Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017509.1 Corchorus olitorius cultivar O-4 contig17542, 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: 56934
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:7319 original size:15 final size:15
Alignment explanation
Indices: 7299--7329 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7289 AAGAATAGGG
7299 GATGAAAACCAAAGT
1 GATGAAAACCAAAGT
*
7314 GATGAAAATCAAAGT
1 GATGAAAACCAAAGT
7329 G
1 G
7330 TATTAGAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.16
Consensus pattern (15 bp):
GATGAAAACCAAAGT
Found at i:7962 original size:12 final size:12
Alignment explanation
Indices: 7945--7987 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
7935 CAAAATTTAT
7945 ATATATATATAC
1 ATATATATATAC
*
7957 ATATATATATAT
1 ATATATATATAC
* *
7969 ATATATATCTGC
1 ATATATATATAC
7981 ATATATA
1 ATATATA
7988 ATAAGGTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (12 bp):
ATATATATATAC
Found at i:7987 original size:2 final size:2
Alignment explanation
Indices: 7942--7976 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
7932 AAGCAAAATT
*
7942 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7977 CTGCATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9790 original size:53 final size:53
Alignment explanation
Indices: 9732--9837 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
9722 GGTGCGATAT
9732 CCCTAGGCTTTTCAACGGGAGATATCATTCTTCAAAGTCTGTAAGTTTTCTTA
1 CCCTAGGCTTTTCAACGGGAGATATCATTCTTCAAAGTCTGTAAGTTTTCTTA
9785 CCCTAGGCTTTTCAACGGGAGATATCATTCTTCAAAGTCTGTAAGTTTTCTTA
1 CCCTAGGCTTTTCAACGGGAGATATCATTCTTCAAAGTCTGTAAGTTTTCTTA
9838 AGTTTCTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (53 bp):
CCCTAGGCTTTTCAACGGGAGATATCATTCTTCAAAGTCTGTAAGTTTTCTTA
Found at i:11609 original size:30 final size:31
Alignment explanation
Indices: 11575--11633 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
11565 TGAGTATATG
11575 TATTTA-TAACTTATAAGTGCAAAACGATGA
1 TATTTAGTAACTTATAAGTGCAAAACGATGA
* *
11605 TATTTATGTTAGTTATAAGTGCAAAACGA
1 TATTTA-GTAACTTATAAGTGCAAAACGA
11634 CATAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
32 19 0.76
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (31 bp):
TATTTAGTAACTTATAAGTGCAAAACGATGA
Found at i:15546 original size:20 final size:20
Alignment explanation
Indices: 15521--15559 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
15511 TTTGCTAAAA
15521 TATAAGTTGATGTTAAGTTC
1 TATAAGTTGATGTTAAGTTC
15541 TATAAGTTGATGTTAAGTT
1 TATAAGTTGATGTTAAGTT
15560 TAATTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.46
Consensus pattern (20 bp):
TATAAGTTGATGTTAAGTTC
Found at i:21859 original size:5 final size:5
Alignment explanation
Indices: 21849--21877 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
21839 GCTTTTAAGA
21849 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
21878 TTTTCCATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:23367 original size:13 final size:13
Alignment explanation
Indices: 23349--23376 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23339 AATTCCAACC
23349 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
23362 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
23375 TT
1 TT
23377 ATTACTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:25663 original size:25 final size:25
Alignment explanation
Indices: 25634--25684 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
25624 AGGCCCAGTG
25634 GTAACAAAATGTGTTGAGGCCAATA
1 GTAACAAAATGTGTTGAGGCCAATA
* *
