Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017520.1 Corchorus olitorius cultivar O-4 contig17553, 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: 107215
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1079 original size:39 final size:39
Alignment explanation
Indices: 1025--1100 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 39
1015 TACATCCCAG
1025 TTCAAATCTTATTCTAAGA-AATCATTGATGGGAAATTTA
1 TTCAAATCTTATTCTAA-ATAATCATTGATGGGAAATTTA
*
1064 TTCAAATCTTATTCTAAATCATCATTGATGGGAAATT
1 TTCAAATCTTATTCTAAATAATCATTGATGGGAAATT
1101 CTAAATTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (39 bp):
TTCAAATCTTATTCTAAATAATCATTGATGGGAAATTTA
Found at i:1995 original size:30 final size:30
Alignment explanation
Indices: 1960--2030 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 30
1950 TACTCAGGAG
1960 GTCCCTCTACTTTCAAAAAAA-ATCAATTTC
1 GTCCCTCTACTTT-AAAAAAAGATCAATTTC
1990 GTCCCTCTAC--TAAAAAAAGGATCAATTTC
1 GTCCCTCTACTTTAAAAAAA-GATCAATTTC
2019 GTCCCTCTACTT
1 GTCCCTCTACTT
2031 GGCACTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
27 7 0.19
28 1 0.03
29 19 0.51
30 10 0.27
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.32
Consensus pattern (30 bp):
GTCCCTCTACTTTAAAAAAAGATCAATTTC
Found at i:2500 original size:45 final size:43
Alignment explanation
Indices: 2406--2502 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 43
2396 AACTAAATTG
* * * *
2406 AAAAAAAAAATGTTGTTTAAACTTTCAACGTTTTTTTTTAAATT
1 AAAAAAAAAACGCTGTTTAAACTTTCAACGTTTTTCTGTAAA-T
2450 GAAAAAAAAAACGCTGTTTAAACTTTCAACGTAATTTTGCTGTAAA-
1 -AAAAAAAAAACGCTGTTTAAACTTTCAACGT--TTTT-CTGTAAAT
2496 AAAAAAA
1 AAAAAAA
2503 CTTTCAACGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 36 0.80
47 4 0.09
48 5 0.11
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (43 bp):
AAAAAAAAAACGCTGTTTAAACTTTCAACGTTTTTCTGTAAAT
Found at i:9504 original size:21 final size:21
Alignment explanation
Indices: 9479--9518 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9469 ACCATGTCAA
9479 CAAATGTAA-AAATAAAAAATT
1 CAAATGTAAGAAA-AAAAAATT
*
9500 CAAATTTAAGAAAAAAAAA
1 CAAATGTAAGAAAAAAAAA
9519 CACTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (21 bp):
CAAATGTAAGAAAAAAAAATT
Found at i:15699 original size:2 final size:2
Alignment explanation
Indices: 15692--15730 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
15682 ATTTATATTT
* *
15692 TA TA TA TA TA TA TA TA GA TA TA GA 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 TA TA TA T
15731 GATGTGATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:17785 original size:22 final size:22
Alignment explanation
Indices: 17760--17811 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
17750 TGAACTATAT
*
17760 AAATATTAAAATAAAATTAT-GA
1 AAATATTAAAA-AAAATTATAAA
*
17782 AAATATATACAAAAAATTATAAA
1 AAATAT-TAAAAAAAATTATAAA
17805 AAATATT
1 AAATATT
17812 TTATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATATTAAAAAAAATTATAAA
Found at i:18297 original size:2 final size:2
Alignment explanation
Indices: 18290--18314 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18280 TTATTTTGTA
18290 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
18315 ATTTCCATAC
