Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015974.1 Corchorus capsularis cultivar CVL-1 contig15995, 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: 135083
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:224 original size:2 final size:2
Alignment explanation
Indices: 219--252 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
209 TAAGATAAAG
219 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
253 TTGGGCATTG
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:3806 original size:21 final size:21
Alignment explanation
Indices: 3780--3819 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3770 AAATGCATCC
* *
3780 CACCTTTGTATACATAACAGG
1 CACCTTCGTATACAGAACAGG
3801 CACCTTCGTATACAGAACA
1 CACCTTCGTATACAGAACA
3820 TCAAACATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (21 bp):
CACCTTCGTATACAGAACAGG
Found at i:5227 original size:2 final size:2
Alignment explanation
Indices: 5220--5252 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5210 TATTTAAAAG
5220 TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5253 TCTTAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:8938 original size:15 final size:15
Alignment explanation
Indices: 8897--8955 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
8887 AACACTTTCA
* *
8897 GTGCCATCACCTTGG
1 GTGCCATCATCTTCG
*
8912 GTGCCGTCATCTTCG
1 GTGCCATCATCTTCG
* *
8927 GTTCCATCATCTTGG
1 GTGCCATCATCTTCG
*
8942 GTGCCATCACCTTC
1 GTGCCATCATCTTC
8956 CTCTATGGCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.12, C:0.34, G:0.22, T:0.32
Consensus pattern (15 bp):
GTGCCATCATCTTCG
Found at i:10260 original size:18 final size:18
Alignment explanation
Indices: 10181--10263 Score: 85
Period size: 18 Copynumber: 4.6 Consensus size: 18
10171 AAGTGTGGCA
*
10181 ACTTGGTGCGGTGCGGCC
1 ACTTGGTGTGGTGCGGCC
* * **
10199 ACTAGGTGCGGTGCGATC
1 ACTTGGTGTGGTGCGGCC
* *
10217 ACTTGGTGTGATGCGACC
1 ACTTGGTGTGGTGCGGCC
*
10235 ACTTGGTGTGGTGCGGCT
1 ACTTGGTGTGGTGCGGCC
*
10253 ACTGGGTGTGG
1 ACTTGGTGTGG
10264 CGCCTGGTGC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.11, C:0.20, G:0.42, T:0.27
Consensus pattern (18 bp):
ACTTGGTGTGGTGCGGCC
Found at i:13495 original size:220 final size:222
Alignment explanation
Indices: 13183--13581 Score: 624
Period size: 220 Copynumber: 1.8 Consensus size: 222
13173 ATACATATAG
13183 GAAGAATTTGTGGTTGAAGTCATTTTCTAGATGATATATATACCATAAGCACTTGGCATTAATCA
1 GAAGAATTTGTGGTTGAAGTCATTTTCTAGATGATATATATACCATAAGCACTTGGCATTAATCA
* * *
13248 AATTAGATACTGTACATATAGGATTATTAGAACAGCGATTGAAACGGAGATTACACTAAAGGTTC
66 AATTAGATACTGTACAGATAAGATTATTAGAACAGCGATTGAAACGGAGA-TACACTAAAGATTC
*
13313 TGTTTGACCGAAGCACCGGTGTACCAGCCC-AA-CG-GCCGGTAAACATTTCTCCTGAGAAATGT
130 CGTTTGACCGAAGCACCGGTGTACCAGCCCAAAGCGCGCCGGTAAACATTTCTCCTGAGAAATGT
13375 TCTAGATGGTATATATACATATATACAC
195 TCTAGATGGTATATATACATATATACAC
* * * *
13403 GAAGAATTTTTTGTTTAAGTCATTTTCTAGATGATATATATACCATAAGCACTTGGCCTTAATCA
1 GAAGAATTTGTGGTTGAAGTCATTTTCTAGATGATATATATACCATAAGCACTTGGCATTAATCA
* * * *
13468 AATTAGGTACTGTACAGATAAGATTATTAGAGCAGTGATTGAAACGGAGATACACTCAAGATTCC
66 AATTAGATACTGTACAGATAAGATTATTAGAACAGCGATTGAAACGGAGATACACTAAAGATTCC
* * * *
13533 GTTTGACTGATGCACGGGTGTACCAGCCCAAAGGGCGCCGGTAAACATT
131 GTTTGACCGAAGCACCGGTGTACCAGCCCAAAGCGCGCCGGTAAACATT
13582 CTAGATGATA
Statistics
Matches: 160, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
219 38 0.24
220 108 0.68
221 1 0.01
222 13 0.08
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (222 bp):
GAAGAATTTGTGGTTGAAGTCATTTTCTAGATGATATATATACCATAAGCACTTGGCATTAATCA
AATTAGATACTGTACAGATAAGATTATTAGAACAGCGATTGAAACGGAGATACACTAAAGATTCC
GTTTGACCGAAGCACCGGTGTACCAGCCCAAAGCGCGCCGGTAAACATTTCTCCTGAGAAATGTT
CTAGATGGTATATATACATATATACAC
Found at i:15342 original size:477 final size:462
Alignment explanation
Indices: 14463--15405 Score: 1483
Period size: 477 Copynumber: 2.0 Consensus size: 462
14453 AAAAGATTTA
* *
14463 GCATCATTACTTCAAGAATAAATTGATAAGGGTATTTCGGTCATTTCATGTTTGGTTTTTTGTTA
1 GCATCATTACTTCAAGAATAAATTGATAAGGGTATTTCGGTCATTTCATGTTCGGTTTTTTATTA
* *
14528 TTTGAGTTGAAGACTGAGGGCATTTTAGGAAGCTTGCCAAAAAAACCCTCCATGGGTCCCATATT
66 TTTGAGTTGAAGACCGAGGGCATTTTAGGAAGCTTACCAAAAAAACCCTCCATGGGTCCCATATT
* *
14593 CCACCATAATCACTTTATAAGTTGGGTAATTTGCCAAACTCTCCTTTATGCTATTTGGTCCTTTG
131 CCACCATAATCACTTTATAAATTGGGTAATTTGCAAAACTCTCCTTTATGCTATTTGGTCCTTTG
* *
14658 TGAATTCTAGCTTGGTCGATTTAACGTTTCGGTTTTGATTGTTTTATTTTTTGTTTTGTTTGTCC
196 TGAATTCTAACTTGGTCGATTTAACGTTTCGGCTTTGATTGTTTTATTTTTTGTTTTGTTTGTCC
* * *
14723 GATTAAGGTGATGCAGGTGTCTACTAAAAGGTGATCTTATGATCTACAACTTTCGTAAATGACTC
261 GATTAAGGTGATCCAGGTGTCTACTAAAAGGTGAGCTCATGATCTACAACTTTCGTAAATGACTC
* * *
14788 AAAAACCAATTTTAATGTTTTGATTCTAAAAATGCTTCTGAATTTTTTTGGTTCGGATTGGCGTT
326 AAAAACCAAATTTAATGTTTTGATCCTAAAAATGCTTCTGAATTTTTTTGGTTCCGATTGGCGTT
14853 CTATTTAATATCGTGTAATTTTTTATCCACATATCCGATTGAAGTCATTCAAGTGTTGGTTC-AA
