Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020383.1 Corchorus olitorius cultivar O-4 contig20416, 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: 58203
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2743 original size:12 final size:12
Alignment explanation
Indices: 2726--2787 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
2716 TCGTTTAATA
2726 ATTATATATATT
1 ATTATATATATT
* *
2738 ATTATATATGTA
1 ATTATATATATT
2750 ATTATATATATT
1 ATTATATATATT
* *
2762 -TAATAT-TACT
1 ATTATATATATT
*
2772 ATATATATATAAT
1 AT-TATATATATT
2785 ATT
1 ATT
2788 TAATTATAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 3 0.08
11 6 0.15
12 25 0.64
13 5 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (12 bp):
ATTATATATATT
Found at i:2795 original size:19 final size:20
Alignment explanation
Indices: 2724--2802 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 20
2714 AATCGTTTAA
2724 TAATTATATATATTATTATATAT
1 TAATTATATATATTA--ATAT-T
2747 GTAATTATATATATTTAATA-T
1 -TAATTATATATA-TTAATATT
*
2768 T-ACTATATATATATAATATT
1 TAATTATATATAT-TAATATT
*
2788 TAATTATAAATATTA
1 TAATTATATATATTA
2803 CTAAACGGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.02
19 14 0.29
20 5 0.10
21 10 0.21
23 3 0.06
24 12 0.25
25 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
TAATTATATATATTAATATT
Found at i:2800 original size:33 final size:34
Alignment explanation
Indices: 2723--2805 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 34
2713 AAATCGTTTA
* *
2723 ATAATTATATATATTA-T-TATATATGTAATTAT
1 ATAATTATAAATATTACTATATATATATAATTAT
2755 ATATATT-T-AATATTACTATATATATATAA-TAT
1 ATA-ATTATAAATATTACTATATATATATAATTAT
*
2787 TTAATTATAAATATTACTA
1 ATAATTATAAATATTACTA
2806 AACGGTCGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
31 9 0.21
32 11 0.26
33 23 0.53
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (34 bp):
ATAATTATAAATATTACTATATATATATAATTAT
Found at i:4838 original size:14 final size:14
Alignment explanation
Indices: 4819--4882 Score: 84
Period size: 14 Copynumber: 4.9 Consensus size: 14
4809 TAAAAAACTA
4819 GGAGAGGGAGGAGG
1 GGAGAGGGAGGAGG
4833 GGAGAGGGAGGAGG
1 GGAGAGGGAGGAGG
4847 GGAGA--GA-GA--
1 GGAGAGGGAGGAGG
4856 GGAGAGGGAGGAGG
1 GGAGAGGGAGGAGG
*
4870 GGAGAGAGAGGAG
1 GGAGAGGGAGGAG
4883 AGGCGGCTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
9 5 0.11
11 4 0.09
12 4 0.09
14 31 0.70
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (14 bp):
GGAGAGGGAGGAGG
Found at i:4859 original size:23 final size:23
Alignment explanation
Indices: 4818--4885 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
4808 CTAAAAAACT
*
4818 AGGAGAGGGAG-GAGGGGAGAGGG
1 AGGAG-GGGAGAGAGAGGAGAGGG
4841 AGGAGGGGAGAGAGAGGAGAGGG
1 AGGAGGGGAGAGAGAGGAGAGGG
4864 AGGAGGGGAGAGAGAGGAGAGG
1 AGGAGGGGAGAGAGAGGAGAGG
4886 CGGCTTAGGG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 5 0.12
23 38 0.88
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (23 bp):
AGGAGGGGAGAGAGAGGAGAGGG
Found at i:7341 original size:34 final size:34
Alignment explanation
Indices: 7298--7369 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
7288 TGACTGTTTT
7298 GAGTGATATGCTAAACAATTCAAAGAACATAAAA
1 GAGTGATATGCTAAACAATTCAAAGAACATAAAA
7332 GAGTGATATGCTAAACAATTCAAAGAACATAAAA
