Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013391.1 Kokia drynarioides strain JFW-HI SEQ_128415, 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: 32336
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Warning! 148 characters in sequence are not A, C, G, or T
Found at i:7028 original size:2 final size:2
Alignment explanation
Indices: 7021--7051 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7011 GAATATGAAA
7021 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 A
7052 GTTTTACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9397 original size:26 final size:27
Alignment explanation
Indices: 9367--9440 Score: 107
Period size: 26 Copynumber: 2.8 Consensus size: 27
9357 ACACAAACTC
*
9367 GCTCCTCAAACTAGCCGTTATCGAA-A
1 GCTCCTCAAACTAGCCGTTACCGAACA
*
9393 GCTCCTCAAACTAGTCGTTACCGAACA
1 GCTCCTCAAACTAGCCGTTACCGAACA
*
9420 -CTCCTCAAACTAGCAGTTACC
1 GCTCCTCAAACTAGCCGTTACC
9441 AAATATTCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 42 0.98
27 1 0.02
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.23
Consensus pattern (27 bp):
GCTCCTCAAACTAGCCGTTACCGAACA
Found at i:9827 original size:27 final size:27
Alignment explanation
Indices: 9797--9851 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
9787 GACTGAAAAG
9797 TTAGCACCTCACGACTCATTCCCCAAA
1 TTAGCACCTCACGACTCATTCCCCAAA
9824 TTAGCACCTCACGACTCATTCCCCAAA
1 TTAGCACCTCACGACTCATTCCCCAAA
9851 T
1 T
9852 CACCTCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.40, G:0.07, T:0.24
Consensus pattern (27 bp):
TTAGCACCTCACGACTCATTCCCCAAA
Found at i:10440 original size:6 final size:6
Alignment explanation
Indices: 10424--10519 Score: 54
Period size: 6 Copynumber: 15.8 Consensus size: 6
10414 AAGCTTTGAT
* * **
10424 TTTAAA ATTAAG TTTAAA TTTATTT TTTAAA TTTAAA TTT--A TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA T-TTAAA
*** **
10472 TTTAAA TTTGTCTT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA -TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
10520 TCAAATTTGA
Statistics
Matches: 65, Mismatches: 18, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
4 2 0.03
5 5 0.08
6 47 0.72
7 10 0.15
8 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:10472 original size:17 final size:18
Alignment explanation
Indices: 10431--10518 Score: 99
Period size: 17 Copynumber: 4.8 Consensus size: 18
10421 GATTTTAAAA
* *
10431 TTAAGTTTAAATTTATTTT
1 TTAAATTTAAATTTA-TCT
10450 TTAAATTTAAATTTATC-
1 TTAAATTTAAATTTATCT
*
10467 TTAAATTTAAATTTGTCTTT
1 TTAAATTTAAATTTATC--T
*
10487 TTAAATTTAAATTT-GCT
1 TTAAATTTAAATTTATCT
10504 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
10519 ATCAAATTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
17 31 0.51
18 1 0.02
19 15 0.25
20 14 0.23
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTAAATTTAAATTTATCT
Found at i:10492 original size:37 final size:36
Alignment explanation
Indices: 10431--10518 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 36
10421 GATTTTAAAA
* *
10431 TTAAGTTTAAATTTATTTTTTAAATTTAAATTT-AT
1 TTAAATTTAAATTTATTTTTTAAATTTAAATTTGCT
*
