Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 100 of 135
Found at i:34344352 original size:40 final size:40
Alignment explanation
Indices: 34344308--34344385 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
34344298 TCACGATAGC
34344308 TTTTGATGGATTTATAAAATTGTTTTAAAAATTTATTTAT
1 TTTTGATGGATTTATAAAATTGTTTTAAAAATTTATTTAT
34344348 TTTTGATGGATTTATAAAATTGTTTTAAAAATTTATTT
1 TTTTGATGGATTTATAAAATTGTTTTAAAAATTTATTT
34344386 CATATTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (40 bp):
TTTTGATGGATTTATAAAATTGTTTTAAAAATTTATTTAT
Found at i:34356849 original size:21 final size:22
Alignment explanation
Indices: 34356825--34356880 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
34356815 AATTAAATTG
34356825 TATAATTTTATATTATAA-AAA
1 TATAATTTTATATTATAATAAA
* *
34356846 TATAATTTTATCATTTTAATAGA
1 TATAATTTTAT-ATTATAATAAA
*
34356869 TATATTTTTATA
1 TATAATTTTATA
34356881 ATTTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.37
22 7 0.23
23 12 0.40
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TATAATTTTATATTATAATAAA
Found at i:34356935 original size:30 final size:30
Alignment explanation
Indices: 34356868--34356937 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
34356858 ATTTTAATAG
*
34356868 ATAT-ATTTTTATAATTTTTAAATGATTAA
1 ATATAATTTTTATAATTTTTAAAAGATTAA
34356897 ATCA-AATTTTTAT-ATTTTTAAAAGATTAAA
1 AT-ATAATTTTTATAATTTTTAAAAGATT-AA
34356927 ATATAATTTTT
1 ATATAATTTTT
34356938 TTCATTATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 16 0.44
30 20 0.56
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
ATATAATTTTTATAATTTTTAAAAGATTAA
Found at i:34356936 original size:29 final size:29
Alignment explanation
Indices: 34356868--34356936 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
34356858 ATTTTAATAG
* *
34356868 ATATATTTTTATAATTTTTAAATGATTAA
1 ATATAATTTTATAATTTTTAAAAGATTAA
34356897 ATCA-AATTTT-TATATTTTTAAAAGATTAAA
1 AT-ATAATTTTATA-ATTTTTAAAAGATT-AA
34356927 ATATAATTTT
1 ATATAATTTT
34356937 TTTCATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.06
29 21 0.62
30 11 0.32
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (29 bp):
ATATAATTTTATAATTTTTAAAAGATTAA
Found at i:34366052 original size:50 final size:50
Alignment explanation
Indices: 34365987--34366086 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
34365977 ATGATTTCAC
* *
34365987 GATGGCTTTCAAATGATATTTTTATTAATAATATTATTATAATATGTAAT
1 GATGGCTTTCAAATGATATTTTTATTAATAATAGTATTATAATAAGTAAT
* *
34366037 GATGGTTTTCGAATGATATTTTTATTAATAATAGTATTATAATAAGTAAT
1 GATGGCTTTCAAATGATATTTTTATTAATAATAGTATTATAATAAGTAAT
34366087 AATATTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (50 bp):
GATGGCTTTCAAATGATATTTTTATTAATAATAGTATTATAATAAGTAAT
Found at i:34366104 original size:18 final size:17
Alignment explanation
Indices: 34366056--34366105 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
34366046 CGAATGATAT
*
34366056 TTTTATTAATAATAGTA
1 TTTTATTAATAATAATA
* *
34366073 TTATAATAAGTAATAATA
1 TTTTATTAA-TAATAATA
34366091 TTTTATTAATTAATA
1 TTTTATTAA-TAATA
34366106 TTATAAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTTATTAATAATAATA
Found at i:34371582 original size:12 final size:12
Alignment explanation
Indices: 34371554--34371588 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
34371544 TATGAGCATT
34371554 ATTATACTTTATA
1 ATTATA-TTTATA
*
34371567 ATTATATTTTTA
1 ATTATATTTATA
34371579 ATTATATTTA
1 ATTATATTTA
34371589 ATTGGATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTATATTTATA
Found at i:34375025 original size:12 final size:12
Alignment explanation
Indices: 34374990--34375028 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
34374980 TCAACTCGGG
34374990 TTAACGGGTCAAA
1 TTAACGGGTC-AA
*
34375003 TTTAACAGGTCAA
1 -TTAACGGGTCAA
34375016 TTAACGGGTCAA
1 TTAACGGGTCAA
34375028 T
1 T
34375029 AGGTCAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 2 0.09
14 9 0.39
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (12 bp):
TTAACGGGTCAA
Found at i:34381576 original size:19 final size:18
Alignment explanation
Indices: 34381542--34381577 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34381532 ATACTTAATA
34381542 TATAATTATAAATTATTT
1 TATAATTATAAATTATTT
*
34381560 TATAATATATTAATTATT
1 TATAAT-TATAAATTATT
34381578 ATCAAAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATAATTATAAATTATTT
Found at i:34382269 original size:26 final size:24
Alignment explanation
Indices: 34382211--34382270 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
34382201 AAATCTCTCC
* *
34382211 TAATTTTTAGTTTATTTAAATTGT
1 TAATTTTTAATTTATTTAAATTAT
34382235 TAACTTTTTAATTTATTTTAAATTAT
1 TAA-TTTTTAATTTA-TTTAAATTAT
34382261 TAATATTTTA
1 TAAT-TTTTA
34382271 TACTAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 3 0.10
25 11 0.35
26 17 0.55
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAAATTAT
Found at i:34384645 original size:32 final size:32
Alignment explanation
Indices: 34384586--34384646 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
34384576 TTTTGGGTCC
* * * *
34384586 AATTTGGTACTCAAACTTGATATTTTTTTCCA
1 AATTAGGTACTCAAACTTAACACTTTTTTCCA
*
34384618 AATTAGGTACTTAAACTTAACACTTTTTT
1 AATTAGGTACTCAAACTTAACACTTTTTT
34384647 TAAGTTGGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (32 bp):
AATTAGGTACTCAAACTTAACACTTTTTTCCA
Found at i:34384703 original size:90 final size:92
Alignment explanation
Indices: 34384530--34384703 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 92
34384520 TATAACATTT
* * *
34384530 GGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGGGTCCAATTTGGTA
1 GGTACCTAAACTTAACACTTTTTCCTAAGTTGGTACCTAAAC-TTTTTTTGGGTCCAATTTGATA
34384595 CTCAAACTTGATATTTTTTTCCAAATTA
65 CTCAAACTTGATATTTTTTTCCAAATTA
* * **
34384623 GGTACTTAAACTTAACACTTTTT-TTAAGTTGGTATTTAAAC-TTTTTTGGGTCCAATTTGATAC
1 GGTACCTAAACTTAACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTTGGGTCCAATTTGATAC
**
34384686 TTGAACTTGACTATTTTT
66 TCAAACTTGA-TATTTTT
34384704 CTTAATTTGG
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
90 29 0.41
91 7 0.10
92 14 0.20
93 21 0.30
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.46
Consensus pattern (92 bp):
GGTACCTAAACTTAACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTTGGGTCCAATTTGATAC
TCAAACTTGATATTTTTTTCCAAATTA
Found at i:34384934 original size:31 final size:30
Alignment explanation
Indices: 34384899--34385054 Score: 123
Period size: 31 Copynumber: 5.3 Consensus size: 30
34384889 AAAAAGCTTG
34384899 GGTACCAAATTAGGAAAACATGTCAAGTTTA
1 GGTACCAAATTAGGAAAA-ATGTCAAGTTTA
* *
34384930 GGTACCAAA-TGGGTTAAAA----AAGTTTA
1 GGTACCAAATTAGG-AAAAATGTCAAGTTTA
*
34384956 GGTACCAAATTAGGAAAAAGTGTCAAGTTCA
1 GGTACCAAATTAGGAAAAA-TGTCAAGTTTA
*
34384987 GGTACCAAATTAGGTAGAAAA----AGGTTTA
1 GGTACCAAATTAGG-A-AAAATGTCAAGTTTA
* ** *
34385015 AGTACCAAATTAAAAAAAATGTCAAGTTCA
1 GGTACCAAATTAGGAAAAATGTCAAGTTTA
*
34385045 AGTACCAAAT
1 GGTACCAAAT
34385055 ATTATATTAA
Statistics
Matches: 100, Mismatches: 12, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
26 24 0.24
27 4 0.04
28 16 0.16
30 19 0.19
31 32 0.32
32 1 0.01
33 4 0.04
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (30 bp):
GGTACCAAATTAGGAAAAATGTCAAGTTTA
Found at i:34384960 original size:57 final size:55
Alignment explanation
Indices: 34384888--34385055 Score: 210
Period size: 57 Copynumber: 2.9 Consensus size: 55
34384878 TGAATCTTAG
* * * *
34384888 AAAAAAGCTTGGGTACCAAATTAGGAAAACATGTCAAGTTTAGGTACCAAATGGGTT
1 AAAAAAGTTTAGGTACCAAATTAGGAAAA-ATGTCAAGTTCAGGTACCAAATAGG-T
34384945 AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTAGGT
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAA-TGTCAAGTTCAGGTACCAAA-TAGGT
* ** *
34385002 AGAAAAAGGTTTAAGTACCAAATTAAAAAAAATGTCAAGTTCAAGTACCAAATA
1 A-AAAAA-GTTTAGGTACCAAATTAGGAAAAATGTCAAGTTCAGGTACCAAATA
34385056 TTATATTAAG
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
56 1 0.01
57 50 0.51
58 27 0.27
59 21 0.21
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (55 bp):
AAAAAAGTTTAGGTACCAAATTAGGAAAAATGTCAAGTTCAGGTACCAAATAGGT
Found at i:34385140 original size:37 final size:38
Alignment explanation
Indices: 34385066--34385141 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 38
34385056 TTATATTAAG
34385066 CCAAAAGAAAAAGAAAAAAAAAATAGAGCATATGTACT
1 CCAAAAGAAAAAGAAAAAAAAAATAGAGCATATGTACT
*
34385104 CCAAAAGAAAAA-AAAGAAGAAAA-AGAGCATGA-GTACT
