Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold576
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: 32587
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.27
Warning! 6754 characters in sequence are not A, C, G, or T
Found at i:6804 original size:10 final size:10
Alignment explanation
Indices: 6789--6862 Score: 82
Period size: 10 Copynumber: 7.3 Consensus size: 10
6779 ATAAGTAAGT
6789 TATTATATTA
1 TATTATATTA
6799 TATTATTATTA
1 TATTA-TATTA
6810 TATTATATTA
1 TATTATATTA
6820 TATTATATTA
1 TATTATATTA
*
6830 CA--ATATTA
1 TATTATATTA
6838 TA-TATATATA
1 TATTATAT-TA
6848 TATATATATATA
1 TAT-TATAT-TA
6860 TAT
1 TAT
6863 AACAAAAGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
8 7 0.12
9 4 0.07
10 25 0.44
11 10 0.18
12 11 0.19
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (10 bp):
TATTATATTA
Found at i:6843 original size:2 final size:2
Alignment explanation
Indices: 6792--6863 Score: 65
Period size: 2 Copynumber: 41.0 Consensus size: 2
6782 AGTAAGTTAT
6792 TA TA T- TA TA T- TA T- TA T- TA TA T- TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
6827 T- TA CA -A TA T- 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
6864 ACAAAAGAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
1 10 0.17
2 49 0.83
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6855 original size:8 final size:8
Alignment explanation
Indices: 6792--6863 Score: 65
Period size: 7 Copynumber: 10.2 Consensus size: 8
6782 AGTAAGTTAT
6792 TATAT-TA
1 TATATATA
6799 TAT-TAT-
1 TATATATA
6805 TAT-TATA
1 TATATATA
6812 T-TATAT-
1 TATATATA
6818 TATAT-TA
1 TATATATA
*
6825 TAT-TACA
1 TATATATA
6832 -ATAT-TA
1 TATATATA
6838 TATATATA
1 TATATATA
6846 TATATATA
1 TATATATA
6854 TATATATA
1 TATATATA
6862 TA
1 TA
6864 ACAAAAGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
6 14 0.26
7 20 0.37
8 20 0.37
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (8 bp):
TATATATA
Found at i:6927 original size:11 final size:11
Alignment explanation
Indices: 6911--6936 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6901 AATTTGAAAC
6911 GAAACAGGGGA
1 GAAACAGGGGA
6922 GAAACAGGGGA
1 GAAACAGGGGA
6933 GAAA
1 GAAA
6937 GCAAGAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:7987 original size:25 final size:23
Alignment explanation
Indices: 7959--8061 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 23
7949 ACTTTAGCGC
* *
7959 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTG--TATTAGCACATTAGT
*
7984 GCTCTCTGATATTTAGCACATCAGT
1 GCTCTCTG-TA-TTAGCACATTAGT
8009 GCTCTCTGT-TTAGCACATCT-GT
1 GCTCTCTGTATTAGCACAT-TAGT
*
8031 GCTCTCTGTA-TAGCACTTTAGT
1 GCTCTCTGTATTAGCACATTAGT
8053 GCTCTCTGT
1 GCTCTCTGT
8062 TCATTAGTGC
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.01
22 38 0.56
24 3 0.04
25 26 0.38
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (23 bp):
GCTCTCTGTATTAGCACATTAGT
Found at i:9858 original size:116 final size:117
Alignment explanation
Indices: 9640--9872 Score: 441
Period size: 116 Copynumber: 2.0 Consensus size: 117
9630 ATCAGACGTT
9640 CCTCATTCAATCTTTTGGATGTTAAAAGAACCGGTAGGGATATCTAGCTAATCATAAATTTTCAT
1 CCTCATTCAATCTTTTGGATGTTAAAAGAACCGGTAGGGATATCTAGCTAATCATAAATTTTCAT
*
9705 GTGGCATACGTTGATGTCATAATGACACCATCATTCGAAAAAAAACTAATAG
66 GTGGCATACGTTGATGTCATAATGACAACATCATTCGAAAAAAAACTAATAG
9757 CCTCATTCAAT-TTTTGGATGTTAAAAGAACCGGTAGGGATATCTAGCTAATCATAAATTTTCAT
1 CCTCATTCAATCTTTTGGATGTTAAAAGAACCGGTAGGGATATCTAGCTAATCATAAATTTTCAT
*
9821 GTGGCATACGTTGATGTCATAATGACAACATCCTTCGAAAAAAAACTAATAG
66 GTGGCATACGTTGATGTCATAATGACAACATCATTCGAAAAAAAACTAATAG
9873 ATCTTTTAAA
Statistics
Matches: 114, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
116 103 0.90
117 11 0.10
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (117 bp):
CCTCATTCAATCTTTTGGATGTTAAAAGAACCGGTAGGGATATCTAGCTAATCATAAATTTTCAT
GTGGCATACGTTGATGTCATAATGACAACATCATTCGAAAAAAAACTAATAG
Found at i:13803 original size:175 final size:175
Alignment explanation
Indices: 13602--13962 Score: 697
Period size: 175 Copynumber: 2.1 Consensus size: 175
13592 TAACTCATCC
13602 TTAA-TAATTGTATATTAAACACAAATTTCTTTTGATTATATGAACTTAAATCTTCTATGCTAAG
1 TTAATTAATT-TATATTAAACACAAATTTCTTTTGATTATATGAACTTAAATCTTCTATGCTAAG
*
13666 CTGAAAACAAAAAAAATCTTTACAATTAATTTAATAATTAATTATTTGAGTTAATTTCATTAAGG
65 CTGAAAACAAAAAAAATCTTTACAATTAATTTAATAATTAATTATTTGAGTTAATTCCATTAAGG
13731 ATAATTTGAAAACATAAAATAAAAATTTAAACTTCAGGAGATTAAT
130 ATAATTTGAAAACATAAAATAAAAATTTAAACTTCAGGAGATTAAT
13777 TTAATTAATTTATATTAAACACAAATTTCTTTTGATTATATGAACTTAAATCTTCTATGCTAAGC
1 TTAATTAATTTATATTAAACACAAATTTCTTTTGATTATATGAACTTAAATCTTCTATGCTAAGC
13842 TGAAAACAAAAAAAATCTTTACAATTAATTTAATAATTAATTATTTGAGTTAATTCCATTAAGGA
66 TGAAAACAAAAAAAATCTTTACAATTAATTTAATAATTAATTATTTGAGTTAATTCCATTAAGGA
13907 TAATTTGAAAACATAAAATAAAAATTTAAACTTCAGGAGATTAAT
131 TAATTTGAAAACATAAAATAAAAATTTAAACTTCAGGAGATTAAT
13952 TTAATTAATTT
1 TTAATTAATTT
13963 CAATATTATA
Statistics
Matches: 184, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
175 179 0.97
176 5 0.03
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (175 bp):
TTAATTAATTTATATTAAACACAAATTTCTTTTGATTATATGAACTTAAATCTTCTATGCTAAGC
TGAAAACAAAAAAAATCTTTACAATTAATTTAATAATTAATTATTTGAGTTAATTCCATTAAGGA
TAATTTGAAAACATAAAATAAAAATTTAAACTTCAGGAGATTAAT
Found at i:15661 original size:30 final size:31
