Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012193.1 Corchorus capsularis cultivar CVL-1 contig12214, 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: 47973
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:1862 original size:2 final size:2
Alignment explanation
Indices: 1855--1880 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1845 ATTCTAGGAC
1855 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1881 TAAGCAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2738 original size:34 final size:34
Alignment explanation
Indices: 2695--2860 Score: 124
Period size: 34 Copynumber: 4.6 Consensus size: 34
2685 AGATAATAGG
2695 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATT
* **
2729 AATCAGTAAAT-TGATAATTAAG-AGTCAAG-GTAATAGT
1 AATCAGTAAATCAG-TAATTAAGTA-AAAAGAG--AT--T
*
2766 AATCAGTTAATCAGTAATTAAGTAAAAAGAGATT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATT
** *
2800 AATCAGT-AATTTGATAATTAAGAGTCAAGGTAAGAGATT
1 AATCAGTAAATCAG-TAATT-A-AGT-AA--AAAGAGATT
2839 AATCAGTAAAGTCAGTAATTAA
1 AATCAGTAAA-TCAGTAATTAA
2861 AGAGACAAAG
Statistics
Matches: 103, Mismatches: 12, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
33 7 0.07
34 35 0.34
35 3 0.03
36 5 0.05
37 24 0.23
38 4 0.04
39 16 0.16
40 7 0.07
41 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (34 bp):
AATCAGTAAATCAGTAATTAAGTAAAAAGAGATT
Found at i:2764 original size:71 final size:71
Alignment explanation
Indices: 2688--2860 Score: 283
Period size: 71 Copynumber: 2.4 Consensus size: 71
2678 GAAGTAAAGA
*
2688 TAATAGGAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAG
1 TAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAG
2753 TCAAGG
66 TCAAGG
* *
2759 TAATAGTAATCAGTTAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAATTTGATAATTAAGAG
1 TAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAG
2824 TCAAGG
66 TCAAGG
*
2830 TAAGAGATTAATCAGTAAAGTCAGTAATTAA
1 TAATAG--TAATCAGTAAA-TCAGTAATTAA
2861 AGAGACAAAG
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
71 73 0.78
73 10 0.11
74 11 0.12
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (71 bp):
TAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAG
TCAAGG
Found at i:3002 original size:40 final size:40
Alignment explanation
Indices: 2940--3049 Score: 157
Period size: 40 Copynumber: 2.8 Consensus size: 40
2930 CAGTAAAATG
* * * **
2940 GAGTGAAAGTAAATGAAATAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
2980 GAGTAAAAGCAAAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
3020 GAGTAACAGTAAAAGAAGTAATCAGTAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAA
3050 GTAAAGAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.22
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
Found at i:3045 original size:16 final size:15
Alignment explanation
Indices: 3021--3050 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3011 GGTAATTAAG
3021 AGTAACAGTAAAAGA
1 AGTAACAGTAAAAGA
3036 AGTAATCAGTAAAAG
1 AGTAA-CAGTAAAAG
3051 TAAAGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.07, G:0.20, T:0.17
Consensus pattern (15 bp):
AGTAACAGTAAAAGA
Found at i:3101 original size:35 final size:36
Alignment explanation
Indices: 3056--3140 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 36
3046 AAAAGTAAAG
* * *
3056 AAAAGAAAAGAAG-AGCCAAAAAAGGAAAAATGGTA
1 AAAAGTAAAGAAGTAACCAAAAAAGGAAAAATAGTA
