Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003360.1 Hibiscus syriacus cultivar Beakdansim tig00007070_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: 89199
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:624 original size:9 final size:9
Alignment explanation
Indices: 605--637 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
595 ATAATTTGTA
605 ATATA-TAT
1 ATATATTAT
613 ATATATTAT
1 ATATATTAT
622 ATATATTAT
1 ATATATTAT
631 A-ATATTA
1 ATATATTA
638 ATAAGCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 11 0.46
9 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATATATTAT
Found at i:627 original size:17 final size:17
Alignment explanation
Indices: 605--637 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
595 ATAATTTGTA
605 ATATATA-TAT-ATATT
1 ATATATATTATAATATT
620 ATATATATTATAATATT
1 ATATATATTATAATATT
637 A
1 A
638 ATAAGCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATTATAATATT
Found at i:13549 original size:14 final size:13
Alignment explanation
Indices: 13511--13563 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
13501 ATTTTAAACG
*
13511 ATTTATATTTAATT
1 ATTT-TATTTTATT
13525 A-TTTATTTTATT
1 ATTTTATTTTATT
*
13537 ATTTTATTCTTATC
1 ATTTTATT-TTATT
13551 ATTTTATCTTTAT
1 ATTTTAT-TTTAT
13564 CTGAAATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 9 0.26
13 8 0.24
14 16 0.47
15 1 0.03
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTATTTTATT
Found at i:16543 original size:12 final size:13
Alignment explanation
Indices: 16470--16551 Score: 60
Period size: 12 Copynumber: 6.2 Consensus size: 13
16460 CAACCCATTA
16470 TTATTTTTATTTT
1 TTATTTTTATTTT
*
16483 TCATTTGTTCAATTTT
1 TTATTT-TT--ATTTT
* *
16499 TTATTTTCA-ATT
1 TTATTTTTATTTT
* **
16511 TTATTTTTCTGAT
1 TTATTTTTATTTT
*
16524 TTATTTTTGTTTT
1 TTATTTTTATTTT
16537 TTA-TTTTATTTT
1 TTATTTTTATTTT
16549 TTA
1 TTA
16552 GATACATCGT
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
12 20 0.38
13 20 0.38
14 2 0.04
15 1 0.02
16 10 0.19
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.74
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:16931 original size:30 final size:30
Alignment explanation
Indices: 16897--16970 Score: 141
Period size: 29 Copynumber: 2.5 Consensus size: 30
16887 GTTCGAACAG
16897 AACAGTGCAGAAAAAAATTGATTTGGTTCA
1 AACAGTGCAGAAAAAAATTGATTTGGTTCA
16927 AACAGTGCAG-AAAAAATTGATTTGGTTCA
1 AACAGTGCAGAAAAAAATTGATTTGGTTCA
16956 AACAGTGCAGAAAAA
1 AACAGTGCAGAAAAA
16971 TACACAGCAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 29 0.67
30 14 0.33
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (30 bp):
AACAGTGCAGAAAAAAATTGATTTGGTTCA
Found at i:16965 original size:117 final size:117
Alignment explanation
Indices: 16729--16941 Score: 311
Period size: 117 Copynumber: 1.8 Consensus size: 117
16719 ATTGTTCAGA
* * *
16729 CAGTGCAGGAAAAAAAGACTTGGTTCGAATTGTGCAGAAAAGTTCAAACAGAACAATGCGAAAAA
1 CAGTGCAGGAAAAAAAGACTTGATTCGAACTATGCAGAAAAGTTCAAACAGAACAATGCGAAAAA
16794 AACTGATTTGGTTCAAACAATGCAGGAAAATACATAACAAATTCAAACAATG
66 AACTGATTTGGTTCAAACAATGCAGGAAAATACATAACAAATTCAAACAATG
* * * *
16846 CAGTGCA-GAAAAAACAGATTTGATTCGAACTATGTAGAAAAGTTCGAACAGAACAGTGCAGAAA
1 CAGTGCAGGAAAAAA-AGACTTGATTCGAACTATGCAGAAAAGTTCAAACAGAACAATGC-GAAA
* * *
16910 AAAATTGATTTGGTTCAAACAGTGCAGAAAAA
64 AAAACTGATTTGGTTCAAACAATGCAGGAAAA
16942 ATTGATTTGG
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 7 0.08
117 44 0.52
118 33 0.39
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (117 bp):
CAGTGCAGGAAAAAAAGACTTGATTCGAACTATGCAGAAAAGTTCAAACAGAACAATGCGAAAAA
AACTGATTTGGTTCAAACAATGCAGGAAAATACATAACAAATTCAAACAATG
Found at i:17048 original size:28 final size:28
Alignment explanation
Indices: 16999--17056 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
16989 AGTGCAATGT
* *
16999 AAAAAAATAGCAGCACAGTTTTGGTTCG
1 AAAAAAATAACAGCACAATTTTGGTTCG
*
17027 AAAAAAATAACAGTACAATTTTGGTTCG
1 AAAAAAATAACAGCACAATTTTGGTTCG
17055 AA
1 AA
17057 CAATGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (28 bp):
AAAAAAATAACAGCACAATTTTGGTTCG
Found at i:29241 original size:22 final size:23
Alignment explanation
