Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000962.1 Hibiscus syriacus cultivar Beakdansim tig00001923_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: 76412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6218 original size:41 final size:42
Alignment explanation
Indices: 6161--6241 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 42
6151 CACGAATTTG
*
6161 TAAATCCTTCAGGTCATCTGT-AATCCTTCGAGCATGATGTT
1 TAAATCCTTCAGGTCATCTGTCAATCCTTCGAGCAAGATGTT
* *
6202 TAAATCCTTCGGGTCATCTGTCAATCTTTCGAGCAAGATG
1 TAAATCCTTCAGGTCATCTGTCAATCCTTCGAGCAAGATG
6242 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 20 0.56
42 16 0.44
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (42 bp):
TAAATCCTTCAGGTCATCTGTCAATCCTTCGAGCAAGATGTT
Found at i:6251 original size:41 final size:41
Alignment explanation
Indices: 6161--6260 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 41
6151 CACGAATTTG
* *
6161 TAAATCCTTCAGGTCATCTGTAATCCTTCGAGCATGATGTT
1 TAAATCCTTCAGGTCATCTGTAATCCTTCGAGCAAGATGTA
* *
6202 TAAATCCTTCGGGTCATCTGTCAATCTTTCGAGCAAGATG-A
1 TAAATCCTTCAGGTCATCTGT-AATCCTTCGAGCAAGATGTA
* * *
6243 TAAGTCCTTAAGGCCATC
1 TAAATCCTTCAGGTCATC
6261 CGTTAGACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
41 34 0.68
42 16 0.32
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (41 bp):
TAAATCCTTCAGGTCATCTGTAATCCTTCGAGCAAGATGTA
Found at i:8708 original size:138 final size:138
Alignment explanation
Indices: 8460--8771 Score: 380
Period size: 138 Copynumber: 2.3 Consensus size: 138
8450 ATTTGTATGG
* *
8460 AATTTAGGCTTAATTTCATATTTAGTCCTTTAATTTATGGGAATTCTTAATTTAGTCATCACTTT
1 AATTTAGGTTTAATTTCATATTTAGTCCTTTAATTTATAGGAATTCTTAATTTAGTCATCACTTT
*
8525 TGATATAGGTTCCATTTTAATTATTCGATTCAATAATTGGCTAAAATG-GACTATGTTAATAATT
66 TGATATAGGTTCCATTTTAATTATTCGATTCAATAATTGGCTAAAATGAG-CTAGGTTAATAATT
*
8589 AGAGCCTCT
130 AGAGCCTCC
* * * **
8598 AATTTAGGTTTAATTTCATATTTAGTCCTTTAATTTATAGGAATTCTTAGTTTGGTCCTTGCTTT
1 AATTTAGGTTTAATTTCATATTTAGTCCTTTAATTTATAGGAATTCTTAATTTAGTCATCACTTT
* ** * * * * **
8663 TGCT-TAAGGTTCCATTTTAATTATTTTATTCGATAATTGGTTAAAATTAGTTAGGTTAATGTTT
66 TGATAT-AGGTTCCATTTTAATTATTCGATTCAATAATTGGCTAAAATGAGCTAGGTTAATAATT
8727 AGAGCCTCC
130 AGAGCCTCC
** *
8736 GTTTTAGTTTTAATTTCAT-TGTTA-TCCTTTAATTTA
1 AATTTAGGTTTAATTTCATAT-TTAGTCCTTTAATTTA
8772 GGAGAATTTT
Statistics
Matches: 150, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
137 14 0.09
138 135 0.90
139 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.48
Consensus pattern (138 bp):
AATTTAGGTTTAATTTCATATTTAGTCCTTTAATTTATAGGAATTCTTAATTTAGTCATCACTTT
TGATATAGGTTCCATTTTAATTATTCGATTCAATAATTGGCTAAAATGAGCTAGGTTAATAATTA
GAGCCTCC
Found at i:12951 original size:20 final size:20
Alignment explanation
Indices: 12922--12967 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
12912 TTGGAAAATG
*
12922 TTCTCATTTCATCTTCATAT
1 TTCTCCTTTCATCTTCATAT
12942 TTCTCCTTTCATCTTCATAT
1 TTCTCCTTTCATCTTCATAT
12962 TTCTCC
1 TTCTCC
12968 AAAATTACAA
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:0.15, C:0.30, G:0.00, T:0.54
Consensus pattern (20 bp):
TTCTCCTTTCATCTTCATAT
Found at i:21082 original size:13 final size:13
Alignment explanation
Indices: 21060--21097 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
21050 TTAATATATG
*
21060 TTGTTGAGCATTT
1 TTGTTTAGCATTT
21073 TTGTTTAGCA-TT
1 TTGTTTAGCATTT
*
21085 TTGTTTAGAATTT
1 TTGTTTAGCATTT
21098 GCATTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.18, C:0.05, G:0.18, T:0.58
