Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 65 of 93
Found at i:9079991 original size:12 final size:11
Alignment explanation
Indices: 9079932--9079992 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 11
9079922 AAACAAACTT
*
9079932 AATTAAATTCA
1 AATTAAATTTA
9079943 AATTAAATTTTA
1 AATTAAA-TTTA
9079955 AATATCAAATTTTA
1 AAT-T-AAA-TTTA
9079969 AATTAAATTTA
1 AATTAAATTTA
9079980 AATTTAAATTTA
1 AA-TTAAATTTA
9079992 A
1 A
9079993 TATGATATCG
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
11 13 0.29
12 19 0.42
13 2 0.04
14 11 0.24
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:9081469 original size:18 final size:17
Alignment explanation
Indices: 9081446--9081479 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9081436 TAATAAAATT
9081446 ATGATATGATAAGATAAG
1 ATGATATGATAA-ATAAG
*
9081464 ATGATATTATAAATAA
1 ATGATATGATAAATAA
9081480 AATTAGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (17 bp):
ATGATATGATAAATAAG
Found at i:9083174 original size:22 final size:22
Alignment explanation
Indices: 9083146--9083207 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
9083136 TTTGAATGAT
* *
9083146 TTTTGGAATTTAAGGTTTGAGA
1 TTTTGGATTTTAAGGTTTGAAA
* *
9083168 TTTTGGATTTTAAGATTTTAAA
1 TTTTGGATTTTAAGGTTTGAAA
*
9083190 TTTTAGATTTTAAGGTTT
1 TTTTGGATTTTAAGGTTT
9083208 TGAAGGTCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.53
Consensus pattern (22 bp):
TTTTGGATTTTAAGGTTTGAAA
Found at i:9083199 original size:14 final size:15
Alignment explanation
Indices: 9083174--9083202 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9083164 GAGATTTTGG
9083174 ATTTTAAGATTTTAA
1 ATTTTAAGATTTTAA
9083189 ATTTT-AGATTTTAA
1 ATTTTAAGATTTTAA
9083203 GGTTTTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
ATTTTAAGATTTTAA
Found at i:9083208 original size:15 final size:15
Alignment explanation
Indices: 9083154--9083208 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
9083144 ATTTTTGGAA
*
9083154 TTTAAGGTTTGAGAT
1 TTTAAGGTTTTAGAT
9083169 TTT--GGATTTTAAGAT
1 TTTAAGG-TTTT-AGAT
*
9083184 TTTAA-ATTTTAGAT
1 TTTAAGGTTTTAGAT
9083198 TTTAAGGTTTT
1 TTTAAGGTTTT
9083209 GAAGGTCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 12 0.38
15 18 0.56
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (15 bp):
TTTAAGGTTTTAGAT
Found at i:9083333 original size:41 final size:41
Alignment explanation
Indices: 9083288--9083370 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
9083278 GTTTGAAAGA
*
9083288 TTTAGGGTTTCGGATTTCAAAGTTTTAAAGGTTTAGAAGTT
1 TTTAGAGTTTCGGATTTCAAAGTTTTAAAGGTTTAGAAGTT
* * ** * *
9083329 TTTAGAGTTTTGGATTTTAGGGTTTTAAGGGTTTGGAAGTT
1 TTTAGAGTTTCGGATTTCAAAGTTTTAAAGGTTTAGAAGTT
9083370 T
1 T
9083371 GGGGTTTAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (41 bp):
TTTAGAGTTTCGGATTTCAAAGTTTTAAAGGTTTAGAAGTT
Found at i:9083823 original size:3 final size:3
Alignment explanation
Indices: 9083815--9083848 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9083805 TTTTTCTACT
9083815 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9083849 TAAAGAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:9084001 original size:9 final size:10
Alignment explanation
Indices: 9083996--9084033 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
9083986 TAGATTTTAT
9083996 TTATTTATTA
1 TTATTTATTA
9084006 TTA-TTATTA
1 TTATTTATTA
*
9084015 TTATTTACTA
1 TTATTTATTA
9084025 TTA-TTATTA
1 TTATTTATTA
9084034 ATATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 14 0.56
10 11 0.44
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTTATTA
Found at i:9084008 original size:3 final size:3
Alignment explanation
Indices: 9084000--9084033 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
9083990 TTTTATTTAT
*
9084000 TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
9084034 ATATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:9084020 original size:19 final size:19
Alignment explanation
Indices: 9083996--9084033 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
9083986 TAGATTTTAT
*
9083996 TTATTTATTATTATTATTA
1 TTATTTACTATTATTATTA
9084015 TTATTTACTATTATTATTA
1 TTATTTACTATTATTATTA
9084034 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTACTATTATTATTA
Found at i:9087575 original size:22 final size:22
Alignment explanation
Indices: 9087562--9087612 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
9087552 AATGAAAATT
9087562 TTAATAAAATTTAAATCAATAAA
1 TTAATAAAATTT-AATCAATAAA
*
9087585 TTAATAAAATTTAAT-ATAAAAA
1 TTAATAAAATTTAATCA-ATAAA
9087607 TTAATA
1 TTAATA
9087613 TAATAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 13 0.50
23 12 0.46
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAATAAAATTTAATCAATAAA
Found at i:9087592 original size:23 final size:22
Alignment explanation
Indices: 9087562--9087612 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
9087552 AATGAAAATT
9087562 TTAATAAAATTTAA-ATCAATAAA
1 TTAATAAAATTTAATAT-AA-AAA
9087585 TTAATAAAATTTAATATAAAAA
1 TTAATAAAATTTAATATAAAAA
9087607 TTAATA
1 TTAATA
9087613 TAATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.33
23 16 0.59
24 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAATAAAATTTAATATAAAAA
Found at i:9087600 original size:10 final size:10
Alignment explanation
Indices: 9087547--9087600 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 10
9087537 TTAAAAAAAT
9087547 AATTTAATGAA
1 AATTTAAT-AA
9087558 AATTTTAATAA
1 AA-TTTAATAA
9087569 AATTTAAATCAA
1 AATTT-AAT-AA
*
9087581 TAAATTAATAA
1 -AATTTAATAA
9087592 AATTTAATA
1 AATTTAATA
9087601 TAAAAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 11 0.30
11 11 0.30
12 11 0.30
13 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
AATTTAATAA
Found at i:9087605 original size:12 final size:11
Alignment explanation
Indices: 9087547--9087615 Score: 52
Period size: 12 Copynumber: 6.0 Consensus size: 11
9087537 TTAAAAAAAT
9087547 AATTT-AATGAA
1 AATTTAAAT-AA
*
9087558 AATTTTAATAA
1 AATTTAAATAA
9087569 AATTTAAATCAA
1 AATTTAAAT-AA
*
9087581 TAAATT-AATAA
1 -AATTTAAATAA
9087592 AATTTAATATAA
1 AATTTAA-ATAA
*
9087604 AAATTAATATAA
1 AATTTAA-ATAA
9087616 TAAAAATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.08
11 18 0.37
12 23 0.47
13 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (11 bp):
AATTTAAATAA
Found at i:9092678 original size:30 final size:30
Alignment explanation
Indices: 9092642--9092704 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
9092632 TTCCGTGGAA
*
9092642 CCAATGGAGCATCAA-TATTTTCTCTTCTTG
1 CCAATGGAGCATCAACT-TTTTCTCTTCATG
9092672 CCAATGGAGCATCAACTTTTTCTCTTCATG
1 CCAATGGAGCATCAACTTTTTCTCTTCATG
9092702 CCA
1 CCA
9092705 TTTTAGTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.37
Consensus pattern (30 bp):
CCAATGGAGCATCAACTTTTTCTCTTCATG
Found at i:9102104 original size:16 final size:16
Alignment explanation
Indices: 9102080--9102110 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9102070 AATAAACAAT
9102080 TGATAATGATGATTTA
1 TGATAATGATGATTTA
*
9102096 TGATTATGATGATTT
1 TGATAATGATGATTT
9102111 GTAATGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (16 bp):
TGATAATGATGATTTA
Found at i:9102936 original size:21 final size:21
Alignment explanation
Indices: 9102910--9102991 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
9102900 AGTTGATTGT
9102910 TGTTGTTGATGTTATTGTTTA
1 TGTTGTTGATGTTATTGTTTA
* * *
9102931 TGTTGTTGATATTAGTGATGT-
1 TGTTGTTGATGTTATTG-TTTA
* *
9102952 TGTTGTTAATCTTATT-TTTA
1 TGTTGTTGATGTTATTGTTTA
* *
9102972 TTATTGTTGTTGTTATTGTT
1 -TGTTGTTGATGTTATTGTT
9102992 AACAGACCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.04
21 40 0.87
22 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.21, T:0.62
Consensus pattern (21 bp):
TGTTGTTGATGTTATTGTTTA
Found at i:9104969 original size:11 final size:11
Alignment explanation
Indices: 9104934--9104974 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
9104924 AGATACTGAT
9104934 TTTATATTTAG
1 TTTATATTTAG
9104945 -TTA-A-TTATG
1 TTTATATTTA-G
9104954 TTTATATTTAG
1 TTTATATTTAG
9104965 TTTATATTTA
1 TTTATATTTA
9104975 TAAAATATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.23
11 12 0.46
12 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (11 bp):
TTTATATTTAG
Found at i:9105077 original size:19 final size:18
Alignment explanation
Indices: 9105035--9105080 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
9105025 TAACATGTTC
9105035 AATATAAAATATAAACAA
1 AATATAAAATATAAACAA
* *
9105053 ATATATAAAGTATAAACATT
1 A-ATATAAAATATAAACA-A
9105073 AATATAAA
1 AATATAAA
9105081 TTGTTAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 22 0.92
20 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (18 bp):
AATATAAAATATAAACAA
Found at i:9108463 original size:21 final size:20
Alignment explanation
Indices: 9108431--9108473 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
9108421 TTAAATATAG
* *
9108431 GTTTCAAAATTTTGGTTTTA
1 GTTTCAAAATTTAGGGTTTA
*
9108451 GTTTTAAAGATTTAGGGTTTA
1 GTTTCAAA-ATTTAGGGTTTA
9108472 GT
1 GT
9108474 GAATGAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (20 bp):
GTTTCAAAATTTAGGGTTTA
Found at i:9119722 original size:17 final size:19
Alignment explanation
Indices: 9119677--9119722 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
9119667 TTATATGTTT
9119677 AATTCAATAATATTTGATTA
1 AATTC-ATAATATTTGATTA
*
9119697 AATTTATAAT-TTTG-TTA
1 AATTCATAATATTTGATTA
*
9119714 TATTCATAA
1 AATTCATAA
9119723 CTTCACTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
19 5 0.22
20 4 0.17
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (19 bp):
