Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001333.1 Hibiscus syriacus cultivar Beakdansim tig00002602_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: 116032
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6447 original size:21 final size:19
Alignment explanation
Indices: 6401--6449 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
6391 TACCCGCGAT
6401 GGCCGCAATAGCGTCCGAC
1 GGCCGCAATAGCGTCCGAC
*
6420 AGCCGCAATAGC-TCCCGTGAC
1 GGCCGCAATAGCGT-CC--GAC
6441 GGCCGCAAT
1 GGCCGCAAT
6450 CACGGTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 1 0.04
19 13 0.52
21 11 0.44
ACGTcount: A:0.22, C:0.37, G:0.29, T:0.12
Consensus pattern (19 bp):
GGCCGCAATAGCGTCCGAC
Found at i:8447 original size:5 final size:5
Alignment explanation
Indices: 8437--8515 Score: 77
Period size: 5 Copynumber: 14.6 Consensus size: 5
8427 TATAAAGTTC
* * *
8437 TTTAT TTTAT TTTAT TTTCT TTTAT TTTAT TTTCT TTTCT TTTCAGGT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-A--T
8485 TTTCAT TTTAT TTTAT TTTAAGT TTTAT TTT
1 TTT-AT TTTAT TTTAT TTT-A-T TTTAT TTT
8516 TAAATATGCT
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
5 49 0.75
6 6 0.09
7 4 0.06
8 6 0.09
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:18474 original size:3 final size:3
Alignment explanation
Indices: 18466--18495 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
18456 CAAGTTGTAA
*
18466 AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18496 TGATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:19274 original size:128 final size:128
Alignment explanation
Indices: 18782--19382 Score: 523
Period size: 128 Copynumber: 4.6 Consensus size: 128
18772 CATCCTTAGG
* * * *
18782 AAGGATGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATC-TGGGTTTACACAACTCCTA
1 AAGG-TGATAACACGGTTCCTACGTGATGAGGACGATTGGTTATCAAGGG-TGACACAGCTCCTA
* * * ** * * * * * *
18846 CATAATGAGGAGATATGGTTGGGCAATGACACGGTTCCTACGCGATGAGGA-TGGCAGGCCATAT
64 CATAATGAGGAGATCTGGTCGGGTAATGACACGACTCATACGTGATGAAGAGT-TCTGGCCATCT
18910 A
128 A
* * * * * **
18911 AGGGTGATAACACGGTTCCTACGTGATGAAGACGGTTGGTTATCAAAGGTGGACAC-GACTTCGG
1 AAGGTGATAACACGGTTCCTACGTGATGAGGACGATTGGTTATCAAGGGT-GACACAG-CTCCTA
* * * * * * *
18975 CGTGATGAAGAGATCAGGTCGGGTGATGACACGGCTCATACGTGATGAAGAGTTATGGCCATCTA
64 CATAATGAGGAGATCTGGTCGGGTAATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCT-
19040 AA
128 -A
* * * * *
19042 AGTGAGGTGATAACACGGCTCATACGTGATGAAGA--ATTCTGGTTATCAAAGGTTGACACGGCT
1 A---AGGTGATAACACGGTTCCTACGTGATGAGGACGA-T-TGGTTATC-AAGGGTGACACAGCT
* * * *
19105 CCTACATGATGAGGAAATCAT-GTCGGGTAATGACACAACTCATACATGATGAAGAGTTCTGGCC
60 CCTACATAATGAGGAGATC-TGGTCGGGTAATGACACGACTCATACGTGATGAAGAGTTCTGGCC
19169 ATCTA
124 ATCTA
* * * * *
19174 AAGGTGATAACATGGTTCCTACATGATGAGGATGACTGGTTATCAGGGGTGACACAGCTCCTACA
1 AAGGTGATAACACGGTTCCTACGTGATGAGGACGATTGGTTATCAAGGGTGACACAGCTCCTACA
* * *
19239 TAATGAGGAGATCTGGTCGGGTGATGACACGACTCATCCGTGATGAAGAGTTTTGGCCATCTA
66 TAATGAGGAGATCTGGTCGGGTAATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTA
* * * * * * *
19302 AAGGTGATAACATGGTTTCTACATGATGAGGACGATTGGTTATCTAA-AGTAACATAGTTCCTAC
1 AAGGTGATAACACGGTTCCTACGTGATGAGGACGATTGGTTATC-AAGGGTGACACAGCTCCTAC
* *
19366 GTAATGAGGACATCTGG
65 ATAATGAGGAGATCTGG
19383 CCATCACTGC
Statistics
Matches: 385, Mismatches: 69, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
127 1 0.00
128 181 0.47
129 93 0.24
130 1 0.00
131 3 0.01
132 2 0.01
133 1 0.00
134 98 0.25
135 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (128 bp):
AAGGTGATAACACGGTTCCTACGTGATGAGGACGATTGGTTATCAAGGGTGACACAGCTCCTACA
TAATGAGGAGATCTGGTCGGGTAATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTA
Found at i:20282 original size:85 final size:84
Alignment explanation
Indices: 19999--20283 Score: 254
Period size: 85 Copynumber: 3.4 Consensus size: 84
19989 AAGGTGTTTT
* * * * *
19999 GTTGAAAGATAACCCTTCTCACCTTGAGTTATACTGTAAACTTGACATGT-CC-TGAAACTGAAT
1 GTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTG--ATGTGCCTTG-AGCTAAAT
* * *
20062 GTAATCAAACTTGAA-GTTTTG
63 GTAATCGAACTCGAAGGTCTTG
* ** * * *
