Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 48 of 73
Found at i:11466696 original size:37 final size:37
Alignment explanation
Indices: 11466637--11466735 Score: 137
Period size: 37 Copynumber: 2.7 Consensus size: 37
11466627 TGTTTGTGTC
* *
11466637 TTAAGGAAGACTGTCTCAAGTGAGACAAAATTT-ATT
1 TTAAAGAAAACTGTCTCAAGTGAGACAAAATTTGATT
*
11466673 TTAAAGAAAAACTGTCTCAAGTGAGACAAAATTTGTTT
1 TTAAAG-AAAACTGTCTCAAGTGAGACAAAATTTGATT
**
11466711 TTAAAGAAAACAATCTCAAGTGAGA
1 TTAAAGAAAACTGTCTCAAGTGAGA
11466736 TTAATTTTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
36 5 0.09
37 43 0.77
38 8 0.14
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (37 bp):
TTAAAGAAAACTGTCTCAAGTGAGACAAAATTTGATT
Found at i:11469283 original size:10 final size:10
Alignment explanation
Indices: 11469261--11469294 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
11469251 TCTTTCCTCA
11469261 TTTT-CTTTCT
1 TTTTCCTTT-T
11469271 TTTTCCTTTT
1 TTTTCCTTTT
11469281 TTTTCCTTTT
1 TTTTCCTTTT
11469291 TTTT
1 TTTT
11469295 TGTTTAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCCTTTT
Found at i:11470741 original size:29 final size:29
Alignment explanation
Indices: 11470705--11470779 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
11470695 TTTATGAATG
*
11470705 ATGCATGTGAAAATGCTTGAATAAATGGA
1 ATGCATGTGAAAATGCTTAAATAAATGGA
11470734 ATGCATGTGAAAATGCTTAAATAAATGGA
1 ATGCATGTGAAAATGCTTAAATAAATGGA
*
11470763 ATGCAGGTGCAAAATGC
1 ATGCATGTG-AAAATGC
11470780 AAAAATACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 36 0.84
30 7 0.16
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.25
Consensus pattern (29 bp):
ATGCATGTGAAAATGCTTAAATAAATGGA
Found at i:11474019 original size:29 final size:30
Alignment explanation
Indices: 11473958--11474033 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
11473948 TTTTTCTTTT
11473958 TTTTCTCTAT-G-TTTTTTCGAAAGCTTCA
1 TTTTCTCTATCGTTTTTTTCGAAAGCTTCA
* *
11473986 TTTTCT-TTTCTGTTTTTTTCGAAAGCTTTA
1 TTTTCTCTATC-GTTTTTTTCGAAAGCTTCA
11474016 -TTTCTCTATCGTTTTTTT
1 TTTTCTCTATCGTTTTTTT
11474034 TGTCTTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 2 0.05
28 6 0.15
29 14 0.34
30 19 0.46
ACGTcount: A:0.13, C:0.16, G:0.09, T:0.62
Consensus pattern (30 bp):
TTTTCTCTATCGTTTTTTTCGAAAGCTTCA
Found at i:11483438 original size:30 final size:29
Alignment explanation
Indices: 11483403--11483490 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
11483393 CACATCTTAA
*
11483403 TATTATCTTAACTTATTAAATATAGTTTAT
1 TATTATCTTAACTTATAAAATATA-TTTAT
*
11483433 TATTATTTTAACTT-TAGAAATATATTTTAT
1 TATTATCTTAACTTATA-AAATATA-TTTAT
* *
11483463 TTTTATCTTAACTTAAAAAATATATTTA
1 TATTATCTTAACTTATAAAATATATTTA
11483491 GTCTATATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.10
30 44 0.88
31 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (29 bp):
TATTATCTTAACTTATAAAATATATTTAT
Found at i:11483661 original size:30 final size:30
Alignment explanation
Indices: 11483625--11483746 Score: 95
Period size: 30 Copynumber: 3.8 Consensus size: 30
11483615 AGATTTTTAA
11483625 AATTAAAATAAGAATAAAATATAAAATTTT
1 AATTAAAATAAGAATAAAATATAAAATTTT
*
11483655 AATTAAATTTAA-AATAATATATATATATATATATATTT
1 AATTAAA-ATAAGAAT-A-A-A-ATATA-A-A-AT-TTT
* *
11483693 AAATTAAGATAAGAATAAAATAT-ATATTTT
1 -AATTAAAATAAGAATAAAATATAAAATTTT
*
11483723 AAGTTAAAATAAGAATAAATTATA
1 AA-TTAAAATAAGAATAAAATATA
11483747 TTTAATTATT
Statistics
Matches: 73, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
29 2 0.03
30 31 0.42
31 6 0.08
32 1 0.01
33 2 0.03
34 5 0.07
35 5 0.07
36 2 0.03
37 3 0.04
38 7 0.10
39 9 0.12
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (30 bp):
AATTAAAATAAGAATAAAATATAAAATTTT
Found at i:11483740 original size:69 final size:65
Alignment explanation
Indices: 11483624--11483759 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 65
11483614 AAGATTTTTA
*
11483624 AAATTAAAATAAGAATAAAATATAAAATTTTAATTAAATTTAAAATAATATATATATATATATAT
1 AAATTAAAATAAGAATAAAATATAAAATTTTAATTAAATATAAAATAA-AT-TATATATA-AT-T
11483689 ATTT
62 ATTT
* * *
11483693 AAATTAAGATAAGAATAAAATAT-ATATTTTAAGTTAAA-ATAAGAATAAATTATATTTAATTAT
1 AAATTAAAATAAGAATAAAATATAAAATTTTAA-TTAAATATAA-AATAAATTATATATAATTAT
11483756 TT
64 TT
11483758 AA
1 AA
11483760 GGTAAGGATA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
65 7 0.11
66 2 0.03
67 7 0.11
68 13 0.21
69 32 0.52
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (65 bp):
AAATTAAAATAAGAATAAAATATAAAATTTTAATTAAATATAAAATAAATTATATATAATTATTT
Found at i:11483747 original size:30 final size:29
Alignment explanation
Indices: 11483681--11483937 Score: 175
Period size: 30 Copynumber: 8.6 Consensus size: 29
11483671 ATATATATAT
*
11483681 ATATATATATTTAAATTAAGATAAGAATAAA
1 ATATATAT-TTTAAGTTAAGATAAGAAT-AA
*
11483712 ATATATATTTTAAGTTAAAATAAGAATAA
1 ATATATATTTTAAGTTAAGATAAGAATAA
* * * *
11483741 AT-TATATTTAATTATTTAAGGTAAGGATAA
1 ATATATATTT--TAAGTTAAGATAAGAATAA
* *
11483771 A-ATATATTTAATAATTTAAGTTAAGAATATA
1 ATATATATTT--TAAGTTAAGATAAGAATA-A
* * ** ** *
11483802 ATTTATGTAATGGGTTAAGATAATAATAA
1 ATATATATTTTAAGTTAAGATAAGAATAA
*
11483831 ATATA-AATTTAGCAGTTAAGATAAGAATAA
1 ATATATATTTTA--AGTTAAGATAAGAATAA
* * *
11483861 A-ATATTTTTTATGTTAAGATAACAATAA
1 ATATATATTTTAAGTTAAGATAAGAATAA
*
11483889 A-ATATATTTAATAAGTTAAGATAAAAATAA
1 ATATATATTT--TAAGTTAAGATAAGAATAA
11483919 A-ATATATTTTTAATGTTAA
1 ATATATA-TTTTAA-GTTAA
11483938 AAATGAATTT
Statistics
Matches: 180, Mismatches: 34, Indels: 25
0.75 0.14 0.10
Matches are distributed among these distances:
28 31 0.17
29 15 0.08
30 117 0.65
31 13 0.07
32 4 0.02
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (29 bp):
ATATATATTTTAAGTTAAGATAAGAATAA
Found at i:11483775 original size:60 final size:60
Alignment explanation
Indices: 11483696--11483927 Score: 224
Period size: 60 Copynumber: 3.9 Consensus size: 60
11483686 TATATTTAAA
* *
11483696 TTAAGATAAGAATAAAATATATATT-TTAAGTTAAAATAAGAATAAATTATATTTAATTAT
1 TTAAGATAAGAATAAAATATAT-TTAATAAGTTAAGATAAGAATAAATTATATTTAATTAT
* * * * * ***
11483756 TTAAGGTAAGGATAAAATATATTTAATAATTTAAGTTAAGAATATAATT-TATGTAATGGG
1 TTAAGATAAGAATAAAATATATTTAATAAGTTAAGATAAGAATA-AATTATATTTAATTAT
* * ** *
11483816 TTAAGATAATAATAAATATAAATTT-AGCAGTTAAGATAAGAATAAA--ATATTT-TTTAT
1 TTAAGATAAGAATAAA-ATATATTTAATAAGTTAAGATAAGAATAAATTATATTTAATTAT
* * *
11483873 GTTAAGATAACAATAAAATATATTTAATAAGTTAAGATAAAAATAAAATATATTT
1 -TTAAGATAAGAATAAAATATATTTAATAAGTTAAGATAAGAATAAATTATATTT
11483928 TTAATGTTAA
Statistics
Matches: 136, Mismatches: 28, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
57 8 0.06
58 37 0.27
59 4 0.03
60 76 0.56
61 11 0.08
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (60 bp):
TTAAGATAAGAATAAAATATATTTAATAAGTTAAGATAAGAATAAATTATATTTAATTAT
Found at i:11483950 original size:18 final size:18
Alignment explanation
Indices: 11483927--11483974 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
11483917 AAAATATATT
11483927 TTTAATGTTAAAAATGAA
1 TTTAATGTTAAAAATGAA
**
11483945 TTTAAT-TTAATATGTGAA
1 TTTAATGTTAA-AAATGAA
11483963 TTTAA-GTTAAAA
1 TTTAATGTTAAAA
11483975 TATATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTAATGTTAAAAATGAA
Found at i:11486377 original size:29 final size:29
Alignment explanation
Indices: 11486338--11486409 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
11486328 TCTCTGTGTT
11486338 TTTTTCGAAAGCTTCATTTTCTTTTTTCC
1 TTTTTCGAAAGCTTCATTTTCTTTTTTCC
11486367 TTTTTCGAAAGCTTCATTTTCTTTTTTCC
1 TTTTTCGAAAGCTTCATTTTCTTTTTTCC
11486396 TTTTTCGAAAGCTT
1 TTTTTCGAAAGCTT
11486410 TCTTTCTCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.57
Consensus pattern (29 bp):
TTTTTCGAAAGCTTCATTTTCTTTTTTCC
Found at i:11487010 original size:3 final size:3
Alignment explanation
Indices: 11487002--11487043 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
11486992 CTACAAAAAT
*
11487002 ATA ATA ATA TTA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11487044 GTTATTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11487691 original size:138 final size:137
Alignment explanation
Indices: 11487246--11487744 Score: 619
Period size: 137 Copynumber: 3.6 Consensus size: 137
11487236 TTTGGAGATA
** * ** * * *
11487246 ACACTGCTCCTACACGATGAGGATATCGGGTCGGTGGATGACACTGTCCCTACGTAATGAGGACA
1 ACACTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACG
** * *
11487311 TTTGGATATCTTTAGGGATAATAGAGATAACACTG-TTCCTACGTGATGAGGAATTTTGGCTATC
66 TTTGGCCATCTTTAGGGATAATAGAGATAACAC-GATTCCTACGTGATGAGGAAGTCTGGCTATC
11487375 TAAGGGTG
130 TAAGGGTG
* * *
11487383 ACACGGCTCCTACGTGATGAGGAGA-ACTGGTCGGTGGATGACACGGTTCCTATGTGATGAGGAC
1 ACACTGCTCCTACGTGATGAGGAGATA-TGGTCGGTGGATGACACTGTTCCTACGTGATGAGGAC
* * * * *
11487447 GTTTGACCATCTTTAGGGATAATGGAGATAACAC-AGTTCTTATGTGAAGAGGAAGTCTGGCTAT
65 GTTTGGCCATCTTTAGGGATAATAGAGATAACACGA-TTCCTACGTGATGAGGAAGTCTGGCTAT
11487511 CTAAGGGTG
129 CTAAGGGTG
* * *
11487520 ACACTGCTCTTACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACG
1 ACACTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACG
* * * *
11487585 TCTGGCCATCTTTAGGGATAAATAGAGATAACACGATTCCTACGCGATTAGGAAGCCTGGCTATC
66 TTTGGCCATCTTTAGGGAT-AATAGAGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATC
*
11487650 TAAGGATG
130 TAAGGGTG
* * * **
11487658 ATGA-TTCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTATTCCTATATGATGAGGAC
1 A-CACTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTGTTCCTACGTGATGAGGAC
*
11487722 GTATGGCCATCTTTAGGGATAAT
65 GTTTGGCCATCTTTAGGGATAAT
11487745 TTGTTTCAAG
Statistics
Matches: 310, Mismatches: 45, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
137 192 0.62
138 116 0.37
139 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (137 bp):
ACACTGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACACTGTTCCTACGTGATGAGGACG
TTTGGCCATCTTTAGGGATAATAGAGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATCT
AAGGGTG
Found at i:11487736 original size:275 final size:274
Alignment explanation
Indices: 11487246--11487744 Score: 707
Period size: 275 Copynumber: 1.8 Consensus size: 274
