Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006354.1 Corchorus capsularis cultivar CVL-1 contig06375, 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: 87822
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2267 original size:22 final size:21
Alignment explanation
Indices: 2221--2267 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
2211 GAATGGCCAT
* *
2221 CTATTTAATTAGGTATGATTT
1 CTATTTAATTAGATATGATTC
2242 CTATTGTAATTAGATGA-GATTC
1 CTATT-TAATTAGAT-ATGATTC
2264 CTAT
1 CTAT
2268 ATGCAATCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 16 0.73
23 1 0.05
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (21 bp):
CTATTTAATTAGATATGATTC
Found at i:2914 original size:21 final size:20
Alignment explanation
Indices: 2879--2939 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
2869 TTTCCTTTAG
* *
2879 TTTTGTTTTTATTTTTCGTA
1 TTTTGTTTTTGTTTTTTGTA
*
2899 TTTTGTTTTTGTTTTTTGTT
1 TTTTGTTTTTGTTTTTTGTA
2919 TTTATGTTTTTGTGTTTTTGT
1 TTT-TGTTTTTGT-TTTTTGT
2940 TAATTTTGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 20 0.56
21 9 0.25
22 7 0.19
ACGTcount: A:0.05, C:0.02, G:0.15, T:0.79
Consensus pattern (20 bp):
TTTTGTTTTTGTTTTTTGTA
Found at i:2939 original size:8 final size:7
Alignment explanation
Indices: 2879--2937 Score: 59
Period size: 7 Copynumber: 8.4 Consensus size: 7
2869 TTTCCTTTAG
2879 TTTTG-T
1 TTTTGTT
*
2885 TTTTATT
1 TTTTGTT
* *
2892 TTTCGTA
1 TTTTGTT
2899 TTTTG-T
1 TTTTGTT
2905 TTTTGTT
1 TTTTGTT
2912 TTTTGTT
1 TTTTGTT
2919 TTTATGTT
1 TTT-TGTT
2927 TTTGTGTT
1 TTT-TGTT
2935 TTT
1 TTT
2938 GTTAATTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 9 0.21
7 20 0.47
8 14 0.33
ACGTcount: A:0.05, C:0.02, G:0.14, T:0.80
Consensus pattern (7 bp):
TTTTGTT
Found at i:6059 original size:18 final size:18
Alignment explanation
Indices: 6018--6060 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
6008 ATTTGTTTGC
*
6018 TTGTCTTTAGTTTTGTTT
1 TTGTTTTTAGTTTTGTTT
** *
6036 AAGTTTTTAGTTTTTTTT
1 TTGTTTTTAGTTTTGTTT
6054 TTGTTTT
1 TTGTTTT
6061 CTAGCTTGCT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.09, C:0.02, G:0.14, T:0.74
Consensus pattern (18 bp):
TTGTTTTTAGTTTTGTTT
Found at i:6908 original size:22 final size:21
Alignment explanation
Indices: 6862--6908 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
6852 GAATGGCCAT
* *
6862 CTATTTAATTAGGTATGATTT
1 CTATTTAATTAGATATGATTC
6883 CTATTGTAATTAGATGA-GATTC
1 CTATT-TAATTAGAT-ATGATTC
6905 CTAT
1 CTAT
6909 ATGCAATCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 16 0.73
23 1 0.05
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (21 bp):
CTATTTAATTAGATATGATTC
Found at i:11070 original size:22 final size:21
Alignment explanation
Indices: 11032--11192 Score: 82
Period size: 22 Copynumber: 8.0 Consensus size: 21
11022 TTAATTATTG
*
11032 ATATG-TTAAGTGTGTTTTTA
1 ATATGTTTAAGTGGGTTTTTA
11052 ATATGTTATAAGTGGGTTTTTA
1 ATATGTT-TAAGTGGGTTTTTA
* * *
11074 AT-TCCCTTTAA-----TTATTG
1 ATAT--GTTTAAGTGGGTTTTTA
11091 ATATG-TTAAGTGGGTTTTTA
1 ATATGTTTAAGTGGGTTTTTA
*
11111 ATATGTTACAAGTGGGTTTTTA
1 ATATGTT-TAAGTGGGTTTTTA
* * *
11133 AT-TCCCTTTAA-----TTATTG
1 ATAT--GTTTAAGTGGGTTTTTA
11150 ATATG-TTAAGTGGGTTTTTA
1 ATATGTTTAAGTGGGTTTTTA
11170 ATATGTTTTAAGTGGGTTTTTA
