Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008695.1 Corchorus capsularis cultivar CVL-1 contig08716, whole genome shotgun sequence
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: 63809
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1271 original size:16 final size:16
Alignment explanation
Indices: 1246--1280 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1236 ATTTTCTTCT
1246 TCTCTATATTCTATTG
1 TCTCTATATTCTATTG
* *
1262 TCTCTTTATTCTCTTG
1 TCTCTATATTCTATTG
1278 TCT
1 TCT
1281 TTTCCATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.06, T:0.60
Consensus pattern (16 bp):
TCTCTATATTCTATTG
Found at i:1920 original size:13 final size:13
Alignment explanation
Indices: 1902--1927 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1892 ATGGCTAAAA
1902 AAGGAAATTTATT
1 AAGGAAATTTATT
1915 AAGGAAATTTATT
1 AAGGAAATTTATT
1928 TTTATGGCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
AAGGAAATTTATT
Found at i:2075 original size:13 final size:13
Alignment explanation
Indices: 2057--2086 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2047 TATATATTTG
2057 TATAAATCCTATA
1 TATAAATCCTATA
2070 TATAAATCCTATA
1 TATAAATCCTATA
2083 TATA
1 TATA
2087 TTTGTAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAAATCCTATA
Found at i:2761 original size:25 final size:25
Alignment explanation
Indices: 2722--2771 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2712 TTTTAGATTT
* *
2722 TTTAATTATTGATTATTATTAATTA
1 TTTAATTAATAATTATTATTAATTA
2747 TTTAATTAATAATTATTATTAATTA
1 TTTAATTAATAATTATTATTAATTA
2772 CAATTTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTAATTAATAATTATTATTAATTA
Found at i:4525 original size:6 final size:6
Alignment explanation
Indices: 4514--4543 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
4504 CTACTCGAAT
4514 AGCTCG AGCTCG AGCTCG AGCTCG -GCTCG A
1 AGCTCG AGCTCG AGCTCG AGCTCG AGCTCG A
4544 TAAAAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
AGCTCG
Found at i:5626 original size:17 final size:17
Alignment explanation
Indices: 5604--5647 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
5594 CCGGTGATGT
*
5604 TCCGACACATCATCAAA
1 TCCGACAAATCATCAAA
5621 TCCGACAAAATCATCAAA
1 TCCGAC-AAATCATCAAA
*
5639 TCTGACAAA
1 TCCGACAAA
5648 ATCTGGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.45, C:0.30, G:0.07, T:0.18
Consensus pattern (17 bp):
TCCGACAAATCATCAAA
Found at i:5635 original size:18 final size:18
Alignment explanation
Indices: 5612--5650 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5602 GTTCCGACAC
5612 ATCATCAAATCCGACAAA
1 ATCATCAAATCCGACAAA
*
5630 ATCATCAAATCTGACAAA
1 ATCATCAAATCCGACAAA
5648 ATC
1 ATC
5651 TGGTTGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.05, T:0.21
Consensus pattern (18 bp):
ATCATCAAATCCGACAAA
Found at i:9098 original size:15 final size:15
Alignment explanation
Indices: 9074--9119 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
9064 TAGGAGAGTG
* *
9074 ATTCTTGGGAGAGTA
1 ATTCTAGGGAAAGTA
*
9089 ATTCCAGGGAAAGTA
1 ATTCTAGGGAAAGTA
*
9104 ACTCTAGGGAAAGTA
1 ATTCTAGGGAAAGTA
9119 A
1 A
9120 CAATTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (15 bp):
ATTCTAGGGAAAGTA
Found at i:10079 original size:2 final size:2
Alignment explanation
Indices: 10072--10121 Score: 55
Period size: 2 Copynumber: 22.5 Consensus size: 2
10062 TTACCAAAGA
