Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003944.1 Hibiscus syriacus cultivar Beakdansim tig00008526_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: 76950
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:1808 original size:24 final size:24
Alignment explanation
Indices: 1780--1826 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1770 TCCTGTAGCA
1780 GCTCCTTAAACTCAGAACTTTCGT
1 GCTCCTTAAACTCAGAACTTTCGT
1804 GCTCCTTAAACTCAGAACTTTCG
1 GCTCCTTAAACTCAGAACTTTCG
1827 AGGAGAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.32
Consensus pattern (24 bp):
GCTCCTTAAACTCAGAACTTTCGT
Found at i:8220 original size:7 final size:7
Alignment explanation
Indices: 8212--8255 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
8202 TGCTTTAGGT
*
8212 GAAAGGT
1 GAAAGGA
8219 GAAAGGA
1 GAAAGGA
8226 GAAAGGA
1 GAAAGGA
8233 GAAAGGA
1 GAAAGGA
8240 GAAAGGA
1 GAAAGGA
8247 GAAAGGA
1 GAAAGGA
8254 GA
1 GA
8256 TGAACTGCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (7 bp):
GAAAGGA
Found at i:8938 original size:15 final size:15
Alignment explanation
Indices: 8883--8940 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
8873 TATAATCCTC
* *
8883 AAATTATAAATATAA
1 AAATTTTAAATATAT
*
8898 AAATATTAAAT-T-T
1 AAATTTTAAATATAT
*
8911 -AATTTAAAAATATAT
1 AAATTT-TAAATATAT
8926 AAATTTTAAATATAT
1 AAATTTTAAATATAT
8941 TTTTTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
12 4 0.12
13 4 0.12
14 2 0.06
15 18 0.55
16 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTTAAATATAT
Found at i:11369 original size:535 final size:535
Alignment explanation
Indices: 10360--11431 Score: 2135
Period size: 535 Copynumber: 2.0 Consensus size: 535
10350 TGAAAGGAGA
10360 CAACAGTTGAGTGGTCACTCATGTAGTTTACTCAGAAATTTAAATTGATTAAAATATTAGCTGAC
1 CAACAGTTGAGTGGTCACTCATGTAGTTTACTCAGAAATTTAAATTGATTAAAATATTAGCTGAC
10425 AAAAACTTTTAGATAATATGGCTTATTTAAGTTGCACAAAATTAAATGCCCTTTTTTAGGATTAA
66 AAAAACTTTTAGATAATATGGCTTATTTAAGTTGCACAAAATTAAATGCCCTTTTTTAGGATTAA
10490 TATAAAAATAAATGCTTAAATTTTATCTTGAAAAATAAGTTGGTGTTTAAAGATTTTTTCGCTAA
131 TATAAAAATAAATGCTTAAATTTTATCTTGAAAAATAAGTTGGTGTTTAAAGATTTTTTCGCTAA
10555 AATTTGATGTCTAATATTTTCTCAGTTACACTTTTAAGTGTCTATACTTATTTTTTGGCTATTTT
196 AATTTGATGTCTAATATTTTCTCAGTTACACTTTTAAGTGTCTATACTTATTTTTTGGCTATTTT
10620 TCCGGTATATCACCGGTGATCGGTATTATTATCGATCTAACATCGATCAGACTATATTTTTTGAT
261 TCCGGTATATCACCGGTGATCGGTATTATTATCGATCTAACATCGATCAGACTATATTTTTTGAT
10685 TTAACACCCTTAACAGGAAAGCACGCCCCCTACCCCACGATATACGGTGATCTGACACCACGTGG
326 TTAACACCCTTAACAGGAAAGCACGCCCCCTACCCCACGATATACGGTGATCTGACACCACGTGG
10750 GTATAACGCGCCCCTGATCCGCGCTATACATGGATATCTGACACGTGGGGTATAGCACGGTGCAG
391 GTATAACGCGCCCCTGATCCGCGCTATACATGGATATCTGACACGTGGGGTATAGCACGGTGCAG
10815 GGGGCGCGCTATACCCCTAATTACCAACCCTTCACGTCCCCATCCTCCCTATAAATACCCCCGTC
456 GGGGCGCGCTATACCCCTAATTACCAACCCTTCACGTCCCCATCCTCCCTATAAATACCCCCGTC
10880 CTTAATCACTTTTAT
521 CTTAATCACTTTTAT
10895 CAACAGTTGAGTGGTCACTCATGTAGTTTACTCAGAAATTTAAATTGATTAAAATATTAGCTGAC
1 CAACAGTTGAGTGGTCACTCATGTAGTTTACTCAGAAATTTAAATTGATTAAAATATTAGCTGAC
10960 AAAAACTTTTAGATAATATGGCTTATTTAAGTTGCACAAAATTAAATGCCCTTTTTTAGGATTAA
66 AAAAACTTTTAGATAATATGGCTTATTTAAGTTGCACAAAATTAAATGCCCTTTTTTAGGATTAA
*
11025 TATAAAAATAAATGTTTAAATTTTATCTTGAAAAATAAGTTGGTGTTTAAAGATTTTTTCGCTAA
131 TATAAAAATAAATGCTTAAATTTTATCTTGAAAAATAAGTTGGTGTTTAAAGATTTTTTCGCTAA
11090 AATTTGATGTCTAATATTTTCTCAGTTACACTTTTAAGTGTCTATACTTATTTTTTGGCTATTTT
196 AATTTGATGTCTAATATTTTCTCAGTTACACTTTTAAGTGTCTATACTTATTTTTTGGCTATTTT
11155 TCCGGTATATCACCGGTGATCGGTATTATTATCGATCTAACATCGATCAGACTATATTTTTTGAT
261 TCCGGTATATCACCGGTGATCGGTATTATTATCGATCTAACATCGATCAGACTATATTTTTTGAT
