Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004801.1 Hibiscus syriacus cultivar Beakdansim tig00010816_pilon, 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: 36191
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:745 original size:15 final size:15
Alignment explanation
Indices: 725--754 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
715 TTTGAAAAAT
*
725 ATGTTTTCAAAACTA
1 ATGTTTCCAAAACTA
740 ATGTTTCCAAAACTA
1 ATGTTTCCAAAACTA
755 TATATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (15 bp):
ATGTTTCCAAAACTA
Found at i:765 original size:38 final size:35
Alignment explanation
Indices: 723--810 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 35
713 ATTTTGAAAA
*
723 ATATGTTTTCAAAACTAATGTTTCCAAAACTATATATT
1 ATATGTTTTCAAAAC-AAT-TTT-AAAAACTATATATT
*
761 ATATGTTTTCATAAACCATTTTAAAAACTATATATT
1 ATATGTTTTCA-AAACAATTTTAAAAACTATATATT
797 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
811 ATATTTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
35 3 0.06
36 24 0.51
37 3 0.06
38 13 0.28
39 4 0.09
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (35 bp):
ATATGTTTTCAAAACAATTTTAAAAACTATATATT
Found at i:823 original size:36 final size:36
Alignment explanation
Indices: 748--823 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
738 TAATGTTTCC
* *
748 AAAACTATATATTATATGTTTTCATAAACCATTTTA
1 AAAACTATATATTATATGTTTTCATAAAACATTTAA
*
784 AAAACTATATATTATATGTTTTCA-AAAATATTTCAA
1 AAAACTATATATTATATGTTTTCATAAAACATTT-AA
820 AAAA
1 AAAA
824 ACTAACTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 7 0.19
36 29 0.81
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (36 bp):
AAAACTATATATTATATGTTTTCATAAAACATTTAA
Found at i:1829 original size:197 final size:198
Alignment explanation
Indices: 1390--2095 Score: 795
Period size: 192 Copynumber: 3.6 Consensus size: 198
1380 AATCGTAGTC
* ** * *
1390 AACATTGGTCTTCTTCTTGGCTTAAAGACCTCGGTTTTAAATTAAACCA-AAAAGTAGTTCCTCG
1 AACATAGGTCTTCTTCTTAACTTAAAGACCTCGGTTTAAAATTCAACCAGAAAAGTAGTTCCTCG
* * * *
1454 CTGCTCCCATGCGGTTGATATGCCCTCGAGCTAAATGGAATCGAAATC-AAAG-TTTCGTTGATA
66 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCGTTGACA
* * **
1517 GACATCTTCTTCGACTTAAGCTATGTTGTAAATTA-TTTGGGAGATAGTTCCTTGTTGCTAAATC
131 GAAACCTTC-TCGACTT-AGCTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATC
*
1581 GCAACC
194 GC-ACA
* * *
1587 AACCTAGGTC-TC-TCTTGAA-TTAAAGACCTCAGTTTAAACTTCAACCAGAAAA-TAGTTCCTC
1 AACATAGGTCTTCTTCTT-AACTTAAAGACCTCGGTTTAAAATTCAACCAGAAAAGTAGTTCCTC
* * *
1648 G-TGCTACCATGCGGTTTATATGCCCTCGAGCTGAATGGAATC-ATCTCGAAAGTTTTTGTTGAC
65 GCTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCGTTGAC
* * * * *
1711 AGATAACCCTTCTCGCCTTGAGCTATGATGTAAATTAGGCTGTGAGATAGCTCCTTGTTACTAAA
130 AGA-AA-CCTTCTCGACTT-AGCTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAA
1776 TCGCACA
192 TCGCACA
* *
1783 AACATAGGTCTTCTTCTTAACTT-AAGACCTCGGTTTAAAATTCAACCAG-AATGTAGTTCCTCA
1 AACATAGGTCTTCTTCTTAACTTAAAGACCTCGGTTTAAAATTCAACCAGAAAAGTAGTTCCTCG
* * * ** *
1846 CTGCTATCATGCGATTGATACGCCCTC--GCTGAATGGAATCGAACTTAAAAGTTTTCATTGACA
66 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCGTTGACA
* *
1909 -ACAACTTTTTCGACTT--CTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCG
131 GA-AACCTTCTCGACTTAGCTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCG
* *
1971 AAGCT
195 CA-CA
* * ** * * *
1976 AACCTAGGTCTTCTT-ATGGCTTAAAGGCCTCGATTT-AAATTCAACC-GAAAAGTAGTTCCTTG
1 AACATAGGTCTTCTTCTTAACTTAAAGACCTCGGTTTAAAATTCAACCAGAAAAGTAGTTCCTCG
2038 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTC
66 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTC
2096 ATTAATAGAT
Statistics
Matches: 427, Mismatches: 64, Indels: 39
0.81 0.12 0.07
Matches are distributed among these distances:
191 1 0.00
192 92 0.22
193 29 0.07
194 69 0.16
195 58 0.14
196 58 0.14
197 92 0.22
198 28 0.07
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (198 bp):
AACATAGGTCTTCTTCTTAACTTAAAGACCTCGGTTTAAAATTCAACCAGAAAAGTAGTTCCTCG
CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCGTTGACA
GAAACCTTCTCGACTTAGCTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGC
ACA
Found at i:2018 original size:192 final size:195
Alignment explanation
Indices: 1370--2098 Score: 775
Period size: 197 Copynumber: 3.7 Consensus size: 195
1360 AAAGTGGTTT
* * * * * * *
1370 CTTGTTGCCAAATCGTAGTCAACATTGGTCTTCTTCTTGGCTTAAAGACCTCGGTTTTAAATTAA
1 CTTGTTGCTAAATCGAACT-AACATAGGTCTTCTTCTTGACTTAAAGACCTC-GATTTAAATTCA
* * * *
1435 ACCAAAAAGTAGTTCCTCGCTGCTCCCATGCGGTTGATATGCCCTCGAGCTAAATGGAATCGAAA
64 ACCAGAAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATGCCCTC-AGCTGAATGGAATCGAAC
* * * * **
1500 TC-AAAG-TTTCGTTGATAGACATCTTCTTCGACTTAAGCTATGTTGTAAATTA-TTTGGGAGAT
128 TCGAAAGTTTTCATTGACAGACAACTTTTTCGACTT-A-CTATGTTGTAAATTAGGCTGGGAGAT
1562 AGTTC
191 AGTTC
* * *
1567 CTTGTTGCTAAATCGCAACCAACCTAGGTC-TC-TCTTGAATTAAAGACCTC-AGTTTAAACTTC
1 CTTGTTGCTAAATCG-AACTAACATAGGTCTTCTTCTTGACTTAAAGACCTCGA-TTTAAA-TTC
* * *
1629 AACCAGAAAATAGTTCCTCG-TGCTACCATGCGGTTTATATGCCCTCGAGCTGAATGGAATC-AT
63 AACCAGAAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATGCCCTC-AGCTGAATGGAATCGAA
** * * * * * *
1692 CTCGAAAGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGATGTAAATTAGGCTGTGAG
127 CTCGAAAGTTTTCATTGACAGACAA-CTTTTTCGACTT-A-CTATGTTGTAAATTAGGCTGGGAG
*
1757 ATAGCTC
189 ATAGTTC
* * * * *
1764 CTTGTTACTAAATCGCACAAACATAGGTCTTCTTCTTAACTT-AAGACCTCGGTTTAAAATTCAA
1 CTTGTTGCTAAATCGAACTAACATAGGTCTTCTTCTTGACTTAAAGACCTCGATTT-AAATTCAA
* * * * * *
1828 CCAGAATGTAGTTCCTCACTGCTATCATGCGATTGATACGCCCTC-GCTGAATGGAATCGAACTT
65 CCAGAAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATGCCCTCAGCTGAATGGAATCGAACTC
*
1892 AAAAGTTTTCATTGACA-ACAACTTTTTCGACTT-CTATGTTGTAAATTAGGCTGGGAGATAGTT
130 GAAAGTTTTCATTGACAGACAACTTTTTCGACTTACTATGTTGTAAATTAGGCTGGGAGATAGTT
1955 C
195 C
* * * *
1956 CTTGTTGCTAAATCGAAGCTAACCTAGGTCTTCTT-ATGGCTTAAAGGCCTCGATTTAAATTCAA
1 CTTGTTGCTAAATCGAA-CTAACATAGGTCTTCTTCTTGACTTAAAGACCTCGATTTAAATTCAA
*
2020 CC-GAAAAGTAGTTCCTTGCTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAAC
65 CCAG-AAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATGCCCTC-AGCTGAATGGAATCGAAC
2084 TCGAAAGTTTTCATT
128 TCGAAAGTTTTCATT
2099 AATAGATAGA
Statistics
Matches: 440, Mismatches: 74, Indels: 39
