Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 73 of 168
Found at i:21441633 original size:30 final size:31
Alignment explanation
Indices: 21441599--21441657 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
21441589 TTCGAGCTTG
**
21441599 GGGACAAAATTGTAATTATG-CAAAAGTTTA
1 GGGACAAAATCATAATTATGACAAAAGTTTA
*
21441629 GGGACAAAATCATAATTTTGACAAAAGTT
1 GGGACAAAATCATAATTATGACAAAAGTT
21441658 GAGTCGAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (31 bp):
GGGACAAAATCATAATTATGACAAAAGTTTA
Found at i:21442302 original size:102 final size:101
Alignment explanation
Indices: 21442126--21442469 Score: 374
Period size: 102 Copynumber: 3.4 Consensus size: 101
21442116 TATCGATGAA
* * * * *
21442126 CACGTGTATAGTACTGTTTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGCAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTA-
21442191 CT-AGTGAAGGCTACAATGTGTACCGAGAAGCTTTAGT
65 CTAAGTGAAGGCTACAATGTGTACCGA-AAGCTTTAGT
* *
21442228 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* * * *
21442293 TAAGTGAAGGTTACTATATGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCG-AAAGCTTTAGT
* * * * ** *
21442330 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAA-ACTTGATCATGTGTGTAGTT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
* * * * *
21442393 CTATGTGAATGCTACTAA-GTGAACCGTAAAACTTGA-T
65 CTAAGTGAAGGCTAC-AATGTGTACCG-AAAGCTTTAGT
* *
21442430 CACGTGTGTAGTACCATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
21442470 ATGATAAAAG
Statistics
Matches: 203, Mismatches: 34, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
100 36 0.18
101 43 0.21
102 123 0.61
103 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAGCTTTAGT
Found at i:21442397 original size:50 final size:50
Alignment explanation
Indices: 21442126--21442459 Score: 280
Period size: 51 Copynumber: 6.6 Consensus size: 50
21442116 TATCGATGAA
* * * * * * * *
21442126 CACGTGTATAGTACTGTTTGAAGGCTACTACGTGTATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAA-ACTTGAT
* * * * * *
21442177 CACATGTGTAGCACCTA-GTGAAGGCTACAATGTGTACCG-AGAAGCTTTAGT
1 CACGTGTGTAGTA-CTATGTGAAGGCTACTATGTGAACCGTA-AAACTTGA-T
* ** *** *
21442228 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATTGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAACTTGAT
* * * * * *
21442279 CACATGTGTAGTACTAAGTGAAGGTTACTATATGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTAAAA-C-TTGAT
21442330 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTAAAACTTGAT
* * * *
21442380 CATGTGTGTAGTTCTATGTGAATGCTACTAAGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTAAAACTTGAT
*
21442430 CACGTGTGTAGTACCATGTGAAGGCTACTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTA
21442460 CGTGTATCGA
Statistics
Matches: 224, Mismatches: 49, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
49 4 0.02
50 82 0.37
51 128 0.57
52 9 0.04
53 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTAAAACTTGAT
Found at i:21444602 original size:31 final size:30
Alignment explanation
Indices: 21444560--21444813 Score: 108
Period size: 29 Copynumber: 8.6 Consensus size: 30
21444550 TGACACATCT
* * * *
21444560 CTTTTCGTAATTCGATGGCTGAAGTTATCC
1 CTTTTCATAATTCGATAGCCGAAGATATCC
* *
21444590 CTTTTTCATAATTTGATAGCCGAAGCTATCC
1 C-TTTTCATAATTCGATAGCCGAAGATATCC
* * *
21444621 CATTTCATAGA-TCGATAGCCAAAGACATCC
1 CTTTTCATA-ATTCGATAGCCGAAGATATCC
* * ** * **
21444651 CTTTTCATAGTTCGATGGTTGTCA-CCATCC
1 CTTTTCATAATTCGATAGCCG-AAGATATCC
** * * ** *
21444681 CTTTTCATTGTT-GATGGTC-ATCACCATCC
1 CTTTTCATAATTCGATAGCCGAAGA-TATCC
* * *
21444710 CTTTTCATAATT-GATAGCTGAAGCTATTC
1 CTTTTCATAATTCGATAGCCGAAGATATCC
* *
21444739 CTTTTCATAA-TCGATAGCCAAAGTTATCC
1 CTTTTCATAATTCGATAGCCGAAGATATCC
* * * * *
21444768 CCTTCCGT-ATTCGATAGCCGAAGCTCTCC
1 CTTTTCATAATTCGATAGCCGAAGATATCC
**
21444797 CTTTTCATTCTTCGATA
1 CTTTTCATAATTCGATA
21444814 ATCACCATTA
Statistics
Matches: 167, Mismatches: 47, Indels: 20
0.71 0.20 0.09
Matches are distributed among these distances:
28 2 0.01
29 77 0.46
30 61 0.37
31 27 0.16
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (30 bp):
CTTTTCATAATTCGATAGCCGAAGATATCC
Found at i:21444629 original size:30 final size:30
Alignment explanation
Indices: 21444604--21444666 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
21444594 TTCATAATTT
*
21444604 GATAGCCGAAG-CTATCCCATTTCATAGATC
1 GATAGCCAAAGAC-ATCCCATTTCATAGATC
* *
21444634 GATAGCCAAAGACATCCCTTTTCATAGTTC
1 GATAGCCAAAGACATCCCATTTCATAGATC
21444664 GAT
1 GAT
21444667 GGTTGTCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (30 bp):
GATAGCCAAAGACATCCCATTTCATAGATC
Found at i:21444723 original size:29 final size:29
Alignment explanation
Indices: 21444646--21444724 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
21444636 TAGCCAAAGA
**
21444646 CATCCCTTTTCATAGTTCGATGGTTGTCAC
1 CATCCCTTTTCATAGTT-GATGGTCATCAC
*
21444676 CATCCCTTTTCATTGTTGATGGTCATCAC
1 CATCCCTTTTCATAGTTGATGGTCATCAC
*
21444705 CATCCCTTTTCATAATTGAT
1 CATCCCTTTTCATAGTTGAT
21444725 AGCTGAAGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 28 0.64
30 16 0.36
ACGTcount: A:0.19, C:0.27, G:0.13, T:0.42
Consensus pattern (29 bp):
CATCCCTTTTCATAGTTGATGGTCATCAC
Found at i:21444768 original size:58 final size:59
Alignment explanation
Indices: 21444581--21444804 Score: 168
Period size: 58 Copynumber: 3.8 Consensus size: 59
21444571 TCGATGGCTG
* * *
21444581 AAGTTATCCCTTTTTCATAATTTGATAGCCGAAGCTATCCCATTTCATAGATCGATAGCCA
1 AAGTCATCCC-TTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATA-ATCGATAGCCA
* * * ** * * ** * * *
21444642 AAGACATCCCTTTTCATAGTTCGATGGTTGTCA-CCATCCCTTTTCATTGTTGATGGTCA
1 AAGTCATCCCTTTTCATAATTCGATAGCCG-AAGCTATCCCTTTTCATAATCGATAGCCA
* * * *
21444701 TCA-CCATCCCTTTTCATAATT-GATAGCTGAAGCTATTCCTTTTCATAATCGATAGCCA
1 -AAGTCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATCGATAGCCA
* * * * *
21444759 AAGTTATCCCCTTCCGT-ATTCGATAGCCGAAGCTCTCCCTTTTCAT
1 AAGTCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCAT
21444805 TCTTCGATAA
Statistics
Matches: 121, Mismatches: 37, Indels: 13
0.71 0.22 0.08
Matches are distributed among these distances:
57 5 0.04
58 56 0.46
59 23 0.19
60 28 0.23
61 9 0.07
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (59 bp):
AAGTCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATCGATAGCCA
Found at i:21446198 original size:3 final size:3
Alignment explanation
Indices: 21446155--21446188 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
21446145 AAGGATTCTT
*
21446155 ATG ATG ATG ATG ATG ATG ATG ATA ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
21446189 ACAATGATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:21453013 original size:17 final size:17
Alignment explanation
Indices: 21452974--21453013 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
21452964 GGAAGGGAAT
*
21452974 GGAAGAGAGAAAAGCTAG
1 GGAA-AGAGAAAAGCAAG
*
21452992 TGAAAGAGAAAAGCAAG
1 GGAAAGAGAAAAGCAAG
21453009 GGAAA
1 GGAAA
21453014 TGAATGGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.55, C:0.05, G:0.35, T:0.05
Consensus pattern (17 bp):
GGAAAGAGAAAAGCAAG
Found at i:21454972 original size:30 final size:30
Alignment explanation
Indices: 21454936--21455007 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
21454926 CATAGATATC
21454936 ATTCCTACCAAGTGTGACAATACTAGTGTT
1 ATTCCTACCAAGTGTGACAATACTAGTGTT
21454966 ATTCCTACCAAGTGTGACAATACTAGTGTT
1 ATTCCTACCAAGTGTGACAATACTAGTGTT
21454996 ATTCCTACCAAG
1 ATTCCTACCAAG
21455008 AGTAAACATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (30 bp):
ATTCCTACCAAGTGTGACAATACTAGTGTT
Found at i:21461070 original size:45 final size:45
Alignment explanation
Indices: 21461006--21461099 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
21460996 AACTGATACT
* * *
21461006 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
*
21461051 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
21461096 CGGT
1 CGGT
21461100 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:21461284 original size:50 final size:50
Alignment explanation
Indices: 21461096--21461332 Score: 280
Period size: 50 Copynumber: 4.7 Consensus size: 50
21461086 CAATGATGTT
* * * * *
21461096 CGGTTCACATAGTAGCCTGCACGTAGTACTACACATGTGACCATTACCA-TC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTC
* * * * * *
21461147 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TC
* *
21461198 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTC
* * *
21461248 CAGTACACGTAGTAGCCTGCACATAGTACTATACATGCGACCTATCATTT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTC
21461298 CGGTACACGTAGTAGCCTGCACATAGTACTACACA
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACA
21461333 CATGACCATC
Statistics
Matches: 159, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 80 0.50
51 76 0.48
52 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTC
Found at i:21464146 original size:42 final size:42
Alignment explanation
Indices: 21464066--21464147 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
21464056 CGTTTTCTCT
* * **
21464066 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACGATGGTCTTACACATATGCACATATTG
*
21464108 ATGCCATAGCCCAGCGATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACGATGGTCTTACACA-TATGCACATAT
21464148 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGCCATAGCCCAACGATGGTCTTACACATATGCACATATTG
Found at i:21466144 original size:18 final size:18
Alignment explanation
Indices: 21466121--21466157 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
21466111 TTCATGGCTA
21466121 TTTTGAATAGATGTGATG
1 TTTTGAATAGATGTGATG
21466139 TTTTGAATAGATGTGATG
1 TTTTGAATAGATGTGATG
21466157 T
1 T
