Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012901.1 Corchorus olitorius cultivar O-4 contig12934, 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: 38078
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:10167 original size:2 final size:2
Alignment explanation
Indices: 10160--10202 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10150 CAAGCGTGCT
10160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10202 T
1 T
10203 TGTACAACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11175 original size:1 final size:1
Alignment explanation
Indices: 11169--11196 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
11159 TTCACACACT
11169 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
11197 CCAACCATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13628 original size:21 final size:20
Alignment explanation
Indices: 13570--13628 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
13560 CTGTTTGGCA
13570 ACTGTACAGATGAAATTA-C
1 ACTGTACAGATGAAATTATC
* *
13589 ACTGTACAGATTAAATTATGT
1 ACTGTACAGATGAAATTAT-C
*
13610 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAAATTAT
13629 TAGAGCAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
ACTGTACAGATGAAATTATC
Found at i:13706 original size:19 final size:19
Alignment explanation
Indices: 13678--13714 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13668 TTTGGTCTCA
*
13678 AAACGGTGGTGAAACGGTC
1 AAACGATGGTGAAACGGTC
13697 AAACGATGGTGAAACGGT
1 AAACGATGGTGAAACGGT
13715 TACAGATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.35, T:0.16
Consensus pattern (19 bp):
AAACGATGGTGAAACGGTC
Found at i:15005 original size:29 final size:27
Alignment explanation
Indices: 14962--15033 Score: 108
Period size: 29 Copynumber: 2.6 Consensus size: 27
14952 TAAAAATTGT
14962 ATAAATCTTATGAAATTTTTTTTTGAAA
1 ATAAATCTTATGAAATTTTTTTTTG-AA
*
14990 ACTAAATCTTATGAAATTTTTTTTTGAC
1 A-TAAATCTTATGAAATTTTTTTTTGAA
15018 ATAAAATCTTATGAAA
1 AT-AAATCTTATGAAA
15034 ATTAAACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 1 0.02
28 16 0.39
29 24 0.59
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (27 bp):
ATAAATCTTATGAAATTTTTTTTTGAA
Found at i:25542 original size:31 final size:31
Alignment explanation
Indices: 25506--25640 Score: 162
Period size: 31 Copynumber: 4.4 Consensus size: 31
25496 TTTGTGCATG
* **
25506 TGGCATGCCACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
*
25537 TGGCATGCCACATGTCACTTTTGGGTACACA
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* ** **
25568 TGGCGTGATACATGTCACTTTTTGGTACATG
1 TGGCATGCCACATGTCACTTTTTGGTACACA
* * *
25599 TGGCGTGCCACATGTCGCTTTTTGGTACACG
1 TGGCATGCCACATGTCACTTTTTGGTACACA
25630 TGGCATGCCAC
1 TGGCATGCCAC
25641 GTCGGATACC
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (31 bp):
TGGCATGCCACATGTCACTTTTTGGTACACA
Found at i:32007 original size:1 final size:1
Alignment explanation
Indices: 32001--32038 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
31991 CCATGACTAG
32001 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32039 CCGGTACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33599 original size:12 final size:12
Alignment explanation
Indices: 33582--33616 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
33572 CAAACATAAA
33582 TATTTTCCTTGG
1 TATTTTCCTTGG
* *
33594 TATTTTCCATAG
1 TATTTTCCTTGG
33606 TATTTTCCTTG
1 TATTTTCCTTG
33617 ATACCAAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.57
Consensus pattern (12 bp):
TATTTTCCTTGG
Found at i:34045 original size:16 final size:16
Alignment explanation
