Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 20 of 125
Found at i:3488966 original size:22 final size:22
Alignment explanation
Indices: 3488941--3488982 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3488931 CAGTACATCA
*
3488941 TTGATAACATAATAATAAATCG
1 TTGATAACATAAAAATAAATCG
3488963 TTGATAACATAAAAATAAAT
1 TTGATAACATAAAAATAAAT
3488983 AAATAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (22 bp):
TTGATAACATAAAAATAAATCG
Found at i:3489391 original size:21 final size:19
Alignment explanation
Indices: 3489367--3489435 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
3489357 ATAAAATAAA
3489367 TTATCAATTTAATATCAAAAG
1 TTATCAATTT--TATCAAAAG
* *
3489388 TTATTAAAATTGTATCCAAAA-
1 TTA-T-CAATTTTAT-CAAAAG
3489409 TTATCAAATTTTATCAAAAG
1 TTATC-AATTTTATCAAAAG
3489429 TTATCAA
1 TTATCAA
3489436 ATTCAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
19 7 0.18
20 13 0.33
21 9 0.23
22 6 0.15
23 4 0.10
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (19 bp):
TTATCAATTTTATCAAAAG
Found at i:3489423 original size:20 final size:20
Alignment explanation
Indices: 3489379--3489438 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
3489369 ATCAATTTAA
* *
3489379 TATCAAAAGTTATTAAAATTG
1 TATCAAAAGTTA-TCAAATTT
3489400 TATCCAAAA-TTATCAAATTT
1 TAT-CAAAAGTTATCAAATTT
3489420 TATCAAAAGTTATCAAATT
1 TATCAAAAGTTATCAAATT
3489439 CAAAATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.14
20 19 0.54
21 6 0.17
22 5 0.14
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TATCAAAAGTTATCAAATTT
Found at i:3489445 original size:27 final size:27
Alignment explanation
Indices: 3489414--3489465 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3489404 CAAAATTATC
* *
3489414 AAATTTTATCAAAAGTTATCAAATTCA
1 AAATTATATCAAAAATTATCAAATTCA
* *
3489441 AAATTATATTAAAAATTATTAAATT
1 AAATTATATCAAAAATTATCAAATT
3489466 TTGTTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATTATATCAAAAATTATCAAATTCA
Found at i:3497466 original size:26 final size:26
Alignment explanation
Indices: 3497427--3497481 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
3497417 ACGGACTCCC
*
3497427 ACAACAAAATATAACAGAAAATTCGA
1 ACAACAAAACATAACAGAAAATTCGA
* *
3497453 ACAACAAAACATAACTGAAAATTTGA
1 ACAACAAAACATAACAGAAAATTCGA
3497479 ACA
1 ACA
3497482 TTCTGAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.16
Consensus pattern (26 bp):
ACAACAAAACATAACAGAAAATTCGA
Found at i:3502876 original size:19 final size:20
Alignment explanation
Indices: 3502837--3502878 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3502827 TTAAAAATTC
*
3502837 AATTGAAAGGCTCAAAATCT
1 AATTGAAAGGCCCAAAATCT
*
3502857 AATTGAAA-GCCCAAAGTCT
1 AATTGAAAGGCCCAAAATCT
3502876 AAT
1 AAT
3502879 ACGACTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (20 bp):
AATTGAAAGGCCCAAAATCT
Found at i:3503457 original size:85 final size:85
Alignment explanation
Indices: 3503309--3503478 Score: 297
Period size: 85 Copynumber: 2.0 Consensus size: 85
3503299 GGTCCGAGCA
* *
3503309 TTTTACCATTACCAAATCCCACCTAAGCCTTGCCTATGCCTTACAGACCAATTGAGACCCCACTT
1 TTTTACCATTACCAAATCCCACCTAAACCTTGCCTATGCCTTACAGACCAACTGAGACCCCACTT
3503374 AAAGACTACCATCACTAACT
66 AAAGACTACCATCACTAACT
*
3503394 TTTTGCCATTACCAAATCCCATCC-AAACCTTGCCTATGCCTTACAGACCAACTGAGACCCCACT
1 TTTTACCATTACCAAATCCCA-CCTAAACCTTGCCTATGCCTTACAGACCAACTGAGACCCCACT
3503458 TAAAGACTACCATCACTAACT
65 TAAAGACTACCATCACTAACT
3503479 ATCGACCTTC
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
85 79 0.98
86 2 0.02
ACGTcount: A:0.32, C:0.35, G:0.08, T:0.25
Consensus pattern (85 bp):
TTTTACCATTACCAAATCCCACCTAAACCTTGCCTATGCCTTACAGACCAACTGAGACCCCACTT
AAAGACTACCATCACTAACT
Found at i:3504040 original size:8 final size:9
Alignment explanation
Indices: 3504018--3504042 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3504008 GACCGAGACC
3504018 CAAAAAACA
1 CAAAAAACA
3504027 CAAAAAACA
1 CAAAAAACA
3504036 CAAAAAA
1 CAAAAAA
3504043 AAAAAGACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAAAACA
Found at i:3504534 original size:2 final size:2
Alignment explanation
Indices: 3504529--3504556 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3504519 AAGGTTGGTT
3504529 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
3504557 AACACAAAAT
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:3504995 original size:20 final size:22
Alignment explanation
Indices: 3504944--3504997 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
3504934 AAATGTGTAT
*
3504944 AAAAATATAAGTAATAATAGGA
1 AAAAATATAAGTAAAAATAGGA
*
3504966 AATAATATATAA-TAAAAATA-TA
1 AA-AA-ATATAAGTAAAAATAGGA
3504988 AAAAATATAA
1 AAAAATATAA
3504998 AATAATAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 5 0.18
23 9 0.32
24 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (22 bp):
AAAAATATAAGTAAAAATAGGA
Found at i:3505277 original size:21 final size:22
Alignment explanation
Indices: 3505245--3505285 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3505235 TATTTTTTAC
3505245 AATAATTAATAATAAAAAAGGT
1 AATAATTAATAATAAAAAAGGT
*
3505267 AATAA-TAATAATAATAAAG
1 AATAATTAATAATAAAAAAG
3505286 AAAATTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (22 bp):
AATAATTAATAATAAAAAAGGT
Found at i:3506912 original size:24 final size:24
Alignment explanation
Indices: 3506885--3506940 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
3506875 TAACAACAAC
3506885 AAAAGAAAAACAAAAATTTTCAAA
1 AAAAGAAAAACAAAAATTTTCAAA
*** *
3506909 AAAA-AAAAATGGAAATTTTCCAA
1 AAAAGAAAAACAAAAATTTTCAAA
3506932 AAAAGAAAA
1 AAAAGAAAA
3506941 TTTTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.16
Consensus pattern (24 bp):
AAAAGAAAAACAAAAATTTTCAAA
Found at i:3506941 original size:23 final size:23
Alignment explanation
Indices: 3506898--3506941 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3506888 AGAAAAACAA
3506898 AAATTTTCAAAAAAAAAAAATGG
1 AAATTTTCAAAAAAAAAAAATGG
* *
3506921 AAATTTTCCAAAAAAGAAAAT
1 AAATTTTCAAAAAAAAAAAAT
3506942 TTTCTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.23
Consensus pattern (23 bp):
AAATTTTCAAAAAAAAAAAATGG
Found at i:3510297 original size:18 final size:17
Alignment explanation
Indices: 3510269--3510321 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
3510259 GGGGAATATG
*
3510269 AAAAGA-AAAAAAAAAG
1 AAAAGACAAAAAAAAAA
*
3510285 AAAAGACAAAAAAAGATA
1 AAAAGACAAAAAAA-AAA
*
3510303 AAAAGAGAAAAACAAAAA
1 AAAAGACAAAAA-AAAAA
3510321 A
1 A
3510322 TGATTATGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 15 0.50
19 2 0.07
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAGACAAAAAAAAAA
Found at i:3510321 original size:16 final size:15
Alignment explanation
Indices: 3510269--3510321 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
3510259 GGGGAATATG
3510269 AAAAGAAAAAAAAAA
1 AAAAGAAAAAAAAAA
3510284 GAAAAGACAAAAAAAGATA
1 -AAAAGA-AAAAAAA-A-A
* *
3510303 AAAAGAGAAAAACAA
1 AAAAGAAAAAAAAAA
3510318 AAAA
1 AAAA
3510322 TGATTATGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 7 0.22
17 12 0.38
18 7 0.22
19 1 0.03
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAAAAAA
Found at i:3510922 original size:16 final size:17
Alignment explanation
Indices: 3510896--3510928 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3510886 AAAAGCTAAA
3510896 AAAATAAAATAAAAAAT
1 AAAATAAAATAAAAAAT
3510913 AAAA-AAAATAAAAAAT
1 AAAATAAAATAAAAAAT
3510929 GATTAAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAATAAAAAAT
Found at i:3512951 original size:14 final size:14
Alignment explanation
Indices: 3512923--3512973 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
3512913 GATATTATAT
*
3512923 TATTA-TTGCATGA
1 TATTATTTGTATGA
3512936 TATTATTTGTATGA
1 TATTATTTGTATGA
*
3512950 TAATTTTTTG-ATGA
1 T-ATTATTTGTATGA
*
3512964 TATTTTTTGT
1 TATTATTTGT
3512974 TTATTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 13 0.39
14 13 0.39
15 7 0.21
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (14 bp):
TATTATTTGTATGA
Found at i:3514970 original size:23 final size:21
Alignment explanation
Indices: 3514944--3514994 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
3514934 AGACAAGATG
3514944 TTTTAAAAC-AAATAGTGAAAAA
1 TTTTAAAACGAAA-AGTG-AAAA
*
3514966 CTTTTTAAACGAAAAGTGAAAA
1 -TTTTAAAACGAAAAGTGAAAA
3514988 TTTTAAA
1 TTTTAAA
3514995 GTAAAAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 6 0.24
22 4 0.16
23 12 0.48
24 3 0.12
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (21 bp):
TTTTAAAACGAAAAGTGAAAA
Found at i:3515130 original size:40 final size:40
Alignment explanation
Indices: 3515045--3515424 Score: 294
Period size: 41 Copynumber: 9.4 Consensus size: 40
3515035 GAATGACTAT
* * * * *
3515045 ATGATTTTCAAGATCTCCAAG-AAAATCTTAAACTTTTGA
1 ATGATTTTCAAGACCTCTAGGCAAAATCTTAAATTTTTAA
* *
3515084 AGGATTTTCAAGACCTCTAGGTAAAA-CTTTAAATTTTTAA
1 ATGATTTTCAAGACCTCTAGGCAAAATC-TTAAATTTTTAA
3515124 ATGA-TTTCTAAGACCTCT-GGACAAAATCTTAAATTTTTAA
1 ATGATTTTC-AAGACCTCTAGG-CAAAATCTTAAATTTTTAA
* * * * * *
3515164 ATAATTTTCAAGATCTCTGGGCAAAATTTTAGATTTTTGA
1 ATGATTTTCAAGACCTCTAGGCAAAATCTTAAATTTTTAA
** ** * *
3515204 ATGATTGCCAAAGATTTCTAGGCAAAATCTTAAAATTTTGA
1 ATGATTTTC-AAGACCTCTAGGCAAAATCTTAAATTTTTAA
* *
3515245 ATGGTTCTCAAGACCTCCT-GGCAAAAGT-TTAAATTTTTGAA
1 ATGATTTTCAAGACCT-CTAGGCAAAA-TCTTAAATTTTT-AA
* * *
