Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014404.1 Corchorus olitorius cultivar O-4 contig14437, 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: 95805
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1656 original size:71 final size:67
Alignment explanation
Indices: 1539--1718 Score: 244
Period size: 71 Copynumber: 2.7 Consensus size: 67
1529 TATATAATAA
1539 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 ATTGATTGATTGATTTG-A-ATA-TTTGATCCAATTAGAATCAATTAGTACT--AATGATATT-A
1604 ATTGATTG
60 ATTGATTG
1612 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAATTGA
1 ATTGATTGATTGATTTGAATAT-TTGATCCAATTAGAATCAATTAGTACTAATGATATTAATTGA
1677 TTG
65 TTG
* *
1680 ATT-A---ATTGATTTGAATA-TTGATCAAATTAAAATCAATTA
1 ATTGATTGATTGATTTGAATATTTGATCCAATTAGAATCAATTA
1719 AAATCAATAA
Statistics
Matches: 104, Mismatches: 2, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
62 20 0.19
64 13 0.12
67 1 0.01
68 12 0.12
69 9 0.09
70 1 0.01
71 30 0.29
72 1 0.01
73 17 0.16
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (67 bp):
ATTGATTGATTGATTTGAATATTTGATCCAATTAGAATCAATTAGTACTAATGATATTAATTGAT
TG
Found at i:2586 original size:3 final size:3
Alignment explanation
Indices: 2578--2651 Score: 139
Period size: 3 Copynumber: 24.3 Consensus size: 3
2568 TTTTTAACAA
2578 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2626 TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT T
2652 TTGTCTTTTA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6972 original size:27 final size:28
Alignment explanation
Indices: 6942--7000 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
6932 GATACGATCA
**
6942 AATTCTTGAAATTTCTC-TTCAAAGGGT
1 AATTCTTGAAATTTAACATTCAAAGGGT
* * *
6969 AATTTTTGTAATTTAACATTCTAAGGGT
1 AATTCTTGAAATTTAACATTCAAAGGGT
6997 AATT
1 AATT
7001 TAGTAATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (28 bp):
AATTCTTGAAATTTAACATTCAAAGGGT
Found at i:7089 original size:3 final size:3
Alignment explanation
Indices: 7081--7193 Score: 226
Period size: 3 Copynumber: 37.7 Consensus size: 3
7071 ATTTATTTAT
7081 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
7129 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
7177 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
7194 TCATTTTCTT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 110 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8229 original size:27 final size:27
Alignment explanation
Indices: 8195--8256 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
8185 ATGTTGATCC
*
8195 TTGGAACTCCACCAATTTTGATTGTTG
1 TTGGAACTCCACCAATGTTGATTGTTG
*
8222 TTTGAACTCCACCAATGTTGATTGTTG
1 TTGGAACTCCACCAATGTTGATTGTTG
8249 TTGGAACT
1 TTGGAACT
8257 GTAGATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (27 bp):
TTGGAACTCCACCAATGTTGATTGTTG
Found at i:10185 original size:20 final size:19
Alignment explanation
Indices: 10152--10227 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 19
10142 GGTAGTTTAT
10152 GGTAGTTTTCTTTTATAAATG
1 GGTAGTTTT-TTTT-TAAATG
10173 GGTAGTTTTTTTTTTTAAATTG
1 GGTAG--TTTTTTTTTAAA-TG
* * *
10195 AGTGGTTTTCTTTTAAATG
1 GGTAGTTTTTTTTTAAATG
*
10214 GATAGTTTTTTTTT
1 GGTAGTTTTTTTTT
10228 TTTTGGTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 12 0.27
20 11 0.24
21 9 0.20
22 9 0.20
23 4 0.09
ACGTcount: A:0.20, C:0.03, G:0.18, T:0.59
Consensus pattern (19 bp):
GGTAGTTTTTTTTTAAATG
Found at i:10228 original size:20 final size:20
Alignment explanation
Indices: 10150--10228 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
10140 AAGGTAGTTT
*
10150 ATGG-TAGTTTTCTTTTATAA
1 ATGGATAGTTTT-TTTTTTAA
*
10170 ATGGGTAGTTTTTTTTTTTAA
