Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011831.1 Corchorus capsularis cultivar CVL-1 contig11852, 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: 35689
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:776 original size:322 final size:321
Alignment explanation
Indices: 129--888 Score: 848
Period size: 322 Copynumber: 2.4 Consensus size: 321
119 AATTCCTAAC
* * *
129 TAAATCGAAACAATATT-AGATGCTCATAAAAACAAATCTCTAAATCCAATATGGCTAAGATTTG
1 TAAATCG-AACAAGATTAAGATGCTCATAAAAACAAATCTTTAAATCCAATATGGCTGAGATTTG
* * * * *
193 GTTAGATGAATATA-ATTATTTCAAGAAGTCTTTCTGCTAAAAATCGTGCAAAACAAAGCTGGGG
65 GTTAGATGAATATAGA-TATTTCAAGAAGTCTTTCTGCCAAAAACCATGCAAAACAAAGCTGAGA
* *
257 CCCCAAAACGTGTTTTTAGCCAAAAACCGTGAAGTACACGATTTTCGGCTAAAAACTGACCAGAA
129 CCCCAAAACGCGTTTTTAGCCAAAAACCGTGAAGTACACGATTTTCGGATAAAAACTGACCAGAA
* *
322 AAGTTTTCCTTAATTTTTTTGCCATAATACTTCGAAAAAAATATATATAATTCAACCCTAAAAAC
194 AAGTTTTCCTCAATTTTTTTGCCACAATACTTCGAAAAAAATATATATAATTCAACCCTAAAAAC
* * *
387 AATTGAATGGTTTTTCACGCTTCTAATATCATTTTTCGATATTTTTCTGAATTTATTTTTAAT
259 AATTGAATGGCTTTACACGCTTCTAATATCATTTTTCGATATTTTTCTGAATTAATTTTTAAT
* * *
450 TAAATCGAAGCACGATTAAGATGCTCGTAAAAAGAAATCTTTAAATCCAATATGGCTGAGATTTG
1 TAAATCGAA-CAAGATTAAGATGCTCATAAAAACAAATCTTTAAATCCAATATGGCTGAGATTTG
* * * **
515 GTTAGATGAATATAGATATTTTAAGGAA-TCTTTTTGCCACAAACCATGCAAAACTGAG-TCGAG
65 GTTAGATGAATATAGATATTTCAA-GAAGTCTTTCTGCCAAAAACCATGCAAAACAAAGCT-GAG
* * * *
578 ACCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGGTACACGATTTTCGGATAAAAACTTACCC
128 ACCCCAAAACGCGTTTTTAGCCAAAAACCGTGA--AGTACACGATTTTCGGATAAAAACTGACCA
* * * **
643 GAAAATTTTATTCTCAA-TTTTTTGCCACAATAC-TC-ATAAAAA-ATATATAATTCAA-TGTCA
191 GAAAAGTTT-TCCTCAATTTTTTTGCCACAATACTTCGAAAAAAATATATATAATTCAACCCT-A
* * *
703 ACAA-AATTGACA-GGCTTTACACGCTTCTAATATCATTTTTCTATTTTTTATCTGAGAATTAAT
254 AAAACAATTGA-ATGGCTTTACACGCTTCTAATATCATTTTTCGATATTTT-TCT--GAATTAAT
766 TTTT-AT
315 TTTTAAT
* * * * * * *
772 TAAATTGAAAAAGATTAAAATGCTCATAAAAACAAAT-TCTTAAATCAAATATGACTGAAATTTT
1 TAAATCGAACAAGATTAAGATGCTCATAAAAACAAATCT-TTAAATCCAATATGGCTGAGATTTG
* * * * *
836 GTTCGATCAATATAGATGTTTCAA-ATAGTTTTTGC-GCCAAAAATCATGCAAAA
65 GTTAGATGAATATAGATATTTCAAGA-AGTCTTT-CTGCCAAAAACCATGCAAAA
889 TTGAACCGGA
Statistics
Matches: 369, Mismatches: 53, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
319 1 0.00
320 44 0.12
321 118 0.32
322 135 0.37
323 17 0.05
324 49 0.13
325 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (321 bp):
TAAATCGAACAAGATTAAGATGCTCATAAAAACAAATCTTTAAATCCAATATGGCTGAGATTTGG
TTAGATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAACCATGCAAAACAAAGCTGAGACC
CCAAAACGCGTTTTTAGCCAAAAACCGTGAAGTACACGATTTTCGGATAAAAACTGACCAGAAAA
GTTTTCCTCAATTTTTTTGCCACAATACTTCGAAAAAAATATATATAATTCAACCCTAAAAACAA
TTGAATGGCTTTACACGCTTCTAATATCATTTTTCGATATTTTTCTGAATTAATTTTTAAT
Found at i:886 original size:321 final size:319
