Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007305.1 Corchorus capsularis cultivar CVL-1 contig07326, 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: 61861
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:71 original size:38 final size:38
Alignment explanation
Indices: 39--351 Score: 473
Period size: 38 Copynumber: 8.2 Consensus size: 38
29 AATTAAGGAC
39 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
77 CAAAGTAATAGTAATCGGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
115 CAAAGTAATAGTAATCAGTAAAATTGATAATTGAGAGC
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
153 CAAAAGTAATAGTAATCAATAAAATTGATAATTAAGAGC
1 C-AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
192 CAAAGTAATAGTAATCAGTAGAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
230 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* * *
268 CAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* * * *
306 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGGGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
344 CAAGGTAA
1 CAAAGTAA
352 AAATATTAAT
Statistics
Matches: 257, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
38 221 0.86
39 36 0.14
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.27
Consensus pattern (38 bp):
CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
Found at i:293 original size:153 final size:152
Alignment explanation
Indices: 29--341 Score: 484
Period size: 153 Copynumber: 2.1 Consensus size: 152
19 ACCCCAGTAA
* * *
29 AATTAAGGACCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCG
1 AATTAAGGACCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCA
* * * *
94 GTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAATTGAGAGCCAAAAG
66 GTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGCC-AAAG
* *
159 TAATAGTAATCAATAAAATTGAT
130 TAAGAATAATCAATAAAATTGAT
*
182 AATTAA-GAGCCAAAGTAATAGTAATCAGTAGAATTGATAATTAAGAGTCAAAGTAAGAATAATC
1 AATTAAGGA-CCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATC
*
246 AGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGTCAAAG
65 AGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGCCAAAG
*
311 TAAGAATAATCAGTAAAATTGAT
130 TAAGAATAATCAATAAAATTGAT
*
334 AATCAAGG
1 AATTAAGG
342 GTCAAGGTAA
Statistics
Matches: 145, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
152 31 0.21
153 114 0.79
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (152 bp):
AATTAAGGACCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCA
GTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTAACAGCCAAAGT
AAGAATAATCAATAAAATTGAT
Found at i:324 original size:19 final size:19
Alignment explanation
Indices: 227--324 Score: 83
Period size: 19 Copynumber: 5.2 Consensus size: 19
217 GATAATTAAG
227 AGTCAAAGTAAGAATAATC
1 AGTCAAAGTAAGAATAATC
* * * * *
246 AGTAAAATTGATAATTAA-G
1 AGTCAAAGTAAGAA-TAATC
265 AGTCAAAGTAAGAATAATC
1 AGTCAAAGTAAGAATAATC
* * * *
284 AGTAAAATTGATAATTAA-C
1 AGTCAAAGTAAGAA-TAATC
303 AGTCAAAGTAAGAATAATC
1 AGTCAAAGTAAGAATAATC
322 AGT
1 AGT
325 AAAATTGATA
Statistics
Matches: 57, Mismatches: 18, Indels: 8
0.69 0.22 0.10
Matches are distributed among these distances:
18 6 0.11
19 45 0.79
20 6 0.11
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (19 bp):
AGTCAAAGTAAGAATAATC
Found at i:337 original size:16 final size:16
Alignment explanation
Indices: 278--338 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 16
268 CAAAGTAAGA
278 ATAATCAGTAAAATTG
1 ATAATCAGTAAAATTG
* *
294 ATAATTAACAGTCAAAGTAAG
1 ATAA-T--CAGT-AAAAT-TG
315 AATAATCAGTAAAATTG
1 -ATAATCAGTAAAATTG
332 ATAATCA
1 ATAATCA
339 AGGGTCAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 11 0.31
17 2 0.06
18 4 0.11
19 8 0.23
20 4 0.11
21 2 0.06
22 4 0.11
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAATCAGTAAAATTG
Found at i:505 original size:33 final size:32
Alignment explanation
Indices: 424--510 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
414 GGGAGAGAGT
*
424 AAAAGAGTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
*
456 AAAAGATTAATCAGTAATTAAGAAAGGAAGTA
1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
488 AAAAGGACTAATCAGTAAATTAA
1 AAAA-GACTAATCAGT-AATTAA
511 TAATTAAGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 35 0.69
33 10 0.20
34 6 0.12