20083 TGTTGACATATGGCCCTTCTCACCTTGAGCTATGCTGTGAATTTGGT-TGTCCTTGAGCTAAATG
1 -GTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATGTG-CCTTGAGCTAAATG
* * *
20147 GAATCGAACTCAAAGGTCTCTT
64 TAATCGAACTCGAAGGTCT-TG
* * * * * * *
20169 GCTGATAGATAACTCTTCTCGCCTTGAGTTATGTTGTAAATTTGATGTGCCTTTGAGCTTAGTGT
1 GTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATGTGCC-TTGAGCTAAATGT
20234 AATCGAACTCGAAGGTCTTG
65 AATCGAACTCGAAGGTCTTG
*
20254 GTTGACAGATAACCCTTCTCGCCTTGAGTT
1 GTTGACAGATAACCCTTCTCACCTTGAGTT
20284 TTACTACCAA
Statistics
Matches: 157, Mismatches: 36, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
82 1 0.01
83 1 0.01
84 19 0.12
85 106 0.68
86 30 0.19
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (84 bp):
GTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATGTGCCTTGAGCTAAATGTA
ATCGAACTCGAAGGTCTTG
Found at i:20465 original size:86 final size:86
Alignment explanation
Indices: 20350--20616 Score: 340
Period size: 86 Copynumber: 3.1 Consensus size: 86
20340 GCAGCTCATA
* * *
20350 ATTCTTCAGGTGGTTCCCCTTAACGAGTCTGAGCCAAGTGAGATGATCTTTGGATAACTCCCCTT
1 ATTCCTCAGGTGGTTCCCCTTAGCGAGTCTGAACCAAGTGAGATGATCTTTGGATAACTCCCCTT
* *
20415 CACGGGAAAACCATGTGGTAT
66 CACAGGAAAGCCATGTGGTAT
* * * * *
20436 ATTCCTCAGGTGATTTCCCTTAGCGAGTCTGAACCGAGTGAGATGAAT-TTTGGATGACTCCACT
1 ATTCCTCAGGTGGTTCCCCTTAGCGAGTCTGAACCAAGTGAGATG-ATCTTTGGATAACTCCCCT
*
20500 TCATAGGAAAGCCATGTGGTAT
65 TCACAGGAAAGCCATGTGGTAT
* * * * * *
20522 ATTCCTCGGGTGGTTCCCCTTAGCGGGTCTAAACCAAATGAGATGATCTTTAGA-ATACTCCCAT
1 ATTCCTCAGGTGGTTCCCCTTAGCGAGTCTGAACCAAGTGAGATGATCTTTGGATA-ACTCCCCT
*
20586 TCACAGGAAAGCCATATGGTAT
65 TCACAGGAAAGCCATGTGGTAT
20608 ATTCCTCAG
1 ATTCCTCAG
20617 TTGAATATCA
Statistics
Matches: 153, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
85 2 0.01
86 149 0.97
87 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (86 bp):
ATTCCTCAGGTGGTTCCCCTTAGCGAGTCTGAACCAAGTGAGATGATCTTTGGATAACTCCCCTT
CACAGGAAAGCCATGTGGTAT
Found at i:22282 original size:51 final size:52
Alignment explanation
Indices: 22164--22337 Score: 244
Period size: 52 Copynumber: 3.4 Consensus size: 52
22154 TTGGTCTGAG
* *
22164 CCTTCAAGATGCCCCACATGGA-TAATATATGTCTTTTTCATACTGATGTGAA
1 CCTTCAAGATGCCCCACATGGATTACT-TCTGTCTTTTTCATACTGATGTGAA
* *
22216 CCTTCAAGATACCTCACATGGATTACTTCTGTCTTTTT-ATACTGATGTGAA
1 CCTTCAAGATGCCCCACATGGATTACTTCTGTCTTTTTCATACTGATGTGAA
* * *
22267 CCTTCAAGATGCCTCACATGGATTACTTCTGTCTTTTTCATGCTGATGTGAG
1 CCTTCAAGATGCCCCACATGGATTACTTCTGTCTTTTTCATACTGATGTGAA
* *
22319 CCTTTAAGATTCCCCACAT
1 CCTTCAAGATGCCCCACAT
22338 AGATAATATA
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
51 50 0.45
52 57 0.52
53 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (52 bp):
CCTTCAAGATGCCCCACATGGATTACTTCTGTCTTTTTCATACTGATGTGAA
Found at i:23640 original size:5 final size:5
Alignment explanation
Indices: 23627--23717 Score: 82
Period size: 5 Copynumber: 17.8 Consensus size: 5
23617 CTTGTTTCAA
*
23627 TTTTT TTTTC TTTTCTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTT- TTTTC
1 TTTTC TTTTC -TTT-TC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
23677 -TTTC TTTTTC TTTTC ATTTGC TTTTTC TTTCTC TTTT- TTTT
1 TTTTC -TTTTC TTTTC -TTTTC -TTTTC TTT-TC TTTTC TTTT
23718 TTCTGATAGA
Statistics
Matches: 74, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
4 14 0.19
5 35 0.47
6 23 0.31
7 2 0.03
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:23662 original size:27 final size:26
Alignment explanation
Indices: 23627--23718 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 26
23617 CTTGTTTCAA
*
23627 TTTTTTTTTCTTTTCTCTTTTCTTTTC
1 TTTTCTTTTCTTTTCT-TTTTCTTTTC
*
23654 TTTTCTTTTCTTTTCTTTTTTTCTTTC
1 TTTTCTTTTCTTTTCTTTTTCT-TTTC
*
23681 TTTTTCTTTTCATTTGCTTTTTCTTTCTC
1 -TTTTCTTTTC-TTTTCTTTTTCTTT-TC
*
23710 TTTTTTTTT
1 TTTTCTTTT
23719 TCTGATAGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
26 5 0.09
27 19 0.34
28 20 0.36
29 12 0.21
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (26 bp):
TTTTCTTTTCTTTTCTTTTTCTTTTC
Found at i:23711 original size:23 final size:22
Alignment explanation
Indices: 23627--23718 Score: 100
Period size: 23 Copynumber: 4.2 Consensus size: 22