1 ATATG-TTTAAGTGGGTTTTTA
11192 A
1 A
11193 GACATCTCAT
Statistics
Matches: 104, Mismatches: 15, Indels: 42
0.65 0.09 0.26
Matches are distributed among these distances:
15 8 0.08
17 12 0.12
18 2 0.02
20 23 0.22
21 4 0.04
22 51 0.49
23 4 0.04
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.51
Consensus pattern (21 bp):
ATATGTTTAAGTGGGTTTTTA
Found at i:11113 original size:59 final size:59
Alignment explanation
Indices: 11016--11192 Score: 318
Period size: 59 Copynumber: 3.0 Consensus size: 59
11006 TAATTTGAGG
* *
11016 TTCCATTTAATTATTGATATGTTAAGTGTGTTTTTAATATGTTATAAGTGGGTTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
*
11075 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTACAAGTGGGTTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
*
11134 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTTTAAGTGGGTTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
11193 GACATCTCAT
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 113 1.00
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.51
Consensus pattern (59 bp):
TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
Found at i:11563 original size:27 final size:27
Alignment explanation
Indices: 11508--11565 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
11498 TTTGCTACTC
* * ** *
11508 AACTTTTCCTACTCCTTTACATTATCA
1 AACTGTTCCTACTCCTTAACAACACCA
11535 AACTGTTCCTACTCCTTAACAACACCA
1 AACTGTTCCTACTCCTTAACAACACCA
11562 AACT
1 AACT
11566 ACACCAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.34
Consensus pattern (27 bp):
AACTGTTCCTACTCCTTAACAACACCA
Found at i:20530 original size:12 final size:12
Alignment explanation
Indices: 20513--20538 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20503 TAGATTCAAA
20513 TTCTCTTCAATT
1 TTCTCTTCAATT
20525 TTCTCTTCAATT
1 TTCTCTTCAATT
20537 TT
1 TT
20539 AATCCACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTCTTCAATT
Found at i:22782 original size:2 final size:2
Alignment explanation
Indices: 22775--22802 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22765 TTGTTAGATA
22775 AT 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 AT
22803 GTTGAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24769 original size:32 final size:32
Alignment explanation
Indices: 24732--24834 Score: 161
Period size: 32 Copynumber: 3.2 Consensus size: 32
24722 GCCCGACTCA
*
24732 AGACCCGAATGACCCGCAACCCAGATGACCCG
1 AGACCCGAATGACCCGTAACCCAGATGACCCG
* * *
24764 AGACCCGAATGACGCGTAACCCAAATAACCCG
1 AGACCCGAATGACCCGTAACCCAGATGACCCG
*
24796 AAACCCGAATGACCCGTAACCCAGATGACCCG
1 AGACCCGAATGACCCGTAACCCAGATGACCCG
24828 AGACCCG
1 AGACCCG
24835 TAACCCGAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.34, C:0.38, G:0.20, T:0.08
Consensus pattern (32 bp):
AGACCCGAATGACCCGTAACCCAGATGACCCG
Found at i:24832 original size:23 final size:23
Alignment explanation
Indices: 24806--24875 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
24796 AAACCCGAAT
*
24806 GACCCGTAACCCAG-ATGACCCGA
1 GACCCGTAACCC-GAATAACCCGA
24829 GACCCGTAACCCGAATAACCCGA
1 GACCCGTAACCCGAATAACCCGA
* *
24852 GA--AGTTAACCCGAATGACCCGA
1 GACCCG-TAACCCGAATAACCCGA
24874 GA
1 GA
24876 ATATTATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 22 0.52