1 ATGGATAG-TTTTTTTTTTAA
* * *
10191 ATTGAGT-GGTTTTCTTTTAA
1 ATGGA-TAGTTTTTTTTTTAA
10211 ATGGATAGTTTTTTTTTT
1 ATGGATAGTTTTTTTTTT
10229 TTTGGTTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 1 0.02
20 27 0.57
21 14 0.30
22 5 0.11
ACGTcount: A:0.20, C:0.03, G:0.18, T:0.59
Consensus pattern (20 bp):
ATGGATAGTTTTTTTTTTAA
Found at i:10229 original size:21 final size:20
Alignment explanation
Indices: 10150--10229 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 20
10140 AAGGTAGTTT
* *
10150 ATGGTAGTTTTCTTTTATAA
1 ATGGTAGTTTTTTTTTTTAA
10170 ATGGGTAGTTTTTTTTTTTAA
1 AT-GGTAGTTTTTTTTTTTAA
* * *
10191 ATTG-AGTGGTTTTCTTTTAA
1 ATGGTAGT-TTTTTTTTTTAA
10211 ATGGATAGTTTTTTTTTTT
1 ATGG-TAGTTTTTTTTTTT
10230 TTGGTTTATA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.06
20 16 0.33
21 26 0.54
22 3 0.06
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (20 bp):
ATGGTAGTTTTTTTTTTTAA
Found at i:11760 original size:14 final size:14
Alignment explanation
Indices: 11738--11771 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11728 CCACGCCAAG
11738 CAGAGGAACATCTTC
1 CAGA-GAACATCTTC
11753 CAGAGAACATCTTC
1 CAGAGAACATCTTC
11767 CAGAG
1 CAGAG
11772 CTCGAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (14 bp):
CAGAGAACATCTTC
Found at i:16059 original size:2 final size:2
Alignment explanation
Indices: 16052--16093 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
16042 AACCTTTATT
16052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16094 CAAATACCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16740 original size:144 final size:138
Alignment explanation
Indices: 16482--16748 Score: 372
Period size: 144 Copynumber: 1.9 Consensus size: 138
16472 AATAACCATG
* *
16482 CTATAAGAACTAAACCGGATTGGATTACAAAAACAAAAAAAAAGAGTAACTTATTTTTTACATTA
1 CTATAAAAACTAAACCGGATTGGATTACAAAAAAAAAAAAAAAGAGTAACTTATTTTTTACATTA
* * * * *
16547 TTTTTATTACTATGTTTGATGATTGCTTAAAACGATTCTTCGAATGAGTTGAATTTTTAAACATA
66 TTTTTATTACTATGTTTGATGATGGCTTAAAACAATTATTCAAAAGAGTTGAATTTTTAAACATA
16612 TAATCGTA
131 TAATCGTA
** *
16620 CTATAAAAACTAAACCGGATTGGATTGTAAAAAAAATAGCAAAAGAAGAGTAACTTATTTTTTTC
1 CTATAAAAACTAAACCGGATTGGATTACAAAAAAAA-A--AAAA-AAGAGTAACTTATTTTTTAC
* *
16685 ATTATTTTTCTTTTACTATGTTTGATGATGGCTTAAAACAATTATTCAAAAGAGTTTAATTTTT
62 ATTA-TTTT-TATTACTATGTTTGATGATGGCTTAAAACAATTATTCAAAAGAGTTGAATTTTT
16749 CTGGCCAAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
138 32 0.29
139 1 0.01
141 4 0.04
142 23 0.21
143 4 0.04
144 47 0.42
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (138 bp):
CTATAAAAACTAAACCGGATTGGATTACAAAAAAAAAAAAAAAGAGTAACTTATTTTTTACATTA
TTTTTATTACTATGTTTGATGATGGCTTAAAACAATTATTCAAAAGAGTTGAATTTTTAAACATA
TAATCGTA
Found at i:18150 original size:22 final size:22
Alignment explanation
Indices: 18124--18179 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
18114 TCACAAGGTA
18124 ATTATCAAAATTTCATA-GAGTG
1 ATTATCAAAATTTCATAGGA-TG
*
18146 GTTATC-AAATTTCATAGGATG
1 ATTATCAAAATTTCATAGGATG
18167 ATTATCAAAATTT
1 ATTATCAAAATTT
18180 TATAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGGATG
Found at i:18488 original size:1 final size:1
Alignment explanation
Indices: 18482--18507 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
18472 TAAGAATATG
18482 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
18508 CCTTATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24952 original size:23 final size:22
Alignment explanation
Indices: 24913--24957 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
24903 CAAATAAGGA
24913 AGAAAAAAATAGAAGAAGAAAG
1 AGAAAAAAATAGAAGAAGAAAG
24935 AGAAAAAAA-AGGAGAGAAGAAAG
1 AGAAAAAAATA-GA-AGAAGAAAG