1 GAGTGATATGCTAAACAATTCAAAGAACATAAAA
7366 GAGT
1 GAGT
7370 TCTTCTGGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (34 bp):
GAGTGATATGCTAAACAATTCAAAGAACATAAAA
Found at i:13077 original size:13 final size:12
Alignment explanation
Indices: 13044--13089 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
13034 AATGTGTTTA
*
13044 AATTAAA-TAAA
1 AATTAAATTAAT
13055 AATTAAATTAAT
1 AATTAAATTAAT
13067 AATTGAAATTAAT
1 AATT-AAATTAAT
*
13080 TA-TAAATTAA
1 AATTAAATTAA
13090 AGTAAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 14 0.45
12 8 0.26
13 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
AATTAAATTAAT
Found at i:13086 original size:29 final size:30
Alignment explanation
Indices: 13043--13100 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
13033 CAATGTGTTT
*
13043 AAATTAAATAAAAATTAAA-TTAATAATTG
1 AAATTAAATAAAAATTAAAGTAAATAATTG
* *
13072 AAATTAATTATAAATTAAAGTAAATAATT
1 AAATTAAATAAAAATTAAAGTAAATAATT
13101 ACATGTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
AAATTAAATAAAAATTAAAGTAAATAATTG
Found at i:13434 original size:19 final size:20
Alignment explanation
Indices: 13410--13451 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
13400 GTCATTTAAA
13410 AATATAT-TAAATTTTTTTT
1 AATATATCTAAATTTTTTTT
13429 AATATATCTAAATTTTTTTT
1 AATATATCTAAATTTTTTTT
13449 AAT
1 AAT
13452 TAAGATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
AATATATCTAAATTTTTTTT
Found at i:15743 original size:13 final size:12
Alignment explanation
Indices: 15720--15749 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
15710 TATAATTCAA
15720 TATTTTAAATAT
1 TATTTTAAATAT
15732 TATTTATAAATAT
1 TATTT-TAAATAT
15745 TATTT
1 TATTT
15750 GGAATTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTAAATAT
Found at i:16717 original size:22 final size:21
Alignment explanation
Indices: 16659--16718 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
16649 TAAAATTACT
* *
16659 TAAAGAATAATTAAATATTTC
1 TAAAAAATAATTAAATATTTA
*
16680 TAAAAAACT-ATAAAAT-TTATGA
1 TAAAAAA-TAATTAAATATT-T-A
16702 TAAAAAATAATTAAATA
1 TAAAAAATAATTAAATA
16719 AACTCAATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
20 2 0.07
21 14 0.47
22 14 0.47
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
TAAAAAATAATTAAATATTTA
Found at i:17123 original size:45 final size:45
Alignment explanation
Indices: 17072--17164 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 45
17062 CATTACCTGA
* *
17072 ATTCTACTCCTCCATCTGAAGGTAATTCATCAAAATAAAACTAAT
1 ATTCTACTCCTCCATCTCAAGATAATTCATCAAAATAAAACTAAT
* * * *
17117 ATTCTACTCCTCCATCTCTATATAGTTCATCAAAATAAAGCTAAT
1 ATTCTACTCCTCCATCTCAAGATAATTCATCAAAATAAAACTAAT
17162 ATT
1 ATT
17165 AGTTGTTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (45 bp):
ATTCTACTCCTCCATCTCAAGATAATTCATCAAAATAAAACTAAT
Found at i:22579 original size:15 final size:16
Alignment explanation
Indices: 22554--22583 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22544 TAATAATTAT
22554 TTTAGATTATAATATA
1 TTTAGATTATAATATA
22570 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
22584 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:23779 original size:334 final size:332
Alignment explanation
Indices: 22939--23863 Score: 1135
Period size: 336 Copynumber: 2.8 Consensus size: 332
