Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2199
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: 52108
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:3938 original size:20 final size:20
Alignment explanation
Indices: 3909--3946 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3899 AAATCAAATA
* *
3909 AATATTTTTATTAATAATTT
1 AATATGTTTAATAATAATTT
3929 AATATGTTTAATAATAAT
1 AATATGTTTAATAATAAT
3947 AAATTCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AATATGTTTAATAATAATTT
Found at i:4880 original size:16 final size:15
Alignment explanation
Indices: 4844--4873 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4834 GAAATAAATA
*
4844 AAACCTAAAATTATT
1 AAACCTAAAAATATT
4859 AAACCTAAAAATATT
1 AAACCTAAAAATATT
4874 CGAACCTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (15 bp):
AAACCTAAAAATATT
Found at i:12360 original size:21 final size:21
Alignment explanation
Indices: 12316--12361 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
12306 TATAAAAGTC
* * *
12316 ATATATTGATACATTGATAAA
1 ATATATCGATACACTAATAAA
*
12337 ATATATCGATACACTAATAGA
1 ATATATCGATACACTAATAAA
12358 ATAT
1 ATAT
12362 TATGATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (21 bp):
ATATATCGATACACTAATAAA
Found at i:12368 original size:21 final size:20
Alignment explanation
Indices: 12316--12368 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
12306 TATAAAAGTC
* *
12316 ATATATTGATACATTGATAAA
1 ATATA-TGATACACTAATAAA
*
12337 ATATATCGATACACTAATAGA
1 ATATAT-GATACACTAATAAA
12358 ATATTATGATA
1 ATA-TATGATA
12369 TTTAGGCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (20 bp):
ATATATGATACACTAATAAA
Found at i:14341 original size:19 final size:19
Alignment explanation
Indices: 14304--14343 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
14294 ATTTAATTAA
*
14304 TATAAATATATAATGATTT
1 TATAAATATACAATGATTT
14323 TATAAATATACACAT-ATTT
1 TATAAATATACA-ATGATTT
14342 TA
1 TA
14344 ATTTATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (19 bp):
TATAAATATACAATGATTT
Found at i:14735 original size:16 final size:15
Alignment explanation
Indices: 14716--14755 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
14706 TAATTTTCTT
14716 ATTTTTTAATTTTAAA
1 ATTTTTT-ATTTTAAA
14732 ATTTTATTATTTTAAA
1 ATTTT-TTATTTTAAA
14748 ATATTTTT
1 AT-TTTTT
14756 TTAGATACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTTATTTTAAA
Found at i:18951 original size:34 final size:33
Alignment explanation
Indices: 18903--19123 Score: 248
Period size: 34 Copynumber: 6.5 Consensus size: 33
18893 TGGTAAAAAC
*
18903 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
18936 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
18970 CACACATTTAATCAATAATGGTAAGCTACTAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
** * *
19004 TTCTCATTTAATCAACAATGATAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* *
19038 CTCCCATTTAGTCAACAATGGTAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGGT-AACCTACCAAAT
*
19072 CACTCATTTAATCAACAATGGTAAACTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
*
19106 CACCATTTAATAAACAAT
1 CACCATTTAATCAACAAT
19124 TCTCCCACTT
Statistics
Matches: 159, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
33 22 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:19019 original size:68 final size:67
Alignment explanation
Indices: 18903--19123 Score: 273
Period size: 68 Copynumber: 3.3 Consensus size: 67
18893 TGGTAAAAAC
* * * *
18903 CACCATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGTAAGCCACCA
1 CACCATTTAATCAACAATGGTAAACTACCAAAT-TACTCATTTAATCAACAATGGTAAGCTACCA
18967 AAT
65 AAT
* * * * *
18970 CACACATTTAATCAATAATGGTAAGCTACTAAATTTCTCATTTAATCAACAATGATAAGCTACCA
1 CAC-CATTTAATCAACAATGGTAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCA
19035 AAT
65 AAT
* * * * *
19038 CTCCCATTTAGTCAACAATGGTAAACCACCAAATCACTCATTTAATCAACAATGGTAAACTACCA
1 C-ACCATTTAATCAACAATGGTAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCA
19103 AAT
65 AAT
*
19106 CACCATTTAATAAACAAT
1 CACCATTTAATCAACAAT
19124 TCTCCCACTT
