Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 89
Found at i:1337540 original size:38 final size:39
Alignment explanation
Indices: 1337437--1337574 Score: 219
Period size: 38 Copynumber: 3.6 Consensus size: 39
1337427 CATATAAAAG
* * *
1337437 ATATCGTATCGTTTAATTATAAAACTATTGGTTTTTAAA
1 ATATCATATCGTTTAATTTTAATACTATTGGTTTTTAAA
1337476 ATATCATAT-GTTT-ATTTTAATACTATTGGTTTTTAAA
1 ATATCATATCGTTTAATTTTAATACTATTGGTTTTTAAA
1337513 ATATCATAT-GTTTAATTTTAATACTATTGGTTTTTAAA
1 ATATCATATCGTTTAATTTTAATACTATTGGTTTTTAAA
*
1337551 ATATCATGTCGTTTAATTTTAATA
1 ATATCATATCGTTTAATTTTAATA
1337575 TTAATACTAA
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
37 35 0.38
38 36 0.39
39 22 0.24
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.51
Consensus pattern (39 bp):
ATATCATATCGTTTAATTTTAATACTATTGGTTTTTAAA
Found at i:1337545 original size:20 final size:19
Alignment explanation
Indices: 1337485--1337545 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
1337475 AATATCATAT
1337485 GTTTATTTTAATACTATTG
1 GTTTATTTTAATACTATTG
**
1337504 GTTT-TTAAAATA-TCATAT-
1 GTTTATTTTAATACT-AT-TG
1337522 GTTTAATTTTAATACTATTG
1 GTTT-ATTTTAATACTATTG
1337542 GTTT
1 GTTT
1337546 TTAAAATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 11
0.68 0.09 0.23
Matches are distributed among these distances:
17 1 0.03
18 12 0.38
19 6 0.19
20 12 0.38
21 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.56
Consensus pattern (19 bp):
GTTTATTTTAATACTATTG
Found at i:1338319 original size:21 final size:21
Alignment explanation
Indices: 1338202--1338313 Score: 188
Period size: 21 Copynumber: 5.3 Consensus size: 21
1338192 TTAGGACAGG
* *
1338202 GAGTATCGGTACTCCTTTAAT
1 GAGTATCGATACTCCATTAAT
*
1338223 AAGTATCGATACTCCATTAAT
1 GAGTATCGATACTCCATTAAT
1338244 GAGTATCGATACTCCATTAAT
1 GAGTATCGATACTCCATTAAT
1338265 GAGTATCGATACTCCATTAAT
1 GAGTATCGATACTCCATTAAT
*
1338286 GAGTATCGATACTCCTTTAAT
1 GAGTATCGATACTCCATTAAT
1338307 GAGTATC
1 GAGTATC
1338314 AGTACTACCT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 86 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (21 bp):
GAGTATCGATACTCCATTAAT
Found at i:1342149 original size:20 final size:21
Alignment explanation
Indices: 1342095--1342152 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1342085 AGAACCCCAG
**
1342095 GGGGTATCGATTCCCTTGTGT
1 GGGGTATCGATTCCCTCATGT
* *
1342116 GGGGAATCGGTTCCCTCATG-
1 GGGGTATCGATTCCCTCATGT
*
1342136 GGTGTATCGATTCCCTC
1 GGGGTATCGATTCCCTC
1342153 TGCACCAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.12, C:0.24, G:0.31, T:0.33
Consensus pattern (21 bp):
GGGGTATCGATTCCCTCATGT
Found at i:1348516 original size:22 final size:23
Alignment explanation
Indices: 1348493--1348534 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
1348483 TTCAGATAAT
1348493 TTTAAAAAT-TTAT-TTAAAAGA
1 TTTAAAAATATTATATTAAAAGA
1348514 TTTAAAAATATTATATTAAAA
1 TTTAAAAATATTATATTAAAA
1348535 AACCTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAAAATATTATATTAAAAGA
Found at i:1348542 original size:24 final size:21
Alignment explanation
Indices: 1348494--1348542 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1348484 TCAGATAATT
* *
1348494 TTAAAAATTTATTTAAAAGAT
1 TTAAAAATTTATTTAAAAAAC
1348515 TTAAAAATATTATATTAAAAAACC
1 TTAAAAAT-TTAT-TTAAAAAA-C
1348539 TTAA
1 TTAA
1348543 TTTCTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 4 0.17
23 7 0.30
24 4 0.17
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
TTAAAAATTTATTTAAAAAAC
Found at i:1349816 original size:16 final size:16
Alignment explanation
Indices: 1349795--1349849 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
1349785 AGTCACATAT
1349795 ATAATTTAGACGAAAA
1 ATAATTTAGACGAAAA
1349811 ATAATTTA-A--AAATA
1 ATAATTTAGACGAAA-A
1349825 TATAATTTAGACGAAAA
1 -ATAATTTAGACGAAAA
1349842 ATAATTTA
1 ATAATTTA
1349850 AAAATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.09
14 1 0.03
15 9 0.26
16 17 0.50
17 1 0.03
18 3 0.09
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATTTAGACGAAAA
Found at i:1349826 original size:31 final size:31
Alignment explanation
Indices: 1349791--1349857 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
1349781 ATTTAGTCAC
1349791 ATATATAATTTAGACGAAAAATAATTTAAAA
1 ATATATAATTTAGACGAAAAATAATTTAAAA
1349822 ATATATAATTTAGACGAAAAATAATTTAAAA
1 ATATATAATTTAGACGAAAAATAATTTAAAA
1349853 ATATA
1 ATATA
1349858 ATTGTTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (31 bp):
ATATATAATTTAGACGAAAAATAATTTAAAA
Found at i:1350599 original size:3 final size:3
Alignment explanation
Indices: 1350585--1350646 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
1350575 GATTGATGGG
*
1350585 TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1350632 TA- TAT ATAT TAT TAT
1 TAT TAT -TAT TAT TAT
1350647 ATATATATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1350639 original size:2 final size:2
Alignment explanation
Indices: 1350632--1350663 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1350622 TTATTATTAT
1350632 TA TA TA TA T- TA T- 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
1350664 AGTTTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1350643 original size:12 final size:12
Alignment explanation
Indices: 1350600--1350662 Score: 78
Period size: 12 Copynumber: 5.2 Consensus size: 12
1350590 TTTTTATTAT
1350600 TATTATTAT-TA
1 TATTATTATATA
1350611 TTATTATTATATTA
1 -TATTATTATA-TA
1350625 TTATTATTATATA
1 -TATTATTATATA
1350638 TATTATTATATA
1 TATTATTATATA
1350650 TA-TA-TATATA
1 TATTATTATATA
1350660 TAT
1 TAT
1350663 AAGTTTTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.17
11 2 0.04
12 23 0.48
13 2 0.04
14 13 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTATTATATA
Found at i:1352745 original size:31 final size:30
Alignment explanation
Indices: 1352681--1352753 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
1352671 TGCTTTCGTG
* *
1352681 CTTTTTATTTATAATTTAATTCAGTTTTTC
1 CTTTTTATTTTTAATTTAATTCAGTCTTTC
*
1352711 CTTTTTATTTTTATTTTAATTTCA-TCCTTTC
1 CTTTTTATTTTTAATTTAA-TTCAGT-CTTTC
1352742 CTTTATT-TTTTT
1 CTTT-TTATTTTT
1352754 CTTTCTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 18 0.49
31 17 0.46
32 2 0.05
ACGTcount: A:0.18, C:0.12, G:0.01, T:0.68
Consensus pattern (30 bp):
CTTTTTATTTTTAATTTAATTCAGTCTTTC
Found at i:1356340 original size:14 final size:13
Alignment explanation
Indices: 1356316--1356387 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 13
1356306 CAATCATAAC
*
1356316 AAAAAGAAAAGAA
1 AAAAAAAAAAGAA
1356329 AAAAAAACAAAGAA
1 AAAAAAA-AAAGAA
1356343 AAAAAGAAAAGAGAA
1 AAAAA-AAAA-AGAA
*
1356358 AATAAAAAAGAGAA
1 AA-AAAAAAAAGAA
* *
1356372 ACAAAACAAAGGAA
1 A-AAAAAAAAAGAA
1356386 AA
1 AA
1356388 TGTGAAGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
13 7 0.14
14 27 0.55
15 12 0.24
16 3 0.06
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:1356350 original size:27 final size:28
Alignment explanation
Indices: 1356316--1356387 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 28
1356306 CAATCATAAC
1356316 AAAAAGAAAAGAAAAA-AAAACAA-AGAA
1 AAAAAGAAAAGAAAAATAAAA-AAGAGAA
1356343 AAAAAGAAAAGAGAAAATAAAAAAGAGAA
1 AAAAAGAAAAGA-AAAATAAAAAAGAGAA
* *
1356372 ACAAAACAAAGGAAAA
1 A-AAAAGAAAAGAAAA
1356388 TGTGAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 12 0.31
28 6 0.15
29 12 0.31
30 9 0.23
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (28 bp):
AAAAAGAAAAGAAAAATAAAAAAGAGAA
Found at i:1357455 original size:32 final size:32
Alignment explanation
Indices: 1357419--1357492 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
1357409 AGGAACAATT
* *
1357419 GGGCATCTTTAAAGATTTAACATCAAATGTTG
1 GGGCATCTTTAAAGATTCAACATCAAATATTG
* ** *
1357451 GGGCATTTTTTTAGATTCAACATCGAATATTG
1 GGGCATCTTTAAAGATTCAACATCAAATATTG
1357483 GGGCATCTTT
1 GGGCATCTTT
1357493 GGGAATTCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (32 bp):
GGGCATCTTTAAAGATTCAACATCAAATATTG
Found at i:1357855 original size:64 final size:64
Alignment explanation
Indices: 1357678--1357970 Score: 344
Period size: 64 Copynumber: 4.6 Consensus size: 64
1357668 TGCAGCTTTT
**
1357678 AGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCA-TC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTC
* * * * * * ** *
1357741 AAAGTCAATTTCAACCTCACAGA-GAATGATGTGGGATTCAACAAATAACTTTATAGTTTTATTC
1 AGAGTCAATTTCAACTTCACA-ACGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTC
* *
1357805 AGAGTCAATTTCAACTTCACAACAAAGGATATTGGACTC-ACAAACAAACTTTCCAGTTTCAATT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAA-TAACTTTCCAGTTTC-ATT
1357869 -
64 C
* * * *
1357869 AGAGTCAATTTTAACTTCACAACGAAGGATATTGGACTCGACAAACAACTTTCTAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTC
* * *
1357933 AGAATCAATTTCAATTTCACATCGAAGGATA-TGGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
1357971 GAAACAATGC
Statistics
Matches: 194, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
63 66 0.34
64 120 0.62
65 8 0.04
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTC
Found at i:1358276 original size:124 final size:124
Alignment explanation
Indices: 1358053--1358397 Score: 477
Period size: 124 Copynumber: 2.8 Consensus size: 124
1358043 GAAACAATCC
* * *
1358053 TGGATTTCAACTTCACAACGAAGGATAT-CAACT-AAAGGTTCAACTTCACAATGAATGAGCCAT
1 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA-GCTCAACTTCACAACGAATGAGCCAT
* * * *
1358116 CTACGATTTCAACTTCACGACGAAGAATATCATGCCCACAAGCAGCATCCATCTCTAGAT
65 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAACCATCTCTAGAT
* * *
1358176 TGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACAAAGGAGCCATC
1 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATC
* *
1358241 CACGATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGCAGCAACTATCTCTAGAT
66 CACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAACCATCTCTAGAT
* * **
1358300 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAACTAAACTTCATGACGAATGAGCCAT-
