Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007101.1 Corchorus capsularis cultivar CVL-1 contig07122, 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: 73396
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2618 original size:27 final size:28
Alignment explanation
Indices: 2551--2634 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 28
2541 TCAAACCCCT
*
2551 ATTTAAGAAAATTGCCAATTACAAACATTAA
1 ATTTAAGAAAATT-CCAATTAGAAAC--TAA
*
2582 ATTTCAGAAAATTCCAATTAGAAAC-AA
1 ATTTAAGAAAATTCCAATTAGAAACTAA
2609 ATTTAAGAAAATTCTCAATT-GAAACT
1 ATTTAAGAAAATTC-CAATTAGAAACT
2635 CTAATTATCC
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 20 0.42
28 5 0.10
30 11 0.23
31 12 0.25
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (28 bp):
ATTTAAGAAAATTCCAATTAGAAACTAA
Found at i:9643 original size:34 final size:34
Alignment explanation
Indices: 9605--9671 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
9595 TTTTATTTTA
* * * *
9605 ATGTAGGTGGAATTGTGATGGCAGCTTGTTGATG
1 ATGTAGGTGAAACTATGATGGCAGCTTGATGATG
*
9639 ATGTAGGTGAAACTATGATGGTAGCTTGATGAT
1 ATGTAGGTGAAACTATGATGGCAGCTTGATGAT
9672 CAGTGTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.25, C:0.06, G:0.34, T:0.34
Consensus pattern (34 bp):
ATGTAGGTGAAACTATGATGGCAGCTTGATGATG
Found at i:9850 original size:14 final size:14
Alignment explanation
Indices: 9831--9903 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
9821 GGTGTTTAAT
9831 TGAGATGTTTATTA
1 TGAGATGTTTATTA
9845 TGAGATG-TT-TTA
1 TGAGATGTTTATTA
* *
9857 TTA-ATGATTGA-TA
1 TGAGATG-TTTATTA
*
9870 TG-G-TGTTTAAT-
1 TGAGATGTTTATTA
9881 TGAGATGTTTATTA
1 TGAGATGTTTATTA
9895 TGAGATGTT
1 TGAGATGTT
9904 CAATTGGTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
11 8 0.17
12 9 0.20
13 13 0.28
14 16 0.35
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.49
Consensus pattern (14 bp):
TGAGATGTTTATTA
Found at i:9908 original size:27 final size:27
Alignment explanation
Indices: 9823--9909 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
9813 GGTAATTTGG
9823 TGTTTAATTGAGATGTTTATTATGAGA
1 TGTTTAATTGAGATGTTTATTATGAGA
* *
9850 TGTTTTATT-A-ATGATTGA-TATG-G-
1 TGTTTAATTGAGATG-TTTATTATGAGA
9873 TGTTTAATTGAGATGTTTATTATGAGA
1 TGTTTAATTGAGATGTTTATTATGAGA
*
9900 TGTTCAATTG
1 TGTTTAATTG
9910 GTTAAATGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
23 8 0.16
24 5 0.10
25 14 0.29
26 5 0.10
27 17 0.35
ACGTcount: A:0.28, C:0.01, G:0.22, T:0.49
Consensus pattern (27 bp):
TGTTTAATTGAGATGTTTATTATGAGA
Found at i:10219 original size:12 final size:12
Alignment explanation
Indices: 10202--10226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10192 ATCCTTAAAA
10202 CAAGAGGATGTT
1 CAAGAGGATGTT
10214 CAAGAGGATGTT
1 CAAGAGGATGTT
10226 C
1 C
10227 TCATGAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (12 bp):
CAAGAGGATGTT
Found at i:19578 original size:35 final size:35
Alignment explanation
Indices: 19537--19770 Score: 292
Period size: 35 Copynumber: 6.7 Consensus size: 35
19527 AGTAATAAGC
* ** **
19537 AACTTAATTCAGGGTAATTACGCAAGTTGGTAATA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATA
*
19572 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATA
* * *
