Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 15 of 325
Found at i:3442670 original size:57 final size:56
Alignment explanation
Indices: 3442582--3442688 Score: 187
Period size: 57 Copynumber: 1.9 Consensus size: 56
3442572 CAAAAAATTG
*
3442582 ACTCATATTGCGAGAGGTGAGTCAAGCCTCAGGGCACCGCTGAGGTATTTTTAGTTT
1 ACTCACATTGCGAGAGGTGAGTCAAGCCTCAGGGCA-CGCTGAGGTATTTTTAGTTT
*
3442639 ACTCACATTGCGAGAGGTGAGTCAAGCCTCAGGTCACGCTGAGGTATTTT
1 ACTCACATTGCGAGAGGTGAGTCAAGCCTCAGGGCACGCTGAGGTATTTT
3442689 AATTCCTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 14 0.29
57 34 0.71
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (56 bp):
ACTCACATTGCGAGAGGTGAGTCAAGCCTCAGGGCACGCTGAGGTATTTTTAGTTT
Found at i:3442809 original size:69 final size:70
Alignment explanation
Indices: 3442638--3442830 Score: 237
Period size: 73 Copynumber: 2.7 Consensus size: 70
3442628 ATTTTTAGTT
* * * * *
3442638 TACTCACATTGCGAGAGGTGAGTCAAGCCTCAGGTCACGCTGAGGTATTTTAATTCCTTTTGTTT
1 TACTCATATTGCGAGAGGTGAGTCAAGCCTCGGGACACGCTGAGGTATTTTAAGT-CTTATGTTT
3442703 CAAAAA
65 CAAAAA
* ** *
3442709 TCAGCTCATATTGCGAGGGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT-TTATGTT
1 T-A-CTCATATTGCGAGAGGTGAGTCAAGCCTCGGGACACGCTGAGGTATTTTAAGTCTTATGTT
3442773 T-AGAAAA
64 TCA-AAAA
* *
3442780 TACTCATATTGCGAGAGGTGAGTCAAGCCTCGGGGCACGCTGAGGTCTTTT
1 TACTCATATTGCGAGAGGTGAGTCAAGCCTCGGGACACGCTGAGGTATTTT
3442831 CAATTTCTGC
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
69 44 0.42
70 2 0.02
71 13 0.12
72 1 0.01
73 45 0.43
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (70 bp):
TACTCATATTGCGAGAGGTGAGTCAAGCCTCGGGACACGCTGAGGTATTTTAAGTCTTATGTTTC
AAAAA
Found at i:3442845 original size:14 final size:14
Alignment explanation
Indices: 3442826--3442860 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3442816 ACGCTGAGGT
* *
3442826 CTTTTCAATTTCTG
1 CTTTTCAATTCCTA
3442840 CTTTTCAATTCCTA
1 CTTTTCAATTCCTA
3442854 CTTTTCA
1 CTTTTCA
3442861 GAAAAATCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.26, G:0.03, T:0.54
Consensus pattern (14 bp):
CTTTTCAATTCCTA
Found at i:3442934 original size:13 final size:13
Alignment explanation
Indices: 3442916--3442949 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3442906 CGTTGAGGTA
*
3442916 TTTTCAATTTCTG
1 TTTTCAATTTATG
3442929 TTTTCAATTTATG
1 TTTTCAATTTATG
3442942 TTGTTCAA
1 TT-TTCAA
3442950 GAATTAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:3443332 original size:159 final size:154
Alignment explanation
Indices: 3443081--3443984 Score: 932
Period size: 159 Copynumber: 5.7 Consensus size: 154
3443071 TTTTAATTTC
* * * *
3443081 AACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGCACGATGAAGTATATTT-AATTTCTGCTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGTAT-TTTCAATTTCT-ATTT
* * * * ** *
3443145 TCAATTCATGCTTCTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACGTGT
63 T-AATTTATGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGA
* *
3443210 TGAGGTAATTTCAATTTATGTTCCAGAATC
125 TGAGGTAATTTCAATTTATGTTCAAAAATC
* * *
3443240 AATTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCGCATGCTGAGGTATTTTCAATTTTTCATT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGG---GCACGCTGAGGTATTTTCAATTTCT-ATT
* *
3443305 TTAATTTTTGTTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGAT
62 TTAATTTATGTTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGAT
*
3443370 GAGGTAATTTCAATTTCTGTTTGTCAAAAATC
126 GAGGTAATTTCAATTTATG--T-TCAAAAATC
* * * *
3443402 AACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTC
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGTATTTTCAATTTCTATTTT-
* * * * * *
3443467 AGTTTATGTTTTTC-AAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAG
64 AATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAG
* * ** **
3443531 GTATTTTCAATTTTTGTGTTTTAATTTC
129 GTAATTTCAA--TTTATGTTCAAAAATC
*
3443559 AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGATGAGGTATCTTT-AATTTCTACTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGTAT-TTTCAATTTCTA-TTT
* * * * * *
3443623 TCAATTCATGCTTCTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACGCGT
63 T-AATTTATGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGA
* *
3443688 TGAGGTAATTTCAATTTATGTTCCAGAATC
125 TGAGGTAATTTCAATTTATGTTCAAAAATC
* * * * * * *
3443718 AACTCATATTGAGAGAGGTGAGTTAAACCTCGACTCGCATGCTGAGGTATTTTCAATTTTTCGTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTCG---GGCACGCTGAGGTATTTTCAATTTCT-ATT
* * *
3443783 TTAATTTCTGTTTTGTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGAT
62 TTAATTTATGTTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGAT
*
3443848 GAGGTAATTTCAATTTCTGTTTGTCAAAAATC
126 GAGGTAATTTCAATTTATG--T-TCAAAAATC
* * *
3443880 AACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTT
1 AACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGTATTTTCAATTTCT-ATTTT
*
3443945 AGTTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAG
64 AATTTATGTTTTTC--AAAAATCAACTCATATTGCGAGAG
3443985 TTTATGAGTC
Statistics
Matches: 618, Mismatches: 98, Indels: 56
0.80 0.13 0.07
Matches are distributed among these distances:
157 55 0.09
158 75 0.12
159 195 0.32
160 97 0.16
161 124 0.20
162 69 0.11
163 3 0.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (154 bp):
AACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAGGTATTTTCAATTTCTATTTTAA
TTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGT
AATTTCAATTTATGTTCAAAAATC
Found at i:3443427 original size:73 final size:73
Alignment explanation
Indices: 3443302--3443605 Score: 261
Period size: 73 Copynumber: 4.0 Consensus size: 73
3443292 TCAATTTTTC
* * * * *
3443302 ATTTTAATTTTTGTTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATAC
1 ATTTCAATTTCTG-TTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACAC
3443367 GATGAGGTA
65 GATGAGGTA
3443376 ATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACG
1 ATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACG
*
3443441 CTGAGGTA
66 ATGAGGTA
* * * * *
3443449 TTTTCAATTTCTGTTTTCAGTTTATGTTTTTCAAAATCAGCTCATATTGCTAGAGGTGAGTTGAG
1 ATTTCAATTTCTG-TTT--G-TCA--------AAAATCAACTCATATTGCAAGAGATGAGTTGAG
* * *
3443514 CCTCGGGGCACGCTGAGGTA
54 CCTCAGGACACGATGAGGTA
* * * ** * * * *
3443534 TTTTCAATTTTTGTGTT-T-TAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
1 ATTTCAATTTCTGT-TTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACAC
3443597 GATGAGGTA
65 GATGAGGTA
3443606 TCTTTAATTT
Statistics
Matches: 197, Mismatches: 20, Indels: 28
0.80 0.08 0.11
Matches are distributed among these distances:
72 48 0.24
73 68 0.35
74 14 0.07
76 1 0.01
77 2 0.01
81 1 0.01
84 1 0.01
85 62 0.31
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (73 bp):
ATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACG
ATGAGGTA
Found at i:3443526 original size:85 final size:86
Alignment explanation
Indices: 3443377--3443557 Score: 256
Period size: 85 Copynumber: 2.1 Consensus size: 86
3443367 GATGAGGTAA
*
3443377 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTATGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGC
3443442 TGAGGTATTTTCAATTTCTGT
66 TGAGGTATTTTCAATTTCTGT
* * * * * * *
3443463 TTTCAGTTTATGTTTTTC-AAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTCAATTTATGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGC
*
3443527 TGAGGTATTTTCAATTTTTGT
66 TGAGGTATTTTCAATTTCTGT
*
3443548 GTTTTAATTT
1 -TTTCAATTT
3443558 CAACTCATAT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
85 61 0.73
86 22 0.27
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (86 bp):
TTTCAATTTATGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGC
TGAGGTATTTTCAATTTCTGT
Found at i:3443899 original size:478 final size:478
Alignment explanation
Indices: 3442997--3443962 Score: 1788
Period size: 478 Copynumber: 2.0 Consensus size: 478
3442987 TAATTTATAC
3442997 TTTTTCAAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
1 TTTTTCAAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
*
3443062 ATTTTTTTGTTTTAATTTCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGCACGATGAAGT
66 ATTTTTGTGTTTTAATTTCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGCACGATGAAGT
*
3443127 ATATTTAATTTCTGCTTTTCAATTCATGCTTCTCAAGAAAATCAACTCATATTGCGAGAGGTGAG
131 ATATTTAATTTCTACTTTTCAATTCATGCTTCTCAAGAAAATCAACTCATATTGCGAGAGGTGAG
* * *
3443192 TTGAGCCTCAAGACGTGTTGAGGTAATTTCAATTTATGTTCCAGAATCAATTCATATTGCGAGAG
196 TTGAGCCTCAAGACGCGTTGAGGTAATTTCAATTTATGTTCCAGAATCAACTCATATTGAGAGAG
* * * *
3443257 GTGAGTTGAGCCTCGGCTCGCATGCTGAGGTATTTTCAATTTTTCATTTTAATTTTTGTTTTGTC
261 GTGAGTTAAACCTCGACTCGCATGCTGAGGTATTTTCAATTTTTCATTTTAATTTCTGTTTTGTC
3443322 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTC
326 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTC
3443387 TGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTT
391 TGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTT
3443452 TCAATTTCTGTTTTCAGTTTATG
456 TCAATTTCTGTTTTCAGTTTATG
