Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016131.1 Corchorus capsularis cultivar CVL-1 contig16152, 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: 39138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:3361 original size:2 final size:2
Alignment explanation
Indices: 3354--3383 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3344 TTCACTAATA
3354 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
3384 GCACTAATAT
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:4089 original size:33 final size:33
Alignment explanation
Indices: 4037--4125 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
4027 TTCTCGGTGC
4037 CGCCCTCCTGGGGCGGCACAGTCCATGGCATGT
1 CGCCCTCCTGGGGCGGCACAGTCCATGGCATGT
* * *
4070 CGCCGTCCTAGGGCGGCACAGTCCATGGTATGT
1 CGCCCTCCTGGGGCGGCACAGTCCATGGCATGT
*
4103 CGCCCTCCTGGGGAGGCAGCAGT
1 CGCCCTCCTGGGGCGGCA-CAGT
4126 TTGTTTTAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.92
34 4 0.08
ACGTcount: A:0.13, C:0.34, G:0.35, T:0.18
Consensus pattern (33 bp):
CGCCCTCCTGGGGCGGCACAGTCCATGGCATGT
Found at i:4187 original size:10 final size:10
Alignment explanation
Indices: 4171--4219 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
4161 TTAAAAAGCT
4171 TTAATTATTGA
1 TTAATTATT-A
4182 TT-ATTATTAA
1 TTAATTATT-A
*
4192 TTATTTAATTA
1 TTAATT-ATTA
4203 TTAATTATTA
1 TTAATTATTA
4213 TTAATTA
1 TTAATTA
4220 CAATTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 20 0.61
11 10 0.30
12 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TTAATTATTA
Found at i:4204 original size:25 final size:25
Alignment explanation
Indices: 4170--4219 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4160 TTTAAAAAGC
*
4170 TTTAATTATTGATTATTATTAATTA
1 TTTAATTATTAATTATTATTAATTA
4195 TTTAATTATTAATTATTATTAATTA
1 TTTAATTATTAATTATTATTAATTA
4220 CAATTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTAATTATTAATTATTATTAATTA
Found at i:6369 original size:18 final size:18
Alignment explanation
Indices: 6346--6385 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6336 GCTCCGACAC
*
6346 ATCATCAGCTCCAACAAA
1 ATCATCAGATCCAACAAA
*
6364 ATCATCAGATCCGACAAA
1 ATCATCAGATCCAACAAA
6382 ATCA
1 ATCA
6386 GGTTGCTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.30, G:0.07, T:0.17
Consensus pattern (18 bp):
ATCATCAGATCCAACAAA
Found at i:7437 original size:32 final size:32
Alignment explanation
Indices: 7370--7473 Score: 106
Period size: 32 Copynumber: 3.2 Consensus size: 32
7360 ACTCCCTCAA
* *
7370 CCGCCCTGCTAGGACGGC-TCGCCATGGTTC-TG
1 CCGCCCTGCTAGGACGGCATC-CCATGG-GCGAG
** *
7402 CCGCTTTAGC-AGGACGGCATGCCATGGGCGAG
1 CCGCCCT-GCTAGGACGGCATCCCATGGGCGAG
*
7434 CCGCCCTGCTAGGACGGCATCCCATGGGCGTG
1 CCGCCCTGCTAGGACGGCATCCCATGGGCGAG
7466 CCGCCCTG
1 CCGCCCTG
7474 TCAGAGCTGC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
31 3 0.05
32 53 0.90
33 3 0.05
ACGTcount: A:0.12, C:0.37, G:0.34, T:0.17
Consensus pattern (32 bp):
CCGCCCTGCTAGGACGGCATCCCATGGGCGAG
Found at i:8953 original size:22 final size:22
Alignment explanation
Indices: 8928--9574 Score: 247
Period size: 22 Copynumber: 29.9 Consensus size: 22
8918 ATGATCCCAT
8928 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
8950 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
8972 TACGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
8994 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* * *
9016 TATGAAATTTTGTTCACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
9038 TAAGGAATTTTGAAAACC-TCAA
1 TATGAAATTTTGATAACCTTC-C
