Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012780.1 Corchorus olitorius cultivar O-4 contig12813, 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: 5701
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Found at i:1709 original size:48 final size:48
Alignment explanation
Indices: 1638--2021 Score: 554
Period size: 48 Copynumber: 8.0 Consensus size: 48
1628 TAAAACGTCG
* *
1638 AAAACAAGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
*
1686 AAAACAGGAATAAAACATTGAAAACAACACCTTCTGACCGGGAAGGGC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
** * * * *
1734 AAAATGGGAATAAAACAATGAAGATAACACCTTCCGATCGGGAAGGGC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
** *
1782 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGATTGGGAAGGTC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
* **
1830 AAAACGGGAATAAAATC-TTGAAAACAACACCTTCCGACTAGGAAGGGC
1 AAAACAGGAATAAAA-CATTGAAAACAACACCTTCCGACCGGGAAGGGC
* * * *
1878 GAAACGGGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
*
1926 AAAACGGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
*
1974 AAAACAGGAATGAAAACATTGAAAACAACACCTTCCGACGGGGAAGGG
1 AAAACAGGAAT-AAAACATTGAAAACAACACCTTCCGACCGGGAAGGG
2022 TATTGAAAAC
Statistics
Matches: 302, Mismatches: 31, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
48 266 0.88
49 36 0.12
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (48 bp):
AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGC
Found at i:1900 original size:144 final size:144
Alignment explanation
Indices: 1638--2202 Score: 635
Period size: 144 Copynumber: 4.1 Consensus size: 144
1628 TAAAACGTCG
* *
1638 AAAACAAGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACA
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACA
* * *
1703 TTGAAAACAACACCTTCTGACCGGGAAGGGCAAAATGGGAATAAAACAATGAAGATAACACCTTC
66 TTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACAATGAAGACAACACCTTC
*
1768 CGATCGGGAAGGGC
131 CGACCGGGAAGGGC
** * *
1782 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGATTGGGAAGGTCAAAACGGGAATAAAATC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAA-C
** * * *
1847 -TTGAAAACAACACCTTCCGACTAGGAAGGGCGAAACGGGAATAAAATATTGAAGACAACACCTT
65 ATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACAATGAAGACAACACCTT
1911 CCGACCGGGAAGGGC
130 CCGACCGGGAAGGGC
*
1926 AAAACGGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAAAC
1 AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAAT-AAAAC
* *
1991 ATTGAAAACAACACCTTCCGA-C--G--GGG---AA-GGG--T-----ATTGAAAACAACACCTT
65 ATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACAATGAAGACAACACCTT
*
2040 TCGACCGGGAAGGGC
130 CCGACCGGGAAGGGC
* *
2055 AAAATAGGAATGAAAACATTGAAAACAACACCTTCTGACCGGGAAGGGCAAAACAGG------A-
1 AAAACAGGAAT-AAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAAC
* * ** * *
2113 A-TGAAATCAACACCTTTCG-GTGAGGAAGGGCAAAACAGGG-ATAAAACATTGAAAACAACACC
65 ATTGAAAACAACACCTTCCGACCG-GGAAGGGCAAAAC-GGGAATAAAACAATGAAGACAACACC
* *
2175 TTCCTACCGGGAAGAGC
128 TTCCGACCGGGAAGGGC
2192 AAAACAGGAAT
1 AAAACAGGAAT
2203 GAAATCAACA
Statistics
Matches: 367, Mismatches: 33, Indels: 49
0.82 0.07 0.11
Matches are distributed among these distances:
121 16 0.04
122 1 0.00
123 1 0.00
124 1 0.00
126 3 0.01
129 41 0.11
130 44 0.12
131 3 0.01
132 1 0.00
134 1 0.00
136 3 0.01
137 41 0.11
140 3 0.01
142 1 0.00
144 182 0.50
145 25 0.07
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (144 bp):
AAAACAGGAATAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAACA
TTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAACAATGAAGACAACACCTTC
CGACCGGGAAGGGC