AATTCATAATATTTGATTA
Found at i:9120792 original size:3 final size:3
Alignment explanation
Indices: 9120784--9120813 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
9120774 ATTTCAAAAG
*
9120784 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9120814 TTTTTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:9121008 original size:3 final size:3
Alignment explanation
Indices: 9121000--9121036 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
9120990 CAAACGTTGT
9121000 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
9121037 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:9121645 original size:12 final size:11
Alignment explanation
Indices: 9121587--9121646 Score: 57
Period size: 11 Copynumber: 5.1 Consensus size: 11
9121577 TTTTTTGTTT
*
9121587 AATTCAAATTA
1 AATTTAAATTA
9121598 AATTTAAATATA
1 AATTTAAAT-TA
*
9121610 AATATATATATTA
1 AAT-T-TAAATTA
*
9121623 AATTCAAATTA
1 AATTTAAATTA
9121634 AATTTTAAATTA
1 AA-TTTAAATTA
9121646 A
1 A
9121647 GAGATAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
11 15 0.38
12 15 0.38
13 6 0.15
14 4 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:9121696 original size:18 final size:19
Alignment explanation
Indices: 9121673--9121711 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
9121663 AATAATCAAC
*
9121673 TATATATTTT-AGTTTTTA
1 TATATATTTTAAATTTTTA
9121691 TATATATTTTAAATTTTTA
1 TATATATTTTAAATTTTTA
9121710 TA
1 TA
9121712 AAATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TATATATTTTAAATTTTTA
Found at i:9121768 original size:13 final size:13
Alignment explanation
Indices: 9121749--9121788 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
9121739 ATTAATTTAA
9121749 ATATATTAAAATT
1 ATATATTAAAATT
* *
9121762 TTATATTAAAATA
1 ATATATTAAAATT
*
9121775 ATATATAAAAATT
1 ATATATTAAAATT
9121788 A
1 A
9121789 AAAAACGATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATATTAAAATT
Found at i:9122563 original size:11 final size:11
Alignment explanation
Indices: 9122547--9122578 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
9122537 TTAATTTTTT
9122547 TATTAAATTTA
1 TATTAAATTTA
*
9122558 TATTAAATATA
1 TATTAAATTTA
9122569 TATTAAATTT
1 TATTAAATTT
9122579 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTAAATTTA
Found at i:9122848 original size:11 final size:11
Alignment explanation
Indices: 9122834--9122882 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
9122824 TTTTATTTAG
9122834 TTTATATTAAA
1 TTTATATTAAA
9122845 TTTACATATTAAA
1 TTT--ATATTAAA
*
9122858 TATATATTAAA
1 TTTATATTAAA
*
9122869 TTTAAATTAAA
1 TTTATATTAAA
9122880 TTT
1 TTT
9122883 TAAATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 23 0.70
13 10 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTATATTAAA
Found at i:9122854 original size:24 final size:24
Alignment explanation
Indices: 9122836--9122880 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
9122826 TTATTTAGTT
9122836 TATATTAAATTTACATATTAAATA
1 TATATTAAATTTACATATTAAATA
9122860 TATATTAAATTTA-A-ATTAAAT
1 TATATTAAATTTACATATTAAAT
9122881 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATTAAATTTACATATTAAATA
Found at i:9122887 original size:18 final size:18
Alignment explanation
Indices: 9122834--9122915 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 18
9122824 TTTTATTTAG
* *
9122834 TTTATATTAAAT-TTACA
1 TTTAAATTAAATATTAAA
*
9122851 TATTAAA-TATATATTAAA
1 T-TTAAATTAAATATTAAA
*
9122869 TTTAAATTAAATTTTAAA
1 TTTAAATTAAATATTAAA
** *
9122887 TAAAAATTAAAAATTAAA
1 TTTAAATTAAATATTAAA
9122905 --TAAATTAAATA
1 TTTAAATTAAATA
9122916 AATTGAATTA
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
16 9 0.18
17 10 0.20
18 32 0.63
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAAATTAAATATTAAA
Found at i:9122888 original size:29 final size:29
Alignment explanation
Indices: 9122853--9122917 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
9122843 AATTTACATA
* * *
9122853 TTAAATATATATT-AAATTTAAATTAAATT
1 TTAAATAAAAATTAAAAATTAAA-TAAATT
9122882 TTAAATAAAAATTAAAAATTAAATAAA--
1 TTAAATAAAAATTAAAAATTAAATAAATT
9122909 TTAAATAAA
1 TTAAATAAA
9122918 TTGAATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 9 0.28
29 15 0.47
30 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAATAAAAATTAAAAATTAAATAAATT
Found at i:9122890 original size:11 final size:11
Alignment explanation
Indices: 9122834--9122914 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 11
9122824 TTTTATTTAG
*
9122834 TTTATATTAAA
1 TTTAAATTAAA
9122845 TTTACATATTAAA
1 TTTA-A-ATTAAA
* *
9122858 TATATATTAAA
1 TTTAAATTAAA
9122869 TTTAAATTAAA
1 TTTAAATTAAA
*
9122880 TTTTAAATAAAAA
1 -TTTAAAT-TAAA
*
9122893 TTAAAAATTAAA
1 TT-TAAATTAAA
9122905 --TAAATTAAA
1 TTTAAATTAAA
9122914 T
1 T
9122915 AAATTGAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.15
11 19 0.35
12 12 0.22
13 16 0.29
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:9123004 original size:20 final size:20
Alignment explanation
Indices: 9122976--9123018 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9122966 TAATTATTTT
* *
9122976 ATATATAAATTTATTTTAAA
1 ATATATAAAATTATATTAAA
*
9122996 ATATTTAAAATTATATTAAA
1 ATATATAAAATTATATTAAA
9123016 ATA
1 ATA
9123019 AGATATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATAAAATTATATTAAA
Found at i:9123649 original size:24 final size:23
Alignment explanation
Indices: 9123622--9123678 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
9123612 TTAATAATAT
*
9123622 AATATATATAAATGTATAAAATTA
1 AATATATATAAA-ATATAAAATTA
* *
9123646 AATAAATAATAAAATATAAAATTT
1 AATATAT-ATAAAATATAAAATTA
*
9123670 TATATATAT
1 AATATATAT
9123679 CTTAAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.07
24 20 0.74
25 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
AATATATATAAAATATAAAATTA
Found at i:9123652 original size:18 final size:18
Alignment explanation
Indices: 9123614--9123665 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
9123604 AAATAATTTT
* *
9123614 AATAATATAATATATATA
1 AATAATAAAATATAAATA
*
9123632 AATGTATAAAAT-TAAATA
1 AAT-AATAAAATATAAATA
9123650 AATAATAAAATATAAA
1 AATAATAAAATATAAA
9123666 ATTTTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.25
18 15 0.54
19 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAATAAAATATAAATA
Found at i:9123830 original size:11 final size:11
Alignment explanation
Indices: 9123814--9123869 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 11
9123804 GTCTCAAAGT
9123814 AAAATATTATA
1 AAAATATTATA
9123825 AAAATA-TATA
1 AAAATATTATA
*
9123835 AATAT-TTA-A
1 AAAATATTATA
*
9123844 AAAATA-AATA
1 AAAATATTATA
*
9123854 AATATATTATA
1 AAAATATTATA
9123865 AAAAT
1 AAAAT
9123870 TTTAAAAGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 6 0.17
10 16 0.46
11 13 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATATTATA
Found at i:9123839 original size:19 final size:20
Alignment explanation
Indices: 9123813--9123869 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
9123803 TGTCTCAAAG
*
9123813 TAAAATATTATAAAAATATA
1 TAAAATATTATAAAAATAAA
9123833 T-AAATATT-TAAAAAATAAA
1 TAAAATATTAT-AAAAATAAA
9123852 TAAATATATTATAAAAAT
1 TAAA-ATATTATAAAAAT
9123870 TTTAAAAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.03
19 16 0.50
20 3 0.09
21 11 0.34
22 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAATATTATAAAAATAAA
Found at i:9124091 original size:12 final size:11
Alignment explanation
Indices: 9124069--9124094 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9124059 TTTTAAAAGA
9124069 TAAAATTTTTT
1 TAAAATTTTTT
9124080 TAAAATTTTTT
1 TAAAATTTTTT
9124091 TAAA
1 TAAA
9124095 TATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TAAAATTTTTT
Found at i:9126744 original size:20 final size:20
Alignment explanation
Indices: 9126704--9126745 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
9126694 TAAATCTAAG
**
9126704 TGCATTAATATTTTATTAAA
1 TGCATTAATATTTTACCAAA
9126724 TGCATTAATATTTTACCAAA
1 TGCATTAATATTTTACCAAA
9126744 TG
1 TG
9126746 AAATTAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (20 bp):
TGCATTAATATTTTACCAAA
Found at i:9127384 original size:36 final size:36
Alignment explanation
Indices: 9127344--9127414 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
9127334 ATAATAAAAT
9127344 TATAAAACGTTACAAATAAAAACAAATGAAATCAAC
1 TATAAAACGTTACAAATAAAAACAAATGAAATCAAC
9127380 TATAAAACGTTACAAATAAAAACAAATGAAATCAA
1 TATAAAACGTTACAAATAAAAACAAATGAAATCAA
9127415 TGCGCATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.20
Consensus pattern (36 bp):
TATAAAACGTTACAAATAAAAACAAATGAAATCAAC
Found at i:9127796 original size:694 final size:677
Alignment explanation
Indices: 9126428--9127796 Score: 1762
Period size: 678 Copynumber: 2.0 Consensus size: 677
9126418 GTTATAGGTT
** *
9126428 AATTAATAAAATAATTTTAAATTATGAAAGTTAATATTGAAATAATAAAAATTGTGGGTGAATAA
1 AATTAATAAAATAATTTTAAATTATGAAAGTTAATATTGAAATAATAAAAATAATGAGTGAATAA
* ** * * *
9126493 TGGTTTAACAATGGTAAGTTGATTAATAGTAAATTATTTTATTTTGCCATTAACATTTAGAGATT
66 TGGTCTAACAATGACAAGTTAATTAATAGTAAAATATTTTATTTTGCCATTAACATTTAGAGATC
* * *
9126558 CCTTAATTTAGAATAATAAAACAAATTAAATTTATTATATTGAATAATATAAATAAAATAAAATA
131 CCTTAATTTAGAACAATAAAAAAAATTAAATATATTATATTGAATAATATAAATAAAATAAAATA
* ** * *
9126623 AATTTTAATTAAATCAACGTGCATTAATATCTAGATTTTAAAATTATAAAACGTTATAAATGAAA
196 AATTTTAATTAAATCAACGTGCATTAATATCTAAATAATAAAATTATAAAACGTTACAAATAAAA
* * *** * *** ** * * ** *
9126688 TCAAATTAAATCTAAGTGCATTAATATTTTATTAAATGCATTAATATTTTACCAAATGAAATTAA
261 ACAAATGAAATCTAAAAACATTAAAATAAAAACAAATGAATCAATACATTA-CAAATGAAATCAA
* * *
