Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1422
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: 293460
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 1 of 3
Found at i:658 original size:13 final size:14
Alignment explanation
Indices: 640--668 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
630 AAATTTTTGA
640 TATATT-AATAATT
1 TATATTAAATAATT
653 TATATTAAATAATT
1 TATATTAAATAATT
667 TA
1 TA
669 CATATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTAAATAATT
Found at i:695 original size:22 final size:21
Alignment explanation
Indices: 670--721 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
660 AATAATTTAC
*
670 ATATTTTTTATTATATT-ATTTT
1 ATATTTTTT-TTAT-TTCATCTT
692 ATATTATTTTTTATTTCATCTT
1 ATATT-TTTTTTATTTCATCTT
714 ATATTTTT
1 ATATTTTT
722 ATGTTCTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 18 0.67
23 4 0.15
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (21 bp):
ATATTTTTTTTATTTCATCTT
Found at i:739 original size:18 final size:18
Alignment explanation
Indices: 685--723 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
675 TTTTATTATA
* *
685 TTATTTTATATTAT-TTT
1 TTATTTCATCTTATATTT
702 TTATTTCATCTTATATTT
1 TTATTTCATCTTATATTT
720 TTAT
1 TTAT
724 GTTCTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTCATCTTATATTT
Found at i:748 original size:10 final size:11
Alignment explanation
Indices: 671--763 Score: 64
Period size: 12 Copynumber: 7.9 Consensus size: 11
661 ATAATTTACA
671 TATTTTTTATT
1 TATTTTTTATT
682 ATATTATTTTATAT
1 -TATT-TTTTAT-T
696 TATTTTTTATT
1 TATTTTTTATT
707 TCATCTTATATT-TT
1 T-AT-TT-T-TTATT
* *
721 TATGTTCTATT
1 TATTTTTTATT
*
732 TAATTTTT-TT
1 TATTTTTTATT
742 TATTTTTATATT
1 TATTTTT-TATT
*
754 TATCTTTTAT
1 TATTTTTTAT
764 AATCGTATCA
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
10 9 0.14
11 14 0.22
12 21 0.32
13 14 0.22
14 5 0.08
15 2 0.03
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:763 original size:13 final size:12
Alignment explanation
Indices: 670--764 Score: 55
Period size: 10 Copynumber: 8.2 Consensus size: 12
660 AATAATTTAC
670 ATATTT-TTTATT
1 ATATTTATTT-TT
682 ATA-TTA-TTTT
1 ATATTTATTTTT
692 ATA-TTATTTTT
1 ATATTTATTTTT
*
703 -TATTTCA-TCTT
1 ATATTT-ATTTTT
714 ATATTT-TTATGTT
1 ATATTTATT-T-TT
* *
727 CTATTTAATTTT
1 ATATTTATTTTT
739 -T-TTTATTTTT
1 ATATTTATTTTT
749 ATATTTATCTTTT
1 ATATTTAT-TTTT
762 ATA
1 ATA
765 ATCGTATCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 23
0.70 0.05 0.24
Matches are distributed among these distances:
10 18 0.27
11 16 0.24
12 16 0.24
13 15 0.23
14 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (12 bp):
ATATTTATTTTT
Found at i:4537 original size:12 final size:12
Alignment explanation
Indices: 4516--4550 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
4506 AAACATGATG
4516 TAAAATATAATA
1 TAAAATATAATA
*
4528 TAAAAAATAATA
1 TAAAATATAATA
4540 TAAAATATAAT
1 TAAAATATAAT
4551 TATATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:6777 original size:14 final size:15
Alignment explanation
Indices: 6749--6779 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6739 AACCTGTTTG
6749 AAGAAAAGAGAAAAT
1 AAGAAAAGAGAAAAT
6764 AAGAAAAG-GAAAAT
1 AAGAAAAGAGAAAAT
6778 AA
1 AA
6780 AGGTCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
AAGAAAAGAGAAAAT
Found at i:6987 original size:24 final size:22
Alignment explanation
Indices: 6959--7012 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
6949 ATTTATCAAT
6959 TTTAATTTAAATTAAAAAAATTAA
1 TTTAATTTAAA-T-AAAAAATTAA
*
6983 TTTAA-TTCAATAAAAAATTAA
1 TTTAATTTAAATAAAAAATTAA
7004 --TAATTTAAA
1 TTTAATTTAAA
7013 ATCAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 4 0.15
21 10 0.37
22 1 0.04
23 4 0.15
24 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAATTTAAATAAAAAATTAA
Found at i:7262 original size:18 final size:18
Alignment explanation
Indices: 7235--7274 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7225 TTATAATCAG
*
7235 AATTTTAAAATTAAAAAT
1 AATTTAAAAATTAAAAAT
* *
7253 AATTTAAAAATTTAAATT
1 AATTTAAAAATTAAAAAT
7271 AATT
1 AATT
7275 CAACTCGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTAAAAATTAAAAAT
Found at i:8543 original size:19 final size:17
Alignment explanation
Indices: 8519--8558 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
8509 TTTGCTTTAG
8519 ATTTAATTATTTAATATAT
1 ATTTAA-TATTT-ATATAT
*
8538 ATTTAATATTTTTATAT
1 ATTTAATATTTATATAT
8555 ATTT
1 ATTT
8559 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 5 0.25
19 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTAATATTTATATAT
Found at i:8551 original size:9 final size:9
Alignment explanation
Indices: 8528--8571 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
8518 GATTTAATTA
8528 TTTAATATAT
1 TTTAATAT-T
8538 ATTTAATATT
1 -TTTAATATT
8548 TTTATATATT
1 TTTA-ATATT
*
8558 TTTAAAATT
1 TTTAATATT
8567 TTTAA
1 TTTAA
8572 AAAATAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 13 0.42
10 10 0.32
11 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTAATATT
Found at i:8561 original size:19 final size:19
Alignment explanation
Indices: 8532--8570 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
8522 TAATTATTTA
*
8532 ATATATATTTAATATTTTT
1 ATATATATTTAAAATTTTT
*
8551 ATATATTTTTAAAATTTTT
1 ATATATATTTAAAATTTTT
8570 A
1 A
8571 AAAAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATATATTTAAAATTTTT
Found at i:9326 original size:23 final size:21
Alignment explanation
Indices: 9300--9342 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9290 TTTTTCCGTA
*
9300 TAAAATTTAAGTAGTTTTTTTAG
1 TAAAAATT-AGTA-TTTTTTTAG
9323 TAAAAATTAGTATTTTTTTA
1 TAAAAATTAGTATTTTTTTA
9343 AAATAAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
TAAAAATTAGTATTTTTTTAG
Found at i:9893 original size:3 final size:3
Alignment explanation
Indices: 9885--9913 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9875 ATCAACCATA
9885 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9914 ATATCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:13895 original size:30 final size:30
Alignment explanation
Indices: 13861--13917 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
13851 TTTTTTTTTT
13861 ATTTTGATCAATTCTATTTAATTTATCCTG
1 ATTTTGATCAATTCTATTTAATTTATCCTG
* * * *
13891 ATTTTGATTAATTTTGTTTATTTTATC
1 ATTTTGATCAATTCTATTTAATTTATC
13918 TAACTTAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.60
Consensus pattern (30 bp):
ATTTTGATCAATTCTATTTAATTTATCCTG
Found at i:16173 original size:25 final size:25
Alignment explanation
Indices: 16145--16238 Score: 66
Period size: 27 Copynumber: 3.6 Consensus size: 25
16135 TAATATAATT
16145 ATAAAATAAAAATATAATATAAAAA
1 ATAAAATAAAAATATAATATAAAAA
* *
16170 AT--AATTAAAATATAATATTTAAATA
1 ATAAAATAAAAATATAATA--TAAAAA
** *
16195 ATATCATAAAAATAATATATATAAAAT
1 ATAAAATAAAAAT-ATA-ATATAAAAA
* *
16222 ATGAATATATAAATATA
1 AT-AAAATAAAAATATA
16239 TCAAAATATA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
23 14 0.26
25 9 0.17
27 16 0.30
28 11 0.21
29 3 0.06
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (25 bp):
ATAAAATAAAAATATAATATAAAAA
Found at i:16184 original size:36 final size:38
Alignment explanation
Indices: 16144--16250 Score: 89
Period size: 39 Copynumber: 2.8 Consensus size: 38
16134 CTAATATAAT
16144 TATAAAATAAAAATATAATATAAAA-AATA-AT-TAAAA
1 TATAAAATAAAAATATAATA-AAAATAATATATATAAAA
* *
16180 TATAATATTTAAATAATATCATAAAAATAATATATATAAAA
1 TATAA-A-ATAAA-AATATAATAAAAATAATATATATAAAA
* * *
16221 TATGAATATATAAATAT-ATCAAAAT-ATATA
1 TAT-AAAATAAAAATATAATAAAAATAATATA
16251 AATTATTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
36 5 0.09
37 6 0.10
38 15 0.26
39 17 0.29
40 5 0.09
41 8 0.14
42 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.34
Consensus pattern (38 bp):
TATAAAATAAAAATATAATAAAAATAATATATATAAAA
Found at i:16221 original size:14 final size:14
Alignment explanation
Indices: 16155--16222 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
16145 ATAAAATAAA
16155 AATATAATATAAAA-
1 AATAT-ATATAAAAT
16169 AATA-AT-TAAAAT
1 AATATATATAAAAT
*
16181 -ATA-ATATTTAAAT
1 AATATATA-TAAAAT
16194 AATATCATA-AAAAT
1 AATAT-ATATAAAAT
16208 AATATATATAAAAT
1 AATATATATAAAAT
16222 A
1 A
16223 TGAATATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 10 0.22
12 2 0.04
13 8 0.18
14 22 0.49
16 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (14 bp):
AATATATATAAAAT
Found at i:16261 original size:16 final size:16
Alignment explanation
Indices: 16211--16272 Score: 51
Period size: 18 Copynumber: 4.0 Consensus size: 16
16201 TAAAAATAAT
* *
16211 ATATATAAAATA-TGA
1 ATATATAAATTATTAA
*
16226 ATATATAAATATATCAAA
1 ATATATAAAT-TAT-TAA
16244 ATATATAAATTATTAA
1 ATATATAAATTATTAA
16260 AT-T-TAAATT-TTAA
1 ATATATAAATTATTAA
16273 TCATTTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.10
14 6 0.15
15 10 0.25
16 6 0.15
17 3 0.08
