Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1142
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: 38790
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Found at i:180 original size:29 final size:29
Alignment explanation
Indices: 22--1232 Score: 1033
Period size: 29 Copynumber: 42.3 Consensus size: 29
12 ATTTGGGCTT
22 CTTTGAAAGGAGTGCCACTGAACTTGTGGG
1 CTTTGAAAGGAGTGCCACTG-ACTTGTGGG
** * *
52 CTTTGAAAGTCGTTGCCACTGAGTTTTGGG
1 CTTTGAAAGGAG-TGCCACTGACTTGTGGG
82 --TTGAAAGG-GTGCCACTGACTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
** *
108 CTTTGAAACGCTGTGCCACTGATTTGTGGG
1 CTTTGAAA-GGAGTGCCACTGACTTGTGGG
*
138 CCTTTGAAAAGAGTGCCACTGAC-TGTGGG
1 -CTTTGAAAGGAGTGCCACTGACTTGTGGG
167 CTTTGATAAGGAGTGCCCACTGACTTGTGGG
1 CTTTGA-AAGGAGTG-CCACTGACTTGTGGG
* *
198 CTTTGAAAGG-GTGCTCACTAATTTTGTGGG
1 CTTTGAAAGGAGTGC-CACTGA-CTTGTGGG
* *
228 CTTTGAAAGGAGTG-CA-TGAATTGTTGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
* *
255 CTTTGAAAAAGAATGCCA-TGACTTGTGGG
1 CTTTG-AAAGGAGTGCCACTGACTTGTGGG
284 CTTTGAAACGG-GTTTTGCCACTGACTTGTGGG
1 CTTTGAAA-GGAG---TGCCACTGACTTGTGGG
*
316 CTTTGAAAGG-GTTCC-CTTGACTTGTGGG
1 CTTTGAAAGGAGTGCCAC-TGACTTGTGGG
* *
344 CTTTGGAAAAGAGTGCCACTGATTTGTGGG
1 CTTT-GAAAGGAGTGCCACTGACTTGTGGG
*
374 CTTTGAAAGGAATGCCACTGACTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
*
403 CTTTGAAAAGAGTGCCACTGGA-TTGT-GG
1 CTTTGAAAGGAGTGCCACT-GACTTGTGGG
* *
431 CTTTGAAATG-GTGCCACTAAC-TGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
*** ** ***
458 CTTTG---GTTTTG----TGAACAAGAAAAG
1 CTTTGAAAGGAGTGCCACTG-ACTTG-TGGG
* *
482 ---TGAAAAGAGTGCCACTTATCTTTGTGGG
1 CTTTGAAAGGAGTGCCACTGA-C-TTGTGGG
* *
510 CTTTGAAAAGATTGCCACTGACTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
* *
539 ATCTGAAAGGAG-GCCAC-GACTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
* *
566 C-TTGAAACGG-GTGCCACTGAGTTTTGGG
1 CTTTGAAA-GGAGTGCCACTGACTTGTGGG
594 CTTTTGAAA-G-GTGCCACTGAC-TGTGGG
1 C-TTTGAAAGGAGTGCCACTGACTTGTGGG
* *
621 C-TTGAAAAGAGGTGCCACTGATTTGTGGG
1 CTTTGAAAGGA-GTGCCACTGACTTGTGGG
*
650 CTTTGAAAAGAGTGCCACTGACTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
679 CTTTGAAAGGAGTGCCACTGACTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
* *
708 C-TTGAAAGG-GTTGCCACCTG-CGTTTTGGC
1 CTTTGAAAGGAG-TGCCA-CTGAC-TTGTGGG
*
737 CTTTCGAACGG-GTGCCAACTGACTTGT-GG
1 CTTT-GAAAGGAGTGCC-ACTGACTTGTGGG
* ** * * *
766 CTTTGAAAAGCTTGCCCCTGATTTGCGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
* *
795 ATTTGAAAGGAGTG-CTCTGACTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
*
823 CTTTGAAAAGGCGTGCCA--GACTTGTGGG
1 CTTTG-AAAGGAGTGCCACTGACTTGTGGG
* *
851 C-TTGAAAGG-GTGCCACTAATTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
878 CTTTGAAAGGAGTGCCACTGACTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
* * *
907 CTTTGAAAAGGAATGCCACTGATTTGGGGG
1 CTTTG-AAAGGAGTGCCACTGACTTGTGGG
*
937 CTTTGAAAGG-GTTGCCACTGACTTGT-TG
1 CTTTGAAAGGAG-TGCCACTGACTTGTGGG
*
965 C-TTGAAAGG-GTTGCCATTGACCTTGTGGG
1 CTTTGAAAGGAG-TGCCACTGA-CTTGTGGG
*
994 CTTTGAAA-GAGTGCCACTGATTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
1022 CTTTGAAAGGAGTGCCACTG-C-TGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
*
1049 CTTTG-AACGAGTGCC-CTTGACTTGTGGG
1 CTTTGAAAGGAGTGCCAC-TGACTTGTGGG
* *
1077 CTTTGAAAGGGGTGCCACCGACTTCGTGGG
1 CTTTGAAAGGAGTGCCACTGACTT-GTGGG
* * *
1107 CTTTGAAAAGAATGCCAC-GATTTGTGGG
1 CTTTGAAAGGAGTGCCACTGACTTGTGGG
*
1135 CGTTGAAAAAGG-GTG-C-CTGACTTGTGGG
1 CTTTG--AAAGGAGTGCCACTGACTTGTGGG
* *
1163 CCTTGAAAAGATGTGCCACTGA-TTGTGGG
1 CTTTGAAAGGA-GTGCCACTGACTTGTGGG
*
1192 CTTTGAAAGGGGTGCCACTGACTTGGTGGG
1 CTTTGAAAGGAGTGCCACTGACTT-GTGGG
1222 CTTTGGAAAGG
1 CTTT-GAAAGG
1233 GAACTATGAA
Statistics
Matches: 968, Mismatches: 123, Indels: 179
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.00
22 2 0.00
23 1 0.00
24 3 0.00
25 15 0.02
26 46 0.05
27 96 0.10
28 227 0.23
29 293 0.30
30 193 0.20
31 70 0.07
32 19 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
CTTTGAAAGGAGTGCCACTGACTTGTGGG
Found at i:881 original size:199 final size:198
Alignment explanation
Indices: 43--1233 Score: 713
Period size: 199 Copynumber: 6.0 Consensus size: 198
33 GTGCCACTGA
* * *
43 ACTTGTGGGCTTTGAAAGTCGTTGCCACTGAGTTTTGGG--TTGAAAGG-GTGCCACTGACTTGT
1 ACTTGTGGGCTTTGAAAG-AG-TGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGT
*** *
105 GGGCTTTGAAACGCTGTGCCACTGATTTGTGGGCCTTTGAAAAGAG-TGCCACTGAC-TGTGGGC
64 GGGCTTTGAAA-GGAATGCCACTGATTTG-GGGCCTTTG-AAAGGGTTGCCACTGACTTGT-GGC
* ** * * * * *
168 TTTGATAAGGAGTGCCCACTGA-CTTGTGGGCTTTGAAAGGGTGCTCACTAATTTTGTGGGCTTT
125 -TTGA-AAAGCTTG-CCACTGACCTTGCGGGATTTGAAAGAGTGC-CACTGA-CTTGTGGGCTTT
232 G-AAAGGAGTG-CATG
185 GAAAAGG-GTGCCA-G
* * *
246 AATTGTTGGCTTTGAAAAAGAATGCCA-TGACTTGTGGGCTTTGAAACGG-GTTTTGCCACTGAC
1 ACTTGTGGGCTTTG--AAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GGAG---TGCCACTGAC
* * * * *
309 TTGTGGGCTTTGAAAGG-GTTCC-CTTGACTTGTGGG-CTTTGGAAAAGAG-TGCCACTGATTTG
60 TTGTGGGCTTTGAAAGGAATGCCAC-TGATTTG-GGGCCTTT-G-AAAGGGTTGCCACTGACTTG
