Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004063.1 Hibiscus syriacus cultivar Beakdansim tig00008885_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: 50045
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2292 original size:172 final size:179
Alignment explanation
Indices: 1991--2352 Score: 553
Period size: 172 Copynumber: 2.1 Consensus size: 179
1981 AGTTAACAAT
*
1991 AAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATC
1 AAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATC
* * *
2056 GACACTTTTGGAATTTAAAAAAGAAGAAGTTATAGTGCTAATAAAGTGTCGATACTTAATAAAAA
66 GACACTTTTGGAATTTAAAAAAGAAGAAGTTACAGCGCCAATAAAGTGTCGATACTTAATAAAAA
*
2121 TATATCGATCCATA-ATATAAACAGGT-AAAA-ATGACAAAATCGGTCTCG
131 TATATC-ATCCATACA-ATAAACAAGTAAAAATATGACAAAATCGGTCTCG
* *
2169 AAATGACAAAACCGGT-AAGAGTTACCGGATAT-TTGA-AGTGTCGATACTTTATTATAA-TATC
1 AAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATC
* *
2230 G-CACTTTTGGAATTTAAAAGA-AAGAAGTTACAGCGCCAATAAAGTGTCGATACTTTATAAAAA
66 GACACTTTTGGAATTTAAAAAAGAAGAAGTTACAGCGCCAATAAAGTGTCGATACTTAATAAAAA
*
2293 TGTATCATCCATACAATAAACAAGTAAAAATATGACAAAATCGGTCTCG
131 TATATCATCCATACAATAAACAAGTAAAAATATGACAAAATCGGTCTCG
2342 AAATGACAAAA
1 AAATGACAAAA
2353 TCGATAGTAA
Statistics
Matches: 171, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
171 16 0.09
172 48 0.28
173 48 0.28
174 5 0.03
175 21 0.12
176 4 0.02
177 14 0.08
178 15 0.09
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (179 bp):
AAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATC
GACACTTTTGGAATTTAAAAAAGAAGAAGTTACAGCGCCAATAAAGTGTCGATACTTAATAAAAA
TATATCATCCATACAATAAACAAGTAAAAATATGACAAAATCGGTCTCG
Found at i:9418 original size:101 final size:101
Alignment explanation
Indices: 9258--9448 Score: 242
Period size: 101 Copynumber: 1.9 Consensus size: 101
9248 AAACCATTTT
* * * * *
9258 TATTATGCAAAACTAAGGAAAAACATGTTTATATGTATAACTTTATAGGTAGCATCTTTTTTAAT
1 TATTATACAAAACTAAGGAAAAACATGTTTAAAAGTATAACATTATAGGTAGCACCTTTTTTAAT
* *
9323 TATCAACCGTTTACG-TTATTTGTTTGGAACCTTCTA
66 TATCAACC-ATTAAGATTATTTGTTTGGAACCTTCTA
* * * *
9359 TATTATACAAAAGTAA-GACAAAACATGTTTAAAAGTATATCATTGTAGGTTGCACCTTTTTTAA
1 TATTATACAAAACTAAGGA-AAAACATGTTTAAAAGTATAACATTATAGGTAGCACCTTTTTTAA
*
9423 TTGTCAACCATTAAGATTATTTGTTT
65 TTATCAACCATTAAGATTATTTGTTT
9449 CAAACTGTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
100 6 0.08
101 70 0.92
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (101 bp):
TATTATACAAAACTAAGGAAAAACATGTTTAAAAGTATAACATTATAGGTAGCACCTTTTTTAAT
TATCAACCATTAAGATTATTTGTTTGGAACCTTCTA
Found at i:9464 original size:101 final size:101
Alignment explanation
Indices: 9237--9465 Score: 232
Period size: 101 Copynumber: 2.3 Consensus size: 101
9227 AAAAATATGT
* * * * * *
9237 TTATATGTTTG-AAACCATTTTTATTATGCAAAACTAAGGAAAAACATGTTTATATGTATAACTT
1 TTATTTGTTTGCAAA-CTTTTTTATTATACAAAACTAAGGAAAAACATGTTTAAAAGTATAACAT
* * *
9301 TATAGGTAGCATCTTTTTTAATTATCAACCGTTTACG
65 TATAGGTAGCACCTTTTTTAATTATCAACCGATTAAG
* * * * * *
9338 TTATTTGTTTGGAACCTTCTATATTATACAAAAGTAA-GACAAAACATGTTTAAAAGTATATCAT
1 TTATTTGTTTGCAAACTTTTTTATTATACAAAACTAAGGA-AAAACATGTTTAAAAGTATAACAT
* * *
9402 TGTAGGTTGCACCTTTTTTAATTGTCAACC-ATTAAG
65 TATAGGTAGCACCTTTTTTAATTATCAACCGATTAAG
9438 ATTATTTGTTT-CAAACTGTTTTTATTAT
1 -TTATTTGTTTGCAAACT-TTTTTATTAT
9466 GTAACAATAA
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
100 10 0.10
101 91 0.88
102 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (101 bp):
TTATTTGTTTGCAAACTTTTTTATTATACAAAACTAAGGAAAAACATGTTTAAAAGTATAACATT
ATAGGTAGCACCTTTTTTAATTATCAACCGATTAAG
Found at i:25709 original size:22 final size:22
Alignment explanation
Indices: 25684--25743 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 22
25674 ATATTTTATA
25684 TATATTAACTTAAAAAATATTT
1 TATATTAACTTAAAAAATATTT
*
25706 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAAAATATTT
25730 TATTATTAACTTAA
1 TA-TATTAACTTAA
25744 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
22 12 0.35
23 1 0.03
24 11 0.32
25 10 0.29
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATTAACTTAAAAAATATTT
Found at i:25989 original size:31 final size:31
Alignment explanation
Indices: 25922--25989 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
25912 TGATGACCAC
* * *
25922 ATCTTAATTAGATAAAAACAAAAGTGGCCAT
1 ATCTTAATTAAATAAAAACAAAAGTGACAAT
* **
25953 GTCTTAATTAAATAAAAATGAAAGTGACAAT
