Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010137.1 Kokia drynarioides strain JFW-HI SEQ_124932, 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: 95205
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 144 characters in sequence are not A, C, G, or T
Found at i:1291 original size:6 final size:6
Alignment explanation
Indices: 1282--1360 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
1272 TTTTAACTTT
* * * * *
1282 ATTTAA ATTTAT A-GTAA TTTTAA ATTTGAA A-ATAA ATTTAA ACTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* *
1329 A-TTAA ATTTAA ATTCAA A-ATAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1361 TTAAACAAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
5 13 0.24
6 39 0.71
7 3 0.05
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:1321 original size:35 final size:35
Alignment explanation
Indices: 1282--1393 Score: 120
Period size: 35 Copynumber: 3.2 Consensus size: 35
1272 TTTTAACTTT
* * *
1282 ATTTAAATTTATAGTAATTTTAAATTTGAAAATAA
1 ATTTAAATTTATAATAAATTTAAATTTCAAAATAA
*
1317 ATTTAAACTTA-AATTAAATTTAAA-TTCAAAATAA
1 ATTTAAATTTATAA-TAAATTTAAATTTCAAAATAA
* * * *
1351 ATTTAAATTTTTAAACAAATTTAATTTTTAAAATAA
1 ATTTAAATTTAT-AATAAATTTAAATTTCAAAATAA
1387 ATTTAAA
1 ATTTAAA
1394 GGGAGTTCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
34 19 0.30
35 27 0.42
36 18 0.28
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (35 bp):
ATTTAAATTTATAATAAATTTAAATTTCAAAATAA
Found at i:1323 original size:18 final size:17
Alignment explanation
Indices: 1282--1393 Score: 116
Period size: 18 Copynumber: 6.4 Consensus size: 17
1272 TTTTAACTTT
* *
1282 ATTTAAATTTATAGTAA
1 ATTTAAATTTAAAATAA
*
1299 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* *
1317 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
1334 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
* *
1351 ATTTAAATTTTTAAACAA
1 ATTTAAA-TTTAAAATAA
*
1369 ATTTAATTTTTAAAATAA
1 ATTTAA-ATTTAAAATAA
1387 ATTTAAA
1 ATTTAAA
1394 GGGAGTTCGA
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
17 36 0.47
18 40 0.53
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:1339 original size:11 final size:11
Alignment explanation
Indices: 1301--1359 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
1291 TATAGTAATT
1301 TTAAATTTGAAA
1 TTAAATTT-AAA
*
1313 ATAAATTTAAA
1 TTAAATTTAAA
1324 CTTAAA-TTAAA
1 -TTAAATTTAAA
*
1335 TTTAAATTCAAA
1 -TTAAATTTAAA
*
1347 ATAAATTTAAA
1 TTAAATTTAAA
1358 TT
1 TT
1360 TTTAAACAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 23 0.61
12 15 0.39
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:5770 original size:16 final size:16
Alignment explanation
Indices: 5726--5772 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5716 GGAGAATGTG
*
5726 TAAAAAAACAT-AAATA
1 TAAATAAACATGAAA-A
*
5742 TAAATAGACATGAAAA
1 TAAATAAACATGAAAA
*
5758 TAAATAAAGATGAAA
1 TAAATAAACATGAAA
5773 TAAGAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:6247 original size:21 final size:21
Alignment explanation
Indices: 6207--6282 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 21
6197 CGGTGATCGG
*
6207 AATTTTTGTTTTTTGCAAAATAA
1 AATTTTT-TTTTTT-AAAAATAA
* *
6230 AATTTTTTTTTTTTAAAACAA
1 AATTTTTTTTTTTAAAAATAA
*
6251 AATCATTATTTTTCTTAAAAATCAA
1 AAT--TT-TTTTTTTTAAAAAT-AA
6276 AATTTTT
1 AATTTTT
6283 ATTTCGAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
21 9 0.20
22 8 0.18
23 11 0.25
24 11 0.25
25 5 0.11
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
AATTTTTTTTTTTAAAAATAA
Found at i:6284 original size:25 final size:23
Alignment explanation
Indices: 6207--6286 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 23
6197 CGGTGATCGG
* *
6207 AATTTTTGTTTTTTGCAAAAT-AA
1 AATTTTTATTTTTT-TAAAATCAA
6230 AATTTTT-TTTTTTTAAAA-CAA
1 AATTTTTATTTTTTTAAAATCAA
**
6251 AATCATTATTTTTCTTAAAAATCAA
1 AATTTTTATTTTT-TT-AAAATCAA
6276 AATTTTTATTT
1 AATTTTTATTT
6287 CGAAATGGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
21 11 0.23
22 11 0.23
23 9 0.19
24 4 0.09
25 12 0.26
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.54
Consensus pattern (23 bp):
AATTTTTATTTTTTTAAAATCAA
Found at i:6477 original size:144 final size:144
Alignment explanation
Indices: 6236--6823 Score: 676
Period size: 144 Copynumber: 4.0 Consensus size: 144
6226 ATAAAATTTT
* * * * **
6236 TTTTTTTTAAAACAAAATCATTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATGGTTAAGA
1 TTTTTTTTAAAA-AAAATAATTACTTTTCTTAAAAATTAAAATTTTTAATTCGAAATAATTAA-A
6301 AAAATC-AAACTTTGTTT-AAAATTT-AACTTTTTTCTTTAAAATGACTAAAAAACAGATTTTTA
64 AAAATCAAAACTTTGTTTAAAAATTTAAAC-TTTTTCTTTAAAATGACTAAAAAACAGATTTTTA
*
6363 TTTTTAAAAACCTAAAC
128 TTTTTAAAAATCTAAAC
* *
6380 TTTTTTTTAAGAAAAAATAATTACGTTTCTTAAAAATTAAAACTTTTAATTCGAAATAATT-AAA
1 TTTTTTTTAA-AAAAAATAATTACTTTTCTTAAAAATTAAAATTTTTAATTCGAAATAATTAAAA