391 CTATTTAATATCGTGTAATTTTTTATCCACATATCCGATTGAAGTCATTCAAGTGTTGGTTCAAA
14917 AGTTTATT
456 AG-TTATT
*
14925 GCATCATTACTTCAAGAATAAATTGATAGGGGTATTTCGGTCATTTCATGTTCGGTTTTTTTATT
1 GCATCATTACTTCAAGAATAAATTGATAAGGGTATTTCGGTCATTTCATGTTCGG-TTTTTTATT
* * ** *
14990 ATTTGAGTTGAAGACCGAGGGCATTTTAGGAAGTTTACCAAAAAAACTCTCTGTGGGTTCCATAT
65 ATTTGAGTTGAAGACCGAGGGCATTTTAGGAAGCTTACCAAAAAAACCCTCCATGGGTCCCATAT
* * *
15055 TCCACCGTAATCACTTTATAAATTGGGTAATTTATCAAATAGCCCTTTAGGTTTTCTCTTTTATG
130 TCCACCATAATCACTTTATAAATTGGGTAATTT-GCAAA-A---C---------TCTCCTTTATG
*
15120 CTATTTGGTCCTTTGTGAATTCTAACTTGGTTGATTTAACGTTTCGGCTTTGATTGTTTTATTTT
181 CTATTTGGTCCTTTGTGAATTCTAACTTGGTCGATTTAACGTTTCGGCTTTGATTGTTTTATTTT
* *
15185 TTGTTTTGTTTGTCCGATTAAGGTGATCCAGGTGTCTATTAAAATGTGAGCTCATGATCTACAAC
246 TTGTTTTGTTTGTCCGATTAAGGTGATCCAGGTGTCTACTAAAAGGTGAGCTCATGATCTACAAC
*
15250 TTTCGTAAATGACTCAAAAACCAAATTTAATGTTTTGATCCTAAAAATGCTTCTGAATTTTTTTT
311 TTTCGTAAATGACTCAAAAACCAAATTTAATGTTTTGATCCTAAAAATGCTTCTGAATTTTTTTG
*
15315 GTTCCGATTGGCGTTCTATTTAATATCGTGTAATTTTTTATCCACATGTCCGATTGAAGTCATTC
376 GTTCCGATTGGCGTTCTATTTAATATCGTGTAATTTTTTATCCACATATCCGATTGAAGTCATTC
15380 AAGTGTTGGTTCAAAAGTTATT
441 AAGTGTTGGTTCAAAAGTTATT
15402 GCAT
1 GCAT
15406 GATCTACGAC
Statistics
Matches: 437, Mismatches: 28, Indels: 17
0.91 0.06 0.04
Matches are distributed among these distances:
462 53 0.12
463 97 0.22
464 3 0.01
465 1 0.00
468 1 0.00
477 278 0.64
478 4 0.01
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (462 bp):
GCATCATTACTTCAAGAATAAATTGATAAGGGTATTTCGGTCATTTCATGTTCGGTTTTTTATTA
TTTGAGTTGAAGACCGAGGGCATTTTAGGAAGCTTACCAAAAAAACCCTCCATGGGTCCCATATT
CCACCATAATCACTTTATAAATTGGGTAATTTGCAAAACTCTCCTTTATGCTATTTGGTCCTTTG
TGAATTCTAACTTGGTCGATTTAACGTTTCGGCTTTGATTGTTTTATTTTTTGTTTTGTTTGTCC
GATTAAGGTGATCCAGGTGTCTACTAAAAGGTGAGCTCATGATCTACAACTTTCGTAAATGACTC
AAAAACCAAATTTAATGTTTTGATCCTAAAAATGCTTCTGAATTTTTTTGGTTCCGATTGGCGTT
CTATTTAATATCGTGTAATTTTTTATCCACATATCCGATTGAAGTCATTCAAGTGTTGGTTCAAA
AGTTATT
Found at i:19209 original size:19 final size:18
Alignment explanation
Indices: 19176--19214 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
19166 CATATTAACT
19176 ATTTTATTTAATTTTATTA
1 ATTTTATTTAATTTT-TTA
**
19195 ATTTTATTTCCTTTTTTA
1 ATTTTATTTAATTTTTTA
19213 AT
1 AT
19215 ATTTCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTATTTAATTTTTTA
Found at i:21039 original size:43 final size:42
Alignment explanation
Indices: 20975--21062 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 42
20965 AGAATGCACG
* *
20975 TTTTGAGTTTTGAAGAATGAAACAAGAAAATGCATATTTTGAA
1 TTTTGAGTTTTGAAGAATGAAACAA-AAAATGCAAATTTTAAA
* * *
21018 TTTTGAGTTTTGATGAGTGAAACAAAAGATGCAAATTTTAAA
1 TTTTGAGTTTTGAAGAATGAAACAAAAAATGCAAATTTTAAA
21060 TTT
1 TTT
21063 GGGGAACCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 17 0.43
43 23 0.57
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.38
Consensus pattern (42 bp):
TTTTGAGTTTTGAAGAATGAAACAAAAAATGCAAATTTTAAA
Found at i:21162 original size:37 final size:37
Alignment explanation
Indices: 21120--21496 Score: 384
Period size: 37 Copynumber: 10.2 Consensus size: 37
21110 GAATAGAGAC
*
21120 CTTAAACAAGAATTTGATAAGAAACCTAAACAGAAAT
1 CTTAAACAAGAATTTGATAAGAAACCTAAACAGGAAT
* ** * *
21157 CTTAAACAAGATTTTCCTAAGACACCTAAACAGGGAT
1 CTTAAACAAGAATTTGATAAGAAACCTAAACAGGAAT
* * *
21194 CTTAAACAAGGATTTAATAAGAAACCTAAACAGGATT
1 CTTAAACAAGAATTTGATAAGAAACCTAAACAGGAAT
* * * * *
21231 CTTGAACAAGATTTTGATGAA-ACACCTAAATAGTG-AC
1 CTTAAACAAGAATTTGAT-AAGAAACCTAAACAG-GAAT
* * *
21268 CTTAAACAAGGATTTAATAAGAAACCTAAACAGGATT
1 CTTAAACAAGAATTTGATAAGAAACCTAAACAGGAAT
* * * * *
21305 CTTAAACAAGATTTTGATGAGACACCTAAACAGGGAC
1 CTTAAACAAGAATTTGATAAGAAACCTAAACAGGAAT
*
21342 CTTAAACAAGGATTTGATAAGAAACCTAAACAGGAAT
1 CTTAAACAAGAATTTGATAAGAAACCTAAACAGGAAT
* * * * * *
21379 CTTAAATAAGATTTTGATGACACACCTAAACA-GAGAC
1 CTTAAACAAGAATTTGATAAGAAACCTAAACAGGA-AT
21416 CTTAAACAA-AGATTTGATAAGAAACCTAAACAGGAAT
1 CTTAAACAAGA-ATTTGATAAGAAACCTAAACAGGAAT
* * * * *
21453 CTTAAACAGGATTTTGATGAGACACCTAAACAGGAAC
1 CTTAAACAAGAATTTGATAAGAAACCTAAACAGGAAT
21490 CTTAAAC
1 CTTAAAC
21497 CAATGTTGTA
Statistics
Matches: 271, Mismatches: 61, Indels: 16
0.78 0.18 0.05
Matches are distributed among these distances:
36 6 0.02
37 259 0.96
38 6 0.02
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (37 bp):
CTTAAACAAGAATTTGATAAGAAACCTAAACAGGAAT
Found at i:21201 original size:74 final size:74
Alignment explanation
Indices: 21117--21496 Score: 580
Period size: 74 Copynumber: 5.1 Consensus size: 74
21107 CCTGAATAGA
* * ** *
21117 GACCTTAAACAAGAATTTGATAAGAAACCTAAACAGAAATCTTAAACAAGATTTTCCTAAGACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
21182 CTAAACAGG
66 CTAAACAGG
* * * * *
21191 GATCTTAAACAAGGATTTAATAAGAAACCTAAACAGGATTCTTGAACAAGATTTTGATGAAACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
* *
21256 CTAAATAGT
66 CTAAACAGG
* *
