Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold16
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: 5287347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 8769 characters in sequence are not A, C, G, or T
File 30 of 35
Found at i:4313135 original size:52 final size:52
Alignment explanation
Indices: 4313079--4313207 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
4313069 CACTGATCTT
*
4313079 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
4313131 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
4313183 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
4313208 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:4315823 original size:13 final size:13
Alignment explanation
Indices: 4315805--4315830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4315795 TACACAAAGT
4315805 ATGTATCGATACA
1 ATGTATCGATACA
4315818 ATGTATCGATACA
1 ATGTATCGATACA
4315831 CGAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4315828 original size:32 final size:34
Alignment explanation
Indices: 4315787--4315851 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
4315777 TAGCCAAACT
**
4315787 TGTATCGATACAC-AAAGTA-TGTATCGATACAA
1 TGTATCGATACACGAAAAAATTGTATCGATACAA
4315819 TGTATCGATACACGAAAAAATTGTATCGATACA
1 TGTATCGATACACGAAAAAATTGTATCGATACA
4315852 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACGAAAAAATTGTATCGATACAA
Found at i:4317312 original size:17 final size:17
Alignment explanation
Indices: 4317278--4317317 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
4317268 GATATTTTAT
4317278 TTAACATTTTTAATAAAA
1 TTAA-ATTTTTAATAAAA
4317296 TCTAAATTTTTAA-AAAA
1 T-TAAATTTTTAATAAAA
4317313 TTAAA
1 TTAAA
4317318 ATAATATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 5 0.24
18 9 0.43
19 3 0.14
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTTTAATAAAA
Found at i:4319906 original size:120 final size:121
Alignment explanation
Indices: 4319773--4319995 Score: 394
Period size: 120 Copynumber: 1.9 Consensus size: 121
4319763 TTCAACCAAG
*
4319773 CATGGATGGCCTAAAAGAAGCTTTTGGATTTTTTACAATTTAGTCCTTAGATATTTTAATGTTAC
1 CATGGATGGCCTAAAAGAAGCTTTTGGATTTTTTACAATTTAGTCCTTAGATATTTTAATATTAC
4319838 AAAATAACC-AAAAAAACATGAAATCATCATCAATTACCAACAACATGATTTCAAC
66 AAAATAACCAAAAAAAACATGAAATCATCATCAATTACCAACAACATGATTTCAAC
* * *
4319893 CATGGATGGCCTAAAAGAAGTTTTTGGATTTTTTACAATTTAGTCCTTCGATCTTTTAATATTAC
1 CATGGATGGCCTAAAAGAAGCTTTTGGATTTTTTACAATTTAGTCCTTAGATATTTTAATATTAC
*
4319958 AAAATAGCCAAAAAAAACATGAAATCATCATCAATTAC
66 AAAATAACCAAAAAAAACATGAAATCATCATCAATTAC
4319996 TAGCCACATG
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
120 69 0.71
121 28 0.29
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (121 bp):
CATGGATGGCCTAAAAGAAGCTTTTGGATTTTTTACAATTTAGTCCTTAGATATTTTAATATTAC
AAAATAACCAAAAAAAACATGAAATCATCATCAATTACCAACAACATGATTTCAAC
Found at i:4320591 original size:3 final size:3
Alignment explanation
Indices: 4320578--4320620 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
4320568 TTTTATTGCT
4320578 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4320621 GTTGTTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:4320625 original size:3 final size:3
Alignment explanation
Indices: 4320619--4320656 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4320609 ATTATTATTA
4320619 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
4320657 ATGATATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:4325626 original size:24 final size:24
Alignment explanation
Indices: 4325594--4325639 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
4325584 GTAGTTCCTT
4325594 TTGTTTGTCAAAAATT-GTGGCTTG
1 TTGTTTGTC-AAAATTGGTGGCTTG
4325618 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTCAAAATTGGTGGCT
4325640 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.20, C:0.09, G:0.26, T:0.46
Consensus pattern (24 bp):
TTGTTTGTCAAAATTGGTGGCTTG
Found at i:4330084 original size:26 final size:27
Alignment explanation
Indices: 4330020--4330121 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
4330010 CAAAAGCCAC
4330020 CCTTTGTGTTTGTCAAAAATAGTGGTT
1 CCTTTGTGTTTGTCAAAAATAGTGGTT
* * *
4330047 ACTTTGTATTTGTCAAAAATGGTGGTT
1 CCTTTGTGTTTGTCAAAAATAGTGGTT
* *
4330074 CCTTT-TGTTTGTTAAAAATTGTGG--
1 CCTTTGTGTTTGTCAAAAATAGTGGTT
*
4330098 -C-TTGTTGTTTGTCAAAATTAGTGG
1 CCTTTG-TGTTTGTCAAAAATAGTGG
4330122 CTAATTTTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.03
23 1 0.02
24 16 0.25
26 16 0.25
27 28 0.44
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46
Consensus pattern (27 bp):
CCTTTGTGTTTGTCAAAAATAGTGGTT
Found at i:4331393 original size:318 final size:319
Alignment explanation
Indices: 4330921--4331520 Score: 897
Period size: 318 Copynumber: 1.9 Consensus size: 319
4330911 TTATAAAAAT
* * * * *
4330921 AATTCATTGTATAATATTAATTTGACCAATTAATTTATTTTATTTATCTTCATTTATTGTTTGTA
1 AATTCAATGTATAATATTAATTTGACCAATTAATTTATCTCATTCATCTTCATTTATTGTGTGTA
* * * *
4330986 ATATAATATATTATTTTTTTCTCAACTTCATTCATTGAATTTAATATAATATATTAATTTTATTC
66 ATATAATATATTAATTTTATCTCAACCTCATTCATTGAATTTAATATAATATATTAATTTCATTC
* *
4331051 ATTGTAGTTTGAATTAAGTTTTAA-TTTTTTTAGTAGAA-TTTGAATCGTTTAAATACCATAAAA
131 ATTATAGTTTCAATTAAGTTTTAATTTTTTTTAGTA-AAGTTTGAATCGTTTAAATA--ATAAAA
* *
4331114 ATAGAATAATAAAAATGATTACCAATTAAT-TTTTCTCATTCATTGAA-TTAAATTTGATATAAT
193 ATAGAATAATAAAAATGATTACCAATTAATATTTTCTCATTCATTAAATTTAAATTTAATATAAT
*
4331177 ATATTAATTTTATTCATTATTTTTTCAAAAAAAAATTCATATATTATAAAAATAATTCATTG
258 ATATTAATTTTATCCATTATTTTTTCAAAAAAAAATTCATATATTATAAAAATAATTCATTG
** *
4331239 AATTCAATGTATAATATTAATTTGATTAATTAATTTTATCTCATTCATCTTTATTTATTGTGTGT
1 AATTCAATGTATAATATTAATTTGACCAATTAA-TTTATCTCATTCATCTTCATTTATTGTGTGT
4331304 AATATAATA-ATTAATTTTATCTCAACCTCATTCATTGAATTTAATATAATATATTAATTTCATT
65 AATATAATATATTAATTTTATCTCAACCTCATTCATTGAATTTAATATAATATATTAATTTCATT
** * * *
4331368 CATTATTTTTTCAATTACA-TTTTAATTTTTTTTAGTAAAGTTTGAATGGTTTAATTATTAAAAA
130 CATTATAGTTTCAATTA-AGTTTTAATTTTTTTTAGTAAAGTTTGAATCGTTTAAATAATAAAAA
* *
4331432 TATAATAATAAAAATTATTACCAATTAATATTTTCTCATTCATTAAATTTAAATTTAATATAATA
194 TAGAATAATAAAAATGATTACCAATTAATATTTTCTCATTCATTAAATTTAAATTTAATATAATA
4331497 TATTAATTTTATCCATTATTTTTT
259 TATTAATTTTATCCATTATTTTTT
4331521 TAATTTCATT
Statistics
Matches: 252, Mismatches: 24, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
317 33 0.13
318 118 0.47
319 101 0.40
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (319 bp):
AATTCAATGTATAATATTAATTTGACCAATTAATTTATCTCATTCATCTTCATTTATTGTGTGTA
ATATAATATATTAATTTTATCTCAACCTCATTCATTGAATTTAATATAATATATTAATTTCATTC
ATTATAGTTTCAATTAAGTTTTAATTTTTTTTAGTAAAGTTTGAATCGTTTAAATAATAAAAATA
GAATAATAAAAATGATTACCAATTAATATTTTCTCATTCATTAAATTTAAATTTAATATAATATA
TTAATTTTATCCATTATTTTTTCAAAAAAAAATTCATATATTATAAAAATAATTCATTG
Found at i:4331577 original size:119 final size:118
Alignment explanation
Indices: 4331454--4331699 Score: 255
Period size: 119 Copynumber: 2.1 Consensus size: 118
4331444 AATTATTACC
** ** *
4331454 AATTAATATTT-TCTCATTCATTAAAT-TTAAATTTAATATAATATATTAATTTTATCCATTATT
1 AATTAATATTTATCTCAGAC-TTAAATATTAAATTTAATATAATATATTAATTCCATCCATTACT
* * *
4331517 TTTTTAATTTCATTTCAACTCTTTGTAATAAAATTTGAATAATTAAATTACTAATA
65 TTTTGAATTTCATTTCAA-TCTTTGTAATAAAATTTGAATAACTAAATTAATAA-A
* * ** * *
4331573 AATTAAT-TTTATGTGAGACTTATTTATTAAATTTAATATGATATATTAATTCCATCCATTGCTT
1 AATTAATATTTATCTCAGACTTAAATATTAAATTTAATATAATATATTAATTCCATCCATTACTT
* * * * * *
4331637 TTTGAATTTTATTTTAATTTTTTTAATAGAATTTGAATGACTAAATTAATAAA
66 TTTGAATTTCATTTCAATCTTTGTAATAAAATTTGAATAACTAAATTAATAAA
4331690 AATATAATAT
1 AAT-TAATAT
4331700 AAAAATTATT
Statistics
Matches: 103, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
117 4 0.04
118 40 0.39
119 59 0.57
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (118 bp):
AATTAATATTTATCTCAGACTTAAATATTAAATTTAATATAATATATTAATTCCATCCATTACTT
TTTGAATTTCATTTCAATCTTTGTAATAAAATTTGAATAACTAAATTAATAAA
Found at i:4333311 original size:23 final size:22
Alignment explanation
Indices: 4333277--4333320 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
4333267 AAATTTTATT
* *
4333277 TTTAAAATAATTTAAATTTAAA
1 TTTAAAAAAATTAAAATTTAAA
4333299 TTTAATAAAAATTAAAATTTAA
1 TTTAA-AAAAATTAAAATTTAA
4333321 TGACAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAAAAAATTAAAATTTAAA
Found at i:4333838 original size:1 final size:1
Alignment explanation
Indices: 4333806--4333831 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4333796 TTTTACGTGA
4333806 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
4333832 CATTTTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4343619 original size:20 final size:20
Alignment explanation
Indices: 4343594--4343672 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
4343584 ACTGCTAAGG
