Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1970
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: 47583
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Found at i:1379 original size:39 final size:40
Alignment explanation
Indices: 1302--1448 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
1292 TAGCTCCTCG
* * *
1302 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
1342 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
1381 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
1421 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
1449 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:1459 original size:80 final size:80
Alignment explanation
Indices: 1348--1528 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
1338 CTCATTCAAT
* * *
1348 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
1411 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
1427 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
1491 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
1508 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
1529 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:1488 original size:40 final size:40
Alignment explanation
Indices: 1345--1528 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
1335 TAACTCATTC
* *
1345 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
1385 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
1425 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
1465 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
1506 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1529 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:9191 original size:39 final size:40
Alignment explanation
Indices: 9114--9260 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
9104 TAGCTCCTCG
* * *
9114 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
9154 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
9193 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
9233 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
9261 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:9271 original size:80 final size:80
Alignment explanation
Indices: 9160--9340 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
9150 CTCATTCAAT
* * *
9160 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
9223 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
9239 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
9303 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
9320 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
9341 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:9300 original size:40 final size:40
Alignment explanation
Indices: 9157--9340 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
9147 TAACTCATTC
* *
9157 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
9197 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
9237 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
9277 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
9318 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
9341 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:12139 original size:46 final size:46
Alignment explanation
Indices: 12081--12255 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
12071 TGATATGTGT
* *
12081 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAAA
1 GCTAATGTAAGACATGTCTGGGACATGCATCAGCCACAATATGAAA
* * * * * *
12127 GCCAATGTAAGACATGTCTGGGACATGCA-CCGGCATTAAGATGAGA
1 GCTAATGTAAGACATGTCTGGGACATGCATCAGCCA-CAATATGAAA
* *
12173 GCTACTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAT-ACAA
1 GCTAATGTAAGACATGTCTGGGACATGCATCAGCCAC-A-ATATGA-AA
* *
12221 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAGC
1 GCTAATGTAAGACATGTCTGGGACAT-GCATCAGC
12256 TTGTTGGGTG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
45 4 0.04
46 60 0.57
47 5 0.05
48 28 0.27
49 8 0.08
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (46 bp):
GCTAATGTAAGACATGTCTGGGACATGCATCAGCCACAATATGAAA
Found at i:14459 original size:42 final size:42
Alignment explanation
Indices: 14413--14524 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 42
14403 ATTTCACATT
* * *
14413 GATGCCATATCCCAGATATGGTCTTATACGAAATCTTATTTC
1 GATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATC
** **
14455 GATGCCAGGTCCCAGACGTGGTCTTACACGAAATCTCATATC
1 GATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATC
* * * *
14497 AACGCCATATCCAAAATATGGTCTTACA
1 GATGCCATATCCCAGATATGGTCTTACA
14525 TGATAACATA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (42 bp):
GATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATC
Found at i:18304 original size:79 final size:81
Alignment explanation
Indices: 18195--18377 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
18185 TACTCGTTCA
* *
18195 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
18258 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
18275 AATGCCTTCGGG-CTTAGCTCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
18338 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
18354 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
18378 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 27 0.30
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:18377 original size:40 final size:40
Alignment explanation
Indices: 18176--18377 Score: 234
Period size: 40 Copynumber: 5.1 Consensus size: 40
18166 GAATTTAACT
** *
18176 GGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCC
1 GGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
