Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1666
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: 77330
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:570 original size:21 final size:21
Alignment explanation
Indices: 528--577 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
518 CTTGTTTAAT
* *
528 AGTTTAAGGTATTTGAATTTA
1 AGTTTAAGGTAATTGAAATTA
549 AGTTTAAGAGTAATT-AAATTA
1 AGTTTAAG-GTAATTGAAATTA
*
570 AATTTAAG
1 AGTTTAAG
578 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (21 bp):
AGTTTAAGGTAATTGAAATTA
Found at i:2521 original size:6 final size:6
Alignment explanation
Indices: 2510--2535 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2500 TTCCAATCTT
2510 TGTTGC TGTTGC TGTTGC TGTTGC TG
1 TGTTGC TGTTGC TGTTGC TGTTGC TG
2536 CTGTTCATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.35, T:0.50
Consensus pattern (6 bp):
TGTTGC
Found at i:5628 original size:3 final size:3
Alignment explanation
Indices: 5620--5648 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5610 CAAATTAAAA
5620 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5649 AAAGCTTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6681 original size:1 final size:1
Alignment explanation
Indices: 6644--6673 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
6634 CAGAAGAAGT
*
6644 GGGGGGGGGGGGGGGGGGGGGGGGGAGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
6674 AAGGGGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:8099 original size:20 final size:20
Alignment explanation
Indices: 8066--8109 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
8056 TAAAAAATTT
* *
8066 TTAAAAAT-ATTTTATATTA
1 TTAAAAATAATTTAATATAA
8085 TTAAATAATAATTTAATATAA
1 TTAAA-AATAATTTAATATAA
8106 TTAA
1 TTAA
8110 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 13 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAAATAATTTAATATAA
Found at i:8124 original size:17 final size:15
Alignment explanation
Indices: 8089--8130 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
8079 ATATTATTAA
8089 ATAA-TAATTT-AAT
1 ATAATTAATTTAAAT
8102 ATAATTAATTTAAATT
1 ATAATTAATTTAAA-T
8118 ATAAATTAATTTA
1 AT-AATTAATTTA
8131 TTTAAATACG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.16
14 6 0.24
15 2 0.08
16 3 0.12
17 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTAATTTAAAT
Found at i:14341 original size:23 final size:23
Alignment explanation
Indices: 14311--14354 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
14301 TCTTTTAGCC
14311 ATAAATAAAACCAAAAAAAAAAT
1 ATAAATAAAACCAAAAAAAAAAT
* *
14334 ATAAATAAAACTACAAAAAAA
1 ATAAATAAAACCAAAAAAAAA
14355 TAGAACAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (23 bp):
ATAAATAAAACCAAAAAAAAAAT
Found at i:14773 original size:14 final size:15
Alignment explanation
Indices: 14754--14784 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
14744 ACAAATATAC
14754 AATTAAAAGAT-GTA
1 AATTAAAAGATGGTA
14768 AATTAAAAGATGGTA
1 AATTAAAAGATGGTA
14783 AA
1 AA
14785 CATTTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (15 bp):
AATTAAAAGATGGTA
Found at i:15055 original size:27 final size:25
Alignment explanation
Indices: 15023--15075 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
