Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012617.1 Corchorus capsularis cultivar CVL-1 contig12638, 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: 40952
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3607 original size:67 final size:67
Alignment explanation
Indices: 3516--3650 Score: 198
Period size: 67 Copynumber: 2.0 Consensus size: 67
3506 TGGGGTTCGA
* * * * * * *
3516 GTCATGCTAACGGTCCTTGTTGGTGGGTGATCTGTAAGTATCATTGTAAGTCCTCTCTGAGACTT
1 GTCACGCTAACGGTCCTCGTTGGTGGATGATCTATAAGTACCACTGTAAGCCCTCTCTGAGACTT
3581 AT
66 AT
*
3583 GTCACGCTAACGGTTCTCGTTGGTGGATGATCTATAAGTACCACTGTAAGCCCTCTCTGAGACTT
1 GTCACGCTAACGGTCCTCGTTGGTGGATGATCTATAAGTACCACTGTAAGCCCTCTCTGAGACTT
3648 AT
66 AT
3650 G
1 G
3651 GCATACCTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (67 bp):
GTCACGCTAACGGTCCTCGTTGGTGGATGATCTATAAGTACCACTGTAAGCCCTCTCTGAGACTT
AT
Found at i:4996 original size:16 final size:16
Alignment explanation
Indices: 4952--5008 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
4942 TGGAATCATA
4952 TGACCCGAAACCGAAAAT
1 TGACCC-AAACC-AAAAT
* * *
4970 AGACACGAACCAAAAT
1 TGACCCAAACCAAAAT
*
4986 TGACCCAAACCCAAA-
1 TGACCCAAACCAAAAT
5001 TGACCCAA
1 TGACCCAA
5009 CATTTGAGCG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 8 0.25
16 16 0.50
17 4 0.12
18 4 0.12
ACGTcount: A:0.47, C:0.32, G:0.12, T:0.09
Consensus pattern (16 bp):
TGACCCAAACCAAAAT
Found at i:7098 original size:12 final size:12
Alignment explanation
Indices: 7077--7124 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
7067 TTTAAGTTAA
7077 AAAAAAAAAAGG
1 AAAAAAAAAAGG
* *
7089 AAAAACAAAATG
1 AAAAAAAAAAGG
*
7101 AAAAAAGAAAAAG
1 AAAAAA-AAAAGG
*
7114 AAAATAAAAAG
1 AAAAAAAAAAG
7125 AGATCTTCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAAGG
Found at i:7104 original size:19 final size:18
Alignment explanation
Indices: 7077--7124 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
7067 TTTAAGTTAA
*
7077 AAAAAAAAAAGGAAAAAC
1 AAAATAAAAAGGAAAAAC
* *
7095 AAAATGAAAAAAGAAAAAG
1 AAAAT-AAAAAGGAAAAAC
7114 AAAATAAAAAG
1 AAAATAAAAAG
7125 AGATCTTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (18 bp):
AAAATAAAAAGGAAAAAC
Found at i:9959 original size:69 final size:71
Alignment explanation
Indices: 9833--9973 Score: 196
Period size: 69 Copynumber: 2.0 Consensus size: 71
9823 ATATACTCCA
* * * **
9833 ACAATTGGAACAAATCAGACGGCCGAGAGAACGGTGTTGTCAAACTTGGACCGGACCGGCCGGTC
1 ACAATTGAAACAAATCAGACGACCGAGAGAACAGTGTTGTCAAACCCGGACCGGACCGGCCGGTC
9898 GAACCG
66 GAACCG
* * *
9904 ACAATTGAAACAAATTAGACGACTGAG-G-ACAGTGTTGTCAAACCCGGATCGGACCGGCCGGTC
1 ACAATTGAAACAAATCAGACGACCGAGAGAACAGTGTTGTCAAACCCGGACCGGACCGGCCGGTC
9967 GAACCG
66 GAACCG
9973 A
1 A
9974 TTCAACCGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 38 0.61
70 1 0.02
71 23 0.37
ACGTcount: A:0.31, C:0.25, G:0.29, T:0.15
Consensus pattern (71 bp):
ACAATTGAAACAAATCAGACGACCGAGAGAACAGTGTTGTCAAACCCGGACCGGACCGGCCGGTC
GAACCG
Found at i:10848 original size:12 final size:12
Alignment explanation
Indices: 10831--10856 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10821 CAATTATCTT
