Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 8 of 32
Found at i:884060 original size:135 final size:136
Alignment explanation
Indices: 883854--884106 Score: 463
Period size: 135 Copynumber: 1.9 Consensus size: 136
883844 TTAAATTTTG
*
883854 TATAATTTGTCATTTGATTCAATTTAAAGAAAATTTGTATGTTTATGTCATGTTCGTGTCGTATC
1 TATAATTTGTCATTTGATTCAATTTAAAGAAAAATTGTATGTTTATGTCATGTTCGTGTCGTATC
* *
883919 TCCATTCATGATATATTTTATATAATTTATCGTAATAATTTATTTAAAGTATCGCATTTCCATTC
66 TCCATTCATGACATATTTTATATAATTTATCATAATAATTTATTTAAAGTATCGCATTTCCATTC
883984 ATGACA
131 ATGACA
*
883990 TATAGTTTGTCATTTGATTCAATTTAAA-AAAAATTGTATGTTTATGTCATGTTCGTGTCGTATC
1 TATAATTTGTCATTTGATTCAATTTAAAGAAAAATTGTATGTTTATGTCATGTTCGTGTCGTATC
884054 TCCATTCATGACATATTTTATATAATTTATCATAATAATTTATTTAAAGTATC
66 TCCATTCATGACATATTTTATATAATTTATCATAATAATTTATTTAAAGTATC
884107 ATATCTCAAT
Statistics
Matches: 113, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
135 86 0.76
136 27 0.24
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (136 bp):
TATAATTTGTCATTTGATTCAATTTAAAGAAAAATTGTATGTTTATGTCATGTTCGTGTCGTATC
TCCATTCATGACATATTTTATATAATTTATCATAATAATTTATTTAAAGTATCGCATTTCCATTC
ATGACA
Found at i:884417 original size:17 final size:16
Alignment explanation
Indices: 884395--884451 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 16
884385 AAATATTTAT
884395 TATAAAAATTATTAATA
1 TATAAAAATTATTAA-A
*
884412 TATAAAATTTATATAAAA
1 TATAAAAATTAT-T-AAA
*
884430 TATAAAAATATTTTAAA
1 TATAAAAAT-TATTAAA
884447 TATAA
1 TATAA
884452 TTATAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 19 0.56
18 11 0.32
19 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATAAAAATTATTAAA
Found at i:884805 original size:21 final size:22
Alignment explanation
Indices: 884779--884819 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
884769 ATTTATAATA
*
884779 AAAAATAATAATTTT-CAAACT
1 AAAAATAACAATTTTACAAACT
884800 AAAAATAACAATTTTACAAA
1 AAAAATAACAATTTTACAAA
884820 TTCCAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATAACAATTTTACAAACT
Found at i:885704 original size:2 final size:2
Alignment explanation
Indices: 885697--885721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
885687 TTAATATTCA
885697 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
885722 ATGGGAAAAT
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:886191 original size:26 final size:25
Alignment explanation
Indices: 886140--886190 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
886130 CACAAATTTT
* *
886140 TATAAAAAAACTTGTAATTTAAAAA
1 TATAAAAAAAATTATAATTTAAAAA
886165 TATAAAAAAAATTATAAATATTAAAA
1 TATAAAAAAAATTAT-AAT-TTAAAA
886191 TTTAAATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 3 0.14
27 6 0.27
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
TATAAAAAAAATTATAATTTAAAAA
Found at i:886198 original size:14 final size:15
Alignment explanation
Indices: 886172--886217 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
886162 AAATATAAAA
886172 AAAATTATAAATATT
1 AAAATTATAAATATT
*
886187 AAAATT-TAAATATC
1 AAAATTATAAATATT
*
886201 AAATTTATTAAATATT
1 AAAATTA-TAAATATT
886217 A
1 A
886218 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 12 0.46
15 6 0.23
16 8 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:887609 original size:21 final size:21
Alignment explanation
Indices: 887566--887615 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
887556 TAATTATTTT
*
887566 TTTAAAA-TATATTTTATAAA
1 TTTAAAATTAAATTTTATAAA
887586 TTTAAAATTAAATTTT-TAATA
1 TTTAAAATTAAATTTTATAA-A
*
887607 TTTATAATT
1 TTTAAAATT
887616 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAATTAAATTTTATAAA
Found at i:887972 original size:19 final size:18
Alignment explanation
Indices: 887921--887972 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
887911 AATAATTAAA
* *
887921 AATAAAAATAAAATACAT
1 AATAAAATTAAAATTCAT
**
887939 AATAAAATTTTAATTCACT
1 AATAAAATTAAAATTCA-T
*
887958 TATAAAATTAAAATT
1 AATAAAATTAAAATT
887973 TTTTAATTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAAATTAAAATTCAT
Found at i:888998 original size:17 final size:16
Alignment explanation
Indices: 888967--889000 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
888957 ATAAAAATTT
*
888967 TAAATAATTATTAAAA
1 TAAATAATAATTAAAA
888983 TAAATATATAATTAAAA
1 TAAATA-ATAATTAAAA
889000 T
1 T
889001 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATAATAATTAAAA
Found at i:889453 original size:29 final size:29
Alignment explanation
Indices: 889430--889490 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 29
889420 AATTAATATT
889430 TATTTTAAAAAATAAAAAAAATT-ATCAAAA
1 TATTTT-AAAAATAAAAAAAATTAAT-AAAA
*
889460 TATTTTAAAAATAAAAAATAATTATTAAAA
1 TATTTTAAAAATAAAAAA-AATTAATAAAA
889490 T
1 T
889491 TATATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 12 0.43
30 15 0.54
31 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (29 bp):
TATTTTAAAAATAAAAAAAATTAATAAAA
Found at i:889466 original size:30 final size:33
Alignment explanation
Indices: 889421--889505 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 33
889411 AAATAAAATA
* *
889421 ATTAATATTTATTTTAAAAAATAAAAAA-AATT
1 ATTAAAATATATTTTAAAAAATAAAAAATAATT
*
889453 A-TCAAA-ATATTTT-AAAAATAAAAAATAATT
1 ATTAAAATATATTTTAAAAAATAAAAAATAATT
889483 ATTAAAATTATATTTTAAAAAAT
1 ATTAAAA-TATATTTTAAAAAAT
889506 TTTAAGATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 12 0.27
30 11 0.25
31 7 0.16
32 1 0.02
33 7 0.16
34 6 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATTAAAATATATTTTAAAAAATAAAAAATAATT
Found at i:889469 original size:19 final size:21
Alignment explanation
Indices: 889447--889494 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
889437 AAAAATAAAA
*
889447 AAAATTATCAAAAT-ATT-TT
1 AAAATTATAAAAATAATTATT
*
889466 AAAAATA-AAAAATAATTATT
1 AAAATTATAAAAATAATTATT
889486 AAAATTATA
1 AAAATTATA
889495 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.22
19 9 0.39
20 8 0.35
21 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTATAAAAATAATTATT
Found at i:889501 original size:33 final size:32
Alignment explanation
Indices: 889410--889503 Score: 106
Period size: 33 Copynumber: 3.0 Consensus size: 32
889400 AATTCGTTAG
* *
889410 AAAATAAAATAATTAATATT-TATTTTAAAAAAT
1 AAAA-AAAATTATTAAAATTATATTTT-AAAAAT
*
889443 AAAAAAAATTA-TCAAA--ATATTTTAAAAAT
1 AAAAAAAATTATTAAAATTATATTTTAAAAAT
889472 AAAAAATAATTATTAAAATTATATTTTAAAAA
1 AAAAAA-AATTATTAAAATTATATTTTAAAAA
889504 ATTTTAAGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
29 12 0.23
30 11 0.21
31 7 0.13
32 6 0.12
33 16 0.31
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (32 bp):
AAAAAAAATTATTAAAATTATATTTTAAAAAT
Found at i:889518 original size:23 final size:25
Alignment explanation
Indices: 889474--889520 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
889464 TTAAAAATAA
*
889474 AAAATAATTATTAAAATTATATTTT
1 AAAATAATTATTAAAATAATATTTT
*
889499 AAAA-AATT-TTAAGATAATATTT
1 AAAATAATTATTAAAATAATATTT
889521 ATTTTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATAATTATTAAAATAATATTTT
Found at i:889582 original size:14 final size:14
Alignment explanation
Indices: 889554--889586 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
889544 AAATATATTT
889554 ATTATAAATATAAA
1 ATTATAAATATAAA
889568 ATTA-AAATATAAA
1 ATTATAAATATAAA
*
889581 AATATA
1 ATTATA
889587 TTTTTTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTATAAATATAAA
Found at i:890196 original size:26 final size:26
Alignment explanation
Indices: 890117--890264 Score: 85
