Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006192.1 Hibiscus syriacus cultivar Beakdansim tig00014732_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: 476961
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:161287 original size:24 final size:24
Alignment explanation
Indices: 161250--161295 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
161240 CGATGGAAAA
*
161250 GGAAAAAGAGAAAA-GATAAAGAGG
1 GGAAAAAGAAAAAATGA-AAAGAGG
*
161274 GGAAAAGGAAAAAATGAAAAGA
1 GGAAAAAGAAAAAATGAAAAGA
161296 TTTTTCGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.04
Consensus pattern (24 bp):
GGAAAAAGAAAAAATGAAAAGAGG
Found at i:161570 original size:2 final size:2
Alignment explanation
Indices: 161563--161602 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
161553 AATCACTGAA
*
161563 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T- TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
161603 GGGTAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:182197 original size:24 final size:24
Alignment explanation
Indices: 182170--182217 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
182160 TTTTTGATTC
182170 GATTTAGCGGTTTGGTGCTTGCTT
1 GATTTAGCGGTTTGGTGCTTGCTT
182194 GATTTAGCGGTTTGGTGCTTGCTT
1 GATTTAGCGGTTTGGTGCTTGCTT
182218 TTTTGCCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.12, G:0.33, T:0.46
Consensus pattern (24 bp):
GATTTAGCGGTTTGGTGCTTGCTT
Found at i:190595 original size:22 final size:22
Alignment explanation
Indices: 190542--190603 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
190532 TAGTGCAGGA
* *
190542 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATTCCCCCTTGAAGG
* *
190564 GGAACCGATTCCCCTTTGAATG
1 GGAACCGATTCCCCCTTGAAGG
*
190586 GGAACTGATTCCCTCCTT
1 GGAACCGATTCCC-CCTT
190604 TAGGGAATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 30 0.91
23 3 0.09
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (22 bp):
GGAACCGATTCCCCCTTGAAGG
Found at i:192314 original size:13 final size:13
Alignment explanation
Indices: 192296--192320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
192286 ACCATGTCAC
192296 ATTGATTATGAAT
1 ATTGATTATGAAT
192309 ATTGATTATGAA
1 ATTGATTATGAA
192321 ACTAATGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:204848 original size:91 final size:91
Alignment explanation
Indices: 204618--204868 Score: 331
Period size: 91 Copynumber: 2.8 Consensus size: 91
204608 GAGGTCAAAC
* *** * *
204618 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTCAAATGGGTTTTTCTCTTTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTTTTCTCATTA
** *
204683 CAAACTCTCCACTGGAAATATTGAGG
66 TGAACTCTCCACAGGAAATATTGAGG
* * *
204709 CAAGGTTGAAAAATTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTTTTCTCATTG
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTTTTCTCATTA
* *
204774 TGAACTCTCCACAGGAAATGTTGATG
66 TGAACTCTCCACAGGAAATATTGAGG
* * * * *
204800 CAAGGATGAACCAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTTTTCTCATTA
204865 TGAA
66 TGAA
204869 GTCCCTGTTG
Statistics
Matches: 138, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
91 138 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (91 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTTTTCTCATTA
TGAACTCTCCACAGGAAATATTGAGG
Found at i:204882 original size:91 final size:91
Alignment explanation
Indices: 204617--204895 Score: 272
Period size: 91 Copynumber: 3.1 Consensus size: 91
204607 TGAGGTCAAA
* * * * * *** * * *
204617 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTCAAATGGGTTTTTCTCTTT
1 CCAAGGATGAACCAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATT
** * * *
204682 ACAAACTCTCCACTGGAAATATTGAG
66 ATGAACTCTCCACAGGAAATGTTGAT
* * ** ** * *
204708 GCAAGGTTGAAAAATTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTTTTCTCATT
1 CCAAGGATGAACCAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATT
*
204773 GTGAACTCTCCACAGGAAATGTTGAT
66 ATGAACTCTCCACAGGAAATGTTGAT
*
204799 GCAAGGATGAACCAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATT
1 CCAAGGATGAACCAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATT
* ***
204864 ATGAAGTC-CCTGTTGGAAATGTTGAT
66 ATGAACTCTCC-ACAGGAAATGTTGAT
204890 CCAAGG
1 CCAAGG
204896 TTGATTCGAA
Statistics
Matches: 159, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
90 2 0.01
91 157 0.99
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (91 bp):
CCAAGGATGAACCAGCTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATT
ATGAACTCTCCACAGGAAATGTTGAT
Found at i:207749 original size:40 final size:40
Alignment explanation
Indices: 207697--208010 Score: 296
Period size: 40 Copynumber: 7.9 Consensus size: 40
207687 CAAGTGAGAT
* * *
207697 AAATCATCTGTTTTGAGTGAAACTATCTCAAGCGAGATAA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGACAA
*
207737 AAATATGT-TGTTTCGAGTGAAACTATCTCAAGCGAGACAA
1 AAATCT-TCTGTTTCGAGTGAAACTATCTCAAGCGAGACAA
* ** * * * *
207777 AAATATGATGTTTCGAGTGAAACTATGTTAAGAGATACAA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGACAA
**
207817 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA-TG
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGACAA
* * **
207856 TAATCTTCCGTTTCGAGTGAAACTATCTCAAAAGAGACAA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGACAA
* ** *
207896 AAATCTTCTATTTCGAGTGAAACTATCTCATA-ATAGACTA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCA-AGCGAGACAA
* * **
207936 AAATCTTTTGTTTCGAGTGAAA-TCATCTCAACCGAGA-TG
1 AAATCTTCTGTTTCGAGTGAAACT-ATCTCAAGCGAGACAA
* * * * *
207975 TAATCTTTTATTTCAAGTGAAACTATCTTAAGCGAG
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAG
208011 TTGTTGATCC
Statistics
Matches: 228, Mismatches: 39, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
39 65 0.29
40 161 0.71
41 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (40 bp):
AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGACAA
Found at i:207910 original size:119 final size:117
Alignment explanation
Indices: 207697--208002 Score: 355
Period size: 119 Copynumber: 2.6 Consensus size: 117
207687 CAAGTGAGAT
* * ** *
207697 AAATCATCTGTTTTGAGTGAAACTATCTCAAGCGAGATAAAAATATGTTGTTTCGAGTGAAACTA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-GTAATCT-TTGTTTCGAGTGAAACTA
** * *
207762 TCTCAAGCGAGACAAAAATATGATGTTTCGAGTGAAACTATGT-TAAGAGATACAA
64 TCTCAAAAGAGACAAAAATATGATATTTCGAGTGAAACTATCTATAAGAG--ACAA
*
207817 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGTAATCTTCCGTTTCGAGTGAAACTAT
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGTAATCTT-TGTTTCGAGTGAAACTAT
* ** * *
207882 CTCAAAAGAGACAAAAATCTTCTATTTCGAGTGAAACTATCTCATAATAGACTA
65 CTCAAAAGAGACAAAAATATGATATTTCGAGTGAAACTATCT-ATAAGAGACAA
* * * *
207936 AAATCTTTTGTTTCGAGTGAAA-TCATCTCAACCGAGATGTAATCTTTTATTTCAAGTGAAACTA
1 AAATCTTCTGTTTCGAGTGAAACT-ATCTCAAGCGAGATGTAATC-TTTGTTTCGAGTGAAACTA
208000 TCT
64 TCT
208003 TAAGCGAGTT
Statistics
Matches: 161, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
118 2 0.01
119 116 0.72
120 38 0.24
121 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (117 bp):
AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGTAATCTTTGTTTCGAGTGAAACTATC
TCAAAAGAGACAAAAATATGATATTTCGAGTGAAACTATCTATAAGAGACAA
Found at i:208294 original size:38 final size:39
Alignment explanation
Indices: 208240--208325 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 39
208230 CTTAGTTTCT
* * * *
208240 TAAAATCTTTTGTTTCGAGCGAAACTATCTCAAGCTAGA
1 TAAAATCTTCTATTTCGAGCGAAACTATCTCAAACGAGA
*
208279 T-AAATCTTCTATTTCGAGTGAAACTATCTCAAACGAGA
1 TAAAATCTTCTATTTCGAGCGAAACTATCTCAAACGAGA
208317 TAAAATCTT
1 TAAAATCTT
208326 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 33 0.80
39 8 0.20
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (39 bp):
TAAAATCTTCTATTTCGAGCGAAACTATCTCAAACGAGA
Found at i:214160 original size:6 final size:5
Alignment explanation
Indices: 214136--214178 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
214126 AATAAAAATT
214136 TAAAA TAAAA TAAACA TAAATA TAAAAA TAAAAA TAAAA TAAA
1 TAAAA TAAAA TAAA-A TAAA-A T-AAAA T-AAAA TAAAA TAAA
214179 CATGCATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
5 17 0.49
6 15 0.43
7 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:215579 original size:3 final size:3
Alignment explanation
Indices: 215562--215615 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
215552 GTCTGGTTTG
* *
215562 TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
215610 T-A TAA T
1 TAA TAA T
215616 CTGGAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:217402 original size:31 final size:31
Alignment explanation
Indices: 217335--217407 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
217325 AAATTATTTT
*
217335 AAATTTGTGATGGAATATGTGGACCCATCAC
1 AAATTTGTGACGGAATATGTGGACCCATCAC
* * *
217366 GAATTTGTGACGGAATATGTGGACTCGTCAC
1 AAATTTGTGACGGAATATGTGGACCCATCAC
*
217397 AAATTTCTGAC
1 AAATTTGTGAC
217408 AGATTCACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (31 bp):
AAATTTGTGACGGAATATGTGGACCCATCAC
Found at i:217428 original size:31 final size:30
Alignment explanation
Indices: 217393--217462 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
217383 TGTGGACTCG
* *
217393 TCACAAATTTCTGACAGATTCACTTATTCCA
1 TCACAAATTT-TGACAGATCCACATATTCCA
* * *
217424 TCACAAATTTTGACTGGTCCACATGTTCCA
1 TCACAAATTTTGACAGATCCACATATTCCA
217454 TCACAAATT
1 TCACAAATT
217463 GTATAGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (30 bp):
TCACAAATTTTGACAGATCCACATATTCCA
Found at i:217553 original size:13 final size:13
Alignment explanation
Indices: 217532--217565 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
217522 AAACTAACCC
217532 TTTTT-TCCCCTT
1 TTTTTCTCCCCTT
217544 TTTTTCTCCCCTT
1 TTTTTCTCCCCTT
