Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017188.1 Corchorus olitorius cultivar O-4 contig17221, 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: 43693
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1026 original size:13 final size:12
Alignment explanation
Indices: 984--1030 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
974 TCATGCACCC
984 AAAACAATTTATTT
1 AAAACAATTTA--T
*
998 AAAACCATTTAT
1 AAAACAATTTAT
1010 AAAACAATTTGAT
1 AAAACAATTT-AT
1023 AAAACAAT
1 AAAACAAT
1031 AATAAAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 10 0.33
13 10 0.33
14 10 0.33
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (12 bp):
AAAACAATTTAT
Found at i:1934 original size:131 final size:132
Alignment explanation
Indices: 1761--2024 Score: 386
Period size: 131 Copynumber: 2.0 Consensus size: 132
1751 ACGTATAATA
* * * *
1761 TTATACAAAACAGTAAGAGGAAGAAATGAAATAACCAAAAAACCAATCAAAAGGTTTAACCTTAT
1 TTATACAAAACAATAAGAGGAAGAAATGAAATAACCAAAAAACCAATAAAAAGATTTAACCTCAT
* * * * *
1826 CAATCCAATAGCA-AATGGGGAGGGGTACTTTAGTCACTTCGTACTTGGTTTTTTTGTTATTTAA
66 CAATCCAATAGCATAATGGAGAGGAGTACTTTAATCACTTCATACTTGGCTTTTTTGTTATTTAA
1890 GT
131 GT
* * * *
1892 TTATACAAAACAATAATAGGAAGAAATGAAATGATCAAAAAACCAATAAAAAGATTTAATCTCAT
1 TTATACAAAACAATAAGAGGAAGAAATGAAATAACCAAAAAACCAATAAAAAGATTTAACCTCAT
* *
1957 CAATCCAATAGCATAATGGAGAGGAGTACTTTAATCATTTCATGCTTGGCTTTTTTGTTATTTAA
66 CAATCCAATAGCATAATGGAGAGGAGTACTTTAATCACTTCATACTTGGCTTTTTTGTTATTTAA
2022 GT
131 GT
2024 T
1 T
2025 GGTAACTAAG
Statistics
Matches: 117, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
131 70 0.60
132 47 0.40
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (132 bp):
TTATACAAAACAATAAGAGGAAGAAATGAAATAACCAAAAAACCAATAAAAAGATTTAACCTCAT
CAATCCAATAGCATAATGGAGAGGAGTACTTTAATCACTTCATACTTGGCTTTTTTGTTATTTAA
GT
Found at i:3075 original size:437 final size:440
Alignment explanation
Indices: 2231--3185 Score: 1027
Period size: 437 Copynumber: 2.2 Consensus size: 440
2221 AAGCTAATTC
* * * * **
2231 AGGTGTCTATTAAAAGGTAATTTCATTA-CTTACAACTTTCATGAAGGACCCACAAGCCAATTTT
1 AGGTGTCTATTAAAAGGTAATTTCATGATC-TACAACTTTCATTAAGGACTCAAAAATCAATTTT
* * *** *
2295 TATGTTTCAATTCAAAAAAATGCTTCCGAAATTTTTTGGTTTCGATTGCCCATCTATTTAATATC
65 TATGTTTCAATTAAAAAAAAAGCTTCCGAAATTTGGCGGTTTCGATTGCCCATCTATTTAATAGC
* *
2360 ATAAAATTTTCGATCCACATGTCCGATTAAAGTTATTAACATGTCAATTAGAAGATTATTGCATC
130 ATAAAATTTTCGATCCACACGTCCGATTAAAGTTATTAACATGTCAATAAGAAGATTATTGCATC
* * *
2425 ATCTACGTCTTTCATGAAGGACCCGAAAGTTAAATTTGATTTACGAGTTTCATGAAGGGCATAAA
195 ATCTACGTCTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGCATAAA
* * *
2490 AGGGAATTTTTATGTTGCAAGATCTCCATCGAAGAACATTTTCTTATTTGGATTATTTTTCAAAT
260 AGGGAATTTTTATGTTGCAAGATCTCCATCGAAAAACATTTTCTTATTTCGATTATTTATCAAAT
* * **
2555 GATCCTCATATTTTAGTACTTTATACTACATAGTCCTTTACTGATTCTATCTTGATTGATTTAAC
325 GACCCTCATATTTTAGTACTTTATAATACATAGTCCTTTACAAATTCTATCTTGATTGATTTAAC
* * * *
2620 GCTTTAGA-TTTATTTTT-TTTTATT-T-TTTGT-TATATTTA-T-CCGATTA
390 GCTTCAGATTTTATTTTTCTTTTATTCTATTTGTCCA-ATTAAGTAACGA-TA
* *
2666 AGGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTAATTAATGACTCAAAAATCAATTTTT
1 AGGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAATCAATTTTT
**
2731 ATGTTTCAATTAAAAAAAAAGCTTCTC-AAATTTGGCGGTTTCGATTGCCGGTCTATTTAATAGC