Period size: 26 Copynumber: 5.5 Consensus size: 26
890107 ATTTTTTTAA
890117 ATTTTAAATATGATATAAAAATATATTAA-
1 ATTTTAAATAT-ATAT--AAATATA-TAAT
* *
890146 AATTTATATA-ATATAAAT-TATTAAT
1 ATTTTAAATATATATAAATATA-TAAT
*
890171 -TTATTAAATTTATATAAATATATAAT
1 ATT-TTAAATATATATAAATATATAAT
*
890197 ATTTTAAATATA-ATTATAATATATAAAA
1 ATTTTAAATATATA-TA-AATATAT-AAT
* *
890225 ATAATTAAAGATA-ATATAATATATAA-
1 AT-TTTAAATATATATA-AATATATAAT
890251 ATTTTTAAATATAT
1 A-TTTTAAATATAT
890265 TAATATTTAT
Statistics
Matches: 97, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
24 7 0.07
25 10 0.10
26 31 0.32
27 18 0.19
28 14 0.14
29 17 0.18
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
ATTTTAAATATATATAAATATATAAT
Found at i:890214 original size:20 final size:19
Alignment explanation
Indices: 890191--890231 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
890181 TATATAAATA
* *
890191 TATAATATTTTAAATATAAT
1 TATAATA-TATAAAAATAAT
890211 TATAATATATAAAAATAAT
1 TATAATATATAAAAATAAT
890230 TA
1 TA
890232 AAGATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAATATATAAAAATAAT
Found at i:890380 original size:27 final size:26
Alignment explanation
Indices: 890324--890376 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
890314 TAAAAATATA
* *
890324 TAATTATGTATTTTATAATTAAAAAT
1 TAATTATGTATTTAATAAATAAAAAT
*
890350 TAATTAATGTA-TTAATAAATATAAAT
1 TAATT-ATGTATTTAATAAATAAAAAT
890376 T
1 T
890377 TAATATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
TAATTATGTATTTAATAAATAAAAAT
Found at i:890389 original size:19 final size:20
Alignment explanation
Indices: 890365--890404 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
890355 AATGTATTAA
890365 TAAAT-ATAAATTTAATATT
1 TAAATAATAAATTTAATATT
*
890384 TAAATAATAAATTTATTATT
1 TAAATAATAAATTTAATATT
890404 T
1 T
890405 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATAATAAATTTAATATT
Found at i:890682 original size:25 final size:25
Alignment explanation
Indices: 890628--890687 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
890618 TAAATTAAAT
* *
890628 AATATTATTAATAATAAAAAATATT
1 AATAATATTAATAATAAAAAATATC
* *
890653 TATAATATTAATAATTTAAAAATA-C
1 AATAATATTAATAA-TAAAAAATATC
890678 AATAAATATT
1 AAT-AATATT
890688 TATGATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AATAATATTAATAATAAAAAATATC
Found at i:891892 original size:33 final size:33
Alignment explanation
Indices: 891852--891922 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
891842 AGATTTTGAG
* *
891852 TTTTTTTTAATTTAAATTTATTTACTT-TTAAAT
1 TTTTTTTTAATTTAAATTT-TTTAATTCATAAAT
*
891885 TTTTTTTTAGTTTAAATTTTTTAATTCATAAAT
1 TTTTTTTTAATTTAAATTTTTTAATTCATAAAT
891918 TTTTT
1 TTTTT
891923 ATTCAGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (33 bp):
TTTTTTTTAATTTAAATTTTTTAATTCATAAAT
Found at i:891904 original size:16 final size:16
Alignment explanation
Indices: 891852--891906 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
891842 AGATTTTGAG
891852 TTTTTTTTAATTTAAA
1 TTTTTTTTAATTTAAA
* *
891868 -TTTATTTACTTTTAAA
1 TTTTTTTTA-ATTTAAA
*
891884 TTTTTTTTTAGTTTAAA
1 -TTTTTTTTAATTTAAA
891901 TTTTTT
1 TTTTTT
891907 AATTCATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 7 0.22
16 12 0.38
17 6 0.19
18 7 0.22
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTTTTTAATTTAAA
Found at i:891920 original size:15 final size:16
Alignment explanation
Indices: 891897--891927 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
891887 TTTTTTAGTT
891897 TAAATTTTTTAATTCA
1 TAAATTTTTTAATTCA
891913 TAAATTTTTT-ATTCA
1 TAAATTTTTTAATTCA
891928 GATGAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAATTTTTTAATTCA
Found at i:893708 original size:18 final size:17
Alignment explanation
Indices: 893663--893708 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
893653 AATGATAAAA
893663 TAAAATATATTT-ATATT
1 TAAAATAT-TTTAATATT
893680 TAAAAT-TTTTAATATTT
1 TAAAATATTTTAATA-TT
*
893697 TTAAATATTTTA
1 TAAAATATTTTA
893709 CATTTGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 3 0.12
16 4 0.16
17 13 0.52
18 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAAAATATTTTAATATT
Found at i:893884 original size:21 final size:18
Alignment explanation
Indices: 893847--893887 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
893837 ATATGAATAT
893847 ATAAATTTTATTATTAAA
1 ATAAATTTTATTATTAAA
893865 ATAAATTATTAATATATTAAA
1 ATAAATT-TT-AT-TATTAAA
893886 AT
1 AT
893888 TTAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 2 0.10
21 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAATTTTATTATTAAA
Found at i:893905 original size:18 final size:17
Alignment explanation
Indices: 893842--893907 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 17
893832 ATATAATATG
893842 AATATATAAATTTTATTA
1 AATATATAAA-TTTATTA
893860 TTAA-A-ATAAA-TTATT-
1 --AATATATAAATTTATTA
893875 AATATATTAAAATTTAATTA
1 AATATA-T-AAATTT-ATTA
893895 AATATATAAATTT
1 AATATATAAATTT
893908 TAAATATGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
13 2 0.05
14 1 0.03
15 1 0.03
16 6 0.15
17 3 0.08
18 13 0.33
19 5 0.13
20 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATATAAATTTATTA
Found at i:896226 original size:34 final size:35
Alignment explanation
Indices: 896187--896261 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 35
896177 CAGGAATGGA
*
896187 CGGATTAAATTATATTAAAAGTTTTGAAATT-GGT
1 CGGATTAAATTATATTAAAAGTTTTAAAATTAGGT
896221 CGGATTAAATTATATTAAAAGTTTTAAAATTAGGT
1 CGGATTAAATTATATTAAAAGTTTTAAAATTAGGT
*
896256 CAGATT
1 CGGATT
896262 GATGATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 30 0.79
35 8 0.21
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (35 bp):
CGGATTAAATTATATTAAAAGTTTTAAAATTAGGT
Found at i:896354 original size:14 final size:14
Alignment explanation
Indices: 896325--896371 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
896315 TACTCTTCTA
*
896325 ATTTTATA-ACTTT
1 ATTTTATATATTTT
896338 ATTTTATATATTTT
1 ATTTTATATATTTT
* *
896352 ATTTTAAATTTTTT
1 ATTTTATATATTTT
896366 AATTTT
1 -ATTTT
896372 TACAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 8 0.28
14 16 0.55
15 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATATATTTT
Found at i:897726 original size:18 final size:17
Alignment explanation
Indices: 897695--897728 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
897685 TTATTTTTAT
*
897695 TTAAAAATATTTAAATA
1 TTAAAAATAATTAAATA
897712 TTAAAAATCAATTAAAT
1 TTAAAAAT-AATTAAAT
897729 TTTTATTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATAATTAAATA
Found at i:899555 original size:20 final size:21
Alignment explanation
Indices: 899513--899557 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
899503 AACTAAAAAC
*
899513 TTAATTGTTTTAATTTTTAAT
1 TTAATTGTTTTAATTTATAAT
899534 TTAATT-TTTTAATATTAT-AT
1 TTAATTGTTTTAAT-TTATAAT
899554 TTAA
1 TTAA
899558 ATTATTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTAATTGTTTTAATTTATAAT
Found at i:900300 original size:21 final size:23
Alignment explanation
Indices: 900276--900323 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
900266 AAAAATCATA
900276 TTATTTA-ATTAAATA-TTATTT
1 TTATTTATATTAAATACTTATTT
*
900297 TTA-TTATATTTAATACTTATTT
1 TTATTTATATTAAATACTTATTT
*
900319 ATATT
1 TTATT
900324 AAAAGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.14
21 10 0.45
22 8 0.36
23 1 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTTATATTAAATACTTATTT
Found at i:900317 original size:37 final size:35
Alignment explanation
Indices: 900276--900355 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 35
