Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006964.1 Corchorus capsularis cultivar CVL-1 contig06985, 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: 54823
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:864 original size:174 final size:175
Alignment explanation
Indices: 649--963 Score: 519
Period size: 174 Copynumber: 1.8 Consensus size: 175
639 AATCTAAACA
* * *
649 TATATTTTTTTTGCAATTAGATCCCTAAACTTTAGAATTTTTCAAATCTATCCCCCTCATTTATA
1 TATAATTTTTTTGCAATTAGATCCCTAAACTTTACAATTTTTCAAATCTATCCCCCTAATTTATA
* *
714 GATTTAATGCATTCACATCCCTCATTCATATATTT-ACACAAAATCAATTTTCACATGGCAATAC
66 GATCT-ATGCATTCACATCCCTCATTCATATATTTAACACAAAATCAATTTTAACATGGCAATAC
*
778 AAACTCATATCAAGCAACAAACACCAATCTACATTCTATAAGATAT
130 AAACTCACATCAAGCAACAAACACCAATCTACATTCTATAAGATAT
* *
824 TATAATTTTTTT-CAATTAGGTCCCTAAACTTGT-CAATTTTTCAATTCTATCCCCCTAATTTAT
1 TATAATTTTTTTGCAATTAGATCCCTAAACTT-TACAATTTTTCAAATCTATCCCCCTAATTTAT
887 AGATCTATGCATTCACATCCCTCATTCATATATTTAACACAAAATCAATTTTAACATGGCAATAC
65 AGATCTATGCATTCACATCCCTCATTCATATATTTAACACAAAATCAATTTTAACATGGCAATAC
952 AAACTCACATCA
130 AAACTCACATCA
964 CCAATCTACG
Statistics
Matches: 130, Mismatches: 8, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
173 29 0.22
174 89 0.68
175 12 0.09
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.37
Consensus pattern (175 bp):
TATAATTTTTTTGCAATTAGATCCCTAAACTTTACAATTTTTCAAATCTATCCCCCTAATTTATA
GATCTATGCATTCACATCCCTCATTCATATATTTAACACAAAATCAATTTTAACATGGCAATACA
AACTCACATCAAGCAACAAACACCAATCTACATTCTATAAGATAT
Found at i:1336 original size:12 final size:12
Alignment explanation
Indices: 1304--1431 Score: 104
Period size: 12 Copynumber: 10.9 Consensus size: 12
1294 TTTTTTTTGG
1304 CTTCAGGAACGA
1 CTTCAGGAACGA
1316 CTTTCAGGAACGA
1 C-TTCAGGAACGA
*
1329 CGTCAGG-A--A
1 CTTCAGGAACGA
*
1338 --TGAGGAACGA
1 CTTCAGGAACGA
* * *
1348 CATAAGGAATGA
1 CTTCAGGAACGA
*
1360 CTTAAGGAACGA
1 CTTCAGGAACGA
1372 CTTCAGGAACGA
1 CTTCAGGAACGA
*
1384 CTTTCAGGAATGA
1 C-TTCAGGAACGA
1397 CTTCAGGAACGA
1 CTTCAGGAACGA
**
1409 CGCCAGGAACGA
1 CTTCAGGAACGA
* *
1421 ATTAAGGAACG
1 CTTCAGGAACG
1432 GGAATATCTT
Statistics
Matches: 94, Mismatches: 15, Indels: 14
0.76 0.12 0.11
Matches are distributed among these distances:
7 4 0.04
8 1 0.01
9 1 0.01
10 1 0.01
11 1 0.01
12 63 0.67
13 23 0.24
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (12 bp):
CTTCAGGAACGA
Found at i:1345 original size:19 final size:19
Alignment explanation
Indices: 1321--1359 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1311 AACGACTTTC
* *
1321 AGGAACGACGTCAGGAATG
1 AGGAACGACATAAGGAATG
1340 AGGAACGACATAAGGAATG
1 AGGAACGACATAAGGAATG
1359 A
1 A
1360 CTTAAGGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.13, G:0.33, T:0.10
Consensus pattern (19 bp):
AGGAACGACATAAGGAATG
Found at i:2293 original size:10 final size:10
Alignment explanation
Indices: 2278--2302 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2268 CTAACCTTTC
2278 AAATCCTCTG
1 AAATCCTCTG
2288 AAATCCTCTG
1 AAATCCTCTG
2298 AAATC
1 AAATC
2303 TTCAAGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (10 bp):
AAATCCTCTG
Found at i:2651 original size:13 final size:13
Alignment explanation
Indices: 2629--2694 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
2619 TTAATTATTA
2629 TTGTATGTAATTT
1 TTGTATGTAATTT
*
2642 TTGTAAGTAATTT
1 TTGTATGTAATTT
2655 TT-TATGTTAATTAT
1 TTGTATG-TAATT-T
*
2669 TAGTGTATGTAATTG
1 T--TGTATGTAATTT
*
2684 TTGTAAGTAAT
1 TTGTATGTAAT
2695 ATTGTTTTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
12 3 0.07
13 28 0.64
14 2 0.05
15 1 0.02
16 6 0.14
17 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.55
Consensus pattern (13 bp):
TTGTATGTAATTT
Found at i:2760 original size:32 final size:32
Alignment explanation
Indices: 2719--2817 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
2709 AATATTTGTT
2719 GTCCTCAGGGGACGGCACGCCATGGACGTGGC
1 GTCCTCAGGGGACGGCACGCCATGGACGTGGC
* * **
2751 GTCCTCAGGGGACGGCAAGCCATGGCCGTATC
1 GTCCTCAGGGGACGGCACGCCATGGACGTGGC
**
2783 GTCCTCA-GGGACGGCACGCCCATGGGTGTGGC
