Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009497.1 Corchorus capsularis cultivar CVL-1 contig09518, 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: 36641
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:854 original size:332 final size:332
Alignment explanation
Indices: 79--2399 Score: 3613
Period size: 332 Copynumber: 7.0 Consensus size: 332
69 CGAAATCGTG
* * *
79 CGGTTTTTGACTAAAATCGCGTTCCGGGGCTCCAGCTCATTTTTGTATGATTTTTAGTGACGAGA
1 CGGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGA
* * * **
144 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCACCCACAATAGATTTGAGGAAATATTTTT
66 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
* *
209 ACTAGCATCTAAATCTTGTTTTGATTGAATCAGAAATTAATTTAGAAAAAAAATTGGAAAACGAT
131 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAG-AAAAAAATTGGAAAACGAT
* * * *
274 ATTAGAAACGTTAAAAGCCCTTCAAAATTTTTGGCCATTGAATTATATATTTTTTATGAT-TATT
195 ATTAGAAACGTTAAAAGCCCTTCAAACTTTTTTG-CATTGAATTATATATTTTTTATG-TGTGTC
* *
338 TTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
258 TAGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
403 CTAACCATCA
323 CTAACCATCA
* * *
413 CGGTTTTTGACTAAAAACGCGTTCCGGGGCAACAACTCATTTTTGTATGATTTTTGGTGACGAGA
1 CGGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGA
*
478 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTCAGGATTTA-TTTT
66 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
*
542 ACGAGCATCTAAATCTTGTTTTGATTTAATCAAAAATTAATTTAGAAAAAAAATTGGAAAACGAT
131 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAG-AAAAAAATTGGAAAACGAT
*
607 ATTAGAAACGTTAAAAGCCCTTCAAATTTTTTTGCATTGAATTATATATTTTTTTATGTGTGTCT
195 ATTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATA-TTTTTTATGTGTGTCT
**
672 AGGCCAAAAAGAAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-C
259 AGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
736 TAACCATCA
324 TAACCATCA
* * *
745 CGGTTTTTGATTAAAAACGCGTTCCGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGA
1 CGGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGA
* * ** * *
810 GCCCTTAAAATTTCTATATTCATCTAATAAAATCTCAGCCACACTAGATTTCAGAATTTATTTTT
66 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
*
875 ACGAGCATCTAAATCTTGTTTTGATTGAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATA
131 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATA
* * * * *
940 TTAGAAACGTTAAAAGCCCTTCAAAATTTTTGGCATTGAATTATATATTTTTTATGAT-TATTTT
196 TTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATG-TGTGTCTA
* *
1004 GGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACT
260 GGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
*
1069 AACCCTCA
325 AACCATCA
* * * *
1077 CAGTTTTTGACTAAAACCGCATTCCGGGGCACCAGCTCA-TTTTGTATGATTTTTGGTAATGAGA
1 CGGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGA
1141 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
66 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
* * *
1206 ACGAGCATCTAAATCTTGTTTTGATATAATCAAAAATTAATCTAGAAAAAAAATTGGAAAACGAT
131 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAG-AAAAAAATTGGAAAACGAT
*
1271 ATTAGAAACGTTAAAAGCCCTTCAAATTTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTA
195 ATTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTA
* * * *
1336 GGCTAAAAATAAAGGAAATATATTTCGGG-CTAATTTTTGCAAAATTTTAGCCGAAATCATGTAC
260 GGCCAAAAATTAAGGAAAAATATTTCGGGTC-AATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
1400 TAACCATCA
324 TAACCATCA
* *
1409 CAGTTTTTGACTAAAACCGCGTTCCGGAGCACCAGCTCA-TTTTGTATGATTTTTGGTGACGAGA