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.10
Consensus pattern (23 bp):
GACCCGTAACCCGAATAACCCGA
Found at i:24833 original size:16 final size:16
Alignment explanation
Indices: 24740--24827 Score: 83
Period size: 16 Copynumber: 5.5 Consensus size: 16
24730 CAAGACCCGA
*
24740 ATGACCCGCAACCCAG
1 ATGACCCGTAACCCAG
24756 ATGACCCG-AGACCC-G
1 ATGACCCGTA-ACCCAG
* *
24771 AATGACGCGTAACCCAA
1 -ATGACCCGTAACCCAG
* *
24788 ATAACCCGAAACCC-G
1 ATGACCCGTAACCCAG
24803 AATGACCCGTAACCCAG
1 -ATGACCCGTAACCCAG
24820 ATGACCCG
1 ATGACCCG
24828 AGACCCGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
15 2 0.03
16 54 0.93
17 2 0.03
ACGTcount: A:0.34, C:0.38, G:0.19, T:0.09
Consensus pattern (16 bp):
ATGACCCGTAACCCAG
Found at i:24863 original size:22 final size:22
Alignment explanation
Indices: 24835--24876 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
24825 CCGAGACCCG
24835 TAACCCGAATAACCCGAGAAGT
1 TAACCCGAATAACCCGAGAAGT
*
24857 TAACCCGAATGACCCGAGAA
1 TAACCCGAATAACCCGAGAA
24877 TATTATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (22 bp):
TAACCCGAATAACCCGAGAAGT
Found at i:25904 original size:30 final size:30
Alignment explanation
Indices: 25870--25966 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 30
25860 TTGGCTCCCA
25870 TCGATTTCCCTCTGTTGACCCATCTCCTCT
1 TCGATTTCCCTCTGTTGACCCATCTCCTCT
* ** ***** *
25900 TCGATTTCCTTCT-CAGATTTGGCT-CTCA
1 TCGATTTCCCTCTGTTGACCCATCTCCTCT
25928 TCGATTTCCCTCTGTTGACCCATCTCCTCT
1 TCGATTTCCCTCTGTTGACCCATCTCCTCT
25958 TCGATTTCC
1 TCGATTTCC
25967 TTCTCAGATT
Statistics
Matches: 47, Mismatches: 18, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
28 15 0.32
29 8 0.17
30 24 0.51
ACGTcount: A:0.11, C:0.36, G:0.11, T:0.41
Consensus pattern (30 bp):
TCGATTTCCCTCTGTTGACCCATCTCCTCT
Found at i:25930 original size:58 final size:58
Alignment explanation
Indices: 25859--26004 Score: 283
Period size: 58 Copynumber: 2.5 Consensus size: 58
25849 TCAAATTCAT
*
25859 TTTGGCTCCCATCGATTTCCCTCTGTTGACCCATCTCCTCTTCGATTTCCTTCTCAGA
1 TTTGGCTCTCATCGATTTCCCTCTGTTGACCCATCTCCTCTTCGATTTCCTTCTCAGA
25917 TTTGGCTCTCATCGATTTCCCTCTGTTGACCCATCTCCTCTTCGATTTCCTTCTCAGA
1 TTTGGCTCTCATCGATTTCCCTCTGTTGACCCATCTCCTCTTCGATTTCCTTCTCAGA
25975 TTTGGCTCTCATCGATTTCCCTCTGTTGAC
1 TTTGGCTCTCATCGATTTCCCTCTGTTGAC
26005 TAGGTTATAC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 87 1.00
ACGTcount: A:0.12, C:0.34, G:0.13, T:0.41
Consensus pattern (58 bp):
TTTGGCTCTCATCGATTTCCCTCTGTTGACCCATCTCCTCTTCGATTTCCTTCTCAGA
Found at i:25936 original size:28 final size:28
Alignment explanation
Indices: 25900--25994 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 28
25890 CATCTCCTCT
25900 TCGATTTCCTTCTCAGATTTGGCTCTCA
1 TCGATTTCCTTCTCAGATTTGGCTCTCA
* ** ***** *
25928 TCGATTTCCCTCTGTTGACCCATCTCCTCT
1 TCGATTTCCTTCT-CAGATTTGGCT-CTCA
25958 TCGATTTCCTTCTCAGATTTGGCTCTCA
1 TCGATTTCCTTCTCAGATTTGGCTCTCA
25986 TCGATTTCC
1 TCGATTTCC
25995 CTCTGTTGAC
Statistics
Matches: 47, Mismatches: 18, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
28 24 0.51
29 8 0.17
30 15 0.32
ACGTcount: A:0.13, C:0.33, G:0.13, T:0.42
Consensus pattern (28 bp):
TCGATTTCCTTCTCAGATTTGGCTCTCA
Found at i:26473 original size:23 final size:23
Alignment explanation
