Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015056.1 Kokia drynarioides strain JFW-HI SEQ_130100, 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: 274517
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 713 characters in sequence are not A, C, G, or T
Found at i:467 original size:2 final size:2
Alignment explanation
Indices: 462--495 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
452 TTTGTAAAAT
*
462 TA TA TA TA TA TA TA TA TA TG TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
496 TATTTGCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:499 original size:8 final size:9
Alignment explanation
Indices: 460--499 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
450 AATTTGTAAA
460 ATTATATAT
1 ATTATATAT
469 ATATATATAT
1 AT-TATATAT
479 ATGTATATAT
1 AT-TATATAT
489 ATTATAT-T
1 ATTATATAT
497 ATT
1 ATT
500 TGCTTGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 4 0.14
9 7 0.24
10 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
ATTATATAT
Found at i:6087 original size:2 final size:2
Alignment explanation
Indices: 6078--6107 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6068 ATATACATGC
6078 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6108 CTTTTGGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9703 original size:5 final size:5
Alignment explanation
Indices: 9693--9721 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9683 GAGCCGCTGA
9693 GGGTC GGGTC GGGTC GGGTC GGGTC GGGT
1 GGGTC GGGTC GGGTC GGGTC GGGTC GGGT
9722 TGGGAAACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.62, T:0.21
Consensus pattern (5 bp):
GGGTC
Found at i:24014 original size:14 final size:14
Alignment explanation
Indices: 23995--24022 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23985 GACACCCAAA
23995 TGATTAAAACTTAC
1 TGATTAAAACTTAC
24009 TGATTAAAACTTAC
1 TGATTAAAACTTAC
24023 CCTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TGATTAAAACTTAC
Found at i:24172 original size:175 final size:174
Alignment explanation
Indices: 23835--24178 Score: 453
Period size: 175 Copynumber: 2.0 Consensus size: 174
23825 TACATCCAAA
* ** ** *
23835 TGATTAAAAGCTTCCCTTTTGGTACAGATATTGGGATTCAACCCCAAATCTGTTGGGTGTCATCT
1 TGATTAAAAGCTTCCCTTTTGGTACAGATATTGGGATTCAACCCCAAATATGCCGAATGCCATCT
* * * * *
23900 TTTAAAGGTGACTAAACGAATCACTCGAAATAAGTCCCATCCGAGCACATTTTTTTGCACGACGA
66 TTTAAAGGTGACTAAACGAATCAATCGAAATAAATCCCATCCGAGCACATTTCTTAGCACCACGA
*
23965 CACATTCTCTGAGTTTTCGAGACACCCAAATGATTAAAACTTAC
131 CACATTCTCTGAATTTTCGAGACACCCAAATGATTAAAACTTAC
* *
24009 TGATTAAAA-CTTACCCTTATT-GTATAGATATTGGGATTCAAACCCCATATATGCCGAATGCCA
1 TGATTAAAAGCTT-CCCTT-TTGGTACAGATATTGGGATTC-AACCCCAAATATGCCGAATGCCA
** * *
24072 TCTTTTAAAGGTGACTGGATGAATCAATCGAAATAAATCCCATCCGAGCATA-TTCTTAGCACCA
63 TCTTTTAAAGGTGACTAAACGAATCAATCGAAATAAATCCCATCCGAGCACATTTCTTAGCACCA
24136 CGACACATTCTCTGAATTTTC-AGTACACCTCAAATGATTAAAA
128 CGACACATTCTCTGAATTTTCGAG-ACACC-CAAATGATTAAAA
24179 GTTTCCCTTT
Statistics
Matches: 147, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
173 5 0.03
174 65 0.44
175 77 0.52
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (174 bp):
TGATTAAAAGCTTCCCTTTTGGTACAGATATTGGGATTCAACCCCAAATATGCCGAATGCCATCT
TTTAAAGGTGACTAAACGAATCAATCGAAATAAATCCCATCCGAGCACATTTCTTAGCACCACGA
CACATTCTCTGAATTTTCGAGACACCCAAATGATTAAAACTTAC
Found at i:25233 original size:31 final size:31
Alignment explanation
Indices: 25198--25262 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
25188 TCAACAATCC
25198 AGTGACTTAAATAAAAACTTTTGAATAATTT
1 AGTGACTTAAATAAAAACTTTTGAATAATTT
* * *
25229 AGTGACTTAAATGAATACTTTTGAATAGTTT
1 AGTGACTTAAATAAAAACTTTTGAATAATTT
25260 AGT
1 AGT
25263 AACCATTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTTGAATAATTT
Found at i:28379 original size:58 final size:57
Alignment explanation
Indices: 28261--28369 Score: 130
Period size: 58 Copynumber: 1.9 Consensus size: 57
28251 ATTTTTGAAA
* * * **
28261 TTTTTTTCTAAAAAAAGGGTGTCCGTCATGCAATGATCAACACCCAAAAATGTAAAT
1 TTTTTTTCTAAAAAAAGGGTGTCCGCCATGAAATGACCAACACAAAAAAATGTAAAT
* *
28318 TTTTTTTCTCAAAAAGAGGGTGT-CGACCATGAAATGACCGACACAAAAAAAT
1 TTTTTTTCT-AAAAAAAGGGTGTCCG-CCATGAAATGACCAACACAAAAAAAT
28370 TGTATTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
57 11 0.26
58 32 0.74
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (57 bp):
TTTTTTTCTAAAAAAAGGGTGTCCGCCATGAAATGACCAACACAAAAAAATGTAAAT
Found at i:34050 original size:32 final size:33
Alignment explanation
Indices: 34014--34075 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
34004 AGGTTATTTT
*
34014 AATTGATAATGAGAATTATGATA-TGTTTTCTA
1 AATTGATAATGAGAATTATGAAATTGTTTTCTA
*
34046 AATTGATGATGAGAATTATGAAATTGTTTT
1 AATTGATAATGAGAATTATGAAATTGTTTT
34076 TTAGTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.44
Consensus pattern (33 bp):
AATTGATAATGAGAATTATGAAATTGTTTTCTA
Found at i:35176 original size:9 final size:10
Alignment explanation
Indices: 35161--35203 Score: 52
Period size: 9 Copynumber: 4.2 Consensus size: 10
35151 AACAAATGAT
35161 TTTAAAATTA
1 TTTAAAATTA
35171 -TTAAAATTA
1 TTTAAAATTA