22929 ATACTTTACA
* * *
22939 TAATCTAACCAAATCTCAGT-AACATTGGATTTAAGAATTTGTTTTTATGAGCATCTGAATCTTG
1 TAATCTAACCAAATCTCA-TCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * *
23003 TTTCGATTTAATTAGAAATTAATTAAG-AAAAATAAGAAATACGATATTAAAAGCGTAAAAAGCC
65 TTTCGATTTAATTAGAAATTAATTAGGAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAA-CC
* * *
23067 CTCCAATCTTTTTGGCGTTGAATTATAT-ATTTTTATGAGAATTTTAGCCAAAAATTGAGGAGAA
129 CTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTTTAGACAAAAATTGAGGA-AA
* * * * **
23131 -ATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACA-AACCATAACAGTT
193 TATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCACCGT---TTTT
* * * * * *
23194 TTTGGCTAAAAACGCGTTCTGGGACCCGGCTCAATTTTGCATGATTTTTGGCTCCGAGACTACTT
255 TTTGGATAAAAAAGCGTTCTGGGACCCAGCTCAATTTTGAATGATTTTTGGCGCCGAGACTACTA
23259 GAAATATCTATAT
320 GAAATATCTATAT
* * * * *
23272 TCATCTAATCAAATCTCATCCACATTAGATTTAAAGATTTGTTTTTACGAGCATCTGAATTTTGT
1 TAATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
23337 TTTGATTTAATTAGAAATTTAATTTGGAAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGC
66 TTCGATTTAATTAGAAA-TTAATTAGG-AAAAAATAGGAAAAACGATATTAGAAGCGT-AAAAAC
*
23402 CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGACAAAAATTGAGGAAA
128 CCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTTTAGACAAAAATTGAGGAAA
* *
23467 TATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAAGCATCACCGTTTTTTT
193 TATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA-CATCACCGTTTTTTT
* * ** * * *
23532 TTGATAAAAAAGCGTTCTGGGGCCCATTTCAGTTTTGAATGATTTTTGGCGCTGAGACTCCTAGA
257 TGGATAAAAAAGCGTTCTGGGACCCAGCTCAATTTTGAATGATTTTTGGCGCCGAGACTACTAGA
*
23597 ATTATCTATAT
322 AATATCTATAT
* *** * * * *
23608 TAATCTAACCAAATCTCATCCACAATGGATTTAAGGATTTG-TAAAACAAGCATCTAAATCATAT
1 TAATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
23672 TTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAACGATATTAGAAGCATGAAAAACC
66 TTCGATTTAATTAGAAATTAATTAGGAAAA-AATAGGAAAAACGATATTAGAAGCGT-AAAAACC
* * *
23737 CTTCAATCTTTTTGGAGTTGAATTATATAATTTTTATGAGTATTGT-GGCTAAAAATTGAGGAAA
129 CTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTTTAGAC-AAAAATTGAGGAAA
* * * * *
23801 TAACTTTCGAGTCAATTTTTGGAAAATTCTAGCCGAAATCGTGTAAATTACATCACGGTTTTT
193 TATCTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-AATAACATCACCGTTTTT
23864 GGCTAGATAT
Statistics
Matches: 509, Mismatches: 71, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
332 1 0.00
333 77 0.15
334 153 0.30
335 35 0.07
336 158 0.31
337 79 0.16
338 2 0.00
339 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (332 bp):
TAATCTAACCAAATCTCATCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTAGGAAAAAATAGGAAAAACGATATTAGAAGCGTAAAAACCCT
TCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTTTAGACAAAAATTGAGGAAATAT
CTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACATCACCGTTTTTTTTGGA
TAAAAAAGCGTTCTGGGACCCAGCTCAATTTTGAATGATTTTTGGCGCCGAGACTACTAGAAATA
TCTATAT
Found at i:27559 original size:22 final size:23
Alignment explanation
Indices: 27517--27568 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
27507 CCTCCATATG
27517 AAATTTTGTTAAATTTCCCTATA
1 AAATTTTGTTAAATTTCCCTATA
*
27540 AAATTTTGTTACA-TTCCCTATA
1 AAATTTTGTTAAATTTCCCTATA