Found at i:2032 original size:32 final size:32
Alignment explanation
Indices: 1991--2053 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1981 GAATGAAAAC
*
1991 ATTGAAAACAACACCTTCCGACGGGGAAGGGT
1 ATTGAAAACAACACCTTCCGACCGGGAAGGGT
*
2023 ATTGAAAACAACACCTTTCGACCGGGAAGGG
1 ATTGAAAACAACACCTTCCGACCGGGAAGGG
2054 CAAAATAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (32 bp):
ATTGAAAACAACACCTTCCGACCGGGAAGGGT
Found at i:2035 original size:81 final size:81
Alignment explanation
Indices: 1942--2188 Score: 291
Period size: 81 Copynumber: 3.0 Consensus size: 81
1932 GGAATAAAAC
1942 ATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACCT
1 ATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACCT
*
2007 TCCGACGGGGAAGGGT
66 TCCGACCGGGAAGGGT
* *
2023 ATTGAAAACAACACCTTTCGACCGGGAAGGGCAAAATAGGAATGAAAACATTGAAAACAACACCT
1 ATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACCT
* *
2088 TCTGACCGGGAAGGGCAAAACAGG
66 TCCGACCGGGAA-GG-------GT
* * * ** *
2112 AATGAAATCAACACCTTTCG-GTGAGGAAGGGCAAAACAGGGAT-AAAACATTGAAAACAACACC
1 ATTGAAAACAACACCTTCCGACCG-GGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACC
*
2175 TTCCTACCGGGAAG
65 TTCCGACCGGGAAG
2189 AGCAAAACAG
Statistics
Matches: 144, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
81 73 0.51
82 2 0.01
87 1 0.01
88 32 0.22
89 36 0.25
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (81 bp):
ATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACCT
TCCGACCGGGAAGGGT
Found at i:2079 original size:49 final size:49
Alignment explanation
Indices: 2023--2206 Score: 203
Period size: 49 Copynumber: 4.0 Consensus size: 49
2013 GGGGAAGGGT
*
2023 ATTGAAAACAACACCTTTCGACCGGGAAGGGCAAAATAGGAATGAAAAC
1 ATTGAAAACAACACCTTTCGACCGGGAAGGGCAAAACAGGAATGAAAAC
2072 ATTGAAAACAACACC-TTCTGACCGGGAAGGGCAAAACAGGAATG--AA-
1 ATTGAAAACAACACCTTTC-GACCGGGAAGGGCAAAACAGGAATGAAAAC
** *
2118 A-T-----CAACACCTTTCG-GTGAGGAAGGGCAAAACAGGGAT-AAAAC
1 ATTGAAAACAACACCTTTCGACCG-GGAAGGGCAAAACAGGAATGAAAAC
* * *
2160 ATTGAAAACAACACCTTCCTACCGGGAAGAGCAAAACAGGAATGAAA
1 ATTGAAAACAACACCTTTCGACCGGGAAGGGCAAAACAGGAATGAAA
2207 TCAACACCTT
Statistics
Matches: 111, Mismatches: 10, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
39 1 0.01
40 26 0.23
41 5 0.05
42 1 0.01
43 1 0.01
45 1 0.01
46 1 0.01
47 2 0.02
48 30 0.27
49 43 0.39
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (49 bp):
ATTGAAAACAACACCTTTCGACCGGGAAGGGCAAAACAGGAATGAAAAC
Found at i:2185 original size:88 final size:88
Alignment explanation
Indices: 2025--2234 Score: 316
Period size: 88 Copynumber: 2.4 Consensus size: 88
2015 GGAAGGGTAT
* ** *
2025 TGAAAACAACACCTTTCGACCGGGAAGGGCAAAATAGGAATGAAAACATTGAAAACAACACCTTC
1 TGAAATCAACACCTTTCG-GTGGGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACCTTC
*
2090 TGACCGGGAAGGGCAAAACAGGAA
65 TGACCGGGAAGAGCAAAACAGGAA
*
2114 TGAAATCAACACCTTTCGGTGAGGAAGGGCAAAACAGGGAT-AAAACATTGAAAACAACACCTTC
1 TGAAATCAACACCTTTCGGTG-GGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACCTT-
2178 CT-ACCGGGAAGAGCAAAACAGGAA
64 CTGACCGGGAAGAGCAAAACAGGAA
2202 TGAAATCAACACCTTTCGGTGGGGAAGGGCAAA
1 TGAAATCAACACCTTTCGGT-GGGAAGGGCAAA
2235 CTGGGAAAAG
Statistics
Matches: 112, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
88 75 0.67
89 37 0.33
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (88 bp):
TGAAATCAACACCTTTCGGTGGGAAGGGCAAAACAGGAATGAAAACATTGAAAACAACACCTTCT
GACCGGGAAGAGCAAAACAGGAA
Found at i:2257 original size:88 final size:86
Alignment explanation
Indices: 2077--2415 Score: 325
Period size: 88 Copynumber: 3.9 Consensus size: 86
2067 AAAACATTGA
*
