Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010780.1 Kokia drynarioides strain JFW-HI SEQ_125745, 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: 19860
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Warning! 145 characters in sequence are not A, C, G, or T
Found at i:1448 original size:139 final size:140
Alignment explanation
Indices: 1198--1500 Score: 448
Period size: 139 Copynumber: 2.2 Consensus size: 140
1188 ACCACAGCTC
* * * * *
1198 CCTGATGAGACACTGAGGAGTAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCCAGATGAGGT
1 CCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCGAAACGAGCAAATCTTCCAAATAAGGT
* * * * * *
1263 ACTGTGAAGTGAACCAAATTCTTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAG-TGATG
66 ACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAACAGACGACG
1327 -GGATCATCTT
131 CGG-TCATCTT
1337 CCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCGAAACGAGCAAATCTTCCAAATAAGGT
1 CCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCGAAACGAGCAAATCTTCCAAATAAGGT
* * *
1402 ACTGAGAAGTGAACCAAATTCGTCTTCTTGGTGAGATATAGAGAAGCGAATTAAAACAGACGACG
66 ACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAACAGACGACG
1467 CGGTCATCTT
131 CGGTCATCTT
*
1477 CCTGATGAGATACTGAGAAGAAGA
1 CCTGATGAGACACTGAGAAGAAGA
1501 GCAAACCAAA
Statistics
Matches: 147, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
139 112 0.76
140 33 0.22
141 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (140 bp):
CCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCGAAACGAGCAAATCTTCCAAATAAGGT
ACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTAAAACAGACGACG
CGGTCATCTT
Found at i:1753 original size:350 final size:350
Alignment explanation
Indices: 1111--1915 Score: 1423
Period size: 350 Copynumber: 2.3 Consensus size: 350
1101 TACCCACAAG
1111 CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAACCAAACCCATGCTCGACATGA
1 CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAACCAAA-CCATGCTCGACATGA
*
1176 GCAAATCTTCGAACCACAGCTCCCTGATGAGACACTGAGGAGTAGACCCAAACGAGGCTCGAAAC
65 GCAAATCTTCGAACCACAGCTCCCTGATGAGACACTGAGGAGAAGACCCAAACGAGGCTCGAAAC
*
1241 GAGCAAATCTTCCAGATGAGGTACTGTGAAGTGAACCAAATTCTTCTTCCTGATGAGATACAGAG
130 GAGCAAATCTTCCAGATGAGGTACTGTGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
1306 AAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAG
195 AAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAG
*
1371 GCTCGAAACGAGCAAATCTTCCAAATAAGGTACTGAGAAGTGAACCAAATTCGTCTTCTTGGTGA
260 GCTCAAAACGAGCAAATCTTCCAAATAAGGTACTGAGAAGTGAACCAAATTCGTCTTCTTGGTGA
*
1436 GATATAGAGAAGCGAATTAAAACAGA
325 GATAAAGAGAAGCGAATTAAAACAGA
*
1462 CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGAGCAAACCAAATCCATGCTCGACATGA
1 CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAACCAAA-CCATGCTCGACATGA
1527 GCAAATCTTCGAACCACAGCTCCCTGATGAGACACTGAGGAGAAGACCCAAAC-AGGCTCGAAAC
65 GCAAATCTTCGAACCACAGCTCCCTGATGAGACACTGAGGAGAAGACCCAAACGAGGCTCGAAAC
1591 GAGCAAATCTTCCAGATGAGGTACTGTGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
130 GAGCAAATCTTCCAGATGAGGTACTGTGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
* *
1656 AAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGATAAGAAGACCCAAACGAG
195 AAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAG
* *
1721 GCTCAAAACGAGCAAATCTTCTAGATAAGGTACTGAGAAGTGAACCAAATTCGTCTTCTTGGTGA
260 GCTCAAAACGAGCAAATCTTCCAAATAAGGTACTGAGAAGTGAACCAAATTCGTCTTCTTGGTGA
* *
1786 GATAAAGAGAAGCGAATTGAAACTGA
325 GATAAAGAGAAGCGAATTAAAACAGA
* **
1812 CGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAACCAAACTCATGCTCGATGTGA
1 CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAACCAAAC-CATGCTCGACATGA
* * *
1877 GCAAATCTTCAAACCACAGCTTCCTGATGAGACATTGAG
65 GCAAATCTTCGAACCACAGCTCCCTGATGAGACACTGAG
1916 AAGCAGGTCG
Statistics
Matches: 434, Mismatches: 19, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
349 1 0.00
350 318 0.73
351 115 0.26
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (350 bp):
CGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAACCAAACCATGCTCGACATGAG
CAAATCTTCGAACCACAGCTCCCTGATGAGACACTGAGGAGAAGACCCAAACGAGGCTCGAAACG
AGCAAATCTTCCAGATGAGGTACTGTGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
AGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGG
CTCAAAACGAGCAAATCTTCCAAATAAGGTACTGAGAAGTGAACCAAATTCGTCTTCTTGGTGAG
ATAAAGAGAAGCGAATTAAAACAGA
Found at i:1798 original size:139 final size:139
Alignment explanation
Indices: 1549--1850 Score: 446
Period size: 139 Copynumber: 2.2 Consensus size: 139
1539 ACCACAGCTC
* * *
1549 CCTGATGAGACACTGAGGAGAAGACCCAAACAGGCTCGAAACGAGCAAATCTTCCAGATGAGGTA
1 CCTGATGAGACACTGAGAAGAAGACCCAAACAGGCTCAAAACGAGCAAATCTTCCAGATAAGGTA
* * * * *
1614 CTGTGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAG-TGATG-
66 CTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAAAGAGAAGCGAATTGAAACAGACGACGT
1677 GGATCATCTT
131 GG-TCATCTT
* *
1687 CCTGATGAGACACTGATAAGAAGACCCAAACGAGGCTCAAAACGAGCAAATCTTCTAGATAAGGT
1 CCTGATGAGACACTGAGAAGAAGACCCAAAC-AGGCTCAAAACGAGCAAATCTTCCAGATAAGGT
* * *
1752 ACTGAGAAGTGAACCAAATTCGTCTTCTTGGTGAGATAAAGAGAAGCGAATTGAAACTGACGACG
65 ACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAAAGAGAAGCGAATTGAAACAGACGACG
1817 TGGTCATCTT
130 TGGTCATCTT
*
1827 CCTGATGAGATACTGAGAAGAAGA
1 CCTGATGAGACACTGAGAAGAAGA
1851 TCAAACCAAA
Statistics
Matches: 146, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
138 29 0.20
139 83 0.57
140 32 0.22
141 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (139 bp):
CCTGATGAGACACTGAGAAGAAGACCCAAACAGGCTCAAAACGAGCAAATCTTCCAGATAAGGTA
CTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAAAGAGAAGCGAATTGAAACAGACGACGT
GGTCATCTT
Found at i:2430 original size:18 final size:18
Alignment explanation
Indices: 2389--2487 Score: 112
Period size: 18 Copynumber: 5.6 Consensus size: 18
2379 CCATACTCTC
2389 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
** *
2407 -TTAAATTCGTTTAAAAA
1 TTTAAATTTATTTTAAAA
2424 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
* *
2442 TTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAA
* *
2459 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAA
2477 TTTAAAGTTTA
1 TTTAAA-TTTA
2488 AAATAAATAA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
17 28 0.42
18 35 0.53
19 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:2448 original size:24 final size:24
Alignment explanation
Indices: 2421--2467 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2411 ATTCGTTTAA
