Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397272.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.0, 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: 3572271
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 44823 characters in sequence are not A, C, G, or T
File 7 of 9
Found at i:2442248 original size:33 final size:34
Alignment explanation
Indices: 2442194--2442258 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
2442184 GAAAGGCAAA
* *
2442194 GGGTTATGCTTGTTATGGTGAAA-GGCATTGTAT
1 GGGTTATACTTGTTATGGTGAAATGGAATTGTAT
*
2442227 GGGTTATACTTGCTT-TTGTGAAATGGAATTGT
1 GGGTTATACTTG-TTATGGTGAAATGGAATTGT
2442259 TATAAAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.42
Consensus pattern (34 bp):
GGGTTATACTTGTTATGGTGAAATGGAATTGTAT
Found at i:2444040 original size:21 final size:22
Alignment explanation
Indices: 2444011--2444058 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2444001 ACCAGCAGAA
* *
2444011 AATCTCTCATAAAATAGCACC-
1 AATCACTCACAAAATAGCACCG
* *
2444032 AATCACTCACAAACTAGTACCG
1 AATCACTCACAAAATAGCACCG
2444054 AATCA
1 AATCA
2444059 GCAGTAGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.44, C:0.29, G:0.06, T:0.21
Consensus pattern (22 bp):
AATCACTCACAAAATAGCACCG
Found at i:2445040 original size:18 final size:18
Alignment explanation
Indices: 2445017--2445055 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2445007 TAATATTTCT
*
2445017 TTAATAATTTTTTATTCA
1 TTAATAATTTCTTATTCA
2445035 TTAATAATTTCTTATTCA
1 TTAATAATTTCTTATTCA
2445053 TTA
1 TTA
2445056 TTTTTATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATAATTTCTTATTCA
Found at i:2445318 original size:13 final size:13
Alignment explanation
Indices: 2445300--2445324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2445290 ACATAAAATA
2445300 AGGATAATATAAC
1 AGGATAATATAAC
2445313 AGGATAATATAA
1 AGGATAATATAA
2445325 ACTCTAAATT
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:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (13 bp):
AGGATAATATAAC
Found at i:2445859 original size:25 final size:23
Alignment explanation
Indices: 2445831--2445890 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
2445821 GAATAGGTGA
2445831 ATATTTTATTAAT-TAACTTAATTTT
1 ATATTTTATTAATATAA-TTAA--TT
2445856 ATATATTT-TTAATATAATTAATT
1 ATAT-TTTATTAATATAATTAATT
2445879 ATATTATTATTA
1 ATATT-TTATTA
2445891 TAAAAATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
22 1 0.03
23 8 0.26
24 3 0.10
25 13 0.42
26 6 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATTTTATTAATATAATTAATT
Found at i:2446466 original size:19 final size:16
Alignment explanation
Indices: 2446426--2446479 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
2446416 AAAGGTAAAC
* *
2446426 TTTTTATTTAATTTTT
1 TTTTTATTTTATTTAT
*
2446442 TCTATTTATATTA-TTAT
1 T-T-TTTATTTTATTTAT
2446459 TTTTTATTTTATTTAT
1 TTTTTATTTTATTTAT
2446475 TTTTT
1 TTTTT
2446480 TCAATTCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 8 0.26
16 11 0.35
17 5 0.16
18 7 0.23
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTATTTTATTTAT
Found at i:2446480 original size:19 final size:19
Alignment explanation
Indices: 2446427--2446481 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
2446417 AAGGTAAACT
*
2446427 TTTTATTTAATTTTTTCTA
1 TTTTATTTATTTTTTTCTA
2446446 -TTTATATTATTATTTTT-TA
1 TTTTAT-TTATT-TTTTTCTA
2446465 TTTTATTTATTTTTTTC
1 TTTTATTTATTTTTTTC
2446482 AATTCTATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 10 0.32
19 11 0.35
20 10 0.32
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATTTATTTTTTTCTA
Found at i:2459173 original size:2 final size:2
Alignment explanation
Indices: 2459166--2459193 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2459156 TACCCTTCAA
2459166 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
2459194 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2463834 original size:35 final size:34
Alignment explanation
Indices: 2463788--2463853 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
2463778 ATTAACACTA
2463788 CTTGTGCTTACTCTAACGTTGTTGTATCTTTCCTG
1 CTTGTGCTTACTCTAACGTTGTTGTA-CTTTCCTG
* *
2463823 CTTGTGCTTACTTTAATGTTGTTGTACTTTC
1 CTTGTGCTTACTCTAACGTTGTTGTACTTTC
2463854 TCGTAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 5 0.17
35 24 0.83
ACGTcount: A:0.12, C:0.20, G:0.17, T:0.52
Consensus pattern (34 bp):
CTTGTGCTTACTCTAACGTTGTTGTACTTTCCTG
Found at i:2464454 original size:27 final size:26
Alignment explanation
Indices: 2464416--2464467 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
2464406 AAATTGCTCC
2464416 AAAAACAACAAAGATG-AAAACACAAG
1 AAAAACAACAAAGA-GAAAAACACAAG
* *
2464442 AAAATCAAGCAAATAGAAAAACACAA
1 AAAAACAA-CAAAGAGAAAAACACAA
2464468 AAATTTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.69, C:0.15, G:0.10, T:0.06
Consensus pattern (26 bp):
AAAAACAACAAAGAGAAAAACACAAG
Found at i:2465033 original size:20 final size:20
Alignment explanation
Indices: 2464994--2465033 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2464984 AACAAAGTTC
*
2464994 AAAAACTGCAACACGATACT
1 AAAAACTGCAACACCATACT
* *
2465014 AAAAATTGCAACACCCTACT
1 AAAAACTGCAACACCATACT
2465034 GCGACTTCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.17
Consensus pattern (20 bp):
AAAAACTGCAACACCATACT
Found at i:2467472 original size:18 final size:19
Alignment explanation
Indices: 2467443--2467478 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2467433 GTTCAGCTCA
*
2467443 ATTTTTTCTTTTTGGTCTC
1 ATTTTTTCTTTTAGGTCTC
2467462 ATTTTTT-TTTTAGGTCT
1 ATTTTTTCTTTTAGGTCT
2467479 TCAAAGATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.08, C:0.11, G:0.11, T:0.69
Consensus pattern (19 bp):
ATTTTTTCTTTTAGGTCTC
Found at i:2468510 original size:6 final size:6
Alignment explanation
Indices: 2468499--2468532 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2468489 GGTTATGCTC
*
2468499 CTTCTG CTTCTG CTTCTG CTTCTG CTTCTA CTTC
1 CTTCTG CTTCTG CTTCTG CTTCTG CTTCTG CTTC
2468533 AGCTGCCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.03, C:0.35, G:0.12, T:0.50
Consensus pattern (6 bp):
CTTCTG
Found at i:2473875 original size:55 final size:55
Alignment explanation
Indices: 2473791--2473953 Score: 245
Period size: 55 Copynumber: 3.0 Consensus size: 55
2473781 AGTAAGATTT
*
2473791 TGGTCCTGTGGATGTGATGTGTGTCCTTAATGAGGACATCAAGGATTTAAGTAGG
1 TGGTCCTGTGGATGTGATGTGTGTCCTTAATGAGGACATCAAGGATTTAAGTAAG
* *
2473846 TGGTCCTGTGGATGTGATGTGTGTCCTTAATGAGAACATCAAGGATTTAAATAAG
1 TGGTCCTGTGGATGTGATGTGTGTCCTTAATGAGGACATCAAGGATTTAAGTAAG
* * ** * *
2473901 TGGTCTTGTGGATGTTATGTGTGTTTTTAATGAAGACATCAAGAATTTAAGTA
1 TGGTCCTGTGGATGTGATGTGTGTCCTTAATGAGGACATCAAGGATTTAAGTA
2473954 TGTGAGATTG
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 97 1.00
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.36
Consensus pattern (55 bp):
TGGTCCTGTGGATGTGATGTGTGTCCTTAATGAGGACATCAAGGATTTAAGTAAG
Found at i:2482821 original size:29 final size:29
Alignment explanation
Indices: 2482775--2482888 Score: 115
Period size: 29 Copynumber: 3.9 Consensus size: 29
2482765 TTTTACCTTA
* *
2482775 TTCTCTTGTACCTGTTCACATACAGCTTC
1 TTCTCTAGTACCTATTCACATACAGCTTC
**
2482804 TTCTCTAGT-CTCTATTCATGTACAGCTTC
1 TTCTCTAGTAC-CTATTCACATACAGCTTC
* * *
2482833 TTCTCTTGTACCAATTCACATGCAGCTTC
1 TTCTCTAGTACCTATTCACATACAGCTTC
* *
2482862 TTTTCTTA-TACCTATTCACATATAGCT
1 TTCTC-TAGTACCTATTCACATACAGCT
2482889 ATTCTTTATT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
28 1 0.01
29 65 0.96
30 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.09, T:0.43
Consensus pattern (29 bp):
TTCTCTAGTACCTATTCACATACAGCTTC
Found at i:2493028 original size:17 final size:17
Alignment explanation
Indices: 2493006--2493061 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 17
2492996 TTGATTCTCC
2493006 ATAAAAAAAATGAAGAA
