Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016433.1 Corchorus capsularis cultivar CVL-1 contig16454, 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: 45600
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:854 original size:8 final size:8
Alignment explanation
Indices: 841--874 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
831 CACCTTCTTG
841 AAAAATTC
1 AAAAATTC
849 AAAAATTC
1 AAAAATTC
*
857 AGAAACTTC
1 A-AAAATTC
866 AAAAATTC
1 AAAAATTC
874 A
1 A
875 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:2594 original size:33 final size:31
Alignment explanation
Indices: 2555--2668 Score: 122
Period size: 33 Copynumber: 3.6 Consensus size: 31
2545 CTAATTGTGA
2555 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAACAATTCTGTTTTGGTTG-A-ATAGCAT
* *
2588 TAAAAACAATTCCGTTTTGGTTGATTATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGA--ATAGCAT
* * *
2621 TGCAAATAATCCTGTTTTGGTTG-ATAGCAT
1 TGAAAACAATTCTGTTTTGGTTGAATAGCAT
* *
2651 TGAAAATAAATCTGTTTT
1 TGAAAACAATTCTGTTTT
2669 TGGTGACGAG
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
30 22 0.32
32 1 0.01
33 46 0.67
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (31 bp):
TGAAAACAATTCTGTTTTGGTTGAATAGCAT
Found at i:9128 original size:16 final size:16
Alignment explanation
Indices: 9109--9140 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9099 CGGTTAAAAC
9109 GTGTTTCGAGTTCATT
1 GTGTTTCGAGTTCATT
9125 GTGTTTCGAGTTCATT
1 GTGTTTCGAGTTCATT
9141 ATTCCATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
GTGTTTCGAGTTCATT
Found at i:15829 original size:34 final size:33
Alignment explanation
Indices: 15768--15833 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
15758 TATAAAAATC
* * *
15768 AAATTAGTGGCTTTTTTTTAAAGAAAAACGCCAA
1 AAATTAGTGGCGTTTTTATAAACAAAAA-GCCAA
**
15802 AAATTAGTGGCGTTTTTATGGACAAAAAGCCA
1 AAATTAGTGGCGTTTTTATAAACAAAAAGCCA
15834 CTATTTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (33 bp):
AAATTAGTGGCGTTTTTATAAACAAAAAGCCAA
Found at i:21533 original size:39 final size:40
Alignment explanation
Indices: 21481--21585 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 40
21471 TGTACATATG
*
21481 TTCATACATGCATTAGT-CAATCATTTGTATATG-TCATACA
1 TTCAT-CATGCATTA-TCCAATCATTTATATATGCTCATACA
* * *
21521 TTCATCATGCATTATCCATTCGTTTATATATGCTCATGCA
1 TTCATCATGCATTATCCAATCATTTATATATGCTCATACA
* * * *
21561 TTGATCATGCCTTATACATTCATTT
1 TTCATCATGCATTATCCAATCATTT
21586 GCACCTAAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.02
39 22 0.40
40 32 0.58
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.43
Consensus pattern (40 bp):
TTCATCATGCATTATCCAATCATTTATATATGCTCATACA
Found at i:23120 original size:20 final size:20
Alignment explanation
Indices: 23074--23130 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
23064 AATTGTTTTT
*
23074 TTAGAAAATGATAAAAAAGAAA
1 TTAGAAAAT-A-ATAAAAGAAA
23096 TTAGAAAATAATAAAA-AAA
1 TTAGAAAATAATAAAAGAAA
*
23115 TGTAGAAAACAATAAA
1 T-TAGAAAATAATAAA
23131 GGATAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.12
20 18 0.56
21 1 0.03
22 9 0.28
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (20 bp):