2077 AAACAACACCTTCTGACCGGGAAGGGCAAAACAGGAATGAAATCAACACCTTTCGGTGAGGAAGG
1 AAACAACACCTTCTGACCGGGAAGGGCAAAACAGGAATGAAA-CAACACCTTCCGGTGAGGAAGG
* *
2142 GCAAAACAGGGATAAA---ACATTGA
65 GC-AAACTGGGA-AAAGTGAC-TT-T
* * *
2165 AAACAACACCTTCCT-ACCGGGAAGAGCAAAACAGGAATGAAATCAACACCTTTCGGTGGGGAAG
1 AAACAACACCTT-CTGACCGGGAAGGGCAAAACAGGAATGAAA-CAACACCTTCCGGTGAGGAAG
*
2229 GGCAAACTGGGAAAAGTGGGCTTT
64 GGCAAACTGGGAAAAGT-GACTTT
* *** * *
2253 AAACAACACCTTCTGA-TGGAGAAGGGCAAATTGGGAATTAAACAACACCTTCCGGTGGGGAAGG
1 AAACAACACCTTCTGACCGG-GAAGGGCAAAACAGGAATGAAACAACACCTTCCGGTGAGGAAGG
2317 GCAAACTGGGAAAAGTAGAC-TT
65 GCAAACTGGGAAAAGT-GACTTT
* ** ** * * *
2339 AGACAACACCTTCCAATGGGGAA-GGC-AAACTGGGAATTTAAACAACACCTTCCGATGAGGAAG
1 AAACAACACCTTCTGACCGGGAAGGGCAAAAC-AGGAA-TGAAACAACACCTTCCGGTGAGGAAG
2402 GGCAAACTGGGAAA
64 GGCAAACTGGGAAA
2416 TTAAACAACA
Statistics
Matches: 219, Mismatches: 22, Indels: 22
0.83 0.08 0.08
Matches are distributed among these distances:
84 2 0.01
85 8 0.04
86 59 0.27
87 53 0.24
88 92 0.42
89 4 0.02
90 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (86 bp):
AAACAACACCTTCTGACCGGGAAGGGCAAAACAGGAATGAAACAACACCTTCCGGTGAGGAAGGG
CAAACTGGGAAAAGTGACTTT
Found at i:2363 original size:47 final size:42
Alignment explanation
Indices: 2208--2819 Score: 259
Period size: 40 Copynumber: 14.6 Consensus size: 42
2198 GGAATGAAAT
* *
2208 CAACACCTTTCGGTGGGGAAGGGCAAACTGGGAAAAGTGGGCTTTAAA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAA------TTTAAA
* * *
2256 CAACACCTTCTGATGGAGAAGGGCAAATTGGG--AA-TTAAA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATTTAAA
* *
2295 CAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAGACTTAGA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAA-T----TTAAA
*
2342 CAACACCTTCCAATGGGGAA-GGCAAACTGGG--AATTTAAA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATTTAAA
*
2381 CAACACCTTCCGATGAGGAAGGGCAAACTGGG-AAA-TTAAA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATTTAAA
* * * * * *
2421 CAACACCTTCCGGTGGGGAAGAGCAGATTGGGCAAATTGGACAAA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATT---TAAA
* * * * *
2466 GGCAATAACACCTCCCGATGAGGAAGGGCAAATTGGGAATA-CT-AA
1 --C---AACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATTTAAA
* ***
2511 CAACACCTTCCGATGAGGAAGGGCAAACT-GGATAAA-GGCAA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGA-AAATTTAAA
* * * * * * * * * *
2552 CAACACCTCCCGATGAGGATGGGAAAATTAGTAATA-CT-GA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATTTAAA
* ***
2592 CAACACCTTCCGAT-GAGAAGGGCAAACT-GGACAAA-GGCAA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGA-AAATTTAAA
* * * * * * *
2632 CAACACCTCCCGATGAGGAAGGGCAAATTGGTAATA-CT-GA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATTTAAA
* * * * * *
2672 CAACACTTTCCGATGAGGAAGGGCAAA-TTGG-TAATGCT-GA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAAT-TTAAA
* * ***
2712 CAATACCTTCCGATGAGGAAGGGCAAACT-GGACAAA-GGCAA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGA-AAATTTAAA
* * * * * * *
2753 CAACACCTCCCGATGAGGAAGGGCAAATTGGTAATA-CT-GA
1 CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATTTAAA
*
2793 CAACACCTTCCGATGAGGAAGGGCAAA
1 CAACACCTTCCGATGGGGAAGGGCAAA
2820 ACAGGAAGTA
Statistics
Matches: 445, Mismatches: 85, Indels: 76
0.73 0.14 0.13
Matches are distributed among these distances:
38 3 0.01
39 71 0.16
40 183 0.41
41 79 0.18
42 9 0.02
43 2 0.00
44 2 0.00
45 5 0.01
46 13 0.03
47 23 0.05
48 27 0.06
50 28 0.06
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.16
Consensus pattern (42 bp):
CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAATTTAAA
Found at i:2390 original size:86 final size:87
