Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 18 of 18
Found at i:3141311 original size:30 final size:33
Alignment explanation
Indices: 3141259--3141330 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 33
3141249 ATAATAAAAA
3141259 TTAAAATTTTAACATTATTTAA-TTA-A-AATT
1 TTAAAATTTTAACATTATTTAATTTAGATAATT
*
3141289 TTAAAATTTTAAATATTA-TTAATTTAGATAATT
1 TTAAAATTTT-AACATTATTTAATTTAGATAATT
*
3141322 TTTAAATTT
1 TTAAAATTT
3141331 AAAAAGTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 14 0.39
31 9 0.25
32 1 0.03
33 12 0.33
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (33 bp):
TTAAAATTTTAACATTATTTAATTTAGATAATT
Found at i:3142902 original size:20 final size:20
Alignment explanation
Indices: 3142877--3142914 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3142867 TTAATTACAT
3142877 TTAAATAAA-AATTAATTTTA
1 TTAAATAAATAA-TAATTTTA
3142897 TTAAATAAATAATAATTT
1 TTAAATAAATAATAATTT
3142915 AAATCAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATAAATAATAATTTTA
Found at i:3145448 original size:2 final size:2
Alignment explanation
Indices: 3145441--3145467 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3145431 TAATTTCTTT
3145441 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3145468 TTGTTTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3146885 original size:2 final size:2
Alignment explanation
Indices: 3146878--3146907 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3146868 ACAACAAAGA
*
3146878 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3146908 TAAATGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3150817 original size:18 final size:19
Alignment explanation
Indices: 3150796--3150842 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
3150786 GAGGGAGAAG
3150796 AAAGAAAGAGAGA-AAGGA
1 AAAGAAAGAGAGAGAAGGA
* *
3150814 AAAGAAATAGAGAGGAGGA
1 AAAGAAAGAGAGAGAAGGA
3150833 AAAG-AAGAGA
1 AAAGAAAGAGA
3150843 AAATTTTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (19 bp):
AAAGAAAGAGAGAGAAGGA
Found at i:3151026 original size:21 final size:23
Alignment explanation
Indices: 3150975--3151026 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 23
3150965 TGTAATATCG
*
3150975 TGTTTTAATTATTTTAATATTTA
1 TGTTTAAATTATTTTAATATTTA
* *
3150998 T-TTAAAATT-TTTTTAT-TTTA
1 TGTTTAAATTATTTTAATATTTA
3151018 TGTTTAAAT
1 TGTTTAAAT
3151027 AACTTATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 5 0.21
21 12 0.50
22 6 0.25
23 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
TGTTTAAATTATTTTAATATTTA
Found at i:3152167 original size:23 final size:23
Alignment explanation
Indices: 3152140--3152195 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
3152130 AATTTTAATA
3152140 TATTTATCTATTTGTGTCATG-TT
1 TATTTAT-TATTTGTGTCATGCTT
*
3152163 TATTT-TTTTTTGTGTCATGCTT
1 TATTTATTATTTGTGTCATGCTT
*
3152185 TAATTA-TATTT
1 TATTTATTATTT
3152196 TTGATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 12 0.43
22 11 0.39
23 5 0.18
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (23 bp):
TATTTATTATTTGTGTCATGCTT
Found at i:3153325 original size:18 final size:17
Alignment explanation
Indices: 3153295--3153328 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3153285 AAATGACATC
*
3153295 AATTTAAATTTCTTCAA
1 AATTTAAAATTCTTCAA
3153312 AATTCTAAAATTCTTCA
1 AATT-TAAAATTCTTCA
3153329 TCCAACTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAAATTCTTCAA
Found at i:3157912 original size:2 final size:2
Alignment explanation
Indices: 3157907--3157933 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3157897 TTGTGAGGCA
3157907 AT 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 AT A
3157934 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3160989 original size:43 final size:44
Alignment explanation
Indices: 3160909--3160996 Score: 103
Period size: 43 Copynumber: 2.0 Consensus size: 44
3160899 AATTTGAAAT
*
3160909 AATATTTATATGATAAAAATATTTTTATTTAAATTT-AATTATA
