Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2062.1
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: 308046
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 82 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:268174 original size:29 final size:29
Alignment explanation
Indices: 268115--268237 Score: 127
Period size: 29 Copynumber: 4.5 Consensus size: 29
268105 TTAATTTATT
* *
268115 TCAT-TTCAATTT-ATACTTTATTTTCATT
1 TCATATTC-ATTTCATATTTTAGTTTCATT
268143 TCATATTCATTT-A-A---TA-TTTCATT
1 TCATATTCATTTCATATTTTAGTTTCATT
*
268166 TCATATTCATTTAATATTTTAGTTTCATT
1 TCATATTCATTTCATATTTTAGTTTCATT
* *
268195 TCAAATTCATTTCATATTTTATTTTCATT
1 TCATATTCATTTCATATTTTAGTTTCATT
*
268224 TCATATTAATTTCA
1 TCATATTCATTTCA
268238 CTTTATTCAC
Statistics
Matches: 83, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
23 19 0.23
24 3 0.04
25 1 0.01
27 1 0.01
28 11 0.13
29 48 0.58
ACGTcount: A:0.28, C:0.13, G:0.01, T:0.58
Consensus pattern (29 bp):
TCATATTCATTTCATATTTTAGTTTCATT
Found at i:268213 original size:18 final size:18
Alignment explanation
Indices: 268192--268230 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
268182 TTTTAGTTTC
268192 ATTTCAAATTCATTTCAT
1 ATTTCAAATTCATTTCAT
* **
268210 ATTTTATTTTCATTTCAT
1 ATTTCAAATTCATTTCAT
268228 ATT
1 ATT
268231 AATTTCACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTCAAATTCATTTCAT
Found at i:268218 original size:23 final size:24
Alignment explanation
Indices: 268133--268233 Score: 100
Period size: 23 Copynumber: 4.0 Consensus size: 24
268123 ATTTATACTT
268133 TATTTTCATTTCATATTCATTTAA
1 TATTTTCATTTCATATTCATTTAA
268157 TA-TTTCATTTCATATTCATTTAA
1 TATTTTCATTTCATATTCATTTAA
* *
268180 TATTTTAGTTTCATTTCAAATTCATTTCA
1 TA---T--TTTCATTTCATATTCATTTAA
268209 TATTTT-ATTTTCAT-TTCATATTAA
1 TATTTTCA-TTTCATATTCAT-TTAA
268233 T
1 T
268234 TTCACTTTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
23 29 0.45
24 14 0.22
26 1 0.02
29 21 0.32
ACGTcount: A:0.29, C:0.12, G:0.01, T:0.58
Consensus pattern (24 bp):
TATTTTCATTTCATATTCATTTAA
Found at i:269424 original size:12 final size:12
Alignment explanation
Indices: 269407--269436 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
269397 TTACCATCAT
269407 GGCCTTTCAGAC
1 GGCCTTTCAGAC
269419 GGCCTTTCAGAC
1 GGCCTTTCAGAC
*
269431 GACCTT
1 GGCCTT
269437 ATCGTGCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.27
Consensus pattern (12 bp):
GGCCTTTCAGAC
Found at i:271200 original size:48 final size:48
Alignment explanation
Indices: 271129--271304 Score: 253
Period size: 48 Copynumber: 3.7 Consensus size: 48
271119 GTAAGATCTC
* * *
271129 GTGTAAGACCATGTCAGGGACATGGTATCGGTGTTGATATGTATGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTATGCCA
*
271177 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGCATGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTATGCCA
* * * *
271225 GTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGTGCAA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTATGCCA
* * *
271273 GTGTAATACCATGTCTAGGATATGGCATCGGC
1 GTGTAAGACCATGTCTGGGACATGGCATCGGC
271305 ACCAATATGT
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 115 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.27
