Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012868.1 Corchorus capsularis cultivar CVL-1 contig12889, 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: 90373
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--25 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1 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 T
26 TTACCAAAGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3362 original size:18 final size:18
Alignment explanation
Indices: 3339--3374 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3329 CATCCCCACG
*
3339 ATACCCAGGTTCACTCCC
1 ATACCCAGATTCACTCCC
*
3357 ATACCCAGATTCATTCCC
1 ATACCCAGATTCACTCCC
3375 TTGAGCATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.42, G:0.08, T:0.25
Consensus pattern (18 bp):
ATACCCAGATTCACTCCC
Found at i:8987 original size:7 final size:7
Alignment explanation
Indices: 8977--9029 Score: 97
Period size: 7 Copynumber: 7.6 Consensus size: 7
8967 GAAGAAGGAA
8977 GTCACAT
1 GTCACAT
8984 GTCACAT
1 GTCACAT
8991 GTCACAT
1 GTCACAT
8998 GTCACAT
1 GTCACAT
9005 GTCACAT
1 GTCACAT
9012 GTCACAT
1 GTCACAT
*
9019 GTCACAG
1 GTCACAT
9026 GTCA
1 GTCA
9030 GTAGATAGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (7 bp):
GTCACAT
Found at i:11377 original size:218 final size:218
Alignment explanation
Indices: 10999--11437 Score: 869
Period size: 218 Copynumber: 2.0 Consensus size: 218
10989 AACATATACA
*
10999 CTTGCGTAGAGATAGACTAAGGTAACATCGTAGCGTTAAACCCGAAAGGGACGAATCTAACTATT
1 CTTGCGTAGAGATAGACTAAGGTAACATCATAGCGTTAAACCCGAAAGGGACGAATCTAACTATT
11064 CTTCTCCAGTGTTAGAAGACATGCTCTTCCCCCTAATTTCCCGAGGATTCCGAGGAGGATTAAAG
66 CTTCTCCAGTGTTAGAAGACATGCTCTTCCCCCTAATTTCCCGAGGATTCCGAGGAGGATTAAAG
11129 ATTTGATATGGAATTATTTTCCTTAAATTCACGATCAATCAAACAGAATGTTAAAGAATAAAAGA
131 ATTTGATATGGAATTATTTTCCTTAAATTCACGATCAATCAAACAGAATGTTAAAGAATAAAAGA
11194 GCAAGGCAATCACACTTATCATT
196 GCAAGGCAATCACACTTATCATT
11217 CTTGCGTAGAGATAGACTAAGGTAACATCATAGCGTTAAACCCGAAAGGGACGAATCTAACTATT
1 CTTGCGTAGAGATAGACTAAGGTAACATCATAGCGTTAAACCCGAAAGGGACGAATCTAACTATT
11282 CTTCTCCAGTGTTAGAAGACATGCTCTTCCCCCTAATTTCCCGAGGATTCCGAGGAGGATTAAAG
66 CTTCTCCAGTGTTAGAAGACATGCTCTTCCCCCTAATTTCCCGAGGATTCCGAGGAGGATTAAAG
11347 ATTTGATATGGAATTATTTTCCTTAAATTCACGATCAATCAAACAGAATGTTAAAGAATAAAAGA
131 ATTTGATATGGAATTATTTTCCTTAAATTCACGATCAATCAAACAGAATGTTAAAGAATAAAAGA
11412 GCAAGGCAATCACACTTATCATT
196 GCAAGGCAATCACACTTATCATT
11435 CTT
1 CTT
11438 CTACGCTCAA
Statistics
Matches: 220, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
218 220 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (218 bp):
CTTGCGTAGAGATAGACTAAGGTAACATCATAGCGTTAAACCCGAAAGGGACGAATCTAACTATT
CTTCTCCAGTGTTAGAAGACATGCTCTTCCCCCTAATTTCCCGAGGATTCCGAGGAGGATTAAAG
ATTTGATATGGAATTATTTTCCTTAAATTCACGATCAATCAAACAGAATGTTAAAGAATAAAAGA
GCAAGGCAATCACACTTATCATT
Found at i:18685 original size:12 final size:11
Alignment explanation
Indices: 18670--18703 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
18660 AAACTTATGA
18670 AAAAAACAAAGG
1 AAAAAA-AAAGG
18682 AAAAAAAAAGG
1 AAAAAAAAAGG
*
18693 AAAAAGAAAGG
1 AAAAAAAAAGG
18704 GGGATTGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:62604 original size:11 final size:12
Alignment explanation
Indices: 62569--62604 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
62559 ATTATTCATA
62569 AAATTTAGACAC
1 AAATTTAGACAC
62581 AAATTTAGCACAC
1 AAATTTAG-ACAC
62594 AAATTTA-ACAC
1 AAATTTAGACAC
62605 CAGGTTTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 8 0.35
13 11 0.48
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (12 bp):
AAATTTAGACAC
Found at i:64581 original size:30 final size:29
Alignment explanation
Indices: 64507--64581 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
64497 TGGGTTTGAT
*
64507 TTTACAAATTCATGGGGCAATGTGGCACAA
1 TTTACAAATTCA-GGGGCAATCTGGCACAA
**
64537 TTTA-AAGCTCAGGGGCAATCTGGC-CTAAA
1 TTTACAAATTCAGGGGCAATCTGGCAC--AA
64566 TTTACAAATTCAGGGG
1 TTTACAAATTCAGGGG
64582 GCAAAATGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 12 0.32
29 11 0.30
30 13 0.35
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (29 bp):
TTTACAAATTCAGGGGCAATCTGGCACAA
Found at i:65650 original size:19 final size:19
Alignment explanation
Indices: 65614--65650 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
65604 ATTTGAACAA
