Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018022.1 Corchorus olitorius cultivar O-4 contig18055, 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: 25311
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Found at i:540 original size:42 final size:42
Alignment explanation
Indices: 481--565 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
471 TGCTAAATTC
481 ACTATACTACCCTCTTCTTCTTAGAAACTTGTTGGAATATTT
1 ACTATACTACCCTCTTCTTCTTAGAAACTTGTTGGAATATTT
523 ACTATACTACCCTCTTCTTCTTAGAAACTTGTTGGAATATTT
1 ACTATACTACCCTCTTCTTCTTAGAAACTTGTTGGAATATTT
565 A
1 A
566 TTAGGAGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.42
Consensus pattern (42 bp):
ACTATACTACCCTCTTCTTCTTAGAAACTTGTTGGAATATTT
Found at i:3512 original size:12 final size:12
Alignment explanation
Indices: 3477--3526 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
3467 AATAATATTT
*
3477 TATGGCAATACT
1 TATGGCAATACC
3489 TATGGCAATACC
1 TATGGCAATACC
*
3501 TATGGAAATACCC
1 TATGGCAATA-CC
*
3514 TATGGTAATACC
1 TATGGCAATACC
3526 T
1 T
3527 TGTCACAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 23 0.68
13 11 0.32
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (12 bp):
TATGGCAATACC
Found at i:6194 original size:46 final size:46
Alignment explanation
Indices: 6065--6448 Score: 536
Period size: 46 Copynumber: 8.3 Consensus size: 46
6055 CTTTGCAAGA
* * *
6065 AGCTACCGTATAGAGAATTCTTTCTGAAGATGGGTGCTCACATAAG
1 AGCTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
* * *
6111 AGCTACCGTGTAGAGTTATTCTTTCTGGAGAAGGGTGCTCACATAAG
1 AGCTACCATATAGAG-TATTCTTTCTGAAGAAGGGTGCTCACATAAG
**
6158 AGCTACTTTATAGAGTATTCTTTCTGAATG-AGGGTGCTCACATAAG
1 AGCTACCATATAGAGTATTCTTTCTGAA-GAAGGGTGCTCACATAAG
*
6204 AGCTAACATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
1 AGCTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
** * *
6250 AGCTACTGTATAGAGTATTCTTTCTGAAGATGGGTGTTCACATAAG
1 AGCTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
* ** * *
6296 AGTTACTGTATAGAGTATTCTTTCTAAAGAAGGGTGCTCACATAGG
1 AGCTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
* * *
6342 AGCTACCATATAGAGTATTTTTTTTCGAAGAAAGGTGCTCACATAAG
1 AGCTACCATATAGAGTATTCTTTCT-GAAGAAGGGTGCTCACATAAG
*
6389 AGCTACCATATAGAGTATTCTTTCTGAATAAGGGTGCTCACATAAG
1 AGCTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
6435 AGCTACCATATAGA
1 AGCTACCATATAGA
6449 TTTCAAAAAT
Statistics
Matches: 301, Mismatches: 33, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.00
46 218 0.72
47 82 0.27
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (46 bp):
AGCTACCATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
Found at i:6384 original size:185 final size:185
Alignment explanation
Indices: 6065--6448 Score: 583
Period size: 185 Copynumber: 2.1 Consensus size: 185
6055 CTTTGCAAGA
*
6065 AGCTACCGTATAGAGAATTCTTTCTGAAGATGGGTGCTCACATAAGAGCTACCGTGTAGAGTTAT
1 AGCTACCGTATAGAGAATTCTTTCTGAAGATGGGTGCTCACATAAGAGCTACCGTATAGAGTTAT
** ** *
6130 TCTTTCTGGAGAAGGGTGCTCACATAAGAGCTACTTTATAGAGTATTCTTTCTGAATGAGGGTGC
66 TCTTTCTAAAGAAGGGTGCTCACATAAGAGCTACCATATAGAGTATTCTTTCTGAATGAAGGTGC
6195 TCACATAAGAGCTAACATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
131 TCACATAAGAGCTAACATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
* * * * *
6250 AGCTACTGTATAGAGTATTCTTTCTGAAGATGGGTGTTCACATAAGAGTTACTGTATAGAG-TAT
1 AGCTACCGTATAGAGAATTCTTTCTGAAGATGGGTGCTCACATAAGAGCTACCGTATAGAGTTAT
* * *
6314 TCTTTCTAAAGAAGGGTGCTCACATAGGAGCTACCATATAGAGTATTTTTTTTCGAA-GAAAGGT
66 TCTTTCTAAAGAAGGGTGCTCACATAAGAGCTACCATATAGAGTATTCTTTCT-GAATG-AAGGT
* *