1 GTCCTCAGGGGACGGCACG-CCATGGACGTGGC
2815 GTC
1 GTC
2818 TTGACAGGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 10 0.18
32 47 0.82
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (32 bp):
GTCCTCAGGGGACGGCACGCCATGGACGTGGC
Found at i:3246 original size:8 final size:7
Alignment explanation
Indices: 3228--3323 Score: 83
Period size: 8 Copynumber: 13.7 Consensus size: 7
3218 AATAGTACTA
3228 ATTAT-T
1 ATTATAT
3234 ATTATAGT
1 ATTATA-T
3242 ATTATAT
1 ATTATAT
3249 A-TATAT
1 ATTATAT
3255 ATATATAT
1 AT-TATAT
*
3263 ATAATAT
1 ATTATAT
*
3270 ATCATATT
1 ATTATA-T
3278 ATTATATT
1 ATTATA-T
3286 ATTATAT
1 ATTATAT
3293 ATTAT-T
1 ATTATAT
*
3299 ATCATAT
1 ATTATAT
*
3306 ATAATA-
1 ATTATAT
*
3312 ATAATAT
1 ATTATAT
3319 ATTAT
1 ATTAT
3324 GCGAGCCGGG
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
6 22 0.29
7 27 0.35
8 28 0.36
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (7 bp):
ATTATAT
Found at i:3251 original size:2 final size:2
Alignment explanation
Indices: 3244--3320 Score: 66
Period size: 2 Copynumber: 42.5 Consensus size: 2
3234 ATTATAGTAT
3244 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TCA TA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
3284 T- TA T- TA TA TA T- TA T- TA TCA TA TA TA -A TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
3320 T
1 T
3321 TATGCGAGCC
Statistics
Matches: 63, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
1 10 0.16
2 49 0.78
3 4 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3292 original size:36 final size:37
Alignment explanation
Indices: 3241--3323 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 37
3231 ATTATTATAG
* *
3241 TATTATA-TATATATATA-TATATATAATATATCATAT
1 TATTATATTATATATATATTAT-TATAATATATAATAA
*
3277 TATTATATTAT-TATATATTATTATCATATATAATAA
1 TATTATATTATATATATATTATTATAATATATAATAA
*
3313 TAATATATTAT
1 TATTATATTAT
3324 GCGAGCCGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 35 0.85
37 6 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (37 bp):
TATTATATTATATATATATTATTATAATATATAATAA
Found at i:3293 original size:44 final size:42
Alignment explanation
Indices: 3230--3323 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
3220 TAGTACTAAT
*
3230 TATTATTATAGTATTATATATATATATAT-ATATATAATATATCA
1 TATTATTATAGTATTATATAT-TAT-TATCATATATAATA-ATAA
*
3274 TATTATTATATTATTATATATTATTATCATATATAATAATAA
1 TATTATTATAGTATTATATATTATTATCATATATAATAATAA
3316 TA-TATTAT
1 TATTATTAT
3324 GCGAGCCGGG
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 6 0.13
42 8 0.17
43 13 0.28
44 20 0.43
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (42 bp):
TATTATTATAGTATTATATATTATTATCATATATAATAATAA
Found at i:7377 original size:13 final size:13
Alignment explanation
Indices: 7359--7383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7349 CTTGCAGAGA
7359 ATTCAAATGTGGG
1 ATTCAAATGTGGG
7372 ATTCAAATGTGG
1 ATTCAAATGTGG
7384 CCGTTGGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (13 bp):
ATTCAAATGTGGG
Found at i:9327 original size:21 final size:24
Alignment explanation
Indices: 9268--9348 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 24
9258 TTTAGTAATT
9268 AAATATATATTATTTATTTATTTTG-
1 AAATATATATTA-TTATTTA-TTTGA
*
9293 AACTCAT-TA-T-TTA-TTATTT-A
1 AAAT-ATATATTATTATTTATTTGA
9313 AAATATAT-TTATTATTTATTTGA
1 AAATATATATTATTATTTATTTGA
*
9336 TAATATATATTAT
1 AAATATATATTAT
9349 ATCTAAGATG
Statistics
Matches: 45, Mismatches: 3, Indels: 17
0.69 0.05 0.26
Matches are distributed among these distances:
19 2 0.04
20 8 0.18
21 6 0.13
22 9 0.20
23 8 0.18
24 5 0.11
25 5 0.11
26 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
AAATATATATTATTATTTATTTGA
Found at i:9343 original size:25 final size:25
Alignment explanation
Indices: 9298--9346 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9288 TTTTGAACTC
*
9298 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
9323 ATTATTTATT-TGATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
9347 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:10138 original size:26 final size:26
