Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002453.1 Hibiscus syriacus cultivar Beakdansim tig00005026_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: 80764
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:350 original size:21 final size:21
Alignment explanation
Indices: 325--614 Score: 180
Period size: 21 Copynumber: 14.0 Consensus size: 21
315 TGCGATTTTG
325 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
346 GACTATCGCAATGAACTTGGA
1 GACTATCGCAACGAACTTGGA
* * * *
367 TATTATCACAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
* *
388 GCCTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
409 GACTATCAC-ACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
* *
429 GACTATCGTAACGAACTTGTAA
1 GACTATCGCAACGAACTTG-GA
* **
451 TAAAATCGCAACGCGAACTT-G-
1 GACTATCGCAA--CGAACTTGGA
*
472 GACTA-CGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
492 -A-TAAATCGCAACGCAAACTT-G-
1 GACT--ATCGCAACG--AACTTGGA
*
513 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
534 -A-AATCGCAACGCAAACTT-G-
1 GACTATCGCAACG--AACTTGGA
*
553 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
* *
574 -A-AATCGCAACGCGAACTT--C
1 GACTATCGCAA--CGAACTTGGA
593 GACTATCGCAACGCGAACTTGG
1 GACTATCGCAA--CGAACTTGG
615 CTATTGCAAT
Statistics
Matches: 207, Mismatches: 35, Indels: 52
0.70 0.12 0.18
Matches are distributed among these distances:
18 7 0.03
19 26 0.13
20 30 0.14
21 122 0.59
22 10 0.05
23 5 0.02
24 7 0.03
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:539 original size:19 final size:19
Alignment explanation
Indices: 477--584 Score: 108
Period size: 19 Copynumber: 5.4 Consensus size: 19
467 ACTTGGACTA
477 CGCAACGAATTTGGAATAAAT
1 CGCAACGAATTTGG-A-AAAT
* **
498 CGCAACGCAAACTTGGACTAT
1 CGCAACG--AATTTGGAAAAT
519 CGCAACGAATTTGGAAAAT
1 CGCAACGAATTTGGAAAAT
* **
538 CGCAACGCAAACTTGGACTAT
1 CGCAACG--AATTTGGAAAAT
559 CGCAACGAATTTGGAAAAT
1 CGCAACGAATTTGGAAAAT
578 CGCAACG
1 CGCAACG
585 CGAACTTCGA
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
19 32 0.45
21 32 0.45
22 1 0.01
23 6 0.08
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.19
Consensus pattern (19 bp):
CGCAACGAATTTGGAAAAT
Found at i:549 original size:40 final size:40
Alignment explanation
Indices: 452--605 Score: 256
Period size: 40 Copynumber: 3.8 Consensus size: 40
442 AACTTGTAAT
*
452 AAAATCGCAACGCGAACTTGGACTA-CGCAACGAATTTGG
1 AAAATCGCAACGCAAACTTGGACTATCGCAACGAATTTGG
491 AATAAATCGCAACGCAAACTTGGACTATCGCAACGAATTTGG
1 -A-AAATCGCAACGCAAACTTGGACTATCGCAACGAATTTGG
533 AAAATCGCAACGCAAACTTGGACTATCGCAACGAATTTGG
1 AAAATCGCAACGCAAACTTGGACTATCGCAACGAATTTGG
* *
573 AAAATCGCAACGCGAACTTCGACTATCGCAACG
1 AAAATCGCAACGCAAACTTGGACTATCGCAACG
606 CGAACTTGGC
Statistics
Matches: 109, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
40 71 0.65
41 24 0.22
42 14 0.13
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (40 bp):
AAAATCGCAACGCAAACTTGGACTATCGCAACGAATTTGG
Found at i:601 original size:61 final size:61
Alignment explanation
Indices: 452--623 Score: 167
Period size: 61 Copynumber: 2.8 Consensus size: 61
442 AACTTGTAAT
* *
452 AAAATCGCAACGCGAACTTGGACTA-CGCAACG-AATTTGGAATAAATCGCAACGCAAACTTGG