* ** * *
370 TGGGCTTTGAAAGGAATGCCACTGA-CTTGTGGGCTTTGAAAAGAGTGCCACTGGA-TTGT-GGC
121 T-GGC-TTGAAAAGCTTGCCACTGACCTTGCGGGATTTG-AAAGAGTGCCACT-GACTTGTGGGC
* *
432 TTTG-AAATGGTGCCACTA
182 TTTGAAAAGGGTGCCA--G
***** ** *** * *
450 AC-TGTGGGCTTTGGTTTTGTG--A---ACAAGAAAAG---TGAAAAGAGTGCCACTTATCTTTG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG-TGGGCTTTGAAAGGAGTGCCACTGA-C-TTG
* * * * *
506 TGGGCTTTGAAAAGATTGCCACTGACTTGTGGG-ATCTGAAAGGAG--GCCAC-GACTTGTGGGC
63 TGGGCTTTGAAAGGAATGCCACTGATTTG-GGGCCTTTGAAAGG-GTTGCCACTGACTTGT-GGC
* ** ** **
567 TTGAAACGGGTGCCACTGAGTTTTG-GGCTTTTGAAAG-GTGCCACTGAC-TGTGGGC-TTGAAA
125 TTGAAAAGCTTGCCACTGA-CCTTGCGGGATTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
628 AGAGGTGCCACTG
189 AG-GGTGCCA--G
*
641 ATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTG
1 ACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTG
** * * *
706 GGC-TTGAAAGGGTTGCCACCTGCGTTT-TGGCCTTTCGAACGGG-TGCCAACTGACTTGTGGCT
65 GGCTTTGAAAGGAATGCCA-CTG-ATTTGGGGCCTTT-GAAAGGGTTGCC-ACTGACTTGTGGC-
* * *
768 TTGAAAAGCTTGCCCCTGA-TTTGCGGGATTTGAAAGGAGTG-CTCTGACTTGTGGGCTTTGAAA
125 TTGAAAAGCTTGCCACTGACCTTGCGGGATTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAA
831 AGGCGTGCCAG
189 AGG-GTGCCAG
* * *
842 ACTTGTGGGC-TTGAAAGGGTGCCACTAATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGG
1 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGG
* *
906 GCTTTGAAAAGGAATGCCACTGATTTGGGGGCTTTGAAAGGGTTGCCACTGACTTGTTGCTTGAA
66 GCTTTG-AAAGGAATGCCACTGATTTGGGGCCTTTGAAAGGGTTGCCACTGACTTGTGGCTTGAA
* * * * * *
971 AGGGTTGCCATTGACCTTGTGGGCTTTGAAAGAGTGCCACTGATTTGTGGGCTTTG-AAAGGAGT
130 AAGCTTGCCACTGACCTTGCGGGATTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGG-GT
1035 GCC--
194 GCCAG
* * *
1038 ACTGCTGTGGGCTTTGAACGAGTGCC-CTTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTC
1 ACT--TGTGGGCTTTGAAAGAGTGCCAC-TGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTT-
* *
1102 GTGGGCTTTGAAAAGAATGCCAC-GATTTGTGGG-CGTTGAAAAAGGG-TG-C-CTGACTTGTGG
62 GTGGGCTTTGAAAGGAATGCCACTGATTTG-GGGCCTTTG--AAAGGGTTGCCACTGACTTGT-G
* * * *
1162 GCCTTGAAAAGATGTGCCACTGA--TTGTGGGCTTTGAAAGGGGTGCCACTGACTTGGTGGGCTT
123 G-CTTGAAAAGCT-TGCCACTGACCTTGCGGGATTTGAAA-GAGTGCCACTGACTT-GTGGGCTT
*
1225 TGGAAAGGG
184 TGAAAAGGG
1234 AACTATGAAA
Statistics
Matches: 808, Mismatches: 108, Indels: 147
0.76 0.10 0.14
Matches are distributed among these distances:
189 8 0.01
190 14 0.02
191 30 0.04
192 35 0.04
193 16 0.02
194 19 0.02
195 23 0.03
196 4 0.00
197 28 0.03
198 83 0.10
199 198 0.25
200 84 0.10
201 56 0.07
202 23 0.03
203 54 0.07
204 12 0.01
205 36 0.04
206 47 0.06
207 13 0.02
208 25 0.03
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (198 bp):
ACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGG
GCTTTGAAAGGAATGCCACTGATTTGGGGCCTTTGAAAGGGTTGCCACTGACTTGTGGCTTGAAA
AGCTTGCCACTGACCTTGCGGGATTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGC
CAG
Found at i:2514 original size:1 final size:1
Alignment explanation
Indices: 2510--2564 Score: 65
Period size: 1 Copynumber: 55.0 Consensus size: 1
2500 TTTTTTGCTA
* * * * *
2510 TTTTTTTCTTTTTTTTTGTTTTGTTTTTTTTTTTTGTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2565 GGTTTAAAGG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:2531 original size:18 final size:17
Alignment explanation
Indices: 2510--2562 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 17
2500 TTTTTTGCTA
2510 TTTTTTTCTTTTTTTTTG
1 TTTTTTT-TTTTTTTTTG
2528 TTTTGTTTTTTTTTTTTG
1 TTTT-TTTTTTTTTTTTG
2546 TTTTTTTTTTGTTTTTT
1 TTTTTTTTTT-TTTTTT
2563 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.18
18 24 0.73
19 3 0.09
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.91
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTTG
Found at i:2537 original size:24 final size:24
Alignment explanation
Indices: 2510--2564 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2500 TTTTTTGCTA
*
2510 TTTTTTTCTTTT-TTTTTGTTTTG
1 TTTTTTTTTTTTGTTTTTGTTTTG
*
2533 TTTTTTTTTTTTGTTTTTTTTTTG
1 TTTTTTTTTTTTGTTTTTGTTTTG
2557 TTTTTTTT
1 TTTTTTTT
2565 GGTTTAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (24 bp):
TTTTTTTTTTTTGTTTTTGTTTTG
Found at i:2562 original size:11 final size:11
Alignment explanation
Indices: 2500--2564 Score: 67
Period size: 11 Copynumber: 5.4 Consensus size: 11
2490 GCCCTTTCTC
2500 TTTTTTGCTATTT
1 TTTTTTG-T-TTT
*
2513 TTTTCTTTTTTT
1 TTTT-TTGTTTT
2525 TTGTTTTGTTTTTT
1 TT-TTTTG--TTTT
2539 TTTTTTGTTTT
1 TTTTTTGTTTT
2550 TTTTTTGTTTT
1 TTTTTTGTTTT
2561 TTTT
1 TTTT
2565 GGTTTAAAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
11 19 0.41
12 7 0.15
13 12 0.26
14 8 0.17
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.88
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:2569 original size:10 final size:10
Alignment explanation
Indices: 2500--2569 Score: 56
Period size: 10 Copynumber: 7.1 Consensus size: 10
2490 GCCCTTTCTC
*
2500 TTTTTTGCTAT
1 TTTTTTGGT-T
*
2511 TTTTTT-CTT
1 TTTTTTGGTT
*
