Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009878.1 Kokia drynarioides strain JFW-HI SEQ_124613, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 135162
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 142 characters in sequence are not A, C, G, or T
Found at i:293 original size:21 final size:20
Alignment explanation
Indices: 264--309 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
254 ATTTTCGAAT
* *
264 TTTTTAAAATATATTTTTCTA
1 TTTTCAAAATAT-TTTTTATA
285 TTTTCAAAATATTTTTTATA
1 TTTTCAAAATATTTTTTATA
305 TTTTC
1 TTTTC
310 GAATTTTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTCAAAATATTTTTTATA
Found at i:386 original size:77 final size:75
Alignment explanation
Indices: 252--394 Score: 171
Period size: 77 Copynumber: 1.9 Consensus size: 75
242 GATGTAAGAT
* * ** * *
252 ATATTTTCGAATTTTTTAAAATATATTTTTCTATTTTCAAAATATTTTTTATATTTTCGAATTTT
1 ATATTTTCGAATTTTTTAAAATATATTTTTATATTTTCAAAAAAAATTTTAGATTTTCAAATTTT
317 TGCATAAATA
66 TGCATAAATA
* * *
327 ATATTTTCGAAATACTTTTT-ACATATATTTTTATATTTTCAAAAAAAATTTTGGCTTTTCAAAT
1 ATATTTTCG-AAT--TTTTTAAAATATATTTTTATATTTTCAAAAAAAATTTTAGATTTTCAAAT
391 TTTT
63 TTTT
395 TAAAAATTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
75 9 0.16
76 3 0.05
77 39 0.70
78 5 0.09
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (75 bp):
ATATTTTCGAATTTTTTAAAATATATTTTTATATTTTCAAAAAAAATTTTAGATTTTCAAATTTT
TGCATAAATA
Found at i:530 original size:25 final size:21
Alignment explanation
Indices: 470--540 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 21
460 TATTAAAAAA
470 TACATTTTGGAAATATTTTTTT
1 TACATTTT-GAAATATTTTTTT
492 TACAAATTTT-AAATCATATATTTTT
1 TAC--ATTTTGAAAT-AT-T-TTTTT
517 TACATTTTCGAAATATTTTTTT
1 TACATTTT-GAAATATTTTTTT
539 TA
1 TA
541 GCCATGAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
22 14 0.33
23 8 0.19
24 8 0.19
25 12 0.29
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.56
Consensus pattern (21 bp):
TACATTTTGAAATATTTTTTT
Found at i:1612 original size:29 final size:30
Alignment explanation
Indices: 1553--1673 Score: 190
Period size: 30 Copynumber: 4.1 Consensus size: 30
1543 TTTTGAATTT
* *
1553 TTTCGTTTATTTTTTAAATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
*
1583 TTTCGTTTATATTTT-AATTTAATTTTTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
1612 TTTCGTTTATATTTTAAATTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
**
1642 TTTCGTTTATATTTTAAATTTCTTTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
1672 TT
1 TT
1674 ATTATTTTTT
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
29 28 0.33
30 57 0.67
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:1661 original size:18 final size:17
Alignment explanation
Indices: 1600--1663 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 17
1590 TATATTTTAA
*
1600 TTTAATTTTTAATTTCG
1 TTTAATTTTAAATTTCG
1617 TTTATATTTTAAA-----
1 TTTA-ATTTTAAATTTCG
1630 TTTAATTTCT-AATTTCG
1 TTTAATTT-TAAATTTCG
1647 TTTATATTTTAAATTTC
1 TTTA-ATTTTAAATTTC
1664 TTTTCTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 17
0.67 0.02 0.31
Matches are distributed among these distances:
12 6 0.16
13 5 0.14
17 9 0.24
18 17 0.46
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTAATTTTAAATTTCG
Found at i:1690 original size:59 final size:58
Alignment explanation
Indices: 1559--1692 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 58
1549 ATTTTTTCGT
* *
1559 TTATTTTTTAAATTTAATTTGTAATTTCGTTTATATTTTAATTTAATTTTTAATTTCGT
1 TTATTTTTTAAATTTAATTTCTAATTTCGTTTATATTTTAATTTAATTTTTAATTTC-A
* *
1618 TTATATTTTAAATTTAATTTCTAATTTCGTTTATATTTTAAATTT-CTTTTCTAA-TT-A
1 TTATTTTTTAAATTTAATTTCTAATTTCGTTTATATTTT-AATTTAATTTT-TAATTTCA
1675 TTATTTTTTCAAAATTTA