15013 AACGTTATTT
15023 TTAAATCAAT-TGATATTATATTAAAAA
1 TTAAATCAATAT-ATATT-T-TTAAAAA
*
15050 TTAAATTAATATATATTTTTAAAAA
1 TTAAATCAATATATATTTTTAAAAA
15075 T
1 T
15076 ATTAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
26 1 0.04
27 14 0.58
28 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TTAAATCAATATATATTTTTAAAAA
Found at i:16892 original size:2 final size:2
Alignment explanation
Indices: 16885--16917 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16875 GATCCTTCAT
16885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16918 TTGTATGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22152 original size:27 final size:27
Alignment explanation
Indices: 22096--22153 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
22086 AATTAAATTT
* * *
22096 ATTAAAATTTAATTCTTAATTATTATA
1 ATTAAAATTTAATACTTAACTAATATA
*
22123 ATTAAAATGTTAATACTTTACTAATA-A
1 ATTAAAAT-TTAATACTTAACTAATATA
22150 ATTA
1 ATTA
22154 TATAGGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTAAAATTTAATACTTAACTAATATA
Found at i:26334 original size:2 final size:2
Alignment explanation
Indices: 26321--26358 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
26311 CCCTTTGTAA
*
26321 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26359 TACACTATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29192 original size:2 final size:2
Alignment explanation
Indices: 29185--29226 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
29175 TTGCCTTTGC
29185 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
29227 AAGCGTGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31442 original size:11 final size:11
Alignment explanation
Indices: 31426--31450 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31416 CTCATGTTAT
31426 TAATTATTGAA
1 TAATTATTGAA
31437 TAATTATTGAA
1 TAATTATTGAA
31448 TAA
1 TAA
31451 ATCTAATTAA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
TAATTATTGAA
Found at i:32241 original size:28 final size:27
Alignment explanation
Indices: 32182--32246 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
32172 TCACCCATTT
*
32182 ATTTGTCAAAAATGATGGTTATTTTGT
1 ATTTGTCAAAAATGATGGTTATTTTGA
* * *
32209 GTTTGTCAAAAATGGTGGTTTTCTTTGA
1 ATTTGTCAAAAATGATGGTTAT-TTTGA
32237 ATTTGTCAAA
1 ATTTGTCAAA
32247 TATAAAGGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 19 0.59
28 13 0.41
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (27 bp):
ATTTGTCAAAAATGATGGTTATTTTGA
Found at i:42666 original size:3 final size:3
Alignment explanation
Indices: 42658--42699 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
42648 CATCTGTCTC
*
42658 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42700 AAATTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42795 original size:19 final size:17
Alignment explanation
Indices: 42752--42784 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42742 CGTGAAAAAC
42752 GCATAAAAAATTACTCA
1 GCATAAAAAATTACTCA
42769 GCATAAAAAATTACTC
1 GCATAAAAAATTACTC
42785 GTATCTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (17 bp):
GCATAAAAAATTACTCA
Found at i:58000 original size:25 final size:25
Alignment explanation
Indices: 57942--58021 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 25
