Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold165.1
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: 1724686
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 30232 characters in sequence are not A, C, G, or T
File 5 of 8
Found at i:1050969 original size:9 final size:9
Alignment explanation
Indices: 1050805--1050956 Score: 135
Period size: 9 Copynumber: 18.0 Consensus size: 9
1050795 TACGTATTAA
*
1050805 GTAAATTAT
1 GTAAGTTAT
1050814 GTAAGTTAT
1 GTAAGTTAT
1050823 GT--GTTAT
1 GTAAGTTAT
*
1050830 GTAAGATAT
1 GTAAGTTAT
1050839 GTAAG-T-T
1 GTAAGTTAT
**
1050846 GTATTTTAT
1 GTAAGTTAT
*
1050855 GTAAGTTCT
1 GTAAGTTAT
1050864 GT-A-TTAT
1 GTAAGTTAT
*
1050871 GTATGTTAT
1 GTAAGTTAT
*
1050880 GTAAGTTGT
1 GTAAGTTAT
*
1050889 GT-AG-AAT
1 GTAAGTTAT
*
1050896 GTAAGCTAT
1 GTAAGTTAT
1050905 GTAAGTTAT
1 GTAAGTTAT
**
1050914 GTAAGTGGT
1 GTAAGTTAT
1050923 GT-A-TTAT
1 GTAAGTTAT
1050930 GTAAGTTAT
1 GTAAGTTAT
1050939 GTAAGTTAT
1 GTAAGTTAT
1050948 GTAAGTTAT
1 GTAAGTTAT
1050957 TATGTAAGTT
Statistics
Matches: 114, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
7 23 0.20
8 9 0.08
9 82 0.72
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:1051056 original size:12 final size:12
Alignment explanation
Indices: 1051006--1051150 Score: 81
Period size: 12 Copynumber: 13.2 Consensus size: 12
1050996 TAACATCAAG
*
1051006 TATTATGTAATT
1 TATTATGTAAGT
*
1051018 TATTATGTTA-T
1 TATTATGTAAGT
*
1051029 TA-TATATAAG-
1 TATTATGTAAGT
1051039 --TTATGTAAGT
1 TATTATGTAAGT
1051049 TATTATGTAAG-
1 TATTATGTAAGT
*
1051060 --TTATGCAAGCT
1 TATTATGTAAG-T
*
1051071 TA-TATATAAGT
1 TATTATGTAAGT
1051082 TATGTAT-TAAG-
1 TAT-TATGTAAGT
1051093 --TTATGTAAGT
1 TATTATGTAAGT
1051103 TATTATGTAAG-
1 TATTATGTAAGT
*
1051114 --TTATGCAAGCT
1 TATTATGTAAG-T
*
1051125 TA-TATATAAGT
1 TATTATGTAAGT
1051136 TATTATGTAAGT
1 TATTATGTAAGT
1051148 TAT
1 TAT
1051151 GTAAGTTTAT
Statistics
Matches: 102, Mismatches: 11, Indels: 40
0.67 0.07 0.26
Matches are distributed among these distances:
8 3 0.03
9 28 0.27
10 5 0.05
11 9 0.09
12 54 0.53
13 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (12 bp):
TATTATGTAAGT
Found at i:1051098 original size:54 final size:54
Alignment explanation
Indices: 1051035--1051157 Score: 230
Period size: 54 Copynumber: 2.3 Consensus size: 54
1051025 TTATTATATA
1051035 TAAGTTATGTAAGTTATTATGTAAGTTATGCAAGCTTATATATAAGTTATGTAT-
1 TAAGTTATGTAAGTTATTATGTAAGTTATGCAAGCTTATATATAAGTTAT-TATG
1051089 TAAGTTATGTAAGTTATTATGTAAGTTATGCAAGCTTATATATAAGTTATTATG
1 TAAGTTATGTAAGTTATTATGTAAGTTATGCAAGCTTATATATAAGTTATTATG
1051143 TAAGTTATGTAAGTT
1 TAAGTTATGTAAGTT
1051158 TATAACATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
53 3 0.04
54 65 0.96
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (54 bp):
TAAGTTATGTAAGTTATTATGTAAGTTATGCAAGCTTATATATAAGTTATTATG
Found at i:1051161 original size:33 final size:33
Alignment explanation
Indices: 1051098--1051161 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1051088 TTAAGTTATG
1051098 TAAGTTATTATGTAAGTTATGCAAGCTTATATA
1 TAAGTTATTATGTAAGTTATGCAAGCTTATATA
* *
1051131 TAAGTTATTATGTAAGTTATGTAAGTTTATA
1 TAAGTTATTATGTAAGTTATGCAAGCTTATA
1051162 ACATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (33 bp):
TAAGTTATTATGTAAGTTATGCAAGCTTATATA
Found at i:1051401 original size:60 final size:60
Alignment explanation
Indices: 1051310--1051454 Score: 254
Period size: 60 Copynumber: 2.4 Consensus size: 60
1051300 AAATATATAA
* * *
1051310 TTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAATAAATTTAGAACAC
1 TTATTTAGAAAACTTAT-AAATTTATACTAATAAATTTTAATACTAATAAATTTAGAAAAC
1051371 TTATTTAGAAAACTTATAAATTTATACTAATAAATTTTAATACTAATAAATTTAGAAAAC
1 TTATTTAGAAAACTTATAAATTTATACTAATAAATTTTAATACTAATAAATTTAGAAAAC
1051431 TTATTTAGAAAACTTATAAATTTA
1 TTATTTAGAAAACTTATAAATTTA
1051455 GAAAACTTAT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
60 64 0.79
61 17 0.21
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (60 bp):
TTATTTAGAAAACTTATAAATTTATACTAATAAATTTTAATACTAATAAATTTAGAAAAC
Found at i:1051415 original size:16 final size:16
Alignment explanation
Indices: 1051331--1051423 Score: 72
Period size: 16 Copynumber: 6.1 Consensus size: 16
1051321 ACTTATAAAA
1051331 TTAATACTAATAAATT
1 TTAATACTAATAAATT
*
1051347 TTATTACTAATAAA-T
1 TTAATACTAATAAATT
* *
1051362 TTAGA-AC-ACT-TATT
1 TTA-ATACTAATAAATT
* * *
1051376 TAGAAAACTTATAAA-T
1 T-TAATACTAATAAATT
1051392 TT-ATACTAATAAATT
1 TTAATACTAATAAATT
1051407 TTAATACTAATAAATT
1 TTAATACTAATAAATT
1051423 T
1 T
1051424 AGAAAACTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
13 1 0.02
14 14 0.24
15 12 0.21
16 30 0.52
17 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (16 bp):
TTAATACTAATAAATT
Found at i:1051423 original size:30 final size:30
Alignment explanation
Indices: 1051328--1051424 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
1051318 AAAACTTATA
* *
1051328 AAATTAATACTAATAAATTTTATTACTAAT
1 AAATTTATACTAATAAATTTTAATACTAAT
* * * * * *
1051358 AAATTTAGAAC-ACT-TATTTAGAAAACTTAT
1 AAATTTA-TACTAATAAATTT-TAATACTAAT
1051388 AAATTTATACTAATAAATTTTAATACTAAT
1 AAATTTATACTAATAAATTTTAATACTAAT
1051418 AAATTTA
1 AAATTTA
1051425 GAAAACTTAT
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
29 6 0.12
30 37 0.76
31 6 0.12
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (30 bp):
AAATTTATACTAATAAATTTTAATACTAAT
Found at i:1051438 original size:13 final size:13
Alignment explanation
Indices: 1051420--1051447 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1051410 ATACTAATAA
1051420 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1051433 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1051446 AT
1 AT
1051448 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:1051450 original size:30 final size:30
Alignment explanation
Indices: 1051356--1051469 Score: 124
Period size: 30 Copynumber: 3.8 Consensus size: 30
1051346 TTTATTACTA
*
1051356 ATAAATTTAGAACACTTATTTAGAAAACTT
1 ATAAATTTAGAAAACTTATTTAGAAAACTT
* * * * * *
1051386 ATAAATTTATACTAA-TAAATTT-TAATACTA
1 ATAAATTTAGA-AAACT-TATTTAGAAAACTT
1051416 ATAAATTTAGAAAACTTATTTAGAAAACTT
1 ATAAATTTAGAAAACTTATTTAGAAAACTT
*
1051446 ATAAATTTAGAAAACTTATATAGA
1 ATAAATTTAGAAAACTTATTTAGA
1051470 TATTAAAACA
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
29 6 0.09
30 55 0.83
31 5 0.08
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (30 bp):
ATAAATTTAGAAAACTTATTTAGAAAACTT
Found at i:1051519 original size:19 final size:19
Alignment explanation
Indices: 1051495--1051537 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1051485 ATATTGGTTA
1051495 TATAATTATTTAGAAAACC
1 TATAATTATTTAGAAAACC
*
1051514 TATAATTATTTAGAAAACT
1 TATAATTATTTAGAAAACC
1051533 TATAA
1 TATAA
1051538 ATTTTATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (19 bp):
TATAATTATTTAGAAAACC
Found at i:1053339 original size:23 final size:23
Alignment explanation
Indices: 1053300--1053345 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1053290 AACGACTTCG
*
1053300 TTTTGCTCTGCTAAAAATCTTTTA
1 TTTTGCTCTACTAAAAAT-TTTTA
1053324 TTTTG-TCTACTAAAAATTTTTA
1 TTTTGCTCTACTAAAAATTTTTA
1053346 GTTAAGTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTTGCTCTACTAAAAATTTTTA
Found at i:1055129 original size:41 final size:41
Alignment explanation
Indices: 1055067--1055471 Score: 510
Period size: 41 Copynumber: 9.9 Consensus size: 41
1055057 AAATCGGAGT
*
1055067 ATTAGCGGCGCTTC-TCTAAAAACACCGCTAAAGCCCCAAGC
1 ATTAGCGGCGCTTCTTC-AAAAACACCGCTAAAGCCCCGAGC
* *
1055108 ATTAGCGGCACTTCTTCAAAAA-ACGTCGCTAAATCCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACAC--CGCTAAAGCCCCGAGC
* *
1055150 ATTAGCGACGCTTCTTCAAAAACACCGCTAAAGCCCCGAAC
1 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGC
* ** *
1055191 ATTAGCGGTGCTTCTTCAAAAACGTCGCTAAAGCCCCGAGA
1 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGC
* **
1055232 ATTAACGGCGCTTCTTCAAAAATGCCGCTAAAGCCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGC
* *
1055273 ATTAGTGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGA
1 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGC
** * *
1055314 ATTAGCGGCGCTTCTTCAAAAATGCCGTTAAAGCCCCAAGC
1 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGC
* * *
1055355 ATTAGCGGTGCTTCTTCAAAAATGA-CGCTAAAGCTCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAA-CACCGCTAAAGCCCCGAGC
* * *
1055396 ATTAGTGGTGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGC
* **
1055437 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCC
1 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCC
1055472 ACGAAAACTC
Statistics
Matches: 315, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
40 2 0.01
41 275 0.87
42 36 0.11
43 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGC
Found at i:1055299 original size:123 final size:123
Alignment explanation
Indices: 1055067--1055471 Score: 571
Period size: 123 Copynumber: 3.3 Consensus size: 123
1055057 AAATCGGAGT
* *
1055067 ATTAGCGGCGCTTC-TCTAAAAACACCGCTAAAGCCCCAAGCATTAGCGGCACTTCTTCAAAAAA
1 ATTAGCGGCGCTTCTTC-AAAAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCTTCTTC-AAAAA
* * * * *
1055131 CGTCGCTAAATCCCCGAGCATTAGCGACGCTTCTTCAAAAACACCGCTAAAGCCCCGAAC
64 TGACGCTAAAGCCCCGAGCATTAGTGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAAC
* * * * *
1055191 ATTAGCGGTGCTTCTTCAAAAACGTCGCTAAAGCCCCGAGAATTAACGGCGCTTCTTCAAAAATG
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCTTCTTCAAAAATG
*
1055256 CCGCTAAAGCCCCGAGCATTAGTGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAGA-
66 ACGCTAAAGCCCCGAGCATTAGTGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGA-AC
* * *
1055314 ATTAGCGGCGCTTCTTCAAAAATGCCGTTAAAGCCCCAAGCATTAGCGGTGCTTCTTCAAAAATG
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCTTCTTCAAAAATG
* * * *
1055379 ACGCTAAAGCTCCGAGCATTAGTGGTGCTTCTTCAAAAACGCCGCTAAAGCCCCGAGC
66 ACGCTAAAGCCCCGAGCATTAGTGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAAC
* *
1055437 ATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
1055472 ACGAAAACTC
Statistics
Matches: 251, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
