Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000656.1 Hibiscus syriacus cultivar Beakdansim tig00001270_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: 80188
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:205 original size:33 final size:33
Alignment explanation
Indices: 168--233 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
158 CATCTTAATA
* *
168 TCACCCCTTAACACC-CCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCCAA-TTCTTTCAACACT
*
201 TCACCCCTCAACACCTCTAATTCTTTCAACACT
1 TCACCCCTCAACACCTCCAATTCTTTCAACACT
234 CTATTTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCTCCAATTCTTTCAACACT
Found at i:297 original size:20 final size:20
Alignment explanation
Indices: 262--322 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
252 CCCCTTATGC
*
262 CTCTCAAG-TGTCTTCGACT
1 CTCTCAAGTTCTCTTCGACT
281 CTCTCAAGTTCTCTTCGACT
1 CTCTCAAGTTCTCTTCGACT
*
301 CTATCAAGTTCTCTTCGACT
1 CTCTCAAGTTCTCTTCGACT
321 CT
1 CT
323 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.16, C:0.33, G:0.11, T:0.39
Consensus pattern (20 bp):
CTCTCAAGTTCTCTTCGACT
Found at i:2563 original size:20 final size:19
Alignment explanation
Indices: 2517--2563 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2507 TCCGGTATCG
*
2517 TTTTATCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
2536 TTGGTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2557 TTTTACC
1 TTTTACC
2564 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2788 original size:181 final size:181
Alignment explanation
Indices: 2484--2955 Score: 687
Period size: 181 Copynumber: 2.6 Consensus size: 181
2474 CGTACTTACG
* * * *
2484 AAAGTATCGACTCTTTCAATATATCCGGTATCGTTTTATCGGTTTTATCATTTTGGTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
2549 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATATTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACAT-TTTTTAAAGTATCGACACATTAT
*
2614 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
2665 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* ** *
2730 TATCATATTTTTACCTGGTATATTATTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT-AAAGTATCGACACATTAT
** *
2795 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * **
2847 AAAGTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
2912 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCG-TACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2956 AATTTGGATC
Statistics
Matches: 260, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
180 5 0.02
181 168 0.65
182 87 0.33
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:4465 original size:2 final size:2
Alignment explanation
Indices: 4458--4483 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4448 AACCAAAGTT
4458 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
4484 CCAGCTTTCT
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):
TA
Found at i:9053 original size:21 final size:20
Alignment explanation
Indices: 9012--9062 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
9002 CAAGTATATA
* *
9012 ATATATTCTTATTAAACATT
1 ATATATTCTTATCAAAAATT
*
9032 ATATATGTGTTATCAAAAATT
1 ATATAT-TCTTATCAAAAATT
9053 AT-T-TTCTTAT
1 ATATATTCTTAT
9063 GTTCAACTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 7 0.27
21 13 0.50
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (20 bp):
ATATATTCTTATCAAAAATT
Found at i:9478 original size:15 final size:16
Alignment explanation
Indices: 9458--9487 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9448 TTTAAATTAA
9458 TTTATA-TTTTAATTT
1 TTTATATTTTTAATTT
9473 TTTATATTTTTAATT
1 TTTATATTTTTAATT
9488 AATAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATATTTTTAATTT
Found at i:10335 original size:24 final size:23
Alignment explanation
Indices: 10285--10335 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
10275 GGTTTATATT
* * *
10285 TGATTTTGTTGGAACTAAGGTCG
1 TGATTTTGTTAGAACTAAGATCA
*