2520 TTTTTTTGTT
1 TTTTTTGGTT
2530 TTGTTTT--TT
1 TT-TTTTGGTT
*
2539 TTTTTTGTTT
1 TTTTTTGGTT
*
2549 TTTTTTTGTT
1 TTTTTTGGTT
2559 TTTTTTGGTT
1 TTTTTTGGTT
2569 T
1 T
2570 AAAGGATGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
8 4 0.08
9 11 0.22
10 26 0.51
11 10 0.20
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (10 bp):
TTTTTTGGTT
Found at i:4561 original size:1 final size:1
Alignment explanation
Indices: 4555--4595 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
4545 ACAAGCCAAC
4555 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4596 CGGACTTGCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13185 original size:79 final size:79
Alignment explanation
Indices: 13080--13285 Score: 220
Period size: 78 Copynumber: 2.6 Consensus size: 79
13070 GAGATAATAA
* * * * * **
13080 CGGGGTTGGAGTGTCCCCTTGAAAATAACGGGGCTGGAGTATCCCCGATTGTGAG-AATTGATGA
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
13144 -TTAGAAAAAAAAAAT
65 TTTAG-AAAAAAAAAT
* * *
13159 CGGGATTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTAT-CCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
13223 TTTGGGAATAAAGT
66 TTAGAAAAAAAAAT
* *
13237 CGGGGTTGGAGTATCCCCTCGGAAGTAAGGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT
13286 GAAATAACGA
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
78 55 0.53
79 49 0.47
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAT
Found at i:13299 original size:28 final size:28
Alignment explanation
Indices: 13240--13308 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
13230 ATAAAGTCGG
** * * *
13240 GGTTGGAGTATCCCCTCGGAAGTAAGGG
1 GGTTGGAGTATCCCCGAGGAAATAACGA
*
13268 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGAGGAAATAACGA
13296 GGTTGGAGTATCC
1 GGTTGGAGTATCC
13309 TTAATTGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGAGGAAATAACGA
Found at i:13386 original size:52 final size:51
Alignment explanation
Indices: 13319--13465 Score: 168
Period size: 51 Copynumber: 2.8 Consensus size: 51
13309 TTAATTGTGA
* * * *
13319 AAAATTGGTGTTTTTGGAAAGAAAATCGAAGTTGGAGTATCGCCGATTAAAGG
1 AAAATTGGTG-TTTTGGAAATAAAACCGAGGTTGGAGTATCCCCGATT-AAGG
* * * **
13372 AAAATTGGTGTTTTGAAAATAAAGCCGGGGTTGGAGTATCCCCGATTGTGG
1 AAAATTGGTGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCGATTAAGG
* * *
13423 AAAATCGATGATTTGGAAATAAAACCGAGGTTGGAGTATCCCC
1 AAAATTGGTGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCC
13466 TCGGAGATAA
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
51 39 0.49
52 30 0.38
53 10 0.13
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (51 bp):
AAAATTGGTGTTTTGGAAATAAAACCGAGGTTGGAGTATCCCCGATTAAGG
Found at i:13455 original size:51 final size:51
Alignment explanation
Indices: 13293--13465 Score: 184
Period size: 52 Copynumber: 3.4 Consensus size: 51
13283 GATGAAATAA
*** * * *
13293 CGAGGTTGGAGTATCCTTAATTGTGAAAAATTGGTGTTTTTGGAAAGAAAAT
1 CGAGGTTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTTGGAAATAAAAC
* * ** * *
13345 CGAAGTTGGAGTATCGCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAGC
1 CGAGGTTGGAGTATCCCCGATT-GTGGAAAATTGGTGTTTTGGAAATAAAAC
* * * *
13397 CGGGGTTGGAGTATCCCCGATTGTGGAAAATCGATGATTTGGAAATAAAAC
1 CGAGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAAC
13448 CGAGGTTGGAGTATCCCC
1 CGAGGTTGGAGTATCCCC
13466 TCGGAGATAA
Statistics
Matches: 97, Mismatches: 23, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
51 39 0.40
52 47 0.48
53 11 0.11
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTGGAAATAAAAC
Found at i:13489 original size:79 final size:80
Alignment explanation
Indices: 13397--13576 Score: 215
Period size: 80 Copynumber: 2.3 Consensus size: 80
13387 AAAATAAAGC
* *
13397 CGGGGTTGGAGTATCCCCGATTGTG-GAAAATCGATGA-TTT-GGAAATAAA-ACCGAGGTTGGA
1 CGGGGTTGGAGTATCCCCGATTATGAG-AAATCAAT-ATTTTAGG-AATAAAGACCGAGGTTGGA
* *
13458 GTATCCCCTCGGAGATAA
63 GTATCCCCTCGAAAATAA
* * *
13476 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGTCGGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGACCGAGGTTGGAGTA
* *
13541 TCCTCTTGAAAATAA
66 TCCCCTCGAAAATAA
*
13556 CGGGGTTAGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
13577 GAATGACGGG
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 40 0.46
80 46 0.53
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGACCGAGGTTGGAGTA
TCCCCTCGAAAATAA
Found at i:13594 original size:27 final size:27
Alignment explanation
Indices: 13529--13606 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
13519 AATAAAGTCG
* *
13529 GGGGTTGGAGTATCCTCTTGA-AAATAAC
1 GGGGTTGGAGTATCC-C-CGATGAATAAC
* *
13557 GGGGTTAGAGTATCCCCGATGAATGAC
1 GGGGTTGGAGTATCCCCGATGAATAAC
13584 GGGGTTGGAGTATCCCCGATGAA
1 GGGGTTGGAGTATCCCCGATGAA
13607 AAATTGATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
26 2 0.05
27 28 0.64
28 14 0.32
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATGAATAAC
Found at i:13677 original size:51 final size:51
Alignment explanation
Indices: 13587--13703 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