Alignment explanation
Indices: 10109--10230 Score: 126
Period size: 26 Copynumber: 4.7 Consensus size: 26
10099 TCGCACGCGC
10109 GAGGTCACGTGTGGAGTTGTACTTCG
1 GAGGTCACGTGTGGAGTTGTACTTCG
* * *
10135 GAGGTCATGTGTTGAAG--GTATCTGTTG
1 GAGGTCACGTG-TGGAGTTGTA-CT-TCG
10162 GAGGTCACGTGTGGAGTTGTACTTCG
1 GAGGTCACGTGTGGAGTTGTACTTCG
* *
10188 GAGATCACGTGTGG-GATCGTACGTT-G
1 GAGGTCACGTGTGGAG-TTGTAC-TTCG
10214 GAGGTCACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
10231 GACAGCTGGC
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
25 4 0.05
26 51 0.65
27 21 0.27
28 3 0.04
ACGTcount: A:0.17, C:0.13, G:0.39, T:0.30
Consensus pattern (26 bp):
GAGGTCACGTGTGGAGTTGTACTTCG
Found at i:10189 original size:53 final size:52
Alignment explanation
Indices: 10109--10230 Score: 174
Period size: 53 Copynumber: 2.3 Consensus size: 52
10099 TCGCACGCGC
* * * *
10109 GAGGTCACGTGTGGAGTTGTACTTCGGAGGTCATGTGT-TGAAGGTATCTGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGGGAACGTA-C-GTTG
*
10162 GAGGTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGGGATCGTACGTTG
1 GAGGTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGGGAACGTACGTTG
10214 GAGGTCACGTGTGGAGT
1 GAGGTCACGTGTGGAGT
10231 GACAGCTGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
52 21 0.33
53 37 0.59
54 5 0.08
ACGTcount: A:0.17, C:0.13, G:0.39, T:0.30
Consensus pattern (52 bp):
GAGGTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGGGAACGTACGTTG
Found at i:10314 original size:15 final size:15
Alignment explanation
Indices: 10270--10314 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
10260 CTTGTGGTCA
*
10270 TAGGTGGTCGAACGC
1 TAGGTGGTCGAGCGC
*
10285 CAGGTGGTCGAGCGC
1 TAGGTGGTCGAGCGC
*
10300 TAGGTGGTCGGGCGC
1 TAGGTGGTCGAGCGC
10315 CGGGCTTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (15 bp):
TAGGTGGTCGAGCGC
Found at i:11407 original size:15 final size:15
Alignment explanation
Indices: 11387--11416 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11377 TTCGTACTTT
*
11387 TATATATATTATAAA
1 TATATATATAATAAA
11402 TATATATATAATAAA
1 TATATATATAATAAA
11417 ATTAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATATATATAATAAA
Found at i:12420 original size:16 final size:16
Alignment explanation
Indices: 12399--12429 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12389 TTGAAAAATA
12399 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
12415 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
12430 AATTTGTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:12764 original size:16 final size:16
Alignment explanation
Indices: 12741--12878 Score: 181
Period size: 16 Copynumber: 8.7 Consensus size: 16
12731 CAAGTCATCT
*
12741 GGGT-TCGGGTTATTC
1 GGGTCTCGGGTCATTC
12756 GGGTCTCGGGTCATTC
1 GGGTCTCGGGTCATTC
* *
12772 GGGTCTCAGGTCATAC
1 GGGTCTCGGGTCATTC
*
12788 GGGTTTCGGGTCATTC
1 GGGTCTCGGGTCATTC
12804 GGGTCTCGGGTCATTC
1 GGGTCTCGGGTCATTC
* *
12820 GGGTTTCGGGTCATTT
1 GGGTCTCGGGTCATTC
*
12836 GGGTTTCGGGTCATTC
1 GGGTCTCGGGTCATTC
*
12852 GGGTCTCGGGTC-TACC
1 GGGTCTCGGGTCAT-TC
12868 GGGTCTCGGGT
1 GGGTCTCGGGT
12879 TGGACGGGTT
Statistics
Matches: 109, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
15 5 0.05
16 104 0.95
ACGTcount: A:0.07, C:0.21, G:0.38, T:0.33
Consensus pattern (16 bp):
GGGTCTCGGGTCATTC
Found at i:12871 original size:48 final size:48
Alignment explanation
Indices: 12712--12878 Score: 205
Period size: 48 Copynumber: 3.5 Consensus size: 48
12702 CATGCAGTTT
* ** * *
12712 TCTCGGTTCATTCGGGT-TACAAGTCATCTGGG-TTCGGGTTATTCGGG
1 TCTCGGGTCATTCGGGTCT-CGGGTCATATGGGTTTCGGGTCATTCGGG
* *
12759 TCTCGGGTCATTCGGGTCTCAGGTCATACGGGTTTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGGTCTCGGGTCATATGGGTTTCGGGTCATTCGGG
* *
12807 TCTCGGGTCATTCGGGTTTCGGGTCATTTGGGTTTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGGTCTCGGGTCATATGGGTTTCGGGTCATTCGGG
*
12855 TCTCGGGTC-TACCGGGTCTCGGGT
1 TCTCGGGTCAT-TCGGGTCTCGGGT
12879 TGGACGGGTT
Statistics
Matches: 106, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
47 27 0.25
48 79 0.75
