Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014961.1 Corchorus capsularis cultivar CVL-1 contig14982, 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: 16139
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1289 original size:18 final size:18
Alignment explanation
Indices: 1260--1316 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
1250 CGAAAAAATG
*
1260 AAAGAAAAAAAGAAAGAAGA
1 AAAGAAAAAGA-AAAGAA-A
1280 AAAGAAAAAGAAAAGAAA
1 AAAGAAAAAGAAAAGAAA
1298 AAAGAGAAGGAAGAAAAGA
1 AAAGA-AA--AAGAAAAGA
1317 GGCTTTAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 10 0.30
21 9 0.27
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGAAAAGAAA
Found at i:1292 original size:11 final size:11
Alignment explanation
Indices: 1267--1299 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
1257 ATGAAAGAAA
1267 AAAAGAAAGAAG
1 AAAAGAAA-AAG
1279 AAAAGAAAAAG
1 AAAAGAAAAAG
1290 AAAAGAAAAA
1 AAAAGAAAAA
1300 AGAGAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:1299 original size:12 final size:12
Alignment explanation
Indices: 1254--1316 Score: 58
Period size: 12 Copynumber: 5.1 Consensus size: 12
1244 AGTGCACGAA
1254 AAAATGAAAGAAA-
1 AAAA-GAAA-AAAG
*
1267 AAAAGAAAGAAG
1 AAAAGAAAAAAG
1279 AAAAG-AAAAAG
1 AAAAGAAAAAAG
1290 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
1302 AGAAGGAAGAAAAG
1 A-AAAGAA-AAAAG
1316 A
1 A
1317 GGCTTTAGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
11 12 0.28
12 16 0.37
13 9 0.21
14 6 0.14
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:1626 original size:26 final size:26
Alignment explanation
Indices: 1597--1683 Score: 65
Period size: 26 Copynumber: 3.4 Consensus size: 26
1587 ATAAGATTGC
1597 ATTCCATTTTTGAGTTCAATATCAAA
1 ATTCCATTTTTGAGTTCAATATCAAA
* * ***
1623 ATTCGATTTTT-A-TAAT-AAGAT-TGC
1 ATTCCATTTTTGAGT--TCAATATCAAA
*
1647 ATTCCATTTGTGAGTTCAATATCAAA
1 ATTCCATTTTTGAGTTCAATATCAAA
*
1673 ATTCGATTTTT
1 ATTCCATTTTT
1684 ATAATAAGAT
Statistics
Matches: 42, Mismatches: 13, Indels: 12
0.63 0.19 0.18
Matches are distributed among these distances:
24 11 0.26
25 10 0.24
26 21 0.50
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (26 bp):
ATTCCATTTTTGAGTTCAATATCAAA
Found at i:1639 original size:50 final size:50
Alignment explanation
Indices: 1580--1775 Score: 331
Period size: 50 Copynumber: 3.9 Consensus size: 50
1570 AACCAAGAAG
*
1580 TTTTATAATAAGATTGCATTCCATTTTTGAGTTCAATATCAAAATTCGAT
1 TTTTATAATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGAT
1630 TTTTATAATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGAT
1 TTTTATAATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGAT
* *
1680 TTTTATAATAAGATTGCATTCCATTTGTGAGTTCAATATCAAGACTCGAT
1 TTTTATAATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGAT
* *
1730 TTTCAAAATAAGATTGCATTCCATTTGTGAG-TCTAATATCAAAATT
1 TTTTATAATAAGATTGCATTCCATTTGTGAGTTC-AATATCAAAATT
1776 TGCTATTCAA
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
49 2 0.01
50 136 0.99
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (50 bp):
TTTTATAATAAGATTGCATTCCATTTGTGAGTTCAATATCAAAATTCGAT
Found at i:2249 original size:8 final size:8
Alignment explanation
Indices: 2236--2269 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
2226 AGGGTGATCT
2236 TTCTTCAA
1 TTCTTCAA
2244 TTCTTCAA
1 TTCTTCAA
*
2252 TTATTCAA
1 TTCTTCAA
*
2260 TACTTCAA
1 TTCTTCAA
2268 TT
1 TT
2270 TACTTCAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (8 bp):
TTCTTCAA
Found at i:2293 original size:58 final size:58
Alignment explanation
Indices: 2226--2417 Score: 294
Period size: 58 Copynumber: 3.3 Consensus size: 58
2216 TATTTTTCAA
* *
2226 AGGGTGATCTTTCTTCAATTCTTCAATTATTCAATACTTCAATTTACTTCAAAGATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATCATTCAATACTTCAATTTACTTCAATGATCC
* * *
2284 AGGGTGATCTCTCTTCAATTCCTCAATCATTCAATCCTTCAATTTACTTCAATGATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATCATTCAATACTTCAATTTACTTCAATGATCC
* * **
2342 AGGGTGGTCTTTCTTCAATTCTTCAATCGTTCAATGTTTCAATTTACTTCAATGATCC
1 AGGGTGATCTTTCTTCAATTCTTCAATCATTCAATACTTCAATTTACTTCAATGATCC
*
2400 AGGGTGGTCTTTCTTCAA
1 AGGGTGATCTTTCTTCAA
2418 ATTCATCGAT
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 123 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (58 bp):
AGGGTGATCTTTCTTCAATTCTTCAATCATTCAATACTTCAATTTACTTCAATGATCC
Found at i:2358 original size:34 final size:34
Alignment explanation
Indices: 2320--2417 Score: 92
Period size: 34 Copynumber: 3.2 Consensus size: 34
2310 TCATTCAATC
2320 CTTCAATTTACTTCAATGATCCAGGGTGGTCTTT
1 CTTCAATTTACTTCAATGATCCAGGGTGGTCTTT
* *
2354 CTTCAA-TT-CTTCAATCG-TTCA--AT-G----T
1 CTTCAATTTACTTCAAT-GATCCAGGGTGGTCTTT
2379 -TTCAATTTACTTCAATGATCCAGGGTGGTCTTT
1 CTTCAATTTACTTCAATGATCCAGGGTGGTCTTT
2412 CTTCAA
1 CTTCAA
2418 ATTCATCGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 24
0.63 0.05 0.32
Matches are distributed among these distances:
24 5 0.10
25 4 0.08
26 10 0.21
28 1 0.02
29 2 0.04
30 1 0.02
32 10 0.21
33 4 0.08
34 11 0.23
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (34 bp):
CTTCAATTTACTTCAATGATCCAGGGTGGTCTTT
Found at i:2448 original size:14 final size:14
Alignment explanation
Indices: 2429--2624 Score: 66
Period size: 14 Copynumber: 14.3 Consensus size: 14
2419 TTCATCGATG
2429 CTTCAATTTCAATT
1 CTTCAATTTCAATT
*
2443 CTTCAAATTCAA--
1 CTTCAATTTCAATT
*
2455 ATTCAATTCTTCAATT
1 CTTCAA-T-TTCAATT
*
2471 C--CAACTTCAATGT
1 CTTCAATTTCAAT-T
**
2484 -TTCAATTTCGTTT
1 CTTCAATTTCAATT
*
2497 CTTCAAATTCAA-T
1 CTTCAATTTCAATT
2510 C--C---TTCAATGT
