Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001927.1 Kokia drynarioides strain JFW-HI SEQ_113728, whole genome shotgun sequence
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: 69046
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:1984 original size:29 final size:30
Alignment explanation
Indices: 1942--2020 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
1932 ATAATTTTAC
**
1942 AATTATTAAAATTATTTT-TTTAAATATAA
1 AATTATTAAAATTATTTTAAATAAATATAA
*
1971 AATTATTAAAATTATTTTAAAATAAATTTAA
1 AATTATTAAAATTATTTT-AAATAAATATAA
*
2002 AATTATT-AAATAATTTTAA
1 AATTATTAAAATTATTTTAA
2021 TTTTCAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 20 0.45
30 9 0.20
31 15 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
AATTATTAAAATTATTTTAAATAAATATAA
Found at i:1992 original size:11 final size:11
Alignment explanation
Indices: 1968--2008 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1958 TTTTTAAATA
1968 TAAAATTA--T
1 TAAAATTATTT
1977 TAAAATTATTT
1 TAAAATTATTT
* *
1988 TAAAATAAATT
1 TAAAATTATTT
1999 TAAAATTATT
1 TAAAATTATT
2009 AAATAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:2030 original size:31 final size:32
Alignment explanation
Indices: 1937--2030 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 32
1927 AACAAATAAT
* *
1937 TTTACAATTATTAAAATTA-TTT--TTTTAAA
1 TTTAAAATTATTAAAATAATTTTAATTTTAAA
* * **
1966 TATAAAATTATTAAAATTATTTTAA-AATAAA
1 TTTAAAATTATTAAAATAATTTTAATTTTAAA
*
1997 TTTAAAATTATT-AAATAATTTTAATTTTCAA
1 TTTAAAATTATTAAAATAATTTTAATTTTAAA
2028 TTT
1 TTT
2031 CATCTTCTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
29 17 0.33
30 14 0.27
31 21 0.40
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTAAAATTATTAAAATAATTTTAATTTTAAA
Found at i:2079 original size:17 final size:17
Alignment explanation
Indices: 2027--2079 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2017 TTAATTTTCA
2027 ATTTCATCTTCTTCCCC
1 ATTTCATCTTCTTCCCC
* *
2044 A-TT-AT-TTATTTCCCA
1 ATTTCATCTT-CTTCCCC
2059 ATTTCATCTTCTTCCCC
1 ATTTCATCTTCTTCCCC
2076 ATTT
1 ATTT
2080 TTCCATCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.07
15 8 0.29
16 4 0.14
17 12 0.43
18 2 0.07
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTCATCTTCTTCCCC
Found at i:2335 original size:99 final size:99
Alignment explanation
Indices: 2164--2361 Score: 333
Period size: 99 Copynumber: 2.0 Consensus size: 99
2154 TTTTGAACTA
*
2164 AACCATGGATACTTCTCCACTTGGATTCTGAACCAAACCATGGCTTCTTCTTCTTCCATCACTCT
1 AACCATGGATACTTCTCCACTTGGATTCTGAACCAAACCATCGCTTCTTCTTCTTCCATCACTCT
*
2229 CCCAACCCTTCAAGGTTCTCTATTTTAATCTCAT
66 CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
* * *
2263 AACCATGGTTACTTCTCCACTTGGATTTTGAATCAAACCATCGCTTCTTCTTCTTCCATCACTCT
1 AACCATGGATACTTCTCCACTTGGATTCTGAACCAAACCATCGCTTCTTCTTCTTCCATCACTCT
**
2328 CTTAACCCTTCAAGGTTCTCTATTTCAATCTCAT
66 CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
2362 TTCTTAGGAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.37
Consensus pattern (99 bp):
AACCATGGATACTTCTCCACTTGGATTCTGAACCAAACCATCGCTTCTTCTTCTTCCATCACTCT
CCCAACCCTTCAAGGTTCTCTATTTCAATCTCAT
Found at i:4133 original size:18 final size:18
Alignment explanation
Indices: 4110--4187 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
4100 TCCAACTCAT
* *
4110 CATCTTCATCTTCATATC
1 CATCTTCATCTCCATCTC
*
4128 CATCTTCACCTCCATCTC
1 CATCTTCATCTCCATCTC
* *
4146 CATCTTGATATCCATCTC
1 CATCTTCATCTCCATCTC
* *
4164 CAACATT-ATCTTCATCTC
1 CATC-TTCATCTCCATCTC
4182 CATCTT
1 CATCTT
4188 GTTCTTTTGT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 2 0.04