ACGTcount: A:0.09, C:0.22, G:0.35, T:0.34
Consensus pattern (48 bp):
TCTCGGGTCATTCGGGTCTCGGGTCATATGGGTTTCGGGTCATTCGGG
Found at i:13350 original size:21 final size:21
Alignment explanation
Indices: 13325--13372 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
13315 TAGCCAATTT
13325 ATAATAGGTAAAATCATAACA
1 ATAATAGGTAAAATCATAACA
* *
13346 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATCATAACA
13367 ATAATA
1 ATAATA
13373 TAAATTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (21 bp):
ATAATAGGTAAAATCATAACA
Found at i:13501 original size:16 final size:16
Alignment explanation
Indices: 13480--13614 Score: 114
Period size: 16 Copynumber: 8.4 Consensus size: 16
13470 GGTTAATGTC
*
13480 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
13496 TCGGGTCATACGGGTC
1 TCGGGTCATTCGGGTT
* *
13512 TCGGGTCATTCAGCTT
1 TCGGGTCATTCGGGTT
* *
13528 TCGGGTTATT-TGGTT
1 TCGGGTCATTCGGGTT
*
13543 TACGGGTCATTCGGGTC
1 T-CGGGTCATTCGGGTT
13560 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* *
13576 GCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
* *
13592 ACGGGTTC-GTCGGGTT
1 TCGGG-TCATTCGGGTT
13608 TCGGGTC
1 TCGGGTC
13615 GGACGGGTTC
Statistics
Matches: 94, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
15 8 0.09
16 78 0.83
17 8 0.09
ACGTcount: A:0.08, C:0.20, G:0.37, T:0.35
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:13596 original size:48 final size:48
Alignment explanation
Indices: 13481--13614 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
13471 GTTAATGTCT
* * *
13481 CGGGTTATTCGGGTTTCGGGTCATACGGGTCTCGGGTCATTCAGCTTT
1 CGGGTTATTCGGGTTACGGGTCATTCGGGTCTCGGGTCATTCAGCTTG
* * * *
13529 CGGGTTATTTGGTTTACGGGTCATTCGGGTCTCGGGTCA-TCTGGGTTG
1 CGGGTTATTCGGGTTACGGGTCATTCGGGTCTCGGGTCATTC-AGCTTG
* * * *
13577 CGGGTCATTCGGGTCACGGGTTC-GTCGGGTTTCGGGTC
1 CGGGTTATTCGGGTTACGGG-TCATTCGGGTCTCGGGTC
13615 GGACGGGTTC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
47 2 0.03
48 67 0.94
49 2 0.03
ACGTcount: A:0.08, C:0.20, G:0.37, T:0.34
Consensus pattern (48 bp):
CGGGTTATTCGGGTTACGGGTCATTCGGGTCTCGGGTCATTCAGCTTG
Found at i:14203 original size:41 final size:43
Alignment explanation
Indices: 14140--14221 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 43
14130 CCCCCCTAAA
14140 AATTAAGGTAACAAATTAAATCT-AGATTTAGCCCCT-CTTAAT
1 AATTAAGGTAACAAATTAAATCTAAG-TTTAGCCCCTACTTAAT
14182 AATTAAGGTAA-AAATTAAATCTAAGTTTAGCCCCTACTTA
1 AATTAAGGTAACAAATTAAATCTAAGTTTAGCCCCTACTTA
14222 TAAATATGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
41 21 0.55
42 17 0.45
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (43 bp):
AATTAAGGTAACAAATTAAATCTAAGTTTAGCCCCTACTTAAT
Found at i:14772 original size:21 final size:19
Alignment explanation
Indices: 14746--14794 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
14736 ATAACTTGAA
*
14746 AACTTTTAGATAATCTTATTT
1 AACTTTTAG-TAAAC-TATTT
*
14767 AGCTTTTTAGTAAACTATTT
1 AAC-TTTTAGTAAACTATTT
14787 AACTTTTA
1 AACTTTTA
14795 TTGTAACTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.21
20 7 0.29
21 6 0.25
22 6 0.25
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (19 bp):
AACTTTTAGTAAACTATTT
Found at i:14933 original size:87 final size:85
Alignment explanation
Indices: 14836--15009 Score: 267
Period size: 87 Copynumber: 2.0 Consensus size: 85
14826 GTAAATTTTC
* *
14836 TTGGTAAGCTTATAAATTTTTCATTAAAGTTAAAAGCTTTTTAAATAATCTTCTTAAATTTATTT
1 TTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTCAAATAATCTTCTTAAATTTATTT
* *
14901 CAATGACCTCGTTTAAGACTTT
66 -AATCAACTCGTTTAAGA-TTT
* * *
14923 TTGGTAAGCTTATAAATTTTTCATTAAACTTGAAAGCTTTTCAAATAGTTTTCTTAAATTTATTT
1 TTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTCAAATAATCTTCTTAAATTTATTT
14988 AATCAACTCGTTTAAGATTT
66 AATCAACTCGTTTAAGATTT
15008 TT
1 TT
15010 AGTGATCTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
85 5 0.06
86 15 0.19
87 60 0.75
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (85 bp):
TTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTCAAATAATCTTCTTAAATTTATTT
AATCAACTCGTTTAAGATTT