11487236 TTTGGAGATA
*
11487246 ACACTGCTCCTACACGATGAGGATATCGGGTCGGTGGATGACACTGTCCCTACGTAATGAGGACA
1 ACACTGCTCCTACACGATGAGGAGATCGGGTCGGTGGATGACACTGTCCCTACGTAATGAGGACA
* * * ***
11487311 TTTGGATATCTTTAGGGATAATAGAGATAACACTGTTCCTACGTGATGAGGAATTTTGGCTATCT
66 TCTGGACATCTTTAGGGATAATAGAGATAACACTGTTCCTACGCGATGAGGAAGCCTGGCTATCT
* * *
11487376 AAGGGTGACACGGCTCCTACGTGATGAGGAGAACTGGTCGGTGGATGACACGGTTCCTATGTGAT
131 AAGGATGACACGGCTCCTACGTGATGAGGAGAACTGGTCGGTGGATGACACGATTCCTATATGAT
*
11487441 GAGGACGTTTGACCATCTTTAGGGATAATGGAGATAACACAGTTCTTATGTGAAGAGGAAGTCTG
196 GAGGACGTATGACCATCTTTAGGGATAATGGAGATAACACAGTTCTTATGTGAAGAGGAAGTCTG
11487506 GCTATCTAAGGGTG
261 GCTATCTAAGGGTG
* ** * * * * *
11487520 ACACTGCTCTTACGTGATGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACG
1 ACACTGCTCCTACACGATGAGGAGATCGGGTCGGTGGATGACACTGTCCCTACGTAATGAGGACA
* *
11487585 TCTGGCCATCTTTAGGGATAAATAGAGATAACAC-GATTCCTACGCGATTAGGAAGCCTGGCTAT
66 TCTGGACATCTTTAGGGAT-AATAGAGATAACACTG-TTCCTACGCGATGAGGAAGCCTGGCTAT
* ** *
11487649 CTAAGGATGATGA-TTCTCCTACGTGATGAGGAGATA-TGGTCGGTGGATGACACTATTCCTATA
129 CTAAGGATGA-CACGGCTCCTACGTGATGAGGAGA-ACTGGTCGGTGGATGACACGATTCCTATA
*
11487712 TGATGAGGACGTATGGCCATCTTTAGGGATAAT
192 TGATGAGGACGTATGACCATCTTTAGGGATAAT
11487745 TTGTTTCAAG
Statistics
Matches: 195, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
274 73 0.37
275 120 0.62
276 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (274 bp):
ACACTGCTCCTACACGATGAGGAGATCGGGTCGGTGGATGACACTGTCCCTACGTAATGAGGACA
TCTGGACATCTTTAGGGATAATAGAGATAACACTGTTCCTACGCGATGAGGAAGCCTGGCTATCT
AAGGATGACACGGCTCCTACGTGATGAGGAGAACTGGTCGGTGGATGACACGATTCCTATATGAT
GAGGACGTATGACCATCTTTAGGGATAATGGAGATAACACAGTTCTTATGTGAAGAGGAAGTCTG
GCTATCTAAGGGTG
Found at i:11488148 original size:37 final size:37
Alignment explanation
Indices: 11488089--11488187 Score: 137
Period size: 37 Copynumber: 2.7 Consensus size: 37
11488079 TGTTTGTGTC
* *
11488089 TTAAGGAAGACTGTCTCAAGTGAGACAAAATTT-ATT
1 TTAAAGAAAACTGTCTCAAGTGAGACAAAATTTGATT
*
11488125 TTAAAGAAAAACTGTCTCAAGTGAGACAAAATTTGTTT
1 TTAAAG-AAAACTGTCTCAAGTGAGACAAAATTTGATT
**
11488163 TTAAAGAAAACAATCTCAAGTGAGA
1 TTAAAGAAAACTGTCTCAAGTGAGA
11488188 TTAATTTTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
36 5 0.09
37 43 0.77
38 8 0.14
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (37 bp):
TTAAAGAAAACTGTCTCAAGTGAGACAAAATTTGATT
Found at i:11490738 original size:11 final size:11
Alignment explanation
Indices: 11490713--11490747 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
11490703 TCTTTCCTCA
*
11490713 TTTTC-TTTCT
1 TTTTCTTTTTT
11490723 TTTTCTTTTTT
1 TTTTCTTTTTT
11490734 TTTTCTTTTTT
1 TTTTCTTTTTT
11490745 TTT
1 TTT
11490748 GTTTAGTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:11490747 original size:10 final size:10
Alignment explanation
Indices: 11490713--11490747 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
11490703 TCTTTCCTCA
*
11490713 TTTTCTTTCT
1 TTTTCTTTTT
11490723 TTTTCTTTTTT
1 TTTTC-TTTTT
11490734 TTTTCTTTTT
1 TTTTCTTTTT
11490744 TTTT
1 TTTT
11490748 GTTTAGTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:11492193 original size:29 final size:29
Alignment explanation
Indices: 11492157--11492231 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
11492147 TTTATGAATG
*
11492157 ATGCATGTGAAAATGCTTGAATAAATGGA
1 ATGCATGTGAAAATGCTTAAATAAATGGA
11492186 ATGCATGTGAAAATGCTTAAATAAATGGA
1 ATGCATGTGAAAATGCTTAAATAAATGGA
*
11492215 ATGCAGGTGTAAAATGC
1 ATGCATGTG-AAAATGC
11492232 AAAAATACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 36 0.84
30 7 0.16
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (29 bp):
ATGCATGTGAAAATGCTTAAATAAATGGA
Found at i:11495469 original size:29 final size:30
Alignment explanation
Indices: 11495408--11495483 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
11495398 TTTTTCTTTT
11495408 TTTTCTCTAT-G-TTTTTTCGAAAGCTTCA
1 TTTTCTCTATCGTTTTTTTCGAAAGCTTCA
* *
11495436 TTTTCT-TTTCTGTTTTTTTCGAAAGCTTTA
1 TTTTCTCTATC-GTTTTTTTCGAAAGCTTCA
11495466 -TTTCTCTATCGTTTTTTT
1 TTTTCTCTATCGTTTTTTT
11495484 TGTCTTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 2 0.05
28 6 0.15
29 14 0.34
30 19 0.46
ACGTcount: A:0.13, C:0.16, G:0.09, T:0.62
Consensus pattern (30 bp):
TTTTCTCTATCGTTTTTTTCGAAAGCTTCA
Found at i:11502739 original size:116 final size:118
Alignment explanation
Indices: 11502524--11502750 Score: 359
Period size: 116 Copynumber: 1.9 Consensus size: 118
11502514 GGGGAAACAA
* *
11502524 TAGTGGCGTTTTTTTGAAAAAACGTCGCAATAGGTCCATCTATAGTGGTGTTTATTGGAAAAACG
1 TAGTGGCGTTTTTTTGAAAAAACGTCACAATAGGTCCATCTATAGTGGCGTTTATTGGAAAAACG
* ***
11502589 CCACTATATATATACTTTTTTTTGGGGGATTTTTTGGG-GCCCTGCACAATAC
66 CCACTATATATATACTTTTTTGTGGCCCATTTTTTGGGAGCCCTGCACAATAC
*
11502641 TAGTGGCGTTTTTTT-AAAAAACGTCACAATAGGTCTATCTATAGTGGCGTTTATTGGAAAAACG
1 TAGTGGCGTTTTTTTGAAAAAACGTCACAATAGGTCCATCTATAGTGGCGTTTATTGGAAAAACG
*
11502705 CCACTATATATATACTTTTTTGGTGTCCCATTTTTTGGGAGCCCTG
66 CCACTATATATATACTTTTTT-GTGGCCCATTTTTTGGGAGCCCTG
11502751 TGCGGTTGCA
Statistics
Matches: 100, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
116 67 0.67
117 27 0.27
118 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (118 bp):
TAGTGGCGTTTTTTTGAAAAAACGTCACAATAGGTCCATCTATAGTGGCGTTTATTGGAAAAACG
CCACTATATATATACTTTTTTGTGGCCCATTTTTTGGGAGCCCTGCACAATAC
Found at i:11503478 original size:18 final size:19
Alignment explanation
Indices: 11503435--11503479 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
11503425 TGTATTTGAT
*
11503435 TTTATTTATAATTTTTTACA
1 TTTATTTATAA-TTTTTAAA
*
11503455 TCTATTTATAA-TTTTAAA
1 TTTATTTATAATTTTTAAA
11503473 TTTATTT
1 TTTATTT
11503480 TATATGTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 12 0.55
20 10 0.45
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTATAATTTTTAAA
Found at i:11503957 original size:31 final size:31
Alignment explanation
Indices: 11503919--11503997 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
11503909 TTAACATCTC
* *
11503919 AGTGACCATATATTAATTAAAATAAAATAAA
1 AGTGACCATATATTAATTAAAACAAAACAAA
* * *
11503950 AGTGACCACATCTTAATTAAAACGAAACAAA
1 AGTGACCATATATTAATTAAAACAAAACAAA
* *
11503981 AGTGACTATGTATTAAT
1 AGTGACCATATATTAAT
11503998 GTTTTTTTGA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (31 bp):
AGTGACCATATATTAATTAAAACAAAACAAA
Found at i:11505881 original size:28 final size:29
Alignment explanation
Indices: 11505819--11505885 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
11505809 TTAAATTTCA
* *
11505819 AAAAAATATTTTATTTTTGCTTTAACTTAT
1 AAAATATATTTTATTTTTACTTTAAC-TAT
* *
11505849 TAAATATATTTTATTTTTATTTTAA-TAT
1 AAAATATATTTTATTTTTACTTTAACTAT
11505877 AAAATATAT
1 AAAATATAT
11505886 GTTTTCATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 11 0.34
30 21 0.66
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (29 bp):
AAAATATATTTTATTTTTACTTTAACTAT
Found at i:11506095 original size:30 final size:30
Alignment explanation
Indices: 11506049--11506256 Score: 124
Period size: 29 Copynumber: 6.7 Consensus size: 30
11506039 CTTTTAAAAG
* *
11506049 TTAAGATAATAATAAAATATAATTTTTAAT
1 TTAAAATAAGAATAAAATATAATTTTTAAT
* *
11506079 TTAAAATAAGAATAAAATAT-ATTGTTAAG
1 TTAAAATAAGAATAAAATATAATTTTTAAT
* *
11506108 TGAAGATAAGAATAAAA-ATATATTTTTATAT
1 TTAAAATAAGAATAAAATATA-ATTTTTA-AT
*
11506139 TGAAATAATAATAA-AATATTAAATAT-ATTTTTAAAAA
1 T----TAA-AATAAGAATA--AAATATAATTTTT--AAT
* * *
11506176 TTAAGATAAGAATAAAATCT-ATTTTTAAG
1 TTAAAATAAGAATAAAATATAATTTTTAAT
* *
11506205 TGAAAATAACG-ATAAAATGTATATTTTT-AT
1 TTAAAATAA-GAATAAAATATA-ATTTTTAAT
*
11506235 ATTAAAATAAAAATAAAATATA
1 -TTAAAATAAGAATAAAATATA
11506257 TTTAATAGGT
Statistics
Matches: 138, Mismatches: 21, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
28 2 0.01
29 39 0.28
30 26 0.19
31 36 0.26
32 4 0.03
33 7 0.05
35 6 0.04
36 10 0.07
37 5 0.04
38 3 0.02
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.38
Consensus pattern (30 bp):
TTAAAATAAGAATAAAATATAATTTTTAAT
Found at i:11506122 original size:59 final size:59
Alignment explanation
Indices: 11506046--11506157 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
11506036 ATACTTTTAA
* *
11506046 AAGTTAAGATAATAAT-AAAATATAATTTTTA-ATTTAAAATAAGAATAAAATATATTGTT
1 AAGTGAAGATAAGAATAAAAATAT-ATTTTTATA-TTAAAATAAGAATAAAATATATTGTT
* *
11506105 AAGTGAAGATAAGAATAAAAATATATTTTTATATTGAAATAATAATAAAATAT
1 AAGTGAAGATAAGAATAAAAATATATTTTTATATTAAAATAAGAATAAAATAT
11506158 TAAATATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 39 0.83
60 8 0.17
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (59 bp):
AAGTGAAGATAAGAATAAAAATATATTTTTATATTAAAATAAGAATAAAATATATTGTT
Found at i:11506124 original size:126 final size:125
Alignment explanation
Indices: 11505994--11506222 Score: 286
Period size: 126 Copynumber: 1.8 Consensus size: 125
11505984 TATTATTAAG
* * *
11505994 TAAAAATATACTTTGATGTT-AAGATATTTAA-AAAATA-AATATATACTTTTAAAAGTTAAGAT
1 TAAAAATATACTTTGATATTGAA-ATA-ATAATAAAATATAA-ATATACTTTTAAAAATTAAGAT
* * *
11506056 AATAATAAAATATAATTTTTAATTTAAAATAA-GAATAAAATATATTGTTAAGTGAAGATAAGAA
63 AAGAATAAAATAT-ATTTTTAAGTGAAAATAACG-ATAAAATATATTGTTAAGTGAAGATAAGAA
* * *
11506120 TAAAAATATATTTTTATATTGAAATAATAATAAAATATTAAATATATTTTTAAAAATTAAGATAA
1 TAAAAATATACTTTGATATTGAAATAATAATAAAATA-TAAATATACTTTTAAAAATTAAGATAA
*
11506185 GAATAAAATCTATTTTTAAGTGAAAATAACGATAAAAT
65 GAATAAAATATATTTTTAAGTGAAAATAACGATAAAAT
11506223 GTATATTTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
125 3 0.03
126 49 0.56
127 34 0.39
128 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (125 bp):
TAAAAATATACTTTGATATTGAAATAATAATAAAATATAAATATACTTTTAAAAATTAAGATAAG
AATAAAATATATTTTTAAGTGAAAATAACGATAAAATATATTGTTAAGTGAAGATAAGAA
Found at i:11506204 original size:97 final size:97
Alignment explanation
Indices: 11506063--11506255 Score: 266
Period size: 97 Copynumber: 2.0 Consensus size: 97
11506053 GATAATAATA
* *
11506063 AAATATAATTTTTAATTTAAAATAAGAATAAAATATATTGTTAAGTGAAGATAA-GAATAAAA-A
1 AAATATAATTTTTAAATTAAAATAAGAATAAAATATATTGTTAAGTGAAAATAACG-ATAAAATA
