Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007746.1 Corchorus capsularis cultivar CVL-1 contig07767, 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: 13146
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Found at i:4225 original size:54 final size:54
Alignment explanation
Indices: 4118--4226 Score: 148
Period size: 53 Copynumber: 2.0 Consensus size: 54
4108 GCCTGCATCA
* * *
4118 CCCAGGTGTGTCAAAAAGAGATACATGTAAATGAGTAGAAGGTAAAGGCTATCT
1 CCCAGGTGTGTCAAAAAGAGATACAAGTAAATGAGTAAAAGGTAAAGACTATCT
* * *
4172 CCCAGGTGTG-CCAAAAGTGATACAAGTAAATGAGTAAAAGGTGAAAGATTATCT
1 CCCAGGTGTGTCAAAAAGAGATACAAGTAAATGAGTAAAAGGT-AAAGACTATCT
4226 C
1 C
4227 TTTTCATCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
53 28 0.58
54 20 0.42
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (54 bp):
CCCAGGTGTGTCAAAAAGAGATACAAGTAAATGAGTAAAAGGTAAAGACTATCT
Found at i:8769 original size:26 final size:26
Alignment explanation
Indices: 8740--8855 Score: 112
Period size: 26 Copynumber: 4.4 Consensus size: 26
8730 CACGCGCGAT
*
8740 GTCACGTGTGGGGTTGTTC-TTCGGAG
1 GTCACGTGTGGGGTTGTACGTT-GGAG
* * *
8766 GTCACGTGTTGAAGG-TATCCGTTGGAG
1 GTCACGTG-TG-GGGTTGTACGTTGGAG
*
8793 GTCACGTGTGGAGTTGTAC-TTCGGAG
1 GTCACGTGTGGGGTTGTACGTT-GGAG
* *
8819 ATCACGTGTGGGGTCGTACGTTGGAG
1 GTCACGTGTGGGGTTGTACGTTGGAG
8845 GTCACGTGTGG
1 GTCACGTGTGG
8856 AGTGCCAGCT
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
25 3 0.04
26 47 0.64
27 19 0.26
28 4 0.05
ACGTcount: A:0.14, C:0.16, G:0.41, T:0.30
Consensus pattern (26 bp):
GTCACGTGTGGGGTTGTACGTTGGAG
Found at i:8804 original size:13 final size:13
Alignment explanation
Indices: 8762--8857 Score: 53
Period size: 13 Copynumber: 7.3 Consensus size: 13
8752 GTTGTTCTTC
8762 GGAGGTCACGTGTT
1 GGAGGTCACGTG-T
*
8776 GAAGGT-ATCCGT-T
1 GGAGGTCA--CGTGT
8789 GGAGGTCACGTGT
1 GGAGGTCACGTGT
8802 GGAGTTGT-AC-T-T
1 GGAG--GTCACGTGT
*
8814 CGGAGATCACGTGT
1 -GGAGGTCACGTGT
8828 GG-GGTCGTACGT-T
1 GGAGGTC--ACGTGT
8841 GGAGGTCACGTGT
1 GGAGGTCACGTGT
8854 GGAG
1 GGAG
8858 TGCCAGCTGG
Statistics
Matches: 64, Mismatches: 4, Indels: 29
0.66 0.04 0.30
Matches are distributed among these distances:
11 1 0.02
12 13 0.20
13 28 0.44
14 17 0.27
15 5 0.08
ACGTcount: A:0.17, C:0.15, G:0.42, T:0.27
Consensus pattern (13 bp):
GGAGGTCACGTGT
Found at i:8824 original size:53 final size:52
Alignment explanation
Indices: 8740--8858 Score: 159
Period size: 53 Copynumber: 2.3 Consensus size: 52
8730 CACGCGCGAT
* * * *
8740 GTCACGTGTGGGGTTGTTCTTCGGAGGTCACGTGTTGAAGGT-ATCCGTTGGAG
1 GTCACGTGTGGAGTTGTACTTCGGAGATCACGTG-TG-AGGTCATACGTTGGAG
* *
8793 GTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGGGGTCGTACGTTGGAG
1 GTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGAGGTCATACGTTGGAG
8845 GTCACGTGTGGAGT
1 GTCACGTGTGGAGT