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:21961 original size:74 final size:72
Alignment explanation
Indices: 21863--22004 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 72
21853 AACAATGTAG
* * * * *
21863 GGAGTTTCTGATGTAGAGGATCCACTTGAGAG-TGGCAATTGTATAGCATATTACTCCTGTTCAT
1 GGAGTTTCTGATGCAGAGGATCCAC-TGAG-GTTGGCAACTGCAGAGCATATGACTCCTG-TCAT
21927 TGCATAGTAA
63 TGCATAGTAA
*
21937 GGAGTTTCT-AGTGCAGAGGATCCACTGAGGTTGGTAACTGCAGAGCATATGACTCCTGTCATTG
1 GGAGTTTCTGA-TGCAGAGGATCCACTGAGGTTGGCAACTGCAGAGCATATGACTCCTGTCATTG
22001 CATA
65 CATA
22005 CTAGGCGTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
72 11 0.18
73 27 0.45
74 22 0.37
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (72 bp):
GGAGTTTCTGATGCAGAGGATCCACTGAGGTTGGCAACTGCAGAGCATATGACTCCTGTCATTGC
ATAGTAA
Found at i:22206 original size:13 final size:13
Alignment explanation
Indices: 22190--22226 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
22180 GTATTTATAG
22190 CCATTATTACACA
1 CCATTATTACACA
*
22203 CCATTATTGCACA
1 CCATTATTACACA
*
22216 CTATTATTACA
1 CCATTATTACA
22227 TAAACTAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (13 bp):
CCATTATTACACA
Found at i:23310 original size:439 final size:432
Alignment explanation
Indices: 22470--23328 Score: 1068
Period size: 437 Copynumber: 2.0 Consensus size: 432
22460 TTAAATCGAG
* ** * *
22470 TAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAAAAAGTATAAGGGTGATTTGACAACTA
1 TAAGATAGAATTTGTAAAGAACTAAGTAGCATAAAATAAAAAGTATAAGGGCCATTTCACAAATA
*
22535 ATTCAAATAAGAAAATATTTGTTAATTAATGGAGATCTTGAAACATAAAAAATTCCCTGTTGAAT
66 ATTCAAATAAGAAAATATTTG---ATTAATGGAGATCTTGAAACATAAAAAATTCCCTGTTGAAC
* * * *
22600 CATTCAAGAAACTCGTAGATTAAATTAACTTTCGGGTTTTCATGAAAGTCATAGATTATACAATA
128 CATTCAAGAAACTCGTAGATCAAATTAACTTTCGGGTCTTCATGAAAGTCATAAATCATACAATA
* * * *
22665 ACCTTTTAACCGACACTTGAATAACTTTAATTGGACATGTGGATCAAAAAATATGGTATTAAATA
193 ACCTTTTAACCGACACTTCAATAACTTCAATTGGACATGTGGAGCAAAAAATATGATATTAAATA
* * * * * * * **
22730 GACCAACAATCGAAACGACCAAATTTAGGAAGCATTTTTTTGAGTTGACATAAAAATTTGCTTTT
258 GACCAACAATCAAAACCACAAAATTTAGAAAGCAATTTTTAGAATAAACATAAAAATTTGCTTTT
** * * * *
22795 GAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTCATT
323 GAGTCCTAAATGAAAATTGTAGATCATGAAATCACCTTTTAATAGACACATGAATCAACTTAATC
*
22860 GGACAAATAGAAAAACAAATAAAAAAAATAAAGCTTAAACGTTAGAT
388 AGACAAATAGAAAAA-AAAT-AAAAAAATAAAGCTTAAACGTTAGAT
* * * * *
22907 TAAGATAGAATTTGTAAAGAATTAAGTAGTATAAAGTAGAAAAGTATGAGGGCCATTTCATAAAT
1 TAAGATAGAATTTGTAAAGAACTAAGTAGCATAAAATA-AAAAGTATAAGGGCCATTTCACAAAT
* * *
22972 AATTCAAATAAGAAAATGTTTG-TTAATGGAGATCTTGAAACAT-AAAAATTCCCTTTTGAACCC
65 AATTCAAATAAGAAAATATTTGATTAATGGAGATCTTGAAACATAAAAAATTCCCTGTTGAACCA
* * *
23035 TT-AACGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAAT
130 TTCAA-GAAACTCGTAGATCAAA-TTAACTTTCGGGT-CTTCATGAAAGTCATAAATCATACAAT
*
23099 AACCTTTTAACCGACACTTCAATAACTTCAATTGGAGATGTGG-GCAAAAAATTATACGATATTA
192 AACCTTTTAACCGACACTTCAATAACTTCAATTGGACATGTGGAGCAAAAAA-TAT--GATATTA
** *
23163 AATTA-ACCGGCAATCAAAACCACAAAATTTCA-AAAGCAATTTTTAGAATCAAAACATTAAAA-
254 AA-TAGACCAACAATCAAAACCACAAAATTT-AGAAAGCAATTTTTAGAAT--AAACATAAAAAT
*
23225 TTGACTTTTGAGTTCTAAATGAAAATTGTAGATCATGAAATCACCTTTTAATAGACA-ATTGAAT
