Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007925.1 Hibiscus syriacus cultivar Beakdansim tig00110331_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: 1316088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:826060 original size:20 final size:20
Alignment explanation
Indices: 826024--826061 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
826014 TTCCTTTGAA
*
826024 GCTTCTCTTTGATTGTGATT
1 GCTTCTCTTTAATTGTGATT
826044 GCTT-TCTTTAATGTGTGA
1 GCTTCTCTTTAAT-TGTGA
826062 CATACATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (20 bp):
GCTTCTCTTTAATTGTGATT
Found at i:826905 original size:15 final size:15
Alignment explanation
Indices: 826872--826905 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
826862 AGAAAATTTG
*
826872 AAAATAAAAGAAAAC
1 AAAATAAAAGAAAAA
*
826887 AAAATTAAAGAAAAA
1 AAAATAAAAGAAAAA
826902 AAAA
1 AAAA
826906 CAACTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAATAAAAGAAAAA
Found at i:827823 original size:25 final size:25
Alignment explanation
Indices: 827795--827854 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
827785 GAATAGGAAA
*
827795 AAGACGAAGAATCGGGTTGAAATTC
1 AAGACGAAGAATCGGGTTAAAATTC
827820 AAGACGAAGAATCGGGTTAAAATTC
1 AAGACGAAGAATCGGGTTAAAATTC
*
827845 AAGACAAAGA
1 AAGACGAAGA
827855 GAATATCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.17
Consensus pattern (25 bp):
AAGACGAAGAATCGGGTTAAAATTC
Found at i:828030 original size:27 final size:27
Alignment explanation
Indices: 827972--828031 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
827962 ATTTTTTTAG
* *
827972 CTGTTCGAATCTGTTGTTTTTTCTACA
1 CTGTTCGAATCTATTGTTTTTTATACA
* *
827999 CTGTTGGAATCTATTGTTTTTTATGCA
1 CTGTTCGAATCTATTGTTTTTTATACA
*
828026 TTGTTC
1 CTGTTC
828032 AAACATTGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (27 bp):
CTGTTCGAATCTATTGTTTTTTATACA
Found at i:832244 original size:34 final size:34
Alignment explanation
Indices: 832201--832278 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
832191 TGTGTCCGTG
832201 AATTCTTCTAGTTCATGTTTCAATCTCTTGATCA
1 AATTCTTCTAGTTCATGTTTCAATCTCTTGATCA
*
832235 AATTCTTCTAGTTCGTGTTTCAATCTCTTGATCA
1 AATTCTTCTAGTTCATGTTTCAATCTCTTGATCA
832269 AATTCTTCTA
1 AATTCTTCTA
832279 ATGTGTCTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (34 bp):
AATTCTTCTAGTTCATGTTTCAATCTCTTGATCA
Found at i:836285 original size:22 final size:22
Alignment explanation
Indices: 836228--836286 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
836218 GTGCTAAGGA
*
836228 ACTTTAGTATCAGTGTGGATGC
1 ACTTTAGTATTAGTGTGGATGC
* *
836250 ACTTCTA-TACTAGTGTTGA-GAC
1 ACTT-TAGTATTAGTGTGGATG-C
836272 ACTTTAGTATTAGTG
1 ACTTTAGTATTAGTG
836287 CTAAGGCACT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 3 0.10
22 25 0.83
23 2 0.07
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (22 bp):
ACTTTAGTATTAGTGTGGATGC
Found at i:836296 original size:22 final size:22
Alignment explanation
Indices: 836218--836297 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
836208 CTCTCCCTCG
* *
836218 GTGCTAAGGAACTTTAGTATCA
1 GTGCTAAGGCACTTTAGTATTA
* * *
836240 GTG-TGGATGCACTTCTA-TACTA
1 GTGCT-AAGGCACTT-TAGTATTA
* * *
836262 GTGTTGAGACACTTTAGTATTA
1 GTGCTAAGGCACTTTAGTATTA
836284 GTGCTAAGGCACTT
1 GTGCTAAGGCACTT
836298 CCATGATAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
21 3 0.07
22 37 0.86
23 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (22 bp):
GTGCTAAGGCACTTTAGTATTA
Found at i:838200 original size:51 final size:52
Alignment explanation
Indices: 838123--838237 Score: 160
Period size: 52 Copynumber: 2.2 Consensus size: 52
838113 TAACTACTAC
* * *
838123 ATAAAATAATAATAAACTAAAGATAAT-GTTTTGATTCTATCCTAATTCCTA
1 ATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCTA
* * * *
838174 ATAAAATATTAATAAACTAAAAATAATATTTTTAACTCTATCTTAATTGCTA
1 ATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCTA
838226 ATAAAATAATAA
1 ATAAAATAATAA
838238 ATATAATCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 25 0.45
52 30 0.55
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (52 bp):
ATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCTA
Found at i:839764 original size:21 final size:21
Alignment explanation
Indices: 839738--839797 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
839728 TTCTAATAAA
*
839738 AATTTAAATGATGTTGATGTT
1 AATTTAAATGATCTTGATGTT
839759 AATTTAAATGATCTTGATGTT
1 AATTTAAATGATCTTGATGTT
839780 AATTTAAATGATCTTGAT
1 AATTTAAATGATCTTGAT
839798 AGTTCTCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (21 bp):
AATTTAAATGATCTTGATGTT
Found at i:841496 original size:5 final size:5
Alignment explanation
Indices: 841486--841523 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
841476 AAATCAAAGA
*
841486 TTATT TTATT TTACAT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTA-TT TTATT TTATT TTATT TTATT TT
841524 TAAATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:841525 original size:16 final size:15
Alignment explanation
Indices: 841486--841523 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
841476 AAATCAAAGA
841486 TTATTTTATTTTACAT
1 TTATTTTATTTTA-AT
*
841502 TTATTTTATTTTATT
1 TTATTTTATTTTAAT
841517 TTATTTT
1 TTATTTT
841524 TAAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTATTTTAAT
Found at i:846799 original size:22 final size:24
Alignment explanation
Indices: 846762--846807 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
846752 CTCTTTTCTA
846762 AAAAGTATTTTCTTTCCTTCTTAG
1 AAAAGTATTTTCTTTCCTTCTTAG
846786 AAAA-TATTTT-TTTCCTTCTTAG
1 AAAAGTATTTTCTTTCCTTCTTAG
846808 TTTTCCAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 12 0.55
23 6 0.27
24 4 0.18
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (24 bp):
AAAAGTATTTTCTTTCCTTCTTAG
Found at i:848987 original size:17 final size:16
Alignment explanation
Indices: 848952--848991 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
848942 TGTTTTCTAA
848952 TATATTATTTATTTAT
1 TATATTATTTATTTAT
848968 TATTATTATTTA-TTATT
1 TA-TATTATTTATTTA-T
848985 TATATTA
1 TATATTA
848992 CACTCCCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTATTTATTTAT
Found at i:848990 original size:13 final size:13
Alignment explanation
Indices: 848954--848984 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
848944 TTTTCTAATA
848954 TATTATTTATTTAT
1 TATTA-TTATTTAT
848968 TATTATTATTTAT
1 TATTATTATTTAT
848981 TATT
1 TATT
848985 TATATTACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:849500 original size:2 final size:2
Alignment explanation
Indices: 849493--849540 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
849483 TCATTTATCA
849493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
849535 AT -T AT A
1 AT AT AT A
849541 GTTTTGAACG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:849973 original size:10 final size:11
Alignment explanation
Indices: 849957--849981 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
849947 AATAAAATTG
849957 AAAAAAAATAA
1 AAAAAAAATAA
849968 AAAAAAAATAA
1 AAAAAAAATAA
849979 AAA
1 AAA
849982 GGTTGATATT
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:851150 original size:74 final size:73
Alignment explanation
Indices: 851027--851206 Score: 213
Period size: 74 Copynumber: 2.4 Consensus size: 73
851017 ATAGGGAGGA
* *
851027 ACCGATACCCCTCATAGGGTGTACCGATAACCCTATTCCAATTTTGGCTCAGAGAAAAACAA-AA
1 ACCGATACCCTTCATA-GG-GTACCGAT-ACCCTATGCCAATTTTGGCTCAGAGAAAAA-AAGAA
*
851091 TGTCAAATGGGT
62 TGCCAAATGGGT
*
851103 ACCGATACCCTTCATAGGGTACCGATACCTCTATGCCAATTTTGGCTCCGAGAAAAAAAGAATGC
1 ACCGATACCCTTCATAGGGTACCGATACC-CTATGCCAATTTTGGCTCAGAGAAAAAAAGAATGC
*
851168 CCAATGGGT
65 CAAATGGGT
* *
851177 ATCGATATCCCCTT-A-AAGGTACCGATACCC
1 ACCGATA--CCCTTCATAGGGTACCGATACCC
851207 CTAGTCATTT
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
73 6 0.06
74 64 0.69
75 3 0.03
76 20 0.22
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (73 bp):
ACCGATACCCTTCATAGGGTACCGATACCCTATGCCAATTTTGGCTCAGAGAAAAAAAGAATGCC
AAATGGGT
Found at i:856972 original size:21 final size:21
Alignment explanation
Indices: 856946--857002 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
856936 TTTGTGCACC
*
856946 AGGTATCGATACCCCCTTGCT
1 AGGTATCGATACCCCCTTACT
856967 AGGTATCGATACCCCCTTACT
1 AGGTATCGATACCCCCTTACT
856988 AGGTATCGATACCCC
1 AGGTATCGATACCCC
857003 TTCAACGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (21 bp):
AGGTATCGATACCCCCTTACT
Found at i:857014 original size:21 final size:20
Alignment explanation
Indices: 856946--857022 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 20
856936 TTTGTGCACC
* *
856946 AGGTATCGATACCCCCTTGCT
1 AGGTATCGATA-CCCCTTACA
*
856967 AGGTATCGATACCCCCTTACT
1 AGGTATCGATA-CCCCTTACA
856988 AGGTATCGATACCCCTT-CA
1 AGGTATCGATACCCCTTACA
857007 ACGTGTATCGATACCC
1 A-G-GTATCGATACCC
857023 TATTTGAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 2 0.04
20 7 0.13
21 43 0.83
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.27
Consensus pattern (20 bp):
AGGTATCGATACCCCTTACA
Found at i:865752 original size:78 final size:78
Alignment explanation
Indices: 865623--865778 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
865613 GTTAAAAAAT
865623 CAGATCAGCACCTTAGAAATATAGATAGAATTAACAAAAATCCAGGCTATAACTCCCTGTAAGAA
1 CAGATCAGCACCTTAGAAATATAGATAGAATTAACAAAAATCCAGGCTATAACTCCCTGTAAGAA