TTAGAAAATAATAAAAGAAA
Found at i:24842 original size:12 final size:12
Alignment explanation
Indices: 24827--24876 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
24817 TTCATCAAAT
24827 AATTCAAATCAA
1 AATTCAAATCAA
*
24839 AATTCGAATCAA
1 AATTCAAATCAA
* *
24851 AGTTTAAATCAA
1 AATTCAAATCAA
*
24863 AGTTCAAATCAA
1 AATTCAAATCAA
24875 AA
1 AA
24877 GTGAATCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (12 bp):
AATTCAAATCAA
Found at i:26531 original size:47 final size:47
Alignment explanation
Indices: 26424--26558 Score: 243
Period size: 47 Copynumber: 2.9 Consensus size: 47
26414 GAAGTCATCG
26424 AAGTTGACTGGAAACAGGTCACCTTTCAGCAATCATCAAAGTTTATCA
1 AAGTTGACTGGAAACAGGTCACCTTTCAGCAATCATC-AAGTTTATCA
26472 AAGTTGACTGGAAACAGGTCACCTTTCAGCAATCATCAAGTTTATCA
1 AAGTTGACTGGAAACAGGTCACCTTTCAGCAATCATCAAGTTTATCA
* *
26519 AAGTTGACTGGAAACAGGTCATCTTTCAGCAATAATCAAG
1 AAGTTGACTGGAAACAGGTCACCTTTCAGCAATCATCAAG
26559 GTTGACTGGA
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
47 48 0.56
48 37 0.44
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (47 bp):
AAGTTGACTGGAAACAGGTCACCTTTCAGCAATCATCAAGTTTATCA
Found at i:26673 original size:37 final size:38
Alignment explanation
Indices: 26594--26684 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 38
26584 AAATTATCAG
* * *
26594 AGGTTATCATTCAGCAGTTATCAAGATCGACTGGAAAC
1 AGGTCATCTTTCAGCACTTATCAAGATCGACTGGAAAC
* * * *
26632 AGGTCGTGTTTCAGCACTTATCAAG-TTGACTGGAAAT
1 AGGTCATCTTTCAGCACTTATCAAGATCGACTGGAAAC
26669 AGGTCATCTTTCAGCA
1 AGGTCATCTTTCAGCA
26685 GTTTTCGGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
37 24 0.55
38 20 0.45
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (38 bp):
AGGTCATCTTTCAGCACTTATCAAGATCGACTGGAAAC
Found at i:26738 original size:15 final size:15
Alignment explanation
Indices: 26718--26775 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 15
26708 GCATTCCAAT
26718 AACTTTTCAATTTAC
1 AACTTTTCAATTTAC
*
26733 AACTTTTCAGCATTCCAAC
1 AACTTTTCA--ATT--TAC
*
26752 AACTTTTCAATCTAC
1 AACTTTTCAATTTAC
26767 AACTTTTCA
1 AACTTTTCA
26776 GTCTTCAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 20 0.56
17 5 0.14
19 11 0.31
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.40
Consensus pattern (15 bp):
AACTTTTCAATTTAC
Found at i:26746 original size:34 final size:34
Alignment explanation
Indices: 26708--26776 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
26698 CCCAAGGGGG
* *
26708 GCATTCCAATAACTTTTCAATTTACAACTTTTCA
1 GCATTCCAACAACTTTTCAATCTACAACTTTTCA
26742 GCATTCCAACAACTTTTCAATCTACAACTTTTCA
1 GCATTCCAACAACTTTTCAATCTACAACTTTTCA
26776 G
1 G
26777 TCTTCAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (34 bp):
GCATTCCAACAACTTTTCAATCTACAACTTTTCA
Found at i:26868 original size:19 final size:19
Alignment explanation
Indices: 26844--26892 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
26834 GAATGGAGAA
26844 CATTCCAACAATTCTTCAG
1 CATTCCAACAATTCTTCAG
26863 CATTCCAACAATTCTTCAG
1 CATTCCAACAATTCTTCAG
26882 CATTCCAACAA
1 CATTCCAACAA
26893 CTTTACAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.29
Consensus pattern (19 bp):
CATTCCAACAATTCTTCAG