18216 GGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* * *
18256 GGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCTC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
*
18295 GGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 GGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCC
* *
18335 GGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 GGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
18375 GGA
1 GGA
18378 CATCATTCGA
Statistics
Matches: 138, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 92 0.67
41 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
Found at i:23858 original size:39 final size:40
Alignment explanation
Indices: 23802--23990 Score: 169
Period size: 39 Copynumber: 4.8 Consensus size: 40
23792 TTGAATGATG
* * *
23802 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAGTGACCATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTGACCAAA
* * *
23841 TCCGGACTAAGATCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTGACCAAA
* *
23881 TCC-GACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTGACCAAA
** * *
23920 TCCGGGTTAAG-TCCCGAAGGCATTTGT--GAGTTACTAAA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTGACCAAA
*
23958 TCCGG-GTCAAG-TCCCGAAGGCATTTGTGCGAGT
1 TCCGGACT-AAGAT-CCGAAGGCATTTGTGCGAGT
23991 TACTATAACC
Statistics
Matches: 133, Mismatches: 10, Indels: 13
0.85 0.06 0.08
Matches are distributed among these distances:
37 1 0.01
38 35 0.26
39 57 0.43
40 40 0.30
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:23990 original size:78 final size:79
Alignment explanation
Indices: 23802--24023 Score: 269
Period size: 78 Copynumber: 2.8 Consensus size: 79
23792 TTGAATGATG
* * * * *
23802 TCCGGG-CTAAGTCCCGAAGGC-TTTGTGCTAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
23864 TTGTACGAGTTACTAAA
64 TTGTA-GAGTTACTAAA
** *
23881 TCCGACT-AAGAT-CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTCAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATT
23944 TGT-GAGTTACTAAA
65 TGTAGAGTTACTAAA
*
23958 TCCGGGTCAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTCAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
24022 TG
65 TG
24024 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
77 17 0.14
78 63 0.51
79 44 0.35
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (79 bp):
TCCGGGTCAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTAGAGTTACTAAA
Found at i:24037 original size:40 final size:39
Alignment explanation
Indices: 23802--24023 Score: 249
Period size: 40 Copynumber: 5.6 Consensus size: 39
23792 TTGAATGATG
* * * *
23802 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGTGACCATA
1 TCCGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
23841 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGG-GTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
**
23881 TCCGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
23920 TCCGGGTTAAGTCCCGAAGGCATTTGT--GAGTTACTAAA
1 TCCGGG-TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
23958 TCCGGGTCAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGT-AAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
23999 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGG-TAAGTCCCGAAGGCATTTG
24024 AACGAGTAGC
Statistics
Matches: 162, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
37 1 0.01
38 36 0.22
39 55 0.34
40 67 0.41
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (39 bp):
TCCGGGTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:24054 original size:78 final size:77
Alignment explanation
Indices: 23815--24055 Score: 249
Period size: 78 Copynumber: 3.1 Consensus size: 77
23805 GGGCTAAGTC
* * * * *
23815 CCGAAGGC-TTTGTGCTAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCATTTG-ACGAGTTACT
**
23878 AAATCCGACTAAGAT
64 AAATCCGGTTAA-AT
* *
23893 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG-TGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGACGAGTTACTAA
* *
23957 ATCCGGGTCAAGT
66 ATCC-GGTTAAAT
*
23970 CCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 -CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTG-ACGAGTTA-
*
24033 CTATATCCGGTTAAAT
62 CTAAATCCGGTTAAAT
*
24049 TCGAAGG
1 CCGAAGG
24056 TACGTGATTT
Statistics
Matches: 137, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
77 15 0.11
78 66 0.48
79 46 0.34
80 10 0.07
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (77 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGACGAGTTACTAA
ATCCGGTTAAAT
Found at i:29737 original size:40 final size:40
Alignment explanation
Indices: 29536--29737 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
29526 TGGAATTTAA
** *
29536 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29576 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29616 CC-GATTTAGTAACTCGCACCAATGCCTTC-GG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
29653 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
29693 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29733 CCGGA
1 CCGGA
29738 CATCATTCGA
Statistics
Matches: 139, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
37 7 0.05
38 28 0.20
39 25 0.18
40 67 0.48
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:32223 original size:81 final size:81
Alignment explanation
Indices: 32079--32230 Score: 184
Period size: 82 Copynumber: 1.9 Consensus size: 81
32069 CTTTGTAAGT
* * * *
32079 TTTGTGAAAATAGAATGCTATCTTGGTATCATTTTTACAATGGGGTATCAATATTTCAGAAAATA
1 TTTGTGAAAATAGAATGCCATCTTGATATCATTTTTACAAAGGGGTATCAATAATTCAGAAAATA
*
32144 TTGATACTTAATTGGG
66 TCGATACTTAATTGGG