865688 TTCTCCAGTAAAC
66 TTCTCCAGTAAAC
865701 CAGATCAGCACCTTAGAAATATAGATAGAATTAACAAAAATCCAGGCTATAACTCCCTGTAAGAA
1 CAGATCAGCACCTTAGAAATATAGATAGAATTAACAAAAATCCAGGCTATAACTCCCTGTAAGAA
865766 TTCTCCAGTAAAC
66 TTCTCCAGTAAAC
865779 TCTATAAACT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (78 bp):
CAGATCAGCACCTTAGAAATATAGATAGAATTAACAAAAATCCAGGCTATAACTCCCTGTAAGAA
TTCTCCAGTAAAC
Found at i:869036 original size:22 final size:22
Alignment explanation
Indices: 869008--869056 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
868998 TTGGTTTTTT
869008 GCTTTCGAATAGAAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
869030 GCTTTCGAATAGAAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
869052 GCTTT
1 GCTTT
869057 TCAAAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (22 bp):
GCTTTCGAATAGAAAAATAATA
Found at i:870159 original size:83 final size:84
Alignment explanation
Indices: 870047--870262 Score: 208
Period size: 84 Copynumber: 2.6 Consensus size: 84
870037 TATATACCTG
* * *
870047 ACTTTTGCGGCG-TTTATATAAAAAACGCCGCAATAGGT-TTACTATATAGT-GATATTT-TATC
1 ACTTTAGCGGCGTTTTA-AT-ACAAACGCCGCAATAGGTGTTA-TATATAGTGGAT-TTTGGAT-
* * *
870108 AAGAAACGTCG-TAAAATATTTGT
61 AACAAACGTCGCAAAAATATTTAT
* *
870131 ACTTTAGCGGCGTTTTAATACAAACGCCGCAATAGGTGTTATCTATAGTGGCTTTTGGATAACAA
1 ACTTTAGCGGCGTTTTAATACAAACGCCGCAATAGGTGTTATATATAGTGGATTTTGGATAACAA
*
870196 ATGTCGCAAAAATATTTAT
66 ACGTCGCAAAAATATTTAT
* * ** * * *
870215 ATTTTAGCGTCGTTTTTGTACAAACGCCGCAATAAGTGTAATCTATAG
1 ACTTTAGCGGCGTTTTAATACAAACGCCGCAATAGGTGTTATATATAG
870263 AGGCATTTGT
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
83 36 0.32
84 72 0.64
85 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (84 bp):
ACTTTAGCGGCGTTTTAATACAAACGCCGCAATAGGTGTTATATATAGTGGATTTTGGATAACAA
ACGTCGCAAAAATATTTAT
Found at i:872645 original size:15 final size:15
Alignment explanation
Indices: 872621--872650 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
872611 CATGGCAGTG
872621 GTATCAGTAGAACTA
1 GTATCAGTAGAACTA
*
872636 GTATCGGTAGAACTA
1 GTATCAGTAGAACTA
872651 AGCTTGCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (15 bp):
GTATCAGTAGAACTA
Found at i:878661 original size:21 final size:21
Alignment explanation
Indices: 878641--878679 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
878631 GATAACAGCA
878641 ATAGA-AGCACAGAGAGAAGC
1 ATAGATAGCACAGAGAGAAGC
*
878661 ATCGATAGCACAGAGAGAA
1 ATAGATAGCACAGAGAGAA
878680 ACATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.49, C:0.15, G:0.28, T:0.08
Consensus pattern (21 bp):
ATAGATAGCACAGAGAGAAGC
Found at i:883625 original size:24 final size:24
Alignment explanation
Indices: 883598--883685 Score: 149
Period size: 24 Copynumber: 3.7 Consensus size: 24
883588 TTCTATTATA
*
883598 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
883622 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
883646 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
883670 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
883686 ATGTTATGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:883701 original size:24 final size:24
Alignment explanation
Indices: 883598--883695 Score: 106
Period size: 24 Copynumber: 4.1 Consensus size: 24
883588 TTCTATTATA
* * **
883598 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTATGATATG
* **
883622 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTATGATATG
* *
883646 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTATGATATG
*
883670 ATACTTGACCTGGATTATGTTATG
1 ATACTTGACCTGGATTATGATATG
883694 AT
1 AT
883696 TTTTGATATA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (24 bp):
ATACTTGACCTGGATTATGATATG
Found at i:885794 original size:18 final size:18
Alignment explanation
Indices: 885771--885823 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
885761 GTCATAACCC
885771 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
885789 GACCCGACCC-A----TT
1 GACCCGACCCGACCCGTT
*
885802 GATCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
885820 GACC
1 GACC
885824 GGTGTTGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
17 1 0.04
18 15 0.54
ACGTcount: A:0.19, C:0.47, G:0.21, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:885823 original size:13 final size:13
Alignment explanation
Indices: 885776--885812 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
885766 AACCCGACCC
885776 GACCCGACCCGTT
1 GACCCGACCCGTT
*
885789 GACCCGACCCATT
1 GACCCGACCCGTT
*
885802 GATCCGACCCG
1 GACCCGACCCG
885813 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:888337 original size:24 final size:24
Alignment explanation
Indices: 888310--888398 Score: 119
Period size: 24 Copynumber: 3.7 Consensus size: 24
888300 TTTCTATTAT
888310 AATACCTT-ACCTGGATTCTGATCG
1 AATA-CTTGACCTGGATTCTGATCG
888334 AATACTTGACCTGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
* *
888358 GATACTTGACCTGGATTTTGATCTG
1 AATACTTGACCTGGATTCTGATC-G
*
888383 -ATTCTTGACCTGGATT
1 AATACTTGACCTGGATT
888399 ATGTTATGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
23 3 0.05
24 56 0.93
25 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATCG
Found at i:888414 original size:24 final size:24
Alignment explanation
Indices: 888338--888414 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
888328 TGATCGAATA
* ** *
888338 CTTGACCTGGATTCTGATCGGATA
1 CTTGACCTGGATTATGATATGATT
* *
888362 CTTGACCTGGATTTTGATCTGATT
1 CTTGACCTGGATTATGATATGATT
*
888386 CTTGACCTGGATTATGTTATGATT
1 CTTGACCTGGATTATGATATGATT
*
888410 TTTGA
1 CTTGA
888415 TATATCCGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (24 bp):
CTTGACCTGGATTATGATATGATT
Found at i:888613 original size:2 final size:2
Alignment explanation
Indices: 888606--888630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
888596 CGGATTGTGT
888606 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
888631 GTTTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:894823 original size:78 final size:77
Alignment explanation
Indices: 894739--894882 Score: 252
Period size: 78 Copynumber: 1.9 Consensus size: 77
894729 TGGAGTACAA
*
894739 TGGTTATCAATCGATTTTGTTTAATGCATATGTTGCATTTTTCATATCAGTACTTTTGTGTACTT
1 TGGTTATCAATCGATTTTGTTTAATGCATATGTTGCA-TTTTCATATCAGTACCTTTGTGTACTT
894804 TCGATACTATATG
65 TCGATACTATATG
* *
894817 TGGTTATCGATCGATTTTGTTTAATGCATATGTTGCATTTTCGTATCAGTACCTTTGTGTACTTT
1 TGGTTATCAATCGATTTTGTTTAATGCATATGTTGCATTTTCATATCAGTACCTTTGTGTACTTT
894882 C
66 C
894883 AGCACTATGT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
77 27 0.43
78 36 0.57
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (77 bp):
TGGTTATCAATCGATTTTGTTTAATGCATATGTTGCATTTTCATATCAGTACCTTTGTGTACTTT
CGATACTATATG
Found at i:901927 original size:77 final size:77
Alignment explanation
Indices: 901846--901994 Score: 262
Period size: 77 Copynumber: 1.9 Consensus size: 77
901836 GAGCGATGGT
* * *
901846 TATCGATCGATTTTGTTTAATGCATATGTTGCATTTTCGTATCAATACCTTTGTGTACTTTCGGC
1 TATCGATCAATTTTGTTTAATGCATACGTTGCATTTTCGTATCAATACCTTTGTGTACTTTCAGC
901911 ACTATGTGTGGC
66 ACTATGTGTGGC
*
901923 TATCGATCAATTTTGTTTAATGCATACGTTGCATTTTCGTATCAGTACCTTTGTGTACTTTCAGC
1 TATCGATCAATTTTGTTTAATGCATACGTTGCATTTTCGTATCAATACCTTTGTGTACTTTCAGC
901988 ACTATGT
66 ACTATGT
901995 TTGCATGCAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (77 bp):
TATCGATCAATTTTGTTTAATGCATACGTTGCATTTTCGTATCAATACCTTTGTGTACTTTCAGC
ACTATGTGTGGC
Found at i:906056 original size:60 final size:60
Alignment explanation
Indices: 905905--906059 Score: 152
Period size: 60 Copynumber: 2.6 Consensus size: 60
905895 ATTTTACTTC
* * *
905905 AATTTTTAAATATTCTAATTTCATCCTTAAACTATGACTATTATTCTAAATTAATCTTCA
1 AATTTTTAAATATTTTAATTTCATCCTCAAACTATGACTATTATTCTAAATTAATCTCCA
* * * * * * * * * *
905965 ATTTTTTTAACATCTCAGTTTCATCCCCAAACTATGACCT-TTGTTTTAAATTGATCTCCAA
1 AATTTTTAAATATTTTAATTTCATCCTCAAACTATGA-CTATTATTCTAAATTAATCTCC-A
*
906026 AATTTTTGAATATTTTAATTTCAT-CTCAAACTAT
1 AATTTTTAAATATTTTAATTTCATCCTCAAACTAT
906060 ATATACATAC
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
60 52 0.71
61 21 0.29
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (60 bp):
AATTTTTAAATATTTTAATTTCATCCTCAAACTATGACTATTATTCTAAATTAATCTCCA
Found at i:906617 original size:35 final size:35
Alignment explanation
Indices: 906566--906641 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
906556 AACACAACCC
*
906566 TCAATTTTATTCTAAACCCCAAATACCAAAATAAT
1 TCAATTATATTCTAAACCCCAAATACCAAAATAAT
* * * *
906601 TCAATTATATTTTAAACCTCAAATTCTAAAATAAT
1 TCAATTATATTCTAAACCCCAAATACCAAAATAAT
*
906636 TTAATT
1 TCAATT
906642 CAGGGTTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATACCAAAATAAT
Found at i:906689 original size:35 final size:35
Alignment explanation
Indices: 906638--906712 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
906628 AAAATAATTT
*
906638 AATTCAGGGTTTAGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
* *
906673 AATTTAGGGTTTAGAATATAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
906708 AATTT
1 AATTT
906713 TGAACATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
Found at i:909911 original size:24 final size:26
Alignment explanation
Indices: 909866--909917 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
909856 CGTTCGTGAA
*
909866 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
