Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002058.1 Hibiscus syriacus cultivar Beakdansim tig00004192_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: 103696
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2208 original size:2 final size:2
Alignment explanation
Indices: 2203--2236 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2193 ACACACACAC
* *
2203 AG AG AG AG AG AG AG AG AG AG GG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2237 GGAAGAGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2237 original size:8 final size:8
Alignment explanation
Indices: 2206--2246 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
2196 CACACACAGA
*
2206 GAGAGAGA
1 GAGAGAGG
2214 GAGAGAGAG
1 GAGAGAG-G
2223 G-GAGAGG
1 GAGAGAGG
2230 GAGAGAGG
1 GAGAGAGG
2238 GA-AGAGG
1 GAGAGAGG
2245 GA
1 GA
2247 CAGGAAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 9 0.30
8 20 0.67
9 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:22117 original size:28 final size:28
Alignment explanation
Indices: 22077--22133 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
22067 AATATCAAAA
*
22077 TAGTCACTCAATTATTTTATTTATGTTT
1 TAGTCACTCAATTATTTTATTTATATTT
22105 TAGTCA-TCTAATTATTTTATTTATATTT
1 TAGTCACTC-AATTATTTTATTTATATTT
22133 T
1 T
22134 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.60
Consensus pattern (28 bp):
TAGTCACTCAATTATTTTATTTATATTT
Found at i:22180 original size:72 final size:73
Alignment explanation
Indices: 22014--22194 Score: 337
Period size: 72 Copynumber: 2.5 Consensus size: 73
22004 CACATTATCT
*
22014 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATGTTTTTAAAAAAATATCAAAATA
1 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATATTTTTAAAAAAATATCAAAATA
22079 GTCACTCA
66 GTCACTCA
22087 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATATTTTT-AAAAAATATCAAAATA
1 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATATTTTTAAAAAAATATCAAAATA
22151 GTCACTCA
66 GTCACTCA
*
22159 ATTATTTTATTTATGTTTTAGTCATCTAATAATTTT
1 ATTATTTTATTTATGTTTTAGTCATCTAATTATTTT
22195 TTTCAAAATC
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
72 59 0.56
73 47 0.44
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (73 bp):
ATTATTTTATTTATGTTTTAGTCATCTAATTATTTTATTTATATTTTTAAAAAAATATCAAAATA
GTCACTCA
Found at i:27371 original size:6 final size:6
Alignment explanation
Indices: 27296--27370 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
27286 GACACGTATT
27296 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
27344 ACCACG ACCACG ACCACG ACCCCG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
27371 CGAGACGAGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:28077 original size:6 final size:6
Alignment explanation
Indices: 28061--28122 Score: 117
Period size: 6 Copynumber: 10.5 Consensus size: 6
28051 TCTCGTCTCG
28061 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
28108 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
28123 AATACGTGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.09
6 51 0.91
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:28257 original size:20 final size:20
Alignment explanation
Indices: 28212--28401 Score: 193
Period size: 20 Copynumber: 9.3 Consensus size: 20
28202 CTTTTGACCG
*
28212 TTGCGATTTTCTAAATCGC-
1 TTGCGATTCTCTAAATCGCA
* *
28231 GTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
28251 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
28271 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
*
28291 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
* *
28314 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
**
28334 TTGCGATTCTAAAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
28354 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
28374 TTGCGATTTTTTCTAAATCGCG
1 TTGCGA--TTCTCTAAATCGCA
28396 TTGCGA
1 TTGCGA
28402 ACTTGGAAGC
Statistics
Matches: 140, Mismatches: 25, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.11
20 89 0.64
21 2 0.01
22 19 0.14
23 14 0.10
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:28290 original size:40 final size:40
Alignment explanation
Indices: 28212--28381 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
28202 CTTTTGACCG
* * *
28212 TTGCGATTTTCTAAATCGC-GTGCGATTCTCTCAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
*
