Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007864.1 Hibiscus syriacus cultivar Beakdansim tig00110236_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: 1537186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1090192 original size:23 final size:24
Alignment explanation
Indices: 1090149--1090202 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
1090139 CAATGATTAA
*
1090149 ATGTAAATTAATGTAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
1090173 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
1090196 ATGTAAA
1 ATGTAAA
1090203 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:1090416 original size:19 final size:20
Alignment explanation
Indices: 1090389--1090443 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1090379 TTGAGAATAT
*
1090389 GTTCTCGCCCTTAA-AATTA
1 GTTCCCGCCCTTAATAATTA
* *
1090408 GTTCCCGCCATTAATGATTA
1 GTTCCCGCCCTTAATAATTA
1090428 GTTCCCGCCCTTAATA
1 GTTCCCGCCCTTAATA
1090444 TAAATTATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.35
Consensus pattern (20 bp):
GTTCCCGCCCTTAATAATTA
Found at i:1090480 original size:6 final size:6
Alignment explanation
Indices: 1090438--1090580 Score: 62
Period size: 6 Copynumber: 25.2 Consensus size: 6
1090428 GTTCCCGCCC
1090438 TTAATA -TAA-A TT-ATA TATAA-A TTATATA TT-ATAA TTAATA TTAATA
1 TTAATA TTAATA TTAATA T-TAATA TTA-ATA TTAAT-A TTAATA TTAATA
* *
1090484 -T-A-A TTAATA TTAATA TTAA-C TT-ATA TTAATA -TAATA -TAATTT
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAA-TA
* * * * * *
1090526 TTAATT TTTA-A TTAATA TTAATA -TAAAA TATAGTC TATAAAA TTAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA T-TAATA T-TAATA TTAATA
1090574 TTAATA T
1 TTAATA T
1090581 AAACTATATT
Statistics
Matches: 105, Mismatches: 14, Indels: 36
0.68 0.09 0.23
Matches are distributed among these distances:
3 1 0.01
4 5 0.05
5 31 0.30
6 52 0.50
7 16 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (6 bp):
TTAATA
Found at i:1090491 original size:9 final size:10
Alignment explanation
Indices: 1090438--1090522 Score: 57
Period size: 11 Copynumber: 7.9 Consensus size: 10
1090428 GTTCCCGCCC
1090438 TTAATATAAA
1 TTAATATAAA
1090448 TTATATATAAA
1 TTA-ATATAAA
1090459 TTATATATTATAA
1 TTA-ATA-TA-AA
*
1090472 TTAATATTAA
1 TTAATATAAA
1090482 TATAAT-TAATA
1 T-TAATATAA-A
*
1090493 TTAATATTAAC
1 TTAATA-TAAA
*
1090504 TT-ATATTAA
1 TTAATATAAA
1090513 TATAATATAA
1 T-TAATATAA
1090523 TTTTTAATTT
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
9 3 0.05
10 16 0.27
11 28 0.47
12 8 0.13
13 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (10 bp):
TTAATATAAA
Found at i:1090510 original size:31 final size:34
Alignment explanation
Indices: 1090438--1090551 Score: 116
Period size: 34 Copynumber: 3.4 Consensus size: 34
1090428 GTTCCCGCCC
*
1090438 TTAATATAAAT-TATATATAAATTA-TATATTA-TAA
1 TTAATATTAATATA-ATAT-AATTATTA-ATTATTAA
1090472 TTAATATTAATATAAT-TAA-TATTAA-TATTAA
1 TTAATATTAATATAATATAATTATTAATTATTAA
* *
1090503 CTT-ATATTAATATAATATAATTTTTAATTTTTAA
1 -TTAATATTAATATAATATAATTATTAATTATTAA
1090537 TTAATATTAATATAA
1 TTAATATTAATATAA
1090552 AATATAGTCT
Statistics
Matches: 69, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
30 2 0.03
31 19 0.28
32 9 0.13
33 8 0.12
34 29 0.42
35 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (34 bp):
TTAATATTAATATAATATAATTATTAATTATTAA
Found at i:1090511 original size:16 final size:16
Alignment explanation
Indices: 1090469--1090549 Score: 87
Period size: 15 Copynumber: 5.0 Consensus size: 16
1090459 TTATATATTA
1090469 TAATTAATATTAATA-
1 TAATTAATATTAATAT
1090484 TAATTAATATTAATAT
1 TAATTAATATTAATAT
1090500 TAACTT-ATATTAATA-
1 TAA-TTAATATTAATAT
* *
1090515 TAATATAATTTTTAATTTT
1 TAAT-TAA-TATTAA-TAT
1090534 TAATTAATATTAATAT
1 TAATTAATATTAATAT
1090550 AAAATATAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.02
15 19 0.35
16 15 0.27
17 12 0.22
18 4 0.07
19 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTAATATTAATAT
Found at i:1090573 original size:31 final size:30
Alignment explanation
Indices: 1090535--1090721 Score: 126
Period size: 31 Copynumber: 5.8 Consensus size: 30
1090525 TTTAATTTTT
*
1090535 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
*
1090566 AATTAATATTAATATAAACTATA-TTTTATA
1 AATTAATATTAATATAAACTATAGTTATA-A
* *
1090596 AATTATATAGTATAGTTTATAAACTATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAACTATAGTT-ATAA
* *
1090632 AATTTATATTAATATAGTA-TATAGTTTATAA
1 AATTAATATTAATATA-AACTATAG-TTATAA
* * *
1090663 ACTATATACTATATTAATATAAATTACAGTTAAAA
1 A--AT-TA--ATATTAATATAAACTATAGTTATAA
*
1090698 TAATTAACATTAATATAAACTATA
1 -AATTAATATTAATATAAACTATA
1090722 CAGTACATTA
Statistics
Matches: 123, Mismatches: 16, Indels: 34
0.71 0.09 0.20
Matches are distributed among these distances:
29 3 0.02
30 7 0.06
31 53 0.43
32 4 0.03
33 8 0.07
34 4 0.03
35 20 0.16
36 22 0.18
37 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:1090587 original size:24 final size:25
Alignment explanation
Indices: 1090542--1090588 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1090532 TTTAATTAAT
**
1090542 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
1090567 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
1090589 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:1090625 original size:66 final size:65
Alignment explanation
Indices: 1090540--1090721 Score: 188
Period size: 66 Copynumber: 2.7 Consensus size: 65
1090530 TTTTTAATTA
* *
1090540 ATATTAATATAAAATATAGTCTATAAAATTAATATTAATATAAACTATATTTTATAAATTATATA
1 ATATT-ATATAAAATATAGT-TATAAAATTAATATTAATATAAACTATAGTTTATAAACTATATA
*
1090605 GT
64 CT
* * * *
1090607 ATAGTT-TATAAACTATAGTTAATATAATTTATATTAATATAGTA-TATAGTTTATAAACTATAT
1 ATA-TTATATAAAATATAGTT-ATAAAATTAATATTAATATA-AACTATAGTTTATAAACTATAT
1090670 ACT
63 ACT
* * * *
1090673 ATATTAATATAAATTACAGTTAAAATAATTAACATTAATATAAACTATA
1 ATATT-ATATAAAATATAGTTATAA-AATTAATATTAATATAAACTATA
1090722 CAGTACATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
65 3 0.03
66 55 0.59
67 34 0.36
68 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (65 bp):
ATATTATATAAAATATAGTTATAAAATTAATATTAATATAAACTATAGTTTATAAACTATATACT
Found at i:1090654 original size:15 final size:16
Alignment explanation
Indices: 1090620--1090670 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1090610 GTTTATAAAC
*
1090620 TATAGTTAATATAATT
1 TATAGTTAATATAATA
*
1090636 TATA-TTAATATAGTA
1 TATAGTTAATATAATA
*
1090651 TATAGTTTATA-AACTA
1 TATAGTTAATATAA-TA
1090667 TATA
1 TATA
1090671 CTATATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (16 bp):
TATAGTTAATATAATA
Found at i:1090783 original size:21 final size:21
Alignment explanation
Indices: 1090733--1090785 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1090723 AGTACATTAA
* *
1090733 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
* *
1090754 TACATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
1090775 TATAAACTATA
1 TATAAACTATA
1090786 TAGTACACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:1090885 original size:22 final size:22
Alignment explanation
Indices: 1090860--1090937 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
1090850 AAATAGATTG
1090860 TATATATACATATACTATAAGT
1 TATATATACATATACTATAAGT
*
1090882 TATATATATATATACTATACATAGTT
1 TATATATACATATACTAT--A-AG-T
* * *
1090908 TATACATACATGTACTATGAGT
1 TATATATACATATACTATAAGT
*
1090930 TACATATA
1 TATATATA
1090938 TAGTTCACAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
22 24 0.53
23 2 0.04
24 1 0.02
25 2 0.04
26 16 0.36
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.41
Consensus pattern (22 bp):
TATATATACATATACTATAAGT
Found at i:1090889 original size:26 final size:25
Alignment explanation
Indices: 1090860--1090939 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
1090850 AAATAGATTG
1090860 TATATATACATATACTATAAGTTATA
1 TATATATACATATACTAT-AGTTATA
*
1090886 TATATATATACTATAC-ATAG-T-T-
1 TATATATACA-TATACTATAGTTATA
* * *
1090908 TATACATACATGTACTATGAGTTACA
1 TATATATACATATACTAT-AGTTATA
1090934 TATATA
1 TATATA
1090940 GTTCACATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
21 4 0.10
22 10 0.24
23 3 0.07
24 2 0.05
25 2 0.05
26 16 0.38
27 5 0.12
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.41
Consensus pattern (25 bp):
TATATATACATATACTATAGTTATA
Found at i:1090924 original size:48 final size:50
Alignment explanation
Indices: 1090838--1090939 Score: 129
Period size: 48 Copynumber: 2.1 Consensus size: 50
1090828 ATATATAGTT
* *
1090838 TATATAACATATAAATAGATTGTATATATACATATACTATAAGTTATATA
1 TATATAACATATAAATAGATTGTATACATACATATACTATAAGTTACATA
* * *
1090888 TATATATAC-TATACATAG-TT-TATACATACATGTACTATGAGTTACATA
1 TATATA-ACATATAAATAGATTGTATACATACATATACTATAAGTTACATA
1090936 TATA
1 TATA
1090940 GTTCACATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 28 0.61
49 2 0.04
50 14 0.30
51 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (50 bp):
TATATAACATATAAATAGATTGTATACATACATATACTATAAGTTACATA
Found at i:1091109 original size:7 final size:7
Alignment explanation
Indices: 1091097--1091176 Score: 72
Period size: 7 Copynumber: 11.6 Consensus size: 7