Indices: 29206--29250 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
29196 TATGCATTTT
**
29206 TAACAATAATATTATTAAAAAAA
1 TAACAATAATATTACAAAAAAAA
*
29229 TAACCATAA-ATTACAAAAAAAA
1 TAACAATAATATTACAAAAAAAA
29251 AACGATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (23 bp):
TAACAATAATATTACAAAAAAAA
Found at i:29366 original size:16 final size:16
Alignment explanation
Indices: 29339--29385 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 16
29329 TAAATTATCT
29339 TTTATATCTTATATATG
1 TTTAT-TCTTATATATG
29356 TTTATTCTTATAT-T-
1 TTTATTCTTATATATG
29370 TTTATT-TTAATATATG
1 TTTATTCTT-ATATATG
29386 AATCATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 2 0.07
16 8 0.30
17 5 0.19
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (16 bp):
TTTATTCTTATATATG
Found at i:32521 original size:14 final size:14
Alignment explanation
Indices: 32504--32532 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32494 GAGATTTCTA
32504 TGTAGGGAATTATT
1 TGTAGGGAATTATT
32518 TGTAGGGAATTATT
1 TGTAGGGAATTATT
32532 T
1 T
32533 ACAGGGATTA
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:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (14 bp):
TGTAGGGAATTATT
Found at i:32761 original size:3 final size:3
Alignment explanation
Indices: 32753--32780 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
32743 AATCAGGGTT
32753 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
32781 GGAGTTAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:34337 original size:14 final size:14
Alignment explanation
Indices: 34318--34349 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
34308 CGTTCGTGAA
34318 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
34332 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
34346 CGTT
1 CGTT
34350 TATGTTCATT
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:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:34366 original size:24 final size:24
Alignment explanation
Indices: 34319--34369 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
34309 GTTCGTGAAC
* *
34319 GTTCGATTATGTTCGTTCGGTTAT
1 GTTCGATTATGTTCATTCAGTTAT
* *
34343 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGATTATGTTCATTCAGTTAT
34367 GTT
1 GTT
34370 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGATTATGTTCATTCAGTTAT
Found at i:35448 original size:16 final size:16
Alignment explanation
Indices: 35427--35493 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
35417 TTTATATTCG
35427 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
35443 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
** *
35459 TTTATGTTCGTGCGCG
1 TTTATGTTCGTGTTCA
35475 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
35489 TTTAT
1 TTTAT
35494 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 5 0.11
16 40 0.89
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:35464 original size:32 final size:32
Alignment explanation
Indices: 35423--35485 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
35413 AACGTTTATA
**
35423 TTCGTTTATGTTCGTGTTCATTTATGTTCGTG
1 TTCGTTTATGTTCGTGCGCATTTATGTTCGTG
*
35455 TTCGTTTATGTTCGTGCGCGTTTATGTTCGT
1 TTCGTTTATGTTCGTGCGCATTTATGTTCGT
35486 TTATTTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.54
Consensus pattern (32 bp):
TTCGTTTATGTTCGTGCGCATTTATGTTCGTG
Found at i:35576 original size:16 final size:16
Alignment explanation
Indices: 35555--35585 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35545 AAAAAAAATT
35555 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
35571 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
35586 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:38232 original size:21 final size:21
Alignment explanation
Indices: 38206--38245 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38196 ATATTTTTTA
* *
38206 ATTTTTTAATAATAAAATATT
1 ATTTTTTAAAAAAAAAATATT
38227 ATTTTTTAAAAAAAAAATA
1 ATTTTTTAAAAAAAAAATA
38246 GCAACAAAAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTTTAAAAAAAAAATATT
Found at i:39004 original size:20 final size:21
Alignment explanation
