Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003232.1 Hibiscus syriacus cultivar Beakdansim tig00006802_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: 85660
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1024 original size:22 final size:23
Alignment explanation
Indices: 989--1034 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
979 TTATTTTTCA
989 TTTTAATTCCTTAACT-TTAATAT
1 TTTTAATTCCTTAA-TATTAATAT
*
1012 TTTTAATT-TTTAATATTAATAT
1 TTTTAATTCCTTAATATTAATAT
1034 T
1 T
1035 AGTTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 12 0.57
23 8 0.38
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAATTCCTTAATATTAATAT
Found at i:3294 original size:25 final size:25
Alignment explanation
Indices: 3261--3313 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
3251 TACACTAAAC
3261 AAATCATACTCTAGTAAATCTCATA
1 AAATCATACTCTAGTAAATCTCATA
* *
3286 AAATTATACTGTAGTAAATCTCATA
1 AAATCATACTCTAGTAAATCTCATA
3311 AAA
1 AAA
3314 GAGTTATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (25 bp):
AAATCATACTCTAGTAAATCTCATA
Found at i:3415 original size:32 final size:31
Alignment explanation
Indices: 3377--3453 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
3367 TGGGGCTGTG
* *
3377 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** **
3409 GGGCCTACCCGAGAATGATCTCAGGGCCACA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
3440 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3454 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:4423 original size:57 final size:56
Alignment explanation
Indices: 4354--4498 Score: 193
Period size: 57 Copynumber: 2.5 Consensus size: 56
4344 ATATTACCTT
*
4354 TTTTTTTCAAAATAATGCCAAGAATGTCACCTTTGCAAAATAATTCCCATA-ATGTCA
1 TTTTTTTCAAAATAATCCCAA-AATGTCACCTTTGCAAAATAATTCCCA-ACATGTCA
* *
4411 TTTTTTTCAAAATAATTCCCAAAATGTCACTTTTTCAAAATAATTCCCAACATGTCA
1 TTTTTTTCAAAATAA-TCCCAAAATGTCACCTTTGCAAAATAATTCCCAACATGTCA
** *
4468 CCTTTTTCAAAATAATTCCCAAAATATCACC
1 TTTTTTTCAAAATAA-TCCCAAAATGTCACC
4499 GAGTCGGGTT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
56 1 0.01
57 73 0.92
58 5 0.06
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (56 bp):
TTTTTTTCAAAATAATCCCAAAATGTCACCTTTGCAAAATAATTCCCAACATGTCA
Found at i:4425 original size:29 final size:27
Alignment explanation
Indices: 4356--4490 Score: 171
Period size: 28 Copynumber: 4.8 Consensus size: 27
4346 ATTACCTTTT
* *
4356 TTTTTCAAAATAATGCCAAGAATGTCAC
1 TTTTTCAAAATAATTCCCA-AATGTCAC
* * *
4384 CTTTGCAAAATAATTCCCATAATGTCATT
1 TTTTTCAAAATAATTCCCA-AATGTCA-C
4413 TTTTTCAAAATAATTCCCAAAATGTCAC
1 TTTTTCAAAATAATTCCC-AAATGTCAC
4441 TTTTTCAAAATAATTCCCAACATGTCACC
1 TTTTTCAAAATAATTCCCAA-ATGTCA-C
4470 TTTTTCAAAATAATTCCCAAA
1 TTTTTCAAAATAATTCCCAAA
4491 ATATCACCGA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
27 2 0.02
28 47 0.50
29 44 0.47
30 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (27 bp):
TTTTTCAAAATAATTCCCAAATGTCAC
Found at i:4497 original size:29 final size:29
Alignment explanation
Indices: 4356--4498 Score: 193
Period size: 29 Copynumber: 5.0 Consensus size: 29
4346 ATTACCTTTT
*
4356 TTTTTCAAAATAA-TGCCAAGAATGTCACC
1 TTTTTCAAAATAATTCCCAA-AATGTCACC
* * **
4385 -TTTGCAAAATAATTCCCATAATGTCATT
1 TTTTTCAAAATAATTCCCAAAATGTCACC
4413 TTTTTCAAAATAATTCCCAAAATGTCA-C
1 TTTTTCAAAATAATTCCCAAAATGTCACC
*
4441 TTTTTCAAAATAATTCCCAACATGTCACC
1 TTTTTCAAAATAATTCCCAAAATGTCACC
*
4470 TTTTTCAAAATAATTCCCAAAATATCACC
1 TTTTTCAAAATAATTCCCAAAATGTCACC
4499 GAGTCGGGTT
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
28 44 0.44
29 56 0.56
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (29 bp):
TTTTTCAAAATAATTCCCAAAATGTCACC
Found at i:4570 original size:19 final size:19
Alignment explanation
Indices: 4548--4584 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4538 ACTGGTCAGA
*
4548 CCGGTTTGGACCGATCAAG
1 CCGGTTTAGACCGATCAAG
*
4567 CCGGTTTAGACCGGTCAA
1 CCGGTTTAGACCGATCAA
4585 CTATTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.22
Consensus pattern (19 bp):
CCGGTTTAGACCGATCAAG
Found at i:22235 original size:20 final size:20
Alignment explanation
Indices: 22210--22249 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22200 TTATTATGTT
*
22210 CGTTCGCTTGTGTTCGTTTA
1 CGTTCGCTTATGTTCGTTTA