66 ATGTTTCAATTAAAAAAAAAGCTTC-CGAAATTTGGCGGTTTCGATTGCCCATCTATTTAATAGC
* * * * * ** * *
2795 ATATAATTTTGGATCTATACGTCTGATTAAAGTTATTCAAGTGTTGGTCAA-AAG-GGGTTATTG
130 ATAAAATTTTCGATCCACACGTCCGATTAAAGTTATT-AA--CAT-GTCAATAAGAAGATTATTG
* * * *
2858 CATGATCTACGAT-TTTCATGACA-AACTCGGAAA-CTAAATTTGATCTACTAGTTTCATGAATG
191 CATCATCTACG-TCTTTCATGA-AGAAC-CCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGG
* * *
2920 G-TTCAATAGGGAATTTTTATGTT-TAATGATCTCCATC-AACAAACATTTTCTTATTTCGATTA
253 GCAT-AAAAGGGAATTTTTATGTTGCAA-GATCTCCATCGAA-AAACATTTTCTTATTTCGATTA
* ** *
2982 TTTATCAAATGACCCTCATACTTTT-TTACTTTATAATATTTTGTCCTTTACAAATTCTATCTT-
315 TTTATCAAATGACCCTCATA-TTTTAGTACTTTATAATACATAGTCCTTTACAAATTCTATCTTG
* * *
3045 ACTCAT-ATTTAACGCTTCA-ACTTTTTTTTTTCTTTTCTTCTATTTGTCCAATTAAGGTAATGA
379 A-T--TGATTTAACGCTTCAGA-TTTTATTTTTCTTTTATTCTATTTGTCCAATTAA-GTAACGA
*
3108 TC
439 TA
* * *
3110 ATGTGTCTATTAATAGTTAATTTCATGATCTACAACTTTCATTAAGGACTC-AAAATCTAATTTT
1 AGGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAATC-AATTTT
*
3174 TATATTTCAATT
65 TATGTTTCAATT
3186 CTAAAAAAGA
Statistics
Matches: 432, Mismatches: 62, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
435 140 0.32
436 10 0.02
437 152 0.35
438 26 0.06
439 14 0.03
440 6 0.01
441 1 0.00
442 9 0.02
443 7 0.02
444 65 0.15
445 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (440 bp):
AGGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATTAAGGACTCAAAAATCAATTTTT
ATGTTTCAATTAAAAAAAAAGCTTCCGAAATTTGGCGGTTTCGATTGCCCATCTATTTAATAGCA
TAAAATTTTCGATCCACACGTCCGATTAAAGTTATTAACATGTCAATAAGAAGATTATTGCATCA
TCTACGTCTTTCATGAAGAACCCGAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGCATAAAA
GGGAATTTTTATGTTGCAAGATCTCCATCGAAAAACATTTTCTTATTTCGATTATTTATCAAATG
ACCCTCATATTTTAGTACTTTATAATACATAGTCCTTTACAAATTCTATCTTGATTGATTTAACG
CTTCAGATTTTATTTTTCTTTTATTCTATTTGTCCAATTAAGTAACGATA
Found at i:4002 original size:6 final size:6
Alignment explanation
Indices: 3991--4041 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
3981 TTATGCTTTA
3991 TATATC TATATC TATATC TATATC TATATC TATATC --TATC TATAT-
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
4036 TATATC
1 TATATC
4042 AAAAAGTAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.10
5 5 0.12
6 33 0.79
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:4299 original size:120 final size:124
Alignment explanation
Indices: 4077--4324 Score: 382
Period size: 120 Copynumber: 2.0 Consensus size: 124
4067 TTAAATCGAC
4077 CATTATACCCTCATTTTTCTAACATATTTCTAAACTGCCATTAATACACAATTAATATTTTAATT
1 CATTATACCCTCATTTTTCTAACATATTTCTAAACTGCCATTAATACACAATTAATATTTTAATT
** *
4142 TTCTTATAATATTCATTAATCAATAGATTTTTAATACAATTAATTATAT-TTTTAATGG
66 TTCTTATAATATTCATTAATCAATAGATTACTAATACAATTAATGATATGTTTTAATGG
* * *
4200 CATTGTACCCTTATTTTTCTAACATATTTCTACACTGCCATT-A-A-ACAATTAATATTTTAATT
1 CATTATACCCTCATTTTTCTAACATATTTCTAAACTGCCATTAATACACAATTAATATTTTAATT
*
4262 TTCTTATAATATTCATTAATCAATATATTAACT-ATACAATTAATGATATGTTTTAATGG
66 TTCTTATAATATTCATTAATCAATAGATT-ACTAATACAATTAATGATATGTTTTAATGG
4321 -ATTA
1 CATTA
4325 AAAAATAAAT
Statistics
Matches: 115, Mismatches: 8, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
120 64 0.56
121 11 0.10
122 1 0.01
123 39 0.34
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.46
Consensus pattern (124 bp):