28251 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
* * *
28291 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAATCGCA
* *
28334 TTGCGATTCTAAAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
28374 TTGCGATT
1 TTGCGATT
28382 TTTTCTAAAT
Statistics
Matches: 114, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
39 17 0.15
40 58 0.51
41 3 0.03
42 3 0.03
43 33 0.29
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:28328 original size:83 final size:82
Alignment explanation
Indices: 28218--28401 Score: 316
Period size: 83 Copynumber: 2.2 Consensus size: 82
28208 ACCGTTGCGA
* * *
28218 TTTTCTAAATCGCG-TGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTC
1 TTTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCTA
*
28282 TCAGTCGCATTGCGATT
66 TCAATCGCATTGCGATT
28299 TTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCT
1 TT-TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCT
28364 ATCAATCGCATTGCGATT
65 ATCAATCGCATTGCGATT
28382 TTTTCTAAATCGCGTTGCGA
1 TTTTCTAAATCGCGTTGCGA
28402 ACTTGGAAGC
Statistics
Matches: 97, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
81 2 0.02
82 30 0.31
83 65 0.67
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (82 bp):
TTTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCTA
TCAATCGCATTGCGATT
Found at i:28478 original size:20 final size:20
Alignment explanation
Indices: 28210--28505 Score: 159
Period size: 20 Copynumber: 14.6 Consensus size: 20
28200 TTCTTTTGAC
28210 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
28230 CG-TGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
28249 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
28269 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
28289 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
28312 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * **
28332 CATTGCGATTCTAAAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
28352 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
28372 CATTGCGATTTTTTCTAAATCG
1 CGTTGCGA--TTTTCTAAATCG
** ** *
28394 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
28415 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
28433 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
28455 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
28475 CGTTGCGACTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
28494 CGTTGCGATTTT
1 CGTTGCGATTTT
28506 ATTGGTCATT
Statistics
Matches: 217, Mismatches: 48, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
18 2 0.01
19 32 0.15
20 135 0.62
21 14 0.06
22 20 0.09
23 14 0.06
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:29498 original size:29 final size:29
Alignment explanation
Indices: 29456--29548 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
29446 GGAACATGTG
*
29456 AATAGTTGGAGGACCATTTTATAAGTTTC
1 AATAGTTGGAGGACCATTTTATAACTTTC
* *
29485 AATAGTAT-GAGGACCATTTTGTAACTTTT
1 AATAGT-TGGAGGACCATTTTATAACTTTC
* * * * *
29514 AATAGTCGAATGATCATTTTATAACTTTT
1 AATAGTTGGAGGACCATTTTATAACTTTC
29543 AATAGT
1 AATAGT
29549 CAAGTAACTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 53 0.98
30 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (29 bp):
AATAGTTGGAGGACCATTTTATAACTTTC
Found at i:31632 original size:60 final size:59
Alignment explanation
Indices: 31498--31633 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
31488 ATTTTAGGCT
* * *
31498 AAAG-TACACAAATGATCCCCGATTATAGGTATTATTTTTGTTGAGTCCCTTGATTATTA
1 AAAGTTACA-AAATGATCCCCAATTATAGGTATTAGTTTTGTTGAGTCCCTTGACTATTA
* ** *
31557 GAAGTTACAGGATGATCCCCTAATTATATGGTGTT-GTTTTGTTGAGTCCCTCT-ACTATTA
1 AAAGTTACAAAATGATCCCC-AATTATA-GGTATTAGTTTTGTTGAGTCCCT-TGACTATTA
*
31617 AAAGTTATAAAATGATC
1 AAAGTTACAAAATGATC
31634 ACCCGACTAT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
59 12 0.19
60 44 0.71
61 6 0.10
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (59 bp):
AAAGTTACAAAATGATCCCCAATTATAGGTATTAGTTTTGTTGAGTCCCTTGACTATTA
Found at i:34256 original size:41 final size:41
Alignment explanation
Indices: 34200--34290 Score: 155
Period size: 41 Copynumber: 2.2 Consensus size: 41
34190 CCCGAAATCA
34200 CGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTCT
1 CGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTCT
* *
34241 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTT
1 CGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTCT
34282 CAGTGTTTG
1 C-GTGTTTG
34291 GTTGGAGGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 40 0.85
42 7 0.15
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (41 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTTCT
Found at i:34549 original size:22 final size:22
Alignment explanation
Indices: 34524--34572 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
34514 ATATATTTAT
34524 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
34546 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
*
34568 AAATA
1 TAATA
34573 ATCAAGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:34605 original size:23 final size:23
Alignment explanation
Indices: 34557--34618 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
34547 AATATTTTTA
*
34557 ATATTATAATAAAATAATCAAGT
1 ATATTATAATAATATAATCAAGT
* *
34580 ATATTATAATAATATAA-GATATT
1 ATATTATAATAATATAATCA-AGT
*
34603 ATATTTTAATAATATA
1 ATATTATAATAATATA
34619 TAATAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (23 bp):
ATATTATAATAATATAATCAAGT
Found at i:34721 original size:53 final size:52
Alignment explanation
Indices: 34612--34723 Score: 122
Period size: 53 Copynumber: 2.2 Consensus size: 52
34602 TATATTTTAA
* * *
34612 TAATATA-TAATAAATTATTAATAAAATTTATATTATTTGTTAATTTCATAG
1 TAATATATTAATAAATTATTAATAAAATTAATATTATTTATTAATTTAATAG
* * *
34663 AAATATATTATTAAATTATTAATAATGAA-TAATATTATTTA-TATATTTAATAT
1 TAATATATTAATAAATTATTAATAA--AATTAATATTATTTATTA-ATTTAATAG
34716 TAATATAT
1 TAATATAT
34724 ATCTAATAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
51 6 0.12
52 18 0.36
53 24 0.48
54 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (52 bp):
TAATATATTAATAAATTATTAATAAAATTAATATTATTTATTAATTTAATAG
Found at i:34724 original size:17 final size:18
Alignment explanation
Indices: 34692--34731 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
34682 TAATAATGAA
* *
34692 TAATATTATTTATATATT
1 TAATATTATATATATATC
34710 TAATATTA-ATATATATC
1 TAATATTATATATATATC
34727 TAATA
1 TAATA
34732 ATATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATATTATATATATATC
Found at i:34764 original size:23 final size:22
Alignment explanation
Indices: 34738--34781 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
34728 AATAATATTT
34738 TAATAAAGATATTTAAAATATAC
1 TAATAAA-ATATTTAAAATATAC
* * *
34761 TAATTAATTTTTTAAAATATA
1 TAATAAAATATTTAAAATATA
34782 TAACACTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAATAAAATATTTAAAATATAC
Found at i:35095 original size:19 final size:20
Alignment explanation
Indices: 35071--35121 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
35061 AATGACCAAT
35071 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
35090 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
35110 AAAATCGCAACG
1 AAAATCGCAACG
35122 GTCAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:35115 original size:20 final size:20
Alignment explanation
Indices: 35071--35368 Score: 152
Period size: 20 Copynumber: 14.6 Consensus size: 20
35061 AATGACCAAT
* *
35071 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
35090 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
**
35110 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
35130 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
35151 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
35174 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
35194 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
35214 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
35234 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
35254 AGAGTCGCAACGTGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
35277 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * * *
35297 AGAATCGCAATGCAACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
35317 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
35337 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
35357 AAAATCGCAACG
1 AAAATCGCAACG
35369 GTCAAAAGAA
Statistics
Matches: 227, Mismatches: 40, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.00
19 18 0.08
20 166 0.73
21 14 0.06
23 28 0.12
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:35273 original size:103 final size:103
Alignment explanation
Indices: 35155--35368 Score: 311
Period size: 103 Copynumber: 2.1 Consensus size: 103
