Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022785.1 Corchorus olitorius cultivar O-4 contig22818, 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: 151783
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1201 original size:100 final size:100
Alignment explanation
Indices: 1028--1228 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
1018 TGGAATTTAG
1028 AATGTTTTCGATTGCTTTCATAATATATGCAAACTTAAGAAATGCTGAGGTTGGTCTATCATAAG
1 AATGTTTTCGATTGCTTTCATAATATATGCAAACTTAAGAAATGCTGAGGTTGGTCTATCATAAG
1093 CTGACGCTAATTTCTTTAGTAACTGGTATTTGTGC
66 CTGACGCTAATTTCTTTAGTAACTGGTATTTGTGC
1128 AATGTTTTCGATTGCTTTCATAATATATGCAAACTTAAGAAATGCTGAGGTTGGTCTATCATAAG
1 AATGTTTTCGATTGCTTTCATAATATATGCAAACTTAAGAAATGCTGAGGTTGGTCTATCATAAG
1193 CTGACGCTAATTTCTTTAGTAACTGGTATTTGTGC
66 CTGACGCTAATTTCTTTAGTAACTGGTATTTGTGC
1228 A
1 A
1229 GTTGGGGACA
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (100 bp):
AATGTTTTCGATTGCTTTCATAATATATGCAAACTTAAGAAATGCTGAGGTTGGTCTATCATAAG
CTGACGCTAATTTCTTTAGTAACTGGTATTTGTGC
Found at i:21796 original size:12 final size:11
Alignment explanation
Indices: 21779--21805 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21769 TTTATTTAGT
21779 AAAAAAAAAAG
1 AAAAAAAAAAG
21790 AAAAAAAAAAG
1 AAAAAAAAAAG
21801 AAAAA
1 AAAAA
21806 GGAAAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:27054 original size:2 final size:2
Alignment explanation
Indices: 27042--27077 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
27032 TGTTAATTAT
*
27042 TA TA GA 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
27078 AGAATGCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:34094 original size:18 final size:18
Alignment explanation
Indices: 34073--34110 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34063 TTGACCCTCC
*
34073 GATTTTCAAAATTAATCA
1 GATTTTCAAAATTAAGCA
*
34091 GATTTTCAATATTAAGCA
1 GATTTTCAAAATTAAGCA
34109 GA
1 GA
34111 CATGACAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
GATTTTCAAAATTAAGCA
Found at i:39637 original size:18 final size:18
Alignment explanation
Indices: 39614--39648 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39604 ACAAAAACTG
39614 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
39632 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
39649 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:43156 original size:12 final size:13
Alignment explanation
Indices: 43134--43163 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
43124 ACTAATAATT
43134 AAAATCAATCAAG
1 AAAATCAATCAAG
43147 AAAA-CAATCAAG
1 AAAATCAATCAAG
43159 AAAAT
1 AAAAT
43164 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:46111 original size:2 final size:2
Alignment explanation
Indices: 46106--46174 Score: 50
Period size: 2 Copynumber: 39.0 Consensus size: 2
46096 TTTTTTTGAG
*
46106 TA TA TA TA TA TA TA T- TA TA TA TA TA -A TG T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46144 T- TA -A T- TA T- TA -A TA TA TA TA TA -A TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
46175 ATAAACGAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 22
0.71 0.01 0.28
