Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3257
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: 54005
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7375 original size:38 final size:41
Alignment explanation
Indices: 7332--7441 Score: 129
Period size: 38 Copynumber: 2.8 Consensus size: 41
7322 GTAATTCAAA
* *
7332 AATAATAAACATTATATAATATCATATTTCCTACATTATAT
1 AATAATAAACATTATATAATATCATATTTCCTAAACTATAT
* * * *
7373 AATAACATAA-ATTATATAATA--A-ACTACATAAACTATAT
1 AATAATA-AACATTATATAATATCATATTTCCTAAACTATAT
7411 AATAATAAACATTATATAATATCATATTTCC
1 AATAATAAACATTATATAATATCATATTTCC
7442 CACAACGCGC
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
37 2 0.04
38 28 0.52
39 1 0.02
40 1 0.02
41 20 0.37
42 2 0.04
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (41 bp):
AATAATAAACATTATATAATATCATATTTCCTAAACTATAT
Found at i:7388 original size:17 final size:17
Alignment explanation
Indices: 7366--7436 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 17
7356 TATTTCCTAC
7366 ATTATATAATAACATAA
1 ATTATATAATAACATAA
7383 ATTATATAATAAACTACATAA
1 ATTATATAAT--A--ACATAA
* *
7404 ACTATATAATAATA-AA
1 ATTATATAATAACATAA
*
7420 CATTATATAATATCATA
1 -ATTATATAATAACATA
7437 TTTCCCACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
16 2 0.05
17 23 0.53
18 1 0.02
19 2 0.05
21 15 0.35
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTATATAATAACATAA
Found at i:7422 original size:21 final size:21
Alignment explanation
Indices: 7371--7422 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
7361 CCTACATTAT
*
7371 ATAAT-AACATAAATTATATA
1 ATAATAAACATAAACTATATA
*
7391 ATAA-ACTACATAAACTATATA
1 ATAATA-AACATAAACTATATA
7412 ATAATAAACAT
1 ATAATAAACAT
7423 TATATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.15
21 21 0.81
22 1 0.04
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATAAACATAAACTATATA
Found at i:7605 original size:113 final size:113
Alignment explanation
Indices: 7448--7797 Score: 357
Period size: 113 Copynumber: 3.1 Consensus size: 113
7438 TTCCCACAAC
* * * *
7448 GCGCCGCTAATAATATGTTTTAGCGGCG-TTTAACCATAAGCGCCAC-AACTGCTAGTATACATC
1 GCGCCACTAATACTATGCTTTAGCGGCGTTTTAA-CATAAGCGCCACTAA-TGCTAATATACATC
*
7511 AAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCACTTTACAATAA
64 AAGACCAAAGCACTGCGTTTTGGTTAATATTTTGCGGCACTTTACAATAA
* * * * * *
7561 GCGCCGCTAATACTTTGCTTTAGCGGCGTTTTCAA-ATAAACGCCACTAATCCTAATGTACCTCA
1 GCGCCACTAATACTATGCTTTAGCGGCGTTTT-AACATAAGCGCCACTAATGCTAATATACATCA
* * * * * * * * * *
7625 AGACCAAA-CTCTGCATTTTTGTTAAGAAATATTGGGGCGCTTTTCAGTAC
65 AGACCAAAGCACTGCGTTTTGGTT-A-ATATTTTGCGGCACTTTACAATAA
* * * * * *
7675 TCGCCACTAATACTATACTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTACTATACATTAA
1 GCGCCACTAATACTATGCTTTAGCGGCGTTTTAACATAAGCGCCACTAATGCTAATATACATCAA
* * *
7740 GACCAAAGCACTGCGTTTTGGTTAATCTTTTGCGGCATTTTCCAATAA
66 GACCAAAGCACTGCGTTTTGGTTAATATTTTGCGGCACTTTACAATAA
7788 GCGCCACTAA
1 GCGCCACTAA
7798 GCCTAATATA
Statistics
Matches: 188, Mismatches: 42, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
112 12 0.06
113 81 0.43
114 81 0.43
115 14 0.07
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (113 bp):
GCGCCACTAATACTATGCTTTAGCGGCGTTTTAACATAAGCGCCACTAATGCTAATATACATCAA
GACCAAAGCACTGCGTTTTGGTTAATATTTTGCGGCACTTTACAATAA
Found at i:7742 original size:114 final size:112
Alignment explanation
Indices: 7448--7797 Score: 312
Period size: 114 Copynumber: 3.1 Consensus size: 112
7438 TTCCCACAAC
* * ** * *
7448 GCGCCGCTAATAATATGTTTTAGCGGCGTTTAACCATAAGCGCCAC-AACTGCTAGTATACATCA
1 GCGCCACTAATACTATACTTTAGCGGCTTTTAA--ATAAGCGCCACTAA-TGCTAATATACATCA
* * *
7512 AGACCAAAGCGCTGCGTTTTGGTT-AATATTTTGCGGCACTTTACAATAA