18 45 0.92
19 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.01, T:0.40
Consensus pattern (18 bp):
CATCTTCATCTCCATCTC
Found at i:4180 original size:30 final size:30
Alignment explanation
Indices: 4110--4180 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
4100 TCCAACTCAT
* *
4110 CATCTTCATCTTCATATCCATCTTCACCTC
1 CATCTTCATCTTCATATCCATCTCCACATC
* *
4140 CATCTCCATCTTGATATCCATCTCCAACAT-
1 CATCTTCATCTTCATATCCATCTCC-ACATC
*
4170 TATCTTCATCT
1 CATCTTCATCT
4181 CCATCTTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 31 0.91
31 3 0.09
ACGTcount: A:0.23, C:0.37, G:0.01, T:0.39
Consensus pattern (30 bp):
CATCTTCATCTTCATATCCATCTCCACATC
Found at i:11372 original size:6 final size:6
Alignment explanation
Indices: 11351--11419 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
11341 TTTAATTTAT
* * *
11351 TTTAAA TTT-GA TTTAAA TTTAAA ATTAAA TTTAAA -TCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
11397 -ATAAA -TTAAA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA
11420 AAATCCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
5 16 0.32
6 29 0.58
7 5 0.10
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:11375 original size:18 final size:18
Alignment explanation
Indices: 11363--11419 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
11353 TAAATTTGAT
* *
11363 TTAAATTTAAAATTAAAT
1 TTAAATTTAAATTTAAAA
*
11381 TTAAA-TCAAATTTAAAA
1 TTAAATTTAAATTTAAAA
11398 -TAAA-TTAAATTTCAAAA
1 TTAAATTTAAATTT-AAAA
11415 TTAAA
1 TTAAA
11420 AAATCCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 11 0.33
17 13 0.39
18 9 0.27
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAATTTAAATTTAAAA
Found at i:11386 original size:11 final size:11
Alignment explanation
Indices: 11352--11408 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
11342 TTAATTTATT
* *
11352 TTAAATTTGAT
1 TTAAATTTAAA
11363 TTAAATTTAAAA
1 TTAAATTT-AAA
11375 TTAAATTTAAA
1 TTAAATTTAAA
*
11386 TCAAATTTAAA
1 TTAAATTTAAA
*
11397 ATAAA-TTAAA
1 TTAAATTTAAA
11407 TT
1 TT
11409 TCAAAATTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
10 6 0.15
11 24 0.62
12 9 0.23
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:11401 original size:16 final size:17
Alignment explanation
Indices: 11382--11415 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11372 AAATTAAATT
11382 TAAATCAAATTT-AAAA
1 TAAATCAAATTTCAAAA
*
11398 TAAATTAAATTTCAAAA
1 TAAATCAAATTTCAAAA
11415 T
1 T
11416 TAAAAAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATCAAATTTCAAAA
Found at i:11412 original size:23 final size:25
Alignment explanation
Indices: 11352--11420 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 25
11342 TTAATTTATT
*
11352 TTAAATTT-GATTT-AAATTTAAAA
1 TTAAATTTAAATTTCAAATTTAAAA
11375 TTAAATTTAAA--TCAAATTTAAAA
1 TTAAATTTAAATTTCAAATTTAAAA
*
11398 -TAAA-TTAAATTTCAAAATTAAAA
1 TTAAATTTAAATTTCAAATTTAAAA
11421 AATCCAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 5 0.12
22 5 0.12
23 29 0.73
24 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (25 bp):
TTAAATTTAAATTTCAAATTTAAAA
Found at i:12091 original size:24 final size:24
Alignment explanation
Indices: 12041--12092 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
12031 AAATATCATT
* **
12041 AATAATATTATTAATTATATTGGC
1 AATAATATTACTAATTATATTAAC
12065 AATAATATTACTAA-TATCATTAAC
1 AATAATATTACTAATTAT-ATTAAC
12089 AATA
1 AATA
12093 TTAATGACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
AATAATATTACTAATTATATTAAC
Found at i:12106 original size:15 final size:15
Alignment explanation