1 AAAATCGCAACGCGAACTTGGACTATCGCAACGCAACTTGGACT--ATCGCAACG-AAACTTGG
** * ** *
514 ACTATCGCAA--CGAATTTGGAAAATCGCAACGCAAACTTGGACTATCGCAACG-AATTTGG
1 AAAATCGCAACGCGAACTTGGACTATCGCAACGC-AACTTGGACTATCGCAACGAAACTTGG
* *
573 AAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGG-CTATTGCAA
1 AAAATCGCAACGCGAACTTGGACTATCGCAACGC-AACTTGGACTATCGCAA
624 TGCGAATATG
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
59 14 0.16
60 18 0.20
61 41 0.46
62 8 0.09
63 8 0.09
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (61 bp):
AAAATCGCAACGCGAACTTGGACTATCGCAACGCAACTTGGACTATCGCAACGAAACTTGG
Found at i:1030 original size:23 final size:25
Alignment explanation
Indices: 979--1032 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
969 ACATCATCCC
* * *
979 TAAAATCATTTAAAAATATATATTT
1 TAAAATCAATTAAAAATATAAATTA
1004 TAAAAT-AATTAAAAA-ATAAATTA
1 TAAAATCAATTAAAAATATAAATTA
1027 TAAAAT
1 TAAAAT
1033 TATCATCGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.46
24 8 0.31
25 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAAATCAATTAAAAATATAAATTA
Found at i:6679 original size:30 final size:31
Alignment explanation
Indices: 6607--6685 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
6597 AAAATTTATA
* *
6607 TACTAAAATGAAATAAAAATTTAACAATAGGG
1 TACTAAAATGAAA-CAAAATGTAACAATAGGG
*
6639 TAGT-AAATGAAACAAAA-GTAA-AATATGGG
1 TACTAAAATGAAACAAAATGTAACAATA-GGG
6668 TACTAAAATGAAACAAAA
1 TACTAAAATGAAACAAAA
6686 AATAAACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 4 0.10
29 9 0.22
30 17 0.41
31 8 0.20
32 3 0.07
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (31 bp):
TACTAAAATGAAACAAAATGTAACAATAGGG
Found at i:11988 original size:30 final size:29
Alignment explanation
Indices: 11954--12024 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 29
11944 AAAACCGAAT
11954 TAAACGGGGATAGAGAAAAACCGTTTATGC
1 TAAACGGGGATAGA-AAAAACCGTTTATGC
* **
11984 TAAACGGGGACTGGAAAAAATTGTTTATGC
1 TAAACGGGGA-TAGAAAAAACCGTTTATGC
12014 TAAACGGGGAT
1 TAAACGGGGAT
12025 GGGTTTGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.03
30 33 0.89
31 3 0.08
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (29 bp):
TAAACGGGGATAGAAAAAACCGTTTATGC
Found at i:12150 original size:2 final size:2
Alignment explanation
Indices: 12145--12193 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
12135 AATTTAAAAA
* * *
12145 AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT 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
12185 AT AT AT AT A
1 AT AT AT AT A
12194 CCCGGCCCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:12575 original size:58 final size:60
Alignment explanation
Indices: 12485--12614 Score: 151
Period size: 58 Copynumber: 2.2 Consensus size: 60
12475 AATGAGATTA
* * *
12485 ATAGTTT-AGGGATGAAATTAGAATGTTAAAAAGTTCAAGGATTAATTT-AAA-ATGAGCC
1 ATAGTTTGA-GGATGAAATTAGAATATTAAAAAGTTCAAGGAATAATTTGAAATAAGAGCC
* * *
12543 ATAGTTTGAGGATGAAATT-GAAATATTTAAAAGTTTAAGGAATAATTTGAAATAAGGGCC
1 ATAGTTTGAGGATGAAATTAG-AATATTAAAAAGTTCAAGGAATAATTTGAAATAAGAGCC
*
12603 AAAGTTTGAGGA
1 ATAGTTTGAGGA
12615 CATATAGTGT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
