Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2631
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: 77731
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2397 original size:19 final size:19
Alignment explanation
Indices: 2373--2413 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2363 AATTTTGTGT
*
2373 ATCTGATATTGTTACATCA
1 ATCTGATATTGTCACATCA
2392 ATCTGATATTGTCACATCA
1 ATCTGATATTGTCACATCA
2411 ATC
1 ATC
2414 GAATTGCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (19 bp):
ATCTGATATTGTCACATCA
Found at i:3553 original size:4 final size:4
Alignment explanation
Indices: 3544--3587 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
3534 TAGAAGTCAG
* * *
3544 ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
3588 TTCCCCAAAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:3555 original size:6 final size:6
Alignment explanation
Indices: 3544--3587 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
3534 TAGAAGTCAG
* * *
3544 ATATAT ATATAT ATATAT ATATAT ATGTAT GTATAT GTATAT AT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT AT
3588 TTCCCCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:3559 original size:10 final size:10
Alignment explanation
Indices: 3544--3587 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
3534 TAGAAGTCAG
3544 ATATATATAT
1 ATATATATAT
3554 ATATATATAT
1 ATATATATAT
*
3564 ATATATGTAT
1 ATATATATAT
* *
3574 GTATATGTAT
1 ATATATATAT
3584 ATAT
1 ATAT
3588 TTCCCCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:4411 original size:3 final size:3
Alignment explanation
Indices: 4403--4436 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4393 TCGGAATATT
4403 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4437 AAGTTTAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6941 original size:3 final size:3
Alignment explanation
Indices: 6935--6960 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6925 CTTCTTCTTC
6935 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
6961 AAGCCCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:10540 original size:20 final size:20
Alignment explanation
Indices: 10512--10555 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
10502 TATTTAATTA
*
10512 TTATTTTAAATA-AATATAT
1 TTATTTTTAATATAATATAT
*
10531 TTATTTTTAATATAATATTT
1 TTATTTTTAATATAATATAT
10551 TTATT
1 TTATT
10556 GAATTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTTTTAATATAATATAT
Found at i:11222 original size:7 final size:7
Alignment explanation
Indices: 11210--11241 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
11200 GGGCAATGAA
11210 ATTAATT
1 ATTAATT
11217 ATTAATT
1 ATTAATT
11224 ATTAATT
1 ATTAATT
*
11231 ATTAATA
1 ATTAATT
11238 ATTA
1 ATTA
11242 TTGGTTGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
ATTAATT
Found at i:11764 original size:25 final size:24
Alignment explanation
Indices: 11731--11794 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 24
11721 TTATAATTAG
11731 TAATATTTATCTATACGTAAGAATTT
1 TAAT-TTTAT-TATACGTAAGAATTT
**
11757 TAATTTTATTATAATTTAAGAATTT
1 TAATTTTATTAT-ACGTAAGAATTT
11782 TAATTTTATTATA
1 TAATTTTATTATA
11795 ATTTTTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 4 0.11
25 27 0.77
26 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (24 bp):
TAATTTTATTATACGTAAGAATTT
Found at i:11795 original size:25 final size:25
Alignment explanation
Indices: 11748--11798 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
11738 TATCTATACG
11748 TAAGAATTTTAATTTTATTATAATT
1 TAAGAATTTTAATTTTATTATAATT
11773 TAAGAATTTTAATTTTATTATAATT
1 TAAGAATTTTAATTTTATTATAATT
11798 T
1 T
11799 TTTTCACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TAAGAATTTTAATTTTATTATAATT
Found at i:11998 original size:18 final size:18
Alignment explanation
Indices: 11958--12009 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
11948 TATTTTAATA
11958 AATTTTGAATATA-TT-TT
1 AATTTT-AATATATTTATT
11975 ACATTTTAATATATTTATT