*
22230 CGTTCGTTTATGTTCGTTTA
1 CGTTCGCTTATGTTCGTTTA
22250 TCATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.17, G:0.23, T:0.53
Consensus pattern (20 bp):
CGTTCGCTTATGTTCGTTTA
Found at i:22250 original size:10 final size:10
Alignment explanation
Indices: 22183--22250 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
22173 GTGTTTGTGT
22183 TGTTCGTTTA
1 TGTTCGTTTA
*
22193 TGTTCATTTA
1 TGTTCGTTTA
22203 T-TAT-G-TT-
1 TGT-TCGTTTA
* * *
22210 CGTTCGCTTG
1 TGTTCGTTTA
22220 TGTTCGTTTA
1 TGTTCGTTTA
*
22230 CGTTCGTTTA
1 TGTTCGTTTA
22240 TGTTCGTTTA
1 TGTTCGTTTA
22250 T
1 T
22251 CATTTAAATG
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
7 1 0.02
8 4 0.09
9 3 0.07
10 37 0.82
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.57
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:27191 original size:34 final size:35
Alignment explanation
Indices: 27143--27215 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
27133 ACAATCATCT
* *
27143 ATTATATTCTAAACCCAAAA-TCCAAAATGCTTAA
1 ATTACATTCTAAACCCAAAATTCCAAAATACTTAA
* * *
27177 ATTACATTCTAAACCTAAAATTCTAAAATACTTCA
1 ATTACATTCTAAACCCAAAATTCCAAAATACTTAA
27212 ATTA
1 ATTA
27216 TATATCCAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (35 bp):
ATTACATTCTAAACCCAAAATTCCAAAATACTTAA
Found at i:33541 original size:20 final size:21
Alignment explanation
Indices: 33485--33541 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
33475 TGTCCCGTAT
* *
33485 GACCTCATGTATGTCCCAAAA
1 GACCTCATATATATCCCAAAA
* *
33506 GACCTCGTATATATCCCAAAG
1 GACCTCATATATATCCCAAAA
33527 GACCTCATATA-ATCC
1 GACCTCATATATATCC
33542 TTGACTCTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (21 bp):
GACCTCATATATATCCCAAAA
Found at i:35344 original size:28 final size:29
Alignment explanation
Indices: 35299--35357 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
35289 CTTAAGGTTG
*
35299 TTTTCATTTATCTGATTTAGT-TTTAAATT
1 TTTTCATTGATCTGATTT-GTCTTTAAATT
* *
35328 TTTTCATTGAT-TTATTTTTCTTTAAATT
1 TTTTCATTGATCTGATTTGTCTTTAAATT
35356 TT
1 TT
35358 CATTTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 15 0.58
29 10 0.38
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (29 bp):
TTTTCATTGATCTGATTTGTCTTTAAATT
Found at i:35369 original size:21 final size:22
Alignment explanation
Indices: 35337--35377 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35327 TTTTTCATTG
35337 ATTTATTTTTCTTTAAATTTTC
1 ATTTATTTTTCTTTAAATTTTC
*
35359 ATTTA-TTTTCTTTTAATTT
1 ATTTATTTTTCTTTAAATTT
35378 CACAACCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTATTTTTCTTTAAATTTTC
Found at i:49126 original size:12 final size:12
Alignment explanation
Indices: 49109--49141 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
49099 TAAAATCACT
49109 AATGATTTTCTA
1 AATGATTTTCTA
49121 AATGATTTTCTA
1 AATGATTTTCTA
*
49133 AAGGATTTT
1 AATGATTTT
49142 ATTTTCTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (12 bp):
AATGATTTTCTA
Found at i:52351 original size:4 final size:4
Alignment explanation
Indices: 52342--52371 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
52332 TCATTTTCCA
52342 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
52372 TATTACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:53080 original size:18 final size:18
Alignment explanation
Indices: 53037--53078 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
53027 TAAAAGGAGG
53037 AAGAAAAAGAGAGCACAA
1 AAGAAAAAGAGAGCACAA
53055 AAGAAAAAGAGA-CA-AA
1 AAGAAAAAGAGAGCACAA
53071 AAGAAAAA
1 AAGAAAAA
53079 AAAGCAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 2 0.08
18 12 0.50
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAGAGCACAA
Found at i:53086 original size:16 final size:16
Alignment explanation
Indices: 53037--53086 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
53027 TAAAAGGAGG
53037 AAGAAAAAGAGAGCACAA
1 AAGAAAAA-AGAGCA-AA
53055 AAG-AAAAAGAGACAAA
1 AAGAAAAAAGAG-CAAA
*
53071 AAGAAAAAAAAGCAAA
1 AAGAAAAAAGAGCAAA
53087 CAAAAAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 13 0.45
17 13 0.45
18 3 0.10
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAGCAAA
Found at i:54004 original size:60 final size:58
Alignment explanation
Indices: 53938--54141 Score: 216
