Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008768.1 Corchorus capsularis cultivar CVL-1 contig08789, 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: 82656
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2361 original size:131 final size:131
Alignment explanation
Indices: 2115--2375 Score: 422
Period size: 131 Copynumber: 2.0 Consensus size: 131
2105 CATAGAAATT
2115 TAGCTGAAATTGTTTTTTTTTCTTTTGGTACTTTATCATTTATCTTGTATTTGAATTCGATCATG
1 TAGCTGAAATTGTTTTTTTTTCTTTTGGTACTTTATCATTTATCTTGTATTTGAATTCGATCATG
2180 ATTGTTTTTCCTGGCTTCTGTTCTTAATTTGTTTTTTCCGTTTTCTTTTAGTCTCCTAGAGGAAA
66 ATTGTTTTTCCTGGCTTCTGTTCTTAATTTGTTTTTTCCGTTTTCTTTTAGTCTCCTAGAGGAAA
2245 A
131 A
*
2246 TAGCTGAAATTG-TTTTTTTT-TTTTGGTATTTTATCATTTATCTTGTATTTGAATTCGATCATG
1 TAGCTGAAATTGTTTTTTTTTCTTTTGGTACTTTATCATTTATCTTGTATTTGAATTCGATCATG
* * *
2309 ATTTTTTTTTTGCTGGCTTCTGTTCTTAAAATTT-TTTTTTCCGTTTTC-TTTAGTCTCTTAGAG
66 A--TTGTTTTTCCTGGCTTCTGTTCTT--AATTTGTTTTTTCCGTTTTCTTTTAGTCTCCTAGAG
2372 GAAA
127 GAAA
2376 GATTAGATTT
Statistics
Matches: 122, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
129 43 0.35
130 8 0.07
131 52 0.43
132 14 0.11
133 5 0.04
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.56
Consensus pattern (131 bp):
TAGCTGAAATTGTTTTTTTTTCTTTTGGTACTTTATCATTTATCTTGTATTTGAATTCGATCATG
ATTGTTTTTCCTGGCTTCTGTTCTTAATTTGTTTTTTCCGTTTTCTTTTAGTCTCCTAGAGGAAA
A
Found at i:2394 original size:131 final size:129
Alignment explanation
Indices: 2126--2375 Score: 380
Period size: 129 Copynumber: 1.9 Consensus size: 129
2116 AGCTGAAATT
2126 GTTTTTTTTTCTTTTGGTACTTTATCATTTATCTTGTATTTGAATTCGATCATGATTGTTTTTCC
1 GTTTTTTTTTCTTTTGGTACTTTATCATTTATCTTGTATTTGAATTCGATCATGATTGTTTTTCC
*
2191 TGGCTTCTGTTCTTAATTTGTTTTTTCCGTTTTCTTTTAGTCTCCTAGAGGAAAATAGCTGAAA
66 TGGCTTCTGTTCTTAATTTGTTTTTTCCGTTTTCTTTTAGTCTCCTAGAGGAAAATAGATGAAA
* * *
2255 -TTGTTTTTTTTTTTTGGTATTTTATCATTTATCTTGTATTTGAATTCGATCATGATTTTTTTTT
1 GTT-TTTTTTTCTTTTGGTACTTTATCATTTATCTTGTATTTGAATTCGATCATGA--TTGTTTT
* *
2319 TGCTGGCTTCTGTTCTTAAAATTT-TTTTTTCCGTTTTC-TTTAGTCTCTTAGAGGAAA
63 TCCTGGCTTCTGTTCTT--AATTTGTTTTTTCCGTTTTCTTTTAGTCTCCTAGAGGAAA
2376 GATTAGATTT
Statistics
Matches: 111, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
128 2 0.02
129 50 0.45
131 40 0.36
132 14 0.13
133 5 0.05
ACGTcount: A:0.17, C:0.12, G:0.14, T:0.56
Consensus pattern (129 bp):
GTTTTTTTTTCTTTTGGTACTTTATCATTTATCTTGTATTTGAATTCGATCATGATTGTTTTTCC
TGGCTTCTGTTCTTAATTTGTTTTTTCCGTTTTCTTTTAGTCTCCTAGAGGAAAATAGATGAAA
Found at i:5897 original size:30 final size:30
Alignment explanation
Indices: 5863--5920 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5853 GGGCCCTGTT
*
5863 GATCCCATCAAGCTTGAAATTTCCTTTGTC
1 GATCCCATCAAGCTTAAAATTTCCTTTGTC
*
5893 GATCCCATCAAGTTTAAAATTTCCTTTG
1 GATCCCATCAAGCTTAAAATTTCCTTTG
5921 CTAATAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (30 bp):
GATCCCATCAAGCTTAAAATTTCCTTTGTC
Found at i:7289 original size:31 final size:31
Alignment explanation
Indices: 7254--7329 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
7244 TTTTCTGTTT
* * *
7254 TTAGGCTCAAATTGAGCAATTTTTGAAATGC
1 TTAGGCTCAAATTGAGCAACTTTAGAAAGGC
* *
7285 TTAGGTTCAAATTGAGCAACTTTAGAAAGGT
1 TTAGGCTCAAATTGAGCAACTTTAGAAAGGC
*
7316 TTAGCCTCAAATTG
1 TTAGGCTCAAATTG
7330 GTAATTTGGC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (31 bp):
