Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 118 of 295
Found at i:40630464 original size:29 final size:28
Alignment explanation
Indices: 40630387--40630465 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
40630377 AAAGTTTAAG
*
40630387 ATTTTTTTACTTTTAGAATTTAGTCTTT
1 ATTTTTTTAATTTTAGAATTTAGTCTTT
* *
40630415 ATTTTTTTATTTTTAATAATTTAGTCTTT
1 ATTTTTTTAATTTT-AGAATTTAGTCTTT
40630444 -TTACTTTTTAAATTTTA-AATTT
1 ATT--TTTTT-AATTTTAGAATTT
40630466 TAGATTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 15 0.34
29 18 0.41
30 6 0.14
31 5 0.11
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (28 bp):
ATTTTTTTAATTTTAGAATTTAGTCTTT
Found at i:40640013 original size:21 final size:21
Alignment explanation
Indices: 40639989--40640038 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
40639979 TTTGTTAGAA
40639989 AATATTTATTTTGATGT-TTTC
1 AATATTTATTTT-ATGTATTTC
*
40640010 AATATTT-TTTTATGTATTTT
1 AATATTTATTTTATGTATTTC
40640030 ATATATTTA
1 A-ATATTTA
40640039 AAAATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 13 0.52
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (21 bp):
AATATTTATTTTATGTATTTC
Found at i:40641591 original size:40 final size:41
Alignment explanation
Indices: 40641517--40641650 Score: 180
Period size: 41 Copynumber: 3.3 Consensus size: 41
40641507 TTAATTATAA
* * *
40641517 CCTAAATTGCACTTATGTGCCCTTGTTTGCACTTCGATACC
1 CCTAAATTGCACTTACGTGCCCTTGTTTGTACTTCGGTACC
** * * * *
40641558 TTTGAATTGCACTTA-GTGCCCCTATTTGTACTTCGGTGCC
1 CCTAAATTGCACTTACGTGCCCTTGTTTGTACTTCGGTACC
40641598 CCTAAATTGCACTTACGTGCCCTTGTTTGTACTTCGGTACC
1 CCTAAATTGCACTTACGTGCCCTTGTTTGTACTTCGGTACC
40641639 CCTAAATTGCAC
1 CCTAAATTGCAC
40641651 ATACATGCTC
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 32 0.41
41 46 0.59
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (41 bp):
CCTAAATTGCACTTACGTGCCCTTGTTTGTACTTCGGTACC
Found at i:40641598 original size:20 final size:20
Alignment explanation
Indices: 40641573--40641642 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
40641563 ATTGCACTTA
40641573 GTGCCCCTATTTGTACTTCG
1 GTGCCCCTATTTGTACTTCG
* *
40641593 GTGCCCCTAAATTGCACTTAC-
1 GTGCCCCT-ATTTGTACTT-CG
* *
40641614 GTGCCCTTGTTTGTACTTCG
1 GTGCCCCTATTTGTACTTCG
*
40641634 GTACCCCTA
1 GTGCCCCTA
40641643 AATTGCACAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.03
20 21 0.55
21 15 0.39
22 1 0.03
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.36
Consensus pattern (20 bp):
GTGCCCCTATTTGTACTTCG
Found at i:40641617 original size:21 final size:20
Alignment explanation
Indices: 40641562--40641619 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
40641552 GATACCTTTG
40641562 AATTGCACTTA-GTGCCCCT
1 AATTGCACTTACGTGCCCCT
* *
40641581 ATTTGTACTT-CGGTGCCCCT
1 AATTGCACTTAC-GTGCCCCT
40641601 AAATTGCACTTACGTGCCC
1 -AATTGCACTTACGTGCCC
40641620 TTGTTTGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 8 0.26
20 8 0.26
21 14 0.45
22 1 0.03
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (20 bp):
AATTGCACTTACGTGCCCCT
Found at i:40643310 original size:47 final size:47
Alignment explanation
Indices: 40643239--40643735 Score: 841
Period size: 47 Copynumber: 10.6 Consensus size: 47
40643229 CCCTTCGGGA
* * * * * *
40643239 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40643286 CCTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40643333 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40643380 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40643427 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40643474 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40643521 CTTATCACATATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
40643568 CTTCTCACATATATACACTTTCACATTCCTCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40643615 CTTATCACATATATACACTTTCACATTCGTCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40643662 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40643709 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
40643736 TATTCAAATA
Statistics
Matches: 429, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 429 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40646571 original size:30 final size:30
Alignment explanation
Indices: 40646537--40646595 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
40646527 GTGTCTTCCA
40646537 GCCGTGTGTGACATACGGCCATGCGACACG
1 GCCGTGTGTGACATACGGCCATGCGACACG
*
40646567 GCCGTGTGTGACATAGGGCCATGCGACAC
1 GCCGTGTGTGACATACGGCCATGCGACAC
40646596 AACCATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.20, C:0.29, G:0.34, T:0.17
Consensus pattern (30 bp):
GCCGTGTGTGACATACGGCCATGCGACACG
Found at i:40646609 original size:30 final size:30
Alignment explanation
Indices: 40646545--40646612 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
40646535 CAGCCGTGTG
** * * *
40646545 TGACATACGGCCATGCGACACGGCCGTGTG
1 TGACATACGGCCATGCGACACAACCATATA
*
40646575 TGACATAGGGCCATGCGACACAACCATATA
1 TGACATACGGCCATGCGACACAACCATATA
40646605 TGACATAC
1 TGACATAC
40646613 AGCTATGTGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (30 bp):
TGACATACGGCCATGCGACACAACCATATA
Found at i:40648878 original size:40 final size:39
Alignment explanation
Indices: 40648814--40649024 Score: 255
Period size: 40 Copynumber: 5.3 Consensus size: 39
40648804 TCTTCGGAAT
* *
40648814 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGGGTC
*
40648853 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
40648893 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
40648933 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * *
40648973 TTAGCCCGGATAAAATCACTAGCACAATTGCCTT-GGGAC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
40649012 TTAGCCCGGATAT
1 TTAGCCCGGATAT
40649025 CATTCAAATG
Statistics
Matches: 147, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
38 1 0.01
39 24 0.16
40 115 0.78
41 7 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
TTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGTC
Found at i:40648941 original size:80 final size:80
Alignment explanation
Indices: 40648814--40649024 Score: 336
Period size: 80 Copynumber: 2.7 Consensus size: 80
40648804 TCTTCGGAAT
* * * * *
40648814 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
40648878 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* *
40648893 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
40648958 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
*
40648973 TTAGCCCGGATAAAATCACTAGCACAATTGCCTT-GGGACTTAGCCCGGATAT
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
40649025 CATTCAAATG
Statistics
Matches: 121, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
79 19 0.16
80 102 0.84
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCAC
AAATGCCTTCGGGTC
Found at i:40651578 original size:53 final size:53
Alignment explanation
Indices: 40651493--40651699 Score: 189
Period size: 53 Copynumber: 3.8 Consensus size: 53
40651483 TTCTTTTTTA
* * *
40651493 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
* * * * *
40651546 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATTG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-TG
** * * * * * * * * *
40651600 TAGTTTATCAATGTCATGTCTTCATATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
* * *
40651655 AACTTACCAATGCCATGCCTTGGCATGTTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
40651700 AAACCCTTAT
Statistics
Matches: 117, Mismatches: 34, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
53 45 0.38
54 36 0.31
55 36 0.31
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
Found at i:40659048 original size:53 final size:55
Alignment explanation
Indices: 40658980--40659186 Score: 159
Period size: 53 Copynumber: 3.8 Consensus size: 55
40658970 TTCCTTTTTA
** *
40658980 AACTTACCATTTCCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTAT-G-
1 AACTTACCATTTCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATCGT
* * * * *
40659033 AACTCACCATTTCCATGCCTTGGCATGGTTTTACATGGGATCTTTGCCTTATCGT
1 AACTTACCATTTCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATCGT
** * * * *** * **
40659088 AGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGT-AA
1 AACTTACCATTTCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATCGT
* * * * * * *
40659142 AACTTACCAATGCCATGCCTTGGCACGGTCTTACTTGGTATCCTT
1 AACTTACCATTTCCATGTCTTGACATGGTCTTACATGGGATCCTT
