Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006655.1 Hibiscus syriacus cultivar Beakdansim tig00016430_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: 456786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 3
Found at i:376370 original size:28 final size:27
Alignment explanation
Indices: 376315--376370 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
376305 TCTCGTACTA
* * *
376315 GTCCCCTCATTTTTAAAATCCAATTTC
1 GTCCCCTAAATTTTAAAATCCAAATTC
*
376342 GTCCCCTAAATTTTAAAAGTTCAAATTC
1 GTCCCCTAAATTTTAAAA-TCCAAATTC
376370 G
1 G
376371 CCCGTTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (27 bp):
GTCCCCTAAATTTTAAAATCCAAATTC
Found at i:377797 original size:11 final size:11
Alignment explanation
Indices: 377781--377806 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
377771 TTCACATTAA
377781 ATTAAATATTT
1 ATTAAATATTT
377792 ATTAAATATTT
1 ATTAAATATTT
377803 ATTA
1 ATTA
377807 GAAAATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTAAATATTT
Found at i:379340 original size:10 final size:10
Alignment explanation
Indices: 379325--379358 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
379315 CAAACAAACA
379325 AAAATCATTC
1 AAAATCATTC
379335 AAAATCATTC
1 AAAATCATTC
*
379345 AAAATCAATC
1 AAAATCATTC
379355 AAAA
1 AAAA
379359 AAGACCAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAATCATTC
Found at i:380125 original size:28 final size:30
Alignment explanation
Indices: 380065--380129 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
380055 ATTCTCTCTT
* * *
380065 ATTTTATTTACTGAAATTTAAATAAAGTTA
1 ATTTTTTTTACTGAAACTTAAATAAACTTA
*
380095 ATTTTTTTTACT-AAACTT-AATATACTTA
1 ATTTTTTTTACTGAAACTTAAATAAACTTA
380123 ATTTTTT
1 ATTTTTT
380130 AATTATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 15 0.48
29 5 0.16
30 11 0.35
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (30 bp):
ATTTTTTTTACTGAAACTTAAATAAACTTA
Found at i:380580 original size:2 final size:2
Alignment explanation
Indices: 380573--380615 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
380563 GTACTGAAAT
380573 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
380615 T
1 T
380616 TTGGGATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:380685 original size:2 final size:2
Alignment explanation
Indices: 380678--380708 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
380668 GTACTGAAAT
380678 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 T
380709 TGCTTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:382378 original size:42 final size:42
Alignment explanation
Indices: 382331--382436 Score: 212
Period size: 42 Copynumber: 2.5 Consensus size: 42
382321 TCTTAAATTG
382331 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
382373 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
382415 ACATTGAAACATAATCACACAA
1 ACATTGAAACATAATCACACAA
382437 ATCCATTAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.23
Consensus pattern (42 bp):
ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
Found at i:382383 original size:23 final size:23
Alignment explanation
Indices: 382357--382425 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
382347 ACACAATAAT
382357 AACACTGGGAATCATTACATTGA
1 AACACTGGGAATCATTACATTGA
* * *
382380 AACA-T---AATCA-CACAATAA
1 AACACTGGGAATCATTACATTGA
382398 TAACACTGGGAATCATTACATTGA
1 -AACACTGGGAATCATTACATTGA
382422 AACA
1 AACA
382426 TAATCACACA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 9 0.26
20 1 0.03
22 1 0.03
23 13 0.38
24 5 0.15
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (23 bp):
AACACTGGGAATCATTACATTGA
Found at i:382402 original size:19 final size:19
Alignment explanation
Indices: 382338--382402 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
382328 TTGACATTGA
382338 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
* * *
382357 AACACTGGGAATCATTACATTGA-
1 AACA-T---AATCA-CACAATAAT
382380 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
382399 AACA
1 AACA
382403 CTGGGAATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 1 0.03
22 1 0.03
23 9 0.26
24 5 0.15
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (19 bp):
AACATAATCACACAATAAT
Found at i:385368 original size:23 final size:22