57 1 0.02
58 40 0.66
59 4 0.07
60 16 0.26
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (60 bp):
ATAGTTTGAGGATGAAATTAGAATATTAAAAAGTTCAAGGAATAATTTGAAATAAGAGCC
Found at i:16056 original size:12 final size:12
Alignment explanation
Indices: 16041--16078 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
16031 GTTATTTAAA
16041 CGGGTATTGGGC
1 CGGGTATTGGGC
*
16053 CGGGTATTGGGT
1 CGGGTATTGGGC
16065 CGGGTATTGGGC
1 CGGGTATTGGGC
16077 CG
1 CG
16079 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:16068 original size:24 final size:24
Alignment explanation
Indices: 16041--16095 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
16031 GTTATTTAAA
* * *
16041 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
16065 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
16089 CGGGTAT
1 CGGGTAT
16096 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:16225 original size:13 final size:13
Alignment explanation
Indices: 16195--16237 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
16185 TTTAATATTT
*
16195 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
16207 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
16220 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
16233 ATCGG
1 ATCGG
16238 ATAATCGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.14, C:0.16, G:0.51, T:0.19
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:17377 original size:5 final size:5
Alignment explanation
Indices: 17367--17405 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
17357 TTCTTCAATC
17367 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
17406 TGCAGCCAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:30675 original size:136 final size:135
Alignment explanation
Indices: 30427--30909 Score: 533
Period size: 136 Copynumber: 3.5 Consensus size: 135
30417 AAACAAGTTA
* * * * * *
30427 AGGTTGAACAAGTTCTTCTCATTACGAACTTCTTTTCTCTC-ATCGGATAAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
* * * *
30491 GAACTCTCCA-CTGAAAATGTTGATCCTTCAAGCGAGGTATTGCTGATTCGAAGTGTTGTGAATC
66 GAACTCTCCATATG-AAATGTTGATCCCTCAAGCGAGGTGTTGCTGATTC-AAATGTTGTGAATC
30555 GAGCAAT
129 GAGCAAT
* *
30562 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
* * ** **
30627 GAACTCTCCATATGAAATG-TCATTCCCTCAAGCGAGGCGTCACTGATTCAAAATGTAATGAATC
66 GAACTCTCCATATGAAATGTTGA-TCCCTCAAGCGAGGTGTTGCTGATTC-AAATGTTGTGAATC
* **
30691 AAGTGAT
129 GAGCAAT
*
30698 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTATCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
* * * * * *
30763 GAACTCTCCATTTGAAGTGTTGATCCCTCAAGTGAGGTGTTGTTGATTCAACTCCATATGCGATG
66 GAACTCTCCATATGAAATGTTGATCCCTCAAGCGAGGTGTTGCTGATTCAA----ATGT-TG-TG
*
30828 AATCGAGCTA-
125 AATCGAGCAAT
* * * * * *
30838 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTTGTTGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
30903 GAACTCT
66 GAACTCT
30910 TCTGGAAATG
Statistics
Matches: 294, Mismatches: 44, Indels: 15
0.83 0.12 0.04
Matches are distributed among these distances:
135 40 0.14
136 171 0.58
137 4 0.01
139 3 0.01
140 67 0.23
141 9 0.03