Found at i:26952 original size:15 final size:15
Alignment explanation
Indices: 26932--26960 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26922 GAGCATTATT
26932 AGCAGTTTTCAGTTC
1 AGCAGTTTTCAGTTC
26947 AGCAGTTTTCAGTT
1 AGCAGTTTTCAGTT
26961 GCTCCGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (15 bp):
AGCAGTTTTCAGTTC
Found at i:27073 original size:8 final size:8
Alignment explanation
Indices: 27060--27168 Score: 71
Period size: 8 Copynumber: 14.9 Consensus size: 8
27050 ATGTTTATAT
27060 TTCAATTC
1 TTCAATTC
*
27068 TTCAATGC
1 TTCAATTC
27076 TTCAA-T-
1 TTCAATTC
27082 TTCAA--C
1 TTCAATTC
* *
27088 TTTAGTTC
1 TTCAATTC
27096 TTCAA-T-
1 TTCAATTC
*
27102 TTCAATCC
1 TTCAATTC
27110 TTCAATGT-
1 TTCAAT-TC
27118 TTCAA-T-
1 TTCAATTC
27124 TTCAATTC
1 TTCAATTC
27132 TTCAATGT-
1 TTCAAT-TC
27140 TTCAA-T-
1 TTCAATTC
27146 TTCAATTC
1 TTCAATTC
*
27154 TTCAATGC
1 TTCAATTC
27162 TTCAATT
1 TTCAATT
27169 TCAACTTTAG
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
6 25 0.31
7 3 0.04
8 51 0.64
9 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.48
Consensus pattern (8 bp):
TTCAATTC
Found at i:27083 original size:22 final size:22
Alignment explanation
Indices: 26984--27199 Score: 212
Period size: 22 Copynumber: 10.0 Consensus size: 22
26974 GGCATTCCAA
* *
26984 CAATCCTTCAATTCCAATTCTT
1 CAATGCTTCAATTTCAATTCTT
* *
27006 GAATACTTCAATTTCAA--CTT
1 CAATGCTTCAATTTCAATTCTT
* * **
27026 CAATTCTTCAAATTCAAACCTT
1 CAATGCTTCAATTTCAATTCTT
*
27048 CAATG-TTTATATTTCAATTCTT
1 CAATGCTTCA-ATTTCAATTCTT
27070 CAATGCTTCAATTTCAA--CTT
1 CAATGCTTCAATTTCAATTCTT
* * * *
27090 TAGTTCTTCAATTTCAATCCTT
1 CAATGCTTCAATTTCAATTCTT
*
27112 CAATGTTTCAATTTCAATTCTT
1 CAATGCTTCAATTTCAATTCTT
*
27134 CAATGTTTCAATTTCAATTCTT
1 CAATGCTTCAATTTCAATTCTT
27156 CAATGCTTCAATTTCAA--CTT
1 CAATGCTTCAATTTCAATTCTT
* *
27176 TAGTGCTTCAATTTCAAATTCTT
1 CAATGCTTCAATTTC-AATTCTT
27199 C
1 C
27200 GAATTCAATC
Statistics
Matches: 161, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
20 50 0.31
21 5 0.03
22 100 0.62
23 6 0.04
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (22 bp):
CAATGCTTCAATTTCAATTCTT
Found at i:27112 original size:14 final size:14
Alignment explanation
Indices: 27058--27359 Score: 108
Period size: 14 Copynumber: 20.3 Consensus size: 14
27048 CAATGTTTAT
27058 ATTTCAATTCTTCA
1 ATTTCAATTCTTCA
27072 ATGCTTCAA-T-TTCA
1 AT--TTCAATTCTTCA
*
27086 ACTTT-AGTTCTTCA
1 A-TTTCAATTCTTCA
*
27100 ATTTCAATCCTTCA
1 ATTTCAATTCTTCA
27114 ATGTTTCAA-T-TTCA
1 A--TTTCAATTCTTCA
27128 ATTCTTCAATGT-TTCA
1 A-T-TTCAAT-TCTTCA
27144 ATTTCAATTCTTCA
1 ATTTCAATTCTTCA
27158 ATGCTTCAA-T-TTCA
1 AT--TTCAATTCTTCA
* *
27172 ACTTT-AGTGCTTCA
1 A-TTTCAATTCTTCA
27186 ATTTCAAATTCTTCGA
1 ATTTC-AATTCTTC-A
* *
27202 A-TTCAATCCTTGA
1 ATTTCAATTCTTCA
*
27215 ATTCCAATTCTTCA
1 ATTTCAATTCTTCA
27229 ATTTTGCAAATTCAAATCCTCCA
1 A-TTT-C-AATTC---T--T-CA
27252 ATGTTTCAA-T-TTCA
1 A--TTTCAATTCTTCA
*
27266 ATATCTCAATGCTTCA
1 AT-T-TCAATTCTTCA
27282 ATTTCAATTCTTCAA
1 ATTTCAATTCTTC-A
* * *
27297 ATTCCAAAT-GTCA
1 ATTTCAATTCTTCA
*
27310 ATGCTTCAATTTTTCA
1 AT--TTCAATTCTTCA
*
27326 ATTTCAATTCCTCA
1 ATTTCAATTCTTCA
*
