Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 20
Found at i:3844469 original size:147 final size:148
Alignment explanation
Indices: 3844213--3844514 Score: 552
Period size: 147 Copynumber: 2.0 Consensus size: 148
3844203 CGAAGTGCCG
3844213 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
* *
3844278 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATAT-
66 CATATAAATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
3844342 ATATATCCCGAAGGACCA
131 ATATATCCCGAAGGACCA
3844360 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
3844425 CATATAAATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACATATGTTCCAAAGAATATA
66 CATATAAATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
3844490 CATATGTCCCGAAGGACCA
131 -ATATATCCCGAAGGACCA
3844509 CGTAGA
1 CGTAGA
3844515 CCCTCGACTC
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
147 126 0.85
149 23 0.15
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (148 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATATAAATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
ATATATCCCGAAGGACCA
Found at i:3845613 original size:16 final size:16
Alignment explanation
Indices: 3845592--3845622 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3845582 TGTAATACAG
*
3845592 ATAATCACATATAATT
1 ATAATCACACATAATT
3845608 ATAATCACACATAAT
1 ATAATCACACATAAT
3845623 CATGTCCATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAATCACACATAATT
Found at i:3845997 original size:21 final size:21
Alignment explanation
Indices: 3845973--3846017 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3845963 TTTTGTTCGT
* *
3845973 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3845994 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3846015 TTG
1 TTG
3846018 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3850951 original size:89 final size:89
Alignment explanation
Indices: 3850800--3851440 Score: 765
Period size: 89 Copynumber: 7.2 Consensus size: 89
3850790 TAAAAGATTC
* * ** *
3850800 CTCGAGTCTGATCTCCCC-AGAAGAGTAATGGAGCAGATTCTTCTTATTTCAGATTTTATCTTCA
1 CTCGAGTCTGATCTCCCCGA-AAGAGTAGTGAAGCAGATTCTTCTTATTTCAGATTTGGTCTTCC
*
3850864 TGAAGAAGTATCGAAGCAAATCAAT
65 TGAAGAAGCATCGAAGCAAATCAAT
* * *
3850889 CTCGAGTTTGATCTCCCCGGAAGAGTAGTGAAGCAGATTCTTCTTGTTTCAGATTTGGTCTTCCT
1 CTCGAGTCTGATCTCCCCGAAAGAGTAGTGAAGCAGATTCTTCTTATTTCAGATTTGGTCTTCCT
* * *
3850954 GAAGAAGCAGT-AAAGAAAATCAGT
66 GAAGAAGCA-TCGAAGCAAATCAAT
* * * * *
3850978 CTTGAGTCTGATCTCCCCGAAAGAGTAG-CAGAGCATATTCTTCTTATTTCATATTTGGTATTCC
1 CTCGAGTCTGATCTCCCCGAAAGAGTAGTGA-AGCAGATTCTTCTTATTTCAGATTTGGTCTTCC
*
3851042 TAAAGAAGCAGT-GAAGCAAATCAAT
65 TGAAGAAGCA-TCGAAGCAAATCAAT
* * * * * *
3851067 CTTGAGTCTGATCTCCCCGGAAGAGTAGTGGAGTATATTCTTCTTATTTCAGATTTGGTTTTCCT
1 CTCGAGTCTGATCTCCCCGAAAGAGTAGTGAAGCAGATTCTTCTTATTTCAGATTTGGTCTTCCT
*
3851132 GAAGAAGTATCGAAGCAAATCAAT
66 GAAGAAGCATCGAAGCAAATCAAT
* *
3851156 CTCGAGTCTGATCTCCTCGAAAGAGTAGTGAAGCAGATTCTT-TATATTTCAAATTTGGTCTTCC
1 CTCGAGTCTGATCTCCCCGAAAGAGTAGTGAAGCAGATTCTTCT-TATTTCAGATTTGGTCTTCC
*
3851220 TGAAGAAGC-TGGTAAGCAAATCAAT
65 TGAAGAAGCATCG-AAGCAAATCAAT
* * *
3851245 CTCGAGTCTGATATCCCTGAAAGAGTAG-CAGAGCAGATTCTTCTTATTTCAGATTTGGTCTTCC
1 CTCGAGTCTGATCTCCCCGAAAGAGTAGTGA-AGCAGATTCTTCTTATTTCAGATTTGGTCTTCC
* *
3851309 TGAAGAAGCAGCGAAGAAAATCAAT
65 TGAAGAAGCATCGAAGCAAATCAAT
* * * * * * *
3851334 CTCGAGTCTGATATCCCCAAAAGAGTAGTGGAGCATATTCTTCTTGTTTCAGATTTTGCCTTCCT
1 CTCGAGTCTGATCTCCCCGAAAGAGTAGTGAAGCAGATTCTTCTTATTTCAGATTTGGTCTTCCT
* * * *
3851399 AAAGAAGAAGCGAAGCAAATCAAC
66 GAAGAAGCATCGAAGCAAATCAAT
*
3851423 CTTGAGTCTGATCTCCCC
1 CTCGAGTCTGATCTCCCC
3851441 TTAAAAAATA
Statistics
Matches: 477, Mismatches: 64, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
88 6 0.01
89 468 0.98
90 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (89 bp):
