Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019361.1 Corchorus olitorius cultivar O-4 contig19394, 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: 94924
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:1105 original size:22 final size:22
Alignment explanation
Indices: 1080--1126 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1070 TTTTTAGTTG
*
1080 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
1102 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
1124 AGT
1 AGT
1127 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:1144 original size:93 final size:94
Alignment explanation
Indices: 1002--1187 Score: 302
Period size: 93 Copynumber: 2.0 Consensus size: 94
992 ACTTTTTAAT
* * *
1002 TAAATTAGTAATATCGTACAAATAAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATA
1 TAAAATAGTAAAATCGTAAAAATAAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATA
*
1067 GAATTTTTAGTTGAGTAAAACTATAAAAG
66 GAATTTTTAGTTGACTAAAACTATAAAAG
* *
1096 TAAAATAGTAAAATGGTAAAAAT-AAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATA
1 TAAAATAGTAAAATCGTAAAAATAAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATA
*
1160 GAGTTTTTAGTTGACTAAAACTATAAAA
66 GAATTTTTAGTTGACTAAAACTATAAAA
1188 ATTTAACCAA
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 66 0.78
94 19 0.22
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (94 bp):
TAAAATAGTAAAATCGTAAAAATAAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATA
GAATTTTTAGTTGACTAAAACTATAAAAG
Found at i:3038 original size:54 final size:54
Alignment explanation
Indices: 2974--3081 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
2964 TCTCCGGGAA
2974 GTAAGATTTTGATAACCACACGCAATAAGGAAGTAGCAATTAATGTTGGATCAC
1 GTAAGATTTTGATAACCACACGCAATAAGGAAGTAGCAATTAATGTTGGATCAC
3028 GTAAGATTTTGATAACCACACGCAATAAGGAAGTAGCAATTAATGTTGGATCAC
1 GTAAGATTTTGATAACCACACGCAATAAGGAAGTAGCAATTAATGTTGGATCAC
3082 TACCAGCAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (54 bp):
GTAAGATTTTGATAACCACACGCAATAAGGAAGTAGCAATTAATGTTGGATCAC
Found at i:6100 original size:6 final size:6
Alignment explanation
Indices: 6092--6126 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
6082 AGAGTTGCAA
*
6092 AAAGTA AAAGT- AAAGTC AAAGTC AAAGTC AAAGTC
1 AAAGTC AAAGTC AAAGTC AAAGTC AAAGTC AAAGTC
6127 GTTGATGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAGTC
Found at i:9778 original size:15 final size:15
Alignment explanation
Indices: 9760--9815 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
9750 AGCATCTGGA
9760 GATGAAGATTCTGAT
1 GATGAAGATTCTGAT
9775 GATGAAGATGT-TGGA-
1 GATGAAGAT-TCT-GAT
* *
9790 GATGAAGATGCTGGT
1 GATGAAGATTCTGAT
*
9805 GATGAATATTC
1 GATGAAGATTC
9816 AAAGGAGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.03
15 29 0.88
16 3 0.09
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.30
Consensus pattern (15 bp):
GATGAAGATTCTGAT
Found at i:9899 original size:45 final size:45
Alignment explanation
Indices: 9831--9922 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
9821 AGCTGTTAAC
*
9831 GCGACAAGCTGAATATTCGAAGGAGCTGTTAACGCTAGAGAAGGA
1 GCGACAAGCTGAATATTCAAAGGAGCTGTTAACGCTAGAGAAGGA
*
9876 GCGACAAGCTGAATATTCAAAGGAGCTGTTAGCGCTAGAGAAGGA
1 GCGACAAGCTGAATATTCAAAGGAGCTGTTAACGCTAGAGAAGGA
9921 GC
1 GC
9923 TGTTGCTGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.32, T:0.17
Consensus pattern (45 bp):
GCGACAAGCTGAATATTCAAAGGAGCTGTTAACGCTAGAGAAGGA