57932 AATTAAAAAA
57942 TTAATAAATAATAATATATTAATTATTATTT
1 TTAA-AAA-AATAATAT-TTAATTA--A-TT
57973 TTAAAAAAATAATATTTAATTAATT
1 TTAAAAAAATAATATTTAATTAATT
* *
57998 TTAAAAAAATTATA-TTAATAAATT
1 TTAAAAAAATAATATTTAATTAATT
58022 AAAATATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.19
25 15 0.32
26 1 0.02
28 7 0.15
29 8 0.17
30 3 0.06
31 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAAAAAATAATATTTAATTAATT
Found at i:58022 original size:28 final size:27
Alignment explanation
Indices: 57956--58023 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 27
57946 TAAATAATAA
* *
57956 TATATTAATTATTATTTTTAAAAAAAT
1 TATATTAATAATTAATTTTAAAAAAAT
*
57983 AATATT--TAATTAATTTTAAAAAAAT
1 TATATTAATAATTAATTTTAAAAAAAT
58008 TATATTAATAAATTAA
1 TATATTAAT-AATTAA
58024 AATATTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 22 0.65
27 6 0.18
28 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATATTAATAATTAATTTTAAAAAAAT
Found at i:58056 original size:13 final size:13
Alignment explanation
Indices: 58038--58062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58028 TTAATTATTT
58038 TTAAAATAAAAAA
1 TTAAAATAAAAAA
58051 TTAAAATAAAAA
1 TTAAAATAAAAA
58063 GGTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAAATAAAAAA
Found at i:58140 original size:21 final size:22
Alignment explanation
Indices: 58082--58149 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
58072 TTACTATTTT
* *
58082 TTAATAAAATT-AAAAATAATA
1 TTAATCAAATTAAAAAATTATA
*
58103 TTTAATTAAATTTAAAAAATTATA
1 -TTAATCAAA-TTAAAAAATTATA
*
58127 TTAA-CAAATTAAAATATTA-A
1 TTAATCAAATTAAAAAATTATA
58147 TTA
1 TTA
58150 TATGTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 4 0.10
21 10 0.25
22 11 0.28
23 6 0.15
24 9 0.22
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAATCAAATTAAAAAATTATA
Found at i:58144 original size:115 final size:111
Alignment explanation
Indices: 57974--58246 Score: 345
Period size: 115 Copynumber: 2.4 Consensus size: 111
57964 TTATTATTTT
* *
57974 TAAAAAAATAATATTTAATTAATTTTAAAAAAATTATATTAATAAATTAAAATATTAATTAT-T-
1 TAAAAAAATAATATTTAATTAAATTT-AAAAAATTATATTAACAAATTAAAATATTAATTATATG
58037 TTTAAAATAAAAAATTAAAATAAAAAGGTTTATTATTACTATTTTTTAATAAAA
65 TTT-AAAT-AAAAA-T-AAA-AAAAA--TTTATTATTACTATTTTTTAATAAAA
*
58091 T-TAAAAATAATATTTAATTAAATTTAAAAAATTATATTAACAAATTAAAATATTAATTATATGT
1 TAAAAAAATAATATTTAATTAAATTTAAAAAATTATATTAACAAATTAAAATATTAATTATATGT
** ** * *
58155 TTTTATAAAAATAAAAATTATTTTTTATTATTATTTTTTAATAAAA
66 TTAAATAAAAATAAAAAAAATTTATTATTACTATTTTTTAATAAAA
*
58201 TAAAAAAATAATATTTAATTAAATTTTAAAAAATTTACATTAACAA
1 TAAAAAAATAATATTTAATTAAA-TTTAAAAAA-TTATATTAACAA
58247 TTTATATATT
Statistics
Matches: 140, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
110 25 0.18
111 20 0.14
112 12 0.09
113 14 0.10
114 1 0.01
115 39 0.28
116 25 0.18
117 4 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (111 bp):
TAAAAAAATAATATTTAATTAAATTTAAAAAATTATATTAACAAATTAAAATATTAATTATATGT
TTAAATAAAAATAAAAAAAATTTATTATTACTATTTTTTAATAAAA
Found at i:59030 original size:122 final size:117
Alignment explanation
Indices: 58762--59115 Score: 471
Period size: 122 Copynumber: 2.9 Consensus size: 117
58752 TATTATTTTT
* * *
58762 AATAAAAATAATATTTAATTAACTTTAAAAAAATTATATTAATAAATTAAAATATTAA-T-TATT