1 ATAAAAAAAATGAAGAA
2493023 AT--AAAAAAT-AA-AA
1 ATAAAAAAAATGAAGAA
*
2493036 ATAAATAAAATG-AGAAA
1 ATAAAAAAAATGAAG-AA
2493053 ATAAAAAAA
1 ATAAAAAAA
2493062 TATTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 14 0.44
17 12 0.38
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (17 bp):
ATAAAAAAAATGAAGAA
Found at i:2493070 original size:17 final size:16
Alignment explanation
Indices: 2493006--2493074 Score: 56
Period size: 17 Copynumber: 4.4 Consensus size: 16
2492996 TTGATTCTCC
*
2493006 ATAAAAAAAATGAAGAA
1 ATAAAAAAAATTAA-AA
2493023 AT--AAAAAA-TAAAA
1 ATAAAAAAAATTAAAA
* *
2493036 ATAAATAAAATGAGAAA
1 ATAAAAAAAATTA-AAA
2493053 ATAAAAAAATATTAAAA
1 ATAAAAAAA-ATTAAAA
2493070 A-AAAA
1 ATAAAA
2493075 TATGAATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
13 4 0.10
14 2 0.05
15 11 0.26
16 5 0.12
17 17 0.40
18 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
ATAAAAAAAATTAAAA
Found at i:2493070 original size:25 final size:23
Alignment explanation
Indices: 2493006--2493074 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
2492996 TTGATTCTCC
*
2493006 ATAAAAAAAATGAAGAAATAAAAA
1 ATAAAAAAAATTAA-AAATAAAAA
*
2493030 ATAAAAATAAA-T-AAAATGAGAAA
1 ATAAAAA-AAATTAAAAAT-AAAAA
2493053 ATAAAAAAATATTAAAAA-AAAA
1 ATAAAAAAA-ATTAAAAATAAAA
2493075 TATGAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
22 6 0.16
23 16 0.43
24 8 0.22
25 7 0.19
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (23 bp):
ATAAAAAAAATTAAAAATAAAAA
Found at i:2495738 original size:2 final size:2
Alignment explanation
Indices: 2495731--2495765 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2495721 TTGTTTGAAC
2495731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2495766 AAGAAGCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2496692 original size:29 final size:29
Alignment explanation
Indices: 2496660--2496720 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2496650 CTTATACTTG
* *
2496660 TTCACGCATAACTTTTTCTCTTGTACCTA
1 TTCACGCACAACTTCTTCTCTTGTACCTA
* * *
2496689 TTCATGTACAGCTTCTTCTCTTGTACCTA
1 TTCACGCACAACTTCTTCTCTTGTACCTA
2496718 TTC
1 TTC
2496721 CTGTACGGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.28, G:0.08, T:0.46
Consensus pattern (29 bp):
TTCACGCACAACTTCTTCTCTTGTACCTA
Found at i:2496725 original size:29 final size:29
Alignment explanation
Indices: 2496675--2496764 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
2496665 GCATAACTTT
2496675 TTCTCTTGTACCTATTCATGTACAGCTTC
1 TTCTCTTGTACCTATTCATGTACAGCTTC
* *
2496704 TTCTCTTGTACCTATTCCTGTACGGCTTC
1 TTCTCTTGTACCTATTCATGTACAGCTTC
* * * *
2496733 TTTTTTTGTACCTATTCATATAGAGC-TC
1 TTCTCTTGTACCTATTCATGTACAGCTTC
2496761 TTCT
1 TTCT
2496765 TAATTAGCTC
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
28 5 0.10
29 47 0.90
ACGTcount: A:0.16, C:0.26, G:0.11, T:0.48
Consensus pattern (29 bp):
TTCTCTTGTACCTATTCATGTACAGCTTC
Found at i:2498710 original size:9 final size:9
Alignment explanation
Indices: 2498696--2498738 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
2498686 CTCATATGTG
*
2498696 TAAAAAAAT
1 TAAAAAAAA
2498705 TAAAAAAAA
1 TAAAAAAAA
2498714 TAAAAAAAA
1 TAAAAAAAA
2498723 T-AAAAAAA
1 TAAAAAAAA
2498731 TAAAAAAA
1 TAAAAAAA
2498739 GTGTCCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.25
9 24 0.75
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:2498718 original size:7 final size:8
Alignment explanation
Indices: 2498696--2498738 Score: 59
Period size: 8 Copynumber: 5.0 Consensus size: 8
2498686 CTCATATGTG
2498696 TAAAAAAA
1 TAAAAAAA
2498704 TTAAAAAAAA
1 -T-AAAAAAA
2498714 TAAAAAAAA
1 T-AAAAAAA
2498723 TAAAAAAA
1 TAAAAAAA
2498731 TAAAAAAA
1 TAAAAAAA
2498739 GTGTCCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.45
9 11 0.33
10 7 0.21
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:2498720 original size:17 final size:17
Alignment explanation
Indices: 2498696--2498738 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2498686 CTCATATGTG
*
2498696 TAAAAAAATTAAAAAAAA
1 TAAAAAAAAT-AAAAAAA
2498714 TAAAAAAAATAAAAAAA
1 TAAAAAAAATAAAAAAA
2498731 TAAAAAAA
1 TAAAAAAA
2498739 GTGTCCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (17 bp):
TAAAAAAAATAAAAAAA
Found at i:2499307 original size:19 final size:18
Alignment explanation
Indices: 2499285--2499324 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2499275 AATTTTATTT
2499285 ATAATTATAAA-ATAAATAA
1 ATAATT-TAAACATAAA-AA
2499304 ATAATTTAAACATAAAAA
1 ATAATTTAAACATAAAAA
2499322 ATA
1 ATA
2499325 TAACATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAATTTAAACATAAAAA
Found at i:2500860 original size:25 final size:24
Alignment explanation
Indices: 2500839--2500921 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 24
2500829 ATTTAAACAT
2500839 TATT-AATATTAATATGATTAAAA
1 TATTAAATATTAATATGATTAAAA
*
2500862 TATTAAAATATTAATAT-TTTAAAA
1 TATT-AAATATTAATATGATTAAAA
* * * *
2500886 TATT-AATGTTTAT-TTATTAAAT
1 TATTAAATATTAATATGATTAAAA
2500908 TATTAATATATTAA
1 TATTAA-ATATTAA
2500922 ATTTTAATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.02
22 16 0.33
23 5 0.10
24 15 0.31
25 11 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTAAATATTAATATGATTAAAA
Found at i:2500868 original size:8 final size:8
Alignment explanation
Indices: 2500843--2500891 Score: 62
Period size: 8 Copynumber: 6.0 Consensus size: 8
2500833 AAACATTATT
2500843 AATATTAA
1 AATATTAA
*
2500851 TATGATTAA
1 AAT-ATTAA
2500860 AATATTAA
1 AATATTAA
2500868 AATATTAA
1 AATATTAA
* *
2500876 TATTTTAA
1 AATATTAA
2500884 AATATTAA
1 AATATTAA
2500892 TGTTTATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 27 0.79
9 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (8 bp):
AATATTAA
Found at i:2500921 original size:16 final size:15
Alignment explanation
Indices: 2500847--2500929 Score: 71
Period size: 16 Copynumber: 5.3 Consensus size: 15
2500837 ATTATTAATA
*
2500847 TTAATATGATTAAAATA
1 TTAATAT-ATT-AAATT
*
2500864 TTAAAATATTAATATT
1 TTAATATATTAA-ATT
*
2500880 TTAAAATATT-AATGT
1 TTAATATATTAAAT-T
*
2500895 TT-ATTTATTAAATT
1 TTAATATATTAAATT
2500909 ATTAATATATTAAATT
1 -TTAATATATTAAATT
2500925 TTAAT
1 TTAAT
2500930 GAGTATAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.14
15 16 0.29
16 26 0.46
17 6 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAATATATTAAATT
Found at i:2500971 original size:16 final size:17
Alignment explanation
Indices: 2500936--2500971 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2500926 TAATGAGTAT
2500936 AAATAAAAAATAAAATA
1 AAATAAAAAATAAAATA
*
2500953 AAATAAAGAA-AAAATA
1 AAATAAAAAATAAAATA
2500969 AAA
1 AAA
2500972 AATTGTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (17 bp):
AAATAAAAAATAAAATA
Found at i:2501229 original size:26 final size:24
Alignment explanation
Indices: 2501186--2501242 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 24
2501176 AATTAATATT
*
2501186 TTAATAATATTATTATTAAATTATA
1 TTAA-AATATTATAATTAAATTATA
2501211 GTTAAAATATTAATAATTAAATTATA
1 -TTAAAATATT-ATAATTAAATTATA
2501237 TTAAAA
1 TTAAAA
2501243 CAATAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TTAAAATATTATAATTAAATTATA
Found at i:2501256 original size:26 final size:26
Alignment explanation
Indices: 2501191--2501264 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
2501181 ATATTTTAAT
* *
2501191 AATATTATTATTAAATTATAGTTAAAAT
1 AATAATATT-TTAAATTATA-TTAAAAC
* *
2501219 ATTAATA-ATTAAATTATATTAAAAC
1 AATAATATTTTAAATTATATTAAAAC
2501244 AATAATATTTTAAA--ATATTAA
1 AATAATATTTTAAATTATATTAA
2501265 TATTTAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 7 0.18
25 12 0.31
26 15 0.38
28 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
AATAATATTTTAAATTATATTAAAAC
Found at i:2501331 original size:26 final size:26
Alignment explanation
Indices: 2501269--2501325 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