10308 TGATTCTTGTTAGACCTAAGATCA
1 TGATT-TTGTTAGAACTAAGATCA
10332 TGAT
1 TGAT
10336 GTATCATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (23 bp):
TGATTTTGTTAGAACTAAGATCA
Found at i:11469 original size:13 final size:13
Alignment explanation
Indices: 11447--11478 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11437 TTTTTTTTCA
*
11447 TTTTATTAGAGAT
1 TTTTACTAGAGAT
11460 TTTTACTAGAGAT
1 TTTTACTAGAGAT
11473 TTTTAC
1 TTTTAC
11479 GATAAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (13 bp):
TTTTACTAGAGAT
Found at i:21883 original size:3 final size:3
Alignment explanation
Indices: 21875--21905 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
21865 GTGAGAAGTC
*
21875 TCT TCT TCT TCT TCG TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
21906 AAACGTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:29198 original size:33 final size:35
Alignment explanation
Indices: 29125--29198 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
29115 AATAAACAAA
29125 ATTAAGCAAAATAAATTAACAAAAAGTCCAACAAGT
1 ATTAA-CAAAATAAATTAACAAAAAGTCCAACAAGT
*
29161 -TTAACAAAATAAATTAA-AATAAA-TCCAACCA-T
1 ATTAACAAAATAAATTAACAA-AAAGTCCAACAAGT
29193 ATTAAC
1 ATTAAC
29199 GAATTAAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
32 1 0.03
33 14 0.40
34 16 0.46
35 4 0.11
ACGTcount: A:0.58, C:0.15, G:0.04, T:0.23
Consensus pattern (35 bp):
ATTAACAAAATAAATTAACAAAAAGTCCAACAAGT
Found at i:29242 original size:13 final size:13
Alignment explanation
Indices: 29224--29297 Score: 73
Period size: 13 Copynumber: 5.8 Consensus size: 13
29214 TTAAATGATA
29224 AATAAAAAAATAC
1 AATAAAAAAATAC
*
29237 AATAAAAAAATCC
1 AATAAAAAAATAC
* *
29250 AATAAACAACTAC
1 AATAAAAAAATAC
29263 AAT-AAAAAATAC
1 AATAAAAAAATAC
*
29275 --TAAATACAAATAT
1 AATAAA-A-AAATAC
29288 AATAAAAAAA
1 AATAAAAAAA
29298 CAAAATCTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.02
11 2 0.04
12 8 0.16
13 33 0.67
14 1 0.02
15 4 0.08
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.18
Consensus pattern (13 bp):
AATAAAAAAATAC
Found at i:31474 original size:9 final size:9
Alignment explanation
Indices: 31460--31493 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
31450 TAAGTAAAAT
31460 ATTAAATAA
1 ATTAAATAA
31469 ATTAAAT-A
1 ATTAAATAA
*
31477 CTTAAATAA
1 ATTAAATAA
31486 ATTAAATA
1 ATTAAATA
31494 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:31492 original size:17 final size:17
Alignment explanation
Indices: 31456--31494 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
31446 TAATTAAGTA
31456 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
31472 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
31489 AAATAC
1 AAATAC
31495 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:31563 original size:20 final size:20
Alignment explanation
Indices: 31538--31575 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31528 ACAAAGATTA
*
31538 TAAGAGTATTTGAGAGAAGT
1 TAAGAGAATTTGAGAGAAGT
31558 TAAGAGAATTTGAGAGAA
1 TAAGAGAATTTGAGAGAA
31576 TTTGGTATGA
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:0.00, G:0.29, T:0.26
Consensus pattern (20 bp):
TAAGAGAATTTGAGAGAAGT
Found at i:31576 original size:10 final size:10
Alignment explanation
Indices: 31540--31579 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
31530 AAAGATTATA
*
31540 AGAGTATTTG
1 AGAGAATTTG
* *
31550 AGAGAAGTTA
1 AGAGAATTTG
31560 AGAGAATTTG
1 AGAGAATTTG
31570 AGAGAATTTG
1 AGAGAATTTG
31580 GTATGATGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:33121 original size:30 final size:30
Alignment explanation
Indices: 33087--33155 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
33077 TTTATAACAT
*
33087 TTGTTATTAAGGGTCTAATTT-TTTTAATGC
1 TTGTTATTAAGGGTCT-ATTTATTTTAATAC
** *
33117 TTGTTAACAAGGGTCTATTTATTTTAATAT
1 TTGTTATTAAGGGTCTATTTATTTTAATAC
33147 TTGTTATTA
1 TTGTTATTA
33156 GGTGTATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (30 bp):
TTGTTATTAAGGGTCTATTTATTTTAATAC