0.80 0.13 0.07
Matches are distributed among these distances:
191 1 0.00
192 92 0.21
193 29 0.07
194 78 0.18
195 57 0.13
196 53 0.12
197 97 0.22
198 33 0.08
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (195 bp):
CTTGTTGCTAAATCGAACTAACATAGGTCTTCTTCTTGACTTAAAGACCTCGATTTAAATTCAAC
CAGAAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATGCCCTCAGCTGAATGGAATCGAACTCG
AAAGTTTTCATTGACAGACAACTTTTTCGACTTACTATGTTGTAAATTAGGCTGGGAGATAGTTC
Found at i:8415 original size:15 final size:16
Alignment explanation
Indices: 8383--8422 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
8373 TAACTTCATT
8383 AAAGAAAATTTATTAA
1 AAAGAAAATTTATTAA
*
8399 AAAGATAATTT-TTAA
1 AAAGAAAATTTATTAA
8414 AAAGAAAAT
1 AAAGAAAAT
8423 ACGTCTCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
AAAGAAAATTTATTAA
Found at i:10028 original size:127 final size:127
Alignment explanation
Indices: 9871--10117 Score: 485
Period size: 127 Copynumber: 1.9 Consensus size: 127
9861 GAATCAAATG
9871 CCCCCTTATATCTAAAAAATGTAAAATTATTCAATATTTGTTGGGATTTTAACCTTTCAATATTT
1 CCCCCTTATATCTAAAAAATGTAAAATTATTCAATATTTGTTGGGATTTTAACCTTTCAATATTT
*
9936 GTTGGTATGAATCAACCGAAAAATTAGTTAATAGAATTGAATTGACCTTTCCAAAATTGATT
66 GTTGGTATGAATCAACCGAAAAATTAGTTAATAGAAGTGAATTGACCTTTCCAAAATTGATT
9998 CCCCCTTATATCTAAAAAATGTAAAATTATTCAATATTTGTTGGGATTTTAACCTTTCAATATTT
1 CCCCCTTATATCTAAAAAATGTAAAATTATTCAATATTTGTTGGGATTTTAACCTTTCAATATTT
10063 GTTGGTATGAATCAACCGAAAAATTAGTTAATAGAAGTGAATTGACCTTTCCAAA
66 GTTGGTATGAATCAACCGAAAAATTAGTTAATAGAAGTGAATTGACCTTTCCAAA
10118 TATTTAGGGG
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 119 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (127 bp):
CCCCCTTATATCTAAAAAATGTAAAATTATTCAATATTTGTTGGGATTTTAACCTTTCAATATTT
GTTGGTATGAATCAACCGAAAAATTAGTTAATAGAAGTGAATTGACCTTTCCAAAATTGATT
Found at i:12254 original size:23 final size:23
Alignment explanation
Indices: 12228--12354 Score: 101
Period size: 23 Copynumber: 5.4 Consensus size: 23
12218 AATATTAGTC
**
12228 TTTATCTCTATCTTTATGACATG
1 TTTATCTCTATCTTTATGACACA
* * * **
12251 TTTATTTCATATTTTTTATGATATG
1 TTTATCTC-TA-TCTTTATGACACA
* * *
12276 TTTATCTCTGTTTTTATGATACA
1 TTTATCTCTATCTTTATGACACA
**
12299 TTTATCTCCGTCTTTATGACACA
1 TTTATCTCTATCTTTATGACACA
* *
12322 TTTATTTATATCTTTATGACACA
1 TTTATCTCTATCTTTATGACACA
*
12345 TTTTTCTCTA
1 TTTATCTCTA
12355 ATTTTTGATT
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
23 64 0.75
24 3 0.04
25 18 0.21
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (23 bp):
TTTATCTCTATCTTTATGACACA
Found at i:14305 original size:37 final size:36
Alignment explanation
Indices: 14244--14431 Score: 179
Period size: 37 Copynumber: 5.0 Consensus size: 36
14234 TTGAAAATAC
14244 ATATATAATATATAGTTTTCTTAAAAACATTTTGAAA
1 ATATATAATATATAGTTTT-TTAAAAACATTTTGAAA
* *
14281 ATGTATAGTATATAGGTTTTTTAAAACACA-TTTGAAA
1 ATATATAATATATA-GTTTTTTAAAA-ACATTTTGAAA
14318 ACTATATAATATATAG-TTTTT-AAAACATTTTAGAAAA
1 A-TATATAATATATAGTTTTTTAAAAACATTTT-G-AAA
** *
14355 ATATATAATATAT-GGGTTTTAAAATCATATTTTTTGAAA
1 ATATATAATATATAGTTTTTTAAAA--ACA--TTTTGAAA
*
14394 ACTTATATAATATATAG-TTTTTAAAAACATTTTTAAA
1 A--TATATAATATATAGTTTTTTAAAAACATTTTGAAA
14431 A
1 A
14432 AATTATATAT
Statistics
Matches: 127, Mismatches: 9, Indels: 30
0.77 0.05 0.18
Matches are distributed among these distances:
34 3 0.02
35 7 0.06
36 22 0.17
37 42 0.33
38 19 0.15
39 8 0.06
40 1 0.01
41 24 0.19
42 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (36 bp):
ATATATAATATATAGTTTTTTAAAAACATTTTGAAA
Found at i:14330 original size:36 final size:36
Alignment explanation
Indices: 14245--14425 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
14235 TGAAAATACA
14245 TATATAATATATAGTTTTCTTAAAA-ACATTTTGAAAA-
1 TATATAATATATAG-TTT-TTAAAACACA-TTTGAAAAC
* *
14282 TGTATAGTATATAGGTTTTTTAAAACACATTTGAAAAC
1 TATATAATATATA-G-TTTTTAAAACACATTTGAAAAC
* *
14320 TATATAATATATAGTTTTTAAAACA-TTTTAGAAAAA
1 TATATAATATATAGTTTTTAAAACACATTT-GAAAAC
* * *
14356 TATATAATATATGGGTTTTAAAATCATATTTTTTGAAAAC
1 TATATAATATATAGTTTTTAAAA-CACA---TTTGAAAAC
14396 TTATATAATATATAGTTTTTAAAA-ACATTT
1 -TATATAATATATAGTTTTTAAAACACATTT
14426 TTAAAAAATT
Statistics
Matches: 121, Mismatches: 13, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
35 3 0.02
36 40 0.33
37 28 0.23
38 19 0.16
39 2 0.02
40 5 0.04
41 24 0.20
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACACATTTGAAAAC
Found at i:14438 original size:38 final size:35
Alignment explanation
Indices: 14244--14459 Score: 164
Period size: 38 Copynumber: 5.7 Consensus size: 35
14234 TTGAAAATAC
*
14244 ATATATAATATATAGTTTTCTTAAAAACATTTTGAAA
1 ATATATAATATATAG-TTT-TTAAAAACATTTTAAAA
* * *
14281 ATGTATAGTATATAGGTTTTTTAAAACACATTTGAAAA
1 ATATATAATATATA-G-TTTTTAAAA-ACATTTTAAAA
*
14319 CTATATAATATATAGTTTTT-AAAACATTTTAGAAAA
1 ATATATAATATATAGTTTTTAAAAACATTTT--AAAA
* * *
14355 ATATATAATATATGGGTTTTAAAATCATATTTTTTGAAAA
1 ATATATAATATATAGTTTTTAAAA--ACA--TTTT-AAAA
*
14395 CTTATATAATATATAGTTTTTAAAAACATTTTTAAAAAA
1 -ATATATAATATATAGTTTTTAAAAACA-TTTT--AAAA
* *
14434 TTATATATAATATATAATTTCTAAAA
1 --ATATATAATATATAGTTTTTAAAA
14460 CTCTTTTGGA
Statistics
Matches: 146, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
34 6 0.04
35 3 0.02
36 26 0.18
37 22 0.15
38 30 0.21
39 8 0.05
40 26 0.18
41 25 0.17
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTAAAAACATTTTAAAA
Found at i:14541 original size:32 final size:32
Alignment explanation
Indices: 14463--14542 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 32
14453 TCTAAAACTC
*
14463 TTTTGGAAATTATATAGTTTTTAAAAAAAACAT
1 TTTTGAAAATTATATAGTTTTT-AAAAAAACAT
**
14496 TTTTGAAAATTATATAGTTTTT-AAAAAATTT
1 TTTTGAAAATTATATAGTTTTTAAAAAAACAT
14527 TTTTGAAAATTTATAT
1 TTTTGAAAA-TTATAT
14543 TTAATAATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 16 0.37
32 6 0.14
33 21 0.49
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (32 bp):
TTTTGAAAATTATATAGTTTTTAAAAAAACAT
Found at i:14638 original size:13 final size:13
Alignment explanation
Indices: 14620--14644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14610 AAATAAATAT
14620 TTATTTATTATTG
1 TTATTTATTATTG
14633 TTATTTATTATT
1 TTATTTATTATT
14645 ATTTGTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTTATTATTG
Found at i:14650 original size:17 final size:17
Alignment explanation