* *
11506126 TATATTTTTATATTGAAATAATAATAAAATATT
65 TATATTTTTATATTAAAATAAAAATAAAATATT
* * *
11506159 AAATAT-ATTTTTAAAAATTAAGATAAGAATAAAATCTATTTTTAAGTGAAAATAACGATAAAAT
1 AAATATAATTTTT--AAATTAAAATAAGAATAAAATATATTGTTAAGTGAAAATAACGATAAAAT
*
11506223 GTATATTTTTATATTAAAATAAAAATAAAATAT
64 ATATATTTTTATATTAAAATAAAAATAAAATAT
11506256 ATTTAATAGG
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 6 0.07
96 6 0.07
97 42 0.49
98 31 0.36
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (97 bp):
AAATATAATTTTTAAATTAAAATAAGAATAAAATATATTGTTAAGTGAAAATAACGATAAAATAT
ATATTTTTATATTAAAATAAAAATAAAATATT
Found at i:11506255 original size:127 final size:128
Alignment explanation
Indices: 11506029--11506259 Score: 301
Period size: 127 Copynumber: 1.8 Consensus size: 128
11506019 ATTTAAAAAA
* * * *
11506029 TAAATATATACTTTTAAAAGTTAAGATAATAATAAAATATAATTTTTAATTTAAAATAAGAATAA
1 TAAATATATA-TTTTAAAAATTAAGATAAGAATAAAATATAATTTTTAAGTGAAAATAAGAATAA
* *
11506094 AATATATTGTTAAGTGAAGATAAGAATAAAAATATATTTTTATATTGAAATAATAATAAAATAT
65 AATATATTGTTAAGTGAAAATAAAAATAAAAATATATTTTTATATTGAAATAATAATAAAATAT
*
11506158 TAAATATAT-TTTTAAAAATTAAGATAAGAATAAAATCT-ATTTTTAAGTGAAAATAACG-ATAA
1 TAAATATATATTTTAAAAATTAAGATAAGAATAAAATATAATTTTTAAGTGAAAATAA-GAATAA
* *
11506220 AATGTATATTTTTATA-TTAAAATAAAAAT-AAAATATATTT
65 AA--TATATTGTTA-AGTGAAAATAAAAATAAAAATATATTT
11506260 AATAGGTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
126 22 0.25
127 38 0.43
128 19 0.21
129 10 0.11
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (128 bp):
TAAATATATATTTTAAAAATTAAGATAAGAATAAAATATAATTTTTAAGTGAAAATAAGAATAAA
ATATATTGTTAAGTGAAAATAAAAATAAAAATATATTTTTATATTGAAATAATAATAAAATAT
Found at i:11506275 original size:24 final size:24
Alignment explanation
Indices: 11506244--11506299 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
11506234 TATTAAAATA
*
11506244 AAAATAAAATATATTTAATAGGTT
1 AAAATAAAATATATTTAATAAGTT
* *
11506268 AAAAT-AAATGTATTTGATAAGTT
1 AAAATAAAATATATTTAATAAGTT
*
11506291 AAGATAAAA
1 AAAATAAAA
11506300 ATAAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (24 bp):
AAAATAAAATATATTTAATAAGTT
Found at i:11506312 original size:30 final size:29
Alignment explanation
Indices: 11506024--11506335 Score: 147
Period size: 30 Copynumber: 10.3 Consensus size: 29
11506014 AAGATATTTA
*
11506024 AAAAATAAATATATACTTTTAAAAGTTAAGAT
1 AAAAATAAA-ATATA--TTTATAAGTTAAGAT
* * * *
11506056 AATAATAAAATATAATTTTTAATTTAAAAT
1 AAAAATAAAATAT-ATTTATAAGTTAAGAT
* *
11506086 AAGAATAAAATATATTGT-TAAGTGAAGAT
1 AAAAATAAAATATATT-TATAAGTTAAGAT
* * *
11506115 AAGAATAAAAATATATTTTTATA-TTGAAATAAT
1 AAAAAT-AAAATATATTTATA-AGTT--AA-GAT
* *
11506148 AATAAAATATTAAATATATTTTTAAAAATTAAGAT
1 -A-AAAATA--AAATATA--TTTATAAGTTAAGAT
* * * * *
11506183 AAGAATAAAATCTATTTTTAAGTGAAAAT
1 AAAAATAAAATATATTTATAAGTTAAGAT
** * *
11506212 AACGATAAAATGTATATTTTTATA-TTAAAAT
1 AAAAATAAAA--TATATTTATA-AGTTAAGAT
*
11506243 AAAAATAAAATATA-TT-TAA--T-AGGT
1 AAAAATAAAATATATTTATAAGTTAAGAT
* *
11506267 TAAAAT-AAATGTATTTGATAAGTTAAGAT
1 AAAAATAAAATATATTT-ATAAGTTAAGAT
*
11506296 AAAAATAAAATATATTTGATAAGTTAAGAC
1 AAAAATAAAATATATTT-ATAAGTTAAGAT
11506326 AAAAATAAAA
1 AAAAATAAAA
11506336 AAAATATTTT
Statistics
Matches: 219, Mismatches: 36, Indels: 52
0.71 0.12 0.17
Matches are distributed among these distances:
23 6 0.03
24 9 0.04
25 1 0.00
26 4 0.02
27 2 0.01
28 3 0.01
29 48 0.22
30 68 0.31
31 34 0.16
32 12 0.05
33 7 0.03
34 3 0.01
35 6 0.03
36 9 0.04
37 1 0.00
38 6 0.03
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (29 bp):
AAAAATAAAATATATTTATAAGTTAAGAT
Found at i:11507853 original size:21 final size:20
Alignment explanation
Indices: 11507823--11507861 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
11507813 AATATAATTT
*
11507823 TGGAGTTAAAGATGGTTTATA
1 TGGAGATAAA-ATGGTTTATA
*
11507844 TGGAGATAAATTGGTTTA
1 TGGAGATAAAATGGTTTA
11507862 AGCATGTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (20 bp):
TGGAGATAAAATGGTTTATA
Found at i:11508090 original size:24 final size:22
Alignment explanation
Indices: 11508048--11508126 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 22
11508038 GAATGCAATT
11508048 AGTGCATCGATGCA---TAAGG
1 AGTGCATCGATGCACTGTAAGG
11508067 AGTGCATCGATGCACATGTAAAGG
1 AGTGCATCGATGCAC-TGT-AAGG
*
11508091 -GATGCATCGATACACTGT-A-G
1 AG-TGCATCGATGCACTGTAAGG
*
11508111 AATGCATCGATGCACT
1 AGTGCATCGATGCACT
11508127 TCAAGGGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
19 14 0.28
20 14 0.28
21 1 0.02
23 5 0.10
24 16 0.32
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.23
Consensus pattern (22 bp):
AGTGCATCGATGCACTGTAAGG
Found at i:11512177 original size:20 final size:22
Alignment explanation
Indices: 11512101--11512177 Score: 65
Period size: 24 Copynumber: 3.6 Consensus size: 22
11512091 ATGCAATTAG
*
11512101 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAA
*
11512120 TGCATCGATGCACATGTAAAGGGA
1 TGCATCGATGCAC-TGT-AAGGAA
* *
11512144 TGCATCCATACACTGT-A-GAA
1 TGCATCGATGCACTGTAAGGAA
11512164 TGCATCGATGCACT
1 TGCATCGATGCACT
11512178 TCAAGGGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
19 12 0.26
20 14 0.30
21 1 0.02
23 4 0.09
24 15 0.33
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAA
Found at i:11519400 original size:21 final size:21
Alignment explanation
Indices: 11519376--11519417 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11519366 CCAGAATGGG
*
11519376 GGGAATCGGTACCCATTCATA
1 GGGAATCGATACCCATTCATA
*
11519397 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCATTCATA
11519418 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCATTCATA
Found at i:11519526 original size:30 final size:31
Alignment explanation
Indices: 11519491--11519551 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
11519481 AAATTTTGAA
11519491 TAAATTCAATTCAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
11519521 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
11519552 CCTTAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:11521015 original size:31 final size:31
Alignment explanation
Indices: 11520917--11521007 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
11520907 CAATTTAAGG
11520917 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
11520948 CAAAATGGTTTTTGGACTTGAATTAAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
11520979 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
11521008 TTCAAAATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.17
30 12 0.21
31 36 0.62
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:11521107 original size:21 final size:21
Alignment explanation
Indices: 11521081--11521122 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11521071 ATTTGAATAT
*
11521081 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11521102 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11521123 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:11522912 original size:18 final size:19
Alignment explanation
Indices: 11522886--11522933 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
11522876 GACGACTCTG
* *
11522886 ACGATGAACCAGAAC-AGC
1 ACGAGGAACAAGAACGAGC
*
11522904 ACGAGGAACAAGCACGAGC
1 ACGAGGAACAAGAACGAGC
11522923 A-GAGGAACAAG
1 ACGAGGAACAAG
11522934 CACATCCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.46, C:0.23, G:0.29, T:0.02
Consensus pattern (19 bp):
ACGAGGAACAAGAACGAGC
Found at i:11522934 original size:18 final size:19
Alignment explanation
Indices: 11522901--11522936 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
11522891 GAACCAGAAC
11522901 AGCACGAGGAACAAGCACG
1 AGCACGAGGAACAAGCACG
11522920 AGCA-GAGGAACAAGCAC
1 AGCACGAGGAACAAGCAC
11522937 ATCCAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.44, C:0.25, G:0.31, T:0.00
Consensus pattern (19 bp):
AGCACGAGGAACAAGCACG
Found at i:11523625 original size:16 final size:16
Alignment explanation
Indices: 11523604--11523635 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11523594 AGGGGGAGTA
11523604 ATTTCAAACTTGATTT
1 ATTTCAAACTTGATTT
11523620 ATTTCAAACTTGATTT
1 ATTTCAAACTTGATTT
11523636 CAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTCAAACTTGATTT
Found at i:11526545 original size:2 final size:2
Alignment explanation
Indices: 11526538--11526572 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11526528 TGATTCAATC
11526538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11526573 ATTTCTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11531495 original size:23 final size:22
Alignment explanation
Indices: 11531469--11531513 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
11531459 AATTTGACAA
*
11531469 ACTAAAAATCCTAATTAATAAAT
1 ACTAAAAATCCTAAATAA-AAAT
11531492 ACTAAAAATCCTAAATAAAAAT
1 ACTAAAAATCCTAAATAAAAAT
11531514 TCCATGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (22 bp):
ACTAAAAATCCTAAATAAAAAT
Found at i:11532426 original size:19 final size:20
Alignment explanation
Indices: 11532394--11532431 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11532384 AATTTTTTCT
*
11532394 TTTTCTTTTATTTTTTGTTA
1 TTTTCTATTATTTTTTGTTA
11532414 TTTTCTATT-TTTTTTGTT
1 TTTTCTATTATTTTTTGTT
11532432 CAAACGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTCTATTATTTTTTGTTA
Found at i:11532563 original size:4 final size:4
Alignment explanation
Indices: 11532554--11532579 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
11532544 ATAGGGGATA
11532554 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
11532580 GGCTTCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:11541224 original size:9 final size:9
Alignment explanation
Indices: 11541210--11541234 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11541200 CATGTTAGAG
11541210 AAGGGTTTC
1 AAGGGTTTC
11541219 AAGGGTTTC
1 AAGGGTTTC
11541228 AAGGGTT
1 AAGGGTT
11541235 ACCTCTGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.36, T:0.32
Consensus pattern (9 bp):
AAGGGTTTC
Found at i:11542403 original size:38 final size:36
Alignment explanation