315 TTG-CTTTTGAGTCCTAAATGAAAATTGTAGATCATGAAATCACCTTTTAATAGACACA-TGAAT
* *
23289 CACCTTAATCAGACAAATAGAAAAAAAATACAAAAATAAA
378 CAACTTAATCAGACAAATAGAAAAAAAATAAAAAAATAAA
23329 AGCGAACGCG
Statistics
Matches: 361, Mismatches: 48, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
432 2 0.01
433 35 0.10
434 40 0.11
435 65 0.18
437 85 0.24
438 52 0.14
439 82 0.23
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (432 bp):
TAAGATAGAATTTGTAAAGAACTAAGTAGCATAAAATAAAAAGTATAAGGGCCATTTCACAAATA
ATTCAAATAAGAAAATATTTGATTAATGGAGATCTTGAAACATAAAAAATTCCCTGTTGAACCAT
TCAAGAAACTCGTAGATCAAATTAACTTTCGGGTCTTCATGAAAGTCATAAATCATACAATAACC
TTTTAACCGACACTTCAATAACTTCAATTGGACATGTGGAGCAAAAAATATGATATTAAATAGAC
CAACAATCAAAACCACAAAATTTAGAAAGCAATTTTTAGAATAAACATAAAAATTTGCTTTTGAG
TCCTAAATGAAAATTGTAGATCATGAAATCACCTTTTAATAGACACATGAATCAACTTAATCAGA
CAAATAGAAAAAAAATAAAAAAATAAAGCTTAAACGTTAGAT
Found at i:23442 original size:439 final size:434
Alignment explanation
Indices: 22474--23442 Score: 994
Period size: 439 Copynumber: 2.2 Consensus size: 434
22464 ATCGAGTAAG
* * * * *** ** * *
22474 ATAGAATTTGTAAAGGACTAAGTAGCATAAAATA-AAAAGTATAAGGGTGATTTGACAACTAATT
1 ATAGAATTTGTAAAGAACTAAATAGCATAAAGTAGAAAAGTATGAGGACCATTACATAAATAATT
* * * *
22538 CAAATAAGAAAATATTTGTTAATTAATGGAGATCTTGAAACATAAAAAATTCCCTGTTGAATCAT
66 CAAACAAGAAAACA----TTAGTTAATGGAGATCTTGAAACATAAAAAATTCCCTGTTGAACCAT
* * * *
22603 TCAAGAAACTCGTAGATTAAATTAACTTTCGGGTTTTCATGAAAGTCATAGATTATACAATAACC
127 TCAAGAAACTCGTAGATCAAATTAACTTTCGGGTCTTCATGAAAGTCATAAATCATACAATAACC
* * * *
22668 TTTTAACCGACACTTGAATAACTTTAATTGGACATGTGGATCAAAAAATATGGTATTAAATAGAC
192 TTTTAACCGACACTTCAATAACTTCAATTGGACATGTGGAGCAAAAAATATGATATTAAATAGAC
* * * * * * * **
22733 CAACAATCGAAACGACCAAATTTAGGAAGCATTTTTTTGAGTTGACATAAAAATTTGCTTTTGAG
257 CAACAATCAAAACCACAAAATTTAGAAAGCAATTTTTAGAATAAACATAAAAATTTGCTTTTGAG
** * * * **
22798 TCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTCATTGGA
322 TCCTAAATGAAAATTGTAGATCATGAAATCACCTTTTAATAGACACATGAATCAACTTAATCAGA
* * *
22863 CAAATAGAAAAACAAATAAAAAAAATAAAGCTTAAACGTTAGATTAAG
387 CAAATAGAAAAACAAATAAAAAAAATAAAGCTGAAACGTTAAATTAAC
* * * * *
22911 ATAGAATTTGTAAAGAATTAAGTAGTATAAAGTAGAAAAGTATGAGGGCCATTTCATAAATAATT
1 ATAGAATTTGTAAAGAACTAAATAGCATAAAGTAGAAAAGTATGAGGACCATTACATAAATAATT
* ** * * *
22976 CAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACAT-AAAAATTCCCTTTTGAACCCTT-AA
66 CAAACAAGAAAACATTAGTTAATGGAGATCTTGAAACATAAAAAATTCCCTGTTGAACCATTCAA
* * *
23039 CGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCT
131 -GAAACTCGTAGATCAAA-TTAACTTTCGGGT-CTTCATGAAAGTCATAAATCATACAATAACCT
*
23104 TTTAACCGACACTTCAATAACTTCAATTGGAGATGTGG-GCAAAAAATTATACGATATTAAATTA
193 TTTAACCGACACTTCAATAACTTCAATTGGACATGTGGAGCAAAAAA-TAT--GATATTAAA-TA
** *
23168 -ACCGGCAATCAAAACCACAAAATTTCA-AAAGCAATTTTTAGAATCAAAACATTAAAA-TTGAC
254 GACCAACAATCAAAACCACAAAATTT-AGAAAGCAATTTTTAGAAT--AAACATAAAAATTTG-C
* *
23230 TTTTGAGTTCTAAATGAAAATTGTAGATCATGAAATCACCTTTTAATAGACA-ATTGAATCACCT
315 TTTTGAGTCCTAAATGAAAATTGTAGATCATGAAATCACCTTTTAATAGACACA-TGAATCAACT
* *
23294 TAATCAGACAAATAGAAAAA-AAAT-ACAAAAATAAAAGC-GAACGCGTTAAATCGTCCAAC
379 TAATCAGACAAATAGAAAAACAAATAAAAAAAAT-AAAGCTGAA-ACGTTAAAT--T--AAC
* * * * * *
23353 CTATAA-TTGTAAAGGACTAAATAGCATAAAGTATAAAAGTATGAGGATCATTAGATAAATAA-T
