Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020776.1 Corchorus olitorius cultivar O-4 contig20809, 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: 47066
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:700 original size:236 final size:239
Alignment explanation
Indices: 287--928 Score: 919
Period size: 236 Copynumber: 2.7 Consensus size: 239
277 CCCGGCTCAG
* * * * * * *
287 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTCAGGCT
1 TTTTGCATGATTTTTGACATAAATACTCTTTGAAATATCTATATTCATCGAACCAATCTCAAGCT
* * * *
352 CTGAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGGATATTGTTTCGATTTAATCAG
66 CTGAGCCACATTAGATTTAAGTATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
*
417 AAACAGATTCGGAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAA-TTTTTTT
131 AAATAGATTCGGAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTT
*
481 TGCGTTGAATTGTGTA-TTTTTTTGCCGAAAATA-TTTTTTTAT
196 TCCGTTGAATTGTGTATTTTTTTTGCCGAAAATATTTTTTTTAT
*
523 TTTTGCATGATTTTTGACATAAATACTCTTTGAAATATCTATATTCATCGAACCAATCTCATGCT
1 TTTTGCATGATTTTTGACATAAATACTCTTTGAAATATCTATATTCATCGAACCAATCTCAAGCT
*
588 CTGAGCCACATTAGATTTAAGTATTTGCTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
66 CTGAGCCACATTAGATTTAAGTATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
*
653 AAATAGATTCGAAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTT
131 AAATAGATTCGGAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTT
*
718 TCCGTTGAATTGTGTATTTTTTTTGCCGAAAATATTTTTTTTTCT
196 TCCGTTGAATTGTGTATTTTTTTTGCCGAAAATA-TTTTTTTTAT
* *
763 TTTTGCATGATTTTTTGACGTAAATACTCTTTGAAATATCTATATTCATCGAA-CAA----AAAC
1 TTTTGCATGA-TTTTTGACATAAATACTCTTTGAAATATCTATATTCATCGAACCAATCTCAAGC
* * ** * *
823 -C-CAGCCACGTCCGATATAAGGTATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
65 TCTGAGCCACATTAGATTTAA-GTATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATT
* * *
886 AGAAATTA-ATTCGGAAAAAAATTGGAAAAATGATATTAAAAGC
129 AGAAA-TAGATTCGGAAAAAAAATAGAAAAATGATATTTAAAGC
929 ATGTAAAGAC
Statistics
Matches: 370, Mismatches: 29, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
234 13 0.04
235 78 0.21
236 178 0.48
237 22 0.06
238 17 0.05
240 21 0.06
241 41 0.11
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (239 bp):
TTTTGCATGATTTTTGACATAAATACTCTTTGAAATATCTATATTCATCGAACCAATCTCAAGCT
CTGAGCCACATTAGATTTAAGTATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
AAATAGATTCGGAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTT
TCCGTTGAATTGTGTATTTTTTTTGCCGAAAATATTTTTTTTAT
Found at i:1681 original size:559 final size:563
Alignment explanation
Indices: 523--1821 Score: 1842
Period size: 559 Copynumber: 2.3 Consensus size: 563
513 ATTTTTTTAT
* * * * *
523 TTTTGCATGATTTTTGACATAAATACTCTTTGAAATATCTATATTCATCGAACCAATCTCATGCT
1 TTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCAAACCAATCTC-TG-T
* *
588 CTGAGCCACATTAGATTTAAGTATTTGCTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
64 CTGAGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
*
653 AAATAGATTCGAAAAAAAAATAGAAAAATGATATTTAAAGCGAG-AAAAATATTTCAATTTTTTT
129 AAATAGATTCG-GAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAAATATTTCAATTTTTTT
*
717 TTCCGTTGAATTGTGTATTTTTTTTGCCGAAAATATTTTTTTTTCTTTTTGCATGATTTTTTGAC