909892 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
909916 CG
1 CG
909918 AACAGAGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:910324 original size:16 final size:16
Alignment explanation
Indices: 910299--910339 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
910289 AAAATAATTT
910299 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
910315 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
910331 T-TT-ATTTAT
1 TGTTCATTTAT
910340 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:911595 original size:31 final size:31
Alignment explanation
Indices: 911559--911618 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
911549 AACTTAAAAG
*
911559 AGTTTTGCAATACT-AAGATTTAAATAATTTT
1 AGTTTTACAATACTGAA-ATTTAAATAATTTT
911590 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
911619 CATACAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:912151 original size:35 final size:36
Alignment explanation
Indices: 912083--912151 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
912073 AATAATTAAA
*
912083 ATAAATATAAAAGTTTAATAATATATAAAATAATTT
1 ATAAATATAAAAGTTAAATAATATATAAAATAATTT
* *
912119 ATAACATATAAAA-TTAAAT-ATCTATAATATAAT
1 ATAA-ATATAAAAGTTAAATAATATATAAAATAAT
912152 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 12 0.41
36 9 0.31
37 8 0.28
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (36 bp):
ATAAATATAAAAGTTAAATAATATATAAAATAATTT
Found at i:912203 original size:64 final size:65
Alignment explanation
Indices: 912127--912283 Score: 243
Period size: 64 Copynumber: 2.5 Consensus size: 65
912117 TTATAACATA
912127 TAAAATTAAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTT-AAAAAATTAATA
1 TAAAATT-AATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAAATTAATA
912191 T
65 T
* *
912192 TAAAATTAATATATATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAAATTAATAT
*
912256 TAAAATTAAAATC-A-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
912284 TTAAATATAA
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
61 1 0.01
62 12 0.14
63 23 0.27
64 43 0.50
65 7 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (65 bp):
TAAAATTAATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAAATTAATAT
Found at i:912262 original size:12 final size:12
Alignment explanation
Indices: 912181--912287 Score: 83
Period size: 12 Copynumber: 8.7 Consensus size: 12
912171 ATTTATTTAA
912181 AAAATTAATATT
1 AAAATTAATATT
912193 AAAATTAATATAT
1 AAAATTAATAT-T
*
912206 ATAATATAATATT
1 AAAAT-TAATATT
912219 AAAAATTAATATT
1 -AAAATTAATATT
* * * **
912232 TAATTTATTTAAA
1 AAAATTA-ATATT
912245 AAAATTAATATT
1 AAAATTAATATT
*
912257 AAAATTAA-AAT
1 AAAATTAATATT
*
912268 CAAATATAATA-T
1 AAAAT-TAATATT
912280 AAAATTAA
1 AAAATTAA
912288 ATATAAAACC
Statistics
Matches: 74, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
11 9 0.12
12 34 0.46
13 21 0.28
14 10 0.14
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:912290 original size:12 final size:12
Alignment explanation
Indices: 912245--912295 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
912235 TTTATTTAAA
912245 AAAATT-AATATT
1 AAAATTAAATA-T
912257 AAAATTAAA-AT
1 AAAATTAAATAT
*
912268 CAAA-TATAATAT
1 AAAATTA-AATAT
912280 AAAATTAAATAT
1 AAAATTAAATAT
912292 AAAA
1 AAAA
912296 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:915068 original size:12 final size:12
Alignment explanation
Indices: 915047--915099 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
915037 ATTACGTATT
915047 TATT-TTATGTA
1 TATTATTATGTA
915058 TATTATTATGTA
1 TATTATTATGTA
*
915070 T-TTATTTTACGTA
1 TATTA--TTATGTA
*
915083 TATTATTATATA
1 TATTATTATGTA
915095 TATTA
1 TATTA
915100 CTTTATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 7 0.20
12 18 0.51
13 7 0.20
14 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (12 bp):
TATTATTATGTA
Found at i:915070 original size:25 final size:25
Alignment explanation
Indices: 915032--915115 Score: 100
Period size: 25 Copynumber: 3.4 Consensus size: 25
915022 AAGTATGTTT
*
915032 TATA-TATTACGTATTTATTTTATG
1 TATATTATTATGTATTTATTTTATG
*
915056 TATATTATTATGTATTTATTTTACG
1 TATATTATTATGTATTTATTTTATG
* *
915081 TATATTATTATATATATTACTTTAT-
1 TATATTATTATGTAT-TTATTTTATG
915106 TATATATATT
1 TATAT-TATT
915116 TATATAATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
24 4 0.08
25 37 0.71
26 11 0.21
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.60
Consensus pattern (25 bp):
TATATTATTATGTATTTATTTTATG
Found at i:915111 original size:27 final size:26
Alignment explanation
Indices: 915056--915126 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
915046 TTATTTTATG
* * *
915056 TATATTATTATGTAT-TTATTTTACG
1 TATATTATTATATATATTACTTTACA
*
915081 TATATTATTATATATATTACTTTA-T
1 TATATTATTATATATATTACTTTACA
*
915106 TATATATATT-TATATAATACT
1 TATAT-TATTATATATATTACT
915127 ACATGTATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
25 29 0.73
26 11 0.28
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (26 bp):
TATATTATTATATATATTACTTTACA
Found at i:917530 original size:11 final size:11
Alignment explanation
Indices: 917516--917601 Score: 77
Period size: 11 Copynumber: 8.0 Consensus size: 11
917506 AAAGGAAAGT
917516 AAAAAAAGAAA
1 AAAAAAAGAAA
* *
917527 AAAAATAGAAG
1 AAAAAAAGAAA
917538 AAAAAAAGAAA
1 AAAAAAAGAAA
* * * *
917549 GAGAAAACAGA
1 AAAAAAAGAAA
* *
917560 AGAAAAAGAGA
1 AAAAAAAGAAA
*
917571 AAAAACA-AAA
1 AAAAAAAGAAA
917581 AAAAAAAG-AA
1 AAAAAAAGAAA
917591 AAAAAAAGAAA
1 AAAAAAAGAAA
917602 GAAGAAAATA
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
10 18 0.32
11 39 0.68
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.01
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:917530 original size:22 final size:22
Alignment explanation
Indices: 917516--917609 Score: 88
Period size: 22 Copynumber: 4.3 Consensus size: 22
917506 AAAGGAAAGT
*
917516 AAAAAAAGAAAAAAAATAGAAG
1 AAAAAAAGAAAAAAAAGAGAAG
*
917538 AAAAAAAGAAAGAGAAAACAGAAG
1 AAAAAAAGAAA-A-AAAAGAGAAG
* *
917562 AAAAAGAGAAAAAACA-A-AA-
1 AAAAAAAGAAAAAAAAGAGAAG
917581 AAAAAAAGAAAAAAAA-AGAAAG
1 AAAAAAAGAAAAAAAAGAG-AAG
*
917603 AAGAAAA
1 AAAAAAA
917610 TAGACATATC
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 15 0.25
20 2 0.03
21 3 0.05
22 20 0.33
23 2 0.03
24 19 0.31
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.01
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAAGAGAAG
Found at i:918289 original size:28 final size:28
Alignment explanation
Indices: 918257--918330 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
918247 GCCAACCCGG
*
918257 AACACATTGCCTCCCCAAATCAACCTGA
1 AACACATTACCTCCCCAAATCAACCTGA
* * *
918285 AACACATTACTTCCCCAAATTAATCTGA
1 AACACATTACCTCCCCAAATCAACCTGA
*
918313 AACACATTACCTTCCCAA
1 AACACATTACCTCCCCAA
918331 GGAATCCTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.38, C:0.35, G:0.04, T:0.23
Consensus pattern (28 bp):
AACACATTACCTCCCCAAATCAACCTGA
Found at i:920245 original size:21 final size:20
Alignment explanation
Indices: 920221--920284 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
920211 TTCTCTTTTC
920221 TTATTTTTTATATATAATATA
1 TTATTTTTTATATAT-ATATA
* *
920242 TTATTTTATATGTATATATA
1 TTATTTTTTATATATATATA
*
920262 CATATTTTTTATATATATATA
1 -TTATTTTTTATATATATATA
920283 TT
1 TT
920285 TTCCCATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATTTTTTATATATATATA
Found at i:920258 original size:18 final size:18
Alignment explanation
Indices: 920222--920286 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 18
920212 TCTCTTTTCT
920222 TATTTTTTATATATAATA
1 TATTTTTTATATATAATA
920240 TATTATTTTATATGTATATATACA
1 TATT-TTTTATA--TATA-AT--A
920264 TATTTTTTATATAT-ATA
1 TATTTTTTATATATAATA
920281 TATTTT
1 TATTTT
920287 CCCATTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
17 7 0.17
18 4 0.10
19 9 0.22
21 7 0.17
22 2 0.05
23 7 0.17
24 5 0.12
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TATTTTTTATATATAATA
Found at i:920271 original size:23 final size:25
Alignment explanation
Indices: 920229--920283 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
920219 TCTTATTTTT
* *
920229 TATATATAATATATTATTTTATATG
1 TATATATAACATATTATTTTATATA
920254 TATATAT-ACATATT-TTTTATATA
1 TATATATAACATATTATTTTATATA
920277 TATATAT
1 TATATAT
920284 TTTCCCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 15 0.54
24 6 0.21
25 7 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TATATATAACATATTATTTTATATA
Found at i:920276 original size:17 final size:17
Alignment explanation
Indices: 920254--920286 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
920244 ATTTTATATG
920254 TATATATACATATTTTT
1 TATATATACATATTTTT
*
920271 TATATATATATATTTT
1 TATATATACATATTTT
920287 CCCATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATACATATTTTT
Found at i:920396 original size:11 final size:12
Alignment explanation
Indices: 920369--920397 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
920359 TTACTACATT
920369 TTTTTGTTTCAA
1 TTTTTGTTTCAA
920381 TTTTTGTTTCAA
1 TTTTTGTTTCAA
920393 TTTTT
1 TTTTT
920398 TATTTTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTGTTTCAA
Found at i:925949 original size:72 final size:72
Alignment explanation
Indices: 925850--926204 Score: 532
Period size: 72 Copynumber: 4.9 Consensus size: 72
925840 TACAGATGAT
*