Alignment explanation
Indices: 148--934 Score: 819
Period size: 321 Copynumber: 2.4 Consensus size: 319
138 ACAATATTAG
148 ATGCTCATAAAAACAAATCTCTAAATCCAATATGGCT-AAGATTTGGTTAGATGAATATA-ATTA
1 ATGCTCATAAAAACAAATCT-TAAATCCAATATGGCTGAA-ATTTGGTTAGATGAATATAGA-TA
* * * ** * * *
211 TTTCAAGAAGTCTTTCTGCTAAAAATCGTGCAAAACAAAGCTGGGGCCCCAAAACGTGTTTTTAG
63 TTTCAA-AAGTTTTTC-GCCAAAAATCATGCAAAACTGAGC--GGACCCCGAAACGCGTTTTTAG
* *
276 CCAAAAACCGTGA--AGTACACGATTTTCGGCTAAAAACTGACCAGAAAAGTTTTCCTTAATTTT
124 CCAAAAACCGTGATGAGTACACGATTTTCGGATAAAAACTGACCAGAAAAGTTTTCCTCAATTTT
* * *
339 TTTGCCATAATACTTCGAAAAAAATATATATAATTCAACCCTAAAAACAATTGAATGGTTTTTCA
189 TTTGCCACAATACTTCGAAAAAAATATATATAATTCAACCCTAAAAACAATTGAATGGCTTTACA
* * *
404 CGCTTCTAATATCATTTTTCGATATTTTTCTGAATTTATTTTTAATTAAATCGAAGCACGATTAA
254 CGCTTCTAATATCATTTTTCGATATTTTTCTGAATTAATTTTTAATTAAATCGAAGAAAGATTAA
*
469 G
319 A
* * *
470 ATGCTCGTAAAAAGAAATCTTTAAATCCAATATGGCTGAGATTTGGTTAGATGAATATAGATATT
1 ATGCTCATAAAAACAAATC-TTAAATCCAATATGGCTGAAATTTGGTTAGATGAATATAGATATT
* * * *
535 TTAAGGAA-TCTTTTTGCCACAAACCATGCAAAACTGAGTCGAGACCCCGAAACGCGTTTTTAGC
65 TCAA--AAGT-TTTTCGCCAAAAATCATGCAAAACTGAG-CG-GACCCCGAAACGCGTTTTTAGC
* * * * *
599 CAAAAACCGTGATGGGTACACGATTTTCGGATAAAAACTTACCCGAAAATTTTATTCTCAA-TTT
125 CAAAAACCGTGATGAGTACACGATTTTCGGATAAAAACTGACCAGAAAAGTTT-TCCTCAATTTT
* ** *
663 TTTGCCACAATAC-TC-ATAAAAA-ATATATAATTCAA-TGTCAACAA-AATTGACA-GGCTTTA
189 TTTGCCACAATACTTCGAAAAAAATATATATAATTCAACCCT-AAAAACAATTGA-ATGGCTTTA
* * *
722 CACGCTTCTAATATCATTTTTCTATTTTTTATCTGAGAATTAATTTTT-ATTAAATTGAA-AAAG
252 CACGCTTCTAATATCATTTTTCGATATTTT-TCT--GAATTAATTTTTAATTAAATCGAAGAAAG
785 ATTAAA
314 ATTAAA
* * * * * *
791 ATGCTCATAAAAACAAATTCTTAAATCAAATATGACTGAAATTTTGTTCGATCAATATAGATGTT
1 ATGCTCATAAAAACAAA-TCTTAAATCCAATATGGCTGAAATTTGGTTAGATGAATATAGATATT
* * * * **
856 TCAAATAGTTTTTGCGCCAAAAATCATGCAAAATTGAACCGGAGCTCCGGAATACGTTTTTAGCC
65 TCAAA-AGTTTTT-CGCCAAAAATCATGCAAAACTG-AGCGGA-CCCCGAAACGCGTTTTTAGCC
*
921 TAAAACCGTGATGA
126 AAAAACCGTGATGA
935 TTAAAACCGT
Statistics
Matches: 387, Mismatches: 57, Indels: 43
0.79 0.12 0.09
Matches are distributed among these distances:
319 1 0.00
320 47 0.12
321 135 0.35
322 127 0.33
323 23 0.06
324 49 0.13
325 5 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (319 bp):
ATGCTCATAAAAACAAATCTTAAATCCAATATGGCTGAAATTTGGTTAGATGAATATAGATATTT
CAAAAGTTTTTCGCCAAAAATCATGCAAAACTGAGCGGACCCCGAAACGCGTTTTTAGCCAAAAA
CCGTGATGAGTACACGATTTTCGGATAAAAACTGACCAGAAAAGTTTTCCTCAATTTTTTTGCCA
CAATACTTCGAAAAAAATATATATAATTCAACCCTAAAAACAATTGAATGGCTTTACACGCTTCT
AATATCATTTTTCGATATTTTTCTGAATTAATTTTTAATTAAATCGAAGAAAGATTAAA
Found at i:958 original size:18 final size:15
Alignment explanation
Indices: 921--953 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
911 GTTTTTAGCC
921 TAAAACCGTGATGAT
1 TAAAACCGTGATGAT
936 TAAAACCGTGATGAT
1 TAAAACCGTGATGAT
951 TAA
1 TAA