* **
3091 AAAAGTAAAG-AGTAATCAGTAAAGGAAAAATAGTA
1 AAAAGTAAAGAAGTAACCAAAAAAGGAAAAATAGTA
*
3126 AAGAGTAAAG-AGTAA
1 AAAAGTAAAGAAGTAA
3141 AGAGTAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 2 0.05
35 40 0.95
ACGTcount: A:0.62, C:0.04, G:0.22, T:0.12
Consensus pattern (36 bp):
AAAAGTAAAGAAGTAACCAAAAAAGGAAAAATAGTA
Found at i:3111 original size:14 final size:13
Alignment explanation
Indices: 3094--3237 Score: 75
Period size: 14 Copynumber: 10.9 Consensus size: 13
3084 AATGGTAAAA
3094 AGTAAAGAGTAAT
1 AGTAAAGAGTAAT
**
3107 CAGTAAAGGAAAAAT
1 -AGTAAA-GAGTAAT
*
3122 AGTAAAGAGTAAAG
1 AGTAAAGAGT-AAT
3136 AGTAAAGAGTAATT
1 AGTAAAGAGTAA-T
* **
3150 ATTAAAGAAAAAT
1 AGTAAAGAGTAAT
*
3163 GGTAAAGAGTAAT
1 AGTAAAGAGTAAT
3176 CAGTAAAG-G-AA-
1 -AGTAAAGAGTAAT
* *
3187 A--AATG-GTAAAG
1 AGTAAAGAGT-AAT
*
3198 AGTAAAGAATAAT
1 AGTAAAGAGTAAT
*
3211 CAGTAAGGAGTAATT
1 -AGTAAAGAGTAA-T
3226 AGTAAAGAGTAA
1 AGTAAAGAGTAA
3238 AATGATAAAA
Statistics
Matches: 97, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
8 4 0.04
10 3 0.03
11 1 0.01
12 2 0.02
13 20 0.21
14 61 0.63
15 6 0.06
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.20
Consensus pattern (13 bp):
AGTAAAGAGTAAT
Found at i:3112 original size:21 final size:21
Alignment explanation
Indices: 3088--3148 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
3078 AGGAAAAATG
3088 GTAAAAAGTAAAGAGTAATCA
1 GTAAAAAGTAAAGAGTAATCA
* **
3109 GTAAAGGAA--AAATAGTAAAGA
1 GTAAA--AAGTAAAGAGTAATCA
*
3130 GTAAAGAGTAAAGAGTAAT
1 GTAAAAAGTAAAGAGTAAT
3149 TATTAAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
19 1 0.03
21 27 0.90
23 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.23, T:0.18
Consensus pattern (21 bp):
GTAAAAAGTAAAGAGTAATCA
Found at i:3147 original size:35 final size:35
Alignment explanation
Indices: 3076--3238 Score: 156
Period size: 35 Copynumber: 4.7 Consensus size: 35
3066 AAGAGCCAAA
* *
3076 AAAGGAAAAATGGTAAAAAGTAAAGAGTAATCAGT
1 AAAGGAAAAATAGTAAAGAGTAAAGAGTAATCAGT
**
3111 AAAGGAAAAATAGTAAAGAGTAAAGAGTAAAGAGT
1 AAAGGAAAAATAGTAAAGAGTAAAGAGTAATCAGT
** *
3146 AATTATTAAAGAA-A--AATG-GTAAAGAGTAATCAGT
1 AA--AGGAAA-AATAGTAAAGAGTAAAGAGTAATCAGT
* *
3180 AAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGT
1 AAAGGAAAAATAGTAAAGAGTAAAGAGTAATCAGT
* *
3215 -AAGGAGTAATTAGTAAAGAGTAAA
1 AAAGGA-AAAATAGTAAAGAGTAAA
3239 ATGATAAAAA
Statistics
Matches: 103, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
31 2 0.02
32 4 0.04
34 24 0.23
35 66 0.64
37 5 0.05
38 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.19
Consensus pattern (35 bp):
AAAGGAAAAATAGTAAAGAGTAAAGAGTAATCAGT
Found at i:3196 original size:28 final size:27
Alignment explanation
Indices: 3137--3202 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 27
3127 AGAGTAAAGA
* *
3137 GTAAAGAGTAATTATTAAAGAAAAATG
1 GTAAAGAGTAATCAGTAAAGAAAAATG
3164 GTAAAGAGTAATCAGTAAAGGAAAAATG
1 GTAAAGAGTAATCAGTAAA-GAAAAATG
3192 GTAAAGAGTAA
1 GTAAAGAGTAA
3203 AGAATAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 17 0.47
28 19 0.53
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.21
Consensus pattern (27 bp):
GTAAAGAGTAATCAGTAAAGAAAAATG
Found at i:3197 original size:41 final size:42
Alignment explanation
Indices: 3088--3198 Score: 104
Period size: 41 Copynumber: 2.7 Consensus size: 42
3078 AGGAAAAATG
* **
3088 GTAAAAAGTAAAGAGTAATCA-GTAAAGGAAAAATAGTAAAGA