Consensus pattern (13 bp):
TTGTTTAGCATTT
Found at i:35137 original size:2 final size:2
Alignment explanation
Indices: 35132--35180 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
35122 AAAAATCGAT
35132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35174 TA TA TA T
1 TA TA TA T
35181 CTTACCGATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38406 original size:23 final size:24
Alignment explanation
Indices: 38361--38418 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
38351 CTGATGACAA
*
38361 GATGAACCCGACGACCCATAACTC
1 GATGAACCCGACGACCCAGAACTC
**
38385 GATGAACCC-ACGACTTAGAACTC
1 GATGAACCCGACGACCCAGAACTC
38408 GATGAACCCGA
1 GATGAACCCGA
38419 TGAATCCTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.34, C:0.33, G:0.19, T:0.14
Consensus pattern (24 bp):
GATGAACCCGACGACCCAGAACTC
Found at i:44388 original size:15 final size:16
Alignment explanation
Indices: 44363--44392 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
44353 ATAATTTATT
44363 AATATTGTATGTATGC
1 AATATTGTATGTATGC
44379 AATA-TGTATGTATG
1 AATATTGTATGTATG
44393 TATATTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (16 bp):
AATATTGTATGTATGC
Found at i:44471 original size:34 final size:34
Alignment explanation
Indices: 44381--44476 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 34
44371 ATGTATGCAA
* * *
44381 TATGTATG-TATGTAT-ATTTTGATACATACATT
1 TATGTATGATATGTATGATATTGATGCATATATT
* *
44413 TACGTATGATA---ATGATA-TGTATGCACATATT
1 TATGTATGATATGTATGATATTG-ATGCATATATT
44444 TATGTATGATATGTATGATATTGATGCATATAT
1 TATGTATGATATGTATGATATTGATGCATATAT
44477 AAACATATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
30 4 0.08
31 20 0.40
32 7 0.14
33 2 0.04
34 15 0.30
35 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (34 bp):
TATGTATGATATGTATGATATTGATGCATATATT
Found at i:44597 original size:28 final size:26
Alignment explanation
Indices: 44566--44634 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 26
44556 TACAATGTGT
*
44566 ATACATACATATATGTTCTACATGCATC
1 ATACATACATAAATGTTCTACAT--ATC
** *
44594 ATACATACATGCATGTTCTACCTATC
1 ATACATACATAAATGTTCTACATATC
44620 -TACATACATAAATGT
1 ATACATACATAAATGT
44635 AATACTGTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.36
26 3 0.08
28 20 0.56
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (26 bp):
ATACATACATAAATGTTCTACATATC
Found at i:49033 original size:137 final size:137
Alignment explanation
Indices: 48671--49003 Score: 490
Period size: 137 Copynumber: 2.4 Consensus size: 137
48661 ATCGTCTGCC
* *
48671 GACCATATCTCCTCAATGCAAAGAAGTAGTGTTATCCTCAGACTATCAGACTTCCTCAACACGAA
1 GACCATATCTCCTCAATGCAAAGAAGTAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAA
* ** *
48736 GGAACCATGTTGTCTCTAAATTATCCAAATACGTCTAGACTTTCTCAACACGAAGGAACGATGTT
66 GGAACCGTGTTGTCTCTAAATTATCCAAATACAACTAGACTTCCTCAACACGAAGGAACGATGTT
*
48801 ATCTACT
131 ATCCACT
* *
48808 GACCATATCTCCTCAATGCAAATG-AGCAGTGTCATCCTCAGACATTCAGACTTCCTCAACACGA
1 GACCATATCTCCTCAATGCAAA-GAAGTAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGA
*
48872 AGGAACCGTGTTGTCTCCAAATTATCCAAATACAACTAGA-TGTCCTCAACACGAAGGAACGATG
65 AGGAACCGTGTTGTCTCTAAATTATCCAAATACAACTAGACT-TCCTCAACACGAAGGAACGATG
*
48936 TTGTCCACT
129 TTATCCACT
* * * * *
48945 GACCAAATCTCCTCAATGCGAAGAAGTAGTGCCATTCTCAGACAATCAAACTTCCTCAA
1 GACCATATCTCCTCAATGCAAAGAAGTAGTGTCATCCTCAGACAATCAGACTTCCTCAA
49004 TGAAAAGGAA
Statistics
Matches: 175, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
136 2 0.01
137 172 0.98
