Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014220.1 Corchorus capsularis cultivar CVL-1 contig14241, 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: 86236
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1699 original size:16 final size:16
Alignment explanation
Indices: 1680--1710 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1670 CCCGAAACCC
1680 GACTAACCCGTGACCT
1 GACTAACCCGTGACCT
*
1696 GACTGACCCGTGACC
1 GACTAACCCGTGACC
1711 CAAATAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.39, G:0.23, T:0.16
Consensus pattern (16 bp):
GACTAACCCGTGACCT
Found at i:1926 original size:13 final size:14
Alignment explanation
Indices: 1908--1944 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1898 AATTTAAATT
1908 ATAGAATAAAG-AA
1 ATAGAATAAAGAAA
*
1921 ATAGAATATAGAAA
1 ATAGAATAAAGAAA
1935 ATAGAATAAA
1 ATAGAATAAA
1945 CTTGTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (14 bp):
ATAGAATAAAGAAA
Found at i:2361 original size:16 final size:16
Alignment explanation
Indices: 2340--2481 Score: 126
Period size: 16 Copynumber: 8.9 Consensus size: 16
2330 CTAAACTCGA
*
2340 ACCCGAATAACCCGAG
1 ACCCGAATGACCCGAG
* * *
2356 ACCCGATTAACCCAAG
1 ACCCGAATGACCCGAG
* *
2372 AACCGAATGACCCGAA
1 ACCCGAATGACCCGAG
* *
2388 ACCCGATTAACCCGAG
1 ACCCGAATGACCCGAG
*
2404 ACCCGAATAACCCGAG
1 ACCCGAATGACCCGAG
* *
2420 A-CCTAATTGACCCGAA
1 ACCCGAA-TGACCCGAG
*
2436 ACCCGATTGACCCGA-
1 ACCCGAATGACCCGAG
* *
2451 ACCCAAATGACCCGAA
1 ACCCGAATGACCCGAG
*
2467 ACCCAAATGACCCGA
1 ACCCGAATGACCCGA
2482 AAAAACTGAC
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
15 17 0.16
16 84 0.81
17 3 0.03
ACGTcount: A:0.37, C:0.37, G:0.16, T:0.10
Consensus pattern (16 bp):
ACCCGAATGACCCGAG
Found at i:2399 original size:48 final size:48
Alignment explanation
Indices: 2339--2483 Score: 170
Period size: 48 Copynumber: 3.0 Consensus size: 48
2329 TCTAAACTCG
* *
2339 AACCCGAATAACCCGAGACCCGATTAACCCAAGAACCGAA-TGACCCGA
1 AACCCGATTAACCCGAGACCCGAATAACCCAAG-ACCGAATTGACCCGA
* *
2387 AACCCGATTAACCCGAGACCCGAATAACCCGAGACCTAATTGACCCGA
1 AACCCGATTAACCCGAGACCCGAATAACCCAAGACCGAATTGACCCGA
* * * * *
2435 AACCCGATTGACCCGA-ACCCAAATGACCCGAA-ACCCAAATGACCCGA
1 AACCCGATTAACCCGAGACCCGAATAACCC-AAGACCGAATTGACCCGA
2482 AA
1 AA
2484 AAACTGACTG
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
47 31 0.36
48 54 0.64
ACGTcount: A:0.39, C:0.36, G:0.16, T:0.10
Consensus pattern (48 bp):
AACCCGATTAACCCGAGACCCGAATAACCCAAGACCGAATTGACCCGA
Found at i:2433 original size:32 final size:32
Alignment explanation
Indices: 2339--2481 Score: 146
Period size: 32 Copynumber: 4.5 Consensus size: 32
2329 TCTAAACTCG
* *
2339 AACCCGAATAACCCGAGACCCGATTAACCC-A
1 AACCCGAATGACCCGAGACCCAATTAACCCGA
* * *
2370 AGAACCGAATGACCCGAAACCCGATTAACCCGA
1 A-ACCCGAATGACCCGAGACCCAATTAACCCGA
* * * *
2403 GACCCGAATAACCCGAGACCTAATTGACCCGA
1 AACCCGAATGACCCGAGACCCAATTAACCCGA
* * *
2435 AACCCGATTGACCCGA-ACCCAAATGACCCGA
1 AACCCGAATGACCCGAGACCCAATTAACCCGA
*
2466 AACCCAAATGACCCGA
1 AACCCGAATGACCCGA
2482 AAAAACTGAC
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
31 28 0.30
32 64 0.69
33 1 0.01
ACGTcount: A:0.38, C:0.36, G:0.16, T:0.10
Consensus pattern (32 bp):
AACCCGAATGACCCGAGACCCAATTAACCCGA
Found at i:3553 original size:15 final size:16
Alignment explanation
Indices: 3531--3568 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3521 CGCTCAAATG
3531 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
* *
3546 TTGGGTCAATTTTGGT
1 TCGGGTCAATTTGGGT
3562 TCGGGTC
1 TCGGGTC
3569 TTTTTCAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.08, C:0.13, G:0.37, T:0.42
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:4334 original size:2 final size:2
Alignment explanation
Indices: 4327--4359 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4317 AATGTATTAT
*
4327 TA TA TA TA TA TA TA TA TA -A TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4360 ATAATACTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4354 original size:15 final size:15
Alignment explanation
Indices: 4330--4362 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4320 GTATTATTAT
*
4330 ATATATATATATATA
1 ATATACATATATATA
4345 ATATACATATATATA
1 ATATACATATATATA
4360 ATA
1 ATA
4363 ATACTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATACATATATATA
Found at i:8090 original size:2 final size:2
Alignment explanation
Indices: 8083--8118 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8073 AATGAAAGGG
8083 AT AT AT 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 AT AT AT
8119 TGTGTCAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9852 original size:237 final size:237
Alignment explanation
Indices: 9437--9914 Score: 956
Period size: 237 Copynumber: 2.0 Consensus size: 237
9427 GCCCATATCT
9437 TTAAATTTGTGAATCGCGAAGTTTGGTGTAAAAGACGAGACATAGGATGGATGATGATATTTGTG
1 TTAAATTTGTGAATCGCGAAGTTTGGTGTAAAAGACGAGACATAGGATGGATGATGATATTTGTG
9502 CATCGATGTAATTACCTACTAAACACACCTGTTAAATGTAAAATAAATACATAGAGTGAAGACAA
66 CATCGATGTAATTACCTACTAAACACACCTGTTAAATGTAAAATAAATACATAGAGTGAAGACAA
9567 CTAACAAGTAGTAATTTTATTTTCCGTCTCGATCGAACAAAATTATTATAATTAAACCTTATGTT
131 CTAACAAGTAGTAATTTTATTTTCCGTCTCGATCGAACAAAATTATTATAATTAAACCTTATGTT
9632 ATGTCATCAACGAACGTCATATATATCATGTCAAACTATAGA
196 ATGTCATCAACGAACGTCATATATATCATGTCAAACTATAGA
