Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006915.1 Hibiscus syriacus cultivar Beakdansim tig00017721_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: 143066
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:8753 original size:13 final size:13
Alignment explanation
Indices: 8735--8761 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8725 GACTGATGAA
8735 GCCCAAACTTTCC
1 GCCCAAACTTTCC
8748 GCCCAAACTTTCC
1 GCCCAAACTTTCC
8761 G
1 G
8762 ACCCCTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.44, G:0.11, T:0.22
Consensus pattern (13 bp):
GCCCAAACTTTCC
Found at i:9229 original size:29 final size:30
Alignment explanation
Indices: 9197--9255 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
9187 GTTCTTTATC
*
9197 TACTCATAATTATTAAAAATATT-AATAAA
1 TACTCACAATTATTAAAAATATTAAATAAA
9226 TACTCACAATTATTAAAAATATTAAATAAA
1 TACTCACAATTATTAAAAATATTAAATAAA
9256 CAGTCATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (30 bp):
TACTCACAATTATTAAAAATATTAAATAAA
Found at i:9268 original size:30 final size:29
Alignment explanation
Indices: 9198--9268 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
9188 TTCTTTATCT
*
9198 ACTCATAATTATTAAAAATATTAATAAAT
1 ACTCATAATTATTAAAAATATTAATAAAC
*
9227 ACTCACAATTATTAAAAATATTAAATAAAC
1 ACTCATAATTATTAAAAATATT-AATAAAC
* *
9257 AGTCATGATTAT
1 ACTCATAATTAT
9269 CGAAAATGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (29 bp):
ACTCATAATTATTAAAAATATTAATAAAC
Found at i:23077 original size:26 final size:26
Alignment explanation
Indices: 23031--23083 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
23021 CATCAAAAAC
23031 ACCAAAACAAGAACATAAACCATGAT
1 ACCAAAACAAGAACATAAACCATGAT
* *
23057 ACCAAAACAA-ATCATTGAACCATGAT
1 ACCAAAACAAGAACA-TAAACCATGAT
23083 A
1 A
23084 TTGATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 21 0.88
ACGTcount: A:0.55, C:0.23, G:0.08, T:0.15
Consensus pattern (26 bp):
ACCAAAACAAGAACATAAACCATGAT
Found at i:27351 original size:24 final size:25
Alignment explanation
Indices: 27306--27361 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
27296 AAATTTTAAG
27306 ATAAAAAATATAATATCAATAAAAAT
1 ATAAAAAATATAATAT-AATAAAAAT
*
27332 ATAAAAAAGTA-AATAT-ATAAATAT
1 ATAAAAAA-TATAATATAATAAAAAT
27356 ATAAAA
1 ATAAAA
27362 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 13 0.46
26 13 0.46
27 2 0.07
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
ATAAAAAATATAATATAATAAAAAT
Found at i:29155 original size:94 final size:95
Alignment explanation
Indices: 29026--29223 Score: 355
Period size: 94 Copynumber: 2.1 Consensus size: 95
29016 TACTTACTAG
*
29026 TTAAATTTAACAACTTTACAATTCAAGTACTTAAAAGTATAATATTAGAACATTAAATATATATT
1 TTAAATTTAACAACTTTACAATTCAAGTACTTAAAAGTATAATATTAGAACATTAAACATATATT
29091 TTTAACGAAAAATCCTTTAAACACTT-AAA
66 TTTAACGAAAAATCCTTTAAACACTTAAAA
29120 TTAAATTTAACAACTTTACAA-TCAAAGTACTTAAAAGTATAATATTAGAACATTAAACATATAT
1 TTAAATTTAACAACTTTACAATTC-AAGTACTTAAAAGTATAATATTAGAACATTAAACATATAT
29184 TTTTAACGAAAAATCCTTTAAACACTTAAAA
65 TTTTAACGAAAAATCCTTTAAACACTTAAAA
*
29215 TTAACTTTA
1 TTAAATTTA
29224 GATATATTAG
Statistics
Matches: 100, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
93 2 0.02
94 87 0.87
95 11 0.11
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (95 bp):
TTAAATTTAACAACTTTACAATTCAAGTACTTAAAAGTATAATATTAGAACATTAAACATATATT
TTTAACGAAAAATCCTTTAAACACTTAAAA
Found at i:31379 original size:10 final size:10
Alignment explanation
Indices: 31353--31418 Score: 66
Period size: 10 Copynumber: 6.8 Consensus size: 10
31343 GCTGGAAAAT
31353 CGGTTTG-AC
1 CGGTTTGAAC
*
31362 CAGTTTTGAAC
1 C-GGTTTGAAC
31373 CGGTTTG-AC
1 CGGTTTGAAC
*
31382 CGGTCTGAAC
1 CGGTTTGAAC
31392 CGGTTTG-AC
1 CGGTTTGAAC
*
31401 CGGTCTGAAC
1 CGGTTTGAAC
*
31411 CGGGTTGA
1 CGGTTTGA
31419 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
9 17 0.37
10 26 0.57
11 3 0.07
ACGTcount: A:0.17, C:0.23, G:0.32, T:0.29
Consensus pattern (10 bp):
CGGTTTGAAC
Found at i:31392 original size:19 final size:19
Alignment explanation
Indices: 31353--31420 Score: 100
Period size: 19 Copynumber: 3.5 Consensus size: 19
31343 GCTGGAAAAT
* *
31353 CGGTTTGACCAGTTTTGAAC
1 CGGTTTGACC-GGTCTGAAC
31373 CGGTTTGACCGGTCTGAAC
1 CGGTTTGACCGGTCTGAAC
31392 CGGTTTGACCGGTCTGAAC
1 CGGTTTGACCGGTCTGAAC
*
31411 CGGGTTGACC
1 CGGTTTGACC
31421 CGACCCGACC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.78
20 10 0.22
