Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007398.1 Hibiscus syriacus cultivar Beakdansim tig00019954_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: 69730
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1486 original size:22 final size:22
Alignment explanation
Indices: 1461--1504 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1451 CCATCATTTC
1461 ATTCAATCAACACCATCAACAT
1 ATTCAATCAACACCATCAACAT
* **
1483 ATTCCATCAAGGCCATCAACAT
1 ATTCAATCAACACCATCAACAT
1505 CTTTTTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.23
Consensus pattern (22 bp):
ATTCAATCAACACCATCAACAT
Found at i:12206 original size:61 final size:61
Alignment explanation
Indices: 12135--12249 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
12125 GAAGGTGGAT
* *
12135 ACGACCTTATGTATCA-TGTCCGAATTAGCACTAT-AGCGTAAGCTTAGTGTAGGTGGTGGGA
1 ACGACCTTATGTAT-ATTATCCGAATTAGCACTATGA-CGTAAGCTTAGTGCAGGTGGTGGGA
* *
12196 ACGACCTTATGTGTATTATCCGGATTAGCACTATGACGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATATTATCCGAATTAGCACTATGACGTAAGCTTAGTGCAGGT
12250 TTAGCACTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 1 0.02
61 46 0.96
62 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (61 bp):
ACGACCTTATGTATATTATCCGAATTAGCACTATGACGTAAGCTTAGTGCAGGTGGTGGGA
Found at i:12423 original size:45 final size:45
Alignment explanation
Indices: 12359--12492 Score: 227
Period size: 45 Copynumber: 3.0 Consensus size: 45
12349 GTAACCATGC
12359 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* *
12404 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
*
12449 AAATAAGATTACGAGCTTATGGGATAAATGGTAA--ATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
12492 A
1 A
12493 GAAATTTTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
43 9 0.11
45 75 0.89
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
Found at i:17411 original size:13 final size:13
Alignment explanation
Indices: 17395--17425 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17385 GTCAACGAGT
*
17395 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
17408 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
17421 CGGGT
1 CGGGT
17426 TGTGACCGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:24482 original size:29 final size:28
Alignment explanation
Indices: 24445--24520 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
24435 TTTTAAAACA
* * *
24445 AATTACCAAAATAGCACCCATCTCGAATT
1 AATTCCCAAAATAGCACCAAACT-GAATT
*
24474 AATTCCCAAAATAGCACTAAAACTGAATT
1 AATTCCCAAAATAGCAC-CAAACTGAATT
*
24503 AATTCCCAGAATAGCACC
1 AATTCCCAAAATAGCACC
24521 GGTCAACGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 37 0.93
30 3 0.08
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.22
Consensus pattern (28 bp):
AATTCCCAAAATAGCACCAAACTGAATT
Found at i:24596 original size:9 final size:9
Alignment explanation
Indices: 24582--24629 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
24572 CGGTGTCGTG
24582 ACCGGTCAA
1 ACCGGTCAA
24591 ACCGGTCAAA
1 ACCGGTC-AA
*
24601 ACCGTTCAAA
1 ACCGGTC-AA
*
24611 ACCGGTTAA
1 ACCGGTCAA
24620 ACCGGTCAA
1 ACCGGTCAA
24629 A
1 A
24630 AACGGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.38, C:0.29, G:0.19, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:24604 original size:10 final size:10
Alignment explanation
Indices: 24582--24635 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
24572 CGGTGTCGTG
24582 ACCGGTC-AA
1 ACCGGTCAAA
24591 ACCGGTCAAA
1 ACCGGTCAAA
*
24601 ACCGTTCAAA
