Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019508.1 Corchorus olitorius cultivar O-4 contig19541, 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: 75024
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:333 original size:2 final size:2
Alignment explanation
Indices: 319--351 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
309 GTAATATTAA
*
319 AT AT AT -T AA 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 AT AT
352 TAAGCGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1297 original size:31 final size:31
Alignment explanation
Indices: 1262--1328 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1252 ATGAATAATG
1262 CTAGTACGTTAAATAAAAAGAATTGATATAA
1 CTAGTACGTTAAATAAAAAGAATTGATATAA
*
1293 CTAGTACGTTAAATAAAAAGAATTTATATAA
1 CTAGTACGTTAAATAAAAAGAATTGATATAA
1324 CTAGT
1 CTAGT
1329 GTTAAAGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.31
Consensus pattern (31 bp):
CTAGTACGTTAAATAAAAAGAATTGATATAA
Found at i:2377 original size:14 final size:14
Alignment explanation
Indices: 2358--2387 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2348 GAAAAAATAC
2358 AATATAGCCACGGA
1 AATATAGCCACGGA
*
2372 AATATAGCTACGGA
1 AATATAGCCACGGA
2386 AA
1 AA
2388 ATCTTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (14 bp):
AATATAGCCACGGA
Found at i:2842 original size:33 final size:33
Alignment explanation
Indices: 2804--2916 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
2794 AAAAAATAAC
***
2804 TGGTGCCGCCCTCCTAGGGCGGCATGCCATGGT
1 TGGTGCCGCCCTAGGAGGGCGGCATGCCATGGT
2837 TGGTGCCGCCCTAGGAGGGCGGCATGCCATGGT
1 TGGTGCCGCCCTAGGAGGGCGGCATGCCATGGT
2870 TGGTGCCGCCCTAGGAGGGCGGCATGCCATGGT
1 TGGTGCCGCCCTAGGAGGGCGGCATGCCATGGT
*
2903 TGGTGTCGCCCTAG
1 TGGTGCCGCCCTAG
2917 TTTTTTTTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.11, C:0.29, G:0.40, T:0.20
Consensus pattern (33 bp):
TGGTGCCGCCCTAGGAGGGCGGCATGCCATGGT
Found at i:2996 original size:8 final size:8
Alignment explanation
Indices: 2976--3019 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
2966 TTAAATTAAT
2976 AATAATT-
1 AATAATTA
2983 AATAATTA
1 AATAATTA
2991 AATAATTA
1 AATAATTA
*
2999 AATAAATA
1 AATAATTA
3007 AATAA--A
1 AATAATTA
3013 AATAATT
1 AATAATT
3020 GGTGCTGCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
6 6 0.18
7 7 0.21
8 20 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AATAATTA
Found at i:4580 original size:23 final size:24
Alignment explanation
Indices: 4554--4622 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 24
4544 ACATTAAAAA
4554 TGACTTTATAAAGATTTA-TAAAT
1 TGACTTTATAAAGATTTATTAAAT
*
4577 TGACTTTGTAAAGATCTTTTTTATTAAAT
1 TGACTTTATAAAGA-----TTTATTAAAT
4606 TGACTTTATAAAGATTT
1 TGACTTTATAAAGATTT
4623 TGACGTTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
23 13 0.34
24 3 0.08
28 4 0.11
29 18 0.47
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (24 bp):
TGACTTTATAAAGATTTATTAAAT