1 CCAAAAGAAAAAGAAA-AAAAAAATAGAGCAT-ATGTACT
34385141 C
1 C
34385142 AAGTTCGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
37 16 0.46
38 19 0.54
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.11
Consensus pattern (38 bp):
CCAAAAGAAAAAGAAAAAAAAAATAGAGCATATGTACT
Found at i:34387559 original size:30 final size:29
Alignment explanation
Indices: 34387508--34387628 Score: 145
Period size: 30 Copynumber: 4.1 Consensus size: 29
34387498 ATGTTAGCAA
34387508 GACACCCCCACATTTTCAAGTGGTTGTAG
1 GACACCCCCACATTTTCAAGTGGTTGTAG
* *
34387537 GACACCTCCCAAATTTTTAAGTGGTTGTAG
1 GACACC-CCCACATTTTCAAGTGGTTGTAG
* *
34387567 GACTCCCCCCACATTTTCAAGTGCTTGTAG
1 GAC-ACCCCCACATTTTCAAGTGGTTGTAG
**
34387597 GATGC-CCCCCACATTTTCAAGTGACTGTAG
1 GA--CACCCCCACATTTTCAAGTGGTTGTAG
34387627 GA
1 GA
34387629 TTGTTTTCTA
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
29 6 0.08
30 71 0.89
31 2 0.03
32 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (29 bp):
GACACCCCCACATTTTCAAGTGGTTGTAG
Found at i:34387613 original size:60 final size:60
Alignment explanation
Indices: 34387512--34387628 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
34387502 TAGCAAGACA
* * * **
34387512 CCCCCACATTTTCAAGTGGTTGTAGGACACCTCCCAAATTTTTAAGTGGTTGTAGGACTC
1 CCCCCACATTTTCAAGTGCTTGTAGGACACCCCCCAAATTTTCAAGTGACTGTAGGACTC
** *
34387572 CCCCCACATTTTCAAGTGCTTGTAGGATGCCCCCCACATTTTCAAGTGACTGTAGGA
1 CCCCCACATTTTCAAGTGCTTGTAGGACACCCCCCAAATTTTCAAGTGACTGTAGGA
34387629 TTGTTTTCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (60 bp):
CCCCCACATTTTCAAGTGCTTGTAGGACACCCCCCAAATTTTCAAGTGACTGTAGGACTC
Found at i:34389934 original size:6 final size:6
Alignment explanation
Indices: 34389923--34389947 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34389913 ACAAATAGAA
34389923 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
34389948 TTCTTTTCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:34390429 original size:23 final size:24
Alignment explanation
Indices: 34390398--34390447 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
34390388 CGGAATGTTG
34390398 GAAAATTCAGAGAG-AAATAGAA-A
1 GAAAATTCA-AGAGTAAATAGAACA
* *
34390421 GAAATTTCAAGAGTGAATAGAACA
1 GAAAATTCAAGAGTAAATAGAACA
34390445 GAA
1 GAA
34390448 TAAAACTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.65
24 4 0.17
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.16
Consensus pattern (24 bp):
GAAAATTCAAGAGTAAATAGAACA
Found at i:34391635 original size:14 final size:14
Alignment explanation
Indices: 34391612--34391649 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
34391602 TATTTCATTG
34391612 AAAATGATTTTCAA
1 AAAATGATTTTCAA
*
34391626 AAAATAATTTTCAA
1 AAAATGATTTTCAA
34391640 AAAATGATTT
1 AAAATGATTT
34391650 ATTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (14 bp):
AAAATGATTTTCAA
Found at i:34392131 original size:15 final size:15
Alignment explanation
Indices: 34392111--34392178 Score: 57
Period size: 15 Copynumber: 4.2 Consensus size: 15
34392101 AATACAAAAC
34392111 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
34392126 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
34392145 ATTTATTATATTAA-AT
1 ATTTA-T-TATTAATAT
*
34392161 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
34392176 ATT
1 ATT
34392179 AATATTGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
14 6 0.14
15 13 0.30
16 8 0.18
17 4 0.09
19 10 0.23
20 2 0.05
21 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:34392154 original size:16 final size:16
Alignment explanation
Indices: 34392111--34392178 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
34392101 AATACAAAAC
*
34392111 ATTTATTATTAATATAT
1 ATTTATTA-TAATAAAT
34392128 -TTATAATTATAATAAAT
1 ATT-T-ATTATAATAAAT
*
34392145 ATTTATTATATTAAAT
1 ATTTATTATAATAAAT
*
34392161 ATTTATTATTA-AAAT
1 ATTTATTATAATAAAT
34392176 ATT
1 ATT
34392179 AATATTGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.16
16 22 0.50
17 9 0.20
18 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTATTATAATAAAT
Found at i:34392191 original size:35 final size:35
Alignment explanation
Indices: 34392117--34392191 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 35
34392107 AAACATTTAT
* *
34392117 TATTAATATATTTATAATTATAATAAATATTTATTA
1 TATTAATATATTTATAATTAAAATAAATATTGA-TA
*
34392153 TATTAA-ATATTTATTATTAAAATATTAATATTGA-A
1 TATTAATATATTTATAATTAAAATA--AATATTGATA
34392188 TATT
1 TATT
34392192 TTCAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 21 0.62
36 6 0.18
37 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (35 bp):
TATTAATATATTTATAATTAAAATAAATATTGATA
Found at i:34392286 original size:16 final size:19
Alignment explanation
Indices: 34392261--34392325 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 19
34392251 TAAAATTGAA
34392261 ATATTAAATAATTTATTAA-
1 ATATT-AATAATTTATTAAT
34392280 A-A-TAATAAATTATATTAATT
1 ATATTAAT-AATT-TATTAA-T
34392300 ATATTAATAATTTATT-AT
1 ATATTAATAATTTATTAAT
34392318 ATGATTAA
1 AT-ATTAA
34392326 ATATAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.08
17 5 0.13
18 10 0.26
19 7 0.18
20 5 0.13
21 5 0.13
22 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATTAATAATTTATTAAT
Found at i:34392374 original size:31 final size:30
Alignment explanation
Indices: 34392331--34392390 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
34392321 ATTAAATATA
34392331 AAAAATTAAATATGTTTAT-TTAATAATATTG
1 AAAAATTAAATAT-TTTATATTAAT-ATATTG
*
34392362 AAAAA-TATAATATTTTTTATTAATATATT
1 AAAAATTA-AATATTTTATATTAATATATT
34392391 AATAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AAAAATTAAATATTTTATATTAATATATTG
Found at i:34393613 original size:19 final size:19
Alignment explanation
Indices: 34393558--34393650 Score: 54
Period size: 19 Copynumber: 4.9 Consensus size: 19
34393548 CAAAAAATTT
34393558 AAATTA-AAAATTAT-T-A
1 AAATTATAAAATTATATAA
*
34393574 AAATTATTTAAAA--ATAGAA
1 AAATTA--TAAAATTATATAA
34393593 AAATTATAAAATTATATAA
1 AAATTATAAAATTATATAA
* * *
34393612 AAAATATATAATATATTTCATA
1 AAATTATAAAAT-TATAT-A-A
*
34393634 AAATTTTAAAA-TATATA
1 AAATTATAAAATTATATA
34393651 TTAGAAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
16 6 0.10
17 7 0.12
19 27 0.47
20 8 0.14
21 1 0.02
22 9 0.16
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
AAATTATAAAATTATATAA
Found at i:34393614 original size:28 final size:28
Alignment explanation
Indices: 34393563--34393617 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
34393553 AATTTAAATT
*
34393563 AAAAATTATTAAAATTATTTAAAAATAG
1 AAAAATTATTAAAATTATTAAAAAATAG
34393591 AAAAATTA-TAAAATTATATAAAAAATA
1 AAAAATTATTAAAATTAT-TAAAAAATA
34393618 TATAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAAATTATTAAAATTATTAAAAAATAG
Found at i:34394022 original size:21 final size:22
Alignment explanation
Indices: 34393974--34394022 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
34393964 ATTTTTAATT
*
34393974 ATTTTTTTAATTTTTTAAAATA
1 ATTTTTTGAATTTTTTAAAATA
*
34393996 AATTTTTGAA-TTTTTAAAATA
1 ATTTTTTGAATTTTTTAAAATA
*
34394017 CTTTTT
1 ATTTTT
34394023 GTAAATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTTTTGAATTTTTTAAAATA
Found at i:34397141 original size:28 final size:28
Alignment explanation
Indices: 34397097--34397248 Score: 171
Period size: 28 Copynumber: 5.4 Consensus size: 28
34397087 AAGGACACGT
* * *
34397097 CTTTGTGGCAAATCTCTGTTAAGAACAC
1 CTTTGTGGAAAACCTCTATTAAGAACAC
* *
34397125 CTTTGTGGAAAAACTCTATTAAGAACTC
1 CTTTGTGGAAAACCTCTATTAAGAACAC
* * *
34397153 CTTTGTGGCAAATCTCTGTTAAGAACGA-
1 CTTTGTGGAAAACCTCTATTAAGAAC-AC
*
34397181 CTTTGTGGCAAACCTCTATTAAGAACAC
1 CTTTGTGGAAAACCTCTATTAAGAACAC
* **
34397209 CTTTTTGGAAAACCTCTATTAAGAATGC
1 CTTTGTGGAAAACCTCTATTAAGAACAC
*
34397237 CTTTTTGGAAAA
1 CTTTGTGGAAAA
34397249 TTTTTTAAAG
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 1 0.01
28 107 0.99
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (28 bp):
CTTTGTGGAAAACCTCTATTAAGAACAC
Found at i:34397185 original size:56 final size:56
Alignment explanation
Indices: 34397097--34397248 Score: 198
Period size: 56 Copynumber: 2.7 Consensus size: 56
34397087 AAGGACACGT
*
34397097 CTTTGTGGCAAATCTCTGTTAAGAAC-ACCTTTGTGGAAAAACTCTATTAAGAACTC
1 CTTTGTGGCAAATCTCTGTTAAGAACGA-CTTTGTGGAAAAACTCTATTAAGAACAC
* *
34397153 CTTTGTGGCAAATCTCTGTTAAGAACGACTTTGTGGCAAACCTCTATTAAGAACAC
1 CTTTGTGGCAAATCTCTGTTAAGAACGACTTTGTGGAAAAACTCTATTAAGAACAC
* * * * * * *