10072 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT ACT AT ACT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT A-T AT A-T AT
10116 ACT AT A
1 A-T AT A
10122 CTACATATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 33 0.77
3 10 0.23
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:10103 original size:5 final size:5
Alignment explanation
Indices: 10073--10124 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
10063 TACCAAAGAA
10073 TATA- TATA- TATA- TATA- TATA- TATAC TATAC TATAC TATAC TATAC
1 TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC
10118 TATAC TA
1 TATAC TA
10125 CATATGATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 20 0.43
5 27 0.57
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAC
Found at i:16961 original size:91 final size:91
Alignment explanation
Indices: 16806--17007 Score: 316
Period size: 91 Copynumber: 2.2 Consensus size: 91
16796 TGGAGTCTCT
* * *
16806 GGTTTGGTTAATGTATAGCAAATTGAAGTATTTTGGTTATCTTTTTGTCATTGGCCAAGATGCTT
1 GGTTTGGTTTATGTATAGCAAACTGAAGTATTTTGGTTATCTTTTTGTCATTGGCAAAGATGCTT
16871 TTGCATTGGATTT-TCATCCAAGATGC
66 TTGCATTGGATTTAT-ATCCAAGATGC
*
16897 GGTTTGGTTTATGTATAGCAGACTGAAGTATTTTGGTTATCTTTTTGTCATTGGCAAAGATGCTT
1 GGTTTGGTTTATGTATAGCAAACTGAAGTATTTTGGTTATCTTTTTGTCATTGGCAAAGATGCTT
* * * *
16962 TTGTATTGTATTTATATCCAAGTTGT
66 TTGCATTGGATTTATATCCAAGATGC
16988 GGTTTGGTTTATGTATAGCA
1 GGTTTGGTTTATGTATAGCA
17008 TAGTGAATTA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 101 0.99
92 1 0.01
ACGTcount: A:0.22, C:0.10, G:0.23, T:0.45
Consensus pattern (91 bp):
GGTTTGGTTTATGTATAGCAAACTGAAGTATTTTGGTTATCTTTTTGTCATTGGCAAAGATGCTT
TTGCATTGGATTTATATCCAAGATGC
Found at i:19057 original size:2 final size:2
Alignment explanation
Indices: 19050--19076 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19040 ACGGAGGGAG
19050 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19077 TTGAAAGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22326 original size:36 final size:36
Alignment explanation
Indices: 22286--22397 Score: 162
Period size: 36 Copynumber: 3.2 Consensus size: 36
22276 TATATTAAAC
22286 TCTTTATTGACTTCACTTAATTACCCTGAATTAAGT
1 TCTTTATTGACTTCACTTAATTACCCTGAATTAAGT
*
22322 TCTTTATT---TT-ACTTAATTAGCCTGAATTAAG-
1 TCTTTATTGACTTCACTTAATTACCCTGAATTAAGT
*
22353 CCTTTTATTGACTTCACTTAATTACCCTGAATTAAGT
1 TC-TTTATTGACTTCACTTAATTACCCTGAATTAAGT
22390 TCTTTATT
1 TCTTTATT
22398 TTACTTAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 26 0.39
33 2 0.03
35 2 0.03
36 34 0.52
37 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (36 bp):
TCTTTATTGACTTCACTTAATTACCCTGAATTAAGT
Found at i:22346 original size:32 final size:32
Alignment explanation
Indices: 22300--22407 Score: 146
Period size: 32 Copynumber: 3.2 Consensus size: 32
22290 TATTGACTTC
22300 ACTTAATTACCCTGAATTAAGTTCTTTATTTT
1 ACTTAATTACCCTGAATTAAGTTCTTTATTTT
* *
22332 ACTTAATTAGCCTGAATTAAG-CCTTTTATTGACTT
1 ACTTAATTACCCTGAATTAAGTTC-TTTATT---TT
22367 CACTTAATTACCCTGAATTAAGTTCTTTATTTT
1 -ACTTAATTACCCTGAATTAAGTTCTTTATTTT
22400 ACTTAATT
1 ACTTAATT
22408 TCCTTTCCTG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 34 0.52
33 2 0.03
35 2 0.03
36 26 0.39
37 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTTCTTTATTTT
Found at i:22482 original size:36 final size:36
Alignment explanation
Indices: 22435--22755 Score: 486
Period size: 36 Copynumber: 9.0 Consensus size: 36