10466 CTTAAATTTAAATTTGTCTTTTTAAATTTAAATTTGCT
1 -TTAAATTTAAATTTAT-TTTTTAAATTTAAATTTGCT
10504 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
10519 ATCAAATTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 14 0.30
37 31 0.67
38 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (36 bp):
TTAAATTTAAATTTATTTTTTAAATTTAAATTTGCT
Found at i:10587 original size:17 final size:18
Alignment explanation
Indices: 10565--10598 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10555 ATTAAAAGCC
10565 CAAATA-AAAATCCAAAA
1 CAAATACAAAATCCAAAA
*
10582 CAAATACAAAGTCCAAA
1 CAAATACAAAATCCAAA
10599 TTACAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.21, G:0.03, T:0.12
Consensus pattern (18 bp):
CAAATACAAAATCCAAAA
Found at i:12399 original size:30 final size:29
Alignment explanation
Indices: 12361--12683 Score: 250
Period size: 30 Copynumber: 11.0 Consensus size: 29
12351 CCCTGGAGGT
* **
12361 CCCT-GAACTATCCGAAAATTATATTTTTA
1 CCCTCGAACT-TCCAAAAATTCCATTTTTA
*
12390 CCCTCGAACTTCCAAAAATTCCATTTTCAA
1 CCCTCGAACTTCCAAAAATTCCATTTT-TA
*
12420 CCC-CGAAACTTCCAAAAATTCTATTTTTA
1 CCCTCG-AACTTCCAAAAATTCCATTTTTA
* *
12449 CCCCCGAACATCCAAAAATTCCATTTTTAA
1 CCCTCGAACTTCCAAAAATTCCATTTTT-A
**
12479 CACC-AAAACTTCCAAAAATTCCATTTTTA
1 C-CCTCGAACTTCCAAAAATTCCATTTTTA
* *
12508 CCCCCGAACTT-TAACAAATTCCATTTTTGA
1 CCCTCGAACTTCCAA-AAATTCCATTTTT-A
* *
12538 TCC-CGAAACTTCCAAAAATTTCATTTTTGA
1 CCCTCG-AACTTCCAAAAATTCCATTTTT-A
* * **
12568 -CCTCAAAACTTCTAAAAATTATATTTTTA
1 CCCTC-GAACTTCCAAAAATTCCATTTTTA
* *
12597 CCCTCGAACCTCCAAAATTTCCATTTTTGA
1 CCCTCGAACTTCCAAAAATTCCATTTTT-A
* *
12627 CCC-CGAAACTTTCAAAAATTACCA-TTTTG
1 CCCTCG-AACTTCCAAAAATT-CCATTTTTA
* *
12656 CCCTCGGA-TGTCCAAAAACTCCATTTTT
1 CCCTCGAACT-TCCAAAAATTCCATTTTT
12684 GACCTTAAAA
Statistics
Matches: 240, Mismatches: 34, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
28 8 0.03
29 104 0.43
30 121 0.50
31 7 0.03
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
CCCTCGAACTTCCAAAAATTCCATTTTTA
Found at i:12467 original size:59 final size:58
Alignment explanation
Indices: 12366--12654 Score: 253
Period size: 59 Copynumber: 4.8 Consensus size: 58
12356 GAGGTCCCTG
* * * *
12366 AACTATCCGAAAATTATATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCAACCCCGA
1 AACT-TCCAAAAATTCTATTTTTACCCCCGAAC-TCCAAAAATTCCATTTTTAACCCCGA
* *
12426 AACTTCCAAAAATTCTATTTTTACCCCCGAACATCCAAAAATTCCATTTTTAACACCAA
1 AACTTCCAAAAATTCTATTTTTACCCCCGAAC-TCCAAAAATTCCATTTTTAACCCCGA
* ** * *
12485 AACTTCCAAAAATTCCATTTTTACCCCCGAACTTTAACAAATTCCATTTTTGATCCCGA
1 AACTTCCAAAAATTCTATTTTTACCCCCGAACTCCAA-AAATTCCATTTTTAACCCCGA
* ** * **
12544 AACTTCCAAAAATT-TCATTTTTGACCTCAAAACTTCTAAAAATTATATTTTT-ACCCTCG-
1 AACTTCCAAAAATTCT-ATTTTT-ACCCCCGAAC-TCCAAAAATTCCATTTTTAACCC-CGA
* * * *
12603 AACCTCCAAAATTTCCATTTTTGA-CCCCGAAACTTTCAAAAATTACCATTTT
1 AACTTCCAAAAATTCTATTTTT-ACCCCCG-AAC-TCCAAAAATT-CCATTTT
12655 GCCCTCGGAT
Statistics
Matches: 189, Mismatches: 32, Indels: 16
0.80 0.14 0.07
Matches are distributed among these distances:
58 5 0.03
59 151 0.80
60 29 0.15
61 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (58 bp):