18 11 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATATATAAATTATTAA
Found at i:17460 original size:29 final size:29
Alignment explanation
Indices: 17394--17460 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
17384 ATGAAAAATT
*
17394 AATTAAAATATGAAATAAAATATATGTAC
1 AATTAAAATATAAAATAAAATATATGTAC
17423 AA-TATAAATATAAAAT-AAATATATGAATA-
1 AATTA-AAATATAAAATAAAATATATG--TAC
17452 AATTAAAAT
1 AATTAAAAT
17461 TTATTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 11 0.33
29 18 0.55
30 4 0.12
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (29 bp):
AATTAAAATATAAAATAAAATATATGTAC
Found at i:17522 original size:13 final size:15
Alignment explanation
Indices: 17499--17536 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
17489 AAATTCAAAA
17499 AAAATATAATT-T-TT
1 AAAA-ATAATTATATT
17513 AAAAATAATTATATT
1 AAAAATAATTATATT
17528 AAAAATAAT
1 AAAAATAAT
17537 AAAAATATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
15 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAATAATTATATT
Found at i:17973 original size:24 final size:22
Alignment explanation
Indices: 17917--17981 Score: 78
Period size: 24 Copynumber: 2.9 Consensus size: 22
17907 TTTTTTAACT
*
17917 TTAAATTTTAATAAA-AAATTA
1 TTAAATTTTAAAAAATAAATTA
*
17938 TTAAATTATTAAAAAATAATATTT
1 TTAAATT-TTAAAAAATAA-ATTA
17962 TTAAAATTTTAAAAAATAAA
1 TT-AAATTTTAAAAAATAAA
17982 ATAAATAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.18
22 7 0.18
23 3 0.08
24 16 0.42
25 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAATTTTAAAAAATAAATTA
Found at i:18375 original size:19 final size:19
Alignment explanation
Indices: 18351--18390 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
18341 TAATATTAAA
18351 TATTTAAA-ATTTTAAAAAT
1 TATTTAAATA-TTTAAAAAT
*
18370 TATTTATATATTTAAAAAT
1 TATTTAAATATTTAAAAAT
18389 TA
1 TA
18391 AAAATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTAAATATTTAAAAAT
Found at i:18380 original size:27 final size:25
Alignment explanation
Indices: 18350--18410 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
18340 TTAATATTAA
* **
18350 ATATTTAAAATTTTAAAAATTATTTAT
1 ATATTTAAAA-ATTAAAAATTAAAT-T
18377 ATATTTAAAAATTAAAAATTAAATT
1 ATATTTAAAAATTAAAAATTAAATT
18402 ATATTTAAA
1 ATATTTAAA
18411 TAATCATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 10 0.32
26 11 0.35
27 10 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATTTAAAAATTAAAAATTAAATT
Found at i:18616 original size:26 final size:27
Alignment explanation
Indices: 18587--18656 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
18577 ATAAATTTAA
18587 TAATTTTTATATTTTTTATA-TTATAT
1 TAATTTTTATATTTTTTATATTTATAT
*
18613 TAATTTTAATATATTTTTATATTTATAT
1 TAATTTTTATAT-TTTTTATATTTATAT
**
18641 TTTTTTATTATATTTT
1 TAATTT-TTATATTTT
18657 ATGTTGTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 11 0.30
27 8 0.22
28 13 0.35
29 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TAATTTTTATATTTTTTATATTTATAT
Found at i:18619 original size:16 final size:14
Alignment explanation
Indices: 18593--18656 Score: 73
Period size: 14 Copynumber: 4.6 Consensus size: 14
18583 TTAATAATTT
18593 TTATATTTTTTATA
1 TTATATTTTTTATA
18607 TTATATTAATTTTA-A
1 TTATATT--TTTTATA
18622 -TATA-TTTTTATA
1 TTATATTTTTTATA
18634 TTTATATTTTTT-TA
1 -TTATATTTTTTATA
18648 TTATATTTT
1 TTATATTTT
18657 ATGTTGTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
11 5 0.11
12 1 0.02
13 10 0.23
14 17 0.39
15 6 0.14
16 5 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATATTTTTTATA
Found at i:18629 original size:27 final size:28
Alignment explanation
Indices: 18587--18656 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
18577 ATAAATTTAA
*
18587 TAATTTTTATAT-TTTTTATA-TTATAT
1 TAATTTTAATATATTTTTATATTTATAT
18613 TAATTTTAATATATTTTTATATTTATAT
1 TAATTTTAATATATTTTTATATTTATAT
* *
18641 T-TTTTTATTATATTTT
1 TAATTTTAATATATTTT
18657 ATGTTGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 11 0.28
27 21 0.54
28 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (28 bp):
TAATTTTAATATATTTTTATATTTATAT
Found at i:22654 original size:2 final size:2
Alignment explanation
Indices: 22647--22679 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22637 GATTGAACAG
22647 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 A
22680 CACACATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23019 original size:16 final size:15
Alignment explanation
Indices: 22998--23031 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
22988 TTGATTGTAA
22998 AATATAAATATGTATT
1 AATATAAATATGT-TT
23014 AATATAAATATGTTT
1 AATATAAATATGTTT
23029 AAT
1 AAT
23032 TTTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (15 bp):
AATATAAATATGTTT
Found at i:23062 original size:12 final size:11
Alignment explanation
Indices: 23036--23060 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23026 TTTAATTTTT
23036 AAATTTTAAAA
1 AAATTTTAAAA
23047 AAATTTTAAAA
1 AAATTTTAAAA
23058 AAA
1 AAA
23061 ATCGTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTTTAAAA
Found at i:23718 original size:22 final size:22
Alignment explanation
Indices: 23684--23735 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
23674 GTGTTAGGTG
* * *
23684 GTGTGCTAGGTAAACGTATTAA
1 GTGTGTTAAGTAAACATATTAA
* *
23706 GTGTGTTAAGTAAATATATTAG
1 GTGTGTTAAGTAAACATATTAA
23728 GTGTGTTA
1 GTGTGTTA
23736 GATAAACTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (22 bp):
GTGTGTTAAGTAAACATATTAA
Found at i:28307 original size:22 final size:24
Alignment explanation
Indices: 28281--28345 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
28271 TTAATATCTT
28281 TATTAAGTGTGTTAGGT-A-AATA
1 TATTAAGTGTGTTAGGTGAGAATA
* * *
28303 TATTATGTATTTTAGGTGAGTAATA
1 TATTAAGTGTGTTAGGTGAG-AATA
28328 TATTAAGTGTGTTAGGTG
1 TATTAAGTGTGTTAGGTG
28346 GTGTGTTAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 14 0.41
23 1 0.03
25 19 0.56
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.45
Consensus pattern (24 bp):
TATTAAGTGTGTTAGGTGAGAATA
Found at i:28595 original size:17 final size:18
Alignment explanation
Indices: 28569--28602 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28559 CGCATTCAAA
*
28569 ATTTATATAT-GATATAT
1 ATTTAAATATAGATATAT
28586 ATTTAAATATAGATATA
1 ATTTAAATATAGATATA
28603 AAATATGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
ATTTAAATATAGATATAT
Found at i:29080 original size:19 final size:18
Alignment explanation
Indices: 29038--29080 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
29028 ATATTATCTT
* *
29038 TTAAAATTTTTTAAAATA
1 TTAAAATTTTTGAAAAAA
29056 TATAAAATTTTTGAAATAAA
1 T-TAAAATTTTTGAAA-AAA
29076 TTAAA
1 TTAAA
29081 CATATTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.81
20 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAAAATTTTTGAAAAAA
Found at i:29655 original size:32 final size:31
Alignment explanation
Indices: 29619--29701 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
29609 TACGTAATAT
* *
29619 AATTATATGTTATAAATATATAAAAATATTAA
1 AATTATAT-ATATAAATATATAAAAATATAAA
* *
29651 AATTATATAATATAAAT-TATTAATATATAAA
1 AATTATAT-ATATAAATATATAAAAATATAAA
29682 AATT-TATATA-AAATATATAA
1 AATTATATATATAAATATATAA
29702 TATTTTAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.09
29 7 0.16
30 3 0.07
31 15 0.34
32 15 0.34
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (31 bp):
AATTATATATATAAATATATAAAAATATAAA
Found at i:29676 original size:13 final size:14
Alignment explanation
Indices: 29613--29704 Score: 55
Period size: 14 Copynumber: 6.4 Consensus size: 14
29603 GATATTTACG
29613 TAATAT-AATTATA
1 TAATATAAATTATA
**
29626 TGTTATAAATATATAA
1 TAATATAAAT-TAT-A
*
29642 AAATATTAAAATTATA
1 TAATA-T-AAATTATA
29658 TAATATAAATTAT-
1 TAATATAAATTATA
**
29671 TAATATATAAAAAT-
1 TAATATA-AATTATA
* *
29685 TTATATAAAATATA
1 TAATATAAATTATA
29699 TAATAT
1 TAATAT
29705 TTTAAATATA
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
13 16 0.26
14 25 0.41
15 4 0.07
16 8 0.13
17 4 0.07
18 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (14 bp):
TAATATAAATTATA
Found at i:29683 original size:39 final size:40
Alignment explanation
Indices: 29628--29704 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
29618 TAATTATATG
29628 TTATAAATATATAAAAA-TAT-TAAAATTATATAATATAAA
1 TTATAAATATATAAAAATTATATAAAA-TATATAATATAAA
*
29667 TTATTAATATATAAAAATTTATATAAAATATATAATAT
1 TTATAAATATATAAAAA-TTATATAAAATATATAATAT
29705 TTTAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
39 16 0.47
41 13 0.38
42 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (40 bp):
TTATAAATATATAAAAATTATATAAAATATATAATATAAA
Found at i:29708 original size:21 final size:21
Alignment explanation
Indices: 29672--29723 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
29662 ATAAATTATT
*
29672 AATATATAAAAATTTATATAA
1 AATATATAAAAATTTAAATAA
* * *
29693 AATATATAATATTTTAAATAT
1 AATATATAAAAATTTAAATAA
29714 AAT-TATAAAA
1 AATATATAAAA