Indices: 26425--26473 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
26415 CTATTGGAAG
*
26425 TTTCTCATCTTTTATCCATTTTC
1 TTTCTCATCTTTTATCCATTTGC
26448 TTTCTCCAT-TTTTATCC-TTTCGC
1 TTTCT-CATCTTTTATCCATTT-GC
26471 TTT
1 TTT
26474 TTTTCTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 17 0.74
24 3 0.13
ACGTcount: A:0.10, C:0.27, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTCTCATCTTTTATCCATTTGC
Found at i:28578 original size:2 final size:2
Alignment explanation
Indices: 28571--28595 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28561 TTGCCGTTAT
28571 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
28596 TTAAATCTTT
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:29793 original size:2 final size:2
Alignment explanation
Indices: 29786--29814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29776 TCTTATAGGT
29786 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 T
29815 TGATTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31994 original size:42 final size:42
Alignment explanation
Indices: 31937--32018 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
31927 TATTGACACA
*
31937 TACCCCACCTAATAATTAATTATGTATTTAATATTCAAAACC
1 TACCCCACCTAATAATAAATTATGTATTTAATATTCAAAACC
* *
31979 TACCTCACCTGATAATAAATTATGTATTTAATATTCAAAA
1 TACCCCACCTAATAATAAATTATGTATTTAATATTCAAAA
32019 TTAATATCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (42 bp):
TACCCCACCTAATAATAAATTATGTATTTAATATTCAAAACC
Found at i:32262 original size:9 final size:9
Alignment explanation
Indices: 32250--32344 Score: 68
Period size: 9 Copynumber: 11.8 Consensus size: 9
32240 CCAACCCGAA
32250 ACCCGAATG
1 ACCCGAATG
*
32259 ACCCGGA--
1 ACCCGAATG
*
32266 ACCTGAATG
1 ACCCGAATG
*
32275 ACCTG-A-G
1 ACCCGAATG
*
32282 ACCCAAATG
1 ACCCGAATG
32291 ACCCG-A-G
1 ACCCGAATG
32298 ACCCGAATG
1 ACCCGAATG
32307 ACCCGAA--
1 ACCCGAATG
*
32314 ACCCGAATA
1 ACCCGAATG
32323 ACCCG-A--
1 ACCCGAATG
32329 ACCCGAATG
1 ACCCGAATG
32338 ACCCGAA
1 ACCCGAA
32345 AAAACTGCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
6 5 0.07
7 23 0.33
8 5 0.07
9 36 0.52
ACGTcount: A:0.36, C:0.36, G:0.20, T:0.08
Consensus pattern (9 bp):
ACCCGAATG
Found at i:32262 original size:16 final size:16
Alignment explanation
Indices: 32243--32345 Score: 136
Period size: 16 Copynumber: 6.5 Consensus size: 16
32233 AACCCGCCCA
32243 ACCCGAAACCCGAATG
1 ACCCGAAACCCGAATG
* *
32259 ACCCGGAACCTGAATG
1 ACCCGAAACCCGAATG
* * *
32275 ACCTGAGACCCAAATG
1 ACCCGAAACCCGAATG
*
32291 ACCCGAGACCCGAATG
1 ACCCGAAACCCGAATG
*
32307 ACCCGAAACCCGAATA
1 ACCCGAAACCCGAATG
32323 ACCCG-AACCCGAATG
1 ACCCGAAACCCGAATG
32338 ACCCGAAA
1 ACCCGAAA
32346 AAACTGCCTG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
15 14 0.19
16 60 0.81
ACGTcount: A:0.37, C:0.36, G:0.19, T:0.08
Consensus pattern (16 bp):
ACCCGAAACCCGAATG
Found at i:37802 original size:11 final size:11
Alignment explanation
Indices: 37769--37802 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
37759 ATTCGGTTTG
37769 TCGGTTTTCGG-
1 TCGG-TTTCGGT
37780 TCGGTTTCGGT
1 TCGGTTTCGGT
37791 TCGGTTTCGGT
1 TCGGTTTCGGT
37802 T
1 T
37803 TAGAGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.00, C:0.18, G:0.35, T:0.47
Consensus pattern (11 bp):
TCGGTTTCGGT