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (32 bp):
AAAAGACTAATCAGTAATTAAGAAAGGAAGTA
Found at i:745 original size:14 final size:14
Alignment explanation
Indices: 722--760 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
712 GAGTTGTATG
722 GTAAAAAGTAATCA
1 GTAAAAAGTAATCA
*
736 GTAAAGAGTAATCA
1 GTAAAAAGTAATCA
750 GTAAAAAGTAA
1 GTAAAAAGTAA
761 AAATGGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (14 bp):
GTAAAAAGTAATCA
Found at i:3501 original size:27 final size:27
Alignment explanation
Indices: 3462--3530 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
3452 GATCAACTGG
*
3462 AACATCCTCTACATTGACTGCATCATC
1 AACATCATCTACATTGACTGCATCATC
*
3489 AACATCATTTACATTGACTGCATCATC
1 AACATCATCTACATTGACTGCATCATC
* *
3516 AACATCCTCCACATT
1 AACATCATCTACATT
3531 CACTCTATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.30
Consensus pattern (27 bp):
AACATCATCTACATTGACTGCATCATC
Found at i:3601 original size:21 final size:21
Alignment explanation
Indices: 3575--3719 Score: 96
Period size: 21 Copynumber: 6.9 Consensus size: 21
3565 TTTCCAGGCA
*
3575 TTTCAACTCCTTCAACTGGCT
1 TTTCAACTCCTTCAACTGGAT
* * **
3596 TTTCAACACCATCTCCTGGAT
1 TTTCAACTCCTTCAACTGGAT
* * * * **
3617 TCTAAACTTCTTCAGCTTCAT
1 TTTCAACTCCTTCAACTGGAT
* **
3638 TTTCAA-TACCATCTCCTGGAT
1 TTTCAACT-CCTTCAACTGGAT
3659 TTTCAACTCCTTCAACTGGAT
1 TTTCAACTCCTTCAACTGGAT
** **
3680 TTTCAA-TACCAACTCCTGGAT
1 TTTCAACT-CCTTCAACTGGAT
3701 TTTCAACTCCTTCAACTGG
1 TTTCAACTCCTTCAACTGG
3720 CCTCTGAACA
Statistics
Matches: 87, Mismatches: 33, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
20 2 0.02
21 83 0.95
22 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (21 bp):
TTTCAACTCCTTCAACTGGAT
Found at i:3607 original size:42 final size:42
Alignment explanation
Indices: 3575--3720 Score: 195
Period size: 42 Copynumber: 3.5 Consensus size: 42
3565 TTTCCAGGCA
3575 TTTCAACTCCTTCAACTGGCTTTTCAACACCATCTCCTGGAT
1 TTTCAACTCCTTCAACTGGCTTTTCAACACCATCTCCTGGAT
* * * * * *
3617 TCTAAACTTCTTCAGCT-TCATTTTCAATACCATCTCCTGGAT
1 TTTCAACTCCTTCAACTGGC-TTTTCAACACCATCTCCTGGAT
* * *
3659 TTTCAACTCCTTCAACTGGATTTTCAATACCAACTCCTGGAT
1 TTTCAACTCCTTCAACTGGCTTTTCAACACCATCTCCTGGAT
3701 TTTCAACTCCTTCAACTGGC
1 TTTCAACTCCTTCAACTGGC
3721 CTCTGAACAT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 87 0.99
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (42 bp):
TTTCAACTCCTTCAACTGGCTTTTCAACACCATCTCCTGGAT
Found at i:4349 original size:29 final size:29
Alignment explanation
Indices: 4311--4366 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
4301 TGAACAAACC
* *
4311 CTAATTCCCAGAAACAATTCATACCCACT
1 CTAATACCCAGAAACAATCCATACCCACT
4340 CTAATACCCAGAAACAATCCATACCCA
1 CTAATACCCAGAAACAATCCATACCCA
4367 TAACTCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.36, G:0.04, T:0.20
Consensus pattern (29 bp):
CTAATACCCAGAAACAATCCATACCCACT
Found at i:5498 original size:178 final size:178
Alignment explanation
Indices: 5200--5597 Score: 489
Period size: 178 Copynumber: 2.2 Consensus size: 178
5190 AATTAGCCAA
** *
5200 CTAAATTTAATGTTTCAAGTATAAAAAA-GCTTCCGAAAAATTAGTAGTTTCGGTTAACGGGAAT
1 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCTAAAAAATTAGTAGTTTCGGTTAACGAGAAT
* * * * ** * *
5264 GGACGGTCCACTTAATATTACATAACTTTTGCTCCATATGTCTAATTGGGGTGATTCAATTGTCT
66 GAACGATCCACTTAATATTACATAACTTTTGCTCCAGATGTCCAATTAAGGTGATTCAAATATCT
* *
5329 CTTAAAAGGTTGTTTCATGATCTACAACTTTCATAAAGGACTCCAAAG
131 CTTAAAAGGTTGTTCCATGATCTACAACTTTCATAAAGAACTCCAAAG
*
5377 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCTAAAAAATTAGTTGTTTCGGTT-ACTGAGAA
1 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCTAAAAAATTAGTAGTTTCGGTTAAC-GAGAA
* *
5441 TGAACCGAT-CACTTAATATTACATAATTTTTGCAT-CAGATGTCCGATTAAGGTGATTCAAATA
65 TGAA-CGATCCACTTAATATTACATAACTTTTGC-TCCAGATGTCCAATTAAGGTGATTCAAATA
* * * * **
5504 TCTGTTAAAAGGTTGTTCCGTGATCTACAACTTTCATGAAGAAGTTGAAAG
128 TCTCTTAAAAGGTTGTTCCATGATCTACAACTTTCATAAAGAACTCCAAAG
* * * * **
5555 CTAAATTTGATATTTTAAATACCAAAAATGCTTCTAAAAAATT
1 CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCTAAAAAATT
5598 TATTATTTCG
Statistics
Matches: 189, Mismatches: 28, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
177 30 0.16
178 155 0.82
179 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (178 bp):
CTAAATTTAATGTTTCAAGTATAAAAAATGCTTCTAAAAAATTAGTAGTTTCGGTTAACGAGAAT
