Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 9 of 14
Found at i:930077 original size:27 final size:27
Alignment explanation
Indices: 929990--930078 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
929980 CATATATATA
* *
929990 ATATAAATAAAATAAAATAAAATATTAAT
1 ATATAAATAAAA-AATAT-AAATATCAAT
* *
930019 ATAT-AA-AAAATATAAAAATATC-AT
1 ATATAAATAAAAAATATAAATATCAAT
*
930043 ATTTTAAATAAAAAATATAAATATCAAT
1 A-TATAAATAAAAAATATAAATATCAAT
930071 ATATAAAT
1 ATATAAAT
930079 TTTTTTTTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
24 3 0.06
25 8 0.17
26 4 0.08
27 24 0.50
28 5 0.10
29 4 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
ATATAAATAAAAAATATAAATATCAAT
Found at i:936570 original size:93 final size:93
Alignment explanation
Indices: 936411--936598 Score: 306
Period size: 93 Copynumber: 2.0 Consensus size: 93
936401 TAAGTAACAT
* *
936411 AGCTTTCTACCATTATATTTCCAACTCAATTAATCAGCTCAGAAACTATACAAGGAAATTAAAAA
1 AGCTTTCAACCATTATATTTCCAACTCAATTAATCAGCTCAGAAACTAAACAAGGAAATTAAAAA
*
936476 CCAAGTGAACAAAAGGG-AAAGTTCACAC
66 CCAAGTGAACAAAAGGGCAAA-ATCACAC
*
936504 AGCTTTCAACCATTATATTTCCAACTCAATTAATCAGCTCAGAAACTAAATAAGGAAATTAAAAA
1 AGCTTTCAACCATTATATTTCCAACTCAATTAATCAGCTCAGAAACTAAACAAGGAAATTAAAAA
* *
936569 CCACGTGAACAAATGGGCAAAATCACAC
66 CCAAGTGAACAAAAGGGCAAAATCACAC
936597 AG
1 AG
936599 TAAAATGTTA
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
93 85 0.97
94 3 0.03
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.23
Consensus pattern (93 bp):
AGCTTTCAACCATTATATTTCCAACTCAATTAATCAGCTCAGAAACTAAACAAGGAAATTAAAAA
CCAAGTGAACAAAAGGGCAAAATCACAC
Found at i:939250 original size:19 final size:20
Alignment explanation
Indices: 939226--939266 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
939216 TAAGTTTATT
939226 AAATTTAAATTAAT-TTTAA
1 AAATTTAAATTAATATTTAA
* *
939245 AAATTTATATTATTATTTAA
1 AAATTTAAATTAATATTTAA
939265 AA
1 AA
939267 TAATATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTTAAATTAATATTTAA
Found at i:939264 original size:31 final size:34
Alignment explanation
Indices: 939222--939311 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
939212 TACTTAAGTT
*
939222 TATTAA-ATTTAAATTAAT-TTTAAAA-A-TTTA
1 TATTAATATTTAAATTAATATTAAAAATATTTTA
* *
939252 TATTATTATTTAAAATAATATTAAAAATATTTTA
1 TATTAATATTTAAATTAATATTAAAAATATTTTA
*
939286 TATTAATATTTATAATTAAAATTAAA
1 TATTAATATTTA-AATTAATATTAAA
939312 TAAAAATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
30 5 0.10
31 11 0.22
32 6 0.12
33 1 0.02
34 15 0.31
35 11 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
TATTAATATTTAAATTAATATTAAAAATATTTTA
Found at i:939599 original size:15 final size:15
Alignment explanation
Indices: 939537--939637 Score: 63
Period size: 15 Copynumber: 6.7 Consensus size: 15
939527 TTATATAAAA
939537 ATAATATTAAT-ATGAT
1 ATAA-ATTAATAAT-AT
939553 ATAAA-T-AT-ATAT
1 ATAAATTAATAATAT
*
939565 ATAAATTAATAAAAT
1 ATAAATTAATAATAT
939580 ATAAATTAATAATAT
1 ATAAATTAATAATAT
*
939595 TTAAAATTTTACATAA-AT
1 AT-AAA--TTA-ATAATAT
939613 ATATAATTAA-AATAT
1 ATA-AATTAATAATAT
*
939628 A-AAAATAATA
1 ATAAATTAATA
939638 TAAATAAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
12 7 0.10
13 10 0.14
14 7 0.10
15 23 0.33
16 10 0.14
17 1 0.01
18 8 0.11
19 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (15 bp):
ATAAATTAATAATAT
Found at i:939648 original size:11 final size:11
Alignment explanation
Indices: 939555--939649 Score: 56
Period size: 11 Copynumber: 8.5 Consensus size: 11
939545 AATATGATAT
*
939555 AAATATATATA
1 AAATATAAATA
939566 TAAAT-T-AATA
1 -AAATATAAATA
939576 AAATATAAATTA
1 AAATATAAA-TA
*
939588 ATAATAT--TTA
1 A-AATATAAATA
* *
939598 AAATTTTACATA
1 AAA-TATAAATA
*
939610 AATATATAATTA
1 AA-ATATAAATA
939622 AAATATAAA-A
1 AAATATAAATA
939632 ATAATATAAATA
1 A-AATATAAATA
939644 AAATAT
1 AAATAT
939650 GCAGATAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
9 6 0.09
10 11 0.17
11 22 0.34
12 20 0.31
13 6 0.09
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATATAAATA
Found at i:939659 original size:22 final size:22
Alignment explanation
Indices: 939529--939649 Score: 55
Period size: 23 Copynumber: 5.2 Consensus size: 22
939519 ATTAATTATT
* **
939529 ATATAAAAATAATATTAATATG
1 ATATAAAAATAATATAAATAAA
*
939551 ATATAAATATATATATAAATTAATA
1 ATATAAAAATA-ATATAAA-TAA-A
* * **
939576 AAATATAAATTAATAATATTTAAA
1 ATATA-AAAATAAT-ATAAATAAA
** * *
939600 AT-TTTACATAAATATATAATTAA
1 ATATAAAAAT-AATATA-AATAAA
939623 AATATAAAAATAATATAAATAAA
1 A-TATAAAAATAATATAAATAAA
939646 ATAT
1 ATAT
939650 GCAGATAATA
Statistics
Matches: 69, Mismatches: 21, Indels: 18
0.64 0.19 0.17
Matches are distributed among these distances:
22 18 0.26
23 20 0.29
24 11 0.16
25 13 0.19
26 7 0.10
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (22 bp):
ATATAAAAATAATATAAATAAA
Found at i:939877 original size:2 final size:2
Alignment explanation
Indices: 939870--939896 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
939860 CTGGTCGACC
939870 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
939897 ATCTTCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:942225 original size:23 final size:24
Alignment explanation
Indices: 942198--942243 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
942188 TAAAATTTTT
*
942198 TTTATATGCAAAT-TTGAATATGC
1 TTTATATACAAATATTGAATATGC
*
942221 TTTATATACAGATATTGAATATG
1 TTTATATACAAATATTGAATATG
942244 TATATTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (24 bp):
TTTATATACAAATATTGAATATGC
Found at i:950224 original size:2 final size:2
Alignment explanation
Indices: 950217--950241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
950207 TCCAGCCCCC
950217 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
950242 AACCTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:950439 original size:27 final size:28
Alignment explanation
Indices: 950409--950481 Score: 67
Period size: 30 Copynumber: 2.5 Consensus size: 28
950399 CAATTTTTGT
950409 AAAAAAAAAAAAAAAGCTTAATT-ATTA
1 AAAAAAAAAAAAAAAGCTTAATTAATTA
** *
950436 AAAATAAAAGTTTAAAAAGCTTAATTAATTG
1 AAAA-AAAA--AAAAAAAGCTTAATTAATTA
* *
950467 TAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAA
950482 TTCAGGTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
27 4 0.11
28 9 0.25
30 17 0.47
31 6 0.17
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.23
Consensus pattern (28 bp):
AAAAAAAAAAAAAAAGCTTAATTAATTA
Found at i:950587 original size:10 final size:10
Alignment explanation
Indices: 950572--950620 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
950562 AAATAAATAA
950572 TAAATTTAAT
1 TAAATTTAAT
*
950582 TAAATTTATT
1 TAAATTTAAT
950592 TAAATAATTAA-
1 TAAAT--TTAAT
*
950603 TAAATATAAT
1 TAAATTTAAT
950613 TAAATTTA
1 TAAATTTA
950621 TTCGTGATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 3 0.09
10 21 0.66
11 5 0.16
12 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAAATTTAAT
Found at i:950604 original size:31 final size:31
Alignment explanation
Indices: 950561--950622 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
950551 CTTTTGATAG
*
950561 TAAATAAATAATAAATTTAATTAAATTTATT
1 TAAATAAATAATAAATATAATTAAATTTATT
*
950592 TAAATAATTAATAAATATAATTAAATTTATT
1 TAAATAAATAATAAATATAATTAAATTTATT
950623 CGTGATTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TAAATAAATAATAAATATAATTAAATTTATT
Found at i:952377 original size:14 final size:15
Alignment explanation
Indices: 952358--952386 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
