Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008859.1 Corchorus capsularis cultivar CVL-1 contig08880, 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: 73087
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:107 original size:19 final size:19
Alignment explanation
Indices: 83--120 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
73 GTTTATTATG
*
83 TTGAATTGAATAAACTAAT
1 TTGAATTGAAAAAACTAAT
102 TTGAATTGAAAAAACTAAT
1 TTGAATTGAAAAAACTAAT
121 CATTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (19 bp):
TTGAATTGAAAAAACTAAT
Found at i:2215 original size:121 final size:121
Alignment explanation
Indices: 2001--2518 Score: 768
Period size: 121 Copynumber: 4.3 Consensus size: 121
1991 GTTATAACTA
* * * * * *
2001 ACCGGCAGGCGATCCGCAAGGACCATTCCTGACCGAGTCTGAAACGATGAAGCCCCCAAGGGGCC
1 ACCGGCAGGCGATCGGCAAGGACCATCCCTGACCGAGTATGAAATGATGAAGCTCCCAAAGGGCC
* *
2066 CAACGCCAACAGGCGAGCAATCAGGCAAGGCCGAGCTCGACCTAGTATGGCAAGCG
66 CAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCAGCG
* * * *
2122 ACCGGCAGGCGATCGGCAAGAACCATCCCTGACCGAATATGAAATGATGAAAC-CCCCAAGTGGC
1 ACCGGCAGGCGATCGGCAAGGACCATCCCTGACCGAGTATGAAATGATGAAGCTCCCAAAG-GGC
* *
2186 CCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGAGCTACTATGGCCAGCG
65 CCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCAGCG
* *
2243 ACCGGCAGGCGATCGGTAAGGACCATCCCTAACCGAGTATGAAATGATGAAGCTCCCAAAGGGCC
1 ACCGGCAGGCGATCGGCAAGGACCATCCCTGACCGAGTATGAAATGATGAAGCTCCCAAAGGGCC
*
2308 CAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGATCTAGTATGGCCAGCG
66 CAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCAGCG
* * * *
2364 ACCGACAGACGATCGGCAAGGACCATCCTTGACCGAGTATGAAATGATGATGCTCCCAAAGGGCC
1 ACCGGCAGGCGATCGGCAAGGACCATCCCTGACCGAGTATGAAATGATGAAGCTCCCAAAGGGCC
* * * *
2429 CAACGCCAATAGGCGAGCGATCGGGCAAGGCCGAGCTCAACCTAGTATGGCCATCG
66 CAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCAGCG
* * *
2485 ACTGGCAGGCGATCGACAAGGACTATCCCTGACC
1 ACCGGCAGGCGATCGGCAAGGACCATCCCTGACC
2519 ATTGATCAAG
Statistics
Matches: 357, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
120 5 0.01
121 346 0.97
122 6 0.02
ACGTcount: A:0.29, C:0.31, G:0.29, T:0.12
Consensus pattern (121 bp):
ACCGGCAGGCGATCGGCAAGGACCATCCCTGACCGAGTATGAAATGATGAAGCTCCCAAAGGGCC
CAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGGCCAGCG
Found at i:2702 original size:25 final size:25
Alignment explanation
Indices: 2621--2702 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
2611 CAATCACGAA
2621 TGTAGAACG-CTGGCCAAGCGTAAAG
1 TGTAGAACGCCT-GCCAAGCGTAAAG
** * **
2646 TGTAGAACGCCCACCGAGCGCCAAG
1 TGTAGAACGCCTGCCAAGCGTAAAG
* * * *
2671 CGGAGAACGCCTGCCAAACGTGAAG
1 TGTAGAACGCCTGCCAAGCGTAAAG
2696 TGTAGAA
1 TGTAGAA
2703 TGTCCGCCGA
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
25 40 0.98
26 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.30, T:0.12
Consensus pattern (25 bp):
TGTAGAACGCCTGCCAAGCGTAAAG
