Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 4 of 311
Found at i:1094942 original size:30 final size:30
Alignment explanation
Indices: 1094906--1094966 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1094896 ATTTTATTGT
*
1094906 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTATTATTATTTTAAAGACATTTGC
* *
1094936 TAATTTTATTATTATTTTAGAGGCATTTGC
1 TAATTTTATTATTATTTTAAAGACATTTGC
1094966 T
1 T
1094967 TGTTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.56
Consensus pattern (30 bp):
TAATTTTATTATTATTTTAAAGACATTTGC
Found at i:1105766 original size:16 final size:16
Alignment explanation
Indices: 1105745--1105778 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1105735 GTATTTAATT
1105745 TAATTTTAATAATGCA
1 TAATTTTAATAATGCA
1105761 TAATTTTAATAATGCA
1 TAATTTTAATAATGCA
1105777 TA
1 TA
1105779 CAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
TAATTTTAATAATGCA
Found at i:1105872 original size:55 final size:55
Alignment explanation
Indices: 1105788--1105998 Score: 191
Period size: 55 Copynumber: 3.8 Consensus size: 55
1105778 ACAAAAAAAA
**
1105788 TTTAATACTGGTGCTAGCCATTGACAGGCCAGCACCAAAAAAATTTCAATTTTTT
1 TTTAATACTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAATTTCAATTTTTT
* *
1105843 TTTAATATTGGTGCCGGCCATTGACAGGCCAGCACC--CAAAATTT---TTTTTT
1 TTTAATACTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAATTTCAATTTTTT
* * * *
1105893 TTGAAAACTCGTATTTTGGTGTCGGCCATTGACAGGCCAGCA-CAAAAAAAATTCAACTTTTTT
1 TT--TAA----TA--CTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAATTTCAA-TTTTTT
* * **
1105956 TTTAATACTAGTGCCGGCCATTGATAGGCCAAAACCAAAAAAA
1 TTTAATACTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAA
1105999 ATAACTTTTT
Statistics
Matches: 126, Mismatches: 15, Indels: 29
0.74 0.09 0.17
Matches are distributed among these distances:
50 8 0.06
52 2 0.02
53 7 0.06
55 54 0.43
56 10 0.08
57 3 0.02
58 26 0.21
59 6 0.05
61 2 0.02
63 8 0.06
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (55 bp):
TTTAATACTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAATTTCAATTTTTT
Found at i:1106697 original size:23 final size:25
Alignment explanation
Indices: 1106653--1106703 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
1106643 ATCCCTAAAT
1106653 TTTTTTTCATTTTGAGCAA-TTTAA
1 TTTTTTTCATTTTGAGCAATTTTAA
* **
1106677 TTTTTTTC-TTTTGTGTTATTTTAA
1 TTTTTTTCATTTTGAGCAATTTTAA
1106701 TTT
1 TTT
1106704 CCCCCCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.69
Consensus pattern (25 bp):
TTTTTTTCATTTTGAGCAATTTTAA
Found at i:1107446 original size:19 final size:18
Alignment explanation
Indices: 1107401--1107446 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1107391 TTTCTCAACA
1107401 AAAAATTTAAAAAAAATC
1 AAAAATTTAAAAAAAATC
* *
1107419 AAAATATTTATAAAAATTCC
1 AAAA-ATTTAAAAAAAAT-C
1107439 AAAAATTT
1 AAAAATTT
1107447 TATATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 15 0.62
20 5 0.21
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATTTAAAAAAAATC
Found at i:1110787 original size:32 final size:32
Alignment explanation
Indices: 1110731--1110817 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 32
1110721 GCAGGGCTAA
* * *
1110731 TATATT-AAATAAACCTTTAAACTTTTTTTAT
1 TATATTCAAATAAATCATTATACTTTTTTTAT
*
1110762 TTTATTTC-AATAAATCATTATAC---TTTTAT
1 TATA-TTCAAATAAATCATTATACTTTTTTTAT
*
1110791 TATATTCAAATAAATTATTATACTTTT
1 TATATTCAAATAAATCATTATACTTTT
1110818 GAATCCCAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
28 3 0.07
29 23 0.52
31 3 0.07
32 15 0.34
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATTCAAATAAATCATTATACTTTTTTTAT
Found at i:1110802 original size:29 final size:29
Alignment explanation
Indices: 1110756--1110817 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
1110746 TTTAAACTTT
*
1110756 TTTTATTTTATTTCAATAAATCATTATAC
1 TTTTATTATATTTCAATAAATCATTATAC
*
1110785 TTTTATTATA-TTCAAATAAATTATTATAC
1 TTTTATTATATTTC-AATAAATCATTATAC
1110814 TTTT
1 TTTT
1110818 GAATCCCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTATTATATTTCAATAAATCATTATAC
Found at i:1112442 original size:22 final size:23
Alignment explanation
Indices: 1112410--1112452 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1112400 GTTATACTAT
1112410 TTTATATGTAAA-CTATTTTATTA
1 TTTATATGTAAACCT-TTTTATTA
1112433 TTTAT-TGTAAACCTTTTTAT
1 TTTATATGTAAACCTTTTTAT
1112453 AATCATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (23 bp):
TTTATATGTAAACCTTTTTATTA
Found at i:1112520 original size:29 final size:30
Alignment explanation
Indices: 1112488--1112558 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
1112478 ATTGCTTACA
*
1112488 TTAAACTTTTTATAT-ATATATTACTTGTT
1 TTAAACTTTTTATATCACATATTACTTGTT
* * *
1112517 TTAAA-TTTATT-TTTCACATGTTATTTGTT
1 TTAAACTTT-TTATATCACATATTACTTGTT
1112546 TTAAACTTTTTAT
1 TTAAACTTTTTAT
1112559 GTTATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
28 5 0.15
29 25 0.74
30 4 0.12
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (30 bp):
TTAAACTTTTTATATCACATATTACTTGTT
Found at i:1112690 original size:26 final size:24
Alignment explanation
Indices: 1112635--1112836 Score: 113
Period size: 26 Copynumber: 8.0 Consensus size: 24
1112625 ATATTAAATG
*
1112635 ATTTTAAATTGTTTTATTCTATTT
1 ATTTTAAATTGTTTTATACTATTT
*
1112659 ATTTTAAATTGCTTTCTATAGTATTT
1 ATTTTAAATTG-TTT-TATACTATTT
*
1112685 ATTTTAAACATGTTTTTCTATA-TATTATT
1 ATTTT-AA-AT-TGTTT-TATACTA-T-TT
* * * *
1112714 CATTTAAAATTGTCTTAAATTATTT
1 -ATTTTAAATTGTTTTATACTATTT
* * *
1112739 AGTTTAAATCGTTTTGTATATTATTT
1 ATTTTAAATTG-TTT-TATACTATTT
* * * *
1112765 GTTTTAAGTT-TCTCTACACATCATTT
1 ATTTTAAATTGT-TTTATAC-T-ATTT
1112791 ATTTTAAATTGTTTTATACTATTT
1 ATTTTAAATTGTTTTATACTATTT
* *
1112815 ACTTCAAATTGTTTTATA-TATT
1 ATTTTAAATTGTTTTATACTATT
1112837 ATTCCGTTTC
Statistics
Matches: 138, Mismatches: 25, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
23 4 0.03
24 43 0.31
25 10 0.07
26 49 0.36
27 10 0.07
28 13 0.09
29 5 0.04
30 4 0.03
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (24 bp):
ATTTTAAATTGTTTTATACTATTT
Found at i:1112829 original size:76 final size:79
Alignment explanation
Indices: 1112635--1112839 Score: 209
Period size: 76 Copynumber: 2.6 Consensus size: 79
1112625 ATATTAAATG
* * * * *
1112635 ATTTTAAATTGTTTTATTCTATTTATTTTAAATTGCTTTCTATAGTATTTATTTTAAACATGTTT
1 ATTTTAAATTGTTTTATACTATTTACTTTAAATTGTTTTATATATTATTTATTTT-AACATGTTT
* * * *
1112700 TTCTATATATTATTC
65 CTCTACACATCATTC
* * * * * * * *
1112715 ATTTAAAATTGTCTTAAATTATTTAGTTTAAATCGTTTTGTATATTATTTGTTTT-A-A-GTTTC
1 ATTTTAAATTGTTTTATACTATTTACTTTAAATTGTTTTATATATTATTTATTTTAACATGTTTC
*
1112777 TCTACACATCATTT
66 TCTACACATCATTC
*
1112791 ATTTTAAATTGTTTTATACTATTTACTTCAAATTGTTTTATATATTATT
1 ATTTTAAATTGTTTTATACTATTTACTTTAAATTGTTTTATATATTATT
1112840 CCGTTTCATT
Statistics
Matches: 101, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
76 55 0.54
77 1 0.01
78 1 0.01
80 44 0.44
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.58
Consensus pattern (79 bp):
ATTTTAAATTGTTTTATACTATTTACTTTAAATTGTTTTATATATTATTTATTTTAACATGTTTC
TCTACACATCATTC
Found at i:1122833 original size:30 final size:30
Alignment explanation
Indices: 1122797--1122869 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
1122787 GAGGACCAAA
* * *
1122797 ATGAAAATTTTTTTTACTGTAGTGCCTAAG
1 ATGAAAATTTTTGTAACAGTAGTGCCTAAG
* * *
1122827 ATGAAAATGATTTGTAAGAGTAGTGCTTAAG
1 ATGAAAAT-TTTTGTAACAGTAGTGCCTAAG
1122858 ATGAAAATTTTT
1 ATGAAAATTTTT
1122870 AGTTTTTAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (30 bp):
ATGAAAATTTTTGTAACAGTAGTGCCTAAG
Found at i:1125066 original size:9 final size:9
Alignment explanation
Indices: 1125022--1125050 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1125012 ATTAAAATTT
1125022 TTTAAATAA
1 TTTAAATAA
1125031 TTT-AATAA
1 TTTAAATAA
1125039 TTTAAATAA
1 TTTAAATAA
1125048 TTT
1 TTT
1125051 TTTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAATAA
Found at i:1125075 original size:21 final size:21
Alignment explanation
Indices: 1125031--1125075 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1125021 TTTTAAATAA
*
1125031 TTTAATAATTTAAATAATTTT
