Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019509.1 Corchorus olitorius cultivar O-4 contig19542, 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: 24112
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Found at i:276 original size:12 final size:12
Alignment explanation
Indices: 259--283 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
249 CCAAGAATAT
259 TATAAACTAAAA
1 TATAAACTAAAA
271 TATAAACTAAAA
1 TATAAACTAAAA
283 T
1 T
284 TATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TATAAACTAAAA
Found at i:628 original size:14 final size:15
Alignment explanation
Indices: 609--639 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
599 ATTAAATTAG
609 TAAAAT-GGTAAAAA
1 TAAAATAGGTAAAAA
623 TAAAATAGGTAAAAA
1 TAAAATAGGTAAAAA
638 TA
1 TA
640 TTAGATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (15 bp):
TAAAATAGGTAAAAA
Found at i:3728 original size:18 final size:18
Alignment explanation
Indices: 3707--3743 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3697 CACCGATGTT
3707 ACCGATGCTGCTGCTGCC
1 ACCGATGCTGCTGCTGCC
3725 ACCGATGCTGCTGCTGCC
1 ACCGATGCTGCTGCTGCC
3743 A
1 A
3744 TCGCCGCTGC
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:0.14, C:0.38, G:0.27, T:0.22
Consensus pattern (18 bp):
ACCGATGCTGCTGCTGCC
Found at i:3752 original size:18 final size:18
Alignment explanation
Indices: 3707--3764 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
3697 CACCGATGTT
*
3707 ACCGATGCTGCTGCTGCC
1 ACCGACGCTGCTGCTGCC
*
3725 ACCGATGCTGCTGCTGCC
1 ACCGACGCTGCTGCTGCC
* *
3743 ATCGCCGCTGCT-CTTGCC
1 ACCGACGCTGCTGC-TGCC
3761 ACCG
1 ACCG
3765 CCAAGCAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 1 0.03
18 34 0.97
ACGTcount: A:0.10, C:0.41, G:0.26, T:0.22
Consensus pattern (18 bp):
ACCGACGCTGCTGCTGCC
Found at i:3766 original size:18 final size:18
Alignment explanation
Indices: 3713--3766 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
3703 TGTTACCGAT
**
3713 GCTGCTGCTGCCACCGAT
1 GCTGCTGCTGCCACCGCC
*
3731 GCTGCTGCTGCCATCGCC
1 GCTGCTGCTGCCACCGCC
3749 GCTGCT-CTTGCCACCGCC
1 GCTGCTGC-TGCCACCGCC
3767 AAGCAGAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.07, C:0.44, G:0.26, T:0.22
Consensus pattern (18 bp):
GCTGCTGCTGCCACCGCC
Found at i:10645 original size:31 final size:31
Alignment explanation
Indices: 10610--10680 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
10600 TTAAACTCTT
** * *
10610 AATTGAGCCTGCAACTTTGCAACTTTGTTCA
1 AATTGAGCCTAAAACTTTGCAACGTTGCTCA
*
10641 AATTGAGACTAAAACTTTGCAACGTTGCTCA
1 AATTGAGCCTAAAACTTTGCAACGTTGCTCA
*
10672 ATTTGAGCC
1 AATTGAGCC
