Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015227.1 Kokia drynarioides strain JFW-HI SEQ_130272, 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: 249131
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 75 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:879 original size:29 final size:29
Alignment explanation
Indices: 837--1302 Score: 409
Period size: 29 Copynumber: 16.0 Consensus size: 29
827 CCTTAGAGGT
837 CCCT-AAACTATCCAAAAATTCCATTTTTA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
* *
866 CCCTCGAACATCCAAAAA-TCTCATTTTTGA
1 CCCTCAAACTTCCAAAAATTC-CATTTTT-A
*
896 CCCTAAAACTTCCAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* * * *
925 CCCTTAAACTTCTAAAAATCCCATTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
*
954 CCC-CAAAACTTCCAAAAATTCCATCTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* * *
983 CCC-CTAAACTTCTAAAAATACTATTTTTGA
1 CCCTC-AAACTTCCAAAAATTCCATTTTT-A
* *
1013 -CCTCAAAACTTCCAAAAATCCCA-TTTGA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
*
1041 CCC-CAAAACTTCCAAAAATTGCATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* *
1070 GCCCT-GAACTTCAAAAAATTCCATTTTTAA
1 -CCCTCAAACTTCCAAAAATTCCATTTTT-A
* *
1100 CACC-GAAACCTCC-AAAATTACCA-TTTTA
1 C-CCTCAAACTTCCAAAAATT-CCATTTTTA
* * *
1128 CCCCCGAACTTCCAAAAATTCCATTTCTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* *
1157 CCCCCAAACTTCTAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* *
1186 ACCTCAAAACTTCCAAAGATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* * * *
1216 CCCCCGAACTTCCAAAAATGCCATTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* *
1245 TCCC-GAAATTTCCAAAAATTCCATTTTTA
1 -CCCTCAAACTTCCAAAAATTCCATTTTTA
* *
1274 CCCTCGAA-TGTCTAAAAATTCCATTTTTA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
1303 AACCCCAAAT
Statistics
Matches: 357, Mismatches: 58, Indels: 44
0.78 0.13 0.10
Matches are distributed among these distances:
27 2 0.01
28 36 0.10
29 232 0.65
30 85 0.24
31 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTA
Found at i:13525 original size:207 final size:204
Alignment explanation
Indices: 13085--13855 Score: 983
Period size: 204 Copynumber: 3.8 Consensus size: 204
13075 TGCGATATCT
* *
13085 ACAAACGACGCAGTCATATTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCAA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGC-A
* * * * * * *
13150 AGTGAGCAAAATCTTTGAACCTCAGCTTTCTGATGAGACACCGAGAAGCAGGTTGAAGCAAT-AA
65 A-TGAAC-AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * * * *
13214 ACGATTAGCTTCCTAATGAGATACTAAGAAGTGAATCAAATTCGTCTTCCTGATGAGATACAGAG
128 ACGAATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
*
13279 AAGCGGATAGAA
193 AAGCGGATTGAA
* * * * * *
13291 ACAAGCGATGCAGTCATCTTTCTGATGAGATACTTAGAAGAAGACCAAATCAAACTCACGCTCAA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGC-A
* * * * *
13356 AGCGAGCAAAATCTTCGAACCCCAACTTCCTGATGAGATACTGATAAGCAGGTCGAAGTAATAAA
65 A-TGAAC-AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * * *
13421 ACGAATAGCTTCTTGATGAGATACTGAGGAGTGAACCAAATTCATCTTCCTAATAAGATACAGAG
128 ACGAATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
13486 AAGCGGATTGAA
193 AAGCGGATTGAA
* * * *
13498 ACAAACGACGCAGTCATCTTCCTGATGAAATACTAAGAAGATGACCAAATCAAACCCACGCGCGA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCAA
** *
13563 TGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAATAACAAAACG
66 TGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACG
* * *
13628 GATAGCTTCCTGATGAGATATTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAA
131 AATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
13693 CGGATTGAA
196 CGGATTGAA
* * * * *
13702 ACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGGAGAAGACCAAATC-AACTCACGCGCGA
1 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCAA
* * *
13766 TGAACAAATCTTCAAACCCTAGCTTCC-GAATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAC
66 TGAACAAATCTTCGAACCCCAGCTTCCTG-ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAC
* * *
13830 -AGTCATCTTCCGGATGAGATACTGAG
130 GAAT-AGCTTCCTGATGAGATACTGAG
13856 AAAAAGGCCA
Statistics
Matches: 496, Mismatches: 66, Indels: 9
0.87 0.12 0.02
Matches are distributed among these distances:
202 2 0.00
203 87 0.18
204 168 0.34
205 3 0.01
206 112 0.23
207 124 0.25
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (204 bp):
ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCGCAA
TGAACAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACG
AATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
CGGATTGAA
Found at i:14212 original size:17 final size:17
Alignment explanation
Indices: 14192--14265 Score: 112
Period size: 17 Copynumber: 4.4 Consensus size: 17
14182 TTGGAAATTG
*
14192 AATTTATTTTAAAATTA
1 AATTTATTTTAAATTTA
*
14209 AATTTATCTTAAATTTA
1 AATTTATTTTAAATTTA
*
14226 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
*
14243 AATTTATTATAAATTTA
1 AATTTATTTTAAATTTA
14260 AATTTA
1 AATTTA
14266 AAATGTCCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:14226 original size:6 final size:6
Alignment explanation
Indices: 14199--14267 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
14189 TTGAATTTAT
*
14199 TTTAAA ATTAAA TTT--A TCTTAAA TTTAAA TTT--A TTTGAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
14245 TTT--A TTATAAA TTTAAA TTTAAA
1 TTTAAA TT-TAAA TTTAAA TTTAAA
14268 ATGTCCAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
4 9 0.17
5 3 0.06
6 31 0.60
7 9 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:14849 original size:3 final size:3
Alignment explanation
Indices: 14833--14884 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
14823 AAACGTTTAT
* ** **
14833 TAA TAA TCAT TAA TAA TAA TAA TTG TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14879 TAA TAA
1 TAA TAA
14885 CATTAATGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:14955 original size:3 final size:3
Alignment explanation
Indices: 14947--14997 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
14937 AATTTTTTAA
* * *
14947 AAT AAT AAT AAT AAT AAT AAT GAAT -AT GAT AAT ATT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
*
14992 AGT AAT
1 AAT AAT
14998 GAATTTATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:15010 original size:30 final size:30
Alignment explanation
Indices: 14947--15023 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
14937 AATTTTTTAA
14947 AATAATAATAATAATAATAATGAATATGAT
1 AATAATAATAATAATAATAATGAATATGAT
* * * *
14977 AATATTAATTATAATAGTAATGAAT-TTATT
1 AATAATAATAATAATAATAATGAATATGA-T
*
15007 AATAGTAATAAATAATA
1 AATAATAAT-AATAATA
15024 TCATTAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 2 0.05
30 31 0.79
31 6 0.15
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (30 bp):
AATAATAATAATAATAATAATGAATATGAT
Found at i:15494 original size:21 final size:21
Alignment explanation
Indices: 15470--15510 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
15460 CCGACCGGTC
15470 GGAGAATTTTCTTGGTTTTTT
1 GGAGAATTTTCTTGGTTTTTT
*
15491 GGAGAGTTTTCTTGGTTTTT
1 GGAGAATTTTCTTGGTTTTT
15511 ATTTTTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.05, G:0.27, T:0.56
Consensus pattern (21 bp):
GGAGAATTTTCTTGGTTTTTT
Found at i:16037 original size:29 final size:29
Alignment explanation
Indices: 15994--16460 Score: 408
Period size: 30 Copynumber: 15.8 Consensus size: 29
15984 AGAGGTCCCT
*
15994 AAACTATCCAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCA
* *** *
16024 AAACTTCCAAAAA-TCTCATTTTAGAAATCG
1 AAACTTCCAAAAATTC-CATTTT-TACCCCA
* * *
16054 AAACTTCCAAAAAAATCAATTTTTACCCCT
1 AAACTTCC-AAAAATTCCATTTTTACCCCA
* *
16084 AAACTTCAAAAAATCCCATTTTTTACCCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCA
* *
16114 AAACATCCAAAAATTCCATTTTTACCATC-
1 AAACTTCCAAAAATTCCATTTTTACC-CCA
* *
16143 AAACTTCCAAAAATGCTATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
16173 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* * *
16203 AAACTT-AAAAAATTCCATTTTTAGCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
* *
16231 AAACTTCAAAAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
*
16261 AAACCTCCAAAAATTACCA-TTTTACACCC-
1 AAACTTCCAAAAATT-CCATTTTTAC-CCCA
16290 AAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCA
* * * *
16320 AAACTTTCAAAAATTCCATTTCTACTCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCA
** *
16349 AAACTTTTAAAAA-TCTCATTTTTAACCCTA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCA
* * *
16379 GAACTTCCAAAGATTCCGTTTTTACACCC-
1 AAACTTCCAAAAATTCCATTTTTAC-CCCA
* * *
16408 GAACTTCCAAAAATGCCATTTTTTATCCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCA
* *
16438 AAATTTCCAAAATTTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
16461 GCCCTCGAAT
Statistics
Matches: 358, Mismatches: 58, Indels: 43
0.78 0.13 0.09
Matches are distributed among these distances:
28 17 0.05
29 150 0.42
30 174 0.49
31 15 0.04
32 2 0.01
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:16138 original size:59 final size:60
Alignment explanation
Indices: 15994--16460 Score: 332
Period size: 59 Copynumber: 7.9 Consensus size: 60
15984 AGAGGTCCCT
* * * ** *** *
15994 AAACTATCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATCTCATTTTAGAAATCG
1 AAACT-TCCAAAAATTCCATTTTTAACCCCAAAACTTCAAAAAATCCCATTTTTTACCCCA
* * *
16054 AAACTTCCAAAAAAATCAATTTTT-ACCCCTAAACTTCAAAAAATCCCATTTTTTACCCCA
1 AAACTTCC-AAAAATTCCATTTTTAACCCCAAAACTTCAAAAAATCCCATTTTTTACCCCA
* * * * * *
16114 AAACATCCAAAAATTCCATTTTT-ACCATC-AAACTTCCAAAAATGCTATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTAACC-CCAAAACTTCAAAAAATCCCATTTTTTACCCCA
* * * * *
16173 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTT-AAAAAATTCCA-TTTTTAGCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCAAAAAATCCCATTTTTTACCCCA
* * * * *
16231 AAACTTCAAAAAATTCCATTTTTAACCCCGAAACCTCCAAAAATTACCA--TTTTACACCC-
1 AAACTTCCAAAAATTCCATTTTTAACCCC-AAAACTTCAAAAAATCCCATTTTTTAC-CCCA
* * * *
16290 AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTTC-AAAAATTCCA-TTTCTACTCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCAAAAC-TTCAAAAAATCCCATTTTTTACCCCA
