Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008312.1 Hibiscus syriacus cultivar Beakdansim tig00111005_pilon, 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: 1258310
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1145264 original size:3 final size:3
Alignment explanation
Indices: 1145256--1145281 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1145246 GAATAAAAAC
1145256 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1145282 TGAGGATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1147238 original size:20 final size:20
Alignment explanation
Indices: 1147213--1147282 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
1147203 AGAAAAATCA
*
1147213 GATTCCCCCCAGAGGGTACC
1 GATTCCCCCCAGGGGGTACC
* *
1147233 GATTCCCCCCAGGGGGAACA
1 GATTCCCCCCAGGGGGTACC
1147253 GATTCCCCCCAGGGGGTACC
1 GATTCCCCCCAGGGGGTACC
1147273 GATTCCCCCC
1 GATTCCCCCC
1147283 TGTCTAACGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.19, C:0.41, G:0.26, T:0.14
Consensus pattern (20 bp):
GATTCCCCCCAGGGGGTACC
Found at i:1152215 original size:30 final size:30
Alignment explanation
Indices: 1152179--1152246 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
1152169 ACTGCAAGTC
1152179 CCATCAACGTGCGTTCCACCA-GTGCCTGCT
1 CCATCAACGTGCGTTCCACCATGTG-CTGCT
* *
1152209 CCATCAACGTGTGTTCCACCATGTGCTTCT
1 CCATCAACGTGCGTTCCACCATGTGCTGCT
1152239 CCATCAAC
1 CCATCAAC
1152247 ACATGACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.19, C:0.38, G:0.16, T:0.26
Consensus pattern (30 bp):
CCATCAACGTGCGTTCCACCATGTGCTGCT
Found at i:1154183 original size:20 final size:20
Alignment explanation
Indices: 1154158--1154198 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1154148 CTTATTTCCT
1154158 GGAGCTCACGCAAGCAACAA
1 GGAGCTCACGCAAGCAACAA
1154178 GGAGCTCACGCAAGCAACAA
1 GGAGCTCACGCAAGCAACAA
1154198 G
1 G
1154199 TTGTTTCTCG
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:0.39, C:0.29, G:0.27, T:0.05
Consensus pattern (20 bp):
GGAGCTCACGCAAGCAACAA
Found at i:1157512 original size:25 final size:26
Alignment explanation
Indices: 1157451--1157554 Score: 72
Period size: 25 Copynumber: 3.9 Consensus size: 26
1157441 AAATAATAAT
*
1157451 AATAAATAAAATAAATCAAAAGGAAAAA
1 AATAAAT-AAATAGATCAAAA-GAAAAA
1157479 AAT-AA-AAATAGATCAAAA-AAAAA
1 AATAAATAAATAGATCAAAAGAAAAA
* * *
1157502 ATTAAATAAATAGGAAAACAAAA-ATAAATC
1 AATAAATAAATA-G--ATCAAAAGA-AAA-A
*
1157532 AATAAAAAAATAGATCAAAAGAA
1 AATAAATAAATAGATCAAAAGAA
1157555 TTTTTTTTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
23 7 0.11
24 2 0.03
25 17 0.28
26 1 0.02
27 9 0.15
28 11 0.18
29 4 0.07
30 10 0.16
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (26 bp):
AATAAATAAATAGATCAAAAGAAAAA
Found at i:1157519 original size:23 final size:22
Alignment explanation
Indices: 1157458--1157535 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
1157448 AATAATAAAT
1157458 AAAATAAATCAAA-AGGAAAAAA
1 AAAATAAAT-AAATAGGAAAAAA
* *
1157480 ATAA-AAATAGATCA--AAAAAA
1 AAAATAAATAAAT-AGGAAAAAA
* *
1157500 AAATTAAATAAATAGGAAAACA
1 AAAATAAATAAATAGGAAAAAA
*
1157522 AAAATAAATCAATA
1 AAAATAAATAAATA
1157536 AAAAAATAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
20 11 0.26
21 11 0.26
22 21 0.49
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAATAAATAAATAGGAAAAAA
Found at i:1157539 original size:42 final size:39
Alignment explanation
Indices: 1157439--1157541 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 39
1157429 AATCAAAGGG
*
1157439 AAAAAT-AATAATAATAAATAAAATAAATCAAAAGGAAAA
1 AAAAATAAATAATAA-AAAAAAAATAAATCAAAAGGAAAA
1157478 AAATAA-AAATAGATCAAAAAAAAAATTAAAT-AAATAGGAAAA
1 AAA-AATAAATA-AT-AAAAAAAAAA-TAAATCAAA-AGGAAAA
1157520 CAAAAATAAATCAATAAAAAAA
1 -AAAAATAAAT-AATAAAAAAA
1157542 TAGATCAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
39 3 0.06
40 6 0.11
41 12 0.22
42 23 0.43
43 9 0.17
44 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.17
Consensus pattern (39 bp):
AAAAATAAATAATAAAAAAAAAATAAATCAAAAGGAAAA
Found at i:1157541 original size:22 final size:21
Alignment explanation
Indices: 1157454--1157541 Score: 59
Period size: 22 Copynumber: 3.9 Consensus size: 21
1157444 TAATAATAAT
1157454 AAATAAAATAAATCAAAAGGAAAAA
1 AAAT-AAATAAAT-AAAA--AAAAA
* * *
1157479 AATAAAAATAGATCAAAAAAAA
1 AA-ATAAATAAATAAAAAAAAA
* * *
1157501 AATTAAATAAATAGGAAAACAA
1 AAATAAATAAATA-AAAAAAAA
*
1157523 AAATAAATCAATAAAAAAA
1 AAATAAATAAATAAAAAAA
1157542 TAGATCAAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
21 11 0.23
22 24 0.50
24 3 0.06
25 9 0.19
26 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.15
Consensus pattern (21 bp):
AAATAAATAAATAAAAAAAAA
Found at i:1158663 original size:19 final size:19
Alignment explanation
Indices: 1158631--1158680 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1158621 ACCCTGACAA
*
1158631 AAATAATAATAAATTAAAT
1 AAATAATAATAAATGAAAT
*
1158650 TAATAA-AATGAAATGAAAT
1 AAATAATAAT-AAATGAAAT
*
1158669 AAATATTAATAA
1 AAATAATAATAA
1158681 TAATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 19 0.76
20 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAATAATAATAAATGAAAT
Found at i:1158703 original size:14 final size:16
Alignment explanation
Indices: 1158666--1158704 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
1158656 AATGAAATGA
*
1158666 AATAAATATTAATAAT
1 AATATATATTAATAAT
1158682 AATATATATT-AT-AT
1 AATATATATTAATAAT
1158696 AATATATAT
1 AATATATAT
1158705 GTTTCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 2 0.09
16 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATATATTAATAAT
Found at i:1158744 original size:29 final size:30
Alignment explanation
Indices: 1158712--1158769 Score: 64
Period size: 31 Copynumber: 1.9 Consensus size: 30
1158702 TATGTTTCAA
* *
1158712 AAAAATATTTTAAAC-TATATATTATATTT
1 AAAAACATTTTAAAACTATATATTATATTT
* *
1158741 AAAAACGTTTTCAAAATTATATATTATAT
1 AAAAACATTTT-AAAACTATATATTATAT
1158770 AGTTTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 3 0.12
31 12 0.50
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (30 bp):
AAAAACATTTTAAAACTATATATTATATTT
Found at i:1158867 original size:110 final size:109
Alignment explanation
Indices: 1158748--1158955 Score: 257
Period size: 110 Copynumber: 1.9 Consensus size: 109
1158738 TTTAAAAACG
* *
1158748 TTTTCAAAATTATATATTATATAGTTTTCAAAAATGATTT-TAAA-A-ATATTATATA-A-GTTT
1 TTTTAAAAATTATATA-T-TATA-TTTTC-AAAATGATTTCAAAACATATATTATATATATGTTT
* *
1158808 TCCAAAAATGTTTTGTTAAATCTATATAT-TATATAAATTTTCAAAAATGT
62 T--AAAAATGTTTT-TAAAATATATATATATATATAAATTTTCAAAAATGT
1158858 TTTTAAAAATTATATATTATATTTTCAAAATGATTTCAAAACTATATATTATATATATGTTTTAA
1 TTTTAAAAATTATATATTATATTTTCAAAATGATTTCAAAAC-ATATATTATATATATGTTTTAA
*
1158923 AAGTGTTTTTAAAATATATATATATATATAAAT
65 AAATGTTTTTAAAATATATATATATATATAAAT
1158956 GGGACGAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
106 10 0.12
107 8 0.09
108 4 0.05
109 14 0.16
110 44 0.51
111 1 0.01
112 5 0.06
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (109 bp):
TTTTAAAAATTATATATTATATTTTCAAAATGATTTCAAAACATATATTATATATATGTTTTAAA
AATGTTTTTAAAATATATATATATATATAAATTTTCAAAAATGT
Found at i:1158909 original size:32 final size:34
Alignment explanation
Indices: 1158691--1158911 Score: 129
Period size: 32 Copynumber: 6.4 Consensus size: 34
1158681 TAATATATAT
** *
1158691 TATATAATATATATGTTTCAAAAAAATATTT-TAAAC
1 TATAT-AT-TATAT-TTTCAAAAATGTATTTAAAAAC
* * *
1158727 TATATATTATA-TTT-AAAAACGT-TTTCAAAAT
1 TATATATTATATTTTCAAAAATGTATTTAAAAAC
1158758 TATATATTATATAGTTTTCAAAAATG-ATTTTAAAAA-
1 TATATA-T-TATA-TTTTCAAAAATGTA-TTTAAAAAC
