Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 29
Found at i:904080 original size:28 final size:28
Alignment explanation
Indices: 904040--904138 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
904030 AGAGTCGAGG
*
904040 GTTCTACATGGTCCTACGGGATATATGT
1 GTTCTACGTGGTCCTACGGGATATATGT
*
904068 GTTCTACGTGGTCTTACGGGATATATGT
1 GTTCTACGTGGTCCTACGGGATATATGT
* *
904096 GTTCTACGTGGTCCTACGAGACATATGT
1 GTTCTACGTGGTCCTACGGGATATATGT
*
904124 GTTCTATGTGGTCCT
1 GTTCTACGTGGTCCT
904139 TCGGAACATA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (28 bp):
GTTCTACGTGGTCCTACGGGATATATGT
Found at i:904147 original size:28 final size:28
Alignment explanation
Indices: 904040--904152 Score: 131
Period size: 28 Copynumber: 4.1 Consensus size: 28
904030 AGAGTCGAGG
* * *
904040 GTTCTACATGGTCCTACGGGATATATGT
1 GTTCTACGTGGTCCTACGGAACATATGT
* * *
904068 GTTCTACGTGGTCTTACGGGATATATGT
1 GTTCTACGTGGTCCTACGGAACATATGT
904096 GTTCTACGTGGTCCTAC-GAGACATATGT
1 GTTCTACGTGGTCCTACGGA-ACATATGT
* *
904124 GTTCTATGTGGTCCTTCGGAACATA-GT
1 GTTCTACGTGGTCCTACGGAACATATGT
904151 GT
1 GT
904153 CATATGGGAC
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
27 5 0.07
28 69 0.91
29 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (28 bp):
GTTCTACGTGGTCCTACGGAACATATGT
Found at i:908107 original size:28 final size:28
Alignment explanation
Indices: 908067--908165 Score: 162
Period size: 28 Copynumber: 3.5 Consensus size: 28
908057 ATAGTCGAGG
908067 GTTCTACGTGGTCCTACGGGATATATGT
1 GTTCTACGTGGTCCTACGGGATATATGT
* *
908095 GTTCTACGTGGTCTTATGGGATATATGT
1 GTTCTACGTGGTCCTACGGGATATATGT
*
908123 GTTCTACGTGGTCCTACGGGACATATGT
1 GTTCTACGTGGTCCTACGGGATATATGT
*
908151 GTTCTATGTGGTCCT
1 GTTCTACGTGGTCCT
908166 TTGGAACATA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.38
Consensus pattern (28 bp):
GTTCTACGTGGTCCTACGGGATATATGT
Found at i:908174 original size:28 final size:28
Alignment explanation
Indices: 908067--908179 Score: 131
Period size: 28 Copynumber: 4.1 Consensus size: 28
908057 ATAGTCGAGG
** *
908067 GTTCTACGTGGTCCTACGGGATATATGT
1 GTTCTACGTGGTCCTTTGGGACATATGT
*
908095 GTTCTACGTGGT-CTTATGGGATATATGT
1 GTTCTACGTGGTCCTT-TGGGACATATGT
**
908123 GTTCTACGTGGTCCTACGGGACATATGT
1 GTTCTACGTGGTCCTTTGGGACATATGT
* *
908151 GTTCTATGTGGTCCTTTGGAACATA-GT
1 GTTCTACGTGGTCCTTTGGGACATATGT
908178 GT
1 GT
908180 CATACGAGAC
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.08
28 66 0.89
29 2 0.03
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.38
Consensus pattern (28 bp):
GTTCTACGTGGTCCTTTGGGACATATGT
Found at i:912116 original size:28 final size:28
Alignment explanation
Indices: 912076--912162 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
912066 TATAGTTGGT
912076 TACGTGGTCCTACGGGACATATGTGTTC
1 TACGTGGTCCTACGGGACATATGTGTTC
* *
912104 TACGTGGTCCTACGAGACATATGTGTTA
1 TACGTGGTCCTACGGGACATATGTGTTC
* * *
912132 TATGTGGTCCTTCGGGACATA-GTGTCC
1 TACGTGGTCCTACGGGACATATGTGTTC
912159 TACG
1 TACG
912163 GGACAAATTC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 7 0.14
28 44 0.86
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.32
Consensus pattern (28 bp):
TACGTGGTCCTACGGGACATATGTGTTC
Found at i:915009 original size:102 final size:101
Alignment explanation
Indices: 914791--915001 Score: 352
Period size: 101 Copynumber: 2.1 Consensus size: 101
914781 AGGGTCTATG
914791 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGTGAGACACATACTTGAT
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGTGAGACACATACTTGAT
* * *
914856 CTTGGCATATGTATATGATTCTTAAGGAATGATATG
66 CCTAGCATATGTATATGATTCTTAAGGAATGATATA
*
914892 TGGTCTTTCGGGACATATATGTATT-TTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCT-GTGAGACACATACTTGA
*
914956 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATA
65 T-CCTAGCATATGTATATGATTCTTAAGGAATGATATA
914994 TGGTCCTT
1 TGGTCCTT
915002 ATGGACATTA
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
100 21 0.21
101 42 0.41
102 39 0.38
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (101 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGTGAGACACATACTTGAT
CCTAGCATATGTATATGATTCTTAAGGAATGATATA
Found at i:917291 original size:3 final size:3
Alignment explanation
Indices: 917285--917399 Score: 167
Period size: 3 Copynumber: 37.7 Consensus size: 3
917275 TCATTTAAAT
** *
917285 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
917333 TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
917379 ATA TTA TATA TTA TTA TTA TT
1 TTA TTA T-TA TTA TTA TTA TT
917400 TAATAAATAA
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
3 94 0.94
4 6 0.06
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:918566 original size:28 final size:26
Alignment explanation
Indices: 918532--918648 Score: 91
Period size: 28 Copynumber: 4.4 Consensus size: 26
918522 TAATTACAAG
918532 TTTTATTACTTTTTATATTTAGTTTTAA
1 TTTTATTA-TTTTTATATTTA-TTTTAA
* *
918560 TTTTATTATTGTTTAAATATATTTTAA
1 TTTTATTATT-TTTATATTTATTTTAA
918587 TTTTA-TATTTTTA-A--TATTTTAA
1 TTTTATTATTTTTATATTTATTTTAA
* *
918609 TTAGTATTATTATTT-TATTTTTTATTAA
1 TT-TTATTATT-TTTATATTTATT-TTAA
*
918637 TATATATTATTT
1 T-TTTATTATTT
918649 GATTAATTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
22 10 0.13
23 2 0.03
24 5 0.07
25 8 0.11
26 4 0.05
27 17 0.23
28 28 0.37
29 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTATTATTTTTATATTTATTTTAA
Found at i:919457 original size:18 final size:18
Alignment explanation
Indices: 919436--919503 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
919426 TTTTATATAC
919436 TTATTATTTTCATAGTAT
1 TTATTATTTTCATAGTAT
*
919454 TTATATATTTTCTTATTAATAT
1 TTAT-TATTTTC--A-TAGTAT
*
919476 TTCATTATTTGCA-AGTATT
1 TT-ATTATTTTCATAGTA-T
919495 TTATTATTT
1 TTATTATTT
919504 ATTTTTCTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 14 0.34
19 10 0.24
20 1 0.02
21 1 0.02
22 13 0.32
23 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TTATTATTTTCATAGTAT
Found at i:926577 original size:85 final size:83
Alignment explanation
Indices: 926194--926794 Score: 923
Period size: 83 Copynumber: 7.2 Consensus size: 83
926184 ACTGCAACAA
* * *
926194 ATGAAAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
*
926259 AATCATTGAAATTGAAAG
66 AATCATTGAATTTGAAAG
* * *
926277 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
*
926342 AATCATTGAAATTGAAAG
66 AATCATTGAATTTGAAAG
* *
926360 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
*
926425 AATCATTGAAATTGAAAG
66 AATCATTGAATTTGAAAG
*
926443 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
* *
926508 AGTTATTGAATTTGGAAAG
66 AATCATTGAATTT-GAAAG
* *
926527 ATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAAC
1 ATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAC
* *
926592 CAGTTATTGAATTTGGAAAG
65 CAATCATTGAATTT-GAAAG
* * *
926612 ATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTGTCTGATCTGATTTGGTAAAAC
1 ATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAC
* * *
926677 TAGTTATTGAATTTGAAAG
65 CAATCATTGAATTTGAAAG
926696 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
*
926761 AATCATTGAATTTAAAAG
66 AATCATTGAATTTGAAAG
* *
926779 ATGAATTTGATCATAG
1 ATGAATGTGCTCATAG
926795 TAGAAATAAG
Statistics
Matches: 495, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
83 314 0.63
84 32 0.06
85 149 0.30
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
AATCATTGAATTTGAAAG
Found at i:930379 original size:76 final size:76
Alignment explanation
Indices: 930141--930773 Score: 1124
Period size: 76 Copynumber: 8.5 Consensus size: 76
930131 CTATTTCCCA
*
930141 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAACCTTC-GGAGC---TTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
930202 AGCCTTCGGGT
66 AGCCTTCGGGT
*
930213 CATCTGTAAGTCCTTCAATGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
930277 AGCCTTCGGGT
66 AGCCTTCGGGT
930288 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
930353 AGCCTTCGGGT
66 AGCCTTCGGGT
930364 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
930429 ATCCTTCGGGT
66 AGCCTTCGGGT
*
930440 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
930505 AGCCTTCGGGT
66 AGCCTTCGGGT
930516 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
930581 AGCCTTCGGGT
66 AGCCTTCGGGT
930592 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
930657 ATCCTTCGGGT
66 AGCCTTCGGGT
*
930668 CATCTGTAAGTCCTACAGTGCATGATGTTTCC---AAGCCTTC-GGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
930729 AACCTTCGGGT
66 AGCCTTCGGGT
*
930740 CATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
930774 CATTTCCATC
Statistics
Matches: 542, Mismatches: 12, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
71 19 0.04
72 82 0.15
73 13 0.02
75 72 0.13
76 356 0.66
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:930905 original size:3 final size:3
Alignment explanation
Indices: 930899--931015 Score: 140
Period size: 3 Copynumber: 40.7 Consensus size: 3
930889 TCATTTAAAT
** *
930899 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TT- TTA TTA TTA GTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
930945 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