Found at i:9921 original size:21 final size:19
Alignment explanation
Indices: 9895--9945 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
9885 TGAATATTCA
9895 AAGGAGCTGTTAGCGCTAGAG
1 AAGGAGCTGTTA--GCTAGAG
*
9916 AAGGAGCTGTT-GCTGGAG
1 AAGGAGCTGTTAGCTAGAG
9934 AAGGAGCTGTTA
1 AAGGAGCTGTTA
9946 ATGCTGACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 17 0.61
21 11 0.39
ACGTcount: A:0.27, C:0.12, G:0.39, T:0.22
Consensus pattern (19 bp):
AAGGAGCTGTTAGCTAGAG
Found at i:10054 original size:46 final size:46
Alignment explanation
Indices: 9929--10061 Score: 209
Period size: 44 Copynumber: 2.9 Consensus size: 46
9919 GAGCTGTTGC
* *
9929 TGGAGAAGGAGCTGTTAA-TGCTGACAGCATTGAAGATGAAGATACT
1 TGGAGAAGGGGCTGTTAACT-CTAACAGCATTGAAGATGAAGATACT
*
9975 TGGAGAAGGGGC--TTAACACTAACAGCATTGAAGATGAAGATACT
1 TGGAGAAGGGGCTGTTAACTCTAACAGCATTGAAGATGAAGATACT
10019 TGGAGAAGGGGCTGTTAACTCTAACAGCATTGAAGATGAAGAT
1 TGGAGAAGGGGCTGTTAACTCTAACAGCATTGAAGATGAAGAT
10062 GAAGGAGCTG
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
44 41 0.51
46 39 0.49
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (46 bp):
TGGAGAAGGGGCTGTTAACTCTAACAGCATTGAAGATGAAGATACT
Found at i:12768 original size:2 final size:2
Alignment explanation
Indices: 12761--12795 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12751 TAGTCTGACC
12761 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12796 GTTTGATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13571 original size:2 final size:2
Alignment explanation
Indices: 13559--13603 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
13549 CGTCCCCGAA
*
13559 AT AT AT A- AT AT AT -T CAT A- AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
13599 AT AT A
1 AT AT A
13604 CACATTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.89
3 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:13604 original size:18 final size:21
Alignment explanation
Indices: 13559--13605 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 21
13549 CGTCCCCGAA
13559 ATATATA-ATATATTCATAAT
1 ATATATACATATATTCATAAT
13579 ATATATACATATA-T-AT-AT
1 ATATATACATATATTCATAAT
13597 ATATATACA
1 ATATATACA
13606 CATTTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.42
19 2 0.08
20 8 0.31
21 5 0.19
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATATACATATATTCATAAT
Found at i:13793 original size:29 final size:29
Alignment explanation
Indices: 13751--13806 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
13741 CCTTGTACGG
*
13751 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTGTGGTGTTGAT
13780 TGTTGAAAACTTGTAATTGTGGTGTTG
1 TGTTGAAAACTTGTAATTGTGGTGTTG
13807 TAAACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.45
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGGTGTTGAT
Found at i:16448 original size:2 final size:2
Alignment explanation
Indices: 16441--16483 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
16431 ATAATTACTC
16441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16483 T
1 T
16484 CAATCATGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18399 original size:32 final size:32
Alignment explanation
Indices: 18347--18441 Score: 127
Period size: 32 Copynumber: 3.0 Consensus size: 32
18337 CCCAAAATCC
* * *
18347 AACCCGAATTAACATGACCCAAATTTGACCCG
1 AACCCGAATCAACCTGACCCAAATTTAACCCG
*
18379 AACCCGAATCAACCTAACCCAAATTTAACCCG
1 AACCCGAATCAACCTGACCCAAATTTAACCCG
* * *
18411 AACCCAAATCAATCTGACTCAAATTTAACCC
1 AACCCGAATCAACCTGACCCAAATTTAACCC
