Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000754.1 Hibiscus syriacus cultivar Beakdansim tig00001457_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: 316703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:195961 original size:30 final size:30
Alignment explanation
Indices: 195910--195981 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
195900 GTTCTTCGAA
* * *
195910 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
195940 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
195970 ACCTCTGGATAG
1 ACCTCTGGATAG
195982 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:196263 original size:2 final size:2
Alignment explanation
Indices: 196251--196292 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
196241 GTATGCGTGG
*
196251 AT AT GT 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
196293 GAAAGGTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197424 original size:19 final size:20
Alignment explanation
Indices: 197400--197438 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
197390 GCAACGGGAT
197400 AATCGCAATGCGAAA-TAAA
1 AATCGCAATGCGAAACTAAA
197419 AATCGCAATGCGAAACTAAA
1 AATCGCAATGCGAAACTAAA
197439 TTCGCGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAACTAAA
Found at i:197472 original size:20 final size:20
Alignment explanation
Indices: 197439--197476 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
197429 CGAAACTAAA
*
197439 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
*
197459 TTCGCATTGTGATTTTCA
1 TTCGCATTGCGATTTTCA
197477 CGTTGCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.50
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:197500 original size:33 final size:33
Alignment explanation
Indices: 197443--197518 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
197433 ACTAAATTCG
* *
197443 CGTTGCGATTTTCATTTTCGCATTGTGATTTTC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATC
*
197476 ACGTTGCGATTTTTA-TTTCGCATTGCGATTATC
1 -CGTTGCGATTTTCATTTTCGCATTGCGATTATC
197509 CTGTTGCGAT
1 C-GTTGCGAT
197519 AGTCAAATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 24 0.63
34 13 0.34
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATC
Found at i:197536 original size:20 final size:20
Alignment explanation
Indices: 197511--197578 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
197501 CGATTATCCT
*
197511 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
197531 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
* *
197551 GTTGCGATAGTCATTTTTGC
1 GTTGCGATAGTCAATTTCGC
197571 GTTGCGAT
1 GTTGCGAT
197579 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:197594 original size:20 final size:20
Alignment explanation
Indices: 197571--197608 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
197561 TCATTTTTGC
197571 GTTGCGATTTTAAGTTTCGT
1 GTTGCGATTTTAAGTTTCGT
197591 GTTGCGATTTTAAGTTTC
1 GTTGCGATTTTAAGTTTC
197609 AGAAACTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.24, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCGT
Found at i:197595 original size:40 final size:40
Alignment explanation
Indices: 197510--197598 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
197500 GCGATTATCC
*
197510 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCCG
1 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAATTTCCG
* ** * **
197550 CGTTGCGATAGTCATTTTTGCGTTGCGATTTTAAGTTT-CG
1 TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAA-TTTCCG
197590 TGTTGCGAT
1 TGTTGCGAT
197599 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 37 0.93
41 3 0.08
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (40 bp):
TGTTGCGATAGTCAAATTCGCGTTGCGATAGTAATTTCCG
Found at i:198163 original size:21 final size:21
Alignment explanation
Indices: 198088--198185 Score: 97
Period size: 21 Copynumber: 4.7 Consensus size: 21
198078 GGCTCACCTG
* *
198088 TCATCGTTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGCCCCTC
** *
198109 TCATCCCTCAAGAGTCCCCTC
1 TCATCATTCAAGAGGCCCCTC
* * *
198130 CCATCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTC
* *
198151 TCATCATTGAAGAGGTCCCTC
1 TCATCATTCAAGAGGCCCCTC
*
198172 TCACCATTCAAGAG
1 TCATCATTCAAGAG
198186 CCCGATTCAC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:198164 original size:42 final size:45
Alignment explanation
Indices: 198089--198178 Score: 123
Period size: 42 Copynumber: 2.1 Consensus size: 45
198079 GCTCACCTGT
*
198089 CATCGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCC-CTC-C
1 CATCGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCTCAC
* * *