1 AATATTAATATGATAAAAATATTTTTATTTAAATTTAAATTATA
*
3160952 AATATTAATAT-A-AAAATATATTTTTAATATT-ATTTTAAATTATA
1 AATATTAATATGATAAAA-ATATTTTT-AT-TTAAATTTAAATTATA
3160996 A
1 A
3160997 TTTTAGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
41 4 0.10
42 9 0.23
43 16 0.41
44 10 0.26
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (44 bp):
AATATTAATATGATAAAAATATTTTTATTTAAATTTAAATTATA
Found at i:3160999 original size:25 final size:25
Alignment explanation
Indices: 3160935--3161001 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
3160925 AAATATTTTT
*
3160935 ATTTAAATT-TAATTATAAATATTA
1 ATTTAAATTATAATTTTAAATATTA
* * *
3160959 ATATAAA-AATATATTTTTAATATTA
1 ATTTAAATTATA-ATTTTAAATATTA
*
3160984 TTTTAAATTATAATTTTA
1 ATTTAAATTATAATTTTA
3161002 GTTTTTTGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
24 8 0.25
25 21 0.66
26 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTAAATTATAATTTTAAATATTA
Found at i:3161909 original size:2 final size:2
Alignment explanation
Indices: 3161902--3161942 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
3161892 GCCCTATGTC
3161902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3161943 TGCATACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3161980 original size:42 final size:42
Alignment explanation
Indices: 3161921--3162004 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
3161911 TATATATATA
3161921 TATATATATATATATATTATATTGCATACTAAAAGTTTGACG
1 TATATATATATATATATTATATTGCATACTAAAAGTTTGACG
3161963 TATATATATATATATATTATATTGCATACTAAAAGTTTGACG
1 TATATATATATATATATTATATTGCATACTAAAAGTTTGACG
3162005 GTGATCATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (42 bp):
TATATATATATATATATTATATTGCATACTAAAAGTTTGACG
Found at i:3162189 original size:2 final size:2
Alignment explanation
Indices: 3162182--3162218 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3162172 ACTAAACGTA
3162182 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3162219 AGACTCAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3162690 original size:18 final size:19
Alignment explanation
Indices: 3162667--3162705 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3162657 GATATATAAC
3162667 TAAAAAAAT-ATTTAAAAA
1 TAAAAAAATAATTTAAAAA
*
3162685 TAAAAAATTAATTTAAAAA
1 TAAAAAAATAATTTAAAAA
3162704 TA
1 TA
3162706 TATAAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAAAATAATTTAAAAA
Found at i:3163042 original size:21 final size:21
Alignment explanation
Indices: 3162995--3163051 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
3162985 AAAAATATTT
*
3162995 TATATTATTAAATAATATATC
1 TATATTTTTAAATAATATATC
* *
3163016 TTTATTTTTAAAT-ATATATG
1 TATATTTTTAAATAATATATC
3163036 TGATA-TTTT-AATAATA
1 T-ATATTTTTAAATAATA
3163052 AAATAACTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.10
20 14 0.47
21 13 0.43
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
TATATTTTTAAATAATATATC
Found at i:3164912 original size:20 final size:20
Alignment explanation
Indices: 3164889--3164927 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3164879 AAATATTAAC
*
3164889 ATAAA-AAATATTTTTAAATT
1 ATAAATAAA-ATTTATAAATT
3164909 ATAAATAAAATTTATAAAT
1 ATAAATAAAATTTATAAAT
3164928 CATATTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAATAAAATTTATAAATT
Found at i:3164936 original size:23 final size:22
Alignment explanation
Indices: 3164910--3164969 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
3164900 TTTTAAATTA
*
3164910 TAAATAAAATT-TATAAATCATAT
1 TAAATAAAATTAAATAAA--ATAT
3164933 TAAACTAAAATTAAATAAAATAT
1 TAAA-TAAAATTAAATAAAATAT
*
3164956 TAAA-AAAATAAAAT
1 TAAATAAAATTAAAT
3164970 TATGACTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 9 0.27
23 12 0.36
24 7 0.21
25 5 0.15
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATAAAATTAAATAAAATAT
Found at i:3166385 original size:20 final size:20
Alignment explanation
Indices: 3166357--3166406 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
3166347 TCCAACAATC
