Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008440.1 Hibiscus syriacus cultivar Beakdansim tig00111239_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: 518054
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:235437 original size:17 final size:17
Alignment explanation
Indices: 235417--235450 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
235407 TTCATCATAT
235417 TATTA-TTATTATTATTA
1 TATTATTTA-TATTATTA
235434 TATTATTTATATTATTA
1 TATTATTTATATTATTA
235451 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTTATATTATTA
Found at i:235752 original size:20 final size:20
Alignment explanation
Indices: 235723--235773 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
235713 AAGCTATTAT
*
235723 GGTGAGTCACCACATAGTTC
1 GGTGACTCACCACATAGTTC
235743 GGTGACTCACCACATAGTTC
1 GGTGACTCACCACATAGTTC
235763 GGTGACTCACC
1 GGTGACTCACC
235774 GAAATCCACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (20 bp):
GGTGACTCACCACATAGTTC
Found at i:236968 original size:17 final size:17
Alignment explanation
Indices: 236948--237011 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
236938 TTTTTAATAA
236948 ATAAATATTTTACTTTT
1 ATAAATATTTTACTTTT
*
236965 ATAAATTATATATATTATTTTT
1 AT-AA--ATAT-T-TTACTTTT
236987 AAATAAATATTTTACTTTT
1 --ATAAATATTTTACTTTT
237006 ATAAAT
1 ATAAAT
237012 TATATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 7 0.18
20 5 0.13
21 5 0.13
22 7 0.18
23 2 0.05
24 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAATATTTTACTTTT
Found at i:236977 original size:22 final size:21
Alignment explanation
Indices: 236939--237011 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
236929 TTTCTGATAT
236939 TTTTAATAAATAAATATTTTAC
1 TTTT-ATAAATAAATATTTTAC
* *
236961 TTTTATAAATTATATATATTA-
1 TTTTATAAA-TAAATATTTTAC
236982 TTTT-TAAATAAATATTTTAC
1 TTTTATAAATAAATATTTTAC
237002 TTTTATAAAT
1 TTTTATAAAT
237012 TATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.20
20 8 0.18
21 14 0.32
22 13 0.30
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAAATAAATATTTTAC
Found at i:236992 original size:24 final size:23
Alignment explanation
Indices: 236936--237029 Score: 76
Period size: 22 Copynumber: 4.3 Consensus size: 23
236926 CATTTTCTGA
*
236936 TATTTTTAATAAA-TAAATATTT
1 TATTTTTAATAAATTAAATATAT
* *
236958 TACTTTT-ATAAATTATATATAT
1 TATTTTTAATAAATTAAATATAT
*
236980 TA-TTTT--TAAA-TAAATATTT
1 TATTTTTAATAAATTAAATATAT
*
236999 TACTTTT-ATAAATTATATATATAT
1 TATTTTTAATAAATTA-A-ATATAT
237023 TATTTTT
1 TATTTTT
237030 TAATGTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
19 9 0.15
20 8 0.14
21 13 0.22
22 17 0.29
23 1 0.02
24 11 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTTTAATAAATTAAATATAT
Found at i:236992 original size:41 final size:43
Alignment explanation
Indices: 236945--237029 Score: 156
Period size: 41 Copynumber: 2.0 Consensus size: 43
236935 ATATTTTTAA
236945 TAAATAAATATTTTACTTTTATAAA-T-TATATATATTATTTT
1 TAAATAAATATTTTACTTTTATAAATTATATATATATTATTTT
236986 TAAATAAATATTTTACTTTTATAAATTATATATATATTATTTT
1 TAAATAAATATTTTACTTTTATAAATTATATATATATTATTTT
237029 T
1 T
237030 TAATGTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 25 0.60
42 1 0.02
43 16 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (43 bp):
TAAATAAATATTTTACTTTTATAAATTATATATATATTATTTT
Found at i:238492 original size:28 final size:28
Alignment explanation
Indices: 238456--238525 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
238446 ATTAGAAACA
238456 TTAGGCACCTAAATTGATCAAAAAGGAT
1 TTAGGCACCTAAATTGATCAAAAAGGAT
*
238484 TTAGGCACCTAAATTGATCAAAAAGGGT
1 TTAGGCACCTAAATTGATCAAAAAGGAT
238512 TTAGGCACCTAAAT
1 TTAGGCACCTAAAT
238526 GGGTATGGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (28 bp):
TTAGGCACCTAAATTGATCAAAAAGGAT
Found at i:238783 original size:28 final size:28
Alignment explanation
Indices: 238751--238832 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 28
238741 TTTGAGGATG
238751 AATTTGGAATGTTCAAAAGTTTGGGACC
1 AATTTGGAATGTTCAAAAGTTTGGGACC
** * * * **
238779 AATTTAAAATGAGTC-ATAGTTTAGAGATG
1 AATTTGGAATG-TTCAAAAGTTT-GGGACC
*
238808 AATTTGGTATGTTCAAAAGTTTGGG
1 AATTTGGAATGTTCAAAAGTTTGGG
238833 GACTAATTCA
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
28 19 0.50
29 19 0.50
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.35
Consensus pattern (28 bp):
AATTTGGAATGTTCAAAAGTTTGGGACC
Found at i:238820 original size:57 final size:57
Alignment explanation
Indices: 238694--238846 Score: 184
Period size: 57 Copynumber: 2.6 Consensus size: 57
238684 GGGGATGTTA
* * *
238694 TTGGAATGTTCAAAAGTTTGAGG-CCTAATTTAGAATAAGGGTCATGTTTTGAGGATGAAT
1 TTGGAATGTTCAAAAGTTTG-GGACC-AATTTA-AA-ATGAGTCATGTTTAGAGGATGAAT
238754 TTGGAATGTTCAAAAGTTTGGGACCAATTTAAAATGAGTCATAGTTTAGA-GATGAAT
1 TTGGAATGTTCAAAAGTTTGGGACCAATTTAAAATGAGTCAT-GTTTAGAGGATGAAT
* * *
238811 TTGGTATGTTCAAAAGTTTGGGGACTAATTCAAAAT
1 TTGGAATGTTCAAAAGTTT-GGGACCAATTTAAAAT
238847 ATTTGTCATA
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
57 32 0.38
58 22 0.26
59 8 0.10
60 22 0.26
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (57 bp):
TTGGAATGTTCAAAAGTTTGGGACCAATTTAAAATGAGTCATGTTTAGAGGATGAAT
Found at i:240724 original size:171 final size:174
Alignment explanation
Indices: 240435--240782 Score: 657
Period size: 171 Copynumber: 2.0 Consensus size: 174
240425 TATGAATAGT
240435 TGAGTGACTGATTTTGTAACTTTTAATAATCGAGAGACTCGACAAAGCAACGCCTCATAATCGAG
1 TGAGTGACTGATTTTGTAACTTTTAATAATCGAGAGACTCGACAAAG--ACGCCTCATAATCGAG
240500 GAATAATTTATAACTTTTAATAGTCATGGGACTAAACAAAATAATATCATATAGTCGAATGATCA
64 GAATAATTTATAACTTTTAATAGTCATGGGACTAAACAAAATAATATCATATAGTCGAATGATCA
240565 TTTGCATACTTTATTCTAA-TTTTTAAAGGATTAGAGCAGGATTGG
129 TTTGCATACTTTATTCTAATTTTTTAAAGGATTAGAGCAGGATTGG
240610 TGAGTGACTGATTTTGTAA-TTTTAATAATCGAGAGACTCGACAAAG-CGCCTCATAATCGAGGA
1 TGAGTGACTGATTTTGTAACTTTTAATAATCGAGAGACTCGACAAAGACGCCTCATAATCGAGGA
240673 ATAATTTATAACTTTTAATAGTCATGGGACTAAACAAAATAATATCATATAGTCGAATGATCATT
66 ATAATTTATAACTTTTAATAGTCATGGGACTAAACAAAATAATATCATATAGTCGAATGATCATT
240738 TGCATACTTTATTCTAATTTTTTAAAGGATTAGAGCAGGATTGG
131 TGCATACTTTATTCTAATTTTTTAAAGGATTAGAGCAGGATTGG
240782 T
1 T
240783 TATTAACTAA
Statistics
Matches: 172, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
171 99 0.58
172 27 0.16
174 27 0.16
175 19 0.11
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (174 bp):
TGAGTGACTGATTTTGTAACTTTTAATAATCGAGAGACTCGACAAAGACGCCTCATAATCGAGGA
ATAATTTATAACTTTTAATAGTCATGGGACTAAACAAAATAATATCATATAGTCGAATGATCATT
TGCATACTTTATTCTAATTTTTTAAAGGATTAGAGCAGGATTGG
Found at i:244942 original size:48 final size:46
Alignment explanation
Indices: 244868--244960 Score: 150
Period size: 48 Copynumber: 2.0 Consensus size: 46
244858 CGAATTGAAT
244868 TATAATTTAATAATTTTTACCATTTTCATTTTGCTTGTCAGAGAAA
1 TATAATTTAATAATTTTTACCATTTTCATTTTGCTTGTCAGAGAAA
* *
244914 TATAATTTAATAGTTTCTTTACCATTTTCATTTTGCTTGTTAGAGAA
1 TATAATTTAATA-ATT-TTTACCATTTTCATTTTGCTTGTCAGAGAA
244961 TGATGAATCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 12 0.28
47 2 0.05
48 29 0.67
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (46 bp):
TATAATTTAATAATTTTTACCATTTTCATTTTGCTTGTCAGAGAAA
Found at i:247442 original size:4 final size:4
Alignment explanation
Indices: 247435--247461 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
247425 GTTCTAACTG
247435 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
247462 TCACAGGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:249378 original size:15 final size:16
Alignment explanation
Indices: 249339--249377 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
249329 GTCTTTTGTC
249339 GAGAAAAAGGGCACTG
1 GAGAAAAAGGGCACTG
249355 GAGAAAAAGGGCACTG
1 GAGAAAAAGGGCACTG
249371 GAAGAAA
1 G-AGAAA
249378 GATGTCCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.49, C:0.10, G:0.36, T:0.05
Consensus pattern (16 bp):
GAGAAAAAGGGCACTG
Found at i:256022 original size:128 final size:126
Alignment explanation
Indices: 255785--256109 Score: 348
Period size: 128 Copynumber: 2.6 Consensus size: 126
255775 TTGAAACTCT
* * ** *
255785 AAAAC-ACAACATTTTATTATCATTATTGGTATGTATCAAAACTACATATTCCAATGAAACTAGA
1 AAAACAACACCATTTTATTATCAATATTGGTGCGTATCAAAACTACATATTCCAATGAAAATAGA
* * * ** * * *
255849 AGCATTGAACTGATAGAATCATTCTTCAAAACGATGACGTTTTAATCAAAATTCTATAA-AT
66 AGCATTGAACCGATAAAAACACACTTCAAAACGACGACGTCTTAATCAAAATTCTA-AAGAA
* * *
255910 ATAACAACGCCATTTTATTAATCAATATCGGTGCGTATCAAAACTACATATTCCAATGAAAAATA
1 AAAACAACACCATTTTATT-ATCAATATTGGTGCGTATCAAAACTACATATTCCAATG-AAAATA
* * *
255975 GAAGCATTGAACCGGTAAAAACACACTTCAAAACGACGATGTCTTAATGAAAATTCTAAAGAA
64 GAAGCATTGAACCGATAAAAACACACTTCAAAACGACGACGTCTTAATCAAAATTCTAAAGAA
* * * ** * * * *
256038 AAAACGATACCGTTCAATTTATCAATATTGGCGCATATTAAAACTACATATTCCAATGAAAGTAG
1 AAAACAACACCATTTTA-TTATCAATATTGGTGCGTATCAAAACTACATATTCCAATGAAAATAG
256103 AAGCATT
65 AAGCATT
256110 TGTTCAACTT
Statistics
Matches: 164, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
125 4 0.02
126 11 0.07
127 49 0.30
128 98 0.60
129 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (126 bp):
AAAACAACACCATTTTATTATCAATATTGGTGCGTATCAAAACTACATATTCCAATGAAAATAGA
AGCATTGAACCGATAAAAACACACTTCAAAACGACGACGTCTTAATCAAAATTCTAAAGAA
Found at i:258180 original size:31 final size:31
Alignment explanation
Indices: 258142--258203 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
258132 TGCTTGTATG
*
258142 AATTTTCTGTGACATTAAAATCACCATTATT
1 AATTTTCTATGACATTAAAATCACCATTATT
*
258173 AATTTTCTATGACATTAAAATCATCATTATT
1 AATTTTCTATGACATTAAAATCACCATTATT
258204 TTTATGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (31 bp):
AATTTTCTATGACATTAAAATCACCATTATT
Found at i:258616 original size:12 final size:10
Alignment explanation
Indices: 258583--258644 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
258573 TTTTTAATAA
258583 TATATATTAT
1 TATATATTAT
258593 TAT-TATTAT
1 TATATATTAT
*
258602 TATATAGTTAG
1 TATATA-TTAT
258613 T-TATATTA-
1 TATATATTAT
*
258621 TA-ATAATA-
1 TATATATTAT
258629 TATGATATTAT
1 TAT-ATATTAT
258640 TATAT
1 TATAT
258645 TCTTGTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
8 8 0.19
9 12 0.28
10 16 0.37
11 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (10 bp):
TATATATTAT
Found at i:258639 original size:23 final size:23
Alignment explanation
Indices: 258577--258639 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
258567 TTAATATTTT
*
258577 TAATAATAT-ATATTATTATTATTA