Alignment explanation
Indices: 385327--385369 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
385317 TCCATTTTAT
*
385327 TATTTTTTTAAAATTTATAAAA
1 TATTTTTTTAAAATGTATAAAA
*
385349 TATTTTTTTATATATGTATAA
1 TATTTTTTTA-AAATGTATAA
385370 TTATTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTTTTTTAAAATGTATAAAA
Found at i:385374 original size:22 final size:22
Alignment explanation
Indices: 385325--385374 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
385315 ACTCCATTTT
*
385325 ATTATTTTTTTAAAATTTATAA
1 ATTATTTTTTTAAAATGTATAA
* *
385347 AATATTTTTTTATATATGTAT-A
1 ATTATTTTTTTA-AAATGTATAA
385369 ATTATT
1 ATTATT
385375 ATAAATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTATTTTTTTAAAATGTATAA
Found at i:395861 original size:11 final size:11
Alignment explanation
Indices: 395845--395870 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
395835 TTCACATTAA
395845 ATTAAATATTT
1 ATTAAATATTT
395856 ATTAAATATTT
1 ATTAAATATTT
395867 ATTA
1 ATTA
395871 GAAAATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTAAATATTT
Found at i:396375 original size:16 final size:17
Alignment explanation
Indices: 396340--396382 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
396330 ATGAGGTGAA
396340 AAAAATAATATTATTGT
1 AAAAATAATATTATTGT
396357 AAAAAT-ATAATTATT-T
1 AAAAATAAT-ATTATTGT
396373 -AAAATAATAT
1 AAAAATAATAT
396383 CTATCACCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAAATAATATTATTGT
Found at i:398526 original size:42 final size:45
Alignment explanation
Indices: 398442--398547 Score: 155
Period size: 48 Copynumber: 2.4 Consensus size: 45
398432 ATTGATATTC
398442 AAACATAATCACACAATAATAACACTGGGAATCATTTTCATTACATTG
1 AAACATAATCACACAATAATAACACTGGGAA-CA--TTCATTACATTG
398490 AAACATAATCACACAATAATAACACTGGG-A-A-TCATTACATTG
1 AAACATAATCACACAATAATAACACTGGGAACATTCATTACATTG
*
398532 AAACATAATCCCACAA
1 AAACATAATCACACAA
398548 ATCCATTAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
42 26 0.46
45 1 0.02
47 1 0.02
48 29 0.51
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.25
Consensus pattern (45 bp):
AAACATAATCACACAATAATAACACTGGGAACATTCATTACATTG
Found at i:403803 original size:20 final size:21
Alignment explanation
Indices: 403778--403836 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
403768 GGCTGCTGGA
403778 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
403798 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
403818 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
403837 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:403814 original size:10 final size:10
Alignment explanation
Indices: 403799--403868 Score: 62
Period size: 10 Copynumber: 7.3 Consensus size: 10
403789 CCGGTTTTCA
403799 ACCGGTTCTG
1 ACCGGTTCTG
*
403809 ACCGGTT-TCA
1 ACCGGTTCT-G
403819 ACCGGTTC-G
1 ACCGGTTCTG
403828 AACCGGTT-TG
1 -ACCGGTTCTG
403838 ACCGG-TCTG
1 ACCGGTTCTG
403847 AACCGGTT-TG
1 -ACCGGTTCTG
403857 ACCGG-TCTG
1 ACCGGTTCTG
403866 ACC
1 ACC
403869 CGACCCGACC
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
8 2 0.04
9 18 0.36
10 29 0.58
11 1 0.02
ACGTcount: A:0.16, C:0.30, G:0.29, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:403843 original size:19 final size:20
Alignment explanation
Indices: 403799--403866 Score: 90
Period size: 19 Copynumber: 3.5 Consensus size: 20
403789 CCGGTTTTCA
*
403799 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
403819 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
403838 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
403857 ACCGG-TCTGA
1 ACCGGTTCTGA
403867 CCCGACCCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 2 0.04
19 27 0.60
20 16 0.36
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.26
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:403867 original size:9 final size:9
Alignment explanation
Indices: 403829--403868 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
403819 ACCGGTTCGA
*
403829 ACCGGTTTG
1 ACCGGTCTG
403838 ACCGGTCTG
1 ACCGGTCTG
*
403847 AACCGGTTTG
1 -ACCGGTCTG
403857 ACCGGTCTG
1 ACCGGTCTG
403866 ACC
1 ACC
403869 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:403892 original size:17 final size:17
Alignment explanation
Indices: 403870--403907 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