9674 TTAAATTTGTGAATCGCGAAGTTTGGTGTAAAAGACGAGACATAGGATGGATGATGATATTTGTG
1 TTAAATTTGTGAATCGCGAAGTTTGGTGTAAAAGACGAGACATAGGATGGATGATGATATTTGTG
9739 CATCGATGTAATTACCTACTAAACACACCTGTTAAATGTAAAATAAATACATAGAGTGAAGACAA
66 CATCGATGTAATTACCTACTAAACACACCTGTTAAATGTAAAATAAATACATAGAGTGAAGACAA
9804 CTAACAAGTAGTAATTTTATTTTCCGTCTCGATCGAACAAAATTATTATAATTAAACCTTATGTT
131 CTAACAAGTAGTAATTTTATTTTCCGTCTCGATCGAACAAAATTATTATAATTAAACCTTATGTT
9869 ATGTCATCAACGAACGTCATATATATCATGTCAAACTATAGA
196 ATGTCATCAACGAACGTCATATATATCATGTCAAACTATAGA
9911 TTAA
1 TTAA
9915 TTTCAGTATT
Statistics
Matches: 241, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 241 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (237 bp):
TTAAATTTGTGAATCGCGAAGTTTGGTGTAAAAGACGAGACATAGGATGGATGATGATATTTGTG
CATCGATGTAATTACCTACTAAACACACCTGTTAAATGTAAAATAAATACATAGAGTGAAGACAA
CTAACAAGTAGTAATTTTATTTTCCGTCTCGATCGAACAAAATTATTATAATTAAACCTTATGTT
ATGTCATCAACGAACGTCATATATATCATGTCAAACTATAGA
Found at i:10584 original size:42 final size:42
Alignment explanation
Indices: 10505--10590 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 42
10495 AATTCCTACT
10505 ATGTAATATATATAATAACTAATTAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAA-TAAATACTTACATTAATTAA
*
10548 ATGTAATAATACTATAATAACT-A-AAATACTTGCATTAATTAA
1 ATGTAAT-ATA-TATAATAACTAATAAATACTTACATTAATTAA
10590 A
1 A
10591 CAAGACACAG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
42 19 0.47
43 7 0.17
44 4 0.10
45 10 0.25
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.37
Consensus pattern (42 bp):
ATGTAATATATATAATAACTAATAAATACTTACATTAATTAA
Found at i:15379 original size:16 final size:16
Alignment explanation
Indices: 15358--15391 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
15348 TACCATCTAC
*
15358 TAGCAGAGGCTTCAAA
1 TAGCAGAGGCTTAAAA
15374 TAGCAGAGGCTTAAAA
1 TAGCAGAGGCTTAAAA
15390 TA
1 TA
15392 CCATCTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (16 bp):
TAGCAGAGGCTTAAAA
Found at i:18447 original size:3 final size:3
Alignment explanation
Indices: 18439--18464 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18429 TATAATTAGT
18439 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
18465 TTTGACATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19225 original size:2 final size:2
Alignment explanation
Indices: 19218--19249 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19208 ATTTGCGTGG
19218 AT 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 AT
19250 GTCCAAAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19401 original size:16 final size:16
Alignment explanation
Indices: 19370--19437 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
19360 AATCCGCCCG
* *
19370 AACCCGAACACAAAAA
1 AACCCGAACCCGAAAA
19386 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
* *
19402 AATCAGAACCCG-AAA
1 AACCCGAACCCGAAAA
* *
19417 AATCTGAAACCCGAAAA
1 AACCCG-AACCCGAAAA
19434 AACC
1 AACC
19438 AAACCTGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
15 8 0.18
16 30 0.68
17 6 0.14
ACGTcount: A:0.54, C:0.31, G:0.10, T:0.04
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:19673 original size:32 final size:32
Alignment explanation
Indices: 19636--19741 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 32
19626 ACCCAATCCG
*
19636 AACCCGAACCCGAATGAACCTGACCCAAAATT
1 AACCCGAACCCGAATCAACCTGACCCAAAATT
* * * *
19668 GACCCGAACCCGAATCAGCATAACCC-AAATT
1 AACCCGAACCCGAATCAACCTGACCCAAAATT
* *
19699 CAACTCGAACCCGAATCAACC-GACCCAAATTT
1 -AACCCGAACCCGAATCAACCTGACCCAAAATT
*
19731 AATCCGAACCC
1 AACCCGAACCC
19742 AACTTAAATC
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
31 18 0.31
32 41 0.69
ACGTcount: A:0.39, C:0.37, G:0.11, T:0.13
Consensus pattern (32 bp):
AACCCGAACCCGAATCAACCTGACCCAAAATT
Found at i:19743 original size:17 final size:17
Alignment explanation
Indices: 19721--19758 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
19711 GAATCAACCG
*
19721 ACCCAAATTTAATCCGA
1 ACCCAAATTAAATCCGA
*
19738 ACCCAACTTAAATCCGA
1 ACCCAAATTAAATCCGA
19755 ACCC
1 ACCC
19759 GAATCCAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.37, G:0.05, T:0.18
Consensus pattern (17 bp):
ACCCAAATTAAATCCGA
Found at i:21934 original size:22 final size:22
Alignment explanation
Indices: 21867--21967 Score: 87
Period size: 22 Copynumber: 4.5 Consensus size: 22
21857 CTTTCATTGC
* *
21867 ATTTTGATAACATCCTTAAGAA
1 ATTTTGATAACATCCATATGAA
* * * *
21889 ATTTCGGTAACCATACACTCTGAA
1 ATTTTGATAA-CATCCA-TATGAA
*
21913 CTTTTGATAACATCCATATGAA
1 ATTTTGATAACATCCATATGAA
* *
21935 ATTTCGATAACCTCTC-TATGAA
1 ATTTTGATAACATC-CATATGAA
21957 ATTTTGATAAC
1 ATTTTGATAAC
21968 CACCCTAAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 6
0.74 0.18 0.07
Matches are distributed among these distances:
22 40 0.66
23 10 0.16
24 11 0.18
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (22 bp):
ATTTTGATAACATCCATATGAA
Found at i:21936 original size:46 final size:44
Alignment explanation
Indices: 21867--21967 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 44
21857 CTTTCATTGC
* * *
21867 ATTTTGATAACATCCTTAAGAAATTTCGGTAACCATACACTCTGAA
1 ATTTTGATAACATCCATAAGAAATTTCGATAACC-T-CACTATGAA
* * *
21913 CTTTTGATAACATCCATATGAAATTTCGATAACCTCTCTATGAA
1 ATTTTGATAACATCCATAAGAAATTTCGATAACCTCACTATGAA
21957 ATTTTGATAAC