34397209 CTTTTTGGAAAACCTCTATTAAGAATGCCTTTTTGGAAAA
1 CTTTGTGGCAAATCTCTGTTAAGAACGACTTTGTGGAAAA
34397249 TTTTTTAAAG
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
56 83 0.99
57 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (56 bp):
CTTTGTGGCAAATCTCTGTTAAGAACGACTTTGTGGAAAAACTCTATTAAGAACAC
Found at i:34397272 original size:84 final size:84
Alignment explanation
Indices: 34397100--34397275 Score: 214
Period size: 84 Copynumber: 2.1 Consensus size: 84
34397090 GACACGTCTT
* * *
34397100 TGTGGCAAATCTCTGTTAAGAACACCTTTGTGGAAAAACTCTATTAAGAACTCCTTTGTGGCAAA
1 TGTGGCAAACCTCTATTAAGAACACCTTTGTGGAAAAACTCTATTAAGAACTCCTTTGTGGAAAA
* *
34397165 TCTCTGTTAAGAACGACTT
66 TCTCTGTTAAGAAAGACTC
* * *
34397184 TGTGGCAAACCTCTATTAAGAACACCTTTTTGGAAAACCTCTATTAAGAA-TGCCTTTTTGGAAA
1 TGTGGCAAACCTCTATTAAGAACACCTTTGTGGAAAAACTCTATTAAGAACT-CCTTTGTGGAAA
* *
34397248 AT-T-TTTTAAAGGAAAGCCTC
65 ATCTCTGTT-AA-GAAAGACTC
34397268 TGTGGCAA
1 TGTGGCAA
34397276 GTATTGAATG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
82 3 0.04
83 4 0.05
84 72 0.91
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (84 bp):
TGTGGCAAACCTCTATTAAGAACACCTTTGTGGAAAAACTCTATTAAGAACTCCTTTGTGGAAAA
TCTCTGTTAAGAAAGACTC
Found at i:34397342 original size:30 final size:30
Alignment explanation
Indices: 34397308--34397395 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 30
34397298 CATTCATGGT
*
34397308 GATCTTTATTAAAGGAAACGCCTTTGTGGC
1 GATCTTTATTAAAGGAAACGCCTTCGTGGC
* *
34397338 GATCTCTATTAAATG-AA-GCCTTCGTGGC
1 GATCTTTATTAAAGGAAACGCCTTCGTGGC
* * *
34397366 TATCTTT-GTAAAGGAAACGACTTCGTGGC
1 GATCTTTATTAAAGGAAACGCCTTCGTGGC
34397395 G
1 G
34397396 TAATCTGTGA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
27 5 0.11
28 17 0.36
29 12 0.26
30 13 0.28
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (30 bp):
GATCTTTATTAAAGGAAACGCCTTCGTGGC
Found at i:34404713 original size:6 final size:6
Alignment explanation
Indices: 34404702--34404726 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34404692 AACAAACTTG
34404702 AACAAA AACAAA AACAAA AACAAA A
1 AACAAA AACAAA AACAAA AACAAA A
34404727 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:34413355 original size:21 final size:19
Alignment explanation
Indices: 34413310--34413356 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
34413300 ACCAACACAA
34413310 TATACATAGATTTCAAGTC
1 TATACATAGATTTCAAGTC
*
34413329 -ATTACATAGTACTTTTAAGTC
1 TA-TACATAG-A-TTTCAAGTC
34413350 TATACAT
1 TATACAT
34413357 CAACTTGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 7 0.30
20 1 0.04
21 13 0.57
22 1 0.04
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (19 bp):
TATACATAGATTTCAAGTC
Found at i:34415973 original size:37 final size:37
Alignment explanation
Indices: 34415931--34416082 Score: 207
Period size: 37 Copynumber: 4.1 Consensus size: 37
34415921 AATCATCAAG
*
34415931 CATTACACTCTAACCGAGACGTAATCCTTCCATATAA
1 CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
* * *
34415968 TATTACGCTCTAACCGAGATGTAAGCCTTCCATA-AA
1 CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
* *
34416004 CATTACACTCTAATCGAGACGTAAGCCTTCCATATGA
1 CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
* * * *
34416041 CATTACGCTCTGACTGAGACATAAGCCTTCCATATAA
1 CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
34416078 CATTA
1 CATTA
34416083 TATCATTTCG
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
36 32 0.32
37 67 0.68
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.28
Consensus pattern (37 bp):
CATTACACTCTAACCGAGACGTAAGCCTTCCATATAA
Found at i:34416094 original size:73 final size:73
Alignment explanation
Indices: 34415900--34416082 Score: 233
Period size: 73 Copynumber: 2.5 Consensus size: 73
34415890 ATGGTCGTAT
** * * *
34415900 GCTCTAACCGAGACATAAGCAAAT-CATCAAGCATTACACTCTAACCGAGACGTAATCCTTCCAT
1 GCTCTAACCGAGACATAAGC-CTTCCAT-AAACATTACACTCTAATCGAGACGTAAGCCTTCCAT
*
34415964 ATAATATTAC
64 ATAACATTAC
**
34415974 GCTCTAACCGAGATGTAAGCCTTCCATAAACATTACACTCTAATCGAGACGTAAGCCTTCCATAT
1 GCTCTAACCGAGACATAAGCCTTCCATAAACATTACACTCTAATCGAGACGTAAGCCTTCCATAT
*
34416039 GACATTAC
66 AACATTAC
* *
34416047 GCTCTGACTGAGACATAAGCCTTCCATATAACATTA
1 GCTCTAACCGAGACATAAGCCTTCCATA-AACATTA
34416083 TATCATTTCG
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
73 66 0.70
74 28 0.30
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.26
Consensus pattern (73 bp):
GCTCTAACCGAGACATAAGCCTTCCATAAACATTACACTCTAATCGAGACGTAAGCCTTCCATAT
AACATTAC
Found at i:34429179 original size:19 final size:19
Alignment explanation
Indices: 34429151--34429189 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
34429141 TTTATGGTTT
34429151 TAAATAATTTTTGGGTAAAA
1 TAAATAA-TTTTGGGTAAAA
*
34429171 TAAAT-ATTTTGGGTTAAA
1 TAAATAATTTTGGGTAAAA
34429189 T
1 T
34429190 TGAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 1 0.06
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (19 bp):
TAAATAATTTTGGGTAAAA
Found at i:34430999 original size:22 final size:22
Alignment explanation
Indices: 34430968--34431030 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
34430958 CCATAGATGT
*
34430968 ATTATGCCAATATAATTGATTG
1 ATTATACCAATATAATTGATTG
34430990 ATTATACCAATATAATTGATTG
1 ATTATACCAATATAATTGATTG
** *
34431012 ATTGCACCATTATAATTGA
1 ATTATACCAATATAATTGA
34431031 ATATTGTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (22 bp):
ATTATACCAATATAATTGATTG
Found at i:34438799 original size:19 final size:18
Alignment explanation
Indices: 34438760--34438796 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
34438750 ATACTAAAAA
*
34438760 TTAATTTTAAAATATATT
1 TTAAATTTAAAATATATT
34438778 TTAAATTT-AAATATATT
1 TTAAATTTAAAATATATT
34438795 TT
1 TT
34438797 TTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTTAAAATATATT
Found at i:34439060 original size:16 final size:16
Alignment explanation
Indices: 34439039--34439073 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34439029 TTAATTTTAT
34439039 TATTTTATATTT-TACA
1 TATTTT-TATTTGTACA
34439055 TATTTTTATTTGTACA
1 TATTTTTATTTGTACA
34439071 TAT
1 TAT
34439074 AAAATGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (16 bp):
TATTTTTATTTGTACA
Found at i:34444571 original size:16 final size:17
Alignment explanation
Indices: 34444540--34444573 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
34444530 ACTTTTTAGC
*
34444540 AATATTTTTGAAATAAA
1 AATATTATTGAAATAAA
34444557 AATATTATT-AAATAAA
1 AATATTATTGAAATAAA
34444573 A
1 A
34444574 TGTTTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AATATTATTGAAATAAA
Found at i:34444606 original size:22 final size:22
Alignment explanation
Indices: 34444570--34444611 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
34444560 ATTATTAAAT
*
34444570 AAAATGTTTTTGAAT-TTTTCG
1 AAAATATTTTTGAATATTTTCG
34444591 AAAATATTTTTAGAATATTTT
1 AAAATATTTTT-GAATATTTT
34444612 TTTAGCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (22 bp):
AAAATATTTTTGAATATTTTCG
Found at i:34445475 original size:2 final size:2
Alignment explanation
Indices: 34445470--34445494 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34445460 TCTCCTCTGG
34445470 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34445495 ATAGTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34446054 original size:12 final size:13
Alignment explanation
Indices: 34446028--34446058 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
34446018 TCCAAATGTA
34446028 TCATTTCTCATTT
1 TCATTTCTCATTT
34446041 TCATTTCT-ATTT
1 TCATTTCTCATTT
34446053 TCATTT
1 TCATTT
34446059 TGAGAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:34452455 original size:16 final size:15
Alignment explanation
Indices: 34452436--34452469 Score: 59
Period size: 15 Copynumber: 2.2 Consensus size: 15
34452426 ACAGAATTAA
34452436 AAATAAAAGAAAATAG
1 AAATAAAAG-AAATAG
34452452 AAATAAAAGAAATAG
1 AAATAAAAGAAATAG
34452467 AAA
1 AAA
34452470 ATAGGGAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAATAAAAGAAATAG
Found at i:34452459 original size:21 final size:22
Alignment explanation
Indices: 34452413--34452473 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
34452403 TGATCTAAGG
* *
34452413 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAAAT
34452434 AAAAATAAAAGAAAATAGAAAT
1 AAAAATAAAAGAAAATAGAAAT
*
34452456 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
34452474 GGAAGTAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAAAT
Found at i:34452471 original size:16 final size:17
Alignment explanation
Indices: 34452435--34452472 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
34452425 AACAGAATTA
34452435 AAAATAAAAGAAAATAG
1 AAAATAAAAGAAAATAG
34452452 -AAATAAAAG-AAATAG
1 AAAATAAAAGAAAATAG
34452467 AAAATA
1 AAAATA
34452473 GGGAAGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (17 bp):
AAAATAAAAGAAAATAG
Found at i:34455184 original size:21 final size:22
Alignment explanation
Indices: 34455138--34455198 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
34455128 TGATCTAAGG
* *
34455138 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAACT
34455159 AAAAATAAAAGAAAATAGAACT
1 AAAAATAAAAGAAAATAGAACT
*
34455181 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
34455199 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:34455189 original size:15 final size:16
Alignment explanation
Indices: 34455164--34455193 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34455154 GAATTAAAAA
34455164 TAAAAGAAAATAGAAC
1 TAAAAGAAAATAGAAC
34455180 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
34455194 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (16 bp):
TAAAAGAAAATAGAAC
Found at i:34456014 original size:19 final size:19
Alignment explanation
Indices: 34455992--34456034 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
34455982 AAATATAAAT
34455992 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
34456011 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
34456030 TAAAT
1 TAAAT
34456035 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:34456855 original size:11 final size:12
Alignment explanation
Indices: 34456832--34456856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34456822 TAATTTAAAA
34456832 TTCGAATTTTTT
1 TTCGAATTTTTT
34456844 TTCGAATTTTTT
1 TTCGAATTTTTT
34456856 T
1 T
34456857 GATTAGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TTCGAATTTTTT
Found at i:34466347 original size:7 final size:7
Alignment explanation
Indices: 34466337--34466390 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
34466327 TCCCTATAAT
34466337 TTTATTA
1 TTTATTA
*
34466344 TTTATTT
1 TTTATTA
34466351 TTTAATT-
1 TTT-ATTA
34466358 TATTATTA
1 T-TTATTA
34466366 TTTATTA
1 TTTATTA
34466373 TTTATTTA
1 TTTA-TTA
*
34466381 TGTATTA
1 TTTATTA
34466388 TTT
1 TTT
34466391 TATGATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 28 0.70
8 12 0.30
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:34466399 original size:25 final size:21
Alignment explanation
Indices: 34466338--34466425 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 21
34466328 CCCTATAATT
*
34466338 TTATTATTTATTTTTTAATTTA
1 TTATTATTTATTATTT-ATTTA
34466360 TTATTATTTATTATTTATTTA
1 TTATTATTTATTATTTATTTA
*
34466381 TGTATTATTTTATGATATTTAATT-
1 T-TATTA-TTTAT--TATTTATTTA
* *
34466405 TTATTGATATCTTATTTATTT
1 TTATT-ATTTATTATTTATTT
34466426 GCATGTCATA
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
21 14 0.25
22 20 0.36
23 12 0.21
24 2 0.04
25 8 0.14
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.68
Consensus pattern (21 bp):
TTATTATTTATTATTTATTTA
Found at i:34466421 original size:16 final size:14
Alignment explanation
Indices: 34466371--34466421 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 14
34466361 TATTATTTAT
34466371 TATTTA-TTTATG-
1 TATTTATTTTATGA
34466383 TA-TTATTTTATGA
1 TATTTATTTTATGA
34466396 TATTTAATTTTATTGA
1 TATTT-ATTTTA-TGA
34466412 TATCTTATTT
1 TAT-TTATTT
34466422 ATTTGCATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.09
12 8 0.24
13 2 0.06
14 2 0.06
15 6 0.18
16 10 0.30
17 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (14 bp):
TATTTATTTTATGA
Found at i:34466810 original size:19 final size:18
Alignment explanation
Indices: 34466775--34466810 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
34466765 GCTCTAATTC
34466775 ATTGGGTCTGGTTTTTTT
1 ATTGGGTCTGGTTTTTTT
*
34466793 ATTGGGTCTAGTTTTTTT
1 ATTGGGTCTGGTTTTTTT
34466811 CTTTGAACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.06, G:0.25, T:0.61
Consensus pattern (18 bp):
ATTGGGTCTGGTTTTTTT
Found at i:34469698 original size:42 final size:42
Alignment explanation
Indices: 34469639--34469722 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
34469629 CTTGTTCGAG
34469639 AACAAGTAACCTGTGGCCACGTTCCATATTTATCAATTCACA
1 AACAAGTAACCTGTGGCCACGTTCCATATTTATCAATTCACA
34469681 AACAAGTAACCTGTGGCCACGTTCCATATTTATCAATTCACA
1 AACAAGTAACCTGTGGCCACGTTCCATATTTATCAATTCACA
34469723 CAATGTCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (42 bp):
AACAAGTAACCTGTGGCCACGTTCCATATTTATCAATTCACA
Found at i:34471419 original size:48 final size:48
Alignment explanation
Indices: 34471345--34471444 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 48
34471335 CTAGGACATA
* * * *
34471345 TGTGGACAAAGCCACTAAATTTGCAGACAAGCTGCCAATACACATAGT
1 TGTGAACAAAGCCACGAAATTCGCAGACAAGCTACCAATACACATAGT
*
34471393 TGTGAACAAAGCCACCGAAA-TCGCAGACAAGCTACCAATACACATGGT
1 TGTGAACAAAGCCA-CGAAATTCGCAGACAAGCTACCAATACACATAGT
34471441 TGTG
1 TGTG
34471445 GATAAACCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 42 0.91
49 4 0.09
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (48 bp):
TGTGAACAAAGCCACGAAATTCGCAGACAAGCTACCAATACACATAGT
Found at i:34477117 original size:36 final size:35
Alignment explanation
Indices: 34477076--34477151 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 35
34477066 TGGAGTCTAT
34477076 GAAAAATAAACACTGTGATTGACTGTCTTGCAAAA
1 GAAAAATAAACACTGTGATTGACTGTCTTGCAAAA
34477111 GGAAAAATAAACACTGTGATTGACTGTCTTGCAAAA
1 -GAAAAATAAACACTGTGATTGACTGTCTTGCAAAA
34477147 GAAAA
1 GAAAA
34477152 GTAAGGCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 5 0.12
36 35 0.88
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (35 bp):
GAAAAATAAACACTGTGATTGACTGTCTTGCAAAA
Found at i:34477629 original size:25 final size:25
Alignment explanation
Indices: 34477599--34477646 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
34477589 AAAAGATAAA
*
34477599 AATAAAAAATCGTGCTACAAAAATT
1 AATAAAAAAACGTGCTACAAAAATT
* *
34477624 AATAAAAAAACGTGTTATAAAAA
1 AATAAAAAAACGTGCTACAAAAA
34477647 CAGATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.23
Consensus pattern (25 bp):
AATAAAAAAACGTGCTACAAAAATT
Found at i:34479108 original size:2 final size:2
Alignment explanation
Indices: 34479053--34479089 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34479043 TTTTTTCTTT
34479053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34479090 TGGTGAATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34486147 original size:21 final size:21
Alignment explanation
Indices: 34486121--34486170 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
34486111 CGATATTTTA
*
34486121 TTAAATTAAATATAAATAAAT
1 TTAAATTAAATACAAATAAAT
* * *
34486142 TTAAATTAATTCCACATAAAT
1 TTAAATTAAATACAAATAAAT
34486163 TTAAATTA
1 TTAAATTA
34486171 TGCTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATTAAATACAAATAAAT
Found at i:34489244 original size:54 final size:54
Alignment explanation
Indices: 34489162--34489299 Score: 215
Period size: 54 Copynumber: 2.6 Consensus size: 54
34489152 GGAAGGAATT
* * *
34489162 GCATACTCGCTCGTTTGAGCACACTGGCTCGTTTA-AGTATACTAGCTCGTTAGA
1 GCATACTAGCTCGTTTGAGCATACTGGCTCG-TTAGAGCATACTAGCTCGTTAGA
*
34489216 GCATACTAGCTCGTTTGAGCATACTGGCTCGTTAGGGCATACTAGCTCGTTAGA
1 GCATACTAGCTCGTTTGAGCATACTGGCTCGTTAGAGCATACTAGCTCGTTAGA
*
34489270 GCATACTAGCTCGTTTGAGCATAATGGCTC
1 GCATACTAGCTCGTTTGAGCATACTGGCTC
34489300 TTAAGAGTAT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 3 0.04
54 75 0.96
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.30
Consensus pattern (54 bp):
GCATACTAGCTCGTTTGAGCATACTGGCTCGTTAGAGCATACTAGCTCGTTAGA
Found at i:34489299 original size:18 final size:18
Alignment explanation
Indices: 34489162--34489292 Score: 172
Period size: 18 Copynumber: 7.3 Consensus size: 18
34489152 GGAAGGAATT
*
34489162 GCATACTCGCTCGTTTGA
1 GCATACTAGCTCGTTTGA
* * *
34489180 GCACACTGGCTCGTTTAA
1 GCATACTAGCTCGTTTGA
* *
34489198 GTATACTAGCTCGTTAGA
1 GCATACTAGCTCGTTTGA
34489216 GCATACTAGCTCGTTTGA
1 GCATACTAGCTCGTTTGA
* * *
34489234 GCATACTGGCTCGTTAGG
1 GCATACTAGCTCGTTTGA
*
34489252 GCATACTAGCTCGTTAGA
1 GCATACTAGCTCGTTTGA
34489270 GCATACTAGCTCGTTTGA
1 GCATACTAGCTCGTTTGA
34489288 GCATA
1 GCATA
34489293 ATGGCTCTTA
