Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009174.1 Hibiscus syriacus cultivar Beakdansim tig00112737_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: 1358226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:524 original size:60 final size:59
Alignment explanation
Indices: 423--551 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 59
413 AATATTATCT
* * * * **
423 CTAAATTATGACTATCATTCTATATTAGTCCTCAAACTTTTGAATATTTTAATTTCACCC
1 CTAAATTATAACTATCATTCTATAATAGTCCCCAAACTTTTGAACATTCCAATTTCA-CC
* *
483 CTAAATTATAACCT-TCATTCTA-AATGGTCCCCAAACTTTTTGACCATTCCAATTTCACC
1 CTAAATTATAA-CTATCATTCTATAATAGTCCCCAAAC-TTTTGAACATTCCAATTTCACC
*
542 CTAAACTATA
1 CTAAATTATA
552 TCTAACTAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 22 0.38
60 34 0.59
61 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (59 bp):
CTAAATTATAACTATCATTCTATAATAGTCCCCAAACTTTTGAACATTCCAATTTCACC
Found at i:877 original size:2 final size:2
Alignment explanation
Indices: 870--898 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
860 AACTCATTTA
870 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
899 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:889 original size:13 final size:13
Alignment explanation
Indices: 871--896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
861 ACTCATTTAA
871 TATATATATATAT
1 TATATATATATAT
884 TATATATATATAT
1 TATATATATATAT
897 ATTATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:890 original size:15 final size:15
Alignment explanation
Indices: 870--901 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
860 AACTCATTTA
870 ATATATATATATATT
1 ATATATATATATATT
885 ATATATATATATATT
1 ATATATATATATATT
900 AT
1 AT
902 TTTAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:2361 original size:14 final size:14
Alignment explanation
Indices: 2342--2373 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2332 TGTTCGTGAA
2342 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
2356 CGTTCGGTTTTGTT
1 CGTTCGGTTATGTT
2370 CGTT
1 CGTT
2374 TATGTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.28, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:3498 original size:16 final size:16
Alignment explanation
Indices: 3477--3508 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3467 GGGTCTCCAA
*
3477 CGTTTATGTTTGTGTT
1 CGTTTATGTTCGTGTT
3493 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
3509 TGTGTTCGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.09, G:0.25, T:0.59
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:5222 original size:9 final size:9
Alignment explanation
Indices: 5204--5243 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
5194 TCTTTCTTCA
5204 TTCTCTTTTT
1 TTCTC-TTTT
5214 TTCTCTTTT
1 TTCTCTTTT
5223 TTCTCTTTT
1 TTCTCTTTT
*
5232 TTCTTTTTT
1 TTCTCTTTT
5241 TTC
1 TTC
5244 CTCTCTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 24 0.83
10 5 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTCTCTTTT
Found at i:5426 original size:42 final size:41
Alignment explanation
Indices: 5355--5458 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 41
5345 AAAATCTTAT
* *
5355 AGATGGCCCGAAGGACTTATCATATTGCTCGAAAGACTAAC
1 AGATGACCCAAAGGACTTATCATATTGCTCGAAAGACTAAC
* *
5396 AGATGACCCAAAGGATTTAATCATCA-TGCTCGAAAGACTTAC
1 AGATGACCCAAAGGACTT-ATCAT-ATTGCTCGAAAGACTAAC
* *
5438 TGAT-AGCCCGAAGGACTTATC
1 AGATGA-CCCAAAGGACTTATC
5459 GATTTTGGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 19 0.36
42 33 0.62
43 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (41 bp):
AGATGACCCAAAGGACTTATCATATTGCTCGAAAGACTAAC
Found at i:5706 original size:20 final size:20
Alignment explanation
Indices: 5681--5719 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5671 TAATCATCAT
5681 GCTCGAAAGACTTACTGATG
1 GCTCGAAAGACTTACTGATG
*
5701 GCTCGAATGACTTACTGAT
1 GCTCGAAAGACTTACTGAT
5720 TTTGGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (20 bp):
GCTCGAAAGACTTACTGATG
Found at i:5823 original size:257 final size:257
Alignment explanation
Indices: 5279--5862 Score: 830
Period size: 258 Copynumber: 2.3 Consensus size: 257
5269 TTTTATTATT
* * ** ** *
5279 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTATCATATGAAAGTATTTTGCCC
1 TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTGAAA--ATCACGTGAAAACATCTTGCCC
* * * *
5344 AAAAATCTTATAGATGGCCCGAAGGACTTATCATATTGCTCGAAAGACTAACAGATGACCCAAAG
64 GAAGATCTTATAGATGGCCCGAAGGACTTATCATATTGCTCAAAAGACTAACAGAAGACCCAAAG
5409 GATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTATCGATTTTGGAAATAGT
129 GATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTATCGATTTTGGAAATAGT
* *
5474 TTAATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTGAAAATA
194 TTAATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTAAAAACA
* *
5538 CTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTATTGAAAATCACGTGAAAACATCTTACCCG
1 TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTT-TTGAAAATCACGTGAAAACATCTTGCCCG
* * * * * * *
5603 AAGGTCTTATAGATGGGCCGAATGACTTATCATCTTGCTCAAAAGCCTGACAGAAGACCCGAAGG
65 AAGATCTTATAGATGGCCCGAAGGACTTATCATATTGCTCAAAAGACTAACAGAAGACCCAAAGG
* * *
5668 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCTCGAATGACTTA-CTGATTTTGGAAATAGT
130 ATTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTATC-GATTTTGGAAATAGT
* * *
5732 TT-ATTGGTAAGAACCTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACA
194 TTAATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTAAAAACA
* * *
5795 TTAAATGATAAACTTTGGAAATCGCTTTCTCATTTTCTGAAAATTACGTGAAAACATCCTGCCCG
1 TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTT-TGAAAATCACGTGAAAACATCTTGCCCG
5860 AAG
65 AAG
5863 TAGGGGTGTT
Statistics
Matches: 289, Mismatches: 33, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
256 1 0.00
257 118 0.41
258 132 0.46
259 33 0.11
260 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (257 bp):
TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTGAAAATCACGTGAAAACATCTTGCCCGA
AGATCTTATAGATGGCCCGAAGGACTTATCATATTGCTCAAAAGACTAACAGAAGACCCAAAGGA
TTTAATCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTATCGATTTTGGAAATAGTTT
AATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTAAAAACA
Found at i:6168 original size:17 final size:17
Alignment explanation
Indices: 6146--6184 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
6136 TGAATCAAAT
*
6146 TAATTAGATATTTTTTA
1 TAATTAGATATTATTTA
*
6163 TAATTAGTTATTATTTA
1 TAATTAGATATTATTTA
6180 -AATTA
1 TAATTA
6185 ATTGTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:6508 original size:42 final size:42
Alignment explanation
Indices: 6407--6514 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
6397 GCCCGAAGGT
* * *
6407 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAAGA
1 CTTACAGATGGCCCGAATGACTTATCATCATGCTCGAAAAGA
** *
6449 CTTACAGATTACTCGAATGA-TTAAATCATCATGCTCG-AAAGA
1 CTTACAGATGGCCCGAATGACTT--ATCATCATGCTCGAAAAGA
*
6491 CTTACTGATGGCCCGAATGACTTA
1 CTTACAGATGGCCCGAATGACTTA
6515 CCAATTTTGA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.06
42 36 0.68
43 14 0.26
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (42 bp):
CTTACAGATGGCCCGAATGACTTATCATCATGCTCGAAAAGA
Found at i:6914 original size:258 final size:258
Alignment explanation
Indices: 6393--7169 Score: 920
Period size: 258 Copynumber: 2.9 Consensus size: 258
6383 AATGAATACC
*
6393 CCTAGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAAGACTTACAGAT
1 CCTA-CCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCG-AAAGACTTACAAAT
* * * * *
6458 TACTCGAATGATTAAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTACCAATTTT
64 AACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTT
6523 GAAAATAGTTTACTAGGTAAGAAAC--T-----TCACTTTCTTACTTTTCAAAAATTTCATTTTA
129 GAAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTA
* *
6581 TGAAAATAGTAAATGAGAAACTTTGGAAATCGATTTCTCATTTTTTAAAAATCATGTGAAAACAT
194 TGAAAATAATAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAACAT
** * ** * *
6646 TATGCCCGAAGGTCTTATAGATGGCTTGAAAGACTTATAATCTTGCTCGAAAGACTTACAAATAA
1 CCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATAA
*
6711 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTACCAATTTTGA
66 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGA
* *
6776 AAATAGTTTACTTGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTTTG
131 AAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATG
* * * * *
6841 AAAATACTAAATGTGAAACTTTGGAAATCGCTTTCCCATTTTTTGAAAATCATGTGAAAATAT
196 AAAATAATAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAACAT
* ** *
6904 CCTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTGAAAAATGA
1 CCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACT------T-A
*
6969 CCCGAAGGATTTAATCATCATGCTCGAAGGAATTAATCATCATGCTCGAAAGACTTACTGATGGC
59 --C-AA--A--T-A--A-C---C-CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
* * * * * *
7034 CCGAAGGACTTACCGATTATGGAAATAGTTTAATGGGTAAGAAACTTTGGAAATCGCTTTCTTAC
109 CCGAAGGACTTACCAATTTTGAAAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTAC
* * ** *
7099 TTTTCAAAAATTTCATTTTCTGAAAAAAATCAAATGAGAAACTTTAAAAATCACTTTCTCATTTT
174 TTTTCAAAAATTTCATTTTATGAAAATAAT-AAATGAGAAACTTTGGAAATCGCTTTCTCATTTT
*
7164 TCAAAA
238 TTAAAA
7170 TAACTTAATG
Statistics
Matches: 443, Mismatches: 51, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
251 96 0.22
252 41 0.09
253 2 0.00
258 135 0.30
264 1 0.00
265 1 0.00
267 1 0.00
268 2 0.00
270 1 0.00
272 1 0.00
273 1 0.00
275 1 0.00
276 1 0.00
279 1 0.00
280 125 0.28
281 33 0.07
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (258 bp):
CCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATAA
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGA
AAATAGTTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATG
AAAATAATAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTTAAAAATCATGTGAAAACAT
Found at i:6999 original size:22 final size:22
Alignment explanation
Indices: 6971--7018 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
6961 AAAAATGACC
*
6971 CGAAGGATTTAATCATCATGCT
1 CGAAGGAATTAATCATCATGCT
6993 CGAAGGAATTAATCATCATGCT
1 CGAAGGAATTAATCATCATGCT
7015 CGAA
1 CGAA
7019 AGACTTACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (22 bp):
CGAAGGAATTAATCATCATGCT
Found at i:10966 original size:19 final size:19
Alignment explanation
Indices: 10942--10984 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
10932 TTTATGTAAG
10942 TATATGT-TATATCATATTA
1 TATATGTATATATC-TATTA
10961 TATATGTATATATCTATTA
1 TATATGTATATATCTATTA
*
10980 AATAT
1 TATAT
10985 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
TATATGTATATATCTATTA
Found at i:10972 original size:10 final size:9
Alignment explanation
Indices: 10916--10973 Score: 50
Period size: 8 Copynumber: 6.6 Consensus size: 9
10906 ACCATGTATG
10916 TATAT-TTA
1 TATATGTTA
10924 TATATGTT-
1 TATATGTTA
* *
10932 TTTATGTAA
1 TATATGTTA
10941 GTATATGTTA
1 -TATATGTTA
*
10951 TATCATATTA
1 TAT-ATGTTA
10961 TATATG-TA
1 TATATGTTA
10969 TATAT
1 TATAT
10974 CTATTAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 18 0.45
9 7 0.17
10 15 0.38
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (9 bp):
TATATGTTA
Found at i:11814 original size:19 final size:19
Alignment explanation
Indices: 11760--11808 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
11750 ATGACGACTC
11760 CAATTCAAAATTTTCAAAT
1 CAATTCAAAATTTTCAAAT
11779 CAATTCAAAATTTTCAAAT
1 CAATTCAAAATTTTCAAAT
*
11798 TAATTCAAAAT
1 CAATTCAAAAT
11809 CGTCAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (19 bp):
CAATTCAAAATTTTCAAAT
Found at i:16721 original size:3 final size:3
Alignment explanation
Indices: 16715--16760 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
16705 AATTTTTTTC
*
16715 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
16761 AATAAATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:25669 original size:93 final size:93
Alignment explanation
Indices: 25528--25717 Score: 278
Period size: 93 Copynumber: 2.0 Consensus size: 93
25518 AGAAGACTCA
* * *
25528 ATAGCATCTTCTGGAAGTGTACTTTGAGTTATCTGATCTGGTTTGGTATGAAAC-CACAGAATCA
1 ATAGCATCTTCTGGAAGTGTACTTTGAATTATCTGATCTGATTTGGTATG-AACTC-CAAAATCA
25592 ATCATTGAATTT-AGAAGATGAA-TATGCTC
64 ATCATTGAATTTGA-AAGATGAATTATGCTC
*
25621 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAATCAAT
1 ATAGCATCTTCTGGAAGTGTACTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAATCAAT
* *
25686 CATTGGATTTGAAAGATGAATTTTGCTC
66 CATTGAATTTGAAAGATGAATTATGCTC
25714 ATAG
1 ATAG
25718 TAGAAATAAG
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
92 29 0.33
93 59 0.67
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTACTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAATCAAT
CATTGAATTTGAAAGATGAATTATGCTC
Found at i:27941 original size:54 final size:54
Alignment explanation
Indices: 27859--27970 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
27849 CAATGATTGA
* ***
27859 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
** *
27913 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGCACTGTTAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
27967 GAAC
1 GAAC
27971 CTGCTATTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
Found at i:28377 original size:22 final size:22
Alignment explanation
Indices: 28347--28401 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
28337 AGATTCTCAC
* *
28347 TTCAGAGATGACAAATTTTCTT
1 TTCAAAGATGACAAATTCTCTT
* * *
28369 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
28391 TTCAAAGATGA
1 TTCAAAGATGA
28402 AAGCTTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCTCTT
Found at i:29164 original size:76 final size:76
Alignment explanation
Indices: 29077--30256 Score: 2104
Period size: 76 Copynumber: 15.6 Consensus size: 76
29067 CTATATCTCA
* *
29077 CATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
29142 AGCCTTAGGGT
66 AGCCTTAGGGT
29153 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
29218 AGCCTTAGGGT
66 AGCCTTAGGGT
*
29229 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
29294 AGCCTTAGGGT
66 AGCCTTAGGGT
*
29305 AATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
29370 AAGCCTTAGGGT
65 AAGCCTTAGGGT
29382 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
29447 AGCCTTAGGGT
66 AGCCTTAGGGT
29458 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
29523 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
29534 CATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
29599 AGCCTTAGGGT
66 AGCCTTAGGGT
*
29610 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
29675 AGCCTTATGGT
66 AGCCTTAGGGT
29686 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
29751 AGCC-------
66 AGCCTTAGGGT
29755 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
29820 AACCTTAAGGT
66 AGCCTTAGGGT
*
29831 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
29896 AGCCTTAAGGT
66 AGCCTTAGGGT
* * *
29907 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGGAACTTTTGGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
29972 AGCCTTCGGGT
66 AGCCTTAGGGT
*
29983 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
30048 AGCCTTCGGGT
66 AGCCTTAGGGT
*
30059 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
30124 AGCCTTCGGGT
66 AGCCTTAGGGT
*
30135 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
30200 AGCCTTCGGGT
66 AGCCTTAGGGT
30211 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
30257 TCATCTGTAA
Statistics
Matches: 1075, Mismatches: 21, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
69 68 0.06
76 933 0.87
77 74 0.07
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:30252 original size:47 final size:47
Alignment explanation
Indices: 30198--30303 Score: 203
Period size: 47 Copynumber: 2.3 Consensus size: 47
30188 TGATGTTTTC
*
30198 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAA
30245 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAA
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAA
30292 AAAGCCTTCGGG
1 AAAGCCTTCGGG
30304 AACTTTTTGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (47 bp):
AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAA
Found at i:30256 original size:123 final size:123
Alignment explanation
Indices: 30122--30379 Score: 507
Period size: 123 Copynumber: 2.1 Consensus size: 123
30112 TGATGTTTTC
*
30122 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
30187 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
66 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
30245 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
30310 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
66 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
30368 AAAGCCTTCGGG
1 AAAGCCTTCGGG
30380 AACTTTTTGA
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 134 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (123 bp):
AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAA
Found at i:30258 original size:199 final size:199
Alignment explanation
Indices: 30046--30455 Score: 811
Period size: 199 Copynumber: 2.1 Consensus size: 199
30036 TGATGTTTTC
*
30046 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
30111 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
66 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
30176 TCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
131 TCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
30241 CCAA
196 CCAA
30245 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
30310 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
66 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
30375 TCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
131 TCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
30440 CCAA
196 CCAA
30444 AAAGCCTTCGGG
1 AAAGCCTTCGGG
30456 AACTTTTTGA
Statistics
Matches: 210, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 210 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (199 bp):
AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
TCGGGAACTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
CCAA
Found at i:30325 original size:76 final size:76
Alignment explanation
Indices: 30245--30564 Score: 588
Period size: 76 Copynumber: 4.2 Consensus size: 76
30235 ATGTTTCCAA
*
30245 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTCCAAAAAGCCTTCGGGAACTTT
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
30310 TTGATGTTTTC
66 TTGATGTTTTC
30321 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
30386 TTGATGTTTTC
66 TTGATGTTTTC
30397 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
30462 TTGATGTTTTC
66 TTGATGTTTTC
* *
30473 AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
30538 TTGATGTTTTC
66 TTGATGTTTTC
*
30549 AAA-CCCTCAGGGTCAT
1 AAAGCCTTC-GGGTCAT
30565 TCATAAGACC
Statistics
Matches: 239, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
75 4 0.02
76 235 0.98
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (76 bp):
AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTT
TTGATGTTTTC
Found at i:30728 original size:3 final size:3
Alignment explanation
Indices: 30722--30756 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
30712 TTCTTACTAT
*
30722 TTA TTA TTA TTA TTA TTA TTA TATA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
30757 AAATAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:33818 original size:5 final size:5
Alignment explanation
Indices: 33808--33855 Score: 96
Period size: 5 Copynumber: 9.6 Consensus size: 5
33798 CTCAGGCAGC
33808 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AAT
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AAT
33856 GGTGTAGGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:35987 original size:17 final size:15
Alignment explanation
Indices: 35965--36006 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
35955 TATGAGATAA
35965 AAAATAATATTATTAT
1 AAAATAATATTATT-T
35981 GAAAAT-ATAATTATTT
1 -AAAATAAT-ATTATTT
35997 AAAATAATAT
1 AAAATAATAT
36007 ATAACTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAATAATATTATTT
Found at i:36225 original size:22 final size:22
Alignment explanation
Indices: 36197--36239 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
36187 GTTAGATAAT
36197 ATTTATAAATTAATATTAAAAC
1 ATTTATAAATTAATATTAAAAC
36219 ATTTATAAATTAATATTAAAA
1 ATTTATAAATTAATATTAAAA
36240 TTTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTATAAATTAATATTAAAAC
Found at i:36258 original size:2 final size:2
Alignment explanation
Indices: 36253--36295 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
36243 ATATTTTTTA
*
36253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36295 A
1 A
36296 ATTTGATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41178 original size:2 final size:2
Alignment explanation
Indices: 41173--41225 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
41163 CTATAATGGG
41173 AT AT AT AT AT 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 AT AT AT AT AT
41215 AT AT AT AT AT A
1 AT AT AT AT AT A
41226 AGTCTCCCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41987 original size:37 final size:37
Alignment explanation
Indices: 41932--42040 Score: 200
Period size: 37 Copynumber: 2.9 Consensus size: 37
41922 AACATAACGT
*
41932 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
41969 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
42006 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAG
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAG
42041 AATTCATAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:42413 original size:3 final size:3
Alignment explanation
Indices: 42407--42469 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
42397 TTTTTCTTAC
42407 TAT TAT TAT TA- TAT ATACT TCAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT -TA-T T-AT TAT TAT TAT TAT TAT TAT TAT TAT
*
42453 TAT T-T TA- TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT T
42470 TTGTTTTATC
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 8 0.16
3 36 0.71
4 5 0.10
5 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:42862 original size:29 final size:30
Alignment explanation
Indices: 42836--42901 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
42826 ATTCATTTTC
*
42836 TTTATTT-TTTTTATCTTCTTTACATTTGT
1 TTTATTTATTTGTATCTTCTTTACATTTGT
* *
42865 TTTATTTATTTGTATTTTCTTCT-TATTT-T
1 TTTATTTATTTGTATCTTCTT-TACATTTGT
42894 TTTATTTA
1 TTTATTTA
42902 CTCGTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 16 0.50
30 15 0.47
31 1 0.03
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (30 bp):
TTTATTTATTTGTATCTTCTTTACATTTGT
Found at i:46859 original size:17 final size:19
Alignment explanation
Indices: 46831--46879 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
46821 TATTTTAAAT
46831 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
46849 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
46868 CACCGATGCACT
1 CATCGATGCACT
46880 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:53853 original size:16 final size:16
Alignment explanation
Indices: 53829--53869 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
53819 AAAGGGAGAG
* *
53829 AAGTGTTAAGTGTTAA
1 AAGTTTTAACTGTTAA
53845 AAGTTTTAACTGTTAA
1 AAGTTTTAACTGTTAA
53861 AAGTTTTAA
1 AAGTTTTAA
53870 AGGGGAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.41
Consensus pattern (16 bp):
AAGTTTTAACTGTTAA
Found at i:54440 original size:19 final size:19
Alignment explanation
Indices: 54413--54450 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54403 ATCGAATGCA
*
54413 CTTGATGCATCGATGCACT
1 CTTGATGCACCGATGCACT
*
54432 CTTGGTGCACCGATGCACT
1 CTTGATGCACCGATGCACT
54451 AAGGGTCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (19 bp):
CTTGATGCACCGATGCACT
Found at i:56628 original size:81 final size:81
Alignment explanation
Indices: 56493--56656 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
56483 TTTTATCTTT
56493 AGATCGATATCTTAGCACTGTCTCTACTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
1 AGATCGATATCTTAGCACTGTCTCTACTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
56558 AAAGAACTGAAATAGA
66 AAAGAACTGAAATAGA
*
56574 AGATCGATATCTTAGCACTGTCTCTGCTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
1 AGATCGATATCTTAGCACTGTCTCTACTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
56639 AAAGAACTGAAATAGA
66 AAAGAACTGAAATAGA
56655 AG
1 AG
56657 TGTTCTAAAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (81 bp):
AGATCGATATCTTAGCACTGTCTCTACTAAAGGAGTTTATGGAGCTTGGACAAATGAGAGATTTC
AAAGAACTGAAATAGA
Found at i:57830 original size:19 final size:19
Alignment explanation
Indices: 57806--57844 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
57796 TCTCAACATG
57806 AAGGAGCAATGTCATCATA
1 AAGGAGCAATGTCATCATA
57825 AAGGAGCAATGTCATCATA
1 AAGGAGCAATGTCATCATA
57844 A
1 A
57845 GCGACTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (19 bp):
AAGGAGCAATGTCATCATA
Found at i:57975 original size:14 final size:14
Alignment explanation
Indices: 57956--57983 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57946 AGATCTCCAG
57956 TCATTCAAATACAA
1 TCATTCAAATACAA
57970 TCATTCAAATACAA
1 TCATTCAAATACAA
57984 CTAGTCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
TCATTCAAATACAA
Found at i:57993 original size:18 final size:18
Alignment explanation
Indices: 57954--58003 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
57944 TCAGATCTCC
57954 AGTCATTCAAATAC-A--
1 AGTCATTCAAATACAACT
57969 A-TCATTCAAATACAACT
1 AGTCATTCAAATACAACT
57986 AGTCATTCAAATACAACT
1 AGTCATTCAAATACAACT
58004 GAAAGAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.39
15 2 0.06
17 1 0.03
18 16 0.52
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (18 bp):
AGTCATTCAAATACAACT
Found at i:60695 original size:19 final size:19
Alignment explanation
Indices: 60671--60723 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
60661 AGAGGGCTAA
**
60671 AAAGTATCAGTACTTATAT
1 AAAGTATCAAAACTTATAT
60690 AAAGTATCAAAACTTATAT
1 AAAGTATCAAAACTTATAT
60709 AAAGTATCAAAACTT
1 AAAGTATCAAAACTT
60724 TAGCAGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
AAAGTATCAAAACTTATAT
Found at i:62195 original size:14 final size:14
Alignment explanation
Indices: 62178--62224 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 14
62168 TACTTATTAT
62178 TATATTATTATTTA
1 TATATTATTATTTA
62192 TATATTATTA-TTA
1 TATATTATTATTTA
*
62205 -ATAATA-TATTTA
1 TATATTATTATTTA
62217 T-TATTATT
1 TATATTATT
62225 GTACACGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
11 2 0.07
12 12 0.43
13 4 0.14
14 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATATTATTATTTA
Found at i:67457 original size:90 final size:90
Alignment explanation
Indices: 67295--67475 Score: 335
Period size: 90 Copynumber: 2.0 Consensus size: 90
67285 TTGCTTGATT
67295 TGGAATCCCAAGAAAAATGAGAGCTCCCCCATCATGCTCATTTCATATTCGCTTTGCATTAGCTT
1 TGGAATCCCAAGAAAAATGAGAGCTCCCCCATCATGCTCATTTCATATTCGCTTTGCATTAGCTT
*
67360 AGAAAATTCTTGGCAACGAACATCA
66 AGAAAATTCTTGGCAAAGAACATCA