Indices: 34024--34081 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
34014 TAAATCTTAC
34024 TACTATATATTATCTA
1 TACTATATATTATCTA
*
34040 TACTATATATATAT-AA
1 TACTATATAT-TATCTA
* *
34056 AAGTATATATTATCTA
1 TACTATATATTATCTA
34072 TACTATATAT
1 TACTATATAT
34082 AAAAGTACGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 3 0.09
16 28 0.82
17 3 0.09
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (16 bp):
TACTATATATTATCTA
Found at i:34079 original size:28 final size:29
Alignment explanation
Indices: 34027--34088 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 29
34017 ATCTTACTAC
34027 TATATATTATCTATACTATATATATATAAAAG
1 TATATATTATCTATAC---ATATATATAAAAG
34059 TATATATTATCTATAC-TATATATAAAAG
1 TATATATTATCTATACATATATATAAAAG
34087 TA
1 TA
34089 CGAATAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 14 0.47
32 16 0.53
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (29 bp):
TATATATTATCTATACATATATATAAAAG
Found at i:34807 original size:13 final size:13
Alignment explanation
Indices: 34789--34827 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
34779 CTAAATTGAC
34789 ATTATTAAAATTA
1 ATTATTAAAATTA
34802 ATTATTTAAAAATTA
1 ATTA-TT-AAAATTA
34817 ATTA-TAAAATT
1 ATTATTAAAATT
34828 TCAATTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.25
13 5 0.21
14 2 0.08
15 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTATTAAAATTA
Found at i:35289 original size:22 final size:22
Alignment explanation
Indices: 35264--35497 Score: 138
Period size: 22 Copynumber: 10.5 Consensus size: 22
35254 TGTTTCTGTG
35264 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
35286 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
35309 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
35330 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
35353 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
35374 AGGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
35396 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
35418 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* ** *
35442 AGGTTATTGAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
35464 TGGTTATCACAAATTTTAT-AGAA
1 TGGTTATCA-AAATTTCATAAG-A
*
35487 AGGTTATCAAA
1 TGGTTATCAAA
35498 GAGATTATCA
Statistics
Matches: 163, Mismatches: 37, Indels: 24
0.73 0.17 0.11
Matches are distributed among these distances:
20 1 0.01
21 5 0.03
22 116 0.71
23 22 0.13
24 19 0.12
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:35334 original size:44 final size:42
Alignment explanation
Indices: 35265--36502 Score: 360
Period size: 44 Copynumber: 28.4 Consensus size: 42
35255 GTTTCTGTGT
* * *
35265 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGGTGGTTATCAAAATTTCAT-AGGA
* *
35309 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATA-GGA
* * * *
35353 AGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGG-TGGTTATCAAAATTTCATAG-GA
* * *
35397 GGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-T--GGTTATCAAAATTTCATAGG-A
** * *
35443 GGTTATTGAAATTTCATAGTGTGGTTATCACAAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GTGGTTATCA-AAATTTCATAG-GA
* * *
35488 GGTTATC---A----A-A-GAGATTATCAAAATGTCATAGCGA
1 GGTTATCAAAATTTCATAGGTGGTTATCAAAATTTCATAG-GA
*
35522 GGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGA
1 GGTTATCAA-AATTTCATAG-GTGGTTATCAAAATTTCAT-AGGA
* * * *
35566 GGTTA-CTAATATTTCATGGGGAGGTTATCAAAATTTCATAAGAA
1 GGTTATC-AAAATTTCAT-AGGTGGTTATCAAAATTTCAT-AGGA
* * * * * * *
35610 GGTTAT-AAAAGTCTCAATTTA-ATAAGGAGTACCAACATTTAATAGAA
1 GGTTATCAAAA-TTTC-A--TAGGT--GG-TTATCAAAATTTCATAGGA
* * * *
35657 GGTTATC-AAATCTCATAGAGTGATTATCGAAATTTCATAGAAA
