Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017042.1 Corchorus olitorius cultivar O-4 contig17075, 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: 101052
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:8082 original size:42 final size:43
Alignment explanation
Indices: 8031--8120 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 43
8021 AGTACATTAC
** *
8031 CTAAATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAAATTCTACTCCACATCTCTAAATAATTCATCAAAACAAAG
*
8072 CTAATATTCTACTCCTACATCTCTAAATAATTTATCAAAACAAAG
1 CTAA-ATTCTACTCC-ACATCTCTAAATAATTCATCAAAACAAAG
8117 CTAA
1 CTAA
8121 CTTGTCTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 8 0.20
43 1 0.02
45 28 0.68
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.32
Consensus pattern (43 bp):
CTAAATTCTACTCCACATCTCTAAATAATTCATCAAAACAAAG
Found at i:9887 original size:13 final size:13
Alignment explanation
Indices: 9869--9907 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
9859 CTAAATTGAC
9869 ATTATTAAAATTA
1 ATTATTAAAATTA
9882 ATTATTTAAAAATTA
1 ATTA-TT-AAAATTA
9897 ATTA-TAAAATT
1 ATTATTAAAATT
9908 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:10080 original size:166 final size:165
Alignment explanation
Indices: 9806--10137 Score: 449
Period size: 166 Copynumber: 2.0 Consensus size: 165
9796 ATAAAAGTAC
* * *
9806 GAATAATGGAAAACTTTATGTTTTCTGATTGTACCTTTTTTTCAAATATATTTCTAAATTGACAT
1 GAATAATGGAAAACTTTATGTTCTCCGATTGTACCTTTTTTCCAAATATATTTCTAAATTGACAT
*
9871 TATTAAAATTAATTATTTAAAAATTAATTATAAAATTTCAATTTAGACCGAA-TTATAAGTTTGT
66 TATTAAAATTAATAATTT--AAATTAATTATAAAATTTCAATTTAGACCGAATTTATAAGTTTGT
*
9935 AAAATTAATTTTCATTGATGAACATGCAAATTTCTAT
129 AAAATTAATTTTCATTAATGAACATGCAAATTTCTAT
*
9972 GAATAAT-GAGAAACTTTATGTTCTCCGATTGTACCCTTTTTTCCAAATATATTTCTAAATTGCC
1 GAATAATGGA-AAACTTTATGTTCTCCGATTGTA-CCTTTTTTCCAAATATATTTCTAAATTGAC
*
10036 ATTATTAAAATTTAGTATAATTT-TATT-ATT-TAAAATTTTCAATTTAGACCGAATTTTTATAA
64 ATTATTAAAA-TTA--ATAATTTAAATTAATTATAAAA-TTTCAATTTAGACCGAA--TTTATAA
* * *
10098 GTTTGTCAAATTGATTTTCGTTAATGAACATGCAAATTTC
123 GTTTGTAAAATTAATTTTCATTAATGAACATGCAAATTTC
10138 CTGTACTATT
Statistics
Matches: 147, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
165 7 0.05
166 48 0.33
167 41 0.28
168 3 0.02
169 42 0.29
170 6 0.04
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.44
Consensus pattern (165 bp):
GAATAATGGAAAACTTTATGTTCTCCGATTGTACCTTTTTTCCAAATATATTTCTAAATTGACAT
TATTAAAATTAATAATTTAAATTAATTATAAAATTTCAATTTAGACCGAATTTATAAGTTTGTAA
AATTAATTTTCATTAATGAACATGCAAATTTCTAT
Found at i:10178 original size:19 final size:20
Alignment explanation
Indices: 10151--10188 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
10141 TACTATTATT
10151 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
10171 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
10189 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:10220 original size:6 final size:6
Alignment explanation
Indices: 10209--10240 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
10199 AAAAGATTAA
10209 ACTAAC ACTAAC ACTAAC ACTAAC ACTAAC AC
1 ACTAAC ACTAAC ACTAAC ACTAAC ACTAAC AC
10241 GTACAATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTAAC
Found at i:10397 original size:22 final size:22
Alignment explanation
Indices: 10372--10525 Score: 143
Period size: 22 Copynumber: 7.0 Consensus size: 22
10362 TGTCCTTGTA
*
10372 TGGTTATCAAAATTTCATAAGC
1 TGGTTATCAAAATTTCATAAGG
* * *
10394 TGGTTATTATAATTTCATGAGG
1 TGGTTATCAAAATTTCATAAGG
* *
10416 AGGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-G
* *
10438 TGGTTACCAAAATTTCATATGG
1 TGGTTATCAAAATTTCATAAGG
** *
10460 AAGTTATCAAAATTATCAT-GGG
1 TGGTTATCAAAATT-TCATAAGG
*
10482 AAGGTTATCAAAATTTCAT-AGTG
1 -TGGTTATCAAAATTTCATAAG-G
10505 TGGTTATCAAAATTTCATAAG
1 TGGTTATCAAAATTTCATAAG
10526 ATCAGGTTAT
Statistics
Matches: 107, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.02
22 84 0.79
23 21 0.20
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGG
Found at i:10502 original size:67 final size:66
Alignment explanation
Indices: 10372--10525 Score: 211
Period size: 67 Copynumber: 2.3 Consensus size: 66
10362 TGTCCTTGTA
** * *
10372 TGGTTATCAAAATTTCATAAGCTGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATAGT
1 TGGTTATCAAAATTTCATAAGCAAGTTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATAGT
10437 G
66 G
* * * *
10438 TGGTTACCAAAATTTCATATGGAAGTTATCAAAATTATCATG-GGAAGGTTATCAAAATTTCATA
1 TGGTTATCAAAATTTCATAAGCAAGTTATCAAAATT-TCATGAGG-AGGTTATCAAAATTCCATA
10502 GTG
64 GTG
10505 TGGTTATCAAAATTTCATAAG
1 TGGTTATCAAAATTTCATAAG
10526 ATCAGGTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
66 31 0.41
67 45 0.59
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (66 bp):
TGGTTATCAAAATTTCATAAGCAAGTTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATAGT
G
Found at i:10655 original size:22 final size:21
Alignment explanation
Indices: 10615--10771 Score: 88
Period size: 22 Copynumber: 7.2 Consensus size: 21
10605 AGAGATTACC
* * *
10615 AAAATGTCATAGCGAGGTTAT
1 AAAATTTCATAGTGTGGTTAT
*
10636 AAGAATTTCATAGTGTGGTTAAC
1 AA-AATTTCATAGTGTGGTT-AT
*
10659 AAAATTTCATAAG-GAGGTTACT
1 AAAATTTCAT-AGTGTGGTTA-T
* * *
10681 AATATTTCATGGGGAT-GTTAT
1 AAAATTTCATAGTG-TGGTTAT
*
10702 CAAAATTTCATAGTGTGGTCAT
1 -AAAATTTCATAGTGTGGTTAT
* *
10724 CAAAATTAT-TTAGTATGGTTAT
1 -AAAATT-TCATAGTGTGGTTAT
*
10746 CAAAATTTCATA-TGAAGGTTAT
1 -AAAATTTCATAGTG-TGGTTAT
10768 AAAA
1 AAAA
10772 GTCTCAATTT
Statistics
Matches: 106, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
21 12 0.11
22 88 0.83
23 6 0.06
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (21 bp):
AAAATTTCATAGTGTGGTTAT
Found at i:10669 original size:44 final size:42
Alignment explanation
Indices: 10614--10771 Score: 131
Period size: 44 Copynumber: 3.6 Consensus size: 42
10604 AAGAGATTAC
* *
10614 CAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAG-GAGGTTATAA-AATTTCATAGTGTGGTTAT
* * *
10658 CAAAATTTCATAAGGAGGTTACTAATATTTCATGGGGAT-GTTAT
1 CAAAATTTCAT-AGGAGGTTA-TAAAATTTCATAGTG-TGGTTAT
* * * *
10702 CAAAATTTCATAGTGTGGTCATCAAAATTAT-TTAGTATGGTTAT
1 CAAAATTTCATAG-GAGGTTAT-AAAATT-TCATAGTGTGGTTAT
*
10746 CAAAATTTCATATGAAGGTTATAAAA
1 CAAAATTTCATA-GGAGGTTATAAAA
10772 GTCTCAATTT
Statistics
Matches: 91, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
43 8 0.09
44 75 0.82
45 8 0.09
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.35
Consensus pattern (42 bp):
