Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_377
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: 83435
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1125 original size:40 final size:39
Alignment explanation
Indices: 1081--1252 Score: 220
Period size: 40 Copynumber: 4.3 Consensus size: 39
1071 GCTCCTCGTT
* * *
1081 CAAATGCCTTCGGGACATAGCCTGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGTT-TAGTAACTCGCA
*
1121 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
*
1161 CAAATGCCTTCGGGACTTAACTCGGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAAC-CCGGTTTAGTAACTCGCA
* * * *
1201 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
1240 CAAATGCCTTCGG
1 CAAATGCCTTCGG
1253 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
38 3 0.03
39 29 0.25
40 81 0.69
41 5 0.04
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGTTTAGTAACTCGCA
Found at i:1193 original size:80 final size:79
Alignment explanation
Indices: 1081--1252 Score: 247
Period size: 80 Copynumber: 2.2 Consensus size: 79
1071 GCTCCTCGTT
* *
1081 CAAATGCCTTCGGGACATAGCCTGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCGGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAACCCGG
* **
1146 ATTTAGTAACTTGCA
65 AATTAGTAACTCACA
* *
1161 CAAATGCCTTCGGGACTTAACTCGGGTT-TAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGG
1 CAAATGCCTTCGGGACATAAC-CGGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGG
*
1225 AATTAGTATCTCACA
65 AATTAGTAACTCACA
1240 CAAATGCCTTCGG
1 CAAATGCCTTCGG
1253 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
79 33 0.40
80 45 0.54
81 5 0.06
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAACCGGGTTATAGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGA
ATTAGTAACTCACA
Found at i:1265 original size:119 final size:120
Alignment explanation
Indices: 1081--1298 Score: 284
Period size: 119 Copynumber: 1.8 Consensus size: 120
1071 GCTCCTCGTT
* * *
1081 CAAATGCCTTCGGGACATAGCCTGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGG
1146 AT-TTAGTAACTT-GCACAAATGCCTTCGGGACTTAACTCGGGTTTAGTAACTCGCA
66 ATATT-GTAACTTAGCACAAA-GCCTTCGGGACTTAACTCGGGTTTAGTAACTCGCA
* * **
1201 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCACACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCACACAAATGCCTTCGGGA-CTTAACCC
* *
1263 GGATATTTTCACTTAGCACAAAGCCTTCGGGACTTA
64 GGATATTGTAACTTAGCACAAAGCCTTCGGGACTTA
1299 GCCCGGACAT
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
118 4 0.05
119 58 0.68
120 23 0.27
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGG
ATATTGTAACTTAGCACAAAGCCTTCGGGACTTAACTCGGGTTTAGTAACTCGCA
Found at i:9341 original size:40 final size:40
Alignment explanation
Indices: 9267--9446 Score: 199
Period size: 40 Copynumber: 4.5 Consensus size: 40
9257 GCTCCTCGTT
*
9267 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
9306 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
9346 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * * *
9385 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCACTTAGCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
9426 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
9447 GGACATCATT
Statistics
Matches: 120, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 44 0.37
40 62 0.52
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:9383 original size:39 final size:39
Alignment explanation
Indices: 9267--9397 Score: 192
Period size: 39 Copynumber: 3.3 Consensus size: 39
9257 GCTCCTCGTT
* *
9267 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATT-TAGTAACTCGCA
*
9306 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATTTAGTAACTCGCA
* *
9346 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
9385 CAAATGCCTTCGG
1 CAAATGCCTTCGG
9398 ATCTTAGTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
39 48 0.57
40 34 0.40
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
Found at i:9449 original size:79 final size:79
Alignment explanation
Indices: 9267--9446 Score: 195
Period size: 79 Copynumber: 2.3 Consensus size: 79
9257 GCTCCTCGTT
* * * *
9267 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
* *
9331 ATTTAGTAACTCGCA
65 ATATAGTAACTAGCA
* **
9346 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCAG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCAG
* * *
9410 ATATGGTCACTTAGCC
65 ATATAGTAAC-TAGCA
9426 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGG-CTTAGCC
9447 GGACATCATT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
78 3 0.04
79 67 0.79
80 15 0.18
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGA
TATAGTAACTAGCA
Found at i:14126 original size:29 final size:29
Alignment explanation
Indices: 14068--14127 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
14058 TAAAGTGATT
* *
14068 TTGAGTAAAAATGTATATTAGGGATTAAA
1 TTGAGTAAAAATGTAAATTAGGGATGAAA
* *