403860 GGTCTGACCC
403870 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
403887 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
403904 GACC
1 GACC
403908 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:403907 original size:24 final size:22
Alignment explanation
Indices: 403854--403914 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
403844 CTGAACCGGT
403854 TTGACCGGTCTGACCCGACCCGAC
1 TTGACC-GT-TGACCCGACCCGAC
**
403878 CCGACCGTTGACCCGACCCGATC
1 TTGACCGTTGACCCGACCCGA-C
403901 GTTGACCGTTGACC
1 -TTGACCGTTGACC
403915 GTTGACTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.42
23 3 0.10
24 15 0.48
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (22 bp):
TTGACCGTTGACCCGACCCGAC
Found at i:411113 original size:20 final size:20
Alignment explanation
Indices: 411088--411165 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
411078 GGCTGCTGGA
*
411088 AACCGGTT-TAACCAGTTTTC
1 AACCGGTTCTAACC-GGTTTC
*
411108 AACCGGTTCTGACCGGTTTC
1 AACCGGTTCTAACCGGTTTC
*
411128 AACCGGTTCGAACCGGTTT-
1 AACCGGTTCTAACCGGTTTC
*
411147 GACCGG-TCTGAACCGGTTT
1 AACCGGTTCT-AACCGGTTT
411166 GACCGGTCTG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
18 2 0.04
19 14 0.28
20 30 0.60
21 4 0.08
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.29
Consensus pattern (20 bp):
AACCGGTTCTAACCGGTTTC
Found at i:411125 original size:30 final size:29
Alignment explanation
Indices: 411108--411178 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
411098 ACCAGTTTTC
411108 AACCGGTTCTGACCGGTTTCAACCGGTTCG
1 AACCGGTT-TGACCGGTTTCAACCGGTTCG
* * *
411138 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 AACCGGTTTGACCGGTTTCAACCGGTTCG
*
411167 -ACCGGTCTGACC
1 AACCGGTTTGACC
411179 CGACCCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 11 0.30
29 18 0.49
30 8 0.22
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:411153 original size:9 final size:9
Alignment explanation
Indices: 411109--411178 Score: 68
Period size: 10 Copynumber: 7.3 Consensus size: 9
411099 CCAGTTTTCA
411109 ACCGGTTCTG
1 ACCGGTT-TG
*
411119 ACCGGTTTCA
1 ACCGGTTT-G
*
411129 ACCGGTTCG
1 ACCGGTTTG
411138 AACCGGTTTG
1 -ACCGGTTTG
*
411148 ACCGGTCTG
1 ACCGGTTTG
411157 AACCGGTTTG
1 -ACCGGTTTG
*
411167 ACCGGTCTG
1 ACCGGTTTG
411176 ACC
1 ACC
411179 CGACCCGACC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 20 0.40
10 30 0.60
ACGTcount: A:0.16, C:0.30, G:0.29, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:411153 original size:19 final size:20
Alignment explanation
Indices: 411109--411176 Score: 90
Period size: 19 Copynumber: 3.5 Consensus size: 20
411099 CCAGTTTTCA
*
411109 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
411129 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
411148 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
411167 ACCGG-TCTGA
1 ACCGGTTCTGA
411177 CCCGACCCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
18 2 0.04
19 27 0.60
20 16 0.36
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.26
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:411202 original size:17 final size:17
Alignment explanation
Indices: 411180--411217 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
411170 GGTCTGACCC
411180 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
411197 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
411214 GACC
1 GACC
411218 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:411217 original size:24 final size:22
Alignment explanation
Indices: 411164--411224 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
411154 CTGAACCGGT
411164 TTGACCGGTCTGACCCGACCCGAC
1 TTGACC-GT-TGACCCGACCCGAC
**
411188 CCGACCGTTGACCCGACCCGATC
1 TTGACCGTTGACCCGACCCGA-C
411211 GTTGACCGTTGACC
1 -TTGACCGTTGACC
411225 GTTGACTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.42
23 3 0.10
24 15 0.48
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (22 bp):
TTGACCGTTGACCCGACCCGAC
Found at i:421374 original size:60 final size:60
Alignment explanation
Indices: 421277--421393 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
421267 GAGAATAATA
* * *
421277 GATGAAATTAGAACGTTCAAAAGTGTAAGGACTAATTTAGAATGAGAGTCATAGTTTAGG