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (135 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
GAACTCTCCATATGAAATGTTGATCCCTCAAGCGAGGTGTTGCTGATTCAAATGTTGTGAATCGA
GCAAT
Found at i:31154 original size:105 final size:105
Alignment explanation
Indices: 30851--31159 Score: 474
Period size: 105 Copynumber: 2.9 Consensus size: 105
30841 TTGAACAAGT
* * *
30851 TCTTCTCATTATGAACTTCTTCTCCTTTTGTTGGATGAGTTCTTCTCATTATGAACTCTTCTGGA
1 TCTTCTCATTACGAAC--CTTCTCC--TT-TAGGACGAGTTCTTCTCATTATGAACTCTTCTGGA
* * *
30916 AATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAAGGAACAGGC
61 AATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
30961 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* * *
31026 TGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGAACATGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
31066 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAGCTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
*
31131 TGGTTCACCTCCTTCTGCAGTGGATTTGA
66 TGGTTCACCTCCTTCTGCGGTGGATTTGA
31160 GTTGTTGTTG
Statistics
Matches: 187, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
105 163 0.87
106 2 0.01
108 7 0.04
110 15 0.08
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (105 bp):
TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
Found at i:32102 original size:8 final size:8
Alignment explanation
Indices: 32091--32192 Score: 65
Period size: 8 Copynumber: 13.0 Consensus size: 8
32081 TTCTTTTTTC
32091 TTTTCATT
1 TTTTCATT
32099 TTTTCATT
1 TTTTCATT
32107 TTTTCATCAT
1 TTTTCAT--T
32117 TTTT--TT
1 TTTTCATT
32123 CTTTT--TT
1 -TTTTCATT
*
32130 TCTTT-TTT
1 T-TTTCATT
*
32138 TTTTCTTT
1 TTTTCATT
32146 TTTTCATTT
1 TTTTCA-TT
* *
32155 TTTTTAGT
1 TTTTCATT
32163 TTTTC--T
1 TTTTCATT
*
32169 TTTTCACT
1 TTTTCATT
32177 TTTTCATT
1 TTTTCATT
32185 TTTTCATT
1 TTTTCATT
32193 CATTCTTTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
6 8 0.10
7 12 0.15
8 48 0.60
9 7 0.09
10 5 0.06
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:32130 original size:11 final size:11
Alignment explanation
Indices: 32124--32172 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 11
32114 CATTTTTTTC
32124 TTTTTTTCTTT
1 TTTTTTTCTTT
32135 TTTTTTTCTTT
1 TTTTTTTCTTT
32146 TTTTCATTT-TTT
1 TTTT--TTTCTTT
32158 TTAGTTTTTCTTT
1 TT--TTTTTCTTT
32171 TT
1 TT
32173 CACTTTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 15 0.45
12 8 0.24
13 8 0.24
14 2 0.06
ACGTcount: A:0.04, C:0.08, G:0.02, T:0.86
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:32140 original size:39 final size:39
Alignment explanation
Indices: 32078--32202 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 39
32068 CGAACCCTCC
32078 TTTTTC-TTTTTTCTTTTCATTTTTTCATTTTTTCATCATT
1 TTTTTCTTTTTTTCTTTT--TTTTTTCATTTTTTCATCATT
32118 TTTTTCTTTTTTTCTTTTTTTTTTC-TTTTTT--TCATT
1 TTTTTCTTTTTTTCTTTTTTTTTTCATTTTTTCATCATT
*
32154 TTTTT-TAGTTTTTCTTTTTCACTTTTTCATTTTTTCATTCATT
1 TTTTTCT-TTTTTTCTTTTT---TTTTTCATTTTTTCA-TCATT
32197 CTTTTT
1 -TTTTT
32203 TTTCAAGCAT
Statistics
Matches: 74, Mismatches: 1, Indels: 16
0.81 0.01 0.18
Matches are distributed among these distances:
35 1 0.01
36 21 0.28
38 6 0.08
39 13 0.18
40 12 0.16
41 11 0.15