217557 TTTTTCTCC
1 TTTTTCTCC
217566 TATTTAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTCTCCCCTT
Found at i:218672 original size:325 final size:325
Alignment explanation
Indices: 218074--218714 Score: 1020
Period size: 325 Copynumber: 2.0 Consensus size: 325
218064 TTTATCAAAT
*
218074 TAATCTAATTATTTGAATTATATTCTTATTAATTTTTGGTACATTAATTAATTAAATAAAAAAAA
1 TAATCTAATTATTTGAATTATATTATTATTAATTTTTGGTACATTAATTAATTAAAT-AAAAAAA
** * *
218139 TTGGATTCATAATAATTTTTTTTTGGAGGAAATTAATATATTTTCGGGTAGAATCCCAATAAAAT
65 TTGGACACATAATAACTTTTTTTTGGAGGAAATAAATATATTTTCGGGTAGAATCCCAATAAAAT
* * * * *
218204 TTTCCTCTTTTTTAAAAAAAATAAGATTTAAATTTCTGATGGAAAAAATGTAGTCTATCGGAAAT
130 TTACCTCTTTTTTAAAAAAAATAAGATTTAAATTTCCGACGGAAAAAATGTAATCTATCGAAAAT
* **
218269 TAAAAAATTCAGATTTTCTTTTTATCTTTATAAATATCCTGAAGGAAAAGATATGTTCATCAGAA
195 TAAAAAATCCAGATTTTCTTTTTATCTTTATAAATATCCCAAAGGAAAAGATATGTTCATCAGAA
** *
218334 ACATAAAATATATTATATTTTATATATATTTATAATATTCCGACGGATTTAAAATATTTCGTTAG
260 ACATAAAATATA-T-TATTAAATATATATTTATAATATTCCGACGAATTTAAAATATTTCGTTAG
218399 TAA
323 TAA
218402 TAATCTAATTATTTGAATTATATTATTATTAATTTTTGGTACATTAATTAATTAAAT-AAAAAAT
1 TAATCTAATTATTTGAATTATATTATTATTAATTTTTGGTACATTAATTAATTAAATAAAAAAAT
* * *
218466 TGGACACATAAT-ACTTTTTTTT-GAGGAAATAAATATATTTTTGGGTAGAATTCCAATATAATT
66 TGGACACATAATAACTTTTTTTTGGAGGAAATAAATATATTTTCGGGTAGAATCCCAATAAAATT
*
218529 TACCTCTTTTTTTTTAAAAAAATAAGATTTAAATTTCCGACGGAAAAAATGTAATCTATCGAAAA
131 TACCTC--TTTTTTAAAAAAAATAAGATTTAAATTTCCGACGGAAAAAATGTAATCTATCGAAAA
218594 TT-AAAAATCCAGATTTTCTTTTTATCTTTATAAATATCCCAAAGGAAAAGATATGTTCATCAGA
194 TTAAAAAATCCAGATTTTCTTTTTATCTTTATAAATATCCCAAAGGAAAAGATATGTTCATCAGA
*
218658 AACATAAAATATATTATTAAATATATATTTATAATATTCCGACGAATTTTAAATATT
259 AACATAAAATATATTATTAAATATATATTTATAATATTCCGACGAATTTAAAATATT
218715 AGATAGTAAT
Statistics
Matches: 290, Mismatches: 21, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
323 39 0.13
324 43 0.15
325 81 0.28
326 71 0.24
328 56 0.19
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (325 bp):
TAATCTAATTATTTGAATTATATTATTATTAATTTTTGGTACATTAATTAATTAAATAAAAAAAT
TGGACACATAATAACTTTTTTTTGGAGGAAATAAATATATTTTCGGGTAGAATCCCAATAAAATT
TACCTCTTTTTTAAAAAAAATAAGATTTAAATTTCCGACGGAAAAAATGTAATCTATCGAAAATT
AAAAAATCCAGATTTTCTTTTTATCTTTATAAATATCCCAAAGGAAAAGATATGTTCATCAGAAA
CATAAAATATATTATTAAATATATATTTATAATATTCCGACGAATTTAAAATATTTCGTTAGTAA
Found at i:220828 original size:21 final size:21
Alignment explanation
Indices: 220802--220846 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
220792 GATTTCTGGG
* *
220802 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
220823 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
220844 CAA
1 CAA
220847 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:222707 original size:103 final size:103
Alignment explanation
Indices: 222379--222699 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
222369 GTCGAAGGTC
222379 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
222444 TTGATTCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
222482 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
222547 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
222585 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
222650 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
222688 TATGTGGTCCTT
1 TATGTGGTCCTT
222700 ATGGACATTA
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:222775 original size:23 final size:23
Alignment explanation
Indices: 222715--222767 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
222705 CATTATTATA
*
222715 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
222738 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
222761 TGGCACT
1 TGGCACT
222768 TTGGTGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:224114 original size:7 final size:8
Alignment explanation
Indices: 224098--224125 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
224088 AGTCTAATTT
224098 AAAATAAA
1 AAAATAAA
224106 AAAATAAA
1 AAAATAAA
224114 AAAATAAA
1 AAAATAAA
224122 AAAA
1 AAAA
224126 GAGAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:224398 original size:10 final size:10
Alignment explanation
Indices: 224391--224435 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
224381 GAACGTTCAG
224391 TTATGTTCGT
1 TTATGTTCGT
224401 TTATGTTCGTT
1 TTATGTTCG-T
224412 CAGTTATGTTCGT
1 ---TTATGTTCGT
224425 TTATGTTCGT
1 TTATGTTCGT
224435 T
1 T
224436 CATTTATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 20 0.65
11 1 0.03
13 1 0.03
14 9 0.29
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.58
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:224401 original size:24 final size:24
Alignment explanation
Indices: 224374--224445 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
224364 CGTTCATTTA
*
224374 CGTTCGTGAACGTTCAGTTATGTT
1 CGTTCATGAACGTTCAGTTATGTT
* **
224398 CGTTTATGTTCGTTCAGTTATGTT
1 CGTTCATGAACGTTCAGTTATGTT
* ** *
224422 CGTTTATGTTCGTTCATTTATGTT
1 CGTTCATGAACGTTCAGTTATGTT
224446 TAACCCAATC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (24 bp):
CGTTCATGAACGTTCAGTTATGTT
Found at i:225544 original size:16 final size:16
Alignment explanation
Indices: 225523--225589 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
225513 GTTTCCAACG
225523 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
225539 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
225555 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
225571 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
225585 TTTAT
1 TTTAT
225590 TAAATGAACA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:225675 original size:16 final size:16
Alignment explanation
Indices: 225654--225684 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
225644 AAAAAATTTG
225654 TTCGTTTATGTTCGTA
1 TTCGTTTATGTTCGTA
225670 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
225685 TTATTTATTA
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:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTA
Found at i:230844 original size:34 final size:33
Alignment explanation
Indices: 230806--230869 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
230796 TTGTATTTTG
230806 TGATTTAAGA-GTTAAATATAAATTATTATTGTTA
1 TGATTTAA-ATGTTAAATATAAATTA-TATTGTTA
*
230840 TGATTTAAATGTTAAATTTAAATTATATTG
1 TGATTTAAATGTTAAATATAAATTATATTG
230870 ATTTATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 6 0.21
34 22 0.79
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (33 bp):
TGATTTAAATGTTAAATATAAATTATATTGTTA
Found at i:230871 original size:28 final size:27
Alignment explanation
Indices: 230840--230904 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
230830 ATTATTGTTA
*
230840 TGATTTAAATGTTAAATTTAAATTATAT
1 TGATTTAAATGTTAAA-ATAAATTATAT
** *
230868 TGATTTATTTTGTTAAAATATATTATAT
1 TGATTTA-AATGTTAAAATAAATTATAT
230896 T-ATTTAAAT
1 TGATTTAAAT
230905 TATTTAGTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.03
27 5 0.17
28 17 0.57
29 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (27 bp):
TGATTTAAATGTTAAAATAAATTATAT
Found at i:230883 original size:23 final size:23
Alignment explanation
Indices: 230857--230900 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
230847 AATGTTAAAT
*
230857 TTAAATTATATTGAT-TTATTTTG
1 TTAAAATATATT-ATATTATTTTG
230880 TTAAAATATATTATATTATTT
1 TTAAAATATATTATATTATTT
230901 AAATTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
TTAAAATATATTATATTATTTTG
Found at i:233670 original size:11 final size:11
Alignment explanation
Indices: 233654--233679 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
233644 ATAAACATAC
233654 AAATAGTTACA
1 AAATAGTTACA
233665 AAATAGTTACA
1 AAATAGTTACA
233676 AAAT
1 AAAT
233680 TATTTAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (11 bp):
AAATAGTTACA
Found at i:234909 original size:21 final size:21
Alignment explanation
Indices: 234871--234910 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
234861 CAACAACCAA
*
234871 AATAGAGAGAAATCGAGAGAG
1 AATAGAGAGAAATAGAGAGAG
234892 AATAGAGA-AAATA-AGAGAG
1 AATAGAGAGAAATAGAGAGAG
234911 TGAGAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.57, C:0.03, G:0.30, T:0.10
Consensus pattern (21 bp):
AATAGAGAGAAATAGAGAGAG
Found at i:240590 original size:102 final size:102
Alignment explanation
Indices: 240410--240646 Score: 325
Period size: 102 Copynumber: 2.3 Consensus size: 102
240400 GAGCATATTG
* * * * * *
240410 TTTGTCTCCCTTGAGACAGTTGCTCTTGAAACAAATTTATTTTCGCTTCAGACAGTTTCTCTTGA
1 TTTGTCTCGCTTGAGACAATTTCTCTTGAAACAAATTTATTCTCACTTCAGACAATTTCTCTTGA
240475 AACATAAAACTTTGAGATTGTTTCTCTT-AAAACAAAT
66 AACATAAAACTTTGAGATTGTTTCTCTTGAAAA-AAAT
* * * *
240512 TTTGTCTCGCTTGAGACATTTTCTCTTTAAACAAATTT-TGTCTCACTTGAGATAATTTCTCTTG
1 TTTGTCTCGCTTGAGACAATTTCTCTTGAAACAAATTTAT-TCTCACTTCAGACAATTTCTCTTG
* *
240576 AAACATAAACCTTTGAGTTTGTTTCTCTTGAAAAAAAT
65 AAACATAAAACTTTGAGATTGTTTCTCTTGAAAAAAAT
*
240614 TTTGTCTCGCTTGAGATAATTTCTCTTGAAACA
1 TTTGTCTCGCTTGAGACAATTTCTCTTGAAACA
240647 TAAACCTTTG
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
101 1 0.01
102 114 0.96
103 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (102 bp):
TTTGTCTCGCTTGAGACAATTTCTCTTGAAACAAATTTATTCTCACTTCAGACAATTTCTCTTGA
AACATAAAACTTTGAGATTGTTTCTCTTGAAAAAAAT
Found at i:240592 original size:66 final size:67
Alignment explanation
Indices: 240531--240811 Score: 381
Period size: 66 Copynumber: 4.2 Consensus size: 67
240521 CTTGAGACAT
* * * *
240531 TTTCTCTTTAAACAAATTTTGTCTCACTTGAGATAATTTCTCTTGAAACATAAACCTTTGAG-TT
1 TTTCTCTTGAAACAAATTTTATATCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATT
240595 TG
66 TG
* * * *
240597 TTTCTCTTGAAAAAAATTTTGTCTCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGATA-T