Matches are distributed among these distances:
1 10 0.18
2 43 0.78
3 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47197 original size:72 final size:72
Alignment explanation
Indices: 47074--47212 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
47064 AAAGACAAGC
*
47074 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGTTATGAGATCATTGGATAT
1 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
47139 CCTGCTG
66 CCTGCTG
* * *
47146 CAAGGTGTGGACATTGTCAAAAGATGGGGCACACGAAATATCAGTGCTATGAGATCATTGGATAT
1 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
47211 CC
66 CC
47213 CTCAGGGTGG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (72 bp):
CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
CCTGCTG
Found at i:52737 original size:76 final size:76
Alignment explanation
Indices: 52611--52768 Score: 307
Period size: 76 Copynumber: 2.1 Consensus size: 76
52601 TGTAAACAAA
52611 ATGAATGGAATATATGATAAAGGTGTTATTTGACCTAAAAAAAGAGTTGATAAGTTCATATATTC
1 ATGAATGGAATATATGATAAAGGTGTTATTTGACCTAAAAAAAGAGTTGATAAGTTCATATATTC
52676 TACCTCCCTAC
66 TACCTCCCTAC
*
52687 ATGAATGGAATATATGATAAAGGTGTTATTTGACCTAAAAAAAGAGTTGATAAGTTCATATATTG
1 ATGAATGGAATATATGATAAAGGTGTTATTTGACCTAAAAAAAGAGTTGATAAGTTCATATATTC
52752 TACCTCCCTAC
66 TACCTCCCTAC
52763 ATGAAT
1 ATGAAT
52769 CTCCTCGCAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 81 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (76 bp):
ATGAATGGAATATATGATAAAGGTGTTATTTGACCTAAAAAAAGAGTTGATAAGTTCATATATTC
TACCTCCCTAC
Found at i:60216 original size:10 final size:10
Alignment explanation
Indices: 60201--60238 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
60191 TTTAGAAATA
60201 TATCTATATC
1 TATCTATATC
60211 TATCTATATC
1 TATCTATATC
60221 TAT-T-TATC
1 TATCTATATC
60229 TATACTATAT
1 TAT-CTATAT
60239 ATAAAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 14 0.56
11 3 0.12
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (10 bp):
TATCTATATC
Found at i:60571 original size:21 final size:22
Alignment explanation
Indices: 60557--60653 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 22
60547 AAAATTCATT
60557 GTGTGGTTACTAAAATTTTATA
1 GTGTGGTTACTAAAATTTTATA
*
60579 GTGCGGTT-CTCAAAATTTTATA
1 GTGTGGTTACT-AAAATTTTATA
* *
60601 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTACTAAAATTTTATA
* **
60623 G-GTAGGATGTTAAAATTTTATA
1 GTGT-GGTTACTAAAATTTTATA
*
60645 GTGTAGTTA
1 GTGTGGTTA
60654 TCACAATTTC
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
21 4 0.07
22 52 0.88
23 3 0.05
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (22 bp):
GTGTGGTTACTAAAATTTTATA
Found at i:60661 original size:22 final size:22
Alignment explanation
Indices: 60568--60683 Score: 85
Period size: 22 Copynumber: 5.3 Consensus size: 22
60558 TGTGGTTACT
** *
60568 AAAATTTTATAGTGCGGTTCTC
1 AAAATTTTATAGTGTAGTTATC
* *
60590 AAAATTTTATAGTGTGGTTACC
1 AAAATTTTATAGTGTAGTTATC
* * * *
60612 AAAATTTCATAG-GTAGGATGTT
1 AAAATTTTATAGTGTA-GTTATC
60634 AAAATTTTATAGTGTAGTTATC
1 AAAATTTTATAGTGTAGTTATC
* * *
60656 ACAATTTCAT-G-GGATGTTATC
1 AAAATTTTATAGTGTA-GTTATC
60677 AAAATTT
1 AAAATTT
60684 CATAAGGAGG
Statistics