11220 TTAACACCCTTAACAGGAAAGCACGCCCCCTACCCCACGATATACGGTGATCTGACACCACGTGG
326 TTAACACCCTTAACAGGAAAGCACGCCCCCTACCCCACGATATACGGTGATCTGACACCACGTGG
11285 GTATAACGCGCCCCTGATCCGCGCTATACATGGATATCTGACACGTGGGGTATAGCACGGTGCAG
391 GTATAACGCGCCCCTGATCCGCGCTATACATGGATATCTGACACGTGGGGTATAGCACGGTGCAG
11350 GGGGCGCGCTATACCCCTAATTACCAACCCTTCACGTCCCCATCCTCCCTATAAATACCCCCGTC
456 GGGGCGCGCTATACCCCTAATTACCAACCCTTCACGTCCCCATCCTCCCTATAAATACCCCCGTC
11415 CTTAATCACTTTTAT
521 CTTAATCACTTTTAT
11430 CA
1 CA
11432 CACCAAATTC
Statistics
Matches: 536, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
535 536 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (535 bp):
CAACAGTTGAGTGGTCACTCATGTAGTTTACTCAGAAATTTAAATTGATTAAAATATTAGCTGAC
AAAAACTTTTAGATAATATGGCTTATTTAAGTTGCACAAAATTAAATGCCCTTTTTTAGGATTAA
TATAAAAATAAATGCTTAAATTTTATCTTGAAAAATAAGTTGGTGTTTAAAGATTTTTTCGCTAA
AATTTGATGTCTAATATTTTCTCAGTTACACTTTTAAGTGTCTATACTTATTTTTTGGCTATTTT
TCCGGTATATCACCGGTGATCGGTATTATTATCGATCTAACATCGATCAGACTATATTTTTTGAT
TTAACACCCTTAACAGGAAAGCACGCCCCCTACCCCACGATATACGGTGATCTGACACCACGTGG
GTATAACGCGCCCCTGATCCGCGCTATACATGGATATCTGACACGTGGGGTATAGCACGGTGCAG
GGGGCGCGCTATACCCCTAATTACCAACCCTTCACGTCCCCATCCTCCCTATAAATACCCCCGTC
CTTAATCACTTTTAT
Found at i:11450 original size:10 final size:10
Alignment explanation
Indices: 11435--11469 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
11425 TTTATCACAC
11435 CAAATTCTCT
1 CAAATTCTCT
11445 CAAATTCTCT
1 CAAATTCTCT
11455 -AAATTTCTCT
1 CAAA-TTCTCT
11465 CAAAT
1 CAAAT
11470 ATTCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:11474 original size:12 final size:12
Alignment explanation
Indices: 11438--11476 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 12
11428 ATCACACCAA
11438 ATTCTCTC-AA-
1 ATTCTCTCAAAT
11448 ATTCTCT-AAAT
1 ATTCTCTCAAAT
11459 -TTCTCTCAAAT
1 ATTCTCTCAAAT
11470 ATTCTCT
1 ATTCTCT
11477 TTTTAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 15 0.60
11 4 0.16
12 6 0.24
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTCTCTCAAAT
Found at i:11793 original size:111 final size:111
Alignment explanation
Indices: 11599--11820 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
11589 TGGAAATCAT
* *
11599 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * *
11664 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAATTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
11710 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
11775 TAATTAATTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
66 TAATTAATTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
11821 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAATTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
Found at i:12210 original size:47 final size:48
Alignment explanation
Indices: 12104--12219 Score: 128
Period size: 47 Copynumber: 2.4 Consensus size: 48
12094 CTACGTGGCG
* * * *
12104 TATAGCGCGGAT-CAGGGGGTGCGCTATACTCACGTGGCGCCAGATCACCG
1 TATAGCGCGG-TGCAAGGGG-G-GCTATACCCACGTGGCGCCAAATCACCA
* * *
12154 TATATCGCGG-GCCAGGGGGGCTATACCCACGTGGCGCCAAATCAGCA
1 TATAGCGCGGTGCAAGGGGGGCTATACCCACGTGGCGCCAAATCACCA
12201 TATAGCGCGGTGCAAGGGG
1 TATAGCGCGGTGCAAGGGG
12220 CGCGCTTTCC
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
47 33 0.60
48 8 0.15
49 5 0.09
50 9 0.16
ACGTcount: A:0.22, C:0.27, G:0.35, T:0.16
Consensus pattern (48 bp):
TATAGCGCGGTGCAAGGGGGGCTATACCCACGTGGCGCCAAATCACCA
Found at i:12357 original size:20 final size:21
Alignment explanation
Indices: 12319--12358 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12309 GAAAATAGCC
*
12319 TTATTTTTTTATTATAAAATA
1 TTATTTTTTAATTATAAAATA
*