23617 CTTGTTTCAA
23627 TTTT-TTTTTCTTTTCTCTTTTC
1 TTTTCTTTTTC-TTTCTCTTTTC
23649 TTTTC-TTTTCTTT-TCTTTTC
1 TTTTCTTTTTCTTTCTCTTTTC
* *
23669 TTTTTTTCTTTCTTTTTCTTTTC
1 TTTTCTT-TTTCTTTCTCTTTTC
* *
23692 ATTTGCTTTTTCTTTCTCTTTTT
1 -TTTTCTTTTTCTTTCTCTTTTC
23715 TTTT
1 TTTT
23719 TCTGATAGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
20 11 0.19
21 4 0.07
22 19 0.32
23 20 0.34
24 5 0.08
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (22 bp):
TTTTCTTTTTCTTTCTCTTTTC
Found at i:23719 original size:17 final size:16
Alignment explanation
Indices: 23627--23721 Score: 93
Period size: 17 Copynumber: 5.7 Consensus size: 16
23617 CTTGTTTCAA
23627 TTTTTTTTTCTTTTCT
1 TTTTTTTTTCTTTTCT
*
23643 CTTTTCTTTTCTTTTCT
1 -TTTTTTTTTCTTTTCT
*
23660 TTTCTTTTCTTTTTTTC-
1 TTT-TTTT-TTCTTTTCT
*
23677 TTTCTTTTTCTTTTCAT
1 TTTTTTTTTCTTTTC-T
**
23694 TTGCTTTTTCTTTCTCT
1 TTTTTTTTTCTTT-TCT
23711 TTTTTTTTTCT
1 TTTTTTTTTCT
23722 GATAGATGAG
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
15 7 0.11
16 6 0.09
17 43 0.66
18 9 0.14
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (16 bp):
TTTTTTTTTCTTTTCT
Found at i:25998 original size:2 final size:2
Alignment explanation
Indices: 25991--26064 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
25981 AAATAACGTA
25991 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
26033 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26065 ACATATAAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27421 original size:20 final size:20
Alignment explanation
Indices: 27396--27438 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27386 TCTAAGAGCC
*
27396 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
27416 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
27436 CAT
1 CAT
27439 GTGGTAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:39440 original size:106 final size:106
Alignment explanation
Indices: 39244--39680 Score: 585
Period size: 106 Copynumber: 4.1 Consensus size: 106
39234 TCCAAGTAGG
* * *
39244 TTGTATTGT-TCCGAGTCCAATATCC-TC-CGTCGTGAAGTTGAAATTGGTTCTGGAACTGGGAA
1 TTGTATTGTCT-CGAGTCCAATATCCTTCAC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAA
*
39306 ATTATTTGTTGACAACTAGCCGTCCCTTCGTTGTGAAGTTGAAC
63 ATTATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
* * * *
39350 TTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAATTTGAAATTGGTTCTGAAATTGGAAAATT
1 TTGTATTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* * *
39415 GTTTGTTGACAACCAGCCGTCCCTTCATTGTGAAGTTGAAT
66 ATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
* * * ** *
39456 TTTTACTGTCTCAAGTCCAATGCCCTTCGA-TGTGAAGTTGAAATTGGCTCTGAAATTAGGAAAT
1 TTGTATTGTCTCGAGTCCAATATCCTTC-ACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
*
39520 TATTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
65 TATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
* * *
39562 TTGTATTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT
1 TTGTATTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
** *
39627 GCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTAAAC
66 ATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
*
39668 TTGTGTTGTCTCG
1 TTGTATTGTCTCG
39681 GGTGGCACGA
Statistics
Matches: 288, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
106 282 0.98
107 5 0.02
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (106 bp):
TTGTATTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
ATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
Found at i:39735 original size:43 final size:42
Alignment explanation
Indices: 39682--39765 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 42
39672 GTTGTCTCGG
* **
39682 GTGGCACGATATCCTCTGTTGTGGAGTTGAAATCGTGGATGT
1 GTGGCACGATATCCTCCGTCATGGAGTTGAAATCGTGGATGT
39724 GTGGCAACGATATCCTCCGTCATGGAGTTGAAATCGTGGATG
1 GTGGC-ACGATATCCTCCGTCATGGAGTTGAAATCGTGGATG
39766 ACCCCTTCGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 5 0.13
43 33 0.87
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (42 bp):
GTGGCACGATATCCTCCGTCATGGAGTTGAAATCGTGGATGT
Found at i:41135 original size:18 final size:18