1 CGGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGA
*
1473 GCCTTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
66 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
* *
1538 ACGAACATCTAAATCTTGTTTTGATTTAATTAGAAATTAATTTAGAAAAAAATTGGAAAACGATA
131 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATA
* * * * * * *
1603 TTAGAAACGTTAATAGCCGTTCAAACTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTG
196 TTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAG
* *
1668 GCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTG-----
261 GCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTA
1728 -------
326 ACCATCA
* * * *
1728 CGGTTTTTGACTAAAATCGTGTTCCGGGGCACCAGCTC-CTTTTGTATGATTTTTGGTGATGAGA
1 CGGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGA
1792 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
66 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
1857 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATA
131 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATA
1922 TTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAG
196 TTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAG
* *
1987 GCCAAAAATTAAGGAAAAATATTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGAACTA
261 GCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTA
2052 ACCATCA
326 ACCATCA
* *
2059 CAGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGATGAGA
1 CGGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGA
* * * * *
2124 GCCATTAAAATATCTATA-TCATCTAACCAAATCTCAACCAAATTGGATTTTAGGATTTATTTTT
66 GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
*
2188 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAAATTAGAAAAAAATTGGAAAACGATA
131 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATA
* * *
2253 TTAGAAATGTTAAAAGTCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTTATCTGTGTCTA
196 TTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATA-TTTTTTATGTGTGTCTA
* * *
2318 GGCCAAAAATAAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTAAT
260 GGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
*
2383 AACCGTCA
325 AACCATCA
2391 CGGTTTTTG
1 CGGTTTTTG
2400 TAATACCGTA
Statistics
Matches: 1832, Mismatches: 131, Indels: 50
0.91 0.07 0.02
Matches are distributed among these distances:
319 300 0.16
331 510 0.28
332 691 0.38
333 216 0.12
334 115 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (332 bp):
CGGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGA
GCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACACTAGATTTTAGGATTTATTTTT
ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATA
TTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAG
GCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTA
ACCATCA
Found at i:1967 original size:982 final size:983
Alignment explanation
Indices: 1--2399 Score: 3683
Period size: 982 Copynumber: 2.4 Consensus size: 983
*
1 ATTTTTTATGAGTATTTTGGCC-AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTT
1 ATTTTTTATGATTATTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTT
* * * *
65 TAACCGAAATCGTG----------CGGTTTTTGACTAAAATCGCGTTCCGGGGCTCCAGCTCATT
66 TAGCCGAAATCGTGACTAACCTCACAGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATT
* * *
120 TTTGTATGATTTTTAGTGACGAGAGCCGTTAAAATATCTATATTCATCTAACCAAATCTCACCCA
131 TTTGTATGATTTTTGGTGATGAGAGCCGTTAAAATATCTATATTCATCTAACCAAATCTCAACCA
* ** *
185 CAATAGATTTGAGGAAATATTTTTACTAGCATCTAAATCTTGTTTTGATTGAATCAGAAATTAAT
