Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022673.1 Corchorus olitorius cultivar O-4 contig22706, 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: 44891
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1003 original size:29 final size:29
Alignment explanation
Indices: 860--1005 Score: 240
Period size: 29 Copynumber: 5.1 Consensus size: 29
850 TACCCCTAGG
*
860 TGTGCAAAAATGACCAAAATGCCCCTGGA
1 TGTGCAAAAATGACCAAAATGCCACTGGA
* * *
889 TGTGC-AAAATGACCAAAATACCCCTAGA
1 TGTGCAAAAATGACCAAAATGCCACTGGA
*
917 TGTGCAAAAATGACCAAAATGCCACTTGA
1 TGTGCAAAAATGACCAAAATGCCACTGGA
946 TGTGCAAAAATGACCAAAATGCCACTGGA
1 TGTGCAAAAATGACCAAAATGCCACTGGA
975 TGTGCAAAAATGACCAAAATGCCACTGGA
1 TGTGCAAAAATGACCAAAATGCCACTGGA
1004 TG
1 TG
1006 AGTGACCCTA
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 26 0.24
29 84 0.76
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.18
Consensus pattern (29 bp):
TGTGCAAAAATGACCAAAATGCCACTGGA
Found at i:1128 original size:19 final size:18
Alignment explanation
Indices: 1088--1127 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1078 ACCCTCTCCT
1088 AAAACTAAAACTAGAGAG
1 AAAACTAAAACTAGAGAG
1106 AAAACTAAAAACTAGA-AG
1 AAAACT-AAAACTAGAGAG
1124 AAAA
1 AAAA
1128 ATAGATGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.68, C:0.10, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAACTAAAACTAGAGAG
Found at i:3077 original size:7 final size:7
Alignment explanation
Indices: 3065--3207 Score: 232
Period size: 7 Copynumber: 20.4 Consensus size: 7
3055 CACTCGATAT
*
3065 ATTCAGA
1 ATTCAAA
*
3072 ATTCAGA
1 ATTCAAA
*
3079 ATTCAGA
1 ATTCAAA
*
3086 ATTCAGA
1 ATTCAAA
*
3093 ATTCAGA
1 ATTCAAA
*
3100 ATTCAGA
1 ATTCAAA
3107 ATTCAAA
1 ATTCAAA
3114 ATTCAAA
1 ATTCAAA
3121 ATTCAAA
1 ATTCAAA
3128 ATTCAAA
1 ATTCAAA
3135 ATTCAAA
1 ATTCAAA
3142 ATTCAAA
1 ATTCAAA
3149 ATTCAAA
1 ATTCAAA
3156 ATTCAAA
1 ATTCAAA
3163 ATTCAAA
1 ATTCAAA
3170 ATTCAAA
1 ATTCAAA
3177 ATTCAAA
1 ATTCAAA
3184 ATTCAAA
1 ATTCAAA
3191 ATTCAAA
1 ATTCAAA
3198 ATTCAAA
1 ATTCAAA
3205 ATT
1 ATT
3208 TTCAAGAAAA
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 135 1.00
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.29
Consensus pattern (7 bp):
ATTCAAA
Found at i:7446 original size:27 final size:27
Alignment explanation
Indices: 7347--7438 Score: 150
Period size: 27 Copynumber: 3.4 Consensus size: 27
7337 AGGATCAACT
7347 AGGGGCATTTCT-GTCATTTGCACATTC
1 AGGGGCATTT-TAGTCATTTGCACATTC
* *
7374 TGGGGCATTTTAGTCATTTGCACATCC
1 AGGGGCATTTTAGTCATTTGCACATTC
7401 AGGGGCATTTTAGTCATTTGCACATTC
1 AGGGGCATTTTAGTCATTTGCACATTC
7428 AGGGGCATTTT
1 AGGGGCATTTT
7439 GGCTATTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 1 0.02
27 59 0.98
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (27 bp):
AGGGGCATTTTAGTCATTTGCACATTC
Found at i:7466 original size:26 final size:26
Alignment explanation
Indices: 7425--7477 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
7415 CATTTGCACA
**
7425 TTCAGGGGCATTTTGG-CTATTTTAAG
1 TTCAGGGGCACGTTGGTC-ATTTTAAG
7451 TTCAGGGGCACGTTGGTCATTTTAAG
1 TTCAGGGGCACGTTGGTCATTTTAAG