* * *
1158794 TAT-TA-TATAAGTTTTCCAAAAATGTTTTGTTAAATC
1 TATATATTAT-A-TTTT-CAAAAATGTATT-TAAAAAC
* *
1158830 TATATATTATATAAATTTTCAAAAATGTTTTTAAAAAT
1 TATATA-T-TAT--ATTTTCAAAAATGTATTTAAAAAC
*
1158868 TATATATTATATTTTC-AAAATG-ATTTCAAAAC
1 TATATATTATATTTTCAAAAATGTATTTAAAAAC
1158900 TATATATTATAT
1 TATATATTATAT
1158912 ATATGTTTTA
Statistics
Matches: 152, Mismatches: 15, Indels: 40
0.73 0.07 0.19
Matches are distributed among these distances:
30 3 0.02
31 15 0.10
32 26 0.17
33 16 0.11
34 20 0.13
35 11 0.07
36 20 0.13
37 10 0.07
38 10 0.07
39 12 0.08
40 7 0.05
41 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (34 bp):
TATATATTATATTTTCAAAAATGTATTTAAAAAC
Found at i:1158913 original size:72 final size:70
Alignment explanation
Indices: 1158727--1158952 Score: 228
Period size: 73 Copynumber: 3.2 Consensus size: 70
1158717 TATTTTAAAC
* * * * *
1158727 TATATATTATA-TTTAAAAACGTTTTCAAAATTATATATTATAT-AGTTTTCAAAAATGATTTTA
1 TATATATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAATTTTCAAAAATGTTTTTA
1158790 AAAA-
66 AAAAT
* *
1158794 TAT-TA-TATAAGTTTTCCAAAAATGTTTTGTTAAATCTATATATTATATAAATTTTCAAAAATG
1 TATATATTAT-A-TTTT-C-AAAATG-TTT-TCAAAACTATATATTATATAAATTTTCAAAAATG
1158857 TTTTTAAAAAT
60 TTTTTAAAAAT
* * * *
1158868 TATATATTATATTTTCAAAATGATTTCAAAACTATATATTATATATATGTTTTAAAAGTGTTTTT
1 TATATATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAAT-TTTCAAAAATGTTTTT
1158933 AAAATAT
65 AAAA-AT
1158940 ATATATATATATA
1 -TATATAT-TATA
1158953 AATGGGACGA
Statistics
Matches: 131, Mismatches: 13, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
65 3 0.02
66 3 0.02
67 3 0.02
68 3 0.02
70 25 0.19
71 23 0.18
72 24 0.18
73 30 0.23
74 11 0.08
75 3 0.02
76 3 0.02
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (70 bp):
TATATATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAATTTTCAAAAATGTTTTTA
AAAAT
Found at i:1158943 original size:39 final size:38
Alignment explanation
Indices: 1158830--1158952 Score: 104
Period size: 37 Copynumber: 3.4 Consensus size: 38
1158820 TTGTTAAATC
**
1158830 TATATATTATATA-A-ATTTTCAAAAATG-TTTTTAAAA
1 TATATATTATATATATATTTTC-AAAATGATTTCAAAAA
*
1158866 -AT-TA-TATAT-TATATTTTCAAAATGATTTCAAAAC
1 TATATATTATATATATATTTTCAAAATGATTTCAAAAA
* **
1158900 TATATATTATATATATGTTTT-AAAAGTG-TTTTTAAAA
1 TATATATTATATATATATTTTCAAAA-TGATTTCAAAAA
1158937 TATATA-TATATATATA
1 TATATATTATATATATA
1158953 AATGGGACGA
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
33 12 0.17
34 14 0.20
35 4 0.06
36 11 0.15
37 21 0.30
38 9 0.13
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (38 bp):
TATATATTATATATATATTTTCAAAATGATTTCAAAAA
Found at i:1159673 original size:84 final size:82
Alignment explanation
Indices: 1159470--1160661 Score: 1069
Period size: 84 Copynumber: 14.5 Consensus size: 82
1159460 ATAATTTTAT
* * * * * * * ** *
1159470 TGACAGATAGCCCTTCTTGCCTTGAGTTATGTTGTAAATGATATGCCTTGAAGCTGAGTATAATC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG-AGCTGAGCGTAGTC
1159535 GAACTCGAAGGTCTTT-G
65 GAACTCGAAGGTCTTTGG
* * ** *
1159552 -G-CAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCATTGAGCTAAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTC
* *
1159615 GAATTCAAAGGTCTTTTGG
65 GAACTCGAAGGTC-TTTGG
* * * * ** * * * *
1159634 AGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGCCCTCGAAGCTAAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGT
*
1159699 CGAACTCGAGGGTCTTT-G
64 CGAACTCGAAGGTCTTTGG
* * * * *
1159717 -G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTC
*
1159780 GAACTTGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* * * * *
1159798 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTTAGCGTAGT
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGT
1159863 CGAACTCGAAGGTCTTTTGG
64 CGAACTCGAAGGTC-TTTGG
* * * * * * *
1159883 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGT
* **
1159948 CGAACTTGGGGGTCTTT-G
64 CGAACTCGAAGGTCTTTGG
* * * * *
1159966 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGTCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAGCTGAGCGTAGTC
* *
1160029 GAACTCAAAGGTCTTTTGT
65 GAACTCGAAGGTC-TTTGG
* * * * * * *
1160048 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCAGCAAATGATATGCCCTCGAAGCTGA-CTGTAA
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGC-GTAG
* *
1160112 TCGAACTCG-AGGGCCTT--
63 TCGAACTCGAAGGTCTTTGG
* *
1160129 TGACAGATAACCCTTCT-GACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTC
* *
1160193 GAACTCAAAGGTCTTTTGT
65 GAACTCGAAGGTC-TTTGG
* * * * *
1160212 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGTCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTC
1160277 GAACTCGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* * * * * * * *
1160295 TGACATATAACCCTTCTAGCCTTATG-T-TG-T--AAATGATATGCCCTCGAAACTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGT
**
1160355 CGAACTCGGGGGTCTTT-G
64 CGAACTCGAAGGTCTTTGG
* * * *
1160373 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTC
* *
1160436 GAACTCAAAGGTCTTTTGT
65 GAACTCGAAGGTC-TTTGG
* * * *
1160455 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTC
*
1160520 GAACTCGAAGGTATTTGG
65 GAACTCGAAGGTCTTTGG
* * * * *
1160538 TGACAGATAACCCTTATCGATTTAAGTTATGTTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTC
1160603 GAACTCGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* * *
1160621 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
1160662 TTGTCTTAAA
Statistics
Matches: 899, Mismatches: 168, Indels: 84
0.78 0.15 0.07
Matches are distributed among these distances:
76 18 0.02
77 2 0.00
78 14 0.02
79 47 0.05
80 158 0.18
81 117 0.13
82 4 0.00
83 128 0.14
84 341 0.38
85 70 0.08
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (82 bp):
TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCG
AACTCGAAGGTCTTTGG
Found at i:1159739 original size:165 final size:162
Alignment explanation
Indices: 1159470--1160661 Score: 1075
Period size: 165 Copynumber: 7.2 Consensus size: 162
1159460 ATAATTTTAT
* * * * * * ** *
1159470 TGACAGATAGCCCTTCTTGCCTTGAGTTATGTTGTAAATGATATG-CCTTGAAGCTGAGTATAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTG-AGCTGAGCGTAGT
* **
1159534 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCAT
65 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-T
* * *
1159599 TGAGCTAAGCGTAGTCGAATTCAAAGGTCTTTTGG
129 TGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* * * * ** * * * * *
1159634 AGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGCCCTCGAAGCTAAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTG-AGCTGAGCGTAGT
* * * * *
1159699 CGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGTCTT
65 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
*
1159764 GGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGG
130 -GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * *
1159798 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTTAGCGTAG
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTT-GAGCTGAGCGTAG
* * * * *
1159862 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAT
64 TCGAACTCGAAGGTC-TTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * * **
1159927 GCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTT-G
125 G-CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * * * *
1159966 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGTCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTC
* * * * * *
1160029 GAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCAGCAAATGATATGC
66 GAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-