952348 TGATTATAAA
952358 CAGAAAACA-GCCAG
1 CAGAAAACATGCCAG
952372 CAGAAAACATGCCAG
1 CAGAAAACATGCCAG
952387 GGCCACCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.28, G:0.21, T:0.03
Consensus pattern (15 bp):
CAGAAAACATGCCAG
Found at i:955617 original size:16 final size:15
Alignment explanation
Indices: 955566--955617 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
955556 ATTTTTTAAA
*
955566 TAAAAATATTATAAAT
1 TAAAAATATAAT-AAT
*
955582 TAAAAGAAATAATAAGT
1 TAAAA-ATATAATAA-T
955599 TAAAAATATAAATAAT
1 TAAAAATAT-AATAAT
955615 TAA
1 TAA
955618 TTAATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
TAAAAATATAATAAT
Found at i:955783 original size:3 final size:3
Alignment explanation
Indices: 955775--955823 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
955765 TCCTATCTGC
955775 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
955823 T
1 T
955824 TCTCCAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:956183 original size:14 final size:13
Alignment explanation
Indices: 956152--956180 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
956142 TATTATTAAA
956152 TTTAATTAAATTT
1 TTTAATTAAATTT
956165 TTTAATTAAATTT
1 TTTAATTAAATTT
956178 TTT
1 TTT
956181 TAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTAATTAAATTT
Found at i:959695 original size:16 final size:16
Alignment explanation
Indices: 959674--959729 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
959664 AATATTATTT
959674 TTTAAATATAATTTAA
1 TTTAAATATAATTTAA
* * *
959690 TTTAAATTTAATTGAT
1 TTTAAATATAATTTAA
959706 TTTATAGATA-AATTTAA
1 TTTA-A-ATATAATTTAA
*
959723 TTAAAAT
1 TTTAAAT
959730 GTGGTTCAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
15 2 0.06
16 18 0.58
17 9 0.29
18 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
TTTAAATATAATTTAA
Found at i:961262 original size:22 final size:20
Alignment explanation
Indices: 961235--961287 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
961225 ATATTTTAAA
**
961235 ATTTAAATTTATTTATTATT
1 ATTTAAATTTATAAATTATT
961255 AATATTAAATTTATAAATTATT
1 -AT-TTAAATTTATAAATTATT
961277 ATTTAAATTTA
1 ATTTAAATTTA
961288 AATTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.31
21 4 0.14
22 16 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAAATTTATAAATTATT
Found at i:961318 original size:31 final size:27
Alignment explanation
Indices: 961205--961321 Score: 88
Period size: 26 Copynumber: 4.4 Consensus size: 27
961195 AATTTTTTAC
*
961205 AATATTTAAATTTAATATAAATA-T-TTT
1 AATATTTAAA-TTAATA-AATTATTATTT
* *
961232 AAAATTTAAATT--T-ATTTATTA-TT
1 AATATTTAAATTAATAAATTATTATTT
*
961255 AATA-TTAAATTTATAAATTATTATTT
1 AATATTTAAATTAATAAATTATTATTT
961281 AA-ATTTAAATTAAATAATATTATCTATTT
1 AATATTTAAATT-AATAA-ATTAT-TATTT
961310 AAATATTTAAAT
1 -AATATTTAAAT
961322 CTATTTAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 20
0.73 0.06 0.20
Matches are distributed among these distances:
22 10 0.14
23 6 0.08
24 2 0.03
25 8 0.11
26 13 0.18
27 13 0.18
28 5 0.07
29 5 0.07
30 2 0.03
31 8 0.11
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
AATATTTAAATTAATAAATTATTATTT
Found at i:961323 original size:18 final size:18
Alignment explanation
Indices: 961302--961338 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
961292 AAATAATATT
*
961302 ATCTATTTAAATATTTAA
1 ATCTATTTAAAAATTTAA
961320 ATCTATTTAAAAATTTAA
1 ATCTATTTAAAAATTTAA
961338 A
1 A
961339 CTCAACAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
ATCTATTTAAAAATTTAA
Found at i:961436 original size:15 final size:14
Alignment explanation
Indices: 961420--961515 Score: 58
Period size: 14 Copynumber: 7.0 Consensus size: 14
961410 TATAATAATA
961420 ATATAAATTTAAAT
1 ATATAAATTTAAAT
*
961434 A-ATAAATTTATAT
1 ATATAAATTTAAAT
* *
961447 GTTTAAATTT--AT
1 ATATAAATTTAAAT
* **
961459 -TATCAATAAAAAT
1 ATATAAATTTAAAT
*
961472 AATATAAATTTTAAT
1 -ATATAAATTTAAAT
961487 A-ATACATATTTAAAT
1 ATATA-A-ATTTAAAT
*
961502 ATTTAAATTTAAAT
1 ATATAAATTTAAAT
961516 TTATTATAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
11 5 0.08
12 2 0.03
13 16 0.26
14 18 0.30
15 18 0.30
16 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (14 bp):
ATATAAATTTAAAT
Found at i:961445 original size:21 final size:21
Alignment explanation
Indices: 961397--961454 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
961387 TATAAATATC
961397 TAAATTTAT-TATTTATAATAA
1 TAAATTTATATATTTA-AATAA
*
961418 T-AA--TATAAATTTAAATAA
1 TAAATTTATATATTTAAATAA
*
961436 TAAATTTATATGTTTAAAT
1 TAAATTTATATATTTAAAT
961455 TTATTATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 9 0.30
19 7 0.23
20 2 0.07
21 12 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAATTTATATATTTAAATAA
Found at i:961458 original size:53 final size:55
Alignment explanation
Indices: 961389--961530 Score: 173
Period size: 53 Copynumber: 2.6 Consensus size: 55
961379 TTAAATTTTA
*
961389 TAAATATCTAAATTTATTATTTATAATAATAATATAAATTTAAATAATA-A-ATT
1 TAAATATTTAAATTTATTATTTATAATAATAATATAAATTTAAATAATACATATT
* * ** * *
961442 TATATGTTTAAATTTATTATCAATAAAAATAATATAAATTTTAATAATACATATT
1 TAAATATTTAAATTTATTATTTATAATAATAATATAAATTTAAATAATACATATT
* *
961497 TAAATATTTAAATTTA-AATTTATTATAAATAATA
1 TAAATATTTAAATTTATTATTTATAAT-AATAATA
961531 ATTATTTATA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
53 42 0.58
54 6 0.08
55 24 0.33
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (55 bp):
TAAATATTTAAATTTATTATTTATAATAATAATATAAATTTAAATAATACATATT
Found at i:962223 original size:34 final size:35
Alignment explanation
Indices: 962162--962233 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
962152 TTTTAATTAA
962162 AAAATCATAATTTATAAATATTAAAATTTAAAATT
1 AAAATCATAATTTATAAATATTAAAATTTAAAATT
* * *
962197 AAAAT-ATATTTTTTAAATAATT-AAATTTAAATTT
1 AAAATCATAATTTATAAAT-ATTAAAATTTAAAATT
962231 AAA
1 AAA
962234 TTCACCTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 25 0.76
35 8 0.24
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (35 bp):
AAAATCATAATTTATAAATATTAAAATTTAAAATT
Found at i:963236 original size:18 final size:18
Alignment explanation
Indices: 963215--963252 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
963205 ATTTTTAATA
*
963215 TATTAAAAATTATAATTT
1 TATTAAAAATAATAATTT
*
963233 TATTAAATATAATAATTT
1 TATTAAAAATAATAATTT
963251 TA
1 TA
963253 AAAAATGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTAAAAATAATAATTT
Found at i:963592 original size:3 final size:3
Alignment explanation
Indices: 963584--963624 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
963574 TTATATTTTA
* *
963584 ATT ATT ATT -TA AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
963625 TTGTTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 32 0.97
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:964222 original size:50 final size:50
Alignment explanation
Indices: 964168--964267 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
964158 GATCATATCC
964168 TACCAAACACAAGATTTTAAAATAAATAAATGAATAGTACGAATAACATA
1 TACCAAACACAAGATTTTAAAATAAATAAATGAATAGTACGAATAACATA
964218 TACCAAACACAAGATTTTAAAATAAATAAATGAATAGTACGAATAACATA
1 TACCAAACACAAGATTTTAAAATAAATAAATGAATAGTACGAATAACATA
964268 GTCCGGAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (50 bp):
TACCAAACACAAGATTTTAAAATAAATAAATGAATAGTACGAATAACATA
Found at i:968998 original size:4 final size:4
Alignment explanation
Indices: 968989--969041 Score: 61
Period size: 4 Copynumber: 13.2 Consensus size: 4
