Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 13 of 26
Found at i:2127054 original size:21 final size:21
Alignment explanation
Indices: 2127017--2127078 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2127007 ATTAATATTT
* *
2127017 ATAATTAAATATAAATAAA-A
1 ATAATTTAATTTAAATAAATA
2127037 ATAATTTTTAA-TTAAATAAATA
1 ATAA--TTTAATTTAAATAAATA
2127059 ATAATTTAATTTAAATAAAT
1 ATAATTTAATTTAAATAAAT
2127079 CTAAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 9 0.25
21 18 0.50
22 9 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATTTAATTTAAATAAATA
Found at i:2127068 original size:27 final size:28
Alignment explanation
Indices: 2127007--2127093 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 28
2126997 TGATATTTTT
2127007 ATTAATATTTATAATTAAATATAAATAAA
1 ATTAAT-TTTATAATTAAATATAAATAAA
*
2127036 AATAATTTT-TAATT-AA-ATAAATAATA
1 ATTAATTTTATAATTAAATATAAATAA-A
* *
2127062 ATTTAATTTAAATAAATCTAAATTTAAATAAA
1 A-TTAATTT-TAT-AAT-TAAATATAAATAAA
2127094 CTTTATTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
25 8 0.17
26 4 0.09
27 11 0.24
28 3 0.07
29 6 0.13
30 3 0.07
31 1 0.02
32 3 0.07
33 7 0.15
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
ATTAATTTTATAATTAAATATAAATAAA
Found at i:2130565 original size:23 final size:23
Alignment explanation
Indices: 2130539--2130582 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2130529 TAACTTATTA
2130539 TATTATATATACATATATATACG
1 TATTATATATACATATATATACG
* * *
2130562 TATTGTGTATATATATATATA
1 TATTATATATACATATATATA
2130583 ATGTTAGCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (23 bp):
TATTATATATACATATATATACG
Found at i:2130877 original size:20 final size:19
Alignment explanation
Indices: 2130839--2130876 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2130829 TTGCTCTTAA
* *
2130839 AATTTTAAAATACTGTTTT
1 AATTTTAAAAAAATGTTTT
2130858 AATTTTAAAAAAATGTTTT
1 AATTTTAAAAAAATGTTTT
2130877 TTAAAACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
AATTTTAAAAAAATGTTTT
Found at i:2135818 original size:2 final size:2
Alignment explanation
Indices: 2135811--2135836 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2135801 TTAATGGACA
2135811 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
2135837 GCAGTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2137092 original size:41 final size:39
Alignment explanation
Indices: 2137017--2137097 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 39
2137007 TTAGATAAAC
*
2137017 AATAAAATTAATTTTAATAAAATTAAAAATAATGATAAT
1 AATAAAATTAATTTTAATAAAATTAAAAATAATGAAAAT
* * * *
2137056 AATAAAATTAATTATTCGATGATATTAAAATTAATGAAAAT
1 AATAAAATTAATT-TT-AATAAAATTAAAAATAATGAAAAT
2137097 A
1 A
2137098 TTTGTTTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 13 0.37
40 2 0.06
41 20 0.57
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (39 bp):
AATAAAATTAATTTTAATAAAATTAAAAATAATGAAAAT
Found at i:2137957 original size:20 final size:20
Alignment explanation
Indices: 2137923--2137968 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2137913 AAAATTATAT
*
2137923 ATATATAAAATATTTAATAG
1 ATATATAAAATATTTAATAA
2137943 ATATA-AAAATAATTTAATAA
1 ATATATAAAAT-ATTTAATAA
2137963 ATATAT
1 ATATAT
2137969 TACAACATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATATATAAAATATTTAATAA
Found at i:2140939 original size:19 final size:19
Alignment explanation
Indices: 2140917--2140961 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2140907 TATTGTTAGA
*
2140917 TATTAAAATATCA-AAAAAT
1 TATTAAAA-ATAATAAAAAT
2140936 TATTAAAAATAATAAAAAT
1 TATTAAAAATAATAAAAAT
*
2140955 TTTTAAA
1 TATTAAA
2140962 TTGTGAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TATTAAAAATAATAAAAAT
Found at i:2142529 original size:21 final size:21
Alignment explanation
Indices: 2142503--2142551 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2142493 ATCACTTATT
*
2142503 TTAATCTCATAATTATAAT-A
1 TTAATCTCATAACTATAATAA
*
2142523 TTCAATCTCATTACTATAATAA
1 TT-AATCTCATAACTATAATAA
2142545 TTAATCT
1 TTAATCT
2142552 TATCATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAATCTCATAACTATAATAA
Found at i:2144865 original size:19 final size:20
Alignment explanation
Indices: 2144825--2144865 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2144815 TGAACAGTGA
**
2144825 TGTATCGATACTATTTATAG
1 TGTATCGATACTATGAATAG
2144845 TGTATCGATAC-ATGAATAG
1 TGTATCGATACTATGAATAG
2144864 TG
1 TG
2144866 ATGAACAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACTATGAATAG
Found at i:2147565 original size:20 final size:20
Alignment explanation
Indices: 2147542--2147601 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 20
2147532 TAGATTGAAT
2147542 TATAACAAAATAAAAAATAA
1 TATAACAAAATAAAAAATAA
**
2147562 TAT-A-AAAATAATTAA-AA
1 TATAACAAAATAAAAAATAA
2147579 TATAACAAACAT-AAAAATAA
1 TATAACAAA-ATAAAAAATAA
2147599 TAT
1 TAT
2147602 TAATACGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 5 0.16
18 10 0.31
19 7 0.22
20 10 0.31
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (20 bp):
TATAACAAAATAAAAAATAA
Found at i:2148088 original size:12 final size:12
Alignment explanation
Indices: 2148071--2148108 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2148061 TATATTATTT
2148071 AAAAATAAAATA
1 AAAAATAAAATA
2148083 AAAAAT-AAATA
1 AAAAATAAAATA
**
2148094 ATTAATAAAATA
1 AAAAATAAAATA
2148106 AAA
1 AAA
2148109 TTTCAACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:2148400 original size:20 final size:20
Alignment explanation
Indices: 2148342--2148422 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
2148332 AATTTAAAAA
2148342 TATATGAA-ATAAAAAA-AT
1 TATATGAATATAAAAAATAT
* * *
2148360 AATATGAAAAATAATGTAAATAT
1 TATATG-AATATAA--AAAATAT
*
2148383 TATATGAATATAAAAAATTT
1 TATATGAATATAAAAAATAT
* *
2148403 TATATAAAT-TAATAAATAT
1 TATATGAATATAAAAAATAT
2148422 T
1 T
2148423 TAAAAATATT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
18 5 0.10
19 11 0.22
20 17 0.35
22 9 0.18
23 7 0.14
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
TATATGAATATAAAAAATAT
Found at i:2148413 original size:29 final size:28
Alignment explanation
Indices: 2148360--2148461 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
2148350 ATAAAAAAAT
* * * *
2148360 AATATGAAAAATAATGTAAATATTATATG
1 AATATAAAAAAT-ATTTAAAAATTATATA
2148389 AATATAAAAAAT-TTTATATAAATTA-ATA
1 AATATAAAAAATATTTA-A-AAATTATATA
* *
2148417 AATATTTAAAAATATTTAAAAATAATATA
1 AATA-TAAAAAATATTTAAAAATTATATA
2148446 AATATAATATAAATAT
1 AATATAA-A-AAATAT
2148462 AAATATAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.05
28 14 0.24
29 32 0.54
30 10 0.17
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
AATATAAAAAATATTTAAAAATTATATA
Found at i:2148424 original size:20 final size:21
Alignment explanation
Indices: 2148376--2148454 Score: 64
Period size: 20 Copynumber: 4.1 Consensus size: 21
2148366 AAAAATAATG
*
2148376 TAAATA-TTATATGAATATAA
1 TAAATATTTATATAAATATAA
*
2148396 AAAAT-TTTATATAAAT-TAA
1 TAAATATTTATATAAATATAA
*
2148415 TAAATATTTA-A-AAATAT-T
1 TAAATATTTATATAAATATAA
* *
2148433 TAAA-AATAATATAAATATAA
1 TAAATATTTATATAAATATAA
2148453 TA
1 TA
2148455 TAAATATAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
17 3 0.07
18 9 0.20
19 15 0.33
20 19 0.41
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
TAAATATTTATATAAATATAA
Found at i:2148431 original size:10 final size:10
