Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019090.1 Corchorus olitorius cultivar O-4 contig19123, 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: 73175
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:34 original size:2 final size:2
Alignment explanation
Indices: 16--49 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
6 TATTCGTATT
*
16 TA TA TT TA TA GTA 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 TA T
50 GAGCTGTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:822 original size:63 final size:62
Alignment explanation
Indices: 723--852 Score: 233
Period size: 63 Copynumber: 2.1 Consensus size: 62
713 ACACTGCCCA
723 ACTCAACACTAAATTAGTTGGGCCCTATGTAATATATAGATGGACACTTGGAATAATATATAT
1 ACTCAACACTAAATTAGTTGGGCCCTATGTAATATATAGATGGA-ACTTGGAATAATATATAT
* *
786 ACTCAACACTAAATTAGTTGGGCCCTATGTAATATATTGATGGAACTTGGAGTAATATATAT
1 ACTCAACACTAAATTAGTTGGGCCCTATGTAATATATAGATGGAACTTGGAATAATATATAT
848 ACTCA
1 ACTCA
853 CTAGTAGACC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 22 0.34
63 43 0.66
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (62 bp):
ACTCAACACTAAATTAGTTGGGCCCTATGTAATATATAGATGGAACTTGGAATAATATATAT
Found at i:1567 original size:38 final size:39
Alignment explanation
Indices: 1493--1574 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 39
1483 ATATTATTAT
*
1493 AATTATCATTATCATAAAGTAACAAAAACCATAATTTTAA
1 AATTATAATTATCATAAAG-AACAAAAACCATAATTTTAA
** *
1533 AATTATAATTATCATAAA-ATGAAAAATCATAATTTTAA
1 AATTATAATTATCATAAAGAACAAAAACCATAATTTTAA
1571 AATT
1 AATT
1575 TTTTAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 21 0.55
40 17 0.45
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (39 bp):
AATTATAATTATCATAAAGAACAAAAACCATAATTTTAA
Found at i:3349 original size:16 final size:17
Alignment explanation
Indices: 3328--3359 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3318 ACAACCTTGT
3328 TTATTTTCCTT-TCAAA
1 TTATTTTCCTTCTCAAA
3344 TTATTTTCCTTCTCAA
1 TTATTTTCCTTCTCAA
3360 TGAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATTTTCCTTCTCAAA
Found at i:3458 original size:32 final size:33
Alignment explanation
Indices: 3397--3463 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
3387 AGTTTTCATA
3397 TTTTGTTGCCAAATAAATATGAAAGAATATGTT
1 TTTTGTTGCCAAATAAATATGAAAGAATATGTT
3430 TTTTGTTGCCAAAATAAA-A-GAAAGAATATGTT
1 TTTTGTTGCC-AAATAAATATGAAAGAATATGTT
3462 TT
1 TT
3464 AAACAAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 15 0.45
33 11 0.33
34 7 0.21
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (33 bp):
TTTTGTTGCCAAATAAATATGAAAGAATATGTT
Found at i:7203 original size:28 final size:30
Alignment explanation
Indices: 7175--7251 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 30
7165 AATATTTATA
*
7175 ATTAAATATATATTATATATATAA-AATAAT
1 ATTAAATATATATTACATATATAATAAT-AT
7205 ATTAGATATATATAATTACATATATAATAATAT
1 ATTA-A-ATATAT-ATTACATATATAATAATAT
*
7238 ATATAAATTTATAT
1 AT-TAAATATATAT
7252 GTACCCAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
30 4 0.10
31 3 0.08
32 11 0.28
33 17 0.43
34 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
ATTAAATATATATTACATATATAATAATAT
Found at i:7241 original size:14 final size:14
Alignment explanation
Indices: 7180--7242 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