1091087 TATATATATA
1091097 GTTTAGG
1 GTTTAGG
1091104 GTTTAGG
1 GTTTAGG
1091111 GTTTAGG
1 GTTTAGG
* *
1091118 ATCTAGG
1 GTTTAGG
1091125 GTTTAGG
1 GTTTAGG
*
1091132 GTTTAAG
1 GTTTAGG
*
1091139 GTTTA-A
1 GTTTAGG
* *
1091145 ATTTATG
1 GTTTAGG
*
1091152 GTTTATG
1 GTTTAGG
1091159 GTTTAGG
1 GTTTAGG
* *
1091166 ATTTAGA
1 GTTTAGG
1091173 GTTT
1 GTTT
1091177 CTATAAACTA
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
6 4 0.07
7 55 0.93
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:1091154 original size:20 final size:20
Alignment explanation
Indices: 1091126--1091163 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1091116 GGATCTAGGG
1091126 TTTAGGGTTTAAGGTTTAAA
1 TTTAGGGTTTAAGGTTTAAA
* *
1091146 TTTATGGTTTATGGTTTA
1 TTTAGGGTTTAAGGTTTA
1091164 GGATTTAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (20 bp):
TTTAGGGTTTAAGGTTTAAA
Found at i:1093783 original size:4 final size:4
Alignment explanation
Indices: 1093768--1093800 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1093758 TACAATATGC
1093768 TTCT TT-T TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1093801 TTCTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:1093859 original size:14 final size:14
Alignment explanation
Indices: 1093821--1093861 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1093811 CATTATGTTT
1093821 TTTTTCTTTTTT-C
1 TTTTTCTTTTTTAC
1093834 TTTTTGC--TTTTAC
1 TTTTT-CTTTTTTAC
1093847 TTTTTCTTTTTTAC
1 TTTTTCTTTTTTAC
1093861 T
1 T
1093862 GAAACATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 5 0.21
13 11 0.46
14 8 0.33
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTTTTAC
Found at i:1093994 original size:16 final size:16
Alignment explanation
Indices: 1093956--1093996 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1093946 CGGTGGTCTA
1093956 CCGGGTCGGGTCAGTT
1 CCGGGTCGGGTCAGTT
* *
1093972 CCAGGTCGGGTTAGTT
1 CCGGGTCGGGTCAGTT
*
1093988 TCGGGTCGG
1 CCGGGTCGG
1093997 ATCCGGGTCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.07, C:0.22, G:0.44, T:0.27
Consensus pattern (16 bp):
CCGGGTCGGGTCAGTT
Found at i:1094249 original size:2 final size:2
Alignment explanation
Indices: 1094242--1094323 Score: 60
Period size: 2 Copynumber: 40.5 Consensus size: 2
1094232 ATGTTTAATG
* *
1094242 AT AT AT AT AT AT AT AT GT -T AT AT AT AT AGT TT AT AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
* * * * *
1094285 AT AT AGT TT AT AT AT AC AT GT AT AT A- AG CT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1094324 GTTCAGGGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
1 2 0.03
2 57 0.90
3 4 0.06
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1094265 original size:13 final size:12
Alignment explanation
Indices: 1094247--1094326 Score: 64
Period size: 11 Copynumber: 7.1 Consensus size: 12
1094237 TAATGATATA
1094247 TATATATATATGT
1 TATATATATA-GT
1094260 TATATATATAGT
1 TATATATATAGT
1094272 T-TATATATA--
1 TATATATATAGT
*
1094281 -CTATATATAGT
1 TATATATATAGT
**
1094292 T-TATATATACA
1 TATATATATAGT
* *
1094303 TGTATATA-AGC
1 TATATATATAGT
1094314 TATATATATAGT
1 TATATATATAGT
1094326 T
1 T
1094327 CAGGGTTTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
9 8 0.15
11 25 0.45
12 12 0.22
13 10 0.18
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (12 bp):
TATATATATAGT
Found at i:1094285 original size:20 final size:20
Alignment explanation
Indices: 1094262--1094301 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1094252 ATATATGTTA
1094262 TATATATAGTTTATATATAC
1 TATATATAGTTTATATATAC
1094282 TATATATAGTTTATATATAC
1 TATATATAGTTTATATATAC
1094302 ATGTATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
TATATATAGTTTATATATAC
Found at i:1094344 original size:7 final size:7
Alignment explanation
Indices: 1094328--1094370 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
1094318 TATATAGTTC
1094328 AGGGTTT
1 AGGGTTT
*
1094335 AGGTTTT
1 AGGGTTT
1094342 AGGGTTT
1 AGGGTTT
* *
1094349 ATGATTT
1 AGGGTTT
*
1094356 AAGGTTT
1 AGGGTTT
1094363 AGGGTTT
1 AGGGTTT
1094370 A
1 A
1094371 TTATTTAGGG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.47
Consensus pattern (7 bp):
AGGGTTT
Found at i:1094385 original size:21 final size:21
Alignment explanation
Indices: 1094340--1094385 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1094330 GGTTTAGGTT
*
1094340 TTAGGGTTTATGATTTAAGGT
1 TTAGGGTTTATGATTTAAGGG
* *
1094361 TTAGGGTTTATTATTTAGGGG
1 TTAGGGTTTATGATTTAAGGG
1094382 TTAG
1 TTAG
1094386 AACTTAGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
TTAGGGTTTATGATTTAAGGG
Found at i:1094528 original size:2 final size:2
Alignment explanation
Indices: 1094516--1094598 Score: 72
Period size: 2 Copynumber: 44.5 Consensus size: 2
1094506 TTATATTAGT
* *
1094516 TA TA CA TA TA TA TA TA TA TA TA TA TA T- TA T- TA -A TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1094555 T- TA TA -A TT TA TA AA CTA TA T- TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
1094594 TA TA T
1 TA TA T
1094599 TAATATAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
1 7 0.11
2 57 0.88
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1094578 original size:19 final size:18
Alignment explanation
Indices: 1094522--1094627 Score: 56
Period size: 19 Copynumber: 5.6 Consensus size: 18
1094512 TAGTTATACA
*
1094522 TATATATATATATATATATAT
1 TATAAATATAT-TATA-AT-T
*
1094543 TATTAATATAAATTATAATT
1 TA-TAA-ATATATTATAATT
*
1094563 TATAAACTATATTATATATA
1 TATAAA-TATATTATA-ATT
*
1094583 TATATATATATTAT-A-T
1 TATAAATATATTATAATT
* * *
1094599 TA-ATATAAATTATAGTT
1 TATAAATATATTATAATT
1094616 TATAAACTATAT
1 TATAAA-TATAT
1094628 ACTTTTTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
15 10 0.15
16 2 0.03
17 4 0.06
18 3 0.04
19 23 0.34
20 10 0.15
21 4 0.06
22 6 0.09
23 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (18 bp):
TATAAATATATTATAATT
Found at i:1094600 original size:53 final size:55
Alignment explanation
Indices: 1094521--1094627 Score: 191
Period size: 53 Copynumber: 2.0 Consensus size: 55
1094511 TTAGTTATAC
1094521 ATATATATATATATATATATATTATTAATATAAATTATAATTTATAAACTATATT
1 ATATATATATATATATATATATTATTAATATAAATTATAATTTATAAACTATATT
*
1094576 ATATATATATATATATAT-TA-TATTAATATAAATTATAGTTTATAAACTATAT
1 ATATATATATATATATATATATTATTAATATAAATTATAATTTATAAACTATAT
1094628 ACTTTTTATA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 31 0.61
54 2 0.04
55 18 0.35
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (55 bp):
ATATATATATATATATATATATTATTAATATAAATTATAATTTATAAACTATATT
Found at i:1096675 original size:8 final size:8
Alignment explanation
Indices: 1096662--1096695 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1096652 TTTCTTGCCA
1096662 TTTATTTT
1 TTTATTTT
1096670 TTTATTTTT
1 TTTA-TTTT
*
1096679 TTTATTTA
1 TTTATTTT
1096687 TTTATTTT
1 TTTATTTT
1096695 T
1 T
1096696 ATTTTACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTATTTT
Found at i:1096682 original size:17 final size:17
Alignment explanation
Indices: 1096662--1096695 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1096652 TTTCTTGCCA
*
1096662 TTTATTTTTTTATTTTT
1 TTTATTTATTTATTTTT
1096679 TTTATTTATTTATTTTT
1 TTTATTTATTTATTTTT
1096696 ATTTTACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTATTTATTTATTTTT
Found at i:1100198 original size:14 final size:15
Alignment explanation
Indices: 1100179--1100211 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1100169 AGCAAAAAAG
1100179 AAAAAACAAGAA-CA
1 AAAAAACAAGAAGCA
*
1100193 AAAAAAGAAGAAGCA
1 AAAAAACAAGAAGCA
1100208 AAAA
1 AAAA
1100212 TCAAAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAACAAGAAGCA
Found at i:1101872 original size:38 final size:36
Alignment explanation
Indices: 1101796--1101865 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
1101786 GAGCTCACCA
*
1101796 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAACT
1101832 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAA
1101866 ACCTTTGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAACT
Found at i:1101887 original size:29 final size:32
Alignment explanation
Indices: 1101849--1101907 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1101839 TCTTGAGACA
1101849 GTTTCCCTTG-AA-A-AAAAACCTTTGAAATT
1 GTTTCCCTTGAAACACAAAAACCTTTGAAATT
*
1101878 GTTTCTCTTGAAACACAAAAACCTTTGAAA
1 GTTTCCCTTGAAACACAAAAACCTTTGAAA
1101908 CATAAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.35
30 2 0.08
31 1 0.04
32 14 0.54
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (32 bp):
GTTTCCCTTGAAACACAAAAACCTTTGAAATT
Found at i:1102114 original size:37 final size:37
Alignment explanation
Indices: 1102044--1102115 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
1102034 TGGAACTAAG
* * * *
1102044 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTCTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
1102081 TTTTCTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTCTCTCCCTTGAGACAGTTTCTCATAAAACAA
1102116 CAGATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTCTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:1102920 original size:106 final size:106
