Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold519
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: 37504
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:274 original size:13 final size:13
Alignment explanation
Indices: 256--287 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
246 CTACCGACAG
256 AGGTGGCTGAGCA
1 AGGTGGCTGAGCA
269 AGGTGGCTGAGCA
1 AGGTGGCTGAGCA
282 AGGTGG
1 AGGTGG
288 TTGAAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.12, G:0.50, T:0.16
Consensus pattern (13 bp):
AGGTGGCTGAGCA
Found at i:2117 original size:13 final size:13
Alignment explanation
Indices: 2099--2124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2089 ACAATTTTTG
2099 TGTATCGATACAT
1 TGTATCGATACAT
2112 TGTATCGATACAT
1 TGTATCGATACAT
2125 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2121 original size:32 final size:32
Alignment explanation
Indices: 2080--2142 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2070 TACAAGCTAA
**
2080 TGTATCGATACAATTTTTG-TGTATCGATACAT
1 TGTATCGATAC-ATACTTGCTGTATCGATACAT
2112 TGTATCGATACATACTTGCTGTATCGATACA
1 TGTATCGATACATACTTGCTGTATCGATACA
2143 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATACTTGCTGTATCGATACAT
Found at i:2867 original size:21 final size:23
Alignment explanation
Indices: 2841--2889 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2831 CCCCGTTATA
2841 TAATTC-T-CCCCCTTAATC-AAG
1 TAATTCATACCCCCTTAA-CAAAG
*
2862 TAATTCATATCCCCTTAACAAAG
1 TAATTCATACCCCCTTAACAAAG
2885 TAATT
1 TAATT
2890 GTAGCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 2 0.08
23 16 0.67
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (23 bp):
TAATTCATACCCCCTTAACAAAG
Found at i:2885 original size:90 final size:91
Alignment explanation
Indices: 2782--2963 Score: 316
Period size: 90 Copynumber: 2.0 Consensus size: 91
2772 GTACATTCTC
*
2782 CCCCTTAATAAAGTAATTGTAGCAATTTACGCATTCTCCCCTTTATCTCCCCCG-TTA-T-ATAA
1 CCCCTTAACAAAGTAATTGTAGCAATTTACGCATTCTCCCCTTTATCT-CCCCGTTTATTAAT-A
2844 TTCTCCCCCTTAATCAAGTAATTCATAT
64 TTCTCCCCCTTAATCAAGTAATTCATAT
2872 CCCCTTAACAAAGTAATTGTAGCAATTTACGCATTCTCCCCTTTATCTCCCCGTTTATTAATATT
1 CCCCTTAACAAAGTAATTGTAGCAATTTACGCATTCTCCCCTTTATCTCCCCGTTTATTAATATT
2937 CTCCCCCTTAATCAAGTAATTCATAT
66 CTCCCCCTTAATCAAGTAATTCATAT
2963 C
1 C
2964 AAAATTTATT
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
89 5 0.06
90 50 0.57
91 31 0.35
92 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.37
Consensus pattern (91 bp):
CCCCTTAACAAAGTAATTGTAGCAATTTACGCATTCTCCCCTTTATCTCCCCGTTTATTAATATT
CTCCCCCTTAATCAAGTAATTCATAT
Found at i:6881 original size:15 final size:15
Alignment explanation
Indices: 6861--6891 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6851 ATTTCGTTTG
*
6861 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
6876 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
6891 G
1 G
6892 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:10912 original size:13 final size:13
Alignment explanation
Indices: 10894--10919 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10884 CAATTTTTTG
10894 TGTATCGATACAT
1 TGTATCGATACAT
10907 TGTATCGATACAT
1 TGTATCGATACAT
10920 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14317 original size:10 final size:10
Alignment explanation
Indices: 14283--14363 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 10
14273 TATGATACGA
14283 ATATATAAAT
1 ATATATAAAT
14293 ATAT-TAAAAT
1 ATATAT-AAAT
*
