Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019386.1 Corchorus olitorius cultivar O-4 contig19419, 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: 21543
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:2742 original size:42 final size:43
Alignment explanation
Indices: 2695--2777 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
2685 CGTGTTTCAC
* *
2695 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTATCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA
*
2737 TTATCGTATTTCGTGTCCTAATCGTGTCAAGACACGATTAA
1 TTATCGTATCTCGTGTCCTAATCGTGTCAAGACACGATTAA
2778 CACGTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 23 0.64
43 13 0.36
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (43 bp):
TTATCGTATCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA
Found at i:2790 original size:20 final size:20
Alignment explanation
Indices: 2765--2804 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2755 TAATCGTGTC
2765 AAGACACGATTAACACGTTT
1 AAGACACGATTAACACGTTT
*
2785 AAGACACGATTGACACGTTT
1 AAGACACGATTAACACGTTT
2805 TAATTAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (20 bp):
AAGACACGATTAACACGTTT
Found at i:3280 original size:12 final size:12
Alignment explanation
Indices: 3263--3293 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3253 TACCCTATGT
3263 AAACACGACACG
1 AAACACGACACG
3275 AAACACGACACG
1 AAACACGACACG
*
3287 GAACACG
1 AAACACG
3294 GATTGCCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.32, G:0.19, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:4283 original size:39 final size:39
Alignment explanation
Indices: 4231--4338 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 39
4221 TAATTTATGG
*
4231 TGATTCGTTAATGATGTTCACACTAAAACTAGAAAATAA
1 TGATTCATTAATGATGTTCACACTAAAACTAGAAAATAA
* * **
4270 TGTTTCATTAATGATGCATGTTCGCACTAAAACTAGATTATAA
1 TGATTCATT-A--ATG-ATGTTCACACTAAAACTAGAAAATAA
*
4313 TGATTCATTAATGATATTCACACTAA
1 TGATTCATTAATGATGTTCACACTAA
4339 GAATGATTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
39 18 0.32
40 4 0.07
42 4 0.07
43 31 0.54
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (39 bp):
TGATTCATTAATGATGTTCACACTAAAACTAGAAAATAA
Found at i:4298 original size:43 final size:43
Alignment explanation
Indices: 4244--4327 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
4234 TTCGTTAATG
*
4244 ATGTTCACACTAAAACTAGAAAATAATGTTTCATTAATGATGC
1 ATGTTCACACTAAAACTAGAAAATAATGATTCATTAATGATGC
* **
4287 ATGTTCGCACTAAAACTAGATTATAATGATTCATTAATGAT
1 ATGTTCACACTAAAACTAGAAAATAATGATTCATTAATGAT
4328 ATTCACACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (43 bp):
ATGTTCACACTAAAACTAGAAAATAATGATTCATTAATGATGC
Found at i:4476 original size:29 final size:29
Alignment explanation
Indices: 4444--4507 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
4434 TACAAAAATG
4444 ATATACTGTAGTAGTAATTATATATGCGT
1 ATATACTGTAGTAGTAATTATATATGCGT
4473 ATATACTGTAGTAGTAATTATATATGCGT
1 ATATACTGTAGTAGTAATTATATATGCGT
4502 ATATAC
1 ATATAC
4508 AGTGAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.41
Consensus pattern (29 bp):
ATATACTGTAGTAGTAATTATATATGCGT
Found at i:14150 original size:163 final size:154
Alignment explanation
Indices: 13904--14235 Score: 551
Period size: 163 Copynumber: 2.1 Consensus size: 154
13894 GTCAATGGAT
13904 TAGTAGAGTTTATAA-TTTTTTTAAATAAACGAAAAATTGAAAAAGGAAAACAAATAGTAGAGAA
1 TAGTAGAGTTTATAATTTTTTTTAAATAAACGAAAAATTGAAAAAGGAAAACAAATAGTAGAGAA
13968 AAATAGTCAACGAATTAGTAGAGTACTCTGGCAAAAAAAAAAGAAGAAAGATTAGTAGAGTAGAA
66 AAATAGTCAACGAATTAGTAGAGTACTCTGGC-----AAAAA-AA-AAA-ATTAGTAGAGTAGAA
14033 TTTCTCTAAAAAATAAATACATTAAAAAATTGA
123 TTTCTCT-AAAAATAAATACATTAAAAAATTGA
14066 TAGTAGAGTTTATAATTTTTTTTTAAATAAACGAAAAATTGAAAAAGGAAAA-AAATAGTAGAGA