3515286 A-GATCTTT-ATAGACCTCCAAGCAAAAT-TTCAAAATTTTAA
1 ATGAT-TTTCA-AGACCTCTAGGCAAAATCTT-AAATTTTTAA
* * *
3515326 ATGATTTTCAAATACCTCCAAGCAAAATCTTAAATTTTTAA
1 ATGATTTTC-AAGACCTCTAGGCAAAATCTTAAATTTTTAA
* * *
3515367 ATGATTTTTCAAAACCT-TATGGCAAAATCTCAAAATTTTAA
1 ATGA-TTTTCAAGACCTCTA-GGCAAAATCTTAAATTTTTAA
3515408 ATGATTTTCTAAGACCT
1 ATGATTTTC-AAGACCT
3515425 TTGAGCAAAA
Statistics
Matches: 278, Mismatches: 41, Indels: 42
0.77 0.11 0.12
Matches are distributed among these distances:
39 24 0.09
40 115 0.41
41 131 0.47
42 8 0.03
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (40 bp):
ATGATTTTCAAGACCTCTAGGCAAAATCTTAAATTTTTAA
Found at i:3515256 original size:81 final size:79
Alignment explanation
Indices: 3515066--3515434 Score: 230
Period size: 81 Copynumber: 4.5 Consensus size: 79
3515056 GATCTCCAAG
* * *
3515066 AAAATCTTAAACTTTTGAA-GGATTTTCAAGACCTCTAGGTAAAACTTTAAATTTTTAAATGATT
1 AAAATCTTAAAATTTTGAATGG-TTTTCAAGACCTCT-GGCAAAACTTTAAATTTTTGAATGATT
* *
3515130 TCTAAGACCTCTGGAC
64 CCAAAGACCTCTGGAC
* * ** * * *
3515146 AAAATCTTAAATTTTTAAATAATTTTCAAGATCTCTGGGCAAAATTTTAGATTTTTGAATGATTG
1 AAAATCTTAAAATTTTGAATGGTTTTCAAGACCTCT-GGCAAAACTTTAAATTTTTGAATGATT-
**
3515211 CCAAAGATTTCTAGG-C
64 CCAAAGACCTCT-GGAC
* * *
3515227 AAAATCTTAAAATTTTGAATGGTTCTCAAGACCTCCTGGCAAAAGTTTAAATTTTTGAAAGATCT
1 AAAATCTTAAAATTTTGAATGGTTTTCAAGACCT-CTGGCAAAACTTTAAATTTTTGAATGAT-T
** * **
3515292 TTATAGACCTC-CAAGC
64 CCAAAGACCTCTGGA-C
* * * ** *
3515308 AAAAT-TTCAAAATTTTAAATGATTTTCAAATACCTCCAAGCAAAA-TCTTAAATTTTTAAATGA
1 AAAATCTT-AAAATTTTGAATGGTTTTC-AAGACCT-CTGGCAAAACT-TTAAATTTTTGAATGA
* *
3515371 TTTTTCAAA-ACCTTATGG-C
62 --TTCCAAAGACC-TCTGGAC
* * * *
3515390 AAAATCTCAAAATTTTAAATGATTTTCTAAGACCTTTGAGCAAAA
1 AAAATCTTAAAATTTTGAATGGTTTTC-AAGACCTCTG-GCAAAA
3515435 ATTCAAATGA
Statistics
Matches: 224, Mismatches: 49, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
80 55 0.25
81 89 0.40
82 73 0.33
83 6 0.03
84 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.36
Consensus pattern (79 bp):
AAAATCTTAAAATTTTGAATGGTTTTCAAGACCTCTGGCAAAACTTTAAATTTTTGAATGATTCC
AAAGACCTCTGGAC
Found at i:3515547 original size:3 final size:3
Alignment explanation
Indices: 3515539--3515577 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3515529 CCTAAATAAA
3515539 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3515578 GTTGTTGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3515582 original size:3 final size:3
Alignment explanation
Indices: 3515576--3515610 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3515566 ATTATTATTA
*
3515576 TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
3515611 CTATATTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:3515941 original size:60 final size:61
Alignment explanation
Indices: 3515850--3515963 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 61
3515840 TCTAATAAGC
* * * *
3515850 AAAAAAAACACAAGATGAGTGATTTTGCC-AAACCAATTTTTTGGTAGATCAAAACCATAAA
1 AAAAAAAAAACAAGATGAGTGATGTTGCCAAAACCAAATTTTT-GTAGATAAAAACCATAAA
*
3515911 AAAAAAAAAACCA-ATGAGTGATGTTGCCAAAACCAAATTTTTGTAGATAAAAA
1 AAAAAAAAAACAAGATGAGTGATGTTGCCAAAACCAAATTTTTGTAGATAAAAA
3515964 AAAAACCTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
60 24 0.51
61 23 0.49
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (61 bp):
AAAAAAAAAACAAGATGAGTGATGTTGCCAAAACCAAATTTTTGTAGATAAAAACCATAAA
Found at i:3516836 original size:22 final size:23
Alignment explanation
Indices: 3516806--3516850 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3516796 ATTTTTTCAC
3516806 CTATATTTTAAATATTTTAATTT
1 CTATATTTTAAATATTTTAATTT
* *
3516829 CTAT-TTTTATATATTTTTATTT
1 CTATATTTTAAATATTTTAATTT
3516851 TTGTGGTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
CTATATTTTAAATATTTTAATTT
Found at i:3518325 original size:17 final size:18
Alignment explanation
Indices: 3518303--3518343 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
3518293 ATTTAAAATG
3518303 AAAAAA-CCAAAAACAACAA
1 AAAAAATCCAAAAAC-A-AA
3518322 AAAAAATCCAAAAACAAA
1 AAAAAATCCAAAAACAAA
3518340 AAAA
1 AAAA
3518344 TAAAGACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 8 0.38
ACGTcount: A:0.80, C:0.17, G:0.00, T:0.02
Consensus pattern (18 bp):
AAAAAATCCAAAAACAAA
Found at i:3518332 original size:20 final size:18
Alignment explanation
Indices: 3518303--3518343 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
3518293 ATTTAAAATG
3518303 AAAAAACCAAAAACAACAA
1 AAAAAACCAAAAACAA-AA
3518322 AAAAAATCCAAAAACAAAA
1 AAAAAA-CCAAAAACAAAA
3518341 AAA
1 AAA
3518344 TAAAGACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.80, C:0.17, G:0.00, T:0.02
Consensus pattern (18 bp):
AAAAAACCAAAAACAAAA
Found at i:3518743 original size:19 final size:19
Alignment explanation
Indices: 3518719--3518769 Score: 86
Period size: 18 Copynumber: 2.7 Consensus size: 19
3518709 CAATTGAGAG
3518719 GCCCAAAATCTAATTGAAA
1 GCCCAAAATCTAATTGAAA
3518738 GCCC-AAATCTAATTGAAA
1 GCCCAAAATCTAATTGAAA
*
3518756 GCCCAAAGTCTAAT
1 GCCCAAAATCTAAT
3518770 GTGAGTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.22
Consensus pattern (19 bp):
GCCCAAAATCTAATTGAAA
Found at i:3524739 original size:20 final size:20
Alignment explanation
Indices: 3524711--3524766 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3524701 GGGTATGATA
3524711 AAATA-AAATTTTAAATTTT
1 AAATATAAATTTTAAATTTT
**
3524730 AAATATAAATTTTATTTTTT
1 AAATATAAATTTTAAATTTT
* *
3524750 AAGTATTAAATTATAAA
1 AAATA-TAAATTTTAAA
3524767 AATTATGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 5 0.17
20 16 0.55
21 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATATAAATTTTAAATTTT
Found at i:3531403 original size:32 final size:32
Alignment explanation
Indices: 3531338--3531404 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
3531328 CCATCTAATT
* *
3531338 ATTTATATATTTTTATCATATAAAATATTAAA
1 ATTTATATATTTATATCATATAAAATATAAAA
* ***
3531370 ATTTATATATTTATATTATATTTTATATAAAA
1 ATTTATATATTTATATCATATAAAATATAAAA
3531402 ATT
1 ATT
3531405 ACGTATTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (32 bp):
ATTTATATATTTATATCATATAAAATATAAAA
Found at i:3532547 original size:34 final size:34
Alignment explanation
Indices: 3532478--3532549 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
3532468 TACGTATAAA
*
3532478 ATATAAAAATTATTATGTTATAATTTGTATTATT
1 ATATAAAAATTATTATGTTATAATTTGTATAATT
* *
3532512 ATATAAAAATATATATTTTTTATAATTT-TA-AATT
1 ATATAAAAAT-TAT-TATGTTATAATTTGTATAATT
3532546 ATAT
1 ATAT
3532550 TGCATTTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 17 0.52
35 5 0.15
36 11 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (34 bp):
ATATAAAAATTATTATGTTATAATTTGTATAATT
Found at i:3540105 original size:19 final size:18
Alignment explanation
Indices: 3540064--3540098 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3540054 TTATAAAAAA
3540064 AAATTAAATATATTTTTG
1 AAATTAAATATATTTTTG
3540082 AAATTAAA-AGTATTTTT
1 AAATTAAATA-TATTTTT
3540099 TAGAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
AAATTAAATATATTTTTG
Found at i:3541709 original size:16 final size:16
Alignment explanation
Indices: 3541685--3541718 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3541675 CAATTTATAC
* *
3541685 TAGTTTTAAATTTTTT
1 TAGTCTTAAAATTTTT
3541701 TAGTCTTAAAATTTTT
1 TAGTCTTAAAATTTTT
3541717 TA
1 TA
3541719 ATAATTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (16 bp):
TAGTCTTAAAATTTTT
Found at i:3543508 original size:304 final size:305
Alignment explanation
Indices: 3542990--3543575 Score: 813
Period size: 304 Copynumber: 1.9 Consensus size: 305
3542980 TAAAACACAT
* * * * *
3542990 TTAATATTTCAGACGATAAATTTTAATTGTCAGATTTTTTAAGGTAGTTATATCTAAAAACGCCT
1 TTAATATTTCAGACGATAAATTTTAATGGTCAGATTATTGAAGGCAGTCATATCTAAAAACGCCT
* * * * *
3543055 TCAATAACATTTTGTTATGGATTATTCAAGACGTTACCCGTATGAAAATGCCCTTCATAATCCAT
66 TCAATAACATTTTATTAGGGATTATTCAAGACATTACCCGTAGGAAAACGCCCTTCATAATCCAT
* **
3543120 TCAATTAATTTTTAGTTTGTATTATTGAAGGCATTTTTTTAAAACGCCTTCAATAATTTATACAA
131 TCAATTAATTTTTAGTTGGTATTATTGAAGGCATTTTTTTAAAACGCCTTCAATAATCCATACAA
* *
3543185 AAAAGACGAGATAGATTCTTGATA-GCATTTTTTGC-CCAAAATACCTTTAATATTCCACACAA-
196 AAAAAACGAGACAGATTCTTGA-AGGCATTTTTTGCTCCAAAATACCTTTAATATTCCACACAAT
*
3543247 TAAATTTTTGGGGAGATTATTGAATGCGATTTTGGTAAAAATTATCA
260 TAAAATTTT-GGGAGATTATTGAATGCGATTTTGGTAAAAATTATCA
* *
3543294 TTAATATTTCAGACGATAAATTTTAATGGTC-GAATTATTGAAGGCGGTCATAT-TCATAAACGC
1 TTAATATTTCAGACGATAAATTTTAATGGTCAG-ATTATTGAAGGCAGTCATATCT-AAAAACGC
* * * *
3543357 CTTCAATAATATTTTATTAGGGATTATTCAAGACATTACTCGTAGGAAAACGTCTTTCATAATCC
64 CTTCAATAACATTTTATTAGGGATTATTCAAGACATTACCCGTAGGAAAACGCCCTTCATAATCC
** *
3543422 ATTTGATTAATTTTTAGTTGGTATTATTGAAGGCGTTTTTTTAAAACGCCTTCAATAATCCATAC
129 ATTCAATTAATTTTTAGTTGGTATTATTGAAGGCATTTTTTTAAAACGCCTTCAATAATCCATAC
* * * * * *
3543487 AAAAAAAATGCGACGGATTCTTGAAGGCATTTTTTTCTCCAAAATGCCTTTCATATTCCACACAA
194 AAAAAAAACGAGACAGATTCTTGAAGGCATTTTTTGCTCCAAAATACCTTTAATATTCCACACAA
*
3543552 TTAAAATTTTGGGTGATTATTGAA
259 TTAAAATTTTGGGAGATTATTGAA
3543576 AGTAGTTTTG
Statistics
Matches: 245, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
303 3 0.01
304 196 0.80
305 38 0.16
306 8 0.03
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (305 bp):
TTAATATTTCAGACGATAAATTTTAATGGTCAGATTATTGAAGGCAGTCATATCTAAAAACGCCT
TCAATAACATTTTATTAGGGATTATTCAAGACATTACCCGTAGGAAAACGCCCTTCATAATCCAT