3443475 TTTTTCAAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
1 TTTTTCAAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
* *
3443540 ATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGATGAGGT
66 ATTTTTGTGTTTTAATTTCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGCACGATGAAGT
*
3443605 ATCTTTAATTTCTACTTTTCAATTCATGCTTCTCAAGAAAATCAACTCATATTGCGAGAGGTGAG
131 ATATTTAATTTCTACTTTTCAATTCATGCTTCTCAAGAAAATCAACTCATATTGCGAGAGGTGAG
3443670 TTGAGCCTCAAGACGCGTTGAGGTAATTTCAATTTATGTTCCAGAATCAACTCATATTGAGAGAG
196 TTGAGCCTCAAGACGCGTTGAGGTAATTTCAATTTATGTTCCAGAATCAACTCATATTGAGAGAG
* *
3443735 GTGAGTTAAACCTCGACTCGCATGCTGAGGTATTTTCAATTTTTCGTTTTAATTTCTGTTTTGTT
261 GTGAGTTAAACCTCGACTCGCATGCTGAGGTATTTTCAATTTTTCATTTTAATTTCTGTTTTGTC
3443800 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTC
326 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTC
*
3443865 TGTTTGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTT
391 TGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTT
*
3443930 TCAATTTCTGTTTTTAGTTTATG
456 TCAATTTCTGTTTTCAGTTTATG
3443953 TTTTTCAAAA
1 TTTTTCAAAA
3443963 AAATCAACTC
Statistics
Matches: 472, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
478 472 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (478 bp):
TTTTTCAAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
ATTTTTGTGTTTTAATTTCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGGCACGATGAAGT
ATATTTAATTTCTACTTTTCAATTCATGCTTCTCAAGAAAATCAACTCATATTGCGAGAGGTGAG
TTGAGCCTCAAGACGCGTTGAGGTAATTTCAATTTATGTTCCAGAATCAACTCATATTGAGAGAG
GTGAGTTAAACCTCGACTCGCATGCTGAGGTATTTTCAATTTTTCATTTTAATTTCTGTTTTGTC
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTC
TGTTTGTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTT
TCAATTTCTGTTTTCAGTTTATG
Found at i:3443905 original size:73 final size:73
Alignment explanation
Indices: 3443785--3443942 Score: 262
Period size: 73 Copynumber: 2.2 Consensus size: 73
3443775 TTTTCGTTTT
* * *
3443785 AATTTCTGTTTTGTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGA
1 AATTTCTG-TTTGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGATGA
3443850 GGTAATTTC
65 GGTAATTTC
*
3443859 AATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGATGAG
*
3443924 GTATTTTC
66 GTAATTTC
3443932 AATTTCTGTTT
1 AATTTCTGTTT
3443943 TTAGTTTATG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 71 0.90
74 8 0.10
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (73 bp):
AATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGATGAG
GTAATTTC
Found at i:3445185 original size:2 final size:2
Alignment explanation
Indices: 3445180--3445222 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
3445170 CCGGAGCTCC
* *
3445180 CT CT CT CT CT CT CT CT CT CT CT CT CT -T C- CT CT CC CT TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3445220 CT C
1 CT C
3445223 CTTTTTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3445736 original size:3 final size:3
Alignment explanation
Indices: 3445677--3445844 Score: 194
Period size: 3 Copynumber: 55.0 Consensus size: 3
3445667 TTTTCATTGT
* * * * *
3445677 TTA TTC TTA TT- TTC TTA TTAA ATA TTC TTA TTA TTCA TATA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A T-TA TTA TTA
* * * * * *
3445724 GTA CTA TTA TTA TTA CTA TTG TTC TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3445772 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3445820 TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA
3445845 GTTTATGTTT
Statistics
Matches: 141, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.01
3 130 0.92
4 8 0.06
5 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3446077 original size:15 final size:15
Alignment explanation
Indices: 3446044--3446082 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3446034 TTTAATGTCG
*
3446044 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
3446060 TATTATATATTTTCA
1 TATTATATATTTTAA
3446075 TATTATAT
1 TATTATAT
3446083 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:3449081 original size:2 final size:2
Alignment explanation
Indices: 3449074--3449196 Score: 67
Period size: 2 Copynumber: 63.5 Consensus size: 2
3449064 CAATGCATGC
* * * *
3449074 AT AT AT AT AT AT AT AT -T AT AT -T TT CT A- AT AC AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
3449113 AT AT AG AT AT AT -T AT GT AC AT AT -T AT CAT GT GT TT AT TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
* * *
3449154 AT AT AT GT AT AT AG AT AT AT AG 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
3449196 A
1 A
3449197 GTAATTTTTA
Statistics
Matches: 92, Mismatches: 23, Indels: 12
0.72 0.18 0.09
Matches are distributed among these distances:
1 5 0.05
2 85 0.92
3 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3449374 original size:23 final size:23
Alignment explanation
Indices: 3449333--3449381 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3449323 TTGTTACACC
*
3449333 TTTTACTATTATTACTATTGTAT
1 TTTTACTATTATTACTATTATAT
**
3449356 TTTTACTATTATTGTTATTATAT
1 TTTTACTATTATTACTATTATAT
3449379 TTT
1 TTT
3449382 CCTCTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTACTATTATTACTATTATAT
Found at i:3449605 original size:22 final size:22
Alignment explanation
Indices: 3449580--3449625 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3449570 TTACTATTTG
3449580 TATTTACCA-TTATTATTACTAT
1 TATTT-CCATTTATTATTACTAT
* *
3449602 TATTTTCATTTTTTATTACTAT
1 TATTTCCATTTATTATTACTAT
3449624 TA
1 TA
3449626 CTAATATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTCCATTTATTATTACTAT
Found at i:3454810 original size:24 final size:25
Alignment explanation
Indices: 3454781--3454863 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
3454771 TAGGTTTTAC
3454781 TTGT-AATAAAACATAATTATCTAT
1 TTGTAAATAAAACATAATTATCTAT
* * *
3454805 TTGTAAATAAAA-AGAGGTT-T-TAC
1 TTGTAAATAAAACATA-ATTATCTAT
* *
3454828 TAGT-AATAAAACATAATTAGCTAT
1 TTGTAAATAAAACATAATTATCTAT
3454852 TTGTAAATAAAA
1 TTGTAAATAAAA
3454864 AGAGGTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
22 9 0.20
23 7 0.16
24 12 0.27
25 16 0.36
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (25 bp):
TTGTAAATAAAACATAATTATCTAT
Found at i:3454826 original size:47 final size:47
Alignment explanation
Indices: 3454772--3454876 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
3454762 CATGTTAATT
*
3454772 AGGTTTTACTTGTAATAAAACATAATTATCTATTTGTAAATAAAAAG
1 AGGTTTTACTTGTAATAAAACATAATTAGCTATTTGTAAATAAAAAG
*
3454819 AGGTTTTACTAGTAATAAAACATAATTAGCTATTTGTAAATAAAAAG
1 AGGTTTTACTTGTAATAAAACATAATTAGCTATTTGTAAATAAAAAG
3454866 AGGTTTTACTT
1 AGGTTTTACTT
3454877 CTAAATCGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (47 bp):
AGGTTTTACTTGTAATAAAACATAATTAGCTATTTGTAAATAAAAAG
Found at i:3460089 original size:2 final size:2
Alignment explanation
Indices: 3460082--3460107 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3460072 ACAGATAAAC
3460082 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
3460108 TATTTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3460331 original size:33 final size:33
Alignment explanation
Indices: 3460289--3460355 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3460279 CGAAAGAGTT
3460289 TAGATTCGATATCAAGTATACCAAGTAATTTCA
1 TAGATTCGATATCAAGTATACCAAGTAATTTCA
3460322 TAGATTCGATATCAAGTATACCAAGTAATTTCA
1 TAGATTCGATATCAAGTATACCAAGTAATTTCA
3460355 T
1 T
3460356 TCTCCTCTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (33 bp):
TAGATTCGATATCAAGTATACCAAGTAATTTCA
Found at i:3464168 original size:3 final size:3
Alignment explanation
Indices: 3464156--3464199 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
3464146 ACGATGTTAA
3464156 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3464200 CAATTTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3466914 original size:17 final size:17
Alignment explanation
Indices: 3466892--3466925 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3466882 TCCAAAAAGT
3466892 CCTATAAAGCAACATGA
1 CCTATAAAGCAACATGA
3466909 CCTATAAAGCAACATGA
1 CCTATAAAGCAACATGA
3466926 AGAAGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (17 bp):
CCTATAAAGCAACATGA
Found at i:3467684 original size:15 final size:15
Alignment explanation
Indices: 3467666--3467699 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3467656 ACTAATTTAG
*
3467666 TAAAAAAATTAATAT
1 TAAAAAAATAAATAT
*
3467681 TAAAAAAATAAATTT
1 TAAAAAAATAAATAT
3467696 TAAA
1 TAAA
3467700 TTAGAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAAAATAAATAT
Found at i:3467871 original size:47 final size:48
Alignment explanation
Indices: 3467771--3467890 Score: 154
Period size: 47 Copynumber: 2.5 Consensus size: 48
3467761 CTCAGAACTT
*
3467771 AATTAGGATTATGAAAATTATATTTTATAAATATATATTAGCTAGAATTG
1 AATTAGGATTACGAAAATTATA-TTTAT-AATATATATTAGCTAGAATTG
* *
3467821 AATTAGGATTAGGAAAATTATATTTAT-GTATAT-TCTAGCTAGAATTG
1 AATTAGGATTACGAAAATTATATTTATAATATATAT-TAGCTAGAATTG