24958 GGCCAACGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 11 0.52
23 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (22 bp):
AGAAAAAAATAGAAGAAGAAAG
Found at i:26741 original size:18 final size:19
Alignment explanation
Indices: 26701--26743 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
26691 GAAAGAATTT
26701 AAAGAAAAAGGAATTGGGGAAG
1 AAAGAAAAAGGAATT---GAAG
26723 AAAGAAAAAGGAATT-AAG
1 AAAGAAAAAGGAATTGAAG
26741 AAA
1 AAA
26744 ATACCGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
22 15 0.71
ACGTcount: A:0.63, C:0.00, G:0.28, T:0.09
Consensus pattern (19 bp):
AAAGAAAAAGGAATTGAAG
Found at i:27251 original size:63 final size:63
Alignment explanation
Indices: 27152--27340 Score: 281
Period size: 63 Copynumber: 3.0 Consensus size: 63
27142 GGTTTAACAT
* * * * *
27152 GGTTTTACTATCAAACTTTGGGGTTTTACTATCAAACTTTGGGGTTTGACCATTAAATTTTGG
1 GGTTTGACCATCAAACTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATAAAAATTTGG
*
27215 GGTTTGACCATCAAACTTTGGGGTTTGACTATCAAACTTTGGGG-TTGACCATCAAAATTTGG
1 GGTTTGACCATCAAACTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATAAAAATTTGG
* * * *
27277 GGTTTGACCATCAAAATTTGGGGTTTGACCATCAAAATTTGGGCTTTGACCATAAAAATTTGG
1 GGTTTGACCATCAAACTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATAAAAATTTGG
27340 G
1 G
27341 CAAAAACACA
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
62 56 0.49
63 59 0.51
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (63 bp):
GGTTTGACCATCAAACTTTGGGGTTTGACTATCAAACTTTGGGGTTTGACCATAAAAATTTGG
Found at i:27341 original size:21 final size:21
Alignment explanation
Indices: 27152--27340 Score: 254
Period size: 21 Copynumber: 9.0 Consensus size: 21
27142 GGTTTAACAT
* * *
27152 GGTTTTACTATCAAACTTTGG
1 GGTTTGACCATCAAAATTTGG
* * *
27173 GGTTTTACTATCAAACTTTGG
1 GGTTTGACCATCAAAATTTGG
* *
27194 GGTTTGACCATTAAATTTTGG
1 GGTTTGACCATCAAAATTTGG
*
27215 GGTTTGACCATCAAACTTTGG
1 GGTTTGACCATCAAAATTTGG
* *
27236 GGTTTGACTATCAAACTTTGG
1 GGTTTGACCATCAAAATTTGG
27257 GG-TTGACCATCAAAATTTGG
1 GGTTTGACCATCAAAATTTGG
27277 GGTTTGACCATCAAAATTTGG
1 GGTTTGACCATCAAAATTTGG
27298 GGTTTGACCATCAAAATTTGG
1 GGTTTGACCATCAAAATTTGG
* *
27319 GCTTTGACCATAAAAATTTGG
1 GGTTTGACCATCAAAATTTGG
27340 G
1 G
27341 CAAAAACACA
Statistics
Matches: 156, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
20 18 0.12
21 138 0.88
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (21 bp):
GGTTTGACCATCAAAATTTGG
Found at i:27476 original size:21 final size:21
Alignment explanation
Indices: 27408--27469 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
27398 TGGTTTGGCT
*
27408 ATCAAATTTTGAGG-TTTGACC
1 ATCAAAATTTG-GGCTTTGACC
27429 ATCAAAATTTGGGCTTTGACC
1 ATCAAAATTTGGGCTTTGACC
*
27450 ATCAAAATTTGGGGTTTGAC
1 ATCAAAATTTGGGCTTTGAC
27470 TGACAAACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTGGGCTTTGACC
Found at i:32057 original size:3 final size:3
Alignment explanation
Indices: 32049--32082 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
32039 TGCCTCTCAA
32049 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
32083 TTTAATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:33179 original size:5 final size:6
Alignment explanation
Indices: 33165--33214 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
33155 TGTTAGCTTC
*
33165 TTTTGT TTTTGT TTTTGT TTTT-T TATTT-T TTATT-T TTTTGT TTTTCT
1 TTTTGT TTTTGT TTTTGT TTTTGT T-TTTGT TT-TTGT TTTTGT TTTTGT
33212 TTT
1 TTT
33215 CAGGATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
5 5 0.12
6 35 0.88
ACGTcount: A:0.04, C:0.02, G:0.08, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:39265 original size:2 final size:2