TCAATTAATTTTTAGTTGGTATTATTGAAGGCATTTTTTTAAAACGCCTTCAATAATCCATACAA
AAAAAACGAGACAGATTCTTGAAGGCATTTTTTGCTCCAAAATACCTTTAATATTCCACACAATT
AAAATTTTGGGAGATTATTGAATGCGATTTTGGTAAAAATTATCA
Found at i:3546985 original size:25 final size:25
Alignment explanation
Indices: 3546957--3547010 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
3546947 AGCAATGTGC
* *
3546957 TCAAACACACCATTCAGCAAACTAT
1 TCAAAAACACCATTCAGCAAACCAT
*
3546982 TCAAAAACACCTTTCAGCAAACCAT
1 TCAAAAACACCATTCAGCAAACCAT
3547007 TCAA
1 TCAA
3547011 CATACGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.31, G:0.04, T:0.20
Consensus pattern (25 bp):
TCAAAAACACCATTCAGCAAACCAT
Found at i:3547143 original size:80 final size:78
Alignment explanation
Indices: 3546997--3547245 Score: 284
Period size: 80 Copynumber: 3.1 Consensus size: 78
3546987 AACACCTTTC
* * * *
3546997 AGCAAACCATTCAACATACGATTTAGCCCTCCAATATCATACAAAACCATTTAGTAAAATAGTAT
1 AGCAAACCATTCAACATACGATTCAGCCCTCCAATATCATACAATACCA-TTCGTAAAA-AATAT
*
3547062 CAGACAATAAGGTTT
64 CAGACAACAAGGTTT
* * ** *
3547077 AGCAAACCATTCAACATATGATTCAACCCTATAATATCATACAATGCCATTCG-ACAATACAATA
1 AGCAAACCATTCAACATACGATTCAGCCCTCCAATATCATACAATACCATTCGTA-AA-A-AATA
* *
3547141 TCATATAACAAGGTTT
63 TCAGACAACAAGGTTT
* * * *
3547157 AGCAAATCATTCAGCATACAATTCAGCCTTCCAATATCATACAATACCATTCAGTAAAAAATATC
1 AGCAAACCATTCAACATACGATTCAGCCCTCCAATATCATACAATACCATTC-GTAAAAAATATC
*
3547222 AGACAACAAAGTTT
65 AGACAACAAGGTTT
3547236 AGCAAACCAT
1 AGCAAACCAT
3547246 AATATTTAAG
Statistics
Matches: 139, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
78 1 0.01
79 31 0.22
80 103 0.74
81 3 0.02
82 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.26
Consensus pattern (78 bp):
AGCAAACCATTCAACATACGATTCAGCCCTCCAATATCATACAATACCATTCGTAAAAAATATCA
GACAACAAGGTTT
Found at i:3547948 original size:16 final size:17
Alignment explanation
Indices: 3547916--3547948 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3547906 CAAATTATTG
*
3547916 AAGACGTTTTATAATAA
1 AAGACGTATTATAATAA
3547933 AAGACGTATT-TAATAA
1 AAGACGTATTATAATAA
3547949 CCCAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
AAGACGTATTATAATAA
Found at i:3548513 original size:172 final size:175
Alignment explanation
Indices: 3548220--3548551 Score: 413
Period size: 173 Copynumber: 1.9 Consensus size: 175
3548210 TAAAAGGAAT
* * *
3548220 TATTGAAGGCTTTTGTCATTAGAAGATGCCTTTAATAATTTCAAAAAAATTTTTTAGAGAGAAAT
1 TATTGAAGGCTTTTGTCAGTAGAAGACGCCTTTAATAA-TTCAAAAAAATTTTTTAGAAAGAAAT
* * * *
3548285 TATTGAAGGTGTGTATTATTAACAAACACTTTCAGTAATTATGTACTAAGTTT-AAAAGAATTAT
65 TATTGAAGGTGTGTATTATTAACAAACACCTTCACTAATTATCTACAAAGTTTAAAAAGAATTAT
*
3548349 TAAAGGTATTTTTTTAGAATAAATACCTTCTATAACTATAGTGATA
130 TAAAGGTATTTTTTTAGAATAAACACCTTCTATAACTATAGTGATA
* ** *
3548395 TATTGAAGG-TATTTTTCAGTAGAAGACGCCTTTAATAA-TCCTAAAATTTTTTTA-AAAGAAAT
1 TATTGAAGGCT-TTTGTCAGTAGAAGACGCCTTTAATAATTCAAAAAAATTTTTTAGAAAGAAAT
* * *** * *
3548457 TATTGATGGTAGT-TGTTATTTGTAAACGCCTTCACTAATTATCTACAAATTTTAAAAAGAATTA
65 TATTGAAGGT-GTGTATTATTAACAAACACCTTCACTAATTATCTACAAAGTTTAAAAAGAATTA
* *
3548521 TTAAAGGTATTTTTTTTGAATATACACCTTC
129 TTAAAGGTATTTTTTTAGAATAAACACCTTC
3548552 AATTACCGTG
Statistics
Matches: 133, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
172 46 0.35
173 53 0.40
174 1 0.01
175 33 0.25
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.40
Consensus pattern (175 bp):
TATTGAAGGCTTTTGTCAGTAGAAGACGCCTTTAATAATTCAAAAAAATTTTTTAGAAAGAAATT
ATTGAAGGTGTGTATTATTAACAAACACCTTCACTAATTATCTACAAAGTTTAAAAAGAATTATT
AAAGGTATTTTTTTAGAATAAACACCTTCTATAACTATAGTGATA
Found at i:3548529 original size:486 final size:469
Alignment explanation
Indices: 3547941--3548834 Score: 1094
Period size: 486 Copynumber: 1.9 Consensus size: 469
3547931 AAAAGACGTA
*
3547941 TTTAATAACCCAAAAATTTTTTAAAAAAATTATTGAAGGTAGTTGTTATCATCAAATGCCTTCAC
1 TTTAATAACCCAAAAATTTTTTAAAAAAATTATTGAAGGTAGTTGTTATCATCAAACGCCTTCAC
* *
3548006 TAATTATCTAAAAATTTAAAAAAGAATTATTAAAGGTATTTTTCTTGAATATACGCATTTAATAA
66 TAATTATCTAAAAATTTAAAAAAGAATTATTAAAGGTATTTTTCTTGAATATACACATTCAATAA
* * * * * * * * * **
3548071 CCATGTTAAAATTTGTGTGGCGTTATATTGAATGTATTTTACAGTAGAAGACGTCTTTAATAATC
131 CCATGTTAAAATTTGTATAGCGGTATATTAAAGGCATTTTACAATAAAAAACACCTTTAATAATC
*
3548136 CCAACAAATTCTAGAAAAAAATTATTGAAGGTATTTATTATCAAGAAACACCTTCAATTTTTATG
196 CCAACAAA-T-T---------TTA--GAAGGTATTTATTATCAAGAAACACCTTCAATATTTATG
* * *
3548201 AAGATAATTTAAAAGGAATTATTGAAGGCTTTTGTCATTAGAAGATGCCTTTAATAATTTCAAAA
248 AAGATAATTTAAAAGAAATTATTGAAGGCTTTTGTCAGTAGAAGATGCCTTTAAGAA--TCAAAA
* * * * *
3548266 AAATTTTTTAGAGAGAAATTATTGAAGGT-GTGTATTATTAACAAACACTTTCAGTAATTATGTA
311 AAATGTTTTAGAGA-AAATTATTGAAGATAGT-TATTATTAACAAACACCTTCACTAATTATCTA
*
3548330 CT-AAGTTT-AAAAGAATTATTAAAGGTATTTTTTTAGAATAAATACCTTCTATAACTATAGTGA
374 -TAAAATTTAAAAAGAATTATTAAAGGTATTTTTTTAGAATAAATACCTTCTATAACTATAGTGA
3548393 TATATTGAAGGTATTTTTCAGTAGAAGACGCC
438 TATATTGAAGGTATTTTTCAGTAGAAGACGCC
* * * * *
3548425 TTTAATAATCCTAAAATTTTTTTAAAAGAAATTATTGATGGTAGTTGTTAT-TTGTAAACGCCTT
1 TTTAATAA-CCCAAAAATTTTTTAAAA-AAATTATTGAAGGTAGTTGTTATCAT-CAAACGCCTT
* * * *
3548489 CACTAATTATCTACAAATTTTAAAAAGAATTATTAAAGGTATTTTTTTTGAATATACACCTTCAA
63 CACTAATTATCTAAAAATTTAAAAAAGAATTATTAAAGGTATTTTTCTTGAATATACACATTCAA
* * * *
3548554 TTACCGTGTTAAAATTTGTATAGTGGTATATTAAAGGCGTTTTACAATAAAAAACACCTTTAATA
128 TAACCATGTTAAAATTTGTATAGCGGTATATTAAAGGCATTTTACAATAAAAAACACCTTTAATA
* * * * * * * *
3548619 ATTCCAATAAATTTTAGAAGGTGTTTATTATCAATAAACGCTTTTAATATTTATGTAGATAATTT
193 ATCCCAACAAATTTTAGAAGGTATTTATTATCAAGAAACACCTTCAATATTTATGAAGATAATTT
* **
3548684 AAATGAAATTATTGAAGGCTTTTGTCAGTAGAAGATGCCTTTAAGAATCCTAAAAATGTTTTAGA
258 AAAAGAAATTATTGAAGGCTTTTGTCAGTAGAAGATGCCTTTAAGAATCAAAAAAATGTTTTAGA
* * ** *
3548749 GAAAATTATTGATGATAGTTGTTATTTGCAAACGCCTTCACTAATTATCTATAAAATTTAAAAAG
323 GAAAATTATTGAAGATAGTTATTATTAACAAACACCTTCACTAATTATCTATAAAATTTAAAAAG
3548814 AATTATTAAAGGTATTTTTTT
388 AATTATTAAAGGTATTTTTTT
3548835 TTAATATATG
Statistics
Matches: 351, Mismatches: 53, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
469 1 0.00
470 42 0.12
471 45 0.13
473 85 0.24
475 3 0.01
484 9 0.03
485 18 0.05
486 148 0.42
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (469 bp):
TTTAATAACCCAAAAATTTTTTAAAAAAATTATTGAAGGTAGTTGTTATCATCAAACGCCTTCAC
TAATTATCTAAAAATTTAAAAAAGAATTATTAAAGGTATTTTTCTTGAATATACACATTCAATAA
CCATGTTAAAATTTGTATAGCGGTATATTAAAGGCATTTTACAATAAAAAACACCTTTAATAATC
CCAACAAATTTTAGAAGGTATTTATTATCAAGAAACACCTTCAATATTTATGAAGATAATTTAAA
AGAAATTATTGAAGGCTTTTGTCAGTAGAAGATGCCTTTAAGAATCAAAAAAATGTTTTAGAGAA
AATTATTGAAGATAGTTATTATTAACAAACACCTTCACTAATTATCTATAAAATTTAAAAAGAAT
TATTAAAGGTATTTTTTTAGAATAAATACCTTCTATAACTATAGTGATATATTGAAGGTATTTTT
CAGTAGAAGACGCC
Found at i:3548931 original size:298 final size:297
Alignment explanation
Indices: 3548395--3549055 Score: 864
Period size: 298 Copynumber: 2.2 Consensus size: 297
3548385 TATAGTGATA
* * * *
3548395 TATTGAAGG-TATTTTTCAGTAGAAGACGCCTTTAATAATCCTAAAATTTTTTTA-AAAGAAATT
1 TATTGAAGGCT-TTTGTCAGTAGAAGACGCCTTTAAGAATCCTAAAA-ATTTTTAGAGA-AAATT
* * *
3548458 ATTGATGGTAGTTGTTATTTGTAAACGCCTTCACTAATTATCTACAAATTTTAAAAAGAATTATT
63 ATTGATGATAGTTGTTATTTGCAAACGCCTTCACTAATTATCTACAAAATTTAAAAAGAATTATT
* *
3548523 AAAGGTATTTTTTTTGAATATACACCTTCAATTACCGTGTTAAAATTTGTATAGTGGTATATTAA
128 AAAGGTATTTTTTTTGAATATACACATTCAATTACCGTGTTAAAATTTGTATAGTGATATATTAA
* * * * **
3548588 AGGCGTTTTACAATAAAAAACACCTTTAATAATTCCAATAAATTTTAGAAGGTGTTTATTATCAA
193 AGGCGTTTTACAATAAAAAACACCCTTAATAATCCCAACAAATTTTAAAAGACGTTTATTATCAA
* * *
3548653 TAAACGCTTTTAATATTTATGTAGATAATTTAAATGAAAT
258 GAAACGCCTTCAATATTTATGTAGATAATTTAAATGAAAT
*
3548693 TATTGAAGGCTTTTGTCAGTAGAAGATGCCTTTAAGAATCCTAAAAATGTTTTAGAGAAAATTAT
1 TATTGAAGGCTTTTGTCAGTAGAAGACGCCTTTAAGAATCCTAAAAAT-TTTTAGAGAAAATTAT
*
3548758 TGATGATAGTTGTTATTTGCAAACGCCTTCACTAATTATCTATAAAATTTAAAAAGAATTATTAA
65 TGATGATAGTTGTTATTTGCAAACGCCTTCACTAATTATCTACAAAATTTAAAAAGAATTATTAA
* ** * *
3548823 AGGTATTTTTTTTTAATATATGCATTCAATTATCGTGTTAAAATTTGTATTGCT-ATATATTAAA
130 AGGTATTTTTTTTGAATATACACATTCAATTACCGTGTTAAAATTTGTATAG-TGATATATTAAA
* ** * * * * * *
3548887 GGTGTTTTGTAGTAGAAGACGCCCTTAATAATCCCAACAAATTTTAAAATACGTTTATTATCAGG
194 GGCGTTTTACAATAAAAAACACCCTTAATAATCCCAACAAATTTTAAAAGACGTTTATTATCAAG
*
3548952 AAATGCCTTCAATATTTATGTAGATAATTTAAATGAAAT
259 AAACGCCTTCAATATTTATGTAGATAATTTAAATGAAAT
* * * * *
3548991 TATTGAAGACCTTTGTTAGTAGAA-ACACTTTTAAGAAT-CTCAAAAATTTTTAGAGGAAAATTA
1 TATTGAAGGCTTTTGTCAGTAGAAGACGCCTTTAAGAATCCT-AAAAATTTTTAGA-GAAAATTA
3549054 TT
64 TT
3549056 AAAAGCATTT
Statistics
Matches: 316, Mismatches: 41, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
296 9 0.03
297 28 0.09
298 275 0.87
299 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (297 bp):
TATTGAAGGCTTTTGTCAGTAGAAGACGCCTTTAAGAATCCTAAAAATTTTTAGAGAAAATTATT
GATGATAGTTGTTATTTGCAAACGCCTTCACTAATTATCTACAAAATTTAAAAAGAATTATTAAA
GGTATTTTTTTTGAATATACACATTCAATTACCGTGTTAAAATTTGTATAGTGATATATTAAAGG
CGTTTTACAATAAAAAACACCCTTAATAATCCCAACAAATTTTAAAAGACGTTTATTATCAAGAA
ACGCCTTCAATATTTATGTAGATAATTTAAATGAAAT
Found at i:3549073 original size:61 final size:63
Alignment explanation
Indices: 3549006--3549132 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 63
3548996 AAGACCTTTG
* *
3549006 TTAGTAGAA-AC-ACTTTTAAGAATCTCAAAAATTTTTAGAGGAAAATTATTAAAAGC-ATT-TT
