Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1569
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: 33308
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Found at i:1263 original size:51 final size:50
Alignment explanation
Indices: 1206--1342 Score: 133
Period size: 51 Copynumber: 2.7 Consensus size: 50
1196 TGAGCCCCGG
1206 AGGGTAAATTA-TGAAATACCCCTGTAGGTAG-AATTACTTAAAATACCCTAAT
1 AGGGTAAATTACTGAAATACCCCTGTAGGTAGAAATTAC---AAATACCCT-AT
* * *
1258 A-GGTAAA-TACTAAAATTACCGCTGTA-GTAGAAATTACGAATACCCTAT
1 AGGGTAAATTACTGAAA-TACCCCTGTAGGTAGAAATTACAAATACCCTAT
*
1306 AGGGTAGAATTACCGAAATA-CCCTGTACGGTAGAAAT
1 AGGGTA-AATTACTGAAATACCCCTGTA-GGTAGAAAT
1343 ACCCGAATAC
Statistics
Matches: 71, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
48 3 0.04
49 18 0.25
50 6 0.08
51 28 0.39
52 16 0.23
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (50 bp):
AGGGTAAATTACTGAAATACCCCTGTAGGTAGAAATTACAAATACCCTAT
Found at i:1337 original size:26 final size:25
Alignment explanation
Indices: 1218--1354 Score: 88
Period size: 26 Copynumber: 5.4 Consensus size: 25
1208 GGTAAATTAT
*
1218 GAAATACCCCTGTAGGTAGAATTACTT
1 GAAATA-CCCTGTAGGTAGAATTAC-C
* * *
1245 AAAATACCCTAATAGGTA-AA-TACT
1 GAAATACCCT-GTAGGTAGAATTACC
*
1269 AAAATTACCGCTGTA-GTAGAAATTA-C
1 GAAA-TACC-CTGTAGGTAG-AATTACC
*
1295 G-AATACCCTATAGGGTAGAATTACC
1 GAAATACCCTGTA-GGTAGAATTACC
*
1320 GAAATACCCTGTACGGTAGAAATACCC
1 GAAATACCCTGTA-GGTAGAATTA-CC
1347 G-AATACCC
1 GAAATACCC
1355 CCTTGGAGTG
Statistics
Matches: 90, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
23 4 0.04
24 17 0.19
25 17 0.19
26 36 0.40
27 16 0.18
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
GAAATACCCTGTAGGTAGAATTACC
Found at i:5134 original size:47 final size:47
Alignment explanation
Indices: 5071--5329 Score: 358
Period size: 47 Copynumber: 5.4 Consensus size: 47
5061 CCCTTCGGGA
* * *
5071 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
5118 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
5165 CTTATCTCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAC-T-TTCACATTCATCACATTGGCCATTCGGC
* *
5214 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
5261 CTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
5310 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
5330 GTACATCAAT
Statistics
Matches: 193, Mismatches: 14, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
47 109 0.56
48 1 0.01
49 82 0.42
50 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:5237 original size:96 final size:96
Alignment explanation
Indices: 5085--5318 Score: 337
Period size: 96 Copynumber: 2.4 Consensus size: 96
5075 TCACATTTAT
* * * *
5085 ACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
1 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACACTTTCACATTCATCA
*
5150 CATTGGCCATTCGGCCTTATCTCACACATAC
66 CATTGGCCATTCGGCCTTATCACACACATAC
5181 ACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTTCACATTCAT
1 ACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACACT-TTCACATTCAT
* * *
5244 CACATTGGCCATTCGGCCTTATCACGCATATAT
64 CACATTGGCCATTCGGCCTTATCACACACATAC
* * *
5277 ATACTTTCACATTCATCACATTGGCCACTCGGCCCTATCACA
1 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACA
5319 TATATATACT
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
95 2 0.02
96 121 0.98
97 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.10, T:0.30
Consensus pattern (96 bp):
ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACACTTTCACATTCATCA
CATTGGCCATTCGGCCTTATCACACACATAC
Found at i:5324 original size:49 final size:49
Alignment explanation
Indices: 5076--5327 Score: 336
Period size: 49 Copynumber: 5.2 Consensus size: 49
5066 CGGGACTTAT
* * *
5076 CACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTAT--
1 CACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCA
*
5123 CACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCT
1 CACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCA
* *
5172 CACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCA
1 CACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCA
*
5221 CAC--ATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCA
1 CACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCA
* * * *
5268 CGCATATATATACTTTCACATTCATCACATTGGCCACTCGGCCCTATCA
1 CACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCA
*
5317 CATATATATAC
1 CACATATATAC
5328 TTGTACATCA
Statistics
Matches: 185, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
47 90 0.49
48 1 0.01
49 93 0.50
50 1 0.01
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31
Consensus pattern (49 bp):
CACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCA
Found at i:8718 original size:40 final size:40
Alignment explanation
Indices: 8658--9019 Score: 532
Period size: 40 Copynumber: 9.1 Consensus size: 40
8648 GCCCGAATAC
* * *
8658 ACATCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * * * * *
8698 ATAACACCAGCACGAATGCTCTTCGGG-TTTAGCACAGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
8737 ATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
8777 ACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
8817 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* *
8857 ACATCACAAGCATGAATGCTCTTCGGGACTTAGCCCGG-T
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
8896 ACATCACTAGCATGAATGCTCTTTGGGACTTAGCACGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
8936 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
8976 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
9016 -CATC
1 ACATC
9020 GTCGAGACCT
Statistics
Matches: 291, Mismatches: 29, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
39 72 0.25
40 219 0.75
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
Found at i:8899 original size:119 final size:120
Alignment explanation
Indices: 8658--9019 Score: 541
Period size: 119 Copynumber: 3.0 Consensus size: 120
8648 GCCCGAATAC
* * * * *
8658 ACATCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
1 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCG
* * * * * *
8723 GG-TTTAGCACAGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGAT
66 GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* *
