Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008612.1 Hibiscus syriacus cultivar Beakdansim tig00111568_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: 105480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:3011 original size:20 final size:20
Alignment explanation
Indices: 2986--3025 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2976 GTTTTGTTTC
2986 TTGAAGAAAAAGAAACGACG
1 TTGAAGAAAAAGAAACGACG
3006 TTGAAGAAAAAGAAACGACG
1 TTGAAGAAAAAGAAACGACG
3026 GTTTTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.25, T:0.10
Consensus pattern (20 bp):
TTGAAGAAAAAGAAACGACG
Found at i:17743 original size:33 final size:32
Alignment explanation
Indices: 17667--17744 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
17657 TTGAGTTCAT
* *
17667 ATCGATTATTTTTTAGCTCGAATCAATATCAG
1 ATCGATTATTTTTTAGCTAGAATCAATATCAA
*
17699 ATTGATTATTTTTTAGCTTAG-ATCAATATCAA
1 ATCGATTATTTTTTAGC-TAGAATCAATATCAA
*
17731 ATCGGTTGATTTTT
1 ATCGATT-ATTTTT
17745 GGGTCAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 31 0.79
33 8 0.21
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (32 bp):
ATCGATTATTTTTTAGCTAGAATCAATATCAA
Found at i:18039 original size:12 final size:12
Alignment explanation
Indices: 18022--18046 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18012 AAGAAAAAAA
18022 TTTATTATAAAT
1 TTTATTATAAAT
18034 TTTATTATAAAT
1 TTTATTATAAAT
18046 T
1 T
18047 AAAATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATTATAAAT
Found at i:18377 original size:32 final size:32
Alignment explanation
Indices: 18331--18408 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
18321 CTAACATGAT
18331 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
1 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
*
18363 TGAGGGACTGAAATTGAACGAGAGTTAACGAC
1 TGAGGGACTAAAATTGAACGAGAGTTAACGAC
18395 TGAGGGACTAAAAT
1 TGAGGGACTAAAAT
18409 CTAATAGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.19
Consensus pattern (32 bp):
TGAGGGACTAAAATTGAACGAGAGTTAACGAC
Found at i:18435 original size:31 final size:31
Alignment explanation
Indices: 18397--18464 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
18387 TTAACGACTG
* * *
18397 AGGGACTAAAATCTAATAGATTGATAACATT
1 AGGGACTAAAATCGAACAGATCGATAACATT
* *
18428 AGGGACTAATATCGAACAGATCGATAGCATT
1 AGGGACTAAAATCGAACAGATCGATAACATT
18459 AGGGAC
1 AGGGAC
18465 CATTTTCCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (31 bp):
AGGGACTAAAATCGAACAGATCGATAACATT
Found at i:18610 original size:21 final size:22
Alignment explanation
Indices: 18586--18626 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18576 ATTATAAATA
18586 AAAAATAA-ATTTTTATATTGT
1 AAAAATAACATTTTTATATTGT
*
18607 AAAAATAACCTTTTTATATT
1 AAAAATAACATTTTTATATT
18627 AAATTTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAAATAACATTTTTATATTGT
Found at i:19146 original size:29 final size:28
Alignment explanation
Indices: 19100--19160 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
19090 TTAGACTTAG
*
19100 ATATTTAATAAATAAAATTAGTTAAATA
1 ATATTTAATAAATAAAATAAGTTAAATA
* *
19128 ATATTTAAATAAA-ATAAATAATTTAAATT
1 ATATTT-AATAAATA-AAATAAGTTAAATA
19157 ATAT
1 ATAT
19161 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
ATATTTAATAAATAAAATAAGTTAAATA
Found at i:23695 original size:60 final size:60
Alignment explanation
Indices: 23610--23747 Score: 151
Period size: 60 Copynumber: 2.3 Consensus size: 60
23600 GTATGACCCC
* * *
23610 TCATTTTAAATTGGTCCTTAAACTTTTAAAT-GTTCCAATT-CTATCC-CTAAACTATGACTA-
1 TCATTCTAAATTAGTCCTTAAACTTTTAAATAGCT-CAATTAC-ATCCTC-AAACTATGA-TAT
*
23670 TCATTCTAAATTAGT-CTTCAAACTTTTGAATAGCTCAATTACATCCTCAAACTATGATAT
1 TCATTCTAAATTAGTCCTT-AAACTTTTAAATAGCTCAATTACATCCTCAAACTATGATAT
*
23730 TCATTCTAAATTGGTCCT
1 TCATTCTAAATTAGTCCT
23748 CTTTTTGAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
59 5 0.07
60 56 0.84
61 6 0.09
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTTAAACTTTTAAATAGCTCAATTACATCCTCAAACTATGATAT
