Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008713.1 Corchorus capsularis cultivar CVL-1 contig08734, 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: 19626
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Found at i:503 original size:37 final size:37
Alignment explanation
Indices: 435--790 Score: 206
Period size: 37 Copynumber: 9.4 Consensus size: 37
425 TACCCCAATA
* *
435 AATTAAGAGTC-AAATAATAGTAACCAATAATTAAGT
1 AATTAAGAGTCAAAATAATAGTAATCAGTAATTAAGT
* *
471 AATTAAGAGTCAAAATGATAGTAACCAGTAATTAAGT
1 AATTAAGAGTCAAAATAATAGTAATCAGTAATTAAGT
* *
508 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGA-T
1 AATTAAGAGTCAAAATAATAGTAATCAGT--AATTAAGT
* * *
546 AATTAAGAGTCAAAAAGAAATAGTAATCAGTAAAT-CGAT
1 AATTAAGAGTC-AAAA-TAATAGTAATCAGTAATTAAG-T
** * *
585 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGT
1 AATTAAGAGTCAAAATAATAGTAATCAGTAATTAAGT
* * * *
622 AATT-A-AG-CAAAAAAAGAGATTAACCAGTAAAATTGA-T
1 AATTAAGAGTCAAAATAATAG--TAATCAGT--AATTAAGT
* * * * * *
659 AATTAAGAGTCAAAGTAATAATAGTCGGCAAAATTGA-T
1 AATTAAGAGTCAAAATAATAGTAATCAG--TAATTAAGT
* * * * *
697 AATTAAGGGTCAAGATAAGAGATTAATCAGTAAAGTCAGT
1 AATTAAGAGTCAAAATAATAG--TAATCAGT-AATTAAGT
* * *
737 AATTAAAGAGTCAAGGTAAAAATAGTAATCAGTAAATCAGT
1 AATT-AAGAGTCAA---AATAATAGTAATCAGTAATTAAGT
*
778 AATTAAGAATCAA
1 AATTAAGAGTCAA
791 GGGATTAATC
Statistics
Matches: 250, Mismatches: 45, Indels: 46
0.73 0.13 0.13
Matches are distributed among these distances:
34 7 0.03
35 2 0.01
36 19 0.08
37 76 0.30
38 50 0.20
39 26 0.10
40 38 0.15
41 19 0.08
42 8 0.03
44 5 0.02
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.26
Consensus pattern (37 bp):
AATTAAGAGTCAAAATAATAGTAATCAGTAATTAAGT
Found at i:623 original size:151 final size:151
Alignment explanation
Indices: 435--790 Score: 411
Period size: 151 Copynumber: 2.3 Consensus size: 151
425 TACCCCAATA
* * * * * * *
435 AATTAAGAGTCAA-ATAATAGTAACCAATAATTAAGTAATTAAGAGTCAAAATGATAGTAACCAG
1 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGA-TCAAAAAGAGAGTAACCAG
* *
499 T-AATTAAGTAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAA-A-A
65 TAAATTAA-TAATTAAGAGTCAAAGTAATAATAATCAGCAAAATTGATAATTAAGAGTCAAGATA
561 AGAAATAGTAATCAGTAAA-TC-GAT
129 AGAAAT--TAATCAGTAAAGTCAG-T
* *
585 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGCA-AAAAAAGAGATTAACCAG
1 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAG-ATCAAAAAGAGAGTAACCAG
* * * *
649 TAAAATTGATAATTAAGAGTCAAAGTAATAATAGTCGGCAAAATTGATAATTAAGGGTCAAGATA
65 T-AAATTAATAATTAAGAGTCAAAGTAATAATAATCAGCAAAATTGATAATTAAGAGTCAAGATA
*
714 AGAGATTAATCAGTAAAGTCAGT
129 AGAAATTAATCAGTAAAGTCAGT
737 AATTAAAGAGTCAAGGTAAAAATAGTAATCAGTAAATCAGTAATTAAGAATCAA
1 AATT-AAGAGTCAAGGT---AATAGTAATCAGTAAATCAGTAATTAAG-ATCAA
791 GGGATTAATC
Statistics
Matches: 175, Mismatches: 18, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
150 28 0.16
151 83 0.47
152 14 0.08
153 19 0.11
156 29 0.17
157 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.26
Consensus pattern (151 bp):
AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGATCAAAAAGAGAGTAACCAGT
AAATTAATAATTAAGAGTCAAAGTAATAATAATCAGCAAAATTGATAATTAAGAGTCAAGATAAG
AAATTAATCAGTAAAGTCAGT
Found at i:984 original size:18 final size:18