Alignment explanation
Indices: 15627--15708 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
15617 AAGAAAAAAG
*
15627 TTTTTACCAACTTTTAAGGGCCCCAAATTTT
1 TTTTTACCAACTTTTAAGGGCCCAAAATTTT
** * ***
15658 TTTTT-TTAGCTTTTAAGGATTCAAAATTTT
1 TTTTTACCAACTTTTAAGGGCCCAAAATTTT
15688 TCTTTTACCAACTTTTAAGGG
1 T-TTTTACCAACTTTTAAGGG
15709 ACTTAAAAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
30 19 0.50
31 9 0.24
32 10 0.26
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTTTACCAACTTTTAAGGGCCCAAAATTTT
Found at i:16366 original size:16 final size:17
Alignment explanation
Indices: 16345--16721 Score: 85
Period size: 18 Copynumber: 21.4 Consensus size: 17
16335 AAAAAAAACG
*
16345 AAATTTTCG-AACACGA
1 AAATTTTAGAAACACGA
16361 AAATTTTAGAAACACGA
1 AAATTTTAGAAACACGA
**
16378 ATTTTTTTTA-AAACACGA
1 A--AATTTTAGAAACACGA
* *
16396 CAATTTTTGAAACACGA
1 AAATTTTAGAAACACGA
*
16413 GAATTTTTCA-AAACAC-A
1 -AAATTTT-AGAAACACGA
* * *
16430 AATTTTATTAAAAAAACATGA
1 AA-ATT-TT--AGAAACACGA
* *
16451 CAATTTGT-GAAACACTA
1 AAATTT-TAGAAACACGA
* * * *
16468 GAGTCATT-GAAAACACGG
1 AAAT-TTTAGA-AACACGA
*
16486 AAATTTGT-GAAAAACGA
1 AAATTT-TAGAAACACGA
* * *
16503 AATTTTTTGAAGCACAGA
1 AAATTTTAGAAACAC-GA
*
16521 AATTTTTAGAAAACACGA
1 AAATTTTAG-AAACACGA
*
16539 AAATTTT-GAATCACCG-
1 AAATTTTAGAAACA-CGA
*
16555 AAATTTTTGAAAACACGA
1 AAATTTTAG-AAACACGA
* *
16573 AGATTTTTGAAACACCG-
1 AAATTTTAGAAACA-CGA
* *
16590 AAATTTTTGAAAACACGT
1 AAATTTTAG-AAACACGA
** *
16608 GGATTTTTGAAACACGA
1 AAATTTTAGAAACACGA
** * *
16625 ATTTTTTTTTGAAAATACGA
1 A--AATTTTAG-AAACACGA
*
16645 AAATTTTTGAAAACACAGA
1 AAATTTTAG-AAACAC-GA
* *
16664 AATTTTTA-AAACACGG
1 AAATTTTAGAAACACGA
* *
16680 GAATTTTTGAAACACTG-
1 AAATTTTAGAAACAC-GA
*
16697 AAATTTTTGAAAACACGA
1 AAATTTTAG-AAACACGA
*
16715 GAATTTT
1 AAATTTT
16722 TTTTACATAA
Statistics
Matches: 273, Mismatches: 55, Indels: 64
0.70 0.14 0.16
Matches are distributed among these distances:
16 32 0.12
17 96 0.35
18 101 0.37
19 26 0.10
20 16 0.06
21 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (17 bp):
AAATTTTAGAAACACGA
Found at i:16376 original size:17 final size:17
Alignment explanation
Indices: 16345--16722 Score: 196
Period size: 17 Copynumber: 21.5 Consensus size: 17
16335 AAAAAAAACG
*
16345 AAATTTTCG-AACACGA
1 AAATTTTTGAAACACGA
*
16361 AAATTTTAGAAACACGA
1 AAATTTTTGAAACACGA
** *
16378 ATTTTTTTTAAAACACGA
1 A-AATTTTTGAAACACGA
*
16396 CAATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
* *
16413 GAATTTTTCAAAACAC-A
1 AAATTTTT-GAAACACGA
* * *
16430 AATTTTATTAAAAAAACATGA
1 AAATTT-TT---GAAACACGA
* * *
16451 CAATTTGTGAAACACTA
1 AAATTTTTGAAACACGA
* * ** *
16468 GAGTCATTGAAAACACGG
1 AAATTTTTG-AAACACGA
* *
16486 AAATTTGTGAAAAACGA
1 AAATTTTTGAAACACGA
* *
16503 AATTTTTTGAAGCAC-A
1 AAATTTTTGAAACACGA
16519 GAAATTTTTAGAAAACACGA
1 -AAATTTTT-G-AAACACGA
*
16539 AAA-TTTTGAATCACCG-
1 AAATTTTTGAAACA-CGA
16555 AAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
*
16573 AGATTTTTGAAACACCG-
1 AAATTTTTGAAACA-CGA
*
16590 AAATTTTTGAAAACACGT
1 AAATTTTTG-AAACACGA
**
16608 GGATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
** *
16625 ATTTTTTTTTGAAAATACGA
1 A--AATTTTTG-AAACACGA
16645 AAATTTTTGAAAACAC-A
1 AAATTTTTG-AAACACGA
* *
16662 GAAATTTTTAAAACACGG
1 -AAATTTTTGAAACACGA
*
16680 GAATTTTTGAAACACTG-
1 AAATTTTTGAAACAC-GA
16697 AAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
*
16715 GAATTTTT
1 AAATTTTT
16723 TTTACATAAA
Statistics
Matches: 274, Mismatches: 61, Indels: 52
0.71 0.16 0.13
Matches are distributed among these distances:
16 16 0.06
17 128 0.47
18 95 0.35
19 14 0.05
20 16 0.06
21 5 0.02
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (17 bp):
AAATTTTTGAAACACGA
Found at i:16394 original size:35 final size:34
Alignment explanation
Indices: 16342--16722 Score: 290
Period size: 35 Copynumber: 10.9 Consensus size: 34
16332 TTTAAAAAAA
* *
16342 ACGAAATTTTCG--AACACGAAAATTTTAGAAAC
1 ACGAAATTTTTGAAAACACGAAAATTTTTGAAAC
* * *
16374 ACGAATTTTTTTTAAAACACGACAATTTTTGAAAC
1 ACGAA-ATTTTTGAAAACACGAAAATTTTTGAAAC
* * *
16409 ACGAGAATTTTTCAAAACAC-AAATTTTATTAAAAAAAC
1 ACGA-AATTTTTGAAAACACGAAAATTT-TT---GAAAC
* * * * * **
16447 ATGACAATTTGTG-AAACACTAGAGTCATTGAAAAC
1 ACGA-AATTTTTGAAAACACGAAAATTTTTG-AAAC
* * *
16482 ACGGAAATTTGTGAAAA-ACGAAATTTTTTGAAGC
1 AC-GAAATTTTTGAAAACACGAAAATTTTTGAAAC
*
16516 ACAGAAATTTTTAGAAAACACGAAAA-TTTTGAATC
1 AC-GAAATTTTT-GAAAACACGAAAATTTTTGAAAC
*
16551 ACCGAAATTTTTGAAAACACGAAGATTTTTGAAAC
1 A-CGAAATTTTTGAAAACACGAAAATTTTTGAAAC
***
16586 ACCGAAATTTTTGAAAACACGTGGATTTTTGAAAC
1 A-CGAAATTTTTGAAAACACGAAAATTTTTGAAAC
* *
16621 ACGAATTTTTTTTTGAAAATACGAAAATTTTTGAAAAC
1 ACGAA---ATTTTTGAAAACACGAAAATTTTTG-AAAC
**
16659 ACAGAAATTTTT-AAAACACGGGAATTTTTGAAAC
1 AC-GAAATTTTTGAAAACACGAAAATTTTTGAAAC
*
16693 ACTGAAATTTTTGAAAACACGAGAATTTTT
1 AC-GAAATTTTTGAAAACACGAAAATTTTT
16723 TTTACATAAA
Statistics
Matches: 282, Mismatches: 45, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
32 5 0.02
33 4 0.01
34 49 0.17
35 153 0.54
36 18 0.06
37 28 0.10
38 22 0.08
39 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (34 bp):
ACGAAATTTTTGAAAACACGAAAATTTTTGAAAC
Found at i:17084 original size:26 final size:25
Alignment explanation
Indices: 17040--17096 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
