Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011157.1 Corchorus capsularis cultivar CVL-1 contig11178, 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: 85121
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:279 original size:30 final size:30
Alignment explanation
Indices: 243--344 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 30
233 CTATGTTATA
*
243 TGTGTTTGGGGACTTTAGTAAAGATGCCTC
1 TGTGTTTAGGGACTTTAGTAAAGATGCCTC
* * *
273 TGTGTTTAGGGACTTTAATATAGGTGCC-C
1 TGTGTTTAGGGACTTTAGTAAAGATGCCTC
*
302 TTGTGCTT-GAGGACTTTGATGT-AA-ATGCCTC
1 -TGTGTTTAG-GGACTTT-A-GTAAAGATGCCTC
333 TGTGTTTAGGGA
1 TGTGTTTAGGGA
345 TGAATACCCT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
29 2 0.04
30 50 0.88
31 4 0.07
32 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.29, T:0.38
Consensus pattern (30 bp):
TGTGTTTAGGGACTTTAGTAAAGATGCCTC
Found at i:416 original size:26 final size:26
Alignment explanation
Indices: 380--481 Score: 91
Period size: 26 Copynumber: 3.7 Consensus size: 26
370 TTGAGAGAGG
380 TGCCTCTGTGTTT-AGGGACTTATAAA
1 TGCC-CTGTGTTTGAGGGACTTATAAA
* *
406 TGCCCGTGTGTTTGAGGAATTTGATATAGAA
1 TGCCC-TGTGTTTGAGGGA-CT--TATA-AA
437 TTGCCTCTGTGTTT-AGGGACTTATAAA
1 -TGCC-CTGTGTTTGAGGGACTTATAAA
464 TGCCCTTGTGTTTGAGGG
1 TGCCC-TGTGTTTGAGGG
482 CTTTAATTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
25 2 0.03
26 22 0.35
27 10 0.16
28 5 0.08
30 5 0.08
31 6 0.10
32 11 0.18
33 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (26 bp):
TGCCCTGTGTTTGAGGGACTTATAAA
Found at i:450 original size:58 final size:57
Alignment explanation
Indices: 243--485 Score: 250
Period size: 58 Copynumber: 4.3 Consensus size: 57
233 CTATGTTATA
* * *
243 TGTGTTTGGGGACTTT-AGTAAAG-ATGCCTCTGTGTTTAGGGACTTTAATATAGGTGCCCT
1 TGTGTTTGAGGACTTTGA-TATAGAATGCCTCTGTGTTTAGGGAC-TT-ATA-A-ATGCCCT
* * * *
303 TGTGCTTGAGGACTTTGATGTA-AATGCCTCTGTGTTTAGGG----ATGAATACCCT
1 TGTGTTTGAGGACTTTGATATAGAATGCCTCTGTGTTTAGGGACTTATAAATGCCCT
* * * *
355 TGTGTTTGAGGACTTTTGAGAGAG-GTGCCTCTGTGTTTAGGGACTTATAAATGCCCG
1 TGTGTTTGAGGAC-TTTGATATAGAATGCCTCTGTGTTTAGGGACTTATAAATGCCCT
*
412 TGTGTTTGAGGAATTTGATATAGAATTGCCTCTGTGTTTAGGGACTTATAAATGCCCT
1 TGTGTTTGAGGACTTTGATATAGAA-TGCCTCTGTGTTTAGGGACTTATAAATGCCCT
*
470 TGTGTTTGAGGGCTTT
1 TGTGTTTGAGGACTTT
486 AATTGTTGGG
Statistics
Matches: 151, Mismatches: 22, Indels: 22
0.77 0.11 0.11
Matches are distributed among these distances:
52 17 0.11
53 24 0.16
54 2 0.01
56 8 0.05
57 20 0.13
58 45 0.30
60 34 0.23
61 1 0.01
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.38
Consensus pattern (57 bp):
TGTGTTTGAGGACTTTGATATAGAATGCCTCTGTGTTTAGGGACTTATAAATGCCCT
Found at i:2232 original size:64 final size:66
Alignment explanation
Indices: 2101--2234 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 66
2091 AGCCAAATTG
* * *
2101 AATTGCCCCACCATTGAAATGCAAACACTAAAATAATTGTAAATCCAAAAAATGAGTTTGCATAA
1 AATTGCCCCACCATTCAAATGCAAACAC-AAAATAATTGTAAATCAAAAAAATGAGTTTGCAGAA
2166 AT
65 AT
2168 AATTGCCCCACCATTCAAATGCAAACAC-AAA-AATTGTAAATCAAAAAAATGAGTTTGCAGAAA
1 AATTGCCCCACCATTCAAATGCAAACACAAAATAATTGTAAATCAAAAAAATGAGTTTGCAGAAA
2231 T
66 T
2232 AAT
1 AAT
2235 AGTAAATTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
64 34 0.53
65 3 0.05
67 27 0.42
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (66 bp):
AATTGCCCCACCATTCAAATGCAAACACAAAATAATTGTAAATCAAAAAAATGAGTTTGCAGAAA
T
Found at i:4098 original size:2 final size:2
Alignment explanation
Indices: 4086--4116 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
4076 ACGATAATGG
4086 AT AT AT GAT 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
4117 CCATATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7351 original size:3 final size:3