Found at i:2726 original size:50 final size:50
Alignment explanation
Indices: 2617--2727 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 50
2607 GGTCCAATCA
* *
2617 CGAATGTAGAACGCTGGCCAAGCGTAAAGTGTAGAACGCCCACCGAGCGC
1 CGAATGGAGAACGCTGGCCAAACGTAAAGTGTAGAACGCCCACCGAGCGC
* * * * *
2667 C-AAGCGGAGAACGCCT-GCCAAACGTGAAGTGTAGAATGTCCGCCGAGCGC
1 CGAA-TGGAGAACG-CTGGCCAAACGTAAAGTGTAGAACGCCCACCGAGCGC
2717 CGAATGGAGAA
1 CGAATGGAGAA
2728 TGCTTCTTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
49 2 0.04
50 44 0.88
51 4 0.08
ACGTcount: A:0.31, C:0.26, G:0.32, T:0.12
Consensus pattern (50 bp):
CGAATGGAGAACGCTGGCCAAACGTAAAGTGTAGAACGCCCACCGAGCGC
Found at i:2821 original size:98 final size:98
Alignment explanation
Indices: 2707--3175 Score: 704
Period size: 98 Copynumber: 4.8 Consensus size: 98
2697 GTAGAATGTC
* *
2707 CGCCGAGCGCCGAATGGAGAATGCTTCTTGAGAGCAGATGGAGAACGCCAGAGAAGGCGAAAAAG
1 CGCCGAGCGCCGAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAAAG
2772 ATGACGCTCGCCAAACGCGAAGCGTAGGACGCT
66 ATGACGCTCGCCAAACGCGAAGCGTAGGACGCT
* **
2805 CGCCGAGCGCCCAATGGAGAATGCTTATTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAAAG
1 CGCCGAGCGCCGAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAAAG
*
2870 ATGACGCTCGCCAAACGCGAAGCGTAGGACACT
66 ATGACGCTCGCCAAACGCGAAGCGTAGGACGCT
* * * *
2903 CGCTGAGCGCCGAACGAAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGTGAAAAAG
1 CGCCGAGCGCCGAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAAAG
* *
2968 ATGACGCTCGCCAAACTCGAAGTGTAGGACGCT
66 ATGACGCTCGCCAAACGCGAAGCGTAGGACGCT
* * * ** *
3001 CACTGAGCGCCGAATGGAGAATGCTCCTTGAGAGCAAATAAAGAACGCCCGAGATGGCGAAAAAG
1 CGCCGAGCGCCGAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAAAG
* *
3066 ATGACGTTCGCCAAACGCGAAGCGTAGAACGCT
66 ATGACGCTCGCCAAACGCGAAGCGTAGGACGCT
* * * ** *
3099 CGTCGATCGCCAAATGGAGAATGCTCCTTGACTGCAGATGGAGAACGCCCGAGATGGCGAAAAAG
1 CGCCGAGCGCCGAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAAAG
3164 ATGACGCTCGCC
66 ATGACGCTCGCC
3176 GAGCGCCAAA
Statistics
Matches: 334, Mismatches: 37, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 334 1.00
ACGTcount: A:0.32, C:0.24, G:0.31, T:0.13
Consensus pattern (98 bp):
CGCCGAGCGCCGAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAAAG
ATGACGCTCGCCAAACGCGAAGCGTAGGACGCT
Found at i:3183 original size:73 final size:73
Alignment explanation
Indices: 3094--3248 Score: 265
Period size: 73 Copynumber: 2.1 Consensus size: 73
3084 GAAGCGTAGA
* * * *
3094 ACGCTCGTCGATCGCCAAATGGAGAATGCTCCTTGACTGCAGATGGAGAACGCCCGAGATGGCGA
1 ACGCTCGCCGAGCGCCAAATGGAGAATGCTCCTTGACAGCAGATGGAGAACGCCCGAGAAGGCGA
3159 AAAAGATG
66 AAAAGATG
*
3167 ACGCTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGA
1 ACGCTCGCCGAGCGCCAAATGGAGAATGCTCCTTGACAGCAGATGGAGAACGCCCGAGAAGGCGA
3232 AAAAGATG
66 AAAAGATG
3240 ACGCTCGCC
1 ACGCTCGCC
3249 AAACGTGAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.30, C:0.25, G:0.31, T:0.14