1 ACCGGTCAAA
*
24611 ACCGGT-TAA
1 ACCGGTCAAA
24620 ACCGGTCAAA
1 ACCGGTCAAA
*
24630 AACGGT
1 ACCGGT
24636 TTCCAGCGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
9 15 0.39
10 23 0.61
ACGTcount: A:0.37, C:0.28, G:0.20, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:24604 original size:19 final size:20
Alignment explanation
Indices: 24582--24635 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
24572 CGGTGTCGTG
24582 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGTCAAA
* *
24601 ACCGTTCAAAACCGGT-TAA
1 ACCGGTCAAAACCGGTCAAA
*
24620 ACCGGTCAAAAACGGT
1 ACCGGTCAAAACCGGT
24636 TTCCAGCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.37, C:0.28, G:0.20, T:0.15
Consensus pattern (20 bp):
ACCGGTCAAAACCGGTCAAA
Found at i:35084 original size:24 final size:24
Alignment explanation
Indices: 35050--35111 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
35040 GAGATATCAA
*
35050 AAATCAAAACAGAATTCAAATAAG
1 AAATCAAAACAGAATCCAAATAAG
* * * * *
35074 ATATCATAACAAAATCCATATTAG
1 AAATCAAAACAGAATCCAAATAAG
*
35098 AAATCAGAACAGAA
1 AAATCAAAACAGAA
35112 ATTATATAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (24 bp):
AAATCAAAACAGAATCCAAATAAG
Found at i:38754 original size:24 final size:24
Alignment explanation
Indices: 38727--38773 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38717 CTGATTTATT
38727 ACAAACAATAAA-AATATATATATC
1 ACAAA-AATAAATAATATATATATC
* *
38751 ACAAAACTAAATTATATATATAT
1 ACAAAAATAAATAATATATATAT
38774 AAGAATACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (24 bp):
ACAAAAATAAATAATATATATATC
Found at i:40547 original size:45 final size:45
Alignment explanation
Indices: 40483--40894 Score: 556
Period size: 45 Copynumber: 9.2 Consensus size: 45
40473 TAATTATTAA
** * *
40483 ATTTATGGCATCCTTTTCATGCCTTTAATGCACATTTATACATTTA
1 ATTTATGGCATCC-TTTCATGCCTTTAATGCACCGTTATGCATTTC
* * *
40529 ATTTATGGCGTCCTTTCATGCCTTTAATGTACCGTTATGTATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
*
40574 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATACATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
* * ** * *
40619 ACTTATGACATCCTTTCATGTGTCTAATGCACCGTTATGCATTTT
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
* * * *
40664 ATTTATGACATCCTTTCATGCGTTTAATGCACCATTATGCATTTA
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
* * * *
40709 ATTTGTGGCATCATTTCATACCTTTAATGCACCGTTATGCATTTA
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
* *
40754 ATTT-TGGCATCCTCTCATGCCTTTAATGCACCTTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
* * *
40798 ATTTAAGGCACCCTTTAATGCCTTTAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
*
40843 ATTTATGGCATCATTTCATGCCTTTAATGCACCGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
40888 ATTTATG
1 ATTTATG
40895 TTATAAAAAC
Statistics
Matches: 322, Mismatches: 43, Indels: 3
0.88 0.12 0.01
Matches are distributed among these distances:
44 39 0.12
45 271 0.84
46 12 0.04
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTC
Found at i:47180 original size:30 final size:30
Alignment explanation
Indices: 47144--47244 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 30
47134 ATTAGAAGTG
47144 AATAAAGTGAATGCTATATGCTATGAAATA
1 AATAAAGTGAATGCTATATGCTATGAAATA
* *
47174 AATAAAGTGAATGCT-TCATGTTGTGAAATA
1 AATAAAGTGAATGCTAT-ATGCTATGAAATA
* * * * * * *
47204 AATGACGTGAATGGTACATACTATTAAATG
1 AATAAAGTGAATGCTATATGCTATGAAATA
47234 AATAAAGTGAA
1 AATAAAGTGAA
47245 AGGAATAAGT
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