14303 CTATATAAAT
1 ATATATAAAT
*
14313 ATATA-ATATT
1 ATATATA-AAT
* *
14323 TTAATATAATT
1 AT-ATATAAAT
*
14334 ATATATAAAA
1 ATATATAAAT
14344 ATATA-AAAT
1 ATATATAAAT
* *
14353 ACAAATAAAT
1 ATATATAAAT
14363 A
1 A
14364 AACTAATTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
9 8 0.15
10 38 0.69
11 8 0.15
12 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
ATATATAAAT
Found at i:18817 original size:32 final size:32
Alignment explanation
Indices: 18767--18830 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
18757 ATTGAAGGGG
18767 TGCCATTAGTTTCCAAATCAGCTGCTGAGAAT
1 TGCCATTAGTTTCCAAATCAGCTGCTGAGAAT
* *
18799 TGCCGTTAGTTTCGAAATCAGCTGCTGAGAAT
1 TGCCATTAGTTTCCAAATCAGCTGCTGAGAAT
18831 GTATCCAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (32 bp):
TGCCATTAGTTTCCAAATCAGCTGCTGAGAAT
Found at i:28281 original size:4 final size:4
Alignment explanation
Indices: 28272--28310 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
28262 ATTGGTAGTG
28272 TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
28311 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:28315 original size:2 final size:2
Alignment explanation
Indices: 28308--28357 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
28298 TCTATCTATC
28308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28350 TA TA TA TA
1 TA TA TA TA
28358 AAAGTATGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28542 original size:29 final size:29
Alignment explanation
Indices: 28466--28561 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
28456 ACTTGCAAAC
* *
28466 AAAAGTAAAGTGCATAAATTCTAAATGCAA
1 AAAAGTAAAATGCATAAATT-TAAATGTAA
* * *
28496 GAAA--AAATTGCATGAATTTAAATGTAA
1 AAAAGTAAAATGCATAAATTTAAATGTAA
*
28523 AAAAGTAAAATGCATAAATTTAAATTTTAA
1 AAAAGTAAAATGCATAAATTTAAA-TGTAA
*
28553 AAAAATAAA
1 AAAAGTAAA
28562 CTACAATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
27 11 0.20
28 12 0.22
29 16 0.30
30 15 0.28
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.27
Consensus pattern (29 bp):
AAAAGTAAAATGCATAAATTTAAATGTAA
Found at i:29043 original size:13 final size:15
Alignment explanation
Indices: 29022--29057 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
29012 AAAAACAGAT
29022 AGAGGAAAGGAA-AA
1 AGAGGAAAGGAAGAA
29036 AG-GGAAAGGAAGAA
1 AGAGGAAAGGAAGAA
29050 AGAGGAAA
1 AGAGGAAA
29058 ATGGGCAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (15 bp):
AGAGGAAAGGAAGAA
Found at i:29466 original size:6 final size:7
Alignment explanation
Indices: 29446--29550 Score: 52
Period size: 7 Copynumber: 13.9 Consensus size: 7
29436 TTTTTCAAAA
29446 TTTAATT
1 TTTAATT
29453 TTTAATT
1 TTTAATT
29460 TTT-ATT
1 TTTAATT
*
29466 TTCTACATA
1 TT-TA-ATT
*
29475 TTTAATA
1 TTTAATT
*
29482 TAT-ATT
1 TTTAATT
*
29488 TTTAGTTT
1 TTTA-ATT
29496 TTTAAATT
1 TTT-AATT
29504 TTTGATATT
1 TTT-A-ATT
*
29513 TTTTATT
1 TTTAATT
29520 TTTATATTTT
1 TTTA-A--TT
29530 TTTAATT
1 TTTAATT
*
29537 TTAAGATT
1 TTTA-ATT
29545 TTTAAT
1 TTTAAT
29551 AATTTTTTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
6 9 0.12
7 29 0.38
8 20 0.26
9 12 0.16
10 6 0.08
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (7 bp):
TTTAATT
Found at i:29511 original size:29 final size:28
Alignment explanation
Indices: 29432--29521 Score: 66
Period size: 28 Copynumber: 3.3 Consensus size: 28
29422 TCTCTCATCC
* *
29432 TTTATTTT-TCAAA-ATTTAATTTTTAATT
1 TTTATTTTCT-AAATATTTAATATAT-ATT
*
29460 TTTATTTTCTACATATTTAATATATATT