925850 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAGGATTTATTTCCCTCAAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
*
925915 ATAGACC
66 ACAGACC
* * *
925922 TTGTCTCACTTGAGACTATTTTACTTGAAAGAGGATTTCTTTCCCTCAAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
925987 ACAGACC
66 ACAGACC
* * * **
925994 TTTTCTCACTTGAGACTGTTTTACTT-AAAAAAGATTTATTTCTCTTGAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
*
926058 ACAAACC
66 ACAGACC
* * **
926065 TTGTCTCACTTGAGACTGTTTTACTTGAAAGCAGATTTATCTCCCTCAAGATTGTTTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
*
926130 ACAGACT
66 ACAGACC
* **
926137 TTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
926202 ACA
66 ACA
926205 ATATTTTATA
Statistics
Matches: 256, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
71 63 0.25
72 193 0.75
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (72 bp):
TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
ACAGACC
Found at i:926021 original size:36 final size:36
Alignment explanation
Indices: 925853--926161 Score: 175
Period size: 36 Copynumber: 8.6 Consensus size: 36
925843 AGATGATTTG
* *
925853 TCTCACTTGAGACTGTTTTACTTGAAAGAGGA-TTTA
1 TCTCACTTGAGACTGTTTTACTTAAAACA-GACTTTA
* * ** * * * * *
925889 TTTCCCTCAAGATTGTCATT-CTTAAAATAGACCTTG
1 TCTCACTTGAGACTGT-TTTACTTAAAACAGACTTTA
* * * *
925925 TCTCACTTGAGACTATTTTACTTGAAAGAGGA-TTTC
1 TCTCACTTGAGACTGTTTTACTTAAAACA-GACTTTA
* * ** * *
925961 TTTCCCTCAAGATTGTCATT-CTTAAAACAGACCTTT-
1 TCTCACTTGAGACTGT-TTTACTTAAAACAGA-CTTTA
*
925997 TCTCACTTGAGACTGTTTTACTTAAAAAAGA-TTTA
1 TCTCACTTGAGACTGTTTTACTTAAAACAGACTTTA
* * * * * * *
926032 TTTCTCTTGAGATTGTCATT-CTTAAAACAAACCTTG
1 TCTCACTTGAGACTGT-TTTACTTAAAACAGACTTTA
*
926068 TCTCACTTGAGACTGTTTTACTTGAAAGCAGA-TTTA
1 TCTCACTTGAGACTGTTTTACTT-AAAACAGACTTTA
* ** * * *
926104 TCTCCCTCAAGATTGTTTTTCTTAAAACAGACTTTG
1 TCTCACTTGAGACTGTTTTACTTAAAACAGACTTTA
926140 TCTCACTTGAGACTGTTTTACT
1 TCTCACTTGAGACTGTTTTACT
926162 CGAAAGAAGA
Statistics
Matches: 194, Mismatches: 65, Indels: 28
0.68 0.23 0.10
Matches are distributed among these distances:
34 3 0.02
35 39 0.20
36 137 0.71
37 15 0.08
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
TCTCACTTGAGACTGTTTTACTTAAAACAGACTTTA
Found at i:926091 original size:143 final size:143
Alignment explanation
Indices: 925849--926205 Score: 529
Period size: 143 Copynumber: 2.5 Consensus size: 143
925839 ATACAGATGA
*
925849 TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAGGATTTATTTCCCTCAAGATTGTCATTCTTAA
1 TTTGTCTCACTTGAGACTGTTTTACTT-AAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAA
* * * *
925914 AATAGACCTTGTCTCACTTGAGACTATTTTACTTGAAAG-AGGATTTCTTTCCCTCAAGATTGTC
65 AACAAACCTTGTCTCACTTGAGACTATTTTACTTGAAAGCA-GATTTATCTCCCTCAAGATTGTC
925978 ATTCTTAAAACAGACC
129 ATTCTTAAAACAGA-C
* * **
925994 TTT-TCTCACTTGAGACTGTTTTACTTAAAAAAGATTTATTTCTCTTGAGATTGTCATTCTTAAA
1 TTTGTCTCACTTGAGACTGTTTTACTTAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
* **
926058 ACAAACCTTGTCTCACTTGAGACTGTTTTACTTGAAAGCAGATTTATCTCCCTCAAGATTGTTTT
66 ACAAACCTTGTCTCACTTGAGACTATTTTACTTGAAAGCAGATTTATCTCCCTCAAGATTGTCAT
926123 TCTTAAAACAGAC
131 TCTTAAAACAGAC
* **
926136 TTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAA
1 TTTGTCTCACTTGAGACTGTTTTACT-TAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAA
926201 AACAA
65 AACAA
926206 TATTTTATAT
Statistics
Matches: 190, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
142 4 0.02
143 123 0.65
144 60 0.32
145 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (143 bp):
TTTGTCTCACTTGAGACTGTTTTACTTAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
ACAAACCTTGTCTCACTTGAGACTATTTTACTTGAAAGCAGATTTATCTCCCTCAAGATTGTCAT
TCTTAAAACAGAC
Found at i:926193 original size:36 final size:35
Alignment explanation
Indices: 926081--926194 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 35
926071 CACTTGAGAC
*
926081 TGTTTTACTTGAAAGCAGATTTATCTCCCTCAAGAT
1 TGTTTTAC-TGAAAGAAGATTTATCTCCCTCAAGAT
* * * * ** *
926117 TGTTTTTCTTAAA-ACAGACTTTGTCTCACTTGAGAC
1 TGTTTTACTGAAAGA-AGA-TTTATCTCCCTCAAGAT
*
926153 TGTTTTACTCGAAAGAAGATTTATTTCCCTCAAGAT
1 TGTTTTACT-GAAAGAAGATTTATCTCCCTCAAGAT
926189 TGTTTT
1 TGTTTT
926195 TCTTAAAACA
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
35 7 0.12
36 44 0.76
37 6 0.10
38 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (35 bp):
TGTTTTACTGAAAGAAGATTTATCTCCCTCAAGAT
Found at i:926336 original size:36 final size:36
Alignment explanation
Indices: 926291--926592 Score: 144
Period size: 36 Copynumber: 8.8 Consensus size: 36
926281 TAAACATTGA
*
926291 AAACA-TTTCCCTTGAAATGAATTTTGTCTCTCTTG
1 AAACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTG
* * *
926326 AAATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
1 AAACAGTTTCCCTTGAAA-TAAATTTTGTCTCTCTTG
* * *
926363 AGACAGTTTCTCTTGAAACATAAA--------C-ATTG
1 AAACAGTTTCCCTTG-AA-ATAAATTTTGTCTCTCTTG
* *
926392 AAAACA-TTTCCCTTAAAATGAATTTTGTCTCTCTTG
1 -AAACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTG
* * * *
926428 AGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG
1 AAACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTG
* * * **
926464 AGACAGTTTCTCTTGAAACATAAA------C-AT-TAA
1 AAACAGTTTCCCTTG-AA-ATAAATTTTGTCTCTCTTG
*
926494 AAACA-TTTCCCTTGAAATGAATTTTGTCTCTCTT-
1 AAACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTG
* * *
926528 AAGATAGTTTCCCTTGAAACAAATTTTGTCTC-CGTAG
1 AA-ACAGTTTCCCTTGAAATAAATTTTGTCTCTC-TTG
* * *
926565 AGACAGTTTCTCTTGAAAAAAATCTTTG
1 AAACAGTTTCCCTTGAAATAAAT-TTTG
926593 AAATTGTTTC
Statistics
Matches: 197, Mismatches: 40, Indels: 58
0.67 0.14 0.20
Matches are distributed among these distances:
27 8 0.04
28 4 0.02
29 18 0.09
30 10 0.05
32 1 0.01
33 1 0.01
34 3 0.02
35 12 0.06
36 96 0.49
37 34 0.17
38 9 0.05
39 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (36 bp):
AAACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTG
Found at i:926363 original size:37 final size:37
Alignment explanation
Indices: 926291--926382 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
926281 TAAACATTGA
** *
926291 AAACA-TTTCCCTTGAAA-TGAATTTTGTCTCTCTTG
1 AAACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
*
926326 AAATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
1 AAACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
* *
926363 AGACAGTTTCTCTTGAAACA
1 AAACAGTTTCCCTTGAAACA
926383 TAAACATTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 4 0.08
36 12 0.25
37 32 0.67
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (37 bp):
AAACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
Found at i:926512 original size:101 final size:102
Alignment explanation
Indices: 926218--926582 Score: 626
Period size: 101 Copynumber: 3.6 Consensus size: 102
926208 TTTTATATCG
* *
926218 CTTGAGATAGTTTCCCTCGAAACATAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATA
1 CTTGAGATAGTTTCCCTTGAAAC--AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
926283 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
64 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
*
926322 CTTGAAATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
*
926387 CATTGAAAACATTTCCCTTAAAATGAATTTTGTCTCT
66 CATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
926424 CTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
*
926488 CATTAAAAACATTTCCCTTGAAATGAATTTTGTCTCT
66 CATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
* * *
926525 CTTAAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCGTAGAGACAGTTTCTCTTGAAA
1 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
926583 AAAATCTTTG
Statistics
Matches: 251, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
101 131 0.52
102 99 0.39
104 21 0.08
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
CATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
Found at i:926629 original size:36 final size:36
Alignment explanation
Indices: 926589--926685 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 36
926579 GAAAAAAATC
926589 TTTGAAATTGTTTCTCTTGGAACACAAAATG-AAACA
1 TTTGAAATTGTTTCTCTTGGAACACAAAA-GAAAACA
*
926625 TTTGAAATTGTTTCTC-TGGAAGCACAAAAGAAAACC
1 TTTGAAATTGTTTCTCTTGGAA-CACAAAAGAAAACA
* *
926661 TTTGAACA-TGTTTATCTTGAAACAC
1 TTTGAA-ATTGTTTCTCTTGGAACAC
926686 TGAACCTATG
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
35 6 0.11
36 43 0.80
37 5 0.09
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (36 bp):
TTTGAAATTGTTTCTCTTGGAACACAAAAGAAAACA
Found at i:928144 original size:2 final size:2
Alignment explanation
Indices: 928139--928196 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
928129 TCATATTTTT
* * *
928139 TA TA TA TA -A TA TA T- TA T- TT TA TA TG TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
928178 TT TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
928197 TCATTTATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:928168 original size:18 final size:18
Alignment explanation
Indices: 928131--928172 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
928121 TTATCTTTTC
928131 ATATTTTTTATATATAAT
1 ATATTTTTTATATATAAT
*
928149 ATATTATTTTATATGTATAT
1 ATATT-TTTTATATATA-AT
928169 ATAT
1 ATAT
928173 ACATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 10 0.48
20 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATATTTTTTATATATAAT
Found at i:929521 original size:54 final size:55
Alignment explanation
Indices: 929334--929639 Score: 320
Period size: 54 Copynumber: 5.6 Consensus size: 55
929324 TGTTTTTTTG
* ** ** * *
929334 GAAACTAAGTCTG-ATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTT-AAG
1 GAAACTAAGCCTGAATTTTCAGGGGTTTCTTGA-TGTTTTCAAATGA-ATTTTCAAA
* ** * **
929389 GAAACTAAGTCTG-ATTTTCAGAAGTTTCTTGATGATTTTTAAATGACCTTTCAAA
1 GAAACTAAGCCTGAATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTTCAAA
* * *
929444 GAAACCAAGTCT-AATTTTAAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAA
1 GAAACTAAGCCTGAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAA
* *
929498 GAAATTAAGCCTGAATTTT-AGGGGTTTCTTGATGTTTTCAAATAAATTTTCAAA
1 GAAACTAAGCCTGAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAA
* * *
929552 GAAATTAAGCCTG-ATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTTAAA
1 GAAACTAAGCCTGAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAA
* * *
929606 GAAACTAAGCCT-AATTTTTAAGAGTTTCTTGATG
1 GAAACTAAGCCTGAATTTTCAGGGGTTTCTTGATG
929640 ATAACTGAAA
Statistics
Matches: 221, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
53 5 0.02
54 137 0.62
55 79 0.36
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (55 bp):
GAAACTAAGCCTGAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAA
Found at i:929576 original size:108 final size:108
Alignment explanation
Indices: 929334--929641 Score: 361
Period size: 108 Copynumber: 2.8 Consensus size: 108
929324 TGTTTTTTTG
** * * * *
929334 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAGGAAACTAAGT
1 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGA-TATTTTCAAATGA-ATTTTAAAGAAACTAAGC
* * * *
929399 CTG-ATTTTCAGAAGTTTCTTGATGATTTTTAAATGACCTTTCAAA
64 CTGAATTTT-AGGAGTTTCTTGATGATTTTCAAATAAACTTTCAAA
* * * * *
929444 GAAACCAAGTCTAATTTTAAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAATTAAGCC
1 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTT-AAAGAAACTAAGCC
* *
929509 TGAATTTTAGGGGTTTCTTGATG-TTTTCAAATAAATTTTCAAA
65 TGAATTTTAGGAGTTTCTTGATGATTTTCAAATAAACTTTCAAA
* *
929552 GAAATTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTTAAAGAAACTAAGCC
1 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAA-TTTTAAAGAAACTAAGCC
*
929617 T-AATTTTTAAGAGTTTCTTGATGAT
65 TGAA-TTTTAGGAGTTTCTTGATGAT
929642 AACTGAAAAA
Statistics
Matches: 167, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
107 2 0.01
108 91 0.54
109 42 0.25
110 32 0.19
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (108 bp):
GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAAAGAAACTAAGCCT
GAATTTTAGGAGTTTCTTGATGATTTTCAAATAAACTTTCAAA
Found at i:930156 original size:275 final size:274
Alignment explanation
Indices: 929662--930204 Score: 874
Period size: 275 Copynumber: 2.0 Consensus size: 274
929652 TGAAAGATTT
*
929662 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCCGGGCCATCAGTAAGTC
1 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCCGGGACATCAGTAAGTC
*
929727 TTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGTGTTTCGAGCAAGATGATAAGTCAT
66 TTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGTGTTTCGAGCAAGATAATAAGTCAT
* * * *
929792 TCGGGCCATCCATATGACCTTCGGGCAGGATGTTTTCAAATGAGTTCTTAAAAATTAAGCCTGAT
131 TCGGACCATCCATAAGACCTTCAGGCAGGATGTTTTCAAATGAGTTCTTAAAAACTAAGCCTGAT
*
929857 TTTCAGAGGTTTCTTAATGATTATCTCCAAAGAATTTTTAAAAGGAAGCTAAGCCTAATTTTTAG
196 TTTCAGAGGTTTCTTAACGATTATCTCCAAAGAATTTTTAAAA-GAAGCTAAGCCTAATTTTTAG
929922 GGGTTCCTTAACAGC
260 GGGTTCCTTAACAGC
* *
929937 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCATT-TGGGACATCAGTAAGT
1 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTC-TTCCGGGACATCAGTAAGT
* * *
930001 CTTTCGAGCGTGATGTTTAAATCTTTC-AGGTCATCTATAAGTGTTTCGAGCAAGATAATAAGTC
65 CTTTCGAGCATGATGCTTAAATCCTTCGA-GTCATCTATAAGTGTTTCGAGCAAGATAATAAGTC
* * * *
930065 CTTCGGACCATCTATAAGACCTTCAGGCAGGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTG
129 ATTCGGACCATCCATAAGACCTTCAGGCAGGATGTTTTCAAATGAGTTCTTAAAAACTAAGCCTG
* * *
930130 ATTTTCAGGGGTTTCTTGACGATTATCTCCAAAGAATTTTTAAAATAAGCTAAGCCTAATTTTTA
194 ATTTTCAGAGGTTTCTTAACGATTATCTCCAAAGAATTTTTAAAAGAAGCTAAGCCTAATTTTTA
930195 GGGGTTCCTT
259 GGGGTTCCTT
930205 GATGACAACT
Statistics
Matches: 247, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
274 30 0.12
275 215 0.87
276 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (274 bp):
TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCCGGGACATCAGTAAGTC
TTTCGAGCATGATGCTTAAATCCTTCGAGTCATCTATAAGTGTTTCGAGCAAGATAATAAGTCAT
TCGGACCATCCATAAGACCTTCAGGCAGGATGTTTTCAAATGAGTTCTTAAAAACTAAGCCTGAT
TTTCAGAGGTTTCTTAACGATTATCTCCAAAGAATTTTTAAAAGAAGCTAAGCCTAATTTTTAGG
GGTTCCTTAACAGC
Found at i:930915 original size:139 final size:139
Alignment explanation
Indices: 930665--931066 Score: 599
Period size: 139 Copynumber: 2.9 Consensus size: 139
930655 AGATGAACCA
** *
930665 ATCAACATTTTAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGCTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* * * *
930730 AATGAGAAGAGCTTGTTCGACCCTAGCTCGATTCATCTCATATGGAGTTGAATCAGCAACACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
*
930795 GCTCGAGGG
131 ACTCGAGGG
* *
930804 ATCAACATTTCCAATGTAGAGTTCATAATGAGAAGAACTTATCCGATGAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* *
930869 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTAAATCAGCAATACCTC
66 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
930934 ACTCGAGGG
131 ACTCGAGGG
* * *
930943 ATCAACATTTCCAGTGGAGAGTTCATAATGATAAGAACTCATCTGAT-AAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAA-GGAGAAGAAGTTCA
* * * * *
931007 TAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCGCATAAGGAGTTGGATCAGCA
65 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCACATATGGAGTTGAATCAGCA
931067 TTACCTTGGA
Statistics
Matches: 238, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
138 2 0.01
139 215 0.90
140 21 0.09
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (139 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
ACTCGAGGG
Found at i:931182 original size:20 final size:19
Alignment explanation
Indices: 931120--931183 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
931110 CCAGTGGATA
931120 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
931139 CATCCGATGATGGAGAAGAA--
1 -GTTC-ATAAT-GAGAAGAACT
931159 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
931179 GTTCA
1 GTTCA
931184 ACCGTGGTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
20 7 0.21
21 4 0.12
22 8 0.24
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:932432 original size:25 final size:25
Alignment explanation
Indices: 932394--932462 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
932384 AAGTATATTT
* *
932394 TATA-TATTACGTATTTATTTTATG
1 TATATTATTATGTATTTATTTTACG
932418 TATATTATTATGTATTTATTTTACG
1 TATATTATTATGTATTTATTTTACG
* *
932443 TATATTATTATATATATATT
1 TATATTATTATGTATTTATT
932463 ACTTTATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 4 0.10
25 36 0.90
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (25 bp):
TATATTATTATGTATTTATTTTACG
Found at i:932462 original size:29 final size:28
Alignment explanation
Indices: 932385--932485 Score: 79
Period size: 28 Copynumber: 3.6 Consensus size: 28
932375 TGTACCATTA
932385 AGTATATT-TTATATATTACGTATTTATTTT
1 AGTATATTATTATATA-TA--TATTTATTTT
* *
932415 A-TGTA-TATTAT-TATGTATTTATTTT
1 AGTATATTATTATATATATATTTATTTT
*
932440 ACGTATATTATTATATATATA-TTACTTT
1 A-GTATATTATTATATATATATTTATTTT
*
932468 ATTATATATATT-TATATA
1 AGTATAT-TATTATATATA
932486 ATACTAAATG
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
25 11 0.19
27 15 0.25
28 20 0.34
29 12 0.20
30 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (28 bp):
AGTATATTATTATATATATATTTATTTT
Found at i:937656 original size:13 final size:13
Alignment explanation
Indices: 937638--937678 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
937628 TTTGGTAATC
937638 CCCGCCCCGATTA
1 CCCGCCCCGATTA
937651 CCCGCCCCGATTA
1 CCCGCCCCGATTA
*
937664 CCCGTCCCGA-TA
1 CCCGCCCCGATTA
937676 CCC
1 CCC
937679 AACCCGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 5 0.19
13 22 0.81
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:937760 original size:19 final size:19
Alignment explanation
Indices: 937736--937775 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
937726 AATAAATTTA
937736 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
937755 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
937774 AT
1 AT
937776 ATATACCCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:937825 original size:12 final size:12
Alignment explanation
Indices: 937778--937831 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
937768 ATATATATAT
* *
937778 ATACCCGGCCCG
1 ATACCCGACCCA
* *
937790 ATTCCCGGCCCA
1 ATACCCGACCCA
*
937802 ATA-CCAACCCA
1 ATACCCGACCCA
937813 ATACCCGACCCA
1 ATACCCGACCCA
937825 ATACCCG
1 ATACCCG
937832 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 9 0.26
12 26 0.74
ACGTcount: A:0.28, C:0.48, G:0.13, T:0.11
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:938925 original size:60 final size:60
Alignment explanation
Indices: 938800--938928 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
938790 AAAGAGGGTC
* * * * *