CTCGAGTCTGATCTCCCCGAAAGAGTAGTGAAGCAGATTCTTCTTATTTCAGATTTGGTCTTCCT
GAAGAAGCATCGAAGCAAATCAAT
Found at i:3851278 original size:267 final size:267
Alignment explanation
Indices: 3850800--3851440 Score: 935
Period size: 267 Copynumber: 2.4 Consensus size: 267
3850790 TAAAAGATTC
* * * *
3850800 CTCGAGTCTGATCTCCCCAGAAGAGTAATGGAGCAGATTCTTCTTATTTCAGATTTTATCTTCAT
1 CTCGAGTCTGATCTCCCCAGAAGAGTAGTGGAGCATATTCTTCTTATTTCAGATTTTGTCTTCCT
* *
3850865 GAAGAAGTATCGAAGCAAATCAATCTCGAGTTTGATCTCCCCGGAAGAGTAGTGAAGCAGATTCT
66 GAAGAAGTATCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGAAAGAGTAGTGAAGCAGATTCT
* * * * *
3850930 TCTTGTTTCAGATTTGGTCTTCCTGAAGAAGCAGTAAAGAAAATCAGTCTTGAGTCTGATCTCCC
131 TCTTATTTCAAATTTGGTCTTCCTGAAGAAGCAGTAAAGAAAATCAATCTCGAGTCTGATATCCC
* * * *
3850995 CGAAAGAGTAGCAGAGCATATTCTTCTTATTTCATATTTGGTATTCCTAAAGAAGCAGTGAAGCA
196 CGAAAGAGTAGCAGAGCAGATTCTTCTTATTTCAGATTTGGTATTCCTAAAGAAGCAGCGAAGAA
3851060 AATCAAT
261 AATCAAT
* * * * *
3851067 CTTGAGTCTGATCTCCCCGGAAGAGTAGTGGAGTATATTCTTCTTATTTCAGATTTGGTTTTCCT
1 CTCGAGTCTGATCTCCCCAGAAGAGTAGTGGAGCATATTCTTCTTATTTCAGATTTTGTCTTCCT
*
3851132 GAAGAAGTATCGAAGCAAATCAATCTCGAGTCTGATCTCCTCGAAAGAGTAGTGAAGCAGATTCT
66 GAAGAAGTATCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGAAAGAGTAGTGAAGCAGATTCT
* *
3851197 T-TATATTTCAAATTTGGTCTTCCTGAAGAAGCTGGT-AAGCAAATCAATCTCGAGTCTGATATC
131 TCT-TATTTCAAATTTGGTCTTCCTGAAGAAGC-AGTAAAGAAAATCAATCTCGAGTCTGATATC
* * *
3851260 CCTGAAAGAGTAGCAGAGCAGATTCTTCTTATTTCAGATTTGGTCTTCCTGAAGAAGCAGCGAAG
194 CCCGAAAGAGTAGCAGAGCAGATTCTTCTTATTTCAGATTTGGTATTCCTAAAGAAGCAGCGAAG
3851325 AAAATCAAT
259 AAAATCAAT
* * * *
3851334 CTCGAGTCTGATATCCCCAAAAGAGTAGTGGAGCATATTCTTCTTGTTTCAGATTTTGCCTTCCT
1 CTCGAGTCTGATCTCCCCAGAAGAGTAGTGGAGCATATTCTTCTTATTTCAGATTTTGTCTTCCT
* * * * *
3851399 AAAGAAGAAGCGAAGCAAATCAACCTTGAGTCTGATCTCCCC
66 GAAGAAGTATCGAAGCAAATCAATCTCGAGTCTGATCTCCCC
3851441 TTAAAAAATA
Statistics
Matches: 331, Mismatches: 41, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
266 1 0.00
267 328 0.99
268 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (267 bp):
CTCGAGTCTGATCTCCCCAGAAGAGTAGTGGAGCATATTCTTCTTATTTCAGATTTTGTCTTCCT
GAAGAAGTATCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGAAAGAGTAGTGAAGCAGATTCT
TCTTATTTCAAATTTGGTCTTCCTGAAGAAGCAGTAAAGAAAATCAATCTCGAGTCTGATATCCC
CGAAAGAGTAGCAGAGCAGATTCTTCTTATTTCAGATTTGGTATTCCTAAAGAAGCAGCGAAGAA
AATCAAT
Found at i:3854192 original size:34 final size:34
Alignment explanation
Indices: 3854154--3854234 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
3854144 ACCATGGTAA
* * *
3854154 GGGTATCGATACCAGTAAACATTGAATTTAAATT
1 GGGTATCGATACCAGGAAACATCGAAGTTAAATT
** *
3854188 GGGTATCGATACCAGGCTACATCGAAGTTAATTT
1 GGGTATCGATACCAGGAAACATCGAAGTTAAATT
*
3854222 TGGTATCGATACC
1 GGGTATCGATACC
3854235 CTAATAGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (34 bp):
GGGTATCGATACCAGGAAACATCGAAGTTAAATT
Found at i:3854705 original size:20 final size:21
Alignment explanation
Indices: 3854680--3854718 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3854670 AATTGAAAAT
3854680 GCATGAAAGGATG-CATAAAG
1 GCATGAAAGGATGCCATAAAG
*
3854700 GCATGAACGGATGCCATAA
1 GCATGAAAGGATGCCATAA
3854719 TTGAAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.15
Consensus pattern (21 bp):
GCATGAAAGGATGCCATAAAG
Found at i:3854739 original size:47 final size:47
Alignment explanation
Indices: 3854670--3854798 Score: 222
Period size: 47 Copynumber: 2.7 Consensus size: 47
3854660 TCGATTTCAA
*
3854670 AATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACGGATGCCAT
1 AATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACAGATGCCAT
*
3854717 AATTGAAAATGCATGAAAGGATGCACAAAGGCATGAACAGATGCCAT
1 AATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACAGATGCCAT
* *
3854764 AATTTAAAATGCATGAAAGGATGCATTAAGGCATG
1 AATTGAAAATGCATGAAAGGATGCATAAAGGCATG
