Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003407.1 Hibiscus syriacus cultivar Beakdansim tig00007179_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: 758105
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 4
Found at i:668505 original size:19 final size:19
Alignment explanation
Indices: 668483--668548 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
668473 CGAAACTAAA
668483 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
668502 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
668517 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
668535 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
668549 CTCTCGTTGC
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
14 8 0.23
16 3 0.09
17 3 0.09
19 21 0.60
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:668529 original size:33 final size:33
Alignment explanation
Indices: 668487--668578 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
668477 ACTAAATTCG
*
668487 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
668520 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* **
668553 CGTTGCCATAGTCATTTCCGCATTGC
1 CGTTGCGATTTTCATTT-CGCATTGC
668579 CATAGTCATT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 45 0.85
34 8 0.15
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:668608 original size:20 final size:20
Alignment explanation
Indices: 668555--668593 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
668545 GATTCTCTCG
668555 TTGCCATAGTCATTTCCGCA
1 TTGCCATAGTCATTTCCGCA
668575 TTGCCATAGTCATTTCCGC
1 TTGCCATAGTCATTTCCGC
668594 GTTGTGATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.31, G:0.15, T:0.36
Consensus pattern (20 bp):
TTGCCATAGTCATTTCCGCA
Found at i:668647 original size:20 final size:20
Alignment explanation
Indices: 668553--668647 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
668543 GCGATTCTCT
*
668553 CGTTGCCATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
668573 CATTGCCATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* * **
668593 CGTTGTGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
668612 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
668634 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
668648 AATGAATGCC
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.05
20 41 0.71
21 11 0.19
22 3 0.05
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:671145 original size:24 final size:24
Alignment explanation
Indices: 671118--671171 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
671108 CTGAAAAATC
*
671118 ATCAAAATCCGAGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
671142 ATCAAAGTTCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
671166 ATCAAA
1 ATCAAA
671172 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:671176 original size:24 final size:24
Alignment explanation
Indices: 671130--671176 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
671120 CAAAATCCGA
*
671130 GTATTGATCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
671154 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
671177 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:671185 original size:24 final size:24
Alignment explanation
Indices: 671138--671185 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
671128 GAGTATTGAT
** *
671138 CAAGATCAAAGTTCGGGTATTGAC
1 CAAGATCAAAGTTCGAATACTGAC
*
671162 CAAGATCAAATTTCGAATACTGAC
1 CAAGATCAAAGTTCGAATACTGAC
671186 TAGTACTCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
CAAGATCAAAGTTCGAATACTGAC
Found at i:672049 original size:20 final size:20
Alignment explanation
Indices: 672033--672178 Score: 215
Period size: 20 Copynumber: 7.3 Consensus size: 20
672023 CAGAATCTCG
672033 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
672053 ATGCGA-TTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
672072 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* *
672092 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAA-TCGCA
672113 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
672133 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
672153 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
672173 TTGCGA
1 TTGCGA