Consensus pattern (73 bp):
ACGCTCGCCGAGCGCCAAATGGAGAATGCTCCTTGACAGCAGATGGAGAACGCCCGAGAAGGCGA
AAAAGATG
Found at i:3288 original size:171 final size:171
Alignment explanation
Indices: 2995--3346 Score: 508
Period size: 171 Copynumber: 2.1 Consensus size: 171
2985 CGAAGTGTAG
* * * *
2995 GACGCTCACTGAGCGCCGAATGGAGAATGCTCCTTGAGAGCAAATAAAGAACGCCCGAGATGGCG
1 GACGCTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAAATAAAGAACGCCCGAGAAGGCG
* * * *
3060 AAAAAGATGACGTTCGCCAAACGCGAAGCGTAGAACGCTCGTCGATCGCCAAATGGAGAATGCTC
66 AAAAAGATGACGCTCGCCAAACGCGAAGCGTAGAACACTCCTCGAGCGCCAAATGGAGAATGCTC
* *
3125 CTTGACTGCAGATGGAGAACGCCCGAGATGGCGAAAAAGAT
131 CTTGACAGCAGATGAAGAACGCCCGAGATGGCGAAAAAGAT
* **
3166 GACGCTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCG
1 GACGCTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAAATAAAGAACGCCCGAGAAGGCG
* * * *
3231 AAAAAGATGACGCTCGCCAAACGTGAAGTGTAGGACACTCACT-GAGCGCCGAATGGAGAATGCT
66 AAAAAGATGACGCTCGCCAAACGCGAAGCGTAGAACACTC-CTCGAGCGCCAAATGGAGAATGCT
* * *
3295 CCTTGAGAGTAGATGAAGAACTCCCGAGATGGCGAAAAAGAT
130 CCTTGACAGCAGATGAAGAACGCCCGAGATGGCGAAAAAGAT
3337 GACGCTCGCC
1 GACGCTCGCC
3347 AAACGCAAAG
Statistics
Matches: 160, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
171 159 0.99
172 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.30, T:0.14
Consensus pattern (171 bp):
GACGCTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAAATAAAGAACGCCCGAGAAGGCG
AAAAAGATGACGCTCGCCAAACGCGAAGCGTAGAACACTCCTCGAGCGCCAAATGGAGAATGCTC
CTTGACAGCAGATGAAGAACGCCCGAGATGGCGAAAAAGAT
Found at i:3299 original size:98 final size:98
Alignment explanation
Indices: 3174--3444 Score: 398
Period size: 98 Copynumber: 2.8 Consensus size: 98
3164 ATGACGCTCG
*
3174 CCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAAAGAT
1 CCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGATGGCGAAAAAGAT
** * *
3239 GACGCTCGCCAAACGTGAAGTGTAGGACACTCA
66 GACGCTCGCCAAACGCAAAGCGTAGAACACTCA
* * * * *
3272 CTGAGCGCCGAATGGAGAATGCTCCTTGAGAGTAGATGAAGAACTCCCGAGATGGCGAAAAAGAT
1 CCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGATGGCGAAAAAGAT
** *
3337 GACGCTCGCCAAACGCAAAGCGTAGAATGCTCG
66 GACGCTCGCCAAACGCAAAGCGTAGAACACTCA
* **
3370 CCGAACGCCAAATGGAGAATGCTCCTTGACTGCAGATGGAGAACGCCCGAGATGGCGAAAAAGAT
1 CCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGATGGCGAAAAAGAT
3435 GACGCTCGCC
66 GACGCTCGCC
3445 GATCGCCAAA
Statistics
Matches: 152, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 152 1.00
ACGTcount: A:0.32, C:0.24, G:0.30, T:0.14
Consensus pattern (98 bp):
CCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGATGGCGAAAAAGAT
GACGCTCGCCAAACGCAAAGCGTAGAACACTCA
Found at i:3368 original size:25 final size:25
Alignment explanation
Indices: 3340--3393 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3330 AAAAGATGAC
3340 GCTCGCCAAACG-CAAA-GCGTAGAAT
1 GCTCGCCAAACGCCAAATG-G-AGAAT
*
3365 GCTCGCCGAACGCCAAATGGAGAAT