1 TTTATTTTCTAAATATTTAATATATATT
*
29488 TTTAGTTTTTTAAAT-TTT--TGATAT-TT
1 TTTA-TTTTCTAAATATTTAAT-ATATATT
29514 TTTATTTT
1 TTTATTTT
29522 TATATTTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.08
26 7 0.13
27 4 0.08
28 20 0.38
29 18 0.34
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (28 bp):
TTTATTTTCTAAATATTTAATATATATT
Found at i:29521 original size:25 final size:26
Alignment explanation
Indices: 29481--29530 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
29471 CATATTTAAT
29481 ATATATTTTTAGTTTTTTAAATTTTTG
1 ATATATTTTTAG-TTTTTAAATTTTTG
*
29508 ATAT-TTTTTA-TTTTTATATTTTT
1 ATATATTTTTAGTTTTTAAATTTTT
29531 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
26 6 0.27
27 4 0.18
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (26 bp):
ATATATTTTTAGTTTTTAAATTTTTG
Found at i:29532 original size:42 final size:42
Alignment explanation
Indices: 29480--29559 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
29470 ACATATTTAA
* *
29480 TATATATTTTTAGTTTTTTAA-ATTTTTGAT-ATTTTTTATTTT
1 TATATATTTTTA--ATTTTAAGATTTTTAATAATTTTTTATTTT
*
29522 TATATTTTTTTAATTTTAAGATTTTTAATAATTTTTTA
1 TATATATTTTTAATTTTAAGATTTTTAATAATTTTTTA
29560 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.18
41 8 0.24
42 19 0.58
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (42 bp):
TATATATTTTTAATTTTAAGATTTTTAATAATTTTTTATTTT
Found at i:29533 original size:16 final size:15
Alignment explanation
Indices: 29501--29531 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
29491 AGTTTTTTAA
29501 ATTTTTGATATTTTTT
1 ATTTTT-ATATTTTTT
29517 ATTTTTATATTTTTT
1 ATTTTTATATTTTTT
29532 TAATTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTATATTTTTT
Found at i:29538 original size:8 final size:8
Alignment explanation
Indices: 29486--29683 Score: 63
Period size: 9 Copynumber: 23.6 Consensus size: 8
29476 TTAATATATA
*
29486 TTTTTAGT
1 TTTTTAAT
29494 TTTTTAAAT
1 TTTTT-AAT
*
29503 TTTTGATAT
1 TTTTTA-AT
29512 TTTTT-AT
1 TTTTTAAT
*
29519 TTTTATATT
1 TTTT-TAAT
29528 TTTTTAA-
1 TTTTTAAT
*
29535 TTTTAAGAT
1 TTTTTA-AT
29544 TTTTAATAAT
1 TTTT--TAAT
29554 TTTTTAAAAT
1 TTTTT--AAT
** *
29564 TTTAAAAAC
1 TTT-TTAAT
29573 TTTTTAAT
1 TTTTTAAT
29581 TCTTTTGAAT
1 T-TTTT-AAT
**
29591 TTATAGAAT
1 TT-TTTAAT
29600 TTTTATAA-
1 TTTT-TAAT
*
29608 TTTTGAA-
1 TTTTTAAT
29615 TTTTT-A-
1 TTTTTAAT
29621 TTTTTATAT
1 TTTTTA-AT
**
29630 TTTAAAAT
1 TTTTTAAT
29638 TTTTTAAAAT
1 TTTTT--AAT
29648 TTTTT-AT
1 TTTTTAAT
29655 TTTTTAGAT
1 TTTTTA-AT
29664 TTTCTT--T
1 TTT-TTAAT
29671 TTTTTAAT
1 TTTTTAAT
29679 TTTTT
1 TTTTT
29684 TGAATAAAAA
Statistics
Matches: 142, Mismatches: 23, Indels: 50
0.66 0.11 0.23
Matches are distributed among these distances:
6 8 0.06
7 28 0.20
8 31 0.22
9 47 0.33
10 27 0.19
11 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (8 bp):
TTTTTAAT
Found at i:29545 original size:17 final size:16
Alignment explanation
Indices: 29487--29547 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 16
29477 TAATATATAT
*
29487 TTTTAG-TTTTTTAAA
1 TTTTAGATTTTTTTAA
* *
29502 TTTTTGATATTTTTTAT
1 TTTTAGAT-TTTTTTAA
*
29519 TTTTATATTTTTTTAA
1 TTTTAGATTTTTTTAA
29535 TTTTAAGATTTTT
1 TTTT-AGATTTTT
29548 AATAATTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 5 0.14
16 12 0.33
17 19 0.53
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (16 bp):
TTTTAGATTTTTTTAA
Found at i:29546 original size:32 final size:32
Alignment explanation
Indices: 29484--29547 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