* *
3166357 TATTTTATTTTAAATAATAT
1 TATTATATTTTAAAAAATAT
*
3166377 TATTATA-TTAAAAAAATAT
1 TATTATATTTTAAAAAATAT
3166396 T-TATATATTTT
1 TAT-TATATTTT
3166407 TATAATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 15 0.62
20 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATATTTTAAAAAATAT
Found at i:3166452 original size:33 final size:34
Alignment explanation
Indices: 3166384--3166456 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
3166374 TATTATTATA
*
3166384 TTAAAAAAATATTTATATATTTTTATAATTAAAT
1 TTAAATAAATATTTATATATTTTTATAATTAAAT
*
3166418 TTAAATAAATATTT-TTTATTATTATATAA-T-AAT
1 TTAAATAAATATTTATATATT-TT-TATAATTAAAT
3166451 TTAAAT
1 TTAAAT
3166457 CGGATTAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 14 0.40
34 16 0.46
35 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TTAAATAAATATTTATATATTTTTATAATTAAAT
Found at i:3170738 original size:15 final size:16
Alignment explanation
Indices: 3170718--3170747 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3170708 AAAAAAAGGA
3170718 AAAATT-ATTAAAAAT
1 AAAATTAATTAAAAAT
3170733 AAAATTAATTAAAAA
1 AAAATTAATTAAAAA
3170748 ATATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTAATTAAAAAT
Found at i:3174839 original size:178 final size:179
Alignment explanation
Indices: 3174540--3174895 Score: 633
Period size: 178 Copynumber: 2.0 Consensus size: 179
3174530 TCCCCTACAA
*
3174540 TGTTGCTTTGTTTATTCTTTTGTTTTGTTCTTTAAAACAACAATTGGCAACAGATCTTTCTTCTT
1 TGTTGCTTTGTTTATTCTTTTGTTTTGTTCTTTAAAACAACAATTGGCAACAGAGCTTTCTTCTT
*
3174605 GAAGGACCTGTGTGTTTGGATAGTCATGGAAACTGAAGTTAATTTCTCCTCAATTGCTCCACCAG
66 GAAAGACCTGTGTGTTTGGATAGTCATGGAAACTGAAGTTAATTTCTCCTCAATTGCTCCACCAG
* *
3174670 TGTTTTACAG-AAACAATTATAAGATTTGGGCTGTATGTATGGAGACAG
131 TGTTTTACAGAAAAAAATTATAAGATTTGGGCTGTACGTATGGAGACAG
*
3174718 TGTTGCTTTGTTTATTCTTTTGTTTTGTTCTTTAAAACAACAATTGGCAGCAGAGCTTTCTTCTT
1 TGTTGCTTTGTTTATTCTTTTGTTTTGTTCTTTAAAACAACAATTGGCAACAGAGCTTTCTTCTT
**
3174783 GAAAGACCTGTGTGTTTGGATAGTCATGGAGGCTGAAGTTAATTTCTCCTCAATTGCTCCACCAG
66 GAAAGACCTGTGTGTTTGGATAGTCATGGAAACTGAAGTTAATTTCTCCTCAATTGCTCCACCAG
*
3174848 TGTTTTACAGAAAAAAATTATAAGATTTGGGCTGTGCGTATGGAGACA
131 TGTTTTACAGAAAAAAATTATAAGATTTGGGCTGTACGTATGGAGACA
3174896 TGCTTAGAGG
Statistics
Matches: 169, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
178 135 0.80
179 34 0.20
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (179 bp):
TGTTGCTTTGTTTATTCTTTTGTTTTGTTCTTTAAAACAACAATTGGCAACAGAGCTTTCTTCTT
GAAAGACCTGTGTGTTTGGATAGTCATGGAAACTGAAGTTAATTTCTCCTCAATTGCTCCACCAG
TGTTTTACAGAAAAAAATTATAAGATTTGGGCTGTACGTATGGAGACAG
Found at i:3182787 original size:38 final size:38
Alignment explanation
Indices: 3182731--3182875 Score: 130
Period size: 38 Copynumber: 3.8 Consensus size: 38
3182721 CAGCCGCCAG
* * *
3182731 CCACCAGCCTATTTCAAATTGAATTCTCTAATTACCAA
1 CCACCAGCCAATTCCAAATTGAATTCTCTAATCACCAA
* * *
3182769 CCACC-GACCAATTCCAAATTAAATTCTCTAGTCATCAA
1 CCACCAG-CCAATTCCAAATTGAATTCTCTAATCACCAA
* * * ** *
3182807 CCGCCAGCTAATTCCAAATTGAATTCTTTAATCGTCAG
1 CCACCAGCCAATTCCAAATTGAATTCTCTAATCACCAA
* ** *
3182845 TCGTCAGCCAATTTCAAATTGAATTCTCTAA
1 CCACCAGCCAATTCCAAATTGAATTCTCTAA
3182876 CTATCAGCCA
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
37 1 0.01
38 85 0.98
39 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (38 bp):
CCACCAGCCAATTCCAAATTGAATTCTCTAATCACCAA
Found at i:3187508 original size:21 final size:20
Alignment explanation
Indices: 3187475--3187513 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3187465 GTAAAAATTA
3187475 TAAAAAAATTATTTTGATCT
1 TAAAAAAATTATTTTGATCT
*
3187495 TAAAAAATTATATTTTGAT
1 TAAAAAAAT-TATTTTGAT
3187514 TCTGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (20 bp):
TAAAAAAATTATTTTGATCT
Found at i:3196942 original size:15 final size:15
Alignment explanation
Indices: 3196922--3196957 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
3196912 ATATTCGATT
3196922 ATATTTTATACACGA
1 ATATTTTATACACGA
3196937 ATA-TTT-TACACGA