1 ATCTTAATTAAATAAAAACAAAAGTGACAAT
25984 ATCTTA
1 ATCTTA
25990 TGTTTTTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACAAT
Found at i:29620 original size:2 final size:2
Alignment explanation
Indices: 29613--29695 Score: 150
Period size: 2 Copynumber: 42.0 Consensus size: 2
29603 ATTTATTTAT
29613 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
*
29655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T- 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
29696 GTTTACAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29874 original size:38 final size:36
Alignment explanation
Indices: 29722--29989 Score: 288
Period size: 37 Copynumber: 7.2 Consensus size: 36
29712 TGAAAATACA
* * *
29722 TATATAATATATAGTTTCTAAAAACATTTTGACAATG
1 TATATAATATATAGTTT-TTAAAACATTTTGAAAATT
* *
29759 TATATAATGTATAGTTTTTAAAACACTTTTGAAAA-C
1 TATATAATATATAGTTTTTAAAACA-TTTTGAAAATT
*
29795 TATATAATATATAGTTTTTAAAACATTTTAGAAAATA
1 TATATAATATATAGTTTTTAAAACATTTT-GAAAATT
29832 TATATAATATATAGTTTTTAAAATCATTTTGAAAGATT
1 TATATAATATATAGTTTTTAAAA-CATTTTGAAA-ATT
* * *
29870 TATATAATATATAGCTTTTGAAAACATTTTTTTAAAACT
1 TATATAATATATAG-TTTTTAAAACA--TTTTGAAAATT
* * * *
29909 TATATAATATATATTTTTTGAAAATATTTTTAAAACT
1 TATATAATATATAGTTTTT-AAAACATTTTGAAAATT
*
29946 TATATAATATATAATTTTTTAAAAACATTTTAGAAAA-T
1 TATATAATATAT-AGTTTTT-AAAACATTTT-GAAAATT
29984 TATATA
1 TATATA
29990 GTTTTAAAAA
Statistics
Matches: 204, Mismatches: 16, Indels: 21
0.85 0.07 0.09
Matches are distributed among these distances:
35 4 0.02
36 36 0.18
37 74 0.36
38 51 0.25
39 32 0.16
40 7 0.03
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAATT
Found at i:30019 original size:32 final size:31
Alignment explanation
Indices: 29966--30053 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 31
29956 ATAATTTTTT
29966 AAAAAC-ATTTTAGAAAATTATATAGTTTTAA
1 AAAAACAATTTT-GAAAATTATATAGTTTTAA
29997 AAAAACAAATTTTGAAAATTATATAGTTTTAA
1 AAAAAC-AATTTTGAAAATTATATAGTTTTAA
*
30029 AAAAACATTTTTGAAAATTTATATA
1 AAAAACAATTTTGAAAA-TTATATA
30054 CAATATATAG
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
31 16 0.30
32 32 0.60
33 5 0.09
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (31 bp):
AAAAACAATTTTGAAAATTATATAGTTTTAA
Found at i:30081 original size:42 final size:38
Alignment explanation
Indices: 30014--30122 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 38
30004 AATTTTGAAA
30014 ATTATATAG-TTTTAAAAAAACATTTTT-GAAAATTTAT
1 ATTATATAGTTTTTAAAAAAACATTTTTAG-AAATTTAT
30051 ATACAATATATAGTTTTTAAAAAAACATTTTTAGAAATTTAT
1 AT----TATATAGTTTTTAAAAAAACATTTTTAGAAATTTAT
*
30093 ATTATATAGTTTTTAAAAAAATACTTTTTA
1 ATTATATAGTTTTTAAAAAAACA-TTTTTA
30123 TATTTATTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
37 2 0.03
38 20 0.31
39 6 0.09
41 7 0.11
42 28 0.44
43 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (38 bp):
ATTATATAGTTTTTAAAAAAACATTTTTAGAAATTTAT
Found at i:31432 original size:26 final size:27
Alignment explanation
Indices: 31335--31433 Score: 87
Period size: 26 Copynumber: 3.6 Consensus size: 27
31325 TTTATGTTCT
*
31335 TTTTATTTTTTAGTATATATTTAT-TTA
1 TTTTATTTTTTA-TATACATTTATATTA
31362 TTTTATTTCTTTAT-TACTATTTAATATTCCA
1 TTTTATTT-TTTATATAC-ATTT-ATATT--A
* * *
31393 TTTTATTATATATATACATATATATTA
1 TTTTATTTTTTATATACATTTATATTA
31420 -TTTATTTTTTATAT
1 TTTTATTTTTTATAT
31434 GTTTTTCTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
26 14 0.24
27 14 0.24
28 6 0.10
29 7 0.12
30 7 0.12
31 11 0.19
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTTATTTTTTATATACATTTATATTA
Found at i:31444 original size:24 final size:24
Alignment explanation
Indices: 31417--31466 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
31407 TACATATATA
31417 TTATT-TATTTTTTATATGTTTTTC
1 TTATTATATTTTTTATAT-TTTTTC
*
31441 TTATTATTTTTTTTATATTTTTTC
1 TTATTATATTTTTTATATTTTTTC
31465 TT
1 TT
31467 TCAAATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (24 bp):
TTATTATATTTTTTATATTTTTTC
Found at i:31445 original size:27 final size:24
Alignment explanation
Indices: 31415--31466 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 24
31405 TATACATATA
31415 TATTATTTATTTTTTATATGTTTTTCT
1 TATTA-TT-TTTTTTATAT-TTTTTCT
31442 TATTATTTTTTTTATATTTTTTCT
1 TATTATTTTTTTTATATTTTTTCT
31466 T
1 T
31467 TCAAATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 8 0.32
25 10 0.40
26 2 0.08
27 5 0.20
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (24 bp):