Indices: 14617--14664 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
14607 TTTAAATAAA
14617 TATTTATTTATTA-TTGT
1 TATTTA-TTATTATTTGT
14634 TATTTATTATTATTTGT
1 TATTTATTATTATTTGT
*
14651 T-TCTATTACTTATT
1 TATTTATTA-TTATT
14665 ATTCATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (17 bp):
TATTTATTATTATTTGT
Found at i:14861 original size:16 final size:15
Alignment explanation
Indices: 14840--14869 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
14830 GCCAGCGAAA
14840 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
14856 ATCCCGGGATGACC
1 ATCCCGGGATGACC
14870 GACCACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:16748 original size:164 final size:164
Alignment explanation
Indices: 16476--17254 Score: 859
Period size: 164 Copynumber: 4.7 Consensus size: 164
16466 TAAAAAAGAT
* * * * * * * * * *
16476 ATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCGAACAAAAGACCTTTGAGCTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TAACCAAAGACCTTCGAGTTCGACT
* * *
16541 ACGCTCAGCT-CAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAG
65 ACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAG
*
16605 ACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCAC
129 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* *
16641 ATCATTTACAGCATAACTCAAGGCTAGAAGGTTTATCTGTAACCGAAGACCTTCGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
* * *
16706 CGCTCAGCTCCAAGGCACATCATTTGTAGAATAGCTTAAGTCGAGAAGGGCTATCTACCAAATAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGAC
* * * *
16771 CCTCGAGTTCGATTACAGTGAGCTTTGAGGGCAC
131 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * ** ** *
16805 ATTATTTGCAGCATAACTTAA-ATTGAGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGAC
1 ATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCT-GTAACCAAAGACCTTCGAGTTCGAC
* * *
16869 TACGCTCAACTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTCCAAAG
64 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAG
*
16934 ACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCAC
129 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * *
16970 ATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAGACCTTCGAGTTTGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
* * * * *
17035 CGCTCAGCTCCACGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTACCAAGCAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTA-C---CAA
** * * * *
17100 AGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCAC
127 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * * * *
17137 GTCATTTGCGGTATAGCTCAAGGCTAGAAGGGCTATCTG---CCAAAGACCTTCGAGTTTGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
* * ** * ***
17199 CGCTCAGCTCTAGGGCACATCATTTATAGCATAGCCTAAGGAAAGAAGGGCTATCT
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
17255 GTCAATAAAA
Statistics
Matches: 520, Mismatches: 86, Indels: 17
0.83 0.14 0.03
Matches are distributed among these distances:
163 1 0.00
164 277 0.53
165 177 0.34
166 1 0.00
167 39 0.08
168 25 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (164 bp):
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGAC
CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:17304 original size:329 final size:326
Alignment explanation
Indices: 16476--17257 Score: 935
Period size: 329 Copynumber: 2.4 Consensus size: 326
16466 TAAAAAAGAT
* * * *
16476 ATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCGAACAAAAGACCTTTGAGCTCGACT
1 ATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGC---C-AAAGACCTTTGAGTTCGACT
* * *
16541 ACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG-CCAAAG
62 ACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTCCAAAG
*
16605 ACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA
127 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA
* * * **
16670 GGTTTATCTGTAACCGAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAG
192 GGGTTATCTATAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAG
* * * * ** *
16735 AATAGCTTAAGTCGAGAAGGGCTATCTACCAAATACCCTCGAGTTCGATTACAGTGAGCTTTGAG
257 AATAACTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGACTACAGTCAGCTTCCAA
16800 GGCAC
322 GGCAC
* * * ** * *
16805 ATTATTTGCAGCATAACTTAA-ATTGAGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAGCTCAAGGCT-AGAAGGGCTATCT----GCCAAAGACCTTTGAGTTCGAC
* * *
16869 TACGCTCAACTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-TCCAAA
61 TACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTCCAAA
* *
16933 GACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGCATAACTCAAGGCTAGA
126 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGA
* * * *
16998 AGGGTTATCTATCACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCACGGCATATCATTTACA
191 AGGGTTATCTATAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACA
* * *
17063 GCATAACTTAAGTCGAGAAGGGTTATCTACCAAGCAAAGACCTTCGAGTTCGACTAC-GCTCAGC
256 GAATAACTTAAGTCGAGAAGGGCTATCTA-C---CAAAGACCCTCGAGTTCGACTACAG-TCAGC
17127 -TCCAAGGCAC
316 TTCCAAGGCAC
* * * * *
17137 GTCATTTGCGGTATAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCTTCGAGTTTGACTACGC
1 ATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGC
* * ** * ***
17202 TCAGCTCTAGGGCACATCATTTATAGCATAGCCTAAGGAAAGAAGGGCTATCTGTC
66 TCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTC
17258 AATAAAATTA
Statistics
Matches: 379, Mismatches: 61, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
328 67 0.18
329 249 0.66
330 2 0.01
332 35 0.09
333 26 0.07
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (326 bp):
ATCATTTGCAGCATAGCTCAAGGCTAGAAGGGCTATCTGCCAAAGACCTTTGAGTTCGACTACGC
TCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTCCAAAGACCC
CCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
TATCTATAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGAATA
ACTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGACTACAGTCAGCTTCCAAGGCA
C
Found at i:17805 original size:2 final size:2
Alignment explanation
Indices: 17798--17864 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
17788 TCATTTTTAT
17798 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17840 TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
17865 GTTCACAAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17973 original size:36 final size:37