AACTTCCAAAAATTCTATTTTTACCCCCGAACTCCAAAAATTCCATTTTTAACCCCGA
Found at i:12552 original size:89 final size:88
Alignment explanation
Indices: 12383--12654 Score: 300
Period size: 89 Copynumber: 3.1 Consensus size: 88
12373 CGAAAATTAT
* * * * *
12383 ATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTCAACCCCGAAACTTCCAAAAATTCTATTTT
1 ATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTACCCCCG-AACTT-CAAAAATTCCATTTT
*
12447 T-ACCCCCG-AACATCCAAAAATTCC
64 TGA-CCCCGAAACTTCCAAAAATTCC
*
12471 ATTTTTAACAC-CAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTTAACAAATTCCATTTT
1 ATTTTTAAC-CTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCAA-AAATTCCATTTT
* *
12535 TGATCCCGAAACTTCCAAAAATTTC
64 TGACCCCGAAACTTCCAAAAATTCC
* * ** * * *
12560 ATTTTTGACCTCAAAACTTCTAAAAATTATATTTTTACCCTCGAACCTCCAAAATTTCCATTTTT
1 ATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAA-CTTCAAAAATTCCATTTTT
*
12625 GACCCCGAAACTTTCAAAAATTACC
65 GACCCCGAAACTTCCAAAAATT-CC
12650 ATTTT
1 ATTTT
12655 GCCCTCGGAT
Statistics
Matches: 156, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
87 2 0.01
88 31 0.20
89 113 0.72
90 10 0.06
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.34
Consensus pattern (88 bp):
ATTTTTAACCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCAAAAATTCCATTTTTG
ACCCCGAAACTTCCAAAAATTCC
Found at i:12660 original size:59 final size:58
Alignment explanation
Indices: 12489--12776 Score: 182
Period size: 59 Copynumber: 4.9 Consensus size: 58
12479 CACCAAAACT
* * *
12489 TCCAAAAATTCCATTTTT-ACCCCCG-AACTTT-AACAAATT-CCATTTTTGATCCCGAAACT
1 TCCAAAATTTCCATTTTTGA-CCCCGAAACTTTCAA-AAATTACCA-TTTTG-CCCCG-AACG
* * * * *
12548 TCCAAAAATTT-CATTTTTGACCTCAAAAC-TTCTAAAAATTA-TATTTTTACCCTCGAACC
1 TCC-AAAATTTCCATTTTTGACCCCGAAACTTTC-AAAAATTACCA-TTTTGCCC-CGAACG
* *
12607 TCCAAAATTTCCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTGCCCTCGGATG
1 TCCAAAATTTCCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTGCCC-CGAACG
** *** * * * *
12666 TCCAAAAACTCCATTTTTGACCTTAAAACTCTC-AAAATTACCCTTTTACCCCTGAATG
1 TCCAAAATTTCCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTGCCCC-GAACG
* * * *
12724 TCTAAAAATTT-CATTTTTAACTCCG-AACTTTCCTAAAATTACCATTTTGCCCC
1 TC-CAAAATTTCCATTTTTGACCCCGAAACTTT-CAAAAATTACCATTTTGCCCC
12777 CCGAGTATCC
Statistics
Matches: 181, Mismatches: 34, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
57 6 0.03
58 39 0.22
59 107 0.59
60 27 0.15
61 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (58 bp):
TCCAAAATTTCCATTTTTGACCCCGAAACTTTCAAAAATTACCATTTTGCCCCGAACG
Found at i:14562 original size:76 final size:76
Alignment explanation
Indices: 14470--14621 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
14460 CTTTGGGTAG
14470 GTTCCTTCTCTTCTTTGGAACATAAATTTGTTCCTATTAGCCTTTCAATGATCTCTCAAGTCTCA
1 GTTCCTTCTCTTCTTTGGAACATAAATTTGTTCCTATTAGCCTTTCAATGATCTCTCAAGTCTCA
14535 ATGTGTATTAA
66 ATGTGTATTAA
*
14546 GTTCCTTCTCTTCTTTGGAACATAAATTTGTTCCTATTAGTCTTTCAATGATCTCTCAAGTCTCA
1 GTTCCTTCTCTTCTTTGGAACATAAATTTGTTCCTATTAGCCTTTCAATGATCTCTCAAGTCTCA
14611 ATGTGTATTAA
66 ATGTGTATTAA