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (19 bp):
CGGTTTGACCGGTCTGAAC
Found at i:31459 original size:17 final size:17
Alignment explanation
Indices: 31437--31490 Score: 99
Period size: 17 Copynumber: 3.2 Consensus size: 17
31427 GACCGACCCA
31437 ACCCGACCCGACTGTTG
1 ACCCGACCCGACTGTTG
31454 ACCCGACCCGACTGTTG
1 ACCCGACCCGACTGTTG
*
31471 ACCCGACCCGACCGTTG
1 ACCCGACCCGACTGTTG
31488 ACC
1 ACC
31491 GTTGACTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.19, C:0.44, G:0.22, T:0.15
Consensus pattern (17 bp):
ACCCGACCCGACTGTTG
Found at i:31462 original size:22 final size:22
Alignment explanation
Indices: 31431--31483 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 22
31421 CGACCCGACC
*
31431 GACCCAACCCGACCCGACTGTT
1 GACCCGACCCGACCCGACTGTT
31453 -----GACCCGACCCGACTGTT
1 GACCCGACCCGACCCGACTGTT
31470 GACCCGACCCGACC
1 GACCCGACCCGACC
31484 GTTGACCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 10
0.69 0.03 0.28
Matches are distributed among these distances:
17 16 0.64
22 9 0.36
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCCGACTGTT
Found at i:38709 original size:10 final size:10
Alignment explanation
Indices: 38680--38748 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
38670 GCTGCTGGAA
38680 AACCGGTTTG
1 AACCGGTTTG
*
38690 -ACCAGTTTTG
1 AACC-GGTTTG
38700 AACCGGTTTG
1 AACCGGTTTG
*
38710 -ACCGGTCTG
1 AACCGGTTTG
38719 AACCGGTTTG
1 AACCGGTTTG
*
38729 -ACCGGTCTG
1 AACCGGTTTG
*
38738 AACCGGGTTG
1 AACCGGTTTG
38748 A
1 A
38749 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:38722 original size:19 final size:19
Alignment explanation
Indices: 38680--38750 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
38670 GCTGCTGGAA
* *
38680 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
38700 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
38719 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
38738 AACCGGGTTGACC
1 AACCGGTTTGACC
38751 CGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:38765 original size:14 final size:14
Alignment explanation
Indices: 38746--38773 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38736 TGAACCGGGT
38746 TGACCCGACCCGAC
1 TGACCCGACCCGAC
38760 TGACCCGACCCGAC
1 TGACCCGACCCGAC
38774 CCGACTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:38769 original size:19 final size:20
Alignment explanation
Indices: 38747--38795 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
38737 GAACCGGGTT
38747 GACCCGACCCGAC-TGACCC
1 GACCCGACCCGACTTGACCC
38766 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGAC--TTGACCC
38788 GACCCGAC
1 GACCCGAC
38796 TGTTGACCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.48
22 14 0.52
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.08
Consensus pattern (20 bp):
GACCCGACCCGACTTGACCC
Found at i:38788 original size:17 final size:17
Alignment explanation
Indices: 38744--38820 Score: 100
Period size: 17 Copynumber: 4.4 Consensus size: 17
38734 TCTGAACCGG
38744 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
38761 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
38780 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
* *
38797 GTTGACCCGACCTGACC
1 GTTGACCCGACCCGACT
38814 GTTGACC
1 GTTGACC
38821 GTTGACCGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
17 37 0.71
19 15 0.29
ACGTcount: A:0.18, C:0.43, G:0.23, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:38821 original size:7 final size:7
Alignment explanation
Indices: 38809--38833 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38799 TGACCCGACC
38809 TGACCGT
1 TGACCGT
38816 TGACCGT
1 TGACCGT
38823 TGACCGT
1 TGACCGT
38830 TGAC
1 TGAC
38834 TTCATTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
TGACCGT
Found at i:54516 original size:24 final size:21
Alignment explanation
Indices: 54463--54519 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 21
54453 ATTTTTAAGA
*
54463 ATTATCTTTAGGAATTATCTC
1 ATTATTTTTAGGAATTATCTC
54484 -TTATTTTTAGGAATTATCTTTTC
1 ATTATTTTTAGGAATTATC---TC
54507 ATTATTTTTAGGA
1 ATTATTTTTAGGA
54520 TTAGAAAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 17 0.55
23 2 0.06
24 12 0.39
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (21 bp):
ATTATTTTTAGGAATTATCTC
Found at i:61052 original size:30 final size:30
Alignment explanation
Indices: 61018--61174 Score: 242
Period size: 30 Copynumber: 5.2 Consensus size: 30