17030 TTAAAAATAT
* *
17040 AAATACAAAAATATAAAAATGCACA
1 AAATACAAAAATATAAAAATGAAAA
* *
17065 AAATACTAATAATATTAAAATGAAAA
1 AAATAC-AAAAATATAAAAATGAAAA
17091 AAATAC
1 AAATAC
17097 GAGCATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATACAAAAATATAAAAATGAAAA
Found at i:17204 original size:16 final size:16
Alignment explanation
Indices: 17183--17224 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
17173 AATTGAACCT
17183 TTTTTTTCTTTTTCCC
1 TTTTTTTCTTTTTCCC
*
17199 -TTTTTTCTTTTTTCTC
1 TTTTTTTC-TTTTTCCC
17215 TTTTTTTCTT
1 TTTTTTTCTT
17225 CTTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 9 0.39
17 7 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTTTCCC
Found at i:17216 original size:24 final size:25
Alignment explanation
Indices: 17181--17238 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
17171 CAAATTGAAC
*
17181 CTTTTTTTTCTTTTTCCCTT-TTTT
1 CTTTTTTCTCTTTTTCCCTTCTTTT
**
17205 CTTTTTTCTCTTTTTTTCTTCTTTT
1 CTTTTTTCTCTTTTTCCCTTCTTTT
*
17230 TTTTTTTCT
1 CTTTTTTCT
17239 GGCCTGCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (25 bp):
CTTTTTTCTCTTTTTCCCTTCTTTT
Found at i:17465 original size:7 final size:7
Alignment explanation
Indices: 17453--17520 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
17443 CTGAATTAAT
17453 TTTTTTC
1 TTTTTTC
17460 TTTTTTC
1 TTTTTTC
17467 TTTCTTT-
1 TTT-TTTC
17474 TTCTTCTTCC
1 TT-TT-TT-C
* *
17484 TTCTTCC
1 TTTTTTC
*
17491 TTTCTTC
1 TTTTTTC
17498 -TTTTTC
1 TTTTTTC
*
17504 TTTCTTC
1 TTTTTTC
17511 TTTTTTC
1 TTTTTTC
17518 TTT
1 TTT
17521 CTTCCCCGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
6 5 0.11
7 32 0.68
8 7 0.15
9 1 0.02
10 2 0.04
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTTC
Found at i:17480 original size:20 final size:20
Alignment explanation
Indices: 17452--17520 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
17442 ACTGAATTAA
17452 TTTTT-TTCTTTTTTCTTTC
1 TTTTTCTTCTTTTTTCTTTC
**
17471 TTTTTCTTCTTCCTTC-TTC
1 TTTTTCTTCTTTTTTCTTTC
*
17490 -CTTTCTTC-TTTTTCTTTC
1 TTTTTCTTCTTTTTTCTTTC
*
17508 TTCTTTTTTCTTT
1 TT-TTTCTTCTTT
17521 CTTCCCCGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 4 0.11
18 10 0.26
19 8 0.21
20 14 0.37
21 2 0.05
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTCTTCTTTTTTCTTTC
Found at i:17498 original size:27 final size:27
Alignment explanation
Indices: 17463--17524 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
17453 TTTTTTCTTT
17463 TTTCTTTCTTTTTC-TTCTTCCTTCTTCC
1 TTTC-TTCTTTTTCTTTCTT-CTTCTTCC
* *
17491 TTTCTTCTTTTTCTTTCTTCTTTTTTC
1 TTTCTTCTTTTTCTTTCTTCTTCTTCC
17518 TTTCTTC
1 TTTCTTC
17525 CCCGTTCAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTCTTCTTTTTCTTTCTTCTTCTTCC
Found at i:17637 original size:17 final size:17
Alignment explanation
Indices: 17605--17681 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 17
17595 ACGCTCCTCC
17605 CTTTTCTTTCTCTTCTTTT
1 CTTTT-TTT-TCTTCTTTT
17624 CTTTTTTTTCTTC--TT
1 CTTTTTTTTCTTCTTTT
*
17639 -TGTTTTTTCTTGCTTGTT
1 CTTTTTTTTCTT-CTT-TT
*
17657 GTTGTTTTTTCTT-TCTTT
1 CTT-TTTTTTCTTCT-TTT
17675 CTTTTTT
1 CTTTTTT
17682 ATTTTTGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
14 10 0.21
15 3 0.06
17 9 0.19
18 10 0.21
19 7 0.15
20 9 0.19
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (17 bp):
CTTTTTTTTCTTCTTTT
Found at i:17686 original size:20 final size:19
Alignment explanation
Indices: 17606--17678 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
17596 CGCTCCTCCC
17606 TTTTCTTTCTCTTCTTT-TCT
1 TTTTCTTTCT-TTCTTTGT-T
17626 TTTT-TTTC-TTCTTTGTT
1 TTTTCTTTCTTTCTTTGTT
*
17643 TTTTCTTGCTTGT-TGTTGTT
1 TTTTCTTTCTT-TCT-TTGTT
17663 TTTTCTTTCTTTCTTT
1 TTTTCTTTCTTTCTTT
17679 TTTATTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
17 11 0.24
18 4 0.09
19 9 0.20
20 21 0.47
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTCTTTGTT
Found at i:18111 original size:59 final size:58
Alignment explanation
Indices: 18019--18165 Score: 179
Period size: 59 Copynumber: 2.5 Consensus size: 58
18009 GGGCCGAATC
*
18019 GTAATTTTGAGAAAGTTTAAGGGTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
1 GTAATTTAGA-AAAGTTT-AGGGTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
* * ** *
18079 GTAATTTAGAAAAGTTTAGGTGTTGAATTGTAATTTTGAGAAAGTTTAGGGGTTAAAAT
1 GTAATTTAGAAAAGTTTAGG-GTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
*
18138 GCAATTTTAGAAAAGTTTAGAGG-TCAAA
1 GTAA-TTTAGAAAAGTTTAG-GGTTCAAA
18166 AAGCAAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
58 3 0.04
59 46 0.61
60 25 0.33
61 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GTAATTTAGAAAAGTTTAGGGTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
Found at i:18157 original size:30 final size:31
Alignment explanation
Indices: 18019--18166 Score: 164
Period size: 30 Copynumber: 5.0 Consensus size: 31
18009 GGGCCGAATC
* *
18019 GTAATTTT-GAGAAAGTTTAAGGGTTCAAAT
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
* *
18049 GTAATTTCA-AGAAAGTTTAGGGGTCAAAAT
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
* * *
18079 GTAA-TTTAGA-AAAGTTTAGGTGTTGAATT
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
18108 GTAATTTT-GAGAAAGTTTAGGGGTTAAAAT
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
* * *
18138 GCAATTTTAGA-AAAGTTTAGAGGTCAAAA
