Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023744.1 Corchorus olitorius cultivar O-4 contig23777, 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: 14727
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Found at i:2742 original size:35 final size:33
Alignment explanation
Indices: 2683--2970 Score: 175
Period size: 35 Copynumber: 8.5 Consensus size: 33
2673 GATTACCATT
*
2683 TTTTTACTCTTTTTAAGTTTAATTACTCAATACCA
1 TTTTTACT-TTTTTAA-CTTAATTACTCAATACCA
* *
2718 TTTTTGCTTTTCTTAACTTGAATTACTGAATACCA
1 TTTTTACTTTT-TTAACTT-AATTACTCAATACCA
* * *
2753 TTTCTT-CTTTTTAAACTTACTTAC-CGATTACCA
1 TTT-TTACTTTTTTAACTTAATTACTC-AATACCA
* *
2786 -TTTTACTTTTTAAACTTATATTACT-AATTACCCT
1 TTTTTACTTTTTTAACTTA-ATTACTCAA-TA-CCA
*
2820 TTTCTTACTCTTCTTT-A--TAGATTACTGAATACCA
1 TTT-TTACT-TT-TTTAACTTA-ATTACTCAATACCA
* *
2854 ATTTTACCCTTTTTTAAACTTAATTACTAAATACCA
1 TTTTTA--CTTTTTT-AACTTAATTACTCAATACCA
*
2890 TTTTTAC---TTCAACTTTAATTACTCAATACCA
1 TTTTTACTTTTTTAAC-TTAATTACTCAATACCA
** **
2921 TTTTTACTTTTTCCT-TTTTAATTACAAAATACCA
1 TTTTTACTTTTT--TAACTTAATTACTCAATACCA
2955 TTTTTACTCTTTTTAA
1 TTTTTACT-TTTTTAA
2971 TCTTTTTACA
Statistics
Matches: 201, Mismatches: 24, Indels: 57
0.71 0.09 0.20
Matches are distributed among these distances:
30 3 0.01
31 27 0.13
32 16 0.08
33 24 0.12
34 45 0.22
35 52 0.26
36 27 0.13
37 5 0.02
38 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.02, T:0.50
Consensus pattern (33 bp):
TTTTTACTTTTTTAACTTAATTACTCAATACCA
Found at i:2911 original size:31 final size:31
Alignment explanation
Indices: 2873--2962 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 31
2863 TTTTTTAAAC
2873 TTAATTACTAAATACCATTTTTACTTCAACT
1 TTAATTACTAAATACCATTTTTACTTCAACT
* ***
2904 TTAATTACTCAATACCATTTTTACTTTTTCCTTT
1 TTAATTACTAAATACCATTTTTAC---TTCAACT
*
2938 TTAATTACAAAATACCATTTTTACT
1 TTAATTACTAAATACCATTTTTACT
2963 CTTTTTAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
31 24 0.48
34 26 0.52
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAATTACTAAATACCATTTTTACTTCAACT
Found at i:2969 original size:9 final size:9
Alignment explanation
Indices: 2955--2993 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2945 CAAAATACCA
2955 TTTTTACTC
1 TTTTTACTC
*
2964 TTTTTAATC
1 TTTTTACTC
**
2973 TTTTTACAA
1 TTTTTACTC
2982 TTTTTACTC
1 TTTTTACTC
2991 TTT
1 TTT
2994 ACCAATACCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTACTC
Found at i:3036 original size:21 final size:22
Alignment explanation
Indices: 3005--3229 Score: 185
Period size: 21 Copynumber: 10.8 Consensus size: 22
2995 CCAATACCCT
*
3005 TTTTAACTGATTACCATTTACTC
1 TTTT-ACTGATTACTATTTACTC
3028 -TTTACTGATTACTA-TTA-TC
1 TTTTACTGATTACTATTTACTC
* * *
3047 ATTTTACTGTTTACTGTTTACCC
1 -TTTTACTGATTACTATTTACTC
*
3070 TTTTATTGATTACTA-TTAC-C
1 TTTTACTGATTACTATTTACTC
* * *
3090 -CTTCCTTGATTACTCTTTACTC
1 TTTTAC-TGATTACTATTTACTC
3112 TTTTACTGATTACTATTT-CTC
1 TTTTACTGATTACTATTTACTC
3133 TTTTAC----T-C--TTTACTC
1 TTTTACTGATTACTATTTACTC
** *
3148 TTTTATAGATTACTCTTTACTC
1 TTTTACTGATTACTATTTACTC