2501259 TATTAATATT
* *
2501269 TAAATTATTAATTATTAATATTTTAA
1 TAAATAATAAATTATTAATATTTTAA
*
2501295 TAAATTATAAATTATTAATA-TTTAA
1 TAAATAATAAATTATTAATATTTTAA
2501320 -AAATAA
1 TAAATAA
2501326 AATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.17
25 5 0.17
26 19 0.66
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAATAATAAATTATTAATATTTTAA
Found at i:2513325 original size:19 final size:18
Alignment explanation
Indices: 2513294--2513347 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
2513284 AGATGCTTTT
2513294 TTTTAAAAA--AATAAAA
1 TTTTAAAAATTAATAAAA
2513310 TTTTAAAAATATAATAATAA
1 TTTTAAAAAT-TAATAA-AA
*
2513330 TTTTTAAAATTAATAAAA
1 TTTTAAAAATTAATAAAA
2513348 AAATATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.27
18 2 0.06
19 11 0.33
20 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTTAAAAATTAATAAAA
Found at i:2513356 original size:22 final size:22
Alignment explanation
Indices: 2513296--2513358 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
2513286 ATGCTTTTTT
*
2513296 TTAA-AAAAATAAAATTTTAAAA
1 TTAATAAAAA-AATATTTTAAAA
* *
2513318 AT-ATAATAATAAT-TTTTAAAA
1 TTAATAA-AAAAATATTTTAAAA
2513339 TTAATAAAAAAATATTTTAA
1 TTAATAAAAAAATATTTTAA
2513359 TTTTTTCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
21 15 0.47
22 15 0.47
23 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAATAAAAAAATATTTTAAAA
Found at i:2514146 original size:23 final size:24
Alignment explanation
Indices: 2514120--2514263 Score: 89
Period size: 23 Copynumber: 5.7 Consensus size: 24
2514110 TTCATTTTTG
2514120 TTAATTTA-TATTTTAATTAAAAT
1 TTAATTTATTATTTTAATTAAAAT
** *
2514143 TTAAAATATTA--ATAATTTAATAAT
1 TTAATTTATTATTTTAA-TTAA-AAT
* * *
2514167 TTAAATATTAATATTTTATTTATAAT
1 TT-AAT-TTATTATTTTAATTAAAAT
* *
2514193 TTAA-ATATTATTATAATTAAAAT
1 TTAATTTATTATTTTAATTAAAAT
2514216 ATTAATTTATTATAATTATAATTGAAAAT
1 -TTAATTTATTAT--TT-TAATT-AAAAT
2514245 TTAAACTTTATTATTTTAA
1 TT-AA-TTTATTATTTTAA
2514264 ATTTTTTTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
22 3 0.03
23 24 0.27
24 11 0.12
25 10 0.11
26 9 0.10
27 7 0.08
28 11 0.12
29 7 0.08
30 8 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
TTAATTTATTATTTTAATTAAAAT
Found at i:2514236 original size:28 final size:30
Alignment explanation
Indices: 2514202--2514258 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
2514192 TTTAAATATT
2514202 ATTATAATT-AAAATATT-AA-TTTATTATA
1 ATTATAATTGAAAAT-TTAAACTTTATTATA
2514230 ATTATAATTGAAAATTTAAACTTTATTAT
1 ATTATAATTGAAAATTTAAACTTTATTAT
2514259 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 11 0.42
29 7 0.27
30 8 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTATAATTGAAAATTTAAACTTTATTATA
Found at i:2514266 original size:28 final size:26
Alignment explanation
Indices: 2514198--2514266 Score: 61
Period size: 28 Copynumber: 2.5 Consensus size: 26
2514188 ATAATTTAAA
*
2514198 TATTATTAT-AATTAAAATATTAATT
1 TATTATTTTAAATTAAAATATTAATT
*
2514223 TATTATAATTATAATTGAAAAT-TTAAACTT
1 TATTAT-TTTA-AATT-AAAATATT-AA-TT
2514253 TATTATTTTAAATT
1 TATTATTTTAAATT
2514267 TTTTTTTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
25 6 0.17
26 1 0.03
28 10 0.29
29 10 0.29
30 8 0.23
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TATTATTTTAAATTAAAATATTAATT
Found at i:2514609 original size:21 final size:21
Alignment explanation
Indices: 2514560--2514601 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2514550 TGAATAATTG
* *
2514560 AAGTTTAAAACTCATTTAAAC
1 AAGTTCAAAACTCATTCAAAC
2514581 AAGTTCAAAACTCATTCAAAC
1 AAGTTCAAAACTCATTCAAAC
2514602 TCATTCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.29
Consensus pattern (21 bp):
AAGTTCAAAACTCATTCAAAC
Found at i:2525851 original size:23 final size:23
Alignment explanation
Indices: 2525817--2525863 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2525807 TTATGAAAAT
2525817 ATAACTTCAAAGAACAAATAAAG
1 ATAACTTCAAAGAACAAATAAAG
* * *
2525840 ATAACTTGAAAGAATAATTAAAG
1 ATAACTTCAAAGAACAAATAAAG
2525863 A
1 A
2525864 GAAAAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.21
Consensus pattern (23 bp):
ATAACTTCAAAGAACAAATAAAG
Found at i:2527029 original size:264 final size:264
Alignment explanation
Indices: 2526558--2527084 Score: 813
Period size: 264 Copynumber: 2.0 Consensus size: 264
2526548 TTATTCTCGT
* * * *
2526558 ATAATGTTGTTGTAATTTCTTTCTTAGTTGACGAGCCATATGTTTCTCGAATATGTTGAGTTACA
1 ATAATGTTGTTGTAATTTCTTTCTTAGTTAACGAGCCACACGTTTCTCGAATATGTTGAATTACA
* * * *
2526623 GATTTGAATCAGACACATTCACGACTTGCTTCATGAATTGCTAAAATTTTTGCATGGTTAGAAGA
66 GATTTGAATCAGACACATTCACGACTTACCTCATGAATTGCTAAAATTTTTGCATGGTCAAAAGA
* * ***
2526688 AGTAGTAACAATAGTTTGTTTTACAGAATACCATGAAGTAGTTGTATCTCCATATGTGAATAAAT
131 AATAGTAACAATAGTTTGTTTTACAGAATACCATGAAATAGCCATATCTCCATATGTGAATAAAT
* ** *
2526753 AACCTGTCTGGGATTGAGCTTTATGTGGATTTGATAAATA-TTTGCATTTGCATAACCTAGTAAA
196 AACCTGTCTGGGATTGAGCTTTACGTCAATCTGATAAATATTTTGCATTTGCATAACCTAGTAAA
2526817 TCTG
261 TCTG
2526821 ATAATGTTGTTGTAATTTCTTTCTTAGTTAACGAGCCACACGTTTCTCGAATATGTTGAATTACA
1 ATAATGTTGTTGTAATTTCTTTCTTAGTTAACGAGCCACACGTTTCTCGAATATGTTGAATTACA
*
2526886 GATTTGAATCAGACACATTTACGACTTAACCTCATGAATTGCTAAAATTTTTGCATGGTCAAAAG
66 GATTTGAATCAGACACATTCACGACTT-ACCTCATGAATTGCTAAAATTTTTGCATGGTCAAAAG
* * *
2526951 AAATAGTAACAATAGTTTGTTTTACATAATGCCATGAAATAGCCATATCTTCATATGTGAATAAA
130 AAATAGTAACAATAGTTTGTTTTACAGAATACCATGAAATAGCCATATCTCCATATGTGAATAAA
* * * *
2527016 TAACCTGTCTGGGATTGAGCTTTGCGTCAATCTGATAAATATTTTGTATTTGTATAACCTATTAA
195 TAACCTGTCTGGGATTGAGCTTTACGTCAATCTGATAAATATTTTGCATTTGCATAACCTAGTAA
2527081 ATCT
260 ATCT
2527085 AATTTTAATG
Statistics
Matches: 237, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
263 87 0.37
264 126 0.53
265 24 0.10
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (264 bp):
ATAATGTTGTTGTAATTTCTTTCTTAGTTAACGAGCCACACGTTTCTCGAATATGTTGAATTACA
GATTTGAATCAGACACATTCACGACTTACCTCATGAATTGCTAAAATTTTTGCATGGTCAAAAGA
AATAGTAACAATAGTTTGTTTTACAGAATACCATGAAATAGCCATATCTCCATATGTGAATAAAT
AACCTGTCTGGGATTGAGCTTTACGTCAATCTGATAAATATTTTGCATTTGCATAACCTAGTAAA
TCTG
Found at i:2530366 original size:40 final size:41
Alignment explanation
Indices: 2530322--2530405 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 41
2530312 TATTTTTTGT
* *
2530322 TTTGGGCTTAATAATATGAT-GAATAAT-GATTTATTAATGA
1 TTTGGGCTTAATAATATGATGGAA-AATGGATTTATGAACGA
* * *
2530362 TTT-GGTTTACTCATATGATGGAAAATGGATTTATGAACGA
1 TTTGGGCTTAATAATATGATGGAAAATGGATTTATGAACGA
2530402 TTTG
1 TTTG
2530406 AGTATACAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
39 16 0.44
40 20 0.56
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (41 bp):
TTTGGGCTTAATAATATGATGGAAAATGGATTTATGAACGA
Found at i:2538765 original size:19 final size:19
Alignment explanation
Indices: 2538725--2538766 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2538715 AATGGAGTTA
*
2538725 TATTTAAATAAATTAGTTG
1 TATTTAAATAAATTAGTGG
*
2538744 TATTTAAATATATTTA-TGG
1 TATTTAAATA-AATTAGTGG
2538763 TATT
1 TATT
2538767 ACGTCACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (19 bp):
TATTTAAATAAATTAGTGG
Found at i:2557719 original size:2 final size:2
Alignment explanation
Indices: 2557714--2557760 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2557704 AAAAAAAGTT
* * *
2557714 AG AG AG CG AG AG AG AG AG CG AG AG AG AG AG AG AG CG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2557756 AG AG A
1 AG AG A
2557761 ACCTGAGATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.45, C:0.06, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2557742 original size:16 final size:16
Alignment explanation
Indices: 2557721--2557760 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2557711 GTTAGAGAGC
2557721 GAGAGAGAGAGCGAGA
1 GAGAGAGAGAGCGAGA
2557737 GAGAGAGAGAGCGAGA
1 GAGAGAGAGAGCGAGA
2557753 GAGAGAGA
1 GAGAGAGA