63 AGACCAAAGCACTGCGTTTTGGTTAAAAATATTGCGGCACTTTACAATAA
* * * * * * *
7561 GCGCCGCTAATACTTTGCTTTAGCGGCGTTTTCAAATAAACGCCACTAATCCTAATGTACCTCAA
1 GCGCCACTAATACTATACTTTAGCGGC-TTTT-AAATAAGCGCCACTAATGCTAATATACATCAA
* * * * * * * *
7626 GACCAAA-CTCTGCATTTTTGTTAAGAAATATTGGGGCGCTTTTCAGTAC
64 GACCAAAGCACTGCGTTTTGGTTAA-AAATATTGCGGCACTTTACAATAA
* * *
7675 TCGCCACTAATACTATACTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTACTATACATTAA
1 GCGCCACTAATACTATACTTTAGCGGC-TTTTAA-ATAAGCGCCACTAATGCTAATATACATCAA
** * * *
7740 GACCAAAGCACTGCGTTTTGGTT-AATCTTTTGCGGCATTTTCCAATAA
64 GACCAAAGCACTGCGTTTTGGTTAAAAATATTGCGGCACTTTACAATAA
7788 GCGCCACTAA
1 GCGCCACTAA
7798 GCCTAATATA
Statistics
Matches: 187, Mismatches: 43, Indels: 14
0.77 0.18 0.06
Matches are distributed among these distances:
112 12 0.06
113 80 0.43
114 81 0.43
115 14 0.07
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (112 bp):
GCGCCACTAATACTATACTTTAGCGGCTTTTAAATAAGCGCCACTAATGCTAATATACATCAAGA
CCAAAGCACTGCGTTTTGGTTAAAAATATTGCGGCACTTTACAATAA
Found at i:7818 original size:74 final size:73
Alignment explanation
Indices: 7692--7837 Score: 188
Period size: 74 Copynumber: 2.0 Consensus size: 73
7682 TAATACTATA
* **
7692 CTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTACTATACATTAAGACCAAAGCACTGCGTT
1 CTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTAATATACAGCAAGACCAAA-CACTGCGTT
7757 TTGGTTAAT
65 TTGGTTAAT
* * * *
7766 CTTTTGCGGCATTTTCCA-ATAAGCGCCACTAA-GCCTAATATACCGCAAGACCAAACTCTGCGT
1 CTTTAGCGGCATTTT-AATATAAGCGCCACTAATG-CTAATATACAGCAAGACCAAACACTGCGT
7829 TTTGGTTAA
64 TTTGGTTAA
7838 GAAATCTTAC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 17 0.27
74 45 0.71
75 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (73 bp):
CTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTAATATACAGCAAGACCAAACACTGCGTTT
TGGTTAAT
Found at i:7924 original size:188 final size:188
Alignment explanation
Indices: 7578--7979 Score: 572
Period size: 188 Copynumber: 2.1 Consensus size: 188
7568 TAATACTTTG
* * * * * *
7578 CTTTAGCGGCGTTTTCAAATAAACGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCATTT
1 CTTTTGCGGCGTTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCATTT
* ** * *
7643 TTGTTAAGAAATATTGGGGCGCTTTTCAGTACTCGCCACTAATACTATACTTTAGCGGCATTTTA
66 TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCACTAATACTATACTTTAGCGACATTTTA
*
7708 ATATAAGCGCCACTAATGCTACTATACATTAAGACCAAAGCACTGCGTTTTGGTTAAT
131 ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGTTAAT
* *
7766 CTTTTGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 CTTTTGCGGCGTTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCATTT
* * *
7831 TGGTTAAGAAATCTTACGGCGCTTTTCACTACTCGCCGCTAATACTATGA-TTTAGCGACGTTTT
66 TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCACTAATACTAT-ACTTTAGCGACATTTT
* * * *
7895 AATATAAGCGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
130 AATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGTTAAT
* * *
7954 ATTTTGCGGCGCTTTACAATAAGCGC
1 CTTTTGCGGCGTTTTCCAATAAGCGC
7980 TGCAAATACT
Statistics
Matches: 188, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
188 187 0.99
189 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (188 bp):
CTTTTGCGGCGTTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCATTT
TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCACTAATACTATACTTTAGCGACATTTTA
ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGTTAAT
Found at i:8080 original size:227 final size:228
Alignment explanation
Indices: 7766--8196 Score: 659
Period size: 227 Copynumber: 1.9 Consensus size: 228
7756 TTTGGTTAAT
*