3170 -TTTACTGATTACTA-TTACTC
1 TTTTACTGATTACTATTTACTC
* * *
3190 TTTTCCTGATTACTCTTTAATC
1 TTTTACTGATTACTATTTACTC
3212 TTTTACTGATTACTATTT
1 TTTTACTGATTACTATTT
3230 TACTGATTGC
Statistics
Matches: 161, Mismatches: 23, Indels: 37
0.73 0.10 0.17
Matches are distributed among these distances:
14 3 0.02
15 8 0.05
16 1 0.01
17 1 0.01
19 5 0.03
20 19 0.12
21 62 0.39
22 58 0.36
23 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTACTGATTACTATTTACTC
Found at i:3111 original size:7 final size:7
Alignment explanation
Indices: 3099--3214 Score: 60
Period size: 7 Copynumber: 16.3 Consensus size: 7
3089 CCTTCCTTGA
3099 TTACTCT
1 TTACTCT
3106 TTACTCTT
1 TTACTC-T
**
3114 TTACTGA
1 TTACTCT
*
3121 TTACTAT
1 TTACTCT
3128 TT-CTCTT
1 TTACTC-T
3135 TTACTCT
1 TTACTCT
3142 TTACTCTT
1 TTACTC-T
**
3150 TTA-TAGA
1 TTACT-CT
3157 TTACTCT
1 TTACTCT
3164 TTACTCT
1 TTACTCT
**
3171 TTACTGA
1 TTACTCT
*
3178 TTACT-A
1 TTACTCT
3184 TTACTCT
1 TTACTCT
*
3191 TTTC-CT
1 TTACTCT
3197 GATTACTCT
1 --TTACTCT
*
3206 TTAATCT
1 TTACTCT
3213 TT
1 TT
3215 TACTGATTAC
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
6 10 0.12
7 55 0.65
8 17 0.20
9 2 0.02
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:3137 original size:29 final size:28
Alignment explanation
Indices: 3098--3193 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 28
3088 CCCTTCCTTG
3098 ATTACTC-TTTACTCTTTTACTGATTACT
1 ATTACTCTTTTACTC-TTTACTGATTACT
* **
3126 ATTTCTCTTTTACTCTTTACTCTTTTA-T
1 ATTACTCTTTTACTCTTTACT-GATTACT
3154 AGATTACTC-TTTACTCTTTACTGATTACT
1 --ATTACTCTTTTACTCTTTACTGATTACT
3183 ATTACTCTTTT
1 ATTACTCTTTT
3194 CCTGATTACT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
27 7 0.12
28 19 0.34
29 24 0.43
30 6 0.11
ACGTcount: A:0.20, C:0.21, G:0.03, T:0.56
Consensus pattern (28 bp):
ATTACTCTTTTACTCTTTACTGATTACT
Found at i:3218 original size:57 final size:57
Alignment explanation
Indices: 3097--3210 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
3087 ACCCTTCCTT
* * *
3097 GATTACTCTTTACTCTTTTACTGATTACTATTTCTCTTTTACTCTTTACTCTTTTATA
1 GATTACTCTTTACTC-TTTACTGATTACTATTACTCTTTTACTCATTACTCTTTAATA
* *
3155 GATTACTCTTTACTCTTTACTGATTACTATTACTCTTTTCCTGATTACTCTTTAAT
1 GATTACTCTTTACTCTTTACTGATTACTATTACTCTTTTACTCATTACTCTTTAAT
3211 CTTTTACTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 36 0.71
58 15 0.29
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.54
Consensus pattern (57 bp):
GATTACTCTTTACTCTTTACTGATTACTATTACTCTTTTACTCATTACTCTTTAATA
Found at i:3225 original size:57 final size:57
Alignment explanation
Indices: 3097--3237 Score: 156
Period size: 57 Copynumber: 2.4 Consensus size: 57
3087 ACCCTTCCTT
* * * *
3097 GATTACTCTTTACTCTTTTACTGATTACTATTTCTCTTTTACTCTTTACTCTTTTATA
1 GATTACTCATTACTC-TTTACTGATTACTATTACTCTTTTACTCATTACTCTTTAATA
* * * *
3155 GATTACTCTTTACTCTTTACTGATTACTATTACTCTTTTCCTGATTACTCTTTAATC
1 GATTACTCATTACTCTTTACTGATTACTATTACTCTTTTACTCATTACTCTTTAATA
** * *
3212 TTTTACTGATTACTATTTTACTGATT
1 GATTACTCATTACT-CTTTACTGATT