35145 GCTTCCAAGT
* * * * *
35155 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCAACTGAGAGAATC
* * * * * *
35220 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAATGCGACTGAGAGAATCGCAACGCGATTGAGAAAA
*
35258 TCGCAACGTGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCAACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCAACTGAGAGAATC
*
35323 GCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAAA
66 GCAATGCGACTGAGAGAATCGCAACGCGATTGAGAAAA
35361 TCGCAACG
1 TCGCAACG
35369 GTCAAAAGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCAACTGAGAGAATC
GCAATGCGACTGAGAGAATCGCAACGCGATTGAGAAAA
Found at i:35283 original size:83 final size:83
Alignment explanation
Indices: 35196--35358 Score: 245
Period size: 83 Copynumber: 2.0 Consensus size: 83
35186 CGATTGATAG
* * * * * * * *
35196 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCAACTGAGAGAATCGCAATGCGACTGAGAGAATCG
*
35261 CAACGTGATTTAGAAGAA
66 CAACGCGATTTAGAAGAA
35279 AATCGCAATGCGACTGAGAGAATCGCAATGCAACTGAGAGAATCGCAATGCGACTGAGAGAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCAACTGAGAGAATCGCAATGCGACTGAGAGAATCG
35344 CAACGCGATTTAGAA
66 CAACGCGATTTAGAA
35359 AATCGCAACG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (83 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCAACTGAGAGAATCGCAATGCGACTGAGAGAATCG
CAACGCGATTTAGAAGAA
Found at i:35363 original size:40 final size:40
Alignment explanation
Indices: 35176--35366 Score: 229
Period size: 40 Copynumber: 4.7 Consensus size: 40
35166 TTTAGAAGAA
* * * *
35176 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTTAGAGAATCGCAATGCGACTGAGAG
* *
35216 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTTAGAGAATCGCAATGCGACTGAGAG
* * *
35256 AGTCGCAACGTGATTTAGAAGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTTAG-AG--AATCGCAATGCGACTGAGAG
* * *
35299 AATCGCAATGCAACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTTAGAGAATCGCAATGCGACTGAGAG
* *
35339 AATCGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAATGCGATTTAGAGAATCGCAA
35367 CGGTCAAAAG
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 95 0.73
41 2 0.02
42 2 0.02
43 31 0.24
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (40 bp):
AATCGCAATGCGATTTAGAGAATCGCAATGCGACTGAGAG
Found at i:35650 original size:6 final size:6
Alignment explanation
Indices: 35455--35646 Score: 258
Period size: 6 Copynumber: 32.0 Consensus size: 6
35445 AGACACGTAT
35455 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
*
35503 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC GACCAC TACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
* * * * *
35551 GACCAC GACCAC GACCAC TACCAC GACCAC GACCAC TACCAC TACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
* * * * * * * *
35599 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC TACCAC
35647 GACCCGACCC
Statistics
Matches: 179, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 179 1.00
ACGTcount: A:0.33, C:0.50, G:0.07, T:0.09
Consensus pattern (6 bp):
TACCAC
Found at i:36348 original size:5 final size:5
Alignment explanation
Indices: 36340--36455 Score: 115
Period size: 5 Copynumber: 22.6 Consensus size: 5
36330 CCGTCTCGTC
* * * * *
36340 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTG TCGTG TCGTG TCGTG TCGTG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
* * * * *
36390 TCGTG TCGTG TCGTG TCGTG TCGTG TCGGG TCGGG TCGGG TCGGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG
36441 TCGTGG TCGTGG TCG
1 TCG-GG TCG-GG TCG
36456 TGGTAATACG
Statistics
Matches: 108, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
5 91 0.84
6 17 0.16
ACGTcount: A:0.00, C:0.20, G:0.49, T:0.31
Consensus pattern (5 bp):
TCGGG
Found at i:36360 original size:15 final size:15
Alignment explanation
Indices: 36335--36455 Score: 134
Period size: 15 Copynumber: 7.9 Consensus size: 15
36325 CGCCGCCGTC
*
36335 TCGTCTCGGGTCGGG
1 TCGTGTCGGGTCGGG
*
36350 TCGGGTCGGGTCGGG
1 TCGTGTCGGGTCGGG
* *
36365 TCGTGTCGTGTCGTG
1 TCGTGTCGGGTCGGG
* *
36380 TCGTGTCGTGTCGTG
1 TCGTGTCGGGTCGGG
* *
36395 TCGTGTCGTGTCGTG
1 TCGTGTCGGGTCGGG
36410 TCGTGTCGGGTCGGG
1 TCGTGTCGGGTCGGG
*
36425 TCGGGTCGGGTCGTGG
1 TCGTGTCGGGTCG-GG
36441 TCGTGGTCGTGGTCG
1 TCGT-GTCG-GGTCG
36456 TGGTAATACG
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
15 80 0.85
16 5 0.05