Alignment explanation
Indices: 7337--7366 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
7327 ATTGAGTGAC
*
7337 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
7367 TCAAGGCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:7582 original size:2 final size:2
Alignment explanation
Indices: 7575--7609 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7565 TTAATTCCAA
7575 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 A
7610 GAAACAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8066 original size:5 final size:5
Alignment explanation
Indices: 8056--8085 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
8046 GTACTACCTC
*
8056 ATAAA ATAAA ATAAA ATAAA ATAAA TTAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
8086 CTACTATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:10730 original size:31 final size:32
Alignment explanation
Indices: 10692--10751 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
10682 TGACCTTGCT
10692 ATGTGGCA-TTTTGATCCAACGTGACATTACC
1 ATGTGGCATTTTTGATCCAACGTGACATTACC
* *
10723 ATGTGGCATTTTTGGTCCAACGTGGCATT
1 ATGTGGCATTTTTGATCCAACGTGACATT
10752 GTCACGCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (32 bp):
ATGTGGCATTTTTGATCCAACGTGACATTACC
Found at i:13611 original size:29 final size:29
Alignment explanation
Indices: 13569--13626 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
13559 GTCTTTTCAT
13569 TTATTCCATGGTTATCACTATTCTGTCAA
1 TTATTCCATGGTTATCACTATTCTGTCAA
13598 TTATTCCATGGTTATCACTATTCTGTCAA
1 TTATTCCATGGTTATCACTATTCTGTCAA
13627 ATGAAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (29 bp):
TTATTCCATGGTTATCACTATTCTGTCAA
Found at i:14361 original size:24 final size:24
Alignment explanation
Indices: 14329--14419 Score: 155
Period size: 24 Copynumber: 3.8 Consensus size: 24
14319 TCAAGTGTTC
*
14329 CTCTTTTTCTCTTTCATGCCCTTT
1 CTCTTTTTCTCTTTCATGCCCTCT
14353 CTCTTTTTCTCTTTCATGCCCTCT
1 CTCTTTTTCTCTTTCATGCCCTCT
14377 CTCTTTTTCTCTTTCATGCCCTCT
1 CTCTTTTTCTCTTTCATGCCCTCT
* *
14401 CTCTTTTTCCCTTCCATGC
1 CTCTTTTTCTCTTTCATGC
14420 TTTGCCTTCC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.04, C:0.37, G:0.04, T:0.54
Consensus pattern (24 bp):
CTCTTTTTCTCTTTCATGCCCTCT
Found at i:18182 original size:168 final size:169
Alignment explanation
Indices: 17901--18240 Score: 558
Period size: 168 Copynumber: 2.0 Consensus size: 169
17891 ATTGGTACGG
* *
17901 AGCTTAATTCCTGTGGGAAATTGACTTAGCATGTATACTAAGGACAATTCATGAGATAAATTTGC
1 AGCTTAATTCCTGTGGGAAATTGACTTAGAATGTATACTAAGGACAATTCATGAGAT--ACTTGC
* * * *
17966 AATGTCTAAATAGATATAATGAGAGTTTTAGCATTAGATTTAGCAGACATACAGAAGATGATAAT
64 AATATCTAAATAGATATAATGAGAGTTTTAGCATTAGATTTAGCAGACATAAAGAACACGATAAT
*
18031 GCACTTGGAAAGGATTACACTA-CATTTTGCATACTAAATCA
129 GCACTTGGAAAGGATTACACAACCA-TTTGCATACTAAATCA
*
18072 AGCTTAATTCCTGTGGGAAATTGTCTTAGAATGTATACTAAGGACAATTCATGAGAT-CTTGCAA
1 AGCTTAATTCCTGTGGGAAATTGACTTAGAATGTATACTAAGGACAATTCATGAGATACTTGCAA
18136 TATCTAAATAGATATAATGAGAGTTTTAGCATTAGATTTAGCAGACATAAAGAACACGATAATGC
66 TATCTAAATAGATATAATGAGAGTTTTAGCATTAGATTTAGCAGACATAAAGAACACGATAATGC
*
18201 ACTTGGAAAGGATTATACAACCATTTGCATACTAAATCA
131 ACTTGGAAAGGATTACACAACCATTTGCATACTAAATCA
18240 A
1 A
18241 CCCGTTAGAA
Statistics
Matches: 159, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
168 102 0.64
169 2 0.01
171 55 0.35
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (169 bp):
AGCTTAATTCCTGTGGGAAATTGACTTAGAATGTATACTAAGGACAATTCATGAGATACTTGCAA
TATCTAAATAGATATAATGAGAGTTTTAGCATTAGATTTAGCAGACATAAAGAACACGATAATGC
ACTTGGAAAGGATTACACAACCATTTGCATACTAAATCA
Found at i:30019 original size:2 final size:2
Alignment explanation