1 TTTAATAATTTAAATAATTAT
*
1125052 TTTAATTAATTT-AATGATTAT
1 TTTAA-TAATTTAAATAATTAT
1125073 TTT
1 TTT
1125076 TTAACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAATAATTTAAATAATTAT
Found at i:1130965 original size:3 final size:3
Alignment explanation
Indices: 1130951--1131007 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
1130941 AATAGAATAG
* * * *
1130951 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTG TTG TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1130999 TTA TTA TTA
1 TTA TTA TTA
1131008 ATAAAAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1131301 original size:17 final size:16
Alignment explanation
Indices: 1131279--1131310 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1131269 GACTCAGTTA
1131279 TAATTAATTGAAACTAG
1 TAATTAATT-AAACTAG
1131296 TAATTAATTAAACTA
1 TAATTAATTAAACTA
1131311 ATTGAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
TAATTAATTAAACTAG
Found at i:1140236 original size:39 final size:39
Alignment explanation
Indices: 1140097--1140253 Score: 133
Period size: 39 Copynumber: 4.0 Consensus size: 39
1140087 ACTTGAAACC
** **
1140097 AATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACATAGCCTGC-GGACCTTAAGTCCGGATAT
* * * * *
1140136 AATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCGGACAT
1 AATTCCAGCAC-ATAGCCTGC-GGACCTTAAGTCCGGATAT
* *
1140175 ATTTCCAGCACGTAGCCTGCGGACCTTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
* *
1140214 AATTCCAGCGCATAGCCTGCGGACCCTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
1140253 A
1 A
1140254 CATCACTGAA
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
38 17 0.18
39 80 0.82
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (39 bp):
AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
Found at i:1141772 original size:132 final size:131
Alignment explanation
Indices: 1141531--1141868 Score: 421
Period size: 132 Copynumber: 2.6 Consensus size: 131
1141521 CATATTCATT
* * *
1141531 TAAAAATTCTTTAAAACGGAGACGA-GATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACG
1 TAAAAATCCTTTAAAACGAAGGCGATG--TTGATATTTGGCAATTCGCGGAATCGTGCCCTAACG
* * *
1141595 TGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCCCTCCAAAATTTCGTTCATGTC
64 TGCTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTCGTTCATGTC
1141660 TTC
129 TTC
*
1141663 TAAAAATCCTTTAAAACGAAGGCGATGTTCGACATTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 TAAAAATCCTTTAAAACGAAGGCGATGTT-GATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * * ** *
1141728 GCTGGGTTGCAATTTCTCATTTGCTCAAAGTAATCGAATGTCCCTTTAGAATCTCGTTCATGTCT
65 GCTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTCGTTCATGTCT
1141793 TC
130 TC
* ** * * * * *
1141795 TAAAAA-CTCTTTAAAACAAAGGAAATACTTGATGTTTGGAAATTTG-GGAATCGTGCCCTATCG
1 TAAAAATC-CTTTAAAACGAAGGCGAT-GTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACG
1141858 TGCTGGGTTGC
64 TGCTGGGTTGC
1141869 GATTCTCCTA
Statistics
Matches: 180, Mismatches: 22, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
131 30 0.17
132 147 0.82
133 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (131 bp):
TAAAAATCCTTTAAAACGAAGGCGATGTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGTG
CTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTCGTTCATGTCTT
C
Found at i:1148925 original size:11 final size:11
Alignment explanation
Indices: 1148887--1148925 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1148877 TAATAATAAT
1148887 AAAATAGTAGC
1 AAAATAGTAGC
* * *
1148898 AACATAATAGT
1 AAAATAGTAGC
1148909 AAAATAGTAGC
1 AAAATAGTAGC
1148920 AAAATA
1 AAAATA
1148926 TAGAGAAAAC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (11 bp):
AAAATAGTAGC
Found at i:1148925 original size:19 final size:22
Alignment explanation
Indices: 1148879--1148921 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1148869 TATCCAAATA
1148879 ATAATAATAAAATAGTAGCAAC
1 ATAATAATAAAATAGTAGCAAC
*
1148901 ATAATAGTAAAATAGTAGCAA
1 ATAATAATAAAATAGTAGCAA
1148922 AATATAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAATAATAAAATAGTAGCAAC
Found at i:1148934 original size:22 final size:22
Alignment explanation
Indices: 1148878--1148934 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
1148868 ATATCCAAAT
**
1148878 AATAATAATAAAATAGTAGCAA
1 AATAATAGGAAAATAGTAGCAA
* *
1148900 CATAATAGTAAAATAGTAGCAA
1 AATAATAGGAAAATAGTAGCAA
1148922 AAT-ATAGAGAAAA
1 AATAATAG-GAAAA
1148935 CAACAAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.21
Consensus pattern (22 bp):
AATAATAGGAAAATAGTAGCAA
Found at i:1151208 original size:24 final size:25
Alignment explanation
Indices: 1151163--1151209 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1151153 ATAACTTACT
*
1151163 TTTATTAATATTTAAATGAATATAA
1 TTTATTAATATTTAAATAAATATAA
1151188 TTTATT-ATATTTATAA-AAATAT
1 TTTATTAATATTTA-AATAAATAT
1151210 TTGTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTATTAATATTTAAATAAATATAA
Found at i:1152494 original size:11 final size:11
Alignment explanation
Indices: 1152478--1152523 Score: 67
Period size: 11 Copynumber: 4.1 Consensus size: 11
1152468 CTAACCTTAA
1152478 ATTAATAAAAT
1 ATTAATAAAAT
1152489 ATTAAT-AAAT
1 ATTAATAAAAT
1152499 ATATAATTAAAAT
1 AT-TAA-TAAAAT
1152512 ATTAATAAAAT
1 ATTAATAAAAT
1152523 A
1 A
1152524 ATATGTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.19
11 16 0.50
12 4 0.12
13 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTAATAAAAT
Found at i:1152526 original size:31 final size:30
Alignment explanation
Indices: 1152491--1152553 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
1152481 AATAAAATAT
1152491 TAATAAATATATAATTAAA-ATATTAATAAAA
1 TAATAAATATATAATTAAATA-ATT-ATAAAA
** *
1152522 TAATATGTATCTAATTAAATAATTATAAAA
1 TAATAAATATATAATTAAATAATTATAAAA
1152552 TA
1 TA
1152554 TCATCAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 8 0.29
31 19 0.68
32 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
TAATAAATATATAATTAAATAATTATAAAA
Found at i:1152555 original size:23 final size:22
Alignment explanation
Indices: 1152477--1152554 Score: 58
Period size: 23 Copynumber: 3.6 Consensus size: 22
1152467 ACTAACCTTA
1152477 AATTAATAAAATATTAA-TAAAT
1 AATT-ATAAAATATTAATTAAAT
* *
1152499 ATATAATTAAAATATTAATAAAAT
1 A-ATTA-TAAAATATTAATTAAAT
*
1152523 AA-TAT---GTATCTAATTAAAT
1 AATTATAAAATAT-TAATTAAAT
1152542 AATTATAAAATAT
1 AATTATAAAATAT
1152555 CATCAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 15
0.67 0.10 0.24
Matches are distributed among these distances:
18 3 0.07
19 10 0.24
20 3 0.07
21 1 0.02
22 3 0.07
23 17 0.40
24 5 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (22 bp):
AATTATAAAATATTAATTAAAT
Found at i:1153265 original size:14 final size:15
Alignment explanation
Indices: 1153246--1153284 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
1153236 GAAAAAGATG
1153246 AATAATTAAAATTT-
1 AATAATTAAAATTTA
1153260 AATAA-TAAAATTTAA
1 AATAATTAAAATTT-A
1153275 AATAATTAAA
1 AATAATTAAA
1153285 TAACTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 5 0.23
15 5 0.23
16 4 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAATTAAAATTTA
Found at i:1156258 original size:16 final size:16
Alignment explanation
Indices: 1156239--1156271 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1156229 TATAAATATT
1156239 ATGT-AAAAAAATTAAA
1 ATGTGAAAAAAA-TAAA
1156255 ATGTGAAAAAAATAAA
1 ATGTGAAAAAAATAAA
1156271 A
1 A
1156272 AAAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
ATGTGAAAAAAATAAA
Found at i:1156272 original size:17 final size:16
Alignment explanation
Indices: 1156239--1156272 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1156229 TATAAATATT
*
1156239 ATGTAAAAAAATTAAA
1 ATGTAAAAAAATAAAA
1156255 ATGTGAAAAAAATAAAA
1 ATGT-AAAAAAATAAAA
1156272 A
1 A
1156273 AAATTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
ATGTAAAAAAATAAAA
Found at i:1158884 original size:16 final size:16
Alignment explanation
Indices: 1158842--1158884 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1158832 TCATTAATAT
*
1158842 TTATTTTTTATTAATA
1 TTATTTTTTATTAAAA
** *
1158858 TTAAATCTTATTAAAA
1 TTATTTTTTATTAAAA
1158874 TTATTTTTTAT
1 TTATTTTTTAT