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 97 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (18 bp):
GCATACTAGCTCGTTTGA
Found at i:34489508 original size:19 final size:19
Alignment explanation
Indices: 34489471--34489508 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
34489461 TACATGTGTA
*
34489471 TTGTTTTTGTTTTGTAGAT
1 TTGTTTTTGTTTTGAAGAT
34489490 TTGTTTTT-TTATTGAAGAT
1 TTGTTTTTGTT-TTGAAGAT
34489509 CGGATCCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.66
Consensus pattern (19 bp):
TTGTTTTTGTTTTGAAGAT
Found at i:34496054 original size:18 final size:18
Alignment explanation
Indices: 34496031--34496129 Score: 103
Period size: 18 Copynumber: 5.4 Consensus size: 18
34496021 GAAGGAATAA
* *
34496031 CATACTCGCTCGTTTGAG
1 CATACTGGCTCGTTAGAG
34496049 CATACTGGCTCGTTAGAG
1 CATACTGGCTCGTTAGAG
* *
34496067 CATATTGGCTTGTTTA-AG
1 CATACTGGCTCG-TTAGAG
*
34496085 -AGTATTGGCTCGTTAGAG
1 CA-TACTGGCTCGTTAGAG
*
34496103 CATACTGGCTCGTAAGAG
1 CATACTGGCTCGTTAGAG
34496121 CATTACTGG
1 CA-TACTGG
34496130 ATCGCATGAG
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.06
18 55 0.80
19 10 0.14
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (18 bp):
CATACTGGCTCGTTAGAG
Found at i:34500966 original size:13 final size:14
Alignment explanation
Indices: 34500942--34501020 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 14
34500932 TTGGATTCAA
34500942 GATTTAAGGTTTAG
1 GATTTAAGGTTTAG
34500956 GATTT-AGGTTT-G
1 GATTTAAGGTTTAG
* **
34500968 GGTTTTGGGTTTAG
1 GATTTAAGGTTTAG
*
34500982 GGTTTAAGGTTTAAG
1 GATTTAAGGTTT-AG
* *
34500997 G--TTACATGTTTGG
1 GATTTA-AGGTTTAG
34501010 GATTTAAGGTT
1 GATTTAAGGTT
34501021 CGGGTTTGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
12 5 0.10
13 16 0.31
14 25 0.48
15 6 0.12
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (14 bp):
GATTTAAGGTTTAG
Found at i:34501039 original size:19 final size:20
Alignment explanation
Indices: 34501004--34501054 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
34500994 AAGGTTACAT
*
34501004 GTTTGGGATTTAAGGTTC-GG
1 GTTTGGG-TTCAAGGTTCAGG
34501024 GTTTGGGTTCAAGGTTCAAGG
1 GTTTGGGTTCAAGGTTC-AGG
34501045 GTTTGTGGTT
1 GTTTG-GGTT
34501055 ATTGGTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 9 0.33
20 7 0.26
21 7 0.26
22 4 0.15
ACGTcount: A:0.14, C:0.06, G:0.39, T:0.41
Consensus pattern (20 bp):
GTTTGGGTTCAAGGTTCAGG
Found at i:34506189 original size:53 final size:53
Alignment explanation
Indices: 34506057--34506235 Score: 297
Period size: 53 Copynumber: 3.4 Consensus size: 53
34506047 GGAAGCCACA
* *
34506057 AAAACCCACCTTTAGAGAAAATTTTGTCTGAAAACCTTAATTTCAACGGAAA-
1 AAAACTCACCTTTAGAGAAAATTTTGTCTGAAAACCTTAATTTCAACGAAAAC
*
34506109 AAAACTCACCTTTAGAGAAAATTTTGTCTGAAAATCTTAATTTCAACGAAAAC
1 AAAACTCACCTTTAGAGAAAATTTTGTCTGAAAACCTTAATTTCAACGAAAAC
* *
34506162 AAAACTCACCTTTAGAAAAAATCTTGTCTGAAAACCTTAATTTCAACGAAAAC
1 AAAACTCACCTTTAGAGAAAATTTTGTCTGAAAACCTTAATTTCAACGAAAAC
*
34506215 AAAACTCGCCTTTAGAGAAAA
1 AAAACTCACCTTTAGAGAAAA
34506236 CCCTAGTTTT
Statistics
Matches: 118, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 49 0.42
53 69 0.58
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (53 bp):
AAAACTCACCTTTAGAGAAAATTTTGTCTGAAAACCTTAATTTCAACGAAAAC
Found at i:34512545 original size:20 final size:20
Alignment explanation
Indices: 34512522--34512559 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34512512 TGCATTAGTG
*
34512522 AGCATCGAGTAGCATCAGCA
1 AGCATCGAGCAGCATCAGCA
34512542 AGCATCGAGCAGCATCAG
1 AGCATCGAGCAGCATCAG
34512560 TAGTAGTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.13
Consensus pattern (20 bp):
AGCATCGAGCAGCATCAGCA
Found at i:34518586 original size:9 final size:9
Alignment explanation
Indices: 34518561--34518603 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
34518551 AATGTTTTAA
*
34518561 ATAATAAAG
1 ATAATAATG
34518570 TATAATAATG
1 -ATAATAATG
* *
34518580 TTAATAATA
1 ATAATAATG
34518589 ATAATAATG
1 ATAATAATG
34518598 ATAATA
1 ATAATA
34518604 GGAAAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (9 bp):
ATAATAATG
Found at i:34523469 original size:21 final size:21
Alignment explanation
Indices: 34523445--34523522 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
34523435 CAATGCAGAC
34523445 TTCTACCAATACAAGAGATAG
1 TTCTACCAATACAAGAGATAG
* * *
34523466 TTCTACCGATACAAGTG-TCAC
1 TTCTACCAATACAAGAGAT-AG
*
34523487 TTCTACCGATACAAGAGATAG
1 TTCTACCAATACAAGAGATAG
34523508 TTCTACCAATACAAG
1 TTCTACCAATACAAG
34523523 TGTCACTTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (21 bp):
TTCTACCAATACAAGAGATAG
Found at i:34523502 original size:42 final size:42
Alignment explanation
Indices: 34523443--34523543 Score: 166
Period size: 42 Copynumber: 2.4 Consensus size: 42
34523433 AACAATGCAG
* *
34523443 ACTTCTACCAATACAAGAGATAGTTCTACCGATACAAGTGTC
1 ACTTCTACCGATACAAGAGATAGTTCTACCAATACAAGTGTC
34523485 ACTTCTACCGATACAAGAGATAGTTCTACCAATACAAGTGTC
1 ACTTCTACCGATACAAGAGATAGTTCTACCAATACAAGTGTC
* *
34523527 ACTTCTATCGACACAAG
1 ACTTCTACCGATACAAG
34523544 TCATGCTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (42 bp):
ACTTCTACCGATACAAGAGATAGTTCTACCAATACAAGTGTC
Found at i:34523542 original size:21 final size:21
Alignment explanation
Indices: 34523443--34523544 Score: 100
Period size: 21 Copynumber: 4.9 Consensus size: 21
34523433 AACAATGCAG
* *
34523443 ACTTCTACCAATACAAGAGAT-
1 ACTTCTACCGATACAAGTG-TC
*
34523464 AGTTCTACCGATACAAGTGTC
1 ACTTCTACCGATACAAGTGTC
*
34523485 ACTTCTACCGATACAAGAGAT-
1 ACTTCTACCGATACAAGTG-TC
* *
34523506 AGTTCTACCAATACAAGTGTC
1 ACTTCTACCGATACAAGTGTC
* *
34523527 ACTTCTATCGACACAAGT
1 ACTTCTACCGATACAAGT
34523545 CATGCTTTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.03
21 63 0.95
22 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGTC
Found at i:34524451 original size:42 final size:41
Alignment explanation
Indices: 34524314--34524454 Score: 119
Period size: 41 Copynumber: 3.4 Consensus size: 41
34524304 CCGAGTCGTA
* * *
34524314 AGTCTTCCTTTA-ACATAA-TCTCATTCTCATCCTGAGATATG
1 AGTCTTCCTTTATACA-AATTCTCATGCTCA-CCCGAGACATG
* * * *
34524355 AGTCTTCCTTTA-ACAATTTCTCATGCTCATTCCGAGTCACG
1 AGTCTTCCTTTATACAAATTCTCATGCTCA-CCCGAGACATG
* *
34524396 AGTCTTCTTTTTATATAAATTCTCATGCTTC-CCCGAGACATG
1 AGTCTTC-CTTTATACAAATTCTCATGC-TCACCCGAGACATG
34524438 AGTCTTCCATTTATACA
1 AGTCTTCC-TTTATACA
34524455 TCAAGTTTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
40 1 0.01
41 39 0.49
42 26 0.32
43 12 0.15
44 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.39
Consensus pattern (41 bp):
AGTCTTCCTTTATACAAATTCTCATGCTCACCCGAGACATG
Found at i:34532376 original size:57 final size:58
Alignment explanation
Indices: 34532307--34532449 Score: 209
Period size: 57 Copynumber: 2.5 Consensus size: 58
34532297 TAATTCATTT
* * *
34532307 TTTAATAATAATTATATTAAAATGTTATTAAATTATATATTA-TTTTATTAAATTGTA
1 TTTAATAATAATTATATTAAAATATAATTAAATTATATATTATTTTTATTAAATTATA
* *
34532364 TTTAATAATAATTATGTTAAAATATAATTAAATTATTTATTATTTTTATTAAATTATA
1 TTTAATAATAATTATATTAAAATATAATTAAATTATATATTATTTTTATTAAATTATA
*
34532422 TTTAATAATAATCT-TATTAAAATTTAAT
1 TTTAATAATAAT-TATATTAAAATATAAT
34532450 AACAATAATC
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
57 38 0.49
58 38 0.49
59 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (58 bp):
TTTAATAATAATTATATTAAAATATAATTAAATTATATATTATTTTTATTAAATTATA
Found at i:34532394 original size:26 final size:26
Alignment explanation
Indices: 34532308--34532394 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
34532298 AATTCATTTT
*
34532308 TTAATAATAATTATATTAAAATGTTA
1 TTAATAATAATTATATTAAAATGTAA
* * *
34532334 TTAAATTATATATTATTTTATTAAATTGTAT
1 TT-AA-TA-ATA--ATTATATTAAAATGTAA
* *
34532365 TTAATAATAATTATGTTAAAATATAA
1 TTAATAATAATTATATTAAAATGTAA
34532391 TTAA
1 TTAA
34532395 ATTATTTATT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
26 18 0.38
27 2 0.04
28 5 0.11
29 5 0.11
30 2 0.04
31 15 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
TTAATAATAATTATATTAAAATGTAA
Found at i:34532642 original size:16 final size:16
Alignment explanation
Indices: 34532613--34532643 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34532603 GATTACAACC
34532613 CTATTCCATTACAGTT
1 CTATTCCATTACAGTT
34532629 CTATTCCATTACAGT
1 CTATTCCATTACAGT
34532644 GAACCAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (16 bp):
CTATTCCATTACAGTT
