Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004716.1 Hibiscus syriacus cultivar Beakdansim tig00010632_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: 129450
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4748 original size:7 final size:7
Alignment explanation
Indices: 4736--4820 Score: 170
Period size: 7 Copynumber: 12.1 Consensus size: 7
4726 TCTATATTCT
4736 CTTTTCA
1 CTTTTCA
4743 CTTTTCA
1 CTTTTCA
4750 CTTTTCA
1 CTTTTCA
4757 CTTTTCA
1 CTTTTCA
4764 CTTTTCA
1 CTTTTCA
4771 CTTTTCA
1 CTTTTCA
4778 CTTTTCA
1 CTTTTCA
4785 CTTTTCA
1 CTTTTCA
4792 CTTTTCA
1 CTTTTCA
4799 CTTTTCA
1 CTTTTCA
4806 CTTTTCA
1 CTTTTCA
4813 CTTTTCA
1 CTTTTCA
4820 C
1 C
4821 AGGCAACTGA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 78 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.56
Consensus pattern (7 bp):
CTTTTCA
Found at i:9147 original size:40 final size:40
Alignment explanation
Indices: 9103--9184 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
9093 ACCGTAGTGC
*
9103 TACACATAAGGTCGTGCCCACCATATACACCGAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAATGTAT
9143 TACACATAAGGTCGTGCCCACCATATACACCAAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAATGTAT
9183 TA
1 TA
9185 TAAACCTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAATGTAT
Found at i:11445 original size:2 final size:2
Alignment explanation
Indices: 11434--11463 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11424 TAATTGTAAT
11434 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11464 TAATAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14311 original size:73 final size:73
Alignment explanation
Indices: 14209--14374 Score: 215
Period size: 73 Copynumber: 2.3 Consensus size: 73
14199 ATACCTAAGT
* * * * *
14209 CATAAGTACCGATAACCTTATGTTGATTTTGGCTCCGAGAAAAACAAAATGGCAAACAGGTACCG
1 CATAGGTACCGATACCCTTATGCTAATTTTGGCTCCGAGAAAAACAAAATGCCAAACAGGTACCG
14274 ATACCCCC
66 ATACCCCC
* * * **
14282 CATAGGTACCGATACCCTTGTGCTAATTTTGGCTCCGAGAAAAATAAAATGCCTAATGGGTACCG
1 CATAGGTACCGATACCCTTATGCTAATTTTGGCTCCGAGAAAAACAAAATGCCAAACAGGTACCG
14347 ATACCCCC
66 ATACCCCC
* * *
14355 TAGAGGTATCGATACCCTTA
1 CATAGGTACCGATACCCTTA
14375 GTCATTTAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (73 bp):
CATAGGTACCGATACCCTTATGCTAATTTTGGCTCCGAGAAAAACAAAATGCCAAACAGGTACCG
ATACCCCC
Found at i:22972 original size:73 final size:72
Alignment explanation
Indices: 22811--22973 Score: 204
Period size: 73 Copynumber: 2.2 Consensus size: 72
22801 TTTAAATGAG
* *
22811 GAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAAAAAACAGAATGCCAAACGGGTATCGATA
1 GAGGTACCGATACCCTTATGCTAATTTTGGCTCCGAAAAAACAGAATGCCAAACGGGTACCGATA
22876 CACCTCA
66 CACCTCA
* * * *
22883 TAGGTACCGATTCCCTTGTGCTAATTTTGGCTCCGAGAAAAACAGAATGTCC-AATGGGTACCGA
1 GAGGTACCGATACCCTTATGCTAATTTTGGCTCCGA-AAAAACAGAATG-CCAAACGGGTACCGA
*
22947 TAC-CCCCTA
64 TACACCTC-A
* *
22956 GAGGTACTGATGCCCTTA
1 GAGGTACCGATACCCTTA
22974 GTCATTTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
72 35 0.45
73 40 0.52
74 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (72 bp):
GAGGTACCGATACCCTTATGCTAATTTTGGCTCCGAAAAAACAGAATGCCAAACGGGTACCGATA
CACCTCA
Found at i:23246 original size:17 final size:18
Alignment explanation
Indices: 23224--23264 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
23214 AGTTTGAGCA
23224 ATTCAAGCAT-ATTTTTC
1 ATTCAAGCATCATTTTTC
*
23241 ATTCAA-TATCATTTTTC
1 ATTCAAGCATCATTTTTC
*
23258 TTTCAAG
1 ATTCAAG
23265 AACACCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTCAAGCATCATTTTTC
Found at i:25612 original size:18 final size:18
Alignment explanation
Indices: 25589--25623 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25579 TAGCATTATC
