Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005670.1 Hibiscus syriacus cultivar Beakdansim tig00013259_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: 132800
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1580 original size:20 final size:20
Alignment explanation
Indices: 1555--1607 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1545 CCCTTAATGC
1555 AAAGGATCGATCCCTCCCCT
1 AAAGGATCGATCCCTCCCCT
* *
1575 AAAGGATCAATCCCTCCTCT
1 AAAGGATCGATCCCTCCCCT
*
1595 AATGGATCGATCC
1 AAAGGATCGATCC
1608 TTATCTCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
AAAGGATCGATCCCTCCCCT
Found at i:8366 original size:107 final size:108
Alignment explanation
Indices: 8199--8851 Score: 777
Period size: 107 Copynumber: 6.1 Consensus size: 108
8189 ACCAAATAGG
* * *
8199 CACTAAGTGTGCAAATCATAAAATTCATCATATGTTGATGAATAACTGTTTC-GTACTAAGTGTA
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGGTACTAAGTGTA
* * *
8263 CAAATCACATAATTCATCATATGTTGATGAATAACCGTTTCGA
66 CAAATCACAGAATTCATCATATGGTGATGAATAACCATTTCGA
* * * * *
8306 CACTAAGTTTGCAAATCACATAA-TCATCATGTGTTGATGAATAACCGTTTCGGTAATAAGTGTG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGGTACTAAGTGTA
* * *
8370 TAAATCACGGAATTCATCATATGGTGATGAATAACTATTTC-A
66 CAAATCACAGAATTCATCATATGGTGATGAATAACCATTTCGA
* * * * * **
8412 GCACTATGTGTGCAAATCACGGAATTAATCATATGGTGATGAATAACTGTTTCGACAC-AAGTGT
1 -CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGGTACTAAGTGT
* *
8476 ACAAATCACAGAATTCATTATATGGTGATGAATAACCGTTTCGA
65 ACAAATCACAGAATTCATCATATGGTGATGAATAACCATTTCGA
* * * *
8520 CACTAAATGTGCAAATCA-TGTAATTCATCATATGATGATGAATAACAGTTTCGGTACTAAGTGT
1 CACTAAGTGTGCAAATCACAG-AATTCATCATATGTTGATGAATAACCGTTTCGGTACTAAGTGT
* * **
8584 GCAAATCACAAAATTCATCATATGGTGATGAATAACTGTTTCGA
65 ACAAATCACAGAATTCATCATATGGTGATGAATAACCATTTCGA
* * * * * **
8628 CACTAATTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCATTTCAGCACTAAGTACA
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGGTACTAAGTGTA
*
8693 TAAATCACAGAA-T--TCATATGGTGATGAATAACCATTTCGGA
66 CAAATCACAGAATTCATCATATGGTGATGAATAACCATTTC-GA
* * * * * *
8734 -ACTAAATGCGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTTGGCACTAAGTGTG
1 CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGGTACTAAGTGTA
*
8798 CAAATCAC-GAAATTCATCATATGTTGATGAATAACCATTTCGA
66 CAAATCACAG-AATTCATCATATGGTGATGAATAACCATTTCGA
*
8841 CACTATGTGTG
1 CACTAAGTGTG
8852 TAAACCATGA
Statistics
Matches: 462, Mismatches: 71, Indels: 25
0.83 0.13 0.04
Matches are distributed among these distances:
104 1 0.00
105 86 0.19
106 31 0.07
107 176 0.38
108 167 0.36
109 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (108 bp):
CACTAAGTGTGCAAATCACAGAATTCATCATATGTTGATGAATAACCGTTTCGGTACTAAGTGTA
CAAATCACAGAATTCATCATATGGTGATGAATAACCATTTCGA
Found at i:8423 original size:54 final size:53
Alignment explanation
Indices: 8198--8851 Score: 719
Period size: 54 Copynumber: 12.2 Consensus size: 53
8188 TACCAAATAG
* * * *
8198 GCACTAAGTGTGCAAATCATAAAATTCATCATATGTTGATGAATAACTGTTTC
1 GCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
* * * *
8251 GTACTAAGTGTACAAATCACATAATTCATCATATGTTGATGAATAACCGTTTC
1 GCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
* * * *
8304 GACACTAAGTTTGCAAATCACATAA-TCATCATGTGTTGATGAATAACCGTTTC
1 G-CACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
* * * * **
8357 GGTAATAAGTGTGTAAATCACGGAATTCATCATATGGTGATGAATAACTATTTC
1 -GCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
* * * *
8411 AGCACTATGTGTGCAAATCACGGAATTAATCATATGGTGATGAATAACTGTTTC