19607 AACTTTAATTCAGGGTAATTAAGTGAGTTAATAAGA
1 AAC-TTAATTCAGGGTAATTAAGTGAGTCAGTAATA
* *
19643 AACTTAATTCAGGGTAATTAAGT-AGTTCAATGAGT-
1 AACTTAATTCAGGGTAATTAAGTGAG-TCAGT-AATA
* *
19678 AACTTAATTCAGGGTAATTAAGTGAGTCGGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATA
*
19713 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATA
*
19748 AACTTAATTCAGGATAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
19771 TTAGTAAGAA
Statistics
Matches: 176, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
34 4 0.02
35 138 0.78
36 34 0.19
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATA
Found at i:19717 original size:70 final size:70
Alignment explanation
Indices: 19536--19770 Score: 330
Period size: 70 Copynumber: 3.3 Consensus size: 70
19526 CAGTAATAAG
* **
19536 CAACTTAATTCAGGGTAATTACGCAAGTTGGTAATAAACTTAATTCAGGGTAATTAAGTGAGTCA
1 CAACTTAATTCAGGGTAATTAAGTGAGTTGGTAATAAACTTAATTCAGGGTAATTAAGTGAGTCA
19601 GTAAT
66 GTAAT
** *
19606 CAACTTTAATTCAGGGTAATTAAGTGAGTTAATAAGAAACTTAATTCAGGGTAATTAAGT-AGTT
1 CAAC-TTAATTCAGGGTAATTAAGTGAGTTGGTAATAAACTTAATTCAGGGTAATTAAGTGAG-T
* *
19670 CAATGAGT
64 CAGT-AAT
* *
19678 -AACTTAATTCAGGGTAATTAAGTGAGTCGGTAATCAACTTAATTCAGGGTAATTAAGTGAGTCA
1 CAACTTAATTCAGGGTAATTAAGTGAGTTGGTAATAAACTTAATTCAGGGTAATTAAGTGAGTCA
19742 GTAAT
66 GTAAT
*
19747 CAACTTAATTCAGGATAATTAAGT
1 CAACTTAATTCAGGGTAATTAAGT
19771 TTAGTAAGAA
Statistics
Matches: 144, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
69 2 0.01
70 82 0.57
71 58 0.40
72 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (70 bp):
CAACTTAATTCAGGGTAATTAAGTGAGTTGGTAATAAACTTAATTCAGGGTAATTAAGTGAGTCA
GTAAT
Found at i:19768 original size:105 final size:106
Alignment explanation
Indices: 19572--19770 Score: 337
Period size: 105 Copynumber: 1.9 Consensus size: 106
19562 GTTGGTAATA
*
19572 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTTA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTCA
*
19637 ATAAGAAACTTAATTCAGGGTAATTAAGTAGTTCAATGAGT
66 ATAAGAAACTTAATTCAGGATAATTAAGTAGTTCAATGAGT
*
19678 AACTTAATTCAGGGTAATTAAGTGAGTCGGTAATCAAC-TTAATTCAGGGTAATTAAGTGAGTCA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTCA
* **
19742 GTAATCAACTTAATTCAGGATAATTAAGT
66 ATAAGAAACTTAATTCAGGATAATTAAGT
19771 TTAGTAAGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
105 50 0.57
106 37 0.43
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (106 bp):
AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTCA
ATAAGAAACTTAATTCAGGATAATTAAGTAGTTCAATGAGT
Found at i:19834 original size:55 final size:56
Alignment explanation
Indices: 19750--19890 Score: 137
Period size: 55 Copynumber: 2.5 Consensus size: 56
19740 CAGTAATCAA
* * * * *
19750 CTTAATTCAGGATAATTAAGTTTAG-TAAGAAGCAGAGATTAG-GGA-A-AATAAATGG
1 CTTAATTCAGGGTAATTGAG-TCAGTTAAGAAGCAGAGA-AAGAGAACAGAATAAAT-G
* *
19805 CTTAATTCAGGGTAATTGAGTCAGTTAAGAATCAGAGAAAGATAATCAGTAATAAATG
1 CTTAATTCAGGGTAATTGAGTCAGTTAAGAAGCAGAGAAAGAGAA-CAG-AATAAATG
*
19863 CTTAATTCAGGGTAATTGAGTCAATTAA
1 CTTAATTCAGGGTAATTGAGTCAGTTAA
19891 AAACAAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
54 5 0.07
55 31 0.43
57 1 0.01
58 28 0.39
59 7 0.10
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (56 bp):
