Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 9 of 204
Found at i:2786129 original size:19 final size:17
Alignment explanation
Indices: 2786105--2786158 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
2786095 AAAATGAAAC
2786105 TAATAATAATTAACAGTAA
1 TAATAATAATTAA-A-TAA
* *
2786124 TAATAA-CATTTAATAA
1 TAATAATAATTAAATAA
2786140 TAATAATAATTAGAATAA
1 TAATAATAATTA-AATAA
2786158 T
1 T
2786159 TAATTAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 9 0.31
17 4 0.14
18 10 0.34
19 6 0.21
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (17 bp):
TAATAATAATTAAATAA
Found at i:2791038 original size:24 final size:24
Alignment explanation
Indices: 2791011--2791063 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2791001 TTTATTGAAG
* *
2791011 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
* *
2791035 ATTTAGCATTTTTTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
2791059 ATTTA
1 ATTTA
2791064 ACTTTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:2791074 original size:24 final size:24
Alignment explanation
Indices: 2791018--2791074 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
2791008 AAGATTTAGT
* * *
2791018 ATTTATGAGTATAATATATTTAGC
1 ATTTATTAGCATAATATATTTAAC
*
2791042 ATTTTTTAGCATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
2791066 -TTTGATTAG
1 ATTT-ATTAG
2791075 AATTAGGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:2804186 original size:28 final size:28
Alignment explanation
Indices: 2804147--2804233 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
2804137 AAAAATAAAA
2804147 AAAAGTTA-TAAAATTATTAAATTTTAAT
1 AAAA-TTATTAAAATTATTAAATTTTAAT
* *
2804175 AAAATTATTAAAATTATTAAATTAGTAAG
1 AAAATTATTAAAATTATTAAATT-TTAAT
* * *
2804204 AAAA-TATAAAAATT-GTAAATTTTTAT
1 AAAATTATTAAAATTATTAAATTTTAAT
2804230 AAAA
1 AAAA
2804234 AATAAAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
26 6 0.12
27 9 0.18
28 28 0.56
29 7 0.14
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
AAAATTATTAAAATTATTAAATTTTAAT
Found at i:2804246 original size:17 final size:19
Alignment explanation
Indices: 2804226--2804261 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2804216 TTGTAAATTT
2804226 TTATAAAA-A-ATAAAAAA
1 TTATAAAATACATAAAAAA
2804243 TTATAAAATACATAAAAAA
1 TTATAAAATACATAAAAAA
2804262 GACTCTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
TTATAAAATACATAAAAAA
Found at i:2804251 original size:28 final size:29
Alignment explanation
Indices: 2804156--2804251 Score: 92
Period size: 28 Copynumber: 3.4 Consensus size: 29
2804146 AAAAAGTTAT
* * *
2804156 AAAATTATTAAATTTTAAT-AAAATTATT
1 AAAATTATTAAATTTTTATAAAAAATATA
** *
2804184 AAAATTATTAAATTAGTA-AGAAAATATA
1 AAAATTATTAAATTTTTATAAAAAATATA
*
2804212 AAAATT-GTAAATTTTTATAAAAAATA-A
1 AAAATTATTAAATTTTTATAAAAAATATA
*
2804239 AAAATTATAAAAT
1 AAAATTATTAAAT
2804252 ACATAAAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
27 15 0.28
28 38 0.72
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTATTAAATTTTTATAAAAAATATA
Found at i:2804545 original size:22 final size:22
Alignment explanation
Indices: 2804517--2804560 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2804507 AATTTATAAC
2804517 TTTTATAAAATTTTACAATTTT
1 TTTTATAAAATTTTACAATTTT
** *
2804539 TTTTATAATTTTTTACGATTTT
1 TTTTATAAAATTTTACAATTTT
2804561 ATAAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTATAAAATTTTACAATTTT
Found at i:2804577 original size:16 final size:18
Alignment explanation
Indices: 2804556--2804594 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2804546 ATTTTTTACG
*
2804556 ATTTTA-TA-AATTTTAT
1 ATTTTATTACAATTTAAT
2804572 ATTTTATTACAATTTAAT
1 ATTTTATTACAATTTAAT
2804590 ATTTT
1 ATTTT
2804595 TTTTATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATTACAATTTAAT
Found at i:2804596 original size:27 final size:27
Alignment explanation
Indices: 2804537--2804607 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
2804527 TTTTACAATT
* *
2804537 TTTTTTATAATTTTTTACGATTTTATA
1 TTTTTTATAATTTTTTACAATTTAATA
**
2804564 AATTTTAT-ATTTTATTACAATTTAATA
1 TTTTTTATAATTTT-TTACAATTTAATA
2804591 TTTTTTTTATAATTTTT
1 --TTTTTTATAATTTTT
2804608 ATTAATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.15
27 17 0.50
29 7 0.21
30 5 0.15
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTTTTATAATTTTTTACAATTTAATA
Found at i:2804610 original size:18 final size:18
Alignment explanation
Indices: 2804534--2804610 Score: 57
Period size: 19 Copynumber: 4.2 Consensus size: 18
2804524 AAATTTTACA
2804534 ATTTTTTTTATAATTTTT
1 ATTTTTTTTATAATTTTT
*** *
2804552 -TACGATTTTATAAATTTT
1 AT-TTTTTTTATAATTTTT
* * *
2804570 ATATTTTATTACAATTTAAT
1 AT-TTTTTTTATAATTT-TT
2804590 ATTTTTTTTATAATTTTT
1 ATTTTTTTTATAATTTTT
2804608 ATT
1 ATT
2804611 AATTTTTCTT
Statistics
Matches: 42, Mismatches: 14, Indels: 6
0.68 0.23 0.10
Matches are distributed among these distances:
17 1 0.02
18 16 0.38
19 22 0.52
20 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
ATTTTTTTTATAATTTTT
Found at i:2804616 original size:56 final size:58
Alignment explanation
Indices: 2804476--2804616 Score: 143
Period size: 56 Copynumber: 2.4 Consensus size: 58
2804466 TTTCTTTACA
*
2804476 TTTTTTATAATTTTTTTCTATATTTCTATATAATTTATAACTTTTATAAAATTTTACAATT
1 TTTTTTATAA-TTTTTT-TACATTT-TATATAATTTATAACTTTTATAAAATTTTACAATT
*
2804537 TTTTTTATAA-TTTTTTACGATTTTATA-AATTT-TATA-TTTTATTACAA-TTTA-ATATT
1 TTTTTTATAATTTTTTTAC-ATTTTATATAATTTATA-ACTTTTA-TAAAATTTTACA-ATT
2804593 TTTTTTATAATTTTTATTA-ATTTT
1 TTTTTTATAATTTTT-TTACATTTT
2804617 TCTTTCTTTC
Statistics
Matches: 72, Mismatches: 2, Indels: 17
0.79 0.02 0.19
Matches are distributed among these distances:
55 1 0.01
56 29 0.40
57 14 0.19
58 9 0.12
59 9 0.12
61 10 0.14
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (58 bp):
TTTTTTATAATTTTTTTACATTTTATATAATTTATAACTTTTATAAAATTTTACAATT
Found at i:2809791 original size:36 final size:36
Alignment explanation
Indices: 2809744--2809813 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2809734 CCATAGATGC
* *
2809744 AGTGGATTCACCATAAGTTACCATAGAAGCAGTGAA
1 AGTGGATTCACCATAAGTAACCAAAGAAGCAGTGAA
*
2809780 AGTGGGTTCACCATAAGTAACCAAAGAAGCAGTG
1 AGTGGATTCACCATAAGTAACCAAAGAAGCAGTG
2809814 TAGTTAACAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (36 bp):
AGTGGATTCACCATAAGTAACCAAAGAAGCAGTGAA
Found at i:2813411 original size:20 final size:19
Alignment explanation
Indices: 2813359--2813417 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
2813349 AGCAATGAAT
2813359 CTGTTCACCAAGAGATACAA
1 CTGTTCA-CAAGAGATACAA
* *
2813379 TTATTCA-AA-AGATACAA
1 CTGTTCACAAGAGATACAA
*
2813396 CTGTTCATCAAGAGATAGAA
1 CTGTTCA-CAAGAGATACAA
2813416 CT
1 CT
2813418 ATTGTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 13 0.42
18 2 0.06
19 2 0.06
20 14 0.45
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (19 bp):
CTGTTCACAAGAGATACAA
Found at i:2816636 original size:21 final size:20
Alignment explanation
Indices: 2816608--2816670 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 20
2816598 TCTCATCTAT
2816608 AAATATTAAAAAATATATTA
1 AAATATTAAAAAATATATTA
* *
2816628 AAATCATTAAAAATTGTATTA
1 AAAT-ATTAAAAAATATATTA
* *
2816649 ATAT-TTTAAAAATA-ATTA
1 AAATATTAAAAAATATATTA
2816667 AAAT
1 AAAT
2816671 TTTATTGAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
18 7 0.20
19 7 0.20
20 4 0.11
21 17 0.49
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATATTAAAAAATATATTA
Found at i:2816639 original size:20 final size:19
Alignment explanation
Indices: 2816608--2816670 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
2816598 TCTCATCTAT
2816608 AAATATTAAAAAATATATTA
1 AAATATT-AAAAATATATTA
*
2816628 AAATCATTAAAAATTGTATTA
1 AAAT-ATTAAAAA-TATATTA
* *
2816649 ATATTTTAAAAATA-ATTA
1 AAATATTAAAAATATATTA
2816667 AAAT
1 AAAT
2816671 TTTATTGAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 7 0.19
19 1 0.03
20 16 0.44
21 12 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATATTAAAAATATATTA
Found at i:2816698 original size:29 final size:30
Alignment explanation
Indices: 2816627--2816698 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 30
2816617 AAAATATATT
* * *
2816627 AAAATCATTAAAAATTGTATTAATATTTTA
1 AAAATAATTAAAAATTGTATTAAGAATTTA
* *
2816657 AAAATAATT-AAAATTTTATTGAGAATTTA
1 AAAATAATTAAAAATTGTATTAAGAATTTA
*
2816686 TAAA-AATTAAAAA
1 AAAATAATTAAAAA
2816699 AATGTTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 4 0.11
29 23 0.66
30 8 0.23
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (30 bp):
AAAATAATTAAAAATTGTATTAAGAATTTA
Found at i:2821011 original size:18 final size:17
Alignment explanation
Indices: 2820984--2821047 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 17
2820974 TTACTTCTCA
*
2820984 AAAAAT-TTTTTAGGAC
1 AAAAATATTTTTAAGAC
*
2821000 AAAAAGTATTTTTAAGAT
1 AAAAA-TATTTTTAAGAC
**
2821018 AAAAATATTGCTAA-AC
1 AAAAATATTTTTAAGAC
*
2821034 -AATATATTTTTAAG
1 AAAAATATTTTTAAG
2821048 CTTTTCAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
15 10 0.27
16 6 0.16
17 8 0.22
18 13 0.35
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (17 bp):
AAAAATATTTTTAAGAC