198131 CATCGTTCAAGAGGCCCCTGTCATCATTGAAGAGGTCCCTCTCAC
1 CATCGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCTCAC
198176 CAT
1 CAT
198179 TCAAGAGCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 29 0.71
43 5 0.12
44 3 0.07
45 4 0.10
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (45 bp):
CATCGTTCAAGAGGCCCCTATCATCACTCAAGAGGTCCCTCTCAC
Found at i:199498 original size:14 final size:14
Alignment explanation
Indices: 199479--199515 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
199469 GATTGTTTAA
199479 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
199493 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
199507 TTGATTTGT
1 TTGATTTGT
199516 TTACTTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:199674 original size:20 final size:20
Alignment explanation
Indices: 199649--199712 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
199639 AACGCTAAAC
199649 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
*
199669 TCAAAATCGTAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
199689 TCAAAATCGCAACGCAAAAG
1 TCAAAATCGCAATGCGAAAG
199709 TCAA
1 TCAA
199713 TTCGCGTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.16
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:199776 original size:20 final size:20
Alignment explanation
Indices: 199751--199839 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
199741 GCGATTTTCT
*
199751 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
199771 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
199791 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
**
199811 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCA
199831 CGTTGCGAT
1 CGTTGCGAT
199840 TTTTGAGTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:199855 original size:94 final size:93
Alignment explanation
Indices: 199707--199881 Score: 235
Period size: 94 Copynumber: 1.9 Consensus size: 93
199697 GCAACGCAAA
* * * * *
199707 AGTCAATTCGCGTTGTGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCC
1 AGTCAATTCACGTTGCGATAGTCAAATACGCGTTGCGATTTTCTAGTTGCGATAGTCAAATTCCC
199772 GTTGCGATAATCAAATTCACGTTGCGAT
66 GTTGCGATAATCAAATTCACGTTGCGAT
** *
199800 AGTCAAATTCACGTTGCGATAGTCAAATTTGCGTTGCGATTTT-TGAGTTGTGATAGTCAAATTC
1 AGTC-AATTCACGTTGCGATAGTCAAATACGCGTTGCGATTTTCT-AGTTGCGATAGTCAAATTC
* *
199864 GCGTTGCGATATTCAAAT
64 CCGTTGCGATAATCAAAT
199882 GAATGTGTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
93 5 0.07
94 65 0.93
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (93 bp):
AGTCAATTCACGTTGCGATAGTCAAATACGCGTTGCGATTTTCTAGTTGCGATAGTCAAATTCCC
GTTGCGATAATCAAATTCACGTTGCGAT
Found at i:199874 original size:20 final size:20
Alignment explanation
Indices: 199751--199881 Score: 139
Period size: 20 Copynumber: 6.8 Consensus size: 20
199741 GCGATTTTCT
*
199751 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
199771 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
199791 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
199811 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
199831 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
199845 AGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
199865 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
199882 GAATGTGTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
14 11 0.12
16 1 0.01
18 1 0.01
20 81 0.86
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:200104 original size:140 final size:140
Alignment explanation
Indices: 199852--200270 Score: 788
Period size: 140 Copynumber: 3.0 Consensus size: 140
199842 TTGAGTTGTG
*
199852 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
199917 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
199982 AATACACATA
131 AATACACATA
* * *
199992 ATAGTCAAATTTGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
200057 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
200122 AATACACATA
131 AATACACATA
200132 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
200197 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACA-AT-A
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
200260 AATACACATA
131 AATACACATA
200270 A
1 A
200271 CAACGTTTGC
Statistics
Matches: 273, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
138 12 0.04
139 2 0.01
140 259 0.95
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:201379 original size:14 final size:14
Alignment explanation
Indices: 201360--201386 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
201350 TCCCGTGGCA
201360 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
201374 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
