Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:343161 original size:21 final size:21
Alignment explanation
Indices: 343084--343155 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
343074 TGCGATTTTG
343084 GACTATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTC
*
343105 GACTATCGCAATGCGAA-TAT-
1 GACTATCGCAACGCGAACT-TC
*
343125 GTA-AATCGCAACGCGAACTTC
1 G-ACTATCGCAACGCGAACTTC
343146 GACTATCGCA
1 GACTATCGCA
343156 TTGCGATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:343196 original size:21 final size:21
Alignment explanation
Indices: 343170--343368 Score: 192
Period size: 21 Copynumber: 9.6 Consensus size: 21
343160 GATTTACATA
343170 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
343191 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
343211 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
343232 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
343253 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
343274 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* * * **
343294 TATCACATTGCGAT-TTACATT
1 T-TCGCATTGCGATAGTCCAAG
*
343315 TTCGCATTGCAATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
343336 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
343357 TTCGCGTTGCGA
1 TTCGCATTGCGA
343369 ATCTGGAAAC
Statistics
Matches: 144, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
20 31 0.22
21 112 0.78
22 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:343196 original size:41 final size:42
Alignment explanation
Indices: 343151--343368 Score: 202
Period size: 41 Copynumber: 5.3 Consensus size: 42
343141 ACTTCGACTA
*
343151 TCGCATTGCGAT-TTAC-ATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGT-CGATATTCGCATTGCGATAGTCCAAGT
* *
343192 TCGCATTGCGATAGTCGACTA-TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTCGA-TATTCGCATTGCGATAGTCCA-AGT
*
343233 TCGCATTGCGATAGTCGA-AGTTCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGATA-TTCGCATTGCGATAGTCCAAGT
* * * **
343275 TCGCATTGCGATAGTCGACTA-TCACATTGCGAT-TTACATTT
1 TCGCATTGCGATAGTCGA-TATTCGCATTGCGATAGTCCAAGT
* * *
343316 TCGCATTGCAATAGTCCA-AGTTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGATA-TTCGCATTGCGATAGTCCAAGT
*
343358 TCGCGTTGCGA
1 TCGCATTGCGA
343369 ATCTGGAAAC
Statistics
Matches: 142, Mismatches: 22, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
39 2 0.01
41 78 0.55
42 59 0.42
43 2 0.01
44 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (42 bp):
TCGCATTGCGATAGTCGATATTCGCATTGCGATAGTCCAAGT
Found at i:343196 original size:62 final size:62
Alignment explanation
Indices: 343130--343257 Score: 204
Period size: 62 Copynumber: 2.1 Consensus size: 62
343120 AATATGTAAA
*
343130 TCGCAACGCGA-ACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCAACGCGATA-GTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
** *
343192 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
1 TCGCAACGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
343254 TCGC
1 TCGC
343258 GTTGCGATAG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 60 0.98
63 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (62 bp):
TCGCAACGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
Found at i:343217 original size:83 final size:83
Alignment explanation
Indices: 343170--343368 Score: 281
Period size: 83 Copynumber: 2.4 Consensus size: 83
343160 GATTTACATA
** *
343170 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCAACGCGATTGACATATTC
343235 GCATTGCGATAGTCGAAG
66 GCATTGCGATAGTCGAAG
* * ** * *
343253 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCACATTGCGATTTACATTTTC
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCAACGCGATTGACATATTC
* *
343318 GCATTGCAATAGTCCAAG
66 GCATTGCGATAGTCGAAG
* *
343336 TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGA
343369 ATCTGGAAAC
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 108 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (83 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCAACGCGATTGACATATTC
GCATTGCGATAGTCGAAG
Found at i:343263 original size:62 final size:62
Alignment explanation
Indices: 343144--343286 Score: 234
Period size: 62 Copynumber: 2.3 Consensus size: 62
343134 AACGCGAACT
343144 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
* *
343206 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
* *
343268 TCCAAGT-TCGCATTGCGAT
1 T-CGACTATCGCATTGCGAT
343287 AGTCGACTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 73 0.96
63 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (62 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
Found at i:345939 original size:18 final size:18
Alignment explanation
Indices: 345918--345952 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
345908 CTTTAATTTT
345918 AAATTATTATTACTAATA
1 AAATTATTATTACTAATA
*
345936 AAATTATTATTATTAAT
1 AAATTATTATTACTAAT
345953 TATTATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTATTATTACTAATA
Found at i:346288 original size:6 final size:6
Alignment explanation
Indices: 346277--346308 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
346267 AAGTGTTCAC
*
346277 ATAAAT ATAAAT ATAAAA ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
346309 TTTTTTATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:346433 original size:60 final size:58
Alignment explanation
Indices: 346360--346515 Score: 172
Period size: 60 Copynumber: 2.7 Consensus size: 58
346350 ACCCTTTTTG
**
346360 AATTAGTCCTTAAACTTTTAGATATTTTAATTTCATCTTTAAACTATGACTCTCATTCT-A
1 AATTAGTCCTTAAACTTTTAGATATTTTAATTTCATCCATAAACTATGACT-T--TTCTAA
* * * * *
346420 AATTAGTCCTTAAACTTTCATACATTCTAATTTCATCCATAAACTATGACTTTTTTAA
1 AATTAGTCCTTAAACTTTTAGATATTTTAATTTCATCCATAAACTATGACTTTTCTAA
** *
346478 AATTAGTCCCCAAACTTTT-GAATATTTCAATTTCATCC
1 AATTAGTCCTTAAACTTTTAG-ATATTTTAATTTCATCC
346516 CCAAATCCAT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
57 3 0.04
58 31 0.39
59 1 0.01
60 45 0.56
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (58 bp):
AATTAGTCCTTAAACTTTTAGATATTTTAATTTCATCCATAAACTATGACTTTTCTAA
Found at i:346757 original size:60 final size:60
Alignment explanation
Indices: 346682--346812 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 60
346672 AAAAATTTGG
* * * * ** * *
346682 GGACCAATTTGGAATGAAAGTCAGAGTTTGGGGATGAAATTGAAATGCTTAAAAGTTTAA
1 GGACTAATTTAGAATGAAAGTAAGAGTTTAGGGATGAAATAAAAATACTTAAAAGTTGAA
* * * * *
346742 GGATTAATTTAGAATGATAGTAATAGTTTATGGATGAAATAAAAATATTTAAAAGTTGAA
1 GGACTAATTTAGAATGAAAGTAAGAGTTTAGGGATGAAATAAAAATACTTAAAAGTTGAA
346802 GGACTAATTTA
1 GGACTAATTTA
346813 AAATAAGAGT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (60 bp):
GGACTAATTTAGAATGAAAGTAAGAGTTTAGGGATGAAATAAAAATACTTAAAAGTTGAA
Found at i:348694 original size:35 final size:35
Alignment explanation
Indices: 348629--348698 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
348619 AATGTTGTTA
**
348629 ATAATAAATCATGTCACTTGATGATTAAACTTATT
1 ATAATAAATCATGTCACTTGATGAAAAAACTTATT
* *
348664 ATAATAAGTCATGTCGC-TGAGTGAAAAAACTTATT
1 ATAATAAATCATGTCACTTGA-TGAAAAAACTTATT
348699 TTTATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 3 0.10
35 27 0.90
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (35 bp):
ATAATAAATCATGTCACTTGATGAAAAAACTTATT
Found at i:349868 original size:10 final size:10
Alignment explanation
Indices: 349840--349876 Score: 60
Period size: 9 Copynumber: 3.9 Consensus size: 10
349830 GCTGTCTTCT
349840 TAAACTGTTG
1 TAAACTGTTG
349850 TAAAC-GTTG
1 TAAACTGTTG
349859 TAAACTGTTG
1 TAAACTGTTG
349869 TAAA-TGTT
1 TAAACTGTT
349877 TGGGCATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (10 bp):
TAAACTGTTG
Found at i:351840 original size:2 final size:2
Alignment explanation
Indices: 351794--351824 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
351784 TTTTATAAAC
351794 AT AT AT 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 AT AT AT A
351825 CACGTCACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:353174 original size:21 final size:21
Alignment explanation
Indices: 353133--353177 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
353123 ATTATTTCAT
* *
353133 TATTTTATTTATTTACTTATA
1 TATTTTATATATATACTTATA
353154 TATTTTATATATATA-TATATA
1 TATTTTATATATATACT-TATA
353175 TAT
1 TAT
353178 ATACATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATATATATACTTATA
Found at i:353197 original size:51 final size:51
Alignment explanation
Indices: 353133--353242 Score: 136
Period size: 51 Copynumber: 2.1 Consensus size: 51
353123 ATTATTTCAT
353133 TATTTTATTTATTTACTTATATA-TTTTATATAT-ATATA-TATATATATACA
1 TATTTTATTTATTT-CTTA-ATACTTTTATATATGATATATTATATATATACA
* *
353183 TATTTTACTTTATTTCTTAATACTTTTTTTATATGTTATATTATATATATACA
1 TATTTTA-TTTATTTCTTAATAC-TTTTATATATGATATATTATATATATACA
353236 TCATTTT
1 T-ATTTT
353243 CTTAATATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
49 3 0.06
50 11 0.21
51 16 0.31
52 4 0.08
53 13 0.25
54 5 0.10
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (51 bp):
TATTTTATTTATTTCTTAATACTTTTATATATGATATATTATATATATACA
Found at i:353265 original size:53 final size:53
Alignment explanation
Indices: 353133--353248 Score: 127
Period size: 53 Copynumber: 2.2 Consensus size: 53
353123 ATTATTTCAT
*
353133 TATTTTA-TTTATTTACTT-ATA-TA-TTTTATATATATATATATATATATACA
1 TATTTTACTTAATTT-CTTAATACTATTTTTATATATATATATATATATATACA
* * *
353183 TATTTTACTTTATTTCTTAATACTTTTTTTATATGT-TATATTATATATATACA
1 TATTTTACTTAATTTCTTAATACTATTTTTATATATATATA-TATATATATACA
353236 TCATTTT-CTTAAT
1 T-ATTTTACTTAAT
353249 ATTTTGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