1 GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAG-GA
* *
35700 TCGGGTTATCAAAATTTCATAGTATGGTTAT-TAAA--T--TAGGAA
1 ---GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAGG-A
* * * * * * *
35742 GGTTATTAAACTTTTATTATGG-AGTAATCAAAATTTGA-GGGA
1 GGTTATCAAAATTTCA-TA-GGTGGTTATCAAAATTTCATAGGA
* ** *
35784 GGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA
1 GGTTATCAAAATTTCATA-GGTGGTTATCAAAATTTCATAG--GA
* * * *
35829 -GTTTTCAAAATTTCATAAGAG-GGTTATTAAAATTTTATAGTA
1 GGTTATCAAAATTTCAT-AG-GTGGTTATCAAAATTTCATAGGA
* * * *
35871 TGTAGATCAAAATTTCATATGGAAGGTTATCAAAATTTCATAGTTTA
1 GGT-TATCAAAATTTCATA-GG-TGGTTATCAAAATTTCATAG--GA
* * * * *
35918 -GTTTTCAAAATTTCATAAGAGGATTATCAAAATTTTATAGTA
1 GGTTATCAAAATTTCATAGGTGG-TTATCAAAATTTCATAGGA
* * * *
35960 TGTAGATCAAAATTTCATAGG-GAGATTAACAAAATTTCATAATGA
1 GGT-TATCAAAATTTCATAGGTG-G-TTATCAAAATTTCAT-AGGA
* ** * * *
36005 GGTTATAAAAAAATCATAGGGAGGTTAT-AAAAATT--T-GTA
1 GGTTATCAAAATTTCATA-GGTGGTTATCAAAATTTCATAGGA
* * *
36044 -GTTATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGA
1 GGTTATCAAAATTTCAT-AGGTGGTTATCAAAATTTCATA-GGA
* *
36087 GGTTTATCAAAATTTTATAGGAAGGTTTATCAAAATTTCATAGCGA
1 GG-TTATCAAAATTTCATAGG-TGG-TTATCAAAATTTCATAG-GA
* * * * *
36133 TGTTATCACAATTTCATAGTGTGATTATCAAAATTTCAGAGTGT
1 GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAG-GA
* * * * *
36177 GATTA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTGCA
1 GGTTATC-AA-AATTTCATA-GGTGGTTATCAAAATTTCAT-A-G-G-A
* * * ** * * *
36224 TAGTTATCAATATATCATATGAAGGTTATCAACATCTCATAGTGTT
1 -GGTTATCAAAATTTCATA-GGTGGTTATCAAAATTTCATAG-G-A
* *
36270 GGTTATCAAAATTTCATTGG-GAAGTTATCAAAATTTCATAATGA
1 GGTTATCAAAATTTCATAGGTG--GTTATCAAAATTTCAT-AGGA
* * * * *
36314 GGTCT-TCAAAATTCCTTAGG-GAGATTAACAAAATTTTATAAGAA
1 GGT-TATCAAAATTTCATAGGTG-G-TTATCAAAATTTCAT-AGGA
* * *** * * * *
36358 GGTTA-AAAAATATTTATAAAAAGGTTCTCGAAATTGCATAGTA
1 GGTTATCAAAAT-TTCAT-AGGTGGTTATCAAAATTTCATAGGA
* * *
36401 TTGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCATAAGGA
1 -GGTTATCAAAATTTCATAGG-TGGTTATCAAAATTTCAT-AGGA
* ** * *
36446 GGTCATCAAAA----ATAGTGTAATTATCATAATTTAATAGGA
1 GGTTATCAAAATTTCATAG-GTGGTTATCAAAATTTCATAGGA
* *
36485 GGTTATCATAGTTTCATA
1 GGTTATCAAAATTTCATA
36503 TGAATATTTC
Statistics
Matches: 889, Mismatches: 197, Indels: 217
0.68 0.15 0.17
Matches are distributed among these distances:
34 16 0.02
35 8 0.01
37 2 0.00
38 22 0.02
39 37 0.04
40 22 0.02
41 9 0.01
42 49 0.06
43 51 0.06
44 380 0.43
45 141 0.16
46 78 0.09
47 37 0.04
48 36 0.04
49 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (42 bp):
GGTTATCAAAATTTCATAGGTGGTTATCAAAATTTCATAGGA
Found at i:35367 original size:66 final size:68
Alignment explanation
Indices: 35261--35497 Score: 290
Period size: 66 Copynumber: 3.5 Consensus size: 68
35251 TCTTGTTTCT
* * * * *
35261 GTGTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCC
1 GTGTGGTTACCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
35324 ATA
66 ATA
35327 GTGTGGTTACCAAAATTTCATATGGA-A-GTTATCAAAATTTCATG-GGAAGGTTATCAAAATTT
1 GTGTGGTTACCAAAATTTCATA-GGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
35389 CATA
65 CATA
* * **
35393 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TTAGGAAGGTTATTGAAATTT
1 GTGTGGTTACCAAAATTTCATAGGAT-AGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
35457 CATA
65 CATA
* * *
35461 GTGTGGTTATCACAAATTTTATA-GAAAGGTTATCAAA
1 GTGTGGTTACCA-AAATTTCATAGGATAGGTTATCAAA
35498 GAGATTATCA
Statistics
Matches: 150, Mismatches: 13, Indels: 15
0.84 0.07 0.08
Matches are distributed among these distances:
65 5 0.03