22425 GCTGTGTCTT
* *
22435 TTTACTTAATTTCCTTGAAA-TCAAGCCAGTCTTTTC
1 TTTACCTAGTTTCCTTGAAACT-AAGCCAGTCTTTTC
* * *
22471 TTTACCTAATTTCCTTGAAATTAAGACAGTCTTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
*
22507 TTTACCTAGTTTCCTTGAGACTAAGCCAGTC-TTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
*
22542 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCGTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
* * *
22578 TTTACTTAGTTTTCTTGAAACTAAGCCAATCTTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
*
22614 TTTACCTAGTTTCCTTGAGACTAAGCCAGTCTTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
* *
22650 TTTACCTAGTTTTCTTGAAACTAAGCCAGTC-TATC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
22685 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
*
22721 ATTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT
22756 ATCAATCTAA
Statistics
Matches: 261, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
35 67 0.26
36 193 0.74
37 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (36 bp):
TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
Found at i:22595 original size:143 final size:143
Alignment explanation
Indices: 22435--22755 Score: 509
Period size: 143 Copynumber: 2.2 Consensus size: 143
22425 GCTGTGTCTT
* *
22435 TTTACTTAATTTCCTTGAAA-TCAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGACA
1 TTTACTTAGTTTCCTTGAAACT-AAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAACTAAGACA
* *
22499 GTCTTTTCTTTACCTAGTTTCCTTGAGACTAAGCCAGTCTTTCTTTACCTAGTTTCCTTGAAACT
65 GTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAACT
22564 AAGCCAGTCGTTTC
130 AAGCCAGTCGTTTC
* * * * *
22578 TTTACTTAGTTTTCTTGAAACTAAGCCAATCTTTTCTTTACCTAGTTTCCTTGAGACTAAGCCAG
1 TTTACTTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAACTAAGACAG
*
22643 TCTTTTCTTTACCTAGTTTTCTTGAAACTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAACTA
66 TCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAACTA
*
22708 AGCCAGTCTTTTC
131 AGCCAGTCGTTTC
* *
22721 ATTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT
1 TTTACTTAGTTTCCTTGAAACTAAGCCAGTCTTTT
22756 ATCAATCTAA
Statistics
Matches: 162, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
143 161 0.99
144 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (143 bp):
TTTACTTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAACTAAGACAG
TCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTATCTTTACCTAGTTTCCTTGAAACTA
AGCCAGTCGTTTC
Found at i:22755 original size:107 final size:108
Alignment explanation
Indices: 22435--22755 Score: 495
Period size: 107 Copynumber: 3.0 Consensus size: 108
22425 GCTGTGTCTT
* * * * * *
22435 TTTACTTAATTTCCTTGAAA-TCAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGACA
1 TTTACCTAGTTTCCTTGAAACT-AAGCCAGTCGTTTCTTTACCTAGTTTCCTTGAAACTAAGCCA
22499 GTCTTTTCTTTACCTAGTTTCCTTGAGACTAAGCCAGTC-TTTC
65 GTCTTTTCTTTACCTAGTTTCCTTGAGACTAAGCCAGTCTTTTC
* * *
22542 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCGTTTCTTTACTTAGTTTTCTTGAAACTAAGCCAA
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCGTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAG
22607 TCTTTTCTTTACCTAGTTTCCTTGAGACTAAGCCAGTCTTTTC
66 TCTTTTCTTTACCTAGTTTCCTTGAGACTAAGCCAGTCTTTTC
* *
22650 TTTACCTAGTTTTCTTGAAACTAAGCCAGTC-TATCTTTACCTAGTTTCCTTGAAACTAAGCCAG