21466158 GGTGTTATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (18 bp):
TTTTGAATAGATGTGATG
Found at i:21469588 original size:30 final size:30
Alignment explanation
Indices: 21469554--21469615 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
21469544 AGTTTGAATG
21469554 ATCATTGCATTCTTTGCGGCTGCTGTTTTC
1 ATCATTGCATTCTTTGCGGCTGCTGTTTTC
21469584 ATCATTGCATTCTTTGCGGCTGCTGTTTTC
1 ATCATTGCATTCTTTGCGGCTGCTGTTTTC
21469614 AT
1 AT
21469616 GACATGCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (30 bp):
ATCATTGCATTCTTTGCGGCTGCTGTTTTC
Found at i:21474070 original size:110 final size:110
Alignment explanation
Indices: 21473818--21474141 Score: 449
Period size: 110 Copynumber: 3.0 Consensus size: 110
21473808 TGGATTAAAA
* ** * *
21473818 TTTAAGAGGATATTTAATTGTTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCATGT
1 TTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCATGT
* * *
21473881 TTTCTCGAATTTCCAAAC-GCAAAACAATGCCTTATTTTAAAATT
66 TTTCTCGAATTTCCAAACGGTAAAACATTGCCTTATTTTGAAATT
* * * * *
21473925 TTTAAAAGGATATTAAGCCATTTAGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGT
1 TTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCATGT
*
21473990 TTTCTCGAATTTCTAAACGGTAAAACATTGCCTTATTTTGAAATT
66 TTTCTCGAATTTCCAAACGGTAAAACATTGCCTTATTTTGAAATT
* *
21474035 TTTGAAAGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCATGT
1 TTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCATGT
* * *
21474100 TTTCTCGAATTTCCAAAAGCT-AAACATTGCCTTATTTAGAAA
66 TTTCTCGAATTTCCAAACGGTAAAACATTGCCTTATTTTGAAA
21474142 AATTCTCCTT
Statistics
Matches: 189, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
107 25 0.13
109 65 0.34
110 99 0.52
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (110 bp):
TTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCATGT
TTTCTCGAATTTCCAAACGGTAAAACATTGCCTTATTTTGAAATT
Found at i:21474650 original size:2 final size:2
Alignment explanation
Indices: 21474645--21474705 Score: 72
Period size: 2 Copynumber: 31.0 Consensus size: 2
21474635 ATATAAAGAG
*
21474645 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
21474686 A- AG AT AT AA AGT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT
21474706 GAAAATTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
1 2 0.04
2 48 0.94
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:21477858 original size:17 final size:17
Alignment explanation
Indices: 21477838--21477870 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21477828 TAGAATTGGG
21477838 TTGAGAAAATAATTTAA
1 TTGAGAAAATAATTTAA
*
21477855 TTGAGAAATTAATTTA
1 TTGAGAAAATAATTTA
21477871 GTTAATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
TTGAGAAAATAATTTAA
Found at i:21478408 original size:15 final size:15
Alignment explanation
Indices: 21478388--21478422 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
21478378 TTAATTGATG
21478388 ATTAAGGTTTAA-TTA
1 ATTAA-GTTTAAGTTA
21478403 ATTAAGTTTAAGTTA
1 ATTAAGTTTAAGTTA
21478418 ATTAA
1 ATTAA
21478423 TTAAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (15 bp):
ATTAAGTTTAAGTTA
Found at i:21478420 original size:19 final size:19
Alignment explanation
Indices: 21478396--21478432 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
21478386 TGATTAAGGT
21478396 TTAATTAATTAAGTTTAAG
1 TTAATTAATTAAGTTTAAG
21478415 TTAATTAATTAAGTTTAA
1 TTAATTAATTAAGTTTAA
21478433 TAATAATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (19 bp):
TTAATTAATTAAGTTTAAG
Found at i:21481368 original size:51 final size:48
Alignment explanation
Indices: 21481220--21481402 Score: 147
Period size: 51 Copynumber: 3.7 Consensus size: 48
21481210 ATCATTCGAT
* * * **
21481220 ACAC-GTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTTCGGT
1 ACACAGTAGTAGCCTGCACATAGTACTACACACATGATC-AAC-TATC-CA
* * *
21481270 TCAC-GTAGTAGCCTGCACATAGTACTACACACATGACCATTAATATCCA
1 ACACAGTAGTAGCCTGCACATAGTACTACACACATGATCA--ACTATCCA
*
21481319 ACACATGTAGTAGCCTGCACATAGTACTACACACATGATCGAAGCTATCCGGT
1 ACACA-GTAGTAGCCTGCACATAGTACTACACACATGATC-AA-CTATCC--A
* * *
21481372 ACGCA-TAGTAGTCTGTACATAGTACTACACA
1 ACACAGTAGTAGCCTGCACATAGTACTACACA
21481403 TGCGACCTTT
Statistics
Matches: 110, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
49 4 0.04
50 38 0.35
51 63 0.57
52 1 0.01
53 4 0.04
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (48 bp):
ACACAGTAGTAGCCTGCACATAGTACTACACACATGATCAACTATCCA
Found at i:21481430 original size:101 final size:101
Alignment explanation
Indices: 21481218--21481453 Score: 249
Period size: 101 Copynumber: 2.3 Consensus size: 101
21481208 TTATCATTCG
* * * * * *
21481218 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTTTTCGGTTCACGTAGTAGCC
1 ATACACGTAGTAGCCTACACATAGTACTACACACATGATCAAACTATCCGGTACACATAGTAGCC
*
21481283 TGCACATAGTACTACACACATGACCATTAATATCCA
66 TGCACATAGTACTACACACACGACCATTAATATCCA
* * * * * *
21481319 ACACATGTAGTAGCCTGCACATAGTACTACACACATGATCGAAGCTATCCGGTACGCATAGTAGT
1 ATACACGTAGTAGCCTACACATAGTACTACACACATGATC-AAACTATCCGGTACACATAGTAGC
* ** * ** **
21481384 CTGTACATAGTACTACACATGCGACCTTTCGT-TCTG
65 CTGCACATAGTACTACACACACGACCATTAATATCCA
* *
21481420 GTACACGTAGTAGCCTACACATTGTACTACACAC
1 ATACACGTAGTAGCCTACACATAGTACTACACAC
21481454 GTGACCATCA
Statistics
Matches: 109, Mismatches: 25, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
101 67 0.61
102 42 0.39
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (101 bp):
ATACACGTAGTAGCCTACACATAGTACTACACACATGATCAAACTATCCGGTACACATAGTAGCC
TGCACATAGTACTACACACACGACCATTAATATCCA
Found at i:21482652 original size:19 final size:19
Alignment explanation
Indices: 21482624--21482749 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
21482614 CTTATGCGCC
*
21482624 AGGATGCACTTTGTGTGAT
1 AGGATGCACTTTGTGTGCT
* * *
21482643 AGGATTCACTTCGTGTGCC
1 AGGATGCACTTTGTGTGCT
* *
21482662 AGGATGCGCTTTGTG-GGT
1 AGGATGCACTTTGTGTGCT
*
21482680 CAGTATGCACTTTGTGTGCT
1 -AGGATGCACTTTGTGTGCT
* ** *
21482700 AGGATGCATTTTGTGCCCC
1 AGGATGCACTTTGTGTGCT
* * *
21482719 AGGATGCGCTCTGTGCGCT
1 AGGATGCACTTTGTGTGCT
*
21482738 AGTATGCACTTT
1 AGGATGCACTTT
21482750 AAGTGCCAGT
Statistics
Matches: 80, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
18 1 0.01
19 77 0.96
20 2 0.03
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (19 bp):
AGGATGCACTTTGTGTGCT
Found at i:21482691 original size:57 final size:57
Alignment explanation
Indices: 21482609--21482749 Score: 160
Period size: 57 Copynumber: 2.5 Consensus size: 57
21482599 GTACGGGTTT
* * * * **
21482609 ATGCGCT-TATGCGCCAGGATGCACTTTGTGTGATAGGATTCACTTCGTGTGCCAGG
1 ATGCGCTCTGTGCGCTAGTATGCACTTTGTGTGATAGGATGCACTTCGTGCCCCAGG
* * * * *
21482665 ATGCGCTTTGTG-GGTCAGTATGCACTTTGTGTGCTAGGATGCATTTTGTGCCCCAGG
1 ATGCGCTCTGTGCGCT-AGTATGCACTTTGTGTGATAGGATGCACTTCGTGCCCCAGG
21482722 ATGCGCTCTGTGCGCTAGTATGCACTTT
1 ATGCGCTCTGTGCGCTAGTATGCACTTT
21482750 AAGTGCCAGT
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
56 8 0.11
57 60 0.86
58 2 0.03
ACGTcount: A:0.16, C:0.21, G:0.30, T:0.33
Consensus pattern (57 bp):
ATGCGCTCTGTGCGCTAGTATGCACTTTGTGTGATAGGATGCACTTCGTGCCCCAGG
Found at i:21484406 original size:20 final size:20
Alignment explanation
Indices: 21484381--21484420 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21484371 AAATGCTAAC
21484381 AGAGGCACCGAAGTGCAAAT
1 AGAGGCACCGAAGTGCAAAT
21484401 AGAGGCACCGAAGTGCAAAT
1 AGAGGCACCGAAGTGCAAAT
21484421 CTCGTACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.30, T:0.10
Consensus pattern (20 bp):
AGAGGCACCGAAGTGCAAAT
Found at i:21490101 original size:24 final size:24
Alignment explanation
Indices: 21490074--21490136 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
21490064 CAGCTCGAAA
*
21490074 GAGCATCCCGTTATTAGCTCTCAT
1 GAGCATCCCGTTATTAGCTCTCAC
* * *
21490098 GAGCATCTCGATATTTGGCTCTCAC
1 GAGCATCCCGTTA-TTAGCTCTCAC
* *
21490123 AAGCTTCCCGTTAT
1 GAGCATCCCGTTAT
21490137 ATGATTCTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTCAC
Found at i:21490243 original size:27 final size:25
Alignment explanation
Indices: 21490164--21490245 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
21490154 CCCGTTTATA
* *
21490164 GCTCT-TCGGAGCTTCCCGATAATTG
1 GCTCTATCAGAGCTTCCTGATAA-TG
21490189 GCTC-ATCAGAGCTTCCTGAGTAGA-G
1 GCTCTATCAGAGCTTCCTGA-TA-ATG
*
21490214 GCTCTTTCATGAGCTTCCTGATTAATG
1 GCTCTATCA-GAGCTTCCTGA-TAATG
21490241 GCTCT
1 GCTCT
21490246 CCGGAGCTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
25 21 0.45
26 6 0.13
27 20 0.43
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (25 bp):
GCTCTATCAGAGCTTCCTGATAATG
Found at i:21497492 original size:5 final size:5
Alignment explanation
Indices: 21497482--21497515 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
21497472 TCCAAAAGTG
21497482 TGAAT TGAAT TGAAT TGAAT TGAAT ATGAAT TGA
1 TGAAT TGAAT TGAAT TGAAT TGAAT -TGAAT TGA
21497516 TGTTAAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
TGAAT
Found at i:21497736 original size:10 final size:10
Alignment explanation
Indices: 21497721--21497747 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21497711 GATCACATAT
21497721 CCGACAATGC
1 CCGACAATGC
21497731 CCGACAATGC
1 CCGACAATGC
21497741 CCGACAA
1 CCGACAA
21497748 ATATTAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.33, C:0.41, G:0.19, T:0.07
Consensus pattern (10 bp):
CCGACAATGC
Found at i:21497877 original size:24 final size:24
Alignment explanation
Indices: 21497845--21497907 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
21497835 CAACTCGAAA
*
21497845 GAGCATCCCGTTATTAGCTCCCAT
1 GAGCATCCCGTTATTAGCTCCCAC
* * *
21497869 GAGCATCCCGATATTTGGCTCTCAC
1 GAGCATCCCGTTA-TTAGCTCCCAC
*
21497894 GAGCTTCCCGTTAT