7170 TTATAATTAA
*
7180 ATATAT-ATTATAT
1 ATATATAATAATAT
*
7193 ATATAAAATAATATT
1 ATATATAATAATA-T
* *
7208 AGATATATATAATTAC
1 ATATATA-ATAA-TAT
7224 ATATATAATAATAT
1 ATATATAATAATAT
7238 ATATA
1 ATATA
7243 AATTTATATG
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
13 5 0.13
14 12 0.31
15 10 0.26
16 10 0.26
17 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
ATATATAATAATAT
Found at i:9839 original size:42 final size:42
Alignment explanation
Indices: 9780--9863 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
9770 TTTGAATTCC
9780 GGCAGAGGAGTCGAACCGATAAATCCTAATATCCACACACAA
1 GGCAGAGGAGTCGAACCGATAAATCCTAATATCCACACACAA
* *
9822 GGCAGATGAGTCGAACCGATAAATCTTAATATCCACACACAA
1 GGCAGAGGAGTCGAACCGATAAATCCTAATATCCACACACAA
9864 TCAATATGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (42 bp):
GGCAGAGGAGTCGAACCGATAAATCCTAATATCCACACACAA
Found at i:15171 original size:19 final size:19
Alignment explanation
Indices: 15147--15187 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
15137 GTGATAGTTA
15147 AGAGAGTGAGTATGAGAAG
1 AGAGAGTGAGTATGAGAAG
15166 AGAGAGTGAGTATGAGAAG
1 AGAGAGTGAGTATGAGAAG
15185 AGA
1 AGA
15188 ATAAGGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (19 bp):
AGAGAGTGAGTATGAGAAG
Found at i:16139 original size:14 final size:14
Alignment explanation
Indices: 16096--16141 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
16086 TCTTGCACCT
16096 AAAATCTATTTAGA
1 AAAATCTATTTAGA
*
16110 AAATTATCT-TTAAGA
1 AAA--ATCTATTTAGA
16125 AAAATCTATTTAGA
1 AAAATCTATTTAGA
16139 AAA
1 AAA
16142 TAGTATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 4 0.15
14 11 0.41
15 8 0.30
16 4 0.15
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.35
Consensus pattern (14 bp):
AAAATCTATTTAGA
Found at i:16142 original size:13 final size:13
Alignment explanation
Indices: 16096--16142 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
16086 TCTTGCACCT
16096 AAAATCTATTTAG
1 AAAATCTATTTAG
16109 AAAAT-TATCTTTAAG
1 AAAATCTA--TTT-AG
16124 AAAAATCTATTTAG
1 -AAAATCTATTTAG
16138 AAAAT
1 AAAAT
16143 AGTATACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 2 0.07
13 10 0.34
14 5 0.17
15 5 0.17
16 5 0.17
17 2 0.07
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.36
Consensus pattern (13 bp):
AAAATCTATTTAG
Found at i:16268 original size:5 final size:5
Alignment explanation
Indices: 16249--16281 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
16239 CCAAACAATC
*
16249 TAAAA -AAAT TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
16282 GAGTCAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:17883 original size:15 final size:16
Alignment explanation
Indices: 17856--17885 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17846 ATGCATGGCT
17856 TCTTTTCTTTTCTTTC
1 TCTTTTCTTTTCTTTC
17872 TCTTTT-TTTTCTTT
1 TCTTTTCTTTTCTTT
17886 TTGGTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TCTTTTCTTTTCTTTC
Found at i:20389 original size:14 final size:15
Alignment explanation
Indices: 20357--20393 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20347 TGAGGACATA
*
20357 CATGGTTGTGCGTTT
1 CATGCTTGTGCGTTT
20372 -ATGCTTGTG-GTTT
1 CATGCTTGTGCGTTT
20385 CATGCTTGT
1 CATGCTTGT
