Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002533.1 Hibiscus syriacus cultivar Beakdansim tig00005149_pilon, 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: 91294
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:447 original size:31 final size:31
Alignment explanation
Indices: 387--463 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
377 CGCTATTCTA
387 AGCTTTGCTAAGCTTTACCCTTTCTCTCTAAT
1 AGCTTTGCTAAGCTTTACCC-TTCTCTCTAAT
*
419 AGCTTTGCTAGGCTTTTACCC-TCTCTCTAAT
1 AGCTTTGCTAAGC-TTTACCCTTCTCTCTAAT
* *
450 AGATTTCCTAAGCT
1 AGCTTTGCTAAGCT
464 ATTATTCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 20 0.50
32 12 0.30
33 7 0.17
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (31 bp):
AGCTTTGCTAAGCTTTACCCTTCTCTCTAAT
Found at i:1026 original size:54 final size:55
Alignment explanation
Indices: 919--1026 Score: 121
Period size: 54 Copynumber: 2.0 Consensus size: 55
909 GCTTCACCTT
* * * * * *
919 TTCTCTCATAGCTTTTCTAAGTTATTTCTCGTCCTTGCTTTGCTAGCTTTTTTCA
1 TTCTCTAATAGCTTTGCTAAGCTATTTCTCATCCTGGCTTTGCTAGCTCTTTTCA
* *
974 TTCTCTAATAGC-TTGCTAAGCTATTTCTCATTCTGGCTTTTCTAAGC-CTTTTC
1 TTCTCTAATAGCTTTGCTAAGCTATTTCTCATCCTGGCTTTGCT-AGCTCTTTTC
1027 TCATCCTTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
54 30 0.68
55 14 0.32
ACGTcount: A:0.15, C:0.24, G:0.11, T:0.50
Consensus pattern (55 bp):
TTCTCTAATAGCTTTGCTAAGCTATTTCTCATCCTGGCTTTGCTAGCTCTTTTCA
Found at i:2913 original size:30 final size:31
Alignment explanation
Indices: 2877--2945 Score: 122
Period size: 30 Copynumber: 2.2 Consensus size: 31
2867 AATGAATAAT
2877 AGCTTAGCAAAGCTATTAGAGAG-AGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAGAAGGGTAA
2907 AGCTTAGCAAAGCTATTAGAGAGAAAGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAG-AAGGGTAA
2939 AGCTTAG
1 AGCTTAG
2946 AATAGCGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 23 0.62
32 14 0.38
ACGTcount: A:0.41, C:0.10, G:0.29, T:0.20
Consensus pattern (31 bp):
AGCTTAGCAAAGCTATTAGAGAGAAGGGTAA
Found at i:8397 original size:2 final size:2
Alignment explanation
Indices: 8351--8379 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8341 ATTTAAACCA
8351 AT AT 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 A
8380 CACACATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9874 original size:3 final size:3
Alignment explanation
Indices: 9866--9907 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
9856 ATTTATTTAT
9866 ATA ATA ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA AT
9908 TTTAATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:10780 original size:76 final size:76
Alignment explanation
Indices: 10040--10753 Score: 1266
Period size: 76 Copynumber: 9.4 Consensus size: 76
10030 GAAATATTGA
** * * *
10040 AAACATCATGCACTAAAGGGCTTACAGATGACCCTAAGGTTTTTAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10105 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
10116 AAACATCATGCATTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10181 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
10192 AAACATCATACACTGCAGGACTTATAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10257 AGGCTTTTTGG
66 AGGCTTTTTGG
*
10268 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10333 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
10344 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10409 AGGCTTTTTGG
66 AGGCTTTTTGG
10420 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10485 AGGCTTTTTGG
66 AGGCTTTTTGG
*
10496 AAACATCATGCACTGTAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10561 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
10572 TAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACCTCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10637 AGGCTTTTTGG
66 AGGCTTTTTGG
10648 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
10713 AGGCTTTTTGG
66 AGGCTTTTTGG
10724 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
10754 TGGGAAATAG
Statistics
Matches: 614, Mismatches: 24, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 614 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:11453 original size:22 final size:22
Alignment explanation
Indices: 11428--11504 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
11418 AATAAAGCTT
*
11428 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
11450 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
11472 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
11494 TCATCTTTGAA
1 TCATCTTTGAA
11505 GAGTGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:18176 original size:12 final size:13
Alignment explanation
Indices: 18152--18180 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18142 AAATGAAAAA
18152 AAATGCTAAATGT
1 AAATGCTAAATGT
18165 AAATGC-AAATGT
1 AAATGCTAAATGT
18177 AAAT
1 AAAT
18181 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (13 bp):
AAATGCTAAATGT
Found at i:18189 original size:20 final size:20
Alignment explanation
Indices: 18161--18199 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18151 AAAATGCTAA
*
18161 ATGTAAATGCAAATGTAAAT
1 ATGTAAATGCAAATATAAAT
* *
18181 ATGTGAATGTAAATATAAA
1 ATGTAAATGCAAATATAAA
18200 AATGCAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTAAATGCAAATATAAAT
Found at i:22175 original size:3 final size:3
Alignment explanation
Indices: 22167--22220 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
22157 ATTTATTTAT
* *
22167 ATA ATA ATA ATA ATA ATA TATA TTA ATA ATA ATA ATA ATA ATA AAA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
22213 ATA ATA AT
1 ATA ATA AT
22221 TTTAATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:26958 original size:22 final size:22
Alignment explanation
Indices: 26896--26963 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
26886 GAGAAAAAAA
* *
26896 AACGTGCCACAAAGACAAAAAT
1 AACGTGTCACAAAGACAAAGAT
26918 AACGTGTCACAAAGACAAAGAT
1 AACGTGTCACAAAGACAAAGAT
*
26940 AACTTGTCACAAA-AGCAAAGAT
1 AACGTGTCACAAAGA-CAAAGAT
26962 AA
1 AA
26964 AAGTGCAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
21 1 0.02
22 41 0.98
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.13
Consensus pattern (22 bp):