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTATGCCA
Found at i:271313 original size:96 final size:96
Alignment explanation
Indices: 271129--271346 Score: 249
Period size: 96 Copynumber: 2.3 Consensus size: 96
271119 GTAAGATCTC
* * * * * *
271129 GTGTAAGACCATGTCAGGGACATGGTATCGGTGTTGATATGTATGCCAGTGTAAGACCATGTCTG
1 GTGTAAGACCATGTCAGGGACATGGCATCAGCGATGATATGTATGCAAGTGTAAGACCATGTCTA
****
271194 GGACATGGCATCGGCGTTGATATGCATGCCA
66 GGACATGGCATCGGCACCAATATGCATGCCA
* * *
271225 GTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATATGTGTGCAAGTGTAATACCATGTCTA
1 GTGTAAGACCATGTCAGGGACATGGCATCAGCGATGATATGTATGCAAGTGTAAGACCATGTCTA
* * *
271290 GGATATGGCATCGGCACCAATATGTGAT-CCC
66 GGACATGGCATCGGCACCAATATG-CATGCCA
* * *
271321 GTATAAGACCATATCAGGGATATGGC
1 GTGTAAGACCATGTCAGGGACATGGC
271347 TTCGACATCA
Statistics
Matches: 101, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
96 99 0.98
97 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (96 bp):
GTGTAAGACCATGTCAGGGACATGGCATCAGCGATGATATGTATGCAAGTGTAAGACCATGTCTA
GGACATGGCATCGGCACCAATATGCATGCCA
Found at i:271332 original size:48 final size:48
Alignment explanation
Indices: 271280--271399 Score: 125
Period size: 48 Copynumber: 2.5 Consensus size: 48
271270 CAAGTGTAAT
* * *
271280 ACCATGTCTAGGATATGGCATCGGCACCAATATGTGATCCCGTATAAG
1 ACCATATCTAGGATATGGCATCGACACCAATAAGTGATCCCGTATAAG
* * * * **
271328 ACCATATC-AGGGATATGGCTTCGACATCATTAAGTTATTTCGTATAAG
1 ACCATATCTA-GGATATGGCATCGACACCAATAAGTGATCCCGTATAAG
* *
271376 ACCATATCTGGGATATGGCGTCGA
1 ACCATATCTAGGATATGGCATCGA
271400 TATGTAGATC
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
47 1 0.02
48 58 0.98
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (48 bp):
ACCATATCTAGGATATGGCATCGACACCAATAAGTGATCCCGTATAAG
Found at i:274503 original size:42 final size:42
Alignment explanation
Indices: 274456--274536 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
274446 GTCTTACGAC
* *
274456 ATACGAGCAGACGTGCATGTGTGTGAACCTTCTAGTTTTCTT
1 ATACGAGCAAACGTGCATGTGTATGAACCTTCTAGTTTTCTT
* * *
274498 ATACGAGCAAATGTGTATGTGTATGGACCTTCTAGTTTT
1 ATACGAGCAAACGTGCATGTGTATGAACCTTCTAGTTTT
274537 TTTACCATCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (42 bp):
ATACGAGCAAACGTGCATGTGTATGAACCTTCTAGTTTTCTT
Found at i:277832 original size:69 final size:69
Alignment explanation
Indices: 277720--277879 Score: 223
Period size: 69 Copynumber: 2.3 Consensus size: 69
277710 TCAACTTTAC
*
277720 CCTTCTCCCTCTTTTTCGTTCTCACGTCTGAAGCAACTTCTTTTTTTTCA-TTCTTCCCATTTCC
1 CCTTCT-CCTCTTTTTCATTCTCACGTCTGAAGCAACTTC-TTTTTTTCATTTCTTCCCATTTCC
277784 TTCCAA
64 TTCCAA
* * *
277790 CCTTCTCCTCTTTTTCATTGTCACGTCTGAATCATCTTCTTTTTTTCATTCTTCTTCCCATTTCC
1 CCTTCTCCTCTTTTTCATTCTCACGTCTGAAGCAACTTCTTTTTTTCA-T-TTCTTCCCATTTCC
277855 TTCCAA
64 TTCCAA
*
277861 CCATCTCTCTCTTTTTCAT
1 CCTTCTC-CTCTTTTTCAT
277880 GCTTATATCC
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
68 9 0.11
69 29 0.36
70 6 0.07
71 26 0.32
72 11 0.14
ACGTcount: A:0.12, C:0.34, G:0.04, T:0.49
Consensus pattern (69 bp):
CCTTCTCCTCTTTTTCATTCTCACGTCTGAAGCAACTTCTTTTTTTCATTTCTTCCCATTTCCTT
CCAA
