Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023599.1 Corchorus olitorius cultivar O-4 contig23632, 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: 21340
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:153 original size:32 final size:32
Alignment explanation
Indices: 112--178 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
102 AATCAGATTG
* * *
112 AACTAGTTTGGATGCTTGGATATTAATGGAAA
1 AACTAGTTTGGATACTTGAATATTAATGAAAA
144 AACTAGTTTGGATACTTGAATATTAATGAAAA
1 AACTAGTTTGGATACTTGAATATTAATGAAAA
176 AAC
1 AAC
179 ATTTGAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (32 bp):
AACTAGTTTGGATACTTGAATATTAATGAAAA
Found at i:1127 original size:131 final size:129
Alignment explanation
Indices: 991--1249 Score: 373
Period size: 131 Copynumber: 2.0 Consensus size: 129
981 AAACTATTAT
**
991 AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATTTTTATA-AT-TTTTAC
1 AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACATATTTTA-
*
1054 CATTTTACTA-ATTACTATTTTAATTAAAAAAACTTATATATATCAGAA-TTTTTTAAATATACT
65 -ATTTTACCATATTACTATTTTAATT-AAAAAACTTATATAT-T-AGAATTTTTTTAAATATA-T
1117 TTTAC
125 TTTAC
* * *
1122 AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTTAATCTAATATCCTTATACCTATTTTAT
1 AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACATATTTTAA
*
1187 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATTAGAATTTTTTTAAATATATTTTA
66 TTTTACCATATTACTATTTTAATTAAAAAACTTATATATTAGAATTTTTTTAAATATATTTTA
1250 AATGAAATTT
Statistics
Matches: 117, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
129 9 0.08
130 14 0.12
131 74 0.63
132 15 0.13
133 5 0.04
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (129 bp):
AGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACATATTTTAA
TTTTACCATATTACTATTTTAATTAAAAAACTTATATATTAGAATTTTTTTAAATATATTTTAC
Found at i:1519 original size:15 final size:15
Alignment explanation
Indices: 1478--1529 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1468 ATAATTCATC
* *
1478 ATTT-TTTAAAACTA
1 ATTTATTTAAAATTT
*
1492 ATTTAGTTAAAAATTT
1 ATTTA-TTTAAAATTT
1508 ATTTATTTAAAATTT
1 ATTTATTTAAAATTT
*
1523 AATTATT
1 ATTTATT
1530 GTGATTAACC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 4 0.13
15 15 0.48
16 12 0.39
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTTAAAATTT
Found at i:2785 original size:12 final size:12
Alignment explanation
Indices: 2768--2794 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2758 CTCTTTCCTA
2768 TTGTTTTTTTTT
1 TTGTTTTTTTTT
2780 TTGTTTTTTTTT
1 TTGTTTTTTTTT
2792 TTG
1 TTG
2795 CAACATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:5283 original size:6 final size:6
Alignment explanation
Indices: 5235--5273 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
5225 AATTTAGAAA
5235 TATATC TATATC TATATC TATATC TATATC TATATC TAT
1 TATATC TATATC TATATC TATATC TATATC TATATC TAT
5274 CTATACCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:5692 original size:22 final size:22
Alignment explanation
Indices: 5610--6655 Score: 127
Period size: 22 Copynumber: 47.7 Consensus size: 22
5600 AATTTTGGAA