8859 GCCAGCTGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 3 0.05
52 25 0.42
53 31 0.53
ACGTcount: A:0.14, C:0.15, G:0.40, T:0.30
Consensus pattern (52 bp):
GTCACGTGTGGAGTTGTACTTCGGAGATCACGTGTGAGGTCATACGTTGGAG
Found at i:8918 original size:15 final size:15
Alignment explanation
Indices: 8898--8927 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8888 CTTGTGGTCA
8898 TAGGTGGTCGAGCGC
1 TAGGTGGTCGAGCGC
*
8913 TAGGTGGTCGGGCGC
1 TAGGTGGTCGAGCGC
8928 CGGGCTTTGG
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:0.20, G:0.50, T:0.20
Consensus pattern (15 bp):
TAGGTGGTCGAGCGC
Found at i:10223 original size:50 final size:50
Alignment explanation
Indices: 10114--10223 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
10104 TCCGCTTCTG
* * *
10114 TTTTGTGTCGCACGCCGCGTAGTAGTTGGCTCTTGATTGCCTTGCTTCCA
1 TTTTGTGTCGCACACCACGTAGTAGTTGGCACTTGATTGCCTTGCTTCCA
** * * * *
10164 TTTAATGTCGCACACCACGTAGTAGTTGGCACTTTATTGCTTTGTTTTCA
1 TTTTGTGTCGCACACCACGTAGTAGTTGGCACTTGATTGCCTTGCTTCCA
10214 TTTTGTGTCG
1 TTTTGTGTCG
10224 TACGTCACAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.42
Consensus pattern (50 bp):
TTTTGTGTCGCACACCACGTAGTAGTTGGCACTTGATTGCCTTGCTTCCA
Found at i:10848 original size:44 final size:43
Alignment explanation
Indices: 10683--11265 Score: 695
Period size: 44 Copynumber: 13.3 Consensus size: 43
10673 TGACCATCTA
* * * * * *
10683 GTTCTTGTCTTCTTGGTTTGATTGTGGTGTGTTCGACCGACTT
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * * * *
10726 GTTGTTTACTTCTTGCTTTTAGTTTGATGTGGTCGATCGACTT
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* *
10769 GTTGTTTACTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
1 GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
*
10812 GTTGTTTAT-TTCTTGCTTTTGAATGTGATGTGGTCGATCGACTT
1 GTTCTTT-TCTTCTTGC-TTTGAATGTGATGTGGTCGATCGACTT
*
10856 GTTCTTGTTCTTCTTGCTTTGTATGTGATGTGGTCGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * *
10900 GTTCTTGTTCTTCTTGCTTTGAATGCGATATGGTTGATCGACTT
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
**
10944 GTTCTTGTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACCG
1 GTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
*
10988 GTTCTTTTCTTCTTTG-TTTGAATGTGATGTGGTCGATCGACTA
1 GTTCTTTTCTTC-TTGCTTTGAATGTGATGTGGTCGATCGACTT
* *
11031 GTTACTTCTCTTCTTTG-TTTGAATGTGATGTGGTCGATCGACTA
1 GTT-CTTTTCTTC-TTGCTTTGAATGTGATGTGGTCGATCGACTT
* * **
11075 GTTACTTCTCTTCTTGCTTTGAATGTGATGTGGTCGATTGACCG
1 GTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
** *
11119 GTTCTTTTCTTCTCACTTCTGAATGTGATGTGGTCGATCGACTA
1 GTTCTTTTCTTCTTGCTT-TGAATGTGATGTGGTCGATCGACTT
* * *
11163 GTTACTTCTCTTCTTGGTTTGAATGTGATGTGGTCGATCGACTA
1 GTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
* * * **
11207 GTTACTTCTCTTTTTGGTTTGAATGTGATGTGGTCGATCGACCG