Indices: 38981--39027 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
38971 AAATTATTTA
38981 AATATATAA-ACAATTAAAAC
1 AATATATAATACAATTAAAAC
* *
39001 AATA-AAAATACAATTAGAAC
1 AATATATAATACAATTAAAAC
39021 AATATAT
1 AATATAT
39028 TTAAAAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AATATATAATACAATTAAAAC
Found at i:40325 original size:3 final size:3
Alignment explanation
Indices: 40317--40439 Score: 201
Period size: 3 Copynumber: 40.7 Consensus size: 3
40307 TTATTTATTA
*
40317 AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
40363 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
40411 AAT ATT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40440 AATGGATAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
3 108 0.97
4 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:41201 original size:118 final size:113
Alignment explanation
Indices: 40736--41420 Score: 1046
Period size: 113 Copynumber: 6.0 Consensus size: 113
40726 GATATCAAAC
* *
40736 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * *
40801 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
*
40850 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
40915 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
*
40963 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
41028 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
41076 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTC
* *
41141 ATTATGAACTCTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
63 ATTATGAA--CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
41194 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTC
* *
41259 ATTATGAACTCTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCA
63 ATTATGAA--CTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
41312 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
41377 ATGAACTTTCTCTGGAAATAATGATCCAACAAATGATGGATTCA
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCA
41421 TCTTTGCTAA
Statistics
Matches: 537, Mismatches: 29, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
113 230 0.43
114 62 0.12
115 19 0.04
116 19 0.04
118 207 0.39
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCA
Found at i:41837 original size:17 final size:18
Alignment explanation
Indices: 41809--41849 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41799 TCCTGAATTC
41809 TGATTC-TGAT-AAAATG
1 TGATTCTTGATAAAAATG
*
41825 TTATTCTTGATAAAAATG
1 TGATTCTTGATAAAAATG
41843 TGATTCT
1 TGATTCT
41850 CAGAAGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 5 0.24
17 4 0.19
18 12 0.57
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (18 bp):
TGATTCTTGATAAAAATG
Found at i:42130 original size:50 final size:50
Alignment explanation
Indices: 42057--42859 Score: 1187
Period size: 50 Copynumber: 15.8 Consensus size: 50
42047 CTTACCAAAC
*
42057 CAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
42107 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
42157 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
42207 CAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
42257 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
* * * *
42307 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTTTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTGTCTAAT
* * * *
42359 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTTTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTGTCTAAT
* * * *
42411 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTTTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTGTCTAAT
* * * *
42463 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTTTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTGTCTAAT
42515 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
42565 CAGATCAGATAACTCAAAGAA-ACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
42614 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
42664 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTGTCTAAT
* * * *
42715 CAGATCTGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTGTCTAAT
* * * *
42767 CAGATCAGATACCTCAAAGAACACTTCCAGAAGATGCTATGTTTTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTGTCTAAT
* * *
42819 CAGATCAGATGATTCAAAGAAAACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
42860 GAGCACATAT
Statistics
Matches: 723, Mismatches: 24, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
49 49 0.07
50 331 0.46
51 49 0.07
52 294 0.41
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
Found at i:43811 original size:1 final size:1
Alignment explanation
Indices: 43800--43882 Score: 76
Period size: 1 Copynumber: 83.0 Consensus size: 1
43790 CCTTGACCCC
* * * * * * *
43800 TTTTTTCTTTTTCTTCTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTCTTTTTTTTCTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
43865 TCTTTTTTCTCTTTTTTT
1 TTTTTTTTTTTTTTTTTT
43883 CTTCTTCAAG
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:43818 original size:16 final size:15
Alignment explanation
Indices: 43799--43881 Score: 107
Period size: 16 Copynumber: 5.5 Consensus size: 15
43789 ACCTTGACCC
43799 CTTTTTTCTTTTTCTT
1 CTTTTTTCTTTTT-TT
43815 CTTTTTT-TTTTTTT
1 CTTTTTTCTTTTTTT
43829 CTTTTTT-TTTTTTT
1 CTTTTTTCTTTTTTT
*
43843 TTTTTTTCTTTTTTTT
1 CTTTTTTC-TTTTTTT
*
43859 CTTCTTTCTTTTTTCT
1 CTTTTTTCTTTTTT-T
43875 CTTTTTT
1 CTTTTTT
43882 TCTTCTTCAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
14 22 0.37
15 11 0.18
16 27 0.45
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
CTTTTTTCTTTTTTT
Found at i:43827 original size:24 final size:24
Alignment explanation
Indices: 43800--43888 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 24
43790 CCTTGACCCC
43800 TTTTTTCTTTTTCTTC-TTTTTTT
1 TTTTTTCTTTTTCTTCTTTTTTTT
*
43823 TTTTTTCTTTTT-TTTTTTTTTTT
1 TTTTTTCTTTTTCTTCTTTTTTTT
*
43846 TTTTCTTTTTTTTCTTCTTTCTTTTT
1 TTTT-TTCTTTTTCTTCTTT-TTTTT
* *
43872 TCTCTT-TTTTTCTTCTT
1 TTTTTTCTTTTTCTTCTT
43889 CAAGCATAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.04
23 23 0.40
24 18 0.32
25 7 0.12
26 7 0.12
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (24 bp):
TTTTTTCTTTTTCTTCTTTTTTTT
Found at i:43887 original size:13 final size:12
Alignment explanation
Indices: 43800--43888 Score: 100
Period size: 12 Copynumber: 7.8 Consensus size: 12
43790 CCTTGACCCC
43800 TTTT-TTCTTTT
1 TTTTCTTCTTTT
*
43811 TCTTCTT-TTTT
1 TTTTCTTCTTTT
*
43822 TTTTTTTCTTTT
1 TTTTCTTCTTTT
43834 TTTT-TT-TTTT
1 TTTTCTTCTTTT
43844 TTTT-TTCTTTT
1 TTTTCTTCTTTT
*
43855 TTTTCTTCTTTC
1 TTTTCTTCTTTT
43867 TTTT-TTCTCTTT
1 TTTTCTTCT-TTT
43879 TTTTCTTCTT
1 TTTTCTTCTT
43889 CAAGCATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
10 10 0.15
11 26 0.39
12 27 0.40
13 4 0.06
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTCTTCTTTT
Found at i:54500 original size:17 final size:17
Alignment explanation
Indices: 54461--54502 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
54451 ATACTTGCAA
54461 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATT
54479 ATAAAAATAATAAATA-T
1 ATAAAAAT-ATAAATATT
54496 ATAAAAA
1 ATAAAAA
54503 AAAATTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATATAAATATT
Found at i:55181 original size:15 final size:16
Alignment explanation
Indices: 55161--55194 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
55151 CTTCGATATA
55161 TAAAAAATA-ATTTAT
1 TAAAAAATATATTTAT
55176 TAAAAAATATTATTTAT
1 TAAAAAATA-TATTTAT
55193 TA
1 TA
55195 TTCATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAAAATATATTTAT
Found at i:55264 original size:20 final size:21
Alignment explanation
Indices: 55241--55287 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
55231 AAATTATTTA
55241 AATATATAA-ACAATTAAAAC
1 AATATATAATACAATTAAAAC
* *
55261 AATA-AAAATACAATTAGAAC
1 AATATATAATACAATTAAAAC
55281 AATATAT
1 AATATAT
55288 TTAAAAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AATATATAATACAATTAAAAC
Found at i:56580 original size:3 final size:3
Alignment explanation
Indices: 56572--56698 Score: 191
Period size: 3 Copynumber: 41.7 Consensus size: 3
56562 TTATTTATTA
* *
56572 AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT ACT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
*
56619 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
