Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015332.1 Corchorus olitorius cultivar O-4 contig15365, 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: 98288
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3378 original size:1 final size:1
Alignment explanation
Indices: 3367--3415 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
3357 CTAGTAAAGC
* * * *
3367 TTTTTTGTTTTTTTTGTTTTTGTTTTTTTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3416 GAGATAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (1 bp):
T
Found at i:3392 original size:14 final size:14
Alignment explanation
Indices: 3367--3416 Score: 91
Period size: 14 Copynumber: 3.5 Consensus size: 14
3357 CTAGTAAAGC
3367 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
3381 TGTTTTTGTTTTTTT
1 T-TTTTTGTTTTTTT
3396 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
3410 TTTTTTG
1 TTTTTTG
3417 AGATAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
14 21 0.60
15 14 0.40
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
TTTTTTGTTTTTTT
Found at i:3397 original size:20 final size:19
Alignment explanation
Indices: 3367--3415 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 19
3357 CTAGTAAAGC
*
3367 TTTTTTGTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTGTTT
3386 TTGTTTTTTTTTTTTTGTTT
1 TT-TTTTTTTTTTTTTGTTT
3406 TTTTTTTTTT
1 TTTTTTTTTT
3416 GAGATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTGTTT
Found at i:9717 original size:15 final size:15
Alignment explanation
Indices: 9697--9730 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
9687 GTTCCACAGA
*
9697 TTTGAGTCAGTTTAG
1 TTTGAGTCAGTTGAG
9712 TTTGAGTCAGTTGAG
1 TTTGAGTCAGTTGAG
9727 TTTG
1 TTTG
9731 TTAAGTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTGAGTCAGTTGAG
Found at i:12232 original size:12 final size:12
Alignment explanation
Indices: 12205--12239 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12195 GAAGTTCGTG
*
12205 TTTGAAGAC-CA
1 TTTGAAGACTTA
12216 TTTGAAGACTTA
1 TTTGAAGACTTA
12228 TTTGAAGACTTA
1 TTTGAAGACTTA
12240 AAGACTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (12 bp):
TTTGAAGACTTA
Found at i:15919 original size:24 final size:26
Alignment explanation
Indices: 15867--15922 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
15857 TTAACCCACT
**
15867 AATCAACTATATAATACTGAACCCGA
1 AATCAACTATATAATACAAAACCCGA
*
15893 AATCAACTATATAAT-CAAAACTC-A
1 AATCAACTATATAATACAAAACCCGA
15917 AATCAA
1 AATCAA
15923 GAAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 7 0.26
25 5 0.19
26 15 0.56
ACGTcount: A:0.52, C:0.21, G:0.04, T:0.23
Consensus pattern (26 bp):
AATCAACTATATAATACAAAACCCGA
Found at i:16792 original size:18 final size:18
Alignment explanation
Indices: 16769--16805 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16759 ACTCTTTTGT
*
16769 GTTTGAGAAAATAAAAAA
1 GTTTGAGAAAACAAAAAA
16787 GTTTGAGAAAACAAAAAA
1 GTTTGAGAAAACAAAAAA
16805 G
1 G
16806 CACTAACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.19, T:0.19
Consensus pattern (18 bp):
GTTTGAGAAAACAAAAAA
Found at i:17070 original size:26 final size:26
Alignment explanation
Indices: 17041--17091 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
17031 GCATAGCTCC
17041 AATTTTAAAATGAGGTTAAATTTTAT
1 AATTTTAAAATGAGGTTAAATTTTAT
17067 AATTTTAAAATGAGGTTAAATTTTA
1 AATTTTAAAATGAGGTTAAATTTTA
17092 GGAATTGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (26 bp):
AATTTTAAAATGAGGTTAAATTTTAT
Found at i:19483 original size:11 final size:11
Alignment explanation
Indices: 19469--19506 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19459 ATTCATAACA
19469 AATTTATAATT
1 AATTTATAATT
19480 AATTTATAATT
1 AATTTATAATT
19491 -ATTTGATAATT
1 AATTT-ATAATT
*
19502 TATTT
1 AATTT
19507 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:20333 original size:14 final size:14
Alignment explanation
Indices: 20314--20343 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20304 ACCTCTCAAG
20314 AATATTAGAAGAAT
1 AATATTAGAAGAAT
20328 AATATTAGAAGAAT
1 AATATTAGAAGAAT
20342 AA
1 AA