10831 TAATTATATATA
1 TAATTATATATA
10843 TAATTATATATA
1 TAATTATATATA
10855 TA
1 TA
10857 GTTTAGTTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTATATATA
Found at i:14605 original size:13 final size:12
Alignment explanation
Indices: 14582--14624 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
14572 TTAATACAGG
14582 TATCGACGGATA
1 TATCGACGGATA
14594 TATCGAACGGATA
1 TATCG-ACGGATA
14607 TATCGACGGATA
1 TATCGACGGATA
14619 TATCGA
1 TATCGA
14625 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:16320 original size:10 final size:10
Alignment explanation
Indices: 16305--16343 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
16295 TTTAATTTAA
16305 TATGGATATT
1 TATGGATATT
16315 TATGGATATT
1 TATGGATATT
*
16325 TACGGATATT
1 TATGGATATT
16335 TATGGATAT
1 TATGGATAT
16344 ATCGAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.46
Consensus pattern (10 bp):
TATGGATATT
Found at i:16355 original size:18 final size:18
Alignment explanation
Indices: 16312--16366 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
16302 TAATATGGAT
* *
16312 ATTTATGGATATTTACGGAT
1 ATTTATGGATATAT-C-GAG
16332 ATTTATGGATATATCGAG
1 ATTTATGGATATATCGAG
* *
16350 ATTTATCGAGATATCGA
1 ATTTATGGATATATCGA
16367 TAAATATCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 17 0.55
19 1 0.03
20 13 0.42
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (18 bp):
ATTTATGGATATATCGAG
Found at i:16471 original size:12 final size:12
Alignment explanation
Indices: 16454--16492 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
16444 GTACAGATAT
16454 CGGATATATCGA
1 CGGATATATCGA
16466 CGGATATATCGA
1 CGGATATATCGA
16478 --G--ATATCGA
1 CGGATATATCGA
16486 CGGATAT
1 CGGATAT
16493 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
10 2 0.09
12 14 0.61
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:19963 original size:96 final size:95
Alignment explanation
Indices: 19799--19991 Score: 350
Period size: 96 Copynumber: 2.0 Consensus size: 95
19789 ACTTTGTACC
* *
19799 TCATCATTGTTTCCATTTTTCTCCACTGCAGCAGTTTTCTCTTCAGTGGTATCTGCATTGTCATC
1 TCATCATTATTTCCATTTTTCTCCACTGCAGCAGTTTTCTCTTCAGTGGTATCTGCATTATCATC
19864 CACCTTAGGACTCTTCCCTTCTACTGCATTT
66 CACCTTAGGACTCTTCCCTTCTACTGC-TTT
*
19895 TCATCATTATTTCCGTTTTTCTCCACTGCAGCAGTTTTCTCTTCAGTGGTATCTGCATTATCATC
1 TCATCATTATTTCCATTTTTCTCCACTGCAGCAGTTTTCTCTTCAGTGGTATCTGCATTATCATC
19960 CACCTTAGGACTCTTCCCTTCTACTGCTTT
66 CACCTTAGGACTCTTCCCTTCTACTGCTTT
19990 TC
1 TC
19992 CATCGCAGGC
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
95 5 0.05
96 89 0.95
ACGTcount: A:0.16, C:0.30, G:0.12, T:0.43
Consensus pattern (95 bp):
TCATCATTATTTCCATTTTTCTCCACTGCAGCAGTTTTCTCTTCAGTGGTATCTGCATTATCATC
CACCTTAGGACTCTTCCCTTCTACTGCTTT
Found at i:20668 original size:6 final size:6
Alignment explanation
Indices: 20657--20684 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20647 CAGGTTTTCT
20657 ATCAAC ATCAAC ATCAAC ATCAAC ATCA
1 ATCAAC ATCAAC ATCAAC ATCAAC ATCA
20685 GTAACCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
ATCAAC
Found at i:26272 original size:28 final size:28