* *
67385 TGGAGTCCTAAGAAAAATGAGAGCTCCCCCATCATGCTCATTTCATATTCGCTTTGCATTAGCTT
1 TGGAATCCCAAGAAAAATGAGAGCTCCCCCATCATGCTCATTTCATATTCGCTTTGCATTAGCTT
67450 AGAAAATTCTTGGCAAAGAACATCA
66 AGAAAATTCTTGGCAAAGAACATCA
67475 T
1 T
67476 TAGTATAACC
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (90 bp):
TGGAATCCCAAGAAAAATGAGAGCTCCCCCATCATGCTCATTTCATATTCGCTTTGCATTAGCTT
AGAAAATTCTTGGCAAAGAACATCA
Found at i:71011 original size:23 final size:23
Alignment explanation
Indices: 70981--71028 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
70971 CAAGAGGGGA
70981 GTGAATTGGTAATTAAAATTTTG
1 GTGAATTGGTAATTAAAATTTTG
71004 GTGAATTGGTAATTAAAATTTTG
1 GTGAATTGGTAATTAAAATTTTG
71027 GT
1 GT
71029 AGAAGCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (23 bp):
GTGAATTGGTAATTAAAATTTTG
Found at i:73989 original size:26 final size:26
Alignment explanation
Indices: 73960--74035 Score: 136
Period size: 26 Copynumber: 3.0 Consensus size: 26
73950 GGAAAGAAAT
*
73960 GTTAGACACCAAACTGAAACGAAAAC
1 GTTAGGCACCAAACTGAAACGAAAAC
73986 GTTAGGCACCAAACTGAAACGAAAAC
1 GTTAGGCACCAAACTGAAACGAAAAC
74012 GTTAGGCACCAAACTGAAAC-AAAA
1 GTTAGGCACCAAACTGAAACGAAAA
74036 TAAATATAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 4 0.08
26 45 0.92
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (26 bp):
GTTAGGCACCAAACTGAAACGAAAAC
Found at i:77105 original size:15 final size:15
Alignment explanation
Indices: 77085--77123 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
77075 TAAAATCAAG
77085 AATAAAAATTAAGAA
1 AATAAAAATTAAGAA
* *
77100 AATAAACATTAAGAT
1 AATAAAAATTAAGAA
*
77115 GATAAAAAT
1 AATAAAAAT
77124 AAATAAAGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.23
Consensus pattern (15 bp):
AATAAAAATTAAGAA
Found at i:79398 original size:12 final size:12
Alignment explanation
Indices: 79381--79409 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
79371 TTGTTGTGCT
79381 TGCTCTTCGGGC
1 TGCTCTTCGGGC
79393 TGCTCTTCGGGC
1 TGCTCTTCGGGC
79405 TGCTC
1 TGCTC
79410 AGGTTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (12 bp):
TGCTCTTCGGGC
Found at i:89458 original size:39 final size:39
Alignment explanation
Indices: 89415--89493 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
89405 ACATCAGGTG
*
89415 GTCTTCCCAAGGAGTTTTGACAAGACTAGATATTGGGTT
1 GTCTTCCCAAGGAGTTTCGACAAGACTAGATATTGGGTT
* *
89454 GTCTTCCTAAGGAGTTTCGACAAGACTGGATATTGGGTT
1 GTCTTCCCAAGGAGTTTCGACAAGACTAGATATTGGGTT
89493 G
1 G
89494 AAATGGTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (39 bp):
GTCTTCCCAAGGAGTTTCGACAAGACTAGATATTGGGTT
Found at i:98989 original size:21 final size:18
Alignment explanation
Indices: 98965--99003 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
98955 AAATTAATCT
98965 ATTACTTAATAATTTATTTTA
1 ATTAC-TAAT-ATTT-TTTTA
98986 ATTACTAATATTTTTTTA
1 ATTACTAATATTTTTTTA
99004 GTATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 4 0.22
21 5 0.28
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTACTAATATTTTTTTA
Found at i:99009 original size:20 final size:22
Alignment explanation
Indices: 98964--99009 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
98954 AAAATTAATC
98964 TATTACTTAATAATTTATTTTA
1 TATTACTTAATAATTTATTTTA
98986 -ATTAC-TAAT-ATTT-TTTTA
1 TATTACTTAATAATTTATTTTA
99004 GTATTA
1 -TATTA
99010 TTTTTGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.23
19 4 0.18
20 8 0.36
21 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTACTTAATAATTTATTTTA
Found at i:102666 original size:3 final size:3
Alignment explanation
Indices: 102658--102735 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
102648 ATAAAGTGTA
102658 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
102706 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
102736 GCATTATTGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:106236 original size:16 final size:16
Alignment explanation
Indices: 106215--106251 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
106205 ATGGGGCCGA
106215 TGCCAACAACCACCGC
1 TGCCAACAACCACCGC
*
106231 TGCCAACAACCTCCGC
1 TGCCAACAACCACCGC
106247 TGCCA
1 TGCCA
106252 CGGCTACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.49, G:0.14, T:0.11
Consensus pattern (16 bp):
TGCCAACAACCACCGC
Found at i:107789 original size:31 final size:31
Alignment explanation
Indices: 107753--107862 Score: 157
Period size: 31 Copynumber: 3.5 Consensus size: 31
107743 ATTCAACGTC
107753 CAAGTGACTAAAACTTAATAAAACAATAACA
1 CAAGTGACTAAAACTTAATAAAACAATAACA
* * * *
107784 TAAGTGACCAAAATTTAATAAAATAATAACA
1 CAAGTGACTAAAACTTAATAAAACAATAACA
107815 CAAGTGACTAAAACTTAATAAAACAATAACA
1 CAAGTGACTAAAACTTAATAAAACAATAACA
* * *
107846 CAATTGACCAAGACTTA
1 CAAGTGACTAAAACTTA
107863 TGTTTTTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.22
Consensus pattern (31 bp):
CAAGTGACTAAAACTTAATAAAACAATAACA
Found at i:108580 original size:18 final size:17
Alignment explanation
Indices: 108547--108579 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
108537 CAGATGAGCA
108547 ATATAAAAGACTAAAAT
1 ATATAAAAGACTAAAAT
108564 ATATCAAAAGA-TAAAA
1 ATAT-AAAAGACTAAAA
108580 AAATGTGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
ATATAAAAGACTAAAAT
Found at i:110143 original size:53 final size:53
Alignment explanation
Indices: 110062--110175 Score: 192
Period size: 53 Copynumber: 2.1 Consensus size: 53
110052 TTATGATGTG
110062 ATTTATAAGGTTTAGAGTACAATACAAAAATAGAAATAATCATAGGCTAATTTC
1 ATTTA-AAGGTTTAGAGTACAATACAAAAATAGAAATAATCATAGGCTAATTTC
* * *
110116 ATTTAAAGGTTTAGAGTACAATACAAAAATAGAAATAATTATGGGCTAATTTT
1 ATTTAAAGGTTTAGAGTACAATACAAAAATAGAAATAATCATAGGCTAATTTC
110169 ATTTAAA
1 ATTTAAA
110176 AATATACTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 52 0.91
54 5 0.09
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (53 bp):
ATTTAAAGGTTTAGAGTACAATACAAAAATAGAAATAATCATAGGCTAATTTC
Found at i:115062 original size:13 final size:14
Alignment explanation
Indices: 115044--115073 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
115034 AGTTGGACAA
115044 TCTTCATATGCA-G
1 TCTTCATATGCACG
115057 TCTTCATATGCACG
1 TCTTCATATGCACG
115071 TCT
1 TCT
115074 GTAATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (14 bp):
TCTTCATATGCACG
Found at i:119771 original size:27 final size:27
Alignment explanation
Indices: 119740--119791 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
119730 AATAAAAATC
* *
119740 AAACTTATTTAAGGAGTATTTTTTTGG
1 AAACTTATTTAAGGAATATTATTTTGG
119767 AAACTTATTTAAGGAATATTATTTT
1 AAACTTATTTAAGGAATATTATTTT
119792 AATAGTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (27 bp):
AAACTTATTTAAGGAATATTATTTTGG
Found at i:125638 original size:39 final size:38
Alignment explanation
Indices: 125595--125672 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 38
125585 GTATTTACAT
*
125595 TTTATT-TTAATAATTTAATATTAATATCCTTAAAAATAA
1 TTTATTCTTAATAATTT-ATATTAAT-TACTTAAAAATAA
*
125634 TTTATTGCTTAATAATTTATTTTAATTACTTAAAAATAA
1 TTTATT-CTTAATAATTTATATTAATTACTTAAAAATAA
125673 ATAAAATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 18 0.51
40 7 0.20
41 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (38 bp):
TTTATTCTTAATAATTTATATTAATTACTTAAAAATAA
Found at i:125708 original size:16 final size:14
Alignment explanation
Indices: 125674--125702 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
125664 TAAAAATAAA
125674 TAAAATTCATATAT
1 TAAAATTCATATAT
125688 TAAAATTCATATAT
1 TAAAATTCATATAT
125702 T
1 T
125703 TTAAAAATAA
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:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAATTCATATAT
Found at i:125736 original size:21 final size:21
Alignment explanation
Indices: 125677--125753 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
125667 AAATAAATAA
* *
125677 AATTCATATATTAAAATTCAT
1 AATTTATATATTAAAATTCAC
*
125698 ATATTT-TA-A-AAATAATTCAC
1 A-ATTTATATATTAA-AATTCAC
125718 AATTTATATATTAAAATTCAC
1 AATTTATATATTAAAATTCAC
**
125739 CGTTTATATATTAAA
1 AATTTATATATTAAA
125754 GTTAACTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 6 0.13
20 10 0.22
21 24 0.53
22 5 0.11
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (21 bp):
AATTTATATATTAAAATTCAC
Found at i:127325 original size:25 final size:25
Alignment explanation
Indices: 127280--127333 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
127270 TTAATTACTT
*
127280 AAAATAATTAAAATTCATATATTTTA
1 AAAATAATTAAAATT-ATATATATTA
*
127306 AAAATAATTCATAATT-TATATATTA
1 AAAATAATT-AAAATTATATATATTA
127331 AAA
1 AAA
127334 TTCACCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 9 0.36
27 5 0.20
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
AAAATAATTAAAATTATATATATTA
Found at i:127337 original size:21 final size:21
Alignment explanation
Indices: 127286--127358 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
127276 ACTTAAAATA
127286 ATTAAAATTCATATATTT-TA-
1 ATTAAAATTCATA-ATTTATAT
*
127306 A-AAATAATTCATAATTTATAT
1 ATTAA-AATTCATAATTTATAT
**
127327 ATTAAAATTCACCATTTATAT
1 ATTAAAATTCATAATTTATAT
