Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019936.1 Corchorus olitorius cultivar O-4 contig19969, 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: 35804
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1703 original size:13 final size:13
Alignment explanation
Indices: 1685--1712 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1675 TCGAAAATCA
1685 GGACATCTAAATG
1 GGACATCTAAATG
1698 GGACATCTAAATG
1 GGACATCTAAATG
1711 GG
1 GG
1713 GTCTTACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (13 bp):
GGACATCTAAATG
Found at i:1926 original size:47 final size:47
Alignment explanation
Indices: 1872--2781 Score: 1091
Period size: 47 Copynumber: 20.2 Consensus size: 47
1862 GAAGATAATT
* * * *
1872 TTAAACTAAATAATAAAAAAAGAGTAGATTAGTTTAATTCTAGGTAG
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
*
1919 TTAAACTAAGTAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
*
1966 TTAAACTAAGTAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
*
2013 CTAAACTAAATAGTAAAAGAAGA-G-G---AG----A-T-TAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
*
2049 TTAAACTAAATAGTAAAAGAAGAGGAAATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
*
2096 CTAAACTAAATAGTAAAAGAAGA-G-G---AG----A-T-TAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
*
2132 TTAAACTAAATAGTAAAAGAAGAGGAAATTAGTTTAA-T-TA---AA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
* * * * *
2174 CT--A--AAATAGTAAAAGAAAAAGAAACTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
** * *
2217 TTAAACTATGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
* * *
2264 TTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCGAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
2311 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
2358 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
2405 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
2452 TTAAACTAAATAGTAAAAGAAGAGGAGATTAG------T-T---TAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
*
2489 TTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
*
2536 TTAAACTAAGTAGTAAAAGAAG-GAGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAG-GAGATTAGTTTAATTCTAGGTAA
** * *
2583 TTAAACTAGGTAGTAAAAGAGGAAGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
**
2630 TTAAACTAGGTAGTAAAAG-AGTAGGAGATTAGTTTAATTCTAGGTAA
1 TTAAACTAAATAGTAAAAGAAG-AGGAGATTAGTTTAATTCTAGGTAA
* * * *
2677 TTAAACTAAGTAGTAAAAGAGGAAGAGATTAATTTAA-TCTTAGGTAA
1 TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTC-TAGGTAA
* * ** * * * *
2724 TTAAACTAAGTAGTAAAAAGAA-AAGAGGCTGGTTTAAGTCCAGATAA
1 TTAAACTAAATAGT-AAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
2771 TTAAACTAAAT
1 TTAAACTAAAT
2782 GGCAAATAAA
Statistics
Matches: 769, Mismatches: 48, Indels: 92
0.85 0.05 0.10
Matches are distributed among these distances:
36 58 0.08
37 38 0.05
38 29 0.04
39 1 0.00
40 4 0.01
41 5 0.01
42 7 0.01
43 4 0.01
44 1 0.00
45 7 0.01
46 6 0.01
47 600 0.78
48 9 0.01
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.29
Consensus pattern (47 bp):
TTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAA
Found at i:2054 original size:36 final size:36
Alignment explanation
Indices: 2006--2190 Score: 217
Period size: 36 Copynumber: 4.8 Consensus size: 36
1996 AGTTTAATTC
*
2006 TAGGTAACTAAACTAAATAGTAAAAGAAGAGGAGAT
1 TAGGTAATTAAACTAAATAGTAAAAGAAGAGGAGAT
2042 TAGGTAATTAAACTAAATAGTAAAAGAAGAGGAAATTAGTTTAATT
1 TAGGTAATTAAACTAAATAGTAAAAGAAGAGG-----AG----A-T
*
2088 CTAGGTAACTAAACTAAATAGTAAAAGAAGAGGAGAT
1 -TAGGTAATTAAACTAAATAGTAAAAGAAGAGGAGAT
*
2125 TAGGTAATTAAACTAAATAGTAAAAGAAGAGGAAAT
1 TAGGTAATTAAACTAAATAGTAAAAGAAGAGGAGAT
*
2161 TAGTTTAATTAAACTAAAATAGTAAAAGAA
1 TAG-GTAATTAAACT-AAATAGTAAAAGAA
2191 AAAGAAACTA
Statistics
Matches: 131, Mismatches: 5, Indels: 24
0.82 0.03 0.15
Matches are distributed among these distances:
36 68 0.52
37 11 0.08
38 15 0.11
41 2 0.02
42 2 0.02
45 1 0.01
46 1 0.01
47 31 0.24
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.24
Consensus pattern (36 bp):
TAGGTAATTAAACTAAATAGTAAAAGAAGAGGAGAT
Found at i:2499 original size:37 final size:37
Alignment explanation
Indices: 2449--2527 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
2439 TAATTCTAGG
*
2449 TAATTAAACTAAATAGTAAAAGAAGAGGAGATTAGTT
1 TAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTT
2486 TAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTT
1 TAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTT
2523 TAATT
1 TAATT
2528 CTAGGTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (37 bp):
TAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTT
Found at i:2509 original size:131 final size:131
Alignment explanation
Indices: 2355--2750 Score: 548
Period size: 131 Copynumber: 2.9 Consensus size: 131
2345 TAATTCTAGG
*
2355 TAATTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAATAGTA
1 TAATTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTA
* *
2420 AAAGAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAGGAGATTAGT
66 AAAGAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGT
2485 T
131 T
*
2486 TAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTA
1 TAATTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTA
* *
2551 AAAGAAG-GAGAGATTAGTTTAATTCTAGGTAATTAAACTAGGTAGTAAAAGAGGAAGAGATTAG
66 AAAGAAGAG-GAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAG
2615 TT
130 TT
*
2617 TAATTCTAGGTAATTAAACTAGGTAGTAAA-AGAGTAGGAGATTAGTTTAATTCTAGGTAATTAA
1 TAA-T-TA---AACTAAA-TA-GTA--AAAGA-AG-AGGAGATTAGTTTAATTCTAGGTAATTAA
* * *
2681 ACTAAGTAGTAAAAGAGGAAGAGATTAATTTAA-TCTTAGGTAATTAAACTAAGTAGTAAAAAGA
55 ACTAAGTAGTAAAAGAAGAGGAGATTAGTTTAATTC-TAGGTAATTAAACTAAGTAGT-AAAAGA
2745 A-AAGAG
118 AGAAGAG
2751 GCTGGTTTAA
Statistics
Matches: 237, Mismatches: 13, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
130 1 0.00
131 126 0.53
132 1 0.00
133 2 0.01
136 6 0.03
137 2 0.01
138 3 0.01
139 1 0.00
140 7 0.03
141 82 0.35
142 6 0.03
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (131 bp):
TAATTAAACTAAATAGTAAAAGAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTA
AAAGAAGAGGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGT
T
Found at i:7534 original size:147 final size:147
Alignment explanation
Indices: 7235--7669 Score: 696