Found at i:34535682 original size:18 final size:18
Alignment explanation
Indices: 34535659--34535696 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
34535649 GTTGCGGGCA
34535659 ATGTTTGCTCAACTCAGT
1 ATGTTTGCTCAACTCAGT
34535677 ATGTTTGCTCAACTCAGT
1 ATGTTTGCTCAACTCAGT
34535695 AT
1 AT
34535697 TAGTGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (18 bp):
ATGTTTGCTCAACTCAGT
Found at i:34542653 original size:17 final size:17
Alignment explanation
Indices: 34542631--34542668 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
34542621 GGGACAAAAT
34542631 AAAATGCAGTAATAA-TA
1 AAAATGCAGTAA-AACTA
*
34542648 AAAATGCATTAAAACTA
1 AAAATGCAGTAAAACTA
34542665 AAAA
1 AAAA
34542669 AAATGTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAATGCAGTAAAACTA
Found at i:34551870 original size:20 final size:19
Alignment explanation
Indices: 34551847--34551892 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
34551837 TTTCAGAGGT
34551847 ATCGATAAATTTCGTTAAAA
1 ATCGATAAATTTC-TTAAAA
** *
34551867 ATCGATACTTTTCTTTAAA
1 ATCGATAAATTTCTTAAAA
34551886 ATCGATA
1 ATCGATA
34551893 CCACGGACCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (19 bp):
ATCGATAAATTTCTTAAAA
Found at i:34558244 original size:19 final size:20
Alignment explanation
Indices: 34558198--34558244 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
34558188 TTTTAGAGGT
*
34558198 ATCGATAATTTTCATTAAAA
1 ATCGATACTTTTCATTAAAA
** *
34558218 ATATATACTTTTC-TTTAAA
1 ATCGATACTTTTCATTAAAA
34558237 ATCGATAC
1 ATCGATAC
34558245 CACAGACCAA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (20 bp):
ATCGATACTTTTCATTAAAA
Found at i:34558901 original size:28 final size:27
Alignment explanation
Indices: 34558859--34558947 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 27
34558849 CCCATAGCCT
*
34558859 TAAT-ACTCGTTCAGCACATAAGTGCGG
1 TAATAACTCGTCCAGCACA-AAGTGCGG
**
34558886 TAATAACTCGTCCAGCACCAAAGTATGG
1 TAATAACTCGTCCAGCA-CAAAGTGCGG
* * *
34558914 TAATAACTCGTCCAACACCGATGTGCGG
1 TAATAACTCGTCCAGCA-CAAAGTGCGG
34558942 TAATAA
1 TAATAA
34558948 GCGCGCAAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
27 4 0.08
28 46 0.88
29 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (27 bp):
TAATAACTCGTCCAGCACAAAGTGCGG
Found at i:34568424 original size:26 final size:26
Alignment explanation
Indices: 34568395--34568445 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
34568385 TGTGATTATT
34568395 TTAAAGTAAATATTTCTTAATAAAAC
1 TTAAAGTAAATATTTCTTAATAAAAC
34568421 TTAAAGTAAATATTTCTTAATAAAA
1 TTAAAGTAAATATTTCTTAATAAAA
34568446 TTTAGGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (26 bp):
TTAAAGTAAATATTTCTTAATAAAAC
Found at i:34568439 original size:16 final size:16
Alignment explanation
Indices: 34568395--34568440 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
34568385 TGTGATTATT
34568395 TTAAAGTAAATATTTC
1 TTAAAGTAAATATTTC
34568411 TT-AA-TAAA-A---C
1 TTAAAGTAAATATTTC
34568421 TTAAAGTAAATATTTC
1 TTAAAGTAAATATTTC
34568437 TTAA
1 TTAA
34568441 TAAAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
10 3 0.12
11 2 0.08
12 4 0.17
13 2 0.08
14 4 0.17
15 2 0.08
16 7 0.29
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (16 bp):
TTAAAGTAAATATTTC
Found at i:34576437 original size:49 final size:49
Alignment explanation
Indices: 34576379--34576473 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
34576369 TTGGATTTAA
* * *
34576379 GATACTTTAGGATTTGATTTTGGGCATTGGGCTTGTAATTTGGGTTTGG
1 GATACTTTAGGATTTGATTTTGAGCATTGAGCTCGTAATTTGGGTTTGG
* *
34576428 GATAGTTTAGGATTTGATTTTGAGTATTGAGCTCGTAATTTGGGTT
1 GATACTTTAGGATTTGATTTTGAGCATTGAGCTCGTAATTTGGGTT
34576474 AAGGGTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.19, C:0.05, G:0.31, T:0.45
Consensus pattern (49 bp):
GATACTTTAGGATTTGATTTTGAGCATTGAGCTCGTAATTTGGGTTTGG
Found at i:34578185 original size:88 final size:88
Alignment explanation
Indices: 34578036--34578212 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
34578026 AATAACAAGG
34578036 TTTTCAAAGTTTGCATTTTAGTCCATCTAACATTCACCTATACCAAGAACCTATATACATGCCAT
1 TTTTCAAAGTTTGCATTTTAGTCCATCTAACATTCACCTATACCAAGAACCTATATACATGCCAT
34578101 ACTAACCCCAAAATTCATACATA
66 ACTAACCCCAAAATTCATACATA
34578124 TTTTCAAAGTTTGCATTTTAGTCCATCTAACATTCACCTATACCAAGAACCTATATACATGCCAT
1 TTTTCAAAGTTTGCATTTTAGTCCATCTAACATTCACCTATACCAAGAACCTATATACATGCCAT
34578189 ACTAACCCCAAAATTCATACATA
66 ACTAACCCCAAAATTCATACATA
34578212 T
1 T
34578213 ATCCTTTCCT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (88 bp):
TTTTCAAAGTTTGCATTTTAGTCCATCTAACATTCACCTATACCAAGAACCTATATACATGCCAT
ACTAACCCCAAAATTCATACATA
Found at i:34578645 original size:28 final size:27
Alignment explanation
Indices: 34578587--34578668 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 27
34578577 CATATATCAC
34578587 TAAGCA-CAAAGTGC-AA-AA-AACGA
1 TAAGCACCAAAGTGCAAATAATAACGA
34578610 TAAGCACCAAAGTGCAAAATAATAACGA
1 TAAGCACCAAAGTGC-AAATAATAACGA
*
34578638 TAAGCACCGAAGTGCGAAATAAT-ACGA
1 TAAGCACCAAAGTGC-AAATAATAACGA
34578665 TAAG
1 TAAG
34578669 TGCGCTAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.12
24 8 0.15
26 2 0.04
27 10 0.19
28 26 0.50
ACGTcount: A:0.51, C:0.17, G:0.18, T:0.13
Consensus pattern (27 bp):
TAAGCACCAAAGTGCAAATAATAACGA
Found at i:34582277 original size:13 final size:13
Alignment explanation
Indices: 34582259--34582283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34582249 AAAGTTAAAG
34582259 TATTAAATTGTGC
1 TATTAAATTGTGC
34582272 TATTAAATTGTG
1 TATTAAATTGTG
34582284 ATTGCTATGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (13 bp):
TATTAAATTGTGC
Found at i:34582379 original size:26 final size:26
Alignment explanation
Indices: 34582343--34582397 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
34582333 TAACATATAA
34582343 TATCATTTACTACATAAAATTAAAAT
1 TATCATTTACTACATAAAATTAAAAT
*
34582369 TATCATTTACTACATAAAATTAGAAT
1 TATCATTTACTACATAAAATTAAAAT
34582395 TAT
1 TAT
34582398 GTTAAAACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (26 bp):
TATCATTTACTACATAAAATTAAAAT
Found at i:34583473 original size:2 final size:2
Alignment explanation
Indices: 34583468--34583494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34583458 ATACACACAC
34583468 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
34583495 ACTTTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34589995 original size:12 final size:12
Alignment explanation
Indices: 34589967--34589997 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34589957 GTATTTTAGC
*
34589967 ATTTATTGGATA
1 ATTTGTTGGATA
34589979 ATTTGTTGGATA
1 ATTTGTTGGATA
34589991 ATTTGTT
1 ATTTGTT
34589998 CCCATTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (12 bp):
ATTTGTTGGATA
Found at i:34590197 original size:37 final size:37
Alignment explanation
Indices: 34590121--34590197 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
34590111 TAATGACGCT
* * *
34590121 GCATGAGCACTTCTAGATTGCACCCAAAACTGTCGTC
1 GCATGAGCACTTCCAAATTGCACCCAAAACTGTCATC
*
34590158 GCATGAGCACTTCCAAATTGCACCCAAAACTGTTATC
1 GCATGAGCACTTCCAAATTGCACCCAAAACTGTCATC
34590195 GCA
1 GCA
34590198 GGAAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (37 bp):
GCATGAGCACTTCCAAATTGCACCCAAAACTGTCATC
Found at i:34592014 original size:17 final size:17
Alignment explanation
Indices: 34591994--34592050 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
34591984 ATTATCATCA
34591994 CATTTCTTTTGTCATTG
1 CATTTCTTTTGTCATTG
*
34592011 CATTT-TTATTGTCACTG
1 CATTTCTT-TTGTCATTG
* *
34592028 CATCTAC-CTTGTCATTG
1 CAT-TTCTTTTGTCATTG
34592045 CATTTC
1 CATTTC
34592051 CATTTATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.12
17 27 0.84
18 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.51
Consensus pattern (17 bp):
CATTTCTTTTGTCATTG
Found at i:34593281 original size:26 final size:26
Alignment explanation
Indices: 34593241--34593298 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
34593231 CACCCAAAAA
* *
34593241 TGTCGCCGCATGAACATGTCTCGAAT
1 TGTCGCCGCAGGAACATGTCTAGAAT
* *
34593267 TGTCGCTGCAGGAACGTGTCTAGAAT
1 TGTCGCCGCAGGAACATGTCTAGAAT
34593293 TG-CGCC
1 TGTCGCC
34593299 TAGAATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (26 bp):
TGTCGCCGCAGGAACATGTCTAGAAT
Found at i:34594018 original size:10 final size:10
Alignment explanation
Indices: 34594003--34594033 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
34593993 TGGTAAGATG
34594003 TTCATTGCAC