40659187 AAACTCTAAT
Statistics
Matches: 119, Mismatches: 33, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 44 0.37
54 37 0.31
55 38 0.32
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (55 bp):
AACTTACCATTTCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATCGT
Found at i:40659135 original size:55 final size:53
Alignment explanation
Indices: 40658992--40659186 Score: 165
Period size: 55 Copynumber: 3.6 Consensus size: 53
40658982 CTTACCATTT
** * *
40658992 CCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTATGAACTCACCATTT
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
* * * * * ** * *
40659045 CCATGCCTTGGCATGGTTTTACATGGGATCTTTGCCTTATCGTAGTTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G-AACTCACCAATG
* * * * *
40659100 CCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATG
* * * *
40659154 CCATGCCTTGGCACGGTCTTACTTGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGTATCCTT
40659187 AAACTCTAAT
Statistics
Matches: 108, Mismatches: 32, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
53 33 0.31
54 37 0.34
55 38 0.35
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
Found at i:40661220 original size:32 final size:32
Alignment explanation
Indices: 40661179--40661285 Score: 126
Period size: 32 Copynumber: 3.3 Consensus size: 32
40661169 GAGGAATATA
40661179 GTTATCATTTAACAAAATTAAAATTGATATTT
1 GTTATCATTTAACAAAATTAAAATTGATATTT
* *
40661211 GTTATCATTTTACAAAATTAAAGTTG-TAATTT
1 GTTATCATTTAACAAAATTAAAATTGAT-ATTT
* * * * *
40661243 GTTATCATTTCATAAAATGAAAAGATAATATTT
1 GTTATCATTTAACAAAATTAAAA-TTGATATTT
40661276 GTTATCATTT
1 GTTATCATTT
40661286 CACAGAACTG
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
31 1 0.02
32 47 0.73
33 15 0.23
34 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (32 bp):
GTTATCATTTAACAAAATTAAAATTGATATTT
Found at i:40662242 original size:17 final size:16
Alignment explanation
Indices: 40662200--40662246 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
40662190 GTGATCGCAT
*
40662200 ACCAAAGAATA-TGAA
1 ACCAAAGAATATTCAA
40662215 ACCAAATAGAATATTACAA
1 ACC-AA-AGAATATT-CAA
40662234 ACCAAAGAATATT
1 ACCAAAGAATATT
40662247 GGTGGCGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.11
16 2 0.07
17 14 0.52
18 3 0.11
19 5 0.19
ACGTcount: A:0.57, C:0.15, G:0.09, T:0.19
Consensus pattern (16 bp):
ACCAAAGAATATTCAA
Found at i:40665521 original size:16 final size:18
Alignment explanation
Indices: 40665488--40665524 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40665478 TAAGTTTGTA
*
40665488 ATATATTATATTATATTT
1 ATATATTATAGTATATTT
40665506 ATATATTAT-GTA-ATTT
1 ATATATTATAGTATATTT
40665522 ATA
1 ATA
40665525 ATATATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATATTATAGTATATTT
Found at i:40666677 original size:17 final size:18
Alignment explanation
Indices: 40666657--40666690 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40666647 AATTTATATC
40666657 TTTTTATGTAT-TTTTTA
1 TTTTTATGTATGTTTTTA
*
40666674 TTTTTATTTATGTTTTT
1 TTTTTATGTATGTTTTT
40666691 CACATGGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTATGTATGTTTTTA
Found at i:40666678 original size:18 final size:18
Alignment explanation
Indices: 40666634--40666681 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
40666624 CTTTCTAAAA
40666634 TTATATTTTTATTAATTT
1 TTATATTTTTATTAATTT
* *
40666652 ATATCTTTTTATGT-ATTT
1 TTATATTTTTAT-TAATTT
40666670 TT-TATTTTTATT
1 TTATATTTTTATT
40666682 TATGTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 8 0.32
18 15 0.60
19 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
TTATATTTTTATTAATTT
Found at i:40667897 original size:22 final size:22
Alignment explanation
Indices: 40667856--40667898 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40667846 ATTTTTTATA
*
40667856 AAATTTTAAAATATATAAATAT
1 AAATTTTAAAATATAAAAATAT
40667878 AAATTTTAAAA-AGTAAAAATA
1 AAATTTTAAAATA-TAAAAATA
40667899 ATACATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATTTTAAAATATAAAAATAT
Found at i:40668127 original size:28 final size:28
Alignment explanation
Indices: 40668094--40668166 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 28
40668084 TTTAAGTTTT
40668094 CTTTTTTCAAAATTTTAAAAACTAAATA
1 CTTTTTTCAAAATTTTAAAAACTAAATA
* **
40668122 CTTTTTTTCAAAAATTTAAAATTTAAATA
1 C-TTTTTTCAAAATTTTAAAAACTAAATA
* *
40668151 CTTTTCTCAAATTTTT
1 CTTTTTTCAAAATTTT
40668167 TTATAAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 13 0.34
29 25 0.66
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (28 bp):
CTTTTTTCAAAATTTTAAAAACTAAATA
Found at i:40668130 original size:29 final size:29
Alignment explanation
Indices: 40668095--40668155 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
40668085 TTAAGTTTTC
*
40668095 TTTTTTCAAAATTTTAAAAACTAAATACT
1 TTTTTTCAAAAATTTAAAAACTAAATACT
**
40668124 TTTTTTCAAAAATTTAAAATTTAAATACT
1 TTTTTTCAAAAATTTAAAAACTAAATACT
40668153 TTT
1 TTT
40668156 CTCAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTTTCAAAAATTTAAAAACTAAATACT
Found at i:40669402 original size:17 final size:17
Alignment explanation
Indices: 40669380--40669416 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
40669370 GGGTTAGGAT
40669380 TTTTTTAAGAATTAAGG
1 TTTTTTAAGAATTAAGG
*
40669397 TTTTTTAAGAATTAGGG
1 TTTTTTAAGAATTAAGG
40669414 TTT
1 TTT
40669417 AGGGTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (17 bp):
TTTTTTAAGAATTAAGG
Found at i:40672942 original size:22 final size:22
Alignment explanation
Indices: 40672917--40672974 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
40672907 CCCGAGTTGA
40672917 TGAACAATAAGCTCTATTGAGC
1 TGAACAATAAGCTCTATTGAGC
**
40672939 TGAAACGGTAAGCTCTATTGAGC
1 TG-AACAATAAGCTCTATTGAGC
* *
40672962 TGAATACTAAGCT
1 TGAACAATAAGCT
40672975 AATACAAGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAACAATAAGCTCTATTGAGC
Found at i:40674542 original size:37 final size:37
Alignment explanation
Indices: 40674448--40674542 Score: 84
Period size: 39 Copynumber: 2.5 Consensus size: 37
40674438 ACACATCAGT
* * *
40674448 TTGGTACCCAGTACCTCATCAGATAATTGAAGCAATAAG
1 TTGGTACCCAGTAACTCATCAGATAATCGAAG--ATAAA
** ** *
40674487 TTGACACCCAGTGTCTCATCAGTTAAATCGAAG-TAAA
1 TTGGTACCCAGTAACTCATCAGAT-AATCGAAGATAAA
40674524 TTGGTACCCAGTAACTCAT
1 TTGGTACCCAGTAACTCAT
40674543 TGAATTAATC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
37 18 0.41
39 19 0.43
40 7 0.16
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (37 bp):
TTGGTACCCAGTAACTCATCAGATAATCGAAGATAAA
Found at i:40675423 original size:17 final size:18
Alignment explanation
Indices: 40675395--40675437 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
40675385 ATCCCTAGCT
*
40675395 TTTCTCCTTTTCTTTCTC
1 TTTCTTCTTTTCTTTCTC
40675413 TTT-TTCTTTTCTTTCTC
1 TTTCTTCTTTTCTTTCTC
40675430 TTTCTTCT
1 TTTCTTCT
40675438 CTGTTTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTCTTTTCTTTCTC
Found at i:40675425 original size:11 final size:12
Alignment explanation
Indices: 40675395--40675434 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
40675385 ATCCCTAGCT
*
40675395 TTTCTCCTTTTC
1 TTTCTCTTTTTC
40675407 TTTCTCTTTTTC
1 TTTCTCTTTTTC
*
40675419 TTT-TCTTTCTC
1 TTTCTCTTTTTC
40675430 TTTCT
1 TTTCT
40675435 TCTCTGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTCTTTTTC
Found at i:40675518 original size:5 final size:5
Alignment explanation
Indices: 40675508--40675542 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
40675498 AATTATTATA
* *
40675508 ATAAT ATAAT AGAAT ATAAA ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
40675543 TAAATATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:40675581 original size:19 final size:17
Alignment explanation
Indices: 40675559--40675596 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
40675549 TTAAGTATTT
40675559 CATATATTATTATTTTATA
1 CATATATT-TTATTTT-TA
40675578 CATATATTTTATTTTTA
1 CATATATTTTATTTTTA
40675595 CA
1 CA
40675597 CGTGTACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (17 bp):
CATATATTTTATTTTTA
Found at i:40681341 original size:23 final size:21
Alignment explanation
Indices: 40681294--40681334 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
40681284 TTTGGTTAAA
40681294 AATTGAATAGAAATGAAGTATG
1 AATTGAATAGAAA-GAAGTATG
40681316 AATTGAGATAGAAA-AAGTA
1 AATTGA-ATAGAAAGAAGTA
40681335 AGTGAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AATTGAATAGAAAGAAGTATG
