Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016382.1 Corchorus capsularis cultivar CVL-1 contig16403, 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: 39020
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:621 original size:199 final size:198
Alignment explanation
Indices: 16--1270 Score: 1683
Period size: 199 Copynumber: 6.3 Consensus size: 198
6 CACATTCAGT
* * * *
16 GTAAATTTTGGACTCCGTAAGCAGGTTAAGAAGTTGACACATACCTCATTTCATATTTAATAAAA
1 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAA
* * *
81 TATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCCTAAACCCTGCACGCGCAGC
66 TATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGT
* * * * * *
146 CTGCTAAACTCCACTAACGGTGTATTGTATAATTGTTCTTATAGAAATATTATACAATAAACTGT
131 CTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGT
211 CAA
196 CAA
* * * * * *
214 TGCAACTTTGGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATATCAGAATTAATTAA
1 -GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAA
279 ATTTATTTAATATTAATACATA-TCCCTTAAGGGGACACATGTCAACCCTTAAA-CCTCGCACGT
65 A--TATTTAATATTAATACATATTCCC-TAAGGGGACACATGTCAACCCTTAAACCCT-GCACGT
* * * * *
342 GCAATCTGCTAAACTCGACTGACAGTGTATAGTATAATTTTTCTTATAGGATTATTATACAATAC
126 GCAGTCTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATAC
407 ACAT-TCAA
191 AC-TGTCAA
* *
415 TGTAAATTTTGGACTCAATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATAAA
1 -GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAA
480 ATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAG
65 ATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAG
*
545 TCTGCTAAACTCCATTGACGGTATATTGTATAAATTTTTCTTATAGGATTATTATACAATACACT
130 TCTGCTAAACTCCATTGACGGTGTATTGTAT-AATTTTTCTTATAGGATTATTATACAATACACT
610 GTCAA
194 GTCAA
* * * *
615 GTAAATTTTGGACTCCATAAGCGGGTTCAGAAGTTGACATATATCTCATTTCATCATTAATTAAA
1 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAA
* *
680 TATATAATATTAATACATATTCCCTAAGGGGACACATGTCAACCTTTAAACCCTGCACGTGCAGT
66 TATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGT
745 CTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGT
131 CTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGT
810 CAAA
196 C-AA
* * * * * * *
814 GTAAATTTTGAACTCCATAAGCGGGTTTAGAAGTTGACATATATCTCATGTCATCATTATTTAAA
1 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAA
* * *
879 TATATAATATTAATACATATTCCCTAAGGGG----ATGTCAATCCTTAAACCCTGGACGTGCAGT
66 TATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGT
* **
940 CTGCTAAACTCCAGTT-ACAGTGTATAATATAATTTTTCTTATAGGATTATTATACAATACACTG
131 CTGCTAAACTCCA-TTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTG
*
1004 TCAGT
195 TCA-A
* * * *
1009 GTAAAATTTGGACTCCATAAGCGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAGA
1 GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAA
* * *
1074 TATTTAATATTAATACATCTTCCCTAAGGGGACACATGTCAACCTTTAAATCCC-GCACGTGCAA
66 TATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-CCCTGCACGTGCAG
* * * * * *
1138 TCAGCTAAAATCCACTT-ACGTTGTATTATATAATTTTTCTTATAGGATTATTATACAACACGCT
130 TCTGCTAAACTCCA-TTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACT
*
1202 GTCAGT
194 GTCA-A
* ** * *
1208 GTAAATTTTTGG-CTCTATAAATGGGTTAAGAA---CACACATACCTCATTTCATCATTAATTAA
1 GTAAA-TTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAA
1269 AT
65 AT
1271 CTATATACTA
Statistics
Matches: 950, Mismatches: 88, Indels: 39
0.88 0.08 0.04
Matches are distributed among these distances:
194 1 0.00
195 172 0.18
196 28 0.03
198 36 0.04
199 486 0.51
200 58 0.06
201 168 0.18
202 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (198 bp):
GTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAA
TATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGT
CTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGT
CAA
Found at i:1121 original size:394 final size:391
Alignment explanation
Indices: 1--1270 Score: 1680
Period size: 394 Copynumber: 3.2 Consensus size: 391
* * *
1 CAATACACAT-TCAGTGTAAATTTTGGACTCCGTAAGCAGGTTAAGAAGTTGACACATACCTCAT
1 CAATACAC-TGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCAT
*
65 TTCATATTTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCCTAA
65 TTCATA-TTAATAAAATATTTAATATTAATACATATTCCCTAAGGGG--A-ATGTCAACCCTTAA
* * * * * *
130 ACCCTGCACGCGCAGCCTGCTAAACTCCACTAACGGTGTATTGTATAATTGTTCTTATAGAAATA
126 ACCCTGCACGTGCAGTCTGCTAAACTCCA-TTACGGTGTATTGTATAATTTTTCTTATAGGATTA
* * * *
195 TTATACAATAAACTGTCAATG-CAACTTTGGGACTCCATAAGCGGGTTAAGAAGTTGACACATAC
190 TTATACAATACACTGTC-ATGTAAAATTT-GGACTCCATAAGCGGGTTAAGAAGTTGACATATAC
