Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_624
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: 55011
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Found at i:5202 original size:27 final size:27
Alignment explanation
Indices: 5162--5249 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 27
5152 AGGAAGCGTC
5162 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
* *
5189 CTGGTGGCTGTGCCACATATT-TCTGCT
1 CTGGTGGCTATGCCACA-ATTATCTGAT
* *
5216 CTGGTGGCTCTGCCACAATTATCTGTTT
1 CTGGTGGCTATGCCACAATTATCTG-AT
5244 CTGGTG
1 CTGGTG
5250 ACTCGATCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.06
27 41 0.76
28 10 0.19
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:7023 original size:39 final size:40
Alignment explanation
Indices: 6923--7107 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
6913 TTGAATGATG
* * *
6923 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
6962 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
7003 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
7042 TCCGGGTTCAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
7081 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
7108 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 34 0.28
40 76 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:7138 original size:79 final size:79
Alignment explanation
Indices: 6975--7140 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
6965 CGGACTAAGA
* ** **
6975 TCCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
* *
7040 AATCCGGGTTCAGT
66 AATCCGGGTTAAAT
* * *
7054 CCCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 TCCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-
*
7117 CTATATCC-GGTTAAAT
63 CTAAATCCGGGTTAAAT
7133 TCCGAAGG
1 TCCGAAGG
7141 TACGTGATTT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
78 2 0.03
79 45 0.62
80 25 0.35
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
AATCCGGGTTAAAT
Found at i:14929 original size:39 final size:41
Alignment explanation
Indices: 14828--15011 Score: 188
Period size: 40 Copynumber: 4.6 Consensus size: 41
14818 TTGAATGATG
* *
14828 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
14868 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
14908 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* * * *
14947 TTCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
14987 ACC-GGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
15012 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 13, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
39 54 0.44
40 56 0.46
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:14968 original size:79 final size:81
Alignment explanation
Indices: 14828--15011 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
14818 TTGAATGATG
* *
14828 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
14892 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * * **
14907 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATTCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
14969 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
14987 ACC-GGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
15012 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
78 7 0.08
79 63 0.71
80 19 0.21
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:15018 original size:39 final size:39
Alignment explanation
Indices: 14832--15011 Score: 188
Period size: 39 Copynumber: 4.6 Consensus size: 39
14822 ATGATGTCCG
* * * *
14832 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCC
* *
14871 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
14911 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATTCG
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA-TCC
* *
14951 GGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA-CC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCC
*
14990 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
15012 AACGAGTAGC
Statistics
Matches: 118, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
39 53 0.45
40 53 0.45
41 12 0.10
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:22207 original size:78 final size:79
Alignment explanation
Indices: 22072--22295 Score: 265
Period size: 78 Copynumber: 2.8 Consensus size: 79
22062 TCGAATGATG
* * * *
22072 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGATTTGTGC-AAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCATT
* *
22136 TGTGCGAGTTACTAAT
64 TGTGCGAGTCACTAAA
* * *
22152 TCCGGGCTAAG-CCCGAAGGATTGGTACAAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGATTTGTGCAAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
22216 TGCGAGTCACTAAA
66 TGCGAGTCACTAAA
* * * * *
22230 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CTGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGG-ATTTGTGCAAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