*
2421 AAATTTAAATTT-ATTTTAAAATTT
1 AAATTT-AATTTAAGTTTAAAATTT
2445 AAATTTAATTTAAGTTTAAAATT
1 AAATTTAATTTAAGTTTAAAATT
2468 ATTTTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AAATTTAATTTAAGTTTAAAATTT
Found at i:2463 original size:35 final size:36
Alignment explanation
Indices: 2389--2488 Score: 116
Period size: 35 Copynumber: 2.8 Consensus size: 36
2379 CCATACTCTC
**
2389 TTTAAATTTATTTTAAAA-TTAAA-TTCGTTTAAAAA
1 TTTAAATTTATTTTAAAATTTAAATTTAATTT-AAAA
*
2424 TTTAAATTTATTTTAAAATTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAAATTTAAATTTAATTTAAAA
* *
2459 TTTAAAATTATTTTCAAATTTAAAGTTTAA
1 TTTAAATTTATTTTAAAATTTAAA-TTTAA
2489 AATAAATAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
35 42 0.74
36 10 0.18
37 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (36 bp):
TTTAAATTTATTTTAAAATTTAAATTTAATTTAAAA
Found at i:3141 original size:18 final size:19
Alignment explanation
Indices: 3107--3148 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
3097 AAAACGTTTC
*
3107 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
3126 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
3144 AATAA
1 AATAA
3149 TAATACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:4464 original size:59 final size:59
Alignment explanation
Indices: 4372--4865 Score: 767
Period size: 59 Copynumber: 8.4 Consensus size: 59
4362 GAGGTCCCTA
*
4372 AACCTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
4431 AACCTTCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACACCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * * *
4490 TATCTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCTCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
*
4549 AACCTTCTAAAAATTACCATTTTACCCACGAACTTCCAAAAATCCCATTTTTGA-CCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
4607 AACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
4666 AACCTTCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
4725 AACCTTCTAAAAAATACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
4784 AACCTCCAAAAAATTACCATTTTACCCCCGAA-TCTCCAAAAATCCCATTTTTGACCCCA
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATCCCATTTTTGACCCCG
4843 AACCTTCTAAAAATTACCATTTT
1 AACCTTCTAAAAATTACCATTTT
4866 GCTGCCGTGC
Statistics
Matches: 396, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
58 56 0.14
59 340 0.86
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (59 bp):
AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:4788 original size:235 final size:236
Alignment explanation
Indices: 4371--4865 Score: 807
Period size: 235 Copynumber: 2.1 Consensus size: 236
4361 GGAGGTCCCT
** *
4371 AAACCTTCTAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
** *
4436 TCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACACCGTATCTTCTAAA
66 TCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACACCAAACCTTCTAAA
* * * * * * *
4501 AATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCTCGAACCTTCTAAAAATTAC
131 AAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTCCAAAAAATTAC
4566 CATTTTACCCACGAA-CTTCCAAAAATCCCATTTTTGA-CCC
196 CATTTTACCCACGAATC-TCCAAAAATCCCATTTTTGACCCC
*
4606 GAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