3854799 TGTCATAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 77 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (47 bp):
AATTGAAAATGCATGAAAGGATGCATAAAGGCATGAACAGATGCCAT
Found at i:3855803 original size:13 final size:13
Alignment explanation
Indices: 3855782--3855814 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3855772 ATCAATTTTT
*
3855782 TTATCTTTTAAAA
1 TTATTTTTTAAAA
3855795 TTATTTTTTAAAA
1 TTATTTTTTAAAA
3855808 TTATTTT
1 TTATTTT
3855815 AAAAGGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTTTTAAAA
Found at i:3855814 original size:12 final size:12
Alignment explanation
Indices: 3855782--3855828 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
3855772 ATCAATTTTT
3855782 TTATCTTTTAAAA
1 TTAT-TTTTAAAA
3855795 TTATTTTTTAAAA
1 TTA-TTTTTAAAA
3855808 TTA-TTTTAAAA
1 TTATTTTTAAAA
*
3855819 GGTATTTTTA
1 -TTATTTTTA
3855829 GGTATTCGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 19 0.63
14 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:3856292 original size:3 final size:3
Alignment explanation
Indices: 3856284--3856354 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
3856274 CTCTTTTGAT
3856284 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3856332 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
3856355 CCATAGGGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3860542 original size:20 final size:20
Alignment explanation
Indices: 3860514--3860551 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3860504 CATATAACAA
*
3860514 ATTATTAAATTTAAATATAT
1 ATTAATAAATTTAAATATAT
*
3860534 ATTAATAAATTTTAATAT
1 ATTAATAAATTTAAATAT
3860552 TGCAAAATAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAATAAATTTAAATATAT
Found at i:3861601 original size:6 final size:6
Alignment explanation
Indices: 3861592--3861617 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3861582 TCGATAGATG
3861592 TACATA TACATA TACATA TACATA TA
1 TACATA TACATA TACATA TACATA TA
3861618 AATGATGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TACATA
Found at i:3863256 original size:21 final size:21
Alignment explanation
Indices: 3863217--3863256 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3863207 GGGTTTTGGG
*
3863217 ATTGAAAATTTTATATTATTT
1 ATTGAAAATTTAATATTATTT
* *
3863238 ATTGATAATTTAATTTTAT
1 ATTGAAAATTTAATATTAT
3863257 ATTTCTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTGAAAATTTAATATTATTT
Found at i:3869219 original size:29 final size:31
Alignment explanation
Indices: 3869164--3869221 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
3869154 TTTAGATACC
*
3869164 TAAATAAAAAAGATGATATATTTTAAGTACT
1 TAAATAAAAAAGATGATATAATTTAAGTACT
*
3869195 TAAATGAAAAA-AT-ATATAATTTAAGTA
1 TAAATAAAAAAGATGATATAATTTAAGTA
3869222 TTTATTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 2 0.08
31 10 0.40
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (31 bp):
TAAATAAAAAAGATGATATAATTTAAGTACT
Found at i:3873683 original size:22 final size:23
Alignment explanation
Indices: 3873658--3873714 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 23
3873648 ATATTATGCA
*
3873658 CTTTACATCAAAAGGA-TAAGTC
1 CTTTACATCGAAAGGATTAAGTC
*
3873680 CTTTA-ATTGAAA-GATTAAGTC
1 CTTTACATCGAAAGGATTAAGTC
3873701 CTTT-CATCGAAAGG
1 CTTTACATCGAAAGG
3873715 TCTTAACCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.07
21 21 0.72
22 6 0.21
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (23 bp):
CTTTACATCGAAAGGATTAAGTC
Found at i:3873878 original size:77 final size:77
Alignment explanation
Indices: 3873751--3873984 Score: 450
Period size: 77 Copynumber: 3.0 Consensus size: 77
3873741 CCCTATATAT
*
3873751 AGGCTAGATTAGAACTTTGGAATAGGAAAAACATTTAGAAAATTCATTCCAAATTCGTTCTTTCC
1 AGGCTAGTTTAGAACTTTGGAATAGGAAAAACATTTAGAAAATTCATTCCAAATTCGTTCTTTCC
3873816 GGTGATAGAGAA
66 GGTGATAGAGAA