66 76 0.51
67 14 0.09
68 46 0.31
69 9 0.06
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (68 bp):
GTGTGGTTACCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
ATA
Found at i:35527 original size:22 final size:21
Alignment explanation
Indices: 35502--36456 Score: 345
Period size: 22 Copynumber: 43.4 Consensus size: 21
35492 ATCAAAGAGA
*
35502 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
35524 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
35546 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
35568 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
*
35590 TTATCAAAATTTCATAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
* **
35612 TTAT-AAAAGTCTCAATTTAATAAGG
1 TTATCAAAA-TTTC-A--T-AGGAGG
* * * * *
35637 AGTACCAACATTTAATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
35659 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
35679 ATTATCGAAATTTCATAGAAATCGGG
1 -TTATCAAAATTTCATAG-GA---GG
*
35705 TTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATAGGA-GG
*
35727 TTAT-TAAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
* * *
35744 TTATTAAACTTTTATTATGGA-G
1 TTATCAAAATTTCA-TA-GGAGG
* * *
35766 TAATCAAAATTTGA-GGGAGG
1 TTATCAAAATTTCATAGGAGG
* *
35786 ATATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
35808 TTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG--GAGG
* *
35830 TTTTCAAAATTTCATAAGAGGG
1 TTATCAAAATTTCATAGGA-GG
* * * *
35852 TTATTAAAATTTTATAGTATG
1 TTATCAAAATTTCATAGGAGG
*
35873 TAGATCAAAATTTCATATGGAAGG
1 T-TATCAAAATTTCATA-GG-AGG
*
35897 TTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATAG--GAGG
* *
35919 TTTTCAAAATTTCATAAGAGG
1 TTATCAAAATTTCATAGGAGG
* * *
35940 ATTATCAAAATTTTATAGTATG
1 -TTATCAAAATTTCATAGGAGG
* *
35962 TAGATCAAAATTTCATAGGGAGA
1 T-TATCAAAATTTCATA-GGAGG
* *
35985 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCAT-AGGAGG
* **
36007 TTATAAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
36029 TTAT-AAAAATT--T-GTA-G
1 TTATCAAAATTTCATAGGAGG
*
36045 TTATCAAGATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
36067 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
36089 TTTATCAAAATTTTATAGGAAGG
1 -TTATCAAAATTTCATAGG-AGG
*
36112 TTTATCAAAATTTCATAGCGATG
1 -TTATCAAAATTTCATAG-GAGG
* * *
36135 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
* * *
36157 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
36179 TTA-CTAACAA-TTCATATGGAGG
1 TTATC-AA-AATTTCATA-GGAGG
* * * *
36201 TTTTTAAATTTTCATAACGTGCATAG
1 TTATCAAAATTTCAT-A-G-G-A-GG
* * *
36227 TTATCAATATATCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
36249 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAG-G-AGG
* *
36272 TTATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCA-TAGGAGG
*
36294 TTATCAAAATTTCATAATGAGG
1 TTATCAAAATTTCAT-AGGAGG
* * *
36316 TCT-TCAAAATTCCTTAGGGAGA
1 T-TATCAAAATTTCATA-GGAGG
* * *
36338 TTAACAAAATTTTATAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
* * **
36360 TTA-AAAAATATTTATAAAAAGG
1 TTATCAAAAT-TTCAT-AGGAGG
* * * * *
36382 TTCTCGAAATTGCATAGTATTG
1 TTATCAAAATTTCATAGGA-GG
*
36404 TTATTAAAATTTCATAGGAAGG
1 TTATCAAAATTTCATAGG-AGG
36426 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
36448 TCATCAAAA
1 TTATCAAAA
36457 ATAGTGTAAT
Statistics
Matches: 699, Mismatches: 157, Indels: 154
0.69 0.16 0.15
Matches are distributed among these distances:
16 5 0.01
17 16 0.02
18 3 0.00
19 8 0.01
20 23 0.03
21 46 0.07
22 440 0.63
23 100 0.14
24 11 0.02
25 27 0.04
26 16 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:35938 original size:89 final size:89