** * * * * * *
16349 AAACTTTTAAAAA-TCTCATTTTTAACCCTAGAACTTCCAAAGATTCC-GTTTTTACACCC-
1 AAACTTCCAAAAATTC-CATTTTTAACCCCAAAACTTCAAAAAATCCCATTTTTTAC-CCCA
* * * * * * * *
16408 GAACTTCCAAAAATGCCATTTTTTATCCCAAAATTTCCAAAATTTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCAAAAAATCCCATTTTT
16461 GCCCTCGAAT
Statistics
Matches: 329, Mismatches: 62, Indels: 32
0.78 0.15 0.08
Matches are distributed among these distances:
58 53 0.16
59 195 0.59
60 81 0.25
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (60 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCAAAAAATCCCATTTTTTACCCCA
Found at i:16478 original size:118 final size:117
Alignment explanation
Indices: 16122--16519 Score: 368
Period size: 118 Copynumber: 3.4 Consensus size: 117
16112 CAAAACATCC
* * * * *
16122 AAAAATTCCATTTTT-ACCAT-CAAACTTCCAAAAA-TGCTATTTTTGAC-CCCAAAACTTCCAA
1 AAAAATTCCATTTTTAACCCTAGAAACCTCCAAAAATTACCA-TTTT-ACACCC-AAACTTCCAA
* * *
16183 AAATCCCATTTTTGACCCCAAAACTTAAAAAATTCCATTTTTAGCCCTAAACTTCA-
63 AAATCCCATTTTTAACCCCAAAATTTCAAAAATTCCATTTTT-GCCCTAAACTT-AT
*
16239 AAAAATTCCATTTTTAACCC-CGAAACCTCCAAAAATTACCATTTTACACCCAAACTTCCAAAAA
1 AAAAATTCCATTTTTAACCCTAGAAACCTCCAAAAATTACCATTTTACACCCAAACTTCCAAAAA
* * * *
16303 TTCCATTTTTAACCCCAAAACTTTCAAAAATTCCATTTCTACTCCTAAACTTTT
66 TCCCATTTTTAACCCCAAAA-TTTCAAAAATTCCATTTTTGC-CCTAAACTTAT
* * * *
16357 AAAAA-TCTCATTTTTAACCCTAG-AACTTCCAAAGATT-CCGTTTTTACACCCGAACTTCCAAA
1 AAAAATTC-CATTTTTAACCCTAGAAACCTCCAAAAATTACC-ATTTTACACCCAAACTTCCAAA
* * * * *
16419 AATGCCATTTTTTATCCCAAAATTTCCAAAATTTCCATTTTTGCCCTCGAA-TGTAT
64 AATCCCATTTTTAACCCCAAAATTT-CAAAAATTCCATTTTTGCCCT-AAACT-TAT
* * ** *
16475 AAAACTTCCATTTTAAACCCTA-AAATTTCCTAAAATTACCATTTT
1 AAAAATTCCATTTTTAACCCTAGAAACCTCCAAAAATTACCATTTT
16520 GCCCCTCGGG
Statistics
Matches: 234, Mismatches: 31, Indels: 31
0.79 0.10 0.10
Matches are distributed among these distances:
117 60 0.26
118 166 0.71
119 8 0.03
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (117 bp):
AAAAATTCCATTTTTAACCCTAGAAACCTCCAAAAATTACCATTTTACACCCAAACTTCCAAAAA
TCCCATTTTTAACCCCAAAATTTCAAAAATTCCATTTTTGCCCTAAACTTAT
Found at i:23128 original size:5 final size:5
Alignment explanation
Indices: 23118--23157 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
23108 GCCCTCCTGG
23118 TGTGC TGTGC TGTGC TGTGC TGTGC TGTGC TGTGC TGTGC
1 TGTGC TGTGC TGTGC TGTGC TGTGC TGTGC TGTGC TGTGC
23158 CACCCCGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
TGTGC
Found at i:25666 original size:20 final size:20
Alignment explanation
Indices: 25622--25659 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25612 ATTTATTTAT
* *
25622 TAAAATTATAATTTTATAAA
1 TAAAATAATAATCTTATAAA
25642 TAAAATAATAATCTTATA
1 TAAAATAATAATCTTATA
25660 TGTAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATAATAATCTTATAAA
Found at i:26962 original size:24 final size:23
Alignment explanation
Indices: 26894--26963 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
26884 TTCATTTAAC
*
26894 TTAATCGAACATGTTCACGAATA
1 TTAATCGAACATGTTCACGAACA
* * *
26917 TTAAACGAACATGTTTATGAACA
1 TTAATCGAACATGTTCACGAACA
*
26940 TATAATTGAACATGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
26964 ATGTTAATGA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:29094 original size:15 final size:15
Alignment explanation
Indices: 29070--29101 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29060 GACAAATGAC
*
29070 CTGTAGTCATGTTTA
1 CTGTAATCATGTTTA
29085 CTGTAATCATGTTTA
1 CTGTAATCATGTTTA
29100 CT
1 CT
29102 TGTCATCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (15 bp):
CTGTAATCATGTTTA
Found at i:30623 original size:16 final size:16
Alignment explanation
Indices: 30586--30623 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
30576 ATATATATTT
*
30586 TATAAATTTATAAAAA
1 TATAAATATATAAAAA
30602 -AGTAAATATATAAAAA
1 TA-TAAATATATAAAAA
30618 TATAAA
1 TATAAA
30624 ATTACTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
15 1 0.05
16 17 0.89
17 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TATAAATATATAAAAA
Found at i:31500 original size:15 final size:15
Alignment explanation
Indices: 31482--31515 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31472 ATTTAAATAT
31482 AATAATAAAAATAAA
1 AATAATAAAAATAAA
* *
31497 AATAATTAAGATAAA
1 AATAATAAAAATAAA
31512 AATA
1 AATA
31516 TAGACATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATAAAAATAAA
Found at i:39238 original size:23 final size:25
Alignment explanation
Indices: 39192--39251 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 25
39182 TTTTCGTAAA
39192 TTTAAAATTTAATTTATTTTTA-TT
1 TTTAAAATTTAATTTATTTTTATTT
39216 TTTAAGAATTTAA-TT-TTTTTATTT
1 TTTAA-AATTTAATTTATTTTTATTT
39240 TTTAAAATTTAA
1 TTTAAAATTTAA
39252 AATTTTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.38
24 14 0.41
25 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTAAAATTTAATTTATTTTTATTT
Found at i:39257 original size:23 final size:22
Alignment explanation
Indices: 39192--39257 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 22
39182 TTTTCGTAAA
39192 TTTAAAATTTAATTTATTTTTATT
1 TTTAAAATTTAA--TATTTTTATT
*
39216 TTTAAGAATTTAATTTTTTTATTT
1 TTTAA-AATTTAATATTTTTA-TT
*
39240 TTTAAAATTTAAAATTTT
1 TTTAAAATTTAATATTTT
39258 GGTTCAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 18 0.49
24 12 0.32
25 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTAAAATTTAATATTTTTATT
Found at i:54411 original size:19 final size:19
Alignment explanation
Indices: 54389--54436 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
54379 ACATAAAGTT
*
54389 ATTAA-AAATATTTAGAAAA
1 ATTAATAAA-ATTTACAAAA
54408 ATTAATAAAATTTACAAAA
1 ATTAATAAAATTTACAAAA
* *
54427 TTTTATAAAA
1 ATTAATAAAA
54437 ACATAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTAATAAAATTTACAAAA
Found at i:54451 original size:17 final size:16
Alignment explanation
Indices: 54429--54490 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 16
54419 TTACAAAATT
54429 TTATAAAAACATAAAAA
1 TTATAAAAA-ATAAAAA
*
54446 TTATAAAACAAACTAAATA
1 TTAT-AAA-AAA-TAAAAA
*
54465 TATATGAAAAAAAAAAAA
1 T-TAT-AAAAAATAAAAA
54483 TTATAAAA
1 TTATAAAA
54491 CAAGTTTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 4 0.11
17 7 0.19
18 9 0.24
19 11 0.30
20 6 0.16
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (16 bp):
TTATAAAAAATAAAAA
Found at i:54712 original size:15 final size:16
Alignment explanation
Indices: 54692--54724 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
54682 TTATAAACAT
54692 TGTTATAC-TTTTTAA
1 TGTTATACATTTTTAA
54707 TGTTATACAATTTTTAA
1 TGTTATAC-ATTTTTAA
54724 T
1 T
54725 AATTTTCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TGTTATACATTTTTAA
Found at i:54740 original size:20 final size:19
Alignment explanation
Indices: 54715--54771 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
54705 AATGTTATAC
54715 AATTTTTAATAATTTTCTG
1 AATTTTTAATAATTTTCTG
* *
54734 CACTTTTCT-AT-ATTTTAATG
1 -AATTTT-TAATAATTTT-CTG
54754 AATTTTTAATAATTTTCT
1 AATTTTTAATAATTTTCT
54772 ATGTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
18 1 0.03
19 13 0.45
20 14 0.48
21 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTTTTAATAATTTTCTG
Found at i:54788 original size:18 final size:19
Alignment explanation
Indices: 54755--54796 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
54745 ATTTTAATGA
*
54755 ATTTTTAATAATTTTCTAT
1 ATTTTTAATAAATTTCTAT
*
54774 GTTTTTAA-AAATTTCTAT
1 ATTTTTAATAAATTTCTAT
54792 ATTTT
1 ATTTT
54797 ATACATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTTAATAAATTTCTAT
Found at i:55102 original size:31 final size:29
Alignment explanation
Indices: 55033--55106 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
55023 ACAAAATAAT
**
55033 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACAAGTCA
55062 AACATAAGTGACTAAAATGTAACTCAAGTCA
1 AACATAAGTGACTAAAATGTAA--CAAGTCA
*
55093 AACAAAAGTGACTA
1 AACATAAGTGACTA
55107 TTTTTGTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 22 0.55
31 18 0.45
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACAAGTCA
Found at i:55339 original size:17 final size:18
Alignment explanation
Indices: 55309--55359 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
55299 TTTTTTGCAC
* *
55309 TTTTATATATTTTTACATA
1 TTTTAT-TAATTTTAAATA
55328 TTTT-TTAATTTTAAATA
1 TTTTATTAATTTTAAATA
*
55345 TTTTATTGATTTTAA
1 TTTTATTAATTTTAA
55360 GTATAAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 14 0.50
18 10 0.36
19 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATTAATTTTAAATA
Found at i:62239 original size:28 final size:28
Alignment explanation
Indices: 62207--62263 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
62197 AAAACTTTCT
*
62207 TATATATAA-TTTGGGATCATAACTCTAA
1 TATATATAACTTTGGCA-CATAACTCTAA
*
62235 TATATATAACTTTGGCACATACCTCTAA
1 TATATATAACTTTGGCACATAACTCTAA
62263 T
1 T
62264 TCCTAATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (28 bp):
TATATATAACTTTGGCACATAACTCTAA
Found at i:66811 original size:17 final size:17
Alignment explanation
Indices: 66786--66867 Score: 101
Period size: 17 Copynumber: 4.8 Consensus size: 17
66776 CTGAGCCCAA
*
66786 TAAACTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
66803 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
*
66820 TAAATTTAAATTTAGTT
1 TAAATTTAAATTTATTT
* *
66837 GAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
66854 TAAATTTAAATTTA
1 TAAATTTAAATTTA
66868 AAATTTATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:66829 original size:6 final size:6
Alignment explanation
Indices: 66786--66874 Score: 55
Period size: 6 Copynumber: 15.3 Consensus size: 6
66776 CTGAGCCCAA
* * * *
66786 TAAACT TAAATT T-ATTT TAAAAT TAAGTT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
* *
66832 T-AGTT GAAATT TAAATT T--ATT ATAAATT TAAATT TAAAATT TA
1 TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT T-AAATT TA
66875 TTTTAAATGT
Statistics
Matches: 63, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
4 5 0.08
5 9 0.14
6 37 0.59
7 12 0.19