1 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATC
* *
1358364 CACGA-TTCAATTTCACAACGAAGG--ATCGTGCCCA
66 CACGATTTCAACTTCACGACGAAGGATATCGTGCCCA
1358398 ACGGATCGAC
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
120 10 0.05
122 16 0.08
123 32 0.16
124 137 0.69
125 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (124 bp):
TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATC
CACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAACCATCTCTAGAT
Found at i:1359022 original size:171 final size:171
Alignment explanation
Indices: 1358465--1359211 Score: 840
Period size: 171 Copynumber: 4.4 Consensus size: 171
1358455 CCAAGTACAT
* * * * * *
1358465 CATAACTCAAGGCGAGAATGGTTATCTGTCAAC-CAAGTCCTTCGAGTTCGATTACATTTAGCTC
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
*
1358529 AAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACTTTCG
66 AAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCG
* * * * * *
1358594 AGTTTGATTAAATTCAGCT-AAAGGCATATCAAATTCATAA
131 AGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAG
* * * **
1358634 CATAACTCAAGGCGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
* * * *
1358699 AAAGGCACATCAAATTTACATCATAGCTCAAGGAC-AGAAAGACTATCTGTCAACAAAATACCTT
66 AAAGGCACATCAAATTTACAACATAGCTCAAGG-CGAGAAGGGCTATCTGTCAAC-AAAGACCTT
* * ** * *
1358763 AGAGTTTGATTACACTCAGCTCAAAGGCACATGGAATTTATAG
129 CGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAG
* * * *
1358806 CATAGCTTAAGGCGAGAAAGGCTATCTGTCAAGAAAAGGCCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
* * * * * *
1358871 AAATGCATATCAAATTTACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAACTAAGACCTTCG
66 AAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCG
* *
1358936 AGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTACAG
131 AGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAG
* * * * *
1358977 CATAGGTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAATTCGATTATATTCATCTC
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
* * * * * * *
1359042 AGAGGCATATCAACTTTACATCATAGCTCAAGGCGATAAGGGCTATTTCTCAATCAAA-ACCTTC
66 AAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAA-CAAAGACCTTC
* * * * **
1359106 GAGTTCGATTCCATTCACCTCAAGGGCATGTCAAATTCACAG
130 GAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAG
* * * * **
1359148 CATAGCTTAAGTCGAGAAAAGCTATCTGTCAACAAAAAATGTT-GAGTTCGATT-CTATTCAGCT
1 CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTAC-ATTCAGCT
1359211 C
65 C
1359212 GACGATACAT
Statistics
Matches: 488, Mismatches: 83, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
169 30 0.06
170 94 0.19
171 244 0.50
172 120 0.25
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (171 bp):
CATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
AAAGGCACATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCG
AGTTCGATTACACTCAGCTCAAAGGCACATCAAATTCACAG
Found at i:1359195 original size:85 final size:86
Alignment explanation
Indices: 1358460--1359211 Score: 811
Period size: 86 Copynumber: 8.8 Consensus size: 86
1358450 CCTAGCCAAG
* * * * * * *
1358460 TACATCATAACTCAAGGCGAGAATGGTTATCTGTCAAC-CAAGTCCTTCGAGTTCGATTACATTT
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
1358524 AGCTCAAAGGCACATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * *
1358545 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAGACTTTCGAGTTTGATTAAATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
*
1358609 AGCT-AAAGGCATATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * * * **
1358629 CATAACATAACTCAAGGCGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGATTACATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
1358694 AGCTCAAAGGCACATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * * * * * *
1358715 TACATCATAGCTCAAGGAC-AGAAAGACTATCTGTCAACAAAATACCTTAGAGTTTGATTACACT
1 TACAACATAGCTCAAGG-CGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATT
**
1358779 CAGCTCAAAGGCACATGGAATT
65 CAGCTCAAAGGCACATCAAATT
* * * * * * *
1358801 TATAGCATAGCTTAAGGCGAGAAAGGCTATCTGTCAAGAAAAGGCCTTCGAGTTCGATTACACTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
* *
1358866 AGCTCAAATGCATATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * * * * *
1358887 TACAACATAACTCAAGGTGAGAAGGGTTATCTGTCAAC-TAAGACCTTCGAGTTCAATTACACTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
1358951 AGCTCAAAGGCACATCAAATT
66 AGCTCAAAGGCACATCAAATT
* * * *
1358972 TACAGCATAGGTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAATTCGATTATATTC
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
* * * *
1359037 ATCTCAGAGGCATATCAACTT
66 AGCTCAAAGGCACATCAAATT
* * * * *
1359058 TACATCATAGCTCAAGGCGATAAGGGCTATTTCTCAATC-AAA-ACCTTCGAGTTCGATTCCATT
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAA-CAAAAGACCTTCGAGTTCGATTACATT
* * **
1359121 CACCTCAAGGGCATGTCAAATT
65 CAGCTCAAAGGCACATCAAATT
* * * * ** * **
1359143 CACAGCATAGCTTAAGTCGAGAAAAGCTATCTGTCAACAAAAAATGTT-GAGTTCGATT-CTATT
1 TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTAC-ATT
1359206 CAGCTC
65 CAGCTC
1359212 GACGATACAT
Statistics
Matches: 557, Mismatches: 101, Indels: 18
0.82 0.15 0.03
Matches are distributed among these distances:
84 49 0.09
85 245 0.44
86 261 0.47
87 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (86 bp):
TACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTC
AGCTCAAAGGCACATCAAATT
Found at i:1361595 original size:21 final size:21
Alignment explanation
Indices: 1361569--1361666 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
1361559 ATCAGTTCCC
1361569 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
1361590 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
* ** * **
1361610 CA-AATTCACATTGCGATTTTCC
1 -AGAA-TCGCAACGCGATTATGA
*
1361632 AGAATCGCAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
1361653 A-AATCGCAACGCGA
1 AGAATCGCAACGCGA
1361667 ACATATAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.31
21 36 0.62
22 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:1361659 original size:20 final size:20
Alignment explanation
Indices: 1361634--1361915 Score: 122
Period size: 20 Copynumber: 13.7 Consensus size: 20
1361624 GATTTTCCAG
*
1361634 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
1361654 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* * *
1361674 AATCGCAACCGCAACGCGATTCTGAC
1 AATCGCAA-CG---CG-AATAC-GAA
* * * *
1361700 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * * *
1361721 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAA
1361741 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
1361762 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
1361782 AATTGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
1361802 AATCACAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
1361822 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
1361842 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
1361862 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
1361883 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
1361903 AATCGCAATGCGA
1 AATCGCAACGCGA
1361916 TTTTTAAAGC
Statistics
Matches: 199, Mismatches: 46, Indels: 34
0.71 0.16 0.12
Matches are distributed among these distances:
19 2 0.01
20 129 0.65
21 54 0.27
22 1 0.01
24 2 0.01
25 3 0.02
26 7 0.04
27 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:1361816 original size:40 final size:41
Alignment explanation
Indices: 1361701--1361910 Score: 325
Period size: 41 Copynumber: 5.2 Consensus size: 41
1361691 GATTCTGACT
* * *
1361701 ATCGCAACGAGTATCCGTAAAATCGCAACGTGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1361742 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
1361783 ATTGCAACGAGAATACGT-AAATCACAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1361823 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
1361863 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
1361904 ATCGCAA
1 ATCGCAA
1361911 TGCGATTTTT
Statistics
Matches: 154, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 73 0.47
41 81 0.53
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:1362496 original size:20 final size:21
Alignment explanation
Indices: 1362471--1362526 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
1362461 TTCTAAACTT
1362471 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1362491 AAAATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1362512 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
1362527 TAATCGCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.54, C:0.16, G:0.20, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1362662 original size:33 final size:33
Alignment explanation
Indices: 1362552--1362684 Score: 122
Period size: 33 Copynumber: 3.8 Consensus size: 33
1362542 ACCAAAATCG
* *
1362552 CATTACGATTTTCATTTCGCGTTGCAATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* * *
1362585 CGTTTCGATTTTAATTTCGCGTTGCGATTTTACTTTCT
1 CATTGCGATTTTCATTTCGCGTTGCGA--TT-C--TCT
* *
1362623 CGTTGCGATTTTCATTTCGTGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
** *
1362656 CATTGCGATAGTCATTTCCGCATTGCGAT
1 CATTGCGATTTTCATTT-CGCGTTGCGAT
1362685 AGTCATTCTC
Statistics
Matches: 82, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
33 40 0.49
34 9 0.11
35 3 0.04
36 3 0.04
38 27 0.33
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1362673 original size:71 final size:73
Alignment explanation
Indices: 1362557--1362713 Score: 194
Period size: 71 Copynumber: 2.2 Consensus size: 73
1362547 AATCGCATTA
* * ** * * *
1362557 CGATTTTCATTTCGCGTTGCAATTCTCTCGTTTCGATTTTAATTT-CGCGTTGCGAT-TTTACTT
1 CGATTTTCATTTCGCGTTGCAATTCTCTCATTGCGATAGTAATTTCCGCATTGCGATAGTCA-TT
1362620 -TCTCGTTG
65 CTCTCGTTG
* * *
1362628 CGATTTTCATTTCGTGTTGCGATTCTCTCATTGCGATAGTCATTTCCGCATTGCGATAGTCATTC
1 CGATTTTCATTTCGCGTTGCAATTCTCTCATTGCGATAGTAATTTCCGCATTGCGATAGTCATTC
1362693 TCTCGTTG
66 TCTCGTTG
1362701 CGATTTTCATTTC
1 CGATTTTCATTTC