Alignment explanation
Indices: 41108--41143 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41098 TGTTGAATCC
*
41108 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
41126 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
41144 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:42226 original size:21 final size:19
Alignment explanation
Indices: 42209--42265 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
42199 TTCCTTTTGA
42209 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
* * *
42228 TTGTT-CTTGTTTT-TTCT
1 TTTTTGCTTCTTTTCTTTT
42245 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
42264 TT
1 TT
42266 GTTCTTGACT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 7 0.23
18 14 0.47
19 9 0.30
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTGCTTCTTTTCTTTT
Found at i:42234 original size:15 final size:16
Alignment explanation
Indices: 42209--42271 Score: 74
Period size: 16 Copynumber: 3.8 Consensus size: 16
42199 TTCCTTTTGA
42209 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
*
42225 TTTTTGTTCTTGTTTTTTCT
1 TTTTTG--C-T-TCTTTTCT
42245 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
42261 TTTTTG-TTCTT
1 TTTTTGCTTCTT
42272 GACTGAATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.12
16 19 0.46
17 1 0.02
18 2 0.05
19 1 0.02
20 13 0.32
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTTGCTTCTTTTCT
Found at i:42271 original size:10 final size:10
Alignment explanation
Indices: 42221--42258 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
42211 TTTGCTTCTT
42221 TTCTTTTTTG
1 TTCTTTTTTG
42231 TTCTTGTTTT-
1 TTCTT-TTTTG
42241 TTCTTTTTTG
1 TTCTTTTTTG
42251 CTTCTTTT
1 -TTCTTTT
42259 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:50762 original size:20 final size:23
Alignment explanation
Indices: 50737--50777 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
50727 ATGTTCAAAT
50737 ATTGTTT-AA-AT-ATTAATTGA
1 ATTGTTTGAACATGATTAATTGA
50757 ATTGTTTGAACATGATTAATT
1 ATTGTTTGAACATGATTAATT
50778 TTCAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 2 0.11
23 7 0.39
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (23 bp):
ATTGTTTGAACATGATTAATTGA
Found at i:50909 original size:22 final size:22
Alignment explanation
Indices: 50874--50924 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
50864 AGGGAATCGG
50874 TCCCCCCTTGA-GGGAACCGAT
1 TCCCCCCTTGAGGGGAACCGAT
* *
50895 TTCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTG-AGGGGAACCGAT
50918 TCCCCCC
1 TCCCCCC
50925 ACAGGGGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.18, C:0.39, G:0.22, T:0.22
Consensus pattern (22 bp):
TCCCCCCTTGAGGGGAACCGAT
Found at i:55082 original size:15 final size:15
Alignment explanation
Indices: 55062--55105 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
55052 AACAGTTAGT
55062 AAAATAAAAAATAA-A
1 AAAATAAAAAA-AATA
55077 AAAATAAAAAAAATA
1 AAAATAAAAAAAATA
* *
55092 ATAATAAAATAAAT
1 AAAATAAAAAAAAT
55106 GGCAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 2 0.08
15 24 0.92
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAAAAAATA
Found at i:55094 original size:20 final size:20
Alignment explanation
Indices: 55061--55104 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
55051 AAACAGTTAG
55061 TAAAATAAAAAATAAAAAAA
1 TAAAATAAAAAATAAAAAAA
*
55081 TAAAA-AAAATAATAATAAAA
1 TAAAATAAAA-AATAAAAAAA
55101 TAAA
1 TAAA
55105 TGGCAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAATAAAAAATAAAAAAA
Found at i:56461 original size:24 final size:23
Alignment explanation
Indices: 56434--56490 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
56424 GGAAATAAAT
56434 AATAATAATATAGGA-GTAATATCA
1 AATAATAATATA--ATGTAATATCA
* *
56458 AATATATACTATAATGTAATATTA
1 AATA-ATAATATAATGTAATATCA
56482 AATAA-AATA
1 AATAATAATA
56491 AGAAGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 3 0.11
23 2 0.07
24 16 0.57
25 7 0.25
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (23 bp):
AATAATAATATAATGTAATATCA
Found at i:59247 original size:14 final size:14
Alignment explanation
Indices: 59228--59256 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59218 CATATACTTA
