Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007618.1 Corchorus capsularis cultivar CVL-1 contig07639, 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: 70652
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8054 original size:15 final size:16
Alignment explanation
Indices: 8023--8056 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8013 AATGAAGAAT
*
8023 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
8039 TAAAAGTAAA-CTAAC
1 TAAAAGTAAATCTAAC
8054 TAA
1 TAA
8057 GAAAGCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:9371 original size:19 final size:18
Alignment explanation
Indices: 9338--9373 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9328 TTGAAATAAG
9338 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
9356 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
9374 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:9574 original size:20 final size:21
Alignment explanation
Indices: 9536--9574 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
9526 TAGAAAATAA
*
9536 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
9557 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
9575 ATAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:12901 original size:19 final size:18
Alignment explanation
Indices: 12877--12913 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12867 TTGAAGATTT
12877 TTTGAAGATAATTTGAAGA
1 TTTGAAGATAA-TTGAAGA
*
12896 TTTGAAGATCATTGAAGA
1 TTTGAAGATAATTGAAGA
12914 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (18 bp):
TTTGAAGATAATTGAAGA
Found at i:18447 original size:19 final size:18
Alignment explanation
Indices: 18423--18458 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18413 TGAAGATTTC
18423 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
18442 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
18459 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:34817 original size:36 final size:36
Alignment explanation
Indices: 34776--35055 Score: 347
Period size: 36 Copynumber: 7.8 Consensus size: 36
34766 TAGTTATTCG
* *
34776 GAATTAAATTACTTACTGACTTTACTTAATTACCCT
1 GAATTAAGTTACTAACTGACTTTACTTAATTACCCT
* *
34812 AAATTAAGTTAACT-ACTGA-TTCACTTAATTACCCT
1 GAATTAAGTT-ACTAACTGACTTTACTTAATTACCCT
*
34847 GAATTAAGTTACTAACTAACTTTACTTAATTACCCT
1 GAATTAAGTTACTAACTGACTTTACTTAATTACCCT
* * *
34883 GAATTAAGTTACTAACTGACTTTACCTAACTGCCCT
1 GAATTAAGTTACTAACTGACTTTACTTAATTACCCT
*
34919 GAATTAAGTTACTAACCGA-TTTGACTTAATTACCCT
1 GAATTAAGTTACTAACTGACTTT-ACTTAATTACCCT
* * *
34955 GAACTAAGTTACTGACTGGCTTTACTTAATTACCCT
1 GAATTAAGTTACTAACTGACTTTACTTAATTACCCT
*
34991 GAATTAAGTTACTGACT-AGCTTTACTTAATTACCCT
1 GAATTAAGTTACTAACTGA-CTTTACTTAATTACCCT
* *
35027 GAATTAAGCTAACT-ACTTA-TTTACTTAAT
1 GAATTAAG-TTACTAACTGACTTTACTTAAT
35056 GCATGGATGC
Statistics
Matches: 215, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
34 3 0.01
35 41 0.19
36 160 0.74
37 11 0.05
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (36 bp):
GAATTAAGTTACTAACTGACTTTACTTAATTACCCT
Found at i:39017 original size:36 final size:36
Alignment explanation
Indices: 38977--39135 Score: 153
Period size: 36 Copynumber: 4.4 Consensus size: 36
38967 CTTAAGAAAC
* *
38977 CCACCCTGGATCATTCCAAACTAAATTGAAGAACGA
1 CCACCCTCGATCATTCCAAACTAAACTGAAGAACGA
* ** *
39013 CCACCCTCGATCATTTCGATGC-AAACTGAAGAAAGA
1 CCACCCTCGATCA-TTCCAAACTAAACTGAAGAACGA
* * * * *
39049 CCACCCTGGGTCA-ACTGAAA-TAAACTGAAAAACGA
1 CCACCCTCGATCATTC-CAAACTAAACTGAAGAACGA
** *
39084 CCACCCTCGATCATTCCGGACTAAACTGAAGAACAA