Found at i:282498 original size:17 final size:17
Alignment explanation
Indices: 282478--282510 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
282468 ATTAAGAATG
282478 TTATTAAATTAAATTTT
1 TTATTAAATTAAATTTT
*
282495 TTATTAAATTATATTT
1 TTATTAAATTAAATTT
282511 AATAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTAAATTAAATTTT
Found at i:282771 original size:16 final size:16
Alignment explanation
Indices: 282750--282788 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
282740 TGAATTACTG
*
282750 ATTACAGCTCTATTCA
1 ATTACAGCCCTATTCA
*
282766 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCA
282782 ATTACAG
1 ATTACAG
282789 TGAACCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (16 bp):
ATTACAGCCCTATTCA
Found at i:288783 original size:45 final size:44
Alignment explanation
Indices: 288719--288807 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 44
288709 AGTTTCTTCT
* *
288719 TCTTCTTCTGTATCTTTATCCTTCATATGTATTCGTCTCAGATA
1 TCTTCTTCTGTATCTTTATCCTTCATATGTAGTCGCCTCAGATA
*
288763 NTCTTCTTCTGTATCTTTATCCTTCATATGTGGTCGCCTCAGATA
1 -TCTTCTTCTGTATCTTTATCCTTCATATGTAGTCGCCTCAGATA
288808 AAATTGTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.17, C:0.24, G:0.11, T:0.47
Consensus pattern (44 bp):
TCTTCTTCTGTATCTTTATCCTTCATATGTAGTCGCCTCAGATA
Found at i:296415 original size:29 final size:28
Alignment explanation
Indices: 296358--296412 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
296348 TTCCTTAAAA
*
296358 AAAAGAAAACGAAGAAAATATAATTTTC
1 AAAAGAAAAAGAAGAAAATATAATTTTC
* *
296386 AAAAGAAAAATAATAAAATATAATTTT
1 AAAAGAAAAAGAAGAAAATATAATTTT
296413 TCAGTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (28 bp):
AAAAGAAAAAGAAGAAAATATAATTTTC
Found at i:297782 original size:20 final size:20
Alignment explanation
Indices: 297759--297799 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
297749 GCCAAAGCAT
297759 ATAGCACTACAGCAAAATAG
1 ATAGCACTACAGCAAAATAG
297779 ATAGCACTACAGCAAAATAG
1 ATAGCACTACAGCAAAATAG
297799 A
1 A
297800 CTTTTAGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.20, G:0.15, T:0.15
Consensus pattern (20 bp):
ATAGCACTACAGCAAAATAG
Found at i:298783 original size:28 final size:29
Alignment explanation
Indices: 298752--298811 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
298742 TAGGAATTAT
* *
298752 GTTTATGGCTTATGGTTTAAG-GGTT-GGG
1 GTTTAAGGCTTATGGGTT-AGTGGTTAGGG
*
298780 GTTTAAGGGTTATGGGTTAGTGGTTAGGG
1 GTTTAAGGCTTATGGGTTAGTGGTTAGGG
298809 GTT
1 GTT
298812 AGGGGTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 19 0.70
29 6 0.22
ACGTcount: A:0.15, C:0.02, G:0.42, T:0.42
Consensus pattern (29 bp):
GTTTAAGGCTTATGGGTTAGTGGTTAGGG
Found at i:298798 original size:7 final size:7
Alignment explanation
Indices: 298772--298863 Score: 87
Period size: 7 Copynumber: 12.9 Consensus size: 7
298762 TATGGTTTAA
298772 GGGTT-G
1 GGGTTAG
*
298778 GGGTTTAA
1 GGG-TTAG
*
298786 GGGTTAT
1 GGGTTAG
298793 GGGTTAG
1 GGGTTAG
*
298800 TGGTTAG
1 GGGTTAG
298807 GGGTTAG
1 GGGTTAG
298814 GGGTTTAG
1 GGG-TTAG
298822 GGGTTAG
1 GGGTTAG
*
298829 GGGTTAAT
1 GGGTT-AG
*
298837 GGTTTAG
1 GGGTTAG
*
298844 GGGTTAA
1 GGGTTAG
*
298851 GGCTTAG
1 GGGTTAG