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:66851 original size:34 final size:34
Alignment explanation
Indices: 66785--66867 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
66775 TCTGAGCCCA
* * * *
66785 ATAAACTTAAATTTATTTTAAAATTAAGTTTATT
1 ATAAATTTAAATTTAGTTGAAAATTAAATTTATT
* *
66819 CTAAATTTAAATTTAGTTGAAATTTAAATTTATT
1 ATAAATTTAAATTTAGTTGAAAATTAAATTTATT
66853 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
66868 AAATTTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (34 bp):
ATAAATTTAAATTTAGTTGAAAATTAAATTTATT
Found at i:66876 original size:24 final size:23
Alignment explanation
Indices: 66838--66882 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
66828 AATTTAGTTG
66838 AAATTTAAATTTATTATAAATTT
1 AAATTTAAATTTATTATAAATTT
*
66861 AAATTTAAAATTTATTTTAAAT
1 AAATTT-AAATTTATTATAAAT
66883 GTTCAAGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTAAATTTATTATAAATTT
Found at i:68637 original size:29 final size:29
Alignment explanation
Indices: 68605--68855 Score: 108
Period size: 30 Copynumber: 8.5 Consensus size: 29
68595 CTAACTTTTG
68605 AAAATCCCATTTTTGACCTCGAAACTTCTA
1 AAAATCCCATTTTTGACCTCGAAACTTC-A
***
68635 AAAATTATATTTTT-ATCCTCG-AACTTCCA
1 AAAATCCCATTTTTGA-CCTCGAAACTT-CA
* *
68664 AAAATCCCATTTTTGACCCCAAAACTTCAA
1 AAAATCCCATTTTTGACCTCGAAACTTC-A
* ** * *
68694 AAAAT-CTATTTTAAACCCCAAAACTTCCAA
1 AAAATCCCATTTTTGACCTCGAAACTT-C-A
* * *
68724 AAAATACCA-ATTT-ACCCCCG-AACTTCTA
1 AAAATCCCATTTTTGA-CCTCGAAACTTC-A
* * *
68752 AAAATCCCATTTTTAACCCCAAAACTTCCA
1 AAAATCCCATTTTTGACCTCGAAACTT-CA
* * **
68782 AAAATTCCA-TTTTAACCTTAAAACTTCCA
1 AAAATCCCATTTTTGACCTCGAAACTT-CA
* *
68811 AAAATTACCA-TTTT-ACCCTCGAAATTTCCAA
1 AAAA-TCCCATTTTTGA-CCTCGAAACTT-C-A
68842 AAAAT-CCATTTTTG
1 AAAATCCCATTTTTG
68856 CCCCGAATGT
Statistics
Matches: 178, Mismatches: 26, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
28 10 0.06
29 79 0.44
30 81 0.46
31 8 0.04
ACGTcount: A:0.39, C:0.27, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATCCCATTTTTGACCTCGAAACTTCA
Found at i:68672 original size:59 final size:59
Alignment explanation
Indices: 68576--68912 Score: 228
Period size: 59 Copynumber: 5.7 Consensus size: 59
68566 TAAGCTGTCC
* * *** * *
68576 AAAAATTCCATTTTT-ACCCCTAACTTTTGAAAATCCCATTTTTGACCTCGAAACTTCT
1 AAAAATTCCATTTTTAACCTCGAACTTCCAAAAATACCATTTTTGACCCCGAAACTTCT
** * * *
68634 AAAAATTATATTTTTATCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTC-
1 AAAAATTCCATTTTTAACCTCGAACTTCCAAAAATACCATTTTTGACCCCGAAACTTCT
* * * * * *
68692 AAAAAATCTATTTTAAACCCCAAAACTTCCAAAAAATACCA-ATTT-ACCCCCG-AACTTCT
1 AAAAATTCCATTTTTAACCTC-GAACTTCC-AAAAATACCATTTTTGA-CCCCGAAACTTCT
* * * * * *** *
68751 AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCA-TTTTAACCTTAAAACTTCC
1 AAAAATTCCATTTTTAACCTC-GAACTTCCAAAAATACCATTTTTGACCCCGAAACTTCT
* *
68810 AAAAATTACCA-TTTTACCCTCGAAATTTCCAAAAA-ATCCATTTTTG-CCCCG-AA-TGTCT
1 AAAAATT-CCATTTTTAACCTCG-AACTTCCAAAAATA-CCATTTTTGACCCCGAAACT-TCT
* *
68868 AAAAATTCCATTTTTAAACCTCGAATTTCCCAAAATTACCATTTT
1 AAAAATTCCATTTTT-AACCTCGAACTT-CCAAAAATACCATTTT
68913 GCCCCTAGGT
Statistics
Matches: 221, Mismatches: 42, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
57 4 0.02
58 70 0.32
59 130 0.59
60 17 0.08
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAAATTCCATTTTTAACCTCGAACTTCCAAAAATACCATTTTTGACCCCGAAACTTCT
Found at i:68862 original size:29 final size:30
Alignment explanation
Indices: 68656--68859 Score: 172
Period size: 30 Copynumber: 6.9 Consensus size: 30
68646 TTTATCCTCG
*
68656 AACTTCC-AAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAAATACCATTTTT-ACCCCAA
* *
68686 AACTT-CAAAAAAT-CTATTTTAAACCCCAA
1 AACTTCCAAAAAATACCATTTT-TACCCCAA
* **
68715 AACTTCCAAAAAATACCA-ATTTACCCCCG
1 AACTTCCAAAAAATACCATTTTTACCCCAA
* *
68744 AACTT-CTAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAAATACCATTTTT-ACCCCAA
* * **
68774 AACTTCC-AAAAATTCCATTTTAACCTTAA
1 AACTTCCAAAAAATACCATTTTTACCCCAA
* *
68803 AACTTCCAAAAATTACCA-TTTTACCCTCGA
1 AACTTCCAAAAAATACCATTTTTACCC-CAA
* *
68833 AATTTCCAAAAAAT-CCATTTTTGCCCC
1 AACTTCCAAAAAATACCATTTTTACCCC
68860 GAATGTCTAA
Statistics
Matches: 139, Mismatches: 25, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
28 10 0.07
29 54 0.39
30 72 0.52
31 3 0.02
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.29
Consensus pattern (30 bp):
AACTTCCAAAAAATACCATTTTTACCCCAA
Found at i:68883 original size:88 final size:89
Alignment explanation
Indices: 68576--68912 Score: 316
Period size: 88 Copynumber: 3.8 Consensus size: 89
68566 TAAGCTGTCC
* * * * * * * *
68576 AAAAATTCCATTTTTACCCC-TAACTTTTGAAAATCCCATTTTTGACCTCGAAACTTCTAAAAAT
1 AAAAATCCCATTTTTACCCCAAAACTTCTAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAAT
* *
68640 TA-TATTTTTATCCTCGAACTTCC-
66 TACCA-TTTTACCCTCGAACTTCCA
* * * *
68663 AAAAATCCCATTTTTGACCCCAAAACTTC-AAAAAATCTATTTTAAACCCCAAAACTTCCAAAAA
1 AAAAATCCCATTTTT-ACCCCAAAACTTCTAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAA
* * * *
68727 ATACCAATTTACCCCCGAACTT-CT
65 TTACCATTTTACCCTCGAACTTCCA
* *
68751 AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCA-TTTTAACCTTAAAACTTCCAAAAA
1 AAAAATCCCATTTTT-ACCCCAAAACTTCTAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAA
*
68815 TTACCATTTTACCCTCGAAATTTCCA
65 TTACCATTTTACCCTCG-AACTTCCA
* * * * *
68841 AAAAAT-CCATTTTTGCCCC-GAA-TGTCTAAAAATTCCATTTTTAAACCTC-GAATTTCCCAAA
1 AAAAATCCCATTTTTACCCCAAAACT-TCTAAAAATTCCATTTTT-AACCTCAAAACTTCCAAAA
68902 ATTACCATTTT
64 ATTACCATTTT
68913 GCCCCTAGGT
Statistics
Matches: 205, Mismatches: 35, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
86 1 0.00
87 29 0.14
88 137 0.67
89 31 0.15
90 7 0.03
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (89 bp):
AAAAATCCCATTTTTACCCCAAAACTTCTAAAAATTCCATTTTTAACCTCAAAACTTCCAAAAAT
TACCATTTTACCCTCGAACTTCCA
Found at i:69243 original size:95 final size:96
Alignment explanation
Indices: 69143--69328 Score: 254
Period size: 96 Copynumber: 1.9 Consensus size: 96
69133 AAGCTTTAAA
*
69143 AATCGAGGCAATATTTT-TTAT-TTCGAGTTTCGAAA-ATTTGTGCCTTAACTCACTAGGTGAAA
1 AATCGAGGCAATATTTTGTTATCTTCGA-TTTCGAAATA-TTGCGCCTTAACTCACTAGGTGAAA
* *
69205 TTTTTCTTCAAATCGAA-ATAATCGAATACCCTT
64 CTTTTCTACAAATC-AAGATAATCGAATACCCTT
* * * *
69238 AATCGAGGCAATGTTTTGTTATCTTCGATTTTGAAATATTGCGCCTTAACTTACTAGGTGCAACT
1 AATCGAGGCAATATTTTGTTATCTTCGATTTCGAAATATTGCGCCTTAACTCACTAGGTGAAACT
69303 TTTCTACAAATCAAGATAATCGAATA
66 TTTCTACAAATCAAGATAATCGAATA
69329 TCCTCTTCGT
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
95 18 0.22
96 56 0.70
97 6 0.08
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTTGTTATCTTCGATTTCGAAATATTGCGCCTTAACTCACTAGGTGAAACT
TTTCTACAAATCAAGATAATCGAATACCCTT
Found at i:73519 original size:12 final size:12
Alignment explanation
Indices: 73504--73531 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
73494 TCTGCATTGC
73504 CATCCTCTTCAT
1 CATCCTCTTCAT
73516 CATCCTCTTCAT
1 CATCCTCTTCAT
73528 CATC
1 CATC
73532 ATCCTCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.43, G:0.00, T:0.39
Consensus pattern (12 bp):
CATCCTCTTCAT
Found at i:73544 original size:12 final size:13
Alignment explanation
Indices: 73504--73544 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
73494 TCTGCATTGC
73504 CATCCTCT-TCAT
1 CATCCTCTATCAT
73516 CATCCTCTTCATCAT
1 CATCCTC-T-ATCAT
73531 CATCCTCTAT-AT
1 CATCCTCTATCAT
73543 CA
1 CA
73545 CTGTCATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.42
13 3 0.12
14 1 0.04
15 11 0.42
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (13 bp):
CATCCTCTATCAT
Found at i:95026 original size:31 final size:32
Alignment explanation
Indices: 94952--95033 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
94942 TCAAAAAAAA
* *
94952 TTTACCAACTTTTAAGGGGCCCCAAATATTTTT
1 TTTATCAACTTTTAA-GGGCCCCAAATAATTTT
* *
94985 TTTTTAAACTTTTAAGGG-CCCATAA-AATTTT
1 TTTATCAACTTTTAAGGGCCCCA-AATAATTTT
95016 TTTATCAACTTTTAAGGG
1 TTTATCAACTTTTAAGGG
95034 ATCTAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
31 25 0.60
32 5 0.12
33 12 0.29
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (32 bp):
TTTATCAACTTTTAAGGGCCCCAAATAATTTT
Found at i:99373 original size:21 final size:21
Alignment explanation
Indices: 99347--99386 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
99337 ATTATTTACA
99347 TGAAGTGAAATTCACCTAAAT
1 TGAAGTGAAATTCACCTAAAT
* *
99368 TGAAGTGACATTTACCTAA
1 TGAAGTGAAATTCACCTAA
99387 GTTACGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
TGAAGTGAAATTCACCTAAAT
Found at i:99409 original size:38 final size:38
Alignment explanation
Indices: 99366--99438 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
99356 ATTCACCTAA
* *
99366 ATTGAAGTGACATTTACCTAAGTTACGTTTAATGTTCG
1 ATTGAAGTGACATTTACCTAACTTACATTTAATGTTCG
* *
99404 ATTGAAGTGACATTTGCCTAACTTGCATTTAATGT
1 ATTGAAGTGACATTTACCTAACTTACATTTAATGT
99439 AAGATGGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (38 bp):
ATTGAAGTGACATTTACCTAACTTACATTTAATGTTCG
Found at i:101381 original size:31 final size:30
Alignment explanation
Indices: 101308--101382 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
101298 TATTTAGGTC
*
101308 AAGATTAAAATTGACCAATTCAAAAAGTCA
1 AAGACTAAAATTGACCAATTCAAAAAGTCA
* * *
101338 TAGACTAGAATTGACTAATTCGAAAAA-TACA
1 AAGACTAAAATTGACCAATTC-AAAAAGT-CA
*
101369 AAGCCTAAAATTGA
1 AAGACTAAAATTGA
101383 TCAAAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24
Consensus pattern (30 bp):
AAGACTAAAATTGACCAATTCAAAAAGTCA
Found at i:112555 original size:11 final size:11
Alignment explanation
Indices: 112539--112610 Score: 54
Period size: 11 Copynumber: 7.3 Consensus size: 11
112529 GGGCTCAAAC
112539 TTATTTTAAAT
1 TTATTTTAAAT
112550 TTATTTT-AA-
1 TTATTTTAAAT
*
112559 -GA-T-TAAAT
1 TTATTTTAAAT
*
112567 TTGTTTTAAA-
1 TTATTTTAAAT
112577 --ATT-TAAAT
1 TTATTTTAAAT
112585 TTATTTTAAAT
1 TTATTTTAAAT
112596 TTATTTTCAAAT
1 TTATTTT-AAAT
112608 TTA
1 TTA
112611 AAATTATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 19
0.67 0.06 0.27
Matches are distributed among these distances:
6 1 0.02
7 7 0.15
8 3 0.06
10 6 0.13
11 23 0.49
12 7 0.15