1 CTTCAATTTCAAT-T
2520 -TTCAATTTCAATT
1 CTTCAATTTCAATT
*
2533 CCTCAATGCTTCAA--
1 CTTCAAT--TTCAATT
* *
2547 ATTCAATTTCAATC
1 CTTCAATTTCAATT
*
2561 CATCAATGTTTCAATT
1 CTTCAA--TTTCAATT
2577 CTTCAACGTTTCAA-T
1 CTTCAA--TTTCAATT
2592 -TTCAATATTTCAATGT
1 CTTC-A-ATTTCAAT-T
2608 -TTCAATTTCAATT
1 CTTCAATTTCAATT
2621 CTTC
1 CTTC
2625 CAGTTCTTCC
Statistics
Matches: 136, Mismatches: 19, Indels: 54
0.65 0.09 0.26
Matches are distributed among these distances:
8 5 0.04
10 1 0.01
11 2 0.01
12 16 0.12
13 6 0.04
14 74 0.54
15 3 0.02
16 29 0.21
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (14 bp):
CTTCAATTTCAATT
Found at i:2459 original size:20 final size:19
Alignment explanation
Indices: 2430--2490 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
2420 TCATCGATGC
*
2430 TTCAATTTCAATTCTTCAAA
1 TTCAAATTCAATTCTTC-AA
2450 TTCAAATTCAATTCTTCAA
1 TTCAAATTCAATTCTTCAA
*
2469 TTCCAACTTCAATGT-TTCAA
1 TT-CAAATTCAAT-TCTTCAA
2489 TT
1 TT
2491 TCGTTTCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.11
20 32 0.86
21 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (19 bp):
TTCAAATTCAATTCTTCAA
Found at i:2523 original size:22 final size:22
Alignment explanation
Indices: 2498--2663 Score: 126
Period size: 22 Copynumber: 7.5 Consensus size: 22
2488 ATTTCGTTTC
*
2498 TTCAAATTCAATCCTTCAATGT
1 TTCAATTTCAATCCTTCAATGT
*
2520 TTCAATTTCAATTCC-TCAATGC
1 TTCAATTTCAA-TCCTTCAATGT
* **
2542 TTCAAATTCAAT--TTCAATCC
1 TTCAATTTCAATCCTTCAATGT
* * *
2562 ATCAATGTTTCAATTCTTCAACGT
1 TTCAA--TTTCAATCCTTCAATGT
**
2586 TTCAATTTCAATATTTCAATGT
1 TTCAATTTCAATCCTTCAATGT
* *
2608 TTCAATTTCAATTCTTCCA-GTT
1 TTCAATTTCAATCCTTCAATG-T
*
2630 CTTCCAA-TTCGATCCTTCAATGT
1 -TT-CAATTTCAATCCTTCAATGT
2653 TTCAATTTCAA
1 TTCAATTTCAA
2664 CATTTCATTG
Statistics
Matches: 113, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
20 10 0.09
21 5 0.04
22 69 0.61
23 16 0.14
24 13 0.12
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.43
Consensus pattern (22 bp):
TTCAATTTCAATCCTTCAATGT
Found at i:2529 original size:28 final size:27
Alignment explanation
Indices: 2498--2576 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
2488 ATTTCGTTTC
2498 TTCAAATTCAATCCTTCAATGTTTCAAT
1 TTCAAATTCAATCC-TCAATGTTTCAAT
* *
2526 TTC-AA-T---TCCTCAATGCTTCAAA
1 TTCAAATTCAATCCTCAATGTTTCAAT
*
2548 TTCAATTTCAATCCATCAATGTTTCAAT
1 TTCAAATTCAATCC-TCAATGTTTCAAT
2576 T
1 T
2577 CTTCAACGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
22 14 0.35
23 4 0.10
24 1 0.03
26 1 0.03
27 5 0.12
28 15 0.38
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (27 bp):
TTCAAATTCAATCCTCAATGTTTCAAT
Found at i:2574 original size:8 final size:8
Alignment explanation
Indices: 2563--2613 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