1 ATATTTTATACACGA
3196950 ATATTTTA
1 ATATTTTA
3196958 AGTAAAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.53
14 6 0.32
15 3 0.16
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (15 bp):
ATATTTTATACACGA
Found at i:3198335 original size:36 final size:37
Alignment explanation
Indices: 3198278--3198349 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
3198268 ACACGAAAAA
* **
3198278 TTTTATTAAAGAAATAATAAAACTTTTTTAAAAGTAT
1 TTTTATTAAAGAAATAATAAAAATTTAATAAAAGTAT
**
3198315 TTTTATTAAA-AAATTTTAAAAATTTAATAAAAGTA
1 TTTTATTAAAGAAATAATAAAAATTTAATAAAAGTA
3198350 AATTTTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTTATTAAAGAAATAATAAAAATTTAATAAAAGTAT
Found at i:3198414 original size:16 final size:17
Alignment explanation
Indices: 3198390--3198430 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3198380 AAGTCAAATA
* *
3198390 ATTAATTATTGATTT-T
1 ATTATTTATTAATTTAT
3198406 ATTATTTATTAATTTAT
1 ATTATTTATTAATTTAT
3198423 ATT-TTTAT
1 ATTATTTAT
3198431 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
ATTATTTATTAATTTAT
Found at i:3198499 original size:3 final size:3
Alignment explanation
Indices: 3198491--3198522 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3198481 ATTAAACTTG
3198491 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3198523 TGTGTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3199581 original size:21 final size:19
Alignment explanation
Indices: 3199556--3199604 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
3199546 CGATTTTGTC
*
3199556 ATTTTAATAAACTTTGATATG
1 ATTTTAATAAACTTT--TATA
*
3199577 ATTTTGAT-AACTTTTATA
1 ATTTTAATAAACTTTTATA
3199595 ATTTTAATAA
1 ATTTTAATAA
3199605 TTTTTTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 10 0.42
19 1 0.04
20 6 0.25
21 7 0.29
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (19 bp):
ATTTTAATAAACTTTTATA
Found at i:3199656 original size:37 final size:37
Alignment explanation
Indices: 3199601--3199673 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
3199591 TATAATTTTA
* * *
3199601 ATAATTTTTTATACAATTTTGATAACATTTGATATAG
1 ATAACTTTTTATACAATTTTAATAACATTTAATATAG
* *
3199638 ATAACTTTTTATATAATTTTAATAACTTTTAATATA
1 ATAACTTTTTATACAATTTTAATAACATTTAATATA
3199674 ATTTGTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (37 bp):
ATAACTTTTTATACAATTTTAATAACATTTAATATAG
Found at i:3199684 original size:21 final size:21
Alignment explanation
Indices: 3199638--3199677 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3199628 TTTGATATAG
*
3199638 ATAACTTTTTATATAATTTTA
1 ATAACTTTTAATATAATTTTA
3199659 ATAACTTTTAATATAATTT
1 ATAACTTTTAATATAATTT
3199678 GTTTAACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAACTTTTAATATAATTTTA
Found at i:3199731 original size:21 final size:22
Alignment explanation
Indices: 3199707--3199804 Score: 82
Period size: 21 Copynumber: 4.7 Consensus size: 22
3199697 TTTGGTAACT
3199707 TTTTGAA-AACTTTTGATTTAA
1 TTTTGAATAACTTTTGATTTAA
* *
3199728 TTTT-AATAACTATTGATATAA
1 TTTTGAATAACTTTTGATTTAA
*
3199749 TTTT-AATAA-TCTTTAATTTAA
1 TTTTGAATAACT-TTTGATTTAA
* *
3199770 TTTTG-ATAATTTTTCATTTAA
1 TTTTGAATAACTTTTGATTTAA
* *
3199791 TGTTG-ATAATTTTT
1 TTTTGAATAACTTTT
3199805 TAAATAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 3 0.05
21 62 0.94
22 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTTGAATAACTTTTGATTTAA
Found at i:3199773 original size:74 final size:73
Alignment explanation
Indices: 3199640--3199783 Score: 168
Period size: 74 Copynumber: 2.0 Consensus size: 73
3199630 TGATATAGAT
* * * *
3199640 AACTTTTTATATAATTTTAATAACTTTTAATATAATTTGTTTAACATGTAATATTATTTTGGTAA
1 AACTTTTGATATAATTTTAATAACTATTAATATAATTTGTATAACATGTAATATTATTTTGATAA
3199705 CTTTTTGAA
66 -TTTTTGAA
* * *
3199714 AACTTTTGATTTAATTTTAATAACTATTGATATAATTT-TAATAATC-TTTAAT-TTAATTTTGA
1 AACTTTTGATATAATTTTAATAACTATTAATATAATTTGT-ATAA-CATGTAATATT-ATTTTGA
3199776 TAATTTTT
63 TAATTTTT
3199784 CATTTAATGT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