7766 CTTTTGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 CTTTAGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
*
7831 TGGTTAAGAAATCTTACGGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACGTTTTA
66 TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACGTTTTA
* * *
7896 ATATAAGCGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATAT-T-TT
131 ATATAAGCGCCACTAATGCTAGTATACATCAAGACCAAA-CGCTGCGTTTTGGTTAAGATGTATT
7959 GCGGCGCTTTACAATAAGCGCTGCAAATACTATG
195 GCGGCGCTTTACAATAAGCGCTGCAAATACTATG
* * * * *
7993 CTTTAGCGGCGTTTTTCGATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTT
1 CTTTAGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
* ** * *
8058 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCGGCGTTTTT
66 TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACGTTTTA
* * * * *
8123 GTATGAGCGCCACTAATGCTAGTGTACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATGTATTG
131 ATATAAGCGCCACTAATGCTAGTATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATGTATTG
8188 CGGCGCTTT
196 CGGCGCTTT
8197 TTGCGACTCG
Statistics
Matches: 182, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
226 18 0.10
227 152 0.84
228 12 0.07
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (228 bp):
CTTTAGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACGTTTTA
ATATAAGCGCCACTAATGCTAGTATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATGTATTG
CGGCGCTTTACAATAAGCGCTGCAAATACTATG
Found at i:8120 original size:114 final size:114
Alignment explanation
Indices: 7783--8253 Score: 570
Period size: 114 Copynumber: 4.1 Consensus size: 114
7773 GGCATTTTCC
* * * *
7783 AATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTTAAGAAATCTTAC
1 AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
* *
7848 GGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACG-TTTTA
66 GGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
* ** * * * * *
7896 ATATAAGCGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTT-A-ATATTTT
1 A-ATAAGCGCCACTAATCCTAATATACCTCAAGACCAAA-CTCTGCGTTTTGGTTAAGAAATATT
* * ** * * *
7959 GCGGCGCTTTACAATAAGCGCTGCAAATACTATGCTTTAGCGGCGTTTTTC
64 GCGGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
*
8010 GATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
1 AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
* *
8075 GGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCGGCGTTTTTG
66 GGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
* * * * * **
8124 TATGAGCGCCACTAATGCTAGTGTACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATGTATTGC
1 AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
** * * * *
8189 GGCGCTTTTTGCGACTCGCCGCTAATTCTATGCTTTAGCGGTGATTTTA
66 GGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
8238 AATAAGCGCCACTAAT
1 AATAAGCGCCACTAAT
8254 ACTTTCTTTA
Statistics
Matches: 299, Mismatches: 54, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
112 14 0.05
113 75 0.25
114 196 0.66
115 14 0.05
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (114 bp):
AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
GGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
Found at i:9132 original size:14 final size:13
Alignment explanation
Indices: 9106--9164 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
9096 AGGCCAACAT
9106 TATATATTGCATA
1 TATATATTGCATA
9119 TATATATATGCATA
1 TATATAT-TGCATA
*
9133 TA-AAAGTGCTGC-TA
1 TATATA-T--TGCATA
9147 TTATATATTGCATA
1 -TATATATTGCATA
9161 TATA
1 TATA
9165 CAATTGGCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 16 0.43
14 13 0.35
15 6 0.16
16 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (13 bp):
TATATATTGCATA