* *
3467868 AATTAAGATCACGAAAATTATAT
1 AATTAGGATTACGAAAATTATAT
3467891 ATAGAGTTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
46 1 0.02
47 37 0.58
49 5 0.08
50 21 0.33
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (48 bp):
AATTAGGATTACGAAAATTATATTTATAATATATATTAGCTAGAATTG
Found at i:3481901 original size:17 final size:17
Alignment explanation
Indices: 3481836--3481901 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 17
3481826 TCTAAACCAA
*
3481836 TATATTTTATATTTT-T
1 TATATATTATATTTTAT
*
3481852 TATATAATTATTATCCTTA-
1 TATAT-ATTA-TAT-TTTAT
*
3481871 TAAATA-TAT-TTTTAT
1 TATATATTATATTTTAT
3481886 TATATATTATATTTTA
1 TATATATTATATTTTA
3481902 AATTTATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 13
0.68 0.09 0.23
Matches are distributed among these distances:
14 3 0.08
15 6 0.16
16 9 0.24
17 10 0.26
18 4 0.11
19 6 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATTATATTTTAT
Found at i:3481925 original size:26 final size:25
Alignment explanation
Indices: 3481878--3481926 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
3481868 TTATAAATAT
* * *
3481878 ATTTTTATTATATATTATATTTTAA
1 ATTTTTATTAAATATCACATTTTAA
3481903 ATTTATTATTAAATATCACATTTT
1 ATTT-TTATTAAATATCACATTTT
3481927 TTTATATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTATTAAATATCACATTTTAA
Found at i:3484586 original size:15 final size:16
Alignment explanation
Indices: 3484551--3484592 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3484541 TGTATCTTAT
3484551 AATTGAAAA-AAAATAA
1 AATT-AAAATAAAATAA
*
3484567 AATTATAATAAAAT-A
1 AATTAAAATAAAATAA
3484582 AATTAAAATAA
1 AATTAAAATAA
3484593 GGTAAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AATTAAAATAAAATAA
Found at i:3487911 original size:26 final size:26
Alignment explanation
Indices: 3487874--3488009 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
3487864 TGATACAAAT
* *
3487874 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3487900 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
3487926 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
3487952 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
3487978 TGATAATGGGTTAGGTAAATGTTTAA
1 TGATAATGGGTTAGGTAAATGTTTCA
3488004 TGATAA
1 TGATAA
3488010 GAATATCATG
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 103 1.00
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:3490039 original size:136 final size:137
Alignment explanation
Indices: 3489794--3490079 Score: 520
Period size: 136 Copynumber: 2.1 Consensus size: 137
3489784 GAGTAGTCTC
3489794 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
3489859 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
3489924 ACTGTTA
131 ACTGTTA
*
3489931 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
3489995 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
3490060 ACTGTTA
131 ACTGTTA
**
3490067 CCTGAATGGGCTT
1 CCCAAATGGGCTT
3490080 AGGCCCAATG
Statistics
Matches: 144, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
136 124 0.86
137 20 0.14
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:3492416 original size:12 final size:13
Alignment explanation
Indices: 3492395--3492423 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3492385 GAAATTAAAT
3492395 CTAAATAATAATC
1 CTAAATAATAATC
3492408 CTAAA-AATAATC
1 CTAAATAATAATC
3492420 CTAA
1 CTAA
3492424 TAACATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (13 bp):
CTAAATAATAATC
Found at i:3493751 original size:27 final size:27
Alignment explanation
Indices: 3493698--3493756 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
3493688 CTGTCGGGAT
* * * *
3493698 AGTAAATACGGGGTAGTCTACCGGGAC
1 AGTAAACACGGGATAGTCCACCAGGAC
*
3493725 AGTAAACACGGGATAGTCCACTAGGAC
1 AGTAAACACGGGATAGTCCACCAGGAC
3493752 A-TAAA
1 AGTAAA
3493757 ATGTGGGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (27 bp):
AGTAAACACGGGATAGTCCACCAGGAC
Found at i:3496697 original size:23 final size:23
Alignment explanation
Indices: 3496636--3496701 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
3496626 CCTGATCAGT
3496636 ATACGACACATAAAGTGCCT-AA
1 ATACGACACATAAAGTGCCTGAA
** *
3496658 A-ACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
*
3496680 ATACAACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
3496702 TTGGTAAAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
21 15 0.43
22 4 0.11
23 16 0.46
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.15
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:3498153 original size:5 final size:5
Alignment explanation
Indices: 3498145--3498171 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3498135 TCTTTAGTTT
3498145 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
3498172 TAAAACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:3498947 original size:73 final size:68
Alignment explanation
Indices: 3498859--3499132 Score: 232
Period size: 66 Copynumber: 3.9 Consensus size: 68
3498849 TTTTAATACC
3498859 TAAATTTAATATTATTCATATCTATTATATTTATTTATTTATTTGTTCGTTATTCTTTTA-TCTT
1 TAAATTTAATATTATT-ATATCTATTATATTTATTTATTTATTT-TTC---ATTCTTTTACT-TT
*
3498923 TCAAATATT
60 TAAAATATT
* * *
3498932 TAAATGTAATATTATTTATAGTTGTTTTATCAATTTATTTATTTATTTTTCATTCTTTTACTTTT
1 TAAATTTAATATTA-TTATA--TCTATTAT--ATTTATTTATTTATTTTTCATTCTTTTACTTTT
3498997 AAAATATT
61 AAAATATT
* * * *
3499005 TAAATTTAATATTATGTATATTTATTTTATCTATTTACTTA--TTT-ATTCTTTTACTTTTAAAA
1 TAAATTTAATATTAT-TATATCTATTATATTTATTTATTTATTTTTCATTCTTTTACTTTTAAAA
*
3499067 CATT
65 TATT
** * * * * ** *
3499071 TAAATTCGATATCATTCATATTTGTTTTATCAATTTATTTATTTATTTATTCTTTTACTTTT
1 TAAATTTAATATTATT-ATATCTATTATATTTATTTATTTATTT-TTCATTCTTTTACTTTT
3499133 TTTAATACTT
Statistics
Matches: 172, Mismatches: 17, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
65 1 0.01
66 54 0.31
67 3 0.02
68 1 0.01
69 13 0.08
70 14 0.08
71 5 0.03
72 1 0.01
73 52 0.30
74 3 0.02
75 6 0.03
76 3 0.02
77 16 0.09
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (68 bp):
TAAATTTAATATTATTATATCTATTATATTTATTTATTTATTTTTCATTCTTTTACTTTTAAAAT
ATT
Found at i:3499180 original size:139 final size:137
Alignment explanation
Indices: 3498908--3499185 Score: 314
Period size: 139 Copynumber: 2.0 Consensus size: 137
3498898 TATTTGTTCG
* * * *
3498908 TTATTCTTTTATCTTTCAAATATTTAAATGTAATATTATTTATAGTTGTTTTATCAATTTATTTA
1 TTATTCTTTTATCTTTAAAACATTTAAATGTAATATCATTCATAGTTGTTTTATCAATTTATTTA
* * *
3498973 TTTATTTTTCATTCTTTTACTTTTAAAATATTTAAATTTAATATTATGTATATTTATTTTATCTA
66 TTTA-TTTTCATTCTTTTACTTTTAAAATACTTAAATTTAATATCATGTATATTTATTTTATCAA
3499038 TTTACTTAT
130 TTTA-TTAT
* *
3499047 TTATTCTTTTA-CTTTTAAAACATTTAAAT-TCGATATCATTCATATTTGTTTTATCAATTTATT
1 TTATTCTTTTATC-TTTAAAACATTTAAATGT-AATATCATTCATAGTTGTTTTATCAATTTATT
** * * * *
3499110 TATTTA-TTT-ATTCTTTTACTTTTTTTAATACTTCAATTTAATGTCATTTGT-TTTATCTATTA
64 TATTTATTTTCATTCTTTTAC-TTTTAAAATACTTAAATTTAATATCATGTATATTTAT-T-TT-
3499172 ATCAATTTATTAT
125 ATCAATTTATTAT
3499185 T
1 T
3499186 CTTTTTTAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
136 15 0.13
137 27 0.23
138 9 0.08
139 67 0.57
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (137 bp):
TTATTCTTTTATCTTTAAAACATTTAAATGTAATATCATTCATAGTTGTTTTATCAATTTATTTA
TTTATTTTCATTCTTTTACTTTTAAAATACTTAAATTTAATATCATGTATATTTATTTTATCAAT
TTATTAT
Found at i:3500769 original size:13 final size:13
Alignment explanation
Indices: 3500751--3500783 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
3500741 AAGACGATCA
3500751 ATAGAAATCATCC
1 ATAGAAATCATCC
3500764 ATAGAAATCATCC
1 ATAGAAATCATCC
3500777 ATAGAAA
1 ATAGAAA
3500784 ACTTCTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (13 bp):
ATAGAAATCATCC
Found at i:3508050 original size:21 final size:23
Alignment explanation
Indices: 3508004--3508052 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
3507994 ATCTAAACTC
3508004 CAAAC-TCAACATCATGAACCCT
1 CAAACTTCAACATCATGAACCCT
*
3508026 -AAACTTCAA-AT-ATGAGCCCT
1 CAAACTTCAACATCATGAACCCT
3508046 CAAACTT
1 CAAACTT
3508053 GAACTAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.33
21 12 0.50
22 4 0.17
ACGTcount: A:0.41, C:0.31, G:0.06, T:0.22
Consensus pattern (23 bp):
CAAACTTCAACATCATGAACCCT
Found at i:3508909 original size:22 final size:22
Alignment explanation
Indices: 3508876--3508935 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3508866 AGCCTAAACT
3508876 TTCTC-TTGTTGCTATTGTTTTG
1 TTCTCATT-TTGCTATTGTTTTG
*
3508898 TTCTCATTTTGCTACTGTTTTG
1 TTCTCATTTTGCTATTGTTTTG
* * *
3508920 CTATCATTTCGCTATT
1 TTCTCATTTTGCTATT
3508936 ATATTGCTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 30 0.94
23 2 0.06
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.58
Consensus pattern (22 bp):
TTCTCATTTTGCTATTGTTTTG
Found at i:3512305 original size:72 final size:72
Alignment explanation
Indices: 3512188--3512334 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 72
3512178 TACCGAAATA
* *
3512188 AATTTAGTTTGCATGGAGATGATTCTTTTTAAGTGAATTTATTAATTTTTTAATCTAAGTTAATA