CATTATACCCTCATTTTTCTAACATATTTCTAAACTGCCATTAATACACAATTAATATTTTAATT
TTCTTATAATATTCATTAATCAATAGATTACTAATACAATTAATGATATGTTTTAATGG
Found at i:4398 original size:6 final size:6
Alignment explanation
Indices: 4389--4413 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4379 CTGACACTAG
4389 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
4414 CTAATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:6925 original size:42 final size:42
Alignment explanation
Indices: 6878--6959 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
6868 AATCAACTTG
* *
6878 TAATTCATTCTATATTTACTTTTATCTTAATTAAACAACATT
1 TAATTCATTCTATATTTACTTTCACCTTAATTAAACAACATT
* *
6920 TAATTCATTTTATGTTTACTTTCACCTTAATTAAACAACA
1 TAATTCATTCTATATTTACTTTCACCTTAATTAAACAACA
6960 AAAATACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.16, G:0.01, T:0.48
Consensus pattern (42 bp):
TAATTCATTCTATATTTACTTTCACCTTAATTAAACAACATT
Found at i:7400 original size:13 final size:13
Alignment explanation
Indices: 7382--7429 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
7372 TTTTGCTATA
7382 TGACCCTCCAATT
1 TGACCCTCCAATT
7395 TGACCCTCCACA--
1 TGACCCTCCA-ATT
7407 TGACCCTCCAATT
1 TGACCCTCCAATT
7420 TGACCCTCCA
1 TGACCCTCCA
7430 CATGTCCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.03
12 10 0.31
13 20 0.62
14 1 0.03
ACGTcount: A:0.23, C:0.44, G:0.08, T:0.25
Consensus pattern (13 bp):
TGACCCTCCAATT
Found at i:7412 original size:12 final size:11
Alignment explanation
Indices: 7381--7440 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 11
7371 GTTTTGCTAT
7381 ATGACCCTCCA
1 ATGACCCTCCA
7392 ATTTGACCCTCCA
1 A--TGACCCTCCA
7405 CATGACCCTCCA
1 -ATGACCCTCCA
7417 ATTTGACCCTCCA
1 A--TGACCCTCCA
*
7430 CATGTCCCTCC
1 -ATGACCCTCC
7441 TAACGTGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
11 2 0.05
12 18 0.43
13 20 0.48
14 2 0.05
ACGTcount: A:0.22, C:0.45, G:0.08, T:0.25
Consensus pattern (11 bp):
ATGACCCTCCA
Found at i:7415 original size:25 final size:25
Alignment explanation
Indices: 7381--7440 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
7371 GTTTTGCTAT
7381 ATGACCCTCCAATTTGACCCTCCAC
1 ATGACCCTCCAATTTGACCCTCCAC
7406 ATGACCCTCCAATTTGACCCTCCAC
1 ATGACCCTCCAATTTGACCCTCCAC
*
7431 ATGTCCCTCC
1 ATGACCCTCC
7441 TAACGTGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.22, C:0.45, G:0.08, T:0.25
Consensus pattern (25 bp):
ATGACCCTCCAATTTGACCCTCCAC
Found at i:8467 original size:19 final size:18
Alignment explanation
Indices: 8445--8481 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
8435 ATATTCATTA
8445 TTATTTAAATATTTGTTTT
1 TTATTTAAATATTT-TTTT
8464 TTATTTAAATATTTTTTT
1 TTATTTAAATATTTTTTT
8482 AATTGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTATTTAAATATTTTTTT
Found at i:8481 original size:16 final size:16
Alignment explanation
Indices: 8445--8493 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
8435 ATATTCATTA
8445 TTATTTAAATATTTGTTTT
1 TTATTTAAATA--T-TTTT
8464 TTATTTAAATATTTTT
1 TTATTTAAATATTTTT
* *
8480 TTAATTGAATATTT
1 TTATTTAAATATTT
8494 GTGATTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 16 0.57
17 1 0.04
19 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (16 bp):
TTATTTAAATATTTTT
Found at i:8641 original size:14 final size:14
Alignment explanation
