Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012062.1 Kokia drynarioides strain JFW-HI SEQ_127060, 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: 258703
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:7345 original size:91 final size:93
Alignment explanation
Indices: 7246--7431 Score: 247
Period size: 93 Copynumber: 2.0 Consensus size: 93
7236 AAATTTTTTC
* *
7246 AAAAAAAGCAATTAAGTC-CTAC-TTCTTTTTGCATTAAATT-AGGTACTTGAA-TTATCAAAAT
1 AAAAAAAGCAATTAAGTCTCTACATTCTTTTTGCACTAAATTGA-ATACTTGAACTT-TCAAAAT
* *
7307 GCA-TAAAAATATCTTCAAACTTAAAAAAAA
64 GCATTAAAAA-ACCCTCAAACTTAAAAAAAA
* *
7337 AAAAAAAGCAATTAAGTCTCTACATTTTTTTTGCACTCAATTGAATACTTGAACTTTCAAAATGC
1 AAAAAAAGCAATTAAGTCTCTACATTCTTTTTGCACTAAATTGAATACTTGAACTTTCAAAATGC
*
7402 ATTAAAAAACCCTCAAACTTTAAAAAAA
66 ATTAAAAAACCCTCAAACTTAAAAAAAA
7430 AA
1 AA
7432 GCAATTAAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
91 18 0.22
92 4 0.05
93 52 0.63
94 9 0.11
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (93 bp):
AAAAAAAGCAATTAAGTCTCTACATTCTTTTTGCACTAAATTGAATACTTGAACTTTCAAAATGC
ATTAAAAAACCCTCAAACTTAAAAAAAA
Found at i:7566 original size:20 final size:20
Alignment explanation
Indices: 7533--7591 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
7523 ATGACATGTG
7533 AAAAAAATGATAAAA-AATA
1 AAAAAAATGATAAAATAATA
*
7552 AAAAAAATTATTAAAATTTAATA
1 AAAAAAATGA-TAAAA--TAATA
7575 AAAAAAACT-ATAAAATA
1 AAAAAAA-TGATAAAATA
7592 TATTTAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
19 9 0.26
20 7 0.21
22 5 0.15
23 12 0.35
24 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAAATGATAAAATAATA
Found at i:7588 original size:22 final size:23
Alignment explanation
Indices: 7548--7590 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
7538 AATGATAAAA
*
7548 AATAAAAAAAATTATTAAAATTT
1 AATAAAAAAAACTATTAAAATTT
7571 AATAAAAAAAACTA-TAAAAT
1 AATAAAAAAAACTATTAAAAT
7591 ATATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
AATAAAAAAAACTATTAAAATTT
Found at i:7738 original size:19 final size:18
Alignment explanation
Indices: 7681--7739 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
7671 AAGTCGTAAG
*
7681 AAAATTATAGAAAATATAA
1 AAAATTATA-AAATTATAA
*
7700 AGAAA-TATAAAATTCGTAA
1 A-AAATTATAAAATT-ATAA
7719 AAAATTATAAATATTATAA
1 AAAATTATAAA-ATTATAA
7738 AA
1 AA
7740 TTTTAAGACT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 7 0.21
19 20 0.61
20 6 0.18
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAATTATAAAATTATAA
Found at i:12274 original size:21 final size:20
Alignment explanation
Indices: 12249--12296 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
12239 TATTCTCACC
*
12249 TTTATTTACTTATTTATTGTT
1 TTTATTTACTTATTAATT-TT
* * *
12270 TTTATATATTTGTTAATTTT
1 TTTATTTACTTATTAATTTT
12290 TTTATTT
1 TTTATTT
12297 TATGTTTTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (20 bp):
TTTATTTACTTATTAATTTT
Found at i:12338 original size:14 final size:15
Alignment explanation
Indices: 12308--12340 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12298 ATGTTTTTCT
*
12308 TTGTCTTTTATTTAA
1 TTGTCATTTATTTAA
12323 TTGTCATTTA-TTAA
1 TTGTCATTTATTTAA
12337 TTGT
1 TTGT
12341 GTTTATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.64
Consensus pattern (15 bp):
TTGTCATTTATTTAA
Found at i:15532 original size:147 final size:148
Alignment explanation
Indices: 15357--15937 Score: 787
Period size: 147 Copynumber: 3.9 Consensus size: 148
15347 TAAAAAAGAG
* *
15357 AGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTCATTTTAAAGAAAAATTTTAAA
1 AGAGAAAGTTTAGATTTTTAAAAATAAAAATCTAGTTTTTAGTCATTTTAAAGAAAAAGTTTAAA
* * *
15422 TTTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAATTTGGA-TTTTAAGTAAAAT
66 TTTTTAAACAAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAAAT
15486 AGTGATTTTCTTTAAAAA
131 AGTGATTTTCTTTAAAAA
* * * *
15504 AGAGAAAGTTTAGATATTCAAAAATAAAAATCTATTTTTTAGTCTTTTTAAAGAAAAAGTTTAAA
1 AGAGAAAGTTTAGATTTTTAAAAATAAAAATCTAGTTTTTAGTCATTTTAAAGAAAAAGTTTAAA
* *
15569 TTTTTAAATAAAGTTTTGATTTTTTTAAACTATTTTGAAATAAAAGTTTGAATTTTTAAGTAAAA
66 TTTTTAAACAAAGTTTTGATTTTTTT-AACTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAAA
*
15634 TAAT-ATTTTTCTTTAAAAA
130 TAGTGA-TTTTCTTTAAAAA
* * * * *
15653 AGAGAAAGTTTAGATTTTAAAAAATAAAAATATGGTTTTTAGTCATTTAAAAG-TAAAGTTTAAA
1 AGAGAAAGTTTAGATTTTTAAAAATAAAAATCTAGTTTTTAGTCATTTTAAAGAAAAAGTTTAAA
* * * *
15717 TTTTTAAACAAAGTTTTGAATTTTTTAATTATTTTGAAATAAAAGTTTGGATTTTTTAGTAAACT
66 TTTTTAAACAAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAAAT
*
15782 AGTGATTTTCATTAAAAA
131 AGTGATTTTCTTTAAAAA
* *
15800 AGAAAGAAAGTTTAGA-TTTTAAAAA-AAAAATCT-GTTTTTAGTGATTTTAAAGAAAAAATTTA
1 AG--AGAAAGTTTAGATTTTTAAAAATAAAAATCTAGTTTTTAGTCATTTTAAAGAAAAAGTTTA
* ** * * * * *
15862 AATTTTTAAATAATTTTTTTATTTTTTTAACTATTTTGTAATAAAAGTTTTGATTTTGAAATAAA
64 AATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAA
*
15927 GTAGTGATTTT
129 ATAGTGATTTT
15938 TGTTTTAATC
Statistics
Matches: 383, Mismatches: 44, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