20394 TCTCATTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.08, C:0.14, G:0.30, T:0.49
Consensus pattern (15 bp):
CATGCTTGTGCGTTT
Found at i:21438 original size:77 final size:75
Alignment explanation
Indices: 21300--21451 Score: 241
Period size: 77 Copynumber: 2.0 Consensus size: 75
21290 AATCTAAAAG
* *
21300 TTCATGATGAAATTTGTTTAATTTCTTGTTGAGTTATGTTTGGTGATTGCAAATGGATTATAGAT
1 TTCATGATGAAATTTGTTTAATTTCTTGTTAAGTTATGTTTGGTGATTGCAAATGGATTATAAAT
21365 ATGTTTAGAA
66 ATGTTTAGAA
* **
21375 TTCATGATGAAATTTGTTTAATTTCCTTTTTAAGTTGATGTTTGGTGATTGGGAATGGATTATAA
1 TTCATGATGAAATTTGTTTAATTT-CTTGTTAAGTT-ATGTTTGGTGATTGCAAATGGATTATAA
21440 ATATGTTTAGAA
64 ATATGTTTAGAA
21452 GTGAAAATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 24 0.34
76 9 0.13
77 37 0.53
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (75 bp):
TTCATGATGAAATTTGTTTAATTTCTTGTTAAGTTATGTTTGGTGATTGCAAATGGATTATAAAT
ATGTTTAGAA
Found at i:24351 original size:13 final size:13
Alignment explanation
Indices: 24328--24359 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
24318 CCATAATGCA
24328 GTTTG-TGCTGCT
1 GTTTGTTGCTGCT
24340 GTTTGTTGCTGCT
1 GTTTGTTGCTGCT
24353 GTTTGTT
1 GTTTGTT
24360 ATTGTCTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.00, C:0.12, G:0.31, T:0.56
Consensus pattern (13 bp):
GTTTGTTGCTGCT
Found at i:24886 original size:37 final size:37
Alignment explanation
Indices: 24845--24918 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
24835 TGCAAACTCT
*
24845 TCTTCATATTTATAACTAGGGACTACACCTGGATTTC
1 TCTTCATATTTATAACTAGGGACTAAACCTGGATTTC
24882 TCTTCATATTTATAACTAGGGACTAAACCTGGATTTC
1 TCTTCATATTTATAACTAGGGACTAAACCTGGATTTC
24919 ATATGAGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (37 bp):
TCTTCATATTTATAACTAGGGACTAAACCTGGATTTC
Found at i:30066 original size:15 final size:16
Alignment explanation
Indices: 30036--30068 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30026 TTACTCTGCT
30036 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
30052 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
30067 TT
1 TT
30069 ACTTTCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:32016 original size:68 final size:68
Alignment explanation
Indices: 31934--32065 Score: 255
Period size: 68 Copynumber: 1.9 Consensus size: 68
31924 TTGAGACTTT
*
31934 GAGTTGTAACTGCATTGATTATTGTAATTAATTATTATCTTAAAAGAGTTTAAGGAGTGTTATCA
1 GAGTTGTAAATGCATTGATTATTGTAATTAATTATTATCTTAAAAGAGTTTAAGGAGTGTTATCA
31999 AAG
66 AAG
32002 GAGTTGTAAATGCATTGATTATTGTAATTAATTATTATCTTAAAAGAGTTTAAGGAGTGTTATC
1 GAGTTGTAAATGCATTGATTATTGTAATTAATTATTATCTTAAAAGAGTTTAAGGAGTGTTATC
32066 TCCTTTGATT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (68 bp):
GAGTTGTAAATGCATTGATTATTGTAATTAATTATTATCTTAAAAGAGTTTAAGGAGTGTTATCA
AAG
Found at i:32103 original size:87 final size:89
Alignment explanation
Indices: 32002--32174 Score: 262
Period size: 90 Copynumber: 2.0 Consensus size: 89
31992 GTTATCAAAG
* * *
32002 GAGTTGTAAATGCATTGATTATTGTAATTAATTA-T-TATCTTAAAAGAGTTTAAGGAGTGTTAT
1 GAGTTGTAAATGCATTCATTATTGTAATCAATTACTATATCTTAAAAGAGTTTAAGGAATGTTAT
32065 CT-CCTTTGATTAGAGAGATATATA
66 CTGCCTTT-ATTAGAGAGATATATA
*
32089 GAGTTGTAAATGCATTCATTATTGTAATCAATTACTACTATCTTAATAGAGTTTAAGGAATGTTA
1 GAGTTGTAAATGCATTCATTATTGTAATCAATTACTA-TATCTTAAAAGAGTTTAAGGAATGTTA
*
32154 TTTGCCTTTATTAGAGAGATA