3238 GCTCTCTTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 46 0.65
58 25 0.35
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.55
Consensus pattern (57 bp):
GATTACTCATTACTCTTTACTGATTACTATTACTCTTTTACTCATTACTCTTTAATA
Found at i:3236 original size:37 final size:37
Alignment explanation
Indices: 3178--3345 Score: 171
Period size: 37 Copynumber: 4.4 Consensus size: 37
3168 TCTTTACTGA
* * *
3178 TTACT-ATTACTCTTTTCCTGATTACTCT-TTAATCTT
1 TTACTGATTACTATTTTACTGATTACTCTCTTATTC-T
*
3214 TTACTGATTACTATTTTACTGATTGCTCTCTTATTCT
1 TTACTGATTACTATTTTACTGATTACTCTCTTATTCT
* *
3251 TTACTGATTACTATTACCATTATGCTGGTTACTCT-TTACTCTT
1 TTACTGATTACTATT----TTA--CTGATTACTCTCTTATTC-T
* *
3294 TTATTGATTACTATTTTACTGATTGCTCTCTTATTCT
1 TTACTGATTACTATTTTACTGATTACTCTCTTATTCT
3331 TTACTGATTACTATT
1 TTACTGATTACTATT
3346 ACCATTGTGC
Statistics
Matches: 110, Mismatches: 12, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
36 5 0.05
37 60 0.55
38 10 0.09
39 3 0.03
41 3 0.03
42 5 0.05
43 24 0.22
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (37 bp):
TTACTGATTACTATTTTACTGATTACTCTCTTATTCT
Found at i:3266 original size:80 final size:80
Alignment explanation
Indices: 3096--3347 Score: 332
Period size: 80 Copynumber: 3.2 Consensus size: 80
3086 TACCCTTCCT
* * ** *
3096 TGATTACTCTTTACTCTTTTACTGATTACTATTT-CTCTTTTACTCTTTACTCTTTTA-TAGATT
1 TGATTACT-ATTACTCTTTTACTGATTACTCTTTACTCTTTTACTGATTACTATTTTACT-GATT
* *
3159 ACTCT-TTACTCTTTAC
64 GCTCTCTTATTCTTTAC
* *
3175 TGATTACTATTACTCTTTTCCTGATTACTCTTTAATCTTTTACTGATTACTATTTTACTGATTGC
1 TGATTACTATTACTCTTTTACTGATTACTCTTTACTCTTTTACTGATTACTATTTTACTGATTGC
3240 TCTCTTATTCTTTAC
66 TCTCTTATTCTTTAC
* * * *
3255 TGATTACTATTAC-CATTATGCTGGTTACTCTTTACTCTTTTATTGATTACTATTTTACTGATTG
1 TGATTACTATTACTC-TTTTACTGATTACTCTTTACTCTTTTACTGATTACTATTTTACTGATTG
3319 CTCTCTTATTCTTTAC
65 CTCTCTTATTCTTTAC
3335 TGATTACTATTAC
1 TGATTACTATTAC
3348 CATTGTGCCG
Statistics
Matches: 155, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
78 22 0.14
79 36 0.23
80 97 0.63
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (80 bp):
TGATTACTATTACTCTTTTACTGATTACTCTTTACTCTTTTACTGATTACTATTTTACTGATTGC
TCTCTTATTCTTTAC
Found at i:3348 original size:80 final size:80
Alignment explanation
Indices: 3131--3374 Score: 332
Period size: 80 Copynumber: 3.1 Consensus size: 80
3121 TTACTATTTC
** * * * *
3131 TCTTTTACTCTTTACTCTTTTA-TAGATTACTCT-TTACTCTTTACTGATTACTATTACTC-TTT
1 TCTTTTACTGATTACTATTTTACT-GATTGCTCTCTTATTCTTTACTGATTACTATTAC-CATTA
* *
3193 TCCTGATTACTCTTTAA
64 TGCTGGTTACTCTTTAA
3210 TCTTTTACTGATTACTATTTTACTGATTGCTCTCTTATTCTTTACTGATTACTATTACCATTATG
1 TCTTTTACTGATTACTATTTTACTGATTGCTCTCTTATTCTTTACTGATTACTATTACCATTATG
*
3275 CTGGTTACTCTTTAC
66 CTGGTTACTCTTTAA
* *
3290 TCTTTTATTGATTACTATTTTACTGATTGCTCTCTTATTCTTTACTGATTACTATTACCATTGTG
1 TCTTTTACTGATTACTATTTTACTGATTGCTCTCTTATTCTTTACTGATTACTATTACCATTATG
* *
3355 CCGGTTACTCTTTAT
66 CTGGTTACTCTTTAA
3370 TCTTT
1 TCTTT
3375 GAGTTTTAAT
Statistics
Matches: 149, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
79 28 0.19