* * * *
6444 AAATCAAAACTTTGTTTAAAATTTTAAAATTTTTCTTTAAAATGACTAAAAAACATATATTTATT
65 AAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACAGATTTTTATT
*
6509 TTTAAAATTCT-AA-
130 TTTAAAAATCTAAAC
* * * * * *
6522 ---TTTTTAAAAAAAATAAAATCACTATTTTTTAAAAAAAATAAAATTTTTATTTTGAAATAGTT
1 TTTTTTTTAAAAAAAAT--AATTACT-TTTCTT--AAAAATTAAAATTTTTAATTCGAAATAATT
* * *
6584 AAAAAAAATAAAAACTTTGTTTAAAAATTTAAACTTTTCCTTTAAAATGACTAAAAAACCGTATT
61 -AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACAG-ATT
6649 TTTATTTTTAAAAATCTAAAC
124 TTTATTTTTAAAAATCTAAAC
*
6670 TTTCTTTTTATTAAAAAAA-AATCAGTATTTTTCTTAAAAATTAAAATTTTT-ATTCGAAATAAT
1 TTT-TTTTTA--AAAAAAATAAT---TACTTTTCTTAAAAATTAAAATTTTTAATTCGAAATAA-
* *
6733 TTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAAAATAAA
59 TTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACT--AAAAAACAGA
*
6798 TTTTTAGTTTTAAAAATCTAAAC
122 TTTTTATTTTTAAAAATCTAAAC
6821 TTT
1 TTT
6824 CAATTTTTTT
Statistics
Matches: 375, Mismatches: 43, Indels: 45
0.81 0.09 0.10
Matches are distributed among these distances:
138 7 0.02
139 7 0.02
140 5 0.01
141 5 0.01
142 7 0.02
143 39 0.10
144 99 0.26
145 57 0.15
146 18 0.05
147 2 0.01
150 57 0.15
151 46 0.12
152 12 0.03
153 5 0.01
154 9 0.02
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (144 bp):
TTTTTTTTAAAAAAAATAATTACTTTTCTTAAAAATTAAAATTTTTAATTCGAAATAATTAAAAA
AATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAACAGATTTTTATTT
TTAAAAATCTAAAC
Found at i:6538 original size:24 final size:24
Alignment explanation
Indices: 6511--6566 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 24
6501 TATTTATTTT
6511 TAAAATTCTAATTTTTAAAAAAAA
1 TAAAATTCTAATTTTTAAAAAAAA
* *
6535 TAAAATCACTATTTTTTAAAAAAAA
1 TAAAAT-TCTAATTTTTAAAAAAAA
6560 TAAAATT
1 TAAAATT
6567 TTTATTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAATTCTAATTTTTAAAAAAAA
Found at i:6574 original size:24 final size:24
Alignment explanation
Indices: 6511--6574 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
6501 TATTTATTTT
* *
6511 TAAAATTCTAATTTTTAAAAAAAA
1 TAAAATTATTATTTTTAAAAAAAA
* *
6535 TAAAATCACTATTTTTTAAAAAAAA
1 TAAAATTATTA-TTTTTAAAAAAAA
*
6560 TAAAATTTTTATTTT
1 TAAAATTATTATTTT
6575 GAAATAGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 11 0.34
25 21 0.66
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATTATTATTTTTAAAAAAAA
Found at i:6639 original size:52 final size:51
Alignment explanation
Indices: 6583--6823 Score: 140
Period size: 52 Copynumber: 4.7 Consensus size: 51
6573 TTGAAATAGT
*
6583 TAAAAAAAATAAAAACTTTGTTTAAAAATTTAAACTTTTCCTTTAAAATGAC
1 TAAAAAAAAT-AAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGAC
** *** * * *
6635 TAAAAAACCGT-ATTTTTATTTTTAAAAATCTAAACTTTCTT-TTT---ATTA-
1 TAAAAAA-AATAAAACTT-TGTTTAAAAATTTAAACTTT-TTCTTTAAAATGAC
** * * * ** * *
6683 -AAAAAAAATCAGTA-TTTTTCTTAAAAA-TTAAAATTTTTATTCGAAATAAT
1 TAAAAAAAAT-AAAACTTTGT-TTAAAAATTTAAACTTTTTCTTTAAAATGAC
*
6733 TTAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGAC
1 TAAAAAAAAT-AAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGAC
** *
6785 TAAAAAAAATAAATTTTTAGTTTTAAAAATCTAAACTTT
1 TAAAAAAAATAAAACTTT-G-TTTAAAAATTTAAACTTT
6824 CAATTTTTTT
Statistics
Matches: 142, Mismatches: 31, Indels: 31
0.70 0.15 0.15
Matches are distributed among these distances:
45 2 0.01
46 13 0.09
47 15 0.11
48 1 0.01
49 6 0.04
51 27 0.19
52 59 0.42
53 19 0.13
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (51 bp):
TAAAAAAAATAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGAC
Found at i:7850 original size:124 final size:126
Alignment explanation
Indices: 7630--7950 Score: 423
Period size: 124 Copynumber: 2.6 Consensus size: 126
7620 CATCTAAACA
* * * *
7630 CAATGAAAAGTAAATGAACTTTCACACTTGGGCCTCTAAAAGCGATGAAAAGTAAATGAAACTCT
1 CAATGAAAAGTAAATGAACCTCCACACTTGGGCCTCTAAATGTGATGAAAAGTAAATGAAACTCT
* * **
7695 ACACCTGAGCCTCTAAATACGATGAAAAGTAAATAGATCTCCACA-TTG-GCCTTTAAATG
66 ACACCTGAGCCTCTAAATACGATGAAAAGTAAATAGACCTCCACACCTGAGCCTCAAAATG
* * * *
7754 CAATGAAAAGTAAATGAACCTCCATACTTGGGCCTCTAAATGTGATGAAAGGTAAATGGACCTCT
1 CAATGAAAAGTAAATGAACCTCCACACTTGGGCCTCTAAATGTGATGAAAAGTAAATGAAACTCT
* * **
7819 ACACTTGGGCCTCTAAATGTGATGAAAAGTAAATAGACCTCCACACCTGAGCCTCAAAATG
66 ACACCTGAGCCTCTAAATACGATGAAAAGTAAATAGACCTCCACACCTGAGCCTCAAAATG
* * * *
7880 CGATGAAAAGTAAATGAACCTCCACACCTAGGCCTTTAAATGTGATGAAAAGTAAAT-AAACCTC
1 CAATGAAAAGTAAATGAACCTCCACACTTGGGCCTCTAAATGTGATGAAAAGTAAATGAAA-CTC
*
7944 CACACCT
65 TACACCT
7951 ATGCCACTAA
Statistics
Matches: 168, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
124 97 0.58
125 3 0.02
126 68 0.40
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (126 bp):
CAATGAAAAGTAAATGAACCTCCACACTTGGGCCTCTAAATGTGATGAAAAGTAAATGAAACTCT
ACACCTGAGCCTCTAAATACGATGAAAAGTAAATAGACCTCCACACCTGAGCCTCAAAATG