CTTAATTCAGGGTAATTGAGTCAGTTAAGAAGCAGAGAAAGAGAACAGAATAAATG
Found at i:24536 original size:17 final size:18
Alignment explanation
Indices: 24504--24538 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24494 AAGTGCATAA
*
24504 AAAAAAGGAGAGAAAAAG
1 AAAAAAGAAGAGAAAAAG
24522 AAAAAAGAAGA-AAAAAG
1 AAAAAAGAAGAGAAAAAG
24539 CTCTAGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAGAGAAAAAG
Found at i:25770 original size:34 final size:35
Alignment explanation
Indices: 25679--25773 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
25669 TCAGTTAATC
* * *
25679 GATCCAGGGCGATCTTTCTTCAGTTAATTTCAATT
1 GATCCAGGGCGATCTTTCTTCAATTTACTTCAATT
* * *
25714 GGTCCAAGGCGATCATTCTTCAATTTACTTCAA-T
1 GATCCAGGGCGATCTTTCTTCAATTTACTTCAATT
* *
25748 GATCCAGGGTGGTCTTTCTTCAATTT
1 GATCCAGGGCGATCTTTCTTCAATTT
25774 TCCTAATTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 22 0.45
35 27 0.55
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (35 bp):
GATCCAGGGCGATCTTTCTTCAATTTACTTCAATT
Found at i:25936 original size:71 final size:71
Alignment explanation
Indices: 25853--26165 Score: 289
Period size: 71 Copynumber: 4.4 Consensus size: 71
25843 GTTCAGTTCC
* * * *
25853 GAATGATCGAGGGTGGTCGTTTC-TCAGTTTATTTCAGTTGACCCAGGGTGGACTTTCTTTAGGT
1 GAATGATCGAGGGTGGTCGTTTCTTCAGTTTATGTCAGATGACCCAGGGTGGTCTTTCTTCA-GT
*
25917 TGAGTCA
65 TGAGTCG
* * * * * * *
25924 GAATGATCGAGGGTGGTTG-TTCTTCAGTTTATGACGGAATGATCGAGGCTGGTCGTTCTTCAGT
1 GAATGATCGAGGGTGGTCGTTTCTTCAGTTTATGTCAG-ATGACCCAGGGTGGTCTTTCTTCAGT
* *
25988 TCAGTTTG
65 TGAG-TCG
* * *
25996 GAATGATCGAGGGTGGT-ATTTCTTCAGTATTGA-GTCAAGATGATCGAGGGTGGT-TGTTCTTC
1 GAATGATCGAGGGTGGTCGTTTCTTCAGT-TT-ATGTC-AGATGACCCAGGGTGGTCT-TTCTTC
*
26058 AGTTTAGTCCG
62 AGTTGAGT-CG
* * *
26069 GAATGATCGAGGGTGGTCG-TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCATTCTTCAGTT
1 GAATGATCGAGGGTGGTCGTTTCTTCAGTTTATGTCAGATGACCCAGGGTGGTCTTTCTTCAG-T
*
26133 TGCGTCG
65 TGAGTCG
*
26140 GAATGATTGAGGGTGGTCG-TTCTTCA
1 GAATGATCGAGGGTGGTCGTTTCTTCA
26166 ATTCAGTTTG
Statistics
Matches: 199, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
70 3 0.02
71 84 0.42
72 53 0.27
73 57 0.29
74 2 0.01
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (71 bp):
GAATGATCGAGGGTGGTCGTTTCTTCAGTTTATGTCAGATGACCCAGGGTGGTCTTTCTTCAGTT
GAGTCG
Found at i:26062 original size:180 final size:180
Alignment explanation
Indices: 25855--26203 Score: 416
Period size: 180 Copynumber: 1.9 Consensus size: 180
25845 TCAGTTCCGA
* * * * *
25855 ATGATCGAGGGTGGTCGTTTCTCAGTTTATTTCAG-TTGACCCAGGGTGGACTTTCTTTAGGTTG
1 ATGATCGAGGGTGGTCGTTTCTCAGTTTAGTCCAGAATGACCCAGGGTGGACGTTCTTCA-GTTG
* * ** *
25919 A-GTCAGAATGATCGAGGGTGGTTGTTCTTCAGTTTATGACGGAATGATCGAGGCTGGTCGTTCT
65 ATGTCAG-ATGACCCAGGGTGGTCATTCTTCAGTTTACGACGGAATGATCGAGGCTGGTCGTTCT
* * *
25983 TCAGTTCAGTTTGGAATGATCGAGGGTGGTATTTCTTCAGTATTGAGTCAAG
129 TCAATTCAGTTTGGAATGATCCAGGGTGGTATTTCTGCAGTATTGAGTCAAG
* * * * * *
26035 ATGATCGAGGGTGGTTG-TTCTTCAGTTTAGTCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTT
1 ATGATCGAGGGTGGTCGTTTC-TCAGTTTAGTCCAGAATGACCCAGGGTGGACGTTCTTCAGTTG
* * * * * *
26099 ATTTCAGTTGACCCAGGGTGGTCATTCTTCAGTTTGCGTCGGAATGATTGAGGGTGGTCGTTCTT
65 ATGTCAGATGACCCAGGGTGGTCATTCTTCAGTTTACGACGGAATGATCGAGGCTGGTCGTTCTT