1 TTATTTTTT--AAATTTA
1693 TATAATCATT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
57 8 0.12
59 50 0.76
60 8 0.12
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (58 bp):
TTATTTTTTAAATTTAATTTCTAATTTCGTTTATATTTTAATTTAATTTTTAATTTCA
Found at i:1863 original size:138 final size:138
Alignment explanation
Indices: 1717--1994 Score: 547
Period size: 138 Copynumber: 2.0 Consensus size: 138
1707 ATAATATTTA
1717 TTTCTCTACATTTTCACAACAACCTATTTAATACTTTTGTATATGATTTGAAATAATTTTAATAC
1 TTTCTCTACATTTTCACAACAACCTATTTAATACTTTTGTATATGATTTGAAATAATTTTAATAC
1782 AAGAAAATACAAATATTGTTGAATATTACTAACCATCAAATTAATTTTTACAGATACAATAAATT
66 AAGAAAATACAAATATTGTTGAATATTACTAACCATCAAATTAATTTTTACAGATACAATAAATT
1847 ACAAATAT
131 ACAAATAT
1855 TTTCTCTACATTTTCACAACAACCTATTTAATACTTTTGTATATGATTTGAAATAATTTTAATAC
1 TTTCTCTACATTTTCACAACAACCTATTTAATACTTTTGTATATGATTTGAAATAATTTTAATAC
*
1920 AAGAAAATACAAATATTGTTGAATATTACTAACCATCAAATTAATTTTTACAGATACAATATATT
66 AAGAAAATACAAATATTGTTGAATATTACTAACCATCAAATTAATTTTTACAGATACAATAAATT
1985 ACAAATAT
131 ACAAATAT
1993 TT
1 TT
1995 GTTAATATTA
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (138 bp):
TTTCTCTACATTTTCACAACAACCTATTTAATACTTTTGTATATGATTTGAAATAATTTTAATAC
AAGAAAATACAAATATTGTTGAATATTACTAACCATCAAATTAATTTTTACAGATACAATAAATT
ACAAATAT
Found at i:2857 original size:60 final size:59
Alignment explanation
Indices: 2646--3275 Score: 461
Period size: 61 Copynumber: 10.6 Consensus size: 59
2636 GAGAAAGGAG
* * * *
2646 AAAAAGTTGATGTCGGCCAATACATGGTCAACA-CAAAAAAATTA-TTTTTTATCAGAT
1 AAAAAGGTGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATTATTTTTTTATCAGAT
** * * * *
2703 AAATAAGGTGGAATGGGCCGA-GCAATGGCCAACA-CAAAAAAAATA-TTTTTTATCTGAT
1 AAA-AAGGTGGTGTCGGCCAATGC-ATGGCCAACACCAAAAAAATTATTTTTTTATCAGAT
** * *
2761 AAAAAGGTGGTGTTAGCCAATGCATGGCCGGA-ACCAAAAAAACTATTTTTTTATCAGAT
1 AAAAAGGTGGTGTCGGCCAATGCATGGCC-AACACCAAAAAAATTATTTTTTTATCAGAT
* * * *
2820 AAATAAGGTGATGTCGGTCAA-GCAATGGCCAACACC----AAATTTTTTTTTTATCTGAT
1 AAA-AAGGTGGTGTCGGCCAATGC-ATGGCCAACACCAAAAAAATTATTTTTTTATCAGAT
* * * * *
2876 AAAAAAGTGGTGTTGGCCAATGCATGACTAACACAAAAAAAAATTATTTATTTTATCAGAT
1 AAAAAGGTGGTGTCGGCCAATGCATGGCCAACAC-CAAAAAAATTATTT-TTTTATCAGAT
* * * * * *
2937 AAAAAAAGTGGTGTCGGCCAA-GTAATGACCTACACTAAAAAAA-TA-TTTTTTATCTGAT
1 -AAAAAGGTGGTGTCGGCCAATG-CATGGCCAACACCAAAAAAATTATTTTTTTATCAGAT
* * * *
2995 AAAAAATTGCTGGTGTCAGCCAATGCATGACCAACACCAAAAAAATTTGAATTTTTTATCAGAT
1 -AAAAA--GGTGGTGTCGGCCAATGCATGGCCAACACCAAAAAAA-TT-ATTTTTTTATCAGAT
* * ** *** * *
3059 AAAAAAAGTGGTGTCGACCAA-GCAATAACCAACA-CAAAATTTTTTTTGCATTTTTATCAAAT
1 -AAAAAGGTGGTGTCGGCCAATGC-ATGGCCAACACCAAAAAAATTATT---TTTTTATCAGAT
* * *
3121 AAAAAAGTGGTGTCTGCCAA-GCAATGGCCAACACCAAAAAAA-TA-TTTTTTATCTGAT
1 AAAAAGGTGGTGTCGGCCAATGC-ATGGCCAACACCAAAAAAATTATTTTTTTATCAGAT
* ** * * **
3178 AAAAAGGTGGTGTCGACCAATGCATAACCAATACTAAAAAAAATCGTTTTTTTATCAGAT
1 AAAAAGGTGGTGTCGGCCAATGCATGGCCAACAC-CAAAAAAATTATTTTTTTATCAGAT
3238 AAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACCAA
1 -AAAAAGGTGGTGTCGGCCAATGCATGGCCAACACCAA
3276 TTTTTTTTTT
Statistics
Matches: 454, Mismatches: 84, Indels: 67
0.75 0.14 0.11
Matches are distributed among these distances:
55 22 0.05
56 22 0.05
57 58 0.13
58 83 0.18
59 21 0.05
60 78 0.17
61 86 0.19
62 65 0.14
63 1 0.00
64 18 0.04
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (59 bp):
AAAAAGGTGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATTATTTTTTTATCAGAT
Found at i:2977 original size:61 final size:59
Alignment explanation
Indices: 2646--3258 Score: 373
Period size: 58 Copynumber: 10.3 Consensus size: 59
2636 GAGAAAGGAG
* **
2646 AAAAAGTTGATGTCGGCCAA-TACATGGTCAACACAAAAAAATTA-TTTTTTATCAGATAA