61008 CCCGAAGGAC
61018 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
61048 CTATCCGGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
61078 CTATCCGGAGGTCATAAAGATCTTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
61108 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* * *
61138 CTATCCGGATGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
61168 CTGTCCA
1 CTATCCA
61175 TATATTCTTT
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 117 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:67551 original size:2 final size:2
Alignment explanation
Indices: 67544--67578 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
67534 TTATTTATTC
67544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
67579 GTAACATTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68700 original size:15 final size:15
Alignment explanation
Indices: 68680--68709 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
68670 TATCACAATC
68680 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
68695 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
68710 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:74277 original size:20 final size:20
Alignment explanation
Indices: 74252--74291 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
74242 AATTTAACTG
74252 CCACCAATTTTGACTTTAAC
1 CCACCAATTTTGACTTTAAC
74272 CCACCAATTTTGACTTTAAC
1 CCACCAATTTTGACTTTAAC
74292 AATCTTCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (20 bp):
CCACCAATTTTGACTTTAAC
Found at i:76600 original size:11 final size:11
Alignment explanation
Indices: 76584--76608 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
76574 CTCCATCCTG
76584 GCATACTGTGA
1 GCATACTGTGA
76595 GCATACTGTGA
1 GCATACTGTGA
76606 GCA
1 GCA
76609 GACTTGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (11 bp):
GCATACTGTGA
Found at i:78114 original size:20 final size:20
Alignment explanation
Indices: 78089--78127 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
78079 ATTTAGTTGT
78089 CACCAATTTTGACTTTAACC
1 CACCAATTTTGACTTTAACC
78109 CACCAATTTTGACTTTAAC
1 CACCAATTTTGACTTTAAC
78128 ACTCTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (20 bp):
CACCAATTTTGACTTTAACC
Found at i:81507 original size:19 final size:17
Alignment explanation
Indices: 81473--81508 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
81463 AATAATCATG
81473 TAAAATATATTATTTAT
1 TAAAATATATTATTTAT
81490 TAAAATTATATATATTTAT
1 TAAAA-TATAT-TATTTAT
81509 GATTAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATATATTATTTAT
Found at i:82934 original size:3 final size:3
Alignment explanation
Indices: 82926--82953 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
82916 AATTATTTAG
82926 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
82954 TAAATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:83716 original size:112 final size:112
Alignment explanation
Indices: 83480--83811 Score: 490
Period size: 112 Copynumber: 3.0 Consensus size: 112
83470 ATAGAGTCAT
** *
83480 GCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
83544 ATTATGAACT-TTCTGGAAATATTGATCCCTAGAGTGATGAATTTGG
66 ATTATGAACTCTTCTGGAAATGTTGATCCATAGAGTGATGGATTCGA
**
83590 GTGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
83655 ATTATGAACTCTTTTGGAAATGTTGATTCATCGAATGATGGATTCGA
66 ATTATGAACTCTTCTGGAAATGTTGATCCATAGAGTGATGGATTCGA
*
83702 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
83766 ATTATGAACTCTCTCTGGAAATGTTGATCCATTGAGTGATGGATTC
66 ATTATGAACTCT-TCTGGAAATGTTGATCCATAGAGTGATGGATTC
83812 AAATCTTGCT
Statistics
Matches: 198, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
110 40 0.20
111 63 0.32
112 95 0.48
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTTCTGGAAATGTTGATCCATAGAGTGATGGATTCGA
Found at i:84994 original size:18 final size:18
Alignment explanation
Indices: 84967--85001 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
84957 TATATGAAAC
84967 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
*
84985 AAATTTAATTTCAAAAA
1 AAATTGAATTTCAAAAA
85002 GATAAACTTG
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:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:85398 original size:14 final size:15
Alignment explanation
Indices: 85363--85416 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 15
85353 ATTATTATTA
*
85363 TTTTTCTTTTTCATCAT
1 TTTTTC-TTTTCAT-TT