Period size: 147 Copynumber: 2.9 Consensus size: 147
7225 GAAGTTCCAC
7235 CATTAAGGTATACA--TTGTCTTGAAATAATGTTTGTTTTATGTTGTGTTCAAATGGTGGATTTT
1 CATTAAGGTATACATTTTGTCTTGAAATAA----TGTTTTATGTTGTGTTCAAATGGTGGATTTT
7298 TTAGAGCATTATGGTGGGTCTTGACTCATTTAAATGATTTGGTATTAATT-TGTTCAAATGAATG
62 TTAGAGCATTATGGTGGGTCTTGACTCATTTAAATGATTTGGTATTAATTCT-TTCAAATGAATG
* *
7362 GTAGTATGTTGGTGGATTCTTT
126 GTAGTACGTTGGTGGATTATTT
7384 CATTAAGGTATACATTTTGTCTTGAAATAATGTTTTATGTTGTGTTCAAATGGTGGATTTTTTAG
1 CATTAAGGTATACATTTTGTCTTGAAATAATGTTTTATGTTGTGTTCAAATGGTGGATTTTTTAG
*
7449 AGCATTATGGTGGGTCTTGACTCATTTCAATGATTTGGTATTAATTCTTTCAAATGAATGGTAGT
66 AGCATTATGGTGGGTCTTGACTCATTTAAATGATTTGGTATTAATTCTTTCAAATGAATGGTAGT
7514 ACGTTGGTGGATTATTT
131 ACGTTGGTGGATTATTT
*
7531 CATTAAGGTATACATTTTGTCTTGAAATCATGTTTGTTTTATGTTGTGTTCAAATGGTGGATTTT
1 CATTAAGGTATACATTTTGTCTTGAAAT-A---ATGTTTTATGTTGTGTTCAAATGGTGGATTTT
*
7596 TTAGAGCATTATTATGGTGGGTCTTGACTCATTTAAATGATTTGGTATTAGTTCTTTCAAATGAA
62 TTAGAGC---ATTATGGTGGGTCTTGACTCATTTAAATGATTTGGTATTAATTCTTTCAAATGAA
7661 TGGTAGTAC
124 TGGTAGTAC
7670 TTTGAAACAT
Statistics
Matches: 270, Mismatches: 6, Indels: 15
0.93 0.02 0.05
Matches are distributed among these distances:
147 140 0.52
148 2 0.01
149 14 0.05
151 52 0.19
154 62 0.23
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (147 bp):
CATTAAGGTATACATTTTGTCTTGAAATAATGTTTTATGTTGTGTTCAAATGGTGGATTTTTTAG
AGCATTATGGTGGGTCTTGACTCATTTAAATGATTTGGTATTAATTCTTTCAAATGAATGGTAGT
ACGTTGGTGGATTATTT
Found at i:16364 original size:33 final size:33
Alignment explanation
Indices: 16300--16457 Score: 136
Period size: 33 Copynumber: 4.8 Consensus size: 33
16290 GCTTGCCAAA
* * * *
16300 ATTGAAGAAGAAAGAAGATAGTATCTTGCTCGC
1 ATTGAAGAAGAAAGAAGACAGGAGCTGGCTCGC
*
16333 ATTGAAGAAGAAAGACGACAGGAGCTGGCTCGC
1 ATTGAAGAAGAAAGAAGACAGGAGCTGGCTCGC
* * * * **
16366 CTTGAATAAGAGAGAAGACATGAATTGGCTCGC
1 ATTGAAGAAGAAAGAAGACAGGAGCTGGCTCGC
* * * *
16399 TTTCAAGAAGAGAGAAGACAAGAGCTGGCTCGC
1 ATTGAAGAAGAAAGAAGACAGGAGCTGGCTCGC
* * * * *
16432 CTTAAAGAATACAGAAGACATGAGCT
1 ATTGAAGAAGAAAGAAGACAGGAGCT
16458 TGATCGTTTA
Statistics
Matches: 102, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 102 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (33 bp):
ATTGAAGAAGAAAGAAGACAGGAGCTGGCTCGC
Found at i:16382 original size:66 final size:66
Alignment explanation
Indices: 16301--16454 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 66
16291 CTTGCCAAAA
* * * * * *
16301 TTGAAGAAGAAAGAAGATA-GTATCTTGCTCGCATTGAAGAAGAAAGACGACAGGAGCTGGCTCG
1 TTGAAGAAGAAAGAAGACATGAAT-TGGCTCGCATTCAAGAAGAAAGAAGACAAGAGCTGGCTCG
16365 CC
65 CC
* * * *
16367 TTGAATAAGAGAGAAGACATGAATTGGCTCGCTTTCAAGAAGAGAGAAGACAAGAGCTGGCTCGC
1 TTGAAGAAGAAAGAAGACATGAATTGGCTCGCATTCAAGAAGAAAGAAGACAAGAGCTGGCTCGC
16432 C
66 C
* * *
16433 TTAAAGAATACAGAAGACATGA
1 TTGAAGAAGAAAGAAGACATGA
16455 GCTTGATCGT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
66 70 0.96
67 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (66 bp):
TTGAAGAAGAAAGAAGACATGAATTGGCTCGCATTCAAGAAGAAAGAAGACAAGAGCTGGCTCGC
C
Found at i:18145 original size:23 final size:23
Alignment explanation