9126753 ATGAAATCATATTTAATGAAATATAAATCTATCAATCAAATATAAATTAATAAAATGTTTTGATC
325 ATGAAATCAGATTTAATAAAATATAAATCTATCAATCAAATATAAATTAATAAAATATTTTGATC
*
9126818 CATTAATTTAATTATGGAGAATTAATTTGATATATTGGATTTCTATATTTACACATAAAGTACAT
390 CATTAATTTAATTATGGAGAATTAATTTGATATATTGGATTTATATATTTACACATAAAGTACAT
* * *
9126883 TAATTACTCAAATTGATACTATATTTAATCAAATATAAATGTATCAAATAATTGATTAGAGAATC
455 CAATTACTCAAATTGATACTATATTTAATCAAACATAAATGTATCAAATAATTAATTAGAGAATC
* *
9126948 AATTATTTTATAATTATAATTGTAGTATTTAATAAATTATTAATTATATATTGATTGATTTAATT
520 AACTATTTTATAATTATAATTGTAGGATTTAATAAATTATTAATTATATATTGATTGATTTAATT
* * * * *
9127013 TGTTAAATTAAGAAAATTTTAATATTTTAATATTTTTATTATGAATTGAATTGAGAGAAATTTAA
585 TGTCAAATTAAGAAAATTTTAACATTTTAATACTTTTAATAAGAATTGAATTGAGAGAAATTTAA
*
9127078 AGTCAATAATAAAAACACAAATATAGTC
650 AATCAATAATAAAAACACAAATATAGTC
*
9127106 AATTAATAAGATAATTTTAAATTATGAAAGTTAATATTGAAATAATAAAAATAATGAGTGAATAA
1 AATTAATAAAATAATTTTAAATTATGAAAGTTAATATTGAAATAATAAAAATAATGAGTGAATAA
* * * *
9127171 TGGTCTAACAATGACAAGTTAATTGATATTAAAATATTTTATTATT-TCATTAATATTTAGAGAT
66 TGGTCTAACAATGACAAGTTAATTAATAGTAAAATATTTTATT-TTGCCATTAACATTTAGAGAT
* *
9127235 CCCTTAATTTAGAACAATAAAAAAAATTAAATATATTATATTTAATAATGA-CAATAAAATAAAA
130 CCCTTAATTTAGAACAATAAAAAAAATTAAATATATTATATTGAATAAT-ATAAATAAAATAAAA
*
9127299 TAAATTTTAATTAAATCAACGTGTATTAATATC-AAATAATAAAATTATAAAACGTTACAAATAA
194 TAAATTTTAATTAAATCAACGTGCATTAATATCTAAATAATAAAATTATAAAACGTTACAAATAA
* * *
9127363 AAACAAATGAAATCAACTATAAAACGTTACAAATAAAAACAAATGAAATCAATGCGCATTA-ATA
259 AAACAAATGAAAT---CTA-AAAACATTA-AAATAAAAACAAATG-AATCAAT--ACATTACAAA
*** * *
9127427 TTTTATCAAATGAAATCAGATTTAATAAAATATAAATGTCTCAATCAAATATAAATTAATAAAAT
316 TGAAATCAAATGAAATCAGATTTAATAAAATATAAATCTATCAATCAAATATAAATTAATAAAAT
* * *
9127492 ATTTT-ATTCTATTAATTTAATTATGGAGAATTAATTT-ATATATTTGCTTTATATATTTACACA
381 ATTTTGA-TCCATTAATTTAATTATGGAGAATTAATTTGATATATTGGATTTATATATTTACAC-
9127555 TGAAATACATCATGGAATACATCAATTACTCAAA-TGAATACTATATTTAATCAAACATAAATGT
444 ----ATA-A--A--G--TACATCAATTACTCAAATTG-ATACTATATTTAATCAAACATAAATGT
* * * * * *
9127619 ATCAAATAATTAATTAGTGAATCGACTATTTTATAATTGTAATTGTTGGATTTATTAATTTATTA
497 ATCAAATAATTAATTAGAGAATCAACTATTTTATAATTATAATTGTAGGATTTAATAAATTATTA
* *
9127684 GTTATATATTGATTGATTTAATTTGTCAAATTAAGAAATTTTTAACATTTTAATACTTTTAATAA
562 ATTATATATTGATTGATTTAATTTGTCAAATTAAGAAAATTTTAACATTTTAATACTTTTAATAA
** *
9127749 GAATTGAATTGAGAGTGATTTAAAATCAATAATAAAAACATAAATATA
627 GAATTGAATTGAGAGAAATTTAAAATCAATAATAAAAACACAAATATA
9127797 ATCGATTTAG
Statistics
Matches: 589, Mismatches: 78, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
677 37 0.06
678 201 0.34
679 3 0.01
680 3 0.01
681 5 0.01
682 32 0.05
683 97 0.16
685 3 0.01
687 3 0.01
688 1 0.00
690 1 0.00
692 1 0.00
693 2 0.00
694 200 0.34
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (677 bp):
AATTAATAAAATAATTTTAAATTATGAAAGTTAATATTGAAATAATAAAAATAATGAGTGAATAA
TGGTCTAACAATGACAAGTTAATTAATAGTAAAATATTTTATTTTGCCATTAACATTTAGAGATC
CCTTAATTTAGAACAATAAAAAAAATTAAATATATTATATTGAATAATATAAATAAAATAAAATA
AATTTTAATTAAATCAACGTGCATTAATATCTAAATAATAAAATTATAAAACGTTACAAATAAAA
ACAAATGAAATCTAAAAACATTAAAATAAAAACAAATGAATCAATACATTACAAATGAAATCAAA
TGAAATCAGATTTAATAAAATATAAATCTATCAATCAAATATAAATTAATAAAATATTTTGATCC
ATTAATTTAATTATGGAGAATTAATTTGATATATTGGATTTATATATTTACACATAAAGTACATC
AATTACTCAAATTGATACTATATTTAATCAAACATAAATGTATCAAATAATTAATTAGAGAATCA
ACTATTTTATAATTATAATTGTAGGATTTAATAAATTATTAATTATATATTGATTGATTTAATTT
GTCAAATTAAGAAAATTTTAACATTTTAATACTTTTAATAAGAATTGAATTGAGAGAAATTTAAA
ATCAATAATAAAAACACAAATATAGTC
Found at i:9128594 original size:391 final size:390
Alignment explanation
Indices: 9127868--9128645 Score: 1138
Period size: 391 Copynumber: 2.0 Consensus size: 390
9127858 TTGGATATTT
* *
9127868 TATTTAATCAAATATAAATGTATCAAATAATTGATTAGTGAATCGATTATTTTATAATTGTAATT
1 TATTTAATCAAATATAAATGTATCAAATAATTGATTAGAGAATCGACTATTTTATAATTGTAATT
* * *
9127933 ATAGTATTTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAGTTAAGAAATTTTT
66 ATAGTATTTTATTAATTTATTAATTATATATTGATTGATTTAATTTATCAAATTAAGAAAATTTT
*
9127998 AAAATTTTAATACTTTTAATATGAATTGAATTAAGAGTGATTTAAAGTTAATAATAAAAACATAA
131 AAAATTTTAATACTTTTAATATAAATTGAATTAAGAGTGATTTAAAGTTAATAATAAAAACATAA
* *
9128063 ATATAAATCAATTTAGTTTTTTAAATTATTTTTAAATTAAAAATATATTAAATAAAATAAAATGC
196 ATATAAATCAATTTAATTTTTTAAATTATTTTTAAATTAAAAATATATTAAATAAAATAAAATAC
* * * * * * * * *
9128128 ATTTATTAGATGTTAAGTGGCGATTTTTTAAACTGTGTACATGTCAATATTTTAAGTCGTCCATA
261 ATTTATTAAATGTCAAGTAGCGAATTTTTAAACCGTCTACATATCAACATTTTAAGTCGTCCACA
* * *
9128193 TAGCATTTTTTTCATTTTTGCCAAAAGCTTTGGCTTTTATATATTTATATAAGATTACTAGATAC
326 TAGCATTTTTTTCATTTTTACCAAAAACTTTGACTTTTATATATTTATATAAGA-TA-TAGATAC
9128258 TA
389 TA
9128260 TATTTAATCAAATATAAATGTATCAAATAATTGATTAGAGAATC-AGCTATTTTATAATTGTAAC
1 TATTTAATCAAATATAAATGTATCAAATAATTGATTAGAGAATCGA-CTATTTTATAATTGTAA-
*
9128324 TT-TAGTA-TTTATTAATTTATTAATTATCTATTGATTGATTTAATTTATCAAATTAAGAAAATT
64 TTATAGTATTTTATTAATTTATTAATTATATATTGATTGATTTAATTTATCAAATTAAGAAAATT
* *
9128387 TTAAAATTTTAATATTTTTAATATAAATTGAATTGAGAGTGATTTAAAGTTAATAATAAAAACAT
129 TTAAAATTTTAATACTTTTAATATAAATTGAATTAAGAGTGATTTAAAGTTAATAATAAAAACAT
** * *
9128452 AAATATAAATTGATTTAATTTTTT-AATTTTTTTTAAATTAAAAATGTATTAAATAAAATAAAAT
194 AAATATAAATCAATTTAATTTTTTAAATTATTTTTAAATTAAAAATATATTAAATAAAATAAAAT
* * *
9128516 ACATTTATTAAATGTCAAGTAG-TAATTTTTAATACCGTCTAATATATTAACATTTTAAG-CTGT
259 ACATTTATTAAATGTCAAGTAGCGAATTTTTAA-ACCGTCT-ACATATCAACATTTTAAGTC-GT
* * *
9128579 CCACATAAG-ATTTTTTTCATTTTTATCAAAAATTTTGATTTTTATATATTTATATAAGATATAG
321 CCACAT-AGCATTTTTTTCATTTTTACCAAAAACTTTGACTTTTATATATTTATATAAGATATAG
9128643 ATA
385 ATA
9128646 TAGATATAGA
Statistics
Matches: 347, Mismatches: 33, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
389 14 0.04
390 64 0.18
391 201 0.58
392 66 0.19
393 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (390 bp):
TATTTAATCAAATATAAATGTATCAAATAATTGATTAGAGAATCGACTATTTTATAATTGTAATT
ATAGTATTTTATTAATTTATTAATTATATATTGATTGATTTAATTTATCAAATTAAGAAAATTTT
AAAATTTTAATACTTTTAATATAAATTGAATTAAGAGTGATTTAAAGTTAATAATAAAAACATAA
ATATAAATCAATTTAATTTTTTAAATTATTTTTAAATTAAAAATATATTAAATAAAATAAAATAC
ATTTATTAAATGTCAAGTAGCGAATTTTTAAACCGTCTACATATCAACATTTTAAGTCGTCCACA
TAGCATTTTTTTCATTTTTACCAAAAACTTTGACTTTTATATATTTATATAAGATATAGATACTA
Found at i:9130271 original size:59 final size:58
Alignment explanation
Indices: 9130147--9130306 Score: 241
Period size: 59 Copynumber: 2.7 Consensus size: 58
9130137 GCTTTTGTAT
**
9130147 AAGAAAAATTGATACTTTCAACTTTTTTTCAAAATA-TTTTTTAAAAAACTTATTTTC
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTAAAAAACTTATTTTC
* *
9130204 AAGAAAAATTAATACTTTCAACTTTTCCTCAAAATTATTTTTTTAGAAAACTTATTTTC
1 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAA-TATTTTTTTAAAAAACTTATTTTC
* *
9130263 AAGGAAAATTGATACTTTTAACTTTTCCTCAAAAATATTTTTTT
1 AAGAAAAATTGATACTTTCAACTTTTCCTC-AAAATATTTTTTT
9130307 TTGGAATTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
57 31 0.33
58 2 0.02
59 56 0.60
60 4 0.04
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (58 bp):
AAGAAAAATTGATACTTTCAACTTTTCCTCAAAATATTTTTTTAAAAAACTTATTTTC
Found at i:9130413 original size:16 final size:17
Alignment explanation
Indices: 9130389--9130421 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9130379 AATTCTAATC
*
9130389 TAATCAATAAATAATAA
1 TAATCAATAAAAAATAA
9130406 TAAT-AATAAAAAATAA
1 TAATCAATAAAAAATAA
9130422 ATAAAACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TAATCAATAAAAAATAA
Found at i:9131186 original size:16 final size:16
Alignment explanation
Indices: 9131165--9131195 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9131155 AACAAAATTC
9131165 AAAATAGATAAATAAA
1 AAAATAGATAAATAAA
*
9131181 AAAATAGCTAAATAA
1 AAAATAGATAAATAA
9131196 TAGAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAATAGATAAATAAA
Found at i:9131244 original size:27 final size:27
Alignment explanation
Indices: 9131183--9131262 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
9131173 TAAATAAAAA
* *
9131183 AATAGCTAAATAATAGAAAATAATATT
1 AATAGATAACTAATAGAAAATAATATT
*
9131210 AATGGATAACTAATA-AAAATATATATT
1 AATAGATAACTAATAGAAAATA-ATATT
* *
9131237 ATTAGATAA-TATATATATAAATAATA
1 AATAGATAACTA-ATAGA-AAATAATA
9131263 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 8 0.18
27 27 0.61
28 4 0.09
29 5 0.11
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (27 bp):
AATAGATAACTAATAGAAAATAATATT
Found at i:9131260 original size:15 final size:16
Alignment explanation
Indices: 9131222--9131262 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
9131212 TGGATAACTA
9131222 ATAAA-AATATATATT
1 ATAAATAATATATATT
*
9131237 ATTAGATAATATATA-T
1 A-TAAATAATATATATT
9131253 ATAAATAATA
1 ATAAATAATA
9131263 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.41
16 5 0.23
17 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
ATAAATAATATATATT
Found at i:9131273 original size:15 final size:15
Alignment explanation
Indices: 9131255--9131290 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
9131245 ATATATATAT
9131255 AAATAATAAAAATAA
1 AAATAATAAAAATAA
* *
9131270 AAATCATAAAACTAA
1 AAATAATAAAAATAA
9131285 AAATAA
1 AAATAA
9131291 AATGGGCCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAATAAAAATAA
Found at i:9131667 original size:41 final size:41
Alignment explanation
Indices: 9131488--9131771 Score: 264
Period size: 43 Copynumber: 6.7 Consensus size: 41
9131478 TTTTGATCAA
* * *
9131488 AGCTCCTCTAAATAAAAGCTCAACGACTTTGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* *
9131529 AAAGCTCCTCTAAACAGAGGCTTAACGACTTTGGAAAATAAAT
1 --AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * *
9131572 AAAGCTCCTCTAAACAGA-GCTCAATGATTTTGGAAAATAAAT
1 --AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * *
9131614 GGCTCCTCTAATCAGAGGCTTAACGACTTTGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * * *
9131655 AGCTCATTTAATCAGAGGCTCAATGATTTTTGGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGA-CTTT-GAAAAATAAAT
* * * * * *
9131698 AAAGCTCCTCCAAACAGAAGCTCAACAACTTTGGACAATAAACAA
1 --AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAAT-AA-AT
*
9131743 AGCTCCTCTAAACAGAGGCCCAACGACTT
1 AGCTCCTCTAAACAGAGGCTCAACGACTT
9131772 AAACAAGCCT
Statistics
Matches: 199, Mismatches: 35, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
40 14 0.07
41 41 0.21
42 24 0.12
43 95 0.48
44 5 0.03
45 20 0.10
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (41 bp):
AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
Found at i:9143412 original size:58 final size:58
Alignment explanation
Indices: 9143282--9143542 Score: 245
Period size: 58 Copynumber: 4.5 Consensus size: 58
9143272 TTGTACAAAG
* * * *
9143282 AAAATTAATACTTTCAACTTTTTCC-C-AAATA-TTTTTCT--GAAACTTTAATTTCGAGA
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAAACTTTTT-TAAGAAAC-TTATTTTCAAGA
* * * * *
9143338 AAATTTGATACATTCAACTTTTCCTTAAAAAACCTTTTTTAAGAAA-TTATTTTTAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAA-CTTTTTTAAGAAACTTATTTTCAAGA
*
9143396 AAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAA-AAAGCTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-ACTTTTTTAAGAAA-CTTATTTTCAAGA
* * * * *
9143454 AAAATTGATACTTTCAATTTTTTCTC--AAAACTATTTTTTAGAAAACTCATTTTCATGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAACT-TTTTTAAG-AAACTTATTTTCAAGA
9143512 AAAATTGATACTTTCAACTTTTCCTCAAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA
9143543 TATATTTTTT
Statistics
Matches: 167, Mismatches: 23, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
55 7 0.04
56 22 0.13
57 18 0.11
58 104 0.62
59 9 0.05
60 7 0.04
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAAACTTTTTTAAGAAACTTATTTTCAAGA
Found at i:9143470 original size:116 final size:115
Alignment explanation
Indices: 9143277--9143551 Score: 287
Period size: 116 Copynumber: 2.4 Consensus size: 115
9143267 TGCTTTTGTA
* * * *
9143277 CAAAGAAAATTAATACTTTCAACTTTTTCC-C--AAATATTTTTCTGAAACTTTAATTTCGAGAA
1 CAAAAAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTT-TAAAACTTTAATTTCAAGAA
*
9143339 AATTTGATACATTCAACTTTTCCTTAAAAAACCT-TTTTTAAG-AAA-TTATTTT
64 AATTTGATACATTCAACTTTTCC-T-AAAAA-CTATTTTTAAGAAAACTCATTTT
* *
9143391 TAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAAGC-TTATTTTCAAGGA
1 CAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-AAAA-CTTTAATTTCAA-GA
* * * * *
9143455 AAA-TTGATACTTTCAATTTTTTCTCAAAACTATTTTTTAGAAAACTCATTTT
63 AAATTTGATACATTCAACTTTTCCTAAAAACTATTTTTAAGAAAACTCATTTT
**
9143507 CATGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTT
1 CAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTT
9143552 TTGTAATTTT
Statistics
Matches: 136, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
113 8 0.06
114 32 0.24
115 5 0.04
116 80 0.59
117 11 0.08
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (115 bp):
CAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAACTTTAATTTCAAGAAAA
TTTGATACATTCAACTTTTCCTAAAAACTATTTTTAAGAAAACTCATTTT
Found at i:9143574 original size:58 final size:56
Alignment explanation
Indices: 9143278--9143574 Score: 237
Period size: 58 Copynumber: 5.2 Consensus size: 56
9143268 GCTTTTGTAC
* *
9143278 AAAGAAAATTAATACTTTCAACTTTTTCC-C--AAATATTTTTCT-GAAACTTTAATTT
1 AAAGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTT-TAGAAA-TTTTATTT
** * *
9143333 CGAGAAAATTTGATACATTCAACTTTTCCTTAAAAA-ACCTTTTTTAAGAAATTATT-TTT
1 AAAGAAAA-TTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTT-AGAAATT-TTATTT
* * **
9143392 AAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAAGCTTATTTT
1 AAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAATTTTA-TTT
* * * * ** *
9143449 CAAGGAAAATTGATACTTTCAATTTTTTCTCAAAACTATTTTTTAGAAAACTCATTTT
1 -AAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAATTTTA-TTT
* * * *
9143507 CATGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGTAATTTTATTT
1 AAAG-AAAATTGATACTTTCAACTTTTCCTC-AAAA-ATATTTTTTAGAAATTTTATTT
9143566 AAAGAAAAT
1 AAAGAAAAT
9143575 CATTTTTAAA
Statistics
Matches: 192, Mismatches: 34, Indels: 29
0.75 0.13 0.11
Matches are distributed among these distances:
55 14 0.07
56 16 0.08
57 12 0.06
58 107 0.56
59 25 0.13
60 18 0.09
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (56 bp):
AAAGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAATTTTATTT
Found at i:9145409 original size:22 final size:19
Alignment explanation
Indices: 9145354--9145412 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 19
9145344 AAATAAATAT
*
9145354 ATAAAATATTTATTT-TT-
1 ATAAAAAATTTATTTATTA
9145371 -TAAAAAATTTATTTATTA
1 ATAAAAAATTTATTTATTA
9145389 ATAAAATAATATTATCTTATTA
1 ATAAAA-AAT-TTAT-TTATTA
9145411 AT
1 AT
9145413 TTTATCAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
16 13 0.37
17 2 0.06
19 5 0.14
20 3 0.09
21 4 0.11
22 8 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAAAAATTTATTTATTA
Found at i:9157174 original size:52 final size:52
Alignment explanation
Indices: 9157096--9157200 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
9157086 TTCAGCAGTC
9157096 GATGGACACGACCCACTGGGAACTACATTGAGAATATACAAAACAATAAGAA
1 GATGGACACGACCCACTGGGAACTACATTGAGAATATACAAAACAATAAGAA
9157148 GATGGACACGACCCACTGGGAACTACATTGAGAATATACAAAACAATAAGAA
1 GATGGACACGACCCACTGGGAACTACATTGAGAATATACAAAACAATAAGAA
9157200 G
1 G
9157201 CAACTGATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (52 bp):
GATGGACACGACCCACTGGGAACTACATTGAGAATATACAAAACAATAAGAA
Found at i:9159283 original size:18 final size:20
Alignment explanation
Indices: 9159228--9159280 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
9159218 TATTAATTTA
*
9159228 ATAAAAATATTAATTTATAT
1 ATAAAAATAATAATTTATAT
*
9159248 ATAATTAATACATAATTTATAT
1 ATAA-AAATA-ATAATTTATAT
9159270 -TAAAAATAATA
1 ATAAAAATAATA
9159281 TTTTTATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.11
20 8 0.29
21 7 0.25
22 10 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAAATAATAATTTATAT
Found at i:9159654 original size:21 final size:20
Alignment explanation
Indices: 9159630--9159688 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
9159620 AAAAAATAAA
9159630 AAAATTAAAAAATTATATAT
1 AAAATTAAAAAATTATATAT
** ** *
9159650 CAAAATTTTAATTTTATTTAT
1 -AAAATTAAAAAATTATATAT
*
9159671 ATAATTAAAAAATTATAT
1 AAAATTAAAAAATTATAT
9159689 TTTTTATTAC
Statistics
Matches: 27, Mismatches: 11, Indels: 1
0.69 0.28 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATTAAAAAATTATATAT
Found at i:9174704 original size:12 final size:12
Alignment explanation
Indices: 9174677--9174711 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
9174667 ATGTAGCTTC
*
9174677 AAATATAATTTTA
1 AAATAT-ATGTTA
9174690 AAATATATGTTA
1 AAATATATGTTA
9174702 AAATATATGT
1 AAATATATGT
9174712 ACATATCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (12 bp):
AAATATATGTTA
Found at i:9175201 original size:34 final size:35
Alignment explanation
Indices: 9175140--9175214 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 35
9175130 TTTGATTTTA
*
9175140 AATTAAAATAAATAGAACAACAACATA-TAAATTT
1 AATTAAAATAAATAGAACAACAACATATTAAACTT
* * ** *
9175174 AATTAAAATAAATATAATATTATCATATTAAACTT
1 AATTAAAATAAATAGAACAACAACATATTAAACTT
9175209 AATTAA
1 AATTAA
9175215 TTAAAATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 22 0.65
35 12 0.35
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (35 bp):
AATTAAAATAAATAGAACAACAACATATTAAACTT
Found at i:9176333 original size:3 final size:3
Alignment explanation
Indices: 9176325--9176351 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9176315 ATGCTAATGC
9176325 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
9176352 CATAAGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9177183 original size:31 final size:29
Alignment explanation
Indices: 9177148--9177222 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
9177138 TATACTTTTT
*
9177148 ATTTTTATATCAATATA-AATCATTACATATA
1 ATTTTTATAT-AATATATAA-CA-TAAATATA
* *
9177179 ATTTTTGTATAAAATATAACATAAATATA
1 ATTTTTATATAATATATAACATAAATATA
9177208 ATATTTTATATAATA
1 AT-TTTTATATAATA
9177223 CAATAATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 9 0.24
30 17 0.46
31 11 0.30
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTTTTATATAATATATAACATAAATATA
Found at i:9186634 original size:44 final size:44
Alignment explanation
Indices: 9186552--9186639 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
9186542 TTTAGTTAGG
* * *
9186552 ATTTTTAAAATTATAATGCCTTTGTTACGGAGGAGCCTTTTCAA
1 ATTTTTAAAATTATAATGCATTTATTACGGAGGAGCCTTGTCAA
*
9186596 ATTTTTAAAATT-TCAATGCATTTATTAGGGAAGG-GCCTTGTCAA
1 ATTTTTAAAATTAT-AATGCATTTATTACGG-AGGAGCCTTGTCAA
9186640 TTAAGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 34 0.89
45 3 0.08
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (44 bp):
ATTTTTAAAATTATAATGCATTTATTACGGAGGAGCCTTGTCAA
Found at i:9187062 original size:15 final size:15
Alignment explanation
Indices: 9187026--9187070 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
9187016 AGGCCCAAAA
*
9187026 ATTTTTTTA-TTCTT
1 ATTTTTTTATTTTTT
9187040 ATTCTTTTTATTTTTT
1 ATT-TTTTTATTTTTT
*
9187056 ATTTTTTGATTTTTT
1 ATTTTTTTATTTTTT
9187071 TCATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 3 0.11
15 17 0.63
16 7 0.26