Alignment explanation
Indices: 26232--26287 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
26222 ATTGGAATAC
26232 TCACAAATTCTGTGTGAAATGAAGATTT
1 TCACAAATTCTGTGTGAAATGAAGATTT
26260 TCACAAATTCTGTGTGAAATGAAGATTT
1 TCACAAATTCTGTGTGAAATGAAGATTT
26288 CCTACTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (28 bp):
TCACAAATTCTGTGTGAAATGAAGATTT
Found at i:26738 original size:31 final size:31
Alignment explanation
Indices: 26669--26831 Score: 146
Period size: 31 Copynumber: 5.5 Consensus size: 31
26659 TCCTTTTGTG
* * * **
26669 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
26700 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
26731 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
26762 CA--T---GTGGCAC--G--AATTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
26784 CATGTGGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
26815 CACGTGGCGTGCCACGT
1 CACGTGGCGTGCCACGT
26832 TGGACACCGT
Statistics
Matches: 107, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
22 12 0.11
24 2 0.02
26 5 0.05
27 6 0.06
29 2 0.02
31 80 0.75
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.33
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:26766 original size:19 final size:20
Alignment explanation
Indices: 26742--26791 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
26732 ACGTGGCGTG
*
26742 ACATGTGTCAC-TTTTTGGT
1 ACATGTGGCACATTTTTGGT
26761 ACATGTGGCACGAATTTTTGGT
1 ACATGTGGCAC--ATTTTTGGT
26783 ACATGTGGC
1 ACATGTGGC
26792 GTGCCACATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.37
22 17 0.63
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (20 bp):
ACATGTGGCACATTTTTGGT
Found at i:26784 original size:53 final size:53
Alignment explanation
Indices: 26722--26822 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 53
26712 CACGTGTCAC
** *
26722 TTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACGAA
1 TTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACGAA
* *
26775 TTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 TTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
26823 GTGCCACGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.37
Consensus pattern (53 bp):
TTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACGAA
Found at i:27696 original size:40 final size:40
Alignment explanation
Indices: 27630--27733 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 40
27620 ACGACATTTA
* * * *
27630 ACAACGA-CTTAAAAATGTCGCTGCTAAATATTGAGTAT-TG
1 ACAACGACCTTTAAAA-GTCGTTGCTAAATATTG-CTATATC
* *
27670 ACAGCGACCTTTAAAAGTCGTTGCTAAATATTGCTTTATC
1 ACAACGACCTTTAAAAGTCGTTGCTAAATATTGCTATATC
*
27710 ACAACGACTTTTAAAAGTCGTTGC
1 ACAACGACCTTTAAAAGTCGTTGC
27734 CCAATCTACA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.04
40 45 0.83
41 7 0.13
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (40 bp):
ACAACGACCTTTAAAAGTCGTTGCTAAATATTGCTATATC
Found at i:28051 original size:132 final size:133
Alignment explanation
Indices: 27878--28461 Score: 1039
Period size: 132 Copynumber: 4.4 Consensus size: 133
27868 AATTCATAGT
* * * *