1 TTTCTCTTGAAACAAATTTTATATCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATT
240661 TG
66 TG
* * *
240663 TTTCTCTCGAAACAAAGTTTCATATCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAG-T
1 TTTCTCTTGAAACAAA-TTTTATATCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGAT
240727 TTG
65 TTG
* * * *
240730 TTTCTCTTAAAACAAATTTTATATCCCTTGTGATAGTTTCTCTTGAAACATAAACCTTTGAGA-T
1 TTTCTCTTGAAACAAATTTTATATCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATT
240794 TG
66 TG
*
240796 TTTCTCTCGAAACAAA
1 TTTCTCTTGAAACAAA
240812 GTTTCGTCTC
Statistics
Matches: 193, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
66 135 0.70
67 58 0.30
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (67 bp):
TTTCTCTTGAAACAAATTTTATATCGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATT
TG
Found at i:240718 original size:133 final size:133
Alignment explanation
Indices: 240557--240843 Score: 443
Period size: 133 Copynumber: 2.2 Consensus size: 133
240547 TTTTGTCTCA
* * *
240557 CTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTTGAAAA-AAATTTTGTCT
1 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTT-AAAACAAATTTTATAT
* *
240621 CGCTTGAGATAATTTCTCTTGAAACATAAACCTTTGATATTGTTTCTCTCGAAACAAAGTTTCAT
65 CCCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCAT
240686 ATCG
130 ATCG
240690 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTTAAAACAAATTTTATATC
1 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTTAAAACAAATTTTATATC
* * * *
240755 CCTTGTGATAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTC
66 CCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCATA
240820 TCG
131 TCG
* *
240823 CATT-AGACAGTTTCCCTTGAA
1 C-TTGAGATAGTTTCTCTTGAA
240844 GCCCAAATTT
Statistics
Matches: 141, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
132 4 0.03
133 135 0.96
134 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (133 bp):
CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTTAAAACAAATTTTATATC
CCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCATA
TCG
Found at i:240723 original size:67 final size:67
Alignment explanation
Indices: 240557--240843 Score: 375
Period size: 66 Copynumber: 4.3 Consensus size: 67
240547 TTTTGTCTCA
* * * ** *
240557 CTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTTGAAA-AAAATTTTGTCT
1 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTCGAAACAAAGTTTCATAT
240621 CG
66 CG
*
240623 CTTGAGATAATTTCTCTTGAAACATAAACCTTTGA-TATTGTTTCTCTCGAAACAAAGTTTCATA
1 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGT-TTGTTTCTCTCGAAACAAAGTTTCATA
240687 TCG
65 TCG
** *
240690 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTTAAAACAAA-TTTTATAT
1 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTCGAAACAAAGTTTCATAT
*
240754 CC
66 CG
* * * *
240756 CTTGTGATAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCT
1 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTCGAAACAAAGTTTCATAT
240821 CG
66 CG
* *
240823 CATT-AGACAGTTTCCCTTGAA
1 C-TTGAGATAGTTTCTCTTGAA
240844 GCCCAAATTT
Statistics
Matches: 195, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 109 0.56
67 82 0.42
68 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (67 bp):
CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTCGAAACAAAGTTTCATAT
CG
Found at i:240779 original size:36 final size:36
Alignment explanation
Indices: 240416--240779 Score: 150
Period size: 36 Copynumber: 10.8 Consensus size: 36
240406 ATTGTTTGTC
* * *
240416 TCCCTTGAGACAGTTGCTCTTGAAACAAA-TTTATTT
1 TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTA-TA
* * *
240452 TCGCTTCAGACAGTTTCTCTTGAAACATAA----A-A
1 TCCCTTGAGATAGTTTCTCTTGAAACA-AATTTTATA
* * * * *
240484 --CTTTGAGATTGTTTCTCTTAAAACAAATTTTGTC
1 TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTATA
* * * * * *
240518 TCGCTTGAGACATTTTCTCTTTAAACAAATTTTGTC
1 TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTATA
* *
240554 TCACTTGAGATAATTTCTCTTGAAAC--A---TA-A
1 TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTATA
* * * * * * *
240584 ACCTTTGAGTTTGTTTCTCTTGAAAAAAATTTTGTC
1 TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTATA
* *
240620 TCGCTTGAGATAATTTCTCTTGAAAC--A---TA-A
1 TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTATA
* * * * * *
240650 ACCTTTGATATTGTTTCTCTCGAAACAAAGTTTCATA
1 TCCCTTGAGATAGTTTCTCTTGAAACAAA-TTTTATA
*
240687 TCGCTTGAGATAGTTTCTCTTGAAAC--A---TA-A
1 TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTATA
* * * * *
240717 ACCTTTGAGTTTGTTTCTCTTAAAACAAATTTTATA
1 TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTATA
*
240753 TCCCTTGTGATAGTTTCTCTTGAAACA
1 TCCCTTGAGATAGTTTCTCTTGAAACA
240780 TAAACCTTTG
Statistics
Matches: 232, Mismatches: 69, Indels: 54
0.65 0.19 0.15
Matches are distributed among these distances:
29 2 0.01
30 78 0.34
31 3 0.01
32 3 0.01
34 3 0.01
35 4 0.02
36 116 0.50
37 23 0.10
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (36 bp):
TCCCTTGAGATAGTTTCTCTTGAAACAAATTTTATA
Found at i:240860 original size:133 final size:132
Alignment explanation
Indices: 240557--240876 Score: 389
Period size: 133 Copynumber: 2.4 Consensus size: 132
240547 TTTTGTCTCA
* * * * * *
240557 CTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTTGAAAAAAATTTTGTCTC
1 CTTGAGACAGTTTCCCTTGAAACACAAA-CTTTGAGTTTGTTTCTCTTGAAAAAAATTTTATATC
* *
240622 GCTTGAGATAATTTCTCTTGAAACATAAACCTTTGATATTGTTTCTCTCGAAACAAAGTTTCATA
65 CCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCATA
240687 TCG
130 TCG
* * *
240690 CTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTT-AAAACAAATTTTATAT
1 CTTGAGACAGTTTCCCTTGAAACACAAA-CTTTGAGTTTGTTTCTCTTGAAAA-AAATTTTATAT
* * *
240754 CCCTTGTGATAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGT
64 CCCTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCAT
*
240819 CTCG
129 ATCG
* *
240823 CATT-AGACAGTTTCCCTTGAAGCCCAAA-TTTCGGAG-TTGTTTCAT-TTGAAAAAA
1 C-TTGAGACAGTTTCCCTTGAAACACAAACTTT--GAGTTTGTTTC-TCTTGAAAAAA
240877 GAAATTGATC
Statistics
Matches: 167, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
131 3 0.02
132 15 0.09
133 147 0.88
134 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (132 bp):
CTTGAGACAGTTTCCCTTGAAACACAAACTTTGAGTTTGTTTCTCTTGAAAAAAATTTTATATCC
CTTGAGATAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCATAT
CG
Found at i:241009 original size:102 final size:102
Alignment explanation
Indices: 240859--241102 Score: 272
Period size: 102 Copynumber: 2.4 Consensus size: 102
240849 AATTTCGGAG
* * * * * * * *
240859 TTGTTTCATTTGAAAAAAGAAATTGATCTCATTTGAGAGTGTTTTCCTAGAAACAAATTTCGTCT
1 TTGTTTCACTTG--AAACGAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATGTCATAT
* *
240924 CACTTGATACAGTTTTCCCTCAAAACATAAAATGTGAAA
64 CACTTGAAACAGTTTTCCCTCAAAACACAAAATGTGAAA
*
240963 TTGTTTCACTTGAAACGAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATGTCATATCG
1 TTGTTTCACTTGAAACGAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATGTCATATCA
* ** * * *
241028 CTTGAAATAGTTTTCCCTTGAAACGCAAATTTTGAAA
66 CTTGAAACAGTTTTCCCTCAAAACACAAAATGTGAAA
* * * *
241065 TTGTTTCACTCGAAACAAAATTTTATCTCACCTGAGAT
1 TTGTTTCACTTGAAACGAAA-TTGATCTCACTTGAGAT
241103 AACTTCTCTT
Statistics
Matches: 118, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
102 92 0.78
103 15 0.13
104 11 0.09
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (102 bp):
TTGTTTCACTTGAAACGAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATGTCATATCA
CTTGAAACAGTTTTCCCTCAAAACACAAAATGTGAAA
Found at i:241079 original size:29 final size:29
Alignment explanation
Indices: 241029--241088 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
241019 GTCATATCGC
* * *
241029 TTGAAATAGTTTTCCCTTGAAACGCAAATT
1 TTGAAATAGTTTTCACTCGAAAC-AAAATT
*
241059 TTGAAATTG-TTTCACTCGAAACAAAATT
1 TTGAAATAGTTTTCACTCGAAACAAAATT
241087 TT
1 TT
241089 ATCTCACCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 7 0.27
29 11 0.42
30 8 0.31
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (29 bp):
TTGAAATAGTTTTCACTCGAAACAAAATT
Found at i:243041 original size:29 final size:29
Alignment explanation
Indices: 243004--243062 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
242994 CCCGGGTATG
* *
243004 ACTTTCATTATTTACGATTCGGGTTAAAT
1 ACTTGCATTATTTACGATTCAGGTTAAAT
*
243033 ACTTGCATTATTTACGATTCATGTTAAAT
1 ACTTGCATTATTTACGATTCAGGTTAAAT
243062 A
1 A
243063 TTAAAGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (29 bp):
ACTTGCATTATTTACGATTCAGGTTAAAT
Found at i:246567 original size:12 final size:12
Alignment explanation
Indices: 246550--246611 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
246540 GTAGACACAA
246550 ATTTTTCATT-TT
1 ATTTTT-ATTATT
246562 ATTTTTATTATT
1 ATTTTTATTATT
* *
246574 ATATTT-TTATA
1 ATTTTTATTATT
* *
246585 AATATTATTATT
1 ATTTTTATTATT
*
246597 ATTTTAATTATT
1 ATTTTTATTATT
246609 ATT
1 ATT
246612 AAATAAAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:246583 original size:20 final size:21
Alignment explanation
Indices: 246558--246612 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
246548 AAATTTTTCA
*
246558 TTTTATTTTTATTATTA-TAT
1 TTTTATTATTATTATTATTAT
* *
246578 TTTTATAAATATTATTATTAT
1 TTTTATTATTATTATTATTAT
*
246599 TTTAATTATTATTA
1 TTTTATTATTATTA
246613 AATAAAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTATTATTATTATTAT
Found at i:248027 original size:11 final size:11
Alignment explanation
Indices: 247998--248042 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
247988 ATATGTTTAA
*
247998 ATTATTACTTTC
1 ATTATTA-TTTT
248010 ATTATTATTTT
1 ATTATTATTTT
*
248021 TTTATTATTTT
1 ATTATTATTTT
248032 ATTATTATTTT
1 ATTATTATTTT
248043 CATCTTAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 23 0.77