Alignment explanation
Indices: 17890--18122 Score: 158
Period size: 39 Copynumber: 6.1 Consensus size: 37
17880 TTGGAAATAC
*
17890 ATATATATATAGTTTTCTTAAAA-ACATTTTGAAAA-T
1 ATATATATATAGTTTTTTTAAAACAC-TTTTGAAAACT
*
17926 GTATAGTATATAGTTTTTTTAAAACACTTTTGAAAACT
1 ATATA-TATATAGTTTTTTTAAAACACTTTTGAAAACT
*
17964 ATATAATATATAG--TTTTTAAAACA-TTTTAGAAAAAT
1 ATAT-ATATATAGTTTTTTTAAAACACTTTT-GAAAACT
** * *
18000 ATATA-ATATA-TGGGTTTTAAAGTCATATTTTTTGAAAACTT
1 ATATATATATAGT-TTTTTTAAA---ACA-CTTTTGAAAAC-T
* *
18041 ATATAATATATAGTTTTTTAAAAACATTTTTGAAAACTT
1 ATAT-ATATATAGTTTTTTTAAAACACTTTTGAAAAC-T
* * * * *
18080 ATATATAATATA-TAATTTCTAAAACTCTTTTGGAAATT
1 ATATAT-ATATAGT-TTTTTTAAAACACTTTTGAAAACT
18118 ATATA
1 ATATA
18123 GTTTTTAAAA
Statistics
Matches: 160, Mismatches: 18, Indels: 36
0.75 0.08 0.17
Matches are distributed among these distances:
34 5 0.03
35 5 0.03
36 32 0.20
37 26 0.16
38 22 0.14
39 41 0.26
40 7 0.04
41 9 0.06
42 1 0.01
43 11 0.07
44 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATATATAGTTTTTTTAAAACACTTTTGAAAACT
Found at i:18078 original size:39 final size:38
Alignment explanation
Indices: 17871--18093 Score: 208
Period size: 36 Copynumber: 5.8 Consensus size: 38
17861 TATAGTTCAC
17871 AAACAGTTTTTGGAAATAC-ATAT-ATATATAGTTTTCTTAA
1 AAACA-TTTTT-GAAA-ACTATATAATATATAGTTTT-TTAA
* * *
17911 AAACA-TTTTGAAAA-TGTATAGTATATAGTTTTTTTA
1 AAACATTTTTGAAAACTATATAATATATAGTTTTTTAA
*
17947 AAACACTTTTGAAAACTATATAATATATAG-TTTTT-A
1 AAACATTTTTGAAAACTATATAATATATAGTTTTTTAA
* * **
17983 AAACATTTTAGAAAAATATATAATATAT-GGGTTTTAA
1 AAACATTTTTGAAAACTATATAATATATAGTTTTTTAA
* *
18020 AGTCATATTTTTTGAAAACTTATATAATATATAGTTTTTTAA
1 A--AACA-TTTTTGAAAAC-TATATAATATATAGTTTTTTAA
18062 AAACATTTTTGAAAACTTATATATAATATATA
1 AAACATTTTTGAAAAC---TATATAATATATA
18094 ATTTCTAAAA
Statistics
Matches: 152, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
35 1 0.01
36 42 0.28
37 31 0.20
38 16 0.11
39 13 0.09
40 16 0.11
41 25 0.16
42 8 0.05
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (38 bp):
AAACATTTTTGAAAACTATATAATATATAGTTTTTTAA
Found at i:18104 original size:39 final size:38
Alignment explanation
Indices: 17871--18122 Score: 177
Period size: 36 Copynumber: 6.6 Consensus size: 38
17861 TATAGTTCAC
* *
17871 AAACAGTTTTTGGAAA-TACATAT-ATATATAGTTTTCTTAA
1 AAACA-TTTTTGAAAACTATATATAATATATAG-TTT-TT-A
* *
17911 AAACA-TTTTGAAAA-TGTATAGT-ATATAGT-TTTTTTA
1 AAACATTTTTGAAAACTATATA-TAATATA-TAGTTTTTA
*
17947 AAACACTTTTGAAAAC--TATATAATATATAGTTTTTA
1 AAACATTTTTGAAAACTATATATAATATATAGTTTTTA
* * *
17983 AAACATTTTAGAAAA--ATATATAATATATGGGTTTTA
1 AAACATTTTTGAAAACTATATATAATATATAGTTTTTA
*
18019 AAGTCATATTTTTTGAAAACT-TATATAATATATAGTTTTTTAA
1 AA---ACA-TTTTTGAAAACTATATATAATATATAG-TTTTT-A
* *
18062 AAACATTTTTGAAAACTTATATATAATATATAATTTCTA
1 AAACATTTTTGAAAAC-TATATATAATATATAGTTTTTA
* *
18101 AAAC-TCTTTTGGAAATTATATA
1 AAACAT-TTTTGAAAACTATATA
18123 GTTTTTAAAA
Statistics
Matches: 176, Mismatches: 18, Indels: 38
0.76 0.08 0.16
Matches are distributed among these distances:
35 2 0.01
36 54 0.31
37 11 0.06
38 22 0.12
39 32 0.18
40 22 0.12
41 26 0.15
42 4 0.02
43 3 0.02
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (38 bp):
AAACATTTTTGAAAACTATATATAATATATAGTTTTTA
Found at i:18269 original size:19 final size:19
Alignment explanation
Indices: 18237--18279 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
18227 AAATTATTAT
* *
18237 TATTATATATATATATATA
1 TATTAAATAAATATATATA
* *
18256 TATTAAATAAATATTTATT
1 TATTAAATAAATATATATA
18275 TATTA
1 TATTA
18280 TTGTTATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTAAATAAATATATATA
Found at i:18286 original size:13 final size:13
Alignment explanation
Indices: 18270--18294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18260 AAATAAATAT
18270 TTATTTATTATTG
1 TTATTTATTATTG
18283 TTATTTATTATT
1 TTATTTATTATT
18295 ATTTGTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTTATTATTG
Found at i:18300 original size:17 final size:17
Alignment explanation
Indices: 18267--18314 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
18257 ATTAAATAAA
18267 TATTTATTTATTA-TTGT
1 TATTTA-TTATTATTTGT
18284 TATTTATTATTATTTGT
1 TATTTATTATTATTTGT
*
18301 T-TCTATTACTTATT
1 TATTTATTA-TTATT
18315 ATTCATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (17 bp):
TATTTATTATTATTTGT
Found at i:19490 original size:17 final size:19
Alignment explanation
Indices: 19452--19501 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
19442 AAGTTTTATT
*
19452 TTATTTTGTTTTATCGTCA
1 TTATTTTATTTTATCGTCA
*
19471 TTATTTT-TTTTCTCGT-A
1 TTATTTTATTTTATCGTCA
19488 TTATTTTATTTTAT
1 TTATTTTATTTTAT
19502 TGCTTCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.29
18 13 0.46
19 7 0.25
ACGTcount: A:0.16, C:0.08, G:0.06, T:0.70
Consensus pattern (19 bp):
TTATTTTATTTTATCGTCA
Found at i:19648 original size:21 final size:20
Alignment explanation
Indices: 19623--19673 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
19613 TTTTTTGCAA
19623 CTTTTATTT-TTATTTTTCATT
1 CTTTTATTTGTTA-TTTT-ATT
*
19644 TTTTTAATTTGTTATTTTATT
1 CTTTT-ATTTGTTATTTTATT
19665 CTTTTATTT
1 CTTTTATTT
19674 ACTCTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 11 0.42
22 8 0.31
23 3 0.12
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (20 bp):
CTTTTATTTGTTATTTTATT
Found at i:19719 original size:17 final size:16
Alignment explanation
Indices: 19681--19721 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
19671 TTTACTCTTG
19681 ATTTATTTATTTGTTT
1 ATTTATTTATTTGTTT
*
19697 ATTTTATTCTATTTTTTT
1 A-TTTATT-TATTTGTTT
19715 ATTTATT
1 ATTTATT
19722 GTCGCTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 12 0.55
18 9 0.41
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (16 bp):
ATTTATTTATTTGTTT
Found at i:19721 original size:12 final size:12
Alignment explanation
Indices: 19625--19721 Score: 54
Period size: 13 Copynumber: 7.5 Consensus size: 12
19615 TTTTGCAACT
19625 TTTATTTTTATT-
1 TTTATTTTT-TTA
19637 TTTCATTTTTTTAA
1 TTT-ATTTTTTT-A
* *
19651 TTTGTTATTTTA
1 TTTATTTTTTTA
*
19663 TTCT-TTTATTTA
1 TT-TATTTTTTTA
*
19675 CTCTTGATTTATTTA
1 -T-TT-ATTTTTTTA
*
19690 TTTGTTTATTTTA
1 TTTATTT-TTTTA
19703 TTCTATTTTTTTA
1 TT-TATTTTTTTA
19716 TTTATT
1 TTTATT
19722 GTCGCTATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