1 GAGCATCCCGTTAT
21497908 ATAATTCTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCCCAC
Found at i:21497946 original size:24 final size:25
Alignment explanation
Indices: 21497919--21497978 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
21497909 TAATTCTTGC
* * * *
21497919 GAGCTTTCCGTTTA-TGGCTCTTTG
1 GAGCTTTCCGATAATTGGCTCATCG
*
21497943 GAGCTTCCCGATAATTGGCTCATCG
1 GAGCTTTCCGATAATTGGCTCATCG
21497968 GAGCTTTCCGA
1 GAGCTTTCCGA
21497979 CTAAAGGCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (25 bp):
GAGCTTTCCGATAATTGGCTCATCG
Found at i:21498027 original size:25 final size:23
Alignment explanation
Indices: 21497935--21498032 Score: 63
Period size: 25 Copynumber: 3.9 Consensus size: 23
21497925 TCCGTTTATG
*
21497935 GCTCTTTGGAGCTTCCCGATAATTG
1 GCTCTTTGGAGCTT-CCGATAA-TA
* *
21497960 GCTCATCGGAGCTTTCCGACTAA-A
1 GCTCTTTGGAGC-TTCCGA-TAATA
*
21497984 GGCTCTTTCATGAGCTTCCTGATTAATA
1 -GCTCTTT--GGAGCTTCC-GA-TAATA
21498012 GCTCTTTGGAGCTTCCCGATA
1 GCTCTTTGGAGCTT-CCGATA
21498033 TTGGTTCGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
24 2 0.04
25 27 0.47
26 11 0.19
27 16 0.28
28 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (23 bp):
GCTCTTTGGAGCTTCCGATAATA
Found at i:21498093 original size:25 final size:25
Alignment explanation
Indices: 21498059--21498141 Score: 114
Period size: 25 Copynumber: 3.3 Consensus size: 25
21498049 TCCCAATTAC
*
21498059 GGCTCTAATGAGCTTCCCGTTATAT
1 GGCTCGAATGAGCTTCCCGTTATAT
* * *
21498084 AGCTCGAATGAGCTTCCTGTTACAT
1 GGCTCGAATGAGCTTCCCGTTATAT
21498109 GGCTC-ACATGAGCTTCCCGTTATAT
1 GGCTCGA-ATGAGCTTCCCGTTATAT
21498134 GGCTCGAA
1 GGCTCGAA
21498142 AAAGAGTTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (25 bp):
GGCTCGAATGAGCTTCCCGTTATAT
Found at i:21511912 original size:20 final size:20
Alignment explanation
Indices: 21511879--21511927 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
21511869 CTCGACGTGC
21511879 ATAATCAAAGCAAGTTCTAGA
1 ATAA-CAAAGCAAGTTCTAGA
*
21511900 ATAACAAATCAAGTTCTAGA
1 ATAACAAAGCAAGTTCTAGA
21511920 ATAACAAA
1 ATAACAAA
21511928 AAATTATGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.22
Consensus pattern (20 bp):
ATAACAAAGCAAGTTCTAGA
Found at i:21514062 original size:9 final size:9
Alignment explanation
Indices: 21514050--21514111 Score: 52
Period size: 9 Copynumber: 6.3 Consensus size: 9
21514040 ACTTAAAAGT
21514050 ATAAAAATA
1 ATAAAAATA
*
21514059 ATAAAACTCA
1 ATAAAAAT-A
*
21514069 ATAATAATA
1 ATAAAAATA
21514078 ATTAAAATGATGA
1 A-TAAAA--AT-A
*
21514091 ATGAAAATA
1 ATAAAAATA
21514100 ATAAAAATA
1 ATAAAAATA
21514109 ATA
1 ATA
21514112 TGAAAAAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
9 21 0.50
10 13 0.31
12 6 0.14
13 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (9 bp):
ATAAAAATA
Found at i:21514208 original size:10 final size:10
Alignment explanation
Indices: 21514162--21514215 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
21514152 AATCACAATA
*
21514162 AAAAAGAAAT
1 AAAAATAAAT
*
21514172 AAAAA-GAAT
1 AAAAATAAAT
21514181 AATAAATAAAAT
1 AA-AAAT-AAAT
21514193 AAAAATAAAT
1 AAAAATAAAT
*
21514203 AAAAATACAT
1 AAAAATAAAT
21514213 AAA
1 AAA
21514216 TAAAATAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
9 5 0.13
10 24 0.63
11 4 0.11
12 5 0.13
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.17
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:21521760 original size:75 final size:76
Alignment explanation
Indices: 21521619--21521772 Score: 213
Period size: 75 Copynumber: 2.0 Consensus size: 76
21521609 ATTTTTTAAA
**
21521619 ATATATACAAATTTCAAATGTTTAAAAAATCAAAAAATAATTTATTATTTATTAATAAAATCTAA
1 ATATATACAAATTTCAAATGCGTAAAAAATCAAAAAATAATTTATTATTTATTAATAAAATCTAA
*
21521684 TATATATTTAT
66 TATATATATAT
* * * * *
21521695 ATATATATAAATTTTAAATGCGTAAAAACTC-AAAAATAATTTATTATTTATTAA-AAACTTGTA
1 ATATATACAAATTTCAAATGCGTAAAAAATCAAAAAATAATTTATTATTTATTAATAAA-ATCTA
21521758 ATATATATATAT
65 ATATATATATAT
21521770 ATA
1 ATA
21521773 GTGCATATAG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 3 0.04
75 40 0.58
76 26 0.38
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (76 bp):
ATATATACAAATTTCAAATGCGTAAAAAATCAAAAAATAATTTATTATTTATTAATAAAATCTAA
TATATATATAT
Found at i:21523738 original size:105 final size:105
Alignment explanation
Indices: 21523627--21523816 Score: 263
Period size: 105 Copynumber: 1.8 Consensus size: 105
21523617 TACTTTTTAT
* * * * * * ** *
21523627 TTTTTTTCAAACATATTTGTGACATAGCCAAATCTTTTGACGTGAAATGAGATGACAACCCAAGC
1 TTTTTTTCAAACAAATTCGAGACATAACCAAATATTTTAACACGAAATAAGATGACAACCCAAGC
*
21523692 ACTTCACCCTAGTTACTCAACTTGACTTGTTTTTTTTTCC
66 ACCTCACCCTAGTTACTCAACTTGACTTGTTTTTTTTTCC
*
21523732 TTTTTTTTAAACAAATTCGAGACATAACCAAATATTTTAACACGAAATAAGATGACAACCCAAGC
1 TTTTTTTCAAACAAATTCGAGACATAACCAAATATTTTAACACGAAATAAGATGACAACCCAAGC
* *
21523797 ACCTCATCTTAGTTACTCAA
66 ACCTCACCCTAGTTACTCAA
21523817 TTTGGCATGT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 72 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.34
Consensus pattern (105 bp):
TTTTTTTCAAACAAATTCGAGACATAACCAAATATTTTAACACGAAATAAGATGACAACCCAAGC
ACCTCACCCTAGTTACTCAACTTGACTTGTTTTTTTTTCC
Found at i:21524652 original size:98 final size:98
Alignment explanation
Indices: 21524480--21524674 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
21524470 ACAATAAAAT
*
21524480 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
21524545 TCTAGAATCCCAAACTCAGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCAGAATATTTCCTTTAC
21524578 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* * * *
21524643 TTTAAAATCCCAAATTCGGAATATTTTCTTTA
66 TCTAAAATCCCAAACTCAGAATATTTCCTTTA
21524675 TTATTTTTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCAGAATATTTCCTTTAC
Found at i:21525372 original size:25 final size:26
Alignment explanation
Indices: 21525342--21525391 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
21525332 ATATAAATAT
21525342 GAAAATATTC-ATTAAAAAAATATAG
1 GAAAATATTCGATTAAAAAAATATAG
*
21525367 GAAAATATTCGTTTAAAAAAATATA
1 GAAAATATTCGATTAAAAAAATATA
21525392 TATGTGTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (26 bp):
GAAAATATTCGATTAAAAAAATATAG
Found at i:21525696 original size:24 final size:25
Alignment explanation
Indices: 21525646--21525697 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
21525636 ATTGGAATTT
* *
21525646 AAAATAAATAAAAGTGTAAATTAAA
1 AAAATAAAGAAAACTGTAAATTAAA
*
21525671 AAAATAAAGAAAACT-T-AATTACA
1 AAAATAAAGAAAACTGTAAATTAAA
21525694 AAAA
1 AAAA
21525698 CATTAAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.42
24 1 0.04
25 13 0.54
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (25 bp):
AAAATAAAGAAAACTGTAAATTAAA
Found at i:21526004 original size:22 final size:21
Alignment explanation
Indices: 21525969--21526102 Score: 77
Period size: 19 Copynumber: 6.7 Consensus size: 21
21525959 AAAGGGTATC
* *
21525969 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
21525990 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
21526013 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
21526032 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
21526051 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
21526070 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
21526089 TGCATATCATATCT
1 TACAAATCATATCT
21526103 AAGATTGCAT
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
17 2 0.02
19 60 0.64
21 7 0.07
22 15 0.16
23 10 0.11
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:21526012 original size:23 final size:22
Alignment explanation
Indices: 21525969--21526026 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
21525959 AAAGGGTATC
* *
21525969 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
21525990 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
21526013 TGCATATCATATCT
1 TACAAATCATATCT
21526027 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:21526029 original size:19 final size:19
Alignment explanation
Indices: 21526005--21526115 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
21525995 AATCATATCT
21526005 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
21526024 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
21526043 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
21526062 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
21526081 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
21526100 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
21526116 CCTGAAGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:21526052 original size:38 final size:38
Alignment explanation
Indices: 21526005--21526108 Score: 199
Period size: 38 Copynumber: 2.7 Consensus size: 38
21525995 AATCATATCT
21526005 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
21526043 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
21526081 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
21526109 GCATATCCCT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:21526669 original size:132 final size:132
Alignment explanation
Indices: 21526482--21527025 Score: 881
Period size: 132 Copynumber: 4.2 Consensus size: 132
21526472 GGGAGATATG
* *
21526482 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGACGTAAAATCCGCTATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
21526547 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
21526612 GA
131 GA
*
21526614 ATTACTGGCTTCAATGTACTCCACTGTAACTACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
21526679 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
21526744 GA
131 GA
* *
21526746 ATTACTGGCTTCAATGTACTCCACTGTAACTACAGGGAGGTAAAATCTGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
