Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015860.1 Corchorus olitorius cultivar O-4 contig15893, 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: 66304
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:388 original size:11 final size:11
Alignment explanation
Indices: 372--396 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
362 AGATAATTTC
372 TTTTCTTCTAG
1 TTTTCTTCTAG
383 TTTTCTTCTAG
1 TTTTCTTCTAG
394 TTT
1 TTT
397 AGGCAAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:1182 original size:15 final size:16
Alignment explanation
Indices: 1151--1190 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
1141 TTACTTTGCT
1151 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
1167 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
*
1182 TTGATTTCT
1 TTGTTTTCT
1191 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:3225 original size:41 final size:41
Alignment explanation
Indices: 3138--3225 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
3128 ATTTAGGCTG
* * *
3138 TTATTTATTCATTAATTTAATTTTGTCCCTGATCTAGAGTA
1 TTATTTATTCATTAATTCAATTTTGTCCCGGATCTAGAATA
* * * * *
3179 ATATTTATTTATTGATTCAATTTTGTCCCGGATTTAGAATT
1 TTATTTATTCATTAATTCAATTTTGTCCCGGATCTAGAATA
3220 TTATTT
1 TTATTT
3226 TTGATTTATG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.53
Consensus pattern (41 bp):
TTATTTATTCATTAATTCAATTTTGTCCCGGATCTAGAATA
Found at i:13588 original size:56 final size:56
Alignment explanation
Indices: 13502--13619 Score: 218
Period size: 56 Copynumber: 2.1 Consensus size: 56
13492 ACCGGCAATC
* *
13502 TCTCCAAATTCAAGGCAAAGTTTTTCTCCATCAAAGCAGATTTGAAGCAAAGTTCT
1 TCTCCAAATTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
13558 TCTCCAAATTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
1 TCTCCAAATTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
13614 TCTCCA
1 TCTCCA
13620 TCAACAAAGC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (56 bp):
TCTCCAAATTCAAGGCAAAGTTCTTCTCCATCAAAGCAGATCTGAAGCAAAGTTCT
Found at i:13666 original size:26 final size:27
Alignment explanation
Indices: 13627--13717 Score: 111
Period size: 26 Copynumber: 3.6 Consensus size: 27
13617 CCATCAACAA
*
13627 AGCAACAACCAAGCAGCAAAGTTCTT-
1 AGCAACAACAAAGCAGCAAAGTTCTTC
13653 AGCAACAACAAAGCAGCAAAGTTCTTC
1 AGCAACAACAAAGCAGCAAAGTTCTTC
13680 A-CAACAAC-AA--AGCAAAGTTCTTC
1 AGCAACAACAAAGCAGCAAAGTTCTTC
** *
13703 TCCATCAACAAAGCA
1 AGCAACAACAAAGCA
13718 ACAACAAAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
23 13 0.23
24 6 0.11
25 4 0.07
26 32 0.56
27 2 0.04
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.15
Consensus pattern (27 bp):
AGCAACAACAAAGCAGCAAAGTTCTTC
Found at i:19140 original size:63 final size:63
Alignment explanation
Indices: 19073--19252 Score: 315
Period size: 63 Copynumber: 2.9 Consensus size: 63
19063 GGTCAAGTCC
19073 ATTTCTTTGGGTTTTCTTTTAATCCTTTTTGGGCCTTTCCATTACTATCTGCTTTGGAACTTT
1 ATTTCTTTGGGTTTTCTTTTAATCCTTTTTGGGCCTTTCCATTACTATCTGCTTTGGAACTTT
* * * * *