*
35180 TTTTAAAAATAA
1 -TTT-AAAATTA
35192 TTTAAAATTA
1 TTTAAAATTA
35202 TT
1 TT
35204 AAATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 9 0.32
10 8 0.29
11 5 0.18
12 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:35182 original size:20 final size:22
Alignment explanation
Indices: 35154--35203 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
35144 TCACATCAAC
* *
35154 AAATGATTTT-AAAATTA-TTA
1 AAATTATTTTAAAAATAATTTA
35174 AAATTATTTTAAAAATAATTTA
1 AAATTATTTTAAAAATAATTTA
35196 AAATTATT
1 AAATTATT
35204 AAATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 9 0.35
21 6 0.23
22 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATTATTTTAAAAATAATTTA
Found at i:35185 original size:11 final size:11
Alignment explanation
Indices: 35154--35203 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
35144 TCACATCAAC
*
35154 AAATGATTTTA
1 AAATTATTTTA
35165 AAATTA--TTA
1 AAATTATTTTA
35174 AAATTATTTTA
1 AAATTATTTTA
* *
35185 AAAATAATTTA
1 AAATTATTTTA
35196 AAATTATT
1 AAATTATT
35204 AAATAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 9 0.28
11 23 0.72
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:38934 original size:22 final size:21
Alignment explanation
Indices: 38891--38937 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
38881 ATTTAGTTCA
**
38891 TTTATTTTTATTTTTTGGAAT
1 TTTATTTTTATTTTTTAAAAT
*
38912 TTTATTTTTTTATTTTTAAAAT
1 TTTATTTTTAT-TTTTTAAAAT
38934 TTTA
1 TTTA
38938 AAATTTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTATTTTTATTTTTTAAAAT
Found at i:39402 original size:27 final size:27
Alignment explanation
Indices: 39372--39424 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
39362 TTAAATTACA
* *
39372 AATTTCTAGAAATAGAAATAAAAAAAT
1 AATTCCTAAAAATAGAAATAAAAAAAT
39399 AATTCCTAAAAATAGAAATAAAAAAA
1 AATTCCTAAAAATAGAAATAAAAAAA
39425 ACTAAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (27 bp):
AATTCCTAAAAATAGAAATAAAAAAAT
Found at i:44903 original size:9 final size:9
Alignment explanation
Indices: 44891--44940 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
44881 AAAATGATGA
44891 TTAAATTAT
1 TTAAATTAT
44900 TTAAATT-T
1 TTAAATTAT
44908 TT---TTAT
1 TTAAATTAT
44914 TTAAATTA-
1 TTAAATTAT
44922 TTAAATTAT
1 TTAAATTAT
*
44931 TAAAATTAT
1 TTAAATTAT
44940 T
1 T
44941 GGTGTATGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
5 2 0.06
6 3 0.09
8 11 0.31
9 19 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAAATTAT
Found at i:46614 original size:16 final size:18
Alignment explanation
Indices: 46575--46608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46565 GAAATTTATA
46575 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
46592 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
46609 AATTTACAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:47497 original size:24 final size:23
Alignment explanation
Indices: 47452--47502 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
47442 ATCTTTTATC
*
47452 ATTTTCTAATTTTTAAATGTTTT
1 ATTTTCTAATTTTTAAACGTTTT
47475 ATTTT-TAATTTTTAAACACGTTTT
1 ATTTTCTAATTTTT-AA-ACGTTTT
47499 ATTT
1 ATTT
47503 GATTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
23 7 0.28
24 10 0.40
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (23 bp):
ATTTTCTAATTTTTAAACGTTTT
Found at i:48958 original size:46 final size:46
Alignment explanation
Indices: 48907--48997 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
48897 CTTTATAAAA
*
48907 TAACAATCATCACTATAAGATTATTTATTTTATTTTATTTAAAATC
1 TAACAATCATCACTATAAGATTATTTATTTTATTTTATGTAAAATC
48953 TAACAATCATCACTATAAGATTATTTATTTTATTTTATGTAAAAT
1 TAACAATCATCACTATAAGATTATTTATTTTATTTTATGTAAAAT
48998 TTAGAAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (46 bp):
TAACAATCATCACTATAAGATTATTTATTTTATTTTATGTAAAATC
Found at i:49351 original size:31 final size:31
Alignment explanation
Indices: 49285--49357 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
49275 TAAAAAATAT
* * * *
49285 AAATTTGATTCTTTTTAAAAGATTAATAATT
1 AAATTTGACTATTTTTAAAAAATTAATAATC
*
49316 AAATTTGACTATTTTTAAAAAATTAGAT-GTC
1 AAATTTGACTATTTTTAAAAAATTA-ATAATC
*
49347 AAATTTAACTA
1 AAATTTGACTA
49358 AATAATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AAATTTGACTATTTTTAAAAAATTAATAATC
Found at i:51002 original size:24 final size:23
Alignment explanation
Indices: 50975--51025 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
50965 AATTTTCGTC
*
50975 AAATATATATA-CTATATTAATAAA
1 AAATATAAATATC-ATATTAA-AAA
50999 AAATATAAATATCATATTAAAAA
1 AAATATAAATATCATATTAAAAA
51022 AAAT
1 AAAT
51026 TATCAAACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 17 0.68
25 1 0.04
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATAAATATCATATTAAAAA
Found at i:51155 original size:26 final size:25
Alignment explanation
Indices: 51126--51181 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
51116 ATGATGTAAA
*
51126 TGCTTTAGCAAAGCT-TATGGAGTTGT
1 TGCTTTAGAAAAG-TAT-TGGAGTTGT
*
51152 TGCTTTGGAAAAGTATTGGAGTTGT
1 TGCTTTAGAAAAGTATTGGAGTTGT
51177 TGCTT
1 TGCTT
51182 AAGTATGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (25 bp):