27340 ATCATTCAATGCTTCA
1 AT--TTCAATTCTTCA
27356 ATTT
1 ATTT
27360 ACTTCAATGA
Statistics
Matches: 219, Mismatches: 28, Indels: 82
0.67 0.09 0.25
Matches are distributed among these distances:
12 3 0.01
13 19 0.09
14 100 0.46
15 31 0.14
16 48 0.22
17 6 0.03
20 1 0.00
21 1 0.00
22 3 0.01
23 4 0.02
24 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (14 bp):
ATTTCAATTCTTCA
Found at i:27135 original size:86 final size:84
Alignment explanation
Indices: 27011--27192 Score: 278
Period size: 86 Copynumber: 2.1 Consensus size: 84
27001 TTCTTGAATA
27011 CTTCAATTTCAACTTCAATTCTTCAAATTCAAACCTTCAATGTTT-ATATTTCAATTCTTCAATG
1 CTTCAATTTCAACTTCAATTCTTCAAATTCAAACCTTCAATGTTTCA-ATTTCAATTCTTCAATG
*
27075 CTTCAATTTCAACTTTAGTT
65 CTTCAATTTCAACTTTAGTG
* **
27095 CTTCAATTTCAATCCTTCAATGT-TTCAATTTCAATTCTTCAATGTTTCAATTTCAATTCTTCAA
1 CTTCAATTTCAA--CTTCAAT-TCTTCAAATTCAAACCTTCAATGTTTCAATTTCAATTCTTCAA
27159 TGCTTCAATTTCAACTTTAGTG
63 TGCTTCAATTTCAACTTTAGTG
27181 CTTCAATTTCAA
1 CTTCAATTTCAA
27193 ATTCTTCGAA
Statistics
Matches: 90, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
84 12 0.13
86 76 0.84
87 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (84 bp):
CTTCAATTTCAACTTCAATTCTTCAAATTCAAACCTTCAATGTTTCAATTTCAATTCTTCAATGC
TTCAATTTCAACTTTAGTG
Found at i:27332 original size:22 final size:22
Alignment explanation
Indices: 27214--27368 Score: 100
Period size: 22 Copynumber: 6.8 Consensus size: 22
27204 TCAATCCTTG
*
27214 AATTCCAATTCTTCAAT-TTTGC
1 AATTTCAATTCTTCAATGTTT-C
* * *
27236 AAATTCAAATCCTCCAATGTTTC
1 AATTTC-AATTCTTCAATGTTTC
*
27259 AATTTCAATATC-TCAATGCTTC
1 AATTTCAAT-TCTTCAATGTTTC
* *
27281 AATTTCAATTCTTCAA-ATTCC
1 AATTTCAATTCTTCAATGTTTC
* * *
27302 AAATGTCAATGCTTCAATTTTTC
1 -AATTTCAATTCTTCAATGTTTC
* **
27325 AATTTCAATTCCTCAATCATTC
1 AATTTCAATTCTTCAATGTTTC
27347 AATGCTTCAATTTACTTCAATG
1 AAT--TTCAA-TT-CTTCAATG
27369 ATCCAGGGTG
Statistics
Matches: 101, Mismatches: 22, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
21 4 0.04
22 62 0.61
23 19 0.19
24 8 0.08
25 2 0.02
26 6 0.06
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (22 bp):
AATTTCAATTCTTCAATGTTTC
Found at i:27341 original size:30 final size:29
Alignment explanation
Indices: 27223--27359 Score: 77
Period size: 30 Copynumber: 4.6 Consensus size: 29
27213 GAATTCCAAT
* *
27223 TCTTCAATTTTGCAAATTCAAATCCTCCAA
1 TCTTCAATTTTTCAATTTCAAATCCT-CAA
* *
27253 TGTTTCAA--TTTCAATATCTC-AATGCTTCAA
1 T-CTTCAATTTTTCAAT-T-TCAAAT-CCTCAA
* * *
27283 T-TTCAATTCTTCAAATTCCAAAT-GTCAA
1 TCTTCAATTTTTC-AATTTCAAATCCTCAA
*
27311 TGCTTCAATTTTTCAATTTCAATTCCTCAA
1 T-CTTCAATTTTTCAATTTCAAATCCTCAA
**
27341 TCATTCAATGCTTCAATTT
1 TC-TTCAATTTTTCAATTT
27360 ACTTCAATGA
Statistics
Matches: 82, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
28 10 0.12
29 15 0.18
30 45 0.55
31 12 0.15
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (29 bp):
TCTTCAATTTTTCAATTTCAAATCCTCAA
Found at i:31031 original size:14 final size:15
Alignment explanation
Indices: 31012--31043 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
31002 TTGGGTTTGT
31012 CTTTTATAT-GTGGG
1 CTTTTATATAGTGGG
31026 CTTTTATATAGTGGG
1 CTTTTATATAGTGGG