1 TAGTAGAGTTTATAA-TTTTTTTTAAATAAACGAAAAATTGAAAAAGGAAAACAAATAGTAGAGA
*
14130 AAAATAGTCAACGGATTAGTAGAGTACTCTGGCAAAAAAAAAAATTAGTAGAGTAGAATTTCTCT
65 AAAATAGTCAACGAATTAGTAGAGTACTCTGGCAAAAAAAAAAATTAGTAGAGTAGAATTTCTCT
14195 AAAAATAAATACATTAAAAAATTGA
130 AAAAATAAATACATTAAAAAATTGA
14220 TAGTAGAGTTTATAAT
1 TAGTAGAGTTTATAAT
14236 CTATACTATA
Statistics
Matches: 167, Mismatches: 1, Indels: 13
0.92 0.01 0.07
Matches are distributed among these distances:
153 1 0.01
154 40 0.24
155 22 0.13
156 3 0.02
157 2 0.01
158 5 0.03
162 15 0.09
163 44 0.26
164 35 0.21
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (154 bp):
TAGTAGAGTTTATAATTTTTTTTAAATAAACGAAAAATTGAAAAAGGAAAACAAATAGTAGAGAA
AAATAGTCAACGAATTAGTAGAGTACTCTGGCAAAAAAAAAAATTAGTAGAGTAGAATTTCTCTA
AAAATAAATACATTAAAAAATTGA
Found at i:15462 original size:22 final size:21
Alignment explanation
Indices: 15407--15637 Score: 124
Period size: 22 Copynumber: 10.5 Consensus size: 21
15397 GTCTCTGTGT
* *
15407 GGTTATC-AATTTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* *
15427 TGGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
15450 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
15472 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
15494 GCTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
* * * *
15516 GGTTATCAAAAATTCCTATTGT
1 GGTTATCAAAATTTCATA-GGA
* * *
15538 GCTTACCTAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* *
15562 GGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
** *
15584 GGTTATTGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
15606 GGTTATCACAATTAT-ATAGAAA
1 GGTTATCAAAATT-TCATAG-GA
15628 GGTTATCAAA
1 GGTTATCAAA
15638 GAGATTATCA
Statistics
Matches: 156, Mismatches: 43, Indels: 21
0.71 0.20 0.10
Matches are distributed among these distances:
21 11 0.07
22 123 0.79
23 7 0.04
24 15 0.10
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:15508 original size:66 final size:67
Alignment explanation
Indices: 15437--15637 Score: 198
Period size: 66 Copynumber: 3.0 Consensus size: 67
15427 TGGTTATTAT
15437 AATTTCATGAGG-AGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATGG-AGCTTAT
1 AATTTCATGAGGAAGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATA-GGAAGCTTAT
15500 CAA
65 CAA
* * * *
15503 AATTTCATG-GGAAGGTTATCAAAAATTCC-TATTGTGCTTACCTAAATTTCATAGGATCAGGTT
1 AATTTCATGAGGAAGGTTATC-AAAATTCCATAGTGTGGTTACCAAAATTTCATAGGA--AGCTT
*
15566 ATTAA
63 ATCAA
* ** * * * * *
15571 AATTTC-TTAGGAAGGTTATTGAAATTTCATAGTGTGGTTATCACAATTAT-ATAGAAAGGTTAT
1 AATTTCATGAGGAAGGTTATCAAAATTCCATAGTGTGGTTACCAAAATT-TCATAGGAAGCTTAT
15634 CAA
65 CAA
15637 A
1 A
15638 GAGATTATCA
Statistics
Matches: 111, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
65 4 0.04
66 48 0.43
67 15 0.14
68 43 0.39
69 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (67 bp):
AATTTCATGAGGAAGGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATAGGAAGCTTATC
AA
Found at i:15753 original size:22 final size:22
Alignment explanation
Indices: 15642--15789 Score: 106
Period size: 22 Copynumber: 6.7 Consensus size: 22
15632 ATCAAAGAGA
* *
15642 TTATCAAAATGTCATAGCGAT-G
1 TTATCAAAATTTCATAGTG-TGG
*
15664 TTAT-AAGAATTTCATAATGTGG
1 TTATCAA-AATTTCATAGTGTGG
* *
15686 TTAGCAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGTGG
* * * * *
15708 TTA-CTAATATATCATGGGGAGG
1 TTATC-AAAATTTCATAGTGTGG
15730 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* ** *
15752 TTATCAAATTTTTTTAGTATGG
1 TTATCAAAATTTCATAGTGTGG
15774 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
15790 TGAAGGTTAT
Statistics
Matches: 98, Mismatches: 21, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
21 5 0.05
22 89 0.91
23 4 0.04
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:15797 original size:22 final size:22