Alignment explanation
Indices: 2198--2415 Score: 305
Period size: 86 Copynumber: 2.5 Consensus size: 87
2188 GAGCAAAACA
* * * *
2198 GGAATGAAATCAACACCTTTCGGTGGGGAAGGGCAAACTGGGAAAAGTGGGCTTTAAACAACACC
1 GGAATTAAA-CAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAGACTTTAAACAACACC
** *
2263 TTCTGATGGAGAAGGGCAAATTG
65 TTCCAATGGAGAAGGGCAAACTG
*
2286 GGAATTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAGAC-TTAGACAACACCT
1 GGAATTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAGACTTTAAACAACACCT
*
2350 TCCAATGGGGAA-GGCAAACTG
66 TCCAATGGAGAAGGGCAAACTG
* *
2371 GGAATTTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAA
1 GGAA-TTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAA
2416 TTAAACAACA
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
85 12 0.10
86 59 0.50
87 39 0.33
88 8 0.07
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (87 bp):
GGAATTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAGTAGACTTTAAACAACACCT
TCCAATGGAGAAGGGCAAACTG
Found at i:2420 original size:40 final size:39
Alignment explanation
Indices: 2341--2819 Score: 349
Period size: 40 Copynumber: 11.7 Consensus size: 39
2331 GTAGACTTAG
* * **
2341 ACAACACCTTCCAATGGGGAA-GGCAAACTGGGAATTTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACT-A
*
2380 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATTAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACT-A
* * *
2420 ACAACACCTTCCGGTGGGGAAGAGCAGATTGGGCAAATTGGACAAAGGC-A
1 ACAACACCTTCCGAT---G-AG-G-A-A--GGGCAAACTGG-GAAA--CTA
* * *
2470 ATAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ACTA
*
2510 ACAACACCTTCCGATGAGGAAGGGCAAACTGGATAAAGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAAA--CTA
* * * * * * *
2551 ACAACACCTCCCGATGAGGATGGGAAAATTAGTAATACTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ACTA
*
2591 ACAACACCTTCCGATGA-GAAGGGCAAACTGGACAAAGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAAA--CTA
* * * *
2631 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ACTA
* * * * *
2671 ACAACACTTTCCGATGAGGAAGGGCAAATTGGTAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ACTA
* *
2711 ACAATACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-A
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-GAAA--CTA
* * * *
2752 ACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ACTA
2792 ACAACACCTTCCGATGAGGAAGGGCAAA
1 ACAACACCTTCCGATGAGGAAGGGCAAA
2820 ACAGGAAGTA
Statistics
Matches: 362, Mismatches: 47, Indels: 61
0.77 0.10 0.13
Matches are distributed among these distances:
39 34 0.09
40 198 0.55
41 90 0.25
42 2 0.01
43 2 0.01
44 3 0.01
45 2 0.01
46 3 0.01
47 2 0.01
49 10 0.03
50 16 0.04
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (39 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTA
Found at i:2660 original size:80 final size:81
Alignment explanation
Indices: 2450--2819 Score: 423
Period size: 81 Copynumber: 4.6 Consensus size: 81
2440 AGAGCAGATT
* * * *
2450 GGGCAAATTGGACAAAGGCAATAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTAACAAC
1 GGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAAC
2515 ACCTTCCGATGAGGAA
66 ACCTTCCGATGAGGAA
* * * *
2531 GGGCAAACTGGATAAAGGCAACAACACCTCCCGATGAGGATGGGAAAATTAGTAATACTGACAAC
1 GGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAAC
2596 ACCTTCCGATGA-GAA
66 ACCTTCCGATGAGGAA
2611 GGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAAC
1 GGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAAC
*
2676 ACTTTCCGATGAGGAA
66 ACCTTCCGATGAGGAA
* * * * * * * * *
2692 GGGCAAATTGG--TAATGCTGACAATACCTTCCGATGAGGAAGGGCAAACTGG-ACAAAGGC-AA