4343594 AAATGTATCGATACATTACT
1 AAATGTATCGATACATTACT
*
4343614 AAATGTATCAATACATGCTTAC-
1 AAATGTATCGATACA---TTACT
* *
4343636 AATTGTATCGATACATTTCT
1 AAATGTATCGATACATTACT
* *
4343656 CATTGTATCGATACATT
1 AAATGTATCGATACATT
4343673 CTGGGTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.06
20 30 0.60
22 13 0.26
23 4 0.08
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (20 bp):
AAATGTATCGATACATTACT
Found at i:4348712 original size:29 final size:29
Alignment explanation
Indices: 4348657--4348712 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4348647 AAGAAAAGCA
* *
4348657 AAATTAGATATATTCTAAATTGGAAAAAG
1 AAATAAGATATATTCTAAATTGAAAAAAG
* *
4348686 AAATAAGATATATTTTAAATTTAAAAA
1 AAATAAGATATATTCTAAATTGAAAAA
4348713 TGGTTAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (29 bp):
AAATAAGATATATTCTAAATTGAAAAAAG
Found at i:4354003 original size:50 final size:50
Alignment explanation
Indices: 4353900--4354005 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
4353890 CATTGTCTCA
* * *
4353900 ATACATCTAGGGTTTTACCCAGACATATCGATACATTATTCATTGTATTG
1 ATACATCTAGGGTTTTACCCAGACATATCGATACATTATTCAATATATCG
** *
4353950 ATACATCCT-GGGTTTTACCCAGATGTATCGATATATT-TCTCAATATATCG
1 ATACAT-CTAGGGTTTTACCCAGACATATCGATACATTAT-TCAATATATCG
4354000 ATACAT
1 ATACAT
4354006 TCAGGCATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.02
50 45 0.94
51 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (50 bp):
ATACATCTAGGGTTTTACCCAGACATATCGATACATTATTCAATATATCG
Found at i:4356714 original size:79 final size:79
Alignment explanation
Indices: 4356348--4356901 Score: 471
Period size: 79 Copynumber: 7.1 Consensus size: 79
4356338 GCATCGATGT
* * * * * ** * * * * *
4356348 TTTTATTTCCAAATCATCGATTTTTCATAATCGAAGATATTCCAACTCCGTTATTTCTGAGGGAA
1 TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
*
4356413 TACTCCAACCCCGG
66 TACTCCAACCCCGA
** * * * *
4356427 CCTTA-TTTCTAAAACATCAAATTTTCACAATC-GGGATACTCCAATCCCGTTATTTTTGAA-AG
1 TTTTATTTTC-AAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTT-AAGGG
*
4356489 GATACT-TAACCCCGA
64 GATACTCCAACCCCGA
* * * * **
4356504 TTTTATTTTCAAAACACCTATTTTCCACAATC--GG---CTTCAACCCCGTTATTTCTGTGGGGA
1 TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
4356564 TACTCCAACCCCGA
66 TACTCCAACCCCGA
* * * * * * * *
4356578 TTTTATTTCCAAAACACCTATTTTCCACCATTGGGGGATACTCTAACCCCATTATTTTTAAGGAG
1 TTTTATTTTCAAAACACCAATTTTTCA-CAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGG
* * *
4356643 ATACTCCAGCCTCGG
65 ATACTCCAACCCCGA
* * *
4356658 TTTTATTTTTAAAATACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGA
1 TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
* *
4356723 TACTTCAACTCCGA
66 TACTCCAACCCCGA
* * * * ** **
4356737 TTTTATTTTCAAAACATCGATTTTTCATAATCGGGGATACTTCAACCCTATTATTTTCGAGGGGA
1 TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
*
4356802 TACTCCAACACCGA
66 TACTCCAACCCCGA
* * * * * *
4356816 TTTTATTTTCAAAACATCAATTTTTCACAATCGAGAATACTCCAACCCCATTA-TTTCAGAAGGG
1 TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTA-AGGGG
*
4356880 ATACTCTAACCCCGA
65 ATACTCCAACCCCGA
4356895 GTTTTAT
1 -TTTTAT
4356902 CTCCAAAATA
Statistics
Matches: 381, Mismatches: 81, Indels: 25
0.78 0.17 0.05
Matches are distributed among these distances:
73 23 0.06
74 34 0.09
75 3 0.01
76 2 0.01
77 30 0.08
78 36 0.09
79 195 0.51
80 58 0.15
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (79 bp):
TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
TACTCCAACCCCGA
Found at i:4361399 original size:33 final size:31
Alignment explanation
Indices: 4361357--4361427 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 31
4361347 GGGTAAAAGC
* *
4361357 AAAAAAATGATAAACACAAGAGAAACAAAAATG
1 AAAAAAATGAAAAAAACAAGAG-AA-AAAAATG
4361390 AAAAAAATGAAAAAAACAAGAGAAAAAAATG
1 AAAAAAATGAAAAAAACAAGAGAAAAAAATG
*
4361421 AACAAAA
1 AAAAAAA
4361428 GGGGAACGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 13 0.37
32 2 0.06
33 20 0.57
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.07
Consensus pattern (31 bp):
AAAAAAATGAAAAAAACAAGAGAAAAAAATG
Found at i:4363565 original size:28 final size:28
Alignment explanation
Indices: 4363484--4363565 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
4363474 TTTTGGAGAT
*
4363484 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
4363512 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
4363540 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
4363566 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:4363708 original size:51 final size:51
Alignment explanation
Indices: 4363548--4363718 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
4363538 GAAATAACGA
* * *
4363548 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
4363600 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
4363653 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
4363704 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
4363719 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:4363792 original size:27 final size:28
Alignment explanation
Indices: 4363701--4363804 Score: 158
Period size: 28 Copynumber: 3.8 Consensus size: 28
4363691 AAAATAAAGT
*
4363701 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
4363729 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
4363757 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
4363784 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
4363805 TGTGAAGAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
27 25 0.35
28 47 0.65
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:4366243 original size:13 final size:13
Alignment explanation
Indices: 4366225--4366250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4366215 ACAAAGATCC
4366225 ATGTATCGATACA
1 ATGTATCGATACA
4366238 ATGTATCGATACA
1 ATGTATCGATACA
4366251 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4366246 original size:33 final size:33
Alignment explanation
Indices: 4366204--4366270 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4366194 AAAATTTCCA
***
4366204 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
4366237 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
4366270 A
1 A
4366271 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:4366314 original size:19 final size:18
Alignment explanation
Indices: 4366290--4366357 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
4366280 CAGTAGCTAA
4366290 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4366309 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4366324 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4366341 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4366358 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4366330 original size:13 final size:13
Alignment explanation
Indices: 4366312--4366336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4366302 ACAATACTTA
4366312 TGTATCGATACAT
1 TGTATCGATACAT
4366325 TGTATCGATACA
1 TGTATCGATACA
4366337 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4366334 original size:32 final size:32
Alignment explanation
Indices: 4366293--4366355 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4366283 TAGCTAATTA
*
4366293 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
4366325 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
4366356 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:4366437 original size:21 final size:21
Alignment explanation
Indices: 4366413--4366469 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
4366403 CATTTGTAGG
4366413 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
4366434 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
4366455 ATGTATCGATACATT
1 ATGTATCGATACATT
4366470 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:4366480 original size:1 final size:1
Alignment explanation
Indices: 4366474--4366521 Score: 69
Period size: 1 Copynumber: 48.0 Consensus size: 1
4366464 TACATTTAAA
***
4366474 TTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4366522 CAAACACTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:4366506 original size:22 final size:22
Alignment explanation
Indices: 4366481--4366524 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4366471 AAATTTTTTT
4366481 TTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTCAA
4366503 TTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTCAA
4366525 ACACTTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.05, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTTTTTTTTTTTTTTTCAA
Found at i:4367201 original size:55 final size:55
Alignment explanation
Indices: 4367117--4367574 Score: 660
Period size: 55 Copynumber: 8.3 Consensus size: 55
4367107 ATAAGTTGTA
* * * * * *