*
65614 ACTTTTTTAACCAAAAAAG
1 ACTTTTTTAACAAAAAAAG
65633 ACTTTTTTAACAAAAAAA
1 ACTTTTTTAACAAAAAAA
65651 TTAAAAGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (19 bp):
ACTTTTTTAACAAAAAAAG
Found at i:66131 original size:41 final size:42
Alignment explanation
Indices: 66052--66138 Score: 140
Period size: 41 Copynumber: 2.0 Consensus size: 42
66042 AGGAAGTATT
66052 ACCTTAATTTCTAACAAGTATATATACGAGTTTCAAGGAAAACCG
1 ACCTTAATTTCTAACAAG---ATATACGAGTTTCAAGGAAAACCG
66097 ACCTTAATTTCTAACAAG-TATACGAGTTTCAAGGAAAACCG
1 ACCTTAATTTCTAACAAGATATACGAGTTTCAAGGAAAACCG
66138 A
1 A
66139 AAACAAAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
41 24 0.57
45 18 0.43
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (42 bp):
ACCTTAATTTCTAACAAGATATACGAGTTTCAAGGAAAACCG
Found at i:69393 original size:3 final size:3
Alignment explanation
Indices: 69387--69429 Score: 59
Period size: 3 Copynumber: 13.3 Consensus size: 3
69377 GTTTTTTTTA
69387 ATT ATT ATT ATT ATT ATT AATT ATT AATT ATT AATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT -ATT ATT -ATT ATT -ATT ATT ATT A
69430 ATTACAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 28 0.76
4 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:69411 original size:10 final size:10
Alignment explanation
Indices: 69384--69433 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
69374 GCCGTTTTTT
69384 TTAATTATTA
1 TTAATTATTA
69394 TT-ATTATTA
1 TTAATTATTA
69403 TTAATTATTAATTA
1 TT-A--ATT-ATTA
69417 TTAATTATTA
1 TTAATTATTA
69427 TTAATTA
1 TTAATTA
69434 CAATTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.26
10 13 0.37
11 3 0.09
13 4 0.11
14 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTAATTATTA
Found at i:69433 original size:7 final size:7
Alignment explanation
Indices: 69384--69426 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
69374 GCCGTTTTTT
69384 TTAATTA
1 TTAATTA
69391 TT-ATTA
1 TTAATTA
69397 TT-ATTA
1 TTAATTA
69403 TTAATTA
1 TTAATTA
69410 TTAATTA
1 TTAATTA
69417 TTAATTA
1 TTAATTA
69424 TTA
1 TTA
69427 TTAATTACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTAATTA
Found at i:73142 original size:7 final size:7
Alignment explanation
Indices: 73130--73156 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
73120 GATTCCACAC
73130 TTGCCAG
1 TTGCCAG
73137 TTGCCAG
1 TTGCCAG
73144 TTGCCAG
1 TTGCCAG
73151 TTGCCA
1 TTGCCA
73157 CTATTGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (7 bp):
TTGCCAG
Found at i:75227 original size:15 final size:15
Alignment explanation
Indices: 75205--75302 Score: 169
Period size: 15 Copynumber: 6.5 Consensus size: 15
75195 CGGCATGGAT
75205 GGCATGGGTGGCATG
1 GGCATGGGTGGCATG
*
75220 GACATGGGTGGCATG
1 GGCATGGGTGGCATG
75235 GGCATGGGTGGCATG
1 GGCATGGGTGGCATG
*
75250 GGCATGGGCGGCATG
1 GGCATGGGTGGCATG
75265 GGCATGGGTGGCATG
1 GGCATGGGTGGCATG
*
75280 GGCATGGGCGGCATG
1 GGCATGGGTGGCATG
75295 GGCATGGG
1 GGCATGGG
75303 CATGGGCGGC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 78 1.00
ACGTcount: A:0.14, C:0.15, G:0.53, T:0.17
Consensus pattern (15 bp):
GGCATGGGTGGCATG
Found at i:75241 original size:30 final size:30
Alignment explanation
Indices: 75190--75302 Score: 181
Period size: 30 Copynumber: 3.7 Consensus size: 30
75180 CTTTGCGAAT
*
75190 ATGGGCGGCATGGATGGCATGGGTGGCATGGAC
1 ATGGGCGGCAT-G--GGCATGGGTGGCATGGGC
*
75223 ATGGGTGGCATGGGCATGGGTGGCATGGGC
1 ATGGGCGGCATGGGCATGGGTGGCATGGGC
75253 ATGGGCGGCATGGGCATGGGTGGCATGGGC
1 ATGGGCGGCATGGGCATGGGTGGCATGGGC
75283 ATGGGCGGCATGGGCATGGG
1 ATGGGCGGCATGGGCATGGG
75303 CATGGGCGGC
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
30 66 0.86
32 1 0.01
33 10 0.13
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.18
Consensus pattern (30 bp):
ATGGGCGGCATGGGCATGGGTGGCATGGGC
Found at i:75263 original size:45 final size:45
Alignment explanation
Indices: 75190--75303 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
75180 CTTTGCGAAT
*
75190 ATGGGCGGCATGGATGGCATGGGTGGCATGGACATGGGTGGCATGGGC
1 ATGGGCGGCAT-G--GGCATGGGCGGCATGGACATGGGTGGCATGGGC
* *
75238 ATGGGTGGCATGGGCATGGGCGGCATGGGCATGGGTGGCATGGGC
1 ATGGGCGGCATGGGCATGGGCGGCATGGACATGGGTGGCATGGGC
75283 ATGGGCGGCATGGGCATGGGC
1 ATGGGCGGCATGGGCATGGGC
75304 ATGGGCGGCA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
45 51 0.82
47 1 0.02
48 10 0.16