1 AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
4671 TCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC-CTCAAACCTTCTAA
66 TCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACAC-CAAACCTTCTAA
*
4735 AAAATACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTCCAAAAAATTA
130 AAAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTCCAAAAAATTA
*
4800 CCATTTTACCCCCGAATCTCCAAAAATCCCATTTTTGACCCC
195 CCATTTTACCCACGAATCTCCAAAAATCCCATTTTTGACCCC
4842 AAACCTTCTAAAAATTACCATTTT
1 AAACCTTCTAAAAATTACCATTTT
4866 GCTGCCGTGC
Statistics
Matches: 240, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
234 1 0.00
235 212 0.88
236 27 0.11
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (236 bp):
AAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
TCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACACCAAACCTTCTAAA
AAATACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTCCAAAAAATTAC
CATTTTACCCACGAATCTCCAAAAATCCCATTTTTGACCCC
Found at i:6003 original size:11 final size:11
Alignment explanation
Indices: 5987--6024 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5977 GGTCCCTATA
5987 ATTTTAATTTT
1 ATTTTAATTTT
5998 ATTTTAA-TTT
1 ATTTTAATTTT
* *
6008 AGTTTAATATT
1 ATTTTAATTTT
6019 ATTTTA
1 ATTTTA
6025 TTTATGTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:6013 original size:21 final size:21
Alignment explanation
Indices: 5989--6064 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 21
5979 TCCCTATAAT
5989 TTTAATTTTATTTTAATTTAG
1 TTTAATTTTATTTTAATTTAG
*
6010 TTTAATATTATTTT-ATTTATG
1 TTTAATTTTATTTTAATTTA-G
*
6031 TTTCTAATTTGTACCTTTAATTTA-
1 -TT-TAATTT-TA-TTTTAATTTAG
6055 TTTACATTTT
1 TTTA-ATTTT
6065 CAATTTAGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
20 5 0.11
21 14 0.31
22 5 0.11
23 11 0.24
24 2 0.04
25 3 0.07
26 5 0.11
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTAATTTTATTTTAATTTAG
Found at i:6188 original size:4 final size:4
Alignment explanation
Indices: 6162--6308 Score: 74
Period size: 4 Copynumber: 36.2 Consensus size: 4
6152 CTCATTTATT
* * *
6162 TTTA TATTA ATTA TATTA TTTTA TTTA -GTA TTTA ATT- TTTA TTTA TTTA
1 TTTA T-TTA TTTA T-TTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * **
6211 TTTA TTT- GTTA TTCA TTT- TTTA TGTTA TTTA TATTC TTGCC TTTA TTTAA
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA T-TTA TT-TA TTTA TTT-A
* *
6261 TCTTA TTTA TTTA -TTG TTT- TTTA TTTA TTTTA TTTA TTTG TTT- TTTA
1 T-TTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
6308 T
1 T
6309 GCCATTTATA
Statistics
Matches: 111, Mismatches: 16, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
3 17 0.15
4 64 0.58
5 27 0.24
6 3 0.03
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:6216 original size:30 final size:31
Alignment explanation
Indices: 6172--6242 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
6162 TTTATATTAA
*
6172 TTATATTATTTTATTTAG-TATTTAATTTTTAT-
1 TTAT-TTA-TTTATTT-GTTATTCAATTTTTATG
*
6204 TTATTTATTTATTTGTTATTCATTTTTTATG
1 TTATTTATTTATTTGTTATTCAATTTTTATG
6235 TTATTTAT
1 TTATTTAT
6243 ATTCTTGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 19 0.54
31 11 0.31
32 4 0.11
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.70
Consensus pattern (31 bp):