65 TCTGCCTTTATTAGAGAGATA
32175 GAATCTCATT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
87 32 0.42
88 1 0.01
90 39 0.51
91 5 0.06
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (89 bp):
GAGTTGTAAATGCATTCATTATTGTAATCAATTACTATATCTTAAAAGAGTTTAAGGAATGTTAT
CTGCCTTTATTAGAGAGATATATA
Found at i:35489 original size:18 final size:18
Alignment explanation
Indices: 35440--35482 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
35430 CTACATTGAA
35440 TCTTGATAAAATACCCTG
1 TCTTGATAAAATACCCTG
35458 TCTTGATAAAATACCCTG
1 TCTTGATAAAATACCCTG
*
35476 TGTTGAT
1 TCTTGAT
35483 GTAATACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (18 bp):
TCTTGATAAAATACCCTG
Found at i:36024 original size:18 final size:18
Alignment explanation
Indices: 35975--36017 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
35965 CTACATTGAA
35975 TCTTGATAAAATACCCTG
1 TCTTGATAAAATACCCTG
35993 TCTTGATAAAATACCCTG
1 TCTTGATAAAATACCCTG
*
36011 TGTTGAT
1 TCTTGAT
36018 GTAATACTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (18 bp):
TCTTGATAAAATACCCTG
Found at i:36277 original size:535 final size:534
Alignment explanation
Indices: 35317--36385 Score: 2066
Period size: 535 Copynumber: 2.0 Consensus size: 534
35307 TGGATCCGGA
35317 GATGCTCCTTCAACTTTAGATCGTCCGGAGTTGCATGTGTAGTAGAGACTAGTAAACTTTATGTA
1 GATGCTCCTTCAACTTTAGATCGTCCGGAGTTGCATGTGTAGTAGAGACTAGTAAACTTTATGTA
*
35382 GTTTTTTGTTTTCTTCATTCGTCTTGTATGAATCCTAATATCTGGTAACTACATTGAATCTTGAT
66 GTTTTTTGTTTTCTTCATCCGTCTTGTATGAATCCTAATATCTGGTAACTACATTGAATCTTGAT
35447 AAAATACCCTGTCTTGATAAAATACCCTGTGTTGATGTAATACTTGGTGGTTTATAAAGCCTATT
131 AAAATACCCTGTCTTGATAAAATACCCTGTGTTGATGTAATACTTGGTGGTTTATAAAGCCTATT
*
35512 GACCGCCTCCAAAAGATTTGATAAAATACCTGGTGGTTTATAAAGCTTATTGATGTAGTTAAAAC
196 GACCGCCTCCAAAAGATTTGATAAAATACCTGGTGGTTTATAAAACTTATTGATGTAGTTAAAAC
35577 CGTTTCTAAAAGATTTAACCCGTTCAAGAAAACCGCCTCTAAATTGCCTACAATTTTATCGGCTC
261 CGTTTCTAAAAGATTTAACCCGTTCAAGAAAACCGCCTCTAAATTGCCTACAATTTTATCGGCTC
*
35642 TATGATTGGAGCTGGATAGAGCTGGTTTGATGCTTGAGTAGGTGTATAATCGCCTCTAAGTCTAA
326 TATGATTGGAGCTGGATAGAGCTGGTTTGATGCTTGAGTAGGTGTATAACCGCCTCTAAGTCTAA
35707 AGCCTAATAAAACCGAACCGAATTTTTGCAATATAATATACCACCTCTTAAGAGGCAGTTTGTTA
391 AGCCTAATAAAACCGAACCGAATTTTTGCAATATAATATACCACCTCTTAAGAGGCAGTTTGTTA
35772 CTTTCTAATTCTATGGATGAGGAGTCATTTCAAGAAGAGTGAAAGACTACTTTCCATGGAGAGTT
456 CTTTCTAATTCTATGGATGAGGAGTCATTTCAAGAAGAGTGAAAGACTACTTTCCATGGAGAGTT
35837 TTTCCCTACTCCTT
521 TTTCCCTACTCCTT
*
35851 GATGCTCCTTCAACTTTAGATCGTCCGGAGTTGCTTGTGTAGTAGAGACTAGTAAACTTTATGTA
1 GATGCTCCTTCAACTTTAGATCGTCCGGAGTTGCATGTGTAGTAGAGACTAGTAAACTTTATGTA
35916 GTTTTTTTGTTTTCTTCATCCGTCTTGTATGAATCCTAATATCTGGTAACTACATTGAATCTTGA
66 G-TTTTTTGTTTTCTTCATCCGTCTTGTATGAATCCTAATATCTGGTAACTACATTGAATCTTGA
35981 TAAAATACCCTGTCTTGATAAAATACCCTGTGTTGATGTAATACTTGGTGGTTTATAAAGCCTAT
130 TAAAATACCCTGTCTTGATAAAATACCCTGTGTTGATGTAATACTTGGTGGTTTATAAAGCCTAT
36046 TGACCGCCTCCAAAAGATTTGATAAAATACCTGGTGGTTTATAAAACTTATTGATGTAGTTAAAA
195 TGACCGCCTCCAAAAGATTTGATAAAATACCTGGTGGTTTATAAAACTTATTGATGTAGTTAAAA
* *
36111 CCGTTTCTAAAATATTTAACTCGTTCAAGAAAACCGCCTCTAAATTGCCTACAATTTTATCGGCT
260 CCGTTTCTAAAAGATTTAACCCGTTCAAGAAAACCGCCTCTAAATTGCCTACAATTTTATCGGCT
*
36176 CTATGATTGGAGCTGGATAGAGCTGGTTTGATGCTTGAGTAGGTGTATAACCGCCTCTAAGTTTA