43 5 0.07
44 5 0.07
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.78
Consensus pattern (39 bp):
TTTTTCTTTTTTTCTTTTTTTTTTCATTTTTTCATCATT
Found at i:32159 original size:31 final size:31
Alignment explanation
Indices: 32124--32207 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 31
32114 CATTTTTTTC
**
32124 TTTTTTTCTTTTTTTTTTCTTTTTTTCATTT
1 TTTTTTTCTTTTTTTTTTCACTTTTTCATTT
* *
32155 TTTTTAGT-TTTTCTTTTTCACTTTTTCATTT
1 TTTTT-TTCTTTTTTTTTTCACTTTTTCATTT
**
32186 TTTCATTCATTCTTTTTTTTCA
1 TTTTTTTC-TT-TTTTTTTTCA
32208 AGCATAGTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
30 1 0.02
31 28 0.68
32 3 0.07
33 9 0.22
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.77
Consensus pattern (31 bp):
TTTTTTTCTTTTTTTTTTCACTTTTTCATTT
Found at i:32205 original size:39 final size:38
Alignment explanation
Indices: 32079--32206 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 38
32069 GAACCCTCCT
32079 TTTTCTTTTTTC-TTTTCATTTTTTCATTTTTTCA-TCA
1 TTTT-TTTTTTCTTTTTCATTTTTTCATTTTTTCATTCA
* ** * *
32116 TTTTTTTCTTTTTTTCTTTTTTTTTTCTTTTTTTCATT-T
1 TTTTTTT-TTTCTTT-TTCATTTTTTCATTTTTTCATTCA
*
32155 TTTTTAGTTTTTCTTTTTCACTTTTTCATTTTTTCATTCA
1 TTTTT--TTTTTCTTTTTCATTTTTTCATTTTTTCATTCA
32195 TTCTTTTTTTTC
1 TT-TTTTTTTTC
32207 AAGCATAGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
36 3 0.04
37 7 0.10
38 2 0.03
39 46 0.64
40 9 0.12
41 5 0.07
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (38 bp):
TTTTTTTTTTCTTTTTCATTTTTTCATTTTTTCATTCA
Found at i:35748 original size:14 final size:14
Alignment explanation
Indices: 35729--35755 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35719 AAATGAATGT
35729 AAAGAATGAAGAAC
1 AAAGAATGAAGAAC
35743 AAAGAATGAAGAA
1 AAAGAATGAAGAA
35756 TGAAAATGTA
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:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAC
Found at i:54989 original size:20 final size:19
Alignment explanation
Indices: 54964--55037 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
54954 CGTTGCAGCT
54964 AGAGTGTAT-GGATACACTGC
1 AGAGTGTATCGG-TACACT-C
54984 AGAGTGTATCGGTACAC-C
1 AGAGTGTATCGGTACACTC
55002 --AGTGTAT-GGATACACTAC
1 AGAGTGTATCGG-TACACT-C
*
55020 AGGGTGTATCGGTACACT
1 AGAGTGTATCGGTACACT
55038 AATTACATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.04
16 12 0.26
18 2 0.04
20 26 0.57
21 4 0.09
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (19 bp):
AGAGTGTATCGGTACACTC
Found at i:55007 original size:16 final size:17
Alignment explanation
Indices: 54986--55036 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
54976 TACACTGCAG
54986 AGTGTATCGGTACAC-C
1 AGTGTATCGGTACACAC
55002 AGTGTAT-GGATACACTAC
1 AGTGTATCGG-TACAC-AC
55020 AGGGTGTATCGGTACAC
1 A--GTGTATCGGTACAC
55037 TAATTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
18 2 0.07
20 11 0.38
21 2 0.07
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (17 bp):
AGTGTATCGGTACACAC
Found at i:55013 original size:36 final size:36
Alignment explanation
Indices: 54966--55136 Score: 139
Period size: 36 Copynumber: 5.0 Consensus size: 36
54956 TTGCAGCTAG
54966 AGTGTATGGATACACTGCAGAGTGTATCGGTACACC