1158885 ATTAAATTTT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTTTTTATTAAAA
Found at i:1159332 original size:60 final size:60
Alignment explanation
Indices: 1159234--1159368 Score: 261
Period size: 60 Copynumber: 2.2 Consensus size: 60
1159224 ACGGGTTGAC
1159234 GACACGACCGTGTGAATACTGGAGCATAATTTTATCTTAGCGAAAACCACGTAGACTGAA
1 GACACGACCGTGTGAATACTGGAGCATAATTTTATCTTAGCGAAAACCACGTAGACTGAA
*
1159294 GACATGACCGTGTGAATACTGGAGCATAATTTTATCTTAGCGAAAACCACGTAGACTGAA
1 GACACGACCGTGTGAATACTGGAGCATAATTTTATCTTAGCGAAAACCACGTAGACTGAA
1159354 GACACGACCGTGTGA
1 GACACGACCGTGTGA
1159369 GCCATACGGG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (60 bp):
GACACGACCGTGTGAATACTGGAGCATAATTTTATCTTAGCGAAAACCACGTAGACTGAA
Found at i:1160808 original size:40 final size:40
Alignment explanation
Indices: 1160763--1160842 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
1160753 TGAGGATGTT
1160763 AAACCTTGTTGAGTTTGAATTTTAAGTAATTATTAAGGTA
1 AAACCTTGTTGAGTTTGAATTTTAAGTAATTATTAAGGTA
* *
1160803 AAACCTTGTTGATTTTGAATTTTAAGTAATTGTTAAGGTA
1 AAACCTTGTTGAGTTTGAATTTTAAGTAATTATTAAGGTA
1160843 GGGGAGACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (40 bp):
AAACCTTGTTGAGTTTGAATTTTAAGTAATTATTAAGGTA
Found at i:1162836 original size:22 final size:22
Alignment explanation
Indices: 1162806--1162849 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1162796 TAGTCATATA
1162806 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
1162828 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
1162850 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:1162909 original size:16 final size:17
Alignment explanation
Indices: 1162873--1162909 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1162863 AATTTTATTT
*
1162873 TAATAATAAATTTTAAA
1 TAATAATAAATTTCAAA
1162890 -AATAAT-AATTTCAAA
1 TAATAATAAATTTCAAA
1162905 TAATA
1 TAATA
1162910 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTCAAA
Found at i:1162962 original size:15 final size:15
Alignment explanation
Indices: 1162942--1162997 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1162932 ATTCAATATT
1162942 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1162957 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
1162976 AATATATTAATAATA
1 AATATTTTAATAATA
1162991 AAT-TTTT
1 AATATTTT
1162998 TGTAGTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 3 0.09
15 13 0.39
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1165642 original size:35 final size:35
Alignment explanation
Indices: 1165573--1165771 Score: 285
Period size: 35 Copynumber: 5.7 Consensus size: 35
1165563 TGGAAAAATG
1165573 TGAAACGTAGGTATGGTA-TTTCCATACTGAGTTA
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGTTA
* * *
1165607 TGATACGTAGGCATGGTATTTTCTATACTGAGTTA
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGTTA
* * *
1165642 TGAAATGTAGGTATGGTA-TTTCCATACCGAGCTA
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGTTA
* * * *
1165676 TGATACATAGGTATGGTATTTTCCATACCGAGTTG
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGTTA
*
1165711 TGAAACGTAGGTATGGTATTTTCCATACTGAGTTG
1 TGAAACGTAGGTATGGTATTTTCCATACTGAGTTA
1165746 TGAAACGTAGGTATGGTATTTTCCAT
1 TGAAACGTAGGTATGGTATTTTCCAT
1165772 GAGGAAAACC
Statistics
Matches: 146, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
34 44 0.30
35 102 0.70
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (35 bp):
TGAAACGTAGGTATGGTATTTTCCATACTGAGTTA
Found at i:1165660 original size:69 final size:69
Alignment explanation
Indices: 1165573--1165771 Score: 299
Period size: 69 Copynumber: 2.9 Consensus size: 69
1165563 TGGAAAAATG
* * *
1165573 TGAAACGTAGGTATGGTATTTCCATACTGAGTTATGATACGTAGGCATGGTATTTTCTATACTGA
1 TGAAACGTAGGTATGGTATTTCCATACTGAGTTATGATACGTAGGTATGGTATTTTCCATACCGA
1165638 GTTA
66 GTTA
* * * *
1165642 TGAAATGTAGGTATGGTATTTCCATACCGAGCTATGATACATAGGTATGGTATTTTCCATACCGA
1 TGAAACGTAGGTATGGTATTTCCATACTGAGTTATGATACGTAGGTATGGTATTTTCCATACCGA
*
1165707 GTTG
66 GTTA
* *
1165711 TGAAACGTAGGTATGGTATTTTCCATACTGAGTTGTGAAACGTAGGTATGGTATTTTCCAT
1 TGAAACGTAGGTATGGTA-TTTCCATACTGAGTTATGATACGTAGGTATGGTATTTTCCAT
1165772 GAGGAAAACC
Statistics
Matches: 115, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 78 0.68
70 37 0.32
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (69 bp):
TGAAACGTAGGTATGGTATTTCCATACTGAGTTATGATACGTAGGTATGGTATTTTCCATACCGA
GTTA
Found at i:1165730 original size:104 final size:104
Alignment explanation
Indices: 1165580--1165771 Score: 305
Period size: 104 Copynumber: 1.8 Consensus size: 104
1165570 ATGTGAAACG
* * *
1165580 TAGGTATGGTATTTCCATACTGAGTTATGATACGTAGGCATGGTATTTTCTATACTGAGTTATGA
1 TAGGTATGGTATTTCCATACCGAGTTATGAAACGTAGGCATGGTATTTTCCATACTGAGTTATGA
*
1165645 AATGTAGGTATGGTA-TTTCCATACCGAGCTATGATACA
66 AACGTAGGTATGGTATTTTCCATACCGAGCTATGATACA
* * *
1165683 TAGGTATGGTATTTTCCATACCGAGTTGTGAAACGTAGGTATGGTATTTTCCATACTGAGTTGTG
1 TAGGTATGGTA-TTTCCATACCGAGTTATGAAACGTAGGCATGGTATTTTCCATACTGAGTTATG
1165748 AAACGTAGGTATGGTATTTTCCAT
65 AAACGTAGGTATGGTATTTTCCAT
1165772 GAGGAAAACC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 11 0.14
104 62 0.77
105 7 0.09
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (104 bp):
TAGGTATGGTATTTCCATACCGAGTTATGAAACGTAGGCATGGTATTTTCCATACTGAGTTATGA
AACGTAGGTATGGTATTTTCCATACCGAGCTATGATACA
Found at i:1174651 original size:12 final size:12
Alignment explanation
Indices: 1174634--1174667 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1174624 CAGCCTGCCC
1174634 ATATTAATTTTT
1 ATATTAATTTTT
*
1174646 ATATTATTTTTT
1 ATATTAATTTTT
1174658 ATA-TAATTTT
1 ATATTAATTTT
1174668 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1176663 original size:3 final size:3
Alignment explanation
Indices: 1176618--1176647 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1176608 TATATTATCC
1176618 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1176648 ATATATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1179699 original size:7 final size:7
Alignment explanation
Indices: 1179689--1179776 Score: 83
Period size: 7 Copynumber: 13.0 Consensus size: 7
1179679 AAAAAATAAA
1179689 AAAATTT
1 AAAATTT
1179696 AAAATTT
1 AAAATTT
1179703 AAAATTT
1 AAAATTT
1179710 AAAATTT
1 AAAATTT
* *
1179717 AAAAATA
1 AAAATTT
*
1179724 AAAATTA
1 AAAATTT
*
1179731 AAAATTA
1 AAAATTT
*
1179738 AAAAATT
1 AAAATTT
*
1179745 AAAAATT
1 AAAATTT
1179752 AAAA---
1 AAAATTT
*
1179756 AAAATTA
1 AAAATTT
1179763 AAAATTT
1 AAAATTT
*
1179770 AATATTT
1 AAAATTT
1179777 TAATCAATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
4 4 0.06
7 67 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
AAAATTT
Found at i:1179699 original size:15 final size:15
Alignment explanation
Indices: 1179681--1179765 Score: 55
Period size: 15 Copynumber: 5.3 Consensus size: 15
1179671 ATAAACTCAA
1179681 AAAATAAAAAAATTT
1 AAAATAAAAAAATTT
1179696 AAAATTTAAAATTTAAAATTT
1 AAAA--T-AAA---AAAATTT
* *
1179717 AAAA-ATAAAAATTA
1 AAAATAAAAAAATTT
* *
1179731 AAAATTAAAAAATTA
1 AAAATAAAAAAATTT
*
1179746 AAAATTAAAAAAAATT
1 AAAA-TAAAAAAATTT
1179762 AAAA
1 AAAA
1179766 ATTTAATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
14 10 0.18
15 16 0.29
16 12 0.22
17 3 0.05
18 3 0.05
21 11 0.20
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAAAAAAATTT
Found at i:1181575 original size:114 final size:113
Alignment explanation
Indices: 1181369--1181700 Score: 520
Period size: 114 Copynumber: 2.9 Consensus size: 113
1181359 ATACTAACAC
* *
1181369 AAAATAACTATAAAATTATTTTTTTAAATACATTACTAAAAAAAAATCACAATACACTAATACGC
1 AAAATAGCTATAAAATTATTTTTTTAAATATATTACT--AAAAAAATCACAATACACTAATA--C
1181434 ACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
62 ACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
* * * * *
1181486 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATTCGCTAATATACT
1 AAAATAGCTATAAAATTATTTTTTT-AAATATATTACTAAAAAAATCACAATACACTAATACACT
1181551 AAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
65 AAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
1181600 AAAATAGCTATAAAATTATTTTTTTTAAATATATTACTAAAAAAATCACAATACACTAATACACT
1 AAAATAGCTATAAAATTA-TTTTTTTAAATATATTACTAAAAAAATCACAATACACTAATACACT