201387 TTTCTTCTTA
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:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:201392 original size:12 final size:13
Alignment explanation
Indices: 201361--201393 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
201351 CCCGTGGCAT
201361 TTTCTTCGGGGAC
1 TTTCTTCGGGGAC
201374 TTTTCTTCGGGGA-
1 -TTTCTTCGGGGAC
201387 TTTCTTC
1 TTTCTTC
201394 TTATTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTCTTCGGGGAC
Found at i:201620 original size:24 final size:24
Alignment explanation
Indices: 201586--201639 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
201576 CTGAAACATC
201586 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
201610 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
201634 ATCAAA
1 ATCAAA
201640 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:201653 original size:24 final size:24
Alignment explanation
Indices: 201586--201653 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
201576 CTGAAACATC
* * *
201586 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
201610 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
201634 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
201654 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:202483 original size:20 final size:20
Alignment explanation
Indices: 202458--202568 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
202448 TTGAAATTCA
*
202458 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
202478 GCGTTGCGTTAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
202498 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* ** *
202518 GAGTTGCGATTATGT-ATTATT
1 GCGTTGCGA-TA-GTCAGAATC
202539 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
202559 GTGTTGCGAT
1 GCGTTGCGAT
202569 TTACATATTA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:202555 original size:41 final size:41
Alignment explanation
Indices: 202458--202569 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 41
202448 TTGAAATTCA
* *
202458 GCGTTGCGACAGTCAGAATCGCGTTGCG-TTAGTCAGAATC
1 GCGTTGCGATAGTCAGAATCGAGTTGCGATTAGTCAGAATC
** *
202498 GCGTTGCGATAGTCAGAATCGAGTTGCGATTATGT-ATTATT
1 GCGTTGCGATAGTCAGAATCGAGTTGCGATTA-GTCAGAATC
*
202539 GCGTTGCGATAGTCAGAATCGTGTTGCGATT
1 GCGTTGCGATAGTCAGAATCGAGTTGCGATT
202570 TACATATTAG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 26 0.41
41 36 0.56
42 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (41 bp):
GCGTTGCGATAGTCAGAATCGAGTTGCGATTAGTCAGAATC
Found at i:202611 original size:21 final size:21
Alignment explanation
Indices: 202587--202628 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
202577 TAGCGTTGCG
*
202587 ATTTCTAAAATCGCAACGCGA
1 ATTTCGAAAATCGCAACGCGA
* *
202608 ATTTGGAAAATCGCAATGCGA
1 ATTTCGAAAATCGCAACGCGA
202629 TAGTCAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
ATTTCGAAAATCGCAACGCGA
Found at i:202698 original size:19 final size:19
Alignment explanation
Indices: 202674--202710 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
202664 TGCGATACTG
* *
202674 GAGATCGCGTTGCTATTTA
1 GAGATCGCATTGCGATTTA
202693 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
202711 TGTTGATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:204398 original size:24 final size:24
Alignment explanation
Indices: 204370--204416 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
204360 TTTTTTTGAC
204370 AGGAGGTGTTTCA-CTTTCACTGTT
1 AGGAGGTGTTTCACCTTT-ACTGTT
204394 AGGAGGTGTTTCACCTTTACTGT
1 AGGAGGTGTTTCACCTTTACTGT
204417 ATCATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (24 bp):
AGGAGGTGTTTCACCTTTACTGTT
Found at i:205475 original size:14 final size:16
Alignment explanation
Indices: 205437--205475 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
205427 CATTTTTTAA
205437 TTATACATATTAACTT
1 TTATACATATTAACTT
*
205453 TTATACATATTTA-TT
1 TTATACATATTAACTT
205468 TT-TACATA
1 TTATACATA
205476 ACATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 4 0.18
16 12 0.55
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATACATATTAACTT
Found at i:205666 original size:2 final size:2
Alignment explanation
Indices: 205659--205751 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
205649 AAATATTCAA
205659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205743 AT AT AT AT A
1 AT AT AT AT A
205752 ACACTAGAAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:214555 original size:24 final size:24
Alignment explanation
Indices: 214526--214575 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
214516 TGGTGGTTGA
*
