Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007252.1 Corchorus capsularis cultivar CVL-1 contig07273, 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: 17751
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Found at i:2151 original size:63 final size:64
Alignment explanation
Indices: 1827--2459 Score: 412
Period size: 64 Copynumber: 9.8 Consensus size: 64
1817 TTTTCAATTC
* * * * * * *
1827 CCCAAAACGCCCTTTTGGACAAAGGTTTAGTTTTGTAAAATTTCTTGCATTTAGGTTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATA-TTCTTGCATTGAAGCTCTAGTTTT
* * *
1892 CCCAGAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCAAATTTCTTGCATTGAGGCTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATA-TTCTTGCATTGAAGCTCTAGTTTT
** * * * *
1957 CCCAAAACGCCC-TTCAAACAAAGGGCTAGTTCTGTCACATTCCATT--ATCT-AAGTTCAACAT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATATT-C-TTGCAT-TGAAG--C-TC-T
*
2018 ATTTGATT
59 AGTT--TT
** * * * * *
2026 CCCAAAATACCCTTTCGGACATAGGGTTAGTTTTCTCATATTCTTGCATTTAGGTTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCATTGAAGCTCTAGTTTT
* * *
2090 CCTAAAACGCCCTTTCAGACAAAGGGTTGGTTTTGTCAT-TTCTTGCATTGAAGCTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCATTGAAGCTCTAGTTTT
* * ** * *
2153 CCCAAAACGCCCTTTCGGACAAAGGGCTAGTTTTGTCACATTCCAGTATCT-AAGTTC-AGGATT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCAT-TGAAGCTCTA-G---
2216 TTTATTT
61 --T-TTT
** * * * * *
2223 CCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCGTCACATTCTTGCATTTAGGATCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCATTGAAGCTCTAGTTTT
* * * * * * * *
2287 CCCAAACCGCCCTTTCAGACAAAGGGTT-GATTTCTCACATTCTTGCATTTAAG-TTTAGTATT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCATTGAAGCTCTAGTTTT
** * * * * *
2349 CCCAAAATACCCTTTCGGACAAATGGTCAGTTTCT-TCACATTCCTGCACTT--AGATTCTAG--
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTT-TGTCATATTCTTGCA-TTGAAG-CTCTAGTT
2409 TT
63 TT
** * * * * *
2411 CCCAAAATACCCTTTCTGACAAAGGGTCAGATTTGTCACATTCTCGCAT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCAT
2460 ATAGTTTCAA
Statistics
Matches: 458, Mismatches: 80, Indels: 64
0.76 0.13 0.11
Matches are distributed among these distances:
61 2 0.00
62 74 0.16
63 98 0.21
64 104 0.23
65 75 0.16
66 5 0.01
67 5 0.01
68 2 0.00
69 16 0.03
70 76 0.17
71 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (64 bp):
CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCATATTCTTGCATTGAAGCTCTAGTTTT
Found at i:2239 original size:197 final size:196
Alignment explanation
Indices: 1731--2392 Score: 832
Period size: 197 Copynumber: 3.4 Consensus size: 196
1721 AGAAATCAAC
* * * * *
1731 TTTCTTGCATTTAGGTTCTAGTTTTCCTAAAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCACA
1 TTTCTTGCATTGAAGCTCTAGTTTTCCCAAAACGCCCTTTCGGACAAAGGGCTAGTTTTGTCACA
* * ** * *
1796 TTCCAGTATCCAAGTTCAGCATTTTCAATTCCCCAAAACGCCCTTTTGGACAAAGGTTTAGTTTT
66 TTCCAGTATCTAAGTTCAGCATTTT-AATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTT
* * * *
1861 GTAAAATTTCTTGCATTTAGGTTCTAGTTTTCCCAGAACGCCCTTTCGGACAAAGGGTTAGTTTT