1 TTAGTAGAAGACGACTTTTAAGAATCTC-AAAA-TTTTAAACGAAAATTATTAAAAGCGATTGTT
* * *
3549067 TTAGTAGAAGACGTCTTTTAATAATCTCAAAATTTTAAACGAAAATTATTGAAAGCGATTGTT
1 TTAGTAGAAGACGACTTTTAAGAATCTCAAAATTTTAAACGAAAATTATTAAAAGCGATTGTT
3549130 TTA
1 TTA
3549133 AAAAACGCCT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
61 30 0.53
62 9 0.16
63 18 0.32
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.37
Consensus pattern (63 bp):
TTAGTAGAAGACGACTTTTAAGAATCTCAAAATTTTAAACGAAAATTATTAAAAGCGATTGTT
Found at i:3549971 original size:201 final size:202
Alignment explanation
Indices: 3549612--3550004 Score: 646
Period size: 201 Copynumber: 1.9 Consensus size: 202
3549602 TAAAAAACCG
* * * *
3549612 TCTTCACTGATATTGTAAGATAAAAATGAGAGAGTTATTGAAGGCGTATTATGTAAAAAATGCCT
1 TCTTCACTAATATTGTAAGATAAAAAT-AGAGAGTTATTAAAGGCATATTATGTAAAAAATCCCT
* ** *
3549677 TCAATAAATACATAAAAAATTTAGATGAAATTAGTGACGGCATTTTTTGTGGCATAAACGCTTTA
65 TCAATAAATACATAAAAAATTTAGATGAAATTAATGACAACATTTTTTATGGCATAAACGCTTTA
* *
3549742 ATAATCTCAAATAATTCTACTACGACTCTGTTGAAGGTGCCTATAATATATTCAAAAAATATTTT
130 ATAATCCCAAATAATTCTACTACGACTCTGTTGAAAGTGCCTATAATATATTCAAAAAATATTTT
3549807 CATTGATA
195 CATTGATA
3549815 TCTTCACTAATATTGTAAGATAAAAAT-GAGAGTTATTAAAGGCATATTATGTAAAAAA-CCCTT
1 TCTTCACTAATATTGTAAGATAAAAATAGAGAGTTATTAAAGGCATATTATGTAAAAAATCCCTT
3549878 CAATAAATACATAAAAAATTTAGATGAAATTAATGACAACATTTTTTATGGCATAAACGCCTTTA
66 CAATAAATACATAAAAAATTTAGATGAAATTAATGACAACATTTTTTATGGCATAAACG-CTTTA
* *
3549943 ATAATCCCAAATAATTTTACTACGACTCTGTTGAAATTGCCTATAATATATTCAAAAAATAT
130 ATAATCCCAAATAATTCTACTACGACTCTGTTGAAAGTGCCTATAATATATTCAAAAAATAT
3550005 GTAGGATGAA
Statistics
Matches: 177, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
200 59 0.33
201 92 0.52
203 26 0.15
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (202 bp):
TCTTCACTAATATTGTAAGATAAAAATAGAGAGTTATTAAAGGCATATTATGTAAAAAATCCCTT
CAATAAATACATAAAAAATTTAGATGAAATTAATGACAACATTTTTTATGGCATAAACGCTTTAA
TAATCCCAAATAATTCTACTACGACTCTGTTGAAAGTGCCTATAATATATTCAAAAAATATTTTC
ATTGATA
Found at i:3570507 original size:20 final size:19
Alignment explanation
Indices: 3570478--3570519 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3570468 TCATAATCCA
* *
3570478 TTAATAGTTTTTAAAATTT
1 TTAATAGTTTTAAAAATAT
3570497 TTAATTAGTTTTAAAAATAT
1 TTAA-TAGTTTTAAAAATAT
3570517 TTA
1 TTA
3570520 TTTATTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTAATAGTTTTAAAAATAT
Found at i:3571480 original size:20 final size:21
Alignment explanation
Indices: 3571430--3571507 Score: 101
Period size: 20 Copynumber: 3.8 Consensus size: 21
3571420 CATCATGCAA
3571430 ATAATA-A-CATGCAATAATAAT
1 ATAATATATCATGCAAT-A-AAT
3571451 ATAATATATCATGCAATAAAT
1 ATAATATATCATGCAATAAAT
*
3571472 ATAA-GTATCATGCAAT-AAT
1 ATAATATATCATGCAATAAAT
3571491 ATAATATATCATGCAAT
1 ATAATATATCATGCAAT
3571508 TAGTATAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
19 7 0.13
20 22 0.42
21 13 0.25
22 2 0.04
23 8 0.15
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.32
Consensus pattern (21 bp):
ATAATATATCATGCAATAAAT
Found at i:3573326 original size:10 final size:11
Alignment explanation
Indices: 3573303--3573330 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3573293 AAAATGAAGT
3573303 AAATTTTTGAA
1 AAATTTTTGAA
3573314 AAATTTTTGAA
1 AAATTTTTGAA
3573325 AAATTT
1 AAATTT
3573331 GAATTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (11 bp):
AAATTTTTGAA
Found at i:3573773 original size:16 final size:15
Alignment explanation
Indices: 3573749--3573784 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
3573739 GCCAATTTTT
3573749 TTTATATTTTATTTA
1 TTTATATTTTATTTA
*
3573764 TTTATGATTTTATTTG
1 TTTAT-ATTTTATTTA
3573780 TTTAT
1 TTTAT
3573785 TTATTGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (15 bp):
TTTATATTTTATTTA
Found at i:3575078 original size:35 final size:35
Alignment explanation
Indices: 3575039--3575117 Score: 115
Period size: 34 Copynumber: 2.3 Consensus size: 35
3575029 ATTTTTTTCT
3575039 AATTTTTAGACAAAAATCTCTTGTATAAAAAATT-A
1 AATTTTTA-ACAAAAATCTCTTGTATAAAAAATTAA
** *
3575074 AATTTCGAACTAAAATCTCTTGTATAAAAAATTAA
1 AATTTTTAACAAAAATCTCTTGTATAAAAAATTAA
3575109 AATTTTTAA
1 AATTTTTAA
3575118 GTTTAATTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 24 0.63
35 14 0.37
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (35 bp):
AATTTTTAACAAAAATCTCTTGTATAAAAAATTAA
Found at i:3576867 original size:3 final size:3
Alignment explanation
Indices: 3576861--3576888 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3576851 TAACCATTGC
3576861 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG C
3576889 CAAGTTGTTG
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:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:3585741 original size:2 final size:2
Alignment explanation
Indices: 3585734--3585759 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3585724 TATGAAGAGA
3585734 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3585760 GTTTTTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3590751 original size:21 final size:20
Alignment explanation
Indices: 3590717--3590820 Score: 90
Period size: 21 Copynumber: 5.2 Consensus size: 20
3590707 ATGAAAACTT
* *
3590717 AATTTTTAAAAAAATCTCAA
1 AATTTTAAAAAAAATCTAAA
*
3590737 AATTTTAATAAAAAATTTAAA
1 AATTTTAA-AAAAAATCTAAA
3590758 AATTTTCAAAAAAAATTCTAAA
1 AATTTT-AAAAAAAA-TCTAAA
* * *
3590780 AA-TTTCAAAATAAT-AAAA
1 AATTTTAAAAAAAATCTAAA
*
3590798 AATTTTAATAAAAA--TAAA
1 AATTTTAAAAAAAATCTAAA
3590816 AATTT
1 AATTT
3590821 CTTACAATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
18 13 0.19
19 9 0.13
20 13 0.19
21 25 0.36
22 9 0.13
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTTTAAAAAAAATCTAAA
Found at i:3590751 original size:22 final size:23
Alignment explanation
Indices: 3590723--3590784 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
3590713 ACTTAATTTT
*
3590723 TAAAAAAATCTCAAAATTTT-AA
1 TAAAAAAATCTAAAAATTTTCAA
*
3590745 T-AAAAAATTTAAAAATTTTCAA
1 TAAAAAAATCTAAAAATTTTCAA
*
3590767 -AAAAAATTCTAAAAATTT
1 TAAAAAAATCTAAAAATTT
3590785 CAAAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAAAAATCTAAAAATTTTCAA
Found at i:3590798 original size:18 final size:18
Alignment explanation
Indices: 3590735--3590821 Score: 59
Period size: 18 Copynumber: 4.4 Consensus size: 18
3590725 AAAAAATCTC
*
3590735 AAAATTTTAATAAAAAATTTA
1 AAAATTTCAAT-AAAAA--TA
*
3590756 AAAATTTTCAAAAAAAATTCTA
1 AAAA-TTTCAATAAAAA---TA
*
3590778 AAAATTTCAA-AATAATAA
1 AAAATTTCAATAAAAAT-A
*
3590796 AAAATTTTAATAAAAATA
1 AAAATTTCAATAAAAATA
3590814 AAAATTTC
1 AAAATTTC
3590822 TTACAATTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
17 1 0.02
18 18 0.33
19 5 0.09
20 4 0.07
21 15 0.27
22 12 0.22
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTTCAATAAAAATA
Found at i:3590810 original size:30 final size:31
Alignment explanation
Indices: 3590721--3590812 Score: 82
Period size: 30 Copynumber: 3.0 Consensus size: 31
3590711 AAACTTAATT
**
3590721 TTTAAAAA-AATCTCAAAATTTTAATAAAAAA
1 TTTAAAAATAATCAAAAAATTTTAAT-AAAAA
** ** *
3590752 TTTAAAAATTTTCAAAAAAAATT-CTAAAAA
1 TTTAAAAATAATCAAAAAATTTTAATAAAAA
*
3590782 TTTCAAAATAAT-AAAAAATTTTAATAAAAA
1 TTTAAAAATAATCAAAAAATTTTAATAAAAA
3590812 T
1 T
3590813 AAAAATTTCT
Statistics
Matches: 46, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
29 8 0.17
30 21 0.46
31 9 0.20
32 8 0.17
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAAATAATCAAAAAATTTTAATAAAAA
Found at i:3590918 original size:37 final size:37
Alignment explanation
Indices: 3590852--3590938 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 37
3590842 ACAAAACTTG
*
3590852 AAAAA-TTGAAAA-TAAAAAATTCTAAAATTT-TTTT
1 AAAAATTTGAAAATTAAAAAATTCTAAAATTTCCTTT
3590886 AAAAATTTTGAAAATTAAACAAATT-TAAAATTTCCTTT
1 AAAAA-TTTGAAAATTAAA-AAATTCTAAAATTTCCTTT
*
3590924 AAAAATCTGAAAATT
1 AAAAATTTGAAAATT
3590939 TATAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 5 0.11
36 7 0.15
37 21 0.46
38 13 0.28
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (37 bp):
AAAAATTTGAAAATTAAAAAATTCTAAAATTTCCTTT
Found at i:3590981 original size:18 final size:19
Alignment explanation
Indices: 3590958--3591001 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3590948 AAAATTCTTA
3590958 AAAATTTTTA-AAAATTTC
1 AAAATTTTTATAAAATTTC
*
3590976 AAAA-TTTTATATAATTTC
1 AAAATTTTTATAAAATTTC
3590994 AAAATTTT
1 AAAATTTT
3591002 GAAATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 15 0.65
19 3 0.13
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATTTTTATAAAATTTC
Found at i:3594127 original size:8 final size:8
Alignment explanation
Indices: 3594114--3594179 Score: 71
Period size: 8 Copynumber: 7.8 Consensus size: 8
3594104 TTACTTATAA
3594114 ATAATATT
1 ATAATATT
3594122 ATAATATATT
1 AT-A-ATATT
3594132 AATAATATT
1 -ATAATATT
3594141 ATAATA-T
1 ATAATATT
3594148 ATAATATT
1 ATAATATT
*
3594156 ATTATATT
1 ATAATATT
3594164 AATTAATATT
1 -A-TAATATT
3594174 ATAATA
1 ATAATA
3594180 ACATATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
7 7 0.14
8 21 0.42
9 8 0.16
10 12 0.24
11 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATAATATT
Found at i:3594172 original size:44 final size:43
Alignment explanation
Indices: 3594121--3594243 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 43
3594111 TAAATAATAT
* *