12 7 0.23
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:248038 original size:22 final size:23
Alignment explanation
Indices: 247999--248042 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
247989 TATGTTTAAA
247999 TTATTACTTTCATTATTATTTTT
1 TTATTACTTTCATTATTATTTTT
*
248022 TTATTA-TTTTATTATTATTTT
1 TTATTACTTTCATTATTATTTT
248043 CATCTTAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (23 bp):
TTATTACTTTCATTATTATTTTT
Found at i:248207 original size:45 final size:47
Alignment explanation
Indices: 248149--248250 Score: 104
Period size: 45 Copynumber: 2.2 Consensus size: 47
248139 CCTATTCTGG
** *
248149 TATTTTAAATAAATAAATATTATAAAAATTAT-ATATATTT-AAT-TT
1 TATTTTATTTAAATAAATATTAGAAAAATTATCATAT-TTTCAATATT
* * * *
248194 TATTTTATTTAAATTATTTTTAGGAAAATTATCATATTTTCAATATT
1 TATTTTATTTAAATAAATATTAGAAAAATTATCATATTTTCAATATT
248241 TA-TTTATTTA
1 TATTTTATTTA
248251 TTTAATATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
45 28 0.60
46 15 0.32
47 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (47 bp):
TATTTTATTTAAATAAATATTAGAAAAATTATCATATTTTCAATATT
Found at i:248384 original size:152 final size:150
Alignment explanation
Indices: 248084--248366 Score: 426
Period size: 152 Copynumber: 1.9 Consensus size: 150
248074 TTTAAATAAT
*
248084 AATATTTATTTATTTTTTAATATTAAGAAAGGGCAGTCTTAATATAACTAGAAGTCCTATTCTGG
1 AATATTTATTTATTTTTTAATATTAAGAAAGGGCAGTCTTAATATAACTAGAAGTCATATTCTGG
*** * **
248149 TATTTTAAATAAATAAATATTATAAAAATTATATATATTTAATTTTATTTTATTTAAATTATTTT
66 TATTTTAAATAAATAAATATTATAAAAATTATATATATTTAATTTTATAAAAATTAAAGCATTTT
248214 TAGGAAAATTATCATATTTTC
131 TA-GAAAATTATCATATTTTC
*
248235 AATATTTATTTATTTATTTAATATTAAGAAAGGGCAGTCTTAATATAACTAGATGTCATATTCTG
1 AATATTTATTTATTT-TTTAATATTAAGAAAGGGCAGTCTTAATATAACTAGAAGTCATATTCTG
* **
248300 GTATTTTAAATTAATAAATATTATAAAAA-T-TATATATTTAATTTTATGAAAAATTATCGCATT
65 GTATTTTAAATAAATAAATATTATAAAAATTATATATATTTAATTTTAT-AAAAATTAAAGCATT
248363 TTTA
129 TTTA
248367 ATATTTATTT
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
150 17 0.14
151 27 0.23
152 75 0.63
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (150 bp):
AATATTTATTTATTTTTTAATATTAAGAAAGGGCAGTCTTAATATAACTAGAAGTCATATTCTGG
TATTTTAAATAAATAAATATTATAAAAATTATATATATTTAATTTTATAAAAATTAAAGCATTTT
TAGAAAATTATCATATTTTC
Found at i:248639 original size:2 final size:2
Alignment explanation
Indices: 248632--248667 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
248622 AACGTCCTAA
248632 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
248668 TTAATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249868 original size:14 final size:14
Alignment explanation
Indices: 249849--249881 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
249839 GGTACTAACC
*
249849 ATTTTATTTTTTTT
1 ATTTTATTTTTCTT
249863 ATTTTATTTTTCTT
1 ATTTTATTTTTCTT
249877 ATTTT
1 ATTTT
249882 TCTCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (14 bp):
ATTTTATTTTTCTT
Found at i:250011 original size:22 final size:19
Alignment explanation
Indices: 249983--250022 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
249973 AGATGTTGAC
249983 TTGAAAGATTGTTCATCAAATT
1 TTGAAAG-TT-TTCAT-AAATT
250005 TTGAAAGTTTTCATAAAT
1 TTGAAAGTTTTCATAAAT
250023 GGACAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 2 0.11
22 7 0.39
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (19 bp):
TTGAAAGTTTTCATAAATT
Found at i:251591 original size:6 final size:6
Alignment explanation
Indices: 251580--251629 Score: 55
Period size: 6 Copynumber: 7.7 Consensus size: 6
251570 ACACCTTTCT
*
251580 CATTTG CATTTG CATTTG CATTTTG CATCTTTG CATTTT CATTTTG CATT
1 CATTTG CATTTG CATTTG CA-TTTG CA--TTTG CATTTG CA-TTTG CATT
251630 CGTACTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
6 21 0.55
7 11 0.29
8 6 0.16
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.54
Consensus pattern (6 bp):
CATTTG
Found at i:251614 original size:21 final size:21
Alignment explanation
Indices: 251588--251628 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
251578 CTCATTTGCA
251588 TTTGCATTTGCATTTTGCATC
1 TTTGCATTTGCATTTTGCATC
*
251609 TTTGCATTTTCATTTTGCAT
1 TTTGCATTTGCATTTTGCAT
251629 TCGTACTTTT
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:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTGCATTTGCATTTTGCATC
Found at i:251737 original size:7 final size:7
Alignment explanation
Indices: 251713--251762 Score: 70
Period size: 6 Copynumber: 7.4 Consensus size: 7
251703 CATTTATATC
251713 TTTGCA-
1 TTTGCAT
251719 TTTGCA-
1 TTTGCAT
251725 TTTGCAT
1 TTTGCAT
251732 TTTGCA-
1 TTTGCAT
251738 TTTGCAT
1 TTTGCAT
251745 TTTGCAT
1 TTTGCAT
251752 CTTTGCAT
1 -TTTGCAT
251760 TTT
1 TTT
251763 TACGTTTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.44
7 16 0.39
8 7 0.17
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.56
Consensus pattern (7 bp):
TTTGCAT
Found at i:251737 original size:13 final size:13
Alignment explanation
Indices: 251713--251807 Score: 86
Period size: 14 Copynumber: 7.1 Consensus size: 13
251703 CATTTATATC
251713 TTTGCA-TTTGCA
1 TTTGCATTTTGCA
251725 TTTGCATTTTGCA
1 TTTGCATTTTGCA
251738 TTTGCATTTTGCA
1 TTTGCATTTTGCA
* *
251751 TCTTTGCATTTTTACG
1 --TTTGCA-TTTTGCA
* *
251767 TTTGTA-TTTACA
1 TTTGCATTTTGCA
*
251779 TTTTCATTTTTGCA
1 TTTGCA-TTTTGCA
251793 TTTGCATATTTGCA
1 TTTGCAT-TTTGCA
251807 T
1 T
251808 AATTACATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
12 15 0.22
13 20 0.29
14 22 0.32
15 6 0.09
16 5 0.07
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.56
Consensus pattern (13 bp):
TTTGCATTTTGCA
Found at i:257872 original size:22 final size:22
Alignment explanation
Indices: 257844--257900 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
257834 ACATCTACAT
257844 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
257866 TCTTCAAATATGATAGATTTTC
1 TCTTCAAAGATGATAGATTCTC
*
257888 TTTTCAAAGATGA
1 TCTTCAAAGATGA
257901 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:258733 original size:76 final size:74
Alignment explanation
Indices: 258607--258748 Score: 241
Period size: 76 Copynumber: 1.9 Consensus size: 74
258597 TTCAGTGCAG
*
258607 GATGTTTTCAAATCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCCTTC
1 GATGTTTTCAAATCCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAA-CCTTC
258672 GGGAGCTTTTT
64 GGGAGCTTTTT
258683 GATGTTTTCAACA-CCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 GATGTTTTCAA-ATCCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
258747 GG
65 GG
258749 TCATCTGTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
74 8 0.12
75 4 0.06
76 51 0.80
77 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (74 bp):
GATGTTTTCAAATCCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGG
GAGCTTTTT
Found at i:258735 original size:45 final size:45
Alignment explanation
Indices: 258682--259029 Score: 543
Period size: 45 Copynumber: 7.7 Consensus size: 45
258672 GGGAGCTTTT
* *
258682 TGATGTTTTCAACACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
258727 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCTTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
258772 TGATGTTTTCAAAACCTTCAGTTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
258817 TGATGTTTTTAAAACCTTCAGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
258862 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* **
258907 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTTTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
258952 TGATATTATCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
** *
258997 TGATGTTTTCAAGGCCTTCGGGTCTTCTGTAAG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
259030 TCTTCCTAGC
Statistics
Matches: 277, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 277 1.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:259235 original size:3 final size:3
Alignment explanation
Indices: 259208--259260 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
259198 CACTGATTTT
* * * *
259208 TTA TT- TTA TTT TTA TTA TAA ATA TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
259255 TTA TTA
1 TTA TTA
259261 AATAAAATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:260760 original size:2 final size:2
Alignment explanation
Indices: 260747--260798 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
260737 CATCTTAGTC
*
260747 AT AT AA 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
260789 AT AT AT AT AT
1 AT AT AT AT AT
260799 TTGTTTAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:268763 original size:20 final size:20
Alignment explanation
Indices: 268740--268791 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
268730 TTGTTATAAT
* *
268740 AATATCGATACTATGGGTTG
1 AATATCGATACTATAGGTGG
* *
268760 AATATTGATATTATAGGTGG
1 AATATCGATACTATAGGTGG
268780 AGA-ATCGATACT
1 A-ATATCGATACT
268792 CAGTTTAAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (20 bp):
AATATCGATACTATAGGTGG
Found at i:268925 original size:20 final size:22
Alignment explanation
Indices: 268874--268927 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
268864 TACTTGCCTT
* *
268874 AGTACCGATACTCCTTTAGGGA
1 AGTATCGATACTCCTATAGGGA
*
268896 AGTATTGATACTCCTATA-GG-
1 AGTATCGATACTCCTATAGGGA
268916 AGTATCGATACT
1 AGTATCGATACT
268928 GCTGAGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 2 0.07
22 15 0.54
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (22 bp):
AGTATCGATACTCCTATAGGGA
Found at i:274133 original size:16 final size:16
Alignment explanation
Indices: 274109--274140 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
274099 TATCACCGAC
*
274109 CAAATTTTACTATTCA
1 CAAAATTTACTATTCA
274125 CAAAATTTACTATTCA
1 CAAAATTTACTATTCA