1 AAAAAG-TGGTGTCGGCCAAGTA-ATGACCAACACAAAAAAATTATTTTTTTATCAGATAA
* * ** * * * * * *
2705 ATAAGGTGGAATGGGCCGAGCAATGGCCAACACAAAAAAAATA-TTTTTTATCTGAT-A
1 AAAAAGTGGTGTCGGCCAAGTAATGACCAACACAAAAAAATTATTTTTTTATCAGATAA
* ** * * *
2762 AAAAGGTGGTGTTAGCCAA-TGCATGGCCGGAAC-CAAAAAAACTATTTTTTTATCAGATAA
1 AAAAAGTGGTGTCGGCCAAGT-AATGACC--AACACAAAAAAATTATTTTTTTATCAGATAA
* * * * * * * * *
2822 ATAAGGTGATGTCGGTCAAGCAATGGCCAACAC---CAAATTTTTTTTTTATCTGAT-A
1 AAAAAGTGGTGTCGGCCAAGTAATGACCAACACAAAAAAATTATTTTTTTATCAGATAA
* * *
2877 AAAAAGTGGTGTTGGCCAA-TGCATGACTAACACAAAAAAAAATTATTTATTTTATCAGATAA
1 AAAAAGTGGTGTCGGCCAAGT-AATGACCAACAC--AAAAAAATTATTT-TTTTATCAGATAA
* *
2939 AAAAAGTGGTGTCGGCCAAGTAATGACCTACACTAAAAAAA-TA-TTTTTTATCTGATAA
1 AAAAAGTGGTGTCGGCCAAGTAATGACCAACAC-AAAAAAATTATTTTTTTATCAGATAA
* * * *
2997 AAAATTGCTGGTGTCAGCCAA-TGCATGACCAACACCAAAAAAATTTGAATTTTTTATCAGATAA
1 AAAA-AG-TGGTGTCGGCCAAGT-AATGACCAACA-CAAAAAAA-TT-ATTTTTTTATCAGATAA
* * * *** * *
3061 AAAAAGTGGTGTCGACCAAGCAATAACCAACACAAAATTTTTTTTGCATTTTTATCAAAT-A
1 AAAAAGTGGTGTCGGCCAAGTAATGACCAACACAAAAAAATTATT---TTTTTATCAGATAA
* * * *
3122 AAAAAGTGGTGTCTGCCAAGCAATGGCCAACACCAAAAAAA-TA-TTTTTTATCTGAT-A
1 AAAAAGTGGTGTCGGCCAAGTAATGACCAACA-CAAAAAAATTATTTTTTTATCAGATAA
* * * * * **
3179 AAAAGGTGGTGTCGACCAA-TGCATAACCAATACTAAAAAAAATCGTTTTTTTATCAGATAA
1 AAAAAGTGGTGTCGGCCAAGT-AATGACCAACAC--AAAAAAATTATTTTTTTATCAGATAA
*
3240 AAAAGGTGGTGTCGGCCAA
1 AAAAAGTGGTGTCGGCCAA
3259 TGCATGGCCA
Statistics
Matches: 429, Mismatches: 89, Indels: 70
0.73 0.15 0.12
Matches are distributed among these distances:
55 24 0.06
56 18 0.04
57 54 0.13
58 75 0.17
59 26 0.06
60 74 0.17
61 72 0.17
62 65 0.15
63 3 0.01
64 18 0.04
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (59 bp):
AAAAAGTGGTGTCGGCCAAGTAATGACCAACACAAAAAAATTATTTTTTTATCAGATAA
Found at i:3031 original size:122 final size:116
Alignment explanation
Indices: 2674--3272 Score: 491
Period size: 117 Copynumber: 5.1 Consensus size: 116
2664 AATACATGGT
* * ** * * *
2674 CAACAC-AAAAAAATTA-TTTTTTATCAGATAAATAAGGTGGAATGGGCCGAGCAATGGCCAACA
1 CAACACAAAAAAAATTATTTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAGCAATGACCAACA
* *
2737 CAAAAAAAATATTTTTTATCTGATAAAAAGGTGGTGTTAGCCAATGCATGGC
66 C-AAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTTAGCCAATGCATGAC
* * * * * *
2789 CGGAAC-C-AAAAAAACTATTTTTTTATCAGATAAATAAGGTGATGTCGGTCAAGCAATGGCCAA
1 C--AACACAAAAAAAATTATTTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAGCAATGACCAA
* ** * *
2852 CAC-CAAATTTTTTTTTTATCTGATAAAAAAGTGGTGTTGGCCAATGCATGAC
64 CACAAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTTAGCCAATGCATGAC
* * *
2904 TAACACAAAAAAAAATTATTTATTTTATCAGATAAAAAAAGTGGTGTCGGCCAAGTAATGACCTA
1 CAACAC-AAAAAAAATTATTT-TTTTATCAGATAAAAAAAGTGGTGTCGGCCAAGCAATGACCAA
*
2969 CACTAAAAAAATATTTTTTATCTGATAAAAAATTGCTGGTGTCAGCCAATGCATGAC
64 CAC-AAAAAAATATTTTTTATCTGATAAAAAA--G-TGGTGTTAGCCAATGCATGAC
* * * *
3026 CAACACCAAAAAAATTTGAATTTTTTATCAGATAAAAAAAGTGGTGTCGACCAAGCAATAACCAA
1 CAACA-CAAAAAAAATT-ATTTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAGCAATGACCAA
*** * ** *
3091 CACAAAATTTTTTTTGCATTTTTATCAAATAAAAAAGTGGTGTCT-GCCAA-GCAATGGC
64 CACAAAA--AAATAT---TTTTTATCTGATAAAAAAGTGGTGT-TAGCCAATGC-ATGAC
* * * * * *
3149 CAACACCAAAAAAA-TA-TTTTTTATCTGAT-AAAAAGGTGGTGTCGACCAATGC-ATAACCAAT
1 CAACACAAAAAAAATTATTTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAA-GCAATGACCAAC
* * ** *
3210 ACTAAAAAAAATCGTTTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAATGCATGGC
65 AC--AAAAAAAT--ATTTTTTATCTGATAAAAAA-GTGGTGTTAGCCAATGCATGAC
3267 CAACAC
1 CAACAC
3273 CAATTTTTTT
Statistics
Matches: 401, Mismatches: 54, Indels: 55
0.79 0.11 0.11
Matches are distributed among these distances:
113 3 0.01