1 ATAGAATTTGTAAAGAACTAAATAGCATAAAGTAGAAAAGTATGAGGACCATTACATAAATAATT
* *
23416 CCAACAA-AAAACATTAGTTTATGGAGA
66 CAAACAAGAAAACATTAGTTAATGGAGA
23443 ATGGGACCCA
Statistics
Matches: 442, Mismatches: 71, Indels: 36
0.81 0.13 0.07
Matches are distributed among these distances:
432 2 0.00
433 35 0.08
434 42 0.10
435 65 0.15
437 80 0.18
438 60 0.14
439 98 0.22
440 7 0.02
441 47 0.11
442 6 0.01
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (434 bp):
ATAGAATTTGTAAAGAACTAAATAGCATAAAGTAGAAAAGTATGAGGACCATTACATAAATAATT
CAAACAAGAAAACATTAGTTAATGGAGATCTTGAAACATAAAAAATTCCCTGTTGAACCATTCAA
GAAACTCGTAGATCAAATTAACTTTCGGGTCTTCATGAAAGTCATAAATCATACAATAACCTTTT
AACCGACACTTCAATAACTTCAATTGGACATGTGGAGCAAAAAATATGATATTAAATAGACCAAC
AATCAAAACCACAAAATTTAGAAAGCAATTTTTAGAATAAACATAAAAATTTGCTTTTGAGTCCT
AAATGAAAATTGTAGATCATGAAATCACCTTTTAATAGACACATGAATCAACTTAATCAGACAAA
TAGAAAAACAAATAAAAAAAATAAAGCTGAAACGTTAAATTAAC
Found at i:31495 original size:32 final size:34
Alignment explanation
Indices: 31459--31524 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 34
31449 CGCGGCATCA
* *
31459 AGGCAGCAGCGCTGC-CTT-GTGCGCGGGCTGGC
1 AGGCAGCAGCGCCGCGCTTGGCGCGCGGGCTGGC
*
31491 AGGCAGCAGCTCCGCGCTTGGCGCGCGGGCTGGC
1 AGGCAGCAGCGCCGCGCTTGGCGCGCGGGCTGGC
31525 CTGGTGGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.45
33 3 0.10
34 13 0.45
ACGTcount: A:0.09, C:0.33, G:0.44, T:0.14
Consensus pattern (34 bp):
AGGCAGCAGCGCCGCGCTTGGCGCGCGGGCTGGC
Found at i:31555 original size:33 final size:33
Alignment explanation
Indices: 31509--31582 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
31499 GCTCCGCGCT
* *
31509 TGGCGCGCGGGCTGGCCTGGTGGTGCCCCGTGC
1 TGGCGCGCGGGCTGCCCTGGTGATGCCCCGTGC
*
31542 TGGCGCGCTGGCTGCCCTGGTGATGCCCCGTGC
1 TGGCGCGCGGGCTGCCCTGGTGATGCCCCGTGC
31575 TGGCGCGC
1 TGGCGCGC
31583 CCTTGCTGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.01, C:0.35, G:0.45, T:0.19
Consensus pattern (33 bp):
TGGCGCGCGGGCTGCCCTGGTGATGCCCCGTGC
Found at i:42725 original size:39 final size:37
Alignment explanation
Indices: 42619--42725 Score: 101
Period size: 39 Copynumber: 2.8 Consensus size: 37
42609 CTAACTGATG
* * *
42619 AAAGCAACAATCCTGAAT-ATGATTCTGAAATTAACTGA
1 AAAGCAATAATCCTAAATCATGA--CTGAAATAAACTGA
* * *
42657 TAAGCAATGATCCTAAATCAGGA-TCGAAATAAAACTGA
1 AAAGCAATAATCCTAAATCATGACT-GAAAT-AAACTGA
42695 CAAAGCAATAATCCTAAATCATGACTGAAAT
1 -AAAGCAATAATCCTAAATCATGACTGAAAT
42726 TGAATCATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
36 1 0.02
37 5 0.09
38 20 0.36
39 28 0.51
40 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (37 bp):
AAAGCAATAATCCTAAATCATGACTGAAATAAACTGA
Found at i:42905 original size:20 final size:20
Alignment explanation
Indices: 42880--42934 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
42870 ACTGATATGG
**
42880 TACCCGGAGGTTTTACCAAT
1 TACCCGGAGGACTTACCAAT
*
42900 TACCCGGAGGACTTACTAAT
1 TACCCGGAGGACTTACCAAT
*
42920 TGCCCGGAGGACTTA
1 TACCCGGAGGACTTA
42935 TCAAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (20 bp):
TACCCGGAGGACTTACCAAT
Found at i:43218 original size:70 final size:70
Alignment explanation
Indices: 43144--43276 Score: 221
Period size: 70 Copynumber: 1.9 Consensus size: 70
43134 AGCCCATGTT
* *
