Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 23 of 168
Found at i:5882164 original size:18 final size:18
Alignment explanation
Indices: 5882141--5882229 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 18
5882131 ATATATAAAG
5882141 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
5882159 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
** * *
5882181 TTTTTGT-ACGTTATATA
1 TTTAAGTAATGTAATATA
*
5882198 TTTAAGTAATGTACTATA
1 TTTAAGTAATGTAATATA
*
5882216 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
5882230 GTAAGTAATG
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
17 10 0.18
18 29 0.53
19 3 0.05
20 3 0.05
21 4 0.07
22 6 0.11
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.47
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:5882210 original size:22 final size:22
Alignment explanation
Indices: 5882154--5882232 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
5882144 AAGTAATGTA
*
5882154 ATATATTTAAGTAATGTAAGTT
1 ATATATTTAAGTAATGTACGTT
*
5882176 ATAAATTT---T--TGTACGTT
1 ATATATTTAAGTAATGTACGTT
5882193 ATATATTTAAGTAATGTAC--T
1 ATATATTTAAGTAATGTACGTT
*
5882213 ATATTTTAGTAAGTAATGTA
1 ATATATT--TAAGTAATGTA
5882233 AGTAATGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
17 14 0.30
19 1 0.02
20 8 0.17
22 23 0.50
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.47
Consensus pattern (22 bp):
ATATATTTAAGTAATGTACGTT
Found at i:5885138 original size:15 final size:15
Alignment explanation
Indices: 5885066--5885147 Score: 62
Period size: 15 Copynumber: 5.5 Consensus size: 15
5885056 TTAATTGACA
*
5885066 CCCTAAA-CCCTAAAT
1 CCCTAAATCCCT-AAC
*
5885081 CCCT-AACCCCTAAC
1 CCCTAAATCCCTAAC
**
5885095 CTTTAAATCTCCTAGAC
1 CCCTAAATC-CCTA-AC
*
5885112 CCC-AAATTCCTAAC
1 CCCTAAATCCCTAAC
*
5885126 CCCTAACTCCCTAAC
1 CCCTAAATCCCTAAC
5885141 CCCTAAA
1 CCCTAAA
5885148 CCTTATATCC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
14 11 0.21
15 30 0.58
16 8 0.15
17 3 0.06
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (15 bp):
CCCTAAATCCCTAAC
Found at i:5886097 original size:14 final size:14
Alignment explanation
Indices: 5886078--5886145 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
5886068 CCGATAATTG
5886078 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
5886092 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
5886107 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
5886120 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
5886133 AAACCTTAAATCT
1 AAACCCTAAATCT
5886146 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:5886101 original size:15 final size:15
Alignment explanation
Indices: 5886081--5886118 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5886071 ATAATTGAAA
5886081 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
5886096 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
5886111 CCCTAAAT
1 CCCTAAAT
5886119 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:5886768 original size:41 final size:41
Alignment explanation
Indices: 5886704--5886982 Score: 203
Period size: 41 Copynumber: 6.8 Consensus size: 41
5886694 TTTTGTTACT
* ** *
5886704 ATTAGCGGCGCTTTTGC-AAAAACGCCGCTAAAGGTAA-ATGC
1 ATTAGCGGCGC-TTAGCTAAAAACGCCGCTAAAGACAAGA-GA
* *
5886745 ATTAGCGGCGCTTAGCTACAAACGCCGCTGAAGACAAGAGA
1 ATTAGCGGCGCTTAGCTAAAAACGCCGCTAAAGACAAGAGA
* * * * *
5886786 ATTAGTGGCGCTCAGTTAAAAACGCCGCTAAAGATC-CGACA
1 ATTAGCGGCGCTTAGCTAAAAACGCCGCTAAAGA-CAAGAGA
* * * *
5886827 ATTACCGGCGCTTA-CATAAAAACGCCGCCAAAGGCCAGAGA
1 ATTAGCGGCGCTTAGC-TAAAAACGCCGCTAAAGACAAGAGA
* * * **
5886868 ATTAGCGGCGC-TAGGATAACAACGCCGCTAAATACCCGAGCA
1 ATTAGCGGCGCTTA-GCTAAAAACGCCGCTAAAGACAAGAG-A
*** * *
5886910 A-TAGCGGCGCTTATAGAAAAACGCCGCTAAAGATC-CGAGC
1 ATTAGCGGCGCTTAGCTAAAAACGCCGCTAAAGA-CAAGAGA
* *
5886950 ATTAGCGTCGCTTAGATAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTTAGCTAAAAACGCCGCTAAAG
5886983 GTTTAAAAAA
Statistics
Matches: 191, Mismatches: 36, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
40 8 0.04
41 176 0.92
42 7 0.04
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTTAGCTAAAAACGCCGCTAAAGACAAGAGA
Found at i:5886850 original size:82 final size:81
Alignment explanation
Indices: 5886745--5886982 Score: 257
Period size: 82 Copynumber: 2.9 Consensus size: 81
5886735 AGGTAAATGC
* * * *
5886745 ATTAGCGGCGCTTAGC-TACAAACGCCGCTGAAGACAAGAGAATTAGTGGCGCTCAGTTAAAAAC
1 ATTAGCGGCGCTTA-CATAAAAACGCCGCTAAAGAC-AGAGAATTAGCGGCGCT-AGATAAAAAC
*
5886809 GCCGCTAAAGATCCGA-CA
63 GCCGCTAAAGACCCGAGCA
* * * *
5886827 ATTACCGGCGCTTACATAAAAACGCCGCCAAAGGCCAGAGAATTAGCGGCGCTAGGATAACAACG
1 ATTAGCGGCGCTTACATAAAAACGCCGCTAAA-GACAGAGAATTAGCGGCGCTA-GATAAAAACG
*
5886892 CCGCTAAATACCCGAGCA
64 CCGCTAAAGACCCGAGCA
* * * * *
5886910 A-TAGCGGCGCTTATAGAAAAACGCCGCTAAAGATCCGAGCATTAGCGTCGCTTAGATAAAAACG
1 ATTAGCGGCGCTTACATAAAAACGCCGCTAAAGA-CAGAGAATTAGCGGCGC-TAGATAAAAACG
5886974 CCGCTAAAG
64 CCGCTAAAG
5886983 GTTTAAAAAA
Statistics
Matches: 130, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
81 3 0.02
82 120 0.92
83 7 0.05
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.16
Consensus pattern (81 bp):
ATTAGCGGCGCTTACATAAAAACGCCGCTAAAGACAGAGAATTAGCGGCGCTAGATAAAAACGCC
GCTAAAGACCCGAGCA
Found at i:5887124 original size:40 final size:40
Alignment explanation
Indices: 5887062--5887137 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
5887052 AATTCCTATT
*
5887062 TTTAGCGGCGCTTCCGGAAAATCGCCACTGATGCTCTACC
1 TTTAGCGGCGCTTCCGGAAAATCGCCACTAATGCTCTACC
* * *
5887102 TTTAGCGGCGCTT-TGGCTAAATCGCCGCTAATGCTC
1 TTTAGCGGCGCTTCCGG-AAAATCGCCACTAATGCTC
5887138 GATTTTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.06
40 29 0.94
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.28
Consensus pattern (40 bp):
TTTAGCGGCGCTTCCGGAAAATCGCCACTAATGCTCTACC
Found at i:5892235 original size:38 final size:38
Alignment explanation
Indices: 5892184--5892261 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
5892174 TACCAGGAAA
*
5892184 ACCAAATGGGACAAAACCTCGGTTAAGGGAAAAATAGT
1 ACCAAATGGGACAAAACCTCGGTTAAGGGAAAAAGAGT
*
5892222 ACCAAATGGGACAAAATCTCGGTTAAGGGAAAAAGAGT
1 ACCAAATGGGACAAAACCTCGGTTAAGGGAAAAAGAGT
5892260 AC
1 AC
5892262 AATGCGTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.15
Consensus pattern (38 bp):
ACCAAATGGGACAAAACCTCGGTTAAGGGAAAAAGAGT
Found at i:5904213 original size:29 final size:27
Alignment explanation
Indices: 5904130--5904215 Score: 97
Period size: 25 Copynumber: 3.1 Consensus size: 27
5904120 TTAAAATGAC
5904130 TTTATATAAAAATAAACAAAATTTATAAA
1 TTTATAT-AAAATAAACAAAA-TTATAAA
*
5904159 ATTATATAAAATCAAAC-AAA-TA-AAA
1 TTTATATAAAAT-AAACAAAATTATAAA
5904184 TTTATATAAAAGTAAACAAAATGTATAAA
1 TTTATATAAAA-TAAACAAAAT-TATAAA
5904213 TTT
1 TTT
5904216 TAATTTTATC
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
25 17 0.35
26 6 0.12
28 10 0.20
29 16 0.33
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTATATAAAATAAACAAAATTATAAA
Found at i:5909478 original size:5 final size:5
Alignment explanation
Indices: 5909449--5909504 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
5909439 AAATATCTCA
* * *
5909449 AAAAT AAATT AAAA- ACAAAA AAACAT AACAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT A-AAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT
5909500 AAAAT
1 AAAAT
5909505 TGGTTAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
4 1 0.02
5 38 0.88
6 4 0.09
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:5910407 original size:21 final size:22
Alignment explanation
Indices: 5910367--5910407 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5910357 ATGTAAAAAT
* *
5910367 AATTTTCCATCTTCTTTTTTAA
1 AATTATCCATCTTCTATTTTAA
5910389 AATTATCCA-CTTCTATTTT
1 AATTATCCATCTTCTATTTT
5910408 GATTACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTATCCATCTTCTATTTTAA
Found at i:5912807 original size:76 final size:76
Alignment explanation
Indices: 5912613--5912824 Score: 253
Period size: 76 Copynumber: 2.8 Consensus size: 76
5912603 GACGTGCCCT
* * * * *
5912613 GCACTAGTCGAATAAATCGACAAAGATTTGCACCCAAAGCTCGTCAGATTAACTGACGGTATTAA
1 GCACTAGTCGAATAAATCGACAAAGATTTGCGCCCAGAGCTAGTCAGATAAACTGACGATATTAA
* *
5912678 TTGTGTGCCCA
66 CTGTGTACCCA
* * * *
5912689 GCACTAGTCGAATAAATTGACAAAGATTTGTGCCCAGTGCTAGTCGGATAAACTGACGATATTAA
1 GCACTAGTCGAATAAATCGACAAAGATTTGCGCCCAGAGCTAGTCAGATAAACTGACGATATTAA
*
5912754 CTGTGTACTCA
66 CTGTGTACCCA
* * * * * * *
5912765 TCACTAGTCGAATAAACCGACAAAGATTTACGCTCAGCGCTAGTAAGATAAACCGACGAT
1 GCACTAGTCGAATAAATCGACAAAGATTTGCGCCCAGAGCTAGTCAGATAAACTGACGAT
5912825 CACATACATA
Statistics
Matches: 114, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
76 114 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (76 bp):
GCACTAGTCGAATAAATCGACAAAGATTTGCGCCCAGAGCTAGTCAGATAAACTGACGATATTAA
CTGTGTACCCA
Found at i:5914100 original size:105 final size:106
Alignment explanation
Indices: 5913764--5914197 Score: 647
Period size: 106 Copynumber: 4.1 Consensus size: 106
5913754 TCAAAAAACA
* * * * *
5913764 TACTTTGAAGTTTTAAAAGGATATTTGGCTATTTGGTC-AACCAAGAAATCAAAACTCAGCACGT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAA-CGAGAAATCGAAACCCAGCACAT
*
5913828 TAGGGCACGCTTTCTCAAATTTCCAAATGCAAAATATTGCCT
65 TAGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* * * *
5913870 CACTTTGAAATTTTAGAAGGATATTTGGTTATTTGGTCAAACGAGAAATCGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
* **
5913935 AGGGTACATTTTCTCGAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* *
5913976 TACTTTGAAATTTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAATTGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
* *
5914041 AGGGCATG-TTTCTCGAATTTGCAAATGCAAAATATTGCCT
66 AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* *
