Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold250
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: 28827
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Found at i:1130 original size:29 final size:28
Alignment explanation
Indices: 1029--1111 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
1019 AGGAAGCGTC
1029 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
*
1057 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGTT
*
1085 CTGGTGGCACTGCCACAAAATATCTGT
1 CTGGTGGCACTGCCACAAATTATCTGT
1112 ATTTGGTGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:1144 original size:56 final size:55
Alignment explanation
Indices: 1029--1144 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 55
1019 AGGAAGCGTC
* *
1029 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTT
* * * *
1085 CTGGTGGC-ACTGCCACAAAATATCTGTATTTGGTGACTCTGTCAC-ATTTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-T
1141 CTGG
1 CTGG
1145 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
55 9 0.18
56 29 0.57
57 13 0.25
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (55 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGTT
Found at i:7922 original size:27 final size:27
Alignment explanation
Indices: 7892--7947 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
7882 CCCATAATTA
7892 ATAAAATGACTGTTATGCCCCTATGTG
1 ATAAAATGACTGTTATGCCCCTATGTG
*
7919 ATAAAATGATTGTTATGCCCCTATGTG
1 ATAAAATGACTGTTATGCCCCTATGTG
7946 AT
1 AT
7948 GTATGATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (27 bp):
ATAAAATGACTGTTATGCCCCTATGTG
Found at i:10994 original size:27 final size:27
Alignment explanation
Indices: 10964--11016 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
10954 CTCATATATG
* * *
10964 TAGGCTAGTATTATTGAAATGCCCTTA
1 TAGGCTAGAATTACTGAAATACCCTTA
*
10991 TAGGGTAGAATTACTGAAATACCCTT
1 TAGGCTAGAATTACTGAAATACCCTT
11017 GGTTTACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (27 bp):
TAGGCTAGAATTACTGAAATACCCTTA
Found at i:11044 original size:26 final size:27
Alignment explanation
Indices: 10999--11068 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
10989 TATAGGGTAG
10999 AATTACTGAAATACCCTTGGTTTACAA
1 AATTACTGAAATACCCTTGGTTTACAA
* * *
11026 AATTATTG-AATACCTTTGGTTTATAA
1 AATTACTGAAATACCCTTGGTTTACAA
**
11052 AATTACCAAAATACCCT
1 AATTACTGAAATACCCT
11069 CGATTAGCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 21 0.60
27 14 0.40
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.36
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGGTTTACAA
Found at i:11080 original size:27 final size:26
Alignment explanation
Indices: 11049--11164 Score: 124
Period size: 27 Copynumber: 4.3 Consensus size: 26
11039 CTTTGGTTTA
*
11049 TAAAATTACCAAAATACCCTCGATTAG
1 TAAAATTACCAAAATACCC-CGATTTG
* * *
11076 CAAAACTACCAAAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCCCGA-TTTG
* *
11103 TAAAATTATCAAAATACCCCTGGTTTG
1 TAAAATTACCAAAATACCCC-GATTTG
**
11130 TAAAATTACCAAAATACCCTCGACCTG
1 TAAAATTACCAAAATACCC-CGATTTG
11157 TAAAATTA
1 TAAAATTA
11165 TTGAAATACC
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
26 2 0.03
27 70 0.96
28 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (26 bp):
TAAAATTACCAAAATACCCCGATTTG
Found at i:11110 original size:54 final size:54
Alignment explanation
Indices: 11044--11148 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
11034 AATACCTTTG
11044 GTTTATAAAATTACCAAAATA-CCCTCGATTAGCAAAACTACCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCT-GATTAGCAAAACTACCAAAATACCCCTA