* *
5610 GTTATCAAAA-TTCATTGTTTG
1 GTTATCAAAATTTCATAGTGTG
*
5631 GTTA-CTAAAATTTTATAGTGTG
1 GTTATC-AAAATTTCATAGTGTG
* *
5653 GTTCTCTAAATTAT-ATAGTGTG
1 GTTATCAAAATT-TCATAGTGTG
*
5675 GTTAGCAAAATTTCATAG-GTAG
1 GTTATCAAAATTTCATAGTGT-G
* * * * * *
5697 GATGTTAAACTTTTATAGTGTA
1 GTTATCAAAATTTCATAGTGTG
* * *
5719 GTTATCACAATTCCAT-GGGAT-
1 GTTATCAAAATTTCATAGTG-TG
*
5740 GTTATCAAAATTTCATAATGAT-
1 GTTATCAAAATTTCATAGTG-TG
* ** **
5762 GTTATTAAAATATTTTTTTTCATAAGGAT
1 GTTA-TCAAA-A-----TTTCATAGTGTG
*
5791 GTTATCAAAATTTTCATA-TGGAG
1 GTTATCAAAA-TTTCATAGT-GTG
* *
5814 GTTATTAAAATTTCATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGTG
* * *
5836 GTTATCGAAA-TTCAT-GGGAAG
1 GTTATCAAAATTTCATAGTG-TG
* * *
5857 GTTGTCAAAATTTCACAAG-GAG
1 GTTATCAAAATTTCA-TAGTGTG
* *
5879 GTTA-CTAAAATTTCATACTCTG
1 GTTATC-AAAATTTCATAGTGTG
*
5901 GTTATC-AAATTTCATAAG-GCG
1 GTTATCAAAATTTCAT-AGTGTG
* ** *
5922 ATTATTGAAATCTT-ATA-TGGAG
1 GTTATCAAAAT-TTCATAGT-GTG
* * *
5944 GTTATTAAAATTTCAT-GGGAAG
1 GTTATCAAAATTTCATAGTG-TG
*
5966 ATTATCAAAATTTCATAGTGT-
1 GTTATCAAAATTTCATAGTGTG
** ** *
5987 AATAGTCCCAATTTCATA--GAG
1 GTTA-TCAAAATTTCATAGTGTG
* * * *
6008 GTTAACAAAATTTCATGGGGCG
1 GTTATCAAAATTTCATAGTGTG
* * * *
6030 ATTATCAAAATTTTAGAGGGAAT-
1 GTTATCAAAATTTCATAGTG--TG
* *
6053 ATTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAGTGTG
*
6075 GTTATCAAAA-TT-ATAATGTG
1 GTTATCAAAATTTCATAGTGTG
* * *
6095 G---T----ATTTCAGAGGGAGAG
1 GTTATCAAAATTTCATA--GTGTG
* *
6112 GTTATCAAATTTTCATTGTGTG
1 GTTATCAAAATTTCATAGTGTG
* * * *
6134 GTAATTAAAATTTCATAATGAG
1 GTTATCAAAATTTCATAGTGTG
* *
6156 TTTATCAAAATTT-ATAGTGAG
1 GTTATCAAAATTTCATAGTGTG
* * *
6177 ATTAACAAAATTTGATAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* * *
6199 GTTCTCAAAATTTTATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGTG
* * *
6221 ATTAACAAAATTTCATAG-GTAA
1 GTTATCAAAATTTCATAGTGT-G
* * * *
6243 GTTATCATAATTTTATGGTGTA
1 GTTATCAAAATTTCATAGTGTG
* * * * * *
6265 ATTAATTATCATAATT--TCATTGGG
1 GTT-ATCA--AAATTTCAT-AGTGTG
* * *
6289 GTTATCAAAAATTTAATAATGTT
1 GTTATC-AAAATTTCATAGTGTG
* * *
6312 CTTATCAAAATTTCGTAG-GAG
1 GTTATCAAAATTTCATAGTGTG
* * * *
6333 GTTAACGAAATTTTATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGTG
* *
6355 GTTATAAAAAATTT-ATAGGGAT-
1 GTTAT-CAAAATTTCATAGTG-TG
* * * *
6377 GATATCAACATTTTATAAG-ATG
1 GTTATCAAAATTTCAT-AGTGTG
*
6399 GTTATCAAAATTCCATGAG-GTG
1 GTTATCAAAATTTCAT-AGTGTG
* *
6421 GTTTTCAAAATTTC--A-TGAG
1 GTTATCAAAATTTCATAGTGTG
* *
6440 GTTATCAAAATTTCA-AATGGAG
1 GTTATCAAAATTTCATAGT-GTG
* * * *
6462 GTTATTAAAATTTTATAGGGAAG
1 GTTATCAAAATTTCATAGTG-TG
* *
6485 TTTATAAAAATTTCATAGTGATG
1 GTTATCAAAATTTCATAGTG-TG
* * * *
6508 G-TATCACAATTTTATGGTATG
1 GTTATCAAAATTTCATAGTGTG
*
6529 GTTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAGTGTG
* * * * * ***
6551 ATTACCAATATTTTATCGAAAG
1 GTTATCAAAATTTCATAGTGTG
* *
6573 GTTATCAAAATATCATAATGTG
1 GTTATCAAAATTTCATAGTGTG
* * * * *
6595 CGCTTACCAACATTTCATTGAGAG
1 -G-TTATCAAAATTTCATAGTGTG
* *
6619 GTTATCAAAGTTTCAT-GGGTG
1 GTTATCAAAATTTCATAGTGTG
*
6640 ATTATCAAAATTTCAT
1 GTTATCAAAATTTCAT