5914081 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTTGAACGAAAAAATCGAAACCCAGCACAT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACG-AGAAATCGAAACCCAGCACAT
* *
5914146 TAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCT
65 TAGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
5914188 TACTTTGAAA
1 TACTTTGAAA
5914198 ACTTTTCCTT
Statistics
Matches: 298, Mismatches: 27, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
105 72 0.24
106 184 0.62
107 42 0.14
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (106 bp):
TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
AGGGCACGCTTTCTCGAATTTCCAAATGCAAAATATTGCCT
Found at i:5914358 original size:15 final size:15
Alignment explanation
Indices: 5914338--5914367 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5914328 GTAAACAAAT
5914338 TATAAAATATATATA
1 TATAAAATATATATA
5914353 TATAAAATATATATA
1 TATAAAATATATATA
5914368 AGTATGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAAAATATATATA
Found at i:5914634 original size:3 final size:3
Alignment explanation
Indices: 5914617--5914701 Score: 63
Period size: 3 Copynumber: 28.7 Consensus size: 3
5914607 AAAGAATTAA
* * *
5914617 AAT AAT AGT ACAT AAT AA- AAT AA- AAT AAT ATAT AA- ACT AAT -AC
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
*
5914660 AAT AAT AAT ACCT -AT AAT AAT AAT AAT AAT AAT AAT CAAT AA
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AA
5914702 CATAACAAGA
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
2 7 0.11
3 49 0.75
4 9 0.14
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5915440 original size:13 final size:14
Alignment explanation
Indices: 5915422--5915450 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5915412 AGGAAACACC
5915422 TTTAGT-TTTTTTT
1 TTTAGTCTTTTTTT
5915435 TTTAGTCTTTTTTT
1 TTTAGTCTTTTTTT
5915449 TT
1 TT
5915451 GAACCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTAGTCTTTTTTT
Found at i:5915993 original size:9 final size:9
Alignment explanation
Indices: 5915973--5916064 Score: 123
Period size: 9 Copynumber: 10.2 Consensus size: 9
5915963 TGTATGATTC
*
5915973 AATTAGGTT
1 AATTCGGTT
*
5915982 AATTCGGGT
1 AATTCGGTT
*
5915991 AATTCGTTT
1 AATTCGGTT
5916000 AATTCAGG-T
1 AATTC-GGTT
5916009 AATTCGGTT
1 AATTCGGTT
*
5916018 AATTCGGGT
1 AATTCGGTT
5916027 AATTCGGTT
1 AATTCGGTT
*
5916036 AATTTGGTT
1 AATTCGGTT
5916045 AATTCGGTT
1 AATTCGGTT
5916054 AATTCGGTT
1 AATTCGGTT
5916063 AA
1 AA
5916065 CCGACCGAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
8 2 0.03
9 69 0.96
10 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:5916326 original size:18 final size:18
Alignment explanation
Indices: 5916305--5916351 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
5916295 TTTGGTCTAC
*
5916305 TGTTTTGTTTTGGGTTTT
1 TGTTTTGTTTTGGGTATT
5916323 TG-TTTGTTTTGGGTATT
1 TGTTTTGTTTTGGGTATT
*
5916340 TGTTTTTTTTTG
1 TGTTTTGTTTTG
5916352 ACTATTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.02, C:0.00, G:0.26, T:0.72
Consensus pattern (18 bp):
TGTTTTGTTTTGGGTATT
Found at i:5917174 original size:45 final size:44
Alignment explanation
Indices: 5917076--5917237 Score: 166
Period size: 45 Copynumber: 3.6 Consensus size: 44
5917066 ATTTTAATCC
* * *
5917076 GCTCCACTGCAACTTCAAGGAGAT-AGGATTAG-TATCTTCAACTT
1 GCTCCACTGCAACTTCAGGGAGATAAGG-TTTGTTATCTTCATC-T
*
5917120 GCTCTACTGCAACTTCAGGGAGATAAGGTTTGTTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTATCTTCA-TCT
** * * *
5917165 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGTGATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTAT-CT-TCATCT
* *
5917211 GCTCTACTGCAACTTCAGAGAGATAAG
1 GCTCCACTGCAACTTCAGGGAGATAAG
5917238 ATCTGTAGCT
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
44 25 0.25
45 45 0.45
46 29 0.29
47 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTATCTTCATCT
Found at i:5917518 original size:128 final size:129
Alignment explanation
Indices: 5917353--5917648 Score: 400
Period size: 128 Copynumber: 2.3 Consensus size: 129
5917343 AATAAAGTCT
**
5917353 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATTTGCT-TCACTGC
1 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCT-ACTGC
* * * *
5917417 AACTTCAG-GAAGATAGGATTAGTTTCTTCAATCTGATCCAGTGCAACTTCAGGGAGATAAGATT
65 AACATCAGAG-AGATAGGATTAGTTTCTTCAATCTGACCCACTGCAACTTCAGGGAGATAAGACT
5917481 G
129 G
** ** *
5917482 GATGTGATCTGCT-TACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCTACTGCG
1 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCTACTGCA
* ** *
5917546 ACATCAGAGAGATAGGATTGGTTTCTTCTGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTG
66 ACATCAGAGAGATAGGATTAGTTTCTTCAATCTGACCCACTGCAACTTCAGGGAGATAAGACTG
* *
5917610 GATGCGATCTGCTCTACTGCAAATTCAGAGAGATAAGAT
1 GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGAT
5917649 TGATAATTTA
Statistics
Matches: 147, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
128 108 0.73
129 39 0.27
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (129 bp):
GATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTCTACTGCA
ACATCAGAGAGATAGGATTAGTTTCTTCAATCTGACCCACTGCAACTTCAGGGAGATAAGACTG
Found at i:5917630 original size:41 final size:41
Alignment explanation
Indices: 5917458--5917647 Score: 141
Period size: 44 Copynumber: 4.5 Consensus size: 41
5917448 TCTGATCCAG
* * *
5917458 TGCAACTTCAGGGAGATAAGATTGGATGTGATCTGCT-TAC
1 TGCAACTTCAGAGAGATAAGACTGGATGCGATCTGCTCTAC
* *** *
5917498 TGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCTAC
1 TGCAACTTCAGAGAGATAAGA-C--TGGATGCGATCTGCTCTAC
* * * * * * * *
5917542 TGCGACATCAGAGAGATAGGATTGGTTTCTTCTG-TCTGCCCCAC
1 TGCAACTTCAGAGAGATAAGACTGG---ATGC-GATCTGCTCTAC
*
5917586 TGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAGACTGGATGCGATCTGCTCTAC
*
5917627 TGCAAATTCAGAGAGATAAGA
1 TGCAACTTCAGAGAGATAAGA
5917648 TTGATAATTT
Statistics
Matches: 114, Mismatches: 27, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
40 21 0.18
41 32 0.28
43 11 0.10
44 50 0.44
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (41 bp):
TGCAACTTCAGAGAGATAAGACTGGATGCGATCTGCTCTAC
Found at i:5917782 original size:50 final size:50
Alignment explanation
Indices: 5917718--5918669 Score: 676
Period size: 50 Copynumber: 19.1 Consensus size: 50
5917708 TTCAGTTTAA
* * ** *
5917718 TTAACTGCAATGTCGGGGAAGTAAGAGTCGTTGTTGTAGCTTTAATCTTT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
* * * * *
5917768 TTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
** ** * * * *
5917818 TCCACTGCACCGCCAGAGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
* ** * *
5917868 TTAATTGCAATGTCAGGGAAACAGGATTTGCCGTTGTAGCTTCAAT-TTGT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTT-T
** ** * *
5917918 TCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
* * *
5917968 TTAATTGCAATGTCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
** * ** * * * * * *
5918018 TCCATTGCACCGCCAGGGAAGTAAGATTCACCGTAGTGGCTTTAATCATT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
* * **
5918068 TTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAAT-TTGT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTT-T
** * * ** *
5918118 TGCACTGCACTGCCAAAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
* * *** * *
5918168 TTAATTGCAATGTCAGGGAAGCAAGATTTATCGTTGTAGTTTCAATCTAT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
** * * * *
5918218 TCCATTGCACTGCCAAGGAAGTAAGATTCGCCGTTGT-GACTTCAATCTTT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAG-CTTCAATCTTT
* * * ** * * *
5918268 TTAATTGTAATGTCGGGGAAACAAGATTCACCGTTTTAGCTTCAATCTGT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
*** ** *
5918318 CCCACTGCACCG-CTA-GGAAGGTAAGATTCGCCGTTGTGGCTTCAATCTTT
1 TTAACTGCAATGTC-AGGGAA-GTAAGATTCGCCGTTGTAGCTTCAATCTTT
* * *
5918368 TTAATTGCAATGTCAGGGAAGTAAGATTTGCCGTTGTAGCTTCAATCTGT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
** **** * * * *
5918418 TCCACTGCACCACCAGTGAAGTAAGATTCGCCATTGTGGCTTCAATGTTT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
* ** * *
5918468 TTAATTGCAATGTCTA-GGAAACAAGATTCACCGTTGTAGCTTCAATCTGT
1 TTAACTGCAATGTC-AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
** * * * * * **
5918518 TCCACTACACTGCCAAGGAAGTAAGATTTGTTGTTGTAGCTTCAATC-TT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
* * * ** * * *
5918567 TTAACTGTAATGTCGGGGAAGCAAGATTCGTTGTTATAGTTTCAATCTGT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
** ** * * ** *
5918617 TCCACTATACTGCCAATGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTT
1 TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
5918667 TTA
1 TTA
5918670 GGGGGACAGG
Statistics
Matches: 676, Mismatches: 213, Indels: 26
0.74 0.23 0.03
Matches are distributed among these distances:
49 46 0.07
50 619 0.92
51 11 0.02
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
TTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTT
Found at i:5917865 original size:100 final size:100
Alignment explanation
Indices: 5917735--5918669 Score: 1162
Period size: 100 Copynumber: 9.4 Consensus size: 100
5917725 CAATGTCGGG
* ** * * * * *
5917735 GAAGTAAGAGTCGTTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACT
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACC
5917800 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * * **
5917835 GAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAACAGGATTTGCC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACC
* *
5917900 GTTGTAGCTTCAATTTGTTCCACTGCACCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
*
5917935 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTCACC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACC
* *
5918000 GTTGTAGCTTCAATCTGTTCCATTGCACCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * * * * * *
5918035 GAAGTAAGATTCACCGTAGTGGCTTTAATCATTTTAATTGCAATGTCGGGGAAACAAGATTCGCC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACC
* * * *
5918100 GTTGTAGCTTCAATTTGTTGCACTGCACTGCCAAA
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* *
5918135 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTTATC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACC
* * * *
5918200 GTTGTAGTTTCAATCTATTCCATTGCACTGCCA-A
66 GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * * *
5918234 GGAAGTAAGATTCGCCGTTGTGACTTCAATCTTTTTAATTGTAATGTCGGGGAAACAAGATTCAC
1 -GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCAC
* * *
5918299 CGTTTTAGCTTCAATCTGTCCCACTGCACCGCTAG-
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* **
5918334 GAAGGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATTTGC
1 GAA-GTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCAC
* *
5918399 CGTTGTAGCTTCAATCTGTTCCACTGCACCACCAGT
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* * *
5918435 GAAGTAAGATTCGCCATTGTGGCTTCAATGTTTTTAATTGCAATGTCTA-GGAAACAAGATTCAC
1 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-AGGGAAGCAAGATTCAC
* *
5918499 CGTTGTAGCTTCAATCTGTTCCACTACACTGCCA-A
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* ** * * * * **
5918534 GGAAGTAAGATTTGTTGTTGTAGCTTCAATC-TTTTAACTGTAATGTCGGGGAAGCAAGATTCGT
1 -GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCAC
* * * ** *
5918598 TGTTATAGTTTCAATCTGTTCCACTATACTGCCA-A
65 CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
* *
5918633 TGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTA
1 -GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTA
5918670 GGGGGACAGG
Statistics
Matches: 723, Mismatches: 104, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
99 89 0.12
100 630 0.87
101 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (100 bp):
GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCACC
GTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGA
Found at i:5919138 original size:132 final size:132
Alignment explanation
Indices: 5918667--5919117 Score: 628
Period size: 132 Copynumber: 3.4 Consensus size: 132
5918657 TTCAATCTTT
* * * *
5918667 TTAGGGGGACAGGATCTATAATCTTCAACCTACTCCACTGCTGCTCAGAAAGATAAGGTTTGTGA
1 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGGTTTGTGG
* * * *
5918732 CTGAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCACCGTCTTTGATCTGCT---CTACT
66 CTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTACT
5918794 AC
131 AC
* * * * *
5918796 TTAGGGAGATAGGACCTGCAATCTTCAACCTACTCCACTGCTGCTCAAAGAGAT-AGGATTGGTG
1 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGG-TTTGTG
*
5918860 GCTTAAATC-GTCTTCCCTACTACCTTGGGAAGATAGGATTCACCGTCTTCGATTTGCTCCACTA
65 GCTTAAATCTG-CTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTA
5918924 CTTA-
129 C-TAC
**
5918928 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACAACTGCTCATG-GAGATAAGGTTTGTG
1 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA-GAGAGATAAGGTTTGTG
* *
5918992 GCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTAACCATCTTCGATTTGCTCCACTAC
65 GCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTAC
*
5919057 TGC
130 TAC
* *
5919060 TTAGGGAGACAGGATCTGCAATCTTTAACCTACTCCACTGCTGCTCAGAGAGATAAGG
1 TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGG
5919118 CTAGTTTTTT
Statistics
Matches: 282, Mismatches: 29, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
128 4 0.01
129 102 0.36
131 2 0.01
132 168 0.60
133 6 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
TTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGGTTTGTGG
CTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATTTGCTCCACTACT
AC
Found at i:5919800 original size:19 final size:19
Alignment explanation
Indices: 5919758--5919804 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5919748 TTGGAGAACT
**
5919758 TAATGCAAATGATGTCATG
1 TAATGCAAATGATGAAATG
5919777 TAATGCAAATGCATGAAATG
1 TAATGCAAATG-ATGAAATG
5919797 -AATGCAAA
1 TAATGCAAA
5919805 ACAGATGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (19 bp):
TAATGCAAATGATGAAATG
Found at i:5921498 original size:106 final size:106
Alignment explanation
Indices: 5921307--5921742 Score: 658
Period size: 106 Copynumber: 4.1 Consensus size: 106
5921297 TCAAAAAACA
* * * * * *
5921307 TACTTTGAAGTTTTAAGAGGATATTTGGCTATTTGGTC-AACCAAGAAATCAAAACTCAGCACGT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAA-CGAGAAATCGAAACCCAGCACAT
* * *
5921371 TAGGGCACGCTTTCTCAAATTTCTAAATGCAAAATATTGCCT
65 TAGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* * * *
5921413 CACTTTGAAATTTTAGAAGGATATTTGGTTATTTGGTCGAACGAGAAACCGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
*
5921478 AGGGTACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
*
5921519 TACTTTGAAATTTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
5921584 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
66 AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
* *
5921625 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAAAAAAATCGAAACTCAGCACA
1 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACG--AGAAATCGAAACCCAGCACA
* * *
5921690 TTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAATATTGCGT
64 TTAGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
5921733 TACTTTGAAA
1 TACTTTGAAA
5921743 AATTTTCCTT
Statistics
Matches: 303, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
106 233 0.77
107 2 0.01
108 68 0.22
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (106 bp):
TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATT
AGGGCACGTTTTCTCGAATTTCCAAATGCAAAATATTGCCT
Found at i:5921986 original size:15 final size:15
Alignment explanation
Indices: 5921968--5921999 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5921958 TATATATATA
5921968 TATATAAAATATTAT
1 TATATAAAATATTAT
5921983 TATATAAAATATTAT
1 TATATAAAATATTAT
5921998 TA
1 TA
5922000 ACTTTTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATAAAATATTAT
Found at i:5921986 original size:17 final size:16
Alignment explanation
Indices: 5921959--5921997 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
5921949 TACAATTTAT
5921959 ATATATATATATATAAA
1 ATAT-TATATATATAAA
5921976 ATATTAT-TATATAAA
1 ATATTATATATATAAA
5921991 ATATTAT
1 ATATTAT
5921998 TAACTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.68
16 3 0.14
17 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTATATATATAAA
Found at i:5922166 original size:3 final size:3
Alignment explanation
Indices: 5922149--5922251 Score: 99
Period size: 3 Copynumber: 34.7 Consensus size: 3
5922139 AAAGAATTAA
* * *
5922149 AAT AAT AGT ACAT AAT AA- AAT AA- AAT AAT ATAT AA- ACT AAT -AC
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
*
5922192 AAT AAT AAT ACCT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5922237 AAT AAT AAT CAAT AA
1 AAT AAT AAT -AAT AA
5922252 CATAACAAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
2 7 0.08
3 67 0.81
4 9 0.11
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5923002 original size:13 final size:14
Alignment explanation
Indices: 5922984--5923012 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5922974 AGGAAACACC
5922984 TTTAGT-TTTTTTT
1 TTTAGTCTTTTTTT
5922997 TTTAGTCTTTTTTT
1 TTTAGTCTTTTTTT
5923011 TT
1 TT
5923013 GAACCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTAGTCTTTTTTT
Found at i:5926825 original size:144 final size:143
Alignment explanation
Indices: 5926627--5927068 Score: 559
Period size: 144 Copynumber: 3.1 Consensus size: 143
5926617 GGGAGTGGGC
* * * * * * * *
5926627 CCAA-AAGCATATTGGAGGATAGATCCAGTGTAACCAAATTCGTTAGCCTACCAATTTCTTGTGG
1 CCAACAAGCATATTAGAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTGG
5926691 AATGGATCCATTAAGTTGGTTATGC-TGAAGGAGCAACGACCCTAGATTGGTTACATTGTTGACA
66 AATGGATCCATTAAGTTGGTT-TGCATGAAGGAGCAACGACCCTAGATTGGTTA-ATTGTTGACA
5926755 GAAGATGGGATTGGA
129 GAAGATGGGATTGGA
*
5926770 CCAACAAGCATATTAAAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTGG
1 CCAACAAGCATATTAGAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTGG
* * * * * ** * *
5926835 AATGGGTCCATTAAGTTGGTTTCCATAAAGAACCAACGATGCAAGATTGGTCAAGTTGTTGACAG
66 AATGGATCCATTAAGTTGGTTTGCATGAAGGAGCAACGACCCTAGATTGGTTAA-TTGTTGACAG
5926900 AAGATGGGATTGGA
130 AAGATGGGATTGGA
* *
5926914 CCAACAAG-ATTATTAGAAGATAGATTCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTCGTG
1 CCAACAAGCA-TATTAGAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTG
* ** * * * *
5926978 GAATGGATCCATTAAGTTGG-TTGCCTTGAAGGAGCAACGACTGTAGATTAGTTAGGTTGGTGAT
65 GAATGGATCCATTAAGTTGGTTTG-CATGAAGGAGCAACGACCCTAGATTGGTTA-ATTGTTGAC
5927042 AGAAGATGGGATTGGA
128 AGAAGATGGGATTGGA
5927058 CCAACAAGCAT
1 CCAACAAGCAT
5927069 GTTGCTTGAG
Statistics
Matches: 256, Mismatches: 36, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
143 10 0.04
144 245 0.96
145 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (143 bp):
CCAACAAGCATATTAGAAGATAGATCCAATGTAATCAAATTTGTCAGTCTCCCAATTTCTTGTGG
AATGGATCCATTAAGTTGGTTTGCATGAAGGAGCAACGACCCTAGATTGGTTAATTGTTGACAGA
AGATGGGATTGGA
Found at i:5932697 original size:6 final size:6
Alignment explanation
Indices: 5932683--5932716 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
5932673 GCTTCTTGCC
*
5932683 CTTGTAG CTTGAG CTTGAG CTCGAG CTTGAG CTT
1 CTTG-AG CTTGAG CTTGAG CTTGAG CTTGAG CTT
5932717 TATTTGCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (6 bp):
CTTGAG
Found at i:5936500 original size:17 final size:17
Alignment explanation
Indices: 5936478--5936547 Score: 122
Period size: 17 Copynumber: 4.1 Consensus size: 17
5936468 ATAGAAAGTC
*
5936478 AAAGATATGGGTATTAG
1 AAAGATATGGGTATCAG
*
5936495 AAAGATATGGGTATTAG
1 AAAGATATGGGTATCAG
5936512 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