ACGTcount: A:0.15, C:0.16, G:0.52, T:0.18
Consensus pattern (45 bp):
ATGGGCGGCATGGGCATGGGCGGCATGGACATGGGTGGCATGGGC
Found at i:75288 original size:21 final size:21
Alignment explanation
Indices: 75190--75272 Score: 59
Period size: 21 Copynumber: 4.0 Consensus size: 21
75180 CTTTGCGAAT
75190 ATGGGCGGCAT-GG-AT-GGC
1 ATGGGCGGCATGGGCATGGGC
* *
75208 ATGGGTGGCATGGACATGGGTGGC
1 ATGGGCGGCATGGGCAT--G-GGC
*
75232 ATGGGCATGG-GT-GGCATGGGC
1 ATGGGC--GGCATGGGCATGGGC
75253 ATGGGCGGCATGGGCATGGG
1 ATGGGCGGCATGGGCATGGG
75273 TGGCATGGGC
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
18 10 0.20
19 3 0.06
20 3 0.06
21 17 0.35
22 1 0.02
24 12 0.24
25 1 0.02
26 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.52, T:0.18
Consensus pattern (21 bp):
ATGGGCGGCATGGGCATGGGC
Found at i:75323 original size:15 final size:15
Alignment explanation
Indices: 75190--75303 Score: 156
Period size: 15 Copynumber: 7.4 Consensus size: 15
75180 CTTTGCGAAT
75190 ATGGGCGGCATGGATGGC
1 ATGGGCGGCAT-G--GGC
* *
75208 ATGGGTGGCATGGAC
1 ATGGGCGGCATGGGC
*
75223 ATGGGTGGCATGGGC
1 ATGGGCGGCATGGGC
*
75238 ATGGGTGGCATGGGC
1 ATGGGCGGCATGGGC
75253 ATGGGCGGCATGGGC
1 ATGGGCGGCATGGGC
*
75268 ATGGGTGGCATGGGC
1 ATGGGCGGCATGGGC
75283 ATGGGCGGCATGGGC
1 ATGGGCGGCATGGGC
75298 ATGGGC
1 ATGGGC
75304 ATGGGCGGCA
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
15 79 0.88
17 1 0.01
18 10 0.11
ACGTcount: A:0.15, C:0.16, G:0.52, T:0.18
Consensus pattern (15 bp):
ATGGGCGGCATGGGC
Found at i:85032 original size:328 final size:328
Alignment explanation
Indices: 84599--87075 Score: 1987
Period size: 329 Copynumber: 7.6 Consensus size: 328
84589 TTTCTGGGCA
* * * * ** * *
84599 AAAAACGTGTTTCGGGGCTCCGACTCAGTTTTGCATGATTTTTGGTTGAAAGGCTTCTTGAAATA
1 AAAAACGAGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
* *
84664 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCTTCTGA
66 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTA
* * * *
84729 ATCTTGATTCGATTTAATTA-AAAATAATTTCGGGAAAATGGAAAAACAATATTAAAAGCGTGAA
131 ATCTTGTTTCGATTTAATTAGAAAATAA-TTCGGAAAAATGGAAAAACGATATTAGAAGCGTGAA
* * * * *
84793 AAACCCTTTAATTTTTTTTTCATTGACTTATATTTTTTTTCTTAGTATTGTGGCAAAGAATTGAG
195 AAACCCTTCAATTTTTTTGTCGTTGAATTATATTTTTTTTCTGAGTATTGTGGCAAAGAATTGAG
*
84858 GAAAAAAATTTCGGGTCAAGTTTGGCAAAATTTTAGTCGAAATCGTGTACTAACCATTACGGTTT
260 GAAAAAATTTTCGGGTCAAGTTT-GCAAAATTTTAGTCGAAATCGTGTACTAACCATTACGGTTT
84923 TTGCT
324 TTGCT
* ** * *
84928 AAAAACGAGTTCCTGGGCATCGACTCATTTTTGCAT-ATTTTTGGCAGAAAGACTCCATGAAATA
1 AAAAACGAGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
* * * * * *
84992 TCTATATTCATTTAACCAATTCTCAGTCACATTGGATTTAAGGATTTGTTTTTATGAGTATTTTA
66 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTA
* * *
85057 ATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATTGGAAAAACGATATTAAAAGCGTGAA
131 ATCTTGTTTCGATTTAATTAGAAAATAATTCGGAAAAA-TGGAAAAACGATATTAGAAGCGTGAA
* * * * * * *
85122 AAATCCTTCAATCTTTTAGACGTTGAATTATATATTTTTTCTGAGTATTATGGCAAATAATTGAG
195 AAACCCTTCAATTTTTTTGTCGTTGAATTATATTTTTTTTCTGAGTATTGTGGCAAAGAATTGAG
* * * * * *
85187 AAAAAAAAATTTCGTGT-AAG--T------TTTTAGGCGAACTCGTGTACTAACCATCACGGTTT
260 -GAAAAAATTTTCGGGTCAAGTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATTACGG---
85243 TTTTTTTGGCT
321 --TTTTT-GCT
* * * * *
85254 AAAAACGTGTTTCAGGGCCCCGGCTCAATTTTGCATGATTATTGGCAGAAAGACTCCTTGAAATA
1 AAAAACGAGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
* * * * * **
85319 TCTATGTTTATCTAACCAAATCTCAGTCACATTGGATTTAAGGATTTGTTCTTACGAGCTTCCAA
66 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTA
* * *
85384 ATGTTGTTTCGATTTAATTAG-AAATAAATTCGGGGAAAATGGAAAAACGATATTAGAAGCGTTA
131 ATCTTGTTTCGATTTAATTAGAAAAT-AATTC-GGAAAAATGGAAAAACGATATTAGAAGCGTGA
** * * * *
85448 AAAACCCATT-AATTTTTTAAT-GTTAAATTATATATTTTTTCTTAGTATTGTGGAAAAGAATTG
194 AAAACCC-TTCAATTTTTTTGTCGTTGAATTATATTTTTTTTCTGAGTATTGTGGCAAAGAATTG
* * ** * * * *
85511 ATG-AAAATTTTTTTGGTC-AGTTTTTGCAGAATTTTAGTCGAAATCGTGTATTAACCGTCACAG
258 AGGAAAAAATTTTCGGGTCAAG--TTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATTAC-G
85574 TGTTTTT-CT
320 -GTTTTTGCT
* * * * * * * * *
85583 AAAAACGTGTTACGGGGCCACGGCTCAATTTTGCATGATTTTTGACAGAAAAACTCATTGAAATA
1 AAAAACGAGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
* * * * * * * * *
