATCTTCCAAAGA
Found at i:100992 original size:137 final size:138
Alignment explanation
Indices: 100739--101334 Score: 760
Period size: 137 Copynumber: 4.4 Consensus size: 138
100729 CAAAGATTTC
* * *
100739 TCAAGTCTAATCTCCCCTGAAAGAAGAGT-GAAGCATACTCA-TCTTCCAAAGATTTCTCAAGTC
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTAG-AGCAGACTCAGTCTTCCAAAGATTTCTCGAGTC
* * * *
100802 TTATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTTCAACGTTGATTTGACTACCCGAAAAAG
65 TTATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAACATTGATCTGACTACCCAAAAAAG
100867 AGGAACAAA
130 AGGAACAAA
* * *
100876 TCAAGTCTGATCTCCCCTAAAAGAAGAGTATAGCAGAC-CAGTGTTCCAAAGATTTCTCGAGTCT
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTAGAGCAGACTCAGTCTTCCAAAGATTTCTCGAGTCT
* * *
100940 TATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAATATTAATATGACTACCCAAAAAAGA
66 TATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAACATTGATCTGACTACCCAAAAAAGA
*
101005 GGAACATA
131 GGAACAAA
* * * * * * *
101013 TCAAGTTTGGTCTCCCCTGAAAAAAGAGTGGAGCAAACTC-GTCTTCCAAAGATTTCTCTAGTTT
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTAGAGCAGACTCAGTCTTCCAAAGATTTCTCGAGTCT
* * *
101077 TATCTCCCTGAAAGAAGAGTGGAGCAGACTCTTCTTCCAACATTGATCTGCCTACCC-AAAAAGA
66 TATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAACATTGATCTGACTACCCAAAAAAGA
*
101141 GGAGCAAA
131 GGAACAAA
* * * * ** *
101149 TCAAGTTTGATATCCCCTGAAAGAATAGTGGAAAAGAC-CCGTCTTCCAAAGATTTCTCGAGTCT
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTAGAGCAGACTCAGTCTTCCAAAGATTTCTCGAGTCT
* *
101213 TATCTCCCTGAAAGAATAGTGGAGCAGATTCGTCTTCCAA-AGTTGATCTGAATACCCAAAAAAG
66 TATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAACA-TTGATCTGACTACCCAAAAAAG
* *
101277 AGGAATATA
130 AGGAACAAA
* *
101286 TCAAGTCTGATCTCCCCTGAAAGAATAGT-GCAACAGACTC-GTCTTCCAA
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTAG-AGCAGACTCAGTCTTCCAA
101335 CATTGATCTG
Statistics
Matches: 400, Mismatches: 51, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
135 2 0.00
136 119 0.30
137 277 0.69
138 2 0.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (138 bp):
TCAAGTCTGATCTCCCCTGAAAGAAGAGTAGAGCAGACTCAGTCTTCCAAAGATTTCTCGAGTCT
TATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAACATTGATCTGACTACCCAAAAAAGA
GGAACAAA
Found at i:101238 original size:273 final size:274
Alignment explanation
Indices: 100739--101334 Score: 856
Period size: 273 Copynumber: 2.2 Consensus size: 274
100729 CAAAGATTTC
* * *
100739 TCAAGTCTAATCTCCCCTGAAAGAAGAGTGAAGCATACTCATCTTCCAAAGATTTCTCAAGTCTT
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTGAAGCAAACTCGTCTTCCAAAGATTTCTCAAGTCTT
* * * *
100804 ATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTTCAACGTTGATTTGACTACCCGAAAAAGAG
66 ATCTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTTCCAACATTGATCTGACTACCCGAAAAAGAG
* * ** *