123 200 0.80
124 49 0.20
125 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (123 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCAAGCATTAGCGGCGCTTCTTCAAAAATG
ACGCTAAAGCCCCGAGCATTAGTGGCGCTTCTTCAAAAACACCGCTAAAGCCCCGAAC
Found at i:1055566 original size:39 final size:38
Alignment explanation
Indices: 1055518--1055635 Score: 137
Period size: 40 Copynumber: 3.0 Consensus size: 38
1055508 CACTTCTTGG
* *
1055518 AAAACGCCGCTAATGCTAATTTTTAGTGGCATTTTTTA
1 AAAACGCCGCTAATGCTGATTTTTAGTGGCTTTTTTTA
* * * *
1055556 AAAAGTGCCGCTAATACTCGATCTTTAGTGGTGTTTTTTTA
1 AAAA-CGCCGCTAATGCT-GATTTTTAGTGG-CTTTTTTTA
*
1055597 AAAACGCCGCTAATGCTTGATTTTTAGCGGCTTTTTTTA
1 AAAACGCCGCTAATGC-TGATTTTTAGTGGCTTTTTTTA
1055636 TCCAAACGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
38 4 0.06
39 19 0.29
40 30 0.46
41 12 0.18
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (38 bp):
AAAACGCCGCTAATGCTGATTTTTAGTGGCTTTTTTTA
Found at i:1056882 original size:17 final size:19
Alignment explanation
Indices: 1056849--1056892 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1056839 ATTTCAAAAT
1056849 AAAA-AAAATGAATGAAA-
1 AAAAGAAAATGAATGAAAG
*
1056866 AAATGAAAATG-ATGAAAG
1 AAAAGAAAATGAATGAAAG
1056884 AAAAGAAAA
1 AAAAGAAAA
1056893 AGAGAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAAGAAAATGAATGAAAG
Found at i:1056900 original size:11 final size:11
Alignment explanation
Indices: 1056880--1056920 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1056870 GAAAATGATG
1056880 AAAGAAAAGAA
1 AAAGAAAAGAA
*
1056891 AAAGAGAAGAA
1 AAAGAAAAGAA
* *
1056902 AAATAAAAGGA
1 AAAGAAAAGAA
1056913 AAAGAAAA
1 AAAGAAAA
1056921 AGGAGAGGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:1056909 original size:17 final size:17
Alignment explanation
Indices: 1056880--1056922 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1056870 GAAAATGATG
1056880 AAAG-AAAAGAAAAAGA
1 AAAGAAAAAGAAAAAGA
* * *
1056896 GAAGAAAAATAAAAGGA
1 AAAGAAAAAGAAAAAGA
1056913 AAAGAAAAAG
1 AAAGAAAAAG
1056923 GAGAGGCCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAGA
Found at i:1057061 original size:42 final size:42
Alignment explanation
Indices: 1057015--1057117 Score: 161
Period size: 42 Copynumber: 2.5 Consensus size: 42
1057005 TGTTGATCAA
* *
1057015 AATGGGCCATGAGGTGATCAGGGTAGCTCAAATTTCGAACAG
1 AATGGGGCATGAGGTGATCAGAGTAGCTCAAATTTCGAACAG
*
1057057 AATGGGGCATGAGGTGATCAGAGTAGCTCAAATTTCGATCAG
1 AATGGGGCATGAGGTGATCAGAGTAGCTCAAATTTCGAACAG
* *
1057099 ATTGGGGCATGTGGTGATC
1 AATGGGGCATGAGGTGATC
1057118 TTGTTATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (42 bp):
AATGGGGCATGAGGTGATCAGAGTAGCTCAAATTTCGAACAG
Found at i:1058551 original size:132 final size:130
Alignment explanation
Indices: 1058412--1058866 Score: 608
Period size: 132 Copynumber: 3.5 Consensus size: 130
1058402 CTCTAAGTTT
* * *
1058412 GCAGTGGAGTAAGTTGAAGATTGTAAATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * *
1058477 AGTGAATCTTATATTCCTAAGGTAATGGGGAAGCAAATTTAAGCCACTAGTCCTATTTCTCT-AG
66 AGTGAATCTTATATTCC-AAGGTAATAGGGAAGCAGATTTAAGCCACTAGTCCTATCTC-CTGA-
1058541 GCA
128 GCA
* *
1058544 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * * * *
1058609 AGTGAATCTTATCTTCCCAAGGTAGTAAGGAAACAGATTTAAGCCACCAGTCCTATCTCCTTGAG
66 AGTGAATCTTATATT-CCAAGGTAATAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCC-TGAG
1058674 CA
129 CA
* * * * * * *
1058676 GCAGTAGAATATGTTAAAGATTGTAGATCATGTCTCTCTAAGCAGTAGTGGAGCAGATCAGAGAC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* *
1058741 GGTGAATCTTATTTTTCCAAGGTAATAGGGAAGCAGATTTAAGCCA-TCAGTCCTATCTCCCTGA
66 AGTGAATCTTA-TATTCCAAGGTAATAGGGAAGCAGATTTAAGCCACT-AGTCCTATCT-CCTGA
1058805 GCA
128 GCA
* *
1058808 GCAATGGAGTAGGTTGAAGATTGTAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATC
1058867 GAAGGCAGCA
Statistics
Matches: 282, Mismatches: 35, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
131 1 0.00
132 273 0.97
133 8 0.03
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (130 bp):
GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
AGTGAATCTTATATTCCAAGGTAATAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCTGAGCA
Found at i:1058982 original size:51 final size:50
Alignment explanation
Indices: 1058901--1059068 Score: 194
Period size: 51 Copynumber: 3.3 Consensus size: 50
1058891 GGCGTTACAA
* * *
1058901 TGGAACGGATTAAAGTTAAAGGTAGTGAATCTTGTTTCCCTGATGTTGCAG
1 TGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGAT-TTGCAG
* * * * * *
1058952 TGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCTTTGTAG
1 TGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCT-GATTTGCAG
*
1059003 TGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTGGCA-TTGCAG
1 TGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCT-G-ATTTGCAG
*
1059054 TGGAATAGATTAAAG
1 TGGAACAGATTAAAG
1059069 TTGAAGTGGA
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
51 96 0.98
52 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (50 bp):
TGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGATTTGCAG
Found at i:1059007 original size:102 final size:102
Alignment explanation
Indices: 1058867--1059074 Score: 272
Period size: 102 Copynumber: 2.0 Consensus size: 102
1058857 GGAGCAGATC
* * * *
1058867 GAAGGCAGCAAATCCTATCTCCTTGGCGTTACAATGGAACGGATTAAAGTTAAAGGTAGTGAATC
1 GAAGGCAGCAAATCCTATCTCCTTGGCGTTACAATGGAACAGATTAAAGCTAAAGATAGCGAATC
**
1058932 TTGTTTCCCTGATGTTGCAGTGGAACAGATTAAAGCT
66 TTGTTTCCCTGACATTGCAGTGGAACAGATTAAAGCT
* * * * ** *
1058969 GAAGGCAGCGAATCTTATTTCCTTGGCTTTGTAGTGGAACAGATTAAAGCTAAAGATAGCGAATC
1 GAAGGCAGCAAATCCTATCTCCTTGGCGTTACAATGGAACAGATTAAAGCTAAAGATAGCGAATC
* * *
1059034 TTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGTT
66 TTGTTTCCCTGACATTGCAGTGGAACAGATTAAAGCT
1059071 GAAG
1 GAAG
1059075 TGGAGTGGAT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (102 bp):
GAAGGCAGCAAATCCTATCTCCTTGGCGTTACAATGGAACAGATTAAAGCTAAAGATAGCGAATC
TTGTTTCCCTGACATTGCAGTGGAACAGATTAAAGCT
Found at i:1059078 original size:21 final size:21
Alignment explanation
Indices: 1059052--1059095 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1059042 CTGGCATTGC
*
1059052 AGTGGAATAGATTAAAGTTGA
1 AGTGGAATAGATTAAAGCTGA
* *
1059073 AGTGGAGTGGATTAAAGCTGA
1 AGTGGAATAGATTAAAGCTGA
1059094 AG
1 AG
1059096 GCAACGAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (21 bp):
AGTGGAATAGATTAAAGCTGA
Found at i:1059322 original size:72 final size:72
Alignment explanation
Indices: 1059239--1059374 Score: 236
Period size: 72 Copynumber: 1.9 Consensus size: 72
1059229 TGTTTCCCTA
*
1059239 GCATTGCAGTGGAATAGATTAAAGCTGAAGTAGAGCGGATTAAAGTAGAAGGCAGCGAGTCCTAC
1 GCATTGCAGTGGAATAGATTAAAGCTGAAGTAGAGCGGATTAAAGTAGAAGGCAACGAGTCCTAC
1059304 CTCATTG
66 CTCATTG
* * *
1059311 GCATTGTAGTGGAATAGATTAAAGCTGAAGTAGAGTGGATTAAAGTTGAAGGCAACGAGTCCTA
1 GCATTGCAGTGGAATAGATTAAAGCTGAAGTAGAGCGGATTAAAGTAGAAGGCAACGAGTCCTA
1059375 TCTCCCTGAG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (72 bp):
GCATTGCAGTGGAATAGATTAAAGCTGAAGTAGAGCGGATTAAAGTAGAAGGCAACGAGTCCTAC
CTCATTG
Found at i:1059332 original size:194 final size:193
Alignment explanation
Indices: 1058996--1059349 Score: 548
Period size: 194 Copynumber: 1.8 Consensus size: 193
1058986 TTTCCTTGGC
* *
1058996 TTTGTAGTGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTGGCATTGCAGTGGAATA
1 TTTGCAGTGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTAGCATTGCAGTGGAATA
* * * * * *
1059061 GATTAAAGTTGAAGTGGAGTGGATTAAAGCTGAAGGCAACGAGTCCTATCTCCTTGGCGTTACAG
66 GATTAAAGCTGAAGTAGAGCGGATTAAAGCTGAAGGCAACGAGTCCTACCTCATTGGCATTACAG
*
1059126 TGGAACAGATTAAAGCTAAAGTTGTAGTGGAGCAGGTTGAAGATACCAACTTTATCTCTCAGAA
131 TGGAACAGATTAAAGCTAAAGTAG-AGTGGAGCAGGTTGAAGATACCAACTTTATCTCTCAGAA
*
1059190 TTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGTGGAATA
1 TTTGCAGTGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTAGCATTGCAGTGGAATA
* **
1059255 GATTAAAGCTGAAGTAGAGCGGATTAAAG-TAGAAGGCAGCGAGTCCTACCTCATTGGCATTGTA
66 GATTAAAGCTGAAGTAGAGCGGATTAAAGCT-GAAGGCAACGAGTCCTACCTCATTGGCATTACA
* *
1059319 GTGGAATAGATTAAAGCTGAAGTAGAGTGGA
130 GTGGAACAGATTAAAGCTAAAGTAGAGTGGA
1059350 TTAAAGTTGA
Statistics
Matches: 144, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
193 7 0.05
194 137 0.95
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (193 bp):
TTTGCAGTGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTAGCATTGCAGTGGAATA
GATTAAAGCTGAAGTAGAGCGGATTAAAGCTGAAGGCAACGAGTCCTACCTCATTGGCATTACAG
TGGAACAGATTAAAGCTAAAGTAGAGTGGAGCAGGTTGAAGATACCAACTTTATCTCTCAGAA
Found at i:1059393 original size:194 final size:194
Alignment explanation
Indices: 1059001--1059394 Score: 497
Period size: 194 Copynumber: 2.0 Consensus size: 194
1058991 TTGGCTTTGT
*
1059001 AGTGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTA
1 AGTGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTAGCATTGCAGTGGAATAGATTA
* * * * * *
1059066 AAGTTGAAGTGGAGTGGATTAAAGCTGAAGGCAACGAGTCCTATCTCCTTGGCGTTACAGTGGAA
66 AAGCTGAAGTAGAGCGGATTAAAGCTGAAGGCAACGAGTCCTACCTCATTGGCATTACAGTGGAA
* * * * * * * * *
1059131 CAGATTAAAGCTAAAGTTGTAGTGGAGCAGGTTGAAGATACCAACTTTATCTCTCAGAATTTGC
131 CAGATTAAAGCTAAAGTAGTAGTGGAGAAAGTTGAAGACAACAACTCTATCTCCCAGAAGTAGC
*
1059195 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGTGGAATAGATTA
1 AGTGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTAGCATTGCAGTGGAATAGATTA
* **
1059260 AAGCTGAAGTAGAGCGGATTAAAG-TAGAAGGCAGCGAGTCCTACCTCATTGGCATTGTAGTGGA
66 AAGCTGAAGTAGAGCGGATTAAAGCT-GAAGGCAACGAGTCCTACCTCATTGGCATTACAGTGGA
* * * * * * *
1059324 ATAGATTAAAGCTGAAGTAG-AGTGGATTAAAGTTGAAGGCAACGAGTCCTATCTCCCTG-AGTA
130 ACAGATTAAAGCTAAAGTAGTAGTGGA-GAAAGTTGAAGACAACAACT-CTATCTCCCAGAAGTA
1059387 GC
193 GC
1059389 AGTGGA
1 AGTGGA
1059395 GCATACTAAA
Statistics
Matches: 170, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
193 7 0.04
194 155 0.91
195 8 0.05
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (194 bp):
AGTGGAACAGATTAAAGCTAAAGATAGCGAATCTTGTTTCCCTAGCATTGCAGTGGAATAGATTA
AAGCTGAAGTAGAGCGGATTAAAGCTGAAGGCAACGAGTCCTACCTCATTGGCATTACAGTGGAA