1 AGTGTATGGATACACTGCAGAGTGTATCGGTACACC
* *
55002 AGTGTATGGATACACTACAGGGTGTATCGGTACA-C
1 AGTGTATGGATACACTGCAGAGTGTATCGGTACACC
* * * * * * *
55037 --T-AAT---TACA-TTCAGTGTTTGAGCAGT-CA-T
1 AGTGTATGGATACACTGCAGAGTGT-ATCGGTACACC
* *
55065 AGGGGTATGGATACATTGCATG-GTGTATCGGTACACC
1 A-GTGTATGGATACACTGCA-GAGTGTATCGGTACACC
55102 AGTGTATGGATACACTGCAGAGTGTATCGGTACAC
1 AGTGTATGGATACACTGCAGAGTGTATCGGTACAC
55137 TTTAACATTT
Statistics
Matches: 104, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
28 9 0.09
29 8 0.08
32 4 0.04
33 1 0.01
35 10 0.10
36 70 0.67
37 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (36 bp):
AGTGTATGGATACACTGCAGAGTGTATCGGTACACC
Found at i:55108 original size:16 final size:18
Alignment explanation
Indices: 55087--55136 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
55077 ACATTGCATG
55087 GTGTATCGGTACAC-C-A
1 GTGTATCGGTACACGCAA
55103 GTGTAT-GGATACACTGCAGA
1 GTGTATCGG-TACAC-GCA-A
55123 GTGTATCGGTACAC
1 GTGTATCGGTACAC
55137 TTTAACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
18 1 0.04
20 12 0.43
21 2 0.07
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (18 bp):
GTGTATCGGTACACGCAA
Found at i:57847 original size:19 final size:17
Alignment explanation
Indices: 57823--57870 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
57813 TGTAGCCAGG
57823 GTGTATGGATACATACAGA
1 GTGTATGGATACA-AC-GA
* *
57842 GTGTATCGATAC-ACTA
1 GTGTATGGATACAACGA
57858 GTGTATGGATACA
1 GTGTATGGATACA
57871 CTGCAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 12 0.48
17 2 0.08
19 11 0.44
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (17 bp):
GTGTATGGATACAACGA
Found at i:57862 original size:16 final size:16
Alignment explanation
Indices: 57841--57872 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57831 ATACATACAG
57841 AGTGTATCGATACACT
1 AGTGTATCGATACACT
*
57857 AGTGTATGGATACACT
1 AGTGTATCGATACACT
57873 GCAGGGTGTA
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:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (16 bp):
AGTGTATCGATACACT
Found at i:57869 original size:35 final size:36
Alignment explanation
Indices: 57823--57893 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
57813 TGTAGCCAGG
57823 GTGTATGGATACA-TACAGAGTGTATCGATACACTA
1 GTGTATGGATACACTACAGAGTGTATCGATACACTA
* * *
57858 GTGTATGGATACACTGCAGGGTGTATCGGTACACTA
1 GTGTATGGATACACTACAGAGTGTATCGATACACTA
57894 ATTACATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (36 bp):
GTGTATGGATACACTACAGAGTGTATCGATACACTA
Found at i:57963 original size:16 final size:16
Alignment explanation
Indices: 57942--57999 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
57932 ACACTGCAGG
57942 GTGTATCGGTACACCA
1 GTGTATCGGTACACCA
57958 GTGTAT-GGATACACTGCA
1 GTGTATCGG-TACAC--CA
57976 GGGTGTATCGGTACACCA
1 --GTGTATCGGTACACCA
57994 GTGTAT
1 GTGTAT
58000 GGATACATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.06
16 17 0.47
18 4 0.11
20 11 0.31
21 2 0.06
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (16 bp):
GTGTATCGGTACACCA
Found at i:57964 original size:36 final size:36
Alignment explanation
Indices: 57924--58135 Score: 316
Period size: 36 Copynumber: 5.9 Consensus size: 36