196 CAATAGATTTTAGGATTTATTTTTACGAGCATCTAAATCTTGTTTTGATT-AATCAGAAATTAA-
*
250 TTAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAATTTTTGGCCATTGA
259 TTAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAATTTTTTG-CATTGA
* * * **
315 ATTATATATTTTTTATGAT-TATTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTG
323 ATTATATATTTTTTATG-TGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCGGGTCAATTTTTG
*
379 CAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGGGCA
387 CAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGAGCA
444 ACAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTATATTCATCTAACCAA
452 ACAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTATATTCATCTAACCAA
*
509 ATCTCAGCCACACTAGATTTCAGGATTTATTTTACGAGCATCTAAATCTTGTTTTGATTTAATCA
517 ATCTCAGCCACACTAGATTTCAGGATTTATTTTACGAACATCTAAATCTTGTTTTGATTTAATCA
*
574 AAAATTAATTTAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAATTTTTT
582 AAAATTAATTTAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTTTTT
* * *
639 TGCATTGAATTATATATTTTTTTATGTGTGTCTAGGCCAAAAAGAAAGGAAAAATATTTCGGGTC
647 GGCATTGAATTATATATTTTTTTATGAGTATCTAGGCCAAAAAGAAAGGAAAAATATTTCGGGTC
* *
704 AATTTTTGCAAAATTTTAGCCGAAATCGTGTCTAACCATCACGGTTTTTGATTAAAAACGCGTTC
712 AATTTTTACAAAATTTTAGCCGAAATCGTG----------ACGGTTTTTGACTAAAAACGCGTTC
* *
769 CGGGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCCTTAAAATTTCTATATTCATC
767 CGGGGCACCAACTCACTTTTGTATGATTTTTGGTGACGAGAGCCCTTAAAATATCTATATTCATC
*
834 TAATAAAATCTCAGCCACACTAGATTTCAGAATTTATTTTTACGAGCATCTAAATCTTGTTTTGA
832 TAACAAAATCTCAGCCACACTAGATTTCAGAATTTATTTTTACGAGCATCTAAATCTTGTTTTGA
899 TTGAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAA
897 TTGAATCAGAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAA
964 AATTTTTGGCATTGAATTATAT
962 AATTTTTGGCATTGAATTATAT
986 ATTTTTTATGATTATTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTT
1 ATTTTTTATGATTATTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTT
* *
1051 TTGCCGAAATCGTGTACTAACCCTCACAGTTTTTGACTAAAACCGCATTCCGGGGCACCAGCTCA
66 TAGCCGAAATCGTG-ACTAA-CCTCACAGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCA
* *
1116 -TTTTGTATGATTTTTGGTAATGAGAGCCGTTAAAATATCTATATTCATCTAACCAAATCTCAGC
129 TTTTTGTATGATTTTTGGTGATGAGAGCCGTTAAAATATCTATATTCATCTAACCAAATCTCAAC
* *
1180 CACACTAGATTTTAGGATTTATTTTTACGAGCATCTAAATCTTGTTTTGATATAATCAAAAATTA
194 CACAATAGATTTTAGGATTTATTTTTACGAGCATCTAAATCTTGTTTTGAT-TAATCAGAAATTA
*
1245 ATCTAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAATTTTTTTGCATTG
258 AT-TAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAATTTTTTGCATTG
* *
1310 AATTATATATTTTTTATGTGTGTCTAGGCTAAAAATAAAGGAAATATATTTCGGG-CTAATTTTT
322 AATTATATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCGGGTC-AATTTTT
* * *
1374 GCAAAATTTTAGCCGAAATCATGTACTAACCATCACAGTTTTTGACTAAAACCGCGTTCCGGAGC
386 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGAGC
* * *
1439 ACCAGCTCA-TTTTGTATGATTTTTGGTGACGAGAGCCTTTAAAATATCTATATTCATCTAACCA
451 AACAACTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTATATTCATCTAACCA
*
1503 AATCTCAGCCACACTAGATTTTAGGATTTATTTTTACGAACATCTAAATCTTGTTTTGATTTAAT
516 AATCTCAGCCACACTAGATTTCAGGATTTA-TTTTACGAACATCTAAATCTTGTTTTGATTTAAT
* * * *
1568 TAGAAATTAATTTAG-AAAAAAATTGGAAAACGATATTAGAAACGTTAATAGCCGTTCAAACTTT
580 CAAAAATTAATTTAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTTT
* * ***
1632 TTGGCATTGAATTATATA-TTTTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATATTTCGGG
645 TTGGCATTGAATTATATATTTTTTTATGAGTATCTAGGCCAAAAAGAAAGGAAAAATATTTCGGG
* *