3873828 AGGCTAGTTTAGAACTTTGGAATAGGAAAAACATTTAGAAAATTCATTCCAAATTCGTTCTTTCC
1 AGGCTAGTTTAGAACTTTGGAATAGGAAAAACATTTAGAAAATTCATTCCAAATTCGTTCTTTCC
3873893 GGTGATAGAGAA
66 GGTGATAGAGAA
*
3873905 AGGCTAGTTTAGAACTTTGGAATAGGAAAAACATTTAGAAAATTCATTCCAAATTCATTCTTTCC
1 AGGCTAGTTTAGAACTTTGGAATAGGAAAAACATTTAGAAAATTCATTCCAAATTCGTTCTTTCC
3873970 GGTGATAGAGAA
66 GGTGATAGAGAA
3873982 AGG
1 AGG
3873985 TAAGATTGTG
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 155 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (77 bp):
AGGCTAGTTTAGAACTTTGGAATAGGAAAAACATTTAGAAAATTCATTCCAAATTCGTTCTTTCC
GGTGATAGAGAA
Found at i:3874255 original size:3 final size:3
Alignment explanation
Indices: 3874241--3874270 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3874231 ACTTCGTTCG
3874241 ATT ATAT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT AT
3874271 CATCTCGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3881240 original size:21 final size:21
Alignment explanation
Indices: 3881193--3881241 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
3881183 CCGGTCATCC
* * *
3881193 AATTTTTTAAACTCCAGACCG
1 AATTTTTTAAACCCCAAACCA
*
3881214 GA-TTTTTAAACCCCAAACCA
1 AATTTTTTAAACCCCAAACCA
3881234 AATTTTTT
1 AATTTTTT
3881242 CCAAATAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (21 bp):
AATTTTTTAAACCCCAAACCA
Found at i:3881559 original size:20 final size:19
Alignment explanation
Indices: 3881534--3881579 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
3881524 CATAACTTTC
3881534 TATTTTGCTTAAATTTAATA
1 TATTTTG-TTAAATTTAATA
*
3881554 TATTTTTGTTTAATTTAATA
1 TA-TTTTGTTAAATTTAATA
*
3881574 TGTTTT
1 TATTTT
3881580 TGTGCCTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 14 0.61
21 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
TATTTTGTTAAATTTAATA
Found at i:3881580 original size:20 final size:20
Alignment explanation
Indices: 3881545--3881582 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3881535 ATTTTGCTTA
3881545 AATTTAATATATTTTTGTTT
1 AATTTAATATATTTTTGTTT
*
3881565 AATTTAATATGTTTTTGT
1 AATTTAATATATTTTTGT
3881583 GCCTGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
AATTTAATATATTTTTGTTT
Found at i:3882498 original size:24 final size:23
Alignment explanation
Indices: 3882471--3882516 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3882461 AAAAAAGGGG
3882471 TAAAAAATAAGAATAATACAAAGC
1 TAAAAAATAAG-ATAATACAAAGC
* **
3882495 TAAACAATCTGATAATACAAAG
1 TAAAAAATAAGATAATACAAAG
3882517 AACACTGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.20
Consensus pattern (23 bp):
TAAAAAATAAGATAATACAAAGC
Found at i:3884180 original size:16 final size:17
Alignment explanation
Indices: 3884159--3884201 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3884149 TAACTCATAT
3884159 AATATTAAAAT-AATAA
1 AATATTAAAATAAATAA
** *
3884175 AATATTGTAATAAATTA
1 AATATTAAAATAAATAA
3884192 AATATTAAAA
1 AATATTAAAA
3884202 AAAAAGTACA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATATTAAAATAAATAA
Found at i:3885057 original size:2 final size:2
Alignment explanation
Indices: 3885050--3885091 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3885040 TCCCAATTCA
3885050 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
3885092 CAATTTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3886085 original size:46 final size:46
Alignment explanation
Indices: 3886035--3886140 Score: 162
Period size: 46 Copynumber: 2.3 Consensus size: 46
3886025 ATGAACTTCC
*
3886035 ATGCATCGATGCACT-CGGGATT-TTATGGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCCAGGATTGTT-T-GAAACATCGAATGCATTTT
*
3886081 ATGCATCGATGCACTCCAGGCTTGTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCATTTT
3886127 ATGCATCGATGCAC
1 ATGCATCGATGCAC
3886141 CCTTACTGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
46 48 0.86
47 6 0.11