9060 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
9082 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
9105 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
9126 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
9149 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
9170 ATATG-AATTATT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
9193 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
9215 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* *
9237 TATGGAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
9260 TATAAAATTTTGATAAACC-TCGC
1 TATGAAATTTTGAT-AACCTTC-C
* * *
9283 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
9305 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
9322 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
9343 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
9365 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
9387 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
9409 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
9431 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
9453 TATGAAATTTTGATAACATTCA
1 TATGAAATTTTGATAACCTTCC
*
9475 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
9496 -CTGAAATTTTGATTA-C-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
9515 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
9539 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
9556 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
9575 CCCCAGAAAT
Statistics
Matches: 459, Mismatches: 125, Indels: 82
0.69 0.19 0.12
Matches are distributed among these distances:
16 11 0.02
17 12 0.03
18 2 0.00
19 5 0.01
20 13 0.03
21 21 0.05
22 320 0.70
23 70 0.15
24 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:9091 original size:44 final size:44
Alignment explanation
Indices: 9016--9983 Score: 328
Period size: 44 Copynumber: 22.4 Consensus size: 44
9006 TTAACCTTCT
* * * * * * *
9016 TATGAAATTTTGTTCACCTCCCTAAGGAATTTTGAAAACCTCAA
1 TATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACCTCAC
* *
9060 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACC-TCAC
* * * * * * * **
9105 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACCTCAC
* * * * * * *
9149 TATGAAAATTTAAAAACCTCCATATG-AATTATT-AGTAATCACAC
1 TATGAAATTTTGATAACTTCCCTATGAAATT-TTGA-TAACCTCAC
* * *
9193 TCTGAAATTTTGATAA--TCACACTATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACTTC-C-CTATGAAATTTTGATAACCTCAC
* * *
9237 TATGGAATTTTGATAAATCTT-CCTATAAAATTTTGATAAACCTCGC
1 TATGAAATTTTGAT-AA-CTTCCCTATGAAATTTTGAT-AACCTCAC
* * * *
9283 TATAAAATTTTGATAACTTTCTTATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACCTCAC
* ** *
9325 ----AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACCTCAC
* * *
9365 TATGAAATTTTGTTAA-TCTCCCTATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGATAACT-TCCCTATGAAATTTTGAT-AACCTCAC
* *
9409 TATGAAATTTTGATAAC--CCTCTTATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACTTCC-C-TATGAAATTTTGATAACCT-CAC
* *
9453 TATGAAATTTTGATAACATT-CATATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAAC-TTCCCTATGAAATTTTGATAACCTCAC
* * * * * *
9496 -CTGAAATTTTGATTAC-TCCATAATAAAAGTTTAATAACCTTC-C
1 TATGAAATTTTGATAACTTCCCT-ATGAAATTTTGATAACC-TCAC
* * * *
9539 --T--AA-TTTGGTAACCAT-ACTATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAA-CTTCCCTATGAAATTTTGATAACCTCAC
* * * * *
9578 CA-G-AA-----AT-AC--CACTATGAAAATTTTG-TAATCACAT
1 TATGAAATTTTGATAACTTCCCTATG-AAATTTTGATAACCTCAC
* * * ** * * * * *
9612 TTTGAAAATTTGATAACCTCTTTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACCTCAC
* * * *
9656 TATGAAATTCTGATAA--TCACATTATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACTTC-C-CTATGAAATTTTGATAACCTCAC
* ** * * **
9700 TTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCTTTC
1 TATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACCTCAC
* * * * *
9744 TAT-AAATTTTGATAATCTGATCTCTATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAA-CT--TCCCTATGAAATTTTGATAACCTCAC
* * *
9790 TATGAGA-TTTGATAACCTT--CTATCAAATTTTGGT-A-CTC-C
1 TATGAAATTTTGATAA-CTTCCCTATGAAATTTTGATAACCTCAC
* * *
9829 TTATGAAATTGAGACTTTTATAACCTT-CATATGAAATTTTGATAACCACAC
1 -TATGAAA-T-----TTTGATAA-CTTCCCTATGAAATTTTGATAACCTCAC
* * * *
9880 TATAAAATTTTGATAACCTCCCCATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGATAACTTCCCTATGAAATTTTGA-TAACCTCAC
* ** * * *
9923 TAATGAAATTTTGTTAACCACACTGTGAAATTCTT-ATAACCTCGC
1 T-ATGAAATTTTGATAACTTCCCTATGAAATT-TTGATAACCTCAC
*
9968 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
9984 TGGTCTAATG
Statistics
Matches: 696, Mismatches: 151, Indels: 154
0.70 0.15 0.15
Matches are distributed among these distances:
34 11 0.02
35 10 0.01
36 3 0.00
37 1 0.00
38 30 0.04
39 24 0.03
40 14 0.02
41 9 0.01
42 51 0.07
43 36 0.05
44 332 0.48
45 81 0.12
46 57 0.08
47 13 0.02
48 13 0.02
49 2 0.00
50 8 0.01
51 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACCTCAC
Found at i:9268 original size:23 final size:23
Alignment explanation
Indices: 9242--9320 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
9232 CTCGCTATGG
9242 AATTTTGATAAATCTTCCTATAA
1 AATTTTGATAAATCTTCCTATAA
*
9265 AATTTTGATAAA-CCTCGCTATAA
1 AATTTTGATAAATCTTC-CTATAA
* * *
9288 AATTTTGATAACT-TTCTTATGA
1 AATTTTGATAAATCTTCCTATAA
*
9310 AATCTTGATAA
1 AATTTTGATAA
9321 CTACAAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
22 17 0.35
23 31 0.65
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (23 bp):
AATTTTGATAAATCTTCCTATAA
Found at i:9681 original size:22 final size:22
Alignment explanation
Indices: 9590--9804 Score: 99
Period size: 22 Copynumber: 9.7 Consensus size: 22
9580 GAAATACCAC
9590 TATGAAAATTTTG-TAATCACAT
1 TATG-AAATTTTGATAATCACAT
* * * * *
9612 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
* * * * *
9634 TATAAAATTTTGTTGA-CCCCT
1 TATGAAATTTTGATAATCACAT
*
9655 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* *
9678 TATGTAATTTTGATAACCTCGC-T
1 TATGAAATTTTGATAA--TCACAT
*
9701 T-TGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATC-ACAT
**
9722 TATGAAATTTTGATAATC-TTT
1 TATGAAATTTTGATAATCACAT
9743 CTAT-AAATTTTGATAATCTGATC-T
1 -TATGAAATTTTGATAATC--A-CAT
*
9767 CTATGAAATTTCGATAATCAC-T
1 -TATGAAATTTTGATAATCACAT
*
9789 CTATGAGA-TTTGATAA
1 -TATGAAATTTTGATAA
9805 CCTTCTATCA
Statistics
Matches: 147, Mismatches: 31, Indels: 31
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 32 0.22
22 85 0.58
23 7 0.05
24 8 0.05
25 13 0.09
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:9708 original size:66 final size:66
Alignment explanation
Indices: 9587--9739 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 66
9577 CCAGAAATAC
* * * *
9587 CACTATGAAAATTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTATAAAATTTTGTTGAC
1 CACTATG-AAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGATAAC
**
9651 CC
65 AA
* * * * *
9653 CTCTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAAC
1 CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATAAAATTTTGATAAC
9717 AA
65 AA
9719 CACTATGAAATTTTGATAATC
1 CACTATGAAATTTTGATAATC
9740 TTTCTATAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
