Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014424.1 Corchorus olitorius cultivar O-4 contig14457, 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: 47163
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:823 original size:56 final size:56
Alignment explanation
Indices: 761--868 Score: 216
Period size: 56 Copynumber: 1.9 Consensus size: 56
751 ATAAGCAGAG
761 GCTTGAGGAATTGAGGGCTTGGGATTCCAAAGCTGCAAAAGACATTGAAAAGCACA
1 GCTTGAGGAATTGAGGGCTTGGGATTCCAAAGCTGCAAAAGACATTGAAAAGCACA
817 GCTTGAGGAATTGAGGGCTTGGGATTCCAAAGCTGCAAAAGACATTGAAAAG
1 GCTTGAGGAATTGAGGGCTTGGGATTCCAAAGCTGCAAAAGACATTGAAAAG
869 ACACCAGTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (56 bp):
GCTTGAGGAATTGAGGGCTTGGGATTCCAAAGCTGCAAAAGACATTGAAAAGCACA
Found at i:3256 original size:18 final size:18
Alignment explanation
Indices: 3233--3269 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3223 TTCTTGGCTT
3233 TAACATCAAGAACCAAAA
1 TAACATCAAGAACCAAAA
3251 TAACATCAAGAACCAAAA
1 TAACATCAAGAACCAAAA
3269 T
1 T
3270 GCAGTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.22, G:0.05, T:0.14
Consensus pattern (18 bp):
TAACATCAAGAACCAAAA
Found at i:10140 original size:22 final size:22
Alignment explanation
Indices: 10115--10310 Score: 82
Period size: 22 Copynumber: 9.0 Consensus size: 22
10105 CTCCAATGTA
*
10115 GAAATATTGATAACCACACTGT
1 GAAATATTGATAACCACACTAT
* * *
10137 GAAA-ATTTGATAACCTCATTTT
1 GAAATA-TTGATAACCACACTAT
* *
10159 GAAAT-TTCAATAACCTC-CTAT
1 GAAATATT-GATAACCACACTAT
*
10180 GAAA-ATTTGATAAGCACACTAT
1 GAAATA-TTGATAACCACACTAT
** * *
10202 GAAAT-TTCGATAACCTTAGTGT
1 GAAATATT-GATAACCACACTAT
* * * *
10224 GAAATTTTGATAATCTCCCTAT
1 GAAATATTGATAACCACACTAT
* * * *
10246 AAAATTTTGATAATCACACTGT
1 GAAATATTGATAACCACACTAT
* * *
10268 -ATA-ATTGGTAACCGCACTAT
1 GAAATATTGATAACCACACTAT
* *
10288 GAAAATTTTAATAACCACACTAT
1 G-AAATATTGATAACCACACTAT
10311 AAGAATGAAA
Statistics
Matches: 128, Mismatches: 34, Indels: 23
0.69 0.18 0.12
Matches are distributed among these distances:
20 12 0.09
21 19 0.15
22 82 0.64
23 15 0.12
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
GAAATATTGATAACCACACTAT
Found at i:10189 original size:43 final size:43
Alignment explanation
Indices: 10136--10217 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
10126 AACCACACTG
* * *
10136 TGAAAATTTGATAACCTCATTTTGAAATTTCAATAACCTCCTA
1 TGAAAATTTGATAACCACACTATGAAATTTCAATAACCTCCTA
* *
10179 TGAAAATTTGATAAGCACACTATGAAATTTCGATAACCT
1 TGAAAATTTGATAACCACACTATGAAATTTCAATAACCT
10218 TAGTGTGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (43 bp):
TGAAAATTTGATAACCACACTATGAAATTTCAATAACCTCCTA
Found at i:10198 original size:65 final size:65
Alignment explanation
Indices: 10116--10267 Score: 173
Period size: 65 Copynumber: 2.3 Consensus size: 65
10106 TCCAATGTAG
* *
10116 AAATATTGATAACCACACTGTGAAAATTT-GATAACCTCATTTTGAAATTTCAATAACCT-CCTA
1 AAAT-TTGATAACCACACTGTG-AAATTTCGATAACCTCAGTGTGAAATTTCAATAACCTCCCTA
10179 TGA
64 T-A