672179 ATTAGGAAAA
Statistics
Matches: 114, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
19 15 0.13
20 81 0.71
21 18 0.16
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:672137 original size:61 final size:60
Alignment explanation
Indices: 672033--672178 Score: 215
Period size: 61 Copynumber: 2.5 Consensus size: 60
672023 CAGAATCTCG
* * * *
672033 TTGCGA-TTTACTAAATCGCAATGCGATTACGTATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTTCCTAATTCGCATTGCGATTACGTAATCGCATTGCGATTTACGTAATCGCA
672092 TTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTTCCTAATTCGCATTGCGA-TTACGTAATCGCATTGCGATTTACGTAATCGCA
* *
672153 TTGCGATTTACGT-ATTCGCATTGCGA
1 TTGCGATTTTCCTAATTCGCATTGCGA
672179 ATTAGGAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
59 6 0.08
60 30 0.38
61 43 0.54
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (60 bp):
TTGCGATTTTCCTAATTCGCATTGCGATTACGTAATCGCATTGCGATTTACGTAATCGCA
Found at i:672199 original size:21 final size:21
Alignment explanation
Indices: 672175--672220 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
672165 TATTCGCATT
672175 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
672196 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
672217 GCGA
1 GCGA
672221 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:677415 original size:6 final size:6
Alignment explanation
Indices: 677404--677434 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
677394 GAGTGAGACA
677404 CCATGT CCATGT CCATGT CCATGT CCATGT C
1 CCATGT CCATGT CCATGT CCATGT CCATGT C
677435 GAACGATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.16, T:0.32
Consensus pattern (6 bp):
CCATGT
Found at i:682566 original size:57 final size:56
Alignment explanation
Indices: 682478--682706 Score: 350
Period size: 57 Copynumber: 4.0 Consensus size: 56
682468 GTTGGAGGAA
*
682478 GAATACTTACAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGTGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGG-GTT
*
682535 GAATACTTGCAGGTTTCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGAC-GGGTT
* *
682592 GAATACTTGTAGGTTCCTCAGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGTTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGG-TT
* * * *
682649 GATTACTTGCAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGACGAGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACG-GGTT
682706 G
1 G
682707 TATGGTTATG
Statistics
Matches: 158, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
56 3 0.02
57 151 0.96
58 4 0.03
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (56 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGTT
Found at i:687862 original size:29 final size:28
Alignment explanation
Indices: 687829--687886 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 28
687819 ATTAGAAATG
687829 AACTACCTAGTAGTTATCCTTATCTATTT
1 AACTA-CTAGTAGTTATCCTTATCTATTT
687858 -A--ACTAGTAGTTATCCTTATCTATTT
1 AACTACTAGTAGTTATCCTTATCTATTT
687883 AACT
1 AACT
687887 TTCTAAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
25 23 0.88
26 2 0.08
28 1 0.04
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (28 bp):
AACTACTAGTAGTTATCCTTATCTATTT
Found at i:687898 original size:29 final size:25
Alignment explanation
Indices: 687835--687886 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
687825 AATGAACTAC
687835 CTAGTAGTTATCCTTATCTATTTAA
1 CTAGTAGTTATCCTTATCTATTTAA
687860 CTAGTAGTTATCCTTATCTATTTAA
1 CTAGTAGTTATCCTTATCTATTTAA
687885 CT
1 CT
687887 TTCTAAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (25 bp):
CTAGTAGTTATCCTTATCTATTTAA
Found at i:692392 original size:25 final size:25
Alignment explanation
Indices: 692364--692414 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
692354 ATAAAATAGT
*
692364 TTAGTTTAATCATCTAAACCACAAG
1 TTAGTTTAATCATCAAAACCACAAG
692389 TTAGTTTAATCATCAAAACCACAAG
1 TTAGTTTAATCATCAAAACCACAAG
692414 T
1 T
692415 AAAGTGTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (25 bp):
TTAGTTTAATCATCAAAACCACAAG
Found at i:696650 original size:23 final size:23
Alignment explanation
Indices: 696624--696684 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
696614 CTCGTATAAA
*
696624 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