65 7 0.10
66 63 0.88
67 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (66 bp):
CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGATAACA
A
Found at i:9752 original size:21 final size:22
Alignment explanation
Indices: 9654--9821 Score: 103
Period size: 22 Copynumber: 7.6 Consensus size: 22
9644 TGTTGACCCC
* **
9654 TCTATGAAATTCTGATAATCACA
1 TCTATGAAATTTTGATAATC-TT
* * *
9677 T-TATGTAATTTTGATAACCTC
1 TCTATGAAATTTTGATAATCTT
* * **
9698 GCTTTGAAATTTTGATAA-CAAC
1 TCTATGAAATTTTGATAATC-TT
*
9720 ACTATGAAATTTTGATAATCTT
1 TCTATGAAATTTTGATAATCTT
9742 TCTAT-AAATTTTGATAATCTGAT
1 TCTATGAAATTTTGATAATCT--T
* **
9765 CTCTATGAAATTTCGATAATCAC
1 -TCTATGAAATTTTGATAATCTT
* *
9788 TCTATGAGA-TTTGATAA-CCT
1 TCTATGAAATTTTGATAATCTT
*
9808 TCTATCAAATTTTG
1 TCTATGAAATTTTG
9822 GTACTCCTTA
Statistics
Matches: 114, Mismatches: 23, Indels: 18
0.74 0.15 0.12
Matches are distributed among these distances:
20 8 0.07
21 27 0.24
22 58 0.51
23 3 0.03
24 5 0.04
25 13 0.11
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TCTATGAAATTTTGATAATCTT
Found at i:9873 original size:22 final size:21
Alignment explanation
Indices: 9844--9983 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
9834 AAATTGAGAC
9844 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
9865 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
9887 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
9909 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* * *
9931 TTTTGTTAACCACACTGTGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
9953 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
9975 TTTTGATAA
1 TTTTGATAA
9984 TGGTCTAATG
Statistics
Matches: 91, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
21 11 0.12
22 76 0.84
23 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:10616 original size:31 final size:32
Alignment explanation
Indices: 10559--10625 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
10549 TGGCAATTTA
* * *
10559 GAAATATGATTTTTAAAAAGATGGTACAATTG
1 GAAATATGATTTTTAAAAAAAGGGTACAATCG
10591 GAAATAT-A-TTTTAAAAATAAGGGTACAATCG
1 GAAATATGATTTTTAAAAA-AAGGGTACAATCG
10622 GAAA
1 GAAA
10626 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.29
31 15 0.48
32 7 0.23
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (32 bp):
GAAATATGATTTTTAAAAAAAGGGTACAATCG
Found at i:10778 original size:169 final size:169
Alignment explanation
Indices: 10499--10838 Score: 671
Period size: 169 Copynumber: 2.0 Consensus size: 169
10489 TAATAATGGA
*
10499 ATAATTTATGATTAAGAAAATAATGGAATAATTAAAATATTGTTTAGTAATGGCAATTTAGAAAT
1 ATAATTTATGATTAAGAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAAT
10564 ATGATTTTTAAAAAGATGGTACAATTGGAAATATATTTTAAAAATAAGGGTACAATCGGAAAACA
66 ATGATTTTTAAAAAGATGGTACAATTGGAAATATATTTTAAAAATAAGGGTACAATCGGAAAACA
10629 TAAAGTTTCCCCTTATTCGTACTTTTATATATAGTATAG
131 TAAAGTTTCCCCTTATTCGTACTTTTATATATAGTATAG
10668 ATAATTTATGATTAAGAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAAT
1 ATAATTTATGATTAAGAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAAT
10733 ATGATTTTTAAAAAGATGGTACAATTGGAAATATATTTTAAAAATAAGGGTACAATCGGAAAACA
66 ATGATTTTTAAAAAGATGGTACAATTGGAAATATATTTTAAAAATAAGGGTACAATCGGAAAACA
10798 TAAAGTTTCCCCTTATTCGTACTTTTATATATAGTATAG
131 TAAAGTTTCCCCTTATTCGTACTTTTATATATAGTATAG
10837 AT
1 AT
10839 TTATAAATTA
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 170 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (169 bp):
ATAATTTATGATTAAGAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAAT
ATGATTTTTAAAAAGATGGTACAATTGGAAATATATTTTAAAAATAAGGGTACAATCGGAAAACA
TAAAGTTTCCCCTTATTCGTACTTTTATATATAGTATAG
Found at i:10785 original size:31 final size:32
Alignment explanation
Indices: 10728--10794 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
10718 TGGCAATTTA
* * *
10728 GAAATATGATTTTTAAAAAGATGGTACAATTG
1 GAAATATGATTTTTAAAAAAAGGGTACAATCG
10760 GAAATAT-A-TTTTAAAAATAAGGGTACAATCG
1 GAAATATGATTTTTAAAAA-AAGGGTACAATCG
10791 GAAA
1 GAAA
10795 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.29
31 15 0.48
32 7 0.23
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (32 bp):
GAAATATGATTTTTAAAAAAAGGGTACAATCG
Found at i:13687 original size:2 final size:2
Alignment explanation
Indices: 13675--13706 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
13665 ATAACCCTTT
13675 TA TA T- TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13707 AATTAATCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:16304 original size:21 final size:22
Alignment explanation
Indices: 16274--16317 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
16264 TGAAATCATT
16274 TTGGTAGTACCACAATA-TATA
1 TTGGTAGTACCACAATATTATA
*
16295 TTGGTGGTACCACAATATTATA
1 TTGGTAGTACCACAATATTATA
16317 T
1 T
16318 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (22 bp):
TTGGTAGTACCACAATATTATA
Found at i:17946 original size:16 final size:17
Alignment explanation
Indices: 17925--17997 Score: 66
Period size: 16 Copynumber: 4.6 Consensus size: 17
17915 ACCCAGCCCG
*
17925 AACCTGAACCCGAA-TT
1 AACCTGAACCCAAATTT
17941 AACCTG-ACCCAAATTT
1 AACCTGAACCCAAATTT
** * *
17957 AACCCAAACTC-GATTT
1 AACCTGAACCCAAATTT
17973 AACCTG-ACCCAAATTT
1 AACCTGAACCCAAATTT
17989 AACCT-AACC
1 AACCTGAACC
17998 TGACTCAAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
15 9 0.20
16 32 0.73
17 3 0.07
ACGTcount: A:0.38, C:0.33, G:0.07, T:0.22
Consensus pattern (17 bp):
AACCTGAACCCAAATTT
Found at i:19760 original size:62 final size:62
Alignment explanation
Indices: 19663--19848 Score: 336
Period size: 62 Copynumber: 3.0 Consensus size: 62
19653 ATACCTTTGT
* *
19663 GGCCTTTTGATTTCCCTTCTAGTTCTCCTTTCTGCTATAGTTTTTGACAGATCATCAGTTTC
1 GGCCTTTTGATTTCCCTTCTAGTTCTCCTTTCTGCTATACTTTTCGACAGATCATCAGTTTC
*
19725 GGCCTTTTGATTTCCCTTCTAGTTCTCCTTTCTGCTATACTTTTCGACAGATCATCAATTTC
1 GGCCTTTTGATTTCCCTTCTAGTTCTCCTTTCTGCTATACTTTTCGACAGATCATCAGTTTC
*
19787 GGCCTTTTGATTTCCCTTCTAGTTCTCGTTTCTGCTATACTTTTCGACAGATCATCAGTTTC
1 GGCCTTTTGATTTCCCTTCTAGTTCTCCTTTCTGCTATACTTTTCGACAGATCATCAGTTTC
19849 AGTTCTAGGC
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 119 1.00
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.46
Consensus pattern (62 bp):
GGCCTTTTGATTTCCCTTCTAGTTCTCCTTTCTGCTATACTTTTCGACAGATCATCAGTTTC
Found at i:22610 original size:18 final size:19
Alignment explanation
Indices: 22587--22629 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
22577 TTATTAATCG
22587 AATATTCATG-TATATATA
1 AATATTCATGATATATATA
* *
22605 AATATTGATGATTTATATA
1 AATATTCATGATATATATA
*
22624 ATTATT
1 AATATT
22630 ATTGAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (19 bp):
AATATTCATGATATATATA
Found at i:22656 original size:2 final size:2
Alignment explanation
Indices: 22649--22673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22639 TTTATTTCTA
22649 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
22674 GTATTCGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29850 original size:18 final size:18
Alignment explanation
Indices: 29827--29862 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29817 GGAATTTTTA