Matches: 74, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.03
21 15 0.20
22 54 0.73
23 3 0.04
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.41
Consensus pattern (22 bp):
AAAATTTTATAGTGTAGTTATC
Found at i:60703 original size:22 final size:22
Alignment explanation
Indices: 60650--60836 Score: 141
Period size: 22 Copynumber: 8.6 Consensus size: 22
60640 TTATAGTGTA
* * *
60650 GTTATCACAATTTCAT-GGGAT
1 GTTATCAAAATTTCATAAGGAG
60671 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* *
60693 GTTATCGAAA-TTCAT-GGGAAG
1 GTTATCAAAATTTCATAAGG-AG
* *
60714 GTTGTCAAAATTTCACT-GGGAG
1 GTTATCAAAATTTCA-TAAGGAG
* ****
60736 GTTACCAAAATTTCATATTCTG
1 GTTATCAAAATTTCATAAGGAG
*
60758 GTTATCAAAATTTCATAAGGCG
1 GTTATCAAAATTTCATAAGGAG
* * *
60780 ATTATCGAAATCTT-ATATGGAG
1 GTTATCAAAAT-TTCATAAGGAG
* *
60802 GTTATTAAAATTTCATAAGAAG
1 GTTATCAAAATTTCATAAGGAG
*
60824 ATTATCAAAATTT
1 GTTATCAAAATTT
60837 TATAGTGTCC
Statistics
Matches: 130, Mismatches: 29, Indels: 13
0.76 0.17 0.08
Matches are distributed among these distances:
20 2 0.02
21 33 0.25
22 89 0.68
23 6 0.05
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAG
Found at i:61013 original size:22 final size:22
Alignment explanation
Indices: 60879--61606 Score: 145
Period size: 22 Copynumber: 33.5 Consensus size: 22
60869 TAGAGTGAGC
*
60879 TTATCAAAATTTCA-AGTGTTG
1 TTATCAAAATTTCATAGTGTGG
* **
60900 TTACCAAAATTTCATAGTGTAA
1 TTATCAAAATTTCATAGTGTGG
* * *
60922 TAATCACAATTTCATA--GAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
60942 -TAACAAAATTTCAT-GCGGAGG
1 TTATCAAAATTTCATAG-TGTGG
* * * * *
60963 TAATCGAAATTTTAAAG-GGGAG
1 TTATCAAAATTTCATAGTGTG-G
60985 ATTATCAAAATTTCATAGTGTGG
1 -TTATCAAAATTTCATAGTGTGG
* *
61008 TTATCAAAATTTTATAATGTGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
61030 ---T----ATTTCAGAGGAAGAGA
1 TTATCAAAATTTCATA-G-TGTGG
* *
61047 TTATCAAATTTTCATTGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
61069 -TAGTTAAAATTTCATAATGAGT
1 TTA-TCAAAATTTCATAGTGTGG
* *
61091 TTATCAAAATTT-ATAGTGAGA
1 TTATCAAAATTTCATAGTGTGG
* *
61112 TTAACAAAATTTGATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
61134 TTCTCAAAATTTTATAAG-GAGA
1 TTATCAAAATTTCAT-AGTGTGG
* * **
61156 TTAACAAAACTTCATAGT-AAG
1 TTATCAAAATTTCATAGTGTGG
** * **
61177 TTATCGTAATTTCATCATGTAATTAA
1 TTATCAAAATTTCAT-A-GT--GTGG
* **
61203 TTATCAAAATTTCATTG-GTAT
1 TTATCAAAATTTCATAGTGTGG
* *
61224 TTATCAAAATTTCATTG-GGGG
1 TTATCAAAATTTCATAGTGTGG
* * **
61245 TTATCAAAATTTGACAGTGTTC
1 TTATCAAAATTTCATAGTGTGG
* *
61267 TTATCAAAATTTCTTAG-GAGG
1 TTATCAAAATTTCATAGTGTGG
* *
61288 TTAACAAAAGTTT-ATAAG-GAGG
1 TTATCAAAA-TTTCAT-AGTGTGG
* *
61310 TTATAAAAAATTT-ATAGGGAT-G
1 TTAT-CAAAATTTCATAGTG-TGG
61332 TTATCAAAATTTCATGAG-GTGG
1 TTATCAAAATTTCAT-AGTGTGG
* * *
61354 TTTTCAAAATCTC--A-TGAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
61373 TTATCAAAATTTGA-AATGGAGG
1 TTATCAAAATTTCATAGT-GTGG
* *
61395 TTATCAAAATGTT-ATAGGGAGG
1 TTATCAAAAT-TTCATAGTGTGG
* **
61417 TTTATAAAAATTTCATAGTAAGG
1 -TTATCAAAATTTCATAGTGTGG
* * * *
61440 -TATCACAATTTCATGGTATGT
1 TTATCAAAATTTCATAGTGTGG
* *
61461 TTATCAAAATTTCATAATGTGA
1 TTATCAAAATTTCATAGTGTGG
* * * * *