10681 CATAAATGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (31 bp):
AATTGAGCCTAAAACTTTGCAACGTTGCTCA
Found at i:12206 original size:14 final size:15
Alignment explanation
Indices: 12187--12215 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12177 AAGAAATTCT
12187 AAAACTATC-AACTA
1 AAAACTATCTAACTA
12201 AAAACTATCTAACTA
1 AAAACTATCTAACTA
12216 TATCTAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAACTATCTAACTA
Found at i:13017 original size:427 final size:427
Alignment explanation
Indices: 12222--13502 Score: 2240
Period size: 427 Copynumber: 3.0 Consensus size: 427
12212 ACTATATCTA
* * *
12222 GGGTTCAAAATAAGGTGGGTATTTATAGTGGACAAATAAAACTCCTAGTAGATTTAGGAATTAAC
1 GGGTTCAACATAAGGTGGGTATTTATAGTGGACTAATAAGACTCCTAGTAGATTTAGGAATTAAC
* *
12287 TTAAACAGCTCCTAGGCCGGTTTAAGCTCTTAACTTGGTCTCCAAGTCGAATTGAAAGTCTCTTT
66 TTAAACAGCTCCTAGGTCGGTTTAAGCTCTTAACTTGGTCTCCAAGTCGAATTGAAAGTCTCCTT
*
12352 GGGCTGAAATTAGGTGAAAATCAGACTTGGCCCCAAAACTGATATTGTGCAGAAACTTCAGGGGC
131 GGGCTGAAATTAGGTGAAAATCGGACTTGGCCCCAAAACTGATATTGTGCAGAAACTTCAGGGGC
* *
12417 AATTTCAGAATTGAAGATGGCAAAATTGGGCTTCGAGCTTCAAAGAAAAGTTGTAGATCATTGAG
196 AATTTCAGAATTGAATATGGCAGAATTGGGCTTCGAGCTTCAAAGAAAAGTTGTAGATCATTGAG
* *
12482 TCTTCTTTCCAACACACTTTGAATAAACTCAAACGGAGGTCTGGATTAAAAGTTATGGCCTTTCT
261 TCTTCTTTCCAACACACTTTGAATCAACTCAAACGGAGGTCTGGATTAAAAGTTATGGCCTTTTT
* *
12547 ACCAAGACCACGCATAAATCCTAGTCCAAGTAGGAAAAGGAAGCATAATCACCATCGGCAAAGGC
326 ACCAAGACCGCGCATAAATCCTAGTCCAAGTAGGAAAAGGAAGCATAATCACCATCGACAAAGGC
*
12612 AAGAGCTTGGCGCGGCATAGGCAACCCAACTCCAGCT
391 AAGGGCTTGGCGCGGCATAGGCAACCCAACTCCAGCT
12649 GGGTTCAACATAAGGTGGGTATTTATAGTGGACTAATAAGACTCCTAGTAGATTTAGGAATTAAC
1 GGGTTCAACATAAGGTGGGTATTTATAGTGGACTAATAAGACTCCTAGTAGATTTAGGAATTAAC
*
12714 TTAAACAGCTTCTAGGTCGGTTTAAGCTCTTAACTTGGTCTCCAAGTCGAATTGAAAGTCTCCTT
66 TTAAACAGCTCCTAGGTCGGTTTAAGCTCTTAACTTGGTCTCCAAGTCGAATTGAAAGTCTCCTT
* * * * *
12779 GGGCTGAAATTAGGTGAAAATTGGACTTGGCCCTAAAACTAATATTGTGCAGAAACTTAAGGGGA
131 GGGCTGAAATTAGGTGAAAATCGGACTTGGCCCCAAAACTGATATTGTGCAGAAACTTCAGGGGC
*
12844 AATTTTC-GAATTGAATATGGCAGAATTGGGCTTCGTGCTTCAAAGAAAAGTTGTAGATCATTGA
196 AA-TTTCAGAATTGAATATGGCAGAATTGGGCTTCGAGCTTCAAAGAAAAGTTGTAGATCATTGA
*
12908 GTCTTCTTTCCAACACACTTTGAATCAACTCAAACGGAGGTCTGGATTAAAAGTCATGGCCTTTT
260 GTCTTCTTTCCAACACACTTTGAATCAACTCAAACGGAGGTCTGGATTAAAAGTTATGGCCTTTT
12973 TACCAAGACCGCGCATAAATCCTAGTCCAAGTAGGAAAAGGAAGCATAATCACCATCGACAAAGG
325 TACCAAGACCGCGCATAAATCCTAGTCCAAGTAGGAAAAGGAAGCATAATCACCATCGACAAAGG
13038 CAAGGGCTTGGCGCGGCATAGGCAACCCAACTCCAGCT
390 CAAGGGCTTGGCGCGGCATAGGCAACCCAACTCCAGCT
* *