59228 GTCTAGGTCATAAG
1 GTCTAGGTCATAAG
59242 GTCTAGGTCATAAG
1 GTCTAGGTCATAAG
59256 G
1 G
59257 GTATTTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (14 bp):
GTCTAGGTCATAAG
Found at i:59958 original size:3 final size:3
Alignment explanation
Indices: 59950--60020 Score: 117
Period size: 3 Copynumber: 24.0 Consensus size: 3
59940 CTTGGTAGCA
* *
59950 TAT TAT TAT TAT TAT CAT TAG TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
59997 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
60021 ACATTTTGAT
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:64900 original size:11 final size:10
Alignment explanation
Indices: 64884--64981 Score: 52
Period size: 11 Copynumber: 8.7 Consensus size: 10
64874 TAACCCATCC
64884 TCGAGCTTAA
1 TCGAGCTTAA
*
64894 GTCGAGCTTGAT
1 -TCGAGCTT-AA
*
64906 TCGAGCTCACAA
1 TCGAGCT--TAA
64918 TCGAGCTTGAA
1 TCGAGCTT-AA
*
64929 TCGAGCTCACAA
1 TCGAGCT--TAA
*
64941 TCAAGCTTGAA
1 TCGAGCTT-AA
*
64952 TCGAGCTCAAAA
1 TCGAGCT--TAA
64964 TCGAGCTTGAA
1 TCGAGCTT-AA
64975 TCGAGCT
1 TCGAGCT
64982 CAAAATTGAG
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
11 41 0.61
12 26 0.39
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (10 bp):
TCGAGCTTAA
Found at i:64924 original size:23 final size:23
Alignment explanation
Indices: 64895--65002 Score: 153
Period size: 23 Copynumber: 4.7 Consensus size: 23
64885 CGAGCTTAAG
*
64895 TCGAGCTTGATTCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
64918 TCGAGCTTGAATCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
* *
64941 TCAAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCACAA
*
64964 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCACAA
* * *
64987 TTGAGATTCAATCGAG
1 TCGAGCTTGAATCGAG
65003 TCTCGAGCTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCACAA
Found at i:66679 original size:5 final size:5
Alignment explanation
Indices: 66669--66694 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
66659 GATTCCGCTA
66669 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
66695 TGTTTCGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:68430 original size:18 final size:17
Alignment explanation
Indices: 68409--68453 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
68399 ATGTTGAATG
68409 CGAAAAAAAATAGCA-GTT
1 CGAAAAAAAAT-G-ATGTT
*
68427 CGAAAAGAAATGATGTT
1 CGAAAAAAAATGATGTT
68444 CGAAAAAAAA
1 CGAAAAAAAA
68454 AAGAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 13 0.54
18 10 0.42
ACGTcount: A:0.58, C:0.09, G:0.18, T:0.16
Consensus pattern (17 bp):
CGAAAAAAAATGATGTT
Found at i:68521 original size:22 final size:21
Alignment explanation
Indices: 68458--68522 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
68448 AAAAAAAAGA
68458 GAAAAAAAAAGACATGAAAAAATG
1 GAAAAAAAAAGA-A-G-AAAAATG
* * * *
68482 GAAAACAAAACAACAAAAGTG
1 GAAAAAAAAAGAAGAAAAATG
68503 TGAAAAAAAAAGAAGAAAAA
1 -GAAAAAAAAAGAAGAAAAA
68523 ATCAAATGCA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 6 0.19
22 15 0.47
23 1 0.03
24 10 0.31
ACGTcount: A:0.72, C:0.06, G:0.15, T:0.06
Consensus pattern (21 bp):
GAAAAAAAAAGAAGAAAAATG
Found at i:76693 original size:2 final size:2
Alignment explanation
Indices: 76686--76717 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
76676 GAATTAACCA
76686 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
76718 TTAATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85112 original size:3 final size:3
Alignment explanation
Indices: 85104--85143 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
85094 TTGTCCGGGA
*
85104 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
85144 ATACTATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:89151 original size:125 final size:125
Alignment explanation
Indices: 88921--89217 Score: 443
Period size: 125 Copynumber: 2.4 Consensus size: 125
88911 GGCCAAGATG
* * * * * *
88921 TTTGGGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAACATTGGGGCACGACTGAGC
1 TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAATATTGGGGAACGACTAAAC
* * *
88986 CCACATCATGTTGAGATGACAAAATTCATACCAAGGAGGCA-TGAAGAATGAGCCTTACAA