146 17 0.04
147 214 0.56
148 66 0.17
149 86 0.22
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (148 bp):
AGAGAAAGTTTAGATTTTTAAAAATAAAAATCTAGTTTTTAGTCATTTTAAAGAAAAAGTTTAAA
TTTTTAAACAAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAAAT
AGTGATTTTCTTTAAAAA
Found at i:15972 original size:147 final size:147
Alignment explanation
Indices: 15319--15972 Score: 766
Period size: 147 Copynumber: 4.4 Consensus size: 147
15309 TAGAGTTTTA
15319 ATTTTTAAG-AAATATAGTGGA-TTTCTTTTAAAAAAGAGAGAGAAAGTTTAGATTTTTAAAAAT
1 ATTTTTAAGTAAA-ATAGT-GATTTTC-TTT-AAAAA-AGA-A-AAAGTTTAGA-TTTTAAAAAT
* * *
15382 AAAAATCTATTTTTTAGTCATTTTAAAGAAAAATTTTAAATTTTTAAACAAAATTTTGATTTTTT
58 AAAAATCTAGTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTT
* *
15447 TAACTATTTCGAAATAAAAATTTGG
123 TAACTATTTTGAAATAAAAGTTTGG
* *
15472 A-TTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAGAAAGTTTAGATATTCAAAAATAAAAATC
1 ATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAAAAAGTTTAGAT-TTTAAAAATAAAAATC
* * *
15536 TATTTTTTAGTCTTTTTAAAGAAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAAACTA
65 TAGTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTT-AACTA
*
15601 TTTTGAAATAAAAGTTTGA
129 TTTTGAAATAAAAGTTTGG
* *
15620 ATTTTTAAGTAAAATAAT-ATTTTTCTTTAAAAAAGAGAAAGTTTAGATTTTAAAAAATAAAAAT
1 ATTTTTAAGTAAAATAGTGA-TTTTCTTTAAAAAAGAAAAAGTTTAGATTTT-AAAAATAAAAAT
* * * * * *
15684 ATGGTTTTTAGTCATTTAAAAG-TAAAGTTTAAATTTTTAAACAAAGTTTTGAATTTTTTAATTA
64 CTAGTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTA
15748 TTTTGAAATAAAAGTTTGG
129 TTTTGAAATAAAAGTTTGG
* * *
15767 ATTTTTTAGTAAACTAGTGATTTTCATTAAAAAAGAAAGAAAGTTTAGATTTTAAAAA-AAAAAT
1 ATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAG-AA-AAAGTTTAGATTTTAAAAATAAAAAT
* * * ** *
15831 CT-GTTTTTAGTGATTTTAAAGAAAAAATTTAAATTTTTAAATAATTTTTTTATTTTTTTAACTA
64 CTAGTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTA
* *
15895 TTTTGTAATAAAAGTTTTG
129 TTTTGAAATAAAAGTTTGG
* * * * * *
15914 ATTTTGAAATAAAGTAGTGATTTTTGTTTTAATCAAAA-AAAAACTTTTGATTTTAAAAA
1 ATTTTTAAGTAAAATAGTGA-TTTT-CTTTAA--AAAAGAAAAAGTTTAGATTTTAAAAA
15973 GAAGAAGAAG
Statistics
Matches: 439, Mismatches: 47, Indels: 35
0.84 0.09 0.07
Matches are distributed among these distances:
146 18 0.04
147 205 0.47
148 87 0.20
149 95 0.22
150 5 0.01
151 9 0.02
152 16 0.04
153 4 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (147 bp):
ATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAGAAAAAGTTTAGATTTTAAAAATAAAAATCT
AGTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATT
TTGAAATAAAAGTTTGG
Found at i:26256 original size:12 final size:13
Alignment explanation
Indices: 26236--26285 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
26226 GAGAATTATG
26236 AGGAGAAAGAAGA
1 AGGAGAAAGAAGA
26249 AGGA-AAAGAAGA
1 AGGAGAAAGAAGA
* *
26261 AGAACGAGAAGAAAA
1 AGGA-GA-AAGAAGA
26276 AGG-GAAAGAA
1 AGGAGAAAGAA
26286 AAAAGAAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 16 0.52
13 6 0.19
14 1 0.03
15 8 0.26
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (13 bp):
AGGAGAAAGAAGA
Found at i:26298 original size:27 final size:27
Alignment explanation
Indices: 26242--26300 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
26232 TATGAGGAGA
* * *
26242 AAGAAGAAGGAAAAGAAGAAGAACGAG
1 AAGAAAAAGGAAAAGAAAAAGAAAGAG
*
26269 AAGAAAAAGGGAAAGAAAAAAGAAAG-G
1 AAGAAAAAGGAAAAG-AAAAAGAAAGAG
26296 AAGAA
1 AAGAA
26301 CCTAATGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.68, C:0.02, G:0.31, T:0.00
Consensus pattern (27 bp):
AAGAAAAAGGAAAAGAAAAAGAAAGAG
Found at i:27379 original size:11 final size:11
Alignment explanation
Indices: 27363--27396 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
27353 AAAAACAAAG
27363 AGAAGAAGAAA
1 AGAAGAAGAAA
27374 AGAAGAAGAAA
1 AGAAGAAGAAA
*
27385 AGAAAAAGAAA
1 AGAAGAAGAAA
27396 A
1 A
27397 AGAAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AGAAGAAGAAA
Found at i:27383 original size:17 final size:17
Alignment explanation
Indices: 27353--27402 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
27343 GTCACATATA
* *
27353 AAAAACAAAGAGAAGAAG
1 AAAAAGAAAAAGAA-AAG
*
27371 -AAAAGAAGAAGAAAAG
1 AAAAAGAAAAAGAAAAG
27387 AAAAAGAAAAAGAAAA
1 AAAAAGAAAAAGAAAA
27403 ATATTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.11
17 24 0.89
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:27402 original size:11 final size:11
Alignment explanation
Indices: 27353--27403 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
27343 GTCACATATA
*
27353 AAAAACAAAGAG
1 AAAAAGAAA-AG
*
27365 AAGAAGAAAAG
1 AAAAAGAAAAG
*
27376 AAGAAGAAAAG
1 AAAAAGAAAAG
27387 AAAAAGAAAAAG
1 AAAAAG-AAAAG
27399 AAAAA
1 AAAAA
27404 TATTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
11 18 0.51
12 17 0.49
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:27403 original size:6 final size:6
Alignment explanation
Indices: 27353--27403 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
27343 GTCACATATA
* * * *