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:112584 original size:18 final size:18
Alignment explanation
Indices: 112543--112598 Score: 80
Period size: 17 Copynumber: 3.2 Consensus size: 18
112533 TCAAACTTAT
*
112543 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAAA
*
112561 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAA
112578 TTTAAATTTATTTT-AAA
1 TTTAAATTTATTTTAAAA
112595 TTTA
1 TTTA
112599 TTTTCAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 22 0.65
18 12 0.35
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:112593 original size:29 final size:29
Alignment explanation
Indices: 112561--112627 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
112551 TATTTTAAGA
* *
112561 TTAAATTTGTTTTAAAATTTAAATTTATT
1 TTAAATTTATTTTAAAATTTAAAATTATT
*
112590 TTAAATTTATTTTCAAATTTAAAATTATT
1 TTAAATTTATTTTAAAATTTAAAATTATT
*
112619 ATAAATTTA
1 TTAAATTTA
112628 AAATAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (29 bp):
TTAAATTTATTTTAAAATTTAAAATTATT
Found at i:112609 original size:12 final size:11
Alignment explanation
Indices: 112578--112610 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
112568 TGTTTTAAAA
112578 TTTAAATTTAT
1 TTTAAATTTAT
112589 TTTAAATTTAT
1 TTTAAATTTAT
112600 TTTCAAATTTA
1 TTT-AAATTTA
112611 AAATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:112625 original size:46 final size:46
Alignment explanation
Indices: 112539--112629 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
112529 GGGCTCAAAC
* * *
112539 TTATTTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAAT
1 TTATTTTAAATTTATTTTAAGATTAAAATTATTATAAAATTTAAAT
112585 TTATTTTAAATTTATTTTCAA-ATTTAAAATTATTAT-AAATTTAAA
1 TTATTTTAAATTTATTTT-AAGA-TTAAAATTATTATAAAATTTAAA
112630 ATAAATAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 28 0.70
47 12 0.30
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (46 bp):
TTATTTTAAATTTATTTTAAGATTAAAATTATTATAAAATTTAAAT
Found at i:112626 original size:17 final size:18
Alignment explanation
Indices: 112589--112631 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
112579 TTAAATTTAT
* *
112589 TTTAAATTTATTTTCAAA
1 TTTAAAATTATTATCAAA
112607 TTTAAAATTATTAT-AAA
1 TTTAAAATTATTATCAAA
112624 TTTAAAAT
1 TTTAAAAT
112632 AAATAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAAATTATTATCAAA
Found at i:113350 original size:3 final size:3
Alignment explanation
Indices: 113342--113409 Score: 66
Period size: 3 Copynumber: 22.0 Consensus size: 3
113332 TTAATGACAT
* **
113342 TAA TAA TAA TAA TAA TAA TAA TAA CT-G TTT TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA
*
113388 TAA TAA TAAA TAT TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA
113410 AAAAAGAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 1 0.02
3 49 0.89
4 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:114515 original size:59 final size:59
Alignment explanation
Indices: 114436--114919 Score: 568
Period size: 59 Copynumber: 8.2 Consensus size: 59
114426 CAAAACTTTT
* * *
114436 AAAAATTACATTTTTGACCCCAAAACTTCCAAAAATTTCATTTTTACCCCTGAACTTCC
1 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
* * * * * *
114495 AAAAATTCCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACACTTGAACTT-A
1 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
* * * *
114553 AAAAATT-CATTTTTTAGCCT-AAAACTTTCAAAAATTACATTTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTTGA-CCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
* * *
114611 AAAAATTCCATTTTTGACCTCGAAACTTCCAAAAAATCTATTTTTA-CCCTCGAACTTCC
1 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCT-GAACTTCC
** * * * *
114670 AAAAATTATATTTTTGACCTCAAAACTTCCAAAAAATCTATTTTTACCCCTAAACTTCT
1 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
* * * * *
114729 AAAAATTCCATTTTTAACCTCGAAACTTCTAAAAATTCCATTTTTACCCCCGAACTTCT
1 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
*
114788 AAAAATTCCATTTTTGACCTTAAAACTTCCAAAAATTCCATTTTTA-CCCTCG-ACTTCC
1 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCT-GAACTTCC
* * * * *
114846 AAAAATTCTATTTTTTACCTCGATACTTCCAAAAATTGCATTTTTGACCCC-GAAACTTCC
1 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTT-ACCCCTG-AACTTCC
114906 AAAAATTACCATTT
1 AAAAATT-CCATTT
114920 GCCCCCAAAT
Statistics
Matches: 363, Mismatches: 50, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
57 38 0.10
58 71 0.20
59 229 0.63
60 20 0.06
61 5 0.01
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
Found at i:114987 original size:29 final size:29
Alignment explanation
Indices: 114397--115030 Score: 508
Period size: 30 Copynumber: 21.6 Consensus size: 29
114387 AGGAGGTCTT
*
114397 GAAACTTCCAAAAATTCCATTTTTGTA-ATC
1 GAAACTTCCAAAAATTCCA-TTTT-TACCTC
* ** * *
114427 AAAACTTTTAAAAATTACATTTTTGACCCC
1 GAAACTTCCAAAAATTCCATTTTT-ACCTC
* * *
114457 AAAACTTCCAAAAATTTCATTTTTACCCC
1 GAAACTTCCAAAAATTCCATTTTTACCTC
*
114486 TG-AACTTCCAAAAATTCCATTTTTAACCCC
1 -GAAACTTCCAAAAATTCCATTTTT-ACCTC
*
114516 GAAACTTCCAAAAATTCCATTTTTACACTT
1 GAAACTTCCAAAAATTCCATTTTTAC-CTC
*
114546 G-AACTT-AAAAAATT-CATTTTTTAGCCT-
1 GAAACTTCCAAAAATTCCA-TTTTTA-CCTC
* * * *
114573 AAAACTTTCAAAAATTACATTTTTACCCC
1 GAAACTTCCAAAAATTCCATTTTTACCTC
*
114602 TAAACTTCCAAAAATTCCATTTTTGACCTC
1 GAAACTTCCAAAAATTCCATTTTT-ACCTC
* *
114632 GAAACTTCCAAAAAATCTATTTTTACCCTC
1 GAAACTTCCAAAAATTCCATTTTTA-CCTC
**
114662 G-AACTTCCAAAAATTATATTTTTGACCTC
1 GAAACTTCCAAAAATTCCATTTTT-ACCTC
* * * *
114691 AAAACTTCCAAAAAATCTATTTTTACCCC
1 GAAACTTCCAAAAATTCCATTTTTACCTC
* *
114720 TAAACTTCTAAAAATTCCATTTTTAACCTC
1 GAAACTTCCAAAAATTCCATTTTT-ACCTC
* *
114750 GAAACTTCTAAAAATTCCATTTTTACCCCC
1 GAAACTTCCAAAAATTCCATTTTTA-CCTC
* *
114780 G-AACTTCTAAAAATTCCATTTTTGACCTT
1 GAAACTTCCAAAAATTCCATTTTT-ACCTC
*
114809 AAAACTTCCAAAAATTCCATTTTTACCCTC
1 GAAACTTCCAAAAATTCCATTTTTA-CCTC
*
114839 G--ACTTCCAAAAATTCTATTTTTTACCTC
1 GAAACTTCCAAAAATTCCA-TTTTTACCTC
* * *
114867 GATACTTCCAAAAATTGCATTTTTGACCCC
1 GAAACTTCCAAAAATTCCATTTTT-ACCTC
* *
114897 GAAACTTCCAAAAATTACCA--TTTGCCCC
1 GAAACTTCCAAAAATT-CCATTTTTACCTC
* * * * * * *
114925 CAAATGTTCAAAAAACTCTATTTTCGACCGC
1 GAAA-CTTCCAAAAATTCCATTTT-TACCTC
114956 GAAAC-TCCAAAAATTCCATTTTTACTCTC
1 GAAACTTCCAAAAATTCCATTTTTAC-CTC
*
114985 G-AA-TGTCTAAAAATTCCATCTTTTAACCTC
1 GAAACT-TCCAAAAATTCCAT-TTTT-ACCTC
*
115015 G-AACTTGCCCAAAATT
1 GAAACTT-CCAAAAATT
115031 ATCATTTCAC
Statistics
Matches: 499, Mismatches: 68, Indels: 73
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.00
28 56 0.11
29 202 0.40
30 221 0.44
31 18 0.04
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
GAAACTTCCAAAAATTCCATTTTTACCTC
Found at i:119757 original size:11 final size:11
Alignment explanation
Indices: 119741--119766 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
119731 ACACTCGATT
119741 GAAGTTATTTG
1 GAAGTTATTTG
119752 GAAGTTATTTG
1 GAAGTTATTTG
119763 GAAG
1 GAAG
119767 GCTAAGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (11 bp):
GAAGTTATTTG
Found at i:123507 original size:120 final size:120
Alignment explanation
Indices: 123364--123607 Score: 409
Period size: 120 Copynumber: 2.0 Consensus size: 120
123354 ACAAACGACG
*
123364 CGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATTAAAC-CTACGCTCGATATAAGCAA
1 CGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACTC-ACGCTCGATATAAGCAA
* *
123428 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTAAAGTAATGAAA
65 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGTAATAAAA
* *
123484 CGGTCATTTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATGAGCAAA
1 CGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATAAGCAAA
* *
123549 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGTAATAAAA
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGTAATAAAA
123604 CGGT
1 CGGT
123608 TAGCTTCCTA
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
120 115 0.99
121 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (120 bp):
CGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCGATATAAGCAAA
TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGTAATAAAA
Found at i:123641 original size:120 final size:120
Alignment explanation
Indices: 123364--123642 Score: 355
Period size: 120 Copynumber: 2.3 Consensus size: 120
123354 ACAAACGACG
* * * * * *
123364 CGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATTAAACCTACGCTCGATATAAGCAAA
1 CGGTCAGCTTCCTAATGAAATACAGAGAAGAAGACCAAATCAAACCTACGCTCGATATAAGCAAA
* *
123429 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTAAAGTAATGAAA
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGTAATAAAA
** * * * * *
123484 CGGTCATTTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAA-CTCACGCTCGATATGAGCAA
1 CGGTCAGCTTCCTAATGAAATACAGAGAAGAAGACCAAATCAAACCT-ACGCTCGATATAAGCAA
* *
123548 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGTAATAAAA
65 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGTAATAAAA
* *
123604 CGGTTAGCTTCCTAATGAAATACAGGGAAGTAA-ACCAAA
1 CGGTCAGCTTCCTAATGAAATACAGAGAAG-AAGACCAAA
123643 ACCATCTTCC
Statistics
Matches: 142, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
119 2 0.01
120 138 0.97
121 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (120 bp):
CGGTCAGCTTCCTAATGAAATACAGAGAAGAAGACCAAATCAAACCTACGCTCGATATAAGCAAA
TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGTAATAAAA
Found at i:124057 original size:6 final size:6
Alignment explanation
Indices: 124046--124116 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
124036 GCCCAAACTC
* * *
124046 AATTTA AATTT- ATTTTA AATTT- AATTTA AGTTTA AATTT- ATTTTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
*
124092 AATTTA AAATT- -ATTATA AATTTA AA
1 AATTTA AATTTA AATT-TA AATTTA AA
124117 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
4 2 0.04
5 14 0.28
6 27 0.54
7 7 0.14
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:124064 original size:11 final size:11
Alignment explanation
Indices: 124046--124115 Score: 54
Period size: 11 Copynumber: 6.2 Consensus size: 11
124036 GCCCAAACTC
124046 AATTTAAATTT
1 AATTTAAATTT
*
124057 ATTTTAAATTT
1 AATTTAAATTT
*
124068 AATTTAAGTTT
1 AATTTAAATTT