22294 TG
64 TG
22296 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
77 1 0.01
78 52 0.42
79 21 0.17
80 47 0.38
81 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGATTTGTGCAAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTCACTAAA
Found at i:22302 original size:40 final size:40
Alignment explanation
Indices: 22072--22295 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
22062 TCGAATGATG
* * *
22072 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
22112 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
22152 TCCGGGCTAAG-CCCGAAGG-ATTGGTACAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
22190 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
22230 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
22271 -CTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
22296 AACGAGTAGC
Statistics
Matches: 159, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 25 0.16
39 15 0.09
40 109 0.69
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:30279 original size:40 final size:40
Alignment explanation
Indices: 30195--30459 Score: 331
Period size: 40 Copynumber: 6.7 Consensus size: 40
30185 TCGAATGATG
* * *
30195 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
30235 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
30275 TCCGGGCTAAG-CTCGAAGGCATTGGTGCGATTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
30314 TCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
30354 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
30394 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
30435 -CTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
30460 AACGAGTAGC
Statistics
Matches: 199, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
39 33 0.17
40 156 0.78
41 10 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:30466 original size:80 final size:78
Alignment explanation
Indices: 30196--30492 Score: 323
Period size: 80 Copynumber: 3.7 Consensus size: 78
30186 CGAATGATGT
* * **
30196 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTAAATCCGGGTTAAG-TCCCGAAGGCATT
*
30259 TGTGCGAGTTACTAATT
63 TGTGCGAGTTACTAA-A
* * * *
30276 CCGGGCTAAG-CTCGAAGGCATTGGTGCGATTTACTAAATCCGGGTTAAGCCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
30340 TGCGAGTTACTAAA
65 TGCGAGTTACTAAA
*
30354 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTT
*
30419 GTGTGAGTTACTATAA
64 GTGCGAGTTACTA-AA
* * ** * * *
30435 CTGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATAT-CGGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTAAATCCGGGTTAAGTCCCGAAGG
30493 TACGTGATTC
Statistics
Matches: 186, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
79 76 0.41
80 108 0.58
81 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
GCGAGTTACTAAA
Found at i:35144 original size:16 final size:15
Alignment explanation
Indices: 35118--35147 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35108 ACTAGATCGG
35118 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
35133 CAAAATGCCGAAAAG
1 CAAAA-GCCGAAAAG
35148 TTGGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.23, G:0.20, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:35585 original size:27 final size:27
Alignment explanation
Indices: 35547--35620 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 27
35537 AGCGTCCTGT
*
35547 TGGCTATGCCACAATTATCTGATCTGG
1 TGGCTCTGCCACAATTATCTGATCTGG
*
35574 TGGCTCTGCCACATATT-TCTGTTCTGG
1 TGGCTCTGCCACA-ATTATCTGATCTGG
35601 TGGCTCTGCCACAATTATCT
1 TGGCTCTGCCACAATTATCT
35621 ATTTCTGGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.07
27 37 0.86
28 3 0.07
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (27 bp):
TGGCTCTGCCACAATTATCTGATCTGG
Found at i:35649 original size:54 final size:54
Alignment explanation
Indices: 35547--35654 Score: 132
Period size: 54 Copynumber: 2.0 Consensus size: 54
35537 AGCGTCCTGT
* *
35547 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTTCTGG
1 TGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTGG
* *
35601 TGGCTCTGCCACAATTATCT-ATTTCTGGTGACTC-GATCACAT-TATCTGTTCTGG
1 TGGCTATGCCACAATTATCTGA--TCTGGTGACTCTG-CCACATATATCTGTTCTGG
35655 CAACCATGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 1 0.02
54 31 0.66
55 15 0.32
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (54 bp):
TGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTGG
Found at i:46957 original size:47 final size:47
Alignment explanation
Indices: 46903--47144 Score: 272
Period size: 47 Copynumber: 5.1 Consensus size: 47
46893 TAGGAATTTT
** * *
46903 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
46950 ATGTGATGAATGTGAACATGCATATAGGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