* * *
259 CCCATATCAGAATTAATTAAATTTATTTAATATTAATACATATCCCTTAAGGGGACACATGTCAA
253 CCCATTTCATAATTAATTAAA--TATTTAATATTAATACATTTCCC-TAAGGGGACACATGTCAA
* * * * *
324 CCCTTAAA-CCTCGCACGTGCAATCTGCTAAACTCGACTGACAGTGTATAGTATAATTTTTCTTA
315 CCTTTAAACCCT-GCACGTGCAATCTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTA
388 TAGGATTATTATA
379 TAGGATTATTATA
*
401 CAATACACAT-TCAATGTAAATTTTGGACTCAATAAGCGGGTTAAGAAGTTGACACATACCTCAT
1 CAATACAC-TGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCAT
465 TTCATAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAA
65 TTCAT-ATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGG--A-ATGTCAACCCTTAA
*
530 ACCCTGCACGTGCAGTCTGCTAAACTCCATTGACGGTATATTGTATAAATTTTTCTTATAGGATT
126 ACCCTGCACGTGCAGTCTGCTAAACTCCATT-ACGGTGTATTGTAT-AATTTTTCTTATAGGATT
* * * *
595 ATTATACAATACACTGTCAAGTAAATTTTGGACTCCATAAGCGGGTTCAGAAGTTGACATATATC
189 ATTATACAATACACTGTCATGTAAAATTTGGACTCCATAAGCGGGTTAAGAAGTTGACATATACC
* * *
660 TCATTTCATCATTAATTAAATATATAATATTAATACATATTCCCTAAGGGGACACATGTCAACCT
254 CCATTTCATAATTAATTAAATATTTAATATTAATACAT-TTCCCTAAGGGGACACATGTCAACCT
*
725 TTAAACCCTGCACGTGCAGTCTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGG
318 TTAAACCCTGCACGTGCAATCTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGG
790 ATTATTATA
383 ATTATTATA
* * * * * *
799 CAATACACTGTCAAAGTAAATTTTGAACTCCATAAGCGGGTTTAGAAGTTGACATATATCTCATG
1 CAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATT
* * * *
864 TCATCATTATTTAAATATATAATATTAATACATATTCCCTAAGGGG-ATGTCAATCCTTAAACCC
66 TCAT-ATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGAATGTCAACCCTTAAACCC
* * **
928 TGGACGTGCAGTCTGCTAAACTCCAGTTACAGTGTATAATATAATTTTTCTTATAGGATTATTAT
130 TGCACGTGCAGTCTGCTAAACTCCA-TTACGGTGTATTGTATAATTTTTCTTATAGGATTATTAT
993 ACAATACACTGTCAGTGTAAAATTTGGACTCCATAAGCGGGTTAAGAAGTTGACATATACCCCAT
194 ACAATACACTGTCA-TGTAAAATTTGGACTCCATAAGCGGGTTAAGAAGTTGACATATACCCCAT
*
1058 TTCATAATTAATTAGATATTTAATATTAATACATCTTCCCTAAGGGGACACATGTCAACCTTTAA
258 TTCATAATTAATTAAATATTTAATATTAATACAT-TTCCCTAAGGGGACACATGTCAACCTTTAA
* * * *
1123 ATCCC-GCACGTGCAATCAGCTAAAATCCACTT-ACGTTGTATTATATAATTTTTCTTATAGGAT
322 A-CCCTGCACGTGCAATCTGCTAAACTCCA-TTGACGGTGTATTGTATAATTTTTCTTATAGGAT
1186 TATTATA
385 TATTATA
* * * * ** *
1193 CAACACGCTGTCAGTGTAAATTTTTGG-CTCTATAAATGGGTTAAGAA---CACACATACCTCAT
1 CAATACACTGTCAATGTAAA-TTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCAT
*
1254 TTCATCATTAATTAAAT
65 TTCAT-ATTAATAAAAT
1271 CTATATACTA
Statistics
Matches: 782, Mismatches: 76, Indels: 33
0.88 0.09 0.04
Matches are distributed among these distances:
391 26 0.03
393 37 0.05
394 247 0.32
395 12 0.02
397 1 0.00
398 200 0.26
399 8 0.01
400 213 0.27
401 38 0.05
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (391 bp):
CAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATT
TCATATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGAATGTCAACCCTTAAACCCT
GCACGTGCAGTCTGCTAAACTCCATTACGGTGTATTGTATAATTTTTCTTATAGGATTATTATAC
AATACACTGTCATGTAAAATTTGGACTCCATAAGCGGGTTAAGAAGTTGACATATACCCCATTTC
ATAATTAATTAAATATTTAATATTAATACATTTCCCTAAGGGGACACATGTCAACCTTTAAACCC
TGCACGTGCAATCTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTAT
A
Found at i:1214 original size:593 final size:596
Alignment explanation
Indices: 11--1275 Score: 1784
Period size: 593 Copynumber: 2.1 Consensus size: 596
1 CAATACACAT
* *
11 TCAGTGTAAATTTTGGACTCCGTAAGCAGGTTAAGAAGTTGACACATACCTCATTTCAT-ATTTA
1 TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATCA-TTA
* *
75 ATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCCTAAACCCTGCACG
65 ATTAAATATATAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCCTAAACCCTGCACG
140 CGCAGCCTGCTAAACTCCACTAACGGTGTATTGTATAATTGTTCTTATAGAAATATTATACAATA
130 CGCAGCCTGCTAAACTCCACTAACGGTGTATTGTATAATTGTTCTTATAGAAATATTATACAATA
* * *
205 AACTGTCAATGCAACTTTGGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATATCAGA
195 AACTGTCAAAGCAAATTTGGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATATCAGA
*
270 ATTAATTAAATTTATTTAATATTAATACATATCCCTTAAGGGGACACATGTCAACCCTTAAACCT
260 ATTAATTAAA-TTATATAATATTAATACATATCCCTTAAGGGG--A-ATGTCAACCCTTAAACCT
* *
335 CGCACGTGCAATCTGCTAAACTCGACTGACAGTGTATAGTATAATTTTTCTTATAGGATTATTAT
321 CGCACGTGCAATCTGCTAAACTCCACTGACAGTGTATAATATAATTTTTCTTATAGGATTATTAT
* *
400 ACAATACACATTCAATGTAAATTTTGGACTCAATAAGCGGGTTAAGAAGTTGACACATACCTCAT
386 ACAATACACATTCAATGTAAAATTTGGACTCAATAAGCGGGTTAAGAAGTTGACACATACCCCAT
465 TTCATAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAA
451 TTCATAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAA
* * * *
530 ACCCTGCACGTGCAGTCTGCTAAACTCCATTGACGGTATATTGTATAAATTTTTCTTATAGGATT
516 ACCCTGCACGTGCAATCAGCTAAAATCCATTGACGGTATATTATATAAATTTTTCTTATAGGATT
*
595 ATTATACAATACACTG
581 ATTATACAACACACTG
* * * *
611 TCA-AGTAAATTTTGGACTCCATAAGCGGGTTCAGAAGTTGACATATATCTCATTTCATCATTAA
1 TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATCATTAA
** *
675 TTAAATATATAATATTAATACATATTCCCTAAGGGGACACATGTCAACCTTTAAACCCTGCACGT
66 TTAAATATATAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCCTAAACCCTGCACGC
* * * * * * *
740 GCAGTCTGCTAAACTCCATTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATAC
131 GCAGCCTGCTAAACTCCACTAACGGTGTATTGTATAATTGTTCTTATAGAAATATTATACAATAA
* * * * * * * **
805 ACTGTCAAAGTAAATTTTGAACTCCATAAGCGGGTTTAGAAGTTGACATATATCTCATGTCATCA
196 ACTGTCAAAGCAAATTTGGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATATCAGAA
* * *
870 TTATTTAAA-TATATAATATTAATACATATTCCC-TAAGGGG-ATGTCAATCCTTAAACC-CTGG
261 TTAATTAAATTATATAATATTAATACATA-TCCCTTAAGGGGAATGTCAACCCTTAAACCTC-GC
* * *
931 ACGTGCAGTCTGCTAAACTCCAGTTACAGTGTATAATATAATTTTTCTTATAGGATTATTATACA
324 ACGTGCAATCTGCTAAACTCCACTGACAGTGTATAATATAATTTTTCTTATAGGATTATTATACA
* * *
996 ATACAC-TGTCAGTGTAAAATTTGGACTCCATAAGCGGGTTAAGAAGTTGACATATACCCCATTT
389 ATACACAT-TCAATGTAAAATTTGGACTCAATAAGCGGGTTAAGAAGTTGACACATACCCCATTT
* * * *
1060 CATAATTAATTAGATATTTAATATTAATACATCTTCCCTAAGGGGACACATGTCAACCTTTAAAT
453 CATAATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA-
* *
1125 CCC-GCACGTGCAATCAGCTAAAATCCACTT-ACGTTGTATTATAT-AATTTTTCTTATAGGATT
517 CCCTGCACGTGCAATCAGCTAAAATCCA-TTGACGGTATATTATATAAATTTTTCTTATAGGATT
*
1187 ATTATACAACACGCTG
581 ATTATACAACACACTG
* ** *
1203 TCAGTGTAAATTTTTGG-CTCTATAAATGGGTTAAGAA---CACACATACCTCATTTCATCATTA
1 TCAGTGTAAA-TTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATCATTA
*
1264 ATTAAATCTATA
65 ATTAAATATATA
1276 TACTACTGTA
Statistics
Matches: 592, Mismatches: 65, Indels: 26
0.87 0.10 0.04
Matches are distributed among these distances:
590 32 0.05
592 37 0.06
593 247 0.42
594 11 0.02
597 25 0.04
598 4 0.01
599 232 0.39
600 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (596 bp):
TCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATCATTAA
TTAAATATATAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCCTAAACCCTGCACGC
GCAGCCTGCTAAACTCCACTAACGGTGTATTGTATAATTGTTCTTATAGAAATATTATACAATAA
ACTGTCAAAGCAAATTTGGAACTCCATAAGCGGGTTAAGAAGTTGACACATACCCCATATCAGAA
TTAATTAAATTATATAATATTAATACATATCCCTTAAGGGGAATGTCAACCCTTAAACCTCGCAC
GTGCAATCTGCTAAACTCCACTGACAGTGTATAATATAATTTTTCTTATAGGATTATTATACAAT
ACACATTCAATGTAAAATTTGGACTCAATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCAT
AATTAATAAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCT
GCACGTGCAATCAGCTAAAATCCATTGACGGTATATTATATAAATTTTTCTTATAGGATTATTAT
ACAACACACTG
Found at i:1409 original size:25 final size:25
Alignment explanation
Indices: 1354--1412 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
1344 TAGAAGTCAC
*
1354 CTAGGGGCATTTTGGTCATTTTGTA
1 CTAGGGGCATTTTGGTCATTTTGAA
*
1379 CCAGGGGCATTTTGGTCATTTTGAA
1 CTAGGGGCATTTTGGTCATTTTGAA
*
1404 TTAGGGGCA
1 CTAGGGGCA
1413 CTTCAGTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.37
Consensus pattern (25 bp):
CTAGGGGCATTTTGGTCATTTTGAA
Found at i:5240 original size:26 final size:27
Alignment explanation
Indices: 5211--5316 Score: 137
Period size: 26 Copynumber: 4.0 Consensus size: 27
5201 AATTGGTAAT
5211 CAGTAATCAGTAAAAAGAGTAAG-AAA
1 CAGTAATCAGTAAAAAGAGTAAGAAAA
*
5237 CAGTATTCAGTAAAAAGAGTAAGAAAA
1 CAGTAATCAGTAAAAAGAGTAAGAAAA
* * *
5264 TAGTCATCAGTAAAAGGAGT-AGAAAA
1 CAGTAATCAGTAAAAAGAGTAAGAAAA
*
5290 CAAT-ATCCAGTAAAAAGAGTAAGAAAA
1 CAGTAAT-CAGTAAAAAGAGTAAGAAAA
5317 GAGCAATAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
25 2 0.03
26 42 0.61
27 25 0.36
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (27 bp):
CAGTAATCAGTAAAAAGAGTAAGAAAA
Found at i:5274 original size:53 final size:53
Alignment explanation
Indices: 5216--5316 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 53
5206 GTAATCAGTA
* *
5216 ATCAGTAAAAAGAGTA-AGAAACAGTATTCAGTAAAAAGAGTAAGAAAATAGTC
1 ATCAGTAAAAAGAGTAGA-AAACAATATCCAGTAAAAAGAGTAAGAAAATAGTC
*
5269 ATCAGTAAAAGGAGTAGAAAACAATATCCAGTAAAAAGAGTAAGAAAA
1 ATCAGTAAAAAGAGTAGAAAACAATATCCAGTAAAAAGAGTAAGAAAA
5317 GAGCAATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
53 43 0.98
54 1 0.02
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (53 bp):
ATCAGTAAAAAGAGTAGAAAACAATATCCAGTAAAAAGAGTAAGAAAATAGTC
Found at i:5440 original size:7 final size:7