GAACGATCCACTTAATATTACATAACTTTTGCTCCAGATGTCCAATTAAGGTGATTCAAATATCT
CTTAAAAGGTTGTTCCATGATCTACAACTTTCATAAAGAACTCCAAAG
Found at i:20529 original size:24 final size:26
Alignment explanation
Indices: 20497--20544 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
20487 TCAATTCAAT
20497 AACAGTAAAAAAAT-GAAA-AAAGGA
1 AACAGTAAAAAAATGGAAAGAAAGGA
*
20521 AACATTAAAAAAATGGAAAGAAAG
1 AACAGTAAAAAAATGGAAAGAAAG
20545 TAGTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 4 0.19
26 4 0.19
ACGTcount: A:0.69, C:0.04, G:0.17, T:0.10
Consensus pattern (26 bp):
AACAGTAAAAAAATGGAAAGAAAGGA
Found at i:21453 original size:75 final size:76
Alignment explanation
Indices: 21368--21527 Score: 241
Period size: 75 Copynumber: 2.1 Consensus size: 76
21358 AATTTAGTTT
* * *
21368 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTATCTTTATTTCCAATC-GTTGTATTTAATTT
1 TTTGTCTCCAACGTCCTATTTAATTTTGCATGTTATCTTTATTTCCAATCTGTTGTATTTAATTT
*
21432 TGTTTTTTGTC
66 TGCTTTTTGTC
* *
21443 TTTGTCTCCAACGTCCTATTTAATTTTGCATGTTGTCTTTGTTTCCAATCGTTGTTGTATTTAAT
1 TTTGTCTCCAACGTCCTATTTAATTTTGCATGTTATCTTTATTTCCAATC--TGTTGTATTTAAT
21508 TTTGCTTTTTGTC
64 TTTGCTTTTTGTC
21521 TTTGTCT
1 TTTGTCT
21528 TTTTTTTTGG
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 45 0.59
78 31 0.41
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.57
Consensus pattern (76 bp):
TTTGTCTCCAACGTCCTATTTAATTTTGCATGTTATCTTTATTTCCAATCTGTTGTATTTAATTT
TGCTTTTTGTC
Found at i:21479 original size:37 final size:38
Alignment explanation
Indices: 21368--21525 Score: 176
Period size: 37 Copynumber: 4.1 Consensus size: 38
21358 AATTTAGTTT
* *
21368 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTATC
1 TTTGTTTCCAATCGTCCTATTTAATTTTGCTTTTTGTC
* ** *
21405 TTTATTTCCAATCGTTGTATTTAATTTTGTTTTTTGTC
1 TTTGTTTCCAATCGTCCTATTTAATTTTGCTTTTTGTC
* * *
21443 TTTGTCTCCAA-CGTCCTATTTAATTTTGCATGTTGTC
1 TTTGTTTCCAATCGTCCTATTTAATTTTGCTTTTTGTC
**
21480 TTTGTTTCCAATCGTTGTTGTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAATC---GTCCTATTTAATTTTGCTTTTTGTC
21521 TTTGT
1 TTTGT
21526 CTTTTTTTTT
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 41 0.42
38 31 0.32
41 26 0.27
ACGTcount: A:0.15, C:0.16, G:0.12, T:0.58
Consensus pattern (38 bp):
TTTGTTTCCAATCGTCCTATTTAATTTTGCTTTTTGTC
Found at i:21845 original size:25 final size:26
Alignment explanation
Indices: 21786--21858 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 26
21776 ATATTTTCCG
* *
21786 ATTATATCATTTTCTAAATATATTTCTA
1 ATTATGTCATTAT-TAAA-ATATTTCTA
*
21814 AAT-TGTCATTATTAAAATATTT-TA
1 ATTATGTCATTATTAAAATATTTCTA
21838 ATTATGTCATTATTAAAATAT
1 ATTATGTCATTATTAAAATAT
21859 AATTTTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 4 0.10
25 23 0.57
26 4 0.10
27 7 0.17
28 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.51
Consensus pattern (26 bp):
ATTATGTCATTATTAAAATATTTCTA
Found at i:21943 original size:27 final size:26
Alignment explanation
Indices: 21895--21959 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
21885 ATTTTTTCCA
*
21895 AAAATAT-TTTTAAATTGTCATTATT
1 AAAATATATTTTAAATTGCCATTATT
*
21920 AAAATATATTTTAACTATGCCATTATT
1 AAAATATATTTTAAAT-TGCCATTATT
21947 AAAATATAATTTT
1 AAAATAT-ATTTT
21960 GTGTACTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 7 0.20
26 7 0.20
27 16 0.46
28 5 0.14
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (26 bp):
AAAATATATTTTAAATTGCCATTATT
Found at i:21970 original size:95 final size:93
Alignment explanation
Indices: 21795--21970 Score: 262
Period size: 95 Copynumber: 1.9 Consensus size: 93
21785 GATTATATCA
* * * *
21795 TTTTCTAAATATATTTCTAAATTGTCATTATTAAAATATTTTAATTATGTCATTATTAAAATATA
1 TTTTCCAAAAATATTTCTAAATTGTCATTATTAAAATATTTTAACTATGCCATTATTAAAATATA
*
21860 ATTTTATATATTTTTTCGATGTACTATT
66 ATTTTATATACTTTTTCGATGTACTATT
*
21888 TTTTCCAAAAATATTTTTAAATTGTCATTATTAAAATATATTTTAACTATGCCATTATTAAAATA
1 TTTTCCAAAAATATTTCTAAATTGTCATTATT-AAA-ATATTTTAACTATGCCATTATTAAAATA
* *
21953 TAATTTTGTGTACTTTTT
64 TAATTTTATATACTTTTT
21971 TTCAAATATA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 29 0.40
94 3 0.04
95 41 0.56
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (93 bp):
TTTTCCAAAAATATTTCTAAATTGTCATTATTAAAATATTTTAACTATGCCATTATTAAAATATA
ATTTTATATACTTTTTCGATGTACTATT
Found at i:22661 original size:344 final size:331