968979 CCATAATTTG
* * * * *
968989 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATGT ATGT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
969037 ATAT A
1 ATAT A
969042 CACATGCAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:971259 original size:17 final size:17
Alignment explanation
Indices: 971230--971273 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
971220 TTTATCAAAA
*
971230 ATTC-AAATCTAAAATG
1 ATTCAAAATTTAAAATG
971246 ATAT-AAAATTTAAAATG
1 AT-TCAAAATTTAAAATG
971263 ATTCAAAATTT
1 ATTCAAAATTT
971274 TAACATCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (17 bp):
ATTCAAAATTTAAAATG
Found at i:971710 original size:18 final size:18
Alignment explanation
Indices: 971689--971728 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
971679 TAAATATAGT
971689 TTTAATATTAAATAAT-TA
1 TTTAATATTAAA-AATATA
971707 TTT-A-ATTAAAAATATA
1 TTTAATATTAAAAATATA
971723 TTTAAT
1 TTTAAT
971729 TTATTGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.16
16 11 0.58
17 2 0.11
18 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATATTAAAAATATA
Found at i:971716 original size:16 final size:16
Alignment explanation
Indices: 971695--971729 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
971685 TAGTTTTAAT
971695 ATTAAATAAT-TATTTA
1 ATTAAA-AATATATTTA
971711 ATTAAAAATATATTTA
1 ATTAAAAATATATTTA
971727 ATT
1 ATT
971730 TATTGACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAAAATATATTTA
Found at i:971745 original size:20 final size:20
Alignment explanation
Indices: 971720--971768 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
971710 AATTAAAAAT
* *
971720 ATATTTAATTTATTGACATA
1 ATATTTAATTGAATGACATA
* *
971740 ATATTTAATTGAATGATATG
1 ATATTTAATTGAATGACATA
971760 ATATTTAAT
1 ATATTTAAT
971769 ATATGTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (20 bp):
ATATTTAATTGAATGACATA
Found at i:977330 original size:2 final size:2
Alignment explanation
Indices: 977323--977347 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
977313 TTAATTTATG
977323 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
977348 GTACATGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:983783 original size:32 final size:32
Alignment explanation
Indices: 983747--983821 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
983737 TTCATACTTA
*
983747 AAAATAATTAAAACTCGAAATAACTCAAATCT
1 AAAATAATTAAAACTCAAAATAACTCAAATCT
* * *
983779 AAAATAACTT-AAATTCAAAATGACTCAAATTT
1 AAAATAA-TTAAAACTCAAAATAACTCAAATCT
*
983811 AAAATGATTAA
1 AAAATAATTAA
983822 TCTCAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 2 0.06
32 32 0.89
33 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.28
Consensus pattern (32 bp):
AAAATAATTAAAACTCAAAATAACTCAAATCT
Found at i:983817 original size:16 final size:16
Alignment explanation
Indices: 983764--983815 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
983754 TTAAAACTCG
*
983764 AAATAACTCAAATCTA
1 AAATAACTCAAATTTA
* *
983780 AAATAACTTAAATTCA
1 AAATAACTCAAATTTA
*
983796 AAATGACTCAAATTTA
1 AAATAACTCAAATTTA
983812 AAAT
1 AAAT
983816 GATTAATCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (16 bp):
AAATAACTCAAATTTA
Found at i:983913 original size:32 final size:33
Alignment explanation
Indices: 983877--983983 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 33
983867 TAAAACTACA
983877 AAAACTTAAAATGATCTAAAACTC-AATAATTT
1 AAAACTTAAAATGATCTAAAACTCAAATAATTT
* ** *
983909 AAAAC-TAAAAT-AACTTAAATTTCAAATTATTT
1 AAAACTTAAAATGATC-TAAAACTCAAATAATTT
* * *
983941 -AAATTTAAAATGATCTAAAACTAAAATTATTT
1 AAAACTTAAAATGATCTAAAACTCAAATAATTT
*
983973 AAATC-TAAAAT
1 AAAACTTAAAAT
983984 CATCCGAACA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
30 2 0.03
31 15 0.25
32 38 0.64
33 4 0.07
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (33 bp):
AAAACTTAAAATGATCTAAAACTCAAATAATTT
Found at i:983959 original size:16 final size:16
Alignment explanation
Indices: 983905--983983 Score: 77
Period size: 16 Copynumber: 4.9 Consensus size: 16
983895 AAACTCAATA
* *
983905 ATTTAAAACTAAAATA
1 ATTTAAATCTAAAATT
* * *
983921 ACTTAAATTTCAAATT
1 ATTTAAATCTAAAATT
* *
983937 ATTTAAATTTAAAATG
1 ATTTAAATCTAAAATT
* *
983953 ATCTAAAACTAAAATT
1 ATTTAAATCTAAAATT
983969 ATTTAAATCTAAAAT
1 ATTTAAATCTAAAAT
983984 CATCCGAACA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (16 bp):
ATTTAAATCTAAAATT
Found at i:992942 original size:4 final size:4
Alignment explanation
Indices: 992915--992957 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
992905 ATGGCACCAG
* *
992915 AGAA ACAA A-AA AGAA A-AA AAAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
992958 AACCTGCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 6 0.17
4 29 0.83
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:992950 original size:12 final size:11
Alignment explanation
Indices: 992915--992959 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
992905 ATGGCACCAG
*
992915 AGAAACAAAAA
1 AGAAAGAAAAA
*
992926 AGAAAAAAAAA
1 AGAAAGAAAAA
992937 AGAAAGAAAGAA
1 AGAAAGAAA-AA
992949 AGAAAGAAAAA
1 AGAAAGAAAAA
992960 CCTGCCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:993922 original size:27 final size:27
Alignment explanation
Indices: 993870--993922 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
993860 TGTATTTTTA
**
993870 TATTTTTTTAATATATATTTAGTAATT
1 TATTTTTTTAATATATAAATAGTAATT
993897 TATTTTTTTAATTATATAAATA-TAAT
1 TATTTTTTTAA-TATATAAATAGTAAT
993923 ATAAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TATTTTTTTAATATATAAATAGTAATT
Found at i:993951 original size:17 final size:19
Alignment explanation
Indices: 993906--993957 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
993896 TTATTTTTTT
993906 AATTATATAAATATAATATA
1 AATTAT-TAAATATAATATA
*
993926 AATTATTAAATATATTA-A
1 AATTATTAAATATAATATA
993944 AATT-TTAAATATAA
1 AATTATTAAATATAA
993958 ATATTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 9 0.30
18 5 0.17
19 10 0.33
20 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATTAAATATAATATA
Found at i:995414 original size:2 final size:2
Alignment explanation
Indices: 995409--995435 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
995399 CATATATATA
995409 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
995436 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1001124 original size:2 final size:2
Alignment explanation
Indices: 1001117--1001160 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1001107 TGCCTCTTCA
*
1001117 AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1001159 AT
1 AT
1001161 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1003168 original size:15 final size:15
Alignment explanation
Indices: 1003150--1003196 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1003140 ATATATTTAA
1003150 AATTTATGATATATT
1 AATTTATGATATATT
*
1003165 AATTTAAGATATATTT
1 AATTTATGATATA-TT
1003181 ATATTTAT-AT-TATT
1 A-ATTTATGATATATT
1003195 AA
1 AA
1003197 CATAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 3 0.11
15 14 0.50
16 5 0.18
17 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (15 bp):
AATTTATGATATATT
Found at i:1003215 original size:25 final size:25
Alignment explanation
Indices: 1003187--1003235 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1003177 ATTTATATTT
1003187 ATATTATTAACATAAA-AAATAAATG
1 ATATTATT-ACATAAATAAATAAATG
*
1003212 ATATTATTATATAAATAAATAAAT
1 ATATTATTACATAAATAAATAAAT