Found at i:7859 original size:84 final size:84
Alignment explanation
Indices: 7632--7970 Score: 389
Period size: 84 Copynumber: 4.1 Consensus size: 84
7622 TCTAAACACA
* * * * * *
7632 ATGAAAAGTAAATGAACTTTCACACTTGGGCCTCTAAAAGCGATGAAAAGTAAATGAAACTCTAC
1 ATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGAACCTCCAC
*
7697 ACCTGAGCCTCTAAATACG
66 ACCTGAGCCTCTAAATGCG
* * * * *
7716 ATGAAAAGTAAATAGATCTCCACA-TT-GGCCTTTAAATGCAATGAAAAGTAAATGAACCTCCAT
1 ATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGAACCTCCAC
* * *
7779 ACTTGGGCCTCTAAATGTG
66 ACCTGAGCCTCTAAATGCG
* * *
7798 ATGAAAGGTAAATGGACCTCTACACTTGGGCCTCTAAATGTGATGAAAAGTAAAT-AGACCTCCA
1 ATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGA-ACCTCCA
*
7862 CACCTGAGCCTCAAAATGCG
65 CACCTGAGCCTCTAAATGCG
* * * * * *
7882 ATGAAAAGTAAATGAACCTCCACACCTAGGCCTTTAAATGTGATGAAAAGTAAATAAACCTCCAC
1 ATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGAACCTCCAC
* *
7947 ACCT-ATGCCACTAAATGCA
66 ACCTGA-GCCTCTAAATGCG
7966 ATGAA
1 ATGAA
7971 TGCTTTCCTT
Statistics
Matches: 214, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
82 66 0.31
83 6 0.03
84 141 0.66
85 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (84 bp):
ATGAAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATGCGATGAAAAGTAAATGAACCTCCAC
ACCTGAGCCTCTAAATGCG
Found at i:7901 original size:42 final size:42
Alignment explanation
Indices: 7632--7970 Score: 348
Period size: 42 Copynumber: 8.1 Consensus size: 42
7622 TCTAAACACA
* * * * *
7632 ATGAAAAGTAAATGAACTTTCACACTTGGGCCTCTAAAAGCG
1 ATGAAAAGTAAATGAACCTCCACACCTGAGCCTCTAAATGCG
* * *
7674 ATGAAAAGTAAATGAAACTCTACACCTGAGCCTCTAAATACG
1 ATGAAAAGTAAATGAACCTCCACACCTGAGCCTCTAAATGCG
* * * *
7716 ATGAAAAGTAAAT-AGATCTCCACA-TTG-GCCTTTAAATGCA
1 ATGAAAAGTAAATGA-ACCTCCACACCTGAGCCTCTAAATGCG
* * * *
7756 ATGAAAAGTAAATGAACCTCCATACTTGGGCCTCTAAATGTG
1 ATGAAAAGTAAATGAACCTCCACACCTGAGCCTCTAAATGCG
* * * * * *
7798 ATGAAAGGTAAATGGACCTCTACACTTGGGCCTCTAAATGTG
1 ATGAAAAGTAAATGAACCTCCACACCTGAGCCTCTAAATGCG
*
7840 ATGAAAAGTAAAT-AGACCTCCACACCTGAGCCTCAAAATGCG
1 ATGAAAAGTAAATGA-ACCTCCACACCTGAGCCTCTAAATGCG
* *
7882 ATGAAAAGTAAATGAACCTCCACACCT-AGGCCTTTAAATGTG
1 ATGAAAAGTAAATGAACCTCCACACCTGA-GCCTCTAAATGCG
* * *
7924 ATGAAAAGTAAATAAACCTCCACACCT-ATGCCACTAAATGCA
1 ATGAAAAGTAAATGAACCTCCACACCTGA-GCCTCTAAATGCG
7966 ATGAA
1 ATGAA
7971 TGCTTTCCTT
Statistics
Matches: 251, Mismatches: 39, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
40 30 0.12
41 8 0.03
42 212 0.84
43 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (42 bp):
ATGAAAAGTAAATGAACCTCCACACCTGAGCCTCTAAATGCG
Found at i:10622 original size:294 final size:292
Alignment explanation
Indices: 10074--10666 Score: 879
Period size: 294 Copynumber: 2.0 Consensus size: 292
10064 ACTTCAAAAC
* *
10074 CCATTTTATATTTTCTCAAGGCTCCCAAATCCAACCAAGGGGCTATCGGTCATTCGTCGTGAGCC
1 CCATTTTATATTTTCTCAAGGCTCCCAAATCCAACCAAGGGGCCATCGATCATTCGTCGTGAGCC
* * * * *
10139 CGTCAATCACTGGCACCGGAGACCATCGCGTACGACGATTGGGAACCTCAAAAGTTGCATTTTTC
66 CGCCAATCACCGGCACCGGAGACCACCGCGTACAACGATCGGGAACCTCAAAAGTTGCATTTTTC
*
10204 TTTCTTTCTTTTTTAATTTGAATCTAGATATAGGGTTTAACCCCTTAGATTTAATTTTGAAACCC
131 TTTCTTTCTTTTTTAATTTGAATCTAGATATAGGGTTTAACCCCTTAGATCTAATTTTGAAACCC
*
10269 TAAAAAAAAGGATAAAGCCTTTAGCTTTCTTAGTTTTTTAAAATAAATCTCTTTTTTTTTCTTAC
196 TAAAAAAAAGGATAAAGCCTTCAGCTTTCTTAGTTTTTTAAAATAAA-CTC-TTTTTTTTCTTAC
*
10334 GACGAAGCCCCGAGTGAGCCAAAGATGCGTTCGT
259 GACGAAGCCCCGAGTGAGCCAAAGACGCGTTCGT
* * * *
10368 CCATTTTATATTCTT-TCAAGGCTCCCAAATTCGACCAAGGGGCCGTCGATCATTCGTCGTGAGT
1 CCATTTTATATT-TTCTCAAGGCTCCCAAATCCAACCAAGGGGCCATCGATCATTCGTCGTGAGC
* * * * *
10432 CTGCCAATCACCGGCATCGGAGACCACCGCGTACAATGGTCGGGAACCTCAAAAGTTGCCTTTTT
65 CCGCCAATCACCGGCACCGGAGACCACCGCGTACAACGATCGGGAACCTCAAAAGTTGCATTTTT
* * *
10497 CTTTCTTTTTTTTTTTTTTAAATTTGAGTCTAGATATAGGGTTTAACCCCTTAGATCTAGTTTTG
130 CTTTC----TTTCTTTTTT-AATTTGAATCTAGATATAGGGTTTAACCCCTTAGATCTAATTTTG
10562 AAACCC-AAAAAAAAGGATAAAGCCTTCAGCTTTCTTAGTTTTTTAAAATAAA-TC-TTTTTTTC
190 AAACCCTAAAAAAAAGGATAAAGCCTTCAGCTTTCTTAGTTTTTTAAAATAAACTCTTTTTTTTC
*
10624 TTACGACGAAGCCCCGATTGAGCCAAAGACGCGTTCGT
255 TTACGACGAAGCCCCGAGTGAGCCAAAGACGCGTTCGT
10662 CCATT
1 CCATT
10667 ATCAGAGATG
Statistics
Matches: 270, Mismatches: 23, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
294 164 0.61
295 2 0.01
296 2 0.01
298 54 0.20
299 48 0.18
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (292 bp):
CCATTTTATATTTTCTCAAGGCTCCCAAATCCAACCAAGGGGCCATCGATCATTCGTCGTGAGCC
CGCCAATCACCGGCACCGGAGACCACCGCGTACAACGATCGGGAACCTCAAAAGTTGCATTTTTC
TTTCTTTCTTTTTTAATTTGAATCTAGATATAGGGTTTAACCCCTTAGATCTAATTTTGAAACCC
TAAAAAAAAGGATAAAGCCTTCAGCTTTCTTAGTTTTTTAAAATAAACTCTTTTTTTTCTTACGA
CGAAGCCCCGAGTGAGCCAAAGACGCGTTCGT
Found at i:11872 original size:193 final size:194
Alignment explanation