930989 TTA -TA TTA -TA TTA -TA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
931016 TAATAAATAA
Statistics
Matches: 100, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
2 14 0.14
3 81 0.81
4 5 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:930990 original size:60 final size:57
Alignment explanation
Indices: 930899--931014 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 57
930889 TCATTTAAAT
*
930899 TTATTATTATTATTATTATTAAAATTATTATTTTATTATTAGTATA-TTATTATTATA
1 TTATTATTATTATTATTATTAAAATTATTATTATATTA-TAGTATATTTATTATTATA
* *
930956 TTATTATTATTATTATTATTATATTATTATTTATTATATTATATTATATTTATTATTAT
1 TTATTATTATTATTATTATTA-A-AATTA-TTATTATATTATAGTATATTTATTATTAT
931015 TTAATAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
57 21 0.40
58 1 0.02
59 10 0.19
60 20 0.38
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (57 bp):
TTATTATTATTATTATTATTAAAATTATTATTATATTATAGTATATTTATTATTATA
Found at i:931015 original size:20 final size:21
Alignment explanation
Indices: 930897--931015 Score: 145
Period size: 20 Copynumber: 5.6 Consensus size: 21
930887 TTTCATTTAA
930897 ATTTATTATTATTATTATTATT
1 ATTTATTATTATTA-TATTATT
** *
930919 A-AAATTATTATTTTATTATT
1 ATTTATTATTATTATATTATT
*
930939 AGTATATTATTATTATATTATT
1 A-TTTATTATTATTATATTATT
930961 ATTATTATTATTATTATATTATT
1 A-T-TTATTATTATTATATTATT
930984 ATTTATTA-TATTATATTA-T
1 ATTTATTATTATTATATTATT
931003 ATTTATTATTATT
1 ATTTATTATTATT
931016 TAATAAATAA
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.10
20 22 0.26
21 15 0.17
22 21 0.24
23 19 0.22
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (21 bp):
ATTTATTATTATTATATTATT
Found at i:932423 original size:27 final size:28
Alignment explanation
Indices: 932363--932431 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
932353 TAATTACAAG
* *
932363 TTTTATTACTT-TTTATATTTAGTTTTAA
1 TTTTATTA-TTGTTTAAATATAGTTTTAA
932391 TTTTATTATTGTTTAAATATA-TTTTAA
1 TTTTATTATTGTTTAAATATAGTTTTAA
932418 TTTTA-TA-TGTTTAA
1 TTTTATTATTGTTTAA
932432 TATTTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
25 7 0.18
26 2 0.05
27 13 0.34
28 16 0.42
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTATTATTGTTTAAATATAGTTTTAA
Found at i:932437 original size:22 final size:26
Alignment explanation
Indices: 932363--932450 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 26
932353 TAATTACAAG
*
932363 TTTTATTACTT-TTTATATTTAGTTTTAA
1 TTTTATTA-TTGTTTA-ATATA-TTTTAA
932391 TTTTATTATTGTTTAAATATATTTTAA
1 TTTTATTATTGTTT-AATATATTTTAA
932418 TTTTA-TA-TGTTT-A-ATATTTTAA
1 TTTTATTATTGTTTAATATATTTTAA
*
932440 TTAGTATTATT
1 TT-TTATTATT
932451 ATTTTATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
22 11 0.21
23 3 0.06
24 2 0.04
25 6 0.11
26 2 0.04
27 13 0.25
28 15 0.28
29 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.65
Consensus pattern (26 bp):
TTTTATTATTGTTTAATATATTTTAA
Found at i:932456 original size:26 final size:26
Alignment explanation
Indices: 932408--932480 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 26
932398 ATTGTTTAAA
*
932408 TATATTTTAATT--T-TATA-TGTTT
1 TATATTTTAATTAATATATATTATTT
* *
932430 AATATTTTAATTAGTAT-TATTATTT
1 TATATTTTAATTAATATATATTATTT
* *
932455 TATTTTTTTATTAATATATATTATTT
1 TATATTTTAATTAATATATATTATTT
932481 GATTAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
22 11 0.28
24 3 0.08
25 18 0.45
26 8 0.20
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (26 bp):
TATATTTTAATTAATATATATTATTT
Found at i:935752 original size:103 final size:103
Alignment explanation
Indices: 935527--935744 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
935517 GTCGAGGGTC
935527 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * * *
935592 TTGATCCTTGGCATTTGTATATGATTCTTAGGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
935630 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
935695 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
935733 TATGTGGTCCTT
1 TATGTGGTCCTT
935745 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:938947 original size:28 final size:28
Alignment explanation
Indices: 938905--938966 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
938895 AGAGTCGAGG
938905 GTTCTACGTAGTCCTACGGGACATATGT
1 GTTCTACGTAGTCCTACGGGACATATGT
938933 GTTCTACGT-GATCCTACGGGACATATGT
1 GTTCTACGTAG-TCCTACGGGACATATGT
*
938961 GCTCTA
1 GTTCTA
938967 TTTGGTCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (28 bp):
GTTCTACGTAGTCCTACGGGACATATGT
Found at i:938975 original size:28 final size:28
Alignment explanation
Indices: 938907--938985 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
938897 AGTCGAGGGT
* *
938907 TCTACGTAGTCCTACGGGACATATGTGT
1 TCTACGTGGTCCTACGGGACATATGTGC
*
938935 TCTACGTGATCCTACGGGACATATGTGC
1 TCTACGTGGTCCTACGGGACATATGTGC
** **
938963 TCTATTTGGTCCTTTGGGACATA
1 TCTACGTGGTCCTACGGGACATA
938986 GTGTCCTACG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (28 bp):
TCTACGTGGTCCTACGGGACATATGTGC
Found at i:949032 original size:21 final size:21
Alignment explanation
Indices: 949006--949203 Score: 176
Period size: 21 Copynumber: 9.5 Consensus size: 21
948996 GTTTCCAGAT
*
949006 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
949027 TCGCAATGCGAGCTTAGACTA
1 TCGCAATGCGAACTTCGACTA
*
949048 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
949068 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
949089 TCGCAATACGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
949110 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
949130 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
949151 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
949172 TTGCAATGCAAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
949193 TCGCATTGCGA
1 TCGCAATGCGA
949204 TAGTCCAAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
20 33 0.23
21 112 0.77
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:949073 original size:62 final size:62
Alignment explanation
Indices: 949006--949180 Score: 262
Period size: 62 Copynumber: 2.8 Consensus size: 62
948996 GTTTCCAGAT
* * *
949006 TCGCAACGCGAACTTCGACTATCGCAATGCGAGCTTAGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
* * *
949068 TCGCAATGCAAACTTGGACTATCGCAATACGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
* *
949130 TCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATTGCAATGC
1 TCGCAATGCGA-ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGC
949181 AAACTTCGAC
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
62 100 0.99
63 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (62 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
Found at i:949103 original size:83 final size:82
Alignment explanation
Indices: 949014--949203 Score: 217
Period size: 83 Copynumber: 2.3 Consensus size: 82
949004 ATTCGCAACG
* *
949014 CGAACTTCGACTATCGCAATGCGAGCT-TAG-ACTATCGCAATGCGAATATGT-A-AATCGCAAT
1 CGAACTTCGACTATCGCAATGCGA-ATAT-GTA-AATCGCAATGCG-ATA-GTCACAATCGCAAT
949075 GCAAACTTGGACTATCGCAATA
61 GCAAACTTGGACTATCGCAATA
* * *
949097 CGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGA
1 CGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC-ACAATCGCAATGCAA
* *
949162 ACTTGGACTATTGCAATG
65 ACTTGGACTATCGCAATA
* *
949180 CAAACTTCGACTATCGCATTGCGA
1 CGAACTTCGACTATCGCAATGCGA
949204 TAGTCCAAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
80 2 0.02
81 3 0.03
82 14 0.15
83 73 0.79
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (82 bp):
CGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCACAATCGCAATGCAAA
CTTGGACTATCGCAATA
Found at i:949805 original size:5 final size:5
Alignment explanation
Indices: 949791--949826 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
949781 CGCGCGCCAC
*
949791 CGTC- CGTCT CGTCT CTTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
949827 GTTCGTGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.00, C:0.42, G:0.19, T:0.39
Consensus pattern (5 bp):
CGTCT
Found at i:949960 original size:21 final size:21
Alignment explanation
Indices: 949934--950099 Score: 153
Period size: 21 Copynumber: 7.8 Consensus size: 21
949924 ATTTTGGACT
*
949934 ATCGCAACGAACTTAGAATAA
1 ATCGCAACGAACTTGGAATAA
*
949955 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
949976 ATCGCAACGCGAACTT-CAACT--
1 ATCGCAA--CGAACTTGGAA-TAA
*
949997 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
950018 ATCGAAATGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
950039 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
950060 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
950081 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
950100 CTATCGTATT
Statistics
Matches: 118, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
19 17 0.14
20 2 0.02
21 72 0.61
22 2 0.02
23 25 0.21
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:950030 original size:63 final size:63
Alignment explanation
Indices: 949931--950089 Score: 264
Period size: 63 Copynumber: 2.5 Consensus size: 63
949921 GCGATTTTGG
* *
949931 ACTATCGCAACGAACTTAGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCA
1 ACTATCGCAACGAACTTGGAATAAATCGAAACGAATTTGGAATAAATCGCAACGCGAACTTCA
* * *