3594121 TATAATATATTAAT-AATATTATAATATATAATATTATTATATTAA
1 TATAATATATTAATAAATATTATAATAAATAATA-TA-CA-ATTAA
3594166 T-TAATAT-TATAATAACATATTATTAATAAATAATATACAATTAA
1 TATAATATAT-TAATAA-ATATTA-TAATAAATAATATACAATTAA
*
3594210 TATAATATATTAATAAATAATATAA-AGAATAATA
1 TATAATATATTAATAAATATTATAATA-AATAATA
3594244 AATAGTTTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
42 1 0.01
43 11 0.16
44 21 0.31
45 15 0.22
46 9 0.13
47 11 0.16
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
TATAATATATTAATAAATATTATAATAAATAATATACAATTAA
Found at i:3594224 original size:31 final size:30
Alignment explanation
Indices: 3594121--3594235 Score: 114
Period size: 31 Copynumber: 3.9 Consensus size: 30
3594111 TAAATAATAT
*
3594121 TATAATATATTAAT-AATATTATAATATATAA
1 TATAATATATTAATAAATAATATAA-AT-TAA
* * *
3594152 TATTATTATATTAATTAATATTAT-AA-TAA
1 TA-TAATATATTAATAAATAATATAAATTAA
*
3594181 CAT-AT-TATTAATAAATAATATACAATTAA
1 TATAATATATTAATAAATAATATA-AATTAA
3594210 TATAATATATTAATAAATAATATAAA
1 TATAATATATTAATAAATAATATAAA
3594236 GAATAATAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
26 14 0.20
27 1 0.01
28 3 0.04
29 9 0.13
30 4 0.06
31 20 0.28
32 12 0.17
33 8 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (30 bp):
TATAATATATTAATAAATAATATAAATTAA
Found at i:3594311 original size:34 final size:35
Alignment explanation
Indices: 3594240--3594342 Score: 92
Period size: 34 Copynumber: 3.0 Consensus size: 35
3594230 TATAAAGAAT
* * *
3594240 AATA-AATAGTTTT-ATTTTAAGTATTTTTATATT
1 AATATAATAGTTTTAATATTAAATATTTTTATATA
3594273 AATATAATA-TTTTAATATTAAATATTTTTAT-TAA
1 AATATAATAGTTTTAATATTAAATATTTTTATAT-A
* *
3594307 AATATAATTATTTTTAAATATT-AATAATTTTA-ATA
1 AATATAA-TAGTTTT-AATATTAAATATTTTTATATA
3594342 A
1 A
3594343 TAATTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
33 9 0.15
34 26 0.44
35 4 0.07
36 14 0.24
37 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (35 bp):
AATATAATAGTTTTAATATTAAATATTTTTATATA
Found at i:3594327 original size:16 final size:16
Alignment explanation
Indices: 3594306--3594354 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
3594296 ATTTTTATTA
3594306 AAATATAATTATTTTT
1 AAATATAATTATTTTT
*
3594322 AAATATTAA-TAATTTT
1 AAATA-TAATTATTTTT
3594338 -AATAATAATT-TTTTT
1 AAAT-ATAATTATTTTT
3594353 AA
1 AA
3594355 TATTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 10 0.37
16 14 0.52
17 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATAATTATTTTT
Found at i:3594345 original size:12 final size:12
Alignment explanation
Indices: 3594328--3594369 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3594318 TTTTAAATAT
3594328 TAATAATTTTAA
1 TAATAATTTTAA
**
3594340 TAATAATTTTTT
1 TAATAATTTTAA
3594352 TAAT-ATTTTAA
1 TAATAATTTTAA
*
3594363 TATTAAT
1 TAATAAT
3594370 ATTCTTTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:3594363 original size:29 final size:31
Alignment explanation
Indices: 3594290--3594370 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
3594280 TATTTTAATA
* **
3594290 TTAAATATTTTTATTAAAAT-ATAATTATTT
1 TTAAATATTTTAATTTTAATAATAATTATTT
*
3594320 TTAAATATTAATAATTTTAATAATAATT-TTT
1 TTAAATATT-TTAATTTTAATAATAATTATTT
*
3594351 TT-AATATTTTAATATTAATA
1 TTAAATATTTTAATTTTAATA
3594371 TTCTTTGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.23
30 15 0.35
31 12 0.28
32 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TTAAATATTTTAATTTTAATAATAATTATTT
Found at i:3595762 original size:22 final size:22
Alignment explanation
Indices: 3595720--3595776 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
3595710 TAATGAGGTG
3595720 GTATCATATAAT-TA-ATTGACA
1 GTAT-ATATAATATATATTGACA
3595741 GTATATATAATATATATTGACA
1 GTATATATAATATATATTGACA
*
3595763 ATATAT-TAA-ATATA
1 GTATATATAATATATA
3595777 ATTATAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 12 0.36
21 9 0.27
22 12 0.36
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
GTATATATAATATATATTGACA
Found at i:3604655 original size:52 final size:51
Alignment explanation
Indices: 3604588--3604744 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 51
3604578 TATAACCATA
* * * * *
3604588 CAAACTTGCCCATTAAGAATCTTTCTCCTCTTAGAATTCTTTTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCATT-TACTCTTAGAATTCTTCTCTTGCAAGT
* *
3604640 CAAACTTGTCTATTAAGAATCCATTTACTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAAT-CATTTACTCTTAGAATTCTTCTCTTGCAAGT
*
3604692 CAAACTTGCCTATTAAGAATCCACTTT-CTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAAT-CA-TTTACTCTTAGAATTCTTCTCTTGCAAGT
3604744 C
1 C
3604745 TTTTTGTCCA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 87 0.94
53 6 0.06
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCATTTACTCTTAGAATTCTTCTCTTGCAAGT
Found at i:3605101 original size:24 final size:24
Alignment explanation
Indices: 3605044--3605142 Score: 94
Period size: 25 Copynumber: 4.0 Consensus size: 24
3605034 CATGCACTTC
**
3605044 CCACATCTTAAACATTT-AGCTCTT
1 CCACATCTCGAAC-TTTCAGCTCTT
3605068 CACACATCTCGAACTTTCAGCTCTT
1 C-CACATCTCGAACTTTCAGCTCTT
* *
3605093 CCACATCTCGAACCTTCGGCTCTTT
1 CCACATCTCGAACTTTCAGCTC-TT
* *
3605118 CCACATCTTGAA-TCTTCAACTCTT
1 CCACATCTCGAACT-TTCAGCTCTT
3605142 C
1 C
3605143 TCACGTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
24 26 0.41
25 37 0.59
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.34
Consensus pattern (24 bp):
CCACATCTCGAACTTTCAGCTCTT
Found at i:3624473 original size:19 final size:17
Alignment explanation
Indices: 3624445--3624480 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
3624435 TTTTTTTATT
3624445 ATTTATTAAAATTTATAG
1 ATTTATT-AAATTTATAG
3624463 ATTTAATTAAATTTATAG
1 ATTT-ATTAAATTTATAG
3624481 TTAACACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTATTAAATTTATAG
Found at i:3626331 original size:38 final size:38
Alignment explanation
Indices: 3626288--3626364 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
3626278 GTGAAAGGCT
3626288 ACCACACCAAATGAGTTTCCCTTAGAATTAGGCTAAAG
1 ACCACACCAAATGAGTTTCCCTTAGAATTAGGCTAAAG
3626326 ACCACACCAAATGAGTTTCCCTTAGAATTAGGCTAAAG
1 ACCACACCAAATGAGTTTCCCTTAGAATTAGGCTAAAG
3626364 A
1 A
3626365 TTGACTTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (38 bp):
ACCACACCAAATGAGTTTCCCTTAGAATTAGGCTAAAG
Found at i:3627957 original size:31 final size:31
Alignment explanation
Indices: 3627922--3627981 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3627912 AAATTTTTAG
* *
3627922 GAGTATAGGGATTAAATTTCAAAATTCAAGT
1 GAGTATAAGGACTAAATTTCAAAATTCAAGT
* *
3627953 GAGTATAATGACTAAATTTCAAATTTCAA
1 GAGTATAAGGACTAAATTTCAAAATTCAA
3627982 ATAAGCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.33
Consensus pattern (31 bp):
GAGTATAAGGACTAAATTTCAAAATTCAAGT
Found at i:3627994 original size:31 final size:31
Alignment explanation
Indices: 3627934--3627994 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3627924 GTATAGGGAT
* * * *
3627934 TAAATTTCAAAATTCAAGTGAGTATAATGAC
1 TAAATTTCAAAATTCAAATAAGCACAATGAC
*
3627965 TAAATTTCAAATTTCAAATAAGCACAATGA
1 TAAATTTCAAAATTCAAATAAGCACAATGA
3627995 TTATTTATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (31 bp):
TAAATTTCAAAATTCAAATAAGCACAATGAC
Found at i:3628059 original size:19 final size:19
Alignment explanation
Indices: 3628030--3628084 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3628020 TTTATTCATC
3628030 TCAATTGTCACGTCAAAAAA
1 TCAA-TGTCACGTCAAAAAA
*
3628050 TCAATGTCACATCAAAAAA
1 TCAATGTCACGTCAAAAAA
*
3628069 TCAAATATCACGTCAA
1 TC-AATGTCACGTCAA
3628085 CATTTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (19 bp):
TCAATGTCACGTCAAAAAA
Found at i:3630456 original size:29 final size:29
Alignment explanation
Indices: 3630415--3630570 Score: 96
Period size: 30 Copynumber: 5.4 Consensus size: 29
3630405 GGATTTTAAG
*
3630415 GGGTTTGGA-TTTAAGTTTTGAGGGTTTTA
1 GGGTTT-GATTTTAAGTTTTGAAGGTTTTA
* * *
3630444 GGGTTTGGTTTTAAGGTATGGAAGG-TTTA
1 GGGTTTGATTTTAA-GTTTTGAAGGTTTTA
*
3630473 GGGTTTTGATTTTAGAG-TTTGAAGATTTTA
1 GGG-TTTGATTTTA-AGTTTTGAAGGTTTTA
**
3630503 GGGTTTCGATTTTAAAATTTG-AGG-TTT-
1 GGGTTT-GATTTTAAGTTTTGAAGGTTTTA
*
3630530 GGAGTTTGA-TTTAAGGGTTTGAA--TTTTA
1 GG-GTTTGATTTTAA-GTTTTGAAGGTTTTA
3630558 GAGGTTTGGATTT
1 G-GGTTT-GATTT
3630571 AAGAGTTAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 29
0.71 0.09 0.21
Matches are distributed among these distances:
26 5 0.05
27 11 0.11
28 14 0.14
29 32 0.32
30 37 0.37
31 1 0.01
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (29 bp):
GGGTTTGATTTTAAGTTTTGAAGGTTTTA
Found at i:3630563 original size:15 final size:15
Alignment explanation
Indices: 3630533--3630719 Score: 77
Period size: 15 Copynumber: 12.3 Consensus size: 15
3630523 GAGGTTTGGA
*
3630533 GTTT-GATTTAAG-G
1 GTTTGGATTTTAGAG
*
3630546 GTTTGAATTTTAGAG
1 GTTTGGATTTTAGAG
*
3630561 GTTTGGATTTAAGA-
1 GTTTGGATTTTAGAG
* *
3630575 G-TTAGAGGTTT-G-G
1 GTTTGGA-TTTTAGAG
* *
3630588 GATTTCGAATTTTATGGG
1 G-TTT-GGATTTTA-GAG
3630606 GTTTTGGATTTTAGAG
1 GT-TTGGATTTTAGAG
*
3630622 GTTTGGATTTAAG-G
1 GTTTGGATTTTAGAG
3630636 GATTTTGGATTTTAAGAG
1 G--TTTGGATTTT-AGAG
*
3630654 TTTTGGATTTTA-AG
1 GTTTGGATTTTAGAG
*
3630668 ATTTTGGATTTTAG-G
1 -GTTTGGATTTTAGAG
* *
3630683 ATTTTGAATTTTAGGAG
1 -GTTTGGATTTTA-GAG
* *
3630700 ATTTTGGATTTTAGGG
1 -GTTTGGATTTTAGAG
3630716 GTTT
1 GTTT
3630720 TAGAAACCTA
Statistics