130 CTCAAA-TTCTTGCATTTAGGTTCTAGTTTTCCCAAAACGCCCTTTCAGACAAAGGGTT-GTTTT
1926 GTCAAA
193 GTC--A
* ** *
1932 TTTCTTGCATTGAGGCTCTAGTTTTCCCAAAACGCCC-TTCAAACAAAGGGCTAGTTCTGTCACA
1 TTTCTTGCATTGAAGCTCTAGTTTTCCCAAAACGCCCTTTCGGACAAAGGGCTAGTTTTGTCACA
* * * *
1996 TTCCATTATCTAAGTTCAACATATTTGA-TTCCCAAAATACCCTTTCGGACATAGGGTTAGTTTT
66 TTCCAGTATCTAAGTTCAGCAT-TTTAATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTT
* *
2060 CTCATATTCTTGCATTTAGGTTCTAGTTTTCCTAAAACGCCCTTTCAGACAAAGGGTTGGTTTTG
130 CTCAAATTCTTGCATTTAGGTTCTAGTTTTCCCAAAACGCCCTTTCAGACAAAGGGTT-GTTTTG
2125 TCA
194 TCA
2128 TTTCTTGCATTGAAGCTCTAGTTTTCCCAAAACGCCCTTTCGGACAAAGGGCTAGTTTTGTCACA
1 TTTCTTGCATTGAAGCTCTAGTTTTCCCAAAACGCCCTTTCGGACAAAGGGCTAGTTTTGTCACA
* *
2193 TTCCAGTATCTAAGTTCAGGATTTTTATTTCCCAAAATACCCTTTCGGACAAAGGGTTAG-TTTC
66 TTCCAGTATCTAAGTTCAGCATTTTAATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTC
* * * * *
2257 GTCACATTCTTGCATTTAGGATCTAGTTTTCCCAAACCGCCCTTTCAGACAAAGGGTTGATTTCT
131 -TCAAATTCTTGCATTTAGGTTCTAGTTTTCCCAAAACGCCCTTTCAGACAAAGGGTTGTTTTGT
2322 CA
195 CA
* * * * ** *
2324 CATTCTTGCATTTAAG-TTTAGTATTCCCAAAATACCCTTTCGGACAAATGG-TCAGTTTCT-TC
1 -TTTCTTGCATTGAAGCTCTAGTTTTCCCAAAACGCCCTTTCGGACAAAGGGCT-AGTTT-TGTC
2386 ACATTCC
63 ACATTCC
2393 TGCACTTAGA
Statistics
Matches: 408, Mismatches: 46, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
195 1 0.00
196 96 0.24
197 141 0.35
198 57 0.14
199 33 0.08
200 43 0.11
201 37 0.09
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (196 bp):
TTTCTTGCATTGAAGCTCTAGTTTTCCCAAAACGCCCTTTCGGACAAAGGGCTAGTTTTGTCACA
TTCCAGTATCTAAGTTCAGCATTTTAATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTTC
TCAAATTCTTGCATTTAGGTTCTAGTTTTCCCAAAACGCCCTTTCAGACAAAGGGTTGTTTTGTC
A
Found at i:2311 original size:64 final size:64
Alignment explanation
Indices: 1827--2459 Score: 459
Period size: 63 Copynumber: 9.8 Consensus size: 64
1817 TTTTCAATTC
* * * * * *
1827 CCCAAAACGCCCTTTTGGACAAAGGTTTAGTTTTGTAAAATTTCTTGCATTTAGGTTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTCGTCACA-TTCTTGCATTTAGGATCTAGTTTT
* * * * *
1892 CCCAGAACGCCCTTTCGGACAAAGGGTTAGTTTTGTCAAATTTCTTGCATTGAGGCTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTCGTCACA-TTCTTGCATTTAGGATCTAGTTTT
** * * * *
1957 CCCAAAACGCCC-TTCAAACAAAGGGCTAG-TTCTGTCACATTCCATT--ATCTAAGTTCAACAT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTC-GTCACATT-C-TTGCAT-TTAG--GATC-T
*
2018 ATTTGATT
59 AGTT--TT
** * * *
2026 CCCAAAATACCCTTTCGGACATAGGGTTAGTTTTC-TCATATTCTTGCATTTAGGTTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAG-TTTCGTCACATTCTTGCATTTAGGATCTAGTTTT
* * * * * * * *
2090 CCTAAAACGCCCTTTCAGACAAAGGGTTGGTTTTGTCA-TTTCTTGCATTGAAGCTCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTCGTCACATTCTTGCATTTAGGATCTAGTTTT
* * *
2153 CCCAAAACGCCCTTTCGGACAAAGGGCTAGTTTTGTCACATTCCAGTAT-CTAAGTTCAGGAT-T
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTCGTCACATT-C--T-TGC--A-TTTAGGATCT
**
2216 TTTATTT
59 AGT-TTT