29474 ATTTAATATA
* * *
29484 TATTTTTAGTTTTTTAAATTTTTGATATTTTT
1 TATTTTTAATTTTTTAAATTTTTAAGATTTTT
*
29516 TATTTTTATATTTTTTTAA-TTTTAAGATTTTT
1 TATTTTTA-ATTTTTTAAATTTTTAAGATTTTT
29548 AATAATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (32 bp):
TATTTTTAATTTTTTAAATTTTTAAGATTTTT
Found at i:29626 original size:22 final size:22
Alignment explanation
Indices: 29598--29641 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29588 AATTTATAGA
*
29598 ATTTTTATAATTTT-GAATTTTT
1 ATTTTTAT-ATTTTAAAATTTTT
29620 ATTTTTATATTTTAAAATTTTT
1 ATTTTTATATTTTAAAATTTTT
29642 TAAAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
ATTTTTATATTTTAAAATTTTT
Found at i:29644 original size:10 final size:10
Alignment explanation
Indices: 29629--29653 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29619 TATTTTTATA
29629 TTTTAAAATT
1 TTTTAAAATT
29639 TTTTAAAATT
1 TTTTAAAATT
29649 TTTTA
1 TTTTA
29654 TTTTTTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:29682 original size:16 final size:15
Alignment explanation
Indices: 29597--29683 Score: 54
Period size: 16 Copynumber: 5.5 Consensus size: 15
29587 GAATTTATAG
* *
29597 AATTTTTATAATTTTG
1 AATTTTT-TATTTTTT
29613 AA-TTTTTA-TTTTT
1 AATTTTTTATTTTTT
**
29626 ATATTTTAAAATTTTTT
1 A-ATTTT-TTATTTTTT
29643 AAAATTTTTTATTTTTT
1 --AATTTTTTATTTTTT
29660 AGATTTTCTT-TTTTTT
1 A-ATTTT-TTATTTTTT
29676 AATTTTTT
1 AATTTTTT
29684 TGAATAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 5 0.09
14 5 0.09
15 13 0.22
16 15 0.26
17 14 0.24
18 5 0.09
19 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.70
Consensus pattern (15 bp):
AATTTTTTATTTTTT
Found at i:30167 original size:135 final size:135
Alignment explanation
Indices: 30048--30298 Score: 341
Period size: 135 Copynumber: 1.9 Consensus size: 135
30038 AGTGTTGCCT
* * * * *
30048 TAAATTAAATAAACTAACAA-AATTTAAATGGAA-GGGATTTTAGCTCTTGTTTGGCCACTAAAA
1 TAAACTAAAT-AACTAACAAGAAATTAAAT-AAACGGGATTTTAGCTCTTGCTTGGCCACCAAAA
30111 T-GATTAGAAAACCATTAAGATCAAGCTATCACCTAAG-TAATGACTTAGGATCATCAAACCTTT
64 TAG-TTAGAAAACCATTAAGATCAAGCTA-CACCTAAGTTAATGACTTAGGATCATCAAACCTTT
30174 AATTACATA
127 AATTACATA
* *
30183 TAAACTAAATAACTAACAAGAAATTAAATAAACTGGATTTTAGCTGTTGCTTGGCCACCAAAATA
1 TAAACTAAATAACTAACAAGAAATTAAATAAACGGGATTTTAGCTCTTGCTTGGCCACCAAAATA
* * *
30248 GTTAGGAAACCATTAAGCTCAAGCTACACCTAAGTTAATGACCT-GGATCAT
66 GTTAGAAAACCATTAAGATCAAGCTACACCTAAGTTAATGACTTAGGATCAT
30299 TAAGCTTTCA
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
134 26 0.25
135 75 0.74
136 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (135 bp):
TAAACTAAATAACTAACAAGAAATTAAATAAACGGGATTTTAGCTCTTGCTTGGCCACCAAAATA
GTTAGAAAACCATTAAGATCAAGCTACACCTAAGTTAATGACTTAGGATCATCAAACCTTTAATT
ACATA
Found at i:30439 original size:27 final size:26
Alignment explanation
Indices: 30409--30469 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
30399 ATCAAAAAAC
30409 TTTCTTTGAATCT-TTTCTTTT-TCTCTT
1 TTTCTTTG--TCTGTTT-TTTTCTCTCTT
30436 TTTCTTCTGTCTGTTTTTTTCTCTCTT
1 TTTCTT-TGTCTGTTTTTTTCTCTCTT
30463 TTTCTTT
1 TTTCTTT
30470 CAAGTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 8 0.26
27 21 0.68
28 2 0.06
ACGTcount: A:0.03, C:0.20, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTCTTTGTCTGTTTTTTTCTCTCTT
Found at i:30440 original size:14 final size:14
Alignment explanation
Indices: 30421--30470 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
30411 TCTTTGAATC
*
30421 TTTTCTTTTTCTCT