CAGATTAAAGCTAAAGTAGTAGTGGAGAAAGTTGAAGACAACAACTCTATCTCCCAGAAGTAGC
Found at i:1060261 original size:10 final size:10
Alignment explanation
Indices: 1060246--1060272 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1060236 GCCACCGTGT
1060246 ACGGTGGCAG
1 ACGGTGGCAG
1060256 ACGGTGGCAG
1 ACGGTGGCAG
1060266 ACGGTGG
1 ACGGTGG
1060273 TAGCCGGCGG
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:0.19, C:0.19, G:0.52, T:0.11
Consensus pattern (10 bp):
ACGGTGGCAG
Found at i:1061590 original size:17 final size:17
Alignment explanation
Indices: 1061548--1061582 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1061538 ACAAATATGC
*
1061548 AAATATATATAATGTTT
1 AAATATATATAATGTAT
1061565 AAATATATATAATGTAT
1 AAATATATATAATGTAT
1061582 A
1 A
1061583 TATTTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
AAATATATATAATGTAT
Found at i:1061771 original size:16 final size:17
Alignment explanation
Indices: 1061750--1061782 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1061740 ATGGAAAATG
1061750 TATAAATAT-TATAAAA
1 TATAAATATATATAAAA
1061766 TATAAATATATATAAAA
1 TATAAATATATATAAAA
1061783 ACTATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAAATATATATAAAA
Found at i:1070856 original size:15 final size:14
Alignment explanation
Indices: 1070832--1070861 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1070822 GGGTTATGGG
1070832 AAACAGTAGAAGAA
1 AAACAGTAGAAGAA
1070846 AAACAAGTAGAAGAA
1 AAAC-AGTAGAAGAA
1070861 A
1 A
1070862 CCAAGAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.67, C:0.07, G:0.20, T:0.07
Consensus pattern (14 bp):
AAACAGTAGAAGAA
Found at i:1075448 original size:41 final size:41
Alignment explanation
Indices: 1075376--1075648 Score: 259
Period size: 41 Copynumber: 6.7 Consensus size: 41
1075366 CATTCGGGGA
*** * *
1075376 TTTAGCGGCGTTTTAAAAAAAAGTGTCGCTAATGCCCAGATC
1 TTTAGCGGCGTTTT-TGTAAAAGTGCCGCTAATGCTCAGATC
*
1075418 TTTAGAGGCGTTTTTGTAAAAGTGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGTAAAAGTGCCGCTAATGCTCAGATC
* *
1075459 TTTAGCAGCGTTTTT-TAAGAAGTACC-CTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGTAA-AAGTGCCGCTAATGCTCAGATC
* * * *
1075499 TTTAGCGGCATTTTTGGAGAAGCGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGTAAAAGTGCCGCTAATGCTCAGATC
* * ** * * *
1075540 TTTATCGGCATTTTTCCAAAA-TCGCCGC-GATACTCAAATC
1 TTTAGCGGCGTTTTTGTAAAAGT-GCCGCTAATGCTCAGATC
* *
1075580 TTTAGCGGCGTTTATAG-AAAAGCGCCGCTAATGCTCAGATC
1 TTTAGCGGCGTTT-TTGTAAAAGTGCCGCTAATGCTCAGATC
* * *
1075621 TTTAGCGACGTTTTTGAAAAAGCGCCGC
1 TTTAGCGGCGTTTTTGTAAAAGTGCCGC
1075649 AAAAACTTTT
Statistics
Matches: 190, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
40 66 0.35
41 111 0.58
42 13 0.07
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGTAAAAGTGCCGCTAATGCTCAGATC
Found at i:1075513 original size:81 final size:78
Alignment explanation
Indices: 1075404--1075635 Score: 243
Period size: 81 Copynumber: 2.9 Consensus size: 78
1075394 AAAAGTGTCG
* * *
1075404 CTAATGCCCAGATCTTTAGAGGCGTTTTTGTAAAAGTGCCGCTAATGCTCAGATCTTTAGCAGCG
1 CTAATGCTCAGATCTTTAGCGGCGTTTTTG-AAAAGCGCCGCTAATGCTCAGATCTTTAGC-GCG
*
1075469 TTTTT-TAAGAAGTAC-C
64 TTTTTCCAA-AA-T-CGC
* * * *
1075485 CTAATGCTCAGATCTTTAGCGGCATTTTTGGAGAAGCGCCGCTAATGCTCAGATCTTTATCGGCA
1 CTAATGCTCAGATCTTTAGCGGCGTTTTT-GAAAAGCGCCGCTAATGCTCAGATCTTTAGC-GCG
1075550 TTTTTCCAAAATCGC
64 TTTTTCCAAAATCGC
** * * *
1075565 CGCGATACTCAAATCTTTAGCGGCGTTTATAGAAAAGCGCCGCTAATGCTCAGATCTTTAGCGAC
1 C-TAATGCTCAGATCTTTAGCGGCGTTT-TTGAAAAGCGCCGCTAATGCTCAGATCTTTAGCG-C
1075630 GTTTTT
63 GTTTTT
1075636 GAAAAAGCGC
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
79 1 0.01
80 4 0.03
81 118 0.93
82 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (78 bp):
CTAATGCTCAGATCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTCAGATCTTTAGCGCGTT
TTTCCAAAATCGC
Found at i:1075793 original size:26 final size:26
Alignment explanation
Indices: 1075745--1075795 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1075735 AAAATGGATA
** * *
1075745 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
1075771 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
1075796 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:1076063 original size:14 final size:15
Alignment explanation
Indices: 1076035--1076067 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1076025 AAGGTTTATA
1076035 GATTATGGAATTAGG
1 GATTATGGAATTAGG
1076050 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
1076064 GATT
1 GATT
1076068 CTGATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:1076235 original size:63 final size:63
Alignment explanation
Indices: 1076160--1076304 Score: 209
Period size: 63 Copynumber: 2.3 Consensus size: 63
1076150 ATTTGGTGTT
* * * * *
1076160 AGGTTAGAGTTTAGGGTTTAGATTAATTAGTGTATTTTAATTTATATGTTAAATGATGTTTAG
1 AGGTTAGGGTTTAGGATTTAGATTAATTAGTATATTTTAATTTATATATTAAATAATGTTTAG
* *
1076223 GGGTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAG
1 AGGTTAGGGTTTAGGATTTAGATTAATTAGTATATTTTAATTTATATATTAAATAATGTTTAG
*
1076286 AGGTTAGGGGTTAGTGATT
1 AGGTTAGGGTTTAG-GATT
1076305 CGGGGTCGGG
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
63 68 0.94
64 4 0.06
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (63 bp):
AGGTTAGGGTTTAGGATTTAGATTAATTAGTATATTTTAATTTATATATTAAATAATGTTTAG
Found at i:1076324 original size:88 final size:89
Alignment explanation
Indices: 1076223--1076387 Score: 296
Period size: 88 Copynumber: 1.9 Consensus size: 89
1076213 TGATGTTTAG
*
1076223 GGGTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGAG
1 GGGTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATATTTAGAG
1076288 GTTAGGGGTTAGTGATTCGGGGTC
66 GTTAGGGGTTAGTGATTCGGGGTC
*
1076312 GGGTTA-GGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATATTTAGGG
1 GGGTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATATTTAGAG
*
1076376 GTTAGTGGTTAG
66 GTTAGGGGTTAG
1076388 GGGTTTGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 67 0.92
89 6 0.08
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.45
Consensus pattern (89 bp):
GGGTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATATTTAGAG
GTTAGGGGTTAGTGATTCGGGGTC
Found at i:1077337 original size:21 final size:21
Alignment explanation
Indices: 1077313--1077362 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 21
1077303 AAAACTAAAA
1077313 TTTATAATTTTA-TCAAAAACT
1 TTTATAATTTTACT-AAAAACT
* *
1077334 TTTA-AATATTACTTAAAACT
1 TTTATAATTTTACTAAAAACT
*
1077354 TTAATAATT
1 TTTATAATT
1077363 ATTTACTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTATAATTTTACTAAAAACT
Found at i:1079764 original size:613 final size:613
Alignment explanation
Indices: 1078599--1079825 Score: 2436
Period size: 613 Copynumber: 2.0 Consensus size: 613
1078589 TGTTAACTTA
*
1078599 TCAAGTCAGATTGGCTCGGCTTTAAATTTGGGTTAATATAGGTGAGGTAAATTTTGAATATCCCT
1 TCAAGTCAGATTGGCTCGACTTTAAATTTGGGTTAATATAGGTGAGGTAAATTTTGAATATCCCT
1078664 AGTAACCTAGATGCAGAAGTCCTCCATTGGGAAATATCGCTTCCAACATCTGTATGTACAATATA
66 AGTAACCTAGATGCAGAAGTCCTCCATTGGGAAATATCGCTTCCAACATCTGTATGTACAATATA
1078729 GAAACGTGATGATGGGTCAGCCAACCCACAAAGGCTAATTGATTGAAAGGCAAAAATAAAAAATA
131 GAAACGTGATGATGGGTCAGCCAACCCACAAAGGCTAATTGATTGAAAGGCAAAAATAAAAAATA
1078794 AAAAATAGATTGCTAGCTGGATCTTTAAGTGGTGGGAAGGATAAATTGATAGTATTTGATAAATT
196 AAAAATAGATTGCTAGCTGGATCTTTAAGTGGTGGGAAGGATAAATTGATAGTATTTGATAAATT
1078859 GATATGCGAATGTCAACAATTTCTAAATCGAGACATCTATTTTAAGCATAGAGGGAGACATCTAA
261 GATATGCGAATGTCAACAATTTCTAAATCGAGACATCTATTTTAAGCATAGAGGGAGACATCTAA
*
1078924 TATCATCTAATTCACTGTCATGTACCTTTTTACAGTAGCAAGCTGATCAGTTTTGATGATAGGTT
326 TATCATCTAATTCACTGTCATGTACCTTTTTACAGTAGCAAGCTGATCAATTTTGATGATAGGTT
1078989 ATAAGCTGATAAATAATGTAATAGTTTTGATGATAGGTTTGCACATGGATGCATTTAGGCTTATT
391 ATAAGCTGATAAATAATGTAATAGTTTTGATGATAGGTTTGCACATGGATGCATTTAGGCTTATT
1079054 TAAAAGAAACAATGTATATGATATGGCTTTAAATCATTTATGCATTTAGGTTTTTTTAGTTTTTT
456 TAAAAGAAACAATGTATATGATATGGCTTTAAATCATTTATGCATTTAGGTTTTTTTAGTTTTTT
1079119 TAGTTTAGCTAACTTCGTGAATATAAACTTTTGTTTTTTTTAGTTTTTTACTTTATTACTTTTGT
521 TAGTTTAGCTAACTTCGTGAATATAAACTTTTGTTTTTTTTAGTTTTTTACTTTATTACTTTTGT
1079184 TTTTTTCGGTACTAATGTATTTCTGTCT
586 TTTTTTCGGTACTAATGTATTTCTGTCT
1079212 TCAAGTCAGATTGGCTCGACTTTAAATTTGGGTTAATATAGGTGAGGTAAATTTTGAATATCCCT
1 TCAAGTCAGATTGGCTCGACTTTAAATTTGGGTTAATATAGGTGAGGTAAATTTTGAATATCCCT
1079277 AGTAACCTAGATGCAGAAGTCCTCCATTGGGAAATATCGCTTCCAACATCTGTATGTACAATATA
66 AGTAACCTAGATGCAGAAGTCCTCCATTGGGAAATATCGCTTCCAACATCTGTATGTACAATATA
1079342 GAAACGTGATGATGGGTCAGCCAACCCACAAAGGCTAATTGATTGAAAGGCAAAAATAAAAAATA
131 GAAACGTGATGATGGGTCAGCCAACCCACAAAGGCTAATTGATTGAAAGGCAAAAATAAAAAATA
1079407 AAAAATAGATTGCTAGCTGGATCTTTAAGTGGTGGGAAGGATAAATTGATAGTATTTGATAAATT
196 AAAAATAGATTGCTAGCTGGATCTTTAAGTGGTGGGAAGGATAAATTGATAGTATTTGATAAATT
1079472 GATATGCGAATGTCAACAATTTCTAAATCGAGACATCTATTTTAAGCATAGAGGGAGACATCTAA
261 GATATGCGAATGTCAACAATTTCTAAATCGAGACATCTATTTTAAGCATAGAGGGAGACATCTAA
1079537 TATCATCTAATTCACTGTCATGTACCTTTTTACAGTAGCAAGCTGATCAATTTTGATGATAGGTT
326 TATCATCTAATTCACTGTCATGTACCTTTTTACAGTAGCAAGCTGATCAATTTTGATGATAGGTT
1079602 ATAAGCTGATAAATAATGTAATAGTTTTGATGATAGGTTTGCACATGGATGCATTTAGGCTTATT
391 ATAAGCTGATAAATAATGTAATAGTTTTGATGATAGGTTTGCACATGGATGCATTTAGGCTTATT
1079667 TAAAAGAAACAATGTATATGATATGGCTTTAAATCATTTATGCATTTAGGTTTTTTTAGTTTTTT
456 TAAAAGAAACAATGTATATGATATGGCTTTAAATCATTTATGCATTTAGGTTTTTTTAGTTTTTT
1079732 TAGTTTAGCTAACTTCGTGAATATAAACTTTTGTTTTTTTTAGTTTTTTACTTTATTACTTTTGT
521 TAGTTTAGCTAACTTCGTGAATATAAACTTTTGTTTTTTTTAGTTTTTTACTTTATTACTTTTGT
1079797 TTTTTTCGGTACTAATGTATTTCTGTCT
586 TTTTTTCGGTACTAATGTATTTCTGTCT
1079825 T
1 T
1079826 TTTTTCCAGG
Statistics
Matches: 612, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
613 612 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.37
Consensus pattern (613 bp):
TCAAGTCAGATTGGCTCGACTTTAAATTTGGGTTAATATAGGTGAGGTAAATTTTGAATATCCCT
AGTAACCTAGATGCAGAAGTCCTCCATTGGGAAATATCGCTTCCAACATCTGTATGTACAATATA
GAAACGTGATGATGGGTCAGCCAACCCACAAAGGCTAATTGATTGAAAGGCAAAAATAAAAAATA
AAAAATAGATTGCTAGCTGGATCTTTAAGTGGTGGGAAGGATAAATTGATAGTATTTGATAAATT
GATATGCGAATGTCAACAATTTCTAAATCGAGACATCTATTTTAAGCATAGAGGGAGACATCTAA