1 ATTTTGATAAC
21968 CACCCTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 17 0.35
45 1 0.02
46 30 0.62
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (44 bp):
ATTTTGATAACATCCATAAGAAATTTCGATAACCTCACTATGAA
Found at i:22615 original size:22 final size:22
Alignment explanation
Indices: 22460--22735 Score: 127
Period size: 22 Copynumber: 12.7 Consensus size: 22
22450 AACAGATTTG
* *
22460 TGAAATTTTTATAACATCCTTA
1 TGAAATTTTGATAACCTCCTTA
* * *
22482 TGAAATTTTGTTAACCTTCGTA
1 TGAAATTTTGATAACCTCCTTA
* * **
22504 TGAAATTTTGATATCCACAGTA
1 TGAAATTTTGATAACCTCCTTA
* *
22526 --AAATTTTGATAATCTGAC-TA
1 TGAAATTTTGATAACCT-CCTTA
* * * * *
22546 TGAAATTTCGATGACCACATTG
1 TGAAATTTTGATAACCTCCTTA
* * * *
22568 TCAAATTTTGGTAACAT-TTCTA
1 TGAAATTTTGATAACCTCCT-TA
*
22590 TGAAATTTTGATAACCTCCTTC
1 TGAAATTTTGATAACCTCCTTA
* * * *
22612 TGAATTTTTTATAATCATGC-TA
1 TGAAATTTTGATAA-CCTCCTTA
** *
22634 TGAAA-TCGGATAACCTCCCTA
1 TGAAATTTTGATAACCTCCTTA
* *
22655 TGAAATTTCGATAACC-GCTCTA
1 TGAAATTTTGATAACCTCCT-TA
* * *
22677 TGAAATTTCGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCCT-TA
* *
22699 TGAAATTTTGATATCATCCTTA
1 TGAAATTTTGATAACCTCCTTA
*
22721 TGAAATTTTGTTAAC
1 TGAAATTTTGATAAC
22736 ATCTATAATA
Statistics
Matches: 183, Mismatches: 59, Indels: 24
0.69 0.22 0.09
Matches are distributed among these distances:
20 17 0.09
21 14 0.08
22 147 0.80
23 5 0.03
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCTTA
Found at i:22863 original size:20 final size:20
Alignment explanation
Indices: 22827--22864 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22817 AATATACATA
*
22827 TAAACAATTATATTTTTATT
1 TAAACAATTATACTTTTATT
22847 TAAAC-ATTCATACTTTTA
1 TAAACAATT-ATACTTTTA
22865 CTTGTAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAACAATTATACTTTTATT
Found at i:34305 original size:26 final size:26
Alignment explanation
Indices: 34269--34320 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
34259 AATTCATTTA
34269 TTTATTACCCAAAATTGTGTAAAGTC
1 TTTATTACCCAAAATTGTGTAAAGTC
34295 TTTATTACCCAAAATTGTGTAAAGTC
1 TTTATTACCCAAAATTGTGTAAAGTC
34321 AGTAAGTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTATTACCCAAAATTGTGTAAAGTC
Found at i:35236 original size:2 final size:2
Alignment explanation
Indices: 35229--35265 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35219 ATAATCACCC
35229 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
35266 TCATATGAAA
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:35776 original size:22 final size:22
Alignment explanation
Indices: 35407--35845 Score: 153
Period size: 22 Copynumber: 20.0 Consensus size: 22
35397 AATTTTTTTT
*
35407 TAACCTTC-TTATGAAATTTTGT
1 TAACC-TCATTATGAAATTTTGA
* * *
35429 TAACCTCCCTGA-GGAATTTTGA
1 TAACCT-CATTATGAAATTTTGA
*
35451 -AGACCTCAATATGAAATTTTGA
1 TA-ACCTCATTATGAAATTTTGA
* *** *
35473 TAACTTCCCAATGAAATTTTGG
1 TAACCTCATTATGAAATTTTGA
* * *
35495 TAACCAACACTAT-AAGATGTTGA
1 TAACC-TCATTATGAA-ATTTTGA
* *
35518 TAACCTCCA-TATGATATATTGA
1 TAACCT-CATTATGAAATTTTGA
* * * *
35540 TAACCACGTTATGAAAATTTAA
1 TAACCTCATTATGAAATTTTGA
*
35562 AAACCTCCA-TATG-AATTGTT-A
1 TAACCT-CATTATGAAATT-TTGA
* * * *
35583 GTAATCACACTCTGAAATTTTGA
1 -TAACCTCATTATGAAATTTTGA
*
35606 TAA--TCATACTATGAAATTGTGA
1 TAACCTCAT--TATGAAATTTTGA
**
35628 TAACCTCGCTATGAAATTTTGA
1 TAACCTCATTATGAAATTTTGA
* ** *
35650 TAAATCTTCCCTATTAAATTTTGA
1 T-AA-CCTCATTATGAAATTTTGA
* *
35674 TAAACCTTC-CTATAAAATTTTGA
1 T-AACC-TCATTATGAAATTTTGA
* *
35697 TAACTTTC-TTATGAAATCTTGA
1 TAAC-CTCATTATGAAATTTTGA
*
35719 TAA---C--TA-CAAATTTTGA
1 TAACCTCATTATGAAATTTTGA
* **
35735 TAACCTCCTTATGATTTTTTGA
1 TAACCTCATTATGAAATTTTGA
*
35757 TAACCTCATTATGAAATTTTGT
1 TAACCTCATTATGAAATTTTGA
* **
35779 TAATCTCCCTATGAAATTTTGA
1 TAACCTCATTATGAAATTTTGA
* * **
35801 TCTACAT-AAAATGAAATTTTGA
1 T-AACCTCATTATGAAATTTTGA
35823 TAACCCTC-TTATGAAATTTTGA
1 TAA-CCTCATTATGAAATTTTGA
35845 T
1 T
35846 TACTCCATAA
Statistics
Matches: 310, Mismatches: 74, Indels: 66
0.69 0.16 0.15
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
19 1 0.00
20 2 0.01
21 14 0.05
22 210 0.68
23 45 0.15
24 24 0.08
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCATTATGAAATTTTGA
Found at i:36017 original size:66 final size:65
Alignment explanation
Indices: 35947--36113 Score: 151
Period size: 66 Copynumber: 2.5 Consensus size: 65
35937 AATCACATTT
** * ** *
35947 TGAAAATTTGATAATTTCTTTATGAAATTTTGATAACCTC-TTTATAAAATTTTGTTAACCCCTC
1 TGAAAATTTGATAATTTC-TTATGAAATTTTGATAACCTCGCGT-TAAAATTTTGATAACAACAC
36011 TA
64 TA
* ** * *
36013 TG-AAATTCTGAAAATCACATTATGTAATTTTGATAACCTCGCGTTAAAATTTTGATAACAACAG
1 TGAAAATT-TGATAATTTC-TTATGAAATTTTGATAACCTCGCGTTAAAATTTTGATAACAACAC
36077 TA
64 TA
* *
36079 TGAAATTTTGATAATCTTCCTAT-AAATTTTGATAA
1 TGAAAATTTGATAAT-TTCTTATGAAATTTTGATAA
36114 TCTGATCTCT
Statistics
Matches: 79, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
65 16 0.20
66 57 0.72
67 6 0.08
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (65 bp):
TGAAAATTTGATAATTTCTTATGAAATTTTGATAACCTCGCGTTAAAATTTTGATAACAACACTA
Found at i:36107 original size:21 final size:24
Alignment explanation
Indices: 36077--36148 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 24
36067 ATAACAACAG
36077 TATGAAATTTTGATAATCT-TC-C
1 TATGAAATTTTGATAATCTATCTC