Found at i:2823706 original size:19 final size:20
Alignment explanation
Indices: 2823655--2823704 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
2823645 CAAAAATTTT
2823655 TTTTAGAAAATTAAAAAAAGTA
1 TTTTA-AAAA-TAAAAAAAGTA
*
2823677 TTTTAAAAATAAAAAAATTA
1 TTTTAAAAATAAAAAAAGTA
2823697 TTTTAAAA
1 TTTTAAAA
2823705 TATTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 18 0.67
21 4 0.15
22 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
TTTTAAAAATAAAAAAAGTA
Found at i:2826354 original size:14 final size:14
Alignment explanation
Indices: 2826271--2826354 Score: 54
Period size: 13 Copynumber: 6.1 Consensus size: 14
2826261 TATATTTTAA
*
2826271 AATATTTTCAATA-
1 AATATTTTTAATAT
2826284 AATATTTTTAAT-T
1 AATATTTTTAATAT
*
2826297 CAATAAGTTTT-ATAT
1 -AAT-ATTTTTAATAT
2826312 AATATTTTTAA-A-
1 AATATTTTTAATAT
* *
2826324 AATTAAGTTCT-ATAT
1 AA-T-ATTTTTAATAT
2826339 AATATTTTTAATAT
1 AATATTTTTAATAT
2826353 AA
1 AA
2826355 AAATATTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 19
0.68 0.09 0.24
Matches are distributed among these distances:
12 2 0.04
13 23 0.43
14 21 0.39
15 8 0.15
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (14 bp):
AATATTTTTAATAT
Found at i:2828962 original size:50 final size:50
Alignment explanation
Indices: 2828847--2829095 Score: 311
Period size: 50 Copynumber: 4.8 Consensus size: 50
2828837 GATCATAACA
* ** *
2828847 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
2828898 TGGCC-ATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 T-GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
2828948 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
2828998 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
2829053 ATGCCAATGCCATGTCCCAGGCATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2829096 TTACCCAAAT
Statistics
Matches: 172, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
49 3 0.02
50 92 0.53
51 30 0.17
52 3 0.02
53 4 0.02
55 1 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:2829468 original size:30 final size:30
Alignment explanation
Indices: 2829434--2829491 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2829424 CCTCGACTCT
* *
2829434 AACTTTTTCAAAATTATAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
2829464 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
2829492 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:2835482 original size:27 final size:29
Alignment explanation
Indices: 2835416--2835474 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2835406 AAAATTGACT
* * *
2835416 TAAATTAATTTTTTTAATAATATAAAAAT
1 TAAATTAATCTATTTAATAATATAAAAAG
2835445 TAAATTAATCTATTTAATAA-A-AAAAAG
1 TAAATTAATCTATTTAATAATATAAAAAG
2835472 TAA
1 TAA
2835475 TTTTATCTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 8 0.30
28 1 0.04
29 18 0.67
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
TAAATTAATCTATTTAATAATATAAAAAG
Found at i:2835928 original size:16 final size:18
Alignment explanation
Indices: 2835909--2835943 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2835899 GTAAATATAC
2835909 AAAAT-AAAGAATA-AAA
1 AAAATGAAAGAATAGAAA
2835925 AAAATGAAAGAATAGAAA
1 AAAATGAAAGAATAGAAA
2835943 A
1 A
2835944 TGGGTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 8 0.47
18 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAATGAAAGAATAGAAA
Found at i:2847665 original size:156 final size:156
Alignment explanation
Indices: 2846976--2847757 Score: 1026
Period size: 156 Copynumber: 5.0 Consensus size: 156
2846966 CAAAAGAAAA
* * *
2846976 GTTCATAGTTCATTATCCTTGATTTGACTTTTATATCCCTATCTCCATCCTCAAACACACGACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
* * * *
2847041 AAACTATAAATACGA-GCACAAGAAAATACCATTTTTTCCTT-TGGGAGTAATTTCTCAGATGGC
66 AAAATATAAATA-AATGCACAAGAACATACCATTTTCTCCTTGT-GGAGTAATTTCTCAGATGGC
* * *
2847104 TTCCTTGATATAGTTTCCTGAAAAGGAT
129 TTCCTCGATACAGTTTCCTGAAAAGGGT
* *
2847132 GCTCGTAGTTTATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
* * *
2847197 AAAATATAAATATATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCATATGGCTT
66 AAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGG---
2847262 CTTCCTCGATACAGTTTCCTG-AAAGGGTT
128 CTTCCTCGATACAGTTTCCTGAAAAGGG-T
* * * * * * * *
2847291 TTTC-TAGTTCATCACCCTTGATTTGAC-CTTATGTTCATATCTCAATCCTAAAACACACAACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
*
2847354 AAAATATAAATACAA-GCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCCCAGATGGCT
66 AAAATATAAATA-AATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGG--
2847418 TCTTCCTCGATACAGTTTCCTGAAAAGGGT
128 -CTTCCTCGATACAGTTTCCTGAAAAGGGT
* * * *
2847448 GTTCCTAGTTCATTATCCTTGATTTGACTTTTATGTTCCTATCTCCATCCTCTAACGCACAACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
*
2847513 AAAGTATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGGCTT
66 AAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGGCTT
* * *
2847578 CCTCGATTCAATTTCCTGAAAAAGGT
131 CCTCGATACAGTTTCCTGAAAAGGGT
* * *
2847604 GTTCGTAGTTCGTTATCCTTGATTTGACATTTATATTCCTATCTCTATCCTCAAACACACAACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
* ** * *
2847669 AAGATATAAATATGTACACAAGAACATACCATTTTCTCCTTG-GAGAGTAATTCCTCAGATGGC-
66 AAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTG-GAGTAATTTCTCAGATGGCT
*
2847732 T--TCGATACAATTTCCTGAAAAGGGT
130 TCCTCGATACAGTTTCCTGAAAAGGGT
2847757 G
1 G
2847758 CATGTAGTTA
Statistics
Matches: 557, Mismatches: 57, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
153 23 0.04
155 3 0.01
156 252 0.45
157 115 0.21
158 55 0.10
159 109 0.20
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.35
Consensus pattern (156 bp):
GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
AAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGGCTT
CCTCGATACAGTTTCCTGAAAAGGGT
Found at i:2847795 original size:130 final size:132
Alignment explanation
Indices: 2847634--2847885 Score: 384
Period size: 130 Copynumber: 1.9 Consensus size: 132
2847624 GATTTGACAT
* * **
2847634 TTATATTCCTATCTCTATCCTCAAACACACAACTCAAGATATAAATATGTACACAAGAACATACC
1 TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACCTACACAAGAACATACC
*
2847699 ATTTTCTCCTTGGAGAGTAA-TTCCTCAGATGGC-TTCGATACAATTTCCTGAAAAGGGTGCATG
66 ATTTTCTCCTTGGAGAGTAACTT-CTCAGATGGCTTTCAATACAATTTCCTGAAAAGGGTGCATG
2847762 TAG
130 TAG
* *
2847765 TTATA-TCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATGCCTGCACAAGAACATACC
1 TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACCTACACAAGAACATACC
*
2847829 GTTTTCTCCTTGGAGAGTAACTTCTCAGATGGCTTGTTCAATACAATTTCCTGAAAA
66 ATTTTCTCCTTGGAGAGTAACTTCTCAGATGGC-T-TTCAATACAATTTCCTGAAAA
2847886 AGATGCAGAG
Statistics
Matches: 109, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
130 82 0.75
131 7 0.06
133 20 0.18
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (132 bp):
TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACCTACACAAGAACATACC
ATTTTCTCCTTGGAGAGTAACTTCTCAGATGGCTTTCAATACAATTTCCTGAAAAGGGTGCATGT
AG
Found at i:2849061 original size:22 final size:22
Alignment explanation
Indices: 2849009--2849061 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
2848999 AAAACAAAAC
* *
2849009 AAATACAGTAATTAAACATTTA
1 AAATACCGTAATTAAACATGTA
* *
2849031 AACAT-CCGTAATTCAATATGTA
1 AA-ATACCGTAATTAAACATGTA
2849053 AAATACCGT
1 AAATACCGT
2849062 TTGAGCTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (22 bp):
AAATACCGTAATTAAACATGTA
Found at i:2849860 original size:65 final size:65
Alignment explanation
Indices: 2849791--2849930 Score: 165
Period size: 65 Copynumber: 2.2 Consensus size: 65
2849781 AGTGTATATA
*** * * * * *
2849791 TATATATGATATTTGTTAATATAAGAGTGTTATTAGATCTATTAAAAATCGTTCTAGAAGGATCT
1 TATATATGATATTTACCAATATAAGAGTATTATCAGATATATTAAAAACCATTCTAGAAGGATCT
* * * *
2849856 TATATATGATATTTACCAATGTAAGAGTATTGTCAGATATATTAGAAACCATTCTAGAAGGGTCT
1 TATATATGATATTTACCAATATAAGAGTATTATCAGATATATTAAAAACCATTCTAGAAGGATCT
2849921 TAT-TATGATA
1 TATATATGATA
2849931 GATCATAGTG
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 7 0.11
65 56 0.89
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (65 bp):
TATATATGATATTTACCAATATAAGAGTATTATCAGATATATTAAAAACCATTCTAGAAGGATCT
Found at i:2853188 original size:39 final size:39
Alignment explanation
Indices: 2853145--2853244 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 39
2853135 ATCGGTGGAT
**
2853145 TCTGGTATGGTGTTTTATGATCTTTTATGCT-ACTTTCAG
1 TCTGGTATGGTGTTTTATGATCTGCTATGCTGA-TTTCAG
* * *
2853184 TCTGGTATGAG-GTTTGATCATCTGCTCTGCTGATTTCAG
1 TCTGGTATG-GTGTTTTATGATCTGCTATGCTGATTTCAG
2853223 TCTGGTATGGTGTTTTACTGAT
1 TCTGGTATGGTGTTTTA-TGAT
2853245 GGTTTCATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
38 1 0.02
39 44 0.88
40 5 0.10
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.47
Consensus pattern (39 bp):
TCTGGTATGGTGTTTTATGATCTGCTATGCTGATTTCAG
Found at i:2855238 original size:74 final size:74
Alignment explanation
Indices: 2855139--2855286 Score: 235
Period size: 74 Copynumber: 2.0 Consensus size: 74
2855129 ATTCACTCGG
* * * *
2855139 TTGTTGTAGTTTAACTCAAATTATTGTTGGAATATTTTCAAATATTTATAGTATTCAAATAATTA
1 TTGTAGTAGTTTAACTCAAACTATTGTTGGAACATTTTCAAATATTTACAGTATTCAAATAATTA