954 TAAAAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (15 bp):
TAAAACCGTGATGAT
Found at i:2251 original size:61 final size:61
Alignment explanation
Indices: 2156--2525 Score: 399
Period size: 51 Copynumber: 6.2 Consensus size: 61
2146 AAGGCTGACA
* *
2156 AGAAGACACGA-GAAGACAAGAGGCTCTACGCAGTGAGGCAAGGCCAGACACGAAGGTACACG
1 AGAAGACAC-ACGAAGAC-AGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACG
*
2218 AGAAGACACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCTAGACACGAAGGTACACAAG
1 AGAAGACACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACAC--G
2281 AAGACACACGAACACACAAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTA
1 -AG--A-A-G-ACACAC--GAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTA
2346 CAC-
58 CACG
* * *
2349 ----G----A-GAAGACAGAGGCTCTCCGCAGTGAGGTGAGGCCAGACATGAAGGTACACA
1 AGAAGACACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACG
* *
2401 AGAAGACATACGAAGACAGAGGCTCTCTGCAGTGAGGCGAGGCCAGACACGAAGGTACAC-
1 AGAAGACACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACG
2461 ----G----A-GAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAA-G-ACACG
1 AGAAGACACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACG
2511 AGAAGACACACGAAG
1 AGAAGACACACGAAG
2526 GCACGAGAAG
Statistics
Matches: 267, Mismatches: 10, Indels: 65
0.78 0.03 0.19
Matches are distributed among these distances:
49 4 0.01
50 1 0.00
51 88 0.33
52 1 0.00
54 2 0.01
56 2 0.01
58 1 0.00
59 5 0.02
60 1 0.00
61 87 0.33
62 15 0.06
63 1 0.00
64 2 0.01
66 1 0.00
67 1 0.00
68 1 0.00
69 6 0.02
71 48 0.18
ACGTcount: A:0.36, C:0.24, G:0.32, T:0.08
Consensus pattern (61 bp):
AGAAGACACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACG
Found at i:2382 original size:71 final size:71
Alignment explanation
Indices: 2223--2357 Score: 243
Period size: 71 Copynumber: 1.9 Consensus size: 71
2213 ACACGAGAAG
* *
2223 ACACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCTAGACACGAAGGTACACAAGAAGACAC
1 ACACAAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACAAGAAGACAC
2288 ACGAAC
66 ACGAAC
*
2294 ACACAAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACA
1 ACACAAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACAAGAAGACA
2358 GAGGCTCTCC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.38, C:0.26, G:0.30, T:0.07
Consensus pattern (71 bp):
ACACAAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACAAGAAGACAC
ACGAAC
Found at i:2521 original size:20 final size:20
Alignment explanation
Indices: 2498--2538 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2488 GCGAGGCCAG
2498 ACACGAAGACACGAGAAGAC
1 ACACGAAGACACGAGAAGAC
*
2518 ACACGAAGGCACGAGAAGAC
1 ACACGAAGACACGAGAAGAC
2538 A
1 A
2539 GAGGCTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.27, T:0.00
Consensus pattern (20 bp):
ACACGAAGACACGAGAAGAC
Found at i:2524 original size:183 final size:182
Alignment explanation