29724 TAAAAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATATAAAAATTTAAATAA
Found at i:34197 original size:21 final size:19
Alignment explanation
Indices: 34154--34198 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
34144 ATTAAATTTT
34154 TTAAAAAAATTAAAATAAA
1 TTAAAAAAATTAAAATAAA
* *
34173 TTAAAATAAATTGAATATGAA
1 TTAAAA-AAATT-AAAATAAA
34194 TTAAA
1 TTAAA
34199 TATGTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 5 0.23
21 11 0.50
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
TTAAAAAAATTAAAATAAA
Found at i:34202 original size:11 final size:10
Alignment explanation
Indices: 34154--34198 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
34144 ATTAAATTTT
34154 TTAAAA-AAA
1 TTAAAATAAA
34163 TTAAAATAAA
1 TTAAAATAAA
34173 TTAAAATAAA
1 TTAAAATAAA
* *
34183 TTGAATATGAA
1 TT-AAAATAAA
34194 TTAAA
1 TTAAA
34199 TATGTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 6 0.19
10 17 0.55
11 8 0.26
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (10 bp):
TTAAAATAAA
Found at i:39782 original size:2 final size:2
Alignment explanation
Indices: 39769--39801 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
39759 AACAATTTTA
*
39769 AT AT AC 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 A
39802 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:39806 original size:2 final size:2
Alignment explanation
Indices: 39801--39826 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39791 ATATATATAT
39801 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
39827 GGGATGAATT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39956 original size:28 final size:29
Alignment explanation
Indices: 39902--39978 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
39892 TGAATAAATT
* *
39902 AAAAATATTTAATTATTTATTAAATATAA
1 AAAAATATTTAATTATTAAATAAATATAA
* *
39931 AAAAAT-TTTAATTGTTAAATATATATTAA
1 AAAAATATTTAATTATTAAATAAATA-TAA
*
39960 AAATAATATTT-TTTATTAA
1 AAA-AATATTTAATTATTAA
39979 TATGATAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 15 0.38
29 12 0.31
30 9 0.23
31 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAAATATTTAATTATTAAATAAATATAA
Found at i:40089 original size:19 final size:19
Alignment explanation
Indices: 40030--40089 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
40020 TTTTTAAAGA
*
40030 TTAATT-TAT-TAAAATA-
1 TTAATTATATATAAATTAT
40046 TTAATTATATATAAATTAT
1 TTAATTATATATAAATTAT
**
40065 AAAATTATATA-AAATTAAT
1 TTAATTATATATAAATT-AT
40084 TTAATT
1 TTAATT
40090 TTATTCTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.17
17 3 0.09
18 11 0.31
19 15 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATTATATATAAATTAT
Found at i:40489 original size:30 final size:30
Alignment explanation
Indices: 40451--40507 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
40441 TAAAGTTTGA
* * *
40451 AATATATATTTGTATCGTATT-ATGTATTT
1 AATATATATATATATCATATTCATGTATTT
40480 AATATTATATATATATCATATTCATGTA
1 AATA-TATATATATATCATATTCATGTA
40508 AATATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.17
30 14 0.61
31 5 0.22
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (30 bp):
AATATATATATATATCATATTCATGTATTT
Found at i:40934 original size:96 final size:97
Alignment explanation
Indices: 40769--40960 Score: 280
Period size: 96 Copynumber: 2.0 Consensus size: 97
40759 GTATAGGAAG
* ** *
40769 GAGGGATTAAAGGGTGTCGAATTTTGATTTTTTTTTATGCATTATAATGCTTAAGTCAATGAAAG
1 GAGGGATTAAAGGGTGTCGAATTTCGATTTTTTTGGATGCATTATAATGCTTAAGTCAATAAAAG
* *
40834 AGATAATGTTATATGTCGTCAATTTATTGAAA
66 AGATAATGTTATATGTCATAAATTTATTGAAA
* *
40866 GAGGGATTAGAGGGTGTCGGATTTCGA-TTTTTTGGATG-AGTTATAATGCTTAAGTCAATAAAA
1 GAGGGATTAAAGGGTGTCGAATTTCGATTTTTTTGGATGCA-TTATAATGCTTAAGTCAATAAAA
*
40929 GAGATAATGTTATATGTCATAAATTTGTTGAA
65 GAGATAATGTTATATGTCATAAATTTATTGAA
40961 GTTTAATGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 1 0.01
96 60 0.71
97 24 0.28
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (97 bp):
GAGGGATTAAAGGGTGTCGAATTTCGATTTTTTTGGATGCATTATAATGCTTAAGTCAATAAAAG
AGATAATGTTATATGTCATAAATTTATTGAAA
Found at i:43831 original size:66 final size:65
Alignment explanation
Indices: 43725--43864 Score: 244
Period size: 66 Copynumber: 2.1 Consensus size: 65
43715 GAAAGCATAA
*
43725 AGATAAAAATAAATTTTACCTTAGTTATCTATTTTGAAAATATAATGGTATAATTCTATAACAAA
1 AGATAAAAATAAATTTTACCTTAGTTATCTATCTTGAAAATA-AATGGTATAATTCTATAACAAA
*
43790 G
65 C
43791 AGATAAAAATAAATTTTACCTTAGTTATCTATCTTGAAAATAAATGGTATAATTCTATAACAAAC
1 AGATAAAAATAAATTTTACCTTAGTTATCTATCTTGAAAATAAATGGTATAATTCTATAACAAAC
43856 AGAATAAAA
1 AG-ATAAAA
43865 CCTTAAAGTA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
65 24 0.34
66 47 0.66
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (65 bp):
AGATAAAAATAAATTTTACCTTAGTTATCTATCTTGAAAATAAATGGTATAATTCTATAACAAAC
Found at i:44218 original size:16 final size:18
Alignment explanation
Indices: 44193--44229 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
44183 AATGGTGATA
44193 TTTTACATTAATTA-AAT
1 TTTTACATTAATTATAAT
*
44210 TTTTA-ATTACTTATAAT
1 TTTTACATTAATTATAAT
44227 TTT
1 TTT
44230 ATATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTACATTAATTATAAT
Found at i:46058 original size:30 final size:28
Alignment explanation
Indices: 45993--46063 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
45983 ATAAATTTTC
*
45993 ATTTATATTCAT-TT-ATTTATTTTTAA
1 ATTTATATTCATATTCATTTAATTTTAA
46019 ATTTA-ATTCATATTCATTAATAATTTTAA
1 ATTTATATTCATATTCATT--TAATTTTAA
46048 ATTTATATTCATATTC
1 ATTTATATTCATATTC
46064 GTATATTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 6 0.15
26 7 0.18
27 3 0.08
29 13 0.33
30 10 0.26
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTATATTCATATTCATTTAATTTTAA
Found at i:46228 original size:83 final size:86
Alignment explanation
Indices: 46094--46249 Score: 239
Period size: 83 Copynumber: 1.8 Consensus size: 86
46084 GTTTATATTT
* *
46094 ATTATTTTTTTCTTTTCACTTTTCTTTCTTTTCCACCAAACACACTAATAAAAATAAAAAATATA
1 ATTATTTTTTTCTTTTCACTTTTCTTTCTTTTCCACCAAACACACCAATAAAAAGAAAAAATATA
46159 TTTTTTATTAGTTGAAAGAAA
66 TTTTTTATTAGTTGAAAGAAA
* *
46180 ATTA-TTTTTTCTTTTCAC-TTT-TTTC-TTTCCTACCAAGCGCACCAATAAAAAGAAAAAATAT
1 ATTATTTTTTTCTTTTCACTTTTCTTTCTTTTCC-ACCAAACACACCAATAAAAAGAAAAAATAT
46241 ATTTTTTAT
65 ATTTTTTAT
46250 CTTTCAACTT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
82 5 0.08
83 39 0.60
84 3 0.05
85 14 0.22
86 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (86 bp):
ATTATTTTTTTCTTTTCACTTTTCTTTCTTTTCCACCAAACACACCAATAAAAAGAAAAAATATA
TTTTTTATTAGTTGAAAGAAA
Found at i:46406 original size:33 final size:32
Alignment explanation
Indices: 46369--46430 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
46359 GAATAATTAA
* *
46369 AAATATATTTATAAAAAATAAATAAATAAATCT
1 AAATAAATTTA-AAAAAATAAACAAATAAATCT
* *
46402 AAATAAATTTAAACAAATTAACAAATAAA
1 AAATAAATTTAAAAAAATAAACAAATAAA
46431 CAAGTATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 15 0.60
33 10 0.40
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (32 bp):
AAATAAATTTAAAAAAATAAACAAATAAATCT
Found at i:46471 original size:15 final size:16
Alignment explanation
Indices: 46451--46480 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46441 TTTTAGTTTT
46451 AAATATAAA-ATAATA
1 AAATATAAATATAATA
46466 AAATATAAATATAAT
1 AAATATAAATATAAT
46481 TAATTACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATAAATATAATA
Found at i:46609 original size:26 final size:28
Alignment explanation
Indices: 46580--46631 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
46570 TAAATAATTC
*
46580 ATAAAT-AAATTTATT-TATTAATATAA
1 ATAAATCAAATATATTATATTAATATAA
*
46606 ATAAATCAAATATATTATATTCATAT
1 ATAAATCAAATATATTATATTAATAT
46632 TCTATTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 8 0.36
28 8 0.36
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
ATAAATCAAATATATTATATTAATATAA
Found at i:46941 original size:6 final size:6
Alignment explanation
Indices: 46930--46954 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
46920 GTCTTTTTTA
46930 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
46955 CATTGTTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:47121 original size:7 final size:7
Alignment explanation
Indices: 47109--47135 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
47099 GAAAGTGAAT
47109 GAGAGAG
1 GAGAGAG
47116 GAGAGAG
1 GAGAGAG
47123 GAGAGAG
1 GAGAGAG
47130 GAGAGA
1 GAGAGA
47136 CAGGAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GAGAGAG
Found at i:48002 original size:3 final size:3
Alignment explanation
Indices: 47996--48028 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
47986 CTACTACTAC
47996 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48029 CTAGAATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48282 original size:9 final size:9
Alignment explanation
Indices: 48270--48317 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
