Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold9_ERROPOS3029511+
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: 59103
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:6149 original size:78 final size:78
Alignment explanation
Indices: 6010--6232 Score: 279
Period size: 78 Copynumber: 2.8 Consensus size: 78
6000 TTGAATGATG
* * * * * *
6010 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCATT
*
6074 TGTGCGAGATACTAAT
63 TGTGCGAGATACTAAA
*
6090 TCCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 TCCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGT
*
6155 GCGAGTTACTAAA
66 GCGAGATACTAAA
* * *
6168 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTT
6232 G
64 G
6233 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
77 1 0.01
78 60 0.47
79 53 0.42
80 13 0.10
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (78 bp):
TCCGGGCTAAGCCCGAAGGCATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGATACTAAA
Found at i:6239 original size:79 final size:78
Alignment explanation
Indices: 6010--6251 Score: 276
Period size: 79 Copynumber: 3.1 Consensus size: 78
6000 TTGAATGATG
* * * * *
6010 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
6073 TTGTGCGAGATACTAAT
63 TTGTGCGAG-TACTAAA
* *
6090 TCCGGGCTAAGCCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATTT
6153 GTGCGAGTTACTAAA
65 GTGCGAG-TACTAAA
* *
6168 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
** *
6233 AACGAGTAGCTATA
66 TGCGAGTA-CTAAA
6247 TCCGG
1 TCCGG
6252 TTAAATTCCG
Statistics
Matches: 140, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.01
78 60 0.43
79 65 0.46
80 13 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTACTAAA
Found at i:6246 original size:40 final size:40
Alignment explanation
Indices: 6010--6232 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
6000 TTGAATGATG
* * * *
6010 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
6050 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
6090 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6128 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
6168 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
6208 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6233 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 25 0.15
39 53 0.33
40 77 0.47
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:10205 original size:37 final size:37
Alignment explanation
Indices: 10155--10233 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
10145 TATTACGAAT
* * * *
10155 GTCTTACCCGGACATAATCTCCACATGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
10192 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
10229 GTCTT
1 GTCTT
10234 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:10430 original size:47 final size:47
Alignment explanation
Indices: 10352--10930 Score: 908
Period size: 47 Copynumber: 12.1 Consensus size: 47
10342 CCCTTCGGGA
* * * * * *
10352 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10399 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10446 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10493 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* **
10544 TTTATCTA-ATATATATGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATC-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10591 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10638 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10687 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10736 CTTATCACACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTAT--CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10785 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10832 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10879 CTTATCACATATAATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT-ATACACTTTCACATTCATCACATCGGCCATTAGGC
10927 CTTA
1 CTTA
10931 CTATCATTTC
Statistics
Matches: 497, Mismatches: 24, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
46 1 0.00
47 274 0.55
48 39 0.08
49 135 0.27
51 47 0.09
52 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:10626 original size:145 final size:144
Alignment explanation
Indices: 10352--10930 Score: 913
Period size: 145 Copynumber: 4.0 Consensus size: 144
10342 CCCTTCGGGA
* * * * * * *
10352 CTTATCAC-AT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATA
1 CTTATCACTATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
10414 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
66 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
10479 ATCGGCCATTAGGC