696647 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
696670 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
696685 TATAAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:698134 original size:63 final size:63
Alignment explanation
Indices: 698026--698175 Score: 164
Period size: 63 Copynumber: 2.4 Consensus size: 63
698016 TCCCCTTGAA
*** *
698026 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTT-TAATATT-ACGGG
1 GTGCATCGATGCACTACTTGTGCATCGATACACAAATCACATTCGATGTTTGT-ATATTAAC-GG
*** * *
698089 GTGCATCGATGCACTACTTGTGCATCGATACATTGATGACATTCGATGTTTGTATTTTAAACGG
1 GTGCATCGATGCACTACTTGTGCATCGATACACAAATCACATTCGATGTTTGTATATT-AACGG
698153 GTGCATCGATGCACTA-TTG-GCAT
1 GTGCATCGATGCACTACTTGTGCAT
698176 TCAATGTTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
62 4 0.05
63 50 0.67
64 19 0.25
65 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACTTGTGCATCGATACACAAATCACATTCGATGTTTGTATATTAACGG
Found at i:700478 original size:9 final size:9
Alignment explanation
Indices: 700464--700492 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
700454 CCGAATAAAT
700464 TTCGGTTAA
1 TTCGGTTAA
700473 TTCGGTTAA
1 TTCGGTTAA
700482 TTCGGTTAA
1 TTCGGTTAA
700491 TT
1 TT
700493 TTCGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:708046 original size:13 final size:13
Alignment explanation
Indices: 708025--708084 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
708015 ATTTTGTTAG
708025 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
708038 TATTGTA-TTATT
1 TATTTTATTTAAT
708050 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
708062 TATTTTATTTAAT
1 TATTTTATTTAAT
708075 TATTTTATTT
1 TATTTTATTT
708085 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:708050 original size:21 final size:20
Alignment explanation
Indices: 708025--708089 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
708015 ATTTTGTTAG
708025 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
708046 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
708062 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
708083 TTTTTTA
1 TATTTTA
708090 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 13 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:708060 original size:29 final size:29
Alignment explanation
Indices: 708027--708089 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
708017 TTTGTTAGTA
708027 TTTTATT-TAATTATTGT-ATTATTTAATTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTT
* *
708056 TTTTATTATTTTATTTAATTATTTTATTT
1 TTTTATTATATTATTTAATTATTTAATTT
708085 TTTTA
1 TTTTA
708090 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATTATTTAATTATTTAATTT
Found at i:708071 original size:16 final size:16
Alignment explanation
Indices: 708029--708071 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
708019 TGTTAGTATT
* *
708029 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
708045 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
708061 TTATTTTATTT
1 TTATTTAATTT
708072 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:708367 original size:20 final size:20
Alignment explanation
Indices: 708342--708379 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
708332 ACTGTAAAAA
*
708342 AATAAAATAATTAAATAAAT
1 AATAAAAAAATTAAATAAAT
708362 AATAAAAAAATTAAATAA
1 AATAAAAAAATTAAATAA
708380 TACAATAATT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAAAAAAATTAAATAAAT
Found at i:708377 original size:28 final size:29
Alignment explanation
Indices: 708336--708397 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
708326 TTTATAACTG
708336 TAAAAAAATAAAATAATTA-AATAAAT-AA
1 TAAAAAAATAAAATAA-TACAATAAATAAA
* *
708364 TAAAAAAATTAAATAATACAATAATTAAA
1 TAAAAAAATAAAATAATACAATAAATAAA
708393 TAAAA
1 TAAAA
708398 TACTAACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 21 0.70
29 7 0.23
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (29 bp):
TAAAAAAATAAAATAATACAATAAATAAA
Found at i:708378 original size:16 final size:16
Alignment explanation
Indices: 708357--708395 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
708347 AATAATTAAA
708357 TAAATAATAAAAAAAT
1 TAAATAATAAAAAAAT
* *
708373 TAAATAATACAATAAT
1 TAAATAATAAAAAAAT