85380 TTTTTCTTTTC-TTT
1 TTTTTCTTTTCATTT
85394 TTTTTC-TTTCATTT
1 TTTTTCTTTTCATTT
85408 TTTCTTCTT
1 TTT-TTCTT
85417 CAAGCATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 4 0.12
14 13 0.39
15 4 0.12
16 6 0.18
17 6 0.18
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTCATTT
Found at i:92716 original size:15 final size:15
Alignment explanation
Indices: 92693--92724 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
92683 TGCAATAAAT
92693 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
92708 AATGCATGTATGCAA
1 AATGAATGTATGCAA
92723 AA
1 AA
92725 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:95648 original size:109 final size:110
Alignment explanation
Indices: 95446--95655 Score: 245
Period size: 109 Copynumber: 1.9 Consensus size: 110
95436 AAGATGTTTA
* * *
95446 TTTATTTAGAAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGCTCTTTTCTTAATATTAAA
1 TTTATTTAGAAATATCAGAAAATGACATCCAGGTGCTTTAAGACAGCTCCTTTCTTAATATTAAA
* *
95511 ATAAATAATATAAAACATTTATCTAATGA-TTAAAATATAGATAAT
66 ATAAATAATAGAAAACATTTA-CAAATGATTTAAAATATAGATAAT
* *
95556 TTTATTTA-AAATATTAGAAAATGGACATCCAGTTGCTTTAAGACTA-C-CCTTTCTTAATATTG
1 TTTATTTAGAAATATCAGAAAAT-GACATCCAGGTGCTTTAAGAC-AGCTCCTTTCTTAATATT-
95618 AAAAATAAAT-AT-GAAAACATAATTA-AAATGATTTAAAA
63 -AAAATAAATAATAGAAAACAT--TTACAAATGATTTAAAA
95656 ATAATATATT
Statistics
Matches: 86, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
109 38 0.44
110 35 0.41
111 13 0.15
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (110 bp):
TTTATTTAGAAATATCAGAAAATGACATCCAGGTGCTTTAAGACAGCTCCTTTCTTAATATTAAA
ATAAATAATAGAAAACATTTACAAATGATTTAAAATATAGATAAT
Found at i:95712 original size:26 final size:26
Alignment explanation
Indices: 95648--95718 Score: 65
Period size: 29 Copynumber: 2.7 Consensus size: 26
95638 AATTAAAATG
*
95648 ATTTA-AAAATAATATATTAAATAGT
1 ATTTATAAAATAATATAATAAATAGT
*
95673 ATTTTAATAGAAATAA-ATAAATAAATATT
1 A-TTT-ATA-AAATAATAT-AATAAATAGT
*
95702 ATTTATAAAATTATATA
1 ATTTATAAAATAATATA
95719 TGTATTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
25 1 0.03
26 9 0.24
27 6 0.16
28 6 0.16
29 15 0.41
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
ATTTATAAAATAATATAATAAATAGT
Found at i:95793 original size:19 final size:17
Alignment explanation
Indices: 95759--95794 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
95749 AATAATCATG
95759 TAAAATATATTATTTAT
1 TAAAATATATTATTTAT
95776 TAAAATTATATATATTTAT
1 TAAAA-TATAT-TATTTAT
95795 GATTAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATATATTATTTAT
Found at i:96987 original size:15 final size:15
Alignment explanation
Indices: 96967--96999 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
96957 GAGATATCGA
96967 CGTGGGGAGACTGAC
1 CGTGGGGAGACTGAC
*
96982 CGTGGGGAGGCTGAC
1 CGTGGGGAGACTGAC
96997 CGT
1 CGT
97000 CGGCAGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (15 bp):
CGTGGGGAGACTGAC
Found at i:97213 original size:3 final size:3
Alignment explanation
Indices: 97205--97229 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
97195 TAAAATTATT
97205 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
97230 CAAATGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:104050 original size:34 final size:34
Alignment explanation
Indices: 103982--104091 Score: 154
Period size: 34 Copynumber: 3.3 Consensus size: 34
103972 GTTTTATTAT
*
103982 TTTCAATCAACAT--AAAATAATAGACTTTCTAC
1 TTTCAATCAACATAAAAAAGAATAGACTTTCTAC
104014 TTTCAATCAACATAAAAAAGAATAGAC-TTCTGAC
1 TTTCAATCAACATAAAAAAGAATAGACTTTCT-AC
** *
104048 TTTCAATCAACATAAAATGGAATAAACTTTCTAC
1 TTTCAATCAACATAAAAAAGAATAGACTTTCTAC
104082 TTTCAATCAA
1 TTTCAATCAA
104092 ATTAGGGTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
32 13 0.19
33 4 0.06
34 49 0.70
35 4 0.06
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (34 bp):
TTTCAATCAACATAAAAAAGAATAGACTTTCTAC
Found at i:107877 original size:65 final size:65
Alignment explanation
Indices: 107168--107876 Score: 1006
Period size: 65 Copynumber: 10.9 Consensus size: 65
107158 GAACAAGTAT
* * * * * *
107168 ATATTACTCATATGACTCATGTACATTTGTGGTGCATGGGGTGAAGTGATAATTGCATACAATAT
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* * *
107233 AGATCACTCATATGACTCATATACCTTTGTGGTGCATG-GTGTGGAGTGATAATTGAATACAGTA
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAG-GTGGAGTGATAATTGAATACAATA
107297 C
65 C
* ** *