274141 TGTGAATAGT
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:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (16 bp):
CAAAATTTACTATTCA
Found at i:274622 original size:22 final size:22
Alignment explanation
Indices: 274595--274640 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
274585 TGCATCAATT
*
274595 TTTCAACCCTTGCTGCCATGCA
1 TTTCAACCCTTGCGGCCATGCA
*
274617 TTTCAACTCTTGCGGCCATGCA
1 TTTCAACCCTTGCGGCCATGCA
274639 TT
1 TT
274641 ATTAAGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (22 bp):
TTTCAACCCTTGCGGCCATGCA
Found at i:277660 original size:24 final size:24
Alignment explanation
Indices: 277604--277652 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
277594 TATAGGAGTC
277604 AAACCGTTTATACCACTGTCTCGG
1 AAACCGTTTATACCACTGTCTCGG
277628 AAACCGTTTATACCACTGTCTCGG
1 AAACCGTTTATACCACTGTCTCGG
277652 A
1 A
277653 GACTGTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (24 bp):
AAACCGTTTATACCACTGTCTCGG
Found at i:285075 original size:34 final size:33
Alignment explanation
Indices: 285034--285097 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
285024 TTGTATTTTG
285034 TGATTTAAATGTTAAATATAAATTATTATTGTTA
1 TGATTTAAATGTTAAATATAAATTA-TATTGTTA
*
285068 TGATTTAAATGTTAAATTTAAATTATATTG
1 TGATTTAAATGTTAAATATAAATTATATTG
285098 ATGTATTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 5 0.17
34 24 0.83
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (33 bp):
TGATTTAAATGTTAAATATAAATTATATTGTTA
Found at i:285244 original size:28 final size:27
Alignment explanation
Indices: 285212--285288 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 27
285202 ATCAATAAAA
*
285212 TTTAATTTAAATATTTTTATGATATACT
1 TTTAATTTAAATATTTTTAT-ATATAAT
* *
285240 TTTAATATAAATATATATTTAATATTTAAT
1 TTTAATTTAAATAT-T-TTT-ATATATAAT
*
285270 TATAATTT-AATATTTTTAT
1 TTTAATTTAAATATTTTTAT
285289 TTGGATTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 2 0.05
27 3 0.07
28 14 0.34
29 6 0.15
30 14 0.34
31 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTAATTTAAATATTTTTATATATAAT
Found at i:285260 original size:17 final size:17
Alignment explanation
Indices: 285240--285282 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
285230 ATGATATACT
285240 TTTAATATAAA-TATATA
1 TTTAATATAAATTATA-A
*
285257 TTTAATATTTAATTATAA
1 TTTAATA-TAAATTATAA
285275 TTTAATAT
1 TTTAATAT
285283 TTTTATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 11 0.48
19 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAATATAAATTATAA
Found at i:291378 original size:46 final size:44
Alignment explanation
Indices: 291313--291398 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 44
291303 TCGATGGTTA
291313 CATTGTTGAGAAAATAAGTTAATCTTATGCTTTCCTATCAGGGT
1 CATTGTTGAGAAAATAAGTTAATCTTATGCTTTCCTATCAGGGT
* *
291357 CATTGATTGA-AAAAGTAAAGTTGATCTTATGTTTTCCTATCA
1 CATTG-TTGAGAAAA-T-AAGTTAATCTTATGCTTTCCTATCA
291399 TGATTGTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 9 0.24
45 5 0.14
46 23 0.62
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (44 bp):
CATTGTTGAGAAAATAAGTTAATCTTATGCTTTCCTATCAGGGT
Found at i:300782 original size:18 final size:17
Alignment explanation
Indices: 300759--300792 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
300749 GCCAAAAAAG
300759 ATTTAACTTTATTAAATA
1 ATTTAACTTTA-TAAATA
*
300777 ATTTAATTTTATAAAT
1 ATTTAACTTTATAAAT
300793 TGTTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAACTTTATAAATA
Found at i:300876 original size:42 final size:42
Alignment explanation
Indices: 300795--300880 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 42
300785 TTATAAATTG
**
300795 TTAAATATATATATATATATATATATAATAAAAGTAATTTGAT
1 TTAAATATATATATATATATATATATAATAAAAAAAATTT-AT
300838 TTAAATATATATAGTATATATAT-T-TAATAAAAAAAATTTAT
1 TTAAATATATATA-TATATATATATATAATAAAAAAAATTTAT
300879 TT
1 TT
300881 TTAAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
41 4 0.10
42 13 0.32
43 14 0.35
44 9 0.22
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.45
Consensus pattern (42 bp):
TTAAATATATATATATATATATATATAATAAAAAAAATTTAT
Found at i:300931 original size:12 final size:12
Alignment explanation
Indices: 300914--300974 Score: 69
Period size: 10 Copynumber: 5.5 Consensus size: 12
300904 TATATGAAAT
300914 TATTAATAAAAA
1 TATTAATAAAAA
*
300926 TATT-A-AAAAT
1 TATTAATAAAAA
300936 TATTAATAAAAA
1 TATTAATAAAAA
*
300948 TATT-A-AAAAT
1 TATTAATAAAAA
300958 TATTAAT-AAAA
1 TATTAATAAAAA
300969 TATTAA
1 TATTAA
300975 AATTATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
10 16 0.39
11 13 0.32
12 12 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATTAATAAAAA
Found at i:300934 original size:9 final size:9
Alignment explanation
Indices: 300920--300982 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 9
300910 AAATTATTAA
300920 TAAAAATAT
1 TAAAAATAT
300929 TAAAAATTATT
1 TAAAAA-TA-T
300940 AATAAAAATAT
1 --TAAAAATAT
300951 TAAAAATTAT
1 TAAAAA-TAT
300961 TAATAAAATAT
1 T-A-AAAATAT
*
300972 TAAAATTAT
1 TAAAAATAT
300981 TA
1 TA
300983 TTTCTTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
9 20 0.43
10 7 0.15
11 7 0.15
12 6 0.13
13 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TAAAAATAT
Found at i:300935 original size:22 final size:22
Alignment explanation
Indices: 300910--300982 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
300900 TATATATATG
300910 AAATTATTAATAAAAATATTAA
1 AAATTATTAATAAAAATATTAA
300932 AAATTATTAATAAAAATATTAA
1 AAATTATTAATAAAAATATTAA
300954 AAATTATTAAT-AAAATATT-A
1 AAATTATTAATAAAAATATTAA
300974 AAATTATTA
1 AAATTATTA
300983 TTTCTTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.20
21 8 0.16
22 33 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTATTAATAAAAATATTAA
Found at i:300984 original size:12 final size:12
Alignment explanation
Indices: 300910--300974 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 12
300900 TATATATATG
300910 AAATTATTAATA
1 AAATTATTAATA
*
300922 AAAATATT-A-A
1 AAATTATTAATA
300932 AAATTATTAATA
1 AAATTATTAATA
*
300944 AAAATATT-A-A
1 AAATTATTAATA
300954 AAATTATTAATA
1 AAATTATTAATA
300966 AAA-TATTAA
1 AAATTATTAA
300975 AATTATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
10 16 0.36
11 10 0.22
12 19 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTATTAATA
Found at i:301073 original size:16 final size:17
Alignment explanation
Indices: 301046--301085 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
301036 AAATTTATTA
*
301046 TATTTATATATATTTAAT
1 TATTTATATATA-TAAAT
301064 TATTTATATATATAAAT
1 TATTTATATATATAAAT
301081 TATTT
1 TATTT
301086 TTACCTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTATATATATAAAT
Found at i:301077 original size:20 final size:19
Alignment explanation
Indices: 301038--301076 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
301028 AAATATTTAA
301038 ATTTATTATATTTATATAT
1 ATTTATTATATTTATATAT
*
301057 ATTTAAT-TATTTATATAT
1 ATTTATTATATTTATATAT
301075 AT
1 AT
301077 AAATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTATTATATTTATATAT
Found at i:301128 original size:16 final size:17
Alignment explanation
Indices: 301097--301129 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
301087 TACCTTTACA
*
301097 AAATAATTTAATTTTAT
1 AAATAATTTAAATTTAT
301114 AAATAA-TTAAATTTAT
1 AAATAATTTAAATTTAT
301130 TATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATAATTTAAATTTAT
Found at i:301362 original size:2 final size:2
Alignment explanation
Indices: 301355--301383 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
301345 GTTTTAAATA
301355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
301384 ATAAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:301431 original size:2 final size:2
Alignment explanation
Indices: 301424--301451 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
301414 ATTGGGTTAA
301424 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
301452 GTGAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:301688 original size:14 final size:13
Alignment explanation
Indices: 301668--301699 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
301658 GATTGGATAG
301668 AAAATAAAATAAA
1 AAAATAAAATAAA
301681 ATAAATAAAATAAA
1 A-AAATAAAATAAA
301695 AAAAT
1 AAAAT
301700 TATCTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:305225 original size:32 final size:32
Alignment explanation
Indices: 305141--305225 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
305131 AATAGCATGT
* * *
305141 GGTGTCTCGGTCACCAGCGGCAGTCCTAGGCG
1 GGTGTCTCGATCACCATCGGCAGACCTAGGCG
* * *
305173 GGTGGCCTCGTTCACCATCGGCAGGAGC-AGGCG
1 GGT-GTCTCGATCACCATCGGCA-GACCTAGGCG
305206 GGTGTCTCGATCACCATCGG
1 GGTGTCTCGATCACCATCGG
305226 TAACCCCCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
32 18 0.41
33 24 0.55
34 2 0.05
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.19
Consensus pattern (32 bp):
GGTGTCTCGATCACCATCGGCAGACCTAGGCG
Found at i:309300 original size:130 final size:132
Alignment explanation
Indices: 309062--309425 Score: 378
Period size: 130 Copynumber: 2.8 Consensus size: 132
309052 AATCCAAGGT
* * * *
309062 TTTTAATTATTGAGTTGTCATAAGTAAAATTAAAAGATTAGTTCCTTTTAATTATTGAGTTGCCC
1 TTTTAATTATTGAGTTGCCAAAAGTAAAATCAAAAGATTAGTTCCTTTTAATTATTGAGTTGCCA
* * *** * * * *
309127 AAAGTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAGTTGCC-AA-AAG-TAAAATGATTATT
66 AAATTAAAATCAAAGGATTAGTTCATTTTGATTACCCAATTGCCAAATAAGATAAAAGGAATAGT
309189 TCC
131 T-C
* * * *
309192 TTTTGATTATTGTGTTGCCAAAAGTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAGTTGCCA
1 TTTTAATTATTGAGTTGCCAAAAGTAAAATCAAAAGATTAGTTCCTTTTAATTATTGAGTTGCCA
* *
309257 AAATTAAAATCAAATGATTAGTTCATTTTGATTACCCAATTGCCGAAATTAAGATCAAAGGAATA
66 AAATTAAAATCAAAGGATTAGTTCATTTTGATTACCCAATTGCC-AAA-TAAGATAAAAGGAATA
