Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013016.1 Corchorus capsularis cultivar CVL-1 contig13037, 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: 123481
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:894 original size:8 final size:7
Alignment explanation
Indices: 870--903 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
860 AAGAAAGATA
*
870 TAAACAG
1 TAAAAAG
877 TAAAAAG
1 TAAAAAG
884 TAAAAAGG
1 TAAAAA-G
892 TAAAAAG
1 TAAAAAG
899 TAAAA
1 TAAAA
904 GGTATCTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.68, C:0.03, G:0.15, T:0.15
Consensus pattern (7 bp):
TAAAAAG
Found at i:896 original size:15 final size:14
Alignment explanation
Indices: 876--907 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
866 GATATAAACA
876 GTAAAAAGTAAAAAG
1 GTAAAAAGT-AAAAG
891 GTAAAAAGTAAAAG
1 GTAAAAAGTAAAAG
905 GTA
1 GTA
908 TCTGTTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (14 bp):
GTAAAAAGTAAAAG
Found at i:965 original size:21 final size:22
Alignment explanation
Indices: 891--979 Score: 94
Period size: 22 Copynumber: 4.2 Consensus size: 22
881 AAGTAAAAAG
* *
891 GTAAAAAGTAAAA-GGT-ATCT
1 GTAAAGAGTAAAATGGTAATCA
* * *
911 GTTAAGGGTAAAATGGTAATTA
1 GTAAAGAGTAAAATGGTAATCA
*
933 GAAAAGAGTAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
955 GTAAA-AGTAAAAGGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
976 GTAA
1 GTAA
980 TCAGGTTCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 10 0.18
21 22 0.39
22 24 0.43
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:1020 original size:14 final size:14
Alignment explanation
Indices: 998--1040 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
988 AAAAGTTATG
* *
998 GTAATCAGTAAGAA
1 GTAAACAGTAAAAA
1012 GTAAACAGTAAAAA
1 GTAAACAGTAAAAA
*
1026 GTAAAAAGGTAAAAA
1 GTAAACA-GTAAAAA
1041 AAGTAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.16
Consensus pattern (14 bp):
GTAAACAGTAAAAA
Found at i:1048 original size:16 final size:17
Alignment explanation
Indices: 1021--1052 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1011 AGTAAACAGT
1021 AAAAAGTAAAAAGGTAA
1 AAAAAGTAAAAAGGTAA
1038 AAAAAGT-AAAAGGTA
1 AAAAAGTAAAAAGGTA
1053 TATGTTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (17 bp):
AAAAAGTAAAAAGGTAA
Found at i:1088 original size:22 final size:21
Alignment explanation
Indices: 1058--1163 Score: 94
Period size: 22 Copynumber: 5.1 Consensus size: 21
1048 AGGTATATGT
* *
1058 TAAGGGTAAAATGGTAATTAG
1 TAAGAGTAAAATGGTAATCAG
1079 TAAAGAGTAAAATGGTAATCAG
1 T-AAGAGTAAAATGGTAATCAG
* *
1101 TAAGAGTAAAATAGTAATCAA
1 TAAGAGTAAAATGGTAATCAG
**
1122 T-A-A--AAAATAATAATCAG
1 TAAGAGTAAAATGGTAATCAG
* *
1139 TAAAGAGTAAAATGATAGTCAG
1 T-AAGAGTAAAATGGTAATCAG
1161 TAA
1 TAA
1164 TTAAATTCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
17 13 0.18
19 2 0.03
20 2 0.03
21 22 0.31
22 32 0.45
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (21 bp):
TAAGAGTAAAATGGTAATCAG
Found at i:1130 original size:17 final size:17
Alignment explanation
Indices: 1108--1142 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1098 CAGTAAGAGT
*
1108 AAAATAGTAATCAATAA
1 AAAATAATAATCAATAA
*
1125 AAAATAATAATCAGTAA
1 AAAATAATAATCAATAA
1142 A
1 A
1143 GAGTAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (17 bp):
AAAATAATAATCAATAA
Found at i:1247 original size:39 final size:37