TGCTTTAGAAAAGTATTGGAGTTGT
Found at i:52963 original size:2 final size:2
Alignment explanation
Indices: 52956--52986 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52946 AAGTAGTAAG
52956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52987 TCTTTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58545 original size:15 final size:16
Alignment explanation
Indices: 58504--58537 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
58494 AAATTGTTCT
*
58504 TTGATTTAATGTACAG
1 TTGATTTAATATACAG
58520 TTGATTTAATATACAG
1 TTGATTTAATATACAG
58536 TT
1 TT
58538 TTTTAATAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (16 bp):
TTGATTTAATATACAG
Found at i:61054 original size:238 final size:238
Alignment explanation
Indices: 60636--61109 Score: 858
Period size: 238 Copynumber: 2.0 Consensus size: 238
60626 TAAGTCTAAG
* * *
60636 TTTTGTTATTTTTATTGATGAATTAACATCTGTCTGGGATGATATGTGTCCTTTATCCTTTTTCT
1 TTTTGTTATTTTTATTGATGAATTAACAACTGTCTGGGATGATATGTGTCCTTTATCCATTTCCT
60701 TCCAAAAGAAGTTGATATAAGCAGGCCTAGAAAGCCTAAGGTTCGAGGACCAAAGCTGGATGTGT
66 TCCAAAAGAAGTTGATATAAGCAGGCCTAGAAAGCCTAAGGTTCGAGGACCAAAGCTGGATGTGT
60766 ATATCCTTTTAAGACCTTTTTTTAGCCCTTTGAAATTTTGGTGATCAATTTTGACCCTTCTATAA
131 ATATCCTTTTAAGACCTTTTTTTAGCCCTTTGAAATTTTGGTGATCAATTTTGACCCTTCTATAA
60831 TTTTGAGAGATTTGCCATGCTTTTTGCTTTCCCCGTTTAAAAA
196 TTTTGAGAGATTTGCCATGCTTTTTGCTTTCCCCGTTTAAAAA
* * *
60874 TTTTGTTATTTTTATTGATGAATTAATAACTGTCTGGGGTGATTTGTGTCCTTTATCCATTTCCT
1 TTTTGTTATTTTTATTGATGAATTAACAACTGTCTGGGATGATATGTGTCCTTTATCCATTTCCT
* *
60939 TCCAAAAGAAGTTGATATAAGCAGGCCTAGAAAGCCTAAGGTTTGAGGACCAATGCTGGATGTGT
66 TCCAAAAGAAGTTGATATAAGCAGGCCTAGAAAGCCTAAGGTTCGAGGACCAAAGCTGGATGTGT
61004 ATATCCTTTTAAGACCTTTTTTTAGCCCTTTGAAATTTTGGTGATCAATTTTGACCCTTCTATAA
131 ATATCCTTTTAAGACCTTTTTTTAGCCCTTTGAAATTTTGGTGATCAATTTTGACCCTTCTATAA
* *
61069 TTTTGAGGGATTTGCCATGCTTTTTGCTTTCCCTGTTTAAA
196 TTTTGAGAGATTTGCCATGCTTTTTGCTTTCCCCGTTTAAA
61110 GAAAGAGTAG
Statistics
Matches: 226, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
238 226 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (238 bp):
TTTTGTTATTTTTATTGATGAATTAACAACTGTCTGGGATGATATGTGTCCTTTATCCATTTCCT
TCCAAAAGAAGTTGATATAAGCAGGCCTAGAAAGCCTAAGGTTCGAGGACCAAAGCTGGATGTGT
ATATCCTTTTAAGACCTTTTTTTAGCCCTTTGAAATTTTGGTGATCAATTTTGACCCTTCTATAA
TTTTGAGAGATTTGCCATGCTTTTTGCTTTCCCCGTTTAAAAA
Found at i:66261 original size:116 final size:119
Alignment explanation
Indices: 66102--66338 Score: 381
Period size: 118 Copynumber: 2.0 Consensus size: 119
66092 ATAACTTTCC
66102 TTATTTTAAATAATGAATGTTCACCAATATTAATATATATG-TTT-GAGATAAATTTGGTTAGCA
1 TTATTTTAAATAATGAATGTTCACCAATATTAATATATATGTTTTGGAGATAAATTTGGTTAGCA
* *
66165 CAATTGGATTTTTTGAATTATTTATGATAATTCGATTTAGATTGATTTA-TTTT
66 CAATTGGATTTTTTGAATTATTTATGACAATTCAATTTAGATTGATTTACTTTT
* * **
66218 TTATTTTAAATAATGAATGTTCACCAATATTAATATATATGTTTTGGGGTTAAATTTGGTTAGTT
1 TTATTTTAAATAATGAATGTTCACCAATATTAATATATATGTTTTGGAGATAAATTTGGTTAGCA
* *
66283 CTATTGGATTTTTTGAATTATTTATGACAATTCAATTTAGATTGGTTTACTTTT
66 CAATTGGATTTTTTGAATTATTTATGACAATTCAATTTAGATTGATTTACTTTT
66337 TT
1 TT
66339 TCATATGGAG
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
116 41 0.37
117 3 0.03
118 60 0.55
119 6 0.05
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (119 bp):
TTATTTTAAATAATGAATGTTCACCAATATTAATATATATGTTTTGGAGATAAATTTGGTTAGCA
CAATTGGATTTTTTGAATTATTTATGACAATTCAATTTAGATTGATTTACTTTT
Found at i:66851 original size:30 final size:30
Alignment explanation
Indices: 66782--66853 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 30
66772 TCTTTTTATT
*
66782 TTTTAA-CAATT-AATTAAATAATAAAATA
1 TTTTAATCAATTAAAATAAATAATAAAATA
66810 TTTT-AT--ATTAAAAT-AATAATAAAATAA
1 TTTTAATCAATTAAAATAAATAATAAAAT-A
66837 TTTTAATCAATTAAAAT
1 TTTTAATCAATTAAAAT
66854 CTACTACCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
26 14 0.38
27 9 0.24
28 6 0.16
30 8 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
TTTTAATCAATTAAAATAAATAATAAAATA
Found at i:71170 original size:140 final size:142
Alignment explanation
Indices: 70868--71203 Score: 378
Period size: 140 Copynumber: 2.4 Consensus size: 142
70858 CAGTAGCATT
* * * * * * *
70868 GAACCCAGAACATT-GCTAAGTTGGTTCAAAGTGGTGACGTGTAACAGGTCAAGTCCGGAGCCGG
1 GAACGCAGAAC-TTAGCTAAGTTGGTTCAAAGTGGTGACATTTAACAGGTCGAGTACAGAGCCAG
* * * * *
70932 AAAACAATACAATCAGTGGTGGTGATGCACAGATAAGAGTCATGAGTAAGATATCCTCATCTGTA
65 AAAACAATACAAGCAGTAGTGATGATGCACAGATAAGAGTCATGACTAAGATATCCTCATCTATA
*
70997 TATGGGAAGCAGC
130 TATAGGAAGCAGC
* *
71010 GAACGCGGAACTTAGCTAAGTTGGTTCAAAGAGGTGACATTTAACAGGT-GAGTACAGAGCCAGA
1 GAACGCAGAACTTAGCTAAGTTGGTTCAAAGTGGTGACATTTAACAGGTCGAGTACAGAGCCAGA
* * * *
71074 AAACAATA-AGGGCAGTAGTGATGATGCACAGGTAAGA-TCATGTCTTAGATATCCAT-ATCTAT
66 AAACAATACA-AGCAGTAGTGATGATGCACAGATAAGAGTCATGACTAAGATATCC-TCATCTAT
* *
71136 TTATAGGTAGCAGC
129 ATATAGGAAGCAGC
* * *
71150 GAAAC-CAGAACTTAGGTAAGTTAGTTCAAAGTGGTAACATTTAACAGGTCGAGT
1 G-AACGCAGAACTTAGCTAAGTTGGTTCAAAGTGGTGACATTTAACAGGTCGAGT
71204 CTACTGCCCT
Statistics
Matches: 163, Mismatches: 26, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