Alignment explanation
Indices: 39258--39285 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39248 ACCTTGCTTT
39258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39286 CACAAATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40884 original size:38 final size:38
Alignment explanation
Indices: 40842--40950 Score: 152
Period size: 38 Copynumber: 2.9 Consensus size: 38
40832 TGTGTGTCCT
*
40842 TATAATTCTTGCCATAAATGTTTATGTCCATTCTGCTG
1 TATAAGTCTTGCCATAAATGTTTATGTCCATTCTGCTG
*
40880 TATAAGTCTTATG-CA-AAATGTTTATGTCCAGTCTGCTG
1 TATAAGTC-T-TGCCATAAATGTTTATGTCCATTCTGCTG
40918 TATAAGTCTT-CCATACAATGTTTATGTCCATTC
1 TATAAGTCTTGCCATA-AATGTTTATGTCCATTC
40951 CACTTTTATG
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
36 3 0.05
37 2 0.03
38 53 0.84
39 3 0.05
40 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (38 bp):
TATAAGTCTTGCCATAAATGTTTATGTCCATTCTGCTG
Found at i:51385 original size:2 final size:2
Alignment explanation
Indices: 51378--51404 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51368 AAGTTGCAGG
51378 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
51405 GTGCATGTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:52458 original size:15 final size:12
Alignment explanation
Indices: 52429--52461 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
52419 TTCCGTGCAA
52429 ATGATGACTCAG
1 ATGATGACTCAG
52441 ATGATGACTCAG
1 ATGATGACTCAG
*
52453 ACGATGACT
1 ATGATGACT
52462 TTAGTGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (12 bp):
ATGATGACTCAG
Found at i:62046 original size:178 final size:178
Alignment explanation
Indices: 61681--62052 Score: 455
Period size: 178 Copynumber: 2.1 Consensus size: 178
61671 CTATAAGCAC
* * *** * * *
61681 AAATTATGTAATATTAAGCAGACCGTCTATTTTTGTTAACTGAAACAACTAATTCTTTGGAATCA
1 AAATTATATAATATTAAGCAGACCGCCTATTCCCGTTAACCGAAACAACTAAATCTTTGGAAGCA
* * * *
61746 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
66 TGTTTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAAC
* * * *
61811 AACCTTTCAAGAGACACTTGAATCATTTCAATCAGACATCTGGAGTAA
131 AACCTTTCAAGAGACACTTAAATCACTTCAATCAGACAACCGGAGTAA
* **
61859 AAGTTATATAATATTAAGTGGACCGCCTATTCCCGTTAACCGAAACAAC-AAATCTTTCGGAAGC
1 AAATTATATAATATTAAGCAGACCGCCTATTCCCGTTAACCGAAACAACTAAATCTTT-GGAAGC
*
61923 ATGTTTGATA-CTTAAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATTAA
65 ATGTTTGATACCTT-AAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAA
* * * * *
61987 ACAATCTTTTAATAGACACTTAAATCACCTT-AATCGGATAACCGGAG-AGA
129 ACAACCTTTCAAGAGACACTTAAATCA-CTTCAATCAGACAACCGGAGTA-A
62037 AAATTATATAATATTA
1 AAATTATATAATATTA
62053 GATATATCGT
Statistics
Matches: 164, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
177 11 0.07
178 151 0.92
179 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (178 bp):
AAATTATATAATATTAAGCAGACCGCCTATTCCCGTTAACCGAAACAACTAAATCTTTGGAAGCA
TGTTTGATACCTTAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGAAAC
AACCTTTCAAGAGACACTTAAATCACTTCAATCAGACAACCGGAGTAA
Found at i:62270 original size:22 final size:22
Alignment explanation
Indices: 62242--62291 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
62232 CTTTCACTTC
62242 TTATAATTATTGTTTTTTATAA
1 TTATAATTATTGTTTTTTATAA
62264 TTATAATTATTGTTTTTTATAA
1 TTATAATTATTGTTTTTTATAA
62286 TTATAA
1 TTATAA
62292 CAAGGAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TTATAATTATTGTTTTTTATAA
Found at i:62303 original size:26 final size:26
Alignment explanation
Indices: 62272--62325 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
62262 AATTATAATT
*
62272 ATTGTTTTTTATAATTATAACAAGGA
1 ATTGTTTTTTATAACTATAACAAGGA
62298 ATTGTTTTTTATAACTATAACAAGGA