4367117 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
4367172 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
4367227 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGAGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
4367282 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
4367337 TCCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
4367392 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
4367447 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
4367502 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAACGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
4367557 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
4367575 AAAAAGCGGA
Statistics
Matches: 375, Mismatches: 19, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
53 2 0.01
54 6 0.02
55 355 0.95
56 10 0.03
57 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:4367281 original size:29 final size:28
Alignment explanation
Indices: 4367248--4367336 Score: 69
Period size: 29 Copynumber: 3.2 Consensus size: 28
4367238 GGGGAATGAA
4367248 AGGTGCCACCAACTTGAGTGGGCTTTAAG
1 AGGTGCCACCAACTTG-GTGGGCTTTAAG
** * * *
4367277 AGGTGTCCTGC-TCTTTGG-GGAC-TGAA-
1 AGGTG-CCACCAAC-TTGGTGGGCTTTAAG
4367303 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTG-GTGGGCTTTAAG
4367332 AGGTG
1 AGGTG
4367337 TCCTGCTCTT
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 6 0.14
26 7 0.16
27 6 0.14
28 6 0.14
29 12 0.28
30 6 0.14
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.27
Consensus pattern (28 bp):
AGGTGCCACCAACTTGGTGGGCTTTAAG
Found at i:4367306 original size:26 final size:26
Alignment explanation
Indices: 4367163--4367307 Score: 64
Period size: 26 Copynumber: 5.3 Consensus size: 26
4367153 GTGTGGGCTT
* *
4367163 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
4367189 TGAAAGGTG-CCACCCACTTGTGTGGG-C
1 TGAAAGGTGTCC-TGCTCTT-TG-GGGAC
* *
4367216 TTTGAAAAGTGTCCTGCTCTTTGGGGAA
1 --TGAAAGGTGTCCTGCTCTTTGGGGAC
** * *
4367244 TGAAAGGTG-CCACCAAC-TTGAGTGGGC
1 TGAAAGGTGTCCTGC-TCTTTG-G-GGAC
*
4367271 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
4367299 TGAAAGGTG
1 TGAAAGGTG
4367308 CCACCAACTT
Statistics
Matches: 83, Mismatches: 22, Indels: 28
0.62 0.17 0.21
Matches are distributed among these distances:
25 8 0.10
26 27 0.33
27 11 0.13
28 10 0.12
29 19 0.23
30 8 0.10
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:4368560 original size:1 final size:1
Alignment explanation
Indices: 4368556--4368605 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
4368546 CTTTTCTCTC
* * * * *
4368556 TTTTTCTTTGTTTTGTTTTTTTTGTTTTTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4368606 GAAGAGAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:4368574 original size:14 final size:13
Alignment explanation
Indices: 4368556--4368604 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
4368546 CTTTTCTCTC
*
4368556 TTTTTCTTTGTTT
1 TTTTTTTTTGTTT
4368569 TGTTTTTTTTGTTT
1 T-TTTTTTTTGTTT
*
4368583 TTTTTTTTTCTTT
1 TTTTTTTTTGTTT
4368596 TTTTTTTTT
1 TTTTTTTTT
4368605 TGAAGAGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 21 0.64
14 12 0.36
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:4368605 original size:14 final size:14
Alignment explanation
Indices: 4368540--4368605 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 14
4368530 CTTAAGTAGG
*
4368540 TTTTTTCTTTTCTCT
1 TTTTTTCTTTT-TTT
*
4368555 CTTTTTCTTTGTTTT
1 TTTTTTCTTT-TTTT
*
4368570 GTTTTTTTTGTTTTTT
1 -TTTTTTCT-TTTTTT
4368586 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
4368600 TTTTTT
1 TTTTTT
4368606 GAAGAGAAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
14 12 0.28
15 18 0.42
16 11 0.26
17 2 0.05
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (14 bp):
TTTTTTCTTTTTTT
Found at i:4381088 original size:28 final size:28
Alignment explanation
Indices: 4381007--4381088 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
4380997 TTTTGGAGAT
*
4381007 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
4381035 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
4381063 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
4381089 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:4381231 original size:51 final size:51
Alignment explanation
Indices: 4381071--4381241 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
4381061 GAAATAACGA
* * *
4381071 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
4381123 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
4381176 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
4381227 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
4381242 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:4381315 original size:27 final size:28
Alignment explanation
Indices: 4381224--4381327 Score: 158
Period size: 28 Copynumber: 3.8 Consensus size: 28
4381214 AAAATAAAGT
*
4381224 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
4381252 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
4381280 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
4381307 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
4381328 TGTGAAGAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
27 25 0.35
28 47 0.65
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:4383765 original size:13 final size:13
Alignment explanation
Indices: 4383747--4383772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4383737 ACAAAGATCC
4383747 ATGTATCGATACA
1 ATGTATCGATACA
4383760 ATGTATCGATACA
1 ATGTATCGATACA
4383773 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4383768 original size:33 final size:33
Alignment explanation
Indices: 4383726--4383792 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4383716 AAAATTTCCA
***
4383726 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
4383759 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
4383792 A
1 A
4383793 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:4383836 original size:19 final size:18
Alignment explanation
Indices: 4383812--4383879 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
4383802 CAGTAGCTAA
4383812 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4383831 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4383846 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4383863 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4383880 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4383852 original size:13 final size:13
Alignment explanation
Indices: 4383834--4383858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4383824 ACAATACTTA
4383834 TGTATCGATACAT
1 TGTATCGATACAT
4383847 TGTATCGATACA
1 TGTATCGATACA
4383859 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4383856 original size:32 final size:32
Alignment explanation
Indices: 4383815--4383877 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4383805 TAGCTAATTA
*
4383815 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
4383847 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
4383878 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:4383959 original size:21 final size:21
Alignment explanation
Indices: 4383935--4383991 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
4383925 CATTTGTAGG
4383935 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
4383956 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
4383977 ATGTATCGATACATT
1 ATGTATCGATACATT
4383992 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:4384002 original size:1 final size:1
Alignment explanation
Indices: 4383996--4384042 Score: 67
Period size: 1 Copynumber: 47.0 Consensus size: 1
4383986 TACATTTAAA
***
4383996 TTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4384043 CAAACACTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:4384028 original size:21 final size:21
Alignment explanation
Indices: 4384004--4384045 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4383994 AATTTTTTTT
4384004 TTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTCAA
4384025 TTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTCAA
4384046 ACACTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTTTTCAA
Found at i:4384495 original size:62 final size:62
Alignment explanation
Indices: 4384417--4385052 Score: 725
Period size: 62 Copynumber: 10.3 Consensus size: 62
4384407 ACCCCTTTTA
* * * * *
4384417 ACCCTCTAATCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAATCCCACATGAGTTGGTGAC
1 ACCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
* ** * * * *
4384479 ACCCTTTAG-CCTTCAAAGAGCAGGACGTTTTTTTCTTTTGAAAGCCCATACGAGTTGGTGAC
1 ACCCTTTAGTCC-TCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
* * * * *