Alignment explanation
Indices: 1172--1255 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 37
1162 AATTAAATTC
* *
1172 AAAGAGT-AAAATGGTAGTCAGTAAAAGAGAAAAAGA
1 AAAGAGTAAAAATGGTAATCAGTAAAAAAGAAAAAGA
* **
1208 AGAAGTGTAAAAAGTGGTAATCAGTAAAAAAGAGTAAGA
1 A-AAGAGTAAAAA-TGGTAATCAGTAAAAAAGAAAAAGA
1247 AAAGAGTAA
1 AAAGAGTAA
1256 TCAGTAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 1 0.03
37 5 0.13
38 11 0.28
39 22 0.56
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.15
Consensus pattern (37 bp):
AAAGAGTAAAAATGGTAATCAGTAAAAAAGAAAAAGA
Found at i:1264 original size:27 final size:28
Alignment explanation
Indices: 1224--1282 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
1214 GTAAAAAGTG
1224 GTAATCAGTAAAAAAGAGTAAGAAAAGA
1 GTAATCAGTAAAAAAGAGTAAGAAAAGA
*
1252 GTAATCAGT-AAAAAGAGTAAGAAATGA
1 GTAATCAGTAAAAAAGAGTAAGAAAAGA
1279 GTAA
1 GTAA
1283 AAAAACGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.17
Consensus pattern (28 bp):
GTAATCAGTAAAAAAGAGTAAGAAAAGA
Found at i:1282 original size:38 final size:37
Alignment explanation
Indices: 1230--1303 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
1220 AGTGGTAATC
*
1230 AGTAAAAAAGAGTAAGAAAA-GAGTAATCAGTAAAAAG
1 AGTAAAAAAGAGTAAAAAAACG-GTAATCAGTAAAAAG
* *
1267 AGTAAGAAATGAGTAAAAAAACGGTGATCAGTAAAAA
1 AGTAA-AAAAGAGTAAAAAAACGGTAATCAGTAAAAA
1304 AGGGTGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 5 0.16
38 26 0.81
39 1 0.03
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.15
Consensus pattern (37 bp):
AGTAAAAAAGAGTAAAAAAACGGTAATCAGTAAAAAG
Found at i:1359 original size:27 final size:26
Alignment explanation
Indices: 1283--1548 Score: 146
Period size: 27 Copynumber: 9.7 Consensus size: 26
1273 AAATGAGTAA
* * *
1283 AAAAACGGTGATCAGTAAAAAAGGGT
1 AAAAATGGTAATCAGTAAAAAAGAGT
* *
1309 GAAAGA-GAGTAATTAG-AAATAAAGAGT
1 -AAAAATG-GTAATCAGTAAA-AAAGAGT
*
1336 AAGAAATGGTGATCAGTAAAAAAGAGT
1 AA-AAATGGTAATCAGTAAAAAAGAGT
* * *
1363 AAAAAGTGGTATTCAGTAAAAAGGGGT
1 AAAAA-TGGTAATCAGTAAAAAAGAGT
* **
1390 AAAAATAGTAAAAAGGAGTAAAAAAGGAGAGT
1 AAAAATGGT---AATCAGT-AAAAA--AGAGT
*
1422 AAAAAATGGTAATTAAGT-AAAAAGAGT
1 -AAAAATGGTAA-TCAGTAAAAAAGAGT
* *
1449 AAAAAGTGGTATTCAGTAAAGACAGTAAG-
1 AAAAA-TGGTAATCAGTAAA-AAAG--AGT
** *
1478 AAAAGGGGTCATCAGTAAAAAAGAGT
1 AAAAATGGTAATCAGTAAAAAAGAGT
*
1504 AAAATATGGTAATCAGT-ACAAAGAGT
1 AAAA-ATGGTAATCAGTAAAAAAGAGT
*
1530 AAAAAATGGTAATTAGTAA
1 -AAAAATGGTAATCAGTAA
1549 TCAAGAAATA
Statistics
Matches: 183, Mismatches: 33, Indels: 46
0.70 0.13 0.18
Matches are distributed among these distances:
25 2 0.01
26 44 0.24
27 84 0.46
28 18 0.10
29 12 0.07
30 9 0.05
31 3 0.02
32 3 0.02
33 8 0.04
ACGTcount: A:0.53, C:0.04, G:0.24, T:0.19
Consensus pattern (26 bp):
AAAAATGGTAATCAGTAAAAAAGAGT
Found at i:1400 original size:9 final size:10
Alignment explanation
Indices: 1377--1418 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1367 AGTGGTATTC
1377 AGTAAAAAGG
1 AGTAAAAAGG
* *
1387 GGTAAAAA-T
1 AGTAAAAAGG
1396 AGTAAAAAGG
1 AGTAAAAAGG
1406 AGTAAAAAAGG
1 AGT-AAAAAGG
1417 AG
1 AG
1419 AGTAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 7 0.27
10 10 0.38
11 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.12
Consensus pattern (10 bp):
AGTAAAAAGG
Found at i:1401 original size:19 final size:19
Alignment explanation
Indices: 1377--1413 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1367 AGTGGTATTC