48 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCATTTT
Found at i:3891447 original size:21 final size:21
Alignment explanation
Indices: 3891421--3891542 Score: 68
Period size: 21 Copynumber: 5.6 Consensus size: 21
3891411 TTGTGCACAA
3891421 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAGG
* *
3891442 TGCATCGATTCATCCCTATGAATG
1 TGCATCGA-T-A-CACTATGAAGG
* * **
3891466 TACATCGATGCAAAATGAAGG
1 TGCATCGATACACTATGAAGG
* * * *
3891487 TGCACCAATACACTCCTTGAATG
1 TGCATCGATACACT--ATGAAGG
* *
3891510 TGCATCGATGCACTCA-GCA-G
1 TGCATCGATACACT-ATGAAGG
3891530 TGCATCGATACAC
1 TGCATCGATACAC
3891543 CCGTCGGGAT
Statistics
Matches: 74, Mismatches: 22, Indels: 11
0.69 0.21 0.10
Matches are distributed among these distances:
20 13 0.18
21 25 0.34
22 2 0.03
23 18 0.24
24 16 0.22
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACTATGAAGG
Found at i:3894232 original size:65 final size:64
Alignment explanation
Indices: 3894100--3894256 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 64
3894090 ACACCCCATT
* * **
3894100 TCGAATGCATTTTATGCATCAATGTACTTCCATGCATCGATGCACTTAGGATTTTATAGAAACA
1 TCGAATGCATTTTATGCATCGATGCACAACCATGCATCGATGCACTTAGGATTTTATAGAAACA
* * *
3894164 TCGAATGTATTTTATGCATCGATGCACAAACCATGCATTGATGCACTCTAGGCTTGTT-T-GAAA
1 TCGAATGCATTTTATGCATCGATGCAC-AACCATGCATCGATGCACT-TAGGATT-TTATAGAAA
*
3894227 TA
63 CA
*
3894229 TCGAATGCATTTTAGTGCACCGATGCAC
1 TCGAATGCATTTTA-TGCATCGATGCAC
3894257 TAAGAGTTCC
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 24 0.30
65 34 0.43
66 19 0.24
67 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATCGATGCACAACCATGCATCGATGCACTTAGGATTTTATAGAAACA
Found at i:3896328 original size:29 final size:29
Alignment explanation
Indices: 3896256--3896345 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
3896246 AGTCCATTAT
* **
3896256 TCTTTTACTCAACAGTGCTTAACCTTTCA
1 TCTTTTACTCAACATTATTTAACCTTTCA
3896285 TCTTTTACTCAACATTATTTAACCTTTCA
1 TCTTTTACTCAACATTATTTAACCTTTCA
* *
3896314 TCTTTTACCCAACATTTTTTAACCATTT-A
1 TCTTTTACTCAACATTATTTAACC-TTTCA
3896343 TCT
1 TCT
3896346 AACTGGCATA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 52 0.95
30 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.47
Consensus pattern (29 bp):
TCTTTTACTCAACATTATTTAACCTTTCA
Found at i:3896815 original size:34 final size:34
Alignment explanation
Indices: 3896777--3896988 Score: 129
Period size: 34 Copynumber: 5.6 Consensus size: 34
3896767 TTTCATGTCA
*
3896777 ATAATGCACCCATATGTATTATTCTTTTATGCTG
1 ATAATGCACCCATATGCATTATTCTTTTATGCTG
* **
3896811 ATAATACA-CCAGTATGCATTTCAGCTATGACATTCTTTCATGCCA
1 ATAATGCACCCA-TATGCA-TT-A--T-T--C--T-TTT-ATGCTG
* *
3896856 ATAATGCACCTATATGCATTATTCTTTAATGCTG
1 ATAATGCACCCATATGCATTATTCTTTTATGCTG
**
3896890 ATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCA
1 ATAATGCACCCATATGCA-TT-A--T-T--C-T--TTT-ATGCTG
*
3896935 ATAATGCACCCATATGCATTATTCTTTTATGTTG
1 ATAATGCACCCATATGCATTATTCTTTTATGCTG
3896969 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
3896989 TCAACTATGG
Statistics
Matches: 138, Mismatches: 16, Indels: 48
0.68 0.08 0.24
Matches are distributed among these distances:
33 3 0.02
34 56 0.41
35 9 0.07
36 3 0.02
37 1 0.01
38 4 0.03
39 2 0.01
40 2 0.01
41 4 0.03
42 1 0.01
43 3 0.02
44 9 0.07
45 39 0.28
46 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.37
Consensus pattern (34 bp):
ATAATGCACCCATATGCATTATTCTTTTATGCTG
Found at i:3896849 original size:79 final size:79
Alignment explanation
Indices: 3896640--3897033 Score: 571
Period size: 79 Copynumber: 5.0 Consensus size: 79
3896630 CAATTATAGC
* * ** * *
3896640 ATTCTTTTAGGTTGATAACGCACCCATATGCATTTCAATG-T-TGGCATCCTGTCATGCCAATAA
1 ATTCTTTTATGCTGATAATACACCCATATGCATTTC-A-GCTATGACATCCTTTCATGCCAATAA
3896703 TGCACCCATATGCATT
64 TGCACCCATATGCATT
* * *
3896719 ATT-TTTTATGTTGATAATACACCCATATGCATTTCAGCTATGGCATCCTTTCATGTCAATAATG
1 ATTCTTTTATGCTGATAATACACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
*
3896783 CACCCATATGTATT
66 CACCCATATGCATT
*
3896797 ATTCTTTTATGCTGATAATACA-CCAGTATGCATTTCAGCTATGACATTCTTTCATGCCAATAAT
1 ATTCTTTTATGCTGATAATACACCCA-TATGCATTTCAGCTATGACATCCTTTCATGCCAATAAT
*
3896861 GCACCTATATGCATT
65 GCACCCATATGCATT
* *
3896876 ATTCTTTAATGCTGATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
1 ATTCTTTTATGCTGATAATACACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
3896941 CACCCATATGCATT
66 CACCCATATGCATT
* * * *
3896955 ATTCTTTTATGTTGATAATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATG
1 ATTCTTTTATGCTGATAATACACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
3897020 CACCCATATGCATT
66 CACCCATATGCATT
3897034 TCAGCTATGA
Statistics
Matches: 290, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
76 1 0.00
77 2 0.01
78 70 0.24
79 214 0.74
80 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (79 bp):
ATTCTTTTATGCTGATAATACACCCATATGCATTTCAGCTATGACATCCTTTCATGCCAATAATG
CACCCATATGCATT
Found at i:3897020 original size:45 final size:45
Alignment explanation
Indices: 3896969--3897063 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
3896959 TTTTATGTTG
* *
3896969 ATAATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACTATGACATACTTTCATGCCA
*
3897014 ATAATGCACCCATATGCATTTCAGCTATGACATACTTTCATGCCA
1 ATAATGCACCCATATGCATTTCAACTATGACATACTTTCATGCCA
3897059 ATAAT
1 ATAAT
3897064 ACACACACAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCAACTATGACATACTTTCATGCCA
Found at i:3897534 original size:20 final size:20
Alignment explanation
Indices: 3897509--3897562 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
3897499 TGTTCTTCAA
3897509 TATCGATACCCCTACCATGG
1 TATCGATACCCCTACCATGG
** *
3897529 TATCGATACTACTATACTATGG
1 TATCGATAC--CCCTACCATGG
3897551 TATCGATACCCC
1 TATCGATACCCC
3897563 CTTCCGGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.30
Consensus pattern (20 bp):
TATCGATACCCCTACCATGG
Found at i:3898850 original size:15 final size:15
Alignment explanation
Indices: 3898832--3898863 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3898822 CTACTAATAG
*
3898832 TGACAAAATTAATTT
1 TGACAAAATTAAATT
3898847 TGACAAAATTAAATT
1 TGACAAAATTAAATT
3898862 TG
1 TG
3898864 TCACAATAAT
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:0.06, G:0.09, T:0.38
Consensus pattern (15 bp):
TGACAAAATTAAATT
Found at i:3900792 original size:20 final size:20
Alignment explanation
Indices: 3900756--3900801 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3900746 TTTGGTATAA
*
3900756 AGACCAGTCTTTAGGTATGG
1 AGACCAGTCGTTAGGTATGG
*
3900776 AGACCAGTCGTTCGGTATGG
1 AGACCAGTCGTTAGGTATGG
3900796 AGACCA
1 AGACCA
3900802 TTGATCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (20 bp):
AGACCAGTCGTTAGGTATGG
Found at i:3907058 original size:31 final size:31
Alignment explanation
Indices: 3907020--3907086 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
3907010 TAGTTACGTC
3907020 GGGGACCATATTGAAAAC-AGACTAAATGTTG
1 GGGGACCATATTGAAAACGA-ACTAAATGTTG
*
3907051 GGGGACCATATTGCAAACGAACTAAATGTTG
1 GGGGACCATATTGAAAACGAACTAAATGTTG
*
3907082 AGGGA
1 GGGGA
3907087 TTGTATTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.21
Consensus pattern (31 bp):
GGGGACCATATTGAAAACGAACTAAATGTTG
Found at i:3907404 original size:3 final size:3
Alignment explanation
Indices: 3907396--3907468 Score: 74
Period size: 3 Copynumber: 23.7 Consensus size: 3
3907386 ATGTTATTTA
* * * *
3907396 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT AAT AAT AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3907444 TAA TAT ATAT TATT TAT TAA TAT TA
1 TAT TAT -TAT TA-T TAT TAT TAT TA
3907469 CAAAACCCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3912935 original size:15 final size:15
Alignment explanation