TTATTTATTTATTTGTTATTCAATTTTTATG
Found at i:6217 original size:18 final size:18
Alignment explanation
Indices: 6155--6299 Score: 88
Period size: 18 Copynumber: 8.0 Consensus size: 18
6145 ATTTGGTCTC
*
6155 ATTTATTTTTATATTAATT
1 ATTTATTTTTAT-TTATTT
*
6174 ATATTA-TTTTATTTA-GT
1 AT-TTATTTTTATTTATTT
6191 ATTTAATTTTTATTTATTT
1 ATTT-ATTTTTATTTATTT
*
6210 ATTTATTTGTTATTCATTT
1 ATTTATTT-TTATTTATTT
*
6229 -TTTA-TGTTATTTATATT
1 ATTTATTTTTATTTAT-TT
* ***
6246 -CTTGCCTTTATTTAATCTT
1 ATTTATTTTTATTT-AT-TT
*
6265 ATTTATTTATTGTTT-TTT
1 ATTTATTT-TTATTTATTT
6283 ATTTA-TTTTATTTATTT
1 ATTTATTTTTATTTATTT
6300 GTTTTTTATG
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
16 14 0.14
17 14 0.14
18 33 0.33
19 27 0.27
20 6 0.06
21 5 0.05
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (18 bp):
ATTTATTTTTATTTATTT
Found at i:6222 original size:11 final size:10
Alignment explanation
Indices: 6155--6299 Score: 61
Period size: 11 Copynumber: 13.8 Consensus size: 10
6145 ATTTGGTCTC
6155 ATTTATTTTT
1 ATTTATTTTT
6165 ATATTAATTATATT
1 AT-TT-ATT-T-TT
*
6179 ATTTTATTTAGT
1 A-TTTATTT-TT
6191 ATTTAATTTTT
1 ATTT-ATTTTT
6202 ATTTA--TTT
1 ATTTATTTTT
6210 ATTTATTTGTT
1 ATTTATTT-TT
*
6221 ATTCATTTTTT
1 ATTTA-TTTTT
*
6232 ATGTTATTTAT
1 AT-TTATTTTT
*
6243 ATTCT-TGCCTTT
1 ATT-TAT--TTTT
* *
6255 ATTTAATCTT
1 ATTTATTTTT
6265 ATTTA--TTT
1 ATTTATTTTT
6273 ATTGT-TTTTT
1 ATT-TATTTTT
6283 ATTTA-TTTT
1 ATTTATTTTT
6292 ATTTATTT
1 ATTTATTT
6300 GTTTTTTATG
Statistics
Matches: 104, Mismatches: 11, Indels: 40
0.67 0.07 0.26
Matches are distributed among these distances:
8 13 0.12
9 11 0.11
10 21 0.20
11 28 0.27
12 21 0.20
13 4 0.04
14 5 0.05
15 1 0.01
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:6283 original size:10 final size:9
Alignment explanation
Indices: 6252--6299 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
6242 TATTCTTGCC
6252 TTTATTTAAT
1 TTTATTT-AT
*
6262 CTTATTTA-
1 TTTATTTAT
*
6270 TTTATTGTTT
1 TTTATT-TAT
6280 TTTATTTAT
1 TTTATTTAT
6289 TTTATTTAT
1 TTTATTTAT
6298 TT
1 TT
6300 GTTTTTTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
8 5 0.16
9 15 0.47
10 12 0.38
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTATTTAT
Found at i:6298 original size:27 final size:27
Alignment explanation
Indices: 6172--6299 Score: 86
Period size: 27 Copynumber: 4.7 Consensus size: 27
6162 TTTATATTAA
*
6172 TTATATTATTTTATTTA-GTATT-TAATTT
1 TTAT-TTATTTTATTTATTTATTGT--TTT
* * *
6200 TTATTTA-TTTATTTATTTGTTATTCAT
1 TTATTTATTTTATTTATTTATTGTT-TT
* * **
6227 TT-TTTATGTTATTTATATTCTTG-CCT
1 TTATTTATTTTATTTAT-TTATTGTTTT
*
6253 TTATTTAATCTTATTTATTTATTGTTTT
1 TTATTT-ATTTTATTTATTTATTGTTTT
6281 TTATTTATTTTATTTATTT
1 TTATTTATTTTATTTATTT
6300 GTTTTTTATG
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
26 16 0.20
27 37 0.47
28 26 0.33
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (27 bp):
TTATTTATTTTATTTATTTATTGTTTT
Found at i:6316 original size:24 final size:22
Alignment explanation
Indices: 6265--6317 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
6255 ATTTAATCTT
**
6265 ATTTATTTATTGTTTTTTATTT
1 ATTTATTTATTGTTTTTTATCC
6287 ATTTTATTTATTTGTTTTTTATGCC
1 A-TTTATTTA-TTGTTTTTTAT-CC
6312 ATTTAT
1 ATTTAT