325 CTATGATTGGAGCTGGATAGAGCTGGTTTGATGCTTGAGTAGGTGTATAACCGCCTCTAAGTCTA
36241 AAGCCTAATAAAACCGAACCGAATTTTTGCAATATAATATACCACCTCTTAAGAGGCAGTTTGTT
390 AAGCCTAATAAAACCGAACCGAATTTTTGCAATATAATATACCACCTCTTAAGAGGCAGTTTGTT
36306 ACTTTCTAATTCTATGGATGAGGAGTCATTTCAAGAAGAGTGAAAGACTACTTTCCATGGAGAGT
455 ACTTTCTAATTCTATGGATGAGGAGTCATTTCAAGAAGAGTGAAAGACTACTTTCCATGGAGAGT
36371 TTTTCCCTACTCCTT
520 TTTTCCCTACTCCTT
36386 CCATGAGAAT
Statistics
Matches: 527, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
534 65 0.12
535 462 0.88
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (534 bp):
GATGCTCCTTCAACTTTAGATCGTCCGGAGTTGCATGTGTAGTAGAGACTAGTAAACTTTATGTA
GTTTTTTGTTTTCTTCATCCGTCTTGTATGAATCCTAATATCTGGTAACTACATTGAATCTTGAT
AAAATACCCTGTCTTGATAAAATACCCTGTGTTGATGTAATACTTGGTGGTTTATAAAGCCTATT
GACCGCCTCCAAAAGATTTGATAAAATACCTGGTGGTTTATAAAACTTATTGATGTAGTTAAAAC
CGTTTCTAAAAGATTTAACCCGTTCAAGAAAACCGCCTCTAAATTGCCTACAATTTTATCGGCTC
TATGATTGGAGCTGGATAGAGCTGGTTTGATGCTTGAGTAGGTGTATAACCGCCTCTAAGTCTAA
AGCCTAATAAAACCGAACCGAATTTTTGCAATATAATATACCACCTCTTAAGAGGCAGTTTGTTA
CTTTCTAATTCTATGGATGAGGAGTCATTTCAAGAAGAGTGAAAGACTACTTTCCATGGAGAGTT
TTTCCCTACTCCTT
Found at i:41199 original size:9 final size:9
Alignment explanation
Indices: 41185--41217 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
41175 ATAAGAGATT
41185 AATATATAA
1 AATATATAA
41194 AATATAATAA
1 AATAT-ATAA
41204 AA-ATATAA
1 AATATATAA
41212 AATATA
1 AATATA
41218 ACGAAGACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.27
9 10 0.45
10 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AATATATAA
Found at i:45131 original size:13 final size:13
Alignment explanation
Indices: 45113--45142 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
45103 GGTTGGTCTG
45113 ACGTGGCAATGCC
1 ACGTGGCAATGCC
*
45126 ACGTGGCATTGCC
1 ACGTGGCAATGCC
45139 ACGT
1 ACGT
45143 CAGCATCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (13 bp):
ACGTGGCAATGCC
Found at i:45208 original size:30 final size:29
Alignment explanation
Indices: 45172--45246 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
45162 TTAGCCTGAT
* *
45172 GGGCAAAACATCTTAAAATTGAAGTTCCGG
1 GGGCAAAACATC-CAAAATTGAAATTCCGG
**
45202 GGGCAAAATGTCCAAAATTGAAATTCCGG
1 GGGCAAAACATCCAAAATTGAAATTCCGG
* *
45231 GAGCAAAACGTCCAAA
1 GGGCAAAACATCCAAA
45247 TGCTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 29 0.74
30 10 0.26
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (29 bp):
GGGCAAAACATCCAAAATTGAAATTCCGG
Found at i:45222 original size:29 final size:29
Alignment explanation
Indices: 45186--45246 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
45176 AAAACATCTT
* * *
45186 AAAATTGAAGTTCCGGGGGCAAAATGTCC
1 AAAATTGAAATTCCGGGAGCAAAACGTCC
45215 AAAATTGAAATTCCGGGAGCAAAACGTCC
1 AAAATTGAAATTCCGGGAGCAAAACGTCC
45244 AAA
1 AAA
45247 TGCTACAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (29 bp):
AAAATTGAAATTCCGGGAGCAAAACGTCC
Found at i:50780 original size:36 final size:36
Alignment explanation
Indices: 50733--50802 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
50723 GGAATATAAT
*
50733 ATGAGTTAATATTTGATGTATTGACAATGTATGATG
1 ATGAGTTAATATTTGATGCATTGACAATGTATGATG
*
50769 ATGAGTTAATATTTGATGCATTGATAATGTATGA
1 ATGAGTTAATATTTGATGCATTGACAATGTATGA
50803 AAATTATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.41