50 10 0.18
51 10 0.18
52 5 0.09
53 27 0.47
54 5 0.09
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (53 bp):
TATTTTACTTAATTTCTTAATACTATTTTTATATATATATATATATATATACA
Found at i:363897 original size:47 final size:47
Alignment explanation
Indices: 363828--363963 Score: 211
Period size: 46 Copynumber: 2.9 Consensus size: 47
363818 AATACTTCGC
* * * *
363828 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAACGT
1 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAACGT
* *
363875 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTG-AAAAAAAAATGT
1 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAACGT
363921 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAA
1 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAA
363964 GAAGAAAAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 44 0.54
47 37 0.46
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (47 bp):
TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAAAAACGT
Found at i:364805 original size:43 final size:43
Alignment explanation
Indices: 364757--365112 Score: 133
Period size: 43 Copynumber: 7.4 Consensus size: 43
364747 CAGAGCCAAT
364757 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
* ** ** * *
364800 TTCAACTTCACGACGAAGGGACTGCTGGTTGTCGATAAACAATGCCAGAG
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAATG-CA-AG
* *
364850 CTAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAG
1 -----TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
** * *
364898 TTCAACTTCATGACGAATGGACCGCTAGTTGTCGA-T--AAACAATTTCAGAGACAAT
1 TTCAACTTCACAACGAA-GGA----TA-TTG--GACTCCAGACAA--T----G-CAAG
364953 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
* *** ** * * *
364996 TTTAACTTCACAACGAAGGGACCGCTGGTTGTCGATAAACAATTTCAGAGCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA--T----G-CAAG
365051 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
*
365094 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
365113 GACCGCTAGT
Statistics
Matches: 226, Mismatches: 45, Indels: 84
0.64 0.13 0.24
Matches are distributed among these distances:
43 71 0.31
44 10 0.04
45 7 0.03
46 4 0.02
47 2 0.01
48 24 0.11
49 10 0.04
50 22 0.10
51 2 0.01
52 4 0.02
53 7 0.03
54 10 0.04
55 53 0.23
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
Found at i:364929 original size:98 final size:98
Alignment explanation
Indices: 364746--365808 Score: 1442
Period size: 98 Copynumber: 10.4 Consensus size: 98
364736 CAGGTTTTAC
*
364746 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * *
364811 GACGAAGGGACTGCTGGTTGTCGATAAACAATG
66 GACGAAGGGACCGCTGGTTGTCAATAAACAATT
* * *
364844 CCAGAGCTAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCAT
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * *
364909 GACGAATGGACCGCTAGTTGTCGATAAACAATT
66 GACGAAGGGACCGCTGGTTGTCAATAAACAATT
* * * *
364942 TCAGAGACAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTTAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
365007 AACGAAGGGACCGCTGGTTGTCGATAAACAATT
66 GACGAAGGGACCGCTGGTTGTCAATAAACAATT
* *
365040 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
365105 GACGAAGGGACCGCTAGTTGTCAATAAACAATT
66 GACGAAGGGACCGCTGGTTGTCAATAAACAATT
* * * * *
365138 TCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGATAATGCAAGTTTAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
365203 GACGAAGGGAACGCTGGTTGTCAATAAATAATT
66 GACGAAGGGACCGCTGGTTGTCAATAAACAATT
* *
365236 TCAGAGCCAATTTCAAGTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
365301 GACGAAGGGACCGCTGGTTGTCAATAAACAAACTTCT
66 GACGAAGGGACCGCTGGTTGTCAATAAAC-AA--T-T
*
365338 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAAC
1 C-----CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
365403 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATT
61 TTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA-----CAATT
365449 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
365514 GACGAAGGGACTGCTGGTTGTCAATAAACAACTTCT
66 GACGAAGGGACCGCTGGTTGTCAATAAACAA--T-T
365550 CAATTTCAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 C-----C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
365615 CTTCACGACGAAGGGACCGCTGGTTTTCAATAAACAACTTCT
60 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA--T-T
365657 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 C-----CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
365722 TTGACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
61 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TT
* *
365761 CCCAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 -CCAG----AG--CCAATTTCAACTTCACAACGAAGGATATTGGACTC
365809 GGAACAATAC
Statistics
Matches: 885, Mismatches: 47, Indels: 58
0.89 0.05 0.06
Matches are distributed among these distances:
98 453 0.51
99 2 0.00
100 4 0.00
101 3 0.00
102 1 0.00
103 2 0.00
104 4 0.00
105 3 0.00
106 213 0.24
107 191 0.22
109 1 0.00
110 2 0.00
111 2 0.00
112 1 0.00
114 2 0.00
115 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (98 bp):
CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAATAAACAATT
Found at i:365418 original size:107 final size:106
Alignment explanation
Indices: 365232--365808 Score: 1019
Period size: 106 Copynumber: 5.4 Consensus size: 106
365222 GTCAATAAAT
*
365232 AATTTCAGAGCCAATTTCAAGTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
365297 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAAACTTCTC
66 TCACGACGAAGGGACCGCTGGTTGTCAATAAAC-AACTTCTC
*
365339 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
365404 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
66 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
*
365445 AATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
365510 TCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCTC
66 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
365551 AATTTCAAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 AATTTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
365616 TTCACGACGAAGGGACCGCTGGTTTTCAATAAACAACTTCTC
65 TTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
365658 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
1 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
365723 TGACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
66 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
* * * * *
365764 AGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
365809 GGAACAATAC
Statistics
Matches: 452, Mismatches: 17, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
106 252 0.56
107 200 0.44
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
Found at i:367677 original size:29 final size:30
Alignment explanation
Indices: 367627--367683 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
367617 TTTTGTTCAT
* *
367627 TTTATCTTATTTTATTTCTATTTTTATTGA
1 TTTATCTTATTTTATCTCTATTATTATTGA
367657 TTTAT-TTATTTT-TCTCATATTATTATT
1 TTTATCTTATTTTATCTC-TATTATTATT
367684 TTTCTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 16 0.67
30 5 0.21
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (30 bp):
TTTATCTTATTTTATCTCTATTATTATTGA
Found at i:372979 original size:126 final size:125
Alignment explanation
Indices: 372775--373153 Score: 386
Period size: 126 Copynumber: 3.0 Consensus size: 125
372765 GACACGACAT
* * * * **
372775 AATGAGGAAATCTAGTCAGGTGATGACAC-GACTCATACGTGATGAA-GAGTTTTGGCCATCTAA
1 AATGAGAAAATCTGGTCAAGTGATGACACTG-CTCATA--TG-TTAATGAGTCGTGGCCATCTAA
** * *
372838 ATGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGCTATCTGGGTTGACACAGCTCCTACAA
62 GGGAGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACAC-GCTCCTACAA
* * * * * *
372903 AATGA-AGAGATCTGGTCAAGTGATGACACTGTTTATATGTTCATGAGTCTTGGCCATGTAAGGG
1 AATGAGA-AAATCTGGTCAAGTGATGACACTGCTCATATGTTAATGAGTCGTGGCCATCTAAGGG
* * * * **
372967 AGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTGAGTTGACATGGTTCCTACGT
65 AGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACA-CGCTCCTACAA
* * * *
373029 GATGAGAAAATCTGGTCATGTGATGACACTGCTCATTTGTTAATGAGTCGTGGCCATCTAAGGGT
1 AATGAGAAAATCTGGTCAAGTGATGACACTGCTCATATGTTAATGAGTCGTGGCCATCTAAGGGA
* * * *
373094 GATAACACGGTTCCTACATGATGAAGACGCCTGGTTATCTATGGTTGACACGACTCCTAC
66 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT-GGGTTGACACG-CTCCTAC
373154 GTGATGAGGA
Statistics
Matches: 206, Mismatches: 38, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
125 2 0.01
126 161 0.78
127 14 0.07
128 28 0.14
129 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (125 bp):
AATGAGAAAATCTGGTCAAGTGATGACACTGCTCATATGTTAATGAGTCGTGGCCATCTAAGGGA
GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTGACACGCTCCTACAA
Found at i:373367 original size:63 final size:67
Alignment explanation
Indices: 373290--373418 Score: 185
Period size: 68 Copynumber: 2.0 Consensus size: 67
373280 AAAGAGACAA
*
373290 AATTCATTTCAAGGG-AATGA-CTCAAAGATG-T-TTTTGTTTCAAGAGAAACAAACTCAAAGAT
1 AATTCATTTCAAGGGAAATAATCTCAAAGATGTTGTTTTGTTTCAAGAGAAACAAACTCAAAGAT
373351 TT
66 TT
* * *
373353 AATTCGTTTTAAGGGAAATAATCTCAAAGATGTTTGTTTTGTTTCAAGAGAAACAGACTCAAAGA
1 AATTCATTTCAAGGGAAATAATCTCAAAGATG-TTGTTTTGTTTCAAGAGAAACAAACTCAAAGA
373418 T
65 T
373419 GGGTATTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
63 13 0.23
64 4 0.07
65 10 0.18
67 1 0.02
68 29 0.51
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (67 bp):
AATTCATTTCAAGGGAAATAATCTCAAAGATGTTGTTTTGTTTCAAGAGAAACAAACTCAAAGAT
TT
Found at i:373582 original size:33 final size:33
Alignment explanation
Indices: 373545--373608 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