12340 TTATTTTTTAATTAAAAAA
1 TTATTTTTTAATTATAAAA
12359 AGGAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTTTTTAATTATAAAATA
Found at i:16666 original size:2 final size:2
Alignment explanation
Indices: 16659--16698 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
16649 AAATATGAAG
* *
16659 AT AT AT AT AT AT AT AT AT AT AT AT AT -T GT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16699 AAAAAATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:19788 original size:18 final size:19
Alignment explanation
Indices: 19765--19803 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19755 TTTAAATAGT
19765 AATAAAAACGATTAAA-TA
1 AATAAAAACGATTAAAGTA
* *
19783 AATAAAAGCTATTAAAGTA
1 AATAAAAACGATTAAAGTA
19802 AA
1 AA
19804 AATAAGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (19 bp):
AATAAAAACGATTAAAGTA
Found at i:21326 original size:12 final size:12
Alignment explanation
Indices: 21309--21341 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
21299 GTGGGAAAAA
21309 GGCTAAATAGAT
1 GGCTAAATAGAT
21321 GGCTAAATAGAT
1 GGCTAAATAGAT
21333 GGCTAAATA
1 GGCTAAATA
21342 TTCAAGGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.24
Consensus pattern (12 bp):
GGCTAAATAGAT
Found at i:27783 original size:22 final size:21
Alignment explanation
Indices: 27742--27783 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
27732 TTTTTAAAAT
**
27742 TTGACACCCAAAATTTTTTTC
1 TTGACACCCAAAATAATTTTC
27763 TTGACACCACAAAATAATTTT
1 TTGACACC-CAAAATAATTTT
27784 TTTAAAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (21 bp):
TTGACACCCAAAATAATTTTC
Found at i:30405 original size:3 final size:3
Alignment explanation
Indices: 30397--30478 Score: 103
Period size: 3 Copynumber: 26.7 Consensus size: 3
30387 ATTTTATTTA
* *
30397 TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TA- TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
30444 TAT TAT TAT TAT ATAT TATT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT -TAT TA-T TA-T TAT TAT TAT TA
30479 CAAAACCCGG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
2 2 0.03
3 59 0.83
4 10 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:30596 original size:16 final size:16
Alignment explanation
Indices: 30575--30621 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
30565 TCTAACCCTA
30575 GCTTCCAGCCGCCTCT
1 GCTTCCAGCCGCCTCT
30591 GCTTCCAGCCGCCTCT
1 GCTTCCAGCCGCCTCT
*
30607 GCCTCCAGCCGCCTC
1 GCTTCCAGCCGCCTC
30622 AGCCAACGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.06, C:0.53, G:0.19, T:0.21
Consensus pattern (16 bp):
GCTTCCAGCCGCCTCT
Found at i:43221 original size:12 final size:12
Alignment explanation
Indices: 43204--43235 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
43194 TATTATGCTT
43204 GAAAAAAAAAGA
1 GAAAAAAAAAGA
43216 GAAAAAAAAAGA
1 GAAAAAAAAAGA
43228 -AAAAAAAA
1 GAAAAAAAA
43236 GAAAAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAGA
Found at i:43222 original size:11 final size:10
Alignment explanation
Indices: 43206--43251 Score: 74
Period size: 10 Copynumber: 4.5 Consensus size: 10
43196 TTATGCTTGA
43206 AAAAAAAAGAG
1 AAAAAAAA-AG
43217 AAAAAAAAAG
1 AAAAAAAAAG
43227 AAAAAAAAAG
1 AAAAAAAAAG
*
43237 AAAAAAGAAG
1 AAAAAAAAAG
43247 AAAAA
1 AAAAA
43252 GGGGGGCGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:44618 original size:83 final size:83
Alignment explanation
Indices: 44392--44791 Score: 692
Period size: 83 Copynumber: 4.8 Consensus size: 83
44382 ATATTAGCTG
*
44392 GAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
44457 AAACCAATTATTGAATTT
66 AAACCAATTATTGAATTT
*