* * * ** *
10182 AAATTTGATAAGCACACTATGAAATTTCGATAACCTTAGTGTGAAATTTTGATAATCTCCCTATA
1 AAATTTGATAACCACACTGTGAAATTTCGATAACCTCAGTGTGAAATTTCAATAACCTCCCTATA
*
10247 AAATTTTGATAATCACACTGT
1 AAA-TTTGATAACCACACTGT
10268 ATAATTGGTA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 6 0.08
65 43 0.59
66 24 0.33
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (65 bp):
AAATTTGATAACCACACTGTGAAATTTCGATAACCTCAGTGTGAAATTTCAATAACCTCCCTATA
Found at i:10229 original size:43 final size:43
Alignment explanation
Indices: 10134--10236 Score: 102
Period size: 43 Copynumber: 2.3 Consensus size: 43
10124 ATAACCACAC
* * *
10134 TGTGAAAATTTGATAACCTCATTTTGAAATTTCAATAACCTCCTA
1 TGTG-AAATTTGATAACCACACTATGAAATTTCAATAACCT-CTA
* * *
10179 TG-AAAATTTGATAAGCACACTATGAAATTTCGATAACCT-TA
1 TGTGAAATTTGATAACCACACTATGAAATTTCAATAACCTCTA
10220 GTGTGAAATTTTGATAA
1 -TGTGAAA-TTTGATAA
10237 TCTCCCTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 2 0.04
42 2 0.04
43 34 0.71
44 8 0.17
45 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36
Consensus pattern (43 bp):
TGTGAAATTTGATAACCACACTATGAAATTTCAATAACCTCTA
Found at i:10482 original size:22 final size:22
Alignment explanation
Indices: 10444--10635 Score: 97
Period size: 22 Copynumber: 8.8 Consensus size: 22
10434 ATTCCCTCCC
10444 TATGAAATTTT-ATTAACCTTCT
1 TATGAAATTTTGA-TAACCTTCT
**
10466 TATGAAATTTTGATAACCAAAC-
1 TATGAAATTTTGATAACC-TTCT
* * * *
10488 TATAAAATTTCGATAACTTTCG
1 TATGAAATTTTGATAACCTTCT
* * * *
10510 TATAAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCT
* * * *
10532 TAGGAAATTTTAATAATCTTTT
1 TATGAAATTTTGATAACCTTCT
* * *
10554 TATGAAAATTTGGTAAGC-T-T
1 TATGAAATTTTGATAACCTTCT
* *
10574 TATGAAATTTTGATAA-CTACAC
1 TATGAAATTTTGATAACCTTC-T
* * ** *
10596 AATGAAGTTTTGATAATTTTCA
1 TATGAAATTTTGATAACCTTCT
*
10618 TATGAAATTTTGGTAACC
1 TATGAAATTTTGATAACC
10636 ACACAATGAA
Statistics
Matches: 124, Mismatches: 39, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
19 1 0.01
20 15 0.12
21 2 0.02
22 102 0.82
23 4 0.03
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCT
Found at i:10601 original size:42 final size:43
Alignment explanation
Indices: 10555--10655 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 43
10545 TAATCTTTTT
* * *
10555 ATGAAAATTTGGTAAGCTT-TATGAAATTTTGATAACTACACA
1 ATGAAATTTTGATAAGCTTATATGAAATTTTGATAACCACACA
* ** *
10597 ATGAAGTTTTGATAATTTTCATATGAAATTTTGGTAACCACACA
1 ATGAAATTTTGATAAGCTT-ATATGAAATTTTGATAACCACACA
10641 ATGAAATTTTGATAA
1 ATGAAATTTTGATAA
10656 CATTCCCATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 14 0.29
44 35 0.71
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (43 bp):
ATGAAATTTTGATAAGCTTATATGAAATTTTGATAACCACACA
Found at i:10644 original size:22 final size:22
Alignment explanation
Indices: 10575--10656 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
10565 GGTAAGCTTT
10575 ATGAAATTTTGATAACTACACA
1 ATGAAATTTTGATAACTACACA
* * * *
10597 ATGAAGTTTTGATAATTTTCA-T
1 ATGAAATTTTGATAA-CTACACA