Found at i:6091 original size:257 final size:256
Alignment explanation
Indices: 5617--6096 Score: 714
Period size: 257 Copynumber: 1.9 Consensus size: 256
5607 GGAATCAACA
*
5617 CTCAACATCAGCCCCCTTTTAGTCAAGGATTGAGATTGTGTTTCTGAGGGGGTTCTTCCAAGGTC
1 CTCAACATCAGCCCCCTTTCAGTCAAGGATTGAGATTGTGTTTCTGAGGGGGTTCTTCCAAGGTC
* * ***
5682 TTGAGTCTGTCTCTCAACGAGAGCACCAATGTTGAGCCGTGGGTCGGAGAATGCGCCATTTTTGA
66 TTGAGTCTGTCTCTCAACGAAAGCACCAATGTTGAGCCGTGGGTCGGAGAATACGCCATTTCAAA
* *** *
5747 GGTATTGTCTCCTTTGAGAAGGGGTTTTGCCCTTTGATAAAAGGCGCCTCGTAAGGGAAGGGGTG
131 GGTATTGTCTCCTTTGAGAAGGAGTTTTGCCCTTTGATAAAAGGCGCCTCGTAAGGGAAGAAATA
*
5812 ACCCTTGTTTATAAAACACATTTTCAACCTTTGACCCAAAAATGTGGGAGCCTTTCCACTC
196 ACCCTTGTTTATAAAACACATTTCCAACCTTTGACCCAAAAATGTGGGAGCCTTTCCACTC
* * *
5873 CTCAACATCAGTCCCCCTTTCAGTCAGGGGTTTAGATTGTGTTT-TCGAGGGGGTTCTTCCAAGG
1 CTCAACATCAG-CCCCCTTTCAGTCAAGGATTGAGATTGTGTTTCT-GAGGGGGTTCTTCCAAGG
* * * *
5937 TCTTGAAT-TCGTTTCTCAACGAAAGCACCAGTGTTGAGCCGTGGGTCGGAGAATACGCCCTTTC
64 TCTTGAGTCT-GTCTCTCAACGAAAGCACCAATGTTGAGCCGTGGGTCGGAGAATACGCCATTTC
*
6001 AAAGGTATTGTC-CTCTTTGAGAAGGAGTTTTGCCTTTTGATAAAAGGCGCCTCGTAAGGGAAGA
128 AAAGGTATTGTCTC-CTTTGAGAAGGAGTTTTGCCCTTTGATAAAAGGCGCCTCGTAAGGGAAGA
*
6065 AATAACCCTTGTTTATAAACCACATTTCCAAC
192 AATAACCCTTGTTTATAAAACACATTTCCAAC
6097 GCTTGAATCA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
256 14 0.07
257 185 0.93
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (256 bp):
CTCAACATCAGCCCCCTTTCAGTCAAGGATTGAGATTGTGTTTCTGAGGGGGTTCTTCCAAGGTC
TTGAGTCTGTCTCTCAACGAAAGCACCAATGTTGAGCCGTGGGTCGGAGAATACGCCATTTCAAA
GGTATTGTCTCCTTTGAGAAGGAGTTTTGCCCTTTGATAAAAGGCGCCTCGTAAGGGAAGAAATA
ACCCTTGTTTATAAAACACATTTCCAACCTTTGACCCAAAAATGTGGGAGCCTTTCCACTC
Found at i:6667 original size:40 final size:41
Alignment explanation
Indices: 6597--6676 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 41
6587 ATATGTGTGA
6597 TGTTTTCTCATCATAAAAAACACATGGAGTCAACAATCTCG
1 TGTTTTCTCATCATAAAAAACACATGGAGTCAACAATCTCG
* *
6638 TGTTTTTTTATCAT-AAAAACACATGGAGTCAACAATCTC
1 TGTTTTCTCATCATAAAAAACACATGGAGTCAACAATCTC
6677 TCGCAGATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 25 0.68
41 12 0.32
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (41 bp):
TGTTTTCTCATCATAAAAAACACATGGAGTCAACAATCTCG
Found at i:8617 original size:26 final size:25
Alignment explanation
Indices: 8566--8628 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
8556 AAAAGGTGAG
8566 TTTTT-TTTTTTTTGGCTTAATGCC
1 TTTTTATTTTTTTTGGCTTAATGCC
8590 TTTTTATTTTTTTTGGCTTAATGCC
1 TTTTTATTTTTTTTGGCTTAATGCC
*
8615 CTTTTATTTTTTTT
1 TTTTTATTTTTTTT
8629 TTTTAAAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 5 0.14
25 32 0.86
ACGTcount: A:0.10, C:0.11, G:0.10, T:0.70
Consensus pattern (25 bp):
TTTTTATTTTTTTTGGCTTAATGCC
Found at i:15287 original size:1 final size:1
Alignment explanation
Indices: 15281--15338 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