6318 ATTTTTGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 8 0.31
24 16 0.62
25 1 0.04
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (22 bp):
ATTTATTTATTGTTTTTTATCC
Found at i:6317 original size:75 final size:77
Alignment explanation
Indices: 6190--6370 Score: 197
Period size: 77 Copynumber: 2.3 Consensus size: 77
6180 TTTTATTTAG
* **
6190 TATTTAATTTTTATTTATTTATTTATTTGTTATTCATTTTTTATGTTATTTATATTCTTGCC-TT
1 TATTT-ATTTTT-TTTATTTATTT-TATGTTATTCATTTTTTATGCCATTTATATTCTTGCCTTT
*
6254 TATTTAA-TCTTATT
63 TATTCAATTCTTATT
** *
6268 TATTTATTGTTTTTTATTTATTTTAT-TTATTTGTTTTTTATGCCATTTATATTTTTGCCTTTTA
1 TATTTATT-TTTTTTATTTATTTTATGTTATTCATTTTTTATGCCATTTATATTCTTGCCTTTTA
*
6332 TTCAATTTTTATT
65 TTCAATTCTTATT
* *
6345 TTTTTATTTTTTATTTTTATATTTTA
1 TATTTATTTTTT-TTATT-TATTTTA
6371 AGCCATTAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
75 28 0.32
76 14 0.16
77 31 0.35
78 15 0.17
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.71
Consensus pattern (77 bp):
TATTTATTTTTTTTATTTATTTTATGTTATTCATTTTTTATGCCATTTATATTCTTGCCTTTTAT
TCAATTCTTATT
Found at i:6348 original size:8 final size:8
Alignment explanation
Indices: 6337--6369 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
6327 TTTTATTCAA
6337 TTTTTATT
1 TTTTTATT
6345 TTTTTA-T
1 TTTTTATT
6352 TTTTTATT
1 TTTTTATT
*
6360 TTTATATT
1 TTTTTATT
6368 TT
1 TT
6370 AAGCCATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:6361 original size:15 final size:15
Alignment explanation
Indices: 6337--6369 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6327 TTTTATTCAA
*
6337 TTTTTATTTTTTTAT
1 TTTTTATTTTTATAT
6352 TTTTTATTTTTATAT
1 TTTTTATTTTTATAT
6367 TTT
1 TTT
6370 AAGCCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTATTTTTATAT
Found at i:7675 original size:55 final size:55
Alignment explanation
Indices: 7599--7732 Score: 180
Period size: 55 Copynumber: 2.4 Consensus size: 55
7589 ATTTTGATTG
* * * * *
7599 AATCGATTGTTATGCAT-GAATATTGCTTCTTTTGAATCGATTGTTTTTATGTTTA
1 AATCGATTGTCATG-TTGGAATACTGCTTCTTTTGAATCGATTGTTTATATATTTA
7654 AATCGATTGTCATGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATATTTA
1 AATCGATTGTCATGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATATTTA
* * *
7709 AATCAACTGTCATGTTGAAATACT
1 AATCGATTGTCATGTTGGAATACT
7733 TTAATGACGG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
54 1 0.01
55 69 0.99
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (55 bp):
AATCGATTGTCATGTTGGAATACTGCTTCTTTTGAATCGATTGTTTATATATTTA
Found at i:8926 original size:55 final size:55
Alignment explanation
Indices: 8851--8985 Score: 164
Period size: 55 Copynumber: 2.5 Consensus size: 55
8841 TACATAAAAT
* * * *
8851 TATTTCAATATGACAATTGATTTAAATATATAAACAATCAATTCAGAA-GAAGCAA
1 TATTCCAACATGACAATTGATTTAAACATAAAAACAATCAATTCA-AATGAAGCAA
* **
8906 TATTGCAACATGACAATTGATTTAAACATAAAAACAATTGATTCAAATGAAGCAA
1 TATTCCAACATGACAATTGATTTAAACATAAAAACAATCAATTCAAATGAAGCAA
* * *
8961 TATTCCAGCATAACAATCGATTTAA
1 TATTCCAACATGACAATTGATTTAA
8986 TCCAAATTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
54 2 0.03
55 67 0.97
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (55 bp):
TATTCCAACATGACAATTGATTTAAACATAAAAACAATCAATTCAAATGAAGCAA
Found at i:13115 original size:3 final size:3