1 TTCATTGCAC
34594013 TTCATTGCAC
1 TTCATTGCAC
34594023 TTCATTGCAC
1 TTCATTGCAC
34594033 T
1 T
34594034 GACAAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (10 bp):
TTCATTGCAC
Found at i:34610383 original size:17 final size:17
Alignment explanation
Indices: 34610358--34610399 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
34610348 GAAAAAAGTA
*
34610358 GTTATAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
34610376 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
34610393 GTTAAAG
1 GTTAAAG
34610400 GTCAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.24
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:34610399 original size:24 final size:24
Alignment explanation
Indices: 34610372--34610419 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
34610362 TAAGAATATG
* *
34610372 AAAGGTTAAAGAAGATGGAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
* *
34610396 AAAGGTCAAGGGAGATGAAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
34610420 GAACATCCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.35, T:0.19
Consensus pattern (24 bp):
AAAGGTCAAAGAAGATGAAAGGTT
Found at i:34613906 original size:17 final size:17
Alignment explanation
Indices: 34613880--34613916 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
34613870 AAGTAGTTAC
*
34613880 AAGAATATGAAAGATTA
1 AAGAAGATGAAAGATTA
*
34613897 AAGAAGATGAAAGGTTA
1 AAGAAGATGAAAGATTA
34613914 AAG
1 AAG
34613917 GTCAAGGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAGATTA
Found at i:34613916 original size:24 final size:24
Alignment explanation
Indices: 34613889--34613936 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
34613879 CAAGAATATG
*
34613889 AAAGATTAAAGAAGATGAAAGGTT
1 AAAGATCAAAGAAGATGAAAGGTT
* *
34613913 AAAGGTCAAGGAAGATGAAAGGTT
1 AAAGATCAAAGAAGATGAAAGGTT
34613937 GAACATCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.29, T:0.19
Consensus pattern (24 bp):
AAAGATCAAAGAAGATGAAAGGTT
Found at i:34614117 original size:18 final size:18
Alignment explanation
Indices: 34614083--34614122 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
34614073 AATTAAAAAG
*
34614083 AAAATATTAAAATATTAT
1 AAAATATTAAAAGATTAT
34614101 AAAATTATT-AAAGATTAT
1 AAAA-TATTAAAAGATTAT
34614119 AAAA
1 AAAA
34614123 ATCTAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAATATTAAAAGATTAT
Found at i:34614226 original size:12 final size:11
Alignment explanation
Indices: 34614198--34614255 Score: 59
Period size: 12 Copynumber: 5.3 Consensus size: 11
34614188 TAAAATATAG
34614198 AAAATTATTAA
1 AAAATTATTAA
*
34614209 AAAATTAGTTAT
1 AAAATTA-TTAA
34614221 AAAATTA-TAGGA
1 AAAATTATTA--A
34614233 AAAATTA-TAA
1 AAAATTATTAA
34614243 AAAATTA-TAA
1 AAAATTATTAA
34614253 AAA
1 AAA
34614256 TGAGAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 16 0.38
11 7 0.17
12 19 0.45
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (11 bp):
AAAATTATTAA
Found at i:34614244 original size:34 final size:32
Alignment explanation
Indices: 34614186--34614249 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 32
34614176 TAGAAAAACA
34614186 TATAAAATATAGAAAATTATTAAAAAATTAGT
1 TATAAAATATAGAAAATTATTAAAAAATTAGT
34614218 TATAAAATTATAGGAAAAATTA-TAAAAAATTA
1 TATAAAA-TATA-G-AAAATTATTAAAAAATTA
34614250 TAAAAATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 7 0.24
33 4 0.14
34 11 0.38
35 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (32 bp):
TATAAAATATAGAAAATTATTAAAAAATTAGT
Found at i:34618563 original size:8 final size:8
Alignment explanation
Indices: 34618550--34618580 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
34618540 GGCATCGAGT
34618550 TTTAATTC
1 TTTAATTC
34618558 TTTAATTC
1 TTTAATTC
34618566 TTTAATTC
1 TTTAATTC
34618574 TTTAATT
1 TTTAATT
34618581 TAGTGGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTAATTC
Found at i:34628926 original size:18 final size:17
Alignment explanation
Indices: 34628905--34628939 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
34628895 GATTTTTGAC
34628905 TTTTTAAGTAATTTTTTA
1 TTTTT-AGTAATTTTTTA
*
34628923 TTTTTATTAATTTTTTA
1 TTTTTAGTAATTTTTTA
34628940 ATGATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAGTAATTTTTTA
Found at i:34631583 original size:32 final size:33
Alignment explanation
Indices: 34631536--34631613 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 33
34631526 TGTGTATATG
* * * *
34631536 AATATGATTACATCTGTATTTTGTATTTCTGTT
1 AATATGATTACATCTGTATTCTGGATATATGTT
34631569 AATATGA-TACATCTGTATTCTGGATATATGTT
1 AATATGATTACATCTGTATTCTGGATATATGTT
34631601 AATATGATTACAT
1 AATATGATTACAT
34631614 GCATTTGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 28 0.70
33 12 0.30
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (33 bp):
AATATGATTACATCTGTATTCTGGATATATGTT
Found at i:34636925 original size:42 final size:41
Alignment explanation
Indices: 34636879--34637027 Score: 113
Period size: 43 Copynumber: 3.5 Consensus size: 41
34636869 CACGCGCATT
* *
34636879 CCGAGTCATGAGTCTTCATTTAATCATATTCTCATTCTCATC
1 CCGAGTCATGAGTCTTCATTTAAT-ATATCCTCATGCTCATC
* * *
34636921 CCGAGGC-TCGAGTCTTCCTTTAATATATCCTCATGCTCATT
1 CCGAGTCAT-GAGTCTTCATTTAATATATCCTCATGCTCATC
* * * * **
34636962 TCTAGTCATGAGTCTTCCATTCATATAAATATTCATGCTCAAT-
1 CCGAGTCATGAGTCTT-CATTTA-ATATATCCTCATGCTC-ATC
* *
34637005 CCAAGACATGAGTCTTCCATTTA
1 CCGAGTCATGAGTCTT-CATTTA
34637028 TACATAAACT
Statistics
Matches: 85, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
41 26 0.31
42 25 0.29
43 32 0.38
44 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (41 bp):
CCGAGTCATGAGTCTTCATTTAATATATCCTCATGCTCATC
Found at i:34636975 original size:41 final size:41
Alignment explanation
Indices: 34636879--34636988 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 41
34636869 CACGCGCATT
* * *
34636879 CCGAGTCATGAGTCTTCATTTAATCATATTCTCATTCTCATC
1 CCGAGTCATGAGTCTTCCTTTAAT-ATATCCTCATGCTCATC
* *
34636921 CCGAGGC-TCGAGTCTTCCTTTAATATATCCTCATGCTCATT
1 CCGAGTCAT-GAGTCTTCCTTTAATATATCCTCATGCTCATC
* * * *
34636962 TCTAGTCATGAGTCTTCCATTCATATA
1 CCGAGTCATGAGTCTTCCTTTAATATA
34636989 AATATTCATG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 35 0.62
42 21 0.38
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (41 bp):
CCGAGTCATGAGTCTTCCTTTAATATATCCTCATGCTCATC
Found at i:34637986 original size:17 final size:17
Alignment explanation
Indices: 34637966--34638000 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
34637956 TTAATCCTTT
34637966 TTACTTAATTAACTATC
1 TTACTTAATTAACTATC
34637983 TTACTTAATTAACTATC
1 TTACTTAATTAACTATC
34638000 T
1 T
34638001 AAACGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (17 bp):
TTACTTAATTAACTATC
Found at i:34640090 original size:29 final size:28
Alignment explanation
Indices: 34640058--34640372 Score: 176
Period size: 29 Copynumber: 10.8 Consensus size: 28
34640048 TGGACTCTCA
*
34640058 GGGGTAAAAATGGAATTTTGGGAAAATTT
1 GGGGTAAAAATGGAATTTTTGG-AAATTT
* *
34640087 GGGGCTAAAAAT-G-ATATTTTGGATATCTA
1 GGGG-TAAAAATGGAAT-TTTTGGAAAT-TT
* * * * *
34640116 GGGGT-AAAACGGTAATCTTTAGAAAATC
1 GGGGTAAAAATGG-AATTTTTGGAAATTT
* * * *
34640144 GGGATAAAAAATGGAGTTTTTGGACATTAA
1 GGGGT-AAAAATGGAATTTTTGGAAATT-T
34640174 GGGGT-AAAATGGTAA-TTTT-GAAAGTTTT
1 GGGGTAAAAATGG-AATTTTTGGAAA--TTT
*
34640202 GAGGTCAAAAATGGAATTTTT-GAAAGTTTTT
1 GGGGT-AAAAATGGAATTTTTGGAAA---TTT
* *
34640233 GGGTTAAAAATGGAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAA-ATTT
* *
34640262 GGGGTTAAAATGGAATTTTTGGAAGTTT
1 GGGGTAAAAATGGAATTTTTGGAAATTT
* * * * *
34640290 CGAGGTCAAAAATGTAATTTTTAGAAGTTC
1 -GGGGT-AAAAATGGAATTTTTGGAAATTT
* * *
34640320 GAGGGTAAAAATGTAATTTTTAGAAGTTT
1 G-GGGTAAAAATGGAATTTTTGGAAATTT
*
34640349 GAGGGTAAAAATGTAATTTTTGGA
1 G-GGGTAAAAATGGAATTTTTGGA
34640373 TAGTTTAGGG
Statistics
Matches: 228, Mismatches: 37, Indels: 42
0.74 0.12 0.14
Matches are distributed among these distances:
27 7 0.03
28 30 0.13
29 110 0.48
30 71 0.31
31 10 0.04
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTTGGAAATTT
Found at i:34640250 original size:59 final size:58
Alignment explanation
Indices: 34640179--34640368 Score: 172
Period size: 59 Copynumber: 3.2 Consensus size: 58
34640169 ATTAAGGGGT
*
34640179 AAAATGGTAATTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGAAAGTTTTTGGGTTA
1 AAAATGG-AATTTTGAAAGTTTTGAGGT-AAAAATGGAATTTTTGAAAGTTTTAGGGTTA
* * * * * *
34640239 AAAATGGAATTTTTGGAAGTTTTGGGGTTAAAATGGAATTTTTGGAAG-TTTCGAGGTCA