708389 TAAATAA
1 TAAATAA
708396 AATACTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAATAATAAAAAAAT
Found at i:708689 original size:175 final size:175
Alignment explanation
Indices: 708398--708749 Score: 704
Period size: 175 Copynumber: 2.0 Consensus size: 175
708388 TTAAATAAAA
708398 TACTAACAAAATATGATTAATTTTATAGAAATTATTTAAAAATTTGCTTGATCTGTAAAATATTC
1 TACTAACAAAATATGATTAATTTTATAGAAATTATTTAAAAATTTGCTTGATCTGTAAAATATTC
708463 TTAAACAGTGCCTAACAAGTAATTAATTTATGTTAAGGTGATATTTGTGTAAAAAGGCCAAATTT
66 TTAAACAGTGCCTAACAAGTAATTAATTTATGTTAAGGTGATATTTGTGTAAAAAGGCCAAATTT
708528 TTTCATGGATTTAAAGTAAAGACGCCTAGAGATCCAAGCAAGGAG
131 TTTCATGGATTTAAAGTAAAGACGCCTAGAGATCCAAGCAAGGAG
708573 TACTAACAAAATATGATTAATTTTATAGAAATTATTTAAAAATTTGCTTGATCTGTAAAATATTC
1 TACTAACAAAATATGATTAATTTTATAGAAATTATTTAAAAATTTGCTTGATCTGTAAAATATTC
708638 TTAAACAGTGCCTAACAAGTAATTAATTTATGTTAAGGTGATATTTGTGTAAAAAGGCCAAATTT
66 TTAAACAGTGCCTAACAAGTAATTAATTTATGTTAAGGTGATATTTGTGTAAAAAGGCCAAATTT
708703 TTTCATGGATTTAAAGTAAAGACGCCTAGAGATCCAAGCAAGGAG
131 TTTCATGGATTTAAAGTAAAGACGCCTAGAGATCCAAGCAAGGAG
708748 TA
1 TA
708750 AAAAAAATCT
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 177 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (175 bp):
TACTAACAAAATATGATTAATTTTATAGAAATTATTTAAAAATTTGCTTGATCTGTAAAATATTC
TTAAACAGTGCCTAACAAGTAATTAATTTATGTTAAGGTGATATTTGTGTAAAAAGGCCAAATTT
TTTCATGGATTTAAAGTAAAGACGCCTAGAGATCCAAGCAAGGAG
Found at i:711176 original size:20 final size:20
Alignment explanation
Indices: 711143--711180 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
711133 AATATCGAAT
* *
711143 AATAATTAATTAAATAAAAA
1 AATAAGTAAATAAATAAAAA
711163 AATAAGTAAATAAATAAA
1 AATAAGTAAATAAATAAA
711181 TCAAAGAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAAGTAAATAAATAAAAA
Found at i:712501 original size:3 final size:3
Alignment explanation
Indices: 712481--712542 Score: 65
Period size: 3 Copynumber: 21.3 Consensus size: 3
712471 GTATTATGTA
* * *
712481 AAT AAT ATT AGT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
712527 AAT TAT TAT AAT AAT A
1 AAT AAT AAT AAT AAT A
712543 TTTTTATTCC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 3 0.06
3 47 0.94
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:727117 original size:37 final size:37
Alignment explanation
Indices: 727075--727150 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
727065 ATCAATTTAA
* ** *
727075 ATATAATATTTTAAGTTAAAAAAATTAACATTTAGAC
1 ATATAACATTTTAAACTAAAAAAATTAACATATAGAC
727112 ATATAACATTTTAAACTAAAAAAATTAACATATAGAC
1 ATATAACATTTTAAACTAAAAAAATTAACATATAGAC
727149 AT
1 AT
727151 GCTCGCACGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (37 bp):
ATATAACATTTTAAACTAAAAAAATTAACATATAGAC
Found at i:730718 original size:22 final size:22
Alignment explanation
Indices: 730693--730736 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
730683 TAGGGTTTAA
730693 AATT-AGAATTTTAGAGATTTGG
1 AATTAAGAA-TTTAGAGATTTGG
* *
730715 AATTAAGGATTTAGAGGTTTGG
1 AATTAAGAATTTAGAGATTTGG
730737 GGTGACACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (22 bp):
AATTAAGAATTTAGAGATTTGG
Found at i:746524 original size:2 final size:2
Alignment explanation
Indices: 746517--746543 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
746507 ACTTAAATTC
746517 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 A
746544 AAGACAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:750945 original size:16 final size:17
Alignment explanation
Indices: 750924--750971 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
750914 ATTTCAGATT
750924 CAGATTCCAATTCCT-A
1 CAGATTCCAATTCCTCA
* *
750940 CAGATTTCAATTCGTTCA
1 CAGATTCCAATTC-CTCA
750958 CAGATTCCAATTCC
1 CAGATTCCAATTCC
750972 CTCATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (17 bp):
CAGATTCCAATTCCTCA
Found at i:755984 original size:14 final size:14
Alignment explanation
Indices: 755965--755995 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
755955 AGAATAAGGT
755965 CCCTGAGCCCTAGG
1 CCCTGAGCCCTAGG
755979 CCCTGAGCCCTAGG
1 CCCTGAGCCCTAGG
755993 CCC
1 CCC
755996 CCTCTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.48, G:0.26, T:0.13
Consensus pattern (14 bp):
CCCTGAGCCCTAGG
Done.