193 TTCCGTTGAATTGTGTA-TTTTTTTGCCGAAAATATTTTTTTTTATTTTTGCATGATTTTTTGAC
*
782 GTAAATACTCTTTGAAATATCTATATTCATCGAACAAAAACCCAGCCACGTCCGATATAAGGTAT
257 GTAAATACTCCTTGAAATATCTATATTCATCGAACAAAAACCCAGCCACGTCCGATATAAGGTAT
* * * *
847 TTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGGA
322 TTGATTTTACGAGCATCTGAATCTTATTTCAATTTAACTAAAAATTAATTCGGAAAAAAATTGGA
* * *
912 AAAATGATATTAAAAGCATGTAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTATCTA
387 AAAACGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGAATTATATATTTTATCTA
* * * * * *
977 AGTATTGTGGCAAAAATTTAGAAAAAAAAATCGGGTCAGTTTTTAGCCGAAAATCGTGTACTAAC
452 AGTATTATGGAAAAAATTAAGAAAAAAAAATCCGATCAGTGTTTAGCCGAAAATCGTGTACTAAC
* * * * *
1042 CATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGGCCTCGGCTCAG
517 CATCATGGTTTTTGGGCTAAAAACGCGTTTCGCGAGCCCCGACTCAA
* ** *
1089 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTGTTCTAACCAATCTCTGGTT
1 TTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCAAACCAATCTCT-G-T
*
1154 CTGAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
64 CTGAGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATTAG
*
1219 AAATAGATTTGGAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAAAT-TTTCAATTTTTTTT
129 AAATAGATTCGGAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAAATATTTCAATTTTTTTT
*
1283 TTCGTTGAATTGTGTA-TTTTTTGCCGAAAATA-TTTTTTTTATTTTTGCATGA-TTTTTGACGT
194 TCCGTTGAATTGTGTATTTTTTTGCCGAAAATATTTTTTTTTATTTTTGCATGATTTTTTGACGT
* *
1345 AAATACTCCTTGAAATATCTATATTCATCGAAC-AAATCCCAGCCACGTTCGATATAA-GTATTT
259 AAATACTCCTTGAAATATCTATATTCATCGAACAAAAACCCAGCCACGTCCGATATAAGGTATTT
*
1408 GTTTTTACGAGCATCTGAATCTTATTTCAATTTAACTAAAAATTAATTCGGAAAAAAA-TGGAAA
324 GATTTTACGAGCATCTGAATCTTATTTCAATTTAACTAAAAATTAATTCGGAAAAAAATTGGAAA
* * * * * *
1472 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAG
389 AACGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGAATTATATATTTTATCTAAG
***
1537 TATTATGGTAAAAAATTAAGAAAAAACTTTTCCGATCAGTGTTTAGCCG-AAATCGTGTACTAAC
454 TATTATGG-AAAAAATTAAGAAAAAA-AAATCCGATCAGTGTTTAGCCGAAAATCGTGTACT---
1601 AACCATCATGGTTTTT-GGCTAAAAACGCG-TTC-CGAGCCCCGACTCAA
514 AACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGCGAGCCCCGACTCAA
*
1648 TTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCAAACCAA---ATGTC-
1 TTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCAAACCAATCTCTGTCT
* ** * *
1709 -AGCCACATTGGACATAAGGATTTGATTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAA
66 GAGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
* * *
1773 ATTA-ATTCGGAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAAA
131 A-TAGATTCGG-AAAAAAA-TAGAAAAATGATATTTAAAGCGAGAAAAAA
1822 CCATCAATCT
Statistics
Matches: 663, Mismatches: 60, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
552 64 0.10
553 9 0.01
554 29 0.04
555 1 0.00
556 1 0.00
558 69 0.10
559 148 0.22
560 41 0.06
561 55 0.08
562 35 0.05
563 16 0.02
565 61 0.09
566 134 0.20
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (563 bp):
TTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCAAACCAATCTCTGTCT
GAGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAA
ATAGATTCGGAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAAATATTTCAATTTTTTTTTC
CGTTGAATTGTGTATTTTTTTGCCGAAAATATTTTTTTTTATTTTTGCATGATTTTTTGACGTAA