1 GTAATTTTAGAGAAAGTTTAGGGGTTAAAA
18167 AGCAAAAAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
29 24 0.24
30 72 0.73
31 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (31 bp):
GTAATTTTAGAGAAAGTTTAGGGGTTAAAAT
Found at i:18533 original size:74 final size:74
Alignment explanation
Indices: 18348--18622 Score: 322
Period size: 74 Copynumber: 3.7 Consensus size: 74
18338 TCGAGAACAG
* * * * * * *
18348 CTCGGCGTGCGACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGATCTTCGAAAAACAAAAA
1 CTCGGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAA
*
18413 TCG-AAAATAC
64 TTGAAAAATAC
* * * *
18423 CTCGACATGTGCCCCGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAACATGAA
1 CTCGGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAA
18488 TTGAAAAATAC
64 TTGAAAAATAC
**
18499 CTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAGACATAAAT
1 CTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-ACATAAAT
18564 T-AAAAATAC
65 TGAAAAATAC
* * * *
18573 CTCAGTGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTT
1 CTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
18623 TTGAAAAAAG
Statistics
Matches: 173, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
73 16 0.09
74 83 0.48
75 60 0.35
76 12 0.07
77 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (74 bp):
CTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATT
GAAAAATAC
Found at i:18630 original size:149 final size:150
Alignment explanation
Indices: 18348--18622 Score: 369
Period size: 149 Copynumber: 1.8 Consensus size: 150
18338 TCGAGAACAG
* * * **
18348 CTCGGCGTGCGACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGATCTTCGAAAAACAAAAA
1 CTCGGCGT-CGACCCGAGACTCAACTCACCTCTCGCAATATGAGTTGATCTTAAAAAAACAAAAA
* * *
18413 TCGAAAATACCTCGACATGTGCCCCGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGA
65 TCAAAAATACCTCGACATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
18478 AAAACATGAATTGAAAAATAC
130 AAAACATGAATTGAAAAATAC
* * *
18499 CTCGGCGT-GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAGACATAAA
1 CTCGGCGTCGACCCGAGACTCAACTCACCTCTCGCAATATGAGTTGATCTTAAAAAA-ACAAAAA
* * * *
18563 TTAAAAATACCTC-A-GTGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTT
65 TCAAAAATACCTCGACATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
18623 TTGAAAAAAG
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
147 17 0.16
148 24 0.22
149 42 0.39
150 17 0.16
151 8 0.07
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (150 bp):
CTCGGCGTCGACCCGAGACTCAACTCACCTCTCGCAATATGAGTTGATCTTAAAAAAACAAAAAT
CAAAAATACCTCGACATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
AAACATGAATTGAAAAATAC
Found at i:27418 original size:18 final size:18
Alignment explanation
Indices: 27395--27429 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27385 GGACACCTTC
*
27395 AAAAATCTCTTTTTAAAG
1 AAAAATCTATTTTTAAAG
*
27413 AAAAATTTATTTTTAAA
1 AAAAATCTATTTTTAAA
27430 TTTTCCTAAA
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:0.03, T:0.43
Consensus pattern (18 bp):
AAAAATCTATTTTTAAAG
Found at i:27706 original size:16 final size:16
Alignment explanation
Indices: 27674--27725 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
27664 TTTTTTTGTT
* *
27674 TTTTAAAAAAACGAAA
1 TTTTAGAAACACGAAA
*
27690 TTTTCG-AACACGAAAA
1 TTTTAGAAACACG-AAA
27706 TTTTAGAAACACGAAA
1 TTTTAGAAACACGAAA
27722 TTTT
1 TTTT
27726 TTTTAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.17
16 19 0.63
17 6 0.20
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (16 bp):
TTTTAGAAACACGAAA
Found at i:27718 original size:17 final size:17
Alignment explanation
Indices: 27674--27762 Score: 58
Period size: 17 Copynumber: 5.2 Consensus size: 17
27664 TTTTTTTGTT
* *
27674 TTTTAAAAAAACG-AAA
1 TTTTAGAAACACGAAAA
*
27690 TTTTCG-AACACGAAAA
1 TTTTAGAAACACGAAAA
*
27706 TTTTAGAAACACGAAATTTT
1 TTTTAGAAACACGAAA---A
*
27726 TTTTA-AAACACGACAA
1 TTTTAGAAACACGAAAA
* * *
27742 TTTTTGACACACGAGAA
1 TTTTAGAAACACGAAAA
27759 TTTT
1 TTTT
27763 TCAAAACACA
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
15 5 0.09
16 16 0.28
17 22 0.39
19 9 0.16
20 5 0.09
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (17 bp):
TTTTAGAAACACGAAAA
Found at i:27734 original size:19 final size:21
Alignment explanation
Indices: 27706--27746 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
27696 AACACGAAAA
27706 TTTTAGAAACACGA-AATTTT
1 TTTTAGAAACACGACAATTTT
27726 TTTTA-AAACACGACAATTTT
1 TTTTAGAAACACGACAATTTT
27746 T
1 T
27747 GACACACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTTAGAAACACGACAATTTT
Found at i:27779 original size:53 final size:51
Alignment explanation
Indices: 27672--27787 Score: 130
Period size: 52 Copynumber: 2.3 Consensus size: 51
27662 TTTTTTTTTG
27672 TTTTTTAAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAACACGAAAT
1 TTTTTTAAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAACACGAAAT
* * * *
27723 TTTTTTTAAAACACGACAATTTTTGACACACGAGAATTTTTCA-AAACAC--AAT
1 TTTTTTAAAAAAACGA-AATTTTCGA-ACACGA-AAATTTT-AGAAACACGAAAT
*
27775 TTTTTAAAAAAAA
1 TTTTTTAAAAAAA
27788 AACATGACAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
51 14 0.26
52 21 0.39
53 6 0.11
54 12 0.22
55 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.33
Consensus pattern (51 bp):