*
21526811 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
21526876 GA
131 GA
* *
21526878 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCAGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
* * * **
21526943 TCACTGTCAATGC--AGGAAGGCAAGATCTG----C-T--ATCTATTCCACTGTTGTCCAGGGAA
66 CCAC--T-ACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAA
21526999 GTAGA
128 GTAGA
21527004 ATTACTGGCTTCAATGTACTCC
1 ATTACTGGCTTCAATGTACTCC
21527026 TCTTTTTACC
Statistics
Matches: 394, Mismatches: 15, Indels: 12
0.94 0.04 0.03
Matches are distributed among these distances:
126 51 0.13
128 1 0.00
129 1 0.00
132 323 0.82
133 13 0.03
134 1 0.00
135 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
GA
Found at i:21526871 original size:44 final size:44
Alignment explanation
Indices: 21526559--21526871 Score: 137
Period size: 44 Copynumber: 7.1 Consensus size: 44
21526549 ACTACTGCTT
*
21526559 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGTCC
* * ** *
21526603 AGGGA-AGT-AGAATTACTG---GCTTCAATGTACTCCACTGTAACTAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTGT-TGTCC
* * * ** * * ** *
21526647 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG-CTT
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGTC-C
*
21526691 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGTCC
* * ** *
21526735 AGGGA-AGT-AGAATTACTG---GCTTCAATGTACTCCACTGTAACTAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTGT-TGTCC
* * ** * * ** *
21526779 AGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTG-CTT
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGTC-C
* *
21526823 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGTCC
21526867 AGGGA
1 AGGGA
21526872 AGTAGAATTA
Statistics
Matches: 188, Mismatches: 57, Indels: 48
0.64 0.19 0.16
Matches are distributed among these distances:
42 5 0.03
43 42 0.22
44 101 0.54
45 34 0.18
46 6 0.03
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGTCC
Found at i:21533826 original size:24 final size:25
Alignment explanation
Indices: 21533776--21533827 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
21533766 ATTGGAATTT
* *
21533776 AAAATAAATAAAAGTGTAAATTAAA
1 AAAATAAAGAAAACTGTAAATTAAA
*
21533801 AAAATAAAGAAAACT-T-AATTACA
1 AAAATAAAGAAAACTGTAAATTAAA
21533824 AAAA
1 AAAA
21533828 CATTAAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.42
24 1 0.04
25 13 0.54
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (25 bp):
AAAATAAAGAAAACTGTAAATTAAA
Found at i:21534205 original size:19 final size:19
Alignment explanation
Indices: 21534135--21534208 Score: 103
Period size: 19 Copynumber: 3.9 Consensus size: 19
21534125 AATCATATCT
*
21534135 TCTAAGATTGCATTTCATA
1 TCTAAGATTGCATATCATA
* ** *
21534154 TATAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
21534173 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
21534192 TCTAAGATTGCATATCA
1 TCTAAGATTGCATATCA
21534209 CTAAAGATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:21535823 original size:12 final size:12
Alignment explanation
Indices: 21535806--21535831 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21535796 CAAAATAGAC
21535806 TTTTAGCGGCGT
1 TTTTAGCGGCGT
21535818 TTTTAGCGGCGT
1 TTTTAGCGGCGT
21535830 TT
1 TT
21535832 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:21536098 original size:41 final size:41
Alignment explanation
Indices: 21536018--21536098 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
21536008 GGCTTTAGAG
* * *
21536018 GCGCTTTTTCAAAAACGCCGCTAATGCTCGGGTCTTTAGCA
1 GCGCTTTTTCAAAAACGCCGCTAAAGCTCGAGTCATTAGCA
*
21536059 GCGCTTTTTTAAAAACGCCGCTAAAGACTCGAG-CATTAGC
1 GCGCTTTTTCAAAAACGCCGCTAAAG-CTCGAGTCATTAGC
21536099 GTTGTTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 30 0.86
42 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (41 bp):
GCGCTTTTTCAAAAACGCCGCTAAAGCTCGAGTCATTAGCA
Found at i:21537775 original size:13 final size:13
Alignment explanation
Indices: 21537759--21537787 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21537749 TTAGATTTAA
21537759 AAAAAACATTGAT
1 AAAAAACATTGAT
21537772 AAAAAACATTGAT
1 AAAAAACATTGAT
21537785 AAA
1 AAA
21537788 TTCGATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAAAACATTGAT
Found at i:21541843 original size:43 final size:43
Alignment explanation
Indices: 21541813--21542028 Score: 276
Period size: 43 Copynumber: 5.0 Consensus size: 43
21541803 AAGTCATGAG
* * * *
21541813 CTTTAGCGGCGTTTGTTGGAAAAGTGTCGCTAAAGGTCTTGTT
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGT
*
21541856 TTTTAGCGGCGTTT-TTGAGAAAAGCGCCGCTAAAGG-CCTTGGT
1 CTTTAGCGGCGTTTGTTG-GAAAAGCGCCGCTAAAGGTCC-TGGT
*
21541899 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGT
**
21541942 CTTTAGTAGCGTTTG-TGGAAAAGGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTTGGAAAA-GCGCCGCTAAAGGTCCTGGT
* * * *
21541985 CTTTAGCAGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGT
21542028 C
1 C
21542029 CGTTTTTAGA
Statistics
Matches: 153, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
42 10 0.07
43 133 0.87
44 10 0.07
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCCTGGT
Found at i:21542151 original size:21 final size:21
Alignment explanation
Indices: 21542125--21542168 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
21542115 TTTAGCGGCA
*
21542125 CTAAAAAGCGCCGCTAAAGGC
1 CTAAAAAGCGCCGCTAAAAGC
*
21542146 CTAAAAAGCGCTGCTAAAAGC
1 CTAAAAAGCGCCGCTAAAAGC
21542167 CT
1 CT
21542169 GTTTTGGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (21 bp):
CTAAAAAGCGCCGCTAAAAGC
Found at i:21554314 original size:19 final size:19
Alignment explanation
Indices: 21554290--21554326 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21554280 AACACACATA
21554290 CTTTGAATAGTTAAAATTC
1 CTTTGAATAGTTAAAATTC
*
21554309 CTTTGAGTAGTTAAAATT
1 CTTTGAATAGTTAAAATT
21554327 TTATCTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (19 bp):
CTTTGAATAGTTAAAATTC
Found at i:21560482 original size:41 final size:41
Alignment explanation
Indices: 21560424--21560629 Score: 279
Period size: 41 Copynumber: 5.0 Consensus size: 41
21560414 GAATAATGAG
* * *
21560424 GAATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACACTT
1 GAATTGCACTTATGTGCCCCTGTTTGTACTTCGGTACCCCT
* * *
21560465 GAATTGCACTTGTGTGCCCCTATTTGTACTTTGGTACCCCT
1 GAATTGCACTTATGTGCCCCTGTTTGTACTTCGGTACCCCT
* * * * *
21560506 AAATTACACTTACGTGCCCCTATTTGTACTTCGATACCCCT
1 GAATTGCACTTATGTGCCCCTGTTTGTACTTCGGTACCCCT
21560547 GAATTGCACTTATGTGCCCCTGTTTGTACTTCGGTACCCCT
1 GAATTGCACTTATGTGCCCCTGTTTGTACTTCGGTACCCCT
* *
21560588 GAATTACA-TATATGTGCCCCTGTTTGTACTTCGATACCCCT
1 GAATTGCACT-TATGTGCCCCTGTTTGTACTTCGGTACCCCT
21560629 G
1 G
21560630 GATGTACTTT
Statistics
Matches: 145, Mismatches: 19, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
40 1 0.01
41 144 0.99
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.36
Consensus pattern (41 bp):
GAATTGCACTTATGTGCCCCTGTTTGTACTTCGGTACCCCT
Found at i:21560504 original size:20 final size:20
Alignment explanation
Indices: 21560440--21560587 Score: 75
Period size: 20 Copynumber: 7.2 Consensus size: 20
21560430 CACTTACGTG
*
21560440 CCCCTGTTTGTACTTCGGTA
1 CCCCTATTTGTACTTCGGTA
* * * * *
21560460 CACTTGAATTGCACTT-GTGTG
1 CCCCT-ATTTGTACTTCG-GTA
*
21560481 CCCCTATTTGTACTTTGGTA
1 CCCCTATTTGTACTTCGGTA
* ** *
21560501 CCCCTAAATTACACTTAC-GTG
1 CCCCT-ATTTGTACTT-CGGTA
*
21560522 CCCCTATTTGTACTTCGATA
1 CCCCTATTTGTACTTCGGTA
* * ** *
21560542 CCCCTGAATTGCACTTATGTG
1 CCCCT-ATTTGTACTTCGGTA
*
21560563 CCCCTGTTTGTACTTCGGTA
1 CCCCTATTTGTACTTCGGTA
21560583 CCCCT
1 CCCCT
21560588 GAATTACATA
Statistics
Matches: 88, Mismatches: 33, Indels: 14
0.65 0.24 0.10
Matches are distributed among these distances:
19 1 0.01
20 46 0.52
21 41 0.47
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.37
Consensus pattern (20 bp):
CCCCTATTTGTACTTCGGTA
Found at i:21567150 original size:9 final size:9
Alignment explanation
Indices: 21567136--21567162 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
21567126 CATGTTGGAT
21567136 CAAAATGAA
1 CAAAATGAA
21567145 CAAAATGAA
1 CAAAATGAA
21567154 CAAAATGAA
1 CAAAATGAA
21567163 TAGAAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (9 bp):
CAAAATGAA
Found at i:21571055 original size:9 final size:9
Alignment explanation
Indices: 21570981--21571090 Score: 68
Period size: 9 Copynumber: 12.2 Consensus size: 9
21570971 TGTTTTGAAG
21570981 AATATATAA
1 AATATATAA
*
21570990 AA-ATTTAA
1 AATATATAA
21570998 AATATATAA
1 AATATATAA
*
21571007 CATAGTAATAA
1 AATA-T-ATAA
* *
21571018 AATGT-TTA
1 AATATATAA
* *
21571026 AATTTATTA
1 AATATATAA
*
21571035 AATTTATAAA
1 AATATAT-AA
21571045 AATATATAA
1 AATATATAA
21571054 AATA-ATTAA
1 AATATA-TAA
*
21571063 AATTTATAA
1 AATATATAA
21571072 TAA-ATAT-A
1 -AATATATAA
21571080 AATATATAA
1 AATATATAA
21571089 AA
1 AA
21571091 CTACTAAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
7 2 0.03
8 19 0.24
9 41 0.51
10 12 0.15
11 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (9 bp):
AATATATAA
Found at i:21572367 original size:19 final size:19
Alignment explanation
Indices: 21572332--21572370 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21572322 GTTCTAATCA
*
21572332 TTATTAAATTCTATTTTAT
1 TTATTAAATTATATTTTAT
21572351 TTATTAAATTGAT-TTTTAT
1 TTATTAAATT-ATATTTTAT
21572370 T
1 T
21572371 ATGAGTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTATTAAATTATATTTTAT
Found at i:21576527 original size:9 final size:9
Alignment explanation
Indices: 21576488--21576576 Score: 53
Period size: 9 Copynumber: 10.0 Consensus size: 9
21576478 ATTATTATTT
21576488 TAAAATATA