TATTATTTTTTTTATATTTTTTCT
Found at i:31478 original size:25 final size:25
Alignment explanation
Indices: 31425--31479 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
31415 TATTATTTAT
* *
31425 TTTTTATATGTTTTTCTTATTATTT
1 TTTTTATATGTTTTTCTTATAATTG
31450 TTTTTATAT-TTTTTCTT-TCAAATTG
1 TTTTTATATGTTTTTCTTAT--AATTG
31475 TTTTT
1 TTTTT
31480 TAAAACTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 8 0.31
25 17 0.65
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTTTATATGTTTTTCTTATAATTG
Found at i:31585 original size:27 final size:25
Alignment explanation
Indices: 31536--31595 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 25
31526 TTTATCTCAT
*
31536 TTTTTTCTTTCGATTTATTCTTTTTTA
1 TTTTTT-TTTCGATTTA-TCCTTTTTA
31563 TATTTTTTTTCTGATTTA-CCTTTTTA
1 T-TTTTTTTTC-GATTTATCCTTTTTA
31589 TTTTTTT
1 TTTTTTT
31596 ATTTATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 6 0.20
26 8 0.27
27 5 0.17
28 11 0.37
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (25 bp):
TTTTTTTTTCGATTTATCCTTTTTA
Found at i:34390 original size:23 final size:23
Alignment explanation
Indices: 34364--34414 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
34354 CTCGTATAAA
*
34364 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
34387 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
34410 TGCAC
1 TGCAC
34415 TGTAGTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:34568 original size:103 final size:102
Alignment explanation
Indices: 34440--34656 Score: 346
Period size: 103 Copynumber: 2.1 Consensus size: 102
34430 TAATGTCCAT
*
34440 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGG-TCAAGTATGTGTCTCCAAA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCT-CAAA
34504 AGACCTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACCTCACACATGTTCCAAAGAATACATATATGT-CCG
* * * **
34543 AATGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAAAA
*
34608 GACTTCACACATGTTCCAAAGAATACATATATGTCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCG
34645 AAGGACCACATA
1 AAGGACCACATA
34657 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
102 14 0.13
103 77 0.73
104 14 0.13
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAAAA
GACCTCACACATGTTCCAAAGAATACATATATGTCCG
Found at i:38729 original size:84 final size:83
Alignment explanation
Indices: 38574--39948 Score: 1214
Period size: 84 Copynumber: 16.7 Consensus size: 83
38564 TTTAAGACAA
* * * * *
38574 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACCAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
38638 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * * *
38657 CATTTGCAACATAGCTCAAGGCAAAAAGGGCTATTTTCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT-CAACCAAAGACCTTCGAGTTCGACTAC
* *
38722 GTTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
38741 AATTTGCAGCATAGCTTAAGTCGAGAAGGGATATC-T--GCCAAAGACCTTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* *
38803 CTCAGCTCAAAGGCACCAG
66 CTCAGCTCCAAGGCA-CAT
* * *
38822 CATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
* * *
38887 GCTCAACTCTAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * ** * **
38906 CATTTGCAGTATAACTTAAG--G-G-A----TATC-T--GCCAAAAACCCCCGAGTTCGATTAAA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* * * *
38960 CTTAGCTTCGAGGGAACAT
66 CTCAGC-TCCAAGGCACAT
* * *
38979 CATTTGCAGCATAACTTAAGTCAAGAAAGGTTATCTGACAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
39044 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
39063 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-T--GCCAAAGACCCTCGAGTTTGACTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* ** *
39125 CTCAACTTTTAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * * *
39144 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACAAAAGACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
*
39208 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * *
39227 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAATACCTTCGAGTACGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT-CAACCAAAGACCTTCGAGTTCGACTAC
39292 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * *
39311 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC-T--GCCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* *
39373 CTCAGCTTCGAGGACACAT
66 CTCAGCTCCAAGG-CACAT
* * * * * *
