Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011879.1 Corchorus capsularis cultivar CVL-1 contig11900, 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: 28809
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3049 original size:38 final size:38
Alignment explanation
Indices: 3007--3191 Score: 187
Period size: 38 Copynumber: 4.8 Consensus size: 38
2997 ACCCCAATAA
*
3007 AATTAAG-GATCAAAACAATAGTAATCAGTAAAATTGAT
1 AATTAAGAG-TCAAAAAAATAGTAATCAGTAAAATTGAT
** * * *
3045 AATTAAGAGTCAAAGTAATAGTAATCAGT-GAATTAAGC
1 AATTAAGAGTCAAAAAAATAGTAATCAGTAAAATTGA-T
* ** *
3083 AATTAAGAATCAAAGTAATAATAATCAGTAAAATTGAT
1 AATTAAGAGTCAAAAAAATAGTAATCAGTAAAATTGAT
* *
3121 AATTAAGAGTAAAAAAAATAGTAATCAGT-AAATCGAT
1 AATTAAGAGTCAAAAAAATAGTAATCAGTAAAATTGAT
*
3158 CATTAAGAGTCAAGGTAAAAATAGTAATCAGTAA
1 AATTAAGAGTCAA---AAAAATAGTAATCAGTAA
3192 GTCAGTAATT
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
37 23 0.19
38 76 0.62
39 6 0.05
40 16 0.13
41 1 0.01
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (38 bp):
AATTAAGAGTCAAAAAAATAGTAATCAGTAAAATTGAT
Found at i:3141 original size:76 final size:76
Alignment explanation
Indices: 3007--3149 Score: 223
Period size: 76 Copynumber: 1.9 Consensus size: 76
2997 ACCCCAATAA
* * * **
3007 AATTAAGGATCAAAACAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCA
1 AATTAAGAATCAAAACAATAATAATCAGTAAAATTGATAATTAAGAGTAAAAAAAATAGTAATCA
3072 GTGAATTAAGC
66 GTGAATTAAGC
**
3083 AATTAAGAATCAAAGTAATAATAATCAGTAAAATTGATAATTAAGAGTAAAAAAAATAGTAATCA
1 AATTAAGAATCAAAACAATAATAATCAGTAAAATTGATAATTAAGAGTAAAAAAAATAGTAATCA
3148 GT
66 GT
3150 AAATCGATCA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 60 1.00
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.27
Consensus pattern (76 bp):
AATTAAGAATCAAAACAATAATAATCAGTAAAATTGATAATTAAGAGTAAAAAAAATAGTAATCA
GTGAATTAAGC
Found at i:3330 original size:21 final size:21
Alignment explanation
Indices: 3305--3344 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3295 TCAAGAGAGT
*
3305 AAAATAGTAATCAGTAAAGGA
1 AAAATAGTAAACAGTAAAGGA
* *
3326 AAAATGGTAAAGAGTAAAG
1 AAAATAGTAAACAGTAAAG
3345 AATAATCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (21 bp):
AAAATAGTAAACAGTAAAGGA
Found at i:3375 original size:14 final size:14
Alignment explanation
Indices: 3338--3377 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3328 AATGGTAAAG
*
3338 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
3352 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
3366 AGTAAAGAGTAA
1 AGTAAAGAGTAA
3378 AATGATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.23
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:3429 original size:50 final size:50
Alignment explanation
Indices: 3310--3406 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 50
3300 AGAGTAAAAT
* * * *
3310 AGTAATCAGTAAAG-GAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGG
1 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAAGG
*
3359 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAGTAATCAGTAA
1 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAA
3407 AGGAAGAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 13 0.31
50 29 0.69
ACGTcount: A:0.55, C:0.03, G:0.22, T:0.21
Consensus pattern (50 bp):
AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAAGG
Found at i:3435 original size:35 final size:35
Alignment explanation