Indices: 8622--8651 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
8612 ATTAGGATGG
8622 TTCTAAAAATAGAC
1 TTCTAAAAATAGAC
8636 TTCTAAAAATAGAC
1 TTCTAAAAATAGAC
8650 TT
1 TT
8652 TTTAGGATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (14 bp):
TTCTAAAAATAGAC
Found at i:10086 original size:47 final size:48
Alignment explanation
Indices: 9997--10088 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 48
9987 AACTCTTGTT
* * *
9997 TGATCAACCCTATCTTTTACTTTTCATGACCTTTGTTTTTACAAGTTG
1 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
* *
10045 TGATCAACCTTGTCATTTAC-TTTCATCACCCTTGTTTTTACAAG
1 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAG
10089 GTGTAATCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 22 0.56
48 17 0.44
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.46
Consensus pattern (48 bp):
TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
Found at i:13182 original size:48 final size:48
Alignment explanation
Indices: 13127--13219 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
13117 AACTCTTGTT
*
13127 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
1 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
* *
13175 TGATCAACCTTGTCATTTACTTTTCATCACCCTTGTTTTTACAAG
1 TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAG
13220 GTGTATTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.45
Consensus pattern (48 bp):
TGATCAACCCTATCATTTACTTTTCATCACCCTTGTTTTTACAAGTTG
Found at i:13208 original size:23 final size:22
Alignment explanation
Indices: 13142--13216 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
13132 AACCCTATCT
*
13142 TTTACTTTTCATCACCCTTGTT
1 TTTACTTTTCATCACCCTTGTA
* * *
13164 TTTACAAGTTGTGATCAACCTTGTCA
1 TTTAC---TTTTCATCACCCTTGT-A
*
13190 TTTACTTTTCATCACCCTTGTT
1 TTTACTTTTCATCACCCTTGTA
13212 TTTAC
1 TTTAC
13217 AAGGTGTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 10 0.24
23 13 0.32
25 13 0.32
26 5 0.12
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (22 bp):
TTTACTTTTCATCACCCTTGTA
Found at i:18472 original size:13 final size:13
Alignment explanation
Indices: 18454--18486 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
18444 TTTGGTGCTT
18454 ATATCACATATGC
1 ATATCACATATGC
18467 ATATCACATATGC
1 ATATCACATATGC
18480 ATATCAC
1 ATATCAC
18487 TTGCATTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (13 bp):
ATATCACATATGC
Found at i:19697 original size:5 final size:5
Alignment explanation
Indices: 19689--19735 Score: 67
Period size: 5 Copynumber: 9.2 Consensus size: 5
19679 AAGAAAAATG
**
19689 AAGAA AAGAA TTGAAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
19736 GAAGTTGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 34 0.92
6 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (5 bp):
AAGAA
Found at i:19730 original size:26 final size:26
Alignment explanation
Indices: 19676--19735 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
19666 AGGGAAAGGA
* **
19676 AAAAAGAAAAATGAAGAAAAGAATTG
1 AAAAAGAAAAATAAAGAAAAGAAAAG
19702 AAAAAGAAAAGA-AAAGAAAAGAAAAG
1 AAAAAGAAAA-ATAAAGAAAAGAAAAG
19728 -AAAAGAAA
1 AAAAAGAAA
19736 GAAGTTGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 8 0.27
26 21 0.70
27 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (26 bp):
AAAAAGAAAAATAAAGAAAAGAAAAG