140 71 0.44
141 51 0.31
142 41 0.25
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.24
Consensus pattern (142 bp):
GAACGCAGAACTTAGCTAAGTTGGTTCAAAGTGGTGACATTTAACAGGTCGAGTACAGAGCCAGA
AAACAATACAAGCAGTAGTGATGATGCACAGATAAGAGTCATGACTAAGATATCCTCATCTATAT
ATAGGAAGCAGC
Found at i:76121 original size:29 final size:28
Alignment explanation
Indices: 76060--76123 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
76050 GCCCACTGTA
*
76060 CTAAAAAAAAGGCAAATTAGTCTGTATG
1 CTAAAAAAAAGGCAAACTAGTCTGTATG
* *
76088 TTAAATAAAAAGGCAAACTAGTCAT-TCTG
1 CTAAA-AAAAAGGCAAACTAGTC-TGTATG
76117 CTAAAAA
1 CTAAAAA
76124 TTTCATTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 6 0.20
29 23 0.77
30 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (28 bp):
CTAAAAAAAAGGCAAACTAGTCTGTATG
Found at i:77599 original size:2 final size:2
Alignment explanation
Indices: 77594--77625 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
77584 AAAAAAACAT
77594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77626 AAACAATCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80300 original size:13 final size:14
Alignment explanation
Indices: 80270--80307 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
80260 TGGGTGGACG
80270 AAAATATATTATATT
1 AAAATATATT-TATT
80285 AAAATATATTTA-T
1 AAAATATATTTATT
80298 AAAAT-TATTT
1 AAAATATATTT
80308 CAACAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.22
13 6 0.26
14 2 0.09
15 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAATATATTTATT
Found at i:90603 original size:81 final size:81
Alignment explanation
Indices: 90459--90624 Score: 235
Period size: 81 Copynumber: 2.0 Consensus size: 81
90449 TATATGTAAT
* * * * * ** *
90459 ATAATAAAAATAATTAGTTTCTTGGTATGCAAGATCGTCCCGGAACCGGATTCCGAACGACAAAC
1 ATAACAAAAAGAACTAGTTTCTCGGCATGCAAGATCGTCCCGGAACCAAATTCCGAACAACAAAC
90524 TTGAATCAACAAACAG
66 TTGAATCAACAAACAG
*
90540 ATAACAAAAAGAACTAGTTTCTCGGCATGCAAGATTTGTCCCGGAA-CAAATTCCGAACAACAAA
1 ATAACAAAAAGAACTAGTTTCTCGGCATGCAAGA-TCGTCCCGGAACCAAATTCCGAACAACAAA
90604 CTTGAATCAACAAACAG
65 CTTGAATCAACAAACAG
90621 ATAA
1 ATAA
90625 TGGTAGTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
81 65 0.87
82 10 0.13
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (81 bp):
ATAACAAAAAGAACTAGTTTCTCGGCATGCAAGATCGTCCCGGAACCAAATTCCGAACAACAAAC
TTGAATCAACAAACAG
Found at i:94183 original size:30 final size:30
Alignment explanation
Indices: 94147--94206 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
94137 GTTTTGGCTT
* *
94147 GGTTCTAAGATGTAATTGTTTTATTATGTC
1 GGTTCTAAGATGTAATTGTTTGATCATGTC
*
94177 GGTTCTAAGTTGTAATTGTTTGATCATGTC
1 GGTTCTAAGATGTAATTGTTTGATCATGTC
94207 AATATAGGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.48
Consensus pattern (30 bp):
GGTTCTAAGATGTAATTGTTTGATCATGTC
Found at i:102474 original size:45 final size:45
Alignment explanation
Indices: 102412--102502 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
102402 TCGAGTCAAT
*
102412 TTTCTCATATTAAAATCAGTTAAGTAAATTCAAAAAACGATTTAA
1 TTTCTCATATTAAAATCAGTTAAATAAATTCAAAAAACGATTTAA
*
102457 TTTCTCATGTTAAAATCAGTTAAATAAATTCAAAAAACGATTTAA
1 TTTCTCATATTAAAATCAGTTAAATAAATTCAAAAAACGATTTAA
102502 T
1 T
102503 CGATCGATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (45 bp):
TTTCTCATATTAAAATCAGTTAAATAAATTCAAAAAACGATTTAA
Found at i:104968 original size:28 final size:27
Alignment explanation
Indices: 104903--104974 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 27
104893 AATAACTCAT
*
104903 ATTTTATAATTTTAAAAATTAAATTAA
1 ATTTTATATTTTTAAAAATTAAATTAA
104930 ATTTTATTATTTTTAAAAGATTAAAGTT-A
1 ATTTTA-TATTTTTAAAA-ATTAAA-TTAA
104959 ATTTTATATTTATTAA
1 ATTTTATATTT-TTAA
104975 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
27 6 0.15
28 15 0.38
29 17 0.43
30 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTTTATATTTTTAAAAATTAAATTAA
Found at i:109824 original size:60 final size:62
Alignment explanation
Indices: 109731--109895 Score: 174
Period size: 62 Copynumber: 2.7 Consensus size: 62
109721 ACACTTTTAT
*
109731 TAATTTGGTACCTAAACTCTTTTTTGGGTCCAATTTGGTACCTGAACTT-G-ATAATTTTTCC
1 TAATTTGGTACCTAAAC-CTTTTTTGGATCCAATTTGGTACCTGAACTTGGCATAATTTTTCC
* * * * * ** *
109792 TAATTTGATACCAAAACCTTTTTTGGACCCAA-TAGAGTACCTTAACTTGGCATTTTTTTTTC
1 TAATTTGGTACCTAAACCTTTTTTGGATCCAATTTG-GTACCTGAACTTGGCATAATTTTTCC
* * * *
109854 TAATTTGGTACCTAAGCTTTTTTTAGATTCAATTTGGTACCT
1 TAATTTGGTACCTAAACCTTTTTTGGATCCAATTTGGTACCT
109896 AAATTTATTA
Statistics
Matches: 83, Mismatches: 17, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
59 2 0.02
60 24 0.29
61 16 0.19
62 39 0.47
63 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (62 bp):
TAATTTGGTACCTAAACCTTTTTTGGATCCAATTTGGTACCTGAACTTGGCATAATTTTTCC
Found at i:110134 original size:30 final size:31
Alignment explanation
Indices: 110098--110176 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
110088 AGACCCCAAA
*
110098 AAGTTTAAGTATCAACTTA-AAAAAACTGTC
1 AAGTTTAAGTATCAAATTAGAAAAAACTGTC
* * *
110128 AAGTTTAGGTATCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTATCAAATTAGAAAAAACTGTC
* * *
110159 AAATTTGAGTACCAAATT
1 AAGTTTAAGTATCAAATT
110177 GGACCAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 17 0.43
31 23 0.57
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.30
Consensus pattern (31 bp):
AAGTTTAAGTATCAAATTAGAAAAAACTGTC
Found at i:110211 original size:89 final size:90
Alignment explanation
Indices: 110051--110222 Score: 215
Period size: 89 Copynumber: 1.9 Consensus size: 90
110041 TATTAAGTAC
* * * *
110051 CAAATTAGGAAAAAGAGTCAAGCTTAGGGACCAAATTAGACCCCAAAAAGTTTAAGTATCAACTT
1 CAAATTAGGAAAAAGAGTCAAACTTAGGGACCAAATTAGACCCAAAAAAGTTTAAGTACCAAATT
110116 AAAAAAA-CTGTCAAGTTTAGGTAT
66 AAAAAAATCTGTCAAGTTTAGGTAT
* * * *
110140 CAAATTAGGAAAAAGTGTCAAA-TTTGAGTACCAAATTGGA-CCAAAAAAGTTTAAGTACCAAAT
1 CAAATTAGGAAAAAGAGTCAAACTTAG-GGACCAAATTAGACCCAAAAAAGTTTAAGTACCAAAT
* *
110203 TAGTAAAAATGTGTCAAGTT
65 TA-AAAAAATCTGTCAAGTT
110223 CACATACCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
88 25 0.36
89 36 0.51
90 9 0.13
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (90 bp):
CAAATTAGGAAAAAGAGTCAAACTTAGGGACCAAATTAGACCCAAAAAAGTTTAAGTACCAAATT
AAAAAAATCTGTCAAGTTTAGGTAT
Found at i:111564 original size:31 final size:29
Alignment explanation
Indices: 111504--111565 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 29
111494 CATAAGTGAT
* * * *
111504 TAAAATGTAACTTTTCAAACATAAGTGAC
1 TAAAATGTAACTTGTAAAACAAAACTGAC
111533 TAAAATGTAACTTGAGTAAAACAAAACTGAC
1 TAAAATGTAACTT--GTAAAACAAAACTGAC
111564 TA
1 TA
111566 TTTTTACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.48
31 14 0.52
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.27
Consensus pattern (29 bp):
TAAAATGTAACTTGTAAAACAAAACTGAC
Found at i:113642 original size:79 final size:79
Alignment explanation
Indices: 113549--113712 Score: 292
Period size: 79 Copynumber: 2.1 Consensus size: 79
113539 TATCAAATTA
113549 ATGTAAAATGATCAAATCAAAAAGCAAAATTTCACCATAAATTTTCGTGCTCGGGTGTCAAATCT
1 ATGTAAAATGATCAAATCAAAAAGCAAAATTTCACCATAAATTTTCGTGCTCGGGTGTCAAATCT
*
113614 GTTAGCTTTATGGG
66 ATTAGCTTTATGGG
* *
113628 ATGTAAAATTATCAAATCAAAAAGCAAAATTTCACCATAGATTTTCGTGCTCGGGTGTCAAATCT
1 ATGTAAAATGATCAAATCAAAAAGCAAAATTTCACCATAAATTTTCGTGCTCGGGTGTCAAATCT
113693 ATTAGCTTTATGGG
66 ATTAGCTTTATGGG
*
113707 ACGTAA
1 ATGTAA
113713 TGGTAGCTTG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (79 bp):
ATGTAAAATGATCAAATCAAAAAGCAAAATTTCACCATAAATTTTCGTGCTCGGGTGTCAAATCT
ATTAGCTTTATGGG
Found at i:115322 original size:31 final size:31
Alignment explanation
Indices: 115286--115363 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
115276 GGACTTCAAA
* *
115286 AAGTTTAAGTACCAACTTAAGA-AAAAGTGTC
1 AAGTTTAAGTACCAAATTAA-ATAAAAATGTC
* *
115317 AAGTTTAGGTACCAAATTAAATAAAAATGTT
1 AAGTTTAAGTACCAAATTAAATAAAAATGTC
115348 AAGTTTAAGTACCAAA
1 AAGTTTAAGTACCAAA
115364 ATGGATAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAATAAAAATGTC
Found at i:115372 original size:31 final size:32
Alignment explanation
Indices: 115286--115374 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
115276 GGACTTCAAA
* * *
115286 AAGTTTAAGTACC-AACTTAAGAAAAAGTGTC
1 AAGTTTAAGTACCAAAATAAATAAAAAGTGTC
* * *
115317 AAGTTTAGGTACCAAATTAAATAAAAA-TGTT
1 AAGTTTAAGTACCAAAATAAATAAAAAGTGTC
**
115348 AAGTTTAAGTACCAAAATGGATAAAAA
1 AAGTTTAAGTACCAAAATAAATAAAAA
115375 AATTTAGGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
31 38 0.79
32 10 0.21
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (32 bp):
AAGTTTAAGTACCAAAATAAATAAAAAGTGTC
Found at i:119672 original size:102 final size:100
Alignment explanation
Indices: 119512--120045 Score: 304
Period size: 102 Copynumber: 5.4 Consensus size: 100
119502 TTTCCTTCCT
* * * * *
119512 TTTTTGCTTTACGTA-TAGTCTTA-TTTAAGGTTATCATAATT-ATGGATTTATCAGATATTAGA
1 TTTTTGCTTTACATATTAGCCTTAGTTAAAGG-TATCGTAATTGAT--ATTTAACAGATATTAGA
*
119574 ATATCAACATTGATAGTAGCCTCTCTCTTCTTTTCTTTC
63 ATATCAATATTGATAGTAGCCTCTCT-TTCTTTTCTTTC
** ** *
119613 TTTTTTGCTTTACATATTA-TTTTAGTTAAAGGTATCGCGATTGCATATTTAACAAATATTAGAA
1 -TTTTTGCTTTACATATTAGCCTTAGTTAAAGGTATCGTAATTG-ATATTTAACAGATATTAGAA
** *
119677 TATTGATATTGAT-GATACCCT-TCTTCTTCTTTTCTCTTC
64 TATCAATATTGATAG-TAGCCTCTC-T-TTCTTTTCT-TTC
* * * * * * * *
119716 CTTTTGCTTTACATA-TAACCTTAGTAAAATGTATTGTAATTGTAGATTTAACA-AAATTAGGAT
1 TTTTTGCTTTACATATTAGCCTTAGTTAAAGGTATCGTAATTG-ATATTTAACAGATATTAGAAT
* * * * * *
119779 ATTAATATTGATGGTATCC-CTTTATTCATTTCTCTCC
65 ATCAATATTGATAGTAGCCTCTCT-TTCTTTTCT-TTC
* * * * *
119816 TTTTTTGATTTACATA-TAGCCTTAGTT-AAGAATATTGTGATTG-TGAATTTAATAGATATTAG
1 -TTTTTGCTTTACATATTAGCCTTAGTTAAAG-GTATCGTAATTGAT--ATTTAACAGATATTAG
* **
119878 AATATCGATATTGATAG-A-CC-CT-TTT-TCCTC-TTC
62 AATATCAATATTGATAGTAGCCTCTCTTTCTTTTCTTTC
** * *
119911 TTTTTGCTTTACATA-TAGTTTTAGTTAAATGTATCGTAATT-ATGAATTTAACAGATATTAAAA
1 TTTTTGCTTTACATATTAGCCTTAGTTAAAGGTATCGTAATTGAT--ATTTAACAGATATT-AGA
* * *
119974 ATATCAATATTGATGGCAGCTTC-CTTTCTTTCTCTTTC
63 ATATCAATATTGATAGTAGCCTCTCTTTCTTT-TCTTTC
* * *
120012 -TTTTGCTTTACATA-TAGCGTTAGTCAAGGGTATC
1 TTTTTGCTTTACATATTAGCCTTAGTTAAAGGTATC
120046 CTTAACTAAG
Statistics
Matches: 340, Mismatches: 67, Indels: 52