Found at i:32980 original size:118 final size:118
Alignment explanation
Indices: 32760--32996 Score: 433
Period size: 118 Copynumber: 2.0 Consensus size: 118
32750 ACTGAATATG
32760 TTCCAAGTTTATAGAAATGGTTCCTAAAGCGATAGCAGACTAACTAGTGAATTTGTTGGAGGAAC
1 TTCCAAGTTTATAGAAATGGTTCCTAAAGCGATAGCAGACTAACTAGTGAATTTGTTGGAGGAAC
32825 CACCCCTCCCAACCCCAAGGGAAAAGAAGAAGAAATTATCAATATTTATGAAC
66 CACCCCTCCCAACCCCAAGGGAAAAGAAGAAGAAATTATCAATATTTATGAAC
32878 TTCCAAGTTTATAGAAAATGGTTCCT-AAGCGATAGCAGACTAACTAGTGAATTTTGTTGGAGGA
1 TTCCAAGTTTATAG-AAATGGTTCCTAAAGCGATAGCAGACTAACTAGTGAA-TTTGTTGGAGGA
*
32942 ACCCCCCCTCCCAACCCCAAGGGAAAAGAAGAAG-AATTATCAATATTTATGAAC
64 ACCACCCCTCCCAACCCCAAGGGAAAAGAAGAAGAAATTATCAATATTTATGAAC
32996 T
1 T
32997 AACTGTGGTA
Statistics
Matches: 116, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
118 60 0.52
119 56 0.48
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (118 bp):
TTCCAAGTTTATAGAAATGGTTCCTAAAGCGATAGCAGACTAACTAGTGAATTTGTTGGAGGAAC
CACCCCTCCCAACCCCAAGGGAAAAGAAGAAGAAATTATCAATATTTATGAAC
Found at i:33208 original size:20 final size:21
Alignment explanation
Indices: 33155--33208 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
33145 AAGTACTACC
* *
33155 AAATAGAGAGAGAGATTAAGA
1 AAATAGAGAAAGAGATGAAGA
*
33176 AAATATGA-TAAGAG-TGAAGA
1 AAATA-GAGAAAGAGATGAAGA
33196 AAATAGAGAAAGA
1 AAATAGAGAAAGA
33209 AAGGGGGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.07
20 14 0.52
21 9 0.33
22 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (21 bp):
AAATAGAGAAAGAGATGAAGA
Found at i:36226 original size:24 final size:24
Alignment explanation
Indices: 36199--36244 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
36189 ACTGAAAATA
36199 TTTTAAATAAATATT-TTATTCAGT
1 TTTTAAATAAAT-TTATTATTCAGT
*
36223 TTTTATATAAATTTATTATTCA
1 TTTTAAATAAATTTATTATTCA
36245 TATGATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTAAATAAATTTATTATTCAGT
Found at i:36467 original size:27 final size:27
Alignment explanation
Indices: 36429--36492 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
36419 GTTGAGATAT
36429 GCTAACTTGTGATATTGATTCACATGG
1 GCTAACTTGTGATATTGATTCACATGG
36456 GCTAACTTGTGATATTGATTCACATGG
1 GCTAACTTGTGATATTGATTCACATGG
36483 GCTAA-TTGTG
1 GCTAACTTGTG
36493 CTTAAAATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.14
27 32 0.86
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (27 bp):
GCTAACTTGTGATATTGATTCACATGG
Found at i:45030 original size:12 final size:12
Alignment explanation
Indices: 45013--45044 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
45003 TTTCTTCATT
45013 TTTATATTATTA
1 TTTATATTATTA
45025 TTTATATTATTA
1 TTTATATTATTA
45037 TTTA-ATTA
1 TTTATATTA
45045 ATTTTATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:45202 original size:19 final size:20
Alignment explanation
Indices: 45178--45228 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
45168 AATGACCAAT
45178 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
45197 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
45217 AAAATCGCAACG
1 AAAATCGCAACG
45229 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:45222 original size:20 final size:20
Alignment explanation
Indices: 45178--45442 Score: 104
Period size: 20 Copynumber: 12.6 Consensus size: 20
45168 AATGACCAAT
* *
45178 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
45197 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
45217 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
45237 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
45257 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
45278 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* *
45301 AAAATCGCAATGCGATTGATTG
1 AAAATCGCAACGCGATT--TAG
* *
45323 AATCGCAATTCGCAATGCGATTGAG
1 AA----AA-TCGCAACGCGATTTAG
* *
45348 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
45368 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * * *
45391 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* *