CAAAATTTCATAGGAGGTTATAAAATTTCATAGTGTGGTTAT
Found at i:10846 original size:22 final size:23
Alignment explanation
Indices: 10794--11048 Score: 132
Period size: 22 Copynumber: 11.6 Consensus size: 23
10784 TAAGGAGTAC
* *
10794 CAAAATTTGATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
10815 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
10836 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
*
10861 CAAAATTT-ATAG-GAAGATTAT
1 CAAAATTTCATAGAGATGATTAT
* * * *
10882 CCAAATTTTATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
10904 CAAAATTTCA-A-A-ATGAGGTTAT
1 CAAAATTTCATAGAGATGA--TTAT
*
10926 CAAAATTACATA-ATG-TGATTAT
1 CAAAATTTCATAGA-GATGATTAT
* * *
10948 CAAAATTTCATAGAG-GGGTTAAA
1 CAAAATTTCATAGAGATGATT-AT
* *
10971 AAAAATTT-ATAGAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
10992 CAAAATTTTATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
11014 CAAATTTTCA-AAATG-TGATTAC
1 CAAAATTTCATAGA-GATGATTAT
11036 CAAAATTTCATAG
1 CAAAATTTCATAG
11049 TGGTATTTAT
Statistics
Matches: 185, Mismatches: 28, Indels: 40
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.01
20 10 0.05
21 32 0.17
22 104 0.56
23 17 0.09
24 7 0.04
25 13 0.07
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:11352 original size:23 final size:23
Alignment explanation
Indices: 11318--11424 Score: 101
Period size: 23 Copynumber: 4.7 Consensus size: 23
11308 AAAATTGTAG
*
11318 TTATCAAGATTTCATAAGGAGGT
1 TTATCAAAATTTCATAAGGAGGT
* * * *
11341 TTGTCAAAATTTTACATGGAGGT
1 TTATCAAAATTTCATAAGGAGGT
*
11364 TTATCAAAATTTTAT-AGGAAGGT
1 TTATCAAAATTTCATAAGG-AGGT
* * *
11387 TTATCAAAATTTCAAAACGAAG-
1 TTATCAAAATTTCATAAGGAGGT
*
11409 TTATCACAATTTCATA
1 TTATCAAAATTTCATA
11425 GTGTGATTAT
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
22 16 0.24
23 50 0.74
24 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTCATAAGGAGGT
Found at i:11567 original size:45 final size:45
Alignment explanation
Indices: 11496--11582 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
11486 TCATAACGTG
* * *
11496 GTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTA
1 GTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGTTA
* *
11541 GTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 GTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
11583 AGGTCTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (45 bp):
GTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGTTA
Found at i:11592 original size:22 final size:22
Alignment explanation
Indices: 11129--11623 Score: 107
Period size: 22 Copynumber: 22.6 Consensus size: 22
11119 TTATGGAGTA
* *
11129 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAAGTT
*
11149 ATCAAAATTTCATA-CGAAGCTT
1 ATCAAAATTTCATAGGGAAG-TT
* ***
11171 ATCAAAAATATCATAGTTTAGTT
1 ATC-AAAATTTCATAGGGAAGTT
* *
11194 TTCAAAATTTTATAAGAGG-A-TT
1 ATCAAAATTTCAT-AG-GGAAGTT
* * * *
11216 ATCAAAATATCATA-GCATGTAG
1 ATCAAAATTTCATAGGGAAGT-T
11238 ATCAAAATTTCATAGGG-AGATT
1 ATCAAAATTTCATAGGGAAG-TT
* ** *
11260 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAAGTT
* ** * *
11282 ATAAAAAAATCATAGGGAGGTA
1 ATCAAAATTTCATAGGGAAGTT
** *
11304 AT-AAAA----A-ATTGTAGTT
1 ATCAAAATTTCATAGGGAAGTT
* * *
11320 ATCAAGATTTCATAAGGAGGTTT