1362714 AACCAAAAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 38 0.52
72 12 0.16
73 23 0.32
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (73 bp):
CGATTTTCATTTCGCGTTGCAATTCTCTCATTGCGATAGTAATTTCCGCATTGCGATAGTCATTC
TCTCGTTG
Found at i:1362701 original size:20 final size:20
Alignment explanation
Indices: 1362649--1362704 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1362639 TCGTGTTGCG
*
1362649 ATTCTCTCATTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
1362669 ATT-TC-CGCATTGCGATAGTC
1 ATTCTCTCG--TTGCGATAGTC
1362689 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1362705 TTTCATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 24 0.77
21 2 0.06
22 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1362710 original size:20 final size:19
Alignment explanation
Indices: 1362582--1362713 Score: 91
Period size: 19 Copynumber: 7.1 Consensus size: 19
1362572 GTTGCAATTC
* *
1362582 TCTCGTTTCGATTTTAATT
1 TCTCGTTGCGATTTTCATT
*
1362601 TCGCGTTGCGATTTT-ACTT
1 TCTCGTTGCGATTTTCA-TT
1362620 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
1362639 TCGT-GTTGCGA--TTC---
1 TC-TCGTTGCGATTTTCATT
* **
1362653 TCTCATTGCGATAGTCATT
1 TCTCGTTGCGATTTTCATT
**
1362672 TC-CGCATTGCGATAGTCATT
1 TCTCG--TTGCGATTTTCATT
1362692 CTCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTTTCATT
1362712 TC
1 TC
1362714 AACCAAAAGA
Statistics
Matches: 92, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
13 1 0.01
14 8 0.09
16 2 0.02
17 3 0.03
18 2 0.02
19 44 0.48
20 28 0.30
21 2 0.02
22 2 0.02
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCTCGTTGCGATTTTCATT
Found at i:1364550 original size:94 final size:94
Alignment explanation
Indices: 1364388--1364767 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
1364378 TAGATTGCTT
* * *
1364388 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1364453 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1364482 AGTAAATTTATTCGGTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1364547 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1364576 AGTAAATTTGTTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1364641 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1364670 AGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1364735 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1364763 AGTAA
1 AGTAA
1364768 TGCAATCCAT
Statistics
Matches: 275, Mismatches: 10, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 249 0.91
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1364914 original size:33 final size:33
Alignment explanation
Indices: 1364859--1364946 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
1364849 ATGACTATCG
*
1364859 CAACGCGAAATG--AATCGTAACGAGAGAATCA
1 CAACGCGAAATGAAAATCGCAACGAGAGAATCA
* *
1364890 CAACGAGAAATGAAAATCGCAACGAGAGAATCG
1 CAACGCGAAATGAAAATCGCAACGAGAGAATCA
**
1364923 CAACGCGAAACCAAAATCGCAACG
1 CAACGCGAAATGAAAATCGCAACG
1364947 CGAAACTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
31 11 0.22
33 38 0.78
ACGTcount: A:0.47, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
CAACGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:1364923 original size:14 final size:14
Alignment explanation
Indices: 1364870--1364927 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
1364860 AACGCGAAAT
*
1364870 GAATCGTAACGAGA
1 GAATCGCAACGAGA
*
1364884 GAATCACAACGAGAAA
1 GAATCGCAACGAG--A
1364900 TGAAAATCGCAACGAGA
1 -G--AATCGCAACGAGA
1364917 GAATCGCAACG
1 GAATCGCAACG
1364928 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 21 0.58
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.10
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:1365048 original size:20 final size:20
Alignment explanation
Indices: 1364996--1365062 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
1364986 GATTCTCTCG
** *
1364996 TTGCGATAGTCAAATTCGAA
1 TTGCGATAGTCATTTTCGCA
1365016 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1365036 TTGCGATCA-TCATTTTCGCG
1 TTGCGAT-AGTCATTTTCGCA
1365056 TTGCGAT
1 TTGCGAT
1365063 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 41 0.98
21 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1365584 original size:18 final size:19
Alignment explanation
Indices: 1365545--1365586 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1365535 CTCACATGTC
1365545 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1365566 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1365584 ATC
1 ATC
1365587 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1369009 original size:20 final size:20
Alignment explanation
Indices: 1368986--1369046 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
1368976 TTGCGATAGT
* *
1368986 CAGATTCTCGTTGCGATTTA
1 CAGATTCGCATTGCGATTTA
1369006 CAGATTCGCATTGCGATTTA
1 CAGATTCGCATTGCGATTTA
1369026 C-GTATTCGCATTGCGATTTA
1 CAG-ATTCGCATTGCGATTTA
1369046 C
1 C
1369047 GTAATCACGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
CAGATTCGCATTGCGATTTA
Found at i:1369061 original size:20 final size:20
Alignment explanation
Indices: 1368996--1369049 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
1368986 CAGATTCTCG
1368996 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
1369016 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1369036 TTGCGATTTACGTA
1 TTGCGATTTACGTA
1369050 ATCACGTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1369082 original size:21 final size:21
Alignment explanation
Indices: 1369058--1369124 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
1369048 TAATCACGTT
* *
1369058 GCGAATTAGGAAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
1369079 GCGAATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
*
1369100 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGGAAATCGCAAC
1369121 GCGA
1 GCGA
1369125 TAGTCAGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (21 bp):
GCGAATTTGGGAAATCGCAAC
Found at i:1369218 original size:20 final size:20
Alignment explanation
Indices: 1369174--1369404 Score: 202
Period size: 20 Copynumber: 11.6 Consensus size: 20
1369164 TACCGGAGAT
*
1369174 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
1369193 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1369213 CGCGTTGTGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
1369233 TGTCGTTGCGATTTACGAATA
1 CG-CGTTGCGATTTACGGATA
* * * * *
1369254 CACATTGCGATTTATGTATT
1 CGCGTTGCGATTTACGGATA
* *
1369274 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
1369294 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
**
1369314 CTTGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1369334 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1369354 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
1369375 C-CGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1369394 CTCGTTGCGAT
1 CGCGTTGCGAT
1369405 AGTCAGAATC
Statistics
Matches: 169, Mismatches: 34, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.01
19 35 0.21
20 102 0.60
21 31 0.18
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1369284 original size:40 final size:40
Alignment explanation
Indices: 1369174--1369404 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
1369164 TACCGGAGAT
* *
1369174 CGCGTTGCGAATTATCG-A-TCGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTA-CGTATTCTCGTTGCGATTTACGGATA
* * *
1369213 CGCGTTGTGATTTTACGTATTGTCGTTGCGATTTACGAATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* * * *
1369254 CACATTGCGATTTATGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* *
1369294 CGCATTGCGATTTACGTATTCTTGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
*
1369334 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* *
1369375 C-CGTTGCGATTTACGGATACTCGTTGCGAT
1 CGCGTTGCGATTTACGTATTCTCGTTGCGAT
1369405 AGTCAGAATC
Statistics
Matches: 166, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 29 0.17
40 83 0.50
41 54 0.33
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:1369381 original size:60 final size:61
Alignment explanation
Indices: 1369195--1369404 Score: 248
Period size: 60 Copynumber: 3.5 Consensus size: 61
1369185 TTATCGATCG
*
1369195 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGTATTGTCGTTGCGATTTACGAATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACA
* * * * * * * * * *
1369256 CATTGCGATTTATGTATTCTCGTTGCGA-TTTACAG-ATACG-CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTAC-GTAT-TGTCGTTGCGATTTACGAATACA
* *
1369316 TGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC-
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACA
*
1369376 CGTTGCGATTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
1369405 AGTCAGAATC
Statistics
Matches: 121, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
60 74 0.61
61 47 0.39
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.39
Consensus pattern (61 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACA
Found at i:1369436 original size:20 final size:20
Alignment explanation
Indices: 1369413--1369465 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1369403 ATAGTCAGAA
*
1369413 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1369433 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
1369453 TCACGTTGCGATT
1 TCGCGTTGCGATT
1369466 GATTCTGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1369568 original size:20 final size:20
Alignment explanation
Indices: 1369518--1369572 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1369508 GATTCTTCAT
1369518 AATCGCGTTGCGATTCTAGG
1 AATCGCGTTGCGATTCTAGG
**
1369538 AA-CTGATTTGCGATTCT-GG
1 AATC-GCGTTGCGATTCTAGG
1369557 AGATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
1369573 TTTATTTCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 4 0.14
20 23 0.82
21 1 0.04
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTAGG
Found at i:1373127 original size:20 final size:21
Alignment explanation