15271 ATGCCCACGG
* * * * * *
15281 AAAAAAAAAAACAAAAACAAAAAAACAAAAAACAAAAAAAAAACAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15339 CTAACTGTTC
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15304 original size:15 final size:15
Alignment explanation
Indices: 15284--15339 Score: 78
Period size: 15 Copynumber: 3.6 Consensus size: 15
15274 CCCACGGAAA
15284 AAAAAAAACAAAAAC
1 AAAAAAAACAAAAAC
15299 -AAAAAAACAAAAAAC
1 AAAAAAAAC-AAAAAC
15314 AAAAAAAAAACAAAAAC
1 --AAAAAAAACAAAAAC
15331 AAAAAAAAC
1 AAAAAAAAC
15340 TAACTGTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.22
15 15 0.41
17 6 0.16
18 8 0.22
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAACAAAAAC
Found at i:15304 original size:17 final size:17
Alignment explanation
Indices: 15282--15338 Score: 91
Period size: 16 Copynumber: 3.5 Consensus size: 17
15272 TGCCCACGGA
15282 AAAAAAAAAACAAAAAC
1 AAAAAAAAAACAAAAAC
*
15299 -AAAAAAACA-AAAAAC
1 AAAAAAAAAACAAAAAC
15314 AAAAAAAAAACAAAAAC
1 AAAAAAAAAACAAAAAC
15331 AAAAAAAA
1 AAAAAAAA
15339 CTAACTGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
15 6 0.17
16 16 0.44
17 14 0.39
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAC
Found at i:15339 original size:26 final size:25
Alignment explanation
Indices: 15281--15339 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
15271 ATGCCCACGG
*
15281 AAAAAAA-AAAACAAAAACAAAAAA
1 AAAAAAACAAAAAAAAAACAAAAAA
15305 ACAAAAAACAAAAAAAAAACAAAAACA
1 A-AAAAAACAAAAAAAAAACAAAAA-A
15332 AAAAAAAC
1 AAAAAAAC
15340 TAACTGTTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 1 0.03
25 6 0.19
26 22 0.71
27 2 0.06
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (25 bp):
AAAAAAACAAAAAAAAAACAAAAAA
Found at i:27590 original size:25 final size:24
Alignment explanation
Indices: 27562--27623 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
27552 GTGGATTGTA
*
27562 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
27587 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
27611 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
27624 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:28788 original size:42 final size:41
Alignment explanation
Indices: 28721--28817 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 41
28711 GTCACTTTGG
* * *
28721 TTGACACTAAAAGTTTTCACCTTGGTAAATTGAAATTACCTT
1 TTGACACCAAAAGTTGTCACCTTGGTAAATTAAAATTACC-T
*
28763 TTGACACCAAAAGTTGTCACTTTGGTAAATTAAAATTACCT
1 TTGACACCAAAAGTTGTCACCTTGGTAAATTAAAATTACCT
*
28804 TTGACACCAGAAGT
1 TTGACACCAAAAGT
28818 GTTACTCCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 14 0.28
42 36 0.72
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (41 bp):
TTGACACCAAAAGTTGTCACCTTGGTAAATTAAAATTACCT
Found at i:32209 original size:25 final size:25
Alignment explanation
Indices: 32175--32222 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
32165 AATCACCATA
32175 TTTGGTATAAATAGAAAAAAAAAGG