Indices: 30008--30040 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
29998 GTATTAATTG
30008 TA TA -A 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
30041 GTTGTGTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:30655 original size:30 final size:30
Alignment explanation
Indices: 30600--30672 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
30590 AAACTTTATG
30600 TTTTCCAATTGTACCCTTATTTTTAAAACATA
1 TTTT-CAATTGTACCCTTATTTTT-AAACATA
30632 TTTTCAATTGTACCCTT-TTTTTAAACATA
1 TTTTCAATTGTACCCTTATTTTTAAACATA
*
30661 TTTCTAAATTGT
1 TTT-TCAATTGT
30673 CATTATTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 10 0.26
30 12 0.31
31 13 0.33
32 4 0.10
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (30 bp):
TTTTCAATTGTACCCTTATTTTTAAACATA
Found at i:31250 original size:22 final size:22
Alignment explanation
Indices: 31133--31326 Score: 123
Period size: 22 Copynumber: 8.9 Consensus size: 22
31123 CACTTTGCAA
*
31133 ATTATCAAAATTTCATAGTGTG
1 ATTATCAAAATTTCATAGTGAG
* * * *
31155 ACTATCAAAATTTCGTAATGTG
1 ATTATCAAAATTTCATAGTGAG
* *
31177 GTTA-CAAAAATTTCATAG-AAG
1 ATTATC-AAAATTTCATAGTGAG
* * *
31198 GTTATCAAAATTTGAT-GTTGTG
1 ATTATCAAAATTTCATAG-TGAG
*
31220 CTTATCAAAATTTCATAGTGAG
1 ATTATCAAAATTTCATAGTGAG
* * *
31242 ATTAACAAAA-CTCTATAGGGA-
1 ATTATCAAAATTTC-ATAGTGAG
* * *
31263 AGTTATCAACA-TTCCTAGGGAG
1 A-TTATCAAAATTTCATAGTGAG
31285 ATTATCAAAATTTCATAGT-ATG
1 ATTATCAAAATTTCATAGTGA-G
* *
31307 GTTATCCAAATTTCATAGTG
1 ATTATCAAAATTTCATAGTG
31327 TACCAAATCA
Statistics
Matches: 133, Mismatches: 28, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 33 0.25
22 98 0.74
23 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGTGAG
Found at i:31428 original size:22 final size:21
Alignment explanation
Indices: 31390--31506 Score: 112
Period size: 22 Copynumber: 5.3 Consensus size: 21
31380 CAGCAAAATT
*
31390 AATTTCAT-GTAGAGGTTATCA
1 AATTTCATAGT-GTGGTTATCA
* *
31411 CTATTTTATAGTGTGGTTATCA
1 -AATTTCATAGTGTGGTTATCA
*
31433 AAGTTTCATAGTGTGGTAATCAA
1 AA-TTTCATAGTGTGGTTATC-A
31456 AATTTCATAG-GATGGTTATCGA
1 AATTTCATAGTG-TGGTTATC-A
*
31478 AATTTCATAGTGTGGGTATCA
1 AATTTCATAGTGTGGTTATCA
31499 AAGTTTCA
1 AA-TTTCA
31507 CAGGGATTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.06
22 69 0.86
23 6 0.08
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (21 bp):
AATTTCATAGTGTGGTTATCA
Found at i:32820 original size:109 final size:109
Alignment explanation
Indices: 32624--32898 Score: 444
Period size: 109 Copynumber: 2.5 Consensus size: 109
32614 ACTATTATAG
* *
32624 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
32689 TATTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
32738 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
32803 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
* *
32847 TTTTATTCTACTTAAAACTCTATTTTCATTTAATTAAATCCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATA
32899 TAATTTTTTT
Statistics
Matches: 155, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
108 6 0.04
109 123 0.79
110 3 0.02
111 2 0.01
114 21 0.14
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
Found at i:35312 original size:29 final size:29
Alignment explanation
Indices: 35280--35336 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
35270 TTGTGGAGTT
35280 TATAATTTAATTTTATCCTTTATGTAGTC
1 TATAATTTAATTTTATCCTTTATGTAGTC
*
35309 TATAATTTAATTTTATCCTTTGTGTAGT
1 TATAATTTAATTTTATCCTTTATGTAGT
35337 TTCTCGCAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (29 bp):
TATAATTTAATTTTATCCTTTATGTAGTC
Found at i:37584 original size:15 final size:15
Alignment explanation
Indices: 37564--37595 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
37554 ACGCCAATAT