1 GTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
11251 GTTCTTTTCTTCTTG
1 GTTCTTTTCTTCTTG
11266 AACCATTTCG
Statistics
Matches: 485, Mismatches: 46, Indels: 18
0.88 0.08 0.03
Matches are distributed among these distances:
43 146 0.30
44 320 0.66
45 19 0.04
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (43 bp):
GTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATCGACTT
Found at i:11160 original size:219 final size:217
Alignment explanation
Indices: 10699--11248 Score: 678
Period size: 219 Copynumber: 2.5 Consensus size: 217
10689 GTCTTCTTGG
* * * * * * * * *
10699 TTTGATTGTGGTGTGTTCGACCGACTTGTTGTTTACTTCTTGCTTTTAGTTTGATGTGGTCGATC
1 TTTGAATGTGATGTGGTCGATCGACTTGTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATC
* * * * **
10764 GACTTGTTGTTTACTTC-TTGCTTTGAATGTGATGTGGTCGATCGACTTGTTGTTTATTTCTTGC
66 GACTAGTTCTTTTCTTCTTTG-TTTGAATGTGATGTGGTCGATCGACTAGTTACTTATTTCTTGC
* * *
10828 TTTTGAATGTGATGTGGTCGATCGACTTGTTCTTGTTCTTCTTGCTTTGTATGTGATGTGGTCGA
130 -TTTGAATGTGATGTGGTCGATCGACTAGTTCTTGCTCTTCTTGCTTTGAATGTGATGTGGTCGA
** **
10893 TCGACTTGTTCTTGTTCTTCTTGC
194 TCGACCGGTTCTTGTTCTTCTCAC
* * *
10917 TTTGAATGCGATATGGTTGATCGACTTGTTCTTGTTCTTCTTGCTTTGAATGTGATGTGGTCGAT
1 TTTGAATGTGATGTGGTCGATCGACTTGTTCTT-TTCTTCTTGCTTTGAATGTGATGTGGTCGAT
** *
10982 CGACCGGTTCTTTTCTTCTTTGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTCTCTTCTTT
65 CGACTAGTTCTTTTCTTCTTTGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTAT-TTC-TT
11047 G-TTTGAATGTGATGTGGTCGATCGACTAGTTACTT-CTCTTCTTGCTTTGAATGTGATGTGGTC
128 GCTTTGAATGTGATGTGGTCGATCGACTAGTT-CTTGCTCTTCTTGCTTTGAATGTGATGTGGTC
*
11110 GATTGACCGGTTCTT-TTCTTCTCAC
192 GATCGACCGGTTCTTGTTCTTCTCAC
* * *
11135 TTCTGAATGTGATGTGGTCGATCGACTAGTTACTTCTCTTCTTGGTTTGAATGTGATGTGGTCGA
1 TT-TGAATGTGATGTGGTCGATCGACTTGTT-CTTTTCTTCTTGCTTTGAATGTGATGTGGTCGA
*
11200 TCGACTAGTTACTTCTCTT-TTTGGTTTGAATGTGATGTGGTCGATCGAC
64 TCGACTAGTT-CTTTTCTTCTTT-GTTTGAATGTGATGTGGTCGATCGAC
11249 CGGTTCTTTT
Statistics
Matches: 286, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
218 35 0.12
219 203 0.71
220 45 0.16
221 3 0.01
ACGTcount: A:0.13, C:0.16, G:0.25, T:0.46
Consensus pattern (217 bp):
TTTGAATGTGATGTGGTCGATCGACTTGTTCTTTTCTTCTTGCTTTGAATGTGATGTGGTCGATC
GACTAGTTCTTTTCTTCTTTGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTATTTCTTGCT
TTGAATGTGATGTGGTCGATCGACTAGTTCTTGCTCTTCTTGCTTTGAATGTGATGTGGTCGATC
GACCGGTTCTTGTTCTTCTCAC
Found at i:11435 original size:57 final size:58
Alignment explanation
Indices: 11256--11435 Score: 267
Period size: 58 Copynumber: 3.1 Consensus size: 58
11246 GACCGGTTCT
11256 TTTCTTCTTGAACCATTTCGGCATGAATGTGATTTTTGGTCGTTCGACACATTAT-TCC
1 TTTCTTCTTGAACCATTTCGGCATGAATGTGATTTTTGGTCGTTCGACACATT-TCTCC
* * * *
11314 TTGCTTCTTGAACCATTTCGGCATGAATGTAATTTTTGGTCGTTCGACACATATCTCA