1 -GCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
* *
8465 GACAC-AAGTGTACAAATCACAGAATTCATTATATGGTGATGAATAACCGTTTC
1 G-CACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
* * * *
8518 GACACTAAATGTGCAAATCA-TGTAATTCATCATATGATGATGAATAACAGTTTC
1 G-CACTAAGTGTGCAAATCACAG-AATTCATCATATGGTGATGAATAACCGTTTC
* * *
8572 GGTACTAAGTGTGCAAATCACAAAATTCATCATATGGTGATGAATAACTGTTTC
1 -GCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
* *
8626 GACACTAATTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCATTTC
1 G-CACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
**** *
8680 AGCACTAAGTACATAAATCACAGAA-T--TCATATGGTGATGAATAACCATTTC
1 -GCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
* * * * * *
8731 GGAACTAAATGCGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTTG
1 -GCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCG-TTTC
* *
8786 GCACTAAGTGTGCAAATCAC-GAAATTCATCATATGTTGATGAATAACCATTTC
1 GCACTAAGTGTGCAAATCACAG-AATTCATCATATGGTGATGAATAACCGTTTC
*
8839 GACACTATGTGTG
1 G-CACTAAGTGTG
8852 TAAACCATGA
Statistics
Matches: 515, Mismatches: 70, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
51 43 0.08
52 1 0.00
53 149 0.29
54 317 0.62
55 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (53 bp):
GCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTC
Found at i:8466 original size:161 final size:162
Alignment explanation
Indices: 8197--8851 Score: 788
Period size: 161 Copynumber: 4.1 Consensus size: 162
8187 TTACCAAATA
* * * *
8197 GGCACTAAGTGTGCAAATCATAAAATTCATCATATGTTGATGAATAACTGTTTC-GTACTAAGTG
1 GGCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACTATTTCGGTACTAAGTG
* * * *
8261 TACAAATCACATAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTTTGCAAATCACA
66 TGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTCGACACTAAGTGTGCAAATCACA
* * * *
8326 TAA-TCATCATGTGTTGATGAATAACCGTTTC
131 GAATTCATCATATGGTGATGAATAACCATTTC
* * * * * * *
8357 GGTAATAAGTGTGTAAATCACGGAATTCATCATATGGTGATGAATAACTATTTCAGCACTATGTG
1 GGCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACTATTTCGGTACTAAGTG
* * * *
8422 TGCAAATCACGGAATTAATCATATGGTGATGAATAACTGTTTCGACAC-AAGTGTACAAATCACA
66 TGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTCGACACTAAGTGTGCAAATCACA
* *
8486 GAATTCATTATATGGTGATGAATAACCGTTTC
131 GAATTCATCATATGGTGATGAATAACCATTTC
* * * *
8518 GACACTAAATGTGCAAATCA-TGTAATTCATCATATGATGATGAATAAC-AGTTTCGGTACTAAG
1 GGCACTAAGTGTGCAAATCACAG-AATTCATCATATGGTGATGAATAACTA-TTTCGGTACTAAG
* * *
8581 TGTGCAAATCACAAAATTCATCATATGGTGATGAATAACTGTTTCGACACTAATTGTGCAAATCA
64 TGTGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTCGACACTAAGTGTGCAAATCA
8646 CAGAATTCATCATATGGTGATGAATAACCATTTC
129 CAGAATTCATCATATGGTGATGAATAACCATTTC
* **** * * *
8680 AGCACTAAGTACATAAATCACAGAA-T--TCATATGGTGATGAATAACCATTTCGGAACTAAATG
1 GGCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACTATTTCGGTACTAAGTG
* * * * *
8742 CGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTTTGGCACTAAGTGTGCAAATCAC-
66 TGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTCGACACTAAGTGTGCAAATCACA
*
8806 GAAATTCATCATATGTTGATGAATAACCATTTC
131 G-AATTCATCATATGGTGATGAATAACCATTTC
* *
8839 GACACTATGTGTG
1 GGCACTAAGTGTG
8852 TAAACCATGA
Statistics
Matches: 422, Mismatches: 65, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
158 1 0.00
159 124 0.29
160 65 0.15
161 172 0.41
162 59 0.14
163 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (162 bp):
GGCACTAAGTGTGCAAATCACAGAATTCATCATATGGTGATGAATAACTATTTCGGTACTAAGTG