45411 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
45431 AAAATCGCAACG
1 AAAATCGCAACG
45443 TTAAAAAGAA
Statistics
Matches: 189, Mismatches: 38, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
19 17 0.09
20 106 0.56
21 16 0.08
22 4 0.02
23 28 0.15
25 3 0.02
26 2 0.01
27 13 0.07
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:45355 original size:27 final size:27
Alignment explanation
Indices: 45305--45357 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
45295 TAGAAGAAAA
**
45305 TCGCAATGCGATTGATTGAATCGCAAT
1 TCGCAATGCGATTGAGAGAATCGCAAT
*
45332 TCGCAATGCGATTGAGAGAGTCGCAA
1 TCGCAATGCGATTGAGAGAATCGCAA
45358 CGCGATTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (27 bp):
TCGCAATGCGATTGAGAGAATCGCAAT
Found at i:45391 original size:43 final size:40
Alignment explanation
Indices: 45332--45442 Score: 141
Period size: 40 Copynumber: 2.7 Consensus size: 40
45322 GAATCGCAAT
* *
45332 TCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAGAA
1 TCGCAATGCGATTGAGAGAATCGCAACGCGA-CT-G-AGAGAA
* *
45375 TCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAATGCGATTGAGAGAATCGCAACGCGACTGAGAGAA
* *
45415 TCGCAACGCGATTGAGAAAATCGCAACG
1 TCGCAATGCGATTGAGAGAATCGCAACG
45443 TTAAAAAGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 30 0.50
41 1 0.02
42 1 0.02
43 28 0.47
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (40 bp):
TCGCAATGCGATTGAGAGAATCGCAACGCGACTGAGAGAA
Found at i:45452 original size:20 final size:20
Alignment explanation
Indices: 45429--45472 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
45419 AACGCGATTG
*
45429 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
45449 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
45469 AGAA
1 AGAA
45473 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:45561 original size:6 final size:6
Alignment explanation
Indices: 45550--45665 Score: 142
Period size: 6 Copynumber: 20.5 Consensus size: 6
45540 GACACGTATT
45550 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
45598 ACCACG ACCACG ACGACCCG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG AC--CACG ACCACG ACCACG ACCACG ACCACG ACCACG
45643 ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
45666 CGAGACGAGA
Statistics
Matches: 107, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
5 45 0.42
6 57 0.53
8 5 0.05
ACGTcount: A:0.28, C:0.54, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:45584 original size:30 final size:26
Alignment explanation
Indices: 45554--45668 Score: 139
Period size: 25 Copynumber: 4.3 Consensus size: 26
45544 CGTATTACCA
45554 CGACCACGACCACGACCACGACCACGACC
1 CGACC-CGACC-CGACC-CGACCACGACC
45583 ACGACCACGACCACGACCACGACCACGA--
1 -CGACC-CGACC-CGACC-CGACCACGACC
45611 CGACCCGACCCGACCCGACC-CGACC
1 CGACCCGACCCGACCCGACCACGACC
45636 CGACCCGACCCGACCCGACC-CGACC
1 CGACCCGACCCGACCCGACCACGACC
45661 CGACCCGA
1 CGACCCGA
45669 GACGAGACGG
Statistics
Matches: 83, Mismatches: 0, Indels: 9
0.90 0.00 0.10
Matches are distributed among these distances:
23 3 0.04
24 5 0.06
25 38 0.46
26 5 0.06
27 5 0.06
30 27 0.33
ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00
Consensus pattern (26 bp):
CGACCCGACCCGACCCGACCACGACC
Found at i:45629 original size:15 final size:15
Alignment explanation
Indices: 45554--45668 Score: 135
Period size: 15 Copynumber: 7.2 Consensus size: 15
45544 CGTATTACCA
45554 CGACCACGACCACGACC
1 CGACC-CGACC-CGACC
45571 ACGACCACGACCACGACC
1 -CGACC-CGACC-CGACC
45589 ACGACCACGACCACGACC
1 -CGACC-CGACC-CGACC
45607 ACGA--CGACCCGACC
1 -CGACCCGACCCGACC
45621 CGACCCGACCCGACC
1 CGACCCGACCCGACC
45636 CGACCCGACCCGACC
1 CGACCCGACCCGACC
45651 CGACCCGACCCGACC
1 CGACCCGACCCGACC
45666 CGA
1 CGA
45669 GACGAGACGG
Statistics
Matches: 95, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
13 3 0.03
14 5 0.05
15 48 0.51
18 39 0.41
ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00
Consensus pattern (15 bp):
CGACCCGACCCGACC
Found at i:46367 original size:6 final size:6
Alignment explanation