1 TTTCTTCTTGAACCATTTCGGCATGAATGTGATTTTTGGTCGTTCGACACATTTCTCC
* *
11372 TTTCTTCTTTG-ACCATTTCGGCATGAACGTGA-TTTTGGTCGTTCGACGCATTTCTCC
1 TTTCTTC-TTGAACCATTTCGGCATGAATGTGATTTTTGGTCGTTCGACACATTTCTCC
11429 TTTCTTC
1 TTTCTTC
11436 GACTTGGGTG
Statistics
Matches: 110, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
57 30 0.27
58 77 0.70
59 3 0.03
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (58 bp):
TTTCTTCTTGAACCATTTCGGCATGAATGTGATTTTTGGTCGTTCGACACATTTCTCC
Found at i:11828 original size:97 final size:96
Alignment explanation
Indices: 11686--11861 Score: 228
Period size: 97 Copynumber: 1.8 Consensus size: 96
11676 CTCGAGGATC
** * *
11686 ATTCTCCATTTGCGCTCGGGGAGCGTCATACGCTTCGCGTTTGGCGAGCATCATCTTTTTCGCCA
1 ATTCTCCATTTGCGCTCGACGAGCGTCATACACTTCGCGTTTGGCGAGCATCATCCTTTTCGCCA
11751 TCTCGGGTATTCTTCATGTGCTCTCAAGGAGA
66 TC-CGGGTATTCTTCATGTGCTCTCAAGGAGA
* * *** *
11783 ATTCTTCC-TTTGCGCTCGACGAGCGTCCTACATTTCGCGTTTGGCGATTGTCATCCTTTTCGCT
1 ATTC-TCCATTTGCGCTCGACGAGCGTCATACACTTCGCGTTTGGCGAGCATCATCCTTTTCGCC
*
11847 ATCCGGGTTTTCTTC
65 ATCCGGGTATTCTTC
11862 TCTTGCTCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
96 11 0.16
97 53 0.79
98 3 0.04
ACGTcount: A:0.13, C:0.28, G:0.23, T:0.36
Consensus pattern (96 bp):
ATTCTCCATTTGCGCTCGACGAGCGTCATACACTTCGCGTTTGGCGAGCATCATCCTTTTCGCCA
TCCGGGTATTCTTCATGTGCTCTCAAGGAGA
Found at i:12390 original size:126 final size:126
Alignment explanation
Indices: 12208--12508 Score: 530
Period size: 126 Copynumber: 2.4 Consensus size: 126
12198 GGACGAGGTC
* **
12208 GATTCATGTCGATCGCCACTTAATCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
1 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
* *
12273 CGCCTGTTGGCGTTGGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
66 CGCCTGTTGGCCTTAGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
*
12334 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCTAGCTCGGCCTTGCCTGATCGCT
1 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
*
12399 CGCCTGTTGGCCTTAGGCCCCTTGTGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
66 CGCCTGTTGGCCTTAGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
*
12460 GATTCAAGTCGATCGCCACTTTGTCGATGGTCATACTAGGTCGAGCTCG
1 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCG
12509 CCTGTTGGCG
Statistics
Matches: 166, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 166 1.00
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.31
Consensus pattern (126 bp):
GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
CGCCTGTTGGCCTTAGGCCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
Found at i:12549 original size:109 final size:108
Alignment explanation
Indices: 12396--12617 Score: 381
Period size: 109 Copynumber: 2.0 Consensus size: 108
12386 TTGCCTGATC
* *