Indices: 11542368--11542437 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
11542358 TACAAATTGT
11542368 AAAATATTTATAT-ATTTTCTTTAAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTT-AAAAAATTAAATTC
* *
11542405 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAATTAAA
11542438 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 10 0.33
37 15 0.50
38 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:11543170 original size:226 final size:225
Alignment explanation
Indices: 11542772--11543181 Score: 565
Period size: 226 Copynumber: 1.8 Consensus size: 225
11542762 GTTTAAACTA
* * * * *
11542772 ATGGAGCCTTATAAATTCAACAATGATAAAATAGGTTAATTATTAGAAACATTATCAACCATAAT
1 ATGGAGCCTTAGAAATCCAACAATAACAAAATAGGTTAATTACTAGAAACATTATCAACCATAAT
** *
11542837 AACATACAAATAGCGCTTATTTAATGCAATGGATAGCGTCTGTTTAAAGCTAACGAGACCTTAGA
66 AACATACAAATAGCAATTATTTAATGCAATGGATAGCGTCTGTTTAAAGCTAACGAGACCATAGA
* * *
11542902 AATCTGACAATAACAAAATAAGTTAATTACTTAATTTGTTATCAGTATTATCAACAAATTAGGTA
131 AATCCGACAATAACAAAATAAGTTAATTACTTAATATGTTATCAATATTATCAACAAATTAGGTA
11542967 GCACCTAAAATGTAACCAAAGTTTTAGTTG
196 GCACCTAAAATGTAACCAAAGTTTTAGTTG
* * *
11542997 ATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTAGATACATTATCAACCATAAT
1 ATGGAGCCTTAGAAATCCAACAATAACAAAATAGGTTAATTACTAGAAACATTATCAACCATAAT
* * * *
11543062 AACATAACAACTAGCAATTATTTAATGTAATAGG-TAGCG-CTTGTTTAAAGCTGATG-GAGCCA
66 AACAT-ACAAATAGCAATTATTTAATGCAAT-GGATAGCGTC-TGTTTAAAGCTAACGAGA-CCA
* * * *
11543124 TAGAAATCCGGCGATAACAAAATAGGTTAATTACTTGATATGTTATCAATATTATCAA
127 TAGAAATCCGACAATAACAAAATAAGTTAATTACTTAATATGTTATCAATATTATCAA
11543182 ATATTACTGT
Statistics
Matches: 159, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
225 65 0.41
226 92 0.58
227 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (225 bp):
ATGGAGCCTTAGAAATCCAACAATAACAAAATAGGTTAATTACTAGAAACATTATCAACCATAAT
AACATACAAATAGCAATTATTTAATGCAATGGATAGCGTCTGTTTAAAGCTAACGAGACCATAGA
AATCCGACAATAACAAAATAAGTTAATTACTTAATATGTTATCAATATTATCAACAAATTAGGTA
GCACCTAAAATGTAACCAAAGTTTTAGTTG
Found at i:11547063 original size:22 final size:18
Alignment explanation
Indices: 11547007--11547057 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
11546997 ACTTTGCTCA
* *
11547007 TCACATACATAATTTCAT
1 TCACATACAAAATTTTAT
11547025 TCACATACAAAATTTTAT
1 TCACATACAAAATTTTAT
11547043 TCACATACAAAATTT
1 TCACATACAAAATTT
11547058 GGTTTACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
TCACATACAAAATTTTAT
Found at i:11550501 original size:19 final size:19
Alignment explanation
Indices: 11550464--11550503 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11550454 GGAAAACTTA
* *
11550464 GTGCATCGGTGCACCAAAT
1 GTGCATCGATGCACAAAAT
*
11550483 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCACAAAAT
11550502 GT
1 GT
11550504 ATTCGATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (19 bp):
GTGCATCGATGCACAAAAT
Found at i:11550595 original size:64 final size:64
Alignment explanation
Indices: 11550482--11550605 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
11550472 GTGCACCAAA
* * ** *
11550482 TGTGCATCGATGCATAAAATGTATTCGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTGCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATTGCT
* *
11550546 TGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAA-AACCCAAGTGCATCGATGCAT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCCAAGTGCATCGATGCAT
11550606 GAAATGCATT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
64 50 0.96
65 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATTGCT
Found at i:11557222 original size:22 final size:21
Alignment explanation
Indices: 11557180--11557219 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11557170 AAGACTATTT
11557180 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
11557201 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
11557220 ATAGAGTCTT
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:11557401 original size:15 final size:15
Alignment explanation
Indices: 11557361--11557401 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
11557351 ACTTCTTGTT
*
11557361 CCTCTTCATCAGAAC
1 CCTCTTCATCGGAAC
11557376 CCTCTTCATCGGAAC
1 CCTCTTCATCGGAAC
11557391 CCTCTTCATCG
1 CCTCTTCATCG
11557402 CTCCATGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.20, C:0.41, G:0.10, T:0.29
Consensus pattern (15 bp):
CCTCTTCATCGGAAC
Found at i:11559190 original size:19 final size:19
Alignment explanation
Indices: 11559153--11559191 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
11559143 GGAACACTTA
* *
11559153 GTGCATCGGTGCACCAAAT
1 GTGCATCGATGCACAAAAT
*
11559172 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCACAAAAT
11559191 G
1 G
11559192 CATTCGATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCACAAAAT
Found at i:11561318 original size:201 final size:196
Alignment explanation
Indices: 11560817--11561337 Score: 495
Period size: 201 Copynumber: 2.6 Consensus size: 196
11560807 TTTTCATTTA
* * * * * * **
11560817 TTTTCAATTCCTAAAGTATCAATACTATGATACATATACTTATAAAAGTATTGATAC---CGTCA
1 TTTTAAATTCATAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
* * * * * *
11560879 A-CATATC-ATGTAG-AGCTTTACCGGTTTTGTCATAGTGAAACCAGTTTTGTCAAATTTCAACA
66 ATCAT-TCTA-GAAGCA-CTTTA-CGGTTTTCTCAAACTGAAACCGGTTTTGTCAAACTTCAACA
*
11560941 TGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCAATACTTTATAGGCGCTATTATTGC
127 TGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCAATACTTTATAGGCGCTATTATTCC
11561006 AATTC
192 AATTC
* *
11561011 TTTTAAATTCCTAAAGTACCAATACTTTGGTGCATATACTTATAAAAGTATCGATACAAATTTCA
1 TTTTAAATTCATAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
* * * * *
11561076 ATCATTCTAGAATCACTTTACAAGTTTTTTCAAACTGAAACCGGTTTTTTTAAACTTCAACATGT
66 ATCATTCTAGAAGCACTTTAC-GGTTTTCTCAAACTGAAACCGGTTTTGTCAAACTTCAACATGT
* * * ** *
11561141 TATATTTTCATGTATCGATACATGTGTGTAAGGTATCGATACTTTCGAGATATTTTC-CT-TTTT
130 TATATTGTCATGTATCGATACATGTGTCTAAGGTATCAATACTTT----ATA--GGCGCTATTAT
*
11561204 TCCATTTC
189 TCCAATTC
* ** * * *
11561212 TTTTAAATTCATACAGTACTGATACTTTGGTACATATACTTATACACGTATCGATACATATTTCA
1 TTTTAAATTCATAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
* * * *
11561277 A-CAATT-TCGATAGCTCTTTATCGGTTTTCTCAAATTGAAACCGGTTTTGTCAAATTTCAAC
66 ATC-ATTCTAGA-AGCACTTTA-CGGTTTTCTCAAACTGAAACCGGTTTTGTCAAACTTCAAC
11561338 TGGTTTTGTC
Statistics
Matches: 268, Mismatches: 43, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
194 51 0.19
196 1 0.00
197 90 0.34
198 5 0.02
200 4 0.01
201 113 0.42
202 3 0.01
203 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (196 bp):
TTTTAAATTCATAAAGTACCAATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
ATCATTCTAGAAGCACTTTACGGTTTTCTCAAACTGAAACCGGTTTTGTCAAACTTCAACATGTT
ATATTGTCATGTATCGATACATGTGTCTAAGGTATCAATACTTTATAGGCGCTATTATTCCAATT
C
Found at i:11561342 original size:20 final size:20
Alignment explanation
Indices: 11561299--11561419 Score: 95
Period size: 20 Copynumber: 6.0 Consensus size: 20
11561289 GCTCTTTATC
* ** *
11561299 GGTTTTCTCAAATTGAAACC
1 GGTTTTGTCAAATTTCAACT
11561319 GGTTTTGTCAAATTTCAACT
1 GGTTTTGTCAAATTTCAACT
11561339 GGTTTTGTC-AATTTCCAA-T
1 GGTTTTGTCAAATTT-CAACT
* * *
11561358 CGATTTTGTCAAATTCGTTACCT
1 -GGTTTTGTCAAATT--TCAACT
**
11561381 -GTTTTGTCAAATTGAAACT
1 GGTTTTGTCAAATTTCAACT
*
11561400 GGATTTGTCAAATTTCAACT
1 GGTTTTGTCAAATTTCAACT
11561420 TGTTATATTC
Statistics
Matches: 80, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
19 9 0.11
20 52 0.65
21 16 0.20
22 1 0.01
23 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (20 bp):
GGTTTTGTCAAATTTCAACT
Found at i:11562014 original size:15 final size:15
Alignment explanation
Indices: 11561990--11562020 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11561980 TGGAAAAAAT
*
11561990 AAATATATTAAATTA
1 AAATAAATTAAATTA
11562005 AAATAAATTAAATTA
1 AAATAAATTAAATTA
11562020 A
1 A
11562021 TTTTAATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATAAATTAAATTA
Found at i:11572253 original size:17 final size:17
Alignment explanation
Indices: 11572231--11572266 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11572221 GAAAATCCGA
* *
11572231 CTCTCAACTTTGAAACT
1 CTCTCAACTCTCAAACT
11572248 CTCTCAACTCTCAAACT
1 CTCTCAACTCTCAAACT
11572265 CT
1 CT
11572267 ATCTACTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.33
Consensus pattern (17 bp):
CTCTCAACTCTCAAACT
Found at i:11572827 original size:26 final size:26
Alignment explanation
Indices: 11572798--11572871 Score: 130
Period size: 26 Copynumber: 2.8 Consensus size: 26
11572788 ATGGAGGGAT
*
11572798 CAATTCAATTATCTTGCAGTGGAAAC
1 CAATTCAATCATCTTGCAGTGGAAAC
11572824 CAATTCAATCATCTTGCAGTGGAAAC
1 CAATTCAATCATCTTGCAGTGGAAAC
*
11572850 CAATTCAATCATCTTGCGGTGG
1 CAATTCAATCATCTTGCAGTGG
11572872 CCCTCCCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (26 bp):
CAATTCAATCATCTTGCAGTGGAAAC
Found at i:11579354 original size:12 final size:12
Alignment explanation
Indices: 11579329--11579362 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
11579319 TTATCTCACC
11579329 TTTATTTTTATA
1 TTTATTTTTATA
11579341 TTTATATTTT-TA
1 TTTAT-TTTTATA
11579353 TTTATTTTTA
1 TTTATTTTTA
11579363 ATCTTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.20
12 12 0.60
13 4 0.20
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTTATA
Found at i:11581814 original size:342 final size:342
Alignment explanation
Indices: 11581189--11581872 Score: 1368
Period size: 342 Copynumber: 2.0 Consensus size: 342
11581179 GAAGGATCAA
11581189 GATATGTTCGCCATGTAACACCTCCAACCCGTACCTGACCCGGATACGAATCTGAGGTGTCACAT
1 GATATGTTCGCCATGTAACACCTCCAACCCGTACCTGACCCGGATACGAATCTGAGGTGTCACAT
11581254 TGACTTTTCAAAACTTTGACTCTTACAAAATCATGAAAATCTAAACTTTCATTAAAATAAAATTA
66 TGACTTTTCAAAACTTTGACTCTTACAAAATCATGAAAATCTAAACTTTCATTAAAATAAAATTA
11581319 GTTAAGTTACATAAGTTTGACCAAAATAATACAAAATAGATCAGAGCATATGTAATTCACAACTT
131 GTTAAGTTACATAAGTTTGACCAAAATAATACAAAATAGATCAGAGCATATGTAATTCACAACTT
11581384 TGTCTACATGCCAACACACTTGATACAACAAAATACATACTTTGCAAATTACTTCTGATCTGATC
