Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010049.1 Corchorus capsularis cultivar CVL-1 contig10070, 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: 9797
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Found at i:522 original size:31 final size:31
Alignment explanation
Indices: 480--553 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
470 GTTATTGATT
*
480 GGACTAAATTGACCCAATCTGCCAAGTAGAG
1 GGACTAAATTGACCCAAACTGCCAAGTAGAG
* *
511 GGACGAAATTGACCCAAAGTGCCAAGTAGAG
1 GGACTAAATTGACCCAAACTGCCAAGTAGAG
542 GGACTAAATTGA
1 GGACTAAATTGA
554 TACTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.18
Consensus pattern (31 bp):
GGACTAAATTGACCCAAACTGCCAAGTAGAG
Found at i:603 original size:31 final size:29
Alignment explanation
Indices: 534--606 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
524 CCAAAGTGCC
*
534 AAGTAGAGGGACTAAATTGATACTTTTTTT
1 AAGTAGAGGGACGAAATTGATA-TTTTTTT
*
564 TAGTAGAGGGACGAAATTGAT-TTTTTTGT
1 AAGTAGAGGGACGAAATTGATATTTTTT-T
593 GAAAGTAGAGGGAC
1 --AAGTAGAGGGAC
607 CTCCTGGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.16
29 1 0.03
30 19 0.51
31 11 0.30
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
AAGTAGAGGGACGAAATTGATATTTTTTT
Found at i:1345 original size:3 final size:3
Alignment explanation
Indices: 1337--1384 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
1327 AAAAAAGAAA
*
1337 AAT AAT AAT AAT ACT AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
1383 AA
1 AA
1385 AAGTAAATCG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1515 original size:36 final size:37
Alignment explanation
Indices: 1468--1537 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
1458 CCGAAAGACA
*
1468 AAATCGATTTAGGTCTAAAGCTAAAAAGA-AGGGGGG
1 AAATCGATTTAGGGCTAAAGCTAAAAAGAGAGGGGGG
1504 AAATCGATTTAGGGCTAAAGCTAAAAAGAGAGGG
1 AAATCGATTTAGGGCTAAAGCTAAAAAGAGAGGG
1538 AAAAAGAGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.19
Consensus pattern (37 bp):
AAATCGATTTAGGGCTAAAGCTAAAAAGAGAGGGGGG
Found at i:4429 original size:46 final size:47
Alignment explanation
Indices: 4366--4460 Score: 156
Period size: 46 Copynumber: 2.0 Consensus size: 47
4356 GATTTTTCTA
4366 TTTTCTTTTTTATTTTCTAAGTTTTTTTT-TATTTTAGGCGGGATTT
1 TTTTCTTTTTTATTTTCTAAGTTTTTTTTATATTTTAGGCGGGATTT
** *
4412 TTTTCTTTTTTATTTTCTCCGTTTTTTTTATATTTTGGGCGGGATTT
1 TTTTCTTTTTTATTTTCTAAGTTTTTTTTATATTTTAGGCGGGATTT
4459 TT
1 TT
4461 CCCGCCGAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 27 0.60
47 18 0.40
ACGTcount: A:0.11, C:0.08, G:0.14, T:0.67
Consensus pattern (47 bp):
TTTTCTTTTTTATTTTCTAAGTTTTTTTTATATTTTAGGCGGGATTT
Found at i:6007 original size:2 final size:2
Alignment explanation
Indices: 6000--6029 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5990 GATAAACATG
*
6000 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6030 GCAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6350 original size:4 final size:4
Alignment explanation
Indices: 6341--6370 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
6331 TGATGATACG
*
6341 TTGA TTGA TTGG TTGA TTGA TTGA TTGA TT
1 TTGA TTGA TTGA TTGA TTGA TTGA TTGA TT
6371 AATAAGATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (4 bp):
TTGA
Found at i:6358 original size:104 final size:103
Alignment explanation
Indices: 6148--6350 Score: 336
Period size: 104 Copynumber: 2.0 Consensus size: 103
6138 AACATGCATA
*
6148 GATTAATAAGATAGTTGATGAGATATTTATATCGTTGATTAATAAGATAATAATAATATGCATGG
1 GATTAATAAGATAGTTGATGAGATATTTATATCGTTGATTAATAAGATAATAATAACATGCATGG
* * *
6213 ATTGATTAGATAGTTGATGGTATGTTTATTGATTAATT
66 ATTGATTAGATAGTTGATGATACGTTGATTGATTAATT
*
6251 GATTAATAAGATAGTTGATGGGATATTTATATCGATTGATTAATGAA-ATAATAATAACATGCAT
1 GATTAATAAGATAGTTGATGAGATATTTATATCG-TTGATTAAT-AAGATAATAATAACATGCAT
6315 GGATTGATTAGATAGTTGATGATACGTTGATTGATT