Found at i:40681688 original size:15 final size:15
Alignment explanation
Indices: 40681665--40681712 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
40681655 TATCAAATTT
40681665 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
40681680 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
40681695 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
40681709 ATAT
1 ATAT
40681713 ATGTTGAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:40682046 original size:23 final size:23
Alignment explanation
Indices: 40682018--40682075 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
40682008 TAATATTCCG
*
40682018 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTAGATATTCT
40682041 GGTGTGTTTGGGTTAGATATTCT
1 GGTGTGTTTGGGTTAGATATTCT
40682064 GGTGTGTTTGGG
1 GGTGTGTTTGGG
40682076 AGGAATCCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.09, C:0.03, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTAGATATTCT
Found at i:40682201 original size:18 final size:19
Alignment explanation
Indices: 40682180--40682220 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40682170 AATGAAATGA
40682180 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
40682198 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
40682217 GAAA
1 GAAA
40682221 ATATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:40684925 original size:14 final size:14
Alignment explanation
Indices: 40684906--40684940 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40684896 AGTAGTAGTA
*
40684906 GAAGGCCTATGTTT
1 GAAGGCCTATGTCT
40684920 GAAGGCCTATGTCT
1 GAAGGCCTATGTCT
40684934 GAAGGCC
1 GAAGGCC
40684941 GGGAAAGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (14 bp):
GAAGGCCTATGTCT
Found at i:40692806 original size:21 final size:20
Alignment explanation
Indices: 40692758--40692814 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
40692748 AACGTCTATT
*
40692758 AATAAT-AAACATATACTTA
1 AATAATAAAACATATACATA
* * *
40692777 TATATTAAAGATATATACATA
1 AATAATAAA-ACATATACATA
40692798 AATAATAAAACATATAC
1 AATAATAAAACATATAC
40692815 TAACAAATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 4 0.14
20 9 0.31
21 16 0.55
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.32
Consensus pattern (20 bp):
AATAATAAAACATATACATA
Found at i:40693387 original size:18 final size:18
Alignment explanation
Indices: 40693366--40693421 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
40693356 GGTATATAAC
40693366 TAATAATATTAAAATATA
1 TAATAATATTAAAATATA
* *
40693384 TAATAGTATATAAAA-ACA
1 TAATAATAT-TAAAATATA
* **
40693402 TAATACTAAAAAAATATA
1 TAATAATATTAAAATATA
40693420 TA
1 TA
40693422 TATATACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (18 bp):
TAATAATATTAAAATATA
Found at i:40693399 original size:20 final size:22
Alignment explanation
Indices: 40693325--40693443 Score: 68
Period size: 22 Copynumber: 5.4 Consensus size: 22
40693315 AGAAATATAC
* *
40693325 AATATAGAAATATACATAC-AAT
1 AATATAAAAATATATA-ACTAAT
*
40693347 AATATAAAAGGTATATAACTAAT
1 AATATAAAA-ATATATAACTAAT
* *
40693370 AATATTAAAATATATAA-TAGT
1 AATATAAAAATATATAACTAAT
* *
40693391 -ATATAAAAACATA-ATACTAAA
1 AATATAAAAATATATA-ACTAAT
* * *
40693412 AAAATATATATATAT-ACATAAT
1 AATATAAAAATATATAAC-TAAT
40693434 ACATATAAAA
1 A-ATATAAAA
40693444 GCAATATATA
Statistics
Matches: 71, Mismatches: 18, Indels: 15
0.68 0.17 0.14
Matches are distributed among these distances:
19 1 0.01
20 12 0.17
21 7 0.10
22 30 0.42
23 21 0.30
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (22 bp):
AATATAAAAATATATAACTAAT
Found at i:40693423 original size:28 final size:31
Alignment explanation
Indices: 40693385--40693455 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 31
40693375 TAAAATATAT
40693385 AATAGTATATAAAAACATAATAC-TA-AAAA-
1 AATA-TATATAAAAACATAATACATATAAAAC
* *
40693414 AATATATATATATACATAATACATATAAAAGC
1 AATATATATAAAAACATAATACATATAAAA-C
40693446 AATATATATA
1 AATATATATA
40693456 TACAATATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 16 0.44
29 6 0.17
30 4 0.11
32 10 0.28
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (31 bp):
AATATATATAAAAACATAATACATATAAAAC
Found at i:40693451 original size:24 final size:25
Alignment explanation
Indices: 40693423--40693482 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
40693413 AAATATATAT
*
40693423 ATATACATAATAC-ATATA-AAAGCA
1 ATATACATAATACAATATAGAAA-AA
*
40693447 ATATATAT-ATACAATATAGAAAAA
1 ATATACATAATACAATATAGAAAAA
*
40693471 ATGTACATAATA
1 ATATACATAATA
40693483 TATGCATCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 4 0.14
24 19 0.66
25 6 0.21
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.28
Consensus pattern (25 bp):
ATATACATAATACAATATAGAAAAA
Found at i:40693563 original size:3 final size:3
Alignment explanation
Indices: 40693555--40693580 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40693545 AAACATTTAC
40693555 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
40693581 TTGGAATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:40709907 original size:16 final size:17
Alignment explanation
Indices: 40709876--40709908 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40709866 ATGTTTAATT
40709876 GAATGTTGAGTTATATG
1 GAATGTTGAGTTATATG
*
40709893 GAATG-TGATTTATATG
1 GAATGTTGAGTTATATG
40709909 ATGTACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.42
Consensus pattern (17 bp):
GAATGTTGAGTTATATG
Found at i:40711228 original size:20 final size:20
Alignment explanation
Indices: 40711203--40711244 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
40711193 GAAACAGAAT
*
40711203 GCTTAGAATTGGGCACATGG
1 GCTTAGAATTGGGCACACGG
40711223 GCTTAGAATTGGGCACACGG
1 GCTTAGAATTGGGCACACGG
40711243 GC
1 GC
40711245 AGAGATACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (20 bp):
GCTTAGAATTGGGCACACGG
Found at i:40716675 original size:21 final size:21
Alignment explanation
Indices: 40716651--40716701 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
40716641 TTTGCCTAAT
* *
40716651 ATGTGAATTGGATTGAATTGA
1 ATGTAAATTGGATTAAATTGA
*
40716672 ATGTAAATTGTATTAAATTGA
1 ATGTAAATTGGATTAAATTGA
40716693 TAT-TAAATT
1 -ATGTAAATT
40716702 CATTCGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (21 bp):
ATGTAAATTGGATTAAATTGA
Found at i:40717169 original size:105 final size:105
Alignment explanation
Indices: 40716982--40717177 Score: 254
Period size: 105 Copynumber: 1.9 Consensus size: 105
40716972 GATACGGGGT
* * *
40716982 TCCCTATTGGCTGTGATCCTGCATGTGTTGCGGACACACCATAGCTGTTACGAGCATCTTGATAT
1 TCCCGATTGGCTGTGATCCTGCATGTGTTGCGGACACACCATAGCTCTTACGAGCATCTCGATAT
* *
40717047 TTGGCTTTCACAAGCTTCCCGTTAATAGCTCTTCAAAGCA
66 ATGGCTCTCACAAGCTTCCCGTTAATAGCTCTTCAAAGCA
* * * *
40717087 TCCCGATTGGTTGTGATCCTGCATGTGTTGTGGACACACTGCA-A-CTCTTATGAGCGTCTCGAT
1 TCCCGATTGGCTGTGATCCTGCATGTGTTGCGGACACAC--CATAGCTCTTACGAGCATCTCGAT
*
40717150 ATATGGCTCTC-CGGAGCTTCCCGTTAAT
64 ATATGGCTCTCAC-AAGCTTCCCGTTAAT
40717178 TATTTCGAGC
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
104 1 0.01
105 74 0.95
106 1 0.01
107 2 0.03
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.33
Consensus pattern (105 bp):
TCCCGATTGGCTGTGATCCTGCATGTGTTGCGGACACACCATAGCTCTTACGAGCATCTCGATAT
ATGGCTCTCACAAGCTTCCCGTTAATAGCTCTTCAAAGCA
Found at i:40717215 original size:34 final size:34
Alignment explanation
Indices: 40717172--40717240 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
40717162 GGAGCTTCCC
40717172 GTTAATTATTTCGAGCTTCCGTTATGGCTCTTAT
1 GTTAATTATTTCGAGCTTCCGTTATGGCTCTTAT
40717206 GTTAATTATTTCGAGCTTCCGTTATGGCTCTTAT
1 GTTAATTATTTCGAGCTTCCGTTATGGCTCTTAT
40717240 G
1 G
40717241 AGCTTCTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.46
Consensus pattern (34 bp):
GTTAATTATTTCGAGCTTCCGTTATGGCTCTTAT
Found at i:40717258 original size:25 final size:25
Alignment explanation
Indices: 40717230--40717311 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
40717220 GCTTCCGTTA
* *
40717230 TGGCTCTTATGAGCTTCTCGATAAT
1 TGGCTCTTATGAGCTTCCCGATAAC
40717255 TGGCTCTTCA-GAGCTTCCCGATAAC
1 TGGCTCTT-ATGAGCTTCCCGATAAC
* *
40717280 TGACTCTTATGAGCTTCCCAATTAA-
1 TGGCTCTTATGAGCTTCCCGA-TAAC
40717305 TGGCTCT
1 TGGCTCT
40717312 CCGGAGCTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.02
25 44 0.90
26 4 0.08
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (25 bp):