Indices: 18119--18166 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
18109 CAAAGTGATC
18119 TTTTGCTTTAGAAGTTTGGTATA
1 TTTTGCTTTAGAAGTTTGGTATA
18142 TTTTGCTTTAGAAGTTTGGTATA
1 TTTTGCTTTAGAAGTTTGGTATA
18165 TT
1 TT
18167 ACAGGTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.54
Consensus pattern (23 bp):
TTTTGCTTTAGAAGTTTGGTATA
Found at i:18175 original size:23 final size:23
Alignment explanation
Indices: 18126--18175 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
18116 ATCTTTTGCT
** *
18126 TTAGAAGTTTGGTATATTTTGCT
1 TTAGAAGTTTGGTATATTCAGCG
18149 TTAGAAGTTTGGTATATTACAG-G
1 TTAGAAGTTTGGTATATT-CAGCG
18172 TTAG
1 TTAG
18176 TGAGTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (23 bp):
TTAGAAGTTTGGTATATTCAGCG
Found at i:18574 original size:15 final size:15
Alignment explanation
Indices: 18554--18583 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18544 GCACAATTTC
18554 AATATACATATATAT
1 AATATACATATATAT
*
18569 AATATATATATATAT
1 AATATACATATATAT
18584 GGTGTATATG
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATACATATATAT
Found at i:18829 original size:32 final size:32
Alignment explanation
Indices: 18793--18904 Score: 145
Period size: 32 Copynumber: 3.5 Consensus size: 32
18783 ACACGCCTCT
* * *
18793 AAATAGTAGCACTTAAAGAACAAAACGTCCCA
1 AAATAGTGGCGCTTAAAGAACAAAACGCCCCA
* *
18825 AAATAGTGGCGCTTAATGAAGAAAACGCCCCA
1 AAATAGTGGCGCTTAAAGAACAAAACGCCCCA
*
18857 AAATAGTGGCGCTTAAA-AACCAAAACACCCCA
1 AAATAGTGGCGCTTAAAGAA-CAAAACGCCCCA
*
18889 AAATAGAGGCGCTTAA
1 AAATAGTGGCGCTTAA
18905 TAAAGAAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
31 2 0.03
32 68 0.97
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (32 bp):
AAATAGTGGCGCTTAAAGAACAAAACGCCCCA
Found at i:18872 original size:64 final size:64
Alignment explanation
Indices: 18793--18923 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 64
18783 ACACGCCTCT
** * * *
18793 AAATAGTAGCACTTAAAGAA-CAAAACGTCCCAAAATAGTGGCGCTTAATGAAGAAAACGCCCCA
1 AAATAGTAGCACTTAAA-AACCAAAACACCCCAAAATAGAGGCGCTTAATAAAGAAAACGCCACA
* * *
18857 AAATAGTGGCGCTTAAAAACCAAAACACCCCAAAATAGAGGCGCTTAATAAAGAAAATGCCACA
1 AAATAGTAGCACTTAAAAACCAAAACACCCCAAAATAGAGGCGCTTAATAAAGAAAACGCCACA
18921 AAA
1 AAA
18924 CACAATATAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 2 0.03
64 56 0.97
ACGTcount: A:0.48, C:0.21, G:0.16, T:0.15
Consensus pattern (64 bp):
AAATAGTAGCACTTAAAAACCAAAACACCCCAAAATAGAGGCGCTTAATAAAGAAAACGCCACA
Found at i:18923 original size:32 final size:32
Alignment explanation
Indices: 18814--18923 Score: 141
Period size: 32 Copynumber: 3.4 Consensus size: 32
18804 CTTAAAGAAC
* *
18814 AAAACGTCCCAAAATAGTGGCGCTTAATGAAG
1 AAAACGCCCCAAAATAGTGGCGCTTAATAAAG
*
18846 AAAACGCCCCAAAATAGTGGCGCTTAA-AAACC
1 AAAACGCCCCAAAATAGTGGCGCTTAATAAA-G
* *
18878 AAAACACCCCAAAATAGAGGCGCTTAATAAAG
1 AAAACGCCCCAAAATAGTGGCGCTTAATAAAG
* *
18910 AAAATGCCACAAAA
1 AAAACGCCCCAAAA
18924 CACAATATAC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.03
32 62 0.93
33 3 0.04
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (32 bp):
AAAACGCCCCAAAATAGTGGCGCTTAATAAAG
Found at i:20052 original size:4 final size:4