*
26164 CAATTCAGTTTGGAATGATCCAGGGTGGTTTTTCTGCAGT
130 CAATTCAGTTTGGAATGATCCAGGGTGGTATTTCTGCAGT
26204 TACTTATTTT
Statistics
Matches: 140, Mismatches: 26, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
179 3 0.02
180 115 0.82
181 22 0.16
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.37
Consensus pattern (180 bp):
ATGATCGAGGGTGGTCGTTTCTCAGTTTAGTCCAGAATGACCCAGGGTGGACGTTCTTCAGTTGA
TGTCAGATGACCCAGGGTGGTCATTCTTCAGTTTACGACGGAATGATCGAGGCTGGTCGTTCTTC
AATTCAGTTTGGAATGATCCAGGGTGGTATTTCTGCAGTATTGAGTCAAG
Found at i:26192 original size:36 final size:36
Alignment explanation
Indices: 25837--26192 Score: 253
Period size: 36 Copynumber: 9.9 Consensus size: 36
25827 GGGTAGTTGC
* *
25837 TCTTAAGTTCAGTTCCGAATGATCGAGGGTGGTCGT
1 TCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGT
* * * * * * * *
25873 T-TCTCAGTTTATTTCAG-TTGACCCAGGGTGGACTT
1 TCT-TCAGTTCAGTTCGGAATGATCGAGGGTGGTCGT
* * * *
25908 TCTTTAGGTTGAG-TCAGAATGATCGAGGGTGGTTGT
1 TCTTCA-GTTCAGTTCGGAATGATCGAGGGTGGTCGT
* * *
25944 TCTTCAGTTTA-TGACGGAATGATCGAGGCTGGTCGT
1 TCTTCAGTTCAGT-TCGGAATGATCGAGGGTGGTCGT
* **
25980 TCTTCAGTTCAGTTTGGAATGATCGAGGGTGGTATT
1 TCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGT
* * *
26016 TCTTCAGTATTGAG-TC-AAGATGATCGAGGGTGGTTGT
1 TCTTCAG--TTCAGTTCGGA-ATGATCGAGGGTGGTCGT
* *
26053 TCTTCAGTTTAGTCCGGAATGATCGAGGGTGGTCGT
1 TCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGT
* * * * * * *
26089 TCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCAT
1 TCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGT
*
26124 TCTTCAGTTTGC-G-TCGGAATGATTGAGGGTGGTCGT
1 TCTTCAG-TT-CAGTTCGGAATGATCGAGGGTGGTCGT
* * *
26160 TCTTCAATTCAGTTTGGAATGATCCAGGGTGGT
1 TCTTCAGTTCAGTTCGGAATGATCGAGGGTGGT
26193 TTTTCTGCAG
Statistics
Matches: 245, Mismatches: 58, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
34 1 0.00
35 56 0.23
36 158 0.64
37 26 0.11
38 4 0.02
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.36
Consensus pattern (36 bp):
TCTTCAGTTCAGTTCGGAATGATCGAGGGTGGTCGT
Found at i:30015 original size:35 final size:35
Alignment explanation
Indices: 29969--30138 Score: 229
Period size: 35 Copynumber: 4.9 Consensus size: 35
29959 GTGAATCAGT
* *
29969 AATAAACAACTTAATTCAGGGTAATTAAGTGAGTT
1 AATAATCAACTTAATTCAGGGTAATTAAGTGAGTC
*
30004 AAT-ATGTAACTTAATTCAGGGTAATTAAGT-AGTTC
1 AATAAT-CAACTTAATTCAGGGTAATTAAGTGAG-TC
*
30039 AATGAGT-AACTTAATTCAGGGTAATTAAGTGAGTC
1 AAT-AATCAACTTAATTCAGGGTAATTAAGTGAGTC
**
30074 GGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AATAATCAACTTAATTCAGGGTAATTAAGTGAGTC
*
30109 AGTAATCAACTTAATTCAGGGTAATTAAGT
1 AATAATCAACTTAATTCAGGGTAATTAAGT
30139 TTAGTAAGAA
Statistics
Matches: 121, Mismatches: 8, Indels: 12
0.86 0.06 0.09
Matches are distributed among these distances:
34 5 0.04
35 113 0.93
36 2 0.02
37 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (35 bp):
AATAATCAACTTAATTCAGGGTAATTAAGTGAGTC
Found at i:30098 original size:19 final size:19
Alignment explanation
Indices: 30074--30133 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
30064 TAAGTGAGTC
30074 GGTAATCAACTTAATTCAG
1 GGTAATCAACTTAATTCAG
* * * *
30093 GGTAATTAA-GTGAGTCA-
1 GGTAATCAACTTAATTCAG