56667 AAT AAT ATT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
56699 AATGGATAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 106 0.95
4 6 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:57560 original size:20 final size:20
Alignment explanation
Indices: 57537--57743 Score: 134
Period size: 20 Copynumber: 10.3 Consensus size: 20
57527 GTTTCCAAAT
*
57537 TCGCAACGTGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
57557 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
*
57577 TCGCAACACAGAA---GTCAAA
1 TCGCAACGC-GAATTTGT-AAA
*
57596 TTCGCAACACAGAA---GTCAAA
1 -TCGCAACGC-GAATTTGT-AAA
*
57616 TTCGCAACGC-AA-TAGTCAAA
1 -TCGCAACGCGAATTTGT-AAA
*
57636 TTCGCAACGCG-A-TAGTCAAA
1 -TCGCAACGCGAATTTGT-AAA
*
57656 TTCGCAACACTGAA---GTCAAA
1 -TCGCAACGC-GAATTTGT-AAA
*
57676 TTCGCAACGCGAATCTGTAAA
1 -TCGCAACGCGAATTTGTAAA
*
57697 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATTTGTAAA
57717 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
57737 TCGCAAC
1 TCGCAAC
57744 ACTGAAGTCA
Statistics
Matches: 170, Mismatches: 6, Indels: 22
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.02
19 6 0.04
20 150 0.88
21 7 0.04
22 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:57596 original size:60 final size:59
Alignment explanation
Indices: 57557--57708 Score: 218
Period size: 60 Copynumber: 2.5 Consensus size: 59
57547 AATTTGTAAA
* *
57557 TCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATCGCAACGC-GAAGTCAAATTCGCAACACTGAAGTCAAAT
*
57617 TCGCAACGC-AA-TAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAAGTCAAAT
1 TCGCAACGCGAATTTGT-AAA-TCGCAACGCGA-AGTCAAATTCGCAACACTGAAGTCAAAT
*
57677 TCGCAACGCGAATCTGTAAATCGCAACGCGAA
1 TCGCAACGCGAATTTGTAAATCGCAACGCGAA
57709 TCTGTAAATC
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
58 3 0.04
59 8 0.10
60 64 0.78
61 5 0.06
62 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (59 bp):
TCGCAACGCGAATTTGTAAATCGCAACGCGAAGTCAAATTCGCAACACTGAAGTCAAAT
Found at i:57661 original size:80 final size:79
Alignment explanation
Indices: 57532--57783 Score: 300
Period size: 80 Copynumber: 3.2 Consensus size: 79
57522 ACCCAGTTTC
* ** * *
57532 CAAATTCGCAACGTGAATTTGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAAT
1 CAAATTCGCAACGCGAATCAGTAAATCGCAACGCGAATTAGTAAATCGCAACACTGAAGTCAAAT
*
57597 TCGCAACACAGAAGT
66 TCGCAACGC-GAAGT
57612 CAAATTCGCAACGC-AAT-AGTCAAATTCGCAACGCG-A-TAGTCAAATTCGCAACACTGAAGTC
1 CAAATTCGCAACGCGAATCAGT-AAA-TCGCAACGCGAATTAGT-AAA-TCGCAACACTGAAGTC
57673 AAATTCGCAACGCGAA-T
62 AAATTCGCAACGCGAAGT
* *
57690 CTGTAAA-TCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATCGCAACACTGAAGTCA
1 C---AAATTCGCAACGCGAATCAGTAAATCGCAACGCGAATTAGTAAATCGCAACACTGAAGTCA
*
57754 AATTCGCAACGCGATAGC
63 AATTCGCAACGCGA-AGT
57772 CAAATTCGCAAC
1 CAAATTCGCAAC
57784 ACTGAATTTC
Statistics
Matches: 150, Mismatches: 8, Indels: 28
0.81 0.04 0.15
Matches are distributed among these distances:
78 7 0.05
79 16 0.11
80 107 0.71
81 14 0.09
82 6 0.04
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (79 bp):
CAAATTCGCAACGCGAATCAGTAAATCGCAACGCGAATTAGTAAATCGCAACACTGAAGTCAAAT
TCGCAACGCGAAGT
Found at i:57760 original size:20 final size:21
Alignment explanation
Indices: 57577--57849 Score: 160
Period size: 20 Copynumber: 13.7 Consensus size: 21
57567 AATTTGTAAA
*
57577 TCGCAACACAGAA-GTCAAAT
1 TCGCAACACTGAATGTCAAAT
*
57597 TCGCAACACAGAA-GTCAAAT
1 TCGCAACACTGAATGTCAAAT
*
57617 TCGCAACGC--AATAGTCAAAT
1 TCGCAACACTGAAT-GTCAAAT
*
57637 TCGCAACGC-G-ATAGTCAAAT
1 TCGCAACACTGAAT-GTCAAAT
57657 TCGCAACACTGAA-GTCAAAT
1 TCGCAACACTGAATGTCAAAT
*
57677 TCGCAACGC-GAATCTGT-AAA-
1 TCGCAACACTGAA--TGTCAAAT
*
57697 TCGCAACGC-GAATCTGT-AAA-
1 TCGCAACACTGAA--TGTCAAAT
*
57717 TCGCAACGC-GAATTTGT-AAA-
1 TCGCAACACTGAA--TGTCAAAT
57737 TCGCAACACTGAA-GTCAAAT
1 TCGCAACACTGAATGTCAAAT
* *
57757 TCGCAACGC-G-ATAGCCAAAT
1 TCGCAACACTGAAT-GTCAAAT
*
57777 TCGCAACACTGAATTTCAAAT
1 TCGCAACACTGAATGTCAAAT
* *
57798 TTGC-A-ACTGAATTTCAAAT
1 TCGCAACACTGAATGTCAAAT
* * * *
57817 TCGCAACTC-GATTTTCGAAT
1 TCGCAACACTGAATGTCAAAT
57837 TCGCAACAC-GAAT
1 TCGCAACACTGAAT
57850 TTAATTTCAC
Statistics