138 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (137 bp):
GACCATATCTCCTCAATGCAAAGAAGTAGTGTCATCCTCAGACAATCAGACTTCCTCAACACGAA
GGAACCGTGTTGTCTCTAAATTATCCAAATACAACTAGACTTCCTCAACACGAAGGAACGATGTT
ATCCACT
Found at i:49202 original size:56 final size:56
Alignment explanation
Indices: 49121--49243 Score: 160
Period size: 56 Copynumber: 2.2 Consensus size: 56
49111 AGTGTCATCT
* * * *
49121 TCAACA-CCATATTATCTCCAGATTGACCCGTTTTCCTCAGAGAA-AAGGAAAAGTG
1 TCAACACCCAAATTATCTCCAGATTGACCCGATGTCCTCAGA-AAGAAGGAAAAATG
* *
49176 TCAACACCCAAATTATCTCCAGATTGACCCGATGTCCTTAGAAAGAATGAAAAATG
1 TCAACACCCAAATTATCTCCAGATTGACCCGATGTCCTCAGAAAGAAGGAAAAATG
*
49232 TCATCACCCAAA
1 TCAACACCCAAA
49244 AGTGGCCATA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
55 8 0.14
56 51 0.86
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (56 bp):
TCAACACCCAAATTATCTCCAGATTGACCCGATGTCCTCAGAAAGAAGGAAAAATG
Found at i:49520 original size:3 final size:3
Alignment explanation
Indices: 49512--49545 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
49502 TTTTAATTGT
49512 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
49546 CATTTTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:51273 original size:2 final size:2
Alignment explanation
Indices: 51268--51341 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
51258 CATAATTTCA
51268 AT AT AT AT A- 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
51309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51342 AATGTTATTA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53072 original size:26 final size:26
Alignment explanation
Indices: 53017--53072 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
53007 AAAATGGCCA
*
53017 AAATACCTCAAGCTCCAAAATAATTG
1 AAATACCTCAAGCTCCAAAATAACTG
* * *
53043 AAATACCCTCGAGCTCCTAAATGACT-
1 AAATA-CCTCAAGCTCCAAAATAACTG
53069 AAAT
1 AAAT
53073 TAACATTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.23
Consensus pattern (26 bp):
AAATACCTCAAGCTCCAAAATAACTG
Found at i:53654 original size:25 final size:25
Alignment explanation
Indices: 53608--53655 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
53598 TCCCATGCAG
* *
53608 AGAAGAAAAACATGAACACAACAAC
1 AGAAAAAAAACAGGAACACAACAAC
53633 AGAAAAAAAACGAGGAAC-CAACA
1 AGAAAAAAAAC-AGGAACACAACA
53656 GCCACCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.65, C:0.19, G:0.15, T:0.02
Consensus pattern (25 bp):
AGAAAAAAAACAGGAACACAACAAC
Found at i:54724 original size:23 final size:23
Alignment explanation
Indices: 54668--54712 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
54658 TAATTTCACA
*
54668 AATTGATTAAATAATAATATTTC
1 AATTGATTTAATAATAATATTTC
54691 AATTGATTTAATAATAATATTT
1 AATTGATTTAATAATAATATTT
54713 ATTTAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
AATTGATTTAATAATAATATTTC
Found at i:56647 original size:20 final size:20
Alignment explanation
Indices: 56622--56670 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
56612 GGTTGAAAAG
56622 GAAAAAT-TCTCCCAACAACT
1 GAAAAATAT-TCCCAACAACT
*
56642 GAAAAATATTCCCAACGACT
1 GAAAAATATTCCCAACAACT
56662 GAAAAATAT
1 GAAAAATAT
56671 AGAAGAAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.20
Consensus pattern (20 bp):
GAAAAATATTCCCAACAACT
Found at i:58313 original size:72 final size:72
Alignment explanation
Indices: 58237--58372 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
58227 ATACAATAAA
* * * *
58237 GCTTGAGTTATCCCCCTAGAGCAATTGGTTGATAGCCCCGGCTTTATAGATAATATTCAGCTAGT