1 AATTTAGTTTGCATGGAGATGATTCTTTTTAAGTGAATTTATTAATTTATTAATATAAGTTAATA
3512253 CAACTTT
66 CAACTTT
3512260 AATTTAGTTTGCATGGAGATGATTCTTTTTAAGTGAATTTATTAATTTATTAATATAAGTTAATA
1 AATTTAGTTTGCATGGAGATGATTCTTTTTAAGTGAATTTATTAATTTATTAATATAAGTTAATA
3512325 CAACTTT
66 CAACTTT
3512332 AAT
1 AAT
3512335 AGGTATTACT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (72 bp):
AATTTAGTTTGCATGGAGATGATTCTTTTTAAGTGAATTTATTAATTTATTAATATAAGTTAATA
CAACTTT
Found at i:3514733 original size:25 final size:23
Alignment explanation
Indices: 3514692--3514739 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
3514682 ATTTTTTAAT
3514692 TATTTTATTTAATATTTTATAAAA
1 TATTTTATTTAATATTTTA-AAAA
3514716 TATTTTAATTTTAA-ATTTTAAAAA
1 TATTTT-A-TTTAATATTTTAAAAA
3514740 CTACATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 10 0.45
25 7 0.32
26 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTTATTTAATATTTTAAAAA
Found at i:3517221 original size:21 final size:21
Alignment explanation
Indices: 3517191--3517232 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3517181 TTTTTTACGT
*
3517191 TTTACGTTTATATGACTTTGA
1 TTTACATTTATATGACTTTGA
3517212 TTTACATTTATATGACTTTGA
1 TTTACATTTATATGACTTTGA
3517233 GTCAGTGCTA
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:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (21 bp):
TTTACATTTATATGACTTTGA
Found at i:3517772 original size:9 final size:9
Alignment explanation
Indices: 3517758--3517789 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3517748 TTCTTATAAT
3517758 TTTTTTTAC
1 TTTTTTTAC
3517767 TTTTTTTAC
1 TTTTTTTAC
*
3517776 TTTTTTAAC
1 TTTTTTTAC
3517785 TTTTT
1 TTTTT
3517790 ATTTTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:3517883 original size:36 final size:36
Alignment explanation
Indices: 3517814--3517887 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 36
3517804 ATTTTGTCTC
*
3517814 TTTCTTAGATTTTTTTCTTTTTTAAGTTTTATATTAT
1 TTTCTTAGATTTTTTTCTTATTTAAG-TTTATATTAT
3517851 TTTCTTA-ATTTATTTTACTTATTTAA-TTTATATTAT
1 TTTCTTAGATTT-TTTT-CTTATTTAAGTTTATATTAT
3517887 T
1 T
3517888 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 15 0.44
37 11 0.32
38 8 0.24
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (36 bp):
TTTCTTAGATTTTTTTCTTATTTAAGTTTATATTAT
Found at i:3517892 original size:18 final size:17
Alignment explanation
Indices: 3517841--3517888 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
3517831 TTTTTTAAGT
*
3517841 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
*
3517859 TTTATTTTACTTATTTAA
1 TTTATATTA-TTATTTAA
3517877 TTTATATTATTA
1 TTTATATTATTA
3517889 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:3517901 original size:23 final size:22
Alignment explanation
Indices: 3517875--3517965 Score: 62
Period size: 23 Copynumber: 4.1 Consensus size: 22
3517865 TTACTTATTT
*
3517875 AATTTATATTATTAATTTTAAAA
1 AATTTATAATATT-ATTTTAAAA
*
3517898 AATTTGTAATA-TATATTTAAAA
1 AATTTATAATATTAT-TTTAAAA
** *
3517920 TGTTTTATAATATT-TTTTTAAA
1 -AATTTATAATATTATTTTAAAA
* * *
3517942 TATTTA-ATTATTATTTTTAAA
1 AATTTATAATATTATTTTAAAA
3517963 AAT
1 AAT
3517966 ATTTTTTAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
20 5 0.09
21 16 0.30
22 14 0.26
23 18 0.33
24 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTATAATATTATTTTAAAA
Found at i:3517947 original size:21 final size:21
Alignment explanation
Indices: 3517923--3517962 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3517913 TTTAAAATGT
3517923 TTTATAATATT-TTTTTAAATA
1 TTTA-AATATTATTTTTAAATA
*
3517944 TTTAATTATTATTTTTAAA
1 TTTAAATATTATTTTTAAA
3517963 AATATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAAATATTATTTTTAAATA
Found at i:3518027 original size:37 final size:36
Alignment explanation
Indices: 3517986--3518056 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
3517976 TTTATATATA
*
3517986 TATTTGTGAAATTAATTATTTATAAATTTTAAAAATG
1 TATTTGTCAAATTAATTATTTA-AAATTTTAAAAATG
* *
3518023 TATTTTTCAAATTAATTTTTTAAAATTTTAAAAA
1 TATTTGTCAAATTAATTATTTAAAATTTTAAAAA
3518057 AATAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 12 0.39
37 19 0.61
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (36 bp):
TATTTGTCAAATTAATTATTTAAAATTTTAAAAATG
Found at i:3518753 original size:10 final size:10
Alignment explanation
Indices: 3518737--3518792 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
3518727 TTTAAAAAAA
3518737 TTAAAATCAT
1 TTAAAATCAT
3518747 TTAAAAT-AT
1 TTAAAATCAT
*
3518756 TAAAAAAT-AT
1 T-TAAAATCAT
*
3518766 TTTAAATCAT
1 TTAAAATCAT
*
3518776 TTTAAATCAT
1 TTAAAATCAT
*
3518786 TTTAAAT
1 TTAAAAT
3518793 GTTTTATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
9 7 0.17
10 34 0.83
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (10 bp):
TTAAAATCAT
Found at i:3518772 original size:9 final size:9
Alignment explanation
Indices: 3518760--3518861 Score: 62
Period size: 10 Copynumber: 10.3 Consensus size: 9
3518750 AAATATTAAA
3518760 AAATATTTT
1 AAATATTTT
3518769 AAATCATTTT
1 AAAT-ATTTT
3518779 AAATCATTTT
1 AAAT-ATTTT
*
3518789 AAATGTTTT
1 AAATATTTT
**
3518798 ATAATATTAA
1 A-AATATTTT
3518808 AAATATATTT
1 AAATAT-TTT
*
3518818 -AATATTTAAA
1 AAATATTT--T
3518828 AAATATTTT
1 AAATATTTT
3518837 GAAAAATATTTT
1 ---AAATATTTT
*
3518849 TAATATTTAT
1 AAATATTT-T
3518859 AAA
1 AAA
3518862 AAAATATATT
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
8 2 0.03
9 26 0.36
10 29 0.40
11 7 0.10
12 9 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (9 bp):
AAATATTTT
Found at i:3518811 original size:19 final size:19
Alignment explanation
Indices: 3518799--3518835 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3518789 AAATGTTTTA
3518799 TAATA-TTAAAAATATATT
1 TAATATTTAAAAATATATT
3518817 TAATATTTAAAAA-ATATT
1 TAATATTTAAAAATATATT
3518835 T
1 T
3518836 TGAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATATTTAAAAATATATT
Found at i:3518883 original size:35 final size:31
Alignment explanation
Indices: 3518801--3518886 Score: 100
Period size: 35 Copynumber: 2.6 Consensus size: 31
3518791 ATGTTTTATA
*
3518801 ATATTAAAAATATATTTAATATTTAAAAAAT
1 ATATTAAAAATATTTTTAATATTTAAAAAAT
*
3518832 ATTTTGAAAAATATTTTTAATATTTATAAAAAAAT
1 ATATT-AAAAATATTTTTAATA-TT-T-AAAAAAT
*
3518867 ATATTATAAAACATTTTTAA
1 ATATTA-AAAATATTTTTAA
3518887 AAAATACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 4 0.09
32 15 0.33
33 2 0.04
34 2 0.04
35 23 0.50
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
ATATTAAAAATATTTTTAATATTTAAAAAAT
Found at i:3522373 original size:30 final size:30
Alignment explanation
Indices: 3522341--3522463 Score: 192
Period size: 30 Copynumber: 4.1 Consensus size: 30
3522331 GGTCAAATGG
* * * *
3522341 ACTCGAACCGCCTATATCCGGGTGATATGG
1 ACTCGAACCACCCATGTCCGGGTGATATGA
3522371 ACTCGAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
3522401 ACTCGAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
* *
3522431 ACTCGAACCACCTATGTCCGGGTTATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
3522461 ACT
1 ACT
3522464 ACTGTGGGAC
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (30 bp):
ACTCGAACCACCCATGTCCGGGTGATATGA
Found at i:3524402 original size:19 final size:19
Alignment explanation
Indices: 3524380--3524416 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3524370 AAGCCCATTA
3524380 AACCCCCAAAAAAAAACCT
1 AACCCCCAAAAAAAAACCT
3524399 AACCCCCAAAAAAAAACC
1 AACCCCCAAAAAAAAACC
3524417 AAGAAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.38, G:0.00, T:0.03
Consensus pattern (19 bp):
AACCCCCAAAAAAAAACCT
Found at i:3524742 original size:17 final size:17
Alignment explanation
Indices: 3524720--3524758 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3524710 CCTAAAGGTG
*
3524720 ATTTTA-TCTTCTTTATT
1 ATTTTACTCTTATTT-TT
3524737 ATTTTACTCTTATTTTT
1 ATTTTACTCTTATTTTT
3524754 ATTTT
1 ATTTT
3524759 TATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTACTCTTATTTTT
Found at i:3525495 original size:2 final size:2
Alignment explanation
Indices: 3525488--3525569 Score: 59
Period size: 2 Copynumber: 43.5 Consensus size: 2
3525478 TTCTAATACG
* * *
3525488 TA TA TA TA TA TA T- TA TA TG TA T- TT TA TA TA TA T- TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3525527 TA TA T- TC T- TA AA TA CTA T- TA TA TA TA CA 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
3525567 TA T
1 TA T
3525570 TTAAAATACC
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
1 6 0.09
2 56 0.88
3 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3525514 original size:11 final size:11
Alignment explanation
Indices: 3525490--3525572 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 11
3525480 CTAATACGTA
*
3525490 TATATATATAT
1 TATATATATTT
*
3525501 TATATGTATTT
1 TATATATATTT
*
3525512 TATATATATTA
1 TATATATATTT
*
3525523 TGTATATATTCT
1 TATATATATT-T
* *
3525535 TAAATACTATTA
1 TATATA-TATTT
* *
3525547 TATATACATATA
1 TATATATAT-TT
3525559 TATATATATATT
1 TATATATAT-TT