4384541 ACCTTTTTGTCCTCAAAGAACAGAACGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
1 ACCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
* ** * * * * *
4384603 ACCCTTTAGTCTTCAAAGAGCAGGGCGCCTTTTCCTTTTCAAAGCTCACACGAGTTGATGTC
1 ACCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
* *
4384665 ACCCTTCTAGTCCTCAAAGAACAGGATGCCTTTTCCTTTTCAAAGCCCACATGAGTTGGTGGC
1 ACCCTT-TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
** *
4384728 ACCCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCCTTTTCAAAGCCCACACAAGTTGATGGC
1 ACCC-TTTAGTCCTCAAAGAGCAGGATGCCTTTTT-CTTTTCAAAGCCCACATGAGTTGGTGGC
* * * * *
4384792 ACCCTTCTAGTCCTCAAAGAGCAGGACGCATTTTCCTTTTCAAAGCCCACACGAGTTGGTGAC
1 ACCCTT-TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
* * *
4384855 ACCCTTCTAGTCCTCAAAGAGTAGGATGTCTTTTTCTTTT-AAAG-AC-CATGAGTTGGTGGC
1 ACCCTT-TAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
* * *
4384915 A-CCTTTTGATCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGCGGC
1 ACCCTTTAG-TCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
* * *
4384977 ACCTTTTAGTCCTTAAAGAGCATGA--CAC-TTTT-TTTT-AAAGCCCACATGAGTTGGTGGC
1 ACCCTTTAGTCCTCAAAGAGCAGGATGC-CTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
*
4385035 ACCCTTTAGTCTTCAAAG
1 ACCCTTTAGTCCTCAAAG
4385053 GGCAAGACAC
Statistics
Matches: 490, Mismatches: 72, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
58 38 0.08
59 35 0.07
60 22 0.04
61 5 0.01
62 187 0.38
63 147 0.30
64 56 0.11
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (62 bp):
ACCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGC
Found at i:4391786 original size:30 final size:30
Alignment explanation
Indices: 4391730--4392055 Score: 183
Period size: 30 Copynumber: 10.9 Consensus size: 30
4391720 TCACCCTTCA
*
4391730 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
4391759 AAAGCCCACAAGTCAGTGGCACCC-TTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * *
4391788 AAAAGCCTACAAATCGGTGGCAACC---TTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* *
4391816 AAAGCCCATAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * *
4391846 GAAGCCCACAAGTCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * *
4391875 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * * *
4391905 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTTCC
1 -----AAAGCCCACAAGTC-AGTGGCACCCTTTTT-C
*
4391941 TTTTAAA-CCCACAAGTTAGTGGCACCC-TTTTC
1 ----AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * *
4391973 AAAAGCCCATAAGTCAATGGCAACC--TTTA
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * *
4392002 AAAGCCCACAAGTCAGTGGCA--ATCTTTA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
*
4392030 AAAGCCCACAAGTCAGTGGCAACCTT
1 AAAGCCCACAAGTCAGTGGCACCCTT
4392056 CAAAAGCACA
Statistics
Matches: 235, Mismatches: 43, Indels: 37
0.75 0.14 0.12
Matches are distributed among these distances:
27 20 0.09
28 47 0.20
29 55 0.23
30 65 0.28
32 1 0.00
33 5 0.02
34 13 0.06
35 28 0.12
36 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTTC
Found at i:4391821 original size:57 final size:57
Alignment explanation
Indices: 4391730--4391902 Score: 168
Period size: 57 Copynumber: 3.0 Consensus size: 57
4391720 TCACCCTTCA
* * * * *
4391730 AAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTC
1 AAAGCCCACAAATCGGTGGCAAC-TCTTCAAAGCCCACAAATCAGTGGCACCCTTTTC
* *
4391788 AAAAGCCTACAAATCGGTGGCAAC-CTTCAAAGCCCATAAATCAGTGGCACCCTTTTTC
1 -AAAGCCCACAAATCGGTGGCAACTCTTCAAAGCCCACAAATCAGTGGCACCC-TTTTC
* * * * * * * *
4391846 GAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTT
1 AAAGCCCACAAATCGGTGGCAACTCTT-CAAAGCCCACAAATCAGTGGCACCCTTTT
4391903 TCTTTTGTAA
Statistics
Matches: 94, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
57 44 0.47
58 11 0.12
59 39 0.41
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (57 bp):
AAAGCCCACAAATCGGTGGCAACTCTTCAAAGCCCACAAATCAGTGGCACCCTTTTC
Found at i:4391828 original size:27 final size:27
Alignment explanation
Indices: 4391721--4391841 Score: 116
Period size: 29 Copynumber: 4.3 Consensus size: 27
4391711 AGACATTCCT
*
4391721 CACCCTTCAAAAGCCCACAAGTCAGTGG
1 CACCCTTC-AAAGCCCACAAATCAGTGG
** *
4391749 CATCTTTTTCAAAGCCCACAAGTCAGTGG
1 CA-C-CCTTCAAAGCCCACAAATCAGTGG
* *
4391778 CACCCTTTTCAAAAGCCTACAAATCGGTGG
1 CACCC--TTC-AAAGCCCACAAATCAGTGG
* *
4391808 CAACCTTCAAAGCCCATAAATCAGTGG
1 CACCCTTCAAAGCCCACAAATCAGTGG
4391835 CACCCTT
1 CACCCTT
4391842 TTTCGAAGCC
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
27 22 0.29
28 6 0.08
29 25 0.33
30 23 0.30
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.21
Consensus pattern (27 bp):
CACCCTTCAAAGCCCACAAATCAGTGG
Found at i:4392014 original size:28 final size:28
Alignment explanation
Indices: 4391939--4392096 Score: 169
Period size: 28 Copynumber: 5.6 Consensus size: 28
4391929 CACTCTTTTT
* * *
4391939 CCTTTTAAA-CCCACAAGTTAGTGGCAC
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
* *
4391966 CCTTTTCAAAAGCCCATAAGTCAATGGCAA
1 CC-TTT-AAAAGCCCACAAGTCAGTGGCAA
4391996 CCTTTAAAAGCCCACAAGTCAGTGGCAA
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
*
4392024 TCTTTAAAAGCCCACAAGTCAGTGGCAA
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
* * *
4392052 CCTTCAAAAGCACACAAGT-TGAT-GCAA
1 CCTTTAAAAGCCCACAAGTCAG-TGGCAA
4392079 TCCTTTTAAAAGCCCACA
1 -CC-TTTAAAAGCCCACA
4392097 CAAGTTGGTG
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
27 7 0.06
28 70 0.63
29 18 0.16
30 16 0.14
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (28 bp):
CCTTTAAAAGCCCACAAGTCAGTGGCAA
Found at i:4392084 original size:84 final size:85
Alignment explanation
Indices: 4391940--4392096 Score: 203
Period size: 85 Copynumber: 1.8 Consensus size: 85
4391930 ACTCTTTTTC
* * * * *
4391940 CTTTTAAACCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCATAAGTCAATGGCAACC-TTTAAA
1 CTTTAAAACCCACAAGTCAGTGGCAACC-TTTCAAAAGCACACAAGTCAATGGCAACCTTTTAAA
4392004 AGCCCACAAGTCAGTGGCAAT
65 AGCCCACAAGTCAGTGGCAAT
**
4392025 CTTTAAAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCACACAAGTTGAT-GCAATCCTTTTAA
1 CTTTAAAA-CCCACAAGTCAGTGGCAACCTTTCAAAAGCACACAAGTCAATGGCAA-CCTTTTAA
4392088 AAGCCCACA
64 AAGCCCACA
4392097 CAAGTTGGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
83 4 0.06
84 19 0.31
85 21 0.34
86 18 0.29
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (85 bp):
CTTTAAAACCCACAAGTCAGTGGCAACCTTTCAAAAGCACACAAGTCAATGGCAACCTTTTAAAA
GCCCACAAGTCAGTGGCAAT
Found at i:4392212 original size:21 final size:21
Alignment explanation
Indices: 4392188--4392255 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
4392178 ATGTAGCTGG
4392188 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* *** *
4392209 CCTTTAAGTCTAGTGTAGCTGGC-
1 CCTTGAA-TC-AGCACA-TTGGCA
4392232 -CTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
4392252 CCTT
1 CCTT
4392256 TAAGTCCAAT
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 11 0.34
22 7 0.22
23 3 0.09
24 4 0.12
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:4392226 original size:43 final size:43
Alignment explanation
Indices: 4392160--4392299 Score: 235
Period size: 43 Copynumber: 3.3 Consensus size: 43
4392150 ATTGGCGCCT
*
4392160 TTGGTACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
1 TTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
* *
4392203 TTGGCACCTTTAAGTCTAGTGTAGCTGGCCTTGAATCAGCACA
1 TTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
* *
4392246 TTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
1 TTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
4392289 TTGGCACCTTT
1 TTGGCACCTTT
4392300 TCCATCTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 90 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (43 bp):
TTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
Found at i:4392331 original size:52 final size:53
Alignment explanation
Indices: 4392253--4392406 Score: 177
Period size: 52 Copynumber: 2.9 Consensus size: 53
4392243 ACATTGGCAC
4392253 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * ** *
4392305 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * *
4392360 CTTTAAGCCCAATATCG-TCGGCCATGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCT-GGCCTTGAATCAGCATATTGGCACCTTT
4392407 ATCACTTTTC
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
52 37 0.45
53 5 0.06
54 7 0.08
55 34 0.41
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:4393272 original size:13 final size:13
Alignment explanation
Indices: 4393254--4393278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4393244 CATAAAGTGT
4393254 TGTATCGATACAA
1 TGTATCGATACAA
4393267 TGTATCGATACA
1 TGTATCGATACA
4393279 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4393276 original size:33 final size:33
Alignment explanation