Indices: 11542--11940 Score: 701
Period size: 193 Copynumber: 2.1 Consensus size: 194
11532 AAGAGATAAA
*
11542 AATGACTTCAATTTAACCCACTGCAACTTTAGAGGTATAAGATTTGGTGCTGAATCTTCACTCCA
1 AATGACTTCAATTTAACCCACTGCAACTTTAGAAGTATAAGATTTGGTGCTGAATCTTCACTCCA
*
11607 TTCCATTATAACTTCATGGAGACTGAGATTCACTTCTGTGAAATGGTAGCTTCAATCTGCCCCTC
66 TTCCATTATAACTTCAGGGAGACTGAGATTCACTTCTGTGAAATGGTAGCTTCAATCTGCCCCTC
*
11672 TTGATTTAGGGGTAAAAGATAGATTAATGGTTTCAATTTACCCTCTGGTTAGGGTAAAAGATTG
131 TTGATTTAAGGGTAAAAGATAGATTAATGGTTTCAATTTACCCTCTGGTTAGGGTAAAAGATTG
* *
11736 AATGACTTCAATTTGACCCACTGCAACTTTA-AAGTATAAGATTTGGTGCTGACTCTTCACTCCA
1 AATGACTTCAATTTAACCCACTGCAACTTTAGAAGTATAAGATTTGGTGCTGAATCTTCACTCCA
* *
11800 TTCCATTATAACTTTAGGGAGACTGAGATTCACTTCTGTGAGATGGTAGCTTCAATCTGCCCCTC
66 TTCCATTATAACTTCAGGGAGACTGAGATTCACTTCTGTGAAATGGTAGCTTCAATCTGCCCCTC
* * *
11865 TTGATTTAAGGGTAAAAGATTGGTTAATGGTTTCAATTTGCCCTCTGGTTAGGGTAAAAGATTG
131 TTGATTTAAGGGTAAAAGATAGATTAATGGTTTCAATTTACCCTCTGGTTAGGGTAAAAGATTG
11929 AATGACTTCAAT
1 AATGACTTCAAT
11941 CTGCCCCATT
Statistics
Matches: 195, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
193 165 0.85
194 30 0.15
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (194 bp):
AATGACTTCAATTTAACCCACTGCAACTTTAGAAGTATAAGATTTGGTGCTGAATCTTCACTCCA
TTCCATTATAACTTCAGGGAGACTGAGATTCACTTCTGTGAAATGGTAGCTTCAATCTGCCCCTC
TTGATTTAAGGGTAAAAGATAGATTAATGGTTTCAATTTACCCTCTGGTTAGGGTAAAAGATTG
Found at i:11959 original size:39 final size:39
Alignment explanation
Indices: 11896--12295 Score: 358
Period size: 39 Copynumber: 9.9 Consensus size: 39
11886 GGTTAATGGT
* * *
11896 TTCAATTTGCCCTC-TGGTTAGGGTAAAAGATTGAATGAC
1 TTCAATCTGCCC-CATGGTTGGGGTAAAAGATTGGATGAC
* * *
11935 TTCAATCTGCCCCATTGTCGGGGTAAGAGATTGGATGGTATC
1 TTCAATCTGCCCCATGGTTGGGGTAAAAGATTGGAT-G-A-C
* * * * *
11977 TTCAATCTACCTTC-TGGTTAGGGTAAAAGATTGGACGGC
1 TTCAATCTGCC-CCATGGTTGGGGTAAAAGATTGGATGAC
* * *
12016 TTCAATCTACCCCATGGTTGGGGTAAGAGATTGGATGGTGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAAAGATTGGA---TGAC
* * * *
12058 TTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGGTGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAAAGATTG---GATGAC
* *
12100 TTCAATCTGCCCTC-TGGTTTGGGTAAAAGATTGGATGGC
1 TTCAATCTGCCC-CATGGTTGGGGTAAAAGATTGGATGAC
* * *
12139 TTCAATCTACCCCATGGTCGGGGTAAAAGATTGGATGGTGTC
1 TTCAATCTGCCCCATGGTTGGGGTAAAAGATTGGA---TGAC
* *
12181 TTCAATCTACCCTC-TGGTTTGGGTAAAAGATTGGATGAC
1 TTCAATCTGCCC-CATGGTTGGGGTAAAAGATTGGATGAC
* *
12220 TTCAATCTGCCTCATGGTCGGGGTAAAAGATTGGATGAC
1 TTCAATCTGCCCCATGGTTGGGGTAAAAGATTGGATGAC
* * *
12259 TTCAATTTGCCCCATGGTTGGGGTAAGAGATTAGATG
1 TTCAATCTGCCCCATGGTTGGGGTAAAAGATTGGATG
12296 GTGATGTAAC
Statistics
Matches: 299, Mismatches: 43, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
38 4 0.01
39 161 0.54
40 1 0.00
41 2 0.01
42 127 0.42
43 3 0.01
45 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (39 bp):
TTCAATCTGCCCCATGGTTGGGGTAAAAGATTGGATGAC
Found at i:11993 original size:81 final size:80
Alignment explanation
Indices: 11916--12297 Score: 391
Period size: 81 Copynumber: 4.7 Consensus size: 80
11906 CCTCTGGTTA
* *
11916 GGGTAAAAGATTGAATGACTTCAATCTGCCCCATTGTCGGGGTAAGAGATTGGATGGTATCTTCA
1 GGGTAAAAGATTGAATGACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTA-CTTCA
**
11981 ATCTACCTTC-TGGTTA
65 ATCTACC-TCATGGTCG
* * * * *
11997 GGGTAAAAGATTGGACGGCTTCAATCTACCCCATGGTTGGGGTAAGAGATTGGATGGTGTCTTCA
1 GGGTAAAAGATTGAATGACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGT-ACTTCA
* *
12062 ATCTGCCCCATGGTCG
65 ATCTACCTCATGGTCG
* * * *
12078 GGGTAAGAGATTGAATGGTGTCTTCAATCTGCCCTC-TGGTTTGGGTAAAAGATTGGATGG--CT
1 GGGTAAAAGATTGAA---TGACTTCAATCTGCCC-CATGGTTGGGGTAAGAGATTGGATGGTACT
*
12140 TCAATCTACCCCATGGTCG
62 TCAATCTACCTCATGGTCG
* * * * *
12159 GGGTAAAAGATTGGATGGTGTCTTCAATCTACCCTC-TGGTTTGGGTAAAAGATTGGAT-G-ACT
1 GGGTAAAAGATT-GA--ATGACTTCAATCTGCCC-CATGGTTGGGGTAAGAGATTGGATGGTACT
*
12221 TCAATCTGCCTCATGGTCG
62 TCAATCTACCTCATGGTCG
* * *
12240 GGGTAAAAGATTGGATGACTTCAATTTGCCCCATGGTTGGGGTAAGAGATTAGATGGT
1 GGGTAAAAGATTGAATGACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGT
12298 GATGTAACTT
Statistics
Matches: 256, Mismatches: 32, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
77 1 0.00
78 32 0.12
79 1 0.00
80 3 0.01
81 181 0.71
82 2 0.01
84 35 0.14
85 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (80 bp):
GGGTAAAAGATTGAATGACTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTACTTCAA
TCTACCTCATGGTCG
Found at i:12064 original size:123 final size:122
Alignment explanation
Indices: 11934--12298 Score: 504
Period size: 123 Copynumber: 3.0 Consensus size: 122
11924 GATTGAATGA
* *
11934 CTTCAATCTGCCCCATTGTCGGGGTAAGAGATTGGATGGTATCTTCAATCTACCTTCTGGTTAGG
1 CTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGGTATCTTCAATCTGCC-TCTGGTTAGG