114 1 0.00
115 43 0.11
116 22 0.05
117 101 0.25
118 53 0.13
119 39 0.10
120 7 0.02
121 6 0.01
122 83 0.21
123 26 0.06
124 1 0.00
126 16 0.04
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (116 bp):
CAACACAAAAAAAATTATTTTTTTATCAGATAAAAAAAGTGGTGTCGGCCAAGCAATGACCAACA
CAAAAAAATATTTTTTATCTGATAAAAAAGTGGTGTTAGCCAATGCATGAC
Found at i:3310 original size:36 final size:36
Alignment explanation
Indices: 3263--3332 Score: 97
Period size: 38 Copynumber: 1.9 Consensus size: 36
3253 GGCCAATGCA
*
3263 TGGCCAACACC-AATTTTTTTTTTAATCTGATAAACT
1 TGGCCAACACCAAATTTGTTTTTT-ATCTGATAAACT
*
3299 TGGCCGACACCAAAATTTGTTTTTTATCTGATAA
1 TGGCCAACACC-AAATTTGTTTTTTATCTGATAA
3333 GAAATATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 10 0.33
37 9 0.30
38 11 0.37
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (36 bp):
TGGCCAACACCAAATTTGTTTTTTATCTGATAAACT
Found at i:10790 original size:20 final size:20
Alignment explanation
Indices: 10765--10806 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
10755 TTGCCATATT
10765 TATGGGCACTAAGCAGAAAC
1 TATGGGCACTAAGCAGAAAC
10785 TATGGGCACTAAGCAGAAAC
1 TATGGGCACTAAGCAGAAAC
10805 TA
1 TA
10807 GGGAGTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (20 bp):
TATGGGCACTAAGCAGAAAC
Found at i:15499 original size:34 final size:35
Alignment explanation
Indices: 15456--15525 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
15446 TAATAGAAGA
15456 TCACTTGGCCACTTGCTT-TGACCTTTTTATAAGG
1 TCACTTGGCCACTTGCTTCTGACCTTTTTATAAGG
15490 TCACTTGGCCACTTGCTTCTGACCTTTTTATAAGG
1 TCACTTGGCCACTTGCTTCTGACCTTTTTATAAGG
15525 T
1 T
15526 TTTGACATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (35 bp):
TCACTTGGCCACTTGCTTCTGACCTTTTTATAAGG
Found at i:16919 original size:4 final size:4
Alignment explanation
Indices: 16910--16934 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
16900 TACAACGGCT
16910 AGGC AGGC AGGC AGGC AGGC AGGC A
1 AGGC AGGC AGGC AGGC AGGC AGGC A
16935 TTCTTGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.48, T:0.00
Consensus pattern (4 bp):
AGGC
Found at i:21504 original size:40 final size:40
Alignment explanation
Indices: 21460--21547 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
21450 TTGTTTAGCA
21460 TCTTTTTCCCCTTCGTGCCATCTCCTACTTCCACCATTCT
1 TCTTTTTCCCCTTCGTGCCATCTCCTACTTCCACCATTCT
21500 TCTTTTTCCCCTTCGTGCCATCTCCTACTTCCACCATTCT
1 TCTTTTTCCCCTTCGTGCCATCTCCTACTTCCACCATTCT
21540 TCTTTTTC
1 TCTTTTTC
21548 TTCCATTGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.09, C:0.41, G:0.05, T:0.45
Consensus pattern (40 bp):
TCTTTTTCCCCTTCGTGCCATCTCCTACTTCCACCATTCT
Found at i:23494 original size:2 final size:2
Alignment explanation
Indices: 23487--23517 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23477 AATAATGCGT
23487 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
23518 GGTGTCAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33936 original size:6 final size:6
Alignment explanation
Indices: 33911--33949 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
33901 ACAATTCATA
* * *
33911 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
33950 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:35203 original size:61 final size:60
Alignment explanation
Indices: 35135--35478 Score: 312
Period size: 61 Copynumber: 5.7 Consensus size: 60
35125 TTATTTATCT
* **
35135 GATAAAAAAAA-TCAAA-TTTTTGAGTGTTGGTCATGCAATGGCCGACATTCTTTTTTCTTA
1 GATAAAAAAAATTCAAATTTTTTGAGTGTTGGCCATGCAATGGCCGACACCCTTTTTTC--A
* * ** *
35195 GATAAAAAAATTTTAAATTTTTTTTGTGTTGGCCATGCAATAGCCGACACCTCCTTTTTT-A
1 GATAAAAAAAATTCAAATTTTTTGAGTGTTGGCCATGCAATGGCCGACA-C-CCTTTTTTCA
** * * * *
35256 GATAAAAAAAATTGC--ATTTTTTTTGTGTTGGTCATGTAATGACCGACACCTTCTTTTTCA