Alignment explanation
Indices: 2148411--2148440 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2148401 TTTATATAAA
2148411 TTAATAAATAT
1 TTAA-AAATAT
2148422 TTAAAAATAT
1 TTAAAAATAT
2148432 TTAAAAATA
1 TTAAAAATA
2148441 ATATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:2148447 original size:11 final size:11
Alignment explanation
Indices: 2148423--2148478 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
2148413 AATAAATATT
*
2148423 TAAAAAT-ATT
1 TAAAAATAATA
2148433 TAAAAATAATA
1 TAAAAATAATA
*
2148444 TAAATATAATA
1 TAAAAATAATA
*
2148455 TAAATATAAATA
1 TAAAAAT-AATA
2148467 TAAAAAATAATA
1 T-AAAAATAATA
2148479 CAAACACAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
10 7 0.17
11 19 0.47
12 9 0.22
13 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:2148451 original size:6 final size:6
Alignment explanation
Indices: 2148440--2148470 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2148430 ATTTAAAAAT
2148440 AATATA AATAT- AATATA AATATA AATATA AA
1 AATATA AATATA AATATA AATATA AATATA AA
2148471 AAATAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:2149776 original size:20 final size:20
Alignment explanation
Indices: 2149751--2149792 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2149741 TTACACCGAC
*
2149751 AATTACATAAAGTCAAATGA
1 AATTACATAAAGTCAAAAGA
*
2149771 AATTACATAAATTCAAAAGA
1 AATTACATAAAGTCAAAAGA
2149791 AA
1 AA
2149793 GGATTAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.24
Consensus pattern (20 bp):
AATTACATAAAGTCAAAAGA
Found at i:2150061 original size:25 final size:24
Alignment explanation
Indices: 2150030--2150076 Score: 85
Period size: 24 Copynumber: 1.9 Consensus size: 24
2150020 TATGGTCATG
2150030 TTCTTGTTTTGTTTTTTTTTTCTTC
1 TTCTTGTTTT-TTTTTTTTTTCTTC
2150055 TTCTTGTTTTTTTTTTTTTTCT
1 TTCTTGTTTTTTTTTTTTTTCT
2150077 GGGATTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (24 bp):
TTCTTGTTTTTTTTTTTTTTCTTC
Found at i:2157048 original size:37 final size:36
Alignment explanation
Indices: 2156959--2157048 Score: 83
Period size: 37 Copynumber: 2.5 Consensus size: 36
2156949 ATTTATGGTA
** **
2156959 TTTATATAATAAAA-ATTATTTTTATTTAAATTTAT
1 TTTATATAATAAAATAAAATTAATATTTAAATTTAT
* * * * *
2156994 TATAAATATTAATATAAAATTAATATTTTAATATTAT
1 TTTATATAATAAAATAAAATTAATATTTAAAT-TTAT
2157031 TTTATATAATAAAATAAA
1 TTTATATAATAAAATAAA
2157049 TTTTTAAATT
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
35 10 0.25
36 12 0.30
37 18 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
TTTATATAATAAAATAAAATTAATATTTAAATTTAT
Found at i:2157198 original size:25 final size:25
Alignment explanation
Indices: 2157147--2157203 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2157137 TAAATTATTA
* *
2157147 ATTTA-ATTTAATTATATATAGTTT
1 ATTTATATTTAATTATAAATAGTAT
2157171 ATTTATATTTAATTATAAAATA-TAT
1 ATTTATATTTAATTAT-AAATAGTAT
*
2157196 ATTAATAT
1 ATTTATAT
2157204 AATATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.18
25 19 0.68
26 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTTATATTTAATTATAAATAGTAT
Found at i:2168476 original size:18 final size:19
Alignment explanation
Indices: 2168449--2168491 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2168439 CATTAACAAG
*
2168449 TAATATTATAT-AATTTAT
1 TAATAATATATAAATTTAT
2168467 TAATAATATATAAATTTAT
1 TAATAATATATAAATTTAT
*
2168486 AAATAA
1 TAATAA
2168492 ATAATACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAATATATAAATTTAT
Found at i:2169814 original size:21 final size:22
Alignment explanation
Indices: 2169772--2169814 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
2169762 AAAATTATTT
*
2169772 TAAAAATTATTTTCGTTCAAAA
1 TAAAAATTATTTTAGTTCAAAA
* *
2169794 TAAAATTTA-TTTAGTTTAAAA
1 TAAAAATTATTTTAGTTCAAAA
2169815 CAATATGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (22 bp):
TAAAAATTATTTTAGTTCAAAA
Found at i:2170378 original size:2 final size:2
Alignment explanation
Indices: 2170371--2170405 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2170361 GCATGTAAAT
2170371 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 T
2170406 GAGAATTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2171018 original size:16 final size:18
Alignment explanation
Indices: 2170990--2171023 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2170980 GATAAATTTG
2170990 ATTTTGAAAAT-AATATA
1 ATTTTGAAAATAAATATA
2171007 ATTTTG-AAATAAATATA
1 ATTTTGAAAATAAATATA
2171024 TTTATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
ATTTTGAAAATAAATATA
Found at i:2171494 original size:21 final size:21
Alignment explanation
Indices: 2171469--2171531 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
2171459 TTAAATTTTT
2171469 AAATTTAAAATATAATAATTA
1 AAATTTAAAATATAATAATTA
* *
2171490 AAATTTTAAAATA-AAAAATAA
1 AAA-TTTAAAATATAATAATTA
*
2171511 AAATTTTAAA-ATAATAATTA
1 AAATTTAAAATATAATAATTA
2171531 A
1 A
2171532 TTAACGAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 13 0.37
21 12 0.34
22 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATTTAAAATATAATAATTA
Found at i:2171762 original size:3 final size:3
Alignment explanation
Indices: 2171754--2171787 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2171744 TCAAAGGGAT
*
2171754 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2171788 ATTTCTGTCA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2172162 original size:9 final size:9
Alignment explanation
Indices: 2172148--2172201 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
2172138 AATGTAGAGA
2172148 ATAAATATT
1 ATAAATATT
2172157 ATAAATA-T
1 ATAAATATT
2172165 -T-AATATT
1 ATAAATATT
2172172 -TAAAT-TT
1 ATAAATATT
2172179 -TAAATATT
1 ATAAATATT
*
2172187 ATAAATGTT
1 ATAAATATT
2172196 A-AAATA
1 ATAAATA
2172202 AATGCATGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 4 0.10
7 10 0.26
8 10 0.26
9 15 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (9 bp):
ATAAATATT
Found at i:2172171 original size:15 final size:15
Alignment explanation
Indices: 2172151--2172197 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2172141 GTAGAGAATA
2172151 AATATTATAAATATT
1 AATATTATAAATATT
*
2172166 AATATT-TAAATTTT
1 AATATTATAAATATT
*
2172180 AAATATTATAAATGTT
1 -AATATTATAAATATT
2172196 AA
1 AA
2172198 AATAAATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 7 0.25
15 14 0.50
16 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTATAAATATT
Found at i:2172512 original size:2 final size:2
Alignment explanation
Indices: 2172507--2172540 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2172497 TGTGTAGATT
2172507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2172541 TTTTATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2173047 original size:29 final size:27
Alignment explanation
Indices: 2173015--2173073 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
2173005 AAATTATAAA
*
2173015 TAATCATGTAAATAATTTGATAAAAATAT
1 TAATCATATAAATAA-TT-ATAAAAATAT
* *
2173044 TAATTATATAAATAATTATAAAATTAT
1 TAATCATATAAATAATTATAAAAATAT
2173071 TAA
1 TAA
2173074 AAAACTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 12 0.44
28 2 0.07
29 13 0.48
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
TAATCATATAAATAATTATAAAAATAT
Found at i:2173737 original size:29 final size:30
Alignment explanation