29827 TTGATTTTACTTGAGCTT
1 TTGATTTTACTTGAGCTT
29845 TTGATTTTACTTGAGCTT
1 TTGATTTTACTTGAGCTT
29863 GGTACTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.56
Consensus pattern (18 bp):
TTGATTTTACTTGAGCTT
Found at i:35182 original size:25 final size:26
Alignment explanation
Indices: 35127--35184 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
35117 CAGACTGAAG
* *
35127 AGAAAGAAGATGAAAGAGAAGAAATA
1 AGAAAGAAGAAGAAACAGAAGAAATA
* *
35153 A-AAAGAAGAAGAAACTGAATAAA-A
1 AGAAAGAAGAAGAAACAGAAGAAATA
35177 AGAAAGAA
1 AGAAAGAA
35185 AAAAACGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.07
25 24 0.89
26 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.22, T:0.07
Consensus pattern (26 bp):
AGAAAGAAGAAGAAACAGAAGAAATA
Found at i:35237 original size:13 final size:13
Alignment explanation
Indices: 35219--35259 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
35209 TTTGTTCTTA
35219 TTTTATTTTTACT
1 TTTTATTTTTACT
*
35232 TTTTATTTTTA-A
1 TTTTATTTTTACT
*
35244 TTTT-CTTTTACT
1 TTTTATTTTTACT
35256 TTTT
1 TTTT
35260 TACCTTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 5 0.21
12 8 0.33
13 11 0.46
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTACT
Found at i:38623 original size:19 final size:19
Alignment explanation
Indices: 38599--38636 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
38589 GCGTTGGTGA
38599 TTGCACGTGCTT-AGGGGAG
1 TTGCACGTG-TTCAGGGGAG
38618 TTGCACGTGTTCAGGGGAG
1 TTGCACGTGTTCAGGGGAG
38637 CATTCGGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.26
Consensus pattern (19 bp):
TTGCACGTGTTCAGGGGAG
Found at i:38748 original size:119 final size:119
Alignment explanation
Indices: 38537--39138 Score: 1012
Period size: 119 Copynumber: 5.1 Consensus size: 119
38527 ATTCAGTGTT
* * * ** * *
38537 AGCATTCTTCATTCGCGCGGTCGGCACTCTAAATTGAGCACTCTTCTTTCGTGCGTTGGTGATTG
1 AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTG
*
38602 CACGTGCTTAG-GGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCGTTA
66 CACGTGCTT-GTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTA
*
38656 AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGCGCATTGGTGATTG
1 AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTG
38721 CACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTA
66 CACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTA
38775 AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTG
1 AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTG
* * *
38840 CACGTGCTTGTGGGAGTTGTACGTGTTCAAGGTAGCATTCGGTGCTCTTCCTTA
66 CACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTA
*
38894 AGCATTGTTCACTCGCGTGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTG
1 AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTG
* *
38959 CACGTGCTTGTGGGAGTTGCACGTGTTCAAGGTAGCATTCGGTGCTCTTCCTTA
66 CACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTA
*
39013 AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGNGCATTGGTGATTG
1 AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTG
* *
39078 CACGTGCTTGTGGGA-TTGGAC-TGTTCAGGGGANCATTCGGTGCTCTTCCTTA
66 CACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTA
39130 AGCATTGTT
1 AGCATTGTT
Statistics
Matches: 461, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
117 37 0.08
118 6 0.01
119 418 0.91
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.35
Consensus pattern (119 bp):
AGCATTGTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTTGTGCATTGGTGATTG
CACGTGCTTGTGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCCTTA
Done.