Found at i:37942 original size:39 final size:34
Alignment explanation
Indices: 37901--37978 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 34
37891 AATAATCATA
*
37901 TATATAAATATAATTATAAACTAAAACTATATTTTAT
1 TATATATATAT-ATT-T-AACTAAAACTATATTTTAT
*
37938 TATATATATATATTTTACTAAAACTATATTTTAT
1 TATATATATATATTTAACTAAAACTATATTTTAT
37972 TATATAT
1 TATATAT
37979 TTTATTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
34 25 0.64
35 1 0.03
36 3 0.08
37 10 0.26
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (34 bp):
TATATATATATATTTAACTAAAACTATATTTTAT
Found at i:37951 original size:18 final size:18
Alignment explanation
Indices: 37928--38001 Score: 84
Period size: 18 Copynumber: 4.2 Consensus size: 18
37918 AAACTAAAAC
37928 TATATTTTATTATATATA
1 TATATTTTATTATATATA
*
37946 TATATTTTACTA-A-A-A
1 TATATTTTATTATATATA
37961 CTATATTTTATTATATAT-
1 -TATATTTTATTATATATA
*
37979 TTTATTATTATTATATATA
1 TATATT-TTATTATATATA
37998 TATA
1 TATA
38002 AGTCGGTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 1 0.02
16 12 0.26
17 7 0.15
18 23 0.50
19 3 0.07
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTTTATTATATATA
Found at i:37979 original size:12 final size:12
Alignment explanation
Indices: 37962--38000 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
37952 TTACTAAAAC
37962 TATATTTTATTA
1 TATATTTTATTA
37974 TATATTTTATTA
1 TATATTTTATTA
*
37986 T-TATTATA-TA
1 TATATTTTATTA
37996 TATAT
1 TATAT
38001 AAGTCGGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 3 0.12
11 9 0.36
12 13 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:40048 original size:9 final size:9
Alignment explanation
Indices: 40034--40067 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
40024 TGGTCGAAAT
40034 ATTTTTTTA
1 ATTTTTTTA
40043 ATTTTTTTA
1 ATTTTTTTA
*
40052 TTTTTTTTA
1 ATTTTTTTA
40061 TATTTTT
1 -ATTTTT
40068 CGATATAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:40066 original size:17 final size:17
Alignment explanation
Indices: 40033--40067 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40023 CTGGTCGAAA
*
40033 TATTTTTTTAATTTTTT
1 TATTTTTTTAATATTTT
*
40050 TATTTTTTTTATATTTT
1 TATTTTTTTAATATTTT
40067 T
1 T
40068 CGATATAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (17 bp):
TATTTTTTTAATATTTT
Found at i:42705 original size:1 final size:1
Alignment explanation
Indices: 42701--42728 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
42691 CTATTTTTTC
42701 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
42729 CTATTTAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:46956 original size:9 final size:9
Alignment explanation
Indices: 46942--46966 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46932 ATTAGGTCCG
46942 AGGCAGATA
1 AGGCAGATA
46951 AGGCAGATA
1 AGGCAGATA
46960 AGGCAGA
1 AGGCAGA
46967 GAATACAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.36, T:0.08
Consensus pattern (9 bp):
AGGCAGATA
Found at i:50250 original size:47 final size:47
Alignment explanation
Indices: 50181--50272 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
50171 TGGTCTTGCA
*
50181 TTTACACATTATCCAGATATTACACAAAAATGTTATAATTAACAAAG
1 TTTACACATTATCCAGATATTACACAAAAATGTTACAATTAACAAAG
50228 TTTACACATTATCCAGATATTACACAAAAATGTTACAATTAACAA