1 A-ATTTTAATATATTTATT
11994 AATTTTAAT-TATTTAT
1 AATTTTAATATATTTAT
12010 ATATCTGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 14 0.44
18 15 0.47
19 3 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTTTAATATATTTATT
Found at i:12293 original size:12 final size:13
Alignment explanation
Indices: 12276--12314 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
12266 TTTTGTTTTG
12276 TTATTAAT-ATTA
1 TTATTAATGATTA
12288 TTATT-ATGATTA
1 TTATTAATGATTA
12300 TTATTAAATGATTA
1 TTATT-AATGATTA
12314 T
1 T
12315 ATATCATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 14 0.58
14 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (13 bp):
TTATTAATGATTA
Found at i:12353 original size:18 final size:18
Alignment explanation
Indices: 12330--12366 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12320 ATAAATTTTT
12330 AAAATT-TATTTGAATTAA
1 AAAATTATATTT-AATTAA
12348 AAAATTATATTTAATTAA
1 AAAATTATATTTAATTAA
12366 A
1 A
12367 TTTTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AAAATTATATTTAATTAA
Found at i:12633 original size:3 final size:3
Alignment explanation
Indices: 12625--12652 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12615 TATTAATAAC
12625 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12653 GTTTTTATAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12683 original size:14 final size:14
Alignment explanation
Indices: 12664--12702 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
12654 TTTTTATAAA
12664 ATTATTTAA-AATTT
1 ATTATTTAATAA-TT
12678 ATTATTTAATAATT
1 ATTATTTAATAATT
12692 ATTATTATAAT
1 ATTATT-TAAT
12703 TTTTTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATTTAATAATT
Found at i:12703 original size:12 final size:12
Alignment explanation
Indices: 12625--12703 Score: 61
Period size: 12 Copynumber: 6.2 Consensus size: 12
12615 TATTAATAAC
*
12625 ATTATTATTATT
1 ATTATTATTATA
*
12637 ATTATTATTATT
1 ATTATTATTATA
*
12649 ATTAGTTTTTATA
1 ATTA-TTATTATA
* *
12662 A-AATTATTTAAA
1 ATTATTA-TTATA
12674 ATTTATTATTTAATA
1 A-TTATTA-TT-ATA
12689 ATTATTATTATA
1 ATTATTATTATA
12701 ATT
1 ATT
12704 TTTTGTTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
11 2 0.04
12 28 0.51
13 9 0.16
14 13 0.24
15 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (12 bp):
ATTATTATTATA
Found at i:13575 original size:11 final size:12
Alignment explanation
Indices: 13560--13588 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
13550 AATGATTATA
13560 ATTTTAAATATT
1 ATTTTAAATATT
13572 -TTTTAAATATT
1 ATTTTAAATATT
13583 ATTTTA
1 ATTTTA
13589 CTAATTTCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTAAATATT
Found at i:14164 original size:37 final size:37
Alignment explanation
Indices: 14105--14180 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
14095 TCCATATAAT
*
14105 ATTTCAATTTTTCAAGTACTAATTATCAAAGAAAATC
1 ATTTCAATTTTTCAAGTACTAATTATCAAAAAAAATC
** *
14142 ATTTCAATTTTTTGAGTCCTAATTATCAAAAAAAATC
1 ATTTCAATTTTTCAAGTACTAATTATCAAAAAAAATC
14179 AT
1 AT
14181 ACCAATACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (37 bp):
ATTTCAATTTTTCAAGTACTAATTATCAAAAAAAATC
Found at i:14519 original size:2 final size:2
Alignment explanation
Indices: 14512--14542 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14502 CTCCTTCTAT
14512 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
14543 AATCTCAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:14949 original size:32 final size:32
Alignment explanation
Indices: 14908--14978 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
14898 GGAAAAGGAA
14908 GCACATGAAATTATCTTAGAGTATTTCTACTC
1 GCACATGAAATTATCTTAGAGTATTTCTACTC
14940 GCACATGAAATTATCTTAGAGTATTTCTACTC
1 GCACATGAAATTATCTTAGAGTATTTCTACTC
14972 GCACATG
1 GCACATG
14979 CACAAAAACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (32 bp):
GCACATGAAATTATCTTAGAGTATTTCTACTC
Found at i:15390 original size:2 final size:2
Alignment explanation