61483 TTACCAATATTTTATCG-GAAGG
1 TTATCAAAATTTCATAGTG-TGG
* * * *
61505 TTACCAAAATATCATAATGTACGC
1 TTATCAAAATTTCATAGTGT--GG
* * * * * * *
61529 TTACCAACATTTAATTGGGAGT
1 TTATCAAAATTTCATAGTGTGG
* * *
61551 TTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATAGTGTGG
61573 TTATCAAAATTTCATTAG-GTGG
1 TTATCAAAATTTCA-TAGTGTGG
* *
61595 TTGTTAAAATTT
1 TTATCAAAATTT
61607 TTATTAGGGA
Statistics
Matches: 511, Mismatches: 145, Indels: 101
0.68 0.19 0.13
Matches are distributed among these distances:
15 6 0.01
17 2 0.00
19 26 0.05
20 3 0.01
21 125 0.24
22 262 0.51
23 51 0.10
24 22 0.04
26 14 0.03
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:61110 original size:21 final size:22
Alignment explanation
Indices: 61074--61587 Score: 147
Period size: 22 Copynumber: 23.5 Consensus size: 22
61064 TGTGGTAGTT
*
61074 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAGTGAGTTTATC
* *
61096 AAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAGTGAGTTTATC
* * * *
61117 AAAATTTGATAGTGTGGTTCTC
1 AAAATTTCATAGTGAGTTTATC
* * *
61139 AAAATTTTATAAG-GAGATTAAC
1 AAAATTTCAT-AGTGAGTTTATC
* *
61161 AAAACTTCATAGTAAG-TTATC
1 AAAATTTCATAGTGAGTTTATC
** * *
61182 GTAATTTCATCATGTAATTAATTATC
1 AAAATTTCAT-A-GTGAGT--TTATC
*
61208 AAAATTTCATTG-GTA-TTTATC
1 AAAATTTCATAGTG-AGTTTATC
* * *
61229 AAAATTTCATTG-GGGGTTATC
1 AAAATTTCATAGTGAGTTTATC
* * *
61250 AAAATTTGACAGTG-TTCTTATC
1 AAAATTTCATAGTGAGT-TTATC
* * *
61272 AAAATTTCTTAG-GAGGTTAAC
1 AAAATTTCATAGTGAGTTTATC
* *
61293 AAAAGTTT-ATAAG-GAGGTTATAA
1 AAAA-TTTCAT-AGTGAGTTTAT-C
*
61316 AAAATTT-ATAGGGA-TGTTATC
1 AAAATTTCATAGTGAGT-TTATC
61337 AAAATTTCATGAGGTG-GTTT-TC
1 AAAATTTCAT-A-GTGAGTTTATC
* *
61359 AAAATCTC--A-TGAGGTTATC
1 AAAATTTCATAGTGAGTTTATC
* * *
61378 AAAATTTGA-AATGGAGGTTATC
1 AAAATTTCATAGT-GAGTTTATC
* *
61400 AAAATGTT-ATAGGGAGGTTTATA
1 AAAAT-TTCATAGTGA-GTTTATC
* *
61423 AAAATTTCATAGTAAG-GTATC
1 AAAATTTCATAGTGAGTTTATC
* *
61444 ACAATTTCATGGT-ATGTTTATC
1 AAAATTTCATAGTGA-GTTTATC
* * * *
61466 AAAATTTCATAATGTGATTACC
1 AAAATTTCATAGTGAGTTTATC
* * * * *
61488 AATATTTTATCG-GAAGGTTACC
1 AAAATTTCATAGTG-AGTTTATC
* * * *
61510 AAAATATCATAATGTACGCTTACC
1 AAAATTTCATAGTG-A-GTTTATC
* * * *
61534 AACATTTAATTGGGAGTTTATC
1 AAAATTTCATAGTGAGTTTATC
* *
61556 AAAATTTAATAGGGTAG-TTATC
1 AAAATTTCATAGTG-AGTTTATC
61578 AAAATTTCAT
1 AAAATTTCAT
61588 TAGGTGGTTG
Statistics
Matches: 366, Mismatches: 88, Indels: 76
0.69 0.17 0.14
Matches are distributed among these distances:
17 2 0.01
18 3 0.01
19 9 0.02
20 2 0.01
21 99 0.27
22 182 0.50
23 37 0.10
24 19 0.05
26 13 0.04
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAGTGAGTTTATC
Found at i:61454 original size:85 final size:85
Alignment explanation
Indices: 61267--61432 Score: 194
Period size: 85 Copynumber: 1.9 Consensus size: 85
61257 GACAGTGTTC
* * * *
61267 TTATCAAAATTTCTTAGGAGGTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGGATG
1 TTATCAAAATCTCAT-GGAGGTTATCAAAA-TTTATAAGGAGGTTATAAAAAATTTATAGGGAGG
*
61332 TTATCAAAATTTCATGAGGTGG
64 TTATAAAAATTTCATGAGGTGG
* *
61354 TTTTCAAAATCTCAT-GAGGTTATCAAAATTTGA-AATGGAGGTTAT-CAAAATGTTATAGGGAG
1 TTATCAAAATCTCATGGAGGTTATCAAAATTT-ATAA-GGAGGTTATAAAAAAT-TTATAGGGAG