214526 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
214550 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
214574 TT
1 TT
214576 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:215081 original size:17 final size:16
Alignment explanation
Indices: 215050--215083 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
215040 CACGTGAGGA
215050 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
215066 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
215083 T
1 T
215084 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:221466 original size:20 final size:20
Alignment explanation
Indices: 221424--221472 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
221414 TAACTTTTTC
*
221424 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
221444 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
*
221463 TTTTACCTTT
1 TTTTATCTTT
221473 TCTCTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:224800 original size:24 final size:24
Alignment explanation
Indices: 224771--224820 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
224761 TGGTGGTTGA
*
224771 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
224795 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
224819 TT
1 TT
224821 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:225326 original size:17 final size:16
Alignment explanation
Indices: 225295--225328 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
225285 CACGTGAGGA
225295 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
225311 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
225328 T
1 T
225329 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:230879 original size:23 final size:22
Alignment explanation
Indices: 230841--230880 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
230831 TCTTTGGGTG
*
230841 TTATATAAGCTTAACAA-AAGA
1 TTATATAAGATTAACAACAAGA
230862 TTATATAAGATTAA-AACAA
1 TTATATAAGATTAACAACAA
230881 CAAGAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
TTATATAAGATTAACAACAAGA
Found at i:231402 original size:35 final size:35
Alignment explanation
Indices: 231337--231407 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 35
231327 GGATAAATCT
*
231337 TCATGAGGTATCGATACTGAAATGATAGTATCGGTA
1 TCATGAGGTATCGATAC-GAAATGAAAGTATCGGTA
231373 TCATG-GGTATCGATAC-AAATGTAGAAGTATCGGTA
1 TCATGAGGTATCGATACGAAATG-A-AAGTATCGGTA
231408 CCATTCTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 5 0.16
34 1 0.03
35 21 0.66
36 5 0.16
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (35 bp):
TCATGAGGTATCGATACGAAATGAAAGTATCGGTA
Found at i:231977 original size:15 final size:15
Alignment explanation
Indices: 231957--231985 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
231947 GGAGAAATGA
231957 TATAAGCTATGTGAC
1 TATAAGCTATGTGAC
231972 TATAAGCTATGTGA
1 TATAAGCTATGTGA
231986 AAATAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (15 bp):
TATAAGCTATGTGAC
Found at i:231991 original size:15 final size:15
Alignment explanation
Indices: 231958--231992 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
231948 GAGAAATGAT
**
231958 ATAAGCTATGTGACT
1 ATAAGCTATGTGAAA
231973 ATAAGCTATGTGAAA
1 ATAAGCTATGTGAAA
231988 ATAAG
1 ATAAG
231993 TTAAATGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.29
Consensus pattern (15 bp):
ATAAGCTATGTGAAA
Found at i:233303 original size:67 final size:67
Alignment explanation
Indices: 233224--233357 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 67
233214 GGTATGAAGA
* * * * ** *
233224 CTCTGGCAGGTTCAGTTGGTTCTGGTAATTACTTGTATAGGTTCAACATTAACTGGTAATTCCTT
1 CTCTGGCAGGTTCAGTCGCTTCTAGTAATTACTCGTATAGGTTCAACACCAACTAGTAATTCCTT
233289 AT
66 AT
* *
233291 CTCTGGCAGGTTCAGTCGCTTCTAGTAATTCCTCGTATAGGTTCAACACCGACTAGTAATTCCTT
1 CTCTGGCAGGTTCAGTCGCTTCTAGTAATTACTCGTATAGGTTCAACACCAACTAGTAATTCCTT
233356 AT
66 AT
233358 GGACCTAAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (67 bp):
CTCTGGCAGGTTCAGTCGCTTCTAGTAATTACTCGTATAGGTTCAACACCAACTAGTAATTCCTT
AT
Found at i:236465 original size:36 final size:36
Alignment explanation
Indices: 236394--236475 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
236384 TAAATTAAAT
* *
236394 TAAATTGATATTCTCAAAATATAAAATTT--ATATA
1 TAAATTTAAATTCTCAAAATATAAAATTTAAATATA
236428 TACAATTTAAATTCTCATAAATA-AAAATTATAAATATA
1 TA-AATTTAAATTCTCA-AAATATAAAATT-TAAATATA
236466 TAAATTTAAA
1 TAAATTTAAA
236476 CTTATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
34 2 0.05
35 18 0.44
36 6 0.15
37 8 0.20
38 7 0.17
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (36 bp):
TAAATTTAAATTCTCAAAATATAAAATTTAAATATA