309322 GTTC
129 GTTC
* * * * * *
309326 TTTTCCATTATTGGGTTGCAAAAATTAAAATCAAATGATTAGTT-TTTTTCAATTATT-AGATTG
1 TTTT-AATTATTGAGTTGCCAAAAGTAAAATCAAAAGATTAGTTCCTTTT-AATTATTGAG-TTG
* * * *
309389 CGAAAATTGAAATCAAAGGGTTAGTTCATTTTTATTA
63 CCAAAATTAAAATCAAAGGATTAGTTCATTTTGATTA
309426 TTGAGTTGCT
Statistics
Matches: 195, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
130 94 0.48
132 2 0.01
134 14 0.07
135 85 0.44
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (132 bp):
TTTTAATTATTGAGTTGCCAAAAGTAAAATCAAAAGATTAGTTCCTTTTAATTATTGAGTTGCCA
AAATTAAAATCAAAGGATTAGTTCATTTTGATTACCCAATTGCCAAATAAGATAAAAGGAATAGT
TC
Found at i:309440 original size:45 final size:45
Alignment explanation
Indices: 309062--309441 Score: 371
Period size: 45 Copynumber: 8.6 Consensus size: 45
309052 AATCCAAGGT
* * * * * *
309062 TTTTAATTATTGAGTTGTCATAAGTAAAATTAAAAGATTAGTTCC
1 TTTTGATTATTGAGTTGCCAAAATTAAAATCAAAGGATTAGTTCC
* * *
309107 TTTTAATTATTGAGTTGCCCAAAGTAAAATCAAAGGATTAGTTCC
1 TTTTGATTATTGAGTTGCCAAAATTAAAATCAAAGGATTAGTTCC
* *
309152 TTTTGATTATTGAGTTGCCAAAAGTAAAAT-----GATTATTTCC
1 TTTTGATTATTGAGTTGCCAAAATTAAAATCAAAGGATTAGTTCC
* *
309192 TTTTGATTATTGTGTTGCCAAAAGTAAAATCAAAGGATTAGTTCC
1 TTTTGATTATTGAGTTGCCAAAATTAAAATCAAAGGATTAGTTCC
* *
309237 TTTTGATTATTGAGTTGCCAAAATTAAAATCAAATGATTAGTTCA
1 TTTTGATTATTGAGTTGCCAAAATTAAAATCAAAGGATTAGTTCC
*** * * * *
309282 TTTTGATTACCCAATTGCCGAAATTAAGATCAAAGGAATAGTT-C
1 TTTTGATTATTGAGTTGCCAAAATTAAAATCAAAGGATTAGTTCC
* * * * *
309326 TTTTCCATTATTGGGTTGCAAAAATTAAAATCAAATGATTAGTT-T
1 TTTT-GATTATTGAGTTGCCAAAATTAAAATCAAAGGATTAGTTCC
* * * * *
309371 TTTTCAATTATT-AGATTGCGAAAATTGAAATCAAAGGGTTAGTTCA
1 TTTT-GATTATTGAG-TTGCCAAAATTAAAATCAAAGGATTAGTTCC
* *
309417 TTTTTATTATTGAGTTGCTAAAATT
1 TTTTGATTATTGAGTTGCCAAAATT
309442 CAATGATTAA
Statistics
Matches: 282, Mismatches: 44, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
40 38 0.13
44 5 0.02
45 233 0.83
46 6 0.02
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (45 bp):
TTTTGATTATTGAGTTGCCAAAATTAAAATCAAAGGATTAGTTCC
Found at i:309692 original size:58 final size:58
Alignment explanation
Indices: 309608--309793 Score: 309
Period size: 58 Copynumber: 3.2 Consensus size: 58
309598 TTGTGTTGAC
* *
309608 TCTAACTTTTTAAGAAAAATAAATAGTTGAATTTATTTCTTTGAGAATCTTAAATGAT
1 TCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
* *
309666 TCTAACTTTGTAAGGAAAATATATAGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
1 TCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
* *
309724 TCTAACTTTGTAAGTAAAATAAATAGTTGAATTTATTTCCATGAGAATCTTAAATGAT
1 TCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
*
309782 TCTAGCTTTGTA
1 TCTAACTTTGTA
309794 TGTATCACTC
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 120 1.00
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (58 bp):
TCTAACTTTGTAAGAAAAATAAATAGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
Found at i:318197 original size:49 final size:49
Alignment explanation
Indices: 318103--318200 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
318093 CAAGCTGGGA
* * **
318103 TTGAGATTGGTGTATGTATCGAGAAGTATTTCTTAAATAGTTTTTATGT
1 TTGAGATTGGTATATGTATCGAGAAGTATTTCTTAAAAAAATTTTATGT
*
318152 TTGAGATTGGTATATGTATC-ACGAAGTATTTGTTAAAAAAATTTTATGT
1 TTGAGATTGGTATATGTATCGA-GAAGTATTTCTTAAAAAAATTTTATGT
318201 CGAATAAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 1 0.02
49 42 0.98
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (49 bp):
TTGAGATTGGTATATGTATCGAGAAGTATTTCTTAAAAAAATTTTATGT
Found at i:319717 original size:22 final size:21
Alignment explanation
Indices: 319661--319717 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
319651 CAACAAAAAA
* *
319661 ATTATATTATATTATTTATTT
1 ATTATATTATTTTATTAATTT
319682 ATTATTATTATTTTATTAATTT
1 ATTA-TATTATTTTATTAATTT
*
319704 ATATATATTTTTTT
1 AT-TATATTATTTT
319718 GCAGGTCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.13
22 25 0.81
23 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTATATTATTTTATTAATTT
Found at i:325058 original size:105 final size:105
Alignment explanation
Indices: 324871--325600 Score: 1130
Period size: 105 Copynumber: 7.0 Consensus size: 105
324861 GGGTCGCTCA
* * * *
324871 AGACAACGCAAGTTCAACTTCACAACGAAGGAACCACTGGTTGTCAATAAACATTTCTCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
* * *
324936 AGAGCCAATTTCAACTTCTCAACGAAGGATCTTGGACTCC
66 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
324976 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
325041 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
325081 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
* *
325146 AGAGCCTATTTCGACTTCATAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
325186 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
325251 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
*
325291 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
* *
325356 AAAGCCAATTTTGACTTCACAACGAAGGATATTGGACTCC
66 AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
* *
325396 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCCATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCCCAATTT
* * * *
325461 CAGAGCCAATTTCAACTTCTCAACGAAGGATCTT-GAATCC
65 CAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
* * * * * * *
325501 AAGACAACACAAGCTCAACTTCATGACGAAGGGGCGGCTGATTGTCAACAAA-ATTT--C-A-TT
1 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTT
* * * * *
325561 CAGAGTCAATTCCAACTTCACAGCGGAGGATATTGGACTC
65 CAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTC
325601 GGAACAATGC
Statistics
Matches: 584, Mismatches: 38, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
100 30 0.05
101 5 0.01
102 1 0.00
104 3 0.01
105 462 0.79
106 83 0.14
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTC
AGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCC
Found at i:326136 original size:22 final size:21
Alignment explanation
Indices: 326080--326136 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
326070 CAACAAAAAA
* *
326080 ATTATATTATATTATTTATTT
1 ATTATATTATTTTATTAATTT
326101 ATTATTATTATTTTATTAATTT
1 ATTA-TATTATTTTATTAATTT
*
326123 ATATATATTTTTTT
1 AT-TATATTATTTT
326137 GCAGGTCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.13
22 25 0.81
23 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTATATTATTTTATTAATTT
Found at i:339305 original size:23 final size:21
Alignment explanation
Indices: 339253--339314 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
339243 TTTTGGTGCA
*
339253 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
339273 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
339294 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
339315 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:339322 original size:21 final size:21
Alignment explanation
Indices: 339296--339335 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
339286 CCCCCTTTGA
*
339296 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
339317 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
339336 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:344016 original size:137 final size:139
Alignment explanation
Indices: 343770--344045 Score: 538
Period size: 137 Copynumber: 2.0 Consensus size: 139
343760 GTGTTCGATT
343770 CACTTGGCTGGAAACCATAAAACAAAAACTTGAGCAAAGACATCACAAATAAGATAGCTCAAGAA
1 CACTTGGCTGGAAACCATAAAACAAAAACTTGAGCAAAGACATCACAAATAAGATAGCTCAAGAA
343835 GAAAAAATAAAGAATTTCACTAGTAGTTTAATTACAGATCTAGGAG-AATAAGACC-ATGAGAAG
66 GAAAAAATAAAGAATTTCACTAGTAGTTTAATTACAGATCTAGGAGAAATAAGACCAATGAGAAG
343898 TAAAATAGG
131 TAAAATAGG
343907 CACTTGGCTGGAAACCATAAAACAAAAACTTGAGCAAAGACATCACAAATAAGATAGCTCAAGAA
1 CACTTGGCTGGAAACCATAAAACAAAAACTTGAGCAAAGACATCACAAATAAGATAGCTCAAGAA
343972 GAAAAAATAAAGAATTTCACTAGTAGTTTAATTACAGATCTAGGAGAAATAAGACCAATGAGAAG
66 GAAAAAATAAAGAATTTCACTAGTAGTTTAATTACAGATCTAGGAGAAATAAGACCAATGAGAAG
344037 TAAAATAGG
131 TAAAATAGG
344046 AAAATATGGT
Statistics
Matches: 137, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
137 111 0.81
138 9 0.07
139 17 0.12
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (139 bp):
CACTTGGCTGGAAACCATAAAACAAAAACTTGAGCAAAGACATCACAAATAAGATAGCTCAAGAA
GAAAAAATAAAGAATTTCACTAGTAGTTTAATTACAGATCTAGGAGAAATAAGACCAATGAGAAG
TAAAATAGG
Found at i:345084 original size:128 final size:127
Alignment explanation
Indices: 344847--345099 Score: 303
Period size: 128 Copynumber: 2.0 Consensus size: 127
344837 ATCTTGAAAG
* **
344847 AGAGGGATATGTTCCACTTCTTCTCGAGGGAAAATCAAATATGGGATGTTGATTTGTTCCACTAT
1 AGAGGGATATGTTCCACTTCTTCTCGAGGGAAAATCAAATATGGGACGTTGATTCATTCCACTAT
* * *
344912 TACTAAGGGAAGATTGAATCGAGGCAGACTTGTTCCATTCTTACTCAG-GGAATATCAAATAT
66 TACTAAGGGAAGATTGAATAGAGGCAGACTTGTTCCACTCTTACTC-GTAGAATATCAAATAT
* * * * * * * * *
344974 AGAGGGATTTGTTTCGCTTTTTCTTGAGGGAAAATTAGATCTAGGGACGTTGATTCATTCCACTG
1 AGAGGGATATGTTCCACTTCTTCTCGAGGGAAAATCAAATAT-GGGACGTTGATTCATTCCACTA
* * *
345039 TT-CTTTAGGGAAGATTGAATAGAGGCAGACTTGTTCTACTGTTACTCGTAGAATATCAAAT
65 TTAC-TAAGGGAAGATTGAATAGAGGCAGACTTGTTCCACTCTTACTCGTAGAATATCAAAT
345100 CTTGAAAGAG
Statistics
Matches: 105, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
127 36 0.34
128 69 0.66
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (127 bp):
AGAGGGATATGTTCCACTTCTTCTCGAGGGAAAATCAAATATGGGACGTTGATTCATTCCACTAT
TACTAAGGGAAGATTGAATAGAGGCAGACTTGTTCCACTCTTACTCGTAGAATATCAAATAT
Found at i:345685 original size:47 final size:47
Alignment explanation
Indices: 345631--345726 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
345621 TTTTCTAGGG
345631 TTTACTCAAATATCAATGTAGAAACTTATAATTTCAAGTTTGCATTC
1 TTTACTCAAATATCAATGTAGAAACTTATAATTTCAAGTTTGCATTC