1003236 TATCAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATTATTACATAAATAAATAAATG
Found at i:1006339 original size:7 final size:7
Alignment explanation
Indices: 1006327--1006356 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1006317 TCCAAGTTTG
1006327 AAATAAA
1 AAATAAA
1006334 AAATAAA
1 AAATAAA
1006341 AAATAAA
1 AAATAAA
1006348 AAA-AAA
1 AAATAAA
1006354 AAA
1 AAA
1006357 GCAAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (7 bp):
AAATAAA
Found at i:1006422 original size:13 final size:13
Alignment explanation
Indices: 1006404--1006428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1006394 GGCACCTCGT
1006404 GGCCATGGGAGGA
1 GGCCATGGGAGGA
1006417 GGCCATGGGAGG
1 GGCCATGGGAGG
1006429 GGCAGCCGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.56, T:0.08
Consensus pattern (13 bp):
GGCCATGGGAGGA
Found at i:1012048 original size:8 final size:8
Alignment explanation
Indices: 1012035--1012059 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1012025 AAGTATGTCG
1012035 TTTTTTTA
1 TTTTTTTA
1012043 TTTTTTTA
1 TTTTTTTA
1012051 TTTTTTTA
1 TTTTTTTA
1012059 T
1 T
1012060 AATTTTATGT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1013820 original size:2 final size:2
Alignment explanation
Indices: 1013813--1013844 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1013803 TCCACCAGCA
1013813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1013845 GTGTAGGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1013977 original size:24 final size:24
Alignment explanation
Indices: 1013950--1013998 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1013940 ATATGATGAG
1013950 TATAGAATATA-AAAATATATTTAA
1 TATA-AATATATAAAATATATTTAA
*
1013974 TATAAATATATAAAATATTTTTAA
1 TATAAATATATAAAATATATTTAA
1013998 T
1 T
1013999 TTTTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TATAAATATATAAAATATATTTAA
Found at i:1014292 original size:28 final size:27
Alignment explanation
Indices: 1014260--1014329 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 27
1014250 AAATAAATAA
* **
1014260 TTTATATATTTATCTTATATTTATATTT
1 TTTATATATTTATATTATATTTA-AAAT
*
1014288 TTTATCATAATTA-ATTATATTTAAAAT
1 TTTAT-ATATTTATATTATATTTAAAAT
*
1014315 ATTATATATTTATAT
1 TTTATATATTTATAT
1014330 ATAATTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 6 0.18
27 8 0.24
28 14 0.41
29 6 0.18
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTATATATTTATATTATATTTAAAAT
Found at i:1014392 original size:12 final size:11
Alignment explanation
Indices: 1014359--1014416 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 11
1014349 ATTTATGTTA
1014359 TATAAAT-TTT
1 TATAAATATTT
*
1014369 AATATAAT-TTT
1 TATA-AATATTT
1014380 TATAACATATTT
1 TATAA-ATATTT
1014392 TATTTAAATATTT
1 TA--TAAATATTT
1014405 TAT-AATATTT
1 TATAAATATTT
1014415 TA
1 TA
1014417 ATTATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 13 0.32
11 12 0.29
12 5 0.12
13 8 0.20
14 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TATAAATATTT
Found at i:1014435 original size:23 final size:22
Alignment explanation
Indices: 1014356--1014435 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
1014346 ATAATTTATG
* *
1014356 TTATATAAATTTTAATATAATTT
1 TTATATATATTTTAAT-TATTTT
* * *
1014379 TTATAACATATTTTATTTAAATATT
1 TTAT-ATATATTTTAATT--ATTTT
1014404 TTATA-ATATTTTAATTATTTT
1 TTATATATATTTTAATTATTTT
1014425 TTATATCATAT
1 TTATAT-ATAT
1014436 AATATTATCC
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
21 9 0.20
23 19 0.42
24 10 0.22
25 7 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATATATTTTAATTATTTT
Found at i:1015501 original size:19 final size:19
Alignment explanation
Indices: 1015460--1015495 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1015450 GAAAAATTAA
*
1015460 TATAAATATAATTTAAATG
1 TATAAATATAATTAAAATG
1015479 TATAAATAT-ATTAAAAT
1 TATAAATATAATTAAAAT
1015496 TTTATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TATAAATATAATTAAAATG
Found at i:1015537 original size:34 final size:36
Alignment explanation
Indices: 1015462--1015537 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 36
1015452 AAAATTAATA
**
1015462 TAAATATAATTTAAATGTATAAATATATTAAAATTT
1 TAAATATAAAATAAATGTATAAATATATTAAAATTT
*
1015498 T--ATATAAAATAAAT-TATTAATATA-TAAAATTT
1 TAAATATAAAATAAATGTATAAATATATTAAAATTT
1015530 TAAATATA
1 TAAATATA
1015538 TTATAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
32 9 0.26
33 9 0.26
34 16 0.46
36 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (36 bp):
TAAATATAAAATAAATGTATAAATATATTAAAATTT
Found at i:1015538 original size:16 final size:16
Alignment explanation
Indices: 1015481--1015538 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1015471 TTTAAATGTA
1015481 TAAATATATTAAAATTT
1 TAAATATA-TAAAATTT
* *
1015498 TATATA-AAATAAATTAT
1 TAAATATATA-AAATT-T
1015515 T-AATATATAAAATTT
1 TAAATATATAAAATTT
1015530 TAAATATAT
1 TAAATATAT
1015539 TATAATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
15 3 0.09
16 21 0.64
17 9 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATATATAAAATTT
Found at i:1015715 original size:2 final size:2
Alignment explanation
Indices: 1015703--1015739 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1015693 CTGAAATTTC
*
1015703 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1015740 CGGCGCCGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1015825 original size:2 final size:2
Alignment explanation
Indices: 1015820--1015846 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1015810 ATTTTTATTT
1015820 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1015847 TTGTTCGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1016779 original size:20 final size:19
Alignment explanation
Indices: 1016756--1016797 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1016746 TATATTTTAT
1016756 TAAAAT-TTAATTATAAAATA
1 TAAAATATTAA-TATAAAA-A
1016776 TAAAATATTAATATAAAAA
1 TAAAATATTAATATAAAAA
1016795 TAA
1 TAA
1016798 TTTTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATATTAATATAAAAA
Found at i:1017232 original size:3 final size:3
Alignment explanation
Indices: 1017224--1017262 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1017214 TCTCTTTTTA
1017224 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1017263 TTCGTATCTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1019622 original size:21 final size:21
Alignment explanation
Indices: 1019596--1019651 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1019586 TTAAAATATA
* * *
1019596 AAATAAAATATGATATTTTAT
1 AAATAAAATATAAAATTTAAT
1019617 AAATAATAATA-AAAATTTAAT
1 AAATAA-AATATAAAATTTAAT
1019638 AAATATAAATATAA
1 AAATA-AAATATAA
1019652 CAAAATTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATAAAATATAAAATTTAAT
Found at i:1019648 original size:24 final size:25
Alignment explanation
Indices: 1019614--1019668 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 25
1019604 TATGATATTT
*
1019614 TATAAATAATAATAAAAATTTAATA-AA
1 TATAAAT-ATAA-CAAAA-TTAATACAA
1019641 TATAAATATAACAAAATTAATACAA
1 TATAAATATAACAAAATTAATACAA
1019666 TAT
1 TAT
1019669 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 9 0.35
26 4 0.15
27 7 0.27
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
TATAAATATAACAAAATTAATACAA
Found at i:1027383 original size:290 final size:283
Alignment explanation
Indices: 1026864--1027973 Score: 1204
Period size: 290 Copynumber: 4.0 Consensus size: 283
1026854 AAAACATGCT
* * *