46997 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
47044 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
47091 ATGTGAAGTATGTATGAGATATG--TATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATG--TGA-ACATGCATATATGTGATAAGGCCGAATGGCCA
47139 ATGTGA
1 ATGTGA
47145 AGTATGTATG
Statistics
Matches: 170, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
47 132 0.78
48 31 0.18
49 3 0.02
50 4 0.02
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:47224 original size:98 final size:96
Alignment explanation
Indices: 47067--47250 Score: 280
Period size: 98 Copynumber: 1.9 Consensus size: 96
47057 GAACATGCAT
* * *
47067 ATATGTGGTAAAGCCGAATGGCTAATGTGAAGTATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATAAGATATGTATATGTGGTAAAGCCGA
*
47132 ATGGCTAATGTGAAGTATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
*
47163 ATATGTGGTAAAGCTGAATGG-TCAATGTGAAATACATATATAAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGCT-AATGTGAAAT--ATATATAAGATATGTATATGTGGTAAAGC
*
47227 CGAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
47251 GGCGATGTGC
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
95 1 0.01
96 29 0.37
98 49 0.62
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.30
Consensus pattern (96 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATAAGATATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:47266 original size:50 final size:48
Alignment explanation
Indices: 47066--47250 Score: 273
Period size: 48 Copynumber: 3.8 Consensus size: 48
47056 TGAACATGCA
*
47066 TATATGTGGTAAAGCCGAATGGCTAATGTGAAGTATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
*
47114 TATATGTGGTAAAGCCGAATGGCTAATGTGAAGTATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* * * *
47162 CATATGTGGTAAAGCTGAATGG-TCAATGTGAAATACATATATAAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTGAAAT--ATGTATGAGATATG
*
47212 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
47251 GGCGATGTGC
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
47 1 0.01
48 81 0.65
50 41 0.33
51 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:47451 original size:37 final size:37
Alignment explanation
Indices: 47396--47541 Score: 247
Period size: 37 Copynumber: 3.9 Consensus size: 37
47386 GGAAATATAT
* *
47396 TCCGGGTAAGACCTGATGACTACGTGTGAAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
47433 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
47470 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
47507 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
47542 CGTCTGAGCT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 103 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:54585 original size:37 final size:41
Alignment explanation
Indices: 54505--54660 Score: 120
Period size: 43 Copynumber: 3.7 Consensus size: 41
54495 TGAGATTACA
* *
54505 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGGT-TACG
1 TGTAAGACCATGTCTGGGACATTGGCA-T-CATTGTGATAT-CG
* * *
54548 TGTAAGACCATGTCTGGGACATTGGCATCATTATACGTTTTCG
1 TGTAAGACCATGTCTGGGACATTGGCATCATTGT--GATATCG
** * *
54591 TGTAAGACCACT-TCTGGGACATTGGCATCAATAAATGATAACA
1 TGTAAGACCA-TGTCTGGGACATTGGCATC-AT-TGTGATATCG
* *
54634 TGTAAGACCATATCTGGGATA-TGGCAT
1 TGTAAGACCATGTCTGGGACATTGGCAT
54661 TGTATGAGCT
Statistics
Matches: 97, Mismatches: 9, Indels: 15
0.80 0.07 0.12
Matches are distributed among these distances:
41 4 0.04
42 8 0.08
43 79 0.81
44 4 0.04
45 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATTGGCATCATTGTGATATCG
Found at i:54619 original size:43 final size:44
Alignment explanation
Indices: 54500--54620 Score: 153
Period size: 43 Copynumber: 2.8 Consensus size: 44
54490 TGAGATGAGA
* *
54500 TTACATGTAAGACCATGTCTGGGACATTGGCAT--TGTATTGTGG
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCATGTATCGT-G
54543 TTACGTGTAAGACCATGTCTGGGACATTGGCATCAT-TATACGT-
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCATGTAT-CGTG
*
54586 TTTCGTGTAAGACCACT-TCTGGGACATTGGCATCA
1 TTACGTGTAAGACCA-TGTCTGGGACATTGGCATCA
54621 ATAAATGATA
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
43 64 0.90
44 4 0.06
45 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (44 bp):
TTACGTGTAAGACCATGTCTGGGACATTGGCATCATGTATCGTG
Found at i:54638 original size:43 final size:43
Alignment explanation
Indices: 54548--54660 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
54538 TGTGGTTACG
* * * * ** *
54548 TGTAAGACCATGTCTGGGACATTGGCATCATTATACGTTTTCG
1 TGTAAGACCATATCTGGGACATTGGCATCAATAAACGATAACA
*
54591 TGTAAGACCACT-TCTGGGACATTGGCATCAATAAATGATAACA
1 TGTAAGACCA-TATCTGGGACATTGGCATCAATAAACGATAACA
*
54634 TGTAAGACCATATCTGGGATA-TGGCAT
1 TGTAAGACCATATCTGGGACATTGGCAT
54661 TGTATGAGCT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 7 0.12
43 52 0.87
44 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGACATTGGCATCAATAAACGATAACA
Done.