* *
10619 ATGAAATTTTGGTAACCACACA
1 ATGAAATTTTGATAACTACACA
10641 ATGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
10657 ATTCCCATGT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
21 2 0.04
22 42 0.89
23 3 0.06
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACTACACA
Found at i:10671 original size:44 final size:44
Alignment explanation
Indices: 10575--10675 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 44
10565 GGTAAGCTTT
* * * ** *
10575 ATGAAATTTTGATAACTACACAATGAAGTTTTGATAATTTTCAT
1 ATGAAATTTTGGTAACCACACAATGAAATTTTGATAACATTCAC
*
10619 ATGAAATTTTGGTAACCACACAATGAAATTTTGATAACATTCCC
1 ATGAAATTTTGGTAACCACACAATGAAATTTTGATAACATTCAC
*
10663 ATGTAATTTTGGT
1 ATGAAATTTTGGT
10676 TTGATTGTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.39
Consensus pattern (44 bp):
ATGAAATTTTGGTAACCACACAATGAAATTTTGATAACATTCAC
Found at i:11412 original size:14 final size:14
Alignment explanation
Indices: 11388--11421 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
11378 TGAATTCCAT
11388 TATAA-AAGTAATA
1 TATAAGAAGTAATA
11401 TATAAGAAGTAATA
1 TATAAGAAGTAATA
11415 TA-AAGAA
1 TATAAGAA
11422 AAAAAAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (14 bp):
TATAAGAAGTAATA
Found at i:12059 original size:32 final size:32
Alignment explanation
Indices: 12009--12069 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
11999 TCGAAATAGC
* *
12009 GGCGTTTCTGTACGGAAACGCCACTATTTAGT
1 GGCGTTTCCGTACAGAAACGCCACTATTTAGT
*
12041 GGCGTTTCCGTACAGAAACGCCGCTATTT
1 GGCGTTTCCGTACAGAAACGCCACTATTT
12070 TGGCTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (32 bp):
GGCGTTTCCGTACAGAAACGCCACTATTTAGT
Found at i:16133 original size:13 final size:13
Alignment explanation
Indices: 16115--16143 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16105 TCGTAATTTT
16115 ATAAGATAGTAAG
1 ATAAGATAGTAAG
16128 ATAAGATAGTAAG
1 ATAAGATAGTAAG
16141 ATA
1 ATA
16144 GTAAGATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (13 bp):
ATAAGATAGTAAG
Found at i:17939 original size:23 final size:22
Alignment explanation
Indices: 17912--17965 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
17902 ATATTAGAAC
*
17912 ATATCTATCTATCCTATATCTGT
1 ATATCTATATAT-CTATATCTGT
17935 ATATCTATATATCTATATC--T
1 ATATCTATATATCTATATCTGT
17955 ATA-CTATATAT
1 ATATCTATATAT
17966 AAAAAGTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 8 0.27
20 4 0.13
22 7 0.23
23 11 0.37
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATCTATATATCTATATCTGT
Found at i:17944 original size:14 final size:14
Alignment explanation
Indices: 17912--17965 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
17902 ATATTAGAAC
*
17912 ATATCTATCTATCCT
1 ATATCTATATAT-CT
*
17927 ATATCTGTATATCT
1 ATATCTATATATCT
* *
17941 ATATATCTATATCT
1 ATATCTATATATCT
17955 ATA-CTATATAT
1 ATATCTATATAT
17966 AAAAAGTGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 6 0.18
14 17 0.52
15 10 0.30
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (14 bp):