Indices: 46351--46394 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
46341 TCTCGTCTCG
46351 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
46395 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:46509 original size:20 final size:20
Alignment explanation
Indices: 46484--46535 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
46474 CTTTTGACCG
46484 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
46504 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
46524 TTGCGATTCTCT
1 TTGCGATTCTCT
46536 TCTAAATCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.29, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:46609 original size:20 final size:20
Alignment explanation
Indices: 46482--46636 Score: 89
Period size: 20 Copynumber: 7.6 Consensus size: 20
46472 TTCTTTTGAC
* *
46482 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
46502 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
46522 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
** ** *
46545 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* ***
46566 TGTTGCGATTTTCTTTTGTC-
1 CGTTGCGATTTTC-TAAATCG
46586 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
46606 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
46625 CGTTGCGATTTT
1 CGTTGCGATTTT
46637 ATTGGTCATT
Statistics
Matches: 104, Mismatches: 25, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
19 20 0.19
20 54 0.52
21 15 0.14
22 1 0.01
23 14 0.13
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:46626 original size:19 final size:20
Alignment explanation
Indices: 46586--46636 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
46576 TTCTTTTGTC
*
46586 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
46606 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
46625 CGTTGCGATTTT
1 CGTTGCGATTTT
46637 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:46855 original size:14 final size:13
Alignment explanation
Indices: 46820--46858 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
46810 TTTAATAATT
46820 TAAAATTT-AAAC
1 TAAAATTTAAAAC
46832 TAAAATTTTAAAAC
1 TAAAA-TTTAAAAC
46846 ATAAAATTTAAAA
1 -TAAAATTTAAAA
46859 TTATTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 3 0.12
14 11 0.46
15 5 0.21
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAATTTAAAAC
Found at i:47079 original size:22 final size:22
Alignment explanation
Indices: 47045--47113 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
47035 GTTTAAAATA
*
47045 AAAAATAATTATTTATATTTTAT
1 AAAATTAA-TATTTATATTTTAT
*
47068 AAAATTAATATTAATTTATTTTA-
1 AAAATTAATATT--TATATTTTAT
47091 AAAATTAA-ATTTATGATATTTAT
1 AAAATTAATATTTAT-AT-TTTAT
47114 TTATGATAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 11 0.29
23 15 0.39
24 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
AAAATTAATATTTATATTTTAT
Found at i:53172 original size:30 final size:30
Alignment explanation
Indices: 53136--53201 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
53126 TTCAAGGGTT
*
53136 AAATTAATATTTTATCTAAAATCTAAGATC
1 AAATTAATATTTTATATAAAATCTAAGATC
* *
53166 AAATTAATATTTTATATAAAGTCTGAGATC
1 AAATTAATATTTTATATAAAATCTAAGATC
53196 AAATTA
1 AAATTA
53202 GCATTTTGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATTAATATTTTATATAAAATCTAAGATC
Found at i:59189 original size:40 final size:40
Alignment explanation
Indices: 59125--59200 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
59115 AAACAATCAA
*
59125 AATGTGGACGTTACCATCCAATATATGAAAGAACCACCAT
1 AATGTGGACGTTACCAACCAATATATGAAAGAACCACCAT
* * * * *
59165 AATGTGGATGTTACTAACCCATATATGGATGAACCA
1 AATGTGGACGTTACCAACCAATATATGAAAGAACCA
59201 TCAGAGTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (40 bp):
AATGTGGACGTTACCAACCAATATATGAAAGAACCACCAT
Found at i:60361 original size:18 final size:18
Alignment explanation
Indices: 60335--60405 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
60325 ACCGGTCACA
60335 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