1696 TCAATTTTTACAAAATTTTAGCCGAAATCGTG-CGGTTTTTGACTAAAATCGTGTTCCGGGGCAC
710 TCAATTTTTACAAAATTTTAGCCGAAATCGTGACGGTTTTTGACTAAAAACGCGTTCCGGGGCAC
* * * *
1760 CAGCTC-CTTTTGTATGATTTTTGGTGATGAGAGCCGTTAAAATATCTATATTCATCTAACCAAA
775 CAACTCACTTTTGTATGATTTTTGGTGACGAGAGCCCTTAAAATATCTATATTCATCTAACAAAA
* * *
1824 TCTCAGCCACACTAGATTTTAGGATTTATTTTTACGAGCATCTAAATCTTGTTTTGATTTAATCA
840 TCTCAGCCACACTAGATTTCAGAATTTATTTTTACGAGCATCTAAATCTTGTTTTGATTGAATCA
* *
1889 GAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTTTTTT
905 GAAATTAATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAATTTTTG
1954 GCATTGAATTATAT
970 GCATTGAATTATAT
* * * * *
1968 ATTTTTTATG-TGTGTCTAGGCCAAAAATTAAGGAAAAATATTTCGGTTCAATTTTTGCAAAATT
1 ATTTTTTATGAT-TATTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATT
2032 TTAGCCGAAATCGTGAACTAACCATCACAGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTC
65 TTAGCCGAAATCGTG-ACTAACC-TCACAGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTC
*
2097 ATTTTTGTATGATTTTTGGTGATGAGAGCCATTAAAATATCTATA-TCATCTAACCAAATCTCAA
128 ATTTTTGTATGATTTTTGGTGATGAGAGCCGTTAAAATATCTATATTCATCTAACCAAATCTCAA
*
2161 CCA-AATTGGATTTTAGGATTTATTTTTACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAAT
193 CCACAA-TAGATTTTAGGATTTATTTTTACGAGCATCTAAATCTTGTTTTGA-TTAATCAGAAAT
* * *
2225 TAAATTAG-AAAAAAATTGGAAAACGATATTAGAAATGTTAAAAGTCCTTCAAACTTTTTTGCAT
256 T-AATTAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAATTTTTTGCAT
*
2289 TGAATTATATATTTTTTTATCTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCGGGTCAATTT
320 TGAATTATATA-TTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCGGGTCAATTT
* * *
2354 TTGCAAAATTTTAGCTGAAATCGTGTAATAACCGTCACGGTTTTTG
384 TTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
2400 TAATACCGTA
Statistics
Matches: 1299, Mismatches: 89, Indels: 55
0.90 0.06 0.04
Matches are distributed among these distances:
981 68 0.05
982 476 0.37
983 80 0.06
985 21 0.02
986 54 0.04
994 70 0.05
995 148 0.11
996 173 0.13
997 173 0.13
998 36 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (983 bp):
ATTTTTTATGATTATTTTGGCCAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTT
TAGCCGAAATCGTGACTAACCTCACAGTTTTTGACTAAAACCGCGTTCCGGGGCACCAGCTCATT
TTTGTATGATTTTTGGTGATGAGAGCCGTTAAAATATCTATATTCATCTAACCAAATCTCAACCA
CAATAGATTTTAGGATTTATTTTTACGAGCATCTAAATCTTGTTTTGATTAATCAGAAATTAATT
AGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAATTTTTTGCATTGAATT
ATATATTTTTTATGTGTGTCTAGGCCAAAAATAAAGGAAAAATATTTCGGGTCAATTTTTGCAAA
ATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCGGAGCAACAA
CTCATTTTTGTATGATTTTTGGTGACGAGAGCCGTTAAAATATCTATATTCATCTAACCAAATCT
CAGCCACACTAGATTTCAGGATTTATTTTACGAACATCTAAATCTTGTTTTGATTTAATCAAAAA
TTAATTTAGAAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAACTTTTTGGCA
TTGAATTATATATTTTTTTATGAGTATCTAGGCCAAAAAGAAAGGAAAAATATTTCGGGTCAATT
TTTACAAAATTTTAGCCGAAATCGTGACGGTTTTTGACTAAAAACGCGTTCCGGGGCACCAACTC
ACTTTTGTATGATTTTTGGTGACGAGAGCCCTTAAAATATCTATATTCATCTAACAAAATCTCAG
CCACACTAGATTTCAGAATTTATTTTTACGAGCATCTAAATCTTGTTTTGATTGAATCAGAAATT
AATTTAGAAAAAAATTGGAAAACGATATTAGAAACGTTAAAAGCCCTTCAAAATTTTTGGCATTG
AATTATAT
Found at i:3351 original size:11 final size:12
Alignment explanation
Indices: 3337--3379 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 12
3327 AAAATAAAAA
3337 AAAAATT-AATT
1 AAAAATTAAATT
3348 AAAAATTAAATT
1 AAAAATTAAATT
3360 AAATTAAATTAAATT
1 -AA--AAATTAAATT
3375 AAAAA
1 AAAAA
3380 CTTTTTGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 2 0.07
14 2 0.07