900266 AAAAATCATA
* *
900276 TTATTTAATTAAATATTATTT-TTATTATATTTAATAC
1 TTATTTAATTAAA-AGTATTTAAT-TTATATTTAA-AC
900313 TTATTTATATTAAAAGTATTTAATTTATATTTAAAC
1 TTATTTA-ATTAAAAGTATTTAATTTATATTTAAAC
900349 TT-TTTAA
1 TTATTTAA
900356 AAACTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
34 1 0.03
35 4 0.10
36 4 0.10
37 23 0.59
38 7 0.18
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (35 bp):
TTATTTAATTAAAAGTATTTAATTTATATTTAAAC
Found at i:900354 original size:20 final size:20
Alignment explanation
Indices: 900315--900355 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
900305 TTTAATACTT
*
900315 ATTTATATTAAAAGTATTTA
1 ATTTATATTAAAACTATTTA
* *
900335 ATTTATATTTAAACTTTTTA
1 ATTTATATTAAAACTATTTA
900355 A
1 A
900356 AAACTAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTATATTAAAACTATTTA
Found at i:900370 original size:19 final size:19
Alignment explanation
Indices: 900346--900385 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
900336 TTTATATTTA
900346 AACTTTTTAAAAACTAAAT
1 AACTTTTTAAAAACTAAAT
* *
900365 AACTTTTTTAAAATTAAAT
1 AACTTTTTAAAAACTAAAT
900384 AA
1 AA
900386 TAAAATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AACTTTTTAAAAACTAAAT
Found at i:900768 original size:21 final size:21
Alignment explanation
Indices: 900732--900785 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
900722 TATAATAATT
*
900732 TATA-TTATA-TAAATTTTAA
1 TATATTTATATTATATTTTAA
900751 TATATTTATATTATATTTTAA
1 TATATTTATATTATATTTTAA
*
900772 T-TAATTTTTATTAT
1 TAT-ATTTATATTAT
900786 TCAAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.13
20 6 0.20
21 20 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTTATATTATATTTTAA
Found at i:900775 original size:25 final size:25
Alignment explanation
Indices: 900703--900776 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
900693 ATCTTATAAG
*
900703 ATATTTAT-TTAAATTTTAATATAAT
1 ATATTTATATTATATTTTAAT-TAAT
*
900728 A-ATTTATATTATA--TAAATTTTAAT
1 ATATTTATATTATATTTTAA--TTAAT
900752 ATATTTATATTATATTTTAATTAAT
1 ATATTTATATTATATTTTAATTAAT
900777 TTTTATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
23 3 0.08
24 11 0.28
25 23 0.57
27 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATTTATATTATATTTTAATTAAT
Found at i:903734 original size:17 final size:18
Alignment explanation
Indices: 903702--903736 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
903692 AAAATTAAAA
903702 TTTTAATATTTATAATTT
1 TTTTAATATTTATAATTT
*
903720 TTTTAAT-TTTTTAATTT
1 TTTTAATATTTATAATTT
903737 ATCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTAATATTTATAATTT
Found at i:904390 original size:30 final size:30
Alignment explanation
Indices: 904355--904423 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
904345 TAAATAATTT
904355 ATTTAATTTAATA-ATTTTAATTTA-ATTTG
1 ATTTAATTTAATATATTTTAATTTATA-TTG
* * *
904384 AATTTAAATTAATATTTTTTTATTTATATTG
1 -ATTTAATTTAATATATTTTAATTTATATTG
904415 ATTTAATTT
1 ATTTAATTT
904424 GATTCGAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 20 0.61
31 12 0.36
32 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
ATTTAATTTAATATATTTTAATTTATATTG
Found at i:905833 original size:3 final size:3
Alignment explanation
Indices: 905825--905860 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
905815 ACGATCAAAA
905825 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
905861 TTATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:905906 original size:27 final size:26
Alignment explanation
Indices: 905859--906019 Score: 84
Period size: 27 Copynumber: 5.9 Consensus size: 26
905849 AATAATAATA
905859 ATTTATATTTT-T-ATATCATTTTAAAT
1 ATTT-TATTTTATAATAT-ATTTTAAAT
*
905885 ATTTTATTTTATAATTATATTTAAAAT
1 ATTTTATTTTATAA-TATATTTTAAAT
*
905912 ATCATATATTTATATAA-AT-TTTTATATAT
1 AT--TTTATTT-TATAATATATTTTA-A-AT
* *
905941 ATTAATAATTTTATAATATA-TTTATAT
1 ATT--TTATTTTATAATATATTTTAAAT
*
905968 ATTCATT-TATTATAATATATTTTATATTAT
1 ATT--TTATTTTATAATATATTTTA-A--AT
*
905998 ATTTTATTATATAAT-TATTTTA
1 ATTTTATTTTATAATATATTTTA
906020 TATCAATTTA
Statistics
Matches: 106, Mismatches: 12, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
25 6 0.06
26 16 0.15
27 27 0.25
28 20 0.19
29 27 0.25
30 10 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
ATTTTATTTTATAATATATTTTAAAT
Found at i:905990 original size:57 final size:58
Alignment explanation
Indices: 905890--906000 Score: 140
Period size: 57 Copynumber: 1.9 Consensus size: 58
905880 TAAATATTTT
905890 ATTTTATAATTATATTTAAAATATCATATATTTATATAAATTTT-TATATATATTAATA
1 ATTTTATAATTATATTTAAAATATCATATATTTATATAAATTTTATAT-TATATTAATA
* * *
905948 ATTTTATAA-TATATTT-ATATATTCATTTA-TTATAATATATTTTATATTATATT
1 ATTTTATAATTATATTTAAAATA-TCATATATTTAT-ATAAATTTTATATTATATT
906001 TTATTATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
56 8 0.17
57 27 0.57
58 12 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (58 bp):
ATTTTATAATTATATTTAAAATATCATATATTTATATAAATTTTATATTATATTAATA
Found at i:905992 original size:12 final size:12
Alignment explanation
Indices: 905889--906010 Score: 69
Period size: 12 Copynumber: 10.2 Consensus size: 12
905879 TTAAATATTT
905889 TATTTTATAATTA
1 TATTTTATAA-TA
* *
905902 TATTTAAAATATCA
1 TATTTTATA-AT-A
905916 TATATTTAT-ATA
1 TAT-TTTATAATA
*
905928 AATTTT-T-ATA
1 TATTTTATAATA
*
905938 TA-TAT-TAATA
1 TATTTTATAATA
905948 -ATTTTATAATA
1 TATTTTATAATA
*
905959 TATTTATATATTCA
1 TATTT-TATAAT-A
905973 T-TTATTATAATA
1 TATT-TTATAATA
*
905985 TATTTTATATTA
1 TATTTTATAATA
*
905997 TATTTTATTATA
1 TATTTTATAATA
906009 TA
1 TA
906011 ATTATTTTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 4 0.05
10 10 0.12
11 8 0.09
12 28 0.33
13 24 0.28
14 8 0.09
15 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTTTATAATA
Found at i:906005 original size:17 final size:17
Alignment explanation
Indices: 905931--906020 Score: 62
Period size: 17 Copynumber: 5.4 Consensus size: 17
905921 TTATATAAAT
905931 TTTTA-TATATATTAATAA
1 TTTTATTATATATT-AT-A
*
905949 TTTTATAATATATT-TA
1 TTTTATTATATATTATA
* *
905965 -TATATTCATTTATTATA
1 TTTTATT-ATATATTATA
* * *
905982 ATATATTTTATATTATA
1 TTTTATTATATATTATA
*
905999 TTTTATTATATAAT-TA
1 TTTTATTATATATTATA
906015 TTTTAT
1 TTTTAT
906021 ATCAATTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
15 4 0.07
16 15 0.26
17 21 0.36
18 11 0.19
19 7 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATTATATATTATA
Found at i:906020 original size:43 final size:43
Alignment explanation
Indices: 905915--906022 Score: 108
Period size: 38 Copynumber: 2.7 Consensus size: 43
905905 TTAAAATATC
905915 ATATATTTA-TATA-AATT-TTTATATATATTAATAATTTTATA
1 ATATATTTATTATATAATTATTT-TATATATTAATAATTTTATA
*
905956 ATATATTTA-TATAT--TCA-TTTAT-TA-TAATATATTTTATA
1 ATATATTTATTATATAATTATTTTATATATTAATA-ATTTTATA
*
905994 TTATATTTTATTATATAATTATTTTATAT
1 ATATA-TTTATTATATAATTATTTTATAT
906023 CAATTTAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
37 5 0.09
38 14 0.25
39 7 0.13
40 8 0.15
41 13 0.24
42 2 0.04
43 5 0.09
44 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (43 bp):
ATATATTTATTATATAATTATTTTATATATTAATAATTTTATA
Found at i:906034 original size:28 final size:28
Alignment explanation
Indices: 905921--906046 Score: 86
Period size: 28 Copynumber: 4.6 Consensus size: 28
905911 TATCATATAT
*
905921 TTATATAAAT-TTTTATAT-ATATTAATAA
1 TTATATAATTATTTTATATCATATT--TAA
* * * *
905949 TTTTATAA-TATATT-TAT-ATATTCAT
1 TTATATAATTATTTTATATCATATTTAA
* *
905974 TTATTATAATATATTTTATATTATATTTTA
1 TTA-TATAAT-TATTTTATATCATATTTAA
