Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011713.1 Corchorus capsularis cultivar CVL-1 contig11734, 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: 20836
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3542 original size:15 final size:15
Alignment explanation
Indices: 3522--3550 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3512 TCGGTTGAAA
3522 TATCGTGTATCGTGT
1 TATCGTGTATCGTGT
3537 TATCGTGTATCGTG
1 TATCGTGTATCGTG
3551 GCGGCCTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (15 bp):
TATCGTGTATCGTGT
Found at i:5874 original size:23 final size:23
Alignment explanation
Indices: 5846--5891 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5836 TAGTTGGATA
5846 ATTGATTTTGTGATAAAATTTGG
1 ATTGATTTTGTGATAAAATTTGG
*
5869 ATTGATTTTGTGTTAAAATTTGG
1 ATTGATTTTGTGATAAAATTTGG
5892 GTAAAATTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (23 bp):
ATTGATTTTGTGATAAAATTTGG
Found at i:10870 original size:22 final size:22
Alignment explanation
Indices: 10845--10944 Score: 96
Period size: 22 Copynumber: 4.5 Consensus size: 22
10835 GAAAGATTAT
10845 CAAAATTTCATAGTGTGGTTAC
1 CAAAATTTCATAGTGTGGTTAC
* *
10867 CAAAATTTCATA-TCAAT-GTTAT
1 CAAAATTTCATAGT--GTGGTTAC
* * *
10889 CAAAACTTCATAGTGTAGTTAT
1 CAAAATTTCATAGTGTGGTTAC
** *
10911 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGTGTGGTTAC
10933 CAAAATTTCATA
1 CAAAATTTCATA
10945 AAAAGAATAC
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.03
22 60 0.94
23 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGTGGTTAC
Found at i:10871 original size:44 final size:43
Alignment explanation
Indices: 10821--10944 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 43
10811 TGACGATCAA
* * *
10821 ACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTGGTT
1 ACCAAAATTTCATACAAAG-TTATCAAAATTTCATAGTGTAGTT
* *
10865 ACCAAAATTTCATATCAATGTTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATA-CAAAGTTATCAAAATTTCATAGTGTAGTT
* * *
10909 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATA
1 ACCAAAATTTCATACA-AAGTTATCAAAATTTCATA
10945 AAAAGAATAC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.03
44 64 0.93
45 3 0.04
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (43 bp):
ACCAAAATTTCATACAAAGTTATCAAAATTTCATAGTGTAGTT
Found at i:10955 original size:22 final size:22
Alignment explanation
Indices: 10911--10963 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
10901 GTGTAGTTAT
* * **
10911 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAAAAAGAATAC
10933 CAAAATTTCATAAAAAGAATAC
1 CAAAATTTCATAAAAAGAATAC
10955 CAAAATTTC
1 CAAAATTTC
10964 TTAGGTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.26
Consensus pattern (22 bp):
CAAAATTTCATAAAAAGAATAC
Found at i:11086 original size:22 final size:22
Alignment explanation
Indices: 11034--11110 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
11024 AAATTTGTGC
**
11034 TTATCAAAATTTCCTAGGGAGT
1 TTATCAAAATTTTATAGGGAGT
* *