Found at i:33311 original size:63 final size:57
Alignment explanation
Indices: 33228--33405 Score: 200
Period size: 57 Copynumber: 3.1 Consensus size: 57
33218 TTTCAGTACT
* *
33228 TTTATTATATGTCT-A-TTTTTAATATTTATTATTATGAACATGCTCTTAAAACTTGTTTA
1 TTTATTAGATGTCTAATTTTTTAATATTTATTATTATGAACATACTCTTAAAA----TTTA
* **
33287 TTATTATTAGATGT-TCAATTTTTTAATATTTATAATTATGAGTATACTCTTAAAATTTA
1 -T-TTATTAGATGTCT-AATTTTTTAATATTTATTATTATGAACATACTCTTAAAATTTA
* * *
33346 TTTATTAGATGTCTAATTTTTTAATATTTATTATTATAAACGTATTCTTAAAATTTA
1 TTTATTAGATGTCTAATTTTTTAATATTTATTATTATGAACATACTCTTAAAATTTA
33403 TTT
1 TTT
33406 TTTAATATTT
Statistics
Matches: 102, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
57 51 0.50
58 2 0.02
59 4 0.04
60 2 0.02
61 10 0.10
62 1 0.01
63 32 0.31
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.54
Consensus pattern (57 bp):
TTTATTAGATGTCTAATTTTTTAATATTTATTATTATGAACATACTCTTAAAATTTA
Found at i:47449 original size:27 final size:27
Alignment explanation
Indices: 47393--47459 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
47383 TGTCTGTAAA
*
47393 TTATAATCATTCTGAATAGATACAACT
1 TTATAATCATTCTGAATAGATAAAACT
* *
47420 TTATAATCATTCTGAACTA-TTAAAATT
1 TTATAATCATTCTGAA-TAGATAAAACT
*
47447 TTATAATTATTCT
1 TTATAATCATTCT
47460 TTTAGCATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (27 bp):
TTATAATCATTCTGAATAGATAAAACT
Found at i:47747 original size:27 final size:29
Alignment explanation
Indices: 47717--47793 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 29
47707 TGTATACCCC
47717 AAATCAAAATTATTAGGACTATGTTAAAAAT
1 AAATCAAAATTATTAGGACTATGTT--AAAT
*
47748 AAATCAAAATTATTTGGACTATGTT-AA-
1 AAATCAAAATTATTAGGACTATGTTAAAT
47775 AAATCAAAATTATTAGGAC
1 AAATCAAAATTATTAGGAC
47794 GCCCTTTGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 18 0.41
28 2 0.05
31 24 0.55
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTATTAGGACTATGTTAAAT
Found at i:60071 original size:22 final size:22
Alignment explanation
Indices: 60041--60099 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
60031 TAGGGCAGAG
*
60041 GGAATCGATACCCCTTTGAAGA
1 GGAACCGATACCCCTTTGAAGA
* *
60063 GGAACCGATTCCCCCTTTGAATA
1 GGAACCGA-TACCCCTTTGAAGA
*
60086 GGAACCGATTCCCC
1 GGAACCGATACCCC
60100 CTAGGGGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (22 bp):
GGAACCGATACCCCTTTGAAGA
Found at i:60077 original size:23 final size:23
Alignment explanation
Indices: 60051--60101 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
60041 GGAATCGATA
60051 CCCCTTTGAAGAGGAACCGATTC
1 CCCCTTTGAAGAGGAACCGATTC
*
60074 CCCCTTTGAATAGGAACCGATTC
1 CCCCTTTGAAGAGGAACCGATTC
60097 CCCCT
1 CCCCT
60102 AGGGGAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (23 bp):
CCCCTTTGAAGAGGAACCGATTC
Found at i:63475 original size:2 final size:2
Alignment explanation
Indices: 63468--63534 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
63458 GAAGTGCACA
63468 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
63510 AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
63535 CGAATATGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:66013 original size:30 final size:30
Alignment explanation
Indices: 65968--66044 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
65958 GGTCTGGCAA
* *
65968 TGAACCGGCTGAAAACCGGTAGAATCGGGG
1 TGAACCGGCTGAAAACCGATAGAACCGGGG
* *
65998 TGAATCGGTTGAAAACCGATAGAACCGGGG
1 TGAACCGGCTGAAAACCGATAGAACCGGGG
66028 TGAACCGGCTGAAAACC
1 TGAACCGGCTGAAAACC
66045 AGCAAAACCG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.21, G:0.32, T:0.14
Consensus pattern (30 bp):
TGAACCGGCTGAAAACCGATAGAACCGGGG
Found at i:66054 original size:30 final size:28
Alignment explanation
Indices: 65968--66064 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 28
65958 GGTCTGGCAA
* *
65968 TGAACCGGCTGAAAACCGGTAGAATCGGGG
1 TGAACCGGCTGAAAACC-G-AAAACCGGGG
* *
65998 TGAATCGGTTGAAAACCGATAGAACCGGGG
1 TGAACCGGCTGAAAACCGA-A-AACCGGGG