Indices: 4393234--4393300 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4393224 TTCAACGATT
4393234 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
4393267 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
4393300 T
1 T
4393301 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:4393359 original size:13 final size:13
Alignment explanation
Indices: 4393341--4393365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4393331 ATCACTTAAA
4393341 TGTATCGATACAT
1 TGTATCGATACAT
4393354 TGTATCGATACA
1 TGTATCGATACA
4393366 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4393418 original size:52 final size:52
Alignment explanation
Indices: 4393354--4393502 Score: 264
Period size: 52 Copynumber: 2.9 Consensus size: 52
4393344 ATCGATACAT
**
4393354 TGTATCGATACACTGA-TCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
4393406 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
4393458 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
4393503 TCATATTTCG
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 1 0.01
52 93 0.99
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:4407365 original size:14 final size:13
Alignment explanation
Indices: 4407343--4407374 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
4407333 CGTCCTCCAC
4407343 AAAAAAAAACAAA
1 AAAAAAAAACAAA
4407356 AAAAACAAAACAAA
1 AAAAA-AAAACAAA
4407370 AAAAA
1 AAAAA
4407375 GGGGTCCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:4408880 original size:30 final size:30
Alignment explanation
Indices: 4408824--4409149 Score: 199
Period size: 30 Copynumber: 10.9 Consensus size: 30
4408814 TCACCCTTCA
*
4408824 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
4408853 AAAGCCCACAAGTCAGTGGCACCC-TTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * *
4408882 AAAAGCCCACAAATCGGTGGCAACC---TTC
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* *
4408910 AAAGCCCATAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * *
4408940 GAAGCCCACAAGTCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * *
4408969 AAAGTCCACAACTCTGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * * *
4408999 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTTCC
1 -----AAAGCCCACAAGTC-AGTGGCACCCTTTTT-C
* *
4409035 TTTTAAGCCCACAAGTTAGTGGCACCC-TTTTC
1 ---AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * * *
4409067 AAAAGCCCATAAGTCAATGGCAACC--TTTA
1 -AAAGCCCACAAGTCAGTGGCACCCTTTTTC
* * *
4409096 AAAGCCCACAAGTCAGTGGCA--ATCTTTA
1 AAAGCCCACAAGTCAGTGGCACCCTTTTTC
*
4409124 AAAGCCCACAAGTCAGTGGCAACCTT
1 AAAGCCCACAAGTCAGTGGCACCCTT
4409150 CAAAAGCACA
Statistics
Matches: 238, Mismatches: 41, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
27 21 0.09
28 47 0.20
29 52 0.22
30 69 0.29
32 1 0.00
33 5 0.02
34 19 0.08
35 23 0.10
36 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTTC
Found at i:4408922 original size:27 final size:27
Alignment explanation
Indices: 4408815--4408935 Score: 125
Period size: 29 Copynumber: 4.3 Consensus size: 27
4408805 AGACATTCCT
*
4408815 CACCCTTCAAAAGCCCACAAGTCAGTGG
1 CACCCTTC-AAAGCCCACAAATCAGTGG
** *
4408843 CATCTTTTTCAAAGCCCACAAGTCAGTGG
1 CA-C-CCTTCAAAGCCCACAAATCAGTGG
*
4408872 CACCCTTTTCAAAAGCCCACAAATCGGTGG
1 CACCC--TTC-AAAGCCCACAAATCAGTGG
* *
4408902 CAACCTTCAAAGCCCATAAATCAGTGG
1 CACCCTTCAAAGCCCACAAATCAGTGG
4408929 CACCCTT
1 CACCCTT
4408936 TTTCGAAGCC
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
27 23 0.29
28 6 0.08
29 25 0.32
30 24 0.31
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.21
Consensus pattern (27 bp):
CACCCTTCAAAGCCCACAAATCAGTGG
Found at i:4409065 original size:34 final size:36
Alignment explanation
Indices: 4408974--4409065 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 36
4408964 TTTCCAAAGT
*
4408974 CCACAACTCT-GTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCCTTTGTAAGC
* *
4409009 TCACAACTCTA-TAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCCTTTGTAAGC
* *
4409043 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCTAGTGGCACTCTTTT
4409066 CAAAAGCCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.04
34 21 0.44
35 25 0.52
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (36 bp):
CCACAACTCTAGTGGCACTCTTTTTCCTTTGTAAGC
Found at i:4409108 original size:28 final size:28
Alignment explanation
Indices: 4409039--4409190 Score: 173
Period size: 28 Copynumber: 5.3 Consensus size: 28
4409029 TTTTCCTTTT
* *
4409039 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
* *
4409069 AAGCCCATAAGTCAATGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
4409097 AAGCCCACAAGTCAGTGGCAATCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
4409125 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* *
4409153 AAGCACACAAGT-TGAT-GCAATCCTTTTAA
1 AAGCCCACAAGTCAG-TGGCAA-CC-TTTAA
4409182 AAGCCCACA
1 AAGCCCACA
4409191 CAAGTTGGTG
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.05
28 67 0.63
29 15 0.14
30 19 0.18
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:4409281 original size:52 final size:52
Alignment explanation
Indices: 4409212--4409429 Score: 166
Period size: 43 Copynumber: 4.5 Consensus size: 52
4409202 CGTCTTCTTC
* * *
4409212 TAAGTCCAATATCGCTGGCCTTGAATCAACATCTTGGCGCCTTTGGTACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAACATCTTGGCGCCTTTGGCACCTT
* *
4409264 TAAGTCCAATGTAGCTGGCCTTG-----A-ATC--GGC-ACATTGGCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAACATCTTGGCGCCTTTGGCACCTT
* * *
4409307 TAAGTCCAGTGTAGCTGGCCTTGAAT---CA-----GC-ACATTGGCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAACATCTTGGCGCCTTTGGCACCTT
* * * * ** *
4409350 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAACATCTTGGCGCCTTTGGCACCTT
*
4409402 TAAGTTCAATGTAGCTGGCCTTGAATCA
1 TAAGTCCAATGTAGCTGGCCTTGAATCA
4409430 GCACGTTGAC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
43 71 0.51
44 3 0.02
46 6 0.04
47 1 0.01
51 2 0.01
52 55 0.40
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (52 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAACATCTTGGCGCCTTTGGCACCTT
Found at i:4409320 original size:43 final size:43
Alignment explanation
Indices: 4409254--4409393 Score: 235
Period size: 43 Copynumber: 3.3 Consensus size: 43
4409244 CTTGGCGCCT
* *
4409254 TTGGTACCTTTAAGTCCAATGTAGCTGGCCTTGAATCGGCACA
1 TTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
*
4409297 TTGGCACCTTTAAGTCCAGTGTAGCTGGCCTTGAATCAGCACA
1 TTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
* *
4409340 TTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATA
1 TTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
4409383 TTGGCACCTTT
1 TTGGCACCTTT
4409394 TCCATCTTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (43 bp):
TTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
Found at i:4409430 original size:52 final size:53
Alignment explanation
Indices: 4409347--4409500 Score: 177
Period size: 52 Copynumber: 2.9 Consensus size: 53
4409337 ACATTGGCAC
4409347 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * ** *
4409399 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * *
4409454 CTTTAAGCCCAATATCG-TCGGCCATGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCT-GGCCTTGAATCAGCATATTGGCACCTTT
4409501 ATCACTTTTC
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
52 37 0.45
53 5 0.06
54 7 0.08
55 34 0.41
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:4410366 original size:13 final size:13
Alignment explanation
Indices: 4410348--4410372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4410338 CATAAAGTGT
4410348 TGTATCGATACAA
1 TGTATCGATACAA
4410361 TGTATCGATACA
1 TGTATCGATACA
4410373 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4410370 original size:33 final size:33
Alignment explanation
Indices: 4410328--4410394 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4410318 TTCAACGATT
4410328 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
4410361 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
4410394 T
1 T
4410395 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:4414310 original size:50 final size:50
Alignment explanation
Indices: 4414235--4414346 Score: 170
Period size: 50 Copynumber: 2.2 Consensus size: 50
4414225 TCACAATTTG
* * * *
4414235 TATCGATATATTCTTCATTGTATCGATACATTCTGGGTTTTACCTAGATA
1 TATCGATACATTATTCATTGTATCGATACATCCTGGATTTTACCTAGATA
*
4414285 TATCGATACATTATTCATTGTATCGATACATCCTGGATTTTATCTAGATA
1 TATCGATACATTATTCATTGTATCGATACATCCTGGATTTTACCTAGATA
*
4414335 TATCAATACATT
1 TATCGATACATT
4414347 TCTCAATGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (50 bp):
TATCGATACATTATTCATTGTATCGATACATCCTGGATTTTACCTAGATA
Found at i:4414361 original size:50 final size:50
Alignment explanation