Indices: 3360--3469 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 35
3350 TCAGTAAGGA
* *
3360 GTAATTAGTAAAGAGTAA-AATGATAAAAAGT-AAAG
1 GTAATCAGTAAAG-G-AAGAATGATAAATAGTAAAAG
*
3395 AGTAATCAGTAAAGGAAGAATGGTAAATAGTAAAAG
1 -GTAATCAGTAAAGGAAGAATGATAAATAGTAAAAG
* *
3431 GTAATCAATAAA-AAAGTAATGAT-AATCAGTAAAAG
1 GTAATCAGTAAAGGAAG-AATGATAAAT-AGTAAAAG
3466 GTAA
1 GTAA
3470 AATAGTAATC
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
34 8 0.12
35 40 0.62
36 16 0.25
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.22
Consensus pattern (35 bp):
GTAATCAGTAAAGGAAGAATGATAAATAGTAAAAG
Found at i:3435 original size:71 final size:73
Alignment explanation
Indices: 3347--3686 Score: 250
Period size: 71 Copynumber: 4.5 Consensus size: 73
3337 GAGTAAAGAA
* *
3347 TAATCAGT-AAGGAGTAATTAGTAAAGAGTAAAATGA-TAAAAAGTAAAGAGTAATCAGTAAAG-
1 TAATCAGTAAAAG-GTAATCAGTAAAGAGTAAAATGAGTAAAAAGTAAAGAGTAATCAGTAAAGA
*
3409 G-AAGAATGG
65 GCAA-AATAG
* * * * *
3418 TAAAT-AGTAAAAGGTAATCAATAAAAAAGTAATGATAATCAGTAAAAGGTAAAATAGTAATCAG
1 T-AATCAGTAAAAGGTAATCAGT-AAAGAGT-A--A-AATGAGTAAAAAGT-AAAGAGTAATCAG
*
3482 TAAAGAGCAAAATGG
59 TAAAGAGCAAAATAG
*
3497 TAATCAATGAGAGAAAAATGGTAATCAGTAAAGAGTAAAATAGTAATTAGTAAAAAGT-AAGAAG
1 TAATC------AGTAAAA-GGTAATCAGTAAAGAGTAAAAT-G-----AGTAAAAAGTAAAG-A-
*
3561 GTAATCAGTAAAGAGTAAAATAG
51 GTAATCAGTAAAGAGCAAAATAG
* **
3584 TAATCAGCAAAAGGTAATCAGT-AAGAGTAAAAT-AGTAATCAGTATAAG-GTAATCAGTAAAGA
1 TAATCAGTAAAAGGTAATCAGTAAAGAGTAAAATGAGTAAAAAGTA-AAGAGTAATCAGTAAAGA
*
3646 GAAAAATAG
65 GCAAAATAG
3655 TAATCAGTAAAAGGTAATCAGT-AAGAGTAAAA
1 TAATCAGTAAAAGGTAATCAGTAAAGAGTAAAA
3687 CAGTAATCAG
Statistics
Matches: 220, Mismatches: 20, Indels: 58
0.74 0.07 0.19
Matches are distributed among these distances:
71 64 0.29
72 20 0.09
73 1 0.00
74 3 0.01
75 1 0.00
76 4 0.02
77 7 0.03
78 20 0.09
79 18 0.08
80 12 0.05
81 9 0.04
82 1 0.00
84 1 0.00
85 14 0.06
86 10 0.05
87 35 0.16
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (73 bp):
TAATCAGTAAAAGGTAATCAGTAAAGAGTAAAATGAGTAAAAAGTAAAGAGTAATCAGTAAAGAG
CAAAATAG
Found at i:3462 original size:85 final size:85
Alignment explanation
Indices: 3310--3477 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 85
3300 AGAGTAAAAT
* ** * *
3310 AGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAAAGAG
1 AGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAATAAAAAGTAATGAGTAAACAG
3375 TAAAATGATAAAA-AGTAAAG
66 TAAAA-GATAAAATAGTAAAG
* * * *
3395 AGTAATCAGTAAAGGAAGAATGGTAAATAGTAAA-AGGTAATCAATAAAAAAGTAATGA-TAATC
1 AGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGA-ATAATCAAT-AAAAAGTAATGAGTAAAC
*
3458 AGTAAAAGGTAAAATAGTAA
64 AGTAAAAGATAAAATAGTAA
3478 TCAGTAAAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 7 0.10
85 54 0.77
86 9 0.13
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (85 bp):
AGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAATAAAAAGTAATGAGTAAACAG
TAAAAGATAAAATAGTAAAG
Found at i:3481 original size:22 final size:21
Alignment explanation
Indices: 3453--3600 Score: 120
Period size: 22 Copynumber: 6.8 Consensus size: 21
3443 AAAGTAATGA
3453 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGT-AAAGGTAAAATAG
* *
3475 TAATCAGTAAAGAGCAAAATGG
1 TAATCAGTAAAG-GTAAAATAG
* * * *
3497 TAATCAAT-GAGAGAAAAATGG
1 TAATCAGTAAAG-GTAAAATAG
3518 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAG-GTAAAATAG