36099 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATCT-ATCTC
36123 TATGAAATTTTGATAATC-A-CTC
1 TATGAAATTTTGATAATCTATCTC
36145 TATG
1 TATG
36149 CGATTTGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
21 15 0.33
22 10 0.22
23 3 0.07
24 4 0.09
25 14 0.30
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (24 bp):
TATGAAATTTTGATAATCTATCTC
Found at i:36148 original size:22 final size:22
Alignment explanation
Indices: 35923--36193 Score: 125
Period size: 22 Copynumber: 12.4 Consensus size: 22
35913 GAAATACCAA
35923 TATGAAATTTTTG-TAATCACAT-
1 TATGAAA-TTTTGATAATCAC-TC
* * ** *
35945 TTTGAAAATTTGATAATTTCTT
1 TATGAAATTTTGATAATCACTC
* * *
35967 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAATCACTC
* * * *
35989 TATAAAATTTTGTTAACCCCTC
1 TATGAAATTTTGATAATCACTC
* *
36011 TATGAAATTCTGAAAATCACAT-
1 TATGAAATTTTGATAATCAC-TC
* * * *
36033 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAATCACTC
* **
36055 GT-TAAAATTTTGATAA-CAACAG
1 -TATGAAATTTTGATAATC-ACTC
*
36077 TATGAAATTTTGATAATC-TTCC
1 TATGAAATTTTGATAATCACT-C
36099 TAT-AAATTTTGATAATCTGATCTC
1 TATGAAATTTTGATAATC--A-CTC
36123 TATGAAATTTTGATAATCACTC
1 TATGAAATTTTGATAATCACTC
**
36145 TATGCGA-TTTGATAA-C-CTTC
1 TATGAAATTTTGATAATCAC-TC
* * *
36165 TATTAAATTTTGGTACTC-CT-
1 TATGAAATTTTGATAATCACTC
36185 TATGAAATT
1 TATGAAATT
36194 AAGACTTTTA
Statistics
Matches: 190, Mismatches: 42, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
19 1 0.01
20 15 0.08
21 36 0.19
22 115 0.61
23 4 0.02
24 4 0.02
25 15 0.08
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACTC
Found at i:36250 original size:22 final size:21
Alignment explanation
Indices: 36213--36338 Score: 71
Period size: 22 Copynumber: 5.8 Consensus size: 21
36203 ATAACCTTCA
**
36213 TATGAAATTTCAATAACCACAC
1 TATGAAATTTTGATAACCAC-C
*
36235 TATAAAATTTTGATAA-CATGCC
1 TATGAAATTTTGATAACCA--CC
* * *
36257 CATGAAATATT-AGTAACCTCC
1 TATGAAATTTTGA-TAACCACC
*
36278 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCAC-C
*
36301 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCAC-C
36323 TAT-AACATTTTGATAA
1 TATGAA-ATTTTGATAA
36339 TCTCTTTGAT
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
21 9 0.11
22 65 0.81
23 6 0.08
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACC
Found at i:36458 original size:22 final size:22
Alignment explanation
Indices: 36373--36557 Score: 130
Period size: 22 Copynumber: 8.3 Consensus size: 22
36363 TTGTGATAAT
* **
36373 TAACCACCCTATGAAATTTCAA
1 TAACCACACTATGAAATTTTGA
* *
36395 TAACCA-ATCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
* *
36417 TAA-CATGATCCTATGAAATTTTGG
1 TAACCA-CA--CTATGAAATTTTGA
*
36441 TAACCACACTGTGAAATTTTGA
1 TAACCACACTATGAAATTTTGA
*
36463 TAACTTC-CA-TATGAAATTTTGG
1 TAAC--CACACTATGAAATTTTGA
*
36485 TAACCACACTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * *
36507 TAACCTC-CTCATGAAATTATAA
1 TAACCACACT-ATGAAATTTTGA
*
36529 TAACCATC-TTATGAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
36551 TAACCAC
1 TAACCAC
36558 GTAGAGACAA
Statistics
Matches: 130, Mismatches: 22, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 7 0.05
22 99 0.76
23 5 0.04
24 16 0.12
25 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:36490 original size:44 final size:43
Alignment explanation
Indices: 36425--36555 Score: 165
Period size: 44 Copynumber: 3.0 Consensus size: 43
36415 AATAACATGA
* *
36425 TCCTATGAAATTTTGGTAACCACACTGTGAAATTTTGATAACT
1 TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
*
36468 TCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
1 TCC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
* ** *
36512 TCCTCATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 TCCT-ATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
36556 ACGTAGAGAC
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
43 4 0.05
44 72 0.94
45 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
Found at i:36752 original size:19 final size:20
Alignment explanation
Indices: 36721--36758 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
36711 TATTGACATT
36721 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
36740 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
36759 ATAATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:37443 original size:37 final size:37
Alignment explanation
Indices: 37355--37446 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 37
37345 ATCTACGCCC
* * *
37355 AAATAGGACGTTGGAGACAAAGACAAAAAGTAAAATT
1 AAATAGGACATTGGAAACAAAGACAAAAAGCAAAATT
** *
37392 AAATACAACGATTGGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGAC-ATTGGAAACAAAGACAAAAAGCAAAATT
37430 AAATAGGACATTGGAAA
1 AAATAGGACATTGGAAA
37447 TAAAAAGGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 15 0.33
38 31 0.67
ACGTcount: A:0.55, C:0.10, G:0.20, T:0.15
Consensus pattern (37 bp):
AAATAGGACATTGGAAACAAAGACAAAAAGCAAAATT
Found at i:38225 original size:22 final size:21
Alignment explanation
Indices: 37843--38277 Score: 138
Period size: 22 Copynumber: 20.0 Consensus size: 21
37833 TAATTTTTTT
*
37843 TAACCTTCTTATGAAATTTTGT
1 TAACC-TCTTATGAAATTTTGA
* * *
37865 TAACCTCCCTAAGGAATTTTGA
1 TAACCT-CTTATGAAATTTTGA
* **
37887 TAACTTCCCAATGAAATTTTGA
1 TAACCT-CTTATGAAATTTTGA
* * * *
37909 TAACCAACAGTATGAGATGTTGA
1 TAACC-TC-TTATGAAATTTTGA