66 CCACATCATGTTGAGATGACAAAATTCAGAACAAGAAGGCATTG-AGAATGAGCCTTACAA
89046 TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAATATTGGGGAACGACTAAAC
1 TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAATATTGGGGAACGACTAAAC
* * * *
89111 CCACATCATGTTGATATGGCAAGATTCAGAACAAGAAGGCATTGAGAATGAGCCTTATAA
66 CCACATCATGTTGAGATGACAAAATTCAGAACAAGAAGGCATTGAGAATGAGCCTTACAA
* *
89171 TTTGAGGTGTTGGGGCATTTTGAAGGCTCGTACCAATATAAGATAAT
1 TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAAT
89218 GTTGTGGCAC
Statistics
Matches: 156, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
125 154 0.99
126 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (125 bp):
TTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGATAATATTGGGGAACGACTAAAC
CCACATCATGTTGAGATGACAAAATTCAGAACAAGAAGGCATTGAGAATGAGCCTTACAA
Found at i:90200 original size:22 final size:22
Alignment explanation
Indices: 90160--90201 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
90150 CAATATGCAT
*
90160 ATATATATATATATTTCATGAC
1 ATATATATATATATGTCATGAC
90182 ATATATATA-ATCATGTCATG
1 ATATATATATAT-ATGTCATG
90202 CACACATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (22 bp):
ATATATATATATATGTCATGAC
Found at i:90432 original size:15 final size:15
Alignment explanation
Indices: 90412--90461 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
90402 CCGTAGGACC
90412 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
90427 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
90442 ACTACATCCCGAAGG
1 ACTACGTCCCGAAGG
90457 ACTAC
1 ACTAC
90462 AATACCCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.30, C:0.34, G:0.22, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:91148 original size:19 final size:20
Alignment explanation
Indices: 91112--91149 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
91102 TTTCATTTAG
91112 GGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
91132 GGGGGAATCGATACCCCC
1 GGGGGAATCGATACCCCC
91150 TGGACATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:92892 original size:42 final size:42
Alignment explanation
Indices: 92820--92916 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
92810 ACTTAGTATG
* * *
92820 TCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAGTAAGCCTTTCGAGCAAGATGATTAAA
* * * *
92862 TCCTTAGGGTCATCTGTAAGCCTTTTGAGCAAGATGA-TAAG
1 TCCTTAGGGCCATCAGTAAGCCTTTCGAGCAAGATGATTAAA
* *
92903 TACTTCGGGCCATC
1 TCCTTAGGGCCATC
92917 CATAAGACCT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 14 0.31
42 31 0.69
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (42 bp):
TCCTTAGGGCCATCAGTAAGCCTTTCGAGCAAGATGATTAAA
Found at i:92986 original size:215 final size:215
Alignment explanation
Indices: 92601--93536 Score: 1101
Period size: 215 Copynumber: 4.3 Consensus size: 215
92591 CCAAAATTTA
* * *
92601 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGTATGATGCTTAAATCCTTAGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * * *
92666 GCCTTTTGAGCAAGACGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCAA
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
*
92731 AGGAATTTG-AAAATGAGAAAATGATGTTTTAAAGAGATGAAATTTTTGAAAACTAAGAATGCGA
131 AAGAATTTGAAAAATGAGAAAATGATGTTTTAAA-AGATGAAATTTTTGAAAACTAAGAATGCGA
*
92795 TTTCCAAAATTTCACACTTAG
195 TTTCCAAAATTTCACAATTAG
* * *
92816 TATGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * *
92881 GCCTTTTGAGCAAGATGATAAGTACTTCGGGCCATCCATAAGACCTTCAGGTAGGATGTTTTCAA
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
* *
92946 AAGAATTTG-AAAATGAGAAAATGATGTTTTAAGAAGATGAAAATTTTGAAAACTATGAATGCGA
131 AAGAATTTGAAAAATGAGAAAATGATGTTTTAA-AAGATGAAATTTTTGAAAACTAAGAATGCGA
*
93010 TTTCCAAAATTTCACATTTAG
195 TTTCCAAAATTTCACAATTAG
* * * *
93031 TAAGTCCTTCGGGCCATCAATAAGTCTTTTGAACATGATGCTTAAATCCTTCGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * * *
93096 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTTGGGCATGATGTTTTCAC
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
** * * ** * *
93161 AAGTCTATCGAAAAATGAG-AAA-GATTTCTCATTAAAATCTGAAGA--TTTGAAAAGTAAGAAA
131 AAGAAT-TTGAAAAATGAGAAAATGATGT-T--TTAAAAGATGAA-ATTTTTGAAAACTAAGAAT