* * *
3540 TAATTAGTAAAAAGTAAGAA-GG
1 TAATCAGT-AAAGGTAA-AATAG
3562 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAG-GTAAAATAG
*
3584 TAATCAGCAAAAGGTAA
1 TAATCAG-TAAAGGTAA
3601 TCAGTAAGAG
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
21 27 0.26
22 67 0.65
23 9 0.09
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.21
Consensus pattern (21 bp):
TAATCAGTAAAGGTAAAATAG
Found at i:3525 original size:65 final size:66
Alignment explanation
Indices: 3428--3671 Score: 207
Period size: 65 Copynumber: 3.7 Consensus size: 66
3418 TAAATAGTAA
* * *
3428 AAGGTAATCAATAAA-A-AAGTAATGATAATCAGTAAAAGGTAAAATAGTAATCAGTAAAGAGCA
1 AAGGTAATCAATAAAGAGAA-AAATGGTAATCAGTAAAAGGTAAAATAGTAATCAGTAAAAAGCA
3491 A-
65 AG
* * *
3492 AATGGTAATCAAT-GAGAGAAAAATGGTAATCAGT-AAAGAGTAAAATAGTAATTAGTAAAAAGT
1 AA-GGTAATCAATAAAGAGAAAAATGGTAATCAGTAAAAG-GTAAAATAGTAATCAGTAAAAAGC
3555 AAG
64 AAG
* * * * *
3558 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGGT--AATCAGTAA-GAGTAAAATAGT
1 AAGGTAATCAATAAAGAGAAAAATGGTAATCAGTAAAAGGTAAAAT-AGTAATCAGTAAAA-AG-
*
3620 AATCAGTAT
63 ---CA--AG
* *
3629 AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGTAAAAGGTAA
1 AAGGTAATCAATAAAGAGAAAAATGGTAATCAGTAAAAGGTAA
3672 TCAGTAAGAG
Statistics
Matches: 147, Mismatches: 16, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
64 17 0.12
65 62 0.42
66 23 0.16
67 4 0.03
69 1 0.01
71 40 0.27
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (66 bp):
AAGGTAATCAATAAAGAGAAAAATGGTAATCAGTAAAAGGTAAAATAGTAATCAGTAAAAAGCAA
G
Found at i:3565 original size:87 final size:79
Alignment explanation
Indices: 3453--3698 Score: 267
Period size: 71 Copynumber: 3.1 Consensus size: 79
3443 AAAGTAATGA
* * *
3453 TAATCAGTAAAAGGTAA-AATAGTAATCAGTAAAGAGCAAAATGGTAATCAATGAGAGAAAAATG
1 TAATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGCAAAATAGTAATC------AGAAAAA-G
3517 GTAATCAGTAAAGAGTAAAATAG
58 GTAATCAGT-AAGAGTAAAATAG
* * *
3540 TAATTAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGGTAATCAG
1 TAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGCAAAATAGTAATCAGAAAAAGGTAATCAG
3605 TAAGAGTAAAATAG
66 TAAGAGTAAAATAG
* *
3619 TAATCAGT----A-T---AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGTAAAAGGTAATCAG
1 TAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGCAAAATAGTAATCAGAAAAAGGTAATCAG
*
3676 TAAGAGTAAAACAG
66 TAAGAGTAAAATAG
3690 TAATCAGTA
1 TAATCAGTA
3699 GGAGCAAAGT
Statistics
Matches: 147, Mismatches: 10, Indels: 19
0.84 0.06 0.11
Matches are distributed among these distances:
71 66 0.45
74 1 0.01
75 1 0.01
79 20 0.14
80 10 0.07
81 6 0.04
87 41 0.28
88 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (79 bp):
TAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGCAAAATAGTAATCAGAAAAAGGTAATCAG
TAAGAGTAAAATAG
Found at i:3598 original size:36 final size:35
Alignment explanation
Indices: 3552--3741 Score: 236
Period size: 35 Copynumber: 5.1 Consensus size: 35
3542 ATTAGTAAAA
3552 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAA-AAGGTAATCAGT-AAGAGTAAAATAGTAATC
*
3589 AGCAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
* *
3624 AGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATC
1 AGTAAAAGGTAATCAGT-AAGAGTAAAATAGTAATC
*
3660 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATC
1 AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
* *