Alignment explanation
Indices: 20039--20080 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
20029 AGTACCCTTC
20039 GAAA -AAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
20081 TAAAAGGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:26701 original size:21 final size:21
Alignment explanation
Indices: 26672--26735 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
26662 AGAGGCTACA
26672 GAAA-AGACAGATACAGAAAT
1 GAAAGAGACAGATACAGAAAT
*
26692 GAAAGAGACAGATTCAGAAAT
1 GAAAGAGACAGATACAGAAAT
* * *
26713 GACAGAGAAAGATACAGGAAT
1 GAAAGAGACAGATACAGAAAT
26734 GA
1 GA
26736 TGATTACAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 4 0.11
21 34 0.89
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAAGAGACAGATACAGAAAT
Found at i:33755 original size:2 final size:2
Alignment explanation
Indices: 33748--33778 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33738 CTTATGCTCT
33748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33779 TGCTCTAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34980 original size:46 final size:47
Alignment explanation
Indices: 34917--35017 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 47
34907 TATTATTACT
34917 TTTTAC-T-TTTTAGCTTAATTAACTCT-A-CTACTGATTACTCTTGC
1 TTTTACTTCTTTTAGCTTAATT-ACTCTAATCTACTGATTACTCTTGC
* *
34961 TTTTACTTCTTTTAGCTTAATTACTCTAATCTTCTGATTACTCTTTC
1 TTTTACTTCTTTTAGCTTAATTACTCTAATCTACTGATTACTCTTGC
35008 TTTTACTTCT
1 TTTTACTTCT
35018 GATTACTCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
44 6 0.12
45 6 0.12
46 14 0.27
47 25 0.49
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (47 bp):
TTTTACTTCTTTTAGCTTAATTACTCTAATCTACTGATTACTCTTGC
Found at i:35017 original size:22 final size:22
Alignment explanation
Indices: 34991--35143 Score: 179
Period size: 22 Copynumber: 7.1 Consensus size: 22
34981 TTACTCTAAT
34991 CTTCTGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
**
35013 CTTCTGATTACTCTTTCTTTGG
1 CTTCTGATTACTCTTTCTTTTA
*
35035 CTTTTGATTACTC-TTCATTTTA
1 CTTCTGATTACTCTTTC-TTTTA
* **
35057 CTT-T-ATTACTCCTTCTTTGG
1 CTTCTGATTACTCTTTCTTTTA
* *
35077 CTTTTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
*
35099 C-TCTGATTACTCTTTCCTTTA
1 CTTCTGATTACTCTTTCTTTTA
*
35120 CTTATGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
35142 CT
1 CT
35144 GCTTAGCTTG
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
20 13 0.12
21 26 0.24
22 71 0.65
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.57
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTTTA
Found at i:35205 original size:47 final size:46
Alignment explanation
Indices: 35154--35797 Score: 400
Period size: 47 Copynumber: 14.1 Consensus size: 46
35144 GCTTAGCTTG
* *
35154 ATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTCT-TTACTCTTTAGTTTA
* * *
35201 ATTACCCAGAATTACACTCTTTTCTTC-T-TTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTCTTTACTCTTTAGTTTA
* *
35245 ATTACCCAGAATTAAATTATTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTCT-TTACTCTTTAGTTTA
* *
35292 ATTACCCAGAATTAAACTATTTCCTTCTTCGTTTACTTTTTTA-TTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTC-TTTAC-TCTTTAGTTTA