ATATCTATATATCT
Found at i:19265 original size:22 final size:22
Alignment explanation
Indices: 19234--19491 Score: 140
Period size: 22 Copynumber: 11.7 Consensus size: 22
19224 GTTTGGGGAG
19234 AGGTTATCAAAATTTCATAGGT
1 AGGTTATCAAAATTTCATAGGT
* * *
19256 AGTTTATCAAAATTTAATTGGGT
1 AGGTTATCAAAATTTCA-TAGGT
* *
19279 GTGGTTGTCAAAATTTCATAAGCG-
1 -AGGTTATCAAAATTTCAT-AG-GT
* * *
19303 AGGTTAACAAAATTGCAGAGTGT
1 AGGTTATCAAAATTTCATAG-GT
* *
19326 -GCTTATC-AAATTTTATA-GT
1 AGGTTATCAAAATTTCATAGGT
*
19345 GAGATTATC-AAATTTCATAGTGT
1 -AGGTTATCAAAATTTCATAG-GT
* *
19368 A-GTTATCAAATTTTCATAGGA
1 AGGTTATCAAAATTTCATAGGT
* * *
19389 AGGTTACCAAAATTTCACAATGT
1 AGGTTATCAAAATTTCA-TAGGT
19412 -GGTTAT-AAAATTTTCATA-GT
1 AGGTTATCAAAA-TTTCATAGGT
* *
19432 GAGATTAACAAAATTTCATAGAG-
1 -AGGTTATCAAAATTTCATAG-GT
* * *
19455 AGGTTATCGAAATTTGATAGGC
1 AGGTTATCAAAATTTCATAGGT
* *
19477 AGATTATCGAAATTT
1 AGGTTATCAAAATTT
19492 TGATTACCTC
Statistics
Matches: 179, Mismatches: 38, Indels: 38
0.70 0.15 0.15
Matches are distributed among these distances:
19 2 0.01
20 2 0.01
21 35 0.20
22 98 0.55
23 26 0.15
24 15 0.08
25 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGT
Found at i:19345 original size:21 final size:20
Alignment explanation
Indices: 19321--19386 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
19311 AAAATTGCAG
19321 AGTGTGCTTATCAAATTTTAT
1 AGTGTG-TTATCAAATTTTAT
* *
19342 AGTGAGATTATCAAATTTCAT
1 AGTGTG-TTATCAAATTTTAT
19363 AGTGTAGTTATCAAATTTTCAT
1 AGTGT-GTTATCAAATTTT-AT
19385 AG
1 AG
19387 GAAGGTTACC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
21 33 0.87
22 5 0.13
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (20 bp):
AGTGTGTTATCAAATTTTAT
Found at i:19417 original size:44 final size:44
Alignment explanation
Indices: 19277--19469 Score: 185
Period size: 44 Copynumber: 4.4 Consensus size: 44
19267 ATTTAATTGG
* * * * * *
19277 GTGTGGTTGTCAAAATTTCATAAGCGAGGTTAACAAAATTGCAGA
1 GTGTGGTTATCAAATTTTCAT-AGTGAGATTAACAAAATTTCACA
* * *
19322 GTGTGCTTATCAAATTTT-ATAGTGAGATTATC-AAATTTCATA
1 GTGTGGTTATCAAATTTTCATAGTGAGATTAACAAAATTTCACA
* * *
19364 GTGTAGTTATCAAATTTTCATAG-GAAGGTTACCAAAATTTCACA
1 GTGTGGTTATCAAATTTTCATAGTG-AGATTAACAAAATTTCACA
* * *
19408 ATGTGGTTATAAAATTTTCATAGTGAGATTAACAAAATTTCATA
1 GTGTGGTTATCAAATTTTCATAGTGAGATTAACAAAATTTCACA
* *
19452 GAGAGGTTATCGAAATTT
1 GTGTGGTTATC-AAATTT
19470 GATAGGCAGA
Statistics
Matches: 120, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
42 25 0.21
43 19 0.16
44 54 0.45
45 22 0.18
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (44 bp):
GTGTGGTTATCAAATTTTCATAGTGAGATTAACAAAATTTCACA
Found at i:19481 original size:44 final size:44
Alignment explanation
Indices: 19231--19491 Score: 160
Period size: 44 Copynumber: 5.9 Consensus size: 44
19221 GTGGTTTGGG
* * * *
19231 GAGAGGTTATCAAAATTTCATAG-GTAGTTTATCAAAATTTAATTGG
1 GAGAGGTTATCAAATTTTCATAGTG-AGATTATCAAAATTTCA-T-A
* * * * * * * * *
19277 GTGTGGTTGTCAAAATTTCATAAGCGAGGTTAACAAAATTGCAGA