Alignment explanation
Indices: 22015--23106 Score: 1028
Period size: 331 Copynumber: 3.3 Consensus size: 331
22005 AATATAATTT
* * * *
22015 TTTAATTAGAAATTAATTCAGAAAAAGGTA-GGAAAAGCGATATTAGAAGCATGAGA-AGCCCTT
1 TTTAATTAGAAATTAATTC-GAAAAA-ATAGGGAAAA-CGATATTAGAAGCGTGAAATAGCCTTT
* * * * * *
22078 CAGTCTTTTTGGCATTGAGTTATTTATTTTTTATTAGTATTGTGGTCC-AAAATTGA-GAAGAAA
63 CAATCTTTTTGGCGTTGA---A-TTATTTTTTATGAATATCGTGG-CCAAAAATTGAGGAA-AAC
* * * ** * * *
22141 TTTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATAGTGTACTAACCATCATGGTTTTT---T
122 TCTTTCGTGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCACCA-GATTTTTGACT
* * * * *
22203 ---ACT-AAAAACGCGTTCCGGAGCCCCGACTTAGTTTTTCATGGTTTTTGGCGCCAAGTCTCAT
186 AAAAATGAAAAACGCGTT-CGG-GGCCCGACTTAGTTTTGCATGATTTTTGGCGTCAAGTCTCAT
* * **
22264 TGAAATATTTATATCCATCTAACCAAATCTTACCCACATTAAATTTAAGGATTTGTTTTTACGAG
249 TGAAATATCTATATCCATCTAACCAAATCTTAACCACATTGGATTT-AGGATTTGTTTTTACGAG
*
22329 C-TATGAATCATGTTTCGA
313 CATCTGAATCATGTTTCGA
* * * *
22347 TCTAATTTGGAATTAATTAATTCAGAAAAAATAGGGAAAACGATATTGGAAACGT-AAATAGCCT
1 TTTAA-TTAG-A--AATTAATTC-GAAAAAATAGGGAAAACGATATTAGAAGCGTGAAATAGCCT
* * *
22411 TTCAATCTTTTTGGTGTTGAATT-TTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTT
61 TTCAATCTTTTTGGCGTTGAATTATTTTTTATGAATATCGTGGCCAAAAATTGAGGAAAACTCTT
* * *
22475 TCAG-GTCAATTTTTACAAAATTTTAGCCAAAATCGTGTACTATATAACTACCACGGTTTTTGGC
126 TC-GTGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTAC----TAACCACCA-GATTTTTGAC
*
22539 TAAAAATGCACAAAAACGCGTTCTGGGGCCCTGACTTAGTTTTGCATGATTTTTGGCGTCAAGAC
185 TAAAAATG---AAAAACGCGTTC-GGGGCCC-GACTTAGTTTTGCATGATTTTTGGCGTCAAGTC
** * * *
22604 TCATTGAAATATCTATATTTATCTAACGAAATCTCAGCCACATTGGATTTGAGGATTTGTTTTTA
245 TCATTGAAATATCTATATCCATCTAACCAAATCTTAACCACATTGGATTT-AGGATTTGTTTTTA
* **
22669 CGAGCATCTCAATCCGGTTTCGA
309 CGAGCATCTGAATCATGTTTCGA
* ** * * *
22692 TTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAAAAATATTAGAAGCATGAGAT-GCCCTTCA
1 TTTAATTAGAAATTAATTCG-AAAAAATAGGGAAAACGATATTAGAAGCGTGAAATAGCCTTTCA
* * ** * *
22756 ATCTTTTTGGCGTTAAATTATATATTTTTTATGAATATGGTGGCCGTAAATTGAGGAGAACTGTT
65 ATCTTTTTGGCGTT-GA--AT-TATTTTTTATGAATATCGTGGCCAAAAATTGAGGAAAACTCTT
* * * * *
22821 TCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATATTTTTTACTAAAAA
126 TCGTGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCACCAGATTTTTGACTAAAAA
* * * *
22886 TG-----CG-TTTCGGGGTCGCGGCTCT-GTTTTGCATGATTTTTGGCGTCAAGTCTAATTGAAA
191 TGAAAAACGCGTTCGGGG-CCCGACT-TAGTTTTGCATGATTTTTGGCGTCAAGTCTCATTGAAA
* *
22944 TATCTATATCCATCTAACCAAATTTTAATCACATTGGATTTAGGGATTTGTTTTTACGAGCATCT
254 TATCTATATCCATCTAACCAAATCTTAACCACATTGGATTTA-GGATTTGTTTTTACGAGCATCT
23009 GAATCATGTTTCGA
318 GAATCATGTTTCGA
23023 TTTAATTAGAAATTAATTCGAAAAAATA-GGAAAACCGATATTAGAAGCGTGAAA-AGCCTTTCA
1 TTTAATTAGAAATTAATTCGAAAAAATAGGGAAAA-CGATATTAGAAGCGTGAAATAGCCTTTCA
23086 ATCTTTTTGGCGTTGAATTAT
65 ATCTTTTTGGCGTTGAATTAT
23107 ATATTTTTTA
Statistics
Matches: 631, Mismatches: 90, Indels: 84
0.78 0.11 0.10
Matches are distributed among these distances:
326 3 0.00
327 2 0.00
329 8 0.01
330 109 0.17
331 134 0.21
332 11 0.02
333 5 0.01
334 17 0.03
335 35 0.06
336 22 0.03
337 1 0.00
340 3 0.00
341 67 0.11
342 11 0.02
343 6 0.01
344 108 0.17
345 19 0.03
346 70 0.11
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (331 bp):
TTTAATTAGAAATTAATTCGAAAAAATAGGGAAAACGATATTAGAAGCGTGAAATAGCCTTTCAA
TCTTTTTGGCGTTGAATTATTTTTTATGAATATCGTGGCCAAAAATTGAGGAAAACTCTTTCGTG
TCAATTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCACCAGATTTTTGACTAAAAATGAAA
AACGCGTTCGGGGCCCGACTTAGTTTTGCATGATTTTTGGCGTCAAGTCTCATTGAAATATCTAT
ATCCATCTAACCAAATCTTAACCACATTGGATTTAGGATTTGTTTTTACGAGCATCTGAATCATG
TTTCGA
Found at i:22961 original size:331 final size:327
Alignment explanation
Indices: 22015--23133 Score: 1177
Period size: 330 Copynumber: 3.4 Consensus size: 327
22005 AATATAATTT
** * *
22015 TTTAATTAGAAATTAATTCAGAAAAAGGTAGGAAAAGCGATATTAGAAGCATGAGAAGCCCTTCA
1 TTTAATTAGAAATTAATTC-GAAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTCA
* * * * * * * * *
22080 GTCTTTTTGGCATTGAGTTATTTATTTTTTATTAGTATTGTGGTCCAAAATTGAGAAGAAATTTT
65 ATCTTTTTGGCGTTGAATTATATATTTTTTATGAATATCGTGG-CCAAAATTGAGGAGAAATCTT
* *
22145 TCGGGTCAATTTTTGCAAAATTTTAGCTGAAATAGTGTACTAACCATCATGGTTTTTTACTAAAA