3695 AGTAGGAGCAAAGTGGTAATTAGTAAGGGTAAAATAGTAATC
1 AGT---A--AAA--GGTAATCAGTAAGAGTAAAATAGTAATC
3737 AGTAA
1 AGTAA
3742 CGAGTAAAAG
Statistics
Matches: 135, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
35 52 0.39
36 45 0.33
37 5 0.04
38 1 0.01
39 1 0.01
40 3 0.02
42 28 0.21
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (35 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
Found at i:3758 original size:21 final size:20
Alignment explanation
Indices: 3453--3762 Score: 143
Period size: 21 Copynumber: 15.5 Consensus size: 20
3443 AAAGTAATGA
* *
3453 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAGA-GTAAAA-GG
*
3475 TAATCAGTAAAGAGCAAAATGG
1 TAATCAGT-AAGAGTAAAA-GG
* * *
3497 TAATCAATGAGAGAAAAATGG
1 TAATCAGTAAGAGTAAAA-GG
*
3518 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGT-AAGAGTAAAA-GG
* *
3540 TAATTAGTAAAAAGTAAGAAGG
1 TAATCAGT-AAGAGTAA-AAGG
3562 TAATCAGTAAAGAGT--AA--
1 TAATCAGT-AAGAGTAAAAGG
* *
3579 -AAT-AGTAATCAGCAAAAGG
1 TAATCAGTAA-GAGTAAAAGG
*
3598 TAATCAGTAAGAGTAAAATAG
1 TAATCAGTAAGAGTAAAA-GG
3619 TAATCAGT---A-T--AAGG
1 TAATCAGTAAGAGTAAAAGG
3633 TAATCAGTAA-AG-AGAAA--
1 TAATCAGTAAGAGTA-AAAGG
*
3650 -AAT-AGTAATCAGTAAAAGG
1 TAATCAGTAA-GAGTAAAAGG
*
3669 TAATCAGTAAGAGTAAAACAG
1 TAATCAGTAAGAGTAAAA-GG
* * *
3690 TAATCAGTAGGAGCAAAGTGG
1 TAATCAGTAAGAGTAAA-AGG
* * *
3711 TAATTAGTAAGGGTAAAATAG
1 TAATCAGTAAGAGTAAAA-GG
3732 TAATCAGTAACGAGTAAAAGG
1 TAATCAGTAA-GAGTAAAAGG
*
3753 TGATCAGTAA
1 TAATCAGTAA
3763 TTCCAAGAGT
Statistics
Matches: 223, Mismatches: 37, Indels: 57
0.70 0.12 0.18
Matches are distributed among these distances:
14 11 0.05
15 12 0.05
16 7 0.03
17 8 0.04
18 2 0.01
19 4 0.02
20 19 0.09
21 87 0.39
22 68 0.30
23 5 0.02
ACGTcount: A:0.51, C:0.06, G:0.22, T:0.22
Consensus pattern (20 bp):
TAATCAGTAAGAGTAAAAGG
Found at i:3762 original size:42 final size:41
Alignment explanation
Indices: 3474--3762 Score: 175
Period size: 35 Copynumber: 7.3 Consensus size: 41
3464 AGGTAAAATA
* ** * *
3474 GTAATCAGTAAAGAGCAAAATGGTAATCAATGA-GAGAAAAATG
1 GTAATCAGT-AAGAGTAAAACAGTAATCAGT-ACGAGTAAAA-G
* * **
3517 GTAATCAGTAAAGAGTAAAATAGTAATTAGTAAAAAGTAAGAAG
1 GTAATCAGT-AAGAGTAAAACAGTAATCAGT-ACGAGTAA-AAG
*
3561 GTAATCAGTAAAGAGTAAAATAGTAATCAG--C----AAAAG
1 GTAATCAGT-AAGAGTAAAACAGTAATCAGTACGAGTAAAAG
*
3597 GTAATCAGTAAGAGTAAAATAGTAATCAGT---A-T--AAG
1 GTAATCAGTAAGAGTAAAACAGTAATCAGTACGAGTAAAAG
* *
3632 GTAATCAGTAAAGAG-AAAA-A-TAGT-AAT-C-AGTAAAAG
1 GTAATCAGT-AAGAGTAAAACAGTAATCAGTACGAGTAAAAG
* * *
3668 GTAATCAGTAAGAGTAAAACAGTAATCAGTAGGAGCAAAGTG
1 GTAATCAGTAAGAGTAAAACAGTAATCAGTACGAGTAAA-AG
* * *
3710 GTAATTAGTAAGGGTAAAATAGTAATCAGTAACGAGTAAAAG
1 GTAATCAGTAAGAGTAAAACAGTAATCAGT-ACGAGTAAAAG
*
3752 GTGATCAGTAA
1 GTAATCAGTAA
3763 TTCCAAGAGT
Statistics
Matches: 204, Mismatches: 24, Indels: 37
0.77 0.09 0.14
Matches are distributed among these distances:
32 2 0.01
33 4 0.02
34 2 0.01
35 41 0.20
36 33 0.16
37 3 0.01
38 3 0.01
39 2 0.01
41 5 0.02
42 38 0.19
43 35 0.17
44 34 0.17
45 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.21
Consensus pattern (41 bp):
GTAATCAGTAAGAGTAAAACAGTAATCAGTACGAGTAAAAG
Found at i:7017 original size:58 final size:58
Alignment explanation
Indices: 6877--7220 Score: 539
Period size: 58 Copynumber: 6.0 Consensus size: 58
6867 ATTCTCTATC
* * * * * *
6877 AAAAAGTCCTTAAACACATGGGCATCCATAAGTCCCTAAACATAGAGGCATCTCT-CA