938800 ATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTAAGGATTAATTTAAAATAAGAATT
1 ATAGTTTAGGGATAAAATTAAAATATTCAAAAATGTAAGAACTAATTTAAAATAAGAATT
* * * **
938860 GTAGTTT-GAGGATAAAATTAAAATATTTAAAAATGTAAGAACTGATTTAAAATAAGGCTT
1 ATAGTTTAG-GGATAAAATTAAAATATTCAAAAATGTAAGAACTAATTTAAAATAAGAATT
938920 ATAGTTTAG
1 ATAGTTTAG
938929 AGACATATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
59 1 0.02
60 54 0.96
61 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.35
Consensus pattern (60 bp):
ATAGTTTAGGGATAAAATTAAAATATTCAAAAATGTAAGAACTAATTTAAAATAAGAATT
Found at i:949990 original size:4 final size:4
Alignment explanation
Indices: 949961--950078 Score: 95
Period size: 4 Copynumber: 29.2 Consensus size: 4
949951 AAAAAACAAT
* * * *
949961 AATA AA-A AAT- AATT AATA TAAT- AATA AATAA AATG GATA AATA TAGATC
1 AATA AATA AATA AATA AATA -AATA AATA AAT-A AATA AATA AATA -A-ATA
950010 AATAA AATA AA-A AA-A GAA-A AATA AATA AATAA AATA AATA AATA AATA
1 AAT-A AATA AATA AATA -AATA AATA AATA AAT-A AATA AATA AATA AATA
950058 AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA A
950079 GGCTAAATAT
Statistics
Matches: 96, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
3 15 0.16
4 63 0.66
5 16 0.17
6 2 0.02
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:951094 original size:19 final size:20
Alignment explanation
Indices: 951070--951111 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
951060 CTTCTAGCCA
951070 TTGAGATCGC-CTCTGGCCG
1 TTGAGATCGCTCTCTGGCCG
* *
951089 TTGAGATTGCTTTCTGGCCG
1 TTGAGATCGCTCTCTGGCCG
951109 TTG
1 TTG
951112 GATTGGGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.10, C:0.24, G:0.31, T:0.36
Consensus pattern (20 bp):
TTGAGATCGCTCTCTGGCCG
Found at i:951258 original size:28 final size:28
Alignment explanation
Indices: 951226--951281 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
951216 ACTTTTACTG
*
951226 GCTGGGTCAAGCCTACCTGATCGGGTTT
1 GCTGGGTCAAGCCTACCCGATCGGGTTT
* * *
951254 GCTGGGTCAGGCTTACCCGATTGGGTTT
1 GCTGGGTCAAGCCTACCCGATCGGGTTT
951282 TCCATGGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.12, C:0.23, G:0.34, T:0.30
Consensus pattern (28 bp):
GCTGGGTCAAGCCTACCCGATCGGGTTT
Found at i:951408 original size:25 final size:25
Alignment explanation
Indices: 951378--951427 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
951368 TAATAATTAT
951378 TATATATATAAAAATTTTCCAAAAACC
1 TATATA-ATAAAAATTTT-CAAAAACC
* *
951405 TATATAATATATATTTTCAAAAA
1 TATATAATAAAAATTTTCAAAAA
951428 TGTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 9 0.43
27 6 0.29
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (25 bp):
TATATAATAAAAATTTTCAAAAACC
Found at i:951427 original size:36 final size:35
Alignment explanation
Indices: 951398--951657 Score: 171
Period size: 36 Copynumber: 7.6 Consensus size: 35
951388 AAAATTTTCC
951398 AAAAACCTATATA-ATATATATTTTCAAAAATGTTT
1 AAAAA-CTATATATATATATATTTTCAAAAATGTTT
* * *
951433 TAAAACTATATAT-TATATA-TGT------T-TTC
1 AAAAACTATATATATATATATTTTCAAAAATGTTT
* *
951459 AAAAACTATAT-TATATATATATTTCAAAATGTTTTT
1 AAAAACTATATATATATATAT-TTTCAAAA-ATGTTT
* *
951495 AAAAATTATATAT-TATATAAGTTTTC-AAAA--TTA
1 AAAAACTATATATATATAT-A-TTTTCAAAAATGTTT
*
951528 AAAAACTATA-ATATATATATTTCCAAAATAT-TTT
1 AAAAACTATATATATATATATTTTCAAAA-ATGTTT
951562 AAAAACTATATAATATATATATTTTC-AAAATGCTTT
1 AAAAACTATAT-ATATATATATTTTCAAAAATG-TTT
*
951598 CAAAAACTATATATTATATATATATTTCAAAAATCATTT
1 -AAAAACTATATA-TATATATAT-TTTCAAAAAT-GTTT
* *
951637 GCAATA-TATATATATATATAT
1 -AAAAACTATATATATATATAT
951658 ATATACATAT
Statistics
Matches: 180, Mismatches: 17, Indels: 54
0.72 0.07 0.22
Matches are distributed among these distances:
25 1 0.01
26 18 0.10
27 1 0.01
28 2 0.01
31 4 0.02
32 6 0.03
33 19 0.11
34 27 0.15
35 8 0.04
36 37 0.21
37 35 0.19
38 11 0.06
39 11 0.06
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (35 bp):
AAAAACTATATATATATATATTTTCAAAAATGTTT
Found at i:951468 original size:24 final size:25
Alignment explanation
Indices: 951441--951487 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
951431 TTTAAAACTA
*
951441 TATATTATATATGT-TTTCAAAAAC
1 TATATTATATATATATTTCAAAAAC
951465 TATATTATATATATATTTCAAAA
1 TATATTATATATATATTTCAAAA
951488 TGTTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (25 bp):
TATATTATATATATATTTCAAAAAC
Found at i:951475 original size:26 final size:26
Alignment explanation
Indices: 951427--951487 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
951417 ATTTTCAAAA
951427 ATGTTTT--AAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
951451 ATGTTTTCAAAAACTATAT-TATATAT
1 ATGTTTTCAAAAACTATATAT-TATAT
*
951477 AT-ATTTCAAAA
1 ATGTTTTCAAAA
951488 TGTTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 7 0.21
25 9 0.27
26 17 0.52
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATATTATAT
Found at i:951562 original size:67 final size:68
Alignment explanation
Indices: 951398--951629 Score: 202
Period size: 67 Copynumber: 3.4 Consensus size: 68
951388 AAAATTTTCC
* *
951398 AAAAACCTATATA-ATATATATTTTCAAAAATG-TTTT-AAAACTATAT-AT-TATATATGTT--
1 AAAAAACTATATATATATATA-TTTC-AAAATGATTTTAAAAACTATATAATATATATATTTTCA
951456 ---TT
64 AAATT
* * * *
951458 CAAAAACTATATTATATATATATTTCAAAATGTTTTTAAAAATTATATATTATATA-AGTTTTCA
1 AAAAAACTATA-TATATATATATTTCAAAATGATTTTAAAAACTATATAATATATATA-TTTTCA
951522 AAATT
64 AAATT
951527 AAAAAACTATA-ATATATATATTTCCAAAAT-ATTTTAAAAACTATATAATATATATATTTTCAA
1 AAAAAACTATATATATATATATTT-CAAAATGATTTTAAAAACTATATAATATATATATTTTCAA
951590 AATGCTTT
65 AA----TT
*
951598 CAAAAACTATATATTATATATATATTTCAAAA
1 AAAAAAC--TATA-TATATATATATTTCAAAA
951630 ATCATTTGCA
Statistics
Matches: 140, Mismatches: 10, Indels: 30
0.78 0.06 0.17
Matches are distributed among these distances:
60 15 0.11
61 10 0.07
62 16 0.11
63 2 0.01
64 7 0.05
67 42 0.30
68 7 0.05
69 12 0.09
71 8 0.06
73 4 0.03
74 5 0.04
75 12 0.09
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (68 bp):
AAAAAACTATATATATATATATTTCAAAATGATTTTAAAAACTATATAATATATATATTTTCAAA
ATT
Found at i:951631 original size:39 final size:37
Alignment explanation
Indices: 951455--951662 Score: 179
Period size: 37 Copynumber: 5.7 Consensus size: 37
951445 TTATATATGT
*
951455 TTTCAAAAAC--TATATTATATATATATTTCAAAATGT
1 TTTCAAAAACTATATATTATATATATATTTCAAAAT-C
* *
951491 TTTTAAAAATTATATATTATATA-AGT-TTTCAAAA--
1 TTTCAAAAACTATATATTATATATA-TATTTCAAAATC
* * *
951525 -TTAAAAAACTATA-A-TATATATAT-TTCCAAAATA
1 TTTCAAAAACTATATATTATATATATATTTCAAAATC
* *
951558 TTTTAAAAACTATATAATATATATAT-TTTCAAAATGC
1 TTTCAAAAACTATATATTATATATATATTTCAAAAT-C
951595 TTTCAAAAACTATATATTATATATATATTTCAAAAATC
1 TTTCAAAAACTATATATTATATATATATTTC-AAAATC
*
951633 ATTTGCAATATA-TATATATATATATATATA
1 -TTT-CAA-AAACTATATAT-TATATATATA
951663 CATATATATA
Statistics
Matches: 145, Mismatches: 11, Indels: 27
0.79 0.06 0.15
Matches are distributed among these distances:
31 14 0.10
32 2 0.01
33 11 0.08
34 12 0.08
35 1 0.01
36 25 0.17
37 33 0.23
38 17 0.12
39 8 0.06
40 10 0.07
41 12 0.08
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (37 bp):
TTTCAAAAACTATATATTATATATATATTTCAAAATC
Found at i:951647 original size:2 final size:2
Alignment explanation
Indices: 951640--951676 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
951630 ATCATTTGCA
*
951640 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
951677 ATAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:953426 original size:13 final size:12
Alignment explanation
Indices: 953407--953440 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
953397 ATGTAATGTG
953407 ATTTTTTTTCAA
1 ATTTTTTTTCAA
953419 ATTTTTTTTCAA
1 ATTTTTTTTCAA
*
953431 AATTTTTTTC
1 ATTTTTTTTC
953441 TCTTTAGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTTTTCAA
Found at i:954277 original size:13 final size:13
Alignment explanation
Indices: 954259--954292 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
954249 TGTCACAGTC
954259 ATATTTTAAAAAA
1 ATATTTTAAAAAA
*
954272 ATATTTTTAAAAA
1 ATATTTTAAAAAA
*
954285 ATACTTTA
1 ATATTTTA
954293 TTTTCTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATTTTAAAAAA
Found at i:954312 original size:2 final size:2
Alignment explanation
Indices: 954307--954331 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
954297 CTTAAAAAAA
954307 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
954332 AATGTGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:956628 original size:17 final size:17
Alignment explanation
Indices: 956606--956640 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
956596 TAACATCATT
956606 TCTGCTCGTCGACGTTC
1 TCTGCTCGTCGACGTTC
*
956623 TCTGCTCGTCGTCGTTC
1 TCTGCTCGTCGACGTTC
956640 T
1 T
956641 GCCCATCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.34, G:0.23, T:0.40
Consensus pattern (17 bp):
TCTGCTCGTCGACGTTC
Found at i:956641 original size:15 final size:16
Alignment explanation
Indices: 956604--956642 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
956594 GTTAACATCA
956604 TTTCTGCTCGTCGACG
1 TTTCTGCTCGTCGACG
*
956620 TTCTCTGCTCGTCGTCG
1 TT-TCTGCTCGTCGACG
956637 -TTCTGC
1 TTTCTGC
956643 CCATCTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 3 0.14
17 13 0.62
ACGTcount: A:0.03, C:0.33, G:0.23, T:0.41
Consensus pattern (16 bp):
TTTCTGCTCGTCGACG
Found at i:958361 original size:130 final size:128
Alignment explanation
Indices: 958117--958362 Score: 282