131 ATCGGCCATTAGGC
*
10493 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCTTTATCTA-ATATA
1 CTTATCAC-TATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC-ACATATA
** *
10557 TATGCTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCACATTCATC
64 TACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATC
10622 ACATCGGCCATTAGGC
129 ACATCGGCCATTAGGC
10638 CTTATCAC-ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 CTTATCACTATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATA
10702 TACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATATACACTTTCACATTCA
64 TACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT--CACATATATACACTTTCACATTCA
*
10767 TCACATCAGCCATTAGGC
127 TCACATCGGCCATTAGGC
* *
10785 CTTAT--CT-CATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATA
1 CTTATCACTATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
10847 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAATACACTTTCACATTCATCA
66 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT-ATACACTTTCACATTCATCA
10912 CATCGGCCATTAGGC
130 CATCGGCCATTAGGC
10927 CTTA
1 CTTA
10931 CTATCATTTC
Statistics
Matches: 407, Mismatches: 19, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
141 15 0.04
142 39 0.10
143 91 0.22
144 1 0.00
145 215 0.53
146 1 0.00
147 45 0.11
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (144 bp):
CTTATCACTATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
ATCGGCCATTAGGC
Found at i:10773 original size:241 final size:240
Alignment explanation
Indices: 10352--10930 Score: 968
Period size: 241 Copynumber: 2.4 Consensus size: 240
10342 CCCTTCGGGA
* * * * * * * * *
10352 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
10415 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
* * *
10480 TCGGCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCT
131 TCGGCCATTAGGCCTTATCACA-ACATATATACACTTTCACATTCATCACATCAGCCATTAGGCC
**
10545 TTATCTAATATATATGCTTTCACATTCATCACATCGGCCATTAGGC
195 TTATCTAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10591 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
10656 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
10721 CATCGGCCATTAGGCCTTATCAC-ACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
129 CATCGGCCATTAGGCCTTATCACAACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
*
10785 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
194 CTTATCTAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10832 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATA-ATAC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
10896 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
10931 CTATCATTTC
Statistics
Matches: 321, Mismatches: 15, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
239 46 0.14
240 39 0.12
241 189 0.59
243 47 0.15
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (240 bp):
CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACAACATATATACACTTTCACATTCATCACATCAGCCATTAGGCCT
TATCTAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:14542 original size:40 final size:39
Alignment explanation
Indices: 14498--14716 Score: 221
Period size: 40 Copynumber: 5.5 Consensus size: 39
14488 GCTACTCGTT
* *
14498 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTT-TAGTAACTCGCA
*
14538 CAAATGCCTTCGGGACTTA-ACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTTAGTAACTCGCA
* *
14577 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGTTTAGTAACTCGCA
* * *
14617 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTTAGTAACTCGCA
* * * * * *
14656 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TTTAGTAAC-TCGCA
14697 CAAA-GCCTTCGGGACTTAGC
1 CAAATGCCTTCGGGACTTAGC
14717 TCGGACATCA
Statistics
Matches: 151, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
38 3 0.02
39 63 0.42
40 73 0.48
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTTAGTAACTCGCA
Found at i:14580 original size:39 final size:39
Alignment explanation
Indices: 14465--14668 Score: 225
Period size: 39 Copynumber: 5.2 Consensus size: 39
14455 AAATCACATA
* * * **
14465 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCAAATG
1 CCTTCGGGACTTAACCGGATTTAG-TAACTCGCACAAATG
* * *
14504 CCTTCGGGACATAGCCCGG-TTATAGTAACTCACACAAATG
1 CCTTCGGGACTTA-ACCGGATT-TAGTAACTCGCACAAATG
14544 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
* *
14583 CCTTCGGGACTTAACCCAGATTTAGTAACTCGCACCAATG
1 CCTTCGGGACTTAA-CCGGATTTAGTAACTCGCACAAATG
* * *
14623 CCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATG
1 CCTTCGGGACTTA-ACCGGATTTAGTAACTCGCACAAATG
14662 CCTTCGG
1 CCTTCGG
14669 ATCTTAGTCT