80 121 0.81
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.53
Consensus pattern (80 bp):
TCTTTTACTGATTACTATTTTACTGATTGCTCTCTTATTCTTTACTGATTACTATTACCATTATG
CTGGTTACTCTTTAA
Found at i:3669 original size:20 final size:20
Alignment explanation
Indices: 3644--3685 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3634 AATACCATCC
3644 GGGCACCCGCCACTCATACT
1 GGGCACCCGCCACTCATACT
3664 GGGCACCCGCCACTCATACT
1 GGGCACCCGCCACTCATACT
3684 GG
1 GG
3686 CTAAGACCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.14
Consensus pattern (20 bp):
GGGCACCCGCCACTCATACT
Found at i:6749 original size:22 final size:23
Alignment explanation
Indices: 6715--6762 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
6705 TAAAAGGATG
6715 AATGCAAAAAGGTGCCATGCAAA
1 AATGCAAAAAGGTGCCATGCAAA
*
6738 AATGC-AAAAGGTGCCATGTAAA
1 AATGCAAAAAGGTGCCATGCAAA
6760 AAT
1 AAT
6763 TCAACTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.17
Consensus pattern (23 bp):
AATGCAAAAAGGTGCCATGCAAA
Found at i:7365 original size:61 final size:61
Alignment explanation
Indices: 7276--7595 Score: 405
Period size: 61 Copynumber: 5.2 Consensus size: 61
7266 TCAACTTACA
* * * ** * **
7276 TGAACTGTCTTCAGGTTCA-TTTCTAAATATCATTCAGAAACTGTCTTCAGATTCATCTTCG
1 TGAACTGTCTTCAGATTCACTCT-TAAATATCTTTTGGGAACTGTCTTCAGACCCATCTTCG
* * * * *
7337 TGAACTGTCTTTAGATTCACGCTCAAATACCTTTTGGGAACTGTCTTCAGAACCCATCTTTG
1 TGAACTGTCTTCAGATTCACTCTTAAATATCTTTTGGGAACTGTCTTCAG-ACCCATCTTCG
* * * * *
7399 TGAACTGTCTTTAGTTTCACTTTTAAATACCTTTTAGGAACTGTCTT-AGACTCCATCTTCG
1 TGAACTGTCTTCAGATTCACTCTTAAATATCTTTTGGGAACTGTCTTCAGAC-CCATCTTCG
7460 TGAACTGTCTTCAGATTCACTCTTAAA-ATCTTTTGGGAACTGTCTTCAGAGCCCATCTTCG
1 TGAACTGTCTTCAGATTCACTCTTAAATATCTTTTGGGAACTGTCTTCAGA-CCCATCTTCG
7521 TGAACTGTCTTCAGATTCACTCTTAAA-ATCTTTTGGGAACTGTCTTCAGAACCCATCTTCG
1 TGAACTGTCTTCAGATTCACTCTTAAATATCTTTTGGGAACTGTCTTCAG-ACCCATCTTCG
7582 TGAACTGTCTTCAG
1 TGAACTGTCTTCAG
7596 TTTTAATCTT
Statistics
Matches: 229, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
60 19 0.08
61 157 0.69
62 53 0.23
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (61 bp):
TGAACTGTCTTCAGATTCACTCTTAAATATCTTTTGGGAACTGTCTTCAGACCCATCTTCG
Found at i:7500 original size:35 final size:35
Alignment explanation
Indices: 7461--7570 Score: 130
Period size: 35 Copynumber: 3.4 Consensus size: 35
7451 CCATCTTCGT
7461 GAACTGTCTTCAGATTCACTCTTAAAATCTTTTGG
1 GAACTGTCTTCAGATTCACTCTTAAAATCTTTTGG
* * *
7496 GAACTGTCTTCAGA-GC-C-C-----ATC-TTCGT
1 GAACTGTCTTCAGATTCACTCTTAAAATCTTTTGG
7522 GAACTGTCTTCAGATTCACTCTTAAAATCTTTTGG
1 GAACTGTCTTCAGATTCACTCTTAAAATCTTTTGG
7557 GAACTGTCTTCAGA
1 GAACTGTCTTCAGA
7571 ACCCATCTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
26 17 0.28
27 4 0.07
28 1 0.02
29 1 0.02
32 1 0.02
33 1 0.02
34 4 0.07
35 31 0.52
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (35 bp):
GAACTGTCTTCAGATTCACTCTTAAAATCTTTTGG
Found at i:8682 original size:1 final size:1
Alignment explanation
Indices: 8676--8732 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
