Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 176 of 195
Found at i:29660963 original size:31 final size:31
Alignment explanation
Indices: 29660923--29660998 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
29660913 ATCAATTTAT
*
29660923 ATTATGAACTTATTTA-AGTACAAATTAAAAG
1 ATTAAGAACTTATTTAGA-TACAAATTAAAAG
* *
29660954 ATTAAGAACTTATTTGGATGCAAATTAAAAG
1 ATTAAGAACTTATTTAGATACAAATTAAAAG
29660985 -TTAA-AGACTTATTT
1 ATTAAGA-ACTTATTT
29660999 GAATATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 1 0.03
30 12 0.30
31 26 0.65
32 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (31 bp):
ATTAAGAACTTATTTAGATACAAATTAAAAG
Found at i:29668734 original size:58 final size:56
Alignment explanation
Indices: 29668642--29669207 Score: 377
Period size: 58 Copynumber: 9.7 Consensus size: 56
29668632 AAACTTTCTA
*
29668642 AAAAAAAATATTTTTAGAGAAAA-TT-AAGAGTATCAATTTTCCTTGAAAATAAGCTTTCC
1 AAAAAAAA-ATTTTGAG-GAAAAGTTGAA-AGTATCAATTTTCCTTGAAAATAAG-TTT-C
* ** * *
29668701 AAAAAAAAAATTTGAGGAAAAGTTGAAAGTATCAATTTTTTTTCAAAATTAAAGATTCC
1 AAAAAAAAATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAA-T-AAG-TTTC
* * * * * *
29668760 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTT
1 AAAAAAAAATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTC
** ** * * *
29668817 AAAACGATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTTT
1 AAAAAAAAATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AA--GTTTC
* * * * ** *
29668876 AAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTACTCGAATTTAAAGTTTA
1 AAAAAA-AAATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTC
* * * *
29668934 AAAAAAAAAGGTTTTTGAAGAAAAGTTGAAAGTCTCAATTTTTCCTCGAAATTAAGGTTTC
1 AAAAAAAAA---TTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTTGAAAATAA-GTTTC
* *
29668995 AAAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTTCTT-AAGAATAAATTTTC
1 AAAAAAAA-A-TTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTGAA-AAT-AAGTTTC
** * * * * *
29669054 AAAAAAAGGTTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTC
1 AAAAAAA-AATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTC
* * * * * * * * * *
29669112 -AAAAAATATTTTGGGGAAAAGTTAAAAATATCAATTTTTCTCGAGATTAAAATTTT
1 AAAAAAAAATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTC
* * *
29669168 TAAAAAATATTTTGGAAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAAATTTT-GAGGAAAAGTTGAAAGTATCAATTTT
29669208 TCCTGCACAA
Statistics
Matches: 419, Mismatches: 67, Indels: 43
0.79 0.13 0.08
Matches are distributed among these distances:
56 40 0.10
57 73 0.17
58 101 0.24
59 84 0.20
60 96 0.23
61 24 0.06
62 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (56 bp):
AAAAAAAAATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTC
Found at i:29668940 original size:60 final size:57
Alignment explanation
Indices: 29668643--29669209 Score: 441
Period size: 60 Copynumber: 9.7 Consensus size: 57
29668633 AACTTTCTAA
* * * *
29668643 AAAAAAATATTTTT-AGAGAAAA-TT-AAGAGTATCAATTTTCCTTGAAAAT-AAGCTTT
1 AAAAAAAGATTTTTGAG-GAAAAGTTGAA-AGTATCAATTTTTCTCGAAATTAAAG-TTT
** * * *
29668699 CCAAAAAAA-AAATTTGAGGAAAAGTTGAAAGTATCAATTTTTTTTCAAAATTAAAGATTC
1 --AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTTCTCGAAATTAAAG-TTT
* * * * ** *
29668759 CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTT
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTT
** * * ** * *
29668815 TTAAAACGATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTTT
1 AAAAAAAGA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAA---GTTT
* * *
29668876 AAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTACTCGAATTTAAAGTTT
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTT
* * * *
29668933 AAAAAAAAAAGGTTTTTGAAGAAAAGTTGAAAGTCTCAATTTTTCCTCGAAATTAAGGTTT
1 ---AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTT-CTCGAAATTAAAGTTT
* * * *
29668994 CAAAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTTCT-TAAGAATAAATTTT
1 --AAAAAAAGATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCTCGAA-ATTAAAGTTT
* * *
29669053 CAAAAAAAGGTTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTCGAAATTAAAGTTT
1 -AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTT
* * * * * * *
29669111 CAAAAAATA-TTTTGGGGAAAAGTTAAAAATATCAATTTTTCTCGAGATTAAAATTTT
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATT-AAAGTTT
* * * *
29669168 TAAAAAATATTTTGGAAGAAAAGTTGAAAGTATCAATTTTTC
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC
29669210 CTGCACAAAA
Statistics
Matches: 416, Mismatches: 72, Indels: 42
0.78 0.14 0.08
Matches are distributed among these distances:
56 41 0.10
57 75 0.18
58 112 0.27
59 48 0.12
60 117 0.28
61 23 0.06
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (57 bp):
AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTT
Found at i:29679604 original size:15 final size:16
Alignment explanation
Indices: 29679576--29679677 Score: 120
Period size: 15 Copynumber: 6.2 Consensus size: 16
29679566 ACTATGCTTG
29679576 AAAAAATGAAAAAATGA
1 AAAAAATG-AAAAATGA
29679593 AAAAAATGAAAAATG-
1 AAAAAATGAAAAATGA
29679608 AAAAAATGAAAAATG-
1 AAAAAATGAAAAATGA
29679623 -AAAAATGAAAAAATGA
1 AAAAAATG-AAAAATGA
*
29679639 AAAAAAGTAAAAAAATGA
1 AAAAAA-T-GAAAAATGA
*
29679657 AAAAAAAGAAAAAGTGA
1 AAAAAATGAAAAA-TGA
29679674 AAAA
1 AAAA
29679678 GGAGGACTCA
Statistics
Matches: 76, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.09
15 22 0.29
16 12 0.16
17 20 0.26
18 15 0.20
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (16 bp):
AAAAAATGAAAAATGA
Found at i:29679678 original size:8 final size:8
Alignment explanation
Indices: 29679574--29679677 Score: 124
Period size: 8 Copynumber: 12.9 Consensus size: 8
29679564 ATACTATGCT
29679574 TGAAAAAA
1 TGAAAAAA
29679582 TGAAAAAA
1 TGAAAAAA
29679590 TGAAAAAAA
1 TG-AAAAAA
29679599 TG-AAAAA
1 TGAAAAAA
29679606 TGAAAAAA
1 TGAAAAAA
29679614 TG-AAAAA
1 TGAAAAAA
29679621 TG-AAAAA
1 TGAAAAAA
29679628 TGAAAAAA
1 TGAAAAAA
29679636 TGAAAAAAA
1 TG-AAAAAA
*
29679645 GTAAAAAAA
1 -TGAAAAAA
29679654 TGAAAAAAA
1 TG-AAAAAA
* *
29679663 AGAAAAAG
1 TGAAAAAA
29679671 TGAAAAA
1 TGAAAAA
29679678 GGAGGACTCA
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
7 21 0.25
8 36 0.42
9 27 0.32
10 1 0.01
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (8 bp):
TGAAAAAA
Found at i:29680833 original size:40 final size:41
Alignment explanation
Indices: 29680682--29680944 Score: 357
Period size: 41 Copynumber: 6.1 Consensus size: 41
29680672 ATGATTGTCA
*
29680682 AGGAGTAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
29680723 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
29680764 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
29680805 AGGAGCAATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTTAGAGAGCAATTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG--T---------TTAG
* *
29680856 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAA-GTCGTGGTGCCTCTGTTTAG
* * *
29680898 AGGAGCAATTTACTTTCCAAAGTCGTTGAGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
29680939 AGGAGC
1 AGGAGC
29680945 TTTGATAAAA
Statistics
Matches: 203, Mismatches: 6, Indels: 26
0.86 0.03 0.11
Matches are distributed among these distances:
40 22 0.11
41 117 0.58
42 26 0.13
51 18 0.09
52 6 0.03
53 14 0.07
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:29680897 original size:53 final size:52
Alignment explanation
Indices: 29680801--29680907 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 52
29680791 GTGCCTCTGT
*
29680801 TTAGAGGAGCAATTTACTTTCAAAGTCGTGGTGCCTCTGTTTAGA-GAGCAA
1 TTAGAGGAGCAATTTACTTTCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAA
29680852 TTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTATTTAGAGGAGCAA
1 TTAGAGGAGCAATTTACTTT-C-AAAGTCGTGGTGCCTCTATTTAGAGGAGCAA
29680906 TT
1 TT
29680908 TACTTTCCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
51 20 0.38
52 1 0.02
53 23 0.44
54 8 0.15
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (52 bp):
TTAGAGGAGCAATTTACTTTCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAA
Found at i:29681292 original size:22 final size:21
Alignment explanation
Indices: 29681241--29681298 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
29681231 TTTGCTTTAG
29681241 ATTTTTTTTCTTTTCATGTTT
1 ATTTTTTTTCTTTTCATGTTT
** * *
29681262 ATCAATTTTTATTTTTATGATTT
1 AT-TTTTTTTCTTTTCATG-TTT
29681285 ATTTTTTTTCTTTT
1 ATTTTTTTTCTTTT
29681299 GATTATCTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 2 0.07
22 21 0.75
23 5 0.18
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (21 bp):
ATTTTTTTTCTTTTCATGTTT
Found at i:29683795 original size:58 final size:57
Alignment explanation
Indices: 29683630--29684136 Score: 526
Period size: 58 Copynumber: 8.7 Consensus size: 57
29683620 AAATTTCCAA
* * * *
29683630 AAAAAATATTTTTAGAGAAAAGTT-AAGAGTATCAATTTTCCTTGAAAAT-AAGCTTTCC
1 AAAAAATATTTTT-GGGAAAAGTTGAA-AGTATCAATTTTTCTCGAAATTAAAG-TTTCC
* * * *
29683688 AAAAAAAAAGATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCCTCGAAATTAAAGATTCC
1 -AAAAAATA-TTTTTG-GGAAAAGTTGAAAGTATCAATTTTT-CTCGAAATTAAAGTTTCC
*
29683749 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGTTTCC
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
* * *
29683807 AAAAAATATTTTTGAGGAAAAGTTGAAAGTGTCAATTTTCCTC-AAATTTAAAGTTTCA
1 AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCTCGAAA-TTAAAGTTTCC
* * * * *
29683865 AAAAAAAAGTTTTTGAGAAAAAGTTGAAAGCATCAATTTTTCTCGAAATTAAGGTTTCAA
1 AAAAAATA-TTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTC-C
* * * *
29683925 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCT-TAAGAATAAATTTTCA
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTCGAA-ATTAAAGTTTCC
** *
29683983 AAAAAAGGTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTT-C
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
* * **
29684040 AAAAAATA-TTTTGGGAAAAAGTTGAAAATATCAATTTTTCTC-AAGATTAAAATTTTT
1 AAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTTCTCGAA-ATTAAAGTTTCC
*
29684097 AAAAAATA-TTTTGGGAAAAAGTTGAAAGTATTAATTTTTC
1 AAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTTC
29684137 CTGCACAAAA
Statistics
Matches: 385, Mismatches: 46, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
55 4 0.01
56 38 0.10
57 48 0.12
58 120 0.31
59 116 0.30
60 43 0.11
61 13 0.03
62 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCC
Found at i:29683887 original size:117 final size:115
Alignment explanation
Indices: 29683618--29684136 Score: 566
Period size: 117 Copynumber: 4.4 Consensus size: 115
29683608 AATTATAAAA
* * *
29683618 TAAAATTTCCAAAAAAAATATTTTTAGAGAAAAGTT-AAGAGTATCAATTTTCCTTGAAAATAAG
1 TAAAATTT-CAAAAAAAA-ATTTTTAGA-AAAAGTTGAA-AGTATCAATTTTTCTCGAAATTAAG
* * * *
29683682 CTTTCCAAAAAAAAAGATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCCTCGAA-AT
62 GTTTCC-AAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCCTC-AAGAT
* * *
29683739 TAAAGA-TTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGT
1 TAAA-ATTTCAAAAAAAAATTTTTA-GAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGT
*
29683803 TTCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTGTCAATTTTCCTCAA-ATT
64 TTCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAGA-T
* *
29683855 TAAAGTTTCAAAAAAAAAGTTTTTGAGAAAAAGTTGAAAGCATCAATTTTTCTCGAAATTAAGGT
1 TAAAATTTCAAAAAAAAA-TTTTT-AGAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGT
* * * * *
29683920 TTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAA
64 TTC-CAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAGAT
* ** * *
29683973 TAAATTTTCAAAAAAAGGTTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTT
1 TAAAATTTCAAAAAAAAATTTTT-AGAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGTT
* *
29684038 T-CAAAAAATA-TTTTG-GGAAAAAGTTGAAAATATCAATTTTTCTCAAGAT
65 TCCAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTCAAGAT
** * ** *
29684087 TAAAATTTTTAAAAAATATTTTGGGAAAAAGTTGAAAGTATTAATTTTTC
1 TAAAATTTCAAAAAAAAATTTTTAGAAAAAGTTGAAAGTATCAATTTTTC
29684137 CTGCACAAAA
Statistics
Matches: 346, Mismatches: 42, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
113 26 0.08
114 50 0.14
115 11 0.03
116 23 0.07
117 113 0.33
118 64 0.18
119 42 0.12
120 10 0.03
121 6 0.02
122 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (115 bp):
TAAAATTTCAAAAAAAAATTTTTAGAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGTTT
CCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAGAT
Found at i:29689036 original size:138 final size:138
Alignment explanation
Indices: 29688783--29689066 Score: 514
Period size: 138 Copynumber: 2.1 Consensus size: 138
29688773 TTTCTTTATT
* *
29688783 GAAGTAGCATGATTATCACATTTTGATGTAAAACTTACTTTCAATTGCTTTACGTTCATCAATGT
1 GAAG-AGCATGATTATCACATTTTGATGTAAAACTTACTTCCAATTACTTTACGTTCATCAATGT
* * *
29688848 CAAAACAAGTGACTTCTGTGGTAATTGAATTGAGTAACATATTTAAATCTCTATGTCAAAAATGT
65 CAAAACAAGTGACTTCTGTGGTAATTGAATTGAGTAACATATTTAAATCTCTATATAAAAAATAT
29688913 ATGAATGTG
130 ATGAATGTG
29688922 GAAGAGCATGATTATCACATTTTGATGTAAAACTTACTTCCAATTACTTTACGTTCATCAATGTC
1 GAAGAGCATGATTATCACATTTTGATGTAAAACTTACTTCCAATTACTTTACGTTCATCAATGTC
29688987 AAAACAAGTGACTTCTGTGGTAATTGAATTGAGTAACATATTTAAATCTCTATATAAAAAATATA
66 AAAACAAGTGACTTCTGTGGTAATTGAATTGAGTAACATATTTAAATCTCTATATAAAAAATATA
29689052 TGAATGTG
131 TGAATGTG
29689060 GAAGAGC
1 GAAGAGC
29689067 TTGACAAAGT
Statistics
Matches: 140, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
138 136 0.97
139 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (138 bp):
GAAGAGCATGATTATCACATTTTGATGTAAAACTTACTTCCAATTACTTTACGTTCATCAATGTC
AAAACAAGTGACTTCTGTGGTAATTGAATTGAGTAACATATTTAAATCTCTATATAAAAAATATA
TGAATGTG
Found at i:29694530 original size:17 final size:18
Alignment explanation
Indices: 29694498--29694531 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29694488 ACATCTGATT
*
29694498 TAAAACAAATAAAAATAC
1 TAAAACAAAGAAAAATAC
29694516 TAAAA-AAAGAAAAATA
1 TAAAACAAAGAAAAATA
29694532 AAAACTAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (18 bp):
TAAAACAAAGAAAAATAC
Found at i:29695173 original size:14 final size:14
Alignment explanation
Indices: 29695138--29695167 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29695128 CGACCCTATC
29695138 TCCTACTTTTTCTT
1 TCCTACTTTTTCTT
29695152 TCCTACTTTTTCTT
1 TCCTACTTTTTCTT
29695166 TC
1 TC
29695168 TAACTTGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (14 bp):
TCCTACTTTTTCTT
Found at i:29696437 original size:15 final size:16
Alignment explanation
Indices: 29696419--29696452 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29696409 TTTCATTCTC
29696419 TTTGCCT-TTTTCATT
1 TTTGCCTCTTTTCATT
*
29696434 TTTGTCTCTTTTCATT
1 TTTGCCTCTTTTCATT
29696450 TTT
1 TTT
29696453 TTCTCGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTGCCTCTTTTCATT
Found at i:29696447 original size:16 final size:16
Alignment explanation
Indices: 29696426--29696457 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29696416 CTCTTTGCCT
29696426 TTTTCATTTTTGTCTC
1 TTTTCATTTTTGTCTC
*
29696442 TTTTCATTTTTTTCTC
1 TTTTCATTTTTGTCTC
29696458 GAATCATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTCATTTTTGTCTC
Found at i:29699847 original size:34 final size:35
Alignment explanation
Indices: 29699809--29699882 Score: 107
Period size: 34 Copynumber: 2.1 Consensus size: 35
29699799 AAATTTTTTG
*
29699809 AAAATAAATTTTTAAAAA-ATTGTATAA-CTTTCCA
1 AAAATAAATTTTCAAAAAGATT-TATAATCTTTCCA
29699843 AAAATAAATTTTCAAAAAGATTTATAATCTTTCCA
1 AAAATAAATTTTCAAAAAGATTTATAATCTTTCCA
*
29699878 GAAAT
1 AAAAT
29699883 TTATTTCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 22 0.61
35 14 0.39
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.36
Consensus pattern (35 bp):
AAAATAAATTTTCAAAAAGATTTATAATCTTTCCA
Found at i:29701981 original size:16 final size:16
Alignment explanation
Indices: 29701957--29701988 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29701947 AGGGTTTATC
*
29701957 TTTAGAATTTATATTT
1 TTTAAAATTTATATTT
29701973 TTTAAAATTTATATTT
1 TTTAAAATTTATATTT
29701989 AATCCACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTAAAATTTATATTT
Found at i:29705763 original size:15 final size:14
Alignment explanation
Indices: 29705740--29705773 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29705730 ATTATTGATT
*
29705740 AATATTTATATTTTA
1 AATAATTATA-TTTA
29705755 AATAATTATATTTA
1 AATAATTATATTTA
29705769 AATAA
1 AATAA
29705774 AATAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATAATTATATTTA
Found at i:29705791 original size:19 final size:19
Alignment explanation
Indices: 29705754--29705793 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29705744 TTTATATTTT
*
29705754 AAATAATTATATTTAAATA
1 AAATAATTATATATAAATA
29705773 AAATAATTAT-TATATAATA
1 AAATAATTATATATA-AATA
29705792 AA
1 AA
29705794 TGATCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATAATTATATATAAATA
Found at i:29705860 original size:18 final size:18
Alignment explanation
Indices: 29705837--29705871 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29705827 ATTCATGAAA
29705837 GTTATGATTATATAAAAG
1 GTTATGATTATATAAAAG
29705855 GTTATGATTATATAAAA
1 GTTATGATTATATAAAA
29705872 ACTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40
Consensus pattern (18 bp):
GTTATGATTATATAAAAG
Found at i:29705877 original size:18 final size:18
Alignment explanation
Indices: 29705838--29705889 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
29705828 TTCATGAAAG
**
29705838 TTATGATTATATAAAAGG
1 TTATGATTATATAAAAAC
29705856 TTATGATTATATAAAAAC
1 TTATGATTATATAAAAAC
* *
29705874 TTATAATTATTTAAAA
1 TTATGATTATATAAAA
29705890 TTATTTGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (18 bp):
TTATGATTATATAAAAAC
Found at i:29712260 original size:4 final size:4
Alignment explanation
Indices: 29712244--29712279 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
29712234 ATAATCAAAC
*
29712244 AATA AACA AATA AATA AATA AATA AATAA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT-A AATA AAT
29712280 GTGAACCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:29717248 original size:9 final size:9
Alignment explanation
Indices: 29717234--29717258 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29717224 CATGCGATGT
29717234 ATTCATTGC
1 ATTCATTGC
29717243 ATTCATTGC
1 ATTCATTGC
29717252 ATTCATT
1 ATTCATT
29717259 ACATATTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (9 bp):
ATTCATTGC
Found at i:29717796 original size:48 final size:47
Alignment explanation
Indices: 29717732--29717864 Score: 116
Period size: 48 Copynumber: 2.8 Consensus size: 47
29717722 ATGTTTATTG
* *
29717732 TTAAA-TTTCAAGCCTTTATTGAAAATGAGCTTT-TTTA-TATAAGAATT
1 TTAAAGTTTCAA-CCTTTATTGAAAATGAGCTTTCTTGAGT-GAA-AATT
*
29717779 TTAAAGTTTCTAACCTTTGTTGAGAAA-GAG-TTTCCTTGAGTGAAAATT
1 TTAAAGTTTC-AACCTTTATTGA-AAATGAGCTTT-CTTGAGTGAAAATT
* *
29717827 TTAAAGTTTCAAACTTTTATTG-AAATGAGCCTTCTTGA
1 TTAAAGTTTC-AACCTTTATTGAAAATGAGCTTTCTTGA
29717865 CATGAATTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
46 3 0.04
47 16 0.23
48 41 0.58
49 10 0.14
50 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (47 bp):
TTAAAGTTTCAACCTTTATTGAAAATGAGCTTTCTTGAGTGAAAATT
Found at i:29717960 original size:74 final size:73
Alignment explanation
Indices: 29717871--29718300 Score: 391
Period size: 74 Copynumber: 5.8 Consensus size: 73
29717861 TTGACATGAA
* * * * * * *
29717871 TTTATTTTTAAAAGTTAAAGTTTTG-TGGAAGAGTTTTTTATTTTTTCCAAGTTGAAGCTTCAGT
1 TTTATTTTTCAAAGTTGAAGCTTCGATAGAAGAGTTCTTTATTTTTT-AAAGTTGAAGCTT-AGT
*
29717935 GGATGAGTAC
64 GGAAGAGTAC
* * * * * * * * *
29717945 TTTATTTTTCAAAGTTAAAGCCTT-GGTGGAGGATTTTTTTATTTTTAAAAGTTGAAGCCTCGAT
1 TTTATTTTTCAAAGTTGAAG-CTTCGATAGAAGAGTTCTTTATTTTTTAAAGTTGAAGCTTAG-T
* *
29718009 GAAAAAGTAC
64 GGAAGAGTAC
* * * * * *
29718019 TTTATTTTT-AAAGTTGAAGCATCGATAGAGGAGTTCTTTATTTTTTCAAGGTGAAGTTTTGGTG
1 TTTATTTTTCAAAGTTGAAGCTTCGATAGAAGAGTTCTTTATTTTTTAAAGTTGAAG-CTTAGTG
*
29718083 GAGGAGTAC
65 GAAGAGTAC
* * * * *
29718092 TTTATTTTTCAAAGTTGAAGCCTCGATAGAAAAGTTCTTTATTTCTCAAAGTTGAAGCCTAGGTG
1 TTTATTTTTCAAAGTTGAAGCTTCGATAGAAGAGTTCTTTATTTTTTAAAGTTGAAGCTTA-GTG
*
29718157 GAAAAGTAC
65 GAAGAGTAC
* * * * * *
29718166 TTTATTTTTTAATGTTGAAGCTTCGATAGAGGAGTTTTTTATTTTTTCAAGTTGAAGTCTTGGTG
1 TTTATTTTTCAAAGTTGAAGCTTCGATAGAAGAGTTCTTTATTTTTTAAAGTTGAAG-CTTAGTG
*
29718231 GATGAGTAC
65 GAAGAGTAC
*
29718240 TTTATTTTTCAAAGTTGAAGCTTCGAT-GCAAGAGTTCTTTATTTTTAAAAAGTTGAAGCTT
1 TTTATTTTTCAAAGTTGAAGCTTCGATAG-AAGAGTTCTTTATTTTT-TAAAGTTGAAGCTT
29718301 TATTTTCTCA
Statistics
Matches: 289, Mismatches: 57, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
72 2 0.01
73 55 0.19
74 201 0.70
75 31 0.11
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (73 bp):
TTTATTTTTCAAAGTTGAAGCTTCGATAGAAGAGTTCTTTATTTTTTAAAGTTGAAGCTTAGTGG
AAGAGTAC
Found at i:29717996 original size:37 final size:36
Alignment explanation
Indices: 29717871--29718300 Score: 142
Period size: 37 Copynumber: 11.6 Consensus size: 36
29717861 TTGACATGAA
* *
29717871 TTTATTTTTAAAAGTTAAAGTTTTGTGGAAGAGTTT
1 TTTATTTTTAAAAGTTAAAGCTTAGTGGAAGAGTTT
** * * **
29717907 TTTATTTTTTCCAAGTTGAAGCTTCAGTGGATGAGTAC
1 TTTA-TTTTTAAAAGTTAAAGCTT-AGTGGAAGAGTTT
* * * *
29717945 TTTATTTTTCAAAGTTAAAGCCTTGGTGGAGGATTTT
1 TTTATTTTTAAAAGTTAAAG-CTTAGTGGAAGAGTTT
* * * * * **
29717982 TTTATTTTTAAAAGTTGAAGCCTCGATGAAAAAGTAC
1 TTTATTTTTAAAAGTTAAAGCTTAG-TGGAAGAGTTT
* * * * * *
29718019 TTTATTTTT-AAAGTTGAAGCATCGATAGAGGAGTTC
1 TTTATTTTTAAAAGTTAAAGCTTAG-TGGAAGAGTTT
** * * * * * **
29718055 TTTATTTTTTCAAGGTGAAGTTTTGGTGGAGGAGTAC
1 TTTATTTTTAAAAGTTAAAG-CTTAGTGGAAGAGTTT
* * * * * * *
29718092 TTTATTTTTCAAAGTTGAAGCCTCGATAGAAAAGTTC
1 TTTATTTTTAAAAGTTAAAGCTTAG-TGGAAGAGTTT
* * * * * **
29718129 TTTATTTCTCAAAGTTGAAGCCTAGGTGGAAAAGTAC
1 TTTATTTTTAAAAGTTAAAGCTTA-GTGGAAGAGTTT
* * * * * *
29718166 TTTATTTTTTAATGTTGAAGCTTCGATAGAGGAGTTT
1 TTTATTTTTAAAAGTTAAAGCTTAG-TGGAAGAGTTT
** * * * **
29718203 TTTATTTTTTCAAGTTGAAGTCTTGGTGGATGAGTAC
1 TTTATTTTTAAAAGTTAAAG-CTTAGTGGAAGAGTTT
* * * * *
29718240 TTTATTTTTCAAAGTTGAAGCTTCGATGCAAGAGTTC
1 TTTATTTTTAAAAGTTAAAGCTTAG-TGGAAGAGTTT
*
29718277 TTTATTTTTAAAAAGTTGAAGCTT
1 TTTATTTTT-AAAAGTTAAAGCTT
29718301 TATTTTCTCA