1026864 ACATCATTCATTTGCCAAACTATTAAATAAGGTAAACTAGCTG-CAAGAAAGAAAAATAACAATA
1 ACATCATTCATTTGCCAAACAATTAAGTGAGGTAAACTAGCTGCCAAGAAAGAAAAATAACAATA
* * * * * *
1026928 AGCATGACAAACTATACAGGTAAACAAATTATGACAGCACTAAAACGAATTAGTACTTGACAGTA
66 AGCATAAGAAACTATTCAGGTAAACAAATTATGACA-CACTAAAATGAATTAGCACTTGACAGGA
* * *
1026993 AAACACGTTAA-GGATAATTCTGAATCCGACAGGCATCGGATCTTAGGGAGACTTAAGGAAAATG
130 AAACACATGAAGGGATAATTCTGAATCCGACAGGCATTGGATCTTA-GGAGACTTAAGGAAAATG
*
1027057 ATGAAAAATGCTTTAAAATTATCTAGATATCAATGTTC-TCTCAACAAACACCCAAAAGCAAAAC
194 ATGAAAAATGCTTTAAAATTATCTGGATATCAATGTTCTTC-CAACAAACACCCAAAAGCAAAAC
1027121 ATGTTACAATGTAGGCAGAGAAAGAA
258 ATGTTACAATGTAGGCAGAGAAAGAA
* * *
1027147 GCATCTTTCATTTGCCAAACCATTAAGTGAGGTAAACTAGCTGCCAAGAAAGAAAAATAACAATA
1 ACATCATTCATTTGCCAAACAATTAAGTGAGGTAAACTAGCTGCCAAGAAAGAAAAATAACAATA
**
1027212 AGCATTAAGAAACTATTCAGGTAAACAAATTATGACACACTAAAATGAATTGAATTAGCACTCAA
66 AGCA-TAAGAAACTATTCAGGTAAACAAATTATGACACACT--AA--AA-TGAATTAGCACTTGA
*
1027277 CAGGAAAA-AGCATGAAGGGATAATTCTGAATCCGACAGGCATTGGATATTAGCGAGACTTAAGG
125 CAGGAAAACA-CATGAAGGGATAATTCTGAATCCGACAGGCATTGGATCTTAG-GAGACTTAAGG
*
1027341 AAAATGATGAAAAATGCTTTAAAATTATATGGATATCAATGTTCTTCCAACAAACA-CCAAGAAG
188 AAAATGATGAAAAATGCTTTAAAATTATCTGGATATCAATGTTCTTCCAACAAACACCCAA-AAG
* *
1027405 CAAAACATGTTACAATGTATGCAGAGGAAGAA
252 CAAAACATGTTACAATGTAGGCAGAGAAAGAA
* * * *
1027437 ACATCATTCATTTGCTAAA-AATAAAAAGTGCA-GTAAACTAGCTGCGAAGAAATAAAAATAACA
1 ACATCATTCATTTGCCAAACAAT--TAAGTG-AGGTAAACTAGCTGCCAAGAAAGAAAAATAACA
* *
1027500 ATAAGCACTAAGAAA-TTTTGCAGGTAAACAAATTATGACAAACTAAAATGAATTAGCACTTGAC
63 ATAAGCA-TAAGAAACTATT-CAGGTAAACAAATTATGACACACTAAAATGAATTAGCACTTGAC
* *
1027564 AGGAAAACACATGAAGGGATAATTCTGAATCTGACAGGCGTTGGATCTTCAGGAGACTTAAGG-A
126 AGGAAAACACATGAAGGGATAATTCTGAATCCGACAGGCATTGGATCTT-AGGAGACTTAAGGAA
** *
1027628 AATGATGAAAAATGCTTTAAAATTATCTGGATATTGAGGTTCTTCCAACAAACACCCAAAAG-AT
190 AATGATGAAAAATGCTTTAAAATTATCTGGATATCAATGTTCTTCCAACAAACACCCAAAAGCA-
1027692 AAACATG---C----T--------------
254 AAACATGTTACAATGTAGGCAGAGAAAGAA
* * * * * *
1027701 ACATCGTTCATTTGCCAAACTATTAAGTGAGCTAAATTAGCTG-CAAGAAAGAATAGTAAC----
1 ACATCATTCATTTGCCAAACAATTAAGTGAGGTAAACTAGCTGCCAAGAAAGAAAAATAACAATA
* * * * * *
1027761 -G-AT-ACAAACCATGCAGGTCAACAAATTATGACAGCACTAAAATG-ATTAGCACTTGACAAGC
66 AGCATAAGAAACTATTCAGGTAAACAAATTATGACA-CACTAAAATGAATTAGCACTTGACAGGA
** * * * *
1027822 AAACATGTGAA-GGATAATTCTGAATCCAACAGGAATTGGATTTTAGGGAGACTTAAGGAATATG
130 AAACACATGAAGGGATAATTCTGAATCCGACAGGCATTGGATCTTA-GGAGACTTAAGGAAAATG
* * * * * *
1027886 ACGAAAAATGCTTTAAAATTATCTAGATATCGATGTTCTTCCAACAAAAACACAAAAGCAAAATA
194 ATGAAAAATGCTTTAAAATTATCTGGATATCAATGTTCTTCCAACAAACACCCAAAAGCAAAACA
* **
1027951 TGCTACAATGTTTGCAGAGAAAG
259 TGTTACAATGTAGGCAGAGAAAG
1027974 GAACGTCCTT
Statistics
Matches: 708, Mismatches: 73, Indels: 102
0.80 0.08 0.12
Matches are distributed among these distances:
252 1 0.00
253 40 0.06
254 109 0.15
255 12 0.02
256 1 0.00
257 2 0.00
261 1 0.00
262 14 0.02
263 15 0.02
264 17 0.02
265 2 0.00
278 1 0.00
282 1 0.00
283 38 0.05
284 30 0.04
285 90 0.13
286 75 0.11
287 5 0.01
288 3 0.00
289 31 0.04
290 146 0.21
291 73 0.10
292 1 0.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (283 bp):
ACATCATTCATTTGCCAAACAATTAAGTGAGGTAAACTAGCTGCCAAGAAAGAAAAATAACAATA
AGCATAAGAAACTATTCAGGTAAACAAATTATGACACACTAAAATGAATTAGCACTTGACAGGAA
AACACATGAAGGGATAATTCTGAATCCGACAGGCATTGGATCTTAGGAGACTTAAGGAAAATGAT
GAAAAATGCTTTAAAATTATCTGGATATCAATGTTCTTCCAACAAACACCCAAAAGCAAAACATG
TTACAATGTAGGCAGAGAAAGAA
Found at i:1029266 original size:18 final size:18
Alignment explanation
Indices: 1029236--1029281 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1029226 TTCGTTTATA
1029236 AAAATTTATTTTATTAT-TT
1 AAAATTTA-TTTA-TATGTT
1029255 AAAATTTATTTATATGTT
1 AAAATTTATTTATATGTT
*
1029273 AATATTTAT
1 AAAATTTAT
1029282 ATAATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 14 0.56
19 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
AAAATTTATTTATATGTT
Found at i:1032159 original size:11 final size:10
Alignment explanation
Indices: 1032138--1032181 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
1032128 AATGTTTAAA
1032138 TTAAATTTTT
1 TTAAATTTTT
1032148 TTAAATTTTT
1 TTAAATTTTT
* * *
1032158 TT-TATATAT
1 TTAAATTTTT
1032167 TTAAATTTTT
1 TTAAATTTTT
1032177 TTAAA
1 TTAAA
1032182 AAAATTATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 6 0.22
10 21 0.78
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTAAATTTTT
Found at i:1035647 original size:11 final size:10
Alignment explanation
Indices: 1035631--1035657 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1035621 TTCTTCCTTT
1035631 AAAAAAAGAA
1 AAAAAAAGAA
1035641 AAAAAAAGAA
1 AAAAAAAGAA
1035651 AAAAAAA
1 AAAAAAA
1035658 TCTGTTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:1037228 original size:17 final size:16
Alignment explanation
Indices: 1037163--1037245 Score: 62
Period size: 17 Copynumber: 5.0 Consensus size: 16
1037153 GTAAAATAAT
1037163 TTTAAATTGAA-TTAAA
1 TTTAAATT-AATTTAAA
* * *
1037179 TCTCAAATTAACTTGAA
1 T-TTAAATTAATTTAAA
*
1037196 TTTTAATT-ATTATAAA
1 TTTAAATTAATT-TAAA
1037212 TATTAAATTAATTTAAA
1 T-TTAAATTAATTTAAA
*
1037229 TTTAAATATAAATTAAA
1 TTTAAAT-TAATTTAAA
1037246 CTATTTAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 2 0.04
16 18 0.34
17 30 0.57
18 3 0.06
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:1038955 original size:14 final size:15
Alignment explanation
Indices: 1038936--1038965 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1038926 TTTTAAGTAT
1038936 ATTTAA-AAAAATTA
1 ATTTAAGAAAAATTA
1038950 ATTTAAGAAAAATTA
1 ATTTAAGAAAAATTA
1038965 A
1 A
1038966 AATATTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
ATTTAAGAAAAATTA
Found at i:1039399 original size:15 final size:13
Alignment explanation
Indices: 1039365--1039415 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 13
1039355 AAATGATAAT
* *
1039365 ATTCTAATAGCAA
1 ATTCAAATATCAA
1039378 TATTCAAATATGACAA
1 -ATTCAAATAT--CAA
1039394 ATTCAAATATCAA
1 ATTCAAATATCAA
1039407 A-TCAAATAT
1 ATTCAAATAT
1039416 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 8 0.24
13 4 0.12
14 8 0.24
15 10 0.30
16 3 0.09
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (13 bp):
ATTCAAATATCAA
Found at i:1039413 original size:12 final size:14
Alignment explanation
Indices: 1039379--1039415 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1039369 TAATAGCAAT
1039379 ATTCAAATATGACAA
1 ATTCAAATAT-ACAA
1039394 ATTCAAATAT-CAA
1 ATTCAAATATACAA
1039407 A-TCAAATAT
1 ATTCAAATAT
1039416 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.36
13 4 0.18
15 10 0.45
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.30
Consensus pattern (14 bp):
ATTCAAATATACAA
Found at i:1042045 original size:21 final size:21
Alignment explanation
Indices: 1042019--1042071 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1042009 TTAATATTTA
1042019 AATTTTAATTTAATGAAA-AAT
1 AATTTTAATTTAAT-AAATAAT
* *
1042040 AATTTTTTATTTTATAAATAAT
1 AA-TTTTAATTTAATAAATAAT
*
1042062 AATTTAAATT
1 AATTTTAATT
1042072 AAATTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTTTAATTTAATAAATAAT
Found at i:1042051 original size:22 final size:22
Alignment explanation
Indices: 1042021--1042066 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1042011 AATATTTAAA
1042021 TTTTAATTTAATGAAA-AATAAT
1 TTTTAATTTAAT-AAATAATAAT
* *
1042043 TTTTTATTTTATAAATAATAAT
1 TTTTAATTTAATAAATAATAAT
1042065 TT