37564 TTAATGTCACTGCCG
1 TTAATGTCACTGCCG
37579 TTAATGTCACTGCCG
1 TTAATGTCACTGCCG
37594 TT
1 TT
37596 TTCATTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (15 bp):
TTAATGTCACTGCCG
Found at i:39922 original size:11 final size:11
Alignment explanation
Indices: 39906--39930 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39896 GATTACAAAG
39906 ATTTCATTCCT
1 ATTTCATTCCT
39917 ATTTCATTCCT
1 ATTTCATTCCT
39928 ATT
1 ATT
39931 GTAGTCTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTCATTCCT
Found at i:42034 original size:33 final size:33
Alignment explanation
Indices: 41992--42061 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
41982 CTACAACCAG
41992 AATCTAGCACCAATCAAGACACCCAAGTTCTTC
1 AATCTAGCACCAATCAAGACACCCAAGTTCTTC
*
42025 AATCTAGCACCAATCAAGACACCCAGGTTCTTC
1 AATCTAGCACCAATCAAGACACCCAAGTTCTTC
42058 AATC
1 AATC
42062 GTCTCAATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (33 bp):
AATCTAGCACCAATCAAGACACCCAAGTTCTTC
Found at i:52236 original size:1 final size:1
Alignment explanation
Indices: 52230--52260 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
52220 ACCTGAAGGG
52230 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
52261 ATACCTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:58636 original size:16 final size:17
Alignment explanation
Indices: 58607--58638 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
58597 GTTTCCAGGT
58607 TAACACGATTACACGAA
1 TAACACGATTACACGAA
58624 TAACACG-TTACACGA
1 TAACACGATTACACGA
58639 CACATTAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (17 bp):
TAACACGATTACACGAA
Found at i:67061 original size:31 final size:31
Alignment explanation
Indices: 66992--67086 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
66982 TCCTTTTGTG
* **
66992 CACGTGGCATGCCACGTGTCACTTTTTGAAA
1 CACGTGGCATACCACGTGTCACTTTTTGGTA
*
67023 CATGTGGCATACCACGTGTCACTTTTTGGTA
1 CACGTGGCATACCACGTGTCACTTTTTGGTA
* * * *
67054 TACGTGGCGTGA-CATGTGTCAATTTTTGGTA
1 CACGTGGCAT-ACCACGTGTCACTTTTTGGTA
67085 CA
1 CA
67087 TATGGCACGA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 52 0.98
32 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (31 bp):
CACGTGGCATACCACGTGTCACTTTTTGGTA
Found at i:71264 original size:2 final size:2
Alignment explanation
Indices: 71257--71289 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
71247 TTGAGGGCAT
*
71257 TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71290 CAATTGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:72784 original size:2 final size:2
Alignment explanation
Indices: 72777--72801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
72767 CCAATCTACA
72777 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 A
72802 CACATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84302 original size:335 final size:333
Alignment explanation
Indices: 83551--85121 Score: 2191
Period size: 335 Copynumber: 4.8 Consensus size: 333
83541 AACAAACCCT
* * *
83551 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTCTTAAATGCAAT
* * * *
83616 GTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCCGCACAAAAAAATCATTCA
66 GTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGC-CAAAAATCATACA
*
83681 AAACTGAGTC-GGGGCCTCGAAACGCGTTTTTCGCCAAAAAACCGTGATGG-TAGTACACGATTT
130 AAACTGAGTCAGGGTCC-CGAAACGCGTTTTTCGCCAAAAAACCGTGATGGTTAGTACACGATTT
* *
83744 TGGCTAAAATTTTGT-AAAAATAACCCGAAAAAATTTTCCTCAATTTTTGGATAAAATACTCATA
194 TGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATA
83808 AATTATATATAATTTAACGCCAAGAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCAT
259 AATTATATATAATTTAACGCCAA-AAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCAT
*
83873 AATTTTTTCTA
