Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1348
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: 233253
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 3 of 3
Found at i:220229 original size:17 final size:17
Alignment explanation
Indices: 220206--220247 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
220196 AATTTAAATC
220206 AAAATTTGAAAATAATTT
1 AAAATTTG-AAATAATTT
220224 -AAATTTG-AATAATTT
1 AAAATTTGAAATAATTT
220239 AAAATTTGA
1 AAAATTTGA
220248 TTTATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.36
16 7 0.32
17 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
AAAATTTGAAATAATTT
Found at i:221418 original size:25 final size:25
Alignment explanation
Indices: 221390--221438 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
221380 AATTGTTAAT
* *
221390 ATATATATTTTACA-AAAATTAAAAA
1 ATATATA-ATTACATAAAAATAAAAA
221415 ATATATAATTACATAAAAATAAAA
1 ATATATAATTACATAAAAATAAAA
221439 GGATGGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATATAATTACATAAAAATAAAAA
Found at i:222494 original size:21 final size:22
Alignment explanation
Indices: 222457--222497 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
222447 ACTCGAATTA
222457 TTATTTAATAATAAAAATATTT
1 TTATTTAATAATAAAAATATTT
*
222479 TTATTTAAT-TTAAAAATAT
1 TTATTTAATAATAAAAATAT
222498 ATATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTAATAATAAAAATATTT
Found at i:223033 original size:18 final size:18
Alignment explanation
Indices: 223010--223054 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
223000 AAAACTTGAC
223010 TATTTTAAATAAA-TTACT
1 TATTTTAAATAAATTTA-T
*
223028 TATTTTAAAAAAATTTAT
1 TATTTTAAATAAATTTAT
223046 T-TTTTAAAT
1 TATTTTAAAT
223055 TTAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 14 0.58
19 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTAAATAAATTTAT
Found at i:223478 original size:20 final size:20
Alignment explanation
Indices: 223428--223512 Score: 88
Period size: 21 Copynumber: 4.3 Consensus size: 20
223418 TATTTATGTT
*
223428 TAAATATTAAAAATTTAAATAA
1 TAAATATT--AAATTTAAAAAA
223450 -AAATATTAAATTTAAAAAA
1 TAAATATTAAATTTAAAAAA
*
223469 TAAATTTTAAATTATAAAAAA
1 TAAATATTAAATT-TAAAAAA
*
223490 TAAATA-T--ATTTAAACAA
1 TAAATATTAAATTTAAAAAA
223507 TAAATA
1 TAAATA
223513 AAATTTTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
17 12 0.21
18 3 0.05
19 11 0.19
20 12 0.21
21 19 0.33
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATATTAAATTTAAAAAA
Found at i:223509 original size:24 final size:21
Alignment explanation
Indices: 223462--223510 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
223452 ATATTAAATT
**
223462 TAAAAAATAAATTTTAAATTA
1 TAAAAAATAAATTTTAAACAA
223483 TAAAAAATAAATATATTTAAACAA
1 TAAAAAAT-AA-AT-TTTAAACAA
223507 TAAA
1 TAAA
223511 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 2 0.09
23 2 0.09
24 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATAAATTTTAAACAA
Found at i:223736 original size:17 final size:17
Alignment explanation
Indices: 223705--223754 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
223695 TTTTAATTTT
223705 TAAAATTTAAT-AAATAA
1 TAAAA-TTAATAAAATAA
223722 TAAAATTAATAAAAT--
1 TAAAATTAATAAAATAA
*
223737 TTAAA-TAATAAAATAA
1 TAAAATTAATAAAATAA
223753 TA
1 TA
223755 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 9 0.32
15 4 0.14
16 6 0.21
17 9 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAATTAATAAAATAA
Found at i:223757 original size:19 final size:21
Alignment explanation
Indices: 223715--223758 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
223705 TAAAATTTAA
223715 TAAATAATAAAATTAATAAAATT
1 TAAATAATAAAATTAAT--AATT
223738 TAAATAATAAAA-TAAT-ATT
1 TAAATAATAAAATTAATAATT
223757 TA
1 TA
223759 TTTTTAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.24