*
1377 AGTAAAAAGGGGTAAAAAT
1 AGTAAAAAGGAGTAAAAAT
1396 AGTAAAAAGGAGTAAAAA
1 AGTAAAAAGGAGTAAAAA
1414 AGGAGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (19 bp):
AGTAAAAAGGAGTAAAAAT
Found at i:1452 original size:26 final size:27
Alignment explanation
Indices: 1417--1548 Score: 137
Period size: 26 Copynumber: 4.9 Consensus size: 27
1407 GTAAAAAAGG
*
1417 AGAGTAAAAAATGGTAATTAAGTAAAA
1 AGAGTAAAAAATGGTAATTCAGTAAAA
* *
1444 AGAGTAAAAAGTGGT-ATTCAGTAAAG
1 AGAGTAAAAAATGGTAATTCAGTAAAA
* * *
1470 ACAGTAAGAAAAGGGGTCA-TCAGTAAAAA
1 AGAGTAA-AAAA-TGGTAATTCAGT-AAAA
* *
1499 AGAGTAAAATATGGTAA-TCAGTACAA
1 AGAGTAAAAAATGGTAATTCAGTAAAA
1525 AGAGTAAAAAATGGTAATT-AGTAA
1 AGAGTAAAAAATGGTAATTCAGTAA
1549 TCAAGAAATA
Statistics
Matches: 86, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
26 38 0.44
27 27 0.31
28 11 0.13
29 10 0.12
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.21
Consensus pattern (27 bp):
AGAGTAAAAAATGGTAATTCAGTAAAA
Found at i:4890 original size:12 final size:12
Alignment explanation
Indices: 4873--4900 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4863 TTCGGGCAAT
4873 TCGTGTTTCGTG
1 TCGTGTTTCGTG
4885 TCGTGTTTCGTG
1 TCGTGTTTCGTG
4897 TCGT
1 TCGT
4901 ATAAACGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:15332 original size:6 final size:6
Alignment explanation
Indices: 15280--15332 Score: 74
Period size: 6 Copynumber: 9.0 Consensus size: 6
15270 TTTATACAAA
*
15280 AAAAAC AAAAAA AAAAAC -AAAAC -AAAAC AAAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC -AAAAAC AAAAAC AAAAAC
15327 AAAAAC
1 AAAAAC
15333 GGAGGGTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 10 0.23
6 28 0.65
7 5 0.12
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:33049 original size:32 final size:32
Alignment explanation
Indices: 32973--33068 Score: 149
Period size: 32 Copynumber: 3.0 Consensus size: 32
32963 CCAAGAGGGC
*
32973 GGCTTACCGTGGCGAAGCCGCCCCACTGGGGA
1 GGCTTACCGTGGTGAAGCCGCCCCACTGGGGA
33005 GGCTTACCGTGGTGAAGCCGCCCCACTGGGGA
1 GGCTTACCGTGGTGAAGCCGCCCCACTGGGGA
* *
33037 GGCTTACCGTGGTTG-AGCCTCCCCAGTGGGGA
1 GGCTTACCGTGG-TGAAGCCGCCCCACTGGGGA
33069 CTCCGCCGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 58 0.97
33 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.17
Consensus pattern (32 bp):
GGCTTACCGTGGTGAAGCCGCCCCACTGGGGA
Found at i:38476 original size:1 final size:1
Alignment explanation
Indices: 38470--38500 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
38460 CCAGAATATT
38470 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38501 CAGATATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:42098 original size:22 final size:22
Alignment explanation
Indices: 42073--42240 Score: 101
Period size: 22 Copynumber: 7.7 Consensus size: 22
42063 ATTCCATTAC
42073 GAAATTTTGATAACCTTCCTAT
1 GAAATTTTGATAACCTTCCTAT
* ** *
42095 GAAATTTTAATAACGATACTAT
1 GAAATTTTGATAACCTTCCTAT
* * * * **
42117 GGAATTTCGAAAATCTTTTTAT
1 GAAATTTTGATAACCTTCCTAT
* ** *
42139 -AATTTTTTTTAACCTTCTTAT
1 GAAATTTTGATAACCTTCCTAT
* *
42160 GAAATTTTGTTAACC-TCTCTAA
1 GAAATTTTGATAACCTTC-CTAT
* *
42182 GGAATTTTGA-AGACC-TCAATAT
1 GAAATTTTGATA-ACCTTC-CTAT
* *
42204 GAAATTTTGATAACTTTCCAAT
1 GAAATTTTGATAACCTTCCTAT
42226 GAAATTTTGATAACC
1 GAAATTTTGATAACC
42241 AACACTATGA
Statistics