129 TC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAT-GTTTTTTACTAAAA
* * * * * * *
22210 ACGCGTTCCGGAGCCCCGACTTAGTTTTTCATGGTTTTTGGCGCCAAGTCTCATTGAAATATTTA
192 ATGCGTTTCGG-GGCCCGACTTAGTTTTGCATGATTTTTGGCGTCAAGTCTCATTGAAATATCTA
* ** *
22275 TATCCATCTAACCAAATCTTACCCACATTAAATTTAAGGATTTGTTTTTACGAGC-TATGAATCA
256 TATCCATCTAACCAAATCTTAACCACATTGGATTT-AGGATTTGTTTTTACGAGCATCTGAATCA
22339 TGTTTCGA
320 TGTTTCGA
* * * * * *
22347 TCTAATTTGGAATTAATTAATTC-AGAAAAAATAGGGAAAACGATATTGGAAACGT-AAATAGCC
1 TTTAA-TTAG-A--AATTAATTCGA-AAAAAATAGGAAAAACGATATTAGAAGCATGAAA-AGCC
* * *
22410 TTTCAATCTTTTTGGTGTTG-A--AT-T-TTTTTTATGAGTATCGTGGCCAAAAATTGAGGA-AA
60 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAATATCGTGGCC-AAAATTGAGGAGAA
* * * * *
22469 ATTCTTTCAGGTCAATTTTTACAAAATTTTAGCCAAAATCGTGTACTATATAACTACCACGGTTT
124 A-TCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC----TAACCATCA-TGTTT
** *
22534 TTGGCTAAAAATGCACAAAAACGCGTTCTGGGGCCCTGACTTAGTTTTGCATGATTTTTGGCGTC
182 TTTACTAAAAATG--------CG-TTTC-GGGGCCC-GACTTAGTTTTGCATGATTTTTGGCGTC
* ** * * *
22599 AAGACTCATTGAAATATCTATATTTATCTAACGAAATCTCAGCCACATTGGATTTGAGGATTTGT
236 AAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTTAACCACATTGGATTT-AGGATTTGT
* **
22664 TTTTACGAGCATCTCAATCCGGTTTCGA
300 TTTTACGAGCATCTGAATCATGTTTCGA
** * *
22692 TTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAAAAATATTAGAAGCATGAGATGCCCTTCAA
1 TTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTCAA
* * * * *
22757 TCTTTTTGGCGTTAAATTATATATTTTTTATGAATATGGTGGCCGTAAATTGAGGAGAACTGTTT
66 TCTTTTTGGCGTTGAATTATATATTTTTTATGAATATCGTGGCC-AAAATTGAGGAGAAATCTTT
*
22822 CGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATATTTTTTACTAAAAAT
130 CG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGTTTTTTACTAAAAAT
* * *
22887 GCGTTTCGGGGTCGCGGCTCT-GTTTTGCATGATTTTTGGCGTCAAGTCTAATTGAAATATCTAT
194 GCGTTTCGGGG-CCCGACT-TAGTTTTGCATGATTTTTGGCGTCAAGTCTCATTGAAATATCTAT
* *
22951 ATCCATCTAACCAAATTTTAATCACATTGGATTTAGGGATTTGTTTTTACGAGCATCTGAATCAT
257 ATCCATCTAACCAAATCTTAACCACATTGGATTTA-GGATTTGTTTTTACGAGCATCTGAATCAT
23016 GTTTCGA
321 GTTTCGA
* * *
23023 TTTAATTAGAAATTAATTCG-AAAAAATAGGAAAACCGATATTAGAAGCGTGAAAAGCCTTTCAA
1 TTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTCAA
23087 TCTTTTTGGCGTTGAATTATATATTTTTTATG-A-ATCGTGG-CAAAATT
66 TCTTTTTGGCGTTGAATTATATATTTTTTATGAATATCGTGGCCAAAATT
23134 TTTTCGGGTA
Statistics
Matches: 648, Mismatches: 102, Indels: 80
0.78 0.12 0.10
Matches are distributed among these distances:
326 5 0.01
327 1 0.00
328 6 0.01
329 6 0.01
330 134 0.21
331 129 0.20
332 12 0.02
333 5 0.01
334 25 0.04
335 43 0.07
336 9 0.01
341 67 0.10
342 13 0.02
343 7 0.01
344 97 0.15
345 19 0.03
346 68 0.10
347 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (327 bp):
TTTAATTAGAAATTAATTCGAAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCCCTTCAA
TCTTTTTGGCGTTGAATTATATATTTTTTATGAATATCGTGGCCAAAATTGAGGAGAAATCTTTC
GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGTTTTTTACTAAAAATGC
GTTTCGGGGCCCGACTTAGTTTTGCATGATTTTTGGCGTCAAGTCTCATTGAAATATCTATATCC
ATCTAACCAAATCTTAACCACATTGGATTTAGGATTTGTTTTTACGAGCATCTGAATCATGTTTC
GA
Found at i:24170 original size:13 final size:13
Alignment explanation
Indices: 24152--24176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24142 GCATAACAAG
24152 AATATTCATATTA
1 AATATTCATATTA
24165 AATATTCATATT
1 AATATTCATATT
24177 GAGCAAGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
AATATTCATATTA
Found at i:26836 original size:16 final size:17
Alignment explanation
Indices: 26804--26841 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
26794 AGAAATGAAA
*
26804 ATTTTCATTTTAGTTTC
1 ATTTTCATTTTAATTTC
26821 ATTTTC-TTTTAATTTC
1 ATTTTCATTTTAATTTC
*
26837 CTTTT
1 ATTTT
26842 AAGCGCCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTCATTTTAATTTC
Found at i:28177 original size:33 final size:32
Alignment explanation
Indices: 28139--28246 Score: 119
Period size: 33 Copynumber: 3.3 Consensus size: 32
28129 GCGCCAAGCG
* *
28139 ATGGCCGGT-TGTGGCCGGACATGTCCATGTCGC
1 ATGGCCGGTGT-TGGCCGGGCATCTCCA-GTCGC
* *
28172 GTGGCCGGTGTTGGCCGGGCATCTCCGAGTCAC
1 ATGGCCGGTGTTGGCCGGGCATCTCC-AGTCGC
* *
28205 TTGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGC
1 ATGGCCGGTGTTGGCCGGGCATCTCC-AGTCGC
28238 ATGGCCGGT
1 ATGGCCGGT