19136 ATTTCTTTAGGTTTTCTTTTAATCCTTTTTGGGCATTTCGATTACTATTTGCTTTGGACCTTT
1 ATTTCTTTGGGTTTTCTTTTAATCCTTTTTGGGCCTTTCCATTACTATCTGCTTTGGAACTTT
19199 ATTTCTTTGGGTTTTCTTTTAATCCTTTTTGGGCCTTTCCATTACTATCTGCTT
1 ATTTCTTTGGGTTTTCTTTTAATCCTTTTTGGGCCTTTCCATTACTATCTGCTT
19253 CACTACTAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 108 1.00
ACGTcount: A:0.13, C:0.18, G:0.14, T:0.55
Consensus pattern (63 bp):
ATTTCTTTGGGTTTTCTTTTAATCCTTTTTGGGCCTTTCCATTACTATCTGCTTTGGAACTTT
Found at i:19689 original size:161 final size:163
Alignment explanation
Indices: 19390--19689 Score: 453
Period size: 161 Copynumber: 1.9 Consensus size: 163
19380 GTAGAAAGAC
* * *
19390 GCCGCCATATTAATATATGGAGGGAGAGATTTTTTTCTCCTTTTTTTGGAGGGAAAAATTCCCTC
1 GCCGCCATATTAATATATGGAGGAAGAAATTTTTTTCTCCTTTTTATGGAGGGAAAAATTCCCTC
*
19455 CCCACTAAAACAAAGAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGGACATCAGA
66 CCCACTAAAACAAAGAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGCACATCAGA
*
19520 CGCCGCTAATTAGTGGCATCTAGAAAAGGAAAA
131 CACCGCTAATTAGTGGCATCTAGAAAAGGAAAA
* *
19553 GCCGCTATTTTAATATATGGAGGAAGAAATTTTTTTC-CCTTTTTATGGAGGGAAAAATTCCCTC
1 GCCGCCATATTAATATATGGAGGAAGAAATTTTTTTCTCCTTTTTATGGAGGGAAAAATTCCCTC
* * * * * *
19617 CTC-CTAAAACAAAGAAATTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCTC-TCTAG
66 CCCACTAAAACAAAGAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGCACATC-AG
19680 ACACCGCTAA
130 ACACCGCTAA
19690 ACGCCGCAAT
Statistics
Matches: 123, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
160 2 0.02
161 60 0.49
162 28 0.23
163 33 0.27
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (163 bp):
GCCGCCATATTAATATATGGAGGAAGAAATTTTTTTCTCCTTTTTATGGAGGGAAAAATTCCCTC
CCCACTAAAACAAAGAAAGTTTACAACTCTACACCTATAATATATAGCGGCGTTTGCACATCAGA
CACCGCTAATTAGTGGCATCTAGAAAAGGAAAA
Found at i:26015 original size:17 final size:17
Alignment explanation
Indices: 25990--26024 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
25980 TGCATAATGT
25990 TAATATACCAACAAGAA
1 TAATATACCAACAAGAA
*
26007 TAATGTACCAACAAGAA
1 TAATATACCAACAAGAA
26024 T
1 T
26025 GCACTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (17 bp):
TAATATACCAACAAGAA
Found at i:29788 original size:27 final size:27
Alignment explanation
Indices: 29758--29861 Score: 165
Period size: 27 Copynumber: 3.9 Consensus size: 27
29748 GACTGTTGCC
*
29758 GCAGTTGG-TCCTCCCACTTCGACCCTA
1 GCAG-TGGATCCTCCCACTTCGACCCCA
*
29785 GCAGTGGATCCTCCCACTCCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
*
29812 GCAGTGCATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
29839 GCAGTGGATCCTCCCACTTCGAC
1 GCAGTGGATCCTCCCACTTCGAC
29862 TCGGGTCGGT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 3 0.04
27 68 0.96
ACGTcount: A:0.17, C:0.44, G:0.18, T:0.20
Consensus pattern (27 bp):
GCAGTGGATCCTCCCACTTCGACCCCA
Found at i:32664 original size:17 final size:17
Alignment explanation
Indices: 32642--32676 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
32632 GAAAAAGTGC
32642 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