27353 AAAAAC AAAGAG AAGAAG -AAAAG AAGAAG -AAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
27399 AAAAA
1 AAAAA
27404 TATTTATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
5 8 0.22
6 28 0.78
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:27784 original size:20 final size:20
Alignment explanation
Indices: 27743--27785 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
27733 TTTTTTAGGA
**
27743 TGCATTTTTAACTTTGTAAT
1 TGCATTTTTAACTCAGTAAT
27763 TGCATTTCTTAACTCAGT-AT
1 TGCATTT-TTAACTCAGTAAT
27783 TGC
1 TGC
27786 TAGGTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (20 bp):
TGCATTTTTAACTCAGTAAT
Found at i:32622 original size:51 final size:50
Alignment explanation
Indices: 32531--32807 Score: 187
Period size: 50 Copynumber: 5.5 Consensus size: 50
32521 GTTACAACCC
* * *
32531 CAAATCTTATATCCTTGAAGTTACAATGGGTCAGATTAAAGTCATGAAAG
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGGTCAGATTAAAGTCATGAAAG
** *
32581 CAAATCTTTATCTCCTTGAAGTTGCAGTGGAG-CAAGA-TAAAG-CTACCACA-
1 CAAATC-TTATCTCCTTGAAGTTGCAGTGG-GTC-AGATTAAAGTC-ATGAAAG
* * *
32631 CACAATCCTATAC-CCCTGAAGTAGCAGTGGGTCAGATTAAAGTCATGAAAG
1 CA-AATCTTAT-CTCCTTGAAGTTGCAGTGGGTCAGATTAAAGTCATGAAAG
* * * * *
32682 CAATTTTTTATCTCCTTGAAGTTGCAGTGGAG-CAAGA-TAAAG-CTATCATAC
1 CAA-ATCTTATCTCCTTGAAGTTGCAGTGG-GTC-AGATTAAAGTC-ATGAAAG
* * * * * *
32733 CAAATCTTATAC-CCCTGAAGTTACAGTAGGTCAGATTGAATTTATGAAAG
1 CAAATCTTAT-CTCCTTGAAGTTGCAGTGGGTCAGATTAAAGTCATGAAAG
*
32783 CAAATCCTATCTTCC-TGAAGTTGCA
1 CAAATCTTATC-TCCTTGAAGTTGCA
32808 ATGAAGTGGA
Statistics
Matches: 173, Mismatches: 33, Indels: 42
0.70 0.13 0.17
Matches are distributed among these distances:
49 9 0.05
50 84 0.49
51 72 0.42
52 8 0.05
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (50 bp):
CAAATCTTATCTCCTTGAAGTTGCAGTGGGTCAGATTAAAGTCATGAAAG
Found at i:32651 original size:101 final size:101
Alignment explanation
Indices: 32530--32807 Score: 375
Period size: 101 Copynumber: 2.8 Consensus size: 101
32520 AGTTACAACC
* * * *
32530 CCAAATCTTATATCCTTGAAGTTACAATGGGTCAGATTAAAGTCATGAAAGCAAATCTTTATCTC
1 CCAAATCCTATACCCCTGAAGTTACAGTGGGTCAGATTAAAGTCATGAAAGCAAATCTTTATCTC
32595 CTTGAAGTTGCAGTGGAGCAAGATAAAGCTACCACA
66 CTTGAAGTTGCAGTGGAGCAAGATAAAGCTACCACA
* *
32631 -CACAATCCTATACCCCTGAAG-TAGCAGTGGGTCAGATTAAAGTCATGAAAGCAATTTTTTATC
1 CCA-AATCCTATACCCCTGAAGTTA-CAGTGGGTCAGATTAAAGTCATGAAAGCAAATCTTTATC
* *
32694 TCCTTGAAGTTGCAGTGGAGCAAGATAAAGCTATCATA
64 TCCTTGAAGTTGCAGTGGAGCAAGATAAAGCTACCACA
* * * * * *
32732 CCAAATCTTATACCCCTGAAGTTACAGTAGGTCAGATTGAATTTATGAAAGCAAATC-CTATCTT
1 CCAAATCCTATACCCCTGAAGTTACAGTGGGTCAGATTAAAGTCATGAAAGCAAATCTTTATC-T
32796 CC-TGAAGTTGCA
65 CCTTGAAGTTGCA
32808 ATGAAGTGGA
Statistics
Matches: 156, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
100 18 0.12
101 134 0.86
102 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (101 bp):
CCAAATCCTATACCCCTGAAGTTACAGTGGGTCAGATTAAAGTCATGAAAGCAAATCTTTATCTC
CTTGAAGTTGCAGTGGAGCAAGATAAAGCTACCACA
Found at i:34374 original size:13 final size:13
Alignment explanation
Indices: 34345--34465 Score: 72
Period size: 13 Copynumber: 9.5 Consensus size: 13
34335 GTTTTATTTG
*
34345 TTATTTAATTTTAT
1 TTATTT-ATTTTCT
34359 TTATTTATTTTCT
1 TTATTTATTTTCT
*
34372 TTATTGATCTTTCAT
1 TTATTTAT-TTTC-T
* *
34387 TTATTTATGTTGT
1 TTATTTATTTTCT
*
34400 TTA--TATTCTC-
1 TTATTTATTTTCT
** *
34410 ACATTTATTTAC-
1 TTATTTATTTTCT
*
34422 TTATTTATTGTCT
1 TTATTTATTTTCT
*
34435 TTATTTATTTTAT
1 TTATTTATTTTCT
* *
34448 TTGTTAATTTT-T
1 TTATTTATTTTCT
34460 TTATTT
1 TTATTT
34466 TATGTTTTTC
Statistics
Matches: 80, Mismatches: 22, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
10 1 0.01
11 4 0.05
12 18 0.22
13 37 0.46
14 12 0.15
15 8 0.10
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.69
Consensus pattern (13 bp):
TTATTTATTTTCT
Found at i:39779 original size:22 final size:21
Alignment explanation
Indices: 39731--39779 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
39721 TTTAGTCTTT
* *
39731 TATTATTAAGCCTTAATTAACC
1 TATT-TTAAACCTTAATAAACC
*
39753 CATTTTAAACCTTAATCAAACC
1 TATTTTAAACCTTAAT-AAACC
39775 TATTT
1 TATTT
39780 ATACTTGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (21 bp):
TATTTTAAACCTTAATAAACC
Found at i:48342 original size:17 final size:17
Alignment explanation
Indices: 48320--48352 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48310 TTTGAAAGAA
48320 TAAAATA-AAAGATAAAC
1 TAAAATAGAAA-ATAAAC
48337 TAAAATAGAAAATAAA
1 TAAAATAGAAAATAAA
48353 GGAAAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAATAGAAAATAAAC
Found at i:50124 original size:21 final size:21
Alignment explanation
Indices: 50099--50141 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
50089 CAATTTTTTC
50099 TTACTC-TATTCTTTTGTGTTT
1 TTACTCATATTCTTTT-TGTTT
*
50120 TTACTCATTTTCTTTTTGTTT
1 TTACTCATATTCTTTTTGTTT
50141 T
1 T
50142 GTTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (21 bp):
TTACTCATATTCTTTTTGTTT
Found at i:54575 original size:21 final size:19
Alignment explanation