1 AATAAAAATAATATTTAATTAAGTTT-AAAAATTTACATTAATAAATTAAAATATTAATTATATT
*
58825 TGTTAAAAATAAAAAAATTTAAATAAAAATAAAAAGGGTTTATTATTATTAATTTTAATAA
65 TTTTAAAAAT-AAAAAATTT---T-AAAATAAAAA-GGTTT-TTATTA-TAATTTTAATAA
* *
58886 AATTAAAAATAATATTTAATTAAGTTTAAAATTTTACATTAACAAATTAAAATATTAATTATTAT
1 AA-TAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAATAAATTAAAATATT-A--ATTAT
58951 ATTTTTATAAAAATAAAAAATTTTAAAATAAAAAGGTTTTTATTATAATTTTTAATAA
62 ATTTTT-TAAAAATAAAAAATTTTAAAATAAAAAGGTTTTTATTATAA-TTTTAATAA
59009 AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAATAAATTAAAATATTAATTATATTT
1 AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAATAAATTAAAATATTAATTATATTT
* * *
59074 TTT-AAAATAAAAAATATTAAATTAAAAAGTTTTTTATTATAA
66 TTTAAAAATAAAAAATTTTAAAATAAAAAGGTTTTTATTATAA
59116 CAATATTTTT
Statistics
Matches: 211, Mismatches: 11, Indels: 23
0.86 0.04 0.09
Matches are distributed among these distances:
117 36 0.17
118 1 0.00
119 11 0.05
121 1 0.00
122 54 0.26
123 17 0.08
124 32 0.15
125 34 0.16
126 1 0.00
127 1 0.00
128 1 0.00
129 15 0.07
130 7 0.03
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (117 bp):
AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAATAAATTAAAATATTAATTATATTT
TTTAAAAATAAAAAATTTTAAAATAAAAAGGTTTTTATTATAATTTTAATAA
Found at i:59405 original size:22 final size:21
Alignment explanation
Indices: 59365--59449 Score: 82
Period size: 22 Copynumber: 4.0 Consensus size: 21
59355 ATAATGATAA
**
59365 ATTATTTTTAATTCCTTAAAT
1 ATTATTTTTAATTTATTAAAT
*
59386 ATTATTTTTTAATTTATTAATGT
1 ATTA-TTTTTAATTTATTAA-AT
*
59409 ATT-TTTTAAATTTAATTAAAT
1 ATTATTTTTAATTT-ATTAAAT
* *
59430 ATCATTTTTACTTTATTAAA
1 ATTATTTTTAATTTATTAAA
59450 AAATAATAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 22 0.42
22 26 0.50
23 4 0.08
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (21 bp):
ATTATTTTTAATTTATTAAAT
Found at i:59411 original size:20 final size:22
Alignment explanation
Indices: 59388--59427 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
59378 CCTTAAATAT
59388 TATTTTTT-AATTT-ATTAATG
1 TATTTTTTAAATTTAATTAATG
59408 TATTTTTTAAATTTAATTAA
1 TATTTTTTAAATTTAATTAA
59428 ATATCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (22 bp):
TATTTTTTAAATTTAATTAATG
Found at i:59525 original size:21 final size:20
Alignment explanation
Indices: 59492--59562 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
59482 TAAAAACATA
*
59492 TAATTAATATTTTAATTTAT
1 TAATTAATTTTTTAATTTAT
59512 TAATGTAATTTTTTAATTTAAT
1 TAAT-TAATTTTTTAATTT-AT
*
59534 TAAAT-ATTATTTTAATTTTAT
1 TAATTAATT-TTTTAA-TTTAT
*
59555 TAAATAAT
1 TAATTAAT
59563 AATAATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.16
21 27 0.61
22 10 0.23
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
TAATTAATTTTTTAATTTAT
Found at i:59565 original size:109 final size:116
Alignment explanation
Indices: 59392--59661 Score: 335
Period size: 109 Copynumber: 2.4 Consensus size: 116
59382 AAATATTATT
* *
59392 TTTTAATTTATTAATGT-ATTTTTTAAATTTAATTAAATATCATTTTTACTTTATT-A-AAAAAT
1 TTTTAATTTATTAATGTAATTTTTTAAATTTAATTAAATATTATTTTAACTTTATTAATAAAAAT
*
59454 AATAATAAT-AA-GTTTTTT-TTT-A-TTTTTA-TAAAAACATATAATTAATA
66 AATAATAATAAATCTTTTTTATTTAATTTTTTATTAAAAA-A-ATAATTAATA