2553 TTTCAATCCA
2563 TCAATGTT
1 TCAATGTT
2571 TCAAT-TCT
1 TCAATGT-T
*
2579 TCAACGTT
1 TCAATGTT
2587 TCAA--TT
1 TCAATGTT
*
2593 TCAATATT
1 TCAATGTT
2601 TCAATGTT
1 TCAATGTT
2609 TCAAT
1 TCAAT
2614 TTCAATTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 6 0.16
7 1 0.03
8 29 0.78
9 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (8 bp):
TCAATGTT
Found at i:2777 original size:8 final size:8
Alignment explanation
Indices: 2764--3178 Score: 80
Period size: 8 Copynumber: 55.2 Consensus size: 8
2754 AGGGTGATCT
2764 TTCTTCAA
1 TTCTTCAA
2772 TTCTTCAA
1 TTCTTCAA
*
2780 TTATTCAA
1 TTCTTCAA
* *
2788 TGCTTTAA
1 TTCTTCAA
*
2796 TTCCTCAA
1 TTCTTCAA
*
2804 TTATTCAA
1 TTCTTCAA
* *
2812 TGCCTCAA
1 TTCTTCAA
2820 -T-TTCAA
1 TTCTTCAA
* **
2826 ATCTTTGA
1 TTCTTCAA
**
2834 CGCTTCAA
1 TTCTTCAA
*
2842 -T-TTGAA
1 TTCTTCAA
2848 TT-TTCAA
1 TTCTTCAA
2855 TTCTTCAA
1 TTCTTCAA
*
2863 TGCTT-AA
1 TTCTTCAA
* *
2870 AT-TTCAG
1 TTCTTCAA
2877 TTCTTCAAA
1 TTCTTC-AA
2886 TTC--CAA
1 TTCTTCAA
* *
2892 AT-GTCAA
1 TTCTTCAA
*
2899 TGCTTCAA
1 TTCTTCAA
2907 -T-TTCAA
1 TTCTTCAA
2913 TTCTTCAA
1 TTCTTCAA
**
2921 CGCTTCAA
1 TTCTTCAA
*
2929 -T-TTCAG
1 TTCTTCAA
2935 TTCTTCAAA
1 TTCTTC-AA
2944 TTC--CAA
1 TTCTTCAA
* *
2950 AT-GTCAA
1 TTCTTCAA
*
2957 TGCTTCAA
1 TTCTTCAA
2965 -T-TTCAA
1 TTCTTCAA
2971 TTCTTCAA
1 TTCTTCAA
* *
2979 TACTTCGA
1 TTCTTCAA
*
2987 TTTTTCAA
1 TTCTTCAA
*
2995 TGCTTCAA
1 TTCTTCAA
3003 -T-TTCAA
1 TTCTTCAA
3009 TAT-TTCAA
1 T-TCTTCAA
* *
3017 TGCTTTAA
1 TTCTTCAA
*
3025 ATC--CAA
1 TTCTTCAA
3031 TTCTTCAAA
1 TTCTTC-AA
3040 TTC--CAA
1 TTCTTCAA
* *
3046 AT-ATCAA
1 TTCTTCAA
3053 TGT-TTCAA
1 T-TCTTCAA
3061 -T-TTCAA
1 TTCTTCAA
*
3067 TAT-GTCAA
1 T-TCTTCAA
*
3075 TGCTTCAA
1 TTCTTCAA
3083 -T-TTCAA
1 TTCTTCAA
*
3089 TTCTTCCA
1 TTCTTCAA
*
3097 TGCTTCAA
1 TTCTTCAA
3105 -T-TTCAA
1 TTCTTCAA
3111 TTCTTCGAA
1 TTCTTC-AA
*
3120 TTCAATCTCGA
1 TTC--T-TCAA
3131 TGT-TTCAA
1 T-TCTTCAA
3139 TTC--CAA
1 TTCTTCAA
3145 TTCTTCAA
1 TTCTTCAA
*
3153 TACTTCAA
1 TTCTTCAA
3161 -TCATTCAA
1 TTC-TTCAA
*
3169 TTCCTCAA
1 TTCTTCAA
3177 TT
1 TT
3179 TATTTTCAAA
Statistics
Matches: 287, Mismatches: 74, Indels: 92
0.63 0.16 0.20
Matches are distributed among these distances:
6 64 0.22
7 31 0.11
8 165 0.57
9 21 0.07
11 3 0.01
12 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.43
Consensus pattern (8 bp):
TTCTTCAA
Found at i:2920 original size:22 final size:22
Alignment explanation
Indices: 2895--3116 Score: 104
Period size: 22 Copynumber: 10.1 Consensus size: 22
2885 ATTCCAAATG
2895 TCAATGCTTCAATTTCAATTCT
1 TCAATGCTTCAATTTCAATTCT
* *
2917 TCAACGCTTCAATTTCAGTTCT
1 TCAATGCTTCAATTTCAATTCT
* * *
2939 TCAAAT--TCCAAATGTCAATGCT
1 TC-AATGCTTC-AATTTCAATTCT
*
2961 TCAAT--TTCAATTCTTCAATACT
1 TCAATGCTTCAA-T-TTCAATTCT
* **