323 AATTTTTTCTG
83884 AATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTCTTAAATGCAAT
* * * * * *
83949 GTGGCTAGGCTGTTTTTAGAGGAATATAGACATTTCAAGGAGTCTCGGCGCCAAAAAGCATACAA
66 GTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATACAA
* *
84014 AACTGAGTCAGGGTCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATTGTTAGTACACGATTTTG
131 AACTGAGTCAGGGTCCCGAAACGCGTTTTTCGCCAAAAAACCGTGATGGTTAGTACACGATTTTG
* * * *
84079 GTTGAAATTTTGTAAAAAAATGACCTGAAAATTTTTTCCTCAATTTTTGGATAAAATACTCATAA
196 GCTAAAATTTTGT-AAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAA
* * *
84144 ATTATATATAATTTAACACCGAAAAGATTGGAGGACTTTTCACGCTTTTAATATCATTTTTTAT-
260 ATTATATATAATTTAACGCC-AAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA
84208 ATTTTTTCTG
324 ATTTTTTCTG
* * *
84218 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTCTTAAATGCAAT
* * *
84283 GTGGCTAAAATTTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAAATCATTC
66 GTGGCTAAGA-TTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGC-CAAAAATCATAC
*
84348 AAAACTGAGTTAGGG-CCTCGAAACGCGTTTTTCGCCAAAAAACCGTGATGGTTAGTACACGATT
129 AAAACTGAGTCAGGGTCC-CGAAACGCGTTTTTCGCCAAAAAACCGTGATGGTTAGTACACGATT
*
84412 TTGGCTAAAATTTTGTAAAAAATAACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCAT
193 TTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCAT
*
84477 GAATTATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCA
258 AAATTATATATAATTTAACGCC-AAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCA
*
84542 TAATTTTTTCGG
322 TAATTTTTTCTG
* * * *
84554 AATTAATTTCTAAATAATTTGAATCAAGATTCAGATGTTCGTAAAAAAAAATTCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTCTTAAATGCAAT
* * *
84619 GTGGC---------TTTAGATGAATATAGACATTTCAAGGAGTCTCGGTGCCAAAAACCATACAA
66 GTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATACAA
* * * * ** *
84675 AACTGATTCAGGGTCCCGAAATGCGTTTTTAGCCAAAAAATCGT-A---ACAGTATACGATTTTG
131 AACTGAGTCAGGGTCCCGAAACGCGTTTTTCGCCAAAAAACCGTGATGGTTAGTACACGATTTTG
* * * *
84736 GTTGAAAA-TTTGTAAAAAAATGACCCGAAACATTTTTACTCAATTTTTGGATAAAATACTTATA
196 GCT-AAAATTTTGT-AAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATA
* * * *
84800 AAATATATATAATTTAATGCCAAAATGATTAGAGGACTTTTCACTCTTTTAATATCGTTTTTCAT
259 AATTATATATAATTTAACGCCAAAA-GATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCAT
84865 -A-TTTTTCTG
323 AATTTTTTCTG
84874 AATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTCTTAAATGCAAT
1 AATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTCTTAAATGCAAT
* * *
84939 GTGGCTAAGATTTTTTTAGATGAA-ACATGATATTTCAAGGAGTCTCGACGCCCAAAATCATACA
66 GTGGCTAAGATTTTTTTAGATGAATATA-GATATTTCAAGGAGTCTCGGCGCCAAAAATCATACA
* * * * * * * * *
85003 AAGCTGAGCCAAGGCCCCGAACCGCGGTTTTCCCCAAAAAACCATGATGGTTA--ACATGATTTT
130 AAACTGAGTCAGGGTCCCGAAACGCGTTTTTCGCCAAAAAACCGTGATGGTTAGTACACGATTTT
* * * *
85066 GGCTAAAATTTTGCAAAAAATGAACCGAAAAATTTGTCCTCAATTTTTAGATAAAA
195 GGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAA
Statistics
Matches: 1094, Mismatches: 116, Indels: 59
0.86 0.09 0.05
Matches are distributed among these distances:
320 73 0.07
321 25 0.02
322 105 0.10
324 1 0.00
325 47 0.04
326 37 0.03
328 2 0.00
329 74 0.07
330 42 0.04
331 15 0.01
332 51 0.05
333 138 0.13
334 78 0.07
335 251 0.23
336 155 0.14
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (333 bp):
AATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTCTTAAATGCAAT
GTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATACAA
AACTGAGTCAGGGTCCCGAAACGCGTTTTTCGCCAAAAAACCGTGATGGTTAGTACACGATTTTG
GCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAA
TTATATATAATTTAACGCCAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATAAT
TTTTTCTG
Done.