373535 GAGAAATTAT
* * *
373545 CTCAAAGATGGTTGTTGTTTCCAGTGAAACAGA
1 CTCAAAGATGATTGTTATTTCAAGTGAAACAGA
*
373578 CTCAAAGATGATTTTTATTTCAAGTGAAACA
1 CTCAAAGATGATTGTTATTTCAAGTGAAACA
373609 ATTTTAGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (33 bp):
CTCAAAGATGATTGTTATTTCAAGTGAAACAGA
Found at i:373971 original size:34 final size:34
Alignment explanation
Indices: 373931--374085 Score: 247
Period size: 34 Copynumber: 4.6 Consensus size: 34
373921 TCTTAGAGAA
*
373931 AAATTGTCTCAAGCGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
**
373965 AAATTGTCTCAAGTGAGATGAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
* * *
373999 AAATTATCTCAAGTGAGACGAAATTTGTTTTAAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
*
374033 AAATTGTCTCAAGTGAGACAAAATTTGTTTTTAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
374067 AAATTGTCTCAAGTGAGAC
1 AAATTGTCTCAAGTGAGAC
374086 GAATTTTTTT
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 112 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (34 bp):
AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
Found at i:374103 original size:68 final size:68
Alignment explanation
Indices: 373931--374103 Score: 244
Period size: 68 Copynumber: 2.5 Consensus size: 68
373921 TCTTAGAGAA
* * **
373931 AAATTGTCTCAAGCGAGACAAAATTTGTTTT-GAGAAATTGTCTCAAGTGAGATGAAATTTGTTT
1 AAATTGTCTCAAGTGAGAC-GAATTTGTTTTAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTT
373995 TGAG
65 TGAG
*
373999 AAATTATCTCAAGTGAGACGAAATTTGTTTTA-AGAAATTGTCTCAAGTGAGACAAAATTTGTTT
1 AAATTGTCTCAAGTGAGACG-AATTTGTTTTAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTT
*
374063 TTAG
65 TGAG
374067 AAATTGTCTCAAGTGAGACGAATTT-TTTTAAGAGAAA
1 AAATTGTCTCAAGTGAGACGAATTTGTTTT-AGAGAAA
374104 CAACATCAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
66 4 0.04
67 6 0.06
68 84 0.89
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (68 bp):
AAATTGTCTCAAGTGAGACGAATTTGTTTTAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTT
GAG
Found at i:375355 original size:7 final size:7
Alignment explanation
Indices: 375281--375425 Score: 71
Period size: 7 Copynumber: 19.1 Consensus size: 7
375271 TTTTTCTTTG
375281 TTTTTTC
1 TTTTTTC
375288 TTTATTTTC
1 -TT-TTTTC
*
375297 TTTTGCTC
1 TTTT-TTC
375305 TTTGTTGCTC
1 TTT-TT--TC
* *
375315 TTTTATA
1 TTTTTTC
*
375322 TTTTCTC
1 TTTTTTC
375329 TTTATTT-
1 TTT-TTTC
375336 TTTCTTTC
1 TTT-TTTC
*
375344 CTTTTTC
1 TTTTTTC
375351 TTTTTTC
1 TTTTTTC
375358 TCTTTTTC
1 T-TTTTTC
*
375366 ATTTTTC
1 TTTTTTC
375373 TCTTTTTC
1 T-TTTTTC
375381 ATTTTTTC
1 -TTTTTTC
375389 TTTGCTTT-
1 TTT--TTTC
375397 TTTTCTT-
1 TTTT-TTC
375404 TTTTTTC
1 TTTTTTC
* *
375411 TCTTCTC
1 TTTTTTC
375418 TTTTTTC
1 TTTTTTC
375425 T
1 T
375426 CTGATTGCTC
Statistics
Matches: 107, Mismatches: 16, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
6 3 0.03
7 54 0.50
8 34 0.32
9 11 0.10
10 5 0.05
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.75
Consensus pattern (7 bp):
TTTTTTC
Found at i:375357 original size:31 final size:31
Alignment explanation
Indices: 375322--375389 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
375312 CTCTTTTATA
**
375322 TTTTCTCTTTATTTTTTCTTTC-CTTTTTC-TT
1 TTTTCTCTTT-TTCATT-TTTCTCTTTTTCATT
375353 TTTTCTCTTTTTCATTTTTCTCTTTTTCATT
1 TTTTCTCTTTTTCATTTTTCTCTTTTTCATT
375384 TTTTCT
1 TTTTCT
375390 TTGCTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 4 0.12
30 11 0.33
31 18 0.55
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTTCTCTTTTTCATTTTTCTCTTTTTCATT
Found at i:375363 original size:14 final size:14
Alignment explanation
Indices: 375283--375427 Score: 79
Period size: 15 Copynumber: 10.1 Consensus size: 14
375273 TTTCTTTGTT
375283 TTTTCTTTATTT-TC
1 TTTTCTTT-TTTCTC
375297 TTTTGCTCTTTGTTGCTC
1 TTTT-CT-TTT-TT-CTC
* *
375315 TTTTATATTTTCTC
1 TTTTCTTTTTTCTC
*
375329 TTTAT-TTTTTCTTTCC
1 TTT-TCTTTTT-TCT-C
375345 TTTTTCTTTTTTCTC
1 -TTTTCTTTTTTCTC
*
375360 TTTTTCATTTTTCTC
1 -TTTTCTTTTTTCTC
*
375375 TTTTTCATTTTT-TC
1 -TTTTCTTTTTTCTC
*
375389 TTTGCTTTTTT-TC
1 TTTTCTTTTTTCTC
375402 --TT-TTTTTTCTC
1 TTTTCTTTTTTCTC
*
375413 TTCTCTTTTTTCTC
1 TTTTCTTTTTTCTC
375427 T
1 T
375428 GATTGCTCTT
Statistics
Matches: 107, Mismatches: 10, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
10 6 0.06
11 3 0.03
13 12 0.11
14 26 0.24
15 35 0.33
16 10 0.09
17 9 0.08
18 6 0.06
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTTCTC
Found at i:376646 original size:8 final size:8
Alignment explanation
Indices: 376626--376655 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
376616 ATAAATGCAT
376626 ATGCAAA-
1 ATGCAAAG
376633 ATGCAAAG
1 ATGCAAAG
376641 ATGCAAAG
1 ATGCAAAG
376649 ATGCAAA
1 ATGCAAA
376656 TGCATATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (8 bp):
ATGCAAAG
Found at i:376654 original size:16 final size:15
Alignment explanation
Indices: 376626--376655 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
376616 ATAAATGCAT
376626 ATGCAAAATGCAAAG
1 ATGCAAAATGCAAAG
376641 ATGCAAAGATGCAAA
1 ATGCAAA-ATGCAAA
376656 TGCATATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (15 bp):
ATGCAAAATGCAAAG
Found at i:378906 original size:23 final size:22
Alignment explanation
Indices: 378855--378907 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
378845 AAACATTCAC
378855 ATAAATATATTTAATTAATAAA
1 ATAAATATATTTAATTAATAAA
* *
378877 AGAAAATATATTTGAATTTAAT-TA
1 A-TAAATATATTT-AA-TTAATAAA
378901 ATAAATA
1 ATAAATA
378908 AGCATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.04
23 15 0.60
24 4 0.16
25 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
ATAAATATATTTAATTAATAAA
Found at i:389382 original size:22 final size:22
Alignment explanation
Indices: 389357--389406 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
389347 TCACTCTCTA
* *
389357 CGGCGATATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATATC
389379 CGGCGAAATCCGTCCCCATATC
1 CGGCGAAATCCGTCCCCATATC
389401 CGGCGA
1 CGGCGA
389407 CCCCCCTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.42, G:0.22, T:0.18
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATATC
Found at i:389846 original size:20 final size:19
Alignment explanation
Indices: 389807--389860 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
389797 AAATCGTAAC
*
389807 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTAGCGTT
*
389826 GCGATTTTCATTTTAGCGTT
1 GCGATTTT-AGTTTAGCGTT
*
389846 GCGAATTTAAGTTTA
1 GCG-ATTTTAGTTTA
389861 AGAAACTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.19, C:0.13, G:0.22, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTAGCGTT
Found at i:391540 original size:21 final size:21
Alignment explanation
Indices: 391513--391562 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
391503 GTTAGGGGAG
391513 TTACGTGATGAGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
* *
391534 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
391555 TTACGTGA
1 TTACGTGA
391563 CAACAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:391661 original size:21 final size:21
Alignment explanation
Indices: 391637--391695 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
391627 GATAATGGTG
* * *
391637 CTTTACATGGTGAGGTATCTA
1 CTTTACGTGATGAGGCATCTA
391658 CTTTACGTGATGAGGCATCTA
1 CTTTACGTGATGAGGCATCTA
391679 CTTTACGTGATGAGGCA
1 CTTTACGTGATGAGGCA
391696 GCCGCTCTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (21 bp):
CTTTACGTGATGAGGCATCTA
Found at i:392021 original size:21 final size:21
Alignment explanation
Indices: 391995--392112 Score: 150
Period size: 21 Copynumber: 5.7 Consensus size: 21
391985 GATTCACCTT
*
391995 TCATCGTTCAAGAGGCTCCTC
1 TCATCGTTCAAGAGGCCCCTC
392016 AT-ATCGTTCAAGAGGCCCCTC
1 -TCATCGTTCAAGAGGCCCCTC
392037 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
392058 -CACCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
392078 TCATCATTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
392099 CCACCGTTTAAGAG
1 TCATCGTTCAAGAG
392113 CCCGATTTAC
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
20 20 0.24
21 64 0.75
22 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:392076 original size:41 final size:41
Alignment explanation
Indices: 391995--392112 Score: 164
Period size: 41 Copynumber: 2.8 Consensus size: 41
391985 GATTCACCTT
* * *
391995 TCATCGTTCAAGAGGCTCCTCATATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC-CACCGTTCAAGAGGCCCCTC
392037 TCATCGTTCAAGAGGCCCCTCCACCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCACCGTTCAAGAGGCCCCTC
* * *
392078 TCATCATTCAAGAGGTCCCTCCCACCGTTTAAGAG
1 TCATCGTTCAAGAGGCCCCT-CCACCGTTCAAGAG
392113 CCCGATTTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
41 36 0.52
42 33 0.48
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (41 bp):
TCATCGTTCAAGAGGCCCCTCCACCGTTCAAGAGGCCCCTC
Found at i:393606 original size:20 final size:20
Alignment explanation
Indices: 393581--393641 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
393571 GTACACTTTT
*
393581 GCAACGCGAAATTCAAATTC
1 GCAACGCGAAAGTCAAATTC
*
393601 GCAACGCAAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
393621 GCAACGCGAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
393641 G
1 G
393642 TATTACAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (20 bp):
GCAACGCGAAAGTCAAATTC
Found at i:393703 original size:20 final size:20
Alignment explanation
Indices: 393654--393703 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
393644 TTACAATTTT
* *
393654 CGCGTTGCGATAGTCAAATT
1 CGCGTTGCGAAAGTCAAATC
***
393674 CGCAAAGCGAAAGTCAAATC
1 CGCGTTGCGAAAGTCAAATC
393694 CGCGTTGCGA
1 CGCGTTGCGA