57914 AGTCATAGGG
*
57924 GTATGGATACACTGCAGGGTGTATCGGTACACCAGT
1 GTATGGATACACTGCAGAGTGTATCGGTACACCAGT
*
57960 GTATGGATACACTGCAGGGTGTATCGGTACACCAGT
1 GTATGGATACACTGCAGAGTGTATCGGTACACCAGT
* * *
57996 GTATGGATACATTGCAGAGTGTATCGATACACTAGT
1 GTATGGATACACTGCAGAGTGTATCGGTACACCAGT
* * *
58032 GTATGGATACACTGTAGGGTGTATCGGTACACTAGT
1 GTATGGATACACTGCAGAGTGTATCGGTACACCAGT
* *
58068 GTATGGATACACTGTAGAGTGTATCGATACACCAGT
1 GTATGGATACACTGCAGAGTGTATCGGTACACCAGT
* *
58104 GCATGGATACACTGTAGAGTGTATCGGTACAC
1 GTATGGATACACTGCAGAGTGTATCGGTACAC
58136 TTTAGCATTT
Statistics
Matches: 163, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 163 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (36 bp):
GTATGGATACACTGCAGAGTGTATCGGTACACCAGT
Found at i:62568 original size:29 final size:30
Alignment explanation
Indices: 62536--62604 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
62526 GATATATCGT
* *
62536 TTATATCACTGAACTTTTAATTT-TATCAA
1 TTATATCACTAAACTTTGAATTTCTATCAA
* *
62565 TTATAAT-ACTAAACTTTGATTTTCGTTTCAA
1 TTAT-ATCACTAAACTTTGAATTTC-TATCAA
62596 TTATATCAC
1 TTATATCAC
62605 AAGCCCGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
29 17 0.53
30 4 0.12
31 11 0.34
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.48
Consensus pattern (30 bp):
TTATATCACTAAACTTTGAATTTCTATCAA
Found at i:65167 original size:24 final size:25
Alignment explanation
Indices: 65140--65190 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
65130 TTTTTATTTT
65140 AAAATA-TTTTAAAATTAAGATAAA
1 AAAATATTTTTAAAATTAAGATAAA
* *
65164 AAAATATTTTTATAGTTAAGATAAA
1 AAAATATTTTTAAAATTAAGATAAA
65189 AA
1 AA
65191 TTAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (25 bp):
AAAATATTTTTAAAATTAAGATAAA
Found at i:65271 original size:59 final size:59
Alignment explanation
Indices: 65164--65290 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
65154 TTAAGATAAA
*
65164 AAAATAT-TTTTATAGTTAAGATAAAAATTAAATATATTTCTTAAATTAAAATAAGAAT
1 AAAATATATTTTATAGTTAAGATAAAAATTAAATATACTTCTTAAATTAAAATAAGAAT
* * *
65222 AAAATATATTTTATAAGTTAAGAT-AAGATTAAAATGTACCTT-TT-AATTAAGATAAGAAT
1 AAAATATATTTTAT-AGTTAAGATAAAAATT-AAATATA-CTTCTTAAATTAAAATAAGAAT
65281 AAAATATATT
1 AAAATATATT
65291 CGATAAATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
58 7 0.11
59 35 0.57
60 17 0.28
61 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (59 bp):
AAAATATATTTTATAGTTAAGATAAAAATTAAATATACTTCTTAAATTAAAATAAGAAT
Found at i:65302 original size:30 final size:30
Alignment explanation
Indices: 65139--65303 Score: 134
Period size: 30 Copynumber: 5.8 Consensus size: 30
65129 ATTTTTATTT
65139 TAAAATAT-TT-TA-AAATTAAGAT-A-AA
1 TAAAATATATTCTATAAATTAAGATAAGAA
* * *
65164 -AAAATAT-TTTTAT-AGTTAAGATAAAAA
1 TAAAATATATTCTATAAATTAAGATAAGAA
* *
65191 TTAAATATATTTCT-TAAATTAAAATAAGAA
1 TAAAATATA-TTCTATAAATTAAGATAAGAA
* * *
65221 TAAAATATATTTTATAAGTTAAGATAAGAT
1 TAAAATATATTCTATAAATTAAGATAAGAA
* * * *
65251 TAAAATGTA-CCTTTTAATTAAGATAAGAA
1 TAAAATATATTCTATAAATTAAGATAAGAA
*
65280 TAAAATATATTCGATAAATTAAGA
1 TAAAATATATTCTATAAATTAAGA
65304 AAAATATATA
Statistics
Matches: 107, Mismatches: 23, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