17 4 0.04
18 5 0.05
ACGTcount: A:0.00, C:0.21, G:0.48, T:0.31
Consensus pattern (15 bp):
TCGTGTCGGGTCGGG
Found at i:36562 original size:20 final size:20
Alignment explanation
Indices: 36537--36576 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36527 TTTTTAACTA
36537 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
* *
36557 TTCTTTTTAGCGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
36577 CTCTCAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.53
Consensus pattern (20 bp):
TTCTTTTGACCGTTGCGATT
Found at i:36592 original size:20 final size:20
Alignment explanation
Indices: 36569--36739 Score: 225
Period size: 20 Copynumber: 8.4 Consensus size: 20
36559 CTTTTTAGCG
36569 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
36589 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
36609 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
*
36629 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
36649 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
*
36672 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
36692 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
36712 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
36732 TTGCGATT
1 TTGCGATT
36740 TTCTTCTAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
20 114 0.86
21 2 0.02
22 3 0.02
23 14 0.11
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:36689 original size:83 final size:83
Alignment explanation
Indices: 36582--36760 Score: 277
Period size: 83 Copynumber: 2.2 Consensus size: 83
36572 CGATTCTCTC
* * * * * * *
36582 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCG
1 AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
36647 CATTGCGATTTTCTTCTA
66 CATTGCGATTTTCTTCTA
* *
36665 AATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
1 AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
36730 CATTGCGATTTTCTTCTA
66 CATTGCGATTTTCTTCTA
36748 AATCGCGTTGCGA
1 AATCGCGTTGCGA
36761 ACTTGGAAGC
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (83 bp):
AATCGCGTTGCGACTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
CATTGCGATTTTCTTCTA
Found at i:36837 original size:20 final size:20
Alignment explanation
Indices: 36547--36864 Score: 147
Period size: 20 Copynumber: 15.6 Consensus size: 20
36537 TTCTTTTGAC
*** *
36547 CGTTGCGATTTTCTTTTTAG
1 CGTTGCGATTTTCTAAATCG
* *
36567 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
36587 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
36607 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
36627 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
36647 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
36670 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
36690 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
36710 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
36730 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
36753 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
36774 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
36792 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
36814 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
36834 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
36853 CGTTGCGATTTT
1 CGTTGCGATTTT
36865 ATTGGTCATT
Statistics
Matches: 240, Mismatches: 47, Indels: 23
0.77 0.15 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.07
20 173 0.72
21 14 0.06
22 6 0.03
23 28 0.12
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:36854 original size:19 final size:20
Alignment explanation
Indices: 36814--36864 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
36804 TTCTTTTTAA
*
36814 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
36834 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
36853 CGTTGCGATTTT
1 CGTTGCGATTTT
36865 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:37091 original size:14 final size:14
Alignment explanation
Indices: 37072--37101 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
37062 CCAGAAATAT
*
37072 AATTTACTTTTCAA
1 AATTTAATTTTCAA
37086 AATTTAATTTTCAA
1 AATTTAATTTTCAA
37100 AA
1 AA
37102 AACCAATTAC
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:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTTAATTTTCAA
Found at i:37753 original size:15 final size:14
Alignment explanation