6378 GCTCACATAAGAGCTACCATATAGAGTATTCTTTCTGAATAAGGGTGCTCACATAAG
129 GCTCACATAAGAGCTAACATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
*
6435 AGCTACCATATAGA
1 AGCTACCGTATAGA
6449 TTTCAAAAAT
Statistics
Matches: 179, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
184 50 0.28
185 129 0.72
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (185 bp):
AGCTACCGTATAGAGAATTCTTTCTGAAGATGGGTGCTCACATAAGAGCTACCGTATAGAGTTAT
TCTTTCTAAAGAAGGGTGCTCACATAAGAGCTACCATATAGAGTATTCTTTCTGAATGAAGGTGC
TCACATAAGAGCTAACATATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
Found at i:6696 original size:50 final size:50
Alignment explanation
Indices: 6635--6804 Score: 141
Period size: 50 Copynumber: 3.3 Consensus size: 50
6625 GATGTATGAG
6635 AGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTA
1 AGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTA
* * * * ** * * *
6685 AGAGGCGCAAGAGCC-AGTGGCA-TAGCTAG-TATGTATTGGGCGCCAGATGTATG-A
1 AGAGGCACAAGAGCCGA-CGGCATTAG-AAGCCA-G--TT--GCATCACA-GCAAGTA
6739 GAGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTA
1 -AGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTA
*
6790 AGAGGCGCAAGAGCC
1 AGAGGCACAAGAGCC
6805 AGTGGGATAG
Statistics
Matches: 88, Mismatches: 19, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
49 5 0.06
50 38 0.43
51 6 0.07
52 2 0.02
53 2 0.02
54 6 0.07
55 24 0.27
56 5 0.06
ACGTcount: A:0.33, C:0.22, G:0.32, T:0.14
Consensus pattern (50 bp):
AGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTA
Found at i:6803 original size:105 final size:105
Alignment explanation
Indices: 6621--6831 Score: 413
Period size: 105 Copynumber: 2.0 Consensus size: 105
6611 GGCATCAAAG
6621 GCCAGATGTATGAGAGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTAA
1 GCCAGATGTATGAGAGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTAA
6686 GAGGCGCAAGAGCCAGTGGCATAGCTAGTATGTATTGGGC
66 GAGGCGCAAGAGCCAGTGGCATAGCTAGTATGTATTGGGC
6726 GCCAGATGTATGAGAGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTAA
1 GCCAGATGTATGAGAGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTAA
*
6791 GAGGCGCAAGAGCCAGTGGGATAGCTAGTATGTATTGGGC
66 GAGGCGCAAGAGCCAGTGGCATAGCTAGTATGTATTGGGC
6831 G
1 G
6832 ACTTAGGCCA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.31, C:0.19, G:0.33, T:0.16
Consensus pattern (105 bp):
GCCAGATGTATGAGAGAGGCACAAGAGCCGACGGCATTAGAAGCCAGTTGCATCACAGCAAGTAA
GAGGCGCAAGAGCCAGTGGCATAGCTAGTATGTATTGGGC
Found at i:7261 original size:19 final size:19
Alignment explanation
Indices: 7237--7303 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
7227 TTGTCACGAA
7237 TACCATACCATATCGCAAG
1 TACCATACCATATCGCAAG
* *
7256 TACCATGCCTTTAGCGTCGCGAA-
1 TACCATACC-ATA---TCGC-AAG
7279 TACCATACCATATCGCAAG
1 TACCATACCATATCGCAAG
7298 TACCAT
1 TACCAT
7304 GCCTTTAGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
18 2 0.05
19 18 0.47
20 2 0.05
22 2 0.05
23 12 0.32
24 2 0.05
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.24
Consensus pattern (19 bp):
TACCATACCATATCGCAAG
Found at i:7265 original size:42 final size:42
Alignment explanation
Indices: 7218--7390 Score: 283
Period size: 42 Copynumber: 4.1 Consensus size: 42
7208 TTGACGCCAA
** * *
7218 ATGCCTTTATTGTCACGAATACCATACCATATCGCAAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCAAGTACC
*
7260 ATGCCTTTAGCGTCGCGAATACCATACCATATCGCAAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCAAGTACC
*
7302 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCAAGTACC
*
7344 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