*
124079 AAATTT-ATTTT
1 -AATTTAAATTT
*
124090 CAAATTTAAAATT
1 --AATTTAAATTT
124103 -ATTATAAATTT
1 AATT-TAAATTT
124114 AA
1 AA
124116 AATAAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 3 0.06
11 29 0.62
12 12 0.26
13 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:124068 original size:17 final size:17
Alignment explanation
Indices: 124059--124116 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
124049 TTAAATTTAT
* *
124059 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
124076 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
124094 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
124111 TTTAAA
1 TTTAAA
124117 ATAAATAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:124117 original size:17 final size:18
Alignment explanation
Indices: 124076--124118 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
124066 TTAATTTAAG
* *
124076 TTTAAATTTATTTTCAAA
1 TTTAAAATTATTATCAAA
124094 TTTAAAATTATTAT-AAA
1 TTTAAAATTATTATCAAA
124111 TTTAAAAT
1 TTTAAAAT
124119 AAATAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAAATTATTATCAAA
Found at i:136625 original size:3 final size:3
Alignment explanation
Indices: 136557--136606 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
136547 TATCATCATC
136557 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
136605 AT
1 AT
136607 CGTACCTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:136806 original size:21 final size:21
Alignment explanation
Indices: 136779--136834 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
136769 GAAGTGAGAG
136779 TTCTACCGATACAACTCTGACC-
1 TTCTACCGATACAAC-CT-ACCT
*
136801 TT-TACCGGTACAACCTACCT
1 TTCTACCGATACAACCTACCT
136821 TTCTACCGATACAA
1 TTCTACCGATACAA
136835 TGAGTTTCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.10
20 4 0.13
21 21 0.70
22 2 0.07
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACAACCTACCT
Found at i:142053 original size:18 final size:17
Alignment explanation
Indices: 142011--142053 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
142001 ATTCTAAATT
*
142011 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
142028 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
142046 TATAATTT
1 TATAATTT
142054 AAAGTATATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:145363 original size:11 final size:12
Alignment explanation
Indices: 145345--145375 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
145335 GAAAATTAAA
145345 ATGATGAAGAAG
1 ATGATGAAGAAG
145357 A-GATGAAGAAG
1 ATGATGAAGAAG
145368 ATGATGAA
1 ATGATGAA
145376 AAATTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
ATGATGAAGAAG
Found at i:145441 original size:22 final size:22
Alignment explanation
Indices: 145398--145442 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
145388 AATATTATTT
*
145398 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATAATTTCAAAAA
*
145420 AATAATTTTAATAATTTTAAAAA
1 AATAATTTT-ATAATTTCAAAAA
145443 TTTATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAATTTTATAATTTCAAAAA
Found at i:145465 original size:13 final size:13
Alignment explanation
Indices: 145429--145471 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
145419 AAATAATTTT
145429 AATAATTTTAAAA
1 AATAATTTTAAAA
* *
145442 ATTTATATTTAAAA
1 AATAAT-TTTAAAA
*
145456 AATAATTTTAATA
1 AATAATTTTAAAA
145469 AAT
1 AAT
145472 TTCAAATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATTTTAAAA
Found at i:146305 original size:10 final size:9
Alignment explanation
Indices: 146281--146327 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
146271 ATATGTGTTG
*
146281 AAAATTAAA
1 AAAATAAAA
146290 AAAATAAAA
1 AAAATAAAA
146299 AACAATAAAA
1 AA-AATAAAA
* *
146309 AATATTAAA
1 AAAATAAAA
146318 AAAATAAAA
1 AAAATAAAA
146327 A
1 A
146328 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 23 0.72
10 9 0.28
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAATAAAA
Found at i:146328 original size:17 final size:17
Alignment explanation
Indices: 146281--146336 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
146271 ATATGTGTTG
* * *
146281 AAAATTAAAAAAATAAA
1 AAAAATAAAAATATTAA
146298 AAACAATAAAAAATATTAA
1 AAA-AAT-AAAAATATTAA
146317 AAAAATAAAAATATTTAA
1 AAAAATAAAAATA-TTAA
146335 AA
1 AA
146337 TTTATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 10 0.30
18 11 0.33
19 12 0.36
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAAAAATATTAA
Found at i:146334 original size:18 final size:19
Alignment explanation
Indices: 146286--146336 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
146276 TGTTGAAAAT
*
146286 TAAAAAA-ATAAAAAACAA
1 TAAAAAATATTAAAAACAA
146304 TAAAAAATATTAAAAA-AA
1 TAAAAAATATTAAAAACAA
146322 T-AAAAATATTTAAAA
1 TAAAAAATA-TTAAAA
146337 TTTATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 7 0.23
18 16 0.53
19 7 0.23
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAAAAATATTAAAAACAA
Found at i:146342 original size:28 final size:28
Alignment explanation
Indices: 146284--146398 Score: 88
Period size: 28 Copynumber: 3.9 Consensus size: 28
146274 TGTGTTGAAA
** **
146284 ATTAAAAAAATAAAAA-ACAATAAAAAAT
1 ATTAAAAAAATAAAAATA-TTTAAAATTT
146312 ATTAAAAAAATAAAAATATTTAAAATTT
1 ATTAAAAAAATAAAAATATTTAAAATTT
* * *
146340 ATTTAAAATATAGAAAAATATTTTAAATTT
1 A-TTAAAA-AAATAAAAATATTTAAAATTT
* *
146370 CTTAAAAAATATAAAGATCATTATAAAAT
1 ATTAAAAAA-ATAAAAAT-ATT-TAAAAT
146399 AAAATTATAG
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
28 24 0.35
29 19 0.28
30 21 0.30
31 5 0.07
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (28 bp):
ATTAAAAAAATAAAAATATTTAAAATTT
Found at i:146345 original size:29 final size:28
Alignment explanation
Indices: 146313--146398 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 28
146303 ATAAAAAATA
*
146313 TTAAAAAAATAAAAATATTTAAAATTTAT
1 TTAAAAAAATAAAAATATTTAAAATTT-C
* * *
146342 TTAAAATATAGAAAAATATTTTAAATTTC
1 TTAAAA-AAATAAAAATATTTAAAATTTC
*
146371 TTAAAAAATATAAAGATCATTATAAAAT
1 TTAAAAAA-ATAAAAAT-ATT-TAAAAT
146399 AAAATTATAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.02
29 18 0.40
30 21 0.47
31 5 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
TTAAAAAAATAAAAATATTTAAAATTTC
Found at i:146379 original size:31 final size:30
Alignment explanation
Indices: 146311--146382 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
146301 CAATAAAAAA
*
146311 TATTAAAAA-A-ATAAAAATATTTAAAATT
1 TATTAAAAATATAGAAAAATATTTAAAATT
* *
146339 TATTTAAAATATAGAAAAATATTTTAAATT
1 TATTAAAAATATAGAAAAATATTTAAAATT
*
146369 TCTTAAAAAATATA
1 TATT-AAAAATATA
146383 AAGATCATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.22
29 1 0.03
30 19 0.53
31 8 0.22
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (30 bp):
TATTAAAAATATAGAAAAATATTTAAAATT
Found at i:146426 original size:23 final size:22
Alignment explanation
Indices: 146389--146442 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
146379 TATAAAGATC
146389 ATTATAAAATAAAATTATAGAAA
1 ATTATAAAATAAAATTATA-AAA
146412 ATTATAGAAAT-AAATTATAAAA
1 ATTATA-AAATAAAATTATAAAA
*
146434 ATCATAAAA
1 ATTATAAAA
146443 GAGTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 3 0.10
22 8 0.28
23 14 0.48
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
ATTATAAAATAAAATTATAAAA
Found at i:146470 original size:39 final size:40
Alignment explanation
Indices: 146426--146525 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
146416 TAGAAATAAA
** *
146426 TTAT-AAAAATCATAAAAGAGTTATAAACATTGTAA-AAAT
1 TTATAAAAAATCATAAAA-AAATATAAAAATTGTAAGAAAT
*
146465 TTATAAAAAATCGTAAAAAAATATAAAAATTGTAAGAAA-
1 TTATAAAAAATCATAAAAAAATATAAAAATTGTAAGAAAT
** *
146504 -TATAAAATTTTATAAAAAAATA
1 TTATAAAAAATCATAAAAAAATA
146526 ATATTTGGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
38 18 0.35
39 18 0.35
40 15 0.29
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (40 bp):
TTATAAAAAATCATAAAAAAATATAAAAATTGTAAGAAAT
Found at i:146473 original size:10 final size:9
Alignment explanation
Indices: 146399--146521 Score: 61
Period size: 10 Copynumber: 12.4 Consensus size: 9
146389 ATTATAAAAT
146399 AAAATTATA
1 AAAATTATA
146408 GAAAATTATAGAA
1 -AAAATTAT---A
146421 ATAAATTATA
1 A-AAATTATA
*
146431 AAAATCATA
1 AAAATTATA
146440 AAAGAGTTATA
1 AAA-A-TTATA
* *
146451 AACATTGTA
1 AAAATTATA
146460 AAAATTTATAA
1 AAAA-TTAT-A
146471 AAAATCGTA-A
1 AAAAT--TATA
*
146481 AAAAATATA
1 AAAATTATA
*
146490 AAAATTGTA
1 AAAATTATA
146499 AGAAA-TATA
1 A-AAATTATA
*
146508 AAATTTTATA
1 AAA-ATTATA
146518 AAAA
1 AAAA
146522 AATAATATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 29
0.68 0.09 0.23
Matches are distributed among these distances:
8 4 0.05
9 30 0.34
10 31 0.36
11 11 0.13
12 3 0.03
13 8 0.09
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:146480 original size:20 final size:19
Alignment explanation
Indices: 146423--146510 Score: 79
Period size: 20 Copynumber: 4.6 Consensus size: 19
146413 TTATAGAAAT
*
146423 AAATTATAAAAATCATAAA
1 AAATTATAAAAATCGTAAA
* * *
146442 AGAGTTATAAACATTGTAAA
1 A-AATTATAAAAATCGTAAA
*
146462 AATTTATAAAAAATCGTAAA
1 AAATTAT-AAAAATCGTAAA
* * *
146482 AAAATATAAAAATTGTAAG
1 AAATTATAAAAATCGTAAA
146501 AAA-TATAAAA
1 AAATTATAAAA
146511 TTTTATAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
18 7 0.12
19 19 0.34
20 30 0.54
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.27
Consensus pattern (19 bp):
AAATTATAAAAATCGTAAA
Found at i:146617 original size:18 final size:20
Alignment explanation
Indices: 146569--146618 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
146559 TTTCTAGGGG
* *
146569 TATAGTAATTTTCTATATTT
1 TATAATAATTTTATATATTT
146589 TATAA-ATATTTTATA-ATTT
1 TATAATA-ATTTTATATATTT
146608 T-TAATAATTTT
1 TATAATAATTTT
146619 TATTGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.31
19 7 0.27
20 11 0.42
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TATAATAATTTTATATATTT
Found at i:151208 original size:12 final size:13
Alignment explanation
Indices: 151176--151208 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
151166 CTCATATAGA
*
151176 GTTGTTTGGAAAT
1 GTTGTTTGAAAAT