ATACTCCTTGAAATATCTATATTCATCGAACAAAAACCCAGCCACGTCCGATATAAGGTATTTGA
TTTTACGAGCATCTGAATCTTATTTCAATTTAACTAAAAATTAATTCGGAAAAAAATTGGAAAAA
CGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGAATTATATATTTTATCTAAGTA
TTATGGAAAAAATTAAGAAAAAAAAATCCGATCAGTGTTTAGCCGAAAATCGTGTACTAACCATC
ATGGTTTTTGGGCTAAAAACGCGTTTCGCGAGCCCCGACTCAA
Found at i:1845 original size:326 final size:325
Alignment explanation
Indices: 1325--2154 Score: 965
Period size: 326 Copynumber: 2.5 Consensus size: 325
1315 TTTTTTTTAT
* ** * *
1325 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAA-CAAATCCCAGCC
1 TTTTGCATGATTTTTGGCACAAATACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCC
* * * * *
1389 ACGTTCGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTATTTCAATTTAACTAAAAATTAA
66 ACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAA-TTAAAATTAA
* * ** *
1454 TTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA
130 TTCGGAAAAAAATGGAAAAATGATATTAAAAGCGTGAAAAAACCATCAATCTTTTTGGCGTTGAA
* * ***
1519 TTATATATTTTTTCTGAGTATTATGGTAAAAAATT-AAGAAAAAACTTTTCCGATCAGTGTTTAG
195 TTATATATTTTTTCTGAGTATTATGGCAAAAAATTAAAAAAAAAAAAATTCCGATCAGTGTTTAG
* *
1583 CC-GAAATCGTGTACTAACAACCATCATGGTTTTTG-GCTAAAAACGCG-TTC-CGAGCCCCGAC
260 CCTAAAATCGTGTACT---AACCATCATGGTTTTTGTGATAAAAACGCGTTTCGCGAGCCCCGAC
1644 TCAA
322 TCAA
* *
1648 TTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCACAAATACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCC
* * *
1713 ACATTGGACATAAGGATTTGATTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAA
66 ACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTA-AAATTAA
*
1778 TTCGGAAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAAACCATCAATCTTTTTGGTGTTG
130 TTCGG-AAAAAAA-TGGAAAAATGATATTAAAAGCGTGAAAAAACCATCAATCTTTTTGGCGTTG
* * * *
1843 AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAAAAATTCGGGTCAGTTT
193 AATTATATATTTTTTCTGAGTATTATGGCAAAAAATT-A-AAAAAAAAAAAATTCCGATCAGTGT
* * * *
1908 TTAGCCTAAAATCGTGTACTAACCATCATGGTTTTTGTGATAAAAACGCGTTTCGGGGGCCTCGG
256 TTAGCCTAAAATCGTGTACTAACCATCATGGTTTTTGTGATAAAAACGCGTTTCGCGAGCCCCGA
*
1973 CTCAT
321 CTCAA
*** * * *
1978 TTTTGCATGATTTTTGGTTGAAATACTCCGTGAAATATGTATATTCATCTAACC-AATCTCAGGC
1 TTTTGCATGATTTTTGGCACAAATACTCCTTGAAATATCTATATTCATCAAACCAAATCTCA-G-
* * * * *
2042 TTTCAACCACATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTACGATTTAATTA
64 ------CCACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTA
* * * * *
2107 AAAATAGATTCGG-AAAAAATAGAAAAATTATATTTAAAGCGAGAAAAA
123 AAATTA-ATTCGGAAAAAAATGGAAAAATGATATTAAAAGCGTGAAAAA
2155 TATTTCTTTT
Statistics
Matches: 430, Mismatches: 57, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
323 49 0.11
324 70 0.16
325 7 0.02
326 80 0.19
327 17 0.04
328 11 0.03
329 33 0.08
330 70 0.16
334 25 0.06
335 6 0.01
336 5 0.01
337 57 0.13
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (325 bp):
TTTTGCATGATTTTTGGCACAAATACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCC
ACATTAGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAAAATTAAT
TCGGAAAAAAATGGAAAAATGATATTAAAAGCGTGAAAAAACCATCAATCTTTTTGGCGTTGAAT
TATATATTTTTTCTGAGTATTATGGCAAAAAATTAAAAAAAAAAAAATTCCGATCAGTGTTTAGC
CTAAAATCGTGTACTAACCATCATGGTTTTTGTGATAAAAACGCGTTTCGCGAGCCCCGACTCAA
Found at i:8836 original size:16 final size:16