Indices: 3912915--3912946 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3912905 ATCAATACCT
3912915 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
3912930 TTTTGCATACATTCA
1 TTTTGCATACATGCA
3912945 TT
1 TT
3912947 ATTCATTTCA
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:3920283 original size:6 final size:6
Alignment explanation
Indices: 3920272--3920314 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
3920262 ATGCTTGAAG
3920272 AGAAAA AG-AAA AGAAAA A-AAAA GAGAAAA AGAAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA AG-AAAA AGAAAA A
3920315 AGGGGGGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 9 0.27
6 14 0.42
7 10 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:3920294 original size:15 final size:14
Alignment explanation
Indices: 3920274--3920315 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
3920264 GCTTGAAGAG
3920274 AAAAAGAAAAGAAAA
1 AAAAAGAAAA-AAAA
*
3920289 AAAAAGAGAAAAAGA
1 AAAAAGA-AAAAAAA
3920304 AAAAAGAAAAAA
1 AAAAAGAAAAAA
3920316 GGGGGGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 5 0.20
15 17 0.68
16 3 0.12
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:3920314 original size:25 final size:23
Alignment explanation
Indices: 3920269--3920316 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
3920259 ATTATGCTTG
3920269 AAGAGAAAAAGAAAAGAAAAAAA
1 AAGAGAAAAAGAAAAGAAAAAAA
*
3920292 AAGAGAAAAAGAAAA-AAGAAAA
1 AAGAGAAAAAGAAAAGAAAAAAA
3920314 AAG
1 AAG
3920317 GGGGGTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (23 bp):
AAGAGAAAAAGAAAAGAAAAAAA
Found at i:3921721 original size:83 final size:83
Alignment explanation
Indices: 3921582--3921793 Score: 424
Period size: 83 Copynumber: 2.6 Consensus size: 83
3921572 AAGAAGACTC
3921582 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAAT
3921647 TTGGAAGAGGAATGTGCT
66 TTGGAAGAGGAATGTGCT
3921665 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAAT
3921730 TTGGAAGAGGAATGTGCT
66 TTGGAAGAGGAATGTGCT
3921748 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
3921794 ATATGAAACC
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 129 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (83 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAAT
TTGGAAGAGGAATGTGCT
Found at i:3921869 original size:198 final size:201
Alignment explanation
Indices: 3921665--3922042 Score: 586
Period size: 207 Copynumber: 1.9 Consensus size: 201
3921655 GGAATGTGCT
*
3921665 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-T-A-A-AACCAGTTATT
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGATAACAGAACCAGTTATT
*
3921726 GAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
66 AAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
* *
3921791 TTGATATGAAACCACAGAACCAATCA-TTAAATTTGAAAGATGAATTTGCTCATAGTAGAAATAA
131 TTGATAT-AAAACACAGAACCAATCATTTAAA-TTAAAAGATGAATTTGCTCATAGTAGAAATAA
3921855 GGAGACCC
194 GGAGACCC
3921863 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAG
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGG-AT--A--ACAGAACCAG
*
3921928 TTATTAAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGAT
61 TTATTAAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
* * *
3921993 TTGGTTTGATATAAAACATAGAACCAATCATTTGAATTAAAAGATGAATT
126 CTGGTTTGATATAAAACACAGAACCAATCATTTAAATTAAAAGATGAATT
3922043 GCATGATCGT
Statistics
Matches: 162, Mismatches: 8, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
198 46 0.28
200 1 0.01
205 1 0.01
206 30 0.19
207 84 0.52
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (201 bp):
AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGATAACAGAACCAGTTATT
AAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT
TTGATATAAAACACAGAACCAATCATTTAAATTAAAAGATGAATTTGCTCATAGTAGAAATAAGG
AGACCC
Found at i:3922926 original size:113 final size:113