Alignment explanation
Indices: 13107--13165 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
13097 GGGGAACGAG
* * * * *
13107 GAT GAT GAT GAT GAG GAAT GGT GAG GAT GAT GAT GAT GAG GAAT GGT
1 GAT GAT GAT GAT GAT G-AT GAT GAT GAT GAT GAT GAT GAT G-AT GAT
13154 GAT GAT GAT GAT
1 GAT GAT GAT GAT
13166 TTTAAAATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 40 0.91
4 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:13132 original size:25 final size:25
Alignment explanation
Indices: 13104--13165 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
13094 GAAGGGGAAC
13104 GAGGATGATGATGATGAGGAATGGT
1 GAGGATGATGATGATGAGGAATGGT
13129 GAGGATGATGATGATGAGGAATGGT
1 GAGGATGATGATGATGAGGAATGGT
*
13154 GATGATGATGAT
1 GAGGATGATGAT
13166 TTTAAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.42, T:0.26
Consensus pattern (25 bp):
GAGGATGATGATGATGAGGAATGGT
Found at i:13158 original size:16 final size:15
Alignment explanation
Indices: 13104--13161 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 15
13094 GAAGGGGAAC
13104 GAGGATGATGATGAT
1 GAGGATGATGATGAT
13119 GAGGA--ATG--G-T
1 GAGGATGATGATGAT
13129 GAGGATGATGATGAT
1 GAGGATGATGATGAT
*
13144 GAGGAATGGTGATGAT
1 GAGG-ATGATGATGAT
13160 GA
1 GA
13162 TGATTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
10 6 0.17
11 1 0.03
12 3 0.08
13 3 0.08
14 1 0.03
15 10 0.28
16 12 0.33
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (15 bp):
GAGGATGATGATGAT
Found at i:18990 original size:30 final size:31
Alignment explanation
Indices: 18956--19026 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 31
18946 TTTCGTCCTT
*
18956 TTTAATTTTAATTCAATTTTAA-TTTTCCCC
1 TTTAATTTTAAATCAATTTTAATTTTTCCCC
18986 TTTAATTTTAAATCAATTTTAATTTTTCCCC
1 TTTAATTTTAAATCAATTTTAATTTTTCCCC
19017 TTTAATTTTA
1 TTTAATTTTA
19027 TTTTTTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 21 0.54
31 18 0.46
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTAATTTTAAATCAATTTTAATTTTTCCCC
Found at i:19298 original size:12 final size:12
Alignment explanation
Indices: 19281--19365 Score: 51
Period size: 12 Copynumber: 7.5 Consensus size: 12
19271 TTGGTCCCAT
19281 TTATTTTTTATA
1 TTATTTTTTATA
19293 TTA---TTTATA
1 TTATTTTTTATA
19302 TTATTTTATT-TA
1 TTATTTT-TTATA
* *
19314 GTATTTAATT-T-
1 TTATTT-TTTATA
19325 TTATTTATTTAT-
1 TTATTT-TTTATA
*
19337 TTATTTGTTATA
1 TTATTTTTTATA
*
19349 -TATTTTTTATG
1 TTATTTTTTATA
19360 TTATTT
1 TTATTT
19366 ATATTTTTGC
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
9 9 0.16
11 21 0.36
12 26 0.45
13 2 0.03
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (12 bp):
TTATTTTTTATA
Found at i:19309 original size:26 final size:26
Alignment explanation
Indices: 19280--19367 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
19270 TTTGGTCCCA
19280 TTTATTT-TTTATATTATTTATATTAT
1 TTTATTTATTTAT-TTATTTATATTAT
* *
19306 TTTATTTA-GTATTTAATT-T-TTA-
1 TTTATTTATTTATTTATTTATATTAT
*
19328 TTTATTTATTTATTTGTTATATATT-T
1 TTTATTTATTTATTTATT-TATATTAT
19354 TTTATGTTATTTAT
1 TTTAT-TTATTTAT
19368 ATTTTTGCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
22 8 0.16
23 9 0.18
24 2 0.04
25 6 0.12
26 17 0.34
27 8 0.16
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (26 bp):