1 GATAAAAAAAATT-CAAATTTTTTGAGTGTTGGCCATGCAATGGCCGACACCCT-TTTTTCA
* * *
35316 GATAAAAAAATTTCAAAATTTTTTG-GTGTTGGCCATGCAATAGCCGACACCCTCTTTTCCCA
1 GATAAAAAAAATTC-AAATTTTTTGAGTGTTGGCCATGCAATGGCCGACACCCT-TTTT-TCA
* * *
35378 GAT-AAAAAAATTTAAATTTTTTTGA-TGTTGGCCATGCAATGACCGATACCCCTTTTTTCA
1 GATAAAAAAAATTCAAA-TTTTTTGAGTGTTGGCCATGCAATGGCCGACA-CCCTTTTTTCA
* *
35438 GATAAAAAAAATT-ACATTTTTTTG-GTGTTGGCCATGTAATG
1 GATAAAAAAAATTCA-AATTTTTTGAGTGTTGGCCATGCAATG
35479 TCGCTCTCTT
Statistics
Matches: 236, Mismatches: 31, Indels: 34
0.78 0.10 0.11
Matches are distributed among these distances:
58 2 0.01
59 7 0.03
60 83 0.35
61 94 0.40
62 43 0.18
64 7 0.03
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (60 bp):
GATAAAAAAAATTCAAATTTTTTGAGTGTTGGCCATGCAATGGCCGACACCCTTTTTTCA
Found at i:35302 original size:60 final size:60
Alignment explanation
Indices: 35135--35478 Score: 315
Period size: 60 Copynumber: 5.7 Consensus size: 60
35125 TTATTTATCT
* * ** * * * *
35135 GATAAAAAAAATCA-AATTTTTGAGTGTTGGTCATGCAATGGCCGACA-TTCTTTTTTCTTA
1 GATAAAAAAAATTACATTTTTTTTGTGTTGGCCATGCAATGACCGACACCTC-CTTTT-TTA
* *
35195 GATAAAAAAATTTTAAATTTTTTTTGTGTTGGCCATGCAAT-AGCCGACACCTCCTTTTTTA
1 GATAAAAAAA-ATTACATTTTTTTTGTGTTGGCCATGCAATGA-CCGACACCTCCTTTTTTA
* * * * *
35256 GATAAAAAAAATTGCATTTTTTTTGTGTTGGTCATGTAATGACCGACACCTTCTTTTTCA
1 GATAAAAAAAATTACATTTTTTTTGTGTTGGCCATGCAATGACCGACACCTCCTTTTTTA
* * * * **
35316 GATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAAT-AGCCGACACC-CTCTTTTCCCA
1 GATAAAAAAAATT-ACATTTTTTTTGTGTTGGCCATGCAATGA-CCGACACCTC-CTTTT-TTA
* * *
35378 GATAAAAAAATTTA-AATTTTTTTGATGTTGGCCATGCAATGACCGATACC-CCTTTTTTCA
1 GATAAAAAAAATTACATTTTTTTTG-TGTTGGCCATGCAATGACCGACACCTCCTTTTTT-A
* *
35438 GATAAAAAAAATTACATTTTTTTGGTGTTGGCCATGTAATG
1 GATAAAAAAAATTACATTTTTTTTGTGTTGGCCATGCAATG
35479 TCGCTCTCTT
Statistics
Matches: 238, Mismatches: 33, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
60 107 0.45
61 82 0.34
62 47 0.20
63 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (60 bp):
GATAAAAAAAATTACATTTTTTTTGTGTTGGCCATGCAATGACCGACACCTCCTTTTTTA
Found at i:35302 original size:122 final size:121
Alignment explanation
Indices: 35135--35473 Score: 409
Period size: 121 Copynumber: 2.8 Consensus size: 121
35125 TTATTTATCT
* * ** *
35135 GATAAAAAAAATCAAATTTTTGAGTGTTGGTCATGCAATGGCCGACA-TTCTTTTTTCTTAGATA
1 GATAAAAAAATTGAAATTTTTTTGTGTTGGTCATGCAATGACCGACACTTCTTTTTTC--AGATA
* **
35199 AAAAAATTTTAAATTTTTTTTGTGTTGGCCATGCAATAGCCGACA-CCTCCTTTT-TTA
64 AAAAAATTTTAAATTTTTTTGGTGTTGGCCATGCAATAGCCGACACCCT-CTTTTCCCA
* * *
35256 GATAAAAAAAATTGCATTTTTTTTGTGTTGGTCATGTAATGACCGACACCTTC-TTTTTCAGATA
1 GAT-AAAAAAATTGAAATTTTTTTGTGTTGGTCATGCAATGACCGACA-CTTCTTTTTTCAGATA
* *
35320 AAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATAGCCGACACCCTCTTTTCCCA
64 AAAAAATTTTAAATTTTTTTGGTGTTGGCCATGCAATAGCCGACACCCTCTTTTCCCA
* * * **
35378 GATAAAAAAATTTAAATTTTTTTGATGTTGGCCATGCAATGACCGATACCCCTTTTTTCAGATAA
1 GATAAAAAAATTGAAATTTTTTTG-TGTTGGTCATGCAATGACCGACACTTCTTTTTTCAGATAA
* *
35443 AAAAA-ATTACATTTTTTTGGTGTTGGCCATG
65 AAAAATTTTAAATTTTTTTGGTGTTGGCCATG
35474 TAATGTCGCT
Statistics
Matches: 186, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
121 97 0.52
122 80 0.43
123 6 0.03
124 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (121 bp):
GATAAAAAAATTGAAATTTTTTTGTGTTGGTCATGCAATGACCGACACTTCTTTTTTCAGATAAA
AAAATTTTAAATTTTTTTGGTGTTGGCCATGCAATAGCCGACACCCTCTTTTCCCA
Found at i:37925 original size:22 final size:22
Alignment explanation
Indices: 37900--37966 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
37890 TAATTCTAGA
37900 ATATTGACTTTGATCCCGTATG
1 ATATTGACTTTGATCCCGTATG
* * *
37922 ATATT-TCGTT-AT-TC-TA-G