1 TTTTCTTTCTCTCT
*
30435 TTTTC-TTCTGTCT
1 TTTTCTTTCTCTCT
30448 GTTTT-TTTCTCTCT
1 -TTTTCTTTCTCTCT
30462 TTTTCTTTC
1 TTTTCTTTC
30471 AAGTTTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTCTTTCTCTCT
Found at i:30476 original size:25 final size:25
Alignment explanation
Indices: 30426--30478 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
30416 GAATCTTTTC
* *
30426 TTTTTCTCTTTTTCTTCTGTCTGTT
1 TTTTTCTCTCTTTCTTCTGTCAGTT
*
30451 TTTTTCTCTCTTT-TTCTTTCAAGTT
1 TTTTTCTCTCTTTCTTCTGTC-AGTT
30476 TTT
1 TTT
30479 CTCTTAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.04, C:0.19, G:0.06, T:0.72
Consensus pattern (25 bp):
TTTTTCTCTCTTTCTTCTGTCAGTT
Found at i:30602 original size:13 final size:13
Alignment explanation
Indices: 30581--30611 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30571 TCTTTTTATT
30581 TTTAATTTCTTTA
1 TTTAATTTCTTTA
*
30594 TTTACTTTCTTTA
1 TTTAATTTCTTTA
30607 TTTAA
1 TTTAA
30612 GCCTCCAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTAATTTCTTTA
Found at i:35450 original size:19 final size:18
Alignment explanation
Indices: 35425--35521 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
35415 ATTTCAACGA
35425 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
35443 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
35459 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
35475 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
35491 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
35507 TTTTGTATCGATACA
1 -TTTGTATCGATACA
35522 ATATATCGCT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 35 0.53
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:35463 original size:32 final size:32
Alignment explanation
Indices: 35427--35529 Score: 188
Period size: 32 Copynumber: 3.2 Consensus size: 32
35417 TTCAACGATT
35427 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
35459 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
35491 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
35523 TATATCG
1 TGTATCG
35530 CTACGAAGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:35464 original size:13 final size:13
Alignment explanation
Indices: 35446--35502 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
35436 ACATAAGTGT
35446 TGTATCGATACAA
1 TGTATCGATACAA
35459 TGTATCGATACATAA
1 TGTATCGATAC--AA
35474 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
35491 TGTATCGATACA
1 TGTATCGATACA
35503 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:35592 original size:13 final size:13
Alignment explanation
Indices: 35574--35598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35564 ATTACTCAAA
35574 TGTATCGATACAT
1 TGTATCGATACAT
35587 TGTATCGATACA
1 TGTATCGATACA
35599 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:35726 original size:53 final size:52
Alignment explanation
Indices: 35609--35736 Score: 211
Period size: 52 Copynumber: 2.4 Consensus size: 52
35599 CTGATCTTTG
* * *
35609 TATCGATACATTCAGGAAAATTTGCCCAGATGTATCGATACACTATGAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
35661 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATTACACTATGAAATA
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGA-TACACTATGAAATA
*
35714 TATTGATACATGCAGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
35737 TCATATTTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
52 36 0.51
53 35 0.49
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
Done.