** *
1181665 AAATTACTAAACACTAACAATTTATATAACCAAATC
65 AAACCACTAAACACTAACAATTTATATAACCTAATC
1181701 AACTATAAAA
Statistics
Matches: 198, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
114 137 0.69
115 7 0.04
116 20 0.10
117 23 0.12
118 11 0.06
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.33
Consensus pattern (113 bp):
AAAATAGCTATAAAATTATTTTTTTAAATATATTACTAAAAAAATCACAATACACTAATACACTA
AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
Found at i:1181769 original size:93 final size:90
Alignment explanation
Indices: 1181607--1181780 Score: 226
Period size: 101 Copynumber: 1.8 Consensus size: 90
1181597 AATAAAATAG
1181607 CTATAAAATTATTTTTTTTAAATATATTACTAAAAAAATCACAATACACTAATACACTAAATTAC
1 CTATAAAATTATTTTTTTTAAATATATTACTAAAAAAATCACAATACACTAATA-AC---A--AC
1181672 TAAACACTAACAATTTATATAACCAAATCAA
60 TAAACACTAACAATTTATATAACCAAATCAA
*
1181703 CTATAAAATTCTTTTTTTTAAAAATATATTATTACTAAAAAAATCACAATACACTAAT-AC-ACT
1 CTATAAAATTATTTTTTTT---AA-ATA-TATTACTAAAAAAATCACAATACACTAATAACAACT
1181766 AAACACTAACAATTT
61 AAACACTAACAATTT
1181781 GTAACCTAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 13
0.84 0.01 0.15
Matches are distributed among these distances:
93 18 0.25
96 18 0.25
99 4 0.06
100 3 0.04
101 29 0.40
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (90 bp):
CTATAAAATTATTTTTTTTAAATATATTACTAAAAAAATCACAATACACTAATAACAACTAAACA
CTAACAATTTATATAACCAAATCAA
Found at i:1181976 original size:3 final size:3
Alignment explanation
Indices: 1181970--1182007 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1181960 ACCCTTTTTT
*
1181970 TTC TTC TTC TTC TTC TTC TTCC TTC TTC TTC TCC TTC T
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC T
1182008 CCTTTCCCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:1181996 original size:19 final size:18
Alignment explanation
Indices: 1181972--1182011 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1181962 CCTTTTTTTT
*
1181972 CTTCTTCTTCTTCTTCTTC
1 CTTCTTCTTCTCCTTC-TC
1181991 CTTCTTCTTCTCCTTCTC
1 CTTCTTCTTCTCCTTCTC
1182009 CTT
1 CTT
1182012 TCCCTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (18 bp):
CTTCTTCTTCTCCTTCTC
Found at i:1183885 original size:8 final size:8
Alignment explanation
Indices: 1183874--1183898 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1183864 ACTAAGAAAC
1183874 CCTAGCCA
1 CCTAGCCA
1183882 CCTAGCCA
1 CCTAGCCA
1183890 CCTAGCCA
1 CCTAGCCA
1183898 C
1 C
1183899 TTTCCCACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.52, G:0.12, T:0.12
Consensus pattern (8 bp):
CCTAGCCA
Found at i:1184126 original size:18 final size:17
Alignment explanation
Indices: 1184087--1184125 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1184077 CCTAAAGGTG
*
1184087 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
1184104 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
1184121 ATTTT
1 ATTTT
1184126 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:1184190 original size:13 final size:13
Alignment explanation
Indices: 1184172--1184224 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
1184162 TATATACATC
1184172 ATAATAAAAAAAT
1 ATAATAAAAAAAT
*
1184185 ATAATAAAAATAT
1 ATAATAAAAAAAT
*
1184198 ATATACAAAACAAAT
1 ATA-ATAAAA-AAAT
1184213 ATAA-AAAAAAAT
1 ATAATAAAAAAAT
1184225 TACCTTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 4 0.11
13 19 0.54
14 6 0.17
15 6 0.17
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:1187146 original size:9 final size:9
Alignment explanation
Indices: 1187128--1187170 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
1187118 GCTTTTATTT
1187128 ATTTTCTATA
1 ATTTT-TATA
1187138 ATTTTTAT-
1 ATTTTTATA
1187146 ATTTTTAATA
1 ATTTTT-ATA
*
1187156 AATTTTATA
1 ATTTTTATA
1187165 ATTTTT
1 ATTTTT
1187171 TTTATAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 6 0.21
9 13 0.45
10 10 0.34
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:1187177 original size:21 final size:23
Alignment explanation
Indices: 1187147--1187191 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
1187137 AATTTTTATA
1187147 TTTTTAATAAATT-TTATA-ATT
1 TTTTTAATAAATTCTTATATATT
*
1187168 TTTTTTATAAATTCTTATATATT
1 TTTTTAATAAATTCTTATATATT
1187191 T
1 T
1187192 GAAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 5 0.24
23 4 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTAATAAATTCTTATATATT
Found at i:1187419 original size:16 final size:16
Alignment explanation
Indices: 1187398--1187462 Score: 78
Period size: 17 Copynumber: 3.9 Consensus size: 16
1187388 CATGTTACAA
1187398 AAAAATTATAAAAAAT
1 AAAAATTATAAAAAAT
1187414 AAAAATTATAAAAAAAT
1 AAAAATTAT-AAAAAAT
*
1187431 AAAATATTA-AAAATTAT
1 AAAA-ATTATAAAA-AAT
*
1187448 AAAAATCATAAAAAA
1 AAAAATTATAAAAAA
1187463 ATATAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
16 17 0.40
17 21 0.50
18 4 0.10
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAATTATAAAAAAT
Found at i:1187424 original size:9 final size:9
Alignment explanation
Indices: 1187398--1187472 Score: 70
Period size: 9 Copynumber: 8.7 Consensus size: 9
1187388 CATGTTACAA
1187398 AAAAATTAT
1 AAAAATTAT
1187407 AAAAA--AT
1 AAAAATTAT
1187414 AAAAATTAT
1 AAAAATTAT
*
1187423 AAAAA-AAT
1 AAAAATTAT
1187431 -AAAA-TATT
1 AAAAATTA-T
1187439 AAAAATTAT
1 AAAAATTAT
*
1187448 AAAAATCAT
1 AAAAATTAT
*
1187457 AAAAAAATAT
1 -AAAAATTAT
1187467 AAAAAT
1 AAAAAT
1187473 AGTGAAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
7 12 0.22
8 3 0.06
9 30 0.56
10 9 0.17
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAAATTAT
Found at i:1187441 original size:25 final size:24
Alignment explanation
Indices: 1187405--1187462 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
1187395 CAAAAAAATT
1187405 ATAAAAAATAAAAATTATAAAAAA
1 ATAAAAAATAAAAATTATAAAAAA
* *
1187429 ATAAAATATTAAAAATTATAAAAATC
1 ATAAAA-AATAAAAATTATAAAAA-A
1187455 ATAAAAAA
1 ATAAAAAA
1187463 ATATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 17 0.59
26 6 0.21
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (24 bp):
ATAAAAAATAAAAATTATAAAAAA
Found at i:1187464 original size:20 final size:20
Alignment explanation
Indices: 1187439--1187550 Score: 65
Period size: 19 Copynumber: 5.8 Consensus size: 20
1187429 ATAAAATATT
1187439 AAAAATTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
*
1187459 AAAAA-TATAAAAAT-AGT-G
1 AAAAATTATAAAAATCA-TAA
** *
1187477 AAATTTTAT-AAAGTCATAA
1 AAAAATTATAAAAATCATAA
* *
1187496 GAAAATTATAAAAA-AATGCAA
1 AAAAATTATAAAAATCAT--AA
* * *
1187517 AGAAA-TATAAAATTCGTAA
1 AAAAATTATAAAAATCATAA
*
1187536 AAAAAATATAAAAAT
1 AAAAATTATAAAAAT
1187551 TATCATACCA
Statistics
Matches: 66, Mismatches: 17, Indels: 18
0.65 0.17 0.18
Matches are distributed among these distances:
18 9 0.14
19 28 0.42
20 23 0.35
21 6 0.09
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (20 bp):
AAAAATTATAAAAATCATAA
Found at i:1188050 original size:3 final size:3
Alignment explanation
Indices: 1188042--1188070 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1188032 TAAAGACTGC
1188042 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1188071 AACAATTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1190266 original size:9 final size:9
Alignment explanation
Indices: 1190248--1190290 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
1190238 GCTTTTATTT
1190248 ATTTTCTATA
1 ATTTT-TATA
1190258 ATTTTTAT-
1 ATTTTTATA
1190266 ATTTTTAATA
1 ATTTTT-ATA
*
1190276 AATTTTATA
1 ATTTTTATA
1190285 ATTTTT
1 ATTTTT
1190291 TTTATAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 6 0.21
9 13 0.45
10 10 0.34
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:1190297 original size:21 final size:23
Alignment explanation
Indices: 1190267--1190311 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
1190257 AATTTTTATA
1190267 TTTTTAATAAATT-TTATA-ATT
1 TTTTTAATAAATTCTTATATATT
*
1190288 TTTTTTATAAATTCTTATATATT
1 TTTTTAATAAATTCTTATATATT
1190311 T
1 T
1190312 GAAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 5 0.24
23 4 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTAATAAATTCTTATATATT
Found at i:1190559 original size:19 final size:20