Indices: 1373091--1373130 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
1373081 GGTTGCGGAA
1373091 TTGATGGTGTTTGATGATGAAG
1 TTGATGGTG-TTGATGATGAAG
1373113 TTGATGGTG-TGATGATGA
1 TTGATGGTGTTGATGATGA
1373131 GAAGGAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.40
Consensus pattern (21 bp):
TTGATGGTGTTGATGATGAAG
Found at i:1373134 original size:22 final size:22
Alignment explanation
Indices: 1373091--1373143 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1373081 GGTTGCGGAA
*
1373091 TTGATGGTGTTTGATGATGAAG
1 TTGATGGTGTATGATGATGAAG
1373113 TTGATGGTGTGATGATGA-GAAG
1 TTGATGGTGT-ATGATGATGAAG
**
1373135 GAGATGGTG
1 TTGATGGTG
1373144 GTGTTGTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.34
Consensus pattern (22 bp):
TTGATGGTGTATGATGATGAAG
Found at i:1375011 original size:23 final size:22
Alignment explanation
Indices: 1374985--1375036 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
1374975 ATTGCACTGA
1374985 AGTGCCACGTAGAATTGCACCAG-
1 AGTGCCACGTAGAATTG-ACC-GT
* *
1375008 AGTGTCGCGTAGAATTGACCGT
1 AGTGCCACGTAGAATTGACCGT
1375030 AGTGCCA
1 AGTGCCA
1375037 TATAATAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 8 0.33
23 15 0.62
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (22 bp):
AGTGCCACGTAGAATTGACCGT
Found at i:1375727 original size:63 final size:64
Alignment explanation
Indices: 1375604--1375755 Score: 175
Period size: 64 Copynumber: 2.4 Consensus size: 64
1375594 TCATTTCATC
*
1375604 TTTAATGGAGGTGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGTGTTTGTA-
1 TTTAATGG-GGTGCATCGATGCACTACACCATGCATCGATGCATAAATCACATTCGTGTTTGTAT
* ** **
1375668 TTTAATGGGGTGCATCGATGCACT-C-CTTATGCATCGATGCATCTATGGCATTCGATGTTTGTA
1 TTTAATGGGGTGCATCGATGCACTACAC-CATGCATCGATGCATAAATCACATTCG-TGTTTGTA
1375731 T
64 T
** *
1375732 TTTAAAAGAGTGCATCGATGCACT
1 TTTAATGGGGTGCATCGATGCACT
1375756 TCATGTGCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
61 1 0.01
62 22 0.29
63 24 0.32
64 29 0.38
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (64 bp):
TTTAATGGGGTGCATCGATGCACTACACCATGCATCGATGCATAAATCACATTCGTGTTTGTAT
Found at i:1375754 original size:64 final size:63
Alignment explanation
Indices: 1375614--1375755 Score: 162
Period size: 63 Copynumber: 2.2 Consensus size: 63
1375604 TTTAATGGAG
* ** *
1375614 GTGCATCGATGCACTACACCATGCATCGATGCATAAATCATATTCGTGTTTGTATTTAATGGG
1 GTGCATCGATGCACTACACCATGCATCGATGCATAAATCACATTCGTGTTTGTATTTAAAAGA
* ** **
1375677 GTGCATCGATGCACT-C-CTTATGCATCGATGCATCTATGGCATTCGATGTTTGTATTTTAAAAG
1 GTGCATCGATGCACTACAC-CATGCATCGATGCATAAATCACATTCG-TGTTTGTA-TTTAAAAG
1375740 A
63 A
1375741 GTGCATCGATGCACT
1 GTGCATCGATGCACT
1375756 TCATGTGCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
61 1 0.01
62 22 0.33
63 23 0.34
64 21 0.31
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACACCATGCATCGATGCATAAATCACATTCGTGTTTGTATTTAAAAGA
Found at i:1381841 original size:23 final size:23
Alignment explanation
Indices: 1381811--1381855 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1381801 TCGTATGCCA
**
1381811 CGTAGAATTGCACCGGAGTTCCG
1 CGTAGAATAACACCGGAGTTCCG
*
1381834 CGTAGAATAACACCGTAGTTCC
1 CGTAGAATAACACCGGAGTTCC
1381856 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATAACACCGGAGTTCCG
Found at i:1382530 original size:63 final size:64
Alignment explanation
Indices: 1382441--1382581 Score: 176
Period size: 63 Copynumber: 2.2 Consensus size: 64
1382431 AATGGAGGTA
* ** *
1382441 TGCATCGATGCACTACACATGCATCGATGCATAAATCATATTCGATGTTTGTA-TTTAATGGGG
1 TGCATCGATGCACTACACATGCATCGATGCATAAATCACATTCGATGTTTGTATTTTAAAAGAG
* ** ** **
1382504 TGCATCGATGCACTCCTTATGCATCGATGCATCTATGGCATTCGATGTTTGTATTTTAAAAGAG
1 TGCATCGATGCACTACACATGCATCGATGCATAAATCACATTCGATGTTTGTATTTTAAAAGAG
1382568 TGCATCGATGCACT
1 TGCATCGATGCACT
1382582 TCATGTGCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
63 45 0.68
64 21 0.32
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
TGCATCGATGCACTACACATGCATCGATGCATAAATCACATTCGATGTTTGTATTTTAAAAGAG
Found at i:1384655 original size:210 final size:210
Alignment explanation
Indices: 1384062--1384873 Score: 1231
Period size: 210 Copynumber: 3.8 Consensus size: 210
1384052 ATTTAAGAAT
1384062 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A--AG
* * *
1384127 GGATCAAATCGAAATTATTTTAAATTGTGAGGTTGAAATTAATACAAAAAA--ACTAAATTATAC
62 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATAC
* * * * *
1384190 CCATTTAAAAAGTTATGGGCTAATTAAAAAAATTGAATTAAGTAATAAGTATGGATTAATTTCAT
127 CCATTTAAAAAGTTATGGGCCAATTAAAAATA-T-AAATAAGTAATAAGTATGG-TCAATTTCAG
1384255 ATGCAAATAAAATTTGGAGGAC
189 ATGCAAATAAAATTTGGAGGAC
*
1384277 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGGG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-AAGGG
* * *
1384342 ATCAAATCTAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
64 ATCAAATCAAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATACCC
*
1384407 ATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGTGTCAATTTCAGATG
129 ATTTAAAAAGTTATGGGCCAA-TTAAAAATATAAATAAGTAATAAGTATG-GTCAATTTCAGATG
1384472 CAAATAAAATTTGGAGGAC
192 CAAATAAAATTTGGAGGAC
* * *
1384491 TAAATTGAACAAATATGAAATTGCAAATAAAAATTTTAATATATTAAACAACACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
*
1384554 CAAATCAAAATAATTTTAAATTTTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATACCCAT
66 CAAATCAAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATACCCAT
*
1384619 TTAAAAAGTTATGGGCCAATTTAAAAATATAAATAAGTAATAAGTATGAGTCAATTTCAGGTGCA
131 TTAAAAAGTTATGGGCCAA-TTAAAAATATAAATAAGTAATAAGTATG-GTCAATTTCAGATGCA
1384684 AATAAAATTTGGAGGAC
194 AATAAAATTTGGAGGAC
* *
1384701 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAAGACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
* * * *
1384764 CAAATCAAAATAATTTTAAATTTTGAGGTTAAAATTAATACAAAAATGTACTAAAATATACTCAT
66 CAAATCAAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATACCCAT
*
1384829 TTAAAAAGTTATGAGCCAATTAATAAATATAAATAAGTAATAAGT
131 TTAAAAAGTTATGGGCCAATTAA-AAATATAAATAAGTAATAAGT
1384874 TGAGAAAAAA
Statistics
Matches: 564, Mismatches: 28, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
209 4 0.01
210 307 0.54
213 50 0.09
214 99 0.18
215 96 0.17
216 8 0.01
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.30
Consensus pattern (210 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
CAAATCAAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAAGTACTAAATTATACCCAT
TTAAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAGTATGGTCAATTTCAGATGCAAA
TAAAATTTGGAGGAC
Found at i:1384971 original size:31 final size:30
Alignment explanation
Indices: 1384904--1385003 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 30
1384894 CTAATATAGA
* **
1384904 TATATATATATATATATATATATAATATAAAG
1 TATATATAT-TATATATATAAAT-ATATAATT
*
1384936 TATATGTATTATATATATAAACTATATAATT
1 TATATATATTATATATATAAA-TATATAATT
*
1384967 TATATATA-TATTATGTATAAAGTATA-AA-T
1 TATATATATTA-TATATATAAA-TATATAATT
1384996 TATATATA
1 TATATATA
1385004 CCAGTATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
29 9 0.15
30 4 0.07
31 37 0.63
32 9 0.15
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (30 bp):
TATATATATTATATATATAAATATATAATT
Found at i:1385020 original size:2 final size:2
Alignment explanation
Indices: 1384897--1385003 Score: 80
Period size: 2 Copynumber: 54.5 Consensus size: 2
1384887 AAAACAACTA
* *
1384897 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
1384939 AT GT AT -T AT AT AT AT AA ACT AT AT A- AT TT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * *
1384979 AT GT AT AA AGT AT AA AT -T AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT A
1385004 CCAGTATAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
1 5 0.06
2 73 0.90
3 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1385173 original size:22 final size:21
Alignment explanation
Indices: 1385140--1385185 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
1385130 AAATAATATA
1385140 TATTGTATAAATTATATAGTT
1 TATTGTATAAATTATATAGTT
1385161 TATTGATATAAATTATATAGTT
1 TATTG-TATAAATTATATAGTT
1385183 TAT
1 TAT
1385186 ATTAGGGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (21 bp):
TATTGTATAAATTATATAGTT
Found at i:1385422 original size:5 final size:5
Alignment explanation
Indices: 1385412--1385438 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1385402 AAAACCGAAA
1385412 AACCG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA
1385439 AAACCCGAAC
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:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:1385613 original size:2 final size:2
Alignment explanation
Indices: 1385606--1385640 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1385596 ACCCCTAGTT
1385606 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 T
1385641 GGTTTAGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1385653 original size:7 final size:7
Alignment explanation
Indices: 1385641--1385674 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1385631 ATATATATAT
1385641 GGTTTAG
1 GGTTTAG
1385648 GGTTTAG
1 GGTTTAG
*
1385655 GGTTTAA
1 GGTTTAG
*
1385662 TGTTTAG
1 GGTTTAG
1385669 GGTTTA
1 GGTTTA
1385675 TATTTATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (7 bp):
GGTTTAG
Found at i:1385682 original size:6 final size:6
Alignment explanation
Indices: 1385671--1385701 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1385661 ATGTTTAGGG
1385671 TTTATA TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA T
1385702 AAACTACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:1385746 original size:22 final size:20
Alignment explanation
Indices: 1385671--1385775 Score: 88
Period size: 22 Copynumber: 5.0 Consensus size: 20
1385661 ATGTTTAGGG
*
1385671 TTTATATTTATAT-TTATA-
1 TTTATATTTATATACTATAT
*
1385689 TTTATATTTATATAAACTACAT
1 TTTATATTTATAT--ACTATAT
**
1385711 ACTATAATTTATATACTATAT
1 TTTAT-ATTTATATACTATAT
*
1385732 TTTATACTTTTATATAAACTATAG
1 TTTATA--TTTATAT--ACTATAT
1385756 TTTATATTTATATACTATAT