906004 TTATATAATTATTTTATATCA-ATTTAAA
1 TTATATAATTATTTTATATCATATTT-AA
*
906032 TTAT-TAATTTTTTTA
1 TTATATAATTATTTTA
906047 ATTACAATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
25 3 0.04
26 5 0.06
27 23 0.29
28 31 0.39
29 9 0.11
30 8 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTATATAATTATTTTATATCATATTTAA
Found at i:907156 original size:17 final size:17
Alignment explanation
Indices: 907134--907208 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 17
907124 TAATTTAATA
907134 TAAATATAAATATTTTT
1 TAAATATAAATATTTTT
*
907151 TAAATATATAAAATTTTT
1 TAAATATA-AATATTTTT
* * *
907169 AAAAAATTAAATA-TATT
1 TAAATA-TAAATATTTTT
* *
907186 TATAT-TAAATATTTAT
1 TAAATATAAATATTTTT
907202 TAAATAT
1 TAAATAT
907209 TTACCTTTAA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
15 6 0.14
16 6 0.14
17 14 0.33
18 15 0.35
19 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATAAATATTTTT
Found at i:908723 original size:37 final size:38
Alignment explanation
Indices: 908652--908731 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 38
908642 TTTTTATCTC
* *
908652 ATATATTTTTAAATATAAATATAAAAATATATATATTT
1 ATATTTTTTTAAATATAAATATAAAAATAAATATATTT
*
908690 -TATTTTTTTAAATATATAA-A-AATAATTAAATATATTT
1 ATATTTTTTTAAATATA-AATATAA-AAATAAATATATTT
908727 ATATT
1 ATATT
908732 CTATACCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 2 0.06
37 28 0.78
38 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
ATATTTTTTTAAATATAAATATAAAAATAAATATATTT
Found at i:911942 original size:22 final size:22
Alignment explanation
Indices: 911917--911962 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
911907 AATGTAAACA
*
911917 AATCAAAATTTTAGAT-AAATTT
1 AATC-AAATTTTAAATCAAATTT
*
911939 AATCACATTTTAAATCAAATTT
1 AATCAAATTTTAAATCAAATTT
911961 AA
1 AA
911963 ATTAAGAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (22 bp):
AATCAAATTTTAAATCAAATTT
Found at i:915034 original size:8 final size:8
Alignment explanation
Indices: 914997--915053 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
914987 ACATCACACT
*
914997 CATACATA
1 CATATATA
*
915005 CATACATA
1 CATATATA
*
915013 CATATACA
1 CATATATA
915021 TCATATATA
1 -CATATATA
915030 CATATACTA
1 CATATA-TA
*
915039 TATATATA
1 CATATATA
*
915047 TATATAT
1 CATATAT
915054 GTTTTTGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 29 0.67
9 14 0.33
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (8 bp):
CATATATA
Found at i:915043 original size:17 final size:17
Alignment explanation
Indices: 914998--915052 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
914988 CATCACACTC
*
914998 ATACATACATACATACAT
1 ATACAT-CATATATACAT
915016 ATACATCATATATACAT
1 ATACATCATATATACAT
*
915033 ATACTAT-ATATATATAT
1 ATAC-ATCATATATACAT
915050 ATA
1 ATA
915053 TGTTTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 26 0.76
18 8 0.24
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (17 bp):
ATACATCATATATACAT
Found at i:915375 original size:19 final size:19
Alignment explanation
Indices: 915351--915388 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
915341 TGGGTTTTCT
* *
915351 TTTTATTTATTTAATTTTA
1 TTTTATATAGTTAATTTTA
915370 TTTTATATAGTTAATTTTA
1 TTTTATATAGTTAATTTTA
915389 ATTGATTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTATATAGTTAATTTTA
Found at i:915514 original size:9 final size:9
Alignment explanation
Indices: 915502--915549 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
915492 CTGGATTAAT
*
915502 TTTAATGGA
1 TTTAATTGA
915511 TTTAATTGA
1 TTTAATTGA
915520 -TTAAGTTGA
1 TTTAA-TTGA
915529 TTTAATTGA
1 TTTAATTGA
*
915538 TTTAATTAA
1 TTTAATTGA
915547 TTT
1 TTT
915550 GATATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 4 0.11
9 27 0.77
10 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (9 bp):
TTTAATTGA
Found at i:920065 original size:30 final size:30
Alignment explanation
Indices: 920031--920106 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
920021 AGTAAAATGT
920031 TAATTTATTT-AGATATAAATTAAGAATTAA
1 TAATTTATTTGA-ATATAAATTAAGAATTAA
* *
920061 TAATTTATTTGAATATAAATTGATAATTAA
1 TAATTTATTTGAATATAAATTAAGAATTAA
*
920091 -AAGATTATTTGAATAT
1 TAA-TTTATTTGAATAT
920107 TATCAAGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 2 0.05
30 38 0.93
31 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (30 bp):
TAATTTATTTGAATATAAATTAAGAATTAA
Found at i:921345 original size:2 final size:2
Alignment explanation
Indices: 921340--921375 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
921330 GTCATTAATT
*
921340 TA TA TA TA TA TA TA CA 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
921376 ATGATAGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:922183 original size:16 final size:16
Alignment explanation
Indices: 922141--922199 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
922131 AAATTAAAAA
922141 ATTAAA-AAAAT-AAT
1 ATTAAATAAAATAAAT
*
922155 ATTAATATTAAATAAAT
1 ATTAA-ATAAAATAAAT
*
922172 GTTAAATAAAATAAAT
1 ATTAAATAAAATAAAT
922188 AATT-AATAAAAT
1 -ATTAAATAAAAT
922200 TATGCATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 5 0.14
15 1 0.03
16 22 0.59
17 9 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTAAATAAAATAAAT
Found at i:922301 original size:16 final size:16
Alignment explanation
Indices: 922276--922306 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
922266 TAAAAGATTA
*
922276 ATTTATATATAAATTT
1 ATTTAGATATAAATTT
922292 ATTTAGATATAAATT
1 ATTTAGATATAAATT
922307 AAAAGTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATTTAGATATAAATTT
Found at i:923326 original size:18 final size:19
Alignment explanation
Indices: 923303--923342 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
923293 TGTATGTATG
923303 TATGTAT-ATATATAAAAT
1 TATGTATCATATATAAAAT
923321 TATGTATGCATATATAAAAT
1 TATGTAT-CATATATAAAAT
923341 TA
1 TA
923343 AGAGTGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
20 13 0.65
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (19 bp):
TATGTATCATATATAAAAT
Found at i:924292 original size:16 final size:16
Alignment explanation
Indices: 924268--924298 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
924258 TAAAAACAAA
*
924268 TTTATAAATTTTAAAT
1 TTTAAAAATTTTAAAT
924284 TTTAAAAATTTTAAA
1 TTTAAAAATTTTAAA
924299 ATAATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAAAATTTTAAAT
Found at i:925852 original size:14 final size:14
Alignment explanation
Indices: 925829--925872 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
925819 ATATTATTTT
925829 AAAA-TAAAATTAA
1 AAAATTAAAATTAA
925842 AAAATTAAAATTAA
1 AAAATTAAAATTAA
* *
925856 TAAATCTAAATTTAA
1 AAAAT-TAAAATTAA
925871 AA
1 AA
925873 TATAAAAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 4 0.15
14 13 0.50
15 9 0.35
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATTAAAATTAA
Found at i:925984 original size:6 final size:6
Alignment explanation
Indices: 925973--926016 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
925963 ATATATAATT
* *
925973 TAAAAA TAAAAA TAAAAT TAAAAA TTAAAAAA TACAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA -T-AAAAA TAAAAA TAAAAA
926017 ATATGAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 25 0.78
7 2 0.06
8 5 0.16
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:925988 original size:26 final size:26
Alignment explanation
Indices: 925959--926020 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
925949 AAATTAACAT
*
925959 TAAAATATATAATTTAAAAATAAAAA
1 TAAAATATATAATTAAAAAATAAAAA
* *
925985 TAAAAT-TAAAAATTAAAAAATACAAA