**
2223 CCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCGTCACATTCTTGCATTTAGGATCTAGTTTT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTCGTCACATTCTTGCATTTAGGATCTAGTTTT
* * * * *
2287 CCCAAACCGCCCTTTCAGACAAAGGGTT-GATTTC-TCACATTCTTGCATTTAAG-TTTAGTATT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAG-TTTCGTCACATTCTTGCATTTAGGATCTAGTTTT
** * * * * *
2349 CCCAAAATACCCTTTCGGACAAATGGTCAGTTTCTTCACATTCCTGCACTTA-GATTCTAG--TT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTCGTCACATTCTTGCATTTAGGA-TCTAGTTTT
** * * *
2411 CCCAAAATACCCTTTCTGACAAAGGGTCAGATTT-GTCACATTCTCGCAT
1 CCCAAAACGCCCTTTCGGACAAAGGGTTAG-TTTCGTCACATTCTTGCAT
2460 ATAGTTTCAA
Statistics
Matches: 457, Mismatches: 79, Indels: 67
0.76 0.13 0.11
Matches are distributed among these distances:
62 75 0.16
63 102 0.22
64 96 0.21
65 76 0.17
66 6 0.01
67 9 0.02
68 3 0.01
69 20 0.04
70 67 0.15
72 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (64 bp):
CCCAAAACGCCCTTTCGGACAAAGGGTTAGTTTCGTCACATTCTTGCATTTAGGATCTAGTTTT
Found at i:2513 original size:63 final size:59
Alignment explanation
Indices: 2221--2523 Score: 200
Period size: 62 Copynumber: 4.8 Consensus size: 59
2211 GGATTTTTAT
* * *
2221 TTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCGTCACATTCTTGCATTTAGGA-TCTAG
1 TTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT-GTCACATTC-CGCA-TTA-GATTCAAG
*** * * * * *
2283 TTTTCCCAAACCGCCCTTTCAGACAAAGGGT-TGATTTCTCACATTCTTGCATTTA-AGTT-TAG
1 --TTCCCAAAATACCCTTTCGGACAAAGGGTCAG-TTTGTCACATTC-CGCA-TTAGA-TTCAAG
* * *
2345 TATTCCCAAAATACCCTTTCGGACAAATGGTCAGTTTCTTCACATTCCTGCACTTAGATTCTAG
1 --TTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT-GTCACATTCC-GCA-TTAGATTCAAG
* * *
2409 TTCCCAAAATACCCTTTCTGACAAAGGGTCAGATTTGTCACATTCTCGCATATAGTTTCAAT
1 TTCCCAAAATACCCTTTCGGACAAAGGGTCAG-TTTGTCACATTC-CGCAT-TAGATTCAAG
** * *
2471 TTCCCAGCATATCCTTTTCGGACAAAGGGTCAGTTTAGTCACACTCCCGCATT
1 TTCCCAAAATA-CCCTTTCGGACAAAGGGTCAGTTT-GTCACA-TTCCGCATT
2524 TAATTTCTGA
Statistics
Matches: 198, Mismatches: 27, Indels: 30
0.78 0.11 0.12
Matches are distributed among these distances:
61 2 0.01
62 92 0.46
63 70 0.35
64 34 0.17
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (59 bp):
TTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTGTCACATTCCGCATTAGATTCAAG
Found at i:2558 original size:63 final size:61
Alignment explanation
Indices: 2218--2705 Score: 313
Period size: 63 Copynumber: 7.6 Consensus size: 61
2208 TCAGGATTTT
* * *
2218 TATTTCCCAAAATACCCTTTCGGACAAAGGGTTAGTTTCGTCACATTCTTGCATTTAGGATC
1 TATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT-GTCACATTCTTGCATTTAAGTTC
*** * * *
2280 TAGTTTTCCCAAACCGCCCTTTCAGACAAAGGGT-TGATTTCTCACATTCTTGCATTTAAGTT-
1 TA--TTTCCCAAAATACCCTTTCGGACAAAGGGTCAG-TTTGTCACATTCTTGCATTTAAGTTC
* * * *
2342 TAGTATTCCCAAAATACCCTTTCGGACAAATGGTCAGTTTCTTCACATTCCTGCACTT-AGATTC
1 TA-T-TTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT-GTCACATTCTTGCATTTAAG-TTC
* * * *
2406 TAGTTCCCAAAATACCCTTTCTGACAAAGGGTCAGATTTGTCACATTCTCGCATAT-AGTTTC
1 TATTTCCCAAAATACCCTTTCGGACAAAGGGTCAG-TTTGTCACATTCTTGCATTTAAG-TTC