*
127348 ATTAAAGTTCA
1 ATTAAAATTCA
127359 CTTTAATTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.14
20 11 0.25
21 25 0.57
22 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (21 bp):
ATTAAAATTCATAATTTATAT
Found at i:127363 original size:19 final size:21
Alignment explanation
Indices: 127319--127359 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
127309 ATAATTCATA
127319 ATTTATATATTAAAATTCACC
1 ATTTATATATTAAAATTCACC
*
127340 ATTTATATATTAAAGTTCAC
1 ATTTATATATTAAAATTCAC
127360 TTTAATTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTTATATATTAAAATTCACC
Found at i:135137 original size:21 final size:21
Alignment explanation
Indices: 135111--135150 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
135101 CCCCCTTTGA
*
135111 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
135132 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
135151 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:140266 original size:20 final size:20
Alignment explanation
Indices: 140193--140275 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
140183 AACAGAACCC
*
140193 CAGGGGGGTATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
*
140213 --GTGGGGGAATCGGTTCCCCTT
1 CAG-GGGGGAATCGATT-CCC-T
** * *
140234 CAAATGAGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
140255 CAGGGGGGAATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
140275 C
1 C
140276 TGCACCAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 1 0.02
19 11 0.23
20 19 0.40
21 3 0.06
22 3 0.06
23 11 0.23
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:147022 original size:17 final size:17
Alignment explanation
Indices: 147000--147034 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
146990 TAAGGGGGAG
147000 TAATTTCAAAACTTGAT
1 TAATTTCAAAACTTGAT
147017 TAATTTCAAAACTTGAT
1 TAATTTCAAAACTTGAT
147034 T
1 T
147035 TCAAAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
TAATTTCAAAACTTGAT
Found at i:150468 original size:16 final size:16
Alignment explanation
Indices: 150447--150491 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
150437 ATATTTTTTC
150447 TTATAAAATATTTCAT
1 TTATAAAATATTTCAT
150463 TTATAAAAATATTTCAT
1 TTAT-AAAATATTTCAT
*
150480 CT-TAAAATATTT
1 TTATAAAATATTT
150492 TTTATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.33
16 5 0.19
17 13 0.48
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATAAAATATTTCAT
Found at i:154415 original size:59 final size:59
Alignment explanation
Indices: 154352--154777 Score: 393
Period size: 59 Copynumber: 7.2 Consensus size: 59
154342 TGGTACTATA
* *
154352 TGTGCTAAAATGGTAGGGGAATCATACTGAGTGTATGAATTCCCATATGGAGCACTGAG
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
*
154411 TGTGCTAAAATGGTAAGGGAATCACACTGAGTGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
*
154470 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCATTGAG
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
** * * * * * * * * *
154529 TGTGCTAAAATAATAAGGAAATCATATTGAATATATGGATTTACAGATAGG-GCA-TTATA
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATAT-GGAGCACTGA-G
* * * *** *
154588 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTTTGGATTTCCAGAAAAAGCACTAAG
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
* * * * * * *
154647 GGTGCTACAA-GGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGG-GCACTTCA-
1 TGTGCTAAAATGG-TAAGGGAATCATACTGAGT-GTATGAATTTCCATAT-GGAGCAC-TGAG
* * * **
154706 TGTGCTAAAAATGGTAAAGGAATCATACT-AATGGTATGGATTCTCGCATA-GG-GCACTTCG
1 TGTGCT-AAAATGGTAAGGGAATCATACTGAGT-GTATGAATT-TC-CATATGGAGCACTGAG
154766 TGTGCTAAAATG
1 TGTGCTAAAATG
154778 AGGAGGAAAT
Statistics
Matches: 306, Mismatches: 48, Indels: 26
0.81 0.13 0.07
Matches are distributed among these distances:
58 6 0.02
59 247 0.81
60 46 0.15
61 3 0.01
62 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (59 bp):
TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
Found at i:154442 original size:31 final size:31
Alignment explanation
Indices: 154404--154503 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
154394 CCATATGGAG
154404 CACTGAGTGTGCTAAAATGGTAAGGGAATCA
1 CACTGAGTGTGCTAAAATGGTAAGGGAATCA
* * * *** * *
154435 CACTGAGTGT-ATGAATTTCCATATGG-A--G
1 CACTGAGTGTGCTAAAATGGTA-AGGGAATCA
154463 CACTGAGTGTGCTAAAATGGTAAGGGAATCA
1 CACTGAGTGTGCTAAAATGGTAAGGGAATCA
*
154494 TACTGAGTGT
1 CACTGAGTGT
154504 ATGAATTTCC
Statistics
Matches: 47, Mismatches: 17, Indels: 10
0.64 0.23 0.14
Matches are distributed among these distances:
28 13 0.28
29 6 0.13
30 6 0.13
31 22 0.47
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (31 bp):
CACTGAGTGTGCTAAAATGGTAAGGGAATCA
Found at i:154495 original size:118 final size:117
Alignment explanation
Indices: 154351--154791 Score: 437
Period size: 118 Copynumber: 3.7 Consensus size: 117
154341 ATGGTACTAT
*
154351 ATGTGCTAAAATGGTAGGGGAATCATACTGAGTGTATGAATTCCCATATGGAGCACTGAGTGTGC
1 ATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTCCCATATGGAGCACTGAGTGTGC
* * * * * *
154416 TAAAATGGTAAGGGAATCACACTGAGTGTATGAATTTCCATAT-GGAGCACTG
66 TAAAATGGTAAGGAAATCATACTGAATGTATGGATTTACATATAGG-GCACTC
* *
154468 AGTGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTTCCATATGGAGCATTGAGTGTG
1 A-TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTCCCATATGGAGCACTGAGTGTG
** * * * * *
154533 CTAAAATAATAAGGAAATCATATTGAATATATGGATTTACAGATAGGGCATTAT
65 CTAAAATGGTAAGGAAATCATACTGAATGTATGGATTTACATATAGGGCACT-C
* * * * *** * *
154587 ATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTTTGGATTTCCAGAAAAAGCACTAAGGGTGC
1 ATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTCCCATATGGAGCACTGAGTGTGC
* *
154652 TACAA-GGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGGCACTTC
66 TAAAATGG-TAAGGAAATCATACTGAAT-GTATGGATTTACATATAGGGCAC-TC
* * * **
154705 ATGTGCTAAAAATGGTAAAGGAATCATACT-AATGGTATGGATTCTCGCATA-GG-GCACTTCGT
1 ATGTGCT-AAAATGGTAAGGGAATCATACTGAGT-GTATGAATTC-C-CATATGGAGCACTGAGT
*
154767 GTGCTAAAATGAG-GAGGAAATCATA
62 GTGCTAAAATG-GTAAGGAAATCATA
154792 TTAAGTATGT
Statistics
Matches: 267, Mismatches: 45, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
117 4 0.01
118 199 0.75
119 58 0.22
120 2 0.01
121 4 0.01
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (117 bp):
ATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGAATTCCCATATGGAGCACTGAGTGTGC
TAAAATGGTAAGGAAATCATACTGAATGTATGGATTTACATATAGGGCACTC
Found at i:154916 original size:44 final size:44
Alignment explanation
Indices: 154867--155112 Score: 384
Period size: 44 Copynumber: 5.6 Consensus size: 44
154857 GTACAAATTT
* * * * *
154867 CTTATGAAATTATAGTAAGTAGATTGATAAAATAAGCTTACGAG
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
* * *
154911 CTTATGGAATAAAGGTAAGTATATTGGTAAAATAAGCTTACAAA
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
154955 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
* *
154999 CTTATTGAATAATGGTAAGTATATTGGTAAAATAAGCTTATGAG
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
155043 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
1 CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
* *
155087 CTTATGGATTAATGGTATGTATATTG
1 CTTATGGAATAATGGTAAGTATATTG
155113 ATAAGAAATC
Statistics
Matches: 185, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 185 1.00
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (44 bp):
CTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAG
Found at i:157913 original size:24 final size:24
Alignment explanation
Indices: 157861--157907 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
157851 TTTAACAAAG
157861 TGGAAGACAAACAAGAATCTTTAC
1 TGGAAGACAAACAAGAATCTTTAC
157885 TGGAAGACAAACAAGAATCTTTA
1 TGGAAGACAAACAAGAATCTTTA
157908 TAGGAAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (24 bp):
TGGAAGACAAACAAGAATCTTTAC
Found at i:170358 original size:23 final size:23
Alignment explanation
Indices: 170332--170393 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
170322 TTTTATTTGT
170332 TAATTATAATTTAA-TATTATATA
1 TAATTATAA-TTAATTATTATATA
170355 TAATTATTAA-TAATTATTATATA
1 TAATTA-TAATTAATTATTATATA
*
170378 T-ATATATAATAAATTA
1 TAAT-TATAATTAATTA
170394 CAATTTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 8 0.24
23 23 0.68
24 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATTATAATTAATTATTATATA
Found at i:171677 original size:64 final size:63
Alignment explanation
Indices: 171592--171752 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
171582 TTATTTAAGG
* * * *
171592 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATATGATTTA
1 TGCATCGATGCATATGTAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * *
171656 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGTAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
171720 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCAT-ATGTAGTGCATCGATGCAT
171753 ACCTTCTTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 60 0.71
65 23 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (63 bp):
TGCATCGATGCATATGTAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:172104 original size:18 final size:18
Alignment explanation
Indices: 172069--172104 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
172059 AAAATGGGTA
* *
172069 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
172087 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
172105 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:173110 original size:18 final size:18
Alignment explanation
Indices: 173083--173152 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
173073 TTAAGGAGTA
*
173083 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
173101 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
* *
173123 GTCCTTCGGGACATATTG
1 GTCCTACGGGACATAGTG
173141 GTCCTACGGGAC
1 GTCCTACGGGAC
173153 GAATACTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 25 0.57
20 4 0.09
22 15 0.34
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:175515 original size:2 final size:2
Alignment explanation
Indices: 175508--175546 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
175498 CATGATATGA
175508 AT AT AT AT AT 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 AT AT AT AT AT A
175547 AAGGAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:176565 original size:64 final size:63
Alignment explanation
Indices: 176480--176640 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
176470 TTGTTTAAGG
* * * *
176480 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
176544 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
176608 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
176641 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:176993 original size:18 final size:18
Alignment explanation
Indices: 176958--176993 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
176948 AAAATGGGTA
* *
176958 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
176976 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
176994 AAAGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:178194 original size:22 final size:18
Alignment explanation
Indices: 178152--178221 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
178142 TTAAGGAGTA
*
178152 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
178170 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
*
178192 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
178210 GTCCTACGGGAC
1 GTCCTACGGGAC
178222 GAATACTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 26 0.58
20 4 0.09
22 15 0.33
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:179929 original size:28 final size:28
Alignment explanation
Indices: 179898--179953 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
179888 TGTCGGACAA
179898 AACCAAAATCCTAAATCATGCGCATTGT
1 AACCAAAATCCTAAATCATGCGCATTGT
*
179926 AACCAAAATCCTAAATCATGTGCATTGT
1 AACCAAAATCCTAAATCATGCGCATTGT
179954 GTGGTAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (28 bp):
AACCAAAATCCTAAATCATGCGCATTGT
Found at i:181030 original size:21 final size:21
Alignment explanation
Indices: 181001--181040 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
180991 CACAGACAAG
*
181001 GGATCGATCCTTTTTGAAAAT
1 GGATCGATCCTTCTTGAAAAT
*
181022 GGATTGATCCTTCTTGAAA
1 GGATCGATCCTTCTTGAAA
181041 GGGATCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (21 bp):
GGATCGATCCTTCTTGAAAAT
Found at i:181140 original size:21 final size:21
Alignment explanation
Indices: 181092--181150 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
181082 TAGTGAGTTT
*
181092 GGGATCGATCTTTTTTGAAAA
1 GGGATCGATCTTTTTTCAAAA
** *
181113 GATATCGATCTTTTTTCACAA
1 GGGATCGATCTTTTTTCAAAA
181134 GGGATCGATCCTTTTTT
1 GGGATCGAT-CTTTTTT
181151 TTAGAAAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 24 0.77
22 7 0.23
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (21 bp):
GGGATCGATCTTTTTTCAAAA
Found at i:182581 original size:12 final size:12
Alignment explanation
Indices: 182546--182596 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
182536 CATAGCACAT
182546 TCACATTTCCATA
1 TCACATTT-CATA
**
182559 -CACATCACATA
1 TCACATTTCATA
**
182570 TCTTATTTCATA
1 TCACATTTCATA
182582 TCACATTTCATA
1 TCACATTTCATA
182594 TCA
1 TCA
182597 ATTAAGTGCA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
11 4 0.14
12 25 0.86
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (12 bp):
TCACATTTCATA
Found at i:183587 original size:13 final size:13
Alignment explanation
Indices: 183569--183605 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
183559 AGAAACGGTT
183569 AATGAGAATTAGA
1 AATGAGAATTAGA
183582 AATGAGAATTAGA
1 AATGAGAATTAGA
183595 AATGAGAATTA
1 AATGAGAATTA
183606 ACAAAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (13 bp):
AATGAGAATTAGA
Found at i:189203 original size:34 final size:35
Alignment explanation
Indices: 189157--189227 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 35
189147 GAAATTGATC
189157 CTTAACATAAATAATCATATCTCTAATGACAATCA
1 CTTAACATAAATAATCATATCTCTAATGACAATCA
*
189192 CTTAA-ATAAATAATTATATCTCTAATGACAATCA
1 CTTAACATAAATAATCATATCTCTAATGACAATCA
189226 CT
1 CT
189228 CAAGTAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 30 0.86
35 5 0.14
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (35 bp):
CTTAACATAAATAATCATATCTCTAATGACAATCA
Found at i:190124 original size:15 final size:15
Alignment explanation
Indices: 190104--190142 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
190094 ATATCTAAAT
190104 AAAATATGTGATTAG
1 AAAATATGTGATTAG
190119 AAAATATGTGATTAG
1 AAAATATGTGATTAG
190134 AAAATATGT
1 AAAATATGT
190143 TTATAAGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (15 bp):
AAAATATGTGATTAG
Found at i:190866 original size:51 final size:51
Alignment explanation
Indices: 190783--191170 Score: 375
Period size: 51 Copynumber: 7.6 Consensus size: 51
190773 CATGAACATA
* * * *
190783 TAAGTGTTAATTTCACTGGGGTAAGTCTATGTTAAGTACCACCATTGGAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACCGTTGGAAT
* * * * *
190834 TAATAGCTAATTTCACCGGTGTAAGTCTATGTTAAGTATCACCATTGAAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACCGTTGGAAT
* * * * * *
190885 TCAGAGTTAATTTCATCGGTGTAAGTATATATTAAGTACCACTGCTGGAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACCGTTGGAAT
* * **
190936 TAAGAGTTAATTTCACAGGTGTACA-TCTATGTTAATTA-CATTTGTTGGAAT
1 TAAGAGTTAATTTCACCGGTGTA-AGTCTATGTTAAGTACCA-CCGTTGGAAT
* * * * *
190987 TAAGAGTTAATTTCACTGGCGTAAGTCTATGTTAAGCACCACCGCTAGAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACCGTTGGAAT
* * * * *
191038 TACGAGTTAATTTGACCAGTGTAAGTCTATGTTAAGTACCATCGTTGAAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACCGTTGGAAT
* ** * * * *
191089 TAAGAGTAAACGTCACCAGTGTATGTCTATGTTAAGTATCACCGTTGTAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACCGTTGGAAT
* * * *
191140 TATGTGTTAAATTTGACTGGTGTAAGTCTAT
1 TAAGAGTT-AATTTCACCGGTGTAAGTCTAT
191171 TGTGAGTTCA
Statistics
Matches: 270, Mismatches: 62, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
50 3 0.01
51 248 0.92
52 19 0.07
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (51 bp):
TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACCGTTGGAAT
Found at i:191201 original size:51 final size:51
Alignment explanation
Indices: 191137--191329 Score: 207
Period size: 51 Copynumber: 3.8 Consensus size: 51
191127 TCACCGTTGT
* *
191137 AATTATGTGTTAAATTTGACTGGTGTAAGTCTATTG-TGAG-TTCAATATTGG
1 AATTATATGTTAAATTTGACTGGTGTAAGT-TATTGATGAGATT-AATATAGG
* *
191188 AATTATATATTAAATTTGAATGGTGTAAGTT-TGTGATGAGATTAATGA-AGG
1 AATTATATGTTAAATTTGACTGGTGTAAGTTAT-TGATGAGATTAAT-ATAGG
* * * *
191239 AATTATATGTTAAATTTGGCTAGTATAAGTTTTTGATGAGATTAAT-TCAGG
1 AATTATATGTTAAATTTGACTGGTGTAAGTTATTGATGAGATTAATAT-AGG
* * *
191290 AATTATGTGTTAAATTTGATTGGTGTAAGTCATTGATGAG
1 AATTATATGTTAAATTTGACTGGTGTAAGTTATTGATGAG
191330 TTCAATGCTA
Statistics
Matches: 119, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
49 1 0.01
50 3 0.03
51 111 0.93
52 4 0.03
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (51 bp):
AATTATATGTTAAATTTGACTGGTGTAAGTTATTGATGAGATTAATATAGG
Found at i:192274 original size:36 final size:36
Alignment explanation
Indices: 192234--192456 Score: 243
Period size: 36 Copynumber: 6.2 Consensus size: 36
192224 ATGTTCCCAC
* *
192234 GCATGATATACATACAATTGCTATTGATGATTATAT
1 GCATGATATACATACACTTGCTACTGATGATTATAT
*** * * *
192270 GCATGATATACATGTGCTTACTACTAATGCTTATAT
1 GCATGATATACATACACTTGCTACTGATGATTATAT
* * * * *
192306 GCATGATATACATGCGCTTGTTACTAATGAATATAT
1 GCATGATATACATACACTTGCTACTGATGATTATAT
* *
192342 G-ATTGATATACACACATTTGCTACTGATGATTATAT
1 GCA-TGATATACATACACTTGCTACTGATGATTATAT
192378 GCATGATATACATGA-ACTTGCTACTGATGATTATAT
1 GCATGATATACAT-ACACTTGCTACTGATGATTATAT
*** *
192414 GCATGATATACATGTGCTTGCTACTGATGGTTATAT
1 GCATGATATACATACACTTGCTACTGATGATTATAT
192450 GCATGAT
1 GCATGAT
192457 CTATTACCAA
Statistics
Matches: 158, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
35 1 0.01
36 155 0.98
37 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (36 bp):