Alignment explanation
Indices: 1102733--1103158 Score: 690
Period size: 106 Copynumber: 4.0 Consensus size: 106
1102723 TCGCGCCACC
*
1102733 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* *
1102798 TTCAGAGCCAATTTCAACTTCACAGCGAAGGAAATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* *
1102839 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* **
1102904 TTCAGAGCCAATTTCAACTTCACAGCGAAGGGCATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * *
1102945 CGAGACAGCACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAATAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1103010 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* *
1103051 CGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
* * * * *
1103116 TCCAAAACCAATTTCAAATTCACGGCGGAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
1103157 CG
1 CG
1103159 GAACAATACA
Statistics
Matches: 299, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 299 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:1105365 original size:18 final size:18
Alignment explanation
Indices: 1105342--1105389 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1105332 ATTTATATAC
*
1105342 ATATAGCTTATAATAATT
1 ATATAGTTTATAATAATT
1105360 ATATAGTTTATAATAATT
1 ATATAGTTTATAATAATT
1105378 ATATAGTTTATA
1 ATATAGTTTATA
1105390 TATATAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (18 bp):
ATATAGTTTATAATAATT
Found at i:1105395 original size:13 final size:13
Alignment explanation
Indices: 1105377--1105406 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1105367 TTATAATAAT
1105377 TATATAGTTTATA
1 TATATAGTTTATA
1105390 TATATAGTTTATA
1 TATATAGTTTATA
1105403 TATA
1 TATA
1105407 AACTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:1105404 original size:15 final size:15
Alignment explanation
Indices: 1105305--1105406 Score: 75
Period size: 15 Copynumber: 6.5 Consensus size: 15
1105295 GCGACAAGTA
1105305 TATATATATATA-TT
1 TATATATATATAGTT
* * *
1105319 TCATATAAACATAATT
1 T-ATATATATATAGTT
* *
1105335 TATATACATATAGCT
1 TATATATATATAGTT
1105350 TATAATAATTATATAGTT
1 TAT-AT-A-TATATAGTT
1105368 TATAATAATTATATAG-T
1 TAT-AT-A-TATATAGTT
1105385 T-TATATATATAGTT
1 TATATATATATAGTT
1105399 TATATATA
1 TATATATA
1105407 AACTTATATT
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
13 7 0.10
14 4 0.05
15 30 0.41
16 6 0.08
17 3 0.04
18 23 0.32
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (15 bp):
TATATATATATAGTT
Found at i:1107044 original size:68 final size:70
Alignment explanation
Indices: 1106935--1107111 Score: 304
Period size: 68 Copynumber: 2.6 Consensus size: 70
1106925 ATTTTTTTTA
* *
1106935 AAAACAATCCCACATGGCTAAGAAACATAGAAGAGAATCCCAAAAGTCTAAAGAGT-AAAA-ATG
1 AAAACAATCCCACATTGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1106998 AGAAC
66 AGAAC
* *
1107003 AAAACAATCTCACATTGCTAAGAAAGATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1 AAAACAATCCCACATTGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
1107068 AGAAC
66 AGAAC
1107073 AAAACAATCCCACATTGCTAAGAAACATAGAAGAGCATC
1 AAAACAATCCCACATTGCTAAGAAACATAGAAGAGCATC
1107112 ACAACTAACT
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
68 52 0.51
69 4 0.04
70 45 0.45
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (70 bp):
AAAACAATCCCACATTGCTAAGAAACATAGAAGAGCATCCCAAAAGTCTAAAGAGTAAAAATATG
AGAAC
Found at i:1107787 original size:24 final size:24
Alignment explanation
Indices: 1107735--1107790 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1107725 TGAACGTTCG
* * *
1107735 GTTATGTTCATTTATGTTCGTTCG
1 GTTATGTTCATTTATATTCATTCA
*
1107759 GTTATGTTCGTTTATATTCATTCA
1 GTTATGTTCATTTATATTCATTCA
*
1107783 TTTATGTT
1 GTTATGTT
1107791 TAACCCAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (24 bp):
GTTATGTTCATTTATATTCATTCA
Found at i:1108828 original size:16 final size:16
Alignment explanation
Indices: 1108807--1108873 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
1108797 GTCTCCAACG
1108807 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1108823 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
1108839 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1108855 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1108869 TTTAT
1 TTTAT
1108874 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1108846 original size:32 final size:32
Alignment explanation
Indices: 1108805--1108865 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1108795 GGGTCTCCAA
1108805 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
1108837 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
1108866 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:1108956 original size:16 final size:16
Alignment explanation
Indices: 1108935--1108967 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1108925 AAAAAAATTT
1108935 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
*
1108951 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
1108967 T
1 T
1108968 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:1110100 original size:11 final size:10
Alignment explanation
Indices: 1110075--1110180 Score: 52
Period size: 11 Copynumber: 9.8 Consensus size: 10
1110065 ATACCAATAT
1110075 AATAAATAAATA
1 AATAAA-AAA-A
1110087 AATAAAACAAA
1 AATAAAA-AAA
*
1110098 AATAAAATAA
1 AATAAAAAAA
1110108 AATAAACAATAAA
1 AAT-AA-AA-AAA
*
1110121 CAATAAAAATA
1 -AATAAAAAAA
**
1110132 AAT-AAAGGA
1 AATAAAAAAA
*
1110141 AATAGAAAATA
1 AATA-AAAAAA
* *
1110152 AATAAAGATA
1 AATAAAAAAA
*
1110162 AAGAAAATAAA
1 AATAAAA-AAA
1110173 AATAAAAA
1 AATAAAAA
1110181 TAGAAATATA
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
9 7 0.09
10 19 0.26
11 29 0.39
12 12 0.16
13 4 0.05
14 3 0.04
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:1110104 original size:6 final size:6
Alignment explanation
Indices: 1110086--1110247 Score: 70
Period size: 6 Copynumber: 25.8 Consensus size: 6
1110076 ATAAATAAAT
*
1110086 AAAT-A AAACAA AAAT-A AAAT-A AAATAA ACAATAA ACAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA A-AATAA A-AATAA AAATAA
* *
1110133 ATAA-AGG AAATAGA AAATAA ATAA-AGA TAAA-GA AAATAA AAATAA
1 A-AATA-A AAATA-A AAATAA A-AATA-A -AAATAA AAATAA AAATAA
*
1110178 AAATAGA AATATAA AATTATAGA AAATAA AAA-AA TATAA-AA TAATAA
1 AAATA-A AA-ATAA AA--ATA-A AAATAA AAATAA -A-AATAA AAATAA
* * *
1110225 AAATAA TAATAA TAATAA TAATA
1 AAATAA AAATAA AAATAA AAATA
1110248 GTCATAATGA
Statistics
Matches: 131, Mismatches: 9, Indels: 33
0.76 0.05 0.19
Matches are distributed among these distances:
5 20 0.15
6 59 0.45
7 41 0.31
8 8 0.06
9 3 0.02
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:1110107 original size:16 final size:16
Alignment explanation
Indices: 1110082--1110120 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1110072 TATAATAAAT
1110082 AAAT-AAATAAAACAA
1 AAATAAAATAAAACAA
*
1110097 AAATAAAATAAAATAA
1 AAATAAAATAAAACAA
1110113 ACAATAAA
1 A-AATAAA
1110121 CAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 11 0.52
17 6 0.29
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATAAAATAAAACAA
Found at i:1110107 original size:20 final size:20
Alignment explanation
Indices: 1110078--1110157 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 20
1110068 CCAATATAAT
1110078 AAAT-AAATAAATAAAACAA
1 AAATAAAATAAATAAAACAA
*
1110097 AAATAAAATAAAATAAACAATAA
1 AAATAAAAT-AAAT-AA-AACAA
**
1110120 ACAATAAAAATAAATAAAGGAA
1 A-AAT-AAAATAAATAAAACAA
* *
1110142 ATAGAAAATAAATAAA
1 AAATAAAATAAATAAA
1110158 GATAAAGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
19 4 0.08
20 16 0.32
21 5 0.10
22 6 0.12
23 7 0.14
24 7 0.14
25 5 0.10
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (20 bp):
AAATAAAATAAATAAAACAA
Found at i:1110158 original size:20 final size:20
Alignment explanation
Indices: 1110122--1110230 Score: 74
Period size: 19 Copynumber: 5.6 Consensus size: 20
1110112 AACAATAAAC
1110122 AATA-AAAATAAATAAAGGA-
1 AATAGAAAATAAATAAA-GAT
1110141 AATAGAAAATAAATAAAGAT
1 AATAGAAAATAAATAAAGAT
*
1110161 AA-AGAAAATAAA-AATA-AA
1 AATAGAAAATAAATAA-AGAT
* *
1110179 AATAGAAATATAAAATTATAGAA
1 AATAGAAA-AT-AAA-TAAAGAT
1110202 AATA-AAAA-AATATAAA-AT
1 AATAGAAAATAA-ATAAAGAT
1110220 AATA-AAAATAA
1 AATAGAAAATAA
1110231 TAATAATAAT
Statistics
Matches: 75, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
18 14 0.19
19 29 0.39
20 17 0.23
21 4 0.05
22 4 0.05
23 7 0.09
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (20 bp):
AATAGAAAATAAATAAAGAT
Found at i:1110187 original size:44 final size:44
Alignment explanation
Indices: 1110142--1110225 Score: 77
Period size: 44 Copynumber: 1.9 Consensus size: 44
1110132 AATAAAGGAA
*
1110142 ATAGAAAATAAATA-AAGATAAAGAAAATAAAAATAAA-AATA-GAA
1 ATAGAAAAT-AATAGAAAATAAA-AAAATAAAAATAAATAA-AGGAA
* *
1110186 ATATAAAATTATAGAAAATAAAAAAATATAAAAT-AATAAA
1 ATAGAAAATAATAGAAAATAAAAAAATA-AAAATAAATAAA
1110226 AATAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
43 12 0.35
44 22 0.65
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (44 bp):
ATAGAAAATAATAGAAAATAAAAAAATAAAAATAAATAAAGGAA