1 TT
1042067 AAATTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTAATTTAATAAATAATAAT
Found at i:1042655 original size:16 final size:16
Alignment explanation
Indices: 1042636--1042669 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1042626 TTTCAATTAA
1042636 TATTTATTAATTAT-TT
1 TATTTATT-ATTATATT
1042652 TATTTATTATTATATT
1 TATTTATTATTATATT
1042668 TA
1 TA
1042670 AATTCGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATTATTATATT
Found at i:1042996 original size:15 final size:15
Alignment explanation
Indices: 1042976--1043023 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
1042966 TACTAATATT
1042976 TATAATAATATTTAA
1 TATAATAATATTTAA
1042991 TATAATTAATTATTATAA
1 TATAA-TAA-TATT-TAA
*
1043009 TATTAATTATATTTA
1 TA-TAATAATATTTA
1043024 TAATTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.18
16 5 0.18
17 8 0.29
18 7 0.25
19 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATAATAATATTTAA
Found at i:1053404 original size:37 final size:38
Alignment explanation
Indices: 1053337--1053414 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 38
1053327 AAGAAATATG
1053337 TTAGTCTACTCTTCAACCCTTATAAGATTGGTGTTTAT
1 TTAGTCTACTCTTCAACCCTTATAAGATTGGTGTTTAT
1053375 TTAGTCTACTCTTCAA-CCTTATAAGATTGGTGTTTAT
1 TTAGTCTACTCTTCAACCCTTATAAGATTGGTGTTTAT
1053412 TTA
1 TTA
1053415 TTTATTACCA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 24 0.60
38 16 0.40
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (38 bp):
TTAGTCTACTCTTCAACCCTTATAAGATTGGTGTTTAT
Found at i:1056421 original size:19 final size:19
Alignment explanation
Indices: 1056397--1056524 Score: 66
Period size: 21 Copynumber: 6.4 Consensus size: 19
1056387 TTGAATGATA
1056397 TAAATAAAATATTATAATT
1 TAAATAAAATATTATAATT
**
1056416 TAAATAAATATAAAATAATT
1 TAAATAAA-ATATTATAATT
* *
1056436 TAAAT--ATTATTATAATA
1 TAAATAAAATATTATAATT
*
1056453 TAAA-AATATATTAATATAATT
1 TAAATAA-A-A-TATTATAATT
1056474 TAAATATATAA-ATTATTAAATT
1 TAAATA-A-AATATTA-T-AATT
* *
1056496 TAATTACAAAAATTTATAATT
1 TAAATA-AAATA-TTATAATT
1056517 ATAAATAA
1 -TAAATAA
1056525 TTTCATTTTA
Statistics
Matches: 83, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
17 11 0.13
18 1 0.01
19 9 0.11
20 17 0.20
21 20 0.24
22 19 0.23
23 6 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATAAAATATTATAATT
Found at i:1056435 original size:20 final size:19
Alignment explanation
Indices: 1056397--1056441 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1056387 TTGAATGATA
**
1056397 TAAATAAAATATTATAATT
1 TAAATAAAATAAAATAATT
1056416 TAAATAAATATAAAATAATT
1 TAAATAAA-ATAAAATAATT
1056436 TAAATA
1 TAAATA
1056442 TTATTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATAAAATAAAATAATT
Found at i:1056451 original size:37 final size:38
Alignment explanation
Indices: 1056406--1056480 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 38
1056396 ATAAATAAAA
*
1056406 TATTATAATTTAAATAA-ATA-TAAAATAATTTAAATAT
1 TATTATAATATAAA-AATATATTAAAATAATTTAAATAT
*
1056443 TATTATAATATAAAAATATATTAATATAATTTAAATAT
1 TATTATAATATAAAAATATATTAAAATAATTTAAATAT
1056481 ATAAATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 2 0.06
37 16 0.47
38 16 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (38 bp):
TATTATAATATAAAAATATATTAAAATAATTTAAATAT
Found at i:1056468 original size:27 final size:27
Alignment explanation
Indices: 1056409--1056492 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 27
1056399 AATAAAATAT
1056409 TATAATTTAAATAAATATAAAATA-ATTTAA
1 TATAATTTAAAT--ATA-AAAATATA-TTAA
*
1056439 -ATATTATTATAATATAAAAATATATTAA
1 TATAAT-TTA-AATATAAAAATATATTAA
*
1056467 TATAATTTAAATATATAAAT-TATTAA
1 TATAATTTAAATATAAAAATATATTAA
1056493 ATTTAATTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
26 6 0.13
27 10 0.21
28 13 0.28
29 12 0.26
30 3 0.06
31 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TATAATTTAAATATAAAAATATATTAA
Found at i:1056481 original size:11 final size:11
Alignment explanation
Indices: 1056409--1056481 Score: 56
Period size: 10 Copynumber: 7.4 Consensus size: 11
1056399 AATAAAATAT
1056409 TATAATTTAAA
1 TATAATTTAAA
*
1056420 TA-AATATAAA
1 TATAATTTAAA
1056430 -ATAATTTAAA
1 TATAATTTAAA
*
1056440 TATTA-TTATAA
1 TATAATTTA-AA
1056451 TATAA---AAA
1 TATAATTTAAA
1056459 TAT-A-TT-AA
1 TATAATTTAAA
1056467 TATAATTTAAA
1 TATAATTTAAA
1056478 TATA
1 TATA
1056482 TAAATTATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
7 1 0.02
8 10 0.20
9 3 0.06
10 19 0.38
11 17 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATAATTTAAA
Found at i:1056499 original size:27 final size:26
Alignment explanation
Indices: 1056400--1056501 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 26
1056390 AATGATATAA
* *
1056400 ATAAAATATTATAATTTAAATAAATAT
1 ATAAATTATTA-AATTTAATTAAATAT
*
1056427 A-AAATAATTTAAATATT-ATTATAATAT
1 ATAAATTA-TTAAAT-TTAATTA-AATAT
* *
1056454 AAAAATATATT-AATATAATTTAAATAT
1 ATAAAT-TATTAAATTTAA-TTAAATAT
1056481 ATAAATTATTAAATTTAATTA
1 ATAAATTATTAAATTTAATTA
1056502 CAAAAATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
26 18 0.30
27 32 0.53
28 9 0.15
29 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAATTATTAAATTTAATTAAATAT
Found at i:1056696 original size:13 final size:13
Alignment explanation
Indices: 1056674--1056709 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1056664 TTTAATTTTT
*
1056674 TAATATATTTAAA
1 TAATAAATTTAAA
1056687 TAATAAATTTAAA
1 TAATAAATTTAAA
*
1056700 TAATTAATTT
1 TAATAAATTT
1056710 TTTCTAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATAAATTTAAA
Found at i:1057062 original size:15 final size:14
Alignment explanation
Indices: 1057026--1057066 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1057016 AAATAAATAA
*
1057026 ATTTTTATTTATTT
1 ATTTTAATTTATTT
1057040 ATTTTAATTTATTT
1 ATTTTAATTTATTT
1057054 ATATTTAATTTAT
1 AT-TTTAATTTAT
1057067 ATTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTAATTTATTT
Found at i:1058731 original size:2 final size:2
Alignment explanation
Indices: 1058724--1058748 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1058714 GAAATACTGT
1058724 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1058749 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1064919 original size:6 final size:7
Alignment explanation
Indices: 1064906--1064941 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1064896 TTTTTATTTT
1064906 TTTAATA
1 TTTAATA
1064913 TTT-ATA
1 TTTAATA
1064919 TTTAATA
1 TTTAATA
1064926 -TTAATA
1 TTTAATA
1064932 TTTAATA
1 TTTAATA
1064939 TTT
1 TTT
1064942 TTTAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTAATA
Found at i:1064924 original size:13 final size:13
Alignment explanation
Indices: 1064906--1064941 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1064896 TTTTTATTTT
1064906 TTTAATATTTATA
1 TTTAATATTTATA
*
1064919 TTTAATATTAATA
1 TTTAATATTTATA
1064932 TTTAATATTT
1 TTTAATATTT
1064942 TTTAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:1064980 original size:23 final size:23
Alignment explanation
Indices: 1064909--1064982 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
1064899 TTATTTTTTT
1064909 AATATTTATATTTA-AT-ATT--
1 AATATTTATATTTATATAATTAA
*
1064928 AATATTTAATATTT-TTTAAATATAA
1 AATATTT-ATATTTATAT-AAT-TAA
1064953 AATATTTATATTTATATAATTAA
1 AATATTTATATTTATATAATTAA
1064976 AATATTT
1 AATATTT
1064983 TAATTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
19 7 0.16
20 7 0.16
22 2 0.04
23 11 0.24
24 9 0.20