**
66028 TGAACCGGCTGAAAACCAGCAAAACCGGTT
1 TGAACCGGCTGAAAACC-G-AAAACCGGGG
66058 TGAACCG
1 TGAACCG
66065 TCGGTTCACT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 50 0.91
31 2 0.04
32 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.31, T:0.14
Consensus pattern (28 bp):
TGAACCGGCTGAAAACCGAAAACCGGGG
Found at i:70786 original size:24 final size:23
Alignment explanation
Indices: 70751--70802 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
70741 GTCATTAAAA
*
70751 ATTAATGATAATATTGAAA-TATT
1 ATTAATGATAATA-TAAAATTATT
*
70774 ATTATATGGTAATATAAAATTATT
1 ATTA-ATGATAATATAAAATTATT
70798 ATTAA
1 ATTAA
70803 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (23 bp):
ATTAATGATAATATAAAATTATT
Found at i:72363 original size:21 final size:22
Alignment explanation
Indices: 72337--72379 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
72327 ATAATCTCTT
* *
72337 GCATGTC-TGAACCTACAACAA
1 GCATGTCATCAACATACAACAA
72358 GCATGTCATCAACATACAACAA
1 GCATGTCATCAACATACAACAA
72380 TAAAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.19
Consensus pattern (22 bp):
GCATGTCATCAACATACAACAA
Found at i:74243 original size:30 final size:30
Alignment explanation
Indices: 74034--74226 Score: 368
Period size: 30 Copynumber: 6.4 Consensus size: 30
74024 TCTGAATGAC
74034 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
74064 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
74094 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
74124 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
74154 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
74184 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
74214 CTATCCATAGGTC
1 CTATCCAGAGGTC
74227 CCGAAGAACC
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 161 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:74243 original size:90 final size:90
Alignment explanation
Indices: 74034--74251 Score: 355
Period size: 90 Copynumber: 2.4 Consensus size: 90
74024 TCTGAATGAC
*
74034 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
*
74099 CAGAGGTCATAAAGATCCTCGGTAA
66 CAAAGGTCATAAAGATCCTCGGTAA
*
74124 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
74189 CAAAGGTCATAAAGATCCTCGGTAA
66 CAAAGGTCATAAAGATCCTCGGTAA
* * * * *
74214 CTATCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
74252 TATGTTCCTT
Statistics
Matches: 120, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 111 0.93
91 9 0.08
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (90 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
CAAAGGTCATAAAGATCCTCGGTAA
Found at i:74266 original size:31 final size:31
Alignment explanation
Indices: 74212--74304 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
74202 GATCCTCGGT
* *
74212 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
74243 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
74274 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
74305 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:77648 original size:30 final size:30
Alignment explanation
Indices: 77499--77631 Score: 248
Period size: 30 Copynumber: 4.4 Consensus size: 30
77489 TCCGAATGAC
77499 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
77529 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
77559 CTATCCAGAGATCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
77589 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
77619 CTATCCAGAGGTC
1 CTATCCAGAGGTC
77632 CCGAAGAACC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 99 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:77901 original size:4 final size:4
Alignment explanation
Indices: 77884--77928 Score: 81
Period size: 4 Copynumber: 11.2 Consensus size: 4
77874 ATATAACCAT
*
77884 TACA TACT TACA TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
77929 GTCATCATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (4 bp):
TACA
Done.