Alignment explanation
Indices: 5430--5675 Score: 93
Period size: 7 Copynumber: 35.7 Consensus size: 7
5420 AATGGTGATC
5430 AGTAAAG
1 AGTAAAG
5437 AGTAAAG
1 AGTAAAG
**
5444 AGTAATC
1 AGTAAAG
5451 AGTAAA-
1 AGTAAAG
5457 A--AAATG
1 AGTAAA-G
5463 -GTAAAG
1 AGTAAAG
*
5469 AGTAAAA
1 AGTAAAG
5476 AGT-AAG
1 AGTAAAG
5482 CAGTAAAG
1 -AGTAAAG
*
5490 A-AAAATG
1 AGTAAA-G
*
5497 -GTAAAA
1 AGTAAAG
5503 AGTAAAG
1 AGTAAAG
**
5510 AGTAATC
1 AGTAAAG
5517 AGTAAAAG
1 AGT-AAAG
** *
5525 AAAAAAT
1 AGTAAAG
5532 AGTAAAG
1 AGTAAAG
5539 AGTAAAG
1 AGTAAAG
5546 AGTAAAG
1 AGTAAAG
**
5553 AGTAATT
1 AGTAAAG
*
5560 ATTAAAG
1 AGTAAAG
*
5567 A-AAAATG
1 AGTAAA-G
*
5574 -GCAAAG
1 AGTAAAG
5580 AGTAAAG
1 AGTAAAG
**
5587 AGTAATC
1 AGTAAAG
5594 AGTAAA-
1 AGTAAAG
**
5600 AAAAAATG
1 AGTAAA-G
5608 -GTAAAG
1 AGTAAAG
5614 AGTAAAG
1 AGTAAAG
* **
5621 AATAATC
1 AGTAAAG
*
5628 AGTAAGG
1 AGTAAAG
**
5635 AGTAATT
1 AGTAAAG
*
5642 AGTAAGG
1 AGTAAAG
5649 AGTAAA-
1 AGTAAAG
*
5655 ATGATAAAA
1 A-G-TAAAG
5664 AGTAAAG
1 AGTAAAG
5671 AGTAA
1 AGTAA
5676 TCAGTAAAAG
Statistics
Matches: 173, Mismatches: 46, Indels: 40
0.67 0.18 0.15
Matches are distributed among these distances:
4 3 0.02
6 17 0.10
7 141 0.82
8 11 0.06
9 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.22, T:0.18
Consensus pattern (7 bp):
AGTAAAG
Found at i:5499 original size:34 final size:34
Alignment explanation
Indices: 5431--5632 Score: 237
Period size: 34 Copynumber: 5.7 Consensus size: 34
5421 ATGGTGATCA
5431 GTAAAGAGTAAAGAGTAATCAGT-AA-AAAAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
* *
5463 GTAAAGAGTAAAAAGTAAGCAGTAAAGAAAAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
*
5497 GTAAAAAGTAAAGAGTAATCAGTAAAAGAAAAAATAGTAAAG
1 GTAAAGAGTAAAGAGTAATCAGT-AAAG--AAAA-A-T---G
* *
5539 AGTAAAGAGTAAAGAGTAATTATTAAAGAAAAATG
1 -GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
* *
5574 GCAAAGAGTAAAGAGTAATCAGTAAAAAAAAATG
1 GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
*
5608 GTAAAGAGTAAAGAATAATCAGTAA
1 GTAAAGAGTAAAGAGTAATCAGTAA
5633 GGAGTAATTA
Statistics
Matches: 145, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
32 21 0.14
33 2 0.01
34 80 0.55
35 5 0.03
37 4 0.03
38 2 0.01
39 2 0.01
40 4 0.03
42 5 0.03
43 20 0.14
ACGTcount: A:0.58, C:0.03, G:0.21, T:0.18
Consensus pattern (34 bp):
GTAAAGAGTAAAGAGTAATCAGTAAAGAAAAATG
Found at i:5762 original size:15 final size:14
Alignment explanation
Indices: 5741--5798 Score: 71
Period size: 15 Copynumber: 4.0 Consensus size: 14
5731 GGAGTAAAGG
5741 GTAATCAGTAAAAA
1 GTAATCAGTAAAAA
*
5755 GATAATCAGTAAAGA
1 G-TAATCAGTAAAAA
* *
5770 GTAATATAGTAAAAG
1 GTAAT-CAGTAAAAA
5785 GTAATCAGTAAAAA
1 GTAATCAGTAAAAA
5799 AAGTAATGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 12 0.33
15 24 0.67
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.22
Consensus pattern (14 bp):
GTAATCAGTAAAAA
Found at i:5766 original size:29 final size:29
Alignment explanation
Indices: 5733--5796 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
5723 GGATGGTAGG
*
5733 AGTAAAGGGTAAT-CAGTAAAAAGATAATC
1 AGTAAAGAGTAATACAGT-AAAAGATAATC
* *
5762 AGTAAAGAGTAATATAGTAAAAGGTAATC
1 AGTAAAGAGTAATACAGTAAAAGATAATC
5791 AGTAAA
1 AGTAAA
5797 AAAAGTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (29 bp):
AGTAAAGAGTAATACAGTAAAAGATAATC
Found at i:5788 original size:44 final size:43
Alignment explanation
Indices: 5741--6041 Score: 216
Period size: 42 Copynumber: 7.0 Consensus size: 43
5731 GGAGTAAAGG
* *
5741 GTAATCAGTAAAAAGATAATCAGTAAAGAGTAATATAGTAA-AA
1 GTAA-CAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATCA
5784 GGTAATCAGTAAAAAAAGTAATGACAATCAGT-AAGAGGTAAAATAGTAATCA
1 -GTAA-CAGT--AAAAAG--AT---AATCAGTAAAGA-GTAAAATAGTAATCA
* * * * *
5836 GTAAGAGCAAAATGGTAATCAGT-AAGAGTAAAATGGTAATCA
1 GTAACAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATCA
* * * *
5878 GTGAA-AGCAAAATGGTAATCAGTAAAGAATAAAATAGTAATCA
1 GT-AACAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATCA
*
5921 GTAAAAAGTAAAAAGATAATCAGTAAAGAGTAAAATAGT-A--A
1 GT-AACAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATCA
* *
5962 -T--CAGT-AAAAGGTAATTAGT-AAGAGTAAAATAGTAATCGA
1 GTAACAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATC-A
** * *
6001 CAAAAAGTAAAAAG-TAATTAGT-AAGAGTAAAATAGTAATCA
1 GTAACAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATCA
6042 ATAAAGAGTA
Statistics
Matches: 218, Mismatches: 19, Indels: 43
0.78 0.07 0.15
Matches are distributed among these distances:
35 14 0.06
36 13 0.06
37 3 0.01
39 1 0.00
40 1 0.00