39392 CATTTACAGCATAACTCAAGGCTAGAAGGGGTATCTGTC-ACCAAAAGACCTTCGAGTTCGACCA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACC-AAAGACCTTCGAGTTCGACTA
*
39456 CGCTCAGCTCCAAGGCATAT
64 CGCTCAGCTCCAAGGCACAT
*
39476 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
* *
39541 GTTCATCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * * * *
39560 CCTTTGCAGCATAGCTTAAGTTGAGAAGGGCTATC-T--GCCAAAGACCCTCAAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
*
39622 CTCAGCTTCAAGGACACAT
66 CTCAGCTCCAAGG-CACAT
* * * * *
39641 CATTTACAACATAACTCAAAG-CTAGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTA
1 CATTTGCAGCATAACT-TAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTA
*
39704 CGCTTAGCTCCAAGGCACAT
64 CGCTCAGCTCCAAGGCACAT
* ** * * * * * * *
39724 AATTTGCAAAATATCTTAAGTCGAGAATGGCTATC-T--GCCAAAGACCTTCGAGTTCAATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
*
39786 CTCAGCTCCGGAGGCACAT
66 CTCAGCTCC-AAGGCACAT
* * * * * * * * * *
39805 CATTTACATCATAACTCAAGACTAAAATGGTTATCTGCCAA-CAAAGACATTCGACTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
*
39869 GCTCAGCTCAAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
** * * * *
39888 CATTTGCAATATAGCTTAAGTCGAGGAGGGTTAT-TTGCCTACCAAAGACTTTCGAGTTCGA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT--CAACCAAAGACCTTCGAGTTCGA
39949 TTTCATTCAA
Statistics
Matches: 1031, Mismatches: 215, Indels: 91
0.77 0.16 0.07
Matches are distributed among these distances:
72 23 0.02
73 27 0.03
76 5 0.00
77 1 0.00
80 155 0.15
81 171 0.17
82 9 0.01
83 142 0.14
84 405 0.39
85 93 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:39231 original size:164 final size:164
Alignment explanation
Indices: 38574--39926 Score: 1388
Period size: 164 Copynumber: 8.2 Consensus size: 164
38564 TTTAAGACAA
* * * * * *
38574 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACCACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCTTCGAGTTCGACTACA
* * * * * * * *
38639 CTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAAAAGGGCTATTTTCCAACCAAAG
63 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAG
* *
38704 ACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCATAT
128 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
38741 AATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGACCTTCGAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
* * * * *
38806 AGCTCAAAGGCACCAGCATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGAC
66 AGCTCCAAGGCA-CATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
* * *
38871 CTTCGAGTTCGACTACGCTCAACTCTAAGGCATAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * ** * * *
38906 CATTTGCAGTATAACTTAAG--G-G-A----TATCTGCCAAAAACCCCCGAGTTCGATTAAACTT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
* * * * * * *
38963 AGCTTCGAGGGAACATCATTTGCAGCATAACTTAAGTCAAGAAAGGTTATCTGACAACCAAAGAC
66 AGC-TCCAAGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
39028 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * *
39063 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGACTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
* ** * * * * * *
39128 AACTTTTAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACAAAAGAC
66 AGC-TCCAAGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
* *
39192 CTTCGAGTTCGACTATGCTCAGCTCCAAGGCATAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * *
39227 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAATACCTTCGAGTACGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC-T---GCCAAAGACCTTCGAGTTCGACTAC
* * *
39292 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAA
62 ACTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAA
* * * * *
39353 GACCCTCGAGTTCGATTACACTCAGCTTCGAGGACACAT
127 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGG-CACAT
* * * * * *
39392 CATTTACAGCATAACTCAAGGCTAGAAGGGGTATCTGTCACCAAAAGACCTTCGAGTTCGACCAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCTTCGAGTTCGACTAC
* * *
39457 GCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAA
62 ACTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAA
* *
39522 GACCTTCGAGTTCGACTACGTTCATCTCCAAGGCACAT
127 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * * *
39560 CCTTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
* * * * *
39625 AGCTTCAAGGACACATCATTTACAACATAACTCAAAG-CTAGAAGGGTTATCTGTC-ACCAAAGA