0.74 0.15 0.11
Matches are distributed among these distances:
94 47 0.14
95 20 0.06
96 1 0.00
97 3 0.01
98 6 0.02
99 2 0.01
100 49 0.14
101 72 0.21
102 127 0.37
103 11 0.03
104 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (100 bp):
TTTTTGCTTTACATATTAGCCTTAGTTAAAGGTATCGTAATTGATATTTAACAGATATTAGAATA
TCAATATTGATAGTAGCCTCTCTTTCTTTTCTTTC
Found at i:119833 original size:101 final size:102
Alignment explanation
Indices: 119659--120027 Score: 263
Period size: 101 Copynumber: 3.7 Consensus size: 102
119649 GCGATTGCAT
* * * *
119659 ATTTAACAAATATTAGAATATTGATATTGATGATACCCTTCTTCTTCTTTTCTCTTCCTTTTGCT
1 ATTTAACAAATATTAGAATATTAATATTGATGATACCCTTCTTATTCATTTCTCTTCCTTTTGAT
119724 TTACATATAACCTTAGTAAAATGTATTGTAATTGTAG
66 TTACATATAACCTTAGTAAAATGTATTGTAATTGTAG
* *
119761 ATTTAACAAA-ATTAGGATATTAATATTGATGGTATCCC-T-TTATTCATTTCTC-TCCTTTTTT
1 ATTTAACAAATATTAGAATATTAATATTGATGATA-CCCTTCTTATTCATTTCTCTTCC--TTTT
* *
119822 GATTTACATATAGCCTTAGTTAAGAA--TATTGTGATTGT-G
63 GATTTACATATAACCTTAG-TAA-AATGTATTGTAATTGTAG
* * ** * * *
119861 AATTTAATAGATATTAGAATATCGATATTGAT-AGACCC-T-TT-TTC----CTCTTCTTTTTGC
1 -ATTTAACAAATATTAGAATATTAATATTGATGATACCCTTCTTATTCATTTCTCTTCCTTTTGA
*** * * *
119918 TTTACATATAGTTTTAGTTAAATGTATCGTAATTAT-G
65 TTTACATATAACCTTAGTAAAATGTATTGTAATTGTAG
* * * ** * * *
119955 AATTTAACAGATATTAAAAATATCAATATTGATGGCA-GCTTCCT-TTC-TTTCTCTTTCTTTTG
1 -ATTTAACAAATATT-AGAATATTAATATTGATGATACCCTTCTTATTCATTTCTCTTCCTTTTG
*
120017 CTTTACATATA
64 ATTTACATATA
120028 GCGTTAGTCA
Statistics
Matches: 218, Mismatches: 32, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
92 2 0.01
93 2 0.01
94 44 0.20
95 19 0.09
96 4 0.02
97 4 0.02
99 6 0.03
100 39 0.18
101 63 0.29
102 33 0.15
103 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (102 bp):
ATTTAACAAATATTAGAATATTAATATTGATGATACCCTTCTTATTCATTTCTCTTCCTTTTGAT
TTACATATAACCTTAGTAAAATGTATTGTAATTGTAG
Found at i:119935 original size:94 final size:98
Alignment explanation
Indices: 119816--120035 Score: 245
Period size: 94 Copynumber: 2.3 Consensus size: 98
119806 ATTTCTCTCC
* * * * * *
119816 TTTTTTGATTTACATATAGCCTTAGTTAAGA-ATATTGTGATTGTGAATTTAATAGATATT-AGA
1 TTTTTTGCTTTACATATAGCCTTAGTTAA-ATATATCGTAATTATGAATTTAACAGATATTAAAA
*
119879 ATATCGATATTGATAG-A-C-CCTTT-TTCCTCT
65 ATATCAATATTGATAGCAGCTCCTTTCTTCCTCT
** *
119909 TCTTTTTGCTTTACATATAGTTTTAGTTAAATGTATCGTAATTATGAATTTAACAGATATTAAAA
1 T-TTTTTGCTTTACATATAGCCTTAGTTAAATATATCGTAATTATGAATTTAACAGATATTAAAA
* *
119974 ATATCAATATTGATGGCAGCTTCCTTTCTTTCTCT
65 ATATCAATATTGATAGCAGC-TCCTTTCTTCCTCT
*
120009 TTCTTTTGCTTTACATATAGCGTTAGT
1 TT-TTTTGCTTTACATATAGCCTTAGT
120036 CAAGGGTATC
Statistics
Matches: 104, Mismatches: 14, Indels: 11
0.81 0.11 0.09
Matches are distributed among these distances:
93 2 0.02
94 49 0.47
95 16 0.15
96 1 0.01
97 1 0.01
99 6 0.06
100 29 0.28
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (98 bp):
TTTTTTGCTTTACATATAGCCTTAGTTAAATATATCGTAATTATGAATTTAACAGATATTAAAAA
TATCAATATTGATAGCAGCTCCTTTCTTCCTCT
Found at i:120375 original size:24 final size:25
Alignment explanation
Indices: 120316--120376 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 25
120306 TAAATTTGAA
* *
120316 TTTAGTTTTTTATTTATTTTTATTT
1 TTTAGATTTTAATTTATTTTTATTT
* * * *
120341 CTAATAATTTAATTT-TTTTTATTT
1 TTTAGATTTTAATTTATTTTTATTT
120365 TTTAGATTTTAA
1 TTTAGATTTTAA
120377 AAAAGTTTAA
Statistics
Matches: 26, Mismatches: 10, Indels: 1
0.70 0.27 0.03
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (25 bp):
TTTAGATTTTAATTTATTTTTATTT
Found at i:120664 original size:63 final size:63
Alignment explanation
Indices: 120586--120709 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
120576 TAACCAAAGG
* * * *
120586 AACTGACTCTATAATTGATTTAACTGCTAAAACTTTTTAAATCGAAATTGATTTAATCGAAGA
1 AACTGACTCTATAATTGATTTAACTACTAAAACTTTTTAAACCAAAATTGACTTAATCGAAGA
* *
120649 AACTGACTCTATAATTGATTTAATTACTACAACTTTTTAAACCAAAATTGACTTAATCGAA
1 AACTGACTCTATAATTGATTTAACTACTAAAACTTTTTAAACCAAAATTGACTTAATCGAA
120710 TTAGTGATTG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (63 bp):
AACTGACTCTATAATTGATTTAACTACTAAAACTTTTTAAACCAAAATTGACTTAATCGAAGA
Found at i:126775 original size:18 final size:18
Alignment explanation
Indices: 126738--126779 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
126728 TCTCGACTCC
***
126738 TTAAAAAAAAATCCTTTT
1 TTAAAAAAAAATCAAATT
126756 TTAAAAAAAAATCAAATT
1 TTAAAAAAAAATCAAATT
126774 TTAAAA
1 TTAAAA
126780 TAATATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAAAAAATCAAATT
Found at i:133108 original size:26 final size:25
Alignment explanation
Indices: 133041--133110 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
133031 ATTGCGCTTC
* *
133041 TAAATTATAATTTTTTATTTTGATAT
1 TAAATTATTA-TTTTCATTTTGATAT
* * *
133067 TTAATCTTTTAATTTCATTTTGATAT
1 TAAAT-TATTATTTTCATTTTGATAT
133093 ATAAATTATTATTTTCAT
1 -TAAATTATTATTTTCAT
133111 CTCAATTTAC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
26 27 0.79
27 7 0.21
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (25 bp):
TAAATTATTATTTTCATTTTGATAT
Found at i:151423 original size:24 final size:24