AACGTGTCACAAAGACAAAGAT
Found at i:28051 original size:13 final size:13
Alignment explanation
Indices: 28033--28059 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28023 AATTCATGTT
28033 GAGTTGGGTATAA
1 GAGTTGGGTATAA
28046 GAGTTGGGTATAA
1 GAGTTGGGTATAA
28059 G
1 G
28060 TTAAATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.41, T:0.30
Consensus pattern (13 bp):
GAGTTGGGTATAA
Found at i:29254 original size:2 final size:2
Alignment explanation
Indices: 29249--29280 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29239 AAAAAAGCAC
29249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29281 TATTTTTTAA
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):
AT
Found at i:34377 original size:18 final size:17
Alignment explanation
Indices: 34354--34388 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
34344 ATGTTCTTCC
34354 ATTCCACAAACAGATATG
1 ATTCCA-AAACAGATATG
*
34372 ATTCCAATACAGATATG
1 ATTCCAAAACAGATATG
34389 CTTCAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (17 bp):
ATTCCAAAACAGATATG
Found at i:34924 original size:14 final size:14
Alignment explanation
Indices: 34905--34933 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34895 ACCAGGTATT
34905 GGTTTCTCATAAAA
1 GGTTTCTCATAAAA
34919 GGTTTCTCATAAAA
1 GGTTTCTCATAAAA
34933 G
1 G
34934 CAGTCTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (14 bp):
GGTTTCTCATAAAA
Found at i:36091 original size:20 final size:20
Alignment explanation
Indices: 36066--36106 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
36056 TAATGAAAAA
*
36066 ATTTATAAACTTAAAAATTT
1 ATTTATAAACATAAAAATTT
**
36086 ATTTATTCACATAAAAATTT
1 ATTTATAAACATAAAAATTT
36106 A
1 A
36107 AAGAAACAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTATAAACATAAAAATTT
Found at i:36287 original size:15 final size:15
Alignment explanation
Indices: 36267--36300 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
36257 ATATTTTGAG
36267 ATATTTTAAATATAT
1 ATATTTTAAATATAT
*
36282 ATATTTTTAATATAT
1 ATATTTTAAATATAT
36297 ATAT
1 ATAT
36301 AAAATTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTTAAATATAT
Found at i:37401 original size:33 final size:34
Alignment explanation
Indices: 37359--37464 Score: 87
Period size: 33 Copynumber: 3.1 Consensus size: 34
37349 GTGGTAAGAA
* *
37359 ATTTATTTTTATGTTAGTAT-TTT-T-TAAATAGTT
1 ATTT-TTTTTATATTAATATATTTATGTAAATA-TT
37392 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATATTTATGTAAATATT
* * *
37427 A-TTTTTTTAT-TAAAATAATATTTATATAATTATT
1 ATTTTTTTTATAT-TAAT-ATATTTATGTAAATATT
37461 ATTT
1 ATTT
37465 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
32 1 0.02
33 27 0.44
34 21 0.34
35 6 0.10
36 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (34 bp):
ATTTTTTTTATATTAATATATTTATGTAAATATT
Found at i:37446 original size:36 final size:34
Alignment explanation
Indices: 37391--37469 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
37381 TTTAAATAGT
*
37391 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
37423 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
37457 TATTATTTATTTA
1 TATTATTTTTTTA
37470 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:39216 original size:21 final size:21
Alignment explanation
Indices: 39186--39233 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39176 GCAGGGGTAC
* *
39186 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
39207 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
39228 ATGCCA
1 ATGCCA
39234 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:39263 original size:21 final size:21
Alignment explanation
Indices: 39237--39330 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
39227 TATGCCATCT
* *
39237 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
39258 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
39279 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
*
39300 CTGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
39321 CCGCAGGGTT
1 CCGCAGGGTT
39331 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:39556 original size:9 final size:9
Alignment explanation
Indices: 39542--39568 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39532 TTTATACAGG
39542 CCCTTCAGC
1 CCCTTCAGC
39551 CCCTTCAGC
1 CCCTTCAGC
39560 CCCTTCAGC
1 CCCTTCAGC
39569 GTCATCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.56, G:0.11, T:0.22
Consensus pattern (9 bp):
CCCTTCAGC
Found at i:40090 original size:14 final size:14
Alignment explanation
Indices: 40071--40100 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40061 TTTTATCATT
*
40071 AACATATATATTAA
1 AACATATACATTAA
40085 AACATATACATTAA
1 AACATATACATTAA
40099 AA
1 AA
40101 TCAACTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:40570 original size:126 final size:126
Alignment explanation
Indices: 40343--40748 Score: 740
Period size: 126 Copynumber: 3.2 Consensus size: 126
40333 TTTAAGTTAT
* *
40343 TCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGAT-A-ATATTCTCTGACGAAATAATGGAAG
40408 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
64 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
40471 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
40536 GCGCCCCCAGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
40597 TCCCCGAGGGACATGAATGATATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
40662 GCGCCCCCGGGAACGTGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
40723 TCCCCGAGGGACATGAATGACATAAT
1 TCCCCGAGGGACATGAATGACATAAT
40749 TAATGGCGGA
Statistics
Matches: 271, Mismatches: 7, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
126 234 0.86
127 1 0.00
128 36 0.13
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:43339 original size:12 final size:13
Alignment explanation
Indices: 43306--43343 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
43296 AAATACATAA
43306 ATATATTTAATAT
1 ATATATTTAATAT
*
43319 ATTTATTTAATAT
1 ATATATTTAATAT
43332 A-ATATTTAATAT
1 ATATATTTAATAT
43344 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:44139 original size:23 final size:23
Alignment explanation
Indices: 44111--44155 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
44101 GATAGATATA