Indices: 12086--12127 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
12076 TAATATCATT
*
12086 AACAATATTAATGAC
1 AACAATAATAATGAC
*
12101 AACAATAATAATGAG
1 AACAATAATAATGAC
*
12116 ATCAATAATAAT
1 AACAATAATAAT
12128 ATTTAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (15 bp):
AACAATAATAATGAC
Found at i:13267 original size:29 final size:28
Alignment explanation
Indices: 13234--13395 Score: 134
Period size: 28 Copynumber: 5.6 Consensus size: 28
13224 CTAGACTATC
13234 CAAAAAATACCATTTTACCCTCGAACTT
1 CAAAAAATACCATTTTACCCTCGAACTT
* * *
13262 CTAAAAATCCCATTTTTGA-CATCGAACCTT
1 CAAAAAATACCA-TTTT-ACCCTCGAA-CTT
* *
13292 CCAAAAATTACCATTTTACCCCCGAACTT
1 -CAAAAAATACCATTTTACCCTCGAACTT
*
13321 CCAAAAAT-CTCATTTTTGA-CCTCGAAACTT
1 CAAAAAATAC-CA-TTTT-ACCCTCG-AACTT
* *
13351 CTAAAAATTACCATTTTACCCCCGAACTT
1 C-AAAAAATACCATTTTACCCTCGAACTT
13380 CAAAAAAT-CACATTTT
1 CAAAAAATAC-CATTTT
13396 TTTACCCCGA
Statistics
Matches: 106, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
27 2 0.02
28 30 0.28
29 29 0.27
30 28 0.26
31 16 0.15
32 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (28 bp):
CAAAAAATACCATTTTACCCTCGAACTT
Found at i:13318 original size:30 final size:29
Alignment explanation
Indices: 13232--13395 Score: 142
Period size: 29 Copynumber: 5.6 Consensus size: 29
13222 CCCTAGACTA
*
13232 TCCAAAAAATACCATTTTACCCTCGAACT
1 TCCAAAAATTACCATTTTACCCTCGAACT
* * *
13261 TCTAAAAA-TCCCATTTTTGA-CATCGAACCT
1 TCCAAAAATTACCA-TTTT-ACCCTCGAA-CT
*
13291 TCCAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATTACCATTTTACCCTCGAACT
13320 TCCAAAAA-T-CTCATTTTTGA-CCTCGAAACT
1 TCCAAAAATTAC-CA-TTTT-ACCCTCG-AACT
* *
13350 TCTAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATTACCATTTTACCCTCGAACT
* *
13379 TCAAAAAATCA-CATTTT
1 TCCAAAAATTACCATTTT
13396 TTTACCCCGA
Statistics
Matches: 111, Mismatches: 12, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
27 1 0.01
28 13 0.12
29 50 0.45
30 39 0.35
31 7 0.06
32 1 0.01
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCGAACT
Found at i:13406 original size:30 final size:29
Alignment explanation
Indices: 13246--13415 Score: 114
Period size: 30 Copynumber: 5.7 Consensus size: 29
13236 AAAAATACCA
* *
13246 TTTTACCCTCGAACTTCTAAAAATCCCATT
1 TTTTACCC-CGAACTTCCAAAAATCACATT
* ** *
13276 TTTGACATCGAACCTTCCAAAAATTACCA--
1 TTTTACCCCGAA-CTTCCAAAAATCA-CATT
*
13305 TTTTACCCCCGAACTTCCAAAAATCTCATT
1 TTTTA-CCCCGAACTTCCAAAAATCACATT
* * * *
13335 TTTGACCTCGAAACTTCTAAAAATTACCA--
1 TTTTACCCCG-AACTTCCAAAAATCA-CATT
*
13364 TTTTACCCCCGAACTTCAAAAAATCACATTT
1 TTTTA-CCCCGAACTTCCAAAAATCACA-TT
*
13395 TTTTACCCCGAAACATCCAAA
1 TTTTACCCCG-AACTTCCAAA
13416 GATTACTATT
Statistics
Matches: 106, Mismatches: 22, Indels: 23
0.70 0.15 0.15
Matches are distributed among these distances:
28 4 0.04
29 40 0.38
30 45 0.42
31 17 0.16
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (29 bp):
TTTTACCCCGAACTTCCAAAAATCACATT
Found at i:13435 original size:59 final size:59
Alignment explanation
Indices: 13231--13429 Score: 254
Period size: 59 Copynumber: 3.4 Consensus size: 59
13221 TCCCTAGACT
* * * * * *
13231 ATCCAAAAAATACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACATCGAACC
1 ATCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACATTTTTGACCTCGAAAC
* * *
13290 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAAAC
1 ATCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACATTTTTGACCTCGAAAC
* * * *
13349 TTCTAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACATTTTTTTACCCCGAAAC
1 ATCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACA-TTTTTGACCTCGAAAC
* *