28247 CACTAGTGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 62 0.97
34 2 0.03
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (32 bp):
ATGGCCGGTGTTGGCCGGGCATCTCCAGTCGC
Found at i:42595 original size:36 final size:35
Alignment explanation
Indices: 42515--42617 Score: 100
Period size: 36 Copynumber: 2.8 Consensus size: 35
42505 GTAAGAAAAT
* *
42515 TTTCAAAGTTTTCAAATTGGCAAAGTTCCCATTAAG
1 TTTCAAAG-TTTCAAATTGGGAAAGTTCCCATCAAG
* *
42551 TCTCCAAAGCTT-ACAATTGGGAAAGTTCCCATCAAG
1 T-TTCAAAGTTTCA-AATTGGGAAAGTTCCCATCAAG
* *
42587 ATTTCAAAGTTGTCGAGTTGGGAAAGTTCCC
1 -TTTCAAAGTT-TCAAATTGGGAAAGTTCCC
42618 GTTCAGTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
35 1 0.02
36 30 0.56
37 23 0.43
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (35 bp):
TTTCAAAGTTTCAAATTGGGAAAGTTCCCATCAAG
Found at i:49184 original size:17 final size:17
Alignment explanation
Indices: 49162--49195 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49152 CAATGTCATG
49162 ATAAAATGCAAAACATA
1 ATAAAATGCAAAACATA
49179 ATAAAATGCAAAACATA
1 ATAAAATGCAAAACATA
49196 TAGCCTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (17 bp):
ATAAAATGCAAAACATA
Found at i:50681 original size:25 final size:26
Alignment explanation
Indices: 50646--50695 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
50636 CATTAGAAGT
** *
50646 CACCTAGGGGCGTTTTGGTCATTTTG
1 CACCTAGGGGCACTTTAGTCATTTTG
50672 CACC-AGGGGCACTTTAGTCATTTT
1 CACCTAGGGGCACTTTAGTCATTTT
50696 TAATTCATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (26 bp):
CACCTAGGGGCACTTTAGTCATTTTG
Found at i:50901 original size:17 final size:18
Alignment explanation
Indices: 50868--50902 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
50858 TCTTAATCGG
*
50868 TAAGTATTTTAATTCGTT
1 TAAGCATTTTAATTCGTT
50886 TAAGCATTTT-ATTCGTT
1 TAAGCATTTTAATTCGTT
50903 GGTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (18 bp):
TAAGCATTTTAATTCGTT
Found at i:53301 original size:50 final size:50
Alignment explanation
Indices: 53239--53370 Score: 228
Period size: 50 Copynumber: 2.6 Consensus size: 50
53229 TCTTTAGCTA
*
53239 AAAGATGGAATTTTTGATTAAGTTGTAAATAAGAATGGAATTTTTAAGTG
1 AAAGATGAAATTTTTGATTAAGTTGTAAATAAGAATGGAATTTTTAAGTG
* *
53289 AGAGATGAAATTTTTGATTAAGTTGTAATTAAGAATGGAATTTTTAAGTG
1 AAAGATGAAATTTTTGATTAAGTTGTAAATAAGAATGGAATTTTTAAGTG
*
53339 AAAGATGAAATTTTTGATTAACTTGTAAATAA
1 AAAGATGAAATTTTTGATTAAGTTGTAAATAA
53371 AAAATGAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.39
Consensus pattern (50 bp):
AAAGATGAAATTTTTGATTAAGTTGTAAATAAGAATGGAATTTTTAAGTG
Found at i:53980 original size:31 final size:31
Alignment explanation
Indices: 53864--54632 Score: 494
Period size: 31 Copynumber: 23.0 Consensus size: 31
53854 GTGAATCAGT
*
53864 AATAAGAAACTTAATTCAGGGTAATTAAGT-
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
* *
53894 AAGTCAGTGAATAACTTAATTCTAGGTAATTAATTAAGT-
1 AA-T-A---AGTAACTTAATTC-AGG---GTAATTAAGTC
*
53933 AATAGGTAACTTAATTCAGGGTAATTAAGTC
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
*
53964 AATAAGTAGCTTAATTCAGGGTAATTAAGT-
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
* * *
53994 AAGTCAGCAACTTAATTCAGGGTAATTAAGTAAGT
1 AA-TAAGTAACTTAATTCAGGGTAATTAAGT---C
54029 AATAAGTAACTTAATTCAGGGTAATTAAGTC
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
* *
54060 AATAAGTAGCTTAATTCAGGGTAATTAAGTAAGT
1 AATAAGTAACTTAATTCAGGGTAATTAAGT---C
54094 AATAAGTAACTTAATTCAGGGTAATTAAGTC
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
*
54125 AATAAGTAGCTTAATTCAGGGTAATTAAGT-
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
*
54155 AAGTAATAGGTAACTTAATTCAGGGTAAATAAGTC
1 AA-T-A-A-GTAACTTAATTCAGGGTAATTAAGTC
*
54190 AATAAGTAGCTTAATTCAGGGTAATTAAGT-
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
54220 AAGTAATAGGTAACTTAATTCAGGGTAATTAAGTC
1 AA-T-A-A-GTAACTTAATTCAGGGTAATTAAGTC
*
54255 AATAAGTAGCTTAATTCAGGGTAATTAATAAAAGTC
1 AATAAGTAACTTAATTCAGGGTAA-T--T--AAGTC
** * * * *
54291 TGTTAGTAGCTTAATTTAGGGTAATTAAGAAAGTTAGT
1 AATAAGTAACTTAATTCAGGGTAATT----AAG-T--C
* *
54329 AAGTCAGTAATTTAATTCAGGGTAATTAAGAAATTC
1 AA-TAAGTAACTTAATTCAGGGTAATTAAG----TC
* * * * *
54365 AGTTATTAATTTAATTTAGGGTAATTAAGT-
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
* *
54395 AATTCAGTAATCAACTTAATTCATGGTAATTAAGT-
1 AA-T-A--AGT-AACTTAATTCAGGGTAATTAAGTC
54430 AAGTAATAGGTAACTTAATTCAGGGTAATTAAGTC