Indices: 15383--15432 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
15373 TTTCATGGAG
15383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15425 AT AT AT AT
1 AT AT AT AT
15433 TCCTTCAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15774 original size:2 final size:2
Alignment explanation
Indices: 15767--15804 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
15757 CATGCAATGC
15767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15805 TCTTATGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16414 original size:12 final size:13
Alignment explanation
Indices: 16380--16411 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16370 TGGTGCTAAT
16380 GTTAAAATTTGAA
1 GTTAAAATTTGAA
16393 GTTAAAATTTGAA
1 GTTAAAATTTGAA
*
16406 TTTAAA
1 GTTAAA
16412 TTTATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (13 bp):
GTTAAAATTTGAA
Found at i:17727 original size:17 final size:17
Alignment explanation
Indices: 17697--17729 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17687 TCGAGAATAT
17697 AAATATTAAAATTATTA
1 AAATATTAAAATTATTA
17714 AAAT-TTAAATATTATT
1 AAATATTAAA-ATTATT
17730 TTTTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATTAAAATTATTA
Found at i:22473 original size:3 final size:3
Alignment explanation
Indices: 22465--22504 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
22455 AAGTCATATC
22465 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
22505 CTTGTAACTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:23773 original size:3 final size:3
Alignment explanation
Indices: 23765--23796 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
23755 CCTTTTAAAG
23765 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23797 GCTTTTTAAT
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:24078 original size:17 final size:17
Alignment explanation
Indices: 24037--24083 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
24027 TCACTTATTA
*
24037 TTCATTATGAAATTGGG
1 TTCATTATGAAATTGGC
*
24054 TTCCTTATGAAATTGGCC
1 TTCATTATGAAATTGG-C
*
24072 TT-ATTATCAAAT
1 TTCATTATGAAAT
24084 GGACTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (17 bp):
TTCATTATGAAATTGGC
Found at i:24273 original size:2 final size:2
Alignment explanation
Indices: 24262--24291 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24252 CTATAACAAT
24262 TA TA TA -A 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 TA TA T
24292 TACTGAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24909 original size:107 final size:107
Alignment explanation
Indices: 24714--24926 Score: 327
Period size: 107 Copynumber: 2.0 Consensus size: 107
24704 GGATAGCAGG
* * *
24714 GCACTAAATAAATAGTGACATAGTAGCAGTGGGTAGAGTGAGGACCACCGCGCGCTAGCTAATGA
1 GCACTAAATAAACAGTGACATAGCAGCAGTGAGTAGAGTGAGGACCACCGCGCGCTAGCTAATGA
* * * * *
24779 TCTGCCAACCCCTGAGCTTTAGACGATGTGACGAACCTACGT
66 TCAGCCAACCCCTGAGATCTAGACAACGTGACGAACCTACGT
* *
24821 GCACTAAATAACCAGTGAGATAGCAGCAGTGAGTAGAGTGAGGACCACCGCGCGCTAGCTAATGA
1 GCACTAAATAAACAGTGACATAGCAGCAGTGAGTAGAGTGAGGACCACCGCGCGCTAGCTAATGA
*
24886 TCAGCCAACCCCTGTGATCTAGACAACGTGACGAACCTACG
66 TCAGCCAACCCCTGAGATCTAGACAACGTGACGAACCTACG
24927 CCTTAAAATA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
107 95 1.00
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (107 bp):
GCACTAAATAAACAGTGACATAGCAGCAGTGAGTAGAGTGAGGACCACCGCGCGCTAGCTAATGA
TCAGCCAACCCCTGAGATCTAGACAACGTGACGAACCTACGT
Found at i:25271 original size:16 final size:17
Alignment explanation
Indices: 25247--25279 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25237 ATTATTTTTA
25247 AAAAATAAT-ATCTAAT
1 AAAAATAATAATCTAAT
*
25263 AAAATTAATAATCTAAT
1 AAAAATAATAATCTAAT
25280 TCTAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATAATAATCTAAT
Found at i:26013 original size:20 final size:21
Alignment explanation
Indices: 25971--26016 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
25961 TTTTTGTAAA
* *
25971 AAAAATATATAATTATATTAT
1 AAAAATATAAAATTATATAAT