Alignment explanation
Indices: 1190517--1190604 Score: 96
Period size: 19 Copynumber: 4.5 Consensus size: 20
1190507 CATGTTACAA
*
1190517 AAAAATTATAAAAAAAATCAAT
1 AAAAATTAT-TAAAAAATC-AT
1190539 AAAAATTATTAAAAAAT-AT
1 AAAAATTATTAAAAAATCAT
1190558 -AAAA-TATT-AAAAATCAT
1 AAAAATTATTAAAAAATCAT
* *
1190575 AAAAATCATAAAAAAAT-AT
1 AAAAATTATTAAAAAATCAT
1190594 AAAAATTATTA
1 AAAAATTATTA
1190605 TACCAAAAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
16 6 0.11
17 6 0.11
18 8 0.14
19 15 0.26
20 6 0.11
21 7 0.12
22 9 0.16
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAATTATTAAAAAATCAT
Found at i:1190565 original size:17 final size:17
Alignment explanation
Indices: 1190536--1190601 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 17
1190526 AAAAAAAATC
1190536 AATA-AAAATTATTAAAA
1 AATATAAAA-TATTAAAA
1190553 AATATAAAATATT-AAA
1 AATATAAAATATTAAAA
*
1190569 AATCATAAAAATCATAAAAA
1 AAT-AT-AAAAT-ATTAAAA
1190589 AATATAAAA-ATTA
1 AATATAAAATATTA
1190602 TTATACCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 9 0.21
17 10 0.24
18 13 0.31
19 4 0.10
20 6 0.14
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AATATAAAATATTAAAA
Found at i:1190578 original size:8 final size:9
Alignment explanation
Indices: 1190529--1190588 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
1190519 AAATTATAAA
1190529 AAAAATCAAT
1 AAAAATC-AT
*
1190539 AAAAATTATT
1 AAAAATCA-T
1190549 AAAAA--AT
1 AAAAATCAT
1190556 ATAAAAT-ATT
1 A-AAAATCA-T
1190566 AAAAATCAT
1 AAAAATCAT
1190575 AAAAATCAT
1 AAAAATCAT
1190584 AAAAA
1 AAAAA
1190589 AATATAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
7 2 0.05
8 5 0.11
9 22 0.50
10 15 0.34
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAAATCAT
Found at i:1190589 original size:36 final size:36
Alignment explanation
Indices: 1190529--1190601 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
1190519 AAATTATAAA
* *
1190529 AAAAATCAATAAAAATTATTAAAAAATATAAAATATT
1 AAAAATCAATAAAAATCATAAAAAAATATAAAA-ATT
1190566 AAAAATC-ATAAAAATCATAAAAAAATATAAAAATT
1 AAAAATCAATAAAAATCATAAAAAAATATAAAAATT
1190601 A
1 A
1190602 TTATACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 4 0.12
36 23 0.68
37 7 0.21
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (36 bp):
AAAAATCAATAAAAATCATAAAAAAATATAAAAATT
Found at i:1190797 original size:27 final size:27
Alignment explanation
Indices: 1190767--1190841 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
1190757 ATGCATTTTA
*
1190767 TAATTTTTTCTAATTTTTAA-TAAAATT
1 TAATTTTTT-TAATTTTTAATTAAAACT
*
1190794 TAATTTTTTT-ATATTTGAATTAAAACT
1 TAATTTTTTTAAT-TTTTAATTAAAACT
1190821 TAATAATTTTTATAATTTTTA
1 TAAT--TTTTT-TAATTTTTA
1190842 TTTATTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 2 0.05
26 6 0.15
27 19 0.49
29 5 0.13
30 5 0.13
31 2 0.05
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (27 bp):
TAATTTTTTTAATTTTTAATTAAAACT
Found at i:1191105 original size:5 final size:5
Alignment explanation
Indices: 1191095--1191120 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1191085 CTTATTTAAC
1191095 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
1191121 AACCTCCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:1191179 original size:3 final size:3
Alignment explanation
Indices: 1191171--1191209 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1191161 TCTTCAGTGG
1191171 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1191210 AACAATTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1194861 original size:29 final size:29
Alignment explanation
Indices: 1194819--1194876 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1194809 ATAAATTTAT
1194819 TCACTTATGACGTTCATAGTGTGGAATAC
1 TCACTTATGACGTTCATAGTGTGGAATAC
1194848 TCACTTATGACGTTCATAGTGTGGAATAC
1 TCACTTATGACGTTCATAGTGTGGAATAC
1194877 CCAAGCGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (29 bp):
TCACTTATGACGTTCATAGTGTGGAATAC
Found at i:1196829 original size:6 final size:6
Alignment explanation
Indices: 1196818--1196847 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1196808 CCCTTGTGCG
1196818 TACTGA TACTGA TACTGA TACTGA TACTGA
1 TACTGA TACTGA TACTGA TACTGA TACTGA
1196848 AAGAGGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (6 bp):
TACTGA
Found at i:1197046 original size:7 final size:7
Alignment explanation
Indices: 1197027--1197060 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1197017 TTTTTGGGCT
*
1197027 TTTACGA
1 TTTATGA
1197034 TTTATGA
1 TTTATGA
*
1197041 TCTATGA
1 TTTATGA
1197048 TTTATGA
1 TTTATGA
1197055 TTTATG
1 TTTATG
1197061 GTTTTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (7 bp):
TTTATGA
Found at i:1197739 original size:7 final size:7
Alignment explanation
Indices: 1197697--1197753 Score: 70
Period size: 6 Copynumber: 8.9 Consensus size: 7
1197687 GGTTTTCTCA
1197697 AAATG-G
1 AAATGAG
1197703 AAATG-G
1 AAATGAG
1197709 AAATG-G
1 AAATGAG
*
1197715 AAGTG-G
1 AAATGAG
1197721 AAATGA-
1 AAATGAG
1197727 AAATGAG
1 AAATGAG
1197734 AAATGAG
1 AAATGAG
1197741 AAATGAG
1 AAATGAG
1197748 AAATGA
1 AAATGA
1197754 TTCATTTGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
6 27 0.57
7 20 0.43
ACGTcount: A:0.54, C:0.00, G:0.30, T:0.16
Consensus pattern (7 bp):
AAATGAG
Found at i:1200458 original size:52 final size:48
Alignment explanation
Indices: 1200379--1200585 Score: 195
Period size: 47 Copynumber: 4.2 Consensus size: 48
1200369 CCATGACAGC
* * * * *
1200379 ATGTGAAATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCTTCGG
1 ATGTGATATGTG-CTTCCGTATAAGACCATATCTGGGATATGGCATCGG
*
1200428 ACAAATGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGG
1 ----ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG
* * *
1200480 -TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG
* * * ** * *
1200527 -TGTGATACGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCGG
1 ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG
1200573 TATGTGATATGTG
1 -ATGTGATATGTG
1200586 ACTATGTGCA
Statistics
Matches: 131, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
46 26 0.20
47 53 0.40
48 10 0.08
52 31 0.24
53 11 0.08
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (48 bp):
ATGTGATATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG
Found at i:1203189 original size:60 final size:60
Alignment explanation
Indices: 1203122--1203260 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 60
1203112 CCAACTGTGT
* *
1203122 TGATATGGGCAAGGCCCAATATA-TCTCGA-CTTGTAATAGGGCTACGGCCCAGATTGATAC
1 TGATATGGGCAAGGCCCAATATACTCT-GATATTGTAA-AGGGCTACGGCCCAGATTAATAC
* * * *
1203182 TGATATGGGCTAGGCCCAATATACTCTGATATTGTAAGGGGCTATGGCCCAGATTAATAT
1 TGATATGGGCAAGGCCCAATATACTCTGATATTGTAAAGGGCTACGGCCCAGATTAATAC
1203242 TGATATGGGCTAAGGCCCA
1 TGATATGGGC-AAGGCCCA
1203261 GTTAACACTA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
60 53 0.77
61 16 0.23
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (60 bp):
TGATATGGGCAAGGCCCAATATACTCTGATATTGTAAAGGGCTACGGCCCAGATTAATAC
Found at i:1203251 original size:28 final size:27
Alignment explanation
Indices: 1203160--1203265 Score: 74
Period size: 28 Copynumber: 3.7 Consensus size: 27
1203150 ACTTGTAATA
* *
1203160 GGGCTACGGCCCAGATTGATACTGATAT
1 GGGCTA-GGCCCAGATTAATATTGATAT
*
1203188 GGGCTAGGCCCA-ATATACTCTGATATTG-TAAG
1 GGGCTAGGCCCAGAT-TA-----ATATTGAT-AT
1203220 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTA-GGCCCAGATTAATATTGATAT
1203248 GGGCTAAGGCCCAG-TTAA
1 GGGCT-AGGCCCAGATTAA
1203266 CACTAAATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
26 2 0.03
27 11 0.17
28 25 0.40
29 2 0.03
31 1 0.02
32 12 0.19
33 8 0.13
34 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (27 bp):
GGGCTAGGCCCAGATTAATATTGATAT
Found at i:1205458 original size:24 final size:26
Alignment explanation
Indices: 1205402--1205469 Score: 95
Period size: 24 Copynumber: 2.7 Consensus size: 26
1205392 GTCTCACCGT
1205402 AGCTCGTATGAGCTTACTGATATATC
1 AGCTCGTATGAGCTTACTGATATATC
* * *
1205428 AGCTCGTAAGATCTTACTG-T-TCTC
1 AGCTCGTATGAGCTTACTGATATATC
1205452 AGCTCGTATGAGCTTACT
1 AGCTCGTATGAGCTTACT
1205470 AATTTAGCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 19 0.51