13076 GGGTTCGACATGAGGTGGGTATTTATAGTGGACTAATAAGACTCCTAGTAGATTTAGGAATTAAC
1 GGGTTCAACATAAGGTGGGTATTTATAGTGGACTAATAAGACTCCTAGTAGATTTAGGAATTAAC
* *
13141 TTAAACATCTCCTAGGTCGGTTTAAGCTCTTAACTTGGTCTCCAAGTCGAATTGAAAGTCTTCTT
66 TTAAACAGCTCCTAGGTCGGTTTAAGCTCTTAACTTGGTCTCCAAGTCGAATTGAAAGTCTCCTT
*
13206 TGGCTGAAATTAGGTGAAAATCGGACTTGGCCCCAAAACTGATATTGTGCAGAAACTTCAGGGGC
131 GGGCTGAAATTAGGTGAAAATCGGACTTGGCCCCAAAACTGATATTGTGCAGAAACTTCAGGGGC
* * * *
13271 AATTTCGGAATTGAATATGGCGGAATTGGGCTTCGAGCTTAAAAGAAAATTTGTAGATCATTGAG
196 AATTTCAGAATTGAATATGGCAGAATTGGGCTTCGAGCTTCAAAGAAAAGTTGTAGATCATTGAG
* *
13336 TCTTCTTTCCAACAAACTTTGAATCAACTCAAACGAAGGTCTGGATTAAAAGTTATGGCCTTTTT
261 TCTTCTTTCCAACACACTTTGAATCAACTCAAACGGAGGTCTGGATTAAAAGTTATGGCCTTTTT
* *
13401 ACCAAGATCGCGCATAAATCCTAGTCCAAGTAGGAAAAGGAAGCATCATCACCATCGACAAAGGC
326 ACCAAGACCGCGCATAAATCCTAGTCCAAGTAGGAAAAGGAAGCATAATCACCATCGACAAAGGC
13466 AAGGGCTTGGCGCGGCATAGGCAACCCAACTCCAGCT
391 AAGGGCTTGGCGCGGCATAGGCAACCCAACTCCAGCT
13503 AGGACCCCAT
Statistics
Matches: 811, Mismatches: 41, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
426 4 0.00
427 803 0.99
428 4 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (427 bp):
GGGTTCAACATAAGGTGGGTATTTATAGTGGACTAATAAGACTCCTAGTAGATTTAGGAATTAAC
TTAAACAGCTCCTAGGTCGGTTTAAGCTCTTAACTTGGTCTCCAAGTCGAATTGAAAGTCTCCTT
GGGCTGAAATTAGGTGAAAATCGGACTTGGCCCCAAAACTGATATTGTGCAGAAACTTCAGGGGC
AATTTCAGAATTGAATATGGCAGAATTGGGCTTCGAGCTTCAAAGAAAAGTTGTAGATCATTGAG
TCTTCTTTCCAACACACTTTGAATCAACTCAAACGGAGGTCTGGATTAAAAGTTATGGCCTTTTT
ACCAAGACCGCGCATAAATCCTAGTCCAAGTAGGAAAAGGAAGCATAATCACCATCGACAAAGGC
AAGGGCTTGGCGCGGCATAGGCAACCCAACTCCAGCT
Found at i:20039 original size:21 final size:21
Alignment explanation
Indices: 19973--20337 Score: 212
Period size: 21 Copynumber: 17.8 Consensus size: 21
19963 ATTAAAATTC
* *
19973 AAAGAAGTAAAAGAATAATCAGA
1 AAAG-AGT-AAAGAGTAATCAGT
* * *
19996 AAAGAGT-AATAGTAGTAAGT
1 AAAGAGTAAAGAGTAATCAGT
*
20016 AAAGAGTAAAGAATAATCAGT
1 AAAGAGTAAAGAGTAATCAGT
* *
20037 AAAAGAGT-AATAGTAATCAAT
1 -AAAGAGTAAAGAGTAATCAGT
20058 AAAGAGTAAAGAGTAATCAAG-
1 AAAGAGTAAAGAGTAATC-AGT
*
20079 AAATG-GTAAAGAGTAATCAGA
1 AAA-GAGTAAAGAGTAATCAGT
* * * *
20100 AAAGGGT-AATAGTAGTAAGT
1 AAAGAGTAAAGAGTAATCAGT
20120 AAAGAGTAAAGAGTAATC-G-
1 AAAGAGTAAAGAGTAATCAGT
* * *
20139 AGAGAGT-AATAGCAATCAGT
1 AAAGAGTAAAGAGTAATCAGT
*
20159 AAAGAGCAAAGAGTAA--A--
1 AAAGAGTAAAGAGTAATCAGT
* * *
20176 AATG-GTAATAGTAATCAGT-A--
1 AAAGAGTAA-AG-AGT-AATCAGT
*
20196 AAAGAGTAAATAGTAATCAGT
1 AAAGAGTAAAGAGTAATCAGT
*
20217 AAAAGAGTAAATAGTAATCAGT
1 -AAAGAGTAAAGAGTAATCAGT
* * *
20239 ACAAGAGT-AATAGTAGTAAGT
1 A-AAGAGTAAAGAGTAATCAGT
* *