*
35339 ATTACCCAGAATTAAACTAGCCTCTGTGTACTTCTTCTTTTGCTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTA---T-T-T-T-CTTCTTC-TTTACT-CTTTAGTTTA
*
35393 ATT---C-GAATTAAACTA---AC--C-TC--T--TCTTTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTCTTTACTCTTTAGTTTA
** * *
35425 ATTACCTGGAATTAAACTAATCTCTTCTTCTTTTACTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTC-TTTACT-CTTTAGTTTA
* * * *
35472 ATTACCTAGAATTAAACT-TATCTCTTCTTCGGTTACTAC-TTAATTTA
1 ATTACCCAGAATTAAACTAT-TTTCTTCTTC-TTTACT-CTTTAGTTTA
* * * *
35519 ACTACCTAGAATTAAACTAATCTT-TTCCTCTTTTACTAC-TTAGTTTA
1 ATTACCCAGAATTAAACT-ATTTTCTTCTTC-TTTACT-CTTTAGTTTA
* *** * * *
35566 ATTACCTAGAATTAAACTAACCTCCTCTCCTTTTGCTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTC-TTTACT-CTTTAGTTTA
* * *
35613 ATTACCTAGAATTAAACTAATCTCTTCTTCTTT--TAC-TTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTCTTTACT-CTTTAGTTTA
* * * *
35657 ATTACCTAGAATTAAACTAATCTCTTCTCCTTT--TAC-TTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTCTTTACT-CTTTAGTTTA
* * *
35701 ATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC-TTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTC-TTTACT-CTTTAGTTTA
* *** *
35748 GTTACCCAGAATTAAACTAACCTCTTC-T-TTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTATTTTCTTCTTCTTTACTCTTTAGTTTA
*
35792 TTTACC
1 ATTACC
35798 TGGAATT
Statistics
Matches: 509, Mismatches: 49, Indels: 81
0.80 0.08 0.13
Matches are distributed among these distances:
31 1 0.00
32 12 0.02
34 1 0.00
36 11 0.02
37 2 0.00
38 1 0.00
39 1 0.00
40 1 0.00
41 1 0.00
42 2 0.00
44 140 0.28
45 6 0.01
46 9 0.02
47 275 0.54
48 8 0.02
49 1 0.00
50 12 0.02
51 2 0.00
52 1 0.00
53 4 0.01
54 18 0.04
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (46 bp):
ATTACCCAGAATTAAACTATTTTCTTCTTCTTTACTCTTTAGTTTA
Found at i:35347 original size:94 final size:92
Alignment explanation
Indices: 35134--35804 Score: 568
Period size: 91 Copynumber: 7.3 Consensus size: 92
35124 TGATTACTCT
* * * * * * *
35134 TTCTTTTACTGCTTAGCTTGATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTACT-CTTTAGT
1 TTCTTTTACT-TTTAGTTTAATTACCTAGAATTAAACTATTTTCTTCTTCTTTTACTAC-TTAGT
* * *
35198 TTAATTACCCAGAATTACACT-CT-TTTC
64 TTAATTACCCAGAATTAAACTAATCCTTC
* * * *
35225 TTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAATTATTTTCTTCTTCTCTTGCT-CTTTAGT
1 TTCTTTTAC-TTTTAGTTTAATTACCTAGAATTAAACTATTTTCTTCTTCTTTTACTAC-TTAGT
*
35289 TTAATTACCCAGAATTAAACTATTTCCTTC
64 TTAATTACCCAGAATTAAACTA-ATCCTTC
* * *
35319 TTCGTTTACTTTTTTA-TTTAATTACCCAGAATTAAACTAGCCTCTGTGTACTTCTTCTTTTGCT
1 TTCTTTTAC--TTTTAGTTTAATTACCTAGAATTAAACTA---T-T-T-T-CTTCTTCTTTTACT
35383 ACTTAGTTTAATT---C-GAATTAAACTAA--C--C
57 ACTTAGTTTAATTACCCAGAATTAAACTAATCCTTC
* * *
35411 -TC--TT-C-TTTAGTTTAATTACCTGGAATTAAACTAATCTCTTCTTCTTTTACTACTTAGTTT
1 TTCTTTTACTTTTAGTTTAATTACCTAGAATTAAACTATTTTCTTCTTCTTTTACTACTTAGTTT
* *
35471 AATTACCTAGAATTAAACTTATCTCTTC
66 AATTACCCAGAATTAAACTAATC-CTTC
** * * * * *
35499 TTCGGTTACTACTTAATTTAACTACCTAGAATTAAACTAATCTT-TTCCTCTTTTACTACTTAGT
1 TTCTTTTACT-TTTAGTTTAATTACCTAGAATTAAACT-ATTTTCTTCTTCTTTTACTACTTAGT