151189 GTTGTTTGAAAAT
1 GTTGTTTGAAAAT
151202 GTT-TTTG
1 GTTGTTTG
151209 TGTGATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (13 bp):
GTTGTTTGAAAAT
Found at i:157462 original size:10 final size:11
Alignment explanation
Indices: 157442--157471 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
157432 CTGACTTTGA
157442 AAAAATCATAG
1 AAAAATCATAG
157453 AAAAAT-ATAG
1 AAAAATCATAG
157463 AAAAATCAT
1 AAAAATCAT
157472 TAGAGACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (11 bp):
AAAAATCATAG
Found at i:158542 original size:20 final size:21
Alignment explanation
Indices: 158504--158542 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
158494 TTTGTACTAA
**
158504 AAATCATATTTTATTTCTTTT
1 AAATCATATTTTAAGTCTTTT
158525 AAATCA-ATTTTAAGTCTT
1 AAATCATATTTTAAGTCTT
158543 GATTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (21 bp):
AAATCATATTTTAAGTCTTTT
Found at i:160448 original size:22 final size:19
Alignment explanation
Indices: 160406--160449 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
160396 CTATGTAAGA
*
160406 TCAGATACATTATCACTTT
1 TCAGATACATTATCACGTT
160425 TCAGATATCAGTTATTCACGTT
1 TCAGATA-CA-TTA-TCACGTT
160447 TCA
1 TCA
160450 CAAATCAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 2 0.10
21 3 0.14
22 9 0.43
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (19 bp):
TCAGATACATTATCACGTT
Found at i:160535 original size:18 final size:18
Alignment explanation
Indices: 160508--160542 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
160498 GCAGATACAA
*
160508 ATACATATACAAATGCAG
1 ATACAGATACAAATGCAG
*
160526 ATACAGATACATATGCA
1 ATACAGATACAAATGCA
160543 ATTTTTCCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (18 bp):
ATACAGATACAAATGCAG
Found at i:163456 original size:25 final size:24
Alignment explanation
Indices: 163427--163480 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
163417 TTTACATGTT
*
163427 TATTTTTTA-AATTTATT-AAATTA
1 TATTTTTTATAATTT-TTAAAAATA
163450 TATATTTTTATAATTTTTAAAAATA
1 TAT-TTTTTATAATTTTTAAAAATA
163475 TATTTT
1 TATTTT
163481 CTAATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.11
24 11 0.41
25 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTTTTATAATTTTTAAAAATA
Found at i:163475 original size:23 final size:24
Alignment explanation
Indices: 163430--163480 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
163420 ACATGTTTAT
*
163430 TTTTTAAATTTATTAAATTATATA
1 TTTTTAAATTTATTAAATAATATA
163454 TTTTTATAATTT-TTAAA-AATATA
1 TTTTTA-AATTTATTAAATAATATA
163477 TTTT
1 TTTT
163481 CTAATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 9 0.36
24 11 0.44
25 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTTAAATTTATTAAATAATATA
Found at i:172569 original size:43 final size:43
Alignment explanation
Indices: 172479--172581 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
172469 CAAAAGACAG
* *
172479 AGGAAGCTACGTGGAAAAAGCCACATTCAAGAAACAACAAAGG
1 AGGAAGCTACGTGGAAAAAACCACATTCAAGAAACAACAAAGA
* * ** *
172522 AGGAAGCTACGTGGAAAAAACCACTTTCATGAAAGGATAAAGA
1 AGGAAGCTACGTGGAAAAAACCACATTCAAGAAACAACAAAGA
* *
172565 AGGAAACTGCGTGGAAA
1 AGGAAGCTACGTGGAAA
172582 GCATCCACAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.13
Consensus pattern (43 bp):
AGGAAGCTACGTGGAAAAAACCACATTCAAGAAACAACAAAGA
Found at i:177138 original size:21 final size:21
Alignment explanation
Indices: 177113--177152 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
177103 AATAATGACT
177113 AAAAGTATTGATACCTTTTCA
1 AAAAGTATTGATACCTTTTCA
177134 AAAAGTATTGATACCTTTT
1 AAAAGTATTGATACCTTTT
177153 ATCAGGTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAAGTATTGATACCTTTTCA
Found at i:180063 original size:27 final size:26
Alignment explanation
Indices: 179998--180073 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 26
179988 TGTGACAGTT
179998 TCTGTTAAAGGTAAGCCTTTGTGGTAAA
1 TCTGTTAAAGGT--GCCTTTGTGGTAAA
* *
180026 CCTCTTAAAAGGTGCCTTTGTGGTAATA
1 TCTGTT-AAAGGTGCCTTTGTGGTAA-A
180054 TCTGTTAAAGGAATGCCTTT
1 TCTGTTAAAGG--TGCCTTT
180074 ATGGCAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.45
28 9 0.22
29 13 0.32
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (26 bp):
TCTGTTAAAGGTGCCTTTGTGGTAAA
Found at i:180257 original size:61 final size:62
Alignment explanation
Indices: 180124--180240 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
180114 GTAAAGGGAA
* * * *
180124 AGCCTTTGTGGTGAGTTCTGAATGTTAAAGGAATGCCTTTGTGGAAATACTCTAAACAAGAG
1 AGCCTTTGTGGAGAGTACTAAATGTTAAAGGAATGCCTTTATGGAAATACTCTAAACAAGAG
180186 AGCCTTTGTGGAGAGTACTAAATGTTAAA-GAATGCCTTTATGGTAAAT-CTCTAAA
1 AGCCTTTGTGGAGAGTACTAAATGTTAAAGGAATGCCTTTATGG-AAATACTCTAAA
180241 AGGAAGCACC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 20 0.40
62 30 0.60
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (62 bp):
AGCCTTTGTGGAGAGTACTAAATGTTAAAGGAATGCCTTTATGGAAATACTCTAAACAAGAG
Found at i:185111 original size:17 final size:16
Alignment explanation
Indices: 185075--185158 Score: 87
Period size: 17 Copynumber: 5.1 Consensus size: 16
185065 CAATTTTAAA
* *
185075 ATTTGAATTTGAATTT
1 ATTTTAATTTAAATTT
*
185091 ATTTTAAGTTTAAATTA
1 ATTTTAA-TTTAAATTT
185108 ATTTTGAATTTAAATTT
1 ATTTT-AATTTAAATTT
* *
185125 ATTTTGAGTTTGAATTT
1 ATTTT-AATTTAAATTT
*
185142 ATTTTAAATTAAATTT
1 ATTTTAATTTAAATTT
185158 A
1 A
185159 AATTTTAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 15 0.26
17 40 0.70
18 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (16 bp):
ATTTTAATTTAAATTT
Found at i:185115 original size:34 final size:34
Alignment explanation
Indices: 185076--185158 Score: 114
Period size: 34 Copynumber: 2.5 Consensus size: 34
185066 AATTTTAAAA
*
185076 TTTGAATTTGAATTTATTTTAAGTTTAAATTAAT
1 TTTGAATTTAAATTTATTTTAAGTTTAAATTAAT
* * *
185110 TTTGAATTTAAATTTATTTTGAGTTTGAATTTAT
1 TTTGAATTTAAATTTATTTTAAGTTTAAATTAAT
*
185144 TTT-AAATTAAATTTA
1 TTTGAATTTAAATTTA
185159 AATTTTAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 11 0.25
34 33 0.75
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (34 bp):
TTTGAATTTAAATTTATTTTAAGTTTAAATTAAT
Found at i:185561 original size:21 final size:22
Alignment explanation
Indices: 185537--185577 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
185527 AGAATACACT
*
185537 CAAAA-TCAATAAAGAAGAACA
1 CAAAATTCAATAAAAAAGAACA
*
185558 CAAAATTGAATAAAAAAGAA
1 CAAAATTCAATAAAAAAGAA
185578 GCAGATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.68, C:0.10, G:0.10, T:0.12
Consensus pattern (22 bp):
CAAAATTCAATAAAAAAGAACA
Found at i:185784 original size:25 final size:25
Alignment explanation
Indices: 185756--185803 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
185746 TTCATCTTTC
*
185756 TGAAATAAATGTTAAATAAATAATT
1 TGAAATAAATGTCAAATAAATAATT
*
185781 TGAAATAAGTGTCAAATAAATAA
1 TGAAATAAATGTCAAATAAATAA
185804 ATGGGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.31
Consensus pattern (25 bp):
TGAAATAAATGTCAAATAAATAATT
Found at i:186893 original size:29 final size:29
Alignment explanation
Indices: 186829--187081 Score: 146
Period size: 29 Copynumber: 8.7 Consensus size: 29
186819 CAAAAGGTCT
* * * *
186829 CTAAACTCTCCAAAAATCACATTTTGACTC
1 CTAAACTTTCCAAAAATTATATTTTG-CCC
*
186859 TTAAACTTTCCAAAAATTATATTTTGCCC
1 CTAAACTTTCCAAAAATTATATTTTGCCC
*
186888 CTAAACTTAT-CAAAAATTATATTTTAACCC
1 CTAAACTT-TCCAAAAATTATATTTT-GCCC
* * *
186918 TCT-AACTTTTCAAAAATTACATTTTGACC
1 -CTAAACTTTCCAAAAATTATATTTTGCCC
* * * * * *
186947 TTGAACTTTTCAAAAATCACATTTTTG-TC
1 CTAAACTTTCCAAAAATTATA-TTTTGCCC
* * *
186976 CTCGAAC-TTCCAAAAATTCTATTTT-TCC
1 CT-AAACTTTCCAAAAATTATATTTTGCCC
* *
187004 CTCGAAC-TTCCAAAAATCATATTTTTGCCTC
1 CT-AAACTTTCCAAAAATTATA-TTTTGCC-C
*
187035 C-AAAC-TTCCAAAAATTATATTTTTAACCC
1 CTAAACTTTCCAAAAATTATA-TTTT-GCCC
*
187064 C-GAACTTTCCAAAAATTA
1 CTAAACTTTCCAAAAATTA
187082 CCATTTTACC
Statistics
Matches: 184, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
28 25 0.14
29 86 0.47
30 69 0.38
31 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.37
Consensus pattern (29 bp):
CTAAACTTTCCAAAAATTATATTTTGCCC
Found at i:186902 original size:59 final size:58
Alignment explanation
Indices: 186839--187088 Score: 204
Period size: 59 Copynumber: 4.3 Consensus size: 58
186829 CTAAACTCTC
* * *
186839 CAAAAATCACA-TTTTGACTCTTAAACTTTCCAAAAATTATATTTTGCCCCTAAACTTAT
1 CAAAAATCACATTTTTGACTCTCAAAC-TTCCAAAAATTATATTTTGACCCTGAACTT-T
* * * * * * * *
186898 CAAAAATTATA-TTTTAACCCTCTAACTTTTCAAAAATTACATTTTGACCTTGAACTTTT
1 CAAAAATCACATTTTTGACTCTCAAAC-TTCCAAAAATTATATTTTGACCCTGAAC-TTT
* * * * *
186957 CAAAAATCACATTTTTGTC-CTCGAACTTCCAAAAATTCTATTTT-TCCCTCGAACTTC
1 CAAAAATCACATTTTTGACTCTCAAACTTCCAAAAATTATATTTTGACCCT-GAACTTT
* * * *
187014 CAAAAATCATATTTTTGCCTC-CAAACTTCCAAAAATTATATTTTTAACCCCGAACTTT
1 CAAAAATCACATTTTTGACTCTCAAACTTCCAAAAATTATA-TTTTGACCCTGAACTTT
*
187072 CCAAAAATTACCATTTT
1 -CAAAAATCA-CATTTT
187089 ACCCCGAACA
Statistics
Matches: 152, Mismatches: 31, Indels: 15
0.77 0.16 0.08
Matches are distributed among these distances:
57 39 0.26
58 30 0.20
59 71 0.47
60 12 0.08
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (58 bp):
CAAAAATCACATTTTTGACTCTCAAACTTCCAAAAATTATATTTTGACCCTGAACTTT
Found at i:187006 original size:28 final size:28
Alignment explanation
Indices: 186975--187108 Score: 139
Period size: 28 Copynumber: 4.7 Consensus size: 28
186965 ACATTTTTGT
186975 CCTCGAACTTCCAAAAATTCTATTTTTC
1 CCTCGAACTTCCAAAAATTCTATTTTTC
*
187003 CCTCGAACTTCCAAAAA-TCATATTTTTG
1 CCTCGAACTTCCAAAAATTC-TATTTTTC
* *
187031 CCTCCAAACTTCCAAAAATTATATTTTTAAC
1 CCT-CGAACTTCCAAAAATTCTATTTTT--C
* *
187062 CC-CGAACTTTCCAAAAATTACCATTTTAC
1 CCTCGAAC-TTCCAAAAATT-CTATTTTTC
*
187091 CC-CGAACATCCAAAAATT
1 CCTCGAACTTCCAAAAATT
187109 ACCAGTTTAC
Statistics
Matches: 90, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.02
28 37 0.41
29 32 0.36
30 12 0.13
31 7 0.08
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
CCTCGAACTTCCAAAAATTCTATTTTTC
Found at i:187089 original size:30 final size:28
Alignment explanation
Indices: 186862--187109 Score: 173
Period size: 29 Copynumber: 8.6 Consensus size: 28
186852 TTGACTCTTA
* *