* * *
37932 TAACCTCCATATGATATATTGA
1 TAACCT-CTTATGAAATTTTGA
* * *
37954 TAACCACGTTATGAAAATTTAA
1 TAACCTC-TTATGAAATTTTGA
* *
37976 AAACCTCCATATG-AATTGTT-A
1 TAACCT-CTTATGAAATT-TTGA
* *
37997 GTAATCACAC-TCTGAAATTTTGA
1 -TAA-C-CTCTTATGAAATTTTGA
* * *
38020 TAATCACAC-TATGAAATTGTAA
1 TAA-C-CTCTTATGAAATTTTGA
* *
38042 TAATCTCGCTATGAAATTTTGA
1 TAACCTC-TTATGAAATTTTGA
*
38064 TAAACCTCTCTATAAAATTTTGA
1 T-AACCTCT-TATGAAATTTTGA
* * **
38087 TAACTTTCTAATGAAATCATGA
1 TAAC-CTCTTATGAAATTTTGA
*
38109 TAA---C-TA-CAAATTTTGA
1 TAACCTCTTATGAAATTTTGA
* **
38125 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CTTATGAAATTTTGA
*
38147 TAACCTCATTATGAAATTTTGT
1 TAACCTC-TTATGAAATTTTGA
* * *
38169 TAATCTCCCTAAGAAATTTTGA
1 TAACCT-CTTATGAAATTTTGA
* *
38191 TCTACATAC-TATGAAATTTTGA
1 T-AACCT-CTTATGAAATTTTGA
*
38213 TAACCCTCTTATGAAAATTTGA
1 TAA-CCTCTTATGAAATTTTGA
* *
38235 -AAACTAAATTATGAAATTTTGA
1 TAACCT--CTTATGAAATTTTGA
* *
38257 TATCCTC-CATGAAATTTTGA
1 TAACCTCTTATGAAATTTTGA
38277 T
1 T
38278 TACTCCATAA
Statistics
Matches: 306, Mismatches: 76, Indels: 64
0.69 0.17 0.14
Matches are distributed among these distances:
16 10 0.03
17 1 0.00
18 1 0.00
20 18 0.06
21 13 0.04
22 210 0.69
23 52 0.17
24 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (21 bp):
TAACCTCTTATGAAATTTTGA
Found at i:38285 original size:19 final size:20
Alignment explanation
Indices: 38245--38285 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
38235 AAACTAAATT
*
38245 ATGAAATTTTGATATCCTCC
1 ATGAAATTTTGATATACTCC
38265 ATGAAATTTTGAT-TACTCC
1 ATGAAATTTTGATATACTCC
38284 AT
1 AT
38286 AATAAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
ATGAAATTTTGATATACTCC
Found at i:38408 original size:22 final size:22
Alignment explanation
Indices: 38383--38629 Score: 145
Period size: 22 Copynumber: 11.3 Consensus size: 22
38373 AATCACATTT
38383 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
38405 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
38427 TAAAATTTCGTTGACACCTC--TA
1 TGAAATTTTGAT-A-ACCTCTTTA
* * * *
38449 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
*
38471 TGTAATTTTGATAACCTCGTTT-
1 TGAAATTTTGATAACCTC-TTTA
* ** **
38493 TAAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
38515 TGAAATTTTGATAA--TCTTACTA
1 TGAAATTTTGATAACCTCTT--TA
* *
38537 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTTTA
* * *
38561 TGAAATTTTGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
38583 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
38603 TCAAATTTTGGT-ACTTC-TTA
1 TGAAATTTTGATAACCTCTTTA
38623 TGAAATT
1 TGAAATT
38630 GAGACTTTTA
Statistics
Matches: 172, Mismatches: 37, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
20 22 0.13
21 28 0.16
22 96 0.56
23 3 0.02
24 8 0.05
25 12 0.07
26 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:38409 original size:44 final size:44
Alignment explanation
Indices: 38359--38574 Score: 171
Period size: 44 Copynumber: 4.9 Consensus size: 44
38349 GAAATACCAC
*
38359 TATGAAATTTTTG-TAATCACATTTTGAAATTTTGATAACCTCTT
1 TATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCTCTT
* * * * * *
38403 TATGAAATTTTGATAACCTCTTTATAAAATTTCGTTGACACCTC--
1 TATGAAATTTTGATAATCACATTATGAAATTTTGAT-A-ACCTCTT
* *
38447 TATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGTT
1 TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTC-TT
* *
38492 T-TAAAATTTTGATAA-CAACACTATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAATC-ACATTATGAAATTTTGATAACCTCTT
38533 ACTAT-AAATTTTGATAATCTGATC-TCTATGAAATTTTGATAA
1 --TATGAAATTTTGATAATC--A-CAT-TATGAAATTTTGATAA
38575 TCACTCTATG
Statistics
Matches: 137, Mismatches: 21, Indels: 26
0.74 0.11 0.14
Matches are distributed among these distances:
41 2 0.01
42 7 0.05
43 20 0.15
44 83 0.61
45 3 0.02
46 22 0.16
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCTT
Found at i:38472 original size:66 final size:66
Alignment explanation
Indices: 38383--38549 Score: 203
Period size: 66 Copynumber: 2.5 Consensus size: 66
38373 AATCACATTT
* * * * * *
38383 TGAAATTTTGATAACCTCTTTATGAAATTTTGATAACCTC-TTTATAAAATTTCGTTGACACCTC
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACCTCGTTT-TAAAATTTCGATAACAACAC
38447 TA
65 TA
* * * *
38449 TGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGTTTTAAAATTTTGATAACAACACT
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACCTCGTTTTAAAATTTCGATAACAACACT
38514 A
66 A
* *
38515 TGAAATTTTGATAATCTTACTAT-AAATTTTGATAA
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAA
38550 TCTGATCTCT
Statistics
Matches: 85, Mismatches: 15, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
65 11 0.13
66 71 0.84
67 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (66 bp):
TGAAATTTTGATAATCTCATTATGAAATTTTGATAACCTCGTTTTAAAATTTCGATAACAACACT
A
Found at i:38521 original size:88 final size:88
Alignment explanation
Indices: 38358--38522 Score: 217
Period size: 88 Copynumber: 1.9 Consensus size: 88
38348 AGAAATACCA
* * * **
38358 CTATGAAATTTTTGTAATCACATTTTGAAATTTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAATTTTGATAACCTCTTTATAAAATTTTGATAACAAC
**
38423 TTTATAAAATTTCGTTGACACCT
66 ACTATAAAATTTCGTTGACACCT
*
38446 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGTTT-TAAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAATTTTGATAACCTC-TTTATAAAATTTTGATAACA