13577 GAATGACGGG
*
13587 GTTGGAGTATCCCCG---ATGAAAAATTGATGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAAAAAATTGATGTTTTAGAAATAAAATCGGA
13635 GTTGGAGTATCCCCGATTATAAAAAATT-AGTGTTTTTA-AAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAAAAAATTGA-TG-TTTTAGAAATAAAATCGGA
13686 GTTGG-GATATCCCCGATT
1 GTTGGAG-TATCCCCGATT
13704 GCGGAGAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
48 15 0.24
50 2 0.03
51 40 0.65
52 5 0.08
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATAAAAAATTGATGTTTTAGAAATAAAATCGGA
Found at i:16091 original size:13 final size:13
Alignment explanation
Indices: 16073--16098 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16063 CAAAGAATAG
16073 ATGTATCGATACA
1 ATGTATCGATACA
16086 ATGTATCGATACA
1 ATGTATCGATACA
16099 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:16095 original size:34 final size:33
Alignment explanation
Indices: 16052--16118 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
16042 AACTTCCTAG
*
16052 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
16086 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
16119 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:16174 original size:19 final size:19
Alignment explanation
Indices: 16150--16233 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
16140 AGCGATACAT
16150 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
16169 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
16188 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
* *
16201 TGCATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
16220 TGTATCGATACAAA
1 TGTATCGATACAAA
16234 TCGCTGAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
13 10 0.18
14 1 0.02
16 2 0.04
18 1 0.02
19 41 0.75
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:23777 original size:21 final size:21
Alignment explanation
Indices: 23751--23798 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
23741 TATATGTATC
*
23751 GATACATAAAGGTTACCTTAG
1 GATACATAAAGGTTAACTTAG
23772 GATACATAAAGGTTAACTTAG
1 GATACATAAAGGTTAACTTAG
*
23793 GCTACA
1 GATACA
23799 AAGGTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (21 bp):
GATACATAAAGGTTAACTTAG
Found at i:27305 original size:40 final size:40
Alignment explanation
Indices: 27194--28095 Score: 480
Period size: 40 Copynumber: 22.3 Consensus size: 40
27184 GGCCCCTGGT
* *
27194 CAACAGATTGGAAGGTTGGCCAAGGTGAAACCGATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
** * * ** *
27234 CAATTGATTGGAAGGGTTGACCAGGGTGAAACTAATAAAAC
1 CAACAGATTGGAA-GGTTGGCCAGGGCGAAACCGATAAAGC
* *
27275 CAACAGATTAGAAGGTTGGCC-GAGGCGAAACCGATAAAAC
1 CAACAGATTGGAAGGTTGGCCAG-GGCGAAACCGATAAAGC
* * *
27315 CAACAGATTGTAAGGTTGGTCAGGGCGAAACTGATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * * * * *
27355 CAACAAATTGGAAGGGCTGACCAAGGCGAAACTGATAAAGT
1 CAACAGATTGGAA-GGTTGGCCAGGGCGAAACCGATAAAGC
** * *
27396 CAATTGATTGGAAGGTTGGCCAGGGCAAAACCAATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * * * * * * *
27436 CAACAGATTAGAAGGGTTGACTACGGCAAAACCAATAGAGT
1 CAACAGATTGGAA-GGTTGGCCAGGGCGAAACCGATAAAGC
* * * * **
27477 CAACCGATTGGAAGGTTAGCTTA-GGTGAAATTGATAAAGC
1 CAACAGATTGGAAGGTTGGC-CAGGGCGAAACCGATAAAGC
* * * * ** * *
27517 TAACA-ATTGGAAGGGTTGACTAGGGCAAAACTAAGAAAGT
1 CAACAGATTGGAA-GGTTGGCCAGGGCGAAACCGATAAAGC
** * * * *
27557 CAATTGATTGGAAGGTTAGCCAAGGCAAAATCGATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * *
27597 CAACAGATTGGAAGGTCGGCCAGGGCAAAACTGATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * * * *
27637 CAACATATTGGAAGGTCGGCTAGGGTGAAACCAATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * * * * * *
27677 AAACAGATTAGAAGGGTTGACCGGGGTGAAACTGATAAAGT
1 CAACAGATTGGAA-GGTTGGCCAGGGCGAAACCGATAAAGC
* * * * * * * * *
27718 CAACGGATTAGATGGATTGCCCATGACAAAATCGATAAAGT
1 CAACAGATTGGAAGG-TTGGCCAGGGCGAAACCGATAAAGC
* * * * *
27759 CAACTGATTAGAAGGTTGGCTAGGGTGAAACCAATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * ** * * * *
27799 CTACAGATTGAGAGGGTTAACTAGGGCAAAATCGATAAAGT
1 CAACAGATTG-GAAGGTTGGCCAGGGCGAAACCGATAAAGC
*** * * ** * ** *
27840 CAATC-GATCAAAAGGCTAGTTAGTGTAAAATCGATAAAGC
1 CAA-CAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * * * * *
27880 CAATAGATTGGAAGTGTTGACTAGGGCAAAACTGATAAAGT
1 CAACAGATTGGAAG-GTTGGCCAGGGCGAAACCGATAAAGC
** * * * *
27921 CAATTGATTGGAAGGTTGGCCAAGACAAAACCAATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * ** * *
27961 CAATAGATTGGAAGGGTTGACCAACGAGAAATCGATAAAGC
1 CAACAGATTGGAA-GGTTGGCCAGGGCGAAACCGATAAAGC
* * ** * * * *
28002 CAATAGATTAGAAAGGTTTACCAAGGCAAAACTGATAAAGT
1 CAACAGATT-GGAAGGTTGGCCAGGGCGAAACCGATAAAGC
* * * *
28043 CAACCGATTGGAATGTTGGCGAGGGTGAAACCGATAAAGC
1 CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
*
28083 TAACAGATTGGAA
1 CAACAGATTGGAA
28096 AATTATTCGA
Statistics
Matches: 650, Mismatches: 195, Indels: 34
0.74 0.22 0.04
Matches are distributed among these distances:
39 10 0.02
40 356 0.55
41 280 0.43