186862 AACTTTCCAAAAATTATATTTTGCCCCTA
1 AACTTTCCAAAAATTATATTTTACCCC-G
*
186891 AACTTAT-CAAAAATTATATTTTAACCCTCT
1 AACTT-TCCAAAAATTATATTTT-ACCC-CG
* * **
186921 AACTTTTCAAAAATTACATTTTGACCTTG
1 AACTTTCCAAAAATTATATTTT-ACCCCG
* * * * *
186950 AACTTTTCAAAAATCACATTTTTGTCCTCG
1 AACTTTCCAAAAATTATA-TTTT-ACCCCG
* *
186980 AAC-TTCCAAAAATTCTATTTTTCCCTCG
1 AACTTTCCAAAAATTATATTTTACCC-CG
* * *
187008 AAC-TTCCAAAAATCATATTTTTGCCTCCA
1 AACTTTCCAAAAATTATA-TTTTACC-CCG
187037 AAC-TTCCAAAAATTATATTTTTAACCCCG
1 AACTTTCCAAAAATTATA-TTTT-ACCCCG
*
187066 AACTTTCCAAAAATTACCATTTTACCCCG
1 AACTTTCCAAAAATTA-TATTTTACCCCG
*
187095 AAC-ATCCAAAAATTA
1 AACTTTCCAAAAATTA
187110 CCAGTTTACG
Statistics
Matches: 184, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
27 3 0.02
28 32 0.17
29 90 0.49
30 57 0.31
31 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (28 bp):
AACTTTCCAAAAATTATATTTTACCCCG
Found at i:187092 original size:29 final size:28
Alignment explanation
Indices: 186862--187168 Score: 162
Period size: 29 Copynumber: 10.6 Consensus size: 28
186852 TTGACTCTTA
* * *
186862 AACTTTCCAAAAATTATATTTTGCCCCTA
1 AACTTTCCAAAAATTACATTTTACCCC-G
* *
186891 AACTTAT-CAAAAATTATATTTTAACCCTCT
1 AACTT-TCCAAAAATTACATTTT-ACCC-CG
* **
186921 AACTTTTCAAAAATTACATTTTGACCTTG
1 AACTTTCCAAAAATTACATTTT-ACCCCG
* * * *
186950 AACTTTTCAAAAATCACATTTTTGTCCTCG
1 AACTTTCCAAAAATTACA-TTTT-ACCCCG
*
186980 AAC-TTCCAAAAATT-CTATTTTTCCCTCG
1 AACTTTCCAAAAATTAC-ATTTTACCC-CG
* * * *
187008 AAC-TTCCAAAAATCATATTTTTGCCTCCA
1 AACTTTCCAAAAATTACA-TTTTACC-CCG
*
187037 AAC-TTCCAAAAATTATATTTTTAACCCCG
1 AACTTTCCAAAAATTACA-TTTT-ACCCCG
187066 AACTTTCCAAAAATTACCATTTTACCCCG
1 AACTTTCCAAAAATTA-CATTTTACCCCG
* * **
187095 AAC-ATCCAAAAATTACCAGTTTACGATCG
1 AACTTTCCAAAAATTA-CATTTTAC-CCCG
* *
187124 GA-TGTCCAAAAATTACATTTTTACCCCCG
1 AACTTTCCAAAAATTACA-TTTTA-CCCCG
* *
187153 -AGTATCCAAAAATTAC
1 AACTTTCCAAAAATTAC
187169 CGTTTTACGC
Statistics
Matches: 229, Mismatches: 31, Indels: 36
0.77 0.10 0.12
Matches are distributed among these distances:
27 3 0.01
28 43 0.19
29 123 0.54
30 58 0.25
31 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (28 bp):
AACTTTCCAAAAATTACATTTTACCCCG
Found at i:187111 original size:28 final size:28
Alignment explanation
Indices: 186978--187207 Score: 143
Period size: 29 Copynumber: 8.1 Consensus size: 28
186968 TTTTTGTCCT
* *
186978 CGAACTTCCAAAAATT-CTATTTTTCCC
1 CGAACTTCCAAAAATTACCATTTTACCC
* * *
187005 TCGAACTTCCAAAAATCA-TATTTTTGCCTC
1 -CGAACTTCCAAAAATTACCA-TTTTACC-C
* *
187035 CAAACTTCCAAAAATTA-TATTTTTAACCC
1 CGAACTTCCAAAAATTACCA-TTTT-ACCC
187064 CGAACTTTCCAAAAATTACCATTTTACCC
1 CGAAC-TTCCAAAAATTACCATTTTACCC
* * **
187093 CGAACATCCAAAAATTACCAGTTTACGAT
1 CGAACTTCCAAAAATTACCATTTTAC-CC
*
187122 CGGA-TGTCCAAAAATTA-CATTTTTACCCC
1 CGAACT-TCCAAAAATTACCA-TTTTA-CCC
* * *
187151 CG-AGTATCCAAAAATTACCGTTTTACGCT
1 CGAACT-TCCAAAAATTACCATTTTAC-CC
* *
187180 CGAACCT-CGAAAA-TACCATTTTACCC
1 CGAACTTCCAAAAATTACCATTTTACCC
187206 CG
1 CG
187208 GGCATCTAAA
Statistics
Matches: 164, Mismatches: 24, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
26 3 0.02
27 10 0.06
28 45 0.27
29 83 0.51
30 22 0.13
31 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (28 bp):
CGAACTTCCAAAAATTACCATTTTACCC
Found at i:189614 original size:10 final size:10
Alignment explanation
Indices: 189599--189627 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
189589 AATTGAGTAT
189599 CAGTTGCAGA
1 CAGTTGCAGA
189609 CAGTTGCAGA
1 CAGTTGCAGA
189619 CAGTTGCAG
1 CAGTTGCAG
189628 CTGAGTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (10 bp):
CAGTTGCAGA
Found at i:192320 original size:18 final size:20
Alignment explanation
Indices: 192294--192331 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
192284 GTAAAAATTC
*
192294 AAATATATATAAATT-TAAA
1 AAATATATAAAAATTATAAA
192313 AAAT-TATAAAAATTATAAA
1 AAATATATAAAAATTATAAA
192332 CTCAATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATATATAAAAATTATAAA
Found at i:192401 original size:19 final size:18
Alignment explanation
Indices: 192356--192419 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 18
192346 CATGCGAATT
*
192356 AAATTAAATAATAATTATAA
1 AAATTAAATAA-AA-AATAA
*
192376 AACATTAAATAAAACATAA
1 AA-ATTAAATAAAAAATAA
192395 ATAATTAAAATAAAAAATAA
1 A-AATT-AAATAAAAAATAA
192415 AAATT
1 AAATT
192420 TTAAAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 12 0.31
20 18 0.46
21 9 0.23
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATTAAATAAAAAATAA
Found at i:192423 original size:21 final size:20
Alignment explanation
Indices: 192382--192429 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
192372 ATAAAACATT
*
192382 AAATAAAACATAAATAATTA
1 AAATAAAAAATAAATAATTA
192402 AAATAAAAAATAAA-AATTTTA
1 AAATAAAAAATAAATAA--TTA
192423 AAATAAA
1 AAATAAA
192430 CTTTTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 13 0.52
21 10 0.40
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAAAAAATAAATAATTA
Found at i:193086 original size:22 final size:22
Alignment explanation
Indices: 193052--193098 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
193042 AATAAATATT
*
193052 AATATATATGATATTTTAGATC
1 AATATATATGATATATTAGATC
*
193074 AATATA-ATAGATATATTAGGTC
1 AATATATAT-GATATATTAGATC
193096 AAT
1 AAT
193099 TCGAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (22 bp):
AATATATATGATATATTAGATC
Found at i:194974 original size:17 final size:18
Alignment explanation
Indices: 194954--194992 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
194944 AAGTTTCTTG
*
194954 TTTAGATTAGTT-AGAGT
1 TTTAGATTAATTAAGAGT
*
194971 TTTAGTTTAATTAAGAGT
1 TTTAGATTAATTAAGAGT
194989 TTTA
1 TTTA
194993 TTTAGATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (18 bp):
TTTAGATTAATTAAGAGT
Found at i:210594 original size:50 final size:52
Alignment explanation
Indices: 210423--210613 Score: 253
Period size: 52 Copynumber: 3.7 Consensus size: 52
210413 AAAAGGGTTT
* *
210423 GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGTGGTAC
1 GATGACTATGTGTCATCGTGAGTATAAGAATCCTTTATGGATTATGTGGTAC
* * * *
210475 AATGATTGTGTGTCATCGTGAGTATATA-AATCCTTTATGGATTATGTGGTCC
1 GATGACTATGTGTCATCGTGAGTATA-AGAATCCTTTATGGATTATGTGGTAC
* *
210527 GATGACTATGTGTCATCGTGAGTATAAGAATCCTTTATGGATTATGAGGTTC
1 GATGACTATGTGTCATCGTGAGTATAAGAATCCTTTATGGATTATGTGGTAC
* * *
210579 GATGA-T-TGTGTCATCGTGAGTGTATGATTCCTTTA
1 GATGACTATGTGTCATCGTGAGTATAAGAATCCTTTA
210614 CGAAACAAGA
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
50 26 0.21
51 2 0.02
52 95 0.77
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.39
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATAAGAATCCTTTATGGATTATGTGGTAC
Found at i:210653 original size:102 final size:104
Alignment explanation
Indices: 210422--210653 Score: 297
Period size: 102 Copynumber: 2.2 Consensus size: 104
210412 AAAAAGGGTT
* *
210422 TGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGTGGTACAATGATTGTGTG
1 TGATGACTAAGTGTCATCGTGAGTATAAGAATCCTTTATGGATTATGAGGTACAATGATTGTGTG
* * ** * * *
210487 TCATCGTGAGTATATAAATCCTTTATGGATTATGTGGTC
66 TCATCGTGAGTATATAAATCCTTTACGAAACAAGAGATC
* * * *
210526 CGATGACTATGTGTCATCGTGAGTATAAGAATCCTTTATGGATTATGAGGTTCGATGA-T-TGTG
1 TGATGACTAAGTGTCATCGTGAGTATAAGAATCCTTTATGGATTATGAGGTACAATGATTGTGTG
* * *
210589 TCATCGTGAGTGTATGATTCCTTTACGAAACAAGAGATC
66 TCATCGTGAGTATATAAATCCTTTACGAAACAAGAGATC
*
210628 TGATGACTACGTGTCATCGTGAGTAT
1 TGATGACTAAGTGTCATCGTGAGTAT
210654 TAAATGAAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
102 57 0.52
103 1 0.01
104 52 0.47
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (104 bp):
TGATGACTAAGTGTCATCGTGAGTATAAGAATCCTTTATGGATTATGAGGTACAATGATTGTGTG
TCATCGTGAGTATATAAATCCTTTACGAAACAAGAGATC
Found at i:211221 original size:11 final size:11
Alignment explanation
Indices: 211205--211229 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
211195 AGAAGTACAG
211205 GGTAGAAGAGA
1 GGTAGAAGAGA
211216 GGTAGAAGAGA
1 GGTAGAAGAGA
211227 GGT
1 GGT
211230 TGTTCACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (11 bp):
GGTAGAAGAGA
Found at i:219192 original size:52 final size:52
Alignment explanation
Indices: 219111--219343 Score: 254
Period size: 52 Copynumber: 4.5 Consensus size: 52
219101 AAAAGGGTTT
* * * *
219111 GATGACTAAGTGTTATTGTGAGTATATGAATCCTTTATTAATTATGTGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATCAATTATGTGGTCC
* *
219163 GAGGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATGTGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATCAATTATGTGGTCC
* * * *
219215 GATGACTATGTCTCATAGTGAGTATAAGAATCCTTTA-CAGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATCA-ATTATGTGGTCC
* * * ** * * * *
219267 GATGACTATGTGTCATCGTGAATGTATGATTCCTTTA-CAGAACAAGAGATCT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATCA-ATTATGTGGTCC
*
219319 GATGACTATGTATCATCGTGAGTAT
1 GATGACTATGTGTCATCGTGAGTAT
219344 TAAATGAAAT
Statistics
Matches: 155, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
51 1 0.01
52 154 0.99
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATCAATTATGTGGTCC
Found at i:221987 original size:5 final size:6
Alignment explanation
Indices: 221970--221997 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
221960 AATACATTAT
221970 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
221998 TTCTCAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:228029 original size:30 final size:30
Alignment explanation
Indices: 227993--228054 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
227983 TATTTTATTA
* *
227993 TTAATTTTGTTATTATTTTAGAGGAATTTG
1 TTAATTTTGCTACTATTTTAGAGGAATTTG
*
228023 TTAATTTTGCTACTATTTTAGAGGCATTTG
1 TTAATTTTGCTACTATTTTAGAGGAATTTG
228053 TT
1 TT
228055 TGTTAAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (30 bp):
TTAATTTTGCTACTATTTTAGAGGAATTTG
Found at i:240493 original size:72 final size:72
Alignment explanation
Indices: 240417--240551 Score: 252
Period size: 72 Copynumber: 1.9 Consensus size: 72
240407 AGGAAAGAAA
240417 CCTAATAAAATTCCTAACTTAAAGTTTATAAGGGAAATAAAAATCTAATATAATAGGGAGAATAG