25 1 0.03
26 17 0.46
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (26 bp):
AGCTCGTATGAGCTTACTGATATATC
Found at i:1206163 original size:19 final size:17
Alignment explanation
Indices: 1206115--1206163 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1206105 GTGATTTGGC
1206115 TTAATTTGGTATAATGT
1 TTAATTTGGTATAATGT
**
1206132 TTAGGTTGTGTATAAGTGT
1 TTAATTTG-GTATAA-TGT
1206151 TTAATTATGGTAT
1 TTAATT-TGGTAT
1206164 GTTTTGACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.24
18 6 0.24
19 11 0.44
20 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAATTTGGTATAATGT
Found at i:1207049 original size:20 final size:21
Alignment explanation
Indices: 1207010--1207057 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 21
1207000 TAAGGGACAA
*
1207010 ATTGTTTGAGTTTGAATGATG
1 ATTGTATGAGTTTGAATGATG
1207031 ATTGTATGA-TTTG-AT--TG
1 ATTGTATGAGTTTGAATGATG
1207048 ATTGTATGAG
1 ATTGTATGAG
1207058 AAAAGTACAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 11 0.44
19 2 0.08
20 4 0.16
21 8 0.32
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (21 bp):
ATTGTATGAGTTTGAATGATG
Found at i:1214585 original size:26 final size:24
Alignment explanation
Indices: 1214556--1214670 Score: 114
Period size: 23 Copynumber: 4.8 Consensus size: 24
1214546 GGACTCACCG
1214556 CAGCTCGTATGAGCTTACTGATATAT
1 CAGCTCGTATGAGCTTACTGAT-T-T
*
1214582 CAGCTCGTAAGAGCTTACTG-TTCT
1 CAGCTCGTATGAGCTTACTGATT-T
*
1214606 TAGCTCGTATGAGCTTACTGATTT
1 CAGCTCGTATGAGCTTACTGATTT
*
1214630 -AGCTCGTCA-GAGCTTACCG-TTT
1 CAGCTCGT-ATGAGCTTACTGATTT
*
1214652 CAGCTC-AATAGAGCTTACT
1 CAGCTCGTAT-GAGCTTACT
1214671 ATCCATCAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
21 1 0.01
22 3 0.04
23 29 0.38
24 22 0.29
25 3 0.04
26 19 0.25
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACTGATTT
Found at i:1217673 original size:42 final size:42
Alignment explanation
Indices: 1217603--1217702 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
1217593 GAAATGAGAA
* * * *
1217603 TACGTGTAAGACCATATCTGGGATATGGCATC-ATTATGATAT
1 TACGTGTAAGACCATATCTGAGACATGGCATCGA-TACGAAAT
*
1217645 TACGTGTAAGACCATGTCTGAGACATGGCATCGATACGAAAT
1 TACGTGTAAGACCATATCTGAGACATGGCATCGATACGAAAT
*
1217687 TTCGTGTAAGACCATA
1 TACGTGTAAGACCATA
1217703 GTTGGGCTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (42 bp):
TACGTGTAAGACCATATCTGAGACATGGCATCGATACGAAAT
Found at i:1217758 original size:85 final size:84
Alignment explanation
Indices: 1217605--1217760 Score: 192
Period size: 85 Copynumber: 1.8 Consensus size: 84
1217595 AATGAGAATA
* * * * *
1217605 CGTGTAAGACCATATCTGGGATATGGCATCATTATGATATTACGTGTAAGACCATGTCTGAGACA
1 CGTGTAAGACCATATCTGGGATATGGCATCATTAAGATATTACATGTAAGACCATATCCGAAACA
1217670 TGGCATCGATACGAAATTT
66 TGGCATCGATACGAAATTT
*
1217689 CGTGTAAGACCATAGT-TGGGCTATTGGCATCGATATAAG-T-TTACATGTAAGACCATATCCGA
1 CGTGTAAGACCATA-TCTGGGATA-TGGCATC-AT-TAAGATATTACATGTAAGACCATATCCGA
*
1217751 AATATGGCAT
62 AACATGGCAT
1217761 TGTACGACCT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
84 20 0.33
85 35 0.57
86 3 0.05
87 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (84 bp):
CGTGTAAGACCATATCTGGGATATGGCATCATTAAGATATTACATGTAAGACCATATCCGAAACA
TGGCATCGATACGAAATTT
Found at i:1222193 original size:18 final size:18
Alignment explanation
Indices: 1222170--1222227 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1222160 TTTGTTTATT
*
1222170 GTTATTCAATAACAATCA
1 GTTATTCAATAACAAACA
*
1222188 GTTATTCAATATCAAACA
1 GTTATTCAATAACAAACA
*
1222206 ---A-TCAATAACAACCA
1 GTTATTCAATAACAAACA
1222220 GTTATTCA
1 GTTATTCA
1222228 GTCCAGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 11 0.34
15 1 0.03
17 1 0.03
18 19 0.59
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (18 bp):
GTTATTCAATAACAAACA
Found at i:1222502 original size:44 final size:44
Alignment explanation
Indices: 1222413--1222502 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
1222403 GAAGTAACAA
* * **
1222413 TAACAGTACGACACACATGGTGCCTCATCGACTCGAAGTTGAAG
1 TAACAGTACGACACACATAGTGCCTCATCAACTCGAAGTCAAAG
**
1222457 TAACAGTACGACACTTATAGTGCCTCATCAACTC-AAGGTCAAAG
1 TAACAGTACGACACACATAGTGCCTCATCAACTCGAA-GTCAAAG
1222501 TA
1 TA
1222503 TCCCTAAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 2 0.05
44 37 0.95
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (44 bp):
TAACAGTACGACACACATAGTGCCTCATCAACTCGAAGTCAAAG
Found at i:1223400 original size:5 final size:5
Alignment explanation
Indices: 1223387--1223423 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
1223377 TTCTTTAGTT
1223387 TATATA TATAA TAT-A -ATAA TATAA TATAA TATAA TAT
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TAT
1223424 TTTATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 21 0.72
6 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:1223408 original size:13 final size:13
Alignment explanation
Indices: 1223392--1223417 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1223382 TAGTTTATAT
1223392 ATATAATATAATA
1 ATATAATATAATA
1223405 ATATAATATAATA
1 ATATAATATAATA
1223418 TAATATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:1223415 original size:18 final size:19
Alignment explanation
Indices: 1223387--1223422 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1223377 TTCTTTAGTT
1223387 TATATATATAATATAATAA
1 TATATATATAATATAATAA
1223406 TATA-ATATAATATAATA
1 TATATATATAATATAATA
1223423 TTTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATATATAATATAATAA
Found at i:1223463 original size:42 final size:42
Alignment explanation
Indices: 1223406--1223491 Score: 109
Period size: 47 Copynumber: 1.9 Consensus size: 42
1223396 AATATAATAA
* *
1223406 TATAATATAATATAATATTTTATAATTAAAACATAAAATATCTTTAT
1 TATAAAATAATATAATA--ATAT-ATT-AAACATAAAA-ATCTTTAT
1223453 TATAAAATAATATAATAATATATTAAACATAAAAATCTT
1 TATAAAATAATATAATAATATATTAAACATAAAAATCTT
1223492 AAATTTTCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
42 5 0.14
43 10 0.27
44 3 0.08
45 3 0.08
47 16 0.43
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (42 bp):
TATAAAATAATATAATAATATATTAAACATAAAAATCTTTAT
Found at i:1229235 original size:8 final size:8
Alignment explanation
Indices: 1229219--1229250 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1229209 AATATGAAAT
*
1229219 TAATGATA
1 TAATAATA
1229227 TAATAATA
1 TAATAATA
1229235 TAATAATA
1 TAATAATA
1229243 TAATAATA
1 TAATAATA
1229251 AGCATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATAATA
Found at i:1234218 original size:60 final size:60
Alignment explanation
Indices: 1234117--1234260 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 60
1234107 TTTAGTGTTA
* *
1234117 ACTGGGCCTTAGCCCATATCAATATTAATCTAGGCCATAGCCC-CTTAC-AGTAAC-AGAGTAT
1 ACTGGGCC-TAGCCCATATCAATATCAATCTAGGCCATAGCCCTATTACAAGT--CGAGA-TAT
* * *
1234178 ACTGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATAT
1 ACTGGGCCTAGCCCATATCAATATCAATCTAGGCCATAGCCCTATTACAAGTCGAGATAT
* *
1234238 ATTGGGCCTTGCCCATATCAATA
1 ACTGGGCCTAGCCCATATCAATA
1234261 CAGTTGGACC
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
60 54 0.75
61 15 0.21
62 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (60 bp):
ACTGGGCCTAGCCCATATCAATATCAATCTAGGCCATAGCCCTATTACAAGTCGAGATAT
Found at i:1241352 original size:2 final size:2
Alignment explanation
Indices: 1241345--1241383 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1241335 TACCCTTAAT
*
1241345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
1241384 CTAATTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1242021 original size:21 final size:20
Alignment explanation
Indices: 1241992--1242034 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1241982 TGAATTTTTT
*
1241992 TTGAATCAAGTTGAGTAAAA
1 TTGAATCAAATTGAGTAAAA
*
1242012 TTGAATTCAAATTGAGTTAAA
1 TTGAA-TCAAATTGAGTAAAA
1242033 TT
1 TT
1242035 AAAAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (20 bp):
TTGAATCAAATTGAGTAAAA
Found at i:1242613 original size:19 final size:19
Alignment explanation
Indices: 1242591--1242659 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
1242581 TAAACTAAGT
1242591 TTTTAGCTGAGTTACCTTC
1 TTTTAGCTGAGTTACCTTC