1 CCACCCTCGATCATTCCAAACTAAACTGAAGAACGA
39120 CCACCCTCGATCATTC
1 CCACCCTCGATCATTC
39136 TGACTTAAAC
Statistics
Matches: 97, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
34 1 0.01
35 26 0.27
36 65 0.67
37 5 0.05
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.18
Consensus pattern (36 bp):
CCACCCTCGATCATTCCAAACTAAACTGAAGAACGA
Found at i:39191 original size:8 final size:8
Alignment explanation
Indices: 39178--39219 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
39168 CATTGAAGTA
39178 AATTGAAG
1 AATTGAAG
39186 AATTGAAG
1 AATTGAAG
*
39194 CATTG-AG
1 AATTGAAG
*
39201 TAATTGAAC
1 -AATTGAAG
39210 AATTGAAG
1 AATTGAAG
39218 AA
1 AA
39220 AGACCACCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 2 0.07
8 25 0.89
9 1 0.04
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (8 bp):
AATTGAAG
Found at i:39207 original size:24 final size:26
Alignment explanation
Indices: 39168--39217 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
39158 CGCCCTGGCT
*
39168 CATTGAAGTAAATTGAAGAATTGAAG
1 CATTGAAGTAAATTGAACAATTGAAG
39194 CATTG-AGT-AATTGAACAATTGAAG
1 CATTGAAGTAAATTGAACAATTGAAG
39218 AAAGACCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.65
25 3 0.13
26 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (26 bp):
CATTGAAGTAAATTGAACAATTGAAG
Found at i:39293 original size:29 final size:29
Alignment explanation
Indices: 39256--39311 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
39246 TTGAAGCATT
*
39256 GATCGCCCTGGACCAATTAACTAAAGAAA
1 GATCACCCTGGACCAATTAACTAAAGAAA
* *
39285 GATCACCCTGGATCAATTAACTTAAGA
1 GATCACCCTGGACCAATTAACTAAAGA
39312 TGGACCACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21
Consensus pattern (29 bp):
GATCACCCTGGACCAATTAACTAAAGAAA
Found at i:39320 original size:29 final size:29
Alignment explanation
Indices: 39261--39324 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
39251 GCATTGATCG
*
39261 CCCTGGACCAATTAACTAAAGAAAGATCA
1 CCCTGGACCAATTAACTAAAGAAAGACCA
* * **
39290 CCCTGGATCAATTAACTTAAGATGGACCA
1 CCCTGGACCAATTAACTAAAGAAAGACCA
39319 CCCTGG
1 CCCTGG
39325 GTTAACTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (29 bp):
CCCTGGACCAATTAACTAAAGAAAGACCA
Found at i:42543 original size:20 final size:20
Alignment explanation
Indices: 42514--42551 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
42504 AAAAAGAAAC
42514 TTTCGGAAGA-GAAAGAGTT
1 TTTCGGAAGAGGAAAGAGTT
42533 TTTCGGGAAGAGGAAAGAG
1 TTTC-GGAAGAGGAAAGAG
42552 AAAGAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 6 0.35
21 7 0.41
ACGTcount: A:0.37, C:0.05, G:0.37, T:0.21
Consensus pattern (20 bp):
TTTCGGAAGAGGAAAGAGTT
Found at i:45012 original size:10 final size:10
Alignment explanation
Indices: 44997--45021 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44987 GTTCCTGCAC
44997 AATTCCAGAA
1 AATTCCAGAA
45007 AATTCCAGAA
1 AATTCCAGAA
45017 AATTC
1 AATTC
45022 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:45953 original size:12 final size:13
Alignment explanation
Indices: 45928--45961 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
45918 ATAATTATTG
45928 TTTGCTTTATTAA
1 TTTGCTTTATTAA
45941 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
45953 TCTGCTTTA
1 TTTGCTTTA
45962 GATTTAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:45977 original size:6 final size:6
Alignment explanation
Indices: 45958--45991 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
45948 TATAATCTGC