25992 AAAAATATAAAATT-TATAAT
1 AAAAATATAAAATTATATAAT
26012 AAAAA
1 AAAAA
26017 AGCTTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAATATAAAATTATATAAT
Found at i:30260 original size:2 final size:2
Alignment explanation
Indices: 30248--30283 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
30238 CACAACTAGA
30248 AT AT A- 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
30284 CACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32532 original size:26 final size:27
Alignment explanation
Indices: 32489--32542 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
32479 TTTTTTTAAT
*
32489 TTTTTTTAATTATTATTTAATAATAAA
1 TTTTTTTAATTATAATTTAATAATAAA
* *
32516 TTTTTTTATTTA-AATTTAATTATAAA
1 TTTTTTTAATTATAATTTAATAATAAA
32542 T
1 T
32543 AATATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTTTTTAATTATAATTTAATAATAAA
Found at i:32997 original size:2 final size:2
Alignment explanation
Indices: 32990--33033 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
32980 AAATTATTAC
*
32990 AT AT AT AT AT AT 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 AT AT AT AT AT AT
33032 AT
1 AT
33034 GCAAGCCCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33489 original size:2 final size:2
Alignment explanation
Indices: 33482--33518 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
33472 GAAATTATTC
*
33482 TA TA TA TA TC 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 TA TA TA TA TA T
33519 GTACACTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35362 original size:19 final size:18
Alignment explanation
Indices: 35320--35374 Score: 76
Period size: 19 Copynumber: 3.1 Consensus size: 18
35310 TTAATGATTT
35320 ATTT-TTTAAAAATTTTA
1 ATTTATTTAAAAATTTTA
*
35337 ATTTATTTAAATATTTATA
1 ATTTATTTAAAAATTT-TA
*
35356 TTTTATTTAAAAATTTTA
1 ATTTATTTAAAAATTTTA
35374 A
1 A
35375 AATATATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 4 0.12
18 12 0.38
19 16 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATTTAAAAATTTTA
Found at i:35398 original size:36 final size:37
Alignment explanation
Indices: 35319--35398 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
35309 ATTAATGATT
* ** *
35319 TATTTTTTAAAAATTTTAATTTATTTAAATATTTATA
1 TATTATTTAAAAATTTTAAAATATATAAATATTTATA
* *
35356 TTTTATTTAAAAATTTTAAAATATAT-AATATTTTTA
1 TATTATTTAAAAATTTTAAAATATATAAATATTTATA
35392 TATTATT
1 TATTATT
35399 ATATTTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 15 0.42
37 21 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (37 bp):
TATTATTTAAAAATTTTAAAATATATAAATATTTATA
Found at i:37192 original size:13 final size:13
Alignment explanation
Indices: 37174--37206 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
37164 ATGCAGATAT
*
37174 TATTTATATTTGA
1 TATTTATATTTAA
37187 TATTTATATTTAA
1 TATTTATATTTAA
37200 TATTTAT
1 TATTTAT
37207 TTAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:37240 original size:21 final size:21
Alignment explanation
Indices: 37214--37270 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
37204 TATTTAAATA
*
37214 TAAATATAAAATATAATATTT
1 TAAATATAAAATATAAAATTT
* *
37235 TAAATATACAATAAAAAAATTT
1 TAAATATAAAAT-ATAAAATTT
* *
37257 AAAAAATAAAATAT
1 TAAATATAAAATAT
37271 TACATATAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATATAAAATATAAAATTT
Found at i:38186 original size:2 final size:2
Alignment explanation
Indices: 38173--38203 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38163 AACACTAGCA
*
38173 AT AT AT AG 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 A
38204 ATTTATTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:38859 original size:2 final size:2
Alignment explanation
Indices: 38854--38887 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
38844 TGTGTGTGTG
*
38854 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38888 AGAATTAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39572 original size:35 final size:34
Alignment explanation