21265 GACCTTAAACAAGGATTTAATAAGAAACCTAAACAGGATTCTTAAACAAGATTTTGATGAGACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
21330 CTAAACAGG
66 CTAAACAGG
* *
21339 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAATAAGATTTTGATGACACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
*
21404 CTAAACAGA
66 CTAAACAGG
* *
21413 GACCTTAAACAAAGATTTGATAAGAAACCTAAACAGGAATCTTAAACAGGATTTTGATGAGACAC
1 GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
21478 CTAAACAGG
66 CTAAACAGG
*
21487 AACCTTAAAC
1 GACCTTAAAC
21497 CAATGTTGTA
Statistics
Matches: 278, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 278 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.23
Consensus pattern (74 bp):
GACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACAC
CTAAACAGG
Found at i:21976 original size:24 final size:23
Alignment explanation
Indices: 21940--21995 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
21930 AACCATGCCT
*
21940 TAAACAAGGATTTGATAAGAAACC
1 TAAAC-AGGATTTGATAACAAACC
* *
21964 TAAACAGGAATTTGATGACACACC
1 TAAACAGG-ATTTGATAACAAACC
21988 TAAACAGG
1 TAAACAGG
21996 GACCTTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (23 bp):
TAAACAGGATTTGATAACAAACC
Found at i:22014 original size:37 final size:37
Alignment explanation
Indices: 21964--22390 Score: 472
Period size: 37 Copynumber: 11.5 Consensus size: 37
21954 ATAAGAAACC
* *
21964 TAAAC-AGGAATTTGATGACACACCTAAACAGGGACCT
1 TAAACAAGG-ATTTGATAAGACACCTAAACAGGGACCT
* * * *
22001 TAAACAAGGATTTGATAAGAAACGTAAACAGGAATCT
1 TAAACAAGGATTTGATAAGACACCTAAACAGGGACCT
* *
22038 TAAACAA-GATTTTGATGAGACACCTAAACAGAGACCT
1 TAAACAAGGA-TTTGATAAGACACCTAAACAGGGACCT
* ** **
22075 TAAACAAGGATTTGATAAGAAACCTAAACAAAGTTCT
1 TAAACAAGGATTTGATAAGACACCTAAACAGGGACCT
*
22112 TAAACAA-GATTTTGATGAGACACCTAAACAGGGACCT
1 TAAACAAGGA-TTTGATAAGACACCTAAACAGGGACCT
* * * *
22149 TAAACAAGGATTTGATAAGAAACCGAAACAGGAATCT
1 TAAACAAGGATTTGATAAGACACCTAAACAGGGACCT
22186 TAAAC-AGGATTTTGA-AGAGACACCTAAACAGGGACCT
1 TAAACAAGGA-TTTGATA-AGACACCTAAACAGGGACCT
22223 TAAACAAGGATTTGATAAGACACCTAAACAGGGACCT
1 TAAACAAGGATTTGATAAGACACCTAAACAGGGACCT
* * *
22260 TAAATAAGGGTTTAATAAGACACCTAAACAGGGACCT
1 TAAACAAGGATTTGATAAGACACCTAAACAGGGACCT
* * * * *
22297 TAAAAAAGGATTTGATAAAACACCTAAACATGAATCT
1 TAAACAAGGATTTGATAAGACACCTAAACAGGGACCT
* *
22334 TGAACAA-AATTTGGATGAA-ACACCTAAACAGGGACCT
1 TAAACAAGGATTT-GAT-AAGACACCTAAACAGGGACCT
* *
22371 TAAATAAGGATTTGACAAGA
1 TAAACAAGGATTTGATAAGA
22391 AAAAGATTTA
Statistics
Matches: 325, Mismatches: 52, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
36 15 0.05
37 292 0.90
38 18 0.06
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (37 bp):
TAAACAAGGATTTGATAAGACACCTAAACAGGGACCT
Found at i:22085 original size:74 final size:74
Alignment explanation
Indices: 21964--22392 Score: 594
Period size: 74 Copynumber: 5.8 Consensus size: 74
21954 ATAAGAAACC
* * * *
21964 TAAACAGGAATTTGATGACACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACGTAAA
1 TAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAA
22029 CAGGAATCT
66 CAGGAATCT
*
22038 TAAACAAGATTTTGATGAGACACCTAAACAGAGACCTTAAACAAGGATTTGATAAGAAACCTAAA
1 TAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAA
22103 CA--AAGTTCT
66 CAGGAA--TCT
*
22112 TAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCGAAA
1 TAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAA
22177 CAGGAATCT
66 CAGGAATCT
* * *
22186 TAAACAGGATTTTGAAGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGACACCTAAA
1 TAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAA
* *
22251 CAGGGACCT
66 CAGGAATCT
* ** * * *
22260 TAAATAAGGGTTTAATAAGACACCTAAACAGGGACCTTAAAAAAGGATTTGATAA-AACACCTAA
1 TAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAA-ACCTAA
*
22324 ACATGAATCT
65 ACAGGAATCT
* * * * * *
22334 TGAACAAAATTTGGATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGACAAGAAA
1 TAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAA
22393 AAGATTTATT
Statistics
Matches: 313, Mismatches: 36, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
72 2 0.01
73 1 0.00
74 306 0.98
75 2 0.01
76 2 0.01
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (74 bp):
TAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAA
CAGGAATCT
Found at i:25791 original size:13 final size:13
Alignment explanation
Indices: 25773--25797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25763 ACCAAAAACA
25773 ATTTATGAATAAG
1 ATTTATGAATAAG
25786 ATTTATGAATAA
1 ATTTATGAATAA
25798 TTATTTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
ATTTATGAATAAG
Found at i:27243 original size:15 final size:16
Alignment explanation
Indices: 27212--27247 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
27202 ATCAAAGCTG
27212 AAATCAACATAGCATA
1 AAATCAACATAGCATA
*
27228 AAATCGACAT-GCATA
1 AAATCAACATAGCATA
27243 AAATC
1 AAATC
27248 CTCCCCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.19