Statistics
Matches: 306, Mismatches: 76, Indels: 22
0.76 0.19 0.05
Matches are distributed among these distances:
36 44 0.14
37 226 0.74
38 36 0.12
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (36 bp):
TTTATTTTTAAAAGTTAAAGCTTAGTGGAAGAGTTT
Found at i:29718053 original size:148 final size:147
Alignment explanation
Indices: 29717901--29718298 Score: 539
Period size: 148 Copynumber: 2.7 Consensus size: 147
29717891 TTTTGTGGAA
* *
29717901 GAGTTTTTTATTTTTTCCAAGTTGAAGCTTCAGTGGATGAGTACTTTATTTTTCAAAGTTAAAGC
1 GAGTTTTTTATTTTTT-CAAGTTGAAGCTT-GGTGGATGAGTACTTTATTTTTCAAAGTTGAAGC
* * * * *
29717966 CTTGGTGGAGGATTTTTTTATTTTTAAAAGTTGAAGCCTCGATGAAAAAGTACTTTA-TTTTTAA
64 CTTGATGGAAGAGTTCTTTATTTTTAAAAGTTGAAGCCTAGATGAAAAAGTACTTTATTTTTTAA
29718030 AGTTGAAGCATCGATAGAG
129 AGTTGAAGCATCGATAGAG
* * * *
29718049 GAGTTCTTTATTTTTTCAAGGTGAAGTTTTGGTGGAGGAGTACTTTATTTTTCAAAGTTGAAGCC
1 GAGTTTTTTATTTTTTCAAGTTGAAG-CTTGGTGGATGAGTACTTTATTTTTCAAAGTTGAAGCC
* * * * * * * *
29718114 TCGATAGAAAAGTTCTTTATTTCTCAAAGTTGAAGCCTAGGTGGAAAAGTACTTTATTTTTTAAT
65 TTGATGGAAGAGTTCTTTATTTTTAAAAGTTGAAGCCTAGATGAAAAAGTACTTTATTTTTTAAA
*
29718179 GTTGAAGCTTCGATAGAG
130 GTTGAAGCATCGATAGAG
29718197 GAGTTTTTTATTTTTTCAAGTTGAAGTCTTGGTGGATGAGTACTTTATTTTTCAAAGTTGAAG-C
1 GAGTTTTTTATTTTTTCAAGTTGAAG-CTTGGTGGATGAGTACTTTATTTTTCAAAGTTGAAGCC
*
29718261 TTCGATGCAAGAGTTCTTTATTTTTAAAAAGTTGAAGC
65 TT-GATGGAAGAGTTCTTTATTTTT-AAAAGTTGAAGC
29718299 TTTATTTTCT
Statistics
Matches: 216, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
147 87 0.40
148 118 0.55
149 11 0.05
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (147 bp):
GAGTTTTTTATTTTTTCAAGTTGAAGCTTGGTGGATGAGTACTTTATTTTTCAAAGTTGAAGCCT
TGATGGAAGAGTTCTTTATTTTTAAAAGTTGAAGCCTAGATGAAAAAGTACTTTATTTTTTAAAG
TTGAAGCATCGATAGAG
Found at i:29718447 original size:43 final size:43
Alignment explanation
Indices: 29718384--29718478 Score: 122
Period size: 43 Copynumber: 2.2 Consensus size: 43
29718374 ACTTTTATTT
* *
29718384 AAAGTTTC-AAGCCTCAATTATAGAAGAA-CATTTTATTTTTTA
1 AAAGTTTCAAAACCTCAATTAT-GAAGAAGCATTTTATTTTTCA
** *
29718426 AAAGTTTCAAAACCTCAATTATGTGGAAGTATTTTATTTTTCA
1 AAAGTTTCAAAACCTCAATTATGAAGAAGCATTTTATTTTTCA
29718469 AAAGTTTCAA
1 AAAGTTTCAA
29718479 TGTCTCAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 12 0.26
43 34 0.74
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (43 bp):
AAAGTTTCAAAACCTCAATTATGAAGAAGCATTTTATTTTTCA
Found at i:29718761 original size:13 final size:13
Alignment explanation
Indices: 29718743--29718778 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
29718733 TTATTTATAT
29718743 TTTAATTTTTTAG
1 TTTAATTTTTTAG
*
29718756 TTTAA-TTTTTGG
1 TTTAATTTTTTAG
29718768 TTTAATTTTTT
1 TTTAATTTTTT
29718779 TTTTAGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTAATTTTTTAG
Found at i:29718783 original size:12 final size:12
Alignment explanation
Indices: 29718743--29718783 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
29718733 TTATTTATAT
29718743 TTTAATTTTTTAG
1 TTTAATTTTTT-G
*
29718756 TTTAATTTTTGG
1 TTTAATTTTTTG
*
29718768 TTTAATTTTTTT
1 TTTAATTTTTTG
29718780 TTTA
1 TTTA
29718784 GTCAAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTAATTTTTTG
Found at i:29719624 original size:20 final size:20
Alignment explanation
Indices: 29719599--29719656 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
29719589 TTTTGTATGA
29719599 ATTTGCA-GAACTAATATTAT
1 ATTTGCATG-ACTAATATTAT
*
29719619 ATTTGCATGATTAATATTAT
1 ATTTGCATGACTAATATTAT
*
29719639 ATTTGCGTGA-TAAT-TTAT
1 ATTTGCATGACTAATATTAT
29719657 TTGCCATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 26 0.74
21 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTTGCATGACTAATATTAT
Found at i:29719683 original size:216 final size:217
Alignment explanation
Indices: 29719289--29719683 Score: 661
Period size: 216 Copynumber: 1.8 Consensus size: 217
29719279 AATGTTTGCT
*
29719289 TTTATTTTTTTGTGCGACTTTTGCATAACTTTTATAGTATTTAATAGCTTACTCTTATTTTTATA
1 TTTATTTTTTTGT-CGACTTTTGCATAACTTTTATAATATTTAATAGCTTACTCTTATTTTTATA
*
29719354 TTTATTACATGGTATTTATTTTTGTATGAATTTACATAACTAATATTATATTTGCATGATTAATA
65 TTTATTACATGGTATTTATTTTTGTATGAATTTACAGAACTAATATTATATTTGCATGATTAATA
* *
29719419 TTATATTTGTGTGATAATTTATTTGCCTAATATATTTATTTGCATGATTATTAAAAGTTGTTGGA
130 TTATATTTGCGTGATAATTTATTTGCCTAATATATTTATTTACATGATTATTAAAAGTTGTTGGA
29719484 ATCCATGATCTATTGAGGTAATA
195 ATCCATGATCTATTGAGGTAATA
* * * *
29719507 TTTACTTTTTTTGT-GATTTTTGCATAACTTTTATAATGTTTAATTGCTTACTTTTATTTTTATA
1 TTTA-TTTTTTTGTCGACTTTTGCATAACTTTTATAATATTTAATAGCTTACTCTTATTTTTATA
*
29719571 TTTATTACATGGTA-TTATTTTTGTATGAATTTGCAGAACTAATATTATATTTGCATGATTAATA
65 TTTATTACATGGTATTTATTTTTGTATGAATTTACAGAACTAATATTATATTTGCATGATTAATA
29719635 TTATATTTGCGTGATAATTTATTTGCC-ATATATATTTATTTACATGATT
130 TTATATTTGCGTGATAATTTATTTGCCTA-ATATATTTATTTACATGATT
29719684 TATTTAATTG
Statistics
Matches: 166, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
215 1 0.01
216 93 0.56
217 59 0.36
218 4 0.02
219 9 0.05
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.53
Consensus pattern (217 bp):
TTTATTTTTTTGTCGACTTTTGCATAACTTTTATAATATTTAATAGCTTACTCTTATTTTTATAT
TTATTACATGGTATTTATTTTTGTATGAATTTACAGAACTAATATTATATTTGCATGATTAATAT
TATATTTGCGTGATAATTTATTTGCCTAATATATTTATTTACATGATTATTAAAAGTTGTTGGAA
TCCATGATCTATTGAGGTAATA
Found at i:29719687 original size:17 final size:17
Alignment explanation
Indices: 29719667--29719700 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29719657 TTGCCATATA
*
29719667 TATTTATTTACATGATT
1 TATTTAATTACATGATT
*
29719684 TATTTAATTGCATGATT
1 TATTTAATTACATGATT
29719701 ATTAATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (17 bp):
TATTTAATTACATGATT
Found at i:29719713 original size:47 final size:46
Alignment explanation
Indices: 29719662--29719802 Score: 135
Period size: 47 Copynumber: 3.0 Consensus size: 46
29719652 TTTATTTGCC
29719662 ATATATATTTAT-TTACATGATTTATTTAATTGCATGATTATTAATAT
1 ATATATATTTATGTTA-AT-ATTTATTTAATTGCATGATTATTAATAT
* * * * * *
29719709 ATATATATTTATGTGATTTATTAATTTATTTACATGATTGTTAATAT
1 ATATATATTTATGTTA-ATATTTATTTAATTGCATGATTATTAATAT
* *
29719756 ATTTAT-TTGTATGATT-ATATTTAATTTGATTGCATGATTATTAATAT
1 ATATATATT-TATG-TTAATATTT-ATTTAATTGCATGATTATTAATAT
29719803 GTTTAATTGC
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
46 6 0.08
47 65 0.87
48 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.55
Consensus pattern (46 bp):
ATATATATTTATGTTAATATTTATTTAATTGCATGATTATTAATAT
Found at i:29719769 original size:24 final size:24
Alignment explanation
Indices: 29719684--29719910 Score: 129
Period size: 24 Copynumber: 9.8 Consensus size: 24
29719674 TTACATGATT
* *
29719684 TATTTAATTGCATGATTATTAATA
1 TATTTATTTGTATGATTATTAATA
* * *
29719708 TATATATATT-TATG-TGATTTAT-
1 TATTTAT-TTGTATGATTATTAATA
** *
29719730 TAATTTATTTACATGATTGTTAATA
1 T-ATTTATTTGTATGATTATTAATA
*
29719755 TATTTATTTGTATGATTA-T-ATT
1 TATTTATTTGTATGATTATTAATA
*
29719777 TAATTTGA-TTGCATGATTATTAATA
1 T-ATTT-ATTTGTATGATTATTAATA
* * *
29719802 TGTTTAATTGCT-TAATTATTAATA
1 TATTTATTTG-TATGATTATTAATA
* *
29719826 TATCTATTTGTAT-A--ATT-ATG
1 TATTTATTTGTATGATTATTAATA
* *
29719846 T-TTTA-TTGCATGATTCTTAATA
1 TATTTATTTGTATGATTATTAATA
* *
29719868 TATTTAATTGTATGATTATTAACA
1 TATTTATTTGTATGATTATTAATA
* *
29719892 TATTTATTCGTGTGATTAT
1 TATTTATTTGTATGATTAT
29719911 ATTTGATTAT
Statistics
Matches: 152, Mismatches: 33, Indels: 36
0.69 0.15 0.16
Matches are distributed among these distances:
18 5 0.03
19 4 0.03
20 3 0.02
21 5 0.03
22 9 0.06
23 36 0.24
24 84 0.55
25 6 0.04
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (24 bp):
TATTTATTTGTATGATTATTAATA
Found at i:29719847 original size:42 final size:42
Alignment explanation
Indices: 29719800--29719886 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
29719790 TGATTATTAA
* *
29719800 TATGTTTAATTGCTTAATTATTAATATATCTATTTGTATAAT
1 TATGTTTAATTGCATAATTATTAATATATCTAATTGTATAAT
* * * * *
29719842 TATGTTTTATTGCATGATTCTTAATATATTTAATTGTATGAT
1 TATGTTTAATTGCATAATTATTAATATATCTAATTGTATAAT
29719884 TAT
1 TAT
29719887 TAACATATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (42 bp):
TATGTTTAATTGCATAATTATTAATATATCTAATTGTATAAT
Found at i:29719910 original size:66 final size:66
Alignment explanation
Indices: 29719784--29719937 Score: 170
Period size: 66 Copynumber: 2.4 Consensus size: 66
29719774 ATTTAATTTG
* * *
29719784 ATTGCATGATTATTAATATGTTTAATTGCTTAATTATTAATATATCTATTTGTATAATTATGTTT
1 ATTGCATGATTATTAATATATTTAATTGCTTAATTATTAACATATCTATTCGTATAATTATGTTT
29719849 T
66 T
* * * * * *
29719850 ATTGCATGATTCTTAATATATTTAATTG-TATGATTATTAACATATTTATTCGTGTGATTATATT
1 ATTGCATGATTATTAATATATTTAATTGCT-TAATTATTAACATATCTATTCGTATAATTATGTT
*
29719914 TG
65 TT
**
29719916 ATTATATGATTA-T-ATATATTTA
1 ATTGCATGATTATTAATATATTTA
29719938 TATGAATGAT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
64 9 0.12
65 2 0.03
66 63 0.85
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (66 bp):
ATTGCATGATTATTAATATATTTAATTGCTTAATTATTAACATATCTATTCGTATAATTATGTTT
T
Found at i:29719938 original size:18 final size:18
Alignment explanation
Indices: 29719904--29719942 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29719894 TTTATTCGTG
*
29719904 TGATTATATTTGATTATA
1 TGATTATATATGATTATA
29719922 TGATTATATAT-ATTTATA
1 TGATTATATATGA-TTATA
29719940 TGA
1 TGA
29719943 ATGATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (18 bp):
TGATTATATATGATTATA
Found at i:29719985 original size:20 final size:20
Alignment explanation
Indices: 29719955--29719999 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
29719945 GATTTTTATG
* *
29719955 TTATT-ATATTATTGCATGA
1 TTATTAATATTACTACATGA
29719974 TTATTAATATTACTACATGA
1 TTATTAATATTACTACATGA
*
29719994 TAATTA
1 TTATTA
29720000 TTGCATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (20 bp):
TTATTAATATTACTACATGA
Found at i:29720035 original size:34 final size:34
Alignment explanation
Indices: 29719997--29720086 Score: 144
Period size: 34 Copynumber: 2.6 Consensus size: 34
29719987 TACATGATAA
29719997 TTATTGCATGATATGATTTTATTTATTGCAGGAT
1 TTATTGCATGATATGATTTTATTTATTGCAGGAT
* *
29720031 TTATTGCATGAAATGATTTTATTTATTGCATGAT
1 TTATTGCATGATATGATTTTATTTATTGCAGGAT
* *
29720065 TTATTGCAAGATATAATTTTAT
1 TTATTGCATGATATGATTTTAT
29720087 ATTTTGGCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.50
Consensus pattern (34 bp):
TTATTGCATGATATGATTTTATTTATTGCAGGAT
Found at i:29720063 original size:17 final size:17
Alignment explanation
Indices: 29720009--29720066 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
29719999 ATTGCATGAT
29720009 ATGATTTTATTTATTGC
1 ATGATTTTATTTATTGC
* * *
29720026 AGGA-TTTATTGCA-TGAA
1 ATGATTTTATT-TATTG-C
29720043 ATGATTTTATTTATTGC
1 ATGATTTTATTTATTGC
29720060 ATGATTT
1 ATGATTT
29720067 ATTGCAAGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 8 0.26
17 15 0.48
18 8 0.26
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.52
Consensus pattern (17 bp):
ATGATTTTATTTATTGC
Found at i:29720125 original size:24 final size:22
Alignment explanation
Indices: 29720098--29720147 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