Indices: 39504--39572 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
39494 AAGAATAGAG
* *
39504 ATCATAATGCTGATGCATAAGCTGGAGAACTAAA
1 ATCATAATGCTAATGCATAAGCTGGACAACTAAA
* *
39538 ATCATTATGCTAATGCATATAGCTGGACAGCTAAA
1 ATCATAATGCTAATGCATA-AGCTGGACAACTAAA
39573 GAATGTATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (34 bp):
ATCATAATGCTAATGCATAAGCTGGACAACTAAA
Found at i:40938 original size:18 final size:18
Alignment explanation
Indices: 40915--40950 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40905 CTTGATAGAT
40915 TGACTCAGGCTCAAGCTC
1 TGACTCAGGCTCAAGCTC
* *
40933 TGACTCTGGCTCAGGCTC
1 TGACTCAGGCTCAAGCTC
40951 AGCCTCAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (18 bp):
TGACTCAGGCTCAAGCTC
Found at i:47775 original size:2 final size:2
Alignment explanation
Indices: 47768--47797 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47758 CATGTGCAGT
47768 TA 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 TA
47798 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47802 original size:2 final size:2
Alignment explanation
Indices: 47797--47831 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
47787 ATATATATAT
47797 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 A
47832 CTGTGGGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49206 original size:2 final size:2
Alignment explanation
Indices: 49199--49225 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49189 CTGAGCAATA
49199 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
49226 AGTGCTTATA
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:51293 original size:3 final size:3
Alignment explanation
Indices: 51285--51343 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
51275 TAATCTATAA
51285 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51332 ATT ATT ATT ATT
1 ATT ATT ATT ATT
51344 TGCATTAGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:57965 original size:88 final size:89
Alignment explanation
Indices: 57801--57979 Score: 315
Period size: 88 Copynumber: 2.0 Consensus size: 89
57791 AAAGTTCACG
*
57801 TACGATAAAGATATTTTGTTGTCATTGGAGTCCCATTTTATTTTTAATAATAGGAATAGGAAGTG
1 TACGATAAAGATATTTTGTTGTCATAGGAGTCCCA-TTTATTTTTAATAATAGGAATAGGAAGTG
57866 AAGTATATTCAACTCCATGTATTCT
65 AAGTATATTCAACTCCATGTATTCT
* *
57891 TACGATAAAGATATTTTGTTGTCATAGGAGTCCCA-TTCTTTTTAATAATAGGAATGGGAAGTGA
1 TACGATAAAGATATTTTGTTGTCATAGGAGTCCCATTTATTTTTAATAATAGGAATAGGAAGTGA
57955 AGTATATTCAACTCCATGTATTCT
66 AGTATATTCAACTCCATGTATTCT
57979 T
1 T
57980 CTATCTGTAG
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
88 52 0.60
90 34 0.40
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (89 bp):
TACGATAAAGATATTTTGTTGTCATAGGAGTCCCATTTATTTTTAATAATAGGAATAGGAAGTGA
AGTATATTCAACTCCATGTATTCT
Found at i:58947 original size:50 final size:46
Alignment explanation
Indices: 58893--58999 Score: 115
Period size: 46 Copynumber: 2.2 Consensus size: 46
58883 AAAGTAGTCG
* * *
58893 TAATTGTTGACGATTCTTCACCGACCTTTGACAATTGAGAGAGGTGACCA
1 TAATTGTTGACGATT-TTCACC-AACTTTGACAA-T-AGAGAAGTAACCA
* * * *
58943 TAATTATTGACTATTTTCACCAACTTTGATAATAGAGAAGTAACCG
1 TAATTGTTGACGATTTTCACCAACTTTGACAATAGAGAAGTAACCA
58989 TAATTGTTGAC
1 TAATTGTTGAC
59000 TCTAAGTAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
46 20 0.41
47 1 0.02
48 9 0.18
49 6 0.12
50 13 0.27
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (46 bp):
TAATTGTTGACGATTTTCACCAACTTTGACAATAGAGAAGTAACCA
Found at i:58993 original size:46 final size:50
Alignment explanation
Indices: 58845--59000 Score: 133
Period size: 50 Copynumber: 3.2 Consensus size: 50
58835 AGTTATTGTC
* * * * * * **
58845 ATTGTTGATTATTCTTCATC-AACTTTTAACAATCGAAAAAAGTAGTCGTA
1 ATTGTTGACTATTCTTCACCGAAC-TTTGACAATTGAGAGAAGTAACCGTA
* * * * *
58895 ATTGTTGACGATTCTTCACCGACCTTTGACAATTGAGAGAGGTGACCATA
1 ATTGTTGACTATTCTTCACCGAACTTTGACAATTGAGAGAAGTAACCGTA
* *
58945 ATTATTGACTATT-TTCACC-AACTTTGATAA-T-AGAGAAGTAACCGTA