22 4 0.19
23 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATAATAAAATTAATAATT
Found at i:224857 original size:2 final size:2
Alignment explanation
Indices: 224850--224890 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
224840 TTGTTCATAC
224850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
224891 CAATCAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:225961 original size:45 final size:49
Alignment explanation
Indices: 225911--226010 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 49
225901 TTACTTTGAT
* *
225911 TTTTTATATTATTATTTATA-A-TTAATAAA-AAATTTAAA-AAAATTA
1 TTTTTATATTAATATTTATATATTTAATAAATAAATTTAAATAAAAATA
*
225956 TTTTTATATTAATATTTATATATTTTATAAATAAATTTAAATAAAAATA
1 TTTTTATATTAATATTTATATATTTAATAAATAAATTTAAATAAAAATA
226005 TTTTTA
1 TTTTTA
226011 ATAATTACGT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
45 19 0.40
46 1 0.02
47 7 0.15
48 9 0.19
49 12 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (49 bp):
TTTTTATATTAATATTTATATATTTAATAAATAAATTTAAATAAAAATA
Found at i:226504 original size:14 final size:15
Alignment explanation
Indices: 226485--226517 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
226475 AATCTTGTTT
*
226485 ATTTATTTA-ATTTA
1 ATTTATTTATATTAA
226499 ATTTATTTATATTAA
1 ATTTATTTATATTAA
226514 ATTT
1 ATTT
226518 TAAATAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATTTATATTAA
Found at i:226591 original size:35 final size:35
Alignment explanation
Indices: 226521--226597 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
226511 TAAATTTTAA
*
226521 ATAAACTTTTTATTAATTTAAATTAATATTTAATAT
1 ATAAA-TTTTTATTAATTTAAATTAATATTAAATAT
* *
226557 TTAAATTTTT-TTTATTTAAAATTAAT-TATAAATAT
1 ATAAATTTTTATTAATTT-AAATTAATAT-TAAATAT
226592 ATAAAT
1 ATAAAT
226598 ATTAATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 7 0.20
35 24 0.69
36 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (35 bp):
ATAAATTTTTATTAATTTAAATTAATATTAAATAT
Found at i:226846 original size:11 final size:11
Alignment explanation
Indices: 226792--226897 Score: 55
Period size: 11 Copynumber: 9.7 Consensus size: 11
226782 AATATTATAA
*
226792 ATTTATATGAT
1 ATTTATATTAT
*
226803 ATTTATA-AATT
1 ATTTATATTA-T
226814 ATTT-T-TTAT
1 ATTTATATTAT
*
226823 ATTT-TATTGTT
1 ATTTATATT-AT
226834 ATATTATATT-T
1 AT-TTATATTAT
*
226845 ATTTTTATTAT
1 ATTTATATTAT
226856 ATTT-TAATTA-
1 ATTTAT-ATTAT
*
226866 ATTTTTATGTCAT
1 ATTTATAT-T-AT
226879 ATTTATATTAT
1 ATTTATATTAT
*
226890 TTTTATAT
1 ATTTATAT
226898 ATAATTAATG
Statistics
Matches: 77, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
9 6 0.08
10 18 0.23
11 38 0.49
12 4 0.05
13 11 0.14
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:226906 original size:43 final size:44
Alignment explanation
Indices: 226824--226906 Score: 109
Period size: 43 Copynumber: 1.9 Consensus size: 44
226814 ATTTTTTATA
* *
226824 TTTTATTGTTATATTATATTTATTTTTATTATATTTTAATTAAT
1 TTTTATTGTCATATTATATTTATTTTTATTATATATTAATTAAT
226868 TTTTA-TGTCATATT-TATATTATTTTTA-TATATAATTAAT
1 TTTTATTGTCATATTATAT-TTATTTTTATTATAT-ATTAAT
226907 GTAGTGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 8 0.23
43 22 0.63
44 5 0.14
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.65
Consensus pattern (44 bp):
TTTTATTGTCATATTATATTTATTTTTATTATATATTAATTAAT
Found at i:227051 original size:9 final size:11
Alignment explanation
Indices: 227024--227052 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
227014 TATGTATTTA
227024 TATATTTTGTT
1 TATATTTTGTT
227035 TATATTTTGTT
1 TATATTTTGTT
227046 TAT-TTTT
1 TATATTTT
227053 AAAGTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
TATATTTTGTT
Found at i:228091 original size:26 final size:27
Alignment explanation
Indices: 228047--228099 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