5936529 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
5936546 AA
1 AA
5936548 TCTGAGATTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.43, C:0.03, G:0.29, T:0.26
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:5939790 original size:24 final size:24
Alignment explanation
Indices: 5939756--5939804 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5939746 CATTAGTTCC
* *
5939756 TTTAATTATTTCTATATACT-ATTA
1 TTTAATGATTTATAT-TACTAATTA
5939780 TTTAATGATTTATATTACTAATTA
1 TTTAATGATTTATATTACTAATTA
5939804 T
1 T
5939805 AGTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTAATGATTTATATTACTAATTA
Found at i:5943729 original size:18 final size:18
Alignment explanation
Indices: 5943706--5943752 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
5943696 AAACATGAGT
* *
5943706 TGAGCTCGCAACTTTCAA
1 TGAGCTTGCAACTTTAAA
5943724 TGAGCTTGCAACTTTAAA
1 TGAGCTTGCAACTTTAAA
5943742 TGAGCTTGCAA
1 TGAGCTTGCAA
5943753 GTGTAGAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (18 bp):
TGAGCTTGCAACTTTAAA
Found at i:5953726 original size:22 final size:22
Alignment explanation
Indices: 5953698--5953742 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5953688 TAAAACAGGT
* *
5953698 CTTTAGCGGCGTTTTTTTATGC
1 CTTTAGCGGCGCTTTTTAATGC
5953720 CTTTAGCGGCGCTTTTTAATGC
1 CTTTAGCGGCGCTTTTTAATGC
5953742 C
1 C
5953743 GCTAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (22 bp):
CTTTAGCGGCGCTTTTTAATGC
Found at i:5953927 original size:43 final size:42
Alignment explanation
Indices: 5953830--5954140 Score: 345
Period size: 43 Copynumber: 7.3 Consensus size: 42
5953820 TTATTTCTAT
* * *
5953830 AAACGCCGCTATAGAGCAAGACCTTTAGTGGCGC-TTTTCCAC
1 AAACGCCGCTATAGA-TAGGACCTTTAGCGGCGCTTTTTCCAC
* * *
5953872 AAACGTCACTATAGAGTAGGACCTTTAGCAGCGCTTTTTCCAC
1 AAACGCCGCTATAGA-TAGGACCTTTAGCGGCGCTTTTTCCAC
* * * *
5953915 AAACGCCGCTATAGAGCAGGACCTTTAACGGCTCTTTTTGCAC
1 AAACGCCGCTATAGA-TAGGACCTTTAGCGGCGCTTTTTCCAC
* * * * **
5953958 AAATGCCACTATAGACCAGGACCTTTAGCGACGCTTTTTATAC
1 AAACGCCGCTATAGA-TAGGACCTTTAGCGGCGCTTTTTCCAC
* *
5954001 AAACGCCGCTATAGATCAGGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAT-AGGACCTTTAGCGGCGCTTTTTCCAC
** *
5954044 CTACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAT-AGGACCTTTAGCGGCGCTTTTTCCAC
* *
5954087 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTATAGAT-AGGACCTTTAGCGGCGCTTTTTCCAC
5954130 AAACGCCGCTA
1 AAACGCCGCTA
5954141 AAAACATATC
Statistics
Matches: 231, Mismatches: 36, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
42 28 0.12
43 203 0.88
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTATAGATAGGACCTTTAGCGGCGCTTTTTCCAC
Found at i:5954067 original size:129 final size:128
Alignment explanation
Indices: 5953830--5954140 Score: 390
Period size: 129 Copynumber: 2.4 Consensus size: 128
5953820 TTATTTCTAT
* * * * * *
5953830 AAACGCCGCTATAGAGCAAGACCTTTAGTGGCGCTTTTCCACAAACGTCACTATAGAGTAGGACC
1 AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGAGTAGGACC
* * **
5953895 TTTAGCAGCGCTTTTTCCACAAACGCCGCTATAGAGCAGGACCTTTAACGGCTCTTTTTGCAC
66 TTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAGCAGGACCTTTAACGGCGCTTTTCCCAC
* * * *
5953958 AAATGCCACTATAGACCAGGACCTTTAGCGACGCTTTTTATACAAACGCCGCTATAGA-TCAGGA
1 AAACGCCACTATAGACCAAGACCTTTAGCGGCGC-TTTTACACAAACGCCGCTATAGAGT-AGGA
** ** * *
5954022 CCTTTAGTGGCGCTTTTCCCACCTACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
64 CCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAGCAGGACCTTTAACGGCGCTTTTCCCAC
* *
5954087 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTA
1 AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTTA-CACAAACGCCGCTA
5954141 AAAACATATC
Statistics
Matches: 154, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
128 34 0.22
129 120 0.78
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (128 bp):
AAACGCCACTATAGACCAAGACCTTTAGCGGCGCTTTTACACAAACGCCGCTATAGAGTAGGACC
TTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAGCAGGACCTTTAACGGCGCTTTTCCCAC
Found at i:5954140 original size:86 final size:85
Alignment explanation
Indices: 5953830--5954136 Score: 391
Period size: 86 Copynumber: 3.6 Consensus size: 85
5953820 TTATTTCTAT
* *
5953830 AAACGCCGCTATAGAGCAAGACCTTTAGTGGCGCTTTTCCACAAACGTCACTATAGAGT-AGGAC
1 AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGCTTTTCCACAAACGCCACTATAGA-TCAGGAC
*
5953894 CTTTAGCAGCGCTTTTTCCAC
65 CTTTAGCGGCGCTTTTTCCAC
* * * * * *
5953915 AAACGCCGCTATAGAGCAGGACCTTTAACGGCTCTTTTTGCACAAATGCCACTATAGACCAGGAC
1 AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGC-TTTTCCACAAACGCCACTATAGATCAGGAC
* **
5953980 CTTTAGCGACGCTTTTTATAC
65 CTTTAGCGGCGCTTTTTCCAC
* * * ** *
5954001 AAACGCCGCTATAGATCAGGACCTTTAGTGGCGCTTTTCCCACCTACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGCTTTT-CCACAAACGCCACTATAGATCAGGAC
*
5954066 CTTTAGCGGCGCTTTTCCCAC
65 CTTTAGCGGCGCTTTTTCCAC
*
5954087 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
1 AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGCTTTT-CCACAAACGCC
5954137 GCTAAAAACA
Statistics
Matches: 188, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
85 34 0.18
86 154 0.82
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (85 bp):
AAACGCCGCTATAGAGCAAGACCTTTAGCGGCGCTTTTCCACAAACGCCACTATAGATCAGGACC
TTTAGCGGCGCTTTTTCCAC
Found at i:5959074 original size:21 final size:20
Alignment explanation
Indices: 5959046--5959089 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
5959036 TATTTTAATT
5959046 AATATAAATAAACAAAATAA
1 AATATAAATAAACAAAATAA
* *
5959066 AATAGTAAATAGACAAGATAA
1 AATA-TAAATAAACAAAATAA
5959087 AAT
1 AAT
5959090 GTTTTTGCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (20 bp):
AATATAAATAAACAAAATAA
Found at i:5960446 original size:19 final size:21
Alignment explanation
Indices: 5960422--5960461 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
5960412 TATCTTATTC
5960422 AATCTTGCT-TTT-AATGTTT
1 AATCTTGCTGTTTGAATGTTT
*
5960441 AATCTTGGTGTTTGAATGTTT
1 AATCTTGCTGTTTGAATGTTT
5960462 CTTAACACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.55
Consensus pattern (21 bp):
AATCTTGCTGTTTGAATGTTT
Found at i:5963578 original size:46 final size:46
Alignment explanation
Indices: 5963498--5963661 Score: 157
Period size: 46 Copynumber: 3.6 Consensus size: 46
5963488 GCTTAATATT
* * * *
5963498 CTTGTATTCTCGAGTCCACAACATATGCAAGAGCTTGGAACCTAAA
1 CTTGTATTCTCGAGTCCGCAACATATGCAGGAGCTCGAAACCTAAA
* * **
5963544 CTTGTATGCTCGAGTCCGCAACATATGTAGGAGCTCGAAACCTATT
1 CTTGTATTCTCGAGTCCGCAACATATGCAGGAGCTCGAAACCTAAA
*** * * **
5963590 CCCCTATTCTCGAGTTCGCAACATATGCAGGAGCTCAAAACCTATT
1 CTTGTATTCTCGAGTCCGCAACATATGCAGGAGCTCGAAACCTAAA
* * **
5963636 CATGTATTCTTGAGTCCATAACATAT
1 CTTGTATTCTCGAGTCCGCAACATAT
5963662 TCAAAAGCTT
Statistics
Matches: 96, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 96 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (46 bp):
CTTGTATTCTCGAGTCCGCAACATATGCAGGAGCTCGAAACCTAAA
Found at i:5969241 original size:15 final size:15
Alignment explanation
Indices: 5969204--5969251 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
5969194 TTGATTACCG
*
5969204 AATTAAATTAATTCTA
1 AATTAATTTAATTC-A
5969220 TAATTAATTTAATTCA
1 -AATTAATTTAATTCA
5969236 AATTAATTTAATTCA
1 AATTAATTTAATTCA
5969251 A
1 A
5969252 GCGACCCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 16 0.53
16 1 0.03
17 13 0.43
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAATTTAATTCA
Found at i:5973564 original size:16 final size:16
Alignment explanation
Indices: 5973533--5973563 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5973523 TTTAGGACTG
5973533 CTATTTTTAATGTTTT
1 CTATTTTTAATGTTTT
5973549 CTATTTTT-ATGTTTT
1 CTATTTTTAATGTTTT
5973564 TTTTATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (16 bp):
CTATTTTTAATGTTTT
Found at i:5974464 original size:17 final size:17
Alignment explanation
Indices: 5974417--5974475 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
5974407 TCACCTAATA
*
5974417 GAGCTTGCACCTTTGTT
1 GAGCTTGCACCTTTGGT
* *
5974434 GA-CATCGCAGCTTTGGT
1 GAGC-TTGCACCTTTGGT
*
5974451 GAGCTTGCATCTTTGGGT
1 GAGCTTGCACCTTT-GGT
5974469 GAGCTTG
1 GAGCTTG
5974476 TAGATGTGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 1 0.03
17 22 0.65
18 11 0.32
ACGTcount: A:0.14, C:0.20, G:0.31, T:0.36
Consensus pattern (17 bp):
GAGCTTGCACCTTTGGT
Found at i:5976703 original size:18 final size:19
Alignment explanation
Indices: 5976661--5976704 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5976651 ACCGGACCGG
*
5976661 CGAACTCCCTAAATTTGGT
1 CGAACTCTCTAAATTTGGT
*
5976680 -GTACTCTCTAAATTT-GT
1 CGAACTCTCTAAATTTGGT
5976697 CGAACTCT
1 CGAACTCT
5976705 TCAGGAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (19 bp):
CGAACTCTCTAAATTTGGT
Found at i:5980427 original size:32 final size:30
Alignment explanation
Indices: 5980386--5980463 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 30
5980376 TTTTGATGCA
*
5980386 TTTTATAATTTTTAAAAAATTTTACAATTTTT
1 TTTTATAATTTTTAAAAAA-TTTA-AATATTT
*
5980418 TTTTCTAATTTTTAATAAAATTTAAATATTT
1 TTTTATAATTTTTAA-AAAATTTAAATATTT
5980449 TTTTAT-ATTTTTAAA
1 TTTTATAATTTTTAAA
5980464 TAGTGTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.02
30 8 0.19
31 11 0.26
32 18 0.43
33 4 0.10
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAAATTTAAATATTT
Found at i:5983028 original size:88 final size:88
Alignment explanation
Indices: 5982903--5983079 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
5982893 TTGCAGTGGT
5982903 TGTTGAATCAATCATTAAAAGAAAAGGAAAGTGGCAAAAGATAGATCGATTTGTACTTTTTTAGA
1 TGTTGAATCAATCATTAAAAGAAAAGGAAAGTGGCAAAAGATAGATCGATTTGTACTTTTTTAGA
5982968 GATGATTTTCAATAAGACGAAGC
66 GATGATTTTCAATAAGACGAAGC
5982991 TGTTGAATCAATCATTAAAAGAAAAGGAAAGTGGCAAAAGATAGATCGATTTGTACTTTTTTAGA