1 CCTAATAAAATTCCTAACTTAAAGTTTATAAGGGAAATAAAAATCTAATATAATAGGGAGAATAG
240482 AAAGAGT
66 AAAGAGT
* *
240489 CCTAATAGAATTCTTAACTTAAAGTTTATAAGGGAAATAAAAATCTAATATAATAGGGAGAAT
1 CCTAATAAAATTCCTAACTTAAAGTTTATAAGGGAAATAAAAATCTAATATAATAGGGAGAAT
240552 TAGTAAAACT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (72 bp):
CCTAATAAAATTCCTAACTTAAAGTTTATAAGGGAAATAAAAATCTAATATAATAGGGAGAATAG
AAAGAGT
Found at i:242238 original size:60 final size:60
Alignment explanation
Indices: 242109--242247 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
242099 TATTGTTATT
* * * *
242109 AAATTTTAATAAAATTATTATTAAATATAATTTAATAAAAATAAGAAAAATAATATAATA
1 AAATCTTAATATAATTATTATTAAAGACAATTTAATAAAAATAAGAAAAATAATATAATA
** * * * *
242169 ATGTTTTAATATAATTATTATTAAAGACAATTTAATAAAAA-ATA-ATATATAATTTAATA
1 AAATCTTAATATAATTATTATTAAAGACAATTTAATAAAAATA-AGAAAAATAATATAATA
242228 AAATACTTAATATAATTATT
1 AAAT-CTTAATATAATTATT
242248 TTCATATTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 15 0.23
60 51 0.77
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (60 bp):
AAATCTTAATATAATTATTATTAAAGACAATTTAATAAAAATAAGAAAAATAATATAATA
Found at i:243026 original size:6 final size:6
Alignment explanation
Indices: 243015--243090 Score: 86
Period size: 6 Copynumber: 13.2 Consensus size: 6
243005 ATTTGTTTAA
* * *
243015 AAATTT AAATTT -ATTTT AAATTT AAATTT -ATTTT AAATTT AAATGT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
243061 -ATTTT AAATTT AAATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT A
243091 TTATCAAATT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
5 11 0.19
6 46 0.81
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:243034 original size:11 final size:11
Alignment explanation
Indices: 243016--243090 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
243006 TTTGTTTAAA
243016 AATTTAAATTT
1 AATTTAAATTT
*
243027 ATTTTAAATTT
1 AATTTAAATTT
*
243038 AAATTT-ATTTT
1 -AATTTAAATTT
*
243049 AAATTTAAATGT
1 -AATTTAAATTT
*
243061 ATTTTAAATTT
1 AATTTAAATTT
*
243072 AAATTTAAGTTT
1 -AATTTAAATTT
243084 AAATTTA
1 -AATTTA
243091 TTATCAAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
11 29 0.56
12 23 0.44
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:243104 original size:18 final size:17
Alignment explanation
Indices: 242983--243090 Score: 146
Period size: 17 Copynumber: 6.2 Consensus size: 17
242973 CAAGCTCCCT
242983 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
243001 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
243018 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
243035 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
243052 TTTAAATGTATTTTAAA
1 TTTAAATTTATTTTAAA
*
243069 TTTAAATTTAAGTTTAAA
1 TTTAAATTT-ATTTTAAA
243087 TTTA
1 TTTA
243091 TTATCAAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
17 56 0.70
18 24 0.30
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:243109 original size:18 final size:17
Alignment explanation
Indices: 243015--243123 Score: 86
Period size: 17 Copynumber: 6.6 Consensus size: 17
243005 ATTTGTTTAA
* *
243015 AAATTTAAATTTATTTT
1 AAATTTAAAATTATTAT
* *
243032 AAATTTAAATTTATTTT
1 AAATTTAAAATTATTAT
*
243049 AAATTT-AAATGTATTTT
1 AAATTTAAAAT-TATTAT
243066 AAATTT--AA--ATT-T
1 AAATTTAAAATTATTAT
* *
243078 AAGTTTAAATTTATTAT
1 AAATTTAAAATTATTAT
243095 CAAATTTAAAATTATTAT
1 -AAATTTAAAATTATTAT
*
243113 GAATTTAAAAT
1 AAATTTAAAAT
243124 AGATAAAGTT
Statistics
Matches: 79, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
12 6 0.08
13 3 0.04
14 1 0.01
16 8 0.10
17 46 0.58
18 15 0.19
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTAAAATTATTAT
Found at i:243119 original size:17 final size:18
Alignment explanation
Indices: 243081--243123 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
243071 TAAATTTAAG
*
243081 TTTAAATTTATTATCAAA
1 TTTAAAATTATTATCAAA
*
243099 TTTAAAATTATTAT-GAA
1 TTTAAAATTATTATCAAA
243116 TTTAAAAT
1 TTTAAAAT
243124 AGATAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTAAAATTATTATCAAA
Found at i:243861 original size:12 final size:12
Alignment explanation
Indices: 243795--243862 Score: 64
Period size: 12 Copynumber: 5.3 Consensus size: 12
243785 TCATTAGGGT
* *
243795 TAATATTGATTA
1 TAATATTAATAA
* *
243807 TTATATTATTAA
1 TAATATTAATAA
243819 TAATATTTATATAA
1 TAATA-TTA-ATAA
243833 TAAATAATTAATAA
1 T-AAT-ATTAATAA
243847 TAATATTAATAA
1 TAATATTAATAA
243859 TAAT
1 TAAT
243863 GACACTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
12 24 0.52
13 6 0.13
14 9 0.20
15 6 0.13
16 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:243861 original size:15 final size:15
Alignment explanation
Indices: 243816--243877 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
243806 ATTATATTAT
*
243816 TAATAATATTTAT-A
1 TAATAATATTAATAA
243830 TAATAA-A-TAATTAA
1 TAATAATATTAA-TAA
243844 TAATAATATTAATAA
1 TAATAATATTAATAA
* * *
243859 TAATGACACTAATAA
1 TAATAATATTAATAA
243874 TAAT
1 TAAT
243878 TTTTAATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.05
13 2 0.05
14 13 0.32
15 20 0.50
16 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (15 bp):
TAATAATATTAATAA
Found at i:245095 original size:59 final size:59
Alignment explanation
Indices: 244948--245404 Score: 387
Period size: 59 Copynumber: 7.8 Consensus size: 59
244938 ATTGTTCAAC
* * * *
244948 AATCCCATTTTTAACCCCAAAACTTC-CAAAATCCCATTTTT-ACCCTC-GAACTTCTAAA
1 AATCCCATTTTT-ACCCTAAAACTTCTAAAAATCCCATTTTTAACCC-CAAAACTTCCAAA
*
245006 AATCCCATTTTTAACCC-AAAACTT-TCAAAAATCCCATTTTTAACTCCAAAACTTCCAAA
1 AATCCCATTTTT-ACCCTAAAACTTCT-AAAAATCCCATTTTTAACCCCAAAACTTCCAAA
* * ** *
245065 AATCCCATTTTTACCCTAGACCTTCTAAAAATCTAATTTTTAACCCCAAAACTTCAAAA
1 AATCCCATTTTTACCCTAAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
* * * * * **
245124 AATCTCATTTTAATCCC-GAAGCTTTTAAAAATCCCAAATTTAACCCCAAAACTTCCAAAA
1 AATCCCATTTTTA-CCCTAAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCC-AAA
*** * *
245184 AATCCCATTTTTACCCCCGAACTTCTAAAAAT-CCAATTTCAACCCCAAAACTTCCAAA
1 AATCCCATTTTTACCCTAAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
* * * * * * * *
245242 AATCCCA-TTTTAACCTCGAAGCTTTTAAAAATCCCAATTTTAACCTCGAAACCTCC-AA
1 AATCCCATTTTTACCCT-AAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
* * * ** *
245300 AATCCCATTTTGACCCTAAAACTACCAAAAATTTCATTTTTAACCCCAAAACTTTCAAA
1 AATCCCATTTTTACCCTAAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
* *** * *
245359 AGGT-CCATTTTTACCCCCTAACTTCT-AAAGTCCCATTTTTGACCCC
1 A-ATCCCATTTTTACCCTAAAACTTCTAAAAATCCCATTTTTAACCCC
245405 GGATTTTTCC
Statistics
Matches: 321, Mismatches: 64, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
57 14 0.04
58 109 0.34
59 168 0.52
60 30 0.09
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (59 bp):
AATCCCATTTTTACCCTAAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCCAAA
Found at i:245173 original size:118 final size:117
Alignment explanation
Indices: 244948--245359 Score: 465
Period size: 118 Copynumber: 3.5 Consensus size: 117
244938 ATTGTTCAAC
* * * ** * *
244948 AATCCCATTTTTAACCCCAAAACTTC-CAAAATCCCATTTTT-ACCCTC-GAACTTCTAAAAATC
1 AATCCCATTTTT-ACCCTAGAACTTCTAAAAATCTAATTTTTAACCC-CAAAACTTCAAAAAATC
* * * * *
245010 CCATTTTTAACCCAAAACTTTCAAAAATCCCATTTTTAACTCCAAAACTTCCAAA
64 CCA-TTTTAACCCGAAGCTTTTAAAAATCCCAATTTTAACCCCAAAACTTCCAAA
* *
245065 AATCCCATTTTTACCCTAGACCTTCTAAAAATCTAATTTTTAACCCCAAAACTTCAAAAAATCTC
1 AATCCCATTTTTACCCTAGAACTTCTAAAAATCTAATTTTTAACCCCAAAACTTCAAAAAATCCC
*
245130 ATTTTAATCCCGAAGCTTTTAAAAATCCCAAATTTAACCCCAAAACTTCCAAAA
66 ATTTTAA-CCCGAAGCTTTTAAAAATCCCAATTTTAACCCCAAAACTTCC-AAA
** * * *
245184 AATCCCATTTTTACCCCCGAACTTCTAAAAATCCAA-TTTCAACCCCAAAACTTCCAAAAATCCC
1 AATCCCATTTTTACCCTAGAACTTCTAAAAATCTAATTTTTAACCCCAAAACTTCAAAAAATCCC
* * *
245248 ATTTTAACCTCGAAGCTTTTAAAAATCCCAATTTTAACCTCGAAACCTCC-AA
66 ATTTTAACC-CGAAGCTTTTAAAAATCCCAATTTTAACCCCAAAACTTCCAAA
* * * * * *
245300 AATCCCATTTTGACCCTAAAACTACCAAAAATTTCATTTTTAACCCCAAAACTTTCAAAA
1 AATCCCATTTTTACCCTAGAACTTCTAAAAATCTAATTTTTAACCCCAAAAC-TTCAAAA
245360 GGTCCATTTT
Statistics
Matches: 250, Mismatches: 37, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
116 39 0.16
117 47 0.19
118 129 0.52
119 35 0.14
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.30
Consensus pattern (117 bp):
AATCCCATTTTTACCCTAGAACTTCTAAAAATCTAATTTTTAACCCCAAAACTTCAAAAAATCCC
ATTTTAACCCGAAGCTTTTAAAAATCCCAATTTTAACCCCAAAACTTCCAAA
Found at i:245368 original size:30 final size:30
Alignment explanation
Indices: 244942--245404 Score: 341
Period size: 29 Copynumber: 15.8 Consensus size: 30
244932 CCCTAAATTG
*
244942 TTCAACAATCCCATTTTTAACCCCAAAAC-
1 TTCAAAAATCCCATTTTTAACCCCAAAACT
* *
244971 TTCCAAAATCCCATTTTT-ACCCTC-GAAC-
1 TTCAAAAATCCCATTTTTAACCC-CAAAACT
244999 TTCTAAAAATCCCATTTTTAA-CCCAAAACT
1 TTC-AAAAATCCCATTTTTAACCCCAAAACT
*
245029 TTCAAAAATCCCATTTTTAACTCCAAAACT
1 TTCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
245059 TCCAAAAATCCCATTTTT-A-CCCTAGACC
1 TTCAAAAATCCCATTTTTAACCCCAAAACT
**
245087 TTCTAAAAATCTAATTTTTAACCCCAAAAC-
1 TTC-AAAAATCCCATTTTTAACCCCAAAACT
* * * *
245117 TTCAAAAAATCTCA-TTTTAATCCCGAAGCT
1 TTC-AAAAATCCCATTTTTAACCCCAAAACT
* **
245147 TTTAAAAATCCCAAATTTAACCCCAAAACT
1 TTCAAAAATCCCATTTTTAACCCCAAAACT
* **
245177 TCCAAAAAATCCCATTTTT-ACCCCCGAAC-
1 TTC-AAAAATCCCATTTTTAACCCCAAAACT
* *
245206 TTCTAAAAAT-CCAATTTCAACCCCAAAACT
1 TTC-AAAAATCCCATTTTTAACCCCAAAACT
* * * *
245236 TCCAAAAATCCCA-TTTTAACCTCGAAGCT
1 TTCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
245265 TTTAAAAATCCCAATTTTAACCTCGAAAC-
1 TTCAAAAATCCCATTTTTAACCCCAAAACT
* * * *
245294 CTCCAAAATCCCA-TTTTGACCCTAAAACT
1 TTCAAAAATCCCATTTTTAACCCCAAAACT
** **
245323 ACCAAAAATTTCATTTTTAACCCCAAAACT
1 TTCAAAAATCCCATTTTTAACCCCAAAACT
* **
245353 TTCAAAAGGT-CCATTTTT-ACCCCCTAAC-
1 TTCAAAA-ATCCCATTTTTAACCCCAAAACT
* * *
245381 TTCTAAAGTCCCATTTTTGACCCC
1 TTCAAAAATCCCATTTTTAACCCC
245405 GGATTTTTCC
Statistics
Matches: 345, Mismatches: 68, Indels: 42
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.01
28 49 0.14
29 164 0.48
30 110 0.32
31 20 0.06
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (30 bp):
TTCAAAAATCCCATTTTTAACCCCAAAACT
Done.