Indices: 4414248--4414362 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
4414238 CGATATATTC
* * * *
4414248 TTCATTGTATCGATACATTCTGGGTTTTACCTAGATATATCGATACATTA
1 TTCAATGTATCGATACATCCTGGATTTTACCTAGATATATCAATACATTA
* *
4414298 TTCATTGTATCGATACATCCTGGATTTTATCTAGATATATCAATACATT-
1 TTCAATGTATCGATACATCCTGGATTTTACCTAGATATATCAATACATTA
*
4414347 TCTCAATGTGTCGATA
1 T-TCAATGTATCGATA
4414363 TATTCAAGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.02
50 57 0.98
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (50 bp):
TTCAATGTATCGATACATCCTGGATTTTACCTAGATATATCAATACATTA
Found at i:4415449 original size:30 final size:30
Alignment explanation
Indices: 4415413--4415472 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4415403 TATGTTTCTC
4415413 TTAATGATATCTTGCCATCACCATGCATTT
1 TTAATGATATCTTGCCATCACCATGCATTT
4415443 TTAATGATATCTTGCCATCACCATGCATTT
1 TTAATGATATCTTGCCATCACCATGCATTT
4415473 GTTCTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (30 bp):
TTAATGATATCTTGCCATCACCATGCATTT
Found at i:4417107 original size:79 final size:79
Alignment explanation
Indices: 4416771--4417108 Score: 273
Period size: 79 Copynumber: 4.3 Consensus size: 79
4416761 TTTTACATTC
* * *
4416771 AGGGATAC-TCAAACCTCAGTTTT-TTTTTAAAACACCAATTTTCCACTATC-AGGATACTCCAA
1 AGGGATACTTC-AACCTCGGTTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAA
* *
4416833 -CCTCATTATTTTCTA
65 CCCT-GTTATTTTCGA
* * * * ** * *
4416848 GGGGATACTTTAACCT-AGTTTTATTTCTAAAATACCAATTTTTTACCATCAAGGATACTCTAAC
1 AGGGATACTTCAACCTCGGTTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAAC
* *
4416912 CCCGTTATTTCCGA
66 CCTGTTATTTTCGA
* * * ** * *
4416926 AGAGATATTTCAATCC-CGGTTTTATTTCTATAACACTGATTTTTCACAATCAAGGATACTCAAA
1 AGGGATACTTCAA-CCTCGGTTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAA
*
4416990 CTCC-GTTA-TTTCTAA
65 C-CCTGTTATTTTC-GA
* * * *
4417005 AGGGATACTTCAACC-CTGGTTTTATTTCTATAACATCGATTTTCCATC-ATCGAGGATACTCCA
1 AGGGATACTTCAACCTC-GGTTTTATTTCTAAAACACCAATTTTCCA-CAATCAAGGATACTCCA
4417068 ACCCTGTTATTTTCGA
64 ACCCTGTTATTTTCGA
* * *
4417084 GGGGATACTCCAACCTCGTTTTTAT
1 AGGGATACTTCAACCTCGGTTTTAT
4417109 CTCCAAAATA
Statistics
Matches: 211, Mismatches: 37, Indels: 24
0.78 0.14 0.09
Matches are distributed among these distances:
76 6 0.03
77 34 0.16
78 37 0.18
79 126 0.60
80 8 0.04
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.37
Consensus pattern (79 bp):
AGGGATACTTCAACCTCGGTTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAAC
CCTGTTATTTTCGA
Found at i:4417107 original size:158 final size:155
Alignment explanation
Indices: 4416771--4417108 Score: 342
Period size: 158 Copynumber: 2.2 Consensus size: 155
4416761 TTTTACATTC
* * *
4416771 AGGGATACTCAAACCTCAGTTTTT-TTTTAAAACACCAATTTTCCACTATCAGGATACTCCAACC
1 AGGGATACTCCAACCTC-GTTTTTATTTTAAAACACCAATTTTCCACAATCAGGATACTCAAACC
* * * **
4416835 TCATTATTTTCTAGGGGATACTTTAACCTAGTTTTATTTCTAAAATACCAATTTTTTACCATCAA
65 TCATTATTTTCTAAGGGATACTTCAACCTAGTTTTATTTCTAAAACACCAATTTTCCACCATCAA
*
4416900 GGATACTCTAACCCCGTTATTTCCGA
130 GGATACTCCAACCCCGTTATTTCCGA
* * * * * ** *
4416926 AGAGATATTTCAATCC-CGGTTTTATTTCTATAACACTGATTTTTCACAATCAAGGATACTCAAA
1 AGGGATACTCCAA-CCTCGTTTTTATTT-TAAAACACCAATTTTCCACAATC-AGGATACTCAAA
* * * * * *
4416990 -CTCCGTTA-TTTCTAAAGGGATACTTCAACCCTGGTTTTATTTCTATAACATCGATTTTCCATC
63 CCT-CATTATTTTCT-AAGGGATACTTCAA-CCTAGTTTTATTTCTAAAACACCAATTTTCCACC
* * *
4417053 ATCGAGGATACTCCAACCCTGTTATTTTCGA
125 ATCAAGGATACTCCAACCCCGTTATTTCCGA
*
4417084 GGGGATACTCCAACCTCGTTTTTAT
1 AGGGATACTCCAACCTCGTTTTTAT
4417109 CTCCAAAATA
Statistics
Matches: 144, Mismatches: 31, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
154 5 0.03
155 13 0.09
156 27 0.19
157 29 0.20
158 70 0.49
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.37
Consensus pattern (155 bp):
AGGGATACTCCAACCTCGTTTTTATTTTAAAACACCAATTTTCCACAATCAGGATACTCAAACCT
CATTATTTTCTAAGGGATACTTCAACCTAGTTTTATTTCTAAAACACCAATTTTCCACCATCAAG
GATACTCCAACCCCGTTATTTCCGA
Found at i:4420489 original size:22 final size:22
Alignment explanation
Indices: 4420454--4420495 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4420444 TAAAGTGTAA
4420454 GACTGCATCAAGAAACTAGCTT
1 GACTGCATCAAGAAACTAGCTT
* * *
4420476 GACTGCCTCCAGAATCTAGC
1 GACTGCATCAAGAAACTAGC
4420496 ACAGTTCCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (22 bp):
GACTGCATCAAGAAACTAGCTT
Found at i:4424796 original size:18 final size:20
Alignment explanation
Indices: 4424757--4424801 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
4424747 AAAAATTTCA
4424757 ATAATATAAAACTTAAAAAT
1 ATAATATAAAACTTAAAAAT
4424777 ATAATA-AAAA-TTAAAAAT
1 ATAATATAAAACTTAAAAAT
*
4424795 ATCATAT
1 ATAATAT
4424802 TTTTATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 6 0.26
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAATATAAAACTTAAAAAT
Found at i:4425116 original size:8 final size:8
Alignment explanation
Indices: 4425088--4425134 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
4425078 GATTATATCT
*
4425088 TTTATATA
1 TTTATAAA
4425096 TTTA-AAA
1 TTTATAAA
4425103 TATTATAAA
1 T-TTATAAA
*
4425112 TTTATAAG
1 TTTATAAA
4425120 TGTTATAAA
1 T-TTATAAA
4425129 TTTATA
1 TTTATA
4425135 TATATAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 3 0.09
8 19 0.58
9 11 0.33
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (8 bp):
TTTATAAA
Found at i:4425164 original size:18 final size:18
Alignment explanation
Indices: 4425149--4425185 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4425139 TAAATTTTAA
4425149 TATATTT-TA-TATTTTT
1 TATATTTATATTATTTTT
4425165 TATATTTATATTATTTTT
1 TATATTTATATTATTTTT
4425183 TAT
1 TAT
4425186 CTCATTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 10 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TATATTTATATTATTTTT
Found at i:4425257 original size:21 final size:21
Alignment explanation
Indices: 4425233--4425272 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4425223 TATCATATCT
*
4425233 TAATTTATTATATATTTTATA
1 TAATTTATCATATATTTTATA
4425254 TAATTTATCATATATTTTA
1 TAATTTATCATATATTTTA
4425273 ATTTTAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATTTATCATATATTTTATA
Found at i:4426791 original size:16 final size:17
Alignment explanation
Indices: 4426772--4426804 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4426762 AATTTATTTA
4426772 AAAATTAA-TTAAAAAT
1 AAAATTAATTTAAAAAT
4426788 AAAATTAATTTAAAAAT
1 AAAATTAATTTAAAAAT
4426805 TGATCACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAATTTAAAAAT
Found at i:4434458 original size:26 final size:24
Alignment explanation
Indices: 4434415--4434479 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
4434405 ATGTTTCTAT
* *
4434415 TATTTTTTATTTG-CTTTATTTTA
1 TATTTTTTATTTGTTTTTAATTTA
4434438 TATTATTTTATTTAGTTTTTAATTTA
1 TATT-TTTTATTT-GTTTTTAATTTA
4434464 TATTTTTTATTTGTTT
1 TATTTTTTATTTGTTT
4434480 GTTGGAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.11
24 12 0.32
25 9 0.24
26 12 0.32
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.74
Consensus pattern (24 bp):
TATTTTTTATTTGTTTTTAATTTA
Found at i:4436724 original size:2 final size:2
Alignment explanation
Indices: 4436717--4436755 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4436707 TTTAGTTGTT
4436717 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4436756 TCTTTTTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4436892 original size:2 final size:2
Alignment explanation
Indices: 4436885--4436914 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4436875 TCTTGATTCC
4436885 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4436915 GTTTGCTTAA
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):
AT
Found at i:4439006 original size:80 final size:81
Alignment explanation
Indices: 4438888--4439091 Score: 211
Period size: 80 Copynumber: 2.5 Consensus size: 81
4438878 GTTAGTATTA
* * * * * * *
4438888 TCTCAGTCTACCTTTTTAACTTATTGACTT-TTAGGTTTCATCCT-GGTCAATCTTTCTTATTTG
1 TCTCAGTCAACCTTTCTCATTTATTGACTTGTTA-GTTTCATCCTCGATCAACCTTTCTTATTCG
* *
4438951 TTGGCTTGCCAATTTTG
65 TTGACCTGCCAATTTTG
* *
4438968 ATCT-AGTCAACGCTTT-TCATTTGTTGACTTGTTAGTTTCAT-CTCGATCAACCTTTTTTATTC
1 -TCTCAGTCAAC-CTTTCTCATTTATTGACTTGTTAGTTTCATCCTCGATCAACCTTTCTTATTC
*
4439030 GTTGACCTGTCAATTTTG
64 GTTGACCTGCCAATTTTG
* * *
4439048 TCTCGGTCAGCCTTTCTCATTTATTGACTTGTTAGTTTTATCCT
1 TCTCAGTCAACCTTTCTCATTTATTGACTTGTTAGTTTCATCCT
4439092 AGTAAACCGC
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
79 9 0.09
80 81 0.79
81 12 0.12
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.49
Consensus pattern (81 bp):
TCTCAGTCAACCTTTCTCATTTATTGACTTGTTAGTTTCATCCTCGATCAACCTTTCTTATTCGT
TGACCTGCCAATTTTG
Found at i:4439018 original size:40 final size:39
Alignment explanation