Period size: 60 Copynumber: 3.4 Consensus size: 58
53928 TTGTAATTAC
* *
53938 ATTTTAGTCCCTTAAGTTTATGGTTTTT-TTATTTTATCCCATTAAATTACTATTTTTGTT
1 ATTTTAGTCCCTTAAGTTTAT--TTTTTATTATTTTAT-CCTTTAAATTTCTATTTTTGTT
* * * *
53998 ATTTTAGTCACTTAAGTTTCTATTTTTACTATTTTAGGCCTTTAAATTTCTA-TTTT-TT
1 ATTTTAGTCCCTTAAGTTTAT-TTTTTATTATTTTA-TCCTTTAAATTTCTATTTTTGTT
* * * *
54056 AATTTAGTCCCTTAAGTTTATTTTTTGTTATTTTAGTCCTTTAAATTTTTATTCTTGTT
1 ATTTTAGTCCCTTAAGTTTATTTTTTATTATTTTA-TCCTTTAAATTTCTATTTTTGTT
*
54115 ATTTTAGTCCCTTGAATCTTTATTTTT
1 ATTTTAGTCCCTT-AA-GTTTATTTTT
54142 GGTATTTAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
57 26 0.21
58 23 0.19
59 23 0.19
60 40 0.33
61 9 0.07
ACGTcount: A:0.21, C:0.12, G:0.08, T:0.59
Consensus pattern (58 bp):
ATTTTAGTCCCTTAAGTTTATTTTTTATTATTTTATCCTTTAAATTTCTATTTTTGTT
Found at i:54148 original size:30 final size:28
Alignment explanation
Indices: 53938--54148 Score: 158
Period size: 30 Copynumber: 7.1 Consensus size: 28
53928 TTGTAATTAC
* *
53938 ATTTTAGTCCCTTAAGTTTATGGTTTTTTT
1 ATTTTAGTCCCTTAATTTTAT--TTTTGTT
*
53968 ATTTTA-TCCCATTAAATTACTATTTTTGTT
1 ATTTTAGTCCC-TT-AATT-TTATTTTTGTT
* **
53998 ATTTTAGTCACTTAAGTTTCTATTTTTACT
1 ATTTTAGTCCCTTAA-TTT-TATTTTTGTT
* *
54028 ATTTTAGGCCTTTAAATTTCTA-TTTT-TT
1 ATTTTAGTCCCTT-AATTT-TATTTTTGTT
* *
54056 AATTTAGTCCCTTAAGTTTATTTTTTGTT
1 ATTTTAGTCCCTTAATTTTA-TTTTTGTT
* *
54085 ATTTTAGTCCTTTAAATTTTTATTCTTGTT
1 ATTTTAGTCCCTT-AA-TTTTATTTTTGTT
*
54115 ATTTTAGTCCCTTGAATCTTTATTTTTGGT
1 ATTTTAGTCCCTT-AAT-TTTATTTTTGTT
54145 ATTT
1 ATTT
54149 AATTTTATCT
Statistics
Matches: 145, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
26 2 0.01
27 4 0.03
28 15 0.10
29 24 0.17
30 85 0.59
31 12 0.08
32 3 0.02
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.59
Consensus pattern (28 bp):
ATTTTAGTCCCTTAATTTTATTTTTGTT
Found at i:57379 original size:5 final size:5
Alignment explanation
Indices: 57369--57489 Score: 54
Period size: 5 Copynumber: 23.8 Consensus size: 5
57359 TAAAGCGAAG
* *
57369 AGAAA AGAAA A-ACAA AGAGAA A-AGA AGCAA AGAAA A-AAA AGAGCAA
1 AGAAA AGAAA AGA-AA AGA-AA AGAAA AGAAA AGAAA AGAAA AGA--AA
* * ** * *
57415 AGAAA AAAAA AGCAA AGAAA AGAAA A-AAA CCAAA ACAAA GGAAAA AGCAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AG-AAA AG-AAA
* *
57466 AGAAAA AGCAA AGAGA A-AAA AGAA
1 AG-AAA AGAAA AGAAA AGAAA AGAA
57490 GACAAGAAGT
Statistics
Matches: 87, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
4 13 0.15
5 51 0.59
6 18 0.21
7 5 0.06
ACGTcount: A:0.75, C:0.07, G:0.17, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:57386 original size:17 final size:17
Alignment explanation
Indices: 57360--57440 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 17
57350 AGATCAAATT
*
57360 AAAGCGAAGAGAAAAGA
1 AAAGCAAAGAGAAAAGA
*
57377 AAAACAAAGAGAAAAG-
1 AAAGCAAAGAGAAAAGA
57393 -AAGCAAAGA-AAAA-A
1 AAAGCAAAGAGAAAAGA
57407 AAGAGCAAAGA-AAAA-A
1 AA-AGCAAAGAGAAAAGA
57423 AAAGC-AA-AGAAAAGA
1 AAAGCAAAGAGAAAAGA
57438 AAA
1 AAA
57441 AAACCAAAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
13 1 0.02
14 10 0.18
15 16 0.29
16 15 0.27
17 14 0.25
ACGTcount: A:0.74, C:0.06, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAGCAAAGAGAAAAGA
Found at i:57393 original size:24 final size:24
Alignment explanation
Indices: 57366--57489 Score: 102
Period size: 24 Copynumber: 5.3 Consensus size: 24
57356 AATTAAAGCG
57366 AAGAGAAAAGAAAAACAAAGAGAA
1 AAGAGAAAAGAAAAACAAAGAGAA
* *
57390 AAGAAGCAAAGAAAAA-AAAGAGCA
1 AAG-AGAAAAGAAAAACAAAGAGAA
*
57414 AAGA-AAAA-AAAAGC-AA-AGAA
1 AAGAGAAAAGAAAAACAAAGAGAA
*
57434 AAGA-AAAAAACCAAAACAAAG-GAA
1 AAGAGAAAAGA--AAAACAAAGAGAA
57458 AA-AGCAAAAGAAAAAGCAAAGAGAA
1 AAGAG-AAAAGAAAAA-CAAAGAGAA
*
57483 AAAAGAA
1 AAGAGAA
57490 GACAAGAAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
20 11 0.14
21 7 0.09
22 3 0.04
23 10 0.12
24 25 0.31
25 23 0.28
26 2 0.02
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (24 bp):
AAGAGAAAAGAAAAACAAAGAGAA
Found at i:57401 original size:15 final size:15
Alignment explanation
Indices: 57369--57441 Score: 94
Period size: 15 Copynumber: 4.7 Consensus size: 15
57359 TAAAGCGAAG
57369 AGAAAAGAAAAA-CAA
1 AGAAAA-AAAAAGCAA
* *
57384 AGAGAAAAGAAGCAA
1 AGAAAAAAAAAGCAA
57399 AGAAAAAAAAGAGCAA
1 AGAAAAAAAA-AGCAA