85648 TATATATTCATTTAACCAATTTTCAACCATATTGGATTTAAGAATTTTTTTTTACAAGCATCTTA
66 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTA
* * * ** *
85713 ATCTTATTTCGATTTAATTA-AAAATTAATTCAGAAAAATAGGAAAAACGATATGAGAAATGTCA
131 ATCTTGTTTCGATTTAATTAGAAAA-TAATTCGGAAAAAT-GGAAAAACGATATTAGAAGCGTGA
** * * * * * * * * **
85777 AAAGGCCTTAAATCTTTTTGGCTTTGAA--ATATTTTTTTTATGAATTTTTTATCCAAA-AATTG
194 AAAACCCTTCAATTTTTTTGTCGTTGAATTATATTTTTTTTCTGAGTATTGT-GGCAAAGAATTG
* * * * * * * * * * *
85839 A-GTAAATATTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCATGAAATAATCATCACAGT
258 AGGAAAAAATTTTCGGGTCAA-GTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATTACGGT
85903 TTTTGGCT
322 TTTT-GCT
* * *
85911 AAAAAAGCA-TT-CAGGAGCCCCGACTCAATTTTTGCATGATTTTTTTGC-GCAAAGACTCCTTG
1 AAAAACG-AGTTCCAGG-GCCCCGACTC-AGTTTTGCATGA-TTTTTGGCAG-AAAGACTCCTTG
* * * * *
85973 AAATATCTATATTCATCGAACTAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGACCA
61 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* * *
86038 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAGAAATGGAAAAACAATATTAGA
126 TCTTAATCTTGTTTCGATTTAATTAGAAAATAATTCGG---AA-AAATGGAAAAACGATATTAGA
** * **
86103 AGCGTGAAAAACCGGTCAATCTTTTTGGT-GTTGAATTATATAATTTTTCTGAGTATTGTGGGGC
187 AGCGTGAAAAACCCTTCAAT-TTTTTTGTCGTTGAATTATATTTTTTTTCTGAGTATTGT--GGC
* * * * *
86167 AAA-AA-TCAAGAAAAAACTTTTCGGGTC-AG--T------TTTTAGCTTGGAAT--TGT-GT-A
249 AAAGAATTGAGGAAAAAA-TTTTCGGGTCAAGTTTGCAAAATTTTAG-TCGAAATCGTGTACTAA
* **
86217 -CGTTACGGTTTTTTTAT
312 CCATTACGG-TTTTTGCT
* * * * * * *
86234 AAAAAAGCGTTCCAAGTCCCCGATTCAGTTTTGCATGATTTTTGGTAGAAAGACTCATTGAAATA
1 AAAAACGAGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
* * * *
86299 TCTATATTTATTTAACTAATTCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTA
66 TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTA
* * * *
86364 ATCTTGTTTCGAATTAATTAGAAATTAATTCGAAAAAAATGGAAAAACTATATTAGAAGCGTG-A
131 ATCTTGTTTCGATTTAATTAGAAAATAATTCG-GAAAAATGGAAAAACGATATTAGAAGCGTGAA
* * * *
86428 AAAGCCTTCCAATATTTTTGGCGATGAATTATATATATATATATATATATATTTCTGAGTATTGT
195 AAACCCTT-CAATTTTTTTGTC---G--TT-GA-AT-TATAT-T-T-T-T-TTTCTGAGTATTGT
* * * * ** * *
86493 GGTAAAAAATTGA-G-AAAAAGTTT----TC-A-TAT--AAGTTTTTAGCCGAAATCGTGCACGT
246 GGCAAAGAATTGAGGAAAAAATTTTCGGGTCAAGTTTGCAAAATTTTAGTCGAAATCGTGTAC-T
**
86548 ---CA-T--GGTCTTAGGGCT
310 AACCATTACGGT-TT-TTGCT
* * *
86563 AAAAACGCGTTTCCA-GGCCTCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAAT
1 AAAAACGAG-TTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAAT
* * * * * ** *
86627 ATTTATATTCATCTAACCAAATCCCAGTCACATTGGACTTAAGGATTTGTTTATACGAGTTTCTG
65 ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTT
* * *
86692 AATCTTGTTTCAATTTAATAAG-AAATAAATTCGGGAAAATGGAAAAACGATATTAGAAGCGTGA
130 AATCTTGTTTCGATTTAATTAGAAAAT-AATTCGGAAAAATGGAAAAACGATATTAGAAGCGTGA
* * * * * *
86756 AAATCCATT-AATTCTTTT-T-GTTGAATTATA-TATTTTTCTGAGTATTATGGAAAAGAATTGA
194 AAAACCCTTCAATTTTTTTGTCGTTGAATTATATTTTTTTTCTGAGTATTGTGGCAAAGAATTGA
* * * * *
86817 TGAAAAATTTTTCGGGTC-AGTTTGCCAAATTTTAGTCGCAATCGTGTACTAACCATTATGGTTT
259 GGAAAAAATTTTCGGGTCAAGTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATTACGGTTT
86881 TTAGGCT
324 TT--GCT
* * * * * *
86888 AAAAACGCA-TTTCGGGGCCCCGACTCAGTTTTGCATGATTGTTGGCAGACATACTTCTTGAAAT
1 AAAAACG-AGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAAT
* *
86952 ATCTATATTCAT-TCAACCAATTCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATGT
65 ATCTATATTCATCT-AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * *
87016 TAATCCTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAATAGG-AAAACGATAATAGAA
129 TAATCTTGTTTCGATTTAATTAGAAAATAATTCGG-AAAAAT-GGAAAAACGATATTAGAA
87076 ACATCAAAAT
Statistics
Matches: 1709, Mismatches: 325, Indels: 231
0.75 0.14 0.10
Matches are distributed among these distances:
311 24 0.01
312 2 0.00
313 8 0.00
315 1 0.00
317 18 0.01
318 34 0.02
319 4 0.00
320 49 0.03
321 111 0.06
322 15 0.01
323 26 0.02
324 30 0.02
325 145 0.08
326 108 0.06
327 163 0.10
328 250 0.15
329 453 0.27
330 130 0.08
331 25 0.01
332 1 0.00
333 35 0.02
334 35 0.02
335 19 0.01
336 13 0.01
337 10 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (328 bp):
AAAAACGAGTTCCAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTA
ATCTTGTTTCGATTTAATTAGAAAATAATTCGGAAAAATGGAAAAACGATATTAGAAGCGTGAAA