Indices: 2173673--2173738 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
2173663 TTCAAATTAC
2173673 TATATATTTACATAAATTTTAACATATTAAT
1 TATAT-TTTACATAAATTTTAACATATTAAT
* * * *
2173704 T-TATTTTATATGAATTTTAATATATT-CT
1 TATATTTTACATAAATTTTAACATATTAAT
2173732 TATATTT
1 TATATTT
2173739 GTGTCATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.07
29 24 0.80
30 3 0.10
31 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (30 bp):
TATATTTTACATAAATTTTAACATATTAAT
Found at i:2173764 original size:21 final size:20
Alignment explanation
Indices: 2173740--2173798 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
2173730 CTTATATTTG
2173740 TGTCATGTTTATCTTTTTTCA
1 TGTCATGTTTAT-TTTTTTCA
*
2173761 TGTCATGTAGTATTTTTTTCA
1 TGTCATGT-TTATTTTTTTCA
* *
2173782 TATTATGTTTATATTTT
1 TGTCATGTTTAT-TTTT
2173799 ATAATCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.09
21 26 0.81
22 3 0.09
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.63
Consensus pattern (20 bp):
TGTCATGTTTATTTTTTTCA
Found at i:2176891 original size:28 final size:28
Alignment explanation
Indices: 2176830--2176892 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
2176820 CAAGGAGTTT
*
2176830 ATTAAAATTTTATATATGATAAAATTCA
1 ATTAAAAATTTATATATGATAAAATTCA
* *
2176858 AATAAAAATTTA-ATCATG-TAAAATTTTA
1 ATTAAAAATTTATAT-ATGATAAAA-TTCA
2176886 ATTAAAA
1 ATTAAAA
2176893 TACCACAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (28 bp):
ATTAAAAATTTATATATGATAAAATTCA
Found at i:2176892 original size:27 final size:28
Alignment explanation
Indices: 2176830--2176893 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
2176820 CAAGGAGTTT
2176830 ATTAAAATTTTATATATGATAAAATTCAA
1 ATTAAAA-TTTATATATGATAAAATTCAA
* **
2176859 ATAAAAATTTA-ATCATG-TAAAATTTTA
1 ATTAAAATTTATAT-ATGATAAAATTCAA
2176886 ATTAAAAT
1 ATTAAAAT
2176894 ACCACAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 17 0.57
28 7 0.23
29 6 0.20
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (28 bp):
ATTAAAATTTATATATGATAAAATTCAA
Found at i:2183906 original size:20 final size:20
Alignment explanation
Indices: 2183883--2183924 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2183873 TTATATATTT
*
2183883 AATTTTTATAATTAATAT-AA
1 AATTATTAT-ATTAATATGAA
*
2183903 AATTATTATTTTAATATGAA
1 AATTATTATATTAATATGAA
2183923 AA
1 AA
2183925 GTATCATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AATTATTATATTAATATGAA
Found at i:2184152 original size:19 final size:19
Alignment explanation
Indices: 2184121--2184159 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2184111 TTACATATTT
2184121 AATTTTATAATTAACATAA
1 AATTTTATAATTAACATAA
*
2184140 AATTATTAT-ATTAATATAA
1 AATT-TTATAATTAACATAA
2184159 A
1 A
2184160 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTTATAATTAACATAA
Found at i:2184391 original size:116 final size:119
Alignment explanation
Indices: 2184120--2184399 Score: 379
Period size: 121 Copynumber: 2.4 Consensus size: 119
2184110 CTTACATATT
** *
2184120 TAATTTTATAATTAACATAAAATTATTATATTAATATAAATAATATTTAATACTAAATTATAATA
1 TAATTTTATAATTAACATAAAATTATTATATTAATATAAAGGATATTTAATACTAAACTATAATA
* *
2184185 TATTTTTGAAAATTAAAACTTCTAAATGAATTTTATTATATAATTTGTAAATAAA
66 TATTTTTGAAAATCAAAACTTCT-AATGAATTTTATTATATAATTTATAAATAAA
* * *
2184240 TAATTTCTATAATTGACATAAAATTATTATGTTAATATCAAGGATATTTAATACTAAACTATAAT
1 TAATTT-TATAATTAACATAAAATTATTATATTAATATAAAGGATATTTAATACTAAACTATAAT
* * * *
2184305 ATATTTTTGGAAATCAAAA-TT-T-CTG-ATTTTTTTATATGATTTATAAATAAA
65 ATATTTTTGAAAATCAAAACTTCTAATGAATTTTATTATATAATTTATAAATAAA
* *
2184356 TAAATTTTATAATCAACATAAAATTATTATATTAATATTAAGGA
1 T-AATTTTATAATTAACATAAAATTATTATATTAATATAAAGGA
2184400 CAATACTAAA
Statistics
Matches: 142, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
116 57 0.40
117 7 0.05
119 1 0.01
120 8 0.06
121 69 0.49
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (119 bp):
TAATTTTATAATTAACATAAAATTATTATATTAATATAAAGGATATTTAATACTAAACTATAATA
TATTTTTGAAAATCAAAACTTCTAATGAATTTTATTATATAATTTATAAATAAA
Found at i:2184733 original size:2 final size:2
Alignment explanation
Indices: 2184692--2184718 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2184682 GTAAGGACCC
2184692 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 T
2184719 TCTCTTTCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2184990 original size:2 final size:2
Alignment explanation
Indices: 2184983--2185023 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2184973 AATGGCATTT
2184983 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2185024 GTAAGTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2185446 original size:20 final size:22
Alignment explanation
Indices: 2185397--2185446 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 22
2185387 TTTATTTAAA
2185397 TTATTATATATTTATATAATTT
1 TTATTATATATTTATATAATTT
2185419 TTA--ATATA-TTA-ATAATTT
1 TTATTATATATTTATATAATTT
*
2185437 TTATTTTATA
1 TTATTATATA
2185447 CAAAATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 10 0.40
19 3 0.12
20 9 0.36
22 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTATATATTTATATAATTT
Found at i:2186168 original size:21 final size:22
Alignment explanation
Indices: 2186144--2186190 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2186134 TTAACATTCT
2186144 CACCAAATATA-TCACCTAACA
1 CACCAAATATACTCACCTAACA
* *
2186165 CACCTAATATACTTTACCTAACA
1 CACCAAATATAC-TCACCTAACA
2186188 CAC
1 CAC
2186191 TTAACAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
23 12 0.55
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (22 bp):
CACCAAATATACTCACCTAACA
Found at i:2193312 original size:19 final size:20
Alignment explanation
Indices: 2193290--2193328 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
2193280 AAATAGCACT
2193290 AAAACTATA-AAATAATTTA
1 AAAACTATATAAATAATTTA
2193309 AAAACTATATTAAATAATTT
1 AAAACTATA-TAAATAATTT
2193329 TACATACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAACTATATAAATAATTTA
Found at i:2196519 original size:34 final size:34
Alignment explanation
Indices: 2196481--2196550 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2196471 GGAGGAATTG
2196481 TTTCAAATGCTAAGCATATGTTCTCTTATCATCT
1 TTTCAAATGCTAAGCATATGTTCTCTTATCATCT
2196515 TTTCAAATGCTAAGCATATGTTCTCTTATCATCT
1 TTTCAAATGCTAAGCATATGTTCTCTTATCATCT
2196549 TT
1 TT
2196551 ATAAAGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (34 bp):
TTTCAAATGCTAAGCATATGTTCTCTTATCATCT
Found at i:2204157 original size:17 final size:19
Alignment explanation
Indices: 2204125--2204159 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2204115 TTAAATTATT
2204125 ATATATTATATAAATTTAA
1 ATATATTATATAAATTTAA
2204144 ATATATTA-AT-AATTTA
1 ATATATTATATAAATTTA
2204160 TTTTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATTATATAAATTTAA
Found at i:2204162 original size:21 final size:23
Alignment explanation
Indices: 2204138--2204185 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
2204128 TATTATATAA
2204138 ATTTAAAT-ATATTAATA-ATTT
1 ATTTAAATAATATTAATATATTT
2204159 ATTTTAAATAAATATTAATATATTT
1 A-TTTAAAT-AATATTAATATATTT
2204184 AT
1 AT
2204186 GTATTCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
21 1 0.04
22 7 0.30
24 10 0.43
25 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTAAATAATATTAATATATTT
Found at i:2212792 original size:2 final size:2
Alignment explanation