73 8 0.13
74 51 0.85
75 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (73 bp):
AACTTTTGATATAATTTTAATAACTATTAATATAATTTGTATAACATGTAATATTATTTTGATAA
TTTTTGAA
Found at i:3199812 original size:21 final size:21
Alignment explanation
Indices: 3199767--3199812 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3199757 ATCTTTAATT
* **
3199767 TAATTTTGATAATTTTTCATT
1 TAATGTTGATAATTTTTCAAA
*
3199788 TAATGTTGATAATTTTTTAAA
1 TAATGTTGATAATTTTTCAAA
3199809 TAAT
1 TAAT
3199813 TTCAGTAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TAATGTTGATAATTTTTCAAA
Found at i:3199857 original size:16 final size:16
Alignment explanation
Indices: 3199838--3199869 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3199828 TATAATTTTG
3199838 TAATAATTTTAATATA
1 TAATAATTTTAATATA
*
3199854 TAATAATTTTGATATA
1 TAATAATTTTAATATA
3199870 ATCTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TAATAATTTTAATATA
Found at i:3200298 original size:22 final size:22
Alignment explanation
Indices: 3200273--3200318 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3200263 TTAAAAGTTT
*
3200273 TATTTATA-TATTAATATTTAAA
1 TATTTATATTATTAA-ATATAAA
*
3200295 TATTTTTATTATTAAATATAAA
1 TATTTATATTATTAAATATAAA
3200317 TA
1 TA
3200319 AAATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTATATTATTAAATATAAA
Found at i:3200874 original size:4 final size:4
Alignment explanation
Indices: 3200860--3200903 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
3200850 TTTTTGTTAA
* *
3200860 AATT GATT AATT AATT GATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT
3200904 CAGGCCATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:3203361 original size:12 final size:12
Alignment explanation
Indices: 3203329--3203377 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3203319 ATAATATTCA
3203329 TATATATTTATAT
1 TATAT-TTTATAT
*
3203342 T-T-TTTTATGT
1 TATATTTTATAT
3203352 TATATTTTATAT
1 TATATTTTATAT
*
3203364 TTTATTTTA-AT
1 TATATTTTATAT
3203375 TAT
1 TAT
3203378 TTTATGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 7 0.23
11 6 0.20
12 16 0.53
13 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:3204439 original size:21 final size:20
Alignment explanation
Indices: 3204413--3204460 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
3204403 TTAAATCATT
*
3204413 TTAAATTAATAA-AATTTATAC
1 TTAAATTAA-AATAATTTA-AA
3204434 TTAAATTAAAATAATTTAAA
1 TTAAATTAAAATAATTTAAA
3204454 TTAAATT
1 TTAAATT
3204461 TACCGAAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAATTAAAATAATTTAAA
Found at i:3204448 original size:46 final size:42
Alignment explanation
Indices: 3204370--3204454 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 42
3204360 TATAATTAAA
*
3204370 TTTAAATAAAAAATTTATTATTAAAATAATAATTTAAATCAT
1 TTTAAATAAAAAATTTATTATTAAAAAAATAATTTAAATCAT
3204412 TTTAAATTAATAAAATTTA-TACTTAAATTAAAATAATTTAAAT
1 TTTAAA-TAA-AAAATTTATTA-TTAAA--AAAATAATTTAAAT
3204455 TAAATTTACC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 6 0.16
43 5 0.14
44 13 0.35
46 13 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (42 bp):
TTTAAATAAAAAATTTATTATTAAAAAAATAATTTAAATCAT
Found at i:3207488 original size:25 final size:29
Alignment explanation
Indices: 3207451--3207502 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
3207441 ATTATATTTT
3207451 ATATATATAAT-AAAAAATAAT-TAAAAA
1 ATATATATAATAAAAAAATAATATAAAAA
3207478 ATATA-AT-ATAAAAAAATAATATAAA
1 ATATATATAATAAAAAAATAATATAAA
3207503 TATCATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.09
26 12 0.52
27 9 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (29 bp):
ATATATATAATAAAAAAATAATATAAAAA
Found at i:3207520 original size:24 final size:23
Alignment explanation
Indices: 3207455--3207524 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
3207445 TATTTTATAT
3207455 ATATAATA-AAAAATAATTAAA-AA
1 ATATAATATAAAAA-AA-TAAATAA
3207478 ATATAATATAAAAAAATAATATAA
1 ATATAATATAAAAAAATAA-ATAA