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCGTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAG
* *
22714 TCTTTTCATTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT
66 TCTTTTCTTTACCTAGTTTCCTTGAGACTAAGCCAGTCTTTT
22756 ATCAATCTAA
Statistics
Matches: 196, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
107 161 0.82
108 35 0.18
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (108 bp):
TTTACCTAGTTTCCTTGAAACTAAGCCAGTCGTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAG
TCTTTTCTTTACCTAGTTTCCTTGAGACTAAGCCAGTCTTTTC
Found at i:22780 original size:22 final size:22
Alignment explanation
Indices: 22755--22799 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
22745 GCCAGTCTTT
* *
22755 TATCAATCTAATTTCAGTTTAA
1 TATCAATCTAATATCAGTCTAA
* *
22777 TATCAGTCTTATATCAGTCTAA
1 TATCAATCTAATATCAGTCTAA
22799 T
1 T
22800 TTCAGTCTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (22 bp):
TATCAATCTAATATCAGTCTAA
Found at i:22806 original size:11 final size:11
Alignment explanation
Indices: 22761--22818 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
22751 CTTTTATCAA
22761 TCTAATTTCAG
1 TCTAATTTCAG
* *
22772 TTTAATATCAG
1 TCTAATTTCAG
* *
22783 TCTTATATCAG
1 TCTAATTTCAG
22794 TCTAATTTCAG
1 TCTAATTTCAG
**
22805 TCTTCTTTCAG
1 TCTAATTTCAG
22816 TCT
1 TCT
22819 CCTTTTCAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.48
Consensus pattern (11 bp):
TCTAATTTCAG
Found at i:42255 original size:405 final size:404
Alignment explanation
Indices: 41502--42287 Score: 1073
Period size: 405 Copynumber: 1.9 Consensus size: 404
41492 ATAATTTTTT
* * *
41502 TCCACATGTCCGATTGAAGTTATTGAAGTGTCAGTTAAAAGGTTATTGCATGATTTACGACTTTC
1 TCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTC
* * * * *
41567 ATGAAGGACCCGGAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGAGAATTTTTAT
66 ATGAAGAACCCGAAAGCTAAATTTGATCTACAAGTTCCATGAAGGATTCAAAAGAGAATTTTTAT
* * * * * *
41632 GCTTCAAGATCTCCGTTAACAAACATTTTCTTATTTGAATTATTTATCAAATAACCCTCCTATTT
131 ACTTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATAACCCTCATACTT
*
41697 TTCTACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCTAACGTTTAAGATTTATTTTT
196 TTCTACTTTATACTACTTAGTCATTTACAAATTCTATCTTAATCT-ACGTTTAAGATTTATTTTT
* * * * * *
41762 TTATGCTTTGTTCTATTTGTTCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATGAT
260 TTATGCTTTGTTCTATTTGTCCAATTAAGGTGATTCAGGTGTCTAATAAAAGATAATTTCATGAT
* * * *
41827 CTACAACTTTCATGAATGACTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAAATGCTTCCTGA
325 CTACAACTTTCATGAAAGACTCAAAAGCAAATTTTCATATTTCAATTCAAAAAAATGCTTCCTGA
41892 ATTTGTTCGTTTCGA
390 ATTTGTTCGTTTCGA
* *
41907 TCCACATGTCCGATTAAAGTTATTCAAGTGTCTGTTAAAAGGTTATTGTATGATCTACGACTTTC
1 TCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTC
* *
41972 ATGAAGAACGCGAAAG-TTAATTTGATCTACAAGTTCCATGAAGGATTCAAAAG-GAAATTTTTA
66 ATGAAGAACCCGAAAGCTAAATTTGATCTACAAGTTCCATGAAGGATTCAAAAGAG-AATTTTTA
* * * *
42035 TATTTCAAGATATCCATTAAGAAATATTTTCTTATTTGAATTAGTTATCAAATGACCCTCATACT
130 TACTTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATAACCCTCATACT
* * * *
42100 TTTCTATTTTATGCTATTTAGTTATTTACAAATTCTATCTT-AT-T-CGATTTAACG-TTTCATT
195 TTTCTACTTTATACTACTTAGTCATTTACAAATTCTATCTTAATCTACG-TTTAA-GATTT-A-T
*
42161 TTTTTTATTTTCTTTGTTCTATTTGTCCAATTAAGGTGATTCAGGTGTCTAATAAAAGATAATTT
256 TTTTTTA--TGCTTTGTTCTATTTGTCCAATTAAGGTGATTCAGGTGTCTAATAAAAGATAATTT
* * *