TTAGGCTCAAATTGAGCAACTTTAGAAAGGC
Found at i:8641 original size:60 final size:59
Alignment explanation
Indices: 8505--8666 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 59
8495 GCTAATTGCT
* *
8505 CAAATAAGGGCTTAACGTT-TGCTAAAATGCTCAAATAAGGGCCCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCATCTTTGAATTTGGC
* * * *
8564 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAGATAAGGATCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG-GCCCATCTTTGAATTTGGC
*
8624 CAAATAAGGATCC-AACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGG-GCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
8667 TAATGTTATC
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
59 37 0.41
60 52 0.57
61 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCATCTTTGAATTTGGC
Found at i:8662 original size:31 final size:32
Alignment explanation
Indices: 8501--8695 Score: 121
Period size: 31 Copynumber: 6.4 Consensus size: 32
8491 GGAGGCTAAT
* *
8501 TGCTCAAATAAGG-GCTTAACGTT-TGCTAAAA
1 TGCTCAAATAAGGAGCCTAACGTTAT-CGAAAA
* * **
8532 TGCTCAAATAAGG-GCCCATC-TT-T-GAATT
1 TGCTCAAATAAGGAGCCTAACGTTATCGAAAA
8560 TGGC-CAAATAAGG-GCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGAGCCTAACGTTATCGAAAA
* * * * * **
8591 TGCTCAGATAAGGATCCGATC-TT-T-TAATT
1 TGCTCAAATAAGGAGCCTAACGTTATCGAAAA
*
8620 TGGC-CAAATAAGGATCC-AACGTTATCGAAAA
1 T-GCTCAAATAAGGAGCCTAACGTTATCGAAAA
*
8651 TGCTCAAATAAGG-GCCTAATGTTATCGAAAA
1 TGCTCAAATAAGGAGCCTAACGTTATCGAAAA
*
8682 TGTTCAAATAAGGA
1 TGCTCAAATAAGGA
8696 CCTGGTTTTA
Statistics
Matches: 126, Mismatches: 25, Indels: 25
0.72 0.14 0.14
Matches are distributed among these distances:
28 19 0.15
29 21 0.17
30 14 0.11
31 68 0.54
32 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (32 bp):
TGCTCAAATAAGGAGCCTAACGTTATCGAAAA
Found at i:8761 original size:31 final size:31
Alignment explanation
Indices: 8726--8890 Score: 162
Period size: 31 Copynumber: 5.5 Consensus size: 31
8716 TGCGTGAGAC
*
8726 AGGCCCTTATTTGAGCATTTTGGCAAACTTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACATT
** * *
8757 AGGCCCTTATTTG-GCCAAATT--CAAAGATG
1 AGGCCCTTATTTGAG-CATTTTGGCAAACATT
*
8786 GGGCCCTTATTTGAGCATTTTGGCAAACATT
1 AGGCCCTTATTTGAGCATTTTGGCAAACATT
** * * *
8817 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACATT
*
8846 AGACCCTTATTTGAGCATTTTGGCAAACATT
1 AGGCCCTTATTTGAGCATTTTGGCAAACATT
8877 AGGCCCTTATTTGA
1 AGGCCCTTATTTGA
8891 ACAATTAGCC
Statistics
Matches: 103, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
29 42 0.41
30 4 0.04
31 57 0.55
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACATT
Found at i:8791 original size:29 final size:29
Alignment explanation
Indices: 8757--8858 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
8747 GGCAAACTTT
*
8757 AGGCCCTTATTTGGCCAAATTCAAAGATG
1 AGGCCCTTATTTGGCCAAATTCAAAGATC
* ** * *
8786 GGGCCCTTATTTGAG-CATTTTGGCAAACATT
1 AGGCCCTTATTTG-GCCAAATT--CAAAGATC
*
8817 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTCAAAGATC
*
8846 AGACCCTTATTTG
1 AGGCCCTTATTTG
8859 AGCATTTTGG
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
29 33 0.58
30 2 0.04
31 22 0.39
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTCAAAGATC
Found at i:8800 original size:60 final size:60
Alignment explanation
Indices: 8725--8889 Score: 285