Statistics
Matches: 141, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
39 79 0.56
40 62 0.44
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
Found at i:14609 original size:79 final size:79
Alignment explanation
Indices: 14465--14668 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 79
14455 AAATCACATA
* * * ** * *
14465 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAG
1 CCTTCGGGACTTAACCGGATTTAG-TAACTCGCACAAATGCCTTCGGGACATAACCCGATTATAG
14529 TAACTCACACAAATG
65 TAACTCACACAAATG
*
14544 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAGATT-TAG
1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACATAACCC-GATTATAG
* *
14608 TAACTCGCACCAATG
65 TAACTCACACAAATG
* * *
14623 CCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG
1 CCTTCGGGACTTA-ACCGGATTTAGTAACTCGCACAAATGCCTTCGG
14669 ATCTTAGTCT
Statistics
Matches: 109, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
78 5 0.05
79 101 0.93
80 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACATAACCCGATTATAGT
AACTCACACAAATG
Found at i:14705 original size:79 final size:79
Alignment explanation
Indices: 14498--14721 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 79
14488 GCTACTCGTT
* * * * *
14498 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-CACAAATGCCTTCGGGACTTA-ACCG
1 CAAATGCCTTCGGGACTTAACCCAGATATAGTAACT-AGCACAAA-GCCTTCGGGACTTAGCCCG
*
14561 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
* * *
14577 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGG
*
14641 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
** ** * * *
14656 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCTCG
1 CAAATGCCTTCGGGA-CTTAACCCAGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCG
14720 GA
64 GA
14722 CATCATTCGA
Statistics
Matches: 119, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
78 7 0.06
79 95 0.80
80 17 0.14
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCAGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:16435 original size:34 final size:33
Alignment explanation
Indices: 16371--16436 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
16361 TTAAAGATGT
* *
16371 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
16404 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
16437 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:19569 original size:11 final size:11
Alignment explanation
Indices: 19549--19598 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
19539 AGAGAAGAGG
19549 AAATTCGAAAA
1 AAATTCGAAAA
*
19560 AAATTTGAAAA
1 AAATTCGAAAA
*
19571 AAAATCGAAAA
1 AAATTCGAAAA
19582 AAATT--AAAA
1 AAATTCGAAAA
19591 AAA-TCGAA
1 AAATTCGAA
19599 GTATAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
8 1 0.03
9 7 0.21
10 2 0.06
11 23 0.70
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (11 bp):
AAATTCGAAAA
Found at i:19578 original size:22 final size:19
Alignment explanation
Indices: 19553--19598 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
19543 AAGAGGAAAT
19553 TCGAAAAAAATTTGAAAAAAAA
1 TCGAAAAAAA-TT--AAAAAAA
19575 TCGAAAAAAATTAAAAAAA
1 TCGAAAAAAATTAAAAAAA
19594 TCGAA
1 TCGAA
19599 GTATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.50
21 2 0.08
22 10 0.42
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.17
Consensus pattern (19 bp):
TCGAAAAAAATTAAAAAAA
Found at i:20561 original size:21 final size:23
Alignment explanation
Indices: 20537--20585 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
20527 AGTACGAGCG
20537 AGAAAAAGAAATCG-AAAG-AAA
1 AGAAAAAGAAATCGAAAAGAAAA
* *
20558 AGAAAAAGAGATTGAAAAGAAAA
1 AGAAAAAGAAATCGAAAAGAAAA
20581 AGAAA
1 AGAAA
20586 TCAAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.50
22 4 0.17
23 8 0.33
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.06
Consensus pattern (23 bp):
AGAAAAAGAAATCGAAAAGAAAA
Found at i:22732 original size:34 final size:33
Alignment explanation
Indices: 22668--22733 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
22658 TTAAAGATGT
* *
22668 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
22701 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
22734 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:23866 original size:12 final size:12
Alignment explanation
Indices: 23849--23875 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23839 AGGAAATTTG
23849 AAAAAAAAATTC
1 AAAAAAAAATTC
23861 AAAAAAAAATTC
1 AAAAAAAAATTC
23873 AAA
1 AAA
23876 TTTTTTTTTT
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:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:26536 original size:11 final size:12