1 TGTTGAATCAATCATTAAAAGAAAAGGAAAGTGGCAAAAGATAGATCGATTTGTACTTTTTTAGA
5983056 GATGATTTTCAATAAGACGAAGC
66 GATGATTTTCAATAAGACGAAGC
5983079 T
1 T
5983080 AACAAAAAGC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (88 bp):
TGTTGAATCAATCATTAAAAGAAAAGGAAAGTGGCAAAAGATAGATCGATTTGTACTTTTTTAGA
GATGATTTTCAATAAGACGAAGC
Found at i:5983832 original size:2 final size:2
Alignment explanation
Indices: 5983827--5983851 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5983817 CAAAAAAATA
5983827 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5983852 AGACATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5984602 original size:30 final size:30
Alignment explanation
Indices: 5984567--5984648 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
5984557 AACCAAAAAT
* *
5984567 ACAAGCCAAAAATGTAAACCAAAGTGACGG
1 ACAAGCCAAAAATGTAAGCCAAAGTGACGA
*
5984597 ACAAGCCAAAGAA--TAAGCCAAAGTGGCGA
1 ACAAGCCAAA-AATGTAAGCCAAAGTGACGA
* *
5984626 ACAAACCAAAAGTGTAAGCCAAA
1 ACAAGCCAAAAATGTAAGCCAAA
5984649 ATGGTAGACA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 22 0.50
30 19 0.43
31 2 0.05
ACGTcount: A:0.51, C:0.21, G:0.20, T:0.09
Consensus pattern (30 bp):
ACAAGCCAAAAATGTAAGCCAAAGTGACGA
Found at i:5989308 original size:23 final size:22
Alignment explanation
Indices: 5989282--5989336 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
5989272 AAAATAGTGG
*
5989282 GAAAAAAAACAAGAAAATAGCAA
1 GAAAAAAAACAAGAAAATAAC-A
* *
5989305 GAAAAAGAAC-AGCAAATAACA
1 GAAAAAAAACAAGAAAATAACA
*
5989326 GTAAAAAAACA
1 GAAAAAAAACA
5989337 GTTGGTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 9 0.35
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (22 bp):
GAAAAAAAACAAGAAAATAACA
Found at i:5989336 original size:21 final size:21
Alignment explanation
Indices: 5989284--5989337 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
5989274 AATAGTGGGA
*
5989284 AAAAAAACAAGAAAATAGCAAG
1 AAAAAAAC-AGAAAATAACAAG
*
5989306 AAAAAGAACAGCAAATAAC-AG
1 AAAAA-AACAGAAAATAACAAG
5989327 TAAAAAAACAG
1 -AAAAAAACAG
5989338 TTGGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 7 0.25
22 18 0.64
23 3 0.11
ACGTcount: A:0.70, C:0.11, G:0.13, T:0.06
Consensus pattern (21 bp):
AAAAAAACAGAAAATAACAAG
Found at i:5990035 original size:29 final size:30
Alignment explanation
Indices: 5990003--5990064 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
5989993 GTTTCACGTG
*
5990003 TATAATT-ATATCAAATTAAAATTCATATA
1 TATAATTAATATCAAATCAAAATTCATATA
*
5990032 TATAATTACATATTAAATCAAAATTCATATA
1 TATAATTA-ATATCAAATCAAAATTCATATA
5990063 TA
1 TA
5990065 ATTTTAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
31 22 0.76
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (30 bp):
TATAATTAATATCAAATCAAAATTCATATA
Found at i:5990065 original size:29 final size:28
Alignment explanation
Indices: 5990003--5990067 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
5989993 GTTTCACGTG
*
5990003 TATAATTATATCAAATTAAAATTCATATA
1 TATAATTATATCAAATCAAAATTCA-ATA
*
5990032 TATAATTACATATTAAATCAAAATTC-ATA
1 TATAATT--ATATCAAATCAAAATTCAATA
5990061 TATAATT
1 TATAATT
5990068 TTAAGATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 17 0.53
31 15 0.47
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (28 bp):
TATAATTATATCAAATCAAAATTCAATA
Found at i:6006133 original size:2 final size:2
Alignment explanation
Indices: 6006128--6006161 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6006118 ATATAGGGTT
6006128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6006162 CGACATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6007099 original size:37 final size:36
Alignment explanation
Indices: 6007028--6007099 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
6007018 GGAGCGCATC
*
6007028 AGTCAGAATAGATCCAAAAGGCTGATGAATTGAATT
1 AGTCAGAATAGATCCAAAAGGCTGATGAACTGAATT
6007064 AGTCAGAATAGATCCGAAAAGGCT-ATTGAACTGAAT
1 AGTCAGAATAGATCC-AAAAGGCTGA-TGAACTGAAT
6007100 AGAGTTTACT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 16 0.48
37 17 0.52
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (36 bp):
AGTCAGAATAGATCCAAAAGGCTGATGAACTGAATT
Found at i:6009782 original size:15 final size:15
Alignment explanation
Indices: 6009756--6009792 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
6009746 TGCCTGAAAG
6009756 CATGATGGAGTCTGTA
1 CATGA-GGAGTCTGTA
*
6009772 CATGAGGAGTCTGTG
1 CATGAGGAGTCTGTA
6009787 CATGAG
1 CATGAG
6009793 TTGCATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.27
Consensus pattern (15 bp):
CATGAGGAGTCTGTA
Found at i:6010284 original size:30 final size:30
Alignment explanation
Indices: 6010250--6010332 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
6010240 TATATGTATC
* * * *
6010250 TGGATGCCCTTGTGGTTATTTAATGATGTG
1 TGGATGCCCTTATGGCTATCTAATGATGTA
* *
6010280 TGGATGCCTTTATGGCTATCTATTGATGTA
1 TGGATGCCCTTATGGCTATCTAATGATGTA
* *
6010310 TGGATG-GCTCTGTGGCTATCTAA
1 TGGATGCCCT-TATGGCTATCTAA
6010333 GTCAAGTGGA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
29 1 0.02
30 41 0.98
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.41
Consensus pattern (30 bp):
TGGATGCCCTTATGGCTATCTAATGATGTA
Found at i:6014876 original size:8 final size:8
Alignment explanation
Indices: 6014863--6014897 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
6014853 TATACATAGC
6014863 TTTTTTAT
1 TTTTTTAT
6014871 TTTTTTAT
1 TTTTTTAT
6014879 TTTTTT-T
1 TTTTTTAT
6014886 ATTTTTTAT
1 -TTTTTTAT
6014895 TTT
1 TTT
6014898 ACATTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 1 0.04
8 23 0.92
9 1 0.04
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTAT
Found at i:6014882 original size:9 final size:9
Alignment explanation
Indices: 6014863--6014892 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6014853 TATACATAGC
6014863 TTTTTTA-T
1 TTTTTTATT
6014871 TTTTTTATT
1 TTTTTTATT
6014880 TTTTTTATT
1 TTTTTTATT
6014889 TTTT
1 TTTT
6014893 ATTTTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTATT
Found at i:6014884 original size:16 final size:16
Alignment explanation
Indices: 6014863--6014897 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
6014853 TATACATAGC
6014863 TTTTTTATTTTTTTATT
1 TTTTTTA-TTTTTTATT
6014880 TTTTTTATTTTTTATT
1 TTTTTTATTTTTTATT
6014896 TT
1 TT
6014898 ACATTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTTATTTTTTATT
Found at i:6015330 original size:109 final size:109
Alignment explanation
Indices: 6015145--6015466 Score: 504
Period size: 109 Copynumber: 3.0 Consensus size: 109
6015135 ATCCTTTTAA
* * *
6015145 AAAAAATTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAGCGTGCCCTAATGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
6015210 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
66 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* *
6015254 AAAAATTTCAAAATAAGGCAATGTTTTGTGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
* * *
6015319 GGTTTCAATTTTTCTCGTTCGAACAAATAGCCAAATATCCTTTT
66 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* * * * *
6015363 AGAAATTTTAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCTCTAATGTGCTG
1 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
*
6015428 GGTTTCGA--TTTCTCGTTGGACCAAATAGCCAAATATCCT
66 GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCT
6015467 CTTAAATCTT
Statistics
Matches: 195, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
107 29 0.15
109 166 0.85
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (109 bp):
AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTG
GGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
Found at i:6019559 original size:9 final size:9
Alignment explanation
Indices: 6019547--6019649 Score: 71
Period size: 9 Copynumber: 10.4 Consensus size: 9
6019537 GTATTTAATT
6019547 AATTTTAAA
1 AATTTTAAA
6019556 AATTTTAAA
1 AATTTTAAA
*
6019565 AATATATAAAA
1 AAT-T-TTAAA
6019576 ATTATTTTAAA
1 A--ATTTTAAA
6019587 AATTTTAAA
1 AATTTTAAA
*
6019596 AATATTAAA
1 AATTTTAAA
*
6019605 ATTATTTAAA
1 AAT-TTTAAA
*
6019615 AATGTGTAAA
1 AAT-TTTAAA
* *
6019625 CATTATAAAAA
1 AATT-T-TAAA
6019636 ATATTTTAAA
1 A-ATTTTAAA
6019646 AATT
1 AATT
6019650 AATTAAATGC
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
9 34 0.47
10 19 0.26
11 14 0.19
12 4 0.05
13 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (9 bp):
AATTTTAAA
Found at i:6019583 original size:31 final size:31
Alignment explanation
Indices: 6019543--6019649 Score: 141
Period size: 31 Copynumber: 3.5 Consensus size: 31
6019533 ATCAGTATTT
6019543 AATTAATTTTAAAAATTTTAAAAATATATAAA
1 AATT-ATTTTAAAAATTTTAAAAATATATAAA
6019575 AATTATTTTAAAAATTTTAAAAATAT-T-AA
1 AATTATTTTAAAAATTTTAAAAATATATAAA
* *
6019604 AATTA-TTTAAAAATGTGTAAACAT-TATAAA
1 AATTATTTTAAAAAT-TTTAAAAATATATAAA
*
6019634 AAATATTTTAAAAATT
1 AATTATTTTAAAAATT
6019650 AATTAAATGC
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
28 10 0.15
29 15 0.22
30 8 0.12
31 31 0.46
32 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (31 bp):
AATTATTTTAAAAATTTTAAAAATATATAAA
Found at i:6019615 original size:50 final size:49
Alignment explanation
Indices: 6019551--6019648 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 49
6019541 TTAATTAATT
**
6019551 TTAAAAATTTTAAAAATATATAAAAATTATTTTAAAA-ATTTTAAAAATA
1 TTAAAAATTTTAAAAATATATAAAAATTA-TAAAAAATATTTTAAAAATA
* * * *
6019600 TTAAAATTATTTAAAAATGTGTAAACATTATAAAAAATATTTTAAAAAT
1 TTAAAAAT-TTTAAAAATATATAAAAATTATAAAAAATATTTTAAAAAT
6019649 TAATTAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
49 12 0.29
50 29 0.71
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (49 bp):
TTAAAAATTTTAAAAATATATAAAAATTATAAAAAATATTTTAAAAATA
Found at i:6022113 original size:31 final size:31
Alignment explanation