61416 GTTTATAAAAATTTCAT
63 G-TTATAAAAATTTCAT
61433 AGTAAGGTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
84 10 0.15
85 32 0.47
86 14 0.21
87 12 0.18
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (85 bp):
TTATCAAAATCTCATGGAGGTTATCAAAATTTATAAGGAGGTTATAAAAAATTTATAGGGAGGTT
ATAAAAATTTCATGAGGTGG
Found at i:61469 original size:107 final size:106
Alignment explanation
Indices: 61283--61475 Score: 232
Period size: 107 Copynumber: 1.8 Consensus size: 106
61273 AAATTTCTTA
* *
61283 GGAGGTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGGATGTTATCAAAATTTCATG
1 GGAGGTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGGAAGGTATCAAAATTTCAT-
61348 AGGTGGTTTTCAAAATCTCATGAGGTTATCAAAATTTGAAAT
65 AGGTGGTTTTCAAAATCTCATGAGGTTATCAAAATTTGAAAT
* * * *
61390 GGAGGTTATCAAAA-TGTTATAGGGAGGTT-TATAAAAATTTCATA-GTAAGGTATCACAATTTC
1 GGAGGTTAACAAAAGT-TTATAAGGAGGTTATA-AAAAATTT-ATAGGGAAGGTATCAAAATTTC
* *
61452 AT-GGTATGTTTATCAAAATTTCAT
63 ATAGGT-GGTTT-TCAAAATCTCAT
61476 AATGTGATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
105 3 0.04
106 7 0.10
107 60 0.82
108 3 0.04
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (106 bp):
GGAGGTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGGAAGGTATCAAAATTTCATA
GGTGGTTTTCAAAATCTCATGAGGTTATCAAAATTTGAAAT
Found at i:61559 original size:46 final size:44
Alignment explanation
Indices: 61459--61560 Score: 114
Period size: 46 Copynumber: 2.3 Consensus size: 44
61449 TTCATGGTAT
* * *
61459 GTTTATCAAAATTTCATAATGTGATTACCAATATTTTATCGGAA
1 GTTTATCAAAATATCATAATGTGATTACCAACATTTAATCGGAA
* * * * *
61503 GGTTACCAAAATATCATAATGTACGCTTACCAACATTTAATTGGGA
1 GTTTATCAAAATATCATAATGT--GATTACCAACATTTAATCGGAA
61549 GTTTATCAAAAT
1 GTTTATCAAAAT
61561 TTAATAGGGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
44 19 0.41
46 27 0.59
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (44 bp):
GTTTATCAAAATATCATAATGTGATTACCAACATTTAATCGGAA
Found at i:61721 original size:22 final size:23
Alignment explanation
Indices: 61696--61753 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
61686 TATCGTCATA
* *
61696 AAAACTTTATAGTGTAA-ATATC
1 AAAATTTTATAGTGGAAGATATC
*
61718 AAAATTTTATA-TGGAAGTTATC
1 AAAATTTTATAGTGGAAGATATC
61740 AAAATTTTATAGTG
1 AAAATTTTATAGTG
61754 ATTATCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.13
22 25 0.81
23 2 0.06
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (23 bp):
AAAATTTTATAGTGGAAGATATC
Found at i:70036 original size:32 final size:32
Alignment explanation
Indices: 69995--70069 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
69985 TTTTGATCTA
69995 ACGTGGCATTGTCACTTGGTATTATATGTCCG
1 ACGTGGCATTGTCACTTGGTATTATATGTCCG
*
70027 ACGTGGCATTGTCACTTGGTATTATATGTCTG
1 ACGTGGCATTGTCACTTGGTATTATATGTCCG
70059 ACGTGGCATTG
1 ACGTGGCATTG
70070 CCACACGTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (32 bp):
ACGTGGCATTGTCACTTGGTATTATATGTCCG
Found at i:72206 original size:13 final size:13
Alignment explanation
Indices: 72188--72216 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
72178 TTGATACTCT
72188 ATCAAGTATTAAC
1 ATCAAGTATTAAC