Indices: 54550--54593 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
54540 CACCGAAAGA
54550 TCTTCCTAAGGATCTTCTTCT
1 TCTTCC-AAGG-TCTTCTTCT
*
54571 TCTT-CAAGGTCTTCTTTT
1 TCTTCCAAGGTCTTCTTCT
54589 TCTTC
1 TCTTC
54594 TTCATCTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.57
19 4 0.19
20 1 0.05
21 4 0.19
ACGTcount: A:0.11, C:0.27, G:0.09, T:0.52
Consensus pattern (19 bp):
TCTTCCAAGGTCTTCTTCT
Found at i:54583 original size:18 final size:19
Alignment explanation
Indices: 54557--54593 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
54547 AGATCTTCCT
54557 AAGGATCTTCTTCTTCTTC
1 AAGGATCTTCTTCTTCTTC
*
54576 AAGG-TCTTCTTTTTCTTC
1 AAGGATCTTCTTCTTCTTC
54594 TTCATCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.14, C:0.24, G:0.11, T:0.51
Consensus pattern (19 bp):
AAGGATCTTCTTCTTCTTC
Found at i:70454 original size:17 final size:17
Alignment explanation
Indices: 70432--70470 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
70422 TAATTGTTCA
*
70432 TGCATTATTAATGTCAT
1 TGCATTATTAATGTCAC
* *
70449 TGCATTTTTATTGTCAC
1 TGCATTATTAATGTCAC
70466 TGCAT
1 TGCAT
70471 CTACATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (17 bp):
TGCATTATTAATGTCAC
Found at i:106191 original size:15 final size:15
Alignment explanation
Indices: 106173--106217 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
106163 AAAAAAGAGA
106173 TAAAATAACAAGAAT
1 TAAAATAACAAGAAT
*
106188 TAAAA-AA-GAG-A-
1 TAAAATAACAAGAAT
106199 TAAAATAACAAGAAT
1 TAAAATAACAAGAAT
106214 TAAA
1 TAAA
106218 CCAAGCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
11 5 0.21
12 3 0.12
13 4 0.17
14 3 0.12
15 9 0.38
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (15 bp):
TAAAATAACAAGAAT
Found at i:106199 original size:26 final size:26
Alignment explanation
Indices: 106163--106217 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
106153 ATTAGTGCAC
106163 AAAAAAGAGATAAAATAACAAGAATT
1 AAAAAAGAGATAAAATAACAAGAATT
106189 AAAAAAGAGATAAAATAACAAGAATT
1 AAAAAAGAGATAAAATAACAAGAATT
106215 AAA
1 AAA
106218 CCAAGCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.15
Consensus pattern (26 bp):
AAAAAAGAGATAAAATAACAAGAATT
Found at i:114976 original size:3 final size:3
Alignment explanation
Indices: 114968--115020 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
114958 TCAGTCACAT
114968 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
115017 ATA A
1 ATA A
115021 ATGTTGTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:117237 original size:14 final size:14
Alignment explanation
Indices: 117198--117238 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 14
117188 TTAGAGTTAG
117198 AAAAA-GAAAATAA
1 AAAAATGAAAATAA
117211 AAACAAGTGAAAATAA
1 AAA-AA-TGAAAATAA
117227 AAAAATGAAAAT
1 AAAAATGAAAAT
117239 GAGTAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 9 0.36
15 2 0.08
16 11 0.44
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (14 bp):
AAAAATGAAAATAA
Found at i:118929 original size:5 final size:5
Alignment explanation
Indices: 118910--118994 Score: 66
Period size: 5 Copynumber: 15.4 Consensus size: 5
118900 ATAGTAGGAT
118910 AAATA AAAGTA AAATA AAATA AAATA AAATA GTAAGATA AAAT- AAATGA
1 AAATA AAA-TA AAATA AAATA AAATA AAATA --AA-ATA AAATA AAAT-A
118959 AAAT- AAATAA ATAATA AATAGTA AAATAA AAATA AA
1 AAATA AAAT-A A-AATA AA-A-TA AAAT-A AAATA AA
118995 GGACAATAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 24
0.74 0.00 0.26
Matches are distributed among these distances:
4 8 0.12
5 27 0.40
6 21 0.31
7 9 0.13
8 3 0.04
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:118972 original size:23 final size:23
Alignment explanation
Indices: 118921--118988 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
118911 AATAAAAGTA
*
118921 AAATAAAATAAAAT-AAAAT-AGT
1 AAATAAAAT-AAATGAAAATAAAT
118943 AAGATAAAATAAATGAAAATAAAT
1 AA-ATAAAATAAATGAAAATAAAT
118967 AAAT--AATAAATAGTAAAATAAA
1 AAATAAAATAAAT-G-AAAATAAA
118989 AATAAAGGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 7 0.17
22 7 0.17
23 22 0.55
24 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (23 bp):
AAATAAAATAAATGAAAATAAAT
Found at i:119013 original size:10 final size:9
Alignment explanation
Indices: 118908--119014 Score: 56
Period size: 10 Copynumber: 10.6 Consensus size: 9
118898 TGATAGTAGG
118908 ATAAATAAA
1 ATAAATAAA
118917 AGTAAAATAAA
1 A-T-AAATAAA
118928 ATAAAATAAAA
1 AT-AAAT-AAA
118939 TAGTAAGATAAA
1 -A-TAA-ATAAA
118951 ATAAATGAAA
1 ATAAAT-AAA
118961 ATAAAT-AA
1 ATAAATAAA
118969 AT-AATAAA
1 ATAAATAAA
118977 TAGTAAAATAAAA
1 -A-T-AAAT-AAA
* *
118990 ATAAAGGACA
1 ATAAA-TAAA
119000 ATAAATAAA
1 ATAAATAAA
119009 TATAAA
1 -ATAAA
119015 AAGAAAAATA
Statistics
Matches: 79, Mismatches: 4, Indels: 29
0.71 0.04 0.26
Matches are distributed among these distances:
7 3 0.04
8 6 0.08
9 6 0.08
10 35 0.44
11 13 0.16
12 10 0.13
13 6 0.08
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (9 bp):
ATAAATAAA
Found at i:119023 original size:38 final size:38
Alignment explanation