6656 TAGGTTGTGT
Statistics
Matches: 728, Mismatches: 215, Indels: 164
0.66 0.19 0.15
Matches are distributed among these distances:
13 1 0.00
14 2 0.00
15 2 0.00
17 4 0.01
19 17 0.02
20 23 0.03
21 133 0.18
22 399 0.55
23 99 0.14
24 27 0.04
25 3 0.00
27 1 0.00
28 4 0.01
29 13 0.02
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:5867 original size:43 final size:44
Alignment explanation
Indices: 5779--6545 Score: 254
Period size: 44 Copynumber: 17.7 Consensus size: 44
5769 AAATATTTTT
* * *
5779 TTTCATAAGGATGTTATCAAAATTTTCATATGGAGGTTATTAAAA
1 TTTCATAAGGAGGTTATCAAAA-TTTCATAGGGAGGTTATCAAAA
* *
5824 TTTCATAAGGAGGTTATCGAAA-TTCAT-GGGAAGGTTGTCAAAA
1 TTTCATAAGGAGGTTATCAAAATTTCATAGGG-AGGTTATCAAAA
* ****
5867 TTTCACAAGGAGGTTA-CTAAAATTTCATACTCTGGTTATC-AAA
1 TTTCATAAGGAGGTTATC-AAAATTTCATAGGGAGGTTATCAAAA
* * ** * *
5910 TTTCATAAGGCGATTATTGAAATCTT-ATATGGAGGTTATTAAAA
1 TTTCATAAGGAGGTTATCAAAAT-TTCATAGGGAGGTTATCAAAA
* * * * **
5954 TTTCAT-GGGAAGATTATCAAAATTTCATAGTGTA--ATAGTCCCAA
1 TTTCATAAGG-AGGTTATCAAAATTTCATAG-GGAGGTTA-TCAAAA
* * * *
5998 TTTCAT-A-GAGGTTAACAAAATTTCATGGGGCGATTATCAAAA
1 TTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAA
* * * ** ** *
6040 TTTTAGAGGGAATATTATCAAAATTTCATAATGTGGTTATCAAAA
1 TTTCATAAGG-AGGTTATCAAAATTTCATAGGGAGGTTATCAAAA
* * * *
6085 -TT-ATAATGTGG---T----ATTTCAGAGGGAGAGGTTATCAAAT
1 TTTCATAAGGAGGTTATCAAAATTTCATA-GG-GAGGTTATCAAAA
* * * * ** *
6122 TTTCAT-TGTGTGGTAATTAAAATTTCATAATGAGTTTATCAAAA
1 TTTCATAAG-GAGGTTATCAAAATTTCATAGGGAGGTTATCAAAA
* * * * * *
6166 TTT-AT-AGTGAGATTAACAAAATTTGATAGTGTGGTTCTCAAAA
1 TTTCATAAG-GAGGTTATCAAAATTTCATAGGGAGGTTATCAAAA
* * * * * *
6209 TTTTATAAGGAGATTAACAAAATTTCATAGGTAAGTTATCATAA
1 TTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAA
* * ** * *
6253 TTTTAT-GGTGTAATTAATTATCATAATTTCAT-TGG-GGTTATCAAAAA
1 TTTCATAAG-G--A--GGTTATCAAAATTTCATAGGGAGGTTATC-AAAA
* * *** * * *
6300 TTTAATAATGTTCTTATCAAAATTTCGTA-GGAGGTTAACGAAA
1 TTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAA
* * * * *
6343 TTTTATAAGGAGGTTATAAAAAATTT-ATAGGGATGATATCAACA
1 TTTCATAAGGAGGTTAT-CAAAATTTCATAGGGAGGTTATCAAAA
* * * *
6387 TTTTATAA-GATGGTTATCAAAATTCCAT-GAGGTGGTTTTCAAAA
1 TTTCATAAGGA-GGTTATCAAAATTTCATAG-GGAGGTTATCAAAA
* * *
6431 TTTCAT---GAGGTTATCAAAATTTCAAATGGAGGTTATTAAAA
1 TTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAA
* * * * * *
6472 TTTTATAGGGAAGTTTATAAAAATTTCATAGTGATGG-TATCACAA
1 TTTCATAAGG-AGGTTATCAAAATTTCATAGGGA-GGTTATCAAAA
*
6517 TTT--TATGGTATGGTTATCAAAATTTCATA
1 TTTCATAAGG-A-GGTTATCAAAATTTCATA
6546 ATGTGATTAC
Statistics
Matches: 527, Mismatches: 144, Indels: 103
0.68 0.19 0.13
Matches are distributed among these distances:
35 7 0.01
37 11 0.02
38 2 0.00
39 7 0.01
41 32 0.06
42 31 0.06
43 153 0.29
44 167 0.32
45 77 0.15
46 16 0.03
47 10 0.02
48 14 0.03
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (44 bp):
TTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAA
Found at i:6622 original size:46 final size:44
Alignment explanation
Indices: 6528--6627 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 44
6518 TTTATGGTAT