1 GTAAACAGTAAAGAGTAAAAATGTAAA-GAAAAATAGTAAAGA
* ** *
3130 GTAAAGAGTAAAGAGTAATTAT-TAAAGAAAAATGGTAAAGA
1 GTAAACAGTAAAGAGTAAAAATGTAAAGAAAAATAGTAAAGA
*
3171 GTAATCAGTAAAG-G-AAAAATGGTAAAGA
1 GTAAACAGTAAAGAGTAAAAAT-GTAAAGA
3199 GTAAAGAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
39 4 0.07
40 1 0.02
41 31 0.53
42 23 0.39
ACGTcount: A:0.57, C:0.02, G:0.23, T:0.19
Consensus pattern (42 bp):
GTAAACAGTAAAGAGTAAAAATGTAAAGAAAAATAGTAAAGA
Found at i:3294 original size:34 final size:36
Alignment explanation
Indices: 3215--3301 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 36
3205 AATAATCAGT
*
3215 AAGGAGTAATTAGTAAAGAGTAAAATGATAAAAAGTA
1 AAGG-GTAATCAGTAAAGAGTAAAATGATAAAAAGTA
* *
3252 AAGAGTAATCAGTAAAG-G-AAGAATGAT-AAGAGTA
1 AAGGGTAATCAGTAAAGAGTAA-AATGATAAAAAGTA
3286 AAGGGTAATCAGTAAA
1 AAGGGTAATCAGTAAA
3302 AAGATAATCG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
34 23 0.51
35 7 0.16
36 12 0.27
37 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.20
Consensus pattern (36 bp):
AAGGGTAATCAGTAAAGAGTAAAATGATAAAAAGTA
Found at i:3314 original size:22 final size:21
Alignment explanation
Indices: 3282--3514 Score: 81
Period size: 22 Copynumber: 11.0 Consensus size: 21
3272 GAATGATAAG
*
3282 AGTAAAGGGTAATCAGTAAAA
1 AGTAAAAGGTAATCAGTAAAA
** **
3303 AGATAATCGGTAAAGAGTAAAA
1 AG-TAAAAGGTAATCAGTAAAA
3325 TAGTAAAAGGTAATCAGTAAAAA
1 -AGTAAAAGGTAATCAGT-AAAA
* * *
3348 AGGGT-AATGATAATGAGTAAAA
1 A--GTAAAAGGTAATCAGTAAAA
* * * *
3370 GGTAAAATAGTGATCAGTAAAG
1 AGTAAAA-GGTAATCAGTAAAA
*
3392 AGTAAAATAGTAATCAGTAAAA
1 AGTAAAA-GGTAATCAGTAAAA
* * *
3414 GGTAATCA-GTAA-GAGT-AAA
1 AGTAA-AAGGTAATCAGTAAAA
* *
3433 A-T---A-GTAATCGGCAAAA
1 AGTAAAAGGTAATCAGTAAAA
* *
3449 AGTAAAGA-GTAATCAATAAGA
1 AGTAAA-AGGTAATCAGTAAAA
**
3470 AGTCAAATTGTAATCAGTAAAA
1 AGT-AAAAGGTAATCAGTAAAA
* *
3492 TGTGAAAAGGCAATCAGTAAAA
1 AGT-AAAAGGTAATCAGTAAAA
3514 A
1 A
3515 AATGGTAAAG
Statistics
Matches: 154, Mismatches: 41, Indels: 33
0.68 0.18 0.14
Matches are distributed among these distances:
14 5 0.03
15 1 0.01
16 4 0.03
17 1 0.01
18 1 0.01
19 3 0.02
20 5 0.03
21 21 0.14
22 94 0.61
23 17 0.11
24 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTAAAAGGTAATCAGTAAAA
Found at i:3332 original size:85 final size:85
Alignment explanation
Indices: 3164--3325 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 85
3154 AAGAAAAATG
* ** *
3164 GTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGT
1 GTAAAGAGTAATCAGTAAAGGAAAAATGATAAAGAGTAAAGAATAATCAGTAAAAAGTAATCAGT
3229 AAAGAGTAAAATGATAAAAA
66 AAAGAGTAAAATGATAAAAA
* ** *
3249 GTAAAGAGTAATCAGTAAAGGAAGAATGAT-AAGAGTAAAGGGTAATCAGTAAAAAGATAATCGG
1 GTAAAGAGTAATCAGTAAAGGAAAAATGATAAAGAGTAAAGAATAATCAGTAAAAAG-TAATCAG
3313 TAAAGAGTAAAAT
65 TAAAGAGTAAAAT
3326 AGTAAAAGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
84 22 0.32
85 46 0.68
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (85 bp):
GTAAAGAGTAATCAGTAAAGGAAAAATGATAAAGAGTAAAGAATAATCAGTAAAAAGTAATCAGT
AAAGAGTAAAATGATAAAAA
Found at i:3344 original size:85 final size:85
Alignment explanation
Indices: 3164--3344 Score: 222
Period size: 85 Copynumber: 2.1 Consensus size: 85
3154 AAGAAAAATG
* * ** *
3164 GTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGT
1 GTAAACAGTAATCAGTAAAGGAAAAATGATAAAGAGTAAAGAATAATCAGTAAAAAGTAATCAGT
3229 AAAGAGTAAAATGATAAAAA