1 GGGCAAACTGGACAAAGGC-AACAACACCTCCCGATGAGGAAGGGCAAATTGGTA-ATA--CTGA
*
2753 CAACACCTCCCGATGAGGAA
62 CAACACCTTCCGATGAGGAA
* * * *
2773 GGGCAAATTGGTA-ATA--CTGACAACACCTTCCGATGAGGAAGGGCAAA
1 GGGCAAACTGG-ACAAAGGC-AACAACACCTCCCGATGAGGAAGGGCAAA
2820 ACAGGAAGTA
Statistics
Matches: 255, Mismatches: 27, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
79 5 0.02
80 106 0.42
81 142 0.56
82 1 0.00
83 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.15
Consensus pattern (81 bp):
GGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAAC
ACCTTCCGATGAGGAA
Found at i:2747 original size:121 final size:121
Alignment explanation
Indices: 2472--2819 Score: 492
Period size: 121 Copynumber: 2.9 Consensus size: 121
2462 CAAAGGCAAT
* * * *
2472 AACACCTCCCGATGAGGAAGGGCAAATTGGGA-ATA--CTAACAACACCTTCCGATGAGGAAGGG
1 AACACCTTCCGATGAGGAAGGGCAAACT-GGACAAAGGC-AACAACACCTCCCGATGAGGAAGGG
* * * * *
2534 CAAACTGGATAA-AGGC-AACAACACCTCCCGATGAGGATGGGAAAATTAGTAATACTGAC
64 CAAATTGG-TAATA--CTGACAACACCTTCCGATGAGGAAGGGCAAATTAGTAATACTGAC
2593 AACACCTTCCGATGA-GAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCA
1 AACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCA
* * *
2657 AATTGGTAATACTGACAACACTTTCCGATGAGGAAGGGCAAATTGGTAATGCTGAC
66 AATTGGTAATACTGACAACACCTTCCGATGAGGAAGGGCAAATTAGTAATACTGAC
*
2713 AATACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCA
1 AACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCA
2778 AATTGGTAATACTGACAACACCTTCCGATGAGGAAGGGCAAA
66 AATTGGTAATACTGACAACACCTTCCGATGAGGAAGGGCAAA
2820 ACAGGAAGTA
Statistics
Matches: 207, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
119 4 0.02
120 66 0.32
121 136 0.66
122 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.16
Consensus pattern (121 bp):
AACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCA
AATTGGTAATACTGACAACACCTTCCGATGAGGAAGGGCAAATTAGTAATACTGAC
Found at i:2948 original size:50 final size:47
Alignment explanation
Indices: 2833--2971 Score: 181
Period size: 50 Copynumber: 2.9 Consensus size: 47
2823 GGAAGTAGAC
*
2833 AACTGGGACCTTCCGACCAGGAAGAGGCATTTTTGGAATAA-AAGAA
1 AACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAAGAA
* * *
2879 AACGGGGACCTTCCAACCAGGAAGGGGCATTTTTGGGATAAGATATCGAA
1 AACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGA-A--GAA
** *
2929 AACTGGGATTTTCCGACCAGGAAGGGGCATTTTTGGTATAAGA
1 AACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGA
2972 GATAAGAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
46 37 0.46
47 1 0.01
48 1 0.01
50 41 0.51
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (47 bp):
AACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGAAGAA
Found at i:4951 original size:13 final size:13
Alignment explanation
Indices: 4914--4970 Score: 68
Period size: 12 Copynumber: 4.7 Consensus size: 13
4904 TTATGCACCC
4914 AAAACATTTAT-T
1 AAAACATTTATAT
4926 AAAACATTT-TAT
1 AAAACATTTATAT
*
4938 AAAGCATTTATAT
1 AAAACATTTATAT
*
4951 AAAACA-GT-TAT
1 AAAACATTTATAT
4962 AAAACATTT
1 AAAACATTT
4971 CCTCAACGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 10 0.26
12 20 0.53
13 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (13 bp):
AAAACATTTATAT
Found at i:4961 original size:24 final size:24
Alignment explanation
Indices: 4914--4970 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
4904 TTATGCACCC
*
4914 AAAACATTTATTAAAACATTTTAT
1 AAAACATTTATTAAAACATGTTAT
*
4938 AAAGCATTTATATAAAACA-GTTAT
1 AAAACATTTAT-TAAAACATGTTAT
4962 AAAACATTT
1 AAAACATTT
4971 CCTCAACGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (24 bp):
AAAACATTTATTAAAACATGTTAT
Done.