42 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (40 bp):
CAACAGATTGGAAGGTTGGCCAGGGCGAAACCGATAAAGC
Found at i:27392 original size:81 final size:81
Alignment explanation
Indices: 27194--27726 Score: 414
Period size: 81 Copynumber: 6.6 Consensus size: 81
27184 GGCCCCTGGT
* * * * *
27194 CAACAGATTGGAA-GGTTGGCCAAGGTGAAACCGATAAAGCCAATTGATTGGAAGGGTTGACCAG
1 CAACAGATTGGAAGGGTTGACCAAGGCGAAACTGATAAAGCCAACTGATTGGAA-GGTTGGCCAG
* *
27258 GGTGAAACTAATAAAAC
65 GGCGAAACTAATAAAGC
* * * * * * * *
27275 CAACAGATTAGAA-GGTTGGCCGAGGCGAAACCGATAAAACCAACAGATTGTAAGGTTGGTCAGG
1 CAACAGATTGGAAGGGTTGACCAAGGCGAAACTGATAAAGCCAACTGATTGGAAGGTTGGCCAGG
*
27339 GCGAAACTGATAAAGC
66 GCGAAACTAATAAAGC
* * * *
27355 CAACAAATTGGAAGGGCTGACCAAGGCGAAACTGATAAAGTCAATTGATTGGAAGGTTGGCCAGG
1 CAACAGATTGGAAGGGTTGACCAAGGCGAAACTGATAAAGCCAACTGATTGGAAGGTTGGCCAGG
* *
27420 GCAAAACCAATAAAGC
66 GCGAAACTAATAAAGC
* * * * ** * * * * *
27436 CAACAGATTAGAAGGGTTGACTACGGCAAAACCAATAGAGTCAACCGATTGGAAGGTTAGCTTA-
1 CAACAGATTGGAAGGGTTGACCAAGGCGAAACTGATAAAGCCAACTGATTGGAAGGTTGGC-CAG
* * *
27500 GGTGAAATTGATAAAGC
65 GGCGAAACTAATAAAGC
* * * * * * * * * *
27517 TAACA-ATTGGAAGGGTTGACTAGGGCAAAACTAAGAAAGTCAATTGATTGGAAGGTTAGCCAAG
1 CAACAGATTGGAAGGGTTGACCAAGGCGAAACTGATAAAGCCAACTGATTGGAAGGTTGGCCAGG
* *
27581 GC-AAAATCGATAAAGC
66 GCGAAACT-AATAAAGC
* * * * * *
27597 CAACAGATTGGAA-GGTCGGCCAGGGCAAAACTGATAAAGCCAACAT-ATTGGAAGGTCGGCTAG
1 CAACAGATTGGAAGGGTTGACCAAGGCGAAACTGATAAAGCCAAC-TGATTGGAAGGTTGGCCAG
* *
27660 GGTGAAACCAATAAAGC
65 GGCGAAACTAATAAAGC
* * ** * * *
27677 AAACAGATTAGAAGGGTTGACCGGGGTGAAACTGATAAAGTCAACGGATT
1 CAACAGATTGGAAGGGTTGACCAAGGCGAAACTGATAAAGCCAACTGATT
27727 AGATGGATTG
Statistics
Matches: 362, Mismatches: 81, Indels: 18
0.79 0.18 0.04
Matches are distributed among these distances:
79 5 0.01
80 152 0.42
81 204 0.56
82 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.18
Consensus pattern (81 bp):
CAACAGATTGGAAGGGTTGACCAAGGCGAAACTGATAAAGCCAACTGATTGGAAGGTTGGCCAGG
GCGAAACTAATAAAGC
Found at i:27410 original size:121 final size:121
Alignment explanation
Indices: 27194--27691 Score: 331
Period size: 121 Copynumber: 4.1 Consensus size: 121
27184 GGCCCCTGGT
* *** * *
27194 CAACAGATTGGAAGGTTGGCCAAGGTGAAACCGATAAAGCCAATTGATTGGAAGGGTTGACCAGG
1 CAACAGATTGGAAGGTTGGCCAAGGCGAAACCGATAAAGCCAACAAATTGGAAGGGCTGACCAAG
* * *
27259 GTGAAACTAATAAAACCAACAGATTAGAAGGTTGGCC-GAGGCGAAACCGATAAAAC
66 GCGAAACTAATAAAACCAACAGATTAGAAGGTTGGCCAG-GGCAAAACCAATAAAAC
* * * *
27315 CAACAGATTGTAAGGTTGGTCAGGGCGAAACTGATAAAGCCAACAAATTGGAAGGGCTGACCAAG
1 CAACAGATTGGAAGGTTGGCCAAGGCGAAACCGATAAAGCCAACAAATTGGAAGGGCTGACCAAG
* ** ** * *
27380 GCGAAACTGATAAAGTCAATTGATTGGAAGGTTGGCCAGGGCAAAACCAATAAAGC
66 GCGAAACTAATAAAACCAACAGATTAGAAGGTTGGCCAGGGCAAAACCAATAAAAC
* * * * * * * * ** * **
27436 CAACAGATTAGAAGGGTTGACTACGGCAAAACCAATAGAGTCAACCGATTGGAA-GG-TTAGCTT
1 CAACAGATTGGAA-GGTTGGCCAAGGCGAAACCGATAAAGCCAACAAATTGGAAGGGCTGA-CCA
* * * * * * * * * * **
27499 AGGTGAAATTGATAAAGCTAACA-ATTGGAAGGGTTGACTAGGGCAAAACTAAGAAAGT
64 AGGCGAAACTAATAAAACCAACAGATTAGAA-GGTTGGCCAGGGCAAAACCAATAAAAC
** * * * * * * *
27557 CAATTGATTGGAAGGTTAGCCAAGGCAAAATCGATAAAGCCAACAGATTGGAAGGTC-GGCCAGG
1 CAACAGATTGGAAGGTTGGCCAAGGCGAAACCGATAAAGCCAACAAATTGGAAGGGCTGACCAAG
* * * * * * * ** *
27621 GCAAAACTGATAAAGCCAACATATTGGAAGGTCGGCTAGGGTGAAACCAATAAAGC
66 GCGAAACTAATAAAACCAACAGATTAGAAGGTTGGCCAGGGCAAAACCAATAAAAC
* *
27677 AAACAGATTAGAAGG
1 CAACAGATTGGAAGG
27692 GTTGACCGGG
Statistics
Matches: 290, Mismatches: 80, Indels: 15
0.75 0.21 0.04
Matches are distributed among these distances:
120 90 0.31
121 170 0.59
122 30 0.10
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.18
Consensus pattern (121 bp):
CAACAGATTGGAAGGTTGGCCAAGGCGAAACCGATAAAGCCAACAAATTGGAAGGGCTGACCAAG
GCGAAACTAATAAAACCAACAGATTAGAAGGTTGGCCAGGGCAAAACCAATAAAAC
Found at i:27829 original size:81 final size:80
Alignment explanation
Indices: 27744--28019 Score: 243
Period size: 81 Copynumber: 3.4 Consensus size: 80
27734 TTGCCCATGA
* *
27744 CAAAATCGATAAAGTCAACTGATTAGAAGGTTGGCTAGGGTGAAACCAATAAAGCCTACAGATT-
1 CAAAATCGATAAAGTCAA-TGATTAGAAGGTTGGCTAGGGTAAAACCAATAAAGCCAACAGATTG
27808 GAGAGGGTTAACTAGGG
65 GA-AGGGTTAACTAGGG
* * * * * * * * *
27825 CAAAATCGATAAAGTCAATCGATCAAAAGGCTAGTTAGTGTAAAATCGATAAAGCCAATAGATTG
1 CAAAATCGATAAAGTCAAT-GATTAGAAGGTTGGCTAGGGTAAAACCAATAAAGCCAACAGATTG
* *
27890 GAAGTGTTGACTAGGG
65 GAAGGGTTAACTAGGG
* * * ** *
27906 CAAAA-CTGATAAAGTCAATTGATTGGAAGGTTGGCCAAGACAAAACCAATAAAGCCAATAGATT
1 CAAAATC-GATAAAGTCAA-TGATTAGAAGGTTGGCTAGGGTAAAACCAATAAAGCCAACAGATT
* * **
27970 GGAAGGGTTGACCAACG
64 GGAAGGGTTAACTAGGG
*
27987 -AGAAATCGATAAAGCCAATAGATTAGAAAGGTT
1 CA-AAATCGATAAAGTCAAT-GATTAG-AAGGTT
28020 TACCAAGGCA
Statistics
Matches: 155, Mismatches: 32, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
80 4 0.03
81 141 0.91
82 10 0.06
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.21
Consensus pattern (80 bp):
CAAAATCGATAAAGTCAATGATTAGAAGGTTGGCTAGGGTAAAACCAATAAAGCCAACAGATTGG
AAGGGTTAACTAGGG