1 TTTATATTTATATACTATAT
1385776 ATACGAACTA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
18 13 0.19
20 7 0.10
21 12 0.17
22 17 0.25
23 8 0.12
24 12 0.17
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (20 bp):
TTTATATTTATATACTATAT
Found at i:1385790 original size:33 final size:31
Alignment explanation
Indices: 1385727--1385792 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1385717 ATTTATATAC
*
1385727 TATATTTTATACTTTTATATAAACTATAGTT
1 TATATTTTATACTTATATATAAACTATAGTT
1385758 TATATTTATATAC-TATATATACGAACTATAGTT
1 TATATTT-TATACTTATATATA--AACTATAGTT
1385791 TA
1 TA
1385793 CATATGAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 14 0.45
32 5 0.16
33 12 0.39
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.50
Consensus pattern (31 bp):
TATATTTTATACTTATATATAAACTATAGTT
Found at i:1385864 original size:18 final size:18
Alignment explanation
Indices: 1385838--1385952 Score: 106
Period size: 18 Copynumber: 5.9 Consensus size: 18
1385828 AAGGTTGATA
*
1385838 TTTATATATGAACTATAG
1 TTTACATATGAACTATAG
*
1385856 TTTACATATAAACTATATAG
1 TTTACATATGAAC--TATAG
*
1385876 TTTATATACT-AACTATAG
1 TTTACATA-TGAACTATAG
*
1385894 TTTACATATAAACTATAG
1 TTTACATATGAACTATAG
1385912 TTAATATTTACATATGAACTATAG
1 ------TTTACATATGAACTATAG
1385936 TTTACATATGAACTATA
1 TTTACATATGAACTATA
1385953 TATATAAACT
Statistics
Matches: 82, Mismatches: 5, Indels: 20
0.77 0.05 0.19
Matches are distributed among these distances:
17 1 0.01
18 48 0.59
20 15 0.18
21 1 0.01
24 17 0.21
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:1385874 original size:20 final size:20
Alignment explanation
Indices: 1385851--1386048 Score: 100
Period size: 20 Copynumber: 10.2 Consensus size: 20
1385841 ATATATGAAC
1385851 TATAGTTTACATATAAACTA
1 TATAGTTTACATATAAACTA
*
1385871 TATAGTTTATATACT-AAC--
1 TATAGTTTACATA-TAAACTA
1385889 TATAGTTTACATATAAACTA
1 TATAGTTTACATATAAACTA
* *
1385909 TAGTTAATATTTACATATGAAC--
1 TA--T-A-GTTTACATATAAACTA
*
1385931 TATAGTTTACATATGAAC--
1 TATAGTTTACATATAAACTA
1385949 TATA---T--ATATAAACTA
1 TATAGTTTACATATAAACTA
* *
1385964 TATAGTTTACATATGAGCTA
1 TATAGTTTACATATAAACTA
* * *
1385984 TATA-TATATATATATA-TA
1 TATAGTTTACATATAAACTA
** *
1386002 CTATAGTTGATATTTATATACTA
1 -TATAGTT--TACATATAAACTA
* *
1386025 TATAGTTTACATATGACCTA
1 TATAGTTTACATATAAACTA
1386045 TATA
1 TATA
1386049 TATATACTAT
Statistics
Matches: 138, Mismatches: 20, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
13 7 0.05
15 5 0.04
17 1 0.01
18 35 0.25
19 12 0.09
20 43 0.31
21 1 0.01
22 19 0.14
23 3 0.02
24 12 0.09
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.42
Consensus pattern (20 bp):
TATAGTTTACATATAAACTA
Found at i:1385970 original size:33 final size:33
Alignment explanation
Indices: 1385931--1386059 Score: 162
Period size: 33 Copynumber: 4.1 Consensus size: 33
1385921 ACATATGAAC
* *
1385931 TATAGTTTACATATGAACTATATATATAAACTA
1 TATAGTTTACATATGAGCTATATATATATACTA
1385964 TATAGTTTACATATGAGCTATATATATATA-TA
1 TATAGTTTACATATGAGCTATATATATATACTA
* *
1385996 TATA---TAC-TAT-AGTTGATATTTATATACTA
1 TATAGTTTACATATGAGCT-ATATATATATACTA
*
1386025 TATAGTTTACATATGACCTATATATATATACTA
1 TATAGTTTACATATGAGCTATATATATATACTA
1386058 TA
1 TA
1386060 GCTTATATTT
Statistics
Matches: 82, Mismatches: 7, Indels: 14
0.80 0.07 0.14
Matches are distributed among these distances:
27 3 0.04
28 13 0.16
29 9 0.11
32 9 0.11
33 46 0.56
34 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (33 bp):
TATAGTTTACATATGAGCTATATATATATACTA
Found at i:1386054 original size:53 final size:53
Alignment explanation
Indices: 1385990--1386101 Score: 163
Period size: 53 Copynumber: 2.1 Consensus size: 53
1385980 GCTATATATA
* *
1385990 TATATATATATACTATAG-TTGATATTTATATACTATATAGTTTACATATGACC
1 TATATATATATACTATAGCTT-ATATTTATATACTATATAGTTTACATATAAAC
* * *
1386043 TATATATATATACTATAGCTTATATTTATATATTATATATTTTATATATAAAC
1 TATATATATATACTATAGCTTATATTTATATACTATATAGTTTACATATAAAC
1386096 TATATA
1 TATATA
1386102 AAATCTATAG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
53 51 0.96
54 2 0.04
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.48
Consensus pattern (53 bp):
TATATATATATACTATAGCTTATATTTATATACTATATAGTTTACATATAAAC
Found at i:1386076 original size:61 final size:60
Alignment explanation
Indices: 1385949--1386081 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 60
1385939 ACATATGAAC
* * * *
1385949 TATATATATAAACTATATAGTTTACATATGAGCTATATATATATATATATATACTATAGTT
1 TATATTTATATACTATATAGTTTACATATGACCTATATATATATATATAGATA-TATAGTT
* *
1386010 GATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGCT-TATA-TT
1 TATATTTATATACTATATAGTTTACATATGACCTATATATATATA-TATAGATATATAGTT
1386069 TATATATTATATA
1 TATAT-TTATATA
1386082 TTTTATATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 6 0.10
60 11 0.17
61 41 0.65
62 5 0.08
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (60 bp):
TATATTTATATACTATATAGTTTACATATGACCTATATATATATATATAGATATATAGTT
Found at i:1386100 original size:20 final size:20
Alignment explanation
Indices: 1385951--1386101 Score: 68
Period size: 20 Copynumber: 7.8 Consensus size: 20
1385941 ATATGAACTA
*
1385951 TATATATAAACTATATAGTT
1 TATATATAAACTATATATTT
* * * *
1385971 TACATATGAGCTATATATATA
1 TATATATAAACTATATAT-TT
* **
1385992 TATATATATACTATAGT-TGA
1 TATATATAAACTATA-TATTT
* * *
1386012 TATTTATATACTATATAGTT
1 TATATATAAACTATATATTT
* * * *
1386032 TACATATGACCTATATA-TA
1 TATATATAAACTATATATTT
*
1386051 TATACTAT-AGCT-TATA-TT
1 TATA-TATAAACTATATATTT
1386069 TATATAT----TATATATTT
1 TATATATAAACTATATATTT
1386085 TATATATAAACTATATA
1 TATATATAAACTATATA
1386102 AAATCTATAG
Statistics
Matches: 98, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
14 1 0.01
15 4 0.04
16 9 0.09
17 3 0.03
18 9 0.09
19 8 0.08
20 50 0.51
21 13 0.13
22 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (20 bp):
TATATATAAACTATATATTT
Found at i:1386101 original size:2 final size:2
Alignment explanation
Indices: 1385982--1386092 Score: 50
Period size: 2 Copynumber: 54.0 Consensus size: 2
1385972 ACATATGAGC
*
1385982 TA TA TA TA TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA
* * ** **
1386025 TA TA GTT TA CA TA TGA CC TA TA TA TA TA TA CTA TA GC T- TA TA
1 TA TA -TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
1386067 TT TA TA TA T- TA TA TA T- TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1386093 AACTATATAA
Statistics
Matches: 82, Mismatches: 16, Indels: 22
0.68 0.13 0.18
Matches are distributed among these distances:
1 4 0.05
2 68 0.83
3 10 0.12
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1386209 original size:18 final size:18
Alignment explanation
Indices: 1386186--1386236 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1386176 AGTTTATTAG
1386186 TATATATAAACTATATAA
1 TATATATAAACTATATAA
* **
1386204 TATATATAGACTATATGG
1 TATATATAAACTATATAA
1386222 TATATATAAACTATA
1 TATATATAAACTATA
1386237 CATATAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (18 bp):
TATATATAAACTATATAA
Found at i:1386236 original size:29 final size:27
Alignment explanation
Indices: 1386197--1386294 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 27
1386187 ATATATAAAC
*
1386197 TATATAA-TATATATAGACT-ATATGGTA
1 TATATAACTATATATA-ACTCAT-TAGTA
*
1386224 TATATAAACTATACATATAATTCATTAGTA
1 TATAT-AACTAT--ATATAACTCATTAGTA
*
1386254 TATATAACTATATATATAGTTCATTAGTA
1 TATATAACTATATATA-A-CTCATTAGTA
1386283 TATA-AACTATAT
1 TATATAACTATAT
1386295 TACATAGTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
27 10 0.16
28 11 0.18
29 23 0.37
30 11 0.18
31 7 0.11
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (27 bp):
TATATAACTATATATAACTCATTAGTA
Found at i:1386258 original size:17 final size:17
Alignment explanation
Indices: 1386238--1386286 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1386228 TAAACTATAC
1386238 ATATAATTCATTAGTAT
1 ATATAATTCATTAGTAT
1386255 ATATAA--C--TA-TAT
1 ATATAATTCATTAGTAT
*
1386267 ATATAGTTCATTAGTAT
1 ATATAATTCATTAGTAT
1386284 ATA
1 ATA
1386287 AACTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
12 8 0.31
13 2 0.08
14 1 0.04
15 1 0.04
16 2 0.08
17 12 0.46
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (17 bp):
ATATAATTCATTAGTAT
Found at i:1386268 original size:58 final size:57
Alignment explanation
Indices: 1386197--1386391 Score: 181
Period size: 58 Copynumber: 3.4 Consensus size: 57
1386187 ATATATAAAC
*
1386197 TATATAA-TATATATAGACTATATGGTATATATAAACTATACATATAATTCATTAGTA
1 TATATAACTATATATAGA-TATATGGTATATATAAACTATATATATAATTCATTAGTA
* * *
1386254 TATATAACTATATATATAGT-TCAT--TAGTATATAAACTATATTACATAGTTCATTAG--
1 TATATAACTATATATAGA-TAT-ATGGTA-TATATAAACTATA-TATATAATTCATTAGTA
* *
1386310 TATATAAC-CTATATAG-TATATGGTATATACAAACTATATATTATATAGTTCATTAGTA
1 TATATAACTATATATAGATATATGGTATATATAAACTATATA-TATA-A-TTCATTAGTA
*
1386368 TATATAAACTATATAGTATATATA
1 TATAT-AACTATATA-TAGATATA
1386392 AACTATATAT
Statistics
Matches: 110, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
53 5 0.05
54 16 0.15
55 8 0.07
56 18 0.16
57 21 0.19
58 29 0.26
59 3 0.03
60 4 0.04
61 2 0.02
62 4 0.04
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.42
Consensus pattern (57 bp):
TATATAACTATATATAGATATATGGTATATATAAACTATATATATAATTCATTAGTA
Found at i:1386270 original size:51 final size:49
Alignment explanation
Indices: 1386215--1386427 Score: 159
Period size: 51 Copynumber: 4.1 Consensus size: 49
1386205 ATATATAGAC
*
1386215 TATATGGTATATATAAACTATACATATAATTCATTAGTATATATAACTATA
1 TATATGGTATATATAAACTATATATATAATTCATTAGTATATA-AAC-ATA
* * * *
1386266 TATATAGTTCATTAGTATATAAACTATATTACATAGTTCATTAGTATATAACCTATATA
1 TATAT-G----GTA-TATATAAACTATA-TATATAATTCATTAGTATATAA---ACATA
*
1386325 GTATATGGTATATACAAACTATATATTATATAGTTCATTAGTATATATAA-ACTA
1 -TATATGGTATATATAAACTATATA-TATA-A-TTCATTAGTATATA-AACA-TA
*
1386379 TATA--GTATATATAAACTATATAT-TAATTTATTA--ATATAAACATA
1 TATATGGTATATATAAACTATATATATAATTCATTAGTATATAAACATA
1386423 TATAT
1 TATAT
1386428 TAATTGAAAG