* * * * * *
11098 GTTTGTAAAATTATCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCC
1 GTTTATAAAATTACCAAAATACCCCTGATTAGCAAAACTACCAAAATACCC
11149 TCGACCTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
54 40 0.91
55 4 0.09
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.28
Consensus pattern (54 bp):
GTTTATAAAATTACCAAAATACCCCTGATTAGCAAAACTACCAAAATACCCCTA
Found at i:11159 original size:54 final size:55
Alignment explanation
Indices: 11049--11179 Score: 135
Period size: 54 Copynumber: 2.4 Consensus size: 55
11039 CTTTGGTTTA
* * **
11049 TAAAATTACCAAAATA-CCCTCGATTAGCAAAACTACCAAAATACCCCTAGTTTG
1 TAAAATTATCAAAATACCCCTCGATTAGCAAAACTACCAAAATACCCCGAGCCTG
* * * *
11103 TAAAATTATCAAAATACCCCT-GGTTTGTAAAATTACCAAAATACCCTCGA-CCTG
1 TAAAATTATCAAAATACCCCTCGATTAGCAAAACTACCAAAATACCC-CGAGCCTG
**
11157 TAAAATTATTGAAATA-CCCTCGA
1 TAAAATTATCAAAATACCCCTCGA
11180 CCTATAAAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
53 4 0.06
54 53 0.84
55 6 0.10
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (55 bp):
TAAAATTATCAAAATACCCCTCGATTAGCAAAACTACCAAAATACCCCGAGCCTG
Found at i:11171 original size:27 final size:27
Alignment explanation
Indices: 11130--11197 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
11120 CCCTGGTTTG
* * *
11130 TAAAATTACCAAAATACCCTCGACCTG
1 TAAAATTATCGAAATACCCTCGACCTA
*
11157 TAAAATTATTGAAATACCCTCGACCTA
1 TAAAATTATCGAAATACCCTCGACCTA
11184 TAAAATTATCGAAA
1 TAAAATTATCGAAA
11198 CTTATTGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (27 bp):
TAAAATTATCGAAATACCCTCGACCTA
Found at i:14569 original size:54 final size:55
Alignment explanation
Indices: 14508--14852 Score: 274
Period size: 54 Copynumber: 6.4 Consensus size: 55
14498 CTTTGGTTTA
* * * *
14508 TAAAATTACCAAAATACCCTCGA-TTAGCAAAACTACCAAAATACCC-CTAGTTTG
1 TAAAATTATCGAAATACCCTCGACTTAGCAAAATTACCAAAATACCCTCGA-TTTG
* * * * **
14562 TAAAATTATCAAAATACCC-CTG-GTTTGTAAAATTACCAAAATACCCTCGACCTG
1 TAAAATTATCGAAATACCCTC-GACTTAGCAAAATTACCAAAATACCCTCGATTTG
* * * * * * *
14616 TAAAATTATTGAAATACCCTCGACCTA-TAAAATTATCGAAACACCCTCGATTAG
1 TAAAATTATCGAAATACCCTCGACTTAGCAAAATTACCAAAATACCCTCGATTTG
* * * *
14670 GAAAATTACCGAAATACCCTCGA-TTAGGAAAATTACCAAAATACCCTTGATTTG
1 TAAAATTATCGAAATACCCTCGACTTAGCAAAATTACCAAAATACCCTCGATTTG
* * * * * * *
14724 GAAAATTATCGAAATACACTTGATTTAG-AAAATTACAAAAATACCCTTGATTTA
1 TAAAATTATCGAAATACCCTCGACTTAGCAAAATTACCAAAATACCCTCGATTTG
* * * * * * * * *
14778 CAAAATTATAGAAATACCCTTGACTT-TCAAAAACTACAAAAATACCATTGGTTTG
1 TAAAATTATCGAAATACCCTCGACTTAGC-AAAATTACCAAAATACCCTCGATTTG
14833 TAAAATTATCGAAATACCCT
1 TAAAATTATCGAAATACCCT
14853 TGGTTTGTAG
Statistics
Matches: 238, Mismatches: 44, Indels: 17
0.80 0.15 0.06
Matches are distributed among these distances:
53 3 0.01
54 187 0.79
55 48 0.20
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (55 bp):
TAAAATTATCGAAATACCCTCGACTTAGCAAAATTACCAAAATACCCTCGATTTG
Found at i:14793 original size:81 final size:82
Alignment explanation
Indices: 14465--14800 Score: 289
Period size: 81 Copynumber: 4.2 Consensus size: 82
14455 TAGAATTACT
* * * * *
14465 GAAATACCCTTGGTTTACAAAATTA-CTG-AATACCTTTGGTTTATAAAATTACCAAAATACCCT
1 GAAATACCCTTGATTTATAAAATTATC-GAAATACCCTTGATTTAGAAAATTACCAAAATACCCT
*
14528 CGATTAGCAAAACTACCA
65 CGATTAGCAAAATTACCA
* * * * *
14546 -AAATACCCCT-AGTTTGTAAAATTATCAAAATACCCCTGGTTT-GTAAAATTACCAAAATACCC
1 GAAATACCCTTGA-TTTATAAAATTATCGAAATACCCTTGATTTAG-AAAATTACCAAAATACCC
* * **
14608 TCGACCT-GTAAAATTA-TT
64 TCGA-TTAGCAAAATTACCA
* ** * * *