1 TAAT-ATATGATATTA-TATTATAA
* *
258601 TTATATA-GTTAGTTATATTATAA
1 TAATATATGATA-TTATATTATAA
258624 TAATATATGATATTAT
1 TAATATATGATATTAT
258640 TATATTCTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
TAATATATGATATTATATTATAA
Found at i:259003 original size:22 final size:23
Alignment explanation
Indices: 258966--259010 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
258956 TAAATTATTC
*
258966 TAAGATTTTTAAAATAATAATAT
1 TAAGATTTTTAAAATAAAAATAT
*
258989 TAAG-TTTTTATAATAAAAATAT
1 TAAGATTTTTAAAATAAAAATAT
259011 CATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TAAGATTTTTAAAATAAAAATAT
Found at i:264105 original size:2 final size:2
Alignment explanation
Indices: 264098--264133 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
264088 TAAAATCAAC
264098 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
264134 CATTATTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264307 original size:54 final size:54
Alignment explanation
Indices: 264268--264589 Score: 491
Period size: 54 Copynumber: 6.0 Consensus size: 54
264258 GGTACCAAAC
*
264268 CGGTTATTCATCTACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* * * *
264322 TGATTATTCATCCACATAGGATAAATTTCGTGAAATGCACACTTAGTGCCGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* * * *
264376 CGGTTATTCATCCACATAGGATGAATTTCGTGAAATACAAACTTAGTGCCAAAA
1 CGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* *
264430 CGATTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* *
264484 CAGTTATGCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
1 CGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* * * *
264538 CGGTTATTCATCCACAAAGGACGAATTTCGTGAAATGCACAATTAGTGCCGA
1 CGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGA
264590 TTTGGTAATC
Statistics
Matches: 241, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 241 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (54 bp):
CGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
Found at i:264912 original size:22 final size:22
Alignment explanation
Indices: 264877--264950 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
264867 TGGCCATTCA
* *
264877 GTATCGATAC--CCCTACCATT
1 GTATCGATACTACCCTACTATG
264897 GTATCGATACTACCCTACTATG
1 GTATCGATACTACCCTACTATG
*
264919 GTATCAATACTACCCTACTATG
1 GTATCGATACTACCCTACTATG
264941 GTATCGATAC
1 GTATCGATAC
264951 CCCCTTCCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.21
22 38 0.79
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (22 bp):
GTATCGATACTACCCTACTATG
Found at i:265080 original size:94 final size:95
Alignment explanation
Indices: 264936--265120 Score: 291
Period size: 94 Copynumber: 2.0 Consensus size: 95
264926 TACTACCCTA
* ** *
264936 CTATGGTATCGATACCCCCTTCCAGTATCGATACCAAAATTAGCTTCGATGTGGCTTGGTATTGA
1 CTATGGTATCGATACCCCCTTCCAGTATCGATACCAAAATTAGCTTCGATGTGACCGGGTATAGA
265001 TACCCTCACCATAGTATCGATACTACTACG
66 TACCCTCACCATAGTATCGATACTACTACG
* * *
265031 CTATGGTATCGATACCCCC-TCCGGTATCGATACCAAAATTAGGTTCGATGTTACCGGGTATAGA
1 CTATGGTATCGATACCCCCTTCCAGTATCGATACCAAAATTAGCTTCGATGTGACCGGGTATAGA
*
265095 TACCCTTACCATAGTATCGATACTAC
66 TACCCTCACCATAGTATCGATACTAC
265121 CTCATTAGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 63 0.77
95 19 0.23
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (95 bp):
CTATGGTATCGATACCCCCTTCCAGTATCGATACCAAAATTAGCTTCGATGTGACCGGGTATAGA
TACCCTCACCATAGTATCGATACTACTACG
Found at i:267947 original size:2 final size:2
Alignment explanation
Indices: 267940--267967 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
267930 AATGAAATCA
267940 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
267968 CATTATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268129 original size:54 final size:54
Alignment explanation
Indices: 268093--268312 Score: 343
Period size: 54 Copynumber: 4.1 Consensus size: 54
268083 TGCACTCATG
*
268093 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGTACACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
* * *
268147 GTGCTGAAACGATTATTCATCCACA-ATGGATGAATTTCGTGAAATGCACACTTA
1 GTGCCGAAACGGTTATTCATCCACATA-GGATGAATTCCGTGAAATGCACACTTA
* *
268201 GTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATACACACTTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
* * *
268255 GGGACGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAATTA
1 GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
268309 GTGC
1 GTGC
268313 TGATTTGGTA
Statistics
Matches: 149, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.01
54 147 0.99
55 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (54 bp):
GTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTA
Found at i:268166 original size:108 final size:108
Alignment explanation
Indices: 268068--268312 Score: 280
Period size: 108 Copynumber: 2.3 Consensus size: 108
268058 TAAATATATT
*** * *
268068 ATAAATTCCGTGTTTTGCACTCATGGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
1 ATAAATTCCGTGAAATGCACACATAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
** * **
268133 GAAATGTACACTTAGTG-CTGAAACGATTATTCATCCACAATGG
66 GAAATACACACTTAGGGAC-GAAACGATTATTCATAAACAATGG
* * * *
268176 ATGAATTTCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
1 ATAAATTCCGTGAAATGCACACATAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
* **
268241 GAAATACACACTTAGGGACGAAACGGTTATTCATCCAC-ATAGG
66 GAAATACACACTTAGGGACGAAACGATTATTCATAAACAAT-GG
*
268284 ATGAATTCCGTGAAATGCACA-ATTAGTGC
1 ATAAATTCCGTGAAATGCACACA-TAGTGC
268313 TGATTTGGTA
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
107 2 0.02
108 115 0.97
109 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (108 bp):
ATAAATTCCGTGAAATGCACACATAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGT
GAAATACACACTTAGGGACGAAACGATTATTCATAAACAATGG
Found at i:285579 original size:24 final size:24
Alignment explanation
Indices: 285552--285653 Score: 82
Period size: 24 Copynumber: 4.2 Consensus size: 24
285542 GATATCAAAA
* *
285552 ATCAAAACAGAATTCAGATTAGAT
1 ATCAGAACAGAATTCAGATCAGAT
* * * * *
285576 ATCATAGCAGAATCCATATCAGAA
1 ATCAGAACAGAATTCAGATCAGAT
* *
285600 ATCAGAACAAAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAGATCA-GAT
*
285624 ATCAGAACAGAATTCA-AGTCAGAA
1 ATCAGAACAGAATTCAGA-TCAGAT
285648 ATCAGA
1 ATCAGA
285654 TAAAACATTT
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
23 1 0.02
24 57 0.97
25 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAGAT
Found at i:285627 original size:48 final size:48
Alignment explanation
Indices: 285543--285653 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
285533 GTAAACGGAG
* * * * * *
285543 ATATCAAAAATCAAAACAGAATTCAGATTAGATATCATAGCAGAATCC
1 ATATCAGAAATCAGAACAAAATTCAGATCAGATATCAGAACAGAATCC
* *
285591 ATATCAGAAATCAGAACAAAATTCAGGTCATG-TATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAAAATTCAGATCA-GATATCAGAACAGAATCC
285639 A-AGTCAGAAATCAGA
1 ATA-TCAGAAATCAGA
285654 TAAAACATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAAAATTCAGATCAGATATCAGAACAGAATCC
Found at i:286553 original size:442 final size:446
Alignment explanation
Indices: 285696--286588 Score: 1447
Period size: 442 Copynumber: 2.0 Consensus size: 446
285686 TGTTTACAGA
* *
285696 TATTATTCAGAGACACTTGATAATCTTATCAAGCAGAGAAATAAGGATCTTCCGTGTACCGATAG
1 TATTATTCAGAGACACTGGATAATCTTATCAAGCAGAGAAACAAGGATCTTCCGTGTACCGATAG
* * * *
285761 AATTCCGAAAGTTAGAATCACTATTGTAAAAGTTCATTAACTGACAAATTCATCAGTTATGCAGA
66 AATTCCGAAAGTTAGAATCACTATTGGAAAAGTTCATTAACTGAAAAAATCATCAATTATGCAGA
* *
285826 ATACGATTTCAGCTGATAAGAAGAAACGAGAATTCAATCTATTTCGATTAATCGGATTATCGAAC
131 ATACGATTTCAACTGATAAGAAGAAACGAGAATTCAATCTATGTCGATTAATC-GATTATCGAAC
* * *
285891 AACTCCCAGAATTTATGCTTGTCGACTGGTTAATTCATTGTCCTGACATGGTATTTACTCTTTAA
195 AACTCCCAGAACTTATGCTTATCGACTGGTTAATTCATTGTCCTGACATAGTATTTACTCTTTAA
285956 TACCAAAAATTCTTATCCATAGATCATCTTCAGAATCATCATTGAATAAATCTTCCAATATTCTT
260 TACCAAAAATTCTTATCCATAGATCATCTTCAGAATCATCATTGAATAAATCTTCCAATATTCTT
*
286021 TATTTAATTTCCACGCCTCCATGATATCATGAAATGATGACGTGCTTGATTTATATTTCATGACC
325 TATTTAATTTCCACGCCTCCATGATATCATGAAATGATGACGTGCTTGATTTATAGTTCATGACC
*
286086 CATAAGAACATTACATCATGTATGTTCATTAATGTTTCCAGAC-TCTCCAAATCACT
390 CATAAGAACATTACATCATGTATGTTCATTAATGTTTCCAGACTTATCCAAATCACT
* * *
286142 TATTATTCAGAGACACTGGATAATCTTATCAGGTAGAGAAACAAGGATCTTTCGTGTACCGATAG
1 TATTATTCAGAGACACTGGATAATCTTATCAAGCAGAGAAACAAGGATCTTCCGTGTACCGATAG
* * * *
286207 AATTTCGGAAGTTAGAATCACTATTGGAAGAGTTCATTAATTGAAAAAATCATCAATTATGCAGA
66 AATTCCGAAAGTTAGAATCACTATTGGAAAAGTTCATTAACTGAAAAAATCATCAATTATGCAGA
* * * *
286272 ATGCGATTTCAACTGATAAGGAAGAAATGATAATTCAATCTATGTCGATTGATC-ATTATCGAAC
131 ATACGATTTCAACTGATAA-GAAGAAACGAGAATTCAATCTATGTCGATTAATCGATTATCGAAC
*
286336 AACT-CCAGAACTTATGCTTATCGACTGGTTAATTCATTGTCCT-TCTATAGTATTTACTCTTTA
195 AACTCCCAGAACTTATGCTTATCGACTGGTTAATTCATTGTCCTGAC-ATAGTATTTACTCTTTA
* * * *
286399 ATACC-AAAATTCTTATCCATATATCATCTT-AGAATCATCGTTGAATAGATCTTCCAATGTTCT
259 ATACCAAAAATTCTTATCCATAGATCATCTTCAGAATCATCATTGAATAAATCTTCCAATATTCT
*
286462 TTATTTAATTTCCACGCCTCCATGATATCATGAAATGATGACGTGCTTGATTTGTAGTTCATGAC
324 TTATTTAATTTCCACGCCTCCATGATATCATGAAATGATGACGTGCTTGATTTATAGTTCATGAC
286527 CCATAAGAACATTACATCATGTATGTTCATTAATGTTTCCAGACTTATCCAAATCACT
389 CCATAAGAACATTACATCATGTATGTTCATTAATGTTTCCAGACTTATCCAAATCACT
286585 TATT
1 TATT
286589 TAATCCTAAG
Statistics
Matches: 414, Mismatches: 30, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
442 137 0.33
443 41 0.10
444 58 0.14
445 14 0.03
446 134 0.32
447 30 0.07
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (446 bp):
TATTATTCAGAGACACTGGATAATCTTATCAAGCAGAGAAACAAGGATCTTCCGTGTACCGATAG
AATTCCGAAAGTTAGAATCACTATTGGAAAAGTTCATTAACTGAAAAAATCATCAATTATGCAGA
ATACGATTTCAACTGATAAGAAGAAACGAGAATTCAATCTATGTCGATTAATCGATTATCGAACA
ACTCCCAGAACTTATGCTTATCGACTGGTTAATTCATTGTCCTGACATAGTATTTACTCTTTAAT
ACCAAAAATTCTTATCCATAGATCATCTTCAGAATCATCATTGAATAAATCTTCCAATATTCTTT
ATTTAATTTCCACGCCTCCATGATATCATGAAATGATGACGTGCTTGATTTATAGTTCATGACCC
ATAAGAACATTACATCATGTATGTTCATTAATGTTTCCAGACTTATCCAAATCACT
Found at i:288447 original size:14 final size:14
Alignment explanation
Indices: 288424--288460 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
288414 GATCAACAGT
288424 AAACGGCTCGACTC
1 AAACGGCTCGACTC
* *
288438 AAATGGCTCGCCTC
1 AAACGGCTCGACTC
288452 AAACGGCTC
1 AAACGGCTC
288461 CCTAGGCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.16
Consensus pattern (14 bp):