Matches: 106, Mismatches: 35, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
21 16 0.15
22 87 0.82
23 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
GAAATTTTGATAACCTTCCTAT
Found at i:42506 original size:13 final size:13
Alignment explanation
Indices: 42470--42508 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
42460 TCTAAATTGA
42470 AATTTT-ATAATT
1 AATTTTAATAATT
42482 AATTTTTAAATAATT
1 AA-TTTT-AATAATT
42497 AATTTTAATAAT
1 AATTTTAATAAT
42509 GTCAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 4 0.17
15 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTAATAATT
Found at i:42516 original size:15 final size:14
Alignment explanation
Indices: 42476--42508 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
42466 TTGAAATTTT
42476 ATAATTAATTTTTAA
1 ATAATTAA-TTTTAA
42491 ATAATTAATTTT-A
1 ATAATTAATTTTAA
42504 ATAAT
1 ATAAT
42509 GTCAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTAATTTTAA
Found at i:44059 original size:31 final size:31
Alignment explanation
Indices: 44023--44088 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
44013 TGACAATTTA
* * *
44023 GAAATATGTTTTAAAAAAAAGGGTACAATTG
1 GAAATATATTTTAAAAAAAAGGATACAATCG
*
44054 GAAATATATTTTAAAAATAAGGATACAATCG
1 GAAATATATTTTAAAAAAAAGGATACAATCG
44085 GAAA
1 GAAA
44089 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.27
Consensus pattern (31 bp):
GAAATATATTTTAAAAAAAAGGATACAATCG
Found at i:45418 original size:166 final size:165
Alignment explanation
Indices: 45142--45617 Score: 535
Period size: 166 Copynumber: 2.9 Consensus size: 165
45132 GAAAATTACT
** * ** * * * *
45142 AAAAGATCCCCACCCCGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTTTCAC-ACAT
1 AAAAGATCCCCACCAAGGATTGATGTTGAGCTAGAAAACTAATTTTTTTCGTCTTTAC-CTACTT
* * * ** *
45206 GATC-GATTACCTAAATGCCCTAACTTTTGATTCTTGAGATGATTAAAAAACTAGACTTTTTGGT
65 G-GCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACTTTTTGGT
* * * *
45270 CATTTCTCAATTGATTTTAATGGAGTAGTGCAATTACC
128 CATTTCTCAATTGACTTGAATAGAGTAGTGCAATTAAC
* * * * * * *
45308 AAAAGATCTCTACCAAGGCTTGATTTTGGAGTTAGAAAACT-TTTTTTTTCGTCTTTTCCTACTT
1 AAAAGATCCCCACCAAGGATTGATGTT-GAGCTAGAAAACTAATTTTTTTCGTCTTTACCTACTT
* * *
45372 GGCAGATTATTTAAATGTCATAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTTGGTC
65 GGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTTTTTGGTC
* * *
45437 ATTTCTCAATGGACTTGAATAGAGTAGTGGAATTAAT
129 ATTTCTCAATTGACTTGAATAGAGTAGTGCAATTAAC
* *
45474 AAAAGATCCCCATCAAGGATTGATGTTGAGCTAGAGAACTAATTTTTTTCGTCTTTACCTACTTG
1 AAAAGATCCCCACCAAGGATTGATGTTGAGCTAGAAAACTAATTTTTTTCGTCTTTACCTACTTG
* * *
45539 GCAGATTACTTAAATGTCCTAATTTTTTTATTTTTGAGGGGATTAAATAACTAAACTTTTTGGTC
66 GCAGATTACTTAAATGTCCTAA-CTTTTGATTCTTGAGGGGATTAAATAACT-AACTTTTTGGTC
45604 ATTTCTCAATTGAC
129 ATTTCTCAATTGAC
45618 AAATGATTAA
Statistics
Matches: 257, Mismatches: 46, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
165 14 0.05
166 183 0.71
167 58 0.23
168 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (165 bp):
AAAAGATCCCCACCAAGGATTGATGTTGAGCTAGAAAACTAATTTTTTTCGTCTTTACCTACTTG
GCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTTTGGTCAT
TTCTCAATTGACTTGAATAGAGTAGTGCAATTAAC
Found at i:45712 original size:14 final size:12
Alignment explanation
Indices: 45691--45723 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
45681 AAGAATTAGT
45691 TTATATAT-TTA
1 TTATATATATTA