Found at i:27839 original size:122 final size:121
Alignment explanation
Indices: 27383--27842 Score: 299
Period size: 122 Copynumber: 3.8 Consensus size: 121
27373 GACCAAGGCG
* * * * * ** *
27383 AAACTGATAAAGTCAA-TTGATTGGAAGGTTGGCCAGGGCAAAACCAATAAAGCCAACAGATTAG
1 AAACTGATAAAGCCAACAT-ATTAGAAGGTCGGCTAGGGTGAAACCAATAAAGCAAACAGATTAG
* * * * * * * * * ** **
27447 AAGGGTTGACTACGGCAAAACCAATAGAGTCAACCGATTGGAAGGTTAGCTTAGG-TG
65 AAGGGTTAACCAGGGCAAAATCGATAAAGTCAACAGATTAGAAGG-TCGCCCAGGACA
* * * * * ** * * ** *
27504 AAATTGATAAAGCTAACA-ATTGGAAGGGTTGACTAGGGCAAAACTAAGAAAGTC-AATTGATTG
1 AAACTGATAAAGCCAACATATTAGAA-GGTCGGCTAGGGTGAAACCAATAAAG-CAAACAGATTA
* * * * * *
27567 GAA-GGTTAGCCAAGGCAAAATCGATAAAGCCAACAGATTGGAAGGTCGGCCAGGGCA
64 GAAGGGTTAACCAGGGCAAAATCGATAAAGTCAACAGATTAGAAGGTCGCCCAGGACA
*
27624 AAACTGATAAAGCCAACATATTGGAAGGTCGGCTAGGGTGAAACCAATAAAGCAAACAGATTAGA
1 AAACTGATAAAGCCAACATATTAGAAGGTCGGCTAGGGTGAAACCAATAAAGCAAACAGATTAGA
* * ** * * * *
27689 AGGGTTGACCGGGGTGAAA-CTGATAAAGTCAACGGATTAGATGGATTGCCCATGACA
66 AGGGTTAACCAGGGCAAAATC-GATAAAGTCAACAGATTAGAAGG-TCGCCCAGGACA
* * **
27746 AAA-TCGATAAAGTCAAC-TGATTAGAAGGTTGGCTAGGGTGAAACCAATAAAGCCTACAGATT-
1 AAACT-GATAAAGCCAACAT-ATTAGAAGGTCGGCTAGGGTGAAACCAATAAAGCAAACAGATTA
*
27808 GAGAGGGTTAACTAGGGCAAAATCGATAAAGTCAA
64 GA-AGGGTTAACCAGGGCAAAATCGATAAAGTCAA
27843 TCGATCAAAA
Statistics
Matches: 265, Mismatches: 61, Indels: 25
0.75 0.17 0.07
Matches are distributed among these distances:
119 6 0.02
120 86 0.32
121 85 0.32
122 87 0.33
123 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (121 bp):
AAACTGATAAAGCCAACATATTAGAAGGTCGGCTAGGGTGAAACCAATAAAGCAAACAGATTAGA
AGGGTTAACCAGGGCAAAATCGATAAAGTCAACAGATTAGAAGGTCGCCCAGGACA
Found at i:28091 original size:122 final size:122
Alignment explanation
Indices: 27867--28095 Score: 307
Period size: 122 Copynumber: 1.9 Consensus size: 122
27857 AGTTAGTGTA
* * * **
27867 AAATCGATAAAGCCAATAGATTGGAAGTGTTGACTAGGGCAAAACTGATAAAGTCAATTGATTGG
1 AAATCGATAAAGCCAATAGATTGAAAGTGTTGACCAAGGCAAAACTGATAAAGTCAACCGATTGG
*
27932 AAGGTTGGCCAAGACAAAACCAATAAAGCCAATAGATTGGAAGGGTTGACCAACGAG
66 AAGGTTGGCCAAGACAAAACCAATAAAGCCAACAGATTGGAAGGGTTGACCAACGAG
*
27989 AAATCGATAAAGCCAATAGATTAGAAAG-GTTTACCAAGGCAAAACTGATAAAGTCAACCGATTG
1 AAATCGATAAAGCCAATAGATT-GAAAGTGTTGACCAAGGCAAAACTGATAAAGTCAACCGATTG
* * * *** * *
28053 GAATGTTGGCGAGGGTGAAACCGATAAAGCTAACAGATTGGAA
65 GAAGGTTGGCCAAGACAAAACCAATAAAGCCAACAGATTGGAA
28096 AATTATTCGA
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
122 87 0.96
123 4 0.04
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (122 bp):
AAATCGATAAAGCCAATAGATTGAAAGTGTTGACCAAGGCAAAACTGATAAAGTCAACCGATTGG
AAGGTTGGCCAAGACAAAACCAATAAAGCCAACAGATTGGAAGGGTTGACCAACGAG
Found at i:29010 original size:90 final size:90
Alignment explanation
Indices: 28799--29674 Score: 799
Period size: 90 Copynumber: 9.9 Consensus size: 90
28789 TCCAAAGGAA
* * * *** *
28799 ATTAGGCTCTGTGATGCATTAGTA-CGATCTAGT-GATTGAAGAAAAAGGATATTACAAGGAACT
1 ATTAGGCTCTGTGATGCATCAATATC-ATCTAGTGGA-TGAAGAAAAAGGATATGATTGGGAAAT
* * *
28862 GTATGGGCTACACCCTTG-CCAAAGGT
64 GGATGGGCTGCACCCTTGCCCCAAGGT
* *
28888 ATTAGGCTCTATGATGCATCAATATCATCTAGTGGATGAAGAAAAAGGATATGATTAGGAAATGG
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAAGAAAAAGGATATGATTGGGAAATGG
*
28953 ATGGGCTGCATCCTTGCCCCAAGGT
66 ATGGGCTGCACCCTTGCCCCAAGGT
* * * * *
28978 ATTAGGCTTTATGACGCATCAATATCATCTAGTGGATGAAGACAAAGGATCTGATTGGGAAATGG
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAAGAAAAAGGATATGATTGGGAAATGG
* * *
29043 ATGGGCTGCACCTTTGCTCTAAGGT
66 ATGGGCTGCACCCTTGCCCCAAGGT
* * * * *
29068 ATTAGGCTCTGTGATGCATTAATATCATTTAGTGGATGAA-AGAAAAGGATATGATTTGAAAATA
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAAGA-AAAAGGATATGATTGGGAAATG
** *
29132 GATGGGCAACACCCTTGTCCCAAGGT
65 GATGGGCTGCACCCTTGCCCCAAGGT
* * * * * * * *
29158 ATTAGGCTTTGTGATGCATCAATATCATTTGGTAGTTGAGGGAAAAA-AATATGTTTGGGAAATG
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGA-AGAAAAAGGATATGATTGGGAAATG
*
29222 TG-TGGGCTGCACCCTTGCCCTAAGGT
65 -GATGGGCTGCACCCTTGCCCCAAGGT
* * *
29248 ATTAGGCTCTGTGATGCACCAATATCATCTAGTGGATGAAGAAAAAAGATATGACTGGGAAATGG
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAAGAAAAAGGATATGATTGGGAAATGG
29313 ATGGGCTGCACCCTTGCCCCAAGGT
66 ATGGGCTGCACCCTTGCCCCAAGGT
* * *
29338 ATTTGGCTTTGTGATGCATCAATATCATCTAGTGGATGAAG-GAAAGGATATGATTGGGAAATGG
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAAGAAAAAGGATATGATTGGGAAATGG
* *
29402 ATGGGCTACACCCTTGCCTCAAGGT
66 ATGGGCTGCACCCTTGCCCCAAGGT
** * * * * * * * * *
29427 ATTAGGCTCAATGATGAATTAATATCAT-TAGTAG-TTAAGGGAAAATGATATGACTAGGAAAAG
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAA-GAAAAAGGATATGATTGGGAAATG
* ** **
29490 TG-TGGG-TCGTA-CCTTGCCTTAAGAAA
65 -GATGGGCT-GCACCCTTGCCCCAAG-GT
* * * **
29516 ATTCGGCTTTGTGATGCATCAATATCATCTAGTTGA--AAG-AAGGGGATATGATTGGG-AATGT
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAAGAAAAAGGATATGATTGGGAAATG-
* **
29577 G-TGGGCTGCA-CCTTGCCCTAAAGAA
65 GATGGGCTGCACCCTTGCCC-CAAGGT