949994 ACTATCGCAACGAATTTGGAATAAATCGAAATGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGAAACGAATTTGGAATAAATCGCAACGCGAACTTCA
*
950057 ACTATCGCAACGAACTTGGAATAAATCGCAACG
1 ACTATCGCAACGAACTTGGAATAAATCGAAACG
950090 CGAACTTGGA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 88 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (63 bp):
ACTATCGCAACGAACTTGGAATAAATCGAAACGAATTTGGAATAAATCGCAACGCGAACTTCA
Found at i:962829 original size:133 final size:133
Alignment explanation
Indices: 962588--962855 Score: 502
Period size: 133 Copynumber: 2.0 Consensus size: 133
962578 TAGTGAGCAA
962588 ACAAATAATTACTTGTTTTAAGTGATTTTGAATTTTTTGGTCGTGGAATCGAGTCTTACGGTAGG
1 ACAAATAATTACTTGTTTTAAGTGATTTTGAATTTTTTGGTCGTGGAATCGAGTCTTACGGTAGG
*
962653 CAATTTATAATTCTGACTGTCGGATGTCTCCCACGGAAACTGCTCTCAACCTGGCGTTGAGGCAG
66 CAATTTATAATTCTGACTGCCGGATGTCTCCCACGGAAACTGCTCTCAACCTGGCGTTGAGGCAG
962718 CCT
131 CCT
962721 ACAAATAATTACTTGTTTTAAGTGATTTTGAATTTTTTGGTCGT-GAGATCGAGTCTTACGGTAG
1 ACAAATAATTACTTGTTTTAAGTGATTTTGAATTTTTTGGTCGTGGA-ATCGAGTCTTACGGTAG
*
962785 GCAATTTATAATTCTGACTGCCGGATGTCTCCCACGGAAGCTGCTCTCAACCTGGCGTTGAGGCA
65 GCAATTTATAATTCTGACTGCCGGATGTCTCCCACGGAAACTGCTCTCAACCTGGCGTTGAGGCA
962850 GCCT
130 GCCT
962854 AC
1 AC
962856 TATCCTACCT
Statistics
Matches: 132, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
132 2 0.02
133 130 0.98
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (133 bp):
ACAAATAATTACTTGTTTTAAGTGATTTTGAATTTTTTGGTCGTGGAATCGAGTCTTACGGTAGG
CAATTTATAATTCTGACTGCCGGATGTCTCCCACGGAAACTGCTCTCAACCTGGCGTTGAGGCAG
CCT
Found at i:963416 original size:2 final size:2
Alignment explanation
Indices: 963409--963441 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
963399 TTTAAATTCA
963409 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 A
963442 AATTATGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:963613 original size:2 final size:2
Alignment explanation
Indices: 963606--963634 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
963596 AAATTCAAAT
963606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
963635 GAATTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:964916 original size:18 final size:18
Alignment explanation
Indices: 964893--964935 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
964883 TCTCTCCTAC
* *
964893 ACCCACTACCCAACTGGT
1 ACCCACCACCCAACTCGT
*
964911 ACCCACCACCCATCTCGT
1 ACCCACCACCCAACTCGT
964929 ACCCACC
1 ACCCACC
964936 TGTGCCTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.53, G:0.07, T:0.14
Consensus pattern (18 bp):
ACCCACCACCCAACTCGT
Found at i:971196 original size:18 final size:18
Alignment explanation
Indices: 971170--971204 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
971160 ACTGAATATT
*
971170 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
971188 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
971205 GATAAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:971461 original size:2 final size:2
Alignment explanation
Indices: 971454--971561 Score: 216
Period size: 2 Copynumber: 54.0 Consensus size: 2
971444 TAATGTTAAC
971454 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
971496 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
971538 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
971562 GCATGTGTGT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 106 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:971960 original size:63 final size:64
Alignment explanation
Indices: 971871--972032 Score: 177
Period size: 63 Copynumber: 2.5 Consensus size: 64
971861 ATCCCTTGAC
* * * **
971871 GGGTGCATCGATGCACTA-TCTATGCATCGGTACA-TAAATCCCATTTGATGTTTGTATTTT-AA
1 GGGTGCATCGATGCACTACT-TGTGCATCGATACACT-AATCACATTCAATGTTTGTATTTTAAA
971933 G
64 G
* * *
971934 GGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGACATTCAATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATCACATTCAATGTTTGTATTTTAAAG
* * * *
971998 GAGTGCATCGATACACTTCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTACTTGTGCATCGATACAC
972033 CTTGAACAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 48 0.57
64 36 0.43
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATCACATTCAATGTTTGTATTTTAAAG
Found at i:974007 original size:23 final size:23
Alignment explanation
Indices: 973976--974036 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
973966 CTAGTATAAA
973976 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
973999 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
974022 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
974037 TATAAAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:978796 original size:65 final size:65
Alignment explanation
Indices: 978721--978845 Score: 191
Period size: 65 Copynumber: 1.9 Consensus size: 65
978711 TGCACTAAGA
*
978721 GTGCACCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGCCTGAGTGCATCGAATGCATGGC
1 GTGCACCGATGCATAAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCG-ATGCATGGC
978784 TG
64 TG
* *
978786 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCAT
1 GTGCACCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCAT
978846 CAAATACATT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
65 33 0.60
66 19 0.35
67 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCACCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGCTG
Found at i:978842 original size:46 final size:46
Alignment explanation
Indices: 978786--978907 Score: 210
Period size: 46 Copynumber: 2.6 Consensus size: 46
978776 TGCATGGCTG
978786 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGA
*
978832 GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAAACCCTGA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGA
978878 GTGCATCGATGCATGGCAAATGCA-TCGATG
1 GTGCATCGATGCAT--CAAATGCATTCGATG
978908 CATAAAATGC
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
46 59 0.82
47 6 0.08
48 7 0.10
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGA
Found at i:978860 original size:111 final size:111
Alignment explanation
Indices: 978719--978927 Score: 314
Period size: 111 Copynumber: 1.9 Consensus size: 111
978709 GGTGCACTAA
* *
978719 GAGTGCACCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGCCTGAGTGCATCGAATGCATG
1 GAGTGCACCGATGCATAAAATACATTCGATGTTTTCATAAA-ACCCTGAGTGCATCG-ATGCATG
*** *
978782 GCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCT
64 GCAAATGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCT
* *
978830 GAGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGC
1 GAGTGCACCGATGCATAAAATACATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGC
978895 AAATGCATCGATGCATAAAATGCATTCGATGTT
66 AAATGCATCGATGCATAAAATGCATTCGATGTT
978928 CAATTTATTC
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
111 66 0.75
112 19 0.22
113 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (111 bp):
GAGTGCACCGATGCATAAAATACATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGC
AAATGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCT
Found at i:978917 original size:17 final size:18
Alignment explanation
Indices: 978879--978925 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
978869 AAACCCTGAG
*
978879 TGCATCGATGCATGGCAAA
1 TGCATCGATGCAT-GAAAA
978898 TGCATCGATGCAT-AAAA
1 TGCATCGATGCATGAAAA
978915 TGCATTCGATG
1 TGCA-TCGATG
978926 TTCAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (18 bp):
TGCATCGATGCATGAAAA
Found at i:979286 original size:14 final size:14
Alignment explanation
Indices: 979251--979289 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
979241 TAAGATTTTC
*
979251 TTTGAAAA-TAAAT
1 TTTGAAAATTAAAG
979264 TTTGAAAAATTAAAG
1 TTTG-AAAATTAAAG
979279 TTTGAAAATTA
1 TTTGAAAATTA
979290 CTCCCCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 11 0.48
15 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (14 bp):
TTTGAAAATTAAAG
Found at i:981567 original size:21 final size:22
Alignment explanation
Indices: 981508--981586 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
981498 TGGCCTTGTT
981508 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACATTC-AGGCGTG
* * * *
981531 CATCGGTGTACCTTCATG-GTG
1 CATCGATGCACATTCAGGCGTG
*
981552 TATCGATGCACATTCAAAGG-GATG
1 CATCGATGCACATTC--AGGCG-TG
981576 CATCGATGCAC
1 CATCGATGCAC
981587 TGTTAAGTGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 14 0.33
22 2 0.05
23 15 0.35
24 12 0.28
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (22 bp):
CATCGATGCACATTCAGGCGTG
Found at i:982005 original size:15 final size:15
Alignment explanation
Indices: 981985--982018 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
981975 TTCTAGAACT
981985 ACATCTTCCTTAGCG
1 ACATCTTCCTTAGCG
*
982000 ACATCTTCCTTAGTG
1 ACATCTTCCTTAGCG
982015 ACAT
1 ACAT
982019 GGTCTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (15 bp):
ACATCTTCCTTAGCG
Found at i:985474 original size:22 final size:21
Alignment explanation
Indices: 985432--985471 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
985422 GAGTTTATTT
*
985432 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
985453 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
985472 ATAATTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:987534 original size:64 final size:65