196 TGTCTACATGCCAACACACTTGATACAACAAAATACATACTTTGCAAATTACTTCTGATCTGATC
11581449 TGCTGGTAGAGGCATGTTGTCTCTGCAAATCTTGATTCAGACCCTCCTGCTTTTTGGTACCTACA
261 TGCTGGTAGAGGCATGTTGTCTCTGCAAATCTTGATTCAGACCCTCCTGCTTTTTGGTACCTACA
11581514 TGTGAAACAGTCACACG
326 TGTGAAACAGTCACACG
11581531 GATATGTTCGCCATGTAACACCTCCAACCCGTACCTGACCCGGATACGAATCTGAGGTGTCACAT
1 GATATGTTCGCCATGTAACACCTCCAACCCGTACCTGACCCGGATACGAATCTGAGGTGTCACAT
11581596 TGACTTTTCAAAACTTTGACTCTTACAAAATCATGAAAATCTAAACTTTCATTAAAATAAAATTA
66 TGACTTTTCAAAACTTTGACTCTTACAAAATCATGAAAATCTAAACTTTCATTAAAATAAAATTA
11581661 GTTAAGTTACATAAGTTTGACCAAAATAATACAAAATAGATCAGAGCATATGTAATTCACAACTT
131 GTTAAGTTACATAAGTTTGACCAAAATAATACAAAATAGATCAGAGCATATGTAATTCACAACTT
11581726 TGTCTACATGCCAACACACTTGATACAACAAAATACATACTTTGCAAATTACTTCTGATCTGATC
196 TGTCTACATGCCAACACACTTGATACAACAAAATACATACTTTGCAAATTACTTCTGATCTGATC
11581791 TGCTGGTAGAGGCATGTTGTCTCTGCAAATCTTGATTCAGACCCTCCTGCTTTTTGGTACCTACA
261 TGCTGGTAGAGGCATGTTGTCTCTGCAAATCTTGATTCAGACCCTCCTGCTTTTTGGTACCTACA
11581856 TGTGAAACAGTCACACG
326 TGTGAAACAGTCACACG
11581873 CTAAGTCACA
Statistics
Matches: 342, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
342 342 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (342 bp):
GATATGTTCGCCATGTAACACCTCCAACCCGTACCTGACCCGGATACGAATCTGAGGTGTCACAT
TGACTTTTCAAAACTTTGACTCTTACAAAATCATGAAAATCTAAACTTTCATTAAAATAAAATTA
GTTAAGTTACATAAGTTTGACCAAAATAATACAAAATAGATCAGAGCATATGTAATTCACAACTT
TGTCTACATGCCAACACACTTGATACAACAAAATACATACTTTGCAAATTACTTCTGATCTGATC
TGCTGGTAGAGGCATGTTGTCTCTGCAAATCTTGATTCAGACCCTCCTGCTTTTTGGTACCTACA
TGTGAAACAGTCACACG
Found at i:11582293 original size:21 final size:19
Alignment explanation
Indices: 11582237--11582294 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
11582227 TTAAGGATCA
* *
11582237 CATATATATTCCAAAGGAC
1 CATATATGTTCCAAAGAAC
*
11582256 CAAATATGTGTCTCAAAGAACC
1 CATATATGT-TC-CAAAGAA-C
11582278 GCATATATGTTCCAAAG
1 -CATATATGTTCCAAAG
11582295 GATTACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 7 0.23
20 2 0.06
21 11 0.35
22 3 0.10
23 8 0.26
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (19 bp):
CATATATGTTCCAAAGAAC
Found at i:11587531 original size:37 final size:36
Alignment explanation
Indices: 11587473--11587542 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
11587463 TATATATATA
*
11587473 TATATATATAATAAATATAATAATGAAAGTAATAATT
1 TATATATATAATAAATATAATAAT-AAAATAATAATT
*
11587510 TATATATATATTAAA-AGTAATAATAAAATAATA
1 TATATATATAATAAATA-TAATAATAAAATAATA
11587543 TTGAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 9 0.30
37 21 0.70
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (36 bp):
TATATATATAATAAATATAATAATAAAATAATAATT
Found at i:11587543 original size:25 final size:24
Alignment explanation
Indices: 11587480--11587543 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
11587470 ATATATATAT
*
11587480 ATAATAAATATAATA-ATGAAAGTA
1 ATAATAAA-ATAATATATAAAAGTA
**
11587504 ATAAT-TTATATATATATTAAAAGTA
1 ATAATAAAATA-ATATA-TAAAAGTA
11587529 ATAATAAAATAATAT
1 ATAATAAAATAATAT
11587544 TGAAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
22 3 0.10
23 3 0.10
24 6 0.19
25 16 0.52
26 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (24 bp):
ATAATAAAATAATATATAAAAGTA
Found at i:11587555 original size:24 final size:23
Alignment explanation
Indices: 11587480--11587559 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 23
11587470 ATATATATAT
* *
11587480 ATAATAAATATAATAATGAAAGTA
1 ATAATAAA-ATAATATTGAAAATA
* *
11587504 ATAATTTATATATATATT-AAAAGTA
1 ATAA-TAAAATA-ATATTGAAAA-TA
11587529 ATAATAAAATAATATTGAAAAT-
1 ATAATAAAATAATATTGAAAATA
11587551 A-AATAAAAT
1 ATAATAAAAT
11587560 TAAATCAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
21 8 0.17
22 1 0.02
23 6 0.13
24 19 0.41
25 12 0.26
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (23 bp):
ATAATAAAATAATATTGAAAATA
Found at i:11587604 original size:23 final size:23
Alignment explanation
Indices: 11587556--11587604 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
11587546 AAAATAAATA
* *
11587556 AAATTAAATCAACTACTAATAAT
1 AAATGAAATCAACAACTAATAAT
*
11587579 AAATGAAATCAA-AACTATATAGT
1 AAATGAAATCAACAACTA-ATAAT
11587602 AAA
1 AAA
11587605 AAGCAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (23 bp):
AAATGAAATCAACAACTAATAAT
Found at i:11588402 original size:3 final size:3
Alignment explanation
Indices: 11588394--11588446 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
11588384 GGCCTATTTG
**
11588394 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
11588439 TAA TAA TA
1 TAA TAA TA
11588447 TCAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:11588414 original size:15 final size:16
Alignment explanation
Indices: 11588389--11588421 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
11588379 ATTTTGGCCT
11588389 ATTTGTAATAATAATA
1 ATTTGTAATAATAATA
11588405 ATTT-TAATAATAATA
1 ATTTGTAATAATAATA
11588420 AT
1 AT
11588422 AATAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATTTGTAATAATAATA
Found at i:11588420 original size:21 final size:21
Alignment explanation
Indices: 11588394--11588455 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
11588384 GGCCTATTTG
* **
11588394 TAATAATAATAATTTTAATAA
1 TAATAATAATAAATAAAATAA
11588415 TAATAATAATAAATAAAATAA
1 TAATAATAATAAATAAAATAA
11588436 TAATAATAATATCAATAAAA
1 TAATAATAATA--AATAAAA
11588456 AATGGGTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 29 0.81
23 7 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TAATAATAATAAATAAAATAA
Found at i:11588452 original size:18 final size:18
Alignment explanation
Indices: 11588394--11588453 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
11588384 GGCCTATTTG
* *
11588394 TAATAATAATAATTTTAA
1 TAATAATAATAATATAAA
11588412 TAATAATAATAATAAATAAAA
1 TAATAATAATAAT--AT-AAA
*
11588433 TAATAATAATAATATCAA
1 TAATAATAATAATATAAA
11588451 TAA
1 TAA
11588454 AAAATGGGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 18 0.50
19 2 0.06
20 1 0.03
21 15 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATATAAA
Found at i:11589494 original size:124 final size:124
Alignment explanation
Indices: 11589356--11590068 Score: 1300
Period size: 124 Copynumber: 5.8 Consensus size: 124
11589346 ATGGATTTGA
*
11589356 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
11589421 ATTATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAT
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
11589480 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
11589545 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATATATCTCCTTCTGTGATAGAGTCAT
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
*
11589604 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
11589669 ATTATGAACTTTCTCTGGAAAAGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCAT
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
* *
11589728 GCAAAAGGTTGAACAAATTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
11589793 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
* * *
11589852 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAAATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
11589917 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTTTTTGATAGAGTCAT
66 ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
*
11589976 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
11590041 ATTATGAGCTTTCTCTGGAAAAGTTGAT
66 ATTATGAACTTTCTCTGGAAAAGTTGAT
11590069 CCATCAAGTG
Statistics
Matches: 569, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 569 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (124 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAT
Found at i:11590515 original size:22 final size:22
Alignment explanation
Indices: 11590436--11590512 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
11590426 AATAAAGCTT
* *
11590436 TCATCTTCGAAAAAAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
11590458 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
11590480 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
11590502 TCATCTTTGAA
1 TCATCTTTGAA
11590513 GAGTGTAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:11595282 original size:17 final size:17
Alignment explanation
Indices: 11595262--11595356 Score: 61
Period size: 17 Copynumber: 5.5 Consensus size: 17
11595252 ATTTCTCCCC
11595262 TTTTTCTTTTTCCTTTT
1 TTTTTCTTTTTCCTTTT
* * **
11595279 TTTTCCTTTTTTCTCAT
1 TTTTTCTTTTTCCTTTT
*
11595296 TTTTCCTTTTTCATCTTTT
1 TTTTTCTTTTTC--CTTTT
*
11595315 TTCTT-TTTTT-C-TTT
1 TTTTTCTTTTTCCTTTT
* *
11595329 TTTCTCATTTTTTCTTTT
1 TTTTTC-TTTTTCCTTTT
11595347 TTCTTTCTTT
1 TT-TTTCTTT
11595357 GTTGGATGAG
Statistics
Matches: 59, Mismatches: 12, Indels: 13
0.70 0.14 0.15
Matches are distributed among these distances:
14 6 0.10
15 1 0.02
16 5 0.08
17 25 0.42
18 13 0.22
19 9 0.15
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTTCCTTTT
Found at i:11595289 original size:24 final size:25
Alignment explanation
Indices: 11595262--11595349 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
11595252 ATTTCTCCCC
*
11595262 TTTTTC-TTTTTCCTTTTTTTTCCTT
1 TTTTTCATTTTTCCTTTTTTATCC-T
*
11595287 TTTTCTCATTTTTCCTTTTTCAT-CT
1 TTTT-TCATTTTTCCTTTTTTATCCT
* * * *
11595312 TTTTTCTTTTTTTCTTTTTTCTCAT
1 TTTTTCATTTTTCCTTTTTTATCCT
*
11595337 TTTTTCTTTTTTC
1 TTTTTCATTTTTC
11595350 TTTCTTTGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
24 14 0.27
25 22 0.42
26 3 0.06
27 13 0.25
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTCATTTTTCCTTTTTTATCCT
Found at i:11595298 original size:10 final size:9
Alignment explanation
Indices: 11595262--11595350 Score: 77
Period size: 8 Copynumber: 10.7 Consensus size: 9
11595252 ATTTCTCCCC
11595262 TTTT-TCTT
1 TTTTCTCTT
* *
11595270 TTTCCTTTT
1 TTTTCTCTT
11595279 TTTTC-CTT
1 TTTTCTCTT
*
11595287 TTTTCTCAT
1 TTTTCTCTT
11595296 TTTTC-C-T
1 TTTTCTCTT
11595303 TTTTCATC-T
1 TTTTC-TCTT
11595312 TTTT-TCTT
1 TTTTCTCTT
11595320 TTTT-TCTT
1 TTTTCTCTT
*
11595328 TTTTCTCAT
1 TTTTCTCTT