1 TAAAATATA
21576497 TAAAA-ATA
1 TAAAATATA
*
21576505 TATACA-AT-
1 TA-AAATATA
21576513 TAAAATATA
1 TAAAATATA
*
21576522 TAAAATGTA
1 TAAAATATA
* *
21576531 TATAATATTT
1 TAAAATA-TA
21576541 TGAAGAATATA
1 T-AA-AATATA
*
21576552 TAAAAT-TT
1 TAAAATATA
21576560 TAAAA-ATA
1 TAAAATATA
*
21576568 TATAATATA
1 TAAAATATA
21576577 GTAATAAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
7 2 0.03
8 20 0.33
9 28 0.46
10 4 0.07
11 3 0.05
12 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (9 bp):
TAAAATATA
Found at i:21576569 original size:18 final size:19
Alignment explanation
Indices: 21576529--21576572 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
21576519 ATATAAAATG
* *
21576529 TATATAATATTTTGAAGAA
1 TATATAAAATTTTGAAAAA
21576548 TATATAAAATTTT-AAAAA
1 TATATAAAATTTTGAAAAA
21576566 TATATAA
1 TATATAA
21576573 TATAGTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TATATAAAATTTTGAAAAA
Found at i:21579063 original size:23 final size:23
Alignment explanation
Indices: 21579031--21579076 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
21579021 TATTATAAAA
21579031 AAAAACCATGCGAGTATAT-TATAT
1 AAAAACCATGC-A-TATATATATAT
21579055 AAAAA-CATGCATATATATATAT
1 AAAAACCATGCATATATATATAT
21579077 TATATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 6 0.29
23 5 0.24
24 5 0.24
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (23 bp):
AAAAACCATGCATATATATATAT
Found at i:21585442 original size:9 final size:9
Alignment explanation
Indices: 21585400--21585509 Score: 59
Period size: 9 Copynumber: 11.9 Consensus size: 9
21585390 GATATATTAT
21585400 TAATTTTTA
1 TAATTTTTA
*
21585409 T-ATTTTTT
1 TAATTTTTA
**
21585417 TAA-TTCAA
1 TAATTTTTA
21585425 TACATTTTTA
1 TA-ATTTTTA
21585435 TAATTTTTA
1 TAATTTTTA
21585444 TATATTTTT-
1 TA-ATTTTTA
*
21585453 TATTTGTTTA
1 TAATT-TTTA
21585463 TGAAATTTTTTA
1 T--AA-TTTTTA
*
21585475 TATATTTTTC
1 TA-ATTTTTA
21585485 TAA-TTTTA
1 TAATTTTTA
*
21585493 -AATCTTATA
1 TAAT-TTTTA
21585502 TAATTTTT
1 TAATTTTT
21585510 TTACAATTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 26
0.67 0.11 0.23
Matches are distributed among these distances:
7 2 0.03
8 17 0.22
9 25 0.33
10 23 0.30
11 1 0.01
12 6 0.08
13 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (9 bp):
TAATTTTTA
Found at i:21585454 original size:20 final size:21
Alignment explanation
Indices: 21585429--21585483 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
21585419 ATTCAATACA
*
21585429 TTTTTATAATTTTTAT-ATAT
1 TTTTTATAATTTTTATGAAAT
21585449 TTTTTAT--TTGTTTATGAAAT
1 TTTTTATAATT-TTTATGAAAT
21585469 TTTTTATATATTTTT
1 TTTTTATA-ATTTTT
21585484 CTAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.07
19 5 0.17
20 17 0.59
22 3 0.10
23 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTATAATTTTTATGAAAT
Found at i:21585489 original size:20 final size:20
Alignment explanation
Indices: 21585429--21585491 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
21585419 ATTCAATACA
21585429 TTTTTATA-ATTTTTATATAT
1 TTTTTATATATTTTTATA-AT
*
21585449 TTTTTAT-T-TGTTTATGAAAT
1 TTTTTATATATTTTTAT--AAT
*
21585469 TTTTTATATATTTTTCTAAT
1 TTTTTATATATTTTTATAAT
21585489 TTT
1 TTT
21585492 AAATCTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
19 6 0.17
20 22 0.63
21 2 0.06
22 5 0.14
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTTATATATTTTTATAAT
Found at i:21585890 original size:15 final size:14
Alignment explanation
Indices: 21585865--21585898 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
21585855 TACCTGCGGT
21585865 TAGTATAAAAACAG
1 TAGTATAAAAACAG
21585879 TAGTACTAAAAACAG
1 TAGTA-TAAAAACAG
21585894 TAGTA
1 TAGTA
21585899 GCGATGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
TAGTATAAAAACAG
Found at i:21587859 original size:21 final size:22
Alignment explanation
Indices: 21587807--21587851 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
21587797 AGCATGAGTA
21587807 TGTTTGATTAAAAATAAAAAAT
1 TGTTTGATTAAAAATAAAAAAT
21587829 TGTTTGATTAAAAATAAAAAAT
1 TGTTTGATTAAAAATAAAAAAT
21587851 T
1 T
21587852 TTATATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (22 bp):
TGTTTGATTAAAAATAAAAAAT
Found at i:21590470 original size:55 final size:55
Alignment explanation
Indices: 21590392--21590531 Score: 210
Period size: 55 Copynumber: 2.6 Consensus size: 55
21590382 TTTTCTTAAT
** *
21590392 TGTTGGAATACTGC-TCTTTTGAATCAATTTTTTATTTGTTGAAATAGATTGTTA
1 TGTTGGAATACTGCTTCTTTTGAATCAATTGCTTATATGTTGAAATAGATTGTTA
* * * *
21590446 TGTTGGAAAACTACTTCTTTTGAATCAATTGCTTATATGTTTAAATTGATTGTTA
1 TGTTGGAATACTGCTTCTTTTGAATCAATTGCTTATATGTTGAAATAGATTGTTA
21590501 TGTTGGAATACTGCTTCTTTTGAATCAATTG
1 TGTTGGAATACTGCTTCTTTTGAATCAATTG
21590532 TTACAGAGCA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
54 12 0.16
55 64 0.84
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.48
Consensus pattern (55 bp):
TGTTGGAATACTGCTTCTTTTGAATCAATTGCTTATATGTTGAAATAGATTGTTA
Found at i:21590766 original size:60 final size:60
Alignment explanation
Indices: 21590697--21590823 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
21590687 CTTTTTCTTT
* * * *** *
21590697 AATTTTTAGAA-TTAGAATTAAATTGACGAATTTTGTAAATGTTG-AGGTTAATTTTATTG
1 AATTTTTAGAATTTA-AACTAAAATGACAAATTTTGTAAACAATGAAGGTTAAATTTATTG
21590756 AATTTGTTAGAATTTAAACTAAAATGACAAATTTTGTAAACAATGAAGGTTAAATTTATTG
1 AATTT-TTAGAATTTAAACTAAAATGACAAATTTTGTAAACAATGAAGGTTAAATTTATTG
21590817 AATTTTT
1 AATTTTT
21590824 TTATATTTAG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
59 5 0.09
60 31 0.53
61 22 0.38
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.43
Consensus pattern (60 bp):
AATTTTTAGAATTTAAACTAAAATGACAAATTTTGTAAACAATGAAGGTTAAATTTATTG
Found at i:21597760 original size:19 final size:19
Alignment explanation
Indices: 21597720--21597761 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
21597710 TCTCACAAGG
**
21597720 TGGAGGCTGTTGGGTTTTT
1 TGGAGGCTGTTGGGTTGGT
21597739 TGGAGGCAT-TTGGGTTGGT
1 TGGAGGC-TGTTGGGTTGGT
21597758 TGGA
1 TGGA
21597762 AGGACTCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.10, C:0.05, G:0.45, T:0.40
Consensus pattern (19 bp):
TGGAGGCTGTTGGGTTGGT
Found at i:21606266 original size:17 final size:17
Alignment explanation
Indices: 21606235--21606278 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
21606225 ACTCTTTTTC
21606235 TTTCTCTTTTC-TTTCAA
1 TTTCT-TTTTCTTTTCAA
*
21606252 TTTCTTTTTCTTTTCTA
1 TTTCTTTTTCTTTTCAA
21606269 TTT-TTTTTCT
1 TTTCTTTTTCT
21606279 CATTTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTCTTTTTCTTTTCAA
Found at i:21607788 original size:14 final size:16
Alignment explanation
Indices: 21607757--21607794 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
21607747 GCACAACACT
21607757 TTTTTTTAATACAAAA
1 TTTTTTTAATACAAAA
*
21607773 TTTTTTTAAT-C-GAA
1 TTTTTTTAATACAAAA
21607787 TTTTTTTA
1 TTTTTTTA
21607795 TGCTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 10 0.48
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTTTTAATACAAAA
Found at i:21612370 original size:22 final size:22
Alignment explanation
Indices: 21612342--21612392 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
21612332 CTCTCTAATC
21612342 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
21612364 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
21612386 CTCTCAA
1 CTCTCAA
21612393 ACCCATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:21612420 original size:51 final size:51
Alignment explanation
Indices: 21612364--21612476 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
21612354 TTCCAAAATT
21612364 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
21612415 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
21612466 CCCTCAATTTC
1 CTCTCAATTTC
21612477 ATTTTTGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
Found at i:21612515 original size:20 final size:20
Alignment explanation
Indices: 21612489--21612536 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
21612479 TTTTGAAAAT
**
21612489 AATTTTTTAAAATTTTTTTA
1 AATTTTTTAAAATAATTTTA
*
21612509 TATTTTTTAAAATAATTTTA
1 AATTTTTTAAAATAATTTTA
21612529 AATTTTTT
1 AATTTTTT
21612537 TATATTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
AATTTTTTAAAATAATTTTA
Found at i:21612534 original size:30 final size:32
Alignment explanation
Indices: 21612477--21612544 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 32
21612467 CCTCAATTTC
21612477 ATTTTTGAAAATAATTTTTTAAAATTTTTTTAT
1 ATTTTTGAAAATAA-TTTTTAAAATTTTTTTAT
*
21612510 ATTTTTTAAAATAA-TTTT-AAATTTTTTTAT
1 ATTTTTGAAAATAATTTTTAAAATTTTTTTAT
21612540 ATTTT
1 ATTTT
21612545 CATCAATGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 17 0.50
31 4 0.12
33 13 0.38
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (32 bp):
ATTTTTGAAAATAATTTTTAAAATTTTTTTAT
Found at i:21612543 original size:10 final size:10
Alignment explanation
Indices: 21612489--21612544 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
21612479 TTTTGAAAAT
*
21612489 AATTTTTTAA
1 AATTTTTTTA
21612499 AATTTTTTTA
1 AATTTTTTTA
* *
21612509 TATTTTTTAA
1 AATTTTTTTA
**
21612519 AATAATTTTA
1 AATTTTTTTA
21612529 AATTTTTTTA
1 AATTTTTTTA
*
21612539 TATTTT
1 AATTTT
21612545 CATCAATGGC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:21614762 original size:25 final size:25
Alignment explanation
Indices: 21614734--21614802 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
21614724 TTTAAATTTA
*
21614734 TTATCTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
21614759 TTATTTAATATAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
21614784 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