1 TTTACACATTATCCAGATATTACACAAAAATGTTACAATTAACAA
50273 GGCTTATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (47 bp):
TTTACACATTATCCAGATATTACACAAAAATGTTACAATTAACAAAG
Found at i:50610 original size:31 final size:31
Alignment explanation
Indices: 50575--50634 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
50565 ACCGAGAATC
50575 ATACCATTCAAAAAA-CCCACACCCATTCATG
1 ATACCATT-AAAAAATCCCACACCCATTCATG
50606 ATACCATTAAAAAATCCCACACCCATTCA
1 ATACCATTAAAAAATCCCACACCCATTCA
50635 CATGTTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.20
Consensus pattern (31 bp):
ATACCATTAAAAAATCCCACACCCATTCATG
Found at i:51391 original size:31 final size:28
Alignment explanation
Indices: 51318--51391 Score: 76
Period size: 32 Copynumber: 2.5 Consensus size: 28
51308 CTGATAGCTG
* *
51318 AGGGATTTATTTGGTTCCAAAAAAAGATT
1 AGGGATTTATTT-GTCCCAAAAAAAGATA
*
51347 AGGGATTTTATTTGTCCCAAAATAAAAAGGTA
1 AGGGA-TTTATTTGTCCC--AA-AAAAAGATA
51379 AGGGATTTATTTG
1 AGGGATTTATTTG
51392 GTATTTAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 9 0.24
30 7 0.18
31 10 0.26
32 12 0.32
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (28 bp):
AGGGATTTATTTGTCCCAAAAAAAGATA
Found at i:54885 original size:2 final size:2
Alignment explanation
Indices: 54878--54902 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54868 TTGCCTTTCA
54878 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 A
54903 GTTGGATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55815 original size:25 final size:24
Alignment explanation
Indices: 55782--55833 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
55772 TGGATTTGTA
55782 AAATAAATTGAACAATAAAGATATT
1 AAATAAATTGAACAATAAA-ATATT
* * *
55807 AAATAAATTTAAGAATTAAATATT
1 AAATAAATTGAACAATAAAATATT
55831 AAA
1 AAA
55834 AAGTTAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (24 bp):
AAATAAATTGAACAATAAAATATT
Found at i:56326 original size:3 final size:3
Alignment explanation
Indices: 56318--56347 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
56308 GATATATAGA
*
56318 TAT TAT TAT TAT TAT TAT GAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56348 CTTCTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:64325 original size:27 final size:28
Alignment explanation
Indices: 64294--64346 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
64284 GCAAAGTATC
*
64294 AAATGCTGTTTTGTCTTTG-TGCAAAAA
1 AAATGCTGTTTTGTCTTGGCTGCAAAAA
64321 AAATGCTGTTTTGTCTTGGCTGCAAA
1 AAATGCTGTTTTGTCTTGGCTGCAAA
64347 CAGGACCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (28 bp):
AAATGCTGTTTTGTCTTGGCTGCAAAAA
Found at i:64767 original size:13 final size:13
Alignment explanation
Indices: 64749--64773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64739 TGTTGTTATT
64749 TTGTAGATCTAAG
1 TTGTAGATCTAAG
64762 TTGTAGATCTAA
1 TTGTAGATCTAA
64774 AATGAAGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTAGATCTAAG
Found at i:64845 original size:32 final size:32
Alignment explanation
Indices: 64803--64900 Score: 110
Period size: 32 Copynumber: 3.0 Consensus size: 32
64793 TCTGTCTCGG
*
64803 TGCCGCCCCAGGTGGGCGGCATG-CCATGGACA
1 TGCCGTCCCAGG-GGGCGGCATGTCCATGGACA
*
64835 TGCCGTCCCAGGAGGGCGGCATGTCTATGG-CA
1 TGCCGTCCCAGG-GGGCGGCATGTCCATGGACA