TGGCTCTTATGAGCTTCCCGATAAC
Found at i:40717369 original size:24 final size:24
Alignment explanation
Indices: 40717288--40717370 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
40717278 ACTGACTCTT
* * *
40717288 ATGAGCTTCCCAATTAATGGCTCTC
1 ATGAGCTTCCTAA-TATTGGCTCAC
** *
40717313 CGGAGCTTCCTAATATTGGCTCGC
1 ATGAGCTTCCTAATATTGGCTCAC
* * *
40717337 TTGAACTTCCTGATATTGGCTCAC
1 ATGAGCTTCCTAATATTGGCTCAC
40717361 ATGAGCTTCC
1 ATGAGCTTCC
40717371 CGTTTATGTG
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 36 0.78
25 10 0.22
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (24 bp):
ATGAGCTTCCTAATATTGGCTCAC
Found at i:40718594 original size:13 final size:13
Alignment explanation
Indices: 40718576--40718609 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
40718566 GCTGTGTGAG
40718576 CCACATGGCCTGA
1 CCACATGGCCTGA
*
40718589 CCACATGGCCTGG
1 CCACATGGCCTGA
40718602 CCACATGG
1 CCACATGG
40718610 GCGCGTGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (13 bp):
CCACATGGCCTGA
Found at i:40721115 original size:25 final size:25
Alignment explanation
Indices: 40721060--40721130 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
40721050 TGCTAGACAG
*
40721060 AATATGCCACAAAGGCAACATACAT
1 AATACGCCACAAAGGCAACATACAT
* *
40721085 AATACGCCACAAAGGCAATATATA-
1 AATACGCCACAAAGGCAACATACAT
*
40721109 AAGTACGCGACAAAGGCTAACA
1 AA-TACGCCACAAAGGC-AACA
40721131 GGATGCCACA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.05
25 34 0.87
26 3 0.08
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.14
Consensus pattern (25 bp):
AATACGCCACAAAGGCAACATACAT
Found at i:40721143 original size:20 final size:20
Alignment explanation
Indices: 40721118--40721168 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
40721108 AAAGTACGCG
* *
40721118 ACAAAGGCTAACAGGATGCC
1 ACAAAGGCTAACAGAATACC
40721138 ACAAAGGCTAACAGAATACC
1 ACAAAGGCTAACAGAATACC
40721158 ACAAAGGCTAA
1 ACAAAGGCTAA
40721169 ACCAGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.10
Consensus pattern (20 bp):
ACAAAGGCTAACAGAATACC
Found at i:40721347 original size:37 final size:37
Alignment explanation
Indices: 40721295--40721368 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
40721285 AGAACACGTA
*
40721295 GATAACCCCAGTTGATAAATGCAGCTTATCTACCTTT
1 GATAACCCCAATTGATAAATGCAGCTTATCTACCTTT
40721332 GATAACCCCAATTGATAAATGCAGCTTATCTACCTTT
1 GATAACCCCAATTGATAAATGCAGCTTATCTACCTTT
40721369 TCTAGAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.32
Consensus pattern (37 bp):
GATAACCCCAATTGATAAATGCAGCTTATCTACCTTT
Found at i:40725597 original size:20 final size:18
Alignment explanation
Indices: 40725574--40725627 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
40725564 TAAGTCGAAG
40725574 AAAATAAAAATAAAACAACT
1 AAAATAAAAATAAAA-AA-T
*
40725594 AAAAGAAAAATAAAAAAT
1 AAAATAAAAATAAAAAAT
*
40725612 AAAACTAAAACTAAAA
1 AAAA-TAAAAATAAAA
40725628 TCAGTGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.17
19 11 0.37
20 14 0.47
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.13
Consensus pattern (18 bp):
AAAATAAAAATAAAAAAT
Found at i:40725627 original size:24 final size:26
Alignment explanation
Indices: 40725574--40725628 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
40725564 TAAGTCGAAG
*
40725574 AAAATAAAAATAAAACAACTAAAAGA
1 AAAATAAAAATAAAACAACTAAAACA
* *
40725600 AAAATAAAAA-ATAA-AACTAAAACT
1 AAAATAAAAATAAAACAACTAAAACA
40725624 AAAAT
1 AAAAT
40725629 CAGTGGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 3 0.12
26 10 0.38
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (26 bp):
AAAATAAAAATAAAACAACTAAAACA
Found at i:40731038 original size:16 final size:16
Alignment explanation
Indices: 40731017--40731059 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
40731007 AAACCAGAAT
40731017 GAAGAAATCCAAGACA
1 GAAGAAATCCAAGACA
*
40731033 GAAG-AATCCAAGATA
1 GAAGAAATCCAAGACA
*
40731048 -AAGATATCCAAG
1 GAAGAAATCCAAG
40731060 GTACAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 17 0.71
16 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (16 bp):
GAAGAAATCCAAGACA
Found at i:40731057 original size:30 final size:30
Alignment explanation
Indices: 40731018--40731077 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
40731008 AACCAGAATG
40731018 AAGAAATCCAA-G-ACAGAAGAATCCAAGATA
1 AAGAAATCCAAGGTACAG-A-AATCCAAGATA
*
40731048 AAGATATCCAAGGTACAGAAATCCAAGATA
1 AAGAAATCCAAGGTACAGAAATCCAAGATA
40731078 CCATATCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 21 0.78
31 2 0.07
32 4 0.15
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.13
Consensus pattern (30 bp):
AAGAAATCCAAGGTACAGAAATCCAAGATA
Found at i:40731071 original size:15 final size:15
Alignment explanation
Indices: 40731019--40731074 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
40731009 ACCAGAATGA
40731019 AGAAATCCAA-G-AC
1 AGAAATCCAAGGTAC
* *
40731032 AGAAGAATCCAAGATAA
1 AG-A-AATCCAAGGTAC
*
40731049 AGATATCCAAGGTAC
1 AGAAATCCAAGGTAC
40731064 AGAAATCCAAG
1 AGAAATCCAAG
40731075 ATACCATATC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 26 0.79
16 1 0.03
17 3 0.09
ACGTcount: A:0.52, C:0.18, G:0.18, T:0.12
Consensus pattern (15 bp):
AGAAATCCAAGGTAC
Found at i:40733751 original size:48 final size:48
Alignment explanation
Indices: 40733699--40733794 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
40733689 TTTCTTCACT
40733699 AAAATTTATTTATCTCAAAGTACGAGACTTGGATAATGTTCCCATCTC
1 AAAATTTATTTATCTCAAAGTACGAGACTTGGATAATGTTCCCATCTC
40733747 AAAATTTATTTATCTCAAAGTACGAGACTTGGATAATGTTCCCATCTC
1 AAAATTTATTTATCTCAAAGTACGAGACTTGGATAATGTTCCCATCTC
40733795 TTTCTCCTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (48 bp):
AAAATTTATTTATCTCAAAGTACGAGACTTGGATAATGTTCCCATCTC
Found at i:40737170 original size:9 final size:10
Alignment explanation
Indices: 40737127--40737174 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
40737117 ACTAAATAAG
40737127 AAAATAAGTA
1 AAAATAAGTA
40737137 AATAATAAGTA
1 AA-AATAAGTA
*
40737148 AAAATAATACTA
1 AAAAT-A-AGTA
40737160 AAAATAA-TA
1 AAAATAAGTA
40737169 AAAATA
1 AAAATA
40737175 CTAACTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
9 8 0.24
10 6 0.18
11 12 0.35
12 8 0.24
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (10 bp):
AAAATAAGTA
Found at i:40737172 original size:22 final size:22
Alignment explanation
Indices: 40737121--40737190 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
40737111 AAAAGTACTA
* *
40737121 AATAAGAA-AATAAGTAAATAAT
1 AATAAAAATAATAACTAAA-AAT
40737143 AAGTAAAAATAAT-ACTAAAAAT
1 AA-TAAAAATAATAACTAAAAAT
*
40737165 AATAAAAATACTAACTAAAAAT
1 AATAAAAATAATAACTAAAAAT
40737187 AATA
1 AATA
40737191 TGAATAAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.21
22 20 0.48
23 10 0.24
24 3 0.07
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (22 bp):
AATAAAAATAATAACTAAAAAT
Found at i:40737378 original size:53 final size:53
Alignment explanation
Indices: 40737264--40737387 Score: 139
Period size: 52 Copynumber: 2.3 Consensus size: 53
40737254 TCAAAATAGT
* ** * *
40737264 AAACAAA-TAATAATAATAAACTAATGATAAAAAATGAAAATAAAAGAAAAAT
1 AAACAAACAAATAATAATAAACTAACAAGAAAAAATGAAAATAAAAGAAAAAC
40737316 AAA-ATAACAAATAATAAT-AACTAACAAGAAAAAATGAAAATAAATA-AATAAAC
1 AAACA-AACAAATAATAATAAACTAACAAGAAAAAATGAAAATAAA-AGAA-AAAC
40737369 AAACAAACAAATAACTAAT
1 AAACAAACAAATAA-TAAT
40737388 TAAATAATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
51 1 0.02
52 30 0.49
53 25 0.41
54 5 0.08
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.18
Consensus pattern (53 bp):
AAACAAACAAATAATAATAAACTAACAAGAAAAAATGAAAATAAAAGAAAAAC
Found at i:40747622 original size:80 final size:80
Alignment explanation
Indices: 40747450--40747706 Score: 396
Period size: 80 Copynumber: 3.2 Consensus size: 80
40747440 CGGATGATAA
* * *
40747450 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAG-CCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-ACCGGGCTAAGTCCCGAAGGCATTT
*
40747513 GTGCGAGTTACTATAA
65 GTGCGAGTTACTATAT
40747529 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
40747594 TGCGAGTTACTATAT
66 TGCGAGTTACTATAT
40747609 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
* *
40747674 AGCAAG-TAGCTATAT
66 TGCGAGTTA-CTATAT
* *
40747689 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
40747707 TACTTGGTTT
Statistics
Matches: 167, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