57415 AGAAAAAAAAAGCAA
1 AGAAAAAAAAAGCAA
57430 AGAAAAGAAAAA
1 AGAAAA-AAAAA
57442 AACCAAAACA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
14 4 0.08
15 27 0.53
16 20 0.39
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAGCAA
Found at i:57413 original size:16 final size:16
Alignment explanation
Indices: 57388--57440 Score: 81
Period size: 16 Copynumber: 3.2 Consensus size: 16
57378 AAACAAAGAG
57388 AAAAGAAGCAAAGAAAA
1 AAAAG-AGCAAAGAAAA
57405 AAAAGAGCAAAGAAAA
1 AAAAGAGCAAAGAAAA
57421 AAAA-AGCAAAGAAAA
1 AAAAGAGCAAAGAAAA
57436 GAAAA
1 -AAAA
57441 AAACCAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.31
16 19 0.54
17 5 0.14
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAGCAAAGAAAA
Found at i:57441 original size:17 final size:17
Alignment explanation
Indices: 57386--57471 Score: 81
Period size: 18 Copynumber: 5.1 Consensus size: 17
57376 AAAAACAAAG
57386 AGAAAAGAAGCAAAGAAA
1 AGAAAA-AAGCAAAGAAA
*
57404 A-AAAAGAGCAAAG-AA
1 AGAAAAAAGCAAAGAAA
57419 A-AAAAAAGCAAAGAAA
1 AGAAAAAAGCAAAGAAA
*
57435 AGAAAAAAACCAAA-ACAA
1 AG-AAAAAAGCAAAGA-AA
*
57453 AGGAAAAAGCAAAAGAAA
1 AGAAAAAAGC-AAAGAAA
57471 A
1 A
57472 AGCAAAGAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
15 14 0.25
16 10 0.18
17 11 0.19
18 21 0.37
19 1 0.02
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAAAAAAGCAAAGAAA
Found at i:57472 original size:13 final size:12
Alignment explanation
Indices: 57371--57485 Score: 61
Period size: 12 Copynumber: 9.8 Consensus size: 12
57361 AAGCGAAGAG
57371 AAAAGAAAAA-C
1 AAAAGAAAAAGC
57382 AAAGAGAAAAGAAGC
1 AAA-AG-AAA-AAGC
57397 -AAAG-AAAA--
1 AAAAGAAAAAGC
*
57405 AAAAGAGCAAAG-
1 AAAAGA-AAAAGC
57417 AAAA-AAAAAGC
1 AAAAGAAAAAGC
57428 -AAAG-AAAAG-
1 AAAAGAAAAAGC
* *
57437 AAAAAAACCAAAAC
1 AAAAGAA--AAAGC
*
57451 AAAGGAAAAAGC
1 AAAAGAAAAAGC
57463 AAAAGAAAAAGC
1 AAAAGAAAAAGC
57475 AAAGAGAAAAA
1 AAA-AGAAAAA
57486 AGAAGACAAG
Statistics
Matches: 80, Mismatches: 8, Indels: 30
0.68 0.07 0.25
Matches are distributed among these distances:
9 4 0.05
10 17 0.21
11 10 0.12
12 24 0.30
13 15 0.19
14 9 0.11
15 1 0.01
ACGTcount: A:0.76, C:0.08, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGC
Found at i:58836 original size:38 final size:38
Alignment explanation
Indices: 58788--58866 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
58778 AAAACCAGAT
* * *
58788 TTTATCTCGCTTGAGATGGTTTCACTCGAAATAGAAGA
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
*
58826 TTTATCTCGCTTGAGATAGTTTCGCTCGAAACAAAAGA
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
58864 TTT
1 TTT
58867 TAAGAAACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (38 bp):
TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
Found at i:58958 original size:42 final size:41
Alignment explanation
Indices: 58899--59024 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 41
58889 AAGGGTTTCT
* *
58899 TGATGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTTGAGCG
1 TGATG-GTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
*
58941 TGATGCGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
* * * * * *
58983 AGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGAGCA
1 TGATGGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
59024 T
1 T
59025 AATGTTTTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 31 0.42
42 42 0.58
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (41 bp):
TGATGGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
Found at i:58973 original size:20 final size:20
Alignment explanation
Indices: 58948--59022 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
58938 GCGTGATGCG
*
58948 TAAGTCCTTCGGGCCATCTA
1 TAAGTCCTTCGAGCCATCTA
* * **
58968 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCCTTCGAGCCATCT-A
*
58989 TAAGTCCTTCGAGCCATCCA
1 TAAGTCCTTCGAGCCATCTA
*
59009 TAAGACCTTCGAGC
1 TAAGTCCTTCGAGC
59023 ATAATGTTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAGTCCTTCGAGCCATCTA
Found at i:59488 original size:67 final size:67
Alignment explanation
Indices: 59377--59733 Score: 411
Period size: 67 Copynumber: 5.4 Consensus size: 67
59367 CAAATTTTAT
* * * *
59377 CTTGAGACGGTTTCTCTTGAAACA-AAAGTCTTTAAATCTATTTCCCTTGAAACAAAATTTAGTC
1 CTTGAGACAGTTTCTCTTGAAACACAAA-TCTTTAAGTCTGTTTCCCTTGAAACAAAATTTTGTC