44475 GAACAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1 GAA-AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT
* *
44540 AAAACCAATCATTGAAATT
65 AAAACCAATTATTGAATTT
* *
44559 GAAAGATGAATGTGCTAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
44624 AAACCAGTTATTGAATTT
66 AAACCAATTATTGAATTT
44642 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
44707 AAACCAGTTATTGAATTT
66 AAACCAATTATTGAATTT
*
44725 GGAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 -GAAAGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
44790 TA
64 TA
44792 TGAACCCCAA
Statistics
Matches: 301, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
83 158 0.52
84 95 0.32
85 48 0.16
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (83 bp):
GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATTATTGAATTT
Found at i:44732 original size:167 final size:168
Alignment explanation
Indices: 44390--44791 Score: 700
Period size: 167 Copynumber: 2.4 Consensus size: 168
44380 AAATATTAGC
* *
44390 TGGAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TGGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
44455 TAAAACCAATTATTGAATTTGAACAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGA
66 TAAAACCAATTATTGAATTTGAACAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGA
44520 GTTATCTGATCTGGTTTGGCAAAACCAATCATTGAAAT
131 GTTATCTGATCTGGTTTGGCAAAACCAATCATTGAAAT
*
44558 T-GAAAGATGAATGTGCTAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TGGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
*
44622 TAAAACCAGTTATTGAATTTGAA-AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGA
66 TAAAACCAATTATTGAATTTGAACAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGA
* * * *
44686 GTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
131 GTTATCTGATCTGGTTTGGCAAAACCAATCATTGAAAT
*
44724 TGGAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TGGAAAGATGAATGTG-CTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
44789 GTA
65 GTA
44792 TGAACCCCAA
Statistics
Matches: 222, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
166 76 0.34
167 96 0.43
168 50 0.23
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (168 bp):
TGGAAAGATGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
TAAAACCAATTATTGAATTTGAACAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGA
GTTATCTGATCTGGTTTGGCAAAACCAATCATTGAAAT
Found at i:45800 original size:113 final size:112
Alignment explanation
Indices: 45602--46226 Score: 749
Period size: 113 Copynumber: 5.5 Consensus size: 112
45592 TAGCAAAGAT
* * *
45602 TCAAATCCATCA-TTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAATAACTCATCTG
1 TCAAATCCATCACTT-GATGGATCAACTTTTCCAGG-CGAGTTCATAATGAGAAGAACTCATCTG
* * *
45666 AAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGC
64 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * **
45715 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAG-GCGAGTTCATAATGAGAAGAACTCATCTGA
* *
45780 AGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * *
45828 TTAAATTCATCA-TATGATGGATTAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCGTC--
1 TCAAATCCATCACT-TGATGGATCAACTTTTCCAGG-CGAGTTCATAATGAGAAGAACTCATCTG
** * * *
45890 ATCTAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTATGC
64 A-AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
45940 TCAAATCTATCACTTGATAGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAG-GCGAGTTCATAATGAGAAGAACTCATCTGA
* *
46005 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
46053 TCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAG-GCGAGTTCATAATGAGAAGAACTCATCTGA
* *
46118 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAGA-TTTTTGC