64 GGATTGATTAGATAGTTGATGATACGTTGATTGATT
6351 GGTTGATTGA
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
103 33 0.35
104 58 0.62
105 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (103 bp):
GATTAATAAGATAGTTGATGAGATATTTATATCGTTGATTAATAAGATAATAATAACATGCATGG
ATTGATTAGATAGTTGATGATACGTTGATTGATTAATT
Found at i:7880 original size:22 final size:22
Alignment explanation
Indices: 7852--7981 Score: 109
Period size: 22 Copynumber: 5.8 Consensus size: 22
7842 TGTCTCTATG
*
7852 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
7874 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* **
7897 -GGTTATCAAAATTCCATAGTC
1 TGGTTATCAAAATTTCATAGGA
*
7918 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
7940 TCAAGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
**
7964 TGGTTATTGAAATTTCAT
1 TGGTTATCAAAATTTCAT
7982 GTGGTGGTTA
Statistics
Matches: 84, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
21 2 0.02
22 62 0.74
23 3 0.04
24 17 0.20
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:8072 original size:22 final size:20
Alignment explanation
Indices: 8032--8165 Score: 97
Period size: 22 Copynumber: 6.2 Consensus size: 20
8022 AGATATCATC
*
8032 AAAATGTCATAGCGAGGTTAT
1 AAAATTTCATAG-GAGGTTAT
* *
8053 AATAATTTCATAGTATGGTTAAC
1 AA-AATTTCATAGGA-GGTT-AT
8076 AAAATTTCATTAGGAGGTTACT
1 AAAATTTCA-TAGGAGGTTA-T
* *
8098 AATATTTCATGGGAGGTTAT
1 AAAATTTCATAGGAGGTTAT
* * *
8118 CAAAATTTTATAGTGTGGCTAT
1 -AAAATTTCATAG-GAGGTTAT
*
8140 CAAAATTTCATATGAAGGTTAT
1 -AAAATTTCATA-GGAGGTTAT
8162 AAAA
1 AAAA
8166 GTCTCAATTT
Statistics
Matches: 89, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 26 0.29
22 54 0.61
23 8 0.09
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (20 bp):
AAAATTTCATAGGAGGTTAT
Found at i:8093 original size:44 final size:43
Alignment explanation
Indices: 8031--8130 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 43
8021 AAGATATCAT
* *
8031 CAAAATGTCATAGCGAGGTTA-TAATAATTTCATAGTATGGTTAA
1 CAAAATTTCATAGCGAGGTTACTAAT-ATTTCATAGGA-GGTTAA
* *
8075 CAAAATTTCATTAG-GAGGTTACTAATATTTCATGGGAGGTTAT
1 CAAAATTTCA-TAGCGAGGTTACTAATATTTCATAGGAGGTTAA
*
8118 CAAAATTTTATAG
1 CAAAATTTCATAG
8131 TGTGGCTATC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
42 3 0.06
43 14 0.29
44 25 0.51
45 7 0.14
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (43 bp):
CAAAATTTCATAGCGAGGTTACTAATATTTCATAGGAGGTTAA
Found at i:8240 original size:22 final size:22
Alignment explanation
Indices: 8171--8442 Score: 125
Period size: 22 Copynumber: 12.5 Consensus size: 22
8161 TAAAAGTCTC
* *
8171 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
8191 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
8211 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
8233 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
*
8258 AATTT-ATATGA-AGATTATCAA
1 AATTTCATA-GAGTGATTATCAA
*
8279 AATTTCATAGTGTTGA-TATCAA
1 AATTTCATAGAG-TGATTATCAA
* * * *
8301 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
8323 AATTACACA-ATGTGATTATCAT
1 AATTTCATAGA-GTGATTATCAA
* * * *
8345 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* ** * * *
8367 CATTTTGTAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
8389 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
8411 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
8433 AATTTCATAG
1 AATTTCATAG
8443 TGGTATTTCT
Statistics
Matches: 192, Mismatches: 42, Indels: 33
0.72 0.16 0.12
Matches are distributed among these distances:
19 2 0.01
20 18 0.09
21 28 0.15
22 121 0.63
23 5 0.03
24 3 0.02
25 15 0.08
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:8484 original size:22 final size:21
Alignment explanation
Indices: 8457--8664 Score: 95
Period size: 22 Copynumber: 9.6 Consensus size: 21
8447 ATTTCTGAGG
8457 AGGTTATCAAAATTTCATAAT