Period size: 130 Copynumber: 1.9 Consensus size: 128
958107 TATTATTTCA
* * * *
958117 ATTAAAACATAAGAAATAATTCCCTTAACATAACTAGGGAGTTATTTTTTTCATTAAGTAGAAAT
1 ATTAAAACACAAGAAATAATTCCCTTAACATAACTAGAGAGTTACTTTCTTCATTAAGTAGAAAT
* ** * * **
958182 AATAATAGATTTTTTTAGTTTTTTTTTCAAATTTCTTACAAATCGAATAATCTTCTAATATTCCG
66 AATAAT--ATTTTTTTAATTTCCTTTTAAAATATCTTACAAATAAAATAATCTTCTAATATTCCG
* *
958247 ATTAAAACACAAGAAATAATTCTCTTAACATAACTAGAGAGTTACTTTCTTCTTTAA-TCAGAAA
1 ATTAAAACACAAGAAATAATTCCCTTAACATAACTAGAGAGTTACTTTCTTCATTAAGT-AGAAA
*
958311 TAATAAT-TTTTTTCCTAAATTTCCTTTTAAAATAT-TTAGAGAATAAAATAAT
65 TAATAATATTTTTT--T-AATTTCCTTTTAAAATATCTTACA-AATAAAATAAT
958363 TATAAATTCA
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
127 6 0.06
129 6 0.06
130 85 0.88
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (128 bp):
ATTAAAACACAAGAAATAATTCCCTTAACATAACTAGAGAGTTACTTTCTTCATTAAGTAGAAAT
AATAATATTTTTTTAATTTCCTTTTAAAATATCTTACAAATAAAATAATCTTCTAATATTCCG
Found at i:963899 original size:351 final size:353
Alignment explanation
Indices: 963237--963939 Score: 1099
Period size: 350 Copynumber: 2.0 Consensus size: 353
963227 TGCTCCTAGG
*
963237 CTATCTCTAGTAACAAACCTGACAGAAAGATGCTACAACAATACCTCTCAGTGTGAACTACAAAA
1 CTATCTCTAGTAACAAACCTGACAGAAAGATGCTACAACAATACCTCTCAGCGTGAACTACAAAA
* * * *
963302 TTATCCTATCGATTACGTCCTACCCCTTTTAGTCGATGAATCACTCTCTTTATCTCTAAGGCAGA
66 CTATCCTATCGATTACATCCTACCCCTTTTAGTCGATGAAACACTCTCCTTATCTCTAAGGCAGA
* * * * *
963367 TTAGAAGCTCACCATTCCAATTTAATTCCATTGGTCACATCGATCTAGCCTAACTTTCTCGATAT
131 TTAGAACCTCACCATCCCAATTTAATTCCATTGGTCACATCGACCTAGCCTAACTCTCTCAATAT
963432 TAAGCATATATACTTAGAAAACTGCTAACTCTCAAAAGCTATTACAAGTCTAAGTAATTAAAATA
196 TAAGCATATATACTTAGAAAACTGCTAACTCTCAAAAGCTATTACAAGTCTAAGTAATTAAAATA
*
963497 TAAATAATGAGAAAACAACATTTAAACATAAAAAACATCCAATAATTCGATT-ACAAAAAAT-AA
261 TAAAAAATGAGAAAACAACATTTAAACATAAAAAACATCCAATAATTCGATTAACAAAAAATAAA
* *
963560 AAATCATCTAAGCAAACCCGTGCCAAAA
326 AAATCATCTAAGAAAACCCATGCCAAAA
* *
963588 CTATCTCTAGTAACGAACCTGACAGAAAGATGCTACGACAATACCTCTCAGCGTGAACTACAAAA
1 CTATCTCTAGTAACAAACCTGACAGAAAGATGCTACAACAATACCTCTCAGCGTGAACTACAAAA
* * **
963653 CTATCCTATCGATTACATCCTA-CCCTTTTAGTTGATGAAACCCTCTCCTTATCTCTAAGGTGGA
66 CTATCCTATCGATTACATCCTACCCCTTTTAGTCGATGAAACACTCTCCTTATCTCTAAGGCAGA
* * *
963717 TTAGAACCTCATCATCCCGATTTAATTCCATTGGTCACGTCGACCTAGCCTAACTCTCTCAATAT
131 TTAGAACCTCACCATCCCAATTTAATTCCATTGGTCACATCGACCTAGCCTAACTCTCTCAATAT
* * *
963782 TAAGCATATATACTTAGAAAAC-GACTAACTCTCGAAAGTTCTTACAAGTCTAAGTAATTAAAAT
196 TAAGCATATATACTTAGAAAACTG-CTAACTCTCAAAAGCTATTACAAGTCTAAGTAATTAAAAT
* * * *
963846 ATAAAAAATGAGCAAAACAACATTTAAACATAAAAAATATTCAATCATTCGATTAACACAAAATA
260 ATAAAAAATGAG-AAAACAACATTTAAACATAAAAAACATCCAATAATTCGATTAACAAAAAATA
963911 AAAAATCATCTAAGAAAACCCATGCCAAA
324 AAAAATCATCTAAGAAAACCCATGCCAAA
963940 TAATTTAGTT
Statistics
Matches: 319, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
349 1 0.00
350 163 0.51
351 120 0.38
352 8 0.03
353 27 0.08
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.27
Consensus pattern (353 bp):
CTATCTCTAGTAACAAACCTGACAGAAAGATGCTACAACAATACCTCTCAGCGTGAACTACAAAA
CTATCCTATCGATTACATCCTACCCCTTTTAGTCGATGAAACACTCTCCTTATCTCTAAGGCAGA
TTAGAACCTCACCATCCCAATTTAATTCCATTGGTCACATCGACCTAGCCTAACTCTCTCAATAT
TAAGCATATATACTTAGAAAACTGCTAACTCTCAAAAGCTATTACAAGTCTAAGTAATTAAAATA
TAAAAAATGAGAAAACAACATTTAAACATAAAAAACATCCAATAATTCGATTAACAAAAAATAAA
AAATCATCTAAGAAAACCCATGCCAAAA
Found at i:966532 original size:62 final size:62
Alignment explanation
Indices: 966443--966563 Score: 242
Period size: 62 Copynumber: 2.0 Consensus size: 62
966433 TCATCAACGG
966443 TTGTCAAGAAAAACCTATGACCCCATGAGTCGAAATTCTATATAAACCCCAAAGATCAACAA
1 TTGTCAAGAAAAACCTATGACCCCATGAGTCGAAATTCTATATAAACCCCAAAGATCAACAA
966505 TTGTCAAGAAAAACCTATGACCCCATGAGTCGAAATTCTATATAAACCCCAAAGATCAA
1 TTGTCAAGAAAAACCTATGACCCCATGAGTCGAAATTCTATATAAACCCCAAAGATCAA
966564 TATGAATGAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (62 bp):
TTGTCAAGAAAAACCTATGACCCCATGAGTCGAAATTCTATATAAACCCCAAAGATCAACAA
Found at i:970181 original size:49 final size:49
Alignment explanation
Indices: 970109--970206 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
970099 AGCTGCAGTG
970109 TTGATAGCTTCAGCCCATAGAAATTTGGGCAATCCGGCATGTACCTCAT
1 TTGATAGCTTCAGCCCATAGAAATTTGGGCAATCCGGCATGTACCTCAT
970158 TTGATAGCTTCAGCCCATAGAAATTTGGGCAATCCGGCATGTACCTCAT
1 TTGATAGCTTCAGCCCATAGAAATTTGGGCAATCCGGCATGTACCTCAT
970207 GCTTCTGGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (49 bp):
TTGATAGCTTCAGCCCATAGAAATTTGGGCAATCCGGCATGTACCTCAT
Found at i:971291 original size:14 final size:14
Alignment explanation
Indices: 971269--971307 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
971259 ACAAGTAAAA
*
971269 TCTTTATTTCCTGT
1 TCTTGATTTCCTGT
971283 TCTTGATTTTCCTGT
1 TCTTGA-TTTCCTGT
*
971298 TCTGGATTTC
1 TCTTGATTTC
971308 GATCTGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.08, C:0.21, G:0.13, T:0.59
Consensus pattern (14 bp):
TCTTGATTTCCTGT
Found at i:971295 original size:15 final size:15
Alignment explanation
Indices: 971275--971306 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
971265 AAAATCTTTA
*
971275 TTTCCTGTTCTTGAT
1 TTTCCTGTTCTGGAT
971290 TTTCCTGTTCTGGAT
1 TTTCCTGTTCTGGAT
971305 TT
1 TT
971307 CGATCTGCCA
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:0.06, C:0.19, G:0.16, T:0.59
Consensus pattern (15 bp):
TTTCCTGTTCTGGAT
Found at i:972557 original size:37 final size:36
Alignment explanation
Indices: 972501--972620 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
972491 ATCCCATTAT
*
972501 CATTTTTC-AACAAACATTTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
972537 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
972573 CA-TTTTCAAAGAAAAATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
972608 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
972621 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 34 0.44
36 13 0.17
37 30 0.39
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:972629 original size:35 final size:36
Alignment explanation
Indices: 972518--972647 Score: 144
Period size: 35 Copynumber: 3.7 Consensus size: 36
972508 CAACAAACAT
* *
972518 TTACCAAACTTTGAAAAAC-TATTTTTCAAAGAAACAT
1 TTACCAAACTTTGAAAACCAT-TTTTTCAAAGAAA-AG
*
972555 TTACCAAACTTTGAAAACCA--TTTTCAAAGAAAAAT
1 TTACCAAACTTTGAAAACCATTTTTTCAAAG-AAAAG
***
972590 TTACCAAACTTTGAAAACCATTTTTTCAAAG-TTGG
1 TTACCAAACTTTGAAAACCATTTTTTCAAAGAAAAG
972625 TTACCAAAC-TTGAAAACCATTTT
1 TTACCAAACTTTGAAAACCATTTT
972648 AATAATTTCA
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
34 14 0.17
35 40 0.48
36 3 0.04
37 27 0.32
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (36 bp):
TTACCAAACTTTGAAAACCATTTTTTCAAAGAAAAG
Found at i:974329 original size:35 final size:35
Alignment explanation
Indices: 974280--974354 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
974270 TTTCGAAGGT
* * *
974280 GTTCGTTTAGATGTTTGTGAACAAGTTTGTTTAGC
1 GTTCGTTTAAATGTTCGTGAACAAGTTTGTTCAGC
* * *
974315 GTTCGTTTAAATGTTCGTGTACATGTTTGTTCAGT
1 GTTCGTTTAAATGTTCGTGAACAAGTTTGTTCAGC
974350 GTTCG
1 GTTCG
974355 GTTAGTGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.11, G:0.25, T:0.47
Consensus pattern (35 bp):
GTTCGTTTAAATGTTCGTGAACAAGTTTGTTCAGC
Found at i:975168 original size:20 final size:21
Alignment explanation
Indices: 975129--975170 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
975119 TTGCTTTTGG
*
975129 GGTATCGATACCCCTGCTACA
1 GGTACCGATACCCCTGCTACA
*
975150 GGTACCGATA-CCTTGCTACA
1 GGTACCGATACCCCTGCTACA
975170 G
1 G
975171 TACTACTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (21 bp):
GGTACCGATACCCCTGCTACA
Found at i:979623 original size:31 final size:31
Alignment explanation
Indices: 979585--979649 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
979575 AACTATCATC
979585 ATTGTTTGCCTGTTTAATTTTATTGATACTA
1 ATTGTTTGCCTGTTTAATTTTATTGATACTA
*
979616 ATTGTTTGCCTGTTTAATTTTATTGATAGTA
1 ATTGTTTGCCTGTTTAATTTTATTGATACTA
979647 ATT
1 ATT
979650 AATTACAGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.08, G:0.14, T:0.55
Consensus pattern (31 bp):
ATTGTTTGCCTGTTTAATTTTATTGATACTA
Found at i:980888 original size:4 final size:4
Alignment explanation
Indices: 980865--980897 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
980855 TATCGATGAT
980865 TTTA TTT- TTTA TTT- TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
980898 TTGCAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTA
Found at i:980897 original size:8 final size:7
Alignment explanation
Indices: 980864--980893 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
980854 ATATCGATGA
980864 TTTTATT
1 TTTTATT
980871 TTTTATT
1 TTTTATT
980878 TTTTATT
1 TTTTATT
980885 TATTTATT
1 T-TTTATT
980893 T
1 T
980894 ATTTTTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTATT
Found at i:986297 original size:214 final size:219
Alignment explanation
Indices: 986060--986492 Score: 815
Period size: 220 Copynumber: 2.0 Consensus size: 219
986050 TTTTTTTAAG
986060 AGAAAAAAAAACATCTGAAATTAAATTAAAAATTAATATTAATTCAAACTAAAA-AATATATC-T
1 AGAAAAAAAAACATCTGAAATTAAATTAAAAATTAATATTAATTCAAACTAAAATAATATATCTT
986123 TAAGCTTATTTATTATAATGTTGACTAATTCCC-AAAAAAAACTTATCATATTGGCATTTTCTGA
66 TAAGCTTATTTATTATAATGTTGACTAATTCCCAAAAAAAAACTTATCATATTGGCATTTTCTGA