1 TTTGGTATAAATAGAAAAAAAAAGG
32200 TTTGGTATAAATAGAAAAAAAAA
1 TTTGGTATAAATAGAAAAAAAAA
32223 TTAATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (25 bp):
TTTGGTATAAATAGAAAAAAAAAGG
Found at i:36912 original size:20 final size:20
Alignment explanation
Indices: 36870--36910 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
36860 TATGTTTAGG
**
36870 ATTCAAACTAATGTGTACAA
1 ATTCAAACTAATGTAAACAA
36890 ATTCAAACTAATGATAAACAA
1 ATTCAAACTAATG-TAAACAA
36911 TTTTTAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (20 bp):
ATTCAAACTAATGTAAACAA
Found at i:45274 original size:21 final size:20
Alignment explanation
Indices: 45232--45271 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
45222 TGAATTACAT
* *
45232 TTTCATTTTTCGAATATAAA
1 TTTCATTTTTAGAAGATAAA
*
45252 TTTCTTTTTTAGAAGATAAA
1 TTTCATTTTTAGAAGATAAA
45272 ATTAATCACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (20 bp):
TTTCATTTTTAGAAGATAAA
Found at i:48057 original size:21 final size:21
Alignment explanation
Indices: 48031--48070 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48021 CGTTATTCTA
* *
48031 ATAATCTCATTTGTACAGTAC
1 ATAATCTAATATGTACAGTAC
48052 ATAATCTAATATGTACAGT
1 ATAATCTAATATGTACAGT
48071 GTAATTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (21 bp):
ATAATCTAATATGTACAGTAC
Found at i:50175 original size:77 final size:77
Alignment explanation
Indices: 50048--50203 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
50038 TATAATGTAG
50048 TAATATTTTATTGAAGAAGGTTAAAAGAGTTAGTAATGCATCAAAATCTTAGTTGTTTTATATTT
1 TAATATTTTATTGAAGAAGGTTAAAAGAGTTAGTAATGCATCAAAATCTTAGTTGTTTTATATTT
50113 TATAAATACGTA
66 TATAAATACGTA
50125 TAATATTTTATTGAAGAAGGTTAAAAGAGTTAGTAATGCATCAAAATCTTAGTTGTTTTATATTT
1 TAATATTTTATTGAAGAAGGTTAAAAGAGTTAGTAATGCATCAAAATCTTAGTTGTTTTATATTT
50190 TATAAATACGTA
66 TATAAATACGTA
50202 TA
1 TA
50204 CTAATTTTTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (77 bp):
TAATATTTTATTGAAGAAGGTTAAAAGAGTTAGTAATGCATCAAAATCTTAGTTGTTTTATATTT
TATAAATACGTA
Found at i:51443 original size:44 final size:45
Alignment explanation
Indices: 51368--51473 Score: 110
Period size: 44 Copynumber: 2.4 Consensus size: 45
51358 TTAACCTTCT
* * *
51368 TATGAAATTTTGTTAACATCCCTAAAGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATAACATCCCGAAAGAATTTTGATA-ACCAACAC
* *
51412 TATGAAATTTTGATAAC-TTCCGAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACATCCCGAAAG-AATTTTGATAACCAACAC
* *
51457 TATGAGATGTTGATAAC
1 TATGAAATTTTGATAAC
51474 CTCTATATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
43 6 0.12
44 27 0.52
45 19 0.37
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (45 bp):
TATGAAATTTTGATAACATCCCGAAAGAATTTTGATAACCAACAC
Found at i:51561 original size:22 final size:22
Alignment explanation
Indices: 51409--51770 Score: 118
Period size: 22 Copynumber: 16.8 Consensus size: 22
51399 TTGAAGACCT
51409 CACTATGAAATTTTGATAACTTC-