Alignment explanation
Indices: 15727--15803 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
15717 TATCATGGGG
15727 AGGTTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
* * **
15749 TGGTTATCAAATTTTTTTA-GTA
1 AGGTTATCAAAATTTCATATG-A
*
15771 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
15793 AGGTTAT-AAAA
1 AGGTTATCAAAA
15804 GTCTCAATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
20 1 0.02
21 4 0.09
22 38 0.86
23 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:18832 original size:35 final size:30
Alignment explanation
Indices: 18786--18851 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 30
18776 TTTGGTTTCG
18786 GTTTTAAATGTTGCAGCGCTTTTACTACTGTATTT
1 GTTTTAAATGTT-C--CGCTTTTACTA-TG-ATTT
*
18821 GTTTTTAATGTTCCGCTTTTACTATGATTT
1 GTTTTAAATGTTCCGCTTTTACTATGATTT
18851 G
1 G
18852 CAAACTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 5 0.17
31 2 0.07
32 11 0.37
34 1 0.03
35 11 0.37
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.52
Consensus pattern (30 bp):
GTTTTAAATGTTCCGCTTTTACTATGATTT
Found at i:19062 original size:21 final size:22
Alignment explanation
Indices: 19013--19143 Score: 106
Period size: 22 Copynumber: 5.9 Consensus size: 22
19003 GTGACAGAGT
* *
19013 GATTATCGAAATTTCATAGAGATCG
1 GATTATCAAAATTTCATAG-G-T-A
19038 GATTATCAAAATTT-ATAGGTA
1 GATTATCAAAATTTCATAGGTA
*
19059 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAG-GTA
* *
19082 G-TTATCAAAATTTCAAAGCTA
1 GATTATCAAAATTTCATAGGTA
* * *
19103 GGTTATCAAAATTACATAATGT-
1 GATTATCAAAATTTCAT-AGGTA
* *
19125 TATTATCAGAATTTCATAG
1 GATTATCAAAATTTCATAG
19144 AGGGGTCAAC
Statistics
Matches: 87, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
21 17 0.20
22 47 0.54
23 6 0.07
24 4 0.05
25 13 0.15
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGGTA
Found at i:19086 original size:22 final size:21
Alignment explanation
Indices: 19040--19233 Score: 115
Period size: 22 Copynumber: 9.0 Consensus size: 21
19030 AGAGATCGGA
* *
19040 TTATCAAAATTT-ATAGGTAGA
1 TTATCAAAATTTCATA-GTGGG
*
19061 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTG-GG
* *
19083 TTATCAAAATTTCAAAGCTAGG
1 TTATCAAAATTTCATAG-TGGG
* * **
19105 TTATCAAAATTACATAATGTTA
1 TTATCAAAATTTCATAGTG-GG
* *
19127 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-TGGG
* *
19149 TCAACAAAATTT-ATCAAG-GGG
1 TTATCAAAATTTCAT--AGTGGG
**
19170 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTG-GG
* * *
19192 TTATCAAAATTTCAAAATGTGA
1 TTATCAAAATTTCATAGTG-GG
*
19214 TTACCAAAATTTCATAGTGG
1 TTATCAAAATTTCATAGTGG
19234 TATTTCTGGG
Statistics
Matches: 132, Mismatches: 31, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.01
21 32 0.24
22 95 0.72
23 4 0.03
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGTGGG
Found at i:19228 original size:44 final size:44
Alignment explanation
Indices: 19038--19229 Score: 164
Period size: 44 Copynumber: 4.4 Consensus size: 44
19028 ATAGAGATCG
* * *
19038 GATTATCAAAATTT-AT-AGGTAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAAAG-AGGTTATCAAAATTTCATAATG-T
*
19082 G-TTATCAAAATTTC--AAAGCTAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAAG--AGGTTATCAAAATTTCATAATGT
* * * * * * *
19125 TATTATCAGAATTTCATAGAGGGGTCAACAAAATTT-ATCAA-GG
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCAT-AATGT
* *
19168 GGTTATCAAAATTTCATAAAGAGGTTATCAAAATTTCAAAATGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
*
19212 GATTACCAAAATTTCATA
1 GATTATCAAAATTTCATA
19230 GTGGTATTTC
Statistics
Matches: 116, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
43 49 0.42
44 64 0.55
46 3 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
Found at i:19358 original size:22 final size:22
Alignment explanation
Indices: 19330--19869 Score: 175