TTTTTTAAAAAAACGAAATTTTCGAACACGAAAATTTTAGAAACACGAAAT
Found at i:27840 original size:18 final size:18
Alignment explanation
Indices: 27818--28101 Score: 202
Period size: 18 Copynumber: 16.1 Consensus size: 18
27808 ACTAGAGTCA
27818 TTGAAAACACGGAAATTT
1 TTGAAAACACGGAAATTT
*
27836 GTGAAAA-AC-GAAATTTT
1 TTGAAAACACGGAAA-TTT
* *
27853 TTG-AAGCACAGAAATTT
1 TTGAAAACACGGAAATTT
*
27870 TTAGAAAACAC-GAAAATT
1 TT-GAAAACACGGAAATTT
*
27888 TTG-AATCACCGG-AATTT
1 TTGAAAACA-CGGAAATTT
*
27905 TTAAAAACAC-GAAGATTT
1 TTGAAAACACGGAA-ATTT
* * *
27923 TTG-AAGCACCGAAAATT
1 TTGAAAACACGGAAATTT
27940 TTGAAAACAC-GAAGATTT
1 TTGAAAACACGGAA-ATTT
*
27958 TTG-AAACACCGAAATTT
1 TTGAAAACACGGAAATTT
*
27975 TTGAAAACACGTG-GATTT
1 TTGAAAACACG-GAAATTT
*
27993 TTG-AAACAC-GAATTTTTT
1 TTGAAAACACGGAA--ATTT
* *
28011 TTGAAAATACGAAAATTT
1 TTGAAAACACGGAAATTT
* * *
28029 TTTAAAACACAGATATTT
1 TTGAAAACACGGAAATTT
*
28047 TT-AAAACACGGGAATTT
1 TTGAAAACACGGAAATTT
**
28064 TTG-AAACACTAAAATTT
1 TTGAAAACACGGAAATTT
28081 TTGAAAACACGAGAAATTT
1 TTGAAAACACG-GAAATTT
28100 TT
1 TT
28102 TTTACATAAA
Statistics
Matches: 208, Mismatches: 34, Indels: 47
0.72 0.12 0.16
Matches are distributed among these distances:
15 1 0.00
16 11 0.05
17 85 0.41
18 90 0.43
19 19 0.09
20 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (18 bp):
TTGAAAACACGGAAATTT
Found at i:27857 original size:35 final size:35
Alignment explanation
Indices: 27822--28101 Score: 241
Period size: 35 Copynumber: 8.0 Consensus size: 35
27812 GAGTCATTGA
*
27822 AAACACGGAAATTTGTGAAAA-ACGAA-ATTTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAGA-TTTTTG
* * *
27856 AAGCACAGAAATTTTTAGAAAACACGAA-AATTTTG
1 AAACACGGAAATTTTT-GAAAACACGAAGATTTTTG
* *
27891 AATCACCGG-AATTTTTAAAAACACGAAGATTTTTG
1 AAACA-CGGAAATTTTTGAAAACACGAAGATTTTTG
* * *
27926 AAGCACCGAAAATTTTGAAAACACGAAGATTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAGATTTTTG
* **
27961 AAACACCGAAATTTTTGAAAACACGTGGATTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAGATTTTTG
* * * *
27996 AAACAC-GAATTTTTTTTGAAAATACGAAAATTTTTTA
1 AAACACGGAA--ATTTTTGAAAACACGAAGA-TTTTTG
* * *
28033 AAACACAGATATTTTT-AAAACACG-GGAATTTTTG
1 AAACACGGAAATTTTTGAAAACACGAAG-ATTTTTG
** *
28067 AAACACTAAAATTTTTGAAAACACGAGAAATTTTT
1 AAACACGGAAATTTTTGAAAACACGA-AGATTTTT
28102 TTTACATAAA
Statistics
Matches: 200, Mismatches: 33, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
34 46 0.23
35 108 0.54
36 33 0.17
37 11 0.05
38 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (35 bp):
AAACACGGAAATTTTTGAAAACACGAAGATTTTTG
Found at i:27980 original size:17 final size:17
Alignment explanation
Indices: 27822--28101 Score: 151
Period size: 17 Copynumber: 15.9 Consensus size: 17
27812 GAGTCATTGA
* *
27822 AAACACGGAAATTTGTG
1 AAACACCGAAATTTTTG
*
27839 AAA-AACGAAATTTTTTG
1 AAACACCGAAA-TTTTTG
* *
27856 AAGCACAGAAATTTTTAG
1 AAACACCGAAATTTTT-G
*
27874 AAA-ACACGAAAATTTTG
1 AAACAC-CGAAATTTTTG
* *
27891 AATCACCGGAATTTTT-
1 AAACACCGAAATTTTTG
*
27907 AAAAACACGAAGATTTTTG
1 AAACAC-CGAA-ATTTTTG
* *
27926 AAGCACCGAAAATTTTG
1 AAACACCGAAATTTTTG
27943 AAA-ACACGAAGATTTTTG
1 AAACAC-CGAA-ATTTTTG
27961 AAACACCGAAATTTTTG
1 AAACACCGAAATTTTTG
**
27978 AAA-ACACGTGGATTTTTG
1 AAACAC-CG-AAATTTTTG
*
27996 AAACA-CGAATTTTTTTTG
1 AAACACCGAA--ATTTTTG
* *
28014 AAA-ATACGAAAATTTTTTA
1 AAACA-CCG-AAA-TTTTTG
* * *
28033 AAACACAGATATTTTTA
1 AAACACCGAAATTTTTG
* *
28050 AAACACGGGAATTTTTG
1 AAACACCGAAATTTTTG
**
28067 AAACACTAAAATTTTTG
1 AAACACCGAAATTTTTG
*
28084 AAAACACGAGAAATTTTT
1 -AAACAC-CGAAATTTTT
28102 TTTACATAAA
Statistics
Matches: 201, Mismatches: 39, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
16 13 0.06
17 91 0.45
18 68 0.34
19 26 0.13
20 3 0.01
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
AAACACCGAAATTTTTG
Found at i:28260 original size:21 final size:20
Alignment explanation
Indices: 28219--28262 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
28209 CGCTGCCTTA
* *
28219 TTTTTGAAAACACGAATATT
1 TTTTTGAAAACAAGAAAATT
28239 TTTTTGAAACACAAGAAAATT
1 TTTTTGAAA-ACAAGAAAATT
28260 TTT
1 TTT
28263 AAAGACACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTTGAAAACAAGAAAATT
Found at i:28285 original size:19 final size:20
Alignment explanation
Indices: 28247--28286 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28237 TTTTTTTGAA
* *
28247 ACACAAGAAAATTTTTAAAG
1 ACACAAGAAAAATTTGAAAG
28267 ACACAA-AAAAATTTGAAAG
1 ACACAAGAAAAATTTGAAAG
28286 A
1 A
28287 TAGAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (20 bp):
ACACAAGAAAAATTTGAAAG
Found at i:28466 original size:6 final size:6
Alignment explanation
Indices: 28446--28495 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
28436 AAAAGTATTC
* *
28446 AAAA-T AAAA-T AAAATT AAAATT -GAATT AAATTT AAAATTT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAATT
28492 AAAA
1 AAAA
28496 ATATAAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
5 13 0.34
6 19 0.50
7 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:28648 original size:28 final size:28
Alignment explanation
Indices: 28580--28635 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28570 AATTAAAAAA
*
28580 TGAAATTACCGAAAAGATCTCGAAACAC
1 TGAAATTACCGAAAAAATCTCGAAACAC
28608 TGAAATTACCGAAAAAATCTCGAAACAC
1 TGAAATTACCGAAAAAATCTCGAAACAC