298858 GGGTTA
1 GGGTTA
298864 TTATTTTATG
Statistics
Matches: 69, Mismatches: 13, Indels: 7
0.78 0.15 0.08
Matches are distributed among these distances:
6 3 0.04
7 51 0.74
8 15 0.22
ACGTcount: A:0.16, C:0.01, G:0.48, T:0.35
Consensus pattern (7 bp):
GGGTTAG
Found at i:298804 original size:22 final size:21
Alignment explanation
Indices: 298772--298863 Score: 87
Period size: 22 Copynumber: 4.3 Consensus size: 21
298762 TATGGTTTAA
*
298772 GGGTT-GGGGTTTAAGGGTTAT
1 GGGTTAGGGG-TTAAGGGTTAG
* *
298793 GGGTTAGTGGTTAGGGGTTAG
1 GGGTTAGGGGTTAAGGGTTAG
* *
298814 GGGTTTAGGGGTTAGGGGTTAAT
1 GGG-TTAGGGGTTAAGGGTT-AG
* *
298837 GGTTTAGGGGTTAAGGCTTAG
1 GGGTTAGGGGTTAAGGGTTAG
298858 GGGTTA
1 GGGTTA
298864 TTATTTTATG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
21 23 0.40
22 32 0.55
23 3 0.05
ACGTcount: A:0.16, C:0.01, G:0.48, T:0.35
Consensus pattern (21 bp):
GGGTTAGGGGTTAAGGGTTAG
Found at i:299079 original size:21 final size:20
Alignment explanation
Indices: 299055--299111 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 20
299045 ATTGTTTGTG
299055 GTTTATGGTTTAAGGGATATA
1 GTTTA-GGTTTAAGGGATATA
*
299076 GTTTAGGGTTTAAGAGATATA
1 GTTTA-GGTTTAAGGGATATA
299097 GTTTAGAGTTTAAGG
1 GTTTAG-GTTTAAGG
299112 TTATGGTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (20 bp):
GTTTAGGTTTAAGGGATATA
Found at i:301426 original size:14 final size:14
Alignment explanation
Indices: 301408--301452 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
301398 TAATGTATAT
301408 ATATATCAATATG-
1 ATATATCAATATGC
*
301421 -TATAT--ATATAC
1 ATATATCAATATGC
301432 ATATATCAATATGC
1 ATATATCAATATGC
301446 ATATATC
1 ATATATC
301453 TTGGGTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
10 4 0.15
12 10 0.38
14 12 0.46
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (14 bp):
ATATATCAATATGC
Found at i:301435 original size:24 final size:24
Alignment explanation
Indices: 301403--301451 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
301393 GATTGTAATG
* *
301403 TATATATATATCAATATGTATATA
1 TATACATATATCAATATGCATATA
301427 TATACATATATCAATATGCATATA
1 TATACATATATCAATATGCATATA
301451 T
1 T
301452 CTTGGGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (24 bp):
TATACATATATCAATATGCATATA
Found at i:301620 original size:25 final size:25
Alignment explanation
Indices: 301563--301625 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
301553 TCCGCATCGT
* * *
301563 CGTCGGCAGCCCTATGCTACATTTT
1 CGTCGGCATCCCTATGCTACATCTC
* * *
301588 CATTGGCATCCCTTTGCTACATCTC
1 CGTCGGCATCCCTATGCTACATCTC
301613 CGTCGGCATCCCT
1 CGTCGGCATCCCT
301626 CTGTTGCTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.14, C:0.37, G:0.17, T:0.32
Consensus pattern (25 bp):
CGTCGGCATCCCTATGCTACATCTC
Found at i:303588 original size:13 final size:14
Alignment explanation
Indices: 303572--303600 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
303562 TTATAAATAT
303572 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
303585 TTATAATGGTTTAA
1 TTATAATGGTTTAA
303599 TT
1 TT
303601 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:304062 original size:21 final size:21
Alignment explanation