Alignment explanation
Indices: 987424--987563 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 65
987414 ACTAAGAGTG
* *
987424 CATCGATGCATAAAATGCATTCGATGTTTCAAACTAGCCTGAGTGCATCGATGCATGG-TAT-GT
1 CATCGATGCATAAAATGCATTCAAAGTTTCAAACTAGCCTGAGTGCATCGATGCATGGAT-TGGT
987487 A
65 A
** *
987488 CATCGATGCATAAAATGCATTCAAAG-TTCAATTTATTCCATG-GTGCATCGATGCATGGATTGG
1 CATCGATGCATAAAATGCATTCAAAGTTTCAAACTA-GCC-TGAGTGCATCGATGCATGGATTGG
*
987551 TG
64 TA
987553 CATCGATGCAT
1 CATCGATGCAT
987564 CACTTTGAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
63 7 0.11
64 43 0.65
65 16 0.24
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (65 bp):
CATCGATGCATAAAATGCATTCAAAGTTTCAAACTAGCCTGAGTGCATCGATGCATGGATTGGTA
Found at i:991531 original size:273 final size:273
Alignment explanation
Indices: 991044--991592 Score: 1053
Period size: 273 Copynumber: 2.0 Consensus size: 273
991034 AAAACATATA
991044 TTCTTATGCTAATTCCACTTTACTTTATCTTTGGATTGCCCATGTACATTATTGAGAACAGAAGG
1 TTCTTATGCTAATTCCACTTTACTTTATCTTTGGATTGCCCATGTACATTATTGAGAACAGAAGG
* *
991109 TACGTGAATAAGCTGAGGTTGTGCAAAATGTTGTCGCCACAACTCGAATAAAATCCCACTAGGGG
66 TACGCGAATAAGCTGAGGTTGTGCAAAATGCTGTCGCCACAACTCGAATAAAATCCCACTAGGGG
*
991174 CACTAAATATTTGCCCCGAAGGACCACTATGTCCCAAAGGACCAGTGATAAACCCTCGACTCTTG
131 CACTAAATATTTGCCCCGAAGGACCACTATGTCCCAAAGGACCACTGATAAACCCTCGACTCTTG
991239 GCATGCCAATTATACATACAGTTCTCATATTAAATAACACGGGCTTAATTATAAATACATTTCTC
196 GCATGCCAATTATACATACAGTTCTCATATTAAATAACACGGGCTTAATTATAAATACATTTCTC
991304 ATTTCATATCTCT
261 ATTTCATATCTCT
991317 TTCTTATGCTAATTCCACTTTACTTTATCTTTGGATTGCCCATGTACATTATTGAGAACAGAAGG
1 TTCTTATGCTAATTCCACTTTACTTTATCTTTGGATTGCCCATGTACATTATTGAGAACAGAAGG
991382 TACGCGAATAAGCTGAGGTTGTGCAAAATGCTGTCGCCACAACTCGAATAAAATCCCACTAGGGG
66 TACGCGAATAAGCTGAGGTTGTGCAAAATGCTGTCGCCACAACTCGAATAAAATCCCACTAGGGG
* *
991447 CACTGAATATTTGCCCCGAAGGACCACTATGTCCCGAAGGACCACTGATAAACCCTCGACTCTTG
131 CACTAAATATTTGCCCCGAAGGACCACTATGTCCCAAAGGACCACTGATAAACCCTCGACTCTTG
991512 GCATGCCAATTATACATACAGTTCTCATATTAAATAACACGGGCTTAATTATAAATACATTTCTC
196 GCATGCCAATTATACATACAGTTCTCATATTAAATAACACGGGCTTAATTATAAATACATTTCTC
991577 ATTTCATATCTCT
261 ATTTCATATCTCT
991590 TTC
1 TTC
991593 ATCAATGTCC
Statistics
Matches: 271, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
273 271 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (273 bp):
TTCTTATGCTAATTCCACTTTACTTTATCTTTGGATTGCCCATGTACATTATTGAGAACAGAAGG
TACGCGAATAAGCTGAGGTTGTGCAAAATGCTGTCGCCACAACTCGAATAAAATCCCACTAGGGG
CACTAAATATTTGCCCCGAAGGACCACTATGTCCCAAAGGACCACTGATAAACCCTCGACTCTTG
GCATGCCAATTATACATACAGTTCTCATATTAAATAACACGGGCTTAATTATAAATACATTTCTC
ATTTCATATCTCT
Found at i:992139 original size:64 final size:64
Alignment explanation
Indices: 992068--992229 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
992058 TCCCTTAACA
* * * *
992068 GGTGCATCGATGCACTA-TCTATGCATTGGTACA-TAAATCCCATTCGATGTTTGTATTTTAAGG
1 GGTGCATCGATACACTACT-TATGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAAG
992131 G
64 G
* * ** *
992132 GGTGCATCGATACACTACTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAGG
1 GGTGCATCGATACACTACTTATGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAGG
* * * *
992196 AGTGCATCGATACACTTCATGTGCATCGATACAC
1 GGTGCATCGATACACTACTTATGCATCGATACAC
992230 CTTGAACAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 82 0.98
65 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
GGTGCATCGATACACTACTTATGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAGG
Found at i:998036 original size:20 final size:20
Alignment explanation
Indices: 998011--998050 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
998001 TTTTGGTGCA
998011 GAGGGAA-TCGATCCCCCCTT
1 GAGGGAACT-GATCCCCCCTT
*
998031 GAGGGAACTGATTCCCCCTT
1 GAGGGAACTGATCCCCCCTT
998051 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GAGGGAACTGATCCCCCCTT
Found at i:998048 original size:21 final size:23
Alignment explanation
Indices: 998013--998072 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
998003 TTGGTGCAGA
*
998013 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCCTTGAAG
* *
998033 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
998056 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
998073 ACAGGGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 7 0.22
21 9 0.28
22 1 0.03
23 15 0.47
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:998080 original size:21 final size:21
Alignment explanation
Indices: 998054--998093 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
998044 CCCCCTTTGA
*
998054 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
998075 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
998094 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1003877 original size:72 final size:72
Alignment explanation
Indices: 1003766--1003899 Score: 259
Period size: 72 Copynumber: 1.9 Consensus size: 72
1003756 ACAGTCACAC
*
1003766 ATATATATATATAGTTTCTCAGCCTACTAACAAATATGATGACCTTATATCTAACACAAGGTTTA
1 ATATATATATATAGTTTCTCAGCCTACTAACAAATATGATGACCTTATATCCAACACAAGGTTTA
1003831 TATATAT
66 TATATAT
1003838 ATATATATATATAGTTTCTCAGCCTACTAACAAATATGATGACCTTATATCCAACACAAGGT
1 ATATATATATATAGTTTCTCAGCCTACTAACAAATATGATGACCTTATATCCAACACAAGGT
1003900 GTTAAAGAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (72 bp):
ATATATATATATAGTTTCTCAGCCTACTAACAAATATGATGACCTTATATCCAACACAAGGTTTA
TATATAT
Found at i:1005714 original size:23 final size:23
Alignment explanation
Indices: 1005680--1005748 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1005670 CACCACAGCT
*
1005680 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
1005703 CGTAGAATTGCACTGTAA-TGTCG
1 CGTAGAAATGCACCG-AAGTGCCA
1005726 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1005749 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 2 0.06
23 31 0.89
24 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1006011 original size:22 final size:23
Alignment explanation
Indices: 1005961--1006004 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1005951 CATTTCACAT
*
1005961 TTTCACATAAACACGTAGTTCAC
1 TTTCACATAAACACGTAGCTCAC
*
1005984 TTTCACAT-AGCACGTAGCTCA
1 TTTCACATAAACACGTAGCTCA
1006005 TATTCACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (23 bp):
TTTCACATAAACACGTAGCTCAC
Found at i:1006156 original size:2 final size:2
Alignment explanation
Indices: 1006149--1006185 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1006139 TTCATCTTCC
1006149 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
1006186 TTTTTGCTAT
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:1010818 original size:23 final size:23
Alignment explanation
Indices: 1010792--1010860 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1010782 CACCACAGCT
*
1010792 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1010815 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1010838 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1010861 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1011270 original size:2 final size:2
Alignment explanation
Indices: 1011263--1011293 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1011253 AATTCATCTT
1011263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1011294 CATTTTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1012434 original size:24 final size:20
Alignment explanation
Indices: 1012377--1012439 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 20
1012367 TTTCCCTTGA
*
1012377 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
1012397 AGTGTATCGATGCATCCCTTATC
1 AGTGCATCGATGCAT-CC-TA-C
1012420 ATGTGCATCGATGCACTCCT
1 A-GTGCATCGATGCA-TCCT
1012440 TACGCATCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.40
21 1 0.03
22 2 0.06
23 3 0.09
24 14 0.40
25 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:1012440 original size:24 final size:21
Alignment explanation
Indices: 1012377--1012454 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 21
1012367 TTTCCCTTGA
*
1012377 AGTGCATCGATGCATTC-TAC
1 AGTGCATCGATGCATCCTTAC
*
1012397 AGTGTATCGATGCATCCCTTATC
1 AGTGCATCGATGCAT-CCTTA-C
1012420 ATGTGCATCGATGCACTCCTTAC
1 A-GTGCATCGATGCA-TCCTTAC
1012443 ---GCATCGATGCAT
1 AGTGCATCGATGCAT
1012455 TAATTGCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 1 0.02
19 11 0.22
20 14 0.28
21 1 0.02
22 2 0.04
23 3 0.06
24 17 0.34
25 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (21 bp):
AGTGCATCGATGCATCCTTAC
Found at i:1018401 original size:31 final size:31
Alignment explanation
Indices: 1018363--1018468 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
1018353 AAACTACCTA
1018363 TTTGGTCACTTATATATTATCTAATTTATGT
1 TTTGGTCACTTATATATTATCTAATTTATGT
* ** ** **
1018394 TTTGGTCACTCGATTATTATTTAGGGTAAACTACCT
1 TTTGGTCACT-TA-TA-TA-TTA-TCTAATTTATGT
1018430 ATTTGGTCACTT-TATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
1018461 TTTGGTCA
1 TTTGGTCA
1018469 TTCGATTATT
Statistics
Matches: 55, Mismatches: 14, Indels: 13
0.67 0.17 0.16
Matches are distributed among these distances:
30 8 0.15
31 16 0.29
32 4 0.07
33 4 0.07
34 4 0.07
35 3 0.05
36 6 0.11
37 10 0.18