13409 ATCCAAAGATTACTATTTTAC
1 ATCCAAAAATTACCATTTTAC
13430 TCCGAATGTC
Statistics
Matches: 123, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 92 0.75
60 31 0.25
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (59 bp):
ATCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACATTTTTGACCTCGAAAC
Found at i:13460 original size:118 final size:117
Alignment explanation
Indices: 13235--13494 Score: 274
Period size: 118 Copynumber: 2.2 Consensus size: 117
13225 TAGACTATCC
* * * * * * *
13235 AAAAAATACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACATCGAACCTTCCAAAAAT
1 AAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACATTTTTGACACCGAAACATCCAAAAAT
*
13300 TACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAAACTTCT
66 TACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTCGACCTCGAAAC-TCT
* * *
13353 AAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACATTTTTTTACCCCGAAACATCCAAAGA
1 AAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACA-TTTTTGACACCGAAACATCCAAAAA
* * ** * *
13418 TTACTATTTTA-CTCCGAA-TGTCTGAAGA-CTCCGTTTTCGACCTCGAAACTCT
65 TTACCATTTTACCCCCGAACT-TCCAAAAATCT-CATTTTCGACCTCGAAACTCT
* * *
13470 CATAATTTCCATTTTTACCCCCGAA
1 AAAAATTACCA-TTTTACCCCCGAA
13495 TTTTTTTAAA
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
117 14 0.12
118 75 0.64
119 29 0.25
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (117 bp):
AAAAATTACCATTTTACCCCCGAACTTCAAAAAATCACATTTTTGACACCGAAACATCCAAAAAT
TACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTCGACCTCGAAACTCT
Found at i:16017 original size:12 final size:12
Alignment explanation
Indices: 16000--16025 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15990 TCTCTATTCC
16000 TTTTTCCTTTTA
1 TTTTTCCTTTTA
16012 TTTTTCCTTTTA
1 TTTTTCCTTTTA
16024 TT
1 TT
16026 ACTTAACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTCCTTTTA
Found at i:27436 original size:30 final size:30
Alignment explanation
Indices: 27362--27436 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
27352 TTAAGATAAG
* * *
27362 ATTAAAATTT-TAAATCTTAAAAATATAAAA
1 ATTAAAATTTATCAAT-TCAAAAATACAAAA
*
27392 ATTAAAATTTATCAATTCAAAAATACATAA
1 ATTAAAATTTATCAATTCAAAAATACAAAA
27422 ATT-AAATTTAATCAA
1 ATTAAAATTT-ATCAA
27437 ATTAAAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.15
30 29 0.74
31 4 0.10
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (30 bp):
ATTAAAATTTATCAATTCAAAAATACAAAA
Found at i:31190 original size:25 final size:27
Alignment explanation
Indices: 31160--31209 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
31150 TGTCAATGTC
*
31160 AAAAGACA-AAA-AACACTTAATTCAA
1 AAAAGACAGAAATAACACTGAATTCAA
*
31185 AAAAGAGAGAAATAACACTGAATTC
1 AAAAGACAGAAATAACACTGAATTC
31210 TTAGAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 3 0.14
27 11 0.52
ACGTcount: A:0.60, C:0.14, G:0.10, T:0.16
Consensus pattern (27 bp):
AAAAGACAGAAATAACACTGAATTCAA
Found at i:32452 original size:31 final size:31
Alignment explanation
Indices: 32395--32454 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
32385 CATCTTCGTC
* *
32395 ATTAAACTGGAAGTTGCAGGTAGCAAGAAAT
1 ATTAAACTGAAAGCTGCAGGTAGCAAGAAAT
*
32426 ATTAAACTGTAAAGCTGCATGT-GCAAGAA
1 ATTAAACTG-AAAGCTGCAGGTAGCAAGAA
32455 TGAATGTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (31 bp):
ATTAAACTGAAAGCTGCAGGTAGCAAGAAAT
Found at i:35739 original size:8 final size:8
Alignment explanation
Indices: 35722--35776 Score: 71
Period size: 8 Copynumber: 7.2 Consensus size: 8
35712 GGAGTTCGAG
35722 TTTAAGGT
1 TTTAAGGT
*
35730 TTTAATGT
1 TTTAAGGT
35738 TTTAAGGT
1 TTTAAGGT