Indices: 304012--304083 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
304002 TTAGAGCGGA
304012 TGCAGCAGCGAGGGAGGCAAC
1 TGCAGCAGCGAGGGAGGCAAC
* *
304033 -GACAACAGCGAGGGAGGCAGC
1 TG-CAGCAGCGAGGGAGGCAAC
** *
304054 TGCAGCAGCGAAAGAGGCAAA
1 TGCAGCAGCGAGGGAGGCAAC
*
304075 GGCAGCAGC
1 TGCAGCAGC
304084 AATGGCAGCA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.40, T:0.03
Consensus pattern (21 bp):
TGCAGCAGCGAGGGAGGCAAC
Found at i:304493 original size:43 final size:43
Alignment explanation
Indices: 304446--304629 Score: 208
Period size: 43 Copynumber: 4.3 Consensus size: 43
304436 GTAACAAAAG
* *
304446 CGCCGTTAAAAGCCATGACTTTTAGCGGCGTTTCACCCACAAA
1 CGCCGCTAAAAGCCATGACTTTTAGCGGCGCTTCACCCACAAA
* * * *
304489 CGCCGCTAAAAGCAATGACTTTTAACGGTGCTTCATCCACAAA
1 CGCCGCTAAAAGCCATGACTTTTAGCGGCGCTTCACCCACAAA
* ** * *
304532 CGCCGCTATAAGCCATGACTTTTAGCAACGCTTCACCTAAAAA
1 CGCCGCTAAAAGCCATGACTTTTAGCGGCGCTTCACCCACAAA
* * * **
304575 TGTCACTAAAAGCCATGACTTTTAGCGGCGCTT-TTCCAGCAAA
1 CGCCGCTAAAAGCCATGACTTTTAGCGGCGCTTCACCCA-CAAA
304618 CGCCGCTAAAAG
1 CGCCGCTAAAAG
304630 TCAGGATCTT
Statistics
Matches: 112, Mismatches: 28, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
42 2 0.02
43 110 0.98
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
CGCCGCTAAAAGCCATGACTTTTAGCGGCGCTTCACCCACAAA
Found at i:305347 original size:57 final size:56
Alignment explanation
Indices: 305278--305393 Score: 187
Period size: 57 Copynumber: 2.1 Consensus size: 56
305268 CCTCTGTTTA
305278 CTACGAACCACATTTATATCTGAAAAAAATTCATATGACTATGAGATTTATTTCTAC
1 CTACGAACCACATTTATATCTGAAAAAAATTCATATGACTATGAGATTTATTTCT-C
* * * *
305335 CTACGAACCACATTTCTCTCTGTAAAAAATTCATATGACTATGAGGTTTATTTCTC
1 CTACGAACCACATTTATATCTGAAAAAAATTCATATGACTATGAGATTTATTTCTC
305391 CTA
1 CTA
305394 AAACTAGACT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
56 4 0.07
57 51 0.93
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (56 bp):
CTACGAACCACATTTATATCTGAAAAAAATTCATATGACTATGAGATTTATTTCTC
Found at i:306446 original size:93 final size:93
Alignment explanation
Indices: 306337--306508 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
306327 CGCCCATAAG
* * *
306337 CGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCATAAGTCAATTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTCAACTCGGACTCAACTCA
306402 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
306430 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTCAACTCGGACTCAACTCA
306495 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
306509 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTCAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:306505 original size:46 final size:46
Alignment explanation
Indices: 306330--306505 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
306320 TGTAACCCGC
* *
306330 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
306376 CCATAAGTC-AATTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAG-CGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
306426 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
306469 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
306506 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.