TATCATCTAATTCACTGTCATGTACCTTTTTACAGTAGCAAGCTGATCAATTTTGATGATAGGTT
ATAAGCTGATAAATAATGTAATAGTTTTGATGATAGGTTTGCACATGGATGCATTTAGGCTTATT
TAAAAGAAACAATGTATATGATATGGCTTTAAATCATTTATGCATTTAGGTTTTTTTAGTTTTTT
TAGTTTAGCTAACTTCGTGAATATAAACTTTTGTTTTTTTTAGTTTTTTACTTTATTACTTTTGT
TTTTTTCGGTACTAATGTATTTCTGTCT
Found at i:1080646 original size:21 final size:23
Alignment explanation
Indices: 1080614--1080671 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
1080604 TTAAAACATC
* *
1080614 TTTTATATATATTTATA-TACAG
1 TTTTATATATATTTATATTAAAA
*
1080636 TTTTA-ATATATATATATTAAAA
1 TTTTATATATATTTATATTAAAA
1080658 TTTTATATATATTT
1 TTTTATATATATTT
1080672 GAAAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 10 0.33
22 13 0.43
23 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTATATATATTTATATTAAAA
Found at i:1080664 original size:19 final size:19
Alignment explanation
Indices: 1080642--1080682 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1080632 ACAGTTTTAA
*
1080642 TATATATATATT-AAAATTT
1 TATATATAT-TTGAAAAATT
1080661 TATATATATTTGAAAAATT
1 TATATATATTTGAAAAATT
1080680 TAT
1 TAT
1080683 CAATCATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATATATTTGAAAAATT
Found at i:1080761 original size:12 final size:11
Alignment explanation
Indices: 1080744--1080831 Score: 85
Period size: 12 Copynumber: 8.1 Consensus size: 11
1080734 TACACAACAC
1080744 ATAACTTACAT
1 ATAACTTACAT
1080755 AATAACTTAC--
1 -ATAACTTACAT
*
1080765 ATAACTTATAT
1 ATAACTTACAT
*
1080776 ATAAACTTATAT
1 AT-AACTTACAT
1080788 ATAACTTAC--
1 ATAACTTACAT
*
1080797 ATAACTTATAT
1 ATAACTTACAT
*
1080808 ATAAACTTATAT
1 AT-AACTTACAT
1080820 ATAACTTACAT
1 ATAACTTACAT
1080831 A
1 A
1080832 CATAATTTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
9 16 0.24
11 19 0.29
12 31 0.47
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAACTTACAT
Found at i:1080768 original size:21 final size:24
Alignment explanation
Indices: 1080742--1080800 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
1080732 CTTACACAAC
1080742 ACATAACTTACATAAT-AAC-T-T
1 ACATAACTTACATAATAAACTTAT
*
1080763 ACATAACTTATAT-ATAAACTTAT
1 ACATAACTTACATAATAAACTTAT
*
1080786 ATATAACTTACATAA
1 ACATAACTTACATAA
1080801 CTTATATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.06
21 15 0.48
22 1 0.03
23 12 0.39
24 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (24 bp):
ACATAACTTACATAATAAACTTAT
Found at i:1080862 original size:36 final size:36
Alignment explanation
Indices: 1080762--1080865 Score: 128
Period size: 32 Copynumber: 3.0 Consensus size: 36
1080752 CATAATAACT
*
1080762 TACATAACTTATATATAAACTTATATATAAC-T---
1 TACATAACTTAAATATAAACTTATATATAACTTACA
*
1080794 TACATAACTTATATATAAACTTATATATAACTTACA
1 TACATAACTTAAATATAAACTTATATATAACTTACA
* *
1080830 TACATAATTTAAATA-AAATTTATATATAAACTTACA
1 TACATAACTTAAATATAAACTTATATAT-AACTTACA
1080866 CAACACATAA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
32 31 0.48
33 1 0.02
35 11 0.17
36 21 0.33
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (36 bp):
TACATAACTTAAATATAAACTTATATATAACTTACA
Found at i:1080871 original size:128 final size:128
Alignment explanation
Indices: 1080688--1080932 Score: 411
Period size: 128 Copynumber: 1.9 Consensus size: 128
1080678 TTTATCAATC
* *
1080688 ATATCATAATTTACATACATAACATATATAAATTTATATATAAACTTACACAACACATAACTTAC
1 ATATCATAACTTACATACATAACATAAATAAATTTATATATAAACTTACACAACACATAACTTAC
*
1080753 ATAATAACTTACATAACTTATATATAAACTTATATATAACTTACATAACTTATATATAAACTT
66 ACAATAACTTACATAACTTATATATAAACTTATATATAACTTACATAACTTATATATAAACTT
**
1080816 ATAT-ATAACTTACATACATAATTTAAATAAAATTTATATATAAACTTACACAACACATAACTTA
1 ATATCATAACTTACATACATAACATAAAT-AAATTTATATATAAACTTACACAACACATAACTTA
* *
1080880 CACAATAACTTACATAATTTATATATAAACTTATATATAACTTTCATAACTTA
65 CACAATAACTTACATAACTTATATATAAACTTATATATAACTTACATAACTTA
1080933 CTTATAATAA
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
127 20 0.18
128 89 0.82
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (128 bp):
ATATCATAACTTACATACATAACATAAATAAATTTATATATAAACTTACACAACACATAACTTAC
ACAATAACTTACATAACTTATATATAAACTTATATATAACTTACATAACTTATATATAAACTT
Found at i:1080939 original size:32 final size:32
Alignment explanation
Indices: 1080774--1080932 Score: 141
Period size: 32 Copynumber: 5.0 Consensus size: 32
1080764 CATAACTTAT
1080774 ATATAAACTTATATATAACTTACATAACTTAT
1 ATATAAACTTATATATAACTTACATAACTTAT
*
1080806 ATATAAACTTATATATAACTTACAT-ACATAATTT
1 ATATAAACTTATATATAACTTACATAAC-T--TAT
* * *
1080840 AAATAAAATTTATATATAAACTTACACAAC----
1 ATAT-AAACTTATATAT-AACTTACATAACTTAT
* * * *
1080870 ACAT-AACTTACACAATAACTTACATAATTTAT
1 ATATAAACTTATA-TATAACTTACATAACTTAT
*
1080902 ATATAAACTTATATATAACTTTCATAACTTA
1 ATATAAACTTATATATAACTTACATAACTTA
1080933 CTTATAATAA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
28 16 0.16
29 2 0.02
30 3 0.03
31 2 0.02
32 44 0.44
33 7 0.07
34 5 0.05
35 11 0.11
36 8 0.08
37 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (32 bp):
ATATAAACTTATATATAACTTACATAACTTAT
Found at i:1080950 original size:23 final size:24
Alignment explanation
Indices: 1080908--1080952 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1080898 TTATATATAA
*
1080908 ACTTATATATAACTTTCATAACTT
1 ACTTATATATAACTTACATAACTT
1080932 ACTTATA-ATAACTTACATAAC
1 ACTTATATATAACTTACATAAC
1080953 ACATAGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (24 bp):
ACTTATATATAACTTACATAACTT
Found at i:1080986 original size:16 final size:16
Alignment explanation
Indices: 1080967--1081033 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 16
1080957 AGCCTACATG
1080967 ACTTACATAATACACA
1 ACTTACATAATACACA
1080983 ACTT--A-AAT--A--
1 ACTTACATAATACACA
*
1080992 ACTTACATAATACATA
1 ACTTACATAATACACA
* *
1081008 ACTTACATTACACACA
1 ACTTACATAATACACA
1081024 ACTTACATAA
1 ACTTACATAA
1081034 CTTACATTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
9 4 0.10
11 2 0.05
12 3 0.08
13 3 0.08
14 2 0.05
16 26 0.65
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.28
Consensus pattern (16 bp):
ACTTACATAATACACA
Found at i:1080987 original size:41 final size:40
Alignment explanation
Indices: 1080941--1081040 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 40
1080931 TACTTATAAT
* * *
1080941 AACTTACATAAC-ACATAGCCTACATGACTTACATAATACAC
1 AACTTACATAACTACATA--ATACATAACTTACATAACACAC
* *
1080982 AACTTAAATAACTTACATAATACATAACTTACATTACACAC
1 AACTTACATAAC-TACATAATACATAACTTACATAACACAC
1081023 AACTTACATAACTTACAT
1 AACTTACATAAC-TACAT
1081041 TCATAACTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
41 46 0.90
43 5 0.10
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (40 bp):
AACTTACATAACTACATAATACATAACTTACATAACACAC
Found at i:1080995 original size:25 final size:25
Alignment explanation
Indices: 1080932--1081012 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
1080922 TTCATAACTT
*
1080932 ACTTATAATAACTTACATAACACATA
1 ACTTA-AATAACTTACATAATACATA
* * * * *
1080958 GCCTACATGACTTACATAATACACA
1 ACTTAAATAACTTACATAATACATA
1080983 ACTTAAATAACTTACATAATACATA
1 ACTTAAATAACTTACATAATACATA
1081008 ACTTA
1 ACTTA
1081013 CATTACACAC
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
25 41 0.93
26 3 0.07
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (25 bp):
ACTTAAATAACTTACATAATACATA
Found at i:1081014 original size:9 final size:9
Alignment explanation
Indices: 1080939--1081234 Score: 115
Period size: 9 Copynumber: 34.9 Consensus size: 9
1080929 CTTACTTATA
1080939 ATAACTTAC
1 ATAACTTAC
1080948 ATAAC--AC
1 ATAACTTAC
* *
1080955 ATAGCCTAC
1 ATAACTTAC
*
1080964 ATGACTTAC
1 ATAACTTAC
1080973 ATAA--TAC
1 ATAACTTAC
* *
1080980 ACAACTTAA
1 ATAACTTAC
1080989 ATAACTTAC
1 ATAACTTAC
1080998 ATAA--TAC
1 ATAACTTAC
1081005 ATAACTTAC
1 ATAACTTAC
*
1081014 ATTAC--AC
1 ATAACTTAC
*
1081021 ACAACTTAC
1 ATAACTTAC
1081030 ATAACTTAC
1 ATAACTTAC
1081039 ---A-TT-C
1 ATAACTTAC
1081043 ATAACTTGA-
1 ATAACTT-AC
* *
1081052 ATAAAATTTATAT
1 AT--AA-CT-TAC
1081065 ATAAACTTAC
1 AT-AACTTAC
*
1081075 ACAAC--AC
1 ATAACTTAC
1081082 ATAACTTAC
1 ATAACTTAC
1081091 AT-A--T--
1 ATAACTTAC
1081095 ATAACTTAC
1 ATAACTTAC
*
1081104 ATAACTTATAT
1 ATAAC-T-TAC
*
1081115 ATAAACTTAT
1 AT-AACTTAC
* *
1081125 ATAGCCTAC
1 ATAACTTAC
* *
1081134 ATGACTTAT
1 ATAACTTAC
1081143 ATAA--TAC
1 ATAACTTAC
* *
1081150 ACAACTTAA
1 ATAACTTAC
1081159 ATAACTTAC
1 ATAACTTAC
1081168 ATAA--TAC
1 ATAACTTAC
*
1081175 ATAACTTTC
1 ATAACTTAC
1081184 ATAACTTAC
1 ATAACTTAC
*
1081193 ATTA--TAC
1 ATAACTTAC
* *
1081200 ACAACTTAT
1 ATAACTTAC
1081209 ATAACTTAC
1 ATAACTTAC
1081218 ATAACTTAC
1 ATAACTTAC
*
1081227 ATAGCTTA
1 ATAACTTA
1081235 ATTATACTTA
Statistics
Matches: 211, Mismatches: 41, Indels: 70
0.66 0.13 0.22
Matches are distributed among these distances:
4 3 0.01
5 3 0.01
6 2 0.01
7 49 0.23
8 3 0.01
9 123 0.58
10 9 0.04
11 8 0.04
12 8 0.04
13 3 0.01
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:1081100 original size:13 final size:13
Alignment explanation
Indices: 1081082--1081106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1081072 TACACAACAC
1081082 ATAACTTACATAT
1 ATAACTTACATAT
1081095 ATAACTTACATA
1 ATAACTTACATA
1081107 ACTTATATAT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAACTTACATAT
Found at i:1081107 original size:61 final size:62
Alignment explanation
Indices: 1081007--1081127 Score: 142
Period size: 61 Copynumber: 2.0 Consensus size: 62
1080997 CATAATACAT
** * *
1081007 AACTTACATTACACACAACTTACATAACTTACATTCATAACTTGA-ATA-AAATTTATATATA
1 AACTTACACAACACACAACTTACATAACTAACATTCATAACTT-ATATATAAACTTATATATA
*
1081068 AACTTACACAACACATAACTTACATATA-TAAC-TTACATAACTTATATATAAACTTATATA
1 AACTTACACAACACACAACTTACATA-ACTAACATT-CATAACTTATATATAAACTTATATA
1081128 GCCTACATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
60 3 0.06
61 37 0.73
62 11 0.22
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (62 bp):
AACTTACACAACACACAACTTACATAACTAACATTCATAACTTATATATAAACTTATATATA
Found at i:1081108 original size:22 final size:21
Alignment explanation
Indices: 1081080--1081123 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
1081070 CTTACACAAC