2557761 ACCTGAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.50, T:0.00
Consensus pattern (16 bp):
GAGAGAGAGAGCGAGA
Found at i:2562476 original size:2 final size:2
Alignment explanation
Indices: 2562469--2562500 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2562459 ACCAGGTGCC
2562469 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2562501 GTGTCTGTGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2577006 original size:41 final size:41
Alignment explanation
Indices: 2576952--2577051 Score: 164
Period size: 41 Copynumber: 2.4 Consensus size: 41
2576942 AGTTCGATGG
* *
2576952 CATGAGCAGCTTCAGATAAGCAATGTTAATCGATTCAATAA
1 CATGAGCAGCTTCAGATAAGCAATGTTAATCAATCCAATAA
* *
2576993 CATGGGCATCTTCAGATAAGCAATGTTAATCAATCCAATAA
1 CATGAGCAGCTTCAGATAAGCAATGTTAATCAATCCAATAA
2577034 CATGAGCAGCTTCAGATA
1 CATGAGCAGCTTCAGATA
2577052 TTGAAAATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (41 bp):
CATGAGCAGCTTCAGATAAGCAATGTTAATCAATCCAATAA
Found at i:2588082 original size:5 final size:5
Alignment explanation
Indices: 2588072--2588096 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2588062 GGGAATAAGA
2588072 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2588097 TTGCACTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2596694 original size:29 final size:30
Alignment explanation
Indices: 2596646--2596707 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
2596636 ATGTCGTTTT
2596646 GAAAAAAAAAACTCAAAAAAAAATATATAAG
1 GAAAAAAAAAACTCAAAAAAAAA-ATATAAG
*
2596677 GAAAAAAAAAGCTC-AAAAAAAAATATAAG
1 GAAAAAAAAAACTCAAAAAAAAAATATAAG
2596706 GA
1 GA
2596708 GGGACTCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 9 0.30
30 8 0.27
31 13 0.43
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.11
Consensus pattern (30 bp):
GAAAAAAAAAACTCAAAAAAAAAATATAAG
Found at i:2597671 original size:20 final size:21
Alignment explanation
Indices: 2597646--2597688 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2597636 ACAATTAAGG
2597646 CAAAAA-ACAAAATAGAGTAC
1 CAAAAACACAAAATAGAGTAC
* *
2597666 CAAAAACTCAAAATCGAGTAC
1 CAAAAACACAAAATAGAGTAC
2597687 CA
1 CA
2597689 CTACTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.58, C:0.21, G:0.09, T:0.12
Consensus pattern (21 bp):
CAAAAACACAAAATAGAGTAC
Found at i:2598310 original size:11 final size:11
Alignment explanation
Indices: 2598294--2598334 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
2598284 TGTCGTTTTG
2598294 AAAAAAAAACT
1 AAAAAAAAACT
2598305 AAAAAAAATA-T
1 AAAAAAAA-ACT
2598316 AAAAAAAAACT
1 AAAAAAAAACT
2598327 CAAAAAAA
1 -AAAAAAA
2598335 TATAAGGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.04
11 18 0.67
12 8 0.30
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAAACT
Found at i:2598319 original size:22 final size:22
Alignment explanation
Indices: 2598294--2598339 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2598284 TGTCGTTTTG
2598294 AAAAAAAAACTAAAAAAAATAT
1 AAAAAAAAACTAAAAAAAATAT
*
2598316 AAAAAAAAACTCAAAAAAATAT
1 AAAAAAAAACTAAAAAAAATAT
2598338 AA
1 AA
2598340 GGAGGGACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (22 bp):
AAAAAAAAACTAAAAAAAATAT
Found at i:2599000 original size:53 final size:54
Alignment explanation
Indices: 2598943--2599060 Score: 211
Period size: 53 Copynumber: 2.2 Consensus size: 54
2598933 CTTTGATTTT
*
2598943 AAGCATTGCGTAACTTAAGCATTGTGTGATTAGG-TTTTGGCATTGTGGGACTA
1 AAGCATTGCGTAACTTAAGCATTGTGTGATTAGGTTTTTGGCATTGTGGGACAA
*
2598996 AAGCATTGCGTAACTTAAGCATTGTGTGATTGGGTTTTTGGCATTGTGGGACAA
1 AAGCATTGCGTAACTTAAGCATTGTGTGATTAGGTTTTTGGCATTGTGGGACAA
2599050 AAGCATTGCGT
1 AAGCATTGCGT
2599061 GACTAGGTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 33 0.53
54 29 0.47
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.35
Consensus pattern (54 bp):
AAGCATTGCGTAACTTAAGCATTGTGTGATTAGGTTTTTGGCATTGTGGGACAA
Found at i:2599211 original size:21 final size:21
Alignment explanation
Indices: 2599187--2599232 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2599177 TGTGATTGGT
* *
2599187 TTTAGGCATTACGTGACTAGA
1 TTTAGACATTACGTAACTAGA
* *
2599208 TTTAGATATTGCGTAACTAGA
1 TTTAGACATTACGTAACTAGA
2599229 TTTA
1 TTTA
2599233 AGTATTGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (21 bp):
TTTAGACATTACGTAACTAGA
Found at i:2600040 original size:13 final size:13
Alignment explanation
Indices: 2600022--2600046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2600012 CATGTATTTT
2600022 AATTGAATCTAAA
1 AATTGAATCTAAA
2600035 AATTGAATCTAA
1 AATTGAATCTAA
2600047 TTTTAGGAGG
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
AATTGAATCTAAA
Found at i:2600611 original size:29 final size:29
Alignment explanation
Indices: 2600579--2600644 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
2600569 TAATTTAGCT
2600579 AAGAAAAT-GTGTTTGTCTTAATATAAGAC
1 AAGAAAATAGTGTTTGTCTTAATAT-AGAC
* * *
2600608 AAGAAAAATATTTTTTGTCTTAATCTAGAC
1 AAG-AAAATAGTGTTTGTCTTAATATAGAC
2600638 AAGAAAA
1 AAGAAAA
2600645 CATATTTGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.22
30 12 0.38
31 13 0.41
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (29 bp):
AAGAAAATAGTGTTTGTCTTAATATAGAC
Found at i:2600627 original size:31 final size:31
Alignment explanation
Indices: 2600590--2600688 Score: 102
Period size: 28 Copynumber: 3.4 Consensus size: 31
2600580 AGAAAATGTG
2600590 TTTGTCTTAATATAAGACAAGAAAAATATTT
1 TTTGTCTTAATATAAGACAAGAAAAATATTT
*
2600621 TTTGTCTTAATCT-AGACAAGAAAACATA---
1 TTTGTCTTAATATAAGACAAGAAAA-ATATTT
* * * *
2600649 TTTGTCTCAATTTAA-ACAATATAAA-ATTT
1 TTTGTCTTAATATAAGACAAGAAAAATATTT
2600678 TTTGTCTTAAT
1 TTTGTCTTAAT
2600689 TAAAGATAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 18 0.32
29 11 0.19
30 11 0.19
31 15 0.26
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
TTTGTCTTAATATAAGACAAGAAAAATATTT
Found at i:2600631 original size:59 final size:57
Alignment explanation
Indices: 2600568--2600689 Score: 138
Period size: 59 Copynumber: 2.1 Consensus size: 57
2600558 ATGTTTGATT
** * *
2600568 TTAATTTAG-CTAAGAAAATGTGTTTGTCTTAATATAAGACAAGAAAAATATTTTTTGTC
1 TTAATTTAGAC-AAGAAAACATATTTGTCTCAATATAA-ACAAGAAAAA-ATTTTTTGTC
* * * *
2600627 TTAATCTAGACAAGAAAACATATTTGTCTCAATTTAAACAATATAAAATTTTTTGTC
1 TTAATTTAGACAAGAAAACATATTTGTCTCAATATAAACAAGAAAAAATTTTTTGTC
2600684 TTAATT
1 TTAATT
2600690 AAAGATAAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
57 15 0.28
58 8 0.15
59 29 0.55
60 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (57 bp):
TTAATTTAGACAAGAAAACATATTTGTCTCAATATAAACAAGAAAAAATTTTTTGTC
Found at i:2603970 original size:22 final size:22
Alignment explanation
Indices: 2603945--2604006 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
2603935 TATCAAGTAG
**
2603945 TCACGTAATGCCTATCAACCAA
1 TCACGTAATGCCTAAAAACCAA
** *
2603967 TCACACAATGCCTAAAAACTAA
1 TCACGTAATGCCTAAAAACCAA
*
2603989 TCATGTAATGCCTAAAAA
1 TCACGTAATGCCTAAAAA
2604007 TCATTCATAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.23
Consensus pattern (22 bp):
TCACGTAATGCCTAAAAACCAA
Found at i:2604153 original size:22 final size:22
Alignment explanation
Indices: 2603964--2604154 Score: 82
Period size: 22 Copynumber: 8.6 Consensus size: 22
2603954 GCCTATCAAC
*
2603964 CAATCACACAATGCCTAAAAA-
1 CAATCACACAATGACTAAAAAT
*** *
2603985 CTAATCATGTAATGCCTAAAAAT
1 C-AATCACACAATGACTAAAAAT
* * * * *
2604008 CATTCATACAACGCCTTATAAAT
1 CAATCACACAATGAC-TAAAAAT
* * *
2604031 CAGTCACATAATAACTAAAAAT
1 CAATCACACAATGACTAAAAAT
* * **
2604053 TAGTCATGCAATGACTAAAAAT
1 CAATCACACAATGACTAAAAAT
**
2604075 TGATCACACAATGACTAAAAA-
1 CAATCACACAATGACTAAAAAT
* ** *
2604096 CAAATCACGCAAT-ACTTTATCAAC
1 C-AATCACACAATGAC--TAAAAAT
* **
2604120 CAGTCATTCAATGACTAAAAAT
1 CAATCACACAATGACTAAAAAT
2604142 CAATCACACAATG
1 CAATCACACAATG
2604155 CCCTATCAAC
Statistics
Matches: 124, Mismatches: 38, Indels: 15
0.70 0.21 0.08