*
25589 ATTTATATTATTATCATT
1 ATTTATATCATTATCATT
25607 ATTTATATCATTATCAT
1 ATTTATATCATTATCAT
25624 CAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATCATTATCATT
Found at i:25765 original size:2 final size:2
Alignment explanation
Indices: 25758--25793 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25748 CATATCCATC
25758 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
25794 TGTATTTGTT
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:28781 original size:4 final size:4
Alignment explanation
Indices: 28774--28800 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28764 ACTATGTATG
28774 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
28801 ACATGCATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:38042 original size:2 final size:2
Alignment explanation
Indices: 38035--38060 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38025 ACAATCATCA
38035 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
38061 GAATCCAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45874 original size:26 final size:26
Alignment explanation
Indices: 45824--45873 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
45814 GCCAAACATT
45824 TGTTGAAAACCAATTTAGCTGCCCCA
1 TGTTGAAAACCAATTTAGCTGCCCCA
* *
45850 TGTTG-AAATCAATTTAGTTGCCCC
1 TGTTGAAAACCAATTTAGCTGCCCC
45874 CTATTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (26 bp):
TGTTGAAAACCAATTTAGCTGCCCCA
Found at i:50468 original size:26 final size:26
Alignment explanation
Indices: 50418--50467 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
50408 GCCAAACATT
50418 TGTTGAAAACCAATTTAGCTACCCCA
1 TGTTGAAAACCAATTTAGCTACCCCA
* *
50444 TGTTG-AAATCAATTTAGCTGCCCC
1 TGTTGAAAACCAATTTAGCTACCCC
50468 CTATTTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (26 bp):
TGTTGAAAACCAATTTAGCTACCCCA
Found at i:52523 original size:12 final size:12
Alignment explanation
Indices: 52506--52536 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
52496 GTACTTAAGG
52506 TTAAGTTTGAGT
1 TTAAGTTTGAGT
52518 TTAAGTTTGAGT
1 TTAAGTTTGAGT
*
52530 TTGAGTT
1 TTAAGTT
52537 CGAGCTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (12 bp):
TTAAGTTTGAGT
Found at i:79873 original size:20 final size:20
Alignment explanation
Indices: 79850--79894 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
79840 CCCGTTGATA
*
79850 GTTGACTTTGACCGTTAATC
1 GTTGACTTTGACCGTCAATC
* *
79870 GTTGACTTTGATCGTCAATT
1 GTTGACTTTGACCGTCAATC
79890 GTTGA
1 GTTGA
79895 TTTTTTGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (20 bp):
GTTGACTTTGACCGTCAATC
Found at i:80532 original size:28 final size:28
Alignment explanation
Indices: 80492--80645 Score: 156
Period size: 28 Copynumber: 5.5 Consensus size: 28
80482 TCTTGTTTCC
*
80492 GTATGAGATTTATTCCTCGATCCGTTCT
1 GTATGAGATTTATTCCTCGATCTGTTCT
* *
80520 GTATTAGATTTATT-CTCCGATATGTTCT
1 GTATGAGATTTATTCCT-CGATCTGTTCT
* * * *
80548 ATATGAGATTTATCCCT-GATATATTCT
1 GTATGAGATTTATTCCTCGATCTGTTCT
80575 GTATGAGATTTA-TCCAT-GATCTGTTCT
1 GTATGAGATTTATTCC-TCGATCTGTTCT
*
80602 GTATTG-GATTTATTCCTCGTTCTGTTTCT
1 GTA-TGAGATTTATTCCTCGATCTG-TTCT
80631 GTATGAGATTATATT
1 GTATGAGATT-TATT
80646 TTGTACTCTG
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.02
27 41 0.39
28 45 0.43
29 13 0.12
30 4 0.04
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.47
Consensus pattern (28 bp):
GTATGAGATTTATTCCTCGATCTGTTCT
Found at i:80579 original size:27 final size:27
Alignment explanation
Indices: 80492--80640 Score: 131
Period size: 27 Copynumber: 5.4 Consensus size: 27
80482 TCTTGTTTCC
* **
80492 GTATGAGATTTATTCCTCGATCCGTTCT
1 GTATGAGATTTATCCCT-GATATGTTCT
*
80520 GTATTAGATTTATTCTCC-GATATGTTCT
1 GTATGAGATTTA-TC-CCTGATATGTTCT
