Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold600
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: 30740
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:2320 original size:21 final size:21
Alignment explanation
Indices: 2287--2327 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2277 CTAAGTAAAA
2287 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
2308 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
2328 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:2392 original size:20 final size:20
Alignment explanation
Indices: 2361--2437 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
2351 GTCAAAACCC
*
2361 TGAAAAGTATCGATACACAT
1 TGAATAGTATCGATACACAT
* *
2381 TTAAGT-GTATCGATACAAAT
1 TGAA-TAGTATCGATACACAT
*
2401 TGCATAGTATCGATACACA-
1 TGAATAGTATCGATACACAT
**
2420 CAAATATGTATCGATACA
1 TGAATA-GTATCGATACA
2438 GGTCATTGGC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 4 0.09
20 41 0.91
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.29
Consensus pattern (20 bp):
TGAATAGTATCGATACACAT
Found at i:2533 original size:10 final size:10
Alignment explanation
Indices: 2514--2544 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2504 AATCTCATTT
2514 TCACTGTTCA
1 TCACTGTTCA
*
2524 TCACTATTCA
1 TCACTGTTCA
2534 TCACTGTTCA
1 TCACTGTTCA
2544 T
1 T
2545 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:2566 original size:21 final size:22
Alignment explanation
Indices: 2532--2587 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
2522 CATCACTATT
2532 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2554 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
2575 CATCACTGTTCAT
1 CATCACTGTTCAT
2588 AGTCACTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:2690 original size:13 final size:13
Alignment explanation
Indices: 2672--2697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2662 ACATATTTGT
2672 GTGTATCGATACA
1 GTGTATCGATACA
2685 GTGTATCGATACA
1 GTGTATCGATACA
2698 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:4222 original size:33 final size:33
Alignment explanation
Indices: 4176--4242 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
4166 GTTGGGCATA
* *
4176 AATGTATCGATACAA-TTCTTCATATATCGATAC
1 AATGTATCAATACAATTTC-CCATATATCGATAC
* *
4209 AATGTATTAATACAATTTCCCATGTATCGATAC
1 AATGTATCAATACAATTTCCCATATATCGATAC
4242 A
1 A
4243 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (33 bp):
AATGTATCAATACAATTTCCCATATATCGATAC
Found at i:5036 original size:20 final size:21
Alignment explanation
Indices: 4992--5065 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
4982 TTCTACAATC
*
4992 TGTATCGATACAAACAGTAAA
1 TGTATCGATACATACAGTAAA
*
5013 TGTATCGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
* *
5033 TGTATCAATACATGCA-TAAAA