1081080 ACATAACTTACATATATAACTT
1 ACATAACTTACATATA-AACTT
*
1081102 ACATAACTTATATATAAACTT
1 ACATAACTTACATATAAACTT
1081123 A
1 A
1081124 TATAGCCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (21 bp):
ACATAACTTACATATAAACTT
Found at i:1081126 original size:30 final size:33
Alignment explanation
Indices: 1081092--1081171 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 33
1081082 ATAACTTACA
1081092 TATATAACTTACATAACTTATAT-AT-A-AACT
1 TATATAACTTACATAACTTATATAATAACAACT
* * *
1081122 TATATAGCCTACATGACTTATATAATACACAACT
1 TATATAACTTACATAACTTATATAATA-ACAACT
*
1081156 TAAATAACTTACATAA
1 TATATAACTTACATAA
1081172 TACATAACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 20 0.51
31 2 0.05
33 1 0.03
34 16 0.41
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (33 bp):
TATATAACTTACATAACTTATATAATAACAACT
Found at i:1081171 original size:25 final size:25
Alignment explanation
Indices: 1081137--1081221 Score: 116
Period size: 25 Copynumber: 3.4 Consensus size: 25
1081127 AGCCTACATG
*
1081137 ACTTATATAATACACAACTTAAATA
1 ACTTACATAATACACAACTTAAATA
* **
1081162 ACTTACATAATACATAACTTTCATA
1 ACTTACATAATACACAACTTAAATA
* *
1081187 ACTTACATTATACACAACTTATATA
1 ACTTACATAATACACAACTTAAATA
1081212 ACTTACATAA
1 ACTTACATAA
1081222 CTTACATAGC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (25 bp):
ACTTACATAATACACAACTTAAATA
Found at i:1083313 original size:29 final size:29
Alignment explanation
Indices: 1083271--1083327 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1083261 ATCCAATATA
* *
1083271 ATGAAAGTCATTTGTGGCAAATTTTTGGT
1 ATGAAAGCCATTTGTGGCAAAGTTTTGGT
1083300 ATGAAAGCCATTTGTGGCAAAGTTTTGG
1 ATGAAAGCCATTTGTGGCAAAGTTTTGG
1083328 ATGTTCAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (29 bp):
ATGAAAGCCATTTGTGGCAAAGTTTTGGT
Found at i:1084027 original size:46 final size:46
Alignment explanation
Indices: 1083960--1084049 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
1083950 ACTGAACATA
1083960 TTTTTAACATAGTGAGTACAAACAAAAATTGAGATCTCGTTCGCGC
1 TTTTTAACATAGTGAGTACAAACAAAAATTGAGATCTCGTTCGCGC
* *
1084006 TTTTTAACATAGTGAGTACAAATAAATATTGAGATCTCGTTCGC
1 TTTTTAACATAGTGAGTACAAACAAAAATTGAGATCTCGTTCGC
1084050 ACTCCCGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (46 bp):
TTTTTAACATAGTGAGTACAAACAAAAATTGAGATCTCGTTCGCGC
Found at i:1088941 original size:43 final size:42
Alignment explanation
Indices: 1088776--1088941 Score: 137
Period size: 43 Copynumber: 4.0 Consensus size: 42
1088766 CATAATAGCT
* * * * *
1088776 CATACAATACC-ATATCCCAGATATGGTCTTACATGTTATCA
1 CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* * * * *
1088817 CATATCGATGCCACTGTCCCAGACAGGGTCTTATACGAAATCA
1 CATA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* *
1088860 TATAACGATGCCAA--T---AGACATGGTCTTACACGTAATCA
1 CAT-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
* *
1088898 CAATACAATGCCAATGTCCCAGACATGGTCTTACATGTTATCA
1 C-ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
1088941 C
1 C
1088942 TTCTCAGTAA
Statistics
Matches: 97, Mismatches: 19, Indels: 16
0.73 0.14 0.12
Matches are distributed among these distances:
38 29 0.30
39 2 0.02
40 1 0.01
41 5 0.05
42 5 0.05
43 54 0.56
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (42 bp):
CATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCA
Found at i:1092683 original size:14 final size:14
Alignment explanation
Indices: 1092664--1092693 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1092654 GAGGTAAATG
1092664 AATATTTATTTATA
1 AATATTTATTTATA
1092678 AATATTTATTTATA
1 AATATTTATTTATA
1092692 AA
1 AA
1092694 GATGAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATATTTATTTATA
Found at i:1094554 original size:24 final size:24
Alignment explanation
Indices: 1094527--1094579 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
1094517 ATTAGTAAGT
1094527 TAAATAAATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
*
1094551 TAAATATATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
1094575 TAAAT
1 TAAAT
1094580 CTTCTAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:1096932 original size:7 final size:7
Alignment explanation
Indices: 1096920--1096945 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1096910 TAGTCGTTTC
1096920 GTATTTA
1 GTATTTA
1096927 GTATTTA
1 GTATTTA
1096934 GTATTTA
1 GTATTTA
1096941 GTATT
1 GTATT
1096946 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:1098036 original size:93 final size:92
Alignment explanation
Indices: 1097873--1098055 Score: 339
Period size: 93 Copynumber: 2.0 Consensus size: 92
1097863 CCCTATGTTG
*
1097873 TTTGTACAAACTATTTTTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTAATATTTTAATA
1 TTTGTACAAACTATTTCTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTAATATTTTAATA
*
1097938 TTAATTTATTTTTTATATTTTTAATATA
66 GTAATTTA-TTTTTATATTTTTAATATA
1097966 TTTGTACAAACTATTTCTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTAATATTTTAATA
1 TTTGTACAAACTATTTCTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTAATATTTTAATA
1098031 GTAATTTATTTTTATATTTTTAATA
66 GTAATTTATTTTTATATTTTTAATA
1098056 AAATAGAAGT
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 17 0.19
93 71 0.81
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (92 bp):
TTTGTACAAACTATTTCTATATTGTTTCATTTAATAAAATAAAAGTTATTTTTAATATTTTAATA
GTAATTTATTTTTATATTTTTAATATA
Found at i:1098060 original size:54 final size:54
Alignment explanation
Indices: 1097995--1098113 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 54
1097985 TATTGTTTCA
* ***
1097995 TTTAATAAAATAAAAGTTATTTTTAATATTTTAATAGTAATT-TATTTTTATATT
1 TTTAATAAAATAAAAGTTATTTTGAATAAGATAATA-TAATTATATTTTTATATT
* * **
1098049 TTTAATAAAATAGAAGTTCTTTTGAATAAGATAATATTTTTAATATTTTTATATT
1 TTTAATAAAATAAAAGTTATTTTGAATAAGATAATATAATT-ATATTTTTATATT
1098104 TTTAATAAAA
1 TTTAATAAAA
1098114 CATAAATAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
53 3 0.05
54 30 0.55
55 22 0.40
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (54 bp):
TTTAATAAAATAAAAGTTATTTTGAATAAGATAATATAATTATATTTTTATATT
Found at i:1098097 original size:8 final size:9
Alignment explanation
Indices: 1098080--1098110 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1098070 TTGAATAAGA
1098080 TAATATTTT
1 TAATATTTT
1098089 TAATATTTT
1 TAATATTTT
1098098 T-ATATTTT
1 TAATATTTT
1098106 TAATA
1 TAATA
1098111 AAACATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATATTTT
Found at i:1101318 original size:126 final size:126
Alignment explanation
Indices: 1101093--1101362 Score: 395
Period size: 126 Copynumber: 2.1 Consensus size: 126
1101083 GGCCAAATAG
1101093 GAACTACTGTAGAAAAAGAGCGTCCACATAGGAGCTTTTTTTCGTAATTTTACTGACAGTGAATC
1 GAACTACTGTAGAAAAAGAGCGTCCACATAGGAGCTTTTTTTCGTAATTTTACTGACAGTGAATC
*
1101158 CTACTTGAAGCATTTTTAACACTATTTGTTTAGAACCGTCTTCTC-AAATTTATTTTTTTAA
66 CTACTTGAAGCATTTTTAACACTATTTGTTTAGAACCGTCTTCTCAAAATTAATTTTTTT-A
* * *
1101219 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGC-TTTTTTCAGTAATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACATAGGAGCTTTTTTTC-GTAATTTTACTGACAGTGAAT
* * * *
1101283 CTTGA-TTGAAGCGTTTTTTACATTATCTT-TTTAGAACCGTCTTCTCAAAATTAATTTTTTTA
65 CCT-ACTTGAAGCATTTTTAACACTAT-TTGTTTAGAACCGTCTTCTCAAAATTAATTTTTTTA
1101345 GAAACTACTGTAGAAAAA
1 G-AACTACTGTAGAAAAA
1101363 AAACAAAAGT
Statistics
Matches: 131, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
125 7 0.05
126 92 0.70
127 32 0.24
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACATAGGAGCTTTTTTTCGTAATTTTACTGACAGTGAATC
CTACTTGAAGCATTTTTAACACTATTTGTTTAGAACCGTCTTCTCAAAATTAATTTTTTTA
Found at i:1101473 original size:34 final size:33
Alignment explanation
Indices: 1101411--1101523 Score: 115
Period size: 34 Copynumber: 3.4 Consensus size: 33
1101401 CTAAACACAA
* *
1101411 AATTATTTAAAAAAC-TAAA-CCATAATTTAATT
1 AATTTTTTAAAAACCATAAATCC-TAATTTAATT
1101443 AATTTTCTTAAAAACCATAAATCCTAATTTAATT
1 AATTTT-TTAAAAACCATAAATCCTAATTTAATT
** *
1101477 AATTTATTTAAACCCCCAAAAAT-CTAATTTAATT
1 AATTT-TTTAAA-AACCATAAATCCTAATTTAATT
*
1101511 AATTTTTAAAAAA
1 AATTTTTTAAAAA
1101524 ATCCTAAACC
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
32 5 0.07
33 13 0.19
34 40 0.59
35 10 0.15
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (33 bp):
AATTTTTTAAAAACCATAAATCCTAATTTAATT
Found at i:1122381 original size:36 final size:34
Alignment explanation
Indices: 1122325--1122397 Score: 83
Period size: 36 Copynumber: 2.1 Consensus size: 34
1122315 TTGTTGCTAG
* *
1122325 AATTGAATATAGCTAAAAAACCTTGGAAAGAATAAT
1 AATTGAATATAGCTAAAAAA-CTT-AAAACAATAAT
* * *
1122361 AATTGAATTTAGGTACAAAACTTAAAACAATAAT
1 AATTGAATATAGCTAAAAAACTTAAAACAATAAT
1122395 AAT
1 AAT
1122398 GAGGGGCTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 12 0.38
35 3 0.09
36 17 0.53
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.27
Consensus pattern (34 bp):
AATTGAATATAGCTAAAAAACTTAAAACAATAAT
Found at i:1122769 original size:19 final size:18
Alignment explanation
Indices: 1122733--1122782 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1122723 TTATTTTTAC
*
1122733 TTTTTTT-ACTTTTGTCT
1 TTTTTTTAAATTTTGTCT
*
1122750 TTTTCTTTAAATTTTTTCT
1 TTTT-TTTAAATTTTGTCT
*
1122769 TTTTTTTAAGTTTT
1 TTTTTTTAAATTTT
1122783 ATACTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 12 0.43
19 12 0.43
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTTTTAAATTTTGTCT
Found at i:1122771 original size:18 final size:19
Alignment explanation
Indices: 1122750--1122793 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1122740 ACTTTTGTCT
*
1122750 TTTTCTTTAAATTTT-TTC
1 TTTTCTTTAAATTTTATAC
* *
1122768 TTTTTTTTAAGTTTTATAC
1 TTTTCTTTAAATTTTATAC
1122787 TTTTCTT
1 TTTTCTT
1122794 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTCTTTAAATTTTATAC
Found at i:1122789 original size:19 final size:19
Alignment explanation
Indices: 1122748--1122790 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1122738 TTACTTTTGT
*
1122748 CTTTTTCTTTAAATTTTTT
1 CTTTTTCTTTAAATTTTTA
*
1122767 CTTTTT-TTTAAGTTTTATA
1 CTTTTTCTTTAAATTTT-TA
1122786 CTTTT
1 CTTTT
1122791 CTTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.72