* * *
32160 TTTGTGAAAAATAGAATGCCATTTTGATATCGTTTTTA-AGAAGGGTGT-T-AATAATTCATAAA
1 TTTGTG-AAAATAGAATGCCATCTTGATATCATTTTTACA-AAGGG-GTATCAATAATTCAGAAA
32222 ATATCGATA
63 ATATCGATA
32231 TTGGGCTGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
81 26 0.43
82 32 0.53
83 2 0.03
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.39
Consensus pattern (81 bp):
TTTGTGAAAATAGAATGCCATCTTGATATCATTTTTACAAAGGGGTATCAATAATTCAGAAAATA
TCGATACTTAATTGGG
Found at i:32585 original size:20 final size:20
Alignment explanation
Indices: 32557--32595 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
32547 AGGGTTTCCA
32557 TGAGCTAGTGTGAAAAAGTT
1 TGAGCTAGTGTGAAAAAGTT
* * *
32577 TGAGGTAGTTTGAGAAAGT
1 TGAGCTAGTGTGAAAAAGT
32596 GAAGAACAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (20 bp):
TGAGCTAGTGTGAAAAAGTT
Found at i:39497 original size:40 final size:39
Alignment explanation
Indices: 39453--39677 Score: 267
Period size: 40 Copynumber: 5.6 Consensus size: 39
39443 GCTCCTCGTT
*
39453 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCA
*
39493 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCA
*
39533 CAAATGCCTTCGGACTTAG-CCGGAATTTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGG-ATTTAGTAACTCGCA
* *
39572 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
39612 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
39653 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
39678 CATCATTCAA
Statistics
Matches: 169, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
38 4 0.02
39 35 0.21
40 113 0.67
41 17 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:39564 original size:79 final size:79
Alignment explanation
Indices: 39453--39677 Score: 278
Period size: 79 Copynumber: 2.8 Consensus size: 79
39443 GCTCCTCGTT
* *
39453 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
39517 GATTTAGTAACTCGCA
64 GATTTAGTAACTCGCA
* *
39533 CAAATGCCTTCGGACTTAG-CCGGAATTTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGACTTAGCCCGG-ATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCG
*
39596 GATTTAGTATCTCGCA
64 GATTTAGTAACTCGCA
* * * * *
39612 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
39676 GA
64 GA
39678 CATCATTCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
78 7 0.06
79 65 0.51
80 40 0.31
81 15 0.12
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
TTTAGTAACTCGCA
Found at i:39637 original size:119 final size:120
Alignment explanation
Indices: 39453--39673 Score: 290
Period size: 119 Copynumber: 1.9 Consensus size: 120
39443 GCTCCTCGTT
39453 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
39518 ATTTAGTAAC-TCGCACAAATGCCTTC-GGACTTAGCCGGAATTTAGTATCTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCGGAATTTAGTATCTCGCA
* * * **
39572 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACC
* *
39634 CGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCC
63 CGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCC
39674 CGGACATCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
118 6 0.07
119 62 0.70
120 20 0.23
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCGGAATTTAGTATCTCGCA
Found at i:43456 original size:41 final size:41
Alignment explanation
Indices: 43411--43540 Score: 121
Period size: 40 Copynumber: 3.3 Consensus size: 41
43401 TCCGGCTAAG
*
43411 CGAAGGC-TTTGGTGCTAAG-TGACCATATCCGGACTAAGATC
1 CGAAGGCATTTGGTGC-AAGAT-ACCAAATCCGGACTAAGATC
* *
43452 CGAAGGCATTT-GTGCGAGATACTAAATCCGGACTAAGATC
1 CGAAGGCATTTGGTGCAAGATACCAAATCCGGACTAAGATC
* * * **
43492 CGAAGGCATTT-GT-CGAGTTACTAAATCCGGGTTAAG-TC
1 CGAAGGCATTTGGTGCAAGATACCAAATCCGGACTAAGATC
43530 CGAAGGC-TTTG
1 CGAAGGCATTTG
43541 TGCGATATTA
Statistics
Matches: 80, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
37 3 0.04
38 9 0.11
39 20 0.25
40 33 0.41
41 12 0.15
42 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (41 bp):
CGAAGGCATTTGGTGCAAGATACCAAATCCGGACTAAGATC
Found at i:43483 original size:40 final size:39
Alignment explanation
Indices: 43437--43581 Score: 170
Period size: 40 Copynumber: 3.7 Consensus size: 39
43427 AAGTGACCAT
43437 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATACTAA
*
43477 ATCCGGACTAAGATCCGAAGGCATTTGT-CGAGTTACTAA
1 ATCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATACTAA
** *
43516 ATCCGGGTTAAGTCCGAAGGC-TTTGTGCGATATTACTATA
1 ATCCGGACTAAGTCCGAAGGCATTTGTGCGAGA-TACTA-A
* *
43556 A-CCGGGCTATGTCCCGAAGGCATTTG
1 ATCCGGACTAAGT-CCGAAGGCATTTG
43582 AATGAGGAGC
Statistics
Matches: 93, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
37 5 0.05
38 12 0.13
39 34 0.37
40 38 0.41
41 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
ATCCGGACTAAGTCCGAAGGCATTTGTGCGAGATACTAA
Found at i:43603 original size:78 final size:77
Alignment explanation
Indices: 43428--43614 Score: 177
Period size: 78 Copynumber: 2.4 Consensus size: 77
43418 TTTGGTGCTA
* *
43428 AGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCC
1 AGTGACTATATCCGG-TTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCC
43493 GAAGGCATTTGTCG
64 GAAGGCATTTGTCG
* * * * *
43507 AGTTACTAAATCCGGGTTAAGTCCGAAGGC-TTTGTGCGATATTACTATAA-CCGGGCTATG-TC
1 AGTGACTATATCC-GGTTAAGTCCGAAGGCATTTGTGCGAGA-TACTA-AATCCGGACTAAGAT-
43569 CCGAAGGCATTTGAAT-G
62 CCGAAGGCATTTG--TCG
*
43586 AG-GAGCTATATCCGGTTAAATTCCGAAGG
1 AGTGA-CTATATCCGGTT-AAGTCCGAAGG
43615 TACGTGATTG
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
77 11 0.12
78 40 0.44
79 36 0.40
80 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (77 bp):
AGTGACTATATCCGGTTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGA
AGGCATTTGTCG
Done.