* * *
6528 GGTTATCAAAATTTCATAATGTGATTACCAATATTTTATCGAAA
1 GGTTATCAAAATATCATAATGTGATTACCAACATTTCATCGAAA
* * *
6572 GGTTATCAAAATATCATAATGTGCGCTTACCAACATTTCATTGAGA
1 GGTTATCAAAATATCATAATGT--GATTACCAACATTTCATCGAAA
6618 GGTTATCAAA
1 GGTTATCAAA
6628 GTTTCATGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 21 0.44
46 27 0.56
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATATCATAATGTGATTACCAACATTTCATCGAAA
Found at i:8868 original size:22 final size:21
Alignment explanation
Indices: 8840--9013 Score: 152
Period size: 22 Copynumber: 7.9 Consensus size: 21
8830 ATCTCGGTGT
8840 GGTTATCAAAATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGGA
* *
8862 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
8884 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* * *
8906 AGTTATCAAAATTTTATGGGAA
1 GGTTATCAAAATTTCATAGG-A
*
8928 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
8950 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
*
8974 GGTTA-CTAAAATTTCTTAGGAA
1 GGTTATC-AAAATTTCATAGG-A
**
8996 GGTTATTGAAATTTCATA
1 GGTTATCAAAATTTCATA
9014 ATACTATCAC
Statistics
Matches: 123, Mismatches: 20, Indels: 18
0.76 0.12 0.11
Matches are distributed among these distances:
21 5 0.04
22 98 0.80
23 3 0.02
24 17 0.14
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:8947 original size:66 final size:66
Alignment explanation
Indices: 8841--8967 Score: 220
Period size: 66 Copynumber: 1.9 Consensus size: 66
8831 TCTCGGTGTG
8841 GTTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGGA
1 GTTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGGA
8906 A
66 A
* *
8907 GTTATCAAAATTTTATG-GGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
1 GTTATCAAAATTTCATGAGG-AGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATA
8968 GGATCAGGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 2 0.03
66 56 0.97
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (66 bp):
GTTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGGA
A
Found at i:9087 original size:22 final size:22
Alignment explanation
Indices: 9051--9491 Score: 181
Period size: 22 Copynumber: 19.9 Consensus size: 22
9041 GTCAAAGAGA
* *
9051 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
9073 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
9095 TTAAT-AAAATTTGATAAG-GAGG
1 TT-ATCAAAATTTCAT-AGTGAGG
* * *
9117 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
9139 TTATCAAAACTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
** *
9161 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
9183 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
9205 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
9230 AGTACCAAAA-TTCAATAG-AAAG
1 -TTATCAAAATTTC-ATAGTGAGG
* * * *
9252 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
9273 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
9297 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
* * *
9319 TTATCGAAATTTCATAGTGTTGT
1 TTATCAAAATTTCATAGTG-AGG
* *
9342 TATATCAAAATTTCAAAGCGAGG
1 T-TATCAAAATTTCATAGTGAGG
* * * *
9365 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