48260 AATAACATAC
*
48270 ATAAAAATT
1 ATAAAAATA
*
48279 ATAATAATA
1 ATAAAAATA
48288 AT-AAAATA
1 ATAAAAATA
*
48296 ATAATAATA
1 ATAAAAATA
*
48305 ATAATAATA
1 ATAAAAATA
48314 ATAA
1 ATAA
48318 CCCATATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
ATAAAAATA
Found at i:48287 original size:3 final size:3
Alignment explanation
Indices: 48279--48317 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
48269 CATAAAAATT
48279 ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
48318 CCCATATTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:48767 original size:12 final size:10
Alignment explanation
Indices: 48736--48766 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
48726 TATTTAATTA
48736 ATATAATTTT
1 ATATAATTTT
48746 ATATAATTTT
1 ATATAATTTT
48756 ATATAAATTTT
1 ATAT-AATTTT
48767 TCGTATGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATATAATTTT
Found at i:49046 original size:16 final size:16
Alignment explanation
Indices: 48987--49074 Score: 65
Period size: 16 Copynumber: 5.2 Consensus size: 16
48977 TTATAATATT
*
48987 AAATATACTATAATTA
1 AAATATAATATAATTA
*
49003 TATAATATTAAAAATAATTA
1 -A-AATA-T-AATATAATTA
49023 AAATATAATATAATATA
1 AAATATAATATAAT-TA
49040 AAA-ATAATATATATT-
1 AAATATAATATA-ATTA
*
49055 TAATATAA-ATATATTA
1 AAATATAATATA-ATTA
49071 AAAT
1 AAAT
49075 TTTAAAATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
15 9 0.15
16 23 0.39
17 9 0.15
18 8 0.14
19 2 0.03
20 8 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATAATATAATTA
Found at i:49053 original size:25 final size:26
Alignment explanation
Indices: 48978--49062 Score: 84
Period size: 25 Copynumber: 3.2 Consensus size: 26
48968 TGGTACCGTT
* * *
48978 TATAATATTAAATATACTATA-ATTA
1 TATAATATTAAAAATAATATATATAA
*
49003 TATAATATTAAAAATAATTAAAATATAA
1 TATAATATTAAAAATAA-T-ATATATAA
49031 TATAATA-TAAAAATAATATATATTTAA
1 TATAATATTAAAAATAATATATA--TAA
49058 TATAA
1 TATAA
49063 ATATATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 19 0.38
26 2 0.04
27 19 0.38
28 10 0.20
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (26 bp):
TATAATATTAAAAATAATATATATAA
Found at i:49646 original size:17 final size:17
Alignment explanation
Indices: 49596--49657 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
49586 GATTATAATG
*
49596 ATTTAATTTAAATTATT-
1 ATTTAATTTTAATT-TTA
*
49613 ATTTAATAATTAA-TTTA
1 ATTTAAT-TTTAATTTTA
49630 ATTTAATTTTAATTTTA
1 ATTTAATTTTAATTTTA
*
49647 A-ATAATTTTAA
1 ATTTAATTTTAA
49658 AAAGTTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 15 0.39
17 20 0.53
18 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAATTTTAATTTTA
Found at i:49646 original size:29 final size:30
Alignment explanation
Indices: 49596--49653 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
49586 GATTATAATG
49596 ATTTAATTTAAATTATTATTT-AATAATTA
1 ATTTAATTTAAATTATTATTTAAATAATTA
49625 ATTTAATTT-AATT-TTAATTTTAAATAATT
1 ATTTAATTTAAATTATT-A-TTTAAATAATT
49654 TTAAAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.08
28 5 0.19
29 12 0.46
30 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTTAATTTAAATTATTATTTAAATAATTA
Found at i:50973 original size:18 final size:18
Alignment explanation
Indices: 50952--50997 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
50942 TTTGATATTT
*
50952 AAATTAATAAAAAAATAA
1 AAATAAATAAAAAAATAA
*
50970 AAATAAATAACAAAATAA
1 AAATAAATAAAAAAATAA
*
50988 TAA-AAATAAA
1 AAATAAATAAA
50998 GATTTAAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (18 bp):
AAATAAATAAAAAAATAA
Found at i:51423 original size:18 final size:18
Alignment explanation
Indices: 51379--51426 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
51369 TTTTCATTAA
51379 ATAA-TAAAATTATTTTT
1 ATAATTAAAATTATTTTT
*
51396 AT-GTTAAAAATTATTTTT
1 ATAATT-AAAATTATTTTT
51414 ATAATTAAAATTA
1 ATAATTAAAATTA
51427 AAAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.12
18 21 0.81
19 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATAATTAAAATTATTTTT
Found at i:52763 original size:19 final size:18
Alignment explanation
Indices: 52739--52787 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
52729 TATTAGATAG
52739 TTTATATATTCATATCATA
1 TTTATATATT-ATATCATA
*
52758 TTTATATATTTTATCATA
1 TTTATATATTATATCATA
52776 -TTATA-ATTATAT
1 TTTATATATTATAT
52788 TTAATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 6 0.21
17 5 0.18
18 7 0.25
19 10 0.36
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATATATTATATCATA
Found at i:52787 original size:29 final size:29
Alignment explanation
Indices: 52721--52799 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
52711 ATAGTACCTT
* * *
52721 TAATTGTATATTAGATAGTTTATATATTCA
1 TAATTATAT-TTATATATTTTATATATTCA
*
52751 T-ATCATATTTATATATTTTATCATATT-A
1 TAATTATATTTATATATTTTAT-ATATTCA
*
52779 TAATTATATTTAATAAATTTT
1 TAATTATATTT-ATATATTTT
52800 TTTAATAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
28 13 0.32
29 18 0.45
30 9 0.22
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
TAATTATATTTATATATTTTATATATTCA
Found at i:52935 original size:14 final size:14
Alignment explanation
Indices: 52918--52983 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 14
52908 TTTGTAATTT
52918 TAAATATAATTATA
1 TAAATATAATTATA
*
52932 TAAATATAATACATA
1 TAAATATAAT-TATA
52947 TAAAATATTTAA-TATA
1 T-AAATA--TAATTATA
*
52963 TAATATATCATTATA
1 TAA-ATATAATTATA
52978 TAAATA
1 TAAATA
52984 CATATTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 15 0.35
15 13 0.30
16 12 0.28
18 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:53431 original size:13 final size:13
Alignment explanation
Indices: 53413--53449 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
53403 TAGTTATAAA
53413 ATAAATAAATATT
1 ATAAATAAATATT
53426 ATAAAT-AATGATT
1 ATAAATAAAT-ATT
53439 A-AAATAAATAT
1 ATAAATAAATAT
53450 ATATTTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
ATAAATAAATATT
Found at i:53586 original size:20 final size:20
Alignment explanation
Indices: 53561--53599 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
53551 CGGTTGCATT
53561 TAAAAATTTAGATTTAAAAG
1 TAAAAATTTAGATTTAAAAG
53581 TAAAAATTTAGATTTAAAA
1 TAAAAATTTAGATTTAAAA
53600 AATAATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAAAATTTAGATTTAAAAG
Found at i:59192 original size:17 final size:17
Alignment explanation
Indices: 59170--59203 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59160 AATGCTATGC
59170 GATATAGTATCATTGCT
1 GATATAGTATCATTGCT
59187 GATATAGTATCATTGCT
1 GATATAGTATCATTGCT
59204 ATGGAGTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
GATATAGTATCATTGCT
Found at i:60553 original size:29 final size:30
Alignment explanation
Indices: 60492--60551 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
60482 TTGGATGAAA
* *
60492 TTAGTAATTTAATTTAATTTTATTTATTTT
1 TTAGTAATTTAATTTAATGTTATTGATTTT
*
60522 TTAGT-ATTTATTTTAATGTT-TTGATTTT
1 TTAGTAATTTAATTTAATGTTATTGATTTT
60550 TT
1 TT
60552 TATTAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 9 0.33
29 13 0.48
30 5 0.19
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (30 bp):
TTAGTAATTTAATTTAATGTTATTGATTTT
Found at i:62132 original size:21 final size:21
Alignment explanation
Indices: 62063--62119 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
62053 GAAAATGTGT
62063 ATTTTTTGAATGAAAGAATGC
1 ATTTTTTGAATGAAAGAATGC
62084 ATTTTTTGAATGAAAGAATGC
1 ATTTTTTGAATGAAAGAATGC
62105 ATTTTTTGAATGAAA
1 ATTTTTTGAATGAAA
62120 AAATTCAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.40
Consensus pattern (21 bp):
ATTTTTTGAATGAAAGAATGC
Found at i:66626 original size:21 final size:21
Alignment explanation
Indices: 66587--66626 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
66577 AAAAGTATAA
* *
66587 TTGGATAAAATGATGTATTAG
1 TTGGATAAAATAATATATTAG
*
66608 TTGGATGAAATAATATATT
1 TTGGATAAAATAATATATT
66627 TTTTGTACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (21 bp):
TTGGATAAAATAATATATTAG
Found at i:69904 original size:31 final size:31
Alignment explanation
Indices: 69882--69948 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
69872 CAAGTAGCTC
*
69882 TACTATCAAAAAGTATTATGCCAACTAACAT
1 TACTACCAAAAAGTATTATGCCAACTAACAT
* * *
69913 TACTACCAAAAAGTGTTGTGCCAAATAACAT
1 TACTACCAAAAAGTATTATGCCAACTAACAT
69944 TACTA
1 TACTA
69949 AAAGTAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.28
Consensus pattern (31 bp):
TACTACCAAAAAGTATTATGCCAACTAACAT
Found at i:72117 original size:20 final size:21
Alignment explanation
Indices: 72094--72133 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
72084 ATACTTTTAA
72094 TTAAA-AATAAATAAAAATTG
1 TTAAATAATAAATAAAAATTG
* *
72114 TTAAATATTAATTAAAAATT
1 TTAAATAATAAATAAAAATT
72134 ATATAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
TTAAATAATAAATAAAAATTG
Found at i:72983 original size:20 final size:20
Alignment explanation
Indices: 72946--73014 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 20