2855204 TAAATGAAA
66 TAAATGAAA
*
2855213 TTGTAGTAGTTTAAC-CTAAACTATTGTTGGAACATTTTCAAATATTTACAGTGTTCAAATAATT
1 TTGTAGTAGTTTAACTC-AAACTATTGTTGGAACATTTTCAAATATTTACAGTATTCAAATAATT
2855277 ATAAATGAAA
65 ATAAATGAAA
2855287 GGATGTAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
73 1 0.01
74 67 0.99
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.42
Consensus pattern (74 bp):
TTGTAGTAGTTTAACTCAAACTATTGTTGGAACATTTTCAAATATTTACAGTATTCAAATAATTA
TAAATGAAA
Found at i:2858081 original size:18 final size:20
Alignment explanation
Indices: 2858058--2858095 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2858048 AAATTATATA
2858058 TATAAAC-TT-GAATTTTTT
1 TATAAACTTTAGAATTTTTT
2858076 TATAAACTTTAGAATTTTTT
1 TATAAACTTTAGAATTTTTT
2858096 AAATAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TATAAACTTTAGAATTTTTT
Found at i:2868308 original size:21 final size:19
Alignment explanation
Indices: 2868271--2868309 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
2868261 AATTAAGATA
*
2868271 AATATTAAAATTTTACACT
1 AATATTAAAATTGTACACT
2868290 AATATTATAAATTGGTACAC
1 AATATTA-AAATT-GTACAC
2868310 ATCGGAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (19 bp):
AATATTAAAATTGTACACT
Found at i:2870244 original size:23 final size:22
Alignment explanation
Indices: 2870214--2870261 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 22
2870204 TAAATCTCAA
2870214 ATTCA-TTTAAAT-TTATATATAT
1 ATTCATTTTAAATATT-TA-ATAT
2870236 ATTCTATTTTAAATATTTAATAT
1 ATTC-ATTTTAAATATTTAATAT
2870259 ATT
1 ATT
2870262 TTTAAAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 9 0.39
25 2 0.09
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTCATTTTAAATATTTAATAT
Found at i:2871008 original size:12 final size:13
Alignment explanation
Indices: 2870987--2871016 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2870977 CATTAAATAA
2870987 AAAAATTTAAAAC
1 AAAAATTTAAAAC
2871000 AAAAA-TTAAAAC
1 AAAAATTTAAAAC
2871012 AAAAA
1 AAAAA
2871017 ACAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATTTAAAAC
Found at i:2871017 original size:13 final size:14
Alignment explanation
Indices: 2870986--2871017 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2870976 TCATTAAATA
2870986 AAAAAATTTAAAAC
1 AAAAAATTTAAAAC
2871000 -AAAAA-TTAAAAC
1 AAAAAATTTAAAAC
2871012 AAAAAA
1 AAAAAA
2871018 CAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAAATTTAAAAC
Found at i:2871570 original size:11 final size:11
Alignment explanation
Indices: 2871532--2871577 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
2871522 ACAACAACAA
2871532 CAAAATAGTAG
1 CAAAATAGTAG
* *
2871543 CAATATAATAG
1 CAAAATAGTAG
*
2871554 CGAAATAGTAG
1 CAAAATAGTAG
*
2871565 CAAAATAGCAG
1 CAAAATAGTAG
2871576 CA
1 CA
2871578 TAACAACAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.17
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:2882651 original size:30 final size:31
Alignment explanation
Indices: 2882616--2882678 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
2882606 AACTCTAAAC
* *
2882616 TCTAAATATTCAAAACAATA-TATCTAAATT
1 TCTAAAAATTCAAAACAATATTACCTAAATT
2882646 TCTAAAAATTCAAAACAATATTACCTAAATT
1 TCTAAAAATTCAAAACAATATTACCTAAATT
2882677 TC
1 TC
2882679 CAAGATAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (31 bp):
TCTAAAAATTCAAAACAATATTACCTAAATT
Found at i:2884473 original size:20 final size:19
Alignment explanation
Indices: 2884419--2884473 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
2884409 TTACACTTTA
* *
2884419 ATATTTTTATTATTTT-CT
1 ATATTTTTATGATTTTATT
*
2884437 ATATTTTTTTG-TTTTATT
1 ATATTTTTATGATTTTATT
2884455 ATATTTTTAATGATTTTAT
1 ATATTTTT-ATGATTTTAT
2884474 AAATAATACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.13
18 18 0.60
19 2 0.07
20 6 0.20
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (19 bp):
ATATTTTTATGATTTTATT
Found at i:2886997 original size:59 final size:61
Alignment explanation
Indices: 2886917--2887039 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 61
2886907 TTTTATTATG
2886917 CCAATATCTCGATACCCATATCTTTGACTTTCCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTTCCAATATTTGATACCCATATCTTTGACTTT
* * * *
2886978 CCAATAT-TTGATA-CCATATCTTTGACTTTCTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATCTCGATACCCATATCTTTGACTTTCCAATATTTGATACCCATATCTTTGACTTT
2887037 CCA
1 CCA
2887040 TAAATATGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
59 46 0.79
60 5 0.09
61 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.44
Consensus pattern (61 bp):
CCAATATCTCGATACCCATATCTTTGACTTTCCAATATTTGATACCCATATCTTTGACTTT
Found at i:2887004 original size:29 final size:30
Alignment explanation
Indices: 2886917--2887039 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
2886907 TTTTATTATG
*
2886917 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
2886948 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
2886978 CCAATATTTGATA-CCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
2887007 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
2887037 CCA
1 CCA
2887040 TAAATATGGA
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
29 27 0.31
30 52 0.60
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:2891652 original size:30 final size:30
Alignment explanation
Indices: 2891606--2891729 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
2891596 TTTTATTATG
*
2891606 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
2891637 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
2891667 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
2891697 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
2891727 CCA
1 CCA
2891730 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:2891661 original size:15 final size:15
Alignment explanation
Indices: 2891616--2891723 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
2891606 CCAATATCTC
2891616 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
2891631 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
2891646 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
2891661 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
2891676 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
2891691 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
2891706 GATACCCATATCTTT
1 GATACCCATATCTTT
2891721 GAT
1 GAT
2891724 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:2893786 original size:3 final size:3
Alignment explanation
Indices: 2893778--2893862 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
2893768 TAGATAAAAG
2893778 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2893826 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2893863 TAGAATAAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2894320 original size:16 final size:17
Alignment explanation
Indices: 2894298--2894337 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2894288 GAATTCTTTA
2894298 AAAATTA-TAAAA-AAT
1 AAAATTATTAAAATAAT
2894313 ATAAATTATTAAAATAAT
1 A-AAATTATTAAAATAAT
2894331 AAAATTA
1 AAAATTA
2894338 CATTTTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.05
16 6 0.27
17 11 0.50
18 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTATTAAAATAAT
Found at i:2899129 original size:302 final size:306
Alignment explanation
Indices: 2898578--2899195 Score: 1082
Period size: 302 Copynumber: 2.0 Consensus size: 306
2898568 ATTATATAAT
* * *
2898578 AAAATTAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCGGG
1 AAAAATAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCAGA
*
2898643 CCCAACCCGGCCCATGGACTCCTCTAGTTCCAAGACACGACTATGTGATGTTTCATTCGGGCATA
66 CCCAACCCGGCCCATGGACACCTCTAGTTCCAAGACACGACTATGTGATGTTTCATTCGGGCATA
2898708 AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGATGATTAAGTCTTAGCTCGATTGGTA
131 AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGATGATTAAGTCTTAGCTCGATTGGTA
*
2898773 CTGGTATTGTTGTTAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
196 CTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
* *
2898838 TAAGGATTAGGAA-GG-A-C-AATGGGTAGTTCTAAGTATTGTATC
261 TAAGGATTAGGAAGGGAAGCTAATAGGCAGTTCTAAGTATTGTATC
2898880 AAAAATAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCAGA
1 AAAAATAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCAGA
* * *
2898945 CCCAGCTCGGCCCATGGACACCTCTAGTTCCAAGACACGGCTATGTGATGTTTCATTCGGGCATA
66 CCCAACCCGGCCCATGGACACCTCTAGTTCCAAGACACGACTATGTGATGTTTCATTCGGGCATA
*
2899010 AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGGTGATTAAGTCTTAGCTCGATTGGTA
131 AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGATGATTAAGTCTTAGCTCGATTGGTA
2899075 CTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
196 CTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
2899140 TAAGGATTAGGAAGGGTAATGGCTAATAGGCAGTTCTAAGTATTGTATC
261 TAAGGATTAGGAAGGG-AA--GCTAATAGGCAGTTCTAAGTATTGTATC
2899189 AAAAATA
1 AAAAATA
2899196 GCAGATATAA
Statistics
Matches: 298, Mismatches: 11, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
302 264 0.89
303 2 0.01
305 1 0.00
308 1 0.00
309 30 0.10
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (306 bp):
AAAAATAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCAGA
CCCAACCCGGCCCATGGACACCTCTAGTTCCAAGACACGACTATGTGATGTTTCATTCGGGCATA
AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGATGATTAAGTCTTAGCTCGATTGGTA
CTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
TAAGGATTAGGAAGGGAAGCTAATAGGCAGTTCTAAGTATTGTATC
Found at i:2905364 original size:13 final size:12
Alignment explanation
Indices: 2905336--2905375 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
2905326 TTGTGACAAA
2905336 TTTTATATTTAT
1 TTTTATATTTAT
2905348 TTTTATATTTAAT
1 TTTTATATTT-AT
2905361 TTTTAT-TATTAT
1 TTTTATAT-TTAT
2905373 TTT
1 TTT
2905376 ACTACATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTATATTTAT
Found at i:2905620 original size:27 final size:27
Alignment explanation
Indices: 2905585--2905639 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2905575 AGAACCCACG
2905585 AACCATGAACCTCAAATCCAAACCTTA
1 AACCATGAACCTCAAATCCAAACCTTA
* * *
2905612 AACCTTGAACTTCGAATCCAAACCTTA
1 AACCATGAACCTCAAATCCAAACCTTA
2905639 A
1 A
2905640 CCCCAAACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.31, G:0.05, T:0.22
Consensus pattern (27 bp):
AACCATGAACCTCAAATCCAAACCTTA
Found at i:2917341 original size:4 final size:4
Alignment explanation
Indices: 2917332--2917461 Score: 170
Period size: 4 Copynumber: 32.5 Consensus size: 4
2917322 AAATTTAGAG
* *
2917332 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAGA CAGA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * *
2917380 CAGA CAGA CAGA CAGA CAGA CAGA CAGA CAGA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2917428 CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA
2917462 GGTAAGCAAC
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 124 1.00
ACGTcount: A:0.50, C:0.25, G:0.08, T:0.17
Consensus pattern (4 bp):
CATA
Found at i:2924979 original size:26 final size:25
Alignment explanation
Indices: 2924950--2925007 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
2924940 AAAAAATATA
2924950 TTTAT-TTTTATTTA-ATACTTAGTAAT
1 TTTATATTTT-TTTATATA-TTA-TAAT
*
2924976 TTTATATTTTTTTATTTATTATAAT
1 TTTATATTTTTTTATATATTATAAT
2925001 TTTATAT
1 TTTATAT
2925008 ATAATTATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 11 0.38
26 12 0.41
27 6 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTATATTTTTTTATATATTATAAT
Found at i:2925015 original size:25 final size:25
Alignment explanation
Indices: 2924972--2925033 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
2924962 TAATACTTAG
* **
2924972 TAATTTTATATTTTTTTAT-TTATTA
1 TAATTTTATATATAATTATCTT-TTA
*
2924997 TAATTTTATATATAATTATCTTTTT
1 TAATTTTATATATAATTATCTTTTA
2925022 TAATGTTTATAT
1 TAAT-TTTATAT
2925034 TATAGTAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 22 0.71
26 9 0.29
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
TAATTTTATATATAATTATCTTTTA
Found at i:2929078 original size:100 final size:100
Alignment explanation
Indices: 2928951--2930210 Score: 1602
Period size: 100 Copynumber: 12.6 Consensus size: 100
2928941 TCAACTACAA
*
2928951 TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAG
1 TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAG
* **
2929016 ATCCGCTGTTGTGGCTTCAATCTTTTTAATTGCAA
66 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * *
2929051 TATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAG
1 TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAG
* * **
2929116 ATCCACCGTTGTGGCTTCAATCTTTTTAATTACAA
66 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * *
2929151 TATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTTCACTGCACTGCTAAGGAAGTAAG
1 TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAG
**
2929216 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAA
66 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * *
2929251 TATCAGGGAAACCAGATCCACCTTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAG
1 TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAG
* *
2929316 ATCCGCCATTGTGGCTTCAATCTTTTTAATTGTGC
66 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * * * * *
2929351 TGTCGGGGAAACCAGATTCGCCGTTGT-GATTTCAATCTGCTCCACTGTACCG-TCAGGGAAGTA
1 TGTCAGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTGCACCGCT-AAGGAAGTA
* * *
2929414 AAATTCGCCGTTGTGGCTTTAATCTTTTTAATTGCGC
64 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * * * *
2929451 TGTCGGGGAAACCAGATCCGCCGTTGT-GACTTCAATCTGCTCCACTGTACCGCCAGGGAAGTAA
1 TGTCAGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAA
*
2929515 GATCCACCGTTGTGGCTTCAATCTTTTTAATTGCGC
65 GATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * * *
2929551 TGTCGGGGAAACCAGATCTGCCATTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAG
1 TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAG
* * **
2929616 ATCCGCCGTTGTGGCTTCAATCTCTTTAATTACAA
66 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* ** *
2929651 TATCAGGGAAACCAGATCTACCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAG
1 TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAG
**
2929716 ATCCATCGTTGTGGCTTCAATCTTTTTAATTGCGC
66 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * *
2929751 TGTC-GGAGAAACCAGATCCGCCGT--TATGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGT
1 TGTCAGG-GAAACCAGATCCGCCGTCGTA-G-CTTCAATCTGTTCCACTGCACCGCTAAGGAAGT
* **
2929813 AAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAA
63 AAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * *
2929851 TATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATTTGTTCCACTGCACTGCTAAGGAAGTAAG
1 TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAG
*
2929916 ATCCGCCATTGTGGCTTCAATCTTTTTAATTGCGC
66 ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * * * * * *
2929951 TGTCGGGGAAACCAAATCCGTCGTTGT-GACTTCAATCTGCTCCACTGCATCGCCAGGGAAGTAA
1 TGTCAGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAA
**
2930015 GATCTACCGTTGTGGCTTCAATCTTTTTAATTGCGC
65 GATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * * ** *
2930051 TGTCGGGGAAACCAGATCCGCCATTGT-GACTTCAATCTGCTCCACTATACCGCCAAGGAAGTAA
1 TGTCAGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAA
2930115 GATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
65 GATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
* * * *
2930151 TGTCAGGGAAACCAGATCCGCCGTTGT-GACTTCAATCTGCTCCACTACAACGCTAAGGAA
1 TGTCAGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTGCACCGCTAAGGAA
2930211 ATAAAAATAT
Statistics
Matches: 1033, Mismatches: 116, Indels: 22
0.88 0.10 0.02
Matches are distributed among these distances:
98 2 0.00
99 6 0.01
100 1019 0.99
101 4 0.00
102 2 0.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (100 bp):
TGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCTAAGGAAGTAAG
ATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGC
Found at i:2929918 original size:50 final size:50
Alignment explanation
Indices: 2928964--2930196 Score: 485
Period size: 50 Copynumber: 24.7 Consensus size: 50
2928954 CAGGGAAACC
* * * *
2928964 AGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * * ** * * * ***
2929014 AGATCCGCTGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* * *
2929064 AGATCCGCCGTCGTAGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * * ** * * * * ***
2929114 AGATCCACCGTTGTGGCTTCAATCTTTTTAATTACAAT-ATCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* * *
2929164 AGATCCGCCGTCGTAGCTTCAATCTGTTTCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * ** * * * ***
2929214 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* *
2929264 AGATCCACC-TTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTT-GTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * * ** * ** * ***
2929314 AGATCCGCCATTGTGGCTTCAATCTTTTTAATTGTGCTG-TCGGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* * * * *
2929364 AGATTCGCCGTTGT-GATTTCAATCTGCTCCACTGTACCG-TCAGGGAAGTA
1 AGATCCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* * * * * ** * * * ***
2929414 AAATTCGCCGTTGTGGCTTTAATCTTTTTAATTGCGCTG-TCGGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* * * *
2929464 AGATCCGCCGTTGT-GACTTCAATCTGCTCCACTGTACCGCCAGGGAAGTA
1 AGATCCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * * ** * * * ***
2929514 AGATCCACCGTTGTGGCTTCAATCTTTTTAATTGCGCTG-TCGGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* * *
2929564 AGATCTGCCATTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * ** * * * * ***
2929614 AGATCCGCCGTTGTGGCTTCAATCTCTTTAATTACAAT-ATCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
** * *
2929664 AGATCTACCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
** * * ** * * * ***
2929714 AGATCCATCGTTGTGGCTTCAATCTTTTTAATTGCGCTG-TCGGAGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAGG-GAAGTA
* * * *
2929764 AGATCCGCCGTTAT-GACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTA
1 AGATCCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * * ** * * * ***
2929814 AGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* * * *
2929864 AGATCTGCCGTCGTAGCTTCAATTTGTTCCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * * ** * * * **