Indices: 6022078--6022136 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6022068 CCCTAGTGAA
*
6022078 TTAAATAAAAACTTTTGAATAGTTTAGTTAC
1 TTAAATAAAAACTTTTGAATAATTTAGTTAC
*
6022109 TTAAATGAAAACTTTTGAATAATTTAGT
1 TTAAATAAAAACTTTTGAATAATTTAGT
6022137 GACCAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (31 bp):
TTAAATAAAAACTTTTGAATAATTTAGTTAC
Found at i:6022849 original size:31 final size:31
Alignment explanation
Indices: 6022788--6022844 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 31
6022778 TTTAACATTT
6022788 AAAAATTCAAAAAATATAAAAATTATTTTAA
1 AAAAATTCAAAAAATATAAAAATTATTTTAA
6022819 AAAAATT---AAAATATAAAAGA-TATTTT
1 AAAAATTCAAAAAATATAAAA-ATTATTTT
6022845 TTTAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 17 0.68
29 1 0.04
31 7 0.28
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (31 bp):
AAAAATTCAAAAAATATAAAAATTATTTTAA
Found at i:6027643 original size:18 final size:18
Alignment explanation
Indices: 6027620--6027655 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6027610 GAATGACTCA
6027620 TATTTCAGAGACAATCTC
1 TATTTCAGAGACAATCTC
*
6027638 TATTTCAGAGATAATCTC
1 TATTTCAGAGACAATCTC
6027656 CTAGTTAAAC
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:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (18 bp):
TATTTCAGAGACAATCTC
Found at i:6032746 original size:20 final size:19
Alignment explanation
Indices: 6032721--6032770 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 19
6032711 AATACAAAAT
6032721 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTC-AA
6032741 AATTCAAAATAATTTTCAA
1 AATTCAAAATAATTTTCAA
*
6032760 AACTCAAAATA
1 AATTCAAAATA
6032771 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTCAAAATAATTTTCAA
Found at i:6032761 original size:12 final size:10
Alignment explanation
Indices: 6032706--6032754 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
6032696 TCTCTCTCAA
*
6032706 CAAAA-AATA
1 CAAAATAATT
6032715 CAAAATAATT
1 CAAAATAATT
6032725 CAAAATAATTTT
1 CAAAATAA--TT
6032737 C-AAA-AATT
1 CAAAATAATT
6032745 CAAAATAATT
1 CAAAATAATT
6032755 TTCAAAACTC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
8 3 0.09
9 8 0.24
10 17 0.50
11 3 0.09
12 3 0.09
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (10 bp):
CAAAATAATT
Found at i:6036546 original size:109 final size:106
Alignment explanation
Indices: 6036409--6036608 Score: 346
Period size: 109 Copynumber: 1.9 Consensus size: 106
6036399 TTGAGCTCAC
6036409 TAACTTGTGGAACTTATGATGTGTATAAGATTTCATAAATTCATGAGTATATTGATAATGAAATT
1 TAACTTGTGGAACTTATGATGTGTATAAGATTTCATAAATTCATG-G-ATA-TGATAATGAAATT
6036474 ATGCATCATTTTATAAAAATTGAGTTTAAGATTTCATAAATTCA
63 ATGCATCATTTTATAAAAATTGAGTTTAAGATTTCATAAATTCA
* * *
6036518 TAACTTGTGGGACTTATGATGTGTATAAGATTTCATAAATTCATGGGTATGGTAATGAAATTATG
1 TAACTTGTGGAACTTATGATGTGTATAAGATTTCATAAATTCATGGATATGATAATGAAATTATG
6036583 CATCATTTTATAAAAATTGAGTTTAA
66 CATCATTTTATAAAAATTGAGTTTAA
6036609 AAAAAAGGTA
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
106 41 0.47
107 2 0.02
108 1 0.01
109 44 0.50
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (106 bp):
TAACTTGTGGAACTTATGATGTGTATAAGATTTCATAAATTCATGGATATGATAATGAAATTATG
CATCATTTTATAAAAATTGAGTTTAAGATTTCATAAATTCA
Found at i:6041153 original size:23 final size:23
Alignment explanation
Indices: 6041127--6041172 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6041117 TTCAAGTTGT
6041127 ACGAAGCTATTCAATACTAAGTC
1 ACGAAGCTATTCAATACTAAGTC
6041150 ACGAAGCTATTCAATACTAAGTC
1 ACGAAGCTATTCAATACTAAGTC
6041173 GTGATACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
ACGAAGCTATTCAATACTAAGTC
Found at i:6051837 original size:15 final size:15
Alignment explanation
Indices: 6051818--6051874 Score: 96
Period size: 15 Copynumber: 3.8 Consensus size: 15
6051808 TTGACTTGCT
*
6051818 ATCTTTTGATTTTTC
1 ATCTTTTGATTTGTC
*
6051833 GTCTTTTGATTTGTC
1 ATCTTTTGATTTGTC
6051848 ATCTTTTGATTTGTC
1 ATCTTTTGATTTGTC
6051863 ATCTTTTGATTT
1 ATCTTTTGATTT
6051875 TTCGCCATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.63
Consensus pattern (15 bp):
ATCTTTTGATTTGTC
Found at i:6051841 original size:30 final size:30
Alignment explanation
Indices: 6051807--6051871 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
6051797 GACTTCATGC
* *
6051807 TTTGACTTG-CTATCTTTTGATTTTTCGTCT
1 TTTGACTTGTC-ATCTTTTGATTTGTCATCT
*
6051837 TTTGATTTGTCATCTTTTGATTTGTCATCT
1 TTTGACTTGTCATCTTTTGATTTGTCATCT
6051867 TTTGA
1 TTTGA
6051872 TTTTTCGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (30 bp):
TTTGACTTGTCATCTTTTGATTTGTCATCT
Found at i:6052396 original size:29 final size:28
Alignment explanation
Indices: 6052337--6052397 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
6052327 CATTTCCAAA
**
6052337 AAAAATTACGGAAATGGGCCATTTTGTT
1 AAAAATTACGGAAATGGGCCATTTTCCT
*
6052365 AAAAATTACTGGAAA-GGGTCGATTTTCCT
1 AAAAATTAC-GGAAATGGG-CCATTTTCCT
6052394 AAAA
1 AAAA
6052398 CGTGCTGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (28 bp):
AAAAATTACGGAAATGGGCCATTTTCCT
Found at i:6052577 original size:32 final size:30
Alignment explanation
Indices: 6052516--6052578 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 30
6052506 GGCCAATTAG
* * *
6052516 GGTTTAGGTTTTTTTTATTTTAAGTGTTTA
1 GGTTTAGGTTTATTTAATTTTAAGGGTTTA
*
6052546 GGTTTAGGGTTATATTTAATTTTTAGGGTTTA
1 GGTTTA-GGTT-TATTTAATTTTAAGGGTTTA
6052578 G
1 G
6052579 AGGTTCTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 6 0.22
31 4 0.15
32 17 0.63
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.57
Consensus pattern (30 bp):
GGTTTAGGTTTATTTAATTTTAAGGGTTTA
Found at i:6052637 original size:29 final size:29
Alignment explanation
Indices: 6052580--6052661 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
6052570 AGGGTTTAGA
6052580 GGTTCTGAAAAAAATAA-TTTGTACAGGATG
1 GGTTCTG-AAAAAATAATTTTG-ACAGGATG
**
6052610 GGTTCTGAAAAAATAATTTTGAGGGGATG
1 GGTTCTGAAAAAATAATTTTGACAGGATG
* *
6052639 GGTTTTGAAGAAATAATTTTGAC
1 GGTTCTGAAAAAATAATTTTGAC
6052662 GAGATGAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 35 0.76
30 11 0.24
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (29 bp):
GGTTCTGAAAAAATAATTTTGACAGGATG
Found at i:6062311 original size:24 final size:25
Alignment explanation
Indices: 6062273--6062334 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
6062263 ATTTTTGTCT
* *
6062273 TTTTTTTTCACCCAACTATCTTGGA
1 TTTTTTGTCACCAAACTATCTTGGA
6062298 TTTTTTGTCACCAAACTATCTTGGA
1 TTTTTTGTCACCAAACTATCTTGGA
*
6062323 TTTTTGGTCACC
1 TTTTTTGTCACC
6062335 TAAAACCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (25 bp):
TTTTTTGTCACCAAACTATCTTGGA
Found at i:6064579 original size:67 final size:66
Alignment explanation
Indices: 6064461--6064591 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 66
6064451 TTTCCATTTC
*
6064461 AGAGAGCACACTCCCGCGAACCTCATCCTTGCAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
1 AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
6064526 A
66 A
* * *
6064527 AGAGAGCACACTCCTGCGAACCTTATTCCTTACAGTGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCA-TCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
6064592 TAATATAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
66 23 0.38
67 37 0.62
ACGTcount: A:0.26, C:0.34, G:0.21, T:0.20
Consensus pattern (66 bp):
AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
A
Found at i:6073359 original size:15 final size:14
Alignment explanation
Indices: 6073322--6073364 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 14
6073312 TTTCAAATTT
6073322 TTAATATAAAAAATA
1 TTAA-ATAAAAAATA
6073337 TATGAAATAAATAAATA
1 T-T-AAATAAA-AAATA
6073354 TTAAATAAAAA
1 TTAAATAAAAA
6073365 TAACATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.08
15 8 0.32
16 7 0.28
17 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
TTAAATAAAAAATA
Found at i:6078866 original size:20 final size:20
Alignment explanation
Indices: 6078841--6078878 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6078831 GTAAAAATAT
6078841 CAAATTTGTTGAGTAATTAC
1 CAAATTTGTTGAGTAATTAC
6078861 CAAATTTGTTGAGTAATT
1 CAAATTTGTTGAGTAATT
6078879 TTCTGCATGT
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:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (20 bp):
CAAATTTGTTGAGTAATTAC
Found at i:6079772 original size:8 final size:8
Alignment explanation
Indices: 6079723--6079780 Score: 63
Period size: 7 Copynumber: 7.8 Consensus size: 8
6079713 CAGTTTTAAC
6079723 ATTTTATTA
1 ATTTTA-TA
6079732 A-TTTATA
1 ATTTTATA
6079739 A-TTTAT-
1 ATTTTATA
6079745 ATTTTAT-
1 ATTTTATA
6079752 ATTTTAT-
1 ATTTTATA
6079759 ATTTTATA
1 ATTTTATA
6079767 ATTTTATA
1 ATTTTATA
*
6079775 AATTTA
1 ATTTTA
6079781 AAAAGATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
6 1 0.02
7 27 0.59
8 17 0.37
9 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
ATTTTATA
Found at i:6085538 original size:2 final size:2
Alignment explanation
Indices: 6085531--6085559 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6085521 TGTTGGGTTT
6085531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6085560 GCAGGAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6087940 original size:15 final size:16
Alignment explanation
Indices: 6087914--6087944 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6087904 AAATTTGATT
6087914 TAAAATATACCAAAAA
1 TAAAATATACCAAAAA
6087930 TAAAA-ATACCAAAAA
1 TAAAATATACCAAAAA
6087945 CTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAATATACCAAAAA
Found at i:6091389 original size:18 final size:18
Alignment explanation
Indices: 6091366--6091401 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6091356 TGATGGTAGG
6091366 ACAACAGAATTCGTTTCC
1 ACAACAGAATTCGTTTCC
6091384 ACAACAGAATTCGTTTCC
1 ACAACAGAATTCGTTTCC
6091402 GGTGATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (18 bp):