12396 GCTCGCCTGTTGGCCTTAGGCCCCTTGTGGGCATCATCATCATTTCTCATACTTGATTGGGGATG
1 GCTCGCCTGTTGGCCTTAGGCCCCTTGGGGGCATCATCACCATTTCTCATACTTGATTGGGGATG
*
12461 ATTCAAGTCGATCGCCACTTTGTCGATGGTCATACTAGGTCGA
66 ATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGA
* * *
12504 GCTCGCCTGTTGGCGTTGGGACCCCTTGGGGGCATTATCACCATTTCTCATACTTGATTGGGGAT
1 GCTCGCCTGTTGGCCTTAGG-CCCCTTGGGGGCATCATCACCATTTCTCATACTTGATTGGGGAT
12569 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGA
65 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGA
12613 GCTCG
1 GCTCG
12618 GCCTTGCCTG
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
108 18 0.17
109 89 0.83
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (108 bp):
GCTCGCCTGTTGGCCTTAGGCCCCTTGGGGGCATCATCACCATTTCTCATACTTGATTGGGGATG
ATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGA
Found at i:12612 original size:126 final size:125
Alignment explanation
Indices: 12504--12922 Score: 676
Period size: 126 Copynumber: 3.3 Consensus size: 125
12494 ACTAGGTCGA
* * * *
12504 GCTCGCCTGTTGGCGTTGGGACCCCTTGGGGGCATTATCACCATTTCTCATACTTGATTGGGGAT
1 GCTCGCCTGTTGGCGTTAGG-CCCCTTGCGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
12569 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATC
65 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGA-CTCGGCCTTGCCTGATC
* *
12631 GCTCGCCTATTGGCGTTAGGCCCCTTGCGGGCATCATCATCATTTTTCATACTTGATTGGGGATG
1 GCTCGCCTGTTGGCGTTAGGCCCCTTGCGGGCATCATCATCATTTCTCATACTTGATTGGGGATG
*
12696 ATTCAAGTCGATCACCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATC
66 ATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGA-CTCGGCCTTGCCTGATC
*
12757 GCTCGCCTGTTGGCGTTAGGCCCCTTGTGGGCATCATCATCATTTCTCATACTTGATTGGGGATG
1 GCTCGCCTGTTGGCGTTAGGCCCCTTGCGGGCATCATCATCATTTCTCATACTTGATTGGGGATG
* *
12822 ATTCAAGTCGATCGCTACTTTGTCGGTGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATC
66 ATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGA-CTCGGCCTTGCCTGATC
* * * *
12883 GCTCGCCTGTTGACGTTGGGCCCCTTGAGGGCATTATCAT
1 GCTCGCCTGTTGGCGTTAGGCCCCTTGCGGGCATCATCAT
12923 TTCCCCGACT
Statistics
Matches: 275, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
126 257 0.93
127 18 0.07
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.31
Consensus pattern (125 bp):
GCTCGCCTGTTGGCGTTAGGCCCCTTGCGGGCATCATCATCATTTCTCATACTTGATTGGGGATG
ATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGACTCGGCCTTGCCTGATC
Found at i:12701 original size:235 final size:235
Alignment explanation
Indices: 12270--12922 Score: 1002
Period size: 235 Copynumber: 2.7 Consensus size: 235
12260 TTGCCTGATC
12270 GCTCGCCTGTTGGCGTTGGG-CCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
1 GCTCGCCTGTTGGCGTTGGGACCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
*