AAACGGCTCGACTC
Found at i:290014 original size:26 final size:26
Alignment explanation
Indices: 289978--290031 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
289968 ACTGAAGTAC
* *
289978 TAATACACATAAGGTCGTGCCCGCCA
1 TAATACACATAAGGTCATGCCCACCA
290004 TAATACACATAAGGTCATGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
290030 TA
1 TA
290032 TGCACTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACCA
Found at i:292534 original size:691 final size:698
Alignment explanation
Indices: 291528--292906 Score: 2393
Period size: 691 Copynumber: 2.0 Consensus size: 698
291518 CTGAAATTAA
* *
291528 TCCATGAATTTAGTAGTTTACAACTTTACCCTTGTAAAGTTCTAAAATTACAATTTTGTCCTTTT
1 TCCATGAAGTTAGTAGTTTACAACTTTACCCTTGTAAAGTTCTAAAATTACAATTTTATCCTTTT
* *
291593 AATTCAATGACTAAGATTTAACATGGAAATCAAATTAAATCCAATAGTCCACATTAAATCTCATC
66 AATCCAATGACTAAGATTTAACATGGAAATCAAATTAAACCCAATAGTCCACATTAAATCTCATC
* *
291658 ATTTTAAAGCATGGAAAATAAATTTTTCCCTTGCTTTATCATCTAGTAAAATTTTCTGAATTTTT
131 ATTTTAAAGCATGGAAAATAAATTTTGCCCTTGCTTTATCATCTAGTAAAATTTCCTGAATTTTT
291723 TATTCGATCCGATTGTCCGAAATTTTCTCGAACTTTCACACTTTATAGCTTTTAACACAAACTCC
196 TATTCGATCCGATTGTCCGAAATTTTCTCGAACTTTCACACTTTATAGCTTTTAACACAAACTCC
* *
291788 GTACGAAAACATGAAACCCACAAAATATCATTCTTGGGGTAAACTATTCGTTTACATGATCAGGT
261 GTACGAAAACATGAAACCCACAAAACATCATTCTTGGGGTAAACTATTCGTTTACATGATCAGAT
* * *
291853 TACATAACTTTTAAAATTATACTTTGGTCCCTAAACTTTTCAAAGTTTTTACTTTAGCCACCAAA
326 TACA-AACTTTTAAAATTATACTTTAGTCCCTAAACTTTTCAAAGTTTATACTTTAACCACCAAA
* * * *
291918 CTTTCAATTTATTTATTTTGGTCACTAACCAAAATTTGGGGTATTACATTTCAAGCCAACTCAAA
390 CTTTCAATTTATTCATATTGGCCACTAACCAAAATTTGAGGTATTACATTTCAAGCCAACTCAAA
**
291983 TCTTCGTTGCAGTTGTTATG-GTTTTATATTCCTTGGTGAAGCGGTATTTTTTGTCTTCAAC-T-
455 TCTTCGTTGCAGTTGTTATGTGTTTTATATTCCTTGGTGAAGCAATATTTTTTGTCTTCAACTTA
*
292045 TCATGGTAGTATCGACTATGTTGAACATATTAATTTCTTGGAATAATGT-AAAAAAATACCTTTA
520 TCATGGTAGTATCCACTATGTTGAACATATTAATTTCTTGGAATAATGTAAAAAAAATACCTTTA
292109 ACGTTTGACTAAATAATCATTTTAGTTC--ATTCTTTTTTTCTTAGCATTCTGGTCCTAACATTT
585 ACGTTTGACTAAATAATCATTTTAGTTCATATTC-TTTTTT-TTAGCATTCTGGTCCTAACATTT
292172 TATTTTGGAATGTGCGGATGAAACCATTAGTTAACAAATGACTAAGATTTG
648 TATTTTGGAATGTGCGGATGAAACCATTAGTTAACAAATGACTAAGATTTG
292223 TCCATGAAGTTAGTAGTTTACAACTTTA-CCTTGTAAAGTTCTAAAATTACAA-TTTATCCTTTT
1 TCCATGAAGTTAGTAGTTTACAACTTTACCCTTGTAAAGTTCTAAAATTACAATTTTATCCTTTT
* *
292286 AATCCAATGACTAAGATTTAACATGGAAATCAAATTAAACCCAATTGTCCACATTAAATCTTATC
66 AATCCAATGACTAAGATTTAACATGGAAATCAAATTAAACCCAATAGTCCACATTAAATCTCATC
292351 ATTTTAAAGCATGGAAAATAAA-TTTGCCCTTGCTTTATCATCTAGTAAAATTTCCTGAATTTTT
131 ATTTTAAAGCATGGAAAATAAATTTTGCCCTTGCTTTATCATCTAGTAAAATTTCCTGAATTTTT
292415 TATTCGATCCGATTGTCC-AAATTTTCTCGAACTTTCACACTTTATAGCTTTTAACACAAACTCC
196 TATTCGATCCGATTGTCCGAAATTTTCTCGAACTTTCACACTTTATAGCTTTTAACACAAACTCC
* *
292479 GTACGAAAAACATG-AACCCACGAAACATCATTCTTGGGGTAAACTATTTGTTTACATGATCAGA
261 GTACG-AAAACATGAAACCCACAAAACATCATTCTTGGGGTAAACTATTCGTTTACATGATCAGA
*
292543 TTATAAACTTTTAAAATTATACTTTAGTCCCTAAACTTTTCAAAGTTTATACTTTAACCACCAAA
325 TTACAAACTTTTAAAATTATACTTTAGTCCCTAAACTTTTCAAAGTTTATACTTTAACCACCAAA
*
292608 CTTTCAATTTATTCATATTGGCCACTAACCAAAATTTGAGGTATTACATTTTAAGCCAACTCAAA
390 CTTTCAATTTATTCATATTGGCCACTAACCAAAATTTGAGGTATTACATTTCAAGCCAACTCAAA
292673 TCTTCGTTGCAGTTGTTATGTGTTTTATATTCCTTGGTGAAGCAATATTTTTTGTCTTCAACTTA
455 TCTTCGTTGCAGTTGTTATGTGTTTTATATTCCTTGGTGAAGCAATATTTTTTGTCTTCAACTTA
*
292738 TCATGGTAGTATCCACTATGTTGAACATATTAATTTCTTGGAATGATGTAAAAAAAAATACCTTT
520 TCATGGTAGTATCCACTATGTTGAACATATTAATTTCTTGGAATAATGT-AAAAAAAATACCTTT
* *
292803 AACGTTTGACTAAATGATTATTTTAGTTCATATTCTTTTTTTTAGCATTCTGGTCCTAACATTTT
584 AACGTTTGACTAAATAATCATTTTAGTTCATATTCTTTTTTTTAGCATTCTGGTCCTAACATTTT
292868 ATTTTGGAATGTGCGGATGAAACCATTAGTTAACAAATG
649 ATTTTGGAATGTGCGGATGAAACCATTAGTTAACAAATG
292907 GTTAATGCTC
Statistics
Matches: 649, Mismatches: 27, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
690 137 0.21
691 140 0.22
692 67 0.10
693 140 0.22
694 24 0.04
695 131 0.20
696 6 0.01
697 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (698 bp):
TCCATGAAGTTAGTAGTTTACAACTTTACCCTTGTAAAGTTCTAAAATTACAATTTTATCCTTTT
AATCCAATGACTAAGATTTAACATGGAAATCAAATTAAACCCAATAGTCCACATTAAATCTCATC
ATTTTAAAGCATGGAAAATAAATTTTGCCCTTGCTTTATCATCTAGTAAAATTTCCTGAATTTTT
TATTCGATCCGATTGTCCGAAATTTTCTCGAACTTTCACACTTTATAGCTTTTAACACAAACTCC
GTACGAAAACATGAAACCCACAAAACATCATTCTTGGGGTAAACTATTCGTTTACATGATCAGAT
TACAAACTTTTAAAATTATACTTTAGTCCCTAAACTTTTCAAAGTTTATACTTTAACCACCAAAC
TTTCAATTTATTCATATTGGCCACTAACCAAAATTTGAGGTATTACATTTCAAGCCAACTCAAAT
CTTCGTTGCAGTTGTTATGTGTTTTATATTCCTTGGTGAAGCAATATTTTTTGTCTTCAACTTAT
CATGGTAGTATCCACTATGTTGAACATATTAATTTCTTGGAATAATGTAAAAAAAATACCTTTAA
CGTTTGACTAAATAATCATTTTAGTTCATATTCTTTTTTTTAGCATTCTGGTCCTAACATTTTAT
TTTGGAATGTGCGGATGAAACCATTAGTTAACAAATGACTAAGATTTG
Found at i:298402 original size:2 final size:2
Alignment explanation
Indices: 298397--298462 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
298387 TGTGTGATTA
298397 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
298439 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
298463 TCTAAACTCG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:304419 original size:17 final size:17
Alignment explanation
Indices: 304394--304437 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
304384 AATAGATAAA
*
304394 ATATATTATCTATTAAT
1 ATATTTTATCTATTAAT
*
304411 ATATTTTATCTATTATT
1 ATATTTTATCTATTAAT
304428 ATTATTTTAT
1 A-TATTTTAT
304438 TGTTAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTTTATCTATTAAT
Found at i:304446 original size:18 final size:18
Alignment explanation
Indices: 304393--304451 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
304383 TAATAGATAA
* *
304393 AATATATTATCTATTAAT
1 AATATTTTATCTATTATT
304411 -ATATTTTATCTATTATT
1 AATATTTTATCTATTATT
* *
304428 ATTATTTTAT-TGTTAATT
1 AATATTTTATCTATT-ATT
304446 AATATT
1 AATATT
304452 CAAGTTGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 18 0.53
18 16 0.47
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (18 bp):
AATATTTTATCTATTATT
Found at i:305054 original size:29 final size:28
Alignment explanation
Indices: 304963--305060 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 28
304953 AAGAATTTGG
*
304963 GGATGAAATTAGAATGTTCAAAAGTTTAA
1 GGATG-AATTAGAATATTCAAAAGTTTAA
* *
304992 GGACT-AATTTAGAATGATATTC-ATAGTTTGA
1 GGA-TGAA-TTAG-A--ATATTCAAAAGTTTAA
305023 GGATGAGATTAGAATATTCAAAAGTTTAA
1 GGATGA-ATTAGAATATTCAAAAGTTTAA
*
305052 GGATCAATT
1 GGATGAATT
305061 TAAAATAAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
28 11 0.20
29 19 0.35
30 4 0.07
31 15 0.27
32 6 0.11
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (28 bp):
GGATGAATTAGAATATTCAAAAGTTTAA
Found at i:309628 original size:32 final size:32
Alignment explanation
Indices: 309539--309660 Score: 127
Period size: 32 Copynumber: 3.8 Consensus size: 32
309529 AAAGGAGTAT
* * *
309539 CTTGGGGCCTGAGAGCCTACCCAAGAGAGTAC
1 CTTGGGGCCTTAGAGCCTACCCAAGGGAATAC
* * * *
309571 CTTAGGGCCTAAGAGCCTATCCAAGGGAATAT
1 CTTGGGGCCTTAGAGCCTACCCAAGGGAATAC
* * * *
309603 CTTGGGACTTTAGAGCCTACCCAAGGAAATGC
1 CTTGGGGCCTTAGAGCCTACCCAAGGGAATAC
**
309635 CTTGGGGCGATAGAGCCTACCCAAGG
1 CTTGGGGCCTTAGAGCCTACCCAAGG
309661 TCACCTTAGG
Statistics
Matches: 73, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.19
Consensus pattern (32 bp):
CTTGGGGCCTTAGAGCCTACCCAAGGGAATAC
Found at i:311250 original size:21 final size:20
Alignment explanation
Indices: 311221--311275 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
311211 AAATTTGTCT
311221 CGAAGGACCTCATGTATATTC
1 CGAAGGACCT-ATGTATATTC
*
311242 CGAATGACCTATGTATATGTCC
1 CGAAGGACCTATGTATAT-T-C
*
311264 CAAAGGACCTAT
1 CGAAGGACCTAT
311276 ATAACCCTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.28
21 10 0.34
22 11 0.38
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (20 bp):
CGAAGGACCTATGTATATTC
Found at i:311257 original size:20 final size:21
Alignment explanation
Indices: 311221--311273 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
311211 AAATTTGTCT
311221 CGAAGGACCTCATGTATATTC
1 CGAAGGACCTCATGTATATTC
*
311242 CGAATGACCT-ATGTATATGTCC
1 CGAAGGACCTCATGTATAT-T-C
*
311264 CAAAGGACCT
1 CGAAGGACCT
311274 ATATAACCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.30
21 10 0.37
22 9 0.33
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (21 bp):
CGAAGGACCTCATGTATATTC
Found at i:319008 original size:151 final size:149
Alignment explanation
Indices: 318828--319144 Score: 528
Period size: 151 Copynumber: 2.1 Consensus size: 149
318818 GAGTCGCGGG
* * * *
318828 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTAGAACATGTATGAAGTCTTGAAAGACACAT
318893 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTA-T-
318958 TATATGGCACTACGGTGCAAT
129 TATATGGCACTACGGTGCAAT
* *
318979 TCTACGCGGTCCTTCGGGATATATATATATTCTGTAGAACATGTATGAAGTCTTTAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTAGAACATGTATGAAGTCTTGAAAGACACAT
* *
319044 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
319109 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
319128 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
319145 TGCAATTATA
Statistics
Matches: 157, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
148 1 0.01
149 36 0.23
150 1 0.01
151 119 0.76
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTAGAACATGTATGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:319145 original size:23 final size:23
Alignment explanation
Indices: 319112--319156 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
319102 ATTATTATAT
*
319112 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
319135 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
319157 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:324014 original size:149 final size:149
Alignment explanation
Indices: 323835--324149 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
323825 GAGTCGCGGG
* *
323835 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
323900 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
323965 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
323984 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
324049 ACTTGATCCCTATTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
324114 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
324133 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