Matches: 136, Mismatches: 19, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
13 10 0.07
14 13 0.10
15 57 0.42
16 27 0.20
17 24 0.18
18 5 0.04
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (15 bp):
GTTTGGATTTTAGAG
Found at i:3630642 original size:16 final size:16
Alignment explanation
Indices: 3630623--3630720 Score: 87
Period size: 16 Copynumber: 6.2 Consensus size: 16
3630613 ATTTTAGAGG
3630623 TTTGGATTTAAGGGAT
1 TTTGGATTTAAGGGAT
*
3630639 TTTGGATTTTAAGAG-T
1 TTTGGA-TTTAAGGGAT
3630655 TTTGGATTTTAA--GAT
1 TTTGGA-TTTAAGGGAT
*
3630670 TTTGGATTTTA-GGAT
1 TTTGGATTTAAGGGAT
* *
3630685 TTTGAATTTTAGGAGAT
1 TTTGGATTTAAGG-GAT
* *
3630702 TTTGGATTTTAGGGGT
1 TTTGGATTTAAGGGAT
3630718 TTT
1 TTT
3630721 AGAAACCTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.07
15 20 0.28
16 25 0.35
17 22 0.31
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (16 bp):
TTTGGATTTAAGGGAT
Found at i:3630645 original size:31 final size:31
Alignment explanation
Indices: 3630598--3630719 Score: 124
Period size: 31 Copynumber: 3.9 Consensus size: 31
3630588 GATTTCGAAT
* *
3630598 TTTATGGGGTTTTGGATTTTAGAGGTTTGGA
1 TTTAAGGGATTTTGGATTTTAGAGGTTTGGA
*
3630629 TTTAAGGGATTTTGGATTTTAAGAGTTTTGGA
1 TTTAAGGGATTTTGGATTTT-AGAGGTTTGGA
* *
3630661 TTTTAA--GATTTTGGATTTTAG-GATTTTGAA
1 -TTTAAGGGATTTTGGATTTTAGAG-GTTTGGA
* *
3630691 TTTTAGGAGATTTTGGATTTTAGGGGTTT
1 TTTAAGG-GATTTTGGATTTTAGAGGTTT
3630720 TAGAAACCTA
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
29 5 0.06
30 8 0.10
31 31 0.40
32 28 0.36
33 6 0.08
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (31 bp):
TTTAAGGGATTTTGGATTTTAGAGGTTTGGA
Found at i:3630665 original size:47 final size:46
Alignment explanation
Indices: 3630533--3630719 Score: 161
Period size: 47 Copynumber: 4.1 Consensus size: 46
3630523 GAGGTTTGGA
* * *
3630533 GTTT-GATTTAAGG-GTTTGAATTTT-AGAGGTTTGGATTTAAGA-
1 GTTTGGATTTAAGGATTTTGAATTTTAAGAGTTTTGGATTTTAGAG
* * * * * *
3630575 GTTAGAGGTTT-GGGATTTCGAATTTTATGGGGTTTTGGATTTTAGAG
1 GTTTG-GATTTAAGGATTTTGAATTTTA-AGAGTTTTGGATTTTAGAG
*
3630622 GTTTGGATTTAAGGGATTTTGGATTTTAAGAGTTTTGGATTTTA-AG
1 GTTTGGATTTAA-GGATTTTGAATTTTAAGAGTTTTGGATTTTAGAG
* * * *
3630668 ATTTTGGATTTTAGGATTTTGAATTTTAGGAGATTTTGGATTTTAGGG
1 -GTTTGGATTTAAGGATTTTGAATTTTAAGAG-TTTTGGATTTTAGAG
3630716 GTTT
1 GTTT
3630720 TAGAAACCTA
Statistics
Matches: 112, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
42 3 0.03
43 2 0.02
44 13 0.12
46 37 0.33
47 43 0.38
48 14 0.12
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (46 bp):
GTTTGGATTTAAGGATTTTGAATTTTAAGAGTTTTGGATTTTAGAG
Found at i:3630672 original size:8 final size:8
Alignment explanation
Indices: 3630635--3630714 Score: 71
Period size: 7 Copynumber: 10.2 Consensus size: 8
3630625 TGGATTTAAG
3630635 GGATTTT-
1 GGATTTTA
3630642 GGATTTTA
1 GGATTTTA
*
3630650 AGAGTTTT-
1 GGA-TTTTA
3630658 GGATTTTA
1 GGATTTTA
*
3630666 AGATTTT-
1 GGATTTTA
3630673 GGATTTTA
1 GGATTTTA
3630681 GGATTTT-
1 GGATTTTA
*
3630688 GAATTTTA
1 GGATTTTA
3630696 GGAGATTTT-
1 -G-GATTTTA
3630705 GGATTTTA
1 GGATTTTA
3630713 GG
1 GG
3630715 GGTTTTAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
7 29 0.49
8 20 0.34
9 5 0.08
10 5 0.08
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (8 bp):
GGATTTTA
Found at i:3630734 original size:32 final size:30
Alignment explanation
Indices: 3630636--3630737 Score: 78
Period size: 32 Copynumber: 3.2 Consensus size: 30
3630626 GGATTTAAGG
* * ***
3630636 GATTTTGGATTTTAAGAGTTTTGGATTTTAA
1 GATTTTGGATTTTAGGA-TTTTGAAACCTAA
***
3630667 GATTTTGGATTTTAGGATTTTGAATTTTAGGA
1 GATTTTGGATTTTAGGATTTTGAAACCTA--A
*
3630699 GATTTTGGATTTTAGGGGTTTTAGAAACCTAA
1 GATTTTGGATTTTA-GGATTTT-GAAACCTAA
3630731 GATTTTG
1 GATTTTG
3630738 AAAATTAAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
30 11 0.18
31 16 0.26
32 23 0.38
33 6 0.10
34 5 0.08
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (30 bp):
GATTTTGGATTTTAGGATTTTGAAACCTAA
Found at i:3631068 original size:30 final size:32
Alignment explanation
Indices: 3630994--3631070 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 32
3630984 ATTATTCTAT
* *
3630994 TATTATTATTATTATTATCTTATTTTAATATA
1 TATTTTTATTATTATTATCTTATCTTAATATA
*
3631026 TATTTTTA--ATTATTATCTTA-CTTACT-T-
1 TATTTTTATTATTATTATCTTATCTTAATATA
3631053 TCATTTTTATTATTATTA
1 T-ATTTTTATTATTATTA
3631071 AAACAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.03
28 8 0.21
29 4 0.10
30 19 0.49
32 7 0.18
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (32 bp):
TATTTTTATTATTATTATCTTATCTTAATATA
Found at i:3631102 original size:22 final size:23
Alignment explanation
Indices: 3631077--3631130 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
3631067 ATTAAAACAA
*
3631077 TTAAAAATTTATCCTA-ATAAAT
1 TTAAAAATTTATCATACATAAAT
*
3631099 TTAAGAATTTATCATACATAAAT
1 TTAAAAATTTATCATACATAAAT
*
3631122 ATATAAAAT
1 TTA-AAAAT
3631131 ACCTAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 14 0.54
23 8 0.31
24 4 0.15
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (23 bp):
TTAAAAATTTATCATACATAAAT
Found at i:3632833 original size:29 final size:29
Alignment explanation
Indices: 3632800--3632918 Score: 84
Period size: 30 Copynumber: 4.1 Consensus size: 29
3632790 GGAGTTTGGA
* *
3632800 TTTAAGTTTTGAGGGTTTTAGGG-TTTGAT
1 TTTAAGTTTGGAAGG-TTTAGGGTTTTGAT
*
3632829 TTTAAGATATGGAAGGTTTAGGGTTTTGAT
1 TTTAAG-TTTGGAAGGTTTAGGGTTTTGAT
* ** *
3632859 TTTAGAGTTT-AAATATTTTAGGGTTTCGAT
1 TTTA-AGTTTGGAA-GGTTTAGGGTTTTGAT
**
3632889 TTTAAAATTGG-AGGTTT-GGAGTTTTGAT
1 TTTAAGTTTGGAAGGTTTAGG-GTTTTGAT
3632917 TT
1 TT
3632919 AAGGGTTTGA
Statistics
Matches: 70, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
27 2 0.03
28 12 0.17
29 19 0.27
30 35 0.50
31 2 0.03
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.49
Consensus pattern (29 bp):
TTTAAGTTTGGAAGGTTTAGGGTTTTGAT
Found at i:3632860 original size:58 final size:53
Alignment explanation
Indices: 3632790--3632950 Score: 146
Period size: 58 Copynumber: 2.8 Consensus size: 53
3632780 CGGATTTTAA
* *
3632790 GGAGTTTGGATTTAAGTTTTGAGGGTTTTAGGGTTTGATTTTAAGATATGGAAGGTTT
1 GGAGTTTTGATTTAAG-TTTGA--ATTTTAGGGTTTGATTTTAAGAT-TGG-AGGTTT
* *
3632848 AGG-GTTTTGATTTTAGAGTTTAAATATTTTAGGGTTTCGATTTTAAAATTGGAGGTTT
1 -GGAGTTTTGA-TTTA-AGTTT-GA-ATTTTAGGGTTT-GATTTTAAGATTGGAGGTTT
3632906 GGAGTTTTGATTTAAGGGTTTGAATTTTAGGGGTTTGA-TTTAAGA
1 GGAGTTTTGATTTAA--GTTTGAATTTTA-GGGTTTGATTTTAAGA
3632951 GTTAAAGGTT
Statistics
Matches: 87, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
55 6 0.07
56 9 0.10
57 13 0.15
58 23 0.26
59 23 0.26
60 13 0.15
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.46
Consensus pattern (53 bp):
GGAGTTTTGATTTAAGTTTGAATTTTAGGGTTTGATTTTAAGATTGGAGGTTT
Found at i:3632932 original size:14 final size:13
Alignment explanation
Indices: 3632911--3632949 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
3632901 GGTTTGGAGT
3632911 TTTGATTTAAGGG
1 TTTGATTTAAGGG
*
3632924 TTTGAATTTTAGGGG
1 TTTG-A-TTTAAGGG
3632939 TTTGATTTAAG
1 TTTGATTTAAG
3632950 AGTTAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 2 0.09
15 11 0.50
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (13 bp):
TTTGATTTAAGGG
Found at i:3633004 original size:15 final size:15
Alignment explanation
Indices: 3632984--3633047 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
3632974 TTTATGAGGT
3632984 TTTGGATTTTAGGGG
1 TTTGGATTTTAGGGG
* *
3632999 TTTGGATTTAAGGGAT
1 TTTGGATTTTAGGG-G
* * **
3633015 TTTAGATTTTTGGAT
1 TTTGGATTTTAGGGG
3633030 TTTGGATTTTAGGGG
1 TTTGGATTTTAGGGG
3633045 TTT
1 TTT
3633048 TAGAAACTTG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 28 0.74
16 10 0.26
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (15 bp):
TTTGGATTTTAGGGG
Found at i:3633014 original size:24 final size:22
Alignment explanation
Indices: 3632987--3633047 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 22
3632977 ATGAGGTTTT
3632987 GGATTTTAGGGGTTTGGATTTAAG
1 GGATTTTAGGGGTTTGGATTT--G
*** *
3633011 GGATTTTAGATTTTTGGATTTT
1 GGATTTTAGGGGTTTGGATTTG
3633033 GGATTTTAGGGGTTT
1 GGATTTTAGGGGTTT
3633048 TAGAAACTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 12 0.40
24 18 0.60
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (22 bp):
GGATTTTAGGGGTTTGGATTTG
Found at i:3633023 original size:31 final size:31
Alignment explanation
Indices: 3632983--3633051 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3632973 TTTTATGAGG
* *
3632983 TTTTGGATTTTAGGGGTTTGGATTTAAGGGA
1 TTTTAGATTTTAGGAGTTTGGATTTAAGGGA
* * * *
3633014 TTTTAGATTTTTGGATTTTGGATTTTAGGGG
1 TTTTAGATTTTAGGAGTTTGGATTTAAGGGA
3633045 TTTTAGA
1 TTTTAGA
3633052 AACTTGAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (31 bp):
TTTTAGATTTTAGGAGTTTGGATTTAAGGGA
Found at i:3633487 original size:2 final size:2
Alignment explanation
Indices: 3633480--3633504 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3633470 AACAAAAATA
3633480 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3633505 AAATTACGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3634340 original size:12 final size:12
Alignment explanation
Indices: 3634323--3634347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3634313 TTGAGGGTTT
3634323 AATCGAAAGATA
1 AATCGAAAGATA
3634335 AATCGAAAGATA
1 AATCGAAAGATA
3634347 A
1 A
3634348 CAAGTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (12 bp):