* *
59501 TTTTAATTTATTAATGTAATTTTTT-AATTTAATTAAATATTATTTTAATTTTATTAAATAATAA
1 TTTTAATTTATTAATGTAATTTTTTAAATTTAATTAAATATTATTTTAACTTTATT-AATAAAAA
*
59565 TAATAATAATAAATCTTTTTTAATTTAATTTTTTATTTTAAAAAATAATTAATA
65 TAATAATAATAAATCTTTTTT-ATTTAATTTTTTA-TTAAAAAAATAATTAATA
* * *
59619 TTTTAATTTATTAATATAATTTTTTTAAAGTTATTTAAATATT
1 TTTTAATTTATTAATGTAA-TTTTTTAAATTTAATTAAATATT
59662 TTTATTAAAA
Statistics
Matches: 138, Mismatches: 9, Indels: 17
0.84 0.05 0.10
Matches are distributed among these distances:
109 44 0.32
110 7 0.05
111 1 0.01
112 14 0.10
113 2 0.01
114 6 0.04
116 3 0.02
117 1 0.01
118 34 0.25
119 7 0.05
120 19 0.14
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (116 bp):
TTTTAATTTATTAATGTAATTTTTTAAATTTAATTAAATATTATTTTAACTTTATTAATAAAAAT
AATAATAATAAATCTTTTTTATTTAATTTTTTATTAAAAAAATAATTAATA
Found at i:59727 original size:118 final size:116
Alignment explanation
Indices: 59392--59730 Score: 268
Period size: 109 Copynumber: 2.9 Consensus size: 116
59382 AAATATTATT
* * * * ** * *
59392 TTTTAATTTATTAATGT-ATTTTTTAAATTTAATTAAATATCATTTT-TACTTTATTAA-AA-AA
1 TTTTAATTTATTAATATAATTTTTT-AAGTTAATTAAATATTATTTTAAAAATAATAAATAATAA
* * *
59453 TAATAATAATAAGT-TT-TT---TTTTATT-TTTATAAAAACATATAATTAATA
65 TAATAATAATAAATCTTATTAAATTTAATTATTTATTAAAA-A-ATAATTAATA
* * *** *
59501 TTTTAATTTATTAATGTAATTTTTTAATTTAATTAAATATTATTTTAATTTTATTAAATAATAAT
1 TTTTAATTTATTAATATAATTTTTTAAGTTAATTAAATATTATTTTAAAAATAATAAATAATAAT
* * *
59566 AATAATAATAAATCTTTTTTAATTTAATTTTTTATTTTAAAAAATAATTAATA
66 AATAATAATAAATCTTATTAAATTTAATTATTTA--TTAAAAAATAATTAATA
* * *
59619 TTTTAATTTATTAATATAATTTTTTTAAAGTTATTTAAATATTTTTATTAAAAATAATAATTAAT
1 TTTTAATTTATTAATATAA-TTTTTT-AAGTTAATTAAATATTATT-TTAAAAATAATAAATAAT
* * * *
59684 ATATATTATTATTAAAT-TTATTAAATTTAATTAATTTATAAAAAAAT
63 A-ATAATAATAATAAATCTTATTAAATTTAATT-ATTTATTAAAAAAT
59731 TACATAATTA
Statistics
Matches: 187, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
109 37 0.20
110 12 0.06
111 2 0.01
112 15 0.08
113 2 0.01
114 2 0.01
117 6 0.03
118 32 0.17
119 7 0.04
120 29 0.16
121 27 0.14
122 16 0.09
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (116 bp):
TTTTAATTTATTAATATAATTTTTTAAGTTAATTAAATATTATTTTAAAAATAATAAATAATAAT
AATAATAATAAATCTTATTAAATTTAATTATTTATTAAAAAATAATTAATA
Found at i:59817 original size:15 final size:15
Alignment explanation
Indices: 59769--59817 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
59759 TTTCTCAACG
* *
59769 TATTCATAAAAAAAT
1 TATTTATAAAAAATT
*
59784 TATTT-TAAAAAATA
1 TATTTATAAAAAATT
59798 T-TTTATAAAAAATT
1 TATTTATAAAAAATT
59812 TATTTA
1 TATTTA
59818 CGAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 3 0.11
14 17 0.61
15 8 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTATAAAAAATT
Found at i:60093 original size:20 final size:20
Alignment explanation
Indices: 60072--60108 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
60062 AATTAAATTA
60072 AAATAA-AATTTATATTATT
1 AAATAATAATTTATATTATT
60091 AAATAATAATTTATATTA
1 AAATAATAATTTATATTA
60109 AATTTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATAATAATTTATATTATT
Found at i:60482 original size:21 final size:21
Alignment explanation
Indices: 60440--60489 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