3525571 TA
1 TA
3525573 AAATACCATA
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
11 29 0.52
12 23 0.41
13 4 0.07
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (11 bp):
TATATATATTT
Found at i:3525568 original size:20 final size:20
Alignment explanation
Indices: 3525487--3525569 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 20
3525477 TTTCTAATAC
*
3525487 GTATATATATATAT-TATAT
1 GTATATATACATATATATAT
* *
3525506 GTAT-TTTATATATAT-TAT
1 GTATATATACATATATATAT
* * *
3525524 GTATATATTCTTAAATACTAT
1 GTATATATACATATATA-TAT
3525545 -TATATATACATATATATAT
1 GTATATATACATATATATAT
*
3525564 ATATAT
1 GTATAT
3525570 TTAAAATACC
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
18 15 0.30
19 14 0.28
20 18 0.36
21 3 0.06
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (20 bp):
GTATATATACATATATATAT
Found at i:3527268 original size:16 final size:16
Alignment explanation
Indices: 3527247--3527297 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
3527237 AAGAAAGAGC
3527247 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
3527263 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
3527279 AAACACGCTAGTAAAT
1 AAATACGCTAGTAAAT
3527295 AAA
1 AAA
3527298 ATACTAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:3528235 original size:16 final size:17
Alignment explanation
Indices: 3528214--3528247 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3528204 AATTAGAGAA
3528214 TTCTATTTAA-TTCTAT
1 TTCTATTTAATTTCTAT
3528230 TTCTATTTAATTTCTAT
1 TTCTATTTAATTTCTAT
3528247 T
1 T
3528248 AAATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTATTTAATTTCTAT
Found at i:3529189 original size:13 final size:13
Alignment explanation
Indices: 3529171--3529198 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3529161 TATATATATA
3529171 AAAGAAACAAAAG
1 AAAGAAACAAAAG
3529184 AAAGAAACAAAAG
1 AAAGAAACAAAAG
3529197 AA
1 AA
3529199 TAAAAGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAG
Found at i:3529406 original size:12 final size:12
Alignment explanation
Indices: 3529389--3529422 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3529379 CTAACCCAAC
3529389 TCAAAAAAAAAA
1 TCAAAAAAAAAA
3529401 TCAAAAAAAAAA
1 TCAAAAAAAAAA
**
3529413 AGAAAAAAAA
1 TCAAAAAAAA
3529423 CCTAATCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (12 bp):
TCAAAAAAAAAA
Found at i:3529636 original size:22 final size:24
Alignment explanation
Indices: 3529610--3529669 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
3529600 TATTTTGGAG
3529610 AGAAGA-A-ATTTTTTGAGATTCA
1 AGAAGAGATATTTTTTGAGATTCA
*
3529632 AGAAGAGATTTTTTTTTGAGATTCA
1 AGAAGAGA-TATTTTTTGAGATTCA
*
3529657 AGAAGGGAT-TTTT
1 AGAAGAGATATTTT
3529670 CTTTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 6 0.18
23 5 0.15
24 1 0.03
25 21 0.64
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (24 bp):
AGAAGAGATATTTTTTGAGATTCA
Found at i:3529690 original size:30 final size:25
Alignment explanation
Indices: 3529618--3529674 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 25
3529608 AGAGAAGAAA
3529618 TTTTTTGAGATTCAAGAAGAGATTT
1 TTTTTTGAGATTCAAGAAGAGATTT
*
3529643 TTTTTTGAGATTCAAGAAGGGATTT
1 TTTTTTGAGATTCAAGAAGAGATTT
3529668 TTCTTTT
1 TT-TTTT
3529675 TTTTGAGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.49
Consensus pattern (25 bp):
TTTTTTGAGATTCAAGAAGAGATTT
Found at i:3530155 original size:3 final size:3
Alignment explanation
Indices: 3530147--3530181 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3530137 TGCATTTTAA
3530147 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3530182 GTGTATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3530283 original size:3 final size:3
Alignment explanation
Indices: 3530275--3530304 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3530265 TGTATTTCTA
3530275 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3530305 ATGGTAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3530430 original size:16 final size:15
Alignment explanation
Indices: 3530399--3530441 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
3530389 CCTTCATTCC
*
3530399 ATTATTATTATTACT
1 ATTATTATTTTTACT
3530414 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
3530430 ATCATTATTTTT
1 ATTATTATTTTT
3530442 CATACGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:3530566 original size:16 final size:16
Alignment explanation
Indices: 3530545--3530576 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3530535 CTATTGTTAC
3530545 TGTTATTATCATCACT
1 TGTTATTATCATCACT
*
3530561 TGTTATTCTCATCACT
1 TGTTATTATCATCACT
3530577 ATTATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTTATTATCATCACT
Found at i:3530618 original size:11 final size:13
Alignment explanation
Indices: 3530588--3530619 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3530578 TTATTATAAT
3530588 TTATTATTGTTAC
1 TTATTATTGTTAC
3530601 TTATTATT-TTAC
1 TTATTATTGTTAC
3530613 -TATTATT
1 TTATTATT
3530620 ATCTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.37
12 4 0.21
13 8 0.42
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (13 bp):
TTATTATTGTTAC
Found at i:3530828 original size:22 final size:22
Alignment explanation
Indices: 3530798--3530886 Score: 67
Period size: 22 Copynumber: 4.1 Consensus size: 22
3530788 TTATTATATC
*
3530798 TTTTACTATTATTATTGTTGTA
1 TTTTACTATTATTATTGTTATA
* * *
3530820 TTTTTCTATTATTGTTATTATA
1 TTTTACTATTATTATTGTTATA
* * *
3530842 TTTTCCT-TTATTTTTGTATTTA
1 TTTTACTATTATTATTGT-TATA
*
3530864 CTTATAC-ATTATTATT-TTATA
1 -TTTTACTATTATTATTGTTATA
3530885 TT
1 TT
3530887 AACTAATTTG
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
20 2 0.04
21 11 0.21
22 28 0.54
23 11 0.21
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.66
Consensus pattern (22 bp):
TTTTACTATTATTATTGTTATA
Found at i:3530832 original size:3 final size:3
Alignment explanation
Indices: 3530576--3530813 Score: 93
Period size: 3 Copynumber: 80.3 Consensus size: 3
3530566 TTCTCATCAC
* * *
3530576 TAT TAT TAT AATT TAT TAT TGT TACT TAT TAT T-T TAC TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
3530622 CTAA TA- TAT CAT CAT TAT CAT TAT T-T TCAT TAT AACT TAA TA- GAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT
* * * *
3530667 CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG CAC TACT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * * ** *
3530716 T-T TAT TAC TAT TAT T-T AAT ATAT TAT T-T TAC TAT TAT CGT CA-
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
3530758 TAT TGT TAC TAT TAC TAT TA- TAT TAT TA- TGT TAT TA- TAT CTTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
3530801 TAC TAT TAT TAT T
1 TAT TAT TAT TAT T
3530814 GTTGTATTTT
Statistics
Matches: 172, Mismatches: 44, Indels: 38
0.68 0.17 0.15
Matches are distributed among these distances:
2 18 0.10
3 138 0.80
4 16 0.09
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:3532859 original size:15 final size:15
Alignment explanation
Indices: 3532841--3532897 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
3532831 TATCTGTTTT
3532841 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
3532856 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
3532871 ATTGAATTTATATTG
1 ATTGAATTTATATTG
3532886 ATTGAA-TTATAT
1 ATTGAATTTATAT
3532898 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:3532876 original size:30 final size:28
Alignment explanation
Indices: 3532837--3532895 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
3532827 TGAATATCTG
3532837 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
3532866 TTTTGATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
3532895 T
1 T
3532896 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:3533307 original size:23 final size:23
Alignment explanation
Indices: 3533281--3533355 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 23
3533271 AGGCACTTTA
3533281 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
3533304 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
3533325 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
3533346 TGTGTCGTAT
1 TGTGTCGTAT
3533356 ACTGATCAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 35 0.76
22 2 0.04
23 9 0.20
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:3534930 original size:18 final size:18
Alignment explanation
Indices: 3534907--3534945 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3534897 ATATATTTAA
* *
3534907 TATATTTTTTTTTAAATT
1 TATATTTATATTTAAATT
3534925 TATATTTATATTTAAATT
1 TATATTTATATTTAAATT
3534943 TAT
1 TAT
3534946 TAATAGTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATATTTATATTTAAATT
Found at i:3535087 original size:21 final size:24
Alignment explanation
Indices: 3535056--3535102 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
3535046 AAAAGAATTT
3535056 AAAAATAATATT-TAAA-ATTGTA
1 AAAAATAATATTATAAACATTGTA
*
3535078 AAAAAT-ATATTATAAACATTTTA
1 AAAAATAATATTATAAACATTGTA
3535101 AA
1 AA