* * *
3207502 ATATCATATAAATATATAAATAA
1 ATATAATATAAAAAAATAAATAA
3207525 CTTAAAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.07
23 15 0.37
24 23 0.56
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (23 bp):
ATATAATATAAAAAAATAAATAA
Found at i:3210969 original size:20 final size:20
Alignment explanation
Indices: 3210932--3210970 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3210922 TGAAGAGTTT
*
3210932 CAATAACATAAGGGGCGCCC
1 CAATAACATAAGGCGCGCCC
3210952 CAATAACATACA-GCGCGCC
1 CAATAACATA-AGGCGCGCC
3210971 TATATATCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.36, C:0.33, G:0.21, T:0.10
Consensus pattern (20 bp):
CAATAACATAAGGCGCGCCC
Found at i:3212525 original size:12 final size:15
Alignment explanation
Indices: 3212494--3212539 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
3212484 ATATATACAT
3212494 TAATAATTTATATTATA
1 TAAT-ATTTATA-TATA
3212511 TAA-A-TTATA-ATA
1 TAATATTTATATATA
3212523 TAATATTTATATATA
1 TAATATTTATATATA
3212538 TA
1 TA
3212540 TTTTAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 6 0.23
13 1 0.04
14 10 0.38
15 6 0.23
17 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATTTATATATA
Found at i:3214230 original size:15 final size:15
Alignment explanation
Indices: 3214207--3214277 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
3214197 AACTTTATTC
*
3214207 ATTTAAAAATTAATT
1 ATTTTAAAATTAATT
*
3214222 ATTTTAAAATTAATC
1 ATTTTAAAATTAATT
*
3214237 A-TTTAAACA-CAATT
1 ATTTTAAA-ATTAATT
*
3214251 AACATTTAAAATTAATT
1 -A-TTTTAAAATTAATT
*
3214268 ATTTTTAAAT
1 ATTTTAAAAT
3214278 CATACTAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
14 9 0.20
15 23 0.52
16 2 0.05
17 10 0.23
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTAAAATTAATT
Found at i:3214962 original size:20 final size:19
Alignment explanation
Indices: 3214937--3215044 Score: 111
Period size: 20 Copynumber: 5.8 Consensus size: 19
3214927 TTTACCTAGA
*
3214937 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTCT-CAT
3214957 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
3214977 TGTATCGAT--A----CAT
1 TGTATCGATACATTCTCAT
3214990 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
* *
3215010 TGTATCGATACATTTTACAA
1 TGTATCGATACATTCT-CAT
3215030 TGTATCGATACATTC
1 TGTATCGATACATTC
3215045 AGGCATTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
13 12 0.16
15 1 0.01
18 1 0.01
19 1 0.01
20 59 0.79
21 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATTCTCAT
Found at i:3214996 original size:33 final size:33
Alignment explanation
Indices: 3214954--3215023 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
3214944 ATACATTTTG
3214954 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
3214987 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
3215020 CATT
1 CATT
3215024 TTACAATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCGATA
Found at i:3215011 original size:53 final size:53
Alignment explanation
Indices: 3214937--3215043 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 53
3214927 TTTACCTAGA
* *
3214937 TGTATCGATACATTTTGCATTGTATCGATACATTGCT-CATTGTATCGATACAT
1 TGTATCGATACATTCTGCATTGTATCGATACATT-CTACAATGTATCGATACAT
*
3214990 TGTATCGATACATTGCT-CATTGTATCGATACATTTTACAATGTATCGATACAT
1 TGTATCGATACATT-CTGCATTGTATCGATACATTCTACAATGTATCGATACAT
3215043 T
1 T
3215044 CAGGCATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
52 1 0.02
53 47 0.96
54 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (53 bp):
TGTATCGATACATTCTGCATTGTATCGATACATTCTACAATGTATCGATACAT
Found at i:3215023 original size:13 final size:13
Alignment explanation
Indices: 3214974--3215004 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3214964 ATACATTGCT
3214974 CATTGTATCGATA
1 CATTGTATCGATA
3214987 CATTGTATCGATA
1 CATTGTATCGATA
3215000 CATTG
1 CATTG
3215005 CTCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3217637 original size:79 final size:78
Alignment explanation
Indices: 3217366--3217645 Score: 316