Found at i:1110212 original size:25 final size:24
Alignment explanation
Indices: 1110073--1110247 Score: 89
Period size: 25 Copynumber: 7.2 Consensus size: 24
1110063 TGATACCAAT
*
1110073 ATAATAAATAAATAAATAAAACA-AAA
1 ATAAT-AA-AAATAAA-AAAATATAAA
* *
1110099 ATAAAATAAAAT-AAACAATA-AACA
1 ATAATA-AAAATAAAAAAATATAA-A
* * *
1110123 ATAAAAATAAATAAAGGAAATAGAAA
1 ATAATAA-AAATAAA-AAAATATAAA
* *
1110149 ATAAATAAAGATAAAGAAA-AT-AA
1 AT-AATAAAAATAAAAAAATATAAA
*
1110172 A-AATAAAAAT--AGAAATATAAA
1 ATAATAAAAATAAAAAAATATAAA
*
1110193 ATTATAGAAAATAAAAAAATATAAA
1 ATAATA-AAAATAAAAAAATATAAA
* *
1110218 ATAATAAAAATAATAATAATA-ATA
1 ATAATAAAAATAA-AAAAATATAAA
1110242 ATAATA
1 ATAATA
1110248 GTCATAATGA
Statistics
Matches: 121, Mismatches: 14, Indels: 30
0.73 0.08 0.18
Matches are distributed among these distances:
19 5 0.04
20 2 0.02
21 11 0.09
22 3 0.02
23 15 0.12
24 29 0.24
25 32 0.26
26 18 0.15
27 6 0.05
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (24 bp):
ATAATAAAAATAAAAAAATATAAA
Found at i:1110218 original size:15 final size:15
Alignment explanation
Indices: 1110140--1110239 Score: 64
Period size: 16 Copynumber: 6.4 Consensus size: 15
1110130 TAAATAAAGG
1110140 AAATAGAAAATAA-ATA
1 AAATA-AAAA-AATATA
1110156 AAGATAAAGAAAATA-A
1 AA-ATAAA-AAAATATA
*
1110172 AAAT--AAAAATAGA
1 AAATAAAAAAATATA
** *
1110185 AATATAAAATTATAGA
1 AA-ATAAAAAAATATA
1110201 AAATAAAAAAATATA
1 AAATAAAAAAATATA
1110216 AAATAATAAAAATAATA
1 AAATAA-AAAAAT-ATA
1110233 ATAATAA
1 A-AATAA
1110240 TAATAATAGT
Statistics
Matches: 69, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
12 6 0.09
13 4 0.06
14 2 0.03
15 18 0.26
16 24 0.35
17 10 0.14
18 5 0.07
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (15 bp):
AAATAAAAAAATATA
Found at i:1110260 original size:6 final size:6
Alignment explanation
Indices: 1110213--1110289 Score: 59
Period size: 6 Copynumber: 12.5 Consensus size: 6
1110203 ATAAAAAAAT
* * * *
1110213 ATAA-A ATAATA AAAATA ATAATA ATAATA ATAATA GTCATA ATGATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
*
1110260 ATTATA TATATATA TATACATA A-AATA ATA
1 ATAATA -ATA-ATA -ATA-ATA ATAATA ATA
1110290 TATATTATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
5 8 0.14
6 38 0.64
7 3 0.05
8 10 0.17
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (6 bp):
ATAATA
Found at i:1110292 original size:20 final size:21
Alignment explanation
Indices: 1110265--1110305 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1110255 TGATAATTAT
1110265 ATATATATATATACATAAAATA
1 ATATATAT-TATACATAAAATA
*
1110287 ATATATATTATATATAAAA
1 ATATATATTATACATAAAA
1110306 AAATTAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATATATTATACATAAAATA
Found at i:1110308 original size:24 final size:27
Alignment explanation
Indices: 1110257--1110309 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
1110247 AGTCATAATG
*
1110257 ATAATTATATATATATATATACATAAA
1 ATAATTATATATATATATATACAAAAA
1110284 ATAA-TATATAT-TATATATA-AAAAA
1 ATAATTATATATATATATATACAAAAA
1110308 AT
1 AT
1110310 TAGAAAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 8 0.32
26 7 0.28
27 4 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAATTATATATATATATATACAAAAA
Found at i:1112854 original size:19 final size:19
Alignment explanation
Indices: 1112830--1112867 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1112820 AAACCTAAAA
1112830 AGATATGCATATATGCGAT
1 AGATATGCATATATGCGAT
1112849 AGATATGCATATATGCGAT
1 AGATATGCATATATGCGAT
1112868 GTTATGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
AGATATGCATATATGCGAT
Found at i:1113601 original size:8 final size:8
Alignment explanation
Indices: 1113588--1113641 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
1113578 CTTATTTTTC
1113588 TTTTCTCT
1 TTTTCTCT
1113596 TTTTCT-T
1 TTTTCTCT
1113603 TTGTTCT-T
1 TT-TTCTCT
1113611 TTTTCTCAT
1 TTTTCTC-T
1113620 TTTTCTCATT
1 TTTTCTC--T
1113630 TTTTCTCT
1 TTTTCTCT
1113638 TTTT
1 TTTT
1113642 TTCAATTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 7 0.17
8 18 0.44
9 8 0.20
10 8 0.20
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTTCTCT
Found at i:1113622 original size:10 final size:10
Alignment explanation
Indices: 1113609--1113644 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1113599 TCTTTTGTTC
1113609 TTTTTTCTCA
1 TTTTTTCTCA
1113619 -TTTTTCTCA
1 TTTTTTCTCA
*
1113628 TTTTTTCTCT
1 TTTTTTCTCA
1113638 TTTTTTC
1 TTTTTTC
1113645 AATTTAAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTCTCA
Found at i:1113642 original size:9 final size:9
Alignment explanation
Indices: 1113595--1113642 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
1113585 TTCTTTTCTC
1113595 TTTT-TCTT
1 TTTTCTCTT
*
1113603 TTGT-TCTT
1 TTTTCTCTT
*
1113611 TTTTCTCAT
1 TTTTCTCTT
1113620 TTTTCTCATT
1 TTTTCTC-TT
1113630 TTTTCTCTT
1 TTTTCTCTT
1113639 TTTT
1 TTTT
1113643 TCAATTTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 10 0.29
9 16 0.47
10 8 0.24
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:1120808 original size:16 final size:18
Alignment explanation
Indices: 1120778--1120814 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
1120768 ATACGAATGT
1120778 AAAAACATGGAAAATATA
1 AAAAACATGGAAAATATA
1120796 AAAAACAT-G-AAATATA
1 AAAAACATGGAAAATATA
1120812 AAA
1 AAA
1120815 TGCAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.70, C:0.05, G:0.08, T:0.16
Consensus pattern (18 bp):
AAAAACATGGAAAATATA
Found at i:1124160 original size:15 final size:15
Alignment explanation
Indices: 1124142--1124248 Score: 89
Period size: 15 Copynumber: 7.2 Consensus size: 15
1124132 TATAATAAAT
*
1124142 AAATAAATAAAACAA
1 AAATAAATAAAATAA
*
1124157 AAATAAAATAAAA-AG
1 AAAT-AAATAAAATAA
**
1124172 AAATAAAGGAAATAGA
1 AAATAAATAAAATA-A
1124188 AAATAAATAAAGATAA
1 AAATAAATAAA-ATAA
*
1124204 AGA-AAATAAAATAA
1 AAATAAATAAAATAA
*
1124218 AAATAAA-AAAGTATA
1 AAATAAATAAAATA-A
1124233 AAAT--ATAAAATAA
1 AAATAAATAAAATAA
1124246 AAA
1 AAA
1124249 AATATATATA
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
13 5 0.07
14 22 0.29
15 25 0.33
16 20 0.27
17 3 0.04
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.16
Consensus pattern (15 bp):
AAATAAATAAAATAA
Found at i:1124175 original size:26 final size:24
Alignment explanation
Indices: 1124146--1124225 Score: 54
Period size: 26 Copynumber: 3.1 Consensus size: 24
1124136 ATAAATAAAT
*
1124146 AAATAAAACAAAAATAAAATAAAAA-G
1 AAAT-AAA-AAAAATAAAA-AAAAATA
** *
1124172 AAATAAAGGAAATAGAAAATAAATA
1 AAATAAAAAAAATA-AAAAAAAATA
*
1124197 AAGATAAAGAAAATAAAATAAAAATA
1 AA-ATAAAAAAAATAAAA-AAAAATA
1124223 AAA
1 AAA
1124226 AAGTATAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 9 0.20
25 12 0.27
26 23 0.52
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (24 bp):
AAATAAAAAAAATAAAAAAAAATA
Found at i:1124195 original size:20 final size:19
Alignment explanation
Indices: 1124162--1124218 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1124152 AACAAAAATA
*
1124162 AAATA-AAAAGAAATAAAGG
1 AAATAGAAAATAAATAAA-G
1124181 AAATAGAAAATAAATAAAG
1 AAATAGAAAATAAATAAAG
1124200 ATAA-AGAAAATAAAATAAA
1 A-AATAGAAAAT-AAATAAA
1124219 AATAAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (19 bp):
AAATAGAAAATAAATAAAG
Found at i:1124254 original size:15 final size:14
Alignment explanation
Indices: 1124142--1124250 Score: 69
Period size: 14 Copynumber: 7.1 Consensus size: 14
1124132 TATAATAAAT
1124142 AAAT-AAATAAAACAA
1 AAATAAAAT-AAA-AA
1124157 AAATAAAATAAAAA
1 AAATAAAATAAAAA
1124171 GAAATAAAGGAAATAGAAAA
1 -AAAT--A--AAATA-AAAA
*
1124191 TAAATAAAGATAAAGA
1 -AAATAAA-ATAAAAA
1124207 AAATAAAATAAAAA
1 AAATAAAATAAAAA
* *
1124221 TAAA-AAAGTATAAA
1 -AAATAAAATAAAAA
*
1124235 ATATAAAATAAAAA
1 AAATAAAATAAAAA
1124249 AA
1 AA
1124251 TATATATAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
13 2 0.03
14 25 0.33
15 21 0.28
16 9 0.12
17 4 0.05
18 1 0.01
19 5 0.07
20 8 0.11
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (14 bp):
AAATAAAATAAAAA
Found at i:1124258 original size:26 final size:25
Alignment explanation
Indices: 1124138--1124259 Score: 72
Period size: 24 Copynumber: 4.8 Consensus size: 25
1124128 CCAATATAAT
* *
1124138 AAATAAATAAATA-AAACAAAAATA
1 AAATAAAAAAATATAAATAAAAATA
* * *
1124162 AAATAAAAAGAA-ATAAAGGAAATAGA
1 AAATAAAAA-AATATAAA-TAAAAATA
* * *
1124188 AAATAAATAAAGATAAA-GAAAATA
1 AAATAAAAAAATATAAATAAAAATA
*
1124212 AAATAAAAATAA-AAAAGTATAAAATATA
1 AAATAAAAA-AATATAA--ATAAAA-ATA
*
1124240 AAATAAAAAAATATATATAA
1 AAATAAAAAAATATAAATAA
1124260 GTTAATAGAA
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
24 24 0.32
25 9 0.12
26 23 0.31
27 5 0.07
28 14 0.19
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (25 bp):
AAATAAAAAAATATAAATAAAAATA
Found at i:1124310 original size:2 final size:2
Alignment explanation
Indices: 1124303--1124350 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
1124293 ATAATTACAA
* *
1124303 AT AT AT AT AT AT AT AT AT AT AT AC AT A- AA AT A- 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
1124343 -T AT AT AT A
1 AT AT AT AT A
1124351 AAAAATAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1124340 original size:20 final size:20