Matches are distributed among these distances:
21 3 0.02
22 90 0.73
23 28 0.23
24 3 0.02
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (22 bp):
CAATCACACAATGACTAAAAAT
Found at i:2604162 original size:45 final size:45
Alignment explanation
Indices: 2604078--2604230 Score: 136
Period size: 45 Copynumber: 3.4 Consensus size: 45
2604068 TAAAAATTGA
* * * *
2604078 TCACACAATGACTAAAAA-CAAATCACGCAATACTTTATCAACCAG
1 TCACGCAATGACTAAAAATC-AATCACACAATGCCTTATCAACCAG
** *
2604123 TCATTCAATGACTAAAAATCAATCACACAATGCCCTATCAACCAAG
1 TCACGCAATGACTAAAAATCAATCACACAATGCCTTATCAACC-AG
* *
2604169 -CACGCAATG-CTTAAAAAT-AAGTCACACAACGTCTTATCAACCAG
1 TCACGCAATGAC-TAAAAATCAA-TCACACAATGCCTTATCAACCAG
*
2604213 TCACGTAATG-CATAAAAA
1 TCACGCAATGAC-TAAAAA
2604231 CTAATAATGC
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
44 5 0.06
45 82 0.91
46 3 0.03
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.21
Consensus pattern (45 bp):
TCACGCAATGACTAAAAATCAATCACACAATGCCTTATCAACCAG
Found at i:2604192 original size:67 final size:66
Alignment explanation
Indices: 2603951--2604192 Score: 159
Period size: 67 Copynumber: 3.6 Consensus size: 66
2603941 GTAGTCACGT
* * * * * *
2603951 AATGCCTATCAACCAATCACACAATGCCTAAAAACTAA-TCATGT-AATGCCTAAAAATCATTCA
1 AATGCCTATAAACCAAGCACACAATACTTAAAAA-TAAGTCAT-TCAATGACTAAAAATCAATCA
*
2604014 TAC
64 CAC
* * * * * **
2604017 AACGCCTTATAAATC-AGTCACATAATAAC-TAAAAATTAGTCATGCAATGACTAAAAATTGATC
1 AATGCC-TATAAACCAAG-CACACAAT-ACTTAAAAATAAGTCATTCAATGACTAAAAATCAATC
2604080 ACAC
63 ACAC
* * * * * ** **
2604084 AATGACTAAAAACAAATCACGCAATACTTTATCAACCAGTCATTCAATGACTAAAAATCAATCAC
1 AATGCCTATAAACCAAGCACACAATAC-TTAAAAATAAGTCATTCAATGACTAAAAATCAATCAC
2604149 AC
65 AC
* * *
2604151 AATGCCCTATCAACCAAGCACGCAATGCTTAAAAATAAGTCA
1 AATG-CCTATAAACCAAGCACACAATACTTAAAAATAAGTCA
2604193 CACAACGTCT
Statistics
Matches: 129, Mismatches: 38, Indels: 17
0.70 0.21 0.09
Matches are distributed among these distances:
65 2 0.02
66 19 0.15
67 90 0.70
68 18 0.14
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.23
Consensus pattern (66 bp):
AATGCCTATAAACCAAGCACACAATACTTAAAAATAAGTCATTCAATGACTAAAAATCAATCACA
C
Found at i:2604266 original size:22 final size:22
Alignment explanation
Indices: 2604211--2604343 Score: 86
Period size: 22 Copynumber: 6.0 Consensus size: 22
2604201 CTTATCAACC
* * *
2604211 AGTCACGTAATGCATAAAAACT
1 AGTCACGCAATGCCTAAAAATT
* * *
2604233 AATAATGCAATGCCTAAAAATT
1 AGTCACGCAATGCCTAAAAATT
* * * *
2604255 AGTCATGTAATGCTTAAAATTT
1 AGTCACGCAATGCCTAAAAATT
*
2604277 AGTCACGCAATGCCTTAAAAATA
1 AGTCACGCAATGCC-TAAAAATT
* * * *
2604300 AGTAACACGATGCCCTAAAAAGT
1 AGTCACGCAATG-CCTAAAAATT
* **
2604323 AATCACGCAATGTTTAAAAAT
1 AGTCACGCAATGCCTAAAAAT
2604344 CGATCATGCA
Statistics
Matches: 81, Mismatches: 28, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
22 50 0.62
23 29 0.36
24 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (22 bp):
AGTCACGCAATGCCTAAAAATT
Found at i:2604349 original size:22 final size:22
Alignment explanation
Indices: 2604324--2604399 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
2604314 CTAAAAAGTA
* *
2604324 ATCACGCAATGTTTAAAAATCG
1 ATCACGCAATGCTTAAAAACCG
* *
2604346 ATCATGCAATGCCTT-AAAACCA
1 ATCACGCAATG-CTTAAAAACCG
*
2604368 ATCACGTAATGCTTAAAAACCG
1 ATCACGCAATGCTTAAAAACCG
2604390 ATCACGCAAT
1 ATCACGCAAT
2604400 CCCTCATCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.07
22 39 0.89
23 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (22 bp):
ATCACGCAATGCTTAAAAACCG
Found at i:2604384 original size:21 final size:23
Alignment explanation
Indices: 2604309--2604395 Score: 63
Period size: 22 Copynumber: 3.9 Consensus size: 23
2604299 AAGTAACACG
* ** *
2604309 ATGCCCTAAAAAGTAATCACGCA
1 ATGCCTTAAAAACCAATCACGTA
* * * * *
2604332 ATG-TTTAAAAATCGATCATGCA
1 ATGCCTTAAAAACCAATCACGTA
2604354 ATGCCTT-AAAACCAATCACGTA
1 ATGCCTTAAAAACCAATCACGTA
*
2604376 ATG-CTTAAAAACCGATCACG
1 ATGCCTTAAAAACCAATCACG
2604396 CAATCCCTCA
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
21 3 0.06
22 42 0.84
23 5 0.10
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (23 bp):
ATGCCTTAAAAACCAATCACGTA
Found at i:2604836 original size:16 final size:16
Alignment explanation
Indices: 2604815--2604858 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2604805 TGGTTTTATT
2604815 AAAAGTAATTTTGTCC
1 AAAAGTAATTTTGTCC
*
2604831 AAAAGTAATTTTGTTC
1 AAAAGTAATTTTGTCC
*
2604847 AAAATTAATTTT
1 AAAAGTAATTTT
2604859 TCTTGGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (16 bp):
AAAAGTAATTTTGTCC
Found at i:2606015 original size:4 final size:4
Alignment explanation
Indices: 2606008--2606048 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
2605998 ATATATAATT
2606008 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
2606049 CCTTCCAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:2608299 original size:30 final size:30
Alignment explanation
Indices: 2608263--2608326 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
2608253 AATCAAGCTC
* *
2608263 TTATATTTTTATTTTAAATTAAATAAATTT
1 TTATATTTTTATTTTAAATCAAATAAATCT
*
2608293 TTATATTTTTATTTTTAATCAAATAAATCT
1 TTATATTTTTATTTTAAATCAAATAAATCT
2608323 TTAT
1 TTAT
2608327 GACTAATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TTATATTTTTATTTTAAATCAAATAAATCT
Found at i:2608595 original size:30 final size:29
Alignment explanation
Indices: 2608553--2608638 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 29
2608543 TTTTACTTGT
*
2608553 AATAATTAATAATAAAATTTATTTAATTTAA
1 AATAA-TAATAATAAAATTTATTTAA-ATAA
* *
2608584 AATAATAATAATAATATTTAATTAAATAA
1 AATAATAATAATAAAATTTATTTAAATAA
2608613 AATAA-AA-AATAAAAATTTATTTAAAT
1 AATAATAATAAT-AAAATTTATTTAAAT
2608639 TTTTTTAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
27 3 0.06
28 15 0.31
29 8 0.16
30 18 0.37
31 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AATAATAATAATAAAATTTATTTAAATAA
Found at i:2608606 original size:26 final size:23
Alignment explanation
Indices: 2608555--2608617 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
2608545 TTACTTGTAA
*
2608555 TAATT-AATAATAA-AATTTATT
1 TAATTAAATAATAATAATATATT
2608576 TAATTTAAAATAATAATAATAATATT
1 TAA-TT-AAATAATAATAAT-ATATT
2608602 TAATTAAATAA-AATAA
1 TAATTAAATAATAATAA
2608618 AAAATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 3 0.08
22 2 0.06
23 5 0.14
24 14 0.39
25 5 0.14
26 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATTAAATAATAATAATATATT
Found at i:2620492 original size:15 final size:15
Alignment explanation
Indices: 2620474--2620516 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2620464 CGCCCATGAG
* *
2620474 TCCCATTCCATCCCA
1 TCCCATCCCAACCCA
2620489 TCCCATCCCAACCCA
1 TCCCATCCCAACCCA
* *
2620504 ACCCAACCCAACC
1 TCCCATCCCAACC
2620517 TTCAATCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.58, G:0.00, T:0.14
Consensus pattern (15 bp):
TCCCATCCCAACCCA
Found at i:2623100 original size:29 final size:29
Alignment explanation
Indices: 2623067--2623132 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
2623057 TGATTAACAA
* *
2623067 TAATTAATT-AAATATTAATTATAAAAATT
1 TAATTAATTAAAATA-AAAATATAAAAATT
*
2623096 TAATTTATTTAAAATAAAAATATAAAAATT
1 TAA-TTAATTAAAATAAAAATATAAAAATT
*
2623126 TTATTAA
1 TAATTAA
2623133 ACATAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
29 6 0.20
30 19 0.63
31 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TAATTAATTAAAATAAAAATATAAAAATT
Found at i:2628190 original size:4 final size:4
Alignment explanation
Indices: 2628183--2628217 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2628173 TATATATATA
*
2628183 TATG TATG TATG TAAG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
2628218 ACAATTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:2642050 original size:19 final size:19
Alignment explanation