31041 CTT
1 CTT
31044 AGGGTTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.16, C:0.09, G:0.25, T:0.50
Consensus pattern (15 bp):
CTTTTATATAGTGGG
Found at i:32389 original size:17 final size:17
Alignment explanation
Indices: 32367--32419 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
32357 ATCACCACCC
32367 AGATCACTAGTGATCTT
1 AGATCACTAGTGATCTT
* * **
32384 AGATCACCATTGATCCA
1 AGATCACTAGTGATCTT
* *
32401 AGATCACTGGTAATCTT
1 AGATCACTAGTGATCTT
32418 AG
1 AG
32420 TCAATTCCAG
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (17 bp):
AGATCACTAGTGATCTT
Found at i:32791 original size:3 final size:3
Alignment explanation
Indices: 32783--32851 Score: 95
Period size: 3 Copynumber: 22.3 Consensus size: 3
32773 GATTTGTATG
32783 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
32828 TATA TGTA TTA TTA TCA TTA TTA T
1 T-TA T-TA TTA TTA TTA TTA TTA T
32852 ATATATCTAC
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.03
3 50 0.83
4 8 0.13
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:32933 original size:2 final size:2
Alignment explanation
Indices: 32922--32957 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
32912 ATATCATTAT
32922 TA TA -A TA TA 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 TA TA TA TA TA T
32958 CTACTACCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32949 original size:34 final size:33
Alignment explanation
Indices: 32884--32949 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 33
32874 GTTATTGTTG
*
32884 TTATTATAATATAATATATCTACGTATTATATCA
1 TTATTATAATATAATATATATAC-TATTATATCA
32918 TTATTATAATATATATATATATA-TATATATAT
1 TTATTATAATATA-ATATATATACTAT-TATAT
32950 ATATATATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 3 0.10
34 18 0.62
35 8 0.28
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (33 bp):
TTATTATAATATAATATATATACTATTATATCA
Found at i:34498 original size:17 final size:17
Alignment explanation
Indices: 34476--34508 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
34466 TGTAGAAGTC
34476 GACAATCTTTTGTTTTT
1 GACAATCTTTTGTTTTT
34493 GACAATCTTTTGTTTT
1 GACAATCTTTTGTTTT
34509 GTATGAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (17 bp):
GACAATCTTTTGTTTTT
Found at i:43094 original size:39 final size:39
Alignment explanation
Indices: 42932--43107 Score: 166
Period size: 40 Copynumber: 4.5 Consensus size: 39
42922 CTTTTTGACA
* *
42932 GGATCTTTCCCTAAATTGAAAAACTTTGAAAAAAAACTGGATG
1 GGATCTTTCCCTAAATTG-AAAACCTTG---AAAAACTTGATG
* * *
42975 AGATCTTTCCCT--A---AAAACTTTG-AAAACTTGGTG
1 GGATCTTTCCCTAAATTGAAAACCTTGAAAAACTTGATG
* * *
43008 GGATCTTTCCCTAAATCGAAAACTTTTAAAAGACTTGATG
1 GGATCTTTCCCTAAATTGAAAACCTTGAAAA-ACTTGATG
* *
43048 GGATCTTTCCCTAAATTGAAAACCTTGGATAACTTGATG
1 GGATCTTTCCCTAAATTGAAAACCTTGAAAAACTTGATG
*
43087 GGTTCTTTCCCTAAATTGAAA
1 GGATCTTTCCCTAAATTGAAA
43108 GCTTTGAGCA
Statistics
Matches: 114, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
33 20 0.18
35 1 0.01
37 9 0.08
38 8 0.07
39 31 0.27
40 33 0.29
41 1 0.01
43 11 0.10
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (39 bp):
GGATCTTTCCCTAAATTGAAAACCTTGAAAAACTTGATG
Done.