41 2 0.01
42 63 0.29
43 40 0.18
44 38 0.17
46 7 0.03
48 7 0.03
50 6 0.03
51 22 0.10
52 1 0.00
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.22
Consensus pattern (43 bp):
GTAACAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATCA
Found at i:5834 original size:22 final size:21
Alignment explanation
Indices: 5809--6054 Score: 169
Period size: 21 Copynumber: 11.8 Consensus size: 21
5799 AAGTAATGAC
5809 AATCAGTAAGAGGTAAAATAGT
1 AATCAGTAA-AGGTAAAATAGT
* *
5831 AATCAGT-AAGAGCAAAATGGT
1 AATCAGTAAAG-GTAAAATAGT
*
5852 AATCAGT-AAGAGTAAAATGGT
1 AATCAGTAAAG-GTAAAATAGT
* *
5873 AATCAGTGAAA-GCAAAATGGT
1 AATCAGT-AAAGGTAAAATAGT
*
5894 AATCAGTAAAGAATAAAATAGT
1 AATCAGTAAAG-GTAAAATAGT
*
5916 AATCAGTAAAAAGTAAAA-AGAT
1 AATCAGT-AAAGGTAAAATAG-T
5938 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAG-GTAAAATAGT
*
5960 AATCAGTAAAAGGT-AATTAGT
1 AATCAGT-AAAGGTAAAATAGT
5981 -A--AG---A-GTAAAATAGT
1 AATCAGTAAAGGTAAAATAGT
** *
5995 AATCGACAAAAAGTAAAA-AGT
1 AATC-AGTAAAGGTAAAATAGT
*
6016 AATTAGT-AAGAGTAAAATAGT
1 AATCAGTAAAG-GTAAAATAGT
*
6037 AATCAATAAAGAGTAAAA
1 AATCAGTAAAG-GTAAAA
6055 GGTGATCAGT
Statistics
Matches: 183, Mismatches: 19, Indels: 44
0.74 0.08 0.18
Matches are distributed among these distances:
13 2 0.01
14 7 0.04
15 1 0.01
18 3 0.02
19 2 0.01
20 13 0.07
21 78 0.43
22 66 0.36
23 11 0.06
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (21 bp):
AATCAGTAAAGGTAAAATAGT
Found at i:5853 original size:21 final size:22
Alignment explanation
Indices: 5809--5969 Score: 195
Period size: 22 Copynumber: 7.5 Consensus size: 22
5799 AAGTAATGAC
*
5809 AATCAGT-AAGAGGTAAAATAGT
1 AATCAGTAAAGA-GTAAAATGGT
*
5831 AATCAGT-AAGAGCAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
5852 AATCAGT-AAGAGTAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
5873 AATCAGTGAA-AGCAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
* *
5894 AATCAGTAAAGAATAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
* * *
5916 AATCAGTAAAAAGTAAAAAGAT
1 AATCAGTAAAGAGTAAAATGGT
*
5938 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGTAAAATGGT
5960 AATCAGTAAA
1 AATCAGTAAA
5970 AGGTAATTAG
Statistics
Matches: 120, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
21 54 0.45
22 66 0.55
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.21
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGGT
Found at i:5875 original size:42 final size:41
Alignment explanation
Indices: 5809--6066 Score: 267
Period size: 42 Copynumber: 6.2 Consensus size: 41
5799 AAGTAATGAC
* *
5809 AATCAGTAAGAGGTAAAATAGTAATCAGTAAGAGCAAAATGGT
1 AATCAGTAAGA-GTAAAATAGTAATCAGTAAAAGTAAAA-GGT
* * *
5852 AATCAGTAAGAGTAAAATGGTAATCAGTGAAAGCAAAATGGT
1 AATCAGTAAGAGTAAAATAGTAATCAGTAAAAGTAAAA-GGT
* *
5894 AATCAGTAAAGAATAAAATAGTAATCAGTAAAAAGTAAAAAGAT
1 AATCAGT-AAGAGTAAAATAGTAATCAGT-AAAAGT-AAAAGGT
5938 AATCAGTAAAGAGTAAAATAGTAATC------AGTAAAAGGT
1 AATCAGT-AAGAGTAAAATAGTAATCAGTAAAAGTAAAAGGT
* ** *
5974 AATTAGTAAGAGTAAAATAGTAATCGACAAAAAGTAAAAAGT
1 AATCAGTAAGAGTAAAATAGTAATC-AGTAAAAGTAAAAGGT
* *
6016 AATTAGTAAGAGTAAAATAGTAATCAATAAAGAGTAAAAGGT
1 AATCAGTAAGAGTAAAATAGTAATCAGTAAA-AGTAAAAGGT
*
6058 GATCAGTAA
1 AATCAGTAA
6067 TTCAAAGAGT
Statistics
Matches: 187, Mismatches: 17, Indels: 23
0.82 0.07 0.10
Matches are distributed among these distances:
35 18 0.10
36 12 0.06
37 3 0.02
41 4 0.02
42 85 0.45
43 30 0.16
44 31 0.17
45 4 0.02
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.22
Consensus pattern (41 bp):
AATCAGTAAGAGTAAAATAGTAATCAGTAAAAGTAAAAGGT
Found at i:5925 original size:15 final size:15
Alignment explanation
Indices: 5907--5970 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
5897 CAGTAAAGAA
*
5907 TAAAATAGTAATCAG
1 TAAAATAGTAAACAG
*
5922 TAAAA-AGTAAAAAG
1 TAAAATAGTAAACAG
* *
5936 -ATAATCAGTAAAGAG
1 TAAAAT-AGTAAACAG
*
5951 TAAAATAGTAATCAG
1 TAAAATAGTAAACAG
5966 TAAAA
1 TAAAA
5971 GGTAATTAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
13 3 0.08
14 7 0.18
15 25 0.64
16 4 0.10
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (15 bp):
TAAAATAGTAAACAG
Found at i:6175 original size:27 final size:28
Alignment explanation
Indices: 6119--6177 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
6109 GTAAAAAGTG
*
6119 GTAATCAATAAAAGAGAGTAAGAAAAGA
1 GTAATCAATAAAAGAGACTAAGAAAAGA
*
6147 GTAATTAATAAAA-AGACTAAGAAAAGA
1 GTAATCAATAAAAGAGACTAAGAAAAGA
6174 GTAA
1 GTAA
6178 AAATGACACC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.61, C:0.03, G:0.19, T:0.17
Consensus pattern (28 bp):
GTAATCAATAAAAGAGACTAAGAAAAGA