*
32659 ATTCTTGTTGGTATATT
1 ATTCTTGTTGGTACATT
32676 A
1 A
32677 ACATTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:34243 original size:32 final size:32
Alignment explanation
Indices: 34177--34350 Score: 259
Period size: 32 Copynumber: 5.5 Consensus size: 32
34167 GTGTGAAAAG
*
34177 AAAACGCCCTTATTTAGCGGCGT-TGTAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
*
34208 AAAACACCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
*
34240 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
34272 AAAACGCCCTTATTTAGCGGCGTCTA-A-AA-
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
34301 AAAACGCCCTTATTTAGCGGCGTCT-TCAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAT-AGAAC
34333 AAAACGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
34351 ACTACTTTTA
Statistics
Matches: 132, Mismatches: 4, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
29 25 0.19
30 3 0.02
31 25 0.19
32 71 0.54
33 2 0.02
34 6 0.05
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
Found at i:34332 original size:61 final size:61
Alignment explanation
Indices: 34172--34350 Score: 254
Period size: 61 Copynumber: 2.9 Consensus size: 61
34162 AGCATGTGTG
* *
34172 AAAAGAAAACGCCCTTATTTAGCGGCGT-TGTAGAACAAAACACCCTTATTTAGCGGCGTCT
1 AAAACAAAACGCCCTTATTTAGCGGCGTCT-TAGAACAAAACGCCCTTATTTAGCGGCGTCT
*
34233 ATAGAACAAAACGCCCTTATTTAGCGGCGTCTAAAGAACAAAACGCCCTTATTTAGCGGCGTCT
1 A-A-AACAAAACGCCCTTATTTAGCGGCGTCT-TAGAACAAAACGCCCTTATTTAGCGGCGTCT
34297 AAAA-AAAACGCCCTTATTTAGCGGCGTCTTCAGAACAAAACGCCGCTATATTTA
1 AAAACAAAACGCCCTTATTTAGCGGCGTCTT-AGAACAAAACGCC-CT-TATTTA
34351 ACTACTTTTA
Statistics
Matches: 107, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
61 39 0.36
62 5 0.05
63 32 0.30
64 31 0.29
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAACAAAACGCCCTTATTTAGCGGCGTCTTAGAACAAAACGCCCTTATTTAGCGGCGTCT
Found at i:34364 original size:61 final size:61
Alignment explanation
Indices: 34172--34367 Score: 223
Period size: 63 Copynumber: 3.1 Consensus size: 61
34162 AGCATGTGTG
** * * *
34172 AAAAGAAAACGCCCTTATTTAGCGGCGT-TGTAGAACAAAACACCCTTATTTAGCGGCGTCT
1 AAAA-AAAACGCCCTTATTTAGCGGCGTCTAAAGAACAAAACGCCCTTATTTAACGACGTCT
* *
34233 ATAGAACAAAACGCCCTTATTTAGCGGCGTCTAAAGAACAAAACGCCCTTATTTAGCGGCGTCT
1 A-A-AA-AAAACGCCCTTATTTAGCGGCGTCTAAAGAACAAAACGCCCTTATTTAACGACGTCT
** * * *
34297 AAAAAAAACGCCCTTATTTAGCGGCGTCTTCAGAACAAAACGCCGCTATATTTAACTACTTTT
1 AAAAAAAACGCCCTTATTTAGCGGCGTCTAAAGAACAAAACGCC-CT-TATTTAACGACGTCT
34360 AAAAAAAA
1 AAAAAAAA
34368 TGTAGTGTTA
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
61 39 0.33
62 5 0.04
63 44 0.37
64 31 0.26
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.24
Consensus pattern (61 bp):
AAAAAAAACGCCCTTATTTAGCGGCGTCTAAAGAACAAAACGCCCTTATTTAACGACGTCT
Found at i:39164 original size:18 final size:18
Alignment explanation
Indices: 39129--39163 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39119 CTCCTCTTGC
*
39129 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