43144 GCTTGGATGGAACCAAGGCTTAAACTGTCTCGTATGGAAACGAGTTTGACTTGTGGAAAAGCCCT
1 GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCCCT
43209 ACGCG
66 ACGCG
* * *
43214 GCTTGGATGGAACCAAGGCTTAAATTGACTCGTATGGAAATGAGTTTGGCTTATGGAAAAGCC
1 GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
43277 AAAGGATTCG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (70 bp):
GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCCCT
ACGCG
Found at i:43461 original size:69 final size:69
Alignment explanation
Indices: 43388--43520 Score: 248
Period size: 69 Copynumber: 1.9 Consensus size: 69
43378 GCTCCTATTA
*
43388 CTTGGATAGAACCAAGGTTTGAACTGACTCGTATGGAAACGAGTTTGGCTCGTGGAAAAGCCTAT
1 CTTGGATAGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTCGTGGAAAAGCCTAT
43453 GCGG
66 GCGG
*
43457 CTTGGATAGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 CTTGGATAGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTCGTGGAAAAGCCTA
43521 AGCATTCAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (69 bp):
CTTGGATAGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTCGTGGAAAAGCCTAT
GCGG
Found at i:44084 original size:1 final size:1
Alignment explanation
Indices: 44078--44108 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
44068 GGATTTCGAG
44078 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44109 CTTGAATTTT
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:44499 original size:50 final size:50
Alignment explanation
Indices: 44445--44599 Score: 229
Period size: 50 Copynumber: 3.1 Consensus size: 50
44435 AATGCCCTTC
* * * * *
44445 GAAAAGCGAACTTTGGTCTTGGTCTCACAAATGGAATGCAACCTTATTTT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTAT
44495 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTAT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTAT
* * *
44545 AAAAAGTGAATTTTGACCTTGGACTCACAAATGGAATGCAATCTTATTAT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTAT
*
44595 AAAAA
1 GAAAA
44600 TTATGGTTCT
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 97 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (50 bp):
GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTAT
Found at i:45240 original size:26 final size:26
Alignment explanation
Indices: 45211--45266 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
45201 TTGTTGACTG
45211 TTTTTGTTGTTGTTG-TTGTTTTTTGT
1 TTTTTGTTGTTGTTGTTTGTTTTTT-T
*
45237 TTTTTTTTGTTGTTGTTTGTTTTTTT
1 TTTTTGTTGTTGTTGTTTGTTTTTTT
45263 TTTT
1 TTTT
45267 GTTTTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (26 bp):
TTTTTGTTGTTGTTGTTTGTTTTTTT
Found at i:45242 original size:10 final size:10
Alignment explanation
Indices: 45223--45274 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
45213 TTTGTTGTTG
*
45223 TTGTTGTTTT
1 TTGTTTTTTT
45233 TTGTTTTTTT
1 TTGTTTTTTT
* *
45243 TTGTTGTTGT
1 TTGTTTTTTT
45253 TTGTTTTTTT
1 TTGTTTTTTT
45263 TT-TTGTTTTT
1 TTGTT-TTTTT
45273 TT
1 TT
45275 ATATTGATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
9 2 0.06
10 34 0.94
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (10 bp):
TTGTTTTTTT
Found at i:45243 original size:29 final size:30
Alignment explanation
Indices: 45211--45274 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