Alignment explanation
Indices: 3922757--3923623 Score: 1307
Period size: 113 Copynumber: 7.7 Consensus size: 113
3922747 TCAACAGTGT
3922757 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
3922822 TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATCAACTTTTC
*
3922870 CAGTTCGAGTTCATAATGAGAACAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
3922935 TTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATCAACTTTTC
3922983 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
3923048 TTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATCAACTTTTC
* *
3923096 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
*
3923161 TTTGTTCAACCTTTTGCTCAAAACTATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATCAACTTTTC
3923209 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
3923274 TTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATCAACTTTTC
* *
3923322 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
** * * *
3923387 TTTGTTCAACCTTTTGCTTGAAT-TCATCATTTGATGGATTAGCTTTTC
66 TTTGTTCAACCTTTTGCTCAAATCT-ATCACTTGATGGATCAACTTTTC
**** * * * *
3923435 CAAAAAGAGTTCATAATAAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* ** * * *
3923500 CTTGTTCAA-CTTTTGCTTGAAT-TCATCACTTAATGGATCAACCTTTA
66 TTTGTTCAACCTTTTGCTCAAATCT-ATCACTTGATGGATCAACTTTTC
**** * * *
3923547 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG-A-AAGTTCATAATAAGAAGAG
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
3923608 CTTATTCAACCTTTTG
66 TTTGTTCAACCTTTTG
3923624 AATGACTCTA
Statistics
Matches: 705, Mismatches: 47, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
108 26 0.04
109 7 0.01
110 2 0.00
111 1 0.00
112 65 0.09
113 604 0.86
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
CAGTTCGAGTTCATAATGAGAAGAACTCATCGGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATCAACTTTTC
Found at i:3923495 original size:24 final size:23
Alignment explanation
Indices: 3923452--3923497 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3923442 AGTTCATAAT
*
3923452 AAGAAGAATTCATCTGAAGAAGG
1 AAGAAGAATTCATATGAAGAAGG
3923475 AAGAAGAAGTTCATAAT-AAGAAG
1 AAGAAGAA-TTCAT-ATGAAGAAG
3923498 AACTTGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 11 0.55
25 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (23 bp):
AAGAAGAATTCATATGAAGAAGG
Found at i:3923863 original size:3 final size:3
Alignment explanation
Indices: 3923855--3923936 Score: 92
Period size: 3 Copynumber: 26.7 Consensus size: 3
3923845 ATGTTATTTA
* * *
3923855 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT TAT TAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3923903 TTT TAT TAT TAA TAT ATAT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TA
3923937 CAAAACCCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
3 61 0.91
4 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3927645 original size:30 final size:31
Alignment explanation
Indices: 3927611--3927679 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
3927601 TACAATACAA
3927611 TCCCTCAACA-TTAGTCCATTTGCAATATGG
1 TCCCTCAACATTTAGTCCATTTGCAATATGG
*
3927641 TCCCTCAACATTTAGTTCATTTGCAATATGG
1 TCCCTCAACATTTAGTCCATTTGCAATATGG
3927672 TCCC-CAAC
1 TCCCTCAAC
3927680 GTAACTATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
30 14 0.38
31 23 0.62
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (31 bp):
TCCCTCAACATTTAGTCCATTTGCAATATGG
Found at i:3928593 original size:28 final size:29
Alignment explanation
Indices: 3928561--3928618 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
3928551 ATCTATGTTT
* * *
3928561 ACATTATGTTGTTGAGCCATTGC-TTGAA
1 ACATTATGCTGGTGAGCCAATGCTTTGAA
3928589 ACATTATGCTGGTGAGCCAATGCTTTGAA
1 ACATTATGCTGGTGAGCCAATGCTTTGAA
3928618 A
1 A
3928619 GTAACAGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (29 bp):
ACATTATGCTGGTGAGCCAATGCTTTGAA
Done.