39147 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
39164 TTAAACTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:48078 original size:36 final size:37
Alignment explanation
Indices: 48031--48109 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 37
48021 AGAGTAATGC
* * *
48031 TTATTAATTGATTCAATTTTGTCACTGATTTAGG-GT
1 TTATTTATTGATTCAATTTCGCCACTGATTTAGGAGT
* *
48067 TTATTTATTGATTCAATTTCGCCCCTGATTTAGGATT
1 TTATTTATTGATTCAATTTCGCCACTGATTTAGGAGT
48104 TTATTT
1 TTATTT
48110 TTAATTTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 30 0.81
37 7 0.19
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (37 bp):
TTATTTATTGATTCAATTTCGCCACTGATTTAGGAGT
Found at i:49299 original size:18 final size:19
Alignment explanation
Indices: 49257--49299 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
49247 ATCTAGAGAT
49257 AGAAAAAAGTACAAAATCC
1 AGAAAAAAGTACAAAATCC
*
49276 AAAAAAAAGTGA-AAAAT-C
1 AGAAAAAAGT-ACAAAATCC
49294 AGAAAA
1 AGAAAA
49300 TGAAAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 14 0.67
20 1 0.05
ACGTcount: A:0.70, C:0.09, G:0.12, T:0.09
Consensus pattern (19 bp):
AGAAAAAAGTACAAAATCC
Found at i:49944 original size:42 final size:44
Alignment explanation
Indices: 49893--49986 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
49883 AATGCATTAC
*
49893 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
**
49934 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATGGAG
1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAG
49979 CTAATATT
1 CTAATATT
49987 AATTTTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 2 0.04
45 32 0.70
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:51776 original size:22 final size:23
Alignment explanation
Indices: 51751--51796 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
51741 TAATATCCAC
51751 ACACAATTAAT-ATATAAT-TAAA
1 ACACAATTAATCATA-AATATAAA
*
51773 ACACAGTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
51796 A
1 A
51797 ATAGTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:52785 original size:2 final size:2
Alignment explanation
Indices: 52778--52802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52768 ATTCACATAA
52778 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
52803 AATGGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59533 original size:35 final size:36
Alignment explanation
Indices: 59449--59658 Score: 144
Period size: 34 Copynumber: 5.8 Consensus size: 36
59439 AAATGCTCTT
** * **
59449 TGATGGGAACTTTCCCACTTTGAAAACTAAAACTGAAAA
1 TGATGGGAACTTTCCCAAATTGAAAACTTAAA---AACC
* *
59488 TGATGCGAACTTTCCCTAAAGTGAAAAC-T-AAAACC
1 TGATGGGAACTTTCCC-AAATTGAAAACTTAAAAACC
* * *
59523 TGATGGGAACTCTCCCAATTTAAAAACTTTGAAAAA-C
1 TGATGGGAACTTTCCCAAATTGAAAAC-TT-AAAAACC
* * * * *
59560 TGGTGGGAACCTTCCCAATTTTAAAACTTAAAAACT
1 TGATGGGAACTTTCCCAAATTGAAAACTTAAAAACC
* *
59596 TGTTGGGACCTTTCCC-AATTGAAAAAC-T-AAAACC
1 TGATGGGAACTTTCCCAAATTG-AAAACTTAAAAACC
* *
59630 TGGTGGGAACTTTCCCAATTTGAAAACTT
1 TGATGGGAACTTTCCCAAATTGAAAACTT