Alignment explanation
Indices: 8815--8847 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8805 ATCAAATTAC
8815 AGAAAACAAAA-GAAAA
1 AGAAAA-AAAAGGAAAA
8831 AGAAAAAAAAGGAAAA
1 AGAAAAAAAAGGAAAA
8847 A
1 A
8848 TAGCTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAGGAAAA
Found at i:14236 original size:81 final size:79
Alignment explanation
Indices: 14097--14257 Score: 286
Period size: 81 Copynumber: 2.0 Consensus size: 79
14087 TAGCGGTGTA
14097 CAGGTCTTCCTGTGCATTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCTCAAAA
1 CAGGTCTTCCTGTGCATTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCT--AAA
14162 AAAAAAACTCTTTCTT
64 AAAAAAACTCTTTCTT
* *
14178 CAGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTTTTATCTAAAAA
1 CAGGTCTTCCTGTGCATTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAA
14243 AAAAACTCTTTCTT
66 AAAAACTCTTTCTT
14257 C
1 C
14258 TTCAGAGTAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
79 20 0.26
81 58 0.74
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (79 bp):
CAGGTCTTCCTGTGCATTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAA
AAAAACTCTTTCTT
Found at i:14321 original size:97 final size:98
Alignment explanation
Indices: 14202--14397 Score: 340
Period size: 100 Copynumber: 2.0 Consensus size: 98
14192 CGTTTGTAAT
14202 CCCAATCTCTTTAAGAAATGAAAATGATTTTTATCT-AAAAAAAAAACTCTTTCTTCTTCAGAGT
1 CCCAATCTCTTTAAGAAATGAAAATGATTTTTATCTAAAAAAAAAAACTCTTTCTTCTTCAGAGT
14266 AAAAATTCGGTAAACTTCCATTAAAAAATATAC
66 AAAAATTCGGTAAACTTCCATTAAAAAATATAC
*
14299 CCCAATCTCTTTAAGAAATGAAAATGATTTTTATCTCAAAAAAAAAAAACTCTTTCTTCTTTAGA
1 CCCAATCTCTTTAAGAAATGAAAATGATTTTTATCT--AAAAAAAAAAACTCTTTCTTCTTCAGA
* *
14364 GTAAAAGTTTGGTAAACTTCCATTAAAAAATATA
64 GTAAAAATTCGGTAAACTTCCATTAAAAAATATA
14398 TCAGGATTAA
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
97 36 0.39
100 57 0.61
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (98 bp):
CCCAATCTCTTTAAGAAATGAAAATGATTTTTATCTAAAAAAAAAAACTCTTTCTTCTTCAGAGT
AAAAATTCGGTAAACTTCCATTAAAAAATATAC
Found at i:22169 original size:31 final size:31
Alignment explanation
Indices: 22131--22189 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
22121 TATTTTCTAC
22131 CAAACAAAAGAAAATTATATTTCCCTCCTAT
1 CAAACAAAAGAAAATTATATTTCCCTCCTAT
** * *
22162 CAAACAAATTAAAATTGTATTTCTCTCC
1 CAAACAAAAGAAAATTATATTTCCCTCC
22190 CATTTTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.32
Consensus pattern (31 bp):
CAAACAAAAGAAAATTATATTTCCCTCCTAT
Found at i:22415 original size:2 final size:2
Alignment explanation
Indices: 22361--22397 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22351 TCATTAAGTG
22361 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22398 GTGGCATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23399 original size:13 final size:13
Alignment explanation
Indices: 23378--23409 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
23368 ATGTGGAGTC
*
23378 TTTATGCTTGATG
1 TTTAAGCTTGATG
23391 TTTAAGCTTGATG
1 TTTAAGCTTGATG
23404 TTTAAG
1 TTTAAG
23410 AGGTAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (13 bp):
TTTAAGCTTGATG
Found at i:23430 original size:12 final size:12
Alignment explanation
Indices: 23413--23454 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