TTTATTTATTTATTTATTTATATTAT
Found at i:19340 original size:30 final size:30
Alignment explanation
Indices: 19293--19423 Score: 96
Period size: 30 Copynumber: 4.3 Consensus size: 30
19283 ATTTTTTATA
*
19293 TTATTTATATTATTTTATTTAG-TATTTAATTT
1 TTATTTAT-TTA-TTTATTT-GTTATATAATTT
*
19325 TTATTTATTTATTTATTTGTTATATATTTT
1 TTATTTATTTATTTATTTGTTATATAATTT
* *
19355 TTATGTTATTTATATT-TTTGCCTTTATTTAA-TC
1 TTAT-TTATTTAT-TTATTTG---TTATATAATTT
*
19388 TTATTTATTTA-TTATTT-TTAT-GAA-TT
1 TTATTTATTTATTTATTTGTTATATAATTT
19414 TTATTTATTT
1 TTATTTATTT
19424 GTTTTTTATG
Statistics
Matches: 85, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
26 13 0.15
27 4 0.05
29 1 0.01
30 21 0.25
31 18 0.21
32 17 0.20
33 5 0.06
34 6 0.07
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (30 bp):
TTATTTATTTATTTATTTGTTATATAATTT
Found at i:19342 original size:18 final size:18
Alignment explanation
Indices: 19279--19404 Score: 82
Period size: 18 Copynumber: 6.8 Consensus size: 18
19269 ATTTGGTCCC
19279 ATTTATTTTTTATATTATTT
1 ATTTA-TTTTTAT-TTATTT
*
19299 ATATTA-TTTTATTTA-GT
1 AT-TTATTTTTATTTATTT
19316 ATTTAATTTTTATTTATTT
1 ATTT-ATTTTTATTTATTT
*
19335 ATTTATTTGTTATATATTT
1 ATTTATTT-TTATTTATTT
*
19354 -TTTA-TGTTATTTATATT
1 ATTTATTTTTATTTAT-TT
***
19371 -TTTGCCTTTATTTAATCTT
1 ATTTATTTTTATTT-AT-TT
19390 ATTTATTTATTATTT
1 ATTTATTT-TTATTT
19405 TTATGAATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
16 9 0.11
17 10 0.12
18 26 0.31
19 24 0.29
20 6 0.07
21 9 0.11
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (18 bp):
ATTTATTTTTATTTATTT
Found at i:19347 original size:11 final size:10
Alignment explanation
Indices: 19293--19423 Score: 53
Period size: 11 Copynumber: 13.0 Consensus size: 10
19283 ATTTTTTATA
*
19293 TTATTTA-TA
1 TTATTTATTT
19302 TTATTTTATTT
1 TTA-TTTATTT
*
19313 AGTATTTAATTT
1 -TTATTT-ATTT
19325 TTATTTA--T
1 TTATTTATTT
19333 TTATTTATTT
1 TTATTTATTT
*
19343 GTTATATATTTT
1 -TTATTTA-TTT
19355 TTATGTTATTT
1 TTAT-TTATTT
*
19366 ATATTT-TTGCCT
1 TTATTTATT---T
* *
19378 TTATTTAATC
1 TTATTTATTT
19388 TTATTTA--T
1 TTATTTATTT
19396 TTA-TTATTT
1 TTATTTATTT
* *
19405 TTA-TGAATT
1 TTATTTATTT
19414 TTATTTATTT
1 TTATTTATTT
19424 GTTTTTTATG
Statistics
Matches: 92, Mismatches: 14, Indels: 31
0.67 0.10 0.23
Matches are distributed among these distances:
7 3 0.03
8 11 0.12
9 16 0.17
10 19 0.21
11 25 0.27
12 17 0.18
13 1 0.01
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (10 bp):
TTATTTATTT
Found at i:19416 original size:59 final size:64
Alignment explanation
Indices: 19315--19441 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 64
19305 TTTTATTTAG
*
19315 TATTTAATTTTTATTTATTTATTTATTTGTTATATATTTTTTATGTTATTTATATTTT-TGCC-T
1 TATTTAATTCTTATTTATTTATTTATTTGTTATATA-TTTTTAT-TTATTTATATTTTATGCCAT
19378 T
64 T
* *
19379 TATTTAA-TCTTATTTATTTA-TTATTT-TTATGA-A-TTTTATTTATTTGTTTTTTATGCCATT
1 TATTTAATTCTTATTTATTTATTTATTTGTTAT-ATATTTTTATTTATTTATATTTTATGCCATT
19439 TAT
1 TAT
19442 ATTTTTGCCT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
58 11 0.19
59 10 0.18
60 5 0.09
61 5 0.09
62 7 0.12
63 12 0.21
64 7 0.12
ACGTcount: A:0.23, C:0.04, G:0.05, T:0.69
Consensus pattern (64 bp):
TATTTAATTCTTATTTATTTATTTATTTGTTATATATTTTTATTTATTTATATTTTATGCCATT
Done.