72936 ATTCAAAATT
*
72946 TTATATTTTTATAA-ATAAAA
1 TTATATTATTA-AATATAAAA
*
72966 TTATATTATTAAATATAACTA
1 TTATATTATTAAATATAA-AA
72987 TTA-ATTTATTAATCATATAAAAA
1 TTATA-TTATTAA--ATAT-AAAA
73010 TTATA
1 TTATA
73015 AAATATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.05
20 15 0.38
21 11 0.28
23 8 0.21
24 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATATTATTAAATATAAAA
Found at i:73258 original size:2 final size:2
Alignment explanation
Indices: 73240--73287 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
73230 GGTGGTACAG
* *
73240 TA TA TA -A TA TT TT 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 TA TA TA TA TA TA
73281 TGA TA TA
1 T-A TA TA
73288 ATTATAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73419 original size:22 final size:22
Alignment explanation
Indices: 73392--73444 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
73382 ATTAAAATTT
*
73392 ATATAAATATAAAATATTTTAA
1 ATATAAATATAAAATATTATAA
*
73414 ATAT-AAT-TATAATATTATAA
1 ATATAAATATAAAATATTATAA
73434 A-A-AAATATAAA
1 ATATAAATATAAA
73445 TACAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.15
20 15 0.58
21 3 0.12
22 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATAAATATAAAATATTATAA
Found at i:73643 original size:2 final size:2
Alignment explanation
Indices: 73638--73668 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
73628 ATTTTTTCCT
*
73638 TA TA TA TA TA TT 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
73669 GTGTGTGTAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:77293 original size:77 final size:78
Alignment explanation
Indices: 77206--77364 Score: 302
Period size: 77 Copynumber: 2.1 Consensus size: 78
77196 GACTTCAGAG
*
77206 TTTATACTTAAAATTATATTTTAATATTTAAATCAATCAAAAATTTT-TAAAAAATAATAAAATA
1 TTTATACTTAAAATTATATTTTAATATTTAAATCAATCAAAAATTTTAAAAAAAATAATAAAATA
77270 ATGAAAATAAAGA
66 ATGAAAATAAAGA
77283 TTTATACTTAAAATTATATTTTAATATTTAAATCAATCAAAAATTTTAAAAAAAATAATAAAATA
1 TTTATACTTAAAATTATATTTTAATATTTAAATCAATCAAAAATTTTAAAAAAAATAATAAAATA
77348 ATGAAAATAAAGA
66 ATGAAAATAAAGA
77361 TTTA
1 TTTA
77365 AGATGAGTTT
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
77 47 0.59
78 33 0.41
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (78 bp):
TTTATACTTAAAATTATATTTTAATATTTAAATCAATCAAAAATTTTAAAAAAAATAATAAAATA
ATGAAAATAAAGA
Found at i:77646 original size:6 final size:6
Alignment explanation
Indices: 77635--77688 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
77625 TTCTCACAAC
* *
77635 AAAAAT AAAAAT AAAAAT AAAAAC AAAAAT AAACAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
77683 AAAAAT
1 AAAAAT
77689 TCGCGTCACT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:77833 original size:22 final size:21
Alignment explanation
Indices: 77806--77847 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
77796 AATATTAAAC
77806 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
77826 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
77847 A
1 A
77848 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:78054 original size:17 final size:17
Alignment explanation
Indices: 78034--78067 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
78024 ATATATATAT
78034 ATTATATTTATATTTTA
1 ATTATATTTATATTTTA
*
78051 ATTATTTTTATATTTTA
1 ATTATATTTATATTTTA
78068 TTCATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTATATTTATATTTTA
Found at i:78253 original size:19 final size:19
Alignment explanation
Indices: 78225--78264 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
78215 ATTAACTAAT
*
78225 AAAATTATTTTA-ATATTAA
1 AAAATAATTTTATA-ATTAA
78244 AAAATAATTTTATAATTAA
1 AAAATAATTTTATAATTAA
78263 AA
1 AA
78265 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAATTTTATAATTAA
Found at i:78256 original size:24 final size:24
Alignment explanation
Indices: 78199--78271 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
78189 TAAAATATTT
* **
78199 ATAAATTTATTTTTATATTAACTA
1 ATAAATTTATTTTAATATTAAAAA
*
78223 ATAAAATTATTTTAATATTAAAAA
1 ATAAATTTATTTTAATATTAAAAA
* * *
78247 ATAATTTTATAATTAAAATTAAAAA
1 ATAAATTTAT-TTTAATATTAAAAA
78272 TATTATTTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 28 0.70
25 12 0.30
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAAATTTATTTTAATATTAAAAA
Found at i:80636 original size:20 final size:22
Alignment explanation
Indices: 80611--80654 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
80601 ATTATTTAAA
80611 AATATTTA-AAATTTTATA-TT
1 AATATTTATAAATTTTATAGTT
*
80631 AATATTTATATATTTTATAGTT
1 AATATTTATAAATTTTATAGTT
80653 AA
1 AA
80655 GTTTAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATATTTATAAATTTTATAGTT
Found at i:84768 original size:18 final size:18
Alignment explanation
Indices: 84745--84780 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
84735 AAATGTAAAG
84745 TCAATTTTAATTAGAATA
1 TCAATTTTAATTAGAATA
*
84763 TCAATTTTCATTAGAATA
1 TCAATTTTAATTAGAATA
84781 ATGGCTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
TCAATTTTAATTAGAATA
Found at i:86516 original size:18 final size:17
Alignment explanation
Indices: 86489--86523 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
86479 TTAATATATT
86489 AAAAATTTTACAAATAA
1 AAAAATTTTACAAATAA
*
86506 AAAATATTTTACATATAA
1 AAAA-ATTTTACAAATAA
86524 TTATGACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATTTTACAAATAA
Found at i:86655 original size:11 final size:11
Alignment explanation
Indices: 86617--86663 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
86607 ATAAACTGTT
86617 TTAATTAAAAA
1 TTAATTAAAAA
* * *
86628 ATAAATAAATA
1 TTAATTAAAAA
*
86639 TT-ATTAAACA
1 TTAATTAAAAA
86649 TTAATTAAAAA
1 TTAATTAAAAA
86660 TTAA
1 TTAA
86664 AAAATTAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TTAATTAAAAA
Found at i:94289 original size:16 final size:16
Alignment explanation
Indices: 94264--94294 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
94254 ATCACATTCA
94264 TGTTCATATTTTTTTG
1 TGTTCATATTTTTTTG
*
94280 TGTTCGTATTTTTTT
1 TGTTCATATTTTTTT
94295 CGTGACATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.13, T:0.71
Consensus pattern (16 bp):
TGTTCATATTTTTTTG
Found at i:100902 original size:13 final size:13
Alignment explanation
Indices: 100884--100908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100874 CATAAAGTGT
100884 TGTATCGATACAA
1 TGTATCGATACAA
100897 TGTATCGATACA
1 TGTATCGATACA
100909 TATTTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:100924 original size:32 final size:33
Alignment explanation
Indices: 100864--100929 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
100854 TTCAACGATT
100864 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
** *
100897 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
100929 T
1 T
100930 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:104214 original size:16 final size:16
Alignment explanation
Indices: 104193--104225 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
104183 CGATACTTAC
104193 CTCTAAATCTAGATAA
1 CTCTAAATCTAGATAA
104209 CTCTAAATCTAGATAA
1 CTCTAAATCTAGATAA
104225 C
1 C
104226 ATAGGTCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (16 bp):
CTCTAAATCTAGATAA
Found at i:112356 original size:18 final size:17
Alignment explanation
Indices: 112324--112357 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
112314 CTTTAATTTT
112324 ATTAAAACTTCTACTAG
1 ATTAAAACTTCTACTAG
*
112341 ATTAAGAACTTTTACTA
1 ATTAA-AACTTCTACTA
112358 TCTTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTAAAACTTCTACTAG
Found at i:112889 original size:28 final size:28
Alignment explanation
Indices: 112858--112928 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
112848 TCTACTTTAT
* *
112858 ACATTGTCTTGTTAAGACGAGTTTATCC
1 ACATTGTCTTGTTAAGACAAGCTTATCC
* *
112886 ACATTATCTTATTAAGACAAGCTTATCC
1 ACATTGTCTTGTTAAGACAAGCTTATCC
**
112914 ATTTTGTCTTGTTAA
1 ACATTGTCTTGTTAA
112929 AACATCAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (28 bp):
ACATTGTCTTGTTAAGACAAGCTTATCC
Found at i:117852 original size:19 final size:18
Alignment explanation
Indices: 117828--117890 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
117818 AGCGATACAT
117828 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
117847 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
117860 TGTACCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
117879 TGTATCGATACA
1 TGTATCGATACA
117891 GTTACAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:117861 original size:32 final size:32
Alignment explanation
Indices: 117815--117890 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
117805 GCAGTAGCTT
* *
117815 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACATTGTACCGATACAAAACTTA
*
117847 TGTATCGATACATTGTACCGATACAACACTTA
1 TGTATCGATACATTGTACCGATACAAAACTTA
117879 TGTATCGATACA
1 TGTATCGATACA