44111 ATATTAACACAAAATCATATAAG
1 ATATTAACACAAAATCATATAAG
44134 ATATTAACACAAAATCATATAA
1 ATATTAACACAAAATCATATAA
44156 AATCTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (23 bp):
ATATTAACACAAAATCATATAAG
Found at i:44911 original size:14 final size:14
Alignment explanation
Indices: 44892--44924 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
44882 TGTTTCACTG
44892 AAAATATTTTTCGA
1 AAAATATTTTTCGA
*
44906 AAAATATTTTTCGT
1 AAAATATTTTTCGA
44920 AAAAT
1 AAAAT
44925 GACTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (14 bp):
AAAATATTTTTCGA
Found at i:45031 original size:45 final size:45
Alignment explanation
Indices: 44967--45057 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
44957 TTTGAAAGAG
44967 ACTGTGTAAACCATTCTCCACTAGTAGATGAAGTTTTTAGAAATT
1 ACTGTGTAAACCATTCTCCACTAGTAGATGAAGTTTTTAGAAATT
45012 ACTGTGTAAACCATTCTCCACTAGTAGATGAAGTTTTTAGAAATT
1 ACTGTGTAAACCATTCTCCACTAGTAGATGAAGTTTTTAGAAATT
45057 A
1 A
45058 TTTATTATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (45 bp):
ACTGTGTAAACCATTCTCCACTAGTAGATGAAGTTTTTAGAAATT
Found at i:45285 original size:24 final size:23
Alignment explanation
Indices: 45258--45331 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
45248 AGTATTATAT
45258 TATATTTTGAAAATTATTAATTAA
1 TATATTTT-AAAATTATTAATTAA
*
45282 TATATTTTAAACA-TATTTATTAA
1 TATATTTTAAA-ATTATTAATTAA
* *
45305 AATATTATT-AGATTATTATATTAA
1 TATATT-TTAAAATTATTA-ATTAA
45329 TAT
1 TAT
45332 TAAATATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.02
23 22 0.54
24 18 0.44
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
TATATTTTAAAATTATTAATTAA
Found at i:45489 original size:28 final size:26
Alignment explanation
Indices: 45425--45490 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
45415 ATAATTGAGT
*
45425 ATATTATATT-ATTAAAAATATTTTA
1 ATATTATATTAATTAAAAATATTTAA
* * *
45450 ATATCATTTTAATTAAAATTATATTAA
1 ATATTATATTAATTAAAAATAT-TTAA
45477 CATATTATATTAAT
1 -ATATTATATTAAT
45491 ATTAAATACA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 8 0.25
26 10 0.31
27 3 0.09
28 11 0.34
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATTATATTAATTAAAAATATTTAA
Found at i:46618 original size:2 final size:2
Alignment explanation
Indices: 46611--46701 Score: 56
Period size: 2 Copynumber: 47.5 Consensus size: 2
46601 TAAATCATAC
*
46611 AT AT AT AT AT AT AT AT AT AT AT AT A- ACT AT AA AT -T AT ACT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
*
46652 AT A- AGT AT AT A- AT AT A- AGT AT AT AT AT AT A- AT -T AT AA AGT
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
46692 AT A- AT AT AT A
1 AT AT AT AT AT A
46702 AGTAAATGTA
Statistics
Matches: 71, Mismatches: 4, Indels: 28
0.69 0.04 0.27
Matches are distributed among these distances:
1 9 0.13
2 57 0.80
3 5 0.07
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:46675 original size:27 final size:27
Alignment explanation
Indices: 46615--46701 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
46605 TCATACATAT
46615 ATATATATATATATA-TATATAACTATA
1 ATATATATATATA-AGTATATAACTATA
46642 A-AT-TATACTTATAAGTATATAA-TATA
1 ATATATATA--TATAAGTATATAACTATA
* *
46668 AGTATATATATATAATTATA-AAGTATA
1 A-TATATATATATAAGTATATAACTATA
46695 ATATATA
1 ATATATA
46702 AGTAAATGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
25 4 0.08
26 16 0.31
27 26 0.50
28 2 0.04
29 4 0.08
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (27 bp):
ATATATATATATAAGTATATAACTATA
Found at i:46713 original size:12 final size:13
Alignment explanation
Indices: 46615--46705 Score: 57
Period size: 13 Copynumber: 6.8 Consensus size: 13
46605 TCATACATAT
46615 ATATATATA-TATA
1 ATATATA-AGTATA
*
46628 TATATATAACTATA
1 -ATATATAAGTATA
**
46642 A-ATTATACTTATA
1 ATA-TATAAGTATA
46655 AGTATATAA-TATA
1 A-TATATAAGTATA
46668 AGTATATATA-TATA
1 A-TATATA-AGTATA
46682 AT-TATAAAGTATA
1 ATATAT-AAGTATA
46695 ATATATAAGTA
1 ATATATAAGTA
46706 AATGTATACA
Statistics
Matches: 66, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.08
13 36 0.55
14 24 0.36
15 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (13 bp):
ATATATAAGTATA
Found at i:46713 original size:19 final size:18
Alignment explanation
Indices: 46612--46702 Score: 69
Period size: 19 Copynumber: 4.7 Consensus size: 18
46602 AAATCATACA
46612 TATATATATATATATATATA-
1 TATA-ATATATA-ATATA-AG
**
46632 TATAACTATA-AATTATACT
1 TATAA-TATATAA-TATAAG
46651 TATAAGTATATAATATAAG
1 TATAA-TATATAATATAAG
46670 TATATATATATAATTATAAAG
1 TATA-ATATATAA-TAT-AAG
46691 TATAATATATAA
1 TATAATATATAA
46703 GTAAATGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.02
19 30 0.50
20 22 0.37
21 7 0.12
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (18 bp):
TATAATATATAATATAAG
Found at i:48469 original size:17 final size:16
Alignment explanation
Indices: 48432--48472 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
48422 ATTATATGGA
48432 TATT-TTATTCATTAT
1 TATTATTATTCATTAT
*
48447 TTTTATTATTCATGTAT
1 TATTATTATTCAT-TAT
48464 TATTATTAT
1 TATTATTAT
48473 ATGTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 3 0.14
16 8 0.36
17 11 0.50
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTATTATTCATTAT
Found at i:52801 original size:18 final size:19
Alignment explanation
Indices: 52780--52822 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
52770 AATAAAAAGG
52780 GCAAAAAGAA-AAAAAAAA
1 GCAAAAAGAAGAAAAAAAA
*
52798 GCAAAAA-AAGAACAAAAA
1 GCAAAAAGAAGAAAAAAAA
52816 G-AAAAAG
1 GCAAAAAG
52823 GGACAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (19 bp):
GCAAAAAGAAGAAAAAAAA
Found at i:53447 original size:22 final size:22
Alignment explanation
Indices: 53419--53462 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
53409 AGCTACCCCA
53419 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
53441 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
53463 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:54472 original size:36 final size:36
Alignment explanation
Indices: 54425--54685 Score: 254
Period size: 36 Copynumber: 7.4 Consensus size: 36
54415 ATTGAAAACA
* * *
54425 TTTCCCTTGAAATAAATTTCGTCTTTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