11056 TTAACAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGT
*
11078 TTATGAAAATTTTAT-GGAGAGT
1 TTATCAAAATTTTATAGG-GAGT
11100 TTATCGAAAAT
1 TTATC-AAAAT
11111 ACATAGGGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
21 2 0.04
22 38 0.84
23 5 0.11
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGT
Found at i:11265 original size:22 final size:22
Alignment explanation
Indices: 11171--11268 Score: 64
Period size: 22 Copynumber: 4.5 Consensus size: 22
11161 CATGGTTTGG
*
11171 TTATCAAAATTTTAT--G-AGG
1 TTATCAAAATTTTATAGGCAGA
*
11190 TTATCAAAATTTTCATAGTGC-GG
1 TTATCAAAATTTT-ATAG-GCAGA
* * *
11213 TTA-C-CAATTTTATTTAGTCTGA
1 TTATCAAAATTTTA--TAGGCAGA
*
11235 TTATTAAAATTTTATAGGCAGA
1 TTATCAAAATTTTATAGGCAGA
11257 TTATCAAAATTT
1 TTATCAAAATTT
11269 CAAACTAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
19 13 0.21
20 3 0.05
21 7 0.11
22 25 0.41
23 6 0.10
24 7 0.11
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGCAGA
Found at i:11333 original size:21 final size:21
Alignment explanation
Indices: 11279--11333 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
11269 CAAACTAAGA
* *
11279 TTATCGAAATTTCATAGCGTGG
1 TTATC-AAATTTCACAACGTGG
* *
11301 TTACTAAAATTTCACAATGTGG
1 TTA-TCAAATTTCACAACGTGG
11323 TTATCAAATTT
1 TTATCAAATTT
11334 TCATAGGGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 7 0.26
22 19 0.70
23 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (21 bp):
TTATCAAATTTCACAACGTGG
Found at i:11482 original size:22 final size:22
Alignment explanation
Indices: 11453--11534 Score: 105
Period size: 22 Copynumber: 3.7 Consensus size: 22
11443 CATAGAAAGA
*
11453 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGTAG
*
11475 TTACCAAAATTTCATA-TCG-AGG
1 TTATCAAAATTTCATAGT-GTA-G
*
11497 TTATCAAAACTTCATAGTGTAG
1 TTATCAAAATTTCATAGTGTAG
11519 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
11535 TAGAGGTTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.02
22 48 0.94
23 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTAG
Found at i:11501 original size:44 final size:44
Alignment explanation
Indices: 11433--11554 Score: 154
Period size: 44 Copynumber: 2.8 Consensus size: 44
11423 TGACGATCAA
* * * * *
11433 ACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTTGTT
1 ACCAAAATTTCATATAGAGGTTATCAAAATTTCATAGTGTAGTT
* *
11477 ACCAAAATTTCATATCGAGGTTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATATAGAGGTTATCAAAATTTCATAGTGTAGTT
* * *
11521 ATCAAAATTTCATATAGAGGTTACCAAATTTTCA
1 ACCAAAATTTCATATAGAGGTTATCAAAATTTCA
11555 AAAAAAGAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (44 bp):
ACCAAAATTTCATATAGAGGTTATCAAAATTTCATAGTGTAGTT
Found at i:11543 original size:22 final size:21
Alignment explanation
Indices: 11453--11554 Score: 98
Period size: 22 Copynumber: 4.7 Consensus size: 21
11443 CATAGAAAGA
**
11453 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATA-TGAGG
*
11475 TTACCAAAATTTCATATCGAGG
1 TTATCAAAATTTCATAT-GAGG