Indices: 2212785--2212816 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2212775 CAAGGTGAAG
2212785 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
2212817 CGCACTTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2215769 original size:40 final size:40
Alignment explanation
Indices: 2215713--2215800 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
2215703 AGTGATCATC
*
2215713 AGAGAATGCCAAGCAAAGTACTGATCATTGTAATATAATCA
1 AGAG-ATGCCAAGCAAAGTACTGATAATTGTAATATAATCA
*
2215754 AGAGATGCCAAGCAAAGTACTGATAATTGTCATATAATCA
1 AGAGATGCCAAGCAAAGTACTGATAATTGTAATATAATCA
2215794 AGAGATG
1 AGAGATG
2215801 ATAATTTCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 41 0.91
41 4 0.09
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (40 bp):
AGAGATGCCAAGCAAAGTACTGATAATTGTAATATAATCA
Found at i:2218215 original size:16 final size:16
Alignment explanation
Indices: 2218194--2218228 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2218184 TACCAAACAA
2218194 ATATACATATATATAT
1 ATATACATATATATAT
*
2218210 ATATACATATATGTAT
1 ATATACATATATATAT
2218226 ATA
1 ATA
2218229 AATTGGATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (16 bp):
ATATACATATATATAT
Found at i:2218874 original size:2 final size:2
Alignment explanation
Indices: 2218867--2218904 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2218857 ACATGCATGC
2218867 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
2218905 TAGATTTGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2220430 original size:21 final size:20
Alignment explanation
Indices: 2220405--2220444 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2220395 AAAAAAAATT
*
2220405 TTAAATTAAATCAATTTAAAC
1 TTAAATAAAAT-AATTTAAAC
*
2220426 TTAAATAAAATATTTTAAA
1 TTAAATAAAATAATTTAAA
2220445 AATTTTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAATAAAATAATTTAAAC
Found at i:2221036 original size:2 final size:2
Alignment explanation
Indices: 2221025--2221057 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2221015 CTTTATCAAG
2221025 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2221058 AGCTTAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2221701 original size:29 final size:30
Alignment explanation
Indices: 2221664--2221742 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 30
2221654 TGCGTTTAGC
* * * * *
2221664 ATAAAAAATATAATATTAATATGATAT-GT
1 ATAATAAATATAAAAATAATATAATATAAT
2221693 ATAATAAATATAAAAATAATATAATATAAT
1 ATAATAAATATAAAAATAATATAATATAAT
* * *
2221723 ATAATATATTTAAATATAAT
1 ATAATAAATATAAAAATAAT
2221743 TAAAAATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 23 0.56
30 18 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
ATAATAAATATAAAAATAATATAATATAAT
Found at i:2221718 original size:5 final size:5
Alignment explanation
Indices: 2221670--2221730 Score: 63
Period size: 5 Copynumber: 12.2 Consensus size: 5
2221660 TAGCATAAAA
* * *
2221670 AATAT AATATT AATAT GATAT -GTAT AATA- AATAT AAAAAT AATAT AATAT
1 AATAT AATA-T AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
2221720 AATAT AATAT A
1 AATAT AATAT A
2221731 TTTAAATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
4 7 0.15
5 31 0.66
6 9 0.19
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:2221738 original size:15 final size:15
Alignment explanation
Indices: 2221692--2221742 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
2221682 ATATGATATG
*
2221692 TATAATAAATATAAA
1 TATAATATATATAAA
*
2221707 AATAATATA-ATATAA
1 TATAATATATATA-AA
*
2221722 TATAATATATTTAAA
1 TATAATATATATAAA
2221737 TATAAT
1 TATAAT
2221743 TAAAAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 3 0.10
15 25 0.83
16 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAATATATATAAA
Found at i:2221747 original size:40 final size:40
Alignment explanation
Indices: 2221666--2221767 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 40
2221656 CGTTTAGCAT
* *
2221666 AAAA-AATATAATATTAATATGATATGTATAATAAATATA
1 AAAATAATATAATATTAATATAATATATATAATAAATATA
*
2221705 AAAATAATATAATA-TAATATAATATATTTAAATATAAT-TA
1 AAAATAATATAATATTAATATAATATATAT-AATA-AATATA
* * *
2221745 AAAATTATTATTATATTTATATA
1 AAAA-TAATATAATATTAATATA
2221768 TAAAATTTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
39 16 0.31
40 19 0.37
41 11 0.21
42 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (40 bp):
AAAATAATATAATATTAATATAATATATATAATAAATATA
Found at i:2221905 original size:22 final size:22
Alignment explanation
Indices: 2221861--2221905 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2221851 AATTAATTTC
* * **
2221861 TAATTTTTAATTTATATTTAAA
1 TAATTTTTAATATAAATCAAAA
2221883 TAATTTTTAATATAAATCAAAA
1 TAATTTTTAATATAAATCAAAA
2221905 T
1 T
2221906 TTTATCTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATTTTTAATATAAATCAAAA
Found at i:2223749 original size:19 final size:21
Alignment explanation
Indices: 2223706--2223753 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
2223696 TCACACTTAC
*
2223706 TTAAAAAGCTATCACTTTTTA
1 TTAAAAAACTATCACTTTTTA
*
2223727 TTAAAAAACTA-CA-TTTTTT
1 TTAAAAAACTATCACTTTTTA
2223746 TTAAAAAA
1 TTAAAAAA
2223754 AATCTGCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 13 0.52
20 2 0.08
21 10 0.40
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAAAAACTATCACTTTTTA
Found at i:2232837 original size:12 final size:13
Alignment explanation
Indices: 2232810--2232839 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2232800 AATATATTTC
2232810 TATATTTAATATT
1 TATATTTAATATT
2232823 TATATTTAA-ATT
1 TATATTTAATATT
2232835 TATAT
1 TATAT
2232840 AATATTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTTAATATT
Found at i:2232973 original size:14 final size:16
Alignment explanation
Indices: 2232944--2232981 Score: 62
Period size: 14 Copynumber: 2.5 Consensus size: 16
2232934 AAAAATAATA
2232944 TTTAATATATTTAAAT
1 TTTAATATATTTAAAT
2232960 TTTAA-ATA-TTAAAT
1 TTTAATATATTTAAAT
2232974 TTTAATAT
1 TTTAATAT
2232982 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.52
15 5 0.24
16 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAATATATTTAAAT
Found at i:2235335 original size:38 final size:38
Alignment explanation
Indices: 2235250--2235366 Score: 96
Period size: 38 Copynumber: 3.0 Consensus size: 38
2235240 TATTTTTATG
* * *
2235250 AAATAAATAAATTTATATATT-GTAATTAAATTAAATAAAT
1 AAAT-AATAAATTTATATATTATTATTTAAA--AAATTAAT
* * *
2235290 ATCAATAA-AATTATTTTTATTTTATT-TTTAAAAATTTAAT
1 A--AATAATAA--ATTTATATATTATTATTTAAAAAATTAAT
2235330 AAATAATAAATTTATATATTATTATTTAAAAAATTAA
1 AAATAATAAATTTATATATTATTATTTAAAAAATTAA
2235367 ATATTATTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
37 12 0.20
38 17 0.28
39 2 0.03
40 10 0.16
41 2 0.03
42 17 0.28
43 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (38 bp):
AAATAATAAATTTATATATTATTATTTAAAAAATTAAT
Found at i:2235400 original size:21 final size:22
Alignment explanation
Indices: 2235359--2235414 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
2235349 TATTATTTAA
2235359 AAAATTAAATATTATTTTATTG
1 AAAATTAAATATTATTTTATTG
*
2235381 AAAA-TAAA-ATTATTTATATTT
1 AAAATTAAATATTATTT-TATTG
**
2235402 AATTTTAAATATT
1 AAAATTAAATATT
2235415 TTTATTTAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.25
21 10 0.36
22 8 0.29
23 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATTAAATATTATTTTATTG
Found at i:2238020 original size:2 final size:2