25 9 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTATATTTATATAATTAA
Found at i:1067809 original size:16 final size:16
Alignment explanation
Indices: 1067780--1067812 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1067770 TATTAATATT
1067780 ATTTATATTTATTTAA
1 ATTTATATTTATTTAA
1067796 ATTTA-ATTTAATTTAA
1 ATTTATATTT-ATTTAA
1067812 A
1 A
1067813 ATATAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATATTTATTTAA
Found at i:1067890 original size:18 final size:19
Alignment explanation
Indices: 1067853--1067895 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1067843 TTATTTTTAA
* *
1067853 AAATTTAATATTTTTTATT
1 AAATTTAATAATTTTAATT
1067872 AAATTTAA-AATTTTAATT
1 AAATTTAATAATTTTAATT
1067890 -AATTTA
1 AAATTTA
1067896 TTTACATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 8 0.36
19 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTTAATAATTTTAATT
Found at i:1068033 original size:13 final size:13
Alignment explanation
Indices: 1068008--1068047 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
1067998 AAACAGATTT
1068008 AATTT-TTTATTTA
1 AATTTATTT-TTTA
1068021 AATTTATTTTTTA
1 AATTTATTTTTTA
1068034 AATTTATTATTTTA
1 AATTTATT-TTTTA
1068048 TTCAAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTTATTTTTTA
Found at i:1068568 original size:2 final size:2
Alignment explanation
Indices: 1068561--1068602 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1068551 TTAGGTTTTA
1068561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1068603 TTCCAACAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1068820 original size:25 final size:23
Alignment explanation
Indices: 1068776--1068822 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1068766 ACATTATATT
*
1068776 AATATTTTTTTTGTCTTTATTAA
1 AATATTTATTTTGTCTTTATTAA
*
1068799 AATATTATATTTTGTTTGTTATTA
1 AATATT-TATTTTGTCT-TTATTA
1068823 GTTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 8 0.40
25 6 0.30
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (23 bp):
AATATTTATTTTGTCTTTATTAA
Found at i:1069365 original size:3 final size:3
Alignment explanation
Indices: 1069347--1069386 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
1069337 TTGAAGCTGC
1069347 ATT ATTT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
1069387 TTTAAGGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 26 0.76
4 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:1070356 original size:70 final size:70
Alignment explanation
Indices: 1070274--1070420 Score: 267
Period size: 70 Copynumber: 2.1 Consensus size: 70
1070264 AGCTTTAAAT
1070274 TTACATTAATATACATAGTATGATCGTAGCAGGAACTTAGCTGGTAACTAGCATTGTCTCAATTT
1 TTACATTAATATACATAGTATGATCGTAGCAGGAACTTAGCTGGTAACTAGCATTGTCTCAATTT
1070339 CTTCA
66 CTTCA
* *
1070344 TTACATTAATATATATAGTATGATTGTAGCAGGAACTTAGCTGGTAACTAGCATTGTCTCAATTT
1 TTACATTAATATACATAGTATGATCGTAGCAGGAACTTAGCTGGTAACTAGCATTGTCTCAATTT
1070409 CTTCA
66 CTTCA
*
1070414 TTCCATT
1 TTACATT
1070421 CTAGGTTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (70 bp):
TTACATTAATATACATAGTATGATCGTAGCAGGAACTTAGCTGGTAACTAGCATTGTCTCAATTT
CTTCA
Found at i:1071394 original size:1 final size:1
Alignment explanation
Indices: 1071388--1071412 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1071378 AGAGTGCTTC
1071388 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
1071413 AGTTTGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1072854 original size:20 final size:19
Alignment explanation
Indices: 1072825--1072865 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1072815 TTATATATAA
1072825 TTATACAAATTAAATTAAAT
1 TTATACAAATT-AATTAAAT
* *
1072845 TTATATAAATTATTTAAAT
1 TTATACAAATTAATTAAAT
1072864 TT
1 TT
1072866 GACATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATACAAATTAATTAAAT
Found at i:1076725 original size:37 final size:38
Alignment explanation
Indices: 1076674--1076747 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
1076664 TCAAGTCTAA
*
1076674 TAAAAAATAAAATATTTCAAATTTGTCCAAACATAACC
1 TAAAAAATAAAATATTTCAAACTTGTCCAAACATAACC
*
1076712 TAAAAAA-AAAATATTTCAAGCTTGTCCAAACATAAC
1 TAAAAAATAAAATATTTCAAACTTGTCCAAACATAAC
1076748 TTATGAACAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 27 0.79
38 7 0.21
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (38 bp):
TAAAAAATAAAATATTTCAAACTTGTCCAAACATAACC
Found at i:1077527 original size:18 final size:18
Alignment explanation
Indices: 1077485--1077521 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1077475 TTGGTAGAAC
1077485 CACCCTGATCAGCAGCAG
1 CACCCTGATCAGCAGCAG
* *
1077503 CACCCTGCTCAGCTGCAG
1 CACCCTGATCAGCAGCAG
1077521 C
1 C
1077522 CTCCTGTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.43, G:0.22, T:0.14
Consensus pattern (18 bp):
CACCCTGATCAGCAGCAG
Found at i:1080857 original size:22 final size:23
Alignment explanation
Indices: 1080800--1080857 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
1080790 AACATTTGGA
*
1080800 ATTTTAAATTTAA-TTTAATATT
1 ATTTAAAATTTAATTTTAATATT
* **
1080822 TTTTAAAAAATAATTTTAAT-TT
1 ATTTAAAATTTAATTTTAATATT
1080844 ATTTAAAATTTAAT
1 ATTTAAAATTTAAT
1080858 ATATTATATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTAAAATTTAATTTTAATATT
Found at i:1083884 original size:24 final size:25
Alignment explanation
Indices: 1083852--1083900 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1083842 TTCTTTGTTG
* *
1083852 AATTAATCAA-TGCTTGATTAAATT
1 AATTAATCAATTGCCTAATTAAATT
1083876 AATTAATCAATTGCCTAATTAAATT
1 AATTAATCAATTGCCTAATTAAATT
1083901 TATAATTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (25 bp):
AATTAATCAATTGCCTAATTAAATT
Found at i:1084296 original size:26 final size:26
Alignment explanation
Indices: 1084248--1084297 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1084238 ATAATTAAAA
* *
1084248 AAATATTTTAATTTAAATTTAATTAT
1 AAATATGTTAATTTAAATATAATTAT
1084274 AAATATGTTAATATT-AATATAATT
1 AAATATGTTAAT-TTAAATATAATT
1084298 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
AAATATGTTAATTTAAATATAATTAT
Found at i:1085460 original size:20 final size:21
Alignment explanation
Indices: 1085432--1085470 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1085422 TTTAAATTTA
1085432 AATATAAATAATTTTATTTTT
1 AATATAAATAATTTTATTTTT
1085453 AATA-AAATAATTTTATTT
1 AATATAAATAATTTTATTT
1085471 GATACATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATAAATAATTTTATTTTT
Found at i:1085756 original size:2 final size:2
Alignment explanation
Indices: 1085749--1085778 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1085739 ACATTAATTC
1085749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1085779 TTACTGGTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1087739 original size:22 final size:22
Alignment explanation
Indices: 1087713--1087754 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1087703 TATTGTATAT
1087713 TTAAAAATAAATTTTAAATTTA
1 TTAAAAATAAATTTTAAATTTA
* * *
1087735 TTAAATATTATTTTTAAATT
1 TTAAAAATAAATTTTAAATT
1087755 ATAATTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAAAATAAATTTTAAATTTA
Found at i:1089290 original size:23 final size:23
Alignment explanation
Indices: 1089253--1089318 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 23
1089243 AAAGTATAAT
* *
1089253 AATTAATTTTATAATTTTTTAAA
1 AATTTATTTTTTAATTTTTTAAA
**
1089276 AATTTATTTTTTAA-TTAATAAA
1 AATTTATTTTTTAATTTTTTAAA
* *
1089298 ATTTTA-ATTTTAATTTTTTAA
1 AATTTATTTTTTAATTTTTTAA