45201 TTGTTGACTG
45211 TTTTTGTTGTTG-TTGTTGTTTTTTGTT-TT
1 TTTTTGTTGTTGTTTGTT-TTTTTTGTTGTT
*
45240 TTTTTGTTGTTGTTTGTTTTTTTTTTTGTT
1 TTTTTGTTGTTGTTTGTTTTTTTTGTTGTT
45270 TTTTT
1 TTTTT
45275 ATATTGATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (30 bp):
TTTTTGTTGTTGTTTGTTTTTTTTGTTGTT
Found at i:45246 original size:20 final size:20
Alignment explanation
Indices: 45223--45273 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
45213 TTTGTTGTTG
45223 TTGTTGTTTTTTGTTTTTTT
1 TTGTTGTTTTTTGTTTTTTT
*
45243 TTGTTGTTGTTTGTTTTTTT
1 TTGTTGTTTTTTGTTTTTTT
45263 TT-TTGTTTTTT
1 TTGTTGTTTTTT
45274 TATATTGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (20 bp):
TTGTTGTTTTTTGTTTTTTT
Found at i:68266 original size:30 final size:30
Alignment explanation
Indices: 68230--68294 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
68220 TAAATGCATT
68230 AGTAAGATGGAAAATTAAAAAGAAGAATAA
1 AGTAAGATGGAAAATTAAAAAGAAGAATAA
* * *
68260 AGTAAGATGGACAATTAGAAAGAAGAATTA
1 AGTAAGATGGAAAATTAAAAAGAAGAATAA
68290 AGTAA
1 AGTAA
68295 AGAGTGTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.02, G:0.22, T:0.18
Consensus pattern (30 bp):
AGTAAGATGGAAAATTAAAAAGAAGAATAA
Found at i:73986 original size:57 final size:57
Alignment explanation
Indices: 73917--74032 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
73907 TTTCTAAGCT
73917 CTGGATCAAAAGATATGGGCTTTATATCGAAACTGCATATAAGAAGTCCTATGTTGA
1 CTGGATCAAAAGATATGGGCTTTATATCGAAACTGCATATAAGAAGTCCTATGTTGA
*
73974 CTGGATCAAAAGATGTGGGCTTTATATCGAAACTGCATATAAGAAGTCCTATGTTGA
1 CTGGATCAAAAGATATGGGCTTTATATCGAAACTGCATATAAGAAGTCCTATGTTGA
74031 CT
1 CT
74033 AGGTCTTGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.30
Consensus pattern (57 bp):
CTGGATCAAAAGATATGGGCTTTATATCGAAACTGCATATAAGAAGTCCTATGTTGA
Found at i:84701 original size:28 final size:28
Alignment explanation
Indices: 84636--84727 Score: 123
Period size: 28 Copynumber: 3.3 Consensus size: 28
84626 AATGCACCTG
* * * *
84636 AAATGACTAAAATGCTCCTGGACGTG-G
1 AAATGACCAAAATGCCCCTGGACATGCA
* *
84663 AAATGATCAAAATGCCCCTAGACATGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
84691 AAATGACCAAAATGCCCCTGGACATGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
84719 AAATGACCA
1 AAATGACCA
84728 GAATAAGAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.38
28 35 0.62
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.17
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGCA
Found at i:84820 original size:18 final size:18
Alignment explanation
Indices: 84797--84831 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
84787 ATCCAACTAT
84797 ACCTAAATGATCAAATGC
1 ACCTAAATGATCAAATGC
84815 ACCTAAATGATCAAATG
1 ACCTAAATGATCAAATG
84832 ACGAGATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (18 bp):
ACCTAAATGATCAAATGC
Found at i:85078 original size:27 final size:27
Alignment explanation
Indices: 85036--85109 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 27
85026 AAGTGGACTT
*
85036 AAAATGACCAACATGCCCCTGAATATG
1 AAAATGACCAAAATGCCCCTGAATATG
* * * *
85063 CAAATGACCAAAATG-CCCTTAGTGTG
1 AAAATGACCAAAATGCCCCTGAATATG
85089 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
85110 GGTAACCTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 22 0.56