393704 TTGTTGCGAA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (20 bp):
CGCGTTGCGAAAGTCAAATC
Found at i:393866 original size:20 final size:20
Alignment explanation
Indices: 393843--393893 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
393833 TTTCGCGTAG
393843 CGAATTTGACTATCACAACA
1 CGAATTTGACTATCACAACA
* *
393863 CGAATTTGACTATCGCAACG
1 CGAATTTGACTATCACAACA
393883 CGAATTTGACT
1 CGAATTTGACT
393894 CAAGTTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (20 bp):
CGAATTTGACTATCACAACA
Found at i:393868 original size:40 final size:40
Alignment explanation
Indices: 393818--393893 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
393808 GCGAAAATTG
* * *
393818 CAACATGAATTTGACTTTCGCGTA-GCGAATTTGACTATCA
1 CAACACGAATTTGACTATCGC-AACGCGAATTTGACTATCA
393858 CAACACGAATTTGACTATCGCAACGCGAATTTGACT
1 CAACACGAATTTGACTATCGCAACGCGAATTTGACT
393894 CAAGTTACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (40 bp):
CAACACGAATTTGACTATCGCAACGCGAATTTGACTATCA
Found at i:394225 original size:11 final size:12
Alignment explanation
Indices: 394183--394217 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
394173 AAGGTGAAGC
*
394183 CGATTGTGATTG
1 CGATTTTGATTG
*
394195 GGATTTTGATTG
1 CGATTTTGATTG
394207 CGATTTTGATT
1 CGATTTTGATT
394218 TCATTTTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.49
Consensus pattern (12 bp):
CGATTTTGATTG
Found at i:396300 original size:12 final size:12
Alignment explanation
Indices: 396283--396308 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
396273 TTCTTCGGGG
396283 TCTTTTTCTTCT
1 TCTTTTTCTTCT
396295 TCTTTTTCTTCT
1 TCTTTTTCTTCT
396307 TC
1 TC
396309 AGGGTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTTTTCTTCT
Found at i:396574 original size:24 final size:24
Alignment explanation
Indices: 396495--396560 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
396485 CAAAATCTGA
396495 GTATTGACCAAGATCAAAGTCCGG
1 GTATTGACCAAGATCAAAGTCCGG
396519 GTATTGACCAAGATCAAAGTCCGG
1 GTATTGACCAAGATCAAAGTCCGG
396543 GTATTGACCAAGATCAAA
1 GTATTGACCAAGATCAAA
396561 TTTCGAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTCCGG
Found at i:396705 original size:12 final size:12
Alignment explanation
Indices: 396684--396717 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
396674 GGTTGTGGGT
*
396684 TTTGAGATTGTG
1 TTTGATATTGTG
396696 TTTGATATTGTG
1 TTTGATATTGTG
*
396708 TTTGGTATTG
1 TTTGATATTG
396718 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:397536 original size:20 final size:19
Alignment explanation
Indices: 397491--397597 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 19
397481 AAACATTTGC
* *
397491 GTTGCGAAAATAAAAGC-T
1 GTTGCGAAATTAAAATCGT
*
397509 GTTACGAAATTAAAATTCGT
1 GTTGCGAAATTAAAA-TCGT
*
397529 GTTGCG-AATTCGAAAATCGA
1 GTTGCGAAATT--AAAATCGT
**
397549 GTTGCGAAAAAAAAATTCGT
1 GTTGCGAAATTAAAA-TCGT
* *
397569 GTTGCG-ATTTAGAAAATCTT
1 GTTGCGAAATT--AAAATCGT
397589 GTTGCGAAA
1 GTTGCGAAA
397598 AGGAAACTTG
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
18 13 0.19
19 10 0.15
20 33 0.49
21 11 0.16
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.29
Consensus pattern (19 bp):
GTTGCGAAATTAAAATCGT
Found at i:397611 original size:20 final size:20
Alignment explanation
Indices: 397521--397636 Score: 90
Period size: 20 Copynumber: 5.8 Consensus size: 20
397511 TACGAAATTA
***
397521 AAATTCGTGTTGCGAATTCG
1 AAATTCGTGTTGCGAAAAAG
* * *
397541 AAAATCGAGTTGCGAAAAAA
1 AAATTCGTGTTGCGAAAAAG
***
397561 AAATTCGTGTTGCGATTTAG
1 AAATTCGTGTTGCGAAAAAG
* * *
397581 AAAATCTTGTTGCGAAAAGG
1 AAATTCGTGTTGCGAAAAAG
*
397601 AAACTT-GTGTTACGAAAAAG
1 AAA-TTCGTGTTGCGAAAAAG
*
397621 AAATTCGCGTTGCGAA
1 AAATTCGTGTTGCGAA
397637 TTCAGAAATC
Statistics
Matches: 70, Mismatches: 24, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
19 2 0.03
20 67 0.96
21 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (20 bp):
AAATTCGTGTTGCGAAAAAG
Found at i:397611 original size:40 final size:40
Alignment explanation
Indices: 397520--397598 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
397510 TTACGAAATT
*
397520 AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAAA
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAA
* **
397560 AAAATTCGTGTTGCGATTTAGAAAATCTTGTTGCGAAAA
1 AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAA
397599 GGAAACTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (40 bp):
AAAATTCGTGTTGCGAATTAGAAAATCGAGTTGCGAAAAA
Found at i:397652 original size:20 final size:19
Alignment explanation
Indices: 397516--397714 Score: 71
Period size: 20 Copynumber: 10.1 Consensus size: 19
397506 GCTGTTACGA
*
397516 AATTA-AAATTCGTGTTGCG
1 AATTAGAAA-TCGAGTTGCG
*
397535 AATTCGAAAATCGAGTTGCG
1 AATTAG-AAATCGAGTTGCG
** * *
397555 AAAAAAAAATTCGTGTTGCG
1 AATTAGAAA-TCGAGTTGCG
* **
397575 ATTTAGAAAATCTTGTTGCG
1 AATTAG-AAATCGAGTTGCG
* * * *
397595 AA-AAGGAAACTTGTGTTACG
1 AATTA-GAAA-TCGAGTTGCG
** *
397615 AAAAAGAAATTCGCGTTGCG
1 AATTAGAAA-TCGAGTTGCG
397635 AATTCAGAAATCGAGTTGCG
1 AATT-AGAAATCGAGTTGCG
* *
397655 AATT-GAAATTCCATGTTGCA
1 AATTAGAAA-TCGA-GTTGCG
* * *
397675 AATTTGGAAATAGCGTTGCG
1 AA-TTAGAAATCGAGTTGCG
* *
397695 AATTTGGAATCGAGTTGCG
1 AATTAGAAATCGAGTTGCG
397714 A
1 A
397715 GAATGAAATT
Statistics
Matches: 134, Mismatches: 34, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
18 4 0.03
19 28 0.21
20 82 0.61
21 16 0.12
22 4 0.03
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (19 bp):
AATTAGAAATCGAGTTGCG
Found at i:397758 original size:21 final size:21
Alignment explanation
Indices: 397734--397778 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
397724 TCGCGTTGCG
397734 ATTTCAGAAACTGAGTTGC-AA
1 ATTT-AGAAACTGAGTTGCGAA
* *
397755 ATTTGGAAACTGTGTTGCGAA
1 ATTTAGAAACTGAGTTGCGAA
397776 ATT
1 ATT
397779 GGAGTTCGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (21 bp):
ATTTAGAAACTGAGTTGCGAA
Found at i:397781 original size:20 final size:20
Alignment explanation
Indices: 397740--397778 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
397730 TGCGATTTCA
397740 GAAACTGAGTTGCAAATTTG
1 GAAACTGAGTTGCAAATTTG
*
397760 GAAACTGTGTTGCGAAATT
1 GAAACTGAGTTGC-AAATT
397779 GGAGTTCGCA
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:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
GAAACTGAGTTGCAAATTTG
Found at i:399343 original size:31 final size:31
Alignment explanation
Indices: 399271--399345 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
399261 AACATCCAAT
* * *
399271 TGACCAAAACGTAATAAAACGATAACATAGG
1 TGACCAAAACTTAATAAAACAATAACATAAG
*
399302 TGACCAAAACTTAATAAAACAATAACGTAAG
1 TGACCAAAACTTAATAAAACAATAACATAAG
399333 TGACCAAAACTTA
1 TGACCAAAACTTA
399346 TGTTTTTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACAATAACATAAG
Found at i:399939 original size:15 final size:15
Alignment explanation
Indices: 399919--399954 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
399909 AAATAATTAT
399919 AAATATATTATCATA
1 AAATATATTATCATA
**
399934 AAATATATTATTTTA
1 AAATATATTATCATA
399949 AAATAT
1 AAATAT
399955 TAATATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATATTATCATA
Found at i:404562 original size:90 final size:90
Alignment explanation
Indices: 404400--404569 Score: 268
Period size: 90 Copynumber: 1.9 Consensus size: 90
404390 CATATACAAA
* * * * *
404400 AGATAATATCCACTAAGCTTCCAAACAAATCGTTTAAAGTCTGGCCGACTTGTGAAATATCCGGT
1 AGATAAAAGCCACTAAGCTTCCAAACAAATCGTTTAAAGGCTGGCCGACTTGTGAAAAATCCAGT
**
404465 CGTATAAGCATTTTGATGTCATACC
66 CCAATAAGCATTTTGATGTCATACC
*
404490 AGATAAAAGCCACTAAGCTTCCGAACAAATCGTTTAAAGGCTGGCCGACTTGTGAAAAATCCAGT
1 AGATAAAAGCCACTAAGCTTCCAAACAAATCGTTTAAAGGCTGGCCGACTTGTGAAAAATCCAGT
404555 CCAATAAGCATTTTG
66 CCAATAAGCATTTTG
404570 CCTGCTTGCA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (90 bp):
AGATAAAAGCCACTAAGCTTCCAAACAAATCGTTTAAAGGCTGGCCGACTTGTGAAAAATCCAGT
CCAATAAGCATTTTGATGTCATACC
Found at i:413343 original size:3 final size:3
Alignment explanation
Indices: 413335--413420 Score: 120
Period size: 3 Copynumber: 28.0 Consensus size: 3
413325 TTTTCTTTAT
* *
413335 TTA TTA TTA TTC TTA TTC TTA TT- TTA TTTA TTTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA T-TA
413382 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
413421 CAGGCCCAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.03
3 64 0.84
4 10 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:414733 original size:40 final size:41
Alignment explanation
Indices: 414654--414747 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 41
414644 ACTTTTTATA
* *
414654 TTTTAATATTATAGTTTTAATTTCATTTATTTTAGTTATTG
1 TTTTAATATTATAGTTTTAATTTCATATATTTTAATTATTG
* * *
414695 TTTTAATTTTATA-TTTTATTTTCA-ATATATTTAATTATTA
1 TTTTAATATTATAGTTTTAATTTCATATAT-TTTAATTATTG
*
414735 TTATTATTATTAT
1 TT-TTAATATTAT
414748 TTAGTCATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.07
40 21 0.48
41 20 0.45
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (41 bp):
TTTTAATATTATAGTTTTAATTTCATATATTTTAATTATTG
Found at i:414739 original size:46 final size:46
Alignment explanation
Indices: 414637--414739 Score: 106
Period size: 46 Copynumber: 2.2 Consensus size: 46
414627 TAATTACTAG
* *
414637 TTTTATTACTTTTTATATTTTAATATTATAGTTTTAATTTCATTTA
1 TTTTATTATTTTTTATATTTTAATATTATAGTTTTAATATCATTTA
*
414683 TTTTAGTTATTGTTTTA-ATTTT-ATATTTTA-TTTTCAATAT-ATTTAA
1 TTTTA-TTATT-TTTTATATTTTAATATTATAGTTTT-AATATCATTT-A
414729 TTATTATTATT
1 TT-TTATTATT
414740 ATTATTATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
45 8 0.16
46 24 0.49
47 12 0.24
48 5 0.10
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (46 bp):