20260 AAAGAGCAAAGAATAATCGAG-
1 AAAGAGTAAAGAGTAATC-AGT
*
20281 AAAGAGT-AATAGTAATCAGT
1 AAAGAGTAAAGAGTAATCAGT
20301 AAAGAGTAAAGGAGTAAT-AGT
1 AAAGAGTAAA-GAGTAATCAGT
**
20322 AATCAGTAAAGAGTAA
1 AAAGAGTAAAGAGTAA
20338 AAAGTAGTCA
Statistics
Matches: 266, Mismatches: 50, Indels: 55
0.72 0.13 0.15
Matches are distributed among these distances:
16 3 0.01
17 5 0.02
18 12 0.05
19 14 0.05
20 77 0.29
21 104 0.39
22 47 0.18
23 4 0.02
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAGAGTAAAGAGTAATCAGT
Found at i:20195 original size:22 final size:22
Alignment explanation
Indices: 20182--20323 Score: 154
Period size: 22 Copynumber: 6.7 Consensus size: 22
20172 TAAAAATGGT
20182 AATAGTAATCAGTAAAAGAGTA
1 AATAGTAATCAGTAAAAGAGTA
20204 AATAGTAATCAGTAAAAGAGTA
1 AATAGTAATCAGTAAAAGAGTA
*
20226 AATAGTAATCAGTACAAGAGT-
1 AATAGTAATCAGTAAAAGAGTA
* * *
20247 AATAGTAGTAAGT-AAAGAGCA
1 AATAGTAATCAGTAAAAGAGTA
* *
20268 AAGAATAATC-G-AGAAAGAGT-
1 AATAGTAATCAGTA-AAAGAGTA
20288 AATAGTAATCAGT-AAAGAGTA
1 AATAGTAATCAGTAAAAGAGTA
*
20309 AAGGAGTAAT-AGTAA
1 AA-TAGTAATCAGTAA
20324 TCAGTAAAGA
Statistics
Matches: 99, Mismatches: 13, Indels: 16
0.77 0.10 0.12
Matches are distributed among these distances:
20 21 0.21
21 29 0.29
22 49 0.49
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (22 bp):
AATAGTAATCAGTAAAAGAGTA
Found at i:20315 original size:28 final size:28
Alignment explanation
Indices: 20284--20338 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
20274 AATCGAGAAA
20284 GAGTAATAGTAATCAGTAAAGAGTAAAG
1 GAGTAATAGTAATCAGTAAAGAGTAAAG
20312 GAGTAATAGTAATCAGTAAAGAGTAAA
1 GAGTAATAGTAATCAGTAAAGAGTAAA
20339 AAGTAGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.22
Consensus pattern (28 bp):
GAGTAATAGTAATCAGTAAAGAGTAAAG
Found at i:20317 original size:8 final size:7
Alignment explanation
Indices: 20013--20343 Score: 59
Period size: 7 Copynumber: 47.6 Consensus size: 7
20003 AATAGTAGTA
20013 AGTAAAG
1 AGTAAAG
20020 AGTAAAG
1 AGTAAAG
* **
20027 AATAATC
1 AGTAAAG
20034 AGTAAAAG
1 AGT-AAAG
*
20042 AGT-AAT
1 AGTAAAG
**
20048 AGTAATC
1 AGTAAAG
*
20055 AATAAAG
1 AGTAAAG
20062 AGTAAAG
1 AGTAAAG
20069 AGTAATCA-
1 AGTAA--AG
20077 AG-AAATG
1 AGTAAA-G
20084 -GTAAAG
1 AGTAAAG
**
20090 AGTAATC
1 AGTAAAG
*
20097 AGAAAAG
1 AGTAAAG
*
20104 GGTAATAG
1 AGTAA-AG
20112 TAGT--A-
1 -AGTAAAG
20117 AGTAAAG
1 AGTAAAG
20124 AGTAAAG
1 AGTAAAG
*
20131 AGTAATCG
1 AGTAA-AG
20139 AG---AG
1 AGTAAAG
*
20143 AGT-AAT
1 AGTAAAG
* **
20149 AGCAATC
1 AGTAAAG
20156 AGTAAAG
1 AGTAAAG
*
20163 AGCAAAG
1 AGTAAAG
*
20170 AGTAAAA
1 AGTAAAG
*
20177 ATGGT-AAT
1 A--GTAAAG
**
20185 AGTAATC