Alignment explanation
Indices: 961--1001 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
951 GTATTAAGTT
961 TGGTAAAAAGAGTA-AAAA
1 TGGTAAAAAGAG-ACAAAA
979 TGGTAAAAAGAGACAAAA
1 TGGTAAAAAGAGACAAAA
997 TGGTA
1 TGGTA
1002 TCATAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.56, C:0.02, G:0.24, T:0.17
Consensus pattern (18 bp):
TGGTAAAAAGAGACAAAA
Found at i:1057 original size:28 final size:27
Alignment explanation
Indices: 1026--1099 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 27
1016 GTAAAAAGGA
1026 TATTAAGAGTAAAAAAAATGGTATTAAG
1 TATTAAGAGT-AAAAAAATGGTATTAAG
1054 TATTAAGAGT--AAAAATGGTATTAAG
1 TATTAAGAGTAAAAAAATGGTATTAAG
1079 TA--AAGAGTAAGAAAAATGGTA
1 TATTAAGAGTAA-AAAAATGGTA
1100 ATTAGCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.14
25 17 0.40
26 10 0.23
28 10 0.23
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (27 bp):
TATTAAGAGTAAAAAAATGGTATTAAG
Found at i:1088 original size:23 final size:24
Alignment explanation
Indices: 993--1088 Score: 87
Period size: 25 Copynumber: 4.0 Consensus size: 24
983 AAAAAGAGAC
* *
993 AAAATGGTATCATAGTAAAAAGAGTA
1 AAAATGGTATTA-AGT-ATAAGAGTA
1019 AAAA-GGATATTAAG-AGTAA-A--A
1 AAAATGG-TATTAAGTA-TAAGAGTA
1040 AAAATGGTATTAAGTATTAAGAGTA
1 AAAATGGTATTAAGTA-TAAGAGTA
1065 AAAATGGTATTAAGTA-AAGAGTA
1 AAAATGGTATTAAGTATAAGAGTA
1088 A
1 A
1089 GAAAAATGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
21 12 0.20
22 6 0.10
23 11 0.18
24 2 0.03
25 21 0.35
26 8 0.13
ACGTcount: A:0.54, C:0.01, G:0.20, T:0.25
Consensus pattern (24 bp):
AAAATGGTATTAAGTATAAGAGTA
Found at i:2031 original size:15 final size:15
Alignment explanation
Indices: 2011--2045 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2001 AGGGTGTGTG
*
2011 TTTTATTTTTTTATT
1 TTTTATTTATTTATT
*
2026 TTTTATTTATTTGTT
1 TTTTATTTATTTATT
2041 TTTTA
1 TTTTA
2046 AAAGGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTATTTATTTATT
Found at i:4269 original size:2 final size:2
Alignment explanation
Indices: 4262--4300 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4252 ACGTGACGCC
4262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4301 CTCATTAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5961 original size:18 final size:17
Alignment explanation
Indices: 5930--5970 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
5920 TAGTAGGCAA
*
5930 GAATAAAAGTATGCAGG
1 GAATAAAAGAATGCAGG
5947 GAATCAAAAGAATGCAGG
1 GAAT-AAAAGAATGCAGG
*
5965 GGATAA
1 GAATAA
5971 CTTCATGGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.49, C:0.07, G:0.29, T:0.15
Consensus pattern (17 bp):
GAATAAAAGAATGCAGG
Found at i:9832 original size:20 final size:20
Alignment explanation
Indices: 9796--9834 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9786 AAATACAAGG
*
9796 CATTTGATTTACGAATTGGA
1 CATTTGATTTACAAATTGGA
*
9816 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
9835 TGCTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:10397 original size:2 final size:2
Alignment explanation
Indices: 10390--10415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10380 TTTTGATTTA
10390 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
10416 GAGCATGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10490 original size:12 final size:12