TGCAAATCACAGAATTCATCATATGGTGATGAATAACCGTTTCGACACTAAGTGTGCAAATCACA
GAATTCATCATATGGTGATGAATAACCATTTC
Found at i:16945 original size:2 final size:2
Alignment explanation
Indices: 16938--16968 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
16928 GTTAATATTA
16938 AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
16969 GGATGTGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23311 original size:2 final size:2
Alignment explanation
Indices: 23304--23392 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
23294 TGTGTCATTA
23304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23388 AT AT A
1 AT AT A
23393 CGCATGTAAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32711 original size:18 final size:18
Alignment explanation
Indices: 32688--32727 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
32678 AAGGAACACT
32688 GAGCATGGAAAAGGTCTA
1 GAGCATGGAAAAGGTCTA
*
32706 GAGCATGGAAAAGTTCTA
1 GAGCATGGAAAAGGTCTA
32724 GAGC
1 GAGC
32728 CTGAAACTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.33, T:0.17
Consensus pattern (18 bp):
GAGCATGGAAAAGGTCTA
Found at i:43466 original size:36 final size:36
Alignment explanation
Indices: 43419--43487 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
43409 TTGTAGTCAG
* *
43419 AGTGTATGGATACACT-GTAGGGTGTATTGGTACACC
1 AGTGTATGGATACACTCATAGGG-GTACTGGTACACC
43455 AGTGTATGGATACACTCATAGGGGTACTGGTAC
1 AGTGTATGGATACACTCATAGGGGTACTGGTAC
43488 CCTTTTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.29
Consensus pattern (36 bp):
AGTGTATGGATACACTCATAGGGGTACTGGTACACC
Found at i:43827 original size:21 final size:21
Alignment explanation
Indices: 43803--43843 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43793 ATGTTTAATG
43803 AAAAAGATACCAATTCTTAAC
1 AAAAAGATACCAATTCTTAAC
* * *
43824 AAAAGGATATCAATTGTTAA
1 AAAAAGATACCAATTCTTAA
43844 AAAGTTACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (21 bp):
AAAAAGATACCAATTCTTAAC
Found at i:47002 original size:19 final size:17
Alignment explanation
Indices: 46978--47028 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
46968 TGTAGCCAAA
*
46978 GTGTATGGATACACTGT
1 GTGTATGGATACACTCT
*
46995 AGGTGTATGGGTACAC-CT
1 --GTGTATGGATACACTCT
47013 GTGTATGGATACACTC
1 GTGTATGGATACACTC
47029 ATAGGGGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
18 1 0.04
19 13 0.46
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (17 bp):
GTGTATGGATACACTCT
Found at i:47024 original size:35 final size:36
Alignment explanation
Indices: 46977--47060 Score: 116
Period size: 36 Copynumber: 2.4 Consensus size: 36
46967 TTGTAGCCAA
* *
46977 AGTGTATGGATACACT-GTAGGTGTATGGGTACACC
1 AGTGTATGGATACACTCATAGGGGTATGGGTACACC
* * *
47012 TGTGTATGGATACACTCATAGGGGTATTGGTACATC
1 AGTGTATGGATACACTCATAGGGGTATGGGTACACC
47048 AGTGTATGGATAC
1 AGTGTATGGATAC
47061 CCTTTGATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 15 0.36
36 27 0.64
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31
Consensus pattern (36 bp):
AGTGTATGGATACACTCATAGGGGTATGGGTACACC
Found at i:57305 original size:24 final size:24
Alignment explanation
Indices: 57175--57293 Score: 204
Period size: 24 Copynumber: 5.0 Consensus size: 24
57165 CATAATTCAT
*
57175 GTCAAGTAGCATAT-AAGAATCCAG
1 GTCAAGTATCATATCAA-AATCCAG
*
57199 GTCAAGTATCATATAAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAG
57223 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAG
57247 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAG
57271 GTCAAGTATCATATCAAAATCCA