14622 ATATATAGGC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (76 bp):
GTTCCTTCTCTTCTTTGGAACATAAATTTGTTCCTATTAGCCTTTCAATGATCTCTCAAGTCTCA
ATGTGTATTAA
Found at i:17397 original size:244 final size:244
Alignment explanation
Indices: 16968--17440 Score: 752
Period size: 244 Copynumber: 1.9 Consensus size: 244
16958 TGAATCATGC
* *
16968 ATATATCTCATATGGAATCTTTGACATGTATTCTCGTTTTGCATAATTCTTTAGCGACATAAAAG
1 ATATATCTCATATGGAATCTTTAACATGTATTCTCGTTTTGCATAATTCTCTAGCGACATAAAAG
** *
17033 CTGTTGGAAATTCGATGAGCCCAACGCACTAACTACAGAAGACCTTGGACCTACAAGTAATGTTA
66 CTGTTGGAAATTCGACAAGCCCAACGCACTAACTACAGAAGACCTAGGACCTACAAGTAATGTTA
* * *
17098 CACCAATTCTATTAAGTCGGTTAACCTTTTTATTTTCTAACTCACAACAAATAGATTTCACCTTA
131 CACCAACTCTATGAAGTCGATTAACCTTTTTATTTTCTAACTCACAACAAATAGATTTCACCTTA
**
17163 GTGAAATATTGAGAAATAGTTAAGTTCCCTTGTGATATACCCACGAGTT
196 GTGAAATAAAGAGAAATAGTTAAGTTCCCTTGTGATATACCCACGAGTT
*
17212 ATATATCTCATATGGAATCTTTAACATGTATTCTCGTTTTGCATAATTCTCTAGCGACATAAAGG
1 ATATATCTCATATGGAATCTTTAACATGTATTCTCGTTTTGCATAATTCTCTAGCGACATAAAAG
* * *
17277 CTGTTGGAAATTTGACAAGCCCAACGCA-TCCACTACAGAAGATCTAGGACCTACAAGTAATGTT
66 CTGTTGGAAATTCGACAAGCCCAACGCACT-AACTACAGAAGACCTAGGACCTACAAGTAATGTT
***
17341 ACACCAACTCTATGAAGTCGATTAACCTTTTTATTTTCTAACTTGTGAA-AAATAGATTTCACCT
130 ACACCAACTCTATGAAGTCGATTAACCTTTTTATTTTCTAAC-TCACAACAAATAGATTTCACCT
*
17405 TATTGAAATAAAGAGAAATAGTTAAGTTCCCTTGTG
194 TAGTGAAATAAAGAGAAATAGTTAAGTTCCCTTGTG
17441 TGATACATGC
Statistics
Matches: 209, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
243 1 0.00
244 205 0.98
245 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (244 bp):
ATATATCTCATATGGAATCTTTAACATGTATTCTCGTTTTGCATAATTCTCTAGCGACATAAAAG
CTGTTGGAAATTCGACAAGCCCAACGCACTAACTACAGAAGACCTAGGACCTACAAGTAATGTTA
CACCAACTCTATGAAGTCGATTAACCTTTTTATTTTCTAACTCACAACAAATAGATTTCACCTTA
GTGAAATAAAGAGAAATAGTTAAGTTCCCTTGTGATATACCCACGAGTT
Found at i:18806 original size:28 final size:28
Alignment explanation
Indices: 18733--18841 Score: 130
Period size: 28 Copynumber: 3.9 Consensus size: 28
18723 ATACAATTAC
* *
18733 TCAGGCAGTAGAGCCGACCATATATTAT
1 TCAGGCAGCAGAGCCGACCATATATCAT
* * *
18761 TTAGGTAG-AGGAGTCGACCATATATCAT
1 TCAGGCAGCA-GAGCCGACCATATATCAT
*
18789 TCAGGCAGCATAGCCGACCATATATCAT
1 TCAGGCAGCAGAGCCGACCATATATCAT
* *
18817 TCAGGCAGCAAAGCCAACCATATAT
1 TCAGGCAGCAGAGCCGACCATATAT
18842 AAAATCTAAC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 1 0.01
28 67 0.97
29 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (28 bp):
TCAGGCAGCAGAGCCGACCATATATCAT
Found at i:25273 original size:7 final size:7
Alignment explanation
Indices: 25261--25321 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
25251 TCAAAGTTCG
25261 AAATTTA
1 AAATTTA
*
25268 AAATTTG
1 AAATTTA
*
25275 AAATTTG
1 AAATTTA
*
25282 AAA-TTC
1 AAATTTA
*
25288 GAATTTA
1 AAATTTA
25295 AAATTTA
1 AAATTTA
**
25302 AAATAAA
1 AAATTTA
25309 AAATATTA
1 AAAT-TTA
25317 AAATT
1 AAATT
25322 ATGTATCGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
6 4 0.09
7 34 0.79
8 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (7 bp):
AAATTTA