28636 GAATTTCGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.18
Consensus pattern (28 bp):
TGAAATTACCGAAAAAATCTCGAAACAC
Found at i:28715 original size:13 final size:12
Alignment explanation
Indices: 28693--28723 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
28683 CCCTTTTTTC
28693 TTTTTTCTCTTT
1 TTTTTTCTCTTT
28705 TTTTCTTCTCTTT
1 TTTT-TTCTCTTT
28718 TTTTTT
1 TTTTTT
28724 TATGGCCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:28720 original size:15 final size:14
Alignment explanation
Indices: 28671--28724 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
28661 ATTGAACCTT
*
28671 TTTTTTCTTTTTCCC
1 TTTTTT-TTTTTCTC
28686 TTTTTTCTTTTT-TC
1 TTTTTT-TTTTTCTC
*
28700 TCTTTTTTTCTTCTC
1 T-TTTTTTTTTTCTC
28715 TTTTTTTTTT
1 TTTTTTTTTT
28725 ATGGCCTGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 14 0.41
15 20 0.59
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTTCTC
Found at i:28721 original size:16 final size:15
Alignment explanation
Indices: 28670--28724 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
28660 AATTGAACCT
*
28670 TTTTTTTCTTTTTCCC
1 TTTTTTT-TTTTTCTC
28686 TTTTTTCTTTTTTCTC
1 TTTTTT-TTTTTTCTC
*
28702 --TTTTTTTCTTCTC
1 TTTTTTTTTTTTCTC
28715 TTTTTTTTTT
1 TTTTTTTTTT
28725 ATGGCCTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 8 0.24
14 4 0.12
15 7 0.21
16 13 0.39
17 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTCTC
Found at i:28984 original size:7 final size:7
Alignment explanation
Indices: 28974--29011 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
28964 TTTTTATTTA
28974 TTTTTCT
1 TTTTTCT
28981 TTTTTCT
1 TTTTTCT
*
28988 TTCTTCT
1 TTTTTCT
28995 TTTCTTCT
1 TTT-TTCT
29003 TTTTTCT
1 TTTTTCT
29010 TT
1 TT
29012 CTTCCCCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:28990 original size:11 final size:11
Alignment explanation
Indices: 28976--29014 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
28966 TTTATTTATT
28976 TTTCTTTTTTC
1 TTTCTTTTTTC
28987 TTTCTTCTTTTC
1 TTTCTT-TTTTC
28999 -TTCTTTTTTC
1 TTTCTTTTTTC
29009 TTTCTT
1 TTTCTT
29015 CCCCGTTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.19
11 16 0.62
12 5 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:29129 original size:17 final size:17
Alignment explanation
Indices: 29097--29173 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 17
29087 ACGCTCCTCC
29097 CTTTTCTTTCTCTTCTTTT
1 CTTTT-TTT-TCTTCTTTT
29116 CTTTTTTTTCTTC--TT
1 CTTTTTTTTCTTCTTTT
*
29131 -TGTTTTTTCTTGCTTGTT
1 CTTTTTTTTCTT-CTT-TT
*
29149 GTTGTTTTTTCTT-TCTTT
1 CTT-TTTTTTCTTCT-TTT
29167 CTTTTTT
1 CTTTTTT
29174 ATTTTTGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
14 10 0.21
15 3 0.06
17 9 0.19
18 10 0.21
19 7 0.15
20 9 0.19
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (17 bp):
CTTTTTTTTCTTCTTTT
Found at i:29178 original size:20 final size:19
Alignment explanation
Indices: 29098--29170 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
29088 CGCTCCTCCC
29098 TTTTCTTTCTCTTCTTT-TCT
1 TTTTCTTTCT-TTCTTTGT-T
29118 TTTT-TTTC-TTCTTTGTT
1 TTTTCTTTCTTTCTTTGTT
*
29135 TTTTCTTGCTTGT-TGTTGTT
1 TTTTCTTTCTT-TCT-TTGTT
29155 TTTTCTTTCTTTCTTT
1 TTTTCTTTCTTTCTTT
29171 TTTATTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
17 11 0.24
18 4 0.09
19 9 0.20
20 21 0.47
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTCTTTGTT
Found at i:29545 original size:30 final size:30
Alignment explanation
Indices: 29511--29660 Score: 180
Period size: 30 Copynumber: 5.0 Consensus size: 30
29501 GGGCCGAATC
*
29511 GTAATTTTGAGAAAGTTTAAGGGTTCAAAT
1 GTAATTTTGAGAAAGTTTAAGGGTTAAAAT
** * *
29541 GTAATTTCAAGAAAGTTTAGGGGTCAAAAT
1 GTAATTTTGAGAAAGTTTAAGGGTTAAAAT
* * *
29571 GTAATTTAGA-AAAGTTT-AGGTGTTGAATT
1 GTAATTTTGAGAAAGTTTAAGG-GTTAAAAT
29600 GTAATTTTGAGAAAGTTTAAGGGTTAAAAT
1 GTAATTTTGAGAAAGTTTAAGGGTTAAAAT
*
29630 GAAATTTT-AGAAAAGTTTAAGGGTTAAAAT
1 GTAATTTTGAG-AAAGTTTAAGGGTTAAAAT
29660 G
1 G
29661 CAAAAAAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
28 2 0.02
29 23 0.23
30 73 0.72
31 3 0.03
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (30 bp):
GTAATTTTGAGAAAGTTTAAGGGTTAAAAT
Found at i:29603 original size:59 final size:58
Alignment explanation
Indices: 29511--29660 Score: 174
Period size: 59 Copynumber: 2.5 Consensus size: 58
29501 GGGCCGAATC
* *
29511 GTAATTTTGAGAAAGTTTAAGGGTTCAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAT
1 GTAATTTAGA-AAAGTTT-AGGGTTCAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAAT
* * ** *
29571 GTAATTTAGAAAAGTTTAGGTGTTGAATTGTAATTTTGAGAAAGTTTAAGGGTTAAAAT
1 GTAATTTAGAAAAGTTTAGG-GTTCAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAAT
* *
29630 GAAATTTTAGAAAAGTTTAAGGGTTAAAATG
1 GTAA-TTTAGAAAAGTTT-AGGGTTCAAATG
29661 CAAAAAAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 3 0.04
59 42 0.55
60 29 0.38
61 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (58 bp):
GTAATTTAGAAAAGTTTAGGGTTCAAATGTAATTTCAAGAAAGTTTAAGGGTCAAAAT
Found at i:30507 original size:152 final size:151
Alignment explanation
Indices: 30158--30977 Score: 1032
Period size: 152 Copynumber: 5.4 Consensus size: 151
30148 GCATGGTCCT
* *
30158 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTT-GAAAA-ACATAAATTTAAAAGAAATA
1 AGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAAGACATAAA-TT--AA-AAATA