Found at i:21279 original size:54 final size:55
Alignment explanation
Indices: 21164--21333 Score: 224
Period size: 54 Copynumber: 3.1 Consensus size: 55
21154 CATAGATCTA
* * *
21164 AGTTGATCCCTAGATGATCCAGTGC-AGTCATTCCAAAGAAGTTTTCAATGATCAG
1 AGTTGATCCCGAAAAGATCCAGTGCGA-TCATTCCAAAGAAGTTTTCAATGATCAG
*
21219 AGTTGATTCCC-AAAAGATCCAGTGCGATCATTCC-AAGAAGTTTTCAATGGTCAG
1 AGTTGA-TCCCGAAAAGATCCAGTGCGATCATTCCAAAGAAGTTTTCAATGATCAG
* * *
21273 AGTTGATCCCGAAAAGATCCAGTGCGGTCATTCCAAAGAAGTTTT--ATGATTAA
1 AGTTGATCCCGAAAAGATCCAGTGCGATCATTCCAAAGAAGTTTTCAATGATCAG
21326 AGTTGATC
1 AGTTGATC
21334 TTCTTTCAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
53 17 0.16
54 47 0.45
55 35 0.34
56 5 0.05
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (55 bp):
AGTTGATCCCGAAAAGATCCAGTGCGATCATTCCAAAGAAGTTTTCAATGATCAG
Found at i:21365 original size:35 final size:35
Alignment explanation
Indices: 21308--21523 Score: 280
Period size: 35 Copynumber: 6.3 Consensus size: 35
21298 GGTCATTCCA
* *
21308 AAGAAGTTTT--ATGATTAAAGTTGATCTTC-TTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATC-TCATTTC
*
21341 AAAAAGTTTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
*
21376 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTT-
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* *
21409 AAGAAGTTTTCGATGATCAAAGTTGATCTCCTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* ** * *
21444 AAAAAGTTTTTTATGATCAGAGTTGGTCTCCTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
*
21479 AAGAAGTTTTCGTTGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
21514 AAGAAGTTTT
1 AAGAAGTTTT
21524 TTTTATGATC
Statistics
Matches: 159, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
33 19 0.12
34 44 0.28
35 96 0.60
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (35 bp):
AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
Found at i:21479 original size:103 final size:102
Alignment explanation
Indices: 21308--21523 Score: 328
Period size: 103 Copynumber: 2.1 Consensus size: 102
21298 GGTCATTCCA
* *
21308 AAGAAGTTTTATGATTAAAGTTGATCTTCTTTCAAAAAGTTTTCGATGATCAGAGTTGATCTCAT
1 AAGAAGTTTTATGATCAAAGTTGATCTCCTTTCAAAAAGTTTTCGATGATCAGAGTTGATCTCAT
21373 TTCAAGAAGTTTT-TATGATCAGAGTTGATCTCATTT-
66 TTCAAGAAGTTTTCT-TGATCAGAGTTGATCTCATTTC
** *
21409 AAGAAGTTTTCGATGATCAAAGTTGATCTCCTTTCAAAAAGTTTTTTATGATCAGAGTTGGTCTC
1 AAGAAGTTTT--ATGATCAAAGTTGATCTCCTTTCAAAAAGTTTTCGATGATCAGAGTTGATCTC
*
21474 CTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCATTTC
64 ATTTCAAGAAGTTTTC-TTGATCAGAGTTGATCTCATTTC
21514 AAGAAGTTTT
1 AAGAAGTTTT
21524 TTTTATGATC
Statistics
Matches: 104, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
101 10 0.10
103 62 0.60
104 21 0.20
105 11 0.11
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (102 bp):
AAGAAGTTTTATGATCAAAGTTGATCTCCTTTCAAAAAGTTTTCGATGATCAGAGTTGATCTCAT
TTCAAGAAGTTTTCTTGATCAGAGTTGATCTCATTTC
Found at i:21547 original size:91 final size:91
Alignment explanation
Indices: 21447--21614 Score: 300
Period size: 91 Copynumber: 1.8 Consensus size: 91
21437 TCCTTTCAAA
* *
21447 AAGTTTTTTATGATCAGAGTTGGTCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCATT
1 AAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
21512 TCAAGAAGTTTTTTTTATGATCAGAG
66 TCAAGAAGTTTTTTTTATGATCAGAG
* *
21538 AAGTTTTTTATGATCAGATTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTT
1 AAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
21603 TCAAGAAGTTTT
66 TCAAGAAGTTTT
21615 CGATGATCAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 73 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (91 bp):
AAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATT
TCAAGAAGTTTTTTTTATGATCAGAG
Found at i:21577 original size:126 final size:126
Alignment explanation
Indices: 21410--21649 Score: 381
Period size: 126 Copynumber: 1.9 Consensus size: 126
21400 ATCTCATTTA
** *
21410 AGAAGTTTTCGATGATCAAAGTTGATCTCCTTTCAAAAAGTTTTTTATGATCAGAGTTGGTCTCC
1 AGAAGTTTTCGATGATCAAAGTTGATCTCCTTTCAAAAAGTTTTCGATGATCAGAGTTGATCTCC
*
21475 TTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTTATGATCAG
66 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTTATGATCAG
** * * * *
21536 AGAAGTTTTTTATGATCAGATTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 AGAAGTTTTCGATGATCAAAGTTGATCTCCTTTCAAAAAGTTTTCGATGATCAGAGTTGATCTCC
*
21601 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTT
66 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTT
21650 CGATGATTAG
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 103 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (126 bp):
AGAAGTTTTCGATGATCAAAGTTGATCTCCTTTCAAAAAGTTTTCGATGATCAGAGTTGATCTCC
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTTATGATCAG
Found at i:21586 original size:35 final size:35
Alignment explanation
Indices: 21536--21737 Score: 314
Period size: 35 Copynumber: 5.8 Consensus size: 35
21526 TTATGATCAG
** * *
21536 AGAAGTTTTTTATGATCAGATTTGATCTCCTTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
21571 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
21606 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
*
21641 AGAAGTTTTCGATGATTAGAGTTGATCTCGTTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
* * *
21676 AGAAGTTTTTGATGATCAGAGTTGATCTCATTCCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
* *
21711 AGAAGTTTTCAATGGTCAGAGTTGATC
1 AGAAGTTTTCGATGATCAGAGTTGATC
21738 CTAAGATGAT
Statistics
Matches: 155, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 155 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (35 bp):
AGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCA
Found at i:21646 original size:161 final size:159
Alignment explanation
Indices: 21377--21685 Score: 492
Period size: 161 Copynumber: 1.9 Consensus size: 159
21367 TCTCATTTCA
21377 AGAAGTTTTTATGATCAGAGTTGATCTCATTTAAGAAGTTTTCGATGATCAAAGTTGATCTCCTT
1 AGAAGTTTTTATGATCAGAGTTGATCTCATTTAAGAAGTTTTCGATGATCAAAGTTGATCTCCTT
** * *
21442 TCAAAAAGTTTTTTATGATCAGAGTTGGTCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATC
66 TCAAAAAGTTTTCGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
21507 TCATTTCAAGAAGTTTTTTTTATGATCAG
131 TCATTTCAAGAAGTTTTTTTTATGATCAG
* * * *
21536 AGAAGTTTTTTATGATCAGATTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 AGAAG-TTTTTATGATCAGAGTTGATCTCATTT-AAGAAGTTTTCGATGATCAAAGTTGATCTCC
* * *
21601 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATTAGAGTTGA
64 TTTCAAAAAGTTTTCGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGA
*
21666 TCTCGTTTCAAGAAGTTTTT
129 TCTCATTTCAAGAAGTTTTT
21686 GATGATCAGA
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