79 61 0.37
80 106 0.63
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT
Found at i:40747687 original size:40 final size:40
Alignment explanation
Indices: 40747446--40747673 Score: 397
Period size: 40 Copynumber: 5.7 Consensus size: 40
40747436 TATTCGGATG
* *
40747446 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40747486 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
40747525 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
40747565 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40747605 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
40747645 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
40747674 AGCAAGTAGC
Statistics
Matches: 179, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
39 35 0.20
40 144 0.80
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40747687 original size:120 final size:119
Alignment explanation
Indices: 40747446--40747706 Score: 411
Period size: 119 Copynumber: 2.2 Consensus size: 119
40747436 TATTCGGATG
*
40747446 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
* *
40747511 TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACT
*
40747565 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-TCCGGGCTAAG-CCCGAAGGC
40747629 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCT
64 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTA-CT
* * *
40747685 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
40747707 TACTTGGTTT
Statistics
Matches: 132, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
118 2 0.02
119 65 0.49
120 65 0.49
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACT
Found at i:40755817 original size:40 final size:40
Alignment explanation
Indices: 40755575--40755803 Score: 413
Period size: 40 Copynumber: 5.7 Consensus size: 40
40755565 TATTCGGATG
* *
40755575 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40755615 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40755655 ATAACCGGGCTAAGTCCCGAAGGAATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
40755695 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40755735 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
40755775 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
40755804 AGCAAGTAGC
Statistics
Matches: 181, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 181 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40758557 original size:23 final size:23
Alignment explanation
Indices: 40758530--40758630 Score: 91
Period size: 23 Copynumber: 4.4 Consensus size: 23
40758520 ATAGCTCGGA
*
40758530 AGAGCTTACTATTTCAGCTCATT
1 AGAGCTTACTATTTCAGCTCAAT
* * *
40758553 GGAGCTTACCGA-TTCAGCTTGAA-
1 AGAGCTTA-CTATTTCAGC-TCAAT
*
40758576 GGAGCTTACTATTT-AGCTCAAT
1 AGAGCTTACTATTTCAGCTCAAT
* *
40758598 AGAGCTTACTGTTTTCAACTCAAT
1 AGAGCTTACT-ATTTCAGCTCAAT
40758622 AGAGCTTAC
1 AGAGCTTAC
40758631 CGACCACGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
21 3 0.05
22 14 0.22
23 26 0.41
24 20 0.32
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (23 bp):
AGAGCTTACTATTTCAGCTCAAT
Found at i:40760374 original size:101 final size:101
Alignment explanation
Indices: 40760248--40760442 Score: 288
Period size: 101 Copynumber: 1.9 Consensus size: 101
40760238 TACGTTCATA
*
40760248 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATG-CGATAGCGTAGCTAT-AGTCTTACATAT
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGTC-ATAGCCTAGCTATGA-TCTTACATAT
**
40760311 A-AGCACTGTCATGGTCCAACCAGGGTCTTACATCCATT
64 ATA-CACTACCATGGTCCAACCAGGGTCTTACATCCATT
* *
40760349 GTGCCATAACCTAGTTATGGTCTTATCATCAGAATGTCATAGCCTAGCTATGATCTTAGATATAT
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGTCATAGCCTAGCTATGATCTTACATATAT
*
40760414 ACACTACCATGGTCCAACCATGGTCTTAC
66 ACACTACCATGGTCCAACCAGGGTCTTAC
40760443 GTTTGAATAA
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
101 82 0.96
102 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (101 bp):
GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGTCATAGCCTAGCTATGATCTTACATATAT
ACACTACCATGGTCCAACCAGGGTCTTACATCCATT
Found at i:40762355 original size:33 final size:34
Alignment explanation
Indices: 40762302--40762381 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
40762292 GGTAGTAATC
* *
40762302 AATATGCTTATAACAATTCAATACAATATCAATT
1 AATATGCTTATAACAATTCAATACAATAACAAGT
* * *
40762336 AATATGCTT-TAACAGTTCAATATAGTAACAAGT
1 AATATGCTTATAACAATTCAATACAATAACAAGT
40762369 AATATGCTTATAA
1 AATATGCTTATAA
40762382 TAGATCAGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 28 0.70
34 12 0.30
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (34 bp):
AATATGCTTATAACAATTCAATACAATAACAAGT
Found at i:40769440 original size:23 final size:22
Alignment explanation
Indices: 40769400--40769454 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
40769390 GGGTATCTAT
*
40769400 AAATCAAATC-TCTAATATTAC
1 AAATCATATCTTCTAATATTAC
40769421 AAAATCATATCTTCTAATATTAC
1 -AAATCATATCTTCTAATATTAC
*
40769444 ATATCATATCT
1 AAATCATATCT
40769455 AAGATTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATCATATCTTCTAATATTAC
Found at i:40769465 original size:19 final size:17
Alignment explanation
Indices: 40769425--40769469 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
40769415 TATTACAAAA
*
40769425 TCATATCTTCTAATATT
1 TCATATCTTCTAAGATT
*
40769442 ACATATCATATCTAAGATT
1 TCATATC-T-TCTAAGATT
40769461 TCATATCTT
1 TCATATCTT
40769470 TGAAGATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.30
18 2 0.09
19 14 0.61
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (17 bp):
TCATATCTTCTAAGATT
Found at i:40774554 original size:22 final size:23
Alignment explanation
Indices: 40774527--40774571 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40774517 GGGTATCTAC
40774527 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
40774549 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
40774572 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:40774575 original size:17 final size:17
Alignment explanation
Indices: 40774553--40774602 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
40774543 ATTACAAAAT
40774553 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
40774570 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
*
40774589 CATATCTTCGAAGA
1 CATATCTTCTAAGA
40774603 ACATGTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 12 0.41
18 2 0.07
19 15 0.52
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:40774576 original size:22 final size:22
Alignment explanation
Indices: 40774524--40774581 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
40774514 AAAGGGTATC
*
40774524 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40774545 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
40774568 TACATATCATATCT
1 TACAAATCATATCT
40774582 AAGATTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.58
23 11 0.33
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40774584 original size:19 final size:20
Alignment explanation
Indices: 40774537--40774594 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
40774527 AAATCAAATC
*
40774537 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
40774560 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
*
40774579 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
40774595 TTCGAAGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
22 7 0.21
23 11 0.33
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:40775887 original size:31 final size:31
Alignment explanation
Indices: 40775852--40775919 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
40775842 ATTTTTTTTT
* *
40775852 ATTTTTG-TGCAAATATACACATTAAAGTTTG
1 ATTTTTGTTG-AAATATACACATAAAAGTTTA
*
40775883 ATTTTTGTTGAAATATACACATAAAATTTTA
1 ATTTTTGTTGAAATATACACATAAAAGTTTA
40775914 ATTTTT
1 ATTTTT
40775920 ATTAATTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (31 bp):
ATTTTTGTTGAAATATACACATAAAAGTTTA
Found at i:40779526 original size:21 final size:21
Alignment explanation
Indices: 40779493--40779549 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
40779483 GTGGGGGTCT
*
40779493 ACACGCCCATGTGA-AGGCCAC
1 ACACG-CCGTGTGAGAGGCCAC
*
40779514 ACACGCCTGTGTGGAGAGGGCAC
1 ACACGCC-GTGT-GAGAGGCCAC
40779537 ACAC-CCGTGTGAG
1 ACACGCCGTGTGAG
40779550 CAACCCGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 5 0.16
21 12 0.39
22 4 0.13