59659 CGAAGACTGA
Statistics
Matches: 136, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
34 32 0.24
35 30 0.22
36 21 0.15
37 24 0.18
38 6 0.04
39 15 0.11
40 8 0.06
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (36 bp):
TGATGGGAACTTTCCCAAATTGAAAACTTAAAAACC
Found at i:63367 original size:8 final size:8
Alignment explanation
Indices: 63350--63398 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
63340 ACTCGAGGCC
*
63350 TTGAATAA
1 TTGAAGAA
63358 TTGAAGAA
1 TTGAAGAA
*
63366 TTGAAGCA
1 TTGAAGAA
* *
63374 TCGAATAA
1 TTGAAGAA
63382 CTTGAAGAA
1 -TTGAAGAA
63391 TTGAAGAA
1 TTGAAGAA
63399 AGACCACCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
8 27 0.82
9 6 0.18
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (8 bp):
TTGAAGAA
Found at i:63512 original size:36 final size:36
Alignment explanation
Indices: 63472--63632 Score: 112
Period size: 36 Copynumber: 4.5 Consensus size: 36
63462 CCGAAAAAAT
*
63472 GACCACCCTCGATCATTTCGACACCAACTAAAGAAA
1 GACCACCCTCGATCATTTCGACACGAACTAAAGAAA
* * ** * ** * *
63508 GACCACCCTGGGTCAACT-GAAATAAACTGAAGAAC
1 GACCACCCTCGATCATTTCGACACGAACTAAAGAAA
* * **
63543 GACCAACCTCGATCATTTCGA-ACTGAACGGAGGGAAA
1 GACCACCCTCGATCATTTCGACAC-GAAC-TAAAGAAA
* *
63580 -ACCACCCTCGATCATTCCGACACGAACTGAAGAAA
1 GACCACCCTCGATCATTTCGACACGAACTAAAGAAA
* * *
63615 GACCTCCCTGGGTCATTT
1 GACCACCCTCGATCATTT
63633 GAAATAAACT
Statistics
Matches: 89, Mismatches: 31, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
35 30 0.34
36 54 0.61
37 5 0.06
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.17
Consensus pattern (36 bp):
GACCACCCTCGATCATTTCGACACGAACTAAAGAAA
Found at i:63547 original size:35 final size:35
Alignment explanation
Indices: 63392--64198 Score: 605
Period size: 35 Copynumber: 22.9 Consensus size: 35
63382 CTTGAAGAAT
* * **
63392 TGAAGAAAGACCACCCTGGGTCATTCTGGAATAATT
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
* *
63428 TGAAGCAAGACCACCCTAGGTC-ACTTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
* * * * ** * **
63463 CGAAAAAATGACCACCCTCGATCATTTCGACACCAAC
1 TGAAGAAA-GACCACCCTGGGTCAACT-GAAATAAAC
*
63500 TAAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * ** * *
63535 TGAAGAACGACCAACCTCGATCATTTCGAACTGAAC
1 TGAAGAAAGACCACCCTGGGTCAACT-GAAATAAAC
* * * * * * * **
63571 GGAGGGAAA-ACCACCCTCGATCATTCCGACACGAAC
1 TGA-AGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
* **
63607 TGAAGAAAGACCTCCCTGGGTCATTTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* **
63642 TGAAGAAAAGACCACCTTGGGTCGAACTGGCATAAAC
1 TGAAG-AAAGACCACCCTGGGTC-AACTGAAATAAAC
*
63679 TGAAGAAAAGACCACCCTGGGTCGACTGAAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* *
63715 TGAAGAACGACCGCCCTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
63750 TGAAGAACGACCGCCCTGGGTCAACT-AAATTAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAA-TAAAC
* * * * *
63785 TGAAGAACGACCACCCTTGATCATTCTGACATAAAC
1 TGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAAC
**
63821 TGAAGAAAAGACCACCCTGGGT---CTTTAATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
63854 TGAAGAAAGACCGCCCTGGGTCATCTGAAATAATC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* *
63889 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAGAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * * * *
63924 TGAAGGATGATCGCCCCGGATCAACTTGAAA-ACAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AAC
* *
63960 TGAAGAAAGACCAACCTGGGTCAACTTGAAATGAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAAC
*
63996 TGAAGAAAGACCACCCTGGGTCGACTGAAATAAAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * ** *
64031 TGAAGAAAGACCGCCCTCGATCTTCCG-AAT----
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
***
64061 TGAAGAAAAGACCACCCTGGGTCAACTTTGATAAAC
1 TGAAG-AAAGACCACCCTGGGTCAACTGAAATAAAC
* * *
64097 TGAAGAAAGACCGCCCTAGGTCAACTGAAATAGAC
1 TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
* * * *
64132 TGAAGAATGATCGCCCTGGATCAACTTGAAA-ACAAC
1 TGAAGAAAGACCACCCTGGGTCAAC-TGAAATA-AAC
* *
64168 TGAAGAAAGACCACCCTGGGTCGATTGAAAT
1 TGAAGAAAGACCACCCTGGGTCAACTGAAAT
64199 TTATTGAATG
Statistics
Matches: 609, Mismatches: 133, Indels: 58
0.76 0.17 0.07
Matches are distributed among these distances:
30 5 0.01
31 15 0.02
32 17 0.03
33 13 0.02
34 7 0.01
35 273 0.45
36 218 0.36
37 61 0.10
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (35 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAAATAAAC
Found at i:63687 original size:107 final size:107
Alignment explanation
Indices: 63392--64189 Score: 469
Period size: 107 Copynumber: 7.5 Consensus size: 107
63382 CTTGAAGAAT
* ** * *
63392 TGAAGAAAGACCACCCTGGGTCATTCTGGAATAATTTGAAGCAAGACCACCCTAGGTC-ACTTGA
1 TGAAGAAAGACCACCCTGGGTCATT-TGAAATAAACTGAAGAAAGACCACCCTGGGTCAAC-TGA
* * * *
63456 AA-TAAACCGAAAAAATGACCACCCTCGATCATTTCGACACCAAC
64 AACTAAACTGAAGAAA-GACCACCCTCGATCATTCCGACACAAAC
* ** * * * * **
63500 TAAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCAACCTCGATCATTTCG-A
1 TGAAGAAAGACCACCCTGGGTCATTTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACT-GAA
* * * *
63564 ACTGAACGGAGGGAAA-ACCACCCTCGATCATTCCGACACGAAC
65 ACTAAACTGA-AGAAAGACCACCCTCGATCATTCCGACACAAAC
* * *
63607 TGAAGAAAGACCTCCCTGGGTCATTTGAAATAAACTGAAGAAAAGACCACCTTGGGTCGAACTGG
1 TGAAGAAAGACCACCCTGGGTCATTTGAAATAAACTGAAG-AAAGACCACCCTGGGTC-AACTGA
* * * * * *
63672 CA-TAAACTGAAGAAAAGACCACCCTGGGTCGA--CTGAAATAAAC
64 AACTAAACTGAAG-AAAGACCACCCTCGATC-ATTCCGACACAAAC
* * ** * *
63715 TGAAGAACGACCGCCCTGGGTCAACTGAAATAAACTGAAGAACGACCGCCCTGGGTCAACT-AAA
1 TGAAGAAAGACCACCCTGGGTCATTTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAA
* * * * *
63779 TTAAACTGAAGAACGACCACCCTTGATCATTCTGACATAAAC
66 CTAAACTGAAGAAAGACCACCCTCGATCATTCCGACACAAAC
* *
63821 TGAAGAAAAGACCACCCTGGGTC-TTT--AATAAACTGAAGAAAGACCGCCCTGGGTCATCTGAA
1 TGAAG-AAAGACCACCCTGGGTCATTTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAA
* * * * * * * * *
63883 A-TAATCTGAAGAAAGACCGCCCTGGGTCA-ACTGAAATAGAC
65 ACTAAACTGAAGAAAGACCACCCTCGATCATTCCGACACAAAC
* * * * * * * *