159 5 0.04
160 25 0.18
161 106 0.78
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (159 bp):
AGAAGTTTTTATGATCAGAGTTGATCTCATTTAAGAAGTTTTCGATGATCAAAGTTGATCTCCTT
TCAAAAAGTTTTCGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
TCATTTCAAGAAGTTTTTTTTATGATCAG
Found at i:21770 original size:54 final size:55
Alignment explanation
Indices: 21703--21909 Score: 273
Period size: 54 Copynumber: 3.9 Consensus size: 55
21693 AGAGTTGATC
* *
21703 TCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCT-AAGATGATCCAGTGCAG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAAGATGATCCAGTGCGG
*
21757 TCATTCCAAGAAGTATTCAATGATCAGAGTTGATCCTCAA-ATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAAGATGATCCAGTGCGG
* ** * *
21811 TCATTCGAAGAAGTTTTTGATGATCAGAGTTGAT-CTCCAGATGATCCAATGCGG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAAGATGATCCAGTGCGG
* * *
21865 TCCTTACAAGAAGTTTT--ATGATCGGAGTTGATCCTC-AGATGATCC
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAAGATGATCC
21910 TGTGATGATC
Statistics
Matches: 137, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
52 23 0.17
53 7 0.05
54 105 0.77
55 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (55 bp):
TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAAGATGATCCAGTGCGG
Found at i:27267 original size:103 final size:104
Alignment explanation
Indices: 27124--27375 Score: 354
Period size: 104 Copynumber: 2.5 Consensus size: 104
27114 AATTTTTCTA
* * *
27124 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGTTAAACTTAGTGAATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAA-ATAAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTATATATTTTAT
* * *
27188 TTTTAAAACCCTATAACAAT-ATTATTAATTATGGATTTT
65 TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
27227 ACCCTTAAAATAAAAATAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTAT
1 ACCCTTAAAATAAAAATAAATTTTAATTTGGGGCTAAACTTAGTG-AATTAGTTATATATTTTAT
*
27292 TTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
27333 ACCCTTAAAAT-AAAA-AAA--TTAATTTGGGGCTAAACTTAGTGAA
1 ACCCTTAAAATAAAAATAAATTTTAATTTGGGGCTAAACTTAGTGAA
27376 ATTAAGGCTA
Statistics
Matches: 136, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
101 2 0.01
102 35 0.26
103 29 0.21
104 39 0.29
105 4 0.03
106 27 0.20
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTATATATTTTATT
TCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:27299 original size:104 final size:105
Alignment explanation
Indices: 27124--27379 Score: 364
Period size: 102 Copynumber: 2.5 Consensus size: 105
27114 AATTTTTCTA
* * *
27124 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGTTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAA-ATAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* * *
27187 TTTTTAAAACCCTATAACAAT-ATTATTAATTATGGATTTT
65 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* *
27227 ACCCTTAAAATAAAAATAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTAT
1 ACCCTTAAAATAAAAATAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
*
27292 TTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
27333 ACCCTTAAAAT-AAAA-AAA--TTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
27380 AGGCTAAACT
Statistics
Matches: 140, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