1 AA-T-A-A-GTAACTTAATTCAGGGTAATTAAGTC
* * ** *
54465 AGTAAGTAGCTTAATTCACAGTAATTAAGTA
1 AATAAGTAACTTAATTCAGGGTAATTAAGTC
* * *
54496 AAGTCAGTTAGTAACTTAGTTCAGAGAAATTAAGT-
1 AA-T-A---AGTAACTTAATTCAGGGTAATTAAGTC
** *
54531 AAGGCAGTAACTTAATTCAGGGTAATTAAAT-
1 AA-TAAGTAACTTAATTCAGGGTAATTAAGTC
* * *
54562 AATTCAGTAATCAACTTAAATCTAGGGTAATTATGTCAGC
1 AA-T-A--AGT-AACTTAATTC-AGGGTAATTAAGT---C
54602 TAATAAGTAACTTAATTCAGGGTAATTAAGT
1 -AATAAGTAACTTAATTCAGGGTAATTAAGT
54633 AAGTCATTGA
Statistics
Matches: 597, Mismatches: 78, Indels: 123
0.75 0.10 0.15
Matches are distributed among these distances:
30 18 0.03
31 204 0.34
32 8 0.01
33 10 0.02
34 145 0.24
35 99 0.17
36 72 0.12
37 3 0.01
38 3 0.01
39 32 0.05
40 1 0.00
41 2 0.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (31 bp):
AATAAGTAACTTAATTCAGGGTAATTAAGTC
Found at i:53997 original size:65 final size:65
Alignment explanation
Indices: 53871--54636 Score: 673
Period size: 65 Copynumber: 11.4 Consensus size: 65
53861 AGTAATAAGA
* * *
53871 AACTTAATTCAGGGTAATTAAGTAAGTCAGTGAATAACTTAATTCTA-GGTAATTAATTAAGTAA
1 AACTTAATTCAGGGTAATTAAGTAAGT-AAT-AGTAACTTAATTC-AGGGTAATTAAGTAAGT-A
53935 TAGGT
62 TA-GT
* *
53940 AACTTAATTCAGGGTAATTAAGTCAA-T-A-AGTAGCTTAATTCAGGGTAATTAAGTAAGT-CAG
1 AACTTAATTCAGGGTAATTAAGT-AAGTAATAGTAACTTAATTCAGGGTAATTAAGTAAGTATAG
*
54001 C
65 T
54002 AACTTAATTCAGGGTAATTAAGTAAGTAATAAGTAACTTAATTCAGGGTAATTAAGTCAA-TA-A
1 AACTTAATTCAGGGTAATTAAGTAAGTAAT-AGTAACTTAATTCAGGGTAATTAAGT-AAGTATA
54065 GT
64 GT
*
54067 AGCTTAATTCAGGGTAATTAAGTAAGTAATAAGTAACTTAATTCAGGGTAATTAAGTCAA-TA-A
1 AACTTAATTCAGGGTAATTAAGTAAGTAAT-AGTAACTTAATTCAGGGTAATTAAGT-AAGTATA
54130 GT
64 GT
* *
54132 AGCTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAAATAAGTCAA-TA-A
1 AACTTAATTCAGGGTAATTAAGTAAGTAATA-GTAACTTAATTCAGGGTAATTAAGT-AAGTATA
54195 GT
64 GT
*
54197 AGCTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAATTAAGTCAA-TA-A
1 AACTTAATTCAGGGTAATTAAGTAAGTAATA-GTAACTTAATTCAGGGTAATTAAGT-AAGTATA
54260 GT
64 GT
* ** * * *
54262 AGCTTAATTCAGGGTAATTAA-TAAAAGTCTGTTAGTAGCTTAATTTAGGGTAATTAAGAAAGTT
1 AACTTAATTCAGGGTAATTAAGT--AAG--TAATAGTAACTTAATTCAGGGTAATT----AAGTA
54326 AGTAAGTCAGT
58 AGT-A-T-AGT
* * * * * * * *
54337 AATTTAATTCAGGGTAATTAAGAAATTCAGTTATTAATTTAATTTAGGGTAATTAAGTAATTCAG
1 AACTTAATTCAGGGTAATTAAGTAAGT-A-ATAGTAACTTAATTCAGGGTAATTAAGTAAGT-A-
*
54402 TAAT
62 TAGT
* *
54406 CAACTTAATTCATGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAATTAAGTCAGTA-A
1 -AACTTAATTCAGGGTAATTAAGTAAGTAATA-GTAACTTAATTCAGGGTAATTAAGTAAGTATA
54470 GT
64 GT
* ** * * * * **
54472 AGCTTAATTCACAGTAATTAAGTAAAGTCAGTTAGTAACTTAGTTCAGAGAAATTAAGTAAG-GC
1 AACTTAATTCAGGGTAATTAAGT-AAGT-A-ATAGTAACTTAATTCAGGGTAATTAAGTAAGTAT
54536 AGT
63 AGT
* * * * * * *
54539 AACTTAATTCAGGGTAATTAAATAATTCAGTAATCAACTTAAATCTAGGGTAATTATGTCAGCTA
1 AACTTAATTCAGGGTAATTAAGTAAGT-AATAGT-AACTTAATTC-AGGGTAATTAAGTAAG-T-
54604 ATAAGT
61 AT-AGT
54610 AACTTAATTCAGGGTAATTAAGTAAGT
1 AACTTAATTCAGGGTAATTAAGTAAGT
54637 CATTGATCGA
Statistics
Matches: 595, Mismatches: 65, Indels: 72
0.81 0.09 0.10
Matches are distributed among these distances:
61 2 0.00
62 25 0.04
63 2 0.00
64 3 0.01
65 287 0.48
66 24 0.04
67 78 0.13
68 8 0.01
69 51 0.09
70 35 0.06
71 33 0.06
72 2 0.00
74 23 0.04
75 22 0.04
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (65 bp):
AACTTAATTCAGGGTAATTAAGTAAGTAATAGTAACTTAATTCAGGGTAATTAAGTAAGTATAGT
Found at i:54100 original size:130 final size:130
Alignment explanation
Indices: 53861--54636 Score: 753
Period size: 130 Copynumber: 5.8 Consensus size: 130
53851 AAGGTGAATC
* * * *
53861 AGTAATAAGAAACTTAATTCAGGGTAATTAAGTAAGTCAGTGAA-TAACTTAATTCTAGGTAATT
1 AGTAATCAGTAACTTAATTCAGGGTAATTAAGTAAGTCAAT-AAGTAACTTAATTC-AGG---GT
* * * *
53925 AATTAAGT-AATAGGTAACTTAATTCAGGGTAATTAAGT---CAATAAGTAGCTTAATTCAGGGT
61 AATTAAGTCAATAAGTAGCTTAATTCAGGGTAATTAAGTAAGTAATAAGTAACTTAATTCAGGGT
53986 AATTA
126 AATTA
*
53991 AGTAAGTCAGCAACTTAATTCAGGGTAATTAAGTAAGT-AATAAGTAACTTAATTCAGGGTAATT
1 AGTAA-TCAGTAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATT
54055 AAGTCAATAAGTAGCTTAATTCAGGGTAATTAAGTAAGTAATAAGTAACTTAATTCAGGGTAATT
65 AAGTCAATAAGTAGCTTAATTCAGGGTAATTAAGTAAGTAATAAGTAACTTAATTCAGGGTAATT
54120 A
130 A
* * * *
54121 AGTCAATAAGTAGCTTAATTCAGGGTAATTAAGTAAGT-AATAGGTAACTTAATTCAGGGTAAAT