1 ATTGTTGACTATTCTTCACCGAACTTTGACAATTGAGAGAAGTAACCGTA
58991 ATTGTTGACT
1 ATTGTTGACT
59001 CTAAGTAACT
Statistics
Matches: 84, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
46 21 0.25
47 1 0.01
48 9 0.11
49 6 0.07
50 45 0.54
51 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCGAACTTTGACAATTGAGAGAAGTAACCGTA
Found at i:63524 original size:99 final size:100
Alignment explanation
Indices: 63352--63708 Score: 535
Period size: 99 Copynumber: 3.6 Consensus size: 100
63342 ATGTGTTGCC
**
63352 ATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATT-T
1 ATTGTTGACTATTCTTCACCAACACTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCT
* * *
63416 TCACCAACCTTTGACAATCGAGAGAGATGTCCATA
66 TCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
*
63451 ATTGTTGACTATTCTTCACCAAC-CTTGACAATCGAGAGAGGTGACCGTAATTGTTGACGATTCT
1 ATTGTTGACTATTCTTCACCAACACTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCT
63515 TCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
66 TCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * *
63550 ATTGTTGACTATTTTTCACCAAC-CTTTGACAATCGAGAGAGATGGCCGTAATTGTTGACTATTC
1 ATTGTTGACTATTCTTCACCAACAC-TTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTC
63614 TTCACCAACC-TTGACAATCGAGAGAGGTGACCGTA
65 TTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * * * *
63649 ATTGTTGACTATTCTTCACCAACATTTGATAATAGAGAAAGGT-AGCCATAATTGTTGACT
1 ATTGTTGACTATTCTTCACCAACACTTGACAATCGAGAGAGGTGA-CCGTAATTGTTGACT
63709 CTAAGCAACT
Statistics
Matches: 237, Mismatches: 17, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
98 37 0.16
99 154 0.65
100 46 0.19
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (100 bp):
ATTGTTGACTATTCTTCACCAACACTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCT
TCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
Found at i:63550 original size:50 final size:50
Alignment explanation
Indices: 63352--63708 Score: 560
Period size: 50 Copynumber: 7.2 Consensus size: 50
63342 ATGTGTTGCC
*
63352 ATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * *
63402 ATTGTTGACTATT-TTCACCAACCTTTGACAATCGAGAGAGATGTCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
63451 ATTGTTGACTATTCTTCACCAACC-TTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
*
63500 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * *
63550 ATTGTTGACTATTTTTCACCAACCTTTGACAATCGAGAGAGATGGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
63600 ATTGTTGACTATTCTTCACCAACC-TTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * * * *
63649 ATTGTTGACTATTCTTCACCAACATTTGATAATAGAGAAAGGT-AGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGA-CCGTA
63699 ATTGTTGACT
1 ATTGTTGACT
63709 CTAAGCAACT
Statistics
Matches: 283, Mismatches: 20, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
49 137 0.48
50 146 0.52
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
Found at i:63628 original size:149 final size:148
Alignment explanation
Indices: 63352--63708 Score: 608
Period size: 149 Copynumber: 2.4 Consensus size: 148
63342 ATGTGTTGCC
*
63352 ATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTTT
1 ATTGTTGACTATTCTTCACCAACATTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTTT
*
63417 CACCAACCTTTGACAATCGAGAGAGATGTCCATAATTGTTGACTATTCTTCACCAACCTTGACAA
66 CACCAACCTTTGACAATCGAGAGAGATGGCCATAATTGTTGACTATTCTTCACCAACCTTGACAA
63482 TCGAGAGAGGTGACCGTA
131 TCGAGAGAGGTGACCGTA
* *
63500 ATTGTTGACGATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTTT
1 ATTGTTGACTATTCTTCACCAACATTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTA-TTT
*
63565 TCACCAACCTTTGACAATCGAGAGAGATGGCCGTAATTGTTGACTATTCTTCACCAACCTTGACA
65 TCACCAACCTTTGACAATCGAGAGAGATGGCCATAATTGTTGACTATTCTTCACCAACCTTGACA
63630 ATCGAGAGAGGTGACCGTA
130 ATCGAGAGAGGTGACCGTA
* * * *
63649 ATTGTTGACTATTCTTCACCAACATTTGATAATAGAGAAAGGT-AGCCATAATTGTTGACT
1 ATTGTTGACTATTCTTCACCAACATTTGACAATCGAGAGAGGTGA-CCGTAATTGTTGACT
63709 CTAAGCAACT
Statistics