1 TGTATCGATACATACAGT-AAA
*
5054 AGTATCGATACA
1 TGTATCGATACA
5066 AAACCACCCT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.27
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:7598 original size:28 final size:26
Alignment explanation
Indices: 7546--7598 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
7536 TCGATTTTAC
*
7546 ATTTCAAGGATACTCCAACCTCATTA
1 ATTTCAAGGATACTCCAACCCCATTA
7572 ATTTCGAAGGGATACTCC-ACCGCCATT
1 ATTTC-AA-GGATACTCCAACC-CCATT
7599 TTTACTTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 5 0.22
27 5 0.22
28 13 0.57
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (26 bp):
ATTTCAAGGATACTCCAACCCCATTA
Found at i:7661 original size:78 final size:78
Alignment explanation
Indices: 7517--7905 Score: 360
Period size: 78 Copynumber: 5.0 Consensus size: 78
7507 AAATTTCTAA
* * * * ** * *
7517 ATTTTTCCTTCCAAAAATATCGATTTTACATTTCAAGGATACTCCAACCTCATTAATTTCGAA-G
1 ATTTTTACTTCC-AAAATATTGATTTTTCATCTCGGGGATACTCCAACCCCATT-ATTTCTAAGG
7581 GGATACTCC-ACCGCC
64 GGATACTCCAACC-CC
* * *
7596 ATTTTTACTTCCAAAATATTGATTTTTCATCTTGGGGATACTCCAACCCCGTTATTTCCTTA-GG
1 ATTTTTACTTCCAAAATATTGATTTTTCATCTCGGGGATACTCCAACCCCATTATTT-CTAAGGG
7660 GATACTCCAACCCC
65 GATACTCCAACCCC
* * * * * * *
7674 ATTTTTATTTCAAAAATATTAAAATTTTAATCTCGGGGATACTCCAACCCCATCAATTCTAAGGG
1 ATTTTTACTTCCAAAATATT-GATTTTTCATCTCGGGGATACTCCAACCCCATTATTTCTAAGGG
* *
7739 GATACTCTAACCTC
65 GATACTCCAACCCC
* * * *
7753 GTTTTTACTTCCAAAATATCGATTTTTCATCTCGGGGATACTCCAATCCCATTATTTCCAAGGGG
1 ATTTTTACTTCCAAAATATTGATTTTTCATCTCGGGGATACTCCAACCCCATTATTTCTAAGGGG
*
7818 ATATTCCAACCCC
66 ATACTCCAACCCC
* * * * ** * *
7831 A-TTTTATTTCAAAAATATTAAAATTTTCAATCTC-GGGATACTTTAACCTCA-TA-TTCTGAGG
1 ATTTTTACTTCCAAAATATT-GATTTTTC-ATCTCGGGGATACTCCAACCCCATTATTTCTAAGG
*
7892 GGACACTCCAACCC
64 GGATACTCCAACCC
7906 TGCCTTTTTT
Statistics
Matches: 253, Mismatches: 51, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
76 18 0.07
77 21 0.08
78 135 0.53
79 79 0.31
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (78 bp):
ATTTTTACTTCCAAAATATTGATTTTTCATCTCGGGGATACTCCAACCCCATTATTTCTAAGGGG
ATACTCCAACCCC
Found at i:7808 original size:157 final size:156
Alignment explanation
Indices: 7553--7872 Score: 459
Period size: 157 Copynumber: 2.0 Consensus size: 156
7543 TACATTTCAA
* * * *
7553 GGATACTCCAACCTCATTAATTTCGAAGGGATACTCCACCGCCATTTTTACTTCCAAAATATTGA
1 GGATACTCCAACCCCATCAATTTCGAAGGGATACTCAACCGCCATTTTTACTTCCAAAATATCGA
* * *
7618 TTTTTCATCTTGGGGATACTCCAACCCCGTTATTTCCTTA-GGGATACTCCAACCCCATTTTTAT
66 TTTTTCATCTCGGGGATACTCCAACCCCATTATTTCC-AAGGGGATACTCCAACCCCA-TTTTAT
7682 TTCAAAAATATTAAAATTTT-AATCTCGG
129 TTCAAAAATATTAAAATTTTCAATCTC-G
* * *
7710 GGATACTCCAACCCCATCAA-TTCTAAGGGGATACTCTAACC-TCGTTTTTACTTCCAAAATATC
1 GGATACTCCAACCCCATCAATTTCGAA-GGGATACTC-AACCGCCATTTTTACTTCCAAAATATC