7477 T
1 T
7478 CCACTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (26 bp):
TTCAGGGGCACGTTGGTCATTTTAAG
Found at i:12211 original size:15 final size:16
Alignment explanation
Indices: 12191--12223 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12181 AATTAATCTA
12191 AAATTAAA-CAAAACT
1 AAATTAAATCAAAACT
*
12206 AAATTAAATCTAAACT
1 AAATTAAATCAAAACT
12222 AA
1 AA
12224 GGAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTAAATCAAAACT
Found at i:21182 original size:37 final size:37
Alignment explanation
Indices: 21138--21208 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
21128 CTTGATCAAC
* *
21138 ATACATGTCTTTTCATATAGACATAACGTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACGTTATGATCA
*
21175 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACGTTATGA
21209 ATAATTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACGTTATGATCA
Found at i:25568 original size:271 final size:273
Alignment explanation
Indices: 25038--25571 Score: 927
Period size: 271 Copynumber: 2.0 Consensus size: 273
25028 CTTTTCAAAG
25038 ACTTGAACAGAACAGAACATACTAGTACTGTTTAAAGACTTTCCACTGTTAAAATGGAACCTGTT
1 ACTTGAACAGAACAGAACATACTAGTA-TGTTTAAAGACTTTCCACTGTTAAAATGGAACCTGTT
*
25103 TTAAGCTGTAACTTGTTCTTTGCCTGCAATTTGCATATTCAAGTTATAACACACCCATTTTGCCT
65 TTAAGCTGTAACTTGTTCTTTACCTGCAATTTGCATATTCAAGTTATAACACACCCATTTTGCCT
25168 TTTGTTTGACAATTCCTTTTTCAGTTTGATAGCAAGGCAGAATTATACTAAGAAAACTGCTCAAA
130 TTTGTTTGACAATTCCTTTTTCAGTTTGATAGCAAGGCAGAATTATACTAAGAAAACTGCTCAAA
25233 TCGTCTTGGACTTTCTTACATTTCAGTAGGCTATTGGTAAGGTATGTTCTCGTACCATTTCAGTT
195 TCGTCTTGGACTTTCTTACATTTCAGTAGGCTATTGGTAAGGTATGTTCTCGTACCATTTCAGTT
25298 TATTGTGTTTCTAA
260 TATTGTGTTTCTAA
* *
25312 ACTTGAATAGAACAGAACA-A-TA-T-TGTTTAAAGACCTTGTCC-TTGGTTAAAATGGAACCTG
1 ACTTGAACAGAACAGAACATACTAGTATGTTTAAAGA-CTT-TCCACT-GTTAAAATGGAACCTG
25372 TTTTAAGCTGTAACTTGTTCTTTACCTGCAATTTGCATATTC-AGTTTATAACACACCCATTTTG
63 TTTTAAGCTGTAACTTGTTCTTTACCTGCAATTTGCATATTCAAG-TTATAACACACCCATTTTG
* * *
25436 CCTTTTGTTTGACAATTCCTTTTTCAGTTTGATAGCAAGGCGGAATTATACTAAGAGAATTGCTC
127 CCTTTTGTTTGACAATTCCTTTTTCAGTTTGATAGCAAGGCAGAATTATACTAAGAAAACTGCTC
25501 AAATCGTCTTGGACTTTCTTACATTTCAGTAGGCTATTGGTAAGGTATGTTCTCGTACCATTTCA
192 AAATCGTCTTGGACTTTCTTACATTTCAGTAGGCTATTGGTAAGGTATGTTCTCGTACCATTTCA
25566 GTTTAT
257 GTTTAT
25572 GTTATATGCT
Statistics
Matches: 250, Mismatches: 6, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
269 10 0.04
270 6 0.02
271 213 0.85
272 2 0.01
273 1 0.00
274 18 0.07
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (273 bp):
ACTTGAACAGAACAGAACATACTAGTATGTTTAAAGACTTTCCACTGTTAAAATGGAACCTGTTT
TAAGCTGTAACTTGTTCTTTACCTGCAATTTGCATATTCAAGTTATAACACACCCATTTTGCCTT
TTGTTTGACAATTCCTTTTTCAGTTTGATAGCAAGGCAGAATTATACTAAGAAAACTGCTCAAAT
CGTCTTGGACTTTCTTACATTTCAGTAGGCTATTGGTAAGGTATGTTCTCGTACCATTTCAGTTT
ATTGTGTTTCTAA
Found at i:25659 original size:25 final size:27
Alignment explanation
Indices: 25599--25674 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 27
25589 ATAATTGGGG
25599 TGCTGCAAACTGTTTCTGTTTTGTTAGT
1 TGCTGCAAACTGTTT-TGTTTTGTTAGT