Found at i:243012 original size:21 final size:20
Alignment explanation
Indices: 242984--243022 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
242974 CACTGTAGGA
*
242984 ATTTATGGCCTCGACAAAAT
1 ATTTATGGCCTCAACAAAAT
*
243004 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
243023 GACCTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAT
Found at i:245821 original size:21 final size:21
Alignment explanation
Indices: 245795--245838 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
245785 ATTCTGGGCT
* *
245795 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
245816 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
245837 AG
1 AG
245839 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:245909 original size:23 final size:22
Alignment explanation
Indices: 245865--245909 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
245855 AATGTCATGG
*
245865 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
245887 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
245910 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:246676 original size:31 final size:31
Alignment explanation
Indices: 246592--246715 Score: 130
Period size: 31 Copynumber: 4.0 Consensus size: 31
246582 GAGTCGAGGG
246592 TACCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTACGGAACATATGGACAGT-A
*
246623 TTACCTATG-TCTTTC-GAGACATATGGACAGTA
1 -TACCTATGTTC-TACGGA-ACATATGGACAGTA
*
246655 TACCTATGTTCTAAGGAACATATGGACAGT-
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
246685 TCACCTAGGTTCTTCGGAACCTATGGACAGT
1 T-ACCTATGTTCTACGGAACATATGGACAGT
246716 TTCCGAGGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
30 1 0.01
31 51 0.65
32 26 0.33
33 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:246754 original size:30 final size:30
Alignment explanation
Indices: 246703--246774 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
246693 GTTCTTCGGA
* * *
246703 ACCTATGGACAGTTTCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
246733 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
246763 ACCTCTGGATAG
1 ACCTCTGGATAG
246775 GTCCTGCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:268492 original size:22 final size:22
Alignment explanation
Indices: 268451--268492 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
268441 ATTGAAGTTA
*
268451 TACTTTTCTTTCGTCTTTTTTT
1 TACTTTTCTTTCGACTTTTTTT
*
268473 TACTTTTCTTTC-ACTATTTT
1 TACTTTTCTTTCGACTTTTTT
268493 CTTTTCACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (22 bp):
TACTTTTCTTTCGACTTTTTTT
Found at i:277997 original size:40 final size:40
Alignment explanation
Indices: 277910--278080 Score: 186
Period size: 41 Copynumber: 4.2 Consensus size: 40
277900 TCATAACGTC
* * **
277910 TATTTTAGTGGTGTTTTTATATAAACGCCGCTAAAGACT-G
1 TATTTTAGTGGCGTTTTTATACAAACG-CATTAAAGACTCG
* *
277950 TAATTTAGTGGCGTTTTT-TACAAACGTCATTAAAGACTCA
1 TATTTTAGTGGCGTTTTTATACAAACG-CATTAAAGACTCG
* * *
277990 TACTTTAGTGGCATTTTTATACAAACAC-TGCTAAAGACTCG
1 TATTTTAGTGGCGTTTTTATACAAACGCAT--TAAAGACTCG
*
278031 TATTTTAGTGGCGTTTTTATACAAATGCAGTTAAAGACTCG
1 TATTTTAGTGGCGTTTTTATACAAACGCA-TTAAAGACTCG
278072 TATTTTAGT
1 TATTTTAGT
278081 ACACATAAGT
Statistics
Matches: 110, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
39 17 0.15
40 33 0.30
41 59 0.54
43 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (40 bp):
TATTTTAGTGGCGTTTTTATACAAACGCATTAAAGACTCG
Found at i:278048 original size:80 final size:81
Alignment explanation
Indices: 277913--278080 Score: 223
Period size: 80 Copynumber: 2.1 Consensus size: 81
277903 TAACGTCTAT
** * *
277913 TTTAGTGGTGTTTTTATATAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTT-TACAAACGT
1 TTTAGTGGCATTTTTATACAAACACCGCTAAAGACTGTAATTTAGTGGCGTTTTTATACAAACG-
277977 CA-TTAAAGACTCATAC
65 CAGTTAAAGACTCATAC
* * *
277993 TTTAGTGGCATTTTTATACAAACACTGCTAAAGACTCGTATTTTAGTGGCGTTTTTATACAAATG
1 TTTAGTGGCATTTTTATACAAACACCGCTAAAGACT-GTAATTTAGTGGCGTTTTTATACAAACG
* *
278058 CAGTTAAAGACTCGTAT
65 CAGTTAAAGACTCATAC
278075 TTTAGT
1 TTTAGT
278081 ACACATAAGT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
80 31 0.41
81 20 0.26
82 25 0.33
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (81 bp):
TTTAGTGGCATTTTTATACAAACACCGCTAAAGACTGTAATTTAGTGGCGTTTTTATACAAACGC
AGTTAAAGACTCATAC
Found at i:278331 original size:20 final size:20
Alignment explanation
Indices: 278306--278358 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
278296 GACCAACAAA
278306 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
278326 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
278346 TTCGCAACGCGAA