30110 -GTAATCAACTTAATTCAG
1 GGTAATCAACTTAATTCAG
30128 GGTAAT
1 GGTAAT
30134 TAAGTTTAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
18 5 0.17
19 13 0.43
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (19 bp):
GGTAATCAACTTAATTCAG
Found at i:31094 original size:25 final size:25
Alignment explanation
Indices: 31036--31099 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
31026 TATGTGATTT
*
31036 CTTAACGCAAGCACAGGCTCGTTTG
1 CTTAACGCAAGCACAGGCGCGTTTG
*
31061 CTAAACGCAAGCACAGGCGCGTTTG
1 CTTAACGCAAGCACAGGCGCGTTTG
* *
31086 CTTAGCGCACGCAC
1 CTTAACGCAAGCAC
31100 GTTATATTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (25 bp):
CTTAACGCAAGCACAGGCGCGTTTG
Found at i:33430 original size:27 final size:27
Alignment explanation
Indices: 33391--33446 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
33381 TAAGAAGCAT
* *
33391 ACTACAATTGCACCTCAGCAATCGCCC
1 ACTAAAATCGCACCTCAGCAATCGCCC
*
33418 ACTAAAATCGCACCTCATCAATCGCCC
1 ACTAAAATCGCACCTCAGCAATCGCCC
33445 AC
1 AC
33447 CTGGATGCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.41, G:0.09, T:0.18
Consensus pattern (27 bp):
ACTAAAATCGCACCTCAGCAATCGCCC
Found at i:38350 original size:7 final size:7
Alignment explanation
Indices: 38327--38366 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
38317 TTTTGAGGAA
38327 ATATATT
1 ATATATT
*
38334 ATTGTATT
1 A-TATATT
38342 ATATATT
1 ATATATT
38349 ATATATT
1 ATATATT
38356 ATATATT
1 ATATATT
38363 ATAT
1 ATAT
38367 CTGAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (7 bp):
ATATATT
Found at i:40065 original size:21 final size:19
Alignment explanation
Indices: 40035--40074 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
40025 CGAGCCCGAT
40035 ATCAAAATAATATTAAAAAA
1 ATCAAAATAAT-TTAAAAAA
40055 ATCAAGAATAATTTATAAAA
1 ATCAA-AATAATTTA-AAAA
40075 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (19 bp):
ATCAAAATAATTTAAAAAA
Found at i:42186 original size:17 final size:17
Alignment explanation
Indices: 42164--42205 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
42154 AAAGTGAACA
42164 CGAACCCGACCCG-GACC
1 CGAACCCGACCCGAG-CC
*
42181 CGAACCCGATCCGAGCC
1 CGAACCCGACCCGAGCC
42198 CGAACCCG
1 CGAACCCG
42206 GAAATACCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.24, C:0.50, G:0.24, T:0.02
Consensus pattern (17 bp):
CGAACCCGACCCGAGCC
Found at i:42217 original size:16 final size:16
Alignment explanation
Indices: 42196--42252 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
42186 CCGATCCGAG
42196 CCCGAACCCGGAAATA
1 CCCGAACCCGGAAATA
*
42212 CCCGAACCCGAAAATA
1 CCCGAACCCGGAAATA
*
42228 CCCGAACCC-GAAGTA
1 CCCGAACCCGGAAATA
42243 CCCGAACCCG
1 CCCGAACCCG
42253 CCCGAACCCG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 13 0.35
16 24 0.65
ACGTcount: A:0.35, C:0.42, G:0.18, T:0.05
Consensus pattern (16 bp):
CCCGAACCCGGAAATA
Found at i:43889 original size:2 final size:2
Alignment explanation
Indices: 43854--43879 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43844 TTATAGTATG
43854 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
43880 AGAAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48054 original size:49 final size:48
Alignment explanation