1 AGT-AATCAGTAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATT
*
54185 AAGTCAATAAGTAGCTTAATTCAGGGTAATTAAGTAAGTAATAGGTAACTTAATTCAGGGTAATT
65 AAGTCAATAAGTAGCTTAATTCAGGGTAATTAAGTAAGTAATAAGTAACTTAATTCAGGGTAATT
54250 A
130 A
* * ** * * *
54251 AGTCAATAAGTAGCTTAATTCAGGGTAATTAA-TAAAAGTCTGTTAGTAGCTTAATTTAGGGTAA
1 AGT-AATCAGTAACTTAATTCAGGGTAATTAAGT--AAGTCAATAAGTAACTTAATTCAGGGTAA
* * * * * * * * *
54315 TTAAGAAAGTTAGTAAGTCAGTAATTTAATTCAGGGTAATTAAGAAATTCAGTTATTAATTTAAT
63 TT----AAGTCAATAAGT-AG---CTTAATTCAGGGTAATTAAGTAAGT-AATAAGTAACTTAAT
*
54380 TTAGGGTAATTA
119 TCAGGGTAATTA
* *
54392 AGTAATTCAGTAATCAACTTAATTCATGGTAATTAAGTAAGT-AATAGGTAACTTAATTCAGGGT
1 AGTAA-TCAG---T-AACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGT
* ** * * * *
54456 AATTAAGTCAGTAAGTAGCTTAATTCACAGTAATTAAGTAAAGTCAGTTAGTAACTTAGTTCAGA
61 AATTAAGTCAATAAGTAGCTTAATTCAGGGTAATTAAGT-AAGT-AATAAGTAACTTAATTCAGG
*
54521 GAAATTA
124 GTAATTA
* * * * *
54528 AGTAAGGCAGTAACTTAATTCAGGGTAATTAAATAATTCAGTAA-TCAACTTAAATCTAGGGTAA
1 AGTAA-TCAGTAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGT-AACTTAATTC-AGGGTAA
* *
54592 TTATGTCAGCTAATAAGTAACTTAATTCAGGGTAATTAAGTAAGT
63 TTAAGT---C-AATAAGTAGCTTAATTCAGGGTAATTAAGTAAGT
54637 CATTGATCGA
Statistics
Matches: 547, Mismatches: 66, Indels: 59
0.81 0.10 0.09
Matches are distributed among these distances:
126 9 0.02
127 28 0.05
129 6 0.01
130 197 0.36
131 36 0.07
132 44 0.08
133 13 0.02
134 12 0.02
135 17 0.03
136 43 0.08
137 7 0.01
138 28 0.05
139 11 0.02
140 24 0.04
141 27 0.05
143 20 0.04
144 5 0.01
145 19 0.03
146 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (130 bp):
AGTAATCAGTAACTTAATTCAGGGTAATTAAGTAAGTCAATAAGTAACTTAATTCAGGGTAATTA
AGTCAATAAGTAGCTTAATTCAGGGTAATTAAGTAAGTAATAAGTAACTTAATTCAGGGTAATTA
Found at i:54365 original size:18 final size:18
Alignment explanation
Indices: 54341--54431 Score: 73
Period size: 18 Copynumber: 5.2 Consensus size: 18
54331 GTCAGTAATT
54341 TAATTCAGGGTAATTAAG
1 TAATTCAGGGTAATTAAG
* * *
54359 AAATTCA--GTTATTAATT
1 TAATTCAGGGTAATTAA-G
*
54376 TAATTTAGGGTAATTAAG
1 TAATTCAGGGTAATTAAG
* *
54394 TAATTCA--GTAATCAACT
1 TAATTCAGGGTAATTAA-G
*
54411 TAATTCATGGTAATTAAG
1 TAATTCAGGGTAATTAAG
54429 TAA
1 TAA
54432 GTAATAGGTA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
16 14 0.25
17 12 0.22
18 15 0.27
19 14 0.25
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (18 bp):
TAATTCAGGGTAATTAAG
Found at i:59816 original size:25 final size:25
Alignment explanation
Indices: 59788--59842 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
59778 AGAGCGAAAA
*
59788 AAAAATGAAAATA-AAAGTGAAAATG
1 AAAAATGAAAAAAGAAAGT-AAAATG
*
59813 AAAATTGAAAAAAGAAAGTAAAATG
1 AAAAATGAAAAAAGAAAGTAAAATG
59838 AAAAA
1 AAAAA
59843 CGAAGGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (25 bp):
AAAAATGAAAAAAGAAAGTAAAATG
Found at i:60154 original size:13 final size:14
Alignment explanation
Indices: 60136--60173 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
60126 TCAAGTGCAT
60136 AAAAAAAGAG-AGA
1 AAAAAAAGAGAAGA
60149 AAAAAAAGAAGAAGA
1 AAAAAAAG-AGAAGA
60164 AGAAAAAAGA
1 A-AAAAAAGA
60174 AGCTCTAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 2 0.09
15 5 0.23
16 7 0.32
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAGAAGA
Found at i:60160 original size:16 final size:16
Alignment explanation
Indices: 60136--60175 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
60126 TCAAGTGCAT
60136 AAAAA-AAGAGAGAA-A
1 AAAAAGAAGA-AGAAGA
60151 AAAAAGAAGAAGAAGA
1 AAAAAGAAGAAGAAGA
60167 AAAAAGAAG
1 AAAAAGAAG
60176 CTCTAGGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAGAAGA
Found at i:61371 original size:25 final size:26
Alignment explanation
Indices: 61336--61385 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
61326 CATTAGAAAT
** *
61336 CACCTAGGGGCGTTTTGGTCATTTTG
1 CACCTAGGGGCACTTTAGTCATTTTG
61362 CACC-AGGGGCACTTTAGTCATTTT
1 CACCTAGGGGCACTTTAGTCATTTT
61386 TAATTCATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (26 bp):
CACCTAGGGGCACTTTAGTCATTTTG
Found at i:61478 original size:2 final size:2
Alignment explanation
Indices: 61471--61495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61461 CAAAACCCAA
61471 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 A
61496 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.