60353 ACCCAACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
60370 ----TA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
60383 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
60401 ACCCG
1 ACCCG
60406 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 10 0.23
13 1 0.02
17 1 0.02
18 32 0.73
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:60377 original size:12 final size:13
Alignment explanation
Indices: 60358--60392 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
60348 CGTTGACCCA
*
60358 ACCCGACCCGTTT
1 ACCCGACCCGTTG
60371 A-CCGACCCGTTG
1 ACCCGACCCGTTG
60383 ACCCGACCCG
1 ACCCGACCCG
60393 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.14
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:60378 original size:30 final size:30
Alignment explanation
Indices: 60342--60399 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
60332 ACAACCCGAC
60342 CCGACCCGTTGACCCAACCCGACCCGTTTA
1 CCGACCCGTTGACCCAACCCGACCCGTTTA
*
60372 CCGACCCGTTGACCCGACCCGACCCGTT
1 CCGACCCGTTGACCCAACCCGACCCGTT
60400 GACCCGTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.17, C:0.48, G:0.19, T:0.16
Consensus pattern (30 bp):
CCGACCCGTTGACCCAACCCGACCCGTTTA
Found at i:60403 original size:8 final size:8
Alignment explanation
Indices: 60392--60420 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
60382 GACCCGACCC
60392 GACCCGTT
1 GACCCGTT
60400 GACCCGTT
1 GACCCGTT
60408 GA-CCGTT
1 GACCCGTT
60415 GACCCG
1 GACCCG
60421 GAGTTGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.14, C:0.38, G:0.28, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:62977 original size:24 final size:24
Alignment explanation
Indices: 62881--62989 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
62871 GAATATTTTA
* *
62881 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
62905 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
62929 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
62953 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
62977 TTTGATTTCTGAT
1 TCTGATATCTGAT
62990 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:65127 original size:18 final size:18
Alignment explanation
Indices: 65104--65174 Score: 91
Period size: 18 Copynumber: 4.3 Consensus size: 18
65094 ACCGGTCACA
65104 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
65122 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
65139 ----TA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
65152 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
65170 ACCCG
1 ACCCG
65175 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
12 10 0.22
13 1 0.02
17 1 0.02
18 33 0.73
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:65146 original size:12 final size:13
Alignment explanation
Indices: 65126--65161 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
65116 CCGTTGACCC
65126 GACCCGACCCGTT
1 GACCCGACCCGTT
*
65139 TA-CCGACCCGTT
1 GACCCGACCCGTT
65151 GACCCGACCCG
1 GACCCGACCCG
65162 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:65147 original size:30 final size:30
Alignment explanation
Indices: 65111--65168 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
65101 ACAACCCGAC
65111 CCGACCCGTTGACCCGACCCGACCCGTTTA
1 CCGACCCGTTGACCCGACCCGACCCGTTTA
65141 CCGACCCGTTGACCCGACCCGACCCGTT
1 CCGACCCGTTGACCCGACCCGACCCGTT
65169 GACCCGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.48, G:0.21, T:0.16
Consensus pattern (30 bp):
CCGACCCGTTGACCCGACCCGACCCGTTTA
Found at i:67738 original size:24 final size:24
Alignment explanation
Indices: 67645--67750 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
67635 ATATTTTATC
* *
67645 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
67669 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * *
67693 TGAT-TCCT-AACTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
67716 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
*
67740 TGATTTCTGAT
1 TGATATCTGAT
67751 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