1 GTCAAGTATCATATCAAAATCCA
57294 AATCGAAAAT
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
24 90 0.98
25 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCATATCAAAATCCAG
Found at i:58337 original size:2 final size:2
Alignment explanation
Indices: 58330--58433 Score: 71
Period size: 2 Copynumber: 56.0 Consensus size: 2
58320 AAATAATTAT
58330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
58369 TA AA TT TA -A TT TA AA T- TA -A AA TA TA TA TA TA -A TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
58407 TA TA TT TA -A TT TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58434 CCCAACCCGA
Statistics
Matches: 77, Mismatches: 17, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
1 8 0.10
2 69 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:58431 original size:38 final size:38
Alignment explanation
Indices: 58345--58433 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 38
58335 ATATATATAT
58345 ATATATATATATATATAATATTAATAAATTTAATTTAA
1 ATATATATATATATATAATATTAATAAATTTAATTTAA
* * *
58383 AT-TAAAATATATATATAATATTTATATATTTAATTTAA
1 ATAT-ATATATATATATAATATTAATAAATTTAATTTAA
58421 ATATATATATATA
1 ATATATATATATA
58434 CCCAACCCGA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 1 0.02
38 43 0.96
39 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
ATATATATATATATATAATATTAATAAATTTAATTTAA
Found at i:60350 original size:22 final size:22
Alignment explanation
Indices: 60312--60353 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
60302 TGTAACAATA
60312 TTTACAAAACTAGCACCCTAGT
1 TTTACAAAACTAGCACCCTAGT
*
60334 TTTACACAAA-TATCACCCTA
1 TTTACA-AAACTAGCACCCTA
60354 ACAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.38, C:0.29, G:0.05, T:0.29
Consensus pattern (22 bp):
TTTACAAAACTAGCACCCTAGT
Found at i:62075 original size:19 final size:19
Alignment explanation
Indices: 62051--62091 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
62041 AGGGTAAAGT
62051 GTTTTGATCCTTTGCTTGA
1 GTTTTGATCCTTTGCTTGA
*
62070 GTTTTGATCCTTTGCTTTA
1 GTTTTGATCCTTTGCTTGA
62089 GTT
1 GTT
62092 CCTTGTGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (19 bp):
GTTTTGATCCTTTGCTTGA
Found at i:63575 original size:26 final size:26
Alignment explanation
Indices: 63498--63575 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
63488 TTTTATGTTA
63498 GGAGT-AACTTATAAAATTTTAGAGG
1 GGAGTAAACTTATAAAATTTTAGAGG
* * *
63523 AGAGCAAACTTATAAAACTTTAGAGG
1 GGAGTAAACTTATAAAATTTTAGAGG
*
63549 GGAGTAAAATTATAAAAATTTTA-AGG
1 GGAGTAAACTTAT-AAAATTTTAGAGG
63575 G
1 G
63576 CGAAAATAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 3 0.07
26 33 0.75
27 8 0.18
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (26 bp):
GGAGTAAACTTATAAAATTTTAGAGG
Found at i:65609 original size:23 final size:23
Alignment explanation
Indices: 65583--65626 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
65573 TTTAATAAAA
*
65583 TTTTAAGATTATTTTTAATTCGG
1 TTTTAAGATTATATTTAATTCGG
* *
65606 TTTTAAGCTTATATTTGATTC
1 TTTTAAGATTATATTTAATTC
65627 AACCATTCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (23 bp):
TTTTAAGATTATATTTAATTCGG
Found at i:75339 original size:25 final size:24
Alignment explanation
Indices: 75290--75340 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
75280 ATAAAGAACC
* *
75290 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAAAAAACCATTA
*
75314 AAAATAAAGTTCAAAAAAACCATTA
1 AAAATAAACTT-AAAAAAACCATTA
75339 AA
1 AA