Period size: 79 Copynumber: 3.6 Consensus size: 78
3217356 CCAATCCCCA
* * * *
3217366 TTTTATTTCTAAAACATC-AATTT--TTCATCGGAGATACTCCAACTCCGTTATTTTCGAGGGGA
1 TTTTATTTCTAAAACA-CAAATTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGA
*
3217428 TACTCCAACCCAGG
65 TACTCCAACCCCGG
* * ** * *
3217442 CTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGTCATTTTCGATGGGA
1 TTTTATTTCTAAAACACAAATTTC-CATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGA
*
3217507 TACTCCAACCTCGG
65 TACTCCAACCCCGG
*
3217521 TTTTATTTCTAAAACATCAAATTTTCATAATCGGGGATACTCCAACCCCGTTA-TTTCTGAGGGG
1 TTTTATTTCTAAAACA-CAAATTTCCATAATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGG
*
3217585 ATACTCCAACCCCGA
64 ATACTCCAACCCCGG
* * * * *
3217600 TTTTATTTTTAAAACACCAATTCTCCACAATCAGGGATATTCCAAC
1 TTTTATTTCTAAAACACAAATT-TCCATAATCGGGGATACTCCAAC
3217646 TTCGATTTTA
Statistics
Matches: 171, Mismatches: 26, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
76 19 0.11
78 9 0.05
79 138 0.81
80 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (78 bp):
TTTTATTTCTAAAACACAAATTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
ACTCCAACCCCGG
Found at i:3217688 original size:51 final size:51
Alignment explanation
Indices: 3217581--3217692 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
3217571 TTATTTCTGA
**
3217581 GGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTCTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
* * ** ** * * *
3217632 AGGGATATTCCAACTTCGATTTTATTTCCAAAACATTAATTTTTCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
3217683 GGGGATACTC
1 GGGGATACTC
3217693 AAATCTCGTT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
Found at i:3217841 original size:158 final size:158
Alignment explanation
Indices: 3217550--3217881 Score: 348
Period size: 158 Copynumber: 2.1 Consensus size: 158
3217540 AATTTTCATA
* * **
3217550 ATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTTATTTTTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCTGAGGGAATACTCCAACCCCGACTTTATTTCCAAAAC
* ** ** *
3217615 ACCAATTCTCCACAATCAGGGATATTCCAACTTCGATTTTATTTCCAAAACATTAATTTTTCACA
66 ACCAATTCTCCACAATCAGAGATATTCCAACCCCGACCTTATTTCCAAAACATTAATTTCTCACA
*
3217680 ATTGGGGATACTCAAATCTCGTTATTTC
131 ATTGAGGATACTCAAATCTCGTTATTTC
* *
3217708 ATCGGGGATATTCCAACCCCGTTATTT-TCGAGGGAATACTCCAACCCCGGCTTTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCT-GAGGGAATACTCCAACCCCGACTTTATTTCCAAAA
* *** * * * * *
3217772 TATTGA-TCTCTCACAATCATAGATACTT-CAACCCCGGCCTTATTTCTAAAATATTGATTTCTC
65 CACCAATTCTC-CACAATCAGAGATA-TTCCAACCCCGACCTTATTTCCAAAACATTAATTTCTC
* * * * *
3217835 ATAATTGAGGATACTCTAACCCCATTATTTTC
128 ACAATTGAGGATACTCAAATCTCGTTA-TTTC
*
3217867 A-CGTGGATACTCCAA
1 ATCGGGGATACTCCAA
3217882 TCTCGATTTT
Statistics
Matches: 141, Mismatches: 29, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
157 5 0.04
158 129 0.91
159 7 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (158 bp):
ATCGGGGATACTCCAACCCCGTTATTTCTGAGGGAATACTCCAACCCCGACTTTATTTCCAAAAC
ACCAATTCTCCACAATCAGAGATATTCCAACCCCGACCTTATTTCCAAAACATTAATTTCTCACA
ATTGAGGATACTCAAATCTCGTTATTTC
Found at i:3217856 original size:51 final size:50
Alignment explanation
Indices: 3217743--3217857 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 50
3217733 TTTCGAGGGA
* *
3217743 ATACTCCAACCCCGGCTTTATTTCCAAAATATTGATCTCTCACAATCATAG
1 ATACTCTAACCCCGGCCTTATTTCCAAAATATTGATCTCTCACAAT-ATAG
* * *
3217794 ATACT-TCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAAT-TGAGG
1 ATACTCT-AACCCCGGCCTTATTTCCAAAATATTGATCTCTCACAATAT-A-G
3217845 ATACTCTAACCCC
1 ATACTCTAACCCC
3217858 ATTATTTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
49 1 0.02
50 1 0.02
51 52 0.95
52 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (50 bp):
ATACTCTAACCCCGGCCTTATTTCCAAAATATTGATCTCTCACAATATAG
Found at i:3218043 original size:130 final size:128
Alignment explanation
Indices: 3217708--3218044 Score: 338