117891 GTTACAGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATTGTACCGATACAAAACTTA
Found at i:118817 original size:49 final size:48
Alignment explanation
Indices: 118652--119832 Score: 1061
Period size: 49 Copynumber: 24.8 Consensus size: 48
118642 CGAAGAATGA
* * * * * * *
118652 CAATGTGCTGATTCATGGCCAGCAATATTAGATTTGAAGAAGAA--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAA-AAGGTGC
* ** * * * *
118699 CAATGTGCTGAGACAAGGCCAACGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-G-AAAAGGTGC
* * * *
118751 CAATATGCTGATTCAAGGCCAACAAAATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGTGC
* * * *
118800 CAATGTGCTAATTCAAGGCCAGGGAGATTGGACTTAAAGATAACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG---A-AAAGGTGC
* * * *
118852 CAATATGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGACAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* * * * *
118900 CAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAGGAATGTTAAAGATG-
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-G-AAAAGGTGC
* * * *
118951 CAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGTGC
*
119000 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG---A-AAAGGTGC
* * *
119052 CAATATGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* * * *
119100 CAATATGCTGATTCAAGGCTAGTGATATTGGGCTT-------A--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* * * *
119139 CAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* *
119187 CAATATGCTGATTC-AGGACCAGTGATATTGGACTTAAAG---A--TGC
1 CAATATGCTGATTCAAGG-CCAGCGACATTGGACTTAAAGAAAAGGTGC
* * *
119230 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
*
119278 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----AAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* * *
119321 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-GA-AAAGGTGC
* * * * *
119373 CAATATGCTGATTCAAGGCCAGTGATATTGGATTTAAAGATGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGTGC
* **
119422 CAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGTGC
* **
119471 CAATATGCTAATTCAAGGCCAGCGACATTGGTTTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGTGC
* *
119520 CAATATGCTAATTCAAGGCCAGCGATATTGGACTT-----AAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* * *
119563 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* * *
119611 CAATATGCTGATTCAAGGCCAACGATATTGGACTT-----AACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* * * *
119654 CAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAAACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGTGC
*
119703 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----AAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
* * * *
119746 CAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAAACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-AAAGGTGC
* *
119795 CAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAA
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA
119833 AGTGCCACGA
Statistics
Matches: 940, Mismatches: 133, Indels: 120
0.79 0.11 0.10
Matches are distributed among these distances:
39 34 0.04
41 1 0.00
43 187 0.20
44 3 0.00
45 1 0.00
46 2 0.00
47 29 0.03
48 189 0.20
49 289 0.31
50 8 0.01
51 36 0.04
52 161 0.17
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAGGTGC
Found at i:119151 original size:39 final size:39
Alignment explanation
Indices: 119097--119174 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
119087 AAAGACAAGG
* *
119097 TGCCAATATGCTGATTCAAGGCTAGTGATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCTAGCGACATTGGGCTTA
* *
119136 TGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTA
1 TGCCAATATGCTGATTCAAGGCTAGCGACATTGGGCTTA
119175 AAGACAAGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (39 bp):
TGCCAATATGCTGATTCAAGGCTAGCGACATTGGGCTTA
Found at i:119260 original size:43 final size:43
Alignment explanation
Indices: 119044--119832 Score: 591
Period size: 43 Copynumber: 17.1 Consensus size: 43
119034 TAAAGATAAC
* *
119044 AAAGGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGTCTT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * * *
119087 AAAGACAAGGTGCCAATATGCTGATTCAAGGCTAGTGATATTGGGCTT
1 AAAG---A--TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* *
119135 ----ATGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * *
119174 AAAGACAAGGTGCCAATATGCTGATTC-AGGACCAGTGATATTGGACTT
1 AAAG---A--TGCCAATATGCTGATTCAAGG-CCAGCGACATTGGTCTT
*
119222 AAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* *
119265 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAG---A--TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* *
119313 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* *
119356 AAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGTGATATTGGAT-TT
1 AAAGAT---------GCCAATATGCTGATTCAAGGCCAGCGACATTGG-TCTT
* *
119408 AAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTT
1 ----A--AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* *
119457 AAAGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGTTTT
1 AAAG----A--TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * *
119506 AAAGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT
1 AAAG----A--TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* *
119555 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * *
119598 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT
1 AAAG---A--TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * * *
119646 AACGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * *
119689 AAAAACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * *
119738 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTT
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * * *
119781 AAAAACAAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
119830 AAA
1 AAA
119833 AGTGCCACGA
Statistics
Matches: 618, Mismatches: 67, Indels: 122
0.77 0.08 0.15
Matches are distributed among these distances:
39 34 0.06
41 1 0.00
43 194 0.31
44 3 0.00
45 2 0.00
46 2 0.00
47 4 0.01
48 145 0.23
49 194 0.31
52 32 0.05
53 1 0.00
56 1 0.00
58 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
Found at i:119307 original size:178 final size:185
Alignment explanation
Indices: 118951--119501 Score: 674
Period size: 178 Copynumber: 2.9 Consensus size: 185
118941 GTTAAAGATG
* * * * * * *
118951 CAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATG---AAGGTGCCAATGTGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTGATT
* * * * *
119013 CAAGGCCAGCGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTGATTCAAGGCTAGCGAC
66 CAAGGCCAGTGATATTGGAC-T-----T-A-AAAGATGCCAATGTGCTGATTCAAGGCCAGCGAC
* * *
119078 ATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCTAGTGATATTGGGCTT-A-TGC
123 ATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGTGC
* *
119139 CAATGTGCTGATTCAAGGCTAGCGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTGATT
119200 C-AGGACCAGTGATATTGGACTT-AAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
66 CAAGG-CCAGTGATATTGGACTTAAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
119263 TTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
130 TTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-GTGC
119321 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTGATT
*
119386 CAAGGCCAGTGATATTGGATTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATT
66 CAAGGCCAGTGATATTGGACTT--A-A--AAGATGCCAATGTGCTGATTCAAGGCCAGCGACATT
* * * *
119451 GGTTTTAAAGATAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGG
126 GGTCTTAAAGA-CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
119502 TTTTAAAGAT
Statistics
Matches: 322, Mismatches: 22, Indels: 33
0.85 0.06 0.09
Matches are distributed among these distances:
178 85 0.26
180 1 0.00
181 1 0.00
182 37 0.11
183 2 0.01
184 1 0.00
185 4 0.01
186 41 0.13
187 38 0.12
188 29 0.09
190 1 0.00
192 46 0.14
193 36 0.11
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (185 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTGATT
CAAGGCCAGTGATATTGGACTTAAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
TAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGTGC
Found at i:119589 original size:92 final size:92
Alignment explanation
Indices: 118696--119839 Score: 873
Period size: 91 Copynumber: 12.1 Consensus size: 92
118686 TGAAGAAGAA
** * * ** *
118696 TGCCAATGTGCTGAGACAAGGCCAACGACATTGGGCTTAGGAATGTTAAAGATGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAAGGTGCCAATATGCTG
* * *
118761 ATTCAAGGCCAACAAAATTGGACTTAAAGATGAAGG
63 ATTCAAGGCCAGCGATATTGGACTT----A--AAGG
* * * *
118797 TGCCAATGTGCTAATTCAAGGCCAGGGAGATTGGACTTAAAGATAACAAAGGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG---ACAAAGGTGCCAATATGCTG
* * *
118862 ATTTAAGGCCAGCGACATTGGTCTTAAAGACAAG
63 ATTCAAGGCCAGCGATATTGGACTTAAAG----G
* * * * ** *
118896 ATGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAGGAATGTTAAAGATG-CAATATGCT