Consensus pattern (16 bp):
AAATCAACATAGCATA
Found at i:36877 original size:157 final size:157
Alignment explanation
Indices: 36501--36908 Score: 461
Period size: 156 Copynumber: 2.6 Consensus size: 157
36491 TATCTTGGCT
* *
36501 AAGTTTCATCTCAAATGGACTTAAGATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTG
1 AAGTTTCATCTCAATTAGACTTAAGATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTG
* * * * * *
36566 GGGTGTGAAACCAACTTCACTATGAAATG-GAGTTCGGTTTTACTTAGAATTTTTTCCATTGTCT
66 GGGTGTGAAACCAAGTTCACCAT-AAAGGAGAGCTCAGTTTTACTTAGAATTTTTTCCATAGTCT
** **
36630 TATGGGGATAATCTAAACCTAATGGTGGA
130 TATGAAGATAATCTAAACCT-ATGGTCAA
*
36659 AA--TTCAGCTTC-ATTAGACTTAAGATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTT
1 AAGTTTCATC-TCAATTAGACTTAAGATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTT
* * * * * *
36721 AGGGAGAGAAACCAAGTTCACCATCAAGGAGAGCTCAGTTTTACTTGGAATTTTTTCCATAGTTT
65 GGGGTGTGAAACCAAGTTCACCATAAAGGAGAGCTCAGTTTTACTTAGAATTTTTTCCATAGTCT
* * **
36786 TGTGAAGATAGTCTTAGTCCCT-TGG-CAA
130 TATGAAGATAATC-TA-AACCTATGGTCAA
* *
36814 AAGTTTCATCTCAATTAGACTT-AGAATGAAAAACTTATGCAAGTTTTTCATTTAAGGATAGTTT
1 AAGTTTCATCTCAATTAGACTTAAG-ATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTT
* * *
36878 GGGGTGTGAAGCCTAGTTCACCATGAAGGAG
65 GGGGTGTGAAACCAAGTTCACCATAAAGGAG
36909 GGCTTGAACC
Statistics
Matches: 210, Mismatches: 32, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
155 6 0.03
156 119 0.57
157 80 0.38
158 5 0.02
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34
Consensus pattern (157 bp):
AAGTTTCATCTCAATTAGACTTAAGATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTG
GGGTGTGAAACCAAGTTCACCATAAAGGAGAGCTCAGTTTTACTTAGAATTTTTTCCATAGTCTT
ATGAAGATAATCTAAACCTATGGTCAA
Found at i:38818 original size:31 final size:31
Alignment explanation
Indices: 38780--38854 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
38770 ACAAAATATA
38780 TACCAAATCCTAATTGACAATTCGTAAGCTT
1 TACCAAATCCTAATTGACAATTCGTAAGCTT
* * * *
38811 TACCAAATCATATTTGCCAATTTGTAAGCTT
1 TACCAAATCCTAATTGACAATTCGTAAGCTT
*
38842 GACCAAATCCTAA
1 TACCAAATCCTAA
38855 CCACTTGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (31 bp):
TACCAAATCCTAATTGACAATTCGTAAGCTT
Found at i:42058 original size:33 final size:33
Alignment explanation
Indices: 41989--42089 Score: 114
Period size: 33 Copynumber: 3.1 Consensus size: 33
41979 TCTTGATCGA
* * *
41989 CATCAGTAGCCCAAGTTTCTTCATTCAAAGGGT
1 CATCAGTAGCCCCAGTTTCTTCATTCACAGGCT
**
42022 CATCAGTAGCCCCAGTTTCTTCATTCACATTCT
1 CATCAGTAGCCCCAGTTTCTTCATTCACAGGCT
* * *
42055 CATCAGTTGCACCA-TTTCCTTCATTCACAGCCT
1 CATCAGTAGCCCCAGTTT-CTTCATTCACAGGCT
42088 CA
1 CA
42090 ACATTTGCAC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 3 0.05
33 55 0.95
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.33
Consensus pattern (33 bp):
CATCAGTAGCCCCAGTTTCTTCATTCACAGGCT
Found at i:42098 original size:33 final size:33
Alignment explanation
Indices: 42004--42115 Score: 100
Period size: 33 Copynumber: 3.4 Consensus size: 33
41994 GTAGCCCAAG
* ** * * * *
42004 TTTCTTCATTCAAAGGGTCATCAGTAGCCCCAG
1 TTTCTTCATTCACAGCCTCAACAGTTGCACCAC
** *
42037 TTTCTTCATTCACATTCTCATCAGTTGCACCA-
1 TTTCTTCATTCACAGCCTCAACAGTTGCACCAC
* *
42069 TTTCCTTCATTCACAGCCTCAACATTTGCACGAC
1 TTT-CTTCATTCACAGCCTCAACAGTTGCACCAC
42103 TTTCTTCATTCAC
1 TTTCTTCATTCAC
42116 GGGATTTTCT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 3 0.05
33 60 0.91
34 3 0.05
ACGTcount: A:0.22, C:0.31, G:0.10, T:0.37
Consensus pattern (33 bp):
TTTCTTCATTCACAGCCTCAACAGTTGCACCAC
Found at i:42735 original size:13 final size:13
Alignment explanation
Indices: 42717--42744 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42707 ATCCCTAAAC
42717 ATGCTTTATAAGT
1 ATGCTTTATAAGT
42730 ATGCTTTATAAGT
1 ATGCTTTATAAGT
42743 AT
1 AT
42745 CAACACAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (13 bp):
ATGCTTTATAAGT
Found at i:54817 original size:22 final size:22
Alignment explanation
Indices: 54785--54826 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54775 TGAGTTAAAT
*
54785 AAAAATGATTTGAAATGACCTA
1 AAAAATGATTTGAAAGGACCTA
*
54807 AAAAATTATTTGAAAGGACC
1 AAAAATGATTTGAAAGGACC
54827 GATTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAAATGATTTGAAAGGACCTA
Found at i:56653 original size:60 final size:60
Alignment explanation
Indices: 56578--56742 Score: 215
Period size: 60 Copynumber: 2.8 Consensus size: 60
56568 GGCTAATTGC
** * *
56578 TCAAATAAGGGTCTAA-AGTTTGATAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGG
1 TCAAATAAGGGTCTAACA-TTTGCCAAAATGCTCAAATAAGGGCCTAATCTTTGAATTTAG
* * * **
56638 TCAAATAAGGATCTAATATTTGCCAAAATGCTCACATAAGGGCCCCATCTTTGAATTTAG
1 TCAAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGGGCCTAATCTTTGAATTTAG
* *
56698 CCAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCT
1 TCAAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGGGCCT
56743 GTCTCACGCG
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 89 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (60 bp):
TCAAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGGGCCTAATCTTTGAATTTAG
Found at i:56737 original size:31 final size:30
Alignment explanation
Indices: 56575--56742 Score: 105
Period size: 31 Copynumber: 5.6 Consensus size: 30
56565 TTAGGCTAAT
* *
56575 TGCTCAAATAAGGGTCTAA-AGTTTGATAAAA
1 TGCTCAAATAAGGGCCTAACA-TTTG-CAAAA
* **
56606 TGCTCAAATAAGGGCCTAATC-TTT-TAATT
1 TGCTCAAATAAGGGCCTAA-CATTTGCAAAA
* ** *
56635 TGGTCAAATAAGGATCTAATATTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACATTTG-CAAAA
* * * **
56666 TGCTCACATAAGGGCCCCATC-TTTG-AATT
1 TGCTCAAATAAGGG-CCTAACATTTGCAAAA
56695 TAGC-CAAATAAGGGCCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACATTTG-CAAAA
56726 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
56743 GTCTCACGCG
Statistics
Matches: 102, Mismatches: 24, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
28 4 0.04
29 38 0.37
30 4 0.04
31 54 0.53
32 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACATTTGCAAAA
Found at i:56814 original size:31 final size:31
Alignment explanation
Indices: 56775--56969 Score: 138
Period size: 31 Copynumber: 6.4 Consensus size: 31
56765 AACACCAGAT
* *
56775 CCTTATTTGAGTATTTTCGATAACGTTAGGT
1 CCTTATTTGAGCATTTTCGATAACGTTAGGC
*
56806 TCTTATTTGAGCATTTTCGATAACGTTAGGC
1 CCTTATTTGAGCATTTTCGATAACGTTAGGC
** * * * *
56837 CCTTATTTG-GC-TAAAT--AAAAAGATCGAGC
1 CCTTATTTGAGCAT-TTTCGATAACGTTAG-GC
56866 CCTTATTTGAGCATTTTCGATAACGTTAGGC
1 CCTTATTTGAGCATTTTCGATAACGTTAGGC
** * * *
56897 CCTTATTTG-GCCAAATT--A-AAAGATCAGAC
1 CCTTATTTGAG-CATTTTCGATAACG-TTAGGC
* *
56926 CCTTATTTGAGCATTTTGGCA-AACATTAGGC
1 CCTTATTTGAGCATTTTCG-ATAACGTTAGGC
56957 CCTTATTTGAGCA
1 CCTTATTTGAGCA
56970 ATTAGCCGAT
Statistics
Matches: 125, Mismatches: 27, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
28 9 0.07
29 30 0.24
30 8 0.06
31 69 0.55
32 9 0.07
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTCGATAACGTTAGGC
Found at i:56876 original size:60 final size:60
Alignment explanation
Indices: 56807--56965 Score: 250
Period size: 60 Copynumber: 2.6 Consensus size: 60
56797 ACGTTAGGTT
*
56807 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCTAAATAAAAAGATC-GAGCC
1 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATAAAAAGATCAGA-CC
*
56867 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACC
1 CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATAAAAAGATCAGACC
* *
56927 CTTATTTGAGCATTTTGGCA-AACATTAGGCCCTTATTTG
1 CTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
56966 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
60 90 0.97
61 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (60 bp):
CTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATAAAAAGATCAGACC
Found at i:70785 original size:1 final size:1
Alignment explanation
Indices: 70779--70808 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
70769 GAACCAATGG
70779 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
70809 CAGTAAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:72526 original size:19 final size:20
Alignment explanation
Indices: 72481--72538 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
72471 GCTGCTCTAA
72481 TAATCTCATCTTTACAGTAAC
1 TAATCTCATCTTTACAGT-AC
* *
72502 TAATCTAATCTTTACAGT-G
1 TAATCTCATCTTTACAGTAC
72521 TAATCTCATCTTTACAGT
1 TAATCTCATCTTTACAGT
72539 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (20 bp):
TAATCTCATCTTTACAGTAC
Found at i:74903 original size:30 final size:31
Alignment explanation
Indices: 74868--75008 Score: 89
Period size: 30 Copynumber: 4.5 Consensus size: 31
74858 CATTTGGAAG
74868 TTTCTATAGAAAGTAAAAAG-GTAGAAAGTT
1 TTTCTATAGAAAGTAAAAAGCGTAGAAAGTT
**
74898 TTTCTATAGAAAGT-TTAAGAC-TAGAAAGTTT
1 TTTCTATAGAAAGTAAAAAG-CGTAGAAAG-TT
* * * *
74929 TTTCT-TAAGAAAATACTTTAAGAGCCCGTTTGGAAG--
1 TTTCTAT-AGAAAGTA----AAAAG--CG-TAGAAAGTT
74965 TTTCTATAGAAAGTAAAAAG-GTAGAAAGTT
1 TTTCTATAGAAAGTAAAAAGCGTAGAAAGTT
74995 TTTCTATAGAAAGT
1 TTTCTATAGAAAGT
75009 TTAAGACTAG
Statistics
Matches: 83, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
28 5 0.06
29 4 0.05
30 36 0.43
31 13 0.16
32 4 0.05
36 14 0.17
37 2 0.02
39 5 0.06
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.34
Consensus pattern (31 bp):
TTTCTATAGAAAGTAAAAAGCGTAGAAAGTT
Found at i:75018 original size:97 final size:97
Alignment explanation
Indices: 74852--75046 Score: 381
Period size: 97 Copynumber: 2.0 Consensus size: 97
74842 CTAACCTCTT
74852 AGAGCCCATTTGGAAGTTTCTATAGAAAGTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAAG
1 AGAGCCCATTTGGAAGTTTCTATAGAAAGTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAAG
74917 ACTAGAAAGTTTTTTCTTAAGAAAATACTTTA
66 ACTAGAAAGTTTTTTCTTAAGAAAATACTTTA
*
74949 AGAGCCCGTTTGGAAGTTTCTATAGAAAGTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAAG
1 AGAGCCCATTTGGAAGTTTCTATAGAAAGTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAAG
75014 ACTAGAAAGTTTTTTCTTAAGAAAATACTTTA
66 ACTAGAAAGTTTTTTCTTAAGAAAATACTTTA
75046 A
1 A
75047 CATGTTTGTT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (97 bp):
AGAGCCCATTTGGAAGTTTCTATAGAAAGTAAAAAGGTAGAAAGTTTTTCTATAGAAAGTTTAAG
ACTAGAAAGTTTTTTCTTAAGAAAATACTTTA
Found at i:75020 original size:30 final size:31
Alignment explanation
Indices: 74889--75027 Score: 92
Period size: 30 Copynumber: 4.4 Consensus size: 31
74879 AGTAAAAAGG
74889 TAGAAAGTTTTTCTATAGAAAGTTTAAGA-C
1 TAGAAAGTTTTTCTATAGAAAGTTTAAGACC
*
74919 TAGAAAGTTTTTTCT-TAAGAAAATACTTTAAGAGCCC
1 TAGAAAG-TTTTTCTAT-AG--AA-AGTTTAAGA--CC
* * * * **
74956 GTTTGGAAG--TTTCTATAGAAAG-TAAAAAGG
1 --TAGAAAGTTTTTCTATAGAAAGTTTAAGACC
74986 TAGAAAGTTTTTCTATAGAAAGTTTAAGA-C
1 TAGAAAGTTTTTCTATAGAAAGTTTAAGACC
75016 TAGAAAGTTTTT
1 TAGAAAGTTTTT
75028 TCTTAAGAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 28
0.67 0.11 0.23
Matches are distributed among these distances:
28 5 0.06
30 33 0.40
31 13 0.16
32 4 0.05
33 3 0.04
34 10 0.12
36 7 0.09
37 2 0.02
39 5 0.06
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (31 bp):
TAGAAAGTTTTTCTATAGAAAGTTTAAGACC
Found at i:75639 original size:24 final size:24
Alignment explanation
Indices: 75612--75670 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
75602 GGATCTTTAG
75612 GAGGGGGCAGAATTTTTGATTCTT
1 GAGGGGGCAGAATTTTTGATTCTT
*
75636 GAGGGGGCACAATTTTTGATTCTT
1 GAGGGGGCAGAATTTTTGATTCTT
* *
75660 AAAGGGGCAGA
1 GAGGGGGCAGA
75671 GTAGACTGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.10, G:0.34, T:0.31
Consensus pattern (24 bp):
GAGGGGGCAGAATTTTTGATTCTT
Found at i:76309 original size:41 final size:41
Alignment explanation
Indices: 76252--76334 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
76242 TCATCTCATC
76252 CTTGACATTGCCTTGTTTCGCCCGAGACTTAGTGAAAGAAT
1 CTTGACATTGCCTTGTTTCGCCCGAGACTTAGTGAAAGAAT
76293 CTTGACATTGCCTTGTTTCGCCCGAGACTTAGTGAAAGAAT
1 CTTGACATTGCCTTGTTTCGCCCGAGACTTAGTGAAAGAAT
76334 C
1 C
76335 ATATAATGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (41 bp):
CTTGACATTGCCTTGTTTCGCCCGAGACTTAGTGAAAGAAT
Found at i:77328 original size:23 final size:23
Alignment explanation
Indices: 77298--77344 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
77288 TGCATTGCAC
77298 ACGTGACCCAATGTGCTTAAATT
1 ACGTGACCCAATGTGCTTAAATT
77321 ACGTGACCCAATGTGCTTAAATT
1 ACGTGACCCAATGTGCTTAAATT
77344 A
1 A
77345 AATGAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (23 bp):
ACGTGACCCAATGTGCTTAAATT
Found at i:79182 original size:2 final size:2
Alignment explanation
Indices: 79127--79162 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
79117 GTATAGTTAG
79127 TA TA 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 TA TA
79163 CCCTAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85633 original size:24 final size:24
Alignment explanation
Indices: 85601--85646 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
85591 TTCTAGATTT
85601 TGCTTTAGATAATTATCCTCTTCG
1 TGCTTTAGATAATTATCCTCTTCG
*
85625 TGCTTTAGATTATTATCCTCTT
1 TGCTTTAGATAATTATCCTCTT
85647 AGATTCTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.50
Consensus pattern (24 bp):
TGCTTTAGATAATTATCCTCTTCG
Found at i:87238 original size:36 final size:36
Alignment explanation
Indices: 87188--87321 Score: 214
Period size: 36 Copynumber: 3.7 Consensus size: 36
87178 AGTTTGATCA
* * *
87188 TAAGTCTTTAACTGATCTTACTTAATTATCCTGAAT
1 TAAGTCTTTGACTGATTTTACTTAATTACCCTGAAT
*
87224 TAAGTCTTTGACTGATTCTACTTAATTACCCTGAAT
1 TAAGTCTTTGACTGATTTTACTTAATTACCCTGAAT
* *
87260 TAAGTCTTTGACTGATTTTACTTAATTGCCCTAAAT
1 TAAGTCTTTGACTGATTTTACTTAATTACCCTGAAT
87296 TAAGTCTTTGACTGATTTTACTTAAT
1 TAAGTCTTTGACTGATTTTACTTAAT
87322 GCATGGATGC
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (36 bp):
TAAGTCTTTGACTGATTTTACTTAATTACCCTGAAT
Found at i:91412 original size:654 final size:657
Alignment explanation
Indices: 90364--91671 Score: 2182
Period size: 654 Copynumber: 2.0 Consensus size: 657
90354 TTATAAAGTA
*
90364 GAAAAGTTTGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATAGAGATCTTGA
1 GAAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATAGAGATCTTGA
*
90429 AACATAACAATTCCCTTTTTAACCCTTAATGAAACTCGTATATCAAATTTAGCTTTCAGGTCCTT
66 AACATAACAATTCCCTTTTTAACCATTAATGAAACTCGTATATCAAATTTAGCTTTCAGGTCCTT
* * *
90494 CATGAAAGTCGTAGATCATGCAATAACCTTTTAACCAACACTTGAATAACATTAATTGGACATGT
131 CATGAAAGTCATAGATCATGCAATAACCTTTTAACCAACACCTGAATAACATTAATCGGACATGT
* *
90559 GGATAAAAGAAACTTATATGATATTAAATAGACCGGCAATCAAAATCACCAAATTTCGGAAGATT
196 GGATAAAAGAAAATTATATGATATTAAATAGACCGGCAATCAAAATCACCAAATTTCGGAACATT
*
90624 TCTTTGAATTGAAACATAAAAATTGGCTTTTGACCCCTTCATGAAAGTTAAAACTCATGAAATTA
261 TCTCTGAATTGAAACATAAAAATTGGCTTTTGACCCCTTCATGAAAGTTAAAACTCATGAAATTA
* * * *