* * * *
1160094 CCTCGAAGCTGA-CTGTAATCGAACTCG-AGGGCCTT--
126 CCTTG-AGCTGAGC-GTAGTCGAACTCGAAGGTCTTTGG
* * * *
1160129 TGACAGATAACCCTTCT-GACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTC
* * * * * *
1160193 GAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGT
66 GAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
1160258 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
127 CTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * * * *
1160295 TGACATATAACCCTTCTAGCCTTATG-T-TG-T--AAATGATATGCCCTCGAAACTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTG-AGCTGAGCGTAGT
** * * *
1160355 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCGT
65 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-T
* *
1160420 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGT
129 TGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* * *
1160455 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTAGAGCTGAGCGTAGT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTT-GAGCTGAGCGTAGT
* * * * *
1160519 CGAACTCGAAGGTATTTGGTGACAGATAACCCTTATCGATTTAAGTTATGTTGCAAATGATGCGC
65 CGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
1160584 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
127 CTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * *
1160621 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
1160662 TTGTCTTAAA
Statistics
Matches: 867, Mismatches: 124, Indels: 71
0.82 0.12 0.07
Matches are distributed among these distances:
159 67 0.08
160 28 0.03
161 1 0.00
162 15 0.02
163 42 0.05
164 220 0.25
165 288 0.33
166 30 0.03
167 110 0.13
168 38 0.04
169 28 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (162 bp):
TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:1159907 original size:249 final size:249
Alignment explanation
Indices: 1159505--1160661 Score: 1149
Period size: 249 Copynumber: 4.7 Consensus size: 249
1159495 GTTATGTTGT
* * ** * *
1159505 AAATGATATGCCTTGAAGCTGAGTATAATCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTC
1 AAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
** * * * *
1159566 TCGACTTAAACTATGCTGCAAATGATGTGCCATT-GAGCTAAGCGTAGTCGAATTCAAAGGTCTT
66 TCGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-T
* * * * * * *
1159630 TTGGAGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGCCCTCGAAGCTAAGTG
129 TTGGTGACAGATAACCCTTCTAGACTTAAGCTATACTGTAAATGATGTGCCCTCG-AGCTGAGCG
* * * * * *
1159695 TAATCGAACTCGAGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGC
193 TAATCGAACTCAAAGGTCTTGTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGC
* *
1159750 AAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTC
1 AAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* *
1159815 TCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTT
66 TCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TT
* * * * * *
1159880 TGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGT
130 TGGTGACAGATAACCCTTCTAGACTTAAGCTATACTGTAAATGATGTGCCCTCG-AGCTGAGCGT
**** * * * *
1159945 AATCGAACTTGGGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTAC
194 AATCGAACTCAAAGGTCTTGTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGC
* * * *
1159999 AAATGATGTGTCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTT
1 AAATGATATGTC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
* * * * * * *
1160063 CTAGACTTAAGTTGTGCAGCAAATGATATGCCCTCGAAGCTGA-CTGTAATCGAACTCG-AGGGC
65 CTCGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGC-GTAGTCGAACTCGAAGGTC
* * * *
1160126 CTT--TGACAGATAACCCTTCT-GACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCG
128 TTTGGTGACAGATAACCCTTCTAGACTTAAGCTATACTGTAAATGATGTGCCCTCGAGCTGAGCG
* * *
1160188 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
193 TAATCGAACTCAAAGGTC--TTGTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGC
* *
1160247 AAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACATATAACCCTTC
1 AAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * * * * * * * **
1160311 TAGCCTTATG-T-TG-T--AAATGATATGCCCTCGAAACTGAGTGTAATCGAACTCGGGGGTCTT
66 TCGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
* * * * *
1160371 T-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCGTTGAGCTGAGCGTA
130 TGGTGACAGATAACCCTTCTAGACTTAAGCTATACTGTAAATGATGTGCCCTCGAGCTGAGCGTA
* * *
1160433 GTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
195 ATCGAACTCAAAGGTC--TTGTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGC
* * * * *
1160490 AAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGG-TGACAGATAACCCTTA
1 AAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * **
1160554 TCGATTTAAGTTATGTTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
66 TCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
* * * * * *
1160619 GGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
131 GG-TGACAGATAACCCTTCTAGACTTAAGCTATACTGTAAATG
1160662 TTGTCTTAAA
Statistics
Matches: 789, Mismatches: 97, Indels: 46
0.85 0.10 0.05
Matches are distributed among these distances:
242 48 0.06
243 170 0.22
244 22 0.03
245 65 0.08
246 19 0.02
247 54 0.07
248 85 0.11
249 269 0.34
250 24 0.03
251 33 0.04
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (249 bp):
AAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
TCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
GGTGACAGATAACCCTTCTAGACTTAAGCTATACTGTAAATGATGTGCCCTCGAGCTGAGCGTAA
TCGAACTCAAAGGTCTTGTTGGCAGACAACCCTTCTAGACTTAAGCTATGCTGC
Found at i:1165796 original size:38 final size:37
Alignment explanation
Indices: 1165739--1165867 Score: 106
Period size: 42 Copynumber: 3.4 Consensus size: 37
1165729 AACAAATATT
*
1165739 AAATAAATC-AAAGG--GAAAAATAATAATAATAAATA
1 AAATAAATCAAAAGGAAAAAAAATAATAATAATAAA-A
*
1165774 AAATAAATCAAAAGGAAAAAAAATAAAAATAGATCAAAAAA
1 AAATAAATCAAAAGGAAAAAAAATAATAATA-AT---AAAA
*
1165815 AAATTAAAT-AAATAGGAAAACAAA-AATAAATCAATAAAA
1 AAA-TAAATCAAA-AGGAAAAAAAATAAT-AAT-AATAAAA
*
1165854 AAATAGATCAAAAG
1 AAATAAATCAAAAG
1165868 AATTTTTTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
35 9 0.12
36 5 0.06
38 18 0.23
39 12 0.16
41 9 0.12
42 23 0.30
43 1 0.01
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (37 bp):
AAATAAATCAAAAGGAAAAAAAATAATAATAATAAAA
Found at i:1165823 original size:26 final size:26
Alignment explanation
Indices: 1165766--1165826 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
1165756 AAATAATAAT
1165766 AATAAAT-AAAATAAATCAAAAGGAAA
1 AATAAATAAAAATAAATCAAAA-GAAA
*
1165792 AA-AAATAAAAATAGATCAAAA-AAA
1 AATAAATAAAAATAAATCAAAAGAAA
1165816 AATTAAATAAA
1 AA-TAAATAAA
1165827 TAGGAAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 5 0.16
25 4 0.13
26 22 0.71
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (26 bp):
AATAAATAAAAATAAATCAAAAGAAA
Found at i:1165834 original size:22 final size:22
Alignment explanation
Indices: 1165773--1165850 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
1165763 AATAATAAAT
1165773 AAAATAAATCAAA-AGG-AAA-A
1 AAAATAAAT-AAATAGGAAAACA
*
1165793 AAAAT-AA-AAATA-GATCAAAAA
1 AAAATAAATAAATAGGA--AAACA
1165814 AAAATTAAATAAATAGGAAAACA
1 AAAA-TAAATAAATAGGAAAACA
*
1165837 AAAATAAATCAATA
1 AAAATAAATAAATA
1165851 AAAAAATAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 2 0.04
20 8 0.17
21 5 0.11
22 10 0.21
23 10 0.21
24 5 0.11
25 2 0.04
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAATAAATAAATAGGAAAACA
Found at i:1165856 original size:22 final size:21
Alignment explanation
Indices: 1165769--1165856 Score: 54
Period size: 22 Copynumber: 3.9 Consensus size: 21