14626 GAAATACCCTCGACCTATAAAATTATCGAAACACCCTCGA-TTAGGAAAATTACCGAAATACCCT
1 GAAATACCCTTGATTTATAAAATTATCGAAATACCCTTGATTTA-GAAAATTACCAAAATACCCT
*
14690 CGATTAGGAAAATTACCA
65 CGATTAGCAAAATTACCA
** * * *
14708 -AAATACCCTTGATTTGGAAAATTATCGAAATACACTTGATTTAGAAAATTACAAAAATACCCTT
1 GAAATACCCTTGATTTATAAAATTATCGAAATACCCTTGATTTAGAAAATTACCAAAATACCCTC
*
14772 GATTTA-CAAAATTA-TA
66 GA-TTAGCAAAATTACCA
14788 GAAATACCCTTGA
1 GAAATACCCTTGA
14801 CTTTCAAAAA
Statistics
Matches: 200, Mismatches: 41, Indels: 28
0.74 0.15 0.10
Matches are distributed among these distances:
80 23 0.12
81 168 0.84
82 9 0.05
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (82 bp):
GAAATACCCTTGATTTATAAAATTATCGAAATACCCTTGATTTAGAAAATTACCAAAATACCCTC
GATTAGCAAAATTACCA
Found at i:14840 original size:55 final size:54
Alignment explanation
Indices: 14465--14854 Score: 272
Period size: 54 Copynumber: 7.2 Consensus size: 54
14455 TAGAATTACT
* * ** * * ** *
14465 GAAATACCCTTGGTTTACAAAATTAC-TGAATACCTTTGGTTTATAAAATTACC
1 GAAATACCCTTGATTTAGAAAATTACAAAAATACCCTTGATTTGCAAAATTATC
* * * * * *
14518 AAAATACCCTCGA-TTAGCAAAACTACCAAAATACCCCT-AGTTTGTAAAATTATC
1 GAAATACCCTTGATTTAG-AAAATTACAAAAATACCCTTGA-TTTGCAAAATTATC
* * * * * ** * *
14572 AAAATACCCCTGGTTT-GTAAAATTACCAAAATACCCTCGACCTGTAAAATTATT
1 GAAATACCCTTGATTTAG-AAAATTACAAAAATACCCTTGATTTGCAAAATTATC
* ** * * * * * * *
14626 GAAATACCCTCGACCTATAAAATTATC-GAAACACCCTCGATTAGGAAAATTACC
1 GAAATACCCTTGATTTAGAAAATTA-CAAAAATACCCTTGATTTGCAAAATTATC
* * *
14680 GAAATACCCTCGA-TTAGGAAAATTACCAAAATACCCTTGATTTGGAAAATTATC
1 GAAATACCCTTGATTTA-GAAAATTACAAAAATACCCTTGATTTGCAAAATTATC
* * *
14734 GAAATACACTTGATTTAGAAAATTACAAAAATACCCTTGATTTACAAAATTATA
1 GAAATACCCTTGATTTAGAAAATTACAAAAATACCCTTGATTTGCAAAATTATC
* * * *
14788 GAAATACCCTTGACTTTCA-AAAACTACAAAAATACCATTGGTTTGTAAAATTATC
1 GAAATACCCTTGA-TTT-AGAAAATTACAAAAATACCCTTGATTTGCAAAATTATC
14843 GAAATACCCTTG
1 GAAATACCCTTG
14855 GTTTGTAGAT
Statistics
Matches: 268, Mismatches: 57, Indels: 22
0.77 0.16 0.06
Matches are distributed among these distances:
52 3 0.01
53 20 0.07
54 192 0.72
55 52 0.19
56 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (54 bp):
GAAATACCCTTGATTTAGAAAATTACAAAAATACCCTTGATTTGCAAAATTATC
Found at i:14859 original size:27 final size:27
Alignment explanation
Indices: 14465--14861 Score: 239
Period size: 27 Copynumber: 14.7 Consensus size: 27
14455 TAGAATTACT
* **
14465 GAAATACCCTTGGTTTACAAAATTA-C
1 GAAATACCCTTGATTTGTAAAATTATC
* * * *
14491 TG-AATACCTTTGGTTTATAAAATTACC
1 -GAAATACCCTTGATTTGTAAAATTATC
* * * * * *
14518 AAAATACCCTCGATTAGCAAAACTACC
1 GAAATACCCTTGATTTGTAAAATTATC
* *
14545 AAAATACCCCT-AGTTTGTAAAATTATC
1 GAAATACCCTTGA-TTTGTAAAATTATC
* * * *
14572 AAAATACCCCTGGTTTGTAAAATTACC
1 GAAATACCCTTGATTTGTAAAATTATC
* * ** *
14599 AAAATACCCTCGACCTGTAAAATTATT
1 GAAATACCCTTGATTTGTAAAATTATC
* ** *
14626 GAAATACCCTCGACCTATAAAATTATC
1 GAAATACCCTTGATTTGTAAAATTATC
* * * * *
14653 GAAACACCCTCGATTAGGAAAATTACC
1 GAAATACCCTTGATTTGTAAAATTATC
* * * *
14680 GAAATACCCTCGATTAGGAAAATTACC
1 GAAATACCCTTGATTTGTAAAATTATC
* *
14707 AAAATACCCTTGATTTGGAAAATTATC
1 GAAATACCCTTGATTTGTAAAATTATC
*
14734 GAAATACACTTGATTTAG-AAAATTA-C
1 GAAATACCCTTGATTT-GTAAAATTATC
* ** *
14760 AAAAATACCCTTGATTTACAAAATTATA
1 -GAAATACCCTTGATTTGTAAAATTATC
** *
14788 GAAATACCCTTGACTTTCAAAAACTA-C
1 GAAATACCCTTGA-TTTGTAAAATTATC
* * *
14815 AAAAATACCATTGGTTTGTAAAATTATC
1 -GAAATACCCTTGATTTGTAAAATTATC
*
14843 GAAATACCCTTGGTTTGTA
1 GAAATACCCTTGATTTGTA
14862 GATTTACCAA
Statistics
Matches: 300, Mismatches: 59, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