59441 TCC
65 TCC
* *
59444 CTTGAGACAGTTTCTCTTGAAACACAAGTCTTTAAGTCTGTTTCCCTTGGAACAAAATTTTGTCT
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTAAGTCTGTTTCCCTTGAAACAAAATTTTGTCT
59509 CC
66 CC
* * * *
59511 CTTGAGACAGTTCCTCTTGAAACACAAATCTTTGAGATC-GTTTCCCTTGAAAC-GAATTTTATC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTAAG-TCTGTTTCCCTTGAAACAAAATTTTGTC
59574 TCC
65 TCC
* * * * * *
59577 CTTGAGACGGTTTCCCTTGGAACACCAATCTTTGAA-TATATTTCCCTTGAAACAAAATTTTGTC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTT-AAGTCTGTTTCCCTTGAAACAAAATTTTGTC
*
59641 TCT
65 TCC
* * * * *
59644 CTTGAGGCAGTTTCTCTTGAAATACAAATCTTTGAGATC-GTTTCCCTTAAAAC-AAATTTTGCC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTAAG-TCTGTTTCCCTTGAAACAAAATTTTGTC
*
59707 TCT
65 TCC
* *
59710 CTTAAGACAGTTTCCCTTGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
59734 AATTTTGTTT
Statistics
Matches: 245, Mismatches: 38, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
65 1 0.00
66 85 0.35
67 154 0.63
68 5 0.02
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (67 bp):
CTTGAGACAGTTTCTCTTGAAACACAAATCTTTAAGTCTGTTTCCCTTGAAACAAAATTTTGTCT
CC
Found at i:59621 original size:133 final size:133
Alignment explanation
Indices: 59377--59733 Score: 461
Period size: 133 Copynumber: 2.7 Consensus size: 133
59367 CAAATTTTAT
* * * *
59377 CTTGAGACGGTTTCTCTTGAAACA-AAAGTCTTT-AAATCTATTTCCCTTGAAACAAAATTTAGT
1 CTTGAGACAGTTTCTCTTGAAACACAAA-TCTTTGAGATC-GTTTCCCTTGAAACAAATTTTA-T
* * * *
59440 CTCCCTTGAGACAGTTTCTCTTGAAACACAAGTCTTTAAGTCTGTTTCCCTTGGAACAAAATTTT
63 CTCCCTTGAGACAGTTTCCCTTGAAACACAAGTCTTTAAGTATATTTCCCTTGAAACAAAATTTT
59505 GTCTCC
128 GTCTCC
* *
59511 CTTGAGACAGTTCCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACGAATTTTATCTC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTC
* *
59576 CCTTGAGACGGTTTCCCTTGGAACACCAA-TCTTTGAA-TATATTTCCCTTGAAACAAAATTTTG
66 CCTTGAGACAGTTTCCCTTGAAACA-CAAGTCTTT-AAGTATATTTCCCTTGAAACAAAATTTTG
*
59639 TCTCT
129 TCTCC
* * * **
59644 CTTGAGGCAGTTTCTCTTGAAATACAAATCTTTGAGATCGTTTCCCTTAAAACAAATTTTGCCTC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTC
* *
59709 TCTTAAGACAGTTTCCCTTGAAACA
66 CCTTGAGACAGTTTCCCTTGAAACA
59734 AATTTTGTTT
Statistics
Matches: 195, Mismatches: 24, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
133 137 0.70
134 51 0.26
135 7 0.04
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (133 bp):
CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTATCTC
CCTTGAGACAGTTTCCCTTGAAACACAAGTCTTTAAGTATATTTCCCTTGAAACAAAATTTTGTC
TCC
Found at i:59786 original size:37 final size:36
Alignment explanation
Indices: 59617--59878 Score: 236
Period size: 36 Copynumber: 7.4 Consensus size: 36
59607 TTTGAATATA
*
59617 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGGCAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
59654 TTTCTCTTGAAATACAAA-------TCT-TTGAGATC-G
1 TTTCCCTTG-AA-ACAAATTTTGTCTCTCTTGAGA-CAG
* * *
59684 TTTCCCTTAAAACAAATTTTGCCTCTCTTAAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
59720 TTTCCCTTGAAACAAATTTTGTTTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
59756 TTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACGG
1 TTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
** * * *
59793 TTTCTTTTAAAAAAAAATTTTGTCTGTCTTGAGACAG
1 TTTCCCTT-GAAACAAATTTTGTCTCTCTTGAGACAG
* * *
59830 TTTCCCTTGAAACAAGTTTTGTCTCTCTTGATACGG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
59866 TTTCTCTTGAAAC
1 TTTCCCTTGAAAC
59879 CATCATACCC
Statistics
Matches: 183, Mismatches: 28, Indels: 29
0.76 0.12 0.12
Matches are distributed among these distances:
28 5 0.03
29 2 0.01
30 13 0.07
31 4 0.02
35 4 0.02
36 86 0.47
37 56 0.31
38 11 0.06
39 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:60635 original size:16 final size:18
Alignment explanation
Indices: 60598--60641 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 18
60588 AAAAATGAGG
60598 AAGAAAAAGAGAACACAA
1 AAGAAAAAGAGAACACAA
*
60616 AAGAACAAGAG-ACA-AA
1 AAGAAAAAGAGAACACAA
60632 AAGAAAAAGA
1 AAGAAAAAGA
60642 AAGCAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 3 0.12
18 10 0.42
ACGTcount: A:0.73, C:0.09, G:0.18, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAGAACACAA
Found at i:61475 original size:60 final size:60
Alignment explanation
Indices: 61401--61533 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 60
61391 GTAATTACTA
* * *
61401 TTTACTCCCTTAAGTTTCTATTTTTACTATTTTGGCCCTTTAAATTTATATTTTTGTTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
* * * * *
61461 TTTAGTCCCTTAAGTTTTTGTTTTTTCTATTTTAGTCCTTTAAATTTCTATTCTTGTTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
*
61521 TTTAGTACCTTAA
1 TTTAGTCCCTTAA
61534 ATGTTTATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.59
Consensus pattern (60 bp):
TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
Found at i:61522 original size:30 final size:30
Alignment explanation
Indices: 61401--61552 Score: 139
Period size: 30 Copynumber: 5.1 Consensus size: 30
61391 GTAATTACTA
* * **
61401 TTTACTCCCTTAAGTTTCTATTTTTACTAT
1 TTTAGTCCCTTAAATTTCTATTTTTGTTAT
* *
61431 TTT-GGCCCTTTAAATTTATATTTTTGTTAT
1 TTTAGTCCC-TTAAATTTCTATTTTTGTTAT
* * *
61461 TTTAGTCCCTTAAGTTTTTGTTTTT-TCTAT
1 TTTAGTCCCTTAAATTTCTATTTTTGT-TAT
* *
61491 TTTAGTCCTTTAAATTTCTATTCTTGTTAT
1 TTTAGTCCCTTAAATTTCTATTTTTGTTAT
* *
61521 TTTAGTACCTTAAATGTT-TATTTTTGGTAT
1 TTTAGTCCCTTAAAT-TTCTATTTTTGTTAT
61551 TT
1 TT
61553 AATTTTATCT
Statistics
Matches: 98, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
29 4 0.04
30 87 0.89
31 7 0.07
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.60
Consensus pattern (30 bp):
TTTAGTCCCTTAAATTTCTATTTTTGTTAT
Found at i:64002 original size:38 final size:37
Alignment explanation
Indices: 63914--64312 Score: 125
Period size: 38 Copynumber: 10.6 Consensus size: 37
63904 TTATATATAC
* **
63914 ATATATATTACATAG-TTTGCGAATGATTTTTGAAAT
1 ATATATATTATATAGTTTTGAAAATGATTTTTGAAAT
63950 ATATATAATATATATAGTTTTGAAAATGATTTTTGAAA-
1 ATATAT-AT-TATATAGTTTTGAAAATGATTTTTGAAAT
* * **
63988 ATGGATATATTATATTGTTTTG-AAATCATTTTAAAAACT
1 AT--ATATATTATATAGTTTTGAAAATGATTTTTGAAA-T
* * * * ** *
64027 -TATATAATATTTGGGTTTT-AAATTTTTTTTTTTAAA-
1 ATATATATTATAT-AGTTTTGAAA-ATGATTTTTGAAAT
* * * * ***
64063 ATTATATAATATATGGTTTTTTAAAA-AAAAATT-AAA-
1 A-TATATATTATATAG-TTTTGAAAATGATTTTTGAAAT
* * * *
64099 ATATATAATATATAGTTTTTAAAA-CA-TGTTGAAAAT
1 ATATATATTATATAGTTTTGAAAATGATTTTTG-AAAT
* * *
64135 ATATATAAATTATATATAGTTTTTAAAA-CATTTTTTAAATAT
1 ATATAT--A-T-TATATAGTTTTGAAAATGA-TTTTTGAA-AT
* *
64177 ATATATATATATATAGTTTTTAAAA-CA-TTTTGAAAAT
1 ATATATAT-TATATAGTTTTGAAAATGATTTTTG-AAAT
* *
64214 ATATATATAATATATAGTTTTTAAAA-CA-TTTTGAAAAT
1 ATATATAT--TATATAGTTTTGAAAATGATTTTTG-AAAT
*
64252 ATATATATAATATATAGTTTT-AAAA-CA-TTTTGAAAAT
1 ATATATAT--TATATAGTTTTGAAAATGATTTTTG-AAAT
* * *
64289 ATATATAATATATATTTTTTAAAA
1 ATATATATTATATAGTTTTGAAAA
64313 CATTTTGAAA
Statistics
Matches: 304, Mismatches: 32, Indels: 54
0.78 0.08 0.14
Matches are distributed among these distances:
33 2 0.01
34 10 0.03
35 26 0.09
36 29 0.10
37 62 0.20
38 96 0.32
39 43 0.14
40 23 0.08
41 2 0.01
42 11 0.04
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (37 bp):
ATATATATTATATAGTTTTGAAAATGATTTTTGAAAT
Found at i:64185 original size:75 final size:75
Alignment explanation
Indices: 64096--64323 Score: 333
Period size: 75 Copynumber: 3.0 Consensus size: 75
64086 AAAAAAAATT
*
64096 AAAATATATA-ATATATAGTTTTTAAAACATGTTGAAAATATATATAAATTATATATAGTTTTTA
1 AAAATATATATATATATAGTTTTTAAAACATTTTGAAAATATATAT-AATTATATATAGTTTTTA
*
64160 AAACATTTTTTA
65 AAACA-TTTTGA
*
64172 AATATATATATATATATATAGTTTTTAAAACATTTTGAAAATATATAT-ATAATATATAGTTTTT
1 AA-A-ATATATATATATATAGTTTTTAAAACATTTTGAAAATATATATAATTATATATAGTTTTT
64236 AAAACATTTTGA
64 AAAACATTTTGA
64248 AAATATATATATAATATATAG-TTTTAAAACATTTTGAAAATATATATAA-TATATAT--TTTTT
1 AAA-ATATATAT-ATATATAGTTTTTAAAACATTTTGAAAATATATATAATTATATATAGTTTTT
64309 AAAACATTTTGA
64 AAAACATTTTGA
64321 AAA
1 AAA
64324 TTTAATTTTA
Statistics
Matches: 143, Mismatches: 4, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
73 20 0.14
75 42 0.29
76 18 0.13
77 22 0.15
78 7 0.05
79 34 0.24
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (75 bp):
AAAATATATATATATATAGTTTTTAAAACATTTTGAAAATATATATAATTATATATAGTTTTTAA
AACATTTTGA
Found at i:64338 original size:37 final size:38
Alignment explanation
Indices: 64099--64324 Score: 359
Period size: 38 Copynumber: 5.9 Consensus size: 38
64089 AAAAATTAAA
*