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.80
Consensus pattern (15 bp):
ATTTTTTTATTTTTT
Found at i:9187603 original size:21 final size:20
Alignment explanation
Indices: 9187579--9187623 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
9187569 ATTCATGTTG
*
9187579 TTTTAGGATTTTTTAGAATTT
1 TTTTAGGAATTTTT-GAATTT
* *
9187600 TTTTGGGAATTTTTGGATTT
1 TTTTAGGAATTTTTGAATTT
9187620 TTTT
1 TTTT
9187624 GAATTTTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (20 bp):
TTTTAGGAATTTTTGAATTT
Found at i:9188157 original size:13 final size:13
Alignment explanation
Indices: 9188130--9188170 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
9188120 AATTTATATA
*
9188130 TTGTAT-ATATTT
1 TTGTATAATATGT
9188142 TTGTATAATATGT
1 TTGTATAATATGT
9188155 TTGTATAATATGT
1 TTGTATAATATGT
9188168 TTG
1 TTG
9188171 CATATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (13 bp):
TTGTATAATATGT
Found at i:9190526 original size:22 final size:23
Alignment explanation
Indices: 9190482--9190526 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
9190472 TTAAAAAAAT
* *
9190482 TAATAACTTAGAATTTATTCAAA
1 TAATAACTTAGAAATTATCCAAA
*
9190505 TAATAA-TTTGAAATTATCCAAA
1 TAATAACTTAGAAATTATCCAAA
9190527 AACAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (23 bp):
TAATAACTTAGAAATTATCCAAA
Found at i:9198133 original size:18 final size:18
Alignment explanation
Indices: 9198027--9198135 Score: 91
Period size: 18 Copynumber: 6.1 Consensus size: 18
9198017 CCTTTGTTCT
*
9198027 TGATACATTTGAGGTGAA
1 TGATACATTTGAGGTGGA
*
9198045 TGATATATTTGA---GGA
1 TGATACATTTGAGGTGGA
*
9198060 TGATACATTT-ATGGTGGG
1 TGATACATTTGA-GGTGGA
* * **
9198078 GGATACATTTGTGGTAAA
1 TGATACATTTGAGGTGGA
9198096 TGATACATTTGAGGAGGTGGA
1 TGATACATTT---GAGGTGGA
9198117 TGATACATTTGAGGTGGA
1 TGATACATTTGAGGTGGA
9198135 T
1 T
9198136 AATAACCATA
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
14 1 0.01
15 11 0.16
18 43 0.61
21 15 0.21
ACGTcount: A:0.29, C:0.05, G:0.31, T:0.35
Consensus pattern (18 bp):
TGATACATTTGAGGTGGA
Found at i:9198489 original size:6 final size:6
Alignment explanation
Indices: 9198478--9198515 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
9198468 CCAAAATTCG
9198478 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CA
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CA
9198516 TCATAATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (6 bp):
CACCAT
Found at i:9202515 original size:40 final size:39
Alignment explanation
Indices: 9202460--9202570 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 39
9202450 ATCCCACCCT
* * * **
9202460 CCTAACACCCCACCACGCCAAATCCCTCCCTGCCTTTCCC
1 CCTAACGCCCCACCACACCCAATCCCTCCCCACC-TTCCC
9202500 CCTAACGCCCCACCACACCCAATCCCTCCCCACCTTCCC
1 CCTAACGCCCCACCACACCCAATCCCTCCCCACCTTCCC
* * *
9202539 CCCAATGCCCCACCATACCCAATCCCTCCCCA
1 CCTAACGCCCCACCACACCCAATCCCTCCCCA
9202571 ACCCATCCAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 34 0.54
40 29 0.46
ACGTcount: A:0.22, C:0.60, G:0.04, T:0.14
Consensus pattern (39 bp):
CCTAACGCCCCACCACACCCAATCCCTCCCCACCTTCCC
Found at i:9202532 original size:20 final size:20
Alignment explanation
Indices: 9202507--9202591 Score: 61
Period size: 20 Copynumber: 4.3 Consensus size: 20
9202497 CCCCCTAACG
9202507 CCCCACCACACCCAATCCCT
1 CCCCACCACACCCAATCCCT
* * *
9202527 CCCCACCTTCCCCCCAAT---G
1 CCCCACC--ACACCCAATCCCT
*
9202546 CCCCACCATACCCAATCCCT
1 CCCCACCACACCCAATCCCT
* *
9202566 CCCCAACC-CATCCAATCTCT
1 CCCC-ACCACACCCAATCCCT
9202586 CCCCAC
1 CCCCAC
9202592 ATGCCTAATA
Statistics
Matches: 49, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
17 6 0.12
19 9 0.18
20 24 0.49
21 3 0.06
22 7 0.14
ACGTcount: A:0.22, C:0.62, G:0.01, T:0.14
Consensus pattern (20 bp):
CCCCACCACACCCAATCCCT
Found at i:9202729 original size:19 final size:20
Alignment explanation
Indices: 9202707--9202747 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
9202697 CTTTCCAAAA
9202707 TTTTCTTATTC-TCTCTC-TT
1 TTTTCTT-TTCATCTCTCATT
9202726 TTTTCTTTTCATCTCTCATT
1 TTTTCTTTTCATCTCTCATT
9202746 TT
1 TT
9202748 CTCTCGCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 13 0.65
20 4 0.20
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTCTTTTCATCTCTCATT
Found at i:9203944 original size:13 final size:13
Alignment explanation
Indices: 9203922--9203952 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9203912 TAAAAAATTT
*
9203922 TAAAATATAATAA
1 TAAAAAATAATAA
9203935 TAAAAAATAATAA
1 TAAAAAATAATAA
9203948 TAAAA
1 TAAAA
9203953 TTTTTCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAAATAATAA
Found at i:9204282 original size:20 final size:20
Alignment explanation
Indices: 9204234--9204285 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
9204224 AACCTTAGGT
*
9204234 AAAACCTT-AAACCCTAAAT
1 AAAACCTTAAAACCCTAAAC
*
9204253 GAAA-CTTAAAACCCTAAAC
1 AAAACCTTAAAACCCTAAAC
9204272 AAAACCTTAAAACC
1 AAAACCTTAAAACC
9204286 TTTGTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 3 0.11
19 16 0.57
20 9 0.32
ACGTcount: A:0.54, C:0.27, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAACCTTAAAACCCTAAAC
Found at i:9207579 original size:10 final size:10
Alignment explanation
Indices: 9207539--9207597 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
9207529 TAGACCAACC
9207539 TTAGTTTTCT
1 TTAGTTTTCT
*
9207549 TTAGTCTT-T
1 TTAGTTTTCT
*
9207558 TT-CTTGTTCT
1 TTAGTT-TTCT
9207568 TTAGTTTTCT
1 TTAGTTTTCT
**
9207578 TTAAACTTTCT
1 TT-AGTTTTCT
9207589 TTAGTTTTC
1 TTAGTTTTC
9207598 AAGATTATGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
8 1 0.03
9 5 0.14
10 21 0.57
11 10 0.27
ACGTcount: A:0.12, C:0.14, G:0.08, T:0.66
Consensus pattern (10 bp):
TTAGTTTTCT
Found at i:9211120 original size:20 final size:20
Alignment explanation
Indices: 9211095--9211136 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
9211085 GAAAAAAGAT
*
9211095 ACGAAAACAATGAAAGAGAA
1 ACGAAAAAAATGAAAGAGAA
9211115 ACGAAAAAAATGAAAGAGAA
1 ACGAAAAAAATGAAAGAGAA
9211135 AC
1 AC
9211137 CAATCCATTC
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:0.67, C:0.10, G:0.19, T:0.05
Consensus pattern (20 bp):
ACGAAAAAAATGAAAGAGAA
Found at i:9220811 original size:28 final size:27
Alignment explanation
Indices: 9220780--9220846 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
9220770 TTTTAGAAGG
* * * *
9220780 TCTTAGAATTTGGTCTTAATTTATGGAT
1 TCTT-GAATTTGATCATAAATTAGGGAT
*
9220808 TCTTGAAATTTTATCATAAATTAGGGAT
1 TCTTG-AATTTGATCATAAATTAGGGAT
9220836 TCTTGGAATTT
1 TCTT-GAATTT
9220847 AGTCCCAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.03
28 30 0.94
29 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.48
Consensus pattern (27 bp):
TCTTGAATTTGATCATAAATTAGGGAT
Found at i:9220911 original size:29 final size:28
Alignment explanation
Indices: 9220876--9220942 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
9220866 TTCAAATCTG
* *
9220876 GTCCCAATTTAGAAATTTTTACAATGTT
1 GTCCCAATTTAGAAATTCTTACAATGTA
* *
9220904 GTCCCCAA-TTAGGAATTCTTAGAATGTA
1 GT-CCCAATTTAGAAATTCTTACAATGTA
9220932 GTCCCAATTTA
1 GTCCCAATTTA
9220943 AGGATTCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.15
28 23 0.70
29 5 0.15
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (28 bp):
GTCCCAATTTAGAAATTCTTACAATGTA
Found at i:9220949 original size:28 final size:26
Alignment explanation
Indices: 9220832--9220963 Score: 81
Period size: 28 Copynumber: 4.8 Consensus size: 26
9220822 CATAAATTAG
* * *
9220832 GGATTCTTGGAATTTAGTCCCAATGTA
1 GGATTCTT-AAATGTAGTCCCAATTTA
* * *
9220859 GGGATTTTTCAAATCTGGTCCCAATTTA
1 -GGATTCTT-AAATGTAGTCCCAATTTA
* * *
9220887 GAAATTTTTACAATGTTGTCCCCAA-TTA
1 G-GATTCTTA-AATGTAGT-CCCAATTTA
9220915 GGAATTCTTAGAATGTAGTCCCAATTTAA
1 GG-ATTCTTA-AATGTAGTCCCAATTT-A
9220944 GGATTCTTAAA--TAGTCCCAA
1 GGATTCTTAAATGTAGTCCCAA
9220964 CTTATCAATT
Statistics
Matches: 85, Mismatches: 13, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
25 9 0.11
27 9 0.11
28 59 0.69
29 8 0.09
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (26 bp):
GGATTCTTAAATGTAGTCCCAATTTA
Found at i:9224064 original size:13 final size:13
Alignment explanation
Indices: 9224046--9224071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9224036 ACAAGGTAAC
9224046 TTGGCAATGTCAT
1 TTGGCAATGTCAT
9224059 TTGGCAATGTCAT
1 TTGGCAATGTCAT
9224072 GTAGGACAAG
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:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
TTGGCAATGTCAT
Found at i:9225814 original size:30 final size:29
Alignment explanation
Indices: 9225743--9225819 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
9225733 GGCTATTTGG
*
9225743 CCTAACAAGTGGTATCAGAGCTATGGTGAT
1 CCTAAC-AGTGGTATCAGAGCTATAGTGAT
* *
9225773 CCAAATAAGTGGTATCAGAGCTATAGTGAT
1 CCTAA-CAGTGGTATCAGAGCTATAGTGAT
9225803 CCCTAACAGTGGTATCA
1 -CCTAACAGTGGTATCA
9225820 AAACTAAAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 36 0.90
31 4 0.10
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (29 bp):
CCTAACAGTGGTATCAGAGCTATAGTGAT
Found at i:9226468 original size:926 final size:939
Alignment explanation
Indices: 9224818--9226672 Score: 2237
Period size: 966 Copynumber: 2.0 Consensus size: 939
9224808 CCTAACAAGA
* * * * ** * *
9224818 GGTATTAGAGCTATGGTGATCCTTAACAGTGGTATCAGAGTTGAAGCTCAAGATGTAAGAAAAGC
1 GGTATCAGAGCTATAGTGATCCCTAACAGTGGTATCAAAACTAAAGCTCAAGATATAAGAAAAGC
* * *
9224883 TGATAGTTTGAGACATGAGAAAAGATAAGCTTAGAGGAGTTCGATTCAAGAAAAAAGTTCAAGTT
66 AGATAGTTCGAGACATGAGAAAAGACAAGCTTAGAGGAGTTCGATTCAAGAAAAAAGTTCAAGTT
* * * * * *
9224948 TGTGTTTTAAAGATCGATTTGCTTGAAACGTAAAAGCATACAAAAGAAAATGATTGTGAGACTTT