324150 TGCAATTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTCATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:324150 original size:23 final size:23
Alignment explanation
Indices: 324117--324161 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
324107 ATTATTATAT
*
324117 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
324140 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
324162 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:326458 original size:20 final size:20
Alignment explanation
Indices: 326435--326494 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
326425 GTTAATTGAC
326435 TAGGGGTATCGGTACCTC-TA
1 TAGGGGTATCGGTACC-CATA
326455 TAGGGGTATCGGTACCCATA
1 TAGGGGTATCGGTACCCATA
*
326475 TGGGGGTATCGGTACCCATA
1 TAGGGGTATCGGTACCCATA
326495 GAGCATTCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.27
Consensus pattern (20 bp):
TAGGGGTATCGGTACCCATA
Found at i:326975 original size:21 final size:20
Alignment explanation
Indices: 326929--326975 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
326919 CTTGTCTTAA
326929 TCCCCTTACTATAACACTTC
1 TCCCCTTACTATAACACTTC
326949 -CCCCTTACTATAACACTTC
1 TCCCCTTACTATAACACTTC
326968 TTCCCCTT
1 -TCCCCTT
326976 TTTGTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 19 0.76
21 6 0.24
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (20 bp):
TCCCCTTACTATAACACTTC
Found at i:332580 original size:22 final size:21
Alignment explanation
Indices: 332538--332577 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
332528 AAGATTATTT
332538 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
332559 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
332578 ATAAAGTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:335081 original size:34 final size:34
Alignment explanation
Indices: 335038--335105 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
335028 TATTTCAAAA
335038 TGGTATTGATACTTA-CCTTATGGTATC-ATACCCT
1 TGGTATTGATAC-TACCCTTA-GGTATCGATACCCT
335072 TGGTATTGATACTACCCCTTAGGTATCGATACCC
1 TGGTATTGATACTA-CCCTTAGGTATCGATACCC
335106 CTTGAATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 2 0.06
34 18 0.58
35 11 0.35
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (34 bp):
TGGTATTGATACTACCCTTAGGTATCGATACCCT
Found at i:336962 original size:4 final size:4
Alignment explanation
Indices: 336953--337050 Score: 77
Period size: 4 Copynumber: 26.5 Consensus size: 4
336943 TCGGGCCGGG
* * *
336953 TATA TATA TATA TAAA T-TA AATA TATA AATA T-TA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
336999 TATA T-TA -ATT TAAA T-TA AATT TAT- TA-A TAT- TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
337041 TATA TATA TA
1 TATA TATA TA
337051 ATAATTATTT
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
3 15 0.21
4 58 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:336964 original size:6 final size:6
Alignment explanation
Indices: 336953--337050 Score: 77
Period size: 6 Copynumber: 17.7 Consensus size: 6
336943 TCGGGCCGGG
* * *
336953 TATATA TATATA TAAAT- TAAATA TATAAA TAT-TA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
336999 TATAT- TA-ATT TAAAT- TAAATT TAT-TA -ATAT- TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
337041 TATATA TATA
1 TATATA TATA
337051 ATAATTATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.05
5 24 0.31
6 50 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:337001 original size:44 final size:44
Alignment explanation
Indices: 336953--337054 Score: 154
Period size: 44 Copynumber: 2.3 Consensus size: 44
336943 TCGGGCCGGG
336953 TATATATATATATAAATTAAATATATAAATATTATATATATATA
1 TATATATATATATAAATTAAATATATAAATATTATATATATATA
* * *
336997 TATATAT-TAATTTAAATTAAATTTATTAATATTATATATATATA
1 TATATATAT-ATATAAATTAAATATATAAATATTATATATATATA
337041 TATATATATA-ATAA
1 TATATATATATATAA
337055 TTATTTTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
43 4 0.08
44 47 0.90
45 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (44 bp):
TATATATATATATAAATTAAATATATAAATATTATATATATATA
Found at i:337164 original size:35 final size:35
Alignment explanation
Indices: 337116--337190 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
337106 GATTACCAAA
*
337116 CCCGTCCCCGTTTA-ACATAAATAGTTTTCCCCATC
1 CCCGTCCCCGTTTAGA-ATAAACAGTTTTCCCCATC
* *
337151 CCCGTCCCTGTTTAGAATAAACAGTTTTCCCCGTC
1 CCCGTCCCCGTTTAGAATAAACAGTTTTCCCCATC
337186 CCCGT
1 CCCGT
337191 TTAATTCGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.20, C:0.37, G:0.12, T:0.31
Consensus pattern (35 bp):
CCCGTCCCCGTTTAGAATAAACAGTTTTCCCCATC
Found at i:339045 original size:16 final size:16
Alignment explanation
Indices: 339024--339068 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
339014 ACAGATCCTC
339024 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
339040 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
339056 TGAATCATTCAGC
1 TGAATCATTCAGC
339069 GCTTAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:339989 original size:2 final size:2
Alignment explanation
Indices: 339982--340006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
339972 TCTATAAAAT
339982 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
340007 TTGTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:341151 original size:14 final size:15
Alignment explanation
Indices: 341124--341158 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
341114 GTATTAATTA
341124 TTTTTCTTTATTTTC
1 TTTTTCTTTATTTTC
341139 TTTTTCTTT-TTTTC
1 TTTTTCTTTATTTTC
341153 TGTTTT
1 T-TTTT
341159 TAAGTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTATTTTC
Found at i:343569 original size:27 final size:27
Alignment explanation
Indices: 343539--343595 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
343529 CTCATCGATG
*
343539 AAATAAATTTGTTATTTAAAGATATTT
1 AAATAAATTTGTTAATTAAAGATATTT
343566 AAATAAATTTGTTAATTAAAGATATTT
1 AAATAAATTTGTTAATTAAAGATATTT
343593 AAA
1 AAA
343596 AAAAATTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (27 bp):
AAATAAATTTGTTAATTAAAGATATTT
Found at i:345473 original size:14 final size:14
Alignment explanation
Indices: 345452--345490 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
345442 ATAATATATA
345452 TATATATATTCGTGTG
1 TATATATA-T-GTGTG
*
345468 TATATATATTTGTG
1 TATATATATGTGTG
345482 TATATATAT
1 TATATATAT
345491 ATTTGAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 1 0.05
16 8 0.36
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (14 bp):
TATATATATGTGTG
Found at i:345494 original size:16 final size:16
Alignment explanation
Indices: 345450--345495 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
345440 AAATAATATA
*
345450 TATATATATATTCGTG
1 TATATATATATTTGTG
*
345466 TGTATATATATTTGTG
1 TATATATATATTTGTG
345482 TATATATATATTTG
1 TATATATATATTTG
345496 AAAACTCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.54
Consensus pattern (16 bp):
TATATATATATTTGTG
Found at i:349550 original size:5 final size:5
Alignment explanation
Indices: 349542--349595 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
349532 TAAAAGGGAA
*
349542 AAAAT AAAAT AACATAA AAAAT AAAAT -AAAT AAAAGT --AAT AAAAT
1 AAAAT AAAAT AA-A-AT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT
349587 AAAAT AAAA
1 AAAAT AAAA
349596 ACATAATGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
3 1 0.02
4 6 0.15
5 28 0.68
6 3 0.07
7 3 0.07
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:349574 original size:9 final size:9
Alignment explanation
Indices: 349543--349595 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
349533 AAAAGGGAAA
349543 AAATAAAAT
1 AAATAAAAT
349552 AACAT-AAA-
1 AA-ATAAAAT
349560 AAATAAAAT
1 AAATAAAAT
349569 AAATAAAAGT
1 AAATAAAA-T
349579 -AATAAAAT
1 AAATAAAAT
349587 AAAATAAAA
1 -AAATAAAA
349596 ACATAATGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
7 2 0.05
8 6 0.16
9 20 0.53
10 10 0.26
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:349601 original size:18 final size:17
Alignment explanation
Indices: 349540--349601 Score: 81
Period size: 17 Copynumber: 3.5 Consensus size: 17
349530 AATAAAAGGG
*
349540 AAAAAATAAAATAACAT
1 AAAAAATAAAATAAAAT
349557 AAAAAATAAAAT-AAAT
1 AAAAAATAAAATAAAAT
349573 AAAAGTAATAAAATAAAAT
1 AAAA--AATAAAATAAAAT
349592 AAAAACATAA
1 AAAAA-ATAA
349602 TGATTGAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 7 0.17
17 13 0.32
18 12 0.30
19 8 0.20
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAAAATAAAATAAAAT
Found at i:352133 original size:22 final size:22
Alignment explanation
Indices: 352092--352172 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
352082 CTCGTATAAA
352092 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
352115 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
352137 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
352159 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
352173 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:352168 original size:13 final size:13
Alignment explanation
Indices: 352106--352168 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
352096 CCGAAGTGCC
352106 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
352119 CC---GAAGTGC-
1 CCGTAGAATTGCA
352128 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
352141 CC---GAAGTGC-
1 CCGTAGAATTGCA
352150 CCGTAGAATTGCA
1 CCGTAGAATTGCA
352163 CCGTAG
1 CCGTAG
352169 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:352504 original size:27 final size:28
Alignment explanation
Indices: 352474--352543 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
352464 TTTTCTGCAT
*
352474 ATTCATGTCATGTAATACATATAAT-GA
1 ATTCATGTCATGTAATACATATAATAAA
*
352501 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATA-AA
352530 ATTCATGTCATGTA
1 ATTCATGTCATGTA
352544 TCATAATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 24 0.62
29 15 0.38
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATAAA
Found at i:352884 original size:19 final size:20
Alignment explanation
Indices: 352847--352884 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
352837 TTTTTTCTCA
*
352847 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
352867 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
352885 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:352940 original size:21 final size:21
Alignment explanation
Indices: 352910--352952 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