64099 ATATATAATATATAGTTTTTAAAACATGTTGAAAATAT
1 ATATATAATATATAGTTTTTAAAACATTTTGAAAATAT
* **
64137 ATATAAATTATATATAGTTTTTAAAACATTTTTTAAATAT
1 ATAT--ATAATATATAGTTTTTAAAACATTTTGAAAATAT
64177 ATATATATATATATAGTTTTTAAAACATTTTGAAAATAT
1 ATATATA-ATATATAGTTTTTAAAACATTTTGAAAATAT
64216 ATATATAATATATAGTTTTTAAAACATTTTGAAAATAT
1 ATATATAATATATAGTTTTTAAAACATTTTGAAAATAT
64254 ATATATAATATATAG-TTTTAAAACATTTTG-AAA-AT
1 ATATATAATATATAGTTTTTAAAACATTTTGAAAATAT
*
64289 ATATATAATATATATTTTTTAAAACATTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAACATTTTGAAAAT
64325 TTAATTTTAT
Statistics
Matches: 174, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
35 16 0.09
36 18 0.10
37 18 0.10
38 52 0.30
39 36 0.21
40 34 0.20
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (38 bp):
ATATATAATATATAGTTTTTAAAACATTTTGAAAATAT
Found at i:65456 original size:32 final size:30
Alignment explanation
Indices: 65390--65456 Score: 71
Period size: 32 Copynumber: 2.2 Consensus size: 30
65380 CTGTAAATTT
* *
65390 TTAGTCATTCATTTTTTAATATTTTTATTT
1 TTAGTCATTCATTTTTTAATATTTTTAATG
* * *
65420 TTAGTTATTCATTTTCTTTATTCTTTTTAATG
1 TTAGTCATTCA-TTT-TTTAATATTTTTAATG
65452 TTAGT
1 TTAGT
65457 ATGTCTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 10 0.33
31 3 0.10
32 17 0.57
ACGTcount: A:0.21, C:0.07, G:0.06, T:0.66
Consensus pattern (30 bp):
TTAGTCATTCATTTTTTAATATTTTTAATG
Found at i:67485 original size:21 final size:21
Alignment explanation
Indices: 67461--67507 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
67451 CCGGAAGAGG
* * *
67461 AGGAGGAGCACGAGAAGTGGT
1 AGGAGGAGCACAAGAAGAGCT
67482 AGGAGGAGCACAAGAAGAGCT
1 AGGAGGAGCACAAGAAGAGCT
67503 AGGAG
1 AGGAG
67508 CAGCTCGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.45, T:0.06
Consensus pattern (21 bp):
AGGAGGAGCACAAGAAGAGCT
Found at i:68077 original size:19 final size:18
Alignment explanation
Indices: 68041--68077 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
68031 TCAGAGAAAA
*
68041 TTTTGAAAAAATGTTTGT
1 TTTTGAAAAAATGATTGT
68059 TTTTGAAAAAATTGATTGT
1 TTTTGAAAAAA-TGATTGT
68078 AAAATATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (18 bp):
TTTTGAAAAAATGATTGT
Found at i:68494 original size:44 final size:45
Alignment explanation
Indices: 68413--68536 Score: 132
Period size: 45 Copynumber: 2.8 Consensus size: 45
68403 AAAACCCGAC
** * * *
68413 GGATGCATCGATGCA-TGGCCTTGTGCATCGATGCACATTC-AA-
1 GGATGCATCGATGCACTTTCATAGTGTATCGATGCACATTCAAAG
*
68455 GGAGTGCATCGGTGCA-TCTTCAT-GATGTATCGATGCACATTCAAAG
1 GGA-TGCATCGATGCACT-TTCATAG-TGTATCGATGCACATTCAAAG
68501 GGATGCATCGATGCACTTTCATAGTGTATCGATGCA
1 GGATGCATCGATGCACTTTCATAGTGTATCGATGCA
68537 TTATGCACAA
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
42 3 0.04
43 13 0.19
44 18 0.26
45 30 0.43
46 5 0.07
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (45 bp):
GGATGCATCGATGCACTTTCATAGTGTATCGATGCACATTCAAAG
Found at i:68497 original size:21 final size:23
Alignment explanation
Indices: 68435--68521 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 23
68425 GCATGGCCTT
68435 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
68458 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
68480 -TGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
*
68502 GATGCATCGATGCACTTTCA
1 G-TGCATCGATGCACATTCA
68522 TAGTGTATCG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.25
22 3 0.06
23 18 0.35
24 16 0.31
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:68533 original size:21 final size:23
Alignment explanation
Indices: 68439--68536 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 23
68429 GGCCTTGTGC
*
68439 ATCGATGCACATTC-AAGGAGTGC
1 ATCGATGCACATTCAAAGGA-TGT
* *
68462 ATCGGTGCATC-TTC--ATGATGT
1 ATCGATGCA-CATTCAAAGGATGT
*
68483 ATCGATGCACATTCAAAGGGATGC
1 ATCGATGCACATTCAAA-GGATGT
* *
68507 ATCGATGCACTTTCATA-G-TGT
1 ATCGATGCACATTCAAAGGATGT
68528 ATCGATGCA
1 ATCGATGCA
68537 TTATGCACAA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 24 0.39
22 4 0.07
23 12 0.20
24 20 0.33
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (23 bp):
ATCGATGCACATTCAAAGGATGT
Found at i:74490 original size:64 final size:63
Alignment explanation
Indices: 74356--74499 Score: 157
Period size: 64 Copynumber: 2.3 Consensus size: 63