12 21 0.31
13 30 0.44
14 9 0.13
15 8 0.12
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:23861 original size:21 final size:21
Alignment explanation
Indices: 23835--23880 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
23825 ATTCAAATCG
23835 AGATGCAGTGGAGAACTTCAT
1 AGATGCAGTGGAGAACTTCAT
*
23856 AGATGCAGTGGAGAACTTCTT
1 AGATGCAGTGGAGAACTTCAT
23877 AGAT
1 AGAT
23881 ATGAATCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (21 bp):
AGATGCAGTGGAGAACTTCAT
Found at i:25844 original size:19 final size:17
Alignment explanation
Indices: 25808--25886 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 17
25798 TAATATAAAT
*
25808 AAAAATAAAACAAGAATAA
1 AAAAATAGAA-AA-AATAA
*
25827 AAAACTAGGAAAAAAATAA
1 AAAAATA-G-AAAAAATAA
25846 AAAAATAGAAAAAATAA
1 AAAAATAGAAAAAATAA
* *
25863 AACAAAAAGTAATAAATAA
1 AA-AAATAG-AAAAAATAA
25882 AAAAA
1 AAAAA
25887 AATAAAACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.22
18 9 0.18
19 27 0.53
20 2 0.04
21 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAATAGAAAAAATAA
Found at i:25849 original size:8 final size:8
Alignment explanation
Indices: 25836--25898 Score: 51
Period size: 8 Copynumber: 8.1 Consensus size: 8
25826 AAAAACTAGG
25836 AAAAAAAT
1 AAAAAAAT
25844 AAAAAAAT
1 AAAAAAAT
25852 AGAAAAAAT
1 A-AAAAAAT
*
25861 AAAACAA-
1 AAAAAAAT
**
25868 AAAGTAAT
1 AAAAAAAT
*
25876 -AAATAA-
1 AAAAAAAT
25882 AAAAAAAT
1 AAAAAAAT
*
25890 AAAACAAT
1 AAAAAAAT
25898 A
1 A
25899 TATATATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 15 0.33
8 22 0.49
9 8 0.18
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:25849 original size:37 final size:37
Alignment explanation
Indices: 25767--25896 Score: 117
Period size: 37 Copynumber: 3.5 Consensus size: 37
25757 AAATAAGTAG
*
25767 AAATAAAAATAAAACAAAATAAACAAAATGGTAATAT
1 AAATAAAAATAAAACAAAATAAACAAAATGGTAATAA
*
25804 AAATAAAAATAAAACAAGAATAAA-AAACTAGG-AA-AA
1 AAATAAAAATAAAACAA-AATAAACAAAAT-GGTAATAA
* *
25840 AAATAAAAA-AATAGAAAAAATAAAACAAAA-AGTAATAAA
1 AAATAAAAATAA-A-ACAAAAT-AAACAAAATGGTAAT-AA
*
25879 TAAAAAAAAATAAAACAA
1 -AAATAAAAATAAAACAA
25897 TATATATATA
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
35 2 0.03
36 15 0.20
37 31 0.41
38 11 0.15
39 5 0.07
40 9 0.12
41 2 0.03
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (37 bp):
AAATAAAAATAAAACAAAATAAACAAAATGGTAATAA
Found at i:25866 original size:47 final size:46
Alignment explanation
Indices: 25808--25898 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 46
25798 TAATATAAAT
* *
25808 AAAAATAAAACAAGAA-TAAAAAACTAGGAAAAAAATAAAAAAATAGA
1 AAAAATAAAACAAAAAGTAAAAAA-TA-AAAAAAAATAAAAAAATAGA
* *
25855 AAAAATAAAACAAAAAGTAATAAATAAAAAAAAATAAAACAATA
1 AAAAATAAAACAAAAAGTAAAAAATAAAAAAAAATAAAAAAATA
25899 TATATATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
46 16 0.41
47 17 0.44
48 6 0.15
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.12
Consensus pattern (46 bp):
AAAAATAAAACAAAAAGTAAAAAATAAAAAAAAATAAAAAAATAGA
Found at i:25869 original size:29 final size:29
Alignment explanation
Indices: 25837--25896 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
25827 AAAACTAGGA
25837 AAAAAATAA-AAA-AATAGAAAAAATAAAAC
1 AAAAAATAATAAATAA-A-AAAAAATAAAAC
*
25866 AAAAAGTAATAAATAAAAAAAAATAAAAC
1 AAAAAATAATAAATAAAAAAAAATAAAAC
25895 AA
1 AA
25897 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 22 0.79
30 4 0.14
31 2 0.07
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (29 bp):
AAAAAATAATAAATAAAAAAAAATAAAAC
Found at i:25876 original size:15 final size:14
Alignment explanation
Indices: 25808--25896 Score: 56
Period size: 14 Copynumber: 5.9 Consensus size: 14
25798 TAATATAAAT
*
25808 AAAAATAAAACAAG
1 AAAAATAAAACAAA
*
25822 AATAA-AAAACTAGGAA
1 AAAAATAAAAC-A--AA
*
25838 AAAAATAAAAAAATAGA
1 AAAAAT-AAAACA-A-A
25855 AAAAATAAAACAAA
1 AAAAATAAAACAAA
*
25869 AAGTAATAAATA-AAA
1 AA-AAATAAA-ACAAA
25884 AAAAATAAAACAA
1 AAAAATAAAACAA
25897 TATATATATA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
13 6 0.10
14 16 0.28
15 12 0.21
16 12 0.21
17 8 0.14
18 4 0.07
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (14 bp):
AAAAATAAAACAAA
Found at i:25952 original size:13 final size:13
Alignment explanation
Indices: 25934--25989 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
25924 ACAAGTGAAA
25934 AAATAATAATAAT
1 AAATAATAATAAT
25947 AAATAATAATAA-
1 AAATAATAATAAT
* * *
25959 ACAATACTAAGAAG
1 A-AATAATAATAAT
25973 AAA-AA-AATAAT
1 AAATAATAATAAT
25984 AAATAA
1 AAATAA
25990 AGTTAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 7 0.20
12 4 0.11
13 23 0.66
14 1 0.03
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:26122 original size:2 final size:2
Alignment explanation
Indices: 26117--26175 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
26107 ATGTGTGTAG
26117 AT AT 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 AT AT
26159 A- AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
26176 ACAACAATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:26184 original size:22 final size:24
Alignment explanation
Indices: 26117--26188 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 24
26107 ATGTGTGTAG
* *
26117 ATATATATATATATATATA-TAT-
1 ATATATATATATATACATACAATA
* *
26139 ATATATATATATATATATATAATA
1 ATATATATATATATACATACAATA
26163 ATATATATATATA-ACA-ACAATA
1 ATATATATATATATACATACAATA
26185 ATAT
1 ATAT
26189 CAATAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 28 0.62
23 4 0.09
24 13 0.29
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATATATATATACATACAATA
Found at i:26286 original size:10 final size:11
Alignment explanation
Indices: 26227--26288 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 11
26217 ATGGTAATAA
*
26227 ATAAAAAATAT
1 ATAAAATATAT
*
26238 AGAAAATA-A-
1 ATAAAATATAT
26247 ATAGAAATATAT
1 ATA-AAATATAT
*
26259 AT-ATATATAT
1 ATAAAATATAT
*
26269 ATATAATAT-T
1 ATAAAATATAT
26279 ATAAAATATA
1 ATAAAATATA
26289 GTACATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
9 2 0.05
10 24 0.62
11 11 0.28
12 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
ATAAAATATAT
Found at i:26489 original size:2 final size:2
Alignment explanation
Indices: 26484--26511 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26474 AAAATAAATA
26484 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