Period size: 22 Copynumber: 24.7 Consensus size: 22
19320 TCAGGGAGGA
19330 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
19352 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
19374 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
19396 TATAAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
*
19418 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
19440 TATCAAAAAATCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
*
19462 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* *
19478 TATCAAGATTTCATGA-GGAGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
19500 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
19523 TATCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
19546 TATCAAAATTTCATAACG-AGAT
1 TATCAAAATTTCAT-ATGAAGGT
* * * *
19568 TATTACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
19590 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
19612 TA-CTAACAATTT-ATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * * *
19634 TTTTAAATTTTCATAACG-TGGC
1 TATCAAAATTTCAT-ATGAAGGT
* * *
19656 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
19678 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
19701 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
19723 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
19745 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
19767 TAACAAAATTTCATAAGAATGT
1 TATCAAAATTTCATATGAAGGT
** * * **
19789 TAAAAAAAATTAATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * * **
19811 TCTCGATATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* * *
19833 CATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
19855 TATCAAAATTTCATA
1 TATCAAAATTTCATA
19870 AGGATGTCAT
Statistics
Matches: 385, Mismatches: 100, Indels: 66
0.70 0.18 0.12
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 2 0.01
21 19 0.05
22 280 0.73
23 69 0.18
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:19529 original size:23 final size:23
Alignment explanation
Indices: 19477--19556 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
19467 AAATTTGTAG
* *
19477 TTATCAAGATTTCAT-GAGGAGG-
1 TTATCAAAATTTTATAG-GGAGGT
19499 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
19522 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
19545 TTATCAAAATTT
1 TTATCAAAATTT
19557 CATAACGAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
22 18 0.34
23 35 0.66
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:19714 original size:23 final size:22
Alignment explanation
Indices: 19311--19781 Score: 276
Period size: 22 Copynumber: 21.6 Consensus size: 22
19301 TTATGAAGTA
* *
19311 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGTGAGGTT
19331 ATCAAAATTTCATA-TGAAGGTT
1 ATCAAAATTTCATAGTG-AGGTT
*
19353 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-TGAGGTT
* *
19375 TTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGTGA-GGTT
* * *
19397 ATAAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGTT
* *
19419 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
** * *
19441 ATCAAAAAATCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGTT
19463 ATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGTGAGGTT
*
19479 ATCAAGATTTCATGAG-GAGGTT
1 ATCAAAATTTCAT-AGTGAGGTT
* *
19501 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGTGAGG-TT
*
19524 ATCAAAATTTTATAG-GAAGGTTT
1 ATCAAAATTTCATAGTG-AGG-TT
** *
19547 ATCAAAATTTCATAACGAGATT
1 ATCAAAATTTCATAGTGAGGTT
* * * *
19569 ATTACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* * *
19591 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
19613 A-CTAACAATTT-ATA-TGGAGGTT
1 ATC-AA-AATTTCATAGT-GAGGTT
* * * ** * *
19635 TTTAAATTTTCATAACGTGGCT
1 ATCAAAATTTCATAGTGAGGTT
* *