27 17 0.44
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATATG
Found at i:87194 original size:15 final size:14
Alignment explanation
Indices: 87169--87198 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
87159 CTATTTTTGA
87169 ATGATATATATATT
1 ATGATATATATATT
87183 ATGATGATATATATT
1 ATGAT-ATATATATT
87198 A
1 A
87199 CATTATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
ATGATATATATATT
Found at i:90315 original size:105 final size:105
Alignment explanation
Indices: 90135--90385 Score: 382
Period size: 106 Copynumber: 2.4 Consensus size: 105
90125 AATTTTTCTA
** **
90135 ACCCTTAAAATAAATTTTTAATTTTAATTT-GGGCTAAACTTAGTGAATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTATATATTTTAT
*
90199 TTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
90238 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTG-AATTAGTTATATATTTTA
*
90303 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
*
90345 A-CCTTAAAATAAAAATAAAATTTGAATTTGGGGCTAAACTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTT
90386 GAAATTAAGG
Statistics
Matches: 135, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 26 0.19
104 15 0.11
105 37 0.27
106 39 0.29
107 18 0.13
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:91321 original size:20 final size:22
Alignment explanation
Indices: 91293--91335 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
91283 ATATGAACTT
*
91293 CACCTAG-AAAATAAGAATAGC
1 CACCTAGAAAAATAAGAACAGC
91314 CACC-AGAAAAATAAGAACAGC
1 CACCTAGAAAAATAAGAACAGC
91335 C
1 C
91336 CACACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.53, C:0.23, G:0.14, T:0.09
Consensus pattern (22 bp):
CACCTAGAAAAATAAGAACAGC
Found at i:92219 original size:22 final size:22
Alignment explanation
Indices: 92194--92237 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
92184 TTTATTGCCT
92194 CTTTTAATTTTCTGAT-TTTTTC
1 CTTTT-ATTTTCTGATCTTTTTC
* *
92216 CTTTTTTTTTTTGATCTTTTTC
1 CTTTTATTTTCTGATCTTTTTC
92238 TAACTCTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.09, C:0.14, G:0.05, T:0.73
Consensus pattern (22 bp):
CTTTTATTTTCTGATCTTTTTC
Found at i:96810 original size:14 final size:16
Alignment explanation
Indices: 96779--96812 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
96769 GAAATTAAGG
96779 AATAATTATTGAATAAT
1 AATAATTA-TGAATAAT
96796 AATAATTATGAAATAAT
1 AATAATTATG-AATAAT
96813 TATTATTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AATAATTATGAATAAT
Found at i:101796 original size:69 final size:69
Alignment explanation
Indices: 101714--102074 Score: 575
Period size: 69 Copynumber: 5.2 Consensus size: 69
101704 CTCATTTAAC
*
101714 TTGGCTTATGGAAAAGCCCTTAT-T-GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
1 TTGGCTTGTGGAAAAG-CC-TATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
*
101777 ACGAAT
64 ACGAGT
* * *
101783 TTGGCTTGTGGAAAAGCCTTTGTGGCTTGGATGAAACCAAGGCTTAAACTGACTCGTACGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
101848 GAGT
66 GAGT
*
101852 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGAAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
101917 GAGT
66 GAGT
101921 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATAGG-ACCAAGGCTTAAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGAT-GGAACCAAGGCTTAAACTGACTCGTATGGAAA