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATCTAATTTATGT
Found at i:1018477 original size:67 final size:68
Alignment explanation
Indices: 1018338--1018480 Score: 261
Period size: 67 Copynumber: 2.1 Consensus size: 68
1018328 CGGTTAGGGA
*
1018338 ATTATTTTTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCAC
1 ATTATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCAC
1018403 TCG
66 TCG
*
1018406 ATTATTATTTAGGGTAAACTACCTATTTGGTCACTT-TATATTATCTAATTTATGTTTTGGTCAT
1 ATTATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCAC
1018470 TCG
66 TCG
1018473 ATTATTAT
1 ATTATTAT
1018481 ATTTTTCAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 38 0.52
68 35 0.48
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.50
Consensus pattern (68 bp):
ATTATTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCAC
TCG
Found at i:1018481 original size:36 final size:35
Alignment explanation
Indices: 1018375--1018483 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 35
1018365 TGGTCACTTA
1018375 TATATTATCTAATTTATGTTTTGGTCACTCGATTAT
1 TATATTATCTAATTTATGTTTTGGTCA-TCGATTAT
** ** **
1018411 TAT-TTAGGGTAAACTACCTATTTGGTCA-C---T-T
1 TATATTA-TCTAATTTATGT-TTTGGTCATCGATTAT
1018442 TATATTATCTAATTTATGTTTTGGTCATTCGATTAT
1 TATATTATCTAATTTATGTTTTGGTCA-TCGATTAT
1018478 TATATT
1 TATATT
1018484 TTTCAAAATT
Statistics
Matches: 52, Mismatches: 12, Indels: 18
0.63 0.15 0.22
Matches are distributed among these distances:
30 8 0.15
31 10 0.19
32 5 0.10
35 5 0.10
36 16 0.31
37 8 0.15
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (35 bp):
TATATTATCTAATTTATGTTTTGGTCATCGATTAT
Found at i:1024668 original size:9 final size:9
Alignment explanation
Indices: 1024654--1024681 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1024644 AATTCTCAAA
1024654 AACCAAATT
1 AACCAAATT
1024663 AACCAAATT
1 AACCAAATT
1024672 AACCAAATT
1 AACCAAATT
1024681 A
1 A
1024682 GGTTAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (9 bp):
AACCAAATT
Found at i:1033340 original size:24 final size:25
Alignment explanation
Indices: 1033313--1033360 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1033303 ATAAAAATTA
**
1033313 TTTATATTTATTATT-AATTTGATT
1 TTTATATTTAAAATTAAATTTGATT
*
1033337 TTTATTTTTAAAATTAAATTTGAT
1 TTTATATTTAAAATTAAATTTGAT
1033361 CTTCAACCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTATATTTAAAATTAAATTTGATT
Found at i:1033714 original size:59 final size:59
Alignment explanation
Indices: 1033651--1033764 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
1033641 ACTGTGACTT
** *
1033651 TCATTCTAAATTAGTCCTTAAACTTTTGGAA-TTTCAATTTCTTCCCCAAA-TTATGGTCC
1 TCATTCTAAATTAGTCCCCAAAC-TTTGGAACTTTCAATTTCAT-CCCAAAGTTATGGTCC
* *
1033710 TCATTTTAAATTGGTCCCCAAACTTTGGAATCTTTCAATTTCATCCCAAAGTTAT
1 TCATTCTAAATTAGTCCCCAAACTTTGGAA-CTTTCAATTTCATCCCAAAGTTAT
1033765 CCAAATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 7 0.15
59 25 0.53
60 15 0.32
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (59 bp):
TCATTCTAAATTAGTCCCCAAACTTTGGAACTTTCAATTTCATCCCAAAGTTATGGTCC
Found at i:1036928 original size:15 final size:15
Alignment explanation
Indices: 1036908--1036941 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1036898 GTTTTATTGC
*
1036908 TGAAAAAGGTGGTAA
1 TGAAAAAGGTGGCAA
1036923 TGAAAAAGGTGGCAA
1 TGAAAAAGGTGGCAA
1036938 TGAA
1 TGAA
1036942 GTCGCAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.32, T:0.18
Consensus pattern (15 bp):
TGAAAAAGGTGGCAA
Found at i:1037704 original size:16 final size:16
Alignment explanation
Indices: 1037682--1037721 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1037672 CGAGCTTAAC
*
1037682 AAACGAGTTTACCAAG
1 AAACGAGTTTAACAAG
* *
1037698 CAACGAGCTTAACAAG
1 AAACGAGTTTAACAAG
1037714 AAACGAGT
1 AAACGAGT
1037722 CGAGCAATAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (16 bp):
AAACGAGTTTAACAAG
Found at i:1039988 original size:5 final size:5
Alignment explanation
Indices: 1039978--1040003 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1039968 ATAAAGTTTC
1039978 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
1040004 ATATATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1043015 original size:61 final size:61
Alignment explanation
Indices: 1042920--1043041 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
1042910 CAATTAAAAT
1042920 GCACCAACCAGTAACACTAAAAATAACACATAAATAGCTAGGATCATCAAACATATGATGA
1 GCACCAACCAGTAACACTAAAAATAACACATAAATAGCTAGGATCATCAAACATATGATGA
*
1042981 GCACCAACCATTAACACTAAAAATAACACATAAATAGCTAGGATCATCAAACATATGATGA
1 GCACCAACCAGTAACACTAAAAATAACACATAAATAGCTAGGATCATCAAACATATGATGA
1043042 TAGCTAGCTG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (61 bp):
GCACCAACCAGTAACACTAAAAATAACACATAAATAGCTAGGATCATCAAACATATGATGA
Found at i:1044150 original size:16 final size:15
Alignment explanation
Indices: 1044109--1044151 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1044099 TGCTCAACTT
**
1044109 AAAATTAAAAATT-A
1 AAAATTAATTATTAA
1044123 AAAATTAATTATTAA
1 AAAATTAATTATTAA
1044138 AAAATTAAGTTATT
1 AAAATTAA-TTATT
1044152 CGAGTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
AAAATTAATTATTAA
Found at i:1052757 original size:27 final size:25
Alignment explanation
Indices: 1052705--1052758 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
1052695 TTAACTTAAA
1052705 ATAAAATATTAAAAGTCAAAATACT
1 ATAAAATATTAAAAGTCAAAATACT
1052730 ATAAAATATATAAGAA-TCAAAATAACT
1 ATAAAATAT-TAA-AAGTCAAAAT-ACT
1052757 AT
1 AT
1052759 TTAATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 9 0.35
26 10 0.38
27 7 0.27
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (25 bp):
ATAAAATATTAAAAGTCAAAATACT
Found at i:1061560 original size:13 final size:13
Alignment explanation
Indices: 1061542--1061586 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
1061532 GTCATAAATC
1061542 TATGACGCACATT
1 TATGACGCACATT
1061555 TATGACGCACATT
1 TATGACGCACATT
* * *
1061568 TATGAAGCGCATG
1 TATGACGCACATT
1061581 TATGAC
1 TATGAC
1061587 TTACATTGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:1061772 original size:85 final size:84
Alignment explanation
Indices: 1061565--1061870 Score: 413
Period size: 85 Copynumber: 3.6 Consensus size: 84
1061555 TATGACGCAC
* *
1061565 ATTTATGAAGCGCATGTATGACTTACATTGCGCGTCATTGAAGC-CTCCGTCATAAATTAATATG
1 ATTTATGAA-CGCATGTATGACTTACATTGCGCGTCATTAAAGCAC-CCGTCATAAATTAAGATG
*
1061629 ACACACATTTGTGTATCATAA
64 ACACACATTTGTGTGTCATAA
*
1061650 ATTTATG-ACGCATGTATGACTTACATTGCGCGTCATTAAAGCACCCGTCATATATTAAGATGAC
1 ATTTATGAACGCATGTATGACTTACATTGCGCGTCATTAAAGCACCCGTCATAAATTAAGATGAC
*
1061714 ACACATTTGTGCGTCATAA
66 ACACATTTGTGTGTCATAA
* *
1061733 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTAAAGCCCCCGTCATAAATCT--GTTT
1 ATTTATGA-ACGCATGTATGACTTACATTGCGCGTCATTAAAGCACCCGTCATAAAT-TAAG-AT
*
1061796 GACATACATTTGTGTGTCATAA
63 GACACACATTTGTGTGTCATAA
* * * * *
1061818 ATTTATGACACACATATATGACTTACATTGCGTGTCATTGAAGCACACGTCAT
1 ATTTATGA-ACGCATGTATGACTTACATTGCGCGTCATTAAAGCACCCGTCAT
1061871 TTAAAAAGAC
Statistics
Matches: 200, Mismatches: 16, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
83 75 0.38
84 3 0.01
85 121 0.61
86 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (84 bp):
ATTTATGAACGCATGTATGACTTACATTGCGCGTCATTAAAGCACCCGTCATAAATTAAGATGAC
ACACATTTGTGTGTCATAA
Found at i:1061925 original size:2 final size:2
Alignment explanation
Indices: 1061918--1061968 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1061908 TTTCGGAAAT
* *
1061918 TA TA TA TA TA TA AA TA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1061960 TA TA TA TA T
1 TA TA TA TA T
1061969 TGTAGATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1063474 original size:12 final size:12
Alignment explanation
Indices: 1063457--1063487 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1063447 ATATATTGAT
1063457 AATCAAATGAAA
1 AATCAAATGAAA
1063469 AATCAAATGAAA
1 AATCAAATGAAA
*
1063481 AAACAAA
1 AATCAAA
1063488 CCCGAGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:1066161 original size:15 final size:15
Alignment explanation
Indices: 1066136--1066177 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1066126 GATGTTTTCT
*
1066136 TTTTCCTTCTTTGACG
1 TTTT-CTTCTTAGACG
1066152 TTTTCTTCTTAGACG
1 TTTTCTTCTTAGACG
*
1066167 TTGTCTTCTTA
1 TTTTCTTCTTA
1066178 CCCCATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.10, C:0.21, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTTCTTCTTAGACG
Found at i:1069525 original size:13 final size:13
Alignment explanation
Indices: 1069486--1069541 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 13
1069476 TTTATCGTAC
* *
1069486 TTTTTGTTTTGAT
1 TTTTTGTTATCAT
*
1069499 TTTTTGATA-CAT
1 TTTTTGTTATCAT
*
1069511 TTTTTGTTATTA-
1 TTTTTGTTATCAT
1069523 TTTTTGTTTATCAT
1 TTTTTG-TTATCAT
1069537 TTTTT
1 TTTTT
1069542 TCAGGACTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
12 16 0.47
13 13 0.38
14 5 0.15
ACGTcount: A:0.14, C:0.04, G:0.09, T:0.73
Consensus pattern (13 bp):
TTTTTGTTATCAT
Found at i:1072207 original size:40 final size:40
Alignment explanation
Indices: 1072152--1072273 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
1072142 TGCAGGTTTA