Alignment explanation
Indices: 10473--10500 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10463 TGTATATTTG
10473 TTTTTATTTGTT
1 TTTTTATTTGTT
10485 TTTTTATTTGTT
1 TTTTTATTTGTT
10497 TTTT
1 TTTT
10501 GTTTGTTGTT
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:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTTATTTGTT
Found at i:10498 original size:11 final size:11
Alignment explanation
Indices: 10467--10512 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
10457 AACAATTGTA
10467 TATTTG-TTTT
1 TATTTGTTTTT
10477 TATTTGTTTTTT
1 TATTTG-TTTTT
10489 TATTTGTTTTT
1 TATTTGTTTTT
* *
10500 TGTTTGTTGTT
1 TATTTGTTTTT
10511 TA
1 TA
10513 CTGTTGGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 6 0.19
11 15 0.48
12 10 0.32
ACGTcount: A:0.09, C:0.00, G:0.13, T:0.78
Consensus pattern (11 bp):
TATTTGTTTTT
Found at i:12082 original size:39 final size:38
Alignment explanation
Indices: 11970--12109 Score: 172
Period size: 38 Copynumber: 3.6 Consensus size: 38
11960 GTGAATTAAG
* *
11970 TAATTAAGAGTCAAAGTAAGGATATTCAGTAAAATTGA
1 TAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGA
* * *
12008 TAATTAAGAGTCAAATTAATAGTAATCAGTAAAAATTGA
1 TAATTAAGAGTCAAAGTAAGAATAATCAGT-AAAATTGA
* *
12047 TAATTAATAAGTCAAAGTAAGAACAATCAGTAAAATTGA
1 TAATTAA-GAGTCAAAGTAAGAATAATCAGTAAAATTGA
* * *
12086 TAATCAAGAGTCAAGGTAAAAATA
1 TAATTAAGAGTCAAAGTAAGAATA
12110 GTAATCAATA
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
38 38 0.45
39 29 0.34
40 18 0.21
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27
Consensus pattern (38 bp):
TAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGA
Found at i:12089 original size:78 final size:77
Alignment explanation
Indices: 11932--12100 Score: 209
Period size: 78 Copynumber: 2.2 Consensus size: 77
11922 TACCCCAATA
* * * * *
11932 AATTAAGAGTCAAGATAATAGTAAACCAGTGAATTAAGTAATTAAGAGTCAAAGTAAGGATATTC
1 AATTAAGAGTCAAGATAATAGTAAACCAGTAAATTAAGTAATTAAAAGTCAAAGTAAGAACAATC
11997 AGTAAAATTGAT
66 AGTAAAATTGAT
* *
12009 AATTAAGAGTCAA-ATTAATAGT-AATCAGTAAAAATTGA-TAATTAATAAGTCAAAGTAAGAAC
1 AATTAAGAGTCAAGA-TAATAGTAAACCAGT--AAATTAAGTAATTAA-AAGTCAAAGTAAGAAC
12071 AATCAGTAAAATTGAT
62 AATCAGTAAAATTGAT
*
12087 AATCAAGAGTCAAG
1 AATTAAGAGTCAAG
12101 GTAAAAATAG
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
76 7 0.09
77 27 0.34
78 45 0.57
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (77 bp):
AATTAAGAGTCAAGATAATAGTAAACCAGTAAATTAAGTAATTAAAAGTCAAAGTAAGAACAATC
AGTAAAATTGAT
Found at i:12138 original size:78 final size:75
Alignment explanation
Indices: 11968--12139 Score: 193
Period size: 78 Copynumber: 2.2 Consensus size: 75
11958 CAGTGAATTA
* * * * **
11968 AGTAATTAAGAGTCAAAGTAAGGATATTCAGTAAAATTGATAATTAAGAGTCAAATTAATAGTAA
1 AGTAATTAAGAGTCAAAGTAAGAACAATCAGTAAAATTGATAATCAAGAGTCAAAAAAATAGTAA
12033 TCAGTAAAAAT
66 TCAG-AAAAAT
* *
12044 TGATAATTAATAAGTCAAAGTAAGAACAATCAGTAAAATTGATAATCAAGAGTCAAGGTAAAAAT
1 AG-TAATTAA-GAGTCAAAGTAAGAACAATCAGTAAAATTGATAATCAAGAGTCAA---AAAAAT
*
12109 AGTAATCA-ATAAAT
61 AGTAATCAGAAAAAT
12123 CAGTAATTAAGAGTCAA
1 -AGTAATTAAGAGTCAA
12140 GGGATTAATC
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
76 1 0.01
77 7 0.09