1 GATGAAATTAGAACATTCAAAAGTGTAAGGACTAATTTAAAATGAAAGTCATAGTTTAGG
* ** * *
421337 GATGAAATTAGAATATTTTAAAGTTTAAGGA-TCAATTTAAAATGAAAGTTATAGTTT
1 GATGAAATTAGAACATTCAAAAGTGTAAGGACT-AATTTAAAATGAAAGTCATAGTTT
421394 TGGAGACACA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (60 bp):
GATGAAATTAGAACATTCAAAAGTGTAAGGACTAATTTAAAATGAAAGTCATAGTTTAGG
Found at i:421851 original size:2 final size:2
Alignment explanation
Indices: 421846--421880 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
421836 ATATGAAGGA
421846 AT 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 AT A
421881 GTTATTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:422402 original size:49 final size:49
Alignment explanation
Indices: 422349--422443 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
422339 GACACTTGTG
** * *
422349 GAGGGGTTGCTTGGGATACCCCGGGCACTATGGAGGTTCACCCCTGGAT
1 GAGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCACCCCTGGAT
* *
422398 GAGGGGTTGCCCGGGATACCCCGGGCTCCATGGAGGTCCGCCCCTG
1 GAGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCACCCCTG
422444 ATCGACACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.14, C:0.29, G:0.38, T:0.19
Consensus pattern (49 bp):
GAGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCACCCCTGGAT
Found at i:423982 original size:11 final size:11
Alignment explanation
Indices: 423966--423991 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
423956 TTCACATTAA
423966 ATTAAATATTT
1 ATTAAATATTT
423977 ATTAAATATTT
1 ATTAAATATTT
423988 ATTA
1 ATTA
423992 GAAAATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTAAATATTT
Found at i:425154 original size:35 final size:35
Alignment explanation
Indices: 425075--425142 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
425065 GTTTATTGAT
* *
425075 CGACTAATACAAATCAAATATTGTAGAGGCAAAAA
1 CGACTAATCCAAATCAAATACTGTAGAGGCAAAAA
*
425110 CGACTAATCCATATCAAATACTGTAGAGGCAAA
1 CGACTAATCCAAATCAAATACTGTAGAGGCAAA
425143 GAAGTCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (35 bp):
CGACTAATCCAAATCAAATACTGTAGAGGCAAAAA
Found at i:425161 original size:35 final size:35
Alignment explanation
Indices: 425075--425162 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
425065 GTTTATTGAT
* * *
425075 CGACTAATACAAATCAAATATTGTAGAGGCAAAAA
1 CGACTAATCCAGATCAAATACTGTAGAGGCAAAAA
*
425110 CGACTAATCCATATCAAATACTGTAGAGGCAAAGAA
1 CGACTAATCCAGATCAAATACTGTAGAGGCAAA-AA
* *
425146 -GTCTAATCCGGATCAAA
1 CGACTAATCCAGATCAAA
425163 CACCGATCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 44 0.96
36 2 0.04
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (35 bp):
CGACTAATCCAGATCAAATACTGTAGAGGCAAAAA
Found at i:426864 original size:2 final size:2
Alignment explanation
Indices: 426859--426902 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
426849 ATATGAAGGA
426859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
426902 A
1 A
426903 GTTATTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:429963 original size:35 final size:35
Alignment explanation
Indices: 429884--429951 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
429874 GTTTATTGAT
* *
429884 CGACTAATACAAATCAAATATTGTAGAGGCAAAAA
1 CGACTAATCCAAATCAAATACTGTAGAGGCAAAAA
*
429919 CGACTAATCCATATCAAATACTGTAGAGGCAAA
1 CGACTAATCCAAATCAAATACTGTAGAGGCAAA
429952 GAAGTCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (35 bp):
CGACTAATCCAAATCAAATACTGTAGAGGCAAAAA
Found at i:429970 original size:35 final size:35
Alignment explanation
Indices: 429884--429971 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
429874 GTTTATTGAT
* * *
429884 CGACTAATACAAATCAAATATTGTAGAGGCAAAAA
1 CGACTAATCCAGATCAAATACTGTAGAGGCAAAAA
*
429919 CGACTAATCCATATCAAATACTGTAGAGGCAAAGAA
1 CGACTAATCCAGATCAAATACTGTAGAGGCAAA-AA
* *
429955 -GTCTAATCCGGATCAAA
1 CGACTAATCCAGATCAAA
429972 CACCGATCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 44 0.96
36 2 0.04
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (35 bp):
CGACTAATCCAGATCAAATACTGTAGAGGCAAAAA
Found at i:437062 original size:24 final size:24
Alignment explanation
Indices: 437030--437084 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
437020 TGTATACATA
437030 TAAATTATATATGATTTTAGAAAC
1 TAAATTATATATGATTTTAGAAAC
437054 TAAATTATATATGATTTTAGAAAC