Found at i:9431 original size:26 final size:25
Alignment explanation
Indices: 9402--9450 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
9392 TCACAAAAAA
9402 TTTTAAAATATCATTTAAACTTTTTT
1 TTTTAAAATATCA-TTAAACTTTTTT
* * *
9428 TTTTCAATTTTCATTAAACTTTT
1 TTTTAAAATATCATTAAACTTTT
9451 AAAATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTAAAATATCATTAAACTTTTTT
Found at i:11479 original size:24 final size:25
Alignment explanation
Indices: 11451--11531 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 25
11441 GTGATATATT
11451 TAATACATAATA-ATTTTAAAATAA
1 TAATACATAATATATTTTAAAATAA
* *
11475 TAATACATAATATCTTTTTTTTAAAT-A
1 TAATACATAATA---TATTTTAAAATAA
*
11502 TGAATACATAATACA-TTTAAAATAA
1 T-AATACATAATATATTTTAAAATAA
11527 TAATA
1 TAATA
11532 TTGGATAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
24 23 0.50
25 2 0.04
27 2 0.04
28 19 0.41
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (25 bp):
TAATACATAATATATTTTAAAATAA
Found at i:11604 original size:23 final size:23
Alignment explanation
Indices: 11516--11640 Score: 87
Period size: 24 Copynumber: 5.3 Consensus size: 23
11506 TACATAATAC
*
11516 ATTTAAAATAATAATAT-TGGATA
1 ATTTAAAATAATAGTATAT-GATA
* * *
11539 AGTTTTAAATTATAGTATACGATAA
1 A-TTTAAAATAATAGTATATGAT-A
* *
11564 ATTTTAAATTAT-GATATATGATA
1 ATTTAAAATAATAG-TATATGATA
* *
11587 ATTTAAAATGATAGTATATTA-A
1 ATTTAAAATAATAGTATATGATA
*
11609 ATATTAAAATAATACTA-ATGATAA
1 AT-TTAAAATAATAGTATATGAT-A
11633 ATTTAAAA
1 ATTTAAAA
11641 CAATGTTAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
22 6 0.07
23 37 0.45
24 38 0.46
25 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (23 bp):
ATTTAAAATAATAGTATATGATA
Found at i:11656 original size:23 final size:25
Alignment explanation
Indices: 11604--11662 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
11594 ATGATAGTAT
*
11604 ATTAAATATTAAAATAATACTAATG
1 ATTAAATATTAAAACAATACTAATG
**
11629 A-TAAAT-TTAAAACAATGTTAA-G
1 ATTAAATATTAAAACAATACTAATG
11651 ATTAAATATTAA
1 ATTAAATATTAA
11663 CTAGCATTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.07
23 17 0.59
24 9 0.31
25 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (25 bp):
ATTAAATATTAAAACAATACTAATG
Found at i:13104 original size:11 final size:11
Alignment explanation
Indices: 13090--13195 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
13080 ATTTTTTTAA
13090 TTTTAAAATAT
1 TTTTAAAATAT
13101 TTTTAAAATACT
1 TTTTAAAATA-T
*
13113 TGTTT-TAAT-T
1 T-TTTAAAATAT
13123 TTTT---A-A-
1 TTTTAAAATAT
13129 TTTTAAAATAT
1 TTTTAAAATAT
13140 TTTTAAAATACT
1 TTTTAAAATA-T
*
13152 TTTT-TAAT-T
1 TTTTAAAATAT
* *
13161 TTTT---TTAA
1 TTTTAAAATAT
13169 TTTTAAAATAT
1 TTTTAAAATAT
13180 TTTTAAAATACT
1 TTTTAAAATA-T
13192 TTTT
1 TTTT
13196 TTTTAATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
6 4 0.05
7 2 0.03
8 4 0.05
9 9 0.12
10 3 0.04
11 35 0.47
12 15 0.20
13 3 0.04
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:13104 original size:40 final size:41
Alignment explanation
Indices: 13038--13196 Score: 254
Period size: 40 Copynumber: 4.0 Consensus size: 41
13028 TAAATATATT
* * *
13038 TATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTTAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
13079 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTGTTTT-A
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTT-TTTTAA
13120 -A-TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
13159 T-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
13197 TTTAATTTTT
Statistics
Matches: 111, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
38 4 0.04
39 33 0.30
40 37 0.33
41 33 0.30
42 4 0.04
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (41 bp):
TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:13145 original size:17 final size:17
Alignment explanation
Indices: 13073--13106 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13063 TTACATACTT
* *
13073 TTTTAATATTTTTTTAA
1 TTTTAAAATATTTTTAA
13090 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
13107 AATACTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:13201 original size:33 final size:33
Alignment explanation
Indices: 13159--13222 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
13149 ACTTTTTTAA
13159 TTTTTTTTAA-TTTTAAAATATTTTTAAAATACT
1 TTTTTTTTAATTTTTAAAA-ATTTTTAAAATACT
*
13192 TTTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTTTTTAATTTTTAAAAATTTTTAAAATA
13223 AAAATGGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (33 bp):
TTTTTTTTAATTTTTAAAAATTTTTAAAATACT
Found at i:13688 original size:11 final size:11
Alignment explanation
Indices: 13671--13700 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
13661 CTATAGAAGA
13671 ATGTAAAATTT
1 ATGTAAAATTT
*
13682 CTGTAAAATTT
1 ATGTAAAATTT
13693 ATGTAAAA
1 ATGTAAAA
13701 ATCAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (11 bp):
ATGTAAAATTT
Found at i:19608 original size:21 final size:22
Alignment explanation
Indices: 19564--19608 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
19554 TTTTTTGTTA
19564 TTAAGTTTTGCATCAAGTTCTT
1 TTAAGTTTTGCATCAAGTTCTT
*
19586 TTAAGTTTTTCATCAAG-TCTT
1 TTAAGTTTTGCATCAAGTTCTT
19607 TT
1 TT
19609 CATAAAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (22 bp):
TTAAGTTTTGCATCAAGTTCTT
Found at i:26441 original size:16 final size:16
Alignment explanation
Indices: 26420--26454 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
26410 AAAACGCACA
* *
26420 TTTTATTTTATTTTAT
1 TTTTATCTTATCTTAT
26436 TTTTATCTTATCTTAT
1 TTTTATCTTATCTTAT
26452 TTT
1 TTT
26455 GCAGTTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATCTTATCTTAT
Found at i:27867 original size:14 final size:13
Alignment explanation
Indices: 27845--27994 Score: 53
Period size: 13 Copynumber: 11.2 Consensus size: 13
27835 AAGTGTTTTC
*
27845 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
27859 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
27873 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* *
27885 TTAATTACCAAGGTTTTTT
1 TT--TCATCAA-G---TTT
* *
27904 TTGTTATTAAGT-T
1 TT-TCATCAAGTTT
*
27917 TTGCATCAAGTTCT
1 TTTCATCAAGTT-T
27931 TTT--T-AAGT-T
1 TTTCATCAAGTTT
*
27940 TTTCATCAAGTCT
1 TTTCATCAAGTTT
*
27953 TTTCATAAAG-TT
1 TTTCATCAAGTTT
*
27965 TTCCATCAAGTTT
1 TTTCATCAAGTTT
*
27978 TTAATCATTAAGTTT
1 TT--TCATCAAGTTT
27993 TT
1 TT
27995 CAATTAAGCT
Statistics
Matches: 104, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
9 4 0.04
11 5 0.05
12 23 0.22
13 26 0.25
14 19 0.18
15 15 0.14
16 1 0.01
17 1 0.01
18 5 0.05
19 5 0.05
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:27936 original size:23 final size:23
Alignment explanation
Indices: 27910--27976 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
27900 TTTTTTGTTA
*
27910 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
*
27933 TTAAGTTTTTCATCAAG-TCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
27955 TCATAAAGTTTTCCATCAAGTT
1 T--T-AAGTTTTCCATCAAGTT
27977 TTTAATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 1 0.03
25 14 0.37
26 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (23 bp):
TTAAGTTTTCCATCAAGTTCTTT
Found at i:27977 original size:12 final size:12
Alignment explanation
Indices: 27912--27984 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
27902 TTTTGTTATT
*
27912 AAGTTTTGCATC
1 AAGTTTTTCATC
*