78 46 0.58
79 12 0.15
80 1 0.01
81 12 0.15
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (75 bp):
AGTAATTAAGAGTCAAAGTAAGAACAATCAGTAAAATTGATAATCAAGAGTCAAAAAAATAGTAA
TCAGAAAAAT
Found at i:12168 original size:27 final size:26
Alignment explanation
Indices: 12120--12170 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12110 GTAATCAATA
*
12120 AATCAGTAATTAAGAGTCAAGGGATT
1 AATCAGTAATTAAGACTCAAGGGATT
* *
12146 AATCAGTAAATTAATACTTAAGGGA
1 AATCAGT-AATTAAGACTCAAGGGA
12171 GAGAGTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (26 bp):
AATCAGTAATTAAGACTCAAGGGATT
Found at i:12209 original size:33 final size:33
Alignment explanation
Indices: 12172--12326 Score: 210
Period size: 33 Copynumber: 4.8 Consensus size: 33
12162 CTTAAGGGAG
12172 AGAGTAAAAGAAATAATCAGTAAAAATGGAGTA
1 AGAGTAAAAGAAATAATCAGTAAAAATGGAGTA
12205 AGAGTAAAAGAAGA-AATCAGTAAAAATGGAGTA
1 AGAGTAAAAGAA-ATAATCAGTAAAAATGGAGTA
*
12238 AGAGTAAAAGAAGA-AATCAGTAAAAATGGAGCA
1 AGAGTAAAAGAA-ATAATCAGTAAAAATGGAGTA
* *
12271 AGAGTAAAAGAAGTAATTAGTAAAAA--GAGTA
1 AGAGTAAAAGAAATAATCAGTAAAAATGGAGTA
* * *
12302 AAAGTAAAAGAAGTAATTAGTAAAA
1 AGAGTAAAAGAAATAATCAGTAAAA
12327 GTAAAAGAGC
Statistics
Matches: 115, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
31 28 0.24
33 86 0.75
34 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.17
Consensus pattern (33 bp):
AGAGTAAAAGAAATAATCAGTAAAAATGGAGTA
Found at i:12210 original size:17 final size:17
Alignment explanation
Indices: 12190--12279 Score: 71
Period size: 17 Copynumber: 5.4 Consensus size: 17
12180 AGAAATAATC
*
12190 AGTAAAAATGGAGTAAG
1 AGTAAAAATGGAGAAAG
* *
12207 AGT-AAAA-GAAGAAATC
1 AGTAAAAATGGAGAAA-G
*
12223 AGTAAAAATGGAGTAAG
1 AGTAAAAATGGAGAAAG
* *
12240 AGT-AAAA-GAAGAAATC
1 AGTAAAAATGGAGAAA-G
*
12256 AGTAAAAATGGAGCAAG
1 AGTAAAAATGGAGAAAG
12273 AGTAAAA
1 AGTAAAA
12280 GAAGTAATTA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
15 10 0.18
16 14 0.25
17 21 0.38
18 10 0.18
ACGTcount: A:0.58, C:0.03, G:0.24, T:0.14
Consensus pattern (17 bp):
AGTAAAAATGGAGAAAG
Found at i:12335 original size:36 final size:31
Alignment explanation
Indices: 12174--12362 Score: 146
Period size: 33 Copynumber: 5.8 Consensus size: 31
12164 TAAGGGAGAG
* * * *
12174 AGTAAAAGAAATAATCAGTAAAAATGGAGTAAG
1 AGTAAAAGAAGTAATTAGTAAAAA--GAGCAAA
* * * *
12207 AGTAAAAGAAGAAATCAGTAAAAATGGAGTAAG
1 AGTAAAAGAAGTAATTAGTAAAAA--GAGCAAA
* * *
12240 AGTAAAAGAAGAAATCAGTAAAAATGGAGCAAG
1 AGTAAAAGAAGTAATTAGTAAAAA--GAGCAAA
*
12273 AGTAAAAGAAGTAATTAGTAAAAAGAGTAAA
1 AGTAAAAGAAGTAATTAGTAAAAAGAGCAAA
12304 AGTAAAAGAAGTAATTAGTAAAAGTAAAAGAGCAAA
1 AGTAAAAGAAGTAATTAGT---A--AAAAGAGCAAA
* *
12340 AGTAGAAGAAGTAATCAG-AAAAA
1 AGTAAAAGAAGTAATTAGTAAAAA
12363 TGGTAATCAA
Statistics
Matches: 141, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
30 4 0.03
31 24 0.17
32 1 0.01
33 85 0.60
34 1 0.01
36 26 0.18
ACGTcount: A:0.59, C:0.03, G:0.22, T:0.16
Consensus pattern (31 bp):
AGTAAAAGAAGTAATTAGTAAAAAGAGCAAA
Found at i:12383 original size:13 final size:15
Alignment explanation
Indices: 12343--12401 Score: 63
Period size: 15 Copynumber: 4.0 Consensus size: 15
12333 GAGCAAAAGT
12343 AGAAGAAGTAATCAG
1 AGAAGAAGTAATCAG
12358 A-AA-AATGGTAATCA-
1 AGAAGAA--GTAATCAG