107298 ATATTACTCATATGACTCATGTACCTTTGTCATGCATGAGGTGAAGTGATAATTGAATACAATAC
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* * * * * *
107363 AGATCACTCATATGACTCGTGTACCTTTGTGGTGCATGGGGTAGAGTGATAATTGAATATAGTAC
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
107428 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* * * * * * * * *
107493 AAATCACTTAAATGACTCATGTACATTTGTGGTGCAAGAAGTAGAGTGATAATTGTATACATTAC
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* * * *
107558 ATATCACTCATATGACTCATGTACCTTTGTAGTGCATGATGTGAAGTGATAATTGAATACAGTAC
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* *
107623 ATATCAGTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAGTAC
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* * * *
107688 AGATCACTCATATGACTCATGTATCTTTGTGGTGCATGATGTGGAGTGATAATTGTATACAATAC
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* * * *
107753 ATACCACTCATATGACTCATGTATCTTTATGGTGCATGAGGTGGAGTGATAATTGAATATAATAC
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
* *
107818 ATATCAATCATATGACTCATGTACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATA
1 ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATA
107877 TTGCAAAGAT
Statistics
Matches: 570, Mismatches: 72, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
64 1 0.00
65 568 1.00
66 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (65 bp):
ATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACAATAC
Found at i:108065 original size:17 final size:17
Alignment explanation
Indices: 108002--108094 Score: 71
Period size: 17 Copynumber: 5.5 Consensus size: 17
107992 AACATCAGAT
* *
108002 ACAAAACAGTAAAAGAT
1 ACAATACAGTAAAAGAA
* *
108019 ACAATACAATAAGAGAA
1 ACAATACAGTAAAAGAA
* ** *
108036 ATAATGTAATAAAAGAA
1 ACAATACAGTAAAAGAA
108053 ACAATACAGT-AAAGAA
1 ACAATACAGTAAAAGAA
* *
108069 ATCAATACAGAAAAAGGA
1 A-CAATACAGTAAAAGAA
*
108087 ACAGTACA
1 ACAATACA
108095 ATGAAAGGAA
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
16 7 0.12
17 46 0.78
18 6 0.10
ACGTcount: A:0.62, C:0.11, G:0.13, T:0.14
Consensus pattern (17 bp):
ACAATACAGTAAAAGAA
Found at i:108084 original size:34 final size:33
Alignment explanation
Indices: 108007--108121 Score: 97
Period size: 34 Copynumber: 3.4 Consensus size: 33
107997 CAGATACAAA
* *
108007 ACAGTAAAAGATACAATACAATAAGAGAAATAAT
1 ACAGAAAAAGAAACAATACAATAA-AGAAATAAT
** *
108041 GTA-ATAAAAGAAACAATACAGTAAAGAAATCAAT
1 ACAGA-AAAAGAAACAATACAATAAAGAAAT-AAT
* * * *
108075 ACAGAAAAAGGAACAGTACAATGAAAGGAATGAT
1 ACAGAAAAAGAAACAATACAAT-AAAGAAATAAT
108109 ACAGGAAAAAGAA
1 ACA-GAAAAAGAA
108122 TAATATAGTG
Statistics
Matches: 63, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
33 6 0.10
34 41 0.65
35 16 0.25
ACGTcount: A:0.61, C:0.09, G:0.17, T:0.14
Consensus pattern (33 bp):
ACAGAAAAAGAAACAATACAATAAAGAAATAAT
Found at i:108134 original size:34 final size:34
Alignment explanation
Indices: 108095--108180 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 34
108085 GAACAGTACA
108095 ATGAAAGGAATGATACAGGAAAAAGAA-TAA-TAT
1 ATGAAAGGAATGATACAGGAAAAA-AATTAAGTAT
* *
108128 AGTGAAAGGATTGGTACAGGAAAAAAATTAAGTAT
1 A-TGAAAGGAATGATACAGGAAAAAAATTAAGTAT
*
108163 ATGATAAGGAACGATACA
1 ATGA-AAGGAATGATACA
108181 AGTTTAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 3 0.07
34 27 0.61
35 14 0.32
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.20
Consensus pattern (34 bp):
ATGAAAGGAATGATACAGGAAAAAAATTAAGTAT
Found at i:115709 original size:8 final size:8
Alignment explanation
Indices: 115696--115736 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
115686 CTCATTTTCA
115696 GAGAATTT
1 GAGAATTT
115704 GAGAATTT
1 GAGAATTT
*
115712 -AGAGTTT
1 GAGAATTT
*
115719 GGGAATTT
1 GAGAATTT
115727 GAGAATTT
1 GAGAATTT
115735 GA
1 GA
115737 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:116192 original size:128 final size:128
Alignment explanation
Indices: 115807--116561 Score: 1460
Period size: 128 Copynumber: 5.9 Consensus size: 128
115797 TAATCGGAGT
*
115807 ACTATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
115872 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
115935 ACTATTCATATGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
115998 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
116061 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
116126 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