Indices: 118910--119030 Score: 129
Period size: 39 Copynumber: 3.1 Consensus size: 38
118900 ATAGTAGGAT
* *
118910 AAATAAAAGTAAAATAAAATAAA-ATAAAATAGTAAGAT-A
1 AAAT-AAAGGAAAAT-AAATAAATATAAAA-AGTAAAATAA
* *
118949 AAATAAATGAAAATAAATAAATAATAAATAGTAAAATAA
1 AAATAAAGGAAAATAAATAAAT-ATAAAAAGTAAAATAA
* *
118988 AAATAAAGGACAATAAATAAATATAAAAAGAAAAATATA
1 AAATAAAGGAAAATAAATAAATATAAAAAGTAAAATA-A
119027 AAAT
1 AAAT
119031 GCTAAAAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
37 7 0.10
38 28 0.40
39 35 0.50
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.21
Consensus pattern (38 bp):
AAATAAAGGAAAATAAATAAATATAAAAAGTAAAATAA
Found at i:120068 original size:15 final size:16
Alignment explanation
Indices: 120048--120088 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
120038 AATTTACACA
120048 TTTTTGTTCTTTT-TT
1 TTTTTGTTCTTTTATT
*
120063 TTTTTGTCCTTTTATT
1 TTTTTGTTCTTTTATT
120079 TGTTTT-TTCT
1 T-TTTTGTTCT
120089 CTCTTACAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 6 0.27
17 4 0.18
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTTGTTCTTTTATT
Found at i:121863 original size:132 final size:130
Alignment explanation
Indices: 121626--121990 Score: 580
Period size: 132 Copynumber: 2.8 Consensus size: 130
121616 ATATTGAATT
121626 ATAAATAAATAAATGTTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAGTT
1 ATAAATAAATAAATGTTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAGTT
* *
121691 GAATACAAAGAATTAATGAAAGA-TTTGAATTGTTATATATATTGATATGCATATTTGGTGGTTA
66 GAATACAAAGGATTAATGAAA-ATTTTGAATTGTTATATATATTGATATGC--ATTTGGTGGCTA
121755 GAA
128 GAA
** *
121758 ATAAATAAATAAATGTTTTTTGCCATGTGAATTATATTGAACATTTCAGATTGTTGAAATGATTT
1 ATAAATAAATAAATGTTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAGTT
*
121823 GAATACAAAGGATTAATGAAAATTTTGAATTGTTATATATATTGATATGCATTTGGTGGCTGGAA
66 GAATACAAAGGATTAATGAAAATTTTGAATTGTTATATATATTGATATGCATTTGGTGGCTAGAA
*
121888 ATAAATAAAT--A--CTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAGTT
1 ATAAATAAATAAATGTTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAGTT
*
121949 GAATATAAAGGATTAATG-AAATATTTGAATTGTTATATATAT
66 GAATACAAAGGATTAATGAAAAT-TTTGAATTGTTATATATAT
121991 AGAGCAATAA
Statistics
Matches: 220, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
125 4 0.02
126 82 0.37
128 1 0.00
130 23 0.10
131 1 0.00
132 109 0.50
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (130 bp):
ATAAATAAATAAATGTTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAGTT
GAATACAAAGGATTAATGAAAATTTTGAATTGTTATATATATTGATATGCATTTGGTGGCTAGAA
Found at i:122471 original size:82 final size:81
Alignment explanation
Indices: 122324--122518 Score: 282
Period size: 82 Copynumber: 2.4 Consensus size: 81
122314 GGGCTCACTC
* * *
122324 TCGCGGTTTATCTGCTAGGCACAGGGTGCTAGGAATTGACGGATTATTCGTTGGTTAATCCAACT
1 TCGCGGTTTATCCGCTAGGCATA-GGTGCCAGGAATTGACGGATTATTCGTTGGTTAATCCAACT
122389 AAAGCTGGACTCACATA
65 AAAGCTGGACTCACATA
* * * *
122406 TCGCAGTTTATCCGCTAGGCATTAGGTGCCAGGAATTGATGGATTATTTGTTGGTTAATCTAACT
1 TCGCGGTTTATCCGCTAGGCA-TAGGTGCCAGGAATTGACGGATTATTCGTTGGTTAATCCAACT
* *
122471 AGAGCTGGACTCGCATA
65 AAAGCTGGACTCACATA
122488 TCGCGGTTTATCCGCTAGGCACTAGGTGCCA
1 TCGCGGTTTATCCGCTAGGCA-TAGGTGCCA
122519 TAATCGTCGG
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
82 100 0.99
83 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (81 bp):
TCGCGGTTTATCCGCTAGGCATAGGTGCCAGGAATTGACGGATTATTCGTTGGTTAATCCAACTA
AAGCTGGACTCACATA
Found at i:122634 original size:102 final size:102
Alignment explanation
Indices: 122484--122723 Score: 320
Period size: 102 Copynumber: 2.4 Consensus size: 102
122474 GCTGGACTCG
* * *
122484 CATATCGCGGTTTATCCGCTAGGCACTAGGTGCCATAATCGTCGGTTTATCCGACTAGCGCTGGG
1 CATATCGCGGTTTATCCGCTAGGCACTAGGTGCCATAACCATCAGTTTATCCGACTAGCGCTGGG
* *
122549 CACAAACCGTTGGTTAATCCAACCA-AATATGGGCTCA
66 CACAAACCATTGGATAATCCAACCAGAAT-TGGGCTCA
* *
122586 CATATCGTGGTTTATCCGCTAGGCACTGGGTGCCATAACCATCAGTTTATCCGACTAGCGCTGGG
1 CATATCGCGGTTTATCCGCTAGGCACTAGGTGCCATAACCATCAGTTTATCCGACTAGCGCTGGG
** * *
122651 TGCAAACCATTGGATAATCCAACTAGAGTTGGGCTCA
66 CACAAACCATTGGATAATCCAACCAGAATTGGGCTCA
* * ** *
122688 CATACCGCGGTATATCTACTAGGCACCAGGTGCCAT
1 CATATCGCGGTTTATCCGCTAGGCACTAGGTGCCAT
122724 GAATTGACGC
Statistics
Matches: 119, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
102 117 0.98
103 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (102 bp):
CATATCGCGGTTTATCCGCTAGGCACTAGGTGCCATAACCATCAGTTTATCCGACTAGCGCTGGG
CACAAACCATTGGATAATCCAACCAGAATTGGGCTCA
Found at i:122650 original size:35 final size:33
Alignment explanation
Indices: 122595--122660 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 33
122585 ACATATCGTG
122595 GTTTATCCGCTAGGCACTGGGTGCCATAACCATCA
1 GTTTATCCGCTAGGCACTGGGTG-CA-AACCATCA
*
122630 GTTTATCCGACTA-GCGCTGGGTGCAAACCAT
1 GTTTATCCG-CTAGGCACTGGGTGCAAACCAT
122661 TGGATAATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.21
34 2 0.07
35 18 0.62
36 3 0.10
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (33 bp):