TTTTATTATTTTTTATATTTTAATATTATAGTTTTAATATCATTTA
Found at i:415025 original size:15 final size:15
Alignment explanation
Indices: 415005--415034 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
414995 TTTAGAGAAA
415005 TATTTTATTAATATT
1 TATTTTATTAATATT
*
415020 TATTTTTTTAATATT
1 TATTTTATTAATATT
415035 AAGAAATGGG
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTATTAATATT
Found at i:415672 original size:13 final size:13
Alignment explanation
Indices: 415654--415695 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
415644 ACTTATAATA
415654 TTTATTATATTTT
1 TTTATTATATTTT
415667 TTTATTATTAATTTT
1 TTTATTA-T-ATTTT
*
415682 TTTATTTTATTTT
1 TTTATTATATTTT
415695 T
1 T
415696 AGATATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 13 0.50
14 2 0.08
15 11 0.42
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTATATTTT
Found at i:416548 original size:36 final size:36
Alignment explanation
Indices: 416500--416569 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
416490 GCTATGCACT
* * *
416500 CAAAGATCCTGTTATATTAATACCAAAAGTATTCCA
1 CAAAGATACTGTTAGATTAATACCAAAAGCATTCCA
*
416536 CAAAGATACTGTTAGATTGATACCAAAAGCATTC
1 CAAAGATACTGTTAGATTAATACCAAAAGCATTC
416570 TACGGTAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (36 bp):
CAAAGATACTGTTAGATTAATACCAAAAGCATTCCA
Found at i:417110 original size:43 final size:44
Alignment explanation
Indices: 417035--417121 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
417025 TGGCTTTAGA
* *
417035 GAAGTTAGGAGAGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGAGAGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
** * *
417078 GAAGTTAGGATTGAAAGCTGTCCTCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGAGAGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
417122 TGATGCACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 26 0.70
44 11 0.30
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (44 bp):
GAAGTTAGGAGAGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
Found at i:417321 original size:15 final size:14
Alignment explanation
Indices: 417295--417326 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
417285 TATATTTCAA
417295 TTTGCATTTTGCAT
1 TTTGCATTTTGCAT
417309 TTTGCATTTTTGCAT
1 TTTGCA-TTTTGCAT
417324 TTT
1 TTT
417327 TATATTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (14 bp):
TTTGCATTTTGCAT
Found at i:417327 original size:8 final size:7
Alignment explanation
Indices: 417295--417326 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
417285 TATATTTCAA
417295 TTTGCAT
1 TTTGCAT
417302 TTTGCAT
1 TTTGCAT
417309 TTTGCATT
1 TTTGCA-T
417317 TTTGCAT
1 TTTGCAT
417324 TTT
1 TTT
417327 TATATTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (7 bp):
TTTGCAT
Found at i:420614 original size:7 final size:8
Alignment explanation
Indices: 420577--420613 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
420567 TAAAAAAATA
420577 AAAAAAGG
1 AAAAAAGG
**
420585 GGAAAAGG
1 AAAAAAGG
420593 AAAAAAGG
1 AAAAAAGG
420601 AAAAAAGG
1 AAAAAAGG
420609 AAAAA
1 AAAAA
420614 GTTAAATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:424857 original size:54 final size:54
Alignment explanation
Indices: 424775--425146 Score: 475
Period size: 54 Copynumber: 6.9 Consensus size: 54
424765 CAGAAATATG
* * *
424775 TGCAGAAGCCACAGGAAATGATAAATGTGTTGTCAAATGTTTTACGAACATTTA
1 TGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATTTA
* *
424829 TGTCA-AAACCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 TG-CAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACAT-TTA
* * *
424884 -GCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTATGAACATCTG
1 TGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATTTA
* * * * * *
424937 TGCAGAAGCCACAGGAAAGGATAAATGTATTGTCAAATATTTTACGAACATCTA
1 TGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATTTA
* * * *
424991 TGCCGAAACCACAGGAAATGATGAATGAGTTGTCAAATGTTTTACGAACATATGA
1 TGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACAT-TTA
* * *
425046 -GCA-AAACCACAGGGAAAGATGAATGTGTTGTCAAATGTTTTAAGAACATCTGA
1 TGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACAT-TTA
*
425099 -GCAGAATCCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
1 TGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
425147 CAATGATTAT
Statistics
Matches: 277, Mismatches: 35, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
53 50 0.18
54 222 0.80
55 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (54 bp):
TGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATTTA
Found at i:425040 original size:162 final size:161
Alignment explanation
Indices: 424773--425146 Score: 595
Period size: 162 Copynumber: 2.3 Consensus size: 161
424763 ACCAGAAATA
* * *
424773 TGTGCAGAAGCCACAGGAAATGATAAATGTGTTGTCAAATGTTTTACGAACATTTATGTCAAAAC
1 TGTGCAGAAGCCACAGGAAAAGATAAATGTGTTGTCAAATGTTTTACGAACATCTATGCCAAAAC
* *
424838 CACAAGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGCAGAAACCACAGGAAAAG
66 CACAAGAAAAGATGAATGAGTTGTCAAATGTTTTACGAACATATGAGCA-AAACCACAGGAAAAG
*
424903 ATGAATGTGTTGTCAAATGTTTTATGAACATC
130 ATGAATGTGTTGTCAAATGTTTTAAGAACATC
* * * *
424935 TGTGCAGAAGCCACAGGAAAGGATAAATGTATTGTCAAATATTTTACGAACATCTATGCCGAAAC
1 TGTGCAGAAGCCACAGGAAAAGATAAATGTGTTGTCAAATGTTTTACGAACATCTATGCCAAAAC
* * *
425000 CACAGGAAATGATGAATGAGTTGTCAAATGTTTTACGAACATATGAGCAAAACCACAGGGAAAGA
66 CACAAGAAAAGATGAATGAGTTGTCAAATGTTTTACGAACATATGAGCAAAACCACAGGAAAAGA
425065 TGAATGTGTTGTCAAATGTTTTAAGAACATC
131 TGAATGTGTTGTCAAATGTTTTAAGAACATC
* * *
425096 TGAGCAGAATCCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
1 TGTGCAGAAGCCACAGGAAAAGATAAATGTGTTGTCAAATGTTTTACGAAC
425147 CAATGATTAT
Statistics
Matches: 194, Mismatches: 18, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
161 90 0.46
162 104 0.54
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (161 bp):
TGTGCAGAAGCCACAGGAAAAGATAAATGTGTTGTCAAATGTTTTACGAACATCTATGCCAAAAC
CACAAGAAAAGATGAATGAGTTGTCAAATGTTTTACGAACATATGAGCAAAACCACAGGAAAAGA
TGAATGTGTTGTCAAATGTTTTAAGAACATC
Found at i:426104 original size:112 final size:111
Alignment explanation
Indices: 425907--426460 Score: 610
Period size: 112 Copynumber: 4.9 Consensus size: 111
425897 CAAAGATTCG
* *
425907 AATTCATCACTCGATGGATCAGCATTACCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 AATTCATCACTCGATGGATCAACATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
*
425972 GGAAGAAGAAGTTCACAATGAGAAGAACTTGTTCAACCTTTTGCTC
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
*
426018 AAATTCATTACTCGATGGATCAACATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 -AATTCATCACTCGATGGATCAACATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
426083 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTC
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * * * *
426130 GAATTCATCACTCGATAGATCAGCTTTGCCGGAAGAGCTCATAATGAGAAGAACTCATTTGAAAA
1 -AATTCATCACTCGATGGATCAACATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
426195 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTAG--C
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* ** * * *
426239 --TTGATCA----ATGGATCAAGTTTTCTAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG-
1 AATTCATCACTCGATGGATCAACATTGC-CGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
426297 AGGAAGAAGAAGTCCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGACTCC
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC--TT--TTG-CT-C
* ** *** * * *
426350 ATTTCCAGAAAGAGATAGAGCAGCAGAGCCATTTTCAGGAAGAGTTCATAATGAGAAGAACTCAT
1 AATT-CATCACTCGAT-G-G-ATCA-A--CA-TTGCCGGAAGAGTTCATAATGAGAAGAACTCAT
*
426415 CTGAAG-AGGAAGAAGAAGTTCATAATAAGAAG-ACTTGTTCAACCTT
58 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
426461 AATTTAATTA
Statistics
Matches: 382, Mismatches: 36, Indels: 39
0.84 0.08 0.09
Matches are distributed among these distances:
102 47 0.12
103 31 0.08
105 2 0.01
106 6 0.02
107 2 0.01
109 1 0.00
111 5 0.01
112 200 0.52
113 2 0.01
114 2 0.01
118 2 0.01
119 1 0.00
120 1 0.00
121 5 0.01
122 1 0.00
123 12 0.03
124 58 0.15
125 4 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (111 bp):
AATTCATCACTCGATGGATCAACATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:426804 original size:3 final size:3
Alignment explanation
Indices: 426798--426858 Score: 72
Period size: 3 Copynumber: 20.0 Consensus size: 3
426788 TTTTCTTTAT
*
426798 TTA TTA TTA TTC TTA TTA TTA TTA -TA TTTA TTTA TTA TTA -TA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA -TTA
426844 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
426859 CAAGCCCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.77
4 8 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:426831 original size:31 final size:31
Alignment explanation
Indices: 426793--426853 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
426783 AGTTTTTTTC
426793 TTTATTTATTATTAT-TCTTATTATTATTATA
1 TTTATTTATTATTATAT-TTATTATTATTATA
426824 TTTATTTATTATTATATTTATTATTATTAT
1 TTTATTTATTATTATATTTATTATTATTAT
426854 TATTACAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (31 bp):
TTTATTTATTATTATATTTATTATTATTATA
Found at i:428327 original size:41 final size:41
Alignment explanation
Indices: 428247--428327 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
428237 ACTTTTTATA
* *
428247 TTTTAATATTATAGTTCTAATTTCATTTATTTTAGTTATTG
1 TTTTAATATTATAGTTCTAATTTCATATATTTTAATTATTG
* *
428288 TTTTAATTTTATATGTT-TAGTTTCA-ATATATTTAATTATT
1 TTTTAATATTATA-GTTCTAATTTCATATAT-TTTAATTATT
428328 ATTATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
40 3 0.09
41 28 0.82
42 3 0.09