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGACCCAGCTTTATAGATAATATTCAGCTAGT
58302 CTGTTAT
66 CTGTTAT
* * * * *
58309 GCTTGAGTTGTCCTCCTAAAGTAATTGGTTAATAGACCTAGCTTTATGGATAATATTCAGCTAG
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGACCCAGCTTTATAGATAATATTCAGCTAG
58373 CCTTTTATTC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGACCCAGCTTTATAGATAATATTCAGCTAGT
CTGTTAT
Found at i:60129 original size:54 final size:54
Alignment explanation
Indices: 60047--60208 Score: 234
Period size: 54 Copynumber: 3.0 Consensus size: 54
60037 TTGACGAGAA
* **
60047 ATCTGGGCAGAAGCTACATAAAAGGATGAATGTGTTGTCAAATGTTTTGCGAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTGCGAAC
* *
60101 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTGTGAAT
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTGCGAAC
* * * * *
60155 ATCTAGGTAGAAGCCATAGGAAAGGATGAATGTGTTGTAAAATGTTTTACGAAC
1 ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTGCGAAC
60209 CAGTATTTAT
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.28
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTGCGAAC
Found at i:61461 original size:123 final size:123
Alignment explanation
Indices: 60994--61937 Score: 1224
Period size: 123 Copynumber: 7.8 Consensus size: 123
60984 CACTCAATGG
*
60994 ATCAACATTTCTAGA-AGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGACA-GAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * * * *
61058 AGTCTGAAGAAC-TATTCAACCTTTTACTTGACTCTATCGTAGAAAGAGATAGAGCAGC
65 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGC
* *
61116 A-GAACCATTTCCAGACAGAGCTCGTAATAAGAAGAACTCATCTG-A-A-GAAGAAG-AGTTCAT
1 ATCAA-CATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * * * **
61176 AGTGTGAAGAACTT-TTCAA-CTTTTACTTGACTCTATCGCAGAAGGAGATAGAGCAAT
65 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGC
* *
61233 AT-AACCATTTCCAGACAAAGTTCGTAAT---AAGAACTCCTCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAA-CATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * * * *
61294 AGTCTGAATAACTTATTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGTAGC
65 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGC
* * *
61353 A-GAACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATATGAAGATGAAGAAGAAGTTCAT
1 ATCAA-CATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * * *
61417 AGTTTGAAGAACTTATTCAACATTTTGCTCGACTTTATCGCAGAAGGATATAAAGCAGC
65 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGC
* *
61476 ATCAACATTTCCAGA-AGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTTAT
1 ATCAACATTTCCAGACAG-AGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* *
61540 AATCTGAAGAACTTATTCAACCTTTTGGTCGACTTTATCGCAGAAGGAGATAAA-CAGC
65 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGC
* * * * * *
61598 ATCAATATTTCCAGACATAGTTCATAATAAGAAGAAGTCATCTGAAGAGGAAGAAAAAATTCATA
1 ATCAACATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
61663 ATCTGAAGAACTTATACAACCTTTTGCTCGACTTTATCGCAGAAGGAGATAAAGCAGC
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGC
* * * * * *
61721 ATCAACATTTTCAGA-AGAAATTCATAATAATAAGAACTCATTTGAAGAGAAAGAAGAAGTTCAT
1 ATCAACATTTCCAGACAG-AGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
*
61785 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCGGC
65 AATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGC
61844 ATCAACATTTCCAGA-AGGAGTTCGTAATGAA-AAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
1 ATCAACATTTCCAGACA-GAGTTCGTAAT-AAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