27562 AAATTTT
1 AAATTTT
27569 AATAACCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (23 bp):
AAATTTTGTTAAATTTCCCTATA
Found at i:27584 original size:22 final size:23
Alignment explanation
Indices: 27559--27603 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
27549 TACATTCCCT
27559 ATAAAATTTTAATAACCA-CCTA
1 ATAAAATTTTAATAACCATCCTA
*
27581 ATAAAATTTTGATAACCATCCTA
1 ATAAAATTTTAATAACCATCCTA
27604 TGATATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAAAATTTTAATAACCATCCTA
Found at i:27628 original size:22 final size:22
Alignment explanation
Indices: 27564--27628 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
27554 TCCCTATAAA
* * *
27564 ATTTTAATAACCA-CCTAATAAA
1 ATTTTCATAACCATCC-AATGAT
* *
27586 ATTTTGATAACCATCCTATGAT
1 ATTTTCATAACCATCCAATGAT
27608 ATTTTCATAACC-TCTCAATGA
1 ATTTTCATAACCATC-CAATGA
27629 AATGTTAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (22 bp):
ATTTTCATAACCATCCAATGAT
Found at i:29146 original size:27 final size:26
Alignment explanation
Indices: 29115--29179 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
29105 AAAATACACA
*
29115 AAAATATATTTTAATAGTGGCATAATTT
1 AAAATATATTTTAATAATGGC--AATTT
*
29143 -AAATATTTTTTAATAATGGCAATTT
1 AAAATATATTTTAATAATGGCAATTT
29168 AGAAATATATTT
1 A-AAATATATTT
29180 GAAAAGAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 5 0.16
27 27 0.84
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (26 bp):
AAAATATATTTTAATAATGGCAATTT
Found at i:31167 original size:19 final size:18
Alignment explanation
Indices: 31130--31174 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
31120 TGAAATTTAT
31130 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
31148 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
31167 TTATTATT
1 TAATTATT
31175 AATATTTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:33062 original size:26 final size:26
Alignment explanation
Indices: 33026--33079 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
33016 GTAAATGCGA
33026 AAACTCTAGCAAGAGATTTTTGGCGC
1 AAACTCTAGCAAGAGATTTTTGGCGC
*
33052 AAACTCTAGCAAGGGATTTTTGGCGC
1 AAACTCTAGCAAGAGATTTTTGGCGC
33078 AA
1 AA
33080 TAGAAACGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (26 bp):
AAACTCTAGCAAGAGATTTTTGGCGC
Found at i:33212 original size:16 final size:16
Alignment explanation
Indices: 33191--33224 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
33181 CTCTAAATGC
33191 GAAAACTCTAGCAAGA
1 GAAAACTCTAGCAAGA
33207 GAAAACTCTAGCAAGA
1 GAAAACTCTAGCAAGA
33223 GA
1 GA
33225 TTTTTGGCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.12
Consensus pattern (16 bp):
GAAAACTCTAGCAAGA
Found at i:35066 original size:41 final size:41
Alignment explanation
Indices: 35006--35310 Score: 229
Period size: 41 Copynumber: 7.2 Consensus size: 41
34996 CGACAAATTA
*
35006 AGTCGTTGCGAAATCTTAAAATTTTCGCAGCGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTT
* *
35047 AGTCGTTGCGAAATATTAAACTTTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTT
* * * * * **
35088 AGTCGTTGCTCAATATATGTTACTAATTGATTTTCGAAGCGAC-CTTGAA
1 AGTCGTTG--CGA-A-ATCTTA--AA---CTTTTCGCAGCGACTTTTGTT
** * * * * * * * *** *
35137 AGTCACTACAAAAAACATGATTACTTTT-GAAACGACAGAT-TA
1 AGTCGTTGC-GAAATC-TTA-AACTTTTCGCAGCGACTTTTGTT
*