* *
7773 GATTTTTCATCTCGGGGATACTCCAATCCCATTATTTCCAAGGGGATATTCCAACCCCATTTTAT
64 GATTTTTCATCTCGGGGATACTCCAACCCCATTATTTCCAAGGGGATACTCCAACCCCATTTTAT
7838 TTCAAAAATATTAAAATTTTCAATCTCG
129 TTCAAAAATATTAAAATTTTCAATCTCG
7866 GGATACT
1 GGATACT
7873 TTAACCTCAT
Statistics
Matches: 147, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
156 40 0.27
157 104 0.71
158 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (156 bp):
GGATACTCCAACCCCATCAATTTCGAAGGGATACTCAACCGCCATTTTTACTTCCAAAATATCGA
TTTTTCATCTCGGGGATACTCCAACCCCATTATTTCCAAGGGGATACTCCAACCCCATTTTATTT
CAAAAATATTAAAATTTTCAATCTCG
Found at i:9653 original size:21 final size:21
Alignment explanation
Indices: 9623--9665 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9613 ATCGATACGA
* *
9623 TACATGATGTATCGATACATT
1 TACATAATGTATCAATACATT
9644 TACATAATGTATCAATACATT
1 TACATAATGTATCAATACATT
9665 T
1 T
9666 CCACTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
TACATAATGTATCAATACATT
Found at i:9747 original size:20 final size:20
Alignment explanation
Indices: 9722--9762 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9712 GCCAACCATA
9722 TGTATCAATACATATAGTAT
1 TGTATCAATACATATAGTAT
* *
9742 TGTATCGATACATTTAGTAT
1 TGTATCAATACATATAGTAT
9762 T
1 T
9763 TTTACTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (20 bp):
TGTATCAATACATATAGTAT
Found at i:12531 original size:3 final size:3
Alignment explanation
Indices: 12523--12553 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
12513 TTCCTTAACC
*
12523 TCA TCA TCA TCA TCA TCA TCA TTA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
12554 TTTGAGTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:13875 original size:21 final size:21
Alignment explanation
Indices: 13849--13900 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
13839 GAAACTAAGT
13849 ACAAAATGAACTTAAAATATC
1 ACAAAATGAACTTAAAATATC
13870 ACAAAATGAACTTAAAATATC
1 ACAAAATGAACTTAAAATATC
13891 ACAAAATGAA
1 ACAAAATGAA
13901 TACAATTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (21 bp):
ACAAAATGAACTTAAAATATC
Found at i:14313 original size:21 final size:21
Alignment explanation
Indices: 14256--14313 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
14246 TGCCAACAAG
*
14256 ATGTATCGATACATTCACATA
1 ATGTATCGATACATTTACATA
*
14277 ATGTATCGATATATTTACATA
1 ATGTATCGATACATTTACATA
14298 ATGTATCGATACATTT
1 ATGTATCGATACATTT
14314 TTACTTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATTTACATA
Found at i:16691 original size:20 final size:20
Alignment explanation
Indices: 16664--16708 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
16654 ATAAAATGTT
16664 AAAT-TTACTTGAAAAATAA
1 AAATATTACTTGAAAAATAA
** *
16683 AAATATTACTTGTTAAATGA
1 AAATATTACTTGAAAAATAA
16703 AAATAT
1 AAATAT