21614803 ACCCTAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 23 0.61
26 15 0.39
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:21614821 original size:18 final size:18
Alignment explanation
Indices: 21614798--21614863 Score: 123
Period size: 18 Copynumber: 3.7 Consensus size: 18
21614788 TTTGATGTAA
21614798 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
21614816 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
21614834 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
21614852 TAAAAACCCTAA
1 TAAAAACCCTAA
21614864 TCTAACCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAACCCTAACTTAAT
Found at i:21614897 original size:29 final size:29
Alignment explanation
Indices: 21614841--21615110 Score: 267
Period size: 29 Copynumber: 9.7 Consensus size: 29
21614831 AATTAAAAAC
* *
21614841 CCTAACTTAATTAAAAACCCTAA-TCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
21614869 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
21614898 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
21614927 CCT-ATTTGAATTAAAAACCCTAACCCTAA
1 CCTAATTT-AATTAAAAACCCTAACCCTAA
* *
21614956 CCTAACTTAATTAAAAACCCTAA-CTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *** * *
21614984 -TTAA---AAACCATAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
21615009 CTTAATTTAATTAAAAACCCTAACACTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
21615038 CCTAATTTAATTAAAAACCCTAA-CTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* * * ** *
21615066 -TTAA--AAACT-CTAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
21615091 CCTAATTTAATTAAAAACCC
1 CCTAATTTAATTAAAAACCC
21615111 CAACTTAATT
Statistics
Matches: 198, Mismatches: 31, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
24 19 0.10
25 9 0.05
26 7 0.04
27 6 0.03
28 37 0.19
29 117 0.59
30 3 0.02
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:21614979 original size:18 final size:18
Alignment explanation
Indices: 21614956--21615120 Score: 91
Period size: 18 Copynumber: 9.7 Consensus size: 18
21614946 CTAACCCTAA
21614956 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
21614974 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* * * **
21614992 CATAACCCTAACT-CTAA-
1 CCTAA-CTTAATTAAAAAC
* *
21615009 CTTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
*
21615027 CCTAAC---ACT---AA-
1 CCTAACTTAATTAAAAAC
*
21615038 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
21615056 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* * * **
21615074 TCTAACCCTAACT-CTAA-
1 CCTAA-CTTAATTAAAAAC
*
21615091 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
*
21615109 CCCAACTTAATT
1 CCTAACTTAATT
21615121 TTACTAACCA
Statistics
Matches: 104, Mismatches: 30, Indels: 26
0.65 0.19 0.16
Matches are distributed among these distances:
11 5 0.05
12 2 0.02
14 2 0.02
15 2 0.02
16 8 0.08
17 14 0.13
18 61 0.59
19 10 0.10
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:21615026 original size:35 final size:34
Alignment explanation
Indices: 21614980--21615049 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
21614970 AAACCCTAAC
*
21614980 TTAATTAAAAACCATAACCCTAACTCTAACTTAAT
1 TTAATTAAAAACCATAACACTAAC-CTAACTTAAT
* *
21615015 TTAATTAAAAACCCTAACACTAACCTAATTTAAT
1 TTAATTAAAAACCATAACACTAACCTAACTTAAT
21615049 T
1 T
21615050 AAAAACCCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (34 bp):
TTAATTAAAAACCATAACACTAACCTAACTTAAT
Found at i:21615048 original size:82 final size:82
Alignment explanation
Indices: 21614798--21615110 Score: 355
Period size: 82 Copynumber: 3.8 Consensus size: 82
21614788 TTTGATGTAA
* ** * ** *
21614798 TAAAAACCCTAACTTAATTAAAAACCCTAA-TTTAATTAAAAACCCTAACTTAATTAAAAACCCT
1 TAAAAACCCTAACTTAATTAAAAACCATAACCCTAACT-CTAA-CCTAATTTAATTAAAAACCCT
*
21614862 AA-TCTAACCTAACTTAAT
64 AACACTAACCTAACTTAAT
* * *** * *
21614880 TAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCT-ATTTGAATTAAAAA
1 TAAAAACCCTAA-CTTAA-TTAA---AAACCATAACCCTAACTCTAACCTAATTT-AATTAAAAA
*
21614944 CCCTAACCCTAACCTAACTTAAT
60 CCCTAACACTAACCTAACTTAAT
*
21614967 TAAAAACCCTAACTTAATTAAAAACCATAACCCTAACTCTAACTTAATTTAATTAAAAACCCTAA
1 TAAAAACCCTAACTTAATTAAAAACCATAACCCTAACTCTAACCTAATTTAATTAAAAACCCTAA
*
21615032 CACTAACCTAATTTAAT
66 CACTAACCTAACTTAAT
21615049 TAAAAACCCTAACTTAATTAAAAACTC-TAACCCTAACTCTAACCTAATTTAATTAAAAACCC
1 TAAAAACCCTAACTTAATTAAAAAC-CATAACCCTAACTCTAACCTAATTTAATTAAAAACCC
21615111 CAACTTAATT
Statistics
Matches: 195, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
82 119 0.61
83 9 0.05
84 3 0.02
85 6 0.03
86 22 0.11
87 33 0.17
88 3 0.02
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (82 bp):
TAAAAACCCTAACTTAATTAAAAACCATAACCCTAACTCTAACCTAATTTAATTAAAAACCCTAA
CACTAACCTAACTTAAT
Found at i:21615175 original size:55 final size:55
Alignment explanation
Indices: 21615116--21615342 Score: 219
Period size: 55 Copynumber: 3.9 Consensus size: 55
21615106 AACCCCAACT
**
21615116 TAATTTTACTAACCATTAACTCAATTGTT-GGACTTAATAATTTAACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATT-TTGGGACTTAATAATTTAACATAATTTGA
* *
21615171 TAATTTTATTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTAACATAATTTGA
* * *
21615226 TAATTTTACCTAA--TTTAATTAAAATTTTTTTGG-CTTAATAATTTTACATAATTTTACATAAT
1 TAATTTTA-CTAACCATTAA-CAAAA--TTTTGGGACTTAATAA--TT---T-A----ACATAAT
21615288 TTGA
52 TTGA
*
21615292 TAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTACATAAT
1 TAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTAACATAAT
21615343 GTTAAATTTG
Statistics
Matches: 141, Mismatches: 13, Indels: 36
0.74 0.07 0.19
Matches are distributed among these distances:
54 6 0.04
55 67 0.48
56 11 0.08
57 6 0.04
58 2 0.01
60 1 0.01
61 1 0.01
63 2 0.01
64 6 0.04
65 12 0.09
66 23 0.16
67 4 0.03
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (55 bp):
TAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTAACATAATTTGA
Found at i:21615230 original size:18 final size:18
Alignment explanation
Indices: 21615207--21615241 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21615197 TTGGGACTTA
21615207 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
*
21615225 ATAATTTTACCTAATTT
1 ATAATTTTACATAATTT
21615242 AATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:21615278 original size:10 final size:10
Alignment explanation
Indices: 21615263--21615289 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21615253 TTTTGGCTTA
21615263 ATAATTTTAC
1 ATAATTTTAC
21615273 ATAATTTTAC
1 ATAATTTTAC
21615283 ATAATTT
1 ATAATTT
21615290 GATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:21615288 original size:66 final size:64
Alignment explanation
Indices: 21615207--21615342 Score: 186
Period size: 66 Copynumber: 2.1 Consensus size: 64
21615197 TTGGGACTTA
* * *
21615207 ATAATTTTACATAATTTGATAATTTTACCTAA-TTTAATTAAAATTTTTTTGG-CTTAATAATTT
1 ATAATTTTACATAATTTGATAATTTTA-CTAACATTAA-CAAAA--TTTTGGGACTTAATAATTT
21615270 TAC
62 TAC
21615273 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAC
1 ATAATTTTACATAATTTGATAATTTTACTAA-CATTAACAAAATTTTGGGACTTAATAATTTTAC
21615338 ATAAT
1 ATAAT
21615343 GTTAAATTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
64 6 0.09
65 23 0.36
66 31 0.48
67 4 0.06
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (64 bp):
ATAATTTTACATAATTTGATAATTTTACTAACATTAACAAAATTTTGGGACTTAATAATTTTAC
Found at i:21618794 original size:124 final size:124
Alignment explanation
Indices: 21618450--21618799 Score: 596
Period size: 124 Copynumber: 2.8 Consensus size: 124
21618440 CCCAAACTTG
*
21618450 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAACATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* * *
21618515 TAGAAGCGATTTTATACTATTTGCTCACAAACGTCAAAAAAATTTATTTCTTACATGAC
66 TAGAATCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
21618574 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
21618639 TAGAGGT-GATTTTATACTATTTGCTCAGAAACATCAAAAAAAATTATTTCTTACATGAC
66 TAGA-ATCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
*
21618698 CTACTGTAGCAAAATCGCGTCCACGAGGGCGTGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
21618763 TAGAATCGATTTTATACTATTTGAC-CGGAAACGTCAA
66 TAGAATCGATTTTATACTATTTG-CTCAGAAACGTCAA
21618800 CTCGAAATAA
Statistics
Matches: 213, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
123 1 0.00
124 211 0.99
125 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAATCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAC
Found at i:21621253 original size:18 final size:16
Alignment explanation
Indices: 21621219--21621254 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
21621209 CAATATAATA
21621219 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
21621235 TATTTTATAATATACTTT
1 TATTTT-TAATA-ACTTT
21621253 TA
1 TA
21621255 AAAGCCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:21623849 original size:102 final size:102
Alignment explanation
Indices: 21623618--21624068 Score: 604
Period size: 102 Copynumber: 4.4 Consensus size: 102
21623608 CTATTATCAT
* * * * * * * *
21623618 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AA-TTTTTACGGTTCACGTAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATAG
* * * * *
21623681 TAGCCTTCACATAGTACTATACACGTGATCAAGT-TTTA
65 TAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTA
* * * * *
21623719 -CGATTCACGTAGTAGTCTTCACATAGTACTACATACGTGACTAAAGCTTTTCGGTACACATAGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
* *
21623783 AGCCTTCACTTAGTACTATACATGTGACCATCATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
* * * * * *
21623820 TCAATTCAAGTAGTAGTCTTCACACAGTACTACACACGTGACCGAAGCTTCTCGGTACATATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
*