1072152 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
1072192 TAATACACTTCGGTGTATATGGTGGGCATGACCTTACGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1072232 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1072272 TA
1 TA
1072274 GCACTACGGT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1072473 original size:47 final size:45
Alignment explanation
Indices: 1072378--1072504 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 45
1072368 GTAACCATGC
* * *
1072378 AAATAAGCTTATGAGCTTACGGAA-ATAATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATA-AATGGTAAGTATATAGGAA
* * *
1072423 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
1072470 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1072505 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
45 33 0.46
47 38 0.53
48 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:1074318 original size:2 final size:2
Alignment explanation
Indices: 1074311--1074428 Score: 68
Period size: 2 Copynumber: 61.0 Consensus size: 2
1074301 TTTCGTCCCC
* * *
1074311 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA -A T- TA TA TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
1074351 TA TT TA TT TA TT TA CTA TA T- TC TT TT TT TA TT TA TA T- TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1074392 TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1074429 GATGTATTAA
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
1 6 0.06
2 83 0.89
3 4 0.04
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:1074488 original size:88 final size:94
Alignment explanation
Indices: 1074311--1074503 Score: 220
Period size: 94 Copynumber: 2.1 Consensus size: 94
1074301 TTTCGTCCCC
* * ** *
1074311 TATATATATATATATATATATATATATTTAATTATATTTTTATTTATTTATTTACTATATTCTTT
1 TATATATATATATATATATATATAGATGTAATTATATTTTTATCGATTTATTTACTATATTCATT
*
1074376 TTTTATTTATATTATATATCTTATATCAT
66 TTTTATTAATATTATATATCTTATATCAT
* *
1074405 TATATATATATATATATATATATAGATGT-ATTA-ATTTTTCTCGATTTA-TTA-TGTATAT-AT
1 TATATATATATATATATATATATAGATGTAATTATATTTTTATCGATTTATTTACTATAT-TCAT
* **
1074465 TTTTTCTTAATATTATAT-T-TTATATGTT
65 TTTTTATTAATATTATATATCTTATATCAT
*
1074493 TTTATATATAT
1 TATATATATAT
1074504 TTTCTTAATA
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
88 17 0.20
89 1 0.01
90 21 0.24
91 4 0.05
92 12 0.14
93 4 0.05
94 27 0.31
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (94 bp):
TATATATATATATATATATATATAGATGTAATTATATTTTTATCGATTTATTTACTATATTCATT
TTTTATTAATATTATATATCTTATATCAT
Found at i:1074499 original size:37 final size:34
Alignment explanation
Indices: 1074458--1074537 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 34
1074448 ATTTATTATG
1074458 TATATATTTTTTCTTAATATTATATTTTATATGTTTT
1 TATATATTTTTTCTTAATATTATA-TTT-T-TGTTTT
* *
1074495 TATATATATTTTCTTAATATTCTATTTTTGTTTT
1 TATATATTTTTTCTTAATATTATATTTTTGTTTT
*
1074529 TATTTATTT
1 TATATATTT
1074538 ATATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
34 13 0.33
35 1 0.03
36 3 0.08
37 22 0.56
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.69
Consensus pattern (34 bp):
TATATATTTTTTCTTAATATTATATTTTTGTTTT
Found at i:1074639 original size:36 final size:38
Alignment explanation
Indices: 1074568--1074660 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 38
1074558 TACTTTATTT
* *
1074568 TATT-TTTTTTATTT-TTTTTCTTAATATCATGTATATC
1 TATTATTTTTTATTTGTTTTACTTAATAT-ATATATATC
* *
1074605 T-TTATTTTTTATTTGTTTTACTTAGTAT-TATATATT
1 TATTATTTTTTATTTGTTTTACTTAATATATATATATC
1074641 TATTA-TTTTTATTTGTTTTA
1 TATTATTTTTTATTTGTTTTA
1074661 GTAAATATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
36 24 0.49
37 14 0.29
38 11 0.22
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (38 bp):
TATTATTTTTTATTTGTTTTACTTAATATATATATATC
Found at i:1074670 original size:36 final size:35
Alignment explanation
Indices: 1074566--1074670 Score: 97
Period size: 36 Copynumber: 2.9 Consensus size: 35
1074556 TTTACTTTAT
* *
1074566 TTTATTTTTTTTATTT-TTTTTCTTAATATCATGTATATC
1 TTTA-TTTTTTTATTTGTTTTAC-TAA-AT-AT-TATATA
* *
1074605 TTTA-TTTTTTATTTGTTTTACTTAGTATTATATA
1 TTTATTTTTTTATTTGTTTTACTAAATATTATATA
*
1074639 TTTATTATTTTTATTTGTTTTAGTAAATATTA
1 TTTATT-TTTTTATTTGTTTTACTAAATATTA
1074671 CTTTATGTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
34 9 0.16
35 3 0.05
36 23 0.41
37 12 0.21
38 5 0.09
39 4 0.07
ACGTcount: A:0.24, C:0.04, G:0.05, T:0.68
Consensus pattern (35 bp):
TTTATTTTTTTATTTGTTTTACTAAATATTATATA
Found at i:1085301 original size:16 final size:16
Alignment explanation
Indices: 1085280--1085324 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1085270 AAAATTAAAA
1085280 AAAGAACAAAAAAGAG
1 AAAGAACAAAAAAGAG
1085296 AAAGAACAAAAAAGAG
1 AAAGAACAAAAAAGAG
1085312 AAAGAACCAAAAA
1 AAAGAA-CAAAAA
1085325 TAAGGTGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 22 0.79
17 6 0.21
ACGTcount: A:0.76, C:0.09, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAACAAAAAAGAG
Found at i:1086485 original size:110 final size:110
Alignment explanation
Indices: 1086287--1086493 Score: 326
Period size: 110 Copynumber: 1.9 Consensus size: 110
1086277 GCTTCCCAGT
*
1086287 TTCAGAGCCAATTTCAACTTCACAGCGAGAGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAGAGATATTGAACTCAAGACAACACAAGCTCAACTTCA
*
1086352 CAACGAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* ** *
1086397 TTCAGAGTCAATTTCAACTTCACAGCGA-AGGATATTGAACTCGGGACAACACAAGCTTAACTTC
1 TTCAGAGCCAATTTCAACTTCACAGCGAGA-GATATTGAACTCAAGACAACACAAGCTCAACTTC
* *
1086461 ACAGCGAAGGGGCGGCTGACTGTCAACAAACAA
65 ACAACGAAGGGGCGACTGACTGTCAACAAACAA
1086494 TTTCCAGAGC
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
109 1 0.01
110 87 0.99
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAGAGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:1087975 original size:181 final size:178
Alignment explanation
Indices: 1087677--1088036 Score: 618
Period size: 181 Copynumber: 2.0 Consensus size: 178
1087667 CGCCGATGAC
**
1087677 CAAAAACGGGTGGGGTTTCAAAGTTTCGAACCTAGATCTCCGAGGCATGTTTTTTTTTAAAGTAT
1 CAAAAACGGGTGGGGTTTCAAAGTTTCGAACCTAGATCTCCGAGGCATGTTCATTTTTAAAGTAT
1087742 TTAATATCCCCTAAGTCAATCTTAATCTTTAATTTATCTTGAAATTTACCCTTTAATTTTACTTT
66 TTAATATCCCCTAAGTCAATCTTAATCTTTAATTTATCTTGAAATTTACCCTTTAATTTTACTTT
1087807 TATATTAATTTCATCCC-ATATATATATTTTT-ATTAT-TATTTTTTA
131 TATATTAATTTCATCCCAATATATATATTTTTAATTATATATTTTTTA
1087852 CAAAAACGGGTGGGGTTTCAAAGTTTCGAACCTAGATCTACTCCCGAGGCATGTTCATTTTTAAA
1 CAAAAACGGGTGGGGTTTCAAAGTTTCGAACCTAGA--T-CT-CCGAGGCATGTTCATTTTTAAA
1087917 GTATTTAATATTCCCCCTAAGTCAATCTTAATCTTTAATTTATCTTGAAATTTACCCTTTAATTT
62 GTATTTAATA-T-CCCCTAAGTCAATCTTAATCTTTAATTTATCTTGAAATTTACCCTTTAATTT
1087982 TACTTTTATATTAATTTCATCCCATATATATATATTTTTAATTATATATTTTTTA
125 TACTTTTATATTAATTTCATCCCA-ATATATATATTTTTAATTATATATTTTTTA
1088037 TTTACTATAT
Statistics
Matches: 173, Mismatches: 2, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
175 36 0.21
177 1 0.01
178 2 0.01
179 30 0.17
180 1 0.01
181 75 0.43
183 14 0.08
184 5 0.03
185 9 0.05
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (178 bp):
CAAAAACGGGTGGGGTTTCAAAGTTTCGAACCTAGATCTCCGAGGCATGTTCATTTTTAAAGTAT
TTAATATCCCCTAAGTCAATCTTAATCTTTAATTTATCTTGAAATTTACCCTTTAATTTTACTTT
TATATTAATTTCATCCCAATATATATATTTTTAATTATATATTTTTTA
Found at i:1088027 original size:16 final size:15
Alignment explanation
Indices: 1088008--1088047 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
1087998 TCATCCCATA
1088008 TATATATATTTTTAAT
1 TATATAT-TTTTTAAT
*
1088024 TATATATTTTTTATT
1 TATATATTTTTTAAT
1088039 TACTATATT
1 TA-TATATT
1088048 CCTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATATTTTTTAAT
Found at i:1088027 original size:18 final size:18
Alignment explanation
Indices: 1088006--1088091 Score: 52
Period size: 21 Copynumber: 4.6 Consensus size: 18
1087996 TTTCATCCCA
1088006 TATATATATATTTTTAA-
1 TATATATATATTTTTAAT
*
1088023 T-TATATAT-TTTTTATT
1 TATATATATATTTTTAAT
* * *
1088039 TACTATATTCCTTTTTTTATT
1 TA-TATA-T-ATATTTTTAAT
*
1088060 TATATTATATTATTTATAAT
1 TATA-TATA-TATTTTTAAT
1088080 ATATATATATAT
1 -TATATATATAT
1088092 ATGTGTATGT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
15 6 0.11
16 8 0.15
17 1 0.02
18 4 0.07
19 4 0.07
20 15 0.28
21 16 0.30
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATATATATTTTTAAT
Found at i:1088074 original size:14 final size:14
Alignment explanation
Indices: 1088055--1088093 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1088045 ATTCCTTTTT
1088055 TTATTTATATTATA
1 TTATTTATATTATA
*
1088069 TTATTTATAATATA
1 TTATTTATATTATA
*
1088083 TATATATATAT
1 T-TATTTATAT
1088094 GTGTATGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:1088195 original size:37 final size:35
Alignment explanation
Indices: 1088135--1088211 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 35
1088125 TATTATGTAC
*
1088135 ATAT-TTTTTCTTAATATTATATTTTCTACGTTTTTAT
1 ATATATTTTTCTTAATATTATATTTT-T--GTTTATAT
*
1088172 ATATATTTTT-TTAATATTCTATTTTTGTTTATAT
1 ATATATTTTTCTTAATATTATATTTTTGTTTATAT
1088206 ATATAT
1 ATATAT
1088212 ATATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 13 0.35
36 1 0.03
37 18 0.49
38 5 0.14