1165759 TAATAATAAT
1165769 AAATAAAATAAATCAAAAGGAAAAA
1 AAAT-AAATAAAT-AAAA--AAAAA
1165794 AAAT-AA-AAATAGATCAAAAAAA
1 AAATAAATAAATA-A--AAAAAAA
* * *
1165816 AATTAAATAAATAGGAAAACAA
1 AAATAAATAAATA-AAAAAAAA
*
1165838 AAATAAATCAATAAAAAAA
1 AAATAAATAAATAAAAAAA
1165857 TAGATCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
21 5 0.10
22 30 0.59
23 4 0.08
24 8 0.16
25 4 0.08
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.15
Consensus pattern (21 bp):
AAATAAATAAATAAAAAAAAA
Found at i:1167019 original size:14 final size:16
Alignment explanation
Indices: 1166982--1167020 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
1166972 AATGAAATGA
*
1166982 AATAAATATTAATAAT
1 AATATATATTAATAAT
1166998 AATATATATT-AT-AT
1 AATATATATTAATAAT
1167012 AATATATAT
1 AATATATAT
1167021 GTTTCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 2 0.09
16 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATATATTAATAAT
Found at i:1167204 original size:34 final size:34
Alignment explanation
Indices: 1167005--1167228 Score: 151
Period size: 32 Copynumber: 6.4 Consensus size: 34
1166995 AATAATATAT
* *
1167005 ATTATATAATATATATGTTTCAAAAAATATTTTT-TAA
1 ATTATAT-AT-TATAT-TTTC-AAAAATGTTTTTAAAA
* * *
1167042 ACTATATATTATA-TTT-AAAAACG-TTTTCAAA
1 ATTATATATTATATTTTCAAAAATGTTTTTAAAA
*
1167073 ATTATATATTATATAGTTTTCAAAAATGATTTTAAAA
1 ATTATATA-T-TATA-TTTTCAAAAATGTTTTTAAAA
1167110 A-TAT-TA-TATAAGTTTTCCAAAAATGTTTTGTTAAAA
1 ATTATATATTAT-A-TTTT-CAAAAATG-TTT-TTAAAA
* *
1167146 CAATATATTATATAAATTTTCAAAAATGTTTTTAAAA
1 -ATTATA-TAT-TATATTTTCAAAAATGTTTTTAAAA
* *
1167183 ATTATATATTATATTTTC-AAAATG-ATTTCAAA
1 ATTATATATTATATTTTCAAAAATGTTTTTAAAA
*
1167215 ACTATATATTATAT
1 ATTATATATTATAT
1167229 ATATGTTTTA
Statistics
Matches: 156, Mismatches: 14, Indels: 39
0.75 0.07 0.19
Matches are distributed among these distances:
30 4 0.03
31 14 0.09
32 23 0.15
33 19 0.12
34 16 0.10
35 14 0.09
36 22 0.14
37 21 0.13
38 6 0.04
39 8 0.05
40 6 0.04
41 1 0.01
42 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (34 bp):
ATTATATATTATATTTTCAAAAATGTTTTTAAAA
Found at i:1167230 original size:34 final size:35
Alignment explanation
Indices: 1167007--1167268 Score: 195
Period size: 36 Copynumber: 7.4 Consensus size: 35
1166997 TAATATATAT
* * *
1167007 TATATAATATATATGTTTCAAAAAATATTTTTTAAAC
1 TATATATTATATAT-TTTC-AAAAATGTTTTTAAAAC
* * *
1167044 TATATA-T-TATA-TTT-AAAAACGTTTTCAAAAT
1 TATATATTATATATTTTCAAAAATGTTTTTAAAAC
* *
1167075 TATATATTATATAGTTTTCAAAAATGATTTTAAAAA
1 TATATATTATATA-TTTTCAAAAATGTTTTTAAAAC
1167111 TAT-TA-TATA-AGTTTTCCAAAAATGTTTTGTTAAAAC
1 TATATATTATATA-TTTT-CAAAAATG-TTT-TTAAAAC
* *
1167147 AATATATTATATAAATTTTCAAAAATGTTTTTAAAAA
1 TATATATTATAT--ATTTTCAAAAATGTTTTTAAAAC
* *
1167184 T-TATA-TATTATATTTTC-AAAATGATTTCAAAAC
1 TATATATTA-TATATTTTCAAAAATGTTTTTAAAAC
**
1167217 TATATATTATATATATGTTTTAAAA-GTGTTTTAAAAC
1 TATATATTATATAT-T-TTCAAAAATGT-TTTTAAAAC
1167254 TATATATATATATAT
1 TATATAT-TATATAT
1167269 ATATATATAT
Statistics
Matches: 184, Mismatches: 20, Indels: 41
0.75 0.08 0.17
Matches are distributed among these distances:
31 18 0.10
32 1 0.01
33 27 0.15
34 27 0.15
35 16 0.09
36 35 0.19
37 33 0.18
38 14 0.08
39 8 0.04
40 4 0.02
41 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (35 bp):
TATATATTATATATTTTCAAAAATGTTTTTAAAAC
Found at i:1167261 original size:2 final size:2
Alignment explanation
Indices: 1167254--1167281 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1167244 GTTTTAAAAC
1167254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1167282 AATGGGACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1167266 original size:70 final size:71
Alignment explanation
Indices: 1167007--1167266 Score: 227
Period size: 70 Copynumber: 3.7 Consensus size: 71
1166997 TAATATATAT
* * * * * *
1167007 TATATAATATATATGTTTCAAAAAAT-ATTTTTTAAACTATATAT-TATA-TTTAAAAACGTTTT
1 TATATTATATATATGTTT-TAAAAATGA-TTTTAAAAATATATATATATATTTTCAAAATGTTTT
*
1167069 CAAAATTA
64 CAAAACTA
1167077 TATA-T-TATATA-GTTTTCAAAAATGATTTTAAAAATAT-TATATA-AGTTTTCCAAAAATGTT
1 TATATTATATATATGTTTT-AAAAATGATTTTAAAAATATATATATATA-TTTT-C-AAAATG-T
* *
1167137 TTGTTAAAACAA
61 TT-TCAAAACTA
* * * *
1167149 TATATTATATAAAT-TTTCAAAAATGTTTTTAAAAAT-TATATATTATATTTTCAAAATGATTTC
1 TATATTATATATATGTTTTAAAAATGATTTTAAAAATATATATA-TATATTTTCAAAATGTTTTC
1167212 AAAACTA
65 AAAACTA
* *
1167219 TATATTATATATATGTTTTAAAAGTG-TTTTAAAACTATATATATATAT
1 TATATTATATATATGTTTTAAAAATGATTTTAAAAATATATATATATAT
1167267 ATATATATAT
Statistics
Matches: 154, Mismatches: 19, Indels: 34
0.74 0.09 0.16
Matches are distributed among these distances:
66 4 0.03
67 22 0.14
68 10 0.06
70 43 0.28
71 20 0.13
72 17 0.11
73 23 0.15
74 14 0.09
75 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (71 bp):
TATATTATATATATGTTTTAAAAATGATTTTAAAAATATATATATATATTTTCAAAATGTTTTCA
AAACTA
Found at i:1168009 original size:84 final size:82
Alignment explanation
Indices: 1167799--1168996 Score: 1184
Period size: 84 Copynumber: 14.5 Consensus size: 82
1167789 ATAATTTTAT
* * * * * * ** *
1167799 TGACAGATAGCCCTTCTTGCCTTGAGTTATGTTGTAAATGATATGCCTTGGAGCTGAGTATAATC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT-GAGCTGAGCGTAGTC
1167864 GAACTCGAAGGTCTTT-G
65 GAACTCGAAGGTCTTTGG
* ** *
1167881 -G-CAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCATTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TTGAGCTGAGCGTAGTC
*
1167944 GAACTCAAAGGTCTTTTGG
65 GAACTCGAAGGTC-TTTGG
* * * * * ** * * * * *
1167963 AGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGCCCTCGAAGCTAAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTTG-AGCTGAGCGTAGT
*
1168028 CGAACTCGAGGGTCTTT-G
64 CGAACTCGAAGGTCTTTGG
* * * *
1168046 -G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT-GAGCTGAGCGTAGTC
*
1168109 GAACTTGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* * *
1168127 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTTAGCGTAGT
1 -TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT-GAGCTGAGCGTAGT
1168192 CGAACTCGAAGGTCTTTTGG
64 CGAACTCGAAGGTC-TTTGG
* * * * * *
1168212 TGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTTG-AGCTGAGCGTAGT
* **
1168277 CGAACTTGGGGGTCTTT-G
64 CGAACTCGAAGGTCTTTGG
* * * *
1168295 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTTGAGCTGAGCGTAGTC
* *
1168358 GAACTCAAAGGTCTTTTGT
65 GAACTCGAAGGTC-TTTGG
* * * * * * * *
1168377 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCAGCAAATGATATGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTTG-AGCTGAGCGTAGT
* *
1168442 CGAACTCG-AGGGCCTT--
64 CGAACTCGAAGGTCTTTGG
* * * * *
1168458 TGACAGATAGCCCTTCTGGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TTGAGCTGAGCGTAGTC
* *
1168523 GAACTCAAAGGTCTTTTGT
65 GAACTCGAAGGTC-TTTGG
* * * * *
1168542 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGTCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT-GAGCTGAGCGTAGTC
1168607 GAACTCGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* * * * * * * *
1168625 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTTG-AGCTGAGCGTAGT
**
1168690 CGAACTCGGGGGTCTTT-G
64 CGAACTCGAAGGTCTTTGG
* * *
1168708 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TTGAGCTGAGCGTAGTC
* *
1168771 GAACTCAAAGGTCTTTTGT
65 GAACTCGAAGGTC-TTTGG
* * * * *
1168790 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTAGAGTTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT-GAGCTGAGCGTAGTC
1168855 GAACTCGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* * **
1168873 TGACAGATAACCCTTCTCGATTTAAGTTATGTTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT-GAGCTGAGCGTAGTC