90689 CCTTTTAATAGACACCTGAATCACCTTAATCGGACAAATAGAAAAAAATATCTAAAGCGTTAAAT
326 CCTTATAATAGACACCTGAACCACCTTAATCGGACAAATAGAAAAAAATACCTAAAGCATTAAAT
* *
90754 CGATTTATAAAGGACTAAATAGCATAAAATAGAAAAGTAT-GCGG-GTCATTTCATAAATAATCC
391 CGATTTATAAAAGACTAAATAACATAAAATAGAAAAGTATGGCGGTGTCATTTCATAAATAATCC
* * *
90817 AAAAAAATTTGGGTTGATAGAGATGGGACCCACCAAGGGTT-T-TTTTTGCTAAAGTTACC-AAA
456 AAAAAAAATTGGGTTGATAGAGATGGGACCCACCAA-GGTTATGTTTTTCCTAAAATT-CCTAAA
* * * *
90879 ATGCCCTTGATCATCAATTCAAATTACAAAAGAACCAAGCATGAAATGACGAAAATACCCCTCCA
519 ATACCCCTGATCATCAACTCAAATAACAAAAGAACCAAGCATGAAATGACGAAAATACCCCTCCA
* *
90944 AATTTGTGCATGAATTCATCCGATCAAATCTTTAGATTGATTTTTTGGTATTTTCACTTCATATT
584 AATTTGTGCATGAATTCATCAGATCAAATCTTTAGATTGATTTTTTGATATTTTCACTTCATATT
91009 CTTATTATT
649 CTTATTATT
*
91018 GAAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATGGAGATCTTGA
1 GAAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATAGAGATCTTGA
91083 AACATAACAATTCCCTTTTTAACCATTAATGAAACTCGTATATCAAATTTAGCTTTCAGGTCCTT
66 AACATAACAATTCCCTTTTTAACCATTAATGAAACTCGTATATCAAATTTAGCTTTCAGGTCCTT
* *
91148 CATGAAAGTCATAGATCATGCAATAACGTTTTAACCGACACCTGAATAACATTAATCGGACATGT
131 CATGAAAGTCATAGATCATGCAATAACCTTTTAACCAACACCTGAATAACATTAATCGGACATGT
91213 GGATAAAA-AAAATTATATGATATTAAATAGACCGGCAATCAAAATCACCAAATTTCGGAACATT
196 GGATAAAAGAAAATTATATGATATTAAATAGACCGGCAATCAAAATCACCAAATTTCGGAACATT
* *
91277 T-TCTGCATTGAAACATAAAAATTGGCTTTTGACCCCTTCATGAAAGTTGTAAA-TCATGAAATT
261 TCTCTGAATTGAAACATAAAAATTGGCTTTTGACCCCTTCATGAAAGTT-AAAACTCATGAAATT
* *
91340 GCCTTATAATAGACACCTGAACCACCTTAATTGGACAAATAGAAAAAAAAATACCTAAAGCATTA
325 ACCTTATAATAGACACCTGAACCACCTTAATCGGACAAATAG--AAAAAAATACCTAAAGCATTA
* * * *
91405 AATCGATTTGTAAAAGATTAAATAACATAAAGTAGAAAAGTATGGGGGTGTCATTTCATAAATAA
388 AATCGATTTATAAAAGACTAAATAACATAAAATAGAAAAGTATGGCGGTGTCATTTCATAAATAA
91470 TCCAAAAAAAATTGGGTTGATAGAGATGGGACCCACCAAGGTTATGTTTTTCCTAAAATTCCTAA
453 TCCAAAAAAAATTGGGTTGATAGAGATGGGACCCACCAAGGTTATGTTTTTCCTAAAATTCCTAA
*
91535 AATACCCCTGGTCATCAACTCAAATAACAAAAGAACCAAGCATGAAATGACGAAAATACCCCTCC
518 AATACCCCTGATCATCAACTCAAATAACAAAAGAACCAAGCATGAAATGACGAAAATACCCCTCC
* *
91600 CAATTTGTGCATGAATTCATTAGATCAAATCTTTAGATTGATTTTTTGATATTTTCACTTCATAT
583 AAATTTGTGCATGAATTCATCAGATCAAATCTTTAGATTGATTTTTTGATATTTTCACTTCATAT
91665 TCTTATT
648 TCTTATT
91672 GTTTTGTTAT
Statistics
Matches: 609, Mismatches: 37, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
652 93 0.15
653 58 0.10
654 252 0.41
655 7 0.01
656 57 0.09
657 142 0.23
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (657 bp):
GAAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTGATAGAGATCTTGA
AACATAACAATTCCCTTTTTAACCATTAATGAAACTCGTATATCAAATTTAGCTTTCAGGTCCTT
CATGAAAGTCATAGATCATGCAATAACCTTTTAACCAACACCTGAATAACATTAATCGGACATGT
GGATAAAAGAAAATTATATGATATTAAATAGACCGGCAATCAAAATCACCAAATTTCGGAACATT
TCTCTGAATTGAAACATAAAAATTGGCTTTTGACCCCTTCATGAAAGTTAAAACTCATGAAATTA
CCTTATAATAGACACCTGAACCACCTTAATCGGACAAATAGAAAAAAATACCTAAAGCATTAAAT
CGATTTATAAAAGACTAAATAACATAAAATAGAAAAGTATGGCGGTGTCATTTCATAAATAATCC
AAAAAAAATTGGGTTGATAGAGATGGGACCCACCAAGGTTATGTTTTTCCTAAAATTCCTAAAAT
ACCCCTGATCATCAACTCAAATAACAAAAGAACCAAGCATGAAATGACGAAAATACCCCTCCAAA
TTTGTGCATGAATTCATCAGATCAAATCTTTAGATTGATTTTTTGATATTTTCACTTCATATTCT
TATTATT
Found at i:91800 original size:54 final size:54
Alignment explanation
Indices: 91718--91822 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
91708 AAACTTAGCC
*
91718 ATTGGAACTAAGACTCCAACATTCTGCCACCATACCAAATATCTAGCATTGGAT
1 ATTGGAACTAAGACTCCAACATTCTGCCAACATACCAAATATCTAGCATTGGAT
* *
91772 ATTGGAACTAAGAGTCCAACATTCTGCCAACGTACCAAATATCTAGCATTG
1 ATTGGAACTAAGACTCCAACATTCTGCCAACATACCAAATATCTAGCATTG
91823 AAGTTTATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (54 bp):
ATTGGAACTAAGACTCCAACATTCTGCCAACATACCAAATATCTAGCATTGGAT
Found at i:94459 original size:26 final size:25
Alignment explanation
Indices: 94416--94465 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
94406 GAAATTAATT
94416 ATAAAGAAAACAATTAAA-CTAAAA
1 ATAAAGAAAACAATTAAATCTAAAA
94440 ATAAAGCAAAACAAATTAAATCTAAA
1 ATAAAG-AAAAC-AATTAAATCTAAA
94466 TCTAAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 5 0.22
26 7 0.30
27 5 0.22
ACGTcount: A:0.68, C:0.10, G:0.04, T:0.18
Consensus pattern (25 bp):
ATAAAGAAAACAATTAAATCTAAAA
Found at i:101425 original size:17 final size:17
Alignment explanation
Indices: 101403--101436 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
101393 GTATGCATGC
101403 GAAAATAAGACGCGTGT
1 GAAAATAAGACGCGTGT
101420 GAAAATAAGACGCGTGT
1 GAAAATAAGACGCGTGT
101437 TATAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (17 bp):
GAAAATAAGACGCGTGT
Found at i:102054 original size:7 final size:7
Alignment explanation
Indices: 102041--102076 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
102031 GGAATTGGAA
102041 ACTTCCC
1 ACTTCCC
*
102048 CCTTCCC
1 ACTTCCC
102055 ACTTCCC
1 ACTTCCC
102062 ACTTCCC
1 ACTTCCC