1 ATATTGACTTTGATCCCGTATG
37939 AATATTGACTTTGATCCCGTATG
1 -ATATTGACTTTGATCCCGTATG
37962 ATATT
1 ATATT
37967 TCGTTCATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
17 1 0.03
18 7 0.21
19 4 0.12
20 4 0.12
21 4 0.12
22 12 0.36
23 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (22 bp):
ATATTGACTTTGATCCCGTATG
Found at i:37984 original size:40 final size:40
Alignment explanation
Indices: 37892--37971 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
37882 TATTTTCATA
37892 ATTCTAGAATATTGACTTTGATCCCGTATGATATTTCGTT
1 ATTCTAGAATATTGACTTTGATCCCGTATGATATTTCGTT
37932 ATTCTAGAATATTGACTTTGATCCCGTATGATATTTCGTT
1 ATTCTAGAATATTGACTTTGATCCCGTATGATATTTCGTT
37972 CATGTTTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (40 bp):
ATTCTAGAATATTGACTTTGATCCCGTATGATATTTCGTT
Found at i:48501 original size:6 final size:6
Alignment explanation
Indices: 48490--48515 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
48480 AAGTAAAACC
48490 ACTCCA ACTCCA ACTCCA ACTCCA AC
1 ACTCCA ACTCCA ACTCCA ACTCCA AC
48516 AGCAGTCGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.00, T:0.15
Consensus pattern (6 bp):
ACTCCA
Found at i:49336 original size:230 final size:230
Alignment explanation
Indices: 48933--49365 Score: 595
Period size: 230 Copynumber: 1.9 Consensus size: 230
48923 TTTATATTTT
* * * *
48933 TTTTTTGTCAACTTTAGTATTTGAATTTAATAACTAGATTCATTTTGATCTATGAACTTGAATTC
1 TTTTTTGTCAACTTTAATATTTGAATTTAATAACTAGATCCATTTTGATCCATGAACTTGAACTC
* * * * **
48998 CTTAAAAATCTGATGATGTGATTAGTGTTACTGAAATATGATTGGATTAGTCGCTCGGACCGATT
66 CTTAAAAATCTGATGATGTGATCAATATTACTGAAACACAATTGGATTAGTCGCTCGGACCGATT
* * * *
49063 GGACCTTAATTGATTGGTACAATGGTCAAAACAAGGCGATTGAACCGATTAAATAGAAAACAACT
131 GGACCTTAAATGATTGGTACAACGATCAAAACAAAGCGATTGAACCGATTAAATAGAAAACAACT
*
49128 TGAAATTGTCAATCAGGTTCACTTTAATATCTGTA
196 TAAAATTGTCAATCAGGTTCACTTTAATATCTGTA
* * * *
49163 TTTTTTGTCCACTTTAATATTTGAATTTGATAACTAGATCCATTTTGGTCCATGAACTTGGACTC
1 TTTTTTGTCAACTTTAATATTTGAATTTAATAACTAGATCCATTTTGATCCATGAACTTGAACTC
*
49228 CATT-AAAATTTGATGATGTGATCAATATTACT-ACAACACAATTGGATTAGTCGCTCGGACCGA
66 C-TTAAAAATCTGATGATGTGATCAATATTACTGA-AACACAATTGGATTAGTCGCTCGGACCGA
* * *
49291 TTGGACTTTAAAAAT-ATTGGTACAACGATC-AAACAAAGTGATTGAACCGATTAAATTGAAAAC
129 TTGGACCTT--AAATGATTGGTACAACGATCAAAACAAAGCGATTGAACCGATTAAATAGAAAAC
49354 AACTTAAAATTG
192 AACTTAAAATTG
49366 ATAAACATAA
Statistics
Matches: 176, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
229 1 0.01
230 157 0.89
231 15 0.09
232 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (230 bp):
TTTTTTGTCAACTTTAATATTTGAATTTAATAACTAGATCCATTTTGATCCATGAACTTGAACTC
CTTAAAAATCTGATGATGTGATCAATATTACTGAAACACAATTGGATTAGTCGCTCGGACCGATT
GGACCTTAAATGATTGGTACAACGATCAAAACAAAGCGATTGAACCGATTAAATAGAAAACAACT
TAAAATTGTCAATCAGGTTCACTTTAATATCTGTA
Found at i:52178 original size:20 final size:21
Alignment explanation
Indices: 52155--52196 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
52145 TTTATATATT
*
52155 TTTTTACGA-TTTTTATAAAA
1 TTTTTACAATTTTTTATAAAA
*
52175 -TTTTGCAATTTTTTATAAAA
1 TTTTTACAATTTTTTATAAAA
52195 TT
1 TT
52197 ACGGATCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
19 6 0.33
20 11 0.61
21 1 0.06
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTTACAATTTTTTATAAAA
Found at i:54871 original size:7 final size:7
Alignment explanation
Indices: 54859--54889 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
54849 AATGTTCAGA
54859 GTCCAAG
1 GTCCAAG
54866 GTCCAAG
1 GTCCAAG
54873 GTCCAAG
1 GTCCAAG
*
54880 GTCCACG
1 GTCCAAG
54887 GTC
1 GTC
54890 TAGGGTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.23, C:0.32, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCCAAG
Found at i:61268 original size:18 final size:16
Alignment explanation
Indices: 61233--61265 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61223 GTATAGAAAC
*
61233 ATGAATTTAAAATATT
1 ATGAATATAAAATATT
61249 ATGAATATAAAAT-TT
1 ATGAATATAAAATATT
61264 AT
1 AT
61266 TATTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
ATGAATATAAAATATT
Found at i:61793 original size:7 final size:7
Alignment explanation
Indices: 61781--61819 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
61771 TGGTAGTGCC
61781 GAGAGTG
1 GAGAGTG
61788 GAGAGTG
1 GAGAGTG
61795 GAGAGTG
1 GAGAGTG
61802 GAGAGTG
1 GAGAGTG
61809 GAGAGTG
1 GAGAGTG
61816 GAGA
1 GAGA
61820 TGGTGCTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.56, T:0.13
Consensus pattern (7 bp):
GAGAGTG
Found at i:62298 original size:28 final size:28
Alignment explanation
Indices: 62266--62322 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
62256 GTGTTAGTTT
**
62266 AGCATTGTCTTTT-AAAAGAGTTTTTAAA
1 AGCATTG-CTTTTGAAAAGAACTTTTAAA
62294 AGCATTGCTTTTGAAAAGAACTTTTAAA
1 AGCATTGCTTTTGAAAAGAACTTTTAAA
62322 A
1 A
62323 AGTGCAGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (28 bp):
AGCATTGCTTTTGAAAAGAACTTTTAAA
Found at i:73720 original size:20 final size:21
Alignment explanation
Indices: 73695--73738 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
73685 TTTTATTAAC
73695 AATAAT-TGTAAAAA-AATAAA
1 AATAATCT-TAAAAATAATAAA
*
73715 AATAATCTTAAAAATAATTAA
1 AATAATCTTAAAAATAATAAA
73736 AAT
1 AAT
73739 GTTTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAATCTTAAAAATAATAAA
Found at i:74282 original size:10 final size:10
Alignment explanation
Indices: 74267--74294 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
74257 TGAATGGATA
74267 TTTATTTTTT
1 TTTATTTTTT
74277 TTTATTTTTT
1 TTTATTTTTT
74287 TTTATTTT
1 TTTATTTT
74295 ATGAAAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:74424 original size:20 final size:21
Alignment explanation
Indices: 74381--74424 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
74371 TTTTATATGA
*
74381 ATTTTTATTTATTTTAAATAT
1 ATTTTAATTTATTTTAAATAT
74402 ATTTTAATTT-TTTTACAAT-T
1 ATTTTAATTTATTTTA-AATAT
74422 ATT
1 ATT
74425 GTTAGGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTAATTTATTTTAAATAT
Found at i:78103 original size:17 final size:17
Alignment explanation
Indices: 78065--78105 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
78055 TCATTTAGTC
78065 AAAAAAATATTTTCTAT
1 AAAAAAATATTTTCTAT
* *
78082 CAAAAAATATTTT-TGT
1 AAAAAAATATTTTCTAT
78098 AAAAAAAT
1 AAAAAAAT
78106 CAATTCCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAAAAATATTTTCTAT
Found at i:81507 original size:21 final size:20
Alignment explanation
Indices: 81482--81526 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 20
81472 ATTTATAAGT
81482 TTTATTTAATGCTAGGAATGG
1 TTTATTT-ATGCTAGGAATGG
81503 TTTA-TTATGCTAGGAATGG
1 TTTATTTATGCTAGGAATGG
81522 TTTAT
1 TTTAT
81527 AAGTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 17 0.74
20 2 0.09
21 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTATTTATGCTAGGAATGG
Found at i:84519 original size:15 final size:15
Alignment explanation
Indices: 84499--84541 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
84489 GAACAACGAC
84499 TATTCTAAACACAAT
1 TATTCTAAACACAAT
*
84514 TATTCTTGAAACACCAT
1 TATTC-T-AAACACAAT
84531 TATTCTAAACA
1 TATTCTAAACA
84542 AGAGTTGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 10 0.40
16 2 0.08
17 13 0.52
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (15 bp):
TATTCTAAACACAAT
Found at i:90409 original size:11 final size:11
Alignment explanation
Indices: 90393--90453 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