8777 ACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCG
1 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCG
* *
8842 GGACTTAGCCCGGATACATCACAAGCATGAATGCTCTTCGGGACTTAGCCCGG-T
66 GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
8896 ACATCACTAGCATGAATGCTCTTTGGGACTTAGCACGGATACATCACTAGCATGAATGCTCTTCG
1 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCG
8961 GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
66 GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
9016 -CATC
1 ACATC
9020 GTCGAGACCT
Statistics
Matches: 219, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
119 176 0.80
120 43 0.20
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCG
GGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
Found at i:8947 original size:159 final size:159
Alignment explanation
Indices: 8658--9019 Score: 541
Period size: 159 Copynumber: 2.3 Consensus size: 159
8648 GCCCGAATAC
* * * * * *
8658 ACATCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCG
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACAAGCACGAATGCTCTTCG
* *
8723 GGTTTAGCACAGATATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGC
66 GGCTTAGCACAGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGC
8788 ACGAATGCTCTTCGAGACTTAGCCCGGAT
131 ACGAATGCTCTTCGAGACTTAGCCCGGAT
*
8817 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACAAGCATGAATGCTCTTCG
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACAAGCACGAATGCTCTTCG
* * * * *
8882 GGACTTAGC-CCGGTACATCACTAGCATGAATGCTCTTTGGGACTTAG-CACGGATACATCACTA
66 GG-CTTAGCACAGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTC-CGGATACATCACTA
* *
8945 GCATGAATGCTCTTCGGGACTTAGCCCGGAT
129 GCACGAATGCTCTTCGAGACTTAGCCCGGAT
8976 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT-CATC
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATC
9020 GTCGAGACCT
Statistics
Matches: 185, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
158 5 0.03
159 175 0.95
160 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (159 bp):
ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACAAGCACGAATGCTCTTCG
GGCTTAGCACAGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGC
ACGAATGCTCTTCGAGACTTAGCCCGGAT
Found at i:9115 original size:38 final size:38
Alignment explanation
Indices: 9073--9147 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
9063 GAATTTTAAT
*
9073 CCGGACATAATCTCTGT-ACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCT-TCACATAGCCAGCGGGTCTTTAC
* *
9111 CCGGACATAATCTCTTCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTA
9148 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTAC
Found at i:11251 original size:40 final size:40
Alignment explanation
Indices: 11192--11403 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
11182 CATTTGAATG
*
11192 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
11232 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
11272 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
11312 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
11352 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
11392 ATATCC-GGCTAA
1 ATATCCGGGCTAA
11404 ATTCCGAAGA
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 7 0.05
40 143 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:14107 original size:40 final size:40
Alignment explanation
Indices: 14047--14410 Score: 532
Period size: 40 Copynumber: 9.1 Consensus size: 40
14037 GCCCGAATAC
* * *
14047 ACATCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * * ** * *
14087 ATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACAGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
14127 ATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
14167 ACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
14207 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
14247 ACATCACAAGCATGAATGCTCTTCGGGACTTAGCCCGGGT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
14287 ACATCACTAGCATGAATGCTCTTTGGGACTTAGCACGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
14327 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
14367 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
14407 -CATC
1 ACATC
14411 GTCGAGACCT
Statistics
Matches: 291, Mismatches: 33, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
39 4 0.01
40 287 0.99
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
Found at i:14506 original size:38 final size:38
Alignment explanation
Indices: 14464--14538 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
14454 GAATTTTAAT
*
14464 CCGGACATAATCTCTGT-ACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCT-TCACATAGCCAGCGGGTCTTTAC
* *
14502 CCGGACATAATCTCTTCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTA
14539 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTAC
Found at i:16639 original size:40 final size:40
Alignment explanation
Indices: 16580--16791 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
16570 CATTTGAATG
*
16580 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
16620 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
16660 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
16700 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
16740 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
16780 ATATCC-GGCTAA
1 ATATCCGGGCTAA
16792 ATTCCGAAGA
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 7 0.05
40 143 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:20624 original size:22 final size:22
Alignment explanation
Indices: 20596--20717 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
20586 TTCCACATCC
20596 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
20618 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
20642 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
20665 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
20689 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
20712 ATCACA
1 ATCACA
20718 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:20631 original size:47 final size:47
Alignment explanation
Indices: 20568--20871 Score: 425
Period size: 47 Copynumber: 6.4 Consensus size: 47
20558 CCCTTCGGGA
* * *
20568 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