Indices: 2642026--2642071 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
2642016 TCAGGTATGT
2642026 GCATTCCCTTAAGGAGCAA
1 GCATTCCCTTAAGGAGCAA
2642045 GCATTCCCTTAAGGAGCAA
1 GCATTCCCTTAAGGAGCAA
*
2642064 GCAATCCC
1 GCATTCCC
2642072 CATATCAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (19 bp):
GCATTCCCTTAAGGAGCAA
Found at i:2643056 original size:45 final size:45
Alignment explanation
Indices: 2643000--2643089 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
2642990 GAAAATGAAG
*
2643000 TTAGCATTCTTTAGGACAATTGTGGATGCTGGGATGCTTCATTTT
1 TTAGCATTCTTTAGGACAATTGTGGATGCTAGGATGCTTCATTTT
* *
2643045 TTAGTATTCTTTGGGACAATTGTGGATGCTAGGATGCTTCATTTT
1 TTAGCATTCTTTAGGACAATTGTGGATGCTAGGATGCTTCATTTT
2643090 GTTAATAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.43
Consensus pattern (45 bp):
TTAGCATTCTTTAGGACAATTGTGGATGCTAGGATGCTTCATTTT
Found at i:2651089 original size:45 final size:45
Alignment explanation
Indices: 2650942--2651091 Score: 165
Period size: 45 Copynumber: 3.3 Consensus size: 45
2650932 TATGCTATGA
* * * * * ** *
2650942 TGTTACACATCATATACAGAAATATATTACACGTCATAATTAAGT
1 TGTTACACGTCATGTACAAAAATATGTTACACATCATGGTTAGGT
* * * * *
2650987 TGTTACACGACATGTACAAAAACATGTGACACTTCATGGTTAGCT
1 TGTTACACGTCATGTACAAAAATATGTTACACATCATGGTTAGGT
2651032 TGTTACACGTCATGTACAAAAATATGTTACACATCATGGTTAGGT
1 TGTTACACGTCATGTACAAAAATATGTTACACATCATGGTTAGGT
* *
2651077 TATTACATGTCATGT
1 TGTTACACGTCATGT
2651092 TAAAAAAAAT
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (45 bp):
TGTTACACGTCATGTACAAAAATATGTTACACATCATGGTTAGGT
Found at i:2651208 original size:29 final size:29
Alignment explanation
Indices: 2651176--2651238 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
2651166 CCATGTTAAA
* * *
2651176 AAAAAATACTGTTATTACATGCCATGTTG
1 AAAAAATACTGTTATTACACGCCATATTC
* *
2651205 AAAAAATATTGTTGTTACACGCCATATTC
1 AAAAAATACTGTTATTACACGCCATATTC
2651234 AAAAA
1 AAAAA
2651239 CATTTTGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (29 bp):
AAAAAATACTGTTATTACACGCCATATTC
Found at i:2657809 original size:22 final size:22
Alignment explanation
Indices: 2657782--2657831 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2657772 AATTGAAATT
2657782 ATTATG-TAATTTTGGTT-TTTC
1 ATTATGTTAATTTT-GTTGTTTC
*
2657803 AATTATGTTAGTTTTGTTGTTTC
1 -ATTATGTTAATTTTGTTGTTTC
2657826 ATTATG
1 ATTATG
2657832 ATTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.60
Consensus pattern (22 bp):
ATTATGTTAATTTTGTTGTTTC
Found at i:2658112 original size:22 final size:22
Alignment explanation
Indices: 2658074--2658123 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2658064 TAAATTAAAC
2658074 AAATTAACATAAAAATTAGATA
1 AAATTAACATAAAAATTAGATA
*
2658096 AAATTACACAT-ATAATTAGATA
1 AAATTA-ACATAAAAATTAGATA
2658118 AAATTA
1 AAATTA
2658124 GATAAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATTAACATAAAAATTAGATA
Found at i:2658135 original size:8 final size:10
Alignment explanation
Indices: 2658085--2658131 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
2658075 AATTAACATA
2658085 AAAATTAGAT
1 AAAATTAGAT
*
2658095 AAAATTACACAT
1 AAAATT--AGAT
*
2658107 ATAATTAGAT
1 AAAATTAGAT
2658117 AAAATTAGAT
1 AAAATTAGAT
2658127 AAAAT
1 AAAAT
2658132 GATATGTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 23 0.74
12 8 0.26
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (10 bp):
AAAATTAGAT
Found at i:2659981 original size:2 final size:2
Alignment explanation
Indices: 2659976--2660000 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2659966 TACAAAAAAA
2659976 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
2660001 AAGTATTGAA
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
Found at i:2680088 original size:14 final size:13
Alignment explanation
Indices: 2680071--2680100 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2680061 AGATAATTTC
2680071 AACCTAAAATATAT
1 AACCTAAAATAT-T
2680085 AACCTAAAATATT
1 AACCTAAAATATT
2680098 AAC
1 AAC
2680101 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (13 bp):
AACCTAAAATATT
Found at i:2680121 original size:15 final size:17
Alignment explanation
Indices: 2680090--2680122 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2680080 TATATAACCT
2680090 AAAATATTAACAAAATA
1 AAAATATTAACAAAATA
2680107 AAAATA-TAA-AAAATA
1 AAAATATTAACAAAATA
2680122 A
1 A
2680123 GCAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATATTAACAAAATA
Found at i:2682176 original size:18 final size:19
Alignment explanation
Indices: 2682141--2682182 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2682131 TTTTTTTCTC
*
2682141 TTTT-TCTTTTTGACTTTA
1 TTTTATCTTTTAGACTTTA
2682159 TTTTATCTTTTAGA-TTTA
1 TTTTATCTTTTAGACTTTA
*
2682177 ATTTAT
1 TTTTAT
2682183 TGTTTCTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTATCTTTTAGACTTTA
Found at i:2682539 original size:44 final size:45
Alignment explanation
Indices: 2682458--2682542 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 45
2682448 CAAACTGTTG
* * *
2682458 AAAATATTTTTTATTGTTTGAATAGTACTTTAAAAAATATTGTCA
1 AAAATATTTTCTATTGTTTGAATAATACTCTAAAAAATATTGTCA
*
2682503 AAAATATTTTCTATT-TTTGAATAATACTCTAGAAAATATT
1 AAAATATTTTCTATTGTTTGAATAATACTCTAAAAAATATT
2682543 TGGAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.61
45 14 0.39
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (45 bp):
AAAATATTTTCTATTGTTTGAATAATACTCTAAAAAATATTGTCA
Found at i:2682819 original size:22 final size:22
Alignment explanation
Indices: 2682794--2682835 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2682784 TGAAATATAT
*
2682794 TTTGTTATAA-TTATTAATAAGA
1 TTTGTT-TAATTTATAAATAAGA
2682816 TTTGTTTAATTTATAAATAA
1 TTTGTTTAATTTATAAATAA
2682836 AAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTGTTTAATTTATAAATAAGA
Found at i:2683005 original size:23 final size:23
Alignment explanation
Indices: 2682957--2683005 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2682947 ATATTAATAT
* * **
2682957 AAAAATATTTTTTTTATTTTCTA
1 AAAAATATTTTTATAATTTTAAA
2682980 AAAAATATTTTTATAATTTTAAA
1 AAAAATATTTTTATAATTTTAAA
2683003 AAA
1 AAA
2683006 GTTACATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAAATATTTTTATAATTTTAAA
Found at i:2692573 original size:13 final size:13
Alignment explanation
Indices: 2692555--2692596 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2692545 AAAATTATAA
2692555 TTTATAAAAAAAT
1 TTTATAAAAAAAT
*
2692568 TTTATAAATAAAAA
1 TTTATAAA-AAAAT
*
2692582 TTTATCAAAAAAT
1 TTTATAAAAAAAT
2692595 TT
1 TT
2692597 CAGCTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTATAAAAAAAT
Found at i:2692594 original size:12 final size:12
Alignment explanation
Indices: 2692553--2692596 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
2692543 ACAAAATTAT
2692553 AATTTATAAAAA
1 AATTTATAAAAA
2692565 AATTTTATAAATAAA
1 AA-TTTAT-AA-AAA
*
2692580 AATTTATCAAAA
1 AATTTATAAAAA
2692592 AATTT
1 AATTT
2692597 CAGCTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 10 0.36
13 6 0.21
14 7 0.25
15 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTTATAAAAA
Found at i:2704919 original size:23 final size:23
Alignment explanation
Indices: 2704893--2704966 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
2704883 CCATATCATA
*
2704893 TCACATATTCTCTTCGAGTCGTG
1 TCACATATTCTCTTCTAGTCGTG
* *
2704916 TCACATATTCTCATCTTGTCGTG
1 TCACATATTCTCTTCTAGTCGTG
*
2704939 TCACATATTCT-TTCTATGGCGTG
1 TCACATATTCTCTTCTA-GTCGTG
2704962 TCACA
1 TCACA
2704967 AACTCTAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
22 3 0.07
23 41 0.93
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.41
Consensus pattern (23 bp):
TCACATATTCTCTTCTAGTCGTG
Found at i:2707180 original size:37 final size:37
Alignment explanation
Indices: 2707125--2707249 Score: 137
Period size: 37 Copynumber: 3.4 Consensus size: 37
2707115 GGTAGAGAGG