25627 TGCTGCAAACTGTTGTTGTTTTGTTAG-
1 TGCTGCAAACTGTT-TTGTTTTGTTAGT
25654 T-C-GCAAACTGTTTTTGTTTTG
1 TGCTGCAAACTG-TTTTGTTTTG
25675 GATCTTGCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
25 16 0.35
26 3 0.07
27 1 0.02
28 25 0.54
29 1 0.02
ACGTcount: A:0.14, C:0.13, G:0.22, T:0.50
Consensus pattern (27 bp):
TGCTGCAAACTGTTTTGTTTTGTTAGT
Found at i:26882 original size:11 final size:11
Alignment explanation
Indices: 26854--26885 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
26844 GAAAAAATAG
*
26854 TATACTATTTC
1 TATACTGTTTC
26865 TATACTGTTTC
1 TATACTGTTTC
26876 TATACTGTTT
1 TATACTGTTT
26886 ATGCTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (11 bp):
TATACTGTTTC
Found at i:30298 original size:37 final size:37
Alignment explanation
Indices: 30226--30298 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
30216 GGGGTCAGTG
* * *
30226 TTTTGACCACCCCATGTTAGGGTGGTGCTATTGAAAA
1 TTTTGACCACCCCAAGTTAGGGTGATGCGATTGAAAA
* *
30263 TTTTGATCACCCCAAGTTGGGGTGATGACGA-TGAAA
1 TTTTGACCACCCCAAGTTAGGGTGATG-CGATTGAAA
30299 TTGAAGGGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 28 0.93
38 2 0.07
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (37 bp):
TTTTGACCACCCCAAGTTAGGGTGATGCGATTGAAAA
Found at i:30932 original size:17 final size:17
Alignment explanation
Indices: 30910--30946 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30900 TCTCTTTAGA
*
30910 GATGCAAACTTTTACTT
1 GATGCAAACTCTTACTT
*
30927 GATGCAAACTCTTATTT
1 GATGCAAACTCTTACTT
30944 GAT
1 GAT
30947 CAACCCTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (17 bp):
GATGCAAACTCTTACTT
Found at i:32656 original size:83 final size:84
Alignment explanation
Indices: 32569--32726 Score: 246
Period size: 83 Copynumber: 1.9 Consensus size: 84
32559 AGACTTTTTG
** * *
32569 ATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT-AAAAAATTATATATATTAT
1 ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGAAAAAATTAGATATATTAA
*
32633 ATTTTTTTAATTAAATCTA
66 AGTTTTTTAATTAAATCTA
* *
32652 ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGCAAAACTTAGATATATTAA
1 ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGAAAAAATTAGATATATTAA
32717 AGTTTTTTAA
66 AGTTTTTTAA
32727 ATATATTTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
83 43 0.64
84 24 0.36
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (84 bp):
ATCTCTTTATAACTATTTTATTTTTACCATTAAACTATTTTAATTGAAAAAATTAGATATATTAA
AGTTTTTTAATTAAATCTA
Found at i:32737 original size:13 final size:14
Alignment explanation
Indices: 32719--32754 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
32709 TATATTAAAG
32719 TTTTTTAAAT-ATA
1 TTTTTTAAATGATA
32732 TTTTTTAAATGATA
1 TTTTTTAAATGATA
*
32746 TTGTTTAAA
1 TTTTTTAAA
32755 CTTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTTTTAAATGATA
Found at i:34967 original size:24 final size:24
Alignment explanation
Indices: 34940--34997 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
34930 AAAATTATTT
*
34940 TCAAAATTTAAATTTTGAATTTAA
1 TCAACATTTAAATTTTGAATTTAA
34964 TCAACA-TTAAATTTTGAATTTAA
1 TCAACATTTAAATTTTGAATTTAA