1 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCAAGTACC
7386 ATGCC
1 ATGCC
7391 ACATGCCACT
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 126 1.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.24
Consensus pattern (42 bp):
ATGCCTTTAGCGTCGCGAATACCATACCACATCGCAAGTACC
Found at i:7282 original size:23 final size:23
Alignment explanation
Indices: 7256--7368 Score: 109
Period size: 23 Copynumber: 5.3 Consensus size: 23
7246 ATATCGCAAG
7256 TACCATGCCTTTAGCGTCGCGAA
1 TACCATGCCTTTAGCGTCGCGAA
* *
7279 TACCATACC-ATA---TCGC-AA
1 TACCATGCCTTTAGCGTCGCGAA
7297 GTACCATGCCTTTAGCGTCGCGAA
1 -TACCATGCCTTTAGCGTCGCGAA
* * *
7321 TACCATACC---A-CATCGCGAG
1 TACCATGCCTTTAGCGTCGCGAA
7340 TACCATGCCTTTAGCGTCGCGAA
1 TACCATGCCTTTAGCGTCGCGAA
7363 TACCAT
1 TACCAT
7369 ACCACATCGC
Statistics
Matches: 70, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
18 2 0.03
19 27 0.39
20 3 0.04
22 3 0.04
23 33 0.47
24 2 0.03
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (23 bp):
TACCATGCCTTTAGCGTCGCGAA
Found at i:7338 original size:19 final size:19
Alignment explanation
Indices: 7272--7394 Score: 86
Period size: 19 Copynumber: 6.1 Consensus size: 19
7262 GCCTTTAGCG
*
7272 TCGCGAATACCATACCATA
1 TCGCGAATACCATACCACA
* *
7291 TCGC-AAGTACCATGCCTTTAGCG
1 TCGCGAA-TACCATACC---A-CA
7314 TCGCGAATACCATACCACA
1 TCGCGAATACCATACCACA
* * *
7333 TCGCGAGTACCATGCCTTTAGCG
1 TCGCGAATACCATACC---A-CA
7356 TCGCGAATACCATACCACA
1 TCGCGAATACCATACCACA
* *
7375 TCGCGAGTACCATGCCACA
1 TCGCGAATACCATACCACA
7394 T
1 T
7395 GCCACTGTAC
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.02
19 46 0.57
20 2 0.02
22 2 0.02
23 27 0.33
24 2 0.02
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.21
Consensus pattern (19 bp):
TCGCGAATACCATACCACA
Found at i:7456 original size:14 final size:14
Alignment explanation
Indices: 7439--7505 Score: 98
Period size: 14 Copynumber: 4.8 Consensus size: 14
7429 ATACTATATC
*
7439 GCGAATGCCACATT
1 GCGAATACCACATT
*
7453 GCGAATACCACATC
1 GCGAATACCACATT
*
7467 GCGAATGCCACATT
1 GCGAATACCACATT
7481 GCGAATACCACATT
1 GCGAATACCACATT
*
7495 GCAAATACCAC
1 GCGAATACCAC
7506 CTTTGATGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 47 1.00
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.18
Consensus pattern (14 bp):
GCGAATACCACATT
Found at i:7459 original size:28 final size:28
Alignment explanation
Indices: 7427--7493 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
7417 TTGGAAGAAG
* *
7427 GAATACTATATCGCGAATGCCACATTGC
1 GAATACCACATCGCGAATGCCACATTGC
7455 GAATACCACATCGCGAATGCCACATTGC
1 GAATACCACATCGCGAATGCCACATTGC
7483 GAATACCACAT
1 GAATACCACAT
7494 TGCAAATACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.21
Consensus pattern (28 bp):
GAATACCACATCGCGAATGCCACATTGC
Found at i:7505 original size:28 final size:28
Alignment explanation
Indices: 7427--7505 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
7417 TTGGAAGAAG
* * * *
7427 GAATACTATATCGCGAATGCCACATTGC
1 GAATACCACATCGCAAATACCACATTGC
* *
7455 GAATACCACATCGCGAATGCCACATTGC
1 GAATACCACATCGCAAATACCACATTGC
*
7483 GAATACCACATTGCAAATACCAC
1 GAATACCACATCGCAAATACCAC
7506 CTTTGATGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.20
Consensus pattern (28 bp):
GAATACCACATCGCAAATACCACATTGC
Found at i:7565 original size:14 final size:14
Alignment explanation
Indices: 7543--7638 Score: 63
Period size: 14 Copynumber: 7.1 Consensus size: 14
7533 GCTTTTGATG
7543 TCGCGAATACCACA
1 TCGCGAATACCACA
* *
7557 TCGCAAATACCATA
1 TCGCGAATACCACA
*
7571 TCGCGAATGCCACA
1 TCGCGAATACCACA
* *** *
7585 T-GC--CTTTGACG
1 TCGCGAATACCACA
*