66 AAAGAGTAAAATGATAAAAA
* * ** *
3249 GTAAAGAGTAATCAGTAAAGGAAGAATGAT-AAGAGTAAAGGGTAATCAGTAAAAAGATAATCGG
1 GTAAACAGTAATCAGTAAAGGAAAAATGATAAAGAGTAAAGAATAATCAGTAAAAAG-TAATCAG
*
3313 TAAAGAGTAAAAT-AGTAAAAG
65 TAAAGAGTAAAATGA-TAAAAA
*
3334 GTAATCAGTAA
1 GTAAACAGTAA
3345 AAAAGGGTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
84 23 0.28
85 60 0.72
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (85 bp):
GTAAACAGTAATCAGTAAAGGAAAAATGATAAAGAGTAAAGAATAATCAGTAAAAAGTAATCAGT
AAAGAGTAAAATGATAAAAA
Found at i:3347 original size:15 final size:15
Alignment explanation
Indices: 3289--3347 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
3279 AAGAGTAAAG
3289 GGTAATCAGTAAAAA
1 GGTAATCAGTAAAAA
* * *
3304 GATAATCGGTAAAGA
1 GGTAATCAGTAAAAA
3319 -GTAAAAT-AGT-AAAA
1 GGT--AATCAGTAAAAA
3333 GGTAATCAGTAAAAA
1 GGTAATCAGTAAAAA
3348 AGGGTAATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
13 3 0.09
14 7 0.21
15 20 0.61
16 3 0.09
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.20
Consensus pattern (15 bp):
GGTAATCAGTAAAAA
Found at i:3376 original size:44 final size:45
Alignment explanation
Indices: 3282--3369 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
3272 GAATGATAAG
* *
3282 AGTAAAGGGTAATCAGT-AAAAAGATAATCGGTAAAGAGTAAAAT
1 AGTAAAAGGTAATCAGTAAAAAAGATAATCGATAAAGAGTAAAAT
* *
3326 AGTAAAAGGTAATCAGTAAAAAAGGGTAAT-GATAATGAGTAAAA
1 AGTAAAAGGTAATCAGTAAAAAA-GATAATCGATAAAGAGTAAAA
3370 GGTAAAATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 16 0.42
45 17 0.45
46 5 0.13
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.20
Consensus pattern (45 bp):
AGTAAAAGGTAATCAGTAAAAAAGATAATCGATAAAGAGTAAAAT
Found at i:3460 original size:35 final size:35
Alignment explanation
Indices: 3384--3460 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
3374 AAATAGTGAT
* * *
3384 CAGTAAAGAGTAAAATAGTAATCAGTAAAAGGTAAT
1 CAGT-AAGAGTAAAATAGTAATCAGCAAAAAGTAAA
*
3420 CAGTAAGAGTAAAATAGTAATCGGCAAAAAGTAAA
1 CAGTAAGAGTAAAATAGTAATCAGCAAAAAGTAAA
*
3455 GAGTAA
1 CAGTAA
3461 TCAATAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 32 0.89
36 4 0.11
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (35 bp):
CAGTAAGAGTAAAATAGTAATCAGCAAAAAGTAAA
Found at i:3545 original size:17 final size:16
Alignment explanation
Indices: 3496--3582 Score: 72
Period size: 17 Copynumber: 5.4 Consensus size: 16
3486 GTAAAATGTG
*
3496 AAAAGGCAATCAGTAAA
1 AAAAGGTAATCAGT-AA
**
3513 AAAATGGTAAAGAGTAA
1 AAAA-GGTAATCAGTAA
*
3530 AAAATGGTAATCAGTAGG
1 AAAA-GGTAATCAGTA-A
*
3548 AAAA-G--ATGAGTAA
1 AAAAGGTAATCAGTAA
3561 AAAAGGTAATCAGTAA
1 AAAAGGTAATCAGTAA
3577 AAAAGG
1 AAAAGG
3583 AAAGTAAGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
13 4 0.07
14 7 0.12
16 14 0.25
17 20 0.36
18 11 0.20
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.16
Consensus pattern (16 bp):
AAAAGGTAATCAGTAA
Found at i:6262 original size:14 final size:14
Alignment explanation
Indices: 6229--6289 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
6219 CAAGAGATAT
*
6229 TTTTCAAAAAAATTG
1 TTTTCAAAAAAA-GG
*
6244 TTTTCAAGAAAAGG
1 TTTTCAAAAAAAGG
*
6258 TTTTC-AAAAATGAG
1 TTTTCAAAAAAAG-G
*
6272 TTTTCAAAAAAAAG
1 TTTTCAAAAAAAGG
6286 TTTT
1 TTTT
6290 TGAGTTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
13 5 0.13
14 17 0.45
15 16 0.42
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (14 bp):