*
38509 ACACTATGAAATTT
64 ACACTATAAAATTT
38523 TGATAATCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 4 0.06
88 59 0.89
89 3 0.05
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAATTTTGATAACCTCTTTATAAAATTTTGATAACAAC
ACTATAAAATTTCGTTGACACCT
Found at i:38678 original size:22 final size:22
Alignment explanation
Indices: 38653--38723 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
38643 CCTTCGTATA
*
38653 AAATTTTGATAACCT-CTCCATG
1 AAATTTTGATAACCTCCT-AATG
*
38675 AAATATT-AGTAACCTCCTAATG
1 AAATTTTGA-TAACCTCCTAATG
* *
38697 AAATTTTGTTAACCACACT-ATG
1 AAATTTTGATAACCTC-CTAATG
38719 AAATT
1 AAATT
38724 CTAATGACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 1 0.03
22 35 0.88
23 4 0.10
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTAATG
Found at i:38858 original size:22 final size:22
Alignment explanation
Indices: 38831--38964 Score: 98
Period size: 22 Copynumber: 6.0 Consensus size: 22
38821 TAAACTAATC
38831 CTATGAAATTTCTG-TAACCACA
1 CTATGAAATTT-TGATAACCACA
*
38853 CTATGAATATTTTTGATAAATTC-CA
1 CTATGAA-A-TTTTGAT-AA-CCACA
*
38878 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
38899 CTATAAAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
38920 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
* *
38943 TTATAAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
38965 TAGAGACAAG
Statistics
Matches: 88, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
20 1 0.01
21 7 0.08
22 59 0.67
23 6 0.07
24 10 0.11
25 4 0.05
26 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:38927 original size:44 final size:42
Alignment explanation
Indices: 38829--38961 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 42
38819 AATAAACTAA
* **
38829 TCCTATGAAATTTCTGTAACCACACTATGAATATTTTTGATAAAT
1 TCCTATGAAATTT-TGTAACCACACTAT-AA-AATTTTGATAACC
38874 TCCATATGAAATTTTGGTAACCACACTATAAAATTTTGATAACC
1 TCC-TATGAAATTTT-GTAACCACACTATAAAATTTTGATAACC
** *
38918 TCCTCATGAAATTATAATAACCATC-TTATAAAATTTTGATAACC
1 TCCT-ATGAAATT-TTGTAACCA-CACTATAAAATTTTGATAACC
38962 ACATAGAGAC
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
43 1 0.01
44 45 0.58
45 8 0.10
46 23 0.30
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (42 bp):
TCCTATGAAATTTTGTAACCACACTATAAAATTTTGATAACC
Found at i:39449 original size:152 final size:152
Alignment explanation
Indices: 39173--39476 Score: 429
Period size: 152 Copynumber: 2.0 Consensus size: 152
39163 AATAGTAAAG
*
39173 GAAATTTACATGTTCATCAACTAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAATTT
1 GAAATTTACATGTTCATCAACTAAAATCAATTTGAAAAACTTATAATTCGGTCTAAATTGAATTT
* * *
39238 TTAATTAATTTTAAATAATAAAATTATACTAAATATATTTTGAAAAAATGGTGCAATCGGGAAAC
66 TTAATTAATTTTAAATAATAAAATTATACGAAATATATTTTGAAAAAATGGTACAATCGGAAAAC
*
39303 ATAAAGTTTCCCATTATTCGTA
131 ATAAAGTTTCACATTATTCGTA
* * *
39325 GAAATTTGCATGTTCATCAA-TGAAAATCAATTTTATAAAACTTATAATTCTGTCTAAATTGAAA
1 GAAATTTACATGTTCATCAACT-AAAATCAATTTGA-AAAACTTATAATTCGGTCTAAATTG-AA
**
39389 TTTTATAATTAATTTT-AATAATGTCAATT-TA-GAAATATA-TTTGAAAAAATGGTACAATCGG
63 TTTT-TAATTAATTTTAAATAAT-AAAATTATACGAAATATATTTTGAAAAAATGGTACAATCGG
*
39450 AAAACATAAAGTTTTACATTATTCGTA
126 AAAACATAAAGTTTCACATTATTCGTA
39477 CTTGTATATA
Statistics
Matches: 136, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
151 1 0.01
152 76 0.56
153 30 0.22
154 14 0.10
155 15 0.11
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (152 bp):
GAAATTTACATGTTCATCAACTAAAATCAATTTGAAAAACTTATAATTCGGTCTAAATTGAATTT
TTAATTAATTTTAAATAATAAAATTATACGAAATATATTTTGAAAAAATGGTACAATCGGAAAAC
ATAAAGTTTCACATTATTCGTA
Found at i:39713 original size:32 final size:32
Alignment explanation
Indices: 39677--39744 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
39667 TTTAGTCATG
*
39677 ACAATTTAGAAATATGTTTTTAAAAA-AATGGT
1 ACAATTTAGAAATAT-ATTTTAAAAATAATGGT
*
39709 ACAA-TTGGAAATATATTTTAAAAATAATGGT
1 ACAATTTAGAAATATATTTTAAAAATAATGGT
39740 ACAAT
1 ACAAT
39745 CGGAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 9 0.28
31 19 0.59
32 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (32 bp):
ACAATTTAGAAATATATTTTAAAAATAATGGT
Found at i:39730 original size:30 final size:32
Alignment explanation
Indices: 39685--39750 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
39675 TGACAATTTA
* *
39685 GAAATATGTTTTTAAAAA-AATGGTACAATTG
1 GAAATATGATTTTAAAAATAATGGTACAATCG
39716 GAAATAT-ATTTTAAAAATAATGGTACAATCG
1 GAAATATGATTTTAAAAATAATGGTACAATCG
39747 GAAA
1 GAAA
39751 ACATAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (32 bp):
GAAATATGATTTTAAAAATAATGGTACAATCG
Found at i:42446 original size:28 final size:28
Alignment explanation
Indices: 42414--42485 Score: 135
Period size: 28 Copynumber: 2.6 Consensus size: 28
42404 CCAGGACGTC
42414 TCCCTCTGATGTATCAGGCGTAAAATCT
1 TCCCTCTGATGTATCAGGCGTAAAATCT
42442 TCCCTCTGATGTATCAGGCGTAAAATCT
1 TCCCTCTGATGTATCAGGCGTAAAATCT
*
42470 TCCCTCTGATGCATCA
1 TCCCTCTGATGTATCA
42486 CATGGCATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.32
Consensus pattern (28 bp):
TCCCTCTGATGTATCAGGCGTAAAATCT
Found at i:43128 original size:17 final size:17
Alignment explanation
Indices: 43102--43150 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
43092 TCCCTCTCAT
43102 GGTACCAGGTAGCATGA
1 GGTACCAGGTAGCATGA
*