29720088 TTTTGGCATA
29720098 ATTTACTATATGATATGATTTAAT
1 ATTTACTATATGAT-TG-TTTAAT
* *
29720122 ATTTATTATATGATTGTTTGAT
1 ATTTACTATATGATTGTTTAAT
29720144 ATTT
1 ATTT
29720148 TGATAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 2 0.08
24 13 0.54
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (22 bp):
ATTTACTATATGATTGTTTAAT
Found at i:29721298 original size:17 final size:17
Alignment explanation
Indices: 29721273--29721311 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
29721263 ATTTTTATTA
*
29721273 TATTTAATAA-ATAAATT
1 TATTAAATAATATAAA-T
29721290 TATTAAATAATATAAAT
1 TATTAAATAATATAAAT
29721307 TATTA
1 TATTA
29721312 TTTTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTAAATAATATAAAT
Found at i:29725591 original size:9 final size:9
Alignment explanation
Indices: 29725579--29725618 Score: 62
Period size: 9 Copynumber: 4.2 Consensus size: 9
29725569 GCTTATTTTA
29725579 CTTAGTTTC
1 CTTAGTTTC
29725588 CTTAGTTTCC
1 CTTAGTTT-C
29725598 TCTTAGTTTC
1 -CTTAGTTTC
29725608 CTTAGTTTC
1 CTTAGTTTC
29725617 CT
1 CT
29725619 CAAAATCCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 19 0.66
10 2 0.07
11 8 0.28
ACGTcount: A:0.10, C:0.25, G:0.10, T:0.55
Consensus pattern (9 bp):
CTTAGTTTC
Found at i:29725604 original size:20 final size:20
Alignment explanation
Indices: 29725579--29725619 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
29725569 GCTTATTTTA
29725579 CTTAGTTTCCTTAGTTTCCT
1 CTTAGTTTCCTTAGTTTCCT
29725599 CTTAGTTTCCTTAGTTTCCT
1 CTTAGTTTCCTTAGTTTCCT
29725619 C
1 C
29725620 AAAATCCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.27, G:0.10, T:0.54
Consensus pattern (20 bp):
CTTAGTTTCCTTAGTTTCCT
Found at i:29726727 original size:30 final size:30
Alignment explanation
Indices: 29726593--29726730 Score: 158
Period size: 30 Copynumber: 4.6 Consensus size: 30
29726583 ATGATTTATG
* *
29726593 TTAAGAG-TTATTTAAATATAAATTAGAAAT
1 TTAAGAGTTTATTTGAATATAAATTA-AAAA
* *
29726623 TTAAAAGTTTATTT-AGATATAAATTAAAAG
1 TTAAGAGTTTATTTGA-ATATAAATTAAAAA
* *
29726653 TTAAGAGTTTATTTTAGTATAAATTAAAAA
1 TTAAGAGTTTATTTGAATATAAATTAAAAA
29726683 TTAA-AGATTTATTTGAATATAAATTAAAAA
1 TTAAGAG-TTTATTTGAATATAAATTAAAAA
29726713 TTAAG-GATTTATTTGAAT
1 TTAAGAG-TTTATTTGAAT
29726731 GTAATAAAAG
Statistics
Matches: 96, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.02
30 77 0.80
31 17 0.18
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (30 bp):
TTAAGAGTTTATTTGAATATAAATTAAAAA
Found at i:29727625 original size:25 final size:25
Alignment explanation
Indices: 29727597--29727647 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
29727587 AGCCCTTGCT
29727597 TTACAAATATGATTAAAGTGTTATA
1 TTACAAATATGATTAAAGTGTTATA
29727622 TTACAAATATGATTAAAGTGTTATA
1 TTACAAATATGATTAAAGTGTTATA
29727647 T
1 T
29727648 AAGGGGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (25 bp):
TTACAAATATGATTAAAGTGTTATA
Found at i:29729413 original size:49 final size:48
Alignment explanation
Indices: 29729360--29729539 Score: 162
Period size: 49 Copynumber: 3.5 Consensus size: 48
29729350 AGGCTAAATA
*
29729360 ACTTTAAAAATTTCATCTTAAAAAAGCTCCTCTAAGCGAAAGTTCAACC
1 ACTTTAAAAATTTCATCTTGAAAAAGCTCCTCTAAGC-AAAGTTCAACC
** * * * *
29729409 ACTTTAAAAAAATTTCATCTTGAAAAATTTTCTCTAAGTAAATGGTCAACA
1 ACTTT--AAAAATTTCATCTTGAAAAAGCTCCTCTAAGCAAA-GTTCAACC
* * * * *
29729460 ATTTTAAAAATTTTATATTGAAAAAGCTCCTCTAAGCAGAGATTTAACC
1 ACTTTAAAAATTTCATCTTGAAAAAGCTCCTCTAAGCAAAG-TTCAACC
29729509 ACTTTAAAGAAAATTTTTCATCTTGAAAAAG
1 ACTTT--A-AAAA--TTTCATCTTGAAAAAG
29729540 GCTTTTCTAG
Statistics
Matches: 101, Mismatches: 21, Indels: 13
0.75 0.16 0.10
Matches are distributed among these distances:
48 1 0.01
49 41 0.41
50 3 0.03
51 38 0.38
52 4 0.04
54 14 0.14
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (48 bp):
ACTTTAAAAATTTCATCTTGAAAAAGCTCCTCTAAGCAAAGTTCAACC
Found at i:29729435 original size:51 final size:50
Alignment explanation
Indices: 29729365--29729539 Score: 174
Period size: 51 Copynumber: 3.4 Consensus size: 50
29729355 AAATAACTTT
*
29729365 AAAAATTTCATCTTAAAAAAGCTCCTCTAAGCGAAAGTTCAACCACTTTAA
1 AAAAATTTCATCTTGAAAAAGCTCCTCTAAGC-AAAGTTCAACCACTTTAA
** * * * * *
29729416 AAAAATTTCATCTTGAAAAATTTTCTCTAAGTAAATGGTCAA-CAATTT-T
1 AAAAATTTCATCTTGAAAAAGCTCCTCTAAGCAAA-GTTCAACCACTTTAA
* * * *
29729465 AAAAATTTTATATTGAAAAAGCTCCTCTAAGCAGAGATTTAACCACTTTAA
1 AAAAATTTCATCTTGAAAAAGCTCCTCTAAGCAAAG-TTCAACCACTTTAA
29729516 AGAAAATTTTTCATCTTGAAAAAG
1 A-AAAA--TTTCATCTTGAAAAAG
29729540 GCTTTTCTAG
Statistics
Matches: 96, Mismatches: 21, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
48 1 0.01
49 31 0.32
50 13 0.14
51 33 0.34
52 4 0.04
54 14 0.15
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (50 bp):
AAAAATTTCATCTTGAAAAAGCTCCTCTAAGCAAAGTTCAACCACTTTAA
Found at i:29742104 original size:31 final size:29
Alignment explanation
Indices: 29742069--29742146 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
29742059 TTCTTTTAAG
*
29742069 AAAATAAATAATAAAAAAAGTGAAATAAAT
1 AAAATAAATAATAAAAAAAGT-AAAAAAAT
* *
29742099 AAAAATAAAAAATTAAAGAAAGTAAAAAAAT
1 -AAAATAAATAA-TAAAAAAAGTAAAAAAAT
* *
29742130 AAAATAGATAAGAAAAA
1 AAAATAAATAATAAAAA
29742147 TATTATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 4 0.10
30 9 0.23
31 17 0.44
32 9 0.23
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.17
Consensus pattern (29 bp):
AAAATAAATAATAAAAAAAGTAAAAAAAT
Found at i:29742552 original size:19 final size:19
Alignment explanation
Indices: 29742509--29742554 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29742499 AGAACACCAG
*
29742509 TGCCGGATTCTGGAAAATT
1 TGCCGGAATCTGGAAAATT
** *
29742528 CACCGGAATCTGGAAATTT
1 TGCCGGAATCTGGAAAATT
29742547 TGCCGGAA
1 TGCCGGAA
29742555 GTTGGCCGAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (19 bp):
TGCCGGAATCTGGAAAATT
Found at i:29742721 original size:25 final size:25
Alignment explanation
Indices: 29742685--29742734 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
29742675 AATCTGGAAA
*
29742685 TTTCCCAGAAATTTCCAGAAAAATT
1 TTTCCCAGAAATTTCCAAAAAAATT
*
29742710 TTTCGCCA-AAATTTCTAAAAAAATT
1 TTTC-CCAGAAATTTCCAAAAAAATT
29742735 CTCCTCACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (25 bp):
TTTCCCAGAAATTTCCAAAAAAATT
Found at i:29743188 original size:11 final size:11
Alignment explanation
Indices: 29743169--29743215 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
29743159 TTAAATTAAG
* *
29743169 AAATAAAAATA
1 AAATGAAAAGA
29743180 AAATGAAAAGA
1 AAATGAAAAGA
*
29743191 AAAAGAAAAGA
1 AAATGAAAAGA
29743202 AAA-GAAAAGGA
1 AAATGAAAA-GA
29743213 AAA
1 AAA
29743216 AAATGTACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
10 5 0.16
11 27 0.84
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
AAATGAAAAGA
Found at i:29743193 original size:16 final size:16
Alignment explanation
Indices: 29743173--29743215 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
29743163 ATTAAGAAAT
*
29743173 AAAAATAAAATGAAAAG
1 AAAAAGAAAA-GAAAAG
29743190 AAAAAGAAAAGAAAAG
1 AAAAAGAAAAGAAAAG
*
29743206 AAAAGGAAAA
1 AAAAAGAAAA
29743216 AAATGTACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAG
Found at i:29743374 original size:7 final size:7
Alignment explanation
Indices: 29743371--29743432 Score: 90
Period size: 7 Copynumber: 8.6 Consensus size: 7
29743361 CATTTTTTGG
29743371 TTTT-TT
1 TTTTGTT
29743377 TTTTGTTT
1 TTTTG-TT
29743385 TTTTGTT
1 TTTTGTT
29743392 TTTTGTT
1 TTTTGTT
29743399 TTTTGTT
1 TTTTGTT
29743406 TTTTGTTT
1 TTTTG-TT
29743414 TTTTGTTT
1 TTTTG-TT
29743422 TTTTGTT
1 TTTTGTT
29743429 TTTT
1 TTTT
29743433 TTTACCAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
6 4 0.08
7 27 0.51
8 22 0.42
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (7 bp):
TTTTGTT
Found at i:29743375 original size:1 final size:1
Alignment explanation
Indices: 29743371--29743435 Score: 67
Period size: 1 Copynumber: 65.0 Consensus size: 1
29743361 CATTTTTTGG
* * * * * * *
29743371 TTTTTTTTTTGTTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29743436 ACCAAAGCTC
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:29743376 original size:8 final size:8
Alignment explanation
Indices: 29743374--29743433 Score: 99
Period size: 8 Copynumber: 7.9 Consensus size: 8
29743364 TTTTTGGTTT
29743374 TTTTTTTG
1 TTTTTTTG
29743382 TTTTTTTG
1 TTTTTTTG
29743390 -TTTTTTG
1 TTTTTTTG
29743397 -TTTTTTG
1 TTTTTTTG
29743404 -TTTTTTG
1 TTTTTTTG
29743411 TTTTTTTG
1 TTTTTTTG
29743419 TTTTTTTG
1 TTTTTTTG
29743427 TTTTTTT
1 TTTTTTT
29743434 TTACCAAAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.41
8 30 0.59
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:29743395 original size:15 final size:15
Alignment explanation
Indices: 29743371--29743433 Score: 103
Period size: 14 Copynumber: 4.3 Consensus size: 15
29743361 CATTTTTTGG
29743371 TTTT-TTTTTTGTTT
1 TTTTGTTTTTTGTTT
29743385 TTTTGTTTTTTG-TT
1 TTTTGTTTTTTGTTT
29743399 TTTTGTTTTTTGTTT
1 TTTTGTTTTTTGTTT
29743414 TTTTGTTTTTTTGTTT
1 TTTTG-TTTTTTGTTT
29743430 TTTT
1 TTTT
29743434 TTACCAAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
14 18 0.39
15 14 0.30
16 14 0.30
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (15 bp):
TTTTGTTTTTTGTTT
Found at i:29743569 original size:41 final size:41
Alignment explanation
Indices: 29743442--29743814 Score: 508
Period size: 41 Copynumber: 9.0 Consensus size: 41
29743432 TTTTACCAAA
* * *
29743442 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-GTAAATT
29743485 GCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATT
*
29743527 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
*
29743568 GCTCCTCTAAACAGA-G-ACAACGAAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGG-AAAGTAAATT
*
29743608 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATT
29743650 GCTCCTCTAAACAGAGGCA--ACGGAC-TTGGAAGAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAC-GACTTTGG-A-AAGTAAATT
*
29743691 GCTCCTCTAAACAGAGGTACCACGACTTTGGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GG-AAAGTAAATT
29743734 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* *
29743775 GCTCCTCTAAACAGAGGCACCA-AACTTTGAAGAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGA-AAGTAAAT
29743815 ACTCCTAGAC
Statistics
Matches: 303, Mismatches: 12, Indels: 32
0.87 0.03 0.09
Matches are distributed among these distances:
39 9 0.03
40 41 0.14
41 103 0.34
42 73 0.24
43 69 0.23
44 8 0.03
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
Found at i:29745077 original size:19 final size:16
Alignment explanation
Indices: 29745043--29745092 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
29745033 AATTTGAATC
**
29745043 TCTTTTTTCATTTTTT
1 TCTTTTTTTTTTTTTT
29745059 TCATTTTTCTTCTTTTTTT
1 TC-TTTTT-TT-TTTTTTT
29745078 TCTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTT
29745093 CATCATCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 8 0.28
17 7 0.24
18 6 0.21
19 8 0.28
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (16 bp):
TCTTTTTTTTTTTTTT
Found at i:29745087 original size:9 final size:9
Alignment explanation