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
6934 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
*
6992 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTTCCTAAACACAGAGGCATCTATACT
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
* * * * * *
7050 AAAAAGTCCTCAAACACATGGGCATCCATAAGTCCCTTAACATAGAGGCATCTCT-CA
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
*
7107 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATACT
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
*
7165 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATA
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
7221 TCAAAGTCCC
Statistics
Matches: 264, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
57 100 0.38
58 164 0.62
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (58 bp):
AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
Found at i:7111 original size:115 final size:116
Alignment explanation
Indices: 6877--7225 Score: 540
Period size: 115 Copynumber: 3.0 Consensus size: 116
6867 ATTCTCTATC
* * * * * *
6877 AAAAAGTCCTTAAACACATGGGCATCCATAAGTCCCTAAACATAGAGGCATCTCT-CAAAAAAGT
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTAAAAAGT
*
6941 CCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
66 CCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACA
*
6992 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTTCCTAAACACAGAGGCATCTATACTAAAAAGT
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTAAAAAGT
* * * * *
7057 CCTCAAACACATGGGCATCCATAAGTCCCTTAACATAGAGGCATCTCT-CA
66 CCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACA
*
7107 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATACTAAAAAGT
1 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTAAAAAGT
*
7172 CCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATATCA
66 CCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA-CA
7224 AA
1 AA
7226 GTCCCTAAGC
Statistics
Matches: 210, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
115 155 0.74
116 51 0.24
117 4 0.02
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (116 bp):
AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTAAAAAGT
CCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACA
Found at i:7166 original size:173 final size:172
Alignment explanation
Indices: 6877--7244 Score: 641
Period size: 173 Copynumber: 2.1 Consensus size: 172
6867 ATTCTCTATC
*
6877 AAAAAGTCCTTAAACACATGGGCATCCATAAGTCCCTAAACATAGAGGCATCTCTCAAAAAAGTC
1 AAAAAGTCCTCAAACACATGGGCATCCATAAGTCCCTAAACATAGAGGCATCTCTCAAAAAAGTC
*
6942 CTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTAAAAAGTCCTCAAAC
66 CTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATACTAAAAAGTCCTCAAAC
* *
7007 ACAAGGGCATTCATAAGTTCCTAAACACAGAGGCATCTATACT
131 ACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATA-T
*
7050 AAAAAGTCCTCAAACACATGGGCATCCATAAGTCCCTTAACATAGAGGCATCTCTCAAAAAAGTC
1 AAAAAGTCCTCAAACACATGGGCATCCATAAGTCCCTAAACATAGAGGCATCTCTCAAAAAAGTC
7115 CTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATACTAAAAAGTCCTCAAAC
66 CTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATACTAAAAAGTCCTCAAAC
7180 ACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATAT
131 ACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATAT
* *
7222 -CAAAGTCC-CTAAGCACATGGGCA
1 AAAAAGTCCTC-AAACACATGGGCA
7245 ATCTCTCAAA
Statistics