1 TTCGCAACGCGAA
278359 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:278463 original size:60 final size:61
Alignment explanation
Indices: 278383--278676 Score: 373
Period size: 60 Copynumber: 4.9 Consensus size: 61
278373 CACATAAGTC
* * * * *
278383 AAATTCTCAACGCAATAGTCAAATCCGCAACGCGATAGTCAAATCCGCAACGCAAATTTGT
1 AAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCAAATTTGT
*
278444 AAA-TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTTGCAACGCAAATTTGT
1 AAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCAAATTTGT
* * * * *
278504 AAA-TCGCAACACAGAAGTCAAATTCGCAACGTGATAGCCAAATTCGCAACACAAA--AGT
1 AAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCAAATTTGT
* * *** *
278562 CAAATTCACAACACAAAAGTCAAATTCGCAATGCGATAGTCAAATTCGCAACATTGAATTT-C
1 -AAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAC-GCAAATTTGT
*
278624 AAATTCGCAACAAAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGC
1 AAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGC
278677 GAAACACAAT
Statistics
Matches: 201, Mismatches: 27, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
58 2 0.01
59 3 0.01
60 143 0.71
61 53 0.26
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (61 bp):
AAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCAAATTTGT
Found at i:278677 original size:20 final size:20
Alignment explanation
Indices: 278346--278678 Score: 234
Period size: 20 Copynumber: 16.6 Consensus size: 20
278336 AGTTTCCAAT
278346 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCG-ATA-GTCAAA
*
278367 -TCGCAACAC-ATAAGTCAAA
1 TTCGCAACGCGAT-AGTCAAA
* *
278386 TTCTCAACGCAATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
*
278406 TCCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
278426 TCCGCAACGCAAATTTGT-AAA
1 TTCGCAACGC-GA-TAGTCAAA
* * *
278447 -TCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
278466 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
278486 TTTGCAACGCAAATTTGT-AAA
1 TTCGCAACGC-GA-TAGTCAAA
*
278507 -TCGCAACACAGA-AGTCAAA
1 TTCGCAACGC-GATAGTCAAA
* *
278526 TTCGCAACGTGATAGCCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
278546 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* * * *
278566 TTCACAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
*
278586 TTCGCAATGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
** *
278606 TTCGCAACATTGA-ATTTCAAA
1 TTCGCAAC-GCGATA-GTCAAA
*** *
278627 TTCGCAACAAAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
278647 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
278667 TTCGCAACGCGA
1 TTCGCAACGCGA
278679 AACACAATAT
Statistics
Matches: 248, Mismatches: 48, Indels: 33
0.75 0.15 0.10
Matches are distributed among these distances:
18 8 0.03
19 14 0.06
20 194 0.78
21 26 0.10
22 6 0.02
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:278815 original size:22 final size:22
Alignment explanation
Indices: 278790--278840 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
278780 CTACGACGAC
278790 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGGCGAA
278812 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGGCGAA
278834 ATCCGTC
1 ATCCGTC
278841 TATCTCCATC
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:0.18, C:0.45, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGGCGAA
Found at i:279253 original size:14 final size:14
Alignment explanation
Indices: 279254--279287 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
279244 TGCGATTTTC
279254 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
279268 ATTTTCTCGTTGTG
1 ATTTTCGCGTTGCG
279282 ATTTTC
1 ATTTTC
279288 ATTTTTGCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.53
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:279261 original size:20 final size:20
Alignment explanation
Indices: 279226--279273 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
279216 AAATCGCAAC
279226 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
279245 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
279265 GCGATTTTC
1 GCGATTTTC
279274 TCGTTGTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:279285 original size:34 final size:34
Alignment explanation
Indices: 279236--279302 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
279226 GCGATTTTAG
279236 TTTCGCGTTGCGATTTTCATTTTCGCGTTGCGAT
1 TTTCGCGTTGCGATTTTCATTTTCGCGTTGCGAT
* * *
279270 TTTCTCGTTGTGATTTTCATTTTTGCGTTGCGA
1 TTTCGCGTTGCGATTTTCATTTTCGCGTTGCGA
279303 ATTTAAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.09, C:0.18, G:0.22, T:0.51
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCATTTTCGCGTTGCGAT
Found at i:281535 original size:21 final size:21
Alignment explanation
Indices: 281475--281566 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 21
281465 CTATCATCAT
* * * *
281475 TCAAAAGGCACCTCCTATCGT
1 TCAAGAGGCCCCTCCCATCGA
*** *
281496 TCAAGAGGCATTTCTCATC-A
1 TCAAGAGGCCCCTCCCATCGA
*
281516 TCGAAGAGGCCCCTCCCATCGT
1 TC-AAGAGGCCCCTCCCATCGA
* *
281538 TCAAGAGGCCCCTCCCACCGT
1 TCAAGAGGCCCCTCCCATCGA
281559 TCAAGAGG
1 TCAAGAGG
281567 TTTCGCCCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.21
Consensus pattern (21 bp):
TCAAGAGGCCCCTCCCATCGA
Found at i:283048 original size:28 final size:28
Alignment explanation
Indices: 283003--283056 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
282993 GCTTGTTTAA
*
283003 TTGATTTGTAAAAGTTGATTTGTAAAAG
1 TTGATTTGTAAAAGTTGATGTGTAAAAG
** *
283031 TTGATTTGTTTAATTTGATGTGTAAA
1 TTGATTTGTAAAAGTTGATGTGTAAA
283057 TAAGAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (28 bp):
TTGATTTGTAAAAGTTGATGTGTAAAAG
Found at i:283049 original size:14 final size:14
Alignment explanation
Indices: 283003--283039 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
282993 GCTTGTTTAA
283003 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
283017 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
283031 TTGATTTGT
1 TTGATTTGT
283040 TTAATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:283091 original size:80 final size:78
Alignment explanation
Indices: 282949--283105 Score: 269
Period size: 80 Copynumber: 2.0 Consensus size: 78
282939 TTTTACATTG
*
282949 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTCATTTGTAA
283014 AAGTTGATTTGTA
66 AAGTTGATTTGTA
* *
283027 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTCATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTCATTTGT
283092 AAAAGTTGATTTGT
64 AAAAGTTGATTTGT
283106 TGTTTTAAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
78 17 0.23
79 19 0.26
80 38 0.51
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.50
Consensus pattern (78 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTCATTTGTAA
AAGTTGATTTGTA
Found at i:283186 original size:20 final size:20
Alignment explanation
Indices: 283161--283198 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
283151 GTTGAAGGTA
*
283161 CAAATTCGCAACGCGAAAGT
1 CAAATTCACAACGCGAAAGT
283181 CAAATTCACAACGCGAAA
1 CAAATTCACAACGCGAAA
283199 TAAGCTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.26, G:0.16, T:0.13
Consensus pattern (20 bp):
CAAATTCACAACGCGAAAGT
Found at i:283569 original size:6 final size:6
Alignment explanation
Indices: 283560--283594 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
283550 TTATGATTGG
*
283560 GATTTT GATTTT GATTAT GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
283595 CCTTTTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (6 bp):
GATTTT
Found at i:285206 original size:17 final size:17
Alignment explanation
Indices: 285184--285225 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
285174 GAACTGAGCA
285184 TTCATGTCATTCATAAT
1 TTCATGTCATTCATAAT
285201 TTCATGTCATTCATAAT
1 TTCATGTCATTCATAAT
285218 TTCATGTC
1 TTCATGTC
285226 CCCGATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (17 bp):
TTCATGTCATTCATAAT
Found at i:286874 original size:19 final size:19
Alignment explanation
Indices: 286849--286980 Score: 131
Period size: 19 Copynumber: 6.7 Consensus size: 19
286839 AAACTAAAAC
*
286849 CTGTTGCGAAATT-AAATT
1 CTGTTGCGAATTTGAAATT
* *
286867 CGTGTTGCGAATTCGAAAAT
1 C-TGTTGCGAATTTGAAATT
286887 CTAGTTGCGAATTTGAAATT
1 CT-GTTGCGAATTTGAAATT
*
286907 CAGTTGCGAATTTGAAATT
1 CTGTTGCGAATTTGAAATT
*
286926 CAGTTGCGAATTTGAAATT
1 CTGTTGCGAATTTGAAATT
* **
286945 CCGCGTTGCGAATTTGACTTTT
1 -C-TGTTGCGAATTTGA-AATT
*
286967 GTGTTGCGAATTTG
1 CTGTTGCGAATTTG
286981 GCTATCGCGT
Statistics
Matches: 97, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
18 1 0.01
19 47 0.48
20 34 0.35
21 13 0.13
22 2 0.02
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.38
Consensus pattern (19 bp):
CTGTTGCGAATTTGAAATT
Found at i:286895 original size:20 final size:19
Alignment explanation
Indices: 286851--286961 Score: 134
Period size: 19 Copynumber: 5.7 Consensus size: 19
286841 ACTAAAACCT
* *
286851 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
* *
286870 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTC-A
286890 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
286909 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
286928 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
286949 GTTGCGAATTTGA
1 GTTGCGAATTTGA