1 TAAAATAT-ATAATTAAAAAATAAAAA
*
926011 TAAAAAATAT
1 TAAAATATAT
926021 GAAGTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 1 0.03
26 27 0.93
27 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (26 bp):
TAAAATATATAATTAAAAAATAAAAA
Found at i:925991 original size:19 final size:19
Alignment explanation
Indices: 925957--926018 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
925947 GCAAATTAAC
*
925957 ATTAAAATATATAATTTAAAA
1 ATTAAAA-ATA-AAATTAAAA
925978 A-TAAAAATAAAATTAAAA
1 ATTAAAAATAAAATTAAAA
*
925996 ATTAAAAAATACAAATAAAAA
1 ATT-AAAAATA-AAATTAAAA
926017 AT
1 AT
926019 ATGAAGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 9 0.25
19 4 0.11
20 12 0.33
21 11 0.31
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
ATTAAAAATAAAATTAAAA
Found at i:925994 original size:12 final size:13
Alignment explanation
Indices: 925957--926019 Score: 56
Period size: 14 Copynumber: 4.8 Consensus size: 13
925947 GCAAATTAAC
*
925957 ATTAAAATATATAA
1 ATTAAAA-ATAAAA
*
925971 TTTAAAAATAAAA
1 ATTAAAAATAAAA
*
925984 A-TAAAATTAAAA
1 ATTAAAAATAAAA
*
925996 ATTAAAAAATACAA
1 ATT-AAAAATAAAA
*
926010 ATAAAAAATA
1 ATTAAAAATA
926020 TGAAGTTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
12 11 0.28
13 13 0.32
14 16 0.40
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
ATTAAAAATAAAA
Found at i:926014 original size:13 final size:13
Alignment explanation
Indices: 925974--926019 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
925964 TATATAATTT
925974 AAAAATAAAAAT-
1 AAAAATAAAAATA
*
925986 AAAATTAAAAATTA
1 AAAAATAAAAA-TA
*
926000 AAAAATACAAATA
1 AAAAATAAAAATA
926013 AAAAATA
1 AAAAATA
926020 TGAAGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 10 0.34
13 10 0.34
14 9 0.31
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:927160 original size:23 final size:23
Alignment explanation
Indices: 927129--927187 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
927119 ACACGCCTAT
*
927129 AACATTAAAAATTAAT-TAAAATAA
1 AACA-TAAAAATAAATATAAAAT-A
* *
927153 AATATAAAAATAAATATAACATA
1 AACATAAAAATAAATATAAAATA
927176 AACATAAAAATA
1 AACATAAAAATA
927188 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (23 bp):
AACATAAAAATAAATATAAAATA
Found at i:927254 original size:23 final size:23
Alignment explanation
Indices: 927228--927272 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
927218 TATAATATTT
* *
927228 TAAATAATAAAAATTATGAATAA
1 TAAATAATAAAAAATATAAATAA
927251 TAAATAATAAAAAATATAAATA
1 TAAATAATAAAAAATATAAATA
927273 TGTATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAATAATAAAAAATATAAATAA
Found at i:927914 original size:2 final size:2
Alignment explanation
Indices: 927907--927935 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
927897 TCTCCTTTGC
927907 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 A
927936 AATCTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:928379 original size:3 final size:3
Alignment explanation
Indices: 928367--928442 Score: 57
Period size: 3 Copynumber: 23.7 Consensus size: 3
928357 AGATAGATAG
928367 ATA ATAA ATA ATA ATA ATA ATA A-A TATA A-A TATA GATAA ATA GATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA -ATA -AT-A ATA -ATA
* *
928413 ATAA AGA ACA ATA ATA ATA ATA ATA ATA AT
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT
928443 TTTTTTATCT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
2 2 0.03
3 44 0.72
4 14 0.23
5 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:928402 original size:43 final size:43
Alignment explanation
Indices: 928349--928432 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
928339 TATATACATG
* * * *
928349 ATAAGTATAGATAGATAGATAATAAATAATAATAATAATAAAT
1 ATAAATATAGATAAATAGATAATAAAGAACAATAATAATAAAT
928392 ATAAATATAGATAAATAGATAATAAAGAACAATAATAATAA
1 ATAAATATAGATAAATAGATAATAAAGAACAATAATAATAA
928433 TAATAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.27
Consensus pattern (43 bp):
ATAAATATAGATAAATAGATAATAAAGAACAATAATAATAAAT
Found at i:928808 original size:29 final size:29
Alignment explanation
Indices: 928767--928833 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 29
928757 AATTTTATTT
*
928767 ATATATAATTTTACATTGTT-AATAAATATAA
1 ATAT-TAATTTTAAATT-TTAAAT-AATATAA
*
928798 ATATTAA-TTTAAATTTTAAATAATTTAA
1 ATATTAATTTTAAATTTTAAATAATATAA
928826 ATAATTAA
1 AT-ATTAA
928834 ATAAAAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 10 0.31
29 15 0.47
30 3 0.09
31 4 0.12
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
ATATTAATTTTAAATTTTAAATAATATAA
Found at i:928821 original size:16 final size:17
Alignment explanation
Indices: 928802--928837 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
928792 ATATAAATAT
*
928802 TAATTTAAAT-TTTAAA
1 TAATTTAAATAATTAAA
928818 TAATTTAAATAATTAAA
1 TAATTTAAATAATTAAA
928835 TAA
1 TAA
928838 AAGTAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTAAATAATTAAA
Found at i:928835 original size:8 final size:9
Alignment explanation
Indices: 928802--928837 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
928792 ATATAAATAT
928802 TAATTTAAA
1 TAATTTAAA
928811 T--TTTAAA
1 TAATTTAAA
928818 TAATTTAAA
1 TAATTTAAA
928827 TAA-TTAAA
1 TAATTTAAA
928835 TAA
1 TAA
928838 AAGTAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.28
8 8 0.32
9 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATTTAAA
Found at i:931069 original size:52 final size:52
Alignment explanation
Indices: 930991--931092 Score: 195
Period size: 52 Copynumber: 2.0 Consensus size: 52
930981 TAAAACTTTC
930991 ATTAAGATTAACTTTGTAGTTCAAAGTCACAACTCTTTCCTATGAATTTTTT
1 ATTAAGATTAACTTTGTAGTTCAAAGTCACAACTCTTTCCTATGAATTTTTT
*
931043 ATTAAGATTAACTTTGTAGTTCAAAGTCACAACTCTTTCCTATGAGTTTT
1 ATTAAGATTAACTTTGTAGTTCAAAGTCACAACTCTTTCCTATGAATTTT
931093 CTAACTCTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (52 bp):
ATTAAGATTAACTTTGTAGTTCAAAGTCACAACTCTTTCCTATGAATTTTTT
Found at i:933821 original size:88 final size:88
Alignment explanation
Indices: 933729--934015 Score: 283
Period size: 88 Copynumber: 3.3 Consensus size: 88
933719 TAGAATGAAG
* * * *
933729 TGATACCCCATGCATCTATTACATTTTTCAGGTTCTAAAAAATTTATTAAGCATTAGTCAAATAT
1 TGATACCACATACATCTGTCACATTTTTCAGGTTCTAAAAAATTTATTAAGCATTAGTCAAATAT
* *
933794 TTTTTATCGTGTCAGAAGGAATT
66 TTTTTATCGTGTCAGAAAGAATC
* * ** *
933817 TGATACCACATACATCTGTCACGTTTTTCAGGTT-TCAATAAATTTATTGGGCATTAATCAAAT-
1 TGATACCACATACATCTGTCACATTTTTCAGGTTCT-AAAAAATTTATTAAGCATTAGTCAAATA
* * * *
933880 TTTTCTGTCGTGTAAGAAATAATC
65 TTTTTTATCGTGTCAGAAAGAATC
* ** * * * * *
933904 TGATATCACATACATCTGTGGCATCTTTCAAGTATC-AAGAAACTTATTAAGCATTAGTTAAATA
1 TGATACCACATACATCTGTCACATTTTTCAGGT-TCTAAAAAATTTATTAAGCATTAGTCAAATA
*
933968 TTTTTTATCGTATCAGAAAGAATC
65 TTTTTTATCGTGTCAGAAAGAATC
* * * *
933992 TAATACCTCATTCATATGTCACAT
1 TGATACCACATACATCTGTCACAT
934016 CTTGAGTAAA
Statistics
Matches: 156, Mismatches: 39, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
87 67 0.43
88 89 0.57
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (88 bp):
TGATACCACATACATCTGTCACATTTTTCAGGTTCTAAAAAATTTATTAAGCATTAGTCAAATAT
TTTTTATCGTGTCAGAAAGAATC
Found at i:934018 original size:88 final size:88
Alignment explanation
Indices: 933772--934018 Score: 271
Period size: 87 Copynumber: 2.8 Consensus size: 88
933762 TCTAAAAAAT
* *
933772 TTATTAAGCATTAGTCAAATATTTTTTATCGTGTCAGAAGGAATTTGATACCACATACATCTGTC
1 TTATTAAGCATTAGTCAAATATTTTTTATCGTGTCAGAAAGAATCTGATACCACATACATCTGTC
* * * * * *
933837 ACGTTTTTCAGGTTTCAATAAAT
66 ACATCTTTCAAGTATCAAGAAAC