Alignment explanation
Indices: 1124313--1124357 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
1124303 ATATATATAT
1124313 ATATATATATATACATAAAATA
1 ATATATAT-TATACATAAAA-A
*
1124335 ATATATATTATATATAAAAA
1 ATATATATTATACATAAAAA
1124355 ATA
1 ATA
1124358 AGAAAAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 10 0.45
22 8 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATATATTATACATAAAAA
Found at i:1124355 original size:23 final size:26
Alignment explanation
Indices: 1124309--1124358 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1124299 ACAAATATAT
1124309 ATATATATATATATATACATAAAATA
1 ATATATATATATATATACATAAAATA
1124335 ATATATAT-TATATATA-A-AAAATA
1 ATATATATATATATATACATAAAATA
1124358 A
1 A
1124359 GAAAAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.29
24 1 0.04
25 8 0.33
26 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATATATATATATATACATAAAATA
Found at i:1132437 original size:15 final size:16
Alignment explanation
Indices: 1132405--1132437 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1132395 AAAATCTTTC
1132405 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
1132421 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
1132436 TT
1 TT
1132438 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:1133214 original size:16 final size:17
Alignment explanation
Indices: 1133187--1133221 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1133177 TATCGCCGAC
1133187 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
1133204 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
1133220 CG
1 CG
1133222 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:1136100 original size:23 final size:21
Alignment explanation
Indices: 1136063--1136107 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
1136053 TTTTTATTGT
1136063 ATTATTTATAATAATAATATA
1 ATTATTTATAATAATAATATA
1136084 ATTATTATAATAATAATAATATA
1 ATTATT-T-ATAATAATAATATA
1136107 A
1 A
1136108 AAATACGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
23 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTATTTATAATAATAATATA
Found at i:1138120 original size:2 final size:2
Alignment explanation
Indices: 1138115--1138142 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1138105 TTTTTAAGAT
1138115 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
1138143 ATCTTAAAAA
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:1149992 original size:14 final size:14
Alignment explanation
Indices: 1149964--1149997 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1149954 AACACAGTGG
1149964 AGAAG-AAAATCAA
1 AGAAGAAAAATCAA
*
1149977 AGAAGAAAAATGAA
1 AGAAGAAAAATCAA
1149991 AGAAGAA
1 AGAAGAA
1149998 GAAGAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.21, T:0.06
Consensus pattern (14 bp):
AGAAGAAAAATCAA
Found at i:1152364 original size:3 final size:3
Alignment explanation
Indices: 1152358--1152401 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1152348 AATTATTATT
1152358 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1152402 TGGGACAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1152705 original size:22 final size:21
Alignment explanation
Indices: 1152674--1152715 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1152664 AAAACCTCAA
*
1152674 AAAATATAAAATATAAAATTTT
1 AAAATAT-AAACATAAAATTTT
*
1152696 AAAATCTAAACATAAAATTT
1 AAAATATAAACATAAAATTT
1152716 AGAAATACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATAAACATAAAATTTT
Found at i:1156904 original size:37 final size:38
Alignment explanation
Indices: 1156846--1156980 Score: 136
Period size: 39 Copynumber: 3.6 Consensus size: 38
1156836 CTTATTTAGT
*
1156846 ATATATATTAATATATAAGTTTTTTAAAACA-TTTTGAAA
1 ATATATA-TAATATAT-AGTTTTTGAAAACATTTTTGAAA
1156885 ATATATATAATATATAGTTTTTGAAAACATTTTTG--A
1 ATATATATAATATATAGTTTTTGAAAACATTTTTGAAA
** ** *
1156921 ACGTATATAATATAT-GGGTTTGAAAGCATTTTTTGAAAA
1 ATATATATAATATATAGTTTTTGAAAACA-TTTTTG-AAA
*
1156960 ATATATATAATAT-TATTTTTT
1 ATATATATAATATATAGTTTTT
1156981 AAATATAATG
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
35 10 0.13
36 20 0.25
37 13 0.16
38 14 0.18
39 22 0.28
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (38 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTTGAAA
Found at i:1156906 original size:36 final size:37
Alignment explanation
Indices: 1156846--1156983 Score: 131
Period size: 36 Copynumber: 3.7 Consensus size: 37
1156836 CTTATTTAGT
1156846 ATATATATTAATATATAAGTTTTTTAAAACA-TTTTGAAA
1 ATATATA-TAATATAT-AG-TTTTTAAAACATTTTTGAAA
1156885 ATATATATAATATATAGTTTTTGAAAACATTTTTG--A
1 ATATATATAATATATAGTTTTT-AAAACATTTTTGAAA
** * * * *
1156921 ACGTATATAATATATGGGTTTGAAAGCATTTTTTGAAAA
1 ATATATATAATATATAGTTTTTAAAACA-TTTTTG-AAA
*
1156960 ATATATATAATAT-TATTTTTTAAA
1 ATATATATAATATATAGTTTTTAAA
1156984 TATAATGCCA
Statistics
Matches: 81, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
35 5 0.06
36 29 0.36
37 8 0.10
38 20 0.25
39 19 0.23
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
Found at i:1158175 original size:18 final size:18
Alignment explanation
Indices: 1158131--1158169 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1158121 CTTTATATTA
*
1158131 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTGTCT
1158149 TTTATTTAATTATTGTCT
1 TTTATTTAATTATTGTCT
1158167 TTT
1 TTT
1158170 TATTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTGTCT
Found at i:1158441 original size:11 final size:11
Alignment explanation
Indices: 1158425--1158524 Score: 53
Period size: 11 Copynumber: 8.5 Consensus size: 11
1158415 ATTTAACACT
1158425 TTTTTTTATTA
1 TTTTTTTATTA
*
1158436 TTTTTTGTTTTA
1 TTTTTT-TATTA
*
1158448 TTTTTATTTTTCCA
1 TTTTT-TTATT--A
1158462 CTTCTTTTTATT-
1 -TT-TTTTTATTA
* *
1158474 TTATTTTATTTTG
1 TT-TTTT-TATTA
1158487 TTTTTTTATT-
1 TTTTTTTATTA
*
1158497 TTCTTTTTATCA
1 TT-TTTTTATTA
1158509 TTTTTTTA-TA
1 TTTTTTTATTA
1158519 TTTTTT
1 TTTTTT
1158525 ATTTTTATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
10 9 0.12
11 28 0.39
12 22 0.31
13 3 0.04
14 1 0.01
15 6 0.08
16 3 0.04
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:1158451 original size:24 final size:23
Alignment explanation
Indices: 1158424--1158527 Score: 74
Period size: 22 Copynumber: 4.5 Consensus size: 23
1158414 AATTTAACAC
*
1158424 TTTTTTTTATTATTTTTTGTTTTA
1 TTTTTTTTATTATCTTTT-TTTTA
*
1158448 TTTTTATTT-TTCCA-CTTCTTTTTA
1 TTTTT-TTTATT--ATCTTTTTTTTA
1158472 TTTTATTTTATT-T-TGTTTTTTTA
1 TTTT-TTTTATTATCT-TTTTTTTA
* *
1158495 TTTTCTTT-TTATCATTTTTTTA
1 TTTTTTTTATTATCTTTTTTTTA
*
1158517 TATTTTTTATT
1 TTTTTTTTATT
1158528 TTTATTTTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
21 2 0.03
22 19 0.30
23 13 0.21
24 19 0.30
25 9 0.14
26 1 0.02
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTTTTTTATTATCTTTTTTTTA
Found at i:1158521 original size:37 final size:34
Alignment explanation
Indices: 1158438--1158537 Score: 98
Period size: 34 Copynumber: 2.9 Consensus size: 34
1158428 TTTTATTATT
* *
1158438 TTTTGTTTTA-TTTTTATTTTTCCA-CTTCTTTTTA
1 TTTTATTTTATTTTTTATTTTT--ATTTTCTTTTTA
1158472 TTTTATTTTATTTTGTT-TTTTTATTTTCTTTTTA
1 TTTTATTTTATTTT-TTATTTTTATTTTCTTTTTA
*
1158506 TCATTTTTTTATATTTTTTATTTTTATTTTCT
1 T--TTTATTT-TATTTTTTATTTTTATTTTCT
1158538 GAAATTTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
33 1 0.02
34 19 0.34
35 8 0.14
36 10 0.18
37 18 0.32
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (34 bp):
TTTTATTTTATTTTTTATTTTTATTTTCTTTTTA
Found at i:1160814 original size:15 final size:15
Alignment explanation
Indices: 1160790--1160825 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1160780 GGGAGTTAGA
1160790 AGAA-AAGATAAACC
1 AGAATAAGATAAACC
*
1160804 ATAATAAGATAAACC
1 AGAATAAGATAAACC
1160819 AGAATAA
1 AGAATAA
1160826 CCAAAGCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (15 bp):
AGAATAAGATAAACC
Found at i:1166113 original size:38 final size:38
Alignment explanation
Indices: 1166004--1166126 Score: 175
Period size: 36 Copynumber: 3.3 Consensus size: 38
1165994 ATATATTAAT
*
1166004 ATATATAGTTTTTGAAAACA-TTTTGAAAATGTATATA
1 ATATATAGTTTTTGAAAACATTTTTGAAAATATATATA
*
1166041 ATATATAGTTTTTGAAAACATTTTTG--AACATATATA
1 ATATATAGTTTTTGAAAACATTTTTGAAAATATATATA
1166077 ATATATAG-TTTTGAAAACATTTTTTGAAAATATATATA
1 ATATATAGTTTTTGAAAACA-TTTTTGAAAATATATATA
*
1166115 ATAT-TATTTTTT
1 ATATATAGTTTTT
1166127 AAATATAATG
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
35 11 0.14
36 22 0.29
37 22 0.29
38 22 0.29
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (38 bp):
ATATATAGTTTTTGAAAACATTTTTGAAAATATATATA
Found at i:1166150 original size:4 final size:4
Alignment explanation
Indices: 1166141--1166185 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
1166131 ATAATGCCAT
* *
1166141 TTTA TTTA TTTC TTTA TTTTCA TTCA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA TTT
1166186 TGTTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 29 0.83
5 5 0.14
6 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:1166174 original size:18 final size:17
Alignment explanation