23 18 0.28
24 46 0.72
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:69895 original size:18 final size:18
Alignment explanation
Indices: 69874--69937 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
69864 AACCCGACGA
69874 CCGACCCGTTGACCCGAC
1 CCGACCCGTTGACCCGAC
*
69892 CCGACCCGTT-----TA-
1 CCGACCCGTTGACCCGAC
69904 CCGACCCGTTGACCCGAC
1 CCGACCCGTTGACCCGAC
69922 CCGACCCGTTGACCCG
1 CCGACCCGTTGACCCG
69938 TTGACCGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
12 10 0.26
13 1 0.03
17 1 0.03
18 26 0.68
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (18 bp):
CCGACCCGTTGACCCGAC
Found at i:69899 original size:30 final size:30
Alignment explanation
Indices: 69865--69929 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
69855 ACCGGTCACA
69865 ACCCGACGACCGACCCGTTGACCCGACCCG
1 ACCCGACGACCGACCCGTTGACCCGACCCG
***
69895 ACCCGTTTACCGACCCGTTGACCCGACCCG
1 ACCCGACGACCGACCCGTTGACCCGACCCG
69925 ACCCG
1 ACCCG
69930 TTGACCCGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (30 bp):
ACCCGACGACCGACCCGTTGACCCGACCCG
Found at i:69909 original size:12 final size:13
Alignment explanation
Indices: 69889--69924 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
69879 CCGTTGACCC
69889 GACCCGACCCGTT
1 GACCCGACCCGTT
*
69902 TA-CCGACCCGTT
1 GACCCGACCCGTT
69914 GACCCGACCCG
1 GACCCGACCCG
69925 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:69930 original size:30 final size:30
Alignment explanation
Indices: 69873--69931 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
69863 CAACCCGACG
69873 ACCGACCCGTTGACCCGACCCGACCCGTTT
1 ACCGACCCGTTGACCCGACCCGACCCGTTT
69903 ACCGACCCGTTGACCCGACCCGACCCGTT
1 ACCGACCCGTTGACCCGACCCGACCCGTT
69932 GACCCGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.15
Consensus pattern (30 bp):
ACCGACCCGTTGACCCGACCCGACCCGTTT
Found at i:74262 original size:17 final size:16
Alignment explanation
Indices: 74251--74306 Score: 66
Period size: 17 Copynumber: 3.7 Consensus size: 16
74241 CCCGACCCGA
74251 CCGTTGACCCGACGAC
1 CCGTTGACCCGACGAC
*
74267 CCGTTTA--C--CGAC
1 CCGTTGACCCGACGAC
74279 CCGTTGACCCGACCGAC
1 CCGTTGACCCGA-CGAC
74296 CCGTTGACCCG
1 CCGTTGACCCG
74307 TTGACCGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
12 10 0.30
14 2 0.06
16 6 0.18
17 15 0.45
ACGTcount: A:0.16, C:0.45, G:0.23, T:0.16
Consensus pattern (16 bp):
CCGTTGACCCGACGAC
Found at i:74286 original size:28 final size:28
Alignment explanation
Indices: 74247--74300 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
74237 ACAACCCGAC
74247 CCGACCGTTGACCCGA-CGACCCGTTTA
1 CCGACCGTTGACCCGACCGACCCGTTTA
74274 CCGACCCGTTGACCCGACCGACCCGTT
1 CCGA-CCGTTGACCCGACCGACCCGTT
74301 GACCCGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 4 0.16
28 12 0.48
29 9 0.36
ACGTcount: A:0.17, C:0.44, G:0.22, T:0.17
Consensus pattern (28 bp):
CCGACCGTTGACCCGACCGACCCGTTTA
Found at i:76703 original size:104 final size:106
Alignment explanation
Indices: 76574--76785 Score: 401
Period size: 104 Copynumber: 2.0 Consensus size: 106
76564 ATTCACATTC
76574 TGAATAACTGATGATTCCGTCAGTTATTGAACTTTTTACAATAGTGATTC-TATTCCGACATTCT
1 TGAATAACTGATGATTCCGTCAGTTATTGAACTTTTTACAATAGTGATTCATATTCCGACATTCT
76638 ATC-GTATACTGAAGATCCATATTTCTCTACTTGCTAAGAT
66 ATCGGTATACTGAAGATCCATATTTCTCTACTTGCTAAGAT
76678 TGAATAACTGATGATTCCGTCAGTTATTGAACTTTTTACAATAGTGATTCTATATTCCGACATTC
1 TGAATAACTGATGATTCCGTCAGTTATTGAACTTTTTACAATAGTGATTC-ATATTCCGACATTC
76743 TATCGGTATACTGAAGATCCATATTTCTCTACTTGCTAAGAT
65 TATCGGTATACTGAAGATCCATATTTCTCTACTTGCTAAGAT
76785 T
1 T
76786 ATCCAGTACC
Statistics
Matches: 105, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
104 50 0.48
106 17 0.16
107 38 0.36
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (106 bp):
TGAATAACTGATGATTCCGTCAGTTATTGAACTTTTTACAATAGTGATTCATATTCCGACATTCT
ATCGGTATACTGAAGATCCATATTTCTCTACTTGCTAAGAT
Found at i:76945 original size:24 final size:24
Alignment explanation
Indices: 76849--76956 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