25659 GTAACAGAATGTGTTGGGGCCAATA
1 GTAACAAAATGTGTTGAGGCCAATA
25684 G
1 G
25685 CCTAAGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (25 bp):
GTAACAAAATGTGTTGAGGCCAATA
Found at i:28971 original size:21 final size:21
Alignment explanation
Indices: 28939--28978 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28929 TTGGTTTTTC
*
28939 TTATTGAAAAAATTTGGTATT
1 TTATTGAAAAAATGTGGTATT
28960 TTATT-AATAAAATGTGGTA
1 TTATTGAA-AAAATGTGGTA
28979 GATTAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (21 bp):
TTATTGAAAAAATGTGGTATT
Found at i:28971 original size:23 final size:23
Alignment explanation
Indices: 28923--28971 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
28913 TTATTTTTTT
* * *
28923 AAAAGTTTGGTTTTTCTTATTGA
1 AAAAATTTGGTTTTTATTAATGA
28946 AAAAATTTGGTATTTTATTAAT-A
1 AAAAATTTGGT-TTTTATTAATGA
28969 AAA
1 AAA
28972 TGTGGTAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (23 bp):
AAAAATTTGGTTTTTATTAATGA
Found at i:31679 original size:2 final size:2
Alignment explanation
Indices: 31672--31718 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
31662 GGGTAAATCA
31672 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31714 TC TC T
1 TC TC T
31719 TTTCAGTGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:33476 original size:21 final size:21
Alignment explanation
Indices: 33431--33470 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33421 ACTGCCTACC
33431 TGGGTGATCAGGCAAACCACA
1 TGGGTGATCAGGCAAACCACA
*
33452 TGGGTGTTCAGGCAAACCA
1 TGGGTGATCAGGCAAACCA
33471 TGTGGGCGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.17
Consensus pattern (21 bp):
TGGGTGATCAGGCAAACCACA
Found at i:35490 original size:6 final size:6
Alignment explanation
Indices: 35479--35508 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
35469 CTTAAAATCG
35479 TATGTT TATGTT TATGTT TATGTT TATGTT
1 TATGTT TATGTT TATGTT TATGTT TATGTT
35509 GTTCAGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (6 bp):
TATGTT
Found at i:38301 original size:36 final size:37
Alignment explanation
Indices: 38182--38353 Score: 226
Period size: 37 Copynumber: 4.7 Consensus size: 37
38172 AAGACCGAAT
* * *
38182 TTGACGGGAACTTTCCCTAAATTGAAAAC--TAAAATC
1 TTGATGGGAACTTTCCC-AATTTGAAAACTTTAAAAAC
*
38218 -TGATGGGAACTTTCCCAATTTGAAAACTTTGAAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAACTTTAAAAAC
* *
38254 TGGATGTGAACTTTCCCAATTTGAAAAC-TTAAAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAACTTTAAAAAC
*
38290 TTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAACTTTAAAAAC
**
38327 TTGATGGGAACTTTTTCAATTTGAAAA
1 TTGATGGGAACTTTCCCAATTTGAAAA
38354 GAGCTAAATT
Statistics
Matches: 120, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 10 0.08
35 15 0.12
36 38 0.32
37 57 0.47
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (37 bp):
TTGATGGGAACTTTCCCAATTTGAAAACTTTAAAAAC
Found at i:38305 original size:73 final size:71
Alignment explanation
Indices: 38187--38353 Score: 253
Period size: 73 Copynumber: 2.3 Consensus size: 71
38177 CGAATTTGAC
* *
38187 GGGAACTTTCCCTAAATTGAAAACTAAAATCTGATGGGAACTTTCCCAATTTGAAAACTTTGAAA
1 GGGAACTTTCCC-AATTTGAAAACTAAAAACTGATGGGAACTTTCCCAATTTGAAAACTTTGAAA
38252 ACTGGAT
65 ACTGGAT
*
38259 GTGAACTTTCCCAATTTGAAAACTTAAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTTGAA
1 GGGAACTTTCCCAATTTGAAAAC-TAAAAAC-TGATGGGAACTTTCCCAATTTGAAAACTTTGAA
*
38324 AACTTGAT
64 AACTGGAT
**
38332 GGGAACTTTTTCAATTTGAAAA
1 GGGAACTTTCCCAATTTGAAAA
38354 GAGCTAAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
71 10 0.12