21623885 AGCCTTCACTTAGTACTACACATGTGACTATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
*
21623922 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGT
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
21623987 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
21624024 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
1 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA
21624069 CACTTTCACT
Statistics
Matches: 314, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
100 39 0.12
101 41 0.13
102 234 0.75
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (102 bp):
TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATAGT
AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
Found at i:21624066 original size:51 final size:51
Alignment explanation
Indices: 21623618--21624067 Score: 387
Period size: 51 Copynumber: 8.9 Consensus size: 51
21623608 CTATTATCAT
* *
21623618 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAATT-TTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA
* * * * *
21623669 -CGGTTCACGTAATAGCCTTCACATAGTACTATACACGTGATCAAGT-TTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGA-CCATTATTTA
* * * *
21623719 -CGATTCACGTAGTAGTCTTCACATAGTACTACATACGTGACTA-AAGCTTT-
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA--TTTA
* * * * * * *
21623769 TCGGTACACATAGTAGCCTTCACTTAGTACTATACATGTGACCATCATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
* * * * * *
21623820 TCAATTCAAGTAGTAGTCTTCACACAGTACTACACACGTGACCGA--AGCTTC
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACC-ATTA-TTTA
* * ** * * * *
21623871 TCGGTACATATTGTAGCCTTCACTTAGTACTACACATGTGACTATTATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
* * * *
21623922 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCA-AAGCTTC
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTA-TTTA
* * * * * *
21623973 TCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
*
21624024 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCA
1 TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCA
21624068 ACACTTTCAC
Statistics
Matches: 311, Mismatches: 76, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
49 2 0.01
50 86 0.28
51 219 0.70
52 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (51 bp):
TCGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTATTTA
Found at i:21625586 original size:16 final size:17
Alignment explanation
Indices: 21625565--21625599 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21625555 TGATATAACA
21625565 AATAAA-AATATTTTTG
1 AATAAACAATATTTTTG
*
21625581 AATAAACATTATTTTTG
1 AATAAACAATATTTTTG
21625598 AA
1 AA
21625600 CAAAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (17 bp):
AATAAACAATATTTTTG
Found at i:21630295 original size:18 final size:19
Alignment explanation
Indices: 21630272--21630307 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21630262 TAAACTAAAT
*
21630272 TTAAATCCCT-AATTTCAC
1 TTAAATCACTAAATTTCAC
21630290 TTAAATCACTAAATTTCA
1 TTAAATCACTAAATTTCA
21630308 AAATTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCACTAAATTTCAC
Found at i:21630621 original size:17 final size:17
Alignment explanation
Indices: 21630580--21630630 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
21630570 TAAGCCTTGT
21630580 CTTTCT-CCTTTCTTT-
1 CTTTCTACCTTTCTTTC
21630595 CTTT-TA--TTTCTTTC
1 CTTTCTACCTTTCTTTC
21630609 CTTTCTACCTTTCTTTC
1 CTTTCTACCTTTCTTTC
21630626 TCTTT
1 -CTTT
21630631 TTCTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 7 0.23
14 5 0.17
15 6 0.20
17 8 0.27
18 4 0.13
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (17 bp):
CTTTCTACCTTTCTTTC
Found at i:21630621 original size:30 final size:28
Alignment explanation
Indices: 21630580--21630636 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
21630570 TAAGCCTTGT
*
21630580 CTTTCTCCTTTCTTTCTTTTATTTCTTTC
1 CTTTCTCCTTTCTTTCTCTT-TTTCTTTC
21630609 CTTTCTACCTTTCTTTCTCTTTTTCTTT
1 CTTTCT-CCTTTCTTTCTCTTTTTCTTT
21630637 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (28 bp):
CTTTCTCCTTTCTTTCTCTTTTTCTTTC
Found at i:21631381 original size:88 final size:88
Alignment explanation
Indices: 21631232--21631406 Score: 280
Period size: 88 Copynumber: 2.0 Consensus size: 88
21631222 ACAAAAACCG
* * *
21631232 ATTTTAAATTATCGAAAACAAAATTCCCCAAAAAATATCTTTCATATTCCAAAAAGTTGAAAATT
1 ATTTTAAACTATCGAAAACAAAAGTCCCCAAAAAATATCTTTCATATTCCAAAAAGCTGAAAATT
*
21631297 AGTAGAGAAATTGGAAATGATCA
66 AGTAGAGAAAGTGGAAATGATCA
* *
21631320 ATTTTGAACTATCGAAAACAAAACGT-CCCAAAAAATATCTTTCATATTCCAAAAAGCTGAAATT
1 ATTTTAAACTATCGAAAACAAAA-GTCCCCAAAAAATATCTTTCATATTCCAAAAAGCTGAAAAT
21631384 TAGTAGAGAAAGTGGAAATGATC
65 TAGTAGAGAAAGTGGAAATGATC
21631407 GCTTCCAATA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 79 0.99
89 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (88 bp):
ATTTTAAACTATCGAAAACAAAAGTCCCCAAAAAATATCTTTCATATTCCAAAAAGCTGAAAATT
AGTAGAGAAAGTGGAAATGATCA
Found at i:21634262 original size:40 final size:40
Alignment explanation
Indices: 21634218--21634546 Score: 186
Period size: 40 Copynumber: 8.6 Consensus size: 40
21634208 TTATTGTCAA
*
21634218 TTTATCTTACTAGTGCTGGGCACATCATTATATCTATCGG
1 TTTATCTGACTAGTGCTGGGCACATCATTATATCTATCGG
* ** * * ** *
21634258 TTTATCCGACTAGCACTGGGCGCA--ACT-T-TC-GCCAG
1 TTTATCTGACTAGTGCTGGGCACATCATTATATCTATCGG
* *
21634293 TTTATCTGACTAGTGTTGGGCACATCATTATATCTGTCGG
1 TTTATCTGACTAGTGCTGGGCACATCATTATATCTATCGG
** ** * *
21634333 TTTAT-TCGACTAGCACTGGGTGCAAC-TT-TA---ATCAG
1 TTTATCT-GACTAGTGCTGGGCACATCATTATATCTATCGG
* * *
21634368 TTTATCTGACTAGTGTTGCGCACATCATTATATCTACCGG
1 TTTATCTGACTAGTGCTGGGCACATCATTATATCTATCGG
* * * **
21634408 TTTATCTAACTAGTGTTGCGCACATCATTATATCTATCAA
1 TTTATCTGACTAGTGCTGGGCACATCATTATATCTATCGG
* **** * *
21634448 TTTTTCTGACTACCATTGGGCACAAC-TT-T-TCT-T-AG
1 TTTATCTGACTAGTGCTGGGCACATCATTATATCTATCGG
* * * *
21634483 TGTATCTGACTAATGCTGGGCACATCATTATATATGTCGG
1 TTTATCTGACTAGTGCTGGGCACATCATTATATCTATCGG
* * *
21634523 TTTATCCGACTAGCGCGGGGCACA
1 TTTATCTGACTAGTGCTGGGCACA
21634547 AAACTTGTTA
Statistics
Matches: 212, Mismatches: 60, Indels: 34
0.69 0.20 0.11
Matches are distributed among these distances:
35 61 0.29
36 8 0.04
37 9 0.04
38 8 0.04
39 8 0.04
40 118 0.56
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (40 bp):
TTTATCTGACTAGTGCTGGGCACATCATTATATCTATCGG
Found at i:21634343 original size:75 final size:75
Alignment explanation
Indices: 21634218--21634413 Score: 302
Period size: 75 Copynumber: 2.6 Consensus size: 75
21634208 TTATTGTCAA
* *
21634218 TTTATCTTACTAGTGCTGGGCACATCATTATATCTATCGGTTTATCCGACTAGCACTGGGCGCAA
1 TTTATCTGACTAGTGTTGGGCACATCATTATATCTATCGGTTTATCCGACTAGCACTGGGCGCAA
**
21634283 CTTTCGCCAG
66 CTTTAACCAG
* * *
21634293 TTTATCTGACTAGTGTTGGGCACATCATTATATCTGTCGGTTTATTCGACTAGCACTGGGTGCAA
1 TTTATCTGACTAGTGTTGGGCACATCATTATATCTATCGGTTTATCCGACTAGCACTGGGCGCAA
*
21634358 CTTTAATCAG
66 CTTTAACCAG
* *
21634368 TTTATCTGACTAGTGTTGCGCACATCATTATATCTACCGGTTTATC
1 TTTATCTGACTAGTGTTGGGCACATCATTATATCTATCGGTTTATC
21634414 TAACTAGTGT
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 109 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (75 bp):
TTTATCTGACTAGTGTTGGGCACATCATTATATCTATCGGTTTATCCGACTAGCACTGGGCGCAA
CTTTAACCAG
Found at i:21634546 original size:115 final size:115
Alignment explanation
Indices: 21634292--21634535 Score: 292
Period size: 115 Copynumber: 2.1 Consensus size: 115
21634282 ACTTTCGCCA
* ** * **
21634292 GTTTATCTGACTAGTGTTGGGCACATCATTATATCTGTCGGTTTATTCGACTAGCACTGGGTGCA
1 GTTTATCTGACTAGTGTTGGGCACATCATTATATCTATCAATTTATTCGACTACCACTGGGCACA
* * * *
21634357 ACTTTAATCAGTTTATCTGACTAGTGTTGCGCACATCATTATATCTACCG
66 ACTTTAATCAGTGTATCTGACTAATGCTGCGCACATCATTATATATACCG
* * *
21634407 GTTTATCTAACTAGTGTTGCGCACATCATTATATCTATCAATTT-TTCTGACTACCATTGGGCAC
1 GTTTATCTGACTAGTGTTGGGCACATCATTATATCTATCAATTTATTC-GACTACCACTGGGCAC
** * * **
21634471 AACTTTTCTTAGTGTATCTGACTAATGCTGGGCACATCATTATATATGTCG
65 AACTTTAATCAGTGTATCTGACTAATGCTGCGCACATCATTATATATACCG
*
21634522 GTTTATCCGACTAG
1 GTTTATCTGACTAG
21634536 CGCGGGGCAC
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
114 3 0.03
115 104 0.97
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (115 bp):
GTTTATCTGACTAGTGTTGGGCACATCATTATATCTATCAATTTATTCGACTACCACTGGGCACA
ACTTTAATCAGTGTATCTGACTAATGCTGCGCACATCATTATATATACCG
Found at i:21646681 original size:28 final size:28
Alignment explanation
Indices: 21646641--21646698 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
21646631 CTGCATACGC
*
21646641 GTAAAAAGTAATATATGCCTCAGATCCA
1 GTAAAAAATAATATATGCCTCAGATCCA
21646669 GTAAAAAATAATATATGCCTCAGATCCA
1 GTAAAAAATAATATATGCCTCAGATCCA
21646697 GT
1 GT
21646699 TCAGTTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (28 bp):
GTAAAAAATAATATATGCCTCAGATCCA
Found at i:21653479 original size:2 final size:2
Alignment explanation
Indices: 21653472--21653511 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
21653462 CCATCTTGAA
21653472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21653512 TTCTCAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21661117 original size:29 final size:29
Alignment explanation
Indices: 21661085--21661156 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
21661075 TAATAACTCC
21661085 TTTATATATATA-ATATAAACATCA-ACTAT
1 TTTATATATATATATATAAACAT-ATA-TAT
* *
21661114 TTTATATATATATATATATATATATATAT
1 TTTATATATATATATATAAACATATATAT
21661143 TTTATATATA-ATAT
1 TTTATATATATATAT
21661157 TTACATGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 4 0.10
29 26 0.67
30 9 0.23
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (29 bp):
TTTATATATATATATATAAACATATATAT