2929914 AGATCCGCCATTGTGGCTTCAATCTTTTTAATTGCGCTG-TCGGGGAAACCA
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGG-AAGTA
* * *
2929965 A-ATCCGTCGTTGT-GACTTCAATCTGCTCCACTGCA-TCGCCAGGGAAGTA
1 AGATCCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACT-GCTAGGGAAGTA
** * * ** * * * ***
2930014 AGATCTACCGTTGTGGCTTCAATCTTTTTAATTGCGCTG-TCGGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
* * ** * * *
2930064 AGATCCGCCATTGT-GACTTCAATCTGCTCCACTATACCGCCAAGGAAGTA
1 AGATCCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
* * ** * * ***
2930114 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCGCTG-TCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCT-AGGGAAGTA
*
2930164 AGATCCGCCGTTGT-GACTTCAATCTGCTCCACT
1 AGATCCGCCGTTGTAG-CTTCAATCTGTTCCACT
2930197 ACAACGCTAA
Statistics
Matches: 818, Mismatches: 327, Indels: 76
0.67 0.27 0.06
Matches are distributed among these distances:
49 21 0.03
50 777 0.95
51 20 0.02
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (50 bp):
AGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAAGTA
Found at i:2934428 original size:19 final size:20
Alignment explanation
Indices: 2934404--2934443 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2934394 AACGGTGTCT
* *
2934404 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
2934423 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
2934443 A
1 A
2934444 TGCGAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:2934494 original size:13 final size:13
Alignment explanation
Indices: 2934476--2934501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2934466 TGTTCAATTT
2934476 TTTACTAGAAAAC
1 TTTACTAGAAAAC
2934489 TTTACTAGAAAAC
1 TTTACTAGAAAAC
2934502 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:2940260 original size:28 final size:29
Alignment explanation
Indices: 2940218--2940298 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
2940208 AAATTTTAAT
*
2940218 AAAAAATACATAAAATTTATTAAAAAT-CAG
1 AAAAAAT-TATAAAATTTA-TAAAAATGCAG
* * * *
2940248 -AAAAATTGTAAAATATATAGAAATGTAG
1 AAAAAATTATAAAATTTATAAAAATGCAG
2940276 AAAAAATTATAAAATTTTATAAA
1 AAAAAATTATAAAA-TTTATAAA
2940299 GTCGTAAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
27 6 0.15
28 10 0.25
29 18 0.45
30 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAAATTATAAAATTTATAAAAATGCAG
Found at i:2940620 original size:23 final size:24
Alignment explanation
Indices: 2940584--2940630 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2940574 TTTTCATATT
*
2940584 TTTTCTTATATTTAATAAATTTTA
1 TTTTCTTATATTTAATAAAATTTA
* *
2940608 TTTT-TTATTTTTATTAAAATTTA
1 TTTTCTTATATTTAATAAAATTTA
2940631 ATAATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTCTTATATTTAATAAAATTTA
Found at i:2944475 original size:37 final size:37
Alignment explanation
Indices: 2944425--2944499 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2944415 TATATTAGTA
2944425 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
1 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
2944462 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
1 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
2944499 A
1 A
2944500 TTGATAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.37
Consensus pattern (37 bp):
AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
Found at i:2945731 original size:38 final size:37
Alignment explanation
Indices: 2945666--2945757 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 37
2945656 ACCAGATTGG
* *
2945666 CACCTAGTGCCTCATCAGATAGTTCGAAGCAAAGTTGA
1 CACCTAGTGTCTCATCGGATAGTTCGAAGCAAAG-TGA
* *
2945704 CACCTAGTGTCTCATCGGCCTAG-TCGAAGTAAAGTGA
1 CACCTAGTGTCTCATCGG-ATAGTTCGAAGCAAAGTGA
* * *
2945741 TACCCAGTATCTCATCG
1 CACCTAGTGTCTCATCG
2945758 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
37 17 0.37
38 26 0.57
39 3 0.07
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (37 bp):
CACCTAGTGTCTCATCGGATAGTTCGAAGCAAAGTGA
Found at i:2945937 original size:18 final size:17
Alignment explanation
Indices: 2945891--2945944 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
2945881 TTTCCAATTC
2945891 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
*
2945908 TCATTTCAAAATGT-ACTT
1 TCAATTC-AAAT-TCACTT
2945926 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
2945944 T
1 T
2945945 TTTCTCACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 7 0.23
18 21 0.68
19 3 0.10
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:2947210 original size:29 final size:29
Alignment explanation
Indices: 2947168--2947224 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
2947158 ATCTTTTCTT
* *
2947168 AATTTATTTTATAATATAATAATATAATC
1 AATTTAATTTATAATATAATAAAATAATC
2947197 AATTTAATTTATAATATAATAAAATAAT
1 AATTTAATTTATAATATAATAAAATAAT
2947225 AACAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTAATTTATAATATAATAAAATAATC
Found at i:2953002 original size:222 final size:222
Alignment explanation
Indices: 2952616--2953062 Score: 894
Period size: 222 Copynumber: 2.0 Consensus size: 222
2952606 TTTTGGTTTA
2952616 GAATGTGTGAGATACTCTCTTTTTATCATTCTAGTTTAATTGATACTTTTCAGACTTACTATTCA
1 GAATGTGTGAGATACTCTCTTTTTATCATTCTAGTTTAATTGATACTTTTCAGACTTACTATTCA
2952681 GCTCTCTTAAATTTGTTTCTAATGTGAGATTCATATGTTGATTTAGTGTTTCAATCCTAAAATGT
66 GCTCTCTTAAATTTGTTTCTAATGTGAGATTCATATGTTGATTTAGTGTTTCAATCCTAAAATGT
2952746 TTTATTGCATACTTTATATTATTGTTTTATGGATATTTGTTGGGATTGGGGAGTCTGGGGTTCAG
131 TTTATTGCATACTTTATATTATTGTTTTATGGATATTTGTTGGGATTGGGGAGTCTGGGGTTCAG
2952811 ACTGAGGCCAGCTGCCCGCCTTAATTG
196 ACTGAGGCCAGCTGCCCGCCTTAATTG
2952838 GAATGTGTGAGATACTCTCTTTTTATCATTCTAGTTTAATTGATACTTTTCAGACTTACTATTCA
1 GAATGTGTGAGATACTCTCTTTTTATCATTCTAGTTTAATTGATACTTTTCAGACTTACTATTCA
2952903 GCTCTCTTAAATTTGTTTCTAATGTGAGATTCATATGTTGATTTAGTGTTTCAATCCTAAAATGT
66 GCTCTCTTAAATTTGTTTCTAATGTGAGATTCATATGTTGATTTAGTGTTTCAATCCTAAAATGT
2952968 TTTATTGCATACTTTATATTATTGTTTTATGGATATTTGTTGGGATTGGGGAGTCTGGGGTTCAG
131 TTTATTGCATACTTTATATTATTGTTTTATGGATATTTGTTGGGATTGGGGAGTCTGGGGTTCAG
2953033 ACTGAGGCCAGCTGCCCGCCTTAATTG
196 ACTGAGGCCAGCTGCCCGCCTTAATTG
2953060 GAA
1 GAA
2953063 ATATTCAACC
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
222 225 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.43
Consensus pattern (222 bp):
GAATGTGTGAGATACTCTCTTTTTATCATTCTAGTTTAATTGATACTTTTCAGACTTACTATTCA
GCTCTCTTAAATTTGTTTCTAATGTGAGATTCATATGTTGATTTAGTGTTTCAATCCTAAAATGT
TTTATTGCATACTTTATATTATTGTTTTATGGATATTTGTTGGGATTGGGGAGTCTGGGGTTCAG
ACTGAGGCCAGCTGCCCGCCTTAATTG
Found at i:2964152 original size:18 final size:18
Alignment explanation
Indices: 2964129--2964166 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2964119 TGTCACCTAA
* *
2964129 TTATTAGTAAGTTTACAC
1 TTATTAATAAATTTACAC
2964147 TTATTAATAAATTTACAC
1 TTATTAATAAATTTACAC
2964165 TT
1 TT
2964167 TGGTCACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (18 bp):
TTATTAATAAATTTACAC
Found at i:2968077 original size:12 final size:12
Alignment explanation
Indices: 2968060--2968084 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2968050 AGTCGATAAG
2968060 AAAAAACAAAAC
1 AAAAAACAAAAC
2968072 AAAAAACAAAAC
1 AAAAAACAAAAC
2968084 A
1 A
2968085 GTAAGACCGA
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:2972165 original size:14 final size:14
Alignment explanation
Indices: 2972143--2972184 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2972133 TCTTTATAAA
2972143 TTTAAAATTTAGTC
1 TTTAAAATTTAGTC
* *
2972157 TTTATAATTTTA-TT
1 TTTA-AAATTTAGTC
2972171 TTTAAAATTTAGTC
1 TTTAAAATTTAGTC
2972185 CCTTTACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (14 bp):
TTTAAAATTTAGTC
Found at i:2972195 original size:28 final size:30
Alignment explanation
Indices: 2972139--2972209 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 30
2972129 TGATTCTTTA
*
2972139 TAAA-TTTAAAATTTAGTCTTTATAA-TTT
1 TAAATTTTAAAATTTAGTCCTTATAATTTT
* *
2972167 T-ATTTTTAAAATTTAGTCCCTT-TACTTTT
1 TAAATTTTAAAATTTAGT-CCTTATAATTTT
2972196 TAAATTTTAAAATT
1 TAAATTTTAAAATT
2972210 CAAATCCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 1 0.03
28 16 0.46
29 7 0.20
30 11 0.31
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (30 bp):
TAAATTTTAAAATTTAGTCCTTATAATTTT
Found at i:2972970 original size:15 final size:15
Alignment explanation
Indices: 2972950--2972978 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2972940 GTTTGGGAAT
2972950 TTTTAGGGTTTTAAA
1 TTTTAGGGTTTTAAA
2972965 TTTTAGGGTTTTAA
1 TTTTAGGGTTTTAA
2972979 GGGAAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (15 bp):
TTTTAGGGTTTTAAA
Found at i:2973761 original size:96 final size:94
Alignment explanation
Indices: 2973634--2973849 Score: 290
Period size: 96 Copynumber: 2.3 Consensus size: 94
2973624 TAAAAATTAC
* *
2973634 ATTTATTAGA-TTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTTAAATTTAT
1 ATTTATTTGATTTTTTCCTT-AAAA-CTTAAACACTAAACCCTAATCTAATTTTTTAAAATTTAT
* *
2973698 AATTAATTTACTCAAGTAACCCTAAACCCTA
64 AATTAATTTAATCAAGAAACCCTAAACCCTA
*
2973729 ATTTATTTGATTTTTTCCTTGAAAACTATAAACGCTAAACCCTAATCTAATTTTTTAAAATTTAT
1 ATTTATTTGATTTTTTCCTT-AAAACT-TAAACACTAAACCCTAATCTAATTTTTTAAAATTTAT
* * * *