20615 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
20662 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
20709 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
20756 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
20803 CTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
20852 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
20872 GTACATCAAT
Statistics
Matches: 239, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 197 0.82
49 40 0.17
50 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:24263 original size:40 final size:40
Alignment explanation
Indices: 24203--24486 Score: 410
Period size: 40 Copynumber: 7.1 Consensus size: 40
24193 GCCCGAATAC
* * *
24203 ACATCACTAGCATGATTGCTCTTCGGGACCTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * * ** *
24243 ATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * *
24283 ATATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
24323 ACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
24363 ACATCACTAGCACGAATGCTCTTTGGGACTTAGCCCGG-T
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
*
24402 AACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 -ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
24443 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
24483 -CATC
1 ACATC
24487 GTCGAGACCT
Statistics
Matches: 217, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 5 0.02
40 211 0.97
41 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
Found at i:24582 original size:38 final size:38
Alignment explanation
Indices: 24540--24614 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
24530 GAATTTTAAT
*
24540 CCGGACATAATCTCTGT-ACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCT-TCACATAGCCAGCGGGTCTTTAC
*
24578 CCGGACATAATCTCTTCATATAGCCAGCGGGTCTTTA
1 CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTA
24615 AACTCGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (38 bp):
CCGGACATAATCTCTTCACATAGCCAGCGGGTCTTTAC
Found at i:26717 original size:40 final size:40
Alignment explanation
Indices: 26658--26869 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
26648 CATTTGAATG
*
26658 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
26698 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
26738 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
26778 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
26818 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
26858 ATATCC-GGCTAA
1 ATATCCGGGCTAA
26870 ATTCCGAAGA
Statistics
Matches: 153, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 7 0.05
40 143 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:30780 original size:47 final size:47
Alignment explanation
Indices: 30647--30988 Score: 480
Period size: 47 Copynumber: 7.3 Consensus size: 47
30637 CCCTTCGGGA
* * *
30647 CTTATCACATTTATACACT-TCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
*
30694 CTTATCACATATACAC-T-TTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
30739 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
*
30786 CTTATCAC--ATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
30831 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
30878 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
* *
30925 CTTATCACGCATATATATACT-TTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
*
30974 CCTATCACATATATA
1 CTTATCACATATATA
30989 TACTTGTACA
Statistics
Matches: 273, Mismatches: 15, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
45 83 0.30
46 1 0.00
47 148 0.54
49 40 0.15
50 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:30807 original size:92 final size:92
Alignment explanation
Indices: 30647--30984 Score: 493
Period size: 92 Copynumber: 3.6 Consensus size: 92
30637 CCCTTCGGGA
* * * *
30647 CTTATCACATTTATACACT-TCCACATCCATCACATTGGCCATTCGGCCTTATCACATATACACT
1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACACA-T
30711 -TTCACATTCATCACATTGGCCATTCGGC
64 GTTCACATTCATCACATTGGCCATTCGGC
* *
30739 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACACATGT
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACACATGT
30804 TCACATTCATCACATTGGCCATTCGGC
66 TCACATTCATCACATTGGCCATTCGGC
* *
30831 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACAT
1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTAT--CACATACACAT
30896 GTTCACATTCATCACATTGGCCATTCGGC
64 GTTCACATTCATCACATTGGCCATTCGGC
* * *
30925 CTTATCACGCATATATATACT-TTCACATTCATCACATTGGCCACTCGGCCCTATCACATA
1 CTTATCA--CATATATACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATA
30985 TATATACTTG
Statistics
Matches: 224, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
91 2 0.01
92 130 0.58
94 53 0.24
96 38 0.17
97 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32
Consensus pattern (92 bp):
CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACACATGT
TCACATTCATCACATTGGCCATTCGGC
Found at i:30897 original size:139 final size:139
Alignment explanation
Indices: 30668--30982 Score: 481
Period size: 139 Copynumber: 2.3 Consensus size: 139
30658 TATACACTTC
* *
30668 CACATCCATCACATTGGCCATTCGGCCTTATCACATATACACTTTCACATTCATCACATTGGCCA
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACTTTCACATTCATCACATTGGCCA
* * **
30733 TTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCA-CATA
66 TTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACCATA
30797 CACAT-GTT
131 CACATAGTT
30805 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGC
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACAC-T-TTCACATTCATCACATTGGC
30870 CATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACGC
64 CATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC-C
* * *
30935 ATATATATACTTT
128 ATACACATA-GTT
* *
30948 CACATTCATCACATTGGCCACTCGGCCCTATCACA
1 CACATTCATCACATTGGCCATTCGGCCTTATCACA
30983 TATATATACT
Statistics
Matches: 161, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
137 40 0.25
138 1 0.01
139 78 0.48
141 7 0.04
143 35 0.22
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.31
Consensus pattern (139 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACTTTCACATTCATCACATTGGCCA
TTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACCATA
CACATAGTT
Done.