1089319 TTTAATATTA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 6 0.18
22 16 0.47
23 12 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTATTTTTTAATTTTTTAAA
Found at i:1089834 original size:17 final size:18
Alignment explanation
Indices: 1089805--1089839 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1089795 TTTTTTAATA
1089805 TTTTATTTAAATTTATTT
1 TTTTATTTAAATTTATTT
1089823 TTTTATTT-AATTTATTT
1 TTTTATTTAAATTTATTT
1089840 ATATTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTAAATTTATTT
Found at i:1089846 original size:18 final size:18
Alignment explanation
Indices: 1089807--1089847 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1089797 TTTTAATATT
*
1089807 TTATTTAAATTTATTTTT
1 TTATTTAAATTTATTTTA
1089825 TTATTT-AATTTATTTATA
1 TTATTTAAATTTATTT-TA
1089843 TTATT
1 TTATT
1089848 ATATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTAAATTTATTTTA
Found at i:1090392 original size:15 final size:15
Alignment explanation
Indices: 1090372--1090404 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1090362 CATGATGACT
*
1090372 ATAACAATAATAATA
1 ATAACAATAATAAAA
1090387 ATAACAATAATAAAA
1 ATAACAATAATAAAA
1090402 ATA
1 ATA
1090405 TTATTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAACAATAATAAAA
Found at i:1090409 original size:3 final size:3
Alignment explanation
Indices: 1090403--1090448 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1090393 ATAATAAAAA
*
1090403 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1090449 CTAAGAGTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1091232 original size:14 final size:15
Alignment explanation
Indices: 1091206--1091254 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 15
1091196 ATTAAAATTA
1091206 AAATTTATTAAATAT
1 AAATTTATTAAATAT
*
1091221 TAATTT-TTAAATAT
1 AAATTTATTAAATAT
*
1091235 AAATTAATTAAAT-T
1 AAATTTATTAAATAT
1091249 AAATTT
1 AAATTT
1091255 TAAGTTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTTATTAAATAT
Found at i:1091807 original size:22 final size:22
Alignment explanation
Indices: 1091771--1091822 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 22
1091761 GTAAAATATT
1091771 ATATATTTATATTAAT-TT-TA
1 ATATATTTATATTAATATTGTA
1091791 ATATATTTATATGTTAATATTGTA
1 ATATATTTATA--TTAATATTGTA
1091815 ATAATATT
1 AT-ATATT
1091823 ATTTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.41
22 5 0.19
23 2 0.07
24 4 0.15
25 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
ATATATTTATATTAATATTGTA
Found at i:1091853 original size:2 final size:2
Alignment explanation
Indices: 1091846--1091875 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1091836 TAAAAATTGG
1091846 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1091876 GCAGCTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1093839 original size:183 final size:184
Alignment explanation
Indices: 1093612--1094041 Score: 460
Period size: 184 Copynumber: 2.3 Consensus size: 184
1093602 GAGTCATTCC
* * * * *
1093612 TGATTGATTTAGAAGATCATAACAATCA-AATGTTGTACTAATTTTTTCAAAATTTAATCA-GAA
1 TGATTAATTTA-AAGACCATAACAAT-AGAATGTTATATTAATTTTTTTAAAATTTAA-CATGAA
* * * * *
1093675 AAAATAAAT-TCAAAAATCTTTTGTCTTTTTCAAATGCATGTCACTACTTTGATACTCATAAACA
63 AAAATAAGTCT-AAAAACCTTTTGTCTTCTTCAAATACATGTCACTACTTTGATACTCAAAAACA
* * * * * *
1093739 GCTTAAGCGGTAAAAAAAATTAA-AA-AAAAA-TAACTTTGAATCATAAGAAACGTCAT
127 ACTTAAGCGGCAAAAAAAA-AAACAATAAAAATTAACTTCGAATCATAAAAAACATCAT
* *
1093795 TGATTAATTTAGAAGACCATAATGAA-AGAATGTTATATTAATTTTTTTTAAAACTTAACATGAA
1 TGATTAATTTA-AAGACCATAA-CAATAGAATGTTATATTAA-TTTTTTTAAAATTTAACATGAA
* * *
1093859 AAAATGAGTCTAAAAACCTTTTGTCTTCTTCAAATACATGTCACTATTTTGATACTCAAAAATAA
63 AAAATAAGTCTAAAAACCTTTTGTCTTCTTCAAATACATGTCACTACTTTGATACTCAAAAACAA
* * *
1093924 TTTAAGTGGCAAAAAAAAAAACTAATAAAAAGTTTAACTTCGAATCATAAAAAACATCTT
128 CTTAAGCGGCAAAAAAAAAAAC-AATAAAAA--TTAACTTCGAATCATAAAAAACATCAT
* ** *
1093984 TGATTTATTTAAAGATTATAACAATCGAATGTTATATTAATTTTTTTAAAATTTAACA
1 TGATTAATTTAAAGACCATAACAATAGAATGTTATATTAATTTTTTTAAAATTTAACA
1094042 AAACAATTGG
Statistics
Matches: 205, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
182 1 0.00
183 35 0.17
184 88 0.43
185 3 0.01
186 5 0.02
187 19 0.09
188 22 0.11
189 32 0.16
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (184 bp):
TGATTAATTTAAAGACCATAACAATAGAATGTTATATTAATTTTTTTAAAATTTAACATGAAAAA
ATAAGTCTAAAAACCTTTTGTCTTCTTCAAATACATGTCACTACTTTGATACTCAAAAACAACTT
AAGCGGCAAAAAAAAAAACAATAAAAATTAACTTCGAATCATAAAAAACATCAT
Found at i:1095118 original size:6 final size:6
Alignment explanation
Indices: 1095107--1095150 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
1095097 GTCTGTGTGA
1095107 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC AT
1095151 GCATGAGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:1095204 original size:59 final size:59
Alignment explanation
Indices: 1095130--1095250 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
1095120 TATACATATA
*
1095130 CATATACATATACATATACATGCATGAGTATTATGTCTAAGTTCAAATATACCTACAAG
1 CATACACATATACATATACATGCATGAGTATTATGTCTAAGTTCAAATATACCTACAAG
1095189 CATACACATATACATATACATGCATGAGTATTATGTCTAAGTTCAAATATACCTACAAG
1 CATACACATATACATATACATGCATGAGTATTATGTCTAAGTTCAAATATACCTACAAG
1095248 CAT
1 CAT
1095251 GTATGTATGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (59 bp):
CATACACATATACATATACATGCATGAGTATTATGTCTAAGTTCAAATATACCTACAAG
Found at i:1099191 original size:20 final size:20
Alignment explanation
Indices: 1099168--1099237 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
1099158 AAATTAAATT
1099168 TTTAAATTTTATTTATTTAA
1 TTTAAATTTTATTTATTTAA
* *
1099188 TTTAAATTAATATTTA-ATAA
1 TTTAAATT-TTATTTATTTAA
*
1099208 TTAAAATTTGTATTTAAATTTAA
1 TTTAAATTT-TATTT--ATTTAA
1099231 TTATAAA
1 TT-TAAA
1099238 ATATATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 23 0.61
21 6 0.16
22 1 0.03
23 5 0.13
24 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
TTTAAATTTTATTTATTTAA
Found at i:1099222 original size:41 final size:43
Alignment explanation
Indices: 1099171--1099255 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 43
1099161 TTAAATTTTT
*
1099171 AAATTTTATTT-ATTTAATT-TAAATTA-ATATTTAA-TAATTA
1 AAATTTTATTTAATTTAATTATAAAATATAT-TTTAATTAATTA
1099211 AAATTTGTATTTAAATTTAATTATAAAATATATTTTAATTAATTA
1 AAATTT-TATTT-AATTTAATTATAAAATATATTTTAATTAATTA
1099256 TTAATTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
40 6 0.16
41 5 0.13
43 8 0.21
44 11 0.29
45 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (43 bp):
AAATTTTATTTAATTTAATTATAAAATATATTTTAATTAATTA
Found at i:1103314 original size:29 final size:28
Alignment explanation
Indices: 1103278--1103332 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1103268 GCTAAAATTT
* *
1103278 TTATATTTATATTAAATTTATATTTTTTA
1 TTATATTTAAAAT-AATTTATATTTTTTA
*
1103307 TTATATTTAAAATATTTTATATTTTT
1 TTATATTTAAAATAATTTATATTTTT
1103333 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TTATATTTAAAATAATTTATATTTTTTA
Found at i:1103342 original size:27 final size:28
Alignment explanation
Indices: 1103294--1103349 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
1103284 TTATATTAAA
*
1103294 TTTATATTTTTTATTATATTTAAAATAT
1 TTTATATTTTTTATAATATTTAAAATAT
*
1103322 TTTATA-TTTTTATAA-ATTTTAATATAT
1 TTTATATTTTTTATAATA-TTTAAAATAT
1103349 T
1 T
1103350 AATAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.04
27 18 0.72
28 6 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTATATTTTTTATAATATTTAAAATAT
Done.