26 23 0.08
27 256 0.85
28 21 0.07
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (27 bp):
GAAATACCCTTGATTTGTAAAATTATC
Found at i:15176 original size:41 final size:41
Alignment explanation
Indices: 15119--15238 Score: 154
Period size: 41 Copynumber: 2.9 Consensus size: 41
15109 GGAGGAAGAA
*
15119 ATTGAGGATCGCATGGTTGCTTGACGACCATGGATCCA-CT
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCT
* **
15159 GATTGAGGATTGCATGGTTGCTTGACGGTCGTGGATCCACCT
1 -ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCT
* *
15201 ATT-ATGGATCACATGGTTGCTTGATGACCGTGGATCCA
1 ATTGA-GGATCGCATGGTTGCTTGACGACCGTGGATCCA
15239 TCGGTGGCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 65 0.96
42 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCT
Found at i:15416 original size:22 final size:22
Alignment explanation
Indices: 15388--15429 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15378 TTATTCTGAT
*
15388 TATGGCTTTGCGCCAACCTACA
1 TATGGCTCTGCGCCAACCTACA
*
15410 TATGGCTCTGTGCCAACCTA
1 TATGGCTCTGCGCCAACCTA
15430 GTTATAGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (22 bp):
TATGGCTCTGCGCCAACCTACA
Found at i:15443 original size:22 final size:22
Alignment explanation
Indices: 15399--15447 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
15389 ATGGCTTTGC
*
15399 GCCAACCTACATATGGCTCTGT
1 GCCAACCTACATATAGCTCTGT
** *
15421 GCCAACCTAGTTATAGCTGTGT
1 GCCAACCTACATATAGCTCTGT
15443 GCCAA
1 GCCAA
15448 ATGTTTTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (22 bp):
GCCAACCTACATATAGCTCTGT
Found at i:18476 original size:31 final size:32
Alignment explanation
Indices: 18421--18493 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
18411 TGAGAGAAAA
*
18421 AGGGGAGGAGTAAGGAGAATGACGGCAAAGAG
1 AGGGGAGGAGTAAGGAGAAGGACGGCAAAGAG
18453 AGGGGAGGAGT-AGGAGAAGGACGGCAAAGAG
1 AGGGGAGGAGTAAGGAGAAGGACGGCAAAGAG
*
18484 AGGAGAGGAG
1 AGGGGAGGAG
18494 AGCAAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 28 0.72
32 11 0.28
ACGTcount: A:0.40, C:0.05, G:0.51, T:0.04
Consensus pattern (32 bp):
AGGGGAGGAGTAAGGAGAAGGACGGCAAAGAG
Found at i:20075 original size:33 final size:33
Alignment explanation
Indices: 20038--20100 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
20028 TACTATCAGG
* *
20038 TAAAGATTAATGGTGATGATGCATCTAAGACAA
1 TAAAGATTAAGGGTGATGATGCACCTAAGACAA
20071 TAAAGATTAAGGGTGATGATGCACCTAAGA
1 TAAAGATTAAGGGTGATGATGCACCTAAGA
20101 TAGCCTTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (33 bp):
TAAAGATTAAGGGTGATGATGCACCTAAGACAA
Found at i:23574 original size:40 final size:39
Alignment explanation
Indices: 23483--23665 Score: 197
Period size: 40 Copynumber: 4.6 Consensus size: 39
23473 TCCTCGTTCA
* * *
23483 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* *
23522 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* * *
23561 GAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* * * * *
23601 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCAC
*
23642 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
23666 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.31
40 76 0.63
41 8 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
Found at i:23674 original size:41 final size:41
Alignment explanation
Indices: 23597--23674 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
23587 TTAGTATCTC
* * *
23597 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
23638 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
23675 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.