1 GCTCGCCAAACGCCAAATGGAGAAT
3390 GCTC
1 GCTC
3394 CTTGACTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 20 0.77
26 5 0.19
27 1 0.04
ACGTcount: A:0.31, C:0.30, G:0.26, T:0.13
Consensus pattern (25 bp):
GCTCGCCAAACGCCAAATGGAGAAT
Found at i:3386 original size:269 final size:269
Alignment explanation
Indices: 2901--3467 Score: 974
Period size: 269 Copynumber: 2.1 Consensus size: 269
2891 GCGTAGGACA
* * * * *
2901 CTCGCTGAGCGCCGAACGAAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGTGAAAA
1 CTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAA
*
2966 AGATGACGCTCGCCAAACTCGAAGTGTAGGACGCTCACTGAGCGCCGAATGGAGAATGCTCCTTG
66 AGATGACGCTCGCCAAACTCGAAGTGTAGGACACTCACTGAGCGCCGAATGGAGAATGCTCCTTG
* *
3031 AGAGCAAATAAAGAACGCCCGAGATGGCGAAAAAGATGACGTTCGCCAAACGCGAAGCGTAGAAC
131 AGAGCAAATAAAGAACGCCCGAGATGGCGAAAAAGATGACGCTCGCCAAACGCAAAGCGTAGAAC
* *
3096 GCTCGTCGATCGCCAAATGGAGAATGCTCCTTGACTGCAGATGGAGAACGCCCGAGATGGCGAAA
196 GCTCGCCGAACGCCAAATGGAGAATGCTCCTTGACTGCAGATGGAGAACGCCCGAGATGGCGAAA
3161 AAGATGACG
261 AAGATGACG
3170 CTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAA
1 CTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAA
3235 AGATGACGCTCGCCAAACGT-GAAGTGTAGGACACTCACTGAGCGCCGAATGGAGAATGCTCCTT
66 AGATGACGCTCGCCAAAC-TCGAAGTGTAGGACACTCACTGAGCGCCGAATGGAGAATGCTCCTT
* * * *
3299 GAGAGTAGATGAAGAACTCCCGAGATGGCGAAAAAGATGACGCTCGCCAAACGCAAAGCGTAGAA
130 GAGAGCAAATAAAGAACGCCCGAGATGGCGAAAAAGATGACGCTCGCCAAACGCAAAGCGTAGAA
*
3364 TGCTCGCCGAACGCCAAATGGAGAATGCTCCTTGACTGCAGATGGAGAACGCCCGAGATGGCGAA
195 CGCTCGCCGAACGCCAAATGGAGAATGCTCCTTGACTGCAGATGGAGAACGCCCGAGATGGCGAA
3429 AAAGATGACG
260 AAAGATGACG
*
3439 CTCGCCGATCGCCAAATGGAGAATGCTCC
1 CTCGCCGAGCGCCAAATGGAGAATGCTCC
3468 AACGCGAAGC
Statistics
Matches: 281, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
269 280 1.00
270 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.30, T:0.14
Consensus pattern (269 bp):
CTCGCCGAGCGCCAAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCGAAAA
AGATGACGCTCGCCAAACTCGAAGTGTAGGACACTCACTGAGCGCCGAATGGAGAATGCTCCTTG
AGAGCAAATAAAGAACGCCCGAGATGGCGAAAAAGATGACGCTCGCCAAACGCAAAGCGTAGAAC
GCTCGCCGAACGCCAAATGGAGAATGCTCCTTGACTGCAGATGGAGAACGCCCGAGATGGCGAAA
AAGATGACG
Found at i:3577 original size:73 final size:73
Alignment explanation
Indices: 3482--3636 Score: 256
Period size: 73 Copynumber: 2.1 Consensus size: 73
3472 CGAAGCGTAG
* * * * *
3482 GACGCTCACTGAGCGACGAATGGAGAATGCTCCTTGAGAGCAGATGGAGAACGCCCGAGAAGGCG
1 GACGCTCGCCGAGCGACAAATGGAGAAAGCTCCTTGAGAGCAGAGGGAGAACGCCCGAGAAGGCG
3547 AAAAAGAT
66 AAAAAGAT
*
3555 GACGCTCGCCGAGCGCCAAATGGAGAAAGCTCCTTGAGAGCAGAGGGAGAACGCCCGAGAAGGCG
1 GACGCTCGCCGAGCGACAAATGGAGAAAGCTCCTTGAGAGCAGAGGGAGAACGCCCGAGAAGGCG
3620 AAAAAGAT
66 AAAAAGAT
3628 GACGCTCGC
1 GACGCTCGC
3637 GAAACGCGAA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.33, C:0.23, G:0.34, T:0.10
Consensus pattern (73 bp):
GACGCTCGCCGAGCGACAAATGGAGAAAGCTCCTTGAGAGCAGAGGGAGAACGCCCGAGAAGGCG