**
64867 TGCCGCTCCCCTGGGGCGGCACTGTCCATGGACA
1 TGCCG-TCCCAGGGGGCGGCA-TGTCCATGGACA
64901 ACAGTTTGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
32 36 0.64
33 18 0.32
34 2 0.04
ACGTcount: A:0.14, C:0.34, G:0.36, T:0.16
Consensus pattern (32 bp):
TGCCGTCCCAGGGGGCGGCATGTCCATGGACA
Found at i:66048 original size:16 final size:16
Alignment explanation
Indices: 66027--66057 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66017 GTAAACAGTA
*
66027 CTGAAATTCATCTGCC
1 CTGAAATACATCTGCC
66043 CTGAAATACATCTGC
1 CTGAAATACATCTGC
66058 TTGAGCTCGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (16 bp):
CTGAAATACATCTGCC
Found at i:69050 original size:42 final size:42
Alignment explanation
Indices: 68991--69076 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 42
68981 AAGGGTCAAG
* *
68991 TGGCCGGTTGTGGCCGGATGG-TCCGTGCGTTGGCCCGTGTGA
1 TGGCCGGTTGTGGCCGGATGGCT-CGTGCGATGGCCCGTGCGA
69033 TGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCGA
1 TGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCGA
69075 TG
1 TG
69077 TCCCATGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.06, C:0.24, G:0.45, T:0.24
Consensus pattern (42 bp):
TGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCGA
Found at i:72821 original size:38 final size:38
Alignment explanation
Indices: 72798--72873 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
72788 ATGTAACGTA
*
72798 CCCAACTTAATGAAAAAGAAAATGAATATGATCACCAT
1 CCCAACTTAATGAAAAAGAAAATGAATATGATAACCAT
*
72836 CCCAACTTAATGAAAAAGAAAATGAATATGATCACCAT
1 CCCAACTTAATGAAAAAGAAAATGAATATGATAACCAT
72874 AACTAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (38 bp):
CCCAACTTAATGAAAAAGAAAATGAATATGATAACCAT
Found at i:73207 original size:28 final size:27
Alignment explanation
Indices: 73115--73215 Score: 100
Period size: 28 Copynumber: 3.7 Consensus size: 27
73105 AGGTGTACTA
* * * *
73115 AAAATTACCAAAATGTCCCTAAATATG
1 AAAATGACCAAAATGCCCCTATATGTG
* *
73142 CAAATGACCAAAAT-ACCCT-TA-GTG
1 AAAATGACCAAAATGCCCCTATATGTG
73166 CAAGAATGACCAAAATGCCCCTATGATGTG
1 -AA-AATGACCAAAATGCCCCTAT-ATGTG
73196 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
73216 GGATGACCCT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
26 16 0.26
27 16 0.26
28 19 0.31
29 3 0.05
30 3 0.05
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.21
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTATATGTG
Found at i:79127 original size:41 final size:42
Alignment explanation
Indices: 79070--79154 Score: 129
Period size: 41 Copynumber: 2.0 Consensus size: 42
79060 AAGGGTCAAG
* *
79070 TGGCCGGTTGTGGCCGGATGG-TCCGTGCG-TTGCCCGTGTGA
1 TGGCCGGTTGTGGCCGGATGGCT-CGTGCGATGGCCCGTGCGA
79111 TGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCGA
1 TGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCGA
79153 TG
1 TG
79155 TCCCATGCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
41 27 0.68
42 13 0.32
ACGTcount: A:0.06, C:0.25, G:0.45, T:0.25
Consensus pattern (42 bp):
TGGCCGGTTGTGGCCGGATGGCTCGTGCGATGGCCCGTGCGA
Found at i:79144 original size:12 final size:12
Alignment explanation
Indices: 79127--79169 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
79117 GTTGTGGCCG
*
79127 GATGGCTCGTGC
1 GATGGCCCGTGC
79139 GATGGCCCGTGC