*
1242610 TTTTAGCTGAGTTA-C--A
1 TTTTAGCTGAGTTACCTTC
*
1242626 TTTGAGCATTGAGTTACCTTC
1 TTTTAGC--TGAGTTACCTTC
*
1242647 TTTTTGCTGAGTT
1 TTTTAGCTGAGTT
1242660 CTTGCTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 6 0.15
18 8 0.20
19 21 0.52
21 5 0.12
ACGTcount: A:0.17, C:0.16, G:0.19, T:0.48
Consensus pattern (19 bp):
TTTTAGCTGAGTTACCTTC
Found at i:1243691 original size:18 final size:18
Alignment explanation
Indices: 1243668--1243703 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1243658 TAATATATAT
1243668 TAACCCAAGTACCCAACC
1 TAACCCAAGTACCCAACC
*
1243686 TAACCCAATTACCCAACC
1 TAACCCAAGTACCCAACC
1243704 CAATCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.44, G:0.03, T:0.14
Consensus pattern (18 bp):
TAACCCAAGTACCCAACC
Found at i:1243743 original size:6 final size:6
Alignment explanation
Indices: 1243732--1243771 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1243722 ATAATTTAAT
* *
1243732 AAATAA AAATAA AATCTAA AACTAA AAATAA AAATAA AAA
1 AAATAA AAATAA AA-ATAA AAATAA AAATAA AAATAA AAA
1243772 GCATACAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:1243771 original size:19 final size:18
Alignment explanation
Indices: 1243732--1243771 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1243722 ATAATTTAAT
*
1243732 AAATAAAAATAAAATCTAA
1 AAATAAAAATAAAA-ATAA
*
1243751 AACTAAAAATAAAAATAA
1 AAATAAAAATAAAAATAA
1243769 AAA
1 AAA
1243772 GCATACAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATAAAAATAAAAATAA
Found at i:1243830 original size:9 final size:9
Alignment explanation
Indices: 1243791--1243849 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 9
1243781 TTTATACAAA
1243791 TAATTCGGT
1 TAATTCGGT
** *
1243800 TAATTTAGA
1 TAATTCGGT
* *
1243809 TAACTCGGG
1 TAATTCGGT
1243818 TAATTCGGT
1 TAATTCGGT
*
1243827 TAATTCGAT
1 TAATTCGGT
1243836 TAATTCGGT
1 TAATTCGGT
1243845 TAATT
1 TAATT
1243850 TTATACTTCT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (9 bp):
TAATTCGGT
Found at i:1244446 original size:27 final size:27
Alignment explanation
Indices: 1244382--1244435 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1244372 CACAAAAAAA
*
1244382 AGTATGATTTTCATTATTATTTGATGT
1 AGTATGATTTTCTTTATTATTTGATGT
1244409 AGTATGATTTTCTTTATTATTTGATGT
1 AGTATGATTTTCTTTATTATTTGATGT
1244436 TTGATAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.15, T:0.57
Consensus pattern (27 bp):
AGTATGATTTTCTTTATTATTTGATGT
Found at i:1244785 original size:23 final size:23
Alignment explanation
Indices: 1244725--1244788 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
1244715 ATCAATTATC
* *
1244725 ATTTAATTAA-TAAATATATATT
1 ATTTAATAAATTAAAAATATATT
*
1244747 -TTTAAAAAAAATTTAAAAATATATT
1 ATTT--AATAAA-TTAAAAATATATT
1244772 ATTTAATAAATTAAAAA
1 ATTTAATAAATTAAAAA
1244789 ATTAATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
21 3 0.09
23 11 0.33
24 5 0.15
25 11 0.33
26 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTAATAAATTAAAAATATATT
Found at i:1248408 original size:18 final size:20
Alignment explanation
Indices: 1248371--1248415 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1248361 CTATAGAAAA
*
1248371 ATAAAAATTACAAAAGTATT
1 ATAAAAATAACAAAAGTATT
*
1248391 A-AAAAATAACTAAA-TATT
1 ATAAAAATAACAAAAGTATT
1248409 ATAAAAA
1 ATAAAAA
1248416 CTTAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 16 0.73
20 1 0.05
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (20 bp):
ATAAAAATAACAAAAGTATT
Found at i:1251346 original size:14 final size:14
Alignment explanation
Indices: 1251327--1251356 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1251317 CAAGTAAGAA
*
1251327 AAGGTTAAAAGTTT
1 AAGGTTAAAAGGTT
1251341 AAGGTTAAAAGGTT
1 AAGGTTAAAAGGTT
1251355 AA
1 AA
1251357 AAAAATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (14 bp):
AAGGTTAAAAGGTT
Found at i:1252576 original size:31 final size:31
Alignment explanation
Indices: 1252522--1252587 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
1252512 CTTGTCACTT
* * *
1252522 GTAGCCGAAGCTATCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
* * *
1252553 GTAGCCGGAGCTACCATTTTTCACTAATCAA
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
1252584 GTAG
1 GTAG
1252588 TCGATGATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTAATCAA
Found at i:1252693 original size:50 final size:50
Alignment explanation
Indices: 1252599--1252825 Score: 346
Period size: 50 Copynumber: 4.5 Consensus size: 50
1252589 CGATGATCAG
* * * * *
1252599 GTAGCCGAAGCTACCACTTTTTACTTGCCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCCTTGATCAGATAAGT
* *
1252650 GTAGCTGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
* * *
1252700 GTAGCCAAAGCTATCACTTATCACTTTCACTTATCCTTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
*
1252750 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1252800 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
1252826 GTTGCCATGG
Statistics
Matches: 162, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
50 140 0.86
51 22 0.14
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
Found at i:1257914 original size:26 final size:26
Alignment explanation
Indices: 1257870--1257978 Score: 112
Period size: 26 Copynumber: 4.1 Consensus size: 26
1257860 ATTTTATTAC
* * *
1257870 AATAAAAAAATATTAAAAATATAGAA
1 AATAGAAAAATATTTAAAATATAAAA
* * *
1257896 ATTATAAAAATATTCAAAATCATAAAAA
1 AATAGAAAAATATTTAAAAT-AT-AAAA
1257924 AATAGAAAAATATTGTAAAA-ATAAAA
1 AATAGAAAAATATT-TAAAATATAAAA
*
1257950 AATAGAAAAATATTTAAAATTTAGAAA
1 AATAGAAAAATATTTAAAATATA-AAA
1257977 AA
1 AA
1257979 ATTTGTTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
25 5 0.07
26 37 0.53
27 9 0.13
28 15 0.21
29 4 0.06
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (26 bp):
AATAGAAAAATATTTAAAATATAAAA
Found at i:1257932 original size:18 final size:18
Alignment explanation
Indices: 1257883--1257932 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1257873 AAAAAAATAT
*
1257883 TAAAAATATAG-AAATTA
1 TAAAAATATAGAAAATCA
**
1257900 TAAAAATATTCAAAATCA
1 TAAAAATATAGAAAATCA
*
1257918 TAAAAAAATAGAAAA
1 TAAAAATATAGAAAA
1257933 ATATTGTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (18 bp):
TAAAAATATAGAAAATCA
Found at i:1257987 original size:21 final size:20
Alignment explanation
Indices: 1257955--1258008 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1257945 TAAAAAATAG
* *
1257955 AAAAATATTTAAAA-TTTAGA
1 AAAAATTTTTAAAACTATA-A
1257975 AAAAATTTGTTAAAACTATAA
1 AAAAATTT-TTAAAACTATAA
1257996 AAAAATTATTTAA
1 AAAAATT-TTTAA
1258009 TTTGTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 18 0.62
22 4 0.14
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAAATTTTTAAAACTATAA
Found at i:1258876 original size:9 final size:9
Alignment explanation
Indices: 1258862--1258918 Score: 64
Period size: 9 Copynumber: 6.2 Consensus size: 9
1258852 GGAGATTAAA
1258862 TTTTATAAT
1 TTTTATAAT
1258871 TTTTAT-AT
1 TTTTATAAT
*
1258879 TTTAATAAACT
1 TTTTAT-AA-T
1258890 TTTTATAAT
1 TTTTATAAT
1258899 TTTTAT-AT
1 TTTTATAAT
1258907 TTTTAATAAT
1 TTTT-ATAAT
1258917 TT
1 TT
1258919 GAATATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 13 0.32
9 15 0.37
10 7 0.17
11 6 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1258918 original size:10 final size:10
Alignment explanation
Indices: 1258862--1259037 Score: 51
Period size: 9 Copynumber: 18.5 Consensus size: 10
1258852 GGAGATTAAA
1258862 TTTT-ATAAT
1 TTTTAATAAT
1258871 TTTT-AT-A-
1 TTTTAATAAT
1258878 TTTTAATAAACT
1 TTTTAAT-AA-T
1258890 TTTT-ATAAT
1 TTTTAATAAT
1258899 TTTT-AT-AT
1 TTTTAATAAT
1258907 TTTTAATAA-
1 TTTTAATAAT
*
1258916 TTTGAAT-AT
1 TTTTAATAAT
* *
1258925 TTTAAACAAGT
1 TTTTAATAA-T
*
1258936 TTATAATGAAT
1 TTTTAAT-AAT
* * *
1258947 TTTAAACAGT
1 TTTTAATAAT
1258957 TTTCT-AT-AT
1 TTT-TAATAAT
* *
1258966 TTTTCATAAA
1 TTTTAATAAT
*
1258976 TTTAAAT-AT
1 TTTTAATAAT
1258985 TTTT-ATAAAT
1 TTTTAAT-AAT
* *
1258995 TTTGAA-CAT
1 TTTTAATAAT
1259004 TTTTAA-AAT
1 TTTTAATAAT
* *
1259013 TTTTATTGA-
1 TTTTAATAAT
1259022 TTTTAATAAAT
1 TTTTAAT-AAT
1259033 TTTTA
1 TTTTA
1259038 TCATTTTCAC
Statistics
Matches: 121, Mismatches: 26, Indels: 38