7596 TCGCGAATACCATA
1 TCGCGAATACCACA
* *
7610 TTGCAAATACCACA
1 TCGCGAATACCACA
*
7624 TCGCGAATGCCACA
1 TCGCGAATACCACA
7638 T
1 T
7639 GCCTTTTGAC
Statistics
Matches: 57, Mismatches: 22, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
11 4 0.07
12 2 0.04
13 2 0.04
14 49 0.86
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.21
Consensus pattern (14 bp):
TCGCGAATACCACA
Found at i:7671 original size:54 final size:54
Alignment explanation
Indices: 7520--7676 Score: 246
Period size: 53 Copynumber: 2.9 Consensus size: 54
7510 GATGTTTGAA
* * * *
7520 GCGAACGCCACATG-CTTTTGATGTCGCGAATACCACATCGCAAATACCATATC
1 GCGAATGCCACATGCCTTTTGACGTCGCGAATACCACATTGCAAATACCACATC
*
7573 GCGAATGCCACATGCC-TTTGACGTCGCGAATACCATATTGCAAATACCACATC
1 GCGAATGCCACATGCCTTTTGACGTCGCGAATACCACATTGCAAATACCACATC
*
7626 GCGAATGCCACATGCCTTTTGACGTCGTGAATACCACATTGCAAATACCAC
1 GCGAATGCCACATGCCTTTTGACGTCGCGAATACCACATTGCAAATACCAC
7677 CACATGCCTT
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 62 0.65
54 33 0.35
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (54 bp):
GCGAATGCCACATGCCTTTTGACGTCGCGAATACCACATTGCAAATACCACATC
Found at i:8113 original size:12 final size:12
Alignment explanation
Indices: 8096--8126 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
8086 CCTGGCAATC
8096 CGTGTTTCGTGT
1 CGTGTTTCGTGT
8108 CGTGTTTCGTGT
1 CGTGTTTCGTGT
8120 CGTGTTT
1 CGTGTTT
8127 ACATAGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:8633 original size:2 final size:2
Alignment explanation
Indices: 8626--8661 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
8616 CATGAATAAG
*
8626 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8662 ATAAAGACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:12490 original size:21 final size:21
Alignment explanation
Indices: 12466--12542 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 21
12456 TATCTTAGAT
12466 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
12487 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
**
12508 ATAAATAATA-AGTTCAAAATAA
1 AT-AATAATATA-TTTTAAATAA
12530 ATAAATAATATAT
1 AT-AATAATATAT
12543 ATATTTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
20 1 0.02
21 18 0.38
22 21 0.44
23 8 0.17
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:18680 original size:51 final size:51
Alignment explanation
Indices: 18625--18792 Score: 105
Period size: 51 Copynumber: 3.3 Consensus size: 51
18615 TAGTTTCGAT
** *
18625 GTTCTCACGGGGAGTCCGTATCGAAATCTAAGGTCAATTACGAATGTTGCC
1 GTTCTCACAAGGAGTCCGTATCGAAATCTAAGGTCAATTACGAACGTTGCC
* ** ** * * * **
18676 GTTCTCCCAAGGAGTCCAGGGCTTTACAT-T-CGGCCAACTTA-G-A--TTCGAT
1 GTTCTCACAAGGAGTCC--GTATCGAAATCTAAGGTCAA-TTACGAACGTT-GCC
**
18725 GTTCTCACGGGGAGTCCGTATCGAAATCTAAGGTCAATTACGAACGTTGCC
1 GTTCTCACAAGGAGTCCGTATCGAAATCTAAGGTCAATTACGAACGTTGCC
* *
18776 GTTCTCCCAAAGAGTCC
1 GTTCTCACAAGGAGTCC
18793 AGGGCTTTAC
Statistics
Matches: 79, Mismatches: 28, Indels: 20
0.62 0.22 0.16
Matches are distributed among these distances:
47 5 0.06
48 6 0.08
49 21 0.27
50 2 0.03
51 34 0.43
52 6 0.08
53 5 0.06
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (51 bp):
GTTCTCACAAGGAGTCCGTATCGAAATCTAAGGTCAATTACGAACGTTGCC
Found at i:18740 original size:100 final size:100
Alignment explanation
Indices: 18558--18894 Score: 561
Period size: 100 Copynumber: 3.4 Consensus size: 100
18548 TTGCTTGTTA
* * * *
18558 CAATTACGAACATTGCCGTTTTCTCAAAGAGTCTAGGGCTTGT--GTTCGGTCACAACTTAGTTT
1 CAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAGGGCTT-TACGTTCGG-C-CAACTTAGTTT