1 GAGAGGTTATCAAATTTTCAT-AGTGAGATTATCAAAATTTCATA
* * *
19322 GTGTGCTTATCAAATTTT-ATAGTGAGATTATC-AAATTTCATA
1 GAGAGGTTATCAAATTTTCATAGTGAGATTATCAAAATTTCATA
* * * *
19364 GTGTA-GTTATCAAATTTTCATAG-GAAGGTTACCAAAATTTCACA
1 GAG-AGGTTATCAAATTTTCATAGTG-AGATTATCAAAATTTCATA
* * *
19408 -ATGTGGTTATAAAATTTTCATAGTGAGATTAACAAAATTTCATA
1 GA-GAGGTTATCAAATTTTCATAGTGAGATTATCAAAATTTCATA
* *
19452 GAGAGGTTATCGAAA-TTTGATAG-GCAGATTATCGAAATTT
1 GAGAGGTTATC-AAATTTTCATAGTG-AGATTATCAAAATTT
19492 TGATTACCTC
Statistics
Matches: 170, Mismatches: 33, Indels: 26
0.74 0.14 0.11
Matches are distributed among these distances:
42 24 0.14
43 20 0.12
44 72 0.42
45 20 0.12
46 18 0.11
47 15 0.09
48 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (44 bp):
GAGAGGTTATCAAATTTTCATAGTGAGATTATCAAAATTTCATA
Found at i:20123 original size:21 final size:21
Alignment explanation
Indices: 20088--20129 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20078 TGGGTGTGTG
*
20088 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
20110 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
20130 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:21369 original size:37 final size:38
Alignment explanation
Indices: 21322--21407 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 38
21312 AATAATTTAT
* * *
21322 TAAAATATTTTATTAAGCATTTAAAT-AAAATCAGTAA
1 TAAAACATTTTATAAAGCATTTAAATAAAAAACAGTAA
21359 TAAAACATTTTATAAAGCATTTAAATAAAAAACAGTAA
1 TAAAACATTTTATAAAGCATTTAAATAAAAAACAGTAA
21397 TAAAACATTTT
1 TAAAACATTTT
21408 CCTCAACGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 24 0.53
38 21 0.47
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (38 bp):
TAAAACATTTTATAAAGCATTTAAATAAAAAACAGTAA
Found at i:22657 original size:28 final size:29
Alignment explanation
Indices: 22626--22690 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
22616 TTCCACTTTA
* *
22626 AAGGGTAAATTTCGTAATTTAACAT-TTT
1 AAGGGTAAATTTAGTAATTTAACATGTTC
* * *
22654 AAGGGT-GATTTAGTAATTTTACCTGTTC
1 AAGGGTAAATTTAGTAATTTAACATGTTC
22682 AAGGGTAAA
1 AAGGGTAAA
22691 ATTATAACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 14 0.48
28 14 0.48
29 1 0.03
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (29 bp):
AAGGGTAAATTTAGTAATTTAACATGTTC
Found at i:30887 original size:24 final size:24
Alignment explanation
Indices: 30852--31066 Score: 223
Period size: 24 Copynumber: 9.0 Consensus size: 24
30842 TACTTGGTCT
30852 TTTCTCACGACCACTATGTGGCCG
1 TTTCTCACGACCACTATGTGGCCG
* * *
30876 TTTTTCATGACCACTATGTGGTCG
1 TTTCTCACGACCACTATGTGGCCG
** * * * *
30900 AATCTCATGACCACCATGTGGTCA
1 TTTCTCACGACCACTATGTGGCCG
**
30924 AATCTCACGACCACTATGTGGCCG
1 TTTCTCACGACCACTATGTGGCCG
*
30948 TTTCTCATGACCACTATGTGGCCG
1 TTTCTCACGACCACTATGTGGCCG
* * * *
30972 TTTCTCACGACCACCATGTAGTCA
1 TTTCTCACGACCACTATGTGGCCG
**
30996 AATCTCACGACCACTATGTGGCCG
1 TTTCTCACGACCACTATGTGGCCG
* * *
31020 TTTCTCACGACCACCATGTGGTCA
1 TTTCTCACGACCACTATGTGGCCG