Period size: 60 Copynumber: 2.8 Consensus size: 60
8715 ATGCGTGAGA
* *
8725 CAGGCCCTTATTTGAGCATTTTGGCAAACTTTAGGCCCTTATTTGGCCAAATTCAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGAT
**
8785 GGGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGAT
*
8845 CAGACCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
8890 AACAATTAGC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:21755 original size:21 final size:21
Alignment explanation
Indices: 21731--21775 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
21721 GGGTAGAAGG
*
21731 AGGAGGAGCAGATGGGGTGGC
1 AGGAGGAGCAGATGGGGTAGC
*
21752 AGGAGGAGGAGATGGGGTAGC
1 AGGAGGAGCAGATGGGGTAGC
21773 AGG
1 AGG
21776 TGGTGGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.07, G:0.58, T:0.09
Consensus pattern (21 bp):
AGGAGGAGCAGATGGGGTAGC
Found at i:23749 original size:23 final size:24
Alignment explanation
Indices: 23690--23752 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
23680 AAAGGGAATG
*
23690 AAAAA-GTATTTTCCTTTTCCTTA
1 AAAAATGTATTTTCCTTTTCCTAA
** *
23713 AAAAATGCT-TTTTTTTTTTTCTAA
1 AAAAATG-TATTTTCCTTTTCCTAA
23737 AAAAATGTATTTTCCT
1 AAAAATGTATTTTCCT
23753 ATATAGAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 6 0.19
24 24 0.77
25 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.51
Consensus pattern (24 bp):
AAAAATGTATTTTCCTTTTCCTAA
Found at i:23841 original size:11 final size:11
Alignment explanation
Indices: 23825--23849 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23815 TCTTTCTGTC
23825 AAAAAAAAAAG
1 AAAAAAAAAAG
23836 AAAAAAAAAAG
1 AAAAAAAAAAG
23847 AAA
1 AAA
23850 TCCCCCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:24525 original size:2 final size:2
Alignment explanation
Indices: 24507--24547 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
24497 TGATTCACAA
24507 AT AT ACT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24548 TATTGTTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 31 0.86
3 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:25904 original size:7 final size:7
Alignment explanation
Indices: 25894--25923 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
25884 GAAATGGTAA
*
25894 GCCGCTG
1 GCCGCCG
25901 GCCGCCG
1 GCCGCCG
25908 GCCGCCG
1 GCCGCCG
25915 GCCGCCG
1 GCCGCCG
25922 GC
1 GC
25924 AGTTGATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.53, G:0.43, T:0.03
Consensus pattern (7 bp):
GCCGCCG
Found at i:28096 original size:31 final size:31
Alignment explanation
Indices: 28053--28111 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28043 AGTTTTGAGA
* *
28053 AACTTTTGAAATACCTATTGTATCCTTATTT
1 AACTTTTAAAATACCTATTATATCCTTATTT
28084 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTATATCCTTA
28112 CTTATCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTATATCCTTATTT
Found at i:28517 original size:12 final size:12
Alignment explanation
Indices: 28500--28525 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28490 GGCCACTCGC
28500 AAAAATGGACCG
1 AAAAATGGACCG
28512 AAAAATGGACCG
1 AAAAATGGACCG
28524 AA
1 AA
28526 GTGTTCCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (12 bp):
AAAAATGGACCG
Found at i:29272 original size:3 final size:3
Alignment explanation
Indices: 29266--29323 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