1 ATCAAAATTTCATAGGGAAG-TT
* * * * *
11343 GTCAAAATTTTACATGGAGGTTT
1 ATCAAAATTTCATAGGGAAG-TT
*
11366 ATCAAAATTTTATA-GGAAGGTTT
1 ATCAAAATTTCATAGGGAA-G-TT
* **
11389 ATCAAAATTTCAAAACGAAGTT
1 ATCAAAATTTCATAGGGAAGTT
*
11411 ATCACAATTTCATAGTGTG-A-TT
1 ATCAAAATTTCATAG-G-GAAGTT
*
11433 ATCAAAATTTCAGAGTGTG-A-TT
1 ATCAAAATTTCATAG-G-GAAGTT
*
11455 A-CTAACAA-TTCATA-TGAAGGTT
1 ATC-AA-AATTTCATAGGGAA-GTT
* * ** **
11477 CTTAAAATTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAAGTT
* * * *
11499 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAAGTT
* * **
11521 ATCAACATCTCATAGTGTTAGTT
1 ATCAAAATTTCATAG-GGAAGTT
*
11544 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAAGTT
* *
11566 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAAGT-T
* * *
11589 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAAGTT
* *
11610 AACAGAATTTCATA
1 ATCAAAATTTCATA
11624 AGAAGGTTAA
Statistics
Matches: 345, Mismatches: 95, Indels: 68
0.68 0.19 0.13
Matches are distributed among these distances:
16 6 0.02
17 4 0.01
19 2 0.01
20 12 0.03
21 14 0.04
22 211 0.61
23 90 0.26
24 6 0.02
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAAGTT
Found at i:11750 original size:22 final size:21
Alignment explanation
Indices: 11725--11780 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
11715 GGTCATCAAA
11725 AATAGTGTAATTATCATAATTT
1 AATAGTG-AATTATCATAATTT
* *
11747 AATAGGGAGGTTATCATAATTT
1 AATAGTGA-ATTATCATAATTT
*
11769 CATA-TGAATTAT
1 AATAGTGAATTAT
11781 TCATTTAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 4 0.14
21 3 0.11
22 21 0.75
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AATAGTGAATTATCATAATTT
Found at i:13137 original size:1 final size:1
Alignment explanation
Indices: 13131--13159 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
13121 AAGAATTTCT
13131 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13160 CAACAAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20207 original size:8 final size:7
Alignment explanation
Indices: 20190--20219 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
20180 CAGCAAAAAT
20190 AAAAAGA
1 AAAAAGA
20197 AAAAAGA
1 AAAAAGA
20204 AAAAAGA
1 AAAAAGA
20211 AAAGAAGA
1 AAA-AAGA
20219 A
1 A
20220 TTATCCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:25742 original size:2 final size:2
Alignment explanation
Indices: 25737--25775 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25727 TTCTTATATA
25737 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
25776 ATTTAGACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:31447 original size:13 final size:13
Alignment explanation
Indices: 31426--31462 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
31416 GATAATTCTT
31426 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
31439 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
31452 CTTGACCCTCC
1 TTTGACCCTCC
31463 TAATAATTAA
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:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:31522 original size:39 final size:39
Alignment explanation
Indices: 31461--31542 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
31451 ACTTGACCCT
*
31461 CCTAATAATTAAGGAAATAAATT-AATACAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATACA-GTTTAGCCC