100869 GAACAAATCAAGTCTGATCTCCCCTAAAAGAAGAGTATAGCAGACCAGTGTTCCAAAGATTTCTC
131 GAACAAATCAAGTCTGATATCCCCTAAAAGAAGAGTAGAAAAGACCAGTCTTCCAAAGATTTCTC
*
100934 GAGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAATA-TTAATATGACTACCCA
196 GAGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAA-AGTTAATATGAATACCCA
100998 AAAAAGAGGAACATA
260 AAAAAGAGGAACATA
* * * * * *
101013 TCAAGTTTGGTCTCCCCTGAAAAAAGAGTGGAGCAAACTCGTCTTCCAAAGATTTCTCTAGTTTT
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTGAAGCAAACTCGTCTTCCAAAGATTTCTCAAGTCTT
* *
101078 ATCTCCCTGAAAGAAGAGTGGAGCAGACTCTTCTTCCAACATTGATCTGCCTACCC-AAAAAGAG
66 ATCTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTTCCAACATTGATCTGACTACCCGAAAAAGAG
* * * * * *
101142 GAGCAAATCAAGTTTGATATCCCCTGAAAGAATAGTGGAAAAGACCCGTCTTCCAAAGATTTCTC
131 GAACAAATCAAGTCTGATATCCCCTAAAAGAAGAGTAGAAAAGACCAGTCTTCCAAAGATTTCTC
* * *
101207 GAGTCTTATCTCCCTGAAAGAATAGTGGAGCAGATTCGTCTTCCAAAGTTGATCTGAATACCCAA
196 GAGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAGTTAATATGAATACCCAA
*
101272 AAAAGAGGAATATA
261 AAAAGAGGAACATA
* *
101286 TCAAGTCTGATCTCCCCTGAAAGAATAGTGCAA-CAGACTCGTCTTCCAA
1 TCAAGTCTGATCTCCCCTGAAAGAAGAGTG-AAGCAAACTCGTCTTCCAA
101335 CATTGATCTG
Statistics
Matches: 283, Mismatches: 37, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
272 1 0.00
273 175 0.62
274 107 0.38
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (274 bp):
TCAAGTCTGATCTCCCCTGAAAGAAGAGTGAAGCAAACTCGTCTTCCAAAGATTTCTCAAGTCTT
ATCTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTTCCAACATTGATCTGACTACCCGAAAAAGAG
GAACAAATCAAGTCTGATATCCCCTAAAAGAAGAGTAGAAAAGACCAGTCTTCCAAAGATTTCTC
GAGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACTCGTCTTCCAAAGTTAATATGAATACCCAA
AAAAGAGGAACATA
Found at i:101312 original size:82 final size:81
Alignment explanation
Indices: 101208--101357 Score: 221
Period size: 82 Copynumber: 1.8 Consensus size: 81
101198 AGATTTCTCG
* * * * *
101208 AGTCTTATCTCCCTGAAAGAATAGTGGAGCAGATTCGTCTTCCAA-AGTTGATCTGAATACCCAA
1 AGTCTGATCTCCCTGAAAGAATAGTGCAACAGACTCGTCTTCCAACA-TTGATCTGAATACCAAA
101272 AAAAGAGGAATATATCA
65 AAAAGAGGAATATATCA
*
101289 AGTCTGATCTCCCCTGAAAGAATAGTGCAACAGACTCGTCTTCCAACATTGATCTGACTACCAAA
1 AGTCTGATCT-CCCTGAAAGAATAGTGCAACAGACTCGTCTTCCAACATTGATCTGAATACCAAA
101354 AAAA
65 AAAA
101358 AAGAAACAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 9 0.15
82 51 0.84
83 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (81 bp):
AGTCTGATCTCCCTGAAAGAATAGTGCAACAGACTCGTCTTCCAACATTGATCTGAATACCAAAA
AAAGAGGAATATATCA
Found at i:101371 original size:82 final size:81
Alignment explanation
Indices: 101208--101374 Score: 219
Period size: 82 Copynumber: 2.0 Consensus size: 81
101198 AGATTTCTCG
* * * * *
101208 AGTCTTATCTCCCTGAAAGAATAGTGGAGCAGATTCGTCTTCCAAAGTTGATCTGAATACCCAAA
1 AGTCTGATCTCCCTGAAAGAATAGTGCAACAGACTCGTCTTCCAAAGTTGATCTGAATACCAAAA
* * * *
101273 AAAGAGGAATATATCA
66 AAAAAGAAACAGATCA