Consensus pattern (36 bp):
ATGAGTTAATATTTGATGCATTGACAATGTATGATG
Found at i:50785 original size:18 final size:19
Alignment explanation
Indices: 50732--50786 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 19
50722 CGGAATATAA
50732 TATGAGTTAATATTTGATG
1 TATGAGTTAATATTTGATG
* * *
50751 TATTGA--CAATGTATGATG
1 TA-TGAGTTAATATTTGATG
50769 -ATGAGTTAATATTTGATG
1 TATGAGTTAATATTTGATG
50787 CATTGATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 7
0.68 0.15 0.17
Matches are distributed among these distances:
16 3 0.11
17 1 0.04
18 18 0.67
19 2 0.07
20 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.44
Consensus pattern (19 bp):
TATGAGTTAATATTTGATG
Found at i:51636 original size:12 final size:13
Alignment explanation
Indices: 51619--51648 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51609 ATAGTTTAAT
51619 TAAAAT-ATTATA
1 TAAAATAATTATA
51631 TAAAATAATTATA
1 TAAAATAATTATA
51644 TAAAA
1 TAAAA
51649 CAGTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAAATAATTATA
Found at i:52859 original size:76 final size:76
Alignment explanation
Indices: 52727--52880 Score: 211
Period size: 76 Copynumber: 2.0 Consensus size: 76
52717 TAATTTTCAC
* * * *
52727 TTCTGAACATATCTATAATCCATTCACAATCACCTAAGAGCAACTTCACAAAAAATTAAACAAAT
1 TTCTAAACATATCTATAATCCATTCACAATCACCAAACAGAAACTTCACAAAAAATTAAACAAAT
*
52792 TTCATCATGAA
66 TTCATCACGAA
* * * *
52803 TTCTAAACATGTCTATAATCCATTCCCAATCACCAAACATAAAC-TCAACAAGAAATTAAACAAA
1 TTCTAAACATATCTATAATCCATTCACAATCACCAAACAGAAACTTC-ACAAAAAATTAAACAAA
52867 TTTCATCACGAA
65 TTTCATCACGAA
52879 TT
1 TT
52881 TTTAGATTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 2 0.03
76 66 0.97
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (76 bp):
TTCTAAACATATCTATAATCCATTCACAATCACCAAACAGAAACTTCACAAAAAATTAAACAAAT
TTCATCACGAA
Found at i:59323 original size:14 final size:15
Alignment explanation
Indices: 59300--59332 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
59290 CAATATCTGA
*
59300 AAAAATTTCTGTTAC
1 AAAAATTTCTGTCAC
59315 AAAAA-TTCTGTCAC
1 AAAAATTTCTGTCAC
59329 AAAA
1 AAAA
59333 TTAAGTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (15 bp):
AAAAATTTCTGTCAC
Found at i:59602 original size:22 final size:22
Alignment explanation
Indices: 59577--60131 Score: 246
Period size: 22 Copynumber: 24.6 Consensus size: 22
59567 CCATAGGAAT
*
59577 GTTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
*
59599 GTTA-CTAAAATTTCACA-TGGAG
1 GTTATC-AAAATTTCATAGT-GAG
***
59621 GTTATCAAAATTTCATACAAAG
1 GTTATCAAAATTTCATAGTGAG
* *** *
59643 GTTACCAAAATTTCATAAAAAT
1 GTTATCAAAATTTCATAGTGAG
* *
59665 GTTATCAAAAATTT-TTAGGGAG
1 GTTATC-AAAATTTCATAGTGAG
*
59687 GTTAATAAACAAAATTTCATACG-AAG
1 GTT-AT---CAAAATTTCATA-GTGAG
* * * * *
59713 CTTATCGAAATTTTATGGTGTG
1 GTTATCAAAATTTCATAGTGAG
*
59735 GTTATCAAAATTTCATAAG-AAG
1 GTTATCAAAATTTCAT-AGTGAG
* * *
59757 TTTAACAAAATTTCATATTGAGCGAG
1 GTTATCAAAATTTC--A-T-AGTGAG
* *
59783 GTTATCAAAATTTCCTAGGGAG
1 GTTATCAAAATTTCATAGTGAG
* * *
59805 GTTAACAAAATTTAATAGGGAG
1 GTTATCAAAATTTCATAGTGAG
* * * * *
59827 GTTATGAAAATTTTATGGAGAT
1 GTTATCAAAATTTCATAGTGAG
* * *
59849 GTTATCAAAATTACGTAGAGAG
1 GTTATCAAAATTTCATAGTGAG
* *
59871 GATATCAAAGTTTCATTCTCATAGAGAG
1 GTTATCAAA-----ATT-TCATAGTGAG
* * * *