35179 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTT
* *
35220 AGTCGTTGCGAAATCGTAAACTTTCCGCAGCGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTT
* *
35261 AGTCGTTGCGAAATCGTAAACTTTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTT
35302 AGTCGTTGC
1 AGTCGTTGC
35311 TTAATATATG
Statistics
Matches: 210, Mismatches: 40, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
39 5 0.02
40 9 0.04
41 139 0.66
42 14 0.07
43 7 0.03
44 1 0.00
45 5 0.02
46 3 0.01
47 6 0.03
48 2 0.01
49 8 0.04
50 11 0.05
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (41 bp):
AGTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTT
Found at i:35121 original size:173 final size:172
Alignment explanation
Indices: 34872--35269 Score: 643
Period size: 173 Copynumber: 2.3 Consensus size: 172
34862 ACCACTTCTA
* ** * * *
34872 TTAGTCGTTGCGAATTCATAGTCTTTTCGCAACGACTTTTGTTAGTCGTTGTTTAATATATTTTA
1 TTAGTCGTTGCGAAAT-ATAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTCAATATATGTTA
*
34937 CAAATTGATTTTCGAAGCGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACAA
65 CAAATTGATTTTCGAAGCGACCTTGAAAGTCACTACAAAAAACATGATTACTTTTGAAACGACAA
*
35002 ATTAAGTCGTTGCGAAATCTTAAAATTTTCGCAGCGACTTTTG
130 ATTAAGTCGTTGCGAAATCTTAAAATTTCCGCAGCGACTTTTG
35045 TTAGTCGTTGCGAAATATTAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTCAATATATGTTA
1 TTAGTCGTTGCGAAATA-TAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTCAATATATGTTA
* *
35110 CTAATTGATTTTCGAAGCGACCTTGAAAGTCACTACAAAAAACATGATTACTTTTGAAACGACAG
65 CAAATTGATTTTCGAAGCGACCTTGAAAGTCACTACAAAAAACATGATTACTTTTGAAACGACAA
*
35175 ATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTG
130 ATTAAGTCGTTGCGAAATCTTAAAATTTCCGCAGCGACTTTTG
* * *
35218 TTAGTCGTTGCGAAATCGTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGC
1 TTAGTCGTTGCGAAAT-ATAAACTTTTCGCAACGACTTTTGTTAGTCGTTGC
35270 GAAATCGTAA
Statistics
Matches: 209, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
172 1 0.00
173 208 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (172 bp):
TTAGTCGTTGCGAAATATAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTCAATATATGTTAC
AAATTGATTTTCGAAGCGACCTTGAAAGTCACTACAAAAAACATGATTACTTTTGAAACGACAAA
TTAAGTCGTTGCGAAATCTTAAAATTTCCGCAGCGACTTTTG
Found at i:35283 original size:214 final size:213
Alignment explanation
Indices: 35006--35395 Score: 663
Period size: 214 Copynumber: 1.8 Consensus size: 213
34996 CGACAAATTA
* * *
35006 AGTCGTTGCGAAATCTTAAAATTTTCGCAGCGACTTTTGTTAGTCGTTGCGAAATATTAAACTTT
1 AGTCGTTGCGAAATCGTAAAATTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATAGTAAACTTT
35071 TCGCAACGACTTTTGTTAGTCGTTGCTCAATATATGTTACTAATTGATTTTCGAAGCGACCTTGA
66 TCGCAACGACTTTTGTTAGTCGTTGCTCAATATATGTTACTAATTGATTTTCGAAGCGACCTTGA
* * *
35136 AAGTCACTACAAAAAACATGATTACTTTTGAAACGACAGATTAAGTCGTTGCGAAATCTTAAACT
131 AAGTCACTAC-AAAAACATAATTACTTTTGAAACCACAAATTAAGTCGTTGCGAAATCTTAAACT
35201 TTCCGCAGCGACTTTTGTT
195 TTCCGCAGCGACTTTTGTT
* *
35220 AGTCGTTGCGAAATCGTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATCGTAAACTTT
1 AGTCGTTGCGAAATCGTAAAATTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATAGTAAACTTT
* * *
35285 TCGCAACGACTTTTGTTAGTCGTTGCTTAATATATGTTACTAATTTATTTTCGCAGCGACCTTGA
66 TCGCAACGACTTTTGTTAGTCGTTGCTCAATATATGTTACTAATTGATTTTCGAAGCGACCTTGA