24 9 0.08
25 10 0.09
26 1 0.01
27 2 0.02
28 6 0.06
29 26 0.24
30 53 0.50
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (30 bp):
TAAAATATATTCTATAAATTAAGATAAGAA
Found at i:66302 original size:20 final size:21
Alignment explanation
Indices: 66269--66307 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
66259 TTAGGGTTTA
66269 TATTTCTTAATTG-ATTTAGG
1 TATTTCTTAATTGAATTTAGG
* *
66289 TATTTTTTATTTGAATTTA
1 TATTTCTTAATTGAATTTA
66308 AAATTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62
Consensus pattern (21 bp):
TATTTCTTAATTGAATTTAGG
Found at i:72368 original size:20 final size:20
Alignment explanation
Indices: 72345--72397 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
72335 CCCTACTAGA
*
72345 AGTATTGATACTCTACCCTC
1 AGTATCGATACTCTACCCTC
72365 AGTATCGATACTCTACCCTC
1 AGTATCGATACTCTACCCTC
*
72385 ATTATCGATACTC
1 AGTATCGATACTC
72398 CCTTAAGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTCTACCCTC
Found at i:73943 original size:23 final size:23
Alignment explanation
Indices: 73917--73961 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
73907 TATAAATGAA
* *
73917 GTTCGTGAACATTAAACAAACAT
1 GTTCATGAACAATAAACAAACAT
*
73940 GTTCATGAACAATAAATAAACA
1 GTTCATGAACAATAAACAAACA
73962 AACATGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (23 bp):
GTTCATGAACAATAAACAAACAT
Found at i:74864 original size:31 final size:29
Alignment explanation
Indices: 74806--74864 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
74796 ACTTTTTTTA
*
74806 GTGGCCAAAATAAAAATGTTAAAAGTTTG
1 GTGGCCAAAATAAAAATGTGAAAAGTTTG
74835 GTGGCCAAAATACAAAGAT-TGGAAAAGTTT
1 GTGGCCAAAATA-AAA-ATGT-GAAAAGTTT
74865 ATAGACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 12 0.46
30 4 0.15
31 10 0.38
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.25
Consensus pattern (29 bp):
GTGGCCAAAATAAAAATGTGAAAAGTTTG
Found at i:74892 original size:31 final size:31
Alignment explanation
Indices: 74857--74917 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
74847 CAAAGATTGG
*
74857 AAAAGTTTATAGACCAAAAAG-GTAATTTTCC
1 AAAAGTTTAGAGA-CAAAAAGTGTAATTTTCC
*
74888 AAAAGTTTAGAGACTAAAAGTGTAATTTTC
1 AAAAGTTTAGAGACAAAAAGTGTAATTTTC
74918 AAAGGTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (31 bp):
AAAAGTTTAGAGACAAAAAGTGTAATTTTCC
Found at i:76114 original size:19 final size:20
Alignment explanation
Indices: 76071--76115 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
76061 TACTATGCTG
*
76071 GAAATTTATGTTAGAGTGTT
1 GAAATTTATGTTAGAATGTT
76091 GAAATTTATGTTAGAATG-T
1 GAAATTTATGTTAGAATGTT
76110 GAAATT
1 GAAATT
76116 GGTTTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (20 bp):
GAAATTTATGTTAGAATGTT
Found at i:79676 original size:15 final size:16
Alignment explanation
Indices: 79654--79695 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
79644 TCATGTAAAA
79654 ATAAATATTTAAATTT
1 ATAAATATTTAAATTT
*
79670 A-AAATA-TAAAATTT
1 ATAAATATTTAAATTT
*
79684 ATTAATATTTAA
1 ATAAATATTTAA
79696 TCAAGTAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
14 8 0.38
15 9 0.43
16 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAATATTTAAATTT
Done.