345678 TTTACTCAAATATCAATGTAGAAACTTATAATTTCAAGTTTGCATTC
1 TTTACTCAAATATCAATGTAGAAACTTATAATTTCAAGTTTGCATTC
345725 TT
1 TT
345727 GAAGAGCCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (47 bp):
TTTACTCAAATATCAATGTAGAAACTTATAATTTCAAGTTTGCATTC
Found at i:347267 original size:27 final size:27
Alignment explanation
Indices: 347231--347392 Score: 147
Period size: 27 Copynumber: 6.5 Consensus size: 27
347221 ATGCCTTAAT
347231 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
* * *
347258 ACATCATTTCATGCATTTTCAATTGTG
1 GCATCCTTTCATGCATTTTCAATTATG
* *
347285 GCATCCGTTCATGC--CTT--A--AT-
1 GCATCCTTTCATGCATTTTCAATTATG
347305 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
* *
347332 GTATCCTTTCATGC--CTT--A--AT-
1 GCATCCTTTCATGCATTTTCAATTATG
347352 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
347379 GCAT-CTGTTCATGC
1 GCATCCT-TTCATGC
347393 CTTAATGCAT
Statistics
Matches: 106, Mismatches: 14, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
20 26 0.25
21 3 0.03
22 4 0.04
23 2 0.02
24 2 0.02
25 4 0.04
26 6 0.06
27 59 0.56
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTCAATTATG
Found at i:347315 original size:47 final size:47
Alignment explanation
Indices: 347259--347425 Score: 280
Period size: 47 Copynumber: 3.6 Consensus size: 47
347249 TCAATTATGA
* *
347259 CATCATTTCATGCATTTTCAATTGTGGCATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
* *
347306 CATCCTTTCATGCATTTTCAATTATGGTATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
*
347353 CATCCTTTCATGCATTTTCAATTATGGCATCTGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
*
347400 CATTCTTTCATGCATTTTCAATTATG
1 CATCCTTTCATGCATTTTCAATTATG
347426 AATTTGATTT
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 112 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.44
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATG
Found at i:347359 original size:20 final size:20
Alignment explanation
Indices: 347285--347365 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 20
347275 TTCAATTGTG
*
347285 GCATCCGTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
347305 GCATCCTTTCATGCATTTTCAATTAT
1 GCATCCTTTCATGC--CTT--A--AT
*
347331 GGTATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
347352 GCATCCTTTCATGC
1 GCATCCTTTCATGC
347366 ATTTTCAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
20 26 0.53
21 2 0.04
22 2 0.04
23 1 0.02
24 1 0.02
25 2 0.04
26 2 0.04
27 13 0.27
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:350873 original size:40 final size:42
Alignment explanation
Indices: 350826--350969 Score: 157
Period size: 45 Copynumber: 3.3 Consensus size: 42
350816 TTTATTGCTT
*
350826 AATAAATGGTAAGCAT-G-AAAATAAGCTTACAAGCTTATGG
1 AATAAATGGTAAGTATGGTAAAATAAGCTTACAAGCTTATGG
*
350866 AATAAATGGTAAGTATATGGATAAAATAAGCTTACTAGCTTATGG
1 AATAAATGGTAAG--TATGG-TAAAATAAGCTTACAAGCTTATGG
* * *
350911 TACAAATGGTAAGTATTTTGGTAAAATAAGCTTACACGCTTATGG
1 AATAAATGGTAAGTA---TGGTAAAATAAGCTTACAAGCTTATGG
350956 TTAATAAATGGTAA
1 --AATAAATGGTAA
350970 AATATTGGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 13
0.80 0.07 0.12
Matches are distributed among these distances:
40 13 0.15
42 2 0.02
43 3 0.03
45 55 0.64
46 3 0.03
47 10 0.12
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (42 bp):
AATAAATGGTAAGTATGGTAAAATAAGCTTACAAGCTTATGG
Found at i:350907 original size:45 final size:44
Alignment explanation
Indices: 350843--350969 Score: 166
Period size: 45 Copynumber: 2.8 Consensus size: 44
350833 GGTAAGCATG
350843 AAAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTA-TATGGAT
1 AAAATAAGCTTAC-AGCTTATGGAATAAATGGTAAGTATTATGG-T
* * *
350888 AAAATAAGCTTACTAGCTTATGGTACAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTAC-AGCTTATGGAATAAATGGTAAGTATTATGGT
350933 AAAATAAGCTTACACGCTTATGGTTAATAAATGGTAA
1 AAAATAAGCTTACA-GCTTATGG--AATAAATGGTAA
350970 AATATTGGAT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
44 1 0.01
45 57 0.79
46 4 0.06
47 10 0.14
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (44 bp):
AAAATAAGCTTACAGCTTATGGAATAAATGGTAAGTATTATGGT
Found at i:354264 original size:19 final size:19
Alignment explanation
Indices: 354226--354266 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
354216 TTGAATCTTT
*
354226 CTTGGATCTACTCGTATGC
1 CTTGGATCTACTCATATGC
*
354245 CTTGGATCTACTCATTTGC
1 CTTGGATCTACTCATATGC
354264 CTT
1 CTT
354267 ATGTAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41
Consensus pattern (19 bp):
CTTGGATCTACTCATATGC
Found at i:357085 original size:20 final size:20
Alignment explanation
Indices: 357060--357136 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 20
357050 GAATACATAC
357060 CCTTTCATGCCTTAATGCAT
1 CCTTTCATGCCTTAATGCAT
*
357080 CCTTTCATGCATTTTCAATTATGGCAT
1 CCTTTCATGC--CTT--A--AT-GCAT
*
357107 CCTTTCATGCCTTAGTGCAT
1 CCTTTCATGCCTTAATGCAT
357127 CCTTTCATGC
1 CCTTTCATGC
357137 ATTTTCAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
20 24 0.51
21 1 0.02
22 2 0.04
23 1 0.02
24 1 0.02
25 2 0.04
26 2 0.04
27 14 0.30
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.42
Consensus pattern (20 bp):
CCTTTCATGCCTTAATGCAT
Found at i:357107 original size:27 final size:27
Alignment explanation
Indices: 357076--357196 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 27
357066 ATGCCTTAAT
357076 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
357103 GCATCCTTTCATGC-----C--TTA-G
1 GCATCCTTTCATGCATTTTCAATTATG
357122 TGCATCCTTTCATGCATTTTCAATTATG
1 -GCATCCTTTCATGCATTTTCAATTATG
* * *
357150 ACATCCGTTCATG-A-CTT-AA-T-T-
1 GCATCCTTTCATGCATTTTCAATTATG
357171 -CATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
357197 AATTTGATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 31
0.67 0.05 0.28
Matches are distributed among these distances:
19 1 0.01
20 28 0.38
21 1 0.01
22 4 0.05
23 3 0.04
24 3 0.04
25 4 0.05
26 1 0.01
27 28 0.38
28 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTCAATTATG
Found at i:357129 original size:47 final size:47
Alignment explanation
Indices: 357060--357197 Score: 231
Period size: 47 Copynumber: 2.9 Consensus size: 47
357050 GAATACATAC
*
357060 CCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGGCAT
1 CCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGACAT
*
357107 CCTTTCATGCCTTAGTGCATCCTTTCATGCATTTTCAATTATGACAT
1 CCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGACAT
* * *
357154 CCGTTCATGACTTAATTCATCCTTTCATGCATTTTCAATTATGA
1 CCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGA
357198 ATTTGATTTA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 85 1.00
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (47 bp):
CCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATGACAT
Found at i:357723 original size:22 final size:20
Alignment explanation
Indices: 357679--357736 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 20
357669 CGTTGTTGTC
357679 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
*
357699 TGGTATCGATACTACCTTACTA
1 TGGTATCGATAC--CCTTACCA
357721 TGGTA-CTGATACCCTT
1 TGGTATC-GATACCCTT
357737 TGTAGTATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 16 0.47
21 1 0.03
22 17 0.50
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (20 bp):
TGGTATCGATACCCTTACCA
Found at i:359026 original size:29 final size:29
Alignment explanation
Indices: 358982--359039 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
358972 CTTATTTGAG
358982 GTAGAATAAGCCTCAACAACTTCTAAGAT
1 GTAGAATAAGCCTCAACAACTTCTAAGAT
* *
359011 GTAGAATAAGCTTCAACAGCTTCTAAGAT
1 GTAGAATAAGCCTCAACAACTTCTAAGAT
359040 CTCCATCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (29 bp):
GTAGAATAAGCCTCAACAACTTCTAAGAT
Found at i:359750 original size:13 final size:12
Alignment explanation
Indices: 359734--359817 Score: 66
Period size: 12 Copynumber: 6.8 Consensus size: 12
359724 CCTTATTCTA
*
359734 TTTCTTATTTATC
1 TTTCTT-TTTTTC
*
359747 TTTCTATCTTTTC
1 TTTCT-TTTTTTC
359760 TTTC-TTTTTTC
1 TTTCTTTTTTTC
*
359771 TATCTTTTTTTC
1 TTTCTTTTTTTC
359783 TTT-TTCTTTTTC
1 TTTCTT-TTTTTC
359795 TTTTTCTTTGTTTT-
1 --TTTCTTT-TTTTC
359809 TTTCTTTTT
1 TTTCTTTTT
359818 ATTATTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
11 13 0.22
12 22 0.37
13 13 0.22
14 5 0.08
15 6 0.10
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:359772 original size:20 final size:20
Alignment explanation
Indices: 359747--359810 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
359737 CTTATTTATC
359747 TTTCTATCTTTTCTTTCTTT
1 TTTCTATCTTTTCTTTCTTT
359767 TTTCTATCTTTT-TTTCTTT
1 TTTCTATCTTTTCTTTCTTT
* * *
359786 TTCTTTTTCTTTTTCTTTGTTT
1 TT-TCTATC-TTTTCTTTCTTT
359808 TTT
1 TTT
359811 TCTTTTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 9 0.24
20 16 0.42
21 5 0.13
22 8 0.21
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTCTATCTTTTCTTTCTTT
Found at i:359775 original size:28 final size:30
Alignment explanation
Indices: 359743--359801 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
359733 ATTTCTTATT
359743 TATCTTTCTATC-TTTTCTTTCT-TTTTTC
1 TATCTTTCTATCTTTTTCTTTCTCTTTTTC
* * *
359771 TATCTTTTTTTCTTTTTCTTTTTCTTTTTC
1 TATCTTTCTATCTTTTTCTTTCTCTTTTTC
359801 T
1 T
359802 TTGTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 10 0.38
29 9 0.35
30 7 0.27
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (30 bp):
TATCTTTCTATCTTTTTCTTTCTCTTTTTC
Found at i:359788 original size:18 final size:18
Alignment explanation
Indices: 359747--359803 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
359737 CTTATTTATC
359747 TTTCTATCTTTTCTTTCTTT
1 TTTCTATCTTTT-TTTC-TT
359767 TTTCTATCTTTTTTTCTT
1 TTTCTATCTTTTTTTCTT
*
359785 TTTCT-TTTTCTTTTTCTT
1 TTTCTATCTT-TTTTTCTT
359803 T
1 T
359804 GTTTTTTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