Found at i:6902 original size:10 final size:10
Alignment explanation
Indices: 6887--6919 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
6877 CATTCATCAT
6887 TAAAACACAC
1 TAAAACACAC
*
6897 TAAAACACAT
1 TAAAACACAC
6907 TAAAACACAC
1 TAAAACACAC
6917 TAA
1 TAA
6920 TTGACAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.15
Consensus pattern (10 bp):
TAAAACACAC
Found at i:8051 original size:198 final size:195
Alignment explanation
Indices: 7702--8197 Score: 670
Period size: 198 Copynumber: 2.5 Consensus size: 195
7692 TCCACTTGTA
* * * * * *
7702 TAATATTAATACATATTCCCTCAGGGGACACATGTCAACCCTTGAACCCTGCACCTGCAGTATGC
1 TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCTGAACGTGCAGTCTGC
* *
7767 TAAACTCCACTGACGGTGCATTGTATAATTGTTCTTATAGGATTATTATACAATACACTGTCAAT
66 TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAAT
* * * * **
7832 GTAAATTTTGGACTTCATAAGCGGGTTAAGAAGTTGGCACATACTTCATTTCATAATTAATTAAA
131 ATAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTC---A-TAATTAAA
7897 TATT
192 TATT
*
7901 TGATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCTGAACGTGCAGTCTGC
1 TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCTGAACGTGCAGTCTGC
* * * * * *
7966 TAAAATCCACTTAC-GTGTATTGTATAATTTTTCTTATATGATTATTATATAATACATTGTCAGT
66 TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAAT
8030 ATAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTCATAATTAAATATT
131 ATAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTCATAATTAAATATT
* * *
8095 TAATATCAATACATATTCCCTAAGGGTACACATGTCAACCCTTAAAGTTAAACCTCACACGTGCA
1 TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAA--T---CCTGA-ACGTGCA
*
8160 GTCTGCTAAACTCTACTGACGGTGTATTGTATAATTTT
60 GTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTT
8198 CTTCCCCCCT
Statistics
Matches: 262, Mismatches: 28, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
194 55 0.21
195 1 0.00
196 1 0.00
198 90 0.34
199 74 0.28
200 24 0.09
201 17 0.06
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (195 bp):
TAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTTAAATCCTGAACGTGCAGTCTGC
TAAACTCCACTGACGGTGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAAT
ATAAATTTTGGACTCCATAAGCGGGTTAAAAAGTTGACACATACCCCATTTCATAATTAAATATT
Found at i:11328 original size:2 final size:2
Alignment explanation
Indices: 11321--11369 Score: 62
Period size: 2 Copynumber: 22.5 Consensus size: 2
11311 ATTGTTTTAA
11321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT GAT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT -AT AT
11364 GAT AT A
1 -AT AT A
11370 AGATATTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 35 0.80
3 9 0.20
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11830 original size:29 final size:29
Alignment explanation
Indices: 11766--11842 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
11756 AGGTGTTGCA
*
11766 AAAAAG-AGGGCCAGGTGTTGGTTGATAC
1 AAAAAGAAGGGCCAGGTGTTGGCTGATAC
* * *
11794 AGAGAGAAGGGCCAGGTGTTGGCTGATGC
1 AAAAAGAAGGGCCAGGTGTTGGCTGATAC
* *
11823 AAAAAGAAGGACCAAGTGTT
1 AAAAAGAAGGGCCAGGTGTT
11843 AGTTTGGGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 4 0.10
29 36 0.90
ACGTcount: A:0.34, C:0.12, G:0.36, T:0.18
Consensus pattern (29 bp):
AAAAAGAAGGGCCAGGTGTTGGCTGATAC
Found at i:15261 original size:21 final size:21
Alignment explanation
Indices: 15237--15484 Score: 118
Period size: 22 Copynumber: 11.6 Consensus size: 21
15227 TCTGCTCCTT
15237 TTTTACTGATTACTCTTTTAC
1 TTTTACTGATTACTCTTTTAC
* *
15258 TTTTTACTGATTGC-CTTTTGC
1 -TTTTACTGATTACTCTTTTAC
*
15279 TTTTTATTGATTAC-CTTTTTAC
1 -TTTTACTGATTACTC-TTTTAC
* * *
15301 TTCTTGCTTATTTGCT-TTTTAC
1 TT-TTACTGA-TTACTCTTTTAC
*
15323 TCTTTACTGATCAC-CTTTTTAC
1 T-TTTACTGATTACTC-TTTTAC
* *
15345 TCTTACTGATTTC-CTTTTAC
1 TTTTACTGATTACTCTTTTAC
* * *
15365 TCCTTACTTATTACTATTTTAC
1 T-TTTACTGATTACTCTTTTAC
* *
15387 TCTTACTGATTACT-ATTTAC
1 TTTTACTGATTACTCTTTTAC
*
15407 TTTT--TGATGGCTACTATTTTAC
1 TTTTACTGAT---TACTCTTTTAC
* **
15429 TCTTGTTGATTA-TCTTCTTAC
1 TTTTACTGATTACTCTT-TTAC
* *
15450 TTTTTACTAATTACTATTTTAC
1 -TTTTACTGATTACTCTTTTAC
*
15472 TCTTTACTAATTA
1 T-TTTACTGATTA
15485 GCATTTTACC
Statistics
Matches: 177, Mismatches: 30, Indels: 38
0.72 0.12 0.16
Matches are distributed among these distances:
18 4 0.02
20 18 0.10
21 66 0.37
22 78 0.44
23 7 0.04
24 4 0.02
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTTACTGATTACTCTTTTAC
Found at i:15283 original size:43 final size:42
Alignment explanation
Indices: 15238--15524 Score: 167
Period size: 42 Copynumber: 6.7 Consensus size: 42