*
35563 TTAATTACCTAGAATTAAACTAA-CCTCCTC
64 TTAATTACCCAGAATTAAACTAATCCT--TC
* * * * *
35593 TCCTTTTGCTACTTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTC-TTT--TACTTAGTT
1 TTCTTTTACT-TTTAGTTTAATTACCTAGAATTAAACTATTTTCTTCTTCTTTTACTACTTAGTT
*
35655 TAATTACCTAGAATTAAACTAATCTCTTC
65 TAATTACCCAGAATTAAACTAATC-CTTC
* * *
35684 TCCTTTTAC--TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTACTTAGTTT
1 TTCTTTTACTTTTAGTTTAATTACCTAGAATTAAACTATTTTCTTCTTCTTTTACTACTTAGTTT
*
35747 AGTTACCCAGAATTAAACTAA-CC-TC
66 AATTACCCAGAATTAAACTAATCCTTC
* *
35772 TTCTTTTACTATTTAGTTTATTTACCTGGAATT
1 TTCTTTTACT-TTTAGTTTAATTACCTAGAATT
Statistics
Matches: 493, Mismatches: 46, Indels: 82
0.79 0.07 0.13
Matches are distributed among these distances:
79 26 0.05
80 1 0.00
82 1 0.00
83 11 0.02
85 4 0.01
86 22 0.04
88 50 0.10
89 8 0.02
90 1 0.00
91 168 0.34
92 6 0.01
93 9 0.02
94 137 0.28
95 8 0.02
97 12 0.02
98 2 0.00
99 1 0.00
100 1 0.00
101 24 0.05
102 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.46
Consensus pattern (92 bp):
TTCTTTTACTTTTAGTTTAATTACCTAGAATTAAACTATTTTCTTCTTCTTTTACTACTTAGTTT
AATTACCCAGAATTAAACTAATCCTTC
Found at i:35426 original size:32 final size:34
Alignment explanation
Indices: 35385--35453 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 34
35375 CTTTTGCTAC
35385 TTAGTTTAATT-C-GAATTAAACTAACCTCTTCT
1 TTAGTTTAATTACGGAATTAAACTAACCTCTTCT
*
35417 TTAGTTTAATTACCTGGAATTAAACTAATCTCTTCT
1 TTAGTTTAATTA-C-GGAATTAAACTAACCTCTTCT
35453 T
1 T
35454 CTTTTACTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 11 0.34
34 1 0.03
36 20 0.62
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (34 bp):
TTAGTTTAATTACGGAATTAAACTAACCTCTTCT
Found at i:35665 original size:44 final size:46
Alignment explanation
Indices: 35417--35804 Score: 520
Period size: 47 Copynumber: 8.5 Consensus size: 46
35407 AACCTCTTCT
*
35417 TTAGTTTAATTACCTGGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTT-CTAC
* * *
35464 TTAGTTTAATTACCTAGAATTAAACTTATCTCTTCTTCGGTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTC-TTTTCTAC
* * * *
35511 TTAATTTAACTACCTAGAATTAAACTAATCTTTTCCTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTT-CTAC
* * *
35558 TTAGTTTAATTACCTAGAATTAAACTAACCTCCTCTCCTTTTGCTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTT-CTAC
35605 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTC-TTT-TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTCTAC
*
35649 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTC-TCCTTT-TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTCTAC
35693 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTT-CTAC
* * *
35740 TTAGTTTAGTTACCCAGAATTAAACTAA-C-C-TCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTT-CTAC
* *
35784 TTAGTTTATTTACCTGGAATT
1 TTAGTTTAATTACCTAGAATT
Statistics
Matches: 306, Mismatches: 29, Indels: 15
0.87 0.08 0.04
Matches are distributed among these distances:
43 2 0.01
44 110 0.36
45 6 0.02
46 6 0.02
47 180 0.59
48 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (46 bp):
TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTCTAC
Done.