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (41 bp):
TTTTAATATTATAGTTCTAATTTCATATATTTTAATTATTG
Found at i:433234 original size:22 final size:22
Alignment explanation
Indices: 433209--433262 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
433199 CAATCCAGTT
433209 ACACCTAAGAGAGACCTTTATA
1 ACACCTAAGAGAGACCTTTATA
433231 ACACCTAAGAGAGACCTTTATA
1 ACACCTAAGAGAGACCTTTATA
* *
433253 TCACCGAAGA
1 ACACCTAAGA
433263 TGAGTATGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (22 bp):
ACACCTAAGAGAGACCTTTATA
Found at i:450965 original size:29 final size:29
Alignment explanation
Indices: 450930--450986 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
450920 ATTGTCACAT
450930 AACTAAATTGATGTAAGCAATGACATCAG
1 AACTAAATTGATGTAAGCAATGACATCAG
450959 AACTAAATTGATGTAAGCAATGACATCA
1 AACTAAATTGATGTAAGCAATGACATCA
450987 AATTAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAG
Found at i:456818 original size:200 final size:197
Alignment explanation
Indices: 456461--456860 Score: 773
Period size: 200 Copynumber: 2.0 Consensus size: 197
456451 AACGTTAGCC
456461 AACTATCACTGTCTTTTCCTGCAACTTATGTCTAAATAATCGATTCAAATAAGCCTTCCACCTTT
1 AACTATCACTGTCTTTTCCTGCAACTTATGTCTAAATAATCGATTCAAATAAGCCTTCCACCTTT
456526 GCAGCTCTACTGATGTCTGATATATATCTGTTCTACTTTCTGTACTTAAATTTTACAAAAGTTTC
66 GCAGCTCTACTGATGTCTGATATATATCTGTTCTACTTTCTGTACTTAAATTTTACAAAAGTTTC
456591 AAGAGATGCCATACTGCGGCCAAAGTGGTGAATGCACCAGCAATGAGAGGCGATGATGCAGGACC
131 AAGAGATGCCATACTGCGGCCAAAGTGGTGAATGCACCAGCAATGAGAGGCGATGATGCAGGACC
456656 GG
196 GG
456658 AACTAATCACTGTCTTTTCCTGCAACTTATGTCTAAATAATCGATTCAAATAAGCCTTCCACCTT
1 AACT-ATCACTGTCTTTTCCTGCAACTTATGTCTAAATAATCGATTCAAATAAGCCTTCCACCTT
456723 TGCCAGCTCTACTGATGTCTGATATATATCTGTTTCTACTTTCTGTACTTAAATTTTACAAAAGT
65 TG-CAGCTCTACTGATGTCTGATATATATCTG-TTCTACTTTCTGTACTTAAATTTTACAAAAGT
456788 TTCAAGAGATGCCATACTGCGGCCAAAGTGGTGAATGCACCAGCAATGAGAGGCGATGATGCAGG
128 TTCAAGAGATGCCATACTGCGGCCAAAGTGGTGAATGCACCAGCAATGAGAGGCGATGATGCAGG
456853 ACCGG
193 ACCGG
456858 AAC
1 AAC
456861 CAGCCGAGAC
Statistics
Matches: 200, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
197 4 0.02
198 62 0.31
199 29 0.14
200 105 0.52
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (197 bp):
AACTATCACTGTCTTTTCCTGCAACTTATGTCTAAATAATCGATTCAAATAAGCCTTCCACCTTT
GCAGCTCTACTGATGTCTGATATATATCTGTTCTACTTTCTGTACTTAAATTTTACAAAAGTTTC
AAGAGATGCCATACTGCGGCCAAAGTGGTGAATGCACCAGCAATGAGAGGCGATGATGCAGGACC
GG
Found at i:459286 original size:17 final size:18
Alignment explanation
Indices: 459252--459289 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
459242 CTAAAACATT
459252 AAACCTAATAAAATACTA
1 AAACCTAATAAAATACTA
* *
459270 AAACCTATTTAAA-ACTA
1 AAACCTAATAAAATACTA
459287 AAA
1 AAA
459290 TACCTAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.24
Consensus pattern (18 bp):
AAACCTAATAAAATACTA
Found at i:461016 original size:17 final size:16
Alignment explanation
Indices: 460994--461025 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
460984 CTGTTTAGAG
460994 AAAAATAAAATGAAATT
1 AAAAATAAAAT-AAATT
461011 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
461026 GGAATGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAAATAAAATAAATT
Found at i:461037 original size:14 final size:15
Alignment explanation
Indices: 460996--461053 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 15
460986 GTTTAGAGAA
460996 AAATAAAATG-AAAT
1 AAATAAAATGAAAAT
*
461010 -TA-AAAAT-AAAAT
1 AAATAAAATGAAAAT
**
461022 AAATGGAATG-AAAT
1 AAATAAAATGAAAAT
461036 AAATAAAATGAAAAT
1 AAATAAAATGAAAAT
461051 AAA
1 AAA
461054 ACGAAATGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
12 9 0.27
13 2 0.06
14 15 0.45
15 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (15 bp):
AAATAAAATGAAAAT
Found at i:461392 original size:16 final size:16
Alignment explanation
Indices: 461368--461407 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
461358 AGTTTTAAAA
461368 GAAATTCTACTATCGT
1 GAAATTCTACTATCGT
*
461384 GATATTCTACTATCGT
1 GAAATTCTACTATCGT
461400 GAAATTCT
1 GAAATTCT
461408 TTAGTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (16 bp):
GAAATTCTACTATCGT
Found at i:464436 original size:18 final size:17
Alignment explanation
Indices: 464405--464471 Score: 95
Period size: 18 Copynumber: 4.0 Consensus size: 17
464395 ATAACATTAA
464405 TTGAAGCT-TAAGTCAC
1 TTGAAGCTCTAAGTCAC
464421 TTGAAGCTCCTAAGTCAC
1 TTGAAGCT-CTAAGTCAC
464439 TTGAAG--CTAAGTCAC
1 TTGAAGCTCTAAGTCAC
464454 TTGAAGCTCTTAAGTCAC
1 TTGAAGCTC-TAAGTCAC
464472 ATTGCATGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
15 15 0.33
16 8 0.17
17 1 0.02
18 22 0.48
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (17 bp):
TTGAAGCTCTAAGTCAC
Found at i:464450 original size:15 final size:15
Alignment explanation
Indices: 464405--464461 Score: 78
Period size: 15 Copynumber: 3.5 Consensus size: 15
464395 ATAACATTAA
464405 TTGAAGCTTAAGTCAC
1 TTGAAGC-TAAGTCAC
464421 TTGAAGCTCCTAAGTCAC
1 TTGAAG---CTAAGTCAC
464439 TTGAAGCTAAGTCAC
1 TTGAAGCTAAGTCAC
464454 TTGAAGCT
1 TTGAAGCT
464462 CTTAAGTCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 17 0.45
16 6 0.16
18 14 0.37
19 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (15 bp):
TTGAAGCTAAGTCAC
Found at i:464453 original size:33 final size:34
Alignment explanation
Indices: 464405--464471 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
464395 ATAACATTAA
464405 TTGAAGCTTAAGTCACTTGAAGCTCCTAAGTCAC
1 TTGAAGCTTAAGTCACTTGAAGCTCCTAAGTCAC
*
464439 TTGAAGC-TAAGTCACTTGAAGCTCTTAAGTCAC
1 TTGAAGCTTAAGTCACTTGAAGCTCCTAAGTCAC
464472 ATTGCATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (34 bp):
TTGAAGCTTAAGTCACTTGAAGCTCCTAAGTCAC
Found at i:464954 original size:68 final size:68
Alignment explanation
Indices: 464845--464980 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
464835 CTCTTGTTCT
464845 TCCTAATGTGTGACTTTTTCTGTTGGAACTTCGGGTGAGATAACTTTTCCACTTCGGAGTGTGAT
1 TCCTAATGTGTGACTTTTTCTGTTGGAACTTCGGGTGAGATAACTTTTCCACTTCGGAGTGTGAT
464910 GAC
66 GAC
464913 TCCTAATGTGTGACTTTTTCTGTTGGAACTTCGGGTGAGATAACTTTTCCACTTCGGAGTGTGAT
1 TCCTAATGTGTGACTTTTTCTGTTGGAACTTCGGGTGAGATAACTTTTCCACTTCGGAGTGTGAT
464978 GAC
66 GAC
464981 ACTAACATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (68 bp):
TCCTAATGTGTGACTTTTTCTGTTGGAACTTCGGGTGAGATAACTTTTCCACTTCGGAGTGTGAT
GAC
Found at i:466338 original size:17 final size:18
Alignment explanation
Indices: 466316--466350 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
466306 ATATATTAAT
466316 AAATAAAATAA-AATAAA
1 AAATAAAATAATAATAAA
*
466333 AAATAATATAATAATAAA
1 AAATAAAATAATAATAAA
466351 TATTAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAAATAATAATAAA
Found at i:466904 original size:12 final size:12
Alignment explanation
Indices: 466884--466913 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
466874 GAAAGTATGC
466884 GAAAAATAGAGA
1 GAAAAATAGAGA
*
466896 GAAAGATAGAGA
1 GAAAAATAGAGA
466908 GAAAAA
1 GAAAAA
466914 AGAAGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:467082 original size:64 final size:63
Alignment explanation
Indices: 467011--467132 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 63
467001 TAAAACATCT
*
467011 TAAATCCTAATTAAAACACTTAAAA-TTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAACA-TTAAAACCTATTTAAACTAAAATACCTAAAAAA-AATATAATATTC
* * *
467075 TAAATCCTGATTAAAATATTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAA
1 TAAATCCTAATTAAAACATTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAA
467133 AATATAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 13 0.25
64 40 0.75
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (63 bp):
TAAATCCTAATTAAAACATTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAATATTC
Found at i:467154 original size:32 final size:32
Alignment explanation
Indices: 467113--467174 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
467103 TTTAAACTAA
467113 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
467144 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
467175 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:468639 original size:12 final size:12
Alignment explanation
Indices: 468624--468653 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
468614 AAAAGTATGC
468624 GAAAAATAGAGA
1 GAAAAATAGAGA
*
468636 GAAAGATAGAGA
1 GAAAAATAGAGA
468648 GAAAAA
1 GAAAAA
468654 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:468827 original size:64 final size:63
Alignment explanation
Indices: 468750--468871 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 63
468740 TAAAACATCT
*
468750 TAAATCCTAATTAAAACACTTAAAA-TTATTTAAACTAAAATACCTTAAAA-ATAATATAATATT
1 TAAATCCTAATTAAAACA-TTAAAACCTATTTAAACTAAAATACC-TAAAACA-AATATAATATT
468813 C
63 C
* *
468814 TAAATCCTGATTAAAATATTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAA
1 TAAATCCTAATTAAAACATTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAA
468872 AATATAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
63 18 0.34
64 35 0.66
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (63 bp):
TAAATCCTAATTAAAACATTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAATATTC
Found at i:468893 original size:32 final size:32
Alignment explanation
Indices: 468852--468913 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
468842 TTTAAACTAA
468852 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
468883 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
468914 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:469086 original size:5 final size:5
Alignment explanation