Statistics
Matches: 133, Mismatches: 11, Indels: 42
0.72 0.06 0.23
Matches are distributed among these distances:
44 8 0.06
45 6 0.05
47 6 0.05
48 1 0.01
49 2 0.02
50 1 0.01
51 22 0.17
52 1 0.01
53 7 0.05
54 18 0.14
55 2 0.02
56 16 0.12
57 15 0.11
58 18 0.14
59 4 0.03
60 6 0.05
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (49 bp):
TATATGGTATATATAAACTATATATATAATTCATTAGTATATAAACATA
Found at i:1386285 original size:66 final size:68
Alignment explanation
Indices: 1386159--1386391 Score: 203
Period size: 56 Copynumber: 3.8 Consensus size: 68
1386149 CCCTAAACCC
*
1386159 TAAACTATACATTATATAGTTTATTAGTATATATAAACTATATAATATATATAGACTATATGGTA
1 TAAACTATACATTATATAGTTCATTAGTATATATAAACTATATAATATATATAGA-TATATGGTA
1386224 TATA
65 TATA
*
1386228 TAAACTATACA-TATA-A-TTCATTAGTATATAT-AACTATAT-ATATAGT-T-CAT-TA--G--
1 TAAACTATACATTATATAGTTCATTAGTATATATAAACTATATAATATA-TATAGATATATGGTA
1386281 TATA
65 TATA
* *
1386285 TAAACTAT--ATTACATAGTTCATTAG--TATAT-AAC--------CTATATAG-TATATGGTAT
1 TAAACTATACATTATATAGTTCATTAGTATATATAAACTATATAATATATATAGATATATGGTAT
1386336 ATA
66 ATA
* * *
1386339 CAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATATA
1 TAAACTATACATTATATAGTTCATTAGTATATATAAACTATATAATATATATA
1386392 AACTATATAT
Statistics
Matches: 132, Mismatches: 8, Indels: 50
0.69 0.04 0.26
Matches are distributed among these distances:
48 1 0.01
49 4 0.03
50 2 0.02
52 1 0.01
54 11 0.08
55 1 0.01
56 27 0.20
57 13 0.10
58 13 0.10
59 4 0.03
61 2 0.02
62 1 0.01
63 1 0.01
64 6 0.05
65 9 0.07
66 14 0.11
67 7 0.05
68 4 0.03
69 11 0.08
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.42
Consensus pattern (68 bp):
TAAACTATACATTATATAGTTCATTAGTATATATAAACTATATAATATATATAGATATATGGTAT
ATA
Found at i:1386301 original size:29 final size:28
Alignment explanation
Indices: 1386224--1386387 Score: 156
Period size: 29 Copynumber: 5.7 Consensus size: 28
1386214 CTATATGGTA
* *
1386224 TATATAAACTATACATATAATTCATTAG
1 TATATAAACTATATATATAGTTCATTAG
1386252 TATATATAACTATATATATAGTTCATTAG
1 TATATA-AACTATATATATAGTTCATTAG
*
1386281 TATATAAACTATATTACATAGTTCATTAG
1 TATATAAACTATA-TATATAGTTCATTAG
* **
1386310 TATATAACCTATATAGTATA--T-GGTA-
1 TATATAAACTATATA-TATAGTTCATTAG
*
1386335 TATACAAACTATATATTATATAGTTCATTAG
1 TATATAAAC--TATA-TATATAGTTCATTAG
1386366 TATATATAAACTATATAGTATA
1 --TATATAAACTATATA-TATA
1386388 TATAAACTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
25 7 0.06
26 2 0.02
27 9 0.08
28 17 0.15
29 56 0.50
30 4 0.04
31 8 0.07
33 8 0.07
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (28 bp):
TATATAAACTATATATATAGTTCATTAG
Found at i:1386354 original size:18 final size:18
Alignment explanation
Indices: 1386326--1386400 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
1386316 ACCTATATAG
* *
1386326 TATATGGTATATACAAAC
1 TATATAGTATATATAAAC
**
1386344 TATATA-T-TATAT-AGT
1 TATATAGTATATATAAAC
1386359 TCAT-TAGTATATATAAAC
1 T-ATATAGTATATATAAAC
1386377 TATATAGTATATATAAAC
1 TATATAGTATATATAAAC
1386395 TATATA
1 TATATA
1386401 TTAATTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
15 4 0.09
16 7 0.15
17 8 0.17
18 27 0.59
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (18 bp):
TATATAGTATATATAAAC
Found at i:1386444 original size:26 final size:26
Alignment explanation
Indices: 1386387--1386453 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 26
1386377 TATATAGTAT
* **
1386387 ATATAAAC-TATATATTAATTTATTA
1 ATATAAACATATATATTAATTAAAGA
1386412 ATATAAACATATATATTAATTGAAAGA
1 ATATAAACATATATATTAATT-AAAGA
*
1386439 AT-TAAAAAATATATA
1 ATAT-AAACATATATA
1386454 AGGATCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 8 0.23
26 13 0.37
27 14 0.40
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (26 bp):
ATATAAACATATATATTAATTAAAGA
Found at i:1386541 original size:61 final size:61
Alignment explanation
Indices: 1386455--1386589 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 61
1386445 AAATATATAA
* * * *
1386455 GGATCAAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATCATAA-CATTAAATTT
1 GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATCA-AATCATTAAATTT
* * *
1386516 GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTAAATTATTAAATTT
1 GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATCAAATCATTAAATTT
* *
1386577 AGACTAAATTGAA
1 GGATTAAATTGAA
1386590 TAAATTTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 2 0.03
61 62 0.97
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (61 bp):
GGATTAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATCAAATCATTAAATTT
Found at i:1388495 original size:18 final size:18
Alignment explanation
Indices: 1388474--1388518 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1388464 TCATTAAGAC
1388474 ACTGGCTTCAGCAATCCA
1 ACTGGCTTCAGCAATCCA
1388492 ACTGGCTTCAGCAATCCA
1 ACTGGCTTCAGCAATCCA
1388510 ACTGGCTTC
1 ACTGGCTTC
1388519 CAACTTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (18 bp):
ACTGGCTTCAGCAATCCA
Found at i:1389143 original size:14 final size:14
Alignment explanation
Indices: 1389124--1389170 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1389114 TATTATTTTT
1389124 TATATAAATTAAAC
1 TATATAAATTAAAC
1389138 TATAT-AATT----
1 TATATAAATTAAAC
1389147 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1389161 TATATTAATT
1 TATATAAATT
1389171 TTCCTTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1389152 original size:23 final size:24
Alignment explanation
Indices: 1389122--1389171 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1389112 AATATTATTT
1389122 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1389145 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1389169 TTT
1 TTT
1389172 TCCTTTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1389364 original size:19 final size:19
Alignment explanation
Indices: 1389340--1389376 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1389330 ACATCATAAC
1389340 TTAAAAACTTATAATTTTA
1 TTAAAAACTTATAATTTTA
*
1389359 TTAAAATCTTATAATTTT
1 TTAAAAACTTATAATTTT
1389377 GTCCATGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAAACTTATAATTTTA
Found at i:1389458 original size:16 final size:16
Alignment explanation
Indices: 1389439--1389490 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
1389429 CAGATTATTT
*
1389439 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
1389455 ACA-G--AGGTTGAAA
1 ACAGGTCAGGTTGAAA
1389468 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
1389484 ACAGGTC
1 ACAGGTC
1389491 GGGTAATACC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 11 0.34
14 1 0.03
15 1 0.03
16 19 0.59
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.17
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:1392335 original size:15 final size:15
Alignment explanation
Indices: 1392314--1392356 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1392304 TAGATGGCTG
*
1392314 CGGAATTGATAGTTG
1 CGGAATTGATAGTTA
*
1392329 TGGAATTGATAGTTA
1 CGGAATTGATAGTTA
*
1392344 CAGAATTGATAGT
1 CGGAATTGATAGT
1392357 GTTTGATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (15 bp):
CGGAATTGATAGTTA
Found at i:1394809 original size:39 final size:39
Alignment explanation
Indices: 1394755--1394853 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
1394745 AAACGATGAG
*
1394755 GAAAATGGTGAATTAGGGATTGAGATGCGAAAGAGAAAT
1 GAAAATGGGGAATTAGGGATTGAGATGCGAAAGAGAAAT
* * *
1394794 GAAAATGGGGAATTAGGGATTGAGGTGCGAGAGGGAAAT
1 GAAAATGGGGAATTAGGGATTGAGATGCGAAAGAGAAAT
1394833 GAAAATGGGGAATTAGGGATT
1 GAAAATGGGGAATTAGGGATT
1394854 TTAGCAAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.39, C:0.02, G:0.38, T:0.20
Consensus pattern (39 bp):
GAAAATGGGGAATTAGGGATTGAGATGCGAAAGAGAAAT
Found at i:1400006 original size:39 final size:39
Alignment explanation
Indices: 1399961--1400059 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
1399951 AAACGAAGAG
*
1399961 GAAAATGGTGAATTAGGGATTGAGATGAGAAAGAGAAAT
1 GAAAATGGGGAATTAGGGATTGAGATGAGAAAGAGAAAT
* * * *
1400000 GAAAATGGGGAATTAGGGATTGAGGTGCGAGAGGGAAAT
1 GAAAATGGGGAATTAGGGATTGAGATGAGAAAGAGAAAT
1400039 GAAAATGGGGAATTAGGGATT
1 GAAAATGGGGAATTAGGGATT
1400060 TTAGCAAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.40, C:0.01, G:0.38, T:0.20
Consensus pattern (39 bp):
GAAAATGGGGAATTAGGGATTGAGATGAGAAAGAGAAAT
Found at i:1403977 original size:2 final size:2
Alignment explanation
Indices: 1403970--1404003 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1403960 TTACATGATT
*
1403970 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1404004 CATGCAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1404966 original size:23 final size:22
Alignment explanation
Indices: 1404919--1404967 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1404909 TCCTTCTCTC
*
1404919 TCGATTTTTTTTATTTTTACTT
1 TCGATTTTTTTTATTTTTACGT
*
1404941 TCGATTATTTTTT-TTTTCTTCGT
1 TCGATT-TTTTTTATTTT-TACGT
1404964 TCGA
1 TCGA
1404968 ATCCTCTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.67
Consensus pattern (22 bp):
TCGATTTTTTTTATTTTTACGT
Found at i:1405442 original size:3 final size:3
Alignment explanation
Indices: 1405434--1405515 Score: 132
Period size: 3 Copynumber: 27.3 Consensus size: 3
1405424 CTACAAAAGC
1405434 AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1405481 AAT AAT AAT -AT AAGT AAT AAT AAT AAT AAAT AAT A
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT -AAT AAT A
1405516 TTTTTTCGAC
Statistics
Matches: 75, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.05
3 65 0.87
4 6 0.08
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1405929 original size:135 final size:134
Alignment explanation
Indices: 1405677--1406168 Score: 608
Period size: 135 Copynumber: 3.7 Consensus size: 134
1405667 TGGGGAGACG
* * * * * *
1405677 ACACGGCTCATACGTGATGAAGAGTTTTGGTCATCTAAGGG-TGACAAGGCTCCTTCGTGATGAT
1 ACACTGCTCATACGTGATGAAGAGTTCTGGTTATC-AAGGGTTGACAAGGCTCCTACATGATGAG
* *
1405741 GAGATCTAGTCAAGG-AATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGGAAG
65 GAGATCTGGTC-AGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTA-GAAG
1405805 GGTGATA
128 GGTGATA
*
1405812 ACACTGCTTATACGTGATGAAGAGTTCTGGTTATCAAGGGTTGACAAGGCTCCTACATGATGAGG
1 ACACTGCTCATACGTGATGAAGAGTTCTGGTTATCAAGGGTTGACAAGGCTCCTACATGATGAGG
*
1405877 AGATCTGGTCAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGAAAGGG
66 AGATCTGGTCAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAG-AAGGG
1405942 TGATA
130 TGATA
* * * *
1405947 ACACTGCTCATACGTGATAAAGAGTTCTGGTTATCAAGGGTTGACACGACTCCTACGTGATGAGG
1 ACACTGCTCATACGTGATGAAGAGTTCTGGTTATCAAGGGTTGACAAGGCTCCTACATGATGAGG
* * * * *
1406012 AGATCTGGTCAGGTGATGACACGGTTCATATGTGATGAAGAGTTC-TAGCCATC--TA-AA-TGA
66 AGATCTGGTCAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGAAGGGT
1406072 GATA
131 GATA
* * * * * * *
1406076 ACATTGTTCCTACGTGATGAGGACG-ACTGGTTATC-TGGGTTGACACA-GCTCCTACATAATGA
1 ACACTGCTCATACGTGATGAAGA-GTTCTGGTTATCAAGGGTTGACA-AGGCTCCTACATGATGA
* *
1406138 AGAGATCTGGTCAGGTGATGACACTACTCAT
64 GGAGATCTGGTCAGGTGATGACACTGCTCAT
1406169 CTTTTCATGA
Statistics
Matches: 316, Mismatches: 36, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
128 48 0.15
129 32 0.10
130 3 0.01
132 2 0.01
134 16 0.05
135 215 0.68
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (134 bp):
ACACTGCTCATACGTGATGAAGAGTTCTGGTTATCAAGGGTTGACAAGGCTCCTACATGATGAGG
AGATCTGGTCAGGTGATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGAAGGGT
GATA
Found at i:1406289 original size:88 final size:87
Alignment explanation
Indices: 1406187--1406363 Score: 273
Period size: 88 Copynumber: 2.0 Consensus size: 87
1406177 GAGTCTTGGC
* *
1406187 CATCTAAGGTGATAACACGGTTCCACACTGATGGGGACGACTGGTTATCTAATTTGACACAGCTC
1 CATCTAAGGTGATAACACGGTTCCACACTAATGGGGACGACTGGTTATCTAAGTTGACACAGCTC
1406252 CTACATAATGAGGAAATATGGT
66 CTACATAATGAGGAAATATGGT
* * *
1406274 CATCTAAAGGTGATAACACGGTTCCACTCTAATGGGGACGACTGGTTATCTAAGTTGACATATCT
1 CATCT-AAGGTGATAACACGGTTCCACACTAATGGGGACGACTGGTTATCTAAGTTGACACAGCT
* * *
1406339 CTTACATAATGAGGAGATCTGGT
65 CCTACATAATGAGGAAATATGGT
1406362 CA
1 CA
1406364 GGTGATTTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 5 0.06
88 76 0.94
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (87 bp):
CATCTAAGGTGATAACACGGTTCCACACTAATGGGGACGACTGGTTATCTAAGTTGACACAGCTC
CTACATAATGAGGAAATATGGT
Found at i:1406697 original size:32 final size:32
Alignment explanation
Indices: 1406629--1406700 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1406619 CATCAGGATG
* * * * * *
1406629 TTGAATCCCCGAAGATGCCTCAATATTTGATG
1 TTGAATCTCCAAAGATACCTCAACATTCGATA
*
1406661 TTGAATCTCCAAAGATACCTCAACATTCGCTA
1 TTGAATCTCCAAAGATACCTCAACATTCGATA
1406693 TTGAATCT
1 TTGAATCT
1406701 TTAAATATGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (32 bp):
TTGAATCTCCAAAGATACCTCAACATTCGATA
Found at i:1415976 original size:2 final size:2
Alignment explanation
Indices: 1415969--1416010 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1415959 ACATGATTTG
1415969 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
1416011 CATGAAATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1416200 original size:24 final size:24
Alignment explanation
Indices: 1416153--1416201 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1416143 ATGTAATCTA
1416153 ATATAATATACACTTACATAAAAAT
1 ATATAATATACAC-TACATAAAAAT
1416178 ATATGAATATACA-TACATGAAAAA
1 ATAT-AATATACACTACAT-AAAAA
1416202 AATAACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (24 bp):
ATATAATATACACTACATAAAAAT
Found at i:1420755 original size:21 final size:21
Alignment explanation
Indices: 1420725--1420773 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1420715 CTTAAGCGAT
* *
1420725 ATCAAACTACTTATCACTTGA
1 ATCAACCTACTGATCACTTGA
*
1420746 ATTAACCTACTGATCACTTGA
1 ATCAACCTACTGATCACTTGA
1420767 ATCAACC
1 ATCAACC
1420774 CTCGTTAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.31
Consensus pattern (21 bp):
ATCAACCTACTGATCACTTGA
Found at i:1422769 original size:30 final size:30
Alignment explanation
Indices: 1422713--1422769 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1422703 ATGTTAGATG
*
1422713 ATAAAATAAAATAAATACAAGGGAAAAATT
1 ATAAAATAAAATAAATACAAGAGAAAAATT
* *
1422743 ATAAGATAAAATAGATA-ACAGAGAAAA
1 ATAAAATAAAATAAATACA-AGAGAAAA
1422770 TTAAAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.04
30 22 0.96
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.18
Consensus pattern (30 bp):
ATAAAATAAAATAAATACAAGAGAAAAATT
Found at i:1422865 original size:21 final size:22
Alignment explanation
Indices: 1422830--1422872 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1422820 AAAAAATTAA
* *
1422830 AATAATAATAGAAAGTCAAATG
1 AATAATAATAAAAAGTAAAATG
1422852 AATAA-AATAAAAAGTAAAATG
1 AATAATAATAAAAAGTAAAATG
1422873 GTTAGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (22 bp):
AATAATAATAAAAAGTAAAATG
Found at i:1424284 original size:83 final size:85
Alignment explanation
Indices: 1424188--1424370 Score: 210
Period size: 84 Copynumber: 2.2 Consensus size: 85
1424178 AATGTAATCA
* *
1424188 AACTCGAAGGTC-TTTGATGACAGATAACCCTTC-TAGCCTTGAGTTATGCTGCAAATGATGTGC
1 AACTCGAAGGTCTTTTGATGACAAATAACCCTTCTTA-CCTTGAGCTATGCTGCAAATGATGTGC
***
1424251 C-TTGGAGCTGAGCGTAGTCG
65 CATCAAAGCTGAGCGTAGTCG
* * * ** *
1424271 AACTCGAATGTCTTTTGTTGGCAAATGGCCCTTCTTACCTTGAGCTATGTTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGATGACAAATAACCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCC
*
1424336 ATCAAAGCTGAGTGTAGTCG
66 ATCAAAGCTGAGCGTAGTCG
* *
1424356 AACTTGAGGGTCTTT
1 AACTCGAAGGTCTTT
1424371 GTGTTTTAAG
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
83 11 0.13
84 42 0.51
85 29 0.35
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (85 bp):
AACTCGAAGGTCTTTTGATGACAAATAACCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCC
ATCAAAGCTGAGCGTAGTCG
Found at i:1424449 original size:33 final size:34
Alignment explanation
Indices: 1424368--1424488 Score: 165
Period size: 33 Copynumber: 3.6 Consensus size: 34
1424358 CTTGAGGGTC
*
1424368 TTTGTGTTTTAAGAGAAAC-ATTTTCAAAGGTTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGG-TTTT
* *
1424403 TTTATGTTACAAGAGAAACGATTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
1424436 TTTGCGTTTCAAGAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
1424470 TTTGTGCTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
1424489 TGTCTCTAGG
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
33 30 0.39
34 20 0.26
35 25 0.33
36 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:1424608 original size:36 final size:36
Alignment explanation
Indices: 1424540--1424790 Score: 227
Period size: 36 Copynumber: 7.1 Consensus size: 36
1424530 CAAAGGTTGG
**
1424540 TGTTTCAATAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
1424577 TGTTTCAAGGGAAAC-GTCTCAAGAGACACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
1424612 TGTTTCAAGAGAAACTGTCTC-AGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * * *
1424648 AGTTCCAAAAGAAAACTGTCCCAAGGGAGACGAAATT
1 TGTTTC-AAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
1424685 TGTTTCAAGGAAAACATAT-TC-A-A-AG-----ATT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT
*
1424713 TGTTTCAAGGGAAACTGTCTCAAGAGATACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
1424749 TGTTTCAAGAGAAACTGTCTCGAGGGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
1424786 TGTTT
1 TGTTT
1424791 TGAGTAAATT
Statistics
Matches: 173, Mismatches: 26, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.01
28 19 0.11
29 1 0.01
30 1 0.01
31 1 0.01
33 2 0.01
35 28 0.16
36 70 0.40
37 39 0.23
38 10 0.06
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1424714 original size:101 final size:100
Alignment explanation
Indices: 1424605--1424790 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 100
1424595 TCAAGAGACA
1424605 CAAAATTTGTTTCAAGAGAAACTGTCTC-AGAGAGACAAAACTTAGTTCCAAAAGAAAACTGTCC
1 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAAG-AAACTGTCC
*
1424669 CAAGGGAGACGAAA-TTTGTTTCAAGGAAAACATATT
64 CAAGGGAGACAAAACTTTGTTTCAAGGAAAACATATT
* * * * * *
1424705 CAAAGATTTGTTTCAAGGGAAACTGTCTCAAGAGATACAAAATTTGTTTCAAGAGAAACTGTCTC
1 CAAA-ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCCC
*
1424770 GAGGGAGACAAAACTTTGTTT
65 AAGGGAGACAAAACTTTGTTT
1424791 TGAGTAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
100 24 0.32
101 40 0.53
102 11 0.15
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (100 bp):
CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCCCA
AGGGAGACAAAACTTTGTTTCAAGGAAAACATATT
Found at i:1424735 original size:28 final size:29
Alignment explanation
Indices: 1424682--1424740 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
1424672 GGGAGACGAA
1424682 ATTTGTTTCAAGGAAAACATATTCAA-AG
1 ATTTGTTTCAAGGAAAACATATTCAAGAG
* *
1424710 ATTTGTTTCAAGGGAAAC-TGTCTCAAGAG
1 ATTTGTTTCAAGGAAAACATAT-TCAAGAG
1424739 AT
1 AT
1424741 ACAAAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 21 0.78
29 4 0.15
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (29 bp):
ATTTGTTTCAAGGAAAACATATTCAAGAG
Found at i:1425800 original size:21 final size:22
Alignment explanation
Indices: 1425760--1425800 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1425750 TTCAGGGGGT
**
1425760 ATCGATTCCCCCTGGGAGGAGA
1 ATCGATTCCCCCTGAAAGGAGA
1425782 ATCGATTCCCCCT-AAAGGA
1 ATCGATTCCCCCTGAAAGGA
1425801 AAAATGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (22 bp):
ATCGATTCCCCCTGAAAGGAGA
Found at i:1426765 original size:38 final size:38
Alignment explanation
Indices: 1426704--1426793 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 38
1426694 CATATGAAAA
* * * *
1426704 GTCCTACGGGACACAGATTACATCCTTCGGGATGACAG
1 GTCCTTCGGGACATAGATGACATCCTTCGAGATGACAG
*
1426742 GTCCTTCGGGACATAGATGACATCCTTCGAGATGATAG
1 GTCCTTCGGGACATAGATGACATCCTTCGAGATGACAG
1426780 GTCCTTCGGGACAT
1 GTCCTTCGGGACAT