*
11999 GTAAAAGATTGGACGGCTTCAATCTACCCCATGGTTGGGGTAAGAGATTGGATGGTGT
65 GTAAAAGATTGGATGGCTTCAATCTACCCCATGGTTGGGGTAAGAGATTGGATGGTGT
* * *
12057 CTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGGTGTCTTCAATCTGCCCTCTGGTTTGG
1 CTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGGTATCTTCAATCTG-CCTCTGGTTAGG
* *
12122 GTAAAAGATTGGATGGCTTCAATCTACCCCATGGTCGGGGTAAAAGATTGGATGGTGT
65 GTAAAAGATTGGATGGCTTCAATCTACCCCATGGTTGGGGTAAGAGATTGGATGGTGT
* ** * **
12180 CTTCAATCTACCCTC-TGGTTTGGGTAAAAGATTGGAT-G-A-CTTCAATCTGCCTCATGGTCGG
1 CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATTGGATGGTATCTTCAATCTGCCTC-TGGTTAG
* * * *
12241 GGTAAAAGATTGGATGACTTCAATTTGCCCCATGGTTGGGGTAAGAGATTAGATGGTG
64 GGTAAAAGATTGGATGGCTTCAATCTACCCCATGGTTGGGGTAAGAGATTGGATGGTG
12299 ATGTAACTTT
Statistics
Matches: 217, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
119 4 0.02
120 67 0.31
122 1 0.00
123 142 0.65
124 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (122 bp):
CTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGGTATCTTCAATCTGCCTCTGGTTAGGG
TAAAAGATTGGATGGCTTCAATCTACCCCATGGTTGGGGTAAGAGATTGGATGGTGT
Found at i:12490 original size:99 final size:98
Alignment explanation
Indices: 12369--12929 Score: 384
Period size: 99 Copynumber: 5.8 Consensus size: 98
12359 TAATCTACTT
* * ** *
12369 CACTGCAACTTCAGGAAG-ATAGGATTTGGTTTTGAAACTTCACTTTATTCCATTGTAACCTCAA
1 CACTGCAACTTCAGG-GGTATAGGATTTGG-TTTGTAACTTCACTCCATTCCACTGTAACCTCAA
* * *
12433 GGACATTGAGATCTGCTTCTGGCTTTAATTTGACC
64 GGACATTGAGATCTGCTTCTCGTTTTAATTCGACC
* *
12468 CACTGCAACTTCAGGGGTATAGGATTTGGTGTTGTAACTTCTCTCCATTCCACTGTATCCTC-AG
1 CACTGCAACTTCAGGGGTATAGGATTTGGT-TTGTAACTTCACTCCATTCCACTGTAACCTCAAG
* * * * *
12532 AGACATTGGGATC--CATATACTCATTTTAATCCAATC
65 -GACATTGAGATCTGC-T-T-CTCGTTTTAATTCGACC
* * * * * *
12568 CACTGTAACTTCAAGGATATAGGATTTGG--TG---CTTCACTCCATTCCGCTGTAACCTTAGGG
1 CACTGCAACTTCAGGGGTATAGGATTTGGTTTGTAACTTCACTCCATTCCACTGTAACCTCAAGG
* * *
12628 ACATTGAGATATGCTTCATTGCTTTAATTCGACC
66 ACATTGAGATCTGCTTC-TCGTTTTAATTCGACC
** * * * ** * * *
12662 CACTATAA-ATCAGTGGTATAGGATTTGGTGTTTTAACTTCTGTCCATTCCACTGTAACTTTAGG
1 CACTGCAACTTCAGGGGTATAGGATTTGGT-TTGTAACTTCACTCCATTCCACTGTAACCTCAAG
* * * * *
12726 GACATTGAG-T-TTCGTTACTCATTTTAATCCAATC
65 GACATTGAGATCTGC-TT-CTCGTTTTAATTCGACC
* * * * * *
12760 CACTACAACTTCAGGGATATAAGATCTGG--TG---CTTCACTCCATTCCACTGTTACTTCAAGG
1 CACTGCAACTTCAGGGGTATAGGATTTGGTTTGTAACTTCACTCCATTCCACTGTAACCTCAAGG
* *
12820 ACATTGAGATCTGCTTCGTTGTTTTAATTTGACC
66 ACATTGAGATCTGCTTC-TCGTTTTAATTCGACC
* * * * * * * *
12854 CACTGCAAC-TCAAGGGTATGGGATTTGATATTGTAACTTCTCTCTATTCCACTGTAACTTTAGG
1 CACTGCAACTTCAGGGGTATAGGATTTGGT-TTGTAACTTCACTCCATTCCACTGTAACCTCAAG
12918 GACATTGAGATC
65 GACATTGAGATC
12930 CCTTACGTAT
Statistics
Matches: 355, Mismatches: 79, Indels: 56
0.72 0.16 0.11
Matches are distributed among these distances:
93 63 0.18
94 70 0.20
95 4 0.01
96 5 0.01
97 5 0.01
98 25 0.07
99 147 0.41
100 36 0.10
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.35
Consensus pattern (98 bp):
CACTGCAACTTCAGGGGTATAGGATTTGGTTTGTAACTTCACTCCATTCCACTGTAACCTCAAGG
ACATTGAGATCTGCTTCTCGTTTTAATTCGACC
Found at i:12824 original size:192 final size:190
Alignment explanation
Indices: 12406--13027 Score: 719
Period size: 192 Copynumber: 3.2 Consensus size: 190
12396 GGTTTTGAAA
** * * *
12406 CTTCACTTTATTCCATTGTAACCTCAAGGACATTGAGATCTGCTTCTGGCTTTAATTTGACCCAC
1 CTTCACTCCATTCCACTGTAACTTCAAGGACATTGAGATCTGCTTCTTGCTTTAATTTGACCCAC
* * * * *
12471 TGCAACTTCAGGGGTATAGGATTTGGTGTTGTAACTTCTCTCCATTCCACTGTATCCTCAGAGAC
66 TGCAA-ATCA-GGGTATAGGATTTGGTGTTGTAACTTCTCTCCATTCCACTGTAACTTTAGGGAC
* ** *
12536 ATTGGGATCCATATACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATTTGGTG
129 ATTGAGATCCAT-TACTCATTTTAATCCAATCCACTACAACTTCAGGGATATAGGATTTGGTG
* * * *
12599 CTTCACTCCATTCCGCTGTAACCTT-AGGGACATTGAGATATGCTTCATTGCTTTAATTCGACCC
1 CTTCACTCCATTCCACTGTAA-CTTCAAGGACATTGAGATCTGCTTC-TTGCTTTAATTTGACCC
** * *
12663 ACTATAAATCAGTGGTATAGGATTTGGTGTTTTAACTTCTGTCCATTCCACTGTAACTTTAGGGA
64 ACTGCAAATCAG-GGTATAGGATTTGGTGTTGTAACTTCTCTCCATTCCACTGTAACTTTAGGGA
* * * * *
12728 CATTGAGTTTCGTTACTCATTTTAATCCAATCCACTACAACTTCAGGGATATAAGATCTGGTG
128 CATTGAGATCCATTACTCATTTTAATCCAATCCACTACAACTTCAGGGATATAGGATTTGGTG
* *
12791 CTTCACTCCATTCCACTGTTACTTCAAGGACATTGAGATCTGCTTCGTTGTTTTAATTTGACCCA
1 CTTCACTCCATTCCACTGTAACTTCAAGGACATTGAGATCTGCTTC-TTGCTTTAATTTGACCCA
* * * * *
12856 CTGCAACTCAAGGGTATGGGATTTGATATTGTAACTTCTCTCTATTCCACTGTAACTTTAGGGAC
65 CTGCAAATC-AGGGTATAGGATTTGGTGTTGTAACTTCTCTCCATTCCACTGTAACTTTAGGGAC
* * *** * *
12921 ATTGAGATCCCTTACGT-ATTTTGATATGATCCACTTCAACTTTAGGGATATAGGATTTGGTG
129 ATTGAGATCCATTAC-TCATTTTAATCCAATCCACTACAACTTCAGGGATATAGGATTTGGTG
* * * * * *
12983 CTCCACTCTATTCCACTATAACCTCAGGGATATTGAGATCT-CTTC
1 CTTCACTCCATTCCACTGTAACTTCAAGGACATTGAGATCTGCTTC