35746 TTTAAGGT
1 TTTAAGGT
35754 TTTAA-GT
1 TTTAAGGT
*
35761 TTT--GAT
1 TTTAAGGT
35767 TTTAAGGT
1 TTTAAGGT
35775 TT
1 TT
35777 GGGGTTCAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 4 0.10
7 5 0.12
8 31 0.77
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (8 bp):
TTTAAGGT
Found at i:38328 original size:102 final size:101
Alignment explanation
Indices: 38152--38355 Score: 354
Period size: 102 Copynumber: 2.0 Consensus size: 101
38142 AAAAAAAAAC
38152 TATATGATTGCATGGTGATTGGGGAAAAGATAGGATGATGCTACCAACCAATCAGGCAACACCGA
1 TATATGATTGCATGGTGATTGGGGAAAAGATAGGATGATGCTACCAACCAATCAGGCAACACCGA
*
38217 TATTCACTATAAAAAAACATTCTATTTTCGTAATTAA
66 TATTCACTAT-AAAAAACATTCTATCTTCGTAATTAA
* * *
38254 TATATGATTGCATGGTGATTGGGGAAAAGATAGGATGGTGCTGCCAACCAGTCAGGCAACACCGA
1 TATATGATTGCATGGTGATTGGGGAAAAGATAGGATGATGCTACCAACCAATCAGGCAACACCGA
*
38319 TATTCACTATAGAAAACATTCTATCTTCGTAATTAA
66 TATTCACTATAAAAAACATTCTATCTTCGTAATTAA
38355 T
1 T
38356 TTGTTTTACA
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 25 0.26
102 72 0.74
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (101 bp):
TATATGATTGCATGGTGATTGGGGAAAAGATAGGATGATGCTACCAACCAATCAGGCAACACCGA
TATTCACTATAAAAAACATTCTATCTTCGTAATTAA
Found at i:39336 original size:3 final size:3
Alignment explanation
Indices: 39328--39356 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39318 ACCTAATTTT
39328 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
39357 AAGCAGGAAC
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:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:46067 original size:10 final size:11
Alignment explanation
Indices: 46028--46068 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
46018 TATTAATTAT
*
46028 CTAATGTTAAA
1 CTAATATTAAA
46039 CTAATATTAAA
1 CTAATATTAAA
*
46050 CTAATATTAAG
1 CTAATATTAAA
46061 C-AATATTA
1 CTAATATTA
46069 CGTGATTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (11 bp):
CTAATATTAAA
Found at i:56693 original size:19 final size:18
Alignment explanation
Indices: 56666--56702 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56656 ATAAAAAATT
56666 AAATATTATTTTATATTTA
1 AAATATTATTTTAT-TTTA
*
56685 AAATTTTATTTTATTTTA
1 AAATATTATTTTATTTTA
56703 CACAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AAATATTATTTTATTTTA
Found at i:59785 original size:2 final size:2
Alignment explanation
Indices: 59780--59805 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59770 GACTCTCTGG
59780 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
59806 TTTTAATGCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:66076 original size:29 final size:28
Alignment explanation
Indices: 66019--66076 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
66009 TCACGACTTG
* *
66019 TTTTTTCCATATATTTTATACTTAGAAT
1 TTTTTTCCATATATTCTATACTTAAAAT
*
66047 TTTTTTCCATAATAATTCTAT-TTTAAAAT
1 TTTTTTCCAT-AT-ATTCTATACTTAAAAT
66076 T
1 T
66077 AACACAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 10 0.40
29 9 0.36
30 6 0.24
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTTTCCATATATTCTATACTTAAAAT
Found at i:66638 original size:31 final size:31
Alignment explanation
Indices: 66573--66643 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
66563 TAGTCCTTTA
* * * *
66573 TTTTAATTTGATCAATTTTAGTTCTTGTACT
1 TTTTAAATTGATCAATTTTAATCCTTATACT
* *
66604 TTTTAAATTGGTCAATTTTAATCCTTATATT
1 TTTTAAATTGATCAATTTTAATCCTTATACT
*
66635 TTTTGAATT
1 TTTTAAATT
66644 TTGAAATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58
Consensus pattern (31 bp):
TTTTAAATTGATCAATTTTAATCCTTATACT
Done.