GTTTATCCGCTAGGCACTGGGTGCAAACCATCA
Found at i:133335 original size:15 final size:14
Alignment explanation
Indices: 133313--133374 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
133303 TTATACTACA
133313 AAATATTTATTATT
1 AAATATTTATTATT
133327 AATATATTTA--A-T
1 AA-ATATTTATTATT
133339 AAATATTTATTATT
1 AAATATTTATTATT
*
133353 AAA-ATATTAATATT
1 AAATAT-TTATTATT
*
133367 GAATATTT
1 AAATATTT
133375 TTAATAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
11 7 0.17
12 3 0.08
13 4 0.10
14 17 0.43
15 9 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
AAATATTTATTATT
Found at i:133342 original size:26 final size:25
Alignment explanation
Indices: 133313--133364 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
133303 TTATACTACA
*
133313 AAATATTTATTATTAATATATTTAAT
1 AAATATTTATTATTAAAATA-TTAAT
133339 AAATATTTATTATTAAAATATTAAT
1 AAATATTTATTATTAAAATATTAAT
133364 A
1 A
133365 TTGAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAATATTTATTATTAAAATATTAAT
Found at i:133489 original size:25 final size:26
Alignment explanation
Indices: 133460--133529 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
133450 TAATTTATTA
* *
133460 AAATAATAAATTGTATTAAT-TATAT
1 AAATAATAAATTGTATGAATAAATAT
* **
133485 TAATAATTTATTGTATGAATAAATAT
1 AAATAATAAATTGTATGAATAAATAT
133511 AAATAATTAAATATGTATG
1 AAATAA-TAAAT-TGTATG
133530 TTTAATAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
25 16 0.47
26 9 0.26
27 3 0.09
28 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (26 bp):
AAATAATAAATTGTATGAATAAATAT
Found at i:138581 original size:21 final size:21
Alignment explanation
Indices: 138531--138583 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
138521 GGAGTTTTTA
138531 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATGACAT
* * * *
138552 ATTTTGGTAGAAGTCAT-ACTT
1 GTATCGGTAGAAG-CATGACAT
138573 GTATCGGTAGA
1 GTATCGGTAGA
138584 TTGTCTCAAG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACAT
Found at i:163212 original size:21 final size:22
Alignment explanation
Indices: 163181--163226 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
163171 ATTCACATGT
163181 TTTCTTACTCA-TGATTCTTTTG
1 TTTCTTACTCATTG-TTCTTTTG
*
163203 TTTC-TACTCATTGTTTTTTTG
1 TTTCTTACTCATTGTTCTTTTG
163224 TTT
1 TTT
163227 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.11, C:0.15, G:0.09, T:0.65
Consensus pattern (22 bp):
TTTCTTACTCATTGTTCTTTTG
Found at i:172499 original size:10 final size:10
Alignment explanation
Indices: 172484--172509 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
172474 TATCAACTAT
172484 ACTTGTATCG
1 ACTTGTATCG
172494 ACTTGTATCG
1 ACTTGTATCG
172504 ACTTGT
1 ACTTGT
172510 GTCCGCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (10 bp):
ACTTGTATCG
Found at i:180097 original size:51 final size:51
Alignment explanation
Indices: 180002--180099 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
179992 CGAAAGGGTC
* * * *
180002 CGATGACTAAGTGTCATCGTGAGTAAATGAATACTTTACAGATTAAAAGTT
1 CGATGACTAAATGTCATCATGAGTAAATGAATACATGACAGATTAAAAGTT
* **
180053 CGATGACTAAATGTCATCATGAGTAAATGAATCCATGATGGATTAAA
1 CGATGACTAAATGTCATCATGAGTAAATGAATACATGACAGATTAAA
180100 GGTCCAAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (51 bp):
CGATGACTAAATGTCATCATGAGTAAATGAATACATGACAGATTAAAAGTT
Found at i:182756 original size:90 final size:90
Alignment explanation
Indices: 182603--182811 Score: 267
Period size: 90 Copynumber: 2.3 Consensus size: 90
182593 TTCCCGGGTC
* * * ** *
182603 ACGATGCTGCTCACACGAGCTATTGAGGATTCGCAACATATGTGGTACCTTAGTCATCGATACGG
1 ACGATGCTGCTCACACGAGCTATCGAGAACTCGCAACATATACGGTACCTCAGTCATCGATACGG
*
182668 TATCTATGCATATAACTATTCCCTA
66 CATCTATGCATATAACTATTCCCTA
* *
182693 ACGATACTGCTCACACGAGCTGTCGAGAACTCGCAACATATACGGTACCTCAG-CTATCGATACG
1 ACGATGCTGCTCACACGAGCTATCGAGAACTCGCAACATATACGGTACCTCAGTC-ATCGATACG
* * * *
182757 GCATTTGTGCATATAACTGTTCCTTA
65 GCATCTATGCATATAACTATTCCCTA
* *
182783 ATGTTGCTGCTCACACGAGCTATCGAGAA
1 ACGATGCTGCTCACACGAGCTATCGAGAA
182812 TATGCACTTT
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 1 0.01
90 100 0.99
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (90 bp):
ACGATGCTGCTCACACGAGCTATCGAGAACTCGCAACATATACGGTACCTCAGTCATCGATACGG
CATCTATGCATATAACTATTCCCTA
Found at i:188039 original size:19 final size:19
Alignment explanation
Indices: 188017--188053 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
188007 GTTTCCAAGG
188017 CTTCTTAGGACGTTATCTA
1 CTTCTTAGGACGTTATCTA
188036 CTTCTTAGGACGTTATCT
1 CTTCTTAGGACGTTATCT
188054 TATCTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (19 bp):
CTTCTTAGGACGTTATCTA
Found at i:192848 original size:21 final size:21
Alignment explanation
Indices: 192795--192848 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
192785 CAAATGCTAA
*
192795 TTCTATCGATACAAGTGACCC
1 TTCTATCGATACAAGTCACCC
* * ***
192816 TTCTACCTATACAAGTCTTTC
1 TTCTATCGATACAAGTCACCC
192837 TTCTATCGATAC
1 TTCTATCGATAC
192849 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (21 bp):