Found at i:21661123 original size:2 final size:2
Alignment explanation
Indices: 21661116--21661156 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
21661106 TCAACTATTT
*
21661116 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21661156 T
1 T
21661157 TTACATGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:21661172 original size:29 final size:29
Alignment explanation
Indices: 21661085--21661173 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
21661075 TAATAACTCC
* * *
21661085 TTTATATATATAATATAAACAT-CAACTAT
1 TTTATATATAT-ATATATACATATAAATAT
* *
21661114 TTTATATATATATATATATATATATATAT
1 TTTATATATATATATATACATATAAATAT
* *
21661143 TTTATATATA-ATATTTACATGTAAAGTAT
1 TTTATATATATATATATACATATAAA-TAT
21661172 TT
1 TT
21661174 ATTTTTTCCA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 19 0.39
29 30 0.61
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (29 bp):
TTTATATATATATATATACATATAAATAT
Found at i:21668927 original size:20 final size:20
Alignment explanation
Indices: 21668904--21668944 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21668894 GAAATGGATG
* * *
21668904 TATGAAATGACAAATTGTTA
1 TATGAAACGAAAAATGGTTA
21668924 TATGAAACGAAAAATGGTTA
1 TATGAAACGAAAAATGGTTA
21668944 T
1 T
21668945 TTGATTTGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (20 bp):
TATGAAACGAAAAATGGTTA
Found at i:21675075 original size:2 final size:2
Alignment explanation
Indices: 21675070--21675103 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21675060 GGTGTGTGGA
21675070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21675104 CGTTTTGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21690951 original size:9 final size:10
Alignment explanation
Indices: 21690927--21690955 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
21690917 ACTAAATTTT
21690927 ATATTTTTAA
1 ATATTTTTAA
21690937 ATATTTTTAA
1 ATATTTTTAA
21690947 A-ATTTTTAA
1 ATATTTTTAA
21690956 TAATGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:21698066 original size:14 final size:15
Alignment explanation
Indices: 21698013--21698064 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
21698003 TGTTTGATAA
21698013 ATTGAAAAAGTAAGT
1 ATTGAAAAAGTAAGT
21698028 ATTG-AAAAGTAAGT
1 ATTGAAAAAGTAAGT
* * *
21698042 GTTGAAAAATTAATT
1 ATTGAAAAAGTAAGT
21698057 ATTGAAAA
1 ATTGAAAA
21698065 TTGAAGTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (15 bp):
ATTGAAAAAGTAAGT
Found at i:21698495 original size:14 final size:14
Alignment explanation
Indices: 21698472--21698504 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
21698462 TGATATGGGT
21698472 TTAT-GGGTTTTAG
1 TTATAGGGTTTTAG
*
21698485 TTATAGGGTTTTGG
1 TTATAGGGTTTTAG
21698499 TTATAG
1 TTATAG
21698505 ACAAATGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.52
Consensus pattern (14 bp):
TTATAGGGTTTTAG
Found at i:21708716 original size:21 final size:23
Alignment explanation
Indices: 21708692--21708736 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
21708682 AATCGATTCA
*
21708692 TATCAA-G-AATAATATCAAATT
1 TATCAATGAAATAACATCAAATT
21708713 TATCAATGAAAATAACATCAAATT
1 TATCAATG-AAATAACATCAAATT
21708737 AGCAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 1 0.05
24 13 0.65
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (23 bp):
TATCAATGAAATAACATCAAATT
Found at i:21728513 original size:27 final size:27
Alignment explanation
Indices: 21728483--21728990 Score: 665
Period size: 27 Copynumber: 18.8 Consensus size: 27
21728473 TATAACAATA
* *
21728483 ATTTTACCCTATGGGGGTATTTTGGCC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
21728510 ATTTTACCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
21728537 ATTCTACCTTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
21728564 ATTCTACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
21728591 ATTCTACCTTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
21728618 ATTCTACCTTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
21728645 ATTTTACCTTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
21728672 ATTTTACCCTATGGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
21728699 ATTTTACCCTATAGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
21728726 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
21728753 ATTTTACCCAATGGGGTTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
21728780 ATTCTACCCTATGGGAGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
21728807 ATTTTACCCTATGGGGGAATTTCAGTT
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
21728834 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* **
21728861 ATTTTATCCTATAAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
21728888 ATTCTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
21728915 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
21728942 ATTATACCCTATGGAGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
21728969 ATTTTACCCTATGGAGGTATTT
1 ATTTTACCCTATGGGGGTATTT
21728991 TAGTCATAAC
Statistics
Matches: 430, Mismatches: 51, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 430 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:21740152 original size:25 final size:25
Alignment explanation
Indices: 21740113--21740194 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
21740103 TGGATACTCC
* *
21740113 ATAGCTCTTGGGAGCATATCGATTT
1 ATAGCTCGTGAGAGCATATCGATTT
*
21740138 ATAGCTCGTGAGAGCATATCGGTTT
1 ATAGCTCGTGAGAGCATATCGATTT
*
21740163 ATAGCTTGTGAGAGCATAGT-GATTT
1 ATAGCTCGTGAGAGCATA-TCGATTT
*
21740188 ACAGCTC
1 ATAGCTC
21740195 ATATAAGCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
25 48 0.98
26 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
ATAGCTCGTGAGAGCATATCGATTT
Found at i:21747636 original size:25 final size:25
Alignment explanation
Indices: 21747554--21747647 Score: 127
Period size: 25 Copynumber: 3.8 Consensus size: 25
21747544 CGAATACTAC
*
21747554 ACAGTTCGTGAGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* *
21747579 ATAGCTCATGAGAGCATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* *
21747604 ATAGCTCGTGAGAGTATACTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
21747629 ACAGCTCGT-ATGAGCATAC
1 ACAGCTCGTGA-GAGCATAC
21747648 ATGTACATGA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 1 0.02
25 60 0.98
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACTGATTT
Found at i:21757572 original size:27 final size:26
Alignment explanation
Indices: 21757542--21757634 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 26
21757532 GTTTCGACCA
*
21757542 ACAGCTCGTGTGACCAGACCCATTGTC
1 ACAGCTCGTGTGAGCAGACCCATT-TC
* * ** **
21757569 ACAGCTCATGTGAGGATTCTGA-TTC
1 ACAGCTCGTGTGAGCAGACCCATTTC
* *
21757594 ACAACTCGTGTGAGCAGACCTATTTTC
1 ACAGCTCGTGTGAGCAGACCCA-TTTC
21757621 ACAGCTCGTGTGAG
1 ACAGCTCGTGTGAG
21757635 GATTCTGATT
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
25 17 0.35
26 1 0.02
27 31 0.63
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.27
Consensus pattern (26 bp):
ACAGCTCGTGTGAGCAGACCCATTTC
Found at i:21757605 original size:25 final size:25
Alignment explanation
Indices: 21757567--21757659 Score: 84
Period size: 25 Copynumber: 3.6 Consensus size: 25
21757557 AGACCCATTG
* *
21757567 TCACAGCTCATGTGAGGATTCTGAT
1 TCACAACTCGTGTGAGGATTCTGAT
*
21757592 TCACAACTCGTGTGAGCAGA-CCT-ATTT
1 TCACAACTCGTGTGAG--GATTCTGA--T
*
21757619 TCACAGCTCGTGTGAGGATTCTGAT
1 TCACAACTCGTGTGAGGATTCTGAT
21757644 TCACAGA-TCGTGTGAG
1 TCACA-ACTCGTGTGAG
21757660 CATACATGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
25 32 0.58
26 4 0.07
27 19 0.35
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (25 bp):
TCACAACTCGTGTGAGGATTCTGAT
Found at i:21757624 original size:52 final size:53
Alignment explanation
Indices: 21757542--21757661 Score: 183
Period size: 52 Copynumber: 2.3 Consensus size: 53
21757532 GTTTCGACCA
*
21757542 ACAG-CTCGTGTGACCAGACCCATTGTCACAGCTCATGTGAGGATTCTGATTC
1 ACAGACTCGTGTGAGCAGACCCATTGTCACAGCTCATGTGAGGATTCTGATTC
* * *
21757594 ACA-ACTCGTGTGAGCAGACCTATTTTCACAGCTCGTGTGAGGATTCTGATTC
1 ACAGACTCGTGTGAGCAGACCCATTGTCACAGCTCATGTGAGGATTCTGATTC
21757646 ACAGA-TCGTGTGAGCA
1 ACAGACTCGTGTGAGCA
21757662 TACATGTACA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
52 61 0.98
53 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (53 bp):
ACAGACTCGTGTGAGCAGACCCATTGTCACAGCTCATGTGAGGATTCTGATTC
Found at i:21764888 original size:25 final size:25
Alignment explanation
Indices: 21764851--21764918 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
21764841 CTTGAATGTC
*
21764851 CACAGCTCATGTGAGCATTCTGATT
1 CACAGCTCGTGTGAGCATTCTGATT
* **
21764876 CACAACTCGTGTGAGGTTTCTGATT
1 CACAGCTCGTGTGAGCATTCTGATT
*
21764901 CACAGCTTGTGTGAGCAT
1 CACAGCTCGTGTGAGCAT
21764919 ACATGTATAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCATTCTGATT
Found at i:21766664 original size:17 final size:17
Alignment explanation
Indices: 21766631--21766664 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21766621 AAATTATTTA
* *
21766631 TTTAATTTTATTTAATT
1 TTTAATTTAATTAAATT
21766648 TTTAATTTAATTAAATT
1 TTTAATTTAATTAAATT
21766665 GATGTTGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATTTAATTAAATT
Found at i:21768117 original size:29 final size:29
Alignment explanation
Indices: 21768059--21768124 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
21768049 GATTTCCCGG
*
21768059 AAAAA-GGACCATTTCGGTAAATAATTAA
1 AAAAAGGGCCCATTTCGGTAAATAATTAA
* **
21768087 AAAATGGGCCCATTTCGGT-AATTTTTGAA
1 AAAAAGGGCCCATTTCGGTAAATAATT-AA
21768116 AAAAAGGGC
1 AAAAAGGGC
21768125 TTTTATTGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (29 bp):
AAAAAGGGCCCATTTCGGTAAATAATTAA
Done.