**** * *
93222 AATTTCTTACCTAGTAAATTATTTCCAAAATTGG
191 GCGAT-TT-CC----AAA--ATTT-CACAATTAG
* * * * *
93256 TATGTCATTCGGGCCATCAGTAAGTCTTTCGAGTATGATGTTTAAACCCTTCGGGTCATCTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * * * *
93321 ACCTTTTGATCAAGGTGATAAGTCCTTCTGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAC
66 GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
* * ** * * * *
93386 AATAAGTTGAAAAATGAGAAAGCGATGTTTTAAGAAAATGAAATATTTGAAAACTACGAAGGCGA
131 AAGAATTTGAAAAATGAGAAAATGATGTTTTAA-AAGATGAAATTTTTGAAAACTAAGAATGCGA
* **
93451 TTTCCAAATTTTTGCAATTAG
195 TTTCCAAAATTTCACAATTAG
* * *
93472 TAAGTCCTTCGGGCCATCAGCAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAA
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
93537 CTTCACGAAA
Statistics
Matches: 613, Mismatches: 87, Indels: 41
0.83 0.12 0.06
Matches are distributed among these distances:
215 324 0.53
216 83 0.14
217 19 0.03
218 7 0.01
219 3 0.00
222 3 0.00
223 7 0.01
224 23 0.04
225 140 0.23
226 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (215 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
GCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTCGGGTAGGATGTTTTCAA
AAGAATTTGAAAAATGAGAAAATGATGTTTTAAAAGATGAAATTTTTGAAAACTAAGAATGCGAT
TTCCAAAATTTCACAATTAG
Found at i:93102 original size:42 final size:41
Alignment explanation
Indices: 93035--93143 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
93025 ATTTAGTAAG
* * * *
93035 TCCTTCGGGCCATCAATAAGTCTTTTGAACATGATGCTTAAA
1 TCCTTCGGGACATCAATAAGCCTTTTGAACAAGATG-ATAAA
* ** * *
93077 TCCTTCGGGTCATCTGTAAGCCTTTTGAGCAAGATGATAAG
1 TCCTTCGGGACATCAATAAGCCTTTTGAACAAGATGATAAA
*
93118 TCCTTCGGGACATCCATAAGACCTTT
1 TCCTTCGGGACATCAATAAG-CCTTT
93144 GGGCATGATG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 20 0.36
42 35 0.64
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGACATCAATAAGCCTTTTGAACAAGATGATAAA
Found at i:93398 original size:440 final size:430
Alignment explanation
Indices: 92596--93536 Score: 1160
Period size: 440 Copynumber: 2.2 Consensus size: 430
92586 TATTTCCAAA
* *
92596 ATTTA-TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGTATGATGCTTAAATCCTTAGGGTCAT
1 ATTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAT
* *
92660 CTGTAAGCCTTTTGAGCAAGACGATAAGTCATTCGGGCCATCCATAAAACCTTCGGGTAGGATGT
66 CTGTAAGCCTTTTGAGCAAGACGATAAGTCATTCGGGACATCCATAAAACCTTCGGGCAGGATGT
* *
92725 TTTCAAAGGAATTTGAAAATGAGAAAATGATGTTTTAAAGAGATGAAATTTTTGAAAACTAAGAA
131 TTTCAAAGCAATTCGAAAATGAGAAAATGATGTTTTAAAGAGATGAAA-TTTTGAAAACTAAGAA
*** * * * *
92790 TGCGATTTCCAAAATTTCACACTTAGTATGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGAT
195 AAAGATTTCCAAAATTTCAAAATTAGTATGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* * *
92855 GATTAAATCCTTAGGGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGTACTTCGGGCCATCCAT
260 GATTAAACCCTTAGGGTCATCTGTAAACCTTTTGAGCAAGATGATAAGTACTTCGGGACATCCAT
* * *
92920 AAGACCTTCAGGTAGGATGTTTTCAAAAGAATTTG-AAAATGAGAAAATGATGTTTTAAGAAGAT
325 AAGACCTTCAGGTAGGATGTTTTCAAAAGAAGTTGAAAAATGAGAAAACGATGTTTTAAGAAAAT
* *
92984 GAAA-ATTTTGAAAACTATGAATGCGATTTCCAAAATTTCAC
390 GAAATA-TTTGAAAACTACGAAGGCGATTTCCAAAATTTCAC
* * *
93025 ATTTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTTGAACATGATGCTTAAATCCTTCGGGTCAT
1 ATTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAT
* * * * *
93090 CTGTAAGCCTTTTGAGCAAGATGATAAGTCCTTCGGGACATCCATAAGACCTTTGGGCATGATGT
66 CTGTAAGCCTTTTGAGCAAGACGATAAGTCATTCGGGACATCCATAAAACCTTCGGGCAGGATGT
* * ** *
93155 TTTCACAAGTCTA-TCGAAAAATGAG-AAA-GATTTCTCATTAAA-ATCTGAAGA-TTTGAAAAG
131 TTTCA-AAG-CAATTCG-AAAATGAGAAAATGATGT-T--TTAAAGAGATGAA-ATTTTGAAAAC
** *
93215 TAAGAAAAATTTCTTACCTAGTAAATTATTTCCAAAATTGGTATGTCATTCGGGCCATCAGTAAG
189 TAAGAAAAAGAT-TT-CC----AAA--ATTT-CAAAATTAGTATGTCATTCGGGCCATCAGTAAG
* * * * * *
93280 TCTTTCGAGTATGATGTTTAAACCCTTCGGGTCATCTGTAAACCTTTTGATCAAGGTGATAAGTC
245 TCTTTCGAGCATGATGATTAAACCCTTAGGGTCATCTGTAAACCTTTTGAGCAAGATGATAAGTA
* * * * *
93345 CTTCTGGACATCCATAAGACCTTCGGGTAGGATGTTTTCACAATAAGTTGAAAAATGAGAAAGCG
310 CTTCGGGACATCCATAAGACCTTCAGGTAGGATGTTTTCAAAAGAAGTTGAAAAATGAGAAAACG