Found at i:15023 original size:21 final size:22
Alignment explanation
Indices: 14999--15053 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
14989 ATCAACTCGT
* *
14999 TTAAGATTTTTAGTGATCTTA-
1 TTAAGATTTTTAGAGACCTTAC
*
15020 TTAACATGTTTTAGAGACCTTAC
1 TTAAGAT-TTTTAGAGACCTTAC
15043 TTAAG-TTTTTA
1 TTAAGATTTTTA
15054 TTTAGTGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.39
22 13 0.46
23 4 0.14
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (22 bp):
TTAAGATTTTTAGAGACCTTAC
Found at i:15095 original size:20 final size:21
Alignment explanation
Indices: 15072--15117 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
15062 CCTTGTAAGA
15072 TTTATAGTTAA-CTTATG-AAT
1 TTTATAG-TAACCTTATGAAAT
15092 TTTATAGTAACCTTATGAAAT
1 TTTATAGTAACCTTATGAAAT
15113 TTTAT
1 TTTAT
15118 TTTTAGTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.12
20 13 0.54
21 8 0.33
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.50
Consensus pattern (21 bp):
TTTATAGTAACCTTATGAAAT
Found at i:15563 original size:20 final size:20
Alignment explanation
Indices: 15526--15564 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15516 TATTTTGCTT
* *
15526 TTTTAGTAACATTGTTAAGC
1 TTTTAATAACATTATTAAGC
*
15546 TTTTAATAACTTTATTAAG
1 TTTTAATAACATTATTAAG
15565 ACTGCTTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTTAATAACATTATTAAGC
Found at i:31387 original size:517 final size:522
Alignment explanation
Indices: 30709--31995 Score: 2097
Period size: 529 Copynumber: 2.5 Consensus size: 522
30699 GCTAATGGTA
*
30709 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATTTATTTGTAATACTATCTATGAACAC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGTAATACTATCTATGAACAC
* * *
30774 ACTACTAACACACATTTGTATATTATGACATTGTGTAAACACTCAATTAAATTCTTTTAAGTAAT
66 ACTACT-A-ACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAAT
*
30839 TACAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGAT
129 TAGAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGAT
*
30904 CATTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCATCTCTCAATTTTCCACA
194 CATTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCATCTCTCAATTTGCCACA
* * * **
30969 GCTTTTGCCAGGGGGTTCTGTAAA-CC-C-G-C-GGTAAATTGAAAAGTTGTGGCAAAGGCCGTG
259 GCTTTTGCCACGGGATTCTGTAAACCCGCTGACAGGCAAATTGAAAAGTCATGG-AAAGGCCGTG
* * *
31029 CCAAATAGCCACGAATTTTCCCACGG-TTTTAAGAAAATCGTTTCAAAAACTGTGGCAAATATAG
323 CCAAACAGCCACGAATTTTCCCACGGTTTTTAAGAAAACCATTTCAAAAACTGTGGCAAATATAG
31093 AATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAATTCCCATAAAATTAAAGGTTT
388 AATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAATTCCCATAAAATTAAAGGTTT
* * * *
31158 TTATGGTGCCCTAATGTGTTTAGCTCGAGTATTTGATGTAGAGTTTAATGTAAAATAGTTTGGGG
453 TTATGGTACCCTAATGTGTTTAGCTCGAGTATTTAATGTAGAATTTAATGTAAAATAGTTCGGGG
31223 AGTGG
518 AGTGG
**
31228 AAAAAAATCAAAATTGTAAAGAGACTTAATTGGCTAAATGTATTTGTAATACTATCTATGAACAC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGTAATACTATCTATGAACAC
* *
31293 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAGATTTTTTTACGTAATTA
66 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
31358 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
131 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
* * *
31423 TTAGCCAATTACTGACTCATATAAGAGTAGGGTTTGAGATCAATCATCTCTCAATTTGCCACAGC
196 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCATCTCTCAATTTGCCACAGC
*
31488 TTTTGCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAGAGTCATGGAAAGGC
261 TTTTGCCACGGGATTCTGTAAACCCGCTG----A--CA-GGCAAATTGAAAAGTCATGGAAAGGC
* * *
31553 CGTGCCAAACATCCACGAATTTTCCCACGGTTTTTAAGATAACCATTTCAAAAACTGTGGTAAAT
319 CGTGCCAAACAGCCACGAATTTTCCCACGGTTTTTAAGAAAACCATTTCAAAAACTGTGGCAAAT
*
31618 ATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAAAG
384 ATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAATTCCCATAAAATTAAAG
* * *
31683 GTTTTTATGGTACCCTATTGTGTTTAGCTCTAGTATTTAATGTAGAATTTAATGTAAAATGGTTC
449 GTTTTTATGGTACCCTAATGTGTTTAGCTCGAGTATTTAATGTAGAATTTAATGTAAAATAGTTC
31748 GGGGAGTGG
514 GGGGAGTGG