1168938 GAACTCGAAGGTCTTTGG
65 GAACTCGAAGGTCTTTGG
* *
1168956 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 -TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1168997 TTGTCTTAAA
Statistics
Matches: 916, Mismatches: 165, Indels: 68
0.80 0.14 0.06
Matches are distributed among these distances:
80 153 0.17
81 166 0.18
82 6 0.01
83 133 0.15
84 387 0.42
85 71 0.08
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (82 bp):
TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGAGCTGAGCGTAGTCG
AACTCGAAGGTCTTTGG
Found at i:1168068 original size:165 final size:162
Alignment explanation
Indices: 1167799--1168996 Score: 1181
Period size: 165 Copynumber: 7.2 Consensus size: 162
1167789 ATAATTTTAT
* * * * * * ** *
1167799 TGACAGATAGCCCTTCTTGCCTTGAGTTATGTTGTAAATGATATG-CCTTGGAGCTGAGTATAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTT-GAGCTGAGCGTAGT
* **
1167863 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCAT
65 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-T
*
1167928 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
129 TGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* * * * ** * * * * *
1167963 AGACAGATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGCCCTCGAAGCTAAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTG-AGCTGAGCGTAGT
* * * *
1168028 CGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT
65 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
*
1168093 GGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGG
130 -GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * *
1168127 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTTAGCGTAG
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTT-GAGCTGAGCGTAG
* * * *
1168191 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATAT
64 TCGAACTCGAAGGTC-TTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * * **
1168256 GCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTT-G
125 G-CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * * *
1168295 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTC
* * * * * *
1168358 GAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCAGCAAATGATATGC
66 GAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-
* * * * *
1168423 CCTCGAAGCTGAGTGTAATCGAACTCG-AGGGCCTT--
126 CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * * *
1168458 TGACAGATAGCCCTTCTGGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTC
* * * * * *
1168523 GAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGT
66 GAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
1168588 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
127 CTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * * * *
1168625 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTG-AGCTGAGCGTAGT
** * *
1168690 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
65 CGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-T
* *
1168755 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGT
129 TGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* * * *
1168790 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTAGAGTTGAGCGTAGT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTT-GAGCTGAGCGTAGT
* * *
1168854 CGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTCGATTTAAGTTATGTTGCAAATGATGCGC
65 CGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
1168919 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
127 CTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * *
1168956 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
1168997 TTGTCTTAAA
Statistics
Matches: 885, Mismatches: 119, Indels: 57
0.83 0.11 0.05
Matches are distributed among these distances:
164 195 0.22
165 441 0.50
166 13 0.01
167 146 0.16
168 61 0.07
169 29 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (162 bp):
TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTTGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:1168391 original size:414 final size:413
Alignment explanation
Indices: 1167799--1168996 Score: 1873
Period size: 414 Copynumber: 2.9 Consensus size: 413
1167789 ATAATTTTAT
* * * * *
1167799 TGACAGATAGCCCTTCTTGCCTTGAGTTATGTTGTAAATGATATG-CCTTGGAGCTGAGTATAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
** * *
1167863 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATGATGTGCCAT
66 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
** * * * * *
1167928 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGAGACAGATAACCCTTCTAGCCTTGAGTTAT
131 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
* * * *
1167993 ACTATAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCT
196 GCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCT
*
1168058 TCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCT
261 TCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
*
1168123 TTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTTAGCG
326 TTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCG
1168188 TAGTCGAACTCGAAGGTCTTTTGG
391 TAGTCGAACTCGAAGGTC-TTTGG
* *
1168212 TGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
* *
1168277 CGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGT
66 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
1168342 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
131 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
* *
1168407 GC-AGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGCCTTTGACAGATAGCCC
196 GCTA-CAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCC
* *
1168471 TTCTGGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGT
260 TTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * * * * *
1168535 CTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGTCTTGGAGCTGAG
324 CTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAG
1168600 CGTAGTCGAACTCGAAGGTCTTTGG
389 CGTAGTCGAACTCGAAGGTCTTTGG
1168625 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
1168690 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
66 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
1168755 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
131 TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
* * * * * * * *
1168820 GCTGCAAATGATATGCCTTAG-AGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAAC
196 GCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-G-CAGATAGC
* * ** *
1168884 CCTTCTCGATTTAAGTTATGTTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
258 CCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1168949 TCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
323 TCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATG
1168997 TTGTCTTAAA
Statistics
Matches: 716, Mismatches: 61, Indels: 14
0.91 0.08 0.02
Matches are distributed among these distances:
412 25 0.03
413 257 0.36
414 327 0.46
415 107 0.15
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (413 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAAT
CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
GCTACAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCT
TCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
TTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCG
TAGTCGAACTCGAAGGTCTTTGG
Found at i:1174107 original size:32 final size:30
Alignment explanation
Indices: 1174071--1174132 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 30
1174061 AACAAATATT
*
1174071 AAATAAATCAAAGGGAAAAATAATAATAAATA
1 AAATAAATCAAAAGGAAAAA-AATAA-AAATA