AATCGAAAGATA
Found at i:3635256 original size:48 final size:50
Alignment explanation
Indices: 3635198--3635295 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 50
3635188 TGCCATTTGT
* *
3635198 CAAATATCATATCTTAA-TTT-AAAGTTTTAATGTCTTTTATGGAATTGA
1 CAAATATCATATCTCAAGTTTGAAAGTTCTAATGTCTTTTATGGAATTGA
*
3635246 CAAATATCATATCTCAATGTTTGAAAGTTCTAATGTCTTTTATGGGATTG
1 CAAATATCATATCTCAA-GTTTGAAAGTTCTAATGTCTTTTATGGAATTG
3635296 GATTAGCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 16 0.36
50 3 0.07
51 25 0.57
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (50 bp):
CAAATATCATATCTCAAGTTTGAAAGTTCTAATGTCTTTTATGGAATTGA
Found at i:3635485 original size:29 final size:27
Alignment explanation
Indices: 3635451--3635507 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
3635441 ATATATTAAT
*
3635451 ATAATTTATGACTTAATTTTATATTTTAC
1 ATAATTTATGA-TT-ACTTTATATTTTAC
*
3635480 ATAATTTGTGATTACTTTATATTTTAC
1 ATAATTTATGATTACTTTATATTTTAC
3635507 A
1 A
3635508 CGACCGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 14 0.54
28 2 0.08
29 10 0.38
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.54
Consensus pattern (27 bp):
ATAATTTATGATTACTTTATATTTTAC
Found at i:3636200 original size:3 final size:3
Alignment explanation
Indices: 3636194--3636218 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3636184 CGCTGCTAAT
3636194 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
3636219 GAACGAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3641022 original size:22 final size:21
Alignment explanation
Indices: 3640973--3641023 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
3640963 GTGTATTTAG
3640973 TTTT-TTAATATAAATTATAA
1 TTTTATTAATATAAATTATAA
* *
3640993 CTTAATTATATATAAA-TATAA
1 TTTTATTA-ATATAAATTATAA
3641014 TTTTTATTAA
1 -TTTTATTAA
3641024 ATTAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 13 0.54
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTATTAATATAAATTATAA
Found at i:3641794 original size:15 final size:15
Alignment explanation
Indices: 3641761--3641802 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3641751 TAATTTTTTT
*
3641761 AATAAA-ATACATTA
1 AATAAATATAAATTA
*
3641775 TATAAATATAAATTA
1 AATAAATATAAATTA
3641790 AATAAATAATAAA
1 AATAAAT-ATAAA
3641803 ATTTATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAATATAAATTA
Found at i:3642339 original size:20 final size:19
Alignment explanation
Indices: 3642310--3642350 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
3642300 AATATAAAAT
3642310 AAAATTAAAAAACA-AATAA
1 AAAATTAAAAAA-AGAATAA
3642329 AAAAGTTAAAAAAAGAATAA
1 AAAA-TTAAAAAAAGAATAA
3642349 AA
1 AA
3642351 TATAAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAATTAAAAAAAGAATAA
Found at i:3642773 original size:16 final size:17
Alignment explanation
Indices: 3642737--3642773 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3642727 ATTTTTTTTT
*
3642737 TAAAAGTCAAAAAATAA
1 TAAAAGTCAAAAAACAA
3642754 -AAAAGT-AAAAAACAA
1 TAAAAGTCAAAAAACAA
3642769 TAAAA
1 TAAAA
3642774 AAAACCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (17 bp):
TAAAAGTCAAAAAACAA
Found at i:3643550 original size:22 final size:21
Alignment explanation
Indices: 3643525--3643565 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3643515 ATTTCATTTC
*
3643525 TAATTTTTTTATTATAATTTTA
1 TAATTTTTTAATTA-AATTTTA
3643547 TAATTTTTTAATTAAATTT
1 TAATTTTTTAATTAAATTT
3643566 AAAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TAATTTTTTAATTAAATTTTA
Found at i:3643572 original size:21 final size:22
Alignment explanation
Indices: 3643526--3643572 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3643516 TTTCATTTCT
* * *
3643526 AATTTTTTTATTATAATTTTAT
1 AATTTTTTAATTATAATTTAAA
3643548 AATTTTTTAATTA-AATTTAAA
1 AATTTTTTAATTATAATTTAAA
3643569 AATT
1 AATT
3643573 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTTTTTAATTATAATTTAAA
Found at i:3643884 original size:15 final size:15
Alignment explanation
Indices: 3643860--3643927 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
3643850 TATAATATTT
*
3643860 TATT-TATTTATTTA
1 TATTATATTTATATA
*
3643874 TTTTATATTTATATA
1 TATTATATTTATATA
*
3643889 TATTATATTAATA-A
1 TATTATATTTATATA
*
3643903 AATTATTATTTA-ATA
1 TATTA-TATTTATATA
*
3643918 TTTTA-ATTTA
1 TATTATATTTA
3643928 AGATATTAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 5 0.12
14 9 0.21
15 29 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATATTTATATA
Found at i:3643892 original size:17 final size:18
Alignment explanation
Indices: 3643848--3643898 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
3643838 CGACTCGATA
3643848 TATATAATATTTTATTTATT
1 TATAT-ATATTTTA-TTATT
3643868 TAT-T-TATTTTA-TATT
1 TATATATATTTTATTATT
*
3643883 TATATATATTATATTA
1 TATATATATTTTATTA
3643899 ATAAAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 7 0.26
16 1 0.04
17 13 0.48
18 2 0.07
19 1 0.04
20 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATATATTTTATTATT
Found at i:3643935 original size:42 final size:45
Alignment explanation
Indices: 3643863--3643953 Score: 118
Period size: 42 Copynumber: 2.1 Consensus size: 45
3643853 AATATTTTAT
* * *
3643863 TTATTTATTTATTTTATATTTATATATATTATA-TTAATAAAATTA
1 TTATTTATATATTTTATATTTATAGATATTA-ACTTAATAAAAATA
3643908 TTATTTA-ATATTTTA-ATTTA-AGATATTAACTTAATAAAAATA
1 TTATTTATATATTTTATATTTATAGATATTAACTTAATAAAAATA
3643950 TTAT
1 TTAT
3643954 ATTTACGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 1 0.02
42 22 0.52
43 5 0.12
44 7 0.17
45 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (45 bp):
TTATTTATATATTTTATATTTATAGATATTAACTTAATAAAAATA
Found at i:3647139 original size:9 final size:9
Alignment explanation
Indices: 3647127--3647160 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
3647117 TATTTTTTCT
3647127 TAAAATATA
1 TAAAATATA
3647136 TAAAATATA
1 TAAAATATA
3647145 TTAATAATATA
1 -TAA-AATATA
3647156 TAAAA
1 TAAAA
3647161 AAGATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 11 0.48
10 6 0.26
11 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAATATA
Found at i:3647479 original size:133 final size:131
Alignment explanation
Indices: 3647313--3647552 Score: 417
Period size: 133 Copynumber: 1.8 Consensus size: 131
3647303 TTTAATGCAA
*
3647313 CATATAAAAACAAAACTTACAATTATAAATATGCCAATATGTGAATATATGTATAACAAAATGAA
1 CATATAAAAACAAAACTTACAATTATAAATATGCCAATATGTAAATATATGTATAACAAAATGAA
*
3647378 TATATTAAGCATGTAAAAATTTCAACTAAACATTTTCTTTTTTTTTTTTCAACCAAACATTTTTT
66 TATATTAAGCATGTAAAAATTTCAACCAAAC-TTTT-TTTTTTTTTTTTCAACCAAACATTTTTT
3647443 CTG
129 CTG
* *
3647446 CATATAAAAACAAAACTTATAATTATAAATATGCTAATATGTAAATATATGTATAACAAAATGAA
1 CATATAAAAACAAAACTTACAATTATAAATATGCCAATATGTAAATATATGTATAACAAAATGAA
*
3647511 TATATTAAGCATGTAAAAATTTTAACCAAACTTTTTTTTTTT
66 TATATTAAGCATGTAAAAATTTCAACCAAACTTTTTTTTTTT
3647553 AAAGCAAACA
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
131 7 0.07
132 4 0.04
133 91 0.89
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (131 bp):
CATATAAAAACAAAACTTACAATTATAAATATGCCAATATGTAAATATATGTATAACAAAATGAA
TATATTAAGCATGTAAAAATTTCAACCAAACTTTTTTTTTTTTTTTTCAACCAAACATTTTTTCT
G
Found at i:3647554 original size:19 final size:21
Alignment explanation
Indices: 3647530--3647568 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3647520 CATGTAAAAA
3647530 TTTT-AACCAAAC-TTTTTTT
1 TTTTAAACCAAACATTTTTTT
*
3647549 TTTTAAAGCAAACATTTTTT
1 TTTTAAACCAAACATTTTTT
3647569 CTTATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.54
Consensus pattern (21 bp):
TTTTAAACCAAACATTTTTTT
Found at i:3654042 original size:21 final size:22
Alignment explanation
Indices: 3654018--3654069 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
3654008 CCTAAAATTA
3654018 ATAAAATATTA-TTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
*
3654039 ATAAAATATTATTTTTTTACAT
1 ATAAAATATTATTTTTTTAAAT
3654061 AT-AAATATT
1 ATAAAATATT
3654070 TAAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAAATATTATTTTTTTAAAT
Found at i:3654075 original size:8 final size:8
Alignment explanation
Indices: 3654059--3654093 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3654049 ATTTTTTTAC
3654059 ATATAAAT
1 ATATAAAT
*
3654067 ATTTAAAT
1 ATATAAAT
*
3654075 ATATAATT
1 ATATAAAT
3654083 ATATAAAT
1 ATATAAAT
3654091 ATA
1 ATA
3654094 CATAAATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:3666700 original size:109 final size:109
Alignment explanation
Indices: 3666504--3666821 Score: 395
Period size: 109 Copynumber: 3.0 Consensus size: 109
3666494 TGTGGAGCTT
*
3666504 TGTCAGTGTACAAGCTTGTACTTTTTAGTTACTAGTGGTGCAAAGCTTGTATTCAGTACATTGTA
1 TGTCAGTGTACAAGCTTATACTTTTTAGTTACTAGTGGTGCAAAGCTTGTATTCAGTACATTGTA
*
3666569 ATAGAACCTGGAATCTATGTATTTCTGCAGAATAATGTTCTCTC
66 ATAGAACCTAGAATCTATGTATTTCTGCAGAATAATGTTCTCTC
* * * **
3666613 TGTCGGTGTACAGGCTTATACTTTTTTGTTACTAGTGGTGCAAATTTTGTATTCAGTACATTGTA
1 TGTCAGTGTACAAGCTTATACTTTTTAGTTACTAGTGGTGCAAAGCTTGTATTCAGTACATTGTA
*
3666678 ATGGAACCTAGAATCTATGTATTTCTGCAGAATAATGTTCTCTC
66 ATAGAACCTAGAATCTATGTATTTCTGCAGAATAATGTTCTCTC
* ** ** * * * *
3666722 --TCACT-TA-TTG-GGATGC-----AGAATAATAGTGGTGCAAAGCTTGTATTCAGTAGATTGT
1 TGTCAGTGTACAAGCTTATACTTTTTAG-TTACTAGTGGTGCAAAGCTTGTATTCAGTACATTGT
*
3666777 AATAGAACCTGGAATCTATGTATTTCTGCAGAATAATGTTCTCTC
65 AATAGAACCTAGAATCTATGTATTTCTGCAGAATAATGTTCTCTC