15228 CTGCTCCTTT
* * *
15238 TTTACTGATTA-CTCTTTTACTTTTTACTGATTGCCTTTTGCTT
1 TTTACTGATTACCT-TTTTAC-TCTTACTGATTGCCTTTTACTC
* * * *
15281 TTTATTGATTACCTTTTTACTTCTTGCTTATTTGCTTTTTACTC
1 TTTACTGATTACCTTTTTAC-TCTTACTGA-TTGCCTTTTACTC
* *
15325 TTTACTGATCACCTTTTTACTCTTACTGATTTCCTTTTACTC
1 TTTACTGATTACCTTTTTACTCTTACTGATTGCCTTTTACTC
* * * *
15367 CTTACTTATTA-CTATTTTACTCTTACTGATT-ACTATTTACTT
1 TTTACTGATTACCT-TTTTACTCTTACTGATTGCCT-TTTACTC
** ** ** *
15409 TTTGA-TGGCTA-CTATTTTACTCTTGTTGATTATCTTCTTACTT
1 TTT-ACTGATTACCT-TTTTACTCTTACTGATTGCCTT-TTACTC
* * * *
15452 TTTACTAATTA-CTATTTTACTCTTTACTAATTAGCATTTTACCC
1 TTTACTGATTACCT-TTTTACTC-TTACTGATT-GCCTTTTACTC
* *
15496 TTT-CAGA-TACCTTTTTACTTTTTACTGAT
1 TTTACTGATTACCTTTTTAC-TCTTACTGAT
15525 GGCATGCTAT
Statistics
Matches: 192, Mismatches: 40, Indels: 25
0.75 0.16 0.10
Matches are distributed among these distances:
41 4 0.02
42 82 0.43
43 61 0.32
44 43 0.22
45 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (42 bp):
TTTACTGATTACCTTTTTACTCTTACTGATTGCCTTTTACTC
Found at i:15778 original size:16 final size:16
Alignment explanation
Indices: 15757--15818 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
15747 GCTTCTTTAA
15757 TTACTGATTACTCAAT
1 TTACTGATTACTCAAT
**
15773 TTACTGATTACTATCTTT
1 TTACTGATTAC--TCAAT
*
15791 TTACCTGATTACT-GAT
1 TTA-CTGATTACTCAAT
15807 TTACTGATTACT
1 TTACTGATTACT
15819 ATTACCTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.23
16 15 0.38
17 1 0.03
18 6 0.15
19 8 0.21
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (16 bp):
TTACTGATTACTCAAT
Found at i:15845 original size:55 final size:55
Alignment explanation
Indices: 15776--16027 Score: 380
Period size: 55 Copynumber: 4.6 Consensus size: 55
15766 ACTCAATTTA
* * * *
15776 CTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTACCTAATTACTGATTTACTGATTACTATTACCTTAACT
* **
15831 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGTCT
1 CTGATTAATCTCTTTTTACCTAATTACTGATTTACTGATTACTATTACCTTAACT
*
15886 CTGAATAATCTCTTTTTA-CTCAATTACTGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACCT-AATTACTGATTTACTGATTACTATTACCTTAACT
* *
15941 CTGATTGATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACT
1 CTGATTAATCTCTTTTTACCTAATTACTGATTTACTGATTACTATTACCTTAACT
* *
15996 CTGATTAATCTCTTTTTACTTAATTATTGATT
1 CTGATTAATCTCTTTTTACCTAATTACTGATT
16028 GCCCCTTTTT
Statistics
Matches: 181, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
54 1 0.01
55 179 0.99
56 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACCTAATTACTGATTTACTGATTACTATTACCTTAACT
Found at i:15962 original size:25 final size:25
Alignment explanation
Indices: 15934--16018 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
15924 TTACTATTAC
*
15934 CTTAACTCTGATTGATCTCTTTTTA
1 CTTAACTCTGATTAATCTCTTTTTA
* * *
15959 CTTAATTACTGATTTA-CTGATTACTATTA
1 CTTAACT-CTGATTAATCT-CTT--T-TTA
15988 CCTTAACTCTGATTAATCTCTTTTTA
1 -CTTAACTCTGATTAATCTCTTTTTA
16014 CTTAA
1 CTTAA
16019 TTATTGATTG
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
25 13 0.28
26 12 0.26
27 1 0.02
28 1 0.02
29 12 0.26
30 8 0.17
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (25 bp):
CTTAACTCTGATTAATCTCTTTTTA
Found at i:17043 original size:50 final size:50
Alignment explanation
Indices: 16897--17132 Score: 242
Period size: 50 Copynumber: 4.7 Consensus size: 50
16887 TATCCAGGAC
* * * * * ***
16897 TTTACCACCTAAAGATTCAATTTTCATTGATAAAATTATCAAGAGTGGCCA
1 TTTACTACTTAAAGATTCAATTTTTATTGATGAAATTATCAA-AATTTTCA
** * * * *
16948 TTTGTTATTTTAAGATCCAATTTTTATTGATGAAATTATCGAAATTTTCA
1 TTTACTACTTAAAGATTCAATTTTTATTGATGAAATTATCAAAATTTTCA
* * *
16998 CTTGCTACTTAAAGATTCAA-TTTTATTGATGAAATTACCAAAAATTATT-A
1 TTTACTACTTAAAGATTCAATTTTTATTGATGAAATTATC-AAAATT-TTCA
* * * *
17048 TTTTCTACTTAAAGATTCAATTTTTATCGATAAAATTATCAAAATTGTCA
1 TTTACTACTTAAAGATTCAATTTTTATTGATGAAATTATCAAAATTTTCA
17098 TTTACTACTTAAAGATTCAATTTTTATTGATGAAA
1 TTTACTACTTAAAGATTCAATTTTTATTGATGAAA
17133 CCTGATATGA
Statistics
Matches: 151, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
49 19 0.13
50 82 0.54
51 50 0.33
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (50 bp):
TTTACTACTTAAAGATTCAATTTTTATTGATGAAATTATCAAAATTTTCA
Found at i:18572 original size:61 final size:61
Alignment explanation
Indices: 18477--18594 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 61
18467 GATTGGGTGC
*
18477 AGTGTGTGCTAGTGTGTTGACCCTTAATGAATTGAGACTGTGACTAAATGTTGCTTAGTAT
1 AGTGTGTGCTAGTGTATTGACCCTTAATGAATTGAGACTGTGACTAAATGTTGCTTAGTAT
* * * *