286962 CTTTTGTGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 46 0.57
20 22 0.27
21 13 0.16
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:286895 original size:39 final size:39
Alignment explanation
Indices: 286851--286958 Score: 139
Period size: 39 Copynumber: 2.8 Consensus size: 39
286841 ACTAAAACCT
* *
286851 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATC-A
* *
286890 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCA
*
286928 GTTGCGAATTTGAAATTCCGCGTTGCGAATT
1 GTTGCGAATTTGAAATT-CGAGTTGCGAATT
286959 TGACTTTTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
38 18 0.30
39 27 0.44
40 16 0.26
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (39 bp):
GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCA
Found at i:286932 original size:58 final size:59
Alignment explanation
Indices: 286851--286961 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 59
286841 ACTAAAACCT
* *
286851 GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAAT-CTAGTTGCGAATTTGAAATTCA
1 GTTGCGAAATTAAATTCGAGTTGCGAATTCGAAAATCCGAGTTGCGAATTTGAAATTCA
* * * *
286909 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCCGCGTTGCGAATTTGA
1 GTTGCGAAATT-AAATTCGAGTTGCGAATTCGAAAATCCGAGTTGCGAATTTGA
286962 CTTTTGTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
58 25 0.56
59 20 0.44
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (59 bp):
GTTGCGAAATTAAATTCGAGTTGCGAATTCGAAAATCCGAGTTGCGAATTTGAAATTCA
Found at i:286974 original size:20 final size:20
Alignment explanation
Indices: 286949--287015 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
286939 GAAATTCCGC
286949 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
286969 GTTGCGAATTTGGCTATCGC
1 GTTGCGAATTTGACTTTTGT
*
286989 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
*
287009 ATTGCGA
1 GTTGCGA
287016 TTTACAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:287029 original size:40 final size:42
Alignment explanation
Indices: 286891--287035 Score: 132
Period size: 40 Copynumber: 3.7 Consensus size: 42
286881 GAAAATCTAG
* * *
286891 TTGCGAATTTG--AAATTC-AGTTGCGAATTTGAAATTCAG--
1 TTGCGAATTTGACAAATTCGCGTTGCGAATTTG-ACTTCTGTA
* *
286929 TTGCGAATTTG--AAATTCCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACAAATT-CGCGTTGCGAATTTGACTTCTGTA
* *
286970 TTGCGAATTTGGC-TA-TCGCGTTGCGAATTTGACTTCTGTA
1 TTGCGAATTTGACAAATTCGCGTTGCGAATTTGACTTCTGTA
287010 TTGCG-ATTT-ACAAATTCGCGTTGCGA
1 TTGCGAATTTGACAAATTCGCGTTGCGA
287036 TTTACATATT
Statistics
Matches: 90, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
38 17 0.19
39 10 0.11
40 50 0.56
41 12 0.13
42 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (42 bp):
TTGCGAATTTGACAAATTCGCGTTGCGAATTTGACTTCTGTA
Found at i:287033 original size:20 final size:20
Alignment explanation
Indices: 287010--287055 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
287000 GACTTCTGTA
287010 TTGCGATTTACAAATTCGCG
1 TTGCGATTTACAAATTCGCG
*
287030 TTGCGATTTACATATTCGCG
1 TTGCGATTTACAAATTCGCG
287050 TTGCGA
1 TTGCGA
287056 AATTGGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCG
Found at i:293925 original size:18 final size:18
Alignment explanation
Indices: 293902--293938 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
293892 ATTAAACATA
293902 AAGTCAAACTAAAATAAC
1 AAGTCAAACTAAAATAAC
293920 AAGTCAAACTAAAATAAC
1 AAGTCAAACTAAAATAAC
293938 A
1 A
293939 GAACAATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AAGTCAAACTAAAATAAC
Found at i:295776 original size:22 final size:23
Alignment explanation
Indices: 295745--295791 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
295735 TAATCGCGAG
295745 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* *
295767 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
295790 TT
1 TT
295792 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:308356 original size:17 final size:17
Alignment explanation
Indices: 308334--308367 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
308324 TGAACTTATT
308334 AGTCTCGTGTGTGAATC
1 AGTCTCGTGTGTGAATC
308351 AGTCTCGTGTGTGAATC
1 AGTCTCGTGTGTGAATC
308368 GTAAGCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (17 bp):
AGTCTCGTGTGTGAATC
Found at i:312718 original size:20 final size:20
Alignment explanation
Indices: 312693--312737 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
312683 ATCATCCAAT
*
312693 TTTTTAAACCTCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
312713 TTTTTAAACCCCAGACCGGA
1 TTTTTAAACCCCAGACCGGA
312733 TTTTT
1 TTTTT
312738 TTCCGAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAGACCGGA
Done.