72201 ATCAAGTATTAAC
1 ATCAAGTATTAAC
72214 ATC
1 ATC
72217 TCACTGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (13 bp):
ATCAAGTATTAAC
Found at i:74753 original size:43 final size:44
Alignment explanation
Indices: 74688--74773 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 44
74678 TCATATATTA
74688 CTTTATAATATATAATATATATAATTTAAATAAAAATAAAAATG
1 CTTTATAATATATAATATATATAATTTAAATAAAAATAAAAATG
*
74732 CTTTATAATATATAATA-ATATAATTTAAATAAAAATCAAAAT
1 CTTTATAATATATAATATATATAATTTAAATAAAAATAAAAAT
74774 CAAAATCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 24 0.59
44 17 0.41
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (44 bp):
CTTTATAATATATAATATATATAATTTAAATAAAAATAAAAATG
Found at i:78818 original size:17 final size:17
Alignment explanation
Indices: 78796--78828 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
78786 CCAAAGTATG
78796 AAAGGTTAAAGTTGTCC
1 AAAGGTTAAAGTTGTCC
78813 AAAGGTTAAAGTTGTC
1 AAAGGTTAAAGTTGTC
78829 TAAACAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (17 bp):
AAAGGTTAAAGTTGTCC
Found at i:79875 original size:17 final size:16
Alignment explanation
Indices: 79838--79884 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
79828 GATTCCTTTC
79838 TTTTTTCTTT-TC-TT
1 TTTTTTCTTTATCATT
79852 TTCTTTTCTTTAATCATT
1 TT-TTTTCTTT-ATCATT
79870 TTTTTTCTTTTATCA
1 TTTTTTC-TTTATCA
79885 GTAGCATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.07
15 8 0.29
17 11 0.39
18 7 0.25
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCTTTATCATT
Found at i:89289 original size:29 final size:31
Alignment explanation
Indices: 89257--89323 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
89247 ATGCAATTTG
* *
89257 GGATATAATGTTAC-ACAACA-AGCAATTAA
1 GGATATAACGTTACGAAAACAGAGCAATTAA
* *
89286 GGATATAACGTTACGAAAAGAGAGTAATTAA
1 GGATATAACGTTACGAAAACAGAGCAATTAA
89317 GGATATA
1 GGATATA
89324 GTCCGTTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
31 15 0.47
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (31 bp):
GGATATAACGTTACGAAAACAGAGCAATTAA
Found at i:89489 original size:31 final size:31
Alignment explanation
Indices: 89454--89532 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
89444 CTAACTGATT
*
89454 ATATCCTTAATTGCTTGAAATCGAAAACGTC
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
*
89485 ATATCCTTAATTGCTTGAAATAGAAAACGTT
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
*
89516 ATATCATTAATTGCTTG
1 ATATCCTTAATTGCTTG
89533 TTTTGTAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAGAAAACGTC
Found at i:90660 original size:31 final size:31
Alignment explanation
Indices: 90621--90702 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
90611 CGTTACAAAA
90621 CAAGCAATTAAGGATATAATGTTTTTGATTT
1 CAAGCAATTAAGGATATAATGTTTTTGATTT
* * *
90652 TAAGCAATTAAGGATATGACGTTTTTGATTT
1 CAAGCAATTAAGGATATAATGTTTTTGATTT
90683 CAAGCAATTAAGGATATAAT
1 CAAGCAATTAAGGATATAAT
90703 CAGTAAAGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAATGTTTTTGATTT
Found at i:90746 original size:11 final size:11
Alignment explanation
Indices: 90727--90763 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