18442 AATCCGATTC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.40, C:0.34, G:0.07, T:0.19
Consensus pattern (32 bp):
AACCCGAATCAACCTGACCCAAATTTAACCCG
Found at i:18416 original size:17 final size:17
Alignment explanation
Indices: 18363--18419 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
18353 AATTAACATG
*
18363 ACCCAAATTTGACCCGA
1 ACCCAAATTTAACCCGA
* * *
18380 ACCCGAA-TCAA-CCTA
1 ACCCAAATTTAACCCGA
18395 ACCCAAATTTAACCCGA
1 ACCCAAATTTAACCCGA
18412 ACCCAAAT
1 ACCCAAAT
18420 CAATCTGACT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 9 0.29
16 5 0.16
17 17 0.55
ACGTcount: A:0.40, C:0.37, G:0.07, T:0.16
Consensus pattern (17 bp):
ACCCAAATTTAACCCGA
Found at i:20209 original size:45 final size:45
Alignment explanation
Indices: 20158--20298 Score: 200
Period size: 45 Copynumber: 3.2 Consensus size: 45
20148 AGCAACAATT
*
20158 AATATTAGGTTTATTTTGATGAATTACCTACAGATGGAGGAGTAG
1 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
* * *
20203 AATATTAGTTTTATTTTGATGAATTACCTAGAGATGTAGGAGTAT
1 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
**
20248 AATATTAACTTTATTTTGATGAATTACCTAGAGAT-GA--AGTAG
1 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
20290 AAT-TTAGGT
1 AATATTAGGT
20299 AATACTCTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 4 0.05
42 7 0.08
44 1 0.01
45 74 0.86
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (45 bp):
AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:26112 original size:25 final size:25
Alignment explanation
Indices: 26078--26127 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
26068 ATAATATATA
26078 GTATATATGAGATTTTAGATCAATT
1 GTATATATGAGATTTTAGATCAATT
26103 GTATATATGAGATTTTAGATCAATT
1 GTATATATGAGATTTTAGATCAATT
26128 TAATTAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (25 bp):
GTATATATGAGATTTTAGATCAATT
Found at i:26479 original size:21 final size:20
Alignment explanation
Indices: 26441--26480 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
26431 TCCTTAGATC
*
26441 AGTTTTGTCAGTTTGTTTTG
1 AGTTTTGTCAGTTAGTTTTG
*
26461 AGTTTTGTTGAGTTAGTTTT
1 AGTTTTG-TCAGTTAGTTTT
26481 TTTCCATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.12, C:0.03, G:0.25, T:0.60
Consensus pattern (20 bp):
AGTTTTGTCAGTTAGTTTTG
Found at i:27041 original size:101 final size:105
Alignment explanation
Indices: 26799--27060 Score: 369
Period size: 107 Copynumber: 2.5 Consensus size: 105
26789 TTTGTATTTA
* * *
26799 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTTAGTTTAG-TCTCAAATTAAAAATT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCT-AAATT-AAAATT
26863 TATTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTATTG
64 TATTTTTATTTTAAGGGTAAATTTCAAAATTAATAA-TTATTG
*
26906 TTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCTAAATT-AAA-TT-
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCTAAATTAAAATTTA
*
26968 TTTTTATTTTAAGGGTAAATTTCATAATTAATAA-TATTG
66 TTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTATTG
* *
27007 TTATAGGGTTTTAGAAATAAAACATATAAA-TAA-TTCACTAAATTTAGCCC-AAAT
1 TTATAGGGTTTTAGAAATAAAATATA-AAACTAATTTCACTAAGTTTAGCCCTAAAT
27061 AGCCATCAGG
Statistics
Matches: 145, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
99 4 0.03
100 16 0.11
101 32 0.22
102 3 0.02
103 33 0.23
104 2 0.01
105 3 0.02
107 50 0.34
108 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (105 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCTAAATTAAAATTTA
TTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTATTG
Found at i:27519 original size:89 final size:88
Alignment explanation
Indices: 27366--27542 Score: 336
Period size: 89 Copynumber: 2.0 Consensus size: 88
27356 AGTGGTGTAC
27366 GGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAAA
1 GGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCT-AAAAA
27431 AAAAAAAAATAGCCCAAATTAAAA
65 AAAAAAAAATAGCCCAAATTAAAA
*
27455 GGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCTCAAAAA
1 GGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAAA
27520 AAAAAAAATAGCCCAAATTAAAA
66 AAAAAAAATAGCCCAAATTAAAA
27543 TTATACATAC
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
88 28 0.32
89 59 0.68
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.29
Consensus pattern (88 bp):
GGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCTTATCTAAAAAA
AAAAAAAATAGCCCAAATTAAAA
Found at i:28177 original size:40 final size:40
Alignment explanation
Indices: 28117--28196 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
28107 AACTAATGAC
* *
28117 TTTCTTTTCTTAATTAAATTTTCTTAAAA-GCACTTATAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAATG-ACTTATAAA
*
28157 TTTCATTTCTTAACTGAATTTTCTTAAAATGACTTATAAA
1 TTTCATTTCTTAACTAAATTTTCTTAAAATGACTTATAAA
28197 ATAAAACAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.49
Consensus pattern (40 bp):
TTTCATTTCTTAACTAAATTTTCTTAAAATGACTTATAAA
Found at i:28445 original size:2 final size:2
Alignment explanation
Indices: 28438--28480 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
28428 TATTATTATT
*
28438 TA TA TA TA TA TA TA GTA TA TA TA TA TA TA TA TA CA TA T- TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28480 T
1 T
28481 CGTTATTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28479 original size:19 final size:18
Alignment explanation
Indices: 28437--28480 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
28427 TTATTATTAT
*
28437 TTATATATATATATAGTA
1 TTATATATATATATAATA
28455 TATATATATATATATACATA
1 T-TATATATATATATA-ATA
28475 TTATAT
1 TTATAT
28481 CGTTATTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 19 0.83
20 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TTATATATATATATAATA
Found at i:28978 original size:15 final size:14
Alignment explanation
Indices: 28949--29006 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
28939 CACCTTTTTA
28949 TTAAAAGAAT-ATTT
1 TTAAAA-AATAATTT
*
28963 TCAAAAAATAATTT
1 TTAAAAAATAATTT
*
28977 TTTAAAAATAATTT
1 TTAAAAAATAATTT
* * *
28991 TGAAAATATTATTT
1 TTAAAAAATAATTT
29005 TT
1 TT
29007 TGAACTAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
13 3 0.09
14 32 0.91
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (14 bp):
TTAAAAAATAATTT
Found at i:30076 original size:27 final size:26
Alignment explanation
Indices: 30028--30083 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
30018 CATTTTTTCC
30028 AAATATACTTCTAATTTGCCATTATT
1 AAATATACTTCTAATTTGCCATTATT
*
30054 AAATAATACTT-TAATTATTCCATTATT
1 AAAT-ATACTTCTAATT-TGCCATTATT
30081 AAA
1 AAA
30084 ATGATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATATACTTCTAATTTGCCATTATT
Found at i:33000 original size:23 final size:22
Alignment explanation
Indices: 32917--33102 Score: 125
Period size: 22 Copynumber: 8.5 Consensus size: 22
32907 GGGAGATTAA
* *
32917 CAAAATATCATAGAAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
32939 CAAAA-CTCATAGGGAGGTT-G