Alignment explanation
Indices: 2238013--2238046 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2238003 GGAAAAGAGA
2238013 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
2238047 GAAAGGAATA
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:2238456 original size:134 final size:134
Alignment explanation
Indices: 2238215--2238616 Score: 635
Period size: 133 Copynumber: 3.0 Consensus size: 134
2238205 GGTAATTTGA
* * * * * * * *
2238215 TACTTCACCCCTAATTCTAAGCCATAGGCTTTAATTGCTCGCTTACTGCTCGCTTCACTTCCACT
1 TACTTTACCCCCAATTCCAAGCCAT-CGCGTTAATTACTCCCTTACTGCTCGCTTCACTTCTACT
* * *
2238280 TGTTTCACTTTCATGGGAACCCCGGAAGCCGTAGTCAAGAAGGATGTGTACTCGCTGTTTGCACT
65 TCTTTCACTTTCATGGGAACCCCAGAAGCCGTAGTCAAGAAGGATGTGTACTCGGTGTTTGCACT
2238345 TCCGC
130 TCCGC
*
2238350 TACTTTACCCCCAATTCCAAGCCATCGTGTTAATTACTCCCTTACTGCTCGCTTCACTTCTACTT
1 TACTTTACCCCCAATTCCAAGCCATCGCGTTAATTACTCCCTTACTGCTCGCTTCACTTCTACTT
*
2238415 CTTTCACTTTCATGGGAACCCCAGTAGCCGTAGTCAAGAAGGATGTGTACTCGGTGTTTGCACTT
66 CTTTCACTTTCATGGGAACCCCAGAAGCCGTAGTCAAGAAGGATGTGTACTCGGTGTTTGCACTT
2238480 -CGC
131 CCGC
*
2238483 TACTTTACCCCCAATTCCAAGCCATCGCGTTAATTACTCCCTTACTGCTCGCTTCACTTCTAATT
1 TACTTTACCCCCAATTCCAAGCCATCGCGTTAATTACTCCCTTACTGCTCGCTTCACTTCTACTT
* * *
2238548 CTTTCACTTTCATGGGAACCCCAGAAGCTGTAGTCAAGAAAGATGTCTACTCGGTGTTTGCACTT
66 CTTTCACTTTCATGGGAACCCCAGAAGCCGTAGTCAAGAAGGATGTGTACTCGGTGTTTGCACTT
2238613 CCGC
131 CCGC
2238617 CGGAAGACGT
Statistics
Matches: 247, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
133 127 0.51
134 98 0.40
135 22 0.09
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (134 bp):
TACTTTACCCCCAATTCCAAGCCATCGCGTTAATTACTCCCTTACTGCTCGCTTCACTTCTACTT
CTTTCACTTTCATGGGAACCCCAGAAGCCGTAGTCAAGAAGGATGTGTACTCGGTGTTTGCACTT
CCGC
Found at i:2241761 original size:10 final size:10
Alignment explanation
Indices: 2241746--2241770 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2241736 AAATTTAAAT
2241746 ATATAAAAAA
1 ATATAAAAAA
2241756 ATATAAAAAA
1 ATATAAAAAA
2241766 ATATA
1 ATATA
2241771 TACATATCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATATAAAAAA
Found at i:2251414 original size:52 final size:51
Alignment explanation
Indices: 2251342--2251449 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 51
2251332 TATATTATCT
*
2251342 ATATTTATTATTTATAATT-AATAAAAAATAAAAAA-ATTATTTTTAT-ATTA
1 ATATTTATTATTTATAATTAAAT-AAAAATAAAAAATATT-TTTTAATAATTA
*
2251392 ATATTTATATATTTTATAATTAAATTAAAATAAAAAATATTTTTTAATAATTA
1 ATATTTAT-TA-TTTATAATTAAATAAAAATAAAAAATATTTTTTAATAATTA
2251445 A-ATTT
1 ATATTT
2251450 CAATTCGAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
50 8 0.16
51 2 0.04
52 30 0.59
53 11 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (51 bp):
ATATTTATTATTTATAATTAAATAAAAATAAAAAATATTTTTTAATAATTA
Found at i:2256751 original size:2 final size:2
Alignment explanation
Indices: 2256740--2256774 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2256730 AAGCTTTGAG
2256740 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2256775 AAGAATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2257118 original size:64 final size:68
Alignment explanation
Indices: 2257007--2257142 Score: 217
Period size: 64 Copynumber: 2.0 Consensus size: 68
2256997 TGATTACTCA
* *
2257007 CAAATTCTTAAAATTTAAAGAAAAATTTGTTACATATTTGAAATCATAATTACGTGAATTTAATA
1 CAAATTCTTAAAATTTAAAGAAAAA-TTGTTACATATTTGAAATCATAATTAAGTGAATTTAACA
2257072 AAAT
65 AAAT
2257076 CAAATTCTTAAAATTT-AA-AAAAA-T-TTACATATTTGAAATCATAATTAAGTGAATTTAACAA
1 CAAATTCTTAAAATTTAAAGAAAAATTGTTACATATTTGAAATCATAATTAAGTGAATTTAACAA
2257137 AAT
66 AAT
2257140 CAA
1 CAA
2257143 TATAAAGTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
64 41 0.63
65 1 0.02
67 5 0.08
68 2 0.03
69 16 0.25
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (68 bp):
CAAATTCTTAAAATTTAAAGAAAAATTGTTACATATTTGAAATCATAATTAAGTGAATTTAACAA
AAT
Found at i:2257557 original size:36 final size:37
Alignment explanation
Indices: 2257512--2257584 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
2257502 TTTCATAAGT
2257512 CATTGAAAAATCGTGTAATTAATAATTCTACCATTAA
1 CATTGAAAAATCGTGTAATTAATAATTCTACCATTAA
*
2257549 CATT-AAAAATTGTGTAATTAATAATTCTACCATTAA
1 CATTGAAAAATCGTGTAATTAATAATTCTACCATTAA
2257585 TATTTTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (37 bp):
CATTGAAAAATCGTGTAATTAATAATTCTACCATTAA
Found at i:2257851 original size:3 final size:3
Alignment explanation
Indices: 2257843--2257881 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2257833 GGTTTACCAA
*
2257843 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2257882 GTGAGATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2258798 original size:16 final size:16
Alignment explanation
Indices: 2258774--2258810 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2258764 AATTTTTTAT
2258774 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
* *
2258790 TTAAGTTTAAATTAAT
1 TTAAATTTAAATTAAA
2258806 TTAAA
1 TTAAA
2258811 AAATTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:2258856 original size:11 final size:11
Alignment explanation
Indices: 2258813--2258862 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
2258803 AATTTAAAAA
*
2258813 ATTATTTTATT
1 ATTATTATATT
2258824 ATTTATTATATT
1 A-TTATTATATT
**
2258836 ATTAAAATATT
1 ATTATTATATT
2258847 ATTATTATATT
1 ATTATTATATT
*
2258858 TTTAT
1 ATTAT
2258863 AATTAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTATATT
Found at i:2259364 original size:68 final size:69
Alignment explanation
Indices: 2259180--2259382 Score: 207
Period size: 68 Copynumber: 3.0 Consensus size: 69
2259170 ATAAATAGAA
* * *
2259180 GTAATA-AAAATTAATTTGAGATAAGTATTTATTGAATCTACTCAAACTCCATTAATTTCA-TTT
1 GTAATAGAAAGTTAATTTGAGATAAGTATATATTGAATCTACTAAAACTCCATTAA-TTCACTTT
*
2259243 TTCTC
65 TTATC
* * * * *
2259248 GTAATAGAAAGCTAATTTGAGATAAATATATATTGAACCCATTAAAACTCCATTAATTCACTTTT
1 GTAATAGAAAGTTAATTTGAGATAAGTATATATTGAATCTACTAAAACTCCATTAATTCACTTTT
2259313 TAT-
66 TATC
* * * * * * * *
2259316 GTGATA-AAAGTTTAATTTAAAATAAGTATATATTAAATTTACTGAAACTCTACTAATTCACTTT
1 GTAATAGAAAG-TTAATTTGAGATAAGTATATATTGAATCTACTAAAACTCCATTAATTCACTTT
2259380 TTA
65 TTA
2259383 CATGATATTT
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
67 4 0.04
68 59 0.54
69 47 0.43
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (69 bp):
GTAATAGAAAGTTAATTTGAGATAAGTATATATTGAATCTACTAAAACTCCATTAATTCACTTTT
TATC
Found at i:2261100 original size:18 final size:20
Alignment explanation
Indices: 2261066--2261102 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
2261056 GTTTGAATAA
2261066 AAATATTAAGTTTAAAAAAT
1 AAATATTAAGTTTAAAAAAT
2261086 AAAT-TTAAG-TTAAAAAA
1 AAATATTAAGTTTAAAAAA
2261103 ACAAAGGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATATTAAGTTTAAAAAAT
Found at i:2261103 original size:19 final size:20
Alignment explanation
Indices: 2261066--2261103 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2261056 GTTTGAATAA
*
2261066 AAATATTAAGTTTAAAAAAT
1 AAATATTAAGTTAAAAAAAT
2261086 AAAT-TTAAGTTAAAAAAA
1 AAATATTAAGTTAAAAAAA
2261104 CAAAGGTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
AAATATTAAGTTAAAAAAAT
Found at i:2261198 original size:24 final size:25
Alignment explanation
Indices: 2261171--2261225 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
2261161 GATTTGATCT