**
31044 AATCTCACGACCACTATGTGGCC
1 TTTCTCACGACCACTATGTGGCC
31067 ATGTGATTTT
Statistics
Matches: 156, Mismatches: 35, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 156 1.00
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (24 bp):
TTTCTCACGACCACTATGTGGCCG
Found at i:30912 original size:48 final size:48
Alignment explanation
Indices: 30854--31066 Score: 273
Period size: 48 Copynumber: 4.4 Consensus size: 48
30844 CTTGGTCTTT
* * * *
30854 TCTCACGACCACTATGTGGCCGTTTTTCATGACCACTATGTGGTCGAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCAAA
* * * *** * * ***
30902 TCTCATGACCACCATGTGGTCAAATCTCACGACCACTATGTGGCCGTT
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCAAA
* *
30950 TCTCATGACCACTATGTGGCCGTTTCTCACGACCACCATGTAGTCAAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCAAA
30998 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCAAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCAAA
31046 TCTCACGACCACTATGTGGCC
1 TCTCACGACCACTATGTGGCC
31067 ATGTGATTTT
Statistics
Matches: 141, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 141 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (48 bp):
TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCAAA
Found at i:30963 original size:72 final size:72
Alignment explanation
Indices: 30854--31064 Score: 332
Period size: 72 Copynumber: 2.9 Consensus size: 72
30844 CTTGGTCTTT
* *
30854 TCTCACGACCACTATGTGGCCGTTTTTCATGACCACTATGTGGTCGAATCTCATGACCACCATGT
1 TCTCACGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAATCTCACGACCACCATGT
30919 GGTCAAA
66 GGTCAAA
* **
30926 TCTCACGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGCCGTTTCTCACGACCACCATGT
1 TCTCACGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAATCTCACGACCACCATGT
*
30991 AGTCAAA
66 GGTCAAA
* * * *
30998 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCAAATCTCACGACCACTATGT
1 TCTCACGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAATCTCACGACCACCATGT
31063 GG
66 GG
31065 CCATGTGATT
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 125 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (72 bp):
TCTCACGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAATCTCACGACCACCATGT
GGTCAAA
Found at i:35370 original size:24 final size:24
Alignment explanation
Indices: 35356--35572 Score: 173
Period size: 24 Copynumber: 9.0 Consensus size: 24
35346 TACTTGGTCT
35356 TTTCTCATGACCACTATGTGGCCG
1 TTTCTCATGACCACTATGTGGCCG
*
35380 TTTCTCATGACCACTATGTGGTCG
1 TTTCTCATGACCACTATGTGGCCG
** * * * *
35404 AATCTCACGACCACCATGTGGTCA
1 TTTCTCATGACCACTATGTGGCCG
** **
35428 AATCTCATGACCACTATGTGGTTG
1 TTTCTCATGACCACTATGTGGCCG
* *
35452 TTTCTCACGACCACCATGTGGCCG
1 TTTCTCATGACCACTATGTGGCCG
* * *
35476 TTTCTCACGACCACCATGTGGTCG
1 TTTCTCATGACCACTATGTGGCCG
** ** * *
35500 AATCTCACAACCACTATATGGTCG
1 TTTCTCATGACCACTATGTGGCCG
* * * *
35524 TTTCTCACGACCACCATGTGGTCA
1 TTTCTCATGACCACTATGTGGCCG
** *
35548 AATCTCACGACCACTATGTGGCCG
1 TTTCTCATGACCACTATGTGGCCG
35572 T
1 T