* * * * **
29602 ATTTGGCTTTGTGATGCATCAATACCATCTAGTTGA--AAG-AAGGGGATATGATTGGG-AATGT
1 ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAAGAAAAAGGATATGATTGGGAAATG-
29663 G-TGGGCTGCACC
65 GATGGGCTGCACC
29675 TTCCCTTATG
Statistics
Matches: 662, Mismatches: 106, Indels: 40
0.82 0.13 0.05
Matches are distributed among these distances:
86 89 0.13
87 20 0.03
88 19 0.03
89 185 0.28
90 343 0.52
91 5 0.01
92 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (90 bp):
ATTAGGCTCTGTGATGCATCAATATCATCTAGTGGATGAAGAAAAAGGATATGATTGGGAAATGG
ATGGGCTGCACCCTTGCCCCAAGGT
Found at i:30788 original size:78 final size:79
Alignment explanation
Indices: 30689--30889 Score: 221
Period size: 78 Copynumber: 2.6 Consensus size: 79
30679 AATAACAGGG
* * * * *
30689 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTT
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTT
*
30752 -AAAAAAAAATCGGGA
64 GAAAAAAAAACCGGGA
* *
30767 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGA
* * * *
30832 GAATAAAGCCGGGG
66 AAAAAAAACCGGGA
* *
30846 TTGGAGTAT-CCTCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCT-TCGAAAATAACGGGGTTGGAGTATCCCCGAT
30890 GAAATAACGA
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
77 7 0.07
78 51 0.49
79 46 0.44
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGA
AAAAAAAACCGGGA
Found at i:30881 original size:28 final size:28
Alignment explanation
Indices: 30841--30914 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
30831 GGAATAAAGC
*
30841 CGGGGTTGGAGTATCCTCTCG-GAAGTAA
1 CGGGGTTGGAGTATCCTC-CGAGAAATAA
30869 CGGGGTTGGAGTATCC-CCGATGAAATAA
1 CGGGGTTGGAGTATCCTCCGA-GAAATAA
*
30897 CGAGGTTGGAGTATCCTC
1 CGGGGTTGGAGTATCCTC
30915 GATTGTGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 37 0.90
29 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCTCCGAGAAATAA
Found at i:30970 original size:52 final size:50
Alignment explanation
Indices: 30900--31025 Score: 135
Period size: 52 Copynumber: 2.4 Consensus size: 50
30890 GAAATAACGA
* * * *
30900 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGG-AGTTTTGAAAATAAAACCG
** * *
30951 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAAATAAAACCG
*
31003 GGATTGGAATATCCCCGATTGTG
1 GG-TTGGAGTATCCCCGATTGTG
31026 GAGAATTGAG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
51 3 0.05
52 49 0.80
53 9 0.15
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAAATAAAACCG
Found at i:33406 original size:13 final size:13
Alignment explanation
Indices: 33388--33413 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33378 ACAAAGATCC
33388 ATGTATCGATACA
1 ATGTATCGATACA
33401 ATGTATCGATACA
1 ATGTATCGATACA
33414 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:33409 original size:33 final size:33
Alignment explanation
Indices: 33367--33433 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
33357 AAAATTTCCA
***
33367 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
33400 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
33433 A
1 A
33434 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:33477 original size:19 final size:18
Alignment explanation
Indices: 33453--33520 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
33443 CAGTAGCTAA
33453 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
33472 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
33487 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
33504 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
33521 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:33493 original size:13 final size:13
Alignment explanation
Indices: 33475--33499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33465 ACAATACTTA
33475 TGTATCGATACAT
1 TGTATCGATACAT
33488 TGTATCGATACA
1 TGTATCGATACA
33500 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:33497 original size:32 final size:32
Alignment explanation
Indices: 33456--33518 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
33446 TAGCTAATTA
*
33456 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
33488 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
33519 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:33600 original size:21 final size:21
Alignment explanation
Indices: 33574--33630 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
33564 TACATTGTAG
33574 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
33595 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
33616 ATGTATCGATACATT
1 ATGTATCGATACATT
33631 TGGAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:33659 original size:13 final size:13
Alignment explanation
Indices: 33641--33666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33631 TGGAATTTTT
33641 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
33654 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
33667 ACACTTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:34344 original size:55 final size:55
Alignment explanation
Indices: 34260--35157 Score: 1340