* *
31500 CCTAATAATTAAGGTAAGAAATTAAATTCAGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATACAGTTTAGCCC
31539 CCTA
1 CCTA
31543 GTTATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
39 34 0.87
40 5 0.13
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (39 bp):
CCTAATAATTAAGGAAAGAAATTAAATACAGTTTAGCCC
Found at i:33078 original size:30 final size:31
Alignment explanation
Indices: 33044--33101 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
33034 AATGAGTCAT
33044 TGAAGTGAACTT-AGTGAGCAATTGAGTCCC
1 TGAAGTGAACTTAAGTGAGCAATTGAGTCCC
* *
33074 TGAAGTGAAGTTAATTGAGCAATTGAGT
1 TGAAGTGAACTTAAGTGAGCAATTGAGT
33102 ATCTGACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (31 bp):
TGAAGTGAACTTAAGTGAGCAATTGAGTCCC
Found at i:34880 original size:190 final size:190
Alignment explanation
Indices: 34557--34937 Score: 762
Period size: 190 Copynumber: 2.0 Consensus size: 190
34547 GAGTACATTA
34557 CTACGACTTCTAAACGTTCTTGGCAGTTATGAGCATTTTAAAAGAATTTGTGGATATTGTCTGGA
1 CTACGACTTCTAAACGTTCTTGGCAGTTATGAGCATTTTAAAAGAATTTGTGGATATTGTCTGGA
34622 ATGAAATGGGATAGGTAGGTGCCTAGAACATAGAACTAATTCTGTTGAGAAGAGGTAAAATGAAA
66 ATGAAATGGGATAGGTAGGTGCCTAGAACATAGAACTAATTCTGTTGAGAAGAGGTAAAATGAAA
34687 TTTACCCCTTTCTTAGGGCTGTACATTACTGCAATTTATCTCTCCTTTAGTCTATTTTTC
131 TTTACCCCTTTCTTAGGGCTGTACATTACTGCAATTTATCTCTCCTTTAGTCTATTTTTC
34747 CTACGACTTCTAAACGTTCTTGGCAGTTATGAGCATTTTAAAAGAATTTGTGGATATTGTCTGGA
1 CTACGACTTCTAAACGTTCTTGGCAGTTATGAGCATTTTAAAAGAATTTGTGGATATTGTCTGGA
34812 ATGAAATGGGATAGGTAGGTGCCTAGAACATAGAACTAATTCTGTTGAGAAGAGGTAAAATGAAA
66 ATGAAATGGGATAGGTAGGTGCCTAGAACATAGAACTAATTCTGTTGAGAAGAGGTAAAATGAAA
34877 TTTACCCCTTTCTTAGGGCTGTACATTACTGCAATTTATCTCTCCTTTAGTCTATTTTTC
131 TTTACCCCTTTCTTAGGGCTGTACATTACTGCAATTTATCTCTCCTTTAGTCTATTTTTC
34937 C
1 C
34938 CCATATAACT
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 191 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (190 bp):
CTACGACTTCTAAACGTTCTTGGCAGTTATGAGCATTTTAAAAGAATTTGTGGATATTGTCTGGA
ATGAAATGGGATAGGTAGGTGCCTAGAACATAGAACTAATTCTGTTGAGAAGAGGTAAAATGAAA
TTTACCCCTTTCTTAGGGCTGTACATTACTGCAATTTATCTCTCCTTTAGTCTATTTTTC
Found at i:36642 original size:11 final size:11
Alignment explanation
Indices: 36618--36652 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
36608 TTGACAGCGT
36618 AACAAAAACAA
1 AACAAAAACAA
* *
36629 AACGAAAACGA
1 AACAAAAACAA
36640 AACAAAAACAA
1 AACAAAAACAA
36651 AA
1 AA
36653 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:43449 original size:11 final size:12
Alignment explanation
Indices: 43428--43454 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43418 GTTGGAACCA
43428 TTTCTTTTTTTT
1 TTTCTTTTTTTT
43440 TTTCTTTTTTTT
1 TTTCTTTTTTTT
43452 TTT
1 TTT
43455 TTGATAACAA
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:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:45870 original size:210 final size:210
Alignment explanation
Indices: 45474--45871 Score: 516
Period size: 210 Copynumber: 1.9 Consensus size: 210
45464 CCAGTCAAGC
* * * * * *
45474 CAATGGAAAGAAGTGACAAGCTTGTTTGATAGAATGGTCGATGAAGGAGTGCAGCCAAATCTCAT
1 CAATGGAAAGAAGCGACAAGCATGTTTAACAGAATGATCGATGAAGGAGTGCAGCCAAATCCCAT
* *