102 41 0.29
103 29 0.21
104 39 0.28
105 4 0.03
106 27 0.19
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:28926 original size:24 final size:25
Alignment explanation
Indices: 28892--28942 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
28882 ATTGGAGTAT
* *
28892 TTATTTATCTTGTTTCTTAATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
*
28917 TTATTT-TCTTGCTTATTTATTTTA
1 TTATTTATCTTGCTTATTAATTTTA
28941 TT
1 TT
28943 GTTACTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGCTTATTAATTTTA
Found at i:32161 original size:167 final size:168
Alignment explanation
Indices: 31760--32260 Score: 642
Period size: 169 Copynumber: 3.0 Consensus size: 168
31750 CGTTGTTGCA
* * * *
31760 AAGATAATAATATGGAGATTTTTGAAGGGGAAATCCGCAATAAAT-TCGTGGAAGCTGATTTGGT
1 AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCT-GTGGAAGCTGATTTGGT
* * *
31824 GGTGAA-AATTTTGTATTCAAATAGCAGTGATGTTGCTAATGGAAAGATTTGGTTATTTATGATA
65 GGTGAATAA-TTTGAATTCAATTAGGAGTGATGTTGCTAATGG-AAG-TTTGGTTATTTATGATA
* * *
31888 GCATTGACTCTAGAAAAGAGGAATTTGTTGCAGAATTTACT-
127 GCATTGACTCTAGTAAAGAGGAATTTGTTGCAGAATCTAATG
* * * * **
31929 ATGATATTAATGTAGGGATTTTTGAAGAGGAATTCGGCAATAAATCCATGGAAGCTGATTTGGTG
1 AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTGGAAGCTGATTTGGTG
* * *
31994 GTGAATAATTTGAATTCAATTAGGAGTGATGGTGCTAAT-GTAGTTTGGTTATTTATGATAGCTT
66 GTGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAAGTTTGGTTATTTATGATAGCAT
32058 TGACTCTAGTAAAGAGGAATTTGTTGCAGAATCTAATG
131 TGACTCTAGTAAAGAGGAATTTGTTGCAGAATCTAATG
* *
32096 AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTTGAAGCTGAGTTGGTG
1 AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTGGAAGCTGATTTGGTG
* * * *
32161 GTGAATAATTTGAATCCAATTATATGAGTGATGTTGCTAATGGAAATTTGG-----TATGATACC
66 GTGAATAATTTGAATTCAA-T-TAGGAGTGATGTTGCTAATGGAAGTTTGGTTATTTATGATAGC
**
32221 ATTGACTCTAGTAAAGAGGTGTTTGTTGCAGAATCTAATG
129 ATTGACTCTAGTAAAGAGGAATTTGTTGCAGAATCTAATG
32261 TTGATATTCA
Statistics
Matches: 290, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
165 45 0.16
166 54 0.19
167 77 0.27
168 2 0.01
169 103 0.36
170 9 0.03
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (168 bp):
AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTGGAAGCTGATTTGGTG
GTGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAAGTTTGGTTATTTATGATAGCAT
TGACTCTAGTAAAGAGGAATTTGTTGCAGAATCTAATG
Found at i:38115 original size:29 final size:30
Alignment explanation
Indices: 38056--38124 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
38046 CAAACAATCT
*
38056 ATCAATCAACTAACAAATAATTGCAATTC-A
1 ATCAATCAA-TAACAAATAATGGCAATTCAA
*
38086 ATCAATCAATAGC-AATATATGGCAATTCAA
1 ATCAATCAATAACAAATA-ATGGCAATTCAA
38116 ATCAA-CAAT
1 ATCAATCAAT
38125 TGAAAGATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 4 0.11
29 16 0.46
30 15 0.43
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.26
Consensus pattern (30 bp):
ATCAATCAATAACAAATAATGGCAATTCAA
Found at i:41663 original size:11 final size:11
Alignment explanation
Indices: 41649--41682 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41639 TTTTCGTTAT
41649 TTTTCTTTTTC
1 TTTTCTTTTTC
41660 TTTTCTTTTTC
1 TTTTCTTTTTC
*
41671 -TTTATTTTTC
1 TTTTCTTTTTC
41681 TT
1 TT
41683 AATTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTTTTC
Done.