54461 TTTCCCTTGAAACAAAATTTTGTCTCTC-TGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
54497 TTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
54533 TTTCCCTTGAAACAAA-------TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* * *
54561 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
54597 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
54634 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
54670 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
54686 ATCTTTGAAT
Statistics
Matches: 185, Mismatches: 27, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.01
28 19 0.10
29 2 0.01
35 15 0.08
36 102 0.55
37 45 0.24
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:54636 original size:101 final size:100
Alignment explanation
Indices: 54467--54650 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 100
54457 ATAGTTTCCC
* *
54467 TTGAAACAAAATTTTGTCTCTCTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 TTGAAACAAAATTTCGTCTCCCTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACA
54532 GTTTCCCTTGAAACAAATATTTGAATATGTTTTCT
66 GTTTCCCTTGAAACAAATATTTGAATATGTTTTCT
* * *
54567 TTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGA
1 TTGAAACAAAATTTCGTCTCCC-TGAGACAGTTTCTCTT-GAAATAAATTTTGTCTCTCTTGAGA
*
54631 CAGTTTCTCTTGAAACAAAT
64 CAGTTTCCCTTGAAACAAAT
54651 TTCGTCTATC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
99 12 0.16
100 22 0.29
101 42 0.55
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (100 bp):
TTGAAACAAAATTTCGTCTCCCTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACA
GTTTCCCTTGAAACAAATATTTGAATATGTTTTCT
Found at i:54640 original size:137 final size:136
Alignment explanation
Indices: 54359--54748 Score: 469
Period size: 137 Copynumber: 2.8 Consensus size: 136
54349 ACTCATGATT
* * * * *
54359 GTTTTTCTTAAAACAAGA-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAA-ACATTGAAA
1 GTTTCTCTTGAAACAA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AATA-TTTGAAT
* * ** *
54422 ACATTTCCCTTGAAATAAATTTCGTCTTTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
63 ATATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTC
54487 TCTGAGACA
128 TCTGAGACA
* *
54496 GTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATTTGAATATG
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATTTGAATATA
* * ** * * *
54561 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
66 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTC-
54626 TGAGACA
130 TGAGACA
* * * *
54633 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATATTTGAATAT
* * * * *
54698 ATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
65 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACA
54749 CAAAATCTTC
Statistics
Matches: 215, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
136 62 0.29
137 100 0.47
138 53 0.25
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (136 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATTTGAATATA
TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
GAGACA
Found at i:54747 original size:65 final size:65
Alignment explanation
Indices: 54643--54817 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 65
54633 GTTTCTCTTG
* ** * **
54643 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
54708 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
54773 TA
64 TA
* * *
54775 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
54818 CATATATCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
65 31 0.33
66 6 0.06
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:55582 original size:105 final size:105
Alignment explanation
Indices: 55421--55870 Score: 687
Period size: 105 Copynumber: 4.3 Consensus size: 105
55411 GCCATCCGCG
* * * *
55421 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACGCAAGTTCAACTTCACGACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
55486 GGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
55529 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
55594 ACCGTTGCTTGTCAACAACAACTTCCCAATCGCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
55634 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
55699 ACCGCTGCTTGTCAACAACAACTTCCCAATCTT-AGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TTCAGAGCCA
55739 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
55804 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
55839 ATTTCAACTTCACGACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
55871 TGAACAATGC
Statistics
Matches: 320, Mismatches: 20, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
99 2 0.01
100 35 0.11
101 1 0.00
102 1 0.00
103 2 0.01
104 2 0.01
105 252 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:57061 original size:18 final size:17
Alignment explanation
Indices: 57022--57064 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
57012 ATTATATGAA
57022 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
57038 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
57056 TATTATTAT
1 TATTATTAT
57065 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:57562 original size:2 final size:2
Alignment explanation
Indices: 57555--57588 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
57545 TAATACTTTG
*
57555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57589 TTTTTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:62393 original size:45 final size:45
Alignment explanation
Indices: 62298--62400 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
62288 TGCACATGAG
* * * **
62298 GTGTATCAATGCACTCCTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATAACATTA
* *
62343 GTGTATCGATGCACCCCCTTAAAATACAAACATCGAATAAGATTTA
1 GTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATAACA-TTA
62389 -TGTATCGATGCA
1 GTGTATCGATGCA
62401 TAGATTGTGC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 47 0.94
46 3 0.06
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (45 bp):
GTGTATCGATGCACCCCCTTAAAATAAAAACATCGAATAACATTA
Found at i:63015 original size:18 final size:19
Alignment explanation
Indices: 62989--63046 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
62979 TCGAGGGATT
62989 ATCAGTGGTCTTTCGGGAC
1 ATCAGTGGTCTTTCGGGAC