45958 TTTAGA TTTAAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTT-AGA TTTAGA TTTAGA TTTAGA TTT
45992 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
TTTAGA
Found at i:54721 original size:11 final size:11
Alignment explanation
Indices: 54678--54715 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
54668 TTCCTATATA
*
54678 AAATAAATTAT
1 AAATTAATTAT
54689 CAAA-TAATTAT
1 -AAATTAATTAT
54700 AAATTAATTAT
1 AAATTAATTAT
54711 AAATT
1 AAATT
54716 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:57350 original size:18 final size:19
Alignment explanation
Indices: 57316--57354 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
57306 TTTGAACCAT
57316 TTCAAGTCGGTGTGGTCGG
1 TTCAAGTCGGTGTGGTCGG
57335 TTCAA-TCGGT-TCGGTCGG
1 TTCAAGTCGGTGT-GGTCGG
57353 TT
1 TT
57355 TTTAGCCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 13 0.68
19 5 0.26
ACGTcount: A:0.10, C:0.18, G:0.36, T:0.36
Consensus pattern (19 bp):
TTCAAGTCGGTGTGGTCGG
Found at i:60758 original size:438 final size:433
Alignment explanation
Indices: 60115--61051 Score: 1091
Period size: 438 Copynumber: 2.1 Consensus size: 433
60105 AAGAGGTAGC
* * *
60115 AGAAAAGTATGAGGTGATTTGATAACTAATTCAAATAAGAAATTATTTGTTAATGGAGATATCTT
1 AGAAAAGTATGAGGTCATTTGATAAATAATTCAAATAAGAAAATATTTGTTAATGGAGA-ATCTT
* * * * *
60180 GAAACATAAAAATTCTCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTTTCGGGTTCTTAA
65 GAAACATAAAAATTCCCTTTTAAACCCTTCACGAAACTCATAGATCAAATTTTTCGGGTCCTTAA
* * * * * * *
60245 TGAAAGTCGTAGATTATACAATAATCTTTTAACCGACACTTGAATAACTTTAATTGGACATGTTG
130 TGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAAGAACTTCAATTGGACATGTAG
* * * * **
60310 ATCGAAAATTATATGGTATTAAA-TAGACCAACAATTGAAATGAAC-AAATTTAGGAAGCATTTT
195 ATCAAAAATTATACGATATTAAATTA-ACCAACAA-TCAAAACAACAAAATTTAGGAAGCATTTT
* * * * * *
60373 TTTGAATTGAAACATAAAAATTTG-CTTTTGAGCCCTTCATGAAAGTTGTAGATCATGAAATTAC
258 TTAGAATTAAAACATAAAAA-TTGACTTTTGAGCCCTTAAAGAAAATTGTAAATCATGAAATTAC
* *
60437 CTTTTAATAGACACATGAATCAACTTAATTGGATAAATAGAACAAAAATAAAAAAAATAAAGCTT
322 CTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAAAAAAAAT-AAAAAAATAAAGCTT
60502 AAACGTTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGT
386 AAACGTTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGT
* *
60550 AGAAAAGTATGAGGGTCATTTGATAAATAATTTAAATAAGAAAATGTTTGTTAATGGAG-ATCTT
1 AGAAAAGTATGA-GGTCATTTGATAAATAATTCAAATAAGAAAATATTTGTTAATGGAGAATCTT
* *
60614 GAAACATAAAAATTCCCTTTTAAACCCTTTACGAAAGTCATAGATCAAATTTAGCTTTCGGGTCC
65 GAAACATAAAAATTCCCTTTTAAACCCTTCACGAAACTCATAGATCAAA-TT---TTTCGGGTCC
* *
60679 TTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAAGAACTTCAATCT-GACA
126 TTAATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAAGAACTTCAAT-TGGACA
** * *
60743 TGTAGA-CAAAAAATTATACGATATTAAATTAACCGGCAATCAAAACCACAAAATTTCGGAAGCA
190 TGTAGATC-AAAAATTATACGATATTAAATTAACCAACAATCAAAACAACAAAATTTAGGAAGCA
* **
60807 TTTTTTAGAATTAAAACATTAAAATTGACTTTTGAGTTCTTAAAGAAAATTGTAAATCATGAAAT
254 TTTTTTAGAATTAAAACATAAAAATTGACTTTTGAGCCCTTAAAGAAAATTGTAAATCATGAAAT
* * *
60872 TACCTTTTAATAGACACTTGAATCACCTTAATTGGACAAATAGAAAAAAAATACAAAAATAAAAG
319 TACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAAAAAAAATAAAAAAAT-AAAG
* * * * * * * * *
60937 -TCAATGCGTTAAATCGTCCAGCCTATAA-TTGTAAAGGACTAAATAGCATAAAGC
383 CTTAA-ACGTTAGAT--T-AAG-ATAGAATTTGTAAAGGACTAAGTAGTATAAAGT
* * * * * * *
60991 ATAAAAGTATGAGGATCATTAGTTAAATAATCCAATTAAG-AAATATTAGTTTATGGAGAAT
1 AGAAAAGTATGAGG-TCATTTGATAAATAATTCAAATAAGAAAATATTTGTTAATGGAGAAT
61052 GGAACCCACA
Statistics