Matches: 187, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
170 1 0.01
171 19 0.10
172 1 0.01
173 166 0.89
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.20
Consensus pattern (172 bp):
AAAAAGTCCTCAAACACATGGGCATCCATAAGTCCCTAAACATAGAGGCATCTCTCAAAAAAGTC
CTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATACTAAAAAGTCCTCAAAC
ACAAGGGCATTCATAAGTCCCTAAACACAGAGACATCTATAT
Found at i:8583 original size:72 final size:73
Alignment explanation
Indices: 8498--8909 Score: 568
Period size: 72 Copynumber: 5.7 Consensus size: 73
8488 TTCTTCTTCT
* * ** *
8498 TCATTGCGATTGTAGCCGAGGCAATTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATT
8563 ATCTTCCA
66 ATCTTCCA
* * ** *
8571 T-ATTGCGGTTGTAGCCGAGGCAGTTCCAACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATT
8635 ATCTTCCA
66 ATCTTCCA
* * *
8643 T-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTATGCGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATT
*
8707 ATATT-CA
66 ATCTTCCA
* * *
8714 TAATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTATGCGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATT
*
8779 ATATT-CA
66 ATCTTCCA
*
8786 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCTCAATCCTTATGTGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATT
8851 ATCTTCC-
66 ATCTTCCA
* * * *
8858 TCATTGCGATTGTAGTCGAGGTAGTTCCTACA--TGCCAGTCCTTCGCACAATC
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATC
8910 TTTGTTCTTC
Statistics
Matches: 315, Mismatches: 22, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
70 18 0.06
71 3 0.01
72 292 0.93
73 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (73 bp):
TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATT
ATCTTCCA
Found at i:9309 original size:19 final size:19
Alignment explanation
Indices: 9285--9321 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9275 GCAACAAAGC
*
9285 TCGAAGCAGACTATCACAT
1 TCGAAGCACACTATCACAT
*
9304 TCGAAGCTCACTATCACA
1 TCGAAGCACACTATCACA
9322 AAATGGAGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
TCGAAGCACACTATCACAT
Found at i:11396 original size:30 final size:31
Alignment explanation
Indices: 11360--11435 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
11350 CTTTCTCCCC
11360 AAAGTCCTCAAGCACAAG-GGCATCC-ATACT
1 AAAGTCCTCAAGCACAAGAGGCA-CCTATACT
* *
11390 AAAGTCCTTAAACAC-AGAGGCACCTATACT
1 AAAGTCCTCAAGCACAAGAGGCACCTATACT
11420 AAAGTCC-CTAAGCACA
1 AAAGTCCTC-AAGCACA
11436 TATAACACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.17
Consensus pattern (31 bp):
AAAGTCCTCAAGCACAAGAGGCACCTATACT
Found at i:13566 original size:17 final size:18
Alignment explanation
Indices: 13544--13581 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
13534 ACATGTAAAT
13544 GTAA-TTAGTGATATATA
1 GTAATTTAGTGATATATA
*
13561 GTAATTTTAGTGATTTATA
1 GTAA-TTTAGTGATATATA
13580 GT
1 GT
13582 CTGAATAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (18 bp):
GTAATTTAGTGATATATA
Found at i:13730 original size:12 final size:12
Alignment explanation
Indices: 13713--13739 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13703 GTCCCCGTTC
13713 CCCGAAAATACT
1 CCCGAAAATACT
13725 CCCGAAAATACT
1 CCCGAAAATACT
13737 CCC
1 CCC
13740 CATCCCCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (12 bp):
CCCGAAAATACT
Found at i:16229 original size:2 final size:2
Alignment explanation
Indices: 16217--16275 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