61907 TAATCTGAAGAACTTATTCAACCTTTTGCTC
64 TAATCTGAAGAACTTATTCAACCTTTTGCTC
61938 AATTCTATTA
Statistics
Matches: 734, Mismatches: 67, Indels: 41
0.87 0.08 0.05
Matches are distributed among these distances:
114 12 0.02
115 1 0.00
116 1 0.00
117 66 0.09
118 42 0.06
119 13 0.02
120 60 0.08
121 3 0.00
122 151 0.21
123 380 0.52
124 5 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGC
Found at i:61701 original size:245 final size:246
Alignment explanation
Indices: 60994--61937 Score: 1231
Period size: 245 Copynumber: 3.9 Consensus size: 246
60984 CACTCAATGG
* *
60994 ATCAACATTTCTAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * * * *
61059 GTCTGAAGAAC-TATTCAACCTTTTACTTGACTCTATCGTAGAAAGAGATAGAGCAGCAGAACCA
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAACAGCACAACCA
* * * *
61123 TTTCCAGACAGAGCTCGTAATAAGAAGAACTCATCTG-A-A-GAAG-AAGAGTTCATAGTGTGAA
131 TTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATCTGAA
* * * * **
61184 GAACTT-TTCAA-CTTTTACTTGACTCTATCGCAGAAGGAGATAGAGCAAT
196 GAACTTATTCAACCTTTTGCTCGACTTTATCGCAGAAGGAGATAAAGCAGC
*
61233 AT-AACCATTTCCAGACA-AAGTTCGTAAT---AAGAACTCCTCTGAAGAGGAAGAAGAAGTTCA
1 ATCAA-CATTTCCAGA-AGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
* * * * ** *
61293 TAGTCTGAATAACTTATTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGTAGCAGAAC
64 TAATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAACAGCACAAC
* * * * *
61358 CATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATATGAAGATGAAGAAGAAGTTCATAGTTTG
129 CATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATCTG
* *
61423 AAGAACTTATTCAACATTTTGCTCGACTTTATCGCAGAAGGATATAAAGCAGC
194 AAGAACTTATTCAACCTTTTGCTCGACTTTATCGCAGAAGGAGATAAAGCAGC
* *
61476 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTTATA
1 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
61541 ATCTGAAGAACTTATTCAACCTTTTGGTCGACTTTATCGCAGAAGGAGATA-AACAGCATCAA-T
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAACAGCA-CAACC
* * * *
61604 ATTTCCAGACATAGTTCATAATAAGAAGAAGTCATCTGAAGAGGAAGAAAAAATTCATAATCTGA
130 ATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATCTGA
*
61669 AGAACTTATACAACCTTTTGCTCGACTTTATCGCAGAAGGAGATAAAGCAGC
195 AGAACTTATTCAACCTTTTGCTCGACTTTATCGCAGAAGGAGATAAAGCAGC
* * * * * *
61721 ATCAACATTTTCAGAAGAAATTCATAATAATAAGAACTCATTTGAAGAGAAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
61786 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATA-AAGCGGCATCAA-
66 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAA-CAGCA-CAAC
*
61849 CATTTCCAGA-AGGAGTTCGTAATGAA-AAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
129 CATTTCCAGACA-GAGTTCGTAAT-AAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATC
61912 TGAAGAACTTATTCAACCTTTTGCTC
192 TGAAGAACTTATTCAACCTTTTGCTC
61938 AATTCTATTA
Statistics
Matches: 622, Mismatches: 65, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
236 43 0.07
237 83 0.13
238 3 0.00
239 22 0.04
240 5 0.01
241 21 0.03
242 6 0.01
243 53 0.09
244 2 0.00
245 219 0.35
246 163 0.26
247 2 0.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (246 bp):
ATCAACATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAACAGCACAACCA
TTTCCAGACAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATCTGAA
GAACTTATTCAACCTTTTGCTCGACTTTATCGCAGAAGGAGATAAAGCAGC
Found at i:61758 original size:368 final size:363
Alignment explanation
Indices: 60994--61937 Score: 1221
Period size: 368 Copynumber: 2.6 Consensus size: 363