** * * * * * * *
933860 TTATTGGGCATTAATCAAAT-TTTTCTGTCGTGTAAGAAATAATCTGATATCACATACATCTGTG
1 TTATTAAGCATTAGTCAAATATTTTTTATCGTGTCAGAAAGAATCTGATACCACATACATCTGTC
*
933924 GCATCTTTCAAGTATCAAGAAAC
66 ACATCTTTCAAGTATCAAGAAAC
* * * * * *
933947 TTATTAAGCATTAGTTAAATATTTTTTATCGTATCAGAAAGAATCTAATACCTCATTCATATGTC
1 TTATTAAGCATTAGTCAAATATTTTTTATCGTGTCAGAAAGAATCTGATACCACATACATCTGTC
934012 ACATCTT
66 ACATCTT
934019 GAGTAAACAT
Statistics
Matches: 124, Mismatches: 34, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
87 68 0.55
88 56 0.45
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (88 bp):
TTATTAAGCATTAGTCAAATATTTTTTATCGTGTCAGAAAGAATCTGATACCACATACATCTGTC
ACATCTTTCAAGTATCAAGAAAC
Found at i:938143 original size:3 final size:3
Alignment explanation
Indices: 938135--938159 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
938125 TATAATGGCT
938135 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
938160 TATTGAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:940292 original size:33 final size:33
Alignment explanation
Indices: 940246--940308 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
940236 TTATGTTTAT
* *
940246 TAATTTATTTAATATGTATTTTTATCATTATTA
1 TAATTTATATAATATGTACTTTTATCATTATTA
*
940279 TAATTTGTATAATATGTACTTTTATCATTA
1 TAATTTATATAATATGTACTTTTATCATTA
940309 AAAAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (33 bp):
TAATTTATATAATATGTACTTTTATCATTATTA
Found at i:940368 original size:12 final size:11
Alignment explanation
Indices: 940338--940370 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
940328 TTTATATTTA
940338 ATCATTTATA-
1 ATCATTTATAT
940348 ATCATTTATAT
1 ATCATTTATAT
940359 ATCATGTTATAT
1 ATCAT-TTATAT
940371 GAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 5 0.24
12 6 0.29
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (11 bp):
ATCATTTATAT
Found at i:941527 original size:20 final size:20
Alignment explanation
Indices: 941491--941538 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
941481 AGTCATACGT
*
941491 TAAAA-AAAATCAGAAACAA
1 TAAAATAAAATCAAAAACAA
*
941510 TAAAATAAAATGAAAAACAA
1 TAAAATAAAATCAAAAACAA
*
941530 -AATATAAAA
1 TAAAATAAAA
941539 GGAAGTAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (20 bp):
TAAAATAAAATCAAAAACAA
Found at i:942421 original size:30 final size:31
Alignment explanation
Indices: 942385--942472 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 31
942375 AGAGGTATCG
*
942385 TAAATTAAAATTTAAATTTAATTA-ATTT-A
1 TAAATTAAAATTTAAATATAATTATATTTAA
** *
942414 TATAATTAATTTTTAAAAATAATTATATTTAA
1 TA-AATTAAAATTTAAATATAATTATATTTAA
*
942446 TAAATTTTAAATTTAAATCA-AATTATA
1 TAAA-TTAAAATTTAAAT-ATAATTATA
942473 ATATTTATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
29 2 0.04
30 18 0.39
31 6 0.13
32 19 0.41
33 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAATTAAAATTTAAATATAATTATATTTAA
Found at i:942453 original size:26 final size:26
Alignment explanation
Indices: 942407--942456 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
942397 TAAATTTAAT
*
942407 TAATTTATATAATTAATTTTTAAAAA
1 TAATTTATATAATTAAATTTTAAAAA
*
942433 TAATTATATTTAA-TAAATTTTAAA
1 TAATT-TATATAATTAAATTTTAAA
942457 TTTAAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAATTTATATAATTAAATTTTAAAAA
Found at i:946601 original size:86 final size:87
Alignment explanation
Indices: 946493--946789 Score: 215
Period size: 86 Copynumber: 3.4 Consensus size: 87
946483 TTTTTGTCGT
* * *
946493 GTTAGAATGAAAC-GATACCCCATGCATCTGTTACATTTTTCAGGTTTCAAAAAATTTATT-GGC
1 GTTAGAAAGAATCTGATA-CCCATGCATCTGTCACATTTTTCAGGTTTCAAAAAATTTATTAGGC
*
946556 ATTAGTCAAATATTTTCTATCAC
65 ATTAGTTAAATATTTTCTATCAC
* * * * * ** * *
946579 GTTAGAAGGAATCTGATACCCATACATTTATCACGTTTTTTGGGTTTCAATAAATTTATTGGGCA
1 GTTAGAAAGAATCTGATACCCATGCATCTGTCACATTTTTCAGGTTTCAAAAAATTTATTAGGCA
* * * ***
946644 TTAATTAAAT-GTTTCTGTTGT
66 TTAGTTAAATATTTTCTATCAC
* * ** * * * * *
946665 GTAAGAAATAATCTGATACCACATGCATCTGTGGCATCTTTCAAGTTTCAAGAAACTTATTAAGC
1 GTTAGAAAGAATCTGATACC-CATGCATCTGTCACATTTTTCAGGTTTCAAAAAATTTATTAGGC
* *
946730 ATTAGTTAAATAATTTT-TGTCAT
65 ATTAGTTAAAT-ATTTTCTATCAC
* * * * *
946753 ATCAGAAAGAATATGATACCTCATTCATCTATCACAT
1 GTTAGAAAGAATCTGATACC-CATGCATCTGTCACAT
946790 CTTAAGTAAA
Statistics
Matches: 159, Mismatches: 47, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
86 68 0.43
87 56 0.35
88 32 0.20
89 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (87 bp):
GTTAGAAAGAATCTGATACCCATGCATCTGTCACATTTTTCAGGTTTCAAAAAATTTATTAGGCA
TTAGTTAAATATTTTCTATCAC
Found at i:947295 original size:155 final size:155
Alignment explanation
Indices: 947128--947432 Score: 513
Period size: 155 Copynumber: 2.0 Consensus size: 155
947118 CTTAAATAAC
* * * *
947128 TTTTTTTTAGTGGCTTTATCTGTAATATCTTAAACCTTACTCATAAATATATTCATAACTGTTGT
1 TTTTTTTTAGTGGCTTCATATGAAATATCTTAAACCTTACTCATAAACATATTCATAACTGTTGT
* *
947193 ACCCAAAAATAGATTTCAGCTATTAGAGGAAA-CAGTACTTGTTGTACCATAAAAAAGATTCAAG
66 ACCCAAAAATAGATTTCAGCTATTAGA-GAAAGCAGTACCTGCTGTACCATAAAAAAGATTCAAG
*
947257 GTAGAAGTATCACCAAAGCCTGAAAT
130 GTACAAGTATCACCAAAGCCTGAAAT
*
947283 TTTTTTTTAGTGGCTTCATATGAAATATCTTAAACCTTACTCATAAACATATTCATAATTGTTGT
1 TTTTTTTTAGTGGCTTCATATGAAATATCTTAAACCTTACTCATAAACATATTCATAACTGTTGT
*
947348 ACCCAAAAATAGATTTCAGCTATTAGAGAAAGCAGTACCTGCTGTACCATAAAATAGATTCAAGG
66 ACCCAAAAATAGATTTCAGCTATTAGAGAAAGCAGTACCTGCTGTACCATAAAAAAGATTCAAGG
947413 TACAAGTATCACCAAAGCCT
131 TACAAGTATCACCAAAGCCT
947433 AAAACTAAAA
Statistics
Matches: 140, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
154 4 0.03
155 136 0.97
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (155 bp):
TTTTTTTTAGTGGCTTCATATGAAATATCTTAAACCTTACTCATAAACATATTCATAACTGTTGT
ACCCAAAAATAGATTTCAGCTATTAGAGAAAGCAGTACCTGCTGTACCATAAAAAAGATTCAAGG
TACAAGTATCACCAAAGCCTGAAAT
Found at i:953206 original size:33 final size:33
Alignment explanation
Indices: 953160--953222 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
953150 TTATGTTTAT
* *
953160 TAATTTATTTAATATGTATTTTTATCATTATTA
1 TAATTTATATAATATGTACTTTTATCATTATTA
*
953193 TAATTTGTATAATATGTACTTTTATCATTA
1 TAATTTATATAATATGTACTTTTATCATTA
953223 AAAAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (33 bp):
TAATTTATATAATATGTACTTTTATCATTATTA
Found at i:953282 original size:12 final size:11
Alignment explanation
Indices: 953252--953284 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
953242 TTTATATTTA
953252 ATCATTTATA-
1 ATCATTTATAT
953262 ATCATTTATAT
1 ATCATTTATAT
953273 ATCATGTTATAT
1 ATCAT-TTATAT
953285 GAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 5 0.24
12 6 0.29
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (11 bp):
ATCATTTATAT
Found at i:954442 original size:20 final size:20
Alignment explanation
Indices: 954406--954453 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
954396 AGTCATACGT
*
954406 TAAAA-AAAATCAGAAACAA
1 TAAAATAAAATCAAAAACAA
*
954425 TAAAATAAAATGAAAAACAA
1 TAAAATAAAATCAAAAACAA
*
954445 -AATATAAAA
1 TAAAATAAAA
954454 GGAAGTAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (20 bp):
TAAAATAAAATCAAAAACAA
Found at i:955336 original size:30 final size:31
Alignment explanation
Indices: 955300--955387 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 31
955290 AGAGGTATCG
*
955300 TAAATTAAAATTTAAATTTAATTA-ATTT-A
1 TAAATTAAAATTTAAATATAATTATATTTAA
** *
955329 TATAATTAATTTTTAAAAATAATTATATTTAA
1 TA-AATTAAAATTTAAATATAATTATATTTAA
*
955361 TAAATTTTAAATTTAAATCA-AATTATA
1 TAAA-TTAAAATTTAAAT-ATAATTATA
955388 ATATTTATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
29 2 0.04