Indices: 4438974--4439085 Score: 107
Period size: 40 Copynumber: 2.8 Consensus size: 39
4438964 TTTGATCTAG
4438974 TCAACGCTTTTCATTTGTTGACTTGTTAGTTTCATCTCGA
1 TCAAC-CTTTTCATTTGTTGACTTGTTAGTTTCATCTCGA
* * * * * ** *
4439014 TCAACCTTTTTTATTCGTTGACCTGTCAATTTTGTCTCGG
1 TCAACC-TTTTCATTTGTTGACTTGTTAGTTTCATCTCGA
* *
4439054 TCAGCCTTTCTCATTTATTGACTTGTTAGTTT
1 TCAACCTTT-TCATTTGTTGACTTGTTAGTTT
4439086 TATCCTAGTA
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
39 4 0.07
40 51 0.93
ACGTcount: A:0.16, C:0.21, G:0.14, T:0.49
Consensus pattern (39 bp):
TCAACCTTTTCATTTGTTGACTTGTTAGTTTCATCTCGA
Found at i:4439349 original size:65 final size:65
Alignment explanation
Indices: 4439274--4439415 Score: 198
Period size: 65 Copynumber: 2.2 Consensus size: 65
4439264 TAGCTAATCC
* * *
4439274 TTTCTGACTTAGGTTTCATCCTAATCACTCTTAGTTGACTATTTTGGTTGCACCTCGATCAA-CC
1 TTTCAGACTTAGGTTTCATCCTAATCACCCTTAGATGACTATTTTGGTTGCACCTCG-TCAACCC
4439338 T
65 T
* * * *
4439339 TTTCAGACTTAGGTTTCATCCTAGTCACCCTTAGATGACTATTTTGGTTTCGCCTTGTCAACCCT
1 TTTCAGACTTAGGTTTCATCCTAATCACCCTTAGATGACTATTTTGGTTGCACCTCGTCAACCCT
4439404 TTT-AGACTTAGG
1 TTTCAGACTTAGG
4439416 ATGAATCCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 13 0.19
65 56 0.81
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (65 bp):
TTTCAGACTTAGGTTTCATCCTAATCACCCTTAGATGACTATTTTGGTTGCACCTCGTCAACCCT
Found at i:4439429 original size:64 final size:65
Alignment explanation
Indices: 4439291--4439434 Score: 175
Period size: 65 Copynumber: 2.2 Consensus size: 65
4439281 CTTAGGTTTC
* * * * **
4439291 ATCCTAATCACTCTTAGTTGACTATTTTGGTTGCACCTCGATCAACCTTTTCAGACTTAGGTTTC
1 ATCCTAGTCACCCTTAGATGACTATTTTGGTTGCACCTCGATCAACCTTTTCAGACTTAGGATGA
* * *
4439356 ATCCTAGTCACCCTTAGATGACTATTTTGGTTTCGCCTTG-TCAACCCTTTT-AGACTTAGGATG
1 ATCCTAGTCACCCTTAGATGACTATTTTGGTTGCACCTCGATCAA-CCTTTTCAGACTTAGGATG
4439419 A
65 A
4439420 ATCCTAGTCATCCCT
1 ATCCTAGTCA-CCCT
4439435 GTTTGATTGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 24 0.35
65 44 0.65
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.38
Consensus pattern (65 bp):
ATCCTAGTCACCCTTAGATGACTATTTTGGTTGCACCTCGATCAACCTTTTCAGACTTAGGATGA
Found at i:4439458 original size:64 final size:65
Alignment explanation
Indices: 4439385--4439540 Score: 171
Period size: 64 Copynumber: 2.4 Consensus size: 65
4439375 GACTATTTTG
*
4439385 GTTTCGCCTT-GTCAACCCTTTTAGACTTAGGATGA-ATCCTAGTCATCC-CTGTTTGATTGTAT
1 GTTTTGCCTTGGTCAACCCTTTTAGACTTAGG-TGACATCCTAGTCATCCTC-GTTTGATTGTAT
4439447 CGA
64 -GA
* * * * *
4439450 -TTTTGCCTTGGTCAACCCTCTT-GACCTAGGTTACATCCTGGTCATCCTCGTTTGATTGTATTA
1 GTTTTGCCTTGGTCAACCCTTTTAGACTTAGGTGACATCCTAGTCATCCTCGTTTGATTGTATGA
* *
4439513 GTTTTGCCTTGGT-TAGCCTTTTAGACTT
1 GTTTTGCCTTGGTCAACCCTTTTAGACTT
4439541 TGGTTTCACC
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
63 9 0.12
64 55 0.72
65 12 0.16
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (65 bp):
GTTTTGCCTTGGTCAACCCTTTTAGACTTAGGTGACATCCTAGTCATCCTCGTTTGATTGTATGA
Found at i:4440804 original size:24 final size:24
Alignment explanation
Indices: 4440771--4440816 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4440761 ATTACTATTA
*
4440771 ATTTTAATTTTCTTTTAATTTTAG
1 ATTTTAATTTTATTTTAATTTTAG
* *
4440795 ATTTTTATTTTATTTTATTTTT
1 ATTTTAATTTTATTTTAATTTT
4440817 TAACTAGTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (24 bp):
ATTTTAATTTTATTTTAATTTTAG
Found at i:4443354 original size:20 final size:20
Alignment explanation
Indices: 4443299--4443354 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
4443289 ATACACATGT
*
4443299 AAATGTATCGATACAATTCAC
1 AAATGTATCGATAC-ATCCAC
*
4443320 -AATGTATTGATACATCCAC
1 AAATGTATCGATACATCCAC
4443339 AAATGTATCGATACAT
1 AAATGTATCGATACAT
4443355 TGAGTTCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATCCAC
Found at i:4444161 original size:33 final size:33
Alignment explanation
Indices: 4444123--4444189 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
4444113 ATTACAAGCT
4444123 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
*
4444156 ATGTATCGCTACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
4444189 A
1 A
4444190 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:4446719 original size:13 final size:13
Alignment explanation
Indices: 4446694--4446735 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
4446684 AAATAGTACC
*
4446694 CAATGTATTGATA
1 CAATGTATCGATA
*
4446707 CATTGTATCGATA
1 CAATGTATCGATA
4446720 CAATGTATCGATA
1 CAATGTATCGATA
4446733 CAA
1 CAA
4446736 GAAATGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:4450554 original size:9 final size:9
Alignment explanation
Indices: 4450542--4450576 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
4450532 TTCATTCGAG
4450542 TCATCATCT
1 TCATCATCT
4450551 TCATCATCAT
1 TCATCATC-T
4450561 T-ATCATCT
1 TCATCATCT
4450569 TCATCATC
1 TCATCATC
4450577 GTTGATGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 20 0.83
10 2 0.08
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (9 bp):
TCATCATCT
Found at i:4452186 original size:13 final size:13
Alignment explanation
Indices: 4452168--4452199 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4452158 TACATTTCTT
4452168 AATGTATCGATAC
1 AATGTATCGATAC
4452181 AATGTATCGATAC
1 AATGTATCGATAC
*
4452194 ATTGTA
1 AATGTA
4452200 CCATGTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:4452288 original size:19 final size:19
Alignment explanation
Indices: 4452244--4452299 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4452234 CTGCCAGTTT
***
4452244 CATGTATCGATACAATTTTC
1 CATGTATCGATACAA-TGAA
4452264 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
4452283 CATGTATCAATACAATG
1 CATGTATCGATACAATG
4452300 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:4453849 original size:16 final size:17
Alignment explanation
Indices: 4453828--4453867 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
4453818 GGATAAAGTG
4453828 AATAAAATGTTACT-AA
1 AATAAAATGTTACTAAA
4453844 AATAAAATGTTACTAAA
1 AATAAAATGTTACTAAA
4453861 AATAAAA
1 AATAAAA
4453868 AAAATCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (17 bp):
AATAAAATGTTACTAAA
Found at i:4454340 original size:19 final size:20
Alignment explanation
Indices: 4454295--4454345 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4454285 CACACCTAGA
*
4454295 TGTATAGATACATATTCCTT
1 TGTATCGATACATATTCCTT
* *
4454315 AGTATCGATACATGTT-CTT
1 TGTATCGATACATATTCCTT
4454334 TGTATCGATACA
1 TGTATCGATACA
4454346 CCATAAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTCCTT
Found at i:4454955 original size:35 final size:35
Alignment explanation
Indices: 4454909--4455008 Score: 148
Period size: 35 Copynumber: 2.9 Consensus size: 35
4454899 CGAAGTGATT
** *
4454909 AAGAGGTTCTATCTTAGTTTTTGTAAAAGATAGAG
1 AAGAGGTTCTATCTTAGCCTTTGTAAAAGATAAAG
* *
4454944 AAGAGGTTCTATCTTGGCCTTTGTTAAAGATAAAG
1 AAGAGGTTCTATCTTAGCCTTTGTAAAAGATAAAG
4454979 AAGAGGTTCTATCTTAGCCTTTG-AAAAGAT
1 AAGAGGTTCTATCTTAGCCTTTGTAAAAGAT
4455009 TGTGTTGTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
34 6 0.10
35 52 0.90
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (35 bp):
AAGAGGTTCTATCTTAGCCTTTGTAAAAGATAAAG
Found at i:4457163 original size:20 final size:19
Alignment explanation
Indices: 4457123--4457166 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4457113 TATTTTAGTG
* *
4457123 TGTATCGATACAATGAATA
1 TGTATCAATACAAAGAATA
4457142 TGTATCAATACAAAGCAATA
1 TGTATCAATACAAAG-AATA
4457162 TGTAT
1 TGTAT
4457167 TGATACATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCAATACAAAGAATA
Found at i:4457172 original size:20 final size:19
Alignment explanation
Indices: 4457123--4457173 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
4457113 TATTTTAGTG
*
4457123 TGTATCGATACAATGAATA
1 TGTATCGATACAAAGAATA
*
4457142 TGTATCAATACAAAGCAATA
1 TGTATCGATACAAAG-AATA
*
4457162 TGTATTGATACA
1 TGTATCGATACA
4457174 TCTGAGTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAGAATA
Found at i:4464360 original size:52 final size:52
Alignment explanation
Indices: 4464303--4464401 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
4464293 CCCGAAATAT
* *
4464303 GAAAATTTGCCTGCATGTATCGATACAAAGAAT-AATGTATTGATACATCTGG
1 GAAAATTTGCATGCATGTATCGATACAAAG-ATCAATGTATCGATACATCTGG
4464355 GAAAATTTGCATGCATGTATCGATACAAAGATCAATGTATCGATACA
1 GAAAATTTGCATGCATGTATCGATACAAAGATCAATGTATCGATACA
4464402 ATGTATCGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.05
52 42 0.95
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (52 bp):
GAAAATTTGCATGCATGTATCGATACAAAGATCAATGTATCGATACATCTGG
Found at i:4464405 original size:13 final size:13
Alignment explanation
Indices: 4464387--4464414 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4464377 ATACAAAGAT