29 1 0.02
30 55 0.98
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.30
Consensus pattern (30 bp):
AATAAAGTGAATGCTATATGCTATGAAATA
Found at i:51095 original size:54 final size:54
Alignment explanation
Indices: 51027--51535 Score: 660
Period size: 54 Copynumber: 9.4 Consensus size: 54
51017 TACATTTTTT
*
51027 CCGTATTGGCACTATGTGTGTAACCCACATAATTCATAATGAGTTTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * * *
51081 CCGCATTGGCACTATGTGTTCAACACACATAATTCATAATGAGTCTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
*
51135 CCGTATTGGCACTATTTGTGCAACCCACATAATTCATAACT-AGTTTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAA-TGAGTTTATGAATTA
* ** ** * *
51189 TCGTATTGATACTATGTGTGCAACCCATGTAATTCATAACGAGTCTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * ** * *
51243 TCGTATTGACACTATGTGTGCAACCCACGCAATTCATATTGAGTTCATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
** *
51297 CCGTATTGGCACTATGTGTGCAACCCATGTAATTCATAATGAGTTTATGGATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * *
51351 CTGTATTGGCACTATGTGTGCATCCCACATAATTCATAATGACTTTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * * * *
51405 CGGTATTGGCACTATGTGTGAAACCCACGTAATTCATAATTAGTTAATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
* * *
51459 CGGTATTAGCACTATGTGTGTAACCCACATAATTCATAATGAGTTTATGAATTA
1 CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
*** * *
51513 TTATATTGGAACTGTGTGTGCAA
1 CCGTATTGGCACTATGTGTGCAA
51536 AACCATAAAA
Statistics
Matches: 396, Mismatches: 57, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
54 395 1.00
55 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (54 bp):
CCGTATTGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTA
Found at i:59610 original size:20 final size:21
Alignment explanation
Indices: 59576--59625 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
59566 AGTTAAAGAA
* *
59576 GTATCGATA-ATAAGATGCAG
1 GTATCGATACATAAGAGGAAG
59596 GTATCGATACA-AAGAGGAAG
1 GTATCGATACATAAGAGGAAG
*
59616 GTATTGATAC
1 GTATCGATAC
59626 CGTAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (21 bp):
GTATCGATACATAAGAGGAAG
Found at i:60097 original size:54 final size:54
Alignment explanation
Indices: 60032--60453 Score: 472
Period size: 54 Copynumber: 7.8 Consensus size: 54
60022 TGTATTACTT
* *
60032 TATTGGCACTATGTGTGTAACCAACATAATTCATAATGAGTTTATGAATTACCA
1 TATTGGCACTATGTGTGCAACCAACATAATTCATAATGAGTTTATGAATTACCG
* * * * * *
60086 TATTAGAACTATGAGTGCAACCCACATAGTTCATAATGAGTTTGTGAATTACCG
1 TATTGGCACTATGTGTGCAACCAACATAATTCATAATGAGTTTATGAATTACCG
*
60140 TATTGGCCTCTATGTGTGCAACC--CATGCAATTCATAATGAGTTTATGAATTACCG
1 TATTGG-CACTATGTGTGCAACCAACAT--AATTCATAATGAGTTTATGAATTACCG
* ** * *
60195 TATTGGCACTATGTGTGCAACCTATGTAATTTATAATGAGTTTATGAATTACCA
1 TATTGGCACTATGTGTGCAACCAACATAATTCATAATGAGTTTATGAATTACCG
* * * *
60249 TATTGGCACTATGTGTGCAA-TACACGTAATTCATAATGATTTTATGAATTATCG
1 TATTGGCACTATGTGTGCAACCA-ACATAATTCATAATGAGTTTATGAATTACCG
* * * * *
60303 TATTGGCACGATTTGTGCAACCCACATAATTCATAATAAGTTTATGAATTACCA
1 TATTGGCACTATGTGTGCAACCAACATAATTCATAATGAGTTTATGAATTACCG
* * * * * * *
60357 TATTGGCAATATGTGTGCAACCCACGTAATTCACACTAACTTTATGAATTACCG
1 TATTGGCACTATGTGTGCAACCAACATAATTCATAATGAGTTTATGAATTACCG
* * * *
60411 TTTTGGAACTATGTGTGCAAAACAACATAATTTATAATGAGTT
1 TATTGGCACTATGTGTGC-AACCAACATAATTCATAATGAGTT
60454 GTAATATTGA
Statistics
Matches: 306, Mismatches: 54, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
53 3 0.01
54 242 0.79
55 60 0.20