Matches: 219, Mismatches: 17, Indels: 34
0.81 0.06 0.13
Matches are distributed among these distances:
18 5 0.02
19 24 0.11
20 168 0.77
21 17 0.08
22 5 0.02
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (21 bp):
TCGCAACACTGAATGTCAAAT
Found at i:57781 original size:40 final size:40
Alignment explanation
Indices: 57577--57804 Score: 186
Period size: 40 Copynumber: 5.7 Consensus size: 40
57567 AATTTGTAAA
* * *
57577 TCGCAACACAGAAGTCAAATTCGCAACACAGA-AGTCAAAT
1 TCGCAACACTGAAGTCAAATTCGCAACGC-GATAGCCAAAT
* * *
57617 TCGCAACGC-AATAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACTGA-AGTCAAATTCGCAACGCGATAGCCAAAT
* *
57657 TCGCAACACTGAAGTCAAATTCGCAACGCGA-ATCTGTAAA-
1 TCGCAACACTGAAGTCAAATTCGCAACGCGATAGC--CAAAT
* * *
57697 TCGCAACGC-GAA-TCTGTAAA-TCGCAACGCGAATTTG-TAAA-
1 TCGCAACACTGAAGTC---AAATTCGCAACGCG-A-TAGCCAAAT
57737 TCGCAACACTGAAGTCAAATTCGCAACGCGATAGCCAAAT
1 TCGCAACACTGAAGTCAAATTCGCAACGCGATAGCCAAAT
* *
57777 TCGCAACACTGAATTTCAAATTTGCAAC
1 TCGCAACACTGAA-GTCAAATTCGCAAC
57805 TGAATTTCAA
Statistics
Matches: 155, Mismatches: 16, Indels: 33
0.76 0.08 0.16
Matches are distributed among these distances:
38 4 0.03
39 14 0.09
40 112 0.72
41 23 0.15
42 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (40 bp):
TCGCAACACTGAAGTCAAATTCGCAACGCGATAGCCAAAT
Found at i:57808 original size:19 final size:19
Alignment explanation
Indices: 57772--57843 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 19
57762 ACGCGATAGC
57772 CAAATTCGCAACACTGAATTT
1 CAAATTCGC-A-ACTGAATTT
*
57793 CAAATTTGCAACTGAATTT
1 CAAATTCGCAACTGAATTT
*
57812 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACT-GAATTT
*
57832 CGAATTCGCAAC
1 CAAATTCGCAAC
57844 ACGAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 21 0.46
20 17 0.37
21 8 0.17
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.31
Consensus pattern (19 bp):
CAAATTCGCAACTGAATTT
Found at i:57815 original size:60 final size:60
Alignment explanation
Indices: 57592--57851 Score: 200
Period size: 60 Copynumber: 4.3 Consensus size: 60
57582 ACACAGAAGT
* *
57592 CAAATTCGCAACACAGAA-GTCAAATTCGCAAC-GCAATAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACTG-AATAGTCAAATTCGCAACGCGATAGC
* * * *
57652 CAAATTCGCAACACTGAA-GTCAAATTCGCAACGCGAATCTGT-AAA-TCGCAACGCGA-ATC
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAAC-TGAAT-AGTCAAATTCGCAACGCGATAGC
* * *
57711 TGTAAA-TCGCAACGCGAATTTGTAAA-TCGCAACACTG-A-AGTCAAATTCGCAACGCGATAGC
1 --CAAATTCGCAACACGAATTT-CAAATTCGC-A-ACTGAATAGTCAAATTCGCAACGCGATAGC
* * * ***
57772 CAAATTCGCAACACTGAATTTCAAATTTGCAACTGAAT-TTCAAATTCGCAACTCGATTTT
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACTGAATAGTCAAATTCGCAACGCGATAGC
*
57832 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
57852 AATTTCACAA
Statistics
Matches: 162, Mismatches: 21, Indels: 35
0.74 0.10 0.16
Matches are distributed among these distances:
58 2 0.01
59 20 0.12
60 110 0.68
61 25 0.15
62 5 0.03
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (60 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACTGAATAGTCAAATTCGCAACGCGATAGC
Found at i:57850 original size:40 final size:40
Alignment explanation
Indices: 57516--57851 Score: 177
Period size: 40 Copynumber: 8.4 Consensus size: 40
57506 GAACTCCAAT
* * * *
57516 TTCGCAACCCAGTTTCCAAATTCGCAAC-GTGAATTTGTAAA
1 TTCGCAACCGAATTT-CAAATTCGCAACACTGAATTT-CAAA
* * *
57557 -TCGCAACGCGAATTTGTAAA-TCGCAACACAGAA-GTCAAA
1 TTCGCAAC-CGAATTT-CAAATTCGCAACACTGAATTTCAAA
* * *
57596 TTCGCAACACAGAA-GTCAAATTCGCAACGC--AATAGTCAAA
1 TTCGCAAC-C-GAATTTCAAATTCGCAACACTGAAT-TTCAAA
* *
57636 TTCGCAACGCG-ATAGTCAAATTCGCAACACTGAA-GTCAAA
1 TTCGCAAC-CGAAT-TTCAAATTCGCAACACTGAATTTCAAA
*
57676 TTCGCAACGCGAATCTGT-AAA-TCGCAACGC-GAATCTGT-AAA
1 TTCGCAAC-CGAAT-T-TCAAATTCGCAACACTGAAT-T-TCAAA
* *
57717 -TCGCAACGCGAATTTGTAAA-TCGCAACACTGAA-GTCAAA
1 TTCGCAAC-CGAATTT-CAAATTCGCAACACTGAATTTCAAA
**
57756 TTCGCAACGCG-ATAGCCAAATTCGCAACACTGAATTTCAAA
1 TTCGCAAC-CGAAT-TTCAAATTCGCAACACTGAATTTCAAA
* * * * *
57797 TTTGCAACTGAATTTCAAATTCGCAACTC-GATTTTCGAA
1 TTCGCAACCGAATTTCAAATTCGCAACACTGAATTTCAAA
57836 TTCGCAACACGAATTT
1 TTCGCAAC-CGAATTT
57852 AATTTCACAA
Statistics