11595337 TTTT-TCTT
1 TTTTCTCTT
11595345 TTTTCT
1 TTTTCT
11595351 TTCTTTGTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
7 8 0.12
8 31 0.46
9 28 0.42
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:11595350 original size:24 final size:23
Alignment explanation
Indices: 11595262--11595352 Score: 101
Period size: 24 Copynumber: 3.7 Consensus size: 23
11595252 ATTTCTCCCC
* *
11595262 TTTTTCTTTTTCCTTTTTTTTCCT
1 TTTTTCTTTTTTCTTTTTTCT-CT
*
11595286 TTTTTCTCATTTTTCCTTTTTCATCT
1 TTTTTCT--TTTTTCTTTTTTC-TCT
11595312 TTTTTCTTTTTTTCTTTTTTCTCAT
1 TTTTTC-TTTTTTCTTTTTTCTC-T
11595337 TTTTTCTTTTTTCTTT
1 TTTTTCTTTTTTCTTT
11595353 CTTTGTTGGA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
24 19 0.33
25 19 0.33
26 18 0.31
27 2 0.03
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTTTTCTTTTTTCTCT
Found at i:11597747 original size:14 final size:15
Alignment explanation
Indices: 11597730--11597763 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11597720 ATAAAAGTAT
*
11597730 AAATGCACA-ATGAA
1 AAATGCAAAGATGAA
11597744 AAATGCAAAGATGAA
1 AAATGCAAAGATGAA
11597759 AAATG
1 AAATG
11597764 AAAATGCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.59, C:0.09, G:0.18, T:0.15
Consensus pattern (15 bp):
AAATGCAAAGATGAA
Found at i:11597759 original size:15 final size:14
Alignment explanation
Indices: 11597730--11597769 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
11597720 ATAAAAGTAT
*
11597730 AAATGCACAATGAA
1 AAATGCAAAATGAA
11597744 AAATGCAAAGATGAA
1 AAATGCAAA-ATGAA
11597759 AAATG-AAAATG
1 AAATGCAAAATG
11597770 CATGTATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 3 0.12
14 11 0.46
15 10 0.42
ACGTcount: A:0.60, C:0.07, G:0.17, T:0.15
Consensus pattern (14 bp):
AAATGCAAAATGAA
Found at i:11601028 original size:2 final size:2
Alignment explanation
Indices: 11601021--11601076 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
11601011 ATTTAAACCA
11601021 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
*
11601063 AT AT A- AT AA AT AT A
1 AT AT AT AT AT AT AT A
11601077 ATAATGAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11601150 original size:10 final size:10
Alignment explanation
Indices: 11601135--11601159 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11601125 ATATTGCAAA
11601135 TAAATAAAAT
1 TAAATAAAAT
11601145 TAAATAAAAT
1 TAAATAAAAT
11601155 TAAAT
1 TAAAT
11601160 CAACTACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TAAATAAAAT
Found at i:11602428 original size:3 final size:3
Alignment explanation
Indices: 11602420--11602475 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
11602410 GGCCTGTTTG
**
11602420 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
11602465 TAA TAA TAA TA
1 TAA TAA TAA TA
11602476 TCAATAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:11602481 original size:21 final size:21
Alignment explanation
Indices: 11602420--11602482 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
11602410 GGCCTGTTTG
* *
11602420 TAATAATAATAATTTTAATAA
1 TAATAATAATAATATAAATAA
11602441 TAATAATAATAA-ATAAAATAA
1 TAATAATAATAATAT-AAATAA
*
11602462 TAATAATAATAATATCAATAA
1 TAATAATAATAATATAAATAA
11602483 AAAATGGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 1 0.03
21 34 0.92
22 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATAATAATAATATAAATAA
Found at i:11603261 original size:5 final size:5
Alignment explanation
Indices: 11603253--11603277 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11603243 TTTCATTCCA
11603253 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
11603278 CAGAGGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:11609843 original size:2 final size:2
Alignment explanation
Indices: 11609803--11609827 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11609793 CTTAATTTAA
11609803 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11609828 ATTTATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11610458 original size:12 final size:12
Alignment explanation
Indices: 11610407--11610521 Score: 51
Period size: 12 Copynumber: 9.7 Consensus size: 12
11610397 TATTATATAA
*
11610407 TTTTGAAAACA-
1 TTTTGAAAATAT
11610418 TTTTGAAAATAT
1 TTTTGAAAATAT
* * *
11610430 ATATT--ATATAA
1 -TTTTGAAAATAT
11610441 TTTTGAAAATAT
1 TTTTGAAAATAT
11610453 TTTTGAAAATAT
1 TTTTGAAAATAT
* * **
11610465 ATATT--ATATGG
1 -TTTTGAAAATAT
*
11610476 TTTTAAAAATATT
1 TTTTGAAAATA-T
**
11610489 TTTTGAAAATGG
1 TTTTGAAAATAT
*
11610501 TTTTGAAAACAAT
1 TTTTGAAAA-TAT
11610514 TTTTGAAA
1 TTTTGAAA
11610522 GTATATATAA
Statistics
Matches: 74, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
10 6 0.08
11 17 0.23
12 28 0.38
13 23 0.31
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.46
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:11610464 original size:35 final size:35
Alignment explanation
Indices: 11610380--11610498 Score: 168
Period size: 35 Copynumber: 3.3 Consensus size: 35
11610370 TTAGAAAACG
*
11610380 ATTTTTGAAAATATATATATTATATAATTTTGAAAAC
1 ATTTTTG-AAA-ATATATATTATATAATTTTGAAAAT
11610417 A-TTTTGAAAATATATATTATATAATTTTGAAAAT
1 ATTTTTGAAAATATATATTATATAATTTTGAAAAT
** *
11610451 ATTTTTGAAAATATATATTATATGGTTTTAAAAAT
1 ATTTTTGAAAATATATATTATATAATTTTGAAAAT
11610486 ATTTTTTGAAAAT
1 A-TTTTTGAAAAT
11610499 GGTTTTGAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
34 25 0.33
35 34 0.45
36 16 0.21
37 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.48
Consensus pattern (35 bp):
ATTTTTGAAAATATATATTATATAATTTTGAAAAT
Found at i:11610503 original size:25 final size:25
Alignment explanation
Indices: 11610472--11610521 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
11610462 TATATATTAT
* *
11610472 ATGGTTTTAAAAATATTTTTTGAAA
1 ATGGTTTTAAAAACAATTTTTGAAA
*
11610497 ATGGTTTTGAAAACAATTTTTGAAA
1 ATGGTTTTAAAAACAATTTTTGAAA
11610522 GTATATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (25 bp):
ATGGTTTTAAAAACAATTTTTGAAA
Found at i:11610616 original size:21 final size:18
Alignment explanation
Indices: 11610589--11610635 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
11610579 ATAAATATTA
11610589 TTTATTTCTATTTATTATTT
1 TTTATTT-TATTTATT-TTT
*
11610609 TATTATTTTTTTTATTTTT
1 T-TTATTTTATTTATTTTT
11610628 TTTATTTT
1 TTTATTTT
11610636 TGTTTAAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 8 0.32
21 6 0.24
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTATTTTATTTATTTTT
Found at i:11610626 original size:8 final size:9
Alignment explanation
Indices: 11610589--11610641 Score: 61
Period size: 9 Copynumber: 5.4 Consensus size: 9
11610579 ATAAATATTA
*
11610589 TTTATTTCTA
1 TTTATTT-TT
11610599 TTTATTATTT
1 TTTATT-TTT
11610609 TATTATTTTT
1 T-TTATTTTT
11610619 TTTATTTTT
1 TTTATTTTT
11610628 TTTATTTTT
1 TTTATTTTT
11610637 GTTTA
1 -TTTA
11610642 AGGTCCAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
9 17 0.44
10 16 0.41
11 6 0.15
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTATTTTT
Found at i:11611511 original size:18 final size:18
Alignment explanation
Indices: 11611488--11611525 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11611478 AGTTGAGAGG
11611488 TTTTTTTAGAGGTTTGGTT
1 TTTTTTTAG-GGTTTGGTT
*
11611507 TTTTTTTTGGGTTTGGTT
1 TTTTTTTAGGGTTTGGTT
11611525 T
1 T
11611526 AAAAATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.05, C:0.00, G:0.26, T:0.68
Consensus pattern (18 bp):
TTTTTTTAGGGTTTGGTT
Found at i:11612081 original size:28 final size:28
Alignment explanation
Indices: 11612050--11612107 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
11612040 TATATCCTTC
11612050 TTTAATTAATTAATTTATTT-AT-TTTCTT
1 TTTAATTAATT--TTTATTTGATATTTCTT
*
11612078 TTTATTTAATTTTTATTTGATATTTCTT
1 TTTAATTAATTTTTATTTGATATTTCTT
11612106 TT
1 TT
11612108 ATTTTACCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 7 0.26
27 2 0.07
28 18 0.67
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (28 bp):
TTTAATTAATTTTTATTTGATATTTCTT
Found at i:11614951 original size:15 final size:15
Alignment explanation
Indices: 11614931--11614961 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11614921 TTTTTCAGGG
*
11614931 TTTTCGGGTTCTTCC
1 TTTTCGGGATCTTCC
11614946 TTTTCGGGATCTTCC
1 TTTTCGGGATCTTCC
11614961 T
1 T
11614962 CTTCTTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.26, G:0.19, T:0.52
Consensus pattern (15 bp):
TTTTCGGGATCTTCC
Found at i:11614969 original size:3 final size:3
Alignment explanation
Indices: 11614955--11615004 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
11614945 CTTTTCGGGA
* * * * *
11614955 TCT TCC TCT TCT TCT TCT TTT TTT TCT TCA TCT TCT TCT TCA TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
11615003 TC
1 TC
11615005 AGGGGGATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:11614993 original size:12 final size:12
Alignment explanation
Indices: 11614955--11615004 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
11614945 CTTTTCGGGA
*
11614955 TCTTCCTCTTCT
1 TCTTCATCTTCT
* * *
11614967 TCTTCTTTTTTT
1 TCTTCATCTTCT
11614979 TCTTCATCTTCT
1 TCTTCATCTTCT
11614991 TCTTCATCTTCT
1 TCTTCATCTTCT
11615003 TC
1 TC
11615005 AGGGGGATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (12 bp):
TCTTCATCTTCT
Found at i:11616934 original size:20 final size:20
Alignment explanation
Indices: 11616909--11616959 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
11616899 ATGTAGTCCT
11616909 TTGACCAACGTTTTTCATCG
1 TTGACCAACGTTTTTCATCG
11616929 TTGACCAACGTTTTTCATCG
1 TTGACCAACGTTTTTCATCG
11616949 TTGACCAACGT
1 TTGACCAACGT
11616960 CTCCATTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (20 bp):
TTGACCAACGTTTTTCATCG
Found at i:11617500 original size:25 final size:25
Alignment explanation
Indices: 11617472--11617553 Score: 101
Period size: 25 Copynumber: 3.1 Consensus size: 25
11617462 TTTATAGAGT
11617472 TTATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
* *
11617497 TTATAATTTTGGGAATATTTTTTATTCAA
1 TTATAATTTT--GAA-A-TTTTAATTTAA
*
11617526 TCATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