131 CGTGTTTTAAAGATAGATTTGCATGAAACGTAAAAGCACACAAAAGAAAATAATTGTGAAACTTT
*
9225013 CATTACAAGTGAAGCCAAGCATGTCTAGCATGAAGATAAATTATTGATAGAATTTGAGTCAAGGT
196 CATTACAAGTGAAGCCAAGCATGTCTAGCATGAAGACAAATTATTGATAGAATTTGAGTCAAGGT
*
9225078 GGAGATTGTTAGGAATAATAACTCAAATCTCATAGGAGATTTATTTGGGATTTGTTAAAGATTTG
261 GGAGATTGTTAGGAATAATAACTCAAATCCCATAGGAG---TATTT-GG--TTGTTAAAGATTTG
* * * * *
9225143 TTAGATATTACTTGATCGACAAGAAGACTTGTAGAAGAAGAATTCTAAAAGAAAAAATATTCTTA
320 TTAGATATTACTTGATCAACAAGAAGACTTGCAAAAAAAGAATTCTAAAAGAAAAAAGATTCTTA
* * * * *
9225208 ATAGGTAAGTTTGACTTACAGAAAAAGAATTCTCAGATGAGAGAGATTCTTAATAGGTAAGTTTG
385 ATAGATAAGTTTGACTTACAGAAAAAGAATTCTAAGAGGAGAGAGATTCTTAATAGGCAAGTTTA
*
9225273 TATGGTTATAAATAAGTAAAGTCTCTATAGGGTTAGGTATGAGAAAAAATGTAAGAGAGTTATAA
450 TATAGTTATAAATAAGTAAAG-CTC------G-T--GTAT-------AA-GT-A-AGAGTTATAA
* * * * *
9225338 GGTTTTATGAGTAGACAACCCATAAGATTATTAAAGATTTATGTCATATGGGCGTGTATGTTTGT
495 GATTTTATGAGTAGACAACCCATAAGACTATGAAAGATTTACGTCATATAGGCGTGTATGTTTGT
*
9225403 TTGTGAGTGGACTAGAGGAAACTGAGAGGGTCCACATAGGTATGATGTATAGGTGCATATGGATA
560 TTGTGAGTGGACTAGAGGAAACTGAGAGGGTCCACATAAGTATGATGTATAGGTGCATATGGATA
* * * *
9225468 TGTGTTTGGTTGTATTGAAATAGTGCATATGAGTACGTATTTATTTTGATTGAGAATACTCTATA
625 TGTGTTTGGTTGTATTGAAATAGTGCACATGAGTACGGATTTATTTAGATTGAGAATACTCCATA
* ** *
9225533 GGACTAGAGGAGATTAAAAAGGTCTATGGGTATTGATTGTTGAG-AGGTTGATATATTTTAATGT
690 AGACTAGAGGAGATTAAAAAGGTCTACAGGTATTGATTGTTGAGTA-GTTGATATATTTTAATAT
* * * *
9225597 ATGTTTGTAGTTCTCTACAACTAGT-GATTTTATTTTTCATCTATGGACGTAGATCGATTAAACT
754 ATGTTTGTAATTCTCTACAACTAGTGGATCTTATTTCTCATCCATGGACGTAGATCGATTAAACT
* * * * *
9225661 AAACCACA-TTAAATTACTGTCTTTTATGTGATTAATTATTTGATTTTGCT-TCCACTGATATGA
819 AAACCA-AGTTAAAGTACTATCTCTTATGTGATTAATTATTTGATTTTGCTGT--ACTAATATAA
* *
9225724 TTGGATTGGGGCTATTTGGCCTAACAAGTGGTATCAGAGCTATGGTGATCCAAATAAGT
881 TTAGATTAGGGCTATTTGGCCTAACAAGTGGTATCAGAGCTATGGTGATCCAAATAAGT
*
9225783 GGTATCAGAGCTATAGTGATCCCTAACAGTGGTATCAAAACTAAAGGTTCAAGATATAAGAAAAG
1 GGTATCAGAGCTATAGTGATCCCTAACAGTGGTATCAAAACTAAA-GCTCAAGATATAAGAAAAG
* * * *
9225848 CAGATGGTTCGAGACATGAGAATAA-ACAAGCTTAGAGGAGTTTGATTCAAGAAAGAAATTTGAA
65 CAGATAGTTCGAGACATGAGAA-AAGACAAGCTTAGAGGAGTTCGATTCAAGAAA-AAAGTTCAA
* * * * * *
9225912 -TTCGTGTTTTAAAGTTAGGTTTGCATGAAGCGTAAAGGCACACAAGAGAAGATAATTGTGAAAC
128 GTTCGTGTTTTAAAGATAGATTTGCATGAAACGTAAAAGCACACAAAAGAAAATAATTGTGAAAC
* * * * *
9225976 TTTCATTACAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGATTATTGATGGAATTTGAGTTAA
193 TTTCATTACAAGTGAAGCCAAGCATGTCTAGCATGAAGACAAATTATTGATAGAATTTGAGTCAA
* *
9226041 GGTGGAGATTGTTAGGAATAATGACTCAAATCCCATAGGAG-ATTT-G-T-TT-AGGATTTGTTA
258 GGTGGAGATTGTTAGGAATAATAACTCAAATCCCATAGGAGTATTTGGTTGTTAAAGATTTGTTA
** * *
9226101 GATATTGTTTGATCAACCAGAAGACTTGCAAAAAAATG-ATTCTAAAAGGAAAAAGATTCTTAAT
323 GATATTACTTGATCAACAAGAAGACTTGCAAAAAAA-GAATTCTAAAAGAAAAAAGATTCTTAAT
* *
9226165 AGATAAGTTTGAC-TGCA-AAAGAAGAATTTTAAGAGGAGAGAGATTCTTAATAGGCAAGTTTAT
387 AGATAAGTTTGACTTACAGAAA-AAGAATTCTAAGAGGAGAGAGATTCTTAATAGGCAAGTTTAT
* * *
9226228 ATAGTTATAAATAGGTGAAG-TC-T-T-T-A-T-AGAGTTATAAGATTTTATGGGTAGAC-ACCT
451 ATAGTTATAAATAAGTAAAGCTCGTGTATAAGTAAGAGTTATAAGATTTTATGAGTAGACAACC-
* *
9226285 CATAAGACTACTGAAA-ATTTACGTCTTATAGGCGTGTATGTTTGTTTGTGAGTGGA-TTGAGGA
515 CATAAGACTA-TGAAAGATTTACGTCATATAGGCGTGTATGTTTGTTTGTGAGTGGACTAGAGGA
* * * * *
9226348 GACTGAGAGGGTCCACATAAGTATGATGTATTGGTGCATATGGGTATTTGTTTGGTTGTGTTGAA
579 AACTGAGAGGGTCCACATAAGTATGATGTATAGGTGCATATGGATATGTGTTTGGTTGTATTGAA
* * * * * * *
9226413 ATGGTGCACATGGGTATGGGTTTGTTTAGGTTGAGAATACTCCATAAGACTAGAGGAGATTAAGA
644 ATAGTGCACATGAGTACGGATTTATTTAGATTGAGAATACTCCATAAGACTAGAGGAGATTAAAA
*
9226478 GGGTCTACAGGTATTGATTGTTGAGTAGTTGATATATTTTAATATATGTTTGTAATTCTCTACAA
709 AGGTCTACAGGTATTGATTGTTGAGTAGTTGATATATTTTAATATATGTTTGTAATTCTCTACAA
* * * * ** * *
9226543 TTAGTGGATCTTGTTTCTCATCCGTGGACGTAGGTCGATTGGACTGAACCAAGTTAAAGTATTAT
774 CTAGTGGATCTTATTTCTCATCCATGGACGTAGATCGATTAAACTAAACCAAGTTAAAGTACTAT
* * *
9226608 CTCTTGTGTGATTGATTATTTGATTTTGCTGTACTAATGTAATTAGATTAGGGCTATTTGGCCTA
839 CTCTTATGTGATTAATTATTTGATTTTGCTGTACTAATATAATTAGATTAGGGCTATTTGGCCTA
9226673 GCTGTCAAAC
Statistics
Matches: 771, Mismatches: 108, Indels: 61
0.82 0.11 0.06
Matches are distributed among these distances:
926 212 0.27
927 143 0.19
928 5 0.01
930 1 0.00
932 1 0.00
940 1 0.00
941 1 0.00
944 1 0.00
952 2 0.00
953 3 0.00
954 57 0.07
955 75 0.10
956 3 0.00
957 1 0.00
960 1 0.00
962 4 0.01
965 38 0.05
966 213 0.28
967 9 0.01
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.33
Consensus pattern (939 bp):
GGTATCAGAGCTATAGTGATCCCTAACAGTGGTATCAAAACTAAAGCTCAAGATATAAGAAAAGC
AGATAGTTCGAGACATGAGAAAAGACAAGCTTAGAGGAGTTCGATTCAAGAAAAAAGTTCAAGTT
CGTGTTTTAAAGATAGATTTGCATGAAACGTAAAAGCACACAAAAGAAAATAATTGTGAAACTTT
CATTACAAGTGAAGCCAAGCATGTCTAGCATGAAGACAAATTATTGATAGAATTTGAGTCAAGGT
GGAGATTGTTAGGAATAATAACTCAAATCCCATAGGAGTATTTGGTTGTTAAAGATTTGTTAGAT
ATTACTTGATCAACAAGAAGACTTGCAAAAAAAGAATTCTAAAAGAAAAAAGATTCTTAATAGAT
AAGTTTGACTTACAGAAAAAGAATTCTAAGAGGAGAGAGATTCTTAATAGGCAAGTTTATATAGT
TATAAATAAGTAAAGCTCGTGTATAAGTAAGAGTTATAAGATTTTATGAGTAGACAACCCATAAG
ACTATGAAAGATTTACGTCATATAGGCGTGTATGTTTGTTTGTGAGTGGACTAGAGGAAACTGAG
AGGGTCCACATAAGTATGATGTATAGGTGCATATGGATATGTGTTTGGTTGTATTGAAATAGTGC
ACATGAGTACGGATTTATTTAGATTGAGAATACTCCATAAGACTAGAGGAGATTAAAAAGGTCTA
CAGGTATTGATTGTTGAGTAGTTGATATATTTTAATATATGTTTGTAATTCTCTACAACTAGTGG
ATCTTATTTCTCATCCATGGACGTAGATCGATTAAACTAAACCAAGTTAAAGTACTATCTCTTAT
GTGATTAATTATTTGATTTTGCTGTACTAATATAATTAGATTAGGGCTATTTGGCCTAACAAGTG
GTATCAGAGCTATGGTGATCCAAATAAGT
Found at i:9229523 original size:28 final size:28
Alignment explanation
Indices: 9229491--9229563 Score: 69
Period size: 30 Copynumber: 2.5 Consensus size: 28
9229481 TCAAAATGAC
*
9229491 AACAAAAAAATTCATCACTA-AGAAAATA
1 AACAAAAAAATTCATCA-TACAAAAAATA
**
9229519 AACAAATCAATTCACTTCATACAAAAAATA
1 AACAAAAAAATTCA--TCATACAAAAAATA
9229549 AA-AAATAAAATTCAT
1 AACAAA-AAAATTCAT
9229564 ATGTGATACA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
28 13 0.36
29 5 0.14
30 18 0.50
ACGTcount: A:0.62, C:0.15, G:0.01, T:0.22
Consensus pattern (28 bp):
AACAAAAAAATTCATCATACAAAAAATA
Found at i:9232173 original size:48 final size:48
Alignment explanation
Indices: 9232117--9232213 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
9232107 TCAAGGTGGA
*
9232117 ATCTAATTTTACCCACATTCGGGTATCAAAGTATGAAATGGATCTTGT
1 ATCTAATTTTACCCACATTCAGGTATCAAAGTATGAAATGGATCTTGT
* *
9232165 ATCTAATTTTACCCGCATTCAGGTATCAATGTATGAAATGGATCTTGT
1 ATCTAATTTTACCCACATTCAGGTATCAAAGTATGAAATGGATCTTGT
9232213 A
1 A
9232214 CCCTTGTGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (48 bp):
ATCTAATTTTACCCACATTCAGGTATCAAAGTATGAAATGGATCTTGT
Found at i:9234802 original size:14 final size:14
Alignment explanation
Indices: 9234785--9234876 Score: 82
Period size: 14 Copynumber: 6.7 Consensus size: 14
9234775 GGATTTAGTT
**
9234785 TTTAAGGTTTGGGA
1 TTTAAGGTTTAAGA
9234799 TTTAAGGTTTAAGA
1 TTTAAGGTTTAAGA
* *
9234813 TTTAAGCTTTAAGG
1 TTTAAGGTTTAAGA
* *
9234827 TTTAAGATTAAAG-
1 TTTAAGGTTTAAGA
*
9234840 TTTAA-GATTAAGA
1 TTTAAGGTTTAAGA
*
9234853 TTT-AGGTTTTAGAA
1 TTTAAGGTTTAAG-A
9234867 TTTAAGGTTT
1 TTTAAGGTTT
9234877 CCTGGAGTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
12 5 0.08
13 13 0.21
14 39 0.62
15 6 0.10
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.45
Consensus pattern (14 bp):
TTTAAGGTTTAAGA
Found at i:9234809 original size:21 final size:21
Alignment explanation
Indices: 9234797--9234856 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
9234787 TAAGGTTTGG
9234797 GATTTAAGGTTTAAGATTTAA
1 GATTTAAGGTTTAAGATTTAA
* *
9234818 GCTTTAAGGTTTAAGATTAAA
1 GATTTAAGGTTTAAGATTTAA
*
9234839 G-TTTAA-GATTAAGATTTA
1 GATTTAAGGTTTAAGATTTA
9234857 GGTTTTAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.29
20 5 0.14
21 20 0.57
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (21 bp):
GATTTAAGGTTTAAGATTTAA
Found at i:9234811 original size:7 final size:7
Alignment explanation
Indices: 9234785--9234876 Score: 57
Period size: 7 Copynumber: 13.4 Consensus size: 7
9234775 GGATTTAGTT
9234785 TTTAAGG
1 TTTAAGG
*
9234792 TTT-GGG
1 TTTAAGG
9234798 ATTTAAGG
1 -TTTAAGG
*
9234806 TTTAAGA
1 TTTAAGG
*
9234813 TTTAAGC
1 TTTAAGG
9234820 TTTAAGG
1 TTTAAGG
9234827 TTTAA-G
1 TTTAAGG
* *
9234833 ATTAAAG
1 TTTAAGG
9234840 TTTAA-G
1 TTTAAGG
* *
9234846 ATTAAGA
1 TTTAAGG
9234853 TTT-AGG
1 TTTAAGG
* *
9234859 TTTTAGAA
1 TTTAAG-G
9234867 TTTAAGG
1 TTTAAGG
9234874 TTT
1 TTT
9234877 CCTGGAGTTG
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
6 17 0.26
7 41 0.63
8 7 0.11
ACGTcount: A:0.33, C:0.01, G:0.22, T:0.45
Consensus pattern (7 bp):
TTTAAGG
Found at i:9234856 original size:13 final size:13
Alignment explanation
Indices: 9234797--9234856 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
9234787 TAAGGTTTGG
*
9234797 GATTTAAGGTTTAA
1 GATTTAA-GATTAA
*
9234811 GATTTAAGCTTTAA
1 GATTTAAG-ATTAA
*
9234825 GGTTTAAGATTAA
1 GATTTAAGATTAA
9234838 -AGTTTAAGATTAA
1 GA-TTTAAGATTAA
9234851 GATTTA
1 GATTTA
9234857 GGTTTTAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 20 0.50
14 20 0.50
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (13 bp):
GATTTAAGATTAA
Found at i:9235461 original size:35 final size:35
Alignment explanation
Indices: 9235415--9235498 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 35
9235405 TCATAATGAT
* *
9235415 TTTTAGTTTACAATCTTCAAATGATTAGGGATTCG
1 TTTTAGTTTACAATCTTCAAATAATTAAGGATTCG
* * *
9235450 TTTTATTTTACATTCTTCGAATAATTAAGGATTCG
1 TTTTAGTTTACAATCTTCAAATAATTAAGGATTCG
9235485 TTTTAGTTTACAAT
1 TTTTAGTTTACAAT