GCATGATATACATACACTTGCTACTGATGATTATAT
Found at i:192317 original size:72 final size:72
Alignment explanation
Indices: 192234--192456 Score: 270
Period size: 72 Copynumber: 3.1 Consensus size: 72
192224 ATGTTCCCAC
* * * *
192234 GCATGATATACATACAATTGCTATTGATGATTATATGCATGATATACATGTGCTTACTACTAATG
1 GCATGATATACATACACTTGCTACTGATGATTATATGCATGATATACATGTGCTTGCTACTGATG
*
192299 CTTATAT
66 ATTATAT
* * * * * *****
192306 GCATGATATACATGCGCTTGTTACTAATGAATATATG-ATTGATATACACACATTTGCTACTGAT
1 GCATGATATACATACACTTGCTACTGATGATTATATGCA-TGATATACATGTGCTTGCTACTGAT
192370 GATTATAT
65 GATTATAT
192378 GCATGATATACATGA-ACTTGCTACTGATGATTATATGCATGATATACATGTGCTTGCTACTGAT
1 GCATGATATACAT-ACACTTGCTACTGATGATTATATGCATGATATACATGTGCTTGCTACTGAT
*
192442 GGTTATAT
65 GATTATAT
192450 GCATGAT
1 GCATGAT
192457 CTATTACCAA
Statistics
Matches: 122, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
71 1 0.01
72 120 0.98
73 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (72 bp):
GCATGATATACATACACTTGCTACTGATGATTATATGCATGATATACATGTGCTTGCTACTGATG
ATTATAT
Found at i:192450 original size:108 final size:108
Alignment explanation
Indices: 192237--192438 Score: 314
Period size: 108 Copynumber: 1.9 Consensus size: 108
192227 TTCCCACGCA
* * ** *
192237 TGATATACATACAATTGCTATTGATGATTATATGCATGATATACATGTGCTTACTACTAATGCTT
1 TGATATACACACAATTGCTACTGATGATTATATGCATGATATACATGAACTTACTACTAATGATT
*
192302 ATATGCATGATATACATGCGCTTGTTACTAATGAATATATGAT
66 ATATGCATGATATACATGCGCTTGCTACTAATGAATATATGAT
* * *
192345 TGATATACACACATTTGCTACTGATGATTATATGCATGATATACATGAACTTGCTACTGATGATT
1 TGATATACACACAATTGCTACTGATGATTATATGCATGATATACATGAACTTACTACTAATGATT
*
192410 ATATGCATGATATACATGTGCTTGCTACT
66 ATATGCATGATATACATGCGCTTGCTACT
192439 GATGGTTATA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 84 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (108 bp):
TGATATACACACAATTGCTACTGATGATTATATGCATGATATACATGAACTTACTACTAATGATT
ATATGCATGATATACATGCGCTTGCTACTAATGAATATATGAT
Found at i:200513 original size:15 final size:15
Alignment explanation
Indices: 200493--200523 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
200483 TTCGGTAAAA
200493 CGTTACCGAAAACAT
1 CGTTACCGAAAACAT
200508 CGTTACCGAAAACAT
1 CGTTACCGAAAACAT
200523 C
1 C
200524 ATTTTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (15 bp):
CGTTACCGAAAACAT
Found at i:201874 original size:15 final size:15
Alignment explanation
Indices: 201854--201882 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
201844 CTACACTTGT
201854 AAATAAAATTATTTA
1 AAATAAAATTATTTA
201869 AAATAAAATTATTT
1 AAATAAAATTATTT
201883 TTGAGGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATAAAATTATTTA
Found at i:202937 original size:102 final size:102
Alignment explanation
Indices: 202751--203136 Score: 432
Period size: 102 Copynumber: 3.8 Consensus size: 102
202741 CGTGAACATA
* * * * * *
202751 TAAGTGTTAATTTCACCAGTGTAAGTATATGTTAAGTACCACCGCTAGAGTTAAGAGTGAATTTC
1 TAAGAGTTAATTTCACCTGTGTAAGTCTATGTTAAGTACCACCGCTGGAATTAAGAGTTAATTTC
* *
202816 ACCGGTACAAGTCTGTGTTAAGTACCATTACTGGAAT
66 ACCGGTGCAAGTCTATGTTAAGTACCATTACTGGAAT
* ** *
202853 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCATTGTTGGAATTAAGAGTTAATTTC
1 TAAGAGTTAATTTCACCTGTGTAAGTCTATGTTAAGTACCACCGCTGGAATTAAGAGTTAATTTC
*** *
202918 ACCGGTGCAAGTCTATGTTAAGTACCATCGTTGGAGT
66 ACCGGTGCAAGTCTATGTTAAGTACCATTACTGGAAT
* * * *
202955 TAAGAGTTAATTTCACTTGTGTAAGTCTATGTTAAGCACTACTGCTGGAATTAAGAGTTAATTTC
1 TAAGAGTTAATTTCACCTGTGTAAGTCTATGTTAAGTACCACCGCTGGAATTAAGAGTTAATTTC
* * * * *
203020 ACTGGAGTAAGTTTATGTTAAGTACGA-TATCTGGAAT
66 ACCGGTGCAAGTCTATGTTAAGTACCATTA-CTGGAAT
* * * * * * *
203057 TAAAAGTAAATTTCACATATGTAAGTCTATGTTAAGTACCACCGTTGGAATTATGTGTTAAATTT
1 TAAGAGTTAATTTCACCTGTGTAAGTCTATGTTAAGTACCACCGCTGGAATTAAGAGTT-AATTT
* **
203122 GATTGGTGCAAGTCT
65 CACCGGTGCAAGTCT
203137 GTTGTGAGTT
Statistics
Matches: 237, Mismatches: 45, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
102 222 0.94
103 15 0.06
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (102 bp):
TAAGAGTTAATTTCACCTGTGTAAGTCTATGTTAAGTACCACCGCTGGAATTAAGAGTTAATTTC
ACCGGTGCAAGTCTATGTTAAGTACCATTACTGGAAT
Found at i:203037 original size:153 final size:153
Alignment explanation
Indices: 202751--203105 Score: 453
Period size: 153 Copynumber: 2.3 Consensus size: 153
202741 CGTGAACATA
* * * *
202751 TAAGTGTTAATTTCACCAGTGTAAGTATATGTTAAGTACCACCGCTAGAGTTAAGAGTGAATTTC
1 TAAGAGTTAATTTCACCAGTGTAAGTCTATGTTAAGTACCACCGTTGGAGTTAAGAGTGAATTTC
* * * *
202816 ACCGGTACAAGTCTGTGTTAAGTACCATTACTGGAATTAAGAGTTAATTTCACCGGTGTAAGTCT
66 ACCGGTACAAGTCTATGTTAAGCACCACTACTGGAATTAAGAGTTAATTTCACCGGAGTAAGTCT
*
202881 ATGTTAAGTACCAT-TGTTGGAAT
131 ATGTTAAGTACCATAT-CTGGAAT
* * * *
202904 TAAGAGTTAATTTCACCGGTGCAAGTCTATGTTAAGTACCATCGTTGGAGTTAAGAGTTAATTTC
1 TAAGAGTTAATTTCACCAGTGTAAGTCTATGTTAAGTACCACCGTTGGAGTTAAGAGTGAATTTC
** ** * * * *
202969 ACTTGTGTAAGTCTATGTTAAGCACTACTGCTGGAATTAAGAGTTAATTTCACTGGAGTAAGTTT
66 ACCGGTACAAGTCTATGTTAAGCACCACTACTGGAATTAAGAGTTAATTTCACCGGAGTAAGTCT
*
203034 ATGTTAAGTACGATATCTGGAAT
131 ATGTTAAGTACCATATCTGGAAT
* * *
203057 TAAAAGTAAATTTCA-CATATGTAAGTCTATGTTAAGTACCACCGTTGGA
1 TAAGAGTTAATTTCACCA-GTGTAAGTCTATGTTAAGTACCACCGTTGGA
203106 ATTATGTGTT
Statistics
Matches: 172, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
152 1 0.01
153 170 0.99
154 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.35
Consensus pattern (153 bp):
TAAGAGTTAATTTCACCAGTGTAAGTCTATGTTAAGTACCACCGTTGGAGTTAAGAGTGAATTTC
ACCGGTACAAGTCTATGTTAAGCACCACTACTGGAATTAAGAGTTAATTTCACCGGAGTAAGTCT
ATGTTAAGTACCATATCTGGAAT
Found at i:203106 original size:51 final size:51
Alignment explanation
Indices: 202751--203109 Score: 389
Period size: 51 Copynumber: 7.0 Consensus size: 51
202741 CGTGAACATA
* * * * * * *
202751 TAAGTGTTAATTTCACCAGTGTAAGTATATGTTAAGTACCACCGCTAGAGT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACTGTTGGAAT
* ** * * **
202802 TAAGAGTGAATTTCACCGGTACAAGTCTGTGTTAAGTACCATTACTGGAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACTGTTGGAAT
*
202853 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCATTGTTGGAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACTGTTGGAAT
* *
202904 TAAGAGTTAATTTCACCGGTGCAAGTCTATGTTAAGTACCA-TCGTTGGAGT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACT-GTTGGAAT
** * * *
202955 TAAGAGTTAATTTCACTTGTGTAAGTCTATGTTAAGCACTACTGCTGGAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACTGTTGGAAT
* * * * *
203006 TAAGAGTTAATTTCACTGGAGTAAGTTTATGTTAAGTACGA-TATCTGGAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACTGT-TGGAAT
* * *** *
203057 TAAAAGTAAATTTCACATATGTAAGTCTATGTTAAGTACCACCGTTGGAAT
1 TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACTGTTGGAAT
203108 TA
1 TA
203110 TGTGTTAAAT
Statistics
Matches: 260, Mismatches: 44, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
50 2 0.01
51 256 0.98
52 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (51 bp):
TAAGAGTTAATTTCACCGGTGTAAGTCTATGTTAAGTACCACTGTTGGAAT
Found at i:206218 original size:22 final size:22
Alignment explanation
Indices: 206191--206243 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
206181 AGTTCTAAGG
* *
206191 CACTTTAGTATCAGTGCAAATA
1 CACTTTAGTAGCAGTGCAAAGA
* * *
206213 CACTTTTGTAGCAGTGCTAAGG
1 CACTTTAGTAGCAGTGCAAAGA
206235 CACTTTAGT
1 CACTTTAGT
206244 TATCCGATGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (22 bp):
CACTTTAGTAGCAGTGCAAAGA
Found at i:209722 original size:20 final size:20
Alignment explanation
Indices: 209689--209735 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
209679 TGATTTTCTA
*
209689 TTGAAAACAAAAATTG-GATT
1 TTGAAAACAAAAA-TGAAATT
209709 TTGAAAAGC-AAAATGAAATT
1 TTGAAAA-CAAAAATGAAATT
209729 TTGAAAA
1 TTGAAAA
209736 ATGATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 21 0.88
21 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (20 bp):
TTGAAAACAAAAATGAAATT
Found at i:211380 original size:232 final size:232
Alignment explanation
Indices: 210974--211440 Score: 934
Period size: 232 Copynumber: 2.0 Consensus size: 232
210964 TCAAAGTCCA
210974 TTAAAGTAGAATTTGAGCACAAAATGTTTTTCTGGGTAAGTAGTATCAATATTGTTCTTATAATA
1 TTAAAGTAGAATTTGAGCACAAAATGTTTTTCTGGGTAAGTAGTATCAATATTGTTCTTATAATA
211039 TTGATATTATAAAAACAATATTGATATTGTTCATGTGGTACTGATACCAAAGGTAAGAGAAGTAT
66 TTGATATTATAAAAACAATATTGATATTGTTCATGTGGTACTGATACCAAAGGTAAGAGAAGTAT
211104 ATATACTCTATAGGTAGTATCGATACTACCAGTTGTTTTCCAACGGCACAAATTCCAAAATGCAA
131 ATATACTCTATAGGTAGTATCGATACTACCAGTTGTTTTCCAACGGCACAAATTCCAAAATGCAA
211169 AATATGTACCGATACCCAAAGGGGTACCGATACTACT
196 AATATGTACCGATACCCAAAGGGGTACCGATACTACT
211206 TTAAAGTAGAATTTGAGCACAAAATGTTTTTCTGGGTAAGTAGTATCAATATTGTTCTTATAATA
1 TTAAAGTAGAATTTGAGCACAAAATGTTTTTCTGGGTAAGTAGTATCAATATTGTTCTTATAATA
211271 TTGATATTATAAAAACAATATTGATATTGTTCATGTGGTACTGATACCAAAGGTAAGAGAAGTAT
66 TTGATATTATAAAAACAATATTGATATTGTTCATGTGGTACTGATACCAAAGGTAAGAGAAGTAT
211336 ATATACTCTATAGGTAGTATCGATACTACCAGTTGTTTTCCAACGGCACAAATTCCAAAATGCAA