*
11497 TTATCAAAACTTCATAGTGTA-G
1 TTATCAAAATTTCATA-TG-AGG
11519 TTATCAAAATTTCATATAGAGG
1 TTATCAAAATTTCATAT-GAGG
* *
11541 TTACCAAATTTTCA
1 TTATCAAAATTTCA
11555 AAAAAAGAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.04
22 62 0.93
23 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATATGAGG
Found at i:11701 original size:22 final size:22
Alignment explanation
Indices: 11649--11993 Score: 73
Period size: 22 Copynumber: 15.6 Consensus size: 22
11639 AAATTTATGC
** *
11649 TTATCAAAATTTCCTAGGGAGT
1 TTATCAAAATTTTATAGGGAGG
*
11671 TTAACAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
* * **
11693 TTATGAAAATTTTAT-GGATAAT
1 TTATCAAAATTTTATAGG-GAGG
**
11715 TTATCGAAAA-TACATAGGGAGG
1 TTATC-AAAATTTTATAGGGAGG
* *
11737 ATATCACAGTTTCATTCTTATA-GGAGG
1 TTATCA-A----AATT-TTATAGGGAGG
* * *
11764 TTATCGAAATTTCAT-GGTGTGG
1 TTATCAAAATTTTATAGG-GAGG
11786 TTATCAAAATTTTAT---GAGG
1 TTATCAAAATTTTATAGGGAGG
** *
11805 TTATCAAAATTTTCATAATGCGG
1 TTATCAAAATTTT-ATAGGGAGG
* * *** *
11828 -TAAC-CAATTTTATTTAGTCTGA
1 TTATCAAAATTTTA--TAGGGAGG
* * *
11850 TTATTAAAATTTTATAGGCAGA
1 TTATCAAAATTTTATAGGGAGG
* * ***
11872 TTATCAAAATTTCAAACTAAGG
1 TTATCAAAATTTTATAGGGAGG
* * * *
11894 TTATCGAAATTTCATAGCGTGG
1 TTATCAAAATTTTATAGGGAGG
* * * ** *
11916 TTACCAAAATTTCACAATGTGG
1 TTATCAAAATTTTATAGGGAGG
11938 TTATC-AAATTTTCATAGGGAGG
1 TTATCAAAATTTT-ATAGGGAGG
** * **
11960 CCATCAAAATTTCATAATGAGG
1 TTATCAAAATTTTATAGGGAGG
11982 TTATC-AAATTTT
1 TTATCAAAATTTT
11994 CAAAATGTGG
Statistics
Matches: 230, Mismatches: 71, Indels: 45
0.66 0.21 0.13
Matches are distributed among these distances:
19 16 0.07
20 3 0.01
21 25 0.11
22 147 0.64
23 17 0.07
24 7 0.03
26 2 0.01
27 10 0.04
28 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGG
Found at i:11911 original size:615 final size:612
Alignment explanation
Indices: 10744--11975 Score: 2203
Period size: 615 Copynumber: 2.0 Consensus size: 612
10734 GATCTAATGC
* *
10744 TCATATTTTGCCTAATAAACAATGAGGAAGATGTACTGACGCAATTGACACAACATAAAAATCAA
1 TCATATTTTGCCTAATAAACAATGAGGAAGATGTAATGACGCAATTGACACAACATAAAAAGCAA
10809 TCTGACGATCAAACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTGGTTACCAAAATT
66 TCTGACGATCAAACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTGGTTACCAAAATT
*
10874 TCATATCAATGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATACAGAGGTTACCAAAAT
131 TCATATCAAGGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATACAGAGGTTACCAAAAT
* *
10939 TTCATAAAAAGAATACCAAAATTTCTTAGGTTTAATAAAATTTCATATGAAAGTTAACAAAATTT
196 TTCAAAAAAAGAATACCAAAATTTCTTAGGTATAATAAAATTTCATATGAAAGTTAACAAAATTT
*
11004 CATAGGGAGGGAGGTTACCAAAATTTGTGCTTATCAAAATTTCCTAGGGAGTTTAACAAAATTTT
261 CATAGGGAGGGAGGTTACCAAAATTTATGCTTATCAAAATTTCCTAGGGAGTTTAACAAAATTTT
* *
11069 ATAGGGAGGTTATGAAAATTTTATGGAGAGTTTATCGAAAATACATAGGGAGGATCTCACAGTTT
326 ATAGGGAGGTTATGAAAATTTTATGGAGAATTTATCGAAAATACATAGGGAGGATATCACAGTTT
*
11134 CATTCTCATAAGAGGTTATCGAAATTTCATGGTTTGGTTATCAAAATTTTATGAGGTTATCAAAA