20344 AAATCTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (14 bp):
AATATTAGAAGAAT
Found at i:20501 original size:13 final size:13
Alignment explanation
Indices: 20483--20509 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20473 ACCCAAAATA
20483 ATAGTATTAGGAT
1 ATAGTATTAGGAT
20496 ATAGTATTAGGAT
1 ATAGTATTAGGAT
20509 A
1 A
20510 ATATTGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (13 bp):
ATAGTATTAGGAT
Found at i:21272 original size:19 final size:19
Alignment explanation
Indices: 21248--21285 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
21238 CAGTATTATC
21248 AATATATAATATTTTAGAT
1 AATATATAATATTTTAGAT
*
21267 AATATATATTATTTTAGAT
1 AATATATAATATTTTAGAT
21286 GAGTGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AATATATAATATTTTAGAT
Found at i:22976 original size:89 final size:89
Alignment explanation
Indices: 22869--23048 Score: 360
Period size: 89 Copynumber: 2.0 Consensus size: 89
22859 CCCCCTGAAC
22869 TTTAATCTTGGACAAAATGCCCCCTCAATTATAAAACCATGCCTCCGTTGCCCCCTTTGTAACGG
1 TTTAATCTTGGACAAAATGCCCCCTCAATTATAAAACCATGCCTCCGTTGCCCCCTTTGTAACGG
22934 ACCGTTAGTCACGTGAGGGCGTCG
66 ACCGTTAGTCACGTGAGGGCGTCG
22958 TTTAATCTTGGACAAAATGCCCCCTCAATTATAAAACCATGCCTCCGTTGCCCCCTTTGTAACGG
1 TTTAATCTTGGACAAAATGCCCCCTCAATTATAAAACCATGCCTCCGTTGCCCCCTTTGTAACGG
23023 ACCGTTAGTCACGTGAGGGCGTCG
66 ACCGTTAGTCACGTGAGGGCGTCG
23047 TT
1 TT
23049 ACGGTGCTGA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (89 bp):
TTTAATCTTGGACAAAATGCCCCCTCAATTATAAAACCATGCCTCCGTTGCCCCCTTTGTAACGG
ACCGTTAGTCACGTGAGGGCGTCG
Found at i:25188 original size:16 final size:15
Alignment explanation
Indices: 25156--25185 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25146 AAAATAGTAA
*
25156 ATACGATTTTCTTTT
1 ATACGATTTCCTTTT
25171 ATACGATTTCCTTTT
1 ATACGATTTCCTTTT
25186 TATGAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (15 bp):
ATACGATTTCCTTTT
Found at i:38471 original size:14 final size:13
Alignment explanation
Indices: 38452--38490 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
38442 ACTCAACACT
38452 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
38466 AACTGACTCAACA
1 AACTGACTCAAAA
38479 AACTGACT-AAAA
1 AACTGACTCAAAA
38491 CCCGATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:38483 original size:13 final size:13
Alignment explanation
Indices: 38441--38486 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
38431 GCCAGACTCA
38441 GACTCAACACTAACT
1 GACTCAACA--AACT
*
38456 GACTCGAAAAAACT
1 GACTC-AACAAACT
38470 GACTCAACAAACT
1 GACTCAACAAACT
38483 GACT
1 GACT
38487 AAAACCCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:39562 original size:19 final size:19
Alignment explanation
Indices: 39538--39576 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39528 TATTATAACC
39538 CTCAATCAAAGAGAACATA
1 CTCAATCAAAGAGAACATA
*
39557 CTCAATCAAAGCGAACATA
1 CTCAATCAAAGAGAACATA
39576 C
1 C
39577 ATGGGCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (19 bp):
CTCAATCAAAGAGAACATA
Found at i:40929 original size:22 final size:22
Alignment explanation
Indices: 40904--40946 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40894 AGGTTATTGA
**
40904 AATTTCATAGTGTGGTTATCAC
1 AATTTCATAGTAAGGTTATCAC
*
40926 AATTTTATAGTAAGGTTATCA
1 AATTTCATAGTAAGGTTATCA
40947 AATAGATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (22 bp):
AATTTCATAGTAAGGTTATCAC
Found at i:41106 original size:22 final size:22
Alignment explanation
Indices: 40953--41369 Score: 153
Period size: 22 Copynumber: 18.9 Consensus size: 22
40943 ATCAAATAGA
* * **
40953 TTATCAAAATATCCTAACGAGG
1 TTATCAAAATTTCATAGTGAGG
*
40975 TTAT-AAGAA-TTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
40996 TTAAT-AAAATTTCATAAG-GAGG
1 TT-ATCAAAATTTCAT-AGTGAGG
* * *
41018 TTA-CTAATATTTCATAGGGAAG
1 TTATC-AAAATTTCATAGTGAGG
*
41040 TTATCAAAATTT-ATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* ** *
41061 TTATTAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
41083 TTATCAAAATTTCAT-GTGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