42226 TATGA-CTTACAACTTTCATGAAAGACTCAAAAGCTAATTTTCATATTTCAATTCTAAAAAAT
319 CATGATC-TACAACTTTCATGAAAGACTCAAAAGCAAATTTTCATATTTCAATTCAAAAAAAT
42288 ACTTTTGAAA
Statistics
Matches: 332, Mismatches: 41, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
400 2 0.01
401 8 0.02
402 3 0.01
403 11 0.03
404 133 0.40
405 175 0.53
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (404 bp):
TCCACATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTC
ATGAAGAACCCGAAAGCTAAATTTGATCTACAAGTTCCATGAAGGATTCAAAAGAGAATTTTTAT
ACTTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATAACCCTCATACTT
TTCTACTTTATACTACTTAGTCATTTACAAATTCTATCTTAATCTACGTTTAAGATTTATTTTTT
TATGCTTTGTTCTATTTGTCCAATTAAGGTGATTCAGGTGTCTAATAAAAGATAATTTCATGATC
TACAACTTTCATGAAAGACTCAAAAGCAAATTTTCATATTTCAATTCAAAAAAATGCTTCCTGAA
TTTGTTCGTTTCGA
Found at i:53886 original size:22 final size:21
Alignment explanation
Indices: 53847--53887 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
53837 TGAAGTAAAT
*
53847 AATTATTTTATTATTATTTCA
1 AATTATTTTATTACTATTTCA
*
53868 AATTATATTTATTCCTATTT
1 AATTAT-TTTATTACTATTT
53888 AAGAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
AATTATTTTATTACTATTTCA
Found at i:55457 original size:30 final size:30
Alignment explanation
Indices: 55423--55481 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
55413 TCACTACTCG
*
55423 AACCCTACATGAACCTGTCACAGGTACTAA
1 AACCCTACATGAACCCGTCACAGGTACTAA
* * *
55453 AACCCTACCTGAGCCCGTCACAGTTACTA
1 AACCCTACATGAACCCGTCACAGGTACTA
55482 CTACCCGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (30 bp):
AACCCTACATGAACCCGTCACAGGTACTAA
Found at i:55640 original size:15 final size:15
Alignment explanation
Indices: 55620--55651 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
55610 AGAATGTATT
*
55620 TTTTTGAAGGATTTA
1 TTTTTGAAGGATATA
55635 TTTTTGAAGGATATA
1 TTTTTGAAGGATATA
55650 TT
1 TT
55652 ATCAATGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (15 bp):
TTTTTGAAGGATATA
Found at i:55788 original size:3 final size:3
Alignment explanation
Indices: 55782--55818 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
55772 CTTGTTGTTG
55782 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55819 ATATAGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58466 original size:30 final size:30
Alignment explanation
Indices: 58425--58868 Score: 521
Period size: 30 Copynumber: 14.6 Consensus size: 30
58415 AGTCTCCAAA
* * *
58425 TGACACTAGAAGTTGTCATGATCTTATAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* * * *
58455 TGACACCAGAAGTTGTCAATGGTCTTAGAAA
1 TGACACCAGAAGTTGTC-ATGATTTTACAAT
* * *
58486 TGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* * * *
58516 TGACACCAAAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* *
58546 TGACACCAAAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
*
58576 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* * *
58606 TGACACCATAAGTTGTCATCATTTTAAAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* *
58636 TGACACTAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* *
58666 TGACACTAGAAGTTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGA-TTTTACAAT
* *
58697 TGACACCAAAAGTTGTCAT-ATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGA-TTTTACAAT
* *
58727 TGACACCACAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
*
58757 TGACACCAGAAGTTGTCATGATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGA-TTTTACAAT