2973794 AGTTAATTTAATTAAGAAATCCTAAACCCTT
64 AATTAATTTAATCAAGAAACCCTAAACCCTA
* *
2973825 ATTTATTTAATTTTTCCCTTAAAAC
1 ATTTATTTGATTTTTTCCTTAAAAC
2973850 CCTAAAATCT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
95 16 0.15
96 91 0.85
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.43
Consensus pattern (94 bp):
ATTTATTTGATTTTTTCCTTAAAACTTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAA
TTAATTTAATCAAGAAACCCTAAACCCTA
Found at i:2974342 original size:9 final size:9
Alignment explanation
Indices: 2974328--2974354 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2974318 CTTGAACACA
2974328 AAAAAGCAC
1 AAAAAGCAC
2974337 AAAAAGCAC
1 AAAAAGCAC
2974346 AAAAAGCAC
1 AAAAAGCAC
2974355 GGCCACCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAGCAC
Found at i:2982149 original size:27 final size:28
Alignment explanation
Indices: 2982094--2982151 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
2982084 TTATCGTGAA
* *
2982094 TTATTTACGTTCAAATGTTTTTTTTTCTT
1 TTATTTACGTTCAAA-GTTTTATATTCTT
2982123 TTATTTACGTTCAAA-TTTTATATTCTT
1 TTATTTACGTTCAAAGTTTTATATTCTT
2982150 TT
1 TT
2982152 GTTTTCATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 12 0.44
29 15 0.56
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (28 bp):
TTATTTACGTTCAAAGTTTTATATTCTT
Found at i:2996224 original size:12 final size:13
Alignment explanation
Indices: 2996207--2996243 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2996197 GAACCGGACA
2996207 CGAACCGAA-CTC
1 CGAACCGAAGCTC
2996219 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
2996231 CGAACCGTAGCTC
1 CGAACCGAAGCTC
2996244 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:2997173 original size:16 final size:16
Alignment explanation
Indices: 2997152--2997183 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2997142 TCACCATTAT
2997152 GGATCAAATCATCCCA
1 GGATCAAATCATCCCA
2997168 GGATCAAATCATCCCA
1 GGATCAAATCATCCCA
2997184 CCTAAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (16 bp):
GGATCAAATCATCCCA
Found at i:2999781 original size:20 final size:20
Alignment explanation
Indices: 2999725--2999772 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2999715 ATTACAAAAG
* *
2999725 AAAAGTTCAAAATAATTTTT
1 AAAATTTCAAAACAATTTTT
2999745 AAAATTTCAAAACAATTTTT
1 AAAATTTCAAAACAATTTTT
2999765 AAATATTT
1 AAA-ATTT
2999773 ATAAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAATTTCAAAACAATTTTT
Found at i:3000527 original size:19 final size:17
Alignment explanation
Indices: 3000505--3000538 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
3000495 TTTTCTCATA
3000505 AAAAATATTAAAAATATT
1 AAAAA-ATTAAAAATATT
3000523 AAAAAATTAAAAATAT
1 AAAAAATTAAAAATAT
3000539 ATTGAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATTAAAAATATT
Found at i:3000535 original size:8 final size:9
Alignment explanation
Indices: 3000505--3000538 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
3000495 TTTTCTCATA
3000505 AAAAATATT
1 AAAAATATT
3000514 AAAAATATT
1 AAAAATATT
3000523 AAAAA-ATT
1 AAAAATATT
3000531 AAAAATAT
1 AAAAATAT
3000539 ATTGAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAATATT
Found at i:3000550 original size:19 final size:18
Alignment explanation
Indices: 3000506--3000550 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
3000496 TTTCTCATAA
3000506 AAAATATT-AAAAATATT
1 AAAATATTAAAAAATATT
*
3000523 AAAAAATTAAAAATATATT
1 AAAATATTAAAAA-ATATT
*
3000542 GAAATATTA
1 AAAATATTA
3000551 TAAGAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 7 0.30
18 4 0.17
19 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATATTAAAAAATATT
Found at i:3000656 original size:20 final size:20
Alignment explanation
Indices: 3000607--3000657 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
3000597 ATTTAAAATT
3000607 TATTA-AAAAAACTAATAAA
1 TATTATAAAAAACTAATAAA
* * *
3000626 AATTCAT-AAAAACTTATAAG
1 TATT-ATAAAAAACTAATAAA
3000646 TATTATAAAAAA
1 TATTATAAAAAA
3000658 TATAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
TATTATAAAAAACTAATAAA
Found at i:3001204 original size:19 final size:19
Alignment explanation
Indices: 3001165--3001228 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
3001155 CAATGACTTT
* *
3001165 TTTTTATATT-TTTAGAA-
1 TTTTTATATTCTTCATAAG
3001182 TTTTTATATTCTTCATAAG
1 TTTTTATATTCTTCATAAG
*
3001201 TTTTTAT-TAACTTCTATAAG
1 TTTTTATAT-TCTTC-ATAAG
3001221 TTTTTATA
1 TTTTTATA
3001229 AAATTTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 10 0.26
18 6 0.15
19 11 0.28
20 12 0.31
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTATATTCTTCATAAG
Found at i:3003264 original size:29 final size:29
Alignment explanation
Indices: 3003230--3003299 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
3003220 ATTAATAATC
*
3003230 ATAAAATTATAGTTTAAT-TTCT-AAAAAT
1 ATAAAATTATAATTTAATCTT-TAAAAAAT
*
3003258 ACTAAAATTTTAATTTAATCTTTAAAAAAT
1 A-TAAAATTATAATTTAATCTTTAAAAAAT
*
3003288 ATAAAAATATAA
1 ATAAAATTATAA
3003300 ATTATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.03
29 25 0.71
30 9 0.26
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAAAATTATAATTTAATCTTTAAAAAAT
Found at i:3003710 original size:12 final size:14
Alignment explanation
Indices: 3003693--3003724 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
3003683 TCTGCATGAG
3003693 AAAAATT-AATA-A
1 AAAAATTAAATATA
3003705 AAAAATTAAATATA
1 AAAAATTAAATATA
3003719 AAAAAT
1 AAAAAT
3003725 CCTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 4 0.22
14 7 0.39
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAATTAAATATA
Found at i:3008321 original size:7 final size:7
Alignment explanation
Indices: 3008309--3008338 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3008299 AGGGGGTTAG
3008309 TACCATA
1 TACCATA
3008316 TACCATA
1 TACCATA
3008323 TACCATA
1 TACCATA
3008330 TACCATA
1 TACCATA
3008337 TA
1 TA
3008339 TCACAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (7 bp):
TACCATA
Found at i:3013522 original size:2 final size:2
Alignment explanation
Indices: 3013515--3013545 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3013505 TTTAGGCTTT
3013515 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 T
3013546 TACTAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3022754 original size:15 final size:13
Alignment explanation
Indices: 3022735--3022784 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
3022725 TAATATTAAA
3022735 ATATATACAATGAT
1 ATATATA-AATGAT
*
3022749 AATATATAAAAGAT
1 -ATATATAAATGAT
*
3022763 ATATATATAATTAT
1 ATATATA-AATGAT
3022777 ATATATAA
1 ATATATAA
3022785 TTAAAATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 8 0.26
14 16 0.52
15 7 0.23
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (13 bp):
ATATATAAATGAT
Found at i:3022779 original size:12 final size:12
Alignment explanation
Indices: 3022762--3022787 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3022752 ATATAAAAGA
3022762 TATATATATAAT
1 TATATATATAAT
3022774 TATATATATAAT
1 TATATATATAAT
3022786 TA
1 TA
3022788 AAATACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATATATAAT
Found at i:3022998 original size:3 final size:3
Alignment explanation
Indices: 3022990--3023031 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
3022980 AAGCATAAAC
*
3022990 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3023032 CATTGAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3023159 original size:3 final size:3
Alignment explanation
Indices: 3023130--3023198 Score: 52
Period size: 3 Copynumber: 23.3 Consensus size: 3
3023120 ATACACGTAC
* * * * *
3023130 ATA ATA AAA AT- ATA CTA ATA CATA ATA ATA GTA ATA GTA ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
3023175 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3023199 CAAGGATATT
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3024368 original size:17 final size:17
Alignment explanation
Indices: 3024346--3024379 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3024336 TTGGGCTTCG
*
3024346 GGTTTATTGGGTTGTTT
1 GGTTTAGTGGGTTGTTT
3024363 GGTTTAGTGGGTTGTTT
1 GGTTTAGTGGGTTGTTT
3024380 AGGATGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.00, G:0.38, T:0.56
Consensus pattern (17 bp):
GGTTTAGTGGGTTGTTT
Found at i:3028588 original size:65 final size:64
Alignment explanation
Indices: 3028491--3028613 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 64
3028481 TAGAGGAGCC
* *
3028491 TAATTAAATTTGCTAAAAACTTCAAAGAAGAAATGAAAATTTTCAAAAACTTTGGGGGTCTAAT
1 TAATTAAATTTGCTAAAAACTTCAAAGAAGAAATCAAAAGTTTCAAAAACTTTGGGGGTCTAAT
* * * *
3028555 TAATTAAAATTTTCTAAAAATTTC-AAGAGAGAAATCAAAAGTTTCCAAAATTTTGGGGG
1 TAATT-AAATTTGCTAAAAACTTCAAAGA-AGAAATCAAAAGTTTCAAAAACTTTGGGGG
3028614 GCATTTGTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 9 0.18
65 42 0.82
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (64 bp):
TAATTAAATTTGCTAAAAACTTCAAAGAAGAAATCAAAAGTTTCAAAAACTTTGGGGGTCTAAT
Found at i:3030100 original size:16 final size:16
Alignment explanation
Indices: 3030075--3030131 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
3030065 ACAATTGTAA
3030075 TAAAAGAAAAAAAATG
1 TAAAAGAAAAAAAATG
*