Indices: 47975--48245 Score: 272
Period size: 49 Copynumber: 5.5 Consensus size: 48
47965 CTTATACTTA
* * *
47975 CAAAAGCGCCCTTACCGAACGGAAGGCACCAATTTTTACTTGTCATTTCC
1 CAAAA-CGCCCTTCCCGGACGGAAGACACCAATTTTTACTTG-CATTTCC
* *
48025 TAAAACGCCCTTCCCGGACGGAAGTCACCAATTTTTACTTGTCATTTCC
1 CAAAACGCCCTTCCCGGACGGAAGACACCAATTTTTACTTG-CATTTCC
* * *** *
48074 CAAAACACCCTTCCCGGGCGGAAGACATTTATTTTTACTTACTATTTCC
1 CAAAACGCCCTTCCCGGACGGAAGACACCAATTTTTACTTGC-ATTTCC
* * ** *
48123 CAAAACGCCCTTCGCGGATGGAAGACACTTATTTTTACTTGCTTTTCCC
1 CAAAACGCCCTTCCCGGACGGAAGACACCAATTTTTACTTGCATTT-CC
* * *
48172 CAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGCTTTTTCC
1 CAAAACGCCCTTCCCGGACGGAAGACACCAATTTTTACTTGC-ATTTCC
* * * *
48221 TAAAAACGGCTTTCTCGGACGGAAG
1 -CAAAACGCCCTTCCCGGACGGAAG
48246 GTATTTTTTT
Statistics
Matches: 187, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
48 4 0.02
49 156 0.83
50 27 0.14
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (48 bp):
CAAAACGCCCTTCCCGGACGGAAGACACCAATTTTTACTTGCATTTCC
Found at i:48256 original size:98 final size:98
Alignment explanation
Indices: 47975--48296 Score: 310
Period size: 98 Copynumber: 3.3 Consensus size: 98
47965 CTTATACTTA
* * *
47975 CAAAAGCGCCCTTACCGAACGGAAGGCACCAATTTTTACTTG-TCATTTCCTAAAACGCCCTTCC
1 CAAAA-CGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGCT-ATTTCCTAAAACGCCCTTCC
** *
48039 CGGACGGAA-GTCACCAATTTTTACTTGTCATTTCC
64 CGGACGGAAGGT-ACTTATTTTTACTTGCCATTTCC
* * * * *** * * *
48074 CAAAACACCCTTCCCGGGCGGAAGACATTTATTTTTACTTACTATTTCCCAAAACGCCCTTCGCG
1 CAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGCTATTTCCTAAAACGCCCTTCCCG
* ** *
48139 GATGGAAGACACTTATTTTTACTTG-CTTTTCCC
66 GACGGAAGGTACTTATTTTTACTTGCCATTT-CC
* * * *
48172 CAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGCTTTTTCCTAAAAACGGCTTTCTC
1 CAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGCTATTTCCT-AAAACGCCCTTCCC
* *
48237 GGACGGAAGGTA-TTTTTTTTACCTGCCATTTCC
65 GGACGGAAGGTACTTATTTTTACTTGCCATTTCC
* * *
48270 CAAAATGCCCTTTCCAGACGAAAGGCA
1 CAAAACGCCCTTCCCGGACGAAAGGCA
48297 AGTTTATTTT
Statistics
Matches: 179, Mismatches: 39, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
97 4 0.02
98 145 0.81
99 30 0.17
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.30
Consensus pattern (98 bp):
CAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGCTATTTCCTAAAACGCCCTTCCCG
GACGGAAGGTACTTATTTTTACTTGCCATTTCC
Found at i:48256 original size:147 final size:147
Alignment explanation
Indices: 48006--48281 Score: 353
Period size: 147 Copynumber: 1.9 Consensus size: 147
47996 GAAGGCACCA
* * *
48006 ATTTTTACTTGTCATTTCCTAAAACGCCCTTCCCGGACGGAAGTCACCAATTTTTACTTGTCATT
1 ATTTTTACTTGTCATTTCCCAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGTCATT
* * *
48071 TCCCAAAACACCCTTCCCGGGCGGAAGACATTTATTTTTACTTACTATTTCCCAAAACGCCCTTC
66 TCCCAAAACACCCTTCCCGGACGGAAGACATTTATTTTTACCTACCATTTCCCAAAACGCCCTTC
48136 GCGGATGGAAGACACTT
131 GCGGATGGAAGACACTT
* *
48153 ATTTTTACTTG-CTTTTCCCCAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTG-CTT
1 ATTTTTACTTGTCATTT-CCCAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGTC-A
* * * ** * *
48216 TTTCCTAAAA-ACGGCTTTCTCGGACGGAAGGTATTT-TTTTTACCTGCCATTTCCCAAAATGCC