* *
80548 ATATGAGATTTATCCCTGATATATTCT
1 GTATGAGATTTATCCCTGATATGTTCT
* *
80575 GTATGAGATTTATCCATGATCTGTTCT
1 GTATGAGATTTATCCCTGATATGTTCT
* * *
80602 GTATTG-GATTTATTCCTCGTTCTGTTTCT
1 GTA-TGAGATTTATCCCT-GATATG-TTCT
80631 GTATGAGATT
1 GTATGAGATT
80641 ATATTTTGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.02
27 46 0.46
28 38 0.38
29 12 0.12
30 2 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (27 bp):
GTATGAGATTTATCCCTGATATGTTCT
Found at i:85182 original size:28 final size:28
Alignment explanation
Indices: 85147--85224 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
85137 TCAAATTTTA
*
85147 TAAATAACTTCAAGACTTCAAATATC-T
1 TAAATAACTTCAATACTTCAAATATCAT
* *
85174 TAGAATAACTTCAATACTAT-AGATTTCAT
1 TA-AATAACTTCAATACT-TCAAATATCAT
85203 TAAATAACTTCAATACTTCAAA
1 TAAATAACTTCAATACTTCAAA
85225 GTTGAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 3 0.07
28 36 0.84
29 4 0.09
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAATAACTTCAATACTTCAAATATCAT
Found at i:87096 original size:13 final size:13
Alignment explanation
Indices: 87078--87112 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
87068 TTAATACCTG
87078 TAAGCAAACGTAA
1 TAAGCAAACGTAA
87091 TAAGCAAACGTAA
1 TAAGCAAACGTAA
87104 TAAGCAAAC
1 TAAGCAAAC
87113 CAGGAAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.54, C:0.17, G:0.14, T:0.14
Consensus pattern (13 bp):
TAAGCAAACGTAA
Found at i:94453 original size:23 final size:23
Alignment explanation
Indices: 94420--94482 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
94410 ATTATTATAT
94420 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
94443 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
94466 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
94483 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:97604 original size:29 final size:29
Alignment explanation
Indices: 97571--97641 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
97561 TATTGCTGAG
97571 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1 CTCGACTCAAACTTTAAAAGTAAGCTCAA
97600 CTCGACTCAAACTTTAAAAGTAAGCTCAA
1 CTCGACTCAAACTTTAAAAGTAAGCTCAA
97629 CTCGACTCAAACT
1 CTCGACTCAAACT
97642 CACGGACTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (29 bp):
CTCGACTCAAACTTTAAAAGTAAGCTCAA
Found at i:104888 original size:20 final size:20
Alignment explanation
Indices: 104863--104908 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
104853 AACTATTCGC
*
104863 TTTCGTTTTCACAACGTGAA
1 TTTCGTTTTCACAACGCGAA
*
104883 TTTCGTTTTCGCAACGCGAA
1 TTTCGTTTTCACAACGCGAA
104903 TTTCGT
1 TTTCGT
104909 AAATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (20 bp):
TTTCGTTTTCACAACGCGAA
Found at i:105309 original size:20 final size:22
Alignment explanation
Indices: 105267--105310 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
105257 GATTTTACAT
105267 TTCGCAACACGAATTTGTCAAA
1 TTCGCAACACGAATTTGTCAAA
*
105289 TTCGCAACTC-AATTT-TCAAA
1 TTCGCAACACGAATTTGTCAAA
105309 TT
1 TT
105311 AGTAAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (22 bp):
TTCGCAACACGAATTTGTCAAA
Found at i:105411 original size:20 final size:20
Alignment explanation
Indices: 105386--105423 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
105376 ATTCGATTTG
*
105386 CGAAATTCACGTTGCGAAAA
1 CGAAATTCACATTGCGAAAA
105406 CGAAATTCACATTGCGAA
1 CGAAATTCACATTGCGAA
105424 TAGTTGTGTT
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:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
CGAAATTCACATTGCGAAAA
Found at i:109787 original size:2 final size:2
Alignment explanation
Indices: 109780--109807 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
109770 TTATCCCTAA