9387 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
9409 TCAACAAAATTTTATA--CAGG
1 TTATCAAAATTTCATAGTGAGG
**
9429 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
** * * * *
9451 TTATCAAGTTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
9473 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
9492 GTATTTTTGG
Statistics
Matches: 314, Mismatches: 77, Indels: 56
0.70 0.17 0.13
Matches are distributed among these distances:
20 22 0.07
21 31 0.10
22 198 0.63
23 15 0.05
24 21 0.07
25 19 0.06
26 4 0.01
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:9705 original size:44 final size:44
Alignment explanation
Indices: 9571--10042 Score: 205
Period size: 44 Copynumber: 10.8 Consensus size: 44
9561 TTATGGAGTA
* *
9571 ATCAAAATTTCAT--GGAGGA-TATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATA-ATGAGGTT
* * * * * *
9613 TTCAAAATTTCGTAAGAGG-G-TAATCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCAT-AG-GGAGATTATCAAAATTTCATAATGAGGT-T
*
9657 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * * *
9701 ATCAAAATATCATAGGGAGGTTATCATAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
* * * *
9739 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGA-GAGGTTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATA-ATGAGG-TT
* * * *
9784 ATCAAAATTTTATTGGAAGATTTATCAAAATTTAATAATGAGGTT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATGAGGTT
* * * * * * * *
9829 ATCACAATTTCATAGTGTGATTATCAAAGTTTTAGAGTGTA-ATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATG-AGGTT
* * * *
9873 A-CTAACAA-TTCATACGGAGGTATT-T-AAATTTTTATAACGTA-GTT
1 ATC-AA-AATTTCATAGGGA-G-ATTATCAAAATTTCATAATG-AGGTT
* * * * * * * *
9917 ATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATG-AGGTT
* * *
9962 ATCAAAATTTCATTGAGA-AGTTATTAAAATTTCATAATGAGGTCT
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATGAGGT-T
* * * *
10007 -TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATAA
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAA
10043 GAAAGTTAAA
Statistics
Matches: 319, Mismatches: 78, Indels: 64
0.69 0.17 0.14
Matches are distributed among these distances:
38 28 0.09
39 3 0.01
40 1 0.00
41 2 0.01
42 16 0.05
43 13 0.04
44 158 0.50
45 74 0.23
46 24 0.08
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAGGTT
Found at i:9720 original size:22 final size:22
Alignment explanation
Indices: 9571--10041 Score: 184
Period size: 22 Copynumber: 21.6 Consensus size: 22
9561 TTATGGAGTA
*
9571 ATCAAAATTTCAT--GGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
**
9591 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * * *
9613 TTCAAAATTTCGTA-AGAGGGTA
1 ATCAAAATTTCATAGGGA-GGTT
* * *
9635 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
9657 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
9679 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
9701 ATCAAAATATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
9723 ATCATAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
9739 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
9761 ATCAAAATTTTATAGAGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * * *
9784 ATCAAAATTTTATTGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
* **
9807 ATCAAAATTTAATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
9829 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
9851 ATCAAAGTTTTAGAGTGTA-ATT
1 ATCAAAATTTCATAG-GGAGGTT
*
9873 A-CTAACAA-TTCATACGGAGG-T
1 ATC-AA-AATTTCATAGGGAGGTT
* * * * *
9894 ATTTAAATTTTTATAACGTA-GTT
1 A-TCAAAATTTCAT-AGGGAGGTT
* * *
9917 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
9939 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
9962 ATCAAAATTTCATTGAGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
9984 ATTAAAATTTCATAATGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
10007 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
10028 AACAAAATTTCATA
1 ATCAAAATTTCATA
10042 AGAAAGTTAA
Statistics
Matches: 323, Mismatches: 100, Indels: 54
0.68 0.21 0.11
Matches are distributed among these distances:
16 8 0.02
17 4 0.01
19 2 0.01
20 14 0.04
21 15 0.05
22 217 0.67
23 63 0.20
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:9742 original size:38 final size:38
Alignment explanation
Indices: 9698--9770 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
9688 TCATAATGAG
* *
9698 GTTATCAAAATATCATAGGGAGGTTATCATAATTTGTA
1 GTTATCAAAATATCATAAGGAGGTTATCAAAATTTGTA
* *
9736 GTTATCAAGATTTCATAAGGAGGTTATCAAAATTT
1 GTTATCAAAATATCATAAGGAGGTTATCAAAATTT
9771 TATAGAGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (38 bp):
GTTATCAAAATATCATAAGGAGGTTATCAAAATTTGTA
Found at i:10050 original size:22 final size:22
Alignment explanation
Indices: 10025--10130 Score: 67
Period size: 22 Copynumber: 4.9 Consensus size: 22
10015 CCTTAGGGAG
10025 GTTAACAAAATTTCATAAGAAA
1 GTTAACAAAATTTCATAAGAAA
*
10047 GTTAAAAAAATTT-ATAA-AAA
1 GTTAACAAAATTTCATAAGAAA
** * * **
10067 GGTTCTCGAAATTCCAT-AGTATC
1 -GTTAACAAAATTTCATAAG-AAA
*
10090 GTT-ACTGAAATTTCATAAGAAA
1 GTTAAC-AAAATTTCATAAGAAA
* *
10112 CTTATCAAAATTTCATAAG
1 GTTAACAAAATTTCATAAG
10131 GAGATCATAA
Statistics
Matches: 62, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
20 3 0.05
21 14 0.23
22 41 0.66
23 4 0.06
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.32
Consensus pattern (22 bp):
GTTAACAAAATTTCATAAGAAA
Found at i:13393 original size:17 final size:17
Alignment explanation
Indices: 13371--13405 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13361 AACATCTATC
13371 TATACAATATATTAATT
1 TATACAATATATTAATT
13388 TATACAATATATTAATT
1 TATACAATATATTAATT
13405 T
1 T
13406 GTGGTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (17 bp):
TATACAATATATTAATT
Found at i:19595 original size:31 final size:31
Alignment explanation
Indices: 19521--19581 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
19511 ACCTGAGGCT
* *
19521 AAATGCTCAATTTGGTACCAAACCTTTTAAG
1 AAATACTCAATTTGGTACCAAACCTTTCAAG
*
19552 AAATGCTCAATTTGGTACCAAACCTTTCAA
1 AAATACTCAATTTGGTACCAAACCTTTCAA
19582 AATCAACTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (31 bp):
AAATACTCAATTTGGTACCAAACCTTTCAAG
Done.