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (35 bp):
ATATATTTTTCTTAATATTATATTTTTGTTTATAT
Found at i:1088208 original size:2 final size:2
Alignment explanation
Indices: 1088201--1088227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1088191 TATTTTTGTT
1088201 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 T
1088228 TATTTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1088309 original size:36 final size:38
Alignment explanation
Indices: 1088239--1088330 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 38
1088229 ATTTTTACTT
*
1088239 TATT-TTTTTTATTT-TTTT-CTTAATATCATGTATATC
1 TATTATTTTTTATTTGTTTTACTTAATAT-ATATATATC
* *
1088275 T-TTATTTTTTATTTGTTTTACTTAGTAT-TATATATT
1 TATTATTTTTTATTTGTTTTACTTAATATATATATATC
1088311 TATTA-TTTTTATTTGTTTTA
1 TATTATTTTTTATTTGTTTTA
1088331 GTATATACTA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
35 2 0.04
36 33 0.67
37 7 0.14
38 7 0.14
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (38 bp):
TATTATTTTTTATTTGTTTTACTTAATATATATATATC
Found at i:1088396 original size:18 final size:17
Alignment explanation
Indices: 1088369--1088402 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1088359 ATTTTTATTC
1088369 TTTTTAATTTCTTTTACA
1 TTTTTAATTT-TTTTACA
*
1088387 TTTTTTATTTTTTTAC
1 TTTTTAATTTTTTTAC
1088403 TCCATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTAATTTTTTTACA
Found at i:1088468 original size:19 final size:19
Alignment explanation
Indices: 1088446--1088487 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1088436 TTTTTAAACA
1088446 TTTTATTCATTTTGT-TTAT
1 TTTTATT-ATTTTGTATTAT
*
1088465 TTTTATTATTTTTTATTAT
1 TTTTATTATTTTGTATTAT
1088484 TTTT
1 TTTT
1088488 TTACGTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTATTATTTTGTATTAT
Found at i:1088490 original size:11 final size:10
Alignment explanation
Indices: 1088446--1088488 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
1088436 TTTTTAAACA
1088446 TTTTATTCATT
1 TTTTATT-ATT
*
1088457 TTGT-TTA-T
1 TTTTATTATT
1088465 TTTTATTATT
1 TTTTATTATT
1088475 TTTTATTATT
1 TTTTATTATT
1088485 TTTT
1 TTTT
1088489 TACGTGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 17 0.61
11 3 0.11
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTATTATT
Found at i:1090754 original size:21 final size:22
Alignment explanation
Indices: 1090719--1090761 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1090709 TGCACTTTCG
1090719 GCAGCCCTATTTCTATGACTTT
1 GCAGCCCTATTTCTATGACTTT
*
1090741 GCAG-CCTTTTTCTATGACTTT
1 GCAGCCCTATTTCTATGACTTT
1090762 TAACAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.16, C:0.26, G:0.14, T:0.44
Consensus pattern (22 bp):
GCAGCCCTATTTCTATGACTTT
Found at i:1101940 original size:104 final size:104
Alignment explanation
Indices: 1101760--1101970 Score: 422
Period size: 104 Copynumber: 2.0 Consensus size: 104
1101750 CATGTATAGA
1101760 TAGTTTGGGGTTGTTTAAGTGCCGTAGTCTCTGACTTGTTGTTTGAGATATAAGATTCTTCTGTG
1 TAGTTTGGGGTTGTTTAAGTGCCGTAGTCTCTGACTTGTTGTTTGAGATATAAGATTCTTCTGTG
1101825 TATTTTAGTCCACCCTAAAGTTTACTCTTTTTTCCTATT
66 TATTTTAGTCCACCCTAAAGTTTACTCTTTTTTCCTATT
1101864 TAGTTTGGGGTTGTTTAAGTGCCGTAGTCTCTGACTTGTTGTTTGAGATATAAGATTCTTCTGTG
1 TAGTTTGGGGTTGTTTAAGTGCCGTAGTCTCTGACTTGTTGTTTGAGATATAAGATTCTTCTGTG
1101929 TATTTTAGTCCACCCTAAAGTTTACTCTTTTTTCCTATT
66 TATTTTAGTCCACCCTAAAGTTTACTCTTTTTTCCTATT
1101968 TAG
1 TAG
1101971 GCTTAGGGGT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 107 1.00
ACGTcount: A:0.18, C:0.15, G:0.19, T:0.47
Consensus pattern (104 bp):
TAGTTTGGGGTTGTTTAAGTGCCGTAGTCTCTGACTTGTTGTTTGAGATATAAGATTCTTCTGTG
TATTTTAGTCCACCCTAAAGTTTACTCTTTTTTCCTATT
Found at i:1105304 original size:64 final size:65
Alignment explanation
Indices: 1105199--1105363 Score: 221
Period size: 64 Copynumber: 2.6 Consensus size: 65
1105189 TTTCAAAGTA
* **
1105199 GTGTACCGATGCACCA-TCTAATGCATCGATGCAC-CCTTGAATAAATTGAATTTCGAATGCATT
1 GTGTACCGATGCA-CAGACT-ATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATT
1105262 TT
64 TT
* **
1105264 GTGTACCGATGCACAAGGC-ATGCATCGATGCACTCC-TGAATATTTTGAACATCGAATGCATTT
1 GTGTACCGATGCAC-AGACTATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTT
1105327 T
65 T
1105328 GTGTACCGATGCACAGACTATGCATCGATGCACTCC
1 GTGTACCGATGCACAGACTATGCATCGATGCACTCC
1105364 AGGCTCATTT
Statistics
Matches: 90, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
63 3 0.03
64 70 0.78
65 16 0.18
66 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (65 bp):
GTGTACCGATGCACAGACTATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTT
Found at i:1105375 original size:64 final size:65
Alignment explanation
Indices: 1105251--1105406 Score: 192
Period size: 64 Copynumber: 2.4 Consensus size: 65
1105241 AAATTGAATT
* *
1105251 TCGAATGCATTTTGTGTACCGATGCACAAGGCATGCATCGATGCACTCCTGAATATTTTG-AACA
1 TCGAATGCATTTTGTGTACCGATGCACAAGACATGCATCGATGCACTCCAGAATATTTTGAAACA
**
1105315 TCGAATGCATTTTGTGTACCGATGCAC-AGACTATGCATCGATGCACTCCAGGCTCA-TTTGAAA
1 TCGAATGCATTTTGTGTACCGATGCACAAGAC-ATGCATCGATGCACTCCAGAAT-ATTTTGAAA
*
1105378 GA
64 CA
* * * *
1105380 TCGAATGTATTTTATGCATCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
1105407 CCCAAGTGTA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
63 3 0.04
64 50 0.62
65 27 0.34
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAGACATGCATCGATGCACTCCAGAATATTTTGAAACA
Found at i:1107320 original size:23 final size:22
Alignment explanation
Indices: 1107290--1107391 Score: 111
Period size: 23 Copynumber: 4.7 Consensus size: 22
1107280 ACACTAGTTA
1107290 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCA-CCCTTGAAT
* *
1107313 GTGCATCGATTCA-CCATGAAT
1 GTGCATCGATGCACCCTTGAAT
*
1107334 GTGCACCGATGCACTCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
* *
1107357 GTGCATCGATGCACTC-TG-CT
1 GTGCATCGATGCACCCTTGAAT
*
1107377 GTGCATCGATACACC
1 GTGCATCGATGCACC
1107392 AGTCGGATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.21
21 20 0.30
22 1 0.01
23 32 0.48
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:1110118 original size:64 final size:64
Alignment explanation
Indices: 1110025--1110169 Score: 202
Period size: 64 Copynumber: 2.3 Consensus size: 64
1110015 GCACCATCTA
* ** ** *
1110025 ATGCATCGATTCAC-CCTTGAATAAATTGAATTTCGAATGCATTTTGTGTACCGATGCACAAGGC
1 ATGCATCGATGCACTCC-TGAATATTTTGAACATCGAATGCATTTTGTGTACCGATGCACAAAGC
* *
1110089 ATGCATTGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTGTGTACCGATGCACAAATC
1 ATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTGTGTACCGATGCACAAAGC
1110153 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
1110170 AGACTCATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 69 0.97
65 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTGTGTACCGATGCACAAAGC
Found at i:1110181 original size:64 final size:65
Alignment explanation
Indices: 1110057--1110198 Score: 198
Period size: 64 Copynumber: 2.2 Consensus size: 65
1110047 AAATTGAATT
* * *
1110057 TCGAATGCATTTTGTGTACCGATGCACAAGGCATGCATTGATGCACTCCTGAATATTTTG-AACA
1 TCGAATGCATTTTGTGTACCGATGCACAAAGCATGCATCGATGCACTCCAGAATATTTTGAAACA
* * *
1110121 TCGAATGCATTTTGTGTACCGATGCACAAATCATGCATCGATGCACTCCAGACTCA-TTTGAAAG
1 TCGAATGCATTTTGTGTACCGATGCACAAAGCATGCATCGATGCACTCCAGAAT-ATTTTGAAAC
1110185 A
65 A
*
1110186 TCGAATGTATTTT
1 TCGAATGCATTTT
1110199 ATGCATCAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 53 0.77
65 16 0.23
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAAGCATGCATCGATGCACTCCAGAATATTTTGAAACA
Found at i:1110437 original size:20 final size:20
Alignment explanation
Indices: 1110408--1110446 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1110398 AGAGCTCATA
*
1110408 TAAGATCATATAGATGCATT
1 TAAGAGCATATAGATGCATT
*
1110428 TAAGAGCATATAGTTGCAT
1 TAAGAGCATATAGATGCAT
1110447 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
TAAGAGCATATAGATGCATT
Found at i:1129446 original size:2 final size:2
Alignment explanation
Indices: 1129439--1129498 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
1129429 AGCTTTCTTT
1129439 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1129481 TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA
1129499 AAATTTTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1130112 original size:31 final size:31
Alignment explanation
Indices: 1130043--1130113 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1130033 GTCACGTGTC
* * *
1130043 ATGATAATAAAATATATTTTTAAAAGTTTAG
1 ATGAGAATAAAATATATTTTTAAAAGTTAAA
* *
1130074 ATAAGAATAAAATATATATTTTTAAA-TTAAA
1 ATGAGAATAAAATATAT-TTTTAAAAGTTAAA
1130105 ATGAGAATA
1 ATGAGAATA
1130114 TATTTTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (31 bp):
ATGAGAATAAAATATATTTTTAAAAGTTAAA
Found at i:1130139 original size:26 final size:26
Alignment explanation
Indices: 1130084--1130161 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
1130074 ATAAGAATAA
* ** * *
1130084 AATATATATTTTTAAATTAAAATGAG
1 AATATATTTTTTTAAATTAAGTTAAT
1130110 AATATATTTTTTTAAATTAAGTTAAT
1 AATATATTTTTTTAAATTAAGTTAAT
* *
1130136 AATAAAATTTATTT--ATTAAGTTAAT
1 AAT-ATATTTTTTTAAATTAAGTTAAT
1130161 A
1 A
1130162 TAAAAATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 12 0.27
26 24 0.55