1174103 AAATAAATCAAAAGGAAAAAAATAAAAATA
1 AAATAAATCAAAAGGAAAAAAATAAAAATA
1174133 GATCAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 5 0.17
31 5 0.17
32 19 0.66
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (30 bp):
AAATAAATCAAAAGGAAAAAAATAAAAATA
Found at i:1174149 original size:24 final size:24
Alignment explanation
Indices: 1174095--1174152 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1174085 GAAAAATAAT
1174095 AATAAAT-AAAATAAATCAAAAGGA
1 AATAAATAAAAATAAATCAAAA-GA
* *
1174119 AAAAAATAAAAATAGATCAAAA-A
1 AATAAATAAAAATAAATCAAAAGA
1174142 AATTAAATAAA
1 AA-TAAATAAA
1174153 TAGGAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 13 0.45
25 13 0.45
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (24 bp):
AATAAATAAAAATAAATCAAAAGA
Found at i:1174180 original size:39 final size:37
Alignment explanation
Indices: 1174086--1174193 Score: 109
Period size: 39 Copynumber: 2.9 Consensus size: 37
1174076 AATCAAAGGG
1174086 AAAAAT-AATAATAAATAAAA-TAAATCAAAAGGAAAA
1 AAAAATAAATAATAAA-AAAATTAAATCAAAAGGAAAA
1174122 AAATAA-AAATAGATCAAAAAAATTAAAT-AAATAGGAAAA
1 AAA-AATAAATA-AT-AAAAAAATTAAATCAAA-AGGAAAA
*
1174161 CAAAAATAAATCAATAAAAAAA-TAGATCAAAAG
1 -AAAAATAAAT-AATAAAAAAATTAAATCAAAAG
1174194 AATTTTTTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 18
0.76 0.01 0.22
Matches are distributed among these distances:
36 3 0.05
37 6 0.10
38 15 0.25
39 27 0.44
40 9 0.15
41 1 0.02
ACGTcount: A:0.72, C:0.05, G:0.06, T:0.17
Consensus pattern (37 bp):
AAAAATAAATAATAAAAAAATTAAATCAAAAGGAAAA
Found at i:1174182 original size:22 final size:23
Alignment explanation
Indices: 1174139--1174182 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1174129 AATAGATCAA
**
1174139 AAAAATTAAATAAATAGGAAAAC
1 AAAAATTAAATAAATAAAAAAAC
*
1174162 AAAAA-TAAATCAATAAAAAAA
1 AAAAATTAAATAAATAAAAAAA
1174183 TAGATCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAAATTAAATAAATAAAAAAAC
Found at i:1175344 original size:14 final size:16
Alignment explanation
Indices: 1175307--1175345 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
1175297 AATGAAATGA
*
1175307 AATAAATATTAATAAT
1 AATATATATTAATAAT
1175323 AATATATATT-AT-AT
1 AATATATATTAATAAT
1175337 AATATATAT
1 AATATATAT
1175346 GTTTCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 2 0.09
16 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATATATTAATAAT
Found at i:1175481 original size:39 final size:38
Alignment explanation
Indices: 1175438--1175592 Score: 121
Period size: 38 Copynumber: 4.2 Consensus size: 38
1175428 TTTAAAAATG
*
1175438 TTATATAAGTTTTCCAAAATGTTTTGTTAAAACTATATA
1 TTATATAAGTTTTCAAAAATGTTTT-TTAAAACTATATA
* * *
1175477 TTATATAAATTTTTCAAAAATGTTTTTAAAAATTATATA
1 TTATAT-AAGTTTTCAAAAATGTTTTTTAAAACTATATA
* * * *
1175516 -T-TAT-A-TTTTC-AAAATG-ATTTCAATATTATATA
1 TTATATAAGTTTTCAAAAATGTTTTTTAAAACTATATA
*
1175548 TTATATATATGTTTT-AAAAGTG-TTTTT-AAACTATATA
1 TTATATA-A-GTTTTCAAAAATGTTTTTTAAAACTATATA
1175585 TATATATA
1 T-TATATA
1175593 TAAATGGGAC
Statistics
Matches: 95, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
32 13 0.14
33 7 0.07
34 8 0.08
35 1 0.01
36 1 0.01
37 12 0.13
38 19 0.20
39 17 0.18
40 17 0.18
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (38 bp):
TTATATAAGTTTTCAAAAATGTTTTTTAAAACTATATA
Found at i:1175544 original size:32 final size:34
Alignment explanation
Indices: 1175474--1175553 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 34
1175464 TTAAAACTAT
* *
1175474 ATATTATATA-AAT-TTTTCAAAAATGTTTTTAA
1 ATATTATATATTATATTTTCAAAAATGTATTTAA
* *
1175506 AAATTATATATTATATTTTC-AAAATG-ATTTCA
1 ATATTATATATTATATTTTCAAAAATGTATTTAA
1175538 ATATTATATATTATAT
1 ATATTATATATTATAT
1175554 ATATGTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 28 0.68
33 8 0.20
34 5 0.12
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (34 bp):
ATATTATATATTATATTTTCAAAAATGTATTTAA
Found at i:1175546 original size:71 final size:71
Alignment explanation
Indices: 1175332--1175577 Score: 238
Period size: 71 Copynumber: 3.5 Consensus size: 71
1175322 TAATATATAT
* * * * * * *
1175332 TATATAATATATATGTTTCAAAAAATATTTTT-TAAACTATATATTATA-TTTAAAAACGTTTTC
1 TATATTATATATATTTTTC-AAAAATGTTTTTAAAAATTATATATTATATTTTCAAAATGTTTTC
1175395 AAAACTA
65 AAAACTA
* *
1175402 TATA-T-TATATAGTTTTCAAAAATGATTTTAAAAATGT-TATA-TA-AGTTTTCCAAAATGTTT
1 TATATTATATATATTTTTCAAAAATGTTTTTAAAAAT-TATATATTATA-TTTT-CAAAATG-TT
*
1175462 TGTTAAAACTA
62 T-TCAAAACTA
* *
1175473 TATATTATATAAATTTTTCAAAAATGTTTTTAAAAATTATATATTATATTTTCAAAATGATTTCA
1 TATATTATATATATTTTTCAAAAATGTTTTTAAAAATTATATATTATATTTTCAAAATGTTTTCA
* *
1175538 ATATTA
66 AAACTA
*
1175544 TATATTATATATATGTTTT-AAAAGTGTTTTTAAA
1 TATATTATATATAT-TTTTCAAAAATGTTTTTAAA
1175578 CTATATATAT
Statistics
Matches: 144, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
66 1 0.01
67 12 0.08
68 20 0.14
69 6 0.04
70 7 0.05
71 45 0.31
72 8 0.06
73 38 0.26
74 6 0.04
75 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (71 bp):
TATATTATATATATTTTTCAAAAATGTTTTTAAAAATTATATATTATATTTTCAAAATGTTTTCA
AAACTA
Found at i:1175555 original size:34 final size:36
Alignment explanation
Indices: 1175414--1175555 Score: 95
Period size: 33 Copynumber: 4.0 Consensus size: 36
1175404 TATTATATAG
*
1175414 TTTTCAAAAATG-ATTTTAAAAATGT-TATA-TA-A-G
1 TTTTCAAAAATGTA-TTTAAAAAT-TATATATTATATA
* * * *
1175447 TTTTCCAAAATGTTTTGTTAAAACTATATATTATATAAA
1 TTTTCAAAAATGTATT-TAAAAATTATATATTATAT--A
*
1175486 TTTTTCAAAAATGTTTTTAAAAATTATATA-T-TATA
1 -TTTTCAAAAATGTATTTAAAAATTATATATTATATA
* *
1175521 TTTTC-AAAATG-ATTTCAATATTATATATTATATA
1 TTTTCAAAAATGTATTTAAAAATTATATATTATATA
1175555 T
1 T
1175556 ATGTTTTAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
32 13 0.15
33 21 0.24
34 19 0.22
35 3 0.03
36 1 0.01
37 3 0.03
38 1 0.01
39 11 0.13
40 15 0.17
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (36 bp):
TTTTCAAAAATGTATTTAAAAATTATATATTATATA
Found at i:1177798 original size:37 final size:36
Alignment explanation
Indices: 1177739--1177850 Score: 124
Period size: 37 Copynumber: 3.2 Consensus size: 36
1177729 ATCCCATTAT
*
1177739 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTG-AAAAC
* *
1177775 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAC
***
1177811 CATTTTTTCAAAG-TTGAT-TACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAACATCTACCAAACTTTGAAAAC
1177845 CATTTT
1 CATTTT
1177851 AATACTTTCA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
33 4 0.06
34 10 0.15
35 8 0.12
36 15 0.22
37 30 0.45
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAC
Found at i:1180138 original size:33 final size:33
Alignment explanation
Indices: 1180060--1180140 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
1180050 ATTTATATAT
1180060 ATATATATATATATATTAATAAATTTAATTTAA
1 ATATATATATATATATTAATAAATTTAATTTAA
* * * * *
1180093 ATAAAAAAATATATATTTATATATTTAATTTAA
1 ATATATATATATATATTAATAAATTTAATTTAA
1180126 ATATATATATATATA
1 ATATATATATATATA
1180141 CCCGACCCGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATATATATATATATTAATAAATTTAATTTAA
Found at i:1180178 original size:12 final size:12
Alignment explanation
Indices: 1180158--1180192 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1180148 CGATTATCGG
1180158 CCCAATACCCGA
1 CCCAATACCCGA
* *
1180170 CCTAATACCCGG
1 CCCAATACCCGA
1180182 CCCAATACCCG
1 CCCAATACCCG
1180193 TTTAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.49, G:0.11, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:1182933 original size:21 final size:21
Alignment explanation