Alignment explanation
Indices: 26520--26574 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
26510 TTGGAGTAAC
26520 AAAAAA-TCAAA
1 AAAAAATTCAAA
26531 AAAAAATTCAAA
1 AAAAAATTCAAA
* *
26543 AAAAATTTGATTGAA
1 AAAAAATTCA---AA
26558 AAAAAATTCAAA
1 AAAAAATTCAAA
26570 AAAAA
1 AAAAA
26575 GTGAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 6 0.17
12 20 0.56
15 10 0.28
ACGTcount: A:0.73, C:0.05, G:0.04, T:0.18
Consensus pattern (12 bp):
AAAAAATTCAAA
Found at i:26598 original size:28 final size:27
Alignment explanation
Indices: 26567--26627 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
26557 AAAAAAATTC
*
26567 AAAAAAAAGTGAAAAAAAA-TCGAGCAAA
1 AAAAAAAAG-AAAAAAAAAGT-GAGCAAA
*
26595 AAAAGAAAGAAAAAAAAAGGTGAGCAAA
1 AAAAAAAAGAAAAAAAAA-GTGAGCAAA
26623 AAAAA
1 AAAAA
26628 TCAAGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 8 0.29
28 19 0.68
29 1 0.04
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (27 bp):
AAAAAAAAGAAAAAAAAAGTGAGCAAA
Found at i:27654 original size:12 final size:12
Alignment explanation
Indices: 27642--27759 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
27632 GAAAGAGATT
*
27642 GAAAAAGAAATT
1 GAAAAAGAAATA
27654 G--AAAGAAA-A
1 GAAAAAGAAATA
*
27663 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
27674 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
27687 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
27699 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
27711 GAAAAAGTGAGA
1 GAAAAAGAAATA
27723 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
27734 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
27750 GAAAAAGAAA
1 GAAAAAGAAA
27760 AAGAGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:27687 original size:6 final size:6
Alignment explanation
Indices: 27655--27768 Score: 77
Period size: 6 Copynumber: 18.5 Consensus size: 6
27645 AAAGAAATTG
* * ** *
27655 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
27702 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
27753 AAAGAA AAAGAGA AAA
1 AAAGAA AAAGA-A AAA
27769 AAGAAATTGA
Statistics
Matches: 80, Mismatches: 24, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
5 3 0.04
6 62 0.77
7 11 0.14
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:27742 original size:15 final size:14
Alignment explanation
Indices: 27721--27774 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
27711 GAAAAAGTGA
27721 GAGAAAAAGAAAAT
1 GAGAAAAAGAAAAT
27735 GA-AGAAAAGAAAAT
1 GAGA-AAAAGAAAAT
* *
27749 -TGAAAAAGAAAAA
1 GAGAAAAAGAAAAT
27762 GAGAAAAAAGAAA
1 GAG-AAAAAGAAA
27775 TTGAAAGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 10 0.30
14 14 0.42
15 9 0.27
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (14 bp):
GAGAAAAAGAAAAT
Found at i:27744 original size:14 final size:13
Alignment explanation
Indices: 27724--27780 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
27714 AAAGTGAGAG
27724 AAAAAGAAAATGA
1 AAAAAGAAAATGA
27737 AGAAAAGAAAATTG-
1 A-AAAAGAAAA-TGA
*
27751 AAAAAGAAAAAGAGA
1 AAAAAG-AAAA-TGA
*
27766 AAAAAGAAATTGA
1 AAAAAGAAAATGA
27779 AA
1 AA
27781 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 10 0.28
14 18 0.50
15 8 0.22
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:27753 original size:27 final size:27
Alignment explanation
Indices: 27723--27780 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
27713 AAAAGTGAGA
* *
27723 GAAAAAGAAAATGA-AGAAAAGAAAATT
1 GAAAAAGAAAAAGAGAAAAAAG-AAATT
27750 GAAAAAGAAAAAGAGAAAAAAGAAATT
1 GAAAAAGAAAAAGAGAAAAAAGAAATT
27777 GAAA
1 GAAA
27781 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (27 bp):
GAAAAAGAAAAAGAGAAAAAAGAAATT
Found at i:27814 original size:33 final size:33
Alignment explanation
Indices: 27777--27839 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
27767 AAAAGAAATT
27777 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
27810 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
27840 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:31213 original size:18 final size:18
Alignment explanation
Indices: 31175--31214 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31165 AAATGAAAAG
* **
31175 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCAA
31193 AAAAGAAAAAGAAATCAA
1 AAAAGAAAAAGAAATCAA
31211 AAAA
1 AAAA
31215 AGAGTGAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.75, C:0.03, G:0.15, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCAA
Found at i:35821 original size:11 final size:11
Alignment explanation
Indices: 35805--35845 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
35795 GTATGCAATT
*
35805 TTTTTTTTCAA