Indices: 29745045--29745092 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
29745035 TTTGAATCTC
*
29745045 TTTTTTCAT
1 TTTTTTCTT
29745054 TTTTTTCATT
1 TTTTTTC-TT
*
29745064 TTTCTTCTT
1 TTTTTTCTT
29745073 TTTTTTCTT
1 TTTTTTCTT
29745082 TTTTTT-TT
1 TTTTTTCTT
29745090 TTT
1 TTT
29745093 CATCATCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
8 5 0.14
9 23 0.66
10 7 0.20
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:29746421 original size:6 final size:6
Alignment explanation
Indices: 29746411--29746476 Score: 66
Period size: 6 Copynumber: 11.2 Consensus size: 6
29746401 AGAGAAAGAG
* **
29746411 GAAAAA -AAAAA GAAAAA GAAAAA GAGAAA GAAAGAA GATGAA GAAAGAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAA-AA GAAAAA GAAA-AA
29746460 -AAAAA GAAAAA -AAAAA G
1 GAAAAA GAAAAA GAAAAA G
29746477 CAGCAGCAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
5 12 0.24
6 31 0.63
7 6 0.12
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:29746454 original size:25 final size:26
Alignment explanation
Indices: 29746398--29746476 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
29746388 GGCGACGCAG
*
29746398 AGAAGAGAAAGAGGAAAAAAAAAAGA
1 AGAAGAAAAAGAGGAAAAAAAAAAGA
* *
29746424 AAAAGAAAAAGA-GAAAGAAAGAAGATGA
1 AGAAGAAAAAGAGGAAA-AAA-AA-AAGA
*
29746452 AGAAAGAAAAA-AAGAAAAAAAAAAG
1 AG-AAGAAAAAGAGGAAAAAAAAAAG
29746477 CAGCAGCAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
25 4 0.09
26 15 0.35
27 4 0.09
28 8 0.19
29 12 0.28
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (26 bp):
AGAAGAAAAAGAGGAAAAAAAAAAGA
Found at i:29761117 original size:276 final size:272
Alignment explanation
Indices: 29760548--29761344 Score: 1344
Period size: 276 Copynumber: 3.0 Consensus size: 272
29760538 TGTAATTGTC
*
29760548 ATTTATTTTTTACAATTTATACAAATAATTCAAATTTTATAACCCAATCATGATATACTTAAAGC
1 ATTTATTTTTTACAATTTATACAAATAATTCAAAATTTATAACCCAATCATGATATACTTAAAGC
*
29760613 GACAAGAATAAACTTTTTAATATAATAGTGGCTAAAAATTATACTTTTAACCGTTTTAACGGTTA
66 GACAAAAATAAACTTTTTAATATAATAGTGGCTAAAAATTATACTTTTAACCGTTTTAACGGTTA
*
29760678 ACATATAAAAGATTTTGATGTCGTATTAG----GTTACACGATAATTACATAAAAGAAAGTAATA
131 ACATATAAAAGATTTTGATGTCGTATTAGTTATGTTACACAATAATTACATAAAAGAAAGTAATA
29760739 ATGTAATGTTTTCAACACCTATAACAACATAACTGAATCAACTAAAAATTTAAATTAACATAATT
196 ATGTAATGTTTTCAACACCTATAACAACATAACTGAATCAACTAAAAATTTAAATTAACATAATT
29760804 TAAATTTAAATT
261 TAAATTTAAATT
* * *
29760816 ATTTATTTCTTACAATTTATACAAATAATTCAAAATTTAAAATCCAATCATGATATACTTAAAGC
1 ATTTATTTTTTACAATTTATACAAATAATTCAAAATTTATAACCCAATCATGATATACTTAAAGC
* *
29760881 GACAAAAATAAACTTTTTAATATAATAGTGGTTAAAAATTATACTTTTAACCATTTTAACGGTTA
66 GACAAAAATAAACTTTTTAATATAATAGTGGCTAAAAATTATACTTTTAACCGTTTTAACGGTTA
29760946 ACATATAAAAGATTTTGATGTCGTATTATGTTACTATGTTACACAATAATTACATAAAAGAAAGT
131 ACATATAAAAGATTTTGATGTCGTATTA-G-T--TATGTTACACAATAATTACATAAAAGAAAGT
*
29761011 AATAATGTAATGTTTTCAACACCTATAACAACATAATTGAATCAACTAAAAATTTAAATTAACAT
192 AATAATGTAATGTTTTCAACACCTATAACAACATAACTGAATCAACTAAAAATTTAAATTAACAT
29761076 AATTTAAATTTAAATT
257 AATTTAAATTTAAATT
*
29761092 ATTTATTTTTTACAATTTATACAAATAATTCAAAATTTATAACCCAATCATGATATACCTAAAGC
1 ATTTATTTTTTACAATTTATACAAATAATTCAAAATTTATAACCCAATCATGATATACTTAAAGC
*** *
29761157 GAC-AAAAT-TTTTTTTTAATATAATAATGGCTAAAAATTATACTTTTAACCGTTTTAACGGTTA
66 GACAAAAATAAACTTTTTAATATAATAGTGGCTAAAAATTATACTTTTAACCGTTTTAACGGTTA
29761220 ACATATAAAAGATTTTGATGTCG---TA-TTATGTTACACAATAATTACATAAAAGAAAGTAATA
131 ACATATAAAAGATTTTGATGTCGTATTAGTTATGTTACACAATAATTACATAAAAGAAAGTAATA
* *
29761281 ATGTAATGTTTTCAACACTTATAACAACATAACCGAATCAACTAAAAATTTAAATTAACATAAT
196 ATGTAATGTTTTCAACACCTATAACAACATAACTGAATCAACTAAAAATTTAAATTAACATAAT
29761345 AAATGATCTT
Statistics
Matches: 499, Mismatches: 22, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
266 96 0.19
268 152 0.30
269 1 0.00
271 2 0.00
274 72 0.14
275 5 0.01
276 171 0.34
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.37
Consensus pattern (272 bp):
ATTTATTTTTTACAATTTATACAAATAATTCAAAATTTATAACCCAATCATGATATACTTAAAGC
GACAAAAATAAACTTTTTAATATAATAGTGGCTAAAAATTATACTTTTAACCGTTTTAACGGTTA
ACATATAAAAGATTTTGATGTCGTATTAGTTATGTTACACAATAATTACATAAAAGAAAGTAATA
ATGTAATGTTTTCAACACCTATAACAACATAACTGAATCAACTAAAAATTTAAATTAACATAATT
TAAATTTAAATT
Found at i:29762326 original size:2 final size:2
Alignment explanation
Indices: 29762319--29762344 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29762309 AGGTAGAACA
29762319 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
29762345 TCATTCAAAT
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:29765327 original size:61 final size:61
Alignment explanation
Indices: 29765248--29765626 Score: 463
Period size: 61 Copynumber: 6.3 Consensus size: 61
29765238 CATTTTAAGG
* *
29765248 TTTTAGTTTTCAAAAAAAATTGATACTTTCAACTTTTCCTTAAAAATGCTTTTTTTTGAAAA
1 TTTTA-TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTTTTTGAAAA
* * * * *
29765310 TTTTAATTTCAAGAAAAATTGAAACTTTCAACTTTTTCTTAAAAACG--CTTTTTTGAAAA
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTTTTTGAAAA
* * * * *
29765369 TTTTAATTTCAATG-AAAATTGACACTATCAACTTTTTCC-CAAAAATATTTTTTTTTGAAAA
1 TTTTATTTTCAA-GAAAAATTGATACTTTCAAC-TTTTCCTTAAAAATGTTTTTTTTTGAAAA
*
29765430 TTTTATTTTCAA-AGAAAATTGATACTTTCAACTTTTCCTTAAAAAT-ATTTTTTTTGAAAA
1 TTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTTTTTGAAAA
* ** * *
29765490 TTTTTATTTTTAAGGGAAATTAATACTTTCAAC-TTTCCTT-CAAAT-TTTTTTTTTGAAAA
1 -TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTTTTTGAAAA
*
29765549 TTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCTTAAAAATGTTTTATTTTTGAAAA
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTT-TTTTTGAAAA
29765611 TTTTATTTTCAA-AAAA
1 TTTTATTTTCAAGAAAA
29765627 TCATTGAAAA
Statistics
Matches: 276, Mismatches: 28, Indels: 27
0.83 0.08 0.08
Matches are distributed among these distances:
58 29 0.11
59 68 0.25
60 36 0.13
61 116 0.42
62 27 0.10
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (61 bp):
TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTTTTTGAAAA
Found at i:29765413 original size:120 final size:118
Alignment explanation
Indices: 29765248--29765622 Score: 441
Period size: 120 Copynumber: 3.1 Consensus size: 118
29765238 CATTTTAAGG
** *
29765248 TTTTAGTTTTCAAAAAAAATTGATACTTTCAACTTTTCCTTAAAAATGCTTTTTTTTGAAAATTT
1 TTTTA-TTTTCAAGGAAAATTGATACTTTCAACTTTTCC-TAAAAAT-TTTTTTTTTGAAAATTT
* * * *
29765313 TAATTTCAAGAAAAATTGAAACTTTCAACTTTTTCTTAAAAACGCTTTTTTGAAAA
63 TATTTTCAAGAAAAATTGAAACTTTCAACTTTTCCTTAAAAAAGTTTTTTTGAAAA
* * * * *
29765369 TTTTAATTTCAATGAAAATTGACACTATCAACTTTTTCCCAAAAATATTTTTTTTTGAAAATTTT
1 TTTTATTTTCAAGGAAAATTGATACTTTCAAC-TTTTCCTAAAAAT-TTTTTTTTTGAAAATTTT
* *
29765434 ATTTTCAA-AGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAA
64 ATTTTCAAGA-AAAATTGAAACTTTCAACTTTTCCTTAAAAA-AGTTTTTTTGAAAA
* * * **
29765490 TTTTTATTTTTAAGGGAAATTAATACTTTCAAC-TTTCCTTCAAATTTTTTTTTTGAAAATTTTA
1 -TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTAAAAATTTTTTTTTTGAAAATTTTA
*
29765554 TTTTCAAGAAAAATT-AATACTTTCAACTTTTCCTTAAAAATGTTTTATTTTTGAAAA
65 TTTTCAAGAAAAATTGAA-ACTTTCAACTTTTCCTTAAAAAAG--TT-TTTTTGAAAA
29765611 TTTTATTTTCAA
1 TTTTATTTTCAA
29765623 AAAATCATTG
Statistics
Matches: 217, Mismatches: 28, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
118 1 0.00
119 55 0.25
120 104 0.48
121 32 0.15
122 25 0.12
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.48
Consensus pattern (118 bp):
TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTAAAAATTTTTTTTTTGAAAATTTTAT
TTTCAAGAAAAATTGAAACTTTCAACTTTTCCTTAAAAAAGTTTTTTTGAAAA
Found at i:29765461 original size:181 final size:181
Alignment explanation
Indices: 29765248--29765626 Score: 507
Period size: 181 Copynumber: 2.1 Consensus size: 181
29765238 CATTTTAAGG
*
29765248 TTTTAGTTTTCAAAAAAAATTGATACTTTCAACTTTTCCTTAAAAATGCTTTTTTTTGAAAA-TT
1 TTTTA-TTTTCAAAAAAAATTGATACTTTCAACTTTTCCTTAAAAAT-ATTTTTTTTGAAAATTT
*
29765312 TTAATTTCAAGAAAAATTGAA-ACTTTCAACTTTTTCTTAAAAACGCTTTTTTGAAAATTTTAAT
64 TTAATTTCAAGAAAAATT-AATACTTTCAAC-TTTCCTTAAAAACGCTTTTTTGAAAATTTTAAT
*
29765376 TTCAATG-AAAATTGACACTATCAACTTTTTCC-CAAAAATATTTT-TTTTTGAAAA
127 TTCAA-GAAAAATTAACACTATCAAC-TTTTCCTCAAAAATATTTTATTTTTGAAAA
*
29765430 TTTTATTTTCAAAGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAATTTTT
1 TTTTATTTTCAAAAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAATTTTT
* * ** * **** *
29765495 ATTTTTAAGGGAAATTAATACTTTCAACTTTCCTTCAAATTTTTTTTTTGAAAATTTTATTTTCA
66 AATTTCAAGAAAAATTAATACTTTCAACTTTCCTTAAAAACGCTTTTTTGAAAATTTTAATTTCA
* * * *
29765560 AGAAAAATTAATACTTTCAACTTTTCCTTAAAAATGTTTTATTTTTGAAAA
131 AGAAAAATTAACACTATCAACTTTTCCTCAAAAATATTTTATTTTTGAAAA
29765611 TTTTATTTTCAAAAAA
1 TTTTATTTTCAAAAAA
29765627 TCATTGAAAA
Statistics
Matches: 173, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
179 7 0.04
180 71 0.41
181 90 0.52
182 5 0.03
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (181 bp):
TTTTATTTTCAAAAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTTGAAAATTTTT
AATTTCAAGAAAAATTAATACTTTCAACTTTCCTTAAAAACGCTTTTTTGAAAATTTTAATTTCA
AGAAAAATTAACACTATCAACTTTTCCTCAAAAATATTTTATTTTTGAAAA
Found at i:29766566 original size:15 final size:16
Alignment explanation
Indices: 29766539--29766571 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
29766529 TATCTTCTAG
29766539 AATAAAAATTAAAAAT
1 AATAAAAATTAAAAAT
29766555 AATAAAAA-TAAAAAT
1 AATAAAAATTAAAAAT
29766570 AA
1 AA
29766572 AATTCATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAAAAATTAAAAAT
Found at i:29766609 original size:6 final size:7
Alignment explanation
Indices: 29766592--29766622 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
29766582 AGATAATTGA
29766592 AAAAAAT
1 AAAAAAT
29766599 AAAAAAT
1 AAAAAAT
29766606 AAAAAAT
1 AAAAAAT
29766613 -AAAAAT
1 AAAAAAT
29766619 AAAA
1 AAAA
29766623 TGGGCTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:29766611 original size:14 final size:13
Alignment explanation
Indices: 29766592--29766622 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
29766582 AGATAATTGA
29766592 AAAAAATAAAAAAT
1 AAAAAAT-AAAAAT
29766606 AAAAAATAAAAAT
1 AAAAAATAAAAAT
29766619 AAAA
1 AAAA
29766623 TGGGCTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:29766976 original size:41 final size:41
Alignment explanation
Indices: 29766823--29767011 Score: 202
Period size: 42 Copynumber: 4.5 Consensus size: 41
29766813 AGGCTAAACA
* * * *
29766823 ACTTTGGAATAATAAATTGC-TCATCTGAATAGAGGTAACCATG
1 ACTTT-GAAAAATAAATTGCTTC-TCTAAACAGAGG-CACCATG
* * * *
29766866 ACTTTGGAAAATAAATTGCTTTTTTAAACAGAGGCAACATG
1 ACTTTGAAAAATAAATTGCTTCTCTAAACAGAGGCACCATG
* *
29766907 ACTTTTGGAAAGTAAATTG-TTCCTCTAAACAGAGGCACCATG
1 AC-TTTGAAAAATAAATTGCTT-CTCTAAACAGAGGCACCATG
*
29766949 ACTTTGAAAAATAAATTGCTTCTCTAAACAGAGGCACCATA
1 ACTTTGAAAAATAAATTGCTTCTCTAAACAGAGGCACCATG
29766990 ACTTTGAAAAAAATAAATTGCT
1 ACTTTG--AAAAATAAATTGCT
29767012 CATTGACAAT
Statistics
Matches: 125, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
41 48 0.38
42 57 0.46
43 20 0.16
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (41 bp):
ACTTTGAAAAATAAATTGCTTCTCTAAACAGAGGCACCATG