30 18 0.39
31 6 0.13
32 19 0.41
33 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAATTAAAATTTAAATATAATTATATTTAA
Found at i:955368 original size:26 final size:26
Alignment explanation
Indices: 955322--955371 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
955312 TAAATTTAAT
*
955322 TAATTTATATAATTAATTTTTAAAAA
1 TAATTTATATAATTAAATTTTAAAAA
*
955348 TAATTATATTTAA-TAAATTTTAAA
1 TAATT-TATATAATTAAATTTTAAA
955372 TTTAAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAATTTATATAATTAAATTTTAAAAA
Found at i:960095 original size:30 final size:31
Alignment explanation
Indices: 960045--960105 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
960035 GCTACAACAA
*
960045 AAATGAGTGTTCTAAAATGTCATCCCAAGTG
1 AAATGAGCGTTCTAAAATGTCATCCCAAGTG
*
960076 AAATGAGCGTT-TTAAATGTCATCCCAAGTG
1 AAATGAGCGTTCTAAAATGTCATCCCAAGTG
960106 TCATAAGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (31 bp):
AAATGAGCGTTCTAAAATGTCATCCCAAGTG
Found at i:962944 original size:18 final size:18
Alignment explanation
Indices: 962921--962956 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
962911 AAAAACCGTA
962921 TACATAGATACTTAGCAT
1 TACATAGATACTTAGCAT
962939 TACATAGATACTTAGCAT
1 TACATAGATACTTAGCAT
962957 ACGCAAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
TACATAGATACTTAGCAT
Found at i:968027 original size:3 final size:3
Alignment explanation
Indices: 968019--968053 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
968009 TTCTCCATTA
968019 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
968054 ATAGCAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:969035 original size:21 final size:21
Alignment explanation
Indices: 968996--969058 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
968986 AATATTTCTT
* *
968996 TTTAATTAAT-ATTTTTATTA
1 TTTAAATAATAATTTATATTA
969016 TTTAAATAATAATTTATATTA
1 TTTAAATAATAATTTATATTA
* *
969037 TAATAAATTA-AATTTA-ATTA
1 T-TTAAATAATAATTTATATTA
969057 TT
1 TT
969059 AAAAAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 14 0.39
21 16 0.44
22 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAAATAATAATTTATATTA
Found at i:969065 original size:21 final size:21
Alignment explanation
Indices: 969026--969093 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
969016 TTTAAATAAT
*
969026 AATTTATATTA-TAATAAATTA
1 AATTTA-ATTATTAAAAAATTA
969047 AATTTAATTATTAAAAAATTA
1 AATTTAATTATTAAAAAATTA
** *
969068 TTTTTAA-AATTAAATTAAATTA
1 AATTTAATTATTAAA--AAATTA
969090 AATT
1 AATT
969094 AAATAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 10 0.26
21 20 0.53
22 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTAATTATTAAAAAATTA
Found at i:969627 original size:17 final size:18
Alignment explanation
Indices: 969593--969631 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
969583 ATATTTAAAA
969593 TTTAAATATTTTAAATAT
1 TTTAAATATTTTAAATAT
*
969611 TTTAAATATTTT-TATAT
1 TTTAAATATTTTAAATAT
969628 TTTA
1 TTTA
969632 TATTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAATATTTTAAATAT
Found at i:970482 original size:18 final size:17
Alignment explanation
Indices: 970448--970498 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
970438 TATATATTTT
970448 ATAA-TTAAATATAAATA
1 ATAATTTAAAT-TAAATA
*
970465 ATAATTATTAATTAAATA
1 ATAATT-TAAATTAAATA
970483 ATAATTTAAATTAAAT
1 ATAATTTAAATTAAAT
970499 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 13 0.43
19 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTTAAATTAAATA
Found at i:970510 original size:20 final size:22
Alignment explanation
Indices: 970445--970515 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 22
970435 GTTTATATAT
970445 TTTATAATTAAATATAAATAATAA
1 TTTA-AATTAAAT-TAAATAATAA
970469 -TT--ATT-AATTAAATAATAA
1 TTTAAATTAAATTAAATAATAA
970487 TTTAAATTAAATTAAA-AA-AA
1 TTTAAATTAAATTAAATAATAA
970507 TTTAAATTA
1 TTTAAATTA
970516 TAAATTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
18 10 0.23
19 5 0.12
20 14 0.33
21 5 0.12
22 7 0.16
23 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAATTAAATTAAATAATAA
Found at i:971032 original size:11 final size:11
Alignment explanation
Indices: 971012--971042 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
971002 TAAATTTAAA
971012 TTTAAATATTT
1 TTTAAATATTT
*
971023 TTTTAATATTT
1 TTTAAATATTT
971034 TTTAAATAT
1 TTTAAATAT
971043 ATTATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAAATATTT
Found at i:973220 original size:18 final size:18
Alignment explanation
Indices: 973194--973228 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
973184 ATTCATAATA
973194 ATATATATTAAACATATC
1 ATATATATTAAACATATC
* *
973212 ATATTTATTAAATATAT
1 ATATATATTAAACATAT
973229 TTTTATCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATATTAAACATATC
Found at i:975659 original size:22 final size:22
Alignment explanation
Indices: 975617--975660 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
975607 ATTTAAATAT
*
975617 TTATAATTTTTTTATTTTTAAA
1 TTATAATTTTTTTATTATTAAA
*
975639 TTATAGTTTTATTTA-TATTAAA
1 TTATAATTTT-TTTATTATTAAA
975661 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATAATTTTTTTATTATTAAA
Found at i:976065 original size:18 final size:16
Alignment explanation
Indices: 976044--976088 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 16
976034 TTTAATGAGA
976044 TAATATTATCTAATAAAT
1 TAATATTAT-T-ATAAAT
976062 TAATATTA-TATAAAT
1 TAATATTATTATAAAT
976077 TATATATTATTA
1 TA-ATATTATTA
976089 GTACATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.32
16 7 0.28
17 2 0.08
18 8 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATTATTATAAAT
Found at i:976085 original size:22 final size:24
Alignment explanation
Indices: 976060--976113 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
976050 TATCTAATAA
* *
976060 ATTAATATTATA-TAAAT-TATAT
1 ATTAATATTACATTAAATATAAAT
* *
976082 ATTATTAGTACATTAAATATAAAT
1 ATTAATATTACATTAAATATAAAT
976106 ATTAATAT
1 ATTAATAT
976114 AAATTTACGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 9 0.38
23 5 0.21
24 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTAATATTACATTAAATATAAAT
Found at i:976101 original size:18 final size:17
Alignment explanation
Indices: 976045--976101 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
976035 TTAATGAGAT
976045 AATATTATCTAATAAATT-
1 AATATTAT-T-ATAAATTA
976063 AATATTA-TATAAATTA
1 AATATTATTATAAATTA
* *
976079 TATATTATTAGTACATTA
1 AATATTATTA-TAAATTA
976097 AATAT
1 AATAT
976102 AAATATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.21
16 7 0.21
17 2 0.06
18 17 0.52
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (17 bp):
AATATTATTATAAATTA
Found at i:980557 original size:2 final size:2
Alignment explanation
Indices: 980550--980582 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
980540 CTCATTTTTC
*
980550 AT AT AT AT AT AT AT AT AT GT 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
980583 ATTATACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:983129 original size:22 final size:22
Alignment explanation
Indices: 983098--983141 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
983088 ATTTAAATAT
* *
983098 TTATAATTTTTTTTATTTTAAA
1 TTATAATTTTATTTATATTAAA
*
983120 TTATAGTTTTATTTATATTAAA
1 TTATAATTTTATTTATATTAAA
983142 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATAATTTTATTTATATTAAA
Found at i:983531 original size:18 final size:16
Alignment explanation
Indices: 983510--983553 Score: 63
Period size: 15 Copynumber: 2.7 Consensus size: 16
983500 TTTAATGAGA
983510 TAATATTATCTAATAAAT