4464387 CAATGTATCGATA
1 CAATGTATCGATA
4464400 CAATGTATCGATA
1 CAATGTATCGATA
4464413 CA
1 CA
4464415 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:4464477 original size:13 final size:13
Alignment explanation
Indices: 4464459--4464510 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
4464449 AGCTTCGTAG
4464459 CGATACATTGTAT
1 CGATACATTGTAT
4464472 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
4464491 CGATACATTGTAT
1 CGATACATTGTAT
4464504 CGATACA
1 CGATACA
4464511 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:4464491 original size:19 final size:19
Alignment explanation
Indices: 4464467--4464529 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
4464457 AGCGATACAT
4464467 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
4464486 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
4464499 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
4464518 TGTGTCGATACA
1 TGTATCGATACA
4464530 GTTACTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 20 0.54
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:4464500 original size:32 final size:32
Alignment explanation
Indices: 4464459--4464529 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
4464449 AGCTTCGTAG
4464459 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
4464491 CGATACATTGTATCGATACAACACTTATGTGT
1 CGATACATTGTATCGATACAACACTTATGTAT
4464523 CGATACA
1 CGATACA
4464530 GTTACTTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:4465779 original size:52 final size:52
Alignment explanation
Indices: 4465677--4465784 Score: 126
Period size: 52 Copynumber: 2.1 Consensus size: 52
4465667 ACCCTAAGTG
* * * *
4465677 AATTGTATCGATGCATGGTAAATTGTATCGATACCTTAAGCCCAAAGGCTAC
1 AATTGTATCGATACATGATAAATTGTATCAATACATTAAGCCCAAAGGCTAC
* * * * * *
4465729 AATTGTATCGATACATTATGAATTGTATCAATACATTGAGTCCAACGGCTAG
1 AATTGTATCGATACATGATAAATTGTATCAATACATTAAGCCCAAAGGCTAC
4465781 AATT
1 AATT
4465785 TTAAATGCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
AATTGTATCGATACATGATAAATTGTATCAATACATTAAGCCCAAAGGCTAC
Found at i:4466241 original size:35 final size:34
Alignment explanation
Indices: 4466193--4466259 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
4466183 CAAAGTGATT
4466193 AAGAGGTTCTATCTTAGCCTTTGTAAAAGATAGGG
1 AAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGGG
*
4466228 AAGAGGTTTTATCTTAGCCTTTGAAAAGATAG
1 AAGAGGTTCTATCTTAGCCTTTGAAAAGATAG
4466260 TGTTGTAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (34 bp):
AAGAGGTTCTATCTTAGCCTTTGAAAAGATAGGG
Found at i:4469394 original size:21 final size:21
Alignment explanation
Indices: 4469370--4469410 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
4469360 ACTTTGGATT
4469370 ATTT-TTACTTGAAAACATATG
1 ATTTGTTACTTGAAAA-ATATG
*
4469391 ATTTGTTGCTTGAAAAATAT
1 ATTTGTTACTTGAAAAATAT
4469411 TTATACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (21 bp):
ATTTGTTACTTGAAAAATATG
Found at i:4477958 original size:33 final size:32
Alignment explanation
Indices: 4477902--4477965 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
4477892 CAATTCAGTG
* *
4477902 TGTATCGATACCAAGAACATGTATCGATACAA
1 TGTAACGATACAAAGAACATGTATCGATACAA
*
4477934 TGTAACGATACAAAGCAATATGTATCGATACA
1 TGTAACGATACAAAG-AACATGTATCGATACA
4477966 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (32 bp):
TGTAACGATACAAAGAACATGTATCGATACAA
Found at i:4481256 original size:16 final size:17
Alignment explanation
Indices: 4481220--4481257 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
4481210 CTCACCCGCA
*
4481220 AAATACATGTCATGAAT
1 AAATGCATGTCATGAAT
*
4481237 AAATGCATGT-ATGTAT
1 AAATGCATGTCATGAAT
4481253 AAATG
1 AAATG
4481258 TATGCTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (17 bp):
AAATGCATGTCATGAAT
Found at i:4483057 original size:25 final size:23
Alignment explanation
Indices: 4483028--4483088 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
4483018 TCGTTGTTTG
*
4483028 TATAGCAAATGATAAATTGTTCACA
1 TATAGCAAATAAT-AATT-TTCACA
** *
4483053 TATAGTGAATAATCATTTTCACA
1 TATAGCAAATAATAATTTTCACA
*
4483076 TATAGCATATAAT
1 TATAGCAAATAAT
4483089 GGAACTTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
23 16 0.55
24 3 0.10
25 10 0.34
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (23 bp):
TATAGCAAATAATAATTTTCACA
Found at i:4487117 original size:20 final size:20
Alignment explanation
Indices: 4487094--4487131 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4487084 ACAATGAGAA
*
4487094 ATGTATCGATACAATTTCTT
1 ATGTATCAATACAATTTCTT
4487114 ATGTATCAATACAATTTC
1 ATGTATCAATACAATTTC
4487132 CTTCCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (20 bp):
ATGTATCAATACAATTTCTT
Found at i:4487738 original size:23 final size:24
Alignment explanation
Indices: 4487699--4487747 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
4487689 TTATCTAAGT
4487699 AAATAAAATTACAAATT-TAATTA
1 AAATAAAATTACAAATTCTAATTA
* *
4487722 AAATTAAATTA-AGAATTCTGATTA
1 AAATAAAATTACA-AATTCTAATTA
4487746 AA
1 AA
4487748 TTTCTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 14 0.64
24 7 0.32
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAAATTACAAATTCTAATTA
Found at i:4489410 original size:37 final size:37
Alignment explanation
Indices: 4489296--4489412 Score: 101
Period size: 40 Copynumber: 3.1 Consensus size: 37
4489286 ATTAAACAAC
*
4489296 ATACTAAAATGACC-TAAAGATTTGGTTTTGACATGAAA
1 ATACTAAAA--ACCTTAAAGATTTGATTTTGACATGAAA
* * * * * **
4489334 ATGCAAAACTAACCCTAAAAGACTCGATTTTGATGTGAAA
1 ATACTAAA--AA-CCTTAAAGATTTGATTTTGACATGAAA
*
4489374 GTACTAAAAACCTTAAAGATTTGATTTTGACATGAAA
1 ATACTAAAAACCTTAAAGATTTGATTTTGACATGAAA
4489411 AT
1 AT
4489413 GCAAAACTAA
Statistics
Matches: 58, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
37 23 0.40
38 9 0.16
39 2 0.03
40 24 0.41
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (37 bp):
ATACTAAAAACCTTAAAGATTTGATTTTGACATGAAA
Found at i:4491320 original size:27 final size:26
Alignment explanation
Indices: 4491290--4491420 Score: 63
Period size: 27 Copynumber: 4.8 Consensus size: 26
4491280 AAGTTTAACA
4491290 AAAAATTTAATTAAAAATTCTATGTCT
1 AAAAATTTAATTAAAAATTCTATGT-T
* * *
4491317 AAAAAGTTAAATTGAAAGA-CCT-TGTAAAT
1 AAAAA-TTTAATT-AAAAATTCTATGT---T
* *
4491346 AATAAAGTTTAATTGAAAATTCCGCATG-T
1 AA-AAA-TTTAATTAAAAATT-C-TATGTT
* *
4491375 AAAAGTTTTATT-AAAATTCTATGTGT
1 AAAAATTTAATTAAAAATTCTATGT-T
*
4491401 AAAAGTTTAATTAAAAATTC
1 AAAAATTTAATTAAAAATTC
4491421 CATTTATGAT
Statistics
Matches: 79, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
24 3 0.04
25 1 0.01
26 18 0.23
27 21 0.27
28 10 0.13
29 13 0.16
30 10 0.13
31 1 0.01
33 2 0.03
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (26 bp):
AAAAATTTAATTAAAAATTCTATGTT
Found at i:4491390 original size:26 final size:27
Alignment explanation
Indices: 4491349--4491422 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
4491339 TGTAAATAAT
* *
4491349 AAAGTTTAATTGAAAATTCCGCATGTA
1 AAAGTTTAATTAAAAATTCCACATGTA
* * **
4491376 AAAGTTTTATT-AAAATTCTATGTGTA
1 AAAGTTTAATTAAAAATTCCACATGTA
4491402 AAAGTTTAATTAAAAATTCCA
1 AAAGTTTAATTAAAAATTCCA
4491423 TTTATGATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (27 bp):
AAAGTTTAATTAAAAATTCCACATGTA
Found at i:4491527 original size:30 final size:29
Alignment explanation
Indices: 4491493--4491549 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
4491483 TTAGGCCTAT
*
4491493 TTGACTTTTCCAACCAATTTTGATTAAAGG
1 TTGACTTTTCCAAACAA-TTTGATTAAAGG
* *
4491523 TTGACTTTTTCAAATAATTTGATTAAA
1 TTGACTTTTCCAAACAATTTGATTAAA
4491550 AATTGATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (29 bp):
TTGACTTTTCCAAACAATTTGATTAAAGG
Found at i:4491555 original size:29 final size:30
Alignment explanation
Indices: 4491493--4491555 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
4491483 TTAGGCCTAT
* **
4491493 TTGACTTTTCCAACCAATTTTGATTAAAGG
1 TTGACTTTTCCAAACAATTTTGATTAAAAA
* *
4491523 TTGACTTTTTCAAATAA-TTTGATTAAAAA
1 TTGACTTTTCCAAACAATTTTGATTAAAAA
4491552 TTGA
1 TTGA
4491556 TTTCTACGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (30 bp):
TTGACTTTTCCAAACAATTTTGATTAAAAA
Found at i:4493197 original size:2 final size:2
Alignment explanation
Indices: 4493176--4493212 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4493166 GGACATCCAC
4493176 AT AT AT -T AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4493213 TTCTATAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:4497091 original size:3 final size:3
Alignment explanation
Indices: 4497083--4497135 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
4497073 TTAAGTTGAA
4497083 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4497131 ATT AT
1 ATT AT
4497136 CTGTTCAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.