34987 TCAACATTTAA
1 TCAACATTTAA
34998 TAAAACCGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 23 0.72
24 9 0.28
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (24 bp):
TCAACATTTAAATTTTGAATTTAA
Found at i:35665 original size:27 final size:27
Alignment explanation
Indices: 35627--35686 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
35617 AGGTTTGCCG
*
35627 CAAAACGCAATTTGGGATATAACGTTA
1 CAAAACGCAATTTGGAATATAACGTTA
35654 CAAAACGCAATTTGGAATATAACGTTA
1 CAAAACGCAATTTGGAATATAACGTTA
35681 CAAAAC
1 CAAAAC
35687 AAGTAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (27 bp):
CAAAACGCAATTTGGAATATAACGTTA
Found at i:35704 original size:29 final size:28
Alignment explanation
Indices: 35627--35731 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 28
35617 AGGTTTGCCG
**
35627 CAAAAC-GCAATTTGGGATATAACGTTA
1 CAAAACAGCAATTAAGGATATAACGTTA
*
35654 CAAAAC-GCAATT-TGGAATATAACGTTA
1 CAAAACAGCAATTAAGG-ATATAACGTTA
* *
35681 CAAAACAAGTAATTAAGGATATAATGTTA
1 CAAAAC-AGCAATTAAGGATATAACGTTA
35710 CGAAAAACGAGCAATTAAGGAT
1 C--AAAAC-AGCAATTAAGGAT
35732 TTTGTCAGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.03
27 29 0.44
29 16 0.24
30 2 0.03
31 17 0.26
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (28 bp):
CAAAACAGCAATTAAGGATATAACGTTA
Found at i:35930 original size:31 final size:31
Alignment explanation
Indices: 35852--35933 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
35842 AACCTAACTG
* *
35852 ATTATATCCTTAATTGATTGAAATTGAAAAC
1 ATTATATCCTTAATTGCTTGAAATCGAAAAC
* *
35883 GTTATACCCTTAATTGCTTGAAATCGAAAAC
1 ATTATATCCTTAATTGCTTGAAATCGAAAAC
35914 ATTATATCCTTAATTGCTTG
1 ATTATATCCTTAATTGCTTG
35934 CTTTGTAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (31 bp):
ATTATATCCTTAATTGCTTGAAATCGAAAAC
Found at i:36475 original size:86 final size:85
Alignment explanation
Indices: 36218--36462 Score: 418
Period size: 86 Copynumber: 2.9 Consensus size: 85
36208 TTTAAACATA
* *
36218 TTTAATTAAATCTAATCTTTTTATAACTATTTTATTTTTACCATTTTACTATTTCAATTAAAAAA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAA
36283 CTTAGATATATTAAAATTTT
66 CTTAGATATATTAAAATTTT
* *
36303 TTTACTTAAATCTAATCTCTTTATAACTATTGTATTTTTACCATTTTACTATTTTAATTAAAAAA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT-AAAAA
*
36368 ACTTAAATATATTAAAATTTT
65 ACTTAGATATATTAAAATTTT
**
36389 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTGCAAAA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAA
36454 CTTAGATAT
66 CTTAGATAT
36463 GTTGGAACTT
Statistics
Matches: 149, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
85 67 0.45
86 82 0.55
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (85 bp):
TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAA
CTTAGATATATTAAAATTTT
Found at i:37370 original size:31 final size:29
Alignment explanation
Indices: 37335--37401 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
37325 TCTAACTGAC
*
37335 TATATCTTTAATTGCTCGCTTTTCGTAATGT
1 TATATCTTTAATTGCTCGC-TTT-GTAACGT
* *
37366 TATATCCTTAATTGCTTGCTTTGTAACGT
1 TATATCTTTAATTGCTCGCTTTGTAACGT
37395 TATATCT
1 TATATCT