Indices: 1166139--1166194 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1166129 ATATAATGCC
* *
1166139 ATTTTATTTATTTCTTT
1 ATTTTATTCATTTATTT
1166156 ATTTTCATTCATTTATTT
1 ATTTT-ATTCATTTATTT
*
1166174 A-TTTATTTATTT-TGTT
1 ATTTTATTCATTTAT-TT
1166190 ATTTT
1 ATTTT
1166195 TCTTTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.03
16 10 0.30
17 11 0.33
18 11 0.33
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTATTCATTTATTT
Found at i:1167302 original size:18 final size:18
Alignment explanation
Indices: 1167279--1167323 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1167269 CTTTAGATTA
*
1167279 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
1167297 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1167315 TTTATTTAA
1 TTTATTTAA
1167324 AAAACCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1167363 original size:15 final size:16
Alignment explanation
Indices: 1167345--1167402 Score: 68
Period size: 15 Copynumber: 3.8 Consensus size: 16
1167335 ATCTTTACTA
1167345 TTATTAT-TTATTATT
1 TTATTATATTATTATT
*
1167360 TTATTATATT-TCTCTT
1 TTATTATATTAT-TATT
1167376 TTATT-TATTATTATT
1 TTATTATATTATTATT
*
1167391 TTATTTTATTAT
1 TTATTATATTAT
1167403 ACCTTTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 20 0.54
16 17 0.46
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTATATTATTATT
Found at i:1167370 original size:36 final size:36
Alignment explanation
Indices: 1167330--1167403 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
1167320 TTAAAAAACC
1167330 TATTTATC-TTTACTATTATTATT-TATTATTTTATTA
1 TATTTATCTTTTA-T-TTATTATTATATTATTTTATTA
* *
1167366 TATTTCTCTTTTATTTATTATTATTTTATTTTATTA
1 TATTTATCTTTTATTTATTATTATATTATTTTATTA
1167402 TA
1 TA
1167404 CCTTTTCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 8 0.24
36 22 0.65
37 4 0.12
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (36 bp):
TATTTATCTTTTATTTATTATTATATTATTTTATTA
Found at i:1167382 original size:20 final size:20
Alignment explanation
Indices: 1167343--1167400 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1167333 TTATCTTTAC
*
1167343 TATTATTA-TTTATTAT-TT
1 TATTATTATTTTATTTTATT
*
1167361 TATTA-TATTTCTCTTTTATT
1 TATTATTATTT-TATTTTATT
1167381 TATTATTATTTTATTTTATT
1 TATTATTATTTTATTTTATT
1167401 ATACCTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 7 0.21
19 4 0.12
20 15 0.45
21 5 0.15
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTATTATTTTATTTTATT
Found at i:1167603 original size:16 final size:16
Alignment explanation
Indices: 1167578--1167608 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1167568 TAACACTTCT
1167578 TTTTAATTTTATTTTG
1 TTTTAATTTTATTTTG
*
1167594 TTTTATTTTTATTTT
1 TTTTAATTTTATTTT
1167609 CCCACTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTAATTTTATTTTG
Found at i:1167743 original size:66 final size:67
Alignment explanation
Indices: 1167622--1167753 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 67
1167612 ACTTCTTTTT
** * *
1167622 TTTATTTTTATTTTCTCTTTTAACATTTTTATATTTTTTTTTTTTCTGAAATTTAATATTTTCTT
1 TTTATTTTTATTTTCTCTTTTAACATTTTTATATAATATTTTTTTCTGAAATTTAATATTTCCTT
1167687 CA
66 CA
*
1167689 TTTA-TTTTATTTTTTTCTTTTAACATTTTTTATATAATATTTTTTT-T-AAATTTAATATTTCC
1 TTTATTTTTA-TTTTCTCTTTTAACA-TTTTTATATAATATTTTTTTCTGAAATTTAATATTTCC
1167751 TTC
64 TTC
1167754 TTTGATATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
66 22 0.38
67 19 0.33
68 17 0.29
ACGTcount: A:0.23, C:0.08, G:0.01, T:0.68
Consensus pattern (67 bp):
TTTATTTTTATTTTCTCTTTTAACATTTTTATATAATATTTTTTTCTGAAATTTAATATTTCCTT
CA
Found at i:1167762 original size:33 final size:30
Alignment explanation
Indices: 1167715--1167798 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 30
1167705 CTTTTAACAT
* * *
1167715 TTTTTATATAATATTTTTTTTAAATTTAATA
1 TTTTTATTTGATATTTTTTTTAAAATTAA-A
*
1167746 TTTCCTTCTTTGATA-TTTTTTTAAAATTAAA
1 TTT--TTATTTGATATTTTTTTTAAAATTAAA
*
1167777 TTTTTATTTGATATTTATTTTA
1 TTTTTATTTGATATTTTTTTTA
1167799 TTTTATAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
29 9 0.20
30 7 0.16
31 7 0.16
32 14 0.32
33 7 0.16
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTTTATTTGATATTTTTTTTAAAATTAAA
Found at i:1171373 original size:19 final size:19
Alignment explanation
Indices: 1171349--1171387 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1171339 TAAGATAGTG
1171349 TTAATTTGTCTTAAAATCT
1 TTAATTTGTCTTAAAATCT
1171368 TTAATTTGTCTTAAAATCT
1 TTAATTTGTCTTAAAATCT
1171387 T
1 T
1171388 ATTAAGTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAATTTGTCTTAAAATCT
Found at i:1178557 original size:40 final size:40
Alignment explanation
Indices: 1178510--1178660 Score: 257
Period size: 40 Copynumber: 3.8 Consensus size: 40
1178500 AGGACACTAA
* *
1178510 GTGTATATGGTGGGCACGACCTTATGTCTAATACACTTCG
1 GTGTATATGGTGGACACGACCTTATGTGTAATACACTTCG
*
1178550 GTGTATATGGTGGACACTACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGACACGACCTTATGTGTAATACACTTCG
*
1178590 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCG
1 GTGTATATGGTGGACACGACCTTATGTGTAATACACTTCG
*
1178630 GTGTATATGGTGGACACTACCTTATGTGTAA
1 GTGTATATGGTGGACACGACCTTATGTGTAA
1178661 CACTACGGTG
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (40 bp):
GTGTATATGGTGGACACGACCTTATGTGTAATACACTTCG
Found at i:1178627 original size:80 final size:80
Alignment explanation
Indices: 1178510--1178660 Score: 293
Period size: 80 Copynumber: 1.9 Consensus size: 80
1178500 AGGACACTAA
1178510 GTGTATATGGTGGGCACGACCTTATGTCTAATACACTTCGGTGTATATGGTGGACACTACCTTAT
1 GTGTATATGGTGGGCACGACCTTATGTCTAATACACTTCGGTGTATATGGTGGACACTACCTTAT
1178575 GTGTAATACACTTCG
66 GTGTAATACACTTCG
*
1178590 GTGTATATGGTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATGGTGGACACTACCTTAT
1 GTGTATATGGTGGGCACGACCTTATGTCTAATACACTTCGGTGTATATGGTGGACACTACCTTAT
1178655 GTGTAA
66 GTGTAA
1178661 CACTACGGTG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (80 bp):
GTGTATATGGTGGGCACGACCTTATGTCTAATACACTTCGGTGTATATGGTGGACACTACCTTAT
GTGTAATACACTTCG
Found at i:1178865 original size:20 final size:20
Alignment explanation
Indices: 1178816--1178870 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1178806 ATGAATAGTA
*
1178816 ATGAACAATACCGATACTGT
1 ATGAACAGTACCGATACTGT
*** *
1178836 GCAAATAGTACCGATACTGT
1 ATGAACAGTACCGATACTGT
1178856 ATGAACAGTACCGAT
1 ATGAACAGTACCGAT
1178871 GCTTAAAAAC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
ATGAACAGTACCGATACTGT
Found at i:1184521 original size:3 final size:3
Alignment explanation
Indices: 1184513--1184540 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1184503 GAGAGTAACT
1184513 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1184541 TTGATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1185739 original size:110 final size:108
Alignment explanation
Indices: 1185523--1185854 Score: 384
Period size: 109 Copynumber: 3.0 Consensus size: 108
1185513 GGGTCAATCA
* *
1185523 CATTTTAAGTGCCCCAAACTTTCCCCTTTTTTTACAAAATGGTCATTGGAAGAGACCTTTCTATA
1 CATTTTAAGT-CCCCAAACTTTCCCATGTTTTTACAAAATGGTCATTGGAAGAGACCTTTCTATA
1185588 ATTTTCCCTTTTCTATTTATGCTTTATAATTTTTGGTATAATTT
65 ATTTTCCCTTTTCTATTTATGCTTTATAATTTTTGGTATAATTT
* * * * *
1185632 CATTTTAAGTCCCCCAAACTTTCCCATGTTTTTAGAAATTGGTCATTGGAAGGGA-TTGTTATTA
1 CATTTTAAGT-CCCCAAACTTTCCCATGTTTTTACAAAATGGTCATTGGAAGAGACCT-TT-CTA
* *
1185696 TAATTTTCCTTTTTCTGTTTATGCTTTATAATTTTTGGTATAATTT
63 TAATTTTCCCTTTTCTATTTATGCTTTATAATTTTTGGTATAATTT
* * * ** * *
1185742 CATTTTAAGTCCCCAAACTTTCCCATGTTTTTACACAATAGTCACTGTCAGGGA-CTATTTTAAT
1 CATTTTAAGTCCCCAAACTTTCCCATGTTTTTACAAAATGGTCATTGGAAGAGACCT-TTCT-AT
* * * *
1185806 AATTTTCCCATTTTAC-ATGTATGCTTTAT-TTTTTTGGTAAAATCT
64 AATTTTCCC-TTTT-CTATTTATGCTTTATAATTTTTGGTATAATTT
1185851 CATT
1 CATT
1185855 CTAGGACCCC
Statistics
Matches: 193, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
108 3 0.02
109 118 0.61
110 71 0.37
111 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (108 bp):
CATTTTAAGTCCCCAAACTTTCCCATGTTTTTACAAAATGGTCATTGGAAGAGACCTTTCTATAA
TTTTCCCTTTTCTATTTATGCTTTATAATTTTTGGTATAATTT
Found at i:1185961 original size:29 final size:28
Alignment explanation
Indices: 1185922--1185977 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1185912 TAATTATTGA
*
1185922 AATTTTATCACCCTGTTTA-TTTTTATTTT
1 AATTTTATCA--CTGTTAATTTTTTATTTT
*
1185951 AATTTTGTCACTGTTAATTTTTTATTT
1 AATTTTATCACTGTTAATTTTTTATTT
1185978 AGCTACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.25
28 9 0.38
29 9 0.38
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.62
Consensus pattern (28 bp):
AATTTTATCACTGTTAATTTTTTATTTT
Found at i:1186015 original size:29 final size:28
Alignment explanation
Indices: 1185964--1186021 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
1185954 TTTGTCACTG
1185964 TTAATTTTTTATTTAGCTACTA-TTATT
1 TTAATTTTTTATTTAGCTACTATTTATT
* *
1185991 TTAATTTTTTCATTTTGGTCACTATTTATT
1 TTAATTTTTT-ATTTAGCT-ACTATTTATT
1186021 T
1 T
1186022 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 6 0.23
29 4 0.15
30 6 0.23
ACGTcount: A:0.22, C:0.09, G:0.05, T:0.64
Consensus pattern (28 bp):
TTAATTTTTTATTTAGCTACTATTTATT