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:3358 original size:5 final size:5
Alignment explanation
Indices: 3350--3377 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3340 AATTAATTAA
3350 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
3378 AACTTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:4315 original size:15 final size:15
Alignment explanation
Indices: 4295--4328 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4285 ATTGGATTTA
4295 TTATTACTAA-TTGTT
1 TTATTA-TAACTTGTT
4310 TTATTATAACTTGTT
1 TTATTATAACTTGTT
4325 TTAT
1 TTAT
4329 AAGTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (15 bp):
TTATTATAACTTGTT
Found at i:6070 original size:332 final size:330
Alignment explanation
Indices: 4890--7066 Score: 2344
Period size: 332 Copynumber: 6.5 Consensus size: 330
4880 GGGTGTGACA
*
4890 GTTTTTGACTAAAAACACGTTCC-GAGGCACCAACTCATTTTTGTATGATTTTTGGTGACGAGAG
1 GTTTTTGA-TAAAAACACGTTCCGGA-GCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAG
4954 CCGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTA
64 CCGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTA
*
5019 CGAGCATCTAAATCTTGTTTTGATTTAATCAGAAAATAATTTAGAAAAAAATTGGAAAACGATAT
129 CGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAG-AAAAAATTGGAAAACGATAT
*
5084 TAGAAACGTTAAAAGCCCTTCAAACTTTTTCGCATTGAATTATATATTTTTTATGAGTATTTTGG
193 TAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGAGTATTTTGG
* * *
5149 CCAAAAATAAAGGGAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAT
258 CCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
5214 CCATCACG
323 CCATCACG
* ** * * * *
5222 GTTCTTGACTAAAAAGGCATTCTGGGGCACCAGCTCATTTTTGTATGATTTTTGGTGACAAGAGC
1 GTTTTTGA-TAAAAACACGTTCCGGAGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGC
5287 CGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTAC
65 CGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTAC
* * *
5352 GAGCATCTAAATCTTGTTTTGATATAATCAAAAATTAATTTTAAAAAAAAATTGGAAAACGATAT
130 GAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAA-TTT-AGAAAAAATTGGAAAACGATAT
* ** * * *
5417 TAGAAACGTTAAAAGCCATTCAAACTTTTTTGCATTGAATTATATATTTTTTATGTCTGTCTAGG
193 TAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGAGTATTTTGG
* * ** *
5482 CCAAAAATAAAGGAAGAATATTTCGAATCAATTTTTGCAAAATTTTAGCTGAAATCGTGTACTAA
258 CCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
*
5547 TCATCACG
323 CCATCACG
* * *
5555 GTTTTTGACTAAAAACGCGTTCCGGGGCACCAGCTCATTTTTGTATGATTTTTGGAGACGAGAGC
1 GTTTTTGA-TAAAAACACGTTCCGGAGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGC
*
5620 CGTTAAAATATCTATATTCATCTAATCAAATCTCAGTCACACTAGATTTGAGGATTTATTTTTAC
65 CGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTAC
5685 GAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAATTGGAAAACGATATTA
130 GAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAATTGGAAAACGATATTA
* * * * *
5750 GAAACGTTAAAAGCCCTTCAAAATTTTTTGCATTGAATTATATATTTTTTATGTGTGTCTAGGCC
195 GAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGAGTATTTTGGCC
*
5815 AAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACC
260 AAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
5880 ATCACG
325 ATCACG
* *
5886 GTTTTTGATAAAAAAACACGTTCCGGAGCACCAGCTCAGTTTTT-TTTAATTTTTGGTGACGAGA
1 GTTTTTGAT--AAAAACACGTTCCGGAGCACCAGCTCA-TTTTTGTATGATTTTTGGTGACGAGA
* * **
5950 GCCGTTAAAATATCCATATTCATCTAACCAAATCTCAGCCATTCTAGATTTGAGGATTTATTTTT
63 GCCGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTT
* *
6015 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAACAATTGGAAAACAATAT
128 ACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAATTGGAAAACGATAT
* * *
6080 TAGAAACGTTAAAAGCCCTTCAAACTTTTTGGCTTTGAATTATATATTTTTTATGTGTATTTTGG
193 TAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGAGTATTTTGG
* * * *
6145 CCAAAAATTGAGGAAAAATATTTAGGGTCAATTTTTGAAAAATTTTAGCTGAAATCGTGTACTAA
258 CCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA
*
6210 CCATCATG
323 CCATCACG
* ** * * * * * *
6218 GTTTTTTGCTAAAAACGTGTTTC-GAGGC-CCCGACTCAGTTTTGCATGATTTTTGGCGCCGAGA
1 G-TTTTTGATAAAAACACGTTCCGGA-GCACCAG-CTCATTTTTGTATGATTTTTGGTGACGAGA
* * * *
6281 -CTCGTTAAAATATTTATATTCATCTGACCAAATCTCAGCCACAATGGATTCAAGATTTTTTTTT
63 GC-CGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCAC-----A--CTAGA------TTT
** * * * ** * * *
6345 GTTTG-TTTGTTTTTAAGAGCATC-AGAAACAGGTTTCGATTTAATTAGAATTTAGAAATTAGTT
114 G-AGGATTTATTTTTACGAGCATCTA-AATCTTGTTTTGATTTAATCAGAAATT---AA-T--TT
* * * * * * *
6408 CTGAAAAACTAGGGAAAACGATATTAGAAGCGTGAAAA-CCCTTCCAATCTTTTTGGCATTGAAT
171 -AGAAAAAAT-TGGAAAACGATATTAGAAACGTTAAAAGCCCTT-CAAACTTTTTTGCATTGAAT
* ** * * * *
6472 TATATATTTCTTATGAGTATTTTGGGGAAAAAATTGAGGGAAAATATTTCGGCTTAATTTTTGCA
233 TATATATTTTTTATGAGTATTTT-GGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCA
* *
6537 AAATTTTATCCGAAATCGTG---T-A-CATCA-T
297 AAATTTTAGCCGAAATCGTGTACTAACCATCACG
* * * * * * *
6565 GTTTTTGGCTAAAAACGCGCTCCGGGACCA-CAGCTCAGTTTTT-CATGATTTTTGGCGCCGA-A
1 GTTTTT-GATAAAAACACGTTCC-GGAGCACCAGCTCA-TTTTTGTATGATTTTTGGTGACGAGA
* * * * * * ** * *
6627 ACTCTTTGAAATATCAATATTCATCTAATCAAATCTCAACCACA-TGGGATTT-AAAATATGTTT
63 GC-CGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACT-AGATTTGAGGATTTATTT
* * * * * *
6690 TTACGAGCATTTGAATCTTATTTCGATTTAATTATAAATTAA-TTAGGAAGAAAATTGGAAAAAC
126 TTACGAGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTA-GAA-AAAATTGG-AAAAC
* * * *
6754 GATATTATAAGCGTTAAAAGCCCTTCAATCTTTTTTGCATTGAATTATATATTTTTTACGAGTAT
188 GATATTAGAAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGAGTAT
* * * * *
6819 TTTGGCCAAAAATTAAGGAAAATTATTTCGGATCAATTTTTGGAAAAATTTAGCCAAAATCGTGT
253 TTTGGCCAAAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
6884 ACTAA--AGT--C-
318 ACTAACCA-TCACG
* * * * * * ** * * * * *
6893 G-TTTTGCTAAAAACGCGTT-CTGAG-ACCCCGACTTAGTTTTAAATGATTTTTTGCGCCAAAAG
1 GTTTTTGATAAAAACACGTTCCGGAGCA-CCAG-CTCATTTTTGTATGATTTTTGGTGACGAGAG
* * * * * * *
6955 TCGTTCAAATATCTATATTCATCTAACCAAATATCAGCCACATTGGATTTGAGGATTTGTTTTTA
64 CCGTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTA
* * * *
7020 CGAGCATC-ACAAACGTGTTTCGATTTAAT-AGAAATTTATTTAGAAAA
129 CGAGCATCTA-AATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAA
7067 TATTTCGGGT
Statistics
Matches: 1589, Mismatches: 192, Indels: 135
0.83 0.10 0.07
Matches are distributed among these distances:
323 1 0.00
324 2 0.00
325 9 0.01
326 139 0.09
327 109 0.07
328 6 0.00
329 2 0.00
330 15 0.01
331 224 0.14
332 450 0.28
333 355 0.22
334 4 0.00
338 4 0.00
340 2 0.00
342 1 0.00
343 1 0.00
344 41 0.03
345 1 0.00
346 6 0.00
347 73 0.05
348 13 0.01
349 3 0.00
350 3 0.00
351 11 0.01
352 62 0.04
353 52 0.03
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (330 bp):
GTTTTTGATAAAAACACGTTCCGGAGCACCAGCTCATTTTTGTATGATTTTTGGTGACGAGAGCC
GTTAAAATATCTATATTCATCTAATCAAATCTCAGCCACACTAGATTTGAGGATTTATTTTTACG
AGCATCTAAATCTTGTTTTGATTTAATCAGAAATTAATTTAGAAAAAATTGGAAAACGATATTAG
AAACGTTAAAAGCCCTTCAAACTTTTTTGCATTGAATTATATATTTTTTATGAGTATTTTGGCCA
AAAATTAAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
TCACG
Found at i:9088 original size:6 final size:6