2261171 ATTTTTTAATTATATAAT-ATAT-TA
1 ATTTTTTAATTATAT-ATGATATGTA
* *
2261195 ATTTTATATTTATATATGATATGTA
1 ATTTTTTAATTATATATGATATGTA
2261220 ATTTTT
1 ATTTTT
2261226 ATCATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.08
24 17 0.65
25 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
ATTTTTTAATTATATATGATATGTA
Found at i:2263237 original size:2 final size:2
Alignment explanation
Indices: 2263230--2263270 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2263220 GACAAGGTTC
2263230 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
2263271 CTTTAACCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2263685 original size:2 final size:2
Alignment explanation
Indices: 2263674--2263708 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2263664 AGGTAGCTTT
2263674 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2263709 TAAAAGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2263752 original size:17 final size:18
Alignment explanation
Indices: 2263730--2263763 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2263720 TATCCTTATT
*
2263730 TAATTTT-TTTGATTTTA
1 TAATTTTGTTTAATTTTA
2263747 TAATTTTGTTTAATTTT
1 TAATTTTGTTTAATTTT
2263764 TTTATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TAATTTTGTTTAATTTTA
Found at i:2266618 original size:2 final size:2
Alignment explanation
Indices: 2266611--2266640 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2266601 CAAGAGGTCC
2266611 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2266641 AATGCAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2267206 original size:2 final size:2
Alignment explanation
Indices: 2267199--2267236 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2267189 TTGATCATCA
2267199 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
2267237 GTTAAAGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2272845 original size:2 final size:2
Alignment explanation
Indices: 2272838--2272862 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2272828 TTAGAAATGC
2272838 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
2272863 ATACAGCAGT
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:2273515 original size:24 final size:23
Alignment explanation
Indices: 2273480--2273525 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
2273470 TGTATCATCT
*
2273480 AATTCAATCATTAGGTTTTAAAG
1 AATTCAATCATTAGATTTTAAAG
*
2273503 AATTCATATCATTTGATTTTAAA
1 AATTCA-ATCATTAGATTTTAAA
2273526 ATGACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (23 bp):
AATTCAATCATTAGATTTTAAAG
Found at i:2274103 original size:2 final size:2
Alignment explanation
Indices: 2274096--2274128 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2274086 ATTCTATGAT
2274096 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2274129 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2274133 original size:2 final size:2
Alignment explanation
Indices: 2274128--2274160 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2274118 ACACACACAC
2274128 AT AT AT 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 AT AT AT A
2274161 GATCCCTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2275108 original size:2 final size:2
Alignment explanation
Indices: 2275103--2275133 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2275093 ATATACGTTT
2275103 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 T
2275134 CATAAGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2277119 original size:13 final size:13
Alignment explanation
Indices: 2277101--2277131 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2277091 AATTTTTAGT
2277101 ATATATAACATAC
1 ATATATAACATAC
*
2277114 ATATATAACATAT
1 ATATATAACATAC
2277127 ATATA
1 ATATA
2277132 ATATTAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATATAACATAC
Found at i:2278556 original size:23 final size:23
Alignment explanation
Indices: 2278521--2278565 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2278511 TTAAATGTAA
2278521 TTATAAATATAATAGA-AAAATAT
1 TTATAAATATAATA-ATAAAATAT
* *
2278544 TTATATATTTAATAATAAAATA
1 TTATAAATATAATAATAAAATA
2278566 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TTATAAATATAATAATAAAATAT
Found at i:2278882 original size:6 final size:6
Alignment explanation
Indices: 2278871--2278896 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2278861 TGAAGAAGGT
2278871 TGAGTG TGAGTG TGAGTG TGAGTG TG
1 TGAGTG TGAGTG TGAGTG TGAGTG TG
2278897 GGGGTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.50, T:0.35
Consensus pattern (6 bp):
TGAGTG
Found at i:2279880 original size:3 final size:3
Alignment explanation
Indices: 2279866--2279898 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
2279856 TTTCATAAAA
2279866 AAT AATT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
2279899 TAATTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2290796 original size:17 final size:17
Alignment explanation
Indices: 2290776--2290810 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2290766 TAAATTTTGT
2290776 ATTTAAAATTGATACAA
1 ATTTAAAATTGATACAA
* *
2290793 ATTTTAAATTGATTCAA
1 ATTTAAAATTGATACAA
2290810 A
1 A
2290811 AATTAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTTAAAATTGATACAA
Found at i:2290869 original size:30 final size:30
Alignment explanation
Indices: 2290835--2290895 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
2290825 TTAATTTCTT
*
2290835 TAAATATATTTTTTTAAAATAAA-ATATATA
1 TAAATATA-TTTTTTAAAATAAATAAATATA
*
2290865 TAAATTTATTTTTTAAAATAAATAAATATA
1 TAAATATATTTTTTAAAATAAATAAATATA
2290895 T
1 T
2290896 TATTTAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAATATATTTTTTAAAATAAATAAATATA
Found at i:2290889 original size:22 final size:24
Alignment explanation
Indices: 2290854--2290902 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
2290844 TTTTTTAAAA
* *
2290854 TAAAATATATATAAATTTATTTTT
1 TAAAATATATATAAATATATTATT
2290878 TAAAATA-A-ATAAATATATTATT
1 TAAAATATATATAAATATATTATT
2290900 TAA
1 TAA
2290903 GAGTCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 1 0.04
24 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAATATATATAAATATATTATT
Found at i:2291564 original size:30 final size:30
Alignment explanation
Indices: 2291528--2291586 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2291518 TTTTTATTGT
*
2291528 TTTAAATAAATTTTTATAATTTAAT-TTAAA
1 TTTAAATAAATTTTTA-AATTAAATATTAAA
2291558 TTTAAATAAATTTTTAAATTAAATATTAA
1 TTTAAATAAATTTTTAAATTAAATATTAA
2291587 TATATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAAATAAATTTTTAAATTAAATATTAAA
Found at i:2291687 original size:6 final size:7
Alignment explanation
Indices: 2291667--2291693 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2291657 TAATTTTTTG
2291667 ATTAAAA
1 ATTAAAA
2291674 ATTAAAA
1 ATTAAAA
2291681 ATTAAAA
1 ATTAAAA
2291688 ATTAAA
1 ATTAAA
2291694 TTTTCTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATTAAAA
Found at i:2293220 original size:19 final size:18
Alignment explanation
Indices: 2293172--2293221 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
2293162 TATAAATATT
2293172 AATATAAAATAATTTTTA
1 AATATAAAATAATTTTTA
** *
2293190 AATATTTTAATATTTTTTA
1 AATA-TAAAATAATTTTTA
2293209 AATATGAAAATAA
1 AATAT-AAAATAA
2293222 GTTTGTGGGT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATATAAAATAATTTTTA
Found at i:2299267 original size:63 final size:63
Alignment explanation
Indices: 2299149--2299267 Score: 141
Period size: 63 Copynumber: 1.9 Consensus size: 63
2299139 TAACAGTGAT
* * * * * *
2299149 GGATATTATCATGTAAGAAGTCCTATGGCGGTTTATTTACCTTAACTGTATGTTTTTATAGTG
1 GGATATTATCATATAAAAAGTCCTATGGCAGTTTATTTACCATAACTATAGGTTTTTATAGTG
* * *
2299212 GGATATTGTCATATAAAAAGTCCTAT-GCAAGTTTATTTATCATAATTATAGGTTTT
1 GGATATTATCATATAAAAAGTCCTATGGC-AGTTTATTTACCATAACTATAGGTTTT
2299268 CTTTTTCTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
62 2 0.04
63 44 0.96
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (63 bp):
GGATATTATCATATAAAAAGTCCTATGGCAGTTTATTTACCATAACTATAGGTTTTTATAGTG
Found at i:2299449 original size:18 final size:17
Alignment explanation
Indices: 2299415--2299448 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2299405 TTGGGCTTAA
2299415 ATAAATTTAAAAGTTTT
1 ATAAATTTAAAAGTTTT
2299432 ATAACATTTAAAA-TTTT
1 ATAA-ATTTAAAAGTTTT
2299449 TGGGCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
ATAAATTTAAAAGTTTT
Found at i:2299463 original size:26 final size:26
Alignment explanation
Indices: 2299428--2299479 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2299418 AATTTAAAAG
* *
2299428 TTTTATAACATTTAAAATTTTTGGGC
1 TTTTAGAACATTTAAAATTATTGGGC
2299454 TTTTAGAACATTTAAAATTATTGGGC
1 TTTTAGAACATTTAAAATTATTGGGC
2299480 CTAAATGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (26 bp):
TTTTAGAACATTTAAAATTATTGGGC
Found at i:2300518 original size:35 final size:30
Alignment explanation
Indices: 2300464--2300569 Score: 94
Period size: 35 Copynumber: 3.5 Consensus size: 30
2300454 TTATCAAAAC
* *
2300464 TATATTAAAAATAAATAAAATTATTATAAATTAA
1 TATATT-AAAATTATTAAAATTATTA-AAA-T-A
2300498 TTATATTAATAATTATTAAAATTATTAAAATA
1 -TATATTAA-AATTATTAAAATTATTAAAATA
* *
2300530 -ATATCAAAATTATTAAAATTA-TAAAA-G
1 TATATTAAAATTATTAAAATTATTAAAATA
2300557 T-TATTAAAATTAT
1 TATATTAAAATTAT
2300570 ATTGAGAGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
27 11 0.17
28 5 0.08
29 14 0.22
30 6 0.09
32 1 0.02
33 1 0.02
34 5 0.08
35 21 0.33
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (30 bp):
TATATTAAAATTATTAAAATTATTAAAATA
Found at i:2300520 original size:9 final size:9
Alignment explanation
Indices: 2300501--2300569 Score: 86
Period size: 9 Copynumber: 7.3 Consensus size: 9
2300491 AAATTAATTA
2300501 TATTAATAAT
1 TATTAA-AAT
2300511 TATTAAAAT
1 TATTAAAAT
2300520 TATTAAAAT
1 TATTAAAAT
*
2300529 AATATCAAAAT
1 --TATTAAAAT
2300540 TATTAAAAT
1 TATTAAAAT
2300549 TA-TAAAAGT
1 TATTAAAA-T
2300558 TATTAAAAT
1 TATTAAAAT
2300567 TAT
1 TAT
2300570 ATTGAGAGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
8 5 0.09
9 29 0.55
10 11 0.21
11 8 0.15
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (9 bp):
TATTAAAAT
Found at i:2300562 original size:18 final size:17
Alignment explanation
Indices: 2300478--2300570 Score: 91
Period size: 18 Copynumber: 5.2 Consensus size: 17
2300468 TTAAAAATAA
2300478 ATAAAATTATTATAAATT
1 ATAAAATTATTA-AAATT
**
2300496 A-ATTA-TATTAATAATT
1 ATAAAATTATTAA-AATT
2300512 ATTAAAATTATTAAAATAAT
1 A-TAAAATTATTAAAAT--T
2300532 ATCAAAATTATTAAAATT
1 AT-AAAATTATTAAAATT
2300550 ATAAAAGTTATTAAAATT
1 ATAAAA-TTATTAAAATT
2300568 ATA
1 ATA
2300571 TTGAGAGTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
15 1 0.02
16 10 0.16
17 6 0.10
18 23 0.37
19 7 0.11
20 16 0.25
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
ATAAAATTATTAAAATT
Found at i:2300572 original size:29 final size:28
Alignment explanation
Indices: 2300466--2300569 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 28
2300456 ATCAAAACTA
* *
2300466 TATTAAAAATAAAT-AAAATTATTATAA-
1 TATT-AAAATATATCAAAATTATTAAAAT
* *
2300493 -ATT-AATTATATTAATAATTATTAAAAT
1 TATTAAAATATATCAA-AATTATTAAAAT
2300520 TATTAAAATAATATCAAAATTATTAAAAT
1 TATTAAAAT-ATATCAAAATTATTAAAAT
*
2300549 TA-TAAAAGT-TATTAAAATTAT
1 TATTAAAA-TATATCAAAATTAT
2300570 ATTGAGAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
24 6 0.09
25 2 0.03
26 13 0.20
27 11 0.17
28 8 0.12
29 18 0.28
30 6 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
TATTAAAATATATCAAAATTATTAAAAT
Found at i:2300579 original size:21 final size:20
Alignment explanation
Indices: 2300511--2300613 Score: 84
Period size: 21 Copynumber: 5.2 Consensus size: 20
2300501 TATTAATAAT
* *
2300511 TATTAAAATTATTAAAATAA
1 TATTAAAGTTATTAAAATTA
* *
2300531 TATCAAAATTATTAAAATTA
1 TATTAAAGTTATTAAAATTA
2300551 TA--AAAGTTATTAAAATTA
1 TATTAAAGTTATTAAAATTA
* * *
2300569 TATTGAGAGTTATTAGAATTT
1 TATT-AAAGTTATTAAAATTA
* * *
2300590 TACTCATAGTTATAAAAATTA
1 TA-TTAAAGTTATTAAAATTA
2300611 TAT
1 TAT
2300614 CAAATATTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
18 17 0.25
20 21 0.31
21 29 0.43
22 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (20 bp):
TATTAAAGTTATTAAAATTA
Found at i:2300638 original size:21 final size:21
Alignment explanation
Indices: 2300604--2300665 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
2300594 CATAGTTATA
*
2300604 AAAATTATATCAAATATTA-AT-
1 AAAATT-TACCAAA-ATTATATG
2300625 AAAATCTTACCAAAATTATATG
1 AAAAT-TTACCAAAATTATATG
*
2300647 AAAATTTACC-GAATTATAT
1 AAAATTTACCAAAATTATAT
2300666 CAATGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 12 0.33
21 18 0.50
22 6 0.17
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAATTTACCAAAATTATATG
Found at i:2300650 original size:22 final size:20
Alignment explanation
Indices: 2300625--2300665 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
2300615 AAATATTAAT
2300625 AAAATCTTACCAAAATTATATG
1 AAAAT-TTACC-AAATTATATG
*
2300647 AAAATTTACCGAATTATAT
1 AAAATTTACCAAATTATAT
2300666 CAATGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATTTACCAAATTATATG
Found at i:2300705 original size:21 final size:21
Alignment explanation
Indices: 2300676--2300855 Score: 112
Period size: 21 Copynumber: 8.5 Consensus size: 21
2300666 CAATGTAAAT
2300676 AAAATTATATAAAAAATTATC
1 AAAATTATATAAAAAATTATC
* ** ***
2300697 AAAACTATATCGAAGGCTATC
1 AAAATTATATAAAAAATTATC
* * *
2300718 AAAATTTTATTAAAGATTATC
1 AAAATTATATAAAAAATTATC
* * ** *
2300739 AAAATCATATCAAGTATTATT
1 AAAATTATATAAAAAATTATC
** *
2300760 AAAATTATATAAAAAATCGTT
1 AAAATTATATAAAAAATTATC
*
2300781 AACAA-TATATAAAAAAGTTATT
1 AA-AATTATATAAAAAA-TTATC
*
2300803 AAAACTATATAAAAAATTATC
1 AAAATTATATAAAAAATTATC
* * **
2300824 AAATTTAT-TACGATTATTATC
1 AAAATTATATA-AAAAATTATC
2300845 AAAATTATATA
1 AAAATTATATA
2300856 TATATATATA
Statistics
Matches: 121, Mismatches: 33, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
20 2 0.02
21 99 0.82
22 20 0.17
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (21 bp):
AAAATTATATAAAAAATTATC
Found at i:2300857 original size:2 final size:2
Alignment explanation
Indices: 2300850--2300874 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2300840 TTATCAAAAT
2300850 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 T
2300875 CTAAGGTTAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2301109 original size:21 final size:21
Alignment explanation
Indices: 2301092--2301169 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
2301082 TTACAAAGAT
*
2301092 TATTAAAATTATATCAAATAC
1 TATTAAAATTATATCAAATGC
* *
2301113 TACTAAAATTATATGAAATGC
1 TATTAAAATTATATCAAATGC
*
2301134 TATTAAAATTATATCAAATGT
1 TATTAAAATTATATCAAATGC
* *
2301155 TATCAAAATTTTATC