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA-ACCTTTTGC
* ** *
46166 TCAAATCCATCACTTGATGGGTCAGTTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATC
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAG-GCGAGTTCATAATGAGAAGAACTCATC
46227 AAGAGCTTAT
Statistics
Matches: 448, Mismatches: 54, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
111 1 0.00
112 116 0.26
113 326 0.73
114 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (112 bp):
TCAAATCCATCACTTGATGGATCAACTTTTCCAGGCGAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:46009 original size:225 final size:220
Alignment explanation
Indices: 45601--46226 Score: 796
Period size: 225 Copynumber: 2.8 Consensus size: 220
45591 TTAGCAAAGA
* * * *
45601 TTCAAATCCATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAATAA--CTCATC
1 TTCAAATTCATCATT-GATGGATTAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCTCATC
*
45664 TGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTCAAATCCATCATT
65 T-AAG---GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CTTTTGCTCAAATCCATCACT
* *
45729 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAA
125 TGATGGATCATCTTTTCCAGAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
45794 GTTCATAATGAGAAGAATTTGTTCAACCTTTTG
188 GTTCATAATGAGAAGAATTTGTTCAACCTTTTG
* *
45827 TTTAAATTCATCATATGATGGATTAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTCAAATTCATCAT-TGATGGATTAACATTACCAGGTCGAGTTCATAATGAGAAGAACTC-TCAT
* * *
45892 CTAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTATGCTCAAATCTATCACTTGA
64 CTAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CTTTTGCTCAAATCCATCACTTGA
* * * *
45957 TAGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTT
128 TGGATCATCTTTTCCAG--AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
46022 CATAATGAGAAGAATTTGTTCAACCTTTTG
191 CATAATGAGAAGAATTTGTTCAACCTTTTG
* * * *
46052 TTCAAA-TCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAA--CTCAT
1 TTCAAATTC-ATCA-TTGATGGATTAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCTCAT
* * *
46114 CTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAGATTTTTGCTCAAATCCATCAC
64 CT----AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA-ACTTTTGCTCAAATCCATCAC
*
46179 TTGATGGGTCAGT-TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATC
124 TTGATGGATCA-TCTTTTCCAGAG-AGTTCATAATGAGAAGAACTCATC
46227 AAGAGCTTAT
Statistics
Matches: 352, Mismatches: 33, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
222 6 0.02
223 1 0.00
224 3 0.01
225 211 0.60
226 117 0.33
227 4 0.01
228 4 0.01
229 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (220 bp):
TTCAAATTCATCATTGATGGATTAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCTCATCT
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTGCTCAAATCCATCACTTGATGG
ATCATCTTTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTG
Found at i:46469 original size:6 final size:5
Alignment explanation
Indices: 46455--46538 Score: 51
Period size: 6 Copynumber: 14.4 Consensus size: 5
46445 AGATATTCTT
*
46455 TTTTT TTTTCA TTTTAA TTTTA TTTATA TTATTA TTATTA TTATTA TTATTA
1 TTTTA TTTT-A TTTT-A TTTTA TTT-TA TT-TTA TT-TTA TT-TTA TT-TTA
46507 TTATTA TTATTA TTATTA TTATTA TTATTA TT
1 TT-TTA TT-TTA TT-TTA TT-TTA TT-TTA TT
46539 ATAATTATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
5 8 0.11
6 65 0.88
7 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:46489 original size:3 final size:3
Alignment explanation
Indices: 46481--46590 Score: 157
Period size: 3 Copynumber: 35.7 Consensus size: 3
46471 ATTTTATTTA
46481 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