Found at i:29775270 original size:15 final size:15
Alignment explanation
Indices: 29775245--29775279 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29775235 TTATTTTGTT
*
29775245 AAATATAATGAATGA
1 AAATGTAATGAATGA
*
29775260 GAATGTAATGAATGA
1 AAATGTAATGAATGA
29775275 AAATG
1 AAATG
29775280 CATGCATGCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (15 bp):
AAATGTAATGAATGA
Found at i:29776546 original size:15 final size:15
Alignment explanation
Indices: 29776513--29776635 Score: 62
Period size: 16 Copynumber: 8.3 Consensus size: 15
29776503 AAGGTTTCAA
* **
29776513 GATTTTAAAGGTTCA
1 GATTTTAAGGGTTTG
29776528 GATTTTAAGGGTTTG
1 GATTTTAAGGGTTTG
*
29776543 GA-TTTAA-GTTTTGAG
1 GATTTTAAGGGTTT--G
*
29776558 GGTTTT-AGGGTTTG
1 GATTTTAAGGGTTTG
*
29776572 G-TTTTAA-GGTATG
1 GATTTTAAGGGTTTG
* *
29776585 GAACGTTT-AGGGTTTT
1 G-A-TTTTAAGGGTTTG
29776601 GA-TTTAAGGGTTTG
1 GATTTTAAGGGTTTG
* *
29776615 GATTTTATGGGGTTTA
1 GATTTTA-AGGGTTTG
29776631 GATTT
1 GATTT
29776636 AAGAGTTTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
13 17 0.20
14 17 0.20
15 23 0.28
16 26 0.31
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (15 bp):
GATTTTAAGGGTTTG
Found at i:29776636 original size:15 final size:14
Alignment explanation
Indices: 29776593--29776644 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
29776583 TGGAACGTTT
*
29776593 AGGGTTTTGATTTA
1 AGGGTTTAGATTTA
*
29776607 AGGGTTTGGATTTTA
1 AGGGTTTAGA-TTTA
*
29776622 TGGGGTTTAGATTTA
1 -AGGGTTTAGATTTA
*
29776637 AGAGTTTA
1 AGGGTTTA
29776645 AAGGTTTGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 15 0.48
15 8 0.26
16 8 0.26
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
AGGGTTTAGATTTA
Found at i:29776710 original size:16 final size:16
Alignment explanation
Indices: 29776662--29776723 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
29776652 GGGATTTCAT
*
29776662 ATTTTATGGGGTTTTGG
1 ATTTTA-GGGATTTTGG
29776679 ATTTTAGGGA-TTTGG
1 ATTTTAGGGATTTTGG
*
29776694 ATTTAAGGGATTTTGG
1 ATTTTAGGGATTTTGG
*
29776710 ATTTTAGGGGTTTT
1 ATTTTAGGGATTTT
29776724 AGAAACCTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
15 14 0.35
16 20 0.50
17 6 0.15
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (16 bp):
ATTTTAGGGATTTTGG
Found at i:29777839 original size:8 final size:8
Alignment explanation
Indices: 29777826--29777856 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
29777816 GCTGTTTGTC
29777826 TTTGTTTT
1 TTTGTTTT
29777834 TTTGTTTT
1 TTTGTTTT
29777842 TTTGTTTT
1 TTTGTTTT
*
29777850 TGTGTTT
1 TTTGTTT
29777857 CCGTTTGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (8 bp):
TTTGTTTT
Found at i:29780258 original size:4 final size:4
Alignment explanation
Indices: 29780249--29780280 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
29780239 AAATAAAAAG
*
29780249 AAAT AAAT AAAT AAAT AACT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
29780281 TAACACATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:29781442 original size:27 final size:27
Alignment explanation
Indices: 29781412--29781502 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
29781402 GAAAATTTTA
29781412 TTTTCAAGAAAAATTGATACTTTCAAC
1 TTTTCAAGAAAAATTGATACTTTCAAC
*** * **
29781439 TTTTCCTTAAAAATCT-ATTCTTGAAATC
1 TTTTCAAGAAAAAT-TGATACTTTCAA-C
29781467 TTTTCTTTTAAGAAAAATTGATACTTTCAAC
1 TTTTC----AAGAAAAATTGATACTTTCAAC
29781498 TTTTC
1 TTTTC
29781503 CTTAAAAATA
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
27 18 0.40
28 7 0.16
31 7 0.16
32 13 0.29
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.45
Consensus pattern (27 bp):
TTTTCAAGAAAAATTGATACTTTCAAC
Found at i:29781492 original size:59 final size:59
Alignment explanation
Indices: 29781300--29781715 Score: 386
Period size: 60 Copynumber: 7.0 Consensus size: 59
29781290 TGCTTTTATG
** * **
29781300 CAAGAAAAATTGATACTTTCAACTACTCCTT--AAA-ACA-TTTT-AAGGTTTTATTTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTGAAATTTTTA-TTTT
** *
29781355 CAAGAAAAATTGATACTATT-AACTTTTCCCCAAAAATATATTTTTTTGAAAATTTTATTTT
1 CAAGAAAAATTGATACT-TTCAACTTTTCCTTAAAAATATA--TTTTTGAAATTTTTATTTT
* * *
29781416 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATCTATTCTTGAAATCTTTTCTTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTGAAAT-TTTTATTTT
*
29781476 -AAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAATTTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTG-AAATTTTTATTTT
* * * *
29781535 CAA-AGGAAATTAATACTTTCAACTTTCCCTTAAAAATATATTTTTTTGAAA-ATTTATTTT
1 CAAGA-AAAATTGATACTTTCAACTTTTCCTTAAAAATATA--TTTTTGAAATTTTTATTTT
** * * * **** *
29781595 TTA-AAAAATTAATATTTTCAACTTTTCCTCAAAAATAT-TTAAAAAAAAAATTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATT--TTTGAAATTTTTATTTT
* * *
29781654 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTAAAATTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATA-TTTTTGAAATTTTTATTTT
29781714 CA
1 CA
29781716 TAAAATCATT
Statistics
Matches: 297, Mismatches: 43, Indels: 37
0.79 0.11 0.10
Matches are distributed among these distances:
55 24 0.08
56 4 0.01
57 3 0.01
58 5 0.02
59 98 0.33
60 103 0.35
61 45 0.15
62 15 0.05
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (59 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTGAAATTTTTATTTT
Found at i:29781568 original size:119 final size:117
Alignment explanation
Indices: 29781346--29781713 Score: 413
Period size: 119 Copynumber: 3.1 Consensus size: 117
29781336 ATTTTAAGGT
* *
29781346 TTTATTTTTCAAGAAAAATTGATACTATT-AACTTTTCCCCAAAAATATATTTTTTTGAAAATTT
1 TTTATTTTTTAAGAAAAATTGATACT-TTCAACTTTT-CCTAAAAA-ATATTTTTTTGAAAATTT
* *
29781410 TATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATCTATTCTTG-AAA
63 TATTTTCAAG-GAAATTGATACTTTCAACTTTTCCTTAAAAATATATTCTTGAAAA
*
29781465 TCTT-TTCTTTTAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAATTTT
1 T-TTATT-TTTTAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTTGAAAA-TTT
* * *
29781529 TATTTTCAAAGGAAATTAATACTTTCAACTTTCCCTTAAAAATATATTTTTTTGAAAA
63 TATTTTC-AAGGAAATTGATACTTTCAACTTTTCCTTAAAAATATA--TTCTTGAAAA
* * * *****
29781587 TTTATTTTTT-A-AAAAATTAATATTTTCAACTTTTCCTCAAAAATATTTAAAAAAAAAATTTTA
1 TTTATTTTTTAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATATTT-TTTTGAAAATTTTA
* *
29781650 TTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTAAAA
65 TTTTCAAGG-AAATTGATACTTTCAACTTTTCCTTAAAAATATA-TTCTTGAAAA
29781705 TTTTATTTT
1 -TTTATTTT
29781714 CATAAAATCA
Statistics
Matches: 218, Mismatches: 19, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
118 29 0.13
119 136 0.62
120 36 0.17
121 11 0.05
122 6 0.03
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (117 bp):
TTTATTTTTTAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTTGAAAATTTTAT
TTTCAAGGAAATTGATACTTTCAACTTTTCCTTAAAAATATATTCTTGAAAA
Found at i:29781570 original size:60 final size:59
Alignment explanation
Indices: 29781345--29781715 Score: 389
Period size: 60 Copynumber: 6.2 Consensus size: 59
29781335 CATTTTAAGG
**
29781345 TTTTATTTTTCAAGAAAAATTGATACTATT-AACTTTTCCCCAAAAATATATTTTTTTGAAAA-
1 TTTTA-TTTTCAAG-AAAATTGATACT-TTCAACTTTT-CCTTAAAA-ATATTTTTTTGAAAAT
* * *
29781407 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATCTATTCTTG-AAAT
1 TTTTATTTTCAAG-AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAAT
*
29781466 CTTTTCTTTT-AAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAAT
1 -TTTTATTTTCAAG-AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAAT
* * *
29781526 TTTTATTTTCAAAGGAAATTAATACTTTCAACTTTCCCTTAAAAATATATTTTTTTGAAAAT
1 TTTTATTTTC-AAGAAAATTGATACTTTCAACTTTTCCTT-AAAA-ATATTTTTTTGAAAAT
* * * ***** *
29781588 TTATT-TTTT-AA-AAAATTAATATTTTCAACTTTTCCTCAAAAATATTTAAAAAAAAAA
1 TT-TTATTTTCAAGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAAT
*
29781645 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATATTTTTTTAAAA-
1 TTTTATTTTCAA-GAAAATTGATACTTTCAACTTTTCCTTAAAAATAT-TTTTTTGAAAAT
29781705 TTTTATTTTCA
1 TTTTATTTTCA
29781716 TAAAATCATT
Statistics
Matches: 264, Mismatches: 31, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
56 2 0.01
57 16 0.06
58 9 0.03
59 80 0.30
60 87 0.33
61 41 0.16
62 27 0.10
63 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (59 bp):
TTTTATTTTCAAGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTGAAAAT
Found at i:29781602 original size:16 final size:16
Alignment explanation
Indices: 29781566--29781604 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29781556 ACTTTCCCTT
* *
29781566 AAAAATATATTTTTTT
1 AAAAATTTATTTTTTA
*
29781582 GAAAATTTATTTTTTA
1 AAAAATTTATTTTTTA
29781598 AAAAATT
1 AAAAATT
29781605 AATATTTTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
AAAAATTTATTTTTTA
Found at i:29782653 original size:15 final size:16
Alignment explanation
Indices: 29782626--29782658 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
29782616 TATCTTCTAG
29782626 AATAAAAATTAAAAAT
1 AATAAAAATTAAAAAT
29782642 AATAAAAA-TAAAAAT
1 AATAAAAATTAAAAAT
29782657 AA
1 AA
29782659 AATTTAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAAAAATTAAAAAT
Found at i:29787888 original size:93 final size:93
Alignment explanation
Indices: 29787774--29787953 Score: 333
Period size: 93 Copynumber: 1.9 Consensus size: 93
29787764 AGACCTAGAT
* *
29787774 TTGCAAAGCGAATAAAAGCCAAGAAACTCCATCTATATATTATGCAATTTTTAAAAATAAAAAAT
1 TTGCAAAGCGAATAAAAGCCAAGAAACTCAATCTATATATTATGCAATTTTTAAAAATAAAAAAG
29787839 TGCAAGCATATATATATATATACTAGTG
66 TGCAAGCATATATATATATATACTAGTG
*
29787867 TTGCGAAGCGAATAAAAGCCAAGAAACTCAATCTATATATTATGCAATTTTTAAAAATAAAAAAG
1 TTGCAAAGCGAATAAAAGCCAAGAAACTCAATCTATATATTATGCAATTTTTAAAAATAAAAAAG
29787932 TGCAAGCATATATATATATATA
66 TGCAAGCATATATATATATATA
29787954 TATAATACAA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.29
Consensus pattern (93 bp):
TTGCAAAGCGAATAAAAGCCAAGAAACTCAATCTATATATTATGCAATTTTTAAAAATAAAAAAG
TGCAAGCATATATATATATATACTAGTG
Found at i:29796294 original size:83 final size:84
Alignment explanation
Indices: 29796197--29796363 Score: 300
Period size: 84 Copynumber: 2.0 Consensus size: 84
29796187 GCTAGTTCAA
29796197 ATTTTTTATTAATTTAAAAACAAATCAG-ATGCAAATAAACATTGCGCTTAGGAAAACAGGAAAT
1 ATTTTTTATTAATTTAAAAACAAATCAGAATGCAAATAAACATTGCGCTTAGGAAAACAGGAAAT
29796261 ATGTCATAACGAATTTCGT
66 ATGTCATAACGAATTTCGT
* **
29796280 ATTTTTTATTAATTTAAAAACAAATCAGAATGCAAATAAACATTGCGTTTAGGAAAGGAGGAAAT
1 ATTTTTTATTAATTTAAAAACAAATCAGAATGCAAATAAACATTGCGCTTAGGAAAACAGGAAAT
29796345 ATGTCATAACGAATTTCGT
66 ATGTCATAACGAATTTCGT
29796364 TTGAGAGATT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 28 0.35
84 52 0.65
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (84 bp):
ATTTTTTATTAATTTAAAAACAAATCAGAATGCAAATAAACATTGCGCTTAGGAAAACAGGAAAT
ATGTCATAACGAATTTCGT
Found at i:29797296 original size:31 final size:31
Alignment explanation
Indices: 29797249--29797335 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
29797239 AAAATCTCTC
* *
29797249 AAAAAAAGATAAAAAATTAAAAATTAAAAAT
1 AAAAAAAGATAAAAAATAAAAAATAAAAAAT
* *
29797280 AAAATAAGTTAAAAAATAAAAAATAAAAAAAAT
1 AAAAAAAGATAAAAAATAAAAAAT--AAAAAAT