3535103 TATACATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 10 0.45
23 7 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAAATAATATTATAAACATTGTA
Found at i:3535247 original size:27 final size:28
Alignment explanation
Indices: 3535217--3535280 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
3535207 TTAAAAAAAA
* * *
3535217 TATTTAAAATATTATGATTTCTTATAT-
1 TATTTAAAAAATTATAATTTCTTAAATG
*
3535244 TA-TTAAAAAATTATAATTTTTTAAATG
1 TATTTAAAAAATTATAATTTCTTAAATG
3535271 TATTTAAAAA
1 TATTTAAAAA
3535281 TTGTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 20 0.65
27 4 0.13
28 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (28 bp):
TATTTAAAAAATTATAATTTCTTAAATG
Found at i:3535288 original size:26 final size:26
Alignment explanation
Indices: 3535217--3535282 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
3535207 TTAAAAAAAA
* *
3535217 TATTTAAAATATTATGATTTCTTATAT
1 TATTTAAAA-ATTATAATTTCTTAAAT
* *
3535244 TATTAAAAAATTATAATTTTTTAAAT
1 TATTTAAAAATTATAATTTCTTAAAT
3535270 GTATTTAAAAATT
1 -TATTTAAAAATT
3535283 GTATTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TATTTAAAAATTATAATTTCTTAAAT
Found at i:3535487 original size:18 final size:18
Alignment explanation
Indices: 3535464--3535502 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3535454 TAATATTTAA
*
3535464 TATATTT-TTTTTAAAATT
1 TATATTTATATTT-AAATT
3535482 TATATTTATATTTAAATT
1 TATATTTATATTTAAATT
3535500 TAT
1 TAT
3535503 TAATAATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATTTATATTTAAATT
Found at i:3535776 original size:21 final size:21
Alignment explanation
Indices: 3535750--3535814 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
3535740 ATATATATAT
3535750 AAAATTAAAAATATTTTTAAA
1 AAAATTAAAAATATTTTTAAA
3535771 AAAATTATAAAATA-TTTTAAA
1 AAAATTA-AAAATATTTTTAAA
* *
3535792 TATATATTACAAAT-TTTTTAAA
1 -A-AAATTAAAAATATTTTTAAA
3535814 A
1 A
3535815 TTAATAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 15 0.39
22 18 0.47
23 5 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTAAAAATATTTTTAAA
Found at i:3535862 original size:18 final size:18
Alignment explanation
Indices: 3535812--3535863 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
3535802 AAATTTTTTA
*
3535812 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
* *
3535830 AAATAAACAAAATAAATT
1 AAATAAATAATATAAATT
3535848 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
3535864 ACTTAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:3540503 original size:15 final size:15
Alignment explanation
Indices: 3540483--3540536 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
3540473 AAAAAACTTA
3540483 ATATAAATAATGTAT
1 ATATAAATAATGTAT
*
3540498 ATATAAAAATAAT-AAT
1 ATAT--AAATAATGTAT
3540514 AATATAAATAATGTAT
1 -ATATAAATAATGTAT
*
3540530 ATGTAAA
1 ATATAAA
3540537 AATAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 17 0.53
16 4 0.12
17 11 0.34
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
ATATAAATAATGTAT
Found at i:3540509 original size:17 final size:17
Alignment explanation
Indices: 3540487--3540542 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
3540477 AACTTAATAT
3540487 AAATAATGTATATATAA
1 AAATAATGTATATATAA
* *
3540504 AAATAAT-AATA-ATAT
1 AAATAATGTATATATAA
*
3540519 AAATAATGTATATGTAA
1 AAATAATGTATATATAA
3540536 AAATAAT
1 AAATAAT
3540543 AATAATATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 10 0.31
16 6 0.19
17 16 0.50
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATAATGTATATATAA
Found at i:3540522 original size:32 final size:32
Alignment explanation
Indices: 3540481--3540551 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
3540471 GAAAAAAACT
3540481 TAATATAAATAATGTATATATAAAAATAATAA
1 TAATATAAATAATGTATATATAAAAATAATAA
*
3540513 TAATATAAATAATGTATATGTAAAAATAATAA
1 TAATATAAATAATGTATATATAAAAATAATAA
3540545 TAATATA
1 TAATATA
3540552 GGAAAGTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (32 bp):
TAATATAAATAATGTATATATAAAAATAATAA
Found at i:3540581 original size:2 final size:2
Alignment explanation
Indices: 3540574--3540607 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3540564 AAATAAACAA
3540574 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
3540608 TAAAATAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3542328 original size:2 final size:2
Alignment explanation
Indices: 3542321--3542364 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3542311 ATATGGTGTT
3542321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
3542362 TA T
1 TA T
3542365 TGGGTAAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3547215 original size:10 final size:9
Alignment explanation
Indices: 3547186--3547218 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3547176 GATTTTATAA
*
3547186 TTTTATATT
1 TTTTAAATT
3547195 TTTTAAATT
1 TTTTAAATT
3547204 TTTTAAATT
1 TTTTAAATT
3547213 TTTTAA
1 TTTTAA
3547219 TTAATTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTAAATT
Found at i:3547889 original size:32 final size:32
Alignment explanation
Indices: 3547853--3547934 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
3547843 CCAACTATAT
*
3547853 AATTATTGCAATTGGATATTAGCATACCCAGA
1 AATTATGGCAATTGGATATTAGCATACCCAGA
3547885 AATTATGGCAATTGGATATTAGCATACCCAGA
1 AATTATGGCAATTGGATATTAGCATACCCAGA
3547917 AATTATGGCAATTGGATA
1 AATTATGGCAATTGGATA
3547935 ATCAGTGTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (32 bp):
AATTATGGCAATTGGATATTAGCATACCCAGA
Found at i:3555274 original size:51 final size:51
Alignment explanation
Indices: 3555114--3555271 Score: 280
Period size: 51 Copynumber: 3.1 Consensus size: 51
3555104 ACTTCTGATC
* * *
3555114 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
3555165 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
3555216 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
3555267 AGTGA
1 AGTGA
3555272 TAAATGTGAT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:3556477 original size:30 final size:30
Alignment explanation
Indices: 3556423--3556479 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3556413 TTTACGAGCA
*
3556423 TTGGGGCAAAAGTGCAAATATGTAAAAGTT
1 TTGGGGCAAAAGTGAAAATATGTAAAAGTT
*
3556453 TTGGGGTCAAAA-TGAAAATTTGTAAAA
1 TTGGGG-CAAAAGTGAAAATATGTAAAA
3556480 ATATGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (30 bp):
TTGGGGCAAAAGTGAAAATATGTAAAAGTT
Found at i:3559470 original size:46 final size:45
Alignment explanation
Indices: 3559414--3559580 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 45
3559404 GACGAGGGCT
3559414 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGAGCC
* * *
3559460 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGAGCC
* * * * * *
3559506 AGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GAGCC
*
3559550 AGTGTAAGACATGTCTGGGACATGCGTCAGC
1 AGTGTAAGACATGTCTGGGACATGCATCAGC
3559581 ACGGTTACAT
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.02
44 33 0.31
46 70 0.65
47 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGAGCC
Found at i:3559522 original size:92 final size:90
Alignment explanation
Indices: 3559363--3559574 Score: 237
Period size: 92 Copynumber: 2.3 Consensus size: 90
3559353 AGATTTGTGT
* * * * * *
3559363 GCCAGTGTAAGACCATGTATGAGACATGGCATTGGCATTGAGACGAGGGCTAGTGTAAGACATGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGT
3559428 CTGGGACATGCATCAGCCAC-AGTATGAGA
64 CTGGGACATGCATCAGCCACGAG-AT--GA
* * * *
3559457 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCCAGTGTCAGACATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
* * * *
3559522 GGGACATGCGTCGGCTACGAGATGT
66 GGGACATGCATCAGCCACGAGATGA
*
3559547 GCTAGTGTAAGACATGTCTGGGACATGC
1 GCCAGTGTAAGACATGTCTGGGACATGC
3559575 GTCAGCACGG
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
90 28 0.27
92 48 0.47
93 14 0.14
94 12 0.12
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (90 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACGAGATGA
Found at i:3559611 original size:46 final size:43
Alignment explanation
Indices: 3559414--3559617 Score: 171
Period size: 46 Copynumber: 4.5 Consensus size: 43
3559404 GACGAGGGCT
* * * *
3559414 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGA-CAT--GTG-C
* * *
3559460 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCGTCAG-CTACGACATG-T-G-C
* * *
3559506 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGTGC
1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC
3559549 TAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGTGTC
1 -AGTGTAAGACATGTCTGGGACATGCGTCAGCTAC-G--ACATGTG-C
*
3559596 AGTGTAAGACCTGTCTGGGACA
1 AGTGTAAGACATGTCTGGGACA
3559618 CGGCATCGAC
Statistics
Matches: 138, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
43 3 0.02
44 32 0.23
45 3 0.02
46 97 0.70
47 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (43 bp):
AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC
Found at i:3559617 original size:90 final size:91
Alignment explanation