*
101289 AGTCTGATCTCCCCTGAAAGAATAGTGCAACAGACTCGTCTTCCAACA-TTGATCTGACTACCAA
1 AGTCTGATCT-CCCTGAAAGAATAGTGCAACAGACTCGTCTTCCAA-AGTTGATCTGAATACCAA
101353 AAAAAAAGAAACAGATCA
64 AAAAAAAGAAACAGATCA
101371 AGTC
1 AGTC
101375 CAATTTACCC
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
81 9 0.12
82 64 0.86
83 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (81 bp):
AGTCTGATCTCCCTGAAAGAATAGTGCAACAGACTCGTCTTCCAAAGTTGATCTGAATACCAAAA
AAAAAGAAACAGATCA
Found at i:107850 original size:16 final size:15
Alignment explanation
Indices: 107829--107862 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
107819 GATGTAGATG
*
107829 AAAATATTTTTATATA
1 AAAATATATTTATA-A
107845 AAAATATATTTATAA
1 AAAATATATTTATAA
107860 AAA
1 AAA
107863 GTTATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATATATTTATAA
Found at i:108905 original size:60 final size:60
Alignment explanation
Indices: 108795--108959 Score: 217
Period size: 60 Copynumber: 2.8 Consensus size: 60
108785 ACCCTCATTT
* * * *
108795 TAAATTAGT-TCTTAAACTTTTG-ATATTCCAATTTCATCACTTAACTATGACTCTCGTTC
1 TAAATTAGTCT-TTAAACTTTTGAATATTCCAATTTCATCCCTAAATTATGACACTCGTTC
* *
108854 TAAATTAGTCTTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATGACACTCTTTC
1 TAAATTAGTCTTTAAACTTTTGAATATTCCAATTTCATCCCTAAATTATGACACTCGTTC
*** *
108914 TAAATTAGTCCCCAAACTTTTGAATATTCCAATTTCATCCCCAAAT
1 TAAATTAGTCTTTAAACTTTTGAATATTCCAATTTCATCCCTAAAT
108960 CCATCCAAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
59 20 0.22
60 73 0.78
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (60 bp):
TAAATTAGTCTTTAAACTTTTGAATATTCCAATTTCATCCCTAAATTATGACACTCGTTC
Found at i:108957 original size:29 final size:29
Alignment explanation
Indices: 108867--108958 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
108857 ATTAGTCTTT
*
108867 AAACTTTTGAATATTCTAATTTCATCCCT
1 AAACTTTTGAATATTCTAATTTCATCCCC
* * *
108896 AAA-TTATGACACTCTTTCTAAATT-AGTCCCC
1 AAACTTTTGA-A-T-ATTCTAATTTCA-TCCCC
*
108927 AAACTTTTGAATATTCCAATTTCATCCCC
1 AAACTTTTGAATATTCTAATTTCATCCCC
108956 AAA
1 AAA
108959 TCCATCCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
28 5 0.10
29 19 0.39
30 4 0.08
31 16 0.33
32 5 0.10
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
AAACTTTTGAATATTCTAATTTCATCCCC
Found at i:109350 original size:149 final size:149
Alignment explanation
Indices: 109080--109377 Score: 560
Period size: 149 Copynumber: 2.0 Consensus size: 149
109070 TTAGTATATA
109080 CGTATAGTTTGGGGTTAAACTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAATGTTGG
1 CGTATAGTTTGGGGTTAAACTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAATGTTGG
*
109145 GGATGAAAACGAAATGTTCAGAAGTTTAAGGACTAACGTAGAATGATAGTTATAGCTTAGGAATG
66 GGATGAAAACGAAATGTTCAGAAGTTTAAGGACTAACATAGAATGATAGTTATAGCTTAGGAATG
109210 AAACTAGAATATTTAAAAG
131 AAACTAGAATATTTAAAAG
*
109229 CGTATAGTTTGGGGTTAAATTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAATGTTGG
1 CGTATAGTTTGGGGTTAAACTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAATGTTGG
109294 GGATGAAAACGAAATGTTCAGAAGTTTAAGGACTAACATAGAATGATAGTTATAGCTTAGGAATG
66 GGATGAAAACGAAATGTTCAGAAGTTTAAGGACTAACATAGAATGATAGTTATAGCTTAGGAATG
* *
109359 AAATTATAATATTTAAAAG
131 AAACTAGAATATTTAAAAG
109378 TTTAGGGATC
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 145 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (149 bp):
CGTATAGTTTGGGGTTAAACTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAATGTTGG
GGATGAAAACGAAATGTTCAGAAGTTTAAGGACTAACATAGAATGATAGTTATAGCTTAGGAATG
AAACTAGAATATTTAAAAG
Found at i:111000 original size:26 final size:26
Alignment explanation
Indices: 110960--111010 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
110950 TTTCTACTAA
110960 TAATTATTAGAACATACATGAGGATG
1 TAATTATTAGAACATACATGAGGATG
**
110986 TAATTATTATTACATACATGAGGAT
1 TAATTATTAGAACATACATGAGGAT
111011 ATGTATTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (26 bp):
TAATTATTAGAACATACATGAGGATG
Found at i:120414 original size:31 final size:31
Alignment explanation
Indices: 120353--120418 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
120343 TAAAACTTAT
* ***
120353 AATACAGTCACCCAATATTTAGTTTGTTTGC
1 AATACAGTCACCCAACATTTAGTCCATTTGC
*
120384 AATACAGTCCCCCAACATTTAGTCCATTTGC
1 AATACAGTCACCCAACATTTAGTCCATTTGC
120415 AATA
1 AATA
120419 TGATCCCTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (31 bp):
AATACAGTCACCCAACATTTAGTCCATTTGC
Found at i:122421 original size:30 final size:30
Alignment explanation
Indices: 122370--122437 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 30
122360 TGAGGGACCA
* *
122370 TATTGCAAACAGACTAAATGTTGGGGAATTG
1 TATTGCAAACAAACTAAATGTTGGGG-ACTG
122401 TATTGCAAACAAAC-AAATGTTGGGGACTG
1 TATTGCAAACAAACTAAATGTTGGGGACTG
122430 TATTGCAA
1 TATTGCAA
122438 GTTTTAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 11 0.31
30 11 0.31
31 13 0.37
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (30 bp):
TATTGCAAACAAACTAAATGTTGGGGACTG
Found at i:124876 original size:60 final size:58
Alignment explanation
Indices: 124774--124943 Score: 162
Period size: 60 Copynumber: 2.8 Consensus size: 58
124764 GTTGAATTGA
* * * * *
124774 AATATTCAAAAGTCTAAGGACCAATTTAGAAAT-AGGGTTATAGTTTAGGGGTGAAAATAT
1 AATATTCAAAAGTTTAAGGATCAATTTA-AAATGA-AGATATAGTTT-GGGGTGAAAATAG
* * * ** * *
124834 AATATTCAAAAGTTTAAGGATTAATTTAGAATGCAAGCTATAGTTTTGGAATGAAATTGG
1 AATATTCAAAAGTTTAAGGATCAATTTAAAATG-AAGATATAG-TTTGGGGTGAAAATAG
*
124894 AATATTTAAAAGTTTAAGGATCAATTTAAAATGAAGATGATAGTTTGGGG
1 AATATTCAAAAGTTTAAGGATCAATTTAAAATGAAGAT-ATAGTTTGGGG
124944 ACATATGATG
Statistics
Matches: 89, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
59 12 0.13
60 73 0.82
61 4 0.04
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (58 bp):
AATATTCAAAAGTTTAAGGATCAATTTAAAATGAAGATATAGTTTGGGGTGAAAATAG
Done.