66 AGCTCCAAGG-CACATCATTTGCAGCATAACTC-AAGTCGAGAAGGGTTATCTGCCAACCAAAGA
* *
39688 CCTTTGAGTTCGACTACGCTTAGCTCCAAGGCACAT
129 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* ** * * * *
39724 AATTTGCAAAATATCTTAAGTCGAGAATGGCTATCTGCCAAAGACCTTCGAGTTCAATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
* * * * * * *
39789 AGCTCCGGAGGCACATCATTTACATCATAACTCAAGACTAAAATGGTTATCTGCCAA-CAAAGAC
66 AGCTCC-AAGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
* * *
39853 ATTCGACTTCGACTACGCTCAGCTCAAAGGCACAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
** * * * *
39888 CATTTGCAATATAGCTTAAGTCGAGGAGGGTTATTTGCC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC
39927 TACCAAAGAC
Statistics
Matches: 997, Mismatches: 161, Indels: 59
0.82 0.13 0.05
Matches are distributed among these distances:
157 128 0.13
158 6 0.01
159 1 0.00
160 1 0.00
161 2 0.00
162 1 0.00
163 4 0.00
164 377 0.38
165 311 0.31
166 4 0.00
167 72 0.07
168 59 0.06
169 31 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (164 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
AGCTCCAAGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:39571 original size:249 final size:247
Alignment explanation
Indices: 38574--39892 Score: 1426
Period size: 248 Copynumber: 5.3 Consensus size: 247
38564 TTTAAGACAA
* * * * * * *
38574 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACCACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGACTACA
* * * * * * * *
38639 CTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAAAAGGGCTAT-TTTCCAACC-AA
63 CTCAGCTTCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-C-ACCAAA
* * *
38702 AGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCATATAATTTGCAGCATAGCTTAAGTCGAGA
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGA
* * * * *
38767 AGGGATATCTG---CCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACCAG
191 AGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CAT
* * * *
38822 CATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGACTAC
* * * * * *
38887 GCTCAAC-TCTAAGGCATATCATTTGCAG--T-A-T-AA--CT-TAAGGGATATCTG---CCAAA
62 ACTCAGCTTC-AAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
** * ** * * * * * *
38940 A-ACCCCCGAGTTCGATTAAACTTAGCTTCGAGGGAACATCATTTGCAGCATAACTTAAGTCAAG
126 AGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
*
39004 AAAGGTTATCTGACAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
190 AAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* *
39063 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTTGACTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
* * *
39128 AACTTTTAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA-CAAAAGAC
66 AGC-TTCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGAC
* *
39192 CTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGGG
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * *
39257 TTATCTTCCAACCAAATACCTTCGAGTACGACTACGCTCAGCTCCAAGGCACAT
195 TTATC-TGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
*
39311 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
* *
39376 AGCTTCGAGGACACATCATTTACAGCATAACTCAAGGCTAGAAGGGGTATCTGTCACCAAAAGAC
66 AGCTTCAAGG-CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGAC
*
39441 CTTCGAGTTCGACCACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* *
39506 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGTTCATCTCCAAGGCACAT
195 TTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * *
39560 CCTTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
* *
39625 AGCTTCAAGGACACATCATTTACAACATAACTCAAAGCTAGAAGGGTTATCTGTCACC-AAAGAC
66 AGCTTCAAGG-CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGAC
* * * * ** * *
39689 CTTTGAGTTCGACTACGCTTAGCTCCAAGGCACATAATTTGCAAAATATCTTAAGTCGAGAATGG
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * * *
39754 CTATCTG---CCAAAGACCTTCGAGTTCAATTACACTCAGCTCCGGAGGCACAT
195 TTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACAT
* * * * * * * * ** * *
39805 CATTTACATCATAACTCAAGACTAAAATGGTTATCTGCCAACAAAGACATTCGACTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGACTACA
39870 CTCAGC-TCAAAGGCACATCATTT
63 CTCAGCTTC-AAGGCACATCATTT
39893 GCAATATAGC
Statistics
Matches: 915, Mismatches: 122, Indels: 69
0.83 0.11 0.06
Matches are distributed among these distances:
237 48 0.05
238 58 0.06
239 1 0.00
240 1 0.00
241 44 0.05
242 40 0.04
243 2 0.00