Found at i:25279 original size:14 final size:14
Alignment explanation
Indices: 25260--25305 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
25250 TTCAAAGTTC
25260 GAAATTTAAAATTT
1 GAAATTTAAAATTT
* *
25274 GAAATTTGAAATTC
1 GAAATTTAAAATTT
25288 G-AATTTAAAATTT
1 GAAATTTAAAATTT
*
25301 AAAAT
1 GAAAT
25306 AAAAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (14 bp):
GAAATTTAAAATTT
Found at i:25312 original size:27 final size:28
Alignment explanation
Indices: 25257--25312 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
25247 TGATTCAAAG
* ***
25257 TTCGAAATTTAAAATTTGAAATTTGAAA
1 TTCGAAATTTAAAATTTAAAATAAAAAA
25285 TTCG-AATTTAAAATTTAAAATAAAAAA
1 TTCGAAATTTAAAATTTAAAATAAAAAA
25312 T
1 T
25313 ATTAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.38
Consensus pattern (28 bp):
TTCGAAATTTAAAATTTAAAATAAAAAA
Found at i:26400 original size:9 final size:9
Alignment explanation
Indices: 26382--26444 Score: 68
Period size: 9 Copynumber: 7.8 Consensus size: 9
26372 GTCAGCAAAT
26382 AATT-TTAA
1 AATTATTAA
26390 AATTATTAA
1 AATTATTAA
26399 AATTATTAA
1 AATTATTAA
26408 AATTATT--
1 AATTATTAA
26415 --TT-TTAA
1 AATTATTAA
*
26421 AAATA-TAA
1 AATTATTAA
26429 AATTATTAA
1 AATTATTAA
26438 AATTATT
1 AATTATT
26445 TTTTTGAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
8 12 0.26
9 30 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTATTAA
Found at i:26431 original size:21 final size:22
Alignment explanation
Indices: 26395--26435 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
26385 TTTAAAATTA
*
26395 TTAAAATTATTAAAATTATTTT
1 TTAAAAATATTAAAATTATTTT
26417 TTAAAAATA-TAAAATTATT
1 TTAAAAATATTAAAATTATT
26436 AAAATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAAATATTAAAATTATTTT
Found at i:26476 original size:30 final size:30
Alignment explanation
Indices: 26384--26469 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 30
26374 CAGCAAATAA
*
26384 TTTTAAAATTATTAAAATTATTAAAATTATT
1 TTTTAAAAATA-TAAAATTATTAAAATTATT
26415 TTTTAAAAATATAAAATTATTAAAATTATT
1 TTTTAAAAATATAAAATTATTAAAATTATT
**
26445 TTTTTGAAATAATAAAATTATTAAA
1 TTTTAAAAAT-ATAAAATTATTAAA
26470 TAATTTTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
30 27 0.53
31 24 0.47
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
TTTTAAAAATATAAAATTATTAAAATTATT
Found at i:27875 original size:154 final size:155
Alignment explanation
Indices: 27640--27950 Score: 606
Period size: 154 Copynumber: 2.0 Consensus size: 155
27630 CCACATCAGC
27640 AAGACCGTTAAAAAATCACCAATTTGACCAAAAAAAAAGATTATGTATGAAAGTGAACCCAAAAA
1 AAGACCGTTAAAAAATCACCAATTTGACCAAAAAAAAAGATTATGTATGAAAGTGAACCCAAAAA
27705 ACCCTTAAGGGTCAAAATGACCAAACACCTAAATGTTAGGGACTAATTTTGTCTTTATGCCTAAA
66 ACCCTTAAGGGTCAAAATGACCAAACACCTAAATGTTAGGGACTAATTTTGTCTTTATGCCTAAA
27770 AATATTAAAAACAACGTTCAAAATG
131 AATATTAAAAACAACGTTCAAAATG
27795 AAGACCGTTAAAAAATCACCAATTTGA-CAAAAAAAAAGATTATGTATGAAAGTGAACCCAAAAA
1 AAGACCGTTAAAAAATCACCAATTTGACCAAAAAAAAAGATTATGTATGAAAGTGAACCCAAAAA
27859 ACCCTTAAGGGTCAAAATGACCAAACACCTAAATGTTAGGGACTAATTTTGTCTTTATGCCTAAA
66 ACCCTTAAGGGTCAAAATGACCAAACACCTAAATGTTAGGGACTAATTTTGTCTTTATGCCTAAA