Indices: 3559414--3559580 Score: 221
Period size: 90 Copynumber: 1.8 Consensus size: 91
3559404 GACGAGGGCT
3559414 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCCAGTGTAAGACATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTAT-AGAGCCAGTGTAAGACATGTCTGGG
* *
3559479 ACATGCATCGGCCTCGAGATGATAGCC
65 ACATGCATCAGCCTCGACATGATAGCC
* * * * * *
3559506 AGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAG-AT-GTGCTAGTGTAAGACATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATAGAGCCAGTGTAAGACATGTCTGGG
*
3559569 ACATGCGTCAGC
65 ACATGCATCAGC
3559581 ACGGTTACAT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 32 0.48
92 32 0.48
93 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (91 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATAGAGCCAGTGTAAGACATGTCTGGGA
CATGCATCAGCCTCGACATGATAGCC
Found at i:3566115 original size:11 final size:12
Alignment explanation
Indices: 3566097--3566130 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3566087 CGTATCCCAC
3566097 ATTTTTTTAATA
1 ATTTTTTTAATA
3566109 ATTTTTTTAA-A
1 ATTTTTTTAATA
*
3566120 ATATTTTTAAT
1 ATTTTTTTAAT
3566131 TTATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTTTAATA
Found at i:3566708 original size:27 final size:27
Alignment explanation
Indices: 3566670--3566729 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
3566660 GACAAATCAA
*
3566670 AAACTAAAAATAAAATCATAATAATAT
1 AAACTAAAAATAAAATCACAATAATAT
3566697 AAACTAAAAATAAAATCACAATAATAT
1 AAACTAAAAATAAAATCACAATAATAT
3566724 AAACTA
1 AAACTA
3566730 GAGGTGTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (27 bp):
AAACTAAAAATAAAATCACAATAATAT
Found at i:3566725 original size:16 final size:16
Alignment explanation
Indices: 3566679--3566726 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
3566669 AAAACTAAAA
3566679 ATAAAATCATAATAAT
1 ATAAAATCATAATAAT
3566695 AT-AAA-C-TAA-AA-
1 ATAAAATCATAATAAT
*
3566706 ATAAAATCACAATAAT
1 ATAAAATCATAATAAT
3566722 ATAAA
1 ATAAA
3566727 CTAGAGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
11 2 0.08
12 5 0.19
13 4 0.15
14 3 0.12
15 5 0.19
16 7 0.27
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAAATCATAATAAT
Found at i:3567223 original size:12 final size:12
Alignment explanation
Indices: 3567193--3567225 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3567183 TATATATTTT
3567193 AAAATT-ATATA
1 AAAATTAATATA
3567204 AAAA-TAATATA
1 AAAATTAATATA
3567215 AAAATTAATAT
1 AAAATTAATAT
3567226 GAGTGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:3568690 original size:15 final size:16
Alignment explanation
Indices: 3568670--3568702 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3568660 GCTCCAAAGT
*
3568670 AGGTTA-TGTTCTTGA
1 AGGTTAGTGATCTTGA
3568685 AGGTTAGTGATCTTGA
1 AGGTTAGTGATCTTGA
3568701 AG
1 AG
3568703 AGTTTTCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.24, C:0.06, G:0.30, T:0.39
Consensus pattern (16 bp):
AGGTTAGTGATCTTGA
Found at i:3569251 original size:20 final size:19
Alignment explanation
Indices: 3569224--3569262 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
3569214 TTAATGAATA
3569224 ATTTAAAA-TTTGTAAAAAT
1 ATTTAAAACTTT-TAAAAAT
3569243 ATTTGAAAACTTTTAAAAAT
1 ATTT-AAAACTTTTAAAAAT
3569263 TAGCATGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 11 0.61
21 3 0.17
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTTAAAACTTTTAAAAAT
Found at i:3574974 original size:23 final size:25
Alignment explanation
Indices: 3574929--3574980 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
3574919 TAAGCTTGCA
3574929 TATATTATTTTTAATTTTGTTAATATT
1 TATATTATTTTTAA--TTGTTAATATT
3574956 TATATTATTTTTAA-T-TTAATATT
1 TATATTATTTTTAATTGTTAATATT
3574979 TA
1 TA
3574981 ATAAATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 10 0.40
24 1 0.04
27 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TATATTATTTTTAATTGTTAATATT
Found at i:3576175 original size:21 final size:20
Alignment explanation
Indices: 3576142--3576190 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
3576132 CCTGCACAGT
3576142 AAAAAAAACGCTGAAAACGAA
1 AAAAAAAACGCTGAAAAC-AA
3576163 AAATAAAAA-GCTGAAAACAA
1 AAA-AAAAACGCTGAAAACAA
3576183 AAAAAAAA
1 AAAAAAAA
3576191 TAAAAAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 12 0.44
22 5 0.19
ACGTcount: A:0.73, C:0.10, G:0.10, T:0.06
Consensus pattern (20 bp):
AAAAAAAACGCTGAAAACAA
Found at i:3576348 original size:3 final size:3
Alignment explanation
Indices: 3576333--3576378 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
3576323 TTCGAGAACA
* * *
3576333 AAG AAG GAG AAG AAG AAA AAG AA- AAG AAG GAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3576379 TGAGGCCGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3576359 original size:23 final size:23
Alignment explanation
Indices: 3576332--3576378 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3576322 TTTCGAGAAC
3576332 AAAGAAGGAGAAGAAGAAAAAGA
1 AAAGAAGGAGAAGAAGAAAAAGA
*
3576355 AAAGAAGGAGAAGAAGAAGAAGA
1 AAAGAAGGAGAAGAAGAAAAAGA
3576378 A
1 A
3576379 TGAGGCCGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (23 bp):
AAAGAAGGAGAAGAAGAAAAAGA
Found at i:3576858 original size:15 final size:15
Alignment explanation
Indices: 3576838--3576906 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
3576828 AAAAATAGTA
3576838 TAAAAAATAAAATAC
1 TAAAAAATAAAATAC
*** *
3576853 TAAAAAATATGTTAA
1 TAAAAAATAAAATAC
*
3576868 TGAAAAATAAAATAC
1 TAAAAAATAAAATAC
*
3576883 GAGAAGAAATAAAATAC
1 TA-AA-AAATAAAATAC
*
3576900 GAAAAAA
1 TAAAAAA
3576907 ACTTTTTCAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
15 24 0.59
16 4 0.10
17 13 0.32
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (15 bp):
TAAAAAATAAAATAC
Found at i:3577130 original size:29 final size:29
Alignment explanation
Indices: 3577098--3577157 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
3577088 TATGTACTAA
3577098 AATA-ATATAAAGAAATAAAATACGAAAAT
1 AATATATATAAA-AAATAAAATACGAAAAT
* *
3577127 AATATATTTAAAAAATAATATACGAAAAT
1 AATATATATAAAAAATAAAATACGAAAAT
3577156 AA
1 AA
3577158 AAAATACGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (29 bp):
AATATATATAAAAAATAAAATACGAAAAT
Found at i:3577558 original size:302 final size:300
Alignment explanation
Indices: 3576944--3577671 Score: 1253
Period size: 302 Copynumber: 2.4 Consensus size: 300
3576934 GCAAGTTTTT
*
3576944 TACTAAAATAATATAAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
1 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
* * *
3577009 AAAAAATACAAATAAAGTGTTAAAATCAGGGTTATCTATT-AAAAAATATAAAAAA-ACTTAAAT
66 AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAAT
3577072 AATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTA
131 AATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTA
*
3577137 AAAAATAATATACGAAAATAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAA
196 AAAAATAAGATACGAAAATAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAA
3577202 ATATAAAAAAACACTTAAATAATACATTTAAAACATTATG
261 ATATAAAAAAACACTTAAATAATACATTTAAAACATTATG
*
3577242 TACTAAAATAATATAAAGAAATAAAATACGAAAATAACATATTTTAAAAAATAATATACGAAAAT
1 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
*
3577307 AAAAAATACGAATAAAGTGCTAAAATCAGGGTTGTTTATTAAAAAAATATAAAAAACACTTAAAT
66 AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAAT
3577372 AATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTT
131 AATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATA-TTT
*
3577437 AAAAAATAAGATACGAAAATAAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAA
195 AAAAAATAAGATACGAAAAT-AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAA
* * *
3577502 AAATATAAAAAAATACTTAAATAATACATTTGAAATATTATG
259 AAATATAAAAAAACACTTAAATAATACATTTAAAACATTATG
*
3577544 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAT
1 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
* * * **
3577609 AAAAAAATACGAAGAAAGTGCCAAAATTAGGGTTATTTATTAAATTAATATAAAAAAACACTT
66 -AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATAT-AAAAAACACTT
3577672 TATAATATAA
Statistics
Matches: 405, Mismatches: 19, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
298 99 0.24
299 15 0.04
300 69 0.17
301 22 0.05
302 145 0.36
303 44 0.11
304 11 0.03
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.28
Consensus pattern (300 bp):
TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAACACTTAAAT
AATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTA
AAAAATAAGATACGAAAATAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAA
ATATAAAAAAACACTTAAATAATACATTTAAAACATTATG
Found at i:3577578 original size:152 final size:151
Alignment explanation
Indices: 3576944--3577671 Score: 1250
Period size: 150 Copynumber: 4.8 Consensus size: 151
3576934 GCAAGTTTTT
*
3576944 TACTAAAATAATATAAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
1 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
* * *
3577009 AAAAAATACAAATAAAGTGTTAAAATCAGGGTTATCTATT-AAAAAATAT-AAAAAA-ACTTAAA