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
67 19 0.15
68 110 0.85
69 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.26
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGTAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:19082 original size:102 final size:101
Alignment explanation
Indices: 18903--19123 Score: 325
Period size: 102 Copynumber: 2.2 Consensus size: 101
18893 TGGTAAAAAC
* *
18903 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
* * *
18968 ATCACACATTTAATCAATAATGGTAAGCTACTAAAT
66 ATCACACATTTAATCAACAATGGTAAACTACCAAAT
** * * *
19004 TTCTCATTTAATCAACAATGATAAGCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCA
1 CAC-CATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCA
*
19069 AATCACTCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACACATTTAATCAACAATGGTAAACTACCAAAT
*
19106 CACCATTTAATAAACAAT
1 CACCATTTAATCAACAAT
19124 TCTCCCACTT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAACCACCAA
ATCACACATTTAATCAACAATGGTAAACTACCAAAT
Found at i:23583 original size:34 final size:33
Alignment explanation
Indices: 23530--23748 Score: 240
Period size: 34 Copynumber: 6.5 Consensus size: 33
23520 TGGTAAAAAC
* * *
23530 CACCATTTAATCAATAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAAACTACCAAAT
* * *
23563 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAACTACCAAAT
* * *
23597 CACACATTTAATCAATAATGGTAAGCTATCAAAT
1 CAC-CATTTAATCAACAATGGTAAACTACCAAAT
** * *
23631 TTCTCATTTAATCAACAATGATAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAACTACCAAAT
* * * *
23665 CTCTCATTTAGTCAACAATGGCAAACTATCAAAT
1 CAC-CATTTAATCAACAATGGTAAACTACCAAAT
23699 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAACTACCAAAT
23733 CACCATTTAATCAACA
1 CACCATTTAATCAACA
23749 CTAAGCGAGT
Statistics
Matches: 158, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
33 17 0.11
34 140 0.89
35 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:23646 original size:68 final size:66
Alignment explanation
Indices: 23530--23746 Score: 272
Period size: 68 Copynumber: 3.2 Consensus size: 66
23520 TGGTAAAAAC
* * * *
23530 CACCATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAATAATGGCAAACTATCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAA
23595 AT
65 AT
* * * *
23597 CACACATTTAATCAATAATGGTAAGCTATCAAATTTCTCATTTAATCAACAATGATAAGCTACCA
1 CAC-CATTTAATCAATAATGGCAAACTATCAAATTAC-CATTTAATCAACAATGGTAAGCTACCA
23662 AAT
64 AAT
* * * * *
23665 CTCTCATTTAGTCAACAATGGCAAACTATCAAATCACCCATTTAATCAACAATGGTAAACTACCA
1 CAC-CATTTAATCAATAATGGCAAACTATCAAATTA-CCATTTAATCAACAATGGTAAGCTACCA
23730 AAT
64 AAT
23733 CACCATTTAATCAA
1 CACCATTTAATCAA
23747 CACTAAGCGA
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
67 15 0.12
68 112 0.88
69 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (66 bp):
CACCATTTAATCAATAATGGCAAACTATCAAATTACCATTTAATCAACAATGGTAAGCTACCAAA
T
Found at i:23675 original size:102 final size:101
Alignment explanation
Indices: 23530--23748 Score: 287
Period size: 102 Copynumber: 2.2 Consensus size: 101
23520 TGGTAAAAAC
* * * *
23530 CACCATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
23595 ATCACACATTTAATCAATAATGGTAAGCTATCAAAT
66 ATCACACATTTAATCAACAATGGTAAACTACCAAAT
** * * * *
23631 TTCTCATTTAATCAACAATGATAAGCTACCAAATCT-CTCATTTAGTCAACAATGGCAAACTATC
1 CAC-CATTTAATCAACAATGACAACCTACCAAATCTAC-CATTTAGTCAACAATGGCAAACCACC
*
23695 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
64 AAATCACACATTTAATCAACAATGGTAAACTACCAAAT
23733 CACCATTTAATCAACA
1 CACCATTTAATCAACA
23749 CTAAGCGAGT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
101 15 0.15
102 85 0.85
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACACATTTAATCAACAATGGTAAACTACCAAAT
Found at i:27355 original size:27 final size:26
Alignment explanation
Indices: 27325--27390 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
27315 GATTGAGAAT
* *
27325 ATATTTTTAATGTATATTTAATAATT-G
1 ATATTTTTAAT-TA-AATAAATAATTAG
27352 ATATTTTTATATTAAATAAATAATTAG
1 ATATTTTTA-ATTAAATAAATAATTAG
27379 ATATTTTTAATT
1 ATATTTTTAATT