1 GATGGCCCGTGC
* *
79151 GATGTCCCATGC
1 GATGGCCCGTGC
*
79163 GTTGGCC
1 GATGGCC
79170 GGTCATGGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.23
Consensus pattern (12 bp):
GATGGCCCGTGC
Found at i:80294 original size:32 final size:32
Alignment explanation
Indices: 80177--80294 Score: 84
Period size: 32 Copynumber: 3.7 Consensus size: 32
80167 CCATGGGAGA
* *
80177 GCCGCCCTAGTAGGACGGCATG-CCATGGTGTAT
1 GCCGCCCTAGCAGGACGGCATGACCAT-G-GCAT
* * * *
80210 GCC-ACCTAGCTAGGACGACAT-CCCATGGTCAG
1 GCCGCCCTAGC-AGGACGGCATGACCATGG-CAT
80242 GCCGCCCT-GTCA-GAGCGGCATGACCATGGCAT
1 GCCGCCCTAG-CAGGA-CGGCATGACCATGGCAT
*
80274 GCCGTCCTAGCAGGACGGCAT
1 GCCGCCCTAGCAGGACGGCAT
80295 CGTCATGGCA
Statistics
Matches: 66, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
31 3 0.05
32 34 0.52
33 29 0.44
ACGTcount: A:0.20, C:0.32, G:0.31, T:0.17
Consensus pattern (32 bp):
GCCGCCCTAGCAGGACGGCATGACCATGGCAT
Found at i:81161 original size:32 final size:32
Alignment explanation
Indices: 81070--81161 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 32
81060 TTCAGTTTGG
* ** * *
81070 TCAGGTTCATTTCGGGAAAGGTTAATTTGGGT
1 TCAGGTTCATTTCAGGTCAGGTTAATTCGGAT
* * * * *
81102 TCAGGTTAAATTCATGTCAAGTAAATTCGGAT
1 TCAGGTTCATTTCAGGTCAGGTTAATTCGGAT
81134 TCAGGTTCATTTCAGGTCAGGTTAATTC
1 TCAGGTTCATTTCAGGTCAGGTTAATTC
81162 AAGTTCGGGT
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (32 bp):
TCAGGTTCATTTCAGGTCAGGTTAATTCGGAT
Found at i:81955 original size:33 final size:33
Alignment explanation
Indices: 81874--81992 Score: 134
Period size: 33 Copynumber: 3.5 Consensus size: 33
81864 CCGCGCAACA
*
81874 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
81909 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
81942 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
81975 CCGGCCACAACCGGCCAC
1 CCGGCCACAACCGGCCAC
81993 ACGATCCTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
32 2 0.03
33 63 0.86
35 7 0.10
36 1 0.01
ACGTcount: A:0.24, C:0.42, G:0.27, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:85249 original size:5 final size:5
Alignment explanation
Indices: 85239--85283 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
85229 TCCAAACCCA
*
85239 ATTAT ATTAT ATTAT ATTAT A-TAT A-TAT ATTAT ATATAT AGTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT A
85284 AAACATGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
4 8 0.22
5 25 0.68
6 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (5 bp):
ATTAT
Found at i:85269 original size:13 final size:13
Alignment explanation
Indices: 85239--85278 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 13
85229 TCCAAACCCA
85239 ATTATATTATATTAT
1 ATTATA-TATA-TAT
85254 ATTATATATATAT
1 ATTATATATATAT
85267 ATTATATATATA
1 ATTATATATATA
85279 GTATAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 15 0.60
14 4 0.16
15 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:85967 original size:11 final size:11
Alignment explanation
Indices: 85924--85961 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
85914 CCTATATATA
*
85924 AAATAAATTAT
1 AAATTAATTAT
85935 CAAA-TAATTAT
1 -AAATTAATTAT
85946 AAATTAATTAT
1 AAATTAATTAT
85957 AAATT
1 AAATT
85962 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Done.