352900 ATCATATTCG
* *
352910 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
352931 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
352952 T
1 T
352953 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:359001 original size:22 final size:22
Alignment explanation
Indices: 358984--359063 Score: 151
Period size: 22 Copynumber: 3.6 Consensus size: 22
358974 CTCGTATAAA
358984 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
359006 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
359028 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
359050 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
359064 ATTTAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:359059 original size:13 final size:13
Alignment explanation
Indices: 358997--359059 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
358987 ACCGAAGTGC
358997 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
359010 CC---GAAGTGC-
1 CCGTAGAATTGCA
359019 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
359032 CC---GAAGTGC-
1 CCGTAGAATTGCA
359041 CCGTAGAATTGCA
1 CCGTAGAATTGCA
359054 CCGTAG
1 CCGTAG
359060 TGCCATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:359398 original size:29 final size:29
Alignment explanation
Indices: 359365--359436 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
359355 TTTTCTGCAT
**
359365 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
359394 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
359423 ATTCATGTCATGTA
1 ATTCATGTCATGTA
359437 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:359777 original size:19 final size:20
Alignment explanation
Indices: 359740--359777 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
359730 TTTTTTCTCA
*
359740 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
359760 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
359778 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:359833 original size:21 final size:21
Alignment explanation
Indices: 359803--359845 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
359793 ATCATATTCG
* *
359803 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
359824 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
359845 T
1 T
359846 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:361220 original size:106 final size:106
Alignment explanation
Indices: 361035--362463 Score: 2276
Period size: 106 Copynumber: 13.5 Consensus size: 106
361025 CATTGTTCCA
* * ** * * *
361035 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGAGAATTTGTGTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * * * * *
361099 CCAGCTGTCCCTTCGTTGTGAATTTAAACTTGTGTTGTCTCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
361141 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
361206 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
361247 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
* * *
361312 CAGCAGTCCCTTCGTCGTAAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * ** * *
361353 AGTTCAATATCTTTCATTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
*
361418 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
361459 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
* * *
361524 CAGCGGTCCCTTCGTCGTGAAGTTGAACATACATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
361565 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
361630 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
361671 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
* *
361736 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
361777 AGTCCACTATCCTTCGCTGTGAAGTTGAAATTGACTCT-AGAATTG-GAAAATTGTTTATTGACA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGAG-AAGTTGTTTATTGACA
361840 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
361883 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
* **
361948 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
361989 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
*
362053 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
362094 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT-AGAATTG-GAAAATTGTTTATTGACA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGAG-AAGTTGTTTATTGACA
362157 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
362200 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
*
362265 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
362306 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
362371 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
362412 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
362464 AATTGAGGTG
Statistics
Matches: 1224, Mismatches: 89, Indels: 20
0.92 0.07 0.02
Matches are distributed among these distances:
104 2 0.00
105 96 0.08
106 1121 0.92
107 5 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:366107 original size:5 final size:5
Alignment explanation
Indices: 366097--366151 Score: 57
Period size: 5 Copynumber: 11.8 Consensus size: 5
366087 TCAAAGGGAA
*
366097 AAAAT AAAAT AACAT -AAA- AAAAT AAAAT -AAAT AAAAGT --AAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT
366143 AAAAT AAAA
1 AAAAT AAAA
366152 ACATAATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
3 1 0.02
4 11 0.26
5 29 0.69
6 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:366118 original size:13 final size:14
Alignment explanation
Indices: 366098--366151 Score: 67
Period size: 13 Copynumber: 3.9 Consensus size: 14
366088 CAAAGGGAAA
*
366098 AAATAAAATAACAT
1 AAATAAAATAAAAT
366112 AAA-AAAATAAAAT
1 AAATAAAATAAAAT
*
366125 AAATAAAAGTAATA-
1 AAATAAAA-TAAAAT
366139 AAATAAAATAAAA
1 AAATAAAATAAAA
366152 ACATAATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 16 0.46
14 15 0.43
15 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:366118 original size:18 final size:17
Alignment explanation
Indices: 366095--366157 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 17
366085 AATCAAAGGG
366095 AAAAAATAAAATAACATA
1 AAAAAATAAAATAA-ATA
366113 AAAAAATAAAATAAATA
1 AAAAAATAAAATAAATA
*
366130 AAAGTAATAAAATAAAATA
1 AAA-AAATAAAAT-AAATA
*
366149 AAAACATAA
1 AAAAAATAA
366158 TGATTGAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.15
18 26 0.65
19 8 0.20
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAAATAAAATAAATA
Found at i:366127 original size:23 final size:24
Alignment explanation
Indices: 366097--366151 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
366087 TCAAAGGGAA
*
366097 AAAATAAAATAACA-TAAAAAAAT
1 AAAATAAAATAAAAGTAAAAAAAT
*
366120 AAAAT-AAATAAAAGTAATAAAAT
1 AAAATAAAATAAAAGTAAAAAAAT
366143 AAAATAAAA
1 AAAATAAAA
366152 ACATAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 7 0.25
23 18 0.64
24 3 0.11
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (24 bp):
AAAATAAAATAAAAGTAAAAAAAT
Found at i:380273 original size:57 final size:58
Alignment explanation
Indices: 380207--380320 Score: 158
Period size: 57 Copynumber: 2.0 Consensus size: 58
380197 ACTATATCTT
* * *
380207 TTATATTAAATTGGTCCTTAAACATTTAAATATTCCAA-TTCATCTCTATACTATGAC
1 TTATATTAAATTAGTCCTTAAACATTTAAATATTCCAATTTCATCCCTAAACTATGAC
* * * *
380264 TTATTTTAAATTAGTCCTTCAACTTTTAAATATTCTAATTTCATCCCTAAACTATGA
1 TTATATTAAATTAGTCCTTAAACATTTAAATATTCCAATTTCATCCCTAAACTATGA
380321 TCCACTTCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 33 0.67
58 16 0.33
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.44
Consensus pattern (58 bp):
TTATATTAAATTAGTCCTTAAACATTTAAATATTCCAATTTCATCCCTAAACTATGAC
Found at i:383201 original size:60 final size:60
Alignment explanation
Indices: 383106--383244 Score: 188
Period size: 60 Copynumber: 2.3 Consensus size: 60
383096 AAATCATATG
* * * *
383106 TCCCCAAACTATAACCCTCACTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCA
1 TCCCCAAACTATGACCCTCACTTTAAATAAATCCTTAAACTTTTGAACATTCCAATTTCA
* * * *
383166 TCCCCAAACCATGACTCTCATTTTAAATAAATCCTTAAACTTTTGAACATTCTAATTTCA
1 TCCCCAAACTATGACCCTCACTTTAAATAAATCCTTAAACTTTTGAACATTCCAATTTCA
* *
383226 TCCCTAAACTATGATCCTC
1 TCCCCAAACTATGACCCTC
383245 TTTCTAAATT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (60 bp):
TCCCCAAACTATGACCCTCACTTTAAATAAATCCTTAAACTTTTGAACATTCCAATTTCA
Found at i:383522 original size:60 final size:59
Alignment explanation
Indices: 383415--383527 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
383405 GTATATATGT
* **
383415 ATAGTTTGGGATAAATTGGAATGTTCAAAAAAGTTTGGGGACCAATTTAGAATGAAGGTC
1 ATAGTTTGGGATAAATTGAAATGTTC-AAAAAGTTTGAAGACCAATTTAGAATGAAGGTC
* * *
383475 ATAGTTTGGGGATGAAATTGAAATTTTC-AAAAGTTTGAAGACTAATTTGGAAT
1 ATAGTTT-GGGAT-AAATTGAAATGTTCAAAAAGTTTGAAGACCAATTTAGAAT
383528 AATAGTCATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 28 0.62
61 5 0.11
62 12 0.27
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (59 bp):
ATAGTTTGGGATAAATTGAAATGTTCAAAAAGTTTGAAGACCAATTTAGAATGAAGGTC
Found at i:383536 original size:60 final size:57
Alignment explanation
Indices: 383415--383589 Score: 131
Period size: 60 Copynumber: 2.9 Consensus size: 57
383405 GTATATATGT
* * ** * * *
383415 ATAGTTTGGGATAAATTGGAATGTTCAAAAAAGTTTGGGGACCAATTTAGAATGAAGGTC
1 ATAGTTTGGGATAAATTGAAATTTTC--AAAAGTTTGAAGACTAATTTGGAAT-AAAGTC
383475 ATAGTTTGGGGATGAAATTGAAATTTTCAAAAGTTTGAAGACTAATTTGGAATAATAGTC
1 ATAGTTT-GGGAT-AAATTGAAATTTTCAAAAGTTTGAAGACTAATTTGGAATAA-AGTC
* * * *
383535 ATA-TTATAAGGATTAAATTGAAACATTT-GAAAGTTT-AAGAACTAATTTGAAATAA
1 ATAGTT-T-GGGA-TAAATTGAAA-TTTTCAAAAGTTTGAAG-ACTAATTTGGAATAA
383590 GACATATAGT
Statistics
Matches: 96, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
59 7 0.07
60 68 0.71
61 9 0.09
62 12 0.12
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (57 bp):
ATAGTTTGGGATAAATTGAAATTTTCAAAAGTTTGAAGACTAATTTGGAATAAAGTC
Found at i:384219 original size:23 final size:23
Alignment explanation
Indices: 384176--384220 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
384166 ATATATTAGG
**
384176 TAGCGCTTATATAATGCAATAGA
1 TAGCGCTTATATAATAAAATAGA
*
384199 TAGCGTTTATATAATAAAATAG
1 TAGCGCTTATATAATAAAATAG
384221 GCATTTAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
TAGCGCTTATATAATAAAATAGA
Found at i:384917 original size:199 final size:200
Alignment explanation
Indices: 384402--384941 Score: 778
Period size: 200 Copynumber: 2.7 Consensus size: 200
384392 CATTTTATGC
* * * * *
384402 GTGTCGATACATTATGTAGACGTATTTTCTCATAAAATCGGTATATTTCTACTGGGTATATTGTA