1 AGTAAAG
20192 AGTAAAAG
1 AGT-AAAG
*
20200 AGTAAAT
1 AGTAAAG
**
20207 AGTAATC
1 AGTAAAG
20214 AGTAAAAG
1 AGT-AAAG
*
20222 AGTAAAT
1 AGTAAAG
**
20229 AGTAATC
1 AGTAAAG
20236 AGTACAAG
1 AGTA-AAG
20244 AGTAATAG
1 AGTAA-AG
20252 TAGT--A-
1 -AGTAAAG
20257 AGTAAAG
1 AGTAAAG
*
20264 AGCAAAG
1 AGTAAAG
* *
20271 AATAATCG
1 AGTAA-AG
20279 AG-AAAG
1 AGTAAAG
*
20285 AGT-AAT
1 AGTAAAG
**
20291 AGTAATC
1 AGTAAAG
20298 AGTAAAG
1 AGTAAAG
20305 AGTAAAGG
1 AGTAAA-G
*
20313 AGT-AAT
1 AGTAAAG
**
20319 AGTAATC
1 AGTAAAG
20326 AGTAAAG
1 AGTAAAG
*
20333 AGTAAAA
1 AGTAAAG
20340 AGTA
1 AGTA
20344 GTCAATAAAA
Statistics
Matches: 226, Mismatches: 65, Indels: 66
0.63 0.18 0.18
Matches are distributed among these distances:
4 9 0.04
5 1 0.00
6 27 0.12
7 143 0.63
8 38 0.17
9 8 0.04
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (7 bp):
AGTAAAG
Found at i:20412 original size:27 final size:25
Alignment explanation
Indices: 20382--20450 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
20372 ATTAAAATTC
*
20382 AAAGAGTAAAAGTGGTAAAAAGATTAA
1 AAAGAGTAAAAATGGTAAAAAG--TAA
***
20409 AAAGAGTAAAAATGGTATTCAGTAA
1 AAAGAGTAAAAATGGTAAAAAGTAA
20434 AAAGAGTAAAAATGGTA
1 AAAGAGTAAAAATGGTA
20451 TTCAGTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 20 0.53
27 18 0.47
ACGTcount: A:0.57, C:0.01, G:0.22, T:0.20
Consensus pattern (25 bp):
AAAGAGTAAAAATGGTAAAAAGTAA
Found at i:20470 original size:25 final size:25
Alignment explanation
Indices: 20406--20458 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
20396 GTAAAAAGAT
20406 TAAAAAGAGTAAAAATGGTATTCAG
1 TAAAAAGAGTAAAAATGGTATTCAG
20431 TAAAAAGAGTAAAAATGGTATTCAG
1 TAAAAAGAGTAAAAATGGTATTCAG
20456 TAA
1 TAA
20459 TTAAAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (25 bp):
TAAAAAGAGTAAAAATGGTATTCAG
Found at i:20533 original size:27 final size:28
Alignment explanation
Indices: 20503--20561 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
20493 AAAAAAAGGG
*
20503 GTAAGAAAA-TGGTCATAAGTAAAAAGA
1 GTAAGAAAATTGGTAATAAGTAAAAAGA
*
20530 GTAA-AAAATTGGTAATCAGTAAAAAGA
1 GTAAGAAAATTGGTAATAAGTAAAAAGA
20557 GTAAG
1 GTAAG
20562 GGTAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.20
Consensus pattern (28 bp):
GTAAGAAAATTGGTAATAAGTAAAAAGA
Found at i:20596 original size:116 final size:114
Alignment explanation
Indices: 20406--20615 Score: 250
Period size: 115 Copynumber: 1.8 Consensus size: 114
20396 GTAAAAAGAT
* * *
20406 TAAAAAGAGTAAAAATGGTATTCAGTAAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTAAAAA
1 TAAAAAGAGTAAAAATGGTAATCAGTAAAAAGAGT--AAAGGGTATTCAATAATTAAAGTAAAAA