18621 CGATGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGT
63 CGATGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGT
* * * *
18659 CAATTACGAATGTTGCCGTTCTCCCAAGGAGTCCAGGGCTTTACATTCGGCCAACTTAGATTCGA
1 CAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGTTTCGA
18724 TGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGT
66 TGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGT
18759 CAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGTTTCGA
1 CAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGTTTCGA
18824 TGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGT
66 TGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGT
18859 CAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAG
1 CAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAG
18895 ATCGAGGTCT
Statistics
Matches: 222, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
100 181 0.82
101 36 0.16
102 5 0.02
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (100 bp):
CAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGTTTCGA
TGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGT
Found at i:18919 original size:151 final size:151
Alignment explanation
Indices: 18751--19043 Score: 507
Period size: 151 Copynumber: 1.9 Consensus size: 151
18741 CGTATCGAAA
* *
18751 TCTAAGGTCAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAGGGCTTTACGTTCGGCCAACTT
1 TCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGACAACTT
* *
18816 AGTTTCGATGTTCTCACGGGGAGTCC-GTATCGAAATCTAAGGTCAATTACGAACGTTGCCGTTC
66 AGATTCGATGTTCTCACGGGGAGTCCAG-ATCGAAATCTAAGGTCAATTACAAACGTTGCCGTTC
*
18880 TCCCAAAGAGTCCAGATCGAGG
130 TCACAAAGAGTCCAGATCGAGG
*
18902 TCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTTACGTTCGGACAACTT
1 TCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGACAACTT
*
18967 AGATTCGATGTTCTCACGGGGAGTCCAGATCGAATTCTAAGGTCAATTACAAACGTTGCCGTTCT
66 AGATTCGATGTTCTCACGGGGAGTCCAGATCGAAATCTAAGGTCAATTACAAACGTTGCCGTTCT
19032 CACAAAGAGTCC
131 CACAAAGAGTCC
19044 GGGGCTTTAC
Statistics
Matches: 134, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
151 133 0.99
152 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.27
Consensus pattern (151 bp):
TCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACGTTCGGACAACTT
AGATTCGATGTTCTCACGGGGAGTCCAGATCGAAATCTAAGGTCAATTACAAACGTTGCCGTTCT
CACAAAGAGTCCAGATCGAGG
Found at i:18980 original size:100 final size:100
Alignment explanation
Indices: 18887--19310 Score: 767
Period size: 100 Copynumber: 4.2 Consensus size: 100
18877 TTCTCCCAAA
**
18887 GAGTCCAGATCGAGGTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
1 GAGTCCAGATCGAATTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
*
18952 ACGTTCGGACAACTTAGATTCGATGTTCTCACGGG
66 ACGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
*
18987 GAGTCCAGATCGAATTCTAAGGTCAATTACAAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
1 GAGTCCAGATCGAATTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
19052 ACGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
66 ACGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
* *
19087 GATTCCGGATCGAATTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
1 GAGTCCAGATCGAATTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
*
19152 GCGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
66 ACGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
19187 GAGTCCAGATCGAATTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
1 GAGTCCAGATCGAATTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
*
19252 ACGTTCGGCCAACTTAGATTTGATGTTCTCACGGG