Found at i:1191402 original size:17 final size:16
Alignment explanation
Indices: 1191380--1191451 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 16
1191370 TAAAAAAGAT
*
1191380 AGAAAAGAAAGGAAAAA
1 AGAAAA-AAAGAAAAAA
1191397 AGAAAAAAA-ATAAAAA
1 AGAAAAAAAGA-AAAAA
1191413 AGAGAAAAAAGAAAAAA
1 AGA-AAAAAAGAAAAAA
1191430 AGAAAAAAAAGAAAAGAA
1 AG-AAAAAAAGAAAA-AA
1191448 AGAA
1 AGAA
1191452 CAAAGAAAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
16 11 0.22
17 32 0.65
18 6 0.12
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (16 bp):
AGAAAAAAAGAAAAAA
Found at i:1191404 original size:9 final size:9
Alignment explanation
Indices: 1191392--1191451 Score: 72
Period size: 9 Copynumber: 7.0 Consensus size: 9
1191382 AAAAGAAAGG
1191392 AAAAAAG-A
1 AAAAAAGAA
*
1191400 AAAAAA-AT
1 AAAAAAGAA
*
1191408 AAAAAAGAG
1 AAAAAAGAA
1191417 AAAAAAG-A
1 AAAAAAGAA
1191425 AAAAAAGAA
1 AAAAAAGAA
1191434 AAAAAAGAA
1 AAAAAAGAA
*
1191443 AAGAAAGAA
1 AAAAAAGAA
1191452 CAAAGAAAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
8 19 0.42
9 26 0.58
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:1191434 original size:33 final size:33
Alignment explanation
Indices: 1191364--1191459 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 33
1191354 TATAGCAAAC
* *
1191364 AAAACATAAAAAAGATAGAAAAGAAAGGAAAAAAGAA
1 AAAAAATAAAAAAG--AG-AAA-AAAGAAAAAAAGAA
1191401 AAAAAATAAAAAAGAGAAAAAAGAAAAAAAGAA
1 AAAAAATAAAAAAGAGAAAAAAGAAAAAAAGAA
* *
1191434 AAAAAAGAAAAGAA-AGAACAAAGAAA
1 AAAAAATAAAA-AAGAGAAAAAAGAAA
1191460 GCGATCATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
33 34 0.63
34 5 0.09
35 2 0.04
37 13 0.24
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (33 bp):
AAAAAATAAAAAAGAGAAAAAAGAAAAAAAGAA
Found at i:1191459 original size:25 final size:23
Alignment explanation
Indices: 1191371--1191448 Score: 56
Period size: 23 Copynumber: 3.4 Consensus size: 23
1191361 AACAAAACAT
* *
1191371 AAAAAAGATAGAAA-AGAAAGGAA
1 AAAAAAGA-AAAAAGAGAAAAGAA
* * *
1191394 AAAAGAA-AAAAAATAAAAAAGAG
1 AAAA-AAGAAAAAAGAGAAAAGAA
1191417 AAAAAAGAAAAAA-AGAAAA-AA
1 AAAAAAGAAAAAAGAGAAAAGAA
1191438 AAGAAAAGAAA
1 AA-AAAAGAAA
1191449 GAACAAAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 3 0.07
22 19 0.42
23 21 0.47
24 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (23 bp):
AAAAAAGAAAAAAGAGAAAAGAA
Found at i:1193703 original size:14 final size:16
Alignment explanation
Indices: 1193679--1193711 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1193669 CCAAGTCAAG
1193679 ACATCAATCAATT-GA
1 ACATCAATCAATTGGA
1193694 ACAT-AATCAATTGGA
1 ACATCAATCAATTGGA
1193709 ACA
1 ACA
1193712 AGTTAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.24
Consensus pattern (16 bp):
ACATCAATCAATTGGA
Found at i:1196476 original size:43 final size:43
Alignment explanation
Indices: 1196428--1196725 Score: 355
Period size: 43 Copynumber: 7.2 Consensus size: 43
1196418 CATATAGCAA
* *
1196428 CGTTTGTCTTTGCAAACGCCGCTATTGAATGTGTATTTAGCGG
1 CGTTTGTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGG
* * * *
1196471 CGTTTGTATATACAAACGCCGTTATTGATTGTGTATTTAGCGG
1 CGTTTGTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGG
*
1196514 C----G--TTT----ACGCCGCTATTGACTGTGTATTTAGTGG
1 CGTTTGTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGG
* * *
1196547 CGTTTTTCTTTACAAACGCCGCTATTGTCTGTGTATTTAGCGC
1 CGTTTGTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGG
* * *
1196590 CGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATTTAGCGA
1 CGTTTGTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGG
* * *
1196633 CGTTTTTCTTTACAAACACCGCTATTGACTGTGTATTTAGCGA
1 CGTTTGTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGG
* *
1196676 CGTTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAGTGG
1 CGTTTGTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGG
*
1196719 CATTTGT
1 CGTTTGT
1196726 AATTAAAAAC
Statistics
Matches: 222, Mismatches: 23, Indels: 20
0.84 0.09 0.08
Matches are distributed among these distances:
33 26 0.12
37 2 0.01
39 4 0.02
43 190 0.86
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (43 bp):
CGTTTGTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGG
Found at i:1196530 original size:33 final size:33
Alignment explanation
Indices: 1196486--1196551 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1196476 GTATATACAA
* *
1196486 ACGCCGTTATTGATTGTGTATTTAGCGGCGTTT
1 ACGCCGCTATTGACTGTGTATTTAGCGGCGTTT
*
1196519 ACGCCGCTATTGACTGTGTATTTAGTGGCGTTT
1 ACGCCGCTATTGACTGTGTATTTAGCGGCGTTT
1196552 TTCTTTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (33 bp):
ACGCCGCTATTGACTGTGTATTTAGCGGCGTTT
Found at i:1199525 original size:10 final size:11
Alignment explanation
Indices: 1199502--1199544 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
1199492 TTTAATGTTT
*
1199502 ATTTTATAATA
1 ATTTAATAATA
1199513 ATTTAATAA-A
1 ATTTAATAATA
*
1199523 ATTTAATAATC
1 ATTTAATAATA
1199534 A-TTAATAATA
1 ATTTAATAATA
1199544 A
1 A
1199545 ATTGATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:1199527 original size:20 final size:20
Alignment explanation
Indices: 1199502--1199541 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1199492 TTTAATGTTT
*
1199502 ATTTTATAATAATTTAATAAA
1 ATTTAATAATAA-TTAATAAA
*
1199523 ATTTAATAATCATTAATAA
1 ATTTAATAATAATTAATAA
1199542 TAAATTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAATAATAATTAATAAA
Found at i:1200001 original size:41 final size:40
Alignment explanation
Indices: 1199953--1200089 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 40
1199943 ATTTGTAAAC
*
1199953 AAAAACGCCACTAAAACACGAGTCTATAACGCCATTTGTA
1 AAAAACGCCACTAAATCACGAGTCTATAACGCCATTTGTA
* * * *
1199993 TAAAAACGCCACTAAATCATGAGTCTATAGCGGCGTTTGTA
1 -AAAAACGCCACTAAATCACGAGTCTATAACGCCATTTGTA
* * * *
1200034 GAAAACGCCACTAAATCACGAGTCTATAGCGGCGTTTGTA
1 AAAAACGCCACTAAATCACGAGTCTATAACGCCATTTGTA
*
1200074 ACAAACACACCACTAA
1 A-AAA-ACGCCACTAA
1200090 TGTATGAGTC
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
40 38 0.45
41 38 0.45
42 9 0.11
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (40 bp):
AAAAACGCCACTAAATCACGAGTCTATAACGCCATTTGTA
Found at i:1200049 original size:40 final size:41
Alignment explanation
Indices: 1199953--1200131 Score: 202
Period size: 41 Copynumber: 4.4 Consensus size: 41
1199943 ATTTGTAAAC
* * * *
1199953 AAAAACGCCACTAAAACACGAGTCTATAACGCCATTTGTAT
1 AAAAACGCCACTAAATCACGAGTCTATAGCGGCGTTTGTAT
*
1199994 AAAAACGCCACTAAATCATGAGTCTATAGCGGCGTTTGTA-
1 AAAAACGCCACTAAATCACGAGTCTATAGCGGCGTTTGTAT
*
1200034 GAAAACGCCACTAAATCACGAGTCTATAGCGGCGTTTGTA-
1 AAAAACGCCACTAAATCACGAGTCTATAGCGGCGTTTGTAT
* * * * *
1200074 ACAAACACACCACT-AATGTATGAGTCTTTAGCAGCGTTTGTAT
1 A-AAA-ACGCCACTAAAT-CACGAGTCTATAGCGGCGTTTGTAT
*
1200117 AAAAACGCCGCTAAA
1 AAAAACGCCACTAAA
1200132 GACGCCACTA
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
40 38 0.32
41 47 0.40
42 32 0.27
43 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAAACGCCACTAAATCACGAGTCTATAGCGGCGTTTGTAT
Found at i:1200184 original size:24 final size:24
Alignment explanation
Indices: 1200152--1200199 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1200142 AAGTACGAGT
1200152 CTTTAGCGGCGTTTGTATAAAAAC
1 CTTTAGCGGCGTTTGTATAAAAAC
1200176 CTTTAGCGGCGTTTGTATAAAAAC
1 CTTTAGCGGCGTTTGTATAAAAAC
1200200 GCCTCTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (24 bp):
CTTTAGCGGCGTTTGTATAAAAAC
Found at i:1200317 original size:40 final size:40
Alignment explanation
Indices: 1200179--1200366 Score: 205
Period size: 41 Copynumber: 4.6 Consensus size: 40
1200169 TAAAAACCTT
* * *
1200179 TAGCGGCGTTTGTATAAAAACGCCTCTAAATCATGAGTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAATTA-CAGTCTA
* * * *
1200220 TAGCGGCGTTTGTATAACAACACCACTAAAGTACGAGTCTT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAATTAC-AGTCTA
*
1200261 TAGCGGCGTTTGTATAAAAACGCCACTAAATTACATTCTA
1 TAGCGGCGTTTGTATAAAAACGCCACTAAATTACAGTCTA
* * * * * *
1200301 AAGCGGCGTTTGTATAAAAACGCCGCTATAGTAGGAGTCTT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAATTA-CAGTCTA
*
1200342 TAGCGGCGTTTGTTCTAAAAACGCC
1 TAGCGGCGTTTG-TATAAAAACGCC
1200367 GCTACAAATG
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
40 33 0.27
41 79 0.64
42 11 0.09
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (40 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAATTACAGTCTA
Found at i:1200351 original size:81 final size:82
Alignment explanation
Indices: 1200176--1200366 Score: 267
Period size: 81 Copynumber: 2.3 Consensus size: 82
1200166 GTATAAAAAC
* * * *
1200176 CTTTAGCGGCGTTTGTATAAAAACGCCTCTAAATCATGAGTCTATAGCGGCGTTTGTATAACAAC
1 CTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATCAGTCTAAAGCGGCGTTTGTATAAAAAC
1200241 ACCACTAAAGTACGAGT
66 ACCACTAAAGTACGAGT
* *
1200258 CTTTAGCGGCGTTTGTATAAAAACGCCACTAAATTA-CATTCTAAAGCGGCGTTTGTATAAAAAC
1 CTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATCAGTCTAAAGCGGCGTTTGTATAAAAAC
* * * *
1200322 GCCGCTATAGTAGGAGT
66 ACCACTAAAGTACGAGT
*
1200339 CTTTAGCGGCGTTTGTTCTAAAAACGCC
1 CTTTAGCGGCGTTTG-TATAAAAACGCC
1200367 GCTACAAATG