ACAACAGAATTCGTTTCC
Found at i:6095165 original size:22 final size:22
Alignment explanation
Indices: 6095137--6095289 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
6095127 TTTATTGTTC
*
6095137 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
6095159 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
6095181 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
6095203 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
6095225 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
6095247 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
6095269 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
6095290 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:6095465 original size:2 final size:2
Alignment explanation
Indices: 6095418--6095446 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6095408 NNNNNNNNNN
6095418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6095447 TACAATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6096090 original size:14 final size:14
Alignment explanation
Indices: 6096071--6096098 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6096061 ATATTAATCA
6096071 AAAGTTATAAAAGT
1 AAAGTTATAAAAGT
6096085 AAAGTTATAAAAGT
1 AAAGTTATAAAAGT
6096099 GTATGTTTCA
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:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (14 bp):
AAAGTTATAAAAGT
Found at i:6097024 original size:22 final size:19
Alignment explanation
Indices: 6096981--6097025 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
6096971 ATATTTTTTT
*
6096981 AAAAATTATAAAAATTTCA
1 AAAAATTATAAAAAGTTCA
6097000 AAAAATATATAAAGAAAGTTCA
1 AAAAAT-TAT-AA-AAAGTTCA
6097022 AAAA
1 AAAA
6097026 TTAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 2 0.09
22 11 0.50
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAAATTATAAAAAGTTCA
Found at i:6097655 original size:21 final size:21
Alignment explanation
Indices: 6097626--6097674 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
6097616 ATAGAATTCA
*
6097626 ATTTAATAACTAAAAATAAAT
1 ATTTAATAAATAAAAATAAAT
* * *
6097647 ATTTGATAAATAAAATTAATT
1 ATTTAATAAATAAAAATAAAT
6097668 A-TTAATA
1 ATTTAATA
6097675 TTTTTATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATTTAATAAATAAAAATAAAT
Found at i:6102730 original size:14 final size:15
Alignment explanation
Indices: 6102708--6102745 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6102698 CAATCAAACA
6102708 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
6102722 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
6102737 ACAGAAAAT
1 CCAGAAAAT
6102746 TAAAACATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:6102772 original size:34 final size:35
Alignment explanation
Indices: 6102712--6102779 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
6102702 CAAACACCAG
*
6102712 AAAATATTTTCCAGTAAATCATTTTACAGAAAATT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
* * *
6102747 AAAACATTTTCCCG-AAATTATTTTACGGAAAAT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAT
6102780 ATTTTACTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
Found at i:6105727 original size:3 final size:3
Alignment explanation
Indices: 6105719--6105788 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
6105709 TTTAGCAATT
6105719 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
6105767 TTA TTA TTG TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
6105789 AATTGTTTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6106073 original size:32 final size:32
Alignment explanation
Indices: 6106037--6106097 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
6106027 AATATTTATG
* * *
6106037 CCTTTCTTAATATATATATGTACATATTTTAA
1 CCTTTCTAAATACATATATATACATATTTTAA
* *
6106069 CCTTTGTAAATACATATATATATATATTT
1 CCTTTCTAAATACATATATATACATATTT
6106098 ATATATATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.49
Consensus pattern (32 bp):
CCTTTCTAAATACATATATATACATATTTTAA
Found at i:6122903 original size:15 final size:17
Alignment explanation
Indices: 6122885--6122930 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
6122875 TTGCCATAAA
6122885 AATATTTAAAA-AA-AT
1 AATATTTAAAATAAGAT
*
6122900 AATATTCAAAATAAGAT
1 AATATTTAAAATAAGAT
*
6122917 AATTATTTTAAATA
1 AA-TATTTAAAATA
6122931 TCTCTACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.40
16 2 0.08
17 4 0.16
18 9 0.36
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AATATTTAAAATAAGAT
Found at i:6123619 original size:19 final size:19
Alignment explanation
Indices: 6123595--6123681 Score: 147
Period size: 19 Copynumber: 4.6 Consensus size: 19
6123585 AGGTTGAAAC
*
6123595 ATAATCTTAGATATAATAT
1 ATAATCTTAGATATGATAT
6123614 ATAATCTTAGATATGATAT
1 ATAATCTTAGATATGATAT
*
6123633 GTAATCTTAGATATGATAT
1 ATAATCTTAGATATGATAT
6123652 ATAATCTTAGATATGATAT
1 ATAATCTTAGATATGATAT
*
6123671 GTAATCTTAGA
1 ATAATCTTAGA
6123682 AGATATGATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (19 bp):
ATAATCTTAGATATGATAT
Found at i:6123652 original size:38 final size:38
Alignment explanation
Indices: 6123596--6123681 Score: 163
Period size: 38 Copynumber: 2.3 Consensus size: 38
6123586 GGTTGAAACA
6123596 TAATCTTAGATATAATATATAATCTTAGATATGATATG
1 TAATCTTAGATATAATATATAATCTTAGATATGATATG
*
6123634 TAATCTTAGATATGATATATAATCTTAGATATGATATG
1 TAATCTTAGATATAATATATAATCTTAGATATGATATG
6123672 TAATCTTAGA
1 TAATCTTAGA
6123682 AGATATGATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.42
Consensus pattern (38 bp):
TAATCTTAGATATAATATATAATCTTAGATATGATATG
Found at i:6123707 original size:22 final size:22
Alignment explanation
Indices: 6123622--6123704 Score: 70
Period size: 19 Copynumber: 4.0 Consensus size: 22
6123612 ATATAATCTT
*
6123622 AGATATGATATGTAATCTT---
1 AGATATGATATGTAAACTTAGA
* *
6123641 AGATATGATATATAATCTTAG-
1 AGATATGATATGTAAACTTAGA
*
6123662 --ATATGATATGTAATCTTAGA
1 AGATATGATATGTAAACTTAGA
*
6123682 AGATATGATTTTGTAAACTTAGA
1 AGATATGA-TATGTAAACTTAGA
6123705 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
19 36 0.67
22 6 0.11
23 12 0.22
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (22 bp):
AGATATGATATGTAAACTTAGA
Found at i:6123714 original size:22 final size:23
Alignment explanation
Indices: 6123670--6123714 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6123660 AGATATGATA
* *
6123670 TGTAATCTTAGAAGATATGATTT
1 TGTAAACTTAGAAGATATAATTT
*
6123693 TGTAAACTTAG-AGATTTAATTT
1 TGTAAACTTAGAAGATATAATTT
6123715 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (23 bp):
TGTAAACTTAGAAGATATAATTT
Found at i:6124047 original size:22 final size:21
Alignment explanation
Indices: 6124002--6124048 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6123992 TTAAGTTTTT
*
6124002 TTTTATTTTTTTAATTTACCA
1 TTTTATTTTTTTAAATTACCA
6124023 TTTTATTTATTTTAAATT-CCA
1 TTTTATTT-TTTTAAATTACCA
*
6124044 ATTTA
1 TTTTA
6124049 ATCCTTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATTTTTTTAAATTACCA
Found at i:6129445 original size:7 final size:7
Alignment explanation
Indices: 6129425--6129467 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
6129415 ACTCAATAGA
*
6129425 CAATCCG
1 CAATCCT
6129432 CAATCCT
1 CAATCCT
6129439 CAATCCT
1 CAATCCT
* *
6129446 AAATTCT
1 CAATCCT
*
6129453 CAATTCT
1 CAATCCT
6129460 CAATCCT
1 CAATCCT
6129467 C
1 C
6129468 GATTCTCGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.30
Consensus pattern (7 bp):
CAATCCT
Found at i:6129538 original size:7 final size:7
Alignment explanation
Indices: 6129432--6129548 Score: 99
Period size: 7 Copynumber: 16.7 Consensus size: 7
6129422 AGACAATCCG
*
6129432 CAATCCT
1 CAATTCT
*
6129439 CAATCCT
1 CAATTCT
*
6129446 AAATTCT
1 CAATTCT
6129453 CAATTCT
1 CAATTCT
*
6129460 CAATCCT
1 CAATTCT
*
6129467 CGATTCT
1 CAATTCT
*
6129474 CGATTCT
1 CAATTCT
*
6129481 CGATTCT
1 CAATTCT
6129488 CAATTCT
1 CAATTCT
**
6129495 CGGTTCT
1 CAATTCT
*
6129502 CGATTCT
1 CAATTCT
6129509 CAATTCT
1 CAATTCT
**
6129516 CGCTTCT
1 CAATTCT
**
6129523 TGATTCT
1 CAATTCT
6129530 CAATTCT
1 CAATTCT
*
6129537 CAAATCT
1 CAATTCT
6129544 CAATT
1 CAATT
6129549 ATTTTTTTAA
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 91 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (7 bp):
CAATTCT
Found at i:6131647 original size:21 final size:21
Alignment explanation
Indices: 6131621--6131663 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6131611 TTTTCGGGTA
6131621 CACACCTAGTTCTGTTTGATG
1 CACACCTAGTTCTGTTTGATG
6131642 CACACCTAGTTCTGTTTGATG
1 CACACCTAGTTCTGTTTGATG
6131663 C
1 C
6131664 TAAAACAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (21 bp):
CACACCTAGTTCTGTTTGATG
Found at i:6138064 original size:14 final size:14
Alignment explanation
Indices: 6138045--6138089 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 14
6138035 TCATAATTTG
*
6138045 TAATTTTTTTTTTA
1 TAATTTTTTTTATA
6138059 TAA--TTTTTTATA
1 TAATTTTTTTTATA
6138071 TAA-TTTTTTTATA
1 TAATTTTTTTTATA
6138084 -AATTTT
1 TAATTTT
6138090 AAATTGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 13 0.46
13 12 0.43
14 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TAATTTTTTTTATA
Found at i:6138067 original size:11 final size:11
Alignment explanation
Indices: 6138051--6138089 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 11
6138041 TTTGTAATTT
6138051 TTTTTTTATAA
1 TTTTTTTATAA
6138062 TTTTTTATATAA
1 TTTTTT-TATAA
6138074 TTTTTTTATAAA
1 TTTTTTTAT-AA
6138086 TTTT
1 TTTT
6138090 AAATTGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTTTATAA
Found at i:6146558 original size:30 final size:30
Alignment explanation
Indices: 6146475--6146561 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
6146465 CAAAATTCAA
* * *
6146475 AATTCAAAAAGTATAGGGACCAAAATTGACC
1 AATTCAAAAAGTATAAGGA-CTAAATTAACC
* * *