43119 GGTACTAGGTAGCATGA
1 GGTACCAGGTAGCATGA
43136 GGTACCAGGTAGCAT
1 GGTACCAGGTAGCAT
43151 CTGCTGTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.20
Consensus pattern (17 bp):
GGTACCAGGTAGCATGA
Found at i:51008 original size:41 final size:41
Alignment explanation
Indices: 50894--51011 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
50884 ATTTCATGGT
* * * ***
50894 TATCTCTCTTAGGGTTTAGCTTGGTTTT-GGGTATTTATTT
1 TATCTCTCTTAAGGTTTAGCTTAGTTTTAGGGCATTTAGCA
* *
50934 TATCTCTCTT-AGGGTTAGCTTAGTTTTAGGGGCATTTGGCA
1 TATCTCTCTTAAGGTTTAGCTTAGTTTTA-GGGCATTTAGCA
*
50975 TCTCTCTCTTAAGGTTTAGCTTAGTTTTAGGGCATTT
1 TATCTCTCTTAAGGTTTAGCTTAGTTTTAGGGCATTT
51012 CTTTCTCTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
39 14 0.22
40 10 0.15
41 24 0.37
42 17 0.26
ACGTcount: A:0.15, C:0.14, G:0.23, T:0.48
Consensus pattern (41 bp):
TATCTCTCTTAAGGTTTAGCTTAGTTTTAGGGCATTTAGCA
Found at i:56861 original size:50 final size:50
Alignment explanation
Indices: 56758--56861 Score: 154
Period size: 50 Copynumber: 2.1 Consensus size: 50
56748 TTCAACCTTC
* * * *
56758 ACAATTAATTGCTTTATAATTTCCCAAATTAGTTTAATACAATTTGGCTA
1 ACAATTAATTGCTTTATAATTTCCCAAATTAGTCTAATACAATCTAGCAA
* *
56808 ACAATTAATTGCTTTATAATTTTCCAACTTAGTCTAATACAATCTAGCAA
1 ACAATTAATTGCTTTATAATTTCCCAAATTAGTCTAATACAATCTAGCAA
56858 ACAA
1 ACAA
56862 AATTCAGGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (50 bp):
ACAATTAATTGCTTTATAATTTCCCAAATTAGTCTAATACAATCTAGCAA
Found at i:56990 original size:50 final size:50
Alignment explanation
Indices: 56923--57027 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
56913 TCCAATATAT
*
56923 AACAATTAAGTGCTTTATAATTTCCCAAATTAGTTTAATACAATCTAGCA
1 AACAATTAAGTGCTTTATAATTTCCCAAATTAGTCTAATACAATCTAGCA
* * * *
56973 AACAATTAATTGTTTTATAATTTTCCAACTTAGTCTAATACAATCTAGCA
1 AACAATTAAGTGCTTTATAATTTCCCAAATTAGTCTAATACAATCTAGCA
57023 AACAA
1 AACAA
57028 AACTCAGGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (50 bp):
AACAATTAAGTGCTTTATAATTTCCCAAATTAGTCTAATACAATCTAGCA
Found at i:61243 original size:23 final size:23
Alignment explanation
Indices: 61193--61251 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
61183 TGTGGTTAAT
* *
61193 AAAATTTCATAAGGAAATTTTATC
1 AAAATTTCAT-AGGAAAGTTTATA
* *
61217 AAAATTTTATAGGGAAGTTTATA
1 AAAATTTCATAGGAAAGTTTATA
61240 AAAATTTCATAG
1 AAAATTTCATAG
61252 TGAGGTATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (23 bp):
AAAATTTCATAGGAAAGTTTATA
Found at i:61268 original size:21 final size:23
Alignment explanation
Indices: 60942--61404 Score: 271
Period size: 22 Copynumber: 20.8 Consensus size: 23
60932 TGTCTTTGTG
* **
60942 TGGTTATCAAAATTTCAGA-ACA
1 TGGTTATCAAAATTTCATAGTGA
* * *
60964 TGGTTATTATAATTTCATGAG-AA
1 TGGTTATCAAAATTTCAT-AGTGA
*
60987 T-GTTATCAAAATTTCATAGT-T
1 TGGTTATCAAAATTTCATAGTGA
*
61008 TGGTTATTAAAATTTCATA-TGGA
1 TGGTTATCAAAATTTCATAGT-GA
*
61031 -GGTTATCAAAATTTCGTAG-GA
1 TGGTTATCAAAATTTCATAGTGA
* * *
61052 AGGTTATTAAAATTTTATAGTG-
1 TGGTTATCAAAATTTCATAGTGA
*
61074 TGGTTA-CTAAGATTTCATAG-GA
1 TGGTTATC-AAAATTTCATAGTGA
* *
61096 TTAGGTTATTAGAATTTCATA-TGA
1 -T-GGTTATCAAAATTTCATAGTGA
*
61120 AGGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAGTGA
*
61142 TGGTTATAAAAATTT-ATAAG-GA
1 TGGTTATCAAAATTTCAT-AGTGA
61164 -GG-TATTCAAAATTTCATAGTG-
1 TGGTTA-TCAAAATTTCATAGTGA
61185 TGGTTAAT-AAAATTTCATAAG-GAAA
1 TGGTT-ATCAAAATTTCAT-AGTG--A
* * *
61210 T-TTTATCAAAATTTTATAGGGA
1 TGGTTATCAAAATTTCATAGTGA
* * *
61232 AGTTTATAAAAATTTCATAGTGA
1 TGGTTATCAAAATTTCATAGTGA
* *
61255 -GG-TATCACAATTTCAT-GTTA
1 TGGTTATCAAAATTTCATAGTGA
*
61275 TGGTTATCAAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAGTGA
* * * * *
61297 TGATTACCAATATTTTATCG-GA
1 TGGTTATCAAAATTTCATAGTGA
* * *
61319 AGGTTATCAAAATATCATAATG-
1 TGGTTATCAAAATTTCATAGTGA
* * *
61341 TGCGCTTACCAAAATTTCATTGGGA
1 TG-G-TTATCAAAATTTCATAGTGA
*
61366 -GGTTATCAAAATTTCATAG-GG
1 TGGTTATCAAAATTTCATAGTGA
61387 TGGTTATCAAAATTTCAT
1 TGGTTATCAAAATTTCAT
61405 TAGGTGATTA
Statistics
Matches: 338, Mismatches: 63, Indels: 80
0.70 0.13 0.17
Matches are distributed among these distances:
20 5 0.01
21 38 0.11
22 213 0.63
23 37 0.11
24 44 0.13
25 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (23 bp):
TGGTTATCAAAATTTCATAGTGA
Found at i:61279 original size:90 final size:89
Alignment explanation
Indices: 60992--61294 Score: 239
Period size: 90 Copynumber: 3.4 Consensus size: 89
60982 GAGAATGTTA
* * * ** * *
60992 TCAAAATTTCATAGTTTGGTTATTAAAATTTCATATGG--AGGTTATCAAAATTTCGTAGGAAGG
1 TCAAAATTTCATAGTATGGTTATCAAAATTTCATAAGGAAATTTTATCAAAATTTCATAGGGAGG
* *
61055 TTATTAAAATTT-TATAGTGTGGT-T
66 TTATAAAAATTTATA-AG-GAGGTAT
* * * * * * ** *
61079 ACTAAGATTTCATAGGATTAGGTTATTAGAATTTCAT-ATG-AAGGTTATCAAAATTTCATAGTG
1 TC-AAAATTTCATAGTA-T-GGTTATCAAAATTTCATAAGGAAATTTTATCAAAATTTCATAGGG
*
61142 TGGTTATAAAAATTTATAAGGAGGTAT
63 AGGTTATAAAAATTTATAAGGAGGTAT
* *
61169 TCAAAATTTCATAGTGTGGTTAAT-AAAATTTCATAAGGAAATTTTATCAAAATTTTATAGGGAA
1 TCAAAATTTCATAGTATGGTT-ATCAAAATTTCATAAGGAAATTTTATCAAAATTTCATAGGG-A
*
61233 GTTTATAAAAATTTCAT-AGTGAGGTA-
64 GGTTATAAAAATTT-ATAAG-GAGGTAT
*
61259 TCACAATTTCAT-GTTATGGTTATCAAAATTTCATAA
1 TCAAAATTTCATAG-TATGGTTATCAAAATTTCATAA
61295 TGTGATTACC
Statistics
Matches: 175, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
87 14 0.08
88 16 0.09
89 39 0.22
90 96 0.55