AAAAAGAT
Found at i:3863 original size:25 final size:25
Alignment explanation
Indices: 3802--3857 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3792 GTGAAGTGTT
* *
3802 GAACGCCTGCCGAGCGCTAAGCGGA
1 GAACGCCGGCCGAGCGCTAAGAGGA
*
3827 GAACGCCGGCCGAGCGCTAGGAGGA
1 GAACGCCGGCCGAGCGCTAAGAGGA
3852 GAACGC
1 GAACGC
3858 TCGCCGGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.30, G:0.39, T:0.05
Consensus pattern (25 bp):
GAACGCCGGCCGAGCGCTAAGAGGA
Found at i:5862 original size:56 final size:56
Alignment explanation
Indices: 5774--5918 Score: 200
Period size: 56 Copynumber: 2.6 Consensus size: 56
5764 CAAGTATCGT
* * * * * * * *
5774 AAATGTAAAAAATGATTATTAGGAGAGCTTTATCGTCTTAGAAGATCTTTGAATTT
1 AAATGTAAAATATAATTGTTGGGAGAGTTTTATCGCCTTAAAAGATCTTTGAATTC
*
5830 GAATGTAAAATATAATTGTTGGGAGAGTTTTATCGCCTTAAAAGATCTTTGAATTC
1 AAATGTAAAATATAATTGTTGGGAGAGTTTTATCGCCTTAAAAGATCTTTGAATTC
*
5886 AAATGTAAAATATCATTGTTGGGAGAGTTTTAT
1 AAATGTAAAATATAATTGTTGGGAGAGTTTTAT
5919 TTCATAATAG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 78 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (56 bp):
AAATGTAAAATATAATTGTTGGGAGAGTTTTATCGCCTTAAAAGATCTTTGAATTC
Found at i:7048 original size:12 final size:12
Alignment explanation
Indices: 7031--7055 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7021 TTTTTAAACC
7031 ATGAAAAACTTG
1 ATGAAAAACTTG
7043 ATGAAAAACTTG
1 ATGAAAAACTTG
7055 A
1 A
7056 CAAAGTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
ATGAAAAACTTG
Found at i:9841 original size:28 final size:28
Alignment explanation
Indices: 9787--9846 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
9777 TAAACTTTTG
* **
9787 AAATATTGTACTAATTTTTTTTGAAGAA
1 AAATATTGTACTAATTATTACTGAAGAA
9815 AAATATTGTACTAATTAATTACT-AAGAA
1 AAATATTGTACTAATT-ATTACTGAAGAA
9843 AAAT
1 AAAT
9847 TATAGGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (28 bp):
AAATATTGTACTAATTATTACTGAAGAA
Found at i:16383 original size:3 final size:3
Alignment explanation
Indices: 16375--16399 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16365 GTTCAACTTT
16375 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
16400 AAAAGTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:24285 original size:180 final size:180
Alignment explanation
Indices: 23981--24325 Score: 530
Period size: 180 Copynumber: 1.9 Consensus size: 180
23971 AATTTTTTTT
* * *
23981 TATCCCATCCGGTATATAAGGCTTTGCCCTGATTAATCCGGATCCGACCCGCGTCGCGCACCTGA
1 TATCCCATCCGGTATACAAGGCTTTGCCCTGACTAATCCGGATCCGACCCGCGTCACGCACCTGA
* * *
24046 TTATGGTGGGTGAGTCTCCTAATAGGGACAGCTGCGTACGCAAGATCTCGAACCCGAGACCTGCT
66 TTATGGTAGGTGAGTCTCCTAACAGGGACAGCTGCGTACGCAAGATCTCGAACCCGAGACCTACT
*
24111 TAAATTGGAACATGCCGCTTACCACTTGATCCAACAGGGGCAGCCGTTGG
131 TAAACTGGAACATGCCGCTTACCACTTGATCCAACAGGGGCAGCCGTTGG
* * * *
24161 TATCCCATCCGGTATCCAGGGCTTTGCCCTGACTAATCCGGATCCGACCCGCGTCACGCATCTGG
1 TATCCCATCCGGTATACAAGGCTTTGCCCTGACTAATCCGGATCCGACCCGCGTCACGCACCTGA