TTCTATCGATACAAGTCACCC
Found at i:197287 original size:24 final size:24
Alignment explanation
Indices: 197255--197317 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
197245 AACCAGTCTA
* *
197255 GGCTCGTAAGAGCTAGCCGTTTTG
1 GGCTCGTAAGAGCTAGCCATTATG
197279 GGCTCGTAAGAGCTAGCCATTATG
1 GGCTCGTAAGAGCTAGCCATTATG
*
197303 GGCTCGTGAGAGCTA
1 GGCTCGTAAGAGCTA
197318 ATGTTGTCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAGCCATTATG
Found at i:201511 original size:24 final size:24
Alignment explanation
Indices: 201483--201581 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
201473 GTATACTGGT
*
201483 TAACCATTTTGGGCTCGTAAGAGA
1 TAACCATTCTGGGCTCGTAAGAGA
* *
201507 TAACCATTTTGGGCTCGTAAGAGG
1 TAACCATTCTGGGCTCGTAAGAGA
* * *
201531 TAACCATTCTAGGCTCATAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGA
* * *
201555 TAACCATTCTGCGCTTGTGAGAGA
1 TAACCATTCTGGGCTCGTAAGAGA
201579 TAA
1 TAA
201582 TGTTGTCTGT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGA
Found at i:202767 original size:55 final size:55
Alignment explanation
Indices: 202640--202771 Score: 158
Period size: 55 Copynumber: 2.4 Consensus size: 55
202630 TCCAGATAGT
* *
202640 TGTCAGATACGACGACAATTCTAGGCGCAATTCTAGACATGCTCATGGAGCGAGT
1 TGTCAGATGCGACGACAATTCTAGGCGCAATTCTAGACATGCTCATGGAGCGAGC
* * * * * * *
202695 TGTCAGATGC-AGTGACAATTCTAGGTGCAATTTTGGATATGCTCATGTAGTGAGC
1 TGTCAGATGCGA-CGACAATTCTAGGCGCAATTCTAGACATGCTCATGGAGCGAGC
*
202750 TGTTAGATGCGACGACAATTCT
1 TGTCAGATGCGACGACAATTCT
202772 TGGTATGCTC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
54 1 0.02
55 62 0.97
56 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (55 bp):
TGTCAGATGCGACGACAATTCTAGGCGCAATTCTAGACATGCTCATGGAGCGAGC
Found at i:203940 original size:17 final size:17
Alignment explanation
Indices: 203918--203951 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
203908 CACTAACATT
203918 AAAATGCAATGACAATG
1 AAAATGCAATGACAATG
*
203935 AAAATGCAATGATAATG
1 AAAATGCAATGACAATG
203952 CTTACTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATG
Found at i:209215 original size:55 final size:55
Alignment explanation
Indices: 209137--209277 Score: 201
Period size: 55 Copynumber: 2.6 Consensus size: 55
209127 TTATCCGGAT
* *
209137 AGCTGTCAGATGTGGCGACAATTTTGGGCATAATTTTGGATATGCTCATGCAACG
1 AGCTGTCAGATGCGGCGACAATTTTGGGCATAATTCTGGATATGCTCATGCAACG
* * * * **
209192 AGCTGTTAGATGCGGTGAAAATTTTGGGCGTAATTCTGGATATGCTCATGCAGTG
1 AGCTGTCAGATGCGGCGACAATTTTGGGCATAATTCTGGATATGCTCATGCAACG
*
209247 AGCTGTCAGATGCGGCGACAATTCTGGGCAT
1 AGCTGTCAGATGCGGCGACAATTTTGGGCAT
209278 TCCATGCAGC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 73 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (55 bp):
AGCTGTCAGATGCGGCGACAATTTTGGGCATAATTCTGGATATGCTCATGCAACG
Found at i:216792 original size:13 final size:14
Alignment explanation
Indices: 216774--216803 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
216764 GTCAATGCAA
216774 TCAAA-GTTAAATG
1 TCAAAGGTTAAATG
216787 TCAAAGGTTAAATG
1 TCAAAGGTTAAATG
216801 TCA
1 TCA
216804 GAGCAACTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (14 bp):
TCAAAGGTTAAATG
Found at i:219162 original size:17 final size:17
Alignment explanation
Indices: 219142--219181 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
219132 TAGAGGTAAC
*
219142 GACAATAAAAATGCAAT
1 GACAATAAAAATGCAAG
* *
219159 GACATTAATAATGCAAG
1 GACAATAAAAATGCAAG
219176 GACAAT
1 GACAAT
219182 TATACTACAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (17 bp):
GACAATAAAAATGCAAG
Found at i:221323 original size:14 final size:14
Alignment explanation
Indices: 221299--221331 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
221289 GTCAATACAA
221299 TCAAA-GTTAAATG
1 TCAAAGGTTAAATG
221312 TCAAAGGTTAAATG
1 TCAAAGGTTAAATG
221326 TCAAAG
1 TCAAAG
221332 CAACTGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (14 bp):
TCAAAGGTTAAATG
Found at i:230214 original size:15 final size:15
Alignment explanation
Indices: 230194--230223 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
230184 CACCAGCCCT
230194 TTGCTTTGCTACCAC
1 TTGCTTTGCTACCAC
*
230209 TTGCTTTGTTACCAC
1 TTGCTTTGCTACCAC
230224 CACTCTAATT
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:0.13, C:0.30, G:0.13, T:0.43
Consensus pattern (15 bp):
TTGCTTTGCTACCAC
Found at i:233466 original size:21 final size:20
Alignment explanation
Indices: 233431--233484 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
233421 AAATTATTAT
*
233431 ATTTTTCTTTATTTTTCTTTC
1 ATTTTTGTTT-TTTTTCTTTC
* *
233452 ATTTTTAGTTTTTTTTGTTTT
1 ATTTTT-GTTTTTTTTCTTTC
*
233473 GTTTTTGTTTTT
1 ATTTTTGTTTTT
233485 GATGTGTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 6 0.21
21 19 0.68
22 3 0.11
ACGTcount: A:0.07, C:0.06, G:0.07, T:0.80
Consensus pattern (20 bp):
ATTTTTGTTTTTTTTCTTTC
Found at i:234282 original size:23 final size:24
Alignment explanation
Indices: 234239--234283 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
234229 TTACCTAAGT