* * ** * * * * **
30221 CATCAGCATGGTCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTT-TGAAAA-ACATA
62 CCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACATA
* * **
30284 AATTTAAAAGAAATACCTCGGCATGGTCCG
126 AA-TT--AA-AAATACCTCAGCGTGACCCG
* *
30314 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTAAAAAAGACATAAATTAAAAATACCTC
1 AGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAAGACATAAATTAAAAATACCTC
*
30377 AGTGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAAAGACATAAATT
66 AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTAAAAAAAGACATAAATT
30442 AAAAATACCTCAGCGTGACCCG
130 AAAAATACCTCAGCGTGACCCG
* *
30464 AGGCTCAATTCACCTCT-TTATTATGAGTTGATTTTTTTTAAAAAAGACATAAATTAAAAATACC
1 AGGCTCAACTCACCTCTCGTATTATGAGTTGA--TTTTTTAAAAAAGACATAAATTAAAAATACC
*
30528 TAAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAAT
64 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAAT
30593 TAAAAATACCTCAGCGTGACCCG
129 TAAAAATACCTCAGCGTGACCCG
* ** * **
30616 AGGCTCAACTCACCTCT-ATATTATGAGTTGATTTTAAAAAAAAAACCGAAATTAAAAATACCTC
1 AGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAAGACATAAATTAAAAATACCTC
* **
30680 AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAGACCGAAATTA
66 AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTA
30745 AAAATACCTCAGCGTGACCCG
131 AAAATACCTCAGCGTGACCCG
* * * ** *
30766 AGGCTTAACTCACCTCT-ATGTTATGAGTTGATTTTAAAAAAAAAAGACATAAATTAAAAACACC
1 AGGCTCAACTCACCTCTCGTATTATGAGTTGATTTT--TTAAAAAAGACATAAATTAAAAATACC
**
30830 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTAAAAAAAGACCGAAAT
64 TCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAAT
30894 TAAAAATACCTCAGCGTGACCCG
129 TAAAAATACCTCAGCGTGACCCG
* * * * *
30917 AGGCTCAACTCACCTCTAGTATTATGAGTTGA-TATTTAAAAAAAACAGAAAGTGAAAAATA
1 AGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAAGACATAAA-TTAAAAATA
30978 TTTCTTGAAA
Statistics
Matches: 600, Mismatches: 51, Indels: 32
0.88 0.07 0.05
Matches are distributed among these distances:
149 23 0.04
150 182 0.30
151 73 0.12
152 188 0.31
153 79 0.13
154 11 0.02
155 6 0.01
156 38 0.06
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (151 bp):
AGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTTAAAAAAGACATAAATTAAAAATACCTC
AGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTA
AAAATACCTCAGCGTGACCCG
Found at i:30556 original size:227 final size:224
Alignment explanation
Indices: 30158--30977 Score: 1021
Period size: 227 Copynumber: 3.6 Consensus size: 224
30148 GCATGGTCCT
* ** *
30158 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT-TGAAAA-ACATAAATTTAAAAGAAATA
1 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACAGAAA-TT--AA-AAATA
* * ** * * * * * *
30221 CATCAGCATGGTCCGAGGCTCAACTCACCTATCGCAATATGAGTTAATTTTTT-GAAAA-ACATA
61 CCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATTTTTTAAAAAAGACATA
* * ** *
30284 AATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
126 AA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-G-ATTATGAGTTGATTT
*
30349 T-AAAAAAGACATAAATTAAAAATACCTCAGTGTGACCCG
185 TAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCG
*
30388 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAAAGACATAAATTAAAAATACCTC
1 AGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTAAAAAAAGACAGAAATTAAAAATACCTC
* *
30453 AGCGTGACCCGAGGCTCAATTCACCTCT-TTATTATGAGTTGATTTTTTTTAAAAAAGACATAAA
65 AGCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGA--TTTTTTAAAAAAGACATAAA
*
30517 TTAAAAATACCTAAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAA
128 TTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTG-ATTATGAGTTGA-TTTTAAAAA
30582 AAGACATAAATTAAAAATACCTCAGCGTGACCCG
191 AAGACATAAATTAAAAATACCTCAGCGTGACCCG
* * * *
30616 AGGCTCAACTCACCTCTATATTATGAGTTGATTTTAAAAAAAAAACCGAAATTAAAAATACCTCA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATACCTCA
** **
30681 GCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTAAAAAAAAGACCGAAATTA
66 GCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATTTTTTAAAAAAGACATAAATTA
*
30745 AAAATACCTCAGCGTGACCCGAGGCTTAACTCACCTCT-ATGTTATGAGTTGATTTTAAAAAAAA
131 AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGA--TTATGAGTTGATTTT---AAAAA
*
30809 AAGACATAAATTAAAAACACCTCAGCGTGACCCG
191 AAGACATAAATTAAAAATACCTCAGCGTGACCCG
*
30843 AGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTAAAAAAAGACCGAAATTAAAAATACCTCA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATACCTCA
* * * *
30907 GCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGA-TATTTAAAAAAAACAGAAAGTG
66 GCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATTTTTTAAAAAAGACATAAA-TT
30971 AAAAATA
130 AAAAATA
30978 TTTCTTGAAA
Statistics
Matches: 529, Mismatches: 45, Indels: 35
0.87 0.07 0.06
Matches are distributed among these distances:
223 1 0.00
224 4 0.01
225 66 0.12
226 84 0.16
227 205 0.39
228 100 0.19
229 21 0.04
230 28 0.05
231 13 0.02
232 7 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (224 bp):
AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATACCTCA
GCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATTTTTTAAAAAAGACATAAATTA
AAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGATTATGAGTTGATTTTAAAAAAAGAC
ATAAATTAAAAATACCTCAGCGTGACCCG
Found at i:30618 original size:75 final size:75