11617551 TTA
1 TTA
11617554 ATATTATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 21 0.45
26 1 0.02
27 6 0.13
28 1 0.02
29 18 0.38
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (25 bp):
TTATAATTTTGAAATTTTAATTTAA
Found at i:11617549 original size:29 final size:28
Alignment explanation
Indices: 11617474--11617555 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
11617464 TATAGAGTTT
*
11617474 ATAATTTTGAAATTTTAA--T-TTAATT
1 ATAATTTTGAAATTTTAATTTATTAATC
*
11617499 ATAATTTTGGGAATATTT--TTTATTCAATC
1 ATAATTTT-GAAAT-TTTAATTTATT-AATC
11617528 ATAATTTTGAAATTTTAATTTAATTAAT
1 ATAATTTTGAAATTTTAATTT-ATTAAT
11617556 ATTATTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
25 8 0.18
26 4 0.09
27 7 0.16
28 6 0.13
29 17 0.38
30 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (28 bp):
ATAATTTTGAAATTTTAATTTATTAATC
Found at i:11618394 original size:5 final size:5
Alignment explanation
Indices: 11618384--11618507 Score: 70
Period size: 5 Copynumber: 25.6 Consensus size: 5
11618374 GAAAACATAG
*
11618384 AAATA AAATA AAA-A CAAAAA CAAATA AAA-A CAAAT- AAAT- AAATA
1 AAATA AAATA AAATA -AAATA -AAATA AAATA -AAATA AAATA AAATA
*
11618428 AAAT- AAATA AATAAA AAATA AAGATA AAA-A CAAAT- AAATA AAAT-
1 AAATA AAATA AA-ATA AAATA AA-ATA AAATA -AAATA AAATA AAATA
* * * *
11618472 AAA-C AAATC AAAGA AAA-A AAATA AAATA AAGTA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
11618508 AATATTAAAC
Statistics
Matches: 98, Mismatches: 7, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
4 29 0.30
5 54 0.55
6 15 0.15
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:11618424 original size:4 final size:4
Alignment explanation
Indices: 11618415--11618532 Score: 75
Period size: 4 Copynumber: 29.0 Consensus size: 4
11618405 AAATAAAAAC
* *
11618415 AAAT AAAT AAAT AAAAT AAAT AAAT AAA- AAAT AAAG ATAA- AAAC AAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
* * *
11618463 AAAT AAAAT AAAC AAAT CAAAGA AAAA AAAT AAAAT AAAGT AAA- AAAT
1 AAAT -AAAT AAAT AAAT -AAA-T AAAT AAAT -AAAT AAA-T AAAT AAAT
* *
11618511 -ATT AAAC AAAT -AAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT
11618533 CAAAGGGAGG
Statistics
Matches: 92, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
3 13 0.14
4 55 0.60
5 24 0.26
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:11618440 original size:31 final size:30
Alignment explanation
Indices: 11618384--11618532 Score: 108
Period size: 31 Copynumber: 4.8 Consensus size: 30
11618374 GAAAACATAG
* *
11618384 AAATAAAATAAAAACAA-AAACAAATAAAAA
1 AAAT-AAATAAAAAAAATAAATAAATAAAAA
*
11618414 CAAATAAATAAATAAAATAAATAAATAAAAA
1 -AAATAAATAAAAAAAATAAATAAATAAAAA
* *
11618445 ATAA-AGATAAAAACAAATAAATAAA-ATAAAC
1 A-AATAAATAAAAA-AAATAAATAAATA-AAAA
*
11618476 AAATCAAAGAAAAAAAATAAAATAAAGTAAAAA
1 AAAT-AAATAAAAAAAAT-AAATAAA-TAAAAA
* * * *
11618509 ATATTAA-ACAAATAATAAATAAAT
1 AAATAAATAAAAAAAATAAATAAAT
11618533 CAAAGGGAGG
Statistics
Matches: 96, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
29 1 0.01
30 28 0.29
31 44 0.46
32 16 0.17
33 6 0.06
34 1 0.01
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.17
Consensus pattern (30 bp):
AAATAAATAAAAAAAATAAATAAATAAAAA
Found at i:11618521 original size:11 final size:10
Alignment explanation
Indices: 11618406--11618532 Score: 50
Period size: 10 Copynumber: 12.0 Consensus size: 10
11618396 AACAAAAACA
11618406 AATAAAAACA-
1 AATAAAAA-AT
11618416 AATAAATAAAT
1 AATAAA-AAAT
*
11618427 AA-AATAAAT
1 AATAAAAAAT
11618436 AAATAAAAAAT
1 -AATAAAAAAT
11618447 AAAGATAAAAACA-
1 --A-ATAAAAA-AT
*
11618460 AATAAATAA-
1 AATAAAAAAT
11618469 AATAAACAAAT
1 AATAAA-AAAT
*
11618480 CAA-AGAAAAAA
1 -AATA-AAAAAT
11618491 AATAAAATAA-
1 AATAAAA-AAT
*
11618501 AGTAAAAAAT
1 AATAAAAAAT
*
11618511 ATTAAACAAAT
1 AATAAA-AAAT
11618522 AATAAATAAAT
1 AATAAA-AAAT
11618533 CAAAGGGAGG
Statistics
Matches: 93, Mismatches: 9, Indels: 29
0.71 0.07 0.22
Matches are distributed among these distances:
9 13 0.14
10 35 0.38
11 31 0.33
12 6 0.06
13 7 0.08
14 1 0.01
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:11619952 original size:40 final size:38
Alignment explanation
Indices: 11619855--11620259 Score: 304
Period size: 40 Copynumber: 10.6 Consensus size: 38
11619845 TTCAAAAACA
*
11619855 TTTTCAAAACTATATATTATATA-TA-TTT-AAAATTGT
1 TTTTAAAAACTATATATTATATATTATTTTCAAAA-TGT
* * *
11619891 TTTCATGAAATTATATATTATATATGTATTTTCAAAATGT
1 TTTTA-AAAACTATATATTATATAT-TATTTTCAAAATGT
* *
11619931 ATTTTAAAAACTATATATTATATATATGTTTTCAAAATAT
1 -TTTTAAAAACTATATATTATATAT-TATTTTCAAAATGT
*
11619971 TTTTAAAAAACTATATATTATATATATGTTTTCAAAATG-
1 TTTT-AAAAACTATATATTATATAT-TATTTTCAAAATGT
* * * *
11620010 TTTTCAAAACTATATAATATATA-TGTTTTCAAATACTAT
1 TTTTAAAAACTATATATTATATATTATTTTCAAA-A-TGT
* * * *
11620049 ATATATATATATA-TATATATATATATATATATATTAAAAATGT
1 -T-T-T-TAAAAACTATATAT-TATATAT-TATTTTCAAAATGT
* *
11620092 TTTCAAAAACTATATATTATATA-TATTTTCGAAAACGT
1 TTTTAAAAACTATATATTATATATTATTTTC-AAAATGT
* * *
11620130 TTTCAAAAACTATATATTATATA-TGTTTTCAAGAA--A
1 TTTTAAAAACTATATATTATATATTATTTTCAA-AATGT
11620166 TTTTAAAAACTATATA--ATATA-TATTTTCAAAATG-
1 TTTTAAAAACTATATATTATATATTATTTTCAAAATGT
*
11620200 TTTTCAAAACTATATA--ATATA-TATTTTCAAAAATCGCT
1 TTTTAAAAACTATATATTATATATTATTTTC-AAAAT-G-T
* *
11620238 TTCTAAAAATTATATATTATAT
1 TTTTAAAAACTATATATTATAT
11620260 TTTTCAGTAA
Statistics
Matches: 305, Mismatches: 36, Indels: 52
0.78 0.09 0.13
Matches are distributed among these distances:
33 2 0.01
34 40 0.13
35 5 0.02
36 29 0.10
37 24 0.08
38 68 0.22
39 19 0.06
40 81 0.27
41 10 0.03
42 8 0.03
43 11 0.04
44 1 0.00
45 7 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTAAAAACTATATATTATATATTATTTTCAAAATGT
Found at i:11620036 original size:25 final size:27
Alignment explanation
Indices: 11620007--11620121 Score: 105
Period size: 26 Copynumber: 4.3 Consensus size: 27
11619997 TGTTTTCAAA
11620007 ATGTTTTCAAA-ACTATATA-ATATAT
1 ATGTTTTCAAATACTATATATATATAT
11620032 ATGTTTTCAAATACTATATATATATAT
1 ATGTTTTCAAATACTATATATATATAT
* * * *
11620059 ATATATATAT-ATATA-TATATATATTAAAA
1 ATGT-T-T-TCAAATACTATATATA-TATAT
*
11620088 ATGTTTTCAAAAACTATATAT-TATAT
1 ATGTTTTCAAATACTATATATATATAT
*
11620114 ATATTTTC
1 ATGTTTTC
11620122 GAAAACGTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
25 11 0.15
26 19 0.26
27 13 0.18
28 17 0.24
29 11 0.15
30 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (27 bp):
ATGTTTTCAAATACTATATATATATAT
Found at i:11620051 original size:2 final size:2
Alignment explanation
Indices: 11620046--11620082 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11620036 TTTCAAATAC
11620046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11620083 TAAAAATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11620056 original size:23 final size:24
Alignment explanation
Indices: 11620007--11620060 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 24
11619997 TGTTTTCAAA
11620007 ATGTTTTCAAAACTATATAATATAT
1 ATGTTTTCAAAAC-ATATAATATAT
11620032 ATGTTTTCAAATACTATATATATATAT
1 ATGTTTTCAAA-AC-ATATA-ATATAT
11620059 AT
1 AT
11620061 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 11 0.41
26 8 0.30
27 8 0.30
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (24 bp):
ATGTTTTCAAAACATATAATATAT
Found at i:11620120 original size:26 final size:26
Alignment explanation
Indices: 11620076--11620127 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
11620066 TATATATATA
*
11620076 TATATATTAAAAATGTTTTCAAAAAC
1 TATATATTAAAAATATTTTCAAAAAC
* * *
11620102 TATATATTATATATATTTTCGAAAAC
1 TATATATTAAAAATATTTTCAAAAAC
11620128 GTTTTCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (26 bp):
TATATATTAAAAATATTTTCAAAAAC
Found at i:11620151 original size:36 final size:35
Alignment explanation
Indices: 11620066--11620265 Score: 201
Period size: 38 Copynumber: 5.5 Consensus size: 35
11620056 TATATATATA
* * *
11620066 TATATATATATATATATTAAAAATGTTTTCAAAAAC
1 TATATAT-TATATATTTTCAAAACGTTTTCAAAAAC
11620102 TATATATTATATATATTTTCGAAAACGTTTTCAAAAAC
1 TATATA-T-TATATATTTTC-AAAACGTTTTCAAAAAC
*
11620140 TATATATTATATATGTTTTCAAGAA-ATTTT-AAAAAC
1 TATATATTATATA--TTTTCAA-AACGTTTTCAAAAAC
* *
11620176 TATATAATATATATTTTCAAAATGTTTTC-AAAAC
1 TATATATTATATATTTTCAAAACGTTTTCAAAAAC
* * *
11620210 TATATAATATATATTTTCAAAAATCGCTTTCTAAAAAT
1 TATATATTATATATTTTC-AAAA-CGTTTTC-AAAAAC
11620248 TATATATTATAT-TTTTCA
1 TATATATTATATATTTTCA
11620266 GTAAATTATT
Statistics
Matches: 143, Mismatches: 10, Indels: 22
0.82 0.06 0.13
Matches are distributed among these distances:
33 2 0.01
34 34 0.24
35 4 0.03
36 36 0.25
37 23 0.16
38 44 0.31
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATATTATATATTTTCAAAACGTTTTCAAAAAC
Found at i:11620180 original size:34 final size:34
Alignment explanation
Indices: 11620066--11620231 Score: 163
Period size: 34 Copynumber: 4.6 Consensus size: 34
11620056 TATATATATA
* * **
11620066 TATATATATATATATATTAAAAATGTTTTCAAAAAC
1 TATATA-ATATATATTTTCAAAACATTTT-AAAAAC
*
11620102 TATATATTATATATATTTTCGAAAACGTTTTCAAAAAC
1 TATATA--ATATATATTTTC-AAAACATTTT-AAAAAC
*
11620140 TATATATTATATATGTTTTCAAGAA-ATTTTAAAAAC
1 TATATA--ATATATATTTTCAA-AACATTTTAAAAAC
** *
11620176 TATATAATATATATTTTCAAAATGTTTTCAAAAC
1 TATATAATATATATTTTCAAAACATTTTAAAAAC
11620210 TATATAATATATATTTTCAAAA
1 TATATAATATATATTTTCAAAA
11620232 ATCGCTTTCT
Statistics
Matches: 118, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
33 2 0.02
34 44 0.37
36 18 0.15
37 17 0.14
38 37 0.31
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (34 bp):
TATATAATATATATTTTCAAAACATTTTAAAAAC
Found at i:11620330 original size:12 final size:12
Alignment explanation
Indices: 11620295--11620341 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
11620285 TATACTATAT
*
11620295 TAATATATATAAA
1 TAATATA-AAAAA
11620308 T-ATATAAAAAA
1 TAATATAAAAAA
11620319 TAATATAAAAAA
1 TAATATAAAAAA
*
11620331 TAAAATAAAAA
1 TAATATAAAAA
11620342 CATATTCGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 5 0.16
12 25 0.81
13 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAATATAAAAAA
Found at i:11621216 original size:85 final size:85
Alignment explanation
Indices: 11621109--11621572 Score: 581
Period size: 85 Copynumber: 5.4 Consensus size: 85
11621099 CGACAGTTTT
* * * *
11621109 TTTGTTAACAGATAGCCCTTCTCACCTTGAGCTATGCTGCAAATTTGATATGTCCTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAA
* *
11621174 TGTAATCGAACTCGAAAGTC
66 TGTAATCGAACTCGAAGGTA
* * *
11621194 TTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTTGACATG-CTCTTGAGCTAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTC-CTTGAGCTGA
* *
11621258 ATGAAATCAAACTCGAAGGTA
65 ATGTAATCGAACTCGAAGGTA
* * * * *
11621279 TTTGTTGACATATAACACTTATCGCCTTGAGCTATGTTGTAAATTCGATATGTCCTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAA
* *
11621344 TGTAATAGAACTCGAAGGTC
66 TGTAATCGAACTCGAAGGTA
* * * *
11621364 TTTGTTGATAGATAGCCCTTCTCTCCTTGAGCTATACTGTAAATTTGATAT-TCCCTTGAGCTGA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGT-CCTTGAGCTGA
11621428 ATGTAATCGAACTCGAAGGTA
65 ATGTAATCGAACTCGAAGGTA
* * * * * *
11621449 TTTGTTGACTGATAACCCTTATCGCCTTAAGTTATACTGTAAATTTGATATGTCCTTGAGCTGAG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAA
* *
11621514 TGTAATCAAACTCGAAGGTTT
66 TGTAATCGAACTCGAAGG-TA
* * * *
11621535 TTTGCTGGCAAATAGCCCTTCTCGCCTTGAGCTATGCT
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCT
11621573 ACAAATAGTT
Statistics
Matches: 323, Mismatches: 51, Indels: 9
0.84 0.13 0.02
Matches are distributed among these distances:
84 2 0.01
85 289 0.89
86 32 0.10
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (85 bp):
TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAA
TGTAATCGAACTCGAAGGTA
Found at i:11621425 original size:255 final size:256
Alignment explanation
Indices: 11621109--11621570 Score: 669
Period size: 255 Copynumber: 1.8 Consensus size: 256
11621099 CGACAGTTTT
*
11621109 TTTGTTAACAGATAGCCCTTCTCACCTTGAGCTATGCTGCAAATTTGATATGTCCTTGAGCTGAA
1 TTTGTTAACAGATAGCCCTTCTCACCTTGAGCTATACTGCAAATTTGATATGTCCTTGAGCTGAA
* * * *
11621174 TGTAATCGAACTCGAAAGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATT
66 TGTAATCGAACTCGAAAGTATTTGTTGACAGATAACCCTTATCACCTTAAGCTATACTGTAAATT
* *
11621239 TGACATG-CTCTTGAGCTAAATGAAATCAAACTCGAAGG-TATTTGTTGACATATAACACTTATC
131 TGACATGTC-CTTGAGCTAAATGAAATCAAACTCGAAGGTTATTTGCTGACAAATAACACTTATC
11621302 GCCTTGAGCTATGTTGTAAATTCGATATGTCCTTGAGCTGAATGTAATAGAACTCGAAGGTC
195 GCCTTGAGCTATGTTGTAAATTCGATATGTCCTTGAGCTGAATGTAATAGAACTCGAAGGTC
* * * *
11621364 TTTGTTGATAGATAGCCCTTCTCTCCTTGAGCTATACTGTAAATTTGATAT-TCCCTTGAGCTGA
1 TTTGTTAACAGATAGCCCTTCTCACCTTGAGCTATACTGCAAATTTGATATGT-CCTTGAGCTGA
* * * *
11621428 ATGTAATCGAACTCGAAGGTATTTGTTGACTGATAACCCTTATCGCCTTAAGTTATACTGTAAAT
65 ATGTAATCGAACTCGAAAGTATTTGTTGACAGATAACCCTTATCACCTTAAGCTATACTGTAAAT
* * * * * * * * *
11621493 TTGATATGTCCTTGAGCTGAGTGTAATCAAACTCGAAGGTTTTTTGCTGGCAAATAGCCCTTCTC
130 TTGACATGTCCTTGAGCTAAATGAAATCAAACTCGAAGGTTATTTGCTGACAAATAACACTTATC
11621558 GCCTTGAGCTATG
195 GCCTTGAGCTATG
11621571 CTACAAATAG
Statistics
Matches: 180, Mismatches: 24, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
254 1 0.01
255 147 0.82
256 32 0.18
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (256 bp):
TTTGTTAACAGATAGCCCTTCTCACCTTGAGCTATACTGCAAATTTGATATGTCCTTGAGCTGAA
TGTAATCGAACTCGAAAGTATTTGTTGACAGATAACCCTTATCACCTTAAGCTATACTGTAAATT
TGACATGTCCTTGAGCTAAATGAAATCAAACTCGAAGGTTATTTGCTGACAAATAACACTTATCG
CCTTGAGCTATGTTGTAAATTCGATATGTCCTTGAGCTGAATGTAATAGAACTCGAAGGTC
Found at i:11622937 original size:95 final size:94
Alignment explanation
Indices: 11622739--11622938 Score: 269
Period size: 95 Copynumber: 2.1 Consensus size: 94
11622729 GGACAACTCA
*
11622739 ATATTATAATCACCTTTATCAGGCTAACTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGATAACTGAATCTTATCCATAAA-CCAGGGCGTTTAACCAATT
* *
11622804 TCTCTAGAGGGACAACTCAAGCTTTATTAT
65 TCTCTAGAGGAACAAATCAAGCTTTATTAT
* * *
11622834 ATATTATAATCACCTTTATCAGGATAGCTGAATCTTATCCATAAA-CTGGGACGTTTAA-CTATT
1 ATATTATAATCACCTTTATCAGGATAACTGAATCTTATCCATAAACCAGGG-CGTTTAACCAATT
* * *
11622897 TACTTTATAGGAACAAATCAAGCTTTATTGT
65 T-CTCTAGAGGAACAAATCAAGCTTTATTAT
11622928 ATATATATAAT
1 ATAT-TATAAT
11622939 TTTATAATAT
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
93 9 0.10
94 35 0.38
95 49 0.53
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.35
Consensus pattern (94 bp):
ATATTATAATCACCTTTATCAGGATAACTGAATCTTATCCATAAACCAGGGCGTTTAACCAATTT
CTCTAGAGGAACAAATCAAGCTTTATTAT
Found at i:11623440 original size:35 final size:34
Alignment explanation
Indices: 11623394--11623465 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 34
11623384 ATTTAAATAT
11623394 AAAAAGAAATATGAGAAAGTTCAAAAA-CAAGTTAC
1 AAAAAGAAATATGAGAAAGTT-AAAAAGCAAGTT-C
11623429 AAAAAGAAATATGAGAAAGTTAAAAAGCAAGTTC
1 AAAAAGAAATATGAGAAAGTTAAAAAGCAAGTTC
11623463 AAA
1 AAA
11623466 TAGGATGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 9 0.25
35 27 0.75
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (34 bp):
AAAAAGAAATATGAGAAAGTTAAAAAGCAAGTTC
Found at i:11626618 original size:4 final size:4
Alignment explanation
Indices: 11626605--11626801 Score: 63
Period size: 4 Copynumber: 49.0 Consensus size: 4
11626595 TGTTAGATAA
* *
11626605 AAAT -AAT AAAT AAAT AAAT -ACT AAAT AAAT CAAAGG AAA- AAATT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAA-T AAAT AAA-T AAAT
* * * * * * * *
11626652 AATT AAAA AACAT AGA- AAAT AAAT AAAT CAAT CAAT CAAT CAAT CAAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
11626700 AAA- AAAT AAAAT AAAAT AAAG ATAA- AAAC AAAT AAAT AAAAT AAAT
1 AAAT AAAT -AAAT -AAAT AAAT A-AAT AAAT AAAT AAAT -AAAT AAAT
* ** * * *
11626746 ATAT CAACG AAAA AAAT AAAAT AAAGC AAA- AAAT -ATT AAAT AAAT -AAT
1 AAAT -AAAT AAAT AAAT -AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT
11626794 AAAT AAAT
1 AAAT AAAT
11626802 CAAAGGGAAA
Statistics
Matches: 150, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
3 25 0.17
4 91 0.61
5 34 0.23
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:11626629 original size:15 final size:15
Alignment explanation
Indices: 11626605--11626801 Score: 63
Period size: 15 Copynumber: 13.0 Consensus size: 15
11626595 TGTTAGATAA
11626605 AAATAATAAATAAAT
1 AAATAATAAATAAAT
*
11626620 AAATACTAAATAAAT
1 AAATAATAAATAAAT
* *
11626635 CAAAGGAAAAAATTAAA-
1 -AAA-TAATAAA-TAAAT
* *
11626652 AATTAA-AAA-ACAT
1 AAATAATAAATAAAT
11626665 AGAA-AATAAATAAAT
1 A-AATAATAAATAAAT
* * *
11626680 CAATCAATCAATCAAT
1 AAAT-AATAAATAAAT
* *
11626696 CAATAAAAAATAAAAT
1 AAATAATAAAT-AAAT
*
11626712 AAAATAA-AGATAAA-
1 -AAATAATAAATAAAT
11626726 AACA-AATAAATAAAAT
1 AA-ATAATAAAT-AAAT
* **
11626742 AAATATATCAACGAA-
1 AAATA-ATAAATAAAT
*
11626757 AAA-AATAAAATAAAGC
1 AAATAAT-AAATAAA-T
* *
11626773 AAAAAAT-ATTAAAT
1 AAATAATAAATAAAT
11626787 AAATAATAAATAAAT
1 AAATAATAAATAAAT
11626802 CAAAGGGAAA
Statistics
Matches: 132, Mismatches: 28, Indels: 44
0.65 0.14 0.22
Matches are distributed among these distances:
12 2 0.02
13 9 0.07
14 24 0.18
15 45 0.34
16 32 0.24
17 16 0.12
18 4 0.03
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:11626724 original size:6 final size:5
Alignment explanation
Indices: 11626702--11626744 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
11626692 CAATCAATAA
11626702 AAAAT AAAAT AAAAT AAAGAT AAAA- ACAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAA-AT AAAAT A-AAAT AAAAT AAAAT AAA
11626745 TATATCAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 5 0.15
5 24 0.71
6 5 0.15
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:11626735 original size:26 final size:27
Alignment explanation
Indices: 11626703--11626771 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
11626693 AATCAATAAA
11626703 AAATAAAATAAAATAAAGATAAAAAC-
1 AAATAAAATAAAATAAAGATAAAAACG
* **
11626729 AAAT-AAATAAAATAAATATATCAACG
1 AAATAAAATAAAATAAAGATAAAAACG
11626755 AAA-AAAATAAAATAAAG
1 AAATAAAATAAAATAAAG
11626772 CAAAAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 18 0.49
26 19 0.51
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (27 bp):
AAATAAAATAAAATAAAGATAAAAACG
Found at i:11626837 original size:25 final size:25
Alignment explanation
Indices: 11626809--11626858 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
11626799 AATCAAAGGG
*
11626809 AAAAA-ATAAAAATAATAAAATAATA
1 AAAAAGATAAAAA-AATAAAACAATA
*
11626834 AAAAAGTTAAAAAAATAAAACAATA
1 AAAAAGATAAAAAAATAAAACAATA
11626859 TGTAGTAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAAAGATAAAAAAATAAAACAATA
Found at i:11628015 original size:17 final size:17
Alignment explanation
Indices: 11627980--11628025 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
11627970 GAAATAAAAT
**
11627980 AAATAAATAAAAATGAA
1 AAATAAATAAAAAACAA
11627997 AAATAAATAAAAAACAA
1 AAATAAATAAAAAACAA
11628014 AAA-AAA-AAAAAA
1 AAATAAATAAAAAA
11628026 TATATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 6 0.22
16 3 0.11
17 18 0.67
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.11
Consensus pattern (17 bp):
AAATAAATAAAAAACAA
Found at i:11628017 original size:26 final size:25
Alignment explanation
Indices: 11627961--11628027 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
11627951 GGAAAAAAGT
* * *
11627961 AAAACAAAAGAAATAAAATAAATAAA
1 AAAAAAAAAAAAAT-AAATAAAAAAA
* **
11627987 TAAAAATGAAAAATAAATAAAAAACA
1 AAAAAAAAAAAAATAAATAAAAAA-A
11628013 AAAAAAAAAAAAATA
1 AAAAAAAAAAAAATA
11628028 TATATTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (25 bp):
AAAAAAAAAAAAATAAATAAAAAAA
Found at i:11628019 original size:21 final size:21
Alignment explanation
Indices: 11627966--11628027 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
11627956 AAAGTAAAAC
*
11627966 AAAAGAAATAAAATAAATAAAT
1 AAAA-AAAAAAAATAAATAAAT
** *
11627988 AAAAATGAAAAATAAATAAAA
1 AAAAAAAAAAAATAAATAAAT
*
11628009 AACAAAAAAAAAAAAAATA
1 AA-AAAAAAAAAATAAATA
11628028 TATATTATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.82, C:0.02, G:0.03, T:0.13
Consensus pattern (21 bp):
AAAAAAAAAAAATAAATAAAT
Done.