63924 TGAAGGATGATCGCCCCGGATCAACTTGAAA-ACAACTGAAGAAAGACCAACCTGGGTCAACTTG
1 TGAAGAAAGACCACCCTGGGTC-ATTTGAAATA-AACTGAAGAAAGACCACCCTGGGTCAAC-TG
* * * * * *
63988 AAA-TGAACTGAAGAAAGACCACCCTGGGTCGA--CTGAAATAAAC
63 AAACTAAACTGAAGAAAGACCACCCTCGATC-ATTCCGACACAAAC
* * * * **
64031 TGAAGAAAGACCGCCCTCGATC-TTCCG-AAT----TGAAGAAAAGACCACCCTGGGTCAACTTT
1 TGAAGAAAGACCACCCTGGGTCATT-TGAAATAAACTGAAG-AAAGACCACCCTGGGTCAACTGA
* * * * * * * * *
64090 GA-TAAACTGAAGAAAGACCGCCCTAGGTCA-ACTGAAATAGAC
64 AACTAAACTGAAGAAAGACCACCCTCGATCATTCCGACACAAAC
* * * * *
64132 TGAAGAATGATCGCCCTGGATCAACTTGAAA-ACAACTGAAGAAAGACCACCCTGGGTC
1 TGAAGAAAGACCACCCTGGGTC-ATTTGAAATA-AACTGAAGAAAGACCACCCTGGGTC
64190 GATTGAAATT
Statistics
Matches: 555, Mismatches: 101, Indels: 70
0.76 0.14 0.10
Matches are distributed among these distances:
100 1 0.00
101 60 0.11
102 31 0.06
103 17 0.03
104 57 0.10
105 22 0.04
106 75 0.14
107 179 0.32
108 95 0.17
109 17 0.03
110 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (107 bp):
TGAAGAAAGACCACCCTGGGTCATTTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAA
CTAAACTGAAGAAAGACCACCCTCGATCATTCCGACACAAAC
Found at i:64121 original size:208 final size:211
Alignment explanation
Indices: 63638--64198 Score: 685
Period size: 208 Copynumber: 2.7 Consensus size: 211
63628 CATTTGAAAT
* * *
63638 AAACTGAAGAAAAGACCACCTTGGGTCGAAC-TGGCATAAACTGAAGAAAAGACCACCCTGGGTC
1 AAACTGAAGAAAAGACCACCCTGGGTC-AACTTAG-ATAAACTGAAG-AAAGACCGCCCTGGGTC
* * * * * * *
63702 GACTGAAATAAACTGAAGAACGACCGCCCTGGGTCAAC-TGAAATA-AACTGAAGAACGACCGCC
63 AACTGAAATAGACTGAAGAATGATCGCCCTGGATCAACTTGAAA-ACAACTGAAGAAAGACCACC
* * *
63765 CTGGGTCAAC-T-AAATTAAACTGAAGAACGACCACCCTTGATCATTCTGACATAAACTGAAGAA
127 CTGGGTCAACTTGAAA-TAAACTGAAGAAAGACCACCCTGGATCA-TCTGAAATAAACTGAAGAA
* * *
63828 AAGACCACCCTGGGTCTTTAAT
190 AAGACCACCCTCGATCTTTAAC
* * * * *
63850 AAACTGAAG-AAAGACCGCCCTGGGTCATCTGAAATAATCTGAAGAAAGACCGCCCTGGGTCAAC
1 AAACTGAAGAAAAGACCACCCTGGGTCAACTTAGATAAACTGAAGAAAGACCGCCCTGGGTCAAC
* * *
63914 TGAAATAGACTGAAGGATGATCGCCCCGGATCAACTTGAAAACAACTGAAGAAAGACCAACCTGG
66 TGAAATAGACTGAAGAATGATCGCCCTGGATCAACTTGAAAACAACTGAAGAAAGACCACCCTGG
* *
63979 GTCAACTTGAAATGAACTGAAGAAAGACCACCCTGGGTCGA-CTGAAATAAACTGAAG-AAAGAC
131 GTCAACTTGAAATAAACTGAAGAAAGACCACCCTGGATC-ATCTGAAATAAACTGAAGAAAAGAC
* *
64042 CGCCCTCGATC-TT-CC
195 CACCCTCGATCTTTAAC
* * * *
64057 GAATTGAAGAAAAGACCACCCTGGGTCAACTTTGATAAACTGAAGAAAGACCGCCCTAGGTCAAC
1 AAACTGAAGAAAAGACCACCCTGGGTCAACTTAGATAAACTGAAGAAAGACCGCCCTGGGTCAAC
64122 TGAAATAGACTGAAGAATGATCGCCCTGGATCAACTTGAAAACAACTGAAGAAAGACCACCCTGG
66 TGAAATAGACTGAAGAATGATCGCCCTGGATCAACTTGAAAACAACTGAAGAAAGACCACCCTGG
*
64187 GTCGA-TTGAAAT
131 GTCAACTTGAAAT
64199 TTATTGAATG
Statistics
Matches: 301, Mismatches: 41, Indels: 19
0.83 0.11 0.05
Matches are distributed among these distances:
207 14 0.05
208 116 0.39
209 62 0.21
210 57 0.19
211 39 0.13
212 13 0.04
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (211 bp):
AAACTGAAGAAAAGACCACCCTGGGTCAACTTAGATAAACTGAAGAAAGACCGCCCTGGGTCAAC