0.65 0.14 0.21
Matches are distributed among these distances:
7 4 0.03
8 13 0.11
9 56 0.46
10 24 0.20
11 18 0.15
12 6 0.05
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:1259043 original size:19 final size:19
Alignment explanation
Indices: 1258964--1259044 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
1258954 AGTTTTCTAT
**
1258964 ATTTTTCATAAATTTAAAT-
1 ATTTTT-ATAAATTTTTATC
* *
1258983 ATTTTTATAAATTTTGAAC
1 ATTTTTATAAATTTTTATC
*
1259002 ATTTTTA-AAATTTTTATTG
1 ATTTTTATAAATTTTTA-TC
*
1259021 ATTTTAATAAATTTTTATC
1 ATTTTTATAAATTTTTATC
1259040 ATTTT
1 ATTTT
1259045 CACCATGTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
18 17 0.33
19 25 0.49
20 9 0.18
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTTATAAATTTTTATC
Found at i:1268307 original size:34 final size:34
Alignment explanation
Indices: 1268264--1268333 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1268254 CGACATGAGC
1268264 ACAGATTCCCTGCACAATGTAACAGTTAAAAAAT
1 ACAGATTCCCTGCACAATGTAACAGTTAAAAAAT
1268298 ACAGATTCCCTGCACAATGTAACAGTTAAAAAAT
1 ACAGATTCCCTGCACAATGTAACAGTTAAAAAAT
1268332 AC
1 AC
1268334 TTTTCACATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.23
Consensus pattern (34 bp):
ACAGATTCCCTGCACAATGTAACAGTTAAAAAAT
Found at i:1269817 original size:21 final size:20
Alignment explanation
Indices: 1269762--1269819 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1269752 TAAAAAATTA
*
1269762 ATTTAATTGATTCAATCAAT
1 ATTTAATTGATTTAATCAAT
1269782 ATTTAATTGATTTTAATCAAT
1 ATTTAATTGA-TTTAATCAAT
* *
1269803 TTTTAGTTCGATTTAAT
1 ATTTAATT-GATTTAAT
1269820 TAGTTCGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.30
21 21 0.64
22 2 0.06
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTAATTGATTTAATCAAT
Found at i:1270190 original size:34 final size:32
Alignment explanation
Indices: 1270130--1270192 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
1270120 TTTAATGTTG
*
1270130 TTTAATTTTTCTATTTTATTGCTATATATTAA
1 TTTAATTTTTCTATTTTATTACTATATATTAA
* *
1270162 TTTAATATTTTGTATTTTTTTACTTATATAT
1 TTTAAT-TTTTCTATTTTATTAC-TATATAT
1270193 GCGAAAGATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 6 0.23
33 13 0.50
34 7 0.27
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (32 bp):
TTTAATTTTTCTATTTTATTACTATATATTAA
Found at i:1272978 original size:37 final size:37
Alignment explanation
Indices: 1272936--1273007 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
1272926 CCCTTATAAT
1272936 CAGGCCTAGCCGAATTTACTAGATGCTTATAGCAAAC
1 CAGGCCTAGCCGAATTTACTAGATGCTTATAGCAAAC
1272973 CAGGCCTAGCCGAATTTACTAGATGCTTATAGCAA
1 CAGGCCTAGCCGAATTTACTAGATGCTTATAGCAA
1273008 CCCATATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (37 bp):
CAGGCCTAGCCGAATTTACTAGATGCTTATAGCAAAC
Found at i:1275204 original size:18 final size:18
Alignment explanation
Indices: 1275177--1275232 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
1275167 AAAAAAAATC
1275177 AAAATAATTTTCAAAAATTT
1 AAAAT-ATTTT-AAAAATTT
*
1275197 -AAATATTTTTTAAAATTT
1 AAAATA-TTTTAAAAATTT
1275215 AAAATATTTATAAAAATT
1 AAAATATTT-TAAAAATT
1275233 CCAAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATATTTTAAAAATTT
Found at i:1275264 original size:10 final size:10
Alignment explanation
Indices: 1275249--1275287 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
1275239 TTTATATTTT
1275249 AAAAATTATA
1 AAAAATTATA
1275259 AAAAATATATA
1 AAAAAT-TATA
1275270 AAGAAATT-TA
1 AA-AAATTATA
1275280 AAAAATTA
1 AAAAATTA
1275288 ATCGTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 5 0.19
10 10 0.38
11 7 0.27
12 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:1275267 original size:23 final size:24
Alignment explanation
Indices: 1275218--1275268 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
1275208 AAAATTTAAA
* **
1275218 ATATTTATAAAAATTCCAAAATTT
1 ATATTTATAAAAATTACAAAAAAT
*
1275242 ATATTT-TAAAAATTATAAAAAAT
1 ATATTTATAAAAATTACAAAAAAT
1275265 ATAT
1 ATAT
1275269 AAAGAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATTTATAAAAATTACAAAAAAT
Found at i:1275371 original size:3 final size:3
Alignment explanation
Indices: 1275363--1275396 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1275353 CTAAAGTTAC
1275363 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1275397 TTGCTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1278728 original size:9 final size:10
Alignment explanation
Indices: 1278714--1278751 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 10
1278704 ATCATATTAT
1278714 TTTTAAAT-A
1 TTTTAAATAA
1278723 TTTTAAATAA
1 TTTTAAATAA
1278733 TTTTTTAAATAA
1 --TTTTAAATAA
1278745 TTTTAAA
1 TTTTAAA
1278752 GATATAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.31
10 8 0.31
12 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:1278740 original size:12 final size:12
Alignment explanation
Indices: 1278723--1278748 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1278713 TTTTTAAATA
1278723 TTTTAAATAATT
1 TTTTAAATAATT
1278735 TTTTAAATAATT
1 TTTTAAATAATT
1278747 TT
1 TT
1278749 AAAGATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAAATAATT
Found at i:1279459 original size:22 final size:21
Alignment explanation
Indices: 1279405--1279461 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1279395 TTTGGATTTG
1279405 ATTTGGCTCTATTAAAAGATA
1 ATTTGGCTCTATTAAAAGATA
1279426 ATTTGGCTCTATTAAAAGATA
1 ATTTGGCTCTATTAAAAGATA
*
1279447 ATTTTGCTGCTATTA
1 ATTTGGCT-CTATTA
1279462 CTAACTCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (21 bp):
ATTTGGCTCTATTAAAAGATA
Found at i:1288907 original size:63 final size:63
Alignment explanation
Indices: 1288829--1288957 Score: 222
Period size: 63 Copynumber: 2.0 Consensus size: 63
1288819 TCCAACTGAG
* * *
1288829 TATGTTCTGTTAACTATTATGTAACTGCTGTAACGCTAATTAAGTTGCGTGCACATACACAGT
1 TATGTTCCGTTAACTATTATGTAACCGCTGTAACGCTAATGAAGTTGCGTGCACATACACAGT
*
1288892 TATGTTCCGTTAACTATTATGTAACCGCTGTAACGCTAATGAAGTTGTGTGCACATACACAGT
1 TATGTTCCGTTAACTATTATGTAACCGCTGTAACGCTAATGAAGTTGCGTGCACATACACAGT
1288955 TAT
1 TAT
1288958 CAAGAAGACA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (63 bp):
TATGTTCCGTTAACTATTATGTAACCGCTGTAACGCTAATGAAGTTGCGTGCACATACACAGT
Found at i:1295179 original size:5 final size:5
Alignment explanation
Indices: 1295169--1295212 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
1295159 AACAACTTAA
*
1295169 ATAAT ATAAT ATGAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
1295213 ACTTAATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:1295229 original size:10 final size:10
Alignment explanation
Indices: 1295169--1295229 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
1295159 AACAACTTAA
*
1295169 ATAATATAAT
1 ATAAAATAAT
* *
1295179 ATGATATAAT
1 ATAAAATAAT
*
1295189 ATAATATAAT
1 ATAAAATAAT
*
1295199 ATAATATAAT
1 ATAAAATAAT
*
1295209 ATAAACTTAAT
1 ATAAA-ATAAT
*
1295220 CTAAAATAAT
1 ATAAAATAAT
1295230 TTGAAATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
10 36 0.82
11 8 0.18
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (10 bp):
ATAAAATAAT
Found at i:1313629 original size:51 final size:51
Alignment explanation
Indices: 1313548--1313654 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 51
1313538 TGATATGAGG
* ** *
1313548 TTGGAGCAGGCTGTTGAATCAAGAAAAGAAGTTGGAATATCGGGGAGAAGT
1 TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCGGGGAGAAGT
* * *
1313599 TTGGAACAGGCTGCCGAATCTAGAAGAGAAGTTGGAATAGCTGGGAGAAGT
1 TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCGGGGAGAAGT
1313650 TTGGA
1 TTGGA
1313655 GCCGAGCCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.34, C:0.09, G:0.36, T:0.21
Consensus pattern (51 bp):
TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCGGGGAGAAGT
Found at i:1325074 original size:19 final size:20
Alignment explanation
Indices: 1325047--1325087 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1325037 AACAAACTTT
1325047 AATTAAAATCCAATTAATGG
1 AATTAAAATCCAATTAATGG
* *
1325067 AATT-AAATTCATTTAATGG
1 AATTAAAATCCAATTAATGG
1325086 AA
1 AA
1325088 ATTTAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (20 bp):
AATTAAAATCCAATTAATGG
Done.