27 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
AATATATTTTTTTAAATTAAGTTAAT
Found at i:1130141 original size:57 final size:56
Alignment explanation
Indices: 1130053--1130182 Score: 135
Period size: 57 Copynumber: 2.4 Consensus size: 56
1130043 ATGATAATAA
*
1130053 AATATATTTTTAAAAGTTTAGATAAGAATAAAATATATATTT-TTAAATTAAAATGAG
1 AATATATTTTTAAAAGTTAAGATAAGAATAAAAT-T-TATTTATTAAATTAAAATGAG
* * * * *
1130110 AATATATTTTTTTAAA-TTAAGTTAATAATAAAATTTATTTATTAAGTTAATAT-A-
1 AATATA-TTTTTAAAAGTTAAGATAAGAATAAAATTTATTTATTAAATTAAAATGAG
*
1130164 AAAATATTTTT-AAAGTTAA
1 AATATATTTTTAAAAGTTAA
1130183 TATATACAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
52 3 0.05
53 9 0.14
54 5 0.08
55 6 0.10
56 11 0.17
57 21 0.33
58 8 0.13
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (56 bp):
AATATATTTTTAAAAGTTAAGATAAGAATAAAATTTATTTATTAAATTAAAATGAG
Found at i:1130179 original size:23 final size:24
Alignment explanation
Indices: 1130125--1130186 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
1130115 ATTTTTTTAA
*
1130125 ATTAAGTTAATAATAAAATTTATTT
1 ATTAAGTTAAT-ATAAAATATATTT
1130150 ATTAAGTTAATATAAAA-ATATTT
1 ATTAAGTTAATATAAAATATATTT
1130173 -TTAAAGTTAATATA
1 ATT-AAGTTAATATA
1130187 TACAGATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
22 2 0.06
23 16 0.46
24 6 0.17
25 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (24 bp):
ATTAAGTTAATATAAAATATATTT
Found at i:1130187 original size:25 final size:26
Alignment explanation
Indices: 1130125--1130188 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
1130115 ATTTTTTTAA
*
1130125 ATTAAGTTAATA-ATAAAATTTATTT
1 ATTAAGTTAATATATAAAATATATTT
1130150 ATTAAGTTAATATA-AAAATAT-TTT
1 ATTAAGTTAATATATAAAATATATTT
*
1130174 -TAAAGTTAATATATA
1 ATTAAGTTAATATATA
1130189 CAGATTATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 12 0.34
24 4 0.11
25 18 0.51
26 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (26 bp):
ATTAAGTTAATATATAAAATATATTT
Found at i:1132380 original size:20 final size:20
Alignment explanation
Indices: 1132350--1132401 Score: 95
Period size: 20 Copynumber: 2.5 Consensus size: 20
1132340 ACCCAGTTTC
1132350 TAAATTCGCAACGCGAATATG
1 TAAA-TCGCAACGCGAATATG
1132371 TAAATCGCAACGCGAATATG
1 TAAATCGCAACGCGAATATG
1132391 TAAATCGCAAC
1 TAAATCGCAAC
1132402 AAAGAAGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGAATATG
Found at i:1132418 original size:20 final size:20
Alignment explanation
Indices: 1132395--1132473 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
1132385 AATATGTAAA
*
1132395 TCGCAACAAAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* **
1132415 TCGCAACGC-GTTTGTCAAAT
1 TCGCAACACAG-AAGTCAAAT
1132435 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
1132455 TCGCAACACAGAAGTCAAA
1 TCGCAACACAGAAGTCAAA
1132474 GCACGTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:1132419 original size:40 final size:40
Alignment explanation
Indices: 1132375--1132461 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
1132365 AATATGTAAA
1132375 TCGCAACGCGAATATGT-AAA-TCGCAACAAAGAAGTCAAAT
1 TCGCAACGCG--TATGTCAAATTCGCAACAAAGAAGTCAAAT
* *
1132415 TCGCAACGCGTTTGTCAAATTCGCAACACAGAAGTCAAAT
1 TCGCAACGCGTATGTCAAATTCGCAACAAAGAAGTCAAAT
1132455 TCGCAAC
1 TCGCAAC
1132462 ACAGAAGTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 4 0.09
39 3 0.07
40 36 0.84
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGTATGTCAAATTCGCAACAAAGAAGTCAAAT
Found at i:1132647 original size:22 final size:22
Alignment explanation
Indices: 1132596--1132647 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1132586 CTACGGCGAC
* * *
1132596 ATCCGTCCCCATCTCTGACGTA
1 ATCCGTCTCCATCTCCGACGAA
1132618 ATCCGTCTCCATCTCCGACGAA
1 ATCCGTCTCCATCTCCGACGAA
*
1132640 ATTCGTCT
1 ATCCGTCT
1132648 ATCTCTATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.38, G:0.13, T:0.29
Consensus pattern (22 bp):
ATCCGTCTCCATCTCCGACGAA
Found at i:1133089 original size:20 final size:20
Alignment explanation
Indices: 1133060--1133118 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1133050 GCGATTTTGT
*
1133060 CATTGTGATTTTAATTTTCG
1 CATTGCGATTTTAATTTTCG
* *
1133080 CGTTGCGATTTTCATTTTCG
1 CATTGCGATTTTAATTTTCG
*
1133100 CATTGCGAATTTAAGTTTT
1 CATTGCGATTTTAA-TTTT
1133119 AGTAACTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.51
Consensus pattern (20 bp):
CATTGCGATTTTAATTTTCG
Found at i:1135241 original size:21 final size:21
Alignment explanation
Indices: 1135215--1135331 Score: 112
Period size: 21 Copynumber: 5.6 Consensus size: 21
1135205 TGCATCTGTC
**
1135215 ATCGTTCAAGAGGCGTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
1135236 ATCGTTCAAGAGGCCCCT-CT
1 ATCGTTCAAGAGGCCCCTCCT
*
1135256 CATCGTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
1135278 ACCGTTCAAGAGGCCCCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
* ** *
1135298 CATCGTTCATGAGATCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
*
1135320 ACCGTTCAAGAG
1 ATCGTTCAAGAG
1135332 CCCGATTCAC
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.03
21 75 0.96
22 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:1135260 original size:42 final size:42
Alignment explanation
Indices: 1135213--1135331 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
1135203 AATGCATCTG
** * *
1135213 TCATCGTTCAAGAGGCGTCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
1135255 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* **
1135297 TCATCGTTCATGAGATCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAG
1135332 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:1136804 original size:64 final size:64
Alignment explanation
Indices: 1136689--1136846 Score: 253
Period size: 64 Copynumber: 2.5 Consensus size: 64
1136679 TTAATTGAAT
* *
1136689 TTTACATTGATTTTTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATGATTTTTTGCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGACGAGGAAATAAGAATGATTTTTTGCTTG
* * * *
1136754 TTTAATTAATTTGTAAAAGTTGATTTGTTTAATTGACGTGTAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGACGAGGAAATAAGAATGATTTTTTGCTTG
1136818 TTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
1136847 GTTTATTCAA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
64 82 0.95
65 4 0.05
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGACGAGGAAATAAGAATGATTTTTTGCTTG
Found at i:1136952 original size:20 final size:20
Alignment explanation
Indices: 1136905--1137004 Score: 110
Period size: 20 Copynumber: 5.0 Consensus size: 20
1136895 TACACTTTTA
*
1136905 CAACGCGAAAGTCAAATTCA
1 CAACGCGAAAGTCAAATTCG
*** *
1136925 CGTTGCGATAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
* * *
1136945 TAACGCGAAAGTTAAATTCA
1 CAACGCGAAAGTCAAATTCG
**
1136965 CAACGTTAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
1136985 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
1137005 TGTTGCGATT
Statistics
Matches: 61, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:1136962 original size:40 final size:40
Alignment explanation
Indices: 1136905--1137013 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
1136895 TACACTTTTA
1136905 CAACGCGAAAGTCAAATTCACGTTGCGATAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCACGTTGCGATAGTCAAATTCG
* * *** ** *
1136945 TAACGCGAAAGTTAAATTCACAACGTTAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCACGTTGCGATAGTCAAATTCG
**
1136985 CAACGCGAAAGTCAAATTCGTGTTGCGAT
1 CAACGCGAAAGTCAAATTCACGTTGCGAT
1137014 TTTCGGTTTT
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (40 bp):
CAACGCGAAAGTCAAATTCACGTTGCGATAGTCAAATTCG
Found at i:1137348 original size:18 final size:18
Alignment explanation
Indices: 1137325--1137360 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1137315 AAGCCGGTTG
*
1137325 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1137343 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1137361 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1140624 original size:19 final size:20
Alignment explanation
Indices: 1140600--1140687 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 20
1140590 AACTAAAACC
1140600 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
* *
1140619 TGTTGCG-AATTCAAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* * *
1140639 AGTTGTGAATTTGAAATTC-
1 TGTTGCGAAATTGAAATTCG
* *
1140658 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
1140679 TGTTGCGAA
1 TGTTGCGAA
1140688 TTTGGAAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.07
19 25 0.45
20 16 0.29
21 11 0.20
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:1140689 original size:40 final size:40
Alignment explanation
Indices: 1140600--1140691 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 40
1140590 AACTAAAACC
* *
1140600 TGTTGCGAAATT-AAATTCGTGTTGCGAATTCAAAAATCG
1 TGTTGCGAATTTGAAATTCGAGTTGCGAATTCAAAAATCG
* * ** *
1140639 AGTTGTGAATTTGAAATTC-AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTCGAGTTGCGAATTCAAAAATC-G
1140679 TGTTGCGAATTTG
1 TGTTGCGAATTTG
1140692 GAAAACGCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
39 24 0.57
40 18 0.43
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (40 bp):
TGTTGCGAATTTGAAATTCGAGTTGCGAATTCAAAAATCG
Done.