46529 TAT TAT TAT TAT AAT TAT AAT TAT TAT TAT TAT TAA TAT ATAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T
*
46576 TATT TAT TAA TAT TA
1 TA-T TAT TAT TAT TA
46591 CAAAATCCGG
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
3 87 0.90
4 10 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:46708 original size:16 final size:16
Alignment explanation
Indices: 46687--46717 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
46677 TCTAACCCTA
46687 GCTTCCAGCCGCCTCT
1 GCTTCCAGCCGCCTCT
46703 GCTTCCAGCCGCCTC
1 GCTTCCAGCCGCCTC
46718 AGCCAACGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.52, G:0.19, T:0.23
Consensus pattern (16 bp):
GCTTCCAGCCGCCTCT
Found at i:51647 original size:18 final size:18
Alignment explanation
Indices: 51624--51658 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
51614 AGTATTGTCT
51624 ATTAAAAGTATTATTGAG
1 ATTAAAAGTATTATTGAG
*
51642 ATTAAAAGTATTCTTGA
1 ATTAAAAGTATTATTGA
51659 AATTTGGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (18 bp):
ATTAAAAGTATTATTGAG
Found at i:53395 original size:15 final size:15
Alignment explanation
Indices: 53371--53417 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
53361 TGACAGATCC
*
53371 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
53386 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
53401 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
53416 AA
1 AA
53418 GAAAGATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.53, C:0.15, G:0.26, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:56613 original size:25 final size:25
Alignment explanation
Indices: 56585--56636 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
56575 AGATTGTTGG
*
56585 AAGTCAAAAGTTGG-GGCTGTAAATC
1 AAGTC-AAAGTTGGAGGCTGGAAATC
*
56610 AAGTCAAATTTGGAGGCTGGAAATC
1 AAGTCAAAGTTGGAGGCTGGAAATC
56635 AA
1 AA
56637 AGCTGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (25 bp):
AAGTCAAAGTTGGAGGCTGGAAATC
Found at i:60373 original size:37 final size:37
Alignment explanation
Indices: 60318--60394 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
60308 CGTATCACAC
* * *
60318 CTGTTCGGACATCATCATGATGTAACTGAAGACTACA
1 CTGTTCAGACATCATCATGACGTAACTGAAAACTACA
*
60355 CTGTTCAGACATCGTCATGACGTAACTGAAAACTACA
1 CTGTTCAGACATCATCATGACGTAACTGAAAACTACA
60392 CTG
1 CTG
60395 CAGCAGAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (37 bp):
CTGTTCAGACATCATCATGACGTAACTGAAAACTACA
Found at i:65023 original size:14 final size:14
Alignment explanation
Indices: 65006--65035 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
64996 ATTTATGTTC
*
65006 ATTTATGTTTATTT
1 ATTTATGTTCATTT
65020 ATTTATGTTCATTT
1 ATTTATGTTCATTT
65034 AT
1 AT
65036 ATTCGAACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (14 bp):
ATTTATGTTCATTT
Found at i:65035 original size:10 final size:10
Alignment explanation
Indices: 64992--65021 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
64982 GAGTTTGTTC
64992 GTTCATTTAT
1 GTTCATTTAT
65002 GTTCATTTAT
1 GTTCATTTAT
*
65012 GTTTATTTAT
1 GTTCATTTAT
65022 TTATGTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:65327 original size:10 final size:10
Alignment explanation
Indices: 65294--65361 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 10
65284 TTGTTTTTTG
65294 TGTTCGTTTA
1 TGTTCGTTTA
*
65304 TGTTCATTTATTA
1 TGTTC--GT-TTA
65317 TGTTCGTTTA
1 TGTTCGTTTA
*
65327 TGTTCGTTCGTTTG
1 ---T-GTTCGTTTA
65341 TGTTCGTTTA
1 TGTTCGTTTA
65351 TGTTCGTTTA
1 TGTTCGTTTA
65361 T
1 T
65362 TATTTAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 27 0.57
11 2 0.04
12 1 0.02
13 9 0.19
14 8 0.17