1 GTGTCGATACATTATGTAGACATATTTTCTCATAAAATCGGTATATTTCTACCGGTTACATTGGA
* * *
384467 AATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGAGATCGATA-TTGTTAATAAATG
66 AATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTT-TTAATAAATG
* * * * *
384531 TATCGACACTTTATGTGTGCACAGCGTTTGGCATTTATTCTGGACAAAATGTATCGACACAAATT
130 TATCGACACTTTATGCGTGCACACCGTTTGACATTCATTCTGGACAAAAAGTATCGACACAAATT
384596 TAAAAA
195 TAAAAA
* * * * * *
384602 GTGTTGATATATTATGTTGACTTATTCTCTCATAAAATAGGTATATTTCTACCGGTTACATTGGA
1 GTGTCGATACATTATGTAGACATATTTTCTCATAAAATCGGTATATTTCTACCGGTTACATTGGA
*
384667 AATTTACCTATTACATTATAATTATCTGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGT
66 AATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGT
* * *
384732 ATCGACACTTTATGCGTGCACCCCGTTTGACATTCATTCTGGATAAAAAGTATCGACATAAATTT
131 ATCGACACTTTATGCGTGCACACCGTTTGACATTCATTCTGGACAAAAAGTATCGACACAAATTT
384797 AAAAA
196 AAAAA
* * * * *
384802 GTGTCGATACATTATGTAGTCATGTTTTCTAAT-TAACCGGTATATTTCTACCGGTTACATTGGA
1 GTGTCGATACATTATGTAGACATATTTTCTCATAAAATCGGTATATTTCTACCGGTTACATTGGA
* * *
384866 AATTTACCTATTACATTATAATAATATGTTTCGATATTTTTGGGATCGATACTTTTAATAAATGT
66 AATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGT
384931 ATCGACACTTT
131 ATCGACACTTT
384942 TGTTTACATT
Statistics
Matches: 302, Mismatches: 37, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
199 100 0.33
200 200 0.66
201 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (200 bp):
GTGTCGATACATTATGTAGACATATTTTCTCATAAAATCGGTATATTTCTACCGGTTACATTGGA
AATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGT
ATCGACACTTTATGCGTGCACACCGTTTGACATTCATTCTGGACAAAAAGTATCGACACAAATTT
AAAAA
Found at i:387895 original size:6 final size:6
Alignment explanation
Indices: 387885--387930 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
387875 CTTGTTTGGA
* * *
387885 TCATCA TCATCA TCATCT TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
387931 TGACCGCTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (6 bp):
TCATCT
Found at i:389775 original size:200 final size:200
Alignment explanation
Indices: 389425--390382 Score: 1271
Period size: 200 Copynumber: 4.8 Consensus size: 200
389415 TTTAAAAAGG
** * ** * * *
389425 TATCGACACAAATTTAAAAAGTGTCGATACATTATGTTA-ACCGCTTTTCTAATTAAA-TCGATA
1 TATCGACACAAATTCCACAAGTGTCGATACATTATG-TAGACCTATTCTCTCATTAAACT-GGTA
* * * *
389488 TATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGG
64 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
*
389553 GATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCA-CCTTGTTGGGCATTGATTCTGG
129 GATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTT-TTGGGCATTCATTCTGG
*
389617 ATAAAAAA
193 ACAAAAAA
* ** * * * ** * * *
389625 TATCGATACAAATTTGAAAAGTGTCGATATATTATGTTGACCGCTTTTCTGATTAAACTAGTATA
1 TATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATTAAACTGGTATA
* * * * * *
389690 CTTATACCGGTTACATTGGAAATTTACCTATTACATTATAATTATTGATTTTGATGTTTTTGGGA
66 TTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGA
* * * *
389755 TCGATACTTTTTATAAATGTATCGACACGTTATGTGTGCACCCTTTTGGGTATTCATTATGGACA
131 TCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTCTGGACA
*
389820 AAAAG
196 AAAAA
* * *
389825 TATCGACACAAATTCCACAAGTGTCAATACATTATGTAGACATATTCTCTCA-TAAAATCGGTAT
1 TATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATTAAACT-GGTAT
389889 ATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
65 ATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
* *** * * *
389954 ATCAATACTTTTTATAAATGTATTTTCACTTTATGCTTGCACCCTTTTAGGTATTC-TATCTGGA
130 ATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCAT-TCTGGA
*
390018 CAAAAAG
194 CAAAAAA
* * * * *
390025 TATCGACACAAATTCCACAAGTGTCAATACATTATATAAACTTATTCTCTCA-TAAACCGGTATA
1 TATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATTAAACTGGTATA
* *
390089 TTTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTCTTGGGA
66 TTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGA
390154 TCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACTCCTTTTGGGCATTCATTCTGGAC
131 TCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCAC-CCTTTTGGGCATTCATTCTGGAC
390219 AAAAAA
195 AAAAAA
* * *
390225 TATTGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATTAAACTGGTATA
* *
390290 TTTATACCGGTTACATTGAAAAATTACATATTACATTATAATTATGGGGTTCGATGTTTTTGGGA
66 TTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGA
* *
390355 TCGATACATTTTATAATTGTATCGACAC
131 TCGATACTTTTTATAAATGTATCGACAC
390383 CTCTGTTAAC
Statistics
Matches: 674, Mismatches: 76, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
199 112 0.17
200 458 0.68
201 104 0.15
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (200 bp):
TATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATTAAACTGGTATA
TTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGA
TCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTCTGGACA
AAAAA
Found at i:390859 original size:19 final size:19
Alignment explanation
Indices: 390832--390878 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
390822 TACATTCACG
* *
390832 TACATAATTGTAAATCATA
1 TACAAAATTATAAATCATA
*
390851 TACAAAATTATAAATCGTA
1 TACAAAATTATAAATCATA
390870 TACAAAATT
1 TACAAAATT
390879 TCTCCTACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (19 bp):
TACAAAATTATAAATCATA
Found at i:392737 original size:17 final size:18
Alignment explanation
Indices: 392702--392737 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
392692 ATTGTTTAAG
392702 GTGCATCGATGCACATGAA
1 GTGCATCGATG-ACATGAA
392721 GTGCATCGATG-CATGAA
1 GTGCATCGATGACATGAA
392738 TTTAAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (18 bp):
GTGCATCGATGACATGAA
Found at i:392771 original size:64 final size:63
Alignment explanation
Indices: 392703--392862 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
392693 TTGTTTAAGG
* * *
392703 TGCATCGATGCACATGAAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TTT
1 TGCATCGATGCACAAGAAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTTT
392766 A
63 A
* * *
392767 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTA
1 TGCATCGATGCACAAGAAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTTA
* *
392831 TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TGCATCGATGCACAAGAAGTGCATCGATGCAT
392863 ACATTCATTG
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 74 0.88
65 7 0.08
66 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACAAGAAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTTA
Found at i:393373 original size:17 final size:19
Alignment explanation
Indices: 393351--393386 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
393341 GATTTACATG
393351 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
393368 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
393387 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:393635 original size:30 final size:30
Alignment explanation
Indices: 393574--393649 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
393564 TAAGGAAATA
* *
393574 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
393605 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
393635 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
393650 GGGTCTGTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 29 0.76
31 9 0.24
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:396974 original size:64 final size:63
Alignment explanation
Indices: 396897--397048 Score: 182
Period size: 64 Copynumber: 2.4 Consensus size: 63
396887 GGTGCATCGT
* * * * *
396897 TGCACATGAAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TTTATGCATCG
1 TGCACAAGGAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTTTATGCACCG
396960 A
63 A
* *
396961 TGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTTATGCACCGA
1 TGCACAAGGAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTTATGCACCGA
*
397025 TGCACAAGTAGTGCATCGATGCAT
1 TGCACAAGGAGTGCATCGATGCAT
397049 ACATTCATTG
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
63 2 0.03
64 66 0.87
65 7 0.09
66 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCACAAGGAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTTATGCACCGA
Found at i:397793 original size:31 final size:31
Alignment explanation
Indices: 397699--397806 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
397689 AGTCGAGGGT
* *
397699 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
397730 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
397761 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
397792 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
397807 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:397813 original size:30 final size:30
Alignment explanation
Indices: 397721--397825 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
397711 TTTCGAGACA
* * * *
397721 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
397752 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
397783 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
397813 TCTGGATAGTTAC
1 TATGGACAGTTAC
397826 TGGGGTCTGT
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
30 27 0.44
31 30 0.49
32 4 0.07
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:402428 original size:182 final size:182
Alignment explanation
Indices: 401768--402432 Score: 931
Period size: 182 Copynumber: 3.7 Consensus size: 182
401758 TTTATTACAC
*
401768 ATACTTAT--TAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTC
1 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
* * * * **
401831 GAGACTGATTTTGTCATATTTTTACCTATTATATTGTTAAGTGTCAATACATTTTTATAAAGTAT
66 GAGACCGGTTTTATCATATTTTTACCTATTATATTGTTATGAATCAATACATTTTTATAAAGTAT
* * * *
401896 TGATACTTTATAGGTGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCG
131 CGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
** *
401948 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACTTGTTTTGTCATTTT
1 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
* * *
402013 GATACCGGTTTTATTATATTTTTACCTATTATATTGTTATGGATCAATACATTTTTATAAAGTAT
66 GAGACCGGTTTTATCATATTTTTACCTATTATATTGTTATGAATCAATACATTTTTATAAAGTAT
* * * * * * *
402078 CGACACTTTATATGCGCTATTATTGTTTGTCTTTTAAATTTCAAAATTATCG
131 CGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
* * * *
402130 ATACTTATAATAAAGTATCAACACTTTCAACATATCCGGTAGCTCTTTACCGGTTTTTTCATTTT
1 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
* **