* **
93410 ATGTTTTAAGAAAATGAAATATTTGAAAACTACGAAGGCGATTTCCAAATTTTTGC
375 ATGTTTTAAGAAAATGAAATATTTGAAAACTACGAAGGCGATTTCCAAAATTTCAC
* * * *
93466 AATTAGTAAGTCCTTCGGGCCATCAGCAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAAT
1 ATTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAT
*
93531 TTGTAA
66 CTGTAA
93537 CTTCACGAAA
Statistics
Matches: 434, Mismatches: 59, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
429 5 0.01
430 121 0.28
431 24 0.06
432 16 0.04
433 8 0.02
437 3 0.01
439 4 0.01
440 129 0.30
441 123 0.28
442 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (430 bp):
ATTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAT
CTGTAAGCCTTTTGAGCAAGACGATAAGTCATTCGGGACATCCATAAAACCTTCGGGCAGGATGT
TTTCAAAGCAATTCGAAAATGAGAAAATGATGTTTTAAAGAGATGAAATTTTGAAAACTAAGAAA
AAGATTTCCAAAATTTCAAAATTAGTATGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
ATTAAACCCTTAGGGTCATCTGTAAACCTTTTGAGCAAGATGATAAGTACTTCGGGACATCCATA
AGACCTTCAGGTAGGATGTTTTCAAAAGAAGTTGAAAAATGAGAAAACGATGTTTTAAGAAAATG
AAATATTTGAAAACTACGAAGGCGATTTCCAAAATTTCAC
Found at i:93729 original size:37 final size:37
Alignment explanation
Indices: 93688--93840 Score: 227
Period size: 37 Copynumber: 4.2 Consensus size: 37
93678 GGCCTTCGGG
93688 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
93725 CCATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-GAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* * *
93761 CCATTTTAAGCTTTCACCGAAGAGTAGTAAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
93798 CCATCTTAAGCCTTCATCGAAGAGTGGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
*
93835 CAATCT
1 CCATCT
93841 CGAGTCTGAT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 31 0.30
37 71 0.70
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (37 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:93781 original size:73 final size:73
Alignment explanation
Indices: 93688--93830 Score: 234
Period size: 73 Copynumber: 2.0 Consensus size: 73
93678 GGCCTTCGGG
*
93688 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCA-CAGAAGAGTAG
1 CCATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATCTTAAGCCTTCATC-GAAGAGTAG
93752 TGAAGCGAT
65 TGAAGCGAT
* * *
93761 CCATTTTAAGCTTTCACCGAAGAGTAGTAAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTGGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTAGT
93826 GAAGC
66 GAAGC
93831 AAATCAATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
73 64 0.98
74 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (73 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATCTTAAGCCTTCATCGAAGAGTAGT
GAAGCGAT
Found at i:94017 original size:3 final size:3
Alignment explanation
Indices: 94009--94039 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
93999 TTGTCCGGGA
94009 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
94040 ATACTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:94031 original size:14 final size:14
Alignment explanation
Indices: 94012--94039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
94002 TCCGGGATAT
94012 TATTATTATTATTA
1 TATTATTATTATTA
94026 TATTATTATTATTA
1 TATTATTATTATTA
94040 ATACTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:99946 original size:13 final size:13
Alignment explanation
Indices: 99928--99952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
99918 ATTACAGACG
99928 TGCATATGAAGAT
1 TGCATATGAAGAT
99941 TGCATATGAAGA
1 TGCATATGAAGA
99953 CTGTTCAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (13 bp):
TGCATATGAAGAT
Found at i:101470 original size:39 final size:40
Alignment explanation
Indices: 101427--101504 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
101417 ACATAGCTTA
* *
101427 CACGT-GGTTATAGCGC-GCCCCTTGATCCGCGCTATACAC
1 CACGTAGGGTATAGCGCTGCCCC-TGATCAGCGCTATACAC
*
101466 CACGTAGGGGTATAGCGCTGCCCCTGCTCAGCGCTATAC
1 CACGTA-GGGTATAGCGCTGCCCCTGATCAGCGCTATAC
101505 CTGGGTATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.15
41 23 0.70
42 5 0.15
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.22
Consensus pattern (40 bp):
CACGTAGGGTATAGCGCTGCCCCTGATCAGCGCTATACAC
Done.