116189 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
116254 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
116317 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
116382 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
116445 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
116510 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
116562 AATAAGGTAA
Statistics
Matches: 620, Mismatches: 5, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
126 122 0.20
127 8 0.01
128 490 0.79
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:117020 original size:33 final size:34
Alignment explanation
Indices: 116959--117058 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
116949 AAATTTAATG
* *
116959 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTAGAATAATATAATTTATATTTTAAAT
* * * *
116993 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTAGAATAATATAATTTATATTTTAAAT
*
117026 TTAAATTTAGAATAATATAATTTGTATTTTAAA
1 TTAAATTTAGAATAATATAATTTATATTTTAAA
117059 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTAGAATAATATAATTTATATTTTAAAT
Found at i:117046 original size:39 final size:39
Alignment explanation
Indices: 116978--117055 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
116968 GAATACTATA
*
116978 ATTTATATTTTAAATTTAAATTTGAATAATAT-TATTTTT
1 ATTTATATTTTAAATTTAAATAT-AATAATATGTATTTTT
* *
117017 ATTTTTATTTTAAATTTAGAATA-ATATAATTTGTATTTT
1 ATTTATATTTTAAATTTA-AATATA-ATAATATGTATTTT
117056 AAAAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
38 1 0.03
39 23 0.70
40 9 0.27
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (39 bp):
ATTTATATTTTAAATTTAAATATAATAATATGTATTTTT
Found at i:117608 original size:21 final size:20
Alignment explanation
Indices: 117581--117671 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 20
117571 GGTATAAAAC
*
117581 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
* *
117601 CCTGGCGGGCTAGGCATGTAT
1 CCT-GCGGGCTAGGAATGTAA
117622 CCTAGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
117643 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
117664 CCCTGCGG
1 -CCTGCGG
117672 AGATGGCATA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.91
22 3 0.05
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.20
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:119486 original size:33 final size:31
Alignment explanation
Indices: 119444--119518 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 31
119434 TTAATAATTC
* *
119444 TAAATAAATAATAATTATATAAATATTATTTAA
1 TAAAAAAATAATAATTACATAAATA-TA-TTAA
*
119477 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTACATAAATATATTAA
119508 TATAAAAAATA
1 TA-AAAAAATA
119519 TTAACTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 6 0.16
32 10 0.26
33 22 0.58
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (31 bp):
TAAAAAAATAATAATTACATAAATATATTAA
Found at i:119491 original size:18 final size:19
Alignment explanation
Indices: 119464--119499 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
119454 ATAATTATAT
*
119464 AAATATTATTTA-ATAAAA
1 AAATAATATTTACATAAAA
119482 AAATAATATTTACATAAA
1 AAATAATATTTACATAAA
119500 TATATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATATTTACATAAAA
Found at i:119519 original size:15 final size:15
Alignment explanation
Indices: 119501--119548 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
119491 TTACATAAAT
119501 ATATTAATATAAAAA
1 ATATTAATATAAAAA
119516 ATATTAACTATTTAAAAA
1 ATATTAA-TA--TAAAAA
* *
119534 ATACTAACATAAAAA
1 ATATTAATATAAAAA
119549 TAAATTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 13 0.46
16 2 0.07
17 1 0.04
18 12 0.43
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATTAATATAAAAA
Found at i:119546 original size:33 final size:33
Alignment explanation
Indices: 119444--119548 Score: 83
Period size: 33 Copynumber: 3.2 Consensus size: 33
119434 TTAATAATTC
* * * * *
119444 TAAATAAATAATAATTATATAAATATTATTTA-A
1 TAAAAAAATAATATTTACATAAATA-TACTAACA
* *
119477 TAAAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAAATAATATTTACATAAATATACTAACA
119510 TAAAAAATATTAACTATTTA-A-AAA-ATACTAACA
1 TAAAAAA-A-TAA-TATTTACATAAATATACTAACA
119543 TAAAAA
1 TAAAAA
119549 TAAATTTCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
32 5 0.08
33 43 0.69
34 4 0.06
35 4 0.06
36 6 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (33 bp):
TAAAAAAATAATATTTACATAAATATACTAACA