986187 TTTGCAT-ATCGATCGTCGGATTACATTTAGATACATTA-TTGTG-TTGTGGAGGGTTTTTTCAC
131 TTTGCATAATCGATCGTCGGATTACATTTAGATACATTATTTGTGTTTGTGGAGGGTTTTTTCAC
986249 GTCGATTGAATTTGATTTGTGGTT
196 GTCGATTGAATTTGATTTGTGGTT
986273 AGAAAAAAAAACAATCTGAAATTAAATTAAAAATTAATATTAATTCAAACTAAAATAATATATCT
1 AGAAAAAAAAAC-ATCTGAAATTAAATTAAAAATTAATATTAATTCAAACTAAAATAATATATCT
986338 TTAAGCTTATTTATTATAATGTTGACTAATTCCCAAAAAAAAACTTATCATATTGGCATTTTCTG
65 TTAAGCTTATTTATTATAATGTTGACTAATTCCCAAAAAAAAACTTATCATATTGGCATTTTCTG
986403 ATTTGCATAATCGATCGTCGGATTACATTTAGATACATTATTTGTGTTTGTGGAGGGTTTTTTCA
130 ATTTGCATAATCGATCGTCGGATTACATTTAGATACATTATTTGTGTTTGTGGAGGGTTTTTTCA
986468 CGTCGATTGAATTTGATTTGTGGTT
195 CGTCGATTGAATTTGATTTGTGGTT
986493 CATCAGTTGT
Statistics
Matches: 213, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
213 12 0.06
214 42 0.20
215 8 0.04
216 34 0.16
217 38 0.18
218 31 0.15
219 5 0.02
220 43 0.20
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (219 bp):
AGAAAAAAAAACATCTGAAATTAAATTAAAAATTAATATTAATTCAAACTAAAATAATATATCTT
TAAGCTTATTTATTATAATGTTGACTAATTCCCAAAAAAAAACTTATCATATTGGCATTTTCTGA
TTTGCATAATCGATCGTCGGATTACATTTAGATACATTATTTGTGTTTGTGGAGGGTTTTTTCAC
GTCGATTGAATTTGATTTGTGGTT
Found at i:987394 original size:20 final size:20
Alignment explanation
Indices: 987358--987395 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
987348 ATCCTATTCC
**
987358 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
987378 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
987396 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:988337 original size:20 final size:23
Alignment explanation
Indices: 988314--988366 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
988304 GATGGTACCG
988314 ATAC-TCCTC-CTT-GGGTATCA
1 ATACTTCCTCTCTTAGGGTATCA
*
988334 ATACTTCCCCTCTTAGGGTATCA
1 ATACTTCCTCTCTTAGGGTATCA
988357 ATACTTCCTC
1 ATACTTCCTC
988367 GGGTATAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 4 0.14
22 3 0.11
23 17 0.61
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (23 bp):
ATACTTCCTCTCTTAGGGTATCA
Found at i:988372 original size:18 final size:18
Alignment explanation
Indices: 988321--988372 Score: 50
Period size: 23 Copynumber: 2.6 Consensus size: 18
988311 CCGATACTCC
*
988321 TCCTTGGGTATCAATACT
1 TCCTCGGGTATCAATACT
988339 TCCCCTCTTAGGGTATCAATACT
1 T--CCTC---GGGTATCAATACT
988362 TCCTCGGGTAT
1 TCCTCGGGTAT
988373 AGATACCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
18 7 0.25
20 3 0.11
21 4 0.14
23 14 0.50
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (18 bp):
TCCTCGGGTATCAATACT
Found at i:989577 original size:31 final size:31
Alignment explanation
Indices: 989539--989645 Score: 178
Period size: 31 Copynumber: 3.5 Consensus size: 31
989529 GCTCGTATAA
*
989539 TAATCTGTCCATATGTCCCGAAGAACATAGG
1 TAATATGTCCATATGTCCCGAAGAACATAGG
* * *
989570 TAATCTGTTCATATGTCCCAAAGAACATAGG
1 TAATATGTCCATATGTCCCGAAGAACATAGG
989601 TAATATGTCCATATGTCCCGAAGAACATAGG
1 TAATATGTCCATATGTCCCGAAGAACATAGG
989632 TAATATGTCCATAT
1 TAATATGTCCATAT
989646 ATTAAATTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (31 bp):
TAATATGTCCATATGTCCCGAAGAACATAGG
Found at i:992606 original size:28 final size:28
Alignment explanation
Indices: 992550--992644 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
992540 CGAATCGTTA
*
992550 TAATTTATAAAAAAATTTCCCTTTATTG
1 TAATTTATAAACAAATTTCCCTTTATTG
* * *
992578 TTATTTATAAACAACTTTATCCTTT-TTG
1 TAATTTATAAACAAATTT-CCCTTTATTG
* *
992606 TAATTTAGAAACAAATTGT-CCTTT-TTCC
1 TAATTTATAAACAAATT-TCCCTTTATT-G
992634 TAATTTATAAA
1 TAATTTATAAA
992645 AATTATCCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
27 7 0.13
28 42 0.76
29 6 0.11
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (28 bp):
TAATTTATAAACAAATTTCCCTTTATTG
Found at i:992717 original size:21 final size:22
Alignment explanation
Indices: 992691--992732 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
992681 GTAATTTCAC
992691 ATTTTTAAAATTT-TAATAAAG
1 ATTTTTAAAATTTATAATAAAG
*
992712 ATTTTTTAAATTTATAATAAA
1 ATTTTTAAAATTTATAATAAA
992733 ATTATGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTTTAAAATTTATAATAAAG
Found at i:996845 original size:31 final size:31
Alignment explanation
Indices: 996802--996959 Score: 183
Period size: 31 Copynumber: 5.1 Consensus size: 31
996792 GCTCGTATAA
* * *
996802 TAATATGTCCATATATTCCGAATAACATAGG
1 TAATCTGTCCATATATCCCGAAGAACATAGG
* *
996833 TAATCTGTCCATATGTCCCGAAGAACATAAG
1 TAATCTGTCCATATATCCCGAAGAACATAGG
* * *
996864 TAATCTGTCCATATGTCTCGAAGAACATATG
1 TAATCTGTCCATATATCCCGAAGAACATAGG
* * * *
996895 TAAACTATCCATATGTCCCTAAGAACATAGG
1 TAATCTGTCCATATATCCCGAAGAACATAGG
*
996926 TAAAT-TGTCCATATATCCCAAAGAACATAGG
1 T-AATCTGTCCATATATCCCGAAGAACATAGG
996957 TAA
1 TAA
996960 CCCTCGACTC
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
30 2 0.02
31 106 0.96
32 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (31 bp):
TAATCTGTCCATATATCCCGAAGAACATAGG
Found at i:997811 original size:20 final size:20
Alignment explanation
Indices: 997788--997861 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
997778 CGTAGGTACA
997788 GGTACCCTCTATAGGGTATC
1 GGTACCCTCTATAGGGTATC
* * *
997808 GGTACACCCCTAATTGAGGTATT
1 GGTAC-CCTCT-ATAG-GGTATC
*
997831 GGTACCCTGC-CTAGGGTATC
1 GGTACCCT-CTATAGGGTATC
*
997851 GATACCC-CTAT
1 GGTACCCTCTAT
997862 TGAAATCTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 16 0.40
21 6 0.15
22 5 0.12
23 11 0.28
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (20 bp):
GGTACCCTCTATAGGGTATC
Found at i:999835 original size:29 final size:30
Alignment explanation
Indices: 999794--999873 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
999784 AAAATGAAAC
999794 AAAAACT-AAAGTTTAGGTATTGTTTAG-A
1 AAAAACTAAAAGTTTAGGTATTGTTTAGAA
*
999822 AAAAACTAAAAGTTGAGGTATTGTTTAGAA
1 AAAAACTAAAAGTTTAGGTATTGTTTAGAA
999852 AAAAACTAAAAGTTTAGGTATT
1 AAAAACTAAAAGTTTAGGTATT
999874 AAAATGGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.15
29 19 0.40
30 22 0.46
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (30 bp):
AAAAACTAAAAGTTTAGGTATTGTTTAGAA
Found at i:1003905 original size:2 final size:2
Alignment explanation
Indices: 1003898--1003968 Score: 124
Period size: 2 Copynumber: 35.0 Consensus size: 2
1003888 TTTAAATGTT
*
1003898 TA TA TA TA TA TA TA TA TA TG 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
1003940 TA TA TA TA TA TA TA TA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
1003969 GAATTAAGGA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 64 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1020503 original size:21 final size:22
Alignment explanation
Indices: 1020456--1020515 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
1020446 CCCCCCATGA
1020456 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC-TTAAAG
*
1020479 GGGAACCGATTCCCCC-TACAG
1 GGGAACCGATTCCCCCTTAAAG
* *
1020500 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
1020516 ATGGGGTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 18 0.53
23 16 0.47
ACGTcount: A:0.25, C:0.35, G:0.23, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTAAAG
Found at i:1026272 original size:21 final size:21
Alignment explanation
Indices: 1026238--1026277 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1026228 TACATATAGC
*
1026238 AGTTTATCTAGTATGGATACA
1 AGTTTATCTAGTATAGATACA
1026259 AGTTTATC-AGGTATAGATA
1 AGTTTATCTA-GTATAGATA
1026278 ACAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (21 bp):
AGTTTATCTAGTATAGATACA
Found at i:1034890 original size:16 final size:17
Alignment explanation
Indices: 1034858--1034891 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1034848 TTATAAATTT
1034858 AAATTTAGGGATTTGAG
1 AAATTTAGGGATTTGAG
*
1034875 AAATTT-GGGTTTTGAG
1 AAATTTAGGGATTTGAG
1034891 A
1 A
1034892 TGATAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.38
Consensus pattern (17 bp):
AAATTTAGGGATTTGAG
Found at i:1035872 original size:20 final size:21
Alignment explanation
Indices: 1035832--1035872 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1035822 AACTTAAAGG
1035832 ATTAAAATGGTAAAAACAGAA
1 ATTAAAATGGTAAAAACAGAA
* *
1035853 ATTAAAA-GGTTAAAATAGAA
1 ATTAAAATGGTAAAAACAGAA
1035873 TGACAGAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22
Consensus pattern (21 bp):
ATTAAAATGGTAAAAACAGAA
Found at i:1035895 original size:28 final size:29
Alignment explanation
Indices: 1035847--1035901 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
1035837 AATGGTAAAA
* *
1035847 ACAGAAATTAAAAGGTTAAAAT-AGAATG
1 ACAGAAACTAAAAGGTCAAAATCAGAATG
1035875 ACAGAAACT-AAAGTGTCAAAATCAGAA
1 ACAGAAACTAAAAG-GTCAAAATCAGAA
1035902 AAATACAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 15 0.65
29 4 0.17
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.18
Consensus pattern (29 bp):
ACAGAAACTAAAAGGTCAAAATCAGAATG
Found at i:1036272 original size:21 final size:21
Alignment explanation
Indices: 1036248--1036293 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1036238 TTTTCTTCTC
1036248 CCTCTCACCTATATATGGCCT
1 CCTCTCACCTATATATGGCCT
** * *
1036269 CCTCTCTTCTATCTATGGCTT
1 CCTCTCACCTATATATGGCCT
1036290 CCTC
1 CCTC
1036294 CCTTTTCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.39, G:0.09, T:0.39
Consensus pattern (21 bp):
CCTCTCACCTATATATGGCCT
Done.