Alignment explanation
Indices: 9079--9106 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9069 ATCAATATCT
9079 CCATCA CCATCA CCATCA CCATCA CCAT
1 CCATCA CCATCA CCATCA CCATCA CCAT
9107 TGTTCACGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CCATCA
Found at i:14253 original size:39 final size:39
Alignment explanation
Indices: 14199--14277 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
14189 GTAACGAACA
*
14199 GAAAGGTAAGAAATTTAAAGGCTGTAATCCAGCAATGGG
1 GAAAGGTAAGAAATTTAAAGACTGTAATCCAGCAATGGG
14238 GAAAGGTAAGAAATTTAAAGACTGTAATCCAGCAATGGG
1 GAAAGGTAAGAAATTTAAAGACTGTAATCCAGCAATGGG
14277 G
1 G
14278 CAATAATTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.42, C:0.10, G:0.28, T:0.20
Consensus pattern (39 bp):
GAAAGGTAAGAAATTTAAAGACTGTAATCCAGCAATGGG
Found at i:16469 original size:24 final size:24
Alignment explanation
Indices: 16441--16512 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
16431 TTCCCCCCCT
16441 AATGTCATGCATCACCCTCTCTAA
1 AATGTCATGCATCACCCTCTCTAA
***
16465 AATGT-ACTGC-T--GTTTC-CT-A
1 AATGTCA-TGCATCACCCTCTCTAA
16484 -ATGTCATGCATCACCCTCTCTAA
1 AATGTCATGCATCACCCTCTCTAA
16507 AATGTC
1 AATGTC
16513 CTGCTGTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 16
0.61 0.11 0.29
Matches are distributed among these distances:
18 7 0.21
19 3 0.09
20 2 0.06
21 4 0.12
22 2 0.06
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (24 bp):
AATGTCATGCATCACCCTCTCTAA
Found at i:16485 original size:42 final size:42
Alignment explanation
Indices: 16438--16519 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
16428 TCTTTCCCCC
16438 CCTAATGTCATGCATCACCCTCTCTAAAATGTACTGCTGTTT
1 CCTAATGTCATGCATCACCCTCTCTAAAATGTACTGCTGTTT
*
16480 CCTAATGTCATGCATCACCCTCTCTAAAATGTCCTGCTGT
1 CCTAATGTCATGCATCACCCTCTCTAAAATGTACTGCTGT
16520 CAAAAATGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (42 bp):
CCTAATGTCATGCATCACCCTCTCTAAAATGTACTGCTGTTT
Found at i:21186 original size:2 final size:2
Alignment explanation
Indices: 21179--21206 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21169 GTATGCAGAG
21179 TA 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 TA
21207 CTCCATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21731 original size:6 final size:6
Alignment explanation
Indices: 21715--21750 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
21705 CATGCTTACT
21715 TCTGCCC TCTGCC TCTGCC TCTGCC TCTGCC TCTGC
1 TCTG-CC TCTGCC TCTGCC TCTGCC TCTGCC TCTGC
21751 TGGGCTATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
TCTGCC
Found at i:22625 original size:16 final size:16
Alignment explanation
Indices: 22604--22634 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
22594 CCGTCTGGTA
22604 TATATGCACTATGCAC
1 TATATGCACTATGCAC
22620 TATATGCACTATGCA
1 TATATGCACTATGCA
22635 ATGCATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (16 bp):
TATATGCACTATGCAC
Found at i:23431 original size:2 final size:2
Alignment explanation
Indices: 23424--23453 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23414 TTATCAATCA
23424 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
23454 TATTAATTAT
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:33333 original size:16 final size:15
Alignment explanation
Indices: 33312--33341 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
33302 GGGAGAGAGA
33312 TTTGAGAAGTAGAAAG
1 TTTGAGAAG-AGAAAG
33328 TTTGAGAAGAGAAA
1 TTTGAGAAGAGAAA
33342 TAGAGAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (15 bp):
TTTGAGAAGAGAAAG
Done.