76839 GAATATTTTA
* *
76849 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
76873 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
76897 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
76921 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
*
76945 T-TGATTTCTGAT
1 TCTGATATCTGAT
76957 ATCTCGTTTA
Statistics
Matches: 66, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
23 11 0.17
24 54 0.82
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:79016 original size:18 final size:18
Alignment explanation
Indices: 78993--79077 Score: 83
Period size: 18 Copynumber: 4.9 Consensus size: 18
78983 ACCGGTCACA
78993 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
79011 ACCCGACCCGTT-----T
1 ACCCGACCCGTTGACCCG
79024 A-CCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
79041 ACCCGACCCTTTGACCCG
1 ACCCGACCCGTTGACCCG
79059 ACCCGTTGACCCGTTGACC
1 ACCC---GACCCGTTGACC
79078 GTTGACCGGA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.19
13 1 0.02
17 1 0.02
18 31 0.57
21 11 0.20
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:79030 original size:12 final size:13
Alignment explanation
Indices: 79010--79071 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
79000 CCGTTGACCC
79010 GACCCGACCCGTT
1 GACCCGACCCGTT
*
79023 TA-CCGACCCGTT
1 GACCCGACCCGTT
79035 GACCCGACCCGACCCTTT
1 GACCCGACCCG-----TT
79053 GACCCGACCCGTT
1 GACCCGACCCGTT
79066 GACCCG
1 GACCCG
79072 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
12 11 0.27
13 17 0.41
18 13 0.32
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:79030 original size:30 final size:31
Alignment explanation
Indices: 78993--79071 Score: 135
Period size: 30 Copynumber: 2.6 Consensus size: 31
78983 ACCGGTCACA
78993 ACCCGACCCGTTGACCCGACCCGACCCGTTT-
1 ACCCGACCCGTTGACCCGACCCGACCC-TTTG
79024 A-CCGACCCGTTGACCCGACCCGACCCTTTG
1 ACCCGACCCGTTGACCCGACCCGACCCTTTG
79054 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
79072 TTGACCGTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
29 3 0.07
30 26 0.57
31 17 0.37
ACGTcount: A:0.16, C:0.48, G:0.20, T:0.15
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCGACCCTTTG
Found at i:91825 original size:16 final size:17
Alignment explanation
Indices: 91793--91829 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
91783 AGGATGTGAT
*
91793 TATTGTCTTAGTAATTA
1 TATTTTCTTAGTAATTA
91810 TATTTTCTTA-TAATTA
1 TATTTTCTTAGTAATTA
91826 -ATTT
1 TATTT
91830 GAATATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 6 0.32
17 9 0.47
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (17 bp):
TATTTTCTTAGTAATTA
Found at i:94545 original size:22 final size:22
Alignment explanation
Indices: 94517--94560 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
94507 ATATTTTCAA
94517 TGTTGATATAACATTAAAGTAT
1 TGTTGATATAACATTAAAGTAT
94539 TGTTGATATAACATTAAAGTAT
1 TGTTGATATAACATTAAAGTAT
94561 GCTCAGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (22 bp):
TGTTGATATAACATTAAAGTAT
Found at i:97057 original size:24 final size:25
Alignment explanation
Indices: 97030--97076 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
97020 TAATTTTTTT
*
97030 AGTTGAATCAAATT-TTAAAATTCG
1 AGTTAAATCAAATTGTTAAAATTCG
* *
97054 AGTTAAATCGAATTGTTTAAATT
1 AGTTAAATCAAATTGTTAAAATT
97077 TTTTATTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (25 bp):
AGTTAAATCAAATTGTTAAAATTCG
Found at i:97168 original size:2 final size:2
Alignment explanation
Indices: 97163--97189 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
97153 TATGTACATG
97163 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 T
97190 TACCTCATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:102573 original size:2 final size:2
Alignment explanation
Indices: 102566--102596 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
102556 ACTTGGGGAA
102566 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 A
102597 AGGGAAAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.