2707125 TTGTGTTTGATTCC-TGAAAGGTAATGGCTTGTATAGA
1 TTGTGTTTGA-TCCTTGAAAGGTAATGGCTTGTATAGA
* ** * *
2707162 TTGTGCTTGATCCTTGAAAGACAGTGGTTTGTATA-A
1 TTGTGTTTGATCCTTGAAAGGTAATGGCTTGTATAGA
* * *
2707198 GTTGTGGTTGATCCTTGAAAGGTAATGGCTTGTAAAGG
1 -TTGTGTTTGATCCTTGAAAGGTAATGGCTTGTATAGA
*
2707236 TTGTATTTGATCCT
1 TTGTGTTTGATCCT
2707250 AAAAAAGCAA
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
36 4 0.06
37 67 0.94
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (37 bp):
TTGTGTTTGATCCTTGAAAGGTAATGGCTTGTATAGA
Found at i:2707817 original size:44 final size:44
Alignment explanation
Indices: 2707754--2707849 Score: 192
Period size: 44 Copynumber: 2.2 Consensus size: 44
2707744 ATCAAGTCCT
2707754 GATCAAGTCCTAATTAAGGTAGGGGACCAATTCTGTGCATTTAA
1 GATCAAGTCCTAATTAAGGTAGGGGACCAATTCTGTGCATTTAA
2707798 GATCAAGTCCTAATTAAGGTAGGGGACCAATTCTGTGCATTTAA
1 GATCAAGTCCTAATTAAGGTAGGGGACCAATTCTGTGCATTTAA
2707842 GATCAAGT
1 GATCAAGT
2707850 TGTCAAGACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (44 bp):
GATCAAGTCCTAATTAAGGTAGGGGACCAATTCTGTGCATTTAA
Found at i:2716718 original size:13 final size:15
Alignment explanation
Indices: 2716701--2716740 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
2716691 CAGCTCTTGA
2716701 TTCCTCTTTTT-TTC
1 TTCCTCTTTTTGTTC
2716715 -TCCT-TTTTTGTTC
1 TTCCTCTTTTTGTTC
2716728 TTGCCTCTTTTTG
1 TT-CCTCTTTTTG
2716741 CCCAAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.23
13 7 0.32
14 1 0.05
15 3 0.14
16 6 0.27
ACGTcount: A:0.00, C:0.25, G:0.07, T:0.68
Consensus pattern (15 bp):
TTCCTCTTTTTGTTC
Found at i:2726574 original size:2 final size:2
Alignment explanation
Indices: 2726567--2726596 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2726557 TTAAAACATT
2726567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2726597 GCTAGTCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2731429 original size:27 final size:29
Alignment explanation
Indices: 2731399--2731471 Score: 96
Period size: 27 Copynumber: 2.5 Consensus size: 29
2731389 TATAATTAAA
*
2731399 CATAAACACACAAAATTAATAATC-TT-T
1 CATAAACACACAAAATCAATAATCTTTCT
*
2731426 CATAAACACACAGAATCAATAATCTTTCT
1 CATAAACACACAAAATCAATAATCTTTCT
2731455 CAATAAACATCACAAAA
1 C-ATAAACA-CACAAAA
2731472 CTAAAACAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 22 0.56
28 2 0.05
29 2 0.05
30 7 0.18
31 6 0.15
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.25
Consensus pattern (29 bp):
CATAAACACACAAAATCAATAATCTTTCT
Found at i:2734958 original size:30 final size:33
Alignment explanation
Indices: 2734922--2734985 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
2734912 TCAATGCATT
*
2734922 GGATTAAGTTA-AGAGA-A-AGGTAAGATTTAG
1 GGATTAAGTTAGAGAGAGAGAGGCAAGATTTAG
2734952 GGATTAAGTTAGGAGAGAGAGAGGCAAGATTTAG
1 GGATTAAGTTA-GAGAGAGAGAGGCAAGATTTAG
2734986 ATCAAGTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 11 0.38
32 5 0.17
33 1 0.03
34 12 0.41
ACGTcount: A:0.41, C:0.02, G:0.34, T:0.23
Consensus pattern (33 bp):
GGATTAAGTTAGAGAGAGAGAGGCAAGATTTAG
Found at i:2755915 original size:2 final size:2
Alignment explanation
Indices: 2755908--2755933 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2755898 TTGTAATTGG
2755908 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
2755934 GTTGTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2758404 original size:17 final size:16
Alignment explanation
Indices: 2758382--2758421 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2758372 GTGATTTGAT
2758382 TTTAAAATAATTTTAAA
1 TTTAAAATAA-TTTAAA
*
2758399 TTTAAATTAATTTAAA
1 TTTAAAATAATTTAAA
*
2758415 TTCAAAA
1 TTTAAAA
2758422 AGATTTCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAATAATTTAAA
Found at i:2758405 original size:16 final size:16
Alignment explanation
Indices: 2758382--2758416 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2758372 GTGATTTGAT
*
2758382 TTTAAAATAATTTTAAA
1 TTTAAATTAA-TTTAAA
2758399 TTTAAATTAATTTAAA
1 TTTAAATTAATTTAAA
2758415 TT
1 TT
2758417 CAAAAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:2763168 original size:2 final size:2
Alignment explanation
Indices: 2763161--2763187 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2763151 ATTTAGATTT
2763161 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 T
2763188 TCTTTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2767623 original size:14 final size:14
Alignment explanation
Indices: 2767604--2767635 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2767594 AAATTATAAT
2767604 TTATAAAAAAAAAC
1 TTATAAAAAAAAAC
*
2767618 TTATAAAAAAAAAT
1 TTATAAAAAAAAAC
2767632 TTAT
1 TTAT
2767636 CAAACAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
TTATAAAAAAAAAC
Found at i:2767784 original size:48 final size:48
Alignment explanation
Indices: 2767728--2768163 Score: 352
Period size: 48 Copynumber: 9.1 Consensus size: 48
2767718 CAAACAAGCT
* * *
2767728 CTTAGTCTTTTTATGTTATTAGTTTGGACTAAAATAATGAACATTGGG
1 CTTAGTCTTTTTATGTTATTAGTTTGGACTAAAATAAAGAATATTGGA
* * *
2767776 CTTAGTCTTTTTTATGTTATTAGTCTAGGTC-AAAATAAACG-ATTTTGGA
1 CTTAGTC-TTTTTATGTTATTAGT-TTGGACTAAAATAAA-GAATATTGGA
* * * * * * * *
2767825 CTTAATCCTTTTATGTTATCAATTT-AAGTCAGAATAAAGTATATTGGA
1 CTTAGTCTTTTTATGTTATTAGTTTGGACT-AAAATAAAGAATATTGGA
* * *
2767873 CTTAGTCGTTTT-TGTTATTTGTTTGGACTAAAATAAAGAACATTGGA
1 CTTAGTCTTTTTATGTTATTAGTTTGGACTAAAATAAAGAATATTGGA
* * ** * * *
2767920 CGTAGTCTTTTTTATGTTATTAGTCTGGGTTAGAATAAACAATATTAGA
1 CTTAGTC-TTTTTATGTTATTAGTTTGGACTAAAATAAAGAATATTGGA
* * * * * *
2767969 CTTAGTCCTTTTATGTTATCAATTT-AAGCCAAAATAAAGTA-ATTGGA
1 CTTAGTCTTTTTATGTTATTAGTTTGGA-CTAAAATAAAGAATATTGGA
* * *
2768016 CTTAGTCTTTTT-TGTTATTAGTTTGG-GTCAGAATAAACAATATTGGA
1 CTTAGTCTTTTTATGTTATTAGTTTGGACT-AAAATAAAGAATATTGGA
* * * * *
2768063 CTTAGTCCTTTTATGTTATTAATTT-AAGCCAAAATAAAGTATATTGGA
1 CTTAGTCTTTTTATGTTATTAGTTTGGA-CTAAAATAAAGAATATTGGA
** * *
2768111 CTTAGTCTTTTT-TGTTATTAGTTTGGGTTAGAATGAAGAATATTGGA
1 CTTAGTCTTTTTATGTTATTAGTTTGGACTAAAATAAAGAATATTGGA
2768158 CTTAGT
1 CTTAGT
2768164 GTTTATTTGA
Statistics
Matches: 296, Mismatches: 75, Indels: 35
0.73 0.18 0.09
Matches are distributed among these distances:
46 18 0.06
47 97 0.33
48 109 0.37
49 67 0.23
50 5 0.02
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (48 bp):
CTTAGTCTTTTTATGTTATTAGTTTGGACTAAAATAAAGAATATTGGA
Found at i:2768005 original size:144 final size:143
Alignment explanation
Indices: 2767728--2768128 Score: 502
Period size: 144 Copynumber: 2.8 Consensus size: 143
2767718 CAAACAAGCT
* *
2767728 CTTAGTCTTTTTATGTTATTAGTTTGGACTAAAATAATGAACATTGGGCTTAGTCTTTTTTATGT
1 CTTAGTCTTTTT-TGTTATTAGTTTGGACTAAAATAAAGAACATTGGACTTAGTCTTTTTTATGT
* * * * *
2767793 TATTAGTCTAGGTCAAAATAAACGATTTTGGACTTAATCCTTTTATGTTATCAATTTAAGTCAGA
65 TATTAGTCTAGGTCAAAATAAACAATATTAGACTTAATCCTTTTATGTTATCAATTTAAGCCAAA
2767858 ATAAAGTATATTGGA
130 ATAAAGTA-ATTGGA
* * *
2767873 CTTAGTCGTTTTTGTTATTTGTTTGGACTAAAATAAAGAACATTGGACGTAGTCTTTTTTATGTT
1 CTTAGTCTTTTTTGTTATTAGTTTGGACTAAAATAAAGAACATTGGACTTAGTCTTTTTTATGTT
* * * *
2767938 ATTAGTCTGGGTTAGAATAAACAATATTAGACTTAGTCCTTTTATGTTATCAATTTAAGCCAAAA
66 ATTAGTCTAGGTCAAAATAAACAATATTAGACTTAATCCTTTTATGTTATCAATTTAAGCCAAAA
2768003 TAAAGTAATTGGA
131 TAAAGTAATTGGA
* * * * *
2768016 CTTAGTCTTTTTTGTTATTAGTTTGG-GTCAGAATAAACAATATTGGACTTAGTC-CTTTTATGT
1 CTTAGTCTTTTTTGTTATTAGTTTGGACT-AAAATAAAGAACATTGGACTTAGTCTTTTTTATGT
* * * * ** * * *
2768079 TATTAATTTAAGCCAAAATAAAGTATATTGGACTTAGT-CTTTTTTGTTAT
65 TATTAGTCTAGGTCAAAATAAACAATATTAGACTTAATCCTTTTATGTTAT
2768129 TAGTTTGGGT
Statistics
Matches: 222, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
141 11 0.05
142 37 0.17
143 51 0.23
144 112 0.50
145 11 0.05
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.44
Consensus pattern (143 bp):
CTTAGTCTTTTTTGTTATTAGTTTGGACTAAAATAAAGAACATTGGACTTAGTCTTTTTTATGTT
ATTAGTCTAGGTCAAAATAAACAATATTAGACTTAATCCTTTTATGTTATCAATTTAAGCCAAAA