90383 AACATCTCAC
90393 ATTAATATTAA
1 ATTAATATTAA
90404 ATTAATA--AA
1 ATTAATATTAA
*
90413 A-TACTATTAA
1 ATTAATATTAA
*
90423 GATAAATATTAA
1 -ATTAATATTAA
90435 ATT--TATTAA
1 ATTAATATTAA
*
90444 AATAATATTA
1 ATTAATATTA
90454 TTTTTGCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
8 4 0.10
9 11 0.28
10 2 0.05
11 15 0.38
12 7 0.18
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:99037 original size:188 final size:190
Alignment explanation
Indices: 98664--99040 Score: 695
Period size: 188 Copynumber: 2.0 Consensus size: 190
98654 GCATTGCAAC
*
98664 ATGTTTGCTGTCATGAAAGATGAGACGAAAAACCAAAGACCCATCACCATGGACCACACCACTTG
1 ATGTTTGCTGTCATGAAAGATGAGACGAAAAACCAAAGACCCACCACCATGGACCACACCACTTG
* * *
98729 GCCATATATGATTAGGCCCCATCAAACACACATCATAGGACATGTTAACTGGACAAATTATAACA
66 CCCATATATGATTAGGCCCAATCAAACACACATCATACGACATGTTAACTGGACAAATTATAACA
98794 GCAATTTGCAGACATTCAACAATTTTGGACAATTATAATCCAAAAGCACCTGCAGGCTGT
131 GCAATTTGCAGACATTCAACAATTTTGGACAATTATAATCCAAAAGCACCTGCAGGCTGT
98854 ATGTTTGCTGTCATGAAAGATGAGACGAAAAACCAAAGACCCACCACCATGGACCACACCACTTG
1 ATGTTTGCTGTCATGAAAGATGAGACGAAAAACCAAAGACCCACCACCATGGACCACACCACTTG
*
98919 CCCATATATGATTAGGCCCAATC-AA-ACACATCATACGACATGTTAACTGGACAAATTATAATA
66 CCCATATATGATTAGGCCCAATCAAACACACATCATACGACATGTTAACTGGACAAATTATAACA
98982 GCAATTTGCAGACATTCAACAATTTTGGACAATTATAATCCAAAAGCACCTGCAGGCTG
131 GCAATTTGCAGACATTCAACAATTTTGGACAATTATAATCCAAAAGCACCTGCAGGCTG
99041 CTTCATCTTG
Statistics
Matches: 182, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
188 95 0.52
189 2 0.01
190 85 0.47
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (190 bp):
ATGTTTGCTGTCATGAAAGATGAGACGAAAAACCAAAGACCCACCACCATGGACCACACCACTTG
CCCATATATGATTAGGCCCAATCAAACACACATCATACGACATGTTAACTGGACAAATTATAACA
GCAATTTGCAGACATTCAACAATTTTGGACAATTATAATCCAAAAGCACCTGCAGGCTGT
Found at i:102461 original size:5 final size:5
Alignment explanation
Indices: 102430--102485 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
102420 TCGTCTTCCC
* * * *
102430 TTTTT TTTTT TTTTC TTTT- TTTGG TTTTG TTTTG TTTTG TTGTTG TTGTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT-TTG TT-TTG
102481 TTTTG
1 TTTTG
102486 GTGTTTTTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
4 3 0.07
5 32 0.70
6 11 0.24
ACGTcount: A:0.00, C:0.02, G:0.18, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:102485 original size:17 final size:16
Alignment explanation
Indices: 102448--102490 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
102438 TTTTTTCTTT
*
102448 TTTTGGTTTTGTTTTG
1 TTTTGGTGTTGTTTTG
*
102464 TTTTGTTGTTGTTGTTG
1 TTTTGGTGTTGTT-TTG
102481 TTTTGGTGTT
1 TTTTGGTGTT
102491 TTTGATGCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (16 bp):
TTTTGGTGTTGTTTTG
Found at i:129394 original size:106 final size:105
Alignment explanation
Indices: 129202--129404 Score: 241
Period size: 106 Copynumber: 1.9 Consensus size: 105
129192 TCTAAAAAAC
* * * *
129202 TTGAAATTGAAATTGATATTAAATATATAAATTAACTAAAAATTATTTAAGATTTTTTATTTTTT
1 TTGAAACTGAAATTGATATTAAATATATAAAGTAACTAAAAATTATTTAAAATTTTTAATTTTTT
* *
129267 AATTTTATATAAAGGCCATAAATTTTATAACTCAAGAAAG
66 AATTTTATATAAAGGACATAAACTTTATAACTCAAGAAAG
* *
129307 TTGAAACTGAAATTGATATTGAATA-A-AAAGTAATTGAAAAA-TATTTAATAATTTTGTAAGTT
1 TTGAAACTGAAATTGATATTAAATATATAAAGTAACT-AAAAATTATTTAA-AATTTT-TAA-TT
** * *
129369 TTTTAATTTTATATTTAGGATATAAACTTTGTAACT
62 TTTTAATTTTATATAAAGGACATAAACTTTATAACT
129405 GTAATCATCT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
103 14 0.17
104 11 0.13
105 25 0.30
106 32 0.39
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (105 bp):
TTGAAACTGAAATTGATATTAAATATATAAAGTAACTAAAAATTATTTAAAATTTTTAATTTTTT
AATTTTATATAAAGGACATAAACTTTATAACTCAAGAAAG
Done.