19657 ATCAATATATCATA-TGGAGGTT
1 ATCAAAATTTCATAGT-GAGGTT
* * *
19679 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGTG-AGGTT
* * *
19702 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGTGAGGTT
19724 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGTGAGGT-T
* * *
19747 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
*
19768 AACAAAATTTCATA
1 ATCAAAATTTCATA
19782 AGAATGTTAA
Statistics
Matches: 348, Mismatches: 73, Indels: 58
0.73 0.15 0.12
Matches are distributed among these distances:
16 8 0.02
17 3 0.01
18 1 0.00
19 2 0.01
20 12 0.03
21 13 0.04
22 242 0.70
23 65 0.19
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGGTT
Found at i:19879 original size:44 final size:43
Alignment explanation
Indices: 19311--19876 Score: 234
Period size: 44 Copynumber: 13.0 Consensus size: 43
19301 TTATGAAGTA
* * * * *
19311 ATCAAAATTTCA-GGGAGGATATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGAGGTTATCAAAATTTCATAAGGATGTT
* * *
19353 ATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAA-GAGGGTT
1 ATCAAAATTTCATAG--GAGGTTATCAAAATTTCATAAGGA-TGTT
* * * * *
19397 ATAAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAAGGATGTT
** * *
19441 ATCAAAAAATCATAGGGAGATTATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAAGGATGTT
* * * *
19479 ATCAAGATTTCATGAGGAGGTTATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAAGGATG-TT
* *
19524 ATCAAAATTTTATAGGAAGGTTTATCAAAATTTCATAACGA-GATT
1 ATCAAAATTTCATAGG-AGG-TTATCAAAATTTCATAAGGATG-TT
* * * * *
19569 ATTACAATTTCATAGTGTGATTATCAAAATTTCA-GAGTG-TGATT
1 ATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAAG-GATG-TT
* * * * *
19613 A-CTAACAATTT-ATATGGAGGTTTTTAAATTTTCATAACG-TGGCT
1 ATC-AA-AATTTCATA-GGAGGTTATCAAAATTTCATAAGGAT-GTT
* * * * *
19657 ATCAATATATCATATGGAGGTTATCAACATCTCAT-AGTGTTGGTT
1 ATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAAG-GAT-GTT
* * *
19702 ATCAAAATTTCATTGGGAAGTTATCAAAATTTCAT-AGTGAGGTCT
1 ATCAAAATTTCA-TAGGAGGTTATCAAAATTTCATAAG-GATGT-T
* * * *
19747 -TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATAAGAATGTT
1 ATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAAGGATGTT
** * * ** * * * * * *
19790 AAAAAAAATTAATAAAAAGGTTCTCGATATTCCAT-AGTATCGTC
1 ATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAAGGAT-GTT
*
19834 ATTAAAATTTCATAGGAAGGTTATCAAAATTTCATAAGGATGT
1 ATCAAAATTTCATAGG-AGGTTATCAAAATTTCATAAGGATGT
19877 CATAAAAAAT
Statistics
Matches: 391, Mismatches: 95, Indels: 74
0.70 0.17 0.13
Matches are distributed among these distances:
38 26 0.07
39 4 0.01
41 2 0.01
42 12 0.03
43 19 0.05
44 221 0.57
45 88 0.23
46 19 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (43 bp):
ATCAAAATTTCATAGGAGGTTATCAAAATTTCATAAGGATGTT
Found at i:19884 original size:22 final size:22
Alignment explanation
Indices: 19831--19884 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
19821 CCATAGTATC
*
19831 GTCATTAAAATTTCATAGGAAG
1 GTCATAAAAATTTCATAGGAAG
* * *
19853 GTTATCAAAATTTCATAAGG-AT
1 GTCATAAAAATTTCAT-AGGAAG
19875 GTCATAAAAA
1 GTCATAAAAA
19885 ATACTAGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (22 bp):
GTCATAAAAATTTCATAGGAAG
Found at i:21035 original size:33 final size:33
Alignment explanation
Indices: 20998--21108 Score: 168
Period size: 33 Copynumber: 3.4 Consensus size: 33
20988 GCCGCCCCCC
* *
20998 TGGGGCGGCACCACCATAGCGGTGTTGCCCTGT
1 TGGGGCGGCACCACCATGGCGGTGTCGCCCTGT
*
21031 TGGGGCGGCACCACCTTGGCGGTGTCGCCCTGT
1 TGGGGCGGCACCACCATGGCGGTGTCGCCCTGT
* * *
21064 TGGAGTGGCACCACCATGGCGGCGTCGCCCTGT
1 TGGGGCGGCACCACCATGGCGGTGTCGCCCTGT
21097 TGGGGCGGCACC
1 TGGGGCGGCACC
21109 GCCACAAAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.10, C:0.32, G:0.39, T:0.19
Consensus pattern (33 bp):
TGGGGCGGCACCACCATGGCGGTGTCGCCCTGT
Done.