31757 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGTAATACTATCTATG-A-AC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGTAATACTATCTATGAACAC
31820 AC-ACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
66 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
* * *
31884 GAAATTACACAATTTTTGGGGACAACATAGAATTTTGAGATGATATAAATGTAATTCTGTGATCA
131 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
31949 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCAT
196 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCAT
31996 GTAATACCAT
Statistics
Matches: 712, Mismatches: 43, Indels: 19
0.92 0.06 0.02
Matches are distributed among these distances:
517 198 0.28
518 3 0.00
519 69 0.10
520 1 0.00
526 166 0.23
527 5 0.01
528 35 0.05
529 235 0.33
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (522 bp):
AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGTAATACTATCTATGAACAC
ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCATCTCTCAATTTGCCACAGC
TTTTGCCACGGGATTCTGTAAACCCGCTGACAGGCAAATTGAAAAGTCATGGAAAGGCCGTGCCA
AACAGCCACGAATTTTCCCACGGTTTTTAAGAAAACCATTTCAAAAACTGTGGCAAATATAGAAT
TCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAATTCCCATAAAATTAAAGGTTTTTA
TGGTACCCTAATGTGTTTAGCTCGAGTATTTAATGTAGAATTTAATGTAAAATAGTTCGGGGAGT
GG
Found at i:39319 original size:14 final size:15
Alignment explanation
Indices: 39300--39330 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39290 TATTAATAAG
39300 TTTTA-TAAATGATT
1 TTTTATTAAATGATT
39314 TTTTATTAAATGATT
1 TTTTATTAAATGATT
39329 TT
1 TT
39331 GAGTGCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTATTAAATGATT
Found at i:50906 original size:529 final size:529
Alignment explanation
Indices: 48738--52396 Score: 6015
Period size: 527 Copynumber: 6.9 Consensus size: 529
48728 CTATAATGGT
* * * * *
48738 AAAAATATCAAAATTGTAACTAGGCTTGATTGGCTAAATTTATTTGCAATACTATCTATGAACAC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
* *
48803 ACTACTAACACACATTTGTATATTATGACATTGTGTAAACATTCAATTAAATTTTTTAAAGTAAT
66 ACTACT-A-ACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAAT
48868 TAGAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGAT
129 TAGAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGAT
*
48933 CATTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATATTTTCTCAATTTGCCACA
194 CATTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACA
* *
48998 GCTTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACTCATCGCAAATTGAAAAGTCGTGGCAAA
259 GCTTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAA
*
49063 GGCCGTGCCAAAGAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCA
324 GGCCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCA
49128 AATATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTA
389 AATATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTA
* * * *
49193 AAGGTTTTTATGGTACCCTATTGTGTTTAGCTCGAGTATTTGATATAGAGTTTAATGTAAAATAG
454 AAGG-TTTTATGGTACCCTATTGTGTTTAGCTCTAGTATTTGATGTAGAATTTAATGTAAAAGAG
49258 TTTGGG-AGTGG
518 TTTGGGCAGTGG
*
49269 AAAAAAATCAAAATTATAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
49334 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
66 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
* *
49399 GAAATTACACAATTTTGGGGGACAATATAGAATTTTGAGATGATATATATGCAATTATGTGATCA
131 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
49464 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACAGC
196 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACAGC
* * *
49529 TTTTTCCACGGGATTCTATAAATCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAGT
261 TTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAGG
* * * *
49594 CCGTGCCAAATAGCCACGAATTTTCCCTCGGTTTTTAAGACAACTGTTTCAAAAATCGTGGCAAA
326 CCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCAAA
* * **
49659 TATAGAATTCATGTCTAAAAATTTTACCCTAAACTAAGATAATTTGAAGTTCACAT-AAAGCAAA
391 TATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAAA
* *
49723 GGTTTTATGGTACCCTATTGTGTTTAGCTCTAGTATATGATGTAGAATTTAATGTAAAAGAGTTA
456 GGTTTTATGGTACCCTATTGTGTTTAGCTCTAGTATTTGATGTAGAATTTAATGTAAAAGAGTTT