45539 AACTTTCAACTCTATAATCGATGCTCTTTGCAAGGAAAGGAGAACTGAAGAAGCCATTGAGCTGT
66 AACTTTCAACTCTATAATCGATGCTCTTTGCAACGAAAGGAGAACCGAAGAAGCCATTGAGCTGT
* * *
45604 GGGATGCAATGGCTGAAAGAGGTGTGAAACCTGATATCTTCATGTATAATTGTTTAATCCTTGGG
131 GGGATGCAATGGCTGAAAGAGGTGTGAAACCTAATATCTTCATGTACAACTGTTTAATCCTTGGG
45669 TTTTGTCGTTCAGGT
196 TTTTGTCGTTCAGGT
* * * *
45684 CAATGGAAGGAAGCGACAAGCATGTTTAACAGAATGATGGATGAAGGAGTGCAGCCAGATCCCGT
1 CAATGGAAAGAAGCGACAAGCATGTTTAACAGAATGATCGATGAAGGAGTGCAGCCAAATCCCAT
* * * * *
45749 AACTTTCAACTGTATGATTGATGCTCTTTGCAACGAAAGTAGAACCGAAGAAGCCATTGAGGT-T
66 AACTTTCAACTCTATAATCGATGCTCTTTGCAACGAAAGGAGAACCGAAGAAGCCATTGAGCTGT
* ** *
45813 ATGGATTTAATGGCTGACAAG-GGTGTGAAACCTAATGTCATT-ACT-TACAACTGTTTAAT
131 -GGGATGCAATGGCTGA-AAGAGGTGTGAAACCTAATATC-TTCA-TGTACAACTGTTTAAT
45872 ACATGGATTA
Statistics
Matches: 160, Mismatches: 24, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
209 1 0.01
210 153 0.96
211 6 0.04
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (210 bp):
CAATGGAAAGAAGCGACAAGCATGTTTAACAGAATGATCGATGAAGGAGTGCAGCCAAATCCCAT
AACTTTCAACTCTATAATCGATGCTCTTTGCAACGAAAGGAGAACCGAAGAAGCCATTGAGCTGT
GGGATGCAATGGCTGAAAGAGGTGTGAAACCTAATATCTTCATGTACAACTGTTTAATCCTTGGG
TTTTGTCGTTCAGGT
Found at i:48642 original size:31 final size:31
Alignment explanation
Indices: 48604--48665 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
48594 GGAGACTCCT
48604 TATCATGCTTTCTTCGGATGTCATTTTAGTC
1 TATCATGCTTTCTTCGGATGTCATTTTAGTC
48635 TATCATGCTTTCTTCGGATGTCATTTTAGTC
1 TATCATGCTTTCTTCGGATGTCATTTTAGTC
48666 GGGCGGTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (31 bp):
TATCATGCTTTCTTCGGATGTCATTTTAGTC
Found at i:55246 original size:2 final size:2
Alignment explanation
Indices: 55239--55268 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55229 TGGGAACATC
55239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55269 TAATTCTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58129 original size:6 final size:6
Alignment explanation
Indices: 58114--58147 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
58104 CGGTCGTCTT
* *
58114 TTTCTA TTTCTC TTTCTC TTTCTC TTTTTC TTTC
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTTC
58148 GCAATTTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTCTC
Found at i:68667 original size:18 final size:18
Alignment explanation
Indices: 68646--68680 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
68636 TTGGGGTTAA
*
68646 TGAGGTTGTTGATGTTTC
1 TGAGGTTGTTAATGTTTC
68664 TGAGGTTGTTAATGTTT
1 TGAGGTTGTTAATGTTT
68681 GAACCAGTTA
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:0.14, C:0.03, G:0.31, T:0.51
Consensus pattern (18 bp):
TGAGGTTGTTAATGTTTC
Found at i:72951 original size:22 final size:22
Alignment explanation
Indices: 72910--72950 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
72900 TATTAAAAGA
*
72910 TAAAAAGAATTAAAAGAAAATC
1 TAAAAAGAATTAAAAAAAAATC
72932 TAAAAAG-ATTAAAAAAAAA
1 TAAAAAGAATTAAAAAAAAA
72951 ACCAGACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (22 bp):
TAAAAAGAATTAAAAAAAAATC
Found at i:78540 original size:22 final size:20
Alignment explanation
Indices: 78501--78541 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
78491 TCTTTTGTTC
*
78501 TTTTTTTTTTTCCGTTTTAA