16207 ATAGTAATAA
*
16217 AT AT AT GT AT AT AT AT AT -T AT -T AT -T AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
16255 AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT A
16276 AACATACATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
1 4 0.08
2 45 0.92
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:17541 original size:2 final size:2
Alignment explanation
Indices: 17534--17558 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17524 TATGATTAAT
17534 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 T
17559 TGGTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24732 original size:16 final size:16
Alignment explanation
Indices: 24711--24742 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
24701 AACAAACAAC
24711 TACAGCCAAGAACCAA
1 TACAGCCAAGAACCAA
*
24727 TACAGCTAAGAACCAA
1 TACAGCCAAGAACCAA
24743 AACAACCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.28, G:0.12, T:0.09
Consensus pattern (16 bp):
TACAGCCAAGAACCAA
Found at i:25604 original size:22 final size:22
Alignment explanation
Indices: 25579--25621 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25569 TTAGTATATT
25579 ATATATATATAATATATATAAC
1 ATATATATATAATATATATAAC
* * *
25601 ATATATTTATATTTTATATAA
1 ATATATATATAATATATATAA
25622 AAAATATCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATATATAATATATATAAC
Found at i:26643 original size:15 final size:15
Alignment explanation
Indices: 26623--26652 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26613 TTGTGGTCAT
26623 AGGTGGTCGAGCGCC
1 AGGTGGTCGAGCGCC
*
26638 AGGTGGTCGGGCGCC
1 AGGTGGTCGAGCGCC
26653 GGGCTTTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.27, G:0.50, T:0.13
Consensus pattern (15 bp):
AGGTGGTCGAGCGCC
Found at i:27115 original size:51 final size:51
Alignment explanation
Indices: 27036--27175 Score: 201
Period size: 51 Copynumber: 2.7 Consensus size: 51
27026 GTCGAGCGTG
* *
27036 GGCGCTC-CACCACATATGGAGATGGTGGGTCGAGCGCCCATATATGGGCTT
1 GGCGCTCGC-CCACACATGAAGATGGTGGGTCGAGCGCCCATATATGGGCTT
* * * *
27087 GGTGCTCGCCCACTCATGAAGATGGTGGGTCGAGTGCCCATATATGGGGTT
1 GGCGCTCGCCCACACATGAAGATGGTGGGTCGAGCGCCCATATATGGGCTT
*
27138 GGCGCTCGCCCACACATGAAGGTGGTGGGTCGAGCGCC
1 GGCGCTCGCCCACACATGAAGATGGTGGGTCGAGCGCC
27176 AATCCCATAT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 77 0.99
52 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.36, T:0.21
Consensus pattern (51 bp):
GGCGCTCGCCCACACATGAAGATGGTGGGTCGAGCGCCCATATATGGGCTT
Found at i:28593 original size:33 final size:34
Alignment explanation
Indices: 28531--28594 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
28521 CTTTTCTTAC
*
28531 TTTCTTTTATTGATTACCACTTTTCACTCTTCTT
1 TTTCTTTTATTGACTACCACTTTTCACTCTTCTT
28565 TTTCTTTATATTGACTACCA-TTTT-ACTCTT
1 TTTCTTT-TATTGACTACCACTTTTCACTCTT
28595 TCAATCACTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 6 0.21
34 11 0.39
35 11 0.39
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (34 bp):
TTTCTTTTATTGACTACCACTTTTCACTCTTCTT
Found at i:28594 original size:24 final size:24
Alignment explanation
Indices: 28567--28622 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
28557 CTCTTCTTTT
* *
28567 TCTTTAT-ATTGACTACCATTTTAC
1 TCTTTATCACTGACCACC-TTTTAC
28591 TCTTTCAATCACTGACCACCTTTTAC
1 TCTTT--ATCACTGACCACCTTTTAC
28617 TCTTTA
1 TCTTTA