74346 GAAAAAGCCT
* * * * * * *
74356 GGGTGCATCGATGCATGGCTTGTGTATCGGTGCATAAAATCAATTCGATGTTAGAATATATAT
1 GGGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAAGCAATTCGATGTTAGAATAAACAA
* *
74419 GGAGTGCATCGATGCATGG-TATGTGCATCGGTACACAAAAGCCATTCGATGTTCA-ATTAAAAC
1 GG-GTGCATCGATGCATGGCT-TGTGCATCGGTACACAAAAGCAATTCGATGTT-AGAAT-AAAC
74482 AA
62 AA
74484 GGGTGCATCGATGCAT
1 GGGTGCATCGATGCAT
74500 TGATTCATGC
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
63 3 0.04
64 59 0.87
65 6 0.09
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (63 bp):
GGGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAAGCAATTCGATGTTAGAATAAACAA
Found at i:74916 original size:24 final size:24
Alignment explanation
Indices: 74888--74942 Score: 87
Period size: 23 Copynumber: 2.3 Consensus size: 24
74878 ATATATATTT
74888 TATTTTTCAT-TTTGATTTATTTAA
1 TATTTTTC-TCTTTGATTTATTTAA
74912 TATTTTT-TCTTTGATTTATTTAA
1 TATTTTTCTCTTTGATTTATTTAA
74935 TATTTTTC
1 TATTTTTC
74943 GAATTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.03
23 21 0.72
24 7 0.24
ACGTcount: A:0.22, C:0.05, G:0.04, T:0.69
Consensus pattern (24 bp):
TATTTTTCTCTTTGATTTATTTAA
Found at i:74941 original size:23 final size:23
Alignment explanation
Indices: 74898--74941 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
74888 TATTTTTCAT
74898 TTTGATTTATTTAATATTTTTTC
1 TTTGATTTATTTAATATTTTTTC
74921 TTTGATTTATTTAATATTTTT
1 TTTGATTTATTTAATATTTTT
74942 CGAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTGATTTATTTAATATTTTTTC
Found at i:76546 original size:17 final size:17
Alignment explanation
Indices: 76526--76558 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
76516 TTACCTTACA
76526 TATTTGTATAT-CTTATT
1 TATTT-TATATACTTATT
76543 TATTTTATATACTTAT
1 TATTTTATATACTTAT
76559 GTTGCATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTTTATATACTTATT
Found at i:77675 original size:14 final size:15
Alignment explanation
Indices: 77645--77676 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
77635 TTCTCGATCC
77645 TTAAGATTAATTTTT
1 TTAAGATTAATTTTT
*
77660 TTAATATTAATTTTT
1 TTAAGATTAATTTTT
77675 TT
1 TT
77677 GTTGCCTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TTAAGATTAATTTTT
Found at i:77892 original size:26 final size:26
Alignment explanation
Indices: 77852--77904 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
77842 TTCGAGAAGT
*
77852 GAAATTGAATAATAATTGAATAGACA
1 GAAATTGAATAATAATTAAATAGACA
*
77878 GAAATTGAATGATAATTAAATAGACA
1 GAAATTGAATAATAATTAAATAGACA
77904 G
1 G
77905 GCGGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (26 bp):
GAAATTGAATAATAATTAAATAGACA
Found at i:78617 original size:8 final size:8
Alignment explanation
Indices: 78604--78648 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
78594 AACAAGTCCC
78604 TTTTGTTT
1 TTTTGTTT
78612 TTTTGTCTT
1 TTTTGT-TT
78621 TTTT-TGTT
1 TTTTGT-TT
78629 TTTTGTTT
1 TTTTGTTT
*
78637 TTTCGTTT
1 TTTTGTTT
78645 TTTT
1 TTTT
78649 TTGGGTGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.84
Consensus pattern (8 bp):
TTTTGTTT
Found at i:78636 original size:25 final size:25
Alignment explanation
Indices: 78604--78651 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
78594 AACAAGTCCC
*
78604 TTTTGTTTTTTTGTCTTTTTTTGTT
1 TTTTGTTTTTTCGTCTTTTTTTGTT
*
78629 TTTTGTTTTTTCGTTTTTTTTTG
1 TTTTGTTTTTTCGTCTTTTTTTG
78652 GGTGACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.83
Consensus pattern (25 bp):
TTTTGTTTTTTCGTCTTTTTTTGTT
Found at i:78647 original size:17 final size:16
Alignment explanation
Indices: 78604--78651 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
78594 AACAAGTCCC
*
78604 TTTTGTTTTTTTGTCT
1 TTTTTTTTTTTTGTCT
*
78620 TTTTTTGTTTTTTGTTT
1 TTTTTT-TTTTTTGTCT
78637 TTTCGTTTTTTTTTG
1 TTT--TTTTTTTTTG
78652 GGTGACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 7 0.26
19 3 0.11
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTTTGTCT
Found at i:84899 original size:3 final size:3
Alignment explanation
Indices: 84893--84926 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
84883 AATTATTATT
84893 ATC ATC ATC ATC ATC ATC ATC ATC ATC -TC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
84927 ATTAACTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Done.