75341 TCAACCACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.63, C:0.14, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAAAAAACCATTA
Found at i:76237 original size:17 final size:19
Alignment explanation
Indices: 76204--76242 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
76194 TTTAACAACT
76204 TATAGAACATTAAATA-TAA
1 TATAGAACA-TAAATATTAA
76223 TATAGAACA-AAATATTAA
1 TATAGAACATAAATATTAA
76241 TA
1 TA
76243 ATACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
TATAGAACATAAATATTAA
Found at i:77617 original size:29 final size:29
Alignment explanation
Indices: 77585--77689 Score: 176
Period size: 29 Copynumber: 3.6 Consensus size: 29
77575 TTTTTAAAAA
77585 AATTACTAAAATAGCACCTATTTCGAATT
1 AATTACTAAAATAGCACCTATTTCGAATT
77614 AATTACTAAAATAGCAGCC-ATTTCGAATT
1 AATTACTAAAATAGCA-CCTATTTCGAATT
* *
77643 AATTACTACAATAGCACCTATTTTGAATT
1 AATTACTAAAATAGCACCTATTTCGAATT
77672 AATTACTAAAATAGCACC
1 AATTACTAAAATAGCACC
77690 CGGTCAACGA
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
28 2 0.03
29 67 0.94
30 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (29 bp):
AATTACTAAAATAGCACCTATTTCGAATT
Found at i:83422 original size:17 final size:19
Alignment explanation
Indices: 83389--83427 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
83379 TTTAACAACT
83389 TATAGAACATTAAATA-TAA
1 TATAGAACA-TAAATATTAA
83408 TATAGAACA-AAATATTAA
1 TATAGAACATAAATATTAA
83426 TA
1 TA
83428 ATACAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
TATAGAACATAAATATTAA
Found at i:84759 original size:58 final size:58
Alignment explanation
Indices: 84677--84803 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
84667 GAATTTACAG
* * * *
84677 AAATAGCACACTTTTTAAAATAATTACTAAAATAGCACATATTTCGAATTAATTATTA
1 AAATAGCACCCATTTCAAAATAATTACTAAAATAGCACATATTTCGAATTAATTACTA
* * * *
84735 AAATAGCACCCATTTCAAATTAATTACTAAAATTGCACCTATTTTGAATTAATTACTA
1 AAATAGCACCCATTTCAAAATAATTACTAAAATAGCACATATTTCGAATTAATTACTA
84793 AAATAGCACCC
1 AAATAGCACCC
84804 GGTCAAAGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.34
Consensus pattern (58 bp):
AAATAGCACCCATTTCAAAATAATTACTAAAATAGCACATATTTCGAATTAATTACTA
Found at i:84802 original size:29 final size:29
Alignment explanation
Indices: 84677--84802 Score: 155
Period size: 29 Copynumber: 4.3 Consensus size: 29
84667 GAATTTACAG
* *
84677 AAATAGCACACT-TTTTAAAATAATTACTA
1 AAATAGCAC-CTATTTCAAATTAATTACTA
* * *
84706 AAATAGCACATATTTCGAATTAATTATTA
1 AAATAGCACCTATTTCAAATTAATTACTA
*
84735 AAATAGCACCCATTTCAAATTAATTACTA
1 AAATAGCACCTATTTCAAATTAATTACTA
* **
84764 AAATTGCACCTATTTTGAATTAATTACTA
1 AAATAGCACCTATTTCAAATTAATTACTA
84793 AAATAGCACC
1 AAATAGCACC
84803 CGGTCAAAGG
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 1 0.01
29 81 0.99
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (29 bp):
AAATAGCACCTATTTCAAATTAATTACTA
Found at i:87209 original size:2 final size:2
Alignment explanation
Indices: 87158--87189 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
87148 TTTTTAACTT
87158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87190 AAAACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:89669 original size:21 final size:21
Alignment explanation
Indices: 89643--89714 Score: 144
Period size: 21 Copynumber: 3.4 Consensus size: 21
89633 TAATGCATGT
89643 AGTATCGATACTCCAAGCCTG
1 AGTATCGATACTCCAAGCCTG
89664 AGTATCGATACTCCAAGCCTG
1 AGTATCGATACTCCAAGCCTG
89685 AGTATCGATACTCCAAGCCTG
1 AGTATCGATACTCCAAGCCTG
89706 AGTATCGAT
1 AGTATCGAT
89715 GCAACATTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (21 bp):
AGTATCGATACTCCAAGCCTG