Indices: 1182909--1182969 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1182899 TTCAAAGAAA
1182909 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1182930 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1182944 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1182965 CATTT
1 CATTT
1182970 TTTCAAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1182943 original size:35 final size:36
Alignment explanation
Indices: 1182858--1183004 Score: 178
Period size: 35 Copynumber: 4.2 Consensus size: 36
1182848 ATCCCATTAT
* * *
1182858 CATTTTTC-AATAAACATCTACCAAACTTTAAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTT-GAAAAC
*
1182894 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1182930 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
***
1182965 CATTTTTTCAAAG--ATGGTTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1182999 CATTTT
1 CATTTT
1183005 AATACTTTCA
Statistics
Matches: 100, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
33 4 0.04
34 10 0.10
35 45 0.45
36 13 0.13
37 28 0.28
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:1182975 original size:72 final size:68
Alignment explanation
Indices: 1182861--1183004 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 68
1182851 CCATTATCAT
* *
1182861 TTTTCAATAAACATCTACCAAACTTTAAAAAACTATTTTTCAAAGAAACATTTACCAAACTTTGA
1 TTTTCAAGAAACATCTACCAAACTTTAAAAAACTATTTTTCAAAG--ACAGTTACCAAAC-TTGA
1182926 AAACCA
63 AAACCA
* * * **
1182932 TTTTCAAAGAAACATTTACCAAACTTT-GAAAACCATTTTTTCAAAGATGGTTACCAAACTTGAA
1 TTTTC-AAGAAACATCTACCAAACTTTAAAAAACTA-TTTTTCAAAGACAGTTACCAAACTTGAA
1182996 AACCA
64 AACCA
1183001 TTTT
1 TTTT
1183005 AATACTTTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
69 14 0.22
70 10 0.16
71 11 0.17
72 29 0.45
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.33
Consensus pattern (68 bp):
TTTTCAAGAAACATCTACCAAACTTTAAAAAACTATTTTTCAAAGACAGTTACCAAACTTGAAAA
CCA
Found at i:1186437 original size:19 final size:19
Alignment explanation
Indices: 1186415--1186460 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1186405 TAATTTATAT
*
1186415 ATTAAGAAATAGTTATCAA
1 ATTAAAAAATAGTTATCAA
*
1186434 ATTAAAAAAATGGTTATCAA
1 ATT-AAAAAATAGTTATCAA
1186454 AGTTAAA
1 A-TTAAA
1186461 GAGCTTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 3 0.13
20 18 0.78
21 2 0.09
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.30
Consensus pattern (19 bp):
ATTAAAAAATAGTTATCAA
Found at i:1186449 original size:20 final size:21
Alignment explanation
Indices: 1186421--1186460 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1186411 ATATATTAAG
1186421 AAATAGTTATCAAA-TTAAAA
1 AAATAGTTATCAAAGTTAAAA
*
1186441 AAATGGTTATCAAAGTTAAA
1 AAATAGTTATCAAAGTTAAA
1186461 GAGCTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (21 bp):
AAATAGTTATCAAAGTTAAAA
Found at i:1191009 original size:28 final size:29
Alignment explanation
Indices: 1190935--1191013 Score: 115
Period size: 29 Copynumber: 2.8 Consensus size: 29
1190925 AAATTCATCG
* *
1190935 TAGGTCGCCATGCCTTCCGGGCGACATAC
1 TAGGTCGCCATGTCTTCCCGGCGACATAC
* *
1190964 TAGGTCGCCATGTTTTCCCGGCGACCTAC
1 TAGGTCGCCATGTCTTCCCGGCGACATAC
1190993 TA-GTCGCCATGTCTTCCCGGC
1 TAGGTCGCCATGTCTTCCCGGC
1191014 AGCTACAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 18 0.40
29 27 0.60
ACGTcount: A:0.14, C:0.35, G:0.25, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGTCTTCCCGGCGACATAC
Found at i:1191134 original size:23 final size:23
Alignment explanation
Indices: 1191083--1191135 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1191073 GACCGAGACC
* *
1191083 ATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGCGAGCTATGCGAGGGA
*
1191106 AGCCGAGCGAGCTATGCGAGGGA
1 ATCCGAGCGAGCTATGCGAGGGA
1191129 ATCCGAG
1 ATCCGAG
1191136 GCAGCCGAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.38, T:0.11
Consensus pattern (23 bp):
ATCCGAGCGAGCTATGCGAGGGA
Found at i:1191207 original size:27 final size:29
Alignment explanation
Indices: 1191156--1191238 Score: 116
Period size: 28 Copynumber: 2.9 Consensus size: 29
1191146 GAGCAAGGGT
* *
1191156 AGGTCGCCCGGAGTGCATGGCGACCTAC-
1 AGGTCGCCCGGAGAGCATGACGACCTACA
*
1191184 AGGTCGCCC-GAGAGCATGTCGACCTACA
1 AGGTCGCCCGGAGAGCATGACGACCTACA
*
1191212 AGGTCGCCCGGAGGGCATGACGACCTA
1 AGGTCGCCCGGAGAGCATGACGACCTA
1191239 TGTGTTGGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 16 0.33
28 18 0.37
29 15 0.31
ACGTcount: A:0.22, C:0.31, G:0.34, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGAGCATGACGACCTACA
Found at i:1191672 original size:29 final size:29
Alignment explanation
Indices: 1191626--1191707 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
1191616 GTGAAATTCG
* *
1191626 TAGGTCGCCATGCCTTCCGGGCGACATAC
1 TAGGTCGCCATGTCTTCCCGGCGACATAC
* *
1191655 TAGGTCGCCATGTTTTCCCGGCGACCTAC
1 TAGGTCGCCATGTCTTCCCGGCGACATAC
1191684 TAGGTCGCCATGTCTTCCCGGCGA
1 TAGGTCGCCATGTCTTCCCGGCGA
1191708 GCTACAAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGTCTTCCCGGCGACATAC
Found at i:1191828 original size:23 final size:23
Alignment explanation
Indices: 1191777--1191829 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1191767 GACCGAGACC
* *
1191777 ATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGCGAGCTATGCGAGGGA
*
1191800 AGCCGAGCGAGCTATGCGAGGGA
1 ATCCGAGCGAGCTATGCGAGGGA
1191823 ATCCGAG
1 ATCCGAG
1191830 GGCAGCCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.38, T:0.11
Consensus pattern (23 bp):
ATCCGAGCGAGCTATGCGAGGGA
Found at i:1191897 original size:29 final size:29
Alignment explanation
Indices: 1191851--1191935 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
1191841 GAGCAAGGGT
* *
1191851 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGAGCATGACGACCTACA
* *
1191880 AGGTCGCCCAGAGAGCATGTCGACCTACA
1 AGGTCGCCCGGAGAGCATGACGACCTACA
*
1191909 AGGTCGCCCGGAGGGCATGACGACCTA
1 AGGTCGCCCGGAGAGCATGACGACCTA
1191936 TGTGTTGGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.24, C:0.31, G:0.33, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGAGCATGACGACCTACA
Found at i:1193708 original size:6 final size:6
Alignment explanation
Indices: 1193697--1193749 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
1193687 ACGGCACGGC
1193697 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T-GTGG TCGT-G
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1193743 TCGTGG T
1 TCGTGG T
1193750 AATGGTAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 10 0.22
6 35 0.78
ACGTcount: A:0.00, C:0.15, G:0.49, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:1194060 original size:22 final size:22
Alignment explanation
Indices: 1194035--1194088 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1194025 CAGGAGTTTA
* *
1194035 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1194057 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
1194079 C-GGAGTTATA
1 CAGGAGTTATA
1194089 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1198071 original size:14 final size:14
Alignment explanation
Indices: 1198052--1198083 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1198042 TGGGGGGAAA
1198052 ATCCGACCACTGCC
1 ATCCGACCACTGCC
1198066 ATCCGACCACTGCC
1 ATCCGACCACTGCC
1198080 ATCC
1 ATCC
1198084 CTAGATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.50, G:0.12, T:0.16
Consensus pattern (14 bp):
ATCCGACCACTGCC
Found at i:1213201 original size:50 final size:48
Alignment explanation
Indices: 1213146--1213249 Score: 131
Period size: 48 Copynumber: 2.1 Consensus size: 48
1213136 AGATACAAAC
*
1213146 ATATATAATTTTAAGA-AAT-AAAAATAATTTATCAAAAGAAAATATAAAAA