234239 GGAGAGAAAAGGAAGGTGAGAGAA
1 GGAGAGAAAAGGAAGGTGAGAGAA
234263 GGAGA-AATAAGG-AGGTGAGAG
1 GGAGAGAA-AAGGAAGGTGAGAG
234284 GGAATCGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.07
Consensus pattern (24 bp):
GGAGAGAAAAGGAAGGTGAGAGAA
Found at i:236177 original size:7 final size:7
Alignment explanation
Indices: 236150--236180 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
236140 ATTGTTTAAA
*
236150 TTTGGAA
1 TTTGGAC
236157 TTTGGAC
1 TTTGGAC
236164 TTTGGAC
1 TTTGGAC
236171 TTTGGAC
1 TTTGGAC
236178 TTT
1 TTT
236181 TTTCTTGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.10, G:0.26, T:0.48
Consensus pattern (7 bp):
TTTGGAC
Found at i:241016 original size:27 final size:27
Alignment explanation
Indices: 240978--241032 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
240968 ATCTTTTCCT
240978 TTTCCTTTTTTTTATGTGACTGAGGGA
1 TTTCCTTTTTTTTATGTGACTGAGGGA
241005 TTTCCTTTTTTTTATGTGACTGAGGGA
1 TTTCCTTTTTTTTATGTGACTGAGGGA
241032 T
1 T
241033 GTCGTTGCAT
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:0.15, C:0.11, G:0.22, T:0.53
Consensus pattern (27 bp):
TTTCCTTTTTTTTATGTGACTGAGGGA
Found at i:243713 original size:3 final size:3
Alignment explanation
Indices: 243705--243775 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
243695 CTCTGAAAGA
* * *
243705 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT TCT TCT CCT ACT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
243753 TCT TCT CCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC
243776 AGCTTACTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.01, C:0.38, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:244706 original size:26 final size:25
Alignment explanation
Indices: 244662--244710 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
244652 GTCTAAAATA
244662 TTAACAATTTAAAATAATTCAAAAAG
1 TTAACAATTTAAAATAATT-AAAAAG
244688 TTAACAATTT-AAATAAATTAAAA
1 TTAACAATTTAAAAT-AATTAAAA
244711 TCAGAATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (25 bp):
TTAACAATTTAAAATAATTAAAAAG
Found at i:246562 original size:20 final size:21
Alignment explanation
Indices: 246537--246575 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
246527 GCAATGAATT
246537 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
246557 TGAAACAAACAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
246576 TAAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.67, C:0.10, G:0.13, T:0.10
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:252147 original size:10 final size:10
Alignment explanation
Indices: 252116--252149 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
252106 TTTGGTTTTC
252116 TTTTTTCTTT
1 TTTTTTCTTT
*
252126 TCTTTTCTTT
1 TTTTTTCTTT
252136 TTTTTTCTTT
1 TTTTTTCTTT
252146 TTTT
1 TTTT
252150 GGCAAAGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:255238 original size:12 final size:12
Alignment explanation
Indices: 255221--255246 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
255211 TGTCTTGATT
255221 TGTTTAATTCCA
1 TGTTTAATTCCA
255233 TGTTTAATTCCA
1 TGTTTAATTCCA
255245 TG
1 TG
255247 AAGAATACAT
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:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (12 bp):
TGTTTAATTCCA
Found at i:256524 original size:13 final size:13
Alignment explanation
Indices: 256506--256532 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
256496 TTCAGATTCA
256506 TTTGATTCATTTT
1 TTTGATTCATTTT
256519 TTTGATTCATTTT
1 TTTGATTCATTTT
256532 T
1 T
256533 GTGGTGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTGATTCATTTT
Found at i:257330 original size:13 final size:13
Alignment explanation
Indices: 257309--257355 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
257299 ATATCATATT
257309 TTTTG-TATATCA
1 TTTTGTTATATCA
257321 TTTTGTTATAT-A
1 TTTTGTTATATCA
*
257333 TTTTTTGTATATCA
1 TTTTGT-TATATCA
257347 TTTTGTTAT
1 TTTTGTTAT
257356 CTTATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 11 0.37
13 13 0.43
14 6 0.20
ACGTcount: A:0.21, C:0.04, G:0.09, T:0.66
Consensus pattern (13 bp):
TTTTGTTATATCA
Found at i:257340 original size:26 final size:26
Alignment explanation
Indices: 257304--257355 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
257294 TCCCTATATC
257304 ATATTTTTTGTATATCATTTTGTTAT
1 ATATTTTTTGTATATCATTTTGTTAT
257330 ATATTTTTTGTATATCATTTTGTTAT
1 ATATTTTTTGTATATCATTTTGTTAT
257356 CTTATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (26 bp):
ATATTTTTTGTATATCATTTTGTTAT
Found at i:257356 original size:11 final size:12
Alignment explanation
Indices: 257309--257356 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
257299 ATATCATATT
257309 TTTTGTATATCA
1 TTTTGTATATCA
257321 TTTTGTTATAT-A
1 TTTTG-TATATCA
257333 TTTTTTGTATATCA
1 --TTTTGTATATCA
257347 TTTTGT-TATC
1 TTTTGTATATC
257357 TTATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 4 0.12
12 12 0.38
13 10 0.31
14 6 0.19
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (12 bp):
TTTTGTATATCA
Done.