28623 CTGATTGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
24 6 0.22
26 13 0.48
27 8 0.30
ACGTcount: A:0.23, C:0.27, G:0.04, T:0.46
Consensus pattern (24 bp):
TCTTTATCACTGACCACCTTTTAC
Found at i:28670 original size:20 final size:20
Alignment explanation
Indices: 28647--28684 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28637 ACTCTTACTG
28647 ATTACCTTCTACTGATTATC
1 ATTACCTTCTACTGATTATC
* *
28667 ATTACTTTTTACTGATTA
1 ATTACCTTCTACTGATTA
28685 CCTTCTTACT
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:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTACCTTCTACTGATTATC
Found at i:28696 original size:22 final size:22
Alignment explanation
Indices: 28668--28809 Score: 99
Period size: 22 Copynumber: 6.9 Consensus size: 22
28658 CTGATTATCA
28668 TTACTTTTTACTGATTACCTTC
1 TTACTTTTTACTGATTACCTTC
* *
28690 TTACTTTTTACTGATTA-ATATT
1 TTACTTTTTACTGATTACCT-TC
*
28712 TTAC-TCTTACTGATTACCTTC
1 TTACTTTTTACTGATTACCTTC
* * *
28733 -TAC---TGA-TTA-T-CATT-
1 TTACTTTTTACTGATTACCTTC
*
28747 TTACTCTTTACTGATTACCTTC
1 TTACTTTTTACTGATTACCTTC
* *
28769 TTACTTTTTACTGATTA-ATATT
1 TTACTTTTTACTGATTACCT-TC
*
28791 TTACTCTTTACTGATTACC
1 TTACTTTTTACTGATTACC
Statistics
Matches: 92, Mismatches: 16, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
15 6 0.07
16 1 0.01
17 2 0.02
18 4 0.04
19 2 0.02
20 4 0.04
21 17 0.18
22 56 0.61
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.53
Consensus pattern (22 bp):
TTACTTTTTACTGATTACCTTC
Found at i:28701 original size:77 final size:78
Alignment explanation
Indices: 28608--28809 Score: 336
Period size: 77 Copynumber: 2.6 Consensus size: 78
28598 ATCACTGACC
* **
28608 ACCTT-TTACTCTTTACTGATTGCTATTTTACTCTTACTGATTACCTTCTACTGATTATCA-TTA
1 ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTACTGATTACCTTCTACTGATTATCATTTA
*
28671 CTTTTTACTGATT
66 CTCTTTACTGATT
28684 ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTACTGATTACCTTCTACTGATTATCATTTT
1 ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTACTGATTACCTTCTACTGATTATCA-TTT
28749 ACTCTTTACTGATT
65 ACTCTTTACTGATT
28763 ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTTACTGATTACC
1 ACCTTCTTACTTTTTACTGATTAATATTTTACTC-TTACTGATTACC
Statistics
Matches: 118, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
76 5 0.04
77 52 0.44
79 49 0.42
80 12 0.10
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.51
Consensus pattern (78 bp):
ACCTTCTTACTTTTTACTGATTAATATTTTACTCTTACTGATTACCTTCTACTGATTATCATTTA
CTCTTTACTGATT
Found at i:28739 original size:35 final size:35
Alignment explanation
Indices: 28613--28769 Score: 147
Period size: 35 Copynumber: 4.3 Consensus size: 35
28603 TGACCACCTT
**
28613 TTACTCTT-TACTGATTGCTATTTTACTCTTACTGA
1 TTAC-CTTCTACTGATTAATATTTTACTCTTACTGA
* **
28648 TTACCTTCTACTGATTATCATTACTTTTTACTGATTACCTTC
1 TTACCTTCTACTGATTA--A-TA--TTTTACT-CTTA-CTGA
* *
28690 TTACTTTTTACTGATTAATATTTTACTCTTACTGA
1 TTACCTTCTACTGATTAATATTTTACTCTTACTGA
28725 TTACCTTCTACTGATT-ATCATTTTACTCTTTACTGA
1 TTACCTTCTACTGATTAAT-ATTTTACTC-TTACTGA
28761 TTACCTTCT
1 TTACCTTCT
28770 TACTTTTTAC
Statistics
Matches: 100, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
34 5 0.05
35 37 0.37
36 19 0.19
37 7 0.07
38 2 0.02
39 2 0.02
40 8 0.08
41 3 0.03
42 17 0.17
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.52
Consensus pattern (35 bp):
TTACCTTCTACTGATTAATATTTTACTCTTACTGA
Done.