*
63008 AT-AGTGGT-TCTTCGGAAC
1 ATCAGTGGTCT-TTCGGGAC
*
63026 AATCAGTGGTCCTTCGGGAC
1 -ATCAGTGGTCTTTCGGGAC
63046 A
1 A
63047 AATATTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 1 0.03
18 13 0.41
19 5 0.16
20 13 0.41
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (19 bp):
ATCAGTGGTCTTTCGGGAC
Found at i:63035 original size:20 final size:20
Alignment explanation
Indices: 62989--63047 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
62979 TCGAGGGATT
62989 ATCAGTGG-TCTTTCGGGAC-
1 ATCAGTGGTTC-TTCGGGACA
*
63008 AT-AGTGGTTCTTCGGAACA
1 ATCAGTGGTTCTTCGGGACA
*
63027 ATCAGTGGTCCTTCGGGACA
1 ATCAGTGGTTCTTCGGGACA
63047 A
1 A
63048 ATATTCACTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 12 0.35
19 6 0.18
20 16 0.47
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCAGTGGTTCTTCGGGACA
Found at i:63304 original size:2 final size:2
Alignment explanation
Indices: 63297--63344 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
63287 AATGTATTGT
*
63297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
63338 TT TA TA T
1 TA TA TA T
63345 TATGTATCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:72472 original size:75 final size:75
Alignment explanation
Indices: 72341--72579 Score: 324
Period size: 75 Copynumber: 3.2 Consensus size: 75
72331 CTTAACCTGT
* * * *
72341 TAAAATAAAATATG-CGCTA-ACTATTATGTTAAGCTACCTACCGATTTGTTTGAAGGTTATTAA
1 TAAAATAAAATA-GACGCTACA-TATTATGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
*
72404 TAATGTAAATGG
64 TAATGCAAATGG
*
72416 TAAAATAAAATAGACGCTACATATTATGTTAAACTACCTACCGGTTTATTTAAAGGTTACTAATA
1 TAAAATAAAATAGACGCTACATATTATGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
*
72481 ATGCAAACGG
66 ATGCAAATGG
* *
72491 TAAAATAAAATA-A-GCATTACCTATTATGTTAAACTACCTATCGGTTTGTTTAAAGGTTACTAA
1 TAAAATAAAATAGACGC--TACATATTATGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
72554 TAATGCAAATGG
64 TAATGCAAATGG
*
72566 TAGAATAAAATAGA
1 TAAAATAAAATAGA
72580 TGAAATGTTA
Statistics
Matches: 147, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
73 2 0.01
74 2 0.01
75 141 0.96
76 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (75 bp):
TAAAATAAAATAGACGCTACATATTATGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGCAAATGG
Found at i:72639 original size:23 final size:23
Alignment explanation
Indices: 72613--72684 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
72603 CGGTAAAATA
*
72613 AAATAGGCGTTACCTATTATGTT
1 AAATAGGCGATACCTATTATGTT
* * *
72636 AAATTGAC-ACTACCTATTTTGTT
1 AAATAGGCGA-TACCTATTATGTT
* * *
72659 AAATAAGTGATACCTATTACGTT
1 AAATAGGCGATACCTATTATGTT
72682 AAA
1 AAA
72685 CTAACTATTG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
AAATAGGCGATACCTATTATGTT
Found at i:73604 original size:17 final size:17
Alignment explanation
Indices: 73584--73616 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
73574 ATATTTATTT
*
73584 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
73601 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
73617 TATGCTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:73682 original size:20 final size:21
Alignment explanation
Indices: 73652--73691 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
73642 TGACCGATTA
*
73652 ACAATATTATATTGTATAATT
1 ACAATATTATATTATATAATT
73673 ACAA-ATTATATTATATAAT
1 ACAATATTATATTATATAAT
73692 AATGTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (21 bp):
ACAATATTATATTATATAATT
Found at i:75203 original size:30 final size:29
Alignment explanation
Indices: 75152--75227 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
75142 TCGTTTCATA
75152 TTTGTTTTATTTT-TTTCCA-TTTATTATTAT
1 TTTGTTTT-TTTTGTTTCCATTTTA-T-TTAT
75182 TTTGTTTTTTTTGTTAT-CATTTTATTTAT
1 TTTGTTTTTTTTGTT-TCCATTTTATTTAT
*
75211 GTTGTTTATTTTTGTTT
1 TTTGTTT-TTTTTGTTT
75228 TTTTTTACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
29 15 0.37
30 21 0.51
31 5 0.12
ACGTcount: A:0.13, C:0.04, G:0.08, T:0.75
Consensus pattern (29 bp):
TTTGTTTTTTTTGTTTCCATTTTATTTAT
Found at i:75233 original size:29 final size:29
Alignment explanation
Indices: 75178--75239 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
75168 CCATTTATTA
* *
75178 TTATTTTGTTTTTTTTGTTATCATTTTAT
1 TTATGTTGTTTTTTTTGTTATCATTTTAC
**
75207 TTATGTTGTTTATTTTTGTT-TTTTTTTAC
1 TTATGTTGTTT-TTTTTGTTATCATTTTAC
75236 TTAT
1 TTAT
75240 TTTATCCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76
Consensus pattern (29 bp):
TTATGTTGTTTTTTTTGTTATCATTTTAC
Found at i:79228 original size:95 final size:93
Alignment explanation
Indices: 79042--79228 Score: 223
Period size: 95 Copynumber: 2.0 Consensus size: 93
79032 AGATTATAAT
* * * * **
79042 ATTATATATATCCAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGTTTTA
1 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATAGGTTAAACGCCCCGACTTTA
* * * *
79107 TAGATAATATTCAACTAGCCTGATAAAG
66 TAGATAAGATTCAACTAACATAATAAAG
*
79135 ATTATTATACTATACAATAAAGCTTGAGCTGTCCCTCTA-AGGCAATAGGTTAAATGCCCCGACT
1 ATTA-TATA-TATACAATAAAGCTTGAGCTGTCCCTCTAGA-GCAATAGGTTAAACGCCCCGACT
* *
79199 TTATGGATAAGATTCAGCTAACATAATAAA
63 TTATAGATAAGATTCAACTAACATAATAAA
79229 TGTGTTTACA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
93 4 0.05
94 5 0.06
95 69 0.88
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (93 bp):
ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATAGGTTAAACGCCCCGACTTTA
TAGATAAGATTCAACTAACATAATAAAG
Found at i:80872 original size:15 final size:15
Alignment explanation
Indices: 80833--80864 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
80823 AAGTTTTGTC
*
80833 TCTCTTGAGACAGTT
1 TCTCTTGAAACAGTT
80848 TCTCTTGAAACAGTT
1 TCTCTTGAAACAGTT
80863 TC
1 TC
80865 CTTTGAAAAA
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:0.22, G:0.16, T:0.41
Consensus pattern (15 bp):
TCTCTTGAAACAGTT
Found at i:80888 original size:36 final size:36
Alignment explanation
Indices: 80848--81135 Score: 181
Period size: 36 Copynumber: 7.9 Consensus size: 36
80838 TGAGACAGTT
*
80848 TCTCTTGAAACAGTTTCCTTTGAAAAAAATTTTGTC
1 TCTCTTGAGACAGTTTCCTTTGAAAAAAATTTTGTC
*
80884 TCTCTTGAGACAGTTTCCCTTGAAACAAAA-------
1 TCTCTTGAGACAGTTTCCTTTGAAA-AAAATTTTGTC
* * * * *