1 AAAATGGAA-TTTTGAAAGTTTTGAGGTAAAAATGGAATTTTTGAAAGTTTTAG-GGTTA
* * * * *
34640298 AAAATGTAATTTTTAGAAG-TTCGAGGGTAAAAATGTAATTTTT-AGAAGTTTGAGGG-TA
1 AAAATGGAATTTTGA-AAGTTTTGA-GGTAAAAATGGAATTTTTGA-AAGTTTTAGGGTTA
*
34640356 AAAATGTAATTTT
1 AAAATGGAATTTT
34640369 TGGATAGTTT
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
58 25 0.23
59 56 0.52
60 26 0.24
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.38
Consensus pattern (58 bp):
AAAATGGAATTTTGAAAGTTTTGAGGTAAAAATGGAATTTTTGAAAGTTTTAGGGTTA
Found at i:34640382 original size:29 final size:28
Alignment explanation
Indices: 34640175--34640382 Score: 186
Period size: 29 Copynumber: 7.1 Consensus size: 28
34640165 GGACATTAAG
* *
34640175 GGGT-AAAATGGTAA-TTTTGAAAGTTTT
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTA
* * *
34640202 GAGGTCAAAAATGGAATTTTTGAAAGTTTTT
1 G-GGT-AAAAATGTAATTTTTGGAAG-TTTA
* *
34640233 GGGTTAAAAATGGAATTTTTGGAAGTTTTG
1 GGG-TAAAAATGTAATTTTTGGAAG-TTTA
* * *
34640263 GGGTTAAAATGGAATTTTTGGAAGTTTC
1 GGGTAAAAATGTAATTTTTGGAAGTTTA
* *
34640291 GAGGTCAAAAATGTAATTTTTAGAAGTTCGA
1 G-GGT-AAAAATGTAATTTTTGGAAGTT-TA
*
34640322 GGGTAAAAATGTAATTTTTAGAAGTTTGA
1 GGGTAAAAATGTAATTTTTGGAAGTTT-A
34640351 GGGTAAAAATGTAATTTTTGGATAGTTTA
1 GGGTAAAAATGTAATTTTTGGA-AGTTTA
34640380 GGG
1 GGG
34640383 ACCTTTAATG
Statistics
Matches: 158, Mismatches: 12, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.01
28 7 0.04
29 74 0.47
30 69 0.44
31 7 0.04
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTA
Found at i:34641486 original size:13 final size:12
Alignment explanation
Indices: 34641459--34641490 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
34641449 TTATTAAAAA
34641459 ATTATTATTAAT
1 ATTATTATTAAT
34641471 ATTATTATTGAAT
1 ATTATTATT-AAT
34641484 ATTATTA
1 ATTATTA
34641491 CCGTTATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:34642294 original size:6 final size:6
Alignment explanation
Indices: 34642269--34642370 Score: 68
Period size: 6 Copynumber: 17.2 Consensus size: 6
34642259 TTTTTGAATT
**
34642269 ATTTCAA ATTTAA AACTAA ATTTAA ATTTAGA A--TAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA
** * ** * *
34642317 AAATGA ATTTAA ATTTAA ATTT-A AGGTAA ATTTAA TTTTAGA A-ATAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA
34642364 ATTTAA A
1 ATTTAA A
34642371 ATCCGTCTAA
Statistics
Matches: 71, Mismatches: 18, Indels: 13
0.70 0.18 0.13
Matches are distributed among these distances:
4 2 0.03
5 7 0.10
6 55 0.77
7 7 0.10
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:34642330 original size:41 final size:41
Alignment explanation
Indices: 34642285--34642370 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
34642275 AATTTAAAAC
*
34642285 TAAATTTAAATTT-AGAATAAATTTAAATTTAAAAATGAATT
1 TAAATTTAAATTTAAG-ATAAATTTAAATTTAAAAATAAATT
* * *
34642326 TAAATTTAAATTTAAGGTAAATTTAATTTTAGAAATAAATT
1 TAAATTTAAATTTAAGATAAATTTAAATTTAAAAATAAATT
34642367 TAAA
1 TAAA
34642371 ATCCGTCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 38 0.95
42 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (41 bp):
TAAATTTAAATTTAAGATAAATTTAAATTTAAAAATAAATT
Found at i:34642347 original size:35 final size:35
Alignment explanation
Indices: 34642274--34642351 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
34642264 GAATTATTTC
* **
34642274 AAATTTAAAACTAAATTTAAATTTAGAATAAATTT
1 AAATTTAAAAATAAATTTAAATTTAGAATAAAGGT
* *
34642309 AAATTTAAAAATGAATTTAAATTTA-AATTTAAGGT
1 AAATTTAAAAATAAATTTAAATTTAGAA-TAAAGGT
34642344 AAATTTAA
1 AAATTTAA
34642352 TTTTAGAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (35 bp):
AAATTTAAAAATAAATTTAAATTTAGAATAAAGGT
Found at i:34642348 original size:17 final size:18
Alignment explanation
Indices: 34642269--34642370 Score: 91
Period size: 18 Copynumber: 5.4 Consensus size: 18
34642259 TTTTTGAATT
34642269 ATTTCAAATTTA-AAACTAA
1 ATTT-AAATTTAGAAA-TAA
34642288 ATTTAAATTTAG-AATAA
1 ATTTAAATTTAGAAATAA
* *
34642305 ATTTAAATTTAAAAATGA
1 ATTTAAATTTAGAAATAA
*
34642323 ATTTAAATTTAAATTTAAGGTAA
1 ATTTAAATTTAGA---AA--TAA
*
34642346 ATTTAATTTTAGAAATAA
1 ATTTAAATTTAGAAATAA
34642364 ATTTAAA
1 ATTTAAA
34642371 ATCCGTCTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
17 14 0.20
18 35 0.50
19 4 0.06
20 2 0.03
21 2 0.03
23 13 0.19
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (18 bp):
ATTTAAATTTAGAAATAA
Found at i:34643405 original size:206 final size:206
Alignment explanation
Indices: 34642723--34643746 Score: 1606
Period size: 206 Copynumber: 5.0 Consensus size: 206
34642713 TCTGGTTTTA
* * * * * * *
34642723 TTGACTTGGCCTTCTTCTTAGTTTCTCATCAGGAAGATGACCGCATCACTTGTTTTAA-TCTACT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATTC-GCT
* * * * * * *
34642787 TCTCTGTGTTTCATCAGGAAGACGGATTTGATTCACTTCTCTGTGTCTCATCAGGAAGCTAACCA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * *
34642852 CTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTATA
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATA
*
34642917 TCGAGTGTGGGT
195 TCGAGCGTGGGT
* * *
34642929 TTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATTCGCTT
* *
34642994 CTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCGT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
34643059 TTGA---CTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGGTTCGAAGACTTGCTCATA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTG-GGGTTCGAAGATTTGCTCATA
34643121 TCGAGCGTGGGT
195 TCGAGCGTGGGT
* *
34643133 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATTCGCTT
* *
34643198 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGACTAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
*
34643263 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
*
34643328 CGAGTGTGGGT
196 CGAGCGTGGGT
* *
34643339 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCGTTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATTCGCTT
* *
34643404 CTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
34643469 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
34643534 CGAGCGTGGGT
196 CGAGCGTGGGT
* *
34643545 TTGATTTGGTCTTTTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATTCGCTT
* *
34643610 CTCTCTATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * **
34643675 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTAGGGTTCAAAGATTTGCTCGCAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
34643740 CGAGCGT
196 CGAGCGT
34643747 CGAGTTGGTA
Statistics
Matches: 758, Mismatches: 55, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
203 35 0.05
204 156 0.21
206 530 0.70
207 37 0.05
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATTCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATAT
CGAGCGTGGGT
Found at i:34645194 original size:6 final size:6
Alignment explanation
Indices: 34645182--34645242 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
34645172 ACCTCTTGTA
* * * *
34645182 TTCTTT TTATTTT TTCTTT TTCTTT TTCTTT TTTTGTT TTGTTT TT-GTT
1 TTCTTT TT-CTTT TTCTTT TTCTTT TTCTTT TTCT-TT TTCTTT TTCTTT
34645231 TT-TTT TTCTTT T
1 TTCTTT TTCTTT T
34645243 ATTCATTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
5 8 0.17
6 28 0.61
7 10 0.22
ACGTcount: A:0.02, C:0.08, G:0.05, T:0.85
Consensus pattern (6 bp):
TTCTTT
Found at i:34645200 original size:13 final size:12
Alignment explanation
Indices: 34645182--34645234 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
34645172 ACCTCTTGTA
34645182 TTCTTTTTATTTT
1 TTCTTTTT-TTTT
*
34645195 TTCTTTTTCTTT
1 TTCTTTTTTTTT
34645207 TTCTTTTTTTGTT
1 TTCTTTTTTT-TT
*
34645220 TTGTTTTTGTTTT
1 TTCTTTTT-TTTT
34645233 TT
1 TT
34645235 TTTCTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 12 0.34
13 21 0.60
14 2 0.06
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.85
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:34645206 original size:19 final size:19
Alignment explanation
Indices: 34645177--34645235 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
34645167 CCTCGACCTC
*
34645177 TTGTATTCTTTTTATTTTT
1 TTGTTTTCTTTTTATTTTT
*
34645196 TCT-TTTTCTTTTTCTTTTT
1 T-TGTTTTCTTTTTATTTTT
* *
34645215 TTGTTTTGTTTTTGTTTTT
1 TTGTTTTCTTTTTATTTTT
34645234 TT
1 TT
34645236 TTCTTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 32 0.94
20 1 0.03
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.83
Consensus pattern (19 bp):
TTGTTTTCTTTTTATTTTT
Done.