1 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAAGGTGCCAATATGCT
* *
118960 GATTCAAGGCCAACAATATTGGACTTAAAGATGAAGG
62 GATTCAAGGCCAGCGATATTGGACTT----A--AAGG
*
118997 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG---ACAAAGGTGCCAATATGCTG
* * *
119062 ATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGG
63 ATTCAAGGCCAGCGATATTGGACTT----A-AAGG
* * * * * *
119097 TGCCAATATGCTGATTCAAGGCTAGTGATATTGGGCTT--------A--TGCCAATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATT
* * *
119152 CAAGGCTAGCGACATTGGTCTTAAAGACAAGG
66 CAAGGCCAGCGATATTGGACTT----A-AAGG
* * * * *
119184 TGCCAATATGCTGATTC-AGGACCAGTGATATTGGACTTAAAG----A--TGCCAATGTGCTGAT
1 TGCCAATGTGCTGATTCAAGG-CCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGAT
* *
119242 TCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
65 TCAAGGCCAGCGATATTGGACTT----A-AAGG
* * * *
119275 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT------AAAGGTGCCAATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATT
* *
119334 CAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGG
66 CAAGGCCAGCGATATTGGAC-T-----T---AAAGG
* * * * ** * *
119370 CGCCAATATGCTGATTCAAGGCCAGTGATATTGGAT-TTAAAGATGAAGATGCCAATGTGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGG-TCTTAAAGACAAAGGTGCCAATATGCTGAT
* **
119434 TCAAGGCCAGCGACATTGGTTTTAAAGATAAAGG
65 TCAAGGCCAGCGATATTGG------ACTTAAAGG
* * * * *
119468 TGCCAATATGCTAATTCAAGGCCAGCGACATTGGTTTTAAAGATAAAGGTGCCAATATGCTAATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATT
119533 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
119560 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATT
* *
119624 CAAGGCCAACGATATTGGACTTAACGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* *
119651 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAAACAAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATT
119716 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* * *
119743 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAAACAAAGGTGCCAATATGTTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATT
*
119808 CAAGGCCAGCGATATTGGACTTAAAAG
66 CAAGGCCAGCGATATTGGACTTAAAGG
119835 TGCCA
1 TGCCA
119840 CGAAGTTGTG
Statistics
Matches: 906, Mismatches: 85, Indels: 113
0.82 0.08 0.10
Matches are distributed among these distances:
86 3 0.00
87 79 0.09
89 2 0.00
91 203 0.22
92 191 0.21
95 41 0.05
96 2 0.00
97 4 0.00
98 80 0.09
99 33 0.04
100 118 0.13
101 143 0.16
102 2 0.00
103 2 0.00
105 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAAGG
Found at i:119873 original size:34 final size:34
Alignment explanation
Indices: 119834--119988 Score: 158
Period size: 34 Copynumber: 4.6 Consensus size: 34
119824 GGACTTAAAA
* *
119834 GTGCCACGAAGTTGTGGCCTT-ATAGGAAAAAGG
1 GTGCCACGAAGTTGTGGACTTAAAAGGAAAAAGG
* * * *
119867 GATGCCATGAAGGTGTGGGCTTAAAAGGGAAAAA-A
1 G-TGCCACGAAGTTGTGGACTTAAAA-GGAAAAAGG
* *
119902 GTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGG
1 GTGCCACGAAGTTGTGGACTTAAAAGGAAAAAGG
*
119936 GTGCCAC-AGAGTTGTGGACTTAAAAAG-AAAA-G
1 GTGCCACGA-AGTTGTGGACTTAAAAGGAAAAAGG
*
119968 GTGCCACGAAGTCGTGGACTT
1 GTGCCACGAAGTTGTGGACTT
119989 TTTGGAAAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
32 19 0.19
33 12 0.12
34 61 0.60
35 3 0.03
36 7 0.07
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.19
Consensus pattern (34 bp):
GTGCCACGAAGTTGTGGACTTAAAAGGAAAAAGG
Found at i:119941 original size:68 final size:66
Alignment explanation
Indices: 119830--119988 Score: 178
Period size: 68 Copynumber: 2.4 Consensus size: 66
119820 TATTGGACTT
* * * *
119830 AAAAGTGCCACGAAGTTGTGGCCTTATAGGAAAAAGGGATGCCA-TGAAGGTGTGGGCTTAAAAG
1 AAAAGTGCCACGAAGTTGTGGACTTAAAGGAAAAAGGGATGCCACAG-AGGTGTGGACTTAAAA-
*
119894 GGAA
64 AG-A
* * *
119898 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGG-TGCCACAGAGTTGTGGACTTAAAAA
1 AAAAGTGCCACGAAGTTGTGGACTT-AAAGGAAAAAGGGATGCCACAGAGGTGTGGACTTAAAAA
119962 GA
65 GA
* *
119964 AAAGGTGCCACGAAGTCGTGGACTT
1 AAAAGTGCCACGAAGTTGTGGACTT
119989 TTTGGAAAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
66 23 0.29
67 1 0.01
68 42 0.54
69 12 0.15
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (66 bp):
AAAAGTGCCACGAAGTTGTGGACTTAAAGGAAAAAGGGATGCCACAGAGGTGTGGACTTAAAAAG
A
Found at i:120004 original size:31 final size:30
Alignment explanation
Indices: 119962--120143 Score: 190
Period size: 31 Copynumber: 5.9 Consensus size: 30
119952 GACTTAAAAA
* *
119962 GAAAAGGTGCCAC-GAAGTCGTGGACTTTTTG
1 GAAAAGATGCCACTG-AGTCGTGGAC-TTTGG
*
119993 GAAAAGATGCCACTGAGTTGTGGACTTT-G
1 GAAAAGATGCCACTGAGTCGTGGACTTTGG
* *
120022 AAAAGAGATTGCCACTGAGTTGTGGACTTTGG
1 GAAA-AGA-TGCCACTGAGTCGTGGACTTTGG
*
120054 AGAAAAAATGCCACTGAGTCGTGGACTTTGG
1 -GAAAAGATGCCACTGAGTCGTGGACTTTGG
* * *
120085 GACAAA-ATGCCACTGAGTCGTGGGCTTAGA
1 GA-AAAGATGCCACTGAGTCGTGGACTTTGG
*
120115 GAAGAGATTGCCACTGAGTCGTGGACTTT
1 GAAAAGA-TGCCACTGAGTCGTGGACTTT
120144 AAGAAAGTAT
Statistics
Matches: 131, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.05
30 32 0.24
31 86 0.66
32 4 0.03
33 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (30 bp):
GAAAAGATGCCACTGAGTCGTGGACTTTGG
Found at i:120016 original size:63 final size:60
Alignment explanation
Indices: 119899--120142 Score: 175
Period size: 61 Copynumber: 3.9 Consensus size: 60
119889 AAAAGGGAAA
* * * * *
119899 AAAGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAG
1 AAAGTGCCACTGAGTCGTGGACTT---TGGGAAAA-GATGCCACTGAGTTGTGGACTTAAAAAG
* *
119963 AAAAGGTGCCAC-GAAGTCGTGGACTTTTTGGAAAAGATGCCACTGAGTTGTGGACTTTGAAAAG
1 -AAA-GTGCCACTG-AGTCGTGGAC-TTTGGGAAAAGATGCCACTGAGTTGTGGAC-TTAAAAAG
* * * * * **** *
120027 AGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCCACTGAGTCGTGGACTTTGGGAC
1 AAAGTGCCACTGAGTCGTGGACTTTGG-GAAAAGATGCCACTGAGTTGTGGACTTAAAAAG
* * * * * *
120088 AAAATGCCACTGAGTCGTGGGCTTAGAGAAGAGATTGCCACTGAGTCGTGGACTT
1 AAAGTGCCACTGAGTCGTGGACTTTGGGAAAAGA-TGCCACTGAGTTGTGGACTT
120143 TAAGAAAGTA
Statistics
Matches: 147, Mismatches: 25, Indels: 18
0.77 0.13 0.09
Matches are distributed among these distances:
60 5 0.03
61 48 0.33
62 38 0.26
63 21 0.14
64 13 0.09
65 4 0.03
66 16 0.11
67 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.23
Consensus pattern (60 bp):
AAAGTGCCACTGAGTCGTGGACTTTGGGAAAAGATGCCACTGAGTTGTGGACTTAAAAAG
Found at i:120128 original size:92 final size:93
Alignment explanation
Indices: 119937--120149 Score: 263
Period size: 92 Copynumber: 2.3 Consensus size: 93
119927 GGGAAAAGGG
* * ** *
119937 TGCCACAGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGAAGTCGTGGACTTTTTGGAAAAGATG
1 TGCCACTGAGTTGTGGACTT-TAAAGAAAAAATGCCACGAAGTCGTGGACTTTTGGGAAAAGATG
* *
120002 CCACTGAGTTGTGGACTTTGAAAAGAGAT
65 CCACTGAGTCGTGGACTTAGAAAAGAGAT
**
120031 TGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCCACTG-AGTCGTGGAC-TTTGGGACAAA-AT
1 TGCCACTGAGTTGTGGACTTTAAAGAAAAAATGCCAC-GAAGTCGTGGACTTTTGGGA-AAAGAT
* *
120093 GCCACTGAGTCGTGGGCTTAGAGAAGAGAT
64 GCCACTGAGTCGTGGACTTAGAAAAGAGAT
*
120123 TGCCACTGAGTCGTGGACTTT-AAGAAA
1 TGCCACTGAGTTGTGGACTTTAAAGAAA
120150 GTATTTGAAG
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
91 5 0.05
92 54 0.52
93 25 0.24
94 20 0.19
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (93 bp):
TGCCACTGAGTTGTGGACTTTAAAGAAAAAATGCCACGAAGTCGTGGACTTTTGGGAAAAGATGC
CACTGAGTCGTGGACTTAGAAAAGAGAT
Found at i:120131 original size:61 final size:62
Alignment explanation
Indices: 119969--120143 Score: 182
Period size: 61 Copynumber: 2.8 Consensus size: 62
119959 AAAGAAAAGG
* * *
119969 TGCCAC-GAAGTCGTGGACTTTTTG-GAAAAGATGCCACTGAGTTGTGGACTTTGAAAAGAGAT
1 TGCCACTG-AGTCGTGGAC-TTTAGAGAAAAAATGCCACTGAGTCGTGGACTTTGAAAAGAGAT
* * *
120031 TGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCCACTGAGTCGTGGACTTTGGGACAA-A-A-
1 TGCCACTGAGTCGTGGACTTTAGAGAAAAAATGCCACTGAGTCGTGGACTTT--GAAAAGAGAT
* * *
120092 TGCCACTGAGTCGTGGGC-TTAGAGAAGAGATTGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTTAGAGAA-AAAATGCCACTGAGTCGTGGACTTT
120144 AAGAAAGTAT
Statistics
Matches: 98, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
60 7 0.07
61 43 0.44
62 42 0.43
63 2 0.02
64 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (62 bp):
TGCCACTGAGTCGTGGACTTTAGAGAAAAAATGCCACTGAGTCGTGGACTTTGAAAAGAGAT
Found at i:122027 original size:21 final size:21
Alignment explanation
Indices: 122003--122084 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
121993 CAGTTTTTAA
122003 TTTAAATTATTAAATTATAAT
1 TTTAAATTATTAAATTATAAT
* *
122024 TTTAAA-TATAAAAATTAAAATT
1 TTTAAATTAT-TAAATTATAA-T
* *
122046 TTTTATTTATTTAATATTAT-AT
1 TTTAAATTA-TTAA-ATTATAAT
*
122068 TTATAAAATATTAAATT
1 TT-TAAATTATTAAATT
122085 TTTAATTTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
20 3 0.07
21 17 0.37
22 12 0.26
23 9 0.20
24 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAATTATTAAATTATAAT
Found at i:128955 original size:14 final size:15