49788 GGGCAGTGG
521 GGGCAGTGG
* *
49797 AAAAAAATCAAAATTGTAACAAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAA
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
*
49862 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAATTTTTTTTAAGTAATTA
66 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
* * *
49927 GAAATTACACAATTTTGGGGGACAATATAGAATTTTGAGATGATATAAAAGCAATTATGTAATCA
131 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
* * * * * *
49992 TTAGCCAATTAATAACTCATATAAGTGTAGGGCTTGAGGTAAATCATCTCTCAATTTGCCACAAC
196 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACAGC
* * *** * * *
50057 TTTTGCCACGAGATTCTGTAAACCCGCTGCAAAACCCGCCGCAAATTGAAAACTTGTTGCAAAGG
261 TTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAGG
* * * *
50122 CCGTGACAAATAGCCACGAATTTTCCCACGG-TTTTAAGAAAACTGTTTCAGAAACCGTGGCAAA
326 CCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCAAA
* *
50186 TATAGAATTGATGTCGAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAAA
391 TATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAAA
* * ** *
50251 TGTTTTAATGGTACCCTATTGTGTTTAGCTCGAGTATTTGATGTAGAGGTTAATGTAAAATAGTT
456 GGTTTT-ATGGTACCCTATTGTGTTTAGCTCTAGTATTTGATGTAGAATTTAATGTAAAAGAGTT
50316 TGGG-AGTGG
520 TGGGCAGTGG
*
50325 AAAAAAATCAAAATTATAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
* *
50390 ACTACTAACACATTTGTATATTCTGACATTGTGTAAAGATTCGATTAAATTTTTTTAAGTAATTA
66 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
50455 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
131 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
*
50520 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTAAGGTCAATCTTTTCTCAATTTGCCACAGC
196 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACAGC
* *
50585 TTTTTCCACGGGATTCTGTAAACCCACTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAAG
261 TTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAGG
*
50650 CCTTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCAAA
326 CCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCAAA
* **
50715 TATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGCTAACGTGAAGTTCCCATAAAATTAAA
391 TATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAAA
* ** *
50780 GGTTTTTATGGTACCCTATTTTGTTTAGCTCTAGTATTTGATGTAGAGGTTAATGTAAAATAGTT
456 GG-TTTTATGGTACCCTATTGTGTTTAGCTCTAGTATTTGATGTAGAATTTAATGTAAAAGAGTT
50845 TGGG-AGTGG
520 TGGGCAGTGG
* *
50854 AAAAAAAACAAAATTATAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
*
50919 ACTACTAGCACATTTGTATATTATGACATTGTGTAAAGATTCAATT-AATTTTTTTAAGTAATTA
66 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
* *
50983 GAAATTACACAA-TTTTGGGGACAATATAGAATTTTGAGATGATATAAACGCAATAATGTGATCA
131 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
* * *
51047 TTAGCCAATTAGTAACTCATATAAGTGTAGGGTTTGAGGTCAATCATCTCTCAATTTGCCACAGC
196 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACAGC
* * *** * * *
51112 TTTTGCCACGGGATTCTGTAAACCTGCTGCAAAACCGGCGGCAAATTGAAAATTTGTTGCAAAGG
261 TTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAGG
* * *
51177 CCGTGACAAATAGCCACGAATTTTCCCACGGTTTTTAAGGTAACCGTTTCAAAAACCCTGGCAAA
326 CCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCAAA
*
51242 TATAGAATTCATGTCTAAAAATTTTACCCAAAACAAAGATAATTTGAAGTTCCCATAAAATTAAA
391 TATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAAA
* *
51307 GGTTTTATGGTACCCTATTGTGTTTAGCTCTAGTATTTGATATAGAATTTAATGTAAAAGAGCTT
456 GGTTTTATGGTACCCTATTGTGTTTAGCTCTAGTATTTGATGTAGAATTTAATGTAAAAGAGTTT
*
51372 GGGCAGTCG
521 GGGCAGTGG
* * *
51381 AGAAAAATCAAAATTGTAACTAGACTTAATTGGCGAAATGTATTTGTAATACTATCTATGAACAC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
*
51446 ACTTCTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
66 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
* *
51511 GAAATTTCACCATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
131 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
* *
51576 TTAGCCAATTACTAACTCATATAAGTGCAGGGTTTGAGGTCAATCATCTTCTCAATTTGCCACAG
196 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATC-TTTTCTCAATTTGCCACAG