391 CATTCTCATAAGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTTTATGAGGTTATCAAAA
* *
11199 TTTTCATAGTGCGGTTACCAATTTTATTTAGTCTGATTATTAAAATTTTATAGGCAGATTATCAA
456 TTTTCATAATGCGGTAACCAATTTTATTTAGTCTGATTATTAAAATTTTATAGGCAGATTATCAA
*
11264 AATTTCAAACTAAGATTATCGAAATTTCATAGCGTGGTTACTAAAATTTCACAATGTGGTTATCA
521 AATTTCAAACTAAGATTATCGAAATTTCATAGCGTGGTTACCAAAATTTCACAATGTGGTTATCA
** *
11329 AATTTTCATAGGGAGGTTATCGAAATT
586 AATTTTCATAGGGAGGCCATCAAAATT
* *
11356 TCATATTTTGCCTAATAAACAATGAGGAAGATGTAATGACGCAATTGATACAATATAAAAAGCAA
1 TCATATTTTGCCTAATAAACAATGAGGAAGATGTAATGACGCAATTGACACAACATAAAAAGCAA
*
11421 TCTGACGATCAAACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTTGTTACCAAAATT
66 TCTGACGATCAAACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTGGTTACCAAAATT
* * *
11486 TCATATCGAGGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATATAGAGGTTACCAAATT
131 TCATATCAAGGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATACAGAGGTTACCAAAAT
*
11551 TTCAAAAAAAGAATACCCAAATTTCTTAGGGATGATAATAAAATTTCATATGAAAGTTAACAAAA
196 TTCAAAAAAAGAATACCAAAATTTCTTA-GG-T-ATAATAAAATTTCATATGAAAGTTAACAAAA
11616 TTTCATAGGGAGGGAGGTTACCAAAATTTATGCTTATCAAAATTTCCTAGGGAGTTTAACAAAAT
258 TTTCATAGGGAGGGAGGTTACCAAAATTTATGCTTATCAAAATTTCCTAGGGAGTTTAACAAAAT
*
11681 TTTATAGGGAGGTTATGAAAATTTTATGGATAATTTATCGAAAATACATAGGGAGGATATCACAG
323 TTTATAGGGAGGTTATGAAAATTTTATGGAGAATTTATCGAAAATACATAGGGAGGATATCACAG
* *
11746 TTTCATTCTTATAGGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTTTATGAGGTTATCA
388 TTTCATTCTCATAAGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTTTATGAGGTTATCA
11811 AAATTTTCATAATGCGGTAACCAATTTTATTTAGTCTGATTATTAAAATTTTATAGGCAGATTAT
453 AAATTTTCATAATGCGGTAACCAATTTTATTTAGTCTGATTATTAAAATTTTATAGGCAGATTAT
*
11876 CAAAATTTCAAACTAAGGTTATCGAAATTTCATAGCGTGGTTACCAAAATTTCACAATGTGGTTA
518 CAAAATTTCAAACTAAGATTATCGAAATTTCATAGCGTGGTTACCAAAATTTCACAATGTGGTTA
11941 TCAAATTTTCATAGGGAGGCCATCAAAATT
583 TCAAATTTTCATAGGGAGGCCATCAAAATT
11971 TCATA
1 TCATA
11976 ATGAGGTTAT
Statistics
Matches: 591, Mismatches: 26, Indels: 3
0.95 0.04 0.00
Matches are distributed among these distances:
612 212 0.36
613 2 0.00
614 1 0.00
615 376 0.64
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (612 bp):
TCATATTTTGCCTAATAAACAATGAGGAAGATGTAATGACGCAATTGACACAACATAAAAAGCAA
TCTGACGATCAAACCAAAATTACATAGAAAGATTATCAAAATTTCATAGTGTGGTTACCAAAATT
TCATATCAAGGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATACAGAGGTTACCAAAAT
TTCAAAAAAAGAATACCAAAATTTCTTAGGTATAATAAAATTTCATATGAAAGTTAACAAAATTT
CATAGGGAGGGAGGTTACCAAAATTTATGCTTATCAAAATTTCCTAGGGAGTTTAACAAAATTTT
ATAGGGAGGTTATGAAAATTTTATGGAGAATTTATCGAAAATACATAGGGAGGATATCACAGTTT
CATTCTCATAAGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTTTATGAGGTTATCAAAA
TTTTCATAATGCGGTAACCAATTTTATTTAGTCTGATTATTAAAATTTTATAGGCAGATTATCAA
AATTTCAAACTAAGATTATCGAAATTTCATAGCGTGGTTACCAAAATTTCACAATGTGGTTATCA
AATTTTCATAGGGAGGCCATCAAAATT
Found at i:11942 original size:66 final size:66