244 31 0.03
245 37 0.04
246 12 0.01
247 17 0.02
248 327 0.36
249 296 0.32
251 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (247 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
AGCTTCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
TATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:40446 original size:73 final size:75
Alignment explanation
Indices: 40338--40619 Score: 285
Period size: 73 Copynumber: 3.7 Consensus size: 75
40328 TGCAAATGGT
* * * *
40338 TTTTG-AAAATACGTATATAATATATAGTTTCTAAAAACATTTT-GACAATGTATATAATGTATA
1 TTTTGAAAAAT-C-TATATAATATATAGTTT-TTAAAACATTTTAGAAAATATATATAATATATA
40401 GTTTTTAAAA-CA
63 GTTTTTAAAATCA
*
40413 CTTTTG-AAAA-CTATATAATATATCGTTTTTAAAACATTTTAGAAAATATATATAATATATAGT
1 -TTTTGAAAAATCTATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGT
40476 TTTTAAAATCA
65 TTTTAAAATCA
* **
40487 TTTTGAAAAATTTATATAATATATAGTTTTTGAAAACATTTTTTTAAAACT-TATATAATATATA
1 TTTTGAAAAATCTATATAATATATAGTTTTT-AAAACA-TTTTAGAAAA-TATATATAATATATA
* *
40551 TATTTTTGAAAAT-G
63 -GTTTTT-AAAATCA
* * *
40565 TTTTTAAAACT-TATATAATATATAATTTTTTAAAAACATTTTAGAAAAT-TATATA
1 TTTTGAAAAATCTATATAATATAT-AGTTTTT-AAAACATTTTAGAAAATATATATA
40620 GTTTTAAAAA
Statistics
Matches: 179, Mismatches: 17, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
72 11 0.06
73 48 0.27
74 7 0.04
75 18 0.10
76 22 0.12
77 41 0.23
78 27 0.15
79 5 0.03
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (75 bp):
TTTTGAAAAATCTATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGTT
TTTAAAATCA
Found at i:40503 original size:38 final size:36
Alignment explanation
Indices: 40351--40619 Score: 254
Period size: 38 Copynumber: 7.2 Consensus size: 36
40341 TGAAAATACG
* * * *
40351 TATATAATATATAGTTTCTAAAAACATTTTGACAATG
1 TATATAATATATAGTTT-TTAAAACATTTTAAAAATT
* * *
40388 TATATAATGTATAGTTTTTAAAACACTTTTGAAAA-C
1 TATATAATATATAGTTTTTAAAACA-TTTTAAAAATT
* *
40424 TATATAATATATCGTTTTTAAAACATTTTAGAAAATA
1 TATATAATATATAGTTTTTAAAACATTTTA-AAAATT
40461 TATATAATATATAGTTTTTAAAATCATTTTGAAAAATT
1 TATATAATATATAGTTTTTAAAA-CATTTT-AAAAATT
* *
40499 TATATAATATATAGTTTTTGAAAACATTTTTTTAAAACT
1 TATATAATATATAGTTTTT-AAAACA--TTTTAAAAATT
* ** * *
40538 TATATAATATATATATTTTTGAAAATGTTTTTAAAACT
1 TATATAATATATA-GTTTTT-AAAACATTTTAAAAATT
*
40576 TATATAATATATAATTTTTTAAAAACATTTTAGAAAA-T
1 TATATAATATAT-AGTTTTT-AAAACATTTTA-AAAATT
40614 TATATA
1 TATATA
40620 GTTTTAAAAA
Statistics
Matches: 201, Mismatches: 20, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
35 4 0.02
36 34 0.17
37 46 0.23
38 75 0.37
39 28 0.14
40 14 0.07
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTAAAAATT
Found at i:40651 original size:34 final size:33
Alignment explanation
Indices: 40596--40687 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 33
40586 ATAATTTTTT
40596 AAAAAC-ATTTTAGAAAATTATATAGTTTTAAAA
1 AAAAACAATTTT-GAAAATTATATAGTTTTAAAA
**
40629 AAAAACAAATTTTGAAAATTATATAGTTTTTTAA
1 AAAAAC-AATTTTGAAAATTATATAGTTTTAAAA
*
40663 AAAAACATTTTTGAAAATTTATATA
1 AAAAACAATTTTGAAAA-TTATATA
40688 CAATATATAG
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
33 16 0.30
34 32 0.60
35 5 0.09
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.39
Consensus pattern (33 bp):
AAAAACAATTTTGAAAATTATATAGTTTTAAAA
Found at i:40743 original size:36 final size:36
Alignment explanation
Indices: 40353--40743 Score: 151
Period size: 36 Copynumber: 10.6 Consensus size: 36
40343 AAAATACGTA
* *
40353 TATAATATATAGTTTCTAAAAACA-TTTT-GACAATGT
1 TATATTATATAGTTTTTAAAAACATTTTTAGA-AAT-T
* * * *
40389 ATATAATGTATAGTTTTT-AAAACACTTTT-GAAAACTA
1 -TATATTATATAGTTTTTAAAAACATTTTTAG-AAA-TT
* *
40426 TATAATATATCGTTTTT-AAAACA-TTTTAGAAAATAT
1 TATATTATATAGTTTTTAAAAACATTTTTAG-AAAT-T
* * * *
40462 ATATAATATATAGTTTTTAAAATCATTTTGAAAAATT
1 -TATATTATATAGTTTTTAAAAACATTTTTAGAAATT
*
40499 TATATAATATATAGTTTTTGAAAACATTTTTTTA-AAACTT
1 TATAT--TATATAGTTTTTAAAAACA--TTTTTAGAAA-TT
* **
40539 ATATAATATATATA-TTTTTGAAAATGTTTTTA-AAACTT
1 -TAT-AT-TATATAGTTTTTAAAAACATTTTTAGAAA-TT
* *
40577 ATATAATATATAATTTTTTAAAAACA-TTTTAG-AA--
1 -TATATTATAT-AGTTTTTAAAAACATTTTTAGAAATT
* *
40611 -A-ATTATATAGTTTTAAAAAAAAACAAATTTT-G-AA--
1 TATATTATATAGTTTT---TAAAAAC-ATTTTTAGAAATT
40645 -A-ATTATATAGTTTTTTAAAAAAACATTTTT-GAAAATT
1 TATATTATATAG-TTTTT--AAAAACATTTTTAG-AAATT
**
40682 TATATACAATATATAGTTTAAAAAAACATTTTTAGAAATT
1 TATAT----TATATAGTTTTTAAAAACATTTTTAGAAATT
40722 TATATTATATAGTTTTTAAAAA