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:65337 original size:14 final size:14
Alignment explanation
Indices: 65318--65358 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
65308 CATTTATTAT
65318 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
65332 GTTCG-TT-TG-T-
1 GTTCGTTTATGTTC
65342 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
65356 GTT
1 GTT
65359 TATTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 5 0.22
11 3 0.13
12 4 0.17
13 3 0.13
14 8 0.35
ACGTcount: A:0.05, C:0.12, G:0.24, T:0.59
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:65349 original size:24 final size:22
Alignment explanation
Indices: 65288--65359 Score: 99
Period size: 24 Copynumber: 3.1 Consensus size: 22
65278 ATAAGTTTGT
*
65288 TTTTTGTGTTCGTTTATGTTCA
1 TTTTTGTGTTCGTTTATGTTCG
*
65310 TTTATTATGTTCGTTTATGTTCG
1 TTT-TTGTGTTCGTTTATGTTCG
65333 TTCGTTTGTGTTCGTTTATGTTCG
1 TT--TTTGTGTTCGTTTATGTTCG
65357 TTT
1 TTT
65360 ATTATTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.09
23 19 0.43
24 20 0.45
25 1 0.02
ACGTcount: A:0.08, C:0.10, G:0.19, T:0.62
Consensus pattern (22 bp):
TTTTTGTGTTCGTTTATGTTCG
Found at i:65914 original size:37 final size:33
Alignment explanation
Indices: 65853--65961 Score: 155
Period size: 33 Copynumber: 3.2 Consensus size: 33
65843 CATATTTTGA
*
65853 TCGGGTCGGGGTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
*
65886 TCGGGTCGGGTCGTTTTTTTTAAGTGTGATATTTGGG
1 TCGGGTC-GG--G-TTTTTTTAAGTGTGATATTCGGG
*
65923 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
65956 TCGGGT
1 TCGGGT
65962 TCGAGTTTAG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
33 34 0.50
34 3 0.04
36 3 0.04
37 28 0.41
ACGTcount: A:0.12, C:0.09, G:0.37, T:0.42
Consensus pattern (33 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
Found at i:67908 original size:24 final size:22
Alignment explanation
Indices: 67857--67933 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 22
67847 ATTTTAATCA
*
67857 AAATATTAATTATTAA-AATAT
1 AAATATTAATTTTTAATAATAT
**
67878 ATTTATTAATATTTCTAATAATAT
1 AAATATTAAT-TTT-TAATAATAT
*
67902 AAATATT-ATTTTTAATATTAT
1 AAATATTAATTTTTAATAATAT
*
67923 AATAAATTAAT
1 AA-ATATTAAT
67934 CAATTATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
21 18 0.41
22 9 0.20
23 7 0.16
24 10 0.23
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATATTAATTTTTAATAATAT
Found at i:67994 original size:31 final size:32
Alignment explanation
Indices: 67906--67994 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 32
67896 TAATATAAAT
67906 ATTAT-TTTTAAT-AT-TATAATAAATTAATCA
1 ATTATATTTTAATAATATATAATAAATT-ATCA
*
67936 ATTATATTATAATAATATA-AGAT--ATTAT-A
1 ATTATATTTTAATAATATATA-ATAAATTATCA
* *
67965 TTTTTATTTTAATAATATATAATAAATTAT
1 ATTATATTTTAATAATATATAATAAATTAT
67995 TAATAAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
29 19 0.40
30 8 0.17
31 14 0.29
32 3 0.06
33 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
ATTATATTTTAATAATATATAATAAATTATCA
Found at i:68132 original size:23 final size:23
Alignment explanation
Indices: 68106--68150 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
68096 AATAATATTT
68106 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
68129 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
68151 ATATAACACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:68499 original size:14 final size:15
Alignment explanation
Indices: 68480--68508 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
68470 TTTCCATAAA
68480 TATAATTC-ATTTTC
1 TATAATTCAATTTTC
68494 TATAATTCAATTTTC
1 TATAATTCAATTTTC
68509 AGAAAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (15 bp):