23403 GTTTAAGAGG
23413 TAATGTTTTATT
1 TAATGTTTTATT
*
23425 TAATGTTTGATT
1 TAATGTTTTATT
23437 T--T-TTTTATT
1 TAATGTTTTATT
23446 TAATGTTTT
1 TAATGTTTT
23455 TCTTTTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 7 0.28
10 1 0.04
11 1 0.04
12 16 0.64
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (12 bp):
TAATGTTTTATT
Found at i:26217 original size:24 final size:24
Alignment explanation
Indices: 26190--26235 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
26180 GTGTCATTGG
26190 TGTATTATTCACAAAGGTAAGGGT
1 TGTATTATTCACAAAGGTAAGGGT
*
26214 TGTATTATTCACATAGGTAAGG
1 TGTATTATTCACAAAGGTAAGG
26236 TTATTGTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.35
Consensus pattern (24 bp):
TGTATTATTCACAAAGGTAAGGGT
Found at i:27985 original size:30 final size:31
Alignment explanation
Indices: 27944--28002 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
27934 TCAAAACCAG
27944 AAAGTCCTTTCCTATCAGGAATTGGAAAAAA
1 AAAGTCCTTTCCTATCAGGAATTGGAAAAAA
** *
27975 AAAG-CCTTTCCTATTTGGGATTGGAAAA
1 AAAGTCCTTTCCTATCAGGAATTGGAAAA
28003 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (31 bp):
AAAGTCCTTTCCTATCAGGAATTGGAAAAAA
Found at i:29315 original size:15 final size:15
Alignment explanation
Indices: 29295--29323 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29285 TATAGTCGAC
29295 TACAAGTACAATGAA
1 TACAAGTACAATGAA
29310 TACAAGTACAATGA
1 TACAAGTACAATGA
29324 CGAAGATCAA
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:0.52, C:0.14, G:0.14, T:0.21
Consensus pattern (15 bp):
TACAAGTACAATGAA
Found at i:34413 original size:18 final size:18
Alignment explanation
Indices: 34372--34414 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
34362 TATACATCCT
* *
34372 TTGAGCTTGAGCTCGAAT
1 TTGAGTTTGAGCTCGAAC
34390 TTGAGTTTGAGCTCGAAC
1 TTGAGTTTGAGCTCGAAC
34408 TTGAGTT
1 TTGAGTT
34415 CGAGTTTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (18 bp):
TTGAGTTTGAGCTCGAAC
Found at i:36288 original size:2 final size:2
Alignment explanation
Indices: 36283--36311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36273 ATGTGTGTAT
36283 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
36312 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:36316 original size:2 final size:2
Alignment explanation
Indices: 36311--36337 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36301 ACACACACAC
36311 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
36338 GGGATTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45820 original size:38 final size:39
Alignment explanation
Indices: 45699--45847 Score: 232
Period size: 39 Copynumber: 3.9 Consensus size: 39
45689 GGCTGTGCAT
45699 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
* *
45738 AGTGGACCTGTGCCTTAGGGGGTTAAACTGATTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
*
45777 AGTGGACCCGTGCCTCAGTGGGTTAAACTG-TTGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
* *
45815 AGTGGACCCCTTCCTCAGGGGGTT-AACTG-TTGG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGG
45848 CTAGACTCGA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
37 9 0.09
38 29 0.28
39 64 0.63
ACGTcount: A:0.21, C:0.18, G:0.35, T:0.26
Consensus pattern (39 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATTGGTAAG
Done.