45702 TTATCATATATTA
1 TTAT-ATATATTA
45715 TTATATATA
1 TTATATATA
45724 AATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATATATATTA
Found at i:51253 original size:31 final size:31
Alignment explanation
Indices: 51217--51278 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
51207 TCCAATTTTG
51217 ATTTTGTTTCAAAAAATGTTTGAGTGTAGTA
1 ATTTTGTTTCAAAAAATGTTTGAGTGTAGTA
51248 ATTTTGTTTCAAAAAATGTTTGAGTGTAGTA
1 ATTTTGTTTCAAAAAATGTTTGAGTGTAGTA
51279 GAGGTGATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (31 bp):
ATTTTGTTTCAAAAAATGTTTGAGTGTAGTA
Found at i:66365 original size:6 final size:6
Alignment explanation
Indices: 66354--66381 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
66344 TGGAGAAGAT
66354 CATGGG CATGGG CATGGG CATGGG CATG
1 CATGGG CATGGG CATGGG CATGGG CATG
66382 AAGTTTTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.46, T:0.18
Consensus pattern (6 bp):
CATGGG
Found at i:66889 original size:2 final size:2
Alignment explanation
Indices: 66882--66912 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
66872 TACTATGGTG
*
66882 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66913 GGATCACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:67082 original size:13 final size:13
Alignment explanation
Indices: 67064--67089 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67054 TACTTCATAA
67064 AATACGAAAAGAT
1 AATACGAAAAGAT
67077 AATACGAAAAGAT
1 AATACGAAAAGAT
67090 TATTGAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (13 bp):
AATACGAAAAGAT
Found at i:78828 original size:27 final size:27
Alignment explanation
Indices: 78788--78843 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
78778 TGAACCTACA
* * *
78788 ATTATATAGGTTTACGTTGTTAATTAT
1 ATTATACAGATTTACATTGTTAATTAT
78815 ATTATACAGATTTACATTGTTAATTAT
1 ATTATACAGATTTACATTGTTAATTAT
78842 AT
1 AT
78844 AGGTGCCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (27 bp):
ATTATACAGATTTACATTGTTAATTAT
Found at i:82381 original size:17 final size:18
Alignment explanation
Indices: 82349--82384 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
82339 TTTTCTCTCT
82349 CTTTTTTTTACTTTCTTC
1 CTTTTTTTTACTTTCTTC
*
82367 CTTTTTTTTTC-TTCTTC
1 CTTTTTTTTACTTTCTTC
82384 C
1 C
82385 CTAACTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTTTTACTTTCTTC
Found at i:86002 original size:21 final size:21
Alignment explanation
Indices: 85976--86017 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
85966 GATATTTTGA
85976 ATTGAAATGAACAATAACCTT
1 ATTGAAATGAACAATAACCTT
85997 ATTGAAATGAACAATAACCTT
1 ATTGAAATGAACAATAACCTT
86018 CTTGTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
ATTGAAATGAACAATAACCTT
Found at i:91315 original size:28 final size:31
Alignment explanation
Indices: 91255--91316 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
91245 TCATTTTGTC
**
91255 AAAATTCAAGGGTTAATATTTTTTGGTACAT
1 AAAATTCAAGGGTTAATATAATTTGGTACAT
*
91286 AAAATTCAAGGGTT-AT-TAATTT-GTCCAT
1 AAAATTCAAGGGTTAATATAATTTGGTACAT
91314 AAA
1 AAA
91317 GTTAGTCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.29
29 4 0.14
30 2 0.07
31 14 0.50
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39
Consensus pattern (31 bp):
AAAATTCAAGGGTTAATATAATTTGGTACAT
Found at i:91490 original size:2 final size:2
Alignment explanation
Indices: 91483--91510 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