* ** * * ** *
2468 AATTTCCCAGCATATCCTTTTCGGACAAAGGGTCAGTTTAGTCACACTCCCGCATTTAATTTC
1 TATTTCCCAAAATA-CCCTTTCGGACAAAGGGTCAGTTT-GTCACATTCTTGCATTTAAGTTC
* * * * * * **
2531 TGATTTCCCCAAATGCCCTTTCAGACAAAGGATCAATTTTCTCACA-TCTCTGCATACAAGTTTA
1 T-ATTTCCCAAAATACCCTTTCGGACAAAGGGTC-AGTTTGTCACATTCT-TGCATTTAAG--T-
2595 ATC
60 -TC
* * * * * * *
2598 TTGGTTTCCTAGAATACCCTTTCGGACAAAGGGTCAATTTCGTCATCCTGCTTGCATTTAGGTTA
1 -T-ATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT-GTCA-CATTCTTGCATTTAAGTT-
2663 AAC
61 --C
*
2666 T-TTCTCCCTAAAATACCCTTTCAGACAAAGGGTCAGTTTG
1 TATT-TCCC-AAAATACCCTTTCGGACAAAGGGTCAGTTTG
2706 GTAATGTTTC
Statistics
Matches: 328, Mismatches: 70, Indels: 52
0.73 0.16 0.12
Matches are distributed among these distances:
61 1 0.00
62 95 0.29
63 103 0.31
64 45 0.14
65 4 0.01
66 4 0.01
67 35 0.11
68 31 0.09
69 8 0.02
70 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (61 bp):
TATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTGTCACATTCTTGCATTTAAGTTC
Found at i:3225 original size:13 final size:14
Alignment explanation
Indices: 3200--3231 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3190 GCATTTTTGT
3200 TTATTTATGCTTAA
1 TTATTTATGCTTAA
3214 TTATTT-TGCTTAA
1 TTATTTATGCTTAA
3227 -TATTT
1 TTATTT
3232 GCATGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 7 0.39
14 6 0.33
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (14 bp):
TTATTTATGCTTAA
Found at i:6702 original size:21 final size:21
Alignment explanation
Indices: 6676--6728 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
6666 AGGAAATAGT
*
6676 GCGTCGGGATGAAGAAGCACG
1 GCGTCGGGAAGAAGAAGCACG
6697 GCGTCGGGAAGAAGAAGCACG
1 GCGTCGGGAAGAAGAAGCACG
6718 GCGTCGGGAAG
1 GCGTCGGGAAG
6729 GAACAACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.45, T:0.08
Consensus pattern (21 bp):
GCGTCGGGAAGAAGAAGCACG
Found at i:15219 original size:62 final size:62
Alignment explanation
Indices: 15070--15237 Score: 178
Period size: 62 Copynumber: 2.7 Consensus size: 62
15060 TATCGAAGTT
* * * * * *
15070 GACCTCAGGCAGGTCATTCTCAATTTCTAAAGTTGACCACCGACTGGTCTTCTTTAAATTCA
1 GACCTCAGACAGATCTTTATCAGTTTCTAAAGTTGACCACAGACTGGTCTTCTTTAAATTCA
* * * * * *
15132 GACCTTAGACAGGTCTTTCTTAGTTTGC-AAAGTTGACCACAGACTGGTTTTC-TTCAATGTCA
1 GACCTCAGACAGATCTTTATCAGTTT-CTAAAGTTGACCACAGACTGGTCTTCTTTAAAT-TCA
* *
15194 GACCTCAGACAGATCTTTATCAGTTTCTAAATTTGACCTCAGAC
1 GACCTCAGACAGATCTTTATCAGTTTCTAAAGTTGACCACAGAC
15238 AAGTCTTTCT
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
61 6 0.07
62 82 0.92
63 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (62 bp):
GACCTCAGACAGATCTTTATCAGTTTCTAAAGTTGACCACAGACTGGTCTTCTTTAAATTCA
Found at i:15278 original size:34 final size:33
Alignment explanation
Indices: 15138--15278 Score: 105
Period size: 34 Copynumber: 4.3 Consensus size: 33
15128 TTCAGACCTT
15138 AGACAGGTCTTTCTTAGTTTGCAAAGTTGACCAC
1 AGACAGGTCTTTCTTAGTTT-CAAAGTTGACCAC
* * * *
15172 AGACTGGT-TTTC-----TTCAATGTCAGACCTC
1 AGACAGGTCTTTCTTAGTTTCAAAGT-TGACCAC
* * * * *