56 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (54 bp):
TATTGGCACTATGTGTGCAACCAACATAATTCATAATGAGTTTATGAATTACCG
Found at i:60306 original size:108 final size:108
Alignment explanation
Indices: 60032--60453 Score: 520
Period size: 108 Copynumber: 3.9 Consensus size: 108
60022 TGTATTACTT
* * * * *
60032 TATTGGCACTATGTGTGTAACCAACATAATTCATAATGAGTTTATGAATTACCATATTAGAACTA
1 TATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGAACTA
* * * *
60097 TGAGTGCAACCCACATAGTTCATAATGAGTTTGTGAATTACCG
66 TGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTACCA
* * * *
60140 TATTGGCCTCTATGTGTGCAACCCATGCAATTCATAATGAGTTTATGAATTACCGTATTGGCACT
1 TATTGG-CACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGAACT
* ** *
60205 ATGTGTGCAACCTATGTAATTTATAATGAGTTTATGAATTACCA
65 ATGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTACCA
** * * * *
60249 TATTGGCACTATGTGTGCAATACACGTAATTCATAATGATTTTATGAATTATCGTATTGGCACGA
1 TATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGAACTA
* *
60314 TTTGTGCAACCCACATAATTCATAATAAGTTTATGAATTACCA
66 TGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTACCA
* * * * * *
60357 TATTGGCAATATGTGTGCAACCCACGTAATTCACACTAACTTTATGAATTACCGTTTTGGAACTA
1 TATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGAACTA
* * *
60422 TGTGTGCAAAACAACATAATTTATAATGAGTT
66 TGTGTGC-AACCCACATAATTCATAATGAGTT
60454 GTAATATTGA
Statistics
Matches: 265, Mismatches: 47, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
108 154 0.58
109 111 0.42
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (108 bp):
TATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGGAACTA
TGTGTGCAACCCACATAATTCATAATGAGTTTATGAATTACCA
Found at i:60444 original size:217 final size:217
Alignment explanation
Indices: 60032--60453 Score: 551
Period size: 217 Copynumber: 1.9 Consensus size: 217
60022 TGTATTACTT
* * *
60032 TATTGGCACTATGTGTGTAACCAACATAATTCATAATGAGTTTATGAATTACCATATTAGAACTA
1 TATTGGCACTATGTGTGCAAACAACATAATTCATAATGAGTTTATGAATTACCATATTAGAACGA
* * * * **
60097 TGAGTGCAACCCACATAGTTCATAATGAGTTTGTGAATTACCGTATTGGCCTCTATGTGTGCAAC
66 TGAGTGCAACCCACATAATTCATAATAAGTTTATGAATTACCATATTGGCCAATATGTGTGCAAC
* * * * * * * **
60162 CCATGCAATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTGCAACCTATGTAATTT
131 CCACGCAATTCACAATAACTTTATGAATTACCGTATTGGAACTATGTGTGCAAACAACATAATTT
60227 ATAATGAGTTTATGAATTACCA
196 ATAATGAGTTTATGAATTACCA
* * * * * *
60249 TATTGGCACTATGTGTGCAATAC-ACGTAATTCATAATGATTTTATGAATTATCGTATTGGCACG
1 TATTGGCACTATGTGTGCAA-ACAACATAATTCATAATGAGTTTATGAATTACCATATTAGAACG
**
60313 ATTTGTGCAACCCACATAATTCATAATAAGTTTATGAATTACCATATTGG-CAATATGTGTGCAA
65 ATGAGTGCAACCCACATAATTCATAATAAGTTTATGAATTACCATATTGGCCAATATGTGTGCAA
* * *
60377 CCCACGTAATTCACACTAACTTTATGAATTACCGTTTTGGAACTATGTGTGCAAAACAACATAAT
130 CCCACGCAATTCACAATAACTTTATGAATTACCGTATTGGAACTATGTGTGC-AAACAACATAAT
60442 TTATAATGAGTT
194 TTATAATGAGTT
60454 GTAATATTGA
Statistics
Matches: 174, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
216 56 0.32
217 117 0.67
218 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (217 bp):
TATTGGCACTATGTGTGCAAACAACATAATTCATAATGAGTTTATGAATTACCATATTAGAACGA
TGAGTGCAACCCACATAATTCATAATAAGTTTATGAATTACCATATTGGCCAATATGTGTGCAAC
CCACGCAATTCACAATAACTTTATGAATTACCGTATTGGAACTATGTGTGCAAACAACATAATTT
ATAATGAGTTTATGAATTACCA
Found at i:61239 original size:54 final size:54
Alignment explanation
Indices: 61172--61676 Score: 602
Period size: 54 Copynumber: 9.4 Consensus size: 54
61162 TTCATTGAGA
* * * * * *