1 CACTATGAAATTTTGATAA--TCA
*
51432 CGA--ATGAAATTTTGATAACCAA
1 C-ACTATGAAATTTTGATAATC-A
* * * *
51454 CACTATGAGATGTTGATAACCT
1 CACTATGAAATTTTGATAATCA
* *
51476 CTA-TATGATATATTGATAATCA
1 C-ACTATGAAATTTTGATAATCA
** * * *
51498 CGTTATGAAAATTTAAAAACCTC-
1 CACTATGAAATTTTGATAA--TCA
* *
51521 CA-TATGAATAGTTAG-TAATCA
1 CACTATGAA-ATTTTGATAATCA
*
51542 CACTTTGAAATTTTGATAATCA
1 CACTATGAAATTTTGATAATCA
* *
51564 CACTATGAAATTGTGATAATCT
1 CACTATGAAATTTTGATAATCA
* * * *
51586 CGCTATAAAATTTTGATAAACCT
1 CACTATGAAATTTTGAT-AATCA
* * * *
51609 CCCTATAAAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCA
*
51631 C-CTTATGAAATCTTG---AT-A
1 CAC-TATGAAATTTTGATAATCA
* * *
51649 -ACTA-CAAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCA
* **
51669 CTCTATGATGTTTTGAT-A--A
1 CACTATGAAATTTTGATAATCA
*
51688 C-CTATGAAATTTTGAT-CTACA
1 CACTATGAAATTTTGATAAT-CA
* *
51709 TACTATGAAATTTTGA-AAACTA
1 CACTATGAAATTTTGATAATC-A
* * *
51731 AACTATGAAATTTTGATAACCTT
1 CACTATGAAATTTTGATAATC-A
51754 CA-TATGAAATTTTGATA
1 CACTATGAAATTTTGATA
51771 CCCTCCCTAA
Statistics
Matches: 257, Mismatches: 53, Indels: 59
0.70 0.14 0.16
Matches are distributed among these distances:
16 7 0.03
17 2 0.01
18 14 0.05
19 3 0.01
20 3 0.01
21 14 0.05
22 165 0.64
23 46 0.18
24 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (22 bp):
CACTATGAAATTTTGATAATCA
Found at i:51854 original size:22 final size:21
Alignment explanation
Indices: 51828--51940 Score: 68
Period size: 22 Copynumber: 5.1 Consensus size: 21
51818 CCTAATTTAG
*
51828 TAACCATAGTATGAAATTTTGA
1 TAACC-TACTATGAAATTTTGA
* * *
51850 TAACCTCCCAATGAAATATT-A
1 TAACCT-ACTATGAAATTTTGA
* *
51871 GTAACCTTCTTATGAAATTTTGT
1 -TAACCTAC-TATGAAATTTTGA
*
51894 TAACCACACTATGAAATTCTT-A
1 TAACC-TACTATGAAATT-TTGA
* *
51916 TAACCTTGCTATGACATTTTGA
1 TAACC-TACTATGAAATTTTGA
51938 TAA
1 TAA
51941 TCTCTTTGAT
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
21 5 0.07
22 61 0.88
23 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
TAACCTACTATGAAATTTTGA
Found at i:51887 original size:44 final size:44
Alignment explanation
Indices: 51837--51940 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
51827 GTAACCATAG
* *
51837 TATGAAATTTTGATAACCTCCCAATGAAA-TATTAGTAACCTT-C
1 TATGAAATTTTGATAACCACACAATGAAATTATTA-TAACCTTGC
* * *
51880 TTATGAAATTTTGTTAACCACACTATGAAATTCTTATAACCTTGC
1 -TATGAAATTTTGATAACCACACAATGAAATTATTATAACCTTGC
*
51925 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
51941 TCTCTTTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
44 46 0.90
45 5 0.10
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACAATGAAATTATTATAACCTTGC
Found at i:51907 original size:66 final size:65
Alignment explanation
Indices: 51827--52180 Score: 211
Period size: 66 Copynumber: 5.2 Consensus size: 65
51817 TCCTAATTTA
* *
51827 GTAACCATAGTATGAAATTTTGATAACC-TCCCAATGAAATATTAGTAACCTTCTTATGAAATTT