66 AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAA
3577071 TAATACATTTGAAACATTATG
131 TAATACATTTGAAACATTATG
3577092 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATA-TTTAAAAAATAATATACGAAAAT
1 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
3577156 AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAA
66 AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAA
*
3577221 TAATACATTTAAAACATTATG
131 TAATACATTTGAAACATTATG
*
3577242 TACTAAAATAATATAAAGAAATAAAATACGAAAATAACATATTTTAAAAAATAATATACGAAAAT
1 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
*
3577307 AAAAAATACGAATAAAGTGCTAAAATCAGGGTTGTTTATTAAAAAAATAT-AAAAAACACTTAAA
66 AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAA
3577371 TAATACATTTGAAACATTATG
131 TAATACATTTGAAACATTATG
*
3577392 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAT
1 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
* *
3577457 AAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAATACTTAA
66 -AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAA
*
3577522 ATAATACATTTGAAATATTATG
130 ATAATACATTTGAAACATTATG
*
3577544 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAT
1 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
* * * **
3577609 AAAAAAATACGAAGAAAGTGCCAAAATTAGGGTTATTTATTAAATTAATATAAAAAAACACTT
66 -AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTT
3577672 TATAATATAA
Statistics
Matches: 553, Mismatches: 21, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
147 60 0.11
148 49 0.09
149 6 0.01
150 164 0.30
151 120 0.22
152 154 0.28
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.28
Consensus pattern (151 bp):
TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAT
AAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAA
TAATACATTTGAAACATTATG
Found at i:3577750 original size:18 final size:19
Alignment explanation
Indices: 3577719--3577754 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3577709 TTTAAAAATT
3577719 AAAATTAAAATTAAAATAA
1 AAAATTAAAATTAAAATAA
*
3577738 AAAATT-AATTTAAAATA
1 AAAATTAAAATTAAAATA
3577755 TATTGATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATTAAAATTAAAATAA
Found at i:3577752 original size:12 final size:13
Alignment explanation
Indices: 3577710--3577745 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3577700 AATATATTTT
3577710 TTAAAAATTAAAA
1 TTAAAAATTAAAA
3577723 TT-AAAATTAAAA
1 TTAAAAATTAAAA
*
3577735 TAAAAAATTAA
1 TTAAAAATTAA
3577746 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAAATTAAAA
Found at i:3579775 original size:72 final size:72
Alignment explanation
Indices: 3579655--3579799 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 72
3579645 AGTCTGAACG
* *
3579655 ATCGCATTCACATTTGACTGATACTTCTTATCATCCTGATTTGACGGGCAATGACTATTTCCTAA
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCTGATTTGACGGGCAATGACTATTTCCCAA
3579720 GCTCGTC
66 GCTCGTC
* **
3579727 ATCGCATTCACATTCGGCTGATACTTCTTATCAT-CTGGATTTTCCGGGCAATGACTATTTCCCA
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCT-GATTTGACGGGCAATGACTATTTCCCA
*
3579791 GGCTCGTC
65 AGCTCGTC
3579799 A
1 A
3579800 GAGGGCGGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.03
72 64 0.97
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCTGATTTGACGGGCAATGACTATTTCCCAA
GCTCGTC
Found at i:3580198 original size:24 final size:24
Alignment explanation
Indices: 3580145--3580201 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
3580135 GTTTCTTGGG
*
3580145 TTTTTATATTAAAAAGTTTGTATT
1 TTTTTGTATTAAAAAGTTTGTATT
3580169 TTTTTGTATTAAAAAGTTTGTATT
1 TTTTTGTATTAAAAAGTTTGTATT
3580193 TTTTTGTAT
1 TTTTTGTAT
3580202 ATATTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (24 bp):
TTTTTGTATTAAAAAGTTTGTATT
Found at i:3580378 original size:17 final size:17
Alignment explanation
Indices: 3580358--3580395 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
3580348 AATACATTAC
3580358 AACATTAATCT-AATTGG
1 AACATTAAT-TAAATTGG
3580375 AACATTAATTAAATTGG
1 AACATTAATTAAATTGG
3580392 AACA
1 AACA
3580396 AATGGCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (17 bp):
AACATTAATTAAATTGG
Found at i:3585289 original size:31 final size:31
Alignment explanation
Indices: 3585251--3585399 Score: 246
Period size: 31 Copynumber: 4.8 Consensus size: 31
3585241 ACAAATGACA
*
3585251 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
3585282 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
3585313 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
3585344 AGTGAAAAGTGGTTG-TACCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCT-TCGGCTACCTGATC
*
3585375 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
3585400 AAGTGACAAG
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
30 1 0.01
31 108 0.98
32 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:3585569 original size:49 final size:47
Alignment explanation
Indices: 3585468--3585639 Score: 205
Period size: 49 Copynumber: 3.7 Consensus size: 47
3585458 TGCTACTGTA
* * * *
3585468 TAAGACCATATCTGGGATATGGCATCA-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
*
3585514 TAAGACCATAGCTGGGCTATGACATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTG
*
3585563 TAAGACCATAGCTGGGCTATGGCATCGATATATGA-A--T-A-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATTCGTG
3585605 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
3585640 AGATGTGTAA
Statistics
Matches: 114, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
41 1 0.01
42 35 0.31
44 1 0.01
45 1 0.01
46 24 0.21
47 1 0.01
48 14 0.12
49 37 0.32
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTG
Found at i:3585606 original size:42 final size:43
Alignment explanation
Indices: 3585511--3585674 Score: 172
Period size: 42 Copynumber: 3.7 Consensus size: 43
3585501 TATGTGATTC
* *
3585511 GTGTAAGACCATAGCTGGGCTATGACATCGATATGTGATATG-TGATT
1 GTGTAAGACCATAGCTGGGCTATGGCATCG--AT-T-ATATGAAGA-T
*
3585558 ACGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 --GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
3585602 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
** **
3585644 GTGTAAGACCATAATTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
3585675 GAAAACGAAG
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.01
42 63 0.61
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
49 29 0.28
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:3587770 original size:24 final size:25
Alignment explanation
Indices: 3587743--3587805 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
3587733 AATAATAATA
*
3587743 ACTAACAATAAT-T-AGGATTTTTTT
1 ACTAACAATAATATAAGG-GTTTTTT
3587767 ACTAACAATAATAATAAGGGTTTTTT
1 ACTAACAATAAT-ATAAGGGTTTTTT
3587793 ACTAACAATAATA
1 ACTAACAATAATA
3587806 ATAACTAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 12 0.34
25 1 0.03
26 19 0.54
27 3 0.09
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (25 bp):
ACTAACAATAATATAAGGGTTTTTT
Found at i:3587944 original size:15 final size:15
Alignment explanation
Indices: 3587926--3587957 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3587916 TCTTTCTTTG
3587926 TTCCTTCTCCTTCTT
1 TTCCTTCTCCTTCTT
3587941 TTCCTTCTCCTTCTT
1 TTCCTTCTCCTTCTT
3587956 TT
1 TT
3587958 TCTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCCTTCTCCTTCTT
Found at i:3588115 original size:18 final size:19
Alignment explanation
Indices: 3588094--3588138 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3588084 TGTTTTTTAT
3588094 TTTTTTTTCGTTTTCAAC-
1 TTTTTTTTCGTTTTCAACA
* *
3588112 TTTTTTTTTGTTTTCAGCA
1 TTTTTTTTCGTTTTCAACA
3588131 TTTTTTTT
1 TTTTTTTT
3588139 TACTGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTTTTTTCGTTTTCAACA
Found at i:3588117 original size:19 final size:19
Alignment explanation
Indices: 3588092--3588139 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
3588082 CCTGTTTTTT
3588092 ATTTTTTTTTCGTTTTCAAC
1 ATTTTTTTTT-GTTTTCAAC
*
3588112 -TTTTTTTTTGTTTTCAGC
1 ATTTTTTTTTGTTTTCAAC
3588130 ATTTTTTTTT
1 ATTTTTTTTT
3588140 ACTGTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.73
Consensus pattern (19 bp):
ATTTTTTTTTGTTTTCAAC
Found at i:3592705 original size:21 final size:20
Alignment explanation
Indices: 3592681--3592720 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3592671 CTTGAAAAAA
*
3592681 AACAAAAATAAAGATAGAAAT
1 AACAAAAAT-AAGAAAGAAAT
*
3592702 AACAAGAATAAGAAAGAAA
1 AACAAAAATAAGAAAGAAA
3592721 GAGATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.10
Consensus pattern (20 bp):
AACAAAAATAAGAAAGAAAT
Found at i:3597260 original size:16 final size:18
Alignment explanation
Indices: 3597221--3597254 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3597211 TAAGTTTATA
3597221 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
3597238 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
3597255 AATTTAGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Done.