64 TTTCCCAAAACAC--CCTTCCCGGACGGAAGACATTTATTTTTACCTACCATTTCCCAAAACGCC
48279 CTT
127 CTT
48282 TCCAGACGAA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
146 7 0.06
147 86 0.78
148 17 0.15
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (147 bp):
ATTTTTACTTGTCATTTCCCAAAACGCCCTTCCCGGACGAAAGGCACCAATTTTTACTTGTCATT
TCCCAAAACACCCTTCCCGGACGGAAGACATTTATTTTTACCTACCATTTCCCAAAACGCCCTTC
GCGGATGGAAGACACTT
Found at i:48808 original size:58 final size:58
Alignment explanation
Indices: 48718--48834 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
48708 CGTTGCAACA
*
48718 GGCATTTAGCCTGGTGATAGAGTACTGGACTCTTAGTTCCAGCCTACCTAGACCATGG
1 GGCATTTAGCCTGGTGATAGAGTACTGGACTCTTAGTTCCAACCTACCTAGACCATGG
* * *
48776 GGCATTTGGCTTGGTGGTAGAGTACTGGACTCTTAGTTCCAACCTACCTAGACCATGG
1 GGCATTTAGCCTGGTGATAGAGTACTGGACTCTTAGTTCCAACCTACCTAGACCATGG
48834 G
1 G
48835 TCTTAGGTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.28
Consensus pattern (58 bp):
GGCATTTAGCCTGGTGATAGAGTACTGGACTCTTAGTTCCAACCTACCTAGACCATGG
Found at i:48908 original size:27 final size:28
Alignment explanation
Indices: 48878--48943 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 28
48868 TTTGTAATTT
*
48878 GTTTATTTATGTATTTGATAG-TAGGTA
1 GTTTATTTATGTATTTGATAGATAGATA
*
48905 GTTTATTTATGTATTTGGTAGATAGATA
1 GTTTATTTATGTATTTGATAGATAGATA
48933 GTTTATTTATG
1 GTTTATTTATG
48944 GGCATAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (28 bp):
GTTTATTTATGTATTTGATAGATAGATA
Found at i:57623 original size:19 final size:21
Alignment explanation
Indices: 57577--57624 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
57567 TGTGGCACGC
*
57577 CACATGTACCAAAAAATCGTGC
1 CACATGTACCAAAAAA-CGTGA
57599 CACATGTACC-AAAAA-GTGA
1 CACATGTACCAAAAAACGTGA
57618 CACATGT
1 CACATGT
57625 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
21 5 0.20
22 10 0.40
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (21 bp):
CACATGTACCAAAAAACGTGA
Found at i:57629 original size:53 final size:53
Alignment explanation
Indices: 57544--57644 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 53
57534 GACATGGCAC
**
57544 GCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAATCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAATCGT
* *
57597 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAA
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAA
57645 GTGACACGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.39, C:0.28, G:0.18, T:0.16
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAATCGT
Found at i:62550 original size:12 final size:12
Alignment explanation
Indices: 62533--62564 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
62523 ATGTTGGAAG
62533 AACCAAACCAAA
1 AACCAAACCAAA
62545 AACCAAACCAAA
1 AACCAAACCAAA
62557 AACCAAAC
1 AACCAAAC
62565 AATTGAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (12 bp):
AACCAAACCAAA
Found at i:62924 original size:13 final size:13
Alignment explanation
Indices: 62906--62932 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62896 TCTTAGTACC
62906 AAAAAAAAAACAA
1 AAAAAAAAAACAA
62919 AAAAAAAAAACAA
1 AAAAAAAAAACAA
62932 A
1 A
62933 TACTTGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Done.