20471 GGCAAAAATGGAAACT-AGTAAAAA-AAAAAGGGGTAAGAAAATGGTCATAAG
64 GGCAAAAAT-GAAA-TAAGTAAAAAGAAAAAGGGGTAAGAAAATGGTCATAAG
* *
20522 TAAAAAGAGTAAAAAATTGGTAATCAGTAAAAAGAGT-AAGGGTAATT-AATAATT-TAGTTAAA
1 TAAAAAGAGT-AAAAA-TGGTAATCAGTAAAAAGAGTAAAGGGT-ATTCAATAATTAAAGTAAAA
*
20584 AGAGTAGAAAATGAAATAAGTAAAAAGAAAAA
63 AG-GCA-AAAATGAAATAAGTAAAAAGAAAAA
20616 AGAAGAGTAA
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
114 9 0.11
115 25 0.31
116 23 0.28
117 5 0.06
118 19 0.23
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.21
Consensus pattern (114 bp):
TAAAAAGAGTAAAAATGGTAATCAGTAAAAAGAGTAAAGGGTATTCAATAATTAAAGTAAAAAGG
CAAAAATGAAATAAGTAAAAAGAAAAAGGGGTAAGAAAATGGTCATAAG
Found at i:20666 original size:28 final size:28
Alignment explanation
Indices: 20613--20747 Score: 73
Period size: 28 Copynumber: 4.6 Consensus size: 28
20603 GTAAAAAGAA
* *
20613 AAAAGAAGAGTAAATAATGGTAATCAGT
1 AAAAGAAGAGTAAAAAAAGGTAATCAGT
* *
20641 AAAA-AAGAGTAAGAAAAAGGTGATCAAT
1 AAAAGAAGAGTAA-AAAAAGGTAATCAGT
* *
20669 AATTTAATTAGAAAGAGTAAAAAATGGTAATAAGT
1 -A---AA--AG-AAGAGTAAAAAAAGGTAATCAGT
* *
20704 --AACAAGAGTAAAAAATGGTAATCAGT
1 AAAAGAAGAGTAAAAAAAGGTAATCAGT
20730 AATCAAG-A-AGTAAAAAAA
1 AA--AAGAAGAGTAAAAAAA
20748 ATAATCAATA
Statistics
Matches: 82, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
26 22 0.27
27 9 0.11
28 24 0.29
29 3 0.04
30 2 0.02
32 2 0.02
34 1 0.01
35 11 0.13
36 8 0.10
ACGTcount: A:0.58, C:0.04, G:0.19, T:0.20
Consensus pattern (28 bp):
AAAAGAAGAGTAAAAAAAGGTAATCAGT
Found at i:20710 original size:26 final size:27
Alignment explanation
Indices: 20681--20746 Score: 107
Period size: 26 Copynumber: 2.4 Consensus size: 27
20671 TTTAATTAGA
20681 AAGAGTAAAAAATGGTAATAAGTAA-C
1 AAGAGTAAAAAATGGTAATAAGTAATC
*
20707 AAGAGTAAAAAATGGTAATCAGTAATC
1 AAGAGTAAAAAATGGTAATAAGTAATC
20734 AAGAAGTAAAAAA
1 AAG-AGTAAAAAA
20747 AATAATCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
26 24 0.65
27 4 0.11
28 9 0.24
ACGTcount: A:0.59, C:0.05, G:0.18, T:0.18
Consensus pattern (27 bp):
AAGAGTAAAAAATGGTAATAAGTAATC
Found at i:20752 original size:27 final size:26
Alignment explanation
Indices: 20681--20754 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
20671 TTTAATTAGA
** *
20681 AAGAGTAAAAAATGGTAATAAGTAAC
1 AAGAGTAAAAAATAATAATCAGTAAC
**
20707 AAGAGTAAAAAATGGTAATCAGTAATC
1 AAGAGTAAAAAATAATAATCAGTAA-C
20734 AAGAAGTAAAAAA-AATAATCA
1 AAG-AGTAAAAAATAATAATCA
20755 ATAGTAAGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 24 0.56
27 10 0.23
28 9 0.21
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.19
Consensus pattern (26 bp):
AAGAGTAAAAAATAATAATCAGTAAC
Done.