9235499 TTTCGAGTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTAGTTTACAATCTTCAAATAATTAAGGATTCG
Found at i:9235534 original size:25 final size:25
Alignment explanation
Indices: 9235485--9235535 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
9235475 TAAGGATTCG
*
9235485 TTTTAGTTTACAATTTTCGAGTGAT
1 TTTTAGTTTACAATTTTCGAATGAT
*
9235510 TTTTAGTTTACAGTCTTT-GAATGAT
1 TTTTAGTTTACAAT-TTTCGAATGAT
9235535 T
1 T
9235536 AGTCACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (25 bp):
TTTTAGTTTACAATTTTCGAATGAT
Found at i:9236082 original size:9 final size:11
Alignment explanation
Indices: 9236058--9236114 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
9236048 AAATTTTCTT
9236058 TCTTTTTTTCC
1 TCTTTTTTTCC
9236069 TCTTTTTTTCC
1 TCTTTTTTTCC
*
9236080 TTTACTTTTTTTTC
1 --T-CTTTTTTTCC
*
9236094 TCTTTTCTTCC
1 TCTTTTTTTCC
9236105 TCTTGTTTTT
1 TCTT-TTTTT
9236115 TGCATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 23 0.61
12 5 0.13
13 1 0.03
14 9 0.24
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.74
Consensus pattern (11 bp):
TCTTTTTTTCC
Found at i:9236096 original size:25 final size:24
Alignment explanation
Indices: 9236051--9236115 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
9236041 CATAAAAAAA
9236051 TTTT-CTTTCTTTTTTTCCTCTTT
1 TTTTCCTTTCTTTTTTTCCTCTTT
*
9236074 TTTTCCTTTACTTTTTTTTCTCTTT
1 TTTTCCTTT-CTTTTTTTCCTCTTT
* *
9236099 TCTTCCTCTTGTTTTTT
1 TTTTCCT-TTCTTTTTT
9236116 GCATTTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 4 0.11
24 4 0.11
25 26 0.72
26 2 0.06
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTCCTTTCTTTTTTTCCTCTTT
Found at i:9237844 original size:46 final size:47
Alignment explanation
Indices: 9237759--9237851 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 47
9237749 AGTCTTAGGT
** *
9237759 AAGTGACTTTAAAAATCATTTTTTGAAAAGTGCTCTTATAAACATAGC
1 AAGTGACTTTAAAAATCA-TCCTTGAAAAGTGCTATTATAAACATAGC
*
9237807 AAGTGACTTTAAAAATC-TCCTTGAAAAGTGCTATTATAAAGATAG
1 AAGTGACTTTAAAAATCATCCTTGAAAAGTGCTATTATAAACATAG
9237852 GTAATAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 24 0.59
48 17 0.41
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (47 bp):
AAGTGACTTTAAAAATCATCCTTGAAAAGTGCTATTATAAACATAGC
Found at i:9238031 original size:49 final size:47
Alignment explanation
Indices: 9237764--9238028 Score: 232
Period size: 49 Copynumber: 5.5 Consensus size: 47
9237754 TAGGTAAGTG
* ***
9237764 ACTTTAAAAATCAT-TTTTTGAAAAGTGCTCTTATAAACAT-AGCAAGTG
1 ACTTTAAAAATC-TCATTTTGAAAAG-GCTCTTATAAA-ATAAGCAACAA
* * * * *
9237812 ACTTTAAAAATCTC--CTTGAAAAGTGCTATTATAAAGATAGGTAATAA
1 ACTTTAAAAATCTCATTTTGAAAAG-GCTCTTATAAA-ATAAGCAACAA
* * * *
9237859 ACTTTAAAATTCTCATTTTGGAAAGGGCTCATATGAAAATGAGCAACAA
1 ACTTTAAAAATCTCATTTT-GAAAAGGCTCTTAT-AAAATAAGCAACAA
* * * **
9237908 ACCTTAAAAATCTCATTTTGAAAGGGCTCTTATGAAAATAAACAGTAA
1 ACTTTAAAAATCTCATTTTGAAAAGGCTCTTAT-AAAATAAGCAACAA
* *
9237956 ACTTTTAAAATCTCATTTTGAAAAAGGCTCTTATAATGATAAGCAACAA
1 ACTTTAAAAATCTCATTTTG-AAAAGGCTCTTATAA-AATAAGCAACAA
9238005 ACTTTAAAAATCTCATTTTGAAAA
1 ACTTTAAAAATCTCATTTTGAAAA
9238029 AGGGCTCCTT
Statistics
Matches: 177, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
46 21 0.12
47 17 0.10
48 60 0.34
49 71 0.40
50 8 0.05
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (47 bp):
ACTTTAAAAATCTCATTTTGAAAAGGCTCTTATAAAATAAGCAACAA
Found at i:9238047 original size:79 final size:79
Alignment explanation
Indices: 9237957--9238107 Score: 230
Period size: 79 Copynumber: 1.9 Consensus size: 79
9237947 AAACAGTAAA
* * * *
9237957 CTTTTAAAATCTCATTTTGAAAAAGGCTCTTATAATGATAAGCAACAAACTTTAAAAATCTCATT
1 CTTTAAAAATCTCATTTTGAAAAAGGCTCCTATAAAGATAAGCAACAAACTTTAAAAACCTCATT
9238022 TTGAAAAAGGGCTC
66 TTGAAAAAGGGCTC
* * * *
9238036 CTTTAAAAATCTCATTTTGAAAAGGGCTCCTATAAAGATAGGCAACAAATTTTAAAAACCTTATT
1 CTTTAAAAATCTCATTTTGAAAAAGGCTCCTATAAAGATAAGCAACAAACTTTAAAAACCTCATT
9238101 TTGAAAA
66 TTGAAAA
9238108 GGCTCTTATA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (79 bp):
CTTTAAAAATCTCATTTTGAAAAAGGCTCCTATAAAGATAAGCAACAAACTTTAAAAACCTCATT
TTGAAAAAGGGCTC
Found at i:9238059 original size:29 final size:30
Alignment explanation
Indices: 9238006--9238071 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
9237996 AAGCAACAAA
9238006 CTTTAAAAATCTCATTTTGAAAAAGGGCTC
1 CTTTAAAAATCTCATTTTGAAAAAGGGCTC
9238036 CTTTAAAAATCTCATTTTG-AAAAGGGCTC
1 CTTTAAAAATCTCATTTTGAAAAAGGGCTC
*
9238065 CTATAAA
1 CTTTAAA
9238072 GATAGGCAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (30 bp):
CTTTAAAAATCTCATTTTGAAAAAGGGCTC
Found at i:9238128 original size:48 final size:48
Alignment explanation
Indices: 9238037--9238298 Score: 227
Period size: 49 Copynumber: 5.5 Consensus size: 48
9238027 AAAGGGCTCC
* * *
9238037 TTTAAAAATCTCATTTTGAAAAGGGCTCCTATAAAGATAGGCAACAAAT
1 TTTAAAAA-CTTATTTTGAAAAGGGCTCTTATAAAGATAGACAACAAAT
* *
9238086 TTTAAAAACCTTATTTTGAAAA-GGCTCTTATAAAGATAGGCAACAAAC
1 TTTAAAAA-CTTATTTTGAAAAGGGCTCTTATAAAGATAGACAACAAAT
*
9238134 TTTAAAAACTTCATTTTGAAAATGGCT-TCTATAAAGAT-------AAAT
1 TTTAAAAACTT-ATTTTGAAAAGGGCTCT-TATAAAGATAGACAACAAAT
* * * *
9238176 TTCAAAAAATTCCATTTTGAAAAGGGTTCTTATAAAGATAGATAACAAAT
1 TTTAAAAACTT--ATTTTGAAAAGGGCTCTTATAAAGATAGACAACAAAT
* * * * *
9238226 TTTAAAAATCTTATTTCGAAAAGGACTTTTATAAAAGATAAACAACAAAC
1 TTTAAAAA-CTTATTTTGAAAAGGGCTCTTAT-AAAGATAGACAACAAAT
**
9238276 TTTAAAATTTTCATTTTGAAAAG
1 TTTAAAAACTT-ATTTTGAAAAG
9238299 TTTTGAAAGT
Statistics
Matches: 177, Mismatches: 21, Indels: 29
0.78 0.09 0.13
Matches are distributed among these distances:
42 12 0.07
43 23 0.13
44 1 0.01
47 3 0.02
48 43 0.24
49 51 0.29
50 42 0.24
51 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (48 bp):
TTTAAAAACTTATTTTGAAAAGGGCTCTTATAAAGATAGACAACAAAT
Found at i:9238137 original size:127 final size:128
Alignment explanation
Indices: 9237911--9238297 Score: 390
Period size: 127 Copynumber: 2.9 Consensus size: 128
9237901 GCAACAAACC
* ** *
9237911 TTAAAAATCTCATTTTG-AAAGGGCTCTTATGAAA-ATAAACAGTAAACTTTT-AAAATCTCATT
1 TTAAAAATCTCATTTTGAAAAGGGCTCTTAT-AAAGATAGACAACAAA-TTTTAAAAATCTTATT
*
9237973 TTGAAAAAGGCTCTTATAATGATAAGCAACAAACTTTAAAAATCTCATTTTGAAAAAGGGCTCCT
64 TTG-AAAAGGCTCTTATAAAGATAAGCAACAAACTTTAAAAATCTCATTTTGAAAAAGGGCTCCT
9238038 -
128 A
* * *
9238038 TTAAAAATCTCATTTTGAAAAGGGCTCCTATAAAGATAGGCAACAAATTTTAAAAACCTTATTTT
1 TTAAAAATCTCATTTTGAAAAGGGCTCTTATAAAGATAGACAACAAATTTTAAAAATCTTATTTT
* * *
9238103 GAAAAGGCTCTTATAAAGATAGGCAACAAACTTTAAAAA-CTTCATTTTG-AAAATGGCTTCTA
66 GAAAAGGCTCTTATAAAGATAAGCAACAAACTTTAAAAATC-TCATTTTGAAAAAGGGCTCCTA
* * *
9238165 TAAAGATAAATTTCAAAAAATTCCATTTTGAAAAGGGTTCTTATAAAGATAGATAACAAATTTTA
1 T-TA-A-AAA--TC-------T-CATTTTGAAAAGGGCTCTTATAAAGATAGACAACAAATTTTA
* * * * *
9238230 AAAATCTTATTTCGAAAAGGACTTTTATAAAAGATAAACAACAAACTTTAAAATTTTCATTTTGA
53 AAAATCTTATTTTGAAAAGG-CTCTTAT-AAAGATAAGCAACAAACTTTAAAAATCTCATTTTGA
9238295 AAA
116 AAA
9238298 GTTTTGAAAG
Statistics
Matches: 215, Mismatches: 23, Indels: 28
0.81 0.09 0.11
Matches are distributed among these distances:
126 11 0.05
127 69 0.32
128 33 0.15
129 1 0.00
130 3 0.01
132 2 0.01
139 1 0.00
140 56 0.26
141 6 0.03
142 30 0.14
143 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (128 bp):
TTAAAAATCTCATTTTGAAAAGGGCTCTTATAAAGATAGACAACAAATTTTAAAAATCTTATTTT
GAAAAGGCTCTTATAAAGATAAGCAACAAACTTTAAAAATCTCATTTTGAAAAAGGGCTCCTA
Found at i:9238247 original size:92 final size:92
Alignment explanation
Indices: 9238098--9238267 Score: 238
Period size: 92 Copynumber: 1.8 Consensus size: 92
9238088 TAAAAACCTT
* *
9238098 ATTTTGAAAAGGCTCTTATAAAGATAGGCAACAAACTTTAAAAACTTCATTTTGAAAATGG-CTT
1 ATTTTGAAAAGGCTCTTATAAAGATAGACAACAAACTTTAAAAACTTCATTTCGAAAA-GGACTT
9238162 CTAT-AAAGATAAATTTCAAAAAATTCC
65 CTATAAAAGATAAATTTCAAAAAATTCC
* * *
9238189 ATTTTGAAAAGGGTTCTTATAAAGATAGATAACAAATTTTAAAAATCTT-ATTTCGAAAAGGACT
1 ATTTTGAAAA-GGCTCTTATAAAGATAGACAACAAACTTTAAAAA-CTTCATTTCGAAAAGGACT
*
9238253 TTTATAAAAGATAAA
64 TCTATAAAAGATAAA
9238268 CAACAAACTT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
91 12 0.17
92 45 0.65
93 12 0.17
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (92 bp):
ATTTTGAAAAGGCTCTTATAAAGATAGACAACAAACTTTAAAAACTTCATTTCGAAAAGGACTTC
TATAAAAGATAAATTTCAAAAAATTCC
Found at i:9238577 original size:31 final size:31
Alignment explanation
Indices: 9238542--9238603 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
9238532 TTATGACAAC
*
9238542 AAGGTTTTCATGATTGCAACTATCTTCAAAT
1 AAGGTTTTCATGACTGCAACTATCTTCAAAT
* *
9238573 AAGGTTTTCATGACTGTAACTATTTTCAAAT
1 AAGGTTTTCATGACTGCAACTATCTTCAAAT
9238604 TCTTGGTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
AAGGTTTTCATGACTGCAACTATCTTCAAAT
Found at i:9239554 original size:13 final size:12
Alignment explanation
Indices: 9239536--9239618 Score: 55
Period size: 12 Copynumber: 6.8 Consensus size: 12
9239526 TTGTCATTTC
9239536 TCTTTTTTTGCTT
1 TCTTTTTTT-CTT
9239549 TCTTTTTTTCTT
1 TCTTTTTTTCTT
* * *
9239561 T-TTGTCTCCTT
1 TCTTTTTTTCTT
*
9239572 TC-CTTTTTCTTT
1 TCTTTTTTTC-TT
*
9239584 TCATTGTTTTCTT
1 TC-TTTTTTTCTT
9239597 CTCTTTTTTT-TT
1 -TCTTTTTTTCTT
9239609 TCATTTTTTT
1 TC-TTTTTTT
9239619 TCAAACTCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
11 13 0.24
12 17 0.31
13 17 0.31
14 7 0.13
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (12 bp):
TCTTTTTTTCTT
Found at i:9239590 original size:25 final size:25
Alignment explanation
Indices: 9239562--9239613 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
9239552 TTTTTTCTTT
9239562 TTGTCTCCTT-TCCTTTTTCTTTTCA
1 TTGTCTCCTTCT-CTTTTTCTTTTCA
* * *
9239587 TTGTTTTCTTCTCTTTTTTTTTTCA
1 TTGTCTCCTTCTCTTTTTCTTTTCA
9239612 TT
1 TT