18538 AGTGTGTGCTAGTGTATTGATCTTTATTGAATTGAGATTGTGACTAAATGTTGCTTA
1 AGTGTGTGCTAGTGTATTGACCCTTAATGAATTGAGACTGTGACTAAATGTTGCTTA
18595 ATGTGGATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (61 bp):
AGTGTGTGCTAGTGTATTGACCCTTAATGAATTGAGACTGTGACTAAATGTTGCTTAGTAT
Found at i:19927 original size:13 final size:13
Alignment explanation
Indices: 19909--19934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19899 ATTAAGATTC
19909 TTTCAATTTTTCA
1 TTTCAATTTTTCA
19922 TTTCAATTTTTCA
1 TTTCAATTTTTCA
19935 ATGCAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTCAATTTTTCA
Found at i:20018 original size:27 final size:28
Alignment explanation
Indices: 19988--20069 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
19978 AGGTGAACTT
*
19988 AAAAATGACTAAAATGCCCC-TGAGTGCA
1 AAAAATGACAAAAATGCCCCTTG-GTGCA
*
20016 AAAAATGACCAAAATGCCCCTTGGTGC-
1 AAAAATGACAAAAATGCCCCTTGGTGCA
*
20043 AAAAATGACAAAAAT-ACCCTTGG-GCA
1 AAAAATGACAAAAATGCCCCTTGGTGCA
20069 A
1 A
20070 CCCTAATGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
25 2 0.04
26 8 0.16
27 14 0.29
28 23 0.47
29 2 0.04
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (28 bp):
AAAAATGACAAAAATGCCCCTTGGTGCA
Found at i:21562 original size:30 final size:31
Alignment explanation
Indices: 21516--21584 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 31
21506 TTCATGTATC
* *
21516 ATATTTAAATTCTATTTATTATT-TTTGAAA
1 ATATGTAAATTCTATTTATTATTAGTTGAAA
*
21546 ATATGTAAATTGTATTTATTATTAGTTGAAA
1 ATATGTAAATTCTATTTATTATTAGTTGAAA
21577 ATATGTAA
1 ATATGTAA
21585 GTTACTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (31 bp):
ATATGTAAATTCTATTTATTATTAGTTGAAA
Found at i:22785 original size:24 final size:22
Alignment explanation
Indices: 22740--22795 Score: 87
Period size: 24 Copynumber: 2.5 Consensus size: 22
22730 GTATAGAACT
22740 AAACTAA-AAAACAACACACAA
1 AAACTAACAAAACAACACACAA
22761 AAACTAACAACAACACACACACAA
1 AAACTAACAA-AACA-ACACACAA
22785 AAACTAACAAA
1 AAACTAACAAA
22796 TGAATACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.22
22 2 0.06
23 5 0.16
24 18 0.56
ACGTcount: A:0.68, C:0.27, G:0.00, T:0.05
Consensus pattern (22 bp):
AAACTAACAAAACAACACACAA
Found at i:30457 original size:21 final size:20
Alignment explanation
Indices: 30432--30475 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 20
30422 TGTTGATTTG
30432 ATTGTCGTTTTGGAGATGATT
1 ATTGT-GTTTTGGAGATGATT
30453 A-T-TGTTTTGGAGATGATT
1 ATTGTGTTTTGGAGATGATT
30471 ATTGT
1 ATTGT
30476 TTGGCTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 16 0.76
19 2 0.10
20 2 0.10
21 1 0.05
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.50
Consensus pattern (20 bp):
ATTGTGTTTTGGAGATGATT
Found at i:30459 original size:18 final size:18
Alignment explanation
Indices: 30438--30477 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
30428 TTTGATTGTC
30438 GTTTTGGAGATGATTATT
1 GTTTTGGAGATGATTATT
30456 GTTTTGGAGATGATTATT
1 GTTTTGGAGATGATTATT
30474 GTTT
1 GTTT
30478 GGCTTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.53
Consensus pattern (18 bp):
GTTTTGGAGATGATTATT
Found at i:35806 original size:183 final size:178
Alignment explanation
Indices: 35451--35813 Score: 618
Period size: 183 Copynumber: 2.0 Consensus size: 178
35441 TCTATAAACA
*
35451 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATGCTATTTAAT
1 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
*
35516 CCTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTTCAATTTGAC
66 CCTTACAATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTTCAATTTGAC
*
35581 CGATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTCCATGGTCTAC
131 CGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
*
35629 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTGTAATTTATACTATTTAA
1 AATCA-TTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
* * *
35694 TCACTTACAATTATGGGTTGGACGATTGAATGTTTCGGCTTTAATTCTTTTATTTTTTTTTCTAT
65 TC-CTTACAATTATAGGTTGGACGATTGAATGTTTCGGCTTTAA-T-TGTT-TTTTTTTTTCAAT
35759 TTGACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
126 TTGACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
35812 AA
1 AA
35814 CTTTCATGAA
Statistics
Matches: 173, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
178 5 0.03
179 59 0.34
180 39 0.23
181 1 0.01
182 3 0.02
183 66 0.38
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (178 bp):
AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
CCTTACAATTATAGGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTTCAATTTGAC
CGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
Done.