16709 AAGGATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (20 bp):
AAATATTACTTGAAAAATAA
Found at i:17335 original size:84 final size:84
Alignment explanation
Indices: 17231--17525 Score: 231
Period size: 84 Copynumber: 3.5 Consensus size: 84
17221 TGATTGGTAA
** * **
17231 AAGAAGTCTCCTAGAACTAAGCTGATGGGTAGACGATGGATTAGGAAGTCTCCCGGGTCTGAGCC
1 AAGAAGTCTCCTAGGTCTAAGCTGATGGGCAGACGAAAGATTAGGAAGTCTCCCGGGTCTGAGCC
17296 GACGGGCAGACGAATGATG
66 GACGGGCAGACGAATGATG
** * * *
17315 AAGAAGTCTCCTAGGTCTAAGAC-GACAGGCAGACGAAAGATAAAAGAAGTCTCTCGGGTCTGAG
1 AAGAAGTCTCCTAGGTCTAAG-CTGATGGGCAGACGAAAGAT-TAGGAAGTCTCCCGGGTCTGAG
** *
17379 CCGATAGGCA-AGCG-ATGGAAG
64 CCGACGGGCAGA-CGAAT-GATG
* * * * * * * * ** * * *
17400 AAAAAATTCTCCTAGGCCTAAGCCGATGGGCAGCCAAAAGA-TGGAGAAGTTTCCCAAGACTAAA
1 -AAGAAGTCTCCTAGGTCTAAGCTGATGGGCAGACGAAAGATTAG-GAAGTCTCCCGGGTCTGAG
*
17464 CCGACGGGTAGACGAATGATG
64 CCGACGGGCAGACGAATGATG
* *
17485 AAGAAGTCTCCTAGGTCTAAG-TCGATGGGTAGATGAAAGAT
1 AAGAAGTCTCCTAGGTCTAAGCT-GATGGGCAGACGAAAGAT
17526 GAAGATTGGA
Statistics
Matches: 158, Mismatches: 42, Indels: 21
0.71 0.19 0.10
Matches are distributed among these distances:
84 66 0.42
85 58 0.37
86 34 0.22
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.18
Consensus pattern (84 bp):
AAGAAGTCTCCTAGGTCTAAGCTGATGGGCAGACGAAAGATTAGGAAGTCTCCCGGGTCTGAGCC
GACGGGCAGACGAATGATG
Found at i:17515 original size:42 final size:42
Alignment explanation
Indices: 17231--17530 Score: 185
Period size: 42 Copynumber: 7.1 Consensus size: 42
17221 TGATTGGTAA
** * * *
17231 AAGAAGTCTCCTAGAACTAAGCTGATGGGTAGACG-ATGGATT
1 AAGAAGTCTCCTAGGTCTAAGCCGATGGGCAGACGAAT-GATG
* ** * *
17273 AGGAAGTCTCCCGGGTCTGAGCCGACGGGCAGACGAATGATG
1 AAGAAGTCTCCTAGGTCTAAGCCGATGGGCAGACGAATGATG
* ** * *
17315 AAGAAGTCTCCTAGGTCTAAGACGACAGGCAGACGAAAGATAA
1 AAGAAGTCTCCTAGGTCTAAGCCGATGGGCAGACGAATGAT-G
* * * *
17358 AAGAAGTCT-CTCGGGTCTGAGCCGATAGGCA-AGCG-ATGGAAG
1 AAGAAGTCTCCT-AGGTCTAAGCCGATGGGCAGA-CGAAT-GATG
* * * * * *
17400 AAAAAATTCTCCTAGGCCTAAGCCGATGGGCAGCCAAAAGATG
1 -AAGAAGTCTCCTAGGTCTAAGCCGATGGGCAGACGAATGATG
* * * * * * * *
17443 GAGAAGTTTCCCAAGACTAAACCGACGGGTAGACGAATGATG
1 AAGAAGTCTCCTAGGTCTAAGCCGATGGGCAGACGAATGATG
* * * *
17485 AAGAAGTCTCCTAGGTCTAAGTCGATGGGTAGATGAAAGATG
1 AAGAAGTCTCCTAGGTCTAAGCCGATGGGCAGACGAATGATG
17527 AAGA
1 AAGA
17531 TTGGAATAAG
Statistics
Matches: 191, Mismatches: 58, Indels: 18
0.72 0.22 0.07
Matches are distributed among these distances:
42 132 0.69
43 56 0.29
44 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (42 bp):
AAGAAGTCTCCTAGGTCTAAGCCGATGGGCAGACGAATGATG
Found at i:18349 original size:11 final size:12
Alignment explanation
Indices: 18331--18357 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18321 GAAAAAATAC
18331 AAAAAAAAGAAA
1 AAAAAAAAGAAA
18343 AAAAAAAAGAAA
1 AAAAAAAAGAAA
18355 AAA