27878 CTTTTCGCAACGACTTCTGCTAGTCATTGT-TTAATATATTTTACAAATTGATTTTCGCAGCGAC
1 CTTTTTGCAACGACTTTTGTTAGTCGTT-TCTTAATATATTTTACAAATTGATTTTCGCAGCGAC
*
27942 CTTGAAAGTCGCTAC-AAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCT
65 CTTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATCT
28006 GAAA
130 GAAA
28010 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
1 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
*
28075 TTGAAAGTCGCTACAAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGTGAAATCT
66 TTGAAAGTCGCTAC-AAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATCT
28140 GAAA
130 GAAA
28144 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
1 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
*
28209 TTGAAAGTCGCTAC-AAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCTG
66 TTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATCTG
28273 AAA
131 AAA
28276 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
1 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
*
28341 TTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATCTT
66 TTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATCTG
28406 AAA
131 AAA
* *
28409 CTTTTCGCAACAACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATT
1 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATT
28462 AAGTCGCAAC
Statistics
Matches: 436, Mismatches: 12, Indels: 7
0.96 0.03 0.02
Matches are distributed among these distances:
131 1 0.00
132 203 0.47
133 102 0.23
134 130 0.30
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (133 bp):
CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
TTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATCTG
AAA
Found at i:28358 original size:266 final size:265
Alignment explanation
Indices: 27878--28461 Score: 1080
Period size: 266 Copynumber: 2.2 Consensus size: 265
27868 AATTCATAGT
* * *
27878 CTTTTCGCAACGACTTCTGCTAGTCATTGT-TTAATATATTTTACAAATTGATTTTCGCAGCGAC
1 CTTTTCGCAACGACTTTTGTTAGTCGTT-TCTTAATATATTTTACAAATTGATTTTCGCAGCGAC
27942 CTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCTG
65 CTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCTG
28007 AAACTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCG
130 AAACTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCG
*
28072 ACCTTGAAAGTCGCTACAAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGTGAAA
195 ACCTTGAAAGTCGCTAC-AAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAA
28137 TCTGAAA
259 TCTGAAA
*
28144 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
1 CTTTTCGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
28209 TTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCTGA
66 TTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCTGA
28274 AACTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGA
131 AACTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGA
28339 CCTTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATC
196 CCTTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATC
*
28404 TTAAA
261 TGAAA
*
28409 CTTTTCGCAACAACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATT
1 CTTTTCGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATT
28462 AAGTCGCAAC
Statistics
Matches: 309, Mismatches: 8, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
265 104 0.34
266 205 0.66
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (265 bp):
CTTTTCGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
TTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCTGA
AACTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGA
CCTTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCATTGCGAAATC
TGAAA
Found at i:35606 original size:202 final size:201
Alignment explanation
Indices: 35171--35942 Score: 1183
Period size: 202 Copynumber: 3.8 Consensus size: 201
35161 AAAGCCATTC
* * *
35171 AAAAGATTTCACAACCAAAACAATGTTGTTGTGTAAGGGTTTTCGCAACGACA--TAATCGCTTT
1 AAAAGATTTCACAACCAAAACAACGTCGTTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
* * * * *
35234 TAAATCACTTTGGCAACTACCTA-AAGGTCGTTCTGTAAGTGTTTTGGAAATGACATTTAATCAA
66 TAAATTATTTTGGCAACTACCTAGAA-GTCGTTGTGTAAGTGTTTTGGAAACGACATTTAATCAT
* * * *
35298 TTCTAAAAGTTATTCGTAACCAATTAAAGTGGCTGCAAAAATTATTACGCAACCAATCAAATGTT
130 TTTTAAAAGTTATTCGTAACCAATTAAAGTGGTTGCGAAAATTATTACACAACCAATCAAATGTT
*
35363 CCTACGT
195 GCTACGT
*
35370 AAAAGATTTTACAACCAAAACAACGTCGTTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
1 AAAAGATTTCACAACCAAAACAACGTCGTTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
* * * *
35435 TAAATTGTTTTGGCAACTACCTACAAGTCGTTGTGTAAGTATTTTGGAAACGACTTTTAATCATT
66 TAAATTATTTTGGCAACTACCTAGAAGTCGTTGTGTAAGTGTTTTGGAAACGACATTTAATCATT
35500 TTTAAAAGTTATTCGTAACCAATTAAAAGTGGTTGCGAAAATTATTACACAACCAATCAAATGTT
131 TTTAAAAGTTATTCGTAACCAATT-AAAGTGGTTGCGAAAATTATTACACAACCAATCAAATGTT
35565 GCTACGT
195 GCTACGT
*
35572 AAAAGATTTCACAACCAAAACAACGTCTTTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
1 AAAAGATTTCACAACCAAAACAACGTCGTTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
* * * ** *
35637 TAAATTGTTTTGGCAACTACCTAGAGGTCGTTGTGTAAGTGTTTCGGAAACGATTTTTACTCATT
66 TAAATTATTTTGGCAACTACCTAGAAGTCGTTGTGTAAGTGTTTTGGAAACGACATTTAATCATT
35702 TTTAAAAGTTATTCGTAACCAATTAAAAGTGGTTGCGAAAATTATTACACAACCAATCAAATGTT
131 TTTAAAAGTTATTCGTAACCAATT-AAAGTGGTTGCGAAAATTATTACACAACCAATCAAATGTT
35767 GCTACGT
195 GCTACGT
* *
35774 AAAAGATTTCACAACCAAAACAACATCGTTGCGTAAGGGTTTTCGC-ACGACATTTAATCGTTTT
1 AAAAGATTTCACAACCAAAACAACGTCGTTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
* * ** *
35838 TAAATTATTTTGGCAACTACCTAGAGGTTGTTACGTAAGTGTTTTGGAAACGACATTTAATCGTT
66 TAAATTATTTTGGCAACTACCTAGAAGTCGTTGTGTAAGTGTTTTGGAAACGACATTTAATCATT
* *
35903 TTTAAAAGTTATCCGTAACCAATTAAAGTGGTTGCCAAAA
131 TTTAAAAGTTATTCGTAACCAATTAAAGTGGTTGCGAAAA
35943 AATTTTCGCA
Statistics
Matches: 530, Mismatches: 39, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
199 50 0.09
200 15 0.03
201 183 0.35
202 282 0.53
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (201 bp):
AAAAGATTTCACAACCAAAACAACGTCGTTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTT
TAAATTATTTTGGCAACTACCTAGAAGTCGTTGTGTAAGTGTTTTGGAAACGACATTTAATCATT
TTTAAAAGTTATTCGTAACCAATTAAAGTGGTTGCGAAAATTATTACACAACCAATCAAATGTTG