Found at i:120450 original size:14 final size:14
Alignment explanation
Indices: 120426--120482 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
120416 CGTTCGTGAA
*
120426 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
*
120440 TGTTTGGTTATGTT
1 CGTTTGGTTATGTT
120454 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
120464 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
120478 CGTTT
1 CGTTT
120483 ATGTTCATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
10 9 0.26
12 1 0.03
14 24 0.71
ACGTcount: A:0.09, C:0.11, G:0.25, T:0.56
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:120454 original size:24 final size:24
Alignment explanation
Indices: 120427--120501 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
120417 GTTCGTGAAC
* * * *
120427 GTTCGGTTATGTTTGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
120451 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
120475 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
120499 GTT
1 GTT
120502 TAACACAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 1 0.02
24 44 0.98
ACGTcount: A:0.12, C:0.09, G:0.21, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:121243 original size:10 final size:10
Alignment explanation
Indices: 121224--121298 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
121214 AGGCCTCCAA
121224 CGTTTATGTT
1 CGTTTATGTT
*
121234 CGTTTTTGTT
1 CGTTTATGTT
121244 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
121255 ATGTTCGTGTT
1 -CGTTTATGTT
121266 CGTTTATGTT
1 CGTTTATGTT
121276 CG----TGTT
1 CGTTTATGTT
121282 CGTTTATGTT
1 CGTTTATGTT
121292 CGTTTAT
1 CGTTTAT
121299 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.67
11 7 0.14
12 3 0.06
ACGTcount: A:0.08, C:0.12, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:121259 original size:16 final size:16
Alignment explanation
Indices: 121230--121294 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
121220 CCAACGTTTA
*
121230 TGTTCGTTTTTGTTCG
1 TGTTCGTTTATGTTCG
*
121246 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
121262 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
121278 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
121294 T
1 T
121295 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.06, C:0.12, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:121388 original size:16 final size:16
Alignment explanation
Indices: 121363--121394 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
121353 AAAAAAAATT
*
121363 TTGTTTGTTTATGTTC
1 TTGTTCGTTTATGTTC
121379 TTGTTCGTTTATGTTC
1 TTGTTCGTTTATGTTC
121395 GTTTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.09, G:0.19, T:0.66
Consensus pattern (16 bp):
TTGTTCGTTTATGTTC
Found at i:123737 original size:14 final size:15
Alignment explanation
Indices: 123712--123744 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
123702 TAAGATTTTT
123712 AAATATTTTTCTTAA
1 AAATATTTTTCTTAA
*
123727 AAATA-TTTTCTTTA
1 AAATATTTTTCTTAA
123741 AAAT
1 AAAT
123745 TTAAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATATTTTTCTTAA
Found at i:125797 original size:182 final size:182
Alignment explanation
Indices: 125504--125891 Score: 607
Period size: 182 Copynumber: 2.1 Consensus size: 182
125494 TACAAATGAA
* * * * * * *
125504 AAATATATCGATCTATAGTAATATAACAGGTAAAAATATGATAAAACTGGTGTCATTATGATAAA
1 AAATATATCGATCCATAGCAATATAACAAGTAAAAATATGACAAAACAGGTCTCATAATGATAAA
* *
125569 ACCGGTAAACCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
66 ACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
* * * *
125634 TAATTTAAAAGAGAAGAAGTTATAGTGTCTAAAAAGTGTCGATACTTTATAC
131 TAATTTAAAAGAGAAGAAGTAATAGCGCCTAAAAAATGTCGATACTTTATAC
*
125686 AAATATATCGATCCATAGCAATATAACAAGTAATAATATGACAAAACAGGTCTCGA-AATGATAA
1 AAATATATCGATCCATAGCAATATAACAAGTAAAAATATGACAAAACAGGTCTC-ATAATGATAA
* *
125750 AACCGGTAAAAGGCTACCGGATATATTGAAAGTGTCGATACATTAATATAAGTATCGACACTTTC
65 AACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTC
125815 GTAATTTAAAAGAGAAGAAGTAATAGCGCCTAAAAAATGTCGATACTTTATAC
130 GTAATTTAAAAGAGAAGAAGTAATAGCGCCTAAAAAATGTCGATACTTTATAC
*
125868 AAATGTATCGATCCATAGCAATAT
1 AAATATATCGATCCATAGCAATAT
125892 TGACATTCAT
Statistics
Matches: 188, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 187 0.99
183 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AAATATATCGATCCATAGCAATATAACAAGTAAAAATATGACAAAACAGGTCTCATAATGATAAA
ACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
TAATTTAAAAGAGAAGAAGTAATAGCGCCTAAAAAATGTCGATACTTTATAC
Found at i:128072 original size:199 final size:195
Alignment explanation
Indices: 127804--128323 Score: 528
Period size: 198 Copynumber: 2.6 Consensus size: 195
127794 AGATTTTGTA
* ** *
127804 TCGATACATTTATAAAAAGTATCGATCCCAAAATCAAAGAGACCGATAATTATAATGTAATAGGT
1 TCGATACATTT-TAAAAAGTATCGATCCCGAAA-CATCGAAACCGATAATTATAATGTAATAGGT
* * *
127869 AAATTTCCAATGTAACCGGTAGAAATATACCGGGTTCATGAGAGAATAGGTCAACATAAAGTATC
64 AAATTTACAATGTAACCGGTA-AAATATACCGGATTAATGAGA-AATAGGTCAACATAAAGTATC
* * * * * * *
127934 GACACTTTTTTAATTTGTGTCGATACATTTTTT-CAAAATGAATG-GCAAACGAGGTGTATGCAT
127 GACACTCTTTAAATATGTGTCGATAC-TTTTTTACAAAAT-AAAGCACAAACGAGGTGCACGCAT
*
127997 AAAGTG
190 AAAATG
* * * *
128003 TCGATACATTTGTAAAAAGTATCGATCCTCGAAACATCGAAATCGATAATTATTATGTAACATGT
1 TCGATACATTT-TAAAAAGTATCGATCC-CGAAACATCGAAACCGATAATTATAATGTAATAGGT
* * * * * * *
128068 AAATTTACAATGTAACTGGTTAAAATATA-CTGATTAATTAGCAAATAGATCTACATTATGTATC
64 AAATTTACAATGTAACCGG-TAAAATATACCGGATTAATGAG-AAATAGGTCAACATAAAGTATC
*
128132 GACACTCTTTAAATATGTGTCGATACTTTTTTACAAAATAAAGCACAAACGAGTTGCACGCATAA
127 GACACTCTTTAAATATGTGTCGATACTTTTTTACAAAATAAAGCACAAACGAGGTGCACGCATAA
128197 AATG
192 AATG
* * *
128201 TCGATACA-TTTAAAATTGTATCGATCCCGAAAATATCGAAACCGAT-ATACATAATGTAATAGG
1 TCGATACATTTTAAAA-AGTATCGATCCCG-AAACATCGAAACCGATAAT-TATAATGTAATAGG
* * * * * * * *
128264 TCAATTTATAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATATGTCAATATAA
63 TAAATTTACAATGTAACCGG-TAAAATATACCGGATTAATGAG-AAATAGGTCAACATAA
128324 GTGCTACCTA
Statistics
Matches: 262, Mismatches: 50, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
196 9 0.03
197 70 0.27
198 101 0.39
199 76 0.29
200 6 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (195 bp):
TCGATACATTTTAAAAAGTATCGATCCCGAAACATCGAAACCGATAATTATAATGTAATAGGTAA
ATTTACAATGTAACCGGTAAAATATACCGGATTAATGAGAAATAGGTCAACATAAAGTATCGACA
CTCTTTAAATATGTGTCGATACTTTTTTACAAAATAAAGCACAAACGAGGTGCACGCATAAAATG
Found at i:128421 original size:86 final size:87
Alignment explanation
Indices: 128318--128479 Score: 263
Period size: 86 Copynumber: 1.9 Consensus size: 87
128308 AAATATGTCA
* *
128318 ATATAAGTGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAAT-TTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
128382 CTGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* * *
128404 ATATAAGCGCTACCTATTATATTATATAAGCGCTACTTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
128469 CCGGTTAAATG
66 CCGGTTAAATG
128480 ATATAACATA
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 56 0.81
87 13 0.19
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:128426 original size:23 final size:23
Alignment explanation
Indices: 128393--128439 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
128383 TGGTTAAATG
*
128393 CCTATTTTATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
128416 CCTATTATATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
128439 C
1 C
128440 TTAATATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (23 bp):
CCTATTATATTATATAAGCGCTA
Found at i:128451 original size:23 final size:23
Alignment explanation
Indices: 128400--128451 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
128390 ATGCCTATTT
*
128400 TATTATATAAGCGCTACCTATTA
1 TATTATATAAGCGCTACCTAATA
*
128423 TATTATATAAGCGCTACTTAATA
1 TATTATATAAGCGCTACCTAATA
*
128446 TGTTAT
1 TATTAT
128452 TGTGCTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TATTATATAAGCGCTACCTAATA
Found at i:128535 original size:17 final size:16
Alignment explanation
Indices: 128502--128537 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
128492 CGATCTAAAT
*
128502 TTTAACCGATCACTTA
1 TTTAACCGATCAATTA
128518 TTTAACCGATCATATTA
1 TTTAACCGATCA-ATTA
128535 TTT
1 TTT
128538 TTTAATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
TTTAACCGATCAATTA
Found at i:131203 original size:19 final size:19
Alignment explanation
Indices: 131169--131219 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
131159 AAAAATTAAA
* *
131169 ATTATGTAATTATAACTAAT
1 ATTAT-TAAATATAACAAAT
131189 ATTATTAAATATAACAAAT
1 ATTATTAAATATAACAAAT
131208 ATTA--AAATATAA
1 ATTATTAAATATAA
131220 TTATACTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
19 16 0.55
20 5 0.17
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTATTAAATATAACAAAT
Done.