Alignment explanation
Indices: 11872--12016 Score: 155
Period size: 66 Copynumber: 2.2 Consensus size: 66
11862 TATAGGCAGA
* ** * * * *
11872 TTATCAAAATTTCAAACTAAGGTTATCGAAATTTCATAGCGTGGTTACCAAAATTTCACAATGTG
1 TTATCAAAATTTCAAACGAAGGCCATCAAAATTTCATAACGAGGTTACCAAAATTTCAAAATGTG
11937 G
66 G
* * * * * * *
11938 TTATCAAATTTTCATAGGGAGGCCATCAAAATTTCATAATGAGGTTATCAAATTTTCAAAATGTG
1 TTATCAAAATTTCAAACGAAGGCCATCAAAATTTCATAACGAGGTTACCAAAATTTCAAAATGTG
12003 G
66 G
*
12004 TTATCAATATTTC
1 TTATCAAAATTTC
12017 TACATTGGAG
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (66 bp):
TTATCAAAATTTCAAACGAAGGCCATCAAAATTTCATAACGAGGTTACCAAAATTTCAAAATGTG
G
Found at i:11994 original size:22 final size:22
Alignment explanation
Indices: 11760--12016 Score: 123
Period size: 22 Copynumber: 11.8 Consensus size: 22
11750 ATTCTTATAG
* **
11760 GAGGTTATCGAAATTTCATGGT
1 GAGGTTATCAAAATTTCATAAT
*
11782 GTGGTTATCAAAATTT--T-AT
1 GAGGTTATCAAAATTTCATAAT
11801 GAGGTTATCAAAATTTTCATAAT
1 GAGGTTATCAAAA-TTTCATAAT
* * * * *
11824 GCGG-TAAC-CAATTTTATTTAGT
1 GAGGTTATCAAAATTTCA--TAAT
** * * * *
11846 CTGATTATTAAAATTTTAT-AG
1 GAGGTTATCAAAATTTCATAAT
*
11867 GCAGATTATCAAAATTTCA-AACT
1 G-AGGTTATCAAAATTTCATAA-T
* * **
11890 AAGGTTATCGAAATTTCATAGC
1 GAGGTTATCAAAATTTCATAAT
* * *
11912 GTGGTTACCAAAATTTCACAAT
1 GAGGTTATCAAAATTTCATAAT
* * **
11934 GTGGTTATCAAATTTTCATAGG
1 GAGGTTATCAAAATTTCATAAT
**
11956 GAGGCCATCAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAAT
* *
11978 GAGGTTATCAAATTTTCAAAAT
1 GAGGTTATCAAAATTTCATAAT
* *
12000 GTGGTTATCAATATTTC
1 GAGGTTATCAAAATTTC
12017 TACATTGGAG
Statistics
Matches: 171, Mismatches: 52, Indels: 24
0.69 0.21 0.10
Matches are distributed among these distances:
19 13 0.08
20 8 0.05
21 2 0.01
22 133 0.78
23 8 0.05
24 7 0.04
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAT
Found at i:12010 original size:44 final size:43
Alignment explanation
Indices: 11872--12016 Score: 148
Period size: 44 Copynumber: 3.3 Consensus size: 43
11862 TATAGGCAGA
*
11872 TTATCAAAATTTCAAACTAAGGTTATCGAAA-TTTCATAGCGTGG
1 TTATCAAAATTTCAAA-TGAGGTTATC-AAATTTTCATAGCGTGG
* * * *
11916 TTACCAAAATTTCACAATGTGGTTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCA-AATGAGGTTATCAAATTTTCATAGCGTGG
** * **
11960 CCATCAAAATTTCATAATGAGGTTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCA-AATGAGGTTATCAAATTTTCATAGCGTGG
*
12004 TTATCAATATTTC
1 TTATCAAAATTTC
12017 TACATTGGAG
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
43 3 0.04
44 77 0.94
45 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTCAAATGAGGTTATCAAATTTTCATAGCGTGG
Found at i:13522 original size:19 final size:19
Alignment explanation
Indices: 13498--13536 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
13488 TATAGTATCA
13498 TAATTTTTTAATTAATATT
1 TAATTTTTTAATTAATATT
13517 TAATTTTTTAATTAATATT
1 TAATTTTTTAATTAATATT
13536 T
1 T
13537 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTTTTTAATTAATATT
Done.