Indices: 37714--37764 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
37704 TAGAATATAA
*
37714 AAATATTAAAAA-AT
1 AAATA-TAAAAATAC
37728 AAATATAAAAATAC
1 AAATATAAAAATAC
37742 AAATACTAAAAATAC
1 AAATA-TAAAAATAC
37757 AAAT-TAAA
1 AAATATAAA
37765 TTACTAGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
13 10 0.29
14 11 0.32
15 13 0.38
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATATAAAAATAC
Found at i:37992 original size:16 final size:17
Alignment explanation
Indices: 37950--37992 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
37940 ATAAATACTA
37950 TAAAATCTTATAAAATT
1 TAAAATCTTATAAAATT
*
37967 TAAAA-GTTATAAAA-T
1 TAAAATCTTATAAAATT
*
37982 TAAAATTTTAT
1 TAAAATCTTAT
37993 GTATAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATCTTATAAAATT
Found at i:42862 original size:105 final size:105
Alignment explanation
Indices: 42680--43466 Score: 1425
Period size: 105 Copynumber: 7.5 Consensus size: 105
42670 CTACTGCCAG
42680 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
*
42745 TTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
42785 TTGCGTTGTCTGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
*
42850 TTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
42890 TTTCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
42955 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
42995 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
43060 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
43100 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGGGA-TTGAGAAAT
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTTGAGAAAT
43164 GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
65 GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
43205 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
43270 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
43310 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGGA-TTGAGAAAT
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTTGAGAAAT
*
43374 GTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAAC
65 GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
43415 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
43467 GGTAAAACCT
Statistics
Matches: 662, Mismatches: 17, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
104 3 0.00
105 655 0.99
106 4 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (105 bp):
TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATG
TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
Found at i:44300 original size:67 final size:66
Alignment explanation
Indices: 44189--44318 Score: 179
Period size: 67 Copynumber: 2.0 Consensus size: 66
44179 ACCCACCTTA
* ** * *
44189 TTTTCTCTTTTTTCCTCTTTTTCTTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCACCCTAAAC
1 TTTTCTCTTTTTTCCTCTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGAGTTTTCACCCTAAAC
44254 G
66 G
* * *
44255 TTTTTTCTTTTTTCCTCTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGAGTTTTCATCCTAA
1 TTTTCTCTTTTTTCCTC-TTTTTCTTTTTTCAACTTAGGACGCCCTCTCGAGTTTTCACCCTAA
44319 GCGAAGTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
66 16 0.29
67 39 0.71
ACGTcount: A:0.12, C:0.24, G:0.10, T:0.55
Consensus pattern (66 bp):
TTTTCTCTTTTTTCCTCTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGAGTTTTCACCCTAAAC
G
Found at i:56832 original size:34 final size:34
Alignment explanation
Indices: 56794--56941 Score: 278
Period size: 34 Copynumber: 4.4 Consensus size: 34
56784 TTATAAAAAA
56794 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
56828 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
*
56862 GGCATTTATATGAGCTTGAGTTACTATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
*
56896 GGCATTTATATGAGCTTGAGTTACTATTAAGGCG
1 GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
56930 GGCATTTATATG
1 GGCATTTATATG
56942 GAGGTATTAA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 113 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (34 bp):
GGCATTTATATGAGCTTGAGTTAATATTAAGGCG
Found at i:58553 original size:232 final size:219
Alignment explanation
Indices: 58209--58652 Score: 485
Period size: 232 Copynumber: 2.0 Consensus size: 219
58199 GAGTTTAAAT
* * * * * *
58209 TGAAGATCTAAATTGAATGTTCATTGAGGAAACAAGTGGGGATAGCTCTGTTGAGAGAGCGTCAG
1 TGAAGATCTAAATGGAACGTTCATTAAGAAAACAAGCGGGGATAGCTCAGTTGAGAGAGCGTCAG