23 10 0.32
ACGTcount: A:0.25, C:0.32, G:0.32, T:0.12
Consensus pattern (21 bp):
ACACGCCGTGTGAGAGGCCAC
Found at i:40781685 original size:46 final size:46
Alignment explanation
Indices: 40781635--40781806 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
40781625 TGGTTGAGCA
40781635 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40781681 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40781726 CATCCGAACTCGTTGAGTTGA-TCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
40781773 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40781807 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 20 0.19
46 52 0.49
47 22 0.21
49 4 0.04
50 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40781790 original size:92 final size:93
Alignment explanation
Indices: 40781632--40781801 Score: 306
Period size: 92 Copynumber: 1.8 Consensus size: 93
40781622 GGATGGTTGA
* *
40781632 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40781697 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40781725 GCATCCGAACTCGTTGAGTTGA-TCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40781789 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40781802 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 52 0.70
93 22 0.30
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40787218 original size:46 final size:45
Alignment explanation
Indices: 40787168--40787433 Score: 256
Period size: 46 Copynumber: 5.8 Consensus size: 45
40787158 TGGTTTAGCA
40787168 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
40787214 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
*
40787259 CATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * * *
40787307 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
* *
40787352 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGGGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-GGAATG
* * *
40787400 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40787434 GGGGCGGGTT
Statistics
Matches: 180, Mismatches: 22, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
42 4 0.02
43 10 0.06
45 6 0.03
46 86 0.48
47 56 0.31
48 5 0.03
50 8 0.04
51 5 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:40787324 original size:93 final size:93
Alignment explanation
Indices: 40787165--40787428 Score: 465
Period size: 93 Copynumber: 2.8 Consensus size: 93
40787155 GGATGGTTTA
40787165 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
*
40787230 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCTGAGTTCGTGAGATGTAACTAG
*
40787258 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
40787323 TGAGTCTGAGTTCGTGAGATGTAACTAG
66 TGAGTCTGAGTTCGTGAGATGTAACTAG
* * * * *
40787351 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGGGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
40787416 TGAGTCTGAGTTC
66 TGAGTCTGAGTTC
40787429 ACTTAGGGGC
Statistics
Matches: 163, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 163 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCTGAGTTCGTGAGATGTAACTAG
Found at i:40791176 original size:12 final size:13
Alignment explanation
Indices: 40791159--40791189 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40791149 ATATATTTAC
40791159 TAAGAAAA-TTGT
1 TAAGAAAATTTGT
40791171 TAAGAAAATTTGT
1 TAAGAAAATTTGT
40791184 TAAGAA
1 TAAGAA
40791190 TATATGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
TAAGAAAATTTGT
Found at i:40793875 original size:30 final size:30
Alignment explanation
Indices: 40793841--40793909 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
40793831 GTGTGTCTGA
40793841 GCCGTGTGTGACACACGGTTAGGTTACACG
1 GCCGTGTGTGACACACGGTTAGGTTACACG
40793871 GCCGTGTGTGACACACGGTTAGGTTACACG
1 GCCGTGTGTGACACACGGTTAGGTTACACG
40793901 GCCGTGTGT
1 GCCGTGTGT
40793910 CCCCTGGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (30 bp):
GCCGTGTGTGACACACGGTTAGGTTACACG
Found at i:40798123 original size:16 final size:16
Alignment explanation
Indices: 40798102--40798133 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40798092 CCTGTAACGC
40798102 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
*
40798118 CCCAAATATCCCGAAA
1 CCCAAAAATCCCGAAA
40798134 TCTTAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.38, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:40799387 original size:16 final size:16
Alignment explanation
Indices: 40799366--40799401 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
40799356 ATGAAACGAC
40799366 AAAAGCCGAAATGCCA
1 AAAAGCCGAAATGCCA
*
40799382 AAAAGCCGAAATTCCA
1 AAAAGCCGAAATGCCA
40799398 AAAA
1 AAAA
40799402 TCCAAAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.22, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAAGCCGAAATGCCA
Found at i:40799655 original size:29 final size:29
Alignment explanation
Indices: 40799613--40799724 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 29
40799603 ATAATATGAT
*
40799613 TTGGGCCTAATGGGCAATATGAATGTGAA
1 TTGGGCCTAATGGGCCATATGAATGTGAA
* * * *
40799642 TTGGGTCTAGTGGGCCATAAGAATATGAA
1 TTGGGCCTAATGGGCCATATGAATGTGAA
* * * *
40799671 CTGGGCCAAATGGGCCTTATGAATGAG-A
1 TTGGGCCTAATGGGCCATATGAATGTGAA
* *
40799699 TTGGGCCTAGTGGGCCATATGCATGT
1 TTGGGCCTAATGGGCCATATGAATGT
40799725 ATGTAGGGGT
Statistics
Matches: 64, Mismatches: 19, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
28 21 0.33
29 43 0.67
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATGAATGTGAA
Found at i:40799677 original size:58 final size:57
Alignment explanation
Indices: 40799605--40799717 Score: 154
Period size: 58 Copynumber: 2.0 Consensus size: 57
40799595 GCATGAGTAT
** * * *
40799605 AATATGATTTGGGCCTAATGGGCAATATGAATGTGAATTGGGTCTAGTGGGCCATAAG
1 AATATGAACTGGGCCAAATGGGCAATATGAATGAG-ATTGGGCCTAGTGGGCCATAAG
**
40799663 AATATGAACTGGGCCAAATGGGCCTTATGAATGAGATTGGGCCTAGTGGGCCATA
1 AATATGAACTGGGCCAAATGGGCAATATGAATGAGATTGGGCCTAGTGGGCCATA
40799718 TGCATGTATG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 19 0.40
58 29 0.60
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (57 bp):
AATATGAACTGGGCCAAATGGGCAATATGAATGAGATTGGGCCTAGTGGGCCATAAG
Found at i:40802141 original size:19 final size:19
Alignment explanation
Indices: 40802117--40802154 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40802107 GTCTTGACAT
40802117 GCATAATCGAAGCAAGTTC
1 GCATAATCGAAGCAAGTTC
40802136 GCATAATCGAAGCAAGTTC
1 GCATAATCGAAGCAAGTTC
40802155 TAGAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GCATAATCGAAGCAAGTTC
Found at i:40807856 original size:55 final size:55
Alignment explanation
Indices: 40807727--40807857 Score: 172
Period size: 55 Copynumber: 2.4 Consensus size: 55
40807717 CATGTCCTTA
* *
40807727 GCCCGTGTGCAACACTGACTTCAACACACGGCCATGGCACACGCCCATGTGACCT
1 GCCCGTGTACAACACTGACTTCAACACACGACCATGGCACACGCCCATGTGACCT
* * * * * *
40807782 GCCCGTGTACGATACTGACTTTAAGACACGACCATGGCACACGCCCGTGTGGCCT
1 GCCCGTGTACAACACTGACTTCAACACACGACCATGGCACACGCCCATGTGACCT
* *
40807837 TCCCGTGTACAACAATGACTT
1 GCCCGTGTACAACACTGACTT
40807858 AAAATTTTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.24, C:0.34, G:0.22, T:0.20
Consensus pattern (55 bp):
GCCCGTGTACAACACTGACTTCAACACACGACCATGGCACACGCCCATGTGACCT
Found at i:40810796 original size:13 final size:13
Alignment explanation
Indices: 40810778--40810816 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
40810768 AGGATTTGCT
40810778 TTATCTAAACTAA
1 TTATCTAAACTAA
40810791 TTATCTAAACTAA
1 TTATCTAAACTAA
*
40810804 TTAACTAAACTAA
1 TTATCTAAACTAA
40810817 GAATACACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:40823547 original size:27 final size:27
Alignment explanation
Indices: 40823474--40823540 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 27
40823464 AATTAAAATT
40823474 TTAAAAATTCAA-AAAATTATTTTTTAAAAA
1 TTAAAAATT-AATAAAATTA---TTTAAAAA
40823504 TTAAAAATTAATAAAATTATTTAAAAA
1 TTAAAAATTAATAAAATTATTTAAAAA
40823531 GTATAAAAAT
1 -T-TAAAAAT
40823541 CATAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
27 8 0.24
28 1 0.03
29 9 0.26
30 16 0.47
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
TTAAAAATTAATAAAATTATTTAAAAA
Found at i:40840092 original size:27 final size:27
Alignment explanation
Indices: 40839925--40840102 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
40839915 TAAATTGTAC
*
40839925 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