AACCCTTCAATTTTTTTGTCGTTGAATTATATTTTTTTTCTGAGTATTGTGGCAAAGAATTGAGG
AAAAAATTTTCGGGTCAAGTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATTACGGTTTTT
GCT
Found at i:86589 original size:980 final size:957
Alignment explanation
Indices: 84502--87064 Score: 2516
Period size: 980 Copynumber: 2.6 Consensus size: 957
84492 TACAATGAAT
* * * *
84502 TATATATTCTTTATGAGTATTGTAGCAAAAAATTGAGAAAAAAAAATTTTCGTGTAAGTTTTTAG
1 TATATATT-TTTCTGAGTATTGT-GGAAAAAATTGAG---AAAAAATTTTCATATAAGTTTTTAG
* * * * * *
84567 CCGAAATCGTGTACCATCACGATTTCTGGGCAAAAAACGTGTTT-CGGGGCTCCGACTCAGTTTT
61 CCGAAATCGTGAACCGTCACG-GTT-TGGGCTAAAAACGTGTTTCCGGGCCT-CGGCTCAGTTTT
** * *
84631 GCATGATTTTTGGTTGAAAGGCTTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAT
123 GCATGATTTTTGGCAGAAAGAC-TCTTGAAATATATATATTCATCTAACCAAATCTCAGCCACAT
84696 TGGATTTAAGGATTTGTTTTTACGAGCTTCTGAATCTTGA-TTCGATTTAATTAAAAA-TAATTT
187 TGGATTTAAGGATTTGTTTTTACGAGCTTCTGAATCTT-ATTTCGATTTAATTAAAAATTAA-TT
* * * * *
84759 CGGGAAAATGGAAAAACAATATTA-AAAGCGTGAAAAACCCTTTAATTTTTTTTTCATTGACTTA
250 CGGGAAAATGGAAAAACGATATTAGAAA-CGTG-AAAACCC-TTAAATCTTTTTGC-TTGA--AA
* * * * * * *
84823 TATTTTTTTTCTTAGTATTGT-GGCAAAGAATTGAGGAAAAAAATTTCGGGTCAAGTTTGGCAAA
309 TATTTTTTTTCTGAATATTTTATGCAAAGAATTGA-GTAAAAATTTTCGGGTCAA-TTTTGCAAA
**
84887 ATTTTAGTCGAAATCGTGTACTAACCATTACGGTTTTT-GCTAAAAACG-AGTTCCTGGGCATCG
372 ATTTTAGTCGAAATCGTGTACTAACCATTACGGTTTTTGGCTAAAAACGCAGTT-C-GGGCCCCG
* * *
84950 ACTCATTTTTGCAT-ATTTTTGGCAG-AAAGACTCCATGAAATATCTATATTCATTTAACCAATT
435 ACTCATTTTTGCATGATTTTTTGC-GCAAAGACTCCTTGAAATATCTATATTCA-TCAACCAATT
* * * *
85013 CTCAGTCACATTGGATTTAAGGATTTGTTTTTATGAGTATTTTAATCTTGTTTCGATTTAATTAG
498 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAG
* * *
85078 AAATTAATTC-G-AAAAAATTGGAAAAACGATATTAAAAGCGTGAAAAATCCTTCAATCTTTTAG
563 AAATTAATTCGGAAAAAAAATGGAAAAACAATATTAAAAGCGTGAAAAATCCGTCAATCTTTTAG
* ** *
85141 ACGTTGAATTATATATTTTTTCTGAGTATTATGGCAAATAATTGAGAAAAAAAAATTTCGTGTAA
628 ACGTTGAATTATATAATTTTTCTGAGTATTATGGCAAATAATCAAGAAAAAAAAATTTCGGGTAA
* * * * *
85206 GTTTTTAGGCGAACTCGTGTACTAACCATCACGGTTTTTTTTTTGGCTAAAAACGTGTTTCAGGG
693 GTTTTTAGGCGAACTCGTGTACT----ATCACGG--TTTTTTTT-GATAAAAAAGCGTTCCAAGG
* * *
85271 CCCCGGCTCAATTTTGCATGATTATTGGCAGAAAGACTCCTTGAAATATCTATGTTTATCTAACC
751 CCCCGACTCAATTTTGCATGATTATTGGCAGAAAGACTCATTGAAATATCTATATTTATCTAACC
* * * *
85336 AAATCTCAGTCACATTGGATTTAAGGATTTGTTCTTACGAGCTTCCAAATGTTGTTTCGATTTAA
816 AAATCTCAGCCACATTGGATTTAAGGATTTGTTCTTACGAGCATCCAAATCTTGTTTCGAATTAA
*** * *
85401 TTAGAAATAAATTCGGGGAAAATGGAAAAACGATATTAGAAGCGTTAAAAACCCATTAATTTTTT
881 TTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCAATAATTTTTT
85466 AATGTTAAATTA
946 AATGTTAAATTA
* ** * * *
85478 TATAT-TTTTTCTTAGTATTGTGGAAAAGAATTGATGAAAATTTTTTTGGTCAGTTTTTGCAGAA
1 TATATATTTTTCTGAGTATTGTGGAAAA-AATTGA-GAAAA--AATTT--TCA---TAT-AAG-T
* ** * * *
85542 TTTTAGTCGAAATCGTGTATTAACCGTCACAGTGTTT-TTCTAAAAACGTGTTACGGGGCCACGG
55 TTTTAGCCGAAATCGTG----AACCGTCAC-G-GTTTGGGCTAAAAACGTGTTTCCGGGCCTCGG
* * * * * *
85606 CTCAATTTTGCATGATTTTTGACAGAAAAACTCATTGAAATATATATATTCATTTAACCAATTTT
114 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTC-TTGAAATATATATATTCATCTAACCAAATCT
* * * * * * *
85671 CAACCATATTGGATTTAAGAATTTTTTTTTACAAGCATCTTAATCTTATTTCGATTTAATTAAAA
178 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCTTCTGAATCTTATTTCGATTTAATTAAAA
* * * * * *
85736 ATTAATTCAGAAAAATAGGAAAAACGATATGAGAAATGTCAAAAGGCCTTAAATCTTTTTGGCTT
243 ATTAATTCGGGAAAAT-GGAAAAACGATATTAGAAACGTGAAAA-CCCTTAAATCTTTTT-GC-T
* * * * *
85801 TGAAATATTTTTTTTATGAATTTTTTATCCAAA-AATTGAGTAAATATTTTCGGGTCAATTTTTA
304 TGAAATATTTTTTTTCTGAATATTTTATGCAAAGAATTGAGTAAAAATTTTCGGGTCAA-TTTTG
* * * * * * * *
85865 CAAAATTTTAGCCGAAATCATGAAATAATCATCACAGTTTTTGGCTAAAAAAGCA-TTCAGGAGC
368 CAAAATTTTAGTCGAAATCGTGTACTAACCATTACGGTTTTTGGCTAAAAACGCAGTTC-GG-GC
85929 CCCGACTCAATTTTTGCATGATTTTTTTGCGCAAAGACTCCTTGAAATATCTATATTCATCGAAC
431 CCCGACTC-ATTTTTGCATGA-TTTTTTGCGCAAAGACTCCTTGAAATATCTATATTCATC-AAC
* * * * * *
85994 TAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGACCATCTGAATCTTGTTTCGATTTA
493 CAATTCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTA
*
86059 ATTAGAAATTAATTCGGAAAAAGAAATGGAAAAACAATATTAGAAGCGTGAAAAA-CCGGTCAAT
558 ATTAGAAATTAATTCGGAAAAA-AAATGGAAAAACAATATTAAAAGCGTGAAAAATCC-GTCAAT
* ** * **