* * ** *
58274 ACTAAAGATCTAAATGTTACATGTTCAATCTGCGTTCATGGCATCTAATTTTAATTGAATTGGAG
66 ACTAAAGATCTAAAGGTCACATGTTCAATCCACGTTCAT-G-A-C--A-TCTAATTGAATTGGAG
* * * *
58339 TATTATTATAATTTGATTCATTAGTTATTTTAAATGTAATAAAAATCATTATATTGTCGATAAGC
125 TATTATTATAATTTGAGTCATTACTTATTTTAAA--T-AT---AATCACTATATTGTCGATAAAC
**
58404 TTAGTTTAAAGAGCACAAGATCTATGGAGTTCAGAC
184 TTAGTCCAAAGAGCACAAGATCTATGGAGTTCAGAC
* *
58440 TGAAGATCTAAATGGAAACGTTCATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCGTTA
1 TGAAGATCTAAATGG-AACGTTCATTAAGAAAACAAGCGGGGATAGCTCAGTTGAGAGAGCGTCA
* ** * ** *
58505 GACTGAAGATCTGGAGGTCACGTGTTGGATCCATGTTCACT-ACATCTAATTGAATTGGAGTATT
65 GACTAAAGATCTAAAGGTCACATGTTCAATCCACGTTCA-TGACATCTAATTGAATTGGAGTATT
* * * *
58569 ATTATGATTTGAGTCATTACTTATTTTAAATATAGTTACTATATTGTCGATAAACTTAGTCCGAA
129 ATTATAATTTGAGTCATTACTTATTTTAAATATAATCACTATATTGTCGATAAACTTAGTCCAAA
58634 GAGCACAAGATCTATGGAG
194 GAGCACAAGATCTATGGAG
58653 CATCTAATAG
Statistics
Matches: 181, Mismatches: 30, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
220 44 0.24
223 2 0.01
224 1 0.01
226 46 0.25
227 1 0.01
229 1 0.01
230 1 0.01
231 14 0.08
232 70 0.39
233 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (219 bp):
TGAAGATCTAAATGGAACGTTCATTAAGAAAACAAGCGGGGATAGCTCAGTTGAGAGAGCGTCAG
ACTAAAGATCTAAAGGTCACATGTTCAATCCACGTTCATGACATCTAATTGAATTGGAGTATTAT
TATAATTTGAGTCATTACTTATTTTAAATATAATCACTATATTGTCGATAAACTTAGTCCAAAGA
GCACAAGATCTATGGAGTTCAGAC
Found at i:74947 original size:17 final size:17
Alignment explanation
Indices: 74925--74962 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
74915 GATAATGATG
*
74925 TTTGTTTGTATT-TATTA
1 TTTGTTTGAATTAT-TTA
74942 TTTGTTTGAATTATTTA
1 TTTGTTTGAATTATTTA
74959 TTTG
1 TTTG
74963 AGCTTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.68
Consensus pattern (17 bp):
TTTGTTTGAATTATTTA
Found at i:83741 original size:15 final size:15
Alignment explanation
Indices: 83715--83757 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
83705 TAATATATAA
83715 TTATATATTTAATGTC
1 TTATA-ATTTAATGTC
*
83731 TTATAATTTAATGTT
1 TTATAATTTAATGTC
*
83746 TTATAAATTAAT
1 TTATAATTTAAT
83758 TTAATGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (15 bp):
TTATAATTTAATGTC
Found at i:87313 original size:22 final size:23
Alignment explanation
Indices: 87278--87325 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
87268 CATTTAAATT
87278 TTTAACTAATTTATAA-TTATACG
1 TTTAACTAATTTATAATTTA-ACG
*
87301 TTTAA-TACTTTATAATTTAACG
1 TTTAACTAATTTATAATTTAACG
87323 TTT
1 TTT
87326 TATGAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAACG
Found at i:95814 original size:12 final size:12
Alignment explanation
Indices: 95797--95821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
95787 ACAAATTGTC
95797 GACTCAAAAACT
1 GACTCAAAAACT
95809 GACTCAAAAACT
1 GACTCAAAAACT
95821 G
1 G
95822 TAGTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (12 bp):
GACTCAAAAACT
Found at i:96123 original size:30 final size:30
Alignment explanation
Indices: 96088--96155 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
96078 ACCCTAACCC
96088 GACGGGGAAAAACCGTTTATACTAAACGGG
1 GACGGGGAAAAACCGTTTATACTAAACGGG
**
96118 GACGGGGAAAAACCGTTTATGTTAAACGGG
1 GACGGGGAAAAACCGTTTATACTAAACGGG
*
96148 GATGGGGA
1 GACGGGGA
96156 CGGGGACGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.34, C:0.13, G:0.35, T:0.18
Consensus pattern (30 bp):
GACGGGGAAAAACCGTTTATACTAAACGGG
Found at i:96245 original size:2 final size:2
Alignment explanation
Indices: 96238--96266 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
96228 AAATAATTAT
96238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
96267 TTTTTTAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96321 original size:39 final size:42
Alignment explanation
Indices: 96247--96334 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 42
96237 TTATATATAT
* * *
96247 ATATATATATATATATATATTTTTTTAATACATTTAAATTAA
1 ATATATAAATATATATATATATATTTAATACATTTAAATTAA
* *
96289 AT-TATAAATATATATATA-ATATTT-ATATATTTAATTTAA
1 ATATATAAATATATATATATATATTTAATACATTTAAATTAA
96328 ATATATA
1 ATATATA
96335 TACCCGGCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 15 0.38
40 8 0.20
41 15 0.38
42 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (42 bp):
ATATATAAATATATATATATATATTTAATACATTTAAATTAA
Done.