Period size: 130 Copynumber: 2.6 Consensus size: 128
3217698 TCGTTATTTC
* * *
3217708 ATCGGGGATATTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGG-ATACTCCAACCCC-GTTTTATTTCCAAAAT
* * * * *
3217773 ATTGATCTCTCACAATCATAGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATA
64 ATTAATTTCTCACAATCATAGACACTTCAACCCCGGCCTTATTTCTAAAATATCGATTTCTCACA
* * * * * * *
3217838 ATTGAGGATACTCTAACCCCATTATTTTC-ACGTGGATACTCCAATCTCGATTTTATTTTCGAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGA-G-GGATACTCCAACCCCG-TTTTATTTCCAAAA
* * * * **** *
3217902 CATCTATTTTCT-ATAATCATGGACACTTCAACTTTTGCCTTATTTCT-AAATCATCGATTTTTC
63 TAT-TAATTTCTCACAATCATAGACACTTCAACCCCGGCCTTATTTCTAAAAT-ATCGATTTCTC
3217965 ACA
126 ACA
*
3217968 ATCGGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGTTATTATCTCCAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTCGAG-GGATACTCCAACCCCGTT-TTATTTCCAAAAT
3218033 ATTAAATTTCTC
64 ATT-AATTTCTC
3218045 GTCGGGAGAT
Statistics
Matches: 163, Mismatches: 35, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
129 9 0.06
130 146 0.90
131 8 0.05
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (128 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGGGATACTCCAACCCCGTTTTATTTCCAAAATAT
TAATTTCTCACAATCATAGACACTTCAACCCCGGCCTTATTTCTAAAATATCGATTTCTCACA
Found at i:3224904 original size:17 final size:17
Alignment explanation
Indices: 3224873--3224933 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
3224863 ATTATATTAT
*
3224873 ATATACAATAAAATAATA
1 ATATAAAATAAAAT-ATA
*
3224891 AT-TAAAATATAATATA
1 ATATAAAATAAAATATA
*
3224907 ATATAAAAAAATAAATATA
1 ATAT-AAAATA-AAATATA
3224926 ATATAAAA
1 ATATAAAA
3224934 ATATTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 5 0.14
17 10 0.28
18 11 0.31
19 10 0.28
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATAAAATAAAATATA
Found at i:3224907 original size:19 final size:18
Alignment explanation
Indices: 3224880--3224937 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
3224870 TATATATACA
* *
3224880 ATAAAATAATAATTAAAAT
1 ATAATATAAT-ATAAAAAT
*
3224899 ATAATATAATATAAAAAA
1 ATAATATAATATAAAAAT
3224917 ATAAATATAATATAAAAAT
1 AT-AATATAATATAAAAAT
3224936 AT
1 AT
3224938 TTATATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.24
19 26 0.76
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATATAATATAAAAAT
Found at i:3224944 original size:19 final size:19
Alignment explanation
Indices: 3224894--3224934 Score: 73
Period size: 19 Copynumber: 2.1 Consensus size: 19
3224884 AATAATAATT
3224894 AAAATATAATATAATATAAA
1 AAAATA-AATATAATATAAA
3224914 AAAATAAATATAATATAAA
1 AAAATAAATATAATATAAA
3224933 AA
1 AA
3224935 TATTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAATAAATATAATATAAA
Found at i:3227757 original size:2 final size:2
Alignment explanation
Indices: 3227750--3227783 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3227740 GATTCCTAGC
3227750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3227784 TTAAACCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3230084 original size:2 final size:2
Alignment explanation
Indices: 3230077--3230101 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3230067 GACTCGCTTA
3230077 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
3230102 GCTAAAAAAT
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:3230613 original size:2 final size:2
Alignment explanation
Indices: 3230606--3230642 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3230596 AAAGAATCTC
3230606 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
3230643 AAGAGTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3231158 original size:13 final size:14
Alignment explanation
Indices: 3231140--3231170 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
3231130 TTAAAAACAA
3231140 AAAAATCATCT-TT
1 AAAAATCATCTATT
3231153 AAAAATCATCTATT
1 AAAAATCATCTATT
3231167 AAAA
1 AAAA
3231171 TTACTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAAATCATCTATT
Done.