402195 GAGACCGGTTTTATCATATTTTTACCTGTTATATTGTTAT-AGATTGATACATTTTTATAAAGTA
66 GAGACCGGTTTTATCATATTTTTACCTATTATATTGTTATGA-ATCAATACATTTTTATAAAGTA
402259 TCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
130 TCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
** * *** *
402312 ATGTTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACTTATTTGGTCATTTC
1 ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
* * *
402377 GAGACCGGTTTTATCATATTTTTACCTGTTATATTGCTATGAATCGATACATTTTT
66 GAGACCGGTTTTATCATATTTTTACCTATTATATTGTTATGAATCAATACATTTTT
402433 TAATGAGAAA
Statistics
Matches: 428, Mismatches: 53, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
180 8 0.02
182 419 0.98
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (182 bp):
ATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC
GAGACCGGTTTTATCATATTTTTACCTATTATATTGTTATGAATCAATACATTTTTATAAAGTAT
CGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCG
Found at i:402624 original size:21 final size:21
Alignment explanation
Indices: 402598--402639 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
402588 CGCAACGCGA
402598 ATAGTCCAAGTTCGCGTTGCG
1 ATAGTCCAAGTTCGCGTTGCG
*
402619 ATAGTCGAAGTTCGCGTTGCG
1 ATAGTCCAAGTTCGCGTTGCG
402640 GTTTATTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (21 bp):
ATAGTCCAAGTTCGCGTTGCG
Found at i:403415 original size:6 final size:6
Alignment explanation
Indices: 403404--403472 Score: 120
Period size: 6 Copynumber: 11.5 Consensus size: 6
403394 TCTCGTCTCG
403404 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
* *
403452 GGTCGT GGTCTT GGTCTT GGT
1 GGTCGT GGTCGT GGTCGT GGT
403473 AATACGTGTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
GGTCGT
Found at i:403595 original size:21 final size:21
Alignment explanation
Indices: 403569--403734 Score: 146
Period size: 21 Copynumber: 7.8 Consensus size: 21
403559 ATTTTGGACT
*
403569 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
403590 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
403611 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
403632 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
403653 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
403674 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
403695 ATCGCAACGAACTTGTAATAA
1 ATCGCAACGAACTTGGAATAA
403716 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
403735 CAATCGTAAC
Statistics
Matches: 116, Mismatches: 15, Indels: 26
0.74 0.10 0.17
Matches are distributed among these distances:
19 29 0.25
21 49 0.42
23 38 0.33
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:403627 original size:42 final size:42
Alignment explanation
Indices: 403565--403761 Score: 326
Period size: 42 Copynumber: 4.7 Consensus size: 42
403555 TGCGATTTTG
*
403565 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
403607 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
403649 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
403691 GACTATCGCAACGAACTTGTAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
403733 GACAATCGTAACGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
403762 TTGCGATAGT
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
40 8 0.05
41 1 0.01
42 139 0.94
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:403739 original size:21 final size:19
Alignment explanation
Indices: 403569--403761 Score: 116
Period size: 21 Copynumber: 9.3 Consensus size: 19
403559 ATTTTGGACT
*
403569 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGG-A-AA
* **
403590 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGGAAA
403611 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGG-A-AA
* **
403632 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGGAAA
403653 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGG-A-AA
* **
403674 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGGAAA
*
403695 ATCGCAACGAACTTGTAATAA
1 ATCGCAACGAACTTG-GA-AA
*
403716 ATCGCAACGCGAACTTGGACA
1 ATCGCAA--CGAACTTGGAAA
* *
403737 ATCGTAACGAATTTGGAAA
1 ATCGCAACGAACTTGGAAA
403756 ATCGCA
1 ATCGCA
403762 TTGCGATAGT
Statistics
Matches: 132, Mismatches: 26, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
19 38 0.29
20 3 0.02
21 56 0.42
22 4 0.03
23 31 0.23
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAACTTGGAAA
Found at i:403786 original size:21 final size:21
Alignment explanation
Indices: 403757--403809 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
403747 ATTTGGAAAA
*
403757 TCGCATTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGATGT
403778 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGATGT
403799 TCGCGTTGCGA
1 TCGCGTTGCGA
403810 ATCTGGAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGATGT
Found at i:413040 original size:48 final size:48
Alignment explanation
Indices: 412984--413088 Score: 183
Period size: 48 Copynumber: 2.2 Consensus size: 48
412974 GCGAGTTAAA
* *
412984 ATCCCTATTGTTTCCATGTTCGGGATCATTGTTATCACGAATTCTCAG
1 ATCCCTATTGTTTCCATGCTCGGGATCATTGTTATCACAAATTCTCAG
*
413032 ATCCCTATTGTTTTCATGCTCGGGATCATTGTTATCACAAATTCTCAG
1 ATCCCTATTGTTTCCATGCTCGGGATCATTGTTATCACAAATTCTCAG
413080 ATCCCTATT
1 ATCCCTATT
413089 ATCCTTTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (48 bp):
ATCCCTATTGTTTCCATGCTCGGGATCATTGTTATCACAAATTCTCAG
Found at i:415401 original size:29 final size:29
Alignment explanation
Indices: 415369--415462 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
415359 AAATTGGTCA
*
415369 TTAAACTTTTAAATATACTAATTTCATCT
1 TTAAACTTTTAAATATATTAATTTCATCT
* * ** * * **
415398 TTAAACTATGACCTTCATTTTAAATTGGTCT
1 TTAAACTTTTA-AAT-ATATTAATTTCATCT
415429 TTAAACTTTTAAATATATTAATTTCATCT
1 TTAAACTTTTAAATATATTAATTTCATCT
415458 TTAAA
1 TTAAA
415463 TTATTACTCT
Statistics
Matches: 46, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
29 25 0.54
30 2 0.04
31 19 0.41
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.48
Consensus pattern (29 bp):
TTAAACTTTTAAATATATTAATTTCATCT
Found at i:415415 original size:60 final size:60
Alignment explanation
Indices: 415344--415462 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
415334 TATATATCTT
415344 TATGACATTCATTTTAAATTGGTCATTAAACTTTTAAATATACTAATTTCATCTTTAAAC
1 TATGACATTCATTTTAAATTGGTCATTAAACTTTTAAATATACTAATTTCATCTTTAAAC
* * *
415404 TATGACCTTCATTTTAAATTGGTCTTTAAACTTTTAAATATATTAATTTCATCTTTAAA
1 TATGACATTCATTTTAAATTGGTCATTAAACTTTTAAATATACTAATTTCATCTTTAAA
415463 TTATTACTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (60 bp):
TATGACATTCATTTTAAATTGGTCATTAAACTTTTAAATATACTAATTTCATCTTTAAAC
Found at i:415875 original size:61 final size:61
Alignment explanation
Indices: 415767--415883 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 61
415757 TAGTTTAGGT
* * *
415767 ATGAAATTAAAATATTCAAAAGTTTAAGAATTAATTAAAAACGATAAT-ACTAATTTTAAGG
1 ATGAAATTAAAATATTCAAAACTTTAAGAACTAATTAAAAACAATAATCA-TAATTTTAAGG
* * * *
415828 ATGAAATTAGAATATTTAAAACTTT-AGAAACTAATTTAAAATAATAATCATAATTT
1 ATGAAATTAAAATATTCAAAACTTTAAG-AACTAATTAAAAACAATAATCATAATTT
415884 GATGCAATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 2 0.04
61 44 0.94
62 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (61 bp):
ATGAAATTAAAATATTCAAAACTTTAAGAACTAATTAAAAACAATAATCATAATTTTAAGG
Found at i:416354 original size:29 final size:30
Alignment explanation
Indices: 416320--416380 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
416310 TATGTTGCTT
*
416320 TTTTAGTTTAGTGTCTAACGTTT-ATTTTG
1 TTTTAGTTTAGTGCCTAACGTTTCATTTTG
416349 TTTTAGTTTAGTGCCTAACGTTTCATTTTG
1 TTTTAGTTTAGTGCCTAACGTTTCATTTTG
416379 TT
1 TT
416381 ACTCAAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.57
Consensus pattern (30 bp):
TTTTAGTTTAGTGCCTAACGTTTCATTTTG
Found at i:417050 original size:29 final size:30
Alignment explanation
Indices: 417005--417061 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
416995 ATTTTTGAGT
*
417005 AACGAAATGAAACGTTAGGCACCAAACTAG
1 AACGAAATGAAACGTTAGACACCAAACTAG
*
417035 AACGAAAT-AAACGTTAGACACTAAACT
1 AACGAAATGAAACGTTAGACACCAAACT
417062 GAAAAACGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (30 bp):
AACGAAATGAAACGTTAGACACCAAACTAG
Found at i:421751 original size:55 final size:55
Alignment explanation
Indices: 421683--422173 Score: 539
Period size: 55 Copynumber: 9.0 Consensus size: 55
421673 CAAATGATAA
** *
421683 GTCTGCTCCCTATTTTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
* * * * *
421738 GTATGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAGCAAACGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
* * * *
421793 GTATGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
* * * * *
421848 GTCTGCTCCCTATTCGTTTAGGGAGTATAAGACTCGAACAATCTTCAATAAAACGG
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-CAAACGT
* * * **
421904 GTCCGCTCTCTATTCCTTCAGAGTGTAT-AGAACTCGAACAATCTTCAACAAATAT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGT
* * *
421959 GTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTTG----ATCTTCAACAAACGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
* * * * * * *
422010 GTCCGCTCCCTATTTCTTCAGAGAGTATAGGACTCGAATAATCTTTATA-AAATGG
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAAACGT
* * *
422065 GTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACGG
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGT
* * *
422120 GTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTTAACAAACG
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACG
422174 GGTTCGCTCC
Statistics
Matches: 383, Mismatches: 43, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
51 47 0.12
54 2 0.01
55 288 0.75
56 46 0.12
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (55 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGT
Found at i:422157 original size:272 final size:272
Alignment explanation
Indices: 421683--422182 Score: 639
Period size: 272 Copynumber: 1.8 Consensus size: 272
421673 CAAATGATAA
* * *
421683 GTCTGCTCCCTATTTTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGTGTATGCTCCC
1 GTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCG---AATCTTCAACAAACGTGTACGCTCCC
* * * * *
421748 TATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAGCAAACGTGTATGCTCCCTATTCGTTCA
63 TATTCATTCAGAGAGTATAAGACTCAAACAATCTTCAGAAAACGGGTACGCTCCCTATTCCTTCA
* * * * * * *
421813 GGGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCTGCTCCCTATTCGTTTAGGGAGTATAA