Indices: 2160--2587 Score: 490
Period size: 183 Copynumber: 2.3 Consensus size: 182
2150 CTGACAAGAA
* *
2160 GACACGAGAAGACAAGAGGCTCTACGCAGTGAGGCAAGGCCAGACACGAAGGTACACGAGAAGAC
1 GACACGAGAAGAC-AGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGAC
*
2225 ACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCTAGACACGAAGGTACACAAGAAGACACAC
65 ACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACAAGAAGACACAC
* * ** ** *
2290 GAACACACAAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAG
130 GAACACACAAGAAGACAGAGGCTCACCGCAGAGACACGAGAACACACACGAAG
* * *
2343 GTACACGAGAAGACAGAGGCTCTCCGCAGTGAGGTGAGGCCAGACATGAAGGTACACAAGAAGAC
1 G-ACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGAC
* * * * *
2408 ATACGAAGACAGAGGCTCTCTGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAG
65 ACACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACAAGAAGACACAC
** * * * * *
2473 GCTCTC-CGCAGTGAGGC-GAGGC-CA--GACACGAAGACACGAGAAGACACACGAAG
130 GAACACAC-AAG-AAGACAGAGGCTCACCG-CA-G-AGACACGAGAACACACACGAAG
* * * *
2526 G-CACGAGAAGACAGAGGCTCTCAGCAGTAAGGCGAGGGCAGACACGAAGCTACACGAGAAGA
1 GACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGA
2588 GGCTCTCCGC
Statistics
Matches: 207, Mismatches: 32, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
180 1 0.00
181 56 0.27
182 3 0.01
183 132 0.64
184 15 0.07
ACGTcount: A:0.36, C:0.24, G:0.32, T:0.07
Consensus pattern (182 bp):
GACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACA
CACGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACAAGAAGACACACG
AACACACAAGAAGACAGAGGCTCACCGCAGAGACACGAGAACACACACGAAG
Found at i:2534 original size:69 final size:71
Alignment explanation
Indices: 2447--2587 Score: 223
Period size: 69 Copynumber: 2.0 Consensus size: 71
2437 GCGAGGCCAG
* *
2447 ACACGAAGGTACACGAGAAGACAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAG-ACACG
1 ACACGAAGG-ACACGAGAAGACAGAGGCTCTCAGCAGTAAGGCGAGGCCAGACACGAAGCACACG
2511 AGAAGAC
65 AGAAGAC
*
2518 ACACGAAGG-CACGAGAAGACAGAGGCTCTCAGCAGTAAGGCGAGGGCAGACACGAAGCTACACG
1 ACACGAAGGACACGAGAAGACAGAGGCTCTCAGCAGTAAGGCGAGGCCAGACACGAAGC-ACACG
2582 AGAAGA
65 AGAAGA
2588 GGCTCTCCGC
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
69 45 0.69
71 20 0.31
ACGTcount: A:0.38, C:0.24, G:0.33, T:0.06
Consensus pattern (71 bp):
ACACGAAGGACACGAGAAGACAGAGGCTCTCAGCAGTAAGGCGAGGCCAGACACGAAGCACACGA
GAAGAC
Found at i:2571 original size:49 final size:48
Alignment explanation
Indices: 2518--2636 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 48
2508 ACGAGAAGAC
*
2518 ACACGAAGGCACGAGAAGACAGAGGCTCTCAGCAGTA-AGGCGAGGGCAG
1 ACACGAAGGCAC-AGAAGACAGAGGCTCTCAGCAG-AGAGGCGAGGCCAG
*
2567 ACACGAA-GCTACACG-AGA-AGAGGCTCTCCGCAGAGAGGCGAGGCCAG
1 ACACGAAGGC-ACA-GAAGACAGAGGCTCTCAGCAGAGAGGCGAGGCCAG
*
2614 ACACAAAGGTACACAAGAAGACA
1 ACACGAAGG--CAC-AGAAGACA
2637 CACGAAGATA
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