8666 GAGCTTTCTC
* * * * * *
8676 TTTTTTTTTGTTTTTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8733 GCCATGTACT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:8732 original size:6 final size:6
Alignment explanation
Indices: 8676--8730 Score: 89
Period size: 6 Copynumber: 9.7 Consensus size: 6
8666 GAGCTTTCTC
8676 TTTT-T TTTTGT TTTT-T TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
8722 TTTT-T TTTT
1 TTTTGT TTTT
8731 TTGCCATGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 14 0.29
6 34 0.71
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (6 bp):
TTTTGT
Found at i:8841 original size:21 final size:20
Alignment explanation
Indices: 8783--8842 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
8773 TTCTAAAAAC
*
8783 CTTTTTGAGAAA-CATTTTTT
1 CTTTTTG-GAAATCATTTCTT
*
8803 C-TTTTGAAAAATCAATTTCTT
1 CTTTTTG-GAAATC-ATTTCTT
8824 CTTTTTGGACAATCATTTC
1 CTTTTTGGA-AATCATTTC
8843 ACCTTCAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 9 0.27
20 2 0.06
21 13 0.39
22 9 0.27
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (20 bp):
CTTTTTGGAAATCATTTCTT
Found at i:10407 original size:14 final size:13
Alignment explanation
Indices: 10383--10432 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
10373 AAAAAACCCT
10383 AAACC-TTTTTGA
1 AAACCATTTTTGA
10395 AAACTCATTTTTGA
1 AAAC-CATTTTTGA
*
10409 AAACCTTTTCTTGA
1 AAACCATTT-TTGA
10423 AAA-CATTTTT
1 AAACCATTTTT
10433 TTTTTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 6 0.18
13 9 0.27
14 18 0.55
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (13 bp):
AAACCATTTTTGA
Found at i:10429 original size:26 final size:25
Alignment explanation
Indices: 10383--10432 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
10373 AAAAAACCCT
10383 AAACCTTTTTGAAAACTCATTTTTGA
1 AAACCTTTTTGAAAAC-CATTTTTGA
10409 AAACCTTTTCTTGAAAA-CATTTTT
1 AAACC-TTT-TTGAAAACCATTTTT
10433 TTTTTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 12 0.55
27 3 0.14
28 7 0.32
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (25 bp):
AAACCTTTTTGAAAACCATTTTTGA
Found at i:13254 original size:37 final size:37
Alignment explanation
Indices: 13209--13301 Score: 113
Period size: 35 Copynumber: 2.6 Consensus size: 37
13199 TCTTTTACTT
*
13209 CTTG-ATTACTGATTACCATTTTTTTACTCTTT-TTAA
1 CTTGAATTACTGAATACCATTTTTTTACT-TTTCTTAA
* * *
13245 CTTTAATTACTCAATACCA--TTTTTGCTTTTCTTAA
1 CTTGAATTACTGAATACCATTTTTTTACTTTTCTTAA
13280 CTTGAATTACTGAATACCATTT
1 CTTGAATTACTGAATACCATTT
13302 CTTCTTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
34 3 0.06
35 28 0.60
36 3 0.06
37 13 0.28
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (37 bp):
CTTGAATTACTGAATACCATTTTTTTACTTTTCTTAA
Found at i:13280 original size:35 final size:34
Alignment explanation
Indices: 13229--13523 Score: 182
Period size: 35 Copynumber: 8.6 Consensus size: 34
13219 GATTACCATT
13229 TTTTTACTCTTTTTAACTTTAATTACTCAATACCA
1 TTTTTACT-TTTTTAACTTTAATTACTCAATACCA
* * *
13264 TTTTTGCTTTTCTTAACTTGAATTACTGAATACCA