TAAAGTAATTGGA
Found at i:2768386 original size:14 final size:14
Alignment explanation
Indices: 2768367--2768393 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2768357 CTAAAATTAT
2768367 AACTTATAAAAAAG
1 AACTTATAAAAAAG
2768381 AACTTATAAAAAA
1 AACTTATAAAAAA
2768394 AATTTACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AACTTATAAAAAAG
Found at i:2770170 original size:13 final size:13
Alignment explanation
Indices: 2770135--2770171 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
2770125 CGAATTCAAG
*
2770135 TAACTAAATTAAT
1 TAACTAAAATAAT
2770148 TAACTAAAAATAAT
1 TAACT-AAAATAAT
2770162 TAACTAAAAT
1 TAACTAAAAT
2770172 TTAAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
TAACTAAAATAAT
Found at i:2772241 original size:2 final size:2
Alignment explanation
Indices: 2772234--2772266 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2772224 ACACTAACTT
2772234 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 T
2772267 GTGCTTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2783949 original size:17 final size:16
Alignment explanation
Indices: 2783929--2783962 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2783919 TAAAAAGGTA
*
2783929 TTTTTATTATAATTAAT
1 TTTTTAATAT-ATTAAT
2783946 TTTTTAATATATTAAT
1 TTTTTAATATATTAAT
2783962 T
1 T
2783963 AATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAATATATTAAT
Found at i:2783998 original size:24 final size:23
Alignment explanation
Indices: 2783933--2783998 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
2783923 AAGGTATTTT
*
2783933 TATTA-TAATTAATTTTTTAATA
1 TATTATTAATTAAATTTTTAATA
*
2783955 TATTAATTAATTAAAATTTTAATA
1 TATT-ATTAATTAAATTTTTAATA
*
2783979 TTATT-TTCATTATAATTTTT
1 -TATTATTAATTA-AATTTTT
2783999 CTTCTTTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 4 0.11
23 7 0.19
24 21 0.58
25 4 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTATTAATTAAATTTTTAATA
Found at i:2784435 original size:16 final size:17
Alignment explanation
Indices: 2784414--2784456 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2784404 CTTAGAGATT
2784414 TAAAATTTTTTA-AAAA
1 TAAAATTTTTTATAAAA
**
2784430 TAAAATAATTTATAAAA
1 TAAAATTTTTTATAAAA
*
2784447 TAATATTTTT
1 TAAAATTTTT
2784457 AATTATATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATTTTTTATAAAA
Found at i:2785423 original size:29 final size:30
Alignment explanation
Indices: 2785380--2785462 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 30
2785370 AACTCTTTAA
2785380 ATTAT-TTTAAATAAATTTTTAATTTT-TT
1 ATTATATTTAAATAAATTTTTAATTTTATT
*
2785408 ATTATATTTAATTAAATTTTTATATTTTATT
1 ATTATATTTAAATAAATTTTTA-ATTTTATT
*
2785439 -TTA-AATTAAATAAATTTTTTAATT
1 ATTATATTTAAATAAA-TTTTTAATT
2785463 AATAATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 5 0.10
29 27 0.56
30 14 0.29
31 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTATATTTAAATAAATTTTTAATTTTATT
Found at i:2785445 original size:25 final size:22
Alignment explanation
Indices: 2785400--2785449 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 22
2785390 ATAAATTTTT
2785400 AATTTTTTATTATATTTAATTA
1 AATTTTTTATTATATTTAATTA
*
2785422 AATTTTTATATTTTATTTTAAATTA
1 AATTTTT-TATTATA-TTT-AATTA
2785447 AAT
1 AAT
2785450 AAATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 3 0.12
25 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTTTTTATTATATTTAATTA
Found at i:2785462 original size:17 final size:16
Alignment explanation
Indices: 2785437--2785478 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2785427 TTATATTTTA
*
2785437 TTTTAAATTAAATAAAT
1 TTTTTAATTAAAT-AAT
2785454 TTTTTAATT-AATAAT
1 TTTTTAATTAAATAAT
*
2785469 TATTTAATTA
1 TTTTTAATTA
2785479 TTAATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 3 0.14
17 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTAATTAAATAAT
Found at i:2785474 original size:15 final size:15
Alignment explanation
Indices: 2785451--2785485 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2785441 AAATTAAATA
*
2785451 AATTTTTTAATTAAT
1 AATTATTTAATTAAT
*
2785466 AATTATTTAATTATT
1 AATTATTTAATTAAT
2785481 AATTA
1 AATTA
2785486 AAATATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTATTTAATTAAT
Found at i:2785594 original size:23 final size:22
Alignment explanation
Indices: 2785560--2785610 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
2785550 ATACCCATCA
2785560 TTATTAATTATGATATCTTAAT
1 TTATTAATTATGATATCTTAAT
* *
2785582 TTATTACATTATGATTTGTTAAT
1 TTATTA-ATTATGATATCTTAAT
*
2785605 ATATTA
1 TTATTA
2785611 TTTTAATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (22 bp):
TTATTAATTATGATATCTTAAT
Found at i:2785687 original size:29 final size:28
Alignment explanation
Indices: 2785655--2785744 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 28
2785645 ATTTTAATCA
*
2785655 AATTAATTATAAATTAAAAGATTTAATTT
1 AATTAATTAAAAATTAAAA-ATTTAATTT
* * *
2785684 AATTTAAAATAAAAATATAAAAATTGAATTA
1 AA-TT-AATTAAAAAT-TAAAAATTTAATTT
*
2785715 AATATAATAAAAAATTAAAAATTT-ATTT
1 AAT-TAATTAAAAATTAAAAATTTAATTT
2785743 AA
1 AA
2785745 ATTTTTTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
28 5 0.10
29 10 0.20
30 11 0.22
31 18 0.37
32 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
AATTAATTAAAAATTAAAAATTTAATTT
Found at i:2785745 original size:29 final size:30
Alignment explanation
Indices: 2785665--2785746 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
2785655 AATTAATTAT
*
2785665 AAATTAAAAGATTTAATTT-AATTTAAAATAA
1 AAATTAAAA-ATTT-ATTTAAATATAAAATAA
* * *
2785696 AAATATAAAAATTGAATTAAATATAATA-AA
1 AAAT-TAAAAATTTATTTAAATATAAAATAA
2785726 AAATTAAAAATTTATTTAAAT
1 AAATTAAAAATTTATTTAAAT
2785747 TTTTTAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 15 0.35
30 9 0.21
31 14 0.33
32 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
AAATTAAAAATTTATTTAAATATAAAATAA
Found at i:2786391 original size:21 final size:23
Alignment explanation
Indices: 2786365--2786407 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2786355 GGATATATTT
*
2786365 ATTTAGG-T-TTTTTTTTTTCTG
1 ATTTAGGATGTTTTGTTTTTCTG
2786386 ATTTAGGATGTTTTGTTTTTCT
1 ATTTAGGATGTTTTGTTTTTCT
2786408 CAGGAATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.12, C:0.05, G:0.16, T:0.67
Consensus pattern (23 bp):
ATTTAGGATGTTTTGTTTTTCTG
Found at i:2788803 original size:14 final size:14
Alignment explanation
Indices: 2788777--2788814 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
2788767 TATCATTGTT
2788777 ATATT-GAATCTTAA
1 ATATTAGAA-CTTAA
2788791 ATATTAGAACTTAA
1 ATATTAGAACTTAA
2788805 ATATTAGAAC
1 ATATTAGAAC
2788815 CCTTGAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (14 bp):
ATATTAGAACTTAA
Found at i:2804793 original size:21 final size:21
Alignment explanation
Indices: 2804783--2804823 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2804773 CTAAGAGAGT
2804783 TCAAATCTCTTCAAAAGAAGG
1 TCAAATCTCTTCAAAAGAAGG
2804804 TCAAATCTCTTCAAAAGAAG
1 TCAAATCTCTTCAAAAGAAG
2804824 TTCCATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (21 bp):
TCAAATCTCTTCAAAAGAAGG
Found at i:2834146 original size:29 final size:29
Alignment explanation
Indices: 2834114--2834170 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
2834104 TTTTAAAGAC
2834114 GAGTGATAGTGGAAATATTTTCTATAGAT
1 GAGTGATAGTGGAAATATTTTCTATAGAT
2834143 GAGTGATAGTGGAAATATTTTCTATAGA
1 GAGTGATAGTGGAAATATTTTCTATAGA
2834171 GTAATCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
GAGTGATAGTGGAAATATTTTCTATAGAT
Found at i:2839015 original size:12 final size:12
Alignment explanation
Indices: 2839000--2839024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2838990 AAATTCCAAG
2839000 AAAAAAAGTCCA
1 AAAAAAAGTCCA
2839012 AAAAAAAGTCCA
1 AAAAAAAGTCCA
2839024 A
1 A
2839025 CATATCAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAAGTCCA
Done.