60430 CTTGTTTAAT
* *
60440 AGTTTAAGATATTTGAATTTA
1 AGTTTAAGATAATTGAAATTA
60461 AGTTTAAGAGTAATT-AAATTA
1 AGTTTAAGA-TAATTGAAATTA
*
60482 AATTTAAG
1 AGTTTAAG
60490 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (21 bp):
AGTTTAAGATAATTGAAATTA
Found at i:62436 original size:6 final size:6
Alignment explanation
Indices: 62425--62450 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
62415 TTCCAATCTT
62425 TGTTGC TGTTGC TGTTGC TGTTGC TG
1 TGTTGC TGTTGC TGTTGC TGTTGC TG
62451 CTGTTCATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.35, T:0.50
Consensus pattern (6 bp):
TGTTGC
Found at i:65367 original size:2 final size:2
Alignment explanation
Indices: 65360--65387 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
65350 GGTTTTCTAC
65360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65388 TGTTGGCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65555 original size:3 final size:3
Alignment explanation
Indices: 65547--65575 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
65537 CAAATTAAAA
65547 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
65576 AAAGCTTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:68021 original size:20 final size:20
Alignment explanation
Indices: 67988--68031 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
67978 TAAAAAATTT
* *
67988 TTAAAAAT-ATTTTATATTA
1 TTAAAAATAATTTAATATAA
68007 TTAAATAATAATTTAATATAA
1 TTAAA-AATAATTTAATATAA
68028 TTAA
1 TTAA
68032 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 13 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAAATAATTTAATATAA
Found at i:68046 original size:17 final size:15
Alignment explanation
Indices: 68011--68052 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
68001 ATATTATTAA
68011 ATAA-TAATTT-AAT
1 ATAATTAATTTAAAT
68024 ATAATTAATTTAAATT
1 ATAATTAATTTAAA-T
68040 ATAAATTAATTTA
1 AT-AATTAATTTA
68053 TTTAAATACG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.16
14 6 0.24
15 2 0.08
16 3 0.12
17 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATAATTAATTTAAAT
Found at i:74258 original size:23 final size:23
Alignment explanation
Indices: 74228--74271 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
74218 TCTTTTAGCC
74228 ATAAATAAAACCAAAAAAAAAAT
1 ATAAATAAAACCAAAAAAAAAAT
* *
74251 ATAAATAAAACTACAAAAAAA
1 ATAAATAAAACCAAAAAAAAA
74272 TAGAACAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (23 bp):
ATAAATAAAACCAAAAAAAAAAT
Found at i:76276 original size:19 final size:20
Alignment explanation
Indices: 76228--76276 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
76218 TTTCTCAAAA
76228 TCTC-TTTTATATTGTCATT
1 TCTCATTTTATATTGTCATT
*
76247 TCTCA-TATATATTGTC-TT
1 TCTCATTTTATATTGTCATT
*
76265 TTTCATTTTATA
1 TCTCATTTTATA
76277 ATGACCCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.20, C:0.14, G:0.04, T:0.61
Consensus pattern (20 bp):
TCTCATTTTATATTGTCATT
Found at i:76770 original size:2 final size:2
Alignment explanation
Indices: 76763--76805 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
76753 GATCCTTCAT
76763 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
76805 T
1 T
76806 TTGTATGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.