41105 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
41130 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
41152 TTATC-AAA-TCCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
41172 TCATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
41196 ATTATCAAAATTTCATAGT-ATTG
1 -TTATCAAAATTTCATAGTGA-GG
* * *
41219 TTATTAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
41241 TTATCAAAATTACATAATGA-A
1 TTATCAAAATTTCATAGTGAGG
*
41262 TATATCAAAATTTCATAGAG-GG
1 T-TATCAAAATTTCATAGTGAGG
** * * *
41284 GCAACACAATTTCATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
* **
41306 TTATTAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
41328 TTATCAAAATTTTCAAAATGTGA
1 TTATCAAAA-TTTCATAGTGAGG
*
41351 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
41370 GTATTTCTAG
Statistics
Matches: 293, Mismatches: 72, Indels: 60
0.69 0.17 0.14
Matches are distributed among these distances:
19 5 0.02
20 8 0.03
21 62 0.21
22 163 0.56
23 24 0.08
24 2 0.01
25 20 0.07
26 5 0.02
27 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:41108 original size:65 final size:65
Alignment explanation
Indices: 40972--41112 Score: 155
Period size: 65 Copynumber: 2.2 Consensus size: 65
40962 TATCCTAACG
*
40972 AGGTTATAAGAATTCATAGTGTGGTTAATAAAATTTCATAAGGAGGTTACTAATATTTCATAGGG
1 AGGTTATAA-AATTCATAGTGTGGTTAATAAAATTTCATAAGGAGGTTACTAAAATTTCATAGGG
41037 A
65 A
* * * * *
41038 A-GTTATCAAAATTTATAGTGTGGTTATTAAAATTT-TTTAGTGTGGTTA-TCAAAATTTCAT-G
1 AGGTTAT-AAAATTCATAGTGTGGTTAATAAAATTTCATAAG-GAGGTTACT-AAAATTTCATAG
*
41099 TGA
63 GGA
41102 AGGTTATAAAA
1 AGGTTATAAAA
41113 GTCTCAATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
64 12 0.19
65 49 0.77
66 3 0.05
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (65 bp):
AGGTTATAAAATTCATAGTGTGGTTAATAAAATTTCATAAGGAGGTTACTAAAATTTCATAGGGA
Found at i:41575 original size:37 final size:37
Alignment explanation
Indices: 41534--41620 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 37
41524 TAGTATGTAG
*
41534 ATCAAAATTTTACATAACAAAATTTCATAATG-AGCTT
1 ATCAAAATTTTACATAACAAAATTTCATAA-GAAGATT
** * *
41571 ATCAAAATTTGTAGTTATCAAGATTTCATAAGAAGATT
1 ATCAAAATTT-TACATAACAAAATTTCATAAGAAGATT
*
41609 ATTAAAATTTTA
1 ATCAAAATTTTA
41621 TAGGGAGGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
37 13 0.31
38 29 0.69
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (37 bp):
ATCAAAATTTTACATAACAAAATTTCATAAGAAGATT
Found at i:41663 original size:23 final size:21
Alignment explanation
Indices: 41613--41669 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
41603 AAGATTATTA
*
41613 AAATTTTATAGGGAGGTTTAC
1 AAATTTTATAGGAAGGTTTAC
41634 ATTAATTTTATAGGAAGGTTTATCC
1 A--AATTTTATAGGAAGGTTTA--C
*
41659 AAATTTCATAG
1 AAATTTTATAG
41670 CGAGGTTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 1 0.03
23 27 0.90
25 2 0.07
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (21 bp):
AAATTTTATAGGAAGGTTTAC
Found at i:41715 original size:22 final size:22
Alignment explanation
Indices: 41653--41721 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
41643 ATAGGAAGGT
* * *
41653 TTATCCAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGA
*
41675 TTATCACAATTTCATAGTGAGA
1 TTATCAAAATTTCATAGTGAGA
* *
41697 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGAGA
41719 TTA
1 TTA
41722 CTAACAATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGA
Found at i:45719 original size:21 final size:21
Alignment explanation
Indices: 45677--45719 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
45667 TGATCTATCG
*
45677 TGATAATAATAGTAATAGTAA
1 TGATAATAATAGTAATACTAA
*
45698 TGATTATAATTAGTAAT-CTAA
1 TGATAATAA-TAGTAATACTAA
45719 T
1 T
45720 TAGTATGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (21 bp):
TGATAATAATAGTAATACTAA
Found at i:55323 original size:19 final size:19
Alignment explanation
Indices: 55299--55335 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55289 GAGGCTTGTA
55299 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
* *
55318 ACCGTTTTATCACCGTTT
1 ACCGTTTCACCACCGTTT