Alignment explanation
Indices: 128938--128973 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
128928 TATTCATATT
*
128938 TAAATATA-TCAAAA
1 TAAATATATTAAAAA
128952 TAAATATATTAAAAA
1 TAAATATATTAAAAA
128967 TAAATAT
1 TAAATAT
128974 CAGATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATATATTAAAAA
Found at i:130254 original size:20 final size:20
Alignment explanation
Indices: 130226--130300 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
130216 TCATACCCTG
130226 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
130246 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
130266 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
130286 ATGTATCGATACATT
1 ATGTATCGATACATT
130301 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:130293 original size:40 final size:39
Alignment explanation
Indices: 130226--130303 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
130216 TCATACCCTG
* *
130226 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
130266 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
130304 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:131248 original size:22 final size:22
Alignment explanation
Indices: 131213--131290 Score: 147
Period size: 22 Copynumber: 3.5 Consensus size: 22
131203 AGCCTTTGAC
131213 CATGCATTTTTTTTATTATGTTT
1 CATGCA-TTTTTTTATTATGTTT
131236 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
131258 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
131280 CATGCATTTTT
1 CATGCATTTTT
131291 AACATGTCCA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 49 0.89
23 6 0.11
ACGTcount: A:0.18, C:0.10, G:0.09, T:0.63
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:143842 original size:10 final size:10
Alignment explanation
Indices: 143827--143887 Score: 61
Period size: 10 Copynumber: 5.6 Consensus size: 10
143817 TTTACACCAA
143827 AAAAAAAAAC
1 AAAAAAAAAC
143837 AAAAAAAAAC
1 AAAAAAAAAC
143847 AAAACAAAAAAAC
1 --AA-AAAAAAAC
143860 AAAAAAAAA-
1 AAAAAAAAAC
143869 AGAAAAAAATAGC
1 A-AAAAAAA-A-C
143882 AAAAAA
1 AAAAAA
143888 TAGAAGGGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.02
10 24 0.55
11 3 0.07
12 7 0.16
13 9 0.20
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:143842 original size:11 final size:11
Alignment explanation
Indices: 143826--143887 Score: 72
Period size: 11 Copynumber: 5.5 Consensus size: 11
143816 ATTTACACCA
143826 AAAAAAAAAAC
1 AAAAAAAAAAC
143837 -AAAAAAAAAC
1 AAAAAAAAAAC
143847 AAAACAAAAAAAC
1 -AAA-AAAAAAAC
*
143860 AAAAAAAAAAG
1 AAAAAAAAAAC
* *
143871 AAAAAAATAGC
1 AAAAAAAAAAC
143882 AAAAAA
1 AAAAAA
143888 TAGAAGGGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
10 10 0.23
11 21 0.48
12 5 0.11
13 8 0.18
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:143859 original size:23 final size:22
Alignment explanation
Indices: 143824--143887 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
143814 TCATTTACAC
143824 CAAAAAAAAAAACAAAAAAAAA
1 CAAAAAAAAAAACAAAAAAAAA
143846 CAAAACAAAAAAACAAAAAAAAA
1 CAAAA-AAAAAAACAAAAAAAAA
* *
143869 -AGAAAAAAATAGCAAAAAA
1 CA-AAAAAAAAAACAAAAAA
143888 TAGAAGGGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.47
23 20 0.53
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (22 bp):
CAAAAAAAAAAACAAAAAAAAA
Found at i:143887 original size:1 final size:1
Alignment explanation
Indices: 143825--143877 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
143815 CATTTACACC
* * * * *
143825 AAAAAAAAAAACAAAAAAAAACAAAACAAAAAAACAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
143878 TAGCAAAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.91, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:145107 original size:29 final size:29
Alignment explanation
Indices: 145065--145981 Score: 1265
Period size: 28 Copynumber: 31.9 Consensus size: 29
145055 AATGTTCATC
145065 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145094 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145123 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
145151 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
145179 CCTTTCAAAGCTCACAGGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
145208 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145237 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145266 CATTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
145295 CCTTTCAAAGCCCACAAATCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
145324 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145352 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145380 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
145409 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
145438 CTTTTCAAAGCCCACAAATCAGTGACACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
145467 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
145495 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
145524 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
145553 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
145582 CTTTTCAAAGCCCACAATTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145610 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
145638 CCTTTCAGAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145666 CCTTTCGAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
145695 -ATTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145723 -CTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145750 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* * * *
145781 CCTTTTAAAGCTTACGCAAGTCAGTGGTAC-
1 CCTTTCAAAGC--CCACAAGTCAGTGGCACT
*
145811 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
145840 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145867 ACTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
145895 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
145923 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
145953 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
145982 ACCCTTTTCA
Statistics
Matches: 802, Mismatches: 71, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
27 1 0.00
28 366 0.46
29 350 0.44
30 61 0.08
31 24 0.03
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:145412 original size:201 final size:199
Alignment explanation
Indices: 145067--145993 Score: 1276
Period size: 201 Copynumber: 4.6 Consensus size: 199
145057 TGTTCATCCC
145067 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTC-TTTCAAA
* *
145132 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCTCACAGG
65 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
*
145197 TCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGG
130 TCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGG
145262 CACTCA
194 CACTCA
*
145268 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCATTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTC-TTTCAAA
* *
145333 GCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAG
65 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
* * * *
145398 TTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGA
130 TCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGG
*
145463 CACTCT
194 CACTCA
* *
145469 TTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACT-CTTTCAAA
* * *
145533 GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACA
65 GCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACA
* * * *
145598 ATTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAGAGCCCACAAGTTAGTG
128 AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTG
*
145662 GCAC-CC
193 GCACTCA
* * * * *
145668 TTTCGAAGCCCACAAGTCAGTGGCACT-ATTGCGAAGCCCACAATTCAGTGGCACTCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTCAAAG
* * * * *
145732 CCCACAAGTTAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCTTACG
66 CCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTTTCAAAGC--CCA
* *
145797 CAAGTCAGTGGTACCTTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAG
126 CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAG
145861 TGGCA-T-A
191 TGGCACTCA
* * * *
145868 CTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTTAGTGGCATTCTTTCAAA
1 -TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTCAAA
* *
145932 GCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCATGCAAGTCAATGGCAACCCTTTTCAAA
65 GCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGC-ACCC-TTTCAAA
145994 TCACCACTGT
Statistics
Matches: 649, Mismatches: 59, Indels: 33
0.88 0.08 0.04
Matches are distributed among these distances:
197 8 0.01
198 28 0.04
199 74 0.11
200 76 0.12
201 392 0.60
202 27 0.04
203 36 0.06
204 8 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (199 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTCAAAG
CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
CAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA
CTCA
Done.