1 TAAATTATATATGATTTTAGAAAC
437078 TAAATTA
1 TAAATTA
437085 CAATAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (24 bp):
TAAATTATATATGATTTTAGAAAC
Found at i:441126 original size:31 final size:31
Alignment explanation
Indices: 441091--441183 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 31
441081 ATGTATCCCC
*
441091 AAACTATGACAATCATTTGAAATTAGTCCTT
1 AAACTATGACAATCATTTCAAATTAGTCCTT
* * * *
441122 AAACTTTTA-AA--A-TTCCAATTAAGTCCTC
1 AAACTATGACAATCATTTCAAATT-AGTCCTT
** *
441150 AAACTATGACTCTCATTTTAAATTAGTCCTT
1 AAACTATGACAATCATTTCAAATTAGTCCTT
441181 AAA
1 AAA
441184 ATTTTGAACA
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
27 6 0.13
28 14 0.31
30 2 0.04
31 17 0.38
32 6 0.13
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (31 bp):
AAACTATGACAATCATTTCAAATTAGTCCTT
Found at i:441226 original size:60 final size:59
Alignment explanation
Indices: 441085--441272 Score: 200
Period size: 60 Copynumber: 3.2 Consensus size: 59
441075 TGCATCATGT
* * *
441085 ATCCCCAAACTATGACA-ATCATTTGAAATTAGTCCTTAAACTTTTAAAATTCCAA-TTA
1 ATCCCCAAACTATGA-ATCTCATTTTAAATTAGTCCTTAAACTTTTAAAATTCCAATTTC
* * * *
441143 AGTCCTCAAACTATGACTCTCATTTTAAATTAGTCCTTAAAATTTTGAACATTCCAATTTC
1 A-TCCCCAAACTATGAATCTCATTTTAAATTAGTCCTTAAACTTTT-AAAATTCCAATTTC
* * * * * * *
441204 ATCCCCAAAATATGAATCTCATTCTAAATTGGTCCCTAGACTTTTAGATATTACAATTTC
1 ATCCCCAAACTATGAATCTCATTTTAAATTAGTCCTTAAACTTTTA-AAATTCCAATTTC
441264 ATCCCCAAA
1 ATCCCCAAA
441273 TTCATCCAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 39 0.36
60 65 0.60
61 3 0.03
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (59 bp):
ATCCCCAAACTATGAATCTCATTTTAAATTAGTCCTTAAACTTTTAAAATTCCAATTTC
Found at i:441557 original size:60 final size:60
Alignment explanation
Indices: 441392--441562 Score: 179
Period size: 60 Copynumber: 2.9 Consensus size: 60
441382 ATATACATAT
* * * *
441392 AATTT-AGGATAAAATTGAAATATTCAAAAAGTTTGGGGACTAATTTAGAATGAATATCAC
1 AATTTAAGGATAAAATTGAAATGTT-AAAAAGTTTAGAGACTAATTTAAAATGAATATCAC
* * *
441452 AATTTAGGGATGAAAA-TGAAATGTTCAAAAGTTTA-AGAACTAATTTAAAATG-ATAGTCAT
1 AATTTAAGGAT-AAAATTGAAATGTTAAAAAGTTTAGAG-ACTAATTTAAAATGAATA-TCAC
* * * *
441512 ATTTTAAGGATAAAATTGAAATGTTTAAAAGTTTAGAGACCAATTTGAAAT
1 AATTTAAGGATAAAATTGAAATGTTAAAAAGTTTAGAGACTAATTTAAAAT
441563 AAGGATAATA
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
59 8 0.09
60 67 0.72
61 14 0.15
62 4 0.04
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (60 bp):
AATTTAAGGATAAAATTGAAATGTTAAAAAGTTTAGAGACTAATTTAAAATGAATATCAC
Found at i:441672 original size:2 final size:2
Alignment explanation
Indices: 441665--441701 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
441655 TAATAATCGT
441665 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 T
441702 TATTGATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:449851 original size:2 final size:2
Alignment explanation
Indices: 449846--449883 Score: 58
Period size: 2 Copynumber: 18.0 Consensus size: 2
449836 ATATGAAGGA
449846 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT
449884 GGTTATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 30 0.88
3 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:452851 original size:35 final size:35
Alignment explanation
Indices: 452803--452878 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
452793 AATAATACGA
* * *
452803 ATCAAATATTGTAGAGGCAAAGACGACTAGTCCAG
1 ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
* *
452838 ATCAAATACTGTAGAGGCAAAGAAGTCTAATCCGG
1 ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
452873 ATCAAA
1 ATCAAA
452879 CACCGATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (35 bp):
ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
Found at i:454599 original size:36 final size:36
Alignment explanation
Indices: 454540--454609 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
454530 GAAATATTCT
* *
454540 TAAATTGGCATTCAAATCAAATCATACAAATCCAAA
1 TAAATTGACATTCAAATCAAATCACACAAATCCAAA
*
454576 TAAATTGACATTGAAA-CATAATCACACAAATCCA
1 TAAATTGACATTCAAATCA-AATCACACAAATCCA
454610 TTAATCACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.50, C:0.20, G:0.06, T:0.24
Consensus pattern (36 bp):
TAAATTGACATTCAAATCAAATCACACAAATCCAAA
Done.