228037 TTTAATACTT
*
228047 TTTAATTTAAATTTATATAATTATTAA
1 TTTAATTTAAATTTATATAAATATTAA
228074 TTTAA-TTAAATATT-TATAAATATTAA
1 TTTAATTTAAAT-TTATATAAATATTAA
228100 AATTCTTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTAATTTAAATTTATATAAATATTAA
Found at i:228198 original size:3 final size:3
Alignment explanation
Indices: 228190--228246 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
228180 CACTTTAAAG
*
228190 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
228238 TAT TGT TAT
1 TAT TAT TAT
228247 AATTTTCACT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:228579 original size:22 final size:25
Alignment explanation
Indices: 228537--228585 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
228527 TTACTTTAAT
228537 TTATTTGTATTAAATTTTAAATAAA
1 TTATTTGTATTAAATTTTAAATAAA
*
228562 TTATTT-TATT-AA-TTTAAATTAA
1 TTATTTGTATTAAATTTTAAATAAA
228584 TT
1 TT
228586 TAAATCGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 2 0.09
24 4 0.17
25 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTATTTGTATTAAATTTTAAATAAA
Found at i:228584 original size:10 final size:10
Alignment explanation
Indices: 228569--228615 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
228559 AAATTATTTT
228569 ATTAATTTAA
1 ATTAATTTAA
228579 ATTAATTTAA
1 ATTAATTTAA
**
228589 ATCGATTTAA
1 ATTAATTTAA
228599 ATTAATATTAA
1 ATTAAT-TTAA
228610 A-TAATT
1 ATTAATT
228616 AAAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 1 0.03
10 26 0.81
11 5 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:228598 original size:20 final size:21
Alignment explanation
Indices: 228573--228611 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
228563 TATTTTATTA
228573 ATTTAAATTAAT-TTAAATCG
1 ATTTAAATTAATATTAAATCG
228593 ATTTAAATTAATATTAAAT
1 ATTTAAATTAATATTAAAT
228612 AATTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTTAAATTAATATTAAATCG
Found at i:228910 original size:21 final size:22
Alignment explanation
Indices: 228880--228920 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
228870 TAAAGGATAA
*
228880 TATATATATTTGT-ATTTAAAT
1 TATATATATTTATAATTTAAAT
*
228901 TATATTTATTTATAATTTAA
1 TATATATATTTATAATTTAA
228921 TATTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATATATATTTATAATTTAAAT
Found at i:228926 original size:14 final size:14
Alignment explanation
Indices: 228907--228960 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
228897 AAATTATATT
*
228907 TATTTATAATTTAA
1 TATTTATAATTAAA
*
228921 TATTTAAAAAATTAAA
1 TATTT--ATAATTAAA
228937 TATTTATAATTAAA
1 TATTTATAATTAAA
228951 TATTTA-AATT
1 TATTTATAATT
228961 TAACTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 4 0.11
14 19 0.54
16 12 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTATAATTAAA
Found at i:228950 original size:22 final size:23
Alignment explanation
Indices: 228915--228959 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
228905 TTTATTTATA
*
228915 ATTTAATATTTAAAAAATTAAAT
1 ATTTAATAATTAAAAAATTAAAT
* *
228938 ATTT-ATAATTAAATATTTAAAT
1 ATTTAATAATTAAAAAATTAAAT
228960 TTAACTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATAATTAAAAAATTAAAT
Found at i:228963 original size:14 final size:14
Alignment explanation
Indices: 228892--228963 Score: 58
Period size: 14 Copynumber: 4.9 Consensus size: 14
228882 TATATATTTG
**
228892 TATTTAAATTATATT
1 TATTTAAATT-TAAA
228907 TATTTATAATTT-AA
1 TATTTA-AATTTAAA
*
228921 TATTTAAAAAATTAAA
1 TATTT--AAATTTAAA
228937 TATTTATAA-TTAAA
1 TATTTA-AATTTAAA
228951 TATTTAAATTTAA
1 TATTTAAATTTAA
228964 CTTTTATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
13 2 0.04
14 21 0.44
15 13 0.27
16 12 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTTAAATTTAAA
Found at i:229537 original size:16 final size:17