14097 TTGAG-AAAAGTGTAAATTGAGGGGTGAAA
1 TTGAGTAAAAATGTAAATT-AGGGATGAAA
14126 TT
1 TT
14128 ATGAAATTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.32
Consensus pattern (29 bp):
TTGAGTAAAAATGTAAATTAGGGATGAAA
Found at i:22233 original size:18 final size:19
Alignment explanation
Indices: 22206--22241 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
22196 GAATGTACTA
22206 TTCATATACA-CATATATT
1 TTCATATACATCATATATT
*
22224 TTCATTTACATCATATAT
1 TTCATATACATCATATAT
22242 AAATTGCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (19 bp):
TTCATATACATCATATATT
Found at i:22532 original size:56 final size:56
Alignment explanation
Indices: 22472--22720 Score: 374
Period size: 56 Copynumber: 4.4 Consensus size: 56
22462 TCCCAGACAG
* * ** *
22472 GGTCTTACTCCCACACATAAATC-AGAATCACATATCGATGCCAATGTATTAAACAT
1 GGTCTTACTCGCACACATATATCGA-AATCACATATCGATGCCAACATATTAAACGT
22528 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGT
* * * *
22584 GGTCTTACTCACACACATATATCGGAATCACATATTGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGT
* * *
22640 GTTCTTACTCGCATACATATATCGAAATCACATATTGATGCCAACATATTAAACGT
1 GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGT
22696 GGTCTTACTCGCACACATATATCGA
1 GGTCTTACTCGCACACATATATCGA
22721 TGCCATGGTC
Statistics
Matches: 176, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
56 175 0.99
57 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCGAAATCACATATCGATGCCAACATATTAAACGT
Found at i:28452 original size:20 final size:20
Alignment explanation
Indices: 28427--28468 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
28417 GGAAAATAAG
28427 TCAAAATTTGGTGTCCATCT
1 TCAAAATTTGGTGTCCATCT
28447 TCAAAATTTGGTGTCCATCT
1 TCAAAATTTGGTGTCCATCT
28467 TC
1 TC
28469 TTAACATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (20 bp):
TCAAAATTTGGTGTCCATCT
Found at i:32998 original size:48 final size:48
Alignment explanation
Indices: 32943--33072 Score: 192
Period size: 48 Copynumber: 2.8 Consensus size: 48
32933 CCACATTATG
32943 AGTGCCAGTATAAGACCATGTCTGGGACATGGCATCGACGTAGAGATA
1 AGTGCCAGTATAAGACCATGTCTGGGACATGGCATCGACGTAGAGATA
* * * *
32991 AGTGCCAGTATAAGACCTTGTTTGGGACATGGCATCGGCGTAGAGATG
1 AGTGCCAGTATAAGACCATGTCTGGGACATGGCATCGACGTAGAGATA
* *
33039 AGTGCCAATGTAAGA-CATGTCTGGGACAT-GCATC
1 AGTGCCAGTATAAGACCATGTCTGGGACATGGCATC
33073 AGCCTCGATG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 5 0.07
47 12 0.16
48 57 0.77
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.23
Consensus pattern (48 bp):
AGTGCCAGTATAAGACCATGTCTGGGACATGGCATCGACGTAGAGATA
Found at i:33064 original size:95 final size:93
Alignment explanation
Indices: 32898--33072 Score: 237
Period size: 95 Copynumber: 1.9 Consensus size: 93
32888 GATTTCTTGT
* * *
32898 GTGCCAGTGTAAGACATGTTTGGGACATGCATCGGCCACATTATGAGTGCCAGTATAAGACCATG
1 GTGCCAGTATAAGACATGTTTGGGACATGCATCGGCCACATGATGAGTGCCAATATAAGACCATG
32963 TCTGGGACATGGCATCGACGTAGAGATAA
66 TCTGGGACAT-GCATCGACGTAGAGATAA
* * * *
32992 GTGCCAGTATAAGACCTTGTTTGGGACATGGCATCGGCGTAGA-GATGAGTGCCAATGTAAGA-C
1 GTGCCAGTATAAGA-CATGTTTGGGACAT-GCATCGGC-CACATGATGAGTGCCAATATAAGACC
33055 ATGTCTGGGACATGCATC
63 ATGTCTGGGACATGCATC
33073 AGCCTCGATG
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
94 18 0.25
95 27 0.38
96 24 0.34
97 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (93 bp):
GTGCCAGTATAAGACATGTTTGGGACATGCATCGGCCACATGATGAGTGCCAATATAAGACCATG
TCTGGGACATGCATCGACGTAGAGATAA
Found at i:40419 original size:47 final size:46
Alignment explanation
Indices: 40351--40718 Score: 250
Period size: 48 Copynumber: 7.8 Consensus size: 46
40341 AATTTCTTGT
*
40351 GTGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCATATTATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCC-TATGATGA
* * * * *
40397 GTGCTAGTATAAGACCATGTCTGGGACATGGCATCCGCGTAGAGATGA
1 GTGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCCTA-TGATGA
* * * * * *
40445 GTGCCAATATAAAACCATGTCTGGGACATGGCATCGACGTAGAGATGA
1 GTGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCCTA-TGATGA
40493 GTGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGATGATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCT--ATGATGA
* * * * * * *
40540 -TAGCCAATGTAAGACGTGTTTGGGACA-CGTATCGG-CTAAGA-GTT
1 GT-GCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTATGATG-A
* * * *
40584 GTGCTAGTGTAAGACATGTCTGTGATAT-GCATCAGCACGTAT-ATACGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGGCATCGGC-C-TATGAT--GA
* * * * *
40632 GAGCTAGTATAAAACCATGTCTGGGACATGGCATCGGCCTCGATAATG-
1 GTGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCCT--ATGATGA
*
40680 CTAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GT-GCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGC
40719 AACTTATCCC
Statistics
Matches: 256, Mismatches: 44, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.00
44 27 0.11
45 1 0.00