13028 GTTATTTTAA
Statistics
Matches: 362, Mismatches: 61, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
191 7 0.02
192 236 0.65
193 97 0.27
194 22 0.06
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (190 bp):
CTTCACTCCATTCCACTGTAACTTCAAGGACATTGAGATCTGCTTCTTGCTTTAATTTGACCCAC
TGCAAATCAGGGTATAGGATTTGGTGTTGTAACTTCTCTCCATTCCACTGTAACTTTAGGGACAT
TGAGATCCATTACTCATTTTAATCCAATCCACTACAACTTCAGGGATATAGGATTTGGTG
Found at i:13669 original size:210 final size:209
Alignment explanation
Indices: 13288--13859 Score: 853
Period size: 210 Copynumber: 2.7 Consensus size: 209
13278 TTCATCTCTC
* *
13288 GGTCTACTTCTCTATATCTCATCAGGAAGATG-ATCGCTTTATTGCTTTGACCCACTTCTCTGTA
1 GGTCCACTTCTCTATATCTCATCAGGAAGATGAAT-GCTTTATTGCTTTGACCCACTTCTCAGTA
13352 TCTCATCA-AGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCT
65 TCTCATCAGA-AAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCT
* *
13416 ACTTCTCTGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATTCGCTTGC-CTGAATCTC
129 ACTTCTCTATATCTCATCAAGAAGATGACCACATCACTTGTTTTAATTCGCTT-CTCTGAATCTC
* *
13480 ATCAAGAAGATGGATTT
193 ATCAAGAAGACGAATTT
*
13497 GGTCCACTTCTCTATATCTCATCAGGAAGACGAATGCTTTATTGCTTTGACCCACTTCTCAGTAT
1 GGTCCACTTCTCTATATCTCATCAGGAAGATGAATGCTTTATTGCTTTGACCCACTTCTCAGTAT
*
13562 CTCATCAGAAAGATGGGGGTTCGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTA
66 CTCATCAGAAAGAT-GGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTA
* * * * *
13627 CTTCTCTATATCACATCAAGAAGATGACCACATCATTTGTTTTAATTCGCTTCTTTGTATCTGAT
130 CTTCTCTATATCTCATCAAGAAGATGACCACATCACTTGTTTTAATTCGCTTCTCTGAATCTCAT
13692 CAAGAAGACGAATTT
195 CAAGAAGACGAATTT
* * * * ** *
13707 GTTCCACGTCTCTGTATCTCATTAGGAAGATGACCGCTTAATTGCTTTGACCCACTTCTCAGTAT
1 GGTCCACTTCTCTATATCTCATCAGGAAGATGAATGCTTTATTGCTTTGACCCACTTCTCAGTAT
* * * * * *
13772 CTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATCGAGCTTCGTTTCATTGATTTGGTTTAC
66 CTCATCAGAAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTAC
13837 TTCTCTATATCTCATCAAGAAGA
131 TTCTCTATATCTCATCAAGAAGA
13860 CGGATTTGGT
Statistics
Matches: 330, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
209 139 0.42
210 191 0.58
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.36
Consensus pattern (209 bp):
GGTCCACTTCTCTATATCTCATCAGGAAGATGAATGCTTTATTGCTTTGACCCACTTCTCAGTAT
CTCATCAGAAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTAC
TTCTCTATATCTCATCAAGAAGATGACCACATCACTTGTTTTAATTCGCTTCTCTGAATCTCATC
AAGAAGACGAATTT
Found at i:13875 original size:37 final size:37
Alignment explanation
Indices: 13825--13896 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
13815 TCGTTTCATT
*
13825 GATTTGGTTTACTTCTCTATATCTCATCAAGAAGACG
1 GATTTGGTCTACTTCTCTATATCTCATCAAGAAGACG
* * *
13862 GATTTGGTCTACTTCTTTGTATCTTATCAAGAAGA
1 GATTTGGTCTACTTCTCTATATCTCATCAAGAAGA
13897 TGACCACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (37 bp):
GATTTGGTCTACTTCTCTATATCTCATCAAGAAGACG
Found at i:14220 original size:45 final size:46
Alignment explanation
Indices: 14159--14247 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
14149 TAAAAGATCG
* *
14159 GATGATGGCTATAATCTGTCC-CATGA-TCGGGGTAAGAGATTGGAT
1 GATGATGGCTACAATCTG-CCTCATGATTAGGGGTAAGAGATTGGAT
* *
14204 GATGATGGCTGCAATCTGCCTTATGATTAGGGGTAAGAGATTGG
1 GATGATGGCTACAATCTGCCTCATGATTAGGGGTAAGAGATTGG
14248 TGTGTCTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 2 0.05
45 20 0.53
46 16 0.42
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (46 bp):
GATGATGGCTACAATCTGCCTCATGATTAGGGGTAAGAGATTGGAT
Found at i:14297 original size:41 final size:41
Alignment explanation
Indices: 14252--14416 Score: 213
Period size: 41 Copynumber: 3.9 Consensus size: 41
14242 GATTGGTGTG
*
14252 TCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAA
1 TCTTCAATCTACCCCTCTTGATTAAGGGTAAAAGATTGGAA
* * *
14293 TCTTCAATCTACCCCTCTTGATTAGGGGTAAAAGACTAGAA
1 TCTTCAATCTACCCCTCTTGATTAAGGGTAAAAGATTGGAA
* *
14334 TCTTCCATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGATGA
1 TCTTCAATCTACCCCTCTTGATTAAGGGTAAAAGATTGGA--A
* *
14377 TGGCTTCAATTTACCCCTCTTGACTTAGGGGTAAAAGATT
1 T--CTTCAATCTACCCCTCTTGA-TTAAGGGTAAAAGATT
14417 TATAGGTCTT
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
41 72 0.68
43 2 0.02
45 17 0.16
46 15 0.14
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (41 bp):
TCTTCAATCTACCCCTCTTGATTAAGGGTAAAAGATTGGAA
Found at i:14344 original size:82 final size:85
Alignment explanation
Indices: 14252--14414 Score: 269
Period size: 82 Copynumber: 1.9 Consensus size: 85
14242 GATTGGTGTG
14252 TCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGA-AT-CTTCAATCTACCCCTCTTGA-
1 TCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAGATGCTTCAATCTACCCCTCTTGAC
14314 TTAGGGGTAAAAGACTAGAA
66 TTAGGGGTAAAAGACTAGAA
* *