131 ATATACTCTATAGGTAGTATCGATACTACCAGTTGTTTTCCAACGGCACAAATTCCAAAATGCAA
211401 AATATGTACCGATACCCAAAGGGGTACCGATACTACT
196 AATATGTACCGATACCCAAAGGGGTACCGATACTACT
211438 TTA
1 TTA
211441 CATAGTAGTA
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 235 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (232 bp):
TTAAAGTAGAATTTGAGCACAAAATGTTTTTCTGGGTAAGTAGTATCAATATTGTTCTTATAATA
TTGATATTATAAAAACAATATTGATATTGTTCATGTGGTACTGATACCAAAGGTAAGAGAAGTAT
ATATACTCTATAGGTAGTATCGATACTACCAGTTGTTTTCCAACGGCACAAATTCCAAAATGCAA
AATATGTACCGATACCCAAAGGGGTACCGATACTACT
Found at i:211562 original size:21 final size:22
Alignment explanation
Indices: 211523--211563 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
211513 TTAAAAATTA
*
211523 TAAAGGAAGTACCGGTACTCAT
1 TAAAGGAAGTACCGATACTCAT
*
211545 TAAAGG-AGTACCTATACTC
1 TAAAGGAAGTACCGATACTC
211564 CCTATCTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:211636 original size:19 final size:20
Alignment explanation
Indices: 211598--211636 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
211588 CAAGAAAATT
*
211598 ATCCCCTAACGGCTCCAAAC
1 ATCCCCTAACGGCTACAAAC
*
211618 ATCCCC-AACGGCTAGAAAC
1 ATCCCCTAACGGCTACAAAC
211637 GACCACAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.33, C:0.41, G:0.13, T:0.13
Consensus pattern (20 bp):
ATCCCCTAACGGCTACAAAC
Found at i:212555 original size:32 final size:31
Alignment explanation
Indices: 212519--212595 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
212509 CGGGGCCGTG
* *
212519 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCCCA
** **
212551 GGGCCTACCCGAGAATGATCTCAGGGCCCCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCCCA
*
212582 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
212596 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCCCA
Found at i:213502 original size:5 final size:5
Alignment explanation
Indices: 213492--213549 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
213482 AACGGTCAAC
* * *
213492 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTTG GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG
213541 GGTCG GGTC
1 GGTCG GGTC
213550 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 36 0.84
7 7 0.16
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:213507 original size:17 final size:17
Alignment explanation
Indices: 213485--213539 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
213475 AACGGTCAAC
213485 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
213502 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
213519 GGTCAACGGTTGGGTCG
1 GGTCAACGGTCGGGTCG
213536 GGTC
1 GGTC
213540 GGGTCGGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:213512 original size:7 final size:7
Alignment explanation
Indices: 213465--213495 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
213455 GTCAAAGAAA
213465 GTCAACG
1 GTCAACG
213472 GTCAACG
1 GTCAACG
213479 GTCAACG
1 GTCAACG
213486 GTCAACG
1 GTCAACG
213493 GTC
1 GTC
213496 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:213564 original size:9 final size:9
Alignment explanation
Indices: 213546--213634 Score: 61
Period size: 9 Copynumber: 9.3 Consensus size: 9
213536 GGTCGGGTCG
*
213546 GGTCAGACC
1 GGTCAAACC
213555 GGTCAAACC
1 GGTCAAACC
* * *
213564 GATTCAGATC
1 G-GTCAAACC
213574 GGTCAAACC
1 GGTCAAACC
*
213583 GGTTCGAACC
1 GG-TCAAACC
*
213593 GGTTGAAACC
1 GG-TCAAACC
213603 GGTCAAACC
1 GGTCAAACC
*
213612 GGTTGAAAACC
1 GG-T-CAAACC
*
213623 GGTTAAACC
1 GGTCAAACC
213632 GGT
1 GGT
213635 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
9 32 0.51
10 24 0.38
11 7 0.11
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:213595 original size:19 final size:18
Alignment explanation
Indices: 213552--213634 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 18
213542 GTCGGGTCAG
*
213552 ACCGGTCAAACCGATTCA
1 ACCGGTCAAACCGGTTCA
*
213570 GATCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTC-A
*
213590 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTC-A
* *
213609 ACCGGTTGAAAACCGGTTAA
1 ACCGG-T-CAAACCGGTTCA
213629 ACCGGT
1 ACCGGT
213635 TTCCAGCAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 30 0.57
20 22 0.42
21 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (18 bp):
ACCGGTCAAACCGGTTCA
Found at i:213603 original size:20 final size:21
Alignment explanation
Indices: 213578--213635 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
213568 CAGATCGGTC
*
213578 AAACCGGTTCGAACCGGTTG-
1 AAACCGGTTCAAACCGGTTGA
213598 AAACCGG-TCAAACCGGTTGA
1 AAACCGGTTCAAACCGGTTGA
213618 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCAAACCGGTT
213636 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 11 0.31
20 23 0.66
21 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
AAACCGGTTCAAACCGGTTGA
Found at i:213605 original size:29 final size:28
Alignment explanation
Indices: 213573--213634 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 28
213563 CGATTCAGAT
213573 CGGTCAAACCGGTTCG-AACCGGTTGAAAC
1 CGGTCAAACCGGTT-GAAACCGGTT-AAAC
213602 CGGTCAAACCGGTTGAAAACCGGTTAAAC
1 CGGTCAAACCGGTTG-AAACCGGTTAAAC
213631 CGGT
1 CGGT
213635 TTCCAGCAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 1 0.03
29 22 0.71
30 8 0.26
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (28 bp):
CGGTCAAACCGGTTGAAACCGGTTAAAC
Found at i:213635 original size:9 final size:10
Alignment explanation
Indices: 213578--213635 Score: 68
Period size: 9 Copynumber: 5.9 Consensus size: 10
213568 CAGATCGGTC
213578 AAACCGGTTCG
1 AAACCGGTT-G
213589 -AACCGGTTG
1 AAACCGGTTG
*
213598 AAACCGG-TC
1 AAACCGGTTG
213607 AAACCGGTTG
1 AAACCGGTTG
213617 AAAACCGGTT-
1 -AAACCGGTTG
213627 AAACCGGTT
1 AAACCGGTT
213636 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 18 0.43
10 15 0.36
11 9 0.21
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:219893 original size:32 final size:31
Alignment explanation
Indices: 219857--219933 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
219847 CGGGGCCGTG
*
219857 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
219889 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
219920 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
219934 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:219916 original size:63 final size:63
Alignment explanation
Indices: 219810--219933 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
219800 CCCTAAGGGA
* * ** *
219810 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
219873 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
219934 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:220832 original size:5 final size:5
Alignment explanation
Indices: 220822--220862 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
220812 AACGGTCAAC
*
220822 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
220863 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:220898 original size:9 final size:9
Alignment explanation
Indices: 220859--220957 Score: 63
Period size: 9 Copynumber: 10.3 Consensus size: 9
220849 GGTCGGGTCG
*
220859 GGTCAGACC
1 GGTCAAACC
*
220868 GGTCAAACT
1 GGTCAAACC
* *
220877 GATTCAGACC
1 G-GTCAAACC
220887 GGTCAAACC
1 GGTCAAACC
*
220896 GGTTCGAACC
1 GG-TCAAACC
* *
220906 GGTTGAAACT
1 GG-TCAAACC
220916 GGTCAAACC
1 GGTCAAACC
220925 GGTCAGAACC
1 GGTCA-AACC
*
220935 GGTTGAAAACC
1 GG-T-CAAACC
*
220946 GGTTAAACC
1 GGTCAAACC
220955 GGT
1 GGT
220958 TTCCAGCAGC
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
9 34 0.49
10 28 0.40
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:220906 original size:19 final size:19
Alignment explanation
Indices: 220865--220958 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 19
220855 GTCGGGTCAG
* *
220865 ACCGGTCAAACTGATTC-A
1 ACCGGTCAAACCGGTTCGA
220883 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
* * *
220903 ACCGGTTGAAACTGG-TCAA
1 ACCGG-TCAAACCGGTTCGA
220922 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACCGGTTCG--A
*
220943 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
220959 TCCAGCAGCC
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.03
19 33 0.55
20 17 0.28
21 8 0.13
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:220921 original size:29 final size:31
Alignment explanation
Indices: 220884--220958 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
220874 ACTGATTCAG
220884 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
220913 ACTGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
220943 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
220959 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
30 14 0.35
31 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:220956 original size:20 final size:21
Alignment explanation
Indices: 220920--220958 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
220910 GAAACTGGTC
220920 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
220941 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
220959 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Done.