* * * *
24226 TTATGGTAGGTGAGTCTTCC-AACAGGGGCAGCTGCGTACGTAAGGTCTCGAATCCGAGACCTAC
66 TTATGGTAGGTGAGTC-TCCTAACAGGGACAGCTGCGTACGCAAGATCTCGAACCCGAGACCTAC
*
24290 TTAAGCTGGAACATGCCGCTTACCACTTGATCCAAC
130 TTAAACTGGAACATGCCGCTTACCACTTGATCCAAC
24326 CCCTTGTTGG
Statistics
Matches: 148, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 145 0.98
181 3 0.02
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.23
Consensus pattern (180 bp):
TATCCCATCCGGTATACAAGGCTTTGCCCTGACTAATCCGGATCCGACCCGCGTCACGCACCTGA
TTATGGTAGGTGAGTCTCCTAACAGGGACAGCTGCGTACGCAAGATCTCGAACCCGAGACCTACT
TAAACTGGAACATGCCGCTTACCACTTGATCCAACAGGGGCAGCCGTTGG
Found at i:25260 original size:2 final size:2
Alignment explanation
Indices: 25253--25283 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25243 GTAGGGAAGA
25253 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
25284 AGAAGAAAGA
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:28805 original size:29 final size:29
Alignment explanation
Indices: 28748--28805 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
28738 AATAATCATC
* * *
28748 TCATCAATTACTTCATCCACCCAACCTTT
1 TCATCAATTACTTCAGCCACCAAAACTTT
28777 TCATCAATTA-TTACAGCCACCAAAACTTT
1 TCATCAATTACTT-CAGCCACCAAAACTTT
28806 CGCCAATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.33
Consensus pattern (29 bp):
TCATCAATTACTTCAGCCACCAAAACTTT
Found at i:32547 original size:171 final size:166
Alignment explanation
Indices: 32326--32674 Score: 398
Period size: 170 Copynumber: 2.1 Consensus size: 166
32316 CAAGGCTTAC
* * * * *
32326 TTGGTCATTTCTCAATTGACTTTAATAGAGTTGTGAAATTACTGAAAGATCC-CTACCAAGCCTT
1 TTGGTCATTTCTCAATGGACTTTAATAGAATAGTGAAATTACTAAAAGATCCAC-ACCAAGCATT
** ** * * * * * * *
32390 TCTTTTGGAG-CTAGAGAACTTATTTTTTTCGTTTTTTCCTACTTTGCAGATTGCTTAAATGTTC
65 GATGAT-GAGTCTA-AGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCC
* *
32454 TAACTTTTGATTCTTGATAGGAGCCATTAAATAAGTAATCTTT
128 TAACTTTTGATTCTTG--AGG-G-CATTAAATAACTAAACTTT
* * *
32497 TTGGTCATTTCTCAATGGA-TTTGAATAGAATAGTGGAATTACTAAAAGATCCACATCAAGGATT
1 TTGGTCATTTCTCAATGGACTTT-AATAGAATAGTGAAATTACTAAAAGATCCACACCAAGCATT
*
32561 GATGATGAGTTTAAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTA
65 GATGATGAGTCTAAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTA
*
32626 ACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTT
130 ACTTTTGATTCTTGAGGGCATTAAATAACTAAACTTT
32663 TTGGTCATTTCT
1 TTGGTCATTTCT
32675 TAATTGACAA
Statistics
Matches: 152, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
166 28 0.18
167 1 0.01
168 3 0.02
170 65 0.43
171 54 0.36
172 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (166 bp):
TTGGTCATTTCTCAATGGACTTTAATAGAATAGTGAAATTACTAAAAGATCCACACCAAGCATTG
ATGATGAGTCTAAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAA
CTTTTGATTCTTGAGGGCATTAAATAACTAAACTTT
Found at i:40491 original size:4 final size:4
Alignment explanation