61172 TGCACAC-TAGTGCCTATACTGTCATTCGTAAACATATTATGAATTCCAT-GGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
* * *
61224 T-CACATATAAAGTGCCTATACGGTCGTTCATCAATATATGATGAATTTCGTGGGT
1 TGCACACAT--AGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
** *
61279 TGCACACATAGTGCCTATACTATCGTTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
*
61333 TGCACACATAGTGCCTATACGGTCATTCATCAACATACGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
* * * * *
61387 TGCATACATAGTGCCTATACGGTCTTTCAACAATAAATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
** ** *
61441 TGCACACATAGTGCCTATATTGTTGTTCATCAACATATGATTAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
* * * * * *
61495 AGCACACATTGTGCATATACGGTCGTTCATCAACATATGACGAATTCCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
* **
61549 TGCACACCTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
*** * * ** *
61603 TGCACACATAGTGCCTATATAATCATTCATCAACATATGATGAATTACTTACGC
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
*
61657 TGTACACATAGTGCCTATAC
1 TGCACACATAGTGCCTATAC
61677 TACACATATT
Statistics
Matches: 387, Mismatches: 61, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
51 4 0.01
52 2 0.01
54 371 0.96
55 4 0.01
56 6 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
Found at i:61446 original size:162 final size:161
Alignment explanation
Indices: 61172--61676 Score: 665
Period size: 162 Copynumber: 3.1 Consensus size: 161
61162 TTCATTGAGA
* * * * * * * *
61172 TGCACAC-TAGTGCCTATACTGTCATTCGTAAACATATTATGAATTCCAT-GGTTCACATATAAA
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCGTGGGTT-GCATACATA
*
61235 GTGCCTATACGGTCGTTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATACT
65 GTGCCTATACGGTCTTTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATA-T
61300 ATCGTTCATCAACATATGATGAATTTCGTGGGT
129 ATCGTTCATCAACATATGATGAATTTCGTGGGT
* *
61333 TGCACACATAGTGCCTATACGGTCATTCATCAACATACGATGAATTTCGTGGGTTGCATACATAG
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCGTGGGTTGCATACATAG
* * *
61398 TGCCTATACGGTCTTTCAACAATAAATGATGAATTTCGTGGGTTGCACACATAGTGCCTATATTG
66 TGCCTATACGGTCTTTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATA-TA
* *
61463 TTGTTCATCAACATATGATTAATTTCGTGGGT
130 TCGTTCATCAACATATGATGAATTTCGTGGGT
* * * * * * *
61495 AGCACACATTGTGCATATACGGTCGTTCATCAACATATGACGAATTCCGTGGGTTGCACACCTAG
1 TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCGTGGGTTGCATACATAG
*
61560 TGCCTATACGGT-TGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATATA
66 TGCCTATACGGTCT-TTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATAT-
* * * ** *
61624 ATCATTCATCAACATATGATGAATTACTTACGC
129 ATCGTTCATCAACATATGATGAATTTCGTGGGT
*
61657 TGTACACATAGTGCCTATAC
1 TGCACACATAGTGCCTATAC
61677 TACACATATT
Statistics
Matches: 298, Mismatches: 42, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
161 9 0.03
162 285 0.96
163 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (161 bp):
TGCACACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTCCGTGGGTTGCATACATAG
TGCCTATACGGTCTTTCATCAATATATGATGAATTTCGTGGGTTGCACACATAGTGCCTATATAT
CGTTCATCAACATATGATGAATTTCGTGGGT
Found at i:62141 original size:18 final size:18
Alignment explanation
Indices: 62097--62141 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
62087 GGAATCAATG
62097 GTATCGATACCCTCATCA
1 GTATCGATACCCTCATCA
*
62115 ATATCGATACCCTCATCA
1 GTATCGATACCCTCATCA
*
62133 GTATTGATA
1 GTATCGATA
62142 TTGTTCATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (18 bp):
GTATCGATACCCTCATCA
Done.