55336 TGGGACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.32, G:0.14, T:0.38
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:55431 original size:19 final size:19
Alignment explanation
Indices: 55407--55443 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55397 GTACGGTACA
*
55407 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGCACAGTG
*
55426 TAATCTCATCTGCACAGT
1 TAATCTAATCTGCACAGT
55444 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (19 bp):
TAATCTAATCTGCACAGTG
Found at i:59144 original size:33 final size:33
Alignment explanation
Indices: 59102--59167 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
59092 TGTTTCCATA
59102 TTCGGCGGCGGTGATGATTCTGATGATTGATTC
1 TTCGGCGGCGGTGATGATTCTGATGATTGATTC
*
59135 TTCGGCGGCGGTGATGATTCTGGTGATTGATTC
1 TTCGGCGGCGGTGATGATTCTGATGATTGATTC
59168 GTTGACTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.14, C:0.15, G:0.35, T:0.36
Consensus pattern (33 bp):
TTCGGCGGCGGTGATGATTCTGATGATTGATTC
Found at i:60719 original size:38 final size:39
Alignment explanation
Indices: 60658--60740 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 39
60648 AGCAACAAGT
60658 AACAACTTTCAAAATGCTAAGCAGAGTAACCAAAGAATA
1 AACAACTTTCAAAATGCTAAGCAGAGTAACCAAAGAATA
60697 AACAACTTTC-AAATGCTAAGCAGAGTAACCAAAGAATA
1 AACAACTTTCAAAATGCTAAGCAGAGTAACCAAAGAATA
60735 AACAAC
1 AACAAC
60741 ACTCAATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 34 0.77
39 10 0.23
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (39 bp):
AACAACTTTCAAAATGCTAAGCAGAGTAACCAAAGAATA
Found at i:70401 original size:23 final size:22
Alignment explanation
Indices: 70371--70418 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
70361 AATCGAAAAG
70371 AAAAAAAA-ATCAAGGACCTTAAA
1 AAAAAAAAGAT-AAGG-CCTTAAA
70394 AAAAAAAAGATAAGGCCTTAAA
1 AAAAAAAAGATAAGGCCTTAAA
70416 AAA
1 AAA
70419 TAATAAGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.42
23 12 0.50
24 2 0.08
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAAAAAAGATAAGGCCTTAAA
Found at i:74097 original size:65 final size:65
Alignment explanation
Indices: 74026--74262 Score: 366
Period size: 65 Copynumber: 3.6 Consensus size: 65
74016 CTATGTAATT
* * * *
74026 GAAAACGCGTGAAAATAGAATATTCGAATTATTCAAGTTAATCCATCAATAGTGAGTCAGCCACA
1 GAAAACGCGTGAAAAGAGAATATTCGAATTATTCGAGTTAATCCATCAATAGTGAGTCAGCAATA
*
74091 GAAAACGCGTGAAAAGAGAATATTCGAATGATTCGAGTTAATCCATCAATAGTGAGTCAGCAATA
1 GAAAACGCGTGAAAAGAGAATATTCGAATTATTCGAGTTAATCCATCAATAGTGAGTCAGCAATA
* * * * *
74156 GAAAACGCGTGAAAAGAGAATATTTGAATAATTCGAGTTAATCTATCAACAGTGAATCAGCAATA
1 GAAAACGCGTGAAAAGAGAATATTCGAATTATTCGAGTTAATCCATCAATAGTGAGTCAGCAATA
* *
74221 GAAAACGCGTGAAAAGAAAATATTTGAATTATTCGAGTTAAT
1 GAAAACGCGTGAAAAGAGAATATTCGAATTATTCGAGTTAAT
74263 ATAACAGAAG
Statistics
Matches: 160, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 160 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (65 bp):
GAAAACGCGTGAAAAGAGAATATTCGAATTATTCGAGTTAATCCATCAATAGTGAGTCAGCAATA
Found at i:87241 original size:17 final size:17
Alignment explanation
Indices: 87219--87259 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
87209 ACCACCTCGT
*
87219 AGAAAAGGGATTAGAGA
1 AGAAAAGGGACTAGAGA
*
87236 AGAAAAAGTGACTAGAGA
1 AG-AAAAGGGACTAGAGA
87254 AGAAAA
1 AGAAAA
87260 ACCAGAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.59, C:0.02, G:0.29, T:0.10
Consensus pattern (17 bp):
AGAAAAGGGACTAGAGA
Found at i:96131 original size:13 final size:14
Alignment explanation
Indices: 96106--96135 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
96096 ACAATAATAT
96106 AAATAAATAACTAA
1 AAATAAATAACTAA
96120 AAATAAAT-ACTAA
1 AAATAAATAACTAA
96133 AAA
1 AAA
96136 CCCTCCCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAATAACTAA
Found at i:97686 original size:12 final size:12
Alignment explanation
Indices: 97669--97699 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
97659 CCAGAGGATC
97669 TTCCTGTAATTG
1 TTCCTGTAATTG
97681 TTCCTGTAATTG
1 TTCCTGTAATTG
97693 TTCCTGT
1 TTCCTGT
97700 TGTTCTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (12 bp):
TTCCTGTAATTG
Done.