1 TATATTATATAGTTTTTAAAAA
40744 AAATATTTTT
Statistics
Matches: 288, Mismatches: 29, Indels: 75
0.73 0.07 0.19
Matches are distributed among these distances:
30 5 0.02
31 6 0.02
32 1 0.00
33 12 0.04
34 20 0.07
35 15 0.05
36 56 0.19
37 48 0.17
38 54 0.19
39 9 0.03
40 39 0.14
41 11 0.04
42 5 0.02
43 7 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
TATATTATATAGTTTTTAAAAACATTTTTAGAAATT
Found at i:40746 original size:40 final size:38
Alignment explanation
Indices: 40353--40745 Score: 141
Period size: 37 Copynumber: 10.6 Consensus size: 38
40343 AAAATACGTA
* * *
40353 TATAATATATAGTTTCT--AAAAACA-TTTTGACAATGT
1 TATATTATATAGTTTTTAAAAAAACATTTTTGAAAAT-T
* * * *
40389 ATATAATGTATAGTTTTT---AAAACACTTTTGAAAACTA
1 -TATATTATATAGTTTTTAAAAAAACATTTTTGAAAA-TT
* * *
40426 TATAATATATCGTTTTT---AAAACATTTTAGAAAATAT
1 TATATTATATAGTTTTTAAAAAAACATTTTTGAAAAT-T
* *
40462 ATATAATATATAGTTTTT--AAAATCA-TTTTGAAAAATT
1 -TATATTATATAGTTTTTAAAAAAACATTTTTG-AAAATT
* *
40499 TATATAATATATAGTTTTT--GAAAACATTTTTTTAAAACTT
1 TATAT--TATATAGTTTTTAAAAAAACA-TTTTTGAAAA-TT
* **
40539 ATATAATATATATA-TTTTT--GAAAATGTTTTT-AAAACTT
1 -TAT-AT-TATATAGTTTTTAAAAAAACATTTTTGAAAA-TT
* * * *
40577 ATATAATATATAATTTTT-TAAAAACA-TTTT-AGAA--
1 -TATATTATATAGTTTTTAAAAAAACATTTTTGAAAATT
* *
40611 -A-ATTATATAGTTTTAAAAAAAAACAAATTTTGAAAA-T
1 TATATTATATAGTTTT-TAAAAAAAC-ATTTTTGAAAATT
*
40648 TATA-TA-GT--TTTTTAAAAAAACATTTTTGAAAATT
1 TATATTATATAGTTTTTAAAAAAACATTTTTGAAAATT
40682 TATATACAATATATAG--TTTAAAAAAACATTTTT-AGAAATT
1 TATAT----TATATAGTTTTTAAAAAAACATTTTTGA-AAATT
40722 TATATTATATAGTTTTTAAAAAAA
1 TATATTATATAGTTTTTAAAAAAA
40746 ATATTTTTTA
Statistics
Matches: 289, Mismatches: 32, Indels: 69
0.74 0.08 0.18
Matches are distributed among these distances:
31 11 0.04
32 1 0.00
33 16 0.06
34 14 0.05
35 9 0.03
36 55 0.19
37 58 0.20
38 56 0.19
39 13 0.04
40 44 0.15
41 10 0.03
42 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (38 bp):
TATATTATATAGTTTTTAAAAAAACATTTTTGAAAATT
Found at i:40754 original size:40 final size:38
Alignment explanation
Indices: 40646--40755 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 38
40636 AATTTTGAAA
*
40646 ATTATATAGTTTTTTAAAAAAACATTTTTGAAAATTTAT
1 ATTATATAG-TTTTTAAAAAAACATTTTTTAAAATTTAT
40685 ATACAATATATAG--TTTAAAAAAACA-TTTTTAGAAATTTAT
1 AT----TATATAGTTTTTAAAAAAACATTTTTTA-AAATTTAT
*
40725 ATTATATAGTTTTTAAAAAAAATATTTTTTA
1 ATTATATAGTTTTT-AAAAAAACATTTTTTA
40756 TATTTATTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
36 7 0.12
38 3 0.05
39 15 0.25
40 28 0.47
43 7 0.12
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (38 bp):
ATTATATAGTTTTTAAAAAAACATTTTTTAAAATTTAT
Found at i:40767 original size:17 final size:17
Alignment explanation
Indices: 40759--40792 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
40749 TTTTTTATAT
40759 TTATTTATTTATTATTA
1 TTATTTATTTATTATTA
40776 TTATTTA-TTATTATTA
1 TTATTTATTTATTATTA
40792 T
1 T
40793 CATTACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTATTTATTATTA
Found at i:40779 original size:13 final size:13
Alignment explanation
Indices: 40763--40792 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40753 TTATATTTAT
40763 TTATTTATTATTA
1 TTATTTATTATTA
40776 TTATTTATTATTA
1 TTATTTATTATTA
40789 TTAT
1 TTAT
40793 CATTACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:42121 original size:25 final size:26
Alignment explanation
Indices: 42077--42128 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
42067 TATACATATA
42077 TATTATTTATTTTTTATATTTTTTCT
1 TATTATTTATTTTTTATATTTTTTCT
42103 TATTATTTA-TTTTTATATTTTTTCT
1 TATTATTTATTTTTTATATTTTTTCT
42128 T
1 T
42129 TCAAATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (26 bp):
TATTATTTATTTTTTATATTTTTTCT
Found at i:42125 original size:10 final size:11
Alignment explanation
Indices: 42086--42125 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
42076 ATATTATTTA
42086 TTTTTTATATT
1 TTTTTTATATT
42097 TTTTCTTATTATT
1 TTTT-TTA-TATT
42110 TATTTTTATATT
1 T-TTTTTATATT
42122 TTTT
1 TTTT
42126 CTTTCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.27
12 8 0.31
13 8 0.31
14 3 0.12
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTATATT
Found at i:42140 original size:25 final size:25
Alignment explanation
Indices: 42087--42141 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
42077 TATTATTTAT
* *
42087 TTTTTATATTTTTTCTTATTATTTA