1 AAA
18358 GGGGTGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:18874 original size:48 final size:50
Alignment explanation
Indices: 18822--18935 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 50
18812 TGAATAGTAC
*
18822 ATGTATCGATACATTCTA-TTTTTACCCAGATATATTGATACATT-TTCA
1 ATGTATCGATACATTCTATTTTTTACCCAGATACATTGATACATTATTCA
* * *
18870 ATGTATCGATACATTCTATTTTTTTTACCTAGATGCATTGATACATTATTCC
1 ATGTATCGATACATTCTA--TTTTTTACCCAGATACATTGATACATTATTCA
18922 ATGTATCGATACAT
1 ATGTATCGATACAT
18936 CTAGTTAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
48 18 0.31
51 23 0.40
52 17 0.29
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.44
Consensus pattern (50 bp):
ATGTATCGATACATTCTATTTTTTACCCAGATACATTGATACATTATTCA
Found at i:26238 original size:50 final size:49
Alignment explanation
Indices: 26162--26344 Score: 249
Period size: 50 Copynumber: 3.7 Consensus size: 49
26152 TTTCACAACT
* * * * *
26162 TGTATCGATACATCTTCATTGTATCGATACAATCTAGATTTTACCCAAA
1 TGTATCGATACATTTTCATTGTATCGATACATTTTGGGTTTTACCCAAA
* *
26211 TGTATCGATACATTATTCATTGCATCGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATT-TTCATTGTATCGATACATTTTGGGTTTTACCCAAA
* *
26261 TGTATCGATACATTTTTCTTTGTATCAATACATTTTGGGTTTTACCCAAA
1 TGTATCGATACA-TTTTCATTGTATCGATACATTTTGGGTTTTACCCAAA
*
26311 TGTATCGATACATTTCTCAATGTATCGATACATT
1 TGTATCGATACATTT-TCATTGTATCGATACATT
26345 CAAGCATTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
49 16 0.14
50 99 0.85
51 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (49 bp):
TGTATCGATACATTTTCATTGTATCGATACATTTTGGGTTTTACCCAAA
Found at i:26270 original size:30 final size:29
Alignment explanation
Indices: 26234--26325 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 29
26224 TATTCATTGC
26234 ATCGATACATTTTGGGTTTTACCCAGATGT
1 ATCGATACATTTTGGGTTTTACCCA-ATGT
*
26264 ATCGATACATTTT---TCTT------TGT
1 ATCGATACATTTTGGGTTTTACCCAATGT
*
26284 ATCAATACATTTTGGGTTTTACCCAAATGT
1 ATCGATACATTTTGGGTTTTACCC-AATGT
26314 ATCGATACATTT
1 ATCGATACATTT
26326 CTCAATGTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 20
0.67 0.06 0.28
Matches are distributed among these distances:
20 15 0.31
23 3 0.06
27 3 0.06
30 27 0.56
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (29 bp):
ATCGATACATTTTGGGTTTTACCCAATGT
Found at i:28769 original size:79 final size:77
Alignment explanation
Indices: 28618--29029 Score: 194
Period size: 79 Copynumber: 5.3 Consensus size: 77
28608 TTTCATCTTG
** * * *
28618 GGGATACTCCAACCTTGATTTATTTCTAAAATATCAATTTTTCACTATCGGGGATACTCTAACCC
1 GGGATACTCCAACCCCGATTTATTTCCAAAATATAAATTTTT-ACTATCGGGGATACTCCAACCC
28683 CATTATTTTCCAA
65 CATTATTTTCCAA
* *
28696 GGGATACTCCAACCCCGTCTTTATTTCCAAAATATTAAATTTTT-C-ATCGGGGATACTCCAATC
1 GGGATACTCCAACCCCG-ATTTATTTCCAAAATA-TAAATTTTTACTATCGGGGATACTCCAACC