27391 TACTTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 12 0.34
27 21 0.60
28 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (26 bp):
ATATTTTTAATTAAATAAATAATTAG
Found at i:27362 original size:22 final size:23
Alignment explanation
Indices: 27337--27392 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
27327 ATTTTTAATG
27337 TATATTTAATAATT-GATATTTT
1 TATATTTAATAATTAGATATTTT
27359 TATATTAAATAAATAATTAGATATTTT
1 TATATT---T-AATAATTAGATATTTT
27386 TA-ATTTA
1 TATATTTA
27393 CTTAAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
22 7 0.24
23 1 0.03
25 1 0.03
26 10 0.34
27 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TATATTTAATAATTAGATATTTT
Found at i:27398 original size:27 final size:26
Alignment explanation
Indices: 27325--27399 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
27315 GATTGAGAAT
* *
27325 ATATTTTTAATGTATATTTAATAATTG
1 ATATTTTTAATAT-TATTAAATAATTG
*
27352 ATATTTTT-ATATTAAATAAATAATTAG
1 ATATTTTTAATATT-ATTAAATAATT-G
27379 ATATTTTTAAT-TTACTTAAAT
1 ATATTTTTAATATTA-TTAAAT
27400 TTGATGTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
25 1 0.03
26 13 0.32
27 24 0.60
28 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (26 bp):
ATATTTTTAATATTATTAAATAATTG
Found at i:27653 original size:16 final size:17
Alignment explanation
Indices: 27612--27653 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
27602 AGTTTAAATA
27612 AAAATTAAAAACATATT
1 AAAATTAAAAACATATT
*
27629 AAAAATAAAAA-ATATT
1 AAAATTAAAAACATATT
*
27645 ATAATTAAA
1 AAAATTAAA
27654 TTTAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTAAAAACATATT
Found at i:29709 original size:32 final size:32
Alignment explanation
Indices: 29660--29755 Score: 96
Period size: 32 Copynumber: 3.1 Consensus size: 32
29650 TATAAGATAT
29660 TTTATA-TATATATAAATTTTAA-TAATTATTAA
1 TTTATATTATATATAAA-TTTAATTAATT-TTAA
29692 TTTATATTATATA-AAATTTAATTAATTTTAA
1 TTTATATTATATATAAATTTAATTAATTTTAA
* * *
29723 TATTACATTATATCT-TATTTAA-T-ATTTTAA
1 T-TTATATTATATATAAATTTAATTAATTTTAA
29753 TTT
1 TTT
29756 TTTTATAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
29 2 0.04
30 8 0.14
31 11 0.19
32 30 0.53
33 6 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTATATTATATATAAATTTAATTAATTTTAA
Found at i:30241 original size:16 final size:16
Alignment explanation
Indices: 30204--30238 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
30194 ATAAATTTGA
*
30204 AAATAATAAGAAATAT
1 AAATAATAAGAAAAAT
30220 AAATAATAAGTAAAAAT
1 AAATAATAAG-AAAAAT
30237 AA
1 AA
30239 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
AAATAATAAGAAAAAT
Found at i:31268 original size:27 final size:26
Alignment explanation
Indices: 31222--31290 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 26
31212 GATTAATTTA
*
31222 TTTAATAATAAAATATTTG-ATTAAT
1 TTTAATAATAAAATAATTGAATTAAT
*
31247 TTTAATATTATAAATAAATTGACATTAA-
1 TTTAATAATA-AAAT-AATTGA-ATTAAT
31275 TTTAATTAA-AAAATAA
1 TTTAA-TAATAAAATAA
31291 AAATAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
25 9 0.25
26 6 0.17
27 8 0.22
28 6 0.17
29 7 0.19
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (26 bp):
TTTAATAATAAAATAATTGAATTAAT
Found at i:36889 original size:3 final size:3
Alignment explanation
Indices: 36883--36907 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
36873 AGTTTTTTTT
36883 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
36908 GAAACACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44283 original size:23 final size:24
Alignment explanation
Indices: 44243--44292 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
44233 TTTAACTCGT
*
44243 TTATTTTTTAATTATATATTAATA
1 TTATTTTTTAATTATATATAAATA
*
44267 TTATTTTTT-ATTTTATATAAATA
1 TTATTTTTTAATTATATATAAATA
44290 TTA
1 TTA
44293 AAAATATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATTTTTTAATTATATATAAATA
Found at i:44384 original size:28 final size:29
Alignment explanation
Indices: 44330--44395 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 29
44320 AAGCTTAATA
*
44330 AAAAAATATAAAATTATTAAACATTAAAT
1 AAAAAATATAAAATTATTAAAAATTAAAT
* *
44359 AAAAAA-ATAATATT-TTAAAAATTTAA-