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 52 0.54
82 45 0.46
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (82 bp):
CTTTAGCGGCGTTTGTATAAAAACGCCACTAAATCATCAGTCTAAAGCGGCGTTTGTATAAAAAC
ACCACTAAAGTACGAGT
Found at i:1205991 original size:15 final size:16
Alignment explanation
Indices: 1205960--1205991 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1205950 TGCAAAGGTG
1205960 CTTGTCTCCACTTAGC
1 CTTGTCTCCACTTAGC
1205976 CTTGTCTCCA-TTAGC
1 CTTGTCTCCACTTAGC
1205991 C
1 C
1205992 ATTACTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38
Consensus pattern (16 bp):
CTTGTCTCCACTTAGC
Found at i:1207216 original size:15 final size:16
Alignment explanation
Indices: 1207185--1207216 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1207175 TGCAAAGGTG
1207185 CTTGTCTCCACTTAGC
1 CTTGTCTCCACTTAGC
1207201 CTTGTCTCCA-TTAGC
1 CTTGTCTCCACTTAGC
1207216 C
1 C
1207217 ATTACTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38
Consensus pattern (16 bp):
CTTGTCTCCACTTAGC
Found at i:1210031 original size:39 final size:39
Alignment explanation
Indices: 1209942--1210378 Score: 564
Period size: 39 Copynumber: 11.4 Consensus size: 39
1209932 AGGGATCAAC
* * *
1209942 ATCTCGCTTTAAATAGTTTCACTCGAAACAAAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
1209980 ATCTCACTTGAGATAGTTTTAATCGAAATAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1210019 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
** *
1210058 ATCTCAATTGAGATAGTTTCACTCGGAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
1210097 TTCTCGCTTGAGATAGTTTTACTCGAAATA-AA-ATATTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAT-TTT
* * *
1210135 ATCTCGCTTGAGACAGTTTTACTCGAAATAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
1210173 ATCTTGCTCGA-ATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
1210211 ATCTCGATTGAGATAGTTTCCCTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
1210250 ATCTCGCTCGAGATATTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
1210288 ATCTAGCTTGAGATAGTTTCACTCGAAATATAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1210327 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
**
1210365 ATCTTACTTGAGAT
1 ATCTCGCTTGAGAT
1210379 TGTTGTTCTT
Statistics
Matches: 345, Mismatches: 47, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
37 22 0.06
38 132 0.38
39 190 0.55
40 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:1210272 original size:192 final size:193
Alignment explanation
Indices: 1209942--1210378 Score: 619
Period size: 192 Copynumber: 2.3 Consensus size: 193
1209932 AGGGATCAAC
* * * * * *
1209942 ATCTCGCTTTAAATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATAGTTTTAATCGAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTTACTCGAGATAGTTTCAATCGAA
* * * *
1210007 ATAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCAATTGAGAT
66 ACAGAAGATTTTATCTCGATTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTCAATCGAGAT
* * * *
1210072 AGTTTCACTCGGAACAGAAGATTTTTTCTCGCTTGAGATAGTTTTACTCGAAATA-AA-ATATTT
131 AGTTTCACTCGAAACAGAAGA-TTTATCTAGCTTGAGATAGTTTCACTCGAAATATAAGAT-TTT
* * * * *
1210135 ATCTCGCTTGAGACAGTTTTACTCGAAATAGAAGATTTATCTTGCTCGA-ATAGTTTCACTCGAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTTACTCGAGATAGTTTCAATCGAA
* **
1210199 ACAGAAGATTTTATCTCGATTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGCTCGAGAT
66 ACAGAAGATTTTATCTCGATTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTCAATCGAGAT
*
1210264 ATTTTCACTCGAAACAGAAGATTTATCTAGCTTGAGATAGTTTCACTCGAAATATAAGATTTT
131 AGTTTCACTCGAAACAGAAGATTTATCTAGCTTGAGATAGTTTCACTCGAAATATAAGATTTT
*
1210327 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTTACTTGAGAT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTTACTCGAGAT
1210379 TGTTGTTCTT
Statistics
Matches: 213, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
191 30 0.14
192 139 0.65
193 44 0.21
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (193 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTTACTCGAGATAGTTTCAATCGAA
ACAGAAGATTTTATCTCGATTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTCAATCGAGAT
AGTTTCACTCGAAACAGAAGATTTATCTAGCTTGAGATAGTTTCACTCGAAATATAAGATTTT
Found at i:1210299 original size:77 final size:76
Alignment explanation
Indices: 1209942--1210378 Score: 556
Period size: 77 Copynumber: 5.7 Consensus size: 76
1209932 AGGGATCAAC
* * * * *
1209942 ATCTCGCTTTAAATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATAGTTTTAATCGAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCT-ACTTGAGATAGTTTCACTCGAA
1210007 ATAGAAGATTTT
65 ATAGAAGATTTT
* *
1210019 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCAATTGAGATAGTTTCACTCGG
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCT-ACTTGAGATAGTTTCACTCGA
*
1210084 AACAGAAGATTTT
64 AATAGAAGATTTT
* * * * * * * *
1210097 TTCTCGCTTGAGATAGTTTTACTCGAAATAAAATATTTATCTCGCTTGAGACAGTTTTACTCGAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCT-ACTTGAGATAGTTTCACTCGAA
1210162 ATAGAAGA-TTT
65 ATAGAAGATTTT
* * *
1210173 ATCTTGCTCGA-ATAGTTTCACTCGAAACAGAAGATTTTATCT-CGATTGAGATAGTTTCCCTCG
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTAC--TTGAGATAGTTTCACTCG
* *
1210236 AAACAAAAGATTTT
63 AAATAGAAGATTTT
* *
1210250 ATCTCGCTCGAGATATTTTCACTCGAAACAGAAGATTTATCTAGCTTGAGATAGTTTCACTCGAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTA-CTTGAGATAGTTTCACTCGAA
*
1210315 ATATAAGATTTT
65 ATAGAAGATTTT
1210327 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTTACTTGAGAT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATC-TACTTGAGAT
1210379 TGTTGTTCTT
Statistics
Matches: 313, Mismatches: 38, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
74 1 0.00
75 19 0.06
76 41 0.13
77 160 0.51
78 91 0.29
79 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (76 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTACTTGAGATAGTTTCACTCGAAA
TAGAAGATTTT
Found at i:1211981 original size:110 final size:110
Alignment explanation
Indices: 1211765--1212054 Score: 368
Period size: 110 Copynumber: 2.6 Consensus size: 110
1211755 ACGTTGTAAA
* ** * * ** *
1211765 TCCCCCAAACTTTCCTGTGTTTTTACAAAATGGTCACTGGAAGTAACCGTTTTTATAATTTTCCC
1 TCCCCAAAACTTTCCCATATTTTTACAAAATGGTCACTGAAAGGGACTGTTTTTATAATTTTCCC
*
1211830 TTTT-TGTTTATGCTTTATGATTTTTGGCATAATTTCATTTTAAG
66 TTTTATGTTTATGCTTTATAATTTTTGGCATAATTTCATTTTAAG
*
1211874 TACCCTAAAACTTTCCCATA-TTTTACAAAATGGTCACTGAAAGGGACTGTTTTTATAATTTTCC
1 T-CCCCAAAACTTTCCCATATTTTTACAAAATGGTCACTGAAAGGGACTGTTTTTATAATTTTCC
* **
1211938 CTTTTATGTTTATGCTTTATAATTTTTGGTATAATTTTGTTTTAAG
65 CTTTTATGTTTATGCTTTATAATTTTTGGCATAATTTCATTTTAAG
* * * ** * *
1211984 TCCCCCAAACTTTCCCATATTTTTACAAAATAGTCATTGTGAGGGACTATTTTCATAATTTTCCC
1 TCCCCAAAACTTTCCCATATTTTTACAAAATGGTCACTGAAAGGGACTGTTTTTATAATTTTCCC
1212049 ATTTTA
66 -TTTTA
1212055 AATGTATGTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
109 62 0.40
110 89 0.57
111 5 0.03
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (110 bp):
TCCCCAAAACTTTCCCATATTTTTACAAAATGGTCACTGAAAGGGACTGTTTTTATAATTTTCCC
TTTTATGTTTATGCTTTATAATTTTTGGCATAATTTCATTTTAAG
Found at i:1212078 original size:110 final size:110
Alignment explanation
Indices: 1211785--1212088 Score: 290
Period size: 110 Copynumber: 2.8 Consensus size: 110
1211775 TTTCCTGTGT
* * ** ** * ** * *
1211785 TTTTACAAAATGGTCACTGGAAGTAACCGTTTTTATAATTTTCCCTTTT-TGTTTATGCTTTATG
1 TTTTACAAAATAGTCACTGAAAGGGACTATTTTCATAATTTTCCCTTTTAAATGTATGCTTTATA
* * *
1211849 ATTTTTGGCATAATTTCATTTTAAGTACCCTAAAACTTTCCCATA
66 ATTTATGGTATAATTTCATTTTAAGTACCCCAAAACTTTCCCATA
* * * ** *
1211894 TTTTACAAAATGGTCACTGAAAGGGACTGTTTTTATAATTTTCCCTTTTATGTTTATGCTTTATA
1 TTTTACAAAATAGTCACTGAAAGGGACTATTTTCATAATTTTCCCTTTTAAATGTATGCTTTATA
* ** *
1211959 ATTTTTGGTATAATTTTGTTTTAAGT-CCCCCAAACTTTCCCATA
66 ATTTATGGTATAATTTCATTTTAAGTACCCCAAAACTTTCCCATA
* ** *
1212003 TTTTTACAAAATAGTCATTGTGAGGGACTATTTTCATAATTTTCCCATTTTAAATGTATGTTTTA
1 -TTTTACAAAATAGTCACTGAAAGGGACTATTTTCATAATTTTCCC-TTTTAAATGTATGCTTTA
* * *
1212068 TTA-TTATGGTAAAATCTCATT
64 TAATTTATGGTATAATTTCATT
1212089 CCAGGTCCTC
Statistics
Matches: 166, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
109 61 0.37
110 89 0.54
111 16 0.10
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (110 bp):
TTTTACAAAATAGTCACTGAAAGGGACTATTTTCATAATTTTCCCTTTTAAATGTATGCTTTATA
ATTTATGGTATAATTTCATTTTAAGTACCCCAAAACTTTCCCATA
Found at i:1212301 original size:50 final size:48
Alignment explanation
Indices: 1212171--1212302 Score: 117
Period size: 50 Copynumber: 2.7 Consensus size: 48
1212161 TCACTCTATT
* * *
1212171 TATTTTTATTTT-TATT-TAGTCACTGTTAATTTCTTATTTAGCTACTA
1 TATTTTAATTTTGCATTCTAGTCACTGTT-ATTTCTTATTTAACTACTA
* * * *
1212218 TTATTTTAATTTTGGATTTTGGTCACTATTTATTTCTTATTTAACTACTA
1 -TATTTTAATTTTGCATTCTAGTCACT-GTTATTTCTTATTTAACTACTA
*
1212268 -ACTTTTATTTTCTTGCATTCTAGTCACTGTTATTT
1 TA-TTTTA-ATT-TTGCATTCTAGTCACTGTTATTT
1212303 TATTTTATGC
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
48 12 0.18
49 8 0.12
50 33 0.49
51 15 0.22
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (48 bp):
TATTTTAATTTTGCATTCTAGTCACTGTTATTTCTTATTTAACTACTA
Done.