CTACGT
Found at i:35922 original size:403 final size:400
Alignment explanation
Indices: 35171--35942 Score: 1197
Period size: 403 Copynumber: 1.9 Consensus size: 400
35161 AAAGCCATTC
*
35171 AAAAGATTTCACAACCAAAACAATGTTGTTGTGTAAGGGTTTTCGCAACGACATAATCGCTTTTA
1 AAAAGATTTCACAACCAAAACAACGTTGTTGTGTAAGGGTTTTCGCAACGACATAATCGCTTTTA
* *
35236 AATCACTTTGGCAACTACCTAAAGGTCGTTCTGTAAGTGTTTTGGAAATGACATTTAATCAATTC
66 AATCACTTTGGCAACTACCTAAAGGTCGTTCTGTAAGTGTTTCGGAAACGACATTTAATCAATTC
*
35301 TAAAAGTTATTCGTAACCAATTAAAGTGGCTGCAAAAATTATTACGCAACCAATCAAATGTTCCT
131 TAAAAGTTATTCGTAACCAATTAAAGTGGCTGCAAAAATTATTACACAACCAATCAAATGTTCCT
* * *
35366 ACGTAAAAGATTTTACAACCAAAACAACGTCGTTGTGTAAGGGTTTTCGCAACGACATTTAATCG
196 ACGTAAAAGATTTCACAACCAAAACAACATCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCG
* ** *
35431 TTTTTAAATTGTTTTGGCAACTACCTACAAGTCGTTGTGTAAGTATTTTGGAAACGACTTTTAAT
261 TTTTTAAATTATTTTGGCAACTACCTACAAGTCGTTACGTAAGTATTTTGGAAACGACATTTAAT
* *
35496 CATTTTTAAAAGTTATTCGTAACCAATTAAAAGTGGTTGCGAAAATTATTACACAACCAATCAAA
326 CATTTTTAAAAGTTATCCGTAACCAATT-AAAGTGGTTGCCAAAATTATTACACAACCAATCAAA
35561 TGTTGCTACGT
390 TGTTGCTACGT
*
35572 AAAAGATTTCACAACCAAAACAACGTCT-TTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTT
1 AAAAGATTTCACAACCAAAACAACGT-TGTTGTGTAAGGGTTTTCGCAACGACA--TAATCGCTT
*** * * ** * *
35636 TTAAATTGTTTTGGCAACTACCTAGAGGTCGTTGTGTAAGTGTTTCGGAAACGATTTTTACTCAT
63 TTAAATCACTTTGGCAACTACCTAAAGGTCGTTCTGTAAGTGTTTCGGAAACGACATTTAATCAA
* * *
35701 TTTTAAAAGTTATTCGTAACCAATTAAAAGTGGTTGCGAAAATTATTACACAACCAATCAAATGT
128 TTCTAAAAGTTATTCGTAACCAATT-AAAGTGGCTGCAAAAATTATTACACAACCAATCAAATGT
*
35766 TGCTACGTAAAAGATTTCACAACCAAAACAACATCGTTGCGTAAGGGTTTTCGC-ACGACATTTA
192 TCCTACGTAAAAGATTTCACAACCAAAACAACATCGTTGCGTAAGGGTTTTCGCAACGACATTTA
* * * *
35830 ATCGTTTTTAAATTATTTTGGCAACTACCTAGAGGTTGTTACGTAAGTGTTTTGGAAACGACATT
257 ATCGTTTTTAAATTATTTTGGCAACTACCTACAAGTCGTTACGTAAGTATTTTGGAAACGACATT
*
35895 TAATCGTTTTTAAAAGTTATCCGTAACCAATTAAAGTGGTTGCCAAAA
322 TAATCATTTTTAAAAGTTATCCGTAACCAATTAAAGTGGTTGCCAAAA
35943 AATTTTCGCA
Statistics
Matches: 335, Mismatches: 32, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
401 50 0.15
402 16 0.05
403 183 0.55
404 86 0.26
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (400 bp):
AAAAGATTTCACAACCAAAACAACGTTGTTGTGTAAGGGTTTTCGCAACGACATAATCGCTTTTA
AATCACTTTGGCAACTACCTAAAGGTCGTTCTGTAAGTGTTTCGGAAACGACATTTAATCAATTC
TAAAAGTTATTCGTAACCAATTAAAGTGGCTGCAAAAATTATTACACAACCAATCAAATGTTCCT
ACGTAAAAGATTTCACAACCAAAACAACATCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCG
TTTTTAAATTATTTTGGCAACTACCTACAAGTCGTTACGTAAGTATTTTGGAAACGACATTTAAT
CATTTTTAAAAGTTATCCGTAACCAATTAAAGTGGTTGCCAAAATTATTACACAACCAATCAAAT
GTTGCTACGT
Found at i:36086 original size:20 final size:20
Alignment explanation
Indices: 36061--36102 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
36051 GCGAACACTC
* *
36061 AAGTCGTTGTGTTAGATTTT
1 AAGTCGTTGCGTTAGATATT
36081 AAGTCGTTGCGTTAGATATT
1 AAGTCGTTGCGTTAGATATT
36101 AA
1 AA
36103 ACAACGGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (20 bp):
AAGTCGTTGCGTTAGATATT
Done.