14334 TCTTCCATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGATGATGGCTTCAATTTACCCCTCTTG
1 TCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGA-GAT-GCTTCAATCTACCCCTCTTG
14399 ACTTAGGGGTAAAAGA
64 ACTTAGGGGTAAAAGA
14415 TTTATAGGTC
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
82 39 0.53
84 2 0.03
86 19 0.26
87 14 0.19
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (85 bp):
TCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGAGATGCTTCAATCTACCCCTCTTGAC
TTAGGGGTAAAAGACTAGAA
Found at i:14873 original size:97 final size:97
Alignment explanation
Indices: 14756--14984 Score: 395
Period size: 97 Copynumber: 2.4 Consensus size: 97
14746 TAAGGTATCA
14756 GTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATAGGGTTCGCCGTTACGGTCTCAACCT
1 GTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATAGGGTTCGCCGTTACGGTCTCAACCT
* *
14821 TTCCTATCACATTTCATGGTACTGGATTCGCT
66 TTCCTATCACATTTCATGGTACCGGATTCACT
* **
14853 GTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATAGGGTTCGTCGTTGTGGTCTCAACCT
1 GTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATAGGGTTCGCCGTTACGGTCTCAACCT
14918 TTCCTATCACATTTCATGGTACCGGATTCACT
66 TTCCTATCACATTTCATGGTACCGGATTCACT
* *
14950 GTTACGGCCTCAACCTTTCCCTTCAAATATTCATG
1 GTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATG
14985 TTTTCTTGAT
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 125 1.00
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.35
Consensus pattern (97 bp):
GTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATAGGGTTCGCCGTTACGGTCTCAACCT
TTCCTATCACATTTCATGGTACCGGATTCACT
Found at i:14914 original size:49 final size:48
Alignment explanation
Indices: 14760--14984 Score: 242
Period size: 48 Copynumber: 4.6 Consensus size: 48
14750 GTATCAGTTG
* *
14760 CGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATAGGGTTCGCCGTTA
1 CGGCCTCAACCTTTCCCTTCAAAT-TTCATGGTATAGGATTCGCTGTTA
* * *
14809 CGGTCTCAACCTTT-CCTATCACATTTCATGGTACT-GGATTCGCTGTTG
1 CGGCCTCAACCTTTCCCT-TCAAATTTCATGGTA-TAGGATTCGCTGTTA
* *
14857 CGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATAGGGTTCG-TCGTTG
1 CGGCCTCAACCTTTCCCTTCAAAT-TTCATGGTATAGGATTCGCT-GTTA
* * * ** *
14906 TGGTCTCAACCTTT-CCTATCACATTTCATGGTACCGGATTCACTGTTA
1 CGGCCTCAACCTTTCCCT-TCAAATTTCATGGTATAGGATTCGCTGTTA
14954 CGGCCTCAACCTTTCCCTTCAAATATTCATG
1 CGGCCTCAACCTTTCCCTTCAAAT-TTCATG
14985 TTTTCTTGAT
Statistics
Matches: 147, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
48 79 0.54
49 68 0.46
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (48 bp):
CGGCCTCAACCTTTCCCTTCAAATTTCATGGTATAGGATTCGCTGTTA
Found at i:15937 original size:10 final size:9
Alignment explanation
Indices: 15916--15963 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 9
15906 TCTCCTTTTC
15916 TTTTTCCTT
1 TTTTTCCTT
15925 TTTTTCCTAT
1 TTTTTCCT-T
*
15935 TTTTT--TA
1 TTTTTCCTT
15942 TTTTTCCTT
1 TTTTTCCTT
15951 TCTTTTCCTT
1 T-TTTTCCTT
15961 TTT
1 TTT
15964 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 5 0.15
8 1 0.03
9 12 0.36
10 15 0.45
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTCCTT
Found at i:15946 original size:26 final size:26
Alignment explanation
Indices: 15911--15973 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
15901 CGACCTCTCC
*
15911 TTTTCTTTTTCCTTT-TTTTCCTATTT
1 TTTTATTTTTCCTTTCTTTTCCT-TTT
15937 TTTTATTTTTCCTTTCTTTTCCTTTT
1 TTTTATTTTTCCTTTCTTTTCCTTTT
15963 TATTTATTTTT
1 T-TTTATTTTT
15974 TCTTCATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTATTTTTCCTTTCTTTTCCTTTT
Found at i:16876 original size:3 final size:3
Alignment explanation
Indices: 16864--16911 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
16854 TTTTGACCCA
*
16864 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
16911 T
1 T
16912 TTGTTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:26120 original size:109 final size:108
Alignment explanation
Indices: 25987--26204 Score: 319
Period size: 109 Copynumber: 2.0 Consensus size: 108
25977 CGAAAATAAA
* * * **
25987 GAACACTTATCGATTTTAAATAGGATGTTCAGTTACTTAGGTTCAAAGAAAAATCATACCCAGTA
1 GAACACTTATCGATTTTAAATAGGATATTCAATTACTTAAGTTCAAAGAAAAATCATA-CCAACA
*
26052 CATTAGGGCATAATTTCTCGAGTTCCCTAAAATAAAAGAACATT
65 CATTAGGGCACAATTTCTCGAGTTCCCTAAAATAAAAGAACATT
* * *
26096 GAACATTTGTCGATTTTAAATAGGATATTTAATTACTTAAGTTCAAAGAAAAATCATACCAACAC
1 GAACACTTATCGATTTTAAATAGGATATTCAATTACTTAAGTTCAAAGAAAAATCATACCAACAC
* * *
26161 GTTAGGGCACAATTTCTCGAGTTCCCTAAAATATAATAACATT
66 ATTAGGGCACAATTTCTCGAGTTCCCTAAAATAAAAGAACATT
26204 G
1 G
26205 CCTCGATTTT
Statistics
Matches: 97, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 45 0.46
109 52 0.54
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (108 bp):
GAACACTTATCGATTTTAAATAGGATATTCAATTACTTAAGTTCAAAGAAAAATCATACCAACAC
ATTAGGGCACAATTTCTCGAGTTCCCTAAAATAAAAGAACATT