26512 GTAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26489 original size:19 final size:21
Alignment explanation
Indices: 26450--26492 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
26440 GAGAAAGTAA
26450 AAAAAAATATAAGAATAATAT
1 AAAAAAATATAAGAATAATAT
*
26471 AAAAAAATA-AATAATATATAT
1 AAAAAAATATAAGAATA-ATAT
26492 A
1 A
26493 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAAAATATAAGAATAATAT
Found at i:28551 original size:80 final size:80
Alignment explanation
Indices: 28238--29020 Score: 890
Period size: 80 Copynumber: 9.7 Consensus size: 80
28228 GATAATTTTG
* * * *
28238 TTGGCAGATAGCCCTTCTTACCTTGAGCTATGCTGTAAATTTGATTTGCCTTTGAGCTGAGTGTA
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTA
* *
28303 ATCGAAAT-AAATGGTCT
64 ATCGAACTCGAA-GGTCT
* * * * *
28320 TTGATGACAAATAACCCTTCTCGCCTTGAGTTATGTTGTAAATGATGTGCC-TTGTAGCTGAGTG
1 TTG--G-CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTG-AGCTGAGTG
*
28384 TAATTGAACTCGAAGGTCT
62 TAATCGAACTCGAAGGTCT
* * * * * *
28403 TTGGTAGATAACCCTTCTAGCCTTGAG-TTTGCTGCAAATGACGTGCCTCTGAGCTTAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
28467 CGAACTTGAAGGTCT
66 CGAACTCGAAGGTCT
* *
28482 TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
28547 CGAACTCGAAGGTCT
66 CGAACTCGAAGGTCT
* * * * * * *
28562 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCATATAATGTTCCTCTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
28627 CGAACTCGAAAGTCT
66 CGAACTCGAAGGTCT
* * *
28642 TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTAAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
28707 CGAACTCGAAAGTCT
66 CGAACTCGAAGGTCT
* * * * * * * *
28722 TTGGCATATAACACTTATAGCCTTAAGTTATGTTGCAAATGATGTGCCTCTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
28787 CGAACTCGAAGGTCT
66 CGAACTCGAAGGTCT
* * * * *
28802 TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATAATGTGTCTTTGAGTTGAGTGTAAT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
* *
28867 TGAACTCGAAGGTAT
66 CGAACTCGAAGGTCT
* * * * * * *
28882 TTGGCAGATAACCCATCTAGCCTTGAGTTATGCTGTAAATGATGCGCCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
28947 CGAACTTGAAGGTCTTTT
66 CGAACTCGAAGGTC---T
* * ** *
28965 GTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGAAAATGATGTGCC-TTGAGCT
1 -TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCT
29021 ATGCTACAAA
Statistics
Matches: 591, Mismatches: 99, Indels: 21
0.83 0.14 0.03
Matches are distributed among these distances:
79 65 0.11
80 407 0.69
81 1 0.00
82 6 0.01
83 41 0.07
84 42 0.07
85 29 0.05
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (80 bp):
TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
CGAACTCGAAGGTCT
Found at i:28682 original size:160 final size:160
Alignment explanation
Indices: 28238--29020 Score: 984
Period size: 160 Copynumber: 4.8 Consensus size: 160
28228 GATAATTTTG
* * * * *
28238 TTGGCAGATAGCCCTTCTTA-CCTTGAGCTATGCTGTAAATTTGATTTGCCTTTGAGCTGAGTGT
1 TTGGCAGATAACCCTTC-TAGCCTTGAGTTATGCTGCAAA--TGATGTGCCTCTGAGCTGAGTGT
* * * * * * **
28302 AATCGAAAT-AAATGGTCTTTGATGACAAATAACCCTTCTCGCCTTGAGTTATGTTGTAAATGAT
63 AATCGAACTCGAA-GGTCTTTG--G-CAGATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGAT
*
28366 GTGCC-TTGTAGCTGAGTGTAATTGAACTCGAAGGTCT
124 GTGCCTTTG-AGCTGAGTGTAATCGAACTCGAAGGTCT
* * *
28403 TTGGTAGATAACCCTTCTAGCCTTGAGTT-TGCTGCAAATGACGTGCCTCTGAGCTTAGTGTAAT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTAAT
* *
28467 CGAACTTGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTT
66 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTT
28532 TGAGCTGAGTGTAATCGAACTCGAAGGTCT
131 TGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * *
28562 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCATATAATGTTCCTCTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTAAT
* *
28627 CGAACTCGAAAGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTT
66 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTT
* *
28692 TGAGCTAAGTGTAATCGAACTCGAAAGTCT
131 TGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * * *
28722 TTGGCATATAACACTTATAGCCTTAAGTTATGTTGCAAATGATGTGCCTCTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTAAT
* * *
28787 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATAATGTGTCTT
66 CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTT
* * *
28852 TGAGTTGAGTGTAATTGAACTCGAAGGTAT
131 TGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * * * *
28882 TTGGCAGATAACCCATCTAGCCTTGAGTTATGCTGTAAATGATGCGCCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTAAT
* * *
28947 CGAACTTGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGA-AAATGATGT
66 CGAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTT-ACAAATGATGT
29011 GCC-TTGAGCT
126 GCCTTTGAGCT
29021 ATGCTACAAA
Statistics
Matches: 545, Mismatches: 64, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
159 92 0.17
160 334 0.61
162 35 0.06
163 9 0.02
164 52 0.10
165 23 0.04
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (160 bp):
TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTAAT
CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTT
TGAGCTGAGTGTAATCGAACTCGAAGGTCT
Found at i:29031 original size:26 final size:26
Alignment explanation
Indices: 28984--29047 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
28974 TAGCCCTTCT
*
28984 TGCCTTGAGCTATATTGAAAATGATG
1 TGCCTTGAGCTATACTGAAAATGATG
* *
29010 TGCCTTGAGCTATGCT-ACAAATGTTG
1 TGCCTTGAGCTATACTGA-AAATGATG
29036 TGCCTTTGAGCT
1 TGCC-TTGAGCT
29048 GAGTGTAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.03
26 25 0.76
27 7 0.21
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (26 bp):
TGCCTTGAGCTATACTGAAAATGATG
Found at i:29102 original size:110 final size:110
Alignment explanation
Indices: 28901--29132 Score: 293
Period size: 110 Copynumber: 2.1 Consensus size: 110
28891 AACCCATCTA
* ** * * *
28901 GCCTTGAGTTATGCTGTAAATGATGCGCCTTTGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTG
1 GCCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTG
* * *
28966 TTGGCAAATAGCCCTTCTTGCCTTGAGCTATATTGAAAATGATGT
66 TTGGCAAATAACCCTTCTAGCCTTGAGCTATACTGAAAATGATGT
* * *
29011 GCCTTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTG
1 GCCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTG
* * * * * *
29076 TTGGCAGATAATCCTTCTAGCTTTGAGTTATGCTGCAAATGATGT
66 TTGGCAAATAACCCTTCTAGCCTTGAGCTATACTGAAAATGATGT
29121 GCCTTGGAGCTA
1 GCCTT-GAGCTA
29133 AGCGTAGTCG
Statistics
Matches: 103, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
110 97 0.94
111 6 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (110 bp):
GCCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTG
TTGGCAAATAACCCTTCTAGCCTTGAGCTATACTGAAAATGATGT
Found at i:29145 original size:194 final size:190
Alignment explanation
Indices: 28820--29215 Score: 533
Period size: 194 Copynumber: 2.1 Consensus size: 190
28810 TAGCCCTTCT
* * * * **
28820 TGCCTTGAGCTATGTTGCAAATAATGTGTCTTTGAGTTGAGTGTAATTGAACTCGAAGGTATTTG
1 TGCCTTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTATTTG
* * *
28885 GCAGATAACCCATCTAGCCTTGAGTTATGCTGTAAATGATGCGCCTTTGAGCTGAGCGTAGTCGA
66 GCAGATAACCCATCTAGCCTTGAGTTATGCTGCAAATGATGCGCCTTGGAGCTAAGCGTAGTCGA
* * *
28950 ACTTGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGA-GCTATATTGAAAATGATG
131 ACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCATT-ATGCTATATTGAAAATGATG
** *
29010 TGCCTTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTT
1 TGCCTTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGG---TAT
* * * *
29075 GTTGGCAGATAATCCTTCTAGCTTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGTAG
63 -TTGGCAGATAACCCATCTAGCCTTGAGTTATGCTGCAAATGATGCGCCTTGGAGCTAAGCGTAG
* * *
29140 TCGAACTCGAAGGTCTTTTGTTGGTAAATAACCCTTCTTGCATTATGCTATGTTGCAAATGATG
127 TCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCATTATGCTATATTGAAAATGATG
29204 TGCCTTGGAGCT
1 TGCCTT-GAGCT
29216 GAGCATAGTC
Statistics
Matches: 178, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
190 51 0.29
193 3 0.02
194 119 0.67
195 5 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (190 bp):
TGCCTTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTATTTG
GCAGATAACCCATCTAGCCTTGAGTTATGCTGCAAATGATGCGCCTTGGAGCTAAGCGTAGTCGA
ACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCATTATGCTATATTGAAAATGATG
Found at i:29155 original size:84 final size:84
Alignment explanation
Indices: 29011--29444 Score: 555
Period size: 84 Copynumber: 5.2 Consensus size: 84
29001 AAAATGATGT
* * * * * *
29011 GCCTTGAGCTATGCTACAAATGTTGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTG
1 GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* *
29076 TTGGCAGATAATCCTTCTA
66 TTGGTAGATAACCCTTCTA
* * *
29095 GCTTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTTG
1 GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* *
29160 TTGGTAAATAACCCTTCTT
66 TTGGTAGATAACCCTTCTA
* * *
29179 GCATT-ATGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTT
1 GCCTTGA-GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
* *
29243 GTTGGTAGATAACGCTTATA
65 GTTGGTAGATAACCCTTCTA
* * * *
29263 GCCTTGAGTTATACTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAG
1 GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* * *
29328 TTGGCAGATAGCCCTTCTT
66 TTGGTAGATAACCCTTCTA
* * * * *
29347 GCCTTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTCTTTTG
1 GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* *
29412 TTGGTAGATAGCCCTTCTC
66 TTGGTAGATAACCCTTCTA
*
29431 GCTTTGAGCTATGC
1 GCCTTGAGCTATGC
29445 CGTAAATAGA
Statistics
Matches: 302, Mismatches: 46, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
83 1 0.00
84 300 0.99
85 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (84 bp):
GCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
TTGGTAGATAACCCTTCTA
Found at i:30823 original size:95 final size:95
Alignment explanation
Indices: 30582--30837 Score: 275
Period size: 95 Copynumber: 2.7 Consensus size: 95
30572 GGCTAGTTGG
* * * * * * *
30582 ATCCATAAAGCCGGGGCGT-TTAACCAATTGCTCTAGAGGGACAACTTAATATCATTGTATAG-A
1 ATCCATAAAGACGAGGCATGTTAACCAATTACTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTA
* *
30645 TATTATAATCACCTTTTTAGGCTAGCTGAATATT
62 TATTATAATCACCTTTTCAAGCTAGCTGAATATT
** *
30679 ATCCATAAAGACGAGGTGTGTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATT
1 ATCCATAAAGACGAGGCATGTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATT
*
30744 ATAATCACCTTTATCAAGCTAGCTGAATCTT
66 ATAATCACCTTT-TCAAGCTAGCTGAATATT
* * * * * *
30775 ATCCATAAAGTCGAGGCAT-TTAACCATTTACTTTAGATGGATAGCTCAAGCTTTATTGTATAT
1 ATCCATAAAGACGAGGCATGTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATAT
30838 ATGCAATATT
Statistics
Matches: 138, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
94 4 0.03
95 57 0.41
96 33 0.24
97 18 0.13
98 26 0.19
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGACGAGGCATGTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATT
ATAATCACCTTTTCAAGCTAGCTGAATATT
Found at i:33628 original size:23 final size:23
Alignment explanation
Indices: 33598--33641 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
33588 AAATAGAAAC
33598 AAAAATAAAACAAAATAATAATA
1 AAAAATAAAACAAAATAATAATA
*
33621 AAAAATAAAAGAAAATAATAA
1 AAAAATAAAACAAAATAATAA
33642 AATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAATAAAACAAAATAATAATA
Found at i:33630 original size:28 final size:28
Alignment explanation
Indices: 33583--33656 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
33573 AATTGGAATT
* *
33583 AAATAA-AATAGAAACA-AAAATAAAACA
1 AAATAATAATA-AAAAATAAAAGAAAACA
*
33610 AAATAATAATAAAAAATAAAAGAAAATA
1 AAATAATAATAAAAAATAAAAGAAAACA
33638 ATAA-AATAATAAAAAATAA
1 A-AATAATAATAAAAAATAA
33657 TATATACATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.24
28 29 0.71
29 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (28 bp):
AAATAATAATAAAAAATAAAAGAAAACA
Found at i:33653 original size:10 final size:11
Alignment explanation
Indices: 33599--33658 Score: 67
Period size: 10 Copynumber: 5.8 Consensus size: 11
33589 AATAGAAACA
*
33599 AAAATAA-AAC
1 AAAATAATAAT
33609 AAAATAATAAT
1 AAAATAATAAT
33620 AAAA-AATAA-
1 AAAATAATAAT
33629 AAGAA-AATAAT
1 AA-AATAATAAT
33640 AAAATAATAA-
1 AAAATAATAAT
33650 AAAATAATA
1 AAAATAATA
33659 TATACATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 2 0.04
10 30 0.67
11 13 0.29
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:33653 original size:23 final size:22
Alignment explanation
Indices: 33598--33658 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