35573 GTGATTTTCC
Statistics
Matches: 159, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 159 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (24 bp):
TTTCTCATGACCACTATGTGGCCG
Found at i:35402 original size:48 final size:48
Alignment explanation
Indices: 35358--35572 Score: 268
Period size: 48 Copynumber: 4.5 Consensus size: 48
35348 CTTGGTCTTT
* * *
35358 TCTCATGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
* * *** * * * **
35406 TCTCACGACCACCATGTGGTCAAATCTCATGACCACTATGTGGTTGTT
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
*
35454 TCTCACGACCACCATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
* * * *
35502 TCTCACAACCACTATATGGTCGTTTCTCACGACCACCATGTGGTCAAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
35550 TCTCACGACCACTATGTGGCCGT
1 TCTCACGACCACTATGTGGCCGT
35573 GTGATTTTCC
Statistics
Matches: 141, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 141 1.00
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (48 bp):
TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
Found at i:35471 original size:72 final size:72
Alignment explanation
Indices: 35358--35568 Score: 305
Period size: 72 Copynumber: 2.9 Consensus size: 72
35348 CTTGGTCTTT
* * *
35358 TCTCATGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAATCTCACGACCACCATGT
1 TCTCATGACCACTATGTGGTCGTTTCTCACGACCACCATGTGGTCGAATCTCACGACCACCATGT
35423 GGTCAAA
66 GGTCAAA
* * **
35430 TCTCATGACCACTATGTGGTTGTTTCTCACGACCACCATGTGGCCGTTTCTCACGACCACCATGT
1 TCTCATGACCACTATGTGGTCGTTTCTCACGACCACCATGTGGTCGAATCTCACGACCACCATGT
*
35495 GGTCGAA
66 GGTCAAA
** * * *
35502 TCTCACAACCACTATATGGTCGTTTCTCACGACCACCATGTGGTCAAATCTCACGACCACTATGT
1 TCTCATGACCACTATGTGGTCGTTTCTCACGACCACCATGTGGTCGAATCTCACGACCACCATGT
35567 GG
66 GG
35569 CCGTGTGATT
Statistics
Matches: 122, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 122 1.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (72 bp):
TCTCATGACCACTATGTGGTCGTTTCTCACGACCACCATGTGGTCGAATCTCACGACCACCATGT
GGTCAAA
Found at i:39668 original size:17 final size:17
Alignment explanation
Indices: 39646--39683 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
39636 CAAACGCATC
39646 GAAAAAATTAAAGTATT
1 GAAAAAATTAAAGTATT
39663 GAAAAAATTAAAGTATT
1 GAAAAAATTAAAGTATT
39680 GAAA
1 GAAA
39684 TTTTTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (17 bp):
GAAAAAATTAAAGTATT
Found at i:41871 original size:19 final size:19
Alignment explanation
Indices: 41844--41880 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41834 AAAAATACAA
41844 TTTTGCTTCCTAAAGATTT
1 TTTTGCTTCCTAAAGATTT
*
41863 TTTTTCTTCCTAAAGATT
1 TTTTGCTTCCTAAAGATT
41881 ATGAGTGATG
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:0.22, C:0.16, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTTGCTTCCTAAAGATTT
Found at i:43324 original size:38 final size:38
Alignment explanation
Indices: 43290--43379 Score: 126
Period size: 38 Copynumber: 2.3 Consensus size: 38
43280 GTTTGAATGT
*