46 1 0.02
47 31 0.53
48 7 0.12
49 13 0.22
50 5 0.09
51 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.32, T:0.06
Consensus pattern (48 bp):
ACACGAAGGCACAGAAGACAGAGGCTCTCAGCAGAGAGGCGAGGCCAG
Found at i:2607 original size:47 final size:47
Alignment explanation
Indices: 2533--2634 Score: 134
Period size: 47 Copynumber: 2.1 Consensus size: 47
2523 AAGGCACGAG
* *
2533 AAGACAGAGGCTCTCAGCAGTAAGGCGAGGGCAGACACGAAGCTACAC
1 AAGA-AGAGGCTCTCAGCAGTAAGGCGAGGCCAGACACAAAGCTACAC
* * *
2581 GAGAAGAGGCTCTCCGCAG-AGAGGCGAGGCCAGACACAAAGGTACAC
1 AAGAAGAGGCTCTCAGCAGTA-AGGCGAGGCCAGACACAAAGCTACAC
2628 AAGAAGA
1 AAGAAGA
2635 CACACGAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 1 0.02
47 43 0.91
48 3 0.06
ACGTcount: A:0.37, C:0.24, G:0.32, T:0.07
Consensus pattern (47 bp):
AAGAAGAGGCTCTCAGCAGTAAGGCGAGGCCAGACACAAAGCTACAC
Found at i:2651 original size:61 final size:59
Alignment explanation
Indices: 2577--2699 Score: 201
Period size: 61 Copynumber: 2.1 Consensus size: 59
2567 ACACGAAGCT
2577 ACACGAGAAGAGGCTCTCCGCAGAGAGGCGAGGCCAGACACAAAGGTACACAAGAAGAC
1 ACACGAGAAGAGGCTCTCCGCAGAGAGGCGAGGCCAGACACAAAGGTACACAAGAAGAC
* * *
2636 ACACGAAGATAGAGGCTCTCCGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGAC
1 ACACG-AGA-AGAGGCTCTCCGCAGAGAGGCGAGGCCAGACACAAAGGTACACAAGAAGAC
2697 ACA
1 ACA
2700 GTGGTGCTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 5 0.08
60 3 0.05
61 51 0.86
ACGTcount: A:0.37, C:0.25, G:0.31, T:0.07
Consensus pattern (59 bp):
ACACGAGAAGAGGCTCTCCGCAGAGAGGCGAGGCCAGACACAAAGGTACACAAGAAGAC
Found at i:2796 original size:2 final size:2
Alignment explanation
Indices: 2791--2821 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2781 GAAAAAAATT
2791 AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2822 CAGCGTGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2811 original size:15 final size:15
Alignment explanation
Indices: 2791--2819 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2781 GAAAAAAATT
2791 AGAGAGAGAGAGAGG
1 AGAGAGAGAGAGAGG
2806 AGAGAGAGAGAGAG
1 AGAGAGAGAGAGAG
2820 AGCAGCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (15 bp):
AGAGAGAGAGAGAGG
Found at i:3180 original size:213 final size:209
Alignment explanation
Indices: 2806--3228 Score: 688
Period size: 213 Copynumber: 2.0 Consensus size: 209
2796 GAGAGAGAGG
*
2806 AGAGAGAGAGAGAGAGCAGCGTGACAGTTCACCTTCATTAAAAAAAGCTCCAAGTGGAAGGAAAT
1 AGAGAGAGAGAGAGAGCAGCGTGACAGTTCACCTTCATTAAAAAAAGCTCCAAATGGAAGGAAAT
2871 CTAGCCAACTCACCAATAGAGAGACAACAGCAACAGAGAGAAATGCAAACAGAAAAGACACAATC
66 CTAGCCAACTCACCAATAGAGAGACAACAGCAACAGAGAGAAATGCAAACAGAAAAGACACAATC
*
2936 AAGCAATCACCAAAAGCAGAAAAGGAAATCAGCAACAAGCAAATGGCGACACAATTCACAAGAAA
131 AAGCAATCAACAAAAGCAGAAAAGGAAATCAGCAACAAGCAAATGGCGACACAATTCACAAGAAA
*
3001 CAACCAGCGCAATC
196 CAACCAGCACAATC
*
3015 AGAGAGAGAGAG-GAGCAGTGTGACAAATAGTTCACCTTCA-TAAAAAAAGCTCCAAATGGAAGG