66 ACGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
*
19287 GAGTCCGGATCGAATTCTAAGGTC
1 GAGTCCAGATCGAATTCTAAGGTC
19311 GAAGATAAAA
Statistics
Matches: 311, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 311 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (100 bp):
GAGTCCAGATCGAATTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTT
ACGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
Found at i:19108 original size:251 final size:251
Alignment explanation
Indices: 18651--19143 Score: 835
Period size: 251 Copynumber: 2.0 Consensus size: 251
18641 CGTATCGAAA
* * * *
18651 TCTAAGGTCAATTACGAATGTTGCCGTTCTCCCAAGGAGTCCAGGGCTTTACATTCGGCCAACTT
1 TCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACATTCGGACAACTT
*
18716 AGATTCGATGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGTCAATTACGAACGTTGCCGTTCT
66 AGATTCGATGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGTCAATTACAAACGTTGCCGTTCT
* * *
18781 CCCAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGTTTCGATGTTCTCACGGGGAGTCCGTAT
131 CACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGATGTTCTCACGGGGAGTCCGGAT
*
18846 CGAAATCTAAGGTCAATTACGAACGTTGCCGTTCTCCCAAAGAGTCCAGATCGAGG
196 CGAAATCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGATCGAGG
* *
18902 TCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCGGGGCTTTACGTTCGGACAACTT
1 TCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACATTCGGACAACTT
*
18967 AGATTCGATGTTCTCACGGGGAGTCCAG-ATCGAATTCTAAGGTCAATTACAAACGTTGCCGTTC
66 AGATTCGATGTTCTCACGGGGAGTCC-GTATCGAAATCTAAGGTCAATTACAAACGTTGCCGTTC
* *
19031 TCACAAAGAGTCCGGGGCTTTACGTTCGGCCAACTTAGATTCGATGTTCTCACGGGGATTCCGGA
130 TCACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGATGTTCTCACGGGGAGTCCGGA
*
19096 TCGAATTCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCC
195 TCGAAATCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCC
19144 GGGGCTTTGC
Statistics
Matches: 226, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
251 225 1.00
252 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (251 bp):
TCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGGGCTTTACATTCGGACAACTT
AGATTCGATGTTCTCACGGGGAGTCCGTATCGAAATCTAAGGTCAATTACAAACGTTGCCGTTCT
CACAAAGAGTCCAGGGCTTTACGTTCGGCCAACTTAGATTCGATGTTCTCACGGGGAGTCCGGAT
CGAAATCTAAGGTCAATTACGAACGTTGCCGTTCTCACAAAGAGTCCAGATCGAGG
Found at i:19191 original size:49 final size:48
Alignment explanation
Indices: 19038--19294 Score: 112
Period size: 49 Copynumber: 5.2 Consensus size: 48
19028 TTCTCACAAA
19038 GAGTCCGGGGCTTTACGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
1 GAGTCCGGGGCTTT-CGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
* * ** ** * ** ***
19087 GATTCCGGATCGAATTC-TAAGGTCAA-TTACGAACGTT-GCCGTTCTCACAAA
1 GAGTCCGG--GGCTTTCGTTCGGCCAACTTA-G-A--TTCGATGTTCTCACGGG
19138 GAGTCCGGGGCTTTGCGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
1 GAGTCCGGGGCTTT-CGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
** ** ** * ** ***
19187 GAGTCCAGATCGAATTC-TAAGGTCAA-TTACGAACGTT-GCCGTTCTCACAAA
1 GAGTCC-G-GGGCTTTCGTTCGGCCAACTTA-G-A--TTCGATGTTCTCACGGG
*
19238 GAGTCCGGGGCTTTACGTTCGGCCAACTTAGATTTGATGTTCTCACGGG
1 GAGTCCGGGGCTTT-CGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
19287 GAGTCCGG
1 GAGTCCGG
19295 ATCGAATTCT
Statistics
Matches: 140, Mismatches: 48, Indels: 40
0.61 0.21 0.18
Matches are distributed among these distances:
48 10 0.07
49 59 0.42
50 10 0.07
51 51 0.36
52 10 0.07
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (48 bp):
GAGTCCGGGGCTTTCGTTCGGCCAACTTAGATTCGATGTTCTCACGGG
Done.