1 AGGTTATCAAAATTTCATAAT
*
8478 ATGGTTATC-AAA-TT-AGAA-
1 A-GGTTATCAAAATTTCATAAT
* * * *
8496 AGGTTATTAAACTTTTATTAT
1 AGGTTATCAAAATTTCATAAT
*
8517 GGAGTAAATATCAAAATTTCAT-AT
1 AG-GT---TATCAAAATTTCATAAT
* *
8541 GAAGGTTAACAAAATTTCATAGTTT
1 --AGGTTATCAAAATTTCATA--AT
* *
8566 A-GTTTTCAAAATTTCATAAG
1 AGGTTATCAAAATTTCATAAT
* *
8586 AGTGTTATGAAAATTTCATAGT
1 AG-GTTATCAAAATTTCATAAT
* * **
8608 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATA-AT
* *
8631 AGATTAACAAAATTTCATAAT
1 AGGTTATCAAAATTTCATAAT
8652 GAGGTTATCAAAA
1 -AGGTTATCAAAA
8665 AATTATAGGG
Statistics
Matches: 136, Mismatches: 32, Indels: 37
0.66 0.16 0.18
Matches are distributed among these distances:
17 6 0.04
18 3 0.02
19 5 0.04
20 5 0.04
21 7 0.05
22 89 0.65
23 4 0.03
24 2 0.01
25 14 0.10
26 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAAT
Found at i:8662 original size:44 final size:44
Alignment explanation
Indices: 8525--8959 Score: 232
Period size: 44 Copynumber: 10.0 Consensus size: 44
8515 ATGGAGTAAA
* * * * *
8525 TATCAAAATTTCATATGAAGGTTAACAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAG-TGAGGT
* * * * *
8569 TTTCAAAATTTCATA-AGAGTGTTATGAAAATTTCATAGT-ATGT
1 TATCAAAATTTCATAGGGAG-ATTATCAAAATTTCATAGTGAGGT
* * *
8612 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * *
8657 TATCAAAAAATT-ATAGGGAGCTTATCAAAA-TT--T-GT-A-AT
1 TATC-AAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * * * *
8695 TATCAAGATTTCATA-AGAAATTTATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGG-T
* * *
8740 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAGGT
* * * * * * *
8785 TATCACAATTTCATAGTGTGATTATCAAAAGTTCAGAGTGTGAT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * * * ** * *
8829 TA-CTAACAA-TTCATATGGAGGTTTTTAATTTTTCATAATGTGGT
1 TATC-AA-AATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
* * * * ** * *
8873 TATCAATATATCATATGGAGGTTATCAACGTCTCATAGTGTTGGT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG-AGGT
* *
8918 TATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATATTGAG
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGTGAG
8960 ATTTACAAAA
Statistics
Matches: 295, Mismatches: 74, Indels: 44
0.71 0.18 0.11
Matches are distributed among these distances:
37 7 0.02
38 17 0.06
39 3 0.01
40 1 0.00
41 2 0.01
42 2 0.01
43 10 0.03
44 150 0.51
45 80 0.27
46 23 0.08
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (44 bp):
TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGT
Found at i:8719 original size:22 final size:22
Alignment explanation
Indices: 8694--8800 Score: 99
Period size: 23 Copynumber: 4.8 Consensus size: 22
8684 AAATTTGTAA
* *
8694 TTATCAAGATTTCATAAGAAAT
1 TTATCAAAATTTCATAGGAAAT
* **
8716 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATA-GGAAAT
*
8739 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGAA-AT
**
8762 TTATCAAAATTTCATAGCG-AGG
1 TTATCAAAATTTCATAG-GAAAT
*
8784 TTATCACAATTTCATAG
1 TTATCAAAATTTCATAG
8801 TGTGATTATC
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
22 33 0.46
23 37 0.52
24 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAAAT
Found at i:8744 original size:23 final size:23
Alignment explanation
Indices: 8715--8800 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
8705 TCATAAGAAA
*
8715 TTTATCAAAATTTTATAGGGAGG
1 TTTATCAAAATTTCATAGGGAGG
* * *
8738 TTTATCAAAATTTTATAGGAAGA
1 TTTATCAAAATTTCATAGGGAGG
*
8761 TTTATCAAAATTTCATAGCGAGG
1 TTTATCAAAATTTCATAGGGAGG
*
8784 -TTATCACAATTTCATAG
1 TTTATCAAAATTTCATAG
8801 TGTGATTATC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
22 16 0.29
23 40 0.71
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (23 bp):
TTTATCAAAATTTCATAGGGAGG
Found at i:8745 original size:45 final size:44
Alignment explanation
Indices: 8694--8799 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 44