3030091 TAAAATAAAAAAAA--
1 TAAAAGAAAAAAAATG
*
3030105 TAAAAGGAAAAAAATTG
1 TAAAA-GAAAAAAAATG
3030122 TAAAAAGAAA
1 T-AAAAGAAA
3030132 GACAAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 13 0.38
17 5 0.15
18 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
TAAAAGAAAAAAAATG
Found at i:3030108 original size:14 final size:14
Alignment explanation
Indices: 3030073--3030119 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
3030063 AGACAATTGT
3030073 AATAAAAGAAAAAA
1 AATAAAAGAAAAAA
*
3030087 AATGTAAAATAAAAAA
1 AA--TAAAAGAAAAAA
*
3030103 AATAAAAGGAAAAA
1 AATAAAAGAAAAAA
3030117 AAT
1 AAT
3030120 TGTAAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 15 0.54
16 13 0.46
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.13
Consensus pattern (14 bp):
AATAAAAGAAAAAA
Found at i:3030116 original size:21 final size:21
Alignment explanation
Indices: 3030073--3030116 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3030063 AGACAATTGT
* *
3030073 AATAAAAGAAAAAAAATGTAA
1 AATAAAAGAAAAAAAAGGAAA
3030094 AATAAAA-AAAATAAAAGGAAA
1 AATAAAAGAAAA-AAAAGGAAA
3030115 AA
1 AA
3030117 AATTGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (21 bp):
AATAAAAGAAAAAAAAGGAAA
Found at i:3031113 original size:17 final size:19
Alignment explanation
Indices: 3031083--3031120 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3031073 AATACAAATT
*
3031083 AACCCTCAGGCC-AAACTA
1 AACCCTCAGCCCAAAACTA
3031101 AACCCT-AGCCCAAAACTA
1 AACCCTCAGCCCAAAACTA
3031119 AA
1 AA
3031121 AAAATTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.45, C:0.37, G:0.08, T:0.11
Consensus pattern (19 bp):
AACCCTCAGCCCAAAACTA
Found at i:3032374 original size:26 final size:29
Alignment explanation
Indices: 3032334--3032394 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 29
3032324 CTATTTGATA
*
3032334 TTATCTATTTTAAATTG-TTTC-A-TATT
1 TTATCTATTTCAAATTGCTTTCTATTATT
*
3032360 TTATTTATTTCAAATTGCTTTCTATTATT
1 TTATCTATTTCAAATTGCTTTCTATTATT
3032389 TTATCT
1 TTATCT
3032395 TAAACTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 15 0.52
27 4 0.14
28 1 0.03
29 9 0.31
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (29 bp):
TTATCTATTTCAAATTGCTTTCTATTATT
Found at i:3040479 original size:3 final size:3
Alignment explanation
Indices: 3040473--3040540 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
3040463 AAGATATTGG
*
3040473 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGAA TTA -GA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG-A TGA TGA
* * *
3040518 GGA TAA TGA TGA TGA CGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TG
3040541 GAGAAGATGA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.95
4 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.32, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:3040561 original size:15 final size:15
Alignment explanation
Indices: 3040537--3040570 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3040527 TGATGACGAT
*
3040537 GATGGAGAAGATGAA
1 GATGGAGAAGAAGAA
*
3040552 GATGGTGAAGAAGAA
1 GATGGAGAAGAAGAA
3040567 GATG
1 GATG
3040571 AGGAGGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (15 bp):
GATGGAGAAGAAGAA
Found at i:3057622 original size:78 final size:78
Alignment explanation
Indices: 3057493--3057649 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
3057483 AACATAAGCA
3057493 ATCTTCAAAGTTGATAATAAGAAGTGTATCTTTTTCTACCATCGTCGAAAATTGCCACTATCAAT
1 ATCTTCAAAGTTGATAATAAGAAGTGTATCTTTTTCTACCATCGTCGAAAATTGCCACTATCAAT
3057558 AACTATGTGAAAC
66 AACTATGTGAAAC
3057571 ATCTTCAAAGTTGATAATAAGAAGTGTATCTTTTTCTACCATCGTCGAAAATTGCCACTATCAAT
1 ATCTTCAAAGTTGATAATAAGAAGTGTATCTTTTTCTACCATCGTCGAAAATTGCCACTATCAAT
3057636 AACTATGTGAAAC
66 AACTATGTGAAAC
3057649 A
1 A
3057650 AGCGAGTAAG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (78 bp):
ATCTTCAAAGTTGATAATAAGAAGTGTATCTTTTTCTACCATCGTCGAAAATTGCCACTATCAAT
AACTATGTGAAAC
Found at i:3061378 original size:25 final size:26
Alignment explanation
Indices: 3061340--3061396 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3061330 TATTTTCTCG
* *
3061340 AAATTTTACTA-GGGAAAAAAGGTTA
1 AAATTTTACCAGGGGAAAAAACGTTA
* *
3061365 AAATTTTACCAGGGGTAAAATCGTTA
1 AAATTTTACCAGGGGAAAAAACGTTA
3061391 AAATTT
1 AAATTT
3061397 GTTGAAGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAGGGGAAAAAACGTTA
Found at i:3067024 original size:20 final size:21
Alignment explanation
Indices: 3066987--3067025 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3066977 GATAAAATAA
3066987 TTTTTCCTATAAAGATCCAAG
1 TTTTTCCTATAAAGATCCAAG
*
3067008 TTTTTCTTATAAA-ATCCA
1 TTTTTCCTATAAAGATCCA
3067026 GTTAATTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTTTCCTATAAAGATCCAAG
Found at i:3067982 original size:12 final size:12
Alignment explanation
Indices: 3067965--3067991 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3067955 TAAGCCCTTT
3067965 TCAGTATTAGTA
1 TCAGTATTAGTA
3067977 TCAGTATTAGTA
1 TCAGTATTAGTA
3067989 TCA
1 TCA
3067992 TTCCAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (12 bp):
TCAGTATTAGTA
Found at i:3076330 original size:55 final size:59
Alignment explanation
Indices: 3076219--3076331 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 59
3076209 AGAAATAGTG
* * *
3076219 AAAATGGAGAAATAGGAAACATTTGGAAATGAAATTTGGTTTTCTCCAAAATGAAAATT
1 AAAATGGAGAAATAGGAAACATTTAGAAATGAAATGTGGTTTTCTCCAAAACGAAAATT
3076278 AAAATGGAGAAATA-GAAACATTTAGAAAT-AAATGT-G-TTTCTCCAAAACGAAAAT
1 AAAATGGAGAAATAGGAAACATTTAGAAATGAAATGTGGTTTTCTCCAAAACGAAAAT
3076332 GAATAAATCA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 17 0.33
56 1 0.02
57 5 0.10
58 14 0.27
59 14 0.27
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.27
Consensus pattern (59 bp):
AAAATGGAGAAATAGGAAACATTTAGAAATGAAATGTGGTTTTCTCCAAAACGAAAATT
Found at i:3079223 original size:18 final size:18
Alignment explanation
Indices: 3079200--3079236 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3079190 TTACACACAC
*
3079200 TTAAATTTAAGAGAAAGT
1 TTAAATTTAAAAGAAAGT
3079218 TTAAATTTAAAAGAAAGT
1 TTAAATTTAAAAGAAAGT
3079236 T
1 T
3079237 GTAGAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (18 bp):
TTAAATTTAAAAGAAAGT
Found at i:3090364 original size:9 final size:9
Alignment explanation
Indices: 3090350--3090385 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3090340 TTTGTTCTCA
*
3090350 ATTTTTTTT
1 ATTTTTGTT
3090359 ATTTTTGTT
1 ATTTTTGTT
3090368 ATTTTTGTT
1 ATTTTTGTT
*
3090377 TTTTTTGTT
1 ATTTTTGTT
3090386 TTCTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.83
Consensus pattern (9 bp):
ATTTTTGTT
Found at i:3096908 original size:39 final size:36
Alignment explanation
Indices: 3096851--3096922 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 36
3096841 AAATTATAAA
*
3096851 TAATAATAAATAATAAATTTTAGAAAATTTATTAAATTT
1 TAATAAGAAATAATAAATTTT---AAATTTATTAAATTT
3096890 TAATAAGAATATAA-AAATTTTAAATTTATTAAA
1 TAATAAGAA-ATAATAAATTTTAAATTTATTAAA
3096923 AATTATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 12 0.39
39 15 0.48
40 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (36 bp):
TAATAAGAAATAATAAATTTTAAATTTATTAAATTT
Found at i:3096961 original size:37 final size:37
Alignment explanation
Indices: 3096920--3096991 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
3096910 TAAATTTATT
** *
3096920 AAAAATTATAATTTTTTATAAAAATCGTAAAAAATAA
1 AAAAATTATAAAATTTTATAAAAATCATAAAAAATAA
* *
3096957 AAAAATTGTAAAATTTTATAAAAATTATAAAAAAT
1 AAAAATTATAAAATTTTATAAAAATCATAAAAAAT
3096992 TAATGACCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (37 bp):
AAAAATTATAAAATTTTATAAAAATCATAAAAAATAA
Found at i:3097210 original size:10 final size:10
Alignment explanation
Indices: 3097195--3097220 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3097185 TTCTTACTAC
3097195 TTTATAAAAT
1 TTTATAAAAT
3097205 TTTATAAAAT
1 TTTATAAAAT
3097215 TTTATA
1 TTTATA
3097221 TTTTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:3097216 original size:57 final size:56
Alignment explanation
Indices: 3097155--3097290 Score: 150
Period size: 57 Copynumber: 2.4 Consensus size: 56
3097145 TTTTTTACGG
* * * *
3097155 AATTTATATTTCTTTACATTTTGTATAATTTTCTTACTA-CTTTATAAAATTTTATAA
1 AATTTATATTT-TTTATATTTTCTATAATTTT-TTACGATCTTTATAAAATTTTACAA
* *
3097212 AATTTTATATTTTTT-TATATTTCTATTATTTTTTACGATTTTTATAAAATTTTACAA
1 AA-TTTATATTTTTTATAT-TTTCTATAATTTTTTACGATCTTTATAAAATTTTACAA
*
3097269 TATATTATATTTTTTATATTTT
1 AAT-TTATATTTTTTATATTTT
3097291 TTTCTAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
56 8 0.12
57 47 0.70
58 12 0.18
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (56 bp):
AATTTATATTTTTTATATTTTCTATAATTTTTTACGATCTTTATAAAATTTTACAA
Found at i:3097302 original size:57 final size:57
Alignment explanation
Indices: 3097195--3097303 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
3097185 TTCTTACTAC
* * *
3097195 TTTATAAAATTTTATAAAATTTTATATTTTTTTATATTTCTATTATTTTTTACGATT
1 TTTATAAAATTTTACAAAATATTATATTTTTTTATATTTCTATTAATTTTTACGATT
* * *
3097252 TTTATAAAATTTTACAATATATTATA-TTTTTTATATTTTTTTCTAATTTTTA
1 TTTATAAAATTTTACAAAATATTATATTTTTTTATATTTCTAT-TAATTTTTA