* ***
28759 CCGTTATATTT-GGG
64 CCATTAT-TTTCCAA
* * * * ** *
28773 GGGATATTCTAACCACGATTT-TATTCCTAAAACATTGATTTTTCCACTATCGGGGATACTCCAT
1 GGGATACTCCAACCCCGATTTAT-TTCC-AAAATATAAATTTTT--ACTATCGGGGATACTCCAA
* * *
28837 CCTCGTTATTTT-CGA
62 CCCCATTATTTTCCAA
* * * * * * *
28852 GGCAATACTCCAACCCTGGTTT-TATTCCTAAAACA-ACGATTTTTGACCATTGGGGATACTCCA
1 GG-GATACTCCAACCCCGATTTAT-TTCC-AAAATATA-AATTTTT-ACTATCGGGGATACTCCA
****
28915 ACTTTGTTA-TTTCCAA
61 ACCCCATTATTTTCCAA
* * * * *** * * *
28931 GTGGATACTCCTACCCCGTTTTATTTCTAAAACACCTATTTTCCACCATCGGAGATACTCCAACC
1 G-GGATACTCCAACCCCGATTTATTTCCAAAATATAAATTTT-TACTATCGGGGATACTCCAACC
** ** *
28996 CTGTTACCTT-CGA
64 CCATTATTTTCCAA
*
29009 GGGATACTCCAACCTCGATTT
1 GGGATACTCCAACCCCGATTT
29030 TATTCCTAAA
Statistics
Matches: 263, Mismatches: 54, Indels: 35
0.75 0.15 0.10
Matches are distributed among these distances:
75 1 0.00
76 14 0.05
77 58 0.22
78 59 0.22
79 66 0.25
80 65 0.25
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.35
Consensus pattern (77 bp):
GGGATACTCCAACCCCGATTTATTTCCAAAATATAAATTTTTACTATCGGGGATACTCCAACCCC
ATTATTTTCCAA
Found at i:28979 original size:78 final size:76
Alignment explanation
Indices: 28618--29078 Score: 284
Period size: 78 Copynumber: 5.9 Consensus size: 76
28608 TTTCATCTTG
** * * * * * * * * *
28618 GGGATACTCCAACCTTGATTTATTTCTAAAATATCAATTTTTCACTATCGGGGATACTCTAACCC
1 GGGATACTCCAACCCCGTTTTATTCCTAAAACACCGATTTTCCACCATCGGGGATACTCCAACCT
** *
28683 CATTATTTTCCAA
66 TGTTA-TTT-CGA
* *** *
28696 GGGATACTCCAACCCCGTCTTTATTTCC-AAAATATTAAATTTT---TCATCGGGGATACTCCAA
1 GGGATACTCCAACCCCGT-TTTA-TTCCTAAAACA-CCGATTTTCCACCATCGGGGATACTCCAA
* * *
28757 TCCCGTT-ATATTTGGG
63 --CC-TTGTTATTTCGA
* * * ** * *
28773 GGGATATTCTAACCACGATTTTATTCCTAAAACATTGATTTTTCCACTATCGGGGATACTCCATC
1 GGGATACTCCAACCCCG-TTTTATTCCTAAAACACCGA-TTTTCCACCATCGGGGATACTCCAAC
*
28838 CTCGTTATTTTCGA
64 CTTGTTA-TTTCGA
* * * ** *
28852 GGCAATACTCCAACCCTGGTTTTATTCCTAAAACAACGATTTTTGACCATTGGGGATACTCCAAC
1 GG-GATACTCCAACCC-CGTTTTATTCCTAAAACACCGATTTTCCACCATCGGGGATACTCCAAC
* *
28917 TTTGTTATTTCCAA
64 CTTGTTATTT-CGA
* * * *
28931 GTGGATACTCCTACCCCGTTTTATTTCTAAAACACCTATTTTCCACCATCGGAGATACTCCAACC
1 G-GGATACTCCAACCCCGTTTTATTCCTAAAACACCGATTTTCCACCATCGGGGATACTCCAACC
* *
28996 CTGTTACCTTCGA
65 TTGTTA-TTTCGA
* ** * *
29009 GGGATACTCCAACCTCGATTTTATTCCTAAAACACCGATTTTCCATAATAGAGGATACTCCAACC
1 GGGATACTCCAACCCCG-TTTTATTCCTAAAACACCGATTTTCCACCATCGGGGATACTCCAACC
*
29074 CTGTT
65 TTGTT
29079 TTTATCTCCA
Statistics
Matches: 298, Mismatches: 65, Indels: 40
0.74 0.16 0.10
Matches are distributed among these distances:
76 6 0.02
77 57 0.19
78 119 0.40
79 62 0.21
80 53 0.18
81 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (76 bp):
GGGATACTCCAACCCCGTTTTATTCCTAAAACACCGATTTTCCACCATCGGGGATACTCCAACCT
TGTTATTTCGA
Done.