9239614 TTTTTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.71
Consensus pattern (25 bp):
TTGTCTCCTTCTCTTTTTCTTTTCA
Found at i:9241641 original size:25 final size:27
Alignment explanation
Indices: 9241607--9241659 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
9241597 CAATCATTCA
9241607 TTTTTTTCT-C-TT-TTTTTTCTTTTT
1 TTTTTTTCTCCATTATTTTTTCTTTTT
9241631 TTTTATTTCTCCATTTATTTTTTCTTTTT
1 TTTT-TTTCTCCA-TTATTTTTTCTTTTT
9241660 CCCCTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 4 0.17
25 5 0.21
26 1 0.04
28 2 0.08
29 12 0.50
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTTTCTCCATTATTTTTTCTTTTT
Found at i:9241657 original size:38 final size:37
Alignment explanation
Indices: 9241605--9241677 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
9241595 CTCAATCATT
***
9241605 CATTTTTTTCTCTTTTTTTTCTTTTTTTTTATTTCTC
1 CATTTTTTTCTCTTTTTCCCCTTTTTTTTTATTTCTC
* *
9241642 CATTTATTTTTTCTTTTTCCCCTTTTTTTTTCTTTC
1 CATTT-TTTTCTCTTTTTCCCCTTTTTTTTTATTTC
9241678 CATCATTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 5 0.17
38 25 0.83
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.75
Consensus pattern (37 bp):
CATTTTTTTCTCTTTTTCCCCTTTTTTTTTATTTCTC
Found at i:9241670 original size:19 final size:18
Alignment explanation
Indices: 9241625--9241677 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
9241615 TCTTTTTTTT
*
9241625 CTTTTTTTTTATTTCTCC
1 CTTTTTTTTTCTTTCTCC
* *
9241643 ATTTATTTTTTCTTTTTCCC
1 CTTT-TTTTTTCTTTCT-CC
9241663 CTTTTTTTTTCTTTC
1 CTTTTTTTTTCTTTC
9241678 CATCATTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTTTTTTTCTTTCTCC
Found at i:9242224 original size:12 final size:13
Alignment explanation
Indices: 9242195--9242232 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
9242185 TTTTTTTCTT
9242195 TTTCATTCTTTTCA
1 TTTCATT-TTTTCA
9242209 TTTCATTTTTTC-
1 TTTCATTTTTTCA
9242221 TTTCATTTTTTC
1 TTTCATTTTTTC
9242233 CTTTTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 5 0.21
14 7 0.29
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCATTTTTTCA
Found at i:9242238 original size:14 final size:13
Alignment explanation
Indices: 9242186--9242245 Score: 68
Period size: 14 Copynumber: 4.5 Consensus size: 13
9242176 TAATCAAAAT
9242186 TTTTTTCTTTTTCA
1 TTTTTTC-TTTTCA
*
9242200 TTCTTTTCATTTCA
1 TT-TTTTCTTTTCA
9242214 TTTTTTC-TTTCA
1 TTTTTTCTTTTCA
*
9242226 TTTTTTCCTTTTCC
1 TTTTTT-CTTTTCA
9242240 TTTTTT
1 TTTTTT
9242246 TTCTTTTCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
12 11 0.27
13 6 0.15
14 19 0.46
15 5 0.12
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTTCTTTTCA
Found at i:9242246 original size:15 final size:16
Alignment explanation
Indices: 9242226--9242263 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
9242216 TTTTCTTTCA
9242226 TTTTTTCCTTTTC-CT
1 TTTTTTCCTTTTCTCT
*
9242241 TTTTTTTCTTTTCTCT
1 TTTTTTCCTTTTCTCT
9242257 TATTTTT
1 T-TTTTT
9242264 TTATTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 3 0.15
17 5 0.25
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCCTTTTCTCT
Found at i:9242247 original size:16 final size:17
Alignment explanation
Indices: 9242216--9242264 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
9242206 TCATTTCATT
9242216 TTTTCT-TTCATTTTTTCC
1 TTTTCTCTT-ATTTTTT-C
9242234 TTTTC-CTT-TTTTTTC
1 TTTTCTCTTATTTTTTC
9242249 TTTTCTCTTATTTTTT
1 TTTTCTCTTATTTTTT
9242265 TATTCTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 6 0.21
18 7 0.25
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTCTTATTTTTTC
Found at i:9245282 original size:37 final size:37
Alignment explanation
Indices: 9245205--9245283 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
9245195 ATGTAGTAAT
* * *
9245205 TATTAAGATATGCATGAAATGAAATGCATGTACCGCC
1 TATTAAAATATGCATGAAATGAAATACATGTACCACC
* * * * *
9245242 TATTAAAATGTGCATGAGATGAAATATATGTACTATC
1 TATTAAAATATGCATGAAATGAAATACATGTACCACC
9245279 TATTA
1 TATTA
9245284 TTTTCAACTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.33
Consensus pattern (37 bp):
TATTAAAATATGCATGAAATGAAATACATGTACCACC
Found at i:9247318 original size:7 final size:7
Alignment explanation
Indices: 9247292--9247334 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
9247282 TTTAAGTTAT
9247292 GGTTTAG
1 GGTTTAG
* *
9247299 GATTTAA
1 GGTTTAG
*
9247306 GATTTAG
1 GGTTTAG
9247313 GGTTTAG
1 GGTTTAG
9247320 GGTTTAG
1 GGTTTAG
*
9247327 AGTTTAG
1 GGTTTAG
9247334 G
1 G
9247335 TTTGAGGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:9247318 original size:21 final size:21
Alignment explanation
Indices: 9247292--9247334 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
9247282 TTTAAGTTAT
9247292 GGTTTAGGATTTA-AGATTTAG
1 GGTTTAGGATTTAGAG-TTTAG
*
9247313 GGTTTAGGGTTTAGAGTTTAG
1 GGTTTAGGATTTAGAGTTTAG
9247334 G
1 G
9247335 TTTGAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (21 bp):
GGTTTAGGATTTAGAGTTTAG
Found at i:9248203 original size:28 final size:28
Alignment explanation
Indices: 9248164--9248236 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
9248154 ATAATTTAGG
* *
9248164 GAATT-TTTAAATTTTGTACAAAATTAT
1 GAATTCTTGAAATTTTGTACAAAATTAA
* * *
9248191 GAATTCTTGAAATTTGGTCCCAAATTAA
1 GAATTCTTGAAATTTTGTACAAAATTAA
*
9248219 GGATTCTTGAAATTTTGT
1 GAATTCTTGAAATTTTGT
9248237 TTCAAATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 5 0.13
28 33 0.87
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (28 bp):
GAATTCTTGAAATTTTGTACAAAATTAA
Found at i:9248242 original size:28 final size:28
Alignment explanation
Indices: 9248172--9248310 Score: 88
Period size: 28 Copynumber: 5.0 Consensus size: 28
9248162 GGGAATTTTT
* * * *
9248172 AAATTTTGTACAAAATTATGAATTCTTG
1 AAATTTTGTCCCAAATTAAGGATTCTTG
*
9248200 AAATTTGGTCCCAAATTAAGGATTCTTG
1 AAATTTTGTCCCAAATTAAGGATTCTTG
**
9248228 AAATTTTGTTTCAAATT-AGTGA-TCTTTG
1 AAATTTTGTCCCAAATTAAG-GATTC-TTG
* *
9248256 AAA-TTTGTTCCC-AATTTAGAAATTCTTG
1 AAATTTTG-TCCCAAATTAAG-GATTCTTG
* * * * *
9248284 CAATTTTATCTCAATTTAGGGATTCTT
1 AAATTTTGTCCCAAATTAAGGATTCTT
9248311 ATAATTTGGA
Statistics
Matches: 85, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
27 12 0.14
28 64 0.75
29 9 0.11
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.44
Consensus pattern (28 bp):
AAATTTTGTCCCAAATTAAGGATTCTTG
Found at i:9249199 original size:5 final size:5
Alignment explanation
Indices: 9249189--9249216 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
9249179 AAAACTTTTT
9249189 TTTCC TTTCC TTTCC TTTCC TTTCC TTT
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTT
9249217 ATTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTCC
Found at i:9255124 original size:2 final size:2
Alignment explanation
Indices: 9255117--9255154 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9255107 ACACTTAACC
9255117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9255155 AAAGAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9255203 original size:2 final size:2
Alignment explanation
Indices: 9255170--9255195 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9255160 AAGAAACCAA
9255170 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
9255196 TAACACACGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9262338 original size:27 final size:27
Alignment explanation
Indices: 9262308--9262361 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
9262298 ATTTTATTAT
*
9262308 ATTTATAATATAACATATTAAATAATA
1 ATTTAAAATATAACATATTAAATAATA
* *
9262335 ATTTAAAATATTATATATTAAATAATA
1 ATTTAAAATATAACATATTAAATAATA
9262362 TAAGCTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
ATTTAAAATATAACATATTAAATAATA
Found at i:9262340 original size:12 final size:14
Alignment explanation
Indices: 9262322--9262363 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
9262312 ATAATATAAC
9262322 ATATTAAATAATA-
1 ATATTAAATAATAT
*
9262335 AT-TTAAAATATTAT
1 ATATT-AAATAATAT
9262349 ATATTAAATAATAT
1 ATATTAAATAATAT
9262363 A
1 A
9262364 AGCTATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 2 0.08
13 9 0.38
14 11 0.46
15 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTAAATAATAT
Found at i:9263927 original size:15 final size:16
Alignment explanation
Indices: 9263889--9263929 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
9263879 TTATTTCATA
*
9263889 TTTATATTTAAATTAG
1 TTTATATTTTAATTAG
*
9263905 TTTA-ATTTTAA-TAT
1 TTTATATTTTAATTAG
9263919 TTTATATTTTA
1 TTTATATTTTA
9263930 TATGTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 6 0.27
15 12 0.55
16 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTATATTTTAATTAG
Found at i:9267610 original size:18 final size:17
Alignment explanation
Indices: 9267537--9267613 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
9267527 TTTTGTTCTT
*
9267537 GATACATTTGAGGTGAAA
1 GATACATTTGTGGT-AAA
* * *
9267555 GATATATTTGAGG-ATA
1 GATACATTTGTGGTAAA
**
9267571 -ATACATTTGTGGTGGA
1 GATACATTTGTGGTAAA
9267587 GATACATTTGTGGTAAA
1 GATACATTTGTGGTAAA
9267604 TGATACATTT
1 -GATACATTT
9267614 AAGGTAGAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
15 10 0.21
16 3 0.06
17 14 0.29
18 21 0.44
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (17 bp):
GATACATTTGTGGTAAA
Found at i:9267619 original size:18 final size:18
Alignment explanation
Indices: 9267587--9267635 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
9267577 TTGTGGTGGA
** *
9267587 GATACATTTGTGGTAAAT
1 GATACATTTAAGGTAAAG
*
9267605 GATACATTTAAGGTAGAG
1 GATACATTTAAGGTAAAG
9267623 GATACATTTAAGG
1 GATACATTTAAGG
9267636 AGGTGGAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (18 bp):
GATACATTTAAGGTAAAG
Done.