6146506 AATTAAAAAAAGTTTAATGACTAAATTAACC
1 AATT-CAAAAAGTATAAGGACTAAATTAACC
*
6146537 AATTCAAAAAGTACAAGGACTAAAT
1 AATTCAAAAAGTATAAGGACTAAAT
6146562 CCATAACTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
30 17 0.38
31 17 0.38
32 11 0.24
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (30 bp):
AATTCAAAAAGTATAAGGACTAAATTAACC
Found at i:6149473 original size:40 final size:39
Alignment explanation
Indices: 6149429--6149505 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
6149419 TCAAACATAT
* *
6149429 ATTTATATTTATACAATA-TTCATAATTGTAATTATATTGA
1 ATTTATAATTATACAATACTTC-TAATTAT-ATTATATTGA
*
6149469 ATTTATAATTATACGATACTTCTAATTATATTATATT
1 ATTTATAATTATACAATACTTCTAATTATATTATATT
6149506 TGTAATCACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 8 0.24
40 22 0.67
41 3 0.09
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (39 bp):
ATTTATAATTATACAATACTTCTAATTATATTATATTGA
Found at i:6149511 original size:17 final size:18
Alignment explanation
Indices: 6149444--6149511 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 18
6149434 TATTTATACA
*
6149444 ATATTCATAATTGTAATT
1 ATATTCATATTTGTAATT
* *
6149462 ATATTGA-ATTTATAATT
1 ATATTCATATTTGTAATT
* *
6149479 ATA--CGATACTTCTAATT
1 ATATTC-ATATTTGTAATT
6149496 ATATT-ATATTTGTAAT
1 ATATTCATATTTGTAAT
6149512 CACAAATCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
16 1 0.03
17 31 0.82
18 6 0.16
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATATTCATATTTGTAATT
Found at i:6154025 original size:20 final size:20
Alignment explanation
Indices: 6154000--6154179 Score: 69
Period size: 20 Copynumber: 9.0 Consensus size: 20
6153990 GAAGTACAAA
6154000 TAGGGGCACATATGTGCAAT
1 TAGGGGCACATATGTGCAAT
* ** * *
6154020 TAGGGGTACCGAAGTACGAA-
1 TAGGGGCACATATGTGC-AAT
*
6154040 TAGGGGGACATATGTGCAAT
1 TAGGGGCACATATGTGCAAT
* * * ** * * *
6154060 CAGGAGTACCGAAGTACAAA
1 TAGGGGCACATATGTGCAAT
*
6154080 TAGGGGCATATATGTGCAAT
1 TAGGGGCACATATGTGCAAT
* * * *
6154100 TAGGGGTAC-TGAAGTACAAA
1 TAGGGGCACAT-ATGTGCAAT
* *
6154120 CAGGGGCACGTATGTGCAAT
1 TAGGGGCACATATGTGCAAT
* * * * *
6154140 CAGGGGTAC-TAAAGTACAAA
1 TAGGGGCACAT-ATGTGCAAT
*
6154160 TAGGGACACATATGTGCAAT
1 TAGGGGCACATATGTGCAAT
6154180 CAGGTGTACC
Statistics
Matches: 107, Mismatches: 47, Indels: 12
0.64 0.28 0.07
Matches are distributed among these distances:
19 4 0.04
20 99 0.93
21 4 0.04
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.21
Consensus pattern (20 bp):
TAGGGGCACATATGTGCAAT
Found at i:6154205 original size:40 final size:40
Alignment explanation
Indices: 6153983--6154221 Score: 334
Period size: 40 Copynumber: 6.0 Consensus size: 40
6153973 GTGCATTTAA
*
6153983 GGGTACCGAAGTACAAATAGGGGCACATATGTGCAATTAG
1 GGGTACCGAAGTACAAATAGGGGCACATATGTGCAATCAG
* *
6154023 GGGTACCGAAGTACGAATAGGGGGACATATGTGCAATCAG
1 GGGTACCGAAGTACAAATAGGGGCACATATGTGCAATCAG
* * *
6154063 GAGTACCGAAGTACAAATAGGGGCATATATGTGCAATTAG
1 GGGTACCGAAGTACAAATAGGGGCACATATGTGCAATCAG
* * *
6154103 GGGTACTGAAGTACAAACAGGGGCACGTATGTGCAATCAG
1 GGGTACCGAAGTACAAATAGGGGCACATATGTGCAATCAG
** *
6154143 GGGTACTAAAGTACAAATAGGGACACATATGTGCAATCAG
1 GGGTACCGAAGTACAAATAGGGGCACATATGTGCAATCAG
* * * *
6154183 GTGTACCGAAGTACAAACAGGGACACGTATGTGCAATCA
1 GGGTACCGAAGTACAAATAGGGGCACATATGTGCAATCA
6154222 TACAATAATC
Statistics
Matches: 176, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 176 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (40 bp):
GGGTACCGAAGTACAAATAGGGGCACATATGTGCAATCAG
Found at i:6161037 original size:40 final size:40
Alignment explanation
Indices: 6160976--6161264 Score: 335
Period size: 40 Copynumber: 7.2 Consensus size: 40
6160966 GTGCACGAAA
* * * * *
6160976 GTGCATTCAAGTGTACCAAAGTACAAATAGGGGCACATAT
1 GTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACGTAT
* * * *
6161016 GTGAAATCAAGGCTACCAAAGTACGAACAGGGGCACGTAT
1 GTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACGTAT
* * * * *
6161056 GTGCCATAAAGAGTACCGAAGTACAAATAGGGGCATGTAT
1 GTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACGTAT
* *
6161096 GTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGCAT
1 GTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACGTAT
* * ** *
6161136 GTGCAATCAAGGGCACTGAAGTACAAACAGGATCACTTAT
1 GTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACGTAT
* *
6161176 GTGCAATCAAGGGTACCAAAGTACAAACAGGGACACGTAT
1 GTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACGTAT
* * *
6161216 GTGCAATCAAGGGTACCGAAGTATAAACAAGGACACGTAT
1 GTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACGTAT
*
6161256 GTACAATCA
1 GTGCAATCA
6161265 TATAATAATT
Statistics
Matches: 209, Mismatches: 40, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 209 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.18
Consensus pattern (40 bp):
GTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACGTAT
Found at i:6164915 original size:2 final size:2
Alignment explanation
Indices: 6164904--6164942 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
6164894 AAACATTTCA
6164904 AT AT -T 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
6164943 TAGTTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6176490 original size:2 final size:2
Alignment explanation
Indices: 6176485--6176515 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6176475 TGATGAACTG
6176485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6176516 CACAACTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6177352 original size:25 final size:26
Alignment explanation
Indices: 6177324--6177374 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
6177314 TTGTAAATCA
**
6177324 GAAAAAATGTCTTTAGA-AATTTTCT
1 GAAAAAACCTCTTTAGAGAATTTTCT
*
6177349 GAAATAACCTCTTTAGAGAATTTTCT
1 GAAAAAACCTCTTTAGAGAATTTTCT
6177375 CTCTACAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (26 bp):
GAAAAAACCTCTTTAGAGAATTTTCT
Found at i:6177507 original size:21 final size:21
Alignment explanation
Indices: 6177483--6177522 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6177473 AATCACATTG
6177483 ATATTAAATTAATATAATAAA
1 ATATTAAATTAATATAATAAA
* *
6177504 ATATTATATTAATTTAATA
1 ATATTAAATTAATATAATA
6177523 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTAAATTAATATAATAAA
Found at i:6180245 original size:14 final size:14
Alignment explanation
Indices: 6180205--6180245 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6180195 GTTACATAAG
* *
6180205 TTATTTTTATATAT
1 TTATATTTATATTT
*
6180219 ATATATTTATATTT
1 TTATATTTATATTT
6180233 TTATATTTATATT
1 TTATATTTATATT
6180246 CTAAGGTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATATTTATATTT
Found at i:6192514 original size:23 final size:24
Alignment explanation
Indices: 6192461--6192514 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
6192451 ACTCCTAGGC
*
6192461 ACCTCAATATGCCATTCAAAACAT
1 ACCTAAATATGCCATTCAAAACAT
*
6192485 ACC-AAATATGTC-TTCAAAATC-T
1 ACCTAAATATGCCATTCAAAA-CAT
6192507 ACCTAAAT
1 ACCTAAAT
6192515 GGTAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 11 0.42
23 12 0.46
24 3 0.12
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.28
Consensus pattern (24 bp):
ACCTAAATATGCCATTCAAAACAT
Found at i:6213582 original size:28 final size:27
Alignment explanation
Indices: 6213528--6213582 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
6213518 AACAAATTTT
* **
6213528 ATTTTTGAAAAAAAAAATTAGTTGTCG
1 ATTTTTAAAAAAAAAAATTAGGAGTCG
*
6213555 ATTTTTAAAAAACAAAAATTGGGAGTCG
1 ATTTTTAAAAAA-AAAAATTAGGAGTCG
6213583 CCACCAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (27 bp):
ATTTTTAAAAAAAAAAATTAGGAGTCG
Found at i:6215069 original size:45 final size:45
Alignment explanation
Indices: 6215007--6215568 Score: 276
Period size: 44 Copynumber: 12.9 Consensus size: 45
6214997 GGATTATCGG
* * *
6215007 CTTTAATCTGCTCCACTGCCACTTCAGGGAGATAAGATTTGCCAT-
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATA
* *
6215052 CTTTAGTCTGC-CTCACTGCAACTTCA-AGAGGATAAGACTTGCTTA
1 CTTTAGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCATA
* *
6215097 C-TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATG
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATA
* * * * * *
6215140 C--GA-TCTGCT-CTCTACAACTTCAGAGAGATAAGATCTAAG-GT-
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCATA
* * * *
6215181 -TTTAATCCGCTCCACTGCAACCTCAGGGAGATAGGA-TT--AT-
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATA
* * * *
6215221 CGGTTTTAATCTGCTCTACTGCAACTTCAAGGAGATAAGATTTGCCAT-
1 C---TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATA
* * * *
6215269 CTTTAGTCTGC-CTAATTGCAACTTCA-AGAGGATAAGACTTGCTTA
1 CTTTAGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCATA
* * *
6215314 CTTT-GTCTGCTCCACTGCAACTTCCGGGAGATAAGACTAG-ATG
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATA
* * * *
6215357 C---AATCTGCT-CTCTGCAACTTCAGAGAGATAAGA--TCCA-A
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATA
* * * * * * * **
6215395 GGTTTTAATCCGCTCCACTGCAACTTTAAGGAGATAGGA-TTATCGGA
1 --CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCATA
* * *
6215442 -TTTAATCTGCTCCAATGCAACTTCAGGAAGATAAGACTTGCCAT-
1 CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATA
* * *
6215486 CTTCAGTCTGC-CTTACTGCAACTTCA-GGAGGATAAGACTTGCTTA
1 CTTTAGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCATA
* *
6215531 C-TTAGTTTGCTCCACTACAACTTTC-GGGAGATAAGACT
1 CTTTAGTCTGCTCCACTGCAAC-TTCAGGGAGATAAGACT
6215569 AGATGCGATC
Statistics
Matches: 397, Mismatches: 76, Indels: 89
0.71 0.14 0.16
Matches are distributed among these distances:
39 1 0.00
40 43 0.11
41 14 0.04
42 6 0.02
43 16 0.04
44 195 0.49
45 117 0.29
46 1 0.00
47 1 0.00
48 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (45 bp):
CTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATA
Done.