90717 TTAATTGATG
90727 ACGTGGCATCC
1 ACGTGGCATCC
*
90738 ACTTGGCATCC
1 ACGTGGCATCC
*
90749 ACGTGGTATCC
1 ACGTGGCATCC
90760 ACGT
1 ACGT
90764 AGATGACACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.19, C:0.32, G:0.24, T:0.24
Consensus pattern (11 bp):
ACGTGGCATCC
Found at i:90877 original size:31 final size:29
Alignment explanation
Indices: 90842--90908 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
90832 CCTAACGGAC
*
90842 TATATCTTTAATTGCTCGTTTTTCGTAACGT
1 TATATCCTTAATTGCTCG-TTTT-GTAACGT
* *
90873 TATATCCTTAATTGTTTGTTTTGTAACGT
1 TATATCCTTAATTGCTCGTTTTGTAACGT
*
90902 TAAATCC
1 TATATCC
90909 CAAATTGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.41
30 4 0.12
31 15 0.47
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (29 bp):
TATATCCTTAATTGCTCGTTTTGTAACGT
Found at i:91011 original size:20 final size:20
Alignment explanation
Indices: 90986--91026 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
90976 CAATACTTGA
90986 ACTTGAGAACTTGTAGGAAT
1 ACTTGAGAACTTGTAGGAAT
91006 ACTTGAGAACTTGTAGGAAT
1 ACTTGAGAACTTGTAGGAAT
91026 A
1 A
91027 TGCCTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (20 bp):
ACTTGAGAACTTGTAGGAAT
Found at i:97356 original size:2 final size:2
Alignment explanation
Indices: 97351--97378 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
97341 CTTTTTGGGT
97351 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
97379 CTTAGCTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:99207 original size:27 final size:27
Alignment explanation
Indices: 99175--99227 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
99165 TCCGACTCAT
* *
99175 CAAGTTTC-AGTTTTGGCGAATCATCAC
1 CAAGTTTCGA-TTTGGGCAAATCATCAC
99202 CAAGTTTCGATTTGGGCAAATCATCA
1 CAAGTTTCGATTTGGGCAAATCATCA
99228 AGTCTCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (27 bp):
CAAGTTTCGATTTGGGCAAATCATCAC
Found at i:99229 original size:24 final size:26
Alignment explanation
Indices: 99171--99230 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
99161 ATCATCCGAC
*
99171 TCATCAAGTTTCAGTTTTGGCGAATCA
1 TCATCAAGTTTCAGTTTGGGCGAA-CA
*
99198 TCACCAAGTTTC-GATTTGGGC-AA-A
1 TCATCAAGTTTCAG-TTTGGGCGAACA
99222 TCATCAAGT
1 TCATCAAGT
99231 CTCAATCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 9 0.31
26 3 0.10
27 17 0.59
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (26 bp):
TCATCAAGTTTCAGTTTGGGCGAACA
Found at i:100193 original size:16 final size:16
Alignment explanation
Indices: 100172--100202 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
100162 ATTTACTTAG
100172 CCAAATGGAAAAGTAC
1 CCAAATGGAAAAGTAC
*
100188 CCAAATGGGAAAGTA
1 CCAAATGGAAAAGTA
100203 AGTGATTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (16 bp):
CCAAATGGAAAAGTAC
Found at i:101964 original size:27 final size:27
Alignment explanation
Indices: 101933--101989 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
101923 CCCTATTGGC
* *
101933 TTCACGATAGCATTGGAAAATATTTGT
1 TTCACGATAACAATGGAAAATATTTGT
* *
101960 TTCACGATAACAATGGGAAATCTTTGT
1 TTCACGATAACAATGGAAAATATTTGT
101987 TTC
1 TTC
101990 TTGAAAAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (27 bp):