**
29797313 AAAAAAA-ATTGAAAA-AAAAAATA
1 AAAAAAAGATAAAAAATAAAAAATA
29797336 TTACGATTCG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 1 0.02
31 28 0.61
32 5 0.11
33 12 0.26
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (31 bp):
AAAAAAAGATAAAAAATAAAAAATAAAAAAT
Found at i:29797315 original size:23 final size:23
Alignment explanation
Indices: 29797250--29797318 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 23
29797240 AAATCTCTCA
* * *
29797250 AAAAAAGATAAAAAATTAAAAAT
1 AAAAAATAAAAAAAATAAAAAAT
* **
29797273 TAAAAATAAAATAAGTTAAAAAAT
1 AAAAAATAAAA-AAAATAAAAAAT
29797297 AAAAAATAAAAAAAATAAAAAA
1 AAAAAATAAAAAAAATAAAAAA
29797319 AATTGAAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (23 bp):
AAAAAATAAAAAAAATAAAAAAT
Found at i:29797318 original size:7 final size:7
Alignment explanation
Indices: 29797251--29797309 Score: 64
Period size: 7 Copynumber: 7.9 Consensus size: 7
29797241 AATCTCTCAA
29797251 AAAAAGAT
1 AAAAA-AT
29797259 AAAAAAT
1 AAAAAAT
*
29797266 TAAAAAT
1 AAAAAAT
*
29797273 TAAAAAT
1 AAAAAAT
29797280 AAAATAAGTT
1 AAAA-AA--T
29797290 AAAAAAT
1 AAAAAAT
29797297 AAAAAAT
1 AAAAAAT
29797304 AAAAAA
1 AAAAAA
29797310 AATAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
7 32 0.70
8 7 0.15
9 2 0.04
10 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (7 bp):
AAAAAAT
Found at i:29797332 original size:16 final size:16
Alignment explanation
Indices: 29797267--29797338 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
29797257 ATAAAAAATT
29797267 AAAAATTAAAAATAAA
1 AAAAATTAAAAATAAA
* *
29797283 ATAAGTTAAAAAATAAA
1 AAAAATT-AAAAATAAA
*
29797300 AAATAA-AAAAAATAAA
1 AAA-AATTAAAAATAAA
*
29797316 AAAAATTGAAAA-AAA
1 AAAAATTAAAAATAAA
*
29797331 AAATATTA
1 AAAAATTA
29797339 CGATTCGATA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
15 11 0.25
16 21 0.48
17 11 0.25
18 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAATTAAAAATAAA
Found at i:29797698 original size:21 final size:22
Alignment explanation
Indices: 29797674--29797716 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29797664 TGTTCTTCTC
*
29797674 AAAAAT-CCAAATTTTTC-CAA
1 AAAAATCCCAAAATTTTCGCAA
29797694 AAAAATCCCAAAATTTTCGCAA
1 AAAAATCCCAAAATTTTCGCAA
29797716 A
1 A
29797717 TTTGGCCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.51, C:0.21, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAATCCCAAAATTTTCGCAA
Found at i:29798126 original size:3 final size:3
Alignment explanation
Indices: 29798120--29798221 Score: 88
Period size: 3 Copynumber: 34.3 Consensus size: 3
29798110 GAAAGAAAAA
* *
29798120 AAT AAT AAT AAT GAT AA- AAT AAT AAT AAT AAT AAT AA- ACCAT AAAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A--AT -AAT
* *
29798166 AAT -AT CAT AAT AAT AAT AAT AAT AGT AA- AAT AAT AAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
*
29798210 -AT AAC AAT AAT A
1 AAT AAT AAT AAT A
29798222 CTATAATATT
Statistics
Matches: 81, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
2 9 0.11
3 66 0.81
4 5 0.06
6 1 0.01
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29798140 original size:17 final size:17
Alignment explanation
Indices: 29798118--29798221 Score: 84
Period size: 17 Copynumber: 5.7 Consensus size: 17
29798108 AGGAAAGAAA
*
29798118 AAAATAATAATAATGAT
1 AAAATAATAATAATAAT
29798135 AAAATAATAATAATAAT
1 AAAATAATAATAATAAT
*
29798152 AATAA-ACCATAAACAATATCAT
1 AA-AATA--AT-AATAATA--AT
*
29798174 AATAATAATAATAATAGT
1 AA-AATAATAATAATAAT
29798192 AAAATAATAATATATAAT
1 AAAATAATAATA-ATAAT
* *
29798210 ATAACAATAATA
1 AAAATAATAATA
29798222 CTATAATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
17 29 0.40
18 19 0.26
19 2 0.03
20 12 0.17
21 2 0.03
22 7 0.10
23 1 0.01
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATAATAATAATAAT
Found at i:29798143 original size:20 final size:19
Alignment explanation
Indices: 29798115--29798230 Score: 96
Period size: 20 Copynumber: 6.0 Consensus size: 19
29798105 GAAAGGAAAG
*
29798115 AAAAAAATAATAATAATGAT
1 AAAATAATAATAATAAT-AT
29798135 AAAATAATAATAATAATA-
1 AAAATAATAATAATAATAT
** *
29798153 ATAAACCAT-A-AACAATAT
1 A-AAATAATAATAATAATAT
*
29798171 CATAATAATAATAATAATAGT
1 -AAAATAATAATAATAATA-T
29798192 AAAATAATAATATATAATAT
1 AAAATAATAATA-ATAATAT
*
29798212 AACAATAATACT-ATAATAT
1 AA-AATAATAATAATAATAT
29798231 TTTGCCATAT
Statistics
Matches: 78, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
17 6 0.08
18 6 0.08
19 15 0.19
20 36 0.46
21 15 0.19
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAATAATAATAATAT
Found at i:29798553 original size:24 final size:22
Alignment explanation
Indices: 29798525--29798570 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
29798515 TATTTTTCTA
29798525 TATAAGCTTATATTTGTTCCTTTT
1 TATAAGCTTA-ATTT-TTCCTTTT
**
29798549 TATAATTTTAATTTTTCCTTTT
1 TATAAGCTTAATTTTTCCTTTT
29798571 CTATTTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (22 bp):
TATAAGCTTAATTTTTCCTTTT
Found at i:29799598 original size:473 final size:472
Alignment explanation
Indices: 29798709--29800125 Score: 2562
Period size: 469 Copynumber: 3.0 Consensus size: 472
29798699 GATAAATACA
* *
29798709 TAGTGATTAAATCACCACATTCGATAAGAATTTAATGGTTTTATGTGACAGTAATCTTAAATTAC
1 TAGTGATTAAATCACCACATTCGATAAGAATTTAATGGTCTTATGTGACAGTAGTCTTAAATTAC
* *
29798774 AAAAGTGATTAGTATTGTCTTAAAAAATTATTTGATTTTCATATAAAAAGATTAGAAACTTTTAT
66 AAAAGTGATTAGTATTGTCTTAAAAAATTATTTGATTTTCATATAAAAA-ATTAGAAAATTTAAT
* * * * *
29798839 CATTAAGACCTCTTTTAACA-TACTGTTGAAAATAATTTTTGCGTTCAAAAATTGCTTTTGATCC
130 CATTAAGACCTCATTTAACATTACTGTTGAAAATAAGTTTTGCATTC-AAAACTGCTTTTGATCT
* *
29798903 AGACCTATTGCTAAACAACAACCAAAATTTTGGCTTTTTAGTTTAAAAGTTTGATATTCCAACCT
194 AGACCTATTGCTAAACAATAACCAAAATTTTGGCTTTTTAGTTTAAAAGTTTGGTATTCCAACCT
29798968 AAACCAAAACATTTCTCAAGAGGTGCTTTTGTAATGAAAAAGTACATTGAGATAAAAAAAAATCA
259 AAACCAAAACATTTCTCAAGAGGTGCTTTTGTAATGAAAAAGTACATTGAGATAAAAAAAAATCA
29799033 CTTTATTTTCCCTATATTTTTAATATTTTATTATTTTGTACATATCTTTTTAAACATTTCATTTA
324 CTTTATTTTCCCTATATTTTTAATATTTTATTATTTTGTACATATCTTTTTAAACATTTCATTTA
29799098 CTCACAACATTTTTCATAATAATATCAAACACTTAAAATTTTATTTCTGAGGCACACTTTTTCCG
389 CTCACAACATTTTTCATAATAATATCAAACACTTAAAATTTTATTTCTGA-GCACACTTTTTCCG
29799163 TCACATTCTTTTAAAAACACT
453 TCACATTCTTTT-AAAACACT
29799184 TAGTGATTAAATCACCACATTCGATAAGAATTTAATGGTCTTATGTGACAGTAGTCTTAAATTAC
1 TAGTGATTAAATCACCACATTCGATAAGAATTTAATGGTCTTATGTGACAGTAGTCTTAAATTAC
29799249 AAAAGTGATTAGTATTGTCTTAAAAAATTATTTGATTTTCATA-AAAAAATTAGAAAATTTAATC
66 AAAAGTGATTAGTATTGTCTTAAAAAATTATTTGATTTTCATATAAAAAATTAGAAAATTTAATC
29799313 ATTAAGACCTCATTTAACATTACTGTTGAAAATAAGTTTTGCATTCAAAACTGCTTTTGATCTAG
131 ATTAAGACCTCATTTAACATTACTGTTGAAAATAAGTTTTGCATTCAAAACTGCTTTTGATCTAG
29799378 ACCTATTGCTAAACAATAACCAAAATTTTGGCTTTTTAGTTTAAAAGTTTGGTATTCCAACCTAA
196 ACCTATTGCTAAACAATAACCAAAATTTTGGCTTTTTAGTTTAAAAGTTTGGTATTCCAACCTAA
* *
29799443 ACCAAAAAATTTCTCAATAGGTGCTTTTGTAATGAAAAAAGTACACTTGAGAT-AAAAAAAATCA
261 ACCAAAACATTTCTCAAGAGGTGCTTTTGTAATG-AAAAAGTACA-TTGAGATAAAAAAAAATCA
*
29799507 CTTTATTTTCCCTATATTTTTAATATTTTATTATTTTATACATATCTTTTTAAACATTTCATTTA
324 CTTTATTTTCCCTATATTTTTAATATTTTATTATTTTGTACATATCTTTTTAAACATTTCATTTA
29799572 CTCACAACATTTTTCATAAT-ATATCAAACACTTAAAAGTTTTATTTCTGAGCACACTTTTTCCG
389 CTCACAACATTTTTCATAATAATATCAAACACTTAAAA-TTTTATTTCTGAGCACACTTTTTCCG
29799636 TCACATTCTTTTAAAACACT
453 TCACATTCTTTTAAAACACT
29799656 TAGTGATTAAATCACCACATTCGATAAGAATTTAATGGTCTTATGTGACAGTAGTCTTAAATTA-
1 TAGTGATTAAATCACCACATTCGATAAGAATTTAATGGTCTTATGTGACAGTAGTCTTAAATTAC
29799720 AAAAGTGATTAGTATTGTCTTAAAAAATTATTTGA-TTTCATATAAAAAATTA-AAAATTTAATC
66 AAAAGTGATTAGTATTGTCTTAAAAAATTATTTGATTTTCATATAAAAAATTAGAAAATTTAATC
29799783 ATTAAGACCTCATTTAACATTACTGTTG-AAATAAGTTTTGCATTCAAAACTGCTTTTGATCTAG
131 ATTAAGACCTCATTTAACATTACTGTTGAAAATAAGTTTTGCATTCAAAACTGCTTTTGATCTAG
29799847 ACCTATTTGCTAAACAATAACCAAAATTTTGGCTTTTTAGTTTAAAAGTTTGGTATTCCAACCTA
196 ACCTA-TTGCTAAACAATAACCAAAATTTTGGCTTTTTAGTTTAAAAGTTTGGTATTCCAACCTA
29799912 AACCAAAACATTTCTCAAGAGGTGCTTTTGTAATGAAAAAGTACATTGAGATAAAAAAAAATCAC
260 AACCAAAACATTTCTCAAGAGGTGCTTTTGTAATGAAAAAGTACATTGAGATAAAAAAAAATCAC
29799977 TTTATTTTCCCTATATTTTTAATATTTTATTATTTTGTACATATCTTTTTAAACATTTCATTTAC
325 TTTATTTTCCCTATATTTTTAATATTTTATTATTTTGTACATATCTTTTTAAACATTTCATTTAC
* *
29800042 TCACAACATTTTTCATAATAATATCAAACACTTAAAATTTTATTTCTAAGCACACTTTTTCAGTC
390 TCACAACATTTTTCATAATAATATCAAACACTTAAAATTTTATTTCTGAGCACACTTTTTCCGTC
29800107 ACATTCTTTTAAAACACT
455 ACATTCTTTTAAAACACT
29800125 T
1 T
29800126 TTTTCAACTT
Statistics
Matches: 915, Mismatches: 19, Indels: 22
0.96 0.02 0.02
Matches are distributed among these distances:
468 7 0.01
469 191 0.21
470 155 0.17
471 44 0.05
472 72 0.08
473 187 0.20
474 146 0.16
475 113 0.12
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (472 bp):
TAGTGATTAAATCACCACATTCGATAAGAATTTAATGGTCTTATGTGACAGTAGTCTTAAATTAC
AAAAGTGATTAGTATTGTCTTAAAAAATTATTTGATTTTCATATAAAAAATTAGAAAATTTAATC
ATTAAGACCTCATTTAACATTACTGTTGAAAATAAGTTTTGCATTCAAAACTGCTTTTGATCTAG
ACCTATTGCTAAACAATAACCAAAATTTTGGCTTTTTAGTTTAAAAGTTTGGTATTCCAACCTAA
ACCAAAACATTTCTCAAGAGGTGCTTTTGTAATGAAAAAGTACATTGAGATAAAAAAAAATCACT
TTATTTTCCCTATATTTTTAATATTTTATTATTTTGTACATATCTTTTTAAACATTTCATTTACT
CACAACATTTTTCATAATAATATCAAACACTTAAAATTTTATTTCTGAGCACACTTTTTCCGTCA
CATTCTTTTAAAACACT
Found at i:29803246 original size:20 final size:22
Alignment explanation
Indices: 29803221--29803263 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
29803211 TGCTTATATA
29803221 ATATATACATAA-ATAT-TTAT
1 ATATATACATAATATATCTTAT
*
29803241 ATATATATATAATATATCTTAT
1 ATATATACATAATATATCTTAT
29803263 A
1 A
29803264 CCCATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 4 0.20
22 5 0.25
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATACATAATATATCTTAT
Found at i:29803819 original size:14 final size:14
Alignment explanation
Indices: 29803800--29803827 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29803790 TTTAAAAAAT
29803800 AAATAATTTTTAAA
1 AAATAATTTTTAAA
29803814 AAATAATTTTTAAA
1 AAATAATTTTTAAA
29803828 GAAAATAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATAATTTTTAAA
Found at i:29805351 original size:19 final size:19
Alignment explanation
Indices: 29805318--29805401 Score: 80
Period size: 19 Copynumber: 4.3 Consensus size: 19
29805308 TGAAACCTTT
29805318 TAAAAAAATTATAAAAATTTC
1 TAAAAAAATTA-AAAAA-TTC
29805339 TAAAAAAATTAAAAAATTC
1 TAAAAAAATTAAAAAATTC
* *
29805358 -AAAATAATTACAAAAATAC
1 TAAAAAAATTA-AAAAATTC
** * *
29805377 TAAAAATTTTAATAATTTC
1 TAAAAAAATTAAAAAATTC
29805396 TAAAAA
1 TAAAAA
29805402 TTTCTAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
18 9 0.17
19 21 0.40
20 12 0.23
21 11 0.21
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAAAATTAAAAAATTC
Found at i:29805405 original size:10 final size:10
Alignment explanation
Indices: 29805329--29805412 Score: 68
Period size: 10 Copynumber: 8.7 Consensus size: 10
29805319 AAAAAAATTA
29805329 TAAAAATTTC
1 TAAAAATTTC
**
29805339 TAAAAAAAT-
1 TAAAAATTTC
*
29805348 TAAAAAATTC
1 TAAAAATTTC
* *
29805358 AAAATAATTAC
1 TAAA-AATTTC
*
29805369 -AAAAA-TAC
1 TAAAAATTTC
29805377 TAAAAATTT-