2983 TCGATTTTTCAATGCTTCAA-T-T
1 TCAATGCTTCAAT--TTCAATTCT
** * *
3005 TCAATATTTCAATGCTTTAAATC-
1 TCAATGCTTCAAT--TTCAATTCT
* * * *
3028 -CAATTCTTCAAATTCCAAAT-A
1 TCAATGCTTC-AATTTCAATTCT
* *
3049 TCAATGTTTCAATTTCAATAT-G
1 TCAATGCTTCAATTTCAAT-TCT
3071 TCAATGCTTCAATTTCAATTCT
1 TCAATGCTTCAATTTCAATTCT
*
3093 TCCATGCTTCAATTTCAATTCT
1 TCAATGCTTCAATTTCAATTCT
3115 TC
1 TC
3117 GAATTCAATC
Statistics
Matches: 159, Mismatches: 27, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.01
21 21 0.13
22 118 0.74
23 7 0.04
24 11 0.07
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (22 bp):
TCAATGCTTCAATTTCAATTCT
Found at i:2931 original size:58 final size:57
Alignment explanation
Indices: 2849--3178 Score: 319
Period size: 58 Copynumber: 5.7 Consensus size: 57
2839 CAATTTGAAT
* *
2849 TTTCAATTCTTCAATGCTTAAATTTCAGTTCTTCAAATTCCAAATGTCAATGCTTCAA
1 TTTCAATTCTTCAATGCTTCAATTTCAATTCTTC-AATTCCAAATGTCAATGCTTCAA
* *
2907 TTTCAATTCTTCAACGCTTCAATTTCAGTTCTTCAAATTCCAAATGTCAATGCTTCAA
1 TTTCAATTCTTCAATGCTTCAATTTCAATTCTTC-AATTCCAAATGTCAATGCTTCAA
* * * * * *
2965 TTTCAATTCTTCAATACTTCGATTTTTCAATGCTTCAATTTCAATATTTCAATGCTTTAA
1 TTTCAATTCTTCAATGCTTC-A-ATTTCAATTCTTCAATTCCAA-ATGTCAATGCTTCAA
* * * * *
3025 ATCCAATTCTTCAAAT--TCCAAATATCAATGT-TTCAATTTCAATATGTCAATGCTTCAA
1 TTTCAATTCTTC-AATGCTTC-AATTTCAAT-TCTTCAATTCCAA-ATGTCAATGCTTCAA
* * * *
3083 TTTCAATTCTTCCATGCTTCAATTTCAATTCTTCGAATT-C-AATCTCGATGTTTCAA
1 TTTCAATTCTTCAATGCTTCAATTTCAATTCTTC-AATTCCAAATGTCAATGCTTCAA
* * *
3139 TTCCAATTCTTCAATACTTCAATCATTCAATTCCTCAATT
1 TTTCAATTCTTCAATGCTTCAAT--TTCAATTCTTCAATT
3179 TATTTTCAAA
Statistics
Matches: 230, Mismatches: 31, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
56 32 0.14
57 8 0.03
58 137 0.60
59 17 0.07
60 33 0.14
61 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.42
Consensus pattern (57 bp):
TTTCAATTCTTCAATGCTTCAATTTCAATTCTTCAATTCCAAATGTCAATGCTTCAA
Found at i:3075 original size:96 final size:96
Alignment explanation
Indices: 2895--3085 Score: 260
Period size: 96 Copynumber: 2.0 Consensus size: 96
2885 ATTCCAAATG
* * * *
2895 TCAATGCTTCAATTTCAATTCTTCAACGCTTCAATTTCAGTTCTTCAAATTCCAAATGTCAATGC
1 TCAATGCTTCAATTTCAATTCTTCAACGCTTCAAATCCAATTCTTCAAATTCCAAATATCAATGC
* *
2960 TTCAATTTCAATTCTTCAATACTTCGATTTT
66 TTCAATTTCAATTCGTCAATACTTCAATTTT
* *
2991 TCAATGCTTCAATTTCAATAT-TTCAATGCTTTAAATCCAATTCTTCAAATTCCAAATATCAATG
1 TCAATGCTTCAATTTCAAT-TCTTCAACGCTTCAAATCCAATTCTTCAAATTCCAAATATCAATG
* *
3055 TTTCAATTTCAATAT-GTCAATGCTTCAATTT
65 CTTCAATTTCAAT-TCGTCAATACTTCAATTT
3086 CAATTCTTCC
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
96 81 0.98
97 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (96 bp):
TCAATGCTTCAATTTCAATTCTTCAACGCTTCAAATCCAATTCTTCAAATTCCAAATATCAATGC
TTCAATTTCAATTCGTCAATACTTCAATTTT