37402 CAAATTGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.38
30 3 0.09
31 17 0.53
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (29 bp):
TATATCTTTAATTGCTCGCTTTGTAACGT
Found at i:37407 original size:29 final size:31
Alignment explanation
Indices: 37335--37409 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
37325 TCTAACTGAC
* *
37335 TATATCTTTAATTGCTCGCTTTTCGTAATGT
1 TATATCTCTAATTGCTCGCTTTTCGTAACGT
*
37366 TATATC-CTTAATTGCTTGC-TTT-GTAACGT
1 TATATCTC-TAATTGCTCGCTTTTCGTAACGT
*
37395 TATATCTCAAATTGC
1 TATATCTCTAATTGC
37410 ATTTTGTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 18 0.47
30 4 0.11
31 16 0.42
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCTCTAATTGCTCGCTTTTCGTAACGT
Found at i:38434 original size:19 final size:18
Alignment explanation
Indices: 38406--38446 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
38396 TTACTTTCTT
38406 CAAAAAAAAAAAAACAAA
1 CAAAAAAAAAAAAACAAA
38424 CAAAAACAAAAAAAACAAA
1 CAAAAA-AAAAAAAACAAA
38443 CAAA
1 CAAA
38447 CAAACTATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAAAAACAAA
Found at i:39779 original size:49 final size:49
Alignment explanation
Indices: 39707--39807 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
39697 AAGTTGATTG
39707 GCGGTACTACCGGAATCTGATGTCGTTAATTGGCTACTGCTGCTTCGTT
1 GCGGTACTACCGGAATCTGATGTCGTTAATTGGCTACTGCTGCTTCGTT
39756 GCGGTACTACCGGAATCTGATGTCGTTAATTGGCTACTGCTGCTTCGTT
1 GCGGTACTACCGGAATCTGATGTCGTTAATTGGCTACTGCTGCTTCGTT
39805 GCG
1 GCG
39808 ATTCCCTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.34
Consensus pattern (49 bp):
GCGGTACTACCGGAATCTGATGTCGTTAATTGGCTACTGCTGCTTCGTT
Found at i:42568 original size:21 final size:21
Alignment explanation
Indices: 42543--42619 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
42533 TATCTTAGAT
42543 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
42564 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
42585 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
42607 ATAAATAATATAT
1 AT-AATAATATAT
42620 ACTATATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 18 0.39
22 21 0.46
23 7 0.15
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:42576 original size:25 final size:25
Alignment explanation
Indices: 42545--42593 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
42535 TCTTAGATAT
*
42545 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
42570 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
42594 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:44822 original size:48 final size:48
Alignment explanation
Indices: 44746--44891 Score: 247
Period size: 48 Copynumber: 3.0 Consensus size: 48
44736 TAAAACTTTG
* * *
44746 AAAACATGAATAAAATATTGAAAGCAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
*
44794 AAAACGGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
*
44842 AAAACAGGAATAAAACATTGGAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
44890 AA
1 AA
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (48 bp):
AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
Done.