80914 TCT-TTGA-ATATGTTTTACATT-AAACAAATTTTTTC
1 TCTCTTGAGACA-G-TTTCCTTTGAAAAAAATTTTGTC
* * * *
80949 TCCCTTGAGACAGTTTCTTTTGGAACTAAGA-TTTGTC
1 TCTCTTGAGACAGTTTCCTTT-GAA-AAAAATTTTGTC
* *
80986 TTTCTTGAGACAGTTT-CTCTTGAAACAAATTTTGTCTTTGTC
1 TCTCTTGAGACAGTTTCCT-TTGAAA-AAA----AT-TTTGTC
* *
81028 TCTCTTGAGACAGTTT-CTCTTGATACAAATTTTGTC
1 TCTCTTGAGACAGTTTCCT-TTGAAAAAAATTTTGTC
* *
81064 TCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
1 TCTCTTGAGACAGTTTCCTTTGAAAAAAATTTTGTC
81100 TCTCTTGAGACAGTTTTCC-TTGAAACAAAATCTTTG
1 TCTCTTGAGACAG-TTTCCTTTGAAA-AAAAT-TTTG
81136 AATATGTTTT
Statistics
Matches: 197, Mismatches: 28, Indels: 52
0.71 0.10 0.19
Matches are distributed among these distances:
28 5 0.03
29 8 0.04
30 9 0.05
35 7 0.04
36 91 0.46
37 40 0.20
38 6 0.03
41 2 0.01
42 29 0.15
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (36 bp):
TCTCTTGAGACAGTTTCCTTTGAAAAAAATTTTGTC
Found at i:81068 original size:21 final size:21
Alignment explanation
Indices: 81043--81107 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
81033 TGAGACAGTT
*
81043 TCTCTTGATACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
81064 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
81081 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
81100 TCTCTTGA
1 TCTCTTGA
81108 GACAGTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 15 0.44
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:81174 original size:101 final size:102
Alignment explanation
Indices: 81041--81229 Score: 308
Period size: 101 Copynumber: 1.9 Consensus size: 102
81031 CTTGAGACAG
* ** *
81041 TTTCTCTTGATACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTT
*
81106 GAGACAGTTTTCCTTGAAACAAAATCTTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
*
81143 TTTC-CTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTT
1 TTTCTCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTT
*
81207 GAGACAGTTTCCCTTTAAACAAA
66 GAGACAGTTTCCCTTGAAACAAA
81230 TTTTGTCTCT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 76 0.95
102 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
Found at i:81280 original size:37 final size:36
Alignment explanation
Indices: 80935--81300 Score: 363
Period size: 36 Copynumber: 10.1 Consensus size: 36
80925 GTTTTACATT
* * **
80935 AAACAAATTTTTTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
* * * *
80971 GAACTAAGA-TTTGTCTTTCTTGAGACAGTTTCTCTTG
1 AAAC-AA-ATTTTATCTCTCTTGAGACAGTTTCCCTTG
* *
81008 AAACAAATTTTGTCTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-----T-TTTATCTCTCTTGAGACAGTTTCCCTTG
* *
81050 ATACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
* *
81086 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
* *
81122 AAACAAA----A--TCT-TTGA-ATATGTTTTCCTTG
1 AAACAAATTTTATCTCTCTTGAGACA-GTTTCCCTTG
* *
81151 AAACAAATTTCATCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
*
81187 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTT
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
*
81223 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
* * * *
81259 AAACAAAGTTTTGTCTCTCTTGATACAATTTCTCTTG
1 AAACAAA-TTTTATCTCTCTTGAGACAGTTTCCCTTG
81296 AAACA
1 AAACA
81301 CCAACCTTTG
Statistics
Matches: 287, Mismatches: 24, Indels: 37
0.82 0.07 0.11
Matches are distributed among these distances:
28 2 0.01
29 21 0.07
30 3 0.01
33 1 0.00
35 4 0.01
36 159 0.55
37 63 0.22
38 1 0.00
42 33 0.11
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.42
Consensus pattern (36 bp):
AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
Found at i:81416 original size:36 final size:34
Alignment explanation
Indices: 81353--81471 Score: 158
Period size: 36 Copynumber: 3.6 Consensus size: 34
81343 CCTGGGGACA
81353 GTTTCTCTTGAAACACAAAAAAATCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAAATCTTTGAAATC
81387 GTTTCTCTTGAAACACAAAAAAAAATCTTTGAAATC
1 GTTTCTCTTGAAACAC--AAAAAAATCTTTGAAATC
* *
81423 GTTTCTCTTG--A-A-AAAAAAACCTTTAAAAAT-
1 GTTTCTCTTGAAACACAAAAAAATCTTT-GAAATC
81453 GTTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
81472 GACCTTCGAG
Statistics
Matches: 76, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
30 21 0.28
31 4 0.05
32 1 0.01
33 2 0.03
34 20 0.26
36 28 0.37
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAATCTTTGAAATC
Found at i:81657 original size:84 final size:84
Alignment explanation
Indices: 81464--81810 Score: 371
Period size: 84 Copynumber: 4.2 Consensus size: 84
81454 TTTCTCTTGA
* * * * * * * *
81464 AACACAAAGACCTTCGAGTTTGACTACACTCAACTTCGAGGGTGCATCATTTACAGCATAACTCA
1 AACA-AAAGACCTTCGAGTTTGATTACACTCAGC-TCAAAGGCGCATCATTTGCAGCATAGCTTA
* * * * *
81529 GGGCTAGAAGGGTTATCTG-C
64 AGTCAAGAAGAGCTATCTGCC
* * *
81549 --C-AAAGACCTTAGAGTTTAATTACACTCAGCTCAAAGGCGCATCATTTGCAGTATAGCTTAAG
1 AACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTTAAG
81611 TCAAGAAGAGCTATCTGCC
66 TCAAGAAGAGCTATCTGCC
* * * *
81630 AACCAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGTGCACCATTTGCAGCATAACTTAAG
1 AACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTTAAG
** * *
81695 TTGAGAAGTGTTATCTGCC
66 TCAAGAAGAGCTATCTGCC
* * * *
81714 AACAAAATACCTTCGAGTTCGATTACACTCAGCTCAAAGACGCATCATTTGCAGCATAGCTCAAG
1 AACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTTAAG
*
81779 GCAAGAA-AGTCTATCTGCC
66 TCAAGAAGAG-CTATCTGCC
81798 AACAAAAGACCTT
1 AACAAAAGACCTT
81811 TGAAATTTAC
Statistics
Matches: 217, Mismatches: 40, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
80 37 0.17
81 26 0.12
83 3 0.01
84 151 0.70
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (84 bp):
AACAAAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCGCATCATTTGCAGCATAGCTTAAG
TCAAGAAGAGCTATCTGCC
Found at i:81762 original size:168 final size:165
Alignment explanation
Indices: 81468--81810 Score: 440
Period size: 168 Copynumber: 2.1 Consensus size: 165
81458 TCTTGAAACA
* * * *
81468 CAAAGACCTTCGAGTTTGACTACACTCAACTTCGAGGGTGCATCATTTACAGCATAACTCAGGGC
1 CAAAGACCTTCGAGTTTGACTACACTCAACTTCAAAGGTGCACCATTTACAGCATAACTCAGAGC
* *
81533 TAGAAGGGTTATCTGCCAAAGACCTTAGAGTTTAATTACACTCAGCTCAAAGGCGCATCATTTGC
66 TAGAAGGGTTATCTGCCAAAGACCTTAGAGTTCAATTACACTCAGCTCAAAGACGCATCATTTGC
* * *