1426794 TTATACGAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (38 bp):
GTCCTTCGGGACATAGATGACATCCTTCGAGATGACAG
Found at i:1430946 original size:15 final size:17
Alignment explanation
Indices: 1430926--1430959 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1430916 TGCAAGTGAT
1430926 GAAAATAA-AAT-AAAA
1 GAAAATAATAATGAAAA
1430941 GAAAATAATAATGAAAA
1 GAAAATAATAATGAAAA
1430958 GA
1 GA
1430960 GTTAGTGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (17 bp):
GAAAATAATAATGAAAA
Found at i:1432268 original size:29 final size:30
Alignment explanation
Indices: 1432219--1432277 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
1432209 ATATTCAAAC
1432219 TAAAATCGTGAAAGAAAAAA-TAATAATAAA
1 TAAAATCGTGAAAGAAAAAATTAA-AATAAA
*
1432249 TAAAA-CG-GAAATGAATAAATTAAAATAAA
1 TAAAATCGTGAAA-GAAAAAATTAAAATAAA
1432278 AGTACAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 4 0.15
29 14 0.54
30 8 0.31
ACGTcount: A:0.66, C:0.03, G:0.10, T:0.20
Consensus pattern (30 bp):
TAAAATCGTGAAAGAAAAAATTAAAATAAA
Found at i:1433022 original size:19 final size:19
Alignment explanation
Indices: 1432989--1433035 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1432979 GTCTACAATT
1432989 ATATCAAAATTTT-AATAAA
1 ATAT-AAAATTTTAAATAAA
*
1433008 ATATAAAATTATTAAATATA
1 ATATAAAATT-TTAAATAAA
1433028 A-ATAAAAT
1 ATATAAAAT
1433036 GAAAAATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 13 0.52
20 6 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATAAAATTTTAAATAAA
Found at i:1434830 original size:26 final size:26
Alignment explanation
Indices: 1434799--1434850 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1434789 GGATTATGCA
*
1434799 CTTTATACTGTCCTGAAGCATATTAT
1 CTTTATACTGCCCTGAAGCATATTAT
1434825 CTTTATACTGCCCTGAAGCATATTAT
1 CTTTATACTGCCCTGAAGCATATTAT
1434851 GCTTCTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (26 bp):
CTTTATACTGCCCTGAAGCATATTAT
Found at i:1445712 original size:19 final size:19
Alignment explanation
Indices: 1445677--1445714 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1445667 ATAAAACTAT
*
1445677 TTTTATTATATTATATTTA
1 TTTTATTATATGATATTTA
1445696 TTTTA-TATATGATTATTTA
1 TTTTATTATATGA-TATTTA
1445715 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTATTATATGATATTTA
Found at i:1448712 original size:23 final size:23
Alignment explanation
Indices: 1448685--1448731 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1448675 AATACCAAAG
*
1448685 ATAAA-TATAAATCTACCATTAAA
1 ATAAAGTATAAA-CAACCATTAAA
*
1448708 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGTATAAACAACCATTAAA
1448731 A
1 A
1448732 CAACCCCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAAAGTATAAACAACCATTAAA
Found at i:1462321 original size:20 final size:20
Alignment explanation
Indices: 1462296--1462335 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1462286 ACCTGAAAAA
1462296 TAAACTATACA-AATATAAAG
1 TAAACTATACACAA-ATAAAG
1462316 TAAACTATACACAAATAAAG
1 TAAACTATACACAAATAAAG
1462336 ATGCAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAACTATACACAAATAAAG
Found at i:1466477 original size:20 final size:20
Alignment explanation
Indices: 1466420--1466477 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1466410 TTTTTATCAA
*
1466420 AATAATATTTTAAT-TATAT
1 AATAATATTTAAATATATAT
* *
1466439 AATGATAATTAAA-AGTATAT
1 AATAATATTTAAATA-TATAT
1466459 AATAATATTTAAATATATA
1 AATAATATTTAAATATATA
1466478 CCTCTGTACC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 10 0.32
20 20 0.65
21 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
AATAATATTTAAATATATAT
Found at i:1470500 original size:28 final size:28
Alignment explanation
Indices: 1470446--1470526 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
1470436 TTCTTTCATG
1470446 TCTTTTTTTTCTCTTTTTCTTTCGAACAT-C
1 TCTTTTTTTT-TCTTTTT-TTTCGAAC-TGC
*
1470476 TCTTTGTTTTTCTTTTTTTTCGAACTGC
1 TCTTTTTTTTTCTTTTTTTTCGAACTGC
*
1470504 TGTTTTTTTTTCTTCCTTTTTTC
1 TCTTTTTTTTTCTT--TTTTTTC
1470527 ATTCAACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.02
28 21 0.47
29 7 0.16
30 16 0.36
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.68
Consensus pattern (28 bp):
TCTTTTTTTTTCTTTTTTTTCGAACTGC
Found at i:1475894 original size:133 final size:133
Alignment explanation
Indices: 1475679--1475941 Score: 438
Period size: 133 Copynumber: 2.0 Consensus size: 133
1475669 CCTTCTTTCG
* *
1475679 TGGATTATTATTTGTATTATTTATAAGGTAAACTACACGGGTGACCATTAAACTATTGTCCATTT
1 TGGATTAATATTTGTATTATTTATAAGGTAAACTACACGGGTGACCATTAAACTATTGCCCATTT
* * *
1475744 TTATTTTGATTATTGACGTTTTAATTTGATCACTCAA-ACAACCTAGCTATTCAAATGCTTCAAT
66 TTATTTTGATCATTGACGTTTCAATTTGATCAAT-AAGACAACCTAGCTATTCAAATGCTTCAAT
1475808 CTTA
130 CTTA
*
1475812 TGGATTAATATTTGTATTATTTATAAGGTAAATTACACGGGTGACCATTAAACTATTGCCCATTT
1 TGGATTAATATTTGTATTATTTATAAGGTAAACTACACGGGTGACCATTAAACTATTGCCCATTT
* *
1475877 TTGTTTTGATCATTGACGTTTCAATTTGATCAATAAGACAACCTAGCTATTTAAATGCTTCAATC
66 TTATTTTGATCATTGACGTTTCAATTTGATCAATAAGACAACCTAGCTATTCAAATGCTTCAATC
1475942 AAGCCACTAA
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
132 2 0.02
133 119 0.98
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (133 bp):
TGGATTAATATTTGTATTATTTATAAGGTAAACTACACGGGTGACCATTAAACTATTGCCCATTT
TTATTTTGATCATTGACGTTTCAATTTGATCAATAAGACAACCTAGCTATTCAAATGCTTCAATC
TTA
Found at i:1476314 original size:2 final size:2
Alignment explanation
Indices: 1476297--1476342 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1476287 ATAAATAAAT
*
1476297 TA TA TT TA TA -A 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
1476338 TA TA T
1 TA TA T
1476343 TAAATTATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
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:1477631 original size:19 final size:20
Alignment explanation
Indices: 1477593--1477631 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1477583 ATTTTTGATT
1477593 TTTTAATAATAAAAATATTA
1 TTTTAATAATAAAAATATTA
1477613 TTTTAA-AATTAAAAA-ATTA
1 TTTTAATAA-TAAAAATATTA
1477632 AACCCACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTAATAATAAAAATATTA
Found at i:1480322 original size:95 final size:95
Alignment explanation
Indices: 1480154--1480343 Score: 317
Period size: 95 Copynumber: 2.0 Consensus size: 95
1480144 GACAGGTAAT
* * * *
1480154 GCCATGATTCTAAGCGTCAACAATTCGGTTGAATCATGGATCTTGGATTCAGGGGCATCTTTCCA
1 GCCATGATTCTAAGCGTCAACAATCCGATTGAATCATGGATCTTGGATGCAGAGGCATCTTTCCA
1480219 CTCCACCCCATACCGAGAAATCATGGAGAA
66 CTCCACCCCATACCGAGAAATCATGGAGAA
*
1480249 GCCATGATTCTAAGCGTCAACAGTCCGATTGAATCATGGATCTTGGATGCAGAGGCATCTTTCCA
1 GCCATGATTCTAAGCGTCAACAATCCGATTGAATCATGGATCTTGGATGCAGAGGCATCTTTCCA
* *
1480314 CTCTACCCCATGCCGAGAAATCATGGAGAA
66 CTCCACCCCATACCGAGAAATCATGGAGAA
1480344 CTGTGTCAGT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 88 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (95 bp):
GCCATGATTCTAAGCGTCAACAATCCGATTGAATCATGGATCTTGGATGCAGAGGCATCTTTCCA
CTCCACCCCATACCGAGAAATCATGGAGAA
Found at i:1495339 original size:20 final size:21
Alignment explanation
Indices: 1495301--1495339 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1495291 AGTGTTGAAG
*
1495301 ATATGCTTATATATTATATGT
1 ATATGCTTATATATAATATGT
*
1495322 ATATG-TTATGTATAATAT
1 ATATGCTTATATATAATAT
1495340 AGTTTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (21 bp):
ATATGCTTATATATAATATGT
Found at i:1495472 original size:14 final size:15
Alignment explanation
Indices: 1495448--1495484 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1495438 TTTTTAGTAA
1495448 TTTAA-ATTTTA-TT
1 TTTAATATTTTATTT
1495461 TTTAATATTTTATTT
1 TTTAATATTTTATTT
1495476 TTTAATATT
1 TTTAATATT
1495485 AGAATACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 6 0.27
15 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATATTTTATTT
Found at i:1495476 original size:13 final size:13
Alignment explanation
Indices: 1495448--1495477 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1495438 TTTTTAGTAA
1495448 TTTAAATTTTATT
1 TTTAAATTTTATT
1495461 TTTAATATTTTATT
1 TTTAA-ATTTTATT
1495475 TTT
1 TTT
1495478 TAATATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTAAATTTTATT
Found at i:1495495 original size:24 final size:23
Alignment explanation
Indices: 1495464--1495514 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1495454 TTTTATTTTT
* *
1495464 AATATTTTAT-TTTTTAATATTAG
1 AATATTTTATATTTATAAT-TTAA
1495487 AATACTTTTATATTTATAATTTAA
1 AATA-TTTTATATTTATAATTTAA
1495511 AATA
1 AATA
1495515 AATAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 13 0.54
25 7 0.29
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AATATTTTATATTTATAATTTAA
Found at i:1497628 original size:24 final size:24
Alignment explanation
Indices: 1497589--1497635 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1497579 TTTTTATATA
*
1497589 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
1497613 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
1497636 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:1498605 original size:39 final size:39
Alignment explanation
Indices: 1498562--1498642 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
1498552 CAAAATTTTC
1498562 TATGCTAAGTCCATCGATAATCTTATAAATATAAACTTT
1 TATGCTAAGTCCATCGATAATCTTATAAATATAAACTTT
* *
1498601 TATGCTAAGTCCATCGGTAATCTTATCAATATAAACTTT
1 TATGCTAAGTCCATCGATAATCTTATAAATATAAACTTT
1498640 TAT
1 TAT
1498643 TAAAGATGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (39 bp):
TATGCTAAGTCCATCGATAATCTTATAAATATAAACTTT
Found at i:1507991 original size:10 final size:9
Alignment explanation
Indices: 1507947--1507991 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
1507937 GTTTGCATTT
1507947 AAAAAAAA-
1 AAAAAAAAC
1507955 AAAAAAAAC
1 AAAAAAAAC
*
1507964 AAAAAAAGCC
1 AAAAAAA-AC
1507974 AAAAAAAAC
1 AAAAAAAAC
1507983 AAAAGAAAA
1 AAAA-AAAA
1507992 ATCAAAAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 8 0.25
9 12 0.38
10 12 0.38
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Done.