Found at i:28390 original size:22 final size:24
Alignment explanation
Indices: 28365--28417 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 24
28355 TCACTCTCTA
*
28365 TTTTTCTTCTTTTTTGT-TGT-TT
1 TTTTTCTTCTTTTTGGTGTGTATT
28387 TTTTTC-TCTTTTTGGTGTGTATT
1 TTTTTCTTCTTTTTGGTGTGTATT
28410 TTTTTCTT
1 TTTTTCTT
28418 GATTTAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 9 0.33
22 9 0.33
23 8 0.30
24 1 0.04
ACGTcount: A:0.02, C:0.09, G:0.11, T:0.77
Consensus pattern (24 bp):
TTTTTCTTCTTTTTGGTGTGTATT
Found at i:47265 original size:20 final size:20
Alignment explanation
Indices: 47240--47284 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
47230 CATGATTTGT
*
47240 ATTAAGAGT-AAATAGGCTTA
1 ATTAAGAGTAAAATA-GATTA
*
47260 ATTAAGATTAAAATAGATTA
1 ATTAAGAGTAAAATAGATTA
47280 ATTAA
1 ATTAA
47285 AGCTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.33
Consensus pattern (20 bp):
ATTAAGAGTAAAATAGATTA
Found at i:69603 original size:30 final size:30
Alignment explanation
Indices: 69567--69704 Score: 111
Period size: 30 Copynumber: 4.6 Consensus size: 30
69557 CGAACTCTTC
* *
69567 TAAAATTGCATTTTGACCCATAAACTTTTT
1 TAAAATTACATTTTAACCCATAAACTTTTT
* *
69597 TAAAATTATATTTTAACCCATGAAC-TTTT
1 TAAAATTACATTTTAACCCATAAACTTTTT
** *
69626 CCAAATTACATTTTAACCTC-TAAACTTTCT
1 TAAAATTACATTTTAACC-CATAAACTTTTT
** * * * *
69656 CGAAATCACATCTTGATCCC-TAAACTTTTC
1 TAAAATTACAT-TTTAACCCATAAACTTTTT
*
69686 TAAAATTATATTTTAACCC
1 TAAAATTACATTTTAACCC
69705 CAAATTCTTC
Statistics
Matches: 84, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
29 29 0.35
30 50 0.60
31 5 0.06
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.41
Consensus pattern (30 bp):
TAAAATTACATTTTAACCCATAAACTTTTT
Found at i:79933 original size:43 final size:43
Alignment explanation
Indices: 79877--80025 Score: 172
Period size: 43 Copynumber: 3.5 Consensus size: 43
79867 CTTTAGGCGC
* *
79877 TTTCCAACAAACGCCGCTAAAGAACATGTTCTTTAACGGCGCT
1 TTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACGGCACT
* * *
79920 TTTCCCACAAACGCCGCTAAAGAACATGTTCTTTATCAGCATT
1 TTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACGGCACT
* * * * * * * *
79963 TTTACCACAAGCGCTGCTATAGAACATGGTCTTTAGCGTCATT
1 TTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACGGCACT
*
80006 TTTCCCACAAATGCCGCTAA
1 TTTCCCACAAACGCCGCTAA
80026 CATTAACAGA
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (43 bp):
TTTCCCACAAACGCCGCTAAAGAACATGTTCTTTAACGGCACT
Found at i:80439 original size:66 final size:65
Alignment explanation
Indices: 80303--80440 Score: 154
Period size: 66 Copynumber: 2.1 Consensus size: 65
80293 TCATATTTTG
* * * *
80303 AAGTTGTAGCTGTAGTTCGTCATACTTTCTTTGAGACTCTGCTTCCCTCGTTGCTACCTTGCCTT
1 AAGTTGTAGCTGAAGTTCATCATACTTTCTTTGAGACTCTGCTT-CCTCGTTGCTACCCTCCCTT
80368 C
65 C
* * *
80369 AAGTTGTAGTTGAAGTTCATCATATTTTCTTTGAGCCTCTGCTT-CTC-TTGCTACTGCCTCCAC
1 AAGTTGTAGCTGAAGTTCATCATACTTTCTTTGAGACTCTGCTTCCTCGTTGCTAC--CCTCC-C
*
80432 TTT
63 TTC
80435 AAGTTG
1 AAGTTG
80441 AGCAATTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
63 7 0.11
64 3 0.05
65 3 0.05
66 48 0.79
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (65 bp):
AAGTTGTAGCTGAAGTTCATCATACTTTCTTTGAGACTCTGCTTCCTCGTTGCTACCCTCCCTTC
Found at i:91167 original size:25 final size:25
Alignment explanation
Indices: 91139--91186 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
91129 TGAGTTTGAA
91139 TGGATTAAATCCATCAGATGCTAAC
1 TGGATTAAATCCATCAGATGCTAAC
91164 TGGATTAAATCCATCAGATGCTA
1 TGGATTAAATCCATCAGATGCTA
91187 GCTCAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (25 bp):
TGGATTAAATCCATCAGATGCTAAC
Found at i:92920 original size:26 final size:26
Alignment explanation
Indices: 92888--93043 Score: 155
Period size: 26 Copynumber: 6.2 Consensus size: 26
92878 ATTTGAATCG
92888 AATATTTGAGTTGTTTTTAATAATTA
1 AATATTTGAGTTGTTTTTAATAATTA
* * * *
92914 AATATTT-AATTAAATAATTAAATAATTA
1 AATATTTGAGTT--GT-TTTTAATAATTA
*
92942 AATATTTGGGTTGTTTTTAATAATTA
1 AATATTTGAGTTGTTTTTAATAATTA
* *
92968 AATATTTGGGTTATTTTTAATAATTA
1 AATATTTGAGTTGTTTTTAATAATTA
* *
92994 AATATTT-A-----ATTAAATAATTA
1 AATATTTGAGTTGTTTTTAATAATTA
93014 AATATTTGAGTTGTTTTTAATAATTA
1 AATATTTGAGTTGTTTTTAATAATTA
93040 AATA
1 AATA
93044 ATTATTTTGT
Statistics
Matches: 105, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
20 17 0.16
21 1 0.01
25 3 0.03
26 63 0.60
27 2 0.02
28 17 0.16
29 2 0.02
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
AATATTTGAGTTGTTTTTAATAATTA
Found at i:92922 original size:8 final size:8
Alignment explanation
Indices: 92920--92945 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
92910 ATTAAATATT
92920 TAATTAAA
1 TAATTAAA
92928 TAATTAAA
1 TAATTAAA
92936 TAATTAAA
1 TAATTAAA
92944 TA
1 TA
92946 TTTGGGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Done.