1 ATATATAA-TATAAGATAATCAAAAAT--TTTAT-AAAAGAAAATATAAAAA
* *
1213196 ATATATAATATATGATAATCTAAAATTTTATAAAAGAAAATATAAAAA
1 ATATATAATATAAGATAATCAAAAATTTTATAAAAGAAAATATAAAAA
1213244 ATATAT
1 ATATAT
1213250 GATAATTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
48 23 0.47
49 10 0.20
50 11 0.22
51 5 0.10
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (48 bp):
ATATATAATATAAGATAATCAAAAATTTTATAAAAGAAAATATAAAAA
Found at i:1215098 original size:26 final size:27
Alignment explanation
Indices: 1215036--1215098 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
1215026 CTCAGTACTC
* * *
1215036 AAGGTTATTTTAGTCATTTTGGGGCTT
1 AAGGATATTTCAGTCATTTTGAGGCTT
1215063 AAGGATATTTCAGTCATTTT-AGG-TAT
1 AAGGATATTTCAGTCATTTTGAGGCT-T
*
1215089 AAGGGTATTT
1 AAGGATATTT
1215099 TGGTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 1 0.03
26 12 0.39
27 18 0.58
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.44
Consensus pattern (27 bp):
AAGGATATTTCAGTCATTTTGAGGCTT
Found at i:1217819 original size:106 final size:105
Alignment explanation
Indices: 1217686--1217899 Score: 320
Period size: 106 Copynumber: 2.0 Consensus size: 105
1217676 TAATTAGTTA
* * * *
1217686 TATGTTCTAAATTCGTTTTTTTATTAAAAATTAATGATCGTTTGAGCTGGACACTAATATATTAA
1 TATGTTCTAAACTCATTTTTTTATTAAAAATTAATGATCGTATGAGCTGGACACTAATATACTAA
**
1217751 TTAAAGTATGATAAAAATCATATTTTAATGATGTCTATTAG
66 TTAAAGTATGAT-AAAATCATATTTTAAAAATGTCTATTAG
* * *
1217792 TATGTTCTAAACTCATTTTTTTGTTAAAAATTAATGGTCGTATGAGCTGGACATTAATATACTAA
1 TATGTTCTAAACTCATTTTTTTATTAAAAATTAATGATCGTATGAGCTGGACACTAATATACTAA
* *
1217857 TTAAAGTATGATAAAATTATATTTTAAAAATGTCTGTTAG
66 TTAAAGTATGATAAAATCATATTTTAAAAATGTCTATTAG
1217897 TAT
1 TAT
1217900 TGTCGTTGCT
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
105 27 0.28
106 70 0.72
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (105 bp):
TATGTTCTAAACTCATTTTTTTATTAAAAATTAATGATCGTATGAGCTGGACACTAATATACTAA
TTAAAGTATGATAAAATCATATTTTAAAAATGTCTATTAG
Found at i:1221639 original size:21 final size:21
Alignment explanation
Indices: 1221614--1221661 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1221604 CCTAATATTG
* *
1221614 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGATACAA
1221635 CAATGTCAAAATTAGATACAA
1 CAATGTCAAAATTAGATACAA
1221656 CAATGT
1 CAATGT
1221662 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
CAATGTCAAAATTAGATACAA
Found at i:1226704 original size:14 final size:14
Alignment explanation
Indices: 1226681--1226715 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1226671 ATTCATTGCC
1226681 GTAA-TAGTTAAGA
1 GTAATTAGTTAAGA
1226694 GTAATTAGTTAAGA
1 GTAATTAGTTAAGA
1226708 GTAATTAG
1 GTAATTAG
1226716 GACAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (14 bp):
GTAATTAGTTAAGA
Found at i:1227127 original size:21 final size:21
Alignment explanation
Indices: 1227101--1227142 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1227091 CAATAGTGTC
*
1227101 CAATAGCACCTGCGACGGCCG
1 CAATAGCACCCGCGACGGCCG
*
1227122 CAATAGCACCCGTGACGGCCG
1 CAATAGCACCCGCGACGGCCG
1227143 TAATCACAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.10
Consensus pattern (21 bp):
CAATAGCACCCGCGACGGCCG
Found at i:1231419 original size:31 final size:31
Alignment explanation
Indices: 1231373--1231446 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
1231363 TAACTCATGG
* *
1231373 GATCACATCTTAATTAAATAAAAACGAAAGT
1 GATCATATATTAATTAAATAAAAACGAAAGT
* * ** *
1231404 GGTCATATATTAATTAAATATAATTGAAATT
1 GATCATATATTAATTAAATAAAAACGAAAGT
1231435 GATCATATATTA
1 GATCATATATTA
1231447 TATATATATT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.35
Consensus pattern (31 bp):
GATCATATATTAATTAAATAAAAACGAAAGT
Found at i:1236759 original size:2 final size:2
Alignment explanation
Indices: 1236752--1236804 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1236742 TACCCAAGTT
1236752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1236794 TA TA TA T- TA TA
1 TA TA TA TA TA TA
1236805 ATTGTGTATA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1244983 original size:19 final size:20
Alignment explanation
Indices: 1244959--1244996 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1244949 ATTGAATTTA
*
1244959 TTCAAAAGT-ATTCAAAGTT
1 TTCAAAAATAATTCAAAGTT
1244978 TTCAAAAATAATTCAAAGT
1 TTCAAAAATAATTCAAAGT
1244997 CCATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (20 bp):
TTCAAAAATAATTCAAAGTT
Found at i:1247468 original size:23 final size:23
Alignment explanation
Indices: 1247442--1247510 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1247432 CACCACAGCT
*
1247442 CGTATAATTGCACC-GAAGTGCCA
1 CGTAGAATTGCACCAG-AGTGCCA
*
1247465 CGTAGAATTGCACCAGAGTGCCG
1 CGTAGAATTGCACCAGAGTGCCA
* *
1247488 CATAGAATTTCACCAGAGTGCCA
1 CGTAGAATTGCACCAGAGTGCCA
1247511 TATAATAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 39 0.98
24 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCAGAGTGCCA
Found at i:1248204 original size:64 final size:66
Alignment explanation
Indices: 1248082--1248238 Score: 189
Period size: 64 Copynumber: 2.4 Consensus size: 66
1248072 CATTTTCATC
1248082 TTTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTT
1 TTTTAATGG-GG-ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTT
1248147 GTA
64 GTA
* * *
1248150 -TTTAATGGGGATGCATCGATGCACT-C-CTTATGCATCGATGCATTAATTGC-ATTCGATGTTT
1 TTTTAATGGGGATGCATCGATGCACTACAC-CATGCATCGATGCA-TAAATCCTATTCGATGTTT
1248211 GTA
64 GTA
** *
1248214 TTTTAAAAGAG-TGCATCGATGCACT
1 TTTTAATGGGGATGCATCGATGCACT
1248239 TCATGTGCAT
Statistics
Matches: 80, Mismatches: 6, Indels: 10
0.83 0.06 0.10
Matches are distributed among these distances:
63 1 0.01
64 42 0.52
65 27 0.34
66 2 0.03
67 8 0.10
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (66 bp):
TTTTAATGGGGATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGT
A
Found at i:1254736 original size:21 final size:21
Alignment explanation
Indices: 1254710--1254754 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1254700 TGATTCTGGG
* *
1254710 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1254731 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1254752 CAA
1 CAA
1254755 AACGACAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1255638 original size:31 final size:31
Alignment explanation
Indices: 1255600--1255752 Score: 238
Period size: 31 Copynumber: 5.0 Consensus size: 31
1255590 GGGTCGAGGG
1255600 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
1255631 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
1255662 TTACCTATGTTCTTCGGAACATATGGACTG-
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * * *
1255692 TTACCTATGTCCTTTGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
1255723 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
1255753 GTTCTTCGGG
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 27 0.24
31 85 0.75
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:1255727 original size:61 final size:62
Alignment explanation
Indices: 1255600--1255752 Score: 238
Period size: 61 Copynumber: 2.5 Consensus size: 62
1255590 GGGTCGAGGG
* *
1255600 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGAACATATGGACTGA
* *
1255662 TTACCTATGTTCTTCGGAACATATGGACTG-TTACCTATGTCCTTTGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGAACATATGGACTGA
*
1255723 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
1255753 GTTCTTCGGG
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
61 54 0.64
62 31 0.36
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGAACATATGGACTGA
Done.