91 10 0.06
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (89 bp):
TCAAAATTTCATAGTATGGTTATCAAAATTTCATAAGGAAATTTTATCAAAATTTCATAGGGAGG
TTATAAAAATTTATAAGGAGGTAT
Found at i:61330 original size:44 final size:45
Alignment explanation
Indices: 61276--61383 Score: 146
Period size: 46 Copynumber: 2.4 Consensus size: 45
61266 TTCATGTTAT
* *
61276 GGTTATCAAAATTTCATAATGT-GATTACCAATATTTTATCGGAA
1 GGTTATCAAAATTTCATAATGTCGATTACCAAAATTTCATCGGAA
* * * *
61320 GGTTATCAAAATATCATAATGTGCGCTTACCAAAATTTCATTGGGA
1 GGTTATCAAAATTTCATAATGT-CGATTACCAAAATTTCATCGGAA
61366 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
61384 GGGTGGTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 21 0.38
46 34 0.62
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAATGTCGATTACCAAAATTTCATCGGAA
Found at i:61537 original size:22 final size:23
Alignment explanation
Indices: 61512--61570 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
61502 TATCGTCATA
*
61512 AAAACTTTATAGTGTAA-TTATC
1 AAAACTTTATAGTGAAAGTTATC
*
61534 AAAACTCTATA-T-AAAGGTTATC
1 AAAACTTTATAGTGAAA-GTTATC
*
61556 AAAATTTTATAGTGA
1 AAAACTTTATAGTGA
61571 TTATTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 2 0.07
21 1 0.03
22 24 0.83
23 1 0.03
24 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (23 bp):
AAAACTTTATAGTGAAAGTTATC
Found at i:61726 original size:54 final size:54
Alignment explanation
Indices: 61644--61748 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
61634 CTTAAACTAA
61644 TAGTTATAAAGTTATAAATATAACAGTTGTGGAGATCATCAAGTGGACTGCTAG
1 TAGTTATAAAGTTATAAATATAACAGTTGTGGAGATCATCAAGTGGACTGCTAG
61698 TAGTTATAAAGTTATAAATATAACAGTTGTGGAGATCATCAAGTGGACTGC
1 TAGTTATAAAGTTATAAATATAACAGTTGTGGAGATCATCAAGTGGACTGC
61749 AATGAGTGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (54 bp):
TAGTTATAAAGTTATAAATATAACAGTTGTGGAGATCATCAAGTGGACTGCTAG
Found at i:61756 original size:14 final size:14
Alignment explanation
Indices: 61739--61767 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61729 GAGATCATCA
61739 AGTGGACTGCAATG
1 AGTGGACTGCAATG
61753 AGTGGACTGCAATG
1 AGTGGACTGCAATG
61767 A
1 A
61768 TTTATAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (14 bp):
AGTGGACTGCAATG
Found at i:69347 original size:2 final size:2
Alignment explanation
Indices: 69340--69375 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
69330 CTATAACTTT
69340 TA TA TA TA TA TA TA TA TA T- 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
69376 GAAGGAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:69361 original size:19 final size:19
Alignment explanation
Indices: 69339--69375 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
69329 ACTATAACTT
69339 TTATATATATATATATATA
1 TTATATATATATATATATA
69358 TTATATATATATATATAT
1 TTATATATATATATATAT
69376 GAAGGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATATATATATATATA
Found at i:69362 original size:17 final size:17
Alignment explanation
Indices: 69342--69375 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
69332 ATAACTTTTA
69342 TATATATATATATATAT
1 TATATATATATATATAT
69359 TATATATATATATATAT
1 TATATATATATATATAT
69376 GAAGGAAAAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:70573 original size:1 final size:1
Alignment explanation
Indices: 70567--70594 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
70557 AGAAGAGAAG
70567 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
70595 TCGGGTAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:71947 original size:42 final size:42
Alignment explanation
Indices: 71888--71975 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
71878 GCAGTTGCAG
71888 GAGGTTTCTGACAAACAATTTTCTTGCCAACCTTAAGACAGC
1 GAGGTTTCTGACAAACAATTTTCTTGCCAACCTTAAGACAGC
*
71930 GAGGTTTCTGACAAACAATTTTCTTTCCAACCTTAAGACAGC
1 GAGGTTTCTGACAAACAATTTTCTTGCCAACCTTAAGACAGC
71972 GAGG
1 GAGG
71976 AGCAGGAGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (42 bp):
GAGGTTTCTGACAAACAATTTTCTTGCCAACCTTAAGACAGC
Found at i:73082 original size:29 final size:27
Alignment explanation
Indices: 73038--73096 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 27
73028 AAAAGACTTT
*
73038 TTTTTTTTTACAAGAGAAAAAAGACAC
1 TTTTTTTTTACAAGAGAAAAAAAACAC
*
73065 TTTTTTTTTGCAATAGAGAAAAAAAACAC
1 TTTTTTTTTAC-A-AGAGAAAAAAAACAC
73094 TTT
1 TTT
73097 ATTAATCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.36
28 1 0.04
29 17 0.61
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (27 bp):
TTTTTTTTTACAAGAGAAAAAAAACAC
Found at i:76144 original size:27 final size:27
Alignment explanation
Indices: 76112--76167 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
76102 CAAAACCTAG
*
76112 TATTTTGAATTTTTGTCATATATTCAC
1 TATTTTGAATTTTTATCATATATTCAC
*
76139 TATTTTGAATTTTTATTATATATTCAC
1 TATTTTGAATTTTTATCATATATTCAC
76166 TA
1 TA
76168 GCACACACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.05, T:0.57
Consensus pattern (27 bp):
TATTTTGAATTTTTATCATATATTCAC
Found at i:79487 original size:17 final size:17
Alignment explanation
Indices: 79465--79498 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
79455 AAATTTTTTC
79465 AATA-TTCAATAATAATA
1 AATATTTCAATAA-AATA
79482 AATATTTCAATAAAATA
1 AATATTTCAATAAAATA
79499 TCAATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
AATATTTCAATAAAATA
Done.