101985 CGAGT
65 CGAGT
* * *
101990 ATGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGGATCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
102055 GAGT
66 GAGT
* *
102059 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
102075 TCAAAGCATT
Statistics
Matches: 275, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
67 2 0.01
68 5 0.02
69 267 0.97
70 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
GAGT
Found at i:102308 original size:86 final size:86
Alignment explanation
Indices: 102161--102372 Score: 343
Period size: 86 Copynumber: 2.4 Consensus size: 86
102151 ATACCTTTCG
* * * *
102161 AAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATTATGAAAGAGGACCAATTT
1 AAATAACTCTG-ATCTGATGTTGTGA-TTAAAACTTCTTAATTGATGATGAAAGAGGACCAATTT
102226 GCGGTCAACTTTGATAACTTAAA
64 GCGGTCAACTTTGATAACTTAAA
*
102249 AAATAACTCTGATCTGATATTGTGATTAAAACTTCTTAATTGATGATGAAAGAGGACCAATTTGC
1 AAATAACTCTGATCTGATGTTGTGATTAAAACTTCTTAATTGATGATGAAAGAGGACCAATTTGC
*
102314 GGTCAACTTTGATAACTTGAA
66 GGTCAACTTTGATAACTTAAA
102335 AAATAACTCTGAGTCTGATGTTGTGATTAAAACTTCTT
1 AAATAACTCTGA-TCTGATGTTGTGATTAAAACTTCTT
102373 GACTGTTGCT
Statistics
Matches: 116, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
86 69 0.59
87 36 0.31
88 11 0.09
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (86 bp):
AAATAACTCTGATCTGATGTTGTGATTAAAACTTCTTAATTGATGATGAAAGAGGACCAATTTGC
GGTCAACTTTGATAACTTAAA
Found at i:103182 original size:15 final size:13
Alignment explanation
Indices: 103162--103201 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
103152 TAAAAACTTA
103162 AAAATTAAAAAAT
1 AAAATTAAAAAAT
103175 AAGTAATTAAAAAAT
1 AA--AATTAAAAAAT
*
103190 TAAATTAAAAAA
1 AAAATTAAAAAA
103202 AACCTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (13 bp):
AAAATTAAAAAAT
Found at i:104575 original size:20 final size:18
Alignment explanation
Indices: 104550--104598 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
104540 GTATTTAATA
104550 TTTTTTTAATTAATTCTGAT
1 TTTTTTTAATTAATTCT--T
* *
104570 TTTTTTTTATTATTTCTT
1 TTTTTTTAATTAATTCTT
104588 TTTTTTTAATT
1 TTTTTTTAATT
104599 TTTTGAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTTAATTAATTCTT
Found at i:105036 original size:31 final size:31
Alignment explanation
Indices: 104998--105056 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
104988 TCGAAAAGCG
104998 AATTTTGATCTTGGACTCACAAATGGAAGTT
1 AATTTTGATCTTGGACTCACAAATGGAAGTT
*
105029 AATTTTGATCTTGGCCTCACAAATGGAA
1 AATTTTGATCTTGGACTCACAAATGGAA
105057 AGCAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (31 bp):
AATTTTGATCTTGGACTCACAAATGGAAGTT
Found at i:105064 original size:31 final size:31
Alignment explanation
Indices: 104992--105065 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
104982 TGCCCCTCGA
104992 AAAGCGAATTTTGATCTTGGACTCACAAATGG
1 AAAGC-AATTTTGATCTTGGACTCACAAATGG
* *
105024 -AAGTTAATTTTGATCTTGGCCTCACAAATGG
1 AAAG-CAATTTTGATCTTGGACTCACAAATGG
105055 AAAGCAATTTT
1 AAAGCAATTTT
105066 ATTTTGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 34 0.92
32 3 0.08
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (31 bp):
AAAGCAATTTTGATCTTGGACTCACAAATGG
Done.