60984 CACTCAATGG
*
60994 ATCAACA-TTTCTAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTTC-AGAA-GAGTTCGTAATAAGAAGAACTCATATGAAGA-GAAGAAGAAGTTCAT
* * * * * *
61058 AGTCTGAAGAAC-TATTCAACCTTTTACTTGACTCTATCGTAGAAAGAGATAGAGCAGCA-GAAC
63 AGTCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGCATCAA-
* * * *
61121 CATTTCCAGACAGAGCTCGTAATAAGAAGAACTCATCTG-A-A-GAAG-AAGAGTTCATAGTGTG
127 CATTTCCAGA-AGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATCTG
* * * *
61182 AAGAACTT-TTCAA-CTTTTACTTGACTCTATCGCAGAAGGAGATAGAGCAATATAACCATTTCC
191 AAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAACAACATAACCATTTCC
* * * * * *
61245 AGACAAAGTTCGTAATAAGAACTCCTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAATAACTTAT
256 AGACAAAGTTCATAATAAGAACTCATCTGAAGAGGAAGAAAAAATTCATAATCTGAAGAACTTAT
* * * *
61310 TCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGTAGC
321 ACAACCTTTTGCTCGACTCTATCACAGAAGGAGATAAAGCAGC
* *
61353 A-GAACCATTTCCAGACAGAGTTCGTAATAAGAAGAACTCATATGAAGATGAAGAAGAAGTTCAT
1 ATCAA-CATTTTCAGA-AGAGTTCGTAATAAGAAGAACTCATATGAAGA-GAAGAAGAAGTTCAT
* * * *
61417 AGTTTGAAGAACTTATTCAACATTTTGCTCGACTTTATCGCAGAAGGATATAAAGCAGCATCAAC
63 AGTCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGCATCAAC
*
61482 ATTTCCAGAAGAAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTTATAATCTGA
128 ATTTCCAGAAG-AGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATCTGA
* * * *
61547 AGAACTTATTCAACCTTTTGGTCGACTTTATCGCAGAAGGAGATA-AACAGCATCAA-TATTTCC
192 AGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAACAACAT-AACCATTTCC
* *
61610 AGACATAGTTCATAATAAGAAGAAGTCATCTGAAGAGGAAGAAAAAATTCATAATCTGAAGAACT
256 AGACAAAGTTCATAAT---AAGAACTCATCTGAAGAGGAAGAAAAAATTCATAATCTGAAGAACT
* *
61675 TATACAACCTTTTGCTCGACTTTATCGCAGAAGGAGATAAAGCAGC
318 TATACAACCTTTTGCTCGACTCTATCACAGAAGGAGATAAAGCAGC
* * * *
61721 ATCAACATTTTCAGAAGAAATTCATAATAATAAGAACTCATTTGAAGAGAAAGAAGAAGTTCATA
1 ATCAACATTTTCAGAAG-AGTTCGTAATAAGAAGAACTCATATGAAGAG-AAGAAGAAGTTCATA
* *
61786 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCGGCATCAACA
64 GTCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGCATCAACA
*
61851 TTTCCAGAAGGAGTTCGTAATGAA-AAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGA
129 TTTCCAGAA-GAGTTCGTAAT-AAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATCTGA
61915 AGAACTTATTCAACCTTTTGCTC
192 AGAACTTATTCAACCTTTTGCTC
61938 AATTCTATTA
Statistics
Matches: 508, Mismatches: 56, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
358 2 0.00
359 64 0.13
360 78 0.15
361 3 0.01
362 1 0.00
363 4 0.01
364 20 0.04
365 30 0.06
366 29 0.06
367 3 0.01
368 269 0.53
369 5 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (363 bp):
ATCAACATTTTCAGAAGAGTTCGTAATAAGAAGAACTCATATGAAGAGAAGAAGAAGTTCATAGT
CTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAAAGCAGCATCAACATT
TCCAGAAGAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATCTGAAGAA
CTTATTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAACAACATAACCATTTCCAGACA
AAGTTCATAATAAGAACTCATCTGAAGAGGAAGAAAAAATTCATAATCTGAAGAACTTATACAAC
CTTTTGCTCGACTCTATCACAGAAGGAGATAAAGCAGC
Found at i:63821 original size:2 final size:2
Alignment explanation
Indices: 63814--63893 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
63804 TAACCCTAAG
63814 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63855 TA TA TA TA 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 TA TA TA TA T
63894 TTATTTACTT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.