1 TATTAAAATTATATC
2301170 CAAAATCATC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (21 bp):
TATTAAAATTATATCAAATGC
Found at i:2301272 original size:40 final size:40
Alignment explanation
Indices: 2301228--2301305 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
2301218 TATTAAAATA
* *
2301228 ATATTAAATGTTATAAAAATCATATCAAAGGTTATCAATT
1 ATATTAAAGGTTATAAAAATCATATCAAAAGTTATCAATT
** *
2301268 ATATTAAAGGTTATCCAAATTATATCAAAAGTTATCAA
1 ATATTAAAGGTTATAAAAATCATATCAAAAGTTATCAA
2301306 AATTATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (40 bp):
ATATTAAAGGTTATAAAAATCATATCAAAAGTTATCAATT
Found at i:2301319 original size:18 final size:19
Alignment explanation
Indices: 2301117--2301346 Score: 90
Period size: 21 Copynumber: 11.3 Consensus size: 19
2301107 AAATACTACT
* *
2301117 AAAATTATATGAAATGCTATT
1 AAAATTATAT-AAA-GTTATC
2301138 AAAATTATATCAAATGTTATC
1 AAAATTATAT-AAA-GTTATC
* * *
2301159 AAAATTTTATCCAAAATCATC
1 AAAATTATAT--AAAGTTATC
* *
2301180 AAAACTGACTA-AAAATATATC
1 AAAA-TTA-TATAAAGT-TATC
* * * *
2301201 AAATATTACAAAGAAGATATT
1 AAA-ATTATATA-AAGTTATC
* *
2301222 AAAATAATATTAAATGTTATA
1 AAAATTATA-TAAA-GTTATC
*
2301243 AAAATCATATCAAAGGTTATC
1 AAAATTATAT-AAA-GTTATC
2301264 --AATTATATTAAAGGTTATC
1 AAAATTATA-TAAA-GTTATC
*
2301283 CAAATTATATCAAAAGTTATC
1 AAAATTATAT--AAAGTTATC
2301304 AAAATTATAT-AAGTTATC
1 AAAATTATATAAAGTTATC
* * *
2301322 AAAATTGTGTAAAAGTTATA
1 AAAATTATAT-AAAGTTATC
2301342 AAAAT
1 AAAAT
2301347 GATAAATCAT
Statistics
Matches: 165, Mismatches: 27, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
18 16 0.10
19 16 0.10
20 27 0.16
21 93 0.56
22 11 0.07
23 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAATTATATAAAGTTATC
Found at i:2301464 original size:10 final size:10
Alignment explanation
Indices: 2301444--2301653 Score: 50
Period size: 11 Copynumber: 20.3 Consensus size: 10
2301434 AATTACAAAG
2301444 ATTAT-TAAA
1 ATTATATAAA
2301453 ATTATATAAA
1 ATTATATAAA
2301463 A-TATTATTAAA
1 ATTA-TA-TAAA
2301474 ATTATATTAAA
1 ATTATA-TAAA
2301485 AGTTAT-TAAA
1 A-TTATATAAA
* *
2301495 AAT-TACAAA
1 ATTATATAAA
2301504 ATGT-TATTAAA
1 AT-TATA-TAAA
2301515 ATGT-TATCAAA
1 AT-TATAT-AAA
2301526 ATTATATTAAAA
1 ATTATA-T-AAA
* *
2301538 AGTAT-TGAA
1 ATTATATAAA
2301547 ATT-TATCAAA
1 ATTATAT-AAA
*
2301557 GTT-TATTAAA
1 ATTATA-TAAA
*
2301567 ATCATATCAAA
1 ATTATAT-AAA
2301578 ATT-TATTAAA
1 ATTATA-TAAA
*
2301588 ATTACACCTAAA
1 ATTATA--TAAA
* *
2301600 GCTTGT-TAAA
1 -ATTATATAAA
2301610 ATTATATTAAA
1 ATTATA-TAAA
*
2301621 GAATA-ATAAA
1 -ATTATATAAA
*
2301631 ATCATATAAAA
1 ATTATAT-AAA
2301642 ATTAT-TAAA
1 ATTATATAAA
2301651 ATT
1 ATT
2301654 TTACAAAGAT
Statistics
Matches: 152, Mismatches: 24, Indels: 50
0.67 0.11 0.22
Matches are distributed among these distances:
8 2 0.01
9 28 0.18
10 48 0.32
11 51 0.34
12 21 0.14
13 2 0.01
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (10 bp):
ATTATATAAA
Found at i:2301468 original size:12 final size:11
Alignment explanation
Indices: 2301444--2301589 Score: 82
Period size: 11 Copynumber: 14.0 Consensus size: 11
2301434 AATTACAAAG
2301444 ATTATT-AAA-
1 ATTATTAAAAT
2301453 ATTATATAAAAT
1 ATTAT-TAAAAT
2301465 ATTATTAAAAT
1 ATTATTAAAAT
2301476 -TATATTAAAA-
1 AT-TATTAAAAT
*
2301486 GTTATTAAAA-
1 ATTATTAAAAT
*
2301496 ATTA-CAAAAT
1 ATTATTAAAAT
*
2301506 GTTATTAAAAT
1 ATTATTAAAAT
* *
2301517 GTTATCAAAAT
1 ATTATTAAAAT
2301528 -TATATTAAAA-
1 AT-TATTAAAAT
* *
2301538 AGTATTGAAAT
1 ATTATTAAAAT
* *
2301549 -TTATCAAAGT
1 ATTATTAAAAT
2301559 -TTATTAAAAT
1 ATTATTAAAAT
*
2301569 CA-TATCAAAAT
1 -ATTATTAAAAT
2301580 -TTATTAAAAT
1 ATTATTAAAAT
2301590 TACACCTAAA
Statistics
Matches: 108, Mismatches: 16, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
9 9 0.08
10 46 0.43
11 48 0.44
12 5 0.05
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (11 bp):
ATTATTAAAAT
Found at i:2301468 original size:21 final size:20
Alignment explanation
Indices: 2301444--2301537 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 20
2301434 AATTACAAAG
2301444 ATTATTAAAATTATATAAAAT
1 ATTATTAAAATT-TATAAAAT
2301465 ATTATTAAAATTATATTAAAA-
1 ATTATTAAAATT-TA-TAAAAT
* * *
2301486 GTTATTAAAAATTACAAAAT
1 ATTATTAAAATTTATAAAAT
*
2301506 GTTATTAAAATGTTATCAAAAT
1 ATTATTAAAAT-TTAT-AAAAT
2301528 -TATATTAAAA
1 AT-TATTAAAA
2301538 AGTATTGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.06
20 12 0.19
21 29 0.46
22 18 0.29
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.40
Consensus pattern (20 bp):
ATTATTAAAATTTATAAAAT
Found at i:2301568 original size:52 final size:53
Alignment explanation
Indices: 2301454--2301588 Score: 163
Period size: 52 Copynumber: 2.6 Consensus size: 53
2301444 ATTATTAAAA
*
2301454 TTATATAAAATATTATTAAAATTATATT-AAAAGTTATTAAAAATTACAAAATG
1 TTAT-TAAAATATTATCAAAATTATATTAAAAAGTTATTAAAAATTACAAAATG
* * * *
2301507 TTATTAAAATGTTATCAAAATTATATTAAAAAG-TATTGAAATTTATCAAAGT-
1 TTATTAAAATATTATCAAAATTATATTAAAAAGTTATTAAAAATTA-CAAAATG
2301559 TTATTAAAATCA-TATCAAAATT-TATTAAAA
1 TTATTAAAAT-ATTATCAAAATTATATTAAAA
2301589 TTACACCTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
51 8 0.11
52 51 0.70
53 14 0.19
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (53 bp):
TTATTAAAATATTATCAAAATTATATTAAAAAGTTATTAAAAATTACAAAATG
Found at i:2301576 original size:21 final size:21
Alignment explanation
Indices: 2301550--2301693 Score: 78
Period size: 21 Copynumber: 6.9 Consensus size: 21
2301540 TATTGAAATT
*
2301550 TATCAAAGTTTATTAAAATCA
1 TATCAAAGATTATTAAAATCA
*
2301571 TATCAAA-ATTTATTAAAATTA
1 TATCAAAGA-TTATTAAAATCA
* * * * *
2301592 CACCTAAAGCTTGTTAAAATTA
1 TATC-AAAGATTATTAAAATCA
* * *
2301614 TATTAAAGAATAATAAAATCA
1 TATCAAAGATTATTAAAATCA
* **
2301635 TAT-AAAAATTATTAAAATTT
1 TATCAAAGATTATTAAAATCA
** * *
2301655 TA-CAAAGATTACCAACATTA
1 TATCAAAGATTATTAAAATCA
* *
2301675 TATCAAAAATTATGAAAAT
1 TATCAAAGATTATTAAAAT
2301694 AATTACAAAA
Statistics
Matches: 90, Mismatches: 28, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
20 28 0.31
21 47 0.52
22 15 0.17
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (21 bp):
TATCAAAGATTATTAAAATCA
Found at i:2301731 original size:21 final size:22
Alignment explanation
Indices: 2301706--2301763 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
2301696 TTACAAAAGG
* **
2301706 CTATCAAAATTATGTT-AAATC
1 CTATCAAAATTATATTAAAAAA
*
2301727 CTATCAACATTATATTAAAAAA
1 CTATCAAAATTATATTAAAAAA
2301749 CTATCAAAATTATAT
1 CTATCAAAATTATAT
2301764 CAATAAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (22 bp):
CTATCAAAATTATATTAAAAAA
Found at i:2304185 original size:17 final size:18
Alignment explanation
Indices: 2304151--2304191 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2304141 TTATTTATAT
*
2304151 TAAT-ATTTATAATTAAA
1 TAATAATTTATAATCAAA
2304168 TAATAATTTA-AATCAAA
1 TAATAATTTATAATCAAA
2304185 TAA-AATT
1 TAATAATT
2304192 GATTCGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 13 0.59
18 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATAATTTATAATCAAA
Found at i:2305805 original size:2 final size:2
Alignment explanation
Indices: 2305800--2305848 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2305790 TTTTTTTGAA
2305800 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2305842 AG AG AG A
1 AG AG AG A
2305849 AATTGAGACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.