Alignment explanation
Indices: 229518--229550 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
229508 AAAATTAATT
229518 TTATAA-ATAAAATAAA
1 TTATAACATAAAATAAA
*
229534 TTATAACTTAAAATAAA
1 TTATAACATAAAATAAA
229551 ATAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TTATAACATAAAATAAA
Found at i:229592 original size:31 final size:31
Alignment explanation
Indices: 229534--229592 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
229524 ATAAAATAAA
* *
229534 TTATAACTTAAAATAAAATAAATTTAAACTT
1 TTATAACTAAAAATAAAATAAACTTAAACTT
*
229565 TTATAA-TAAAAATAAACTTAAACTTAAA
1 TTATAACTAAAAATAAA-ATAAACTTAAA
229593 TAATTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (31 bp):
TTATAACTAAAAATAAAATAAACTTAAACTT
Found at i:229595 original size:25 final size:22
Alignment explanation
Indices: 229523--229596 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 22
229513 TAATTTTATA
229523 AATAAAATAAATTATAACTTAA-
1 AATAAAATAAATTA-AACTTAAT
*
229545 AATAAAATAAATTTAAACTTTTAT
1 AATAAAATAAA-TTAAAC-TTAAT
229569 AATAAAAATAAACTTAAACTTAAAT
1 AAT-AAAATAAA-TTAAACTT-AAT
229594 AAT
1 AAT
229597 TATATTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 14 0.32
23 6 0.14
24 5 0.11
25 19 0.43
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
AATAAAATAAATTAAACTTAAT
Found at i:229645 original size:19 final size:16
Alignment explanation
Indices: 229590--229636 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
229580 ACTTAAACTT
229590 AAATAATTATATTTAA
1 AAATAATTATATTTAA
*
229606 AAATAATTTTATAATTAA
1 AAATAA--TTATATTTAA
229624 AAATAAATTATAT
1 AAAT-AATTATAT
229637 CTTATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.23
17 5 0.19
18 13 0.50
19 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATAATTATATTTAA
Found at i:230072 original size:11 final size:13
Alignment explanation
Indices: 230057--230085 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
230047 TAAAAATATA
230057 AAAAAATATTT-T
1 AAAAAATATTTAT
230069 AAAAAATATTTAT
1 AAAAAATATTTAT
230082 AAAA
1 AAAA
230086 CACATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAAATATTTAT
Found at i:230529 original size:14 final size:13
Alignment explanation
Indices: 230501--230535 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
230491 TAAATTGAAA
*
230501 TTATTAATAATAT
1 TTATAAATAATAT
230514 TTATAAATATATAT
1 TTATAAATA-ATAT
230528 TTATAAAT
1 TTATAAAT
230536 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATAAATAATAT
Found at i:230969 original size:37 final size:34
Alignment explanation
Indices: 230922--230995 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
230912 TTTTTATTTA
*
230922 AATTTATTTATAAAATATATAAATATTAATATAAAAT
1 AATTTATTTAT-AAAT-TATAAATAATAATAT-AAAT
* *
230959 AATTTTTTTATTAATTATAAATAATAATATAAAT
1 AATTTATTTATAAATTATAAATAATAATATAAAT
230993 AAT
1 AAT
230996 ATAAATGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 7 0.21
35 14 0.41
36 3 0.09
37 10 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
AATTTATTTATAAATTATAAATAATAATATAAAT
Found at i:231271 original size:19 final size:20
Alignment explanation
Indices: 231227--231271 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
231217 AGTAATATTT
*
231227 TAATAATATTTAATATTAAA
1 TAATTATATTTAATATTAAA
231247 -ATATTATATTT-ATATTAAA
1 TA-ATTATATTTAATATTAAA
231266 TAATTA
1 TAATTA
231272 AAAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTATATTTAATATTAAA
Found at i:232973 original size:22 final size:22
Alignment explanation
Indices: 232945--232987 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
232935 ATAATATTTT
232945 TATTTAAAT-TTAATTATAAAAA
1 TATTTAAATATTAA-TATAAAAA
*
232967 TATTTAAGTATTAATATAAAA
1 TATTTAAATATTAATATAAAA
232988 CTAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTTAAATATTAATATAAAAA
Done.