59899 GTTATTAAAA-TTCTGTGGTGTG
1 GTTATCAAAATTTC-ATAGTGAG
*
59921 GTTATCAAAATTTTCATAGTGTG
1 GTTATCAAAA-TTTCATAGTGAG
* * **
59944 GTTA-C-CAATTTTATAGTTTG
1 GTTATCAAAATTTCATAGTGAG
* *
59964 ATTATCAAAATTTCTTAG-GAAG
1 GTTATCAAAATTTCATAGTG-AG
* * *
59986 ATTATCAAAATTTCACACTGAG
1 GTTATCAAAATTTCATAGTGAG
* ** *
60008 ATTATCGGAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
* * *
60030 GTTATCAAAATTTGACAGTGTG
1 GTTATCAAAATTTCATAGTGAG
* * * *
60052 GTAATCAAATTTTTATAGGGAG
1 GTTATCAAAATTTCATAGTGAG
*
60074 GTTATCAAAATTTCATAATGAG
1 GTTATCAAAATTTCATAGTGAG
* * *
60096 GTTATCACATTTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
*
60118 GTTATCAATATTTC
1 GTTATCAAAATTTC
60132 TACGTTGGAA
Statistics
Matches: 400, Mismatches: 103, Indels: 60
0.71 0.18 0.11
Matches are distributed among these distances:
20 13 0.03
21 8 0.02
22 299 0.75
23 24 0.06
24 4 0.01
25 12 0.03
26 21 0.05
27 4 0.01
28 15 0.04
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAG
Found at i:59768 original size:44 final size:43
Alignment explanation
Indices: 59641--59839 Score: 132
Period size: 48 Copynumber: 4.3 Consensus size: 43
59631 TTTCATACAA
* * *
59641 AGGTTACCAAAATTTCATAAAAATG-TTATCAAAAATTTT-TAGGG
1 AGGTTATCAAAATTTCATAAGAA-GCTTAAC-AAAATTTTAT-GGG
* * *
59685 AGGTTAATAAACAAAATTTCATACGAAGCTTATCGAAATTTTATGGTG
1 AGGTT-AT---CAAAATTTCATAAGAAGCTTAACAAAATTTTATGG-G
* *
59733 TGGTTATCAAAATTTCATAAGAAGTTTAACAAAATTTCATATTGAGCG
1 AGGTTATCAAAATTTCATAAGAAGCTTAACAAAATTT--TA-TG-G-G
* * * * *
59781 AGGTTATCAAAATTTCCTAGGGAGGTTAACAAAATTTAATAGGG
1 AGGTTATCAAAATTTCATAAGAAGCTTAACAAAATTTTAT-GGG
*
59825 AGGTTATGAAAATTT
1 AGGTTATCAAAATTT
59840 TATGGAGATG
Statistics
Matches: 126, Mismatches: 17, Indels: 24
0.75 0.10 0.14
Matches are distributed among these distances:
44 46 0.37
45 3 0.02
46 4 0.03
47 14 0.11
48 59 0.47
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (43 bp):
AGGTTATCAAAATTTCATAAGAAGCTTAACAAAATTTTATGGG
Found at i:61248 original size:48 final size:47
Alignment explanation
Indices: 61172--61267 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 47
61162 AATTTTTAGG
*
61172 AATTCGGACAAATTTAACCTTTTCAAAATTTACAAAAAATATTATATT
1 AATTCGGACAAATTTAACCTTTTCAAAATTTAC-AAAAACATTATATT
* * *
61220 AATTTGGACATATTTAATCTTTTCAAAATTTACAAAAACATTATATT
1 AATTCGGACAAATTTAACCTTTTCAAAATTTACAAAAACATTATATT
61267 A
1 A
61268 CGTACACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 14 0.32
48 30 0.68
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (47 bp):
AATTCGGACAAATTTAACCTTTTCAAAATTTACAAAAACATTATATT
Found at i:62373 original size:75 final size:73
Alignment explanation
Indices: 62227--62442 Score: 262
Period size: 73 Copynumber: 3.0 Consensus size: 73
62217 CAACTAAGAG
*
62227 AGGTTTAACCAAGCAAGAGCAACATGCGATGGCAATG-TT--GCCAACAAAAAATAATATCAACA
1 AGGTTCAACCAAGCAAGAGCAACATGCGATGGCAATGTTTAAGCCAACAAAAAATAATATCAACA
62289 TGTGCCTA
66 TGTGCCTA
* *
62297 AGTTTTTCAACCAAGCAAGAGCAACATGCGATTGCAATGTTTAAGCCAACAAAAAATAATATCAA
1 AG--GTTCAACCAAGCAAGAGCAACATGCGATGGCAATGTTTAAGCCAACAAAAAATAATATCAA
*
62362 CATCTGCCTA
64 CATGTGCCTA
** * * * * *
62372 AGGTTCAATTAAGCAAG-GCCTATATAG-GATGGCAATGTTTAATCCAACAAAAAATAAGATCGA
1 AGGTTCAACCAAGCAAGAG-CAACAT-GCGATGGCAATGTTTAAGCCAACAAAAAATAATATCAA
62435 CATGTGCC
64 CATGTGCC
62443 CATAATGTTT