TTTTCAAAAAAAGG
Found at i:6946 original size:15 final size:17
Alignment explanation
Indices: 6926--6960 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6916 CATTCAATTC
6926 AAAGG-AAAA-AAAGAA
1 AAAGGAAAAAGAAAGAA
6941 AAAGGAAAAAGAAAGAA
1 AAAGGAAAAAGAAAGAA
6958 AAA
1 AAA
6961 AACTCAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 4 0.22
17 9 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAGGAAAAAGAAAGAA
Found at i:7557 original size:17 final size:18
Alignment explanation
Indices: 7533--7586 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 18
7523 ATAGTGCATG
7533 GAAAAAAAGAAAAAGAAA
1 GAAAAAAAGAAAAAGAAA
7551 GAAAAAAAAGAAAGAAGAAA
1 G-AAAAAAAGAAA-AAGAAA
*
7571 G-AAAAAAGAAGAAGAA
1 GAAAAAAAGAAAAAGAA
7587 GAAGCTCGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 5 0.15
18 10 0.30
19 11 0.33
20 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
GAAAAAAAGAAAAAGAAA
Found at i:7559 original size:20 final size:19
Alignment explanation
Indices: 7534--7589 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 19
7524 TAGTGCATGG
7534 AAAAAAAGAAAAAGAAAGA
1 AAAAAAAGAAAAAGAAAGA
7553 AAAAAAAGAAAGAAGAAAGA
1 AAAAAAAGAAA-AAGAAAGA
*
7573 AAAAAGAAGAAGAAGAA
1 AAAAA-AAGAAAAAGAA
7590 GCTCGAGGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 11 0.32
20 18 0.53
21 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAGAAAGA
Found at i:18672 original size:16 final size:16
Alignment explanation
Indices: 18651--18682 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18641 GAAGTCTTCC
18651 CATCTTAATATCAGAG
1 CATCTTAATATCAGAG
18667 CATCTTAATATCAGAG
1 CATCTTAATATCAGAG
18683 GCAAGGCTCT
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:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
CATCTTAATATCAGAG
Found at i:23792 original size:110 final size:110
Alignment explanation
Indices: 23671--23881 Score: 359
Period size: 110 Copynumber: 1.9 Consensus size: 110
23661 ATGTCTAAAG
* *
23671 AACAAAATCAATACCTTGAAGAAATCATAATTTTGTTCTAATTAAGACTAACAAACCAATAATTC
1 AACAAAATCAATACCCTGAAGAAATCATAATTTTGTTCTAATTAAAACTAACAAACCAATAATTC
* * *
23736 ATTAATTAGAACAAAATTAAACATGGTTGATTATCATGTAAAAAA
66 ATCAATCAGAACAAAATTAAACACGGTTGATTATCATGTAAAAAA
* *
23781 AACAAAATCAATACCCTGAAGAAATCATAATTTTGTTCTAATTAAAACTAATAAACCAATTATTC
1 AACAAAATCAATACCCTGAAGAAATCATAATTTTGTTCTAATTAAAACTAACAAACCAATAATTC
23846 ATCAATCAGAACAAAATTAAACACGGTTGATTATCA
66 ATCAATCAGAACAAAATTAAACACGGTTGATTATCA
23882 AAACAAAATA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 94 1.00
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (110 bp):
AACAAAATCAATACCCTGAAGAAATCATAATTTTGTTCTAATTAAAACTAACAAACCAATAATTC
ATCAATCAGAACAAAATTAAACACGGTTGATTATCATGTAAAAAA
Found at i:25957 original size:33 final size:33
Alignment explanation
Indices: 25920--25983 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
25910 AACTCATAAT
25920 TGTAAAGGATTAAATAGCATAAAGCATAAAAAG
1 TGTAAAGGATTAAATAGCATAAAGCATAAAAAG
25953 TGTAAAGGATTAAATAGCATAAAGCATAAAA
1 TGTAAAGGATTAAATAGCATAAAGCATAAAA
25984 GTGCGAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.22
Consensus pattern (33 bp):
TGTAAAGGATTAAATAGCATAAAGCATAAAAAG
Found at i:25975 original size:17 final size:17
Alignment explanation
Indices: 25922--25976 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
25912 CTCATAATTG
25922 TAAAGGATTAAATAGCA
1 TAAAGGATTAAATAGCA