3666822 ACTTATTGGG
Statistics
Matches: 185, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
99 1 0.01
100 74 0.40
104 3 0.02
105 1 0.01
106 2 0.01
107 3 0.02
109 101 0.55
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (109 bp):
TGTCAGTGTACAAGCTTATACTTTTTAGTTACTAGTGGTGCAAAGCTTGTATTCAGTACATTGTA
ATAGAACCTAGAATCTATGTATTTCTGCAGAATAATGTTCTCTC
Found at i:3666818 original size:100 final size:98
Alignment explanation
Indices: 3666645--3666836 Score: 321
Period size: 100 Copynumber: 1.9 Consensus size: 98
3666635 TTTTTGTTAC
** *
3666645 TAGTGGTGCAAATTTTGTATTCAGTACATTGTAATGGAACCTAGAATCTATGTATTTCTGCAGAA
1 TAGTGGTGCAAAGCTTGTATTCAGTACATTGTAATAGAACCTAGAATCTATGTATTTCTGCAGAA
3666710 TAATGTTCTCTCTCACTTATTGGGATGCAGAATAA
66 TAATG-T-TCTCTCACTTATTGGGATGCAGAATAA
* *
3666745 TAGTGGTGCAAAGCTTGTATTCAGTAGATTGTAATAGAACCTGGAATCTATGTATTTCTGCAGAA
1 TAGTGGTGCAAAGCTTGTATTCAGTACATTGTAATAGAACCTAGAATCTATGTATTTCTGCAGAA
3666810 TAATGTTCTCTCACTTATTGGGATGCA
66 TAATGTTCTCTCACTTATTGGGATGCA
3666837 AGTATAAAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 21 0.24
99 1 0.01
100 65 0.75
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.36
Consensus pattern (98 bp):
TAGTGGTGCAAAGCTTGTATTCAGTACATTGTAATAGAACCTAGAATCTATGTATTTCTGCAGAA
TAATGTTCTCTCACTTATTGGGATGCAGAATAA
Found at i:3675142 original size:134 final size:134
Alignment explanation
Indices: 3674972--3675227 Score: 365
Period size: 134 Copynumber: 1.9 Consensus size: 134
3674962 TCATGATAAC
**
3674972 GTGCATGTTAGTTGAATTTTTCTCTTGCATCTATTTTTCTTTCGTTTAAAACAAGATAACATTAG
1 GTGCATGTTAGTTGAATTTTTCTCTTGCATCTATTTTTCTTTAATTTAAAACAAGATAACATTAG
* * * ** * *
3675037 GTTGTATATA-TTTTTGCATTCATTTCGTATGTTTTAACTTGAAATTTTGGTAGTTGAAATCATT
66 GCTGCATATATTTTTTACATTCATTTCACATGTGTTAACTTGAAATCTTGGTAGTTGAAATCATT
3675101 AAAA
131 AAAA
*
3675105 GTGCATGTTAGTTGAAGTTTTT-TCCTT-CAATTTATTTTTCTTTAATTTAAAACAAGATAACAT
1 GTGCATGTTAGTTGAA-TTTTTCT-CTTGC-ATCTATTTTTCTTTAATTTAAAACAAGATAACAT
*
3675168 TAGGCTGCATATATTTTTTACATTCATTTCACATGTGTTAACTTGAAATCTTGGTGGTTG
63 TAGGCTGCATATATTTTTTACATTCATTTCACATGTGTTAACTTGAAATCTTGGTAGTTG
3675228 CATATTAATA
Statistics
Matches: 108, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
133 18 0.17
134 50 0.46
135 40 0.37
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.47
Consensus pattern (134 bp):
GTGCATGTTAGTTGAATTTTTCTCTTGCATCTATTTTTCTTTAATTTAAAACAAGATAACATTAG
GCTGCATATATTTTTTACATTCATTTCACATGTGTTAACTTGAAATCTTGGTAGTTGAAATCATT
AAAA
Found at i:3677826 original size:8 final size:8
Alignment explanation
Indices: 3677810--3677860 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
3677800 ATAATAGATG
*
3677810 AAATAAAA
1 AAATGAAA
3677818 AAATGAAA
1 AAATGAAA
3677826 AAA-GTAAA
1 AAATG-AAA
*
3677834 AAA-AAAA
1 AAATGAAA
3677841 AATATGAAA
1 AA-ATGAAA
3677850 AAATGAAA
1 AAATGAAA
3677858 AAA
1 AAA
3677861 AAGAGACAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.16
8 26 0.70
9 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:3677847 original size:24 final size:22
Alignment explanation
Indices: 3677814--3677862 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
3677804 TAGATGAAAT
3677814 AAAAAAATGAAAAAAGTAAAAAA
1 AAAAAAATGAAAAAA-TAAAAAA
*
3677837 AAAAAATATGAAAAAATGAAAAA
1 AAAAAA-ATGAAAAAATAAAAAA
3677860 AAA
1 AAA
3677863 GAGACAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (22 bp):
AAAAAAATGAAAAAATAAAAAA
Found at i:3679059 original size:20 final size:22
Alignment explanation
Indices: 3679011--3679059 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
3679001 TAATCTCTAA
3679011 GAATTTTCAAATGAGAATCTTT
1 GAATTTTCAAATGAGAATCTTT
*
3679033 GAGTTTT-AAATGAGAATC-TT
1 GAATTTTCAAATGAGAATCTTT
3679053 GAATTTT
1 GAATTTT
3679060 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 11 0.44
22 6 0.24
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (22 bp):
GAATTTTCAAATGAGAATCTTT
Found at i:3679330 original size:17 final size:17
Alignment explanation
Indices: 3679283--3679331 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
3679273 AAAATCTTGA
* *
3679283 AATCTTCAATTTTTACG
1 AATCTTCAATTCTTGCG
* *
3679300 AAT-TTGAGTTCTTGCG
1 AATCTTCAATTCTTGCG
3679316 AATCTTCAATTCTTGC
1 AATCTTCAATTCTTGC
3679332 AAACTTTTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
AATCTTCAATTCTTGCG
Found at i:3679448 original size:17 final size:17
Alignment explanation
Indices: 3679428--3679460 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3679418 ATCTAAAAGG
*
3679428 TTAAAAATTTAAAAATT
1 TTAAAAATCTAAAAATT
3679445 TTAAAAATCTAAAAAT
1 TTAAAAATCTAAAAAT
3679461 CTTGTGAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAAATCTAAAAATT
Found at i:3679569 original size:18 final size:17
Alignment explanation
Indices: 3679528--3679570 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3679518 ACGAAATTTT
*
3679528 AAAATTTTTGCGAACCA
1 AAAATTTTTGCAAACCA
* *
3679545 AACATTTTTGCAAAGCTA
1 AAAATTTTTGCAAA-CCA
3679563 AAAATTTT
1 AAAATTTT
3679571 ACGAATCTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (17 bp):
AAAATTTTTGCAAACCA
Found at i:3679629 original size:51 final size:51
Alignment explanation
Indices: 3679564--3679672 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 51
3679554 GCAAAGCTAA
* * *
3679564 AAATT-TTACGAATCT-AAAATTCTTGTTAATCTCTAATTTTTAAAAATTTG
1 AAATTCTTACAAATCTCAAAA-TCTTGTGAAGCTCTAATTTTTAAAAATTTG
* * **
3679614 AAATTCTTACAAATCTCCAAATCTTGTGAAGCTTTAATTTTTACGAATTTG
1 AAATTCTTACAAATCTCAAAATCTTGTGAAGCTCTAATTTTTAAAAATTTG
3679665 AAATTCTT
1 AAATTCTT
3679673 GTGAATTTCC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 5 0.10
51 42 0.84
52 3 0.06
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (51 bp):
AAATTCTTACAAATCTCAAAATCTTGTGAAGCTCTAATTTTTAAAAATTTG
Found at i:3679686 original size:17 final size:16
Alignment explanation
Indices: 3679666--3679724 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
3679656 ACGAATTTGA
3679666 AATTCTTGTGAATTTCC
1 AATTCTTGTGAATTT-C
***
3679683 AATTCTTACAAATTTTC
1 AATTCTTGTGAA-TTTC
*
3679700 AATTTTTGTGAATATTC
1 AATTCTTGTGAAT-TTC
3679717 AATTCTTG
1 AATTCTTG
3679725 CAAATTTGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 1 0.03
17 28 0.88
18 3 0.09
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (16 bp):
AATTCTTGTGAATTTC
Found at i:3679697 original size:34 final size:33
Alignment explanation
Indices: 3679615--3679732 Score: 105
Period size: 34 Copynumber: 3.5 Consensus size: 33
3679605 AAAAATTTGA
**
3679615 AATTCTTACAAATCTCCAAA-TCTTGTGAAGCTTT-
1 AATTCTTACAAAT-TTGAAATTCTTGTGAA--TTTC
* *
3679649 AATTTTTACGAATTTGAAATTCTTGTGAATTTCC
1 AATTCTTACAAATTTGAAATTCTTGTGAATTT-C
** *
3679683 AATTCTTACAAATTTTCAATTTTTGTGAATATTC
1 AATTCTTACAAATTTGAAATTCTTGTGAAT-TTC
*
3679717 AATTCTTGCAAATTTG
1 AATTCTTACAAATTTG
3679733 TGTTCTTGCG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
32 3 0.04
33 4 0.06
34 60 0.87
35 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.45
Consensus pattern (33 bp):
AATTCTTACAAATTTGAAATTCTTGTGAATTTC
Found at i:3679773 original size:17 final size:17
Alignment explanation
Indices: 3679736--3679787 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
3679726 AAATTTGTGT
3679736 TCTTGCGAATC--TGAAA
1 TCTTGCGAATCTTTG-AA
3679752 TTCTTGCGAATCTTTGAA
1 -TCTTGCGAATCTTTGAA
*
3679770 TCTTACGAATCTTTGAA
1 TCTTGCGAATCTTTGAA
3679787 T
1 T
3679788 TGTGAATCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 28 0.88
18 2 0.06
19 2 0.06
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (17 bp):
TCTTGCGAATCTTTGAA
Found at i:3680228 original size:13 final size:13
Alignment explanation
Indices: 3680210--3680234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3680200 AAAAATAAAT
3680210 AAAAAGATAAAAA
1 AAAAAGATAAAAA
3680223 AAAAAGATAAAA
1 AAAAAGATAAAA
3680235 CAAGTGATAA
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAAGATAAAAA
Found at i:3681292 original size:46 final size:45
Alignment explanation
Indices: 3681241--3681328 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 45
3681231 TAAATTTCAC
* * **
3681241 AAAAAACATTTTTAAGGAAAATTTGAAAGTATAAAATTTTCTTAAAT
1 AAAAAAAAGTTTT-AGGAAAAAATGAAAGTAT-AAATTTTCTTAAAT
3681288 AAAAAAAAGTTTTAGGAAAAAATGAAAGTATAAATTTTCTT
1 AAAAAAAAGTTTTAGGAAAAAATGAAAGTATAAATTTTCTT
3681329 TGAAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 10 0.27
46 16 0.43
47 11 0.30
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (45 bp):
AAAAAAAAGTTTTAGGAAAAAATGAAAGTATAAATTTTCTTAAAT
Found at i:3683857 original size:38 final size:38
Alignment explanation
Indices: 3683813--3683889 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
3683803 ATTTAATGGT
* * *
3683813 TCAATTGATTCGAAATAAAAAATTTAAGGTTTGATTGA
1 TCAATTGATTCAAAATAAAAAATTTAAGATTTCATTGA
3683851 TCAATTGATTCAAAATAAAAAATTTAAGATTTCATTGA
1 TCAATTGATTCAAAATAAAAAATTTAAGATTTCATTGA
3683889 T
1 T
3683890 TATAATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (38 bp):
TCAATTGATTCAAAATAAAAAATTTAAGATTTCATTGA
Found at i:3684033 original size:21 final size:21
Alignment explanation
Indices: 3684009--3684048 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3683999 TTGATAAAAT
3684009 ATTAAAATATTAATT-TTAATA
1 ATTAAAAT-TTAATTGTTAATA
3684030 ATTAAAATTTAATTGTTAA
1 ATTAAAATTTAATTGTTAA
3684049 CCGTTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
ATTAAAATTTAATTGTTAATA
Done.