Matches: 236, Mismatches: 33, Indels: 53
0.73 0.10 0.16
Matches are distributed among these distances:
38 5 0.02
39 34 0.14
40 154 0.65
41 39 0.17
42 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (40 bp):
TTCGCAACCGAATTTCAAATTCGCAACACTGAATTTCAAA
Found at i:58054 original size:16 final size:15
Alignment explanation
Indices: 58019--58057 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
58009 TCCCCATCTC
*
58019 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
58034 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
58050 TAATTTTT
1 TAATTTTT
58058 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:58840 original size:24 final size:24
Alignment explanation
Indices: 58789--58842 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
58779 GTATTCAAAA
*
58789 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
58813 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
58837 TTTGAT
1 TTTGAT
58843 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:59028 original size:3 final size:3
Alignment explanation
Indices: 59020--59044 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
59010 TAACCCTGAG
59020 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
59045 TCTCCGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:61075 original size:18 final size:18
Alignment explanation
Indices: 61049--61084 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61039 AAGCAAAAGG
*
61049 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
*
61067 AAATTAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
61085 CAACCGGCTT
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:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:61596 original size:66 final size:65
Alignment explanation
Indices: 61514--61689 Score: 248
Period size: 66 Copynumber: 2.6 Consensus size: 65
61504 AATTTAAAAC
61514 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
61579 A
65 A
* * *
61580 AACAAATCAACTTTTACAAATCAATTAAGCAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
61644 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
61690 GTGTACCACA
Statistics
Matches: 99, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 33 0.33
68 4 0.04
69 15 0.15
70 6 0.06
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:63077 original size:42 final size:42
Alignment explanation
Indices: 63018--63111 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 42
63008 GTGAATCGGA
*
63018 CTCTTGAACGGTGGGAGGGACC-CATTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTC-TTGAACGATGACAGGAGC
* *
63060 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGAGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGAGC
63102 CTCTTGAACG
1 CTCTTGAACG
63112 ATAGGATGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.37, T:0.19
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGAGC
Found at i:63112 original size:21 final size:21
Alignment explanation
Indices: 63018--63113 Score: 113
Period size: 21 Copynumber: 4.6 Consensus size: 21
63008 GTGAATCGGA
* * *
63018 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGGC
*
63039 C-CATTGAACGATGACAGGGGC
1 CTC-TTGAACGATGAGAGGGGC
* *
63060 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
63081 CTCTTGAACGATGAGAGGAGC
1 CTCTTGAACGATGAGAGGGGC
63102 CTCTTGAACGAT
1 CTCTTGAACGAT
63114 AGGATGTGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:63129 original size:42 final size:42
Alignment explanation
Indices: 63018--63140 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
63008 GTGAATCGGA
* * * *
63018 CTCTTGAACGGTGGGAGGGACC-CATTGAACGATGACAGGGGC
1 CTCTTGAACGATAGGAGGGGCCGC-TTGAACGATGACAGGAGC
* * * *
63060 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGAGC
1 CTCTTGAACGATAGGAGGGGCCGCTTGAACGATGACAGGAGC
* * *
63102 CTCTTGAACGATAGGATGTGTCGCTTGAACGATGACAGG
1 CTCTTGAACGATAGGAGGGGCCGCTTGAACGATGACAGG
63141 TGAATCAGAC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 69 0.99
43 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGATAGGAGGGGCCGCTTGAACGATGACAGGAGC
Found at i:65301 original size:14 final size:14
Alignment explanation