27924 AAGTTCTTT--TT
1 AAGTT-TTTCATC
27935 AAGTTTTTCATC
1 AAGTTTTTCATC
*
27947 AAGTCTTTTCATA
1 AAGT-TTTTCATC
*
27960 AAGTTTTCCATC
1 AAGTTTTTCATC
*
27972 AAGTTTTTAATC
1 AAGTTTTTCATC
27984 A
1 A
27985 TTAAGTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 27 0.55
13 13 0.27
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:28002 original size:13 final size:12
Alignment explanation
Indices: 27909--28007 Score: 67
Period size: 12 Copynumber: 7.8 Consensus size: 12
27899 TTTTTTTGTT
*
27909 ATTAAGTTTTGC
1 ATTAAGTTTTTC
*
27921 ATCAAGTTCTTT-
1 ATTAAGTT-TTTC
27933 -TTAAGTTTTTC
1 ATTAAGTTTTTC
*
27944 ATCAAGTCTTTTC
1 ATTAAGT-TTTTC
* *
27957 ATAAAGTTTTCC
1 ATTAAGTTTTTC
*
27969 ATCAAGTTTTTAATC
1 ATTAAG-TTTT--TC
27984 ATTAAGTTTTTC
1 ATTAAGTTTTTC
27996 AATTAAGCTTTT
1 -ATTAAG-TTTT
28008 ATCTCTTGCA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.04
11 6 0.09
12 23 0.33
13 23 0.33
14 8 0.12
15 6 0.09
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (12 bp):
ATTAAGTTTTTC
Found at i:28861 original size:36 final size:37
Alignment explanation
Indices: 28790--28861 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 37
28780 TTATTTAACT
* **
28790 GCATTTTATTATTTTATTTTCAGCTTTTACTTTTTAC
1 GCATTTTATTATTTTATTTTCAGCTTTCAAATTTTAC
*
28827 GCATTTTATT-TATTTA-TTTCAGGTTTCAAATTTTA
1 GCATTTTATTAT-TTTATTTTCAGCTTTCAAATTTTA
28862 TCCCCCCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (37 bp):
GCATTTTATTATTTTATTTTCAGCTTTCAAATTTTAC
Found at i:37001 original size:25 final size:25
Alignment explanation
Indices: 36967--37023 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
36957 CCTTGCCTTC
36967 AGCTTGAATAAGATGACCATTTCCT
1 AGCTTGAATAAGATGACCATTTCCT
36992 AGCTTGAATAAGATGACCATTTCCT
1 AGCTTGAATAAGATGACCATTTCCT
*
37017 ATCTTGA
1 AGCTTGA
37024 CTTTAGTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (25 bp):
AGCTTGAATAAGATGACCATTTCCT
Found at i:42370 original size:3 final size:3
Alignment explanation
Indices: 42362--42394 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
42352 GTGAGATAAG
42362 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42395 GAGTGGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42454 original size:39 final size:39
Alignment explanation
Indices: 42400--42477 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
42390 ATTATGAGTG
42400 GGAATTAAATTGAATAATTGATATGAATTAATATTTGAA
1 GGAATTAAATTGAATAATTGATATGAATTAATATTTGAA
42439 GGAATTAAATTGAATAATTGATATGAATTAATATTTGAA
1 GGAATTAAATTGAATAATTGATATGAATTAATATTTGAA
42478 TTGTTTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (39 bp):
GGAATTAAATTGAATAATTGATATGAATTAATATTTGAA
Found at i:42479 original size:22 final size:22
Alignment explanation
Indices: 42415--42480 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 22
42405 TAAATTGAAT
42415 AATTGATATGAATTAATATTTG
1 AATTGATATGAATTAATATTTG
* * *
42437 AA-GGA-ATTAAATTGA-A--T-
1 AATTGATA-TGAATTAATATTTG
42454 AATTGATATGAATTAATATTTG
1 AATTGATATGAATTAATATTTG
42476 AATTG
1 AATTG
42481 TTTGTTGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 14
0.61 0.12 0.27
Matches are distributed among these distances:
17 2 0.06
18 9 0.29
19 2 0.06
20 2 0.06
21 9 0.29
22 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (22 bp):
AATTGATATGAATTAATATTTG
Found at i:47161 original size:16 final size:16
Alignment explanation
Indices: 47140--47171 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
47130 TTACTACTGA
47140 AGGTTTGTCAAAGGAT
1 AGGTTTGTCAAAGGAT
*
47156 AGGTTTGTCGAAGGAT
1 AGGTTTGTCAAAGGAT
47172 TTTCTCTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.31
Consensus pattern (16 bp):
AGGTTTGTCAAAGGAT
Done.