86123 CTTTTTGGTGTTGAATTATATAATTTTTCTGAGTATTGTGGGGCAAA-AATCAAG-AAAAAACTT
621 CTTTTAGACGTTGAATTATATAATTTTTCTGAGTATTAT--GGCAAATAATCAAGAAAAAAAAAT
* *
86186 TTCGGGTCAGTTTTTA-GCTTGGAA-TTGTGTACGT-T-ACGG-TTTTTTT-ATAAAAAAGCGTT
684 TTCGGGTAAGTTTTTAGGC---GAACTCGTGTAC-TATCACGGTTTTTTTTGATAAAAAAGCGTT
* * * * *
86245 CCAAGTCCCCGATTCAGTTTTGCATGATTTTTGGTAGAAAGACTCATTGAAATATCTATATTTAT
745 CCAAGGCCCCGACTCAATTTTGCATGATTATTGGCAGAAAGACTCATTGAAATATCTATATTTAT
* * * * **
86310 TTAACTAATTCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCG
810 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTCTTACGAGCATCCAAATCTTGTTTCG
* * *
86375 AATTAATTAGAAATTAATTCGAAAAAAATGGAAAAACTATATTAGAAGCGTGAAAAGCCTTCCAA
875 AATTAATTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA-AC--CCAA
86440 T-ATTTTTGGCGATGAAT-TATATATATATA
937 TAATTTTT-----T-AATGT-TA-A-AT-TA
*
86469 TATATATATATTTCTGAGTATTGTGGTAAAAAATTGAGAAAAAGTTTTCATATAAGTTTTTAGCC
1 TATATAT-T-TTTCTGAGTATTGTGG-AAAAAATTGAGAAAAAATTTTCATATAAGTTTTTAGCC
* * * *
86534 GAAATCGTGCA-CGTCATGGTCTTAGGGCTAAAAACGCGTTTCCAGGCCTCGGCTCAGTTTTGCA
63 GAAATCGTGAACCGTCACGGT-TT-GGGCTAAAAACGTGTTTCCGGGCCTCGGCTCAGTTTTGCA
* * *
86598 TGATTTTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCTAACCAAATCCCAGTCACATTGG
126 TGATTTTTGGCAGAAAGACT-CTTGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGG
* * * * * *
86663 ACTTAAGGATTTGTTTATACGAGTTTCTGAATCTTGTTTCAATTTAA-TAAGAAATAAATTCGGG
190 ATTTAAGGATTTGTTTTTACGAGCTTCTGAATCTTATTTCGATTTAATTAA-AAATTAATTCGGG
* * * * *
86727 AAAATGGAAAAACGATATTAGAAGCGTGAAAATCCATTAATTCTTTTTG-TTGAATTATATATTT
254 AAAATGGAAAAACGATATTAGAAACGTGAAAA-CCCTTAAATCTTTTTGCTTGAAATAT-TTTTT
* * * *
86791 TTCTGAGTA--TTATGGAAAAGAATTGA-TGAAAAATTTTTCGGGTC-AGTTTGCCAAATTTTAG
317 TTCTGAATATTTTAT-GCAAAGAATTGAGT-AAAAA-TTTTCGGGTCAATTTTGCAAAATTTTAG
* * * *
86852 TCGCAATCGTGTACTAACCATTATGGTTTTTAGGCTAAAAACGCATTTCGGGGCCCCGACTCAGT
379 TCGAAATCGTGTACTAACCATTACGGTTTTT-GGCTAAAAACGCAGTTC-GGGCCCCGACTCATT
* * *
86917 TTTGCATGA-TTGTTG-GCAGACATACTTCTTGAAATATCTATATTCATTCAACCAATTCTCAGC
442 TTTGCATGATTTTTTGCGCA-A-AGACTCCTTGAAATATCTATATTCA-TCAACCAATTCTCAGC
* * *
86980 CACATTGGATTTAAGGATTTGTTTTTACGAGCATGTTAATCCTGTTTCAATTTAATTAGAAATTA
504 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTA
*
87045 ATTCGGAAAAAATA-GGAAAA
569 ATTCGGAAAAAAAATGGAAAA
87065 CGATAATAGA
Statistics
Matches: 1293, Mismatches: 219, Indels: 153
0.78 0.13 0.09
Matches are distributed among these distances:
972 4 0.00
973 14 0.01
974 29 0.02
975 111 0.09
976 67 0.05
977 45 0.03
978 19 0.01
979 45 0.03
980 309 0.24
981 18 0.01
982 70 0.05
983 49 0.04
984 177 0.14
985 46 0.04
986 115 0.09
987 3 0.00
988 13 0.01
989 93 0.07
990 14 0.01
991 20 0.02
992 1 0.00
993 6 0.00
994 21 0.02
995 4 0.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (957 bp):
TATATATTTTTCTGAGTATTGTGGAAAAAATTGAGAAAAAATTTTCATATAAGTTTTTAGCCGAA
ATCGTGAACCGTCACGGTTTGGGCTAAAAACGTGTTTCCGGGCCTCGGCTCAGTTTTGCATGATT
TTTGGCAGAAAGACTCTTGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAA
GGATTTGTTTTTACGAGCTTCTGAATCTTATTTCGATTTAATTAAAAATTAATTCGGGAAAATGG
AAAAACGATATTAGAAACGTGAAAACCCTTAAATCTTTTTGCTTGAAATATTTTTTTTCTGAATA
TTTTATGCAAAGAATTGAGTAAAAATTTTCGGGTCAATTTTGCAAAATTTTAGTCGAAATCGTGT
ACTAACCATTACGGTTTTTGGCTAAAAACGCAGTTCGGGCCCCGACTCATTTTTGCATGATTTTT
TGCGCAAAGACTCCTTGAAATATCTATATTCATCAACCAATTCTCAGCCACATTGGATTTAAGGA
TTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGG
AAAAACAATATTAAAAGCGTGAAAAATCCGTCAATCTTTTAGACGTTGAATTATATAATTTTTCT
GAGTATTATGGCAAATAATCAAGAAAAAAAAATTTCGGGTAAGTTTTTAGGCGAACTCGTGTACT
ATCACGGTTTTTTTTGATAAAAAAGCGTTCCAAGGCCCCGACTCAATTTTGCATGATTATTGGCA
GAAAGACTCATTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTT
GTTCTTACGAGCATCCAAATCTTGTTTCGAATTAATTAGAAATAAATTCGAAAAAAATGGAAAAA
CGATATTAGAAGCGTGAAAAACCCAATAATTTTTTAATGTTAAATTA
Found at i:87202 original size:146 final size:146
Alignment explanation
Indices: 86992--87277 Score: 371
Period size: 146 Copynumber: 2.0 Consensus size: 146
86982 CATTGGATTT
* * *
86992 AAGGATTTGTTTTTACGAGCATGTTAATCCTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAA
1 AAGGATTTGTTTTTACGACCATCTGAATCCTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAA
* * ** *
87057 TAGG-AAAACGATAATAGAAACATCAAAATACTTTTAATCTTTTTGGCATTGAAATATAT-ATTT
66 T-GGAAAAACAATAATAGAAACATCAAAAGACCGTCAATCTTTTTGGCATTGAAATATATGATTT