Consensus pattern (19 bp):
CTTTTTCTTTAAATTTTTA
Found at i:1122812 original size:13 final size:13
Alignment explanation
Indices: 1122796--1122838 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1122786 CTTTTCTTAT
*
1122796 TTTATTTTGTTTA
1 TTTATTTTATTTA
1122809 TTTATTTTATTTA
1 TTTATTTTATTTA
* *
1122822 TTTTTTGTTATTAA
1 TTTATT-TTATTTA
1122836 TTT
1 TTT
1122839 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:1122818 original size:23 final size:23
Alignment explanation
Indices: 1122796--1122840 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1122786 CTTTTCTTAT
*
1122796 TTTATTTTGT-TTATTTATTTTA
1 TTTATTTTGTGTTATTAATTTTA
*
1122818 TTTATTTTTTGTTATTAATTTTA
1 TTTATTTTGTGTTATTAATTTTA
1122841 AAAAATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTATTTTGTGTTATTAATTTTA
Found at i:1122833 original size:10 final size:9
Alignment explanation
Indices: 1122792--1122825 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1122782 TATACTTTTC
1122792 TTATTTTAT
1 TTATTTTAT
1122801 TT-TGTTTAT
1 TTAT-TTTAT
1122810 TTATTTTAT
1 TTATTTTAT
1122819 TTATTTT
1 TTATTTT
1122826 TTGTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 21 0.91
10 1 0.04
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:1122937 original size:21 final size:20
Alignment explanation
Indices: 1122903--1122944 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1122893 TTTAAATATT
*
1122903 ATTTTTAAATTATTTTTTAA
1 ATTTTAAAATTATTTTTTAA
1122923 ATTTTAAATATTATTTTTTAA
1 ATTTTAAA-ATTATTTTTTAA
1122944 A
1 A
1122945 ATTATGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTAAAATTATTTTTTAA
Found at i:1122999 original size:36 final size:32
Alignment explanation
Indices: 1122884--1123003 Score: 132
Period size: 36 Copynumber: 3.5 Consensus size: 32
1122874 AATATATATA
*
1122884 TTTTAAAATTTTAAATATTATTTTTAAATTAT
1 TTTTTAAATTTTAAATATTATTTTTAAATTAT
1122916 TTTTTAAATTTTAAATATTATTTTTTAAAATTAT
1 TTTTTAAATTTTAAATATTA-TTTTT-AAATTAT
* * *
1122950 GTCTTATACATTTTAAAAATATATTTTTGAAATTAAT
1 -T-TTTTAAATTTTAAATAT-TATTTTT-AAATT-AT
1122987 TTTTCTAAATTTTAAAT
1 TTTT-TAAATTTTAAAT
1123004 TTTAAATATA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
32 19 0.26
33 5 0.07
34 7 0.10
35 3 0.04
36 35 0.48
37 4 0.05
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.57
Consensus pattern (32 bp):
TTTTTAAATTTTAAATATTATTTTTAAATTAT
Found at i:1123024 original size:14 final size:14
Alignment explanation
Indices: 1123007--1123035 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1122997 TTTAAATTTT
1123007 AAATATATTTTTAA
1 AAATATATTTTTAA
1123021 AAATATATTTTTAA
1 AAATATATTTTTAA
1123035 A
1 A
1123036 CAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATTTTTAA
Found at i:1123084 original size:26 final size:28
Alignment explanation
Indices: 1123055--1123125 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 28
1123045 ATAATTTCAA
*
1123055 AAATATATTTTTAAAT-TTTAAATA-TT
1 AAATATATTTTTAAATATTTAAACATTT
1123081 AAATATATTTTTAATAATATTTAAACATTT
1 AAATATATTTTT-A-AATATTTAAACATTT
1123111 AAA-AT-TTTTTAAATA
1 AAATATATTTTTAAATA
1123126 AAATTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 16 0.40
27 2 0.05
28 8 0.20
29 9 0.22
30 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATATATTTTTAAATATTTAAACATTT
Found at i:1123125 original size:29 final size:29
Alignment explanation
Indices: 1123055--1123131 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
1123045 ATAATTTCAA
* *
1123055 AAATATA-TTTT--TAAATTTTAAATATT
1 AAATATATTTTTAATAAAATTTAAACATT
*
1123081 AAATATATTTTTAATAATATTTAAACATTT
1 AAATATATTTTTAATAAAATTTAAACA-TT
1123111 AAA-AT-TTTTTAAATAAAATTT
1 AAATATATTTTT-AATAAAATTT
1123132 TTATAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 7 0.17
27 4 0.10
28 5 0.12
29 21 0.50
30 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
AAATATATTTTTAATAAAATTTAAACATT
Found at i:1123129 original size:14 final size:14
Alignment explanation
Indices: 1123110--1123150 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1123100 TTTAAACATT
1123110 TAAAATTTTTTAAA
1 TAAAATTTTTTAAA
*
1123124 TAAAA-TTTTTATA
1 TAAAATTTTTTAAA
1123137 -AAAATTATTTTAAA
1 TAAAATT-TTTTAAA
1123151 AACGTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.17
13 8 0.35
14 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAAATTTTTTAAA
Found at i:1123496 original size:20 final size:20
Alignment explanation
Indices: 1123468--1123510 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1123458 AAATATATAT
1123468 ATTTGAAATTATT-TTTCTAA
1 ATTTGAAA-TATTATTTCTAA
* *
1123488 ATTTTAAATATTATTTTTAA
1 ATTTGAAATATTATTTCTAA
1123508 ATT
1 ATT
1123511 ATTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTGAAATATTATTTCTAA
Found at i:1123510 original size:33 final size:32
Alignment explanation
Indices: 1123443--1123543 Score: 121
Period size: 33 Copynumber: 3.0 Consensus size: 32
1123433 TTATAATATA
* *
1123443 TATTTTTTAATTTTTAAATATATATATTTGAAAT
1 TATTTTTTAAATTTTAAATAT-TAT-TTTTAAAT
1123477 TATTTTTCTAAATTTTAAATATTATTTTTAAAT
1 TATTTTT-TAAATTTTAAATATTATTTTTAAAT
* *
1123510 TATTGTTTAAAAATTTAAATATTATTTTATAAAT
1 TATT-TTTTAAATTTTAAATATTATTTT-TAAAT
1123544 ATTAAATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
33 29 0.48
34 18 0.30
35 13 0.22
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (32 bp):
TATTTTTTAAATTTTAAATATTATTTTTAAAT
Found at i:1123533 original size:22 final size:21
Alignment explanation
Indices: 1123508--1123569 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1123498 TTATTTTTAA
1123508 ATTATTGTTTAAAAATTTAAAT
1 ATTATT-TTTAAAAATTTAAAT
*
1123530 ATTA-TTTTATAAATATTAAAT
1 ATTATTTTTAAAAAT-TTAAAT
* *
1123551 A-TATTTTTAATAATATAAA
1 ATTATTTTTAAAAATTTAAA
1123570 ACATTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 14 0.41
21 16 0.47
22 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTATTTTTAAAAATTTAAAT
Found at i:1123558 original size:21 final size:20
Alignment explanation
Indices: 1123503--1123560 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
1123493 AAATATTATT
1123503 TTTAAAT-TATTGTTTAAAAA
1 TTTAAATATATT-TTTAAAAA
*
1123523 TTTAAATAT-TATTTTATAAA
1 TTTAAATATAT-TTTTAAAAA
1123543 TATTAAATATATTTTTAA
1 T-TTAAATATATTTTTAA
1123561 TAATATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 16 0.50
21 15 0.47
22 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTAAATATATTTTTAAAAA
Found at i:1123675 original size:34 final size:34
Alignment explanation
Indices: 1123614--1123692 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
1123604 TTTATTAGTA
* *
1123614 ATTTTATAA-TATTTTAAATGTATATTTTAATTT
1 ATTTTATAATTATTTTAAATATATATTTTAAATT
* *
1123647 GTTTTATAATTTTTTTAAATATGA-ATTTTAAATT
1 ATTTTATAATTATTTTAAATAT-ATATTTTAAATT
1123681 ATTTTA-AATTAT
1 ATTTTATAATTAT
1123693 GATTTTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
33 13 0.34
34 24 0.63
35 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (34 bp):
ATTTTATAATTATTTTAAATATATATTTTAAATT
Found at i:1123685 original size:24 final size:24
Alignment explanation
Indices: 1123624--1123708 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 24
1123614 ATTTTATAAT
*
1123624 ATTTTAAATGTATATTTT-AATTTG-
1 ATTTTAAAT-TAT-TTTTAAATATGA
1123648 -TTTTATAATT-TTTTTAAATATGA
1 ATTTTA-AATTATTTTTAAATATGA
1123671 ATTTTAAATTA-TTTTAAATTATGA
1 ATTTTAAATTATTTTTAAA-TATGA
*
1123695 TTTTTAAATTATTT
1 ATTTTAAATTATTT
1123709 AAAATATATT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 4 0.08
22 6 0.12
23 17 0.33
24 23 0.44
25 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (24 bp):
ATTTTAAATTATTTTTAAATATGA
Found at i:1123686 original size:10 final size:10
Alignment explanation
Indices: 1123614--1123692 Score: 52
Period size: 10 Copynumber: 7.2 Consensus size: 10
1123604 TTTATTAGTA
1123614 ATTTTATAA-T
1 ATTTTA-AATT
1123624 ATTTTAAATGTAT
1 ATTTTAAA--T-T
*
1123637 ATTTTAATTT
1 ATTTTAAATT
*
1123647 GTTTTATAATT
1 ATTTTA-AATT
*
1123658 TTTTTAAATAT
1 ATTTTAAAT-T
1123669 GAATTTTAAATT
1 --ATTTTAAATT
1123681 ATTTTAAATT
1 ATTTTAAATT
1123691 AT
1 AT
1123693 GATTTTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
9 2 0.04
10 27 0.48
11 10 0.18
12 1 0.02
13 16 0.29
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:1123706 original size:14 final size:13
Alignment explanation
Indices: 1123658--1123703 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
1123648 TTTTATAATT
1123658 TTTTTAAATATGA
1 TTTTTAAATATGA
*
1123671 ATTTTAAAT-T-A
1 TTTTTAAATATGA
1123682 -TTTTAAATTATGA
1 TTTTTAAA-TATGA
1123695 TTTTTAAAT
1 TTTTTAAAT
1123704 TATTTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 7 0.25
11 2 0.07
12 2 0.07
13 10 0.36
14 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (13 bp):
TTTTTAAATATGA
Found at i:1123713 original size:24 final size:24
Alignment explanation
Indices: 1123648--1123727 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
1123638 TTTTAATTTG
* *
1123648 TTTTATAATTTTTTTAAA-TATGAA
1 TTTTA-AATTATTTTAAATTATGAT
1123672 TTTTAAATTATTTTAAATTATGAT
1 TTTTAAATTATTTTAAATTATGAT
* *
1123696 TTTTAAATTATTTAAAATATATTAT
1 TTTTAAATTATTTTAAAT-TATGAT
1123721 TTTTAAA
1 TTTTAAA
1123728 GATATGACCT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 11 0.22
24 27 0.54
25 12 0.24
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (24 bp):
TTTTAAATTATTTTAAATTATGAT
Found at i:1123778 original size:11 final size:11
Alignment explanation
Indices: 1123762--1123798 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1123752 TTGTTTTATA
1123762 ATTTTTTAAAT
1 ATTTTTTAAAT
1123773 ATTTTTTTAAAT
1 A-TTTTTTAAAT
1123785 A-TTTTTAAA-
1 ATTTTTTAAAT
1123794 ATTTT
1 ATTTT
1123799 AAATATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.04
10 11 0.46
11 1 0.04
12 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:1123778 original size:12 final size:12
Alignment explanation
Indices: 1123763--1123790 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1123753 TGTTTTATAA
1123763 TTTTTTAAATAT
1 TTTTTTAAATAT
1123775 TTTTTTAAATAT
1 TTTTTTAAATAT
1123787 TTTT
1 TTTT
1123791 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTAAATAT
Found at i:1123780 original size:22 final size:22
Alignment explanation
Indices: 1123749--1123817 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
1123739 TCAAATTTAT
1123749 TATTTGTTTTATAATTTTTTAAA
1 TATTT-TTTTATAATTTTTTAAA
1123772 TATTTTTTTA-AATATTTTTAAA
1 TATTTTTTTATAAT-TTTTTAAA
**
1123794 -ATTTTAAATATAATTTTTATAAA
1 TATTTT-TTTATAATTTTT-TAAA
1123817 T
1 T
1123818 TATTAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
21 8 0.21
22 19 0.49
23 12 0.31
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (22 bp):
TATTTTTTTATAATTTTTTAAA
Found at i:1123808 original size:12 final size:13
Alignment explanation
Indices: 1123793--1123842 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 13
1123783 ATATTTTTAA
1123793 AATTTTAAATA-T
1 AATTTTAAATATT
1123805 AATTTTTATAAATTATT
1 AA--TTT-TAAA-TATT
1123822 AATTTTAAA-ATT
1 AATTTTAAATATT
1123834 AATTTTAAA
1 AATTTTAAA
1123843 GATATTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 14 0.42
14 7 0.21
15 7 0.21
16 2 0.06
17 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTAAATATT
Found at i:1126985 original size:16 final size:18
Alignment explanation
Indices: 1126946--1126986 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
1126936 ACTAATACAA
1126946 AAAATATTACATAACACTT
1 AAAAT-TTACATAACACTT
*
1126965 GAAATTTACAT-A-ACTT
1 AAAATTTACATAACACTT
1126981 AAAATT
1 AAAATT
1126987 GGAAAGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 6 0.30
19 4 0.20
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATTTACATAACACTT
Found at i:1127223 original size:30 final size:30
Alignment explanation
Indices: 1127170--1127302 Score: 176
Period size: 30 Copynumber: 4.4 Consensus size: 30
1127160 GGTTGCTCTT
* * *
1127170 GGTGAAATAAACTCGAACCGCCTATGTCTG
1 GGTGATATGAACTTGAACCGCCTATGTCTG
*
1127200 GGTGATATGAACTTGAACTGCCTATGTCTG
1 GGTGATATGAACTTGAACCGCCTATGTCTG
1127230 GGTGATATGAACTTGAACCGCCTATGTCTG
1 GGTGATATGAACTTGAACCGCCTATGTCTG
* *** *
1127260 GGTGATATGAACTTTAACCGAAAATGTCCG
1 GGTGATATGAACTTGAACCGCCTATGTCTG
*
1127290 AGTGATATGAACT
1 GGTGATATGAACT
1127303 GCTCTGCGAC
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 92 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (30 bp):
GGTGATATGAACTTGAACCGCCTATGTCTG
Found at i:1129683 original size:41 final size:42
Alignment explanation
Indices: 1129629--1129711 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 42
1129619 GAAAATATAT
*
1129629 ATTAAGTACATAAATTTATGAATGTGTACTAAAATTAAAAAA
1 ATTAAGTACATAAATTTATAAATGTGTACTAAAATTAAAAAA
*
1129671 ATTAA-TATATAAATTTATAAATGTGTACTAAAATTAAAAAA
1 ATTAAGTACATAAATTTATAAATGTGTACTAAAATTAAAAAA
1129712 TTATAACCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 34 0.87
42 5 0.13
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (42 bp):
ATTAAGTACATAAATTTATAAATGTGTACTAAAATTAAAAAA
Found at i:1129704 original size:20 final size:20
Alignment explanation
Indices: 1129640--1129705 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
1129630 TTAAGTACAT
*
1129640 AAATTTATGAATGTGTACTA
1 AAATTTATAAATGTGTACTA
* * *
1129660 AAATTAAAAAAAT-TAATA-TA
1 AAATT-TATAAATGT-GTACTA
1129680 TAAATTTATAAATGTGTACTA
1 -AAATTTATAAATGTGTACTA
1129701 AAATT
1 AAATT
1129706 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (20 bp):
AAATTTATAAATGTGTACTA
Found at i:1130794 original size:9 final size:9
Alignment explanation
Indices: 1130769--1130811 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1130759 AAATTTTTTT
*
1130769 AAATTAATA
1 AAATAAATA
1130778 ACAATAAATA
1 A-AATAAATA
1130788 AAATAAAT-
1 AAATAAATA
*
1130796 AAATAAACA
1 AAATAAATA
1130805 AAATAAA
1 AAATAAA
1130812 ATAAGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:1130829 original size:9 final size:9
Alignment explanation
Indices: 1130783--1130858 Score: 55
Period size: 9 Copynumber: 8.2 Consensus size: 9
1130773 TAATAACAAT
*
1130783 AAATAAAAT
1 AAATAAAAA
1130792 AAATAAATAA
1 AAATAAA-AA
* *
1130802 ACA-AAATA
1 AAATAAAAA
1130810 AAATAAGAAA
1 AAATAA-AAA
*
1130820 AAATATAAA
1 AAATAAAAA
**
1130829 ACTTAAAAA
1 AAATAAAAA
*
1130838 AAAGAAAAA
1 AAATAAAAA
1130847 AAATTAAAAA
1 AAA-TAAAAA
1130857 AA
1 AA
1130859 GAGAGACAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
8 3 0.06
9 30 0.60
10 17 0.34
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (9 bp):
AAATAAAAA
Found at i:1136975 original size:13 final size:12
Alignment explanation
Indices: 1136944--1136974 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1136934 AAAAAATTAT
1136944 AAAAAAACATAA
1 AAAAAAACATAA
*
1136956 AAAAAAACGTAA
1 AAAAAAACATAA
1136968 AAAAAAA
1 AAAAAAA
1136975 AGAAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (12 bp):
AAAAAAACATAA
Found at i:1148463 original size:10 final size:12
Alignment explanation
Indices: 1148437--1148464 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1148427 TAAAAGTATC
1148437 ATATAGGCTCTT
1 ATATAGGCTCTT
1148449 ATATAGGCTCTT
1 ATATAGGCTCTT
1148461 ATAT
1 ATAT
1148465 TAAGAGTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (12 bp):
ATATAGGCTCTT
Found at i:1150659 original size:5 final size:5
Alignment explanation
Indices: 1150649--1150686 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
1150639 TGCTTTTATT
1150649 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAT
1150687 CCACTTATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:1152475 original size:7 final size:7
Alignment explanation
Indices: 1152459--1152501 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
1152449 CAGAAATACA
*
1152459 TTAGGCT
1 TTAGGGT
1152466 TTAGGGT
1 TTAGGGT
1152473 TTAGGGT
1 TTAGGGT
*
1152480 TTAAGGT
1 TTAGGGT
1152487 TTAGGGT
1 TTAGGGT
1152494 TTAGGGT
1 TTAGGGT
1152501 T
1 T
1152502 GAGGATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.16, C:0.02, G:0.37, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:1153047 original size:70 final size:70
Alignment explanation
Indices: 1152925--1153078 Score: 290
Period size: 70 Copynumber: 2.2 Consensus size: 70
1152915 CATGCTAGTT
1152925 AATTATTCATATATGTTTTCACTATTTACTTATATGTTCCTTCAAAGCTATCTATTTGAGTCACT
1 AATTATT--TATATGTTTTCACTATTTACTTATATGTTCCTTCAAAGCTATCTATTTGAGTCACT
1152990 GTTACTA
64 GTTACTA
1152997 AATTATTTATATGTTTTCACTATTTACTTATATGTTCCTTCAAAGCTATCTATTTGAGTCACTGT
1 AATTATTTATATGTTTTCACTATTTACTTATATGTTCCTTCAAAGCTATCTATTTGAGTCACTGT
1153062 TACTA
66 TACTA
1153067 AATTATTTATAT
1 AATTATTTATAT
1153079 CTTGAGCTAC
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
70 75 0.91
72 7 0.09
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.49
Consensus pattern (70 bp):
AATTATTTATATGTTTTCACTATTTACTTATATGTTCCTTCAAAGCTATCTATTTGAGTCACTGT
TACTA
Found at i:1159109 original size:25 final size:25
Alignment explanation
Indices: 1159081--1159135 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1159071 AAGCTCCTTT
* *
1159081 GAGCTAAATAACGGTAAGCTCATAC
1 GAGCTAAATAACGGTAAGCACATAA
* * *
1159106 GAGCTGAGTATCGGTAAGCACATAA
1 GAGCTAAATAACGGTAAGCACATAA
1159131 GAGCT
1 GAGCT
1159136 GGAATCAGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (25 bp):
GAGCTAAATAACGGTAAGCACATAA
Found at i:1161964 original size:41 final size:41
Alignment explanation
Indices: 1161905--1161987 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1161895 TAAATAAAAA
*
1161905 TTCAAATCCCTTTGTTTTAGTTGTGTTGGTTGAAGGGAAAG
1 TTCAAATCCCTTTATTTTAGTTGTGTTGGTTGAAGGGAAAG
* *
1161946 TTCAAATCCTTTTATTTTATTTGTGTTGGTTGAAGGGAAAG
1 TTCAAATCCCTTTATTTTAGTTGTGTTGGTTGAAGGGAAAG
1161987 T
1 T
1161988 GGTTGCCCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.23, C:0.08, G:0.24, T:0.45
Consensus pattern (41 bp):
TTCAAATCCCTTTATTTTAGTTGTGTTGGTTGAAGGGAAAG
Found at i:1163440 original size:43 final size:43
Alignment explanation
Indices: 1163393--1163796 Score: 519
Period size: 43 Copynumber: 9.4 Consensus size: 43
1163383 GTTTCTAGGA
* *
1163393 ACAAACGCCGCTAAA-AGCCAAGACCTTTAGAGGCGCTTCCAAA
1 ACAAACGCCGCTAAAGA-CCAAGACCTTTAGCGGCGCTTCCAAC
*
1163436 ACAAACGCTGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAAC
* *
1163479 ACAAACGCCGCTAATGACCAAGACCTTTAGCGACGCTTCCAAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAAC
* *
1163522 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCACTTCCCAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAAC
* * *
1163565 ACAAACGCCGCTAAAGACCAAGACTTTTAGCGGCGCTACCCAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAAC
* * *
1163608 ACAAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTACCCAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAAC
* * * *
1163651 ACAAACGCTGCTAAAGACTAGGACCTTTTAGCGGCGCTTCCTAC
1 ACAAACGCCGCTAAAGACCAAGACC-TTTAGCGGCGCTTCCAAC
* * *
1163695 ACAAACGTCGCTAAAGACCAAGACCTTTAGCGGCACGTTTC-AC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCAAC
** * *
1163738 ACAAACATCGCTAAAGACCAAGA-CTTTAGCAGCGCTTTCC-GC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTCCAAC
*
1163780 ACAAACGCTGCTAAAGA
1 ACAAACGCCGCTAAAGA
1163797 TATCGACCAT
Statistics
Matches: 322, Mismatches: 36, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.09
43 253 0.79
44 41 0.13
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.16
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCCAAC
Found at i:1163627 original size:129 final size:130
Alignment explanation
Indices: 1163393--1163881 Score: 514
Period size: 129 Copynumber: 3.8 Consensus size: 130
1163383 GTTTCTAGGA
* * * *
1163393 ACAAACGCCGCTAAA-AGCCAAGACC-TTTAGAGGCGCTTCCAAAACAAACGCTGCTAAAGACCA
1 ACAAACGCCGCTAAAGA-CCAAGACCTTTTAGCGGCGCTTCCCACACAAACGCCGCTAAAGACCA
* *
1163456 AGACCTTTAGCGGCGC-TTCCAACACAAACGCCGCTAATGACCAAGACCTTTAGCGACGCTTCCA
65 AGACCTTTAGCGGCGCGTTCCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTCC-
1163520 AC
129 AC
*
1163522 ACAAACGCCGCTAAAGACCAAGACC-TTTAGCGGCACTTCCCACACAAACGCCGCTAAAGACCAA
1 ACAAACGCCGCTAAAGACCAAGACCTTTTAGCGGCGCTTCCCACACAAACGCCGCTAAAGACCAA
* * * * *
1163586 GACTTTTAGCGGCGC-TACCCACACAAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTACCCA
66 GACCTTTAGCGGCGCGTTCCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCT-TCCA
1163650 C
130 C
* * * * *