TATAATTCAATTTTC
Found at i:69903 original size:28 final size:28
Alignment explanation
Indices: 69859--69945 Score: 156
Period size: 28 Copynumber: 3.1 Consensus size: 28
69849 TGGTAAGATT
69859 AATCTCATCAACCAGAGTTCACAATAGG
1 AATCTCATCAACCAGAGTTCACAATAGG
*
69887 AATCTCATCAACAAGAGTTCACAATAGG
1 AATCTCATCAACCAGAGTTCACAATAGG
*
69915 AATCTCATCAACCAGAGTTCACGATAGG
1 AATCTCATCAACCAGAGTTCACAATAGG
69943 AAT
1 AAT
69946 TAAATATTAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (28 bp):
AATCTCATCAACCAGAGTTCACAATAGG
Found at i:70950 original size:15 final size:14
Alignment explanation
Indices: 70941--71066 Score: 67
Period size: 13 Copynumber: 9.2 Consensus size: 14
70931 CTTTTAGTTG
70941 TTTTTATTTTATTA
1 TTTTTATTTTATTA
*
70955 TTTTTAAGATTTA--A
1 TTTTT-A-TTTTATTA
70969 CTTTTTATTTTTATT-
1 -TTTTTA-TTTTATTA
*
70984 TATTTA-TTTATTCA
1 TTTTTATTTTATT-A
70998 TTCATTTA-TTTATT-
1 TT--TTTATTTTATTA
*
71012 TATTTATTTTACTT-
1 TTTTTATTTTA-TTA
*
71026 CTTTTA-TTT-TTA
1 TTTTTATTTTATTA
71038 TTTTTATTTT-TTA
1 TTTTTATTTTATTA
71051 TTTTTATTTT-TTA
1 TTTTTATTTTATTA
71064 TTT
1 TTT
71067 CATTCATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 27
0.71 0.07 0.21
Matches are distributed among these distances:
11 2 0.02
12 15 0.17
13 29 0.32
14 24 0.27
15 6 0.07
16 14 0.16
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.75
Consensus pattern (14 bp):
TTTTTATTTTATTA
Found at i:70987 original size:4 final size:4
Alignment explanation
Indices: 70978--71066 Score: 73
Period size: 4 Copynumber: 22.8 Consensus size: 4
70968 ACTTTTTATT
* *
70978 TTTA TTTA TTTA TTTA TTCA TTCA TTTA TTTA TTTA TTTA TTTTA CTTCT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA -TT-TA
*
71028 TTTA TTT- TTATT TTTA TTT- TTTA -TT- TTTA TTT- TTTA TTT
1 TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
71067 CATTCATTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
3 13 0.18
4 50 0.69
5 8 0.11
6 1 0.01
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:75039 original size:110 final size:110
Alignment explanation
Indices: 74667--75146 Score: 626
Period size: 110 Copynumber: 4.5 Consensus size: 110
74657 TACAGCTTTT
* *
74667 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAA
* **
74732 CGAAGGGGTGACTGACTT-TCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGCGACTGA-TTGTCAACAAACAACTTCCCAGTTTCATTC
**
74777 AGAGTCAATTTCAACTTCACAGCGAA-G---TTGGACTTAAGACAACACAAGCTCAACTAT-ACA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACT-TCACA
*
74837 ACGAAGGGGCGACTGGTTGTCAAC-AA-AACTTCCCAG--T--TTC
65 ACGAAGGGGCGACTGATTGTCAACAAACAACTTCCCAGTTTCATTC
* *
74877 AGAG-CTAATTTCAACTTCACAGCGAAGGATATTGGGCTCAAGACAACACAAGCTCAACTTCACA
1 AGAGTC-AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACA
* **
74941 ACGAAGGGGTGACTGATTGTCAACAAACAACTTTTCAGTTTCATTC
65 ACGAAGGGGCGACTGATTGTCAACAAACAACTTCCCAGTTTCATTC
* * *
74987 ATAGTCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAA
* * ** *
75052 TGAAGGGGCGGCTGCCTGTCAACAAACAACTTCCCAATTTCATTC
66 CGAAGGGGCGACTGATTGTCAACAAACAACTTCCCAGTTTCATTC
* * *
75097 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTGAAACAACACA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
75147 TACTTAGATT
Statistics
Matches: 323, Mismatches: 32, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
99 1 0.00
100 27 0.08
101 1 0.00
102 1 0.00
103 1 0.00
104 59 0.18
105 6 0.02
106 54 0.17
107 1 0.00
108 1 0.00
109 1 0.00
110 169 0.52
111 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (110 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAA
CGAAGGGGCGACTGATTGTCAACAAACAACTTCCCAGTTTCATTC
Done.