Found at i:3528 original size:3 final size:3
Alignment explanation
Indices: 3520--3546 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3510 TTCATTAGAT
3520 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3547 CAAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5074 original size:20 final size:20
Alignment explanation
Indices: 5030--5071 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
5020 CTATCGCATA
5030 TTGGGTATTCATTTCTTACT
1 TTGGGTATTCATTTCTTACT
5050 TTGGGTATACTCA-TTCTTACT
1 TTGGGTAT--TCATTTCTTACT
5071 T
1 T
5072 GGGCTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 9 0.45
22 3 0.15
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (20 bp):
TTGGGTATTCATTTCTTACT
Found at i:5887 original size:52 final size:51
Alignment explanation
Indices: 5774--5898 Score: 171
Period size: 52 Copynumber: 2.4 Consensus size: 51
5764 GAATTTCACC
*
5774 TCAAGTTTTCAAACCATTCAATTTAGGTCTTTTCAAATTGGGAAAGTTCCA
1 TCAAGTTTTCAAACCATTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCA
* ***
5825 TTAAGTTTTTCAAAGTGTTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCCA
1 TCAAG-TTTTCAAACCATTCAATTTAGGTCTTTTCAAAGTGGGAAAGTT-CCA
5878 TCAAGTTTTCAAGA-CATTCAA
1 TCAAGTTTTCAA-ACCATTCAA
5899 ACACAATTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
51 4 0.06
52 51 0.81
53 8 0.13
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (51 bp):
TCAAGTTTTCAAACCATTCAATTTAGGTCTTTTCAAAGTGGGAAAGTTCCA
Found at i:9537 original size:11 final size:11
Alignment explanation
Indices: 9521--9548 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
9511 ATTTCAACTG
9521 AAGATTATCTA
1 AAGATTATCTA
9532 AAGATTATCTA
1 AAGATTATCTA
9543 AAGATT
1 AAGATT
9549 TAAGTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (11 bp):
AAGATTATCTA
Found at i:9885 original size:40 final size:38
Alignment explanation
Indices: 9826--9915 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 38
9816 CTTCTGTTTA
**
9826 AGAAGTTGTCACTTTGGTAAATTAAAATTACCTTCGACACC
1 AGAAGTTGTCACTCCGGTAAATTAAAATTA-C-T-GACACC
*
9867 AGAAG-TGTCACTCCGGTAAATTATAATTACTGACACC
1 AGAAGTTGTCACTCCGGTAAATTAAAATTACTGACACC
9904 AGAAGTTGTCAC
1 AGAAGTTGTCAC
9916 CTTGAATTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
37 11 0.24
38 7 0.16
39 1 0.02
40 21 0.47
41 5 0.11
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (38 bp):
AGAAGTTGTCACTCCGGTAAATTAAAATTACTGACACC
Found at i:13062 original size:20 final size:20
Alignment explanation
Indices: 13027--13064 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13017 AATACAAGGC
*
13027 ATTTGATTTACGAATTGGAT
1 ATTTGATTTACAAATTGGAT
*
13047 ATTTGATTTGCAAATTGG
1 ATTTGATTTACAAATTGG
13065 TGCTCTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGATTTACAAATTGGAT
Done.