1 TAAAAATTTC
*
29805386 TAATAATTTC
1 TAAAAATTTC
29805396 TAAAAATTTC
1 TAAAAATTTC
29805406 TAAAAAT
1 TAAAAAT
29805413 ATTGCAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
8 3 0.05
9 23 0.38
10 30 0.50
11 4 0.07
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAATTTC
Found at i:29805474 original size:10 final size:9
Alignment explanation
Indices: 29805321--29805478 Score: 53
Period size: 9 Copynumber: 17.0 Consensus size: 9
29805311 AACCTTTTAA
29805321 AAAAATTAT
1 AAAAATTAT
*
29805330 AAAAATTTCTAA
1 AAAAA--T-TAT
29805342 AAAAATTA-
1 AAAAATTAT
29805350 AAAAATTCA-
1 AAAAATT-AT
*
29805359 AAATAATTAC
1 AAA-AATTAT
29805369 AAAAA-TACT
1 AAAAATTA-T
*
29805378 AAAAATTTT
1 AAAAATTAT
* *
29805387 AATAATTTCT
1 AA-AAATTAT
*
29805397 AAAAATTTCT
1 AAAAA-TTAT
29805407 AAAAA-TATT
1 AAAAATTA-T
* *
29805416 GCAAAAACTAA
1 --AAAAATTAT
*
29805427 AAAAATTTT
1 AAAAATTAT
29805436 AAAAA--AT
1 AAAAATTAT
29805443 AAAAA--AT
1 AAAAATTAT
*
29805450 GAAATATTATT
1 -AAAAATTA-T
29805461 AAAAATTAT
1 AAAAATTAT
29805470 AAAAATTAT
1 AAAAATTAT
29805479 GATAACTAGA
Statistics
Matches: 117, Mismatches: 14, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
7 8 0.07
8 14 0.12
9 46 0.39
10 33 0.28
11 7 0.06
12 9 0.08
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29805562 original size:38 final size:38
Alignment explanation
Indices: 29805490--29805566 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
29805480 ATAACTAGAT
* *
29805490 AAATTCAAAAATATATGAAAATTTTAACTCAAATTCAAA
1 AAATTCAAAAACATATGAAAATTTTAACTAAAATT-AAA
* *
29805529 AAATTCAACAACA-ATGAAAATTTTAATTAAAATTAAA
1 AAATTCAAAAACATATGAAAATTTTAACTAAAATTAAA
29805566 A
1 A
29805567 TTTCTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 4 0.12
38 19 0.56
39 11 0.32
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (38 bp):
AAATTCAAAAACATATGAAAATTTTAACTAAAATTAAA
Found at i:29805656 original size:38 final size:36
Alignment explanation
Indices: 29805613--29805716 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 36
29805603 AAACTGAAAA
* *
29805613 TTAAAACAATCTAAATTTTTTTGAAAACTTTTAAAATT
1 TTAAAA-AATCTAAAATTTTTTGAAAA-TCTTAAAATT
* *
29805651 TTAAAAAATATTAAAAATTTTTAGAAAATCTTAAAATT
1 TTAAAAAAT-CT-AAAATTTTTTGAAAATCTTAAAATT
29805689 TTAAAAAAATTCTAAAATTTTTTGAAAA
1 TT-AAAAAA-TCTAAAATTTTTTGAAAA
29805717 ATTAAATAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
37 3 0.05
38 32 0.57
39 20 0.36
40 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (36 bp):
TTAAAAAATCTAAAATTTTTTGAAAATCTTAAAATT
Found at i:29805658 original size:19 final size:18
Alignment explanation
Indices: 29805631--29805709 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 18
29805621 ATCTAAATTT
* *
29805631 TTTTGAAAACTTTTAAAA
1 TTTTAAAAAATTTTAAAA
*
29805649 TTTTAAAAAATATTAAAAA
1 TTTTAAAAAAT-TTTAAAA
* *
29805668 TTTTTAGAAAATCTTAAAA
1 -TTTTAAAAAATTTTAAAA
*
29805687 TTTTAAAAAAATTCTAAAA
1 TTTT-AAAAAATTTTAAAA
29805706 TTTT
1 TTTT
29805710 TTGAAAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
18 13 0.27
19 26 0.53
20 10 0.20
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (18 bp):
TTTTAAAAAATTTTAAAA
Found at i:29805716 original size:19 final size:19
Alignment explanation
Indices: 29805622--29805716 Score: 70
Period size: 19 Copynumber: 4.9 Consensus size: 19
29805612 ATTAAAACAA
* *
29805622 TCTAAATTTTTTTGAAAACT
1 TCTAAAATTTTTAGAAAA-T
* *
29805642 TTTAAAA-TTTTAAAAAAT
1 TCTAAAATTTTTAGAAAAT
29805660 AT-TAAAAATTTTTAGAAAA-
1 -TCT-AAAATTTTTAGAAAAT
* *
29805679 TCTTAAAATTTTAAAAAAAT
1 TC-TAAAATTTTTAGAAAAT
*
29805699 TCTAAAATTTTTTGAAAA
1 TCTAAAATTTTTAGAAAA
29805717 ATTAAATAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.05
19 39 0.66
20 17 0.29
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (19 bp):
TCTAAAATTTTTAGAAAAT
Found at i:29805825 original size:12 final size:11
Alignment explanation
Indices: 29805805--29805841 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
29805795 ATTTTAGTAA
29805805 AAATAAAAAAT
1 AAATAAAAAAT
*
29805816 AAATTCAAAAAT
1 AAA-TAAAAAAT
29805828 AAATAAAAAAT
1 AAATAAAAAAT
29805839 AAA
1 AAA
29805842 ATTTGTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:29805843 original size:12 final size:12
Alignment explanation
Indices: 29805804--29805843 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
29805794 AATTTTAGTA
29805804 AAAATAAAAAAT
1 AAAATAAAAAAT
* *
29805816 AAATTCAAAAAT
1 AAAATAAAAAAT
29805828 -AAATAAAAAAT
1 AAAATAAAAAAT
29805839 AAAAT
1 AAAAT
29805844 TTGTAAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:29805909 original size:40 final size:40
Alignment explanation
Indices: 29805865--29805942 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
29805855 AAAACTCAAC
29805865 AATTTTAAGAAT-TTTAAAAAAAAATTTACAATTTTTTAAA
1 AATTTTAA-AATCTTTAAAAAAAAATTTACAATTTTTTAAA
* * * * *
29805905 AATTTTTATATCTTTAAAAAAAATTTTAGATTTTTTTA
1 AATTTTAAAATCTTTAAAAAAAAATTTACAATTTTTTA
29805943 TTTTAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (40 bp):
AATTTTAAAATCTTTAAAAAAAAATTTACAATTTTTTAAA
Found at i:29805988 original size:20 final size:19
Alignment explanation
Indices: 29805947--29805991 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
29805937 TTTTTATTTT
*
29805947 AAATATTTTTAAGTTTTTGC
1 AAAT-TTTTTAAGTTTTAGC
*
29805967 AAATTTTTTTAGTTTTAAGC
1 AAATTTTTTAAGTTTT-AGC
29805987 AAATT
1 AAATT
29805992 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (19 bp):
AAATTTTTTAAGTTTTAGC
Found at i:29809016 original size:21 final size:21
Alignment explanation
Indices: 29808992--29809074 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
29808982 CCCTAAACTC
29808992 AAACTTTAAACTTTAAAACCT
1 AAACTTTAAACTTTAAAACCT
* * *
29809013 AAACTCT-AATTCTTAAAAACT
1 AAACTTTAAACT-TTAAAACCT
** *
29809034 AAACAATATAACTTTAAACCCT
1 AAACTTTA-AACTTTAAAACCT
*
29809056 AAAAC-TTAAACTATAAAAC
1 -AAACTTTAAACTTTAAAAC
29809075 TTGCATCCAA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
20 3 0.06
21 28 0.60
22 9 0.19
23 7 0.15
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (21 bp):
AAACTTTAAACTTTAAAACCT
Found at i:29821814 original size:31 final size:31
Alignment explanation
Indices: 29821779--29821838 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
29821769 AAATGATTTC
29821779 TATACTCATACAAAATTTAAAATTTAATCCT
1 TATACTCATACAAAATTTAAAATTTAATCCT
** * *
29821810 TATACTTGTATAAAATTTGAAATTTAATC
1 TATACTCATACAAAATTTAAAATTTAATC
29821839 TATGTACTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (31 bp):
TATACTCATACAAAATTTAAAATTTAATCCT
Found at i:29821847 original size:31 final size:30
Alignment explanation
Indices: 29821790--29821869 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
29821780 ATACTCATAC
*
29821790 AAAATTTAAAATTTAATCCTTATACTTGTAT
1 AAAATTTAAAATTTAAT-CTTATACTTGCAT
* *
29821821 AAAATTTGAAATTTAATCTATGTACTTGCAT
1 AAAATTTAAAATTTAATCT-TATACTTGCAT
* *
29821852 GAAATTTAAAACTTAATC
1 AAAATTTAAAATTTAATC
29821870 CTTCTAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 2 0.05
31 40 0.95
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.41
Consensus pattern (30 bp):
AAAATTTAAAATTTAATCTTATACTTGCAT
Found at i:29822043 original size:29 final size:25
Alignment explanation
Indices: 29821976--29822051 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 25
29821966 TATATAACTA
*
29821976 ATTATTAATAATATTATCTTAATATT
1 ATTATTAATAAT-TTATATTAATATT
*
29822002 ATTATT-ATCATTTATATTAATCAATTAT
1 ATTATTAATAATTTATATTAAT--A-T-T
*
29822030 ATTATTAATAATTTAAATTAAT
1 ATTATTAATAATTTATATTAAT
29822052 GTATCAAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 9 0.22
25 4 0.10
26 7 0.17
27 1 0.02
28 7 0.17
29 13 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTATTAATAATTTATATTAATATT
Found at i:29822237 original size:20 final size:21
Alignment explanation
Indices: 29822207--29822249 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
29822197 ACATAAAATT
29822207 AATATAGTAAAAA-TATATTAA
1 AATATAGTAAAAATTA-ATTAA
29822228 AATA-AGTAAAAATTAATTAA
1 AATATAGTAAAAATTAATTAA
29822248 AA
1 AA
29822250 ATAATATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AATATAGTAAAAATTAATTAA
Found at i:29824533 original size:20 final size:20
Alignment explanation
Indices: 29824486--29824535 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
29824476 ATAAATAATC
*
29824486 ATGAATCAAACTTAAATTAA
1 ATGAATCTAACTTAAATTAA
29824506 ATGAATCTAACTTAAATTAA
1 ATGAATCTAACTTAAATTAA
29824526 ATGAATCTAA
1 ATGAATCTAA
29824536 TTGATCACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (20 bp):
ATGAATCTAACTTAAATTAA
Found at i:29826653 original size:37 final size:37
Alignment explanation
Indices: 29826600--29826675 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
29826590 ACAAAGACTA
29826600 GAAAACTAGTTAAAGTAGAGGCCATGGCTTCATCTCT
1 GAAAACTAGTTAAAGTAGAGGCCATGGCTTCATCTCT
*
29826637 GAAAACTAGTTGAAGTAGAGGCCATGGCTTCATCTCT
1 GAAAACTAGTTAAAGTAGAGGCCATGGCTTCATCTCT
29826674 GA
1 GA
29826676 TTTTTTGGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (37 bp):
GAAAACTAGTTAAAGTAGAGGCCATGGCTTCATCTCT
Found at i:29828755 original size:26 final size:26
Alignment explanation
Indices: 29828719--29828773 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
29828709 TTGAATATTG
* *
29828719 CTTCATAATCTTTTGGGCCCATGAAC
1 CTTCATAATCTCTTAGGCCCATGAAC
29828745 CTTCATAATCTCTTAGGCCCATGAAC
1 CTTCATAATCTCTTAGGCCCATGAAC
29828771 CTT
1 CTT
29828774 TAACTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.35
Consensus pattern (26 bp):
CTTCATAATCTCTTAGGCCCATGAAC
Found at i:29828859 original size:8 final size:8
Alignment explanation
Indices: 29828846--29828879 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
29828836 GCGAAAGCGA
29828846 AATCAAAC
1 AATCAAAC
*
29828854 AATCAAAT
1 AATCAAAC
29828862 AATCAAAC
1 AATCAAAC
*
29828870 AATCACAC
1 AATCAAAC
29828878 AA
1 AA
29828880 GAAACAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.15
Consensus pattern (8 bp):
AATCAAAC
Found at i:29830601 original size:14 final size:14
Alignment explanation
Indices: 29830584--29830610 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29830574 TATTATTGGG
29830584 TGTTTTATATTTTA
1 TGTTTTATATTTTA
29830598 TGTTTTATATTTT
1 TGTTTTATATTTT
29830611 TAAAAGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (14 bp):
TGTTTTATATTTTA
Found at i:29830791 original size:14 final size:14
Alignment explanation
Indices: 29830742--29830844 Score: 58
Period size: 14 Copynumber: 7.6 Consensus size: 14
29830732 CATTTGTTAT
* *
29830742 TAATAGTATATTAA
1 TAATATTATATAAA
*
29830756 TAAATATTAT-TATA
1 T-AATATTATATAAA
*
29830770 T-TTATTATATAAA
1 TAATATTATATAAA
*
29830783 TAATATTATATTAA
1 TAATATTATATAAA
*
29830797 TAATA-TA-ATATA
1 TAATATTATATAAA
*
29830809 TTAT-TTAT-TAATA
1 TAATATTATATAA-A
29830822 TAATATT-TATAAAA
1 TAATATTATAT-AAA
*
29830836 TAAAATTAT
1 TAATATTAT
29830845 TATTTTATTA
Statistics
Matches: 66, Mismatches: 13, Indels: 19
0.67 0.13 0.19
Matches are distributed among these distances:
12 16 0.24
13 11 0.17
14 29 0.44
15 10 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (14 bp):
TAATATTATATAAA
Done.