Alignment explanation
Indices: 35788--36000 Score: 367
Period size: 89 Copynumber: 2.4 Consensus size: 89
35778 GAGGGAGGAT
*
35788 ATCAAAATTTCATAT-GAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGG
1 ATCAAAATTTCATATGGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGA
*
35852 TTATTAAAATTTTATAGTATGTAG
66 TTATCAAAATTTTATAGTATGTAG
35876 ATCAAAATTTCATATGGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGA
1 ATCAAAATTTCATATGGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGA
35941 TTATCAAAATTTTATAGTATGTAG
66 TTATCAAAATTTTATAGTATGTAG
* * *
35965 ATCAAAATTTCATA-GGGAGATTAACAAAATTTCATA
1 ATCAAAATTTCATATGGAAGGTTATCAAAATTTCATA
36001 ATGAGGTTAT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 34 0.29
89 85 0.71
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (89 bp):
ATCAAAATTTCATATGGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGA
TTATCAAAATTTTATAGTATGTAG
Found at i:37889 original size:335 final size:332
Alignment explanation
Indices: 37323--38078 Score: 972
Period size: 335 Copynumber: 2.3 Consensus size: 332
37313 AATAAGAAAT
* *
37323 ACGTAAAAAGCCCTCCAATCTTTTTGGCGTTGAATTTTATA-TTTTTATGAGTATTTTAGTCAAA
1 ACGTAAAAA-CCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAA
* * * *
37387 AACTGA-GAAGAAATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACAAA
65 AATTGAGGAA-AAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATTGCGTACTAACAAA
* * * *
37451 CCATCACGGTTTTTGACTAAAATCGCATTCTAGGTACCGGCTCAATTTTGCATGATTTTTGGCTC
129 CCATCACAGTTTTTGACTAAAATCGCATTCTAGGTACCGACTCAATTATGCATGATTTTTGGCGC
* **
37516 CAAGACTACTTGAAATATCTAAATTCATCTAATCAAATCTCAGCCACATTAGATTTAAGGGTTTG
194 CAAGACTACTTGAAATATCCAAATTCATCTAATCAAATCTCAGCCACATTAGATTTAAGAATTTG
* *
37581 TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAAATAGGAAA
259 TTTTTACAAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAA-TT-G-AAAAAAATAGGAAA
37646 AACGATATTAGAA
321 AACGATATTA-AA
*
37659 ACGTCAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAA
1 ACGT-AAAAACCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAA
* * *
37724 AATTGAGGAAATATCTTTCGGGTCAATTTTTTACATAATTTTAGCCGAAA-T-CGTA-TAA-TAA
65 AATTGAGGAAAAATCTTTCGGGTCAA-TTTTTACAAAATTTTAGCCGAAATTGCGTACTAACAAA
* * * * * *
37785 TCATCACAGTTTTTGGCTAAAAAT-GCGTTTTAGG-ACCCCGACTCAGTTATGCCTGATTTTTGG
129 CCATCACAGTTTTTGACT-AAAATCGCATTCTAGGTA--CCGACTCAATTATGCATGATTTTTGG
* * * *
37848 CGCCAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGAAT
191 CGCCAAGACTACTTGAAATATCCAAATTCATCTAATCAAATCTCAGCCACATTAGATTTAAGAAT
* * *
37913 TTGTTTTTACAAGCATCTATATCTTGTTTCGATTTAATCAGAAATTAATTGAGAAAAATATGAAA
256 TTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTGAAAAAAATAGGAAA
*
37978 AATGATATTAAA
321 AACGATATTAAA
** * *
37990 AGCGTGAAAAGTCCTCCAAT-TGTTTTGGCGTTAAATTATATATTTTTTATGAGTATTTTACCCA
1 A-CGT-AAAAACCCTCCAATCT-TTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCA
* *
38054 AAAATTGAGGAAAAATTTTTAGGGT
63 AAAATTGAGGAAAAATCTTTCGGGT
Statistics
Matches: 369, Mismatches: 42, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
331 4 0.01
332 97 0.26
333 2 0.01
334 27 0.07
335 132 0.36
336 36 0.10
337 47 0.13
338 24 0.07
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (332 bp):
ACGTAAAAACCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAA
ATTGAGGAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATTGCGTACTAACAAACC
ATCACAGTTTTTGACTAAAATCGCATTCTAGGTACCGACTCAATTATGCATGATTTTTGGCGCCA
AGACTACTTGAAATATCCAAATTCATCTAATCAAATCTCAGCCACATTAGATTTAAGAATTTGTT
TTTACAAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTGAAAAAAATAGGAAAAACGA
TATTAAA
Done.