* *
58788 TGACACCAGAAGTTGTCATGATTTTTCTAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
** *
58818 TGACACTTGAAGATGTCATGATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGATTTTA--CAAT
58850 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
58869 ATACACCATG
Statistics
Matches: 374, Mismatches: 34, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
30 271 0.72
31 84 0.22
32 19 0.05
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATTTTACAAT
Found at i:58553 original size:91 final size:91
Alignment explanation
Indices: 58425--58868 Score: 520
Period size: 91 Copynumber: 4.9 Consensus size: 91
58415 AGTCTCCAAA
* * * * * * *
58425 TGACACTAGAAGTTGTCATGATCTTATAATTGACACCAGAAGTTGTCAATGGTCTTAG-AAATGA
1 TGACACCAAAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTC-ATGAT-TTTGCAATTGA
* * * *
58489 CACCAGAAGTTGTCATG-GTCTTACAAA
64 CACCAGAAGTTGTCATGATTTTTGCAAT
* *
58516 TGACACCAAAAGTTGTCATGGTCTTACAAATGACACCAAAAGTTGTCATGATTTTGCAATTGACA
1 TGACACCAAAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGATTTTGCAATTGACA
58581 CCAGAAGTTGTCATGA-TTTTGCAAT
66 CCAGAAGTTGTCATGATTTTTGCAAT
* * * *
58606 TGACACCATAAGTTGTCATCATTTTA-AAATTGACACTAGAAGTTGTCATGATTTTGCAATTGAC
1 TGACACCAAAAGTTGTCATGATCTTACAAA-TGACACCAGAAGTTGTCATGATTTTGCAATTGAC
*
58670 ACTAGAAGTTGTCATGATTTTTGCAAT
65 ACCAGAAGTTGTCATGATTTTTGCAAT
* * * *
58697 TGACACCAAAAGTTGTCAT-ATTTTTGCAATTGACACCACAAGTTGTCATGATTTTGCAATTGAC
1 TGACACCAAAAGTTGTCATGA-TCTTACAAATGACACCAGAAGTTGTCATGATTTTGCAATTGAC
58761 ACCAGAAGTTGTCATGATTTTTGCAAT
65 ACCAGAAGTTGTCATGATTTTTGCAAT
* * * * * ** * *
58788 TGACACCAGAAGTTGTCATGATTTTTCTATTGACACTTGAAGATGTCATGATTTTATTCAATTGA
1 TGACACCAAAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGA-TTT-TGCAATTGA
58853 CACCAGAAGTTGTCAT
64 CACCAGAAGTTGTCAT
58869 ATACACCATG
Statistics
Matches: 311, Mismatches: 33, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
89 6 0.02
90 103 0.33
91 172 0.55
92 6 0.02
93 24 0.08
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (91 bp):
TGACACCAAAAGTTGTCATGATCTTACAAATGACACCAGAAGTTGTCATGATTTTGCAATTGACA
CCAGAAGTTGTCATGATTTTTGCAAT
Found at i:59138 original size:118 final size:118
Alignment explanation
Indices: 58925--59160 Score: 418
Period size: 118 Copynumber: 2.0 Consensus size: 118
58915 ACTAATTCCC
* *
58925 ATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGAGTT
1 ATTTGACACTAGAAGTTGTCATTGTACTTTAATTACATGTCTAGGCAAATTCTGTATAAGGAGTT
* * *
58990 GGATTTTAAGTGAGACCGTTTGTGGCTCCTCCATCTTTCTTGGGAATTTACCT
66 GGATTTTAAGTGAGACCGTATGTGACTCCTCCATCTTTCCTGGGAATTTACCT
59043 ATTTGACACTAGAAGTTGTCATTGTACTTTAATTACATGTCTAGGCAAATTCTGTATAAGGAGTT
1 ATTTGACACTAGAAGTTGTCATTGTACTTTAATTACATGTCTAGGCAAATTCTGTATAAGGAGTT
*
59108 GGATTTTAAGTGAGACCGTATGTGATTCCTCCATCTTTCCTGGGAATTTACCT
66 GGATTTTAAGTGAGACCGTATGTGACTCCTCCATCTTTCCTGGGAATTTACCT
59161 GGTGTAATTT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 112 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (118 bp):
ATTTGACACTAGAAGTTGTCATTGTACTTTAATTACATGTCTAGGCAAATTCTGTATAAGGAGTT
GGATTTTAAGTGAGACCGTATGTGACTCCTCCATCTTTCCTGGGAATTTACCT
Found at i:60187 original size:2 final size:2
Alignment explanation
Indices: 60180--60209 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60170 GGCTTTGAGC
60180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60210 TATTCTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.