1 CAAAATTTCATAGGAAGGTTAT
32959 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
32982 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
33004 CAAAGTTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
33026 CACAATTTAATAGGTAA--TTAT
1 CAAAATTTCATAGG-AAGGTTAT
* *
33047 CAAAATTTCATAACG-TGGTTAT
1 CAAAATTTCAT-AGGAAGGTTAT
* *
33069 CAAAATTTAATA-GAATAGTTAT
1 CAAAATTTCATAGGAA-GGTTAT
*
33091 CAAATTTTCATA
1 CAAAATTTCATA
33103 AAAATATTCA
Statistics
Matches: 127, Mismatches: 26, Indels: 22
0.73 0.15 0.13
Matches are distributed among these distances:
20 6 0.05
21 37 0.29
22 67 0.53
23 17 0.13
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:33012 original size:22 final size:23
Alignment explanation
Indices: 32917--33058 Score: 97
Period size: 21 Copynumber: 6.5 Consensus size: 23
32907 GGGAGATTAA
* *
32917 CAAAATATCATAGAAAGG-TTAT
1 CAAAATTTCATAGGAAGGTTTAT
* * *
32939 CAAAA-CTCATAGGGAGG-TT-G
1 CAAAATTTCATAGGAAGGTTTAT
32959 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGGTTTAT
* **
32982 TAAAATTTCATAGTTAGG-TTAT
1 CAAAATTTCATAGGAAGGTTTAT
*
33004 CAAAGTTTCATATGG-A-GTTTAT
1 CAAAATTTCATA-GGAAGGTTTAT
* *
33026 CACAATTTAATAGGTAA---TTAT
1 CAAAATTTCATAGG-AAGGTTTAT
33047 CAAAATTTCATA
1 CAAAATTTCATA
33059 ACGTGGTTAT
Statistics
Matches: 95, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
20 5 0.05
21 38 0.40
22 35 0.37
23 17 0.18
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (23 bp):
CAAAATTTCATAGGAAGGTTTAT
Found at i:43555 original size:32 final size:32
Alignment explanation
Indices: 43514--43579 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
43504 AACCACATCT
43514 CATAATCAAATACAAAAACCAATTCATTTCAA
1 CATAATCAAATACAAAAACCAATTCATTTCAA
* *
43546 CATAATCAAATACAACAGCCAATTCATTTCAA
1 CATAATCAAATACAAAAACCAATTCATTTCAA
43578 CA
1 CA
43580 GAAATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (32 bp):
CATAATCAAATACAAAAACCAATTCATTTCAA
Found at i:54757 original size:3 final size:3
Alignment explanation
Indices: 54749--54805 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
54739 AGGCATGCGA
* **
54749 AAT AAT AATT AAT AAT AAT AAT AAT ATT TCT CAA- AA- AAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
54794 AAT AAT AAT AAT
1 AAT AAT AAT AAT
54806 CAAGCAACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:54808 original size:26 final size:26
Alignment explanation
Indices: 54759--54808 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
54749 AATAATAATT
* **
54759 AATAATAATAATAATATTTCTCAAAA
1 AATAATAATAATAATAATAATCAAAA
54785 AATAATAATAATAATAATAATCAA
1 AATAATAATAATAATAATAATCAA
54809 GCAACATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (26 bp):
AATAATAATAATAATAATAATCAAAA
Found at i:91323 original size:26 final size:26
Alignment explanation
Indices: 91294--91346 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
91284 GCACAAATGA
91294 ATTTAATTAGTGCAA-GATTTTGTAGT
1 ATTTAATTAGTG-AAGGATTTTGTAGT
91320 ATTTAATTAGTGAAGGATTTTGTAGT
1 ATTTAATTAGTGAAGGATTTTGTAGT
91346 A
1 A
91347 ATGACAGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (26 bp):
ATTTAATTAGTGAAGGATTTTGTAGT
Found at i:94576 original size:12 final size:12
Alignment explanation
Indices: 94559--94584 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
94549 CCTTAAAGCC
94559 CAATCATTAGTT
1 CAATCATTAGTT
94571 CAATCATTAGTT
1 CAATCATTAGTT
94583 CA
1 CA
94585 TTGTCTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (12 bp):
CAATCATTAGTT
Done.