Statistics
Matches: 125, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
70 2 0.02
72 33 0.26
73 57 0.46
74 1 0.01
75 32 0.26
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (73 bp):
AGGTTCAACCAAGCAAGAGCAACATGCGATGGCAATGTTTAAGCCAACAAAAAATAATATCAACA
TGTGCCTA
Found at i:63671 original size:64 final size:64
Alignment explanation
Indices: 63598--63726 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
63588 CTTGCAACAT
*
63598 AGCAGAAATAAATTAAGAATAGTCAGTCATAAATAACAGGAAATAAACAGTGCATTGAGAACTA
1 AGCAGAAATAAATTAAGAACAGTCAGTCATAAATAACAGGAAATAAACAGTGCATTGAGAACTA
63662 AGCAGAAATAAATTAAGAACAGTCAGTCATAAATAACAGGAAATAAACAGTGCATTGAGAACTA
1 AGCAGAAATAAATTAAGAACAGTCAGTCATAAATAACAGGAAATAAACAGTGCATTGAGAACTA
63726 A
1 A
63727 ACAAAGAAGC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (64 bp):
AGCAGAAATAAATTAAGAACAGTCAGTCATAAATAACAGGAAATAAACAGTGCATTGAGAACTA
Found at i:64483 original size:74 final size:74
Alignment explanation
Indices: 64362--64505 Score: 270
Period size: 74 Copynumber: 1.9 Consensus size: 74
64352 GTTGTGAGAA
* *
64362 GCGAAAGGAAGAGGAAAAGCAAGCATGCAAGGGACTGAGCCAGCGCTGAGGGGCTTTTGAAGAGT
1 GCGAAAGGAAGAGGAAAACCAAGCAGGCAAGGGACTGAGCCAGCGCTGAGGGGCTTTTGAAGAGT
64427 GGAAACAAC
66 GGAAACAAC
64436 GCGAAAGGAAGAGGAAAACCAAGCAGGCAAGGGACTGAGCCAGCGCTGAGGGGCTTTTGAAGAGT
1 GCGAAAGGAAGAGGAAAACCAAGCAGGCAAGGGACTGAGCCAGCGCTGAGGGGCTTTTGAAGAGT
64501 GGAAA
66 GGAAA
64506 TGGGAAATGG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.36, C:0.16, G:0.38, T:0.10
Consensus pattern (74 bp):
GCGAAAGGAAGAGGAAAACCAAGCAGGCAAGGGACTGAGCCAGCGCTGAGGGGCTTTTGAAGAGT
GGAAACAAC
Found at i:65138 original size:15 final size:15
Alignment explanation
Indices: 65118--65146 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
65108 ACATCTGCAG
65118 GCGGATCAACCACAT
1 GCGGATCAACCACAT
65133 GCGGATCAACCACA
1 GCGGATCAACCACA
65147 GGCAGATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.10
Consensus pattern (15 bp):
GCGGATCAACCACAT
Found at i:65160 original size:15 final size:15
Alignment explanation
Indices: 65142--65172 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
65132 TGCGGATCAA
65142 CCACAGGCAGATTAG
1 CCACAGGCAGATTAG
*
65157 CCACAGGCGGATTAG
1 CCACAGGCAGATTAG
65172 C
1 C
65173 ACCTTCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.13
Consensus pattern (15 bp):
CCACAGGCAGATTAG
Found at i:71445 original size:37 final size:38
Alignment explanation
Indices: 71396--71479 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
71386 TACTTGTTGA
*
71396 AATTTAAATTAAA-TTTAAAATAGATTTCTATAATCAC
1 AATTCAAATTAAATTTTAAAATAGATTTCTATAATCAC
* * *
71433 AATTCAAATTAAATTTTAGAATTGATTTTTATAATCAC
1 AATTCAAATTAAATTTTAAAATAGATTTCTATAATCAC
71471 AATTCAAAT
1 AATTCAAAT
71480 AACAATTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 12 0.29
38 30 0.71
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (38 bp):
AATTCAAATTAAATTTTAAAATAGATTTCTATAATCAC
Found at i:71626 original size:2 final size:2
Alignment explanation
Indices: 71619--71674 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
71609 CTGTTATAGA
71619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71660 A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
71675 CAAAAATCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.