15200 AGACAGATCTTTATCAGTTTCTAAATTTGACCTC
1 AGACAGGTCTTTCTTAGTTTC-AAAGTTGACCAC
*
15234 AGACAAGTCTTTCTTAGTTTTCAAAGTTGACCAC
1 AGACAGGTCTTTCTTAG-TTTCAAAGTTGACCAC
*
15268 AGACTGGTCTT
1 AGACAGGTCTT
15279 CTTCAATTTT
Statistics
Matches: 80, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
27 5 0.06
28 13 0.16
29 3 0.04
33 4 0.05
34 48 0.60
35 7 0.09
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.35
Consensus pattern (33 bp):
AGACAGGTCTTTCTTAGTTTCAAAGTTGACCAC
Found at i:15294 original size:62 final size:61
Alignment explanation
Indices: 15228--15499 Score: 254
Period size: 62 Copynumber: 4.5 Consensus size: 61
15218 TTCTAAATTT
* * *
15228 GACCTCAGACAAGTCTTTCTTAGTTTTCAAAGTTGACCACAGACTGGTCTTCTTCAATTTTA
1 GACCTCAGACAGGTCTTTCTCAGTTTTC-AAGTTGACCACAGACTGGTCTTCTTCAATTTCA
* * * * *
15290 GACCTCAGACAGGTTTTTCTCA-ATTTC-A---GACCTCAGACAGGTC-TCTCTCAACTTCA
1 GACCTCAGACAGGTCTTTCTCAGTTTTCAAGTTGACCACAGACTGGTCTTCT-TCAATTTCA
* ** *
15346 GACCTCAGACAGGTCTTTCTTAGTTTTCAAAGTTGACCATGGATTGGTCTTCTTCAATTTCA
1 GACCTCAGACAGGTCTTTCTCAGTTTTC-AAGTTGACCACAGACTGGTCTTCTTCAATTTCA
* * * * * * *
15408 GACTTTAGACAGGTCTTTCTCAATTAT-AAGATAGATCACATACTGGTCTTCTTCAATTTCA
1 GACCTCAGACAGGTCTTTCTCAGTTTTCAAG-TTGACCACAGACTGGTCTTCTTCAATTTCA
* * *
15469 GACCTTAGACAGGTCCTTCTCAATTTT-AAGT
1 GACCTCAGACAGGTCTTTCTCAGTTTTCAAGT
15500 CAACCACGAA
Statistics
Matches: 170, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
55 3 0.02
56 40 0.24
57 4 0.02
59 2 0.01
60 4 0.02
61 55 0.32
62 59 0.35
63 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (61 bp):
GACCTCAGACAGGTCTTTCTCAGTTTTCAAGTTGACCACAGACTGGTCTTCTTCAATTTCA
Found at i:15298 original size:28 final size:29
Alignment explanation
Indices: 15262--15362 Score: 136
Period size: 28 Copynumber: 3.6 Consensus size: 29
15252 TTTCAAAGTT
* * *
15262 GACCACAGACTGGTCTTCT-TCAATTTTA
1 GACCTCAGACAGGTCTTCTCTCAATTTCA
*
15290 GACCTCAGACAGGT-TTTTCTCAATTTCA
1 GACCTCAGACAGGTCTTCTCTCAATTTCA
*
15318 GACCTCAGACAGGTC-TCTCTCAACTTCA
1 GACCTCAGACAGGTCTTCTCTCAATTTCA
15346 GACCTCAGACAGGTCTT
1 GACCTCAGACAGGTCTT
15363 TCTTAGTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
27 3 0.05
28 60 0.94
29 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.31
Consensus pattern (29 bp):
GACCTCAGACAGGTCTTCTCTCAATTTCA
Found at i:15423 original size:28 final size:28
Alignment explanation
Indices: 15391--15494 Score: 70
Period size: 28 Copynumber: 3.5 Consensus size: 28
15381 ACCATGGATT
15391 GGTCTTCTTCAATTTCAGACTTTAGACA
1 GGTCTTCTTCAATTTCAGACTTTAGACA
* * * *
15419 GGTCTT-TCTCAATTATAAGA-TAGATCACATACT
1 GGTCTTCT-TCAATT-TCAGACT---T--TAGACA
*
15452 GGTCTTCTTCAATTTCAGACCTTAGACA
1 GGTCTTCTTCAATTTCAGACTTTAGACA
15480 GGTCCTTC-TCAATTT
1 GGT-CTTCTTCAATTT
15495 TAAGTCAACC
Statistics
Matches: 57, Mismatches: 9, Indels: 20
0.66 0.10 0.23
Matches are distributed among these distances:
27 1 0.02
28 26 0.46
29 8 0.14
30 1 0.02
31 1 0.02
32 4 0.07
33 15 0.26
34 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (28 bp):
GGTCTTCTTCAATTTCAGACTTTAGACA
Done.