72 17 0.20
73 59 0.69
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (71 bp):
GGGAACTTTCCCAATTTGAAAACTAAAAACTGATGGGAACTTTCCCAATTTGAAAACTTTGAAAA
CTGGAT
Found at i:38447 original size:54 final size:52
Alignment explanation
Indices: 38310--38473 Score: 283
Period size: 52 Copynumber: 3.1 Consensus size: 52
38300 CTTTCCCAAT
* **
38310 TTGAAAACTTTGAAAACTTGATGGGAACTTTTTCAATTTGAAAAGAGCTAAA
1 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAA
38362 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTTAAA
1 TTGAATACTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGC-TAAA
38415 TTGAATACTTTGAAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAA
1 TTGAATACTTTG-AAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAA
38468 TTGAAT
1 TTGAAT
38474 TGAATACTTT
Statistics
Matches: 107, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
52 45 0.42
53 26 0.24
54 36 0.34
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (52 bp):
TTGAATACTTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAA
Found at i:45088 original size:27 final size:27
Alignment explanation
Indices: 44964--45092 Score: 186
Period size: 27 Copynumber: 4.8 Consensus size: 27
44954 TTGAATTAAA
*
44964 AAATGACCAAAACACCCCTGAACATGC
1 AAATGACCAAAACACCCCTGGACATGC
* *
44991 AAATGACCAAAACCCCCCTGGACGTGC
1 AAATGACCAAAACACCCCTGGACATGC
*
45018 AAATGACCAAAACACCCCTGAACATGC
1 AAATGACCAAAACACCCCTGGACATGC
* *
45045 AAATGACCAAAACGCCCCTGGACGTGC
1 AAATGACCAAAACACCCCTGGACATGC
**
45072 AAATGACCAAAATGCCCCTGG
1 AAATGACCAAAACACCCCTGG
45093 GTGCCCCTAA
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 92 1.00
ACGTcount: A:0.39, C:0.33, G:0.16, T:0.12
Consensus pattern (27 bp):
AAATGACCAAAACACCCCTGGACATGC
Found at i:45091 original size:54 final size:54
Alignment explanation
Indices: 44964--45083 Score: 231
Period size: 54 Copynumber: 2.2 Consensus size: 54
44954 TTGAATTAAA
44964 AAATGACCAAAACACCCCTGAACATGCAAATGACCAAAACCCCCCTGGACGTGC
1 AAATGACCAAAACACCCCTGAACATGCAAATGACCAAAACCCCCCTGGACGTGC
*
45018 AAATGACCAAAACACCCCTGAACATGCAAATGACCAAAACGCCCCTGGACGTGC
1 AAATGACCAAAACACCCCTGAACATGCAAATGACCAAAACCCCCCTGGACGTGC
45072 AAATGACCAAAA
1 AAATGACCAAAA
45084 TGCCCCTGGG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.42, C:0.33, G:0.15, T:0.11
Consensus pattern (54 bp):
AAATGACCAAAACACCCCTGAACATGCAAATGACCAAAACCCCCCTGGACGTGC
Found at i:45449 original size:23 final size:23
Alignment explanation
Indices: 45423--45499 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
45413 AAGAACCGTT
45423 TTCCGCTTATCCTTTGAACTGTC
1 TTCCGCTTATCCTTTGAACTGTC
** * *
45446 TTCCAATTCAAT-CTTAAAAGAACCGTC
1 TTCCGCTT--ATCCTT---TGAACTGTC
45473 TTCCGCTTATCCTTTGAACTGTC
1 TTCCGCTTATCCTTTGAACTGTC
45496 TTCC
1 TTCC
45500 AATTCAATCT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
23 17 0.43
24 3 0.08
25 4 0.10
26 3 0.08
27 13 0.32
ACGTcount: A:0.21, C:0.30, G:0.10, T:0.39
Consensus pattern (23 bp):
TTCCGCTTATCCTTTGAACTGTC
Found at i:45449 original size:50 final size:50
Alignment explanation
Indices: 45384--45579 Score: 329
Period size: 50 Copynumber: 3.9 Consensus size: 50
45374 GAATCAACTT
* * *
45384 CTTTGAACTGTCTTCCAATCCAATATTAAAAGAACCGTTTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGAACCGTCTTCCGCTTATC
45434 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGAACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGAACCGTCTTCCGCTTATC
*
45484 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGAACCGTCTTCCGCTTATC
* * *
45534 CTTTAAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCT
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGAACCGTCTTCCGCT
45580 CGTGTTTCAA
Statistics
Matches: 140, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 140 1.00
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGAACCGTCTTCCGCTTATC
Found at i:45476 original size:27 final size:27
Alignment explanation
Indices: 45438--45576 Score: 82
Period size: 27 Copynumber: 5.4 Consensus size: 27
45428 CTTATCCTTT
*
45438 GAACTGTCTTCCAATTCAATCTTAAAA
1 GAACCGTCTTCCAATTCAATCTTAAAA
** *
45465 GAACCGTCTTCCGCTT--ATCCTT---T
1 GAACCGTCTTCCAATTCAAT-CTTAAAA
*
45488 GAACTGTCTTCCAATTCAATCTTAAAA
1 GAACCGTCTTCCAATTCAATCTTAAAA
* ** *
45515 GGACCGTCTTCCGCTT--ATCCTT--TA
1 GAACCGTCTTCCAATTCAAT-CTTAAAA
*
45539 -AACTGTCTTCCAATTCAATCTTAAAA
1 GAACCGTCTTCCAATTCAATCTTAAAA
* *
45565 GGATCGTCTTCC
1 GAACCGTCTTCC
45577 GCTCGTGTTT
Statistics
Matches: 79, Mismatches: 21, Indels: 24
0.64 0.17 0.19
Matches are distributed among these distances:
23 24 0.30
24 7 0.09
25 8 0.10
26 7 0.09
27 33 0.42
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (27 bp):
GAACCGTCTTCCAATTCAATCTTAAAA
Found at i:45546 original size:23 final size:23
Alignment explanation
Indices: 45470--45549 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
45460 TAAAAGAACC
*
45470 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTAAACT
** * *
45493 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCGCTT--ATCCTT-TAA--ACT
45520 GTCTTCCGCTTATCCTTTAAACT
1 GTCTTCCGCTTATCCTTTAAACT
45543 GTCTTCC
1 GTCTTCC
45550 AATTCAATCT
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
23 18 0.43
24 3 0.07
25 7 0.17
26 3 0.07
27 11 0.26
ACGTcount: A:0.20, C:0.30, G:0.11, T:0.39
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTAAACT
Found at i:45921 original size:65 final size:64
Alignment explanation
Indices: 45852--46206 Score: 505
Period size: 65 Copynumber: 5.5 Consensus size: 64
45842 GGTGTATCTC
* *
45852 TTAACAAGATCGTCTTCCGATCAACTTCTGAAACCTT-TTCGAGAAACTATCTTCTGGTGTACTT
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTGTT-GAGAAACCATCTTCTGGTGTACTT
45916 T
64 T
* * * *
45917 TTAACAACATCGTCCTCCGATCAACTTCTGAAAATTTTTTAGAAACCATCTTCTGGTGTACTTCT
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTT-T
* * *
45982 TTAAGAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAAATCATCTTCTGGTGTACTTC
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAG-AAACCATCTTCTGGTGTACTTT
* * * *
46047 TTGACAAGATCATCTTCCGATCCACTTCTGAAAAATTGTTGAGAAACCATCTTCTGGTGTACTTC
1 TTAACAAGATCGTCTTCCGATCAACTTCTG-AAAATTGTTGAGAAACCATCTTCTGGTGTACTTT
* *
46112 CTGACAAGATCGTCTTCCGATCAACTTCTGAAAAATTGTTGAGAAACCATCTTCTGGTGTACTTT
1 TTAACAAGATCGTCTTCCGATCAACTTCTG-AAAATTGTTGAGAAACCATCTTCTGGTGTACTTT
*
46177 TTGACAAGATCGTCTTCCGATCAACTTCTG
1 TTAACAAGATCGTCTTCCGATCAACTTCTG
46207 GAGAATTCTT
Statistics
Matches: 264, Mismatches: 22, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
64 24 0.09
65 208 0.79
66 32 0.12
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (64 bp):
TTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTT
Found at i:46002 original size:130 final size:128
Alignment explanation
Indices: 45836--46268 Score: 521
Period size: 130 Copynumber: 3.3 Consensus size: 128
45826 TAAATAACTG
*
45836 TCTTCCGGTGTA-TCTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAACCTT-TTCGAGAAAC
1 TCTTCCGGTGTATTCT-TTAACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTGTT-GAGAAAC
* * *
45899 TATCTTCTGGTGTACTTTTTAACAACATCGTCCTCCGATCAACTTCTGAAAATTTTTTAGAAACC
63 TATCTTCTGGTGTACTTTTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTTAGAAACC
45964 A
128 A
* * *
45965 TCTTCTGGTGTACTTCTTTAAGAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAAATC
1 TCTTCCGGTGTA-TTCTTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACT-
* * * * *
46030 ATCTTCTGGTGTACTTCTTGACAAGATCATCTTCCGATCCACTTCTGAAAAATTGTTGAGAAACC
64 ATCTTCTGGTGTACTTTTTGACAAGATCGTCTTCCGATCAACTTCTG-AAAATTTTTTAGAAACC
46095 A
128 A
* * * *
46096 TCTTCTGGTGTACTTC-CTGACAAGATCGTCTTCCGATCAACTTCTGAAAAATTGTTGAGAAACC
1 TCTTCCGGTGTA-TTCTTTAACAAGATCGTCTTCCGATCAACTTCTG-AAAATTGTTGAGAAACT
*
46160 ATCTTCTGGTGTACTTTTTGACAAGATCGTCTTCCGATCAACTTCTGGAGAATTCTTTCTAGCAA
64 ATCTTCTGGTGTACTTTTTGACAAGATCGTCTTCCGATCAACTTCT-GAAAATT-TTT-TAG-AA
*
46225 ACCG
125 ACCA
* * ** * *
46229 TCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAA
1 TCTTCCGGTGTATTCTTTAACAAGATCGTCTTCCGATCAA
46269 GATTTGAAAA
Statistics
Matches: 261, Mismatches: 32, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
129 20 0.08
130 150 0.57
131 53 0.20
132 5 0.02
133 33 0.13
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (128 bp):
TCTTCCGGTGTATTCTTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACTAT
CTTCTGGTGTACTTTTTGACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTTAGAAACCA
Found at i:46370 original size:67 final size:67
Alignment explanation
Indices: 46183--46370 Score: 279
Period size: 67 Copynumber: 2.8 Consensus size: 67
46173 CTTTTTGACA
* * * **
46183 AGATCGTCTTCCGATCAAC-TTCTGGAGAATTCTTTCTAGCAAACCGTCTTCCGATGTATTCCTT
1 AGATTGTCTTCCAATCAACATT-T-GAAAATTCTTTCTAGCAAACCGTCTTCCGGGGTATTCCTT
46247 AATG
64 AATG
* *
46251 AGATTGTCTTCCAATCAAGATTTGAAAATTATTTCTAGCAAACCGTCTTCCGGGGTATTCCTTAA
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGGGTATTCCTTAA
46316 TG
66 TG
*
46318 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAAACCGTCTTCCGG
1 AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGG
46371 ATCATCTTTG
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
67 90 0.83
68 17 0.16
69 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (67 bp):
AGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGGGTATTCCTTAA
TG
Found at i:51344 original size:30 final size:30
Alignment explanation
Indices: 51301--52173 Score: 1097
Period size: 30 Copynumber: 29.1 Consensus size: 30
51291 CAAATAAACC
* * *
51301 AAAGTAATAATCCT-AAATCAGGATAAAAAT
1 AAAGCAATGATCCTCAAA-CAGGATTAAAAT
* * *
51331 AAAGCGATGATCCTCAACCAGCATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* ** *
51361 AAAGCAATGGTCCTCATCCAAGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
** *
51391 AAAGCAACAATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
51421 GATGCAAAT-ATCCTCAACCAGGATTAAAAT
1 AAAGC-AATGATCCTCAAACAGGATTAAAAT
* * * * *
51451 GGAGGAAAT-ATACTCAATCAGGATTAAAAT
1 -AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
51481 GAAGCAATGATCCTTAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
51511 GATGCAACGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
51541 AAAGCAATGATCCTC-AACTAGGATTAAAAT
1 AAAGCAATGATCCTCAAAC-AGGATTAAAAT
** * *
51571 AAAGCAACAATCCTCAACCATGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
51601 AAAGCAGTGCTCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
51631 AAAGCAACGCTCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
51661 ACAGCAATGATCCTCAAACAAGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
51691 AAAGCAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
** *
51721 AAAGCAACAATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
51751 AAAGCAGTGCTCCTCTAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
51781 AAAACAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
51811 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* * *
51841 AAAGCACTGATCCTCAAACATGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
51871 AAAGCAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
** *
51901 AAAGCAACAATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
51931 AAAGCAGTGCTCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
51961 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
51991 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
52021 AAAGCAATGATCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
** *
52051 AAAGCAACAATCCTCAACCAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
* *
52081 AAAGCAGTGCTCCTCAAACAGGATTAAAAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
52111 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
*
52141 AAAGCAATGATCCTCAAACAGGATTAACAT
1 AAAGCAATGATCCTCAAACAGGATTAAAAT
52171 AAA
1 AAA
52174 CTGAAGAAAG
Statistics
Matches: 737, Mismatches: 100, Indels: 12
0.87 0.12 0.01
Matches are distributed among these distances:
29 9 0.01
30 719 0.98
31 9 0.01
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (30 bp):
AAAGCAATGATCCTCAAACAGGATTAAAAT
Found at i:52244 original size:36 final size:36
Alignment explanation
Indices: 52169--52402 Score: 170
Period size: 36 Copynumber: 6.3 Consensus size: 36
52159 CAGGATTAAC
* *
52169 ATAAACTGAAG-AAAGACCGCCCTTGG-TCAACTGAA
1 ATAAACTGAAGAAAAGATCGCCC-TGGATCAAATGAA
** * *
52204 ATAAACTGAAGGGAGGATCGCCCTGGATC-AATTAA
1 ATAAACTGAAGAAAAGATCGCCCTGGATCAAATGAA
52239 TATAAACTGAAGAAAAGATCGCCCTGGATCAAATGAA
1 -ATAAACTGAAGAAAAGATCGCCCTGGATCAAATGAA
** *
52276 ATAAACTGAAATGAATTGAACAAGGATTACCCTGGATCAACTGAA
1 ATAAAC-----TGAA--GAA-AA-GATCGCCCTGGATCAAATGAA
* * * *
52321 GTGAATTGAAGAAAAGATCGCCCTGGATCAATTGAA
1 ATAAACTGAAGAAAAGATCGCCCTGGATCAAATGAA
* * * * *
52357 ATAAACTGAA-TAAAGACCGTCCTGGGTCAACTGAA
1 ATAAACTGAAGAAAAGATCGCCCTGGATCAAATGAA
*
52392 ATGAACTGAAG
1 ATAAACTGAAG
52403 CATCTGAAAT
Statistics
Matches: 158, Mismatches: 27, Indels: 27
0.75 0.13 0.13
Matches are distributed among these distances:
35 47 0.30
36 67 0.42
37 7 0.04
38 3 0.02
40 4 0.03
41 4 0.03
43 3 0.02
44 2 0.01
45 21 0.13
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (36 bp):
ATAAACTGAAGAAAAGATCGCCCTGGATCAAATGAA
Found at i:52381 original size:35 final size:36
Alignment explanation
Indices: 52305--52402 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 36
52295 ACAAGGATTA
* * *
52305 CCCTGGATCAACTGAAGTGAATTGAAGAAAAGATCG
1 CCCTGGATCAACTGAAATGAACTGAAGAAAAGACCG
* * *
52341 CCCTGGATCAATTGAAATAAACTGAA-TAAAGACCG
1 CCCTGGATCAACTGAAATGAACTGAAGAAAAGACCG
* *
52376 TCCTGGGTCAACTGAAATGAACTGAAG
1 CCCTGGATCAACTGAAATGAACTGAAG
52403 CATCTGAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 29 0.57
36 22 0.43
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (36 bp):
CCCTGGATCAACTGAAATGAACTGAAGAAAAGACCG
Found at i:53934 original size:15 final size:15
Alignment explanation
Indices: 53914--53961 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
53904 ACAAATTTTG
53914 AAAACCATTTTTGAA
1 AAAACCATTTTTGAA
53929 AAAACCATTTTTTTGAA
1 AAAACCA--TTTTTGAA
53946 AAAA--ATCTTTTGAA
1 AAAACCAT-TTTTGAA
53960 AA
1 AA
53962 CATGTGACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.03
14 9 0.30
15 8 0.27
17 12 0.40
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (15 bp):
AAAACCATTTTTGAA
Done.