Period size: 55 Copynumber: 16.3 Consensus size: 55
34250 ATAAATTGTA
* * * * * *
34260 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
34315 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
34370 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
34425 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
34480 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
34535 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
34590 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
34645 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
34700 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
34755 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
34810 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
34865 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
34920 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* ** *
34975 TCCTGCTCTTTGAGGACTGGAACATGCCACCGACTTAG-GTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTT-GTGTGGGCTTT-AAGAGGTG
* *
35030 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTAGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
35085 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
35140 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
35158 AAAAAGCGGA
Statistics
Matches: 779, Mismatches: 37, Indels: 54
0.90 0.04 0.06
Matches are distributed among these distances:
54 38 0.05
55 705 0.91
56 36 0.05
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:34453 original size:110 final size:110
Alignment explanation
Indices: 34260--35157 Score: 1536
Period size: 110 Copynumber: 8.2 Consensus size: 110
34250 ATAAATTGTA
* * * * * *
34260 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCT
*
34324 TTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
65 TTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
34370 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
34435 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
34480 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
* *
34545 TGAGGACTAGAAAATGCCACCAACTTGGGTGGGCTTTGAAAGGTG
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
34590 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
34655 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
34700 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
34765 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
34810 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
34875 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
34920 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
* *
34985 TGAGGACTGGAACATGCCACCGACTTAG-GTGGGCTTTGAAAGGTG
66 TGAGGACTGGAAAATGCCACCAACTT-GTGTGGGCTTTGAAAGGTG
* *
35030 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTAGGCTTTAAGAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCT
***
35094 TTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
65 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
35140 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
35158 AAAAAGCGGA
Statistics
Matches: 760, Mismatches: 22, Indels: 12
0.96 0.03 0.02
Matches are distributed among these distances:
109 5 0.01
110 746 0.98
111 9 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (110 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:34500 original size:26 final size:26
Alignment explanation
Indices: 34471--34615 Score: 73
Period size: 26 Copynumber: 5.3 Consensus size: 26
34461 GTGTGGGCTT
34471 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
34497 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
34524 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
* ** * * *
34552 TAGAAA-ATG-CCACCAACTTGGGTGGGC
1 T-GAAAGGTGTCCTGC-TCTTTGG-GGAC
34579 TTTGAAAGGTGTCCTGCTCTTTGGGGAC
1 --TGAAAGGTGTCCTGCTCTTTGGGGAC
34607 TGAAAGGTG
1 TGAAAGGTG
34616 CCACCAACTT
Statistics
Matches: 83, Mismatches: 22, Indels: 28
0.62 0.17 0.21
Matches are distributed among these distances:
25 6 0.07
26 27 0.33
27 10 0.12
28 18 0.22
29 16 0.19
30 6 0.07
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:36141 original size:1 final size:1
Alignment explanation
Indices: 36137--36197 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
36127 CTTTTCTCTC
* * * * ** *
36137 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTGCTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
36198 GAAGAGAAGG
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.89
Consensus pattern (1 bp):
T
Found at i:36191 original size:15 final size:13
Alignment explanation
Indices: 36137--36198 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
36127 CTTTTCTCTC
*
36137 TTTTTCTTTGTTT
1 TTTTTTTTTGTTT
*
36150 TGTTTTTTTGTTT
1 TTTTTTTTTGTTT
36163 TTTTTTTTT-TTT
1 TTTTTTTTTGTTT
*
36175 TTTTTTTTTGCTCT
1 TTTTTTTTTG-TTT
36189 TTTTTTTTTG
1 TTTTTTTTTG
36199 AAGAGAAGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
12 12 0.28
13 19 0.44
14 12 0.28
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Done.