29256 GGTTTAATGC
29266 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29314 TTA TTA TTA T
1 TTA TTA TTA T
29324 CTTTTCTGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31567 original size:47 final size:47
Alignment explanation
Indices: 31482--31572 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 47
31472 GTGTTATTGG
* *
31482 AAAAGTTTACTATAATTTCTAAAATCATATATATTTAATAATATCCT
1 AAAAGTTTACTATAATTTCTAAAACCATATACATTTAATAATATCCT
* * *
31529 AAAAGTTTGCTTTAATTTCTAAAAACCCTATACA-TTAATAATAT
1 AAAAGTTTACTATAATTTCT-AAAACCATATACATTTAATAATAT
31573 TCTGAAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 28 0.74
48 10 0.26
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (47 bp):
AAAAGTTTACTATAATTTCTAAAACCATATACATTTAATAATATCCT
Found at i:34293 original size:30 final size:32
Alignment explanation
Indices: 34243--34307 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
34233 AAATCATCTT
*
34243 TCTCTTTCCTCCTCCTCCT-CCTTTCTCTCCGC
1 TCTCTTTACTCCTCCTCCTCCCTTTC-CTCCGC
34275 TCTCTTTACT-CT-CTCCTCCCTTTCCTCCGC
1 TCTCTTTACTCCTCCTCCTCCCTTTCCTCCGC
34305 TCT
1 TCT
34308 TCTCCGCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 14 0.45
31 8 0.26
32 9 0.29
ACGTcount: A:0.02, C:0.51, G:0.03, T:0.45
Consensus pattern (32 bp):
TCTCTTTACTCCTCCTCCTCCCTTTCCTCCGC
Found at i:35954 original size:27 final size:28
Alignment explanation
Indices: 35924--35982 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
35914 GTCATGCCTC
*
35924 CCATGGTTG-TACCCATCATCATGATCA
1 CCATGGATGATACCCATCATCATGATCA
*
35951 CCAT-GATGATGCCCATCATCATGATCA
1 CCATGGATGATACCCATCATCATGATCA
*
35978 TCATG
1 CCATG
35983 ACCACCGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (28 bp):
CCATGGATGATACCCATCATCATGATCA
Found at i:36000 original size:27 final size:26
Alignment explanation
Indices: 35970--36050 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 26
35960 TGCCCATCAT
35970 CATGATCATCATGACCACCGACACGAA
1 CATGATCATCATGACCACC-ACACGAA
* *
35997 CATG---ATCATG--C-CCA-TC-AT
1 CATGATCATCATGACCACCACACGAA
36015 CATGATCATCATGACCACCAACACGAA
1 CATGATCATCATGACCACC-ACACGAA
36042 CATGATCAT
1 CATGATCAT
36051 GGAGCAGGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
18 5 0.12
19 1 0.02
20 1 0.02
21 8 0.20
22 1 0.02
23 1 0.02
24 8 0.20
25 1 0.02
26 1 0.02
27 14 0.34
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (26 bp):
CATGATCATCATGACCACCACACGAA
Found at i:36016 original size:45 final size:45
Alignment explanation
Indices: 35952--36051 Score: 182
Period size: 45 Copynumber: 2.2 Consensus size: 45
35942 TCATGATCAC
* *
35952 CATGATGATGCCCATCATCATGATCATCATGACCACCGACACGAA
1 CATGATCATGCCCATCATCATGATCATCATGACCACCAACACGAA
35997 CATGATCATGCCCATCATCATGATCATCATGACCACCAACACGAA
1 CATGATCATGCCCATCATCATGATCATCATGACCACCAACACGAA
36042 CATGATCATG
1 CATGATCATG
36052 GAGCAGGCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (45 bp):
CATGATCATGCCCATCATCATGATCATCATGACCACCAACACGAA
Found at i:42421 original size:19 final size:20
Alignment explanation
Indices: 42397--42441 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 20
42387 AGTATATATA
42397 TTATTATATTA-TTATTTAT
1 TTATTATATTATTTATTTAT
42416 TTATTATATTATTTATTTAT
1 TTATTATATTATTTATTTAT
42436 TCTATT
1 T-TATT
42442 CTTACTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.46
20 9 0.38