40839952 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
40839978 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
40840006 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
40840034 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
40840061 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
40840088 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40840103 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:40840093 original size:82 final size:81
Alignment explanation
Indices: 40839922--40840102 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
40839912 GATTAAATTG
* * * *
40839922 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40839987 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
40840003 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40840067 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
40840085 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40840103 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:40843618 original size:21 final size:22
Alignment explanation
Indices: 40843595--40843646 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
40843585 ACCCTTAAAA
*
40843595 CCCTAAATCCCTAACTCTTAAC
1 CCCTAAACCCCTAACTCTTAAC
*
40843617 CCCT-AACCCCTAACTCTTAAT
1 CCCTAAACCCCTAACTCTTAAC
40843638 CCCTAAACC
1 CCCTAAACC
40843647 TTAAATCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.31, C:0.44, G:0.00, T:0.25
Consensus pattern (22 bp):
CCCTAAACCCCTAACTCTTAAC
Found at i:40843864 original size:24 final size:24
Alignment explanation
Indices: 40843837--40843889 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
40843827 ATTATATATG
*
40843837 AAAT-TATTTAATATATAAATTAAA
1 AAATATATTTAA-AAATAAATTAAA
40843861 AAATATATTTAAAAATAAATTAAA
1 AAATATATTTAAAAATAAATTAAA
40843885 AAATA
1 AAATA
40843890 ATTAATCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATATATTTAAAAATAAATTAAA
Found at i:40843874 original size:12 final size:12
Alignment explanation
Indices: 40843851--40843894 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
40843841 TATTTAATAT
40843851 ATAAATTAAAAA
1 ATAAATTAAAAA
* *
40843863 ATATATTTAAAA
1 ATAAATTAAAAA
40843875 ATAAATTAAAAA
1 ATAAATTAAAAA
40843887 AT-AATTAA
1 ATAAATTAA
40843895 TCTAAACCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 6 0.21
12 22 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAATTAAAAA
Found at i:40843986 original size:22 final size:22
Alignment explanation
Indices: 40843945--40844024 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 22
40843935 CCCTAAATCC
*
40843945 CTAACTCTT-AACCCCATAACAT
1 CTAACCCTTAAACCCC-TAACAT
*
40843967 CTAACCCCTAAACCCCTAACCA-
1 CTAACCCTTAAACCCCTAA-CAT
*
40843989 CTAACCTCTTAAA-CCTTAA-AT
1 CTAACC-CTTAAACCCCTAACAT
40844010 CTCAACCCTTAAACC
1 CT-AACCCTTAAACC
40844025 ATAATCCCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 1 0.02
21 8 0.17
22 26 0.54
23 13 0.27
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (22 bp):
CTAACCCTTAAACCCCTAACAT
Found at i:40844052 original size:15 final size:15
Alignment explanation
Indices: 40844016--40844056 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
40844006 AAATCTCAAC
40844016 CCTTAAA-CCATAAT
1 CCTTAAATCCATAAT
*
40844030 CCCT-AATCCATAAT
1 CCTTAAATCCATAAT
40844044 CCTTAAATCCATA
1 CCTTAAATCCATA
40844057 CTCCCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (15 bp):
CCTTAAATCCATAAT
Found at i:40844069 original size:22 final size:22
Alignment explanation
Indices: 40843998--40844072 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
40843988 ACTAACCTCT
*
40843998 TAAACCTTAAATCTCA-AC-CCT
1 TAAACCTTAAATC-CATACTCCA
* * *
40844019 TAAACCAT-AATCCCTAATCCA
1 TAAACCTTAAATCCATACTCCA
* *
40844040 TAATCCTTAAATCCATACTCCC
1 TAAACCTTAAATCCATACTCCA
40844062 TAAACCTTAAA
1 TAAACCTTAAA
40844073 ACAGTAACTC
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 15 0.37
22 20 0.49
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAACCTTAAATCCATACTCCA
Found at i:40844351 original size:41 final size:41
Alignment explanation
Indices: 40844289--40844404 Score: 164
Period size: 41 Copynumber: 2.8 Consensus size: 41
40844279 TAAAATGTTT
40844289 TTAGCGGCGCTTTAT-CAAAAACGCCGCTAAAGCCCCTA-CCA
1 TTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAGCCCC-AGCCA
* * *
40844330 TTAGTGGCGCTTTTCCAAAAACGCCGCTAAAGGCCCAGGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAGCCA
*
40844371 TTAGCGGCGCTTTTCCAAAAACGCTGCTAAAGCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
40844405 ACGAAATGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.03
41 65 0.97
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAGCCA
Found at i:40844484 original size:39 final size:39
Alignment explanation
Indices: 40844440--40844518 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
40844430 TGGGCTAAGG
* *
40844440 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGA-TAATGCTCA
1 TTTTTAGCGGCATTTTTTT-AAAAACGCC-ACTAATGCTCA
40844480 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
40844519 ATCTTTAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 1 0.03
39 18 0.50
40 17 0.47
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
Found at i:40844490 original size:40 final size:40
Alignment explanation
Indices: 40844440--40844577 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 40
40844430 TGGGCTAAGG
*
40844440 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGATAATGCTCA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGATAATGCTCA
*
40844480 TTTTTAGCGGCATTTTTTT-AAAAACGCC-ACTAATGCTCAA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGA-TAATGCTC-A
* * * *** * * *
40844520 TCTTTAGTGGCGATTTCCAG-AAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGATAATGC-TCA
*
40844560 TTTTTACCGGCGTTTTTT
1 TTTTTAGCGGCGTTTTTT
40844578 GTCCAAACGC
Statistics
Matches: 75, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
38 1 0.01
39 17 0.23
40 56 0.75
41 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTTGAAAAACGCCGATAATGCTCA
Found at i:40845857 original size:2 final size:2
Alignment explanation
Indices: 40845850--40845876 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40845840 TGTTTTCTTG
40845850 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
40845877 ACTCCACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:40847031 original size:2 final size:2
Alignment explanation
Indices: 40847024--40847053 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40847014 AACCACAGTG
40847024 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
40847054 AAATTAAAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40848688 original size:18 final size:18
Alignment explanation
Indices: 40848665--40848700 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
40848655 GTTTTATGCT
40848665 GAGAAGAAGAAGATGAAG
1 GAGAAGAAGAAGATGAAG
*
40848683 GAGAAGAAGATGATGAAG
1 GAGAAGAAGAAGATGAAG
40848701 AGTATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.39, T:0.08
Consensus pattern (18 bp):
GAGAAGAAGAAGATGAAG
Found at i:40854154 original size:16 final size:15
Alignment explanation
Indices: 40854133--40854185 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
40854123 GAGCAAAAAG
40854133 AAAATTGGAAGGATGA
1 AAAATT-GAAGGATGA
* *
40854149 AAAATTAAAGGGTAGA
1 AAAATTGAAGGAT-GA
*
40854165 AAAACTAGAAGGATGA
1 AAAA-TTGAAGGATGA
40854181 AAAAT
1 AAAAT
40854186 ATAATTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.17
Consensus pattern (15 bp):
AAAATTGAAGGATGA
Found at i:40860250 original size:21 final size:20
Alignment explanation
Indices: 40860221--40860260 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40860211 CGTGTATTAG
*
40860221 ATTTGATTATAAAATTTTGAC
1 ATTTAATTA-AAAATTTTGAC
*
40860242 ATTTAATTAATAATTTTGA
1 ATTTAATTAAAAATTTTGA
40860261 TATCTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTTAATTAAAAATTTTGAC
Found at i:40860472 original size:20 final size:21
Alignment explanation
Indices: 40860447--40860491 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
40860437 CGAATACCGA
40860447 AATTAAA-ATCATAAATAA-AT
1 AATTAAATATCA-AAATAATAT
40860467 AATTAAATTATCAAAATAATAT
1 AATTAAA-TATCAAAATAATAT
40860489 AAT
1 AAT
40860492 CAGGTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTAAATATCAAAATAATAT
Found at i:40863545 original size:163 final size:163
Alignment explanation
Indices: 40863357--40863668 Score: 500