109780 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
109808 GATAGAATTA
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:110216 original size:30 final size:31
Alignment explanation
Indices: 110171--110239 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
110161 AATATAAGTT
* *
110171 TGGTTACTTTTATTTC-TTTTAATTAAAATC
1 TGGTCACTTTCATTTCGTTTTAATTAAAATC
* *
110201 TGGTCACTTTCATTTCGTTTTAATTAAGATG
1 TGGTCACTTTCATTTCGTTTTAATTAAAATC
110232 TGGTCACT
1 TGGTCACT
110240 GAAGCTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (31 bp):
TGGTCACTTTCATTTCGTTTTAATTAAAATC
Found at i:110416 original size:31 final size:31
Alignment explanation
Indices: 110379--110447 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
110369 AGTTCTGGTG
* ** *
110379 GTCACTTACGTTATTGTTTTATTAAGTTTTA
1 GTCACTTACATTATCATGTTATTAAGTTTTA
110410 GTCACTTACATTATCATGTTATTAAGTTTTA
1 GTCACTTACATTATCATGTTATTAAGTTTTA
110441 GTCACTT
1 GTCACTT
110448 GAACGTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.51
Consensus pattern (31 bp):
GTCACTTACATTATCATGTTATTAAGTTTTA
Found at i:110871 original size:31 final size:31
Alignment explanation
Indices: 110798--110874 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
110788 TTCAACGTCC
*
110798 AAGTGACCAAAACTTAATAAAACTATAACGT
1 AAGTCACCAAAACTTAATAAAACTATAACGT
* * *
110829 AAGTGACCAAAACTTAATAAAA-TAGTGATGT
1 AAGTCACCAAAACTTAATAAAACTA-TAACGT
*
110860 AAGTCAGCAAAACTT
1 AAGTCACCAAAACTT
110875 GTGTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.05
31 39 0.95
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.23
Consensus pattern (31 bp):
AAGTCACCAAAACTTAATAAAACTATAACGT
Found at i:116211 original size:30 final size:31
Alignment explanation
Indices: 116137--116213 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
116127 AAAATCATCT
116137 TTTAAATATAA-TTAAAAGATTCAAACTCATG
1 TTTAAATA-AATTTAAAAGATTCAAACTCATG
* * * **
116168 TTT-AATTATTTTAAAATATT-AAACTTTTG
1 TTTAAATAAATTTAAAAGATTCAAACTCATG
116197 TTTAAATAAATTTAAAA
1 TTTAAATAAATTTAAAA
116214 ATAATGAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 11 0.30
30 23 0.62
31 3 0.08
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (31 bp):
TTTAAATAAATTTAAAAGATTCAAACTCATG
Found at i:117244 original size:2 final size:2
Alignment explanation
Indices: 117199--117229 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
117189 ATTTTAAAAT
117199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
117230 TAAATAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117275 original size:16 final size:18
Alignment explanation
Indices: 117241--117276 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
117231 AAATAAGTAT
117241 ATATGAATTATACTTAAA
1 ATATGAATTATACTTAAA
117259 ATAT-AATTATA-TTAAA
1 ATATGAATTATACTTAAA
117275 AT
1 AT
117277 TTTATTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
ATATGAATTATACTTAAA
Found at i:117501 original size:26 final size:26
Alignment explanation
Indices: 117446--117494 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
117436 AAGCAAAATC
*
117446 AATTTATTTTCTTAAATATCCAATTA
1 AATTTATATTCTTAAATATCCAATTA
*
117472 AATTTATATTC-TAAATATTCAAT
1 AATTTATATTCTTAAATATCCAAT
117495 GTGAATTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (26 bp):
AATTTATATTCTTAAATATCCAATTA
Found at i:127457 original size:21 final size:21
Alignment explanation
Indices: 127433--127479 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
127423 AGTGTCAAAC
*
127433 AATAACAAAATCAGTAGAAAA
1 AATAACAAAACCAGTAGAAAA
*
127454 AATAACAAAACCAGTAGAAAT
1 AATAACAAAACCAGTAGAAAA
127475 AATAA
1 AATAA
127480 TGTTTCCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.15
Consensus pattern (21 bp):
AATAACAAAACCAGTAGAAAA
Done.