43290 TTTGAAAACTTGATGGGAGCTTTCCCTGAATTGAATAC
1 TTTGAAAACTTGATGGGAGCTTTCCCTAAATTGAATAC
* * *
43328 TTTGAAAACTTGATGGGATCTTTTCCTAAATTGAAAAC
1 TTTGAAAACTTGATGGGAGCTTTCCCTAAATTGAATAC
*
43366 TATGGAAAACTTGA
1 T-TTGAAAACTTGA
43380 ATTGAATACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 35 0.76
39 11 0.24
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (38 bp):
TTTGAAAACTTGATGGGAGCTTTCCCTAAATTGAATAC
Found at i:43382 original size:61 final size:61
Alignment explanation
Indices: 43316--43536 Score: 343
Period size: 61 Copynumber: 3.6 Consensus size: 61
43306 GAGCTTTCCC
* * * * *
43316 TGAATTGAATACTTTGAAAACTTGATGGGATCTTTTCCTAAATTGAAAACTATGGAAAACT
1 TGAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCTAAATTGAACACTTTGAAAAACT
*
43377 TGAATTGAATACTTTGGAAACTTGATGGGAACTTTCCCTAAATTGAACACTTTGAAAAACT
1 TGAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCTAAATTGAACACTTTGAAAAACT
* *
43438 TGAATTGAATACTTGGAAAACTTGATGGGAACTTTCCCTAAACTGAACACTTTGAAAAACT
1 TGAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCTAAATTGAACACTTTGAAAAACT
* * *
43499 TGAATTTAATATTTTGAAAACTTGATGGGAATTTTCCC
1 TGAATTGAATACTTTGAAAACTTGATGGGAACTTTCCC
43537 ACTTTGAAAA
Statistics
Matches: 147, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 147 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (61 bp):
TGAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCTAAATTGAACACTTTGAAAAACT
Found at i:43394 original size:23 final size:23
Alignment explanation
Indices: 43356--43462 Score: 70
Period size: 23 Copynumber: 5.0 Consensus size: 23
43346 TCTTTTCCTA
* *
43356 AATTGAAAACTATGGAAAACTTG
1 AATTGAATACTTTGGAAAACTTG
43379 AATTGAATACTTTGG-AAACTTG
1 AATTGAATACTTTGGAAAACTTG
* * * * *
43401 -ATGGGA-ACTTT-----CCCTA
1 AATTGAATACTTTGGAAAACTTG
* *
43417 AATTGAACACTTTGAAAAACTTG
1 AATTGAATACTTTGGAAAACTTG
43440 AATTGAATAC-TTGGAAAACTTG
1 AATTGAATACTTTGGAAAACTTG
43462 A
1 A
43463 TGGGAACTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 15
0.68 0.15 0.16
Matches are distributed among these distances:
16 2 0.03
17 4 0.06
18 5 0.08
20 5 0.08
21 4 0.06
22 19 0.30
23 24 0.38
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (23 bp):
AATTGAATACTTTGGAAAACTTG
Found at i:43460 original size:22 final size:23
Alignment explanation
Indices: 43417--43462 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
43407 ACTTTCCCTA
43417 AATTGAACACTTTGAAAAACTTG
1 AATTGAACACTTTGAAAAACTTG
* *
43440 AATTGAATAC-TTGGAAAACTTG
1 AATTGAACACTTTGAAAAACTTG
43462 A
1 A
43463 TGGGAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (23 bp):
AATTGAACACTTTGAAAAACTTG
Found at i:45626 original size:51 final size:50
Alignment explanation
Indices: 45525--45626 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
45515 GTTCTTCTTA
* **
45525 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
45575 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
45626 T
1 T
45627 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Done.