* * **
25939 TAAAGCA-TAAAAAGTG
1 TAAAGGATTAAATAGCA
25955 TAAAGGATTAAATAGCA
1 TAAAGGATTAAATAGCA
25972 TAAAG
1 TAAAG
25977 CATAAAAGTG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (17 bp):
TAAAGGATTAAATAGCA
Found at i:26670 original size:2 final size:2
Alignment explanation
Indices: 26656--26691 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
26646 AAATGTATGT
*
26656 TA TA TA TG T- 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
26692 GACCCAATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:27139 original size:18 final size:18
Alignment explanation
Indices: 27118--27179 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 18
27108 TATTACTAAA
27118 TAAATAATAAATATATTT
1 TAAATAATAAATATATTT
27136 TAAATAATAAATAATGAGTTT
1 TAAATAATAAAT-AT-A-TTT
*
27157 AAAATAAATAAATATATATT
1 TAAAT-AATAAATATAT-TT
27177 TAA
1 TAA
27180 TTATTATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 6 0.16
21 9 0.24
22 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
TAAATAATAAATATATTT
Found at i:27144 original size:21 final size:24
Alignment explanation
Indices: 27100--27150 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
27090 AATCTTAGAT
27100 ATAATATATATTACTAAATAAATA
1 ATAATATATATTACTAAATAAATA
*
27124 ATAA-ATATATT-TTAAAT-AATAA
1 ATAATATATATTACTAAATAAAT-A
27146 ATAAT
1 ATAAT
27151 GAGTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.12
22 10 0.42
23 7 0.29
24 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAATATATATTACTAAATAAATA
Found at i:27178 original size:21 final size:21
Alignment explanation
Indices: 27102--27179 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 21
27092 TCTTAGATAT
27102 AATATATA-TTACTAAATAAATA
1 AATATATATTTA--AAATAAATA
* *
27124 ATAAATATATTTTAAAT-AATA
1 A-ATATATATTTAAAATAAATA
27145 AATA-ATGAGTTTAAAATAAATA
1 AATATAT-A-TTTAAAATAAATA
27167 AATATATATTTAA
1 AATATATATTTAA
27180 TTATTATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
19 2 0.04
20 3 0.07
21 17 0.37
22 14 0.30
23 8 0.17
24 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (21 bp):
AATATATATTTAAAATAAATA
Found at i:38232 original size:15 final size:13
Alignment explanation
Indices: 38192--38247 Score: 89
Period size: 13 Copynumber: 4.5 Consensus size: 13
38182 TTAATACAGG
38192 TATCG-ACGGATA
1 TATCGAACGGATA
38204 TATCGAACGGATA
1 TATCGAACGGATA
38217 TATCGAACGGATA
1 TATCGAACGGATA
*
38230 TATCG-ATGGATA
1 TATCGAACGGATA
38242 TATCGA
1 TATCGA
38248 GGTATCAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
12 16 0.39
13 25 0.61
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:38240 original size:25 final size:26
Alignment explanation
Indices: 38192--38247 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
38182 TTAATACAGG
38192 TATCG-ACGGATATATCGAACGGATA
1 TATCGAACGGATATATCGAACGGATA
*
38217 TATCGAACGGATATATCG-ATGGATA
1 TATCGAACGGATATATCGAACGGATA
38242 TATCGA
1 TATCGA
38248 GGTATCAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (26 bp):
TATCGAACGGATATATCGAACGGATA
Found at i:42539 original size:20 final size:21
Alignment explanation
Indices: 42511--42549 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42501 TTATGGCTAT
*
42511 TTTTCTATAC-TTTTTACCAC
1 TTTTATATACATTTTTACCAC
42531 TTTTATATACATTTTTACC
1 TTTTATATACATTTTTACC
42550 TTATTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATATACATTTTTACCAC
Done.