1 TTTTTTTTCGA
35816 TTTTTTTTCGA
1 TTTTTTTTCGA
35827 TTTTTTTTCGA
1 TTTTTTTTCGA
35838 TTTTTTTT
1 TTTTTTTT
35846 TAATCTACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:38537 original size:12 final size:11
Alignment explanation
Indices: 38511--38536 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38501 TTTGTCTAGT
38511 AAAATTTTTCC
1 AAAATTTTTCC
38522 AAAATTTTTCC
1 AAAATTTTTCC
38533 AAAA
1 AAAA
38537 AAAAAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATTTTTCC
Found at i:43931 original size:11 final size:11
Alignment explanation
Indices: 43915--43959 Score: 81
Period size: 11 Copynumber: 4.0 Consensus size: 11
43905 TAGTAGTTTC
43915 TTCAAAAAAAA
1 TTCAAAAAAAA
43926 TTCAAAAAAAA
1 TTCAAAAAAAA
43937 TTCAAAAAAAAA
1 TTC-AAAAAAAA
43949 TTCAAAAAAAA
1 TTCAAAAAAAA
43960 ATTTGGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:43935 original size:12 final size:12
Alignment explanation
Indices: 43918--43962 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
43908 TAGTTTCTTC
43918 AAAAAAAATTC-
1 AAAAAAAATTCA
43929 AAAAAAAATTCA
1 AAAAAAAATTCA
43941 AAAAAAAATTCA
1 AAAAAAAATTCA
43953 AAAAAAAATT
1 AAAAAAAATT
43963 TGGTTTCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 11 0.33
12 22 0.67
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:44022 original size:15 final size:15
Alignment explanation
Indices: 44002--44053 Score: 95
Period size: 15 Copynumber: 3.4 Consensus size: 15
43992 TATCAAGTTG
44002 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
44017 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTG-A
44033 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
44048 AAAAAA
1 AAAAAA
44054 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 21 0.58
16 15 0.42
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (15 bp):
AAAAAAAATTCGTGA
Found at i:44023 original size:16 final size:16
Alignment explanation
Indices: 44002--44053 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
43992 TATCAAGTTG
44002 AAAAAAAATTCGTG-A
1 AAAAAAAATTCGTGAA
44017 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
44033 AAAAAAAATTCGTGAA
1 AAAAAAAATTCGTGAA
44049 AAAAA
1 AAAAA
44054 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 14 0.39
16 22 0.61
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (16 bp):
AAAAAAAATTCGTGAA
Found at i:53912 original size:19 final size:18
Alignment explanation
Indices: 53876--53915 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53866 TTTCCACTCG
*
53876 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
53894 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
53913 TTT
1 TTT
53916 ATTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:56207 original size:12 final size:12
Alignment explanation
Indices: 56190--56234 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
56180 TAGTTTCTCG
56190 AAAAAAAATTCA
1 AAAAAAAATTCA
*
56202 AAAAAAAAATCA
1 AAAAAAAATTCA
56214 AAAAAAAATTCGA
1 AAAAAAAATTC-A
56227 AAAAAAAA
1 AAAAAAAA
56235 ACTAGTTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 21 0.70
13 9 0.30
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:58696 original size:9 final size:9
Alignment explanation
Indices: 58682--58719 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
58672 GGAGTAAGTG
58682 ATTAAAAAA
1 ATTAAAAAA
58691 ATTAAAAAA
1 ATTAAAAAA
*
58700 ATCAAAAAAA
1 AT-TAAAAAA
58710 ATTAAAAAA
1 ATTAAAAAA
58719 A
1 A
58720 AAAAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:58700 original size:10 final size:10
Alignment explanation
Indices: 58685--58720 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
58675 GTAAGTGATT
58685 AAAAAAATT-
1 AAAAAAATTA
*
58694 AAAAAAATCA
1 AAAAAAATTA
58704 AAAAAAATTA
1 AAAAAAATTA
58714 AAAAAAA
1 AAAAAAA
58721 AAAGTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:58719 original size:13 final size:13
Alignment explanation
Indices: 58703--58734 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
58693 TAAAAAAATC
*
58703 AAAAAAAATTAAA
1 AAAAAAAAGTAAA
58716 AAAAAAAAGTAAA
1 AAAAAAAAGTAAA
58729 AAAAAA
1 AAAAAA
58735 TTCGTGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (13 bp):
AAAAAAAAGTAAA
Found at i:58729 original size:19 final size:18
Alignment explanation
Indices: 58685--58723 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
58675 GTAAGTGATT
58685 AAAAAAATTAAAAAAATCA
1 AAAAAAATTAAAAAAA-CA
58704 AAAAAAATTAAAAAAA-A
1 AAAAAAATTAAAAAAACA
58721 AAA
1 AAA
58724 GTAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
19 16 0.80
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAAAAATTAAAAAAACA
Done.