8684 AAATTTGTAA
* *
8694 TTATCAAGATTTCATAAGAA-ATTTATCAAAATTTTATAGGGAGG
1 TTATCAA-ATTTCATAAGAAGATTTATCAAAATTTCATAGCGAGG
* *
8738 TTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGG
1 -TTATC-AAATTTCATAAGAAGATTTATCAAAATTTCATAGCGAGG
8784 TTATCACAATTTCATA
1 TTATCA-AATTTCATA
8800 GTGTGATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
44 1 0.02
45 28 0.53
46 24 0.45
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (44 bp):
TTATCAAATTTCATAAGAAGATTTATCAAAATTTCATAGCGAGG
Found at i:8809 original size:22 final size:22
Alignment explanation
Indices: 8525--8830 Score: 116
Period size: 22 Copynumber: 14.1 Consensus size: 22
8515 ATGGAGTAAA
* *
8525 TATCAAAATTTCATA-TGAAGGT
1 TATCAAAATTTCATAGTG-TGAT
* *
8547 TAACAAAATTTCATAGT-TTAGT
1 TATCAAAATTTCATAGTGTGA-T
* *
8569 TTTCAAAATTTCATAAGAGTG-T
1 TATCAAAATTTCAT-AGTGTGAT
* *
8591 TATGAAAATTTCATAGTATG-T
1 TATCAAAATTTCATAGTGTGAT
* * *
8612 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTGTGAT
* * * *
8635 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTGTGAT
* * * *
8657 TATCAAAAAATT-ATAGGGAGCT
1 TATC-AAAATTTCATAGTGTGAT
*
8679 TATCAAAA--T--T--TGTAAT
1 TATCAAAATTTCATAGTGTGAT
* * **
8695 TATCAAGATTTCATA-AGAAATT
1 TATCAAAATTTCATAGTGTGA-T
* * * *
8717 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGTG-TGAT
* *
8740 TATCAAAATTTTATAG-GAAGATT
1 TATCAAAATTTCATAGTG-TGA-T
* * *
8763 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGTGTGAT
*
8785 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
* *
8807 TATCAAAAGTTCAGAGTGTGAT
1 TATCAAAATTTCATAGTGTGAT
8829 TA
1 TA
8831 CTAACAATTC
Statistics
Matches: 216, Mismatches: 51, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
16 9 0.04
18 2 0.01
19 1 0.00
20 1 0.00
21 12 0.06
22 143 0.66
23 46 0.21
24 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGAT
Found at i:8886 original size:22 final size:22
Alignment explanation
Indices: 8861--8923 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
8851 TTTTAATTTT
*
8861 TCATAATGTGGTTATCAATATA
1 TCATAATGTGGTTATCAACATA
* * *
8883 TCAT-ATGGAGGTTATCAACGTC
1 TCATAAT-GTGGTTATCAACATA
*
8905 TCATAGTGTTGGTTATCAA
1 TCATAATG-TGGTTATCAA
8924 AATTTCATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 2 0.06
22 20 0.62
23 10 0.31
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (22 bp):
TCATAATGTGGTTATCAACATA
Found at i:8942 original size:45 final size:44
Alignment explanation
Indices: 8861--8945 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
8851 TTTTAATTTT
* *
8861 TCATAATGTGGTTATCAATATATCATATGGAGGTTATCAACGTC
1 TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAACGTC
* *
8905 TCATAGTGTTGGTTATCAAAATTTCAT-TGGGAAGTTATCAA
1 TCATAATG-TGGTTATCAAAATATCATAT-GGAAGTTATCAA
8946 AATTTCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
44 8 0.23
45 27 0.77
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (44 bp):
TCATAATGTGGTTATCAAAATATCATATGGAAGTTATCAACGTC
Found at i:8991 original size:22 final size:21
Alignment explanation
Indices: 8966--9020 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
8956 TGAGATTTAC
* *
8966 AAAATTCCTTAGATAGGTTAAA
1 AAAATTCATAAGA-AGGTTAAA
8988 AAAATTTCATAAGAAGGTTAAA
1 AAAA-TTCATAAGAAGGTTAAA
*
9010 AAAATTTATAA
1 AAAATTCATAA
9021 AAATATTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 16 0.55
23 7 0.24
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.31
Consensus pattern (21 bp):
AAAATTCATAAGAAGGTTAAA
Found at i:9010 original size:21 final size:21
Alignment explanation
Indices: 8980--9020 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
8970 TTCCTTAGAT
8980 AGGTTAAAAAAATTTCATAAGA
1 AGGTTAAAAAAATTT-ATAAGA
9002 AGGTTAAAAAAATTTATAA
1 AGGTTAAAAAAATTTATAA
9021 AAATATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.29
Consensus pattern (21 bp):
AGGTTAAAAAAATTTATAAGA
Done.