TTCACGATAACAATGGAAAATATTTGT
Found at i:117004 original size:7 final size:7
Alignment explanation
Indices: 116989--117044 Score: 58
Period size: 7 Copynumber: 7.4 Consensus size: 7
116979 AAGGCCTGCT
*
116989 AAAATGA
1 AAAAGGA
116996 AAAAGGA
1 AAAAGGA
117003 AAAAGGA
1 AAAAGGA
*
117010 AAGAGAGA
1 AAAAG-GA
117018 AAAAGGAA
1 AAAAGG-A
117026 AGAAAGAGA
1 A-AAAG-GA
117035 AAAAGGA
1 AAAAGGA
117042 AAA
1 AAA
117045 TCATGCGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
7 23 0.55
8 12 0.29
9 6 0.14
10 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (7 bp):
AAAAGGA
Found at i:117021 original size:15 final size:16
Alignment explanation
Indices: 116989--117043 Score: 71
Period size: 17 Copynumber: 3.6 Consensus size: 16
116979 AAGGCCTGCT
*
116989 AAAATGAAA-AAG-GA
1 AAAAGGAAAGAAGAGA
117003 AAAAGGAAAG-AGAGA
1 AAAAGGAAAGAAGAGA
117018 AAAAGGAAAGAAAGAGA
1 AAAAGGAAAG-AAGAGA
117035 AAAAGGAAA
1 AAAAGGAAA
117044 ATCATGCGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 10 0.28
15 12 0.33
17 14 0.39
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (16 bp):
AAAAGGAAAGAAGAGA
Found at i:117035 original size:17 final size:17
Alignment explanation
Indices: 116997--117043 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
116987 CTAAAATGAA
116997 AAAG-GAAAAAGGAAAG
1 AAAGAGAAAAAGGAAAG
117013 --AGAGAAAAAGGAAAG
1 AAAGAGAAAAAGGAAAG
117028 AAAGAGAAAAAGGAAA
1 AAAGAGAAAAAGGAAA
117044 ATCATGCGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 12 0.43
17 14 0.50
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAAGAGAAAAAGGAAAG
Found at i:126577 original size:14 final size:14
Alignment explanation
Indices: 126558--126585 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
126548 CTATTGCATA
126558 TGCATATCAACTTT
1 TGCATATCAACTTT
126572 TGCATATCAACTTT
1 TGCATATCAACTTT
126586 GAAGTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
TGCATATCAACTTT
Found at i:127325 original size:14 final size:14
Alignment explanation
Indices: 127306--127335 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
127296 AATTTATTAC
127306 TAGTAAGTAACAAT
1 TAGTAAGTAACAAT
127320 TAGTAAGTAACAAT
1 TAGTAAGTAACAAT
127334 TA
1 TA
127336 ATTAACACTA
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:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (14 bp):
TAGTAAGTAACAAT
Found at i:129260 original size:26 final size:26
Alignment explanation
Indices: 129208--129260 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
129198 TCCTTCGACT
** *
129208 TGACTAAATACATTGGGTTGGCTATA
1 TGACTAAATACATTGGGTTCACCATA
129234 TGACTAAATA-AGTTGGGTTCACCATA
1 TGACTAAATACA-TTGGGTTCACCATA
129260 T
1 T
129261 AACTTGACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (26 bp):
TGACTAAATACATTGGGTTCACCATA
Found at i:130180 original size:12 final size:12
Alignment explanation
Indices: 130162--130197 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
130152 GCTGAGGTAC
130162 CTCTGTCTCTCT
1 CTCTGTCTCTCT
*
130174 GTCTGTCTCTCT
1 CTCTGTCTCTCT
*
130186 CTCTCTCTCTCT
1 CTCTGTCTCTCT
130198 ATGTATGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (12 bp):
CTCTGTCTCTCT
Done.