46 25 0.10
47 65 0.25
48 78 0.30
49 48 0.19
50 9 0.04
51 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTATGATGA
Found at i:42302 original size:12 final size:12
Alignment explanation
Indices: 42282--42313 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
42272 GATAGAGATC
42282 CTCGATTTACAT
1 CTCGATTTACAT
*
42294 CTTGATTTACAT
1 CTCGATTTACAT
42306 CTCGATTT
1 CTCGATTT
42314 TGGAATAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (12 bp):
CTCGATTTACAT
Found at i:43962 original size:14 final size:14
Alignment explanation
Indices: 43943--43969 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43933 TCGAATAAGA
43943 ATTAAATTGCATGG
1 ATTAAATTGCATGG
43957 ATTAAATTGCATG
1 ATTAAATTGCATG
43970 AATTTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (14 bp):
ATTAAATTGCATGG
Found at i:44248 original size:21 final size:22
Alignment explanation
Indices: 44218--44258 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
44208 TAGATTATAT
44218 ATGTTAATTTGTT-TGAATTGA
1 ATGTTAATTTGTTGTGAATTGA
* *
44239 ATGTTGATTTTTTGTGAATT
1 ATGTTAATTTGTTGTGAATT
44259 TTATAAATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (22 bp):
ATGTTAATTTGTTGTGAATTGA
Found at i:44715 original size:25 final size:25
Alignment explanation
Indices: 44642--44715 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
44632 TTCCCAATAG
* *
44642 GCTCTTCATGAGCTTCCCGATTAAAA
1 GCTCTT-ATGAGCTTCCTGATTTAAA
* * *
44668 GCTCTTTATGAACTTCTTG-TTTATA
1 GCTC-TTATGAGCTTCCTGATTTAAA
44693 GCTCTTATGAGCTTCCTGATTTA
1 GCTCTTATGAGCTTCCTGATTTA
44716 GCCTAAGTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 12 0.31
25 12 0.31
26 13 0.33
27 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCTGATTTAAA
Found at i:47851 original size:40 final size:40
Alignment explanation
Indices: 47797--48030 Score: 387
Period size: 40 Copynumber: 5.8 Consensus size: 40
47787 ATTACCACAA
* ** *
47797 GCACAATTGCCTTCGGGTCTTAGCCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
47837 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
47877 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
47917 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
47957 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
47997 GCACAAATGCCTGCGGGTCTTAGCCCGGATATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
48031 ATACAAATGC
Statistics
Matches: 181, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 181 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:56206 original size:40 final size:40
Alignment explanation
Indices: 56152--56345 Score: 298
Period size: 40 Copynumber: 4.8 Consensus size: 40
56142 ATTACCACAA
* ** *
56152 GCACAATTGCCTTCGGGTCTTAGCCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
56192 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
56232 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
56272 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
56312 GCACAAATGCCTGCGGGTCTTAGCCCGAATATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
56346 ATACAAATGC
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:61142 original size:43 final size:42
Alignment explanation
Indices: 61045--61154 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
61035 AACTTCTGTT
*
61045 TTACGTGTAAGACCATGTCTGGGACATCGACATCATATCTGA
1 TTACGTGTAAGACCATGTCCGGGACATCGACATCATATCTGA
* * * *
61087 TTTCGTGTAAGACCCTGTCCGGGACAGT-GGCATCGATATTTGA
1 TTACGTGTAAGACCATGTCCGGGACA-TCGACATC-ATATCTGA
* * *
61130 TTACATGTAAGACCACGTCTGGGAC
1 TTACGTGTAAGACCATGTCCGGGAC
61155 GTTGGCATTG
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
42 28 0.50
43 28 0.50
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCCGGGACATCGACATCATATCTGA
Found at i:61161 original size:43 final size:42
Alignment explanation
Indices: 61005--61162 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 42
60995 ATGTGATTTT
* * *
61005 GTGTAAGACCACATATGGGACATTGGCATCA-ACTTCTGTTTTAC
1 GTGTAAGACCACGTCTGGGACATTGGCATCATA-TT-TG-ATTAC
* * * * *
61049 GTGTAAGACCATGTCTGGGACATCGACATCATATCTGATTTC
1 GTGTAAGACCACGTCTGGGACATTGGCATCATATTTGATTAC
* *
61091 GTGTAAGACC-CTGTCCGGGACAGTGGCATCGATATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGACATTGGCATC-ATATTTGATTAC
* *
61134 ATGTAAGACCACGTCTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACATTGGCAT
61163 TGTCTATGTT
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
42 27 0.30
43 35 0.38
44 28 0.31
45 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCATATTTGATTAC
Found at i:74761 original size:30 final size:30
Alignment explanation
Indices: 74727--74787 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
74717 TTTTCGAGCC
74727 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
74757 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
74787 T
1 T
74788 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Done.