17 3 0.09
18 16 0.46
19 4 0.11
20 12 0.34
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTATCTTTTTTTCTT
Found at i:359792 original size:12 final size:12
Alignment explanation
Indices: 359755--359817 Score: 69
Period size: 12 Copynumber: 5.3 Consensus size: 12
359745 TCTTTCTATC
*
359755 TTTTCTTTCT-T
1 TTTTCTTTTTCT
*
359766 TTTTCTATCTT-T
1 TTTTCT-TTTTCT
359778 TTTTCTTTTTCT
1 TTTTCTTTTTCT
359790 TTTTCTTTTTCT
1 TTTTCTTTTTCT
359802 TTGTT-TTTTTCT
1 TT-TTCTTTTTCT
359814 TTTT
1 TTTT
359818 ATTATTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
11 11 0.24
12 33 0.72
13 2 0.04
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:359810 original size:18 final size:18
Alignment explanation
Indices: 359755--359817 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
359745 TCTTTCTATC
*
359755 TTTTCTTTCT-TTTTTCT
1 TTTTCTTTTTCTTTTTCT
*
359772 ATCTT-TTTTTCTTTTTCT
1 -TTTTCTTTTTCTTTTTCT
359790 TTTTCTTTTTCTTTGTT-T
1 TTTTCTTTTTCTTT-TTCT
359808 TTTTCTTTTT
1 TTTTCTTTTT
359818 ATTATTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.18
18 30 0.77
19 2 0.05
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTTCT
Found at i:359826 original size:18 final size:18
Alignment explanation
Indices: 359789--359829 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
359779 TTTCTTTTTC
*
359789 TTTTTCTTTTTCTTTGTT
1 TTTTTCTTTTTATTTGTT
*
359807 TTTTTCTTTTTA-TTATT
1 TTTTTCTTTTTATTTGTT
359824 TTTTTC
1 TTTTTC
359830 GAGTGTGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.05, C:0.10, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTTATTTGTT
Found at i:361391 original size:10 final size:10
Alignment explanation
Indices: 361363--361395 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
361353 AAGTGTCAAA
361363 AATGATAAAG
1 AATGATAAAG
361373 AATG-TAAAG
1 AATGATAAAG
*
361382 AATGAAAAAG
1 AATGATAAAG
361392 AATG
1 AATG
361396 TGAAATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (10 bp):
AATGATAAAG
Found at i:363323 original size:15 final size:15
Alignment explanation
Indices: 363303--363333 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
363293 AAATAGAATT
*
363303 AATAATAATGTTAAA
1 AATAATAATATTAAA
363318 AATAATAATATTAAA
1 AATAATAATATTAAA
363333 A
1 A
363334 GGGAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
AATAATAATATTAAA
Found at i:365431 original size:15 final size:15
Alignment explanation
Indices: 365369--365432 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
365359 TTAAGTATGT
365369 TTTATGTAT-TATATA
1 TTTAT-TATATATATA
* ** *
365384 TTTATTTTACGTACA
1 TTTATTATATATATA
365399 -TTATTATATAT-TA
1 TTTATTATATATATA
365412 CTTTATTATATATATA
1 -TTTATTATATATATA
365428 TTTAT
1 TTTAT
365433 ATAATACTAC
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
13 1 0.03
14 10 0.27
15 24 0.65
16 2 0.05
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (15 bp):
TTTATTATATATATA
Found at i:366691 original size:20 final size:20
Alignment explanation
Indices: 366668--366743 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
366658 CGATTTTATT
366668 TCTTCTTTTCTTTTTTTCTC
1 TCTTCTTTTCTTTTTTTCTC
* * *
366688 TCTTTTTTTATTTTTTTTTC
1 TCTTCTTTTCTTTTTTTCTC
*
366708 T-TTCTCTT-TTTTTTTCTC
1 TCTTCTTTTCTTTTTTTCTC
366726 TC-T-TTTTCTTTCTTTTCT
1 TCTTCTTTTCTTT-TTTTCT
366744 ATTTATCTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
17 3 0.07
18 14 0.30
19 11 0.24
20 18 0.39
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTCTTTTCTTTTTTTCTC
Found at i:366726 original size:36 final size:35
Alignment explanation
Indices: 366660--366759 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 35
366650 TGTTTGATCG
*
366660 ATTTTATTTCTTCTTTTCTTTTTTTCTCTCTTTTTTT
1 ATTTT-TTT-TTCTTTTCTTTTTTTCTCTCTCTTTTT
*
366697 ATTTTTTTTTCTTTCTCTTTTTTTTTCTCTCTTTTT
1 ATTTTTTTTTCTTT-TCTTTTTTTCTCTCTCTTTTT
* * * *
366733 CTTTCTTTTCTATTTATCTTTCTTTCT
1 ATTT-TTTTTTCTTT-TCTTTTTTTCT
366760 TTTTTGTGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 6 0.11
36 25 0.47
37 22 0.42
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (35 bp):
ATTTTTTTTTCTTTTCTTTTTTTCTCTCTCTTTTT
Found at i:366733 original size:10 final size:10
Alignment explanation
Indices: 366674--366763 Score: 67
Period size: 10 Copynumber: 8.9 Consensus size: 10
366664 TATTTCTTCT
366674 TTTCTTTTT-
1 TTTCTTTTTC
366683 TTCTCTCTTTT-
1 TT-TCT-TTTTC
* *
366694 TTTATTTTTT
1 TTTCTTTTTC
*
366704 TTTCTTTCTC
1 TTTCTTTTTC
*
366714 TTTTTTTTTC
1 TTTCTTTTTC
*
366724 TCTCTTTTTC
1 TTTCTTTTTC
*
366734 TTTCTTTTCTA
1 TTTCTTTT-TC
* *
366745 TTTATCTTTC
1 TTTCTTTTTC
366755 TTTCTTTTT
1 TTTCTTTTT
366764 TGTGTGTATT
Statistics
Matches: 62, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
9 6 0.10
10 43 0.69
11 13 0.21
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:366755 original size:31 final size:30
Alignment explanation
Indices: 366661--366763 Score: 85
Period size: 26 Copynumber: 3.6 Consensus size: 30
366651 GTTTGATCGA
* *
366661 TTTTATTTCT-TC-TTTTCTTTTTTTCTCT
1 TTTTCTTTCTCTCTTTTTCTTTCTTTCTCT
* *
366689 CTTT-TTT-TAT-TTTTT-TTTCTTTCTCT
1 TTTTCTTTCTCTCTTTTTCTTTCTTTCTCT
*
366715 TTTTTTTTCTCTCTTTTTCTTTCTTT-TCT
1 TTTTCTTTCTCTCTTTTTCTTTCTTTCTCT
*
366744 ATTTATCTTTCTTTCTTTTT
1 -TTT-TCTTTCTCTCTTTTT
366764 TGTGTGTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
26 14 0.23
27 11 0.18
28 5 0.08
29 8 0.13
30 10 0.16
31 13 0.21
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (30 bp):
TTTTCTTTCTCTCTTTTTCTTTCTTTCTCT
Found at i:367548 original size:19 final size:19
Alignment explanation
Indices: 367503--367539 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
367493 AGGGCATGGC
*
367503 TTTATTGTTTTAGAGGAAA
1 TTTATTGTTTCAGAGGAAA
367522 TTTATTGTTTCAGAGGAA
1 TTTATTGTTTCAGAGGAA
367540 TTCTCTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.46
Consensus pattern (19 bp):
TTTATTGTTTCAGAGGAAA
Found at i:367772 original size:295 final size:295
Alignment explanation
Indices: 367242--367834 Score: 1150
Period size: 295 Copynumber: 2.0 Consensus size: 295
367232 CCAATTATTC
367242 GAATTCTCTTGTGAAACTTGATCTGCAACATTCCATCTTGTCTTTCTTTCAAGAGTGGTTCTCGT
1 GAATTCTCTTGTGAAACTTGATCTGCAACATTCCATCTTGTCTTTCTTTCAAGAGTGGTTCTCGT
367307 GCACATGACAATCTCATACTTTATGTCTTCAAGTTTTATTTAAGTTGGGAAATGAATGATGATTC
66 GCACATGACAATCTCATACTTTATGTCTTCAAGTTTTATTTAAGTTGGGAAATGAATGATGATTC
367372 CATGTTTAGGAAGGGAAATATGTGACTTTAAAATTAGAATTCTGAAAAATGGTAATGTTATGGAA
131 CATGTTTAGGAAGGGAAATATGTGACTTTAAAATTAGAATTCTGAAAAATGGTAATGTTATGGAA
367437 AAGTTATTTCTGTATGGGAAGGTAAAAGTACATGTTTTAGTGCCTCAGGGAGGATAAGGGCATGG
196 AAGTTATTTCTGTATGGGAAGGTAAAAGTACATGTTTTAGTGCCTCAGGGAGGATAAGGGCATGG
* *
367502 CTTTATTGTTTTAGAGGAAATTTATTGTTTCAGAG
261 CTTTATTATTTTAGAGGAAATTTATTATTTCAGAG
*
367537 GAATTCTCTTGTGAAACTTGATCTGCAACATTCCATCTTGTCTTTCTTTCAAGAGTGGTTCTTGT
1 GAATTCTCTTGTGAAACTTGATCTGCAACATTCCATCTTGTCTTTCTTTCAAGAGTGGTTCTCGT
367602 GCACATGACAATCTCATACTTTATGTCTTCAAGTTTTATTTAAGTTGGGAAATGAATGATGATTC
66 GCACATGACAATCTCATACTTTATGTCTTCAAGTTTTATTTAAGTTGGGAAATGAATGATGATTC
367667 CATGTTTAGGAAGGGAAATATGTGACTTTAAAATTAGAATTCTGAAAAATGGTAATGTTATGGAA
131 CATGTTTAGGAAGGGAAATATGTGACTTTAAAATTAGAATTCTGAAAAATGGTAATGTTATGGAA
*
367732 AAGTTATTTCTGTATGGGAAGGTTAAAGTACATGTTTTAGTGCCTCAGGGAGGATAAGGGCATGG
196 AAGTTATTTCTGTATGGGAAGGTAAAAGTACATGTTTTAGTGCCTCAGGGAGGATAAGGGCATGG
367797 CTTTATTATTTTAGAGGAAATTTATTATTTCAGAG
261 CTTTATTATTTTAGAGGAAATTTATTATTTCAGAG
367832 GAA
1 GAA
367835 AGTGATGTCA
Statistics
Matches: 294, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
295 294 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (295 bp):
GAATTCTCTTGTGAAACTTGATCTGCAACATTCCATCTTGTCTTTCTTTCAAGAGTGGTTCTCGT
GCACATGACAATCTCATACTTTATGTCTTCAAGTTTTATTTAAGTTGGGAAATGAATGATGATTC
CATGTTTAGGAAGGGAAATATGTGACTTTAAAATTAGAATTCTGAAAAATGGTAATGTTATGGAA
AAGTTATTTCTGTATGGGAAGGTAAAAGTACATGTTTTAGTGCCTCAGGGAGGATAAGGGCATGG
CTTTATTATTTTAGAGGAAATTTATTATTTCAGAG
Found at i:367822 original size:19 final size:19
Alignment explanation
Indices: 367798--367835 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
367788 AGGGCATGGC
*
367798 TTTATTATTTTAGAGGAAA
1 TTTATTATTTCAGAGGAAA
367817 TTTATTATTTCAGAGGAAA
1 TTTATTATTTCAGAGGAAA
367836 GTGATGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (19 bp):
TTTATTATTTCAGAGGAAA
Found at i:370717 original size:28 final size:28
Alignment explanation
Indices: 370673--370740 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
370663 GTGAGAAGCC
* *
370673 AACCTGAAATACATTACCTCCCTAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
* *
370701 AACTTGAAACACATTACTTCCCCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
*
370729 AACCTAAAACAC
1 AACCTGAAACAC
370741 GTCACCTTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.43, C:0.29, G:0.03, T:0.25
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCCAAATT
Found at i:372055 original size:55 final size:55
Alignment explanation
Indices: 371996--372179 Score: 201
Period size: 55 Copynumber: 3.3 Consensus size: 55
371986 GTTTTTTAGG
* *
371996 AACTAAGTCCGATTTTCGGAAGTTTCTTGATCATTTTTAAATGATCTTTTAAAGA
1 AACTAAGTCCGATTTTCAGAAGTTTCTTGATCATTTTTAAATGAGCTTTTAAAGA
* * * *
372051 AACTATG-CCTGATTTTTAGAACTTTCTTGA-CGATTTTCAAATGAGCTTTTAAAGA
1 AACTAAGTCC-GATTTTCAGAAGTTTCTTGATC-ATTTTTAAATGAGCTTTTAAAGA
* * * * *
372106 AACTAAGACTGATTTTCAGAAGTTTTTTTGATGATTTTTAAATGAGCTTTCAAAGA
1 AACTAAGTCCGATTTTCAGAAG-TTTCTTGATCATTTTTAAATGAGCTTTTAAAGA
* **
372162 AATTAAGTATGATTTTCA
1 AACTAAGTCCGATTTTCA
372180 TAGATTTCTT
Statistics
Matches: 107, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
54 3 0.03
55 60 0.56
56 44 0.41
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (55 bp):
AACTAAGTCCGATTTTCAGAAGTTTCTTGATCATTTTTAAATGAGCTTTTAAAGA
Done.