*
27924 AATATTTAAAACAACGTTCAAAATG
131 AATATTAAAAACAACGTTCAAAATG
27949 AA
1 AA
27951 CACCAAGTTC
Statistics
Matches: 155, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
154 128 0.83
155 27 0.17
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (155 bp):
AAGACCGTTAAAAAATCACCAATTTGACCAAAAAAAAAGATTATGTATGAAAGTGAACCCAAAAA
ACCCTTAAGGGTCAAAATGACCAAACACCTAAATGTTAGGGACTAATTTTGTCTTTATGCCTAAA
AATATTAAAAACAACGTTCAAAATG
Found at i:28027 original size:29 final size:26
Alignment explanation
Indices: 27973--28030 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 26
27963 TATGAGGTGG
* *
27973 TTTCTTATAATTTATAATTTTGTATA
1 TTTCTTATAATTTAAAATTTTCTATA
27999 TTTCTTAATAATTTTAAATATTTTCTATA
1 TTTCTT-ATAA-TTTAAA-ATTTTCTATA
28028 TTT
1 TTT
28031 TTTAGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 6 0.22
27 4 0.15
28 5 0.19
29 12 0.44
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTCTTATAATTTAAAATTTTCTATA
Found at i:28764 original size:19 final size:20
Alignment explanation
Indices: 28740--28783 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28730 AAATCATGTG
28740 AAAAATTAAA-TAAAACAAA
1 AAAAATTAAATTAAAACAAA
**
28759 AAAAATTAAATTAAATTAAA
1 AAAAATTAAATTAAAACAAA
28779 AAAAA
1 AAAAA
28784 AATAACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAATTAAATTAAAACAAA
Found at i:30555 original size:19 final size:20
Alignment explanation
Indices: 30514--30560 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
30504 CCTTTGAAAA
* *
30514 ATTTTA-AATTTTAAATATT
1 ATTTTATAAATTTAAATATC
30533 ATTTTATAAATTTAAATA-C
1 ATTTTATAAATTTAAATATC
30552 ATTTTATAA
1 ATTTTATAA
30561 TTGAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTATAAATTTAAATATC
Found at i:30567 original size:18 final size:19
Alignment explanation
Indices: 30533--30568 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30523 TTTAAATATT
*
30533 ATTTTATAAATTTAAATAC
1 ATTTTATAAATTGAAATAC
30552 ATTTTAT-AATTGAAATA
1 ATTTTATAAATTGAAATA
30569 GAATAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTTATAAATTGAAATAC
Found at i:31656 original size:18 final size:18
Alignment explanation
Indices: 31633--31685 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 18
31623 ATTGTAAGAT
31633 AATTTAACAAATAACATA
1 AATTTAACAAATAACATA
31651 AATTTAA-AAACTAA-A-A
1 AATTTAACAAA-TAACATA
*
31667 AATTTAACTAATAAC-TA
1 AATTTAACAAATAACATA
31684 AA
1 AA
31686 ATAATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
16 11 0.37
17 9 0.30
18 10 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (18 bp):
AATTTAACAAATAACATA
Found at i:31671 original size:16 final size:16
Alignment explanation
Indices: 31650--31706 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 16
31640 CAAATAACAT
31650 AAATTTAAAAACTAAA
1 AAATTTAAAAACTAAA
31666 AAATTTAACTAATAACTAAA
1 AAATTT-A--AA-AACTAAA
31686 ATAATTT-AAAACTAAA
1 A-AATTTAAAAACTAAA
31702 TAAAT
1 -AAAT
31707 CATTATACGT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 16 0.46
17 4 0.11
19 2 0.06
20 8 0.23
21 5 0.14
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTTAAAAACTAAA
Done.