91473 TAGCTGTTAG
91483 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
91511 CTCCTTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:97250 original size:21 final size:22
Alignment explanation
Indices: 97226--97268 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
97216 TTATTTTCTG
*
97226 TTAGCAAATTACTTAAC-CCTT
1 TTAGAAAATTACTTAACACCTT
97247 TTAGAAAATTACTTAACACCTT
1 TTAGAAAATTACTTAACACCTT
97269 AATTTTACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (22 bp):
TTAGAAAATTACTTAACACCTT
Found at i:101812 original size:23 final size:23
Alignment explanation
Indices: 101769--101812 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
101759 AGGAGTTTGA
* *
101769 AGGGGTGAGAGTGTGTTTGGTTG
1 AGGGGTGAGAGTGGGTGTGGTTG
101792 AGGGGTAGAGAG-GGGTGTGGT
1 AGGGGT-GAGAGTGGGTGTGGT
101813 GTAGGAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.16, C:0.00, G:0.57, T:0.27
Consensus pattern (23 bp):
AGGGGTGAGAGTGGGTGTGGTTG
Found at i:107125 original size:35 final size:35
Alignment explanation
Indices: 107083--107660 Score: 773
Period size: 35 Copynumber: 16.3 Consensus size: 35
107073 TATAATTAAT
* *
107083 GGGTAATTAAGTAATTCAGTAATTAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
*
107118 GGATAATTAAGTGAA-TCAGTAATAAGCAACTTAATTCA
1 GGGTAATTAAGT-AAGTCAGTAAT---CAACTTAATTCA
* * *
107156 GGGTAATTAAGTAATTTAGTAATTAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
*
107191 GGGTAATTAAGTGAGTCAGTAATCAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
* * * *
107226 GGATAATTAAGTAATTCGGTAATTAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
* *
107261 GAGTAATTAAGTGAA-TCAGTAATAAGCAACTTAATTTA
1 GGGTAATTAAGT-AAGTCAGTAAT---CAACTTAATTCA
* *
107299 GGGTAATTAAGTAATTCAGTAATTAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
* *
107334 GGTTAATTAAGTGAGTCAGTAATCAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
* *
107369 GGGTGATTAAGTAAGTCAGTAATAAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
*
107404 GGGTAATTAAGTGAGTCAGTAATCAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
* *
107439 GGGTGATTAAGTAAGTCAGTAATAAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
*
107474 GGGTAATTAAGTAAGTCATTAATCAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
* *
107509 GGGTAATTAAGTGAGTCAGTAATTAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
* *
107544 GGGTGATTAAGTAAGTCAGTAATAAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
*
107579 GGGTAATTAAGTAAGTCATTAATCAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
* * * * *
107614 GGATAATTAAGTGAGTCAATAGTTAACTTAATTCA
1 GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
107649 GGGTAATTAAGT
1 GGGTAATTAAGT
107661 TTAGCAAGAA
Statistics
Matches: 479, Mismatches: 54, Indels: 20
0.87 0.10 0.04
Matches are distributed among these distances:
35 413 0.86
36 4 0.01
37 4 0.01
38 58 0.12
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (35 bp):
GGGTAATTAAGTAAGTCAGTAATCAACTTAATTCA
Found at i:110912 original size:9 final size:9
Alignment explanation
Indices: 110898--110936 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
110888 TTAGTTTCTT
*
110898 TTAATTTAA
1 TTAATTAAA
110907 TTAATTAAA
1 TTAATTAAA
**
110916 TTAAAGAAA
1 TTAATTAAA
110925 TTAATTAAA
1 TTAATTAAA
110934 TTA
1 TTA
110937 TATTGAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Done.