Matches: 421, Mismatches: 63, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
434 48 0.11
435 14 0.03
436 41 0.10
437 20 0.05
438 215 0.51
439 3 0.01
440 18 0.04
441 58 0.14
442 4 0.01
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (433 bp):
AGAAAAGTATGAGGTCATTTGATAAATAATTCAAATAAGAAAATATTTGTTAATGGAGAATCTTG
AAACATAAAAATTCCCTTTTAAACCCTTCACGAAACTCATAGATCAAATTTTTCGGGTCCTTAAT
GAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAAGAACTTCAATTGGACATGTAGA
TCAAAAATTATACGATATTAAATTAACCAACAATCAAAACAACAAAATTTAGGAAGCATTTTTTA
GAATTAAAACATAAAAATTGACTTTTGAGCCCTTAAAGAAAATTGTAAATCATGAAATTACCTTT
TAATAGACACATGAATCAACTTAATTGGACAAATAGAAAAAAAATAAAAAAATAAAGCTTAAACG
TTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGT
Found at i:64955 original size:21 final size:19
Alignment explanation
Indices: 64919--64958 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
64909 GATATGCTTT
64919 ATCTATACACACAAAAAAA
1 ATCTATACACACAAAAAAA
64938 ATCTATACACACAAAAAAA
1 ATCTATACACACAAAAAAA
64957 AT
1 AT
64959 AAATAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.62, C:0.20, G:0.00, T:0.17
Consensus pattern (19 bp):
ATCTATACACACAAAAAAA
Found at i:65289 original size:3 final size:3
Alignment explanation
Indices: 65281--65306 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
65271 CTAGTAGGGT
65281 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
65307 TTTTTCGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:65636 original size:107 final size:105
Alignment explanation
Indices: 65465--65722 Score: 378
Period size: 107 Copynumber: 2.5 Consensus size: 105
65455 AGTTTAGCCT
* *
65465 TAATTTGACTAAGTTTAGCCCCAAATT-AAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
65529 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
65571 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
65636 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAT
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * ** *
65676 TTA-TTCACTATGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAG
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAG
65723 AGTTAGAAAA
Statistics
Matches: 140, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 27 0.19
104 13 0.09
105 34 0.24
106 26 0.19
107 40 0.29
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:66989 original size:23 final size:23
Alignment explanation
Indices: 66954--66997 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
66944 TAAATTGCAA
* *
66954 CAAAATAGTCACCACTAACCCAT
1 CAAAACAGACACCACTAACCCAT
66977 CAAAACAGACACCACTAACCC
1 CAAAACAGACACCACTAACCC
66998 TCTTCCTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.39, G:0.05, T:0.11
Consensus pattern (23 bp):
CAAAACAGACACCACTAACCCAT
Found at i:67592 original size:75 final size:75
Alignment explanation
Indices: 67513--67676 Score: 172
Period size: 75 Copynumber: 2.2 Consensus size: 75
67503 GATGCTCAAA
* * *
67513 ATTTGAATTCGAATC-AGAAACCTGATAA-AGTGAATCAGCTTTAAGATGTTG-CAAATCATCTT
1 ATTTGAATTCGAATCAAGAAA-CTGATAAGA-TGAATCAGCTTCAAGATGTTGTCAAA-CACCAT
* *
67575 CAGAGAACTTAGT
63 CAGAAAACTCAGT
* * * * * *
67588 ATTTGAATTCAAAACAAGAAACTGATCAGATGAATCATCTTCAAGATTTTGTCTAACACCATCAG
1 ATTTGAATTCGAATCAAGAAACTGATAAGATGAATCAGCTTCAAGATGTTGTCAAACACCATCAG
*
67653 AAAACTCATT
66 AAAACTCAGT
67663 ATTTGAATTCGAAT
1 ATTTGAATTCGAAT
67677 TTGCAAACTT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
75 63 0.88
76 9 0.12
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (75 bp):
ATTTGAATTCGAATCAAGAAACTGATAAGATGAATCAGCTTCAAGATGTTGTCAAACACCATCAG
AAAACTCAGT
Done.