1 TTTTTATATTTTTTCTTATAAATTA
*
42112 TTTTTATATTTTTTCTT-TCAAATTG
1 TTTTTATATTTTTTCTTAT-AAATTA
42137 TTTTT
1 TTTTT
42142 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTTATATTTTTTCTTATAAATTA
Found at i:42241 original size:12 final size:12
Alignment explanation
Indices: 42214--42281 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
42204 TTCTTTCGAC
42214 TTATTATTATTA-
1 TTATTATT-TTAT
42226 TTATTATTTTAT
1 TTATTATTTTAT
*
42238 TTATTTATTCTGAT
1 TTA-TTATT-TTAT
42252 TTATCT-TTTTAT
1 TTAT-TATTTTAT
42264 TTATT-TATTTA-
1 TTATTAT-TTTAT
42275 TTATTAT
1 TTATTAT
42282 ATTTTTTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
11 10 0.21
12 23 0.48
13 8 0.17
14 7 0.15
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (12 bp):
TTATTATTTTAT
Found at i:42242 original size:4 final size:4
Alignment explanation
Indices: 42233--42285 Score: 56
Period size: 4 Copynumber: 12.8 Consensus size: 4
42223 TTATTATTAT
42233 TTTA TTTA TTTA TTCTGA TTTA TCTT- TTTA TTTA TTTA TTTA -TTA TTATA
1 TTTA TTTA TTTA TT-T-A TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TT-TA
42283 TTT
1 TTT
42286 TTTTTGTCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
3 5 0.12
4 27 0.63
5 8 0.19
6 3 0.07
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:42281 original size:26 final size:25
Alignment explanation
Indices: 42220--42287 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
42210 CGACTTATTA
42220 TTATTATTATTATTTTATTTATTTAT
1 TTATTATTATT-TTTTATTTATTTAT
42246 TCTGA-T-TTATCTTTTTATTTATTTAT
1 T-T-ATTATTAT-TTTTTATTTATTTAT
42272 TTATTATTATATTTTT
1 TTATTATTAT-TTTTT
42288 TTTGTCTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
24 1 0.03
25 2 0.06
26 29 0.81
27 3 0.08
28 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (25 bp):
TTATTATTATTTTTTATTTATTTAT
Found at i:43515 original size:17 final size:18
Alignment explanation
Indices: 43489--43523 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43479 AAAATGTTTT
*
43489 CAATTCATTT-ATTTTAA
1 CAATTAATTTAATTTTAA
43506 CAATTAATTTAATTTTAA
1 CAATTAATTTAATTTTAA
43524 TAGTAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
CAATTAATTTAATTTTAA
Found at i:44510 original size:29 final size:30
Alignment explanation
Indices: 44477--44533 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
44467 TAATTTTTTC
* *
44477 AGTTTAGTGTCTCACGTTT-ATTTCGTTCT
1 AGTTTAGTGTCTAACGTTTCATTCCGTTCT
*
44506 AGTTTGGTGTCTAACGTTTCATTCCGTT
1 AGTTTAGTGTCTAACGTTTCATTCCGTT
44534 ACTCAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.14, C:0.18, G:0.19, T:0.49
Consensus pattern (30 bp):
AGTTTAGTGTCTAACGTTTCATTCCGTTCT
Found at i:44577 original size:13 final size:13
Alignment explanation
Indices: 44559--44593 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
44549 AGGTGTGACG
44559 GACCGTTAAGTTT
1 GACCGTTAAGTTT
44572 GACCGTTAAGTTT
1 GACCGTTAAGTTT
44585 GACCGTTAA
1 GACCGTTAA
44594 CCTATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (13 bp):
GACCGTTAAGTTT
Found at i:45014 original size:29 final size:29
Alignment explanation
Indices: 44982--45040 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
44972 CTTCACCTTC
44982 AAGGAAGGTGTCATGGTTGCTATTGATTT
1 AAGGAAGGTGTCATGGTTGCTATTGATTT
*
45011 AAGGAAGGTGTCATGGTTGCTGTTGATTT
1 AAGGAAGGTGTCATGGTTGCTATTGATTT
45040 A
1 A
45041 GGGTTCTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.07, G:0.32, T:0.37
Consensus pattern (29 bp):
AAGGAAGGTGTCATGGTTGCTATTGATTT
Found at i:45320 original size:29 final size:30
Alignment explanation
Indices: 45264--45331 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
45254 CCATTTTGAG
*
45264 TAACGAAATGAAACCTTAGGCACCAAACTA
1 TAACAAAATGAAACCTTAGGCACCAAACTA
* *
45294 TAACAAAAT-AAACGTTAGGCACTAAACTA
1 TAACAAAATGAAACCTTAGGCACCAAACTA
*
45323 GAA-AAAATG
1 TAACAAAATG
45332 GCATAGGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.15
29 20 0.61
30 8 0.24
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (30 bp):
TAACAAAATGAAACCTTAGGCACCAAACTA
Found at i:47028 original size:21 final size:21
Alignment explanation
Indices: 47002--47049 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
46992 AAGGACTTCT
47002 GAATTTCATAACAGAGAATCA
1 GAATTTCATAACAGAGAATCA
47023 GAATTTCATAACAGAGAATCA
1 GAATTTCATAACAGAGAATCA
47044 GAATTT
1 GAATTT
47050 TATTAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (21 bp):
GAATTTCATAACAGAGAATCA
Done.