Alignment explanation
Indices: 30158--30977 Score: 1044
Period size: 75 Copynumber: 10.8 Consensus size: 75
30148 GCATGGTCCT
* **
30158 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTT-TGAAAA-ACATAAATTTAAAAGAAATA
1 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACATAAA-TT--AA-AAATA
* * **
30221 CATCAGCATGGTCCG
61 CCTCAGCGTGACCCG
* * * * **
30236 AGGCTCAACTCACCTATCGCAATATGAGTTAATTTTT-TGAAAA-ACATAAATTTAAAAGAAATA
1 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACATAAA-TT--AA-AAATA
* * **
30299 CCTCGGCATGGTCCG
61 CCTCAGCGTGACCCG
* *
30314 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT-AAAAAAGACATAAATTAAAAATACCTC
1 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTC
*
30377 AGTGTGACCCG
65 AGCGTGACCCG
30388 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAAAGACATAAATTAAAAATACCTC
1 AGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTTAAAAAAAGACATAAATTAAAAATACCTC
30453 AGCGTGACCCG
65 AGCGTGACCCG
* * *
30464 AGGCTCAATTCACCTCTTTATTATGAGTTGATTTTTTTTAAAAAAGACATAAATTAAAAATACCT
1 AGGCTCAACTCACCTCTGTATTATGAGTTGA--TTTTTAAAAAAAGACATAAATTAAAAATACCT
*
30529 AAGCGTGACCCG
64 CAGCGTGACCCG
30541 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCA
30606 GCGTGACCCG
66 GCGTGACCCG
* * * **
30616 AGGCTCAACTCACCTCTATATTATGAGTTGATTTTAAAAAAAAAACCGAAATTAAAAATACCTCA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCA
30681 GCGTGACCCG
66 GCGTGACCCG
* **
30691 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAAGACCGAAATTAAAAATACCTCA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCA
30756 GCGTGACCCG
66 GCGTGACCCG
* * * * *
30766 AGGCTTAACTCACCTCTATGTTATGAGTTGATTTTAAAAAAAAAAGACATAAATTAAAAACACCT
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTT--TAAAAAAAGACATAAATTAAAAATACCT
30831 CAGCGTGACCCG
64 CAGCGTGACCCG
**
30843 AGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTAAAAAAAGACCGAAATTAAAAATACCTCA
1 AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCA
30907 GCGTGACCCG
66 GCGTGACCCG
* * *
30917 AGGCTCAACTCACCTCTAGTATTATGAGTTGATATTTAAAAAAA-ACAGAAAGTGAAAAATA
1 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACATAAA-TTAAAAATA
30978 TTTCTTGAAA
Statistics
Matches: 684, Mismatches: 48, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
73 12 0.02
74 85 0.12
75 243 0.36
76 87 0.13
77 147 0.21
78 110 0.16
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCA
GCGTGACCCG
Found at i:30977 original size:302 final size:302
Alignment explanation
Indices: 30311--30977 Score: 1070
Period size: 302 Copynumber: 2.2 Consensus size: 302
30301 TCGGCATGGT
* * * * *
30311 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAGACATAAATTAAAAATACCT
1 CCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATTTTAAAAAAAACAGAAATTAAAAATACCT
* * *
30376 CAGTGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAAAGACATAAAT
66 CAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACAGAAAT
* * ****
30441 TAAAAATACCTCAGCGTGACCCGAGGCTCAATTCACCTCTTTATTATGAGTTGATTTTTTTTAAA
131 TAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTAAAAAAA
*
30506 AAAGACATAAATTAAAAATACCTAAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTG
196 AAAGACATAAATTAAAAACACCTAAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTG
*
30571 ATTTTTAAAAAAAGACATAAATTAAAAATACCTCAGCGTGAC
261 ATTTTTAAAAAAAGACAGAAATTAAAAATACCTCAGCGTGAC
*
30613 CCGAGGCTCAACTCACCTCTA-TATTATGAGTTGATTTTAAAAAAAAAACCGAAATTAAAAATAC
1 CCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATTTT--AAAAAAAACAGAAATTAAAAATAC
*
30677 CTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTTAAAAAAAAGACCGAA
64 CTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACAGAA
* *
30741 ATTAAAAATACCTCAGCGTGACCCGAGGCTTAACTCACCTCTATGTTATGAGTTGATTTTAAAAA
129 ATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTAAAAA
*
30806 AAAAAGACATAAATTAAAAACACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
194 AAAAAGACATAAATTAAAAACACCTAAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGT
*
30871 TGA-TTTTAAAAAAAGACCGAAATTAAAAATACCTCAGCGTGAC
259 TGATTTTTAAAAAAAGACAGAAATTAAAAATACCTCAGCGTGAC
*
30914 CCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATATTTAAAAAAAACAGAAAGTGAAAAATA
1 CCGAGGCTCAACTCACCTCTAGTATTATGAGTTGAT-TTTAAAAAAAACAGAAA-TTAAAAATA
30978 TTTCTTGAAA
Statistics
Matches: 336, Mismatches: 24, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
301 87 0.26
302 181 0.54
303 68 0.20
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (302 bp):
CCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATTTTAAAAAAAACAGAAATTAAAAATACCT
CAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAAGACAGAAAT
TAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTATATTATGAGTTGATTTTAAAAAAA
AAAGACATAAATTAAAAACACCTAAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTG
ATTTTTAAAAAAAGACAGAAATTAAAAATACCTCAGCGTGAC
Found at i:31858 original size:15 final size:14
Alignment explanation
Indices: 31834--31872 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
31824 TTGATTTTTC
31834 TTTTTCTTTTCTTTG
1 TTTTT-TTTTCTTTG
*
31849 TTTTGTTTTTGTTTG
1 TTTT-TTTTTCTTTG
31864 TTTTTTTTT
1 TTTTTTTTT
31873 GTCCTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 16 0.73
16 1 0.05
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Done.