1163651 ACAAACGCTGCTAAAGACTAGGACCTTTTAGCGGCGCTTCCTACACAAACGTCGCTAAAGACCAA
1 ACAAACGCCGCTAAAGACCAAGACCTTTTAGCGGCGCTTCCCACACAAACGCCGCTAAAGACCAA
* * **
1163716 GACCTTTAGCGGCACGTT-TCACACAAACATCGCTAAAGACCAAGA-CTTTAGC-AGCGCTTTCC
66 GACCTTTAGCGGCGCGTTCCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGA-CGC-TTCC
*
1163778 GC
129 AC
* * * ** ** *
1163780 ACAAACGCTGCTAAAGA-TATCGACCATTTTAGCGGCGCTTTTCTGACAAACGCCGCAAAAGA-C
1 ACAAACGCCGCTAAAGACCA-AGACC-TTTTAGCGGCGCTTCCCACACAAACGCCGCTAAAGACC
* * * * *
1163843 TAGGCCTTTTAGCGGCGCTTTTCC-CACAAATGCCGCTAA
64 AAGACC-TTTAGCGGCGCGTTCCCACACAAACGCCGCTAA
1163882 TTTTGGCAGA
Statistics
Matches: 306, Mismatches: 44, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
128 2 0.01
129 173 0.57
130 129 0.42
131 2 0.01
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (130 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTTAGCGGCGCTTCCCACACAAACGCCGCTAAAGACCAA
GACCTTTAGCGGCGCGTTCCCACACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTCCAC
Found at i:1163865 original size:43 final size:42
Alignment explanation
Indices: 1163436--1163881 Score: 240
Period size: 43 Copynumber: 10.3 Consensus size: 42
1163426 CGCTTCCAAA
* * * * *
1163436 ACAAACGCTGCTAAAGACCAAGACC-TTTAGCGGCGCTTCCAAC
1 ACAAACGCCGCTAAAGA-CTAGGCCTTTTAGCGGCGCTTTC-TC
* * * * * *
1163479 ACAAACGCCGCTAATGACCAAGACC-TTTAGCGACGCTTCCAAC
1 ACAAACGCCGCTAAAGA-CTAGGCCTTTTAGCGGCGCTTTC-TC
* * * * *
1163522 ACAAACGCCGCTAAAGACCAAGACC-TTTAGCGGCACTTCCCAC
1 ACAAACGCCGCTAAAGA-CTAGGCCTTTTAGCGGCGCTT-TCTC
* * * ** *
1163565 ACAAACGCCGCTAAAGACCAAGACTTTTAGCGGCGCTACCCAC
1 ACAAACGCCGCTAAAGACTAGGCCTTTTAGCGGCGCT-TTCTC
* * * ** *
1163608 ACAAATGCCGCTAAAGACCAAGACC-TTTAGCGGCGCTACCCAC
1 ACAAACGCCGCTAAAGA-CTAGGCCTTTTAGCGGCGCT-TTCTC
* *
1163651 ACAAACGCTGCTAAAGACTAGGACCTTTTAGCGGCGCTTCCTAC
1 ACAAACGCCGCTAAAGACTAGG-CCTTTTAGCGGCGCTTTCT-C
* * * * *
1163695 ACAAACGTCGCTAAAGACCAAGACC-TTTAGCGGCACGTTTCAC
1 ACAAACGCCGCTAAAGA-CTAGGCCTTTTAGCGGCGC-TTTCTC
** * * * * *
1163738 ACAAACATCGCTAAAGACCAAGAC-TTTAGCAGCGCTTTCCGC
1 ACAAACGCCGCTAAAGACTAGGCCTTTTAGCGGCGCTTT-CTC
* * *
1163780 ACAAACGCTGCTAAAGA-TATCGACCATTTTAGCGGCGCTTTTCTG
1 ACAAACGCCGCTAAAGACTA--GGCC-TTTTAGCGGCGC-TTTCTC
* *
1163825 ACAAACGCCGCAAAAGACTAGGCCTTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACTAGGCCTTTTAGCGGCGC-TTTCTC
*
1163868 ACAAATGCCGCTAA
1 ACAAACGCCGCTAA
1163882 TTTTGGCAGA
Statistics
Matches: 332, Mismatches: 55, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
41 4 0.01
42 34 0.10
43 219 0.66
44 41 0.12
45 29 0.09
46 5 0.02
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.18
Consensus pattern (42 bp):
ACAAACGCCGCTAAAGACTAGGCCTTTTAGCGGCGCTTTCTC
Found at i:1164139 original size:9 final size:9
Alignment explanation
Indices: 1164125--1164163 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1164115 GTCTAAAACG
*
1164125 GCGGCTGTC
1 GCGGCTGTT
1164134 GCGGCTGTT
1 GCGGCTGTT
*
1164143 GCGTCTGTT
1 GCGGCTGTT
*
1164152 GCGGATGTT
1 GCGGCTGTT
1164161 GCG
1 GCG
1164164 ATTGCTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.03, C:0.23, G:0.44, T:0.31
Consensus pattern (9 bp):
GCGGCTGTT
Found at i:1168492 original size:22 final size:22
Alignment explanation
Indices: 1168466--1168507 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1168456 TAATTTAGTT
*
1168466 ATGTACGTTACGTATCATATTA
1 ATGTAAGTTACGTATCATATTA
* *
1168488 ATGTAAGTTATGTATTATAT
1 ATGTAAGTTACGTATCATAT
1168508 AAGTTATTTA
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:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (22 bp):
ATGTAAGTTACGTATCATATTA
Found at i:1168528 original size:18 final size:18
Alignment explanation
Indices: 1168488--1168582 Score: 72
Period size: 16 Copynumber: 5.3 Consensus size: 18
1168478 TATCATATTA
1168488 ATGTAAGTTATGT-A-TT
1 ATGTAAGTTATGTAAGTT
* *
1168504 ATATAAGTTATTTAAGTT
1 ATGTAAGTTATGTAAGTT
* *
1168522 ATGTAAGTTGTGCAAGTT
1 ATGTAAGTTATGTAAGTT
* *
1168540 ATGTATAATATTACGGTAAGTT
1 ATG--TAA-GTTA-TGTAAGTT
1168562 ATGT-A-TTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
1168578 ATGTA
1 ATGTA
1168583 TAATATTAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
16 22 0.36
17 4 0.07
18 19 0.31
19 1 0.02
20 4 0.07
21 2 0.03
22 9 0.15
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (18 bp):
ATGTAAGTTATGTAAGTT
Found at i:1168563 original size:22 final size:20
Alignment explanation
Indices: 1168535--1168605 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 20
1168525 TAAGTTGTGC
1168535 AAGTTATGTATAATATTACGGT
1 AAGTTATGTATAATATTA--GT
1168557 AAGTTATGTAT--TA-T-GT
1 AAGTTATGTATAATATTAGT
1168573 AAGTTATGTATAATATTAATGT
1 AAGTTATGTATAATATT-A-GT
1168595 AAGTTATGTAT
1 AAGTTATGTAT
1168606 TATGTTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
16 13 0.30
18 2 0.05
19 2 0.05
20 2 0.05
22 24 0.56
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (20 bp):
AAGTTATGTATAATATTAGT
Found at i:1168577 original size:38 final size:38
Alignment explanation
Indices: 1168516--1168610 Score: 136
Period size: 38 Copynumber: 2.4 Consensus size: 38
1168506 ATAAGTTATT
* * *
1168516 TAAGTTATGTAAGTTGTGCAAGTTATGTATAATATTACGG
1 TAAGTTATGT-A-TTATGTAAGTTATGTATAATATTAAGG
*
1168556 TAAGTTATGTATTATGTAAGTTATGTATAATATTAATG
1 TAAGTTATGTATTATGTAAGTTATGTATAATATTAAGG
1168594 TAAGTTATGTATTATGT
1 TAAGTTATGTATTATGT
1168611 TAATATTTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 40 0.78
39 1 0.02
40 10 0.20
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (38 bp):
TAAGTTATGTATTATGTAAGTTATGTATAATATTAAGG
Found at i:1168581 original size:9 final size:9
Alignment explanation
Indices: 1168488--1168582 Score: 72
Period size: 9 Copynumber: 10.6 Consensus size: 9
1168478 TATCATATTA
1168488 ATGTAAGTT
1 ATGTAAGTT
1168497 ATGT-A-TT
1 ATGTAAGTT
*
1168504 ATATAAGTT
1 ATGTAAGTT
*
1168513 ATTTAAGTT
1 ATGTAAGTT
1168522 ATGTAAGTT
1 ATGTAAGTT
* *
1168531 GTGCAAGTT
1 ATGTAAGTT
*
1168540 ATGTATAATATT
1 ATG--TAA-GTT
*
1168552 ACGGTAAGTT
1 A-TGTAAGTT
1168562 ATGT-A-TT
1 ATGTAAGTT
1168569 ATGTAAGTT
1 ATGTAAGTT
1168578 ATGTA
1 ATGTA
1168583 TAATATTAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
7 11 0.16
8 4 0.06
9 40 0.60
10 3 0.04
11 5 0.07
12 3 0.04
13 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:1168613 original size:22 final size:22
Alignment explanation
Indices: 1168560--1168614 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1168550 TTACGGTAAG
*
1168560 TTATGTATTATGTAAGTTATGTA
1 TTATGT-TAATGTAAGTTATGTA
* *
1168583 TAATATTAATGTAAGTTATGTA
1 TTATGTTAATGTAAGTTATGTA
1168605 TTATGTTAAT
1 TTATGTTAAT
1168615 ATTTAGAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.51
Consensus pattern (22 bp):
TTATGTTAATGTAAGTTATGTA
Found at i:1168674 original size:21 final size:21
Alignment explanation
Indices: 1168644--1168771 Score: 64
Period size: 21 Copynumber: 5.8 Consensus size: 21
1168634 CAATTATTTC
1168644 TAAAATTATAAAATTTATTATT
1 TAAAA-TATAAAATTTATTATT
* * *
1168666 GAAAATAT-AGATGTTAATATT
1 TAAAATATAAAAT-TTATTATT
*
1168687 TAGAAA-ATAACATTTACAATTATTT
1 TA-AAATATAAAATTT---ATTA-TT
*
1168712 CTAAAATTATAAAAATTATTATT
1 -TAAAA-TATAAAATTTATTATT
* ***
1168735 GAAAATATAGGTTTTATTATT
1 TAAAATATAAAATTTATTATT
*
1168756 TAAAA-ATAACATTTAT
1 TAAAATATAAAATTTAT
1168772 CATTATTTTT
Statistics
Matches: 79, Mismatches: 17, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
20 11 0.14
21 31 0.39
22 14 0.18
23 2 0.03
24 7 0.09
25 5 0.06
26 2 0.03
27 7 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (21 bp):
TAAAATATAAAATTTATTATT
Found at i:1168795 original size:26 final size:26
Alignment explanation
Indices: 1168748--1168797 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1168738 AATATAGGTT
*
1168748 TTATTATTTAAAAATAACATTTATCA
1 TTATTATTTAAAAATAAAATTTATCA
*
1168774 TTATT-TTTAAAATTAAAAATTTAT
1 TTATTATTTAAAAAT-AAAATTTAT
1168798 TATCAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
TTATTATTTAAAAATAAAATTTATCA
Found at i:1168809 original size:69 final size:69
Alignment explanation
Indices: 1168607--1168800 Score: 304
Period size: 69 Copynumber: 2.8 Consensus size: 69
1168597 GTTATGTATT
*
1168607 ATGTTAATATTTAGAAAATAGCATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
1 ATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
1168672 ATAG
66 ATAG
*
1168676 ATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAAATTATTATTGAAAAT
1 ATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
1168741 ATAG
66 ATAG
* * * *
1168745 GTTTTATTATTTA-AAAATAACATTTATC-ATTATTTTTAAAATTA-AAAATTTATTAT
1 ATGTTAATATTTAGAAAATAACATTTA-CAATTATTTCTAAAATTATAAAATTTATTAT
1168801 CAATAAAATT
Statistics
Matches: 117, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
67 11 0.09
68 28 0.24
69 78 0.67
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (69 bp):
ATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
ATAG
Found at i:1169506 original size:16 final size:16
Alignment explanation
Indices: 1169485--1169515 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1169475 TATGGAACCA
1169485 TATTAAATAATACTAG
1 TATTAAATAATACTAG
1169501 TATTAAATAATACTA
1 TATTAAATAATACTA
1169516 TTTGCATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
TATTAAATAATACTAG
Found at i:1170010 original size:26 final size:26
Alignment explanation
Indices: 1169981--1170038 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
1169971 TTAGATTTAT
*
1169981 ATTATTTTATAAGCTATAGAGTAAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
*
1170007 ATTATTTGATAAGCTATAGAGTGAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
1170033 ATTATT
1 ATTATT
1170039 ATGCAACGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (26 bp):
ATTATTTGATAAGCTATAGAGTAAGA
Found at i:1171158 original size:24 final size:22
Alignment explanation
Indices: 1171120--1171165 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
1171110 CTAGGGTTCT
1171120 AAATTTGGGGGATTTTTGGGGA
1 AAATTTGGGGGATTTTTGGGGA
1171142 AAATTTGGGGGGAATTTTTGGGGA
1 AAATTT-GGGGG-ATTTTTGGGGA
1171166 GAAAAGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (22 bp):
AAATTTGGGGGATTTTTGGGGA
Done.