1 TTTTTTTTTTTCCCTTTTAA
78521 TTTTTTTTCTTTCCCCTTTTA
1 TTTTTTTT-TTT-CCCTTTTA
78542 CTAGTAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTTTTTTTCCCTTTTAA
Found at i:83052 original size:31 final size:30
Alignment explanation
Indices: 83010--83071 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
83000 AACAGCCCAT
83010 AAAGCCCAATACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAACCT-AAATAA-AAAATA
*
83041 AAAGCCTAATACTAACCTAAATAAAAAATA
1 AAAGCCCAATACTAACCTAAATAAAAAATA
83071 A
1 A
83072 TGGCAGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 20 0.69
32 2 0.07
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (30 bp):
AAAGCCCAATACTAACCTAAATAAAAAATA
Found at i:83171 original size:6 final size:6
Alignment explanation
Indices: 83160--83236 Score: 124
Period size: 6 Copynumber: 13.3 Consensus size: 6
83150 GGCGGGAGCC
*
83160 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGGGGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
83208 AGAGGG AGAGGG AG-GGG -GAGGG -GAGGG AG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AG
83237 GGAGGGATGT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
4 1 0.01
5 11 0.16
6 55 0.82
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:94874 original size:24 final size:24
Alignment explanation
Indices: 94842--94903 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
94832 ACCAGCTTGA
94842 GTTTGTTCCTCCTGTTACTCCTGG
1 GTTTGTTCCTCCTGTTACTCCTGG
*
94866 GTTTGTTCCCCCTGTTACTCCTGG
1 GTTTGTTCCTCCTGTTACTCCTGG
* *
94890 GTGTATTCCTCCTG
1 GTTTGTTCCTCCTG
94904 AATATTGGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.05, C:0.31, G:0.21, T:0.44
Consensus pattern (24 bp):
GTTTGTTCCTCCTGTTACTCCTGG
Found at i:98371 original size:6 final size:6
Alignment explanation
Indices: 98360--98389 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
98350 CATTCTTTAA
*
98360 CCATTT CCATTT CCATTT CCATTT CGATTT
1 CCATTT CCATTT CCATTT CCATTT CCATTT
98390 TTTTGCTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.03, T:0.50
Consensus pattern (6 bp):
CCATTT
Found at i:100473 original size:39 final size:40
Alignment explanation
Indices: 100420--100500 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
100410 TTTAATTCCT
100420 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
* * ** *
100460 ATGTAATA-CTATAATAACTGAAATCCTTATATTAATTAA
1 ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
100499 AT
1 AT
100501 TCTTAGATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATAATTACATTAATTAA
Found at i:100526 original size:24 final size:23
Alignment explanation
Indices: 100491--100536 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
100481 AATCCTTATA
100491 TTAATTAAATTCTTAGATATTTT
1 TTAATTAAATTCTTAGATATTTT
*
100514 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGATATTT
100537 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (23 bp):
TTAATTAAATTCTTAGATATTTT
Found at i:100728 original size:2 final size:2
Alignment explanation
Indices: 100723--100752 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
100713 TGGTATAGTT
100723 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
100753 ATAGTAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.