3097304 ATATTTGAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 14 0.31
57 31 0.69
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (57 bp):
TTTATAAAATTTTACAAAATATTATATTTTTTTATATTTCTATTAATTTTTACGATT
Found at i:3097489 original size:86 final size:87
Alignment explanation
Indices: 3097387--3097608 Score: 283
Period size: 86 Copynumber: 2.5 Consensus size: 87
3097377 AATTTTTAAT
* *
3097387 AAAATAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTT-ATGCATTTTGAAAGT
1 AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG-CTTTTTTGATACATTTTGAAAGT
*
3097451 TCAAATACCCAATTGAATGC-AA
65 TCAAATACCCAAATGAATGCAAA
*
3097473 AAAAAAGGGGCCTAATTGCTTTTTTTG-AAAAGATTTGAGGGCTTTTTTGATACATTTTGAAAGT
1 AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAAG-TTTGAGGGCTTTTTTGATACATTTTGAAAGT
* * *
3097537 TCAAGTATCCAAATGAGTGCAAA
65 TCAAATACCCAAATGAATGCAAA
*
3097560 AAAAAGCAGGGGCTTAATTG-TATTTTTTCTAAAAA-TTTGAGGGCTTTTT
1 AAAAA--AGGGGCTTAATTGCT-TTTTTT-GAAAAAGTTTGAGGGCTTTTT
3097609 GCACCCTTAA
Statistics
Matches: 119, Mismatches: 9, Indels: 13
0.84 0.06 0.09
Matches are distributed among these distances:
85 12 0.10
86 63 0.53
87 7 0.06
88 1 0.01
89 32 0.27
91 4 0.03
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (87 bp):
AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTTTGATACATTTTGAAAGTT
CAAATACCCAAATGAATGCAAA
Found at i:3103712 original size:18 final size:19
Alignment explanation
Indices: 3103679--3103717 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3103669 ATGTTTTAAT
3103679 AAATAAAAATTATTTTGAA
1 AAATAAAAATTATTTTGAA
* *
3103698 AAATATAAA-TATTTTTAA
1 AAATAAAAATTATTTTGAA
3103716 AA
1 AA
3103718 GTTTTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATAAAAATTATTTTGAA
Found at i:3110201 original size:22 final size:22
Alignment explanation
Indices: 3110176--3110243 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
3110166 CACTTAAAAG
3110176 TTTAATCTGGTTTAACTCTAAA
1 TTTAATCTGGTTTAACTCTAAA
3110198 TTTAA------TTAACT-TAAAA
1 TTTAATCTGGTTTAACTCT-AAA
3110214 GTTTAATCTGGTTTAACTCTAAA
1 -TTTAATCTGGTTTAACTCTAAA
3110237 TTTAATC
1 TTTAATC
3110244 AAGAATAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 18
0.67 0.00 0.33
Matches are distributed among these distances:
15 1 0.03
16 9 0.24
17 5 0.14
22 12 0.32
23 9 0.24
24 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTAATCTGGTTTAACTCTAAA
Found at i:3110221 original size:39 final size:39
Alignment explanation
Indices: 3110167--3110242 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
3110157 ATATTCTCTC
3110167 ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAATTA
1 ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAATTA
3110206 ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAAT
1 ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAAT
3110243 CAAGAATAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (39 bp):
ACTTAAAAGTTTAATCTGGTTTAACTCTAAATTTAATTA
Found at i:3120063 original size:20 final size:20
Alignment explanation
Indices: 3120021--3120065 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3120011 AAATTTTGTT
*
3120021 ATAATTTTAATACTTTTTTAA
1 ATAATTTTAATAC-TTTTAAA
3120042 ATAATTTTAATGA-TTTTAAA
1 ATAATTTTAAT-ACTTTTAAA
3120062 ATAA
1 ATAA
3120066 AAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 11 0.50
22 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAATTTTAATACTTTTAAA
Found at i:3120110 original size:26 final size:25
Alignment explanation
Indices: 3120056--3120110 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
3120046 TTTTAATGAT
* * * *
3120056 TTTAAAATAAAAAATTATTTTATTT
1 TTTAAAATAAAAAATTAATTAAATG
3120081 TTTAAAATTAAAAAATTAATTAAATG
1 TTTAAAA-TAAAAAATTAATTAAATG
3120107 TTTA
1 TTTA
3120111 TGTGGAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTAAAATAAAAAATTAATTAAATG
Found at i:3127869 original size:42 final size:40
Alignment explanation
Indices: 3127810--3127890 Score: 144
Period size: 42 Copynumber: 2.0 Consensus size: 40
3127800 CCCGCGATCA
3127810 TGTTAGAATAAACTACCCCTTTAGTACTCTGTCATTTATTGT
1 TGTTAGAATAAACTACCCCTTTAGTA--CTGTCATTTATTGT
3127852 TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTG
1 TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTG
3127891 GTGTAATCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 13 0.33
42 26 0.67
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (40 bp):
TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTGT
Found at i:3133611 original size:144 final size:144
Alignment explanation
Indices: 3133348--3133633 Score: 464
Period size: 144 Copynumber: 2.0 Consensus size: 144
3133338 TGTTCTTTAT
** *
3133348 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGTTATTGAGTGAGCTTTAT
1 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGCCATTGAGCGAGCTTTAT
** *
3133413 CATTGTAATATCTTCCTTGAGAGGTGTCTTTAATCATTGTTATTATTTAACATATTTGTAAGGGG
66 CATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGGG
3133478 TTGCTTAAGGTTAC
131 TTGCTTAAGGTTAC
* * * *
3133492 ACACACTTGGGTAACCATCTCTTTTATTCTTTTCAATTGTTGTATTGCCATTGAGCGAGCTTTAT
1 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGCCATTGAGCGAGCTTTAT
* *
3133557 CATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTATCATATTTGTAAGGGT
66 CATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGGG
3133622 TTGCTTAAGGTT
131 TTGCTTAAGGTT
3133634 TTTGAGTAGA
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 130 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (144 bp):
ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGCCATTGAGCGAGCTTTAT
CATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGGG
TTGCTTAAGGTTAC
Found at i:3134642 original size:6 final size:7
Alignment explanation
Indices: 3134624--3134652 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3134614 TTATAATAAT
3134624 ATTTTTA
1 ATTTTTA
3134631 ATTTTTA
1 ATTTTTA
3134638 ATTTTTA
1 ATTTTTA
3134645 ATTTTTA
1 ATTTTTA
3134652 A
1 A
3134653 AATATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTTTTA
Found at i:3134824 original size:22 final size:23
Alignment explanation
Indices: 3134783--3134825 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3134773 ATTTTATGTT
*
3134783 AATAATATATTTTAGCATTTTTA
1 AATAATATATTTTAACATTTTTA
*
3134806 AATAATAT-TTTTAATATTTT
1 AATAATATATTTTAACATTTT
3134826 ATTGAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
AATAATATATTTTAACATTTTTA
Found at i:3134825 original size:21 final size:22
Alignment explanation
Indices: 3134783--3134826 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3134773 ATTTTATGTT
3134783 AATAATATATTTTAGCATTTTTA
1 AATAATATATTTTA-CATTTTTA
3134806 AATAATAT-TTTTA-ATATTTTA
1 AATAATATATTTTACAT-TTTTA
3134827 TTGAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.10
21 5 0.25
22 5 0.25
23 8 0.40
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
AATAATATATTTTACATTTTTA
Found at i:3141712 original size:40 final size:40
Alignment explanation
Indices: 3141653--3141864 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
3141643 CATTTGAATG
* *
3141653 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * *
3141693 TTATCCGGGCTAAGACCCGAAGGCATTTGTCCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
3141733 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * * * *
3141773 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
3141813 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
3141853 ATATCC-GGCTAA
1 ATATCCGGGCTAA
3141865 ATTCCAAAGA
Statistics
Matches: 138, Mismatches: 32, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
39 8 0.06
40 128 0.93
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:3141793 original size:80 final size:79
Alignment explanation
Indices: 3141657--3141864 Score: 299
Period size: 80 Copynumber: 2.6 Consensus size: 79
3141647 TGAATGATAT
*
3141657 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCC-GGCTAAGACCCGAAGGCATTTG
* *
3141722 TCCGAGTTGCTATAC
65 TCCGAGTTACTAAAC
* *
3141737 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGG-CTAAGACCCGAAGGCATTTG
* *
3141802 TGCGAGTTACTAAAT
65 TCCGAGTTACTAAAC
* * * *
3141817 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCCGGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAA
3141865 ATTCCAAAGA
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
79 6 0.05
80 109 0.95
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGCTAAGACCCGAAGGCATTTGT
CCGAGTTACTAAAC
Found at i:3145783 original size:21 final size:21
Alignment explanation
Indices: 3145757--3145797 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3145747 AGACGAGCAA
* *
3145757 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3145778 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3145798 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3149192 original size:18 final size:19
Alignment explanation
Indices: 3149155--3149192 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3149145 TAATTAAATA
* *
3149155 AAAAATTAAATTTATTTAT
1 AAAAATAAAATTTATATAT
3149174 AAAAATAAAATTT-TATAT
1 AAAAATAAAATTTATATAT
3149192 A
1 A
3149193 CATTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATAAAATTTATATAT
Done.