Indices: 40478--40513 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
40468 ATAAAAAGCA
40478 CTTT -TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
40514 CCTTCCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:43041 original size:65 final size:64
Alignment explanation
Indices: 42954--43105 Score: 177
Period size: 62 Copynumber: 2.4 Consensus size: 64
42944 GCATTAATTT
* ** * **
42954 GACCAAACCCAAGACTGCAAGTCCATAATAATCAAATTATGTTCAAAACCCAAACTT-TATTTAT
1 GACCAAACCCAAGATTAAAAGTCCAT-ATAATCAAACTACATTCAAAACCC-AACTTCTATTTAT
43018 G
64 G
* *
43019 GACCAAACCCAAGATTAAAAGTCC--ATGATCAAACTACATTCAAAACCCAAGTTCTATTTATG
1 GACCAAACCCAAGATTAAAAGTCCATATAATCAAACTACATTCAAAACCCAACTTCTATTTATG
*
43081 GACCAAACCCAAGATTATAA-TCCAT
1 GACCAAACCCAAGATTAAAAGTCCAT
43106 GATCAAACTA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
61 7 0.09
62 47 0.63
65 21 0.28
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (64 bp):
GACCAAACCCAAGATTAAAAGTCCATATAATCAAACTACATTCAAAACCCAACTTCTATTTATG
Found at i:43077 original size:62 final size:61
Alignment explanation
Indices: 42995--43153 Score: 203
Period size: 62 Copynumber: 2.5 Consensus size: 61
42985 TCAAATTATG
42995 TTCAAAACCCAAACTTTATTTATGGACCAAACCCAAGATTAAAAGTCCATGATCAAACTACA
1 TTCAAAACCCAAACTTTATTTATGGACCAAACCCAAGATTAAAA-TCCATGATCAAACTACA
* *
43057 TTCAAAACCC-AAGTTCTATTTATGGACCAAACCCAAGATTATAATCCATGATCAAACTATGTTC
1 TTCAAAACCCAAACTT-TATTTATGGACCAAACCCAAGATTAAAATCCATGATCAAACTA----C
43121 AAAA
61 ---A
*
43125 ATCAAAACCCAAACTTTATTTATGGACCA
1 TTCAAAACCCAAACTTTATTTATGGACCA
43154 CGTCCCGAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
61 19 0.23
62 37 0.44
65 1 0.01
68 23 0.27
69 4 0.05
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.26
Consensus pattern (61 bp):
TTCAAAACCCAAACTTTATTTATGGACCAAACCCAAGATTAAAATCCATGATCAAACTACA
Found at i:47472 original size:14 final size:14
Alignment explanation
Indices: 47453--47482 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47443 GAAGTAAACT
47453 ATGAGGCAGAAAGC
1 ATGAGGCAGAAAGC
47467 ATGAGGCAGAAAGC
1 ATGAGGCAGAAAGC
47481 AT
1 AT
47483 AAGTCCTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.33, T:0.10
Consensus pattern (14 bp):
ATGAGGCAGAAAGC
Found at i:60698 original size:19 final size:19
Alignment explanation
Indices: 60674--60711 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
60664 ATGAAAATAT
60674 TAATCAATGTCACATTTTC
1 TAATCAATGTCACATTTTC
*
60693 TAATCAATGTCATATTTTC
1 TAATCAATGTCACATTTTC
60712 CCTTGCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (19 bp):
TAATCAATGTCACATTTTC
Found at i:72696 original size:10 final size:10
Alignment explanation
Indices: 72683--72713 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
72673 TCTTTCTCTC
*
72683 TCTATATGTA
1 TCTATATATA
72693 TCTATATATA
1 TCTATATATA
72703 TCTATATATA
1 TCTATATATA
72713 T
1 T
72714 GTGTGTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (10 bp):
TCTATATATA
Done.