*
35350 AAGTCGCTACAAAAACATAATTACTTTTGAAACCACAAATTAAGTC
131 AAGTCACTACAAAAACATAATTACTTTTGAAACCACAAATTAAGTC
35396 TCAACGACAA
Statistics
Matches: 164, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
213 33 0.20
214 131 0.80
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (213 bp):
AGTCGTTGCGAAATCGTAAAATTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATAGTAAACTTT
TCGCAACGACTTTTGTTAGTCGTTGCTCAATATATGTTACTAATTGATTTTCGAAGCGACCTTGA
AAGTCACTACAAAAACATAATTACTTTTGAAACCACAAATTAAGTCGTTGCGAAATCTTAAACTT
TCCGCAGCGACTTTTGTT
Found at i:39000 original size:19 final size:20
Alignment explanation
Indices: 38974--39029 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 20
38964 TGAAAAAAGC
38974 TCATTTAGGAACAAAAAAAA
1 TCATTTAGGAACAAAAAAAA
* **
38994 TTA-TTA-G-AC-AAAAAGC
1 TCATTTAGGAACAAAAAAAA
39010 TCATTTAGGAACAAAAAAAA
1 TCATTTAGGAACAAAAAAAA
39030 AATTAGACTT
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
16 7 0.27
17 5 0.19
18 2 0.08
19 5 0.19
20 7 0.27
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.21
Consensus pattern (20 bp):
TCATTTAGGAACAAAAAAAA
Found at i:39007 original size:36 final size:35
Alignment explanation
Indices: 38967--39037 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
38957 TCTTATCTGA
*
38967 AAAAAGCTCATTTAGGAACAAAAAAAATTATTAGAC
1 AAAAAGCTCATTTAGGAACAAAAAAAA-AATTAGAC
39003 AAAAAGCTCATTTAGGAACAAAAAAAAAATTAGAC
1 AAAAAGCTCATTTAGGAACAAAAAAAAAATTAGAC
39038 TTGGGAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 7 0.21
36 27 0.79
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (35 bp):
AAAAAGCTCATTTAGGAACAAAAAAAAAATTAGAC
Found at i:43084 original size:62 final size:61
Alignment explanation
Indices: 42966--43094 Score: 197
Period size: 62 Copynumber: 2.1 Consensus size: 61
42956 AAAAAAAATG
* * *
42966 AAAAAGAAGCTCGCTAAGTTGAAAATCCTGTAAAGGACGGCTTAGGCAAAAGTTAGAGCGAA
1 AAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC-AA
*
43028 AAAAAAAAGCCTCGCTAAGTTGAAAATCCTGCAAAGGA-GGCTTAGGCAAAACTTAGAGCAC
1 AAAAAAAAG-CTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCAA
43089 AAAAAA
1 AAAAAA
43095 TAAATGAACT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
61 7 0.11
62 28 0.45
63 27 0.44
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (61 bp):
AAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGCAA
Found at i:46673 original size:54 final size:54
Alignment explanation
Indices: 46600--46708 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
46590 GCGTTTGGTT
*
46600 TCACCCCTGGTGATCTTGGGTGGTAATCTCATATCACCAC-GTTTGGTTTGCAGA
1 TCACCCCTGGTGATCTTGGGTGGTAATCTCAGATCACC-CTGTTTGGTTTGCAGA
* * * *
46654 TCACCCGTGGTGATCTTGGGTGTTAATTTTAGATCACCCTGTTTGGTTTGCAGA
1 TCACCCCTGGTGATCTTGGGTGGTAATCTCAGATCACCCTGTTTGGTTTGCAGA
46708 T
1 T
46709 TTTGCACTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 1 0.02
54 48 0.98
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (54 bp):
TCACCCCTGGTGATCTTGGGTGGTAATCTCAGATCACCCTGTTTGGTTTGCAGA
Found at i:48255 original size:41 final size:44
Alignment explanation
Indices: 48202--48294 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
48192 AGTGCATTAC
* *
48202 CTAA-ATTGTA-C-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTGTACCATCCATCTCTAGATAATTCATCAAAATAAAA