Found at i:94707 original size:18 final size:18
Alignment explanation
Indices: 94681--94715 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
94671 TCGAAAGGAC
*
94681 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
94699 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
94716 CCAGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:104002 original size:16 final size:17
Alignment explanation
Indices: 103981--104012 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
103971 ATTGTCCTAA
103981 TAGAGAAAA-TTAAAGT
1 TAGAGAAAATTTAAAGT
103997 TAGAGAAAATTTAAAG
1 TAGAGAAAATTTAAAG
104013 AAAATATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (17 bp):
TAGAGAAAATTTAAAGT
Found at i:104185 original size:2 final size:2
Alignment explanation
Indices: 104178--104211 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
104168 AAATACTAGA
104178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104212 GTACGAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112414 original size:15 final size:15
Alignment explanation
Indices: 112390--112421 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
112380 TCTTTCATTT
*
112390 ATATTTATTTTCATA
1 ATATTGATTTTCATA
112405 ATATTGATTTTCATA
1 ATATTGATTTTCATA
112420 AT
1 AT
112422 CTTAATCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (15 bp):
ATATTGATTTTCATA
Found at i:117894 original size:32 final size:32
Alignment explanation
Indices: 117853--117931 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
117843 TTATAAATTT
117853 TGCATTCAGATAATGAACAACAAAGTCAGTGC
1 TGCATTCAGATAATGAACAACAAAGTCAGTGC
* * ** *
117885 TGCATTCAGATAATGCACAGCAGTGTCAGTGT
1 TGCATTCAGATAATGAACAACAAAGTCAGTGC
117917 TGCAATT-AGATAATG
1 TGC-ATTCAGATAATG
117932 TGTAGTAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 38 0.93
33 3 0.07
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (32 bp):
TGCATTCAGATAATGAACAACAAAGTCAGTGC
Found at i:119766 original size:16 final size:16
Alignment explanation
Indices: 119731--119767 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
119721 AATTTGAAAG
*
119731 AAAAAAGGAAAAAATC
1 AAAAAAGGAAAAAACC
119747 AAAAAAGG-AAAAACC
1 AAAAAAGGAAAAAACC
119762 AAAAAA
1 AAAAAA
119768 CCTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.78, C:0.08, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAAAAGGAAAAAACC
Found at i:122930 original size:19 final size:19
Alignment explanation
Indices: 122883--122932 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
122873 ATGACATCTT
*
122883 TAATGAATCACACAAACATA
1 TAATGAA-CAGACAAACATA
*
122903 CACAT-AACAGACAAACATA
1 TA-ATGAACAGACAAACATA
122922 TAATGAACAGA
1 TAATGAACAGA
122933 TTTGTAGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.08
19 18 0.72
20 3 0.12
21 2 0.08
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (19 bp):
TAATGAACAGACAAACATA
Found at i:125435 original size:18 final size:20
Alignment explanation
Indices: 125369--125468 Score: 65
Period size: 19 Copynumber: 5.3 Consensus size: 20
125359 TAGATATTAC
* *
125369 ATTTATTT-AATATTTTCACT
1 ATTTATTTAAATA-TTTAAAT
*
125389 A-TTATTTAATTATTTAAAT
1 ATTTATTTAAATATTTAAAT
125408 CA-TT-TTTAAATATTT-AAT
1 -ATTTATTTAAATATTTAAAT
*
125426 -TTTATTTAAA-ATTTTATAT
1 ATTTATTTAAATA-TTTAAAT
125445 ATTTA-TTAAAT-TTTAAAT
1 ATTTATTTAAATATTTAAAT
*
125463 TTTTAT
1 ATTTAT
125469 ACTTTTCTTG
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
17 3 0.05
18 22 0.34
19 28 0.44
20 11 0.17
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATTTAAATATTTAAAT
Done.