Indices: 65282--65308 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65272 ACGCGAAAAT
65282 GAAAATCGCAACGA
1 GAAAATCGCAACGA
65296 GAAAATCGCAACG
1 GAAAATCGCAACG
65309 CAAAACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:65732 original size:20 final size:21
Alignment explanation
Indices: 65707--65764 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
65697 TCTGAGAGAT
65707 GGAGAT-AGACGGATTTTGCC
1 GGAGATGAGACGGATTTTGCC
*
65727 GGAGATGGGGACGGATTTTGCC
1 GGAGAT-GAGACGGATTTTGCC
*
65749 GGAGATGGGGACGGAT
1 GGAGAT-GAGACGGAT
65765 GTCGCCGTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 6 0.17
22 29 0.83
ACGTcount: A:0.22, C:0.12, G:0.45, T:0.21
Consensus pattern (21 bp):
GGAGATGAGACGGATTTTGCC
Found at i:65771 original size:22 final size:22
Alignment explanation
Indices: 65714--65764 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
65704 GATGGAGATA
65714 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTTGCCGGAGATGGG
65736 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTTGCCGGAGATGGG
65758 GACGGAT
1 GACGGAT
65765 GTCGCCGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTTGCCGGAGATGGG
Found at i:65948 original size:20 final size:20
Alignment explanation
Indices: 65923--66194 Score: 236
Period size: 20 Copynumber: 13.6 Consensus size: 20
65913 TAAACGCGTT
*
65923 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGTG
* *
65943 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
65963 TTGCGAATTTGA-TTATCGTG
1 TTGCGAATTTGACTT-TCGTG
*
65983 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGTG
**
66003 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTTTC-GTG
* *
66024 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
* *
66044 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
*
66064 TTGCAAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
* **
66084 TTGTGAATTTGACTTTTATG
1 TTGCGAATTTGACTTTCGTG
* * *
66104 TTGTG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC--TTTCGTG
66124 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
66144 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
* *
66164 TTGTG-ATTT-ACATATTCGCG
1 TTGCGAATTTGAC-T-TTCGTG
66184 TTGCGAATTTG
1 TTGCGAATTTG
66195 GAAACTGAGT
Statistics
Matches: 210, Mismatches: 27, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
18 4 0.02
19 14 0.07
20 158 0.75
21 32 0.15
22 2 0.01
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGTG
Found at i:65994 original size:60 final size:59
Alignment explanation
Indices: 65923--66234 Score: 285
Period size: 60 Copynumber: 5.2 Consensus size: 59
65913 TAAACGCGTT
* *
65923 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGATTATCGTG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACT-TCTGTGTTGCGAATTTGACT-TCGTG
* * * * *
65983 TTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTG-ACTTCTGTGTTGCGAATTTGACT-TCGTG
* * * **
66044 TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGTGAATTTGACTTTTATG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-TTCGTG
* *
66104 TTGTG-ATTT-ACAGATTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGAC--TTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTC-GTG
* ** * * * *
66164 TTGTG-ATTT-ACATATTCGCGTTGCGAATTTGGA-AACTGAGTTGCGAAATTGGAGTTCGCG
1 TTGCGAATTTGAC-T-TTCGCGTTGCGAATTT-GACTTCTGTGTTGCG-AATTTGACTTCGTG
66224 TTGCGAATTTG
1 TTGCGAATTTG
66235 TTGGTCATTT
Statistics
Matches: 209, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.01
59 6 0.03
60 136 0.65
61 65 0.31
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.41
Consensus pattern (59 bp):
TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTCGTG
Found at i:86065 original size:19 final size:19
Alignment explanation
Indices: 86017--86068 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
86007 TGGAGCGTGG
86017 GGGGAATCGGTACCCCTCAT
1 GGGGAATCGGTACCCCT-AT
86037 GGGGAATCGGTACCCCT-T
1 GGGGAATCGGTACCCCTAT
86055 GGGGTAATCGGTAC
1 GGGG-AATCGGTAC
86069 TTTCTTGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.16
19 9 0.29
20 17 0.55
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (19 bp):
GGGGAATCGGTACCCCTAT
Done.