12334 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCTAGCTCGGCCTTGCCTGATCGCT
66 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
* *
12399 CGCCTGTTGGCCTTAGGCCCCTTGTGGGCATCATCATCATTTCTCATACTTGATTGGGGATGATT
131 CGCCTGTTGGCGTTAGGCCCCTTGAGGGCATCATCATCATTTCTCATACTTGATTGGGGATGATT
* *
12464 CAAGTCGATCGCCACTTTGTCGATGGTCATACTAGGTCGA
196 CAAGTCGATCACCACTTTGTCGATGGCCATACTAGGTCGA
* *
12504 GCTCGCCTGTTGGCGTTGGGACCCCTTGGGGGCATTATCACCATTTCTCATACTTGATTGGGGAT
1 GCTCGCCTGTTGGCGTTGGGACCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
12569 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
66 GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
* * *
12634 CGCCTATTGGCGTTAGGCCCCTTGCGGGCATCATCATCATTTTTCATACTTGATTGGGGATGATT
131 CGCCTGTTGGCGTTAGGCCCCTTGAGGGCATCATCATCATTTCTCATACTTGATTGGGGATGATT
12699 CAAGTCGATCACCACTTTGTCGATGGCCATACTAGGTCGA
196 CAAGTCGATCACCACTTTGTCGATGGCCATACTAGGTCGA
*
12739 GCTCGGCCTTGCCTGATCGCTCGCCTGTTGGCGTTAGGCCCCTTGTGGGCATCATCATCATTTCT
1 GCTC-GCC-TG--T--T-G---G-C-GTTGG-G--A--CCCCTTGGGGGCATCATCATCATTTCT
* *
12804 CATACTTGATTGGGGATGATTCAAGTCGATCGCTACTTTGTCGGTGGCCATACTAGGTCGAGCTC
49 CATACTTGATTGGGGATGATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTC
* * *
12869 GGCCTTGCCTGATCGCTCGCCTGTTGACGTTGGGCCCCTTGAGGGCATTATCAT
114 GGCCTTGCCTGATCGCTCGCCTGTTGGCGTTAGGCCCCTTGAGGGCATCATCAT
12923 TTCCCCGACT
Statistics
Matches: 382, Mismatches: 19, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
234 20 0.05
235 209 0.55
236 3 0.01
237 2 0.01
239 1 0.00
241 1 0.00
242 1 0.00
245 1 0.00
246 1 0.00
247 5 0.01
248 1 0.00
250 1 0.00
252 136 0.36
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (235 bp):
GCTCGCCTGTTGGCGTTGGGACCCCTTGGGGGCATCATCATCATTTCTCATACTTGATTGGGGAT
GATTCAAGTCGATCGCCACTTTGTCGATGGCCATACTAGGTCGAGCTCGGCCTTGCCTGATCGCT
CGCCTGTTGGCGTTAGGCCCCTTGAGGGCATCATCATCATTTCTCATACTTGATTGGGGATGATT
CAAGTCGATCACCACTTTGTCGATGGCCATACTAGGTCGA
Found at i:13122 original size:90 final size:90
Alignment explanation
Indices: 12969--13136 Score: 239
Period size: 90 Copynumber: 1.9 Consensus size: 90
12959 CCTGCCAGTC
* * *
12969 GGGGGCCATGTTAGGTCAAGGTCGATTCTTGTCGATCGCATAGCCTCCTGGCGTTGAGCCCCTTG
1 GGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCGCATAGCCTCCTGGCGTTGAGCCCCTTG
*
13034 GGGGCGTTCGTCATTCCCATAAGTT
66 GGGGCGTCCGTCATTCCCATAAGTT
** * * *
13059 GGGGGCCATGCTAGGTCTGGGTCAAATCTTGTTGATCGCCCT-GCCTGCTGGCGTTGAGCCCCTT
1 GGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCG-CATAGCCTCCTGGCGTTGAGCCCCTT
13123 GGGGGCGTCCGTCA
65 GGGGGCGTCCGTCA
13137 AGTATAATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
90 66 0.97
91 2 0.03
ACGTcount: A:0.12, C:0.27, G:0.33, T:0.27
Consensus pattern (90 bp):
GGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCGCATAGCCTCCTGGCGTTGAGCCCCTTG
GGGGCGTCCGTCATTCCCATAAGTT
Done.