* * *
51641 TTTTTTCGAAGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAG
260 CTTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAG
* * *
51706 GCCGTGCCAAATAGCCACGAATTTTCGCACGATTTTTAAGATAACCGTTTCCAAAACCGTGGCAA
325 GCCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCAA
51771 ATATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCAT-AAATTAA
390 ATATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAA
*
51835 AGGTTTTATGGTACCCTATTGTG-TTA-CTATAGTATTTGATGTAGAATTTAATGTAAAAGAGTT
455 AGGTTTTATGGTACCCTATTGTGTTTAGCTCTAGTATTTGATGTAGAATTTAATGTAAAAGAGTT
51898 TGGGCAGTGG
520 TGGGCAGTGG
* *
51908 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGTAATGCTATCTATGAACAC
1 AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
* * * *
51973 ACTACTAACAGATTTGTATATTATGACATTGTGTAAAGACTCAATTAAAATTTTTTAACTAATTA
66 ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
* *
52038 GAAATTACACAATTTTTGGGAACAATATAGAATTTTGAGATGATATAAATGCAATAATGTGATCA
131 GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
52103 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACAGC
196 TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACAGC
* *
52168 TTTTTCCACGGGATTATATAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAGG
261 TTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAGG
* **
52233 CCATGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACTATTTCAAAAACCGTGGCAAA
326 CCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCAAA
* * * *
52298 TATAGAATTTATGTCTAAAAATTTTACCCTAAACTAAGATAATTTGAAGTTCACATAAAACTAAA
391 TATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAAA
52363 GGTTTTATGGTACCCTATTGTGTTTAGCTCTAGT
456 GGTTTTATGGTACCCTATTGTGTTTAGCTCTAGT
52397 TGTAATACTA
Statistics
Matches: 2901, Mismatches: 215, Indels: 26
0.92 0.07 0.01
Matches are distributed among these distances:
526 251 0.09
527 839 0.29
528 751 0.26
529 805 0.28
530 190 0.07
531 65 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (529 bp):
AAAAAAATCAAAATTGTAACTAGACTTAATTGGCTAAATGTATTTGAAATACTATCTATGAACAC
ACTACTAACACATTTGTATATTATGACATTGTGTAAAGATTCAATTAAATTTTTTTAAGTAATTA
GAAATTACACAATTTTTGGGGACAATATAGAATTTTGAGATGATATAAATGCAATTATGTGATCA
TTAGCCAATTACTAACTCATATAAGTGTAGGGTTTGAGGTCAATCTTTTCTCAATTTGCCACAGC
TTTTTCCACGGGATTCTGTAAACCCGCTGCAAAACCCATGGCAAATTGAAAAGTCGTGGCAAAGG
CCGTGCCAAATAGCCACGAATTTTCCCACGGTTTTTAAGATAACCGTTTCAAAAACCGTGGCAAA
TATAGAATTCATGTCTAAAAATTTTACCCTAAACAAAGATAATTTGAAGTTCCCATAAAATTAAA
GGTTTTATGGTACCCTATTGTGTTTAGCTCTAGTATTTGATGTAGAATTTAATGTAAAAGAGTTT
GGGCAGTGG
Found at i:53482 original size:37 final size:38
Alignment explanation
Indices: 53441--53519 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
53431 GCCTGGTGCA
*
53441 GCCCAAAC-ACCAGGCCAGGCGCGCGGGCCAGCGCTTG
1 GCCCAAACGACCAGGCCAGGCGCGCGGGCCAGCGCTAG
* * * *
53478 GCCC-AGCGGCTAGGCCTGGCGCGCGGGCCAGCGCTAG
1 GCCCAAACGACCAGGCCAGGCGCGCGGGCCAGCGCTAG
53515 GCCCA
1 GCCCA
53520 GGCGCTGGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 2 0.06
37 33 0.94
ACGTcount: A:0.15, C:0.41, G:0.38, T:0.06
Consensus pattern (38 bp):
GCCCAAACGACCAGGCCAGGCGCGCGGGCCAGCGCTAG
Found at i:53669 original size:20 final size:21
Alignment explanation
Indices: 53631--53672 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
53621 AAGAAAAAGG
53631 AAAAAGGAGAAATAAGGAAAT
1 AAAAAGGAGAAATAAGGAAAT
**
53652 AAAAAGG-GAAATTTGGAAAT
1 AAAAAGGAGAAATAAGGAAAT
53672 A
1 A
53673 TATAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (21 bp):
AAAAAGGAGAAATAAGGAAAT
Found at i:54393 original size:26 final size:25
Alignment explanation
Indices: 54333--54393 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
54323 CCTGTTGAGG
*
54333 AAATTATTTTAATTATGGTTTTATT
1 AAATTATTTTAATAATGGTTTTATT
*
54358 AACA-TGTTTT-ATAAATGGTTTTTATT
1 AA-ATTATTTTAAT-AATGG-TTTTATT
54384 AAATTATTTT
1 AAATTATTTT
54394 GGGTGCATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
24 2 0.07
25 12 0.41
26 15 0.52
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (25 bp):
AAATTATTTTAATAATGGTTTTATT
Done.