Alignment explanation
Indices: 151381--151433 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
151371 ACTTAAATCT
151381 TTAAA-TCTGAAAAATAAA-TACA
1 TTAAATTCTGAAAAATAAATTACA
*
151403 TTAAATTCTTAAAAATAAAATTACA
1 TTAAATTCTGAAAAAT-AAATTACA
151428 -TAAATT
1 TTAAATT
151434 AATTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 5 0.19
23 9 0.33
24 9 0.33
25 4 0.15
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (24 bp):
TTAAATTCTGAAAAATAAATTACA
Found at i:158496 original size:24 final size:24
Alignment explanation
Indices: 158415--158480 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
158405 GTTAATTCGT
158415 GAGCATAAACATATAGTGGCTAGC
1 GAGCATAAACATATAGTGGCTAGC
*
158439 GAGCATAAACGTATAGTGGCTAGC
1 GAGCATAAACATATAGTGGCTAGC
158463 GAGCATAAACATATAGTG
1 GAGCATAAACATATAGTG
158481 ATTGACGAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (24 bp):
GAGCATAAACATATAGTGGCTAGC
Found at i:159196 original size:24 final size:23
Alignment explanation
Indices: 159156--159200 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
159146 TTATACATAT
*
159156 AAAATATAAAAATATTTTATGTAA
1 AAAATATAAAAA-AATTTATGTAA
159180 AAAATA-AATAAAAATTTATGT
1 AAAATATAA-AAAAATTTATGT
159201 GAGTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
AAAATATAAAAAAATTTATGTAA
Found at i:164141 original size:15 final size:15
Alignment explanation
Indices: 164121--164171 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
164111 ACAAAACGAT
164121 AACATAAGTGATTAA
1 AACATAAGTGATTAA
* *
164136 AACATAA--CATTTCA
1 AACATAAGTGA-TTAA
164150 AACATAAGTGATTAA
1 AACATAAGTGATTAA
*
164165 AATATAA
1 AACATAA
164172 CATAAGGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 1 0.04
14 10 0.36
15 16 0.57
16 1 0.04
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (15 bp):
AACATAAGTGATTAA
Found at i:170736 original size:18 final size:18
Alignment explanation
Indices: 170715--170785 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 18
170705 TTAAAATTTT
170715 ATTTCAAAATAAATTTAA
1 ATTTCAAAATAAATTTAA
*
170733 ATTTTAAAATAAATTTAA
1 ATTTCAAAATAAATTTAA
* * **
170751 A-CTCCAAATAAGCTTAA
1 ATTTCAAAATAAATTTAA
*
170768 ATTT-ACAATAAATTTAA
1 ATTTCAAAATAAATTTAA
170785 A
1 A
170786 CTTAAATTGA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
17 22 0.54
18 19 0.46
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (18 bp):
ATTTCAAAATAAATTTAA
Found at i:172125 original size:16 final size:16
Alignment explanation
Indices: 172106--172136 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
172096 GAAGTGTGGT
172106 TTCATTGAATTAAATA
1 TTCATTGAATTAAATA
*
172122 TTCATTTAATTAAAT
1 TTCATTGAATTAAAT
172137 TTAAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TTCATTGAATTAAATA
Found at i:188254 original size:8 final size:8
Alignment explanation
Indices: 188241--188265 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
188231 CCACTCTCTT
188241 TTTAAATA
1 TTTAAATA
188249 TTTAAATA
1 TTTAAATA
188257 TTTAAATA
1 TTTAAATA
188265 T
1 T
188266 CATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAATA
Found at i:193241 original size:11 final size:10
Alignment explanation
Indices: 193208--193242 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
193198 ATACGATATT
193208 CAAATAATAA
1 CAAATAATAA
*
193218 CAAATAGTAA
1 CAAATAATAA
193228 CAATATAATAA
1 CAA-ATAATAA
193239 CAAA
1 CAAA
193243 ATGACAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (10 bp):
CAAATAATAA
Found at i:193628 original size:19 final size:19
Alignment explanation
Indices: 193591--193627 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
193581 ATACATCAAG
193591 TAAATGAATAACATTAAAA
1 TAAATGAATAACATTAAAA
193610 TAAATGAAT-ACATTAAAA
1 TAAATGAATAACATTAAAA
193628 AAAGTAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
TAAATGAATAACATTAAAA
Found at i:193703 original size:11 final size:10
Alignment explanation
Indices: 193670--193704 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
193660 ATACGATATT
193670 CAAATAATAA
1 CAAATAATAA
*
193680 CAAATAGTAA
1 CAAATAATAA
193690 CAATATAATAA
1 CAA-ATAATAA
193701 CAAA
1 CAAA
193705 ATGACAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (10 bp):
CAAATAATAA
Found at i:196278 original size:2 final size:2
Alignment explanation
Indices: 196271--196303 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
196261 TTCTCAAATT
196271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
196304 TTAGAGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:211003 original size:68 final size:68
Alignment explanation
Indices: 210894--211029 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
210884 GCTGAAGGCC
*
210894 ACAAATTCAAGTCAAAGACACACTACTCATATAACCATGTGAGCTTTCATTTTAATCAAAAGTCT
1 ACAAATTCAAGTAAAAGACACACTACTCATATAACCATGTGAGCTTTCATTTTAATCAAAAGTCT
210959 AAT
66 AAT
210962 ACAAATTCAAGTAAAAGACACACTACTCATATAACCATGTGAGCTTTCATTTTAATCAAAAGTCT
1 ACAAATTCAAGTAAAAGACACACTACTCATATAACCATGTGAGCTTTCATTTTAATCAAAAGTCT
211027 AAT
66 AAT
211030 CATACTTCAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (68 bp):
ACAAATTCAAGTAAAAGACACACTACTCATATAACCATGTGAGCTTTCATTTTAATCAAAAGTCT