1 TAATATTAT-T-ATAAAT
983528 TAATATTA-TATAAAT
1 TAATATTATTATAAAT
983543 TAATATTATTA
1 TAATATTATTA
983554 GTACATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.56
16 3 0.12
18 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATATTATTATAAAT
Found at i:985620 original size:20 final size:20
Alignment explanation
Indices: 985576--985621 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
985566 CATATTAACG
985576 TATATT-TTTATTATAATAT
1 TATATTATTTATTATAATAT
985595 T-T-TTATTTATTA-AATAT
1 TATATTATTTATTATAATAT
985612 TAATATTATT
1 T-ATATTATT
985622 AATCGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 2 0.09
20 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTATTTATTATAATAT
Found at i:1025783 original size:11 final size:11
Alignment explanation
Indices: 1025767--1025794 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1025757 AGATGAATTT
1025767 ATAATATAATA
1 ATAATATAATA
1025778 ATAATATAATA
1 ATAATATAATA
1025789 ATAATA
1 ATAATA
1025795 ATATAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATATAATA
Found at i:1025791 original size:14 final size:14
Alignment explanation
Indices: 1025772--1025799 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1025762 AATTTATAAT
1025772 ATAATAATAATATA
1 ATAATAATAATATA
1025786 ATAATAATAATATA
1 ATAATAATAATATA
1025800 GCAAAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAATAATAATATA
Found at i:1030346 original size:2 final size:2
Alignment explanation
Indices: 1030339--1030377 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1030329 TTGAGTTAAA
1030339 AT AT AT 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 AT AT AT A
1030378 AGAAATGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1036361 original size:3 final size:3
Alignment explanation
Indices: 1036353--1036385 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1036343 AGATGAATTT
1036353 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1036386 GCAAAAGGAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1044290 original size:121 final size:121
Alignment explanation
Indices: 1044150--1044384 Score: 389
Period size: 121 Copynumber: 1.9 Consensus size: 121
1044140 TGATAATAAA
* *
1044150 TTTTCAATTTTATAAATAAAATTAAAATATTATCTTATTAATTTTATTAAAGTAAATGAGATAAT
1 TTTTCAATTTTATAAATAAAATTAAAATATTATCTTATTAATTTTACTAAAGTAAATGAAATAAT
* * *
1044215 TTTTAATTATAATATACTTGAATGAATTAAAATTATGAATTAAATTACAATAAATT
66 TTTTAATTATAAAATACTTAAATAAATTAAAATTATGAATTAAATTACAATAAATT
* *
1044271 TTTTTAATTTTATAAATAAAATTAAAATATTATTTTATTAATTTTACTAAAGTAAATGAAATAAT
1 TTTTCAATTTTATAAATAAAATTAAAATATTATCTTATTAATTTTACTAAAGTAAATGAAATAAT
**
1044336 TTTTAATTATAAAATTTTTAAATAAATTAAAATTATGAATTAAATTACA
66 TTTTAATTATAAAATACTTAAATAAATTAAAATTATGAATTAAATTACA
1044385 TCAATTTAAT
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 105 1.00
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (121 bp):
TTTTCAATTTTATAAATAAAATTAAAATATTATCTTATTAATTTTACTAAAGTAAATGAAATAAT
TTTTAATTATAAAATACTTAAATAAATTAAAATTATGAATTAAATTACAATAAATT
Found at i:1044348 original size:58 final size:58
Alignment explanation
Indices: 1044165--1044351 Score: 148
Period size: 58 Copynumber: 3.1 Consensus size: 58
1044155 AATTTTATAA
* *
1044165 ATAAAATTAAAATATTATCTTATTAATTTTATTAAAGTAAATGAGATAATTTTTAATT
1 ATAAAATTAAAATATTATATTATTAATTTTATTAAAGTAAATGAAATAATTTTTAATT
* * * ** ****
1044223 ATAATATACTTGAATGAAT-TAAAATTATGAATTAAATTACAA-TAAATTTTTTTAATTTTATAA
1 ATAA-A-A-TT-AA--AATATTATATTATTAATTTTATTA-AAGTAAA-TGAAATAATTTT-TAA
1044286 --
57 TT
* *
1044286 ATAAAATTAAAATATTATTTTATTAATTTTACTAAAGTAAATGAAATAATTTTTAATT
1 ATAAAATTAAAATATTATATTATTAATTTTATTAAAGTAAATGAAATAATTTTTAATT
1044344 ATAAAATT
1 ATAAAATT
1044352 TTTAAATAAA
Statistics
Matches: 95, Mismatches: 21, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
56 3 0.03
57 13 0.14
58 29 0.31
59 3 0.03
60 3 0.03
61 3 0.03
62 3 0.03
63 22 0.23
64 13 0.14
65 3 0.03
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (58 bp):
ATAAAATTAAAATATTATATTATTAATTTTATTAAAGTAAATGAAATAATTTTTAATT
Found at i:1045269 original size:16 final size:17
Alignment explanation
Indices: 1045248--1045279 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1045238 TAAATAATCA
1045248 AAATTTAA-AAAATATT
1 AAATTTAATAAAATATT
1045264 AAATTTAATAAAATAT
1 AAATTTAATAAAATAT
1045280 ATTGTGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAATAAAATATT
Found at i:1045521 original size:2 final size:2
Alignment explanation
Indices: 1045516--1045553 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1045506 ATAATCTCTC
1045516 AT AT AT AT 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
1045554 GTATTGAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1048161 original size:6 final size:6
Alignment explanation
Indices: 1048144--1048196 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
1048134 TGCACATAAA
*
1048144 TATATAT TATATT TATATT TATATT TGATAATT TATA-T TAAATT TA-ATT
1 TATAT-T TATATT TATATT TATATT T-AT-ATT TATATT TATATT TATATT
1048193 TATA
1 TATA
1048197 AAACTCATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
5 9 0.22
6 19 0.46
7 9 0.22
8 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TATATT
Found at i:1048179 original size:14 final size:12
Alignment explanation
Indices: 1048144--1048196 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 12
1048134 TGCACATAAA
1048144 TATATATTATATT
1 TATAT-TTATATT
1048157 TATATTTATATT
1 TATATTTATATT
1048169 TGATAATTTATA-T
1 T-AT-ATTTATATT
*
1048182 TAAATTTA-ATT
1 TATATTTATATT
1048193 TATA
1 TATA
1048197 AAACTCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 1 0.03
11 9 0.26
12 9 0.26
13 9 0.26
14 7 0.20
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TATATTTATATT
Found at i:1049106 original size:24 final size:25
Alignment explanation
Indices: 1049078--1049132 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1049068 ATACGAATCT
*
1049078 AATTTTAA-TATT-TAAAATTAATTA
1 AATTTTAATTATTATAAAA-TAATAA
*
1049102 AATTTAAATTATTATAAAATAATAA
1 AATTTTAATTATTATAAAATAATAA
1049127 AATTTT
1 AATTTT
1049133 TATTTGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 7 0.27
25 14 0.54
26 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTTAATTATTATAAAATAATAA
Found at i:1049239 original size:23 final size:23
Alignment explanation
Indices: 1049186--1049240 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1049176 AGATTCATTT
**
1049186 TTTATTTAAAATTTTATTTAATA
1 TTTATTTAAAAAATTATTTAATA
*
1049209 -TTATTTTAAAAAATTATTTTATA
1 TTTA-TTTAAAAAATTATTTAATA
1049232 TTTATTTAA
1 TTTATTTAA
1049241 CATTTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.11
23 21 0.78
24 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTATTTAAAAAATTATTTAATA
Found at i:1049261 original size:22 final size:25
Alignment explanation
Indices: 1049224--1049275 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
1049214 TTAAAAAATT
1049224 ATTTTATATTTATTTAACATTT-AA
1 ATTTTATATTTATTTAACATTTAAA
*
1049248 ATTTTAT-TTT-TTTAATATTTAAA
1 ATTTTATATTTATTTAACATTTAAA
1049271 ATTTT
1 ATTTT
1049276 TACCAGCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 10 0.38
24 7 0.27
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTTATATTTATTTAACATTTAAA
Found at i:1049992 original size:2 final size:2
Alignment explanation
Indices: 1049987--1050021 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1049977 TCTCTCTCTC
1049987 TA 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 TA T
1050022 TTCAAAATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.