1 ATTGTTTTTTATAACTATAACAAGGA
62324 AT
1 AT
62326 CATGAGGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (26 bp):
ATTGTTTTTTATAACTATAACAAGGA
Found at i:63137 original size:34 final size:34
Alignment explanation
Indices: 63094--63163 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
63084 GAAGAGGCCT
63094 GCAATATTTGTGACATTAAAACCGAATAAGTATA
1 GCAATATTTGTGACATTAAAACCGAATAAGTATA
63128 GCAATATTTGTGACATTAAAACCGAATAAGTATA
1 GCAATATTTGTGACATTAAAACCGAATAAGTATA
63162 GC
1 GC
63164 TATAGCTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (34 bp):
GCAATATTTGTGACATTAAAACCGAATAAGTATA
Found at i:66868 original size:2 final size:2
Alignment explanation
Indices: 66861--66891 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
66851 ATATTAATTG
66861 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66892 ATTACTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71621 original size:33 final size:31
Alignment explanation
Indices: 71584--71644 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 31
71574 ATGAAAGATA
71584 AATTATTTTAAGAAGCTAAAAAGAGAAAAAAAG
1 AATTATTTTAAGAAGC-AAAAAGA-AAAAAAAG
* *
71617 AATTATTTTAAGGATCAAAAAGAAAAAA
1 AATTATTTTAAGAAGCAAAAAGAAAAAA
71645 GTTCAACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 5 0.19
32 7 0.27
33 14 0.54
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.23
Consensus pattern (31 bp):
AATTATTTTAAGAAGCAAAAAGAAAAAAAAG
Found at i:72562 original size:16 final size:16
Alignment explanation
Indices: 72536--72571 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
72526 TTACATAAAT
72536 AAATCATATAATATATC
1 AAATCATATAATA-ATC
72553 AAAT-ATATAATAATC
1 AAATCATATAATAATC
72568 AAAT
1 AAAT
72572 TTTTTGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 8 0.42
17 4 0.21
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATCATATAATAATC
Found at i:73295 original size:159 final size:160
Alignment explanation
Indices: 72985--73298 Score: 542
Period size: 159 Copynumber: 1.9 Consensus size: 160
72975 TGGAAAACTG
72985 GATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCTACTGTTTA
1 GATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTG--T-TATAATGTCTACTGTTTA
*
73050 AAAACATACAATACCTAAATGATTAACCTATTTTTTATCTAGTATCACAAAAATTAAAGTCTACG
63 AAAACATACAATACCTAAATGATTAACCTATTTTTTATCTAATATCACAAAAATTAAAGTCTACG
73115 CCAATTGGAGAAAATAATTGCATGTGAAAATTT
128 CCAATTGGAGAAAATAATTGCATGTGAAAATTT
*
73148 GATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTG-T-TAATGTCTACTGTTTAAGA
1 GATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTATAATGTCTACTGTTTAAAA
* *
73211 ACATATAATACCTAAATGATTAACCTATTTTTTTATCTAATATCACAAAAATTAAAGTCTACTCC
66 ACATACAATACCTAAATGATTAACCTA-TTTTTTATCTAATATCACAAAAATTAAAGTCTACGCC
73276 AATTGGAGAAAATAATTGCATGT
130 AATTGGAGAAAATAATTGCATGT
73299 CTTAAGCCAT
Statistics
Matches: 146, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
158 44 0.30
159 59 0.40
163 43 0.29
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (160 bp):
GATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTATAATGTCTACTGTTTAAAA
ACATACAATACCTAAATGATTAACCTATTTTTTATCTAATATCACAAAAATTAAAGTCTACGCCA
ATTGGAGAAAATAATTGCATGTGAAAATTT
Found at i:76009 original size:14 final size:14
Alignment explanation
Indices: 75990--76037 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
75980 TTGCACTTTT
75990 TATATCTATA-ATAA
1 TATATCTATATAT-A
*
76004 TATATCTATATATC
1 TATATCTATATATA
*
76018 TATATCTATCTATA
1 TATATCTATATATA
76032 CTATAT
1 -TATAT
76038 TAAAAAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 22 0.76
15 7 0.24
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATCTATATATA
Found at i:76199 original size:62 final size:62
Alignment explanation
Indices: 76128--76249 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 62
76118 AGATTTATAG
*
76128 TTTTACTCAACAAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTA
1 TTTTACTCAACAAAAAACTATATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTA
* *
76190 TTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATTTAATATCTTTATAACTATTT
1 TTTTACTCAACAAAAAACTATATTTTTATTTAATTAAATCTAATATCTTTATAACTATTT
76250 CAGTCTACCA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (62 bp):
TTTTACTCAACAAAAAACTATATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTA
Found at i:76910 original size:13 final size:13
Alignment explanation
Indices: 76873--76910 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
76863 TAATTCTTAA
*
76873 ATTTATTTAATAT
1 ATTTATTTAATCT
76886 ATTTATTTAATCT
1 ATTTATTTAATCT
76899 ATTTATTTAATC
1 ATTTATTTAATC
76911 CACTACAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTATTTAATCT
Found at i:78293 original size:174 final size:174
Alignment explanation
Indices: 77996--78316 Score: 475
Period size: 174 Copynumber: 1.8 Consensus size: 174
77986 ACAAATTATG
* * * *
77996 TAATATTAAGTAGACCGTCTATTTCCGTTAATTGAAACAACTAATTCTTTGGAAGCATTTTTTAT
1 TAATATTAAGTAGACCGTCTATTCCCGTTAATCGAAACAACAAATTCTTTGGAAGCATTTTTGAT
* * * *
78061 ACCTTGAACATTAAATTTAGTTTTCGAGTCCTACATGAAAGTTGTAGATTATGGAACAACCTTTC
66 ACCTTGAACATTAAATTTAGTTTTCGAGACCTACATGAAAGTTGTAGATCACGGAACAACCTTTA
* *
78126 AAGAGATACTTGAATCATCTCAATCATACATCTGAAGCAAAAGT
131 AAGAGACACTTAAATCATCTCAATCATACATCTGAAGCAAAAGT
*
78170 TAATATTAAGTGGACCGTCTATTCCCGTTAATCGAAACAACAAATT-TTTCGGAAGCATTTTTGA
1 TAATATTAAGTAGACCGTCTATTCCCGTTAATCGAAACAACAAATTCTTT-GGAAGCATTTTTGA
* * *
78234 TA-CTTGAAACATTAAATTTAGTTTTTGAGACCTTCATGAAAGTTGTAGATCACGGAACAATCTT
65 TACCTTG-AACATTAAATTTAGTTTTCGAGACCTACATGAAAGTTGTAGATCACGGAACAACCTT
*
78298 TAAATAGACACTTAAATCA
129 TAAAGAGACACTTAAATCA
78317 CCTTAATCGG
Statistics
Matches: 130, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
173 7 0.05
174 123 0.95
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (174 bp):
TAATATTAAGTAGACCGTCTATTCCCGTTAATCGAAACAACAAATTCTTTGGAAGCATTTTTGAT
ACCTTGAACATTAAATTTAGTTTTCGAGACCTACATGAAAGTTGTAGATCACGGAACAACCTTTA
AAGAGACACTTAAATCATCTCAATCATACATCTGAAGCAAAAGT
Found at i:79457 original size:25 final size:25
Alignment explanation
Indices: 79419--79470 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
79409 ATGCAATCTC
79419 TCATAGAAAGACACATTTTCATGTT
1 TCATAGAAAGACACATTTTCATGTT
* *
79444 TCATAGAAATACACCTTTTCATGTT
1 TCATAGAAAGACACATTTTCATGTT
79469 TC
1 TC
79471 TGCAGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (25 bp):
TCATAGAAAGACACATTTTCATGTT
Found at i:83207 original size:25 final size:25
Alignment explanation
Indices: 83169--83216 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
83159 ATGCAATCTC
83169 TCATAGAAAGACACATTTTCATGCT
1 TCATAGAAAGACACATTTTCATGCT
* *
83194 TCATAGAAATACACCTTTTCATG
1 TCATAGAAAGACACATTTTCATG
83217 TTTCTGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.33
Consensus pattern (25 bp):
TCATAGAAAGACACATTTTCATGCT
Found at i:84028 original size:27 final size:29
Alignment explanation
Indices: 83966--84028 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
83956 TACATTTGAC
83966 TTTTATTTAAAACAAGATATATACAATCAA
1 TTTT-TTTAAAACAAGATATATACAATCAA
**
83996 -AATTTTAAAA-AAGATATATACAAT-AA
1 TTTTTTTAAAACAAGATATATACAATCAA
84022 TTTTTTT
1 TTTTTTT
84029 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 2 0.07
27 18 0.64
28 7 0.25
29 1 0.04
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTTTTTAAAACAAGATATATACAATCAA
Done.