33588 AAATAGAAAC
33598 AAAAATAAAACAAAATAATAATA
1 AAAAATAAAA-AAAATAATAATA
33621 AAAAATAAAAGAAAATAAT-A-A
1 AAAAATAAAA-AAAATAATAATA
*
33642 AATAATAAAAAATAATA
1 AAAAATAAAAAA-AATA
33659 TATACATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.06
21 14 0.40
22 1 0.03
23 18 0.51
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAAAAATAATAATA
Found at i:33657 original size:18 final size:18
Alignment explanation
Indices: 33584--33658 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
33574 ATTGGAATTA
*
33584 AATAAAATAGAAA-CAAA-
1 AATAAAATA-AAAGAAAAT
* *
33601 AATAAAACAAAATAATAAT
1 AATAAAATAAAAGAA-AAT
33620 AA-AAAATAAAAGAAAAT
1 AATAAAATAAAAGAAAAT
33637 AATAAAATAATAA-AAAAT
1 AATAAAATAA-AAGAAAAT
33655 AATA
1 AATA
33659 TATACATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.06
17 14 0.29
18 28 0.57
19 4 0.08
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
AATAAAATAAAAGAAAAT
Found at i:33881 original size:2 final size:2
Alignment explanation
Indices: 33874--33936 Score: 96
Period size: 2 Copynumber: 32.5 Consensus size: 2
33864 ATGTCGGTAG
33874 AT 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 AT AT
33915 AT AGT A- AT A- AT AT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT A
33937 ACAATAATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.05
2 52 0.91
3 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:33943 original size:28 final size:29
Alignment explanation
Indices: 33894--33965 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
33884 ATATATATAT
*
33894 ATATATATATATATATATATAATAGT-AATA
1 ATATATATATATA-ACATATAATA-TCAATA
33924 ATATATATATATAACA-ATAATATCAATA
1 ATATATATATATAACATATAATATCAATA
* *
33952 AAATAAATATATAA
1 ATATATATATATAA
33966 TGGTAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 1 0.03
28 22 0.58
29 2 0.05
30 13 0.34
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (29 bp):
ATATATATATATAACATATAATATCAATA
Found at i:33965 original size:22 final size:22
Alignment explanation
Indices: 33943--34021 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
33933 TATAACAATA
33943 ATATCAATAAAATAAATATATA-
1 ATAT-AATAAAATAAATATATAG
*
33965 ATGGTAAT-AAATAAAATATATAG
1 AT-ATAATAAAAT-AAATATATAG
*
33988 A-A-AATAAATATAAATATATAT
1 ATATAATAAA-ATAAATATATAG
*
34009 ATATTATAAAATA
1 ATATAATAAAATA
34022 TAGTACTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
20 3 0.07
21 16 0.35
22 20 0.43
23 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (22 bp):
ATATAATAAAATAAATATATAG
Found at i:34136 original size:28 final size:28
Alignment explanation
Indices: 34088--34151 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
34078 GTTATAAATA
*
34088 AAATATTAAAAAAATATACACACATATAT
1 AAATA-TAAAAAAATACACACACATATAT
* *
34117 AAATATAACAAAATACACACGCATATAT
1 AAATATAAAAAAATACACACACATATAT
*
34145 ATATATA
1 AAATATA
34152 TATAACAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (28 bp):
AAATATAAAAAAATACACACACATATAT
Found at i:34177 original size:21 final size:21
Alignment explanation
Indices: 34147--34191 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
34137 GCATATATAT
*
34147 ATATATATAACAAAA-TAAGTA
1 ATATAAATAACAAAAGTAA-TA
*
34168 ATATAAATAATAAAAGTAATA
1 ATATAAATAACAAAAGTAATA
34189 ATA
1 ATA
34192 AAAGGGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
ATATAAATAACAAAAGTAATA
Found at i:34275 original size:33 final size:34
Alignment explanation
Indices: 34220--34288 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 34
34210 AAAGAAGTAA
34220 AAATAAAATATATAAGAATAAT-ATAAAATA-AAT
1 AAATAAAATATATAAG-ATAATAATAAAATATAAT
34253 AAATAAAATATATATATG-TAATAATAAAATATAAT
1 AAATAAAATATATA-A-GATAATAATAAAATATAAT
34288 A
1 A
34289 TTTAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
33 18 0.56
34 9 0.28
35 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (34 bp):
AAATAAAATATATAAGATAATAATAAAATATAAT
Found at i:34279 original size:39 final size:41
Alignment explanation
Indices: 34219--34303 Score: 95
Period size: 43 Copynumber: 2.1 Consensus size: 41
34209 GAAAGAAGTA
34219 AAAATAAAATATATAAGAAT-AATATAA-A-ATAAATAAAT
1 AAAATAAAATATATAAGAATAAATATAATATATAAATAAAT
* * * *
34257 AAAATATATATATGTAATAATAAAATATAATATTTAAATAAAT
1 AAAATA-AAATATATAAGAAT-AAATATAATATATAAATAAAT
34300 AAAA
1 AAAA
34304 ATAAGAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
38 6 0.16
39 11 0.29
41 7 0.18
42 1 0.03
43 13 0.34
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (41 bp):
AAAATAAAATATATAAGAATAAATATAATATATAAATAAAT
Found at i:34280 original size:21 final size:22
Alignment explanation
Indices: 34248--34307 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
34238 TAATATAAAA
34248 TAAATAAATAAAATATATATATG
1 TAAATAAATAAAATATA-ATATG
*
34271 T-AAT-AATAAAATATAATATT
1 TAAATAAATAAAATATAATATG
34291 TAAATAAATAAAA-ATAA
1 TAAATAAATAAAATATAA
34308 GAAAAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 5 0.15
21 18 0.53
22 10 0.29
23 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATAAATAAAATATAATATG
Found at i:35152 original size:37 final size:37
Alignment explanation
Indices: 35100--35203 Score: 163
Period size: 37 Copynumber: 2.8 Consensus size: 37
35090 ATTTTCGTCC
*
35100 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTTAAACTCCTAAAAATAGGATAGAATTT
* *
35137 TGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTTT
1 TACTAGGATTTAAACTCCTAAAAATAGGATAGAATTT
* *
35174 TACTATGATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTTAAACTCCTAAAAATAGGAT
35204 CAACAAGTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (37 bp):
TACTAGGATTTAAACTCCTAAAAATAGGATAGAATTT
Found at i:35215 original size:37 final size:37
Alignment explanation
Indices: 35100--35216 Score: 103
Period size: 37 Copynumber: 3.2 Consensus size: 37
35090 ATTTTCGTCC
* * **
35100 TACTAGGATTCAAACTCCTAAAAATAGGATAGA-ATTT
1 TACTATGATTTAAACTCCTAAAAATAGGATAGACA-AG
* * ****
35137 TGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTTT
1 TACTATGATTTAAACTCCTAAAAATAGGATAGACAAG
*
35174 TACTATGATTTAAACTCCTAAAGATAGGATCA-ACAAG
1 TACTATGATTTAAACTCCTAAAAATAGGAT-AGACAAG
35211 TACTAT
1 TACTAT
35217 AAATAGCCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
37 67 0.99
38 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (37 bp):
TACTATGATTTAAACTCCTAAAAATAGGATAGACAAG
Done.