128 GAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAA
421878 GACTCGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAGAGTGTATAGAACTCGAAC
193 GACTCGAACAATCTTCAA-AAAACGGGTCCGCTCTCTATTCCTTCAGAGTGTATAGAACTCGAAC
421943 AATCTTCAACAAATAT
257 AATCTTCAACAAATAT
* * *
421959 GTCTGCTCCCTATTTCTTCAGAGAGTATAGGACTTG-ATCTTCAACAAACGTGTCCGCTCCCTAT
1 GTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAATCTTCAACAAACGTGTACGCTCCCTA-
* * * * * * * *
422023 TTC-TTCAGAGAGTATAGGACTCGAATAATCTTTATAAAATGGGTCCGCTCTCTATTCCTTCAGA
65 TTCATTCAGAGAGTATAAGACTCAAACAATCTTCAGAAAACGGGTACGCTCCCTATTCCTTCAGA
*
422087 GAGTAT-AGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AG
130 GAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAG
* * *
422150 AACTCGAACAATCTTTAACAAACGGGTTCGCTC
194 -ACTCGAACAATCTTCAAAAAACGGGTCCGCTC
422183 CCTCTTTCTC
Statistics
Matches: 191, Mismatches: 30, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
271 17 0.09
272 139 0.73
273 3 0.02
276 32 0.17
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (272 bp):
GTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAATCTTCAACAAACGTGTACGCTCCCTAT
TCATTCAGAGAGTATAAGACTCAAACAATCTTCAGAAAACGGGTACGCTCCCTATTCCTTCAGAG
AGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGAC
TCGAACAATCTTCAAAAAACGGGTCCGCTCTCTATTCCTTCAGAGTGTATAGAACTCGAACAATC
TTCAACAAATAT
Found at i:422245 original size:54 final size:54
Alignment explanation
Indices: 422175--422277 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
422165 TAACAAACGG
*
422175 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACAA
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATTTTCTTCTTACAA
422229 GTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATTTTCTTCT
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATTTTCTTCT
422278 GCTTTACTAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (54 bp):
GTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATTTTCTTCTTACAA
Found at i:422705 original size:37 final size:37
Alignment explanation
Indices: 422654--422769 Score: 112
Period size: 37 Copynumber: 3.2 Consensus size: 37
422644 TTGCTCTAAC
* *
422654 ACTCTTCCGA-GAAGGTTTAAAAAAGATATGCTTCACT
1 ACTCTT-CGATGAAGGCTTAAAAAAGATTTGCTTCACT
* * *
422691 ACTCTTCGATGAAGGCTT-AAGATGGTTTGCTTCACT
1 ACTCTTCGATGAAGGCTTAAAAAAGATTTGCTTCACT
* * **
422727 ACTCGTTAG-TGAAGGCTCAAAATGGATTTGCTTCACT
1 ACTC-TTCGATGAAGGCTTAAAAAAGATTTGCTTCACT
422764 ACTCTT
1 ACTCTT
422770 TGGTGAAGAC
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
36 31 0.48
37 34 0.52
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (37 bp):
ACTCTTCGATGAAGGCTTAAAAAAGATTTGCTTCACT
Found at i:422776 original size:37 final size:36
Alignment explanation
Indices: 422682--422777 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 36
422672 AAAAAAGATA
* * * *
422682 TGCTTCACTACTCTTCGATGAAGGCTTAAGATGGTT
1 TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGGTT
* *
422718 TGCTTCACTACTCGTTAGTGAAGGCTCAAAATGGATT
1 TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGG-TT
422755 TGCTTCACTACTCTTTGGTGAAG
1 TGCTTCACTACTCTTTGGTGAAG
422778 ACTTGGCTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 28 0.55
37 23 0.45
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (36 bp):
TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGGTT
Found at i:424166 original size:125 final size:126
Alignment explanation
Indices: 423945--424190 Score: 307
Period size: 125 Copynumber: 2.0 Consensus size: 126
423935 CAATAATACC
* * ** *
423945 TTTAGCTGGAACAAGCCTTCAAAATGCCCTAACATTTCAAGTTGTAAGACTCACTCTCAACGTCC
1 TTTAGCTGGAACAAGCCTTCAAAATGCCCCAAAACCTCAAATTGTAAGACTCACTCTCAACGTCC
* * * * ** *
424010 TCTTGGTCTGAATCTTGTCATTTCATCATGATGTGGGTTCAGTCATGCCCCAATATTATCT
66 TCTTCGTCCGAATCATGTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATATTATCT
* * * * * *
424071 TTTA-CTGGTACAAGTCTTCAAAATGCCCCAAAACCTCAAATTGTAAGGCTTATTCTCAATG-CC
1 TTTAGCTGGAACAAGCCTTCAAAATGCCCCAAAACCTCAAATTGTAAGACTCACTCTCAACGTCC
424134 TTCTTCGTCCGAATCATGTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATAT
66 -TCTTCGTCCGAATCATGTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATAT
424191 GGGTATTCAT
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
124 2 0.02
125 95 0.94
126 4 0.04
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (126 bp):
TTTAGCTGGAACAAGCCTTCAAAATGCCCCAAAACCTCAAATTGTAAGACTCACTCTCAACGTCC
TCTTCGTCCGAATCATGTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATATTATCT
Found at i:427602 original size:72 final size:72
Alignment explanation
Indices: 427485--427635 Score: 248
Period size: 72 Copynumber: 2.1 Consensus size: 72
427475 CCCCTAACAG
*
427485 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACTCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
427550 TTCATCT
66 TTCATAT
* * *
427557 GTTCTTGATCATTTGCTATCATCACATTGGCTGTATCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
427622 TTCATAT
66 TTCATAT
*
427629 TTTCTTG
1 GTTCTTG
427636 TGTAATAGGG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:428388 original size:55 final size:55
Alignment explanation
Indices: 428317--428481 Score: 276
Period size: 55 Copynumber: 3.0 Consensus size: 55
428307 TGTGGATCTG
* * *
428317 TCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCATTCTTCATGAATCGT
1 TCTTCAGTCAGGTTCAAATTTCTTCATTCATCGGATGTCATTCTTCATGAATCAT
*
428372 TCTTCAGTCAGGTTCAAATTTCTTCATTCATCGGATGCCATTCTTCATGAATCAT
1 TCTTCAGTCAGGTTCAAATTTCTTCATTCATCGGATGTCATTCTTCATGAATCAT
* *
428427 TCTTCAGTCAGGTTCAAATTTCTTCATTCATCGGATTTCATTGTTCATGAATCAT
1 TCTTCAGTCAGGTTCAAATTTCTTCATTCATCGGATGTCATTCTTCATGAATCAT
428482 CTGAACGCCT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 103 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (55 bp):
TCTTCAGTCAGGTTCAAATTTCTTCATTCATCGGATGTCATTCTTCATGAATCAT
Found at i:428882 original size:46 final size:45
Alignment explanation
Indices: 428795--428882 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 45
428785 TGCAAAAAAT
* *
428795 CCTAACCGCATGATATCTAATTCACATGCTTGTTCGAGAAAATAAA
1 CCTAACCACATGATATCTAATTCACATGCTTATTC-AGAAAATAAA
*
428841 CCTAACCACATGATATCTAGTTCACATGCATTTATTC-GAAAA
1 CCTAACCACATGATATCTAATTCACATGC--TTATTCAGAAAA
428883 ACGAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 32 0.86
48 5 0.14
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (45 bp):
CCTAACCACATGATATCTAATTCACATGCTTATTCAGAAAATAAA
Found at i:435113 original size:23 final size:23
Alignment explanation
Indices: 435086--435129 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
435076 AACACAATTT
*
435086 AATTTGCCTA-GACATTTCCATCC
1 AATTTGCC-ACGACATATCCATCC
435109 AATTTGCCACGACATATCCAT
1 AATTTGCCACGACATATCCAT
435130 TTGCTACTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (23 bp):
AATTTGCCACGACATATCCATCC
Found at i:444187 original size:31 final size:31
Alignment explanation
Indices: 444149--444302 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
444139 CCCGAAGGAC
* *
444149 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
444180 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
444211 CAGTCCATATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
444242 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
444273 CAGTCCGTATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
444303 CCCTCGACCC
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:445465 original size:13 final size:15
Alignment explanation
Indices: 445434--445469 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
445424 TTCACACGTG
445434 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
445449 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
445461 GAGAAGAGA
1 GAGAAGAGA
445470 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:448559 original size:31 final size:31
Alignment explanation
Indices: 448521--448674 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
448511 CCCGAAGGAC
* *
448521 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
448552 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
448583 CAGTCCATATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
448614 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
448645 CAGTCCGTATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
448675 CCCTCGACCC
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:449839 original size:13 final size:15
Alignment explanation
Indices: 449808--449843 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
449798 TTCACACGTG
449808 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
449823 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
449835 GAGAAGAGA
1 GAGAAGAGA
449844 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:452809 original size:23 final size:23
Alignment explanation
Indices: 452782--452825 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
452772 AACACAATTA
*
452782 AATTTGCCAAGACATTTCCATCC
1 AATTTGCCAAGACATATCCATCC
*
452805 AATTTGCCACGACATATCCAT
1 AATTTGCCAAGACATATCCAT
452826 TTGCTACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.30
Consensus pattern (23 bp):
AATTTGCCAAGACATATCCATCC
Found at i:455867 original size:59 final size:59
Alignment explanation
Indices: 455796--455976 Score: 222
Period size: 59 Copynumber: 3.1 Consensus size: 59
455786 GTCCTTAAAT
* * *
455796 TATAATTCTCATTTTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCTAAAC
1 TATAATTTTCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCAAAC
* * *
455855 TATAATTTTCATTCTAAATTAAT-CCTCAAAATTTTGAACATTTCAATTTCATCCCAAAC
1 TATAATTTTCATTCTAAATTAGTCCCT-AAACTTTTAAACATTTCAATTTCATCCCAAAC
* * * * * *
455914 TATGACTTTCATTGTAAATTAG-CCCCAAACTTTTTAAACATTTTAATTCCATCCCAAAC
1 TATAATTTTCATTCTAAATTAGTCCCTAAAC-TTTTAAACATTTCAATTTCATCCCAAAC
455973 TATA
1 TATA
455977 CATATATACT
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 6 0.06
59 97 0.94
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (59 bp):
TATAATTTTCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCAAAC
Found at i:457443 original size:12 final size:12
Alignment explanation
Indices: 457426--457469 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
457416 GTGGTTGTGC
*
457426 AGGAGGTGTTGG
1 AGGAGGAGTTGG
* **
457438 AGGAGGGGAAGG
1 AGGAGGAGTTGG
457450 AGGAGGAGTTGG
1 AGGAGGAGTTGG
457462 AGGAGGAG
1 AGGAGGAG
457470 GAGGTATGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.61, T:0.11
Consensus pattern (12 bp):
AGGAGGAGTTGG
Done.