Matches: 197, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
148 60 0.30
149 137 0.70
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (148 bp):
ATTGTTGACTATTCTTCACCAACATTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTTT
CACCAACCTTTGACAATCGAGAGAGATGGCCATAATTGTTGACTATTCTTCACCAACCTTGACAA
TCGAGAGAGGTGACCGTA
Found at i:68847 original size:61 final size:61
Alignment explanation
Indices: 68772--68893 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
68762 GATCATGTAT
68772 ATATCATATTTTGTTTCTGTATGGATGCTGCTAGGTTAAATTATGTATGAAATTAACTACA
1 ATATCATATTTTGTTTCTGTATGGATGCTGCTAGGTTAAATTATGTATGAAATTAACTACA
68833 ATATCATATTTTGTTTCTGTATGGATGCTGCTAGGTTAAATTATGTATGAAATTAACTACA
1 ATATCATATTTTGTTTCTGTATGGATGCTGCTAGGTTAAATTATGTATGAAATTAACTACA
68894 GTAATTTGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (61 bp):
ATATCATATTTTGTTTCTGTATGGATGCTGCTAGGTTAAATTATGTATGAAATTAACTACA
Found at i:69847 original size:45 final size:45
Alignment explanation
Indices: 69780--69870 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
69770 CAACAAGCAA
* * *
69780 GCAGAAAATGTCACTGAGCTGAAGGTTTTTGAAGATCGAAAGCTT
1 GCAGAAAATGTCACTGAACTGAAGGCTTTTGAAGATCAAAAGCTT
69825 GCAGAAAATGTCACTGAACTGAAGGCTTTTGAAGATCAAAAGCTT
1 GCAGAAAATGTCACTGAACTGAAGGCTTTTGAAGATCAAAAGCTT
69870 G
1 G
69871 GGGAGTTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (45 bp):
GCAGAAAATGTCACTGAACTGAAGGCTTTTGAAGATCAAAAGCTT
Found at i:71493 original size:30 final size:30
Alignment explanation
Indices: 71457--71527 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
71447 TTTAGGACAT
71457 AGCACATTGGACTCTTAGTGCAGCTACTCC
1 AGCACATTGGACTCTTAGTGCAGCTACTCC
71487 AGCACATTGGACTCTTAGTGCAGCTACTCC
1 AGCACATTGGACTCTTAGTGCAGCTACTCC
71517 AGCACATTGGA
1 AGCACATTGGA
71528 ATTGCCTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (30 bp):
AGCACATTGGACTCTTAGTGCAGCTACTCC
Found at i:75904 original size:13 final size:15
Alignment explanation
Indices: 75886--75917 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
75876 AATATAAATT
75886 TTTATATTA-AT-AA
1 TTTATATTATATAAA
75899 TTTATATTATATAAA
1 TTTATATTATATAAA
75914 TTTA
1 TTTA
75918 AAATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:75971 original size:23 final size:25
Alignment explanation
Indices: 75930--75975 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
75920 ATATTTATAT
75930 ATAAAATATTTATACTATTTTTTAG
1 ATAAAATATTTATACTATTTTTTAG
*
75955 ATAATATATTT-TA-TATTTTTT
1 ATAAAATATTTATACTATTTTTT
75976 TAATTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
ATAAAATATTTATACTATTTTTTAG
Found at i:76771 original size:14 final size:15
Alignment explanation
Indices: 76747--76775 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
76737 TTTATAAAAG
76747 TTTATATTTTATTAA
1 TTTATATTTTATTAA
76762 TTTA-ATTTTATTAA
1 TTTATATTTTATTAA
76776 AATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATATTTTATTAA
Found at i:77255 original size:3 final size:3
Alignment explanation
Indices: 77249--77288 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
77239 CCACCAAGTT
77249 TTG TTG TTG TTG -TG TTG TTG TTG TTG TTG TTG -TG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
77289 CCTTGTGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:77271 original size:17 final size:17
Alignment explanation
Indices: 77249--77288 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
77239 CCACCAAGTT
77249 TTGTTGTTGTTG-TGTTG
1 TTGTTGTTGTTGTTG-TG
77266 TTGTTGTTGTTGTTGTG
1 TTGTTGTTGTTGTTGTG
77283 TTGTTG
1 TTGTTG
77289 CCTTGTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (17 bp):
TTGTTGTTGTTGTTGTG
Found at i:77274 original size:20 final size:20
Alignment explanation
Indices: 77249--77288 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
77239 CCACCAAGTT
77249 TTGTTGTTGTTGTGTTGTTG
1 TTGTTGTTGTTGTGTTGTTG
77269 TTGTTGTTGTTGTGTTGTTG
1 TTGTTGTTGTTGTGTTGTTG
77289 CCTTGTGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (20 bp):
TTGTTGTTGTTGTGTTGTTG
Done.