102069 ACTTCCC
1 ACTTCCC
102076 A
1 A
102077 GGTTTGTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.58, G:0.00, T:0.28
Consensus pattern (7 bp):
ACTTCCC
Found at i:103506 original size:13 final size:13
Alignment explanation
Indices: 103488--103515 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
103478 ATATATTCAA
103488 ATTTCTAATTTAT
1 ATTTCTAATTTAT
103501 ATTTCTAATTTAT
1 ATTTCTAATTTAT
103514 AT
1 AT
103516 AGTAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTCTAATTTAT
Found at i:103542 original size:3 final size:3
Alignment explanation
Indices: 103534--103579 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
103524 ATATGCAATT
103534 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
103580 GATTGTACGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:113819 original size:2 final size:2
Alignment explanation
Indices: 113812--113840 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
113802 TATGATAACC
113812 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 A
113841 CAAATCTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:115124 original size:14 final size:14
Alignment explanation
Indices: 115107--115146 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
115097 TTAAAGTTAC
115107 TTATTTAATTTTAA
1 TTATTTAATTTTAA
115121 TTATTTAA--TT-A
1 TTATTTAATTTTAA
*
115132 TTATTTAATTATAA
1 TTATTTAATTTTAA
115146 T
1 T
115147 ACAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 1 0.05
14 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTAATTTTAA
Found at i:116744 original size:24 final size:25
Alignment explanation
Indices: 116717--116763 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
116707 TATTAATAGG
*
116717 TAAC-AAACTATAAGCCCAAATGGA
1 TAACAAAACTAGAAGCCCAAATGGA
*
116741 TAACAAAATTAGAAGCCCAAATG
1 TAACAAAACTAGAAGCCCAAATG
116764 CCTAAAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (25 bp):
TAACAAAACTAGAAGCCCAAATGGA
Found at i:119653 original size:23 final size:24
Alignment explanation
Indices: 119610--119659 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
119600 TCTCTTTCTT
* *
119610 TTTTTGTCTGTTTAGAGCTAGATC
1 TTTTTGTCTGATTAGAGCTAGAGC
119634 TTTTTGT-TGATT-GAGTCTAGAGC
1 TTTTTGTCTGATTAGAG-CTAGAGC
119657 TTT
1 TTT
119660 CCTTTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 13 0.57
24 7 0.30
ACGTcount: A:0.16, C:0.10, G:0.22, T:0.52
Consensus pattern (24 bp):
TTTTTGTCTGATTAGAGCTAGAGC
Found at i:123086 original size:21 final size:20
Alignment explanation
Indices: 123047--123091 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
123037 AATTATCAAT
* *
123047 TAAAAATAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
123067 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
123088 TAAA
1 TAAA
123092 TTTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.07, T:0.18
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:129153 original size:142 final size:144
Alignment explanation
Indices: 128893--129185 Score: 493
Period size: 142 Copynumber: 2.0 Consensus size: 144
128883 ACAAAATTTT
*
128893 CATTATGCCATCATGACATTTACAAGCTGATGATCAAAGGGAGGCTGAGATCAAAGCTCGATTCC
1 CATTATGCCATCATGACATTTACAAGCTGATGAGCAAAGGGAGGCTGAGATCAAAGCTCGATTCC
* *
128958 ATATCATAGAGGAATACCATTTTCTAGATTGAAAAATCTCTCTGCCCTTTATCATGTCATTTGGA
66 ATATCATAGAAGAATACCATTTTCTAGATTGAAAAATCTCTCTGCCCTCTATCATGTCATTTGGA
129023 CCATAAGAGGAT-A
131 CCATAAGAGGATGA
* * *
129036 -ATTATGCCATCATGATATTTACAAGCTGATGAGCAAAGGGAGGCTGATATCAAAGCTTGATTCC
1 CATTATGCCATCATGACATTTACAAGCTGATGAGCAAAGGGAGGCTGAGATCAAAGCTCGATTCC
129100 A-ATTCATAGAAGAATACCATTTTCTAGATTGAAAAATCTCTCTGCCCTCTATCATGTCATTTGG
66 ATA-TCATAGAAGAATACCATTTTCTAGATTGAAAAATCTCTCTGCCCTCTATCATGTCATTTGG
*
129164 ACCATTAGAGGATGA
130 ACCATAAGAGGATGA
129179 CATTATG
1 CATTATG
129186 TTAGCTTTCA
Statistics
Matches: 140, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
141 1 0.01
142 132 0.94
143 1 0.01
144 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (144 bp):
CATTATGCCATCATGACATTTACAAGCTGATGAGCAAAGGGAGGCTGAGATCAAAGCTCGATTCC
ATATCATAGAAGAATACCATTTTCTAGATTGAAAAATCTCTCTGCCCTCTATCATGTCATTTGGA
CCATAAGAGGATGA
Found at i:130266 original size:12 final size:12
Alignment explanation
Indices: 130245--130275 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
130235 ACATTTTAAC
130245 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
130257 AAAAAGAAAAAG
1 AAAAAAAAAAAG
130269 AAAAAAA
1 AAAAAAA
130276 GACCAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:135043 original size:24 final size:25
Alignment explanation
Indices: 135016--135068 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
135006 ATATATTCGC
135016 TAAAAAAA-TTATTATAAATATGTA
1 TAAAAAAATTTATTATAAATATGTA
135040 TAAAAAAATTTATTATAAATATGTA
1 TAAAAAAATTTATTATAAATATGTA
135065 TAAA
1 TAAA
135069 GAATAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TAAAAAAATTTATTATAAATATGTA
Done.