1 GTAACCACACTATGAAATTTT-ATAACCTTCCCAATGAAAT-TTAGTAACCTTCTTATGAAATTT
51891 TG
64 TG
* * * *
51893 TTAACCACACTATGAAATTCTTATAACCTTGCTATGACATTTTGATAATCTCTTTGATAACCTT-
1 GTAACCACACTATGAAATT-TTATAACCTT-C----CCA--ATGA-AA--T-TTAG-TAACCTTC
* *
51957 TCTATAAAATTGTG
53 T-TATGAAATTTTG
* * * * * * *
51971 ATAACCACATTATGAAATTTCAATAACCTTTCTAA-GAAATTTTAATAACCTGATCCTATGAAAT
1 GTAACCACACTATGAAATTT-TATAACCTTCCCAATGAAA-TTTAGTAACCT--TCTTATGAAAT
52035 TTTG
62 TTTG
*
52039 GTAACCACACTATGAAATTTTAGTAACCTTCCC-ATGAAATTTTGATAA-CTTCTATATGAAATT
1 GTAACCACACTATGAAATTTTA-TAACCTTCCCAATGAAATTTAG-TAACCTTCT-TATGAAATT
52102 TTG
63 TTG
* * **
52105 GTAACCACACGATTG-AATTTTGATAACC-TCCTC-ATGAAATTATAATAACCACCTTATGAAAT
1 GTAACCACACTA-TGAAATTTT-ATAACCTTCC-CAATGAAATT-TAGTAACCTTCTTATGAAAT
*
52167 TTTT
62 TTTG
*
52171 ATAACCACAC
1 GTAACCACAC
52181 AGAAACAAGA
Statistics
Matches: 224, Mismatches: 37, Indels: 54
0.71 0.12 0.17
Matches are distributed among these distances:
65 5 0.02
66 94 0.42
67 19 0.08
68 46 0.21
69 2 0.01
70 2 0.01
72 2 0.01
73 1 0.00
74 3 0.01
75 2 0.01
77 6 0.03
78 42 0.19
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (65 bp):
GTAACCACACTATGAAATTTTATAACCTTCCCAATGAAATTTAGTAACCTTCTTATGAAATTTTG
Found at i:52013 original size:78 final size:78
Alignment explanation
Indices: 51872--52018 Score: 181
Period size: 78 Copynumber: 1.9 Consensus size: 78
51862 GAAATATTAG
* * * * * * *
51872 TAACCTTCTTATGAAATTTTGTTAACCACACTATGAAATTCTTATAACCTTGCTATGACATTTTG
1 TAACCTTCTTATAAAATTGTGATAACCACACTATGAAATTCTAATAACCTTGCTAAGAAATTTTA
51937 ATAATCTCTTTGA
66 ATAATCTCTTTGA
* *
51950 TAACCTT-TCTATAAAATTGTGATAACCACATTATGAAATT-TCAATAACCTTTCTAAGAAATTT
1 TAACCTTCT-TATAAAATTGTGATAACCACACTATGAAATTCT-AATAACCTTGCTAAGAAATTT
52013 TAATAA
64 TAATAA
52019 CCTGATCCTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
77 2 0.03
78 56 0.97
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.40
Consensus pattern (78 bp):
TAACCTTCTTATAAAATTGTGATAACCACACTATGAAATTCTAATAACCTTGCTAAGAAATTTTA
ATAATCTCTTTGA
Found at i:52054 original size:22 final size:22
Alignment explanation
Indices: 51958--52180 Score: 127
Period size: 22 Copynumber: 10.0 Consensus size: 22
51948 GATAACCTTT
* *
51958 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
* ** ***
51980 TTATGAAATTTCAATAACCTTT
1 CTATGAAATTTTGATAACCACA
* *
52002 CTAAGAAATTTTAATAACCTGATC-
1 CTATGAAATTTTGATAACC--A-CA
*
52026 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
52048 CTATGAAATTTT-AGTAACCTTC-
1 CTATGAAATTTTGA-TAACC-ACA
* **
52070 CCATGAAATTTTGATAACTTCTA
1 CTATGAAATTTTGATAACCAC-A
*
52093 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
52114 CGATTG-AATTTTGATAACCTC-
1 CTA-TGAAATTTTGATAACCACA
* *
52135 CTCATGAAATTATAATAACCAC-
1 CT-ATGAAATTTTGATAACCACA
*
52157 CTTATGAAATTTTTATAACCACA
1 C-TATGAAATTTTGATAACCACA
52180 C
1 C
52181 AGAAACAAGA
Statistics
Matches: 153, Mismatches: 33, Indels: 29
0.71 0.15 0.13
Matches are distributed among these distances:
21 7 0.05
22 124 0.81
23 6 0.04
24 16 0.10
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:71545 original size:31 final size:32
Alignment explanation
Indices: 71499--71562 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
71489 ATAAAAAAGA
*
71499 ATTGGAATGCCCAAATTATCCTCAAGGCTTAT
1 ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
* * *
71531 ATTGG-ATGTCCAAATTACCCTCGAGTCTTAT
1 ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
71562 A
1 A
71563 CGAAATAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (32 bp):
ATTGGAATGCCCAAATTACCCTCAAGGCTTAT
Found at i:72441 original size:131 final size:129
Alignment explanation
Indices: 72300--72562 Score: 402
Period size: 131 Copynumber: 2.0 Consensus size: 129
72290 GTTTTTTTAG
*
72300 AAATAAACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCT
1 AAATAAACTTTTATAGTTTTACTCAACTAAAAACTCCATTTTTATTTAATTAAATCTAATAT--T
* * * *
72365 TATAACTATTTGATTTTTACCATTTTACTATTTTAATT-GAAAAACTTATATATATTAGAATCTT
64 TATAACTATTTGATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAAAAT-TT
72429 TT
128 TT
* *
72431 AAATATACTTTTATAGTTTTACTCAACTAAAAGCTCCATTTTTATTTAATTAAATCTAATATTTA
1 AAATAAACTTTTATAGTTTTACTCAACTAAAAACTCCATTTTTATTTAATTAAATCTAATATTTA
* * *
72496 TACCTATTTTATTTTTACCATTTTACTAATTTAATTAAAAAAATTTAGATATATTAAAATTTTT
66 TAACTATTTGATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAAAATTTTT
72560 AAA
1 AAA
72563 AATATTTCAT
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
129 43 0.36
130 19 0.16
131 59 0.49
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.48
Consensus pattern (129 bp):
AAATAAACTTTTATAGTTTTACTCAACTAAAAACTCCATTTTTATTTAATTAAATCTAATATTTA
TAACTATTTGATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAAAATTTTT
Found at i:72602 original size:129 final size:130
Alignment explanation
Indices: 72322--72581 Score: 337
Period size: 129 Copynumber: 2.0 Consensus size: 130
72312 ATAGTTTTAC
* *
72322 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTGATTTTTACCA
1 TCAACTAAAAGCTCCATTTTTATTTAATTAAATCTAATAT-CTTATAACTATTTGATTTTTACCA
* * * * * * ** **
72387 TTTTACTATTTTAATTGAAAAACTTATATATATTAGAATCTTTTAAATATACTTTTATAGTTTTA
65 TTTTACTAATTTAATTAAAAAACTTAGATATATTAAAATCTTTTAAAAATACTTTCATAAATGAA
*
72452 C
130 A
* *
72453 TCAACTAAAAGCTCCATTTTTATTTAATTAAATCTAATAT-TTATACCTATTTTATTTTTACCAT
1 TCAACTAAAAGCTCCATTTTTATTTAATTAAATCTAATATCTTATAACTATTTGATTTTTACCAT
*
72517 TTTACTAATTTAATTAAAAAAATTTAGATATATTAAAAT-TTTTAAAAATA-TTTCATAAATGAA
66 TTTACTAATTTAATT-AAAAAACTTAGATATATTAAAATCTTTTAAAAATACTTTCATAAATGAA
72580 A
130 A
72581 T
1 T
72582 TGTTTAAATT
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
128 9 0.08
129 46 0.41
130 19 0.17
131 38 0.34
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (130 bp):
TCAACTAAAAGCTCCATTTTTATTTAATTAAATCTAATATCTTATAACTATTTGATTTTTACCAT
TTTACTAATTTAATTAAAAAACTTAGATATATTAAAATCTTTTAAAAATACTTTCATAAATGAAA
Done.