1 AAAAAATATAAAATTATTAAAAATTAAAT
*
44385 AAATAATATAA
1 AAAAAATATAA
44396 GTGACTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 5 0.16
27 14 0.44
28 7 0.22
29 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAAAATATAAAATTATTAAAAATTAAAT
Found at i:44544 original size:2 final size:2
Alignment explanation
Indices: 44490--44525 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44480 ACTTAAATAA
44490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44526 GATGTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44894 original size:20 final size:21
Alignment explanation
Indices: 44854--44902 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
44844 CTATAATTTA
*
44854 TATCGATACAACAAGTTAATG
1 TATCGATACAACAAGTGAATG
*
44875 TATCGATAC-ATAAGTGAATG
1 TATCGATACAACAAGTGAATG
44895 TATCGATA
1 TATCGATA
44903 TTGGATCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (21 bp):
TATCGATACAACAAGTGAATG
Found at i:45355 original size:198 final size:198
Alignment explanation
Indices: 45017--45409 Score: 601
Period size: 198 Copynumber: 2.0 Consensus size: 198
45007 TTCTTTAATA
* * * *
45017 TATCAATACATCCAGTTAAATTTGAAAATTTCGATCCATATTTTCAGCCACAGTAGTAGCCATAT
1 TATCAATACATCCAATTAAATTTGAAAATTTCGAGCCATATTTTCAGCCACAGTACTAACCATAT
* *
45082 CTCAACCAAAAGCATCAACACAAAACACTTAAGAAAAATCAATTCCTGTAGCTCTTCAACACCTC
66 CTCAACCAAAAGCATCAACACAAAACACTCAAGAAAAATCAATTCCCGTAGCTCTTCAACACCTC
* * *
45147 TCGAAAAAAACAAC-TCTAAACACTTCATCCTTTGCCAATACAGAGCTCCAATCCATCTCTCCTC
131 TAGAAAAAAACAACTTC-AAACACTTCATCCTTTACCAATACAGAGCTCAAATCCATCTCTCCTC
45211 AATG
195 AATG
** *
45215 TATCAATACATCCAATTAAATTTGAACTTTTCGAGCTATATTTTCAGCCACAGTACTAACCATAT
1 TATCAATACATCCAATTAAATTTGAAAATTTCGAGCCATATTTTCAGCCACAGTACTAACCATAT
* *
45280 CTCAGCCAAAAGCATCAACACAAAACACTCAAGAAAAATCAATTCCCGTAGCTCTTCAACA-CTT
66 CTCAACCAAAAGCATCAACACAAAACACTCAAGAAAAATCAATTCCCGTAGCTCTTCAACACCTC
* * *
45344 TAGAAAAAAAACACCTTCAAACACTTCCTCCTTTACCAATACATAGCTCAAATCCATCTCTCCTC
131 TAG-AAAAAAACAACTTCAAACACTTCATCCTTTACCAATACAGAGCTCAAATCCATCTCTCCTC
45409 A
195 A
45410 TGCAATAACC
Statistics
Matches: 176, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
197 4 0.02
198 170 0.97
199 2 0.01
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.26
Consensus pattern (198 bp):
TATCAATACATCCAATTAAATTTGAAAATTTCGAGCCATATTTTCAGCCACAGTACTAACCATAT
CTCAACCAAAAGCATCAACACAAAACACTCAAGAAAAATCAATTCCCGTAGCTCTTCAACACCTC
TAGAAAAAAACAACTTCAAACACTTCATCCTTTACCAATACAGAGCTCAAATCCATCTCTCCTCA
ATG
Found at i:48171 original size:17 final size:16
Alignment explanation
Indices: 48150--48211 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 16
48140 TCACGACACT
48150 TATAAATAAAAAATAA
1 TATAAATAAAAAATAA
48166 TTATAATATAATATAAAATAA
1 -TATAA-AT-A-A-AAAATAA
*
48187 AATAAAATAAAAAATAA
1 TAT-AAATAAAAAATAA
48204 TATAAATA
1 TATAAATA
48212 TAATAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
16 5 0.13
17 14 0.37
18 3 0.08
19 2 0.05
20 5 0.13
21 9 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAAATAAAAAATAA
Found at i:48183 original size:21 final size:20
Alignment explanation
Indices: 48154--48223 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
48144 GACACTTATA
48154 AATAAAAAATAATTATAATAT
1 AATAAAAAATAA-TATAATAT
* *
48175 AATATAAAAT-A-A-AATAA
1 AATAAAAAATAATATAATAT
48192 AATAAAAAATAATATAAATAT
1 AATAAAAAATAATAT-AATAT
48213 AATAAAAAATA
1 AATAAAAAATA
48224 TTAATTTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 13 0.32
18 2 0.05
19 1 0.02
20 1 0.02
21 24 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AATAAAAAATAATATAATAT
Found at i:48234 original size:22 final size:22
Alignment explanation
Indices: 48186--48250 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
48176 ATATAAAATA
* *
48186 AAATAAAATAAAAAATAAT-AT
1 AAATATAATAAAAAATATTAAT
48207 AAATATAATAAAAAATATTAAT
1 AAATATAATAAAAAATATTAAT
** *
48229 TTATATAAT-AAAATTATTAAT
1 AAATATAATAAAAAATATTAAT
48250 A
1 A
48251 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 28 0.76
22 9 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATATAATAAAAAATATTAAT
Done.