AAT
Found at i:218034 original size:7 final size:7
Alignment explanation
Indices: 218022--218072 Score: 102
Period size: 7 Copynumber: 7.3 Consensus size: 7
218012 TATTATCTAA
218022 ATCATAT
1 ATCATAT
218029 ATCATAT
1 ATCATAT
218036 ATCATAT
1 ATCATAT
218043 ATCATAT
1 ATCATAT
218050 ATCATAT
1 ATCATAT
218057 ATCATAT
1 ATCATAT
218064 ATCATAT
1 ATCATAT
218071 AT
1 AT
218073 AAAGTAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (7 bp):
ATCATAT
Found at i:224839 original size:15 final size:16
Alignment explanation
Indices: 224821--224854 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
224811 AATTTTATCA
*
224821 TTATTAATT-TAAAAT
1 TTATAAATTATAAAAT
224836 TTATAAATTATAAAAT
1 TTATAAATTATAAAAT
224852 TTA
1 TTA
224855 CTATTTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATAAATTATAAAAT
Found at i:232051 original size:3 final size:3
Alignment explanation
Indices: 232045--232076 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
232035 TGATGATGTT
*
232045 GAA GAA GAG GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
232077 CCTTTCCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:232956 original size:2 final size:2
Alignment explanation
Indices: 232949--232980 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
232939 TCCTTTCACC
*
232949 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
232981 CTTCCCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:244031 original size:20 final size:18
Alignment explanation
Indices: 243997--244048 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
243987 TCTTATATTT
* *
243997 TTTTTTATAAATTTTATA
1 TTTTTAATAAATTTTACA
244015 TTTTGTAATAAACTTTTACA
1 TTTT-TAATAAA-TTTTACA
244035 TTTTTAATAAATTT
1 TTTTTAATAAATTT
244049 CTAATTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 7 0.23
19 13 0.43
20 10 0.33
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTAATAAATTTTACA
Found at i:246283 original size:29 final size:30
Alignment explanation
Indices: 246251--246331 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
246241 TATCTAATTT
* *
246251 TTTTTTTAATTTAGTACTTAAATTTGACA-
1 TTTTTTTAATTTGGTACTTAAACTTGACAC
* *
246280 TTTTTTTGATTTGGTA-TCTAAACTTGATAC
1 TTTTTTTAATTTGGTACT-TAAACTTGACAC
*
246310 TTTTTCTTAAGTTGGTACTTAA
1 TTTTT-TTAATTTGGTACTTAA
246332 TCTTATCGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 23 0.55
30 5 0.12
31 12 0.29
32 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (30 bp):
TTTTTTTAATTTGGTACTTAAACTTGACAC
Found at i:250929 original size:20 final size:20
Alignment explanation
Indices: 250877--250930 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
250867 TTTATTAAAC
**
250877 ATAAATAAAATTTTCAAAATTT
1 ATAAAT-AAA-TTTCAAAATAA
250899 A-AAATATAATTTCAAAATAA
1 ATAAATA-AATTTCAAAATAA
250919 ATAAATAAATTT
1 ATAAATAAATTT
250931 TATTTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 16 0.57
21 11 0.39
22 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAATAAATTTCAAAATAA
Found at i:257153 original size:2 final size:2
Alignment explanation
Indices: 257146--257171 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
257136 ATTTTCCCTT
257146 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
257172 CATATTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:267789 original size:4 final size:4
Alignment explanation
Indices: 267780--267820 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
267770 CATCAATAGC
267780 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
267821 GTGAACTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:268253 original size:31 final size:33
Alignment explanation
Indices: 268190--268254 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 33
268180 AGATTAATTT
*
268190 ATATTTTATGTATTATTATATTAAATTATTTAA
1 ATATTTTATGTATTATTATATTAAAATATTTAA
268223 ATATTTT-T-TATTATTATATTTAAAAT-TTTAA
1 ATATTTTATGTATTATTATA-TTAAAATATTTAA
268254 A
1 A
268255 AAATTTCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 16 0.53
32 7 0.23
33 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
ATATTTTATGTATTATTATATTAAAATATTTAA
Found at i:268678 original size:13 final size:13
Alignment explanation
Indices: 268662--268698 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
268652 CCTTCTTCCC
*
268662 TTCTTTCATTTTT
1 TTCTTCCATTTTT
268675 TTCTTCCATTTTT
1 TTCTTCCATTTTT
268688 TTC-TCCATTTT
1 TTCTTCCATTTT
268699 CTTCACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (13 bp):
TTCTTCCATTTTT
Found at i:268770 original size:33 final size:33
Alignment explanation
Indices: 268733--268817 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 33
268723 ATGATTATAT
*
268733 TTAAATATTTAAAATATAATTTATA-TAATCTAA
1 TTAAATATTTAAAATATAATTAATATTAAT-TAA
* *
268766 TTAAAT-TTTATAA-ATAATTAATATTAATTAC
1 TTAAATATTTAAAATATAATTAATATTAATTAA
268797 TTAGAAATATTTAAAAT-TAAT
1 TT--AAATATTTAAAATATAAT
268818 ATTTCATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
31 13 0.30
32 10 0.23
33 10 0.23
34 10 0.23
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (33 bp):
TTAAATATTTAAAATATAATTAATATTAATTAA
Done.