Period size: 163 Copynumber: 1.9 Consensus size: 163
40863347 AGGTATCAAC
* * * * *
40863357 TTGACAATTGAGTCCATTTTAGTCCCAAACTTGAAACCTATAAAAGTTTGATGATGTGGCATTAT
1 TTGACAACTGAGTCAATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGACGTGACATTAT
* *
40863422 GAGATTGTGCAACATCATCACTTGAAAATT-AAAAAAATATATATGAATTTTTAGGTGATGATGT
66 GAGATTGTGCAACATCATCACTTGAAAATTCAAAAAAAT-TATATGAATTTTCAAGTGATGATGT
40863486 GGTACAATTTCAAAGTTTCACATGGCACTTAAAT
130 GGTACAATTTCAAAGTTTCACATGGCACTTAAAT
*
40863520 TTGACAACTGAGTCAATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATTACGTGACATTAT
1 TTGACAACTGAGTCAATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGACGTGACATTAT
* * *
40863585 GAGATTGTGCTACATCATCACTTGAAAATTCATATAAATTATATGAATTTTCAAGTGATGATGTG
66 GAGATTGTGCAACATCATCACTTGAAAATTCAAAAAAATTATATGAATTTTCAAGTGATGATGTG
*
40863650 GTACAATTTCAATGTTTCA
131 GTACAATTTCAAAGTTTCA
40863669 TATACAATAT
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
163 130 0.96
164 6 0.04
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (163 bp):
TTGACAACTGAGTCAATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGACGTGACATTAT
GAGATTGTGCAACATCATCACTTGAAAATTCAAAAAAATTATATGAATTTTCAAGTGATGATGTG
GTACAATTTCAAAGTTTCACATGGCACTTAAAT
Found at i:40864626 original size:13 final size:13
Alignment explanation
Indices: 40864608--40864632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40864598 TCTCTTTCTA
40864608 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
40864621 TTTTCTTTTCTT
1 TTTTCTTTTCTT
40864633 CTGTAAATTT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:40867231 original size:45 final size:46
Alignment explanation
Indices: 40867167--40867262 Score: 126
Period size: 45 Copynumber: 2.1 Consensus size: 46
40867157 TAATTTGACC
*
40867167 TACTAAATAATTAACTAAATT-GCATAGTATATATT-TTAAATTATTTA
1 TACTAAAT-ATTAACTAAATTAG-ATAGTATATATTATT-AATTATCTA
*
40867214 TACTAAAT-TTAACTAAATTAGATAGTATTTATTATTAATTATCTA
1 TACTAAATATTAACTAAATTAGATAGTATATATTATTAATTATCTA
40867259 TACT
1 TACT
40867263 TGATCAAGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
45 34 0.76
46 3 0.07
47 8 0.18
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (46 bp):
TACTAAATATTAACTAAATTAGATAGTATATATTATTAATTATCTA
Found at i:40868105 original size:25 final size:25
Alignment explanation
Indices: 40868077--40868126 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40868067 TTAGGTGTTG
40868077 TATAGGGGTGTAATCCAGCCAAGTT
1 TATAGGGGTGTAATCCAGCCAAGTT
40868102 TATAGGGGTGTAATCCAGCCAAGTT
1 TATAGGGGTGTAATCCAGCCAAGTT
40868127 GAGCTCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (25 bp):
TATAGGGGTGTAATCCAGCCAAGTT
Found at i:40868620 original size:3 final size:3
Alignment explanation
Indices: 40868612--40868658 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
40868602 TGGATTATAG
40868612 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40868659 AAGAATTGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40872996 original size:13 final size:13
Alignment explanation
Indices: 40872978--40873010 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40872968 TTGACCACAC
40872978 GCCCGTGTGTCTA
1 GCCCGTGTGTCTA
40872991 GCCCGTGTGTCTA
1 GCCCGTGTGTCTA
40873004 GCCCGTG
1 GCCCGTG
40873011 GTCGAAACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.33, G:0.33, T:0.27
Consensus pattern (13 bp):
GCCCGTGTGTCTA
Found at i:40874324 original size:15 final size:15
Alignment explanation
Indices: 40874285--40874329 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
40874275 GTGCTGTAAA
40874285 TTGGATTTCTTTATC
1 TTGGATTTCTTTATC
* *
40874300 ATGTATTTTCTTTATC
1 TTGGA-TTTCTTTATC
40874316 TTGGATTTCTTTAT
1 TTGGATTTCTTTAT
40874330 TCTGGGCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (15 bp):
TTGGATTTCTTTATC
Found at i:40876398 original size:16 final size:15
Alignment explanation
Indices: 40876370--40876418 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
40876360 TGATGTAAAT
*
40876370 TGGATTTCCTTATCA
1 TGGATTTCTTTATCA
*
40876385 TGGATTTTCTTTATCT
1 TGGA-TTTCTTTATCA
*
40876401 TGGATTTCTTTATTA
1 TGGATTTCTTTATCA
40876416 TGG
1 TGG
40876419 GCTTTTCCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.55
Consensus pattern (15 bp):
TGGATTTCTTTATCA
Found at i:40877860 original size:24 final size:25
Alignment explanation
Indices: 40877833--40877883 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
40877823 TGTATGGTAA
* *
40877833 TAAAAATATATATGTGTAATA-AAT
1 TAAAAACATACATGTGTAATACAAT
* *
40877857 TAAATACATACATTTGTAATACAAT
1 TAAAAACATACATGTGTAATACAAT
40877882 TA
1 TA
40877884 TATAATTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (25 bp):
TAAAAACATACATGTGTAATACAAT
Found at i:40878027 original size:9 final size:9
Alignment explanation
Indices: 40878017--40878045 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
40878007 ACAGAGAAGA
40878017 AAAG-AAGG
1 AAAGAAAGG
40878025 AAAGAAAGG
1 AAAGAAAGG
40878034 AAAGAAAGG
1 AAAGAAAGG
40878043 AAA
1 AAA
40878046 ATTAGGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (9 bp):
AAAGAAAGG
Found at i:40879278 original size:18 final size:18
Alignment explanation
Indices: 40879255--40879337 Score: 121
Period size: 18 Copynumber: 4.6 Consensus size: 18
40879245 TAAATAAAAG
* * *
40879255 TACTGAATGACTGACTGT
1 TACTGAATAATTGATTGT
40879273 TACTGAATAATTGATTGT
1 TACTGAATAATTGATTGT
*
40879291 TACTGAATAATTGATTGC
1 TACTGAATAATTGATTGT
40879309 TACTGAATAATTGATTGT
1 TACTGAATAATTGATTGT
*
40879327 TACTGCATAAT
1 TACTGAATAAT
40879338 ATTGACAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGAATAATTGATTGT
Found at i:40879359 original size:18 final size:19
Alignment explanation
Indices: 40879336--40879380 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
40879326 TTACTGCATA
* *
40879336 ATATTGACAA-ATTGATTG
1 ATATTGAAAATATTGACTG
40879354 ATATTGAAAAATATTGACTG
1 ATATTG-AAAATATTGACTG
40879374 ATATTGA
1 ATATTGA
40879381 GCTTGGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 4 0.17
20 13 0.57
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (19 bp):
ATATTGAAAATATTGACTG
Found at i:40879366 original size:28 final size:28
Alignment explanation
Indices: 40879317--40879371 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
40879307 GCTACTGAAT
* * *
40879317 AATTGATTGTTACTGCATAATATTGACA
1 AATTGATTGATACTGAAAAATATTGACA
*
40879345 AATTGATTGATATTGAAAAATATTGAC
1 AATTGATTGATACTGAAAAATATTGAC
40879372 TGATATTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (28 bp):
AATTGATTGATACTGAAAAATATTGACA
Found at i:40885695 original size:30 final size:29
Alignment explanation
Indices: 40885661--40885728 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
40885651 ATCGTATCTT
40885661 GGGTTTCTTTATCCTGGATCTCTTTATTCC
1 GGGTTTCTTTATCCTGGATCTCTTTATT-C
* * *
40885691 GGGTTTCTCTATCTTGGATTTCTTTATTC
1 GGGTTTCTTTATCCTGGATCTCTTTATTC
*
40885720 GGTTTTCTT
1 GGGTTTCTT
40885729 GTTATCTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.09, C:0.19, G:0.18, T:0.54
Consensus pattern (29 bp):
GGGTTTCTTTATCCTGGATCTCTTTATTC
Found at i:40900830 original size:114 final size:114
Alignment explanation
Indices: 40900593--40900898 Score: 512
Period size: 114 Copynumber: 2.7 Consensus size: 114
40900583 CTTTTATTCT
* *
40900593 ATATTTCAGTATCAAATAATGTGTACATCTTTGATTTGATAAAGTAGATATTATTTGACAT-C-T
1 ATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTAGATATTATTTGACATCCAT
* * *
40900656 --ATTACAGAAAAAATTGAAATTTCTAAATATTGCAATTCCATTATTCA
66 CCATTACAGAAAATATTAAAATTTCTAAATATTGCAATTCCATTAGTCA
*
40900703 ATATTTCACTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTAGATATTATTTGACATCCAT
1 ATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTAGATATTATTTGACATCCAT
*
40900768 CCATTACAGAAAATATTAAAATTTCTAAATATTGCAATTCCATTAGTCG
66 CCATTACAGAAAATATTAAAATTTCTAAATATTGCAATTCCATTAGTCA
*
40900817 ATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTACATATTATTTGACATCCAT
1 ATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTAGATATTATTTGACATCCAT
40900882 CCATTACAGAAAATATT
66 CCATTACAGAAAATATT
40900899 GCAATTCCAT
Statistics
Matches: 183, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
110 58 0.32
111 1 0.01
112 1 0.01
114 123 0.67
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (114 bp):
ATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTAGATATTATTTGACATCCAT
CCATTACAGAAAATATTAAAATTTCTAAATATTGCAATTCCATTAGTCA
Done.