21 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTATATTATTTATTTAT
Found at i:42425 original size:16 final size:16
Alignment explanation
Indices: 42406--42441 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
42396 ATTATTATAT
42406 TATTATTTATTTATTA
1 TATTATTTATTTATTA
*
42422 TATTATTTATTTATTC
1 TATTATTTATTTATTA
42438 TATT
1 TATT
42442 CTTACTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTATTTATTTATTA
Found at i:55667 original size:24 final size:24
Alignment explanation
Indices: 55635--55682 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
55625 TTTATTATTG
55635 TTTCAACTAACCAATAATATAAGA
1 TTTCAACTAACCAATAATATAAGA
55659 TTTCAACTAACCAATAATATAAGA
1 TTTCAACTAACCAATAATATAAGA
55683 AGAACAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (24 bp):
TTTCAACTAACCAATAATATAAGA
Found at i:72829 original size:26 final size:26
Alignment explanation
Indices: 72800--72854 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
72790 ATTAAATAAG
72800 AATGATCCAAGGGATGTATAAATGGT
1 AATGATCCAAGGGATGTATAAATGGT
72826 AATGATCCAAGGGATGTATAAATGGT
1 AATGATCCAAGGGATGTATAAATGGT
72852 AAT
1 AAT
72855 TCCTTGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.27
Consensus pattern (26 bp):
AATGATCCAAGGGATGTATAAATGGT
Found at i:74472 original size:69 final size:69
Alignment explanation
Indices: 74268--74477 Score: 233
Period size: 69 Copynumber: 3.0 Consensus size: 69
74258 CAACTCACAT
* * * * * *
74268 ATACTGCTTGGAATATTTTGAACCTCTGTCTCACTCATGTTTAACCACCACAGTTTCTTTAGGGA
1 ATACTGCTTGGAATATTTTGAACCTTTGTGTCACTCATGTCTAACCTCCTCAGTTTCTTTAGAGA
*
74333 CCCA
66 CCCG
* * * * * *
74337 ATACTGCTTGGAATGTTTTGAACCTTTGTGCCCCTCATGTCTAACCAT-GTTAGTTCCTTTAGAG
1 ATACTGCTTGGAATATTTTGAACCTTTGTGTCACTCATGTCTAACC-TCCTCAGTTTCTTTAGAG
74401 ACCCG
65 ACCCG
* ** ** *
74406 ATACTGTTTGGAATATTTTGAACCTTTGTGTGGCTCATGTCTAACCTCCTCAGTTTCTCCAAAGA
1 ATACTGCTTGGAATATTTTGAACCTTTGTGTCACTCATGTCTAACCTCCTCAGTTTCTTTAGAGA
74471 CCCG
66 CCCG
74475 ATA
1 ATA
74478 AATGAGGGCA
Statistics
Matches: 115, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
68 1 0.01
69 114 0.99
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (69 bp):
ATACTGCTTGGAATATTTTGAACCTTTGTGTCACTCATGTCTAACCTCCTCAGTTTCTTTAGAGA
CCCG
Found at i:76381 original size:75 final size:75
Alignment explanation
Indices: 76297--76447 Score: 248
Period size: 75 Copynumber: 2.0 Consensus size: 75
76287 TGCAAAAGTT
* * * *
76297 TATACAATGTCACTTAAGAAATATATTTAAGAAATTCTAATATATCTAAGTTTCTTAATTAAGAT
1 TATACAATGTCACTTAAGAAATATATTTAAAAAATTCTAATACATCTAACTTTCTTAATTAAAAT
76362 AGTAAAATGG
66 AGTAAAATGG
* *
76372 TATACAATGTCATTTAAGAAATATATTTAAAAAATTCTAATACATCTAACTTTTTTAATTAAAAT
1 TATACAATGTCACTTAAGAAATATATTTAAAAAATTCTAATACATCTAACTTTCTTAATTAAAAT
76437 AGTAAAATGG
66 AGTAAAATGG
76447 T
1 T
76448 GAAAATAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (75 bp):
TATACAATGTCACTTAAGAAATATATTTAAAAAATTCTAATACATCTAACTTTCTTAATTAAAAT
AGTAAAATGG
Found at i:79537 original size:16 final size:16
Alignment explanation
Indices: 79516--79554 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
79506 TGGGTTGTAT
79516 AAATGAATTCTTGAAG
1 AAATGAATTCTTGAAG
79532 AAATGAATTCTTGAAG
1 AAATGAATTCTTGAAG
79548 AAATGAA
1 AAATGAA
79555 ACATGGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (16 bp):
AAATGAATTCTTGAAG
Done.