87120 TTCATGAGTATTTTATCC
130 TTC-TGAGTATTTTATCC
* *
87138 AAGGATTT-TTGTTTACGACCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
1 AAGGATTTGTT-TTTACGACCATCTGAATCCTGTTTCAATTTAATTAGAAATTAATTCGGAAAAA
* * * * * * *
87202 ATGGAAAAACAATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGCGTTGAATTATATGATTT
65 ATGGAAAAACAATAATAGAAACATCAAAAGACCGTCAATCTTTTTGGCATTGAAATATATGATTT
87267 TTCTGAGTATT
130 TTCTGAGTATT
87278 GTGGGGAAAA
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
145 4 0.03
146 109 0.91
147 7 0.06
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (146 bp):
AAGGATTTGTTTTTACGACCATCTGAATCCTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAA
TGGAAAAACAATAATAGAAACATCAAAAGACCGTCAATCTTTTTGGCATTGAAATATATGATTTT
TCTGAGTATTTTATCC
Found at i:88535 original size:656 final size:648
Alignment explanation
Indices: 87138--88561 Score: 1723
Period size: 656 Copynumber: 2.2 Consensus size: 648
87128 TATTTTATCC
* * * * * *
87138 AAGGATTT-TTGTTTACGACCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
1 AAGGATTTGTT-TTTACGAGCTTCCGAATCTTGTTTCGATTTAATTAAAAATAAATTCGGGAAAA
** * * * *
87202 ATGGAAAAACAATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGCGTTGAATTATATGA-TT
65 ATGGAAAAACAATATTAGAAGCGTGAAAAACCCATTAATTTTTTTTGCGTTGAATTATAT-ATTT
* * * * ** ** **
87266 -TTTCTGAGTATTGTGGGGAAA-AATTGAGAAAAAAAACATTCCGGG-ACA-GTTTTAGCTCGGA
129 GTTTCTTAGTATTAT-GGCAAAGAATTGAG--GAAAAATTTTATGGGTA-AGGTTTT-G-T-AAA
* * * * *
87327 A---TCG-TG-TA-CGT-TAGTTACCATCAACGGTTTTTTACTAAAAACGCGTTACAGGGCCCCG
187 ATTTTAGTTGAAATCGTATACTAACCATCAACGGTTTTTTACTAAAAACGAGTTACAGGGCCCCG
* * * * * * *
87385 ATTTAGTTTTGCATGATTTTTGACAGAAAGATTCCTTGAAATATCTATATTCATTTAATCAAATC
252 ACTAAATTTTGCATGATTTTTGACAGAAAGACTCCATAAAATATCTATATTCATTTAACCAAATC
* *
87450 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTTTTTTGATTTAATTACA
317 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTACA
* * **
87515 AATTAATTCTAAAAAAATGAAAAAACTATATTAGAAGCGTGAAAAAAACCCTTCAACATTTTTTA
382 AATTAATTCGAAAAAAATGAAAAAACGATATTAGAAGCGTG-AAAAAACCCTTCAACATTTTAGA
* * * * * ** *
87580 CGGTGAATTATATATTTTTTCTGGGTATTGTGGCAAAAAATTGAGATAAAACTTTTCGTTTAAGT
446 CAGTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATCGAGAAAAAAAATTTCGTGTAAGT
* * * * *
87645 TTTTAGTCGAAATCGTGTACGTGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTT
511 TTTTAGCCGAAATCGTCTACATAGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTT
* * *
87710 TGCATGATTTTTGGCTGAAAGACTCCTTGAAATATCTTTATTTAACTAACCAAATCTCAGCCACA
576 TGCATGATTATTGGCAGAAACACTCCTTGAAATATCTTTATTTAACTAACCAAATCTCAGCCACA
87775 TTGGACTT
641 TTGGACTT
* * * *
87783 AAGTATTTGTTTTTACGAGTTTCTGAATCTTGTTTCGATTTAATTAAAAATAATTTCGGGAAAAA
1 AAGGATTTGTTTTTACGAGCTTCCGAATCTTGTTTCGATTTAATTAAAAATAAATTCGGGAAAAA
* *
87848 TGGAAAAACTATATTAGAAGCGTGAAAAACCCTTTAA-TTTTTTTGCGTTGAATTATATATTTGT
66 TGGAAAAACAATATTAGAAGCGTGAAAAACCCATTAATTTTTTTTGCGTTGAATTATATATTTGT
87912 TTCTTAGTATTATGGCAAAGAATTGAGGAAAAATTTTATGGGTAAGGTTTTGTAAAATTTTAGTT
131 TTCTTAGTATTATGGCAAAGAATTGAGGAAAAATTTTATGGGTAAGGTTTTGTAAAATTTTAGTT
* * * * *
87977 GAAATCGTATACTAACCATC-ACGGTTTTTTGCTAAAAACGAGTTCCTGGGCCTCGGCTAAATTT
196 GAAATCGTATACTAACCATCAACGGTTTTTTACTAAAAACGAGTTACAGGGCCCCGACTAAATTT
* *
88041 TGCATGATTTTTGACAGAAAGACTCCATAAAATATCTATATTCATTTAACCAATTCTCAGTCACA
261 TGCATGATTTTTGACAGAAAGACTCCATAAAATATCTATATTCATTTAACCAAATCTCAGCCACA
* *
88106 TTGGTTTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTC
326 TTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTACAAATTAATTC
* * * * *
88171 GAAAAAATTTGGAAAAACGATATTAGAAGCGTG-AAAGATCCTTCAATC-TTTTAGACATTGAAT
391 GAAAAAA-ATGAAAAAACGATATTAGAAGCGTGAAAAAACCCTTCAA-CATTTTAGACAGTGAAT
* *
88234 TGTATTTTTTTTTCTGAGTATTATGG-AAAATAATCGAGAAAAAAAAATTTCGTGTAAGTTTTTA
454 TATA-TATTTTTTCTGAGTATTATGGCAAAA-AATCGAG-AAAAAAAATTTCGTGTAAGTTTTTA
*
88298 GCCGAAATCATGTACTAACCATCACAGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGACTTAG
516 GCCGAAATC--GT-CT-A-CAT---AGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAG
* * * *
88363 TTTTGCATTATTATTGGCAGAAACACTCCTTGAAATATCTTTATTTATCTAACCAAATTTCAGTC
573 TTTTGCATGATTATTGGCAGAAACACTCCTTGAAATATCTTTATTTAACTAACCAAATCTCAGCC
*
88428 ACATTGGATTT
638 ACATTGGACTT
*
88439 AAGGATTTGTTTTTACGAGCTTCCGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGGAAAAA
1 AAGGATTTGTTTTTACGAGCTTCCGAATCTTGTTTCGATTTAATTAAAAATAAATTCGGGAAAAA
* * *
88504 TGGAAAAACAATATTGGAAGCTTGAAAAACCCATTAATTTTTTTTGTGTTGAATTATA
66 TGGAAAAACAATATTAGAAGCGTGAAAAACCCATTAATTTTTTTTGCGTTGAATTATA
88562 CTCTCCCTGT
Statistics
Matches: 661, Mismatches: 91, Indels: 42
0.83 0.11 0.05
Matches are distributed among these distances:
641 2 0.00
642 1 0.00
643 13 0.02
644 34 0.05
645 107 0.16
646 32 0.05
647 189 0.29
648 60 0.09
650 2 0.00
651 1 0.00
652 1 0.00
653 2 0.00
656 198 0.30
657 19 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (648 bp):
AAGGATTTGTTTTTACGAGCTTCCGAATCTTGTTTCGATTTAATTAAAAATAAATTCGGGAAAAA
TGGAAAAACAATATTAGAAGCGTGAAAAACCCATTAATTTTTTTTGCGTTGAATTATATATTTGT
TTCTTAGTATTATGGCAAAGAATTGAGGAAAAATTTTATGGGTAAGGTTTTGTAAAATTTTAGTT
GAAATCGTATACTAACCATCAACGGTTTTTTACTAAAAACGAGTTACAGGGCCCCGACTAAATTT
TGCATGATTTTTGACAGAAAGACTCCATAAAATATCTATATTCATTTAACCAAATCTCAGCCACA
TTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAATTACAAATTAATTC
GAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAAACCCTTCAACATTTTAGACAGTGAATTA
TATATTTTTTCTGAGTATTATGGCAAAAAATCGAGAAAAAAAATTTCGTGTAAGTTTTTAGCCGA
AATCGTCTACATAGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTA
TTGGCAGAAACACTCCTTGAAATATCTTTATTTAACTAACCAAATCTCAGCCACATTGGACTT
Found at i:89677 original size:324 final size:321
Alignment explanation
Indices: 89228--90066 Score: 795
Period size: 324 Copynumber: 2.6 Consensus size: 321
89218 AATCATCACA
* * *
89228 GTTTTTGGCTAAAAAAGCGTTCAGGAGCCCCGACTCAATTTTTGCATGATTTTTTGCGCAAAGAC
1 GTTTTTGGCTAAAAAAGCGTTCAGGAGCCCCGACTCAAGTTTTACATGAATTTTTGCGCAAAGAC
* *
89293 TCCTTGAAATATCTATATTTATCGAAACAAATCTCAGCCACATTGGATATAAATATTTGTTTTTA
66 TCCTTAAAATATCTATATTTATCGAAACAAATCTCAGCCACATTGGATATAAAGATTTGTTTTTA
89358 CGA-CTATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAGAAATGGAAAAACAA
131 CGAGC-ATCTAAATCTTATTTCGATTTAATTAGAAATTAATTC-G--AAA-AAATGGAAAAACAA
* * * *
89422 TATTAGGAGCGAGAAAAACCCGT-C-TCTTTTTGGCGTTGAATTATATAATTTTTCTGAGTATTG
191 TATTAGAAGCGAGAAAAACCC-TCCATATTTTTGACGATGAATTATATAATTTTTCTGAGTATTG
** *
89485 TGGGGATAAATTGAGGAAAAAAAATTTCAGGTCAGTTTTTAGATCGGAATCGTGTACTAACCATT
255 TGGCAAAAAATTGA-GAAAAAAAATTTCAGGTCAGTTTTTAGATCGGAATCGTGTACTAACCATT
89550 ACG
319 ACG
* * * * *
89553 GTTTTTTGCTAAAAACGCGTTCCGGGGCCCCGATTC-AGTTTTACA-GAATTTTTGACAG-AAAG
1 GTTTTTGGCTAAAAAAGCGTTCAGGAGCCCCGACTCAAGTTTTACATGAATTTTTG-C-GCAAAG
** * * * *
89615 ACTCCTTAAAATATCTATATTTATTTAACCAATTCTCAGCTACATTGGATTTAAAGATTTGTTTT
64 ACTCCTTAAAATATCTATATTTATCGAAACAAATCTCAGCCACATTGGATATAAAGATTTGTTTT
* ** * * *
89680 TATGAGCATCTTGATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAACTGGAAAAACTATAT
129 TACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCGAAAAAATGGAAAAACAATAT
* * *
89745 TAGAAGCGTGAAAAACCCTCCAATATTTTTTACGATGAATTATATATTTTTTCTGAGTATTGTGG
194 TAGAAGCGAGAAAAACCCTCC-ATATTTTTGACGATGAATTATATAATTTTTCTGAGTATTGTGG
* * * *
89810 CAAAAAATTGAGAAAAATATTTTC-GTGTAAGTTTTTAG--CGGAAATCATGTACGT---CA-T-
258 CAAAAAATTGAGAAAAAAAATTTCAG-GTCAGTTTTTAGATCGG-AATCGTGTAC-TAACCATTA
89867 -G
320 CG
** * ** * *
89868 GTATTAGGGCTAAAAACGCGTTTC--GAGTCCTTGGCT-TAGTTTTACATG-ATTTTTG-GCTGA
1 GT-TTTTGGCTAAAAAAGCG-TTCAGGAG-CCCCGACTCAAGTTTTACATGAATTTTTGCGC--A
* * * * * * *
89928 AAGACTCCTTGAAATATCTAT-TTTCATCTAATCAAATCT-AGCCACATTGAATTTAAGGATTCG
61 AAGACTCCTTAAAATATCTATATTT-ATCGAAACAAATCTCAGCCACATTGGATATAAAGATTTG
* * * * * * * * *
89991 TTTTAACGAGCTTCTTAATTTTGTATCGATTTAATTGGAAATAAATTCGGGGAAAAATGGAAAAA
125 TTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTC--GAAAAAATGGAAAAA
*
90056 CGATATTAGAA
188 CAATATTAGAA
90067 AAATGAAAAG
Statistics
Matches: 431, Mismatches: 63, Indels: 48
0.80 0.12 0.09
Matches are distributed among these distances:
313 1 0.00
315 68 0.16
316 66 0.15
317 28 0.06
318 2 0.00
319 4 0.01
320 42 0.10
321 26 0.06
322 45 0.10
323 9 0.02
324 107 0.25
325 33 0.08
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (321 bp):
GTTTTTGGCTAAAAAAGCGTTCAGGAGCCCCGACTCAAGTTTTACATGAATTTTTGCGCAAAGAC
TCCTTAAAATATCTATATTTATCGAAACAAATCTCAGCCACATTGGATATAAAGATTTGTTTTTA
CGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCGAAAAAATGGAAAAACAATATTA
GAAGCGAGAAAAACCCTCCATATTTTTGACGATGAATTATATAATTTTTCTGAGTATTGTGGCAA
AAAATTGAGAAAAAAAATTTCAGGTCAGTTTTTAGATCGGAATCGTGTACTAACCATTACG
Done.