81598 AGTATAGCTTAAGTCAAGAAGAG-CTATCTGCCAAC
131 AGCATAGCTCAAGGCAAGAA-AGTCTATCTGCCAAC
* * * * *
81633 CAAAGACCTTCGAGTTTGATTACACTCAGC-TCAAAGGTGCACCATTTGCAGCATAACTTA-AGT
1 CAAAGACCTTCGAGTTTGACTACACTCAACTTCAAAGGTGCACCATTTACAGCATAACTCAGAGC
* * * *
81696 TGAGAAGTGTTATCTGCCAACAAAATACCTTCGAGTTCGATTACACTCAGCTCAAAGACGCATCA
66 T-AGAAGGGTTATCTG-C--C-AAAGACCTTAGAGTTCAATTACACTCAGCTCAAAGACGCATCA
81761 TTTGCAGCATAGCTCAAGGCAAGAAAGTCTATCTGCCAAC
126 TTTGCAGCATAGCTCAAGGCAAGAAAGTCTATCTGCCAAC
*
81801 AAAAGACCTT
1 CAAAGACCTT
81811 TGAAATTTAC
Statistics
Matches: 153, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
163 2 0.01
164 38 0.25
165 29 0.19
167 3 0.02
168 81 0.53
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (165 bp):
CAAAGACCTTCGAGTTTGACTACACTCAACTTCAAAGGTGCACCATTTACAGCATAACTCAGAGC
TAGAAGGGTTATCTGCCAAAGACCTTAGAGTTCAATTACACTCAGCTCAAAGACGCATCATTTGC
AGCATAGCTCAAGGCAAGAAAGTCTATCTGCCAAC
Found at i:83738 original size:14 final size:14
Alignment explanation
Indices: 83706--83747 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
83696 TTTTTAAAAT
*
83706 TTTTTA-TTATTAA
1 TTTTTATTTATTTA
*
83719 TATTTATTTATTTA
1 TTTTTATTTATTTA
*
83733 TTTTTATTTACTTA
1 TTTTTATTTATTTA
83747 T
1 T
83748 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:83953 original size:22 final size:22
Alignment explanation
Indices: 83934--83998 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
83924 TTTGTTTTAT
*
83934 TTTATTTATTTATTATTTTTTG
1 TTTATTTTTTTATTATTTTTTG
*
83956 TTT-TTTTTGTTATCATTTTTTTG
1 TTTATTTTT-TTATTA-TTTTTTG
83979 TTTATTTTTTTACTTATTTT
1 TTTATTTTTTTA-TTATTTT
83999 ATCCTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 4 0.11
22 8 0.22
23 17 0.47
24 7 0.19
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (22 bp):
TTTATTTTTTTATTATTTTTTG
Found at i:83958 original size:50 final size:47
Alignment explanation
Indices: 83867--83997 Score: 122
Period size: 50 Copynumber: 2.7 Consensus size: 47
83857 TTTCTCTTAT
* * *
83867 TTTCTTATTTGTGTT-TTTTATTTAATTCCATTTCTTTTGTTTTATTTTCG
1 TTTCATATTTGTTTTATTTTATTT-ATT-TATTTCTTTTGTTTT-TTTT-G
*
83917 TTTCATATTTGTTTTATTTTATTTATTTATTATTTTTTGTTTTTTTTG
1 TTTCATATTTGTTTTATTTTATTTATTTATT-TCTTTTGTTTTTTTTG
* * *
83965 TTATCATTTTTTTGTTTATTTT-TTTACTTATTT
1 TT-TCATATTTGT-TTTATTTTATTTATTTATTT
83998 TATCCTTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
48 4 0.06
49 24 0.34
50 34 0.49
51 8 0.11
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (47 bp):
TTTCATATTTGTTTTATTTTATTTATTTATTTCTTTTGTTTTTTTTG
Found at i:83959 original size:23 final size:21
Alignment explanation
Indices: 83928--83998 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 21
83918 TTCATATTTG
*
83928 TTTTATTTTATTTATTTATTAT
1 TTTTTTTTTATTT-TTTATTAT
*
83950 TTTTTGTTTT-TTTTGTTATCAT
1 TTTTT-TTTTATTTT-TTATTAT
83972 TTTTTTGTTTATTTTTTTACTTAT
1 TTTTTT-TTTA-TTTTTTA-TTAT
83996 TTT
1 TTT
83999 ATCCTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.05
22 21 0.52
23 7 0.17
24 10 0.25
ACGTcount: A:0.14, C:0.03, G:0.04, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTATTTTTTATTAT
Found at i:83976 original size:14 final size:12
Alignment explanation
Indices: 83924--83989 Score: 55
Period size: 14 Copynumber: 5.2 Consensus size: 12
83914 TCGTTTCATA
83924 TTTGTTTTATTTT
1 TTTG-TTTATTTT
*
83937 ATTTATTTATTATT
1 -TTTGTTTATT-TT
*
83951 TTT-TGT-TTTT
1 TTTGTTTATTTT
83961 TTTGTTATCATTTT
1 TTTGTT-T-ATTTT
83975 TTTGTTTATTTT
1 TTTGTTTATTTT
83987 TTT
1 TTT
83990 ACTTATTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
10 5 0.11
11 3 0.07
12 11 0.25
13 10 0.23
14 15 0.34
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (12 bp):
TTTGTTTATTTT
Found at i:83995 original size:27 final size:26
Alignment explanation
Indices: 83924--83995 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 26
83914 TCGTTTCATA
* *
83924 TTTGTTTTATTTTATTTATTTATTATTT
1 TTTG-TTTATTTT-TTTACTTATCATTT
*
83952 TTTG--T-TTTTTTT-GTTATCATTTT
1 TTTGTTTATTTTTTTACTTATCA-TTT
83975 TTTGTTTATTTTTTTACTTAT
1 TTTGTTTATTTTTTTACTTAT
83996 TTTATCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
22 5 0.14
23 10 0.28
24 4 0.11
25 2 0.06
26 7 0.19
27 4 0.11
28 4 0.11
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (26 bp):
TTTGTTTATTTTTTTACTTATCATTT
Found at i:86180 original size:21 final size:21
Alignment explanation
Indices: 86129--86181 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
86119 ATTATGACTA
86129 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
86150 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
86171 TCGCAATGCGA
1 TCGCAATGCGA
86182 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:86196 original size:20 final size:21
Alignment explanation
Indices: 86171--86222 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
86161 TTTTCCCAAT
*
86171 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
86191 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
86212 TCGCAATGCGA
1 TCGCAATGCGA
86223 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:86201 original size:41 final size:41
Alignment explanation
Indices: 86156--86363 Score: 136
Period size: 41 Copynumber: 5.1 Consensus size: 41
86146 AATTTCGCGT
*
86156 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
86197 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
86238 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
86279 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
86320 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
86361 TGC
1 TGC
86364 AAATACGTAA
Statistics
Matches: 124, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
39 2 0.02
40 25 0.20
41 95 0.77
43 1 0.01
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:86266 original size:21 final size:21
Alignment explanation
Indices: 86232--86304 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
86222 ATACTGACTA
* *
86232 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
86253 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
86273 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
86294 TCGCAATGCGA
1 TCGCAATGCGA
86305 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:86319 original size:20 final size:20