1 TTTTTACTTTT-TTAACTTTAATTACTCAATACCA
* * *
13299 TTTCTT-CTTTTTAAAC-ATACTTAC-CAATTACCA
1 TTT-TTACTTTTTTAACTTTAATTACTCAA-TACCA
*
13332 -TTTTAC-TTTTTATACTTATAAATTACT-AATTACCCT
1 TTTTTACTTTTTTA-ACTT-T-AATTACTCAA-TA-CCA
* * * *
13368 TTTCTTACTCTTCTTCAC--TGATTACTGAATACCA
1 TTT-TTACT-TTTTTAACTTTAATTACTCAATACCA
* *
13402 ATTTTACCCTTTTTTAAAC-TTAATTACTAAATACCA
1 TTTTTA--CTTTTTT-AACTTTAATTACTCAATACCA
*
13438 TTTTTAC---TTCAACTTTAATTACTCAATACCA
1 TTTTTACTTTTTTAACTTTAATTACTCAATACCA
**** **
13469 TTTTTACTTTTTCCTTTTTAATTACAAAATACCA
1 TTTTTACTTTTTTAACTTTAATTACTCAATACCA
13503 TTTTTACTCTTTTTAATCTTT
1 TTTTTACT-TTTTTAA-CTTT
13524 TTACCATTTT
Statistics
Matches: 202, Mismatches: 33, Indels: 49
0.71 0.12 0.17
Matches are distributed among these distances:
30 3 0.01
31 32 0.16
32 7 0.03
33 13 0.06
34 44 0.22
35 62 0.31
36 29 0.14
37 2 0.01
38 4 0.02
39 2 0.01
40 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.02, T:0.50
Consensus pattern (34 bp):
TTTTTACTTTTTTAACTTTAATTACTCAATACCA
Found at i:13459 original size:31 final size:31
Alignment explanation
Indices: 13421--13510 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 31
13411 TTTTTTAAAC
13421 TTAATTACTAAATACCATTTTTACTTCAACT
1 TTAATTACTAAATACCATTTTTACTTCAACT
* ***
13452 TTAATTACTCAATACCATTTTTACTTTTTCCTTT
1 TTAATTACTAAATACCATTTTTAC---TTCAACT
*
13486 TTAATTACAAAATACCATTTTTACT
1 TTAATTACTAAATACCATTTTTACT
13511 CTTTTTAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
31 24 0.48
34 26 0.52
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAATTACTAAATACCATTTTTACTTCAACT
Found at i:13517 original size:9 final size:9
Alignment explanation
Indices: 13503--13541 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
13493 CAAAATACCA
13503 TTTTTACTC
1 TTTTTACTC
*
13512 TTTTTAATC
1 TTTTTACTC
13521 TTTTTAC-C
1 TTTTTACTC
13529 ATTTTTACTC
1 -TTTTTACTC
13539 TTT
1 TTT
13542 ACCAATACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 24 0.92
10 1 0.04
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTACTC
Found at i:13565 original size:22 final size:22
Alignment explanation
Indices: 13525--13567 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13515 TTAATCTTTT
*
13525 TACCATTTTTACTCTTTACCAA
1 TACCATTTTTACTCATTACCAA
* *
13547 TACCCTTTTTACTGATTACCA
1 TACCATTTTTACTCATTACCA
13568 TTTACTCTTT
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:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (22 bp):
TACCATTTTTACTCATTACCAA
Found at i:13599 original size:21 final size:21
Alignment explanation
Indices: 13553--13634 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
13543 CCAATACCCT
*
13553 TTTTACTGATTACCATT-T-A
1 TTTTACTGATTACTATTATCA
13572 CTCTTTACTGATTACTATTATCA
1 -T-TTTACTGATTACTATTATCA
*
13595 TTTTACTGTTTAC-AGTGTACTC-
1 TTTTACTGATTACTA-T-TA-TCA
*
13617 TTTTATTGATTACTATTA
1 TTTTACTGATTACTATTA
13635 CCCTTCCTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.04
21 29 0.57
22 16 0.31
23 4 0.08
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTACTGATTACTATTATCA
Done.