48243 CTAATATT-TACTCATCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTGTAC-CATCCATCTCTAGATAATTCATCAAAATAAAA
*
48287 CTAGTATT
1 CTAATATT
48295 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
41 6 0.13
42 3 0.07
43 1 0.02
44 35 0.78
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.34
Consensus pattern (44 bp):
CTAATATTGTACCATCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:54364 original size:26 final size:25
Alignment explanation
Indices: 54323--54375 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
54313 TGTATTTTTA
*
54323 TATATGTTAATCATACTTAAACAATT
1 TATATGTTAATAATACTTAAAC-ATT
*
54349 TATATGTTGATAATACTTAAACATT
1 TATATGTTAATAATACTTAAACATT
54374 TA
1 TA
54376 AGATGTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (25 bp):
TATATGTTAATAATACTTAAACATT
Found at i:54381 original size:26 final size:26
Alignment explanation
Indices: 54326--54381 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
54316 ATTTTTATAT
* *
54326 ATGTTAATCATACTTAAACAATTTAT
1 ATGTTAATAATACTTAAACAATTTAG
*
54352 ATGTTGATAATACTTAAAC-ATTTAAG
1 ATGTTAATAATACTTAAACAATTT-AG
54378 ATGT
1 ATGT
54382 CATCGGACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (26 bp):
ATGTTAATAATACTTAAACAATTTAG
Found at i:57684 original size:2 final size:2
Alignment explanation
Indices: 57679--57704 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57669 TTGGTATAGT
57679 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
57705 ATAGTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58048 original size:200 final size:203
Alignment explanation
Indices: 57695--58190 Score: 885
Period size: 200 Copynumber: 2.5 Consensus size: 203
57685 TATATATATA
57695 TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAA
1 TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAA
*
57760 AAAATTAATAACATTCACCATTGATAAATAAATCGGATTTTTAATATCTTTTATAATTTTGAAAT
66 AAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAAT
* *
57825 TTTGTTTGACATTGATCTAATTTAATTTAATAAATCAATCACTAATGTTCAACTA-ATTTTTTTG
131 TTTGTTTGACATTGATCTAATTTAATTCAATAAATCAACCACTAATGTTCAACTACATTTTTTTG
57889 GTATAGTT
196 GTATAGTT
57897 CTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTT-
1 -TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTA
*
57961 AAAAATT-ATAACATTTACC-TTGATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAA
65 AAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAA
*
58024 TTTTGTTTGACATTGATCTAATTTAATTCAATAAATCAACCACTAATGTTCAACTACTTTTTTTT
130 TTTTGTTTGACATTGATCTAATTTAATTCAATAAATCAACCACTAATGTTCAACTAC-ATTTTTT
58089 TGGTATAGTT
194 TGGTATAGTT
*
58099 T-TATATATAATAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAA
1 TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAA
58163 AAAATTAATAACATTCACCATTGATAAA
66 AAAATTAATAACATTCACCATTGATAAA
58191 GTTATTAAGC
Statistics
Matches: 281, Mismatches: 7, Indels: 10
0.94 0.02 0.03
Matches are distributed among these distances:
200 157 0.56
201 19 0.07
202 34 0.12
203 71 0.25
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (203 bp):
TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAA
AAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAAT
TTTGTTTGACATTGATCTAATTTAATTCAATAAATCAACCACTAATGTTCAACTACATTTTTTTG
GTATAGTT
Done.