Alignment explanation
Indices: 86294--86405 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
86284 TTTTCATAAT
86294 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
86314 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
86334 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
86355 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
86375 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
86395 TCGCAATGCGA
1 TCGCAATGCGA
86406 TTTACATAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.74
21 17 0.22
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:86344 original size:61 final size:61
Alignment explanation
Indices: 86156--86385 Score: 164
Period size: 61 Copynumber: 3.8 Consensus size: 61
86146 AATTTCGCGT
** * ** *
86156 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATGCG-ATTAAGTAAATCGCAA
** * * * * * * * **
86218 TGCGATACTGACT-A-TCGCAATGC-AATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCA-TAATTCGCAATGCGAA--TACGTAAATCGCAATGCGA-TTAAGTAAATCGCAA
*
86279 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATGCGATTAAGTAAATCGCAA
*** * *
86340 TGCGAATTAGGA-AAATCGCAATGCAAATACGTAAATCGCAATGCGA
1 TGCG-ATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATGCGA
86386 ATCTTACTAT
Statistics
Matches: 125, Mismatches: 34, Indels: 19
0.70 0.19 0.11
Matches are distributed among these distances:
60 8 0.06
61 78 0.62
62 37 0.30
63 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (61 bp):
TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAATGCGATTAAGTAAATCGCAA
Found at i:86374 original size:41 final size:41
Alignment explanation
Indices: 86294--86387 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
86284 TTTTCATAAT
* * *
86294 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCAAATAAGTAAA
* * *
86334 TCGCAATGCGAATTAGGAAAATCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCAAATAAGTAAA
86375 TCGCAATGCGAAT
1 TCGCAATGCGAAT
86388 CTTACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCAAATAAGTAAA
Found at i:86672 original size:27 final size:27
Alignment explanation
Indices: 86615--86667 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
86605 CATCGCCGGC
* *
86615 GAAATCCCTCACAACCATTCACAGTCA
1 GAAATCCCTCACAACCATTCAAAATCA
*
86642 GAAATCCCTCACAATCATTCAGAAAT
1 GAAATCCCTCACAACCATTCA-AAAT
86668 GGAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.32, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCAAAATCA
Found at i:87060 original size:20 final size:19
Alignment explanation
Indices: 86971--87083 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
86961 GAAACCAAAA
*
86971 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
86990 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
87009 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
87023 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
87042 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
87062 ATCTG-GTTGCGATTTTCATT
1 -TC-GCGTTGCGATTTTCATT
87082 TC
1 TC
87084 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 30 0.39
20 30 0.39
21 2 0.03
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:87082 original size:40 final size:38
Alignment explanation
Indices: 86976--87083 Score: 118
Period size: 34 Copynumber: 2.9 Consensus size: 38
86966 CAAAATCGCA
* *
86976 TTGCGATTTTCATTTCGCGTTGTGATTTTCATTT-CGCG
1 TTGCGATTCTCATTTCG-GTTGCGATTTTCATTTCCGCG
**
87014 TTGCGATTCTC---TC-GTTGCGATAGTCATTTCCGCG
1 TTGCGATTCTCATTTCGGTTGCGATTTTCATTTCCGCG
87048 TTGCGATTCTCATTATCTGGTTGCGATTTTCATTTC
1 TTGCGATTCTCATT-TC-GGTTGCGATTTTCATTTC
87084 AACCAAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
33 13 0.23
34 15 0.26
35 2 0.04
38 12 0.21
40 15 0.26
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.46
Consensus pattern (38 bp):
TTGCGATTCTCATTTCGGTTGCGATTTTCATTTCCGCG
Found at i:90637 original size:13 final size:14
Alignment explanation
Indices: 90606--90640 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
90596 GATTGTTTAA
90606 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
90620 TGATTTGTAAAA-G
1 TGATTTGTAAAAGG
90633 TGATTTGT
1 TGATTTGT
90641 TTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:90862 original size:19 final size:18
Alignment explanation
Indices: 90834--90963 Score: 95
Period size: 19 Copynumber: 7.7 Consensus size: 18
90824 GCGAACTAAA
*
90834 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGA-TTTCAT
*
90853 TTCGCATTGCGA-TTC-C
1 TTCGCATTGCGATTTCAT
*
90869 CTCG--TTGCGATTTCAT
1 TTCGCATTGCGATTTCAT
*
90885 TTCGCATTGCGA----AA
1 TTCGCATTGCGATTTCAT
*
90899 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGA-TTTCAT
90918 TTCGCATTGCGA-TTC-T
1 TTCGCATTGCGATTTCAT
*
90934 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGA-TTTCAT
90951 TTCGCATTGCGAT
1 TTCGCATTGCGAT
90964 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 29
0.68 0.09 0.23
Matches are distributed among these distances:
14 24 0.28
15 3 0.03
16 13 0.15
17 10 0.12
18 7 0.08
19 29 0.34
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (18 bp):
TTCGCATTGCGATTTCAT
Found at i:90875 original size:33 final size:32
Alignment explanation
Indices: 90838--90963 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
90828 ACTAAATTCG
90838 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
90871 CGTTGCGA-TTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
90903 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
90936 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
90964 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
31 3 0.03
32 26 0.30
33 54 0.63
34 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:90910 original size:65 final size:66
Alignment explanation
Indices: 90831--90962 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 66
90821 AACGCGAACT
90831 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGA-TTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
90895 G
66 G
*
90896 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
90961 G
66 G
90962 A
1 A
90963 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 47 0.72
66 18 0.28
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Done.