Indices: 469078--469136 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
469068 TACAGAAAAG
* * *
469078 AATAA AAT-A AATAA AAGGAA AA-AA AA-AA AATAA AAAAA TAAAAA AATAA
1 AATAA AATAA AATAA AA-TAA AATAA AATAA AATAA AATAA -AATAA AATAA
469127 AATAA AATAA
1 AATAA AATAA
469137 TAGCTCAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
4 12 0.26
5 26 0.55
6 9 0.19
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:469107 original size:8 final size:8
Alignment explanation
Indices: 469096--469128 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
469086 AAATAAAAGG
469096 AAAAA-AA
1 AAAAATAA
469103 AAAAATAA
1 AAAAATAA
469111 AAAAATAA
1 AAAAATAA
469119 AAAAATAA
1 AAAAATAA
469127 AA
1 AA
469129 TAAAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (8 bp):
AAAAATAA
Found at i:469112 original size:13 final size:13
Alignment explanation
Indices: 469081--469133 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
469071 AGAAAAGAAT
*
469081 AAAATAAATAAAA
1 AAAAAAAATAAAA
469094 GGAAAAAAAA-AAAA
1 --AAAAAAAATAAAA
*
469108 TAAAAAAATAAAA
1 AAAAAAAATAAAA
*
469121 AAATAAAATAAAA
1 AAAAAAAATAAAA
469134 TAATAGCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 7 0.21
13 15 0.45
14 4 0.12
15 7 0.21
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.11
Consensus pattern (13 bp):
AAAAAAAATAAAA
Found at i:469138 original size:13 final size:13
Alignment explanation
Indices: 469099--469138 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
469089 TAAAAGGAAA
* *
469099 AAAAAAAAATAAA
1 AAAATAAAATAAT
*
469112 AAAATAAAAAAAT
1 AAAATAAAATAAT
469125 AAAATAAAATAAT
1 AAAATAAAATAAT
469138 A
1 A
469139 GCTCAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:469138 original size:21 final size:19
Alignment explanation
Indices: 469098--469138 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
469088 ATAAAAGGAA
469098 AAAAAAAAAATAAAAAAAT
1 AAAAAAAAAATAAAAAAAT
*
469117 AAAAAAATAAAATAAAATAAT
1 -AAAAAA-AAAATAAAAAAAT
469138 A
1 A
469139 GCTCAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAAAAAAATAAAAAAAT
Found at i:471282 original size:35 final size:35
Alignment explanation
Indices: 471240--471314 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
471230 TCTAAACCCT
*
471240 AAATTAAAATATTTTAGAATTTAGGGTTTAAAATG
1 AAATTAAAATATTCTAGAATTTAGGGTTTAAAATG
* * *
471275 TAATTAAATTATTCTAGAATTTAGGGTTTAGAATG
1 AAATTAAAATATTCTAGAATTTAGGGTTTAAAATG
471310 AAATT
1 AAATT
471315 GAGGATTGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.01, G:0.15, T:0.41
Consensus pattern (35 bp):
AAATTAAAATATTCTAGAATTTAGGGTTTAAAATG
Found at i:471870 original size:19 final size:19
Alignment explanation
Indices: 471846--471886 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
471836 TTATAAAAAG
*
471846 TAAATTATAAGTTTGTATT
1 TAAATTATAACTTTGTATT
* *
471865 TAAATTATTACTTTTTATT
1 TAAATTATAACTTTGTATT
471884 TAA
1 TAA
471887 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (19 bp):
TAAATTATAACTTTGTATT
Found at i:474827 original size:3 final size:3
Alignment explanation
Indices: 474819--474852 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
474809 AAATTAGTTA
474819 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
474853 GAAAATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:474841 original size:19 final size:18
Alignment explanation
Indices: 474817--474852 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
474807 AAAAATTAGT
474817 TAAATAATAATAATAATAA
1 TAAATAATAATAA-AATAA
474836 TAAATAATAATAAAATA
1 TAAATAATAATAAAATA
474853 GAAAATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATAATAATAAAATAA
Found at i:474843 original size:16 final size:15
Alignment explanation
Indices: 474818--474852 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
474808 AAAATTAGTT
474818 AAAT-AATAATAATA
1 AAATAAATAATAATA
474832 ATAATAAATAATAATA
1 A-AATAAATAATAATA
474848 AAATA
1 AAATA
474853 GAAAATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 7 0.37
16 11 0.58
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAAATAATAATA
Found at i:476892 original size:106 final size:106
Alignment explanation
Indices: 476707--477592 Score: 1264
Period size: 106 Copynumber: 8.5 Consensus size: 106
476697 GCATTGTTCT
* * * ** *
476707 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTAGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * *
476771 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
476813 GAGTCCAATATGCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
476878 CCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
476919 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
476984 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGCTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
477025 GAGTTCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
477090 CCAGCGGTCCCTTCGTCGTGAAGTTAAACATACGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
477131 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
477196 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
477237 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
477302 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
477343 GAGTCCACTATCCTTCGCTGTGAAGTTGAAATTGACTCT-AGAATTGGAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAATTGTTTATTGACA
*
477407 ACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
477449 GAGTCCAATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * *
477502 ACAGCGGTCCCCTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
477543 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AGAATTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAA
477593 GCCCCTTCGT
Statistics
Matches: 706, Mismatches: 57, Indels: 34
0.89 0.07 0.04
Matches are distributed among these distances:
94 78 0.11
95 3 0.00
96 1 0.00
99 3 0.00
100 4 0.01
101 3 0.00
104 2 0.00
105 5 0.01
106 606 0.86
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:477545 original size:94 final size:94
Alignment explanation
Indices: 477384--477577 Score: 336
Period size: 94 Copynumber: 2.1 Consensus size: 94
477374 TTGACTCTAG
*
477384 AATTGGAAAATTGTTTATTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1 AATTGGAAAATTGTTTATTGACAACTAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
477449 GAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GAGTCCAATATCCTTCGCTGTGAAGTTGA
* *
477478 AATTGGGAAATTGTTTATTGACAAAC-AGCGGTCCCCTCGTCGTGAAGTTGAACTTGTGTTGTCT
1 AATTGGAAAATTGTTTATTGAC-AACTAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCT
477542 GGAGTCCAATATCCTTCGCTGTGAAGTTGA
65 GGAGTCCAATATCCTTCGCTGTGAAGTTGA
477572 AATTGG
1 AATTGG
477578 CTCTAGAATT
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 92 0.97
95 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (94 bp):
AATTGGAAAATTGTTTATTGACAACTAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCTG
GAGTCCAATATCCTTCGCTGTGAAGTTGA
Found at i:477666 original size:35 final size:35
Alignment explanation
Indices: 477626--477693 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
477616 CTCAAATGGC
* *
477626 ACGATATCCTCTATTATAGAGTTGAAATCGTGGGT
1 ACGATATCCTCCATCATAGAGTTGAAATCGTGGGT
* *
477661 ACGATATCCTCCGTCATGGAGTTGAAATCGTGG
1 ACGATATCCTCCATCATAGAGTTGAAATCGTGG
477694 ATGGCCCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (35 bp):
ACGATATCCTCCATCATAGAGTTGAAATCGTGGGT
Found at i:481799 original size:16 final size:16
Alignment explanation
Indices: 481778--481811 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
481768 TTATAGACTG
481778 AAAGTTAAAATCTATA
1 AAAGTTAAAATCTATA
*
481794 AAAGTTGAAATCTATA
1 AAAGTTAAAATCTATA
481810 AA
1 AA
481812 CATTAGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (16 bp):
AAAGTTAAAATCTATA
Found at i:482975 original size:2 final size:2
Alignment explanation
Indices: 482968--483029 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
482958 CCCTCTCAGA
482968 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
483010 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
483030 GCTGAGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:484840 original size:12 final size:12
Alignment explanation
Indices: 484823--484863 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
484813 CTAAAGTGTG
484823 ATAAATCTAAAT
1 ATAAATCTAAAT
484835 ATAAATCTAAAT
1 ATAAATCTAAAT
484847 ATAAATCTAAAT
1 ATAAATCTAAAT
*
484859 CTAAA
1 ATAAA
484864 GGATAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAATCTAAAT
Found at i:484851 original size:18 final size:18
Alignment explanation
Indices: 484824--484882 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
484814 TAAAGTGTGA
*
484824 TAAATCTAAATATAAATC
1 TAAATATAAATATAAATC
*
484842 TAAATATAAATCTAAATC
1 TAAATATAAATATAAATC
* *
484860 TAAAGGATAAATTTAAAGTC
1 TAAA-TATAAATATAAA-TC
484880 TAA
1 TAA
484883 GGCTCTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 20 0.57
19 10 0.29
20 5 0.14
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (18 bp):
TAAATATAAATATAAATC
Found at i:484876 original size:6 final size:6
Alignment explanation
Indices: 484824--484863 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
484814 TAAAGTGTGA
* *
484824 TAAATC TAAATA TAAATC TAAATA TAAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
484864 GGATAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATC
Found at i:486574 original size:22 final size:22
Alignment explanation
Indices: 486546--486591 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
486536 AATTTTACTG
486546 CTTTTACATGGGATGAAATGGT
1 CTTTTACATGGGATGAAATGGT
486568 CTTTTACATGGGATGAAATGGT
1 CTTTTACATGGGATGAAATGGT
486590 CT