12372 AG-AGAAGTAATCAG
1 AGAAGAAGTAATCAG
12386 TAGAAGAAGTAATCAG
1 -AGAAGAAGTAATCAG
12402 TAAAATGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.24
14 4 0.11
15 12 0.32
16 12 0.32
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.17
Consensus pattern (15 bp):
AGAAGAAGTAATCAG
Found at i:12427 original size:32 final size:33
Alignment explanation
Indices: 12375--12456 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 33
12365 GTAATCAAGA
* *
12375 GAAGTAATCAGTAGAAGAAGTAATCAGT-AAAAT
1 GAAGTAA-AAGTAAAAGAAGTAATCAGTAAAAAT
12408 GAAG-AAAGAGTAAAAGAAGTAATCAGTAAAAAT
1 GAAGTAAA-AGTAAAAGAAGTAATCAGTAAAAAT
*
12441 GGAGTAAAAGTAAAAG
1 GAAGTAAAAGTAAAAG
12457 GAGTGTTTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
32 20 0.47
33 20 0.47
34 3 0.07
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (33 bp):
GAAGTAAAAGTAAAAGAAGTAATCAGTAAAAAT
Found at i:12436 original size:16 final size:16
Alignment explanation
Indices: 12174--12438 Score: 131
Period size: 16 Copynumber: 16.4 Consensus size: 16
12164 TAAGGGAGAG
*
12174 AGTAAAAGAAATAATC
1 AGTAAAAGAAGTAATC
* *
12190 AGTAAAAATGGAGTAA-G
1 AGT-AAAA-GAAGTAATC
*
12207 AGTAAAAGAAGAAATC
1 AGTAAAAGAAGTAATC
* *
12223 AGTAAAAATGGAGTAA-G
1 AGT-AAAA-GAAGTAATC
*
12240 AGTAAAAGAAGAAATC
1 AGTAAAAGAAGTAATC
* * *
12256 AGTAAAAATGGAGCAA-G
1 AGT-AAAA-GAAGTAATC
*
12273 AGTAAAAGAAGTAATT
1 AGTAAAAGAAGTAATC
*
12289 AGTAAAA-AGAGTAA-A
1 AGTAAAAGA-AGTAATC
*
12304 AGTAAAAGAAGTAATT
1 AGTAAAAGAAGTAATC
**
12320 AGTAAAAGTAAAAG-AGCAAA
1 AGTAAAAG---AAGTA--ATC
*
12340 AGTAGAAGAAGTAATC
1 AGTAAAAGAAGTAATC
*
12356 AG-AAAA-ATGGTAATC
1 AGTAAAAGA-AGTAATC
*
12371 ---AAGAGAAGTAATC
1 AGTAAAAGAAGTAATC
*
12384 AGTAGAAGAAGTAATC
1 AGTAAAAGAAGTAATC
**
12400 AGTAAAATGAAG-AAAG
1 AGTAAAA-GAAGTAATC
12416 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
12432 AGTAAAA
1 AGTAAAA
12439 ATGGAGTAAA
Statistics
Matches: 188, Mismatches: 36, Indels: 50
0.69 0.13 0.18
Matches are distributed among these distances:
13 9 0.05
14 2 0.01
15 41 0.22
16 80 0.43
17 28 0.15
18 17 0.09
19 3 0.02
20 8 0.04
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.17
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:12455 original size:16 final size:15
Alignment explanation
Indices: 12374--12456 Score: 51
Period size: 16 Copynumber: 5.1 Consensus size: 15
12364 GGTAATCAAG
* *
12374 AGAAGTAATCAGTAGA
1 AGAAGTAA-AAGTAAA
*
12390 AGAAGTAATCAGTAAA
1 AGAAGTAA-AAGTAAA
12406 ATGAAG-AAAGAGTAAA
1 A-GAAGTAAA-AGTAAA
*
12422 AGAAGTAATCAGTAAAA
1 AGAAGTAA-AAGT-AAA
*
12439 ATGGAGTAAAAGTAAA
1 A-GAAGTAAAAGTAAA
12455 AG
1 AG
12457 GAGTGTTTAG
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
15 5 0.09
16 34 0.61
17 11 0.20
18 6 0.11
ACGTcount: A:0.57, C:0.04, G:0.23, T:0.17
Consensus pattern (15 bp):
AGAAGTAAAAGTAAA
Found at i:12790 original size:14 final size:14
Alignment explanation
Indices: 12749--12793 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
12739 AGTGGTAAAA
12749 AAGTAATCAGGTAA-
1 AAGTAATCA-GTAAG
12763 AAGTAATCAGTAAG
1 AAGTAATCAGTAAG
*
12777 AAGTAATGAGTAAG
1 AAGTAATCAGTAAG
12791 AAG
1 AAG
12794 GTCAAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.20
Consensus pattern (14 bp):
AAGTAATCAGTAAG
Done.