TGAAATAGACTGAAGAATGATCGCCCTGGATCAACTTGAAAACAACTGAAGAAAGACCACCCTGG
GTCAACTTGAAATAAACTGAAGAAAGACCACCCTGGATCATCTGAAATAAACTGAAGAAAAGACC
ACCCTCGATCTTTAAC
Found at i:64218 original size:71 final size:69
Alignment explanation
Indices: 63604--64232 Score: 488
Period size: 71 Copynumber: 9.0 Consensus size: 69
63594 TTCCGACACG
* ** * * * *
63604 AACTGAAGAAAGACCTCCCTGGGTCATTTGAAATAAACTGAAGAAAAGACCACCTTGGGTCGAAC
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAG-AACGACCGCCCTGGATC-AAC
* *
63669 TGGCATA
64 T-GAAAA
* *
63676 AACTGAAGAAAAGACCACCCTGGGTCGACTGAAATAAACTGAAGAACGACCGCCCTGGGTCAACT
1 AACTGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCGCCCTGGATCAACT
63741 GAAATA
65 GAAA-A
* * * * *
63747 AACTGAAGAACGACCGCCCTGGGTCAACT-AAATTAAACTGAAGAACGACCACCCTTGATCATTC
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAA-TAAACTGAAGAACGACCGCCCTGGATCA-AC
*
63811 TGACATA
64 TGA-AAA
** * * *
63818 AACTGAAGAAAAGACCACCCTGGGT---CTTTAATAAACTGAAGAAAGACCGCCCTGGGTCATCT
1 AACTGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCGCCCTGGATCAACT
63880 GAAATA
65 GAAA-A
* * * * * * *
63886 ATCTGAAGAAAGACCGCCCTGGGTCAACTGAAATAGACTGAAGGATGATCGCCCCGGATCAACTT
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCGCCCTGGATCAAC-T
63951 GAAAA
65 GAAAA
* * * * * *
63956 CAACTGAAGAAAGACCAACCTGGGTCAACTTGAAATGAACTGAAGAAAGACCACCCTGGGTCGAC
1 -AACTGAAGAAAGACCACCCTGGGTCAAC-TGAAATAAACTGAAGAACGACCGCCCTGGATCAAC
64021 TGAAATA
64 TGAAA-A
* * * ** * * * * *
64028 AACTGAAGAAAGACCGCCCTCGATCTTCCGAATTGAA--GAA-AA-GACCACCCTGGGTCAACTT
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCGCCCTGGATCAAC--
*
64089 TG-ATA
64 TGAAAA
* * * * *
64094 AACTGAAGAAAGACCGCCCTAGGTCAACTGAAATAGACTGAAGAATGATCGCCCTGGATCAACTT
1 AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCGCCCTGGATCAAC-T
64159 GAAAA
65 GAAAA
* * ** * *
64164 CAACTGAAGAAAGACCACCCTGGGTCGATTGAAATTTATTGAATGGA-GACCGCCCT-GAGTCAA
1 -AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAA-GAACGACCGCCCTGGA-TCAA
64227 CTGAAA
63 CTGAAA
64233 CTTTGAACAT
Statistics
Matches: 453, Mismatches: 79, Indels: 52
0.78 0.14 0.09
Matches are distributed among these distances:
66 46 0.10
67 19 0.04
68 21 0.05
69 34 0.08
70 105 0.23
71 131 0.29
72 66 0.15
73 31 0.07
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (69 bp):
AACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAACGACCGCCCTGGATCAACTG
AAAA
Found at i:65901 original size:14 final size:14
Alignment explanation
Indices: 65879--65911 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
65869 TGAAAACAAA
65879 TTTTG-GAAACCAT
1 TTTTGAGAAACCAT
*
65892 TTTTGAGAAATCAT
1 TTTTGAGAAACCAT
65906 TTTTGA
1 TTTTGA
65912 AAAATCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (14 bp):
TTTTGAGAAACCAT
Found at i:66278 original size:2 final size:2
Alignment explanation
Indices: 66271--66303 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
66261 GAACAGTAGA
66271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66304 A
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.