1 CT
486592 CTCGAGCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (22 bp):
CTTTTACATGGGATGAAATGGT
Found at i:487387 original size:24 final size:23
Alignment explanation
Indices: 487353--487519 Score: 143
Period size: 24 Copynumber: 7.4 Consensus size: 23
487343 ATTATTTATA
*
487353 TATATATTATACTATTTTTAAAAT
1 TATATAATATA-TATTTTTAAAAT
*
487377 TATAT-A-ATATATTTTTAAAAA
1 TATATAATATATATTTTTAAAAT
487398 TATATAATATATTATTTTTAAAAT
1 TATATAATATA-TATTTTTAAAAT
* *
487422 TATAT-A-ACATATTTTCAAAA-
1 TATATAATATATATTTTTAAAAT
**
487442 -ATATAATATACTATTTTTCATGAT
1 TATATAATATA-TATTTTT-AAAAT
* *
487466 TGTAT-A-ATATATTTTAAAAAT
1 TATATAATATATATTTTTAAAAT
* *
487487 ATATATAATATATATTTTCAAAAC
1 -TATATAATATATATTTTTAAAAT
487511 TATATAATA
1 TATATAATA
487520 AGTTATCATA
Statistics
Matches: 115, Mismatches: 16, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
19 4 0.03
20 1 0.01
21 31 0.27
22 22 0.19
23 19 0.17
24 35 0.30
25 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (23 bp):
TATATAATATATATTTTTAAAAT
Found at i:487402 original size:45 final size:45
Alignment explanation
Indices: 487352--487519 Score: 200
Period size: 45 Copynumber: 3.8 Consensus size: 45
487342 TATTATTTAT
487352 ATATATATTATACTATTTTTAAAATTATATAATATATTTTTAAAA
1 ATATATATTATACTATTTTTAAAATTATATAATATATTTTTAAAA
* * * *
487397 ATATATAATATATTATTTTTAAAATTATATAACATATTTTCAAAA
1 ATATATATTATACTATTTTTAAAATTATATAATATATTTTTAAAA
** *
487442 ATATA-A-TATACTATTTTTCATGATTGTATAATATA-TTTTAAAA
1 ATATATATTATACTATTTTT-AAAATTATATAATATATTTTTAAAA
* *
487485 ATATATATAATATA-TATTTTCAAAACTATATAATA
1 ATATATAT--TATACTATTTTTAAAATTATATAATA
487520 AGTTATCATA
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
43 23 0.22
44 14 0.14
45 56 0.54
46 6 0.06
47 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (45 bp):
ATATATATTATACTATTTTTAAAATTATATAATATATTTTTAAAA
Found at i:487493 original size:22 final size:22
Alignment explanation
Indices: 487352--487499 Score: 126
Period size: 22 Copynumber: 6.7 Consensus size: 22
487342 TATTATTTAT
* *
487352 ATATATATTATACTATTTTTAAA
1 ATATATATAATA-TATTTTAAAA
487375 AT-TATATAATATATTTTTAAAA
1 ATATATATAATATA-TTTTAAAA
*
487397 ATATATA-ATATATTATTTTTAAA
1 ATATATATA-ATA-TATTTTAAAA
*
487420 AT-TATATAACATATTTTCAAAA
1 ATATATATAATATATTTT-AAAA
* * **
487442 ATATAATATACTAT-TTTTCATG
1 ATAT-ATATAATATATTTTAAAA
*
487464 AT-TGTATAATATATTTTAAAA
1 ATATATATAATATATTTTAAAA
487485 ATATATATAATATAT
1 ATATATATAATATAT
487500 ATTTTCAAAA
Statistics
Matches: 99, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
20 7 0.07
21 16 0.16
22 43 0.43
23 24 0.24
24 9 0.09
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (22 bp):
ATATATATAATATATTTTAAAA
Found at i:491114 original size:19 final size:19
Alignment explanation
Indices: 491063--491115 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
491053 TTTACTTTTG
*
491063 GTATTGATACTTAAGGAAA
1 GTATTGATACTTATGGAAA
491082 GTATTGATACTTATGGAAA
1 GTATTGATACTTATGGAAA
491101 GTATTGATACTTATG
1 GTATTGATACTTATG
491116 ACTTGATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.38
Consensus pattern (19 bp):
GTATTGATACTTATGGAAA
Found at i:491525 original size:22 final size:22
Alignment explanation
Indices: 491497--491548 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
491487 GTCTTTATGA
491497 CATGTTTTCTTATGCCTTTTGG
1 CATGTTTTCTTATGCCTTTTGG
491519 CATGTTTTCTTATGCCTTTTGG
1 CATGTTTTCTTATGCCTTTTGG
491541 CATGTTTT
1 CATGTTTT
491549 ACGGTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.10, C:0.17, G:0.17, T:0.56
Consensus pattern (22 bp):
CATGTTTTCTTATGCCTTTTGG
Found at i:492444 original size:142 final size:142
Alignment explanation
Indices: 492175--492459 Score: 498
Period size: 142 Copynumber: 2.0 Consensus size: 142
492165 ATACATTCCT
492175 AATGCGCATGCGATCCATGTCTCACTTGATATACTTGGCCATTTTAGGCTAGCGGATGTACGTTC
1 AATGCGCATGCGATCCATGTCTCACTTGATATACTTGGCCATTTTAGGCTAGCGGATGTACGTTC
* * *
492240 CAAATGCATGTAACTCAGGTCTCATCCAAAGTATCATGTTAGTAAACTAGAAATATGGGAGTTCT
66 CAAATGCATGTAACTCAGGTCTCATCCAAAATATCATGTTAGTAAACTAGAAAGATGAGAGTTCT
492305 GAGACTACGGTG
131 GAGACTACGGTG
* * *
492317 AATGTGCATGCGATCCATGTTTCACTTGATATACTTGGCCATTTTAGGCTAGTGGATGTACGTTC
1 AATGCGCATGCGATCCATGTCTCACTTGATATACTTGGCCATTTTAGGCTAGCGGATGTACGTTC
* *
492382 CTAATGCGTGTAACTCAGGTCTCATCCAAAATATCATGTTAGTAAACTAGAAAGATGAGAGTTCT
66 CAAATGCATGTAACTCAGGTCTCATCCAAAATATCATGTTAGTAAACTAGAAAGATGAGAGTTCT
492447 GAGACTACGGTG
131 GAGACTACGGTG
492459 A
1 A
492460 CGTTGGACTA
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 135 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (142 bp):
AATGCGCATGCGATCCATGTCTCACTTGATATACTTGGCCATTTTAGGCTAGCGGATGTACGTTC
CAAATGCATGTAACTCAGGTCTCATCCAAAATATCATGTTAGTAAACTAGAAAGATGAGAGTTCT
GAGACTACGGTG
Found at i:494057 original size:41 final size:43
Alignment explanation
Indices: 494003--494120 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 43
493993 TTTATTATAA
*
494003 AAATGTCGTAATAGAGTATAAATTTTGCGGCGTTTTA-ACC-C
1 AAATGTCGCAATAGAGTATAAATTTTGCGGCGTTTTATACCAC
* * *
494044 AAATGCCGCAATAGAGTGGT-AATTTTACGGCG-TTTATACCAC
1 AAATGTCGCAATAGAGT-ATAAATTTTGCGGCGTTTTATACCAC
* * * *
494086 AAACGTCGCAATAGAGTATACATATAGCGGCGTTT
1 AAATGTCGCAATAGAGTATAAATTTTGCGGCGTTT
494121 ATTCCTCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
40 4 0.07
41 30 0.49
42 25 0.41
43 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (43 bp):
AAATGTCGCAATAGAGTATAAATTTTGCGGCGTTTTATACCAC
Found at i:494117 original size:42 final size:40
Alignment explanation
Indices: 494012--494141 Score: 129
Period size: 42 Copynumber: 3.1 Consensus size: 40
494002 AAAATGTCGT
* *
494012 AATAGAGTATAAATTTTGCGGCGTTT-TAACCCAAATGCCGC
1 AATAGAGTAT-AATTTAGCGGCGTTTAT-ACCCAAACGCCGC
* *
494053 AATAGAGTGGTAATTTTA-CGGCGTTTATACCACAAACGTCGC
1 AATAGAGT-ATAA-TTTAGCGGCGTTTATACC-CAAACGCCGC
* *
494095 AATAGAGTATACATATAGCGGCGTTTATTCCTCAAACGCCGC
1 AATAGAGTATA-ATTTAGCGGCGTTTATACC-CAAACGCCGC
494137 AATAG
1 AATAG
494142 TATTAATCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
41 26 0.35
42 48 0.65
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (40 bp):
AATAGAGTATAATTTAGCGGCGTTTATACCCAAACGCCGC
Found at i:494183 original size:41 final size:41
Alignment explanation
Indices: 494127--494263 Score: 175
Period size: 41 Copynumber: 3.3 Consensus size: 41
494117 GTTTATTCCT
*
494127 CAAACGCCGCAATAGTATTAATCAATAGTGGAGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGAGTTTTTAGA
* * *
494168 CAAATGCCGTAATAGTGTTAATCAATAGTGGCGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGAGTTTTTAGA
* * * *
494209 CAAACACCACAATAGTGTTAATCAATAGTGGCATTTTTTTGTA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGG-AGTTTTTAG-A
*
494252 TAAACGCCGCAA
1 CAAACGCCGCAA
494264 AAAACATGTG
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 64 0.80
42 6 0.08
43 10 0.12
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (41 bp):
CAAACGCCGCAATAGTGTTAATCAATAGTGGAGTTTTTAGA
Found at i:494496 original size:137 final size:133
Alignment explanation
Indices: 494320--494621 Score: 340
Period size: 137 Copynumber: 2.2 Consensus size: 133
494310 TAAATAATAC
* * * * * * *
494320 TTTAGTGGTGTTTTTAAAAACAACGCCGCAA-AATGGTTGTATATTTTCATTTCTAGCGGCG-TT
1 TTTAATGGCGTTTTTAAATA-AACACCGCAATAA-AGTTGTATATTGTCATTTATAGCGGCGCTT
*** *
494383 TTTAAATCAATTGCCG-AAAAATACTCTTAATTTAGTGGTGTTTCTAAACCCCAAATGCCACTAA
64 TTT-AATCAAACACCGTAAAAA-ACTCTTAATTTAGTGGTGTTTCT-AA--CCAAACGCCACTAA
*
494447 AGAGTTGTAC
124 AGAGTTGTAA
*
494457 TTTAATGGCGTTTTTTACATAAACACCGCAATAAAGTTGTATATTGTCATTTATAGCGGCGCTTT
1 TTTAATGGCG-TTTTTAAATAAACACCGCAATAAAGTTGTATATTGTCATTTATAGCGGCGCTTT
* * * *
494522 TTAATCAAACACCGTAAAAAACTCTTTATTTAGTGGTGTTTGTTACCAAACGCCGCTAAAGAGTT
65 TTAATCAAACACCGTAAAAAACTCTTAATTTAGTGGTGTTTCTAACCAAACGCCACTAAAGAGTT
494587 GTAA
130 GTAA
* *
494591 TTTAGTGGCGTTTTTAAATAAACGCCGCAAT
1 TTTAATGGCGTTTTTAAATAAACACCGCAAT
494622 TGTATTCTCC
Statistics
Matches: 141, Mismatches: 20, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
133 19 0.13
134 30 0.21
136 1 0.01
137 71 0.50
138 20 0.14
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (133 bp):
TTTAATGGCGTTTTTAAATAAACACCGCAATAAAGTTGTATATTGTCATTTATAGCGGCGCTTTT
TAATCAAACACCGTAAAAAACTCTTAATTTAGTGGTGTTTCTAACCAAACGCCACTAAAGAGTTG
TAA
Found at i:494636 original size:41 final size:40
Alignment explanation
Indices: 494591--494736 Score: 115
Period size: 41 Copynumber: 3.6 Consensus size: 40
494581 AGAGTTGTAA
494591 TTTAGTGGCGTTTTTAAATAAACGCCGCAATTGTATTCTCC
1 TTTAGTGGCGTTTTTAAATAAACGCCGCAATTGT-TTCTCC
*
494632 TTTAGTGGC-TTTTTGTAATAAA---CGCAATTGTTTTCTCC
1 TTTAGTGGCGTTTTT-AAATAAACGCCGCAATTG-TTTCTCC
* * * * * *
494670 GTTAATGGCATTTTCGT-AATAAACGCCGTAATAGTTTATCCC
1 TTTAGTGGCGTTTT--TAAATAAACGCCGCAATTGTTTCT-CC
*
494712 ATT-GTGGCGTTTTTAATATAAACGC
1 TTTAGTGGCGTTTTTAA-ATAAACGC
494737 TGCCATTTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
38 21 0.25
39 12 0.14
40 6 0.07
41 36 0.42
42 10 0.12
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (40 bp):
TTTAGTGGCGTTTTTAAATAAACGCCGCAATTGTTTCTCC
Found at i:494668 original size:38 final size:39
Alignment explanation
Indices: 494616--494695 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
494606 AAATAAACGC
* * *
494616 CGCAATTGTATTCTCCTTTAGTGGC-TTTTTGTAATAAA
1 CGCAATTGTATTCTCCGTTAATGGCATTTTCGTAATAAA
*
494654 CGCAATTGTTTTCTCCGTTAATGGCATTTTCGTAATAAA
1 CGCAATTGTATTCTCCGTTAATGGCATTTTCGTAATAAA
494693 CGC
1 CGC
494696 CGTAATAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 22 0.59
39 15 0.41
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (39 bp):
CGCAATTGTATTCTCCGTTAATGGCATTTTCGTAATAAA
Done.