1 AGAGAGAGAGAGAGAGCAGCGTGAC----AGTTCACCTTCATTAAAAAAAGCTCCAAATGGAAGG
* * * *
3078 AAATCTAGCCAACTACACCAATAGAGAGACAACAGCAACAGAGAGAACTGCAAAACAGGAAGGTC
62 AAATCTAGCCAACT-CACCAATAGAGAGACAACAGCAACAGAGAGAAATGC-AAACAGAAAAGAC
* *
3143 ACAATCAAGCAATCAACAAAAGCAGAAAAGGAAATCAGCAACAAGCAAATGGTGACACGATTCAC
125 ACAATCAAGCAATCAACAAAAGCAGAAAAGGAAATCAGCAACAAGCAAATGGCGACACAATTCAC
3208 AAGAAACAACCAGCACAATC
190 AAGAAACAACCAGCACAATC
3228 A
1 A
3229 ATGACAAGCA
Statistics
Matches: 198, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
208 11 0.06
209 12 0.06
211 36 0.18
212 47 0.24
213 92 0.46
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (209 bp):
AGAGAGAGAGAGAGAGCAGCGTGACAGTTCACCTTCATTAAAAAAAGCTCCAAATGGAAGGAAAT
CTAGCCAACTCACCAATAGAGAGACAACAGCAACAGAGAGAAATGCAAACAGAAAAGACACAATC
AAGCAATCAACAAAAGCAGAAAAGGAAATCAGCAACAAGCAAATGGCGACACAATTCACAAGAAA
CAACCAGCACAATC
Found at i:8667 original size:25 final size:25
Alignment explanation
Indices: 8633--8683 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
8623 AATTAATCAA
*
8633 CCAAAAACCATAAATCATTGATCTT
1 CCAAAAACCAGAAATCATTGATCTT
8658 CCAAAAACCAGAAATCATTGATCTT
1 CCAAAAACCAGAAATCATTGATCTT
8683 C
1 C
8684 ATCCAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.25
Consensus pattern (25 bp):
CCAAAAACCAGAAATCATTGATCTT
Found at i:16751 original size:6 final size:6
Alignment explanation
Indices: 16706--16747 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
16696 CAGCTTGAAG
*
16706 ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA GCAGCA
1 ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA
16748 GCAGTAATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.48, C:0.33, G:0.19, T:0.00
Consensus pattern (6 bp):
ACAGCA
Found at i:25866 original size:23 final size:23
Alignment explanation
Indices: 25839--25882 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
25829 CTTCACCTTC
*
25839 TTTTAATTAGCAATAATATGTTT
1 TTTTAATTAACAATAATATGTTT
25862 TTTTAATTAACAATAATATGT
1 TTTTAATTAACAATAATATGT
25883 CACCATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTTAATTAACAATAATATGTTT
Found at i:26199 original size:14 final size:15
Alignment explanation
Indices: 26172--26202 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
26162 GAATTGAATA
26172 AATTATTAAAAAATT
1 AATTATTAAAAAATT
26187 AATTATT-AAAAATT
1 AATTATTAAAAAATT
26201 AA
1 AA
26203 ATTCAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATTATTAAAAAATT
Found at i:26205 original size:15 final size:16
Alignment explanation
Indices: 26170--26205 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
26160 TTGAATTGAA
26170 TAAATTATTAAAAAAT
1 TAAATTATTAAAAAAT
26186 T-AATTATT-AAAAAT
1 TAAATTATTAAAAAAT
26200 TAAATT
1 TAAATT
26206 CAAGTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.37
15 11 0.58
16 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTATTAAAAAAT
Found at i:27741 original size:22 final size:22
Alignment explanation
Indices: 27711--27755 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
27701 AACTGATTAG
27711 AGTCATTTTTTACCATATTTAT
1 AGTCATTTTTTACCATATTTAT
* **
27733 AGTCTTTTTTTTTCATATTTAT
1 AGTCATTTTTTACCATATTTAT
27755 A
1 A
27756 ATGGTATTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.60
Consensus pattern (22 bp):
AGTCATTTTTTACCATATTTAT
Found at i:27946 original size:24 final size:24
Alignment explanation
Indices: 27914--27965 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
27904 ATGAAACCCT
*
27914 TTAAAGGGACTGCTAATAGACAGC
1 TTAAAGGGACTGCTAATAAACAGC
27938 TTAAAGGGACTGCTAATAAACAGC
1 TTAAAGGGACTGCTAATAAACAGC
27962 TTAA
1 TTAA
27966 TAATTTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.23
Consensus pattern (24 bp):
TTAAAGGGACTGCTAATAAACAGC
Found at i:33700 original size:15 final size:15
Alignment explanation
Indices: 33680--33709 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33670 GATTTAGTAT
*
33680 GTTTGAGTCAGTTGA
1 GTTTGAATCAGTTGA
33695 GTTTGAATCAGTTGA
1 GTTTGAATCAGTTGA
33710 ATTTCTTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (15 bp):
GTTTGAATCAGTTGA
Found at i:33821 original size:245 final size:245
Alignment explanation
Indices: 33391--33877 Score: 920
Period size: 245 Copynumber: 2.0 Consensus size: 245
33381 CCCACAAATT
* *
33391 TGATCTGTTTGGGTTTTTAGTCTCCAGAACTTTAGATTTAGGATGTTTGAGTCGGTTGAGTTTGA
1 TGATCTGTTTGGGTTTTTAGTCTCCAGAACTCTAGATTTAGGATGTTTGAGTCAGTTGAGTTTGA
33456 ATCAGTTGAATTTCTTGTGTTAGTTTGTTTTGAGTTTACAATAAATTGTGATTATTTACTCCATA
66 ATCAGTTGAATTTCTTGTGTTAGTTTGTTTTGAGTTTACAATAAATTGTGATTATTTACTCCATA
*
33521 TTAATATGAGTTTACTTTATAATCATTGGATCTAAAAGTAGTTTTTTGGATCTCTCACTTTTTTA
131 TTAATATGAGTTTACTTTATAATCATTGGATCTAAAAGTAGTTTTTTGGATCTCTCACCTTTTTA
*
33586 ACGTTGGTGAAAGTATTCTGTTGGAACAGAAGCAAAAGTGAGAAGTATTC
196 ACGTTGGTGAAAGTATTCTGTTGGAACAAAAGCAAAAGTGAGAAGTATTC
*
33636 TGATCTGTTTGGGTTTTTAGTCTCCAGAACTCTAGATTTAGTATGTTTGAGTCAGTTGAGTTTGA
1 TGATCTGTTTGGGTTTTTAGTCTCCAGAACTCTAGATTTAGGATGTTTGAGTCAGTTGAGTTTGA
33701 ATCAGTTGAATTTCTTGTGTTAGTTTGTTTTGAGTTTACAATAAATTGTGATTATTTACTCCATA
66 ATCAGTTGAATTTCTTGTGTTAGTTTGTTTTGAGTTTACAATAAATTGTGATTATTTACTCCATA
*
33766 TTAATATGGGTTTACTTTATAATCATTGGATCTAAAAGTAGTTTTTTGGATCTCTCACCTTTTTA
131 TTAATATGAGTTTACTTTATAATCATTGGATCTAAAAGTAGTTTTTTGGATCTCTCACCTTTTTA
33831 ACGTTGGTGAAAGTATTCTGTTGGAACAAAAGCAAAAGTGAGAAGTA
196 ACGTTGGTGAAAGTATTCTGTTGGAACAAAAGCAAAAGTGAGAAGTA
33878 ATGAGAAGGT
Statistics
Matches: 236, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
245 236 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (245 bp):
TGATCTGTTTGGGTTTTTAGTCTCCAGAACTCTAGATTTAGGATGTTTGAGTCAGTTGAGTTTGA
ATCAGTTGAATTTCTTGTGTTAGTTTGTTTTGAGTTTACAATAAATTGTGATTATTTACTCCATA
TTAATATGAGTTTACTTTATAATCATTGGATCTAAAAGTAGTTTTTTGGATCTCTCACCTTTTTA
ACGTTGGTGAAAGTATTCTGTTGGAACAAAAGCAAAAGTGAGAAGTATTC
Done.