Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold166
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: 2719372
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17868 characters in sequence are not A, C, G, or T
File 8 of 18
Found at i:1332944 original size:24 final size:24
Alignment explanation
Indices: 1332911--1332996 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1332901 AAGAGAAAGA
*
1332911 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1332935 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1332953 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1332977 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1332997 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1332963 original size:42 final size:42
Alignment explanation
Indices: 1332902--1333020 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1332892 TAGCCCTCAA
* *
1332902 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1332944 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1332986 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1333021 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1342867 original size:42 final size:42
Alignment explanation
Indices: 1342829--1342919 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
1342819 CTTCTCCTTT
* *
1342829 TGTCATCCATTCTCT-TTCTATTATCTTTCTTATCTCTCCTCC
1 TGTCATCCATTCTATCTT-TACTATCTTTCTTATCTCTCCTCC
* * *
1342871 TATCATCCCTTCTATCTTTACTATCTCTCTTATCTCTCCTCC
1 TGTCATCCATTCTATCTTTACTATCTTTCTTATCTCTCCTCC
1342913 TGTCATC
1 TGTCATC
1342920 TCTCCTATCT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.13, C:0.35, G:0.02, T:0.49
Consensus pattern (42 bp):
TGTCATCCATTCTATCTTTACTATCTTTCTTATCTCTCCTCC
Found at i:1342940 original size:42 final size:42
Alignment explanation
Indices: 1342850--1342929 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
1342840 CTCTTTCTAT
* *
1342850 TATCTTTCTTATCTCTCCTCCTATCATCCCTTCTATCTTTAC
1 TATCTCTCTTATCTCTCCTCCTATCATCCCTCCTATCTTTAC
* *
1342892 TATCTCTCTTATCTCTCCTCCTGTCATCTCTCCTATCT
1 TATCTCTCTTATCTCTCCTCCTATCATCCCTCCTATCT
1342930 CTTCTTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.12, C:0.38, G:0.01, T:0.49
Consensus pattern (42 bp):
TATCTCTCTTATCTCTCCTCCTATCATCCCTCCTATCTTTAC
Found at i:1348366 original size:9 final size:9
Alignment explanation
Indices: 1348354--1348411 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
1348344 CTCTCTCTAT
1348354 TATCTCTCC
1 TATCTCTCC
1348363 TATCTCTCC
1 TATCTCTCC
* *
1348372 T-CCTAT-C
1 TATCTCTCC
*
1348379 -ATCCCTCC
1 TATCTCTCC
*
1348387 TATCTCTAC
1 TATCTCTCC
1348396 TATCTCTCC
1 TATCTCTCC
1348405 TATCTCT
1 TATCTCT
1348412 TCTTTCTCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
7 3 0.08
8 4 0.11
9 31 0.82
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:1348368 original size:18 final size:18
Alignment explanation
Indices: 1348341--1348411 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
1348331 CCTGTCATCC
*
1348341 CTCCTCTCTCTATTATCT
1 CTCCTATCTCTATTATCT
*
1348359 CTCCTATCTCTCCTCCTATCAT
1 CTCCTATCTCT-AT--TATC-T
*
1348381 CCCTCCTATCTCTACTATCT
1 --CTCCTATCTCTATTATCT
1348401 CTCCTATCTCT
1 CTCCTATCTCT
1348412 TCTTTCTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 21 0.49
19 1 0.02
20 1 0.02
21 8 0.19
22 1 0.02
24 11 0.26
ACGTcount: A:0.13, C:0.44, G:0.00, T:0.44
Consensus pattern (18 bp):
CTCCTATCTCTATTATCT
Found at i:1348372 original size:42 final size:42
Alignment explanation
Indices: 1348325--1348411 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
1348315 CTTCTTCTCT
* * *
1348325 TCTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
1348367 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
1348409 TCT
1 TCT
1348412 TCTTTCTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.11, C:0.45, G:0.01, T:0.43
Consensus pattern (42 bp):
TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
Found at i:1348374 original size:12 final size:12
Alignment explanation
Indices: 1348359--1348393 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1348349 TCTATTATCT
1348359 CTCCTATCTCTC
1 CTCCTATCTCTC
1348371 CTCCTATCATC-C
1 CTCCTATC-TCTC
1348383 CTCCTATCTCT
1 CTCCTATCTCT
1348394 ACTATCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:1359217 original size:12 final size:11
Alignment explanation
Indices: 1359195--1359270 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1359185 AGAGAAAGAA
*
1359195 GAGAGAGGAGG
1 GAGATAGGAGG
1359206 GATGATAGGAGG
1 GA-GATAGGAGG
*
1359218 AGAGACAGGA--
1 -GAGATAGGAGG
*
1359228 GAGATAGTA--
1 GAGATAGGAGG
1359237 GAGATAGGAGG
1 GAGATAGGAGG
1359248 GATGATAGGAGG
1 GA-GATAGGAGG
*
1359260 AGAGACAGGAG
1 -GAGATAGGAG
1359271 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1359246 original size:42 final size:42
Alignment explanation
Indices: 1359185--1359303 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1359175 TAGCCCTCAA
* *
1359185 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1359227 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1359269 AGAGATAATAGAGAGAAGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1359304 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.44, C:0.02, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1367046 original size:20 final size:20
Alignment explanation
Indices: 1367008--1367047 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1366998 TTTCAAATTT
1367008 CTTCATTTTCATCTCAAAATA
1 CTTCATTTTCA-CTCAAAATA
1367029 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
1367048 TATCAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:1367766 original size:21 final size:21
Alignment explanation
Indices: 1367740--1367784 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1367730 TTTTAAACTA
1367740 TTATC-AAGAAGGAGAAAATTT
1 TTATCAAAG-AGGAGAAAATTT
*
1367761 TTATCAAAGGGGAGAAAATTT
1 TTATCAAAGAGGAGAAAATTT
1367782 TTA
1 TTA
1367785 AATGAGAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (21 bp):
TTATCAAAGAGGAGAAAATTT
Found at i:1368435 original size:20 final size:19
Alignment explanation
Indices: 1368410--1368463 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
1368400 CTACCACTAT
1368410 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
1368430 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGA-GAA
1368450 TTGTATCGATACAT
1 TTGTATCGATACAT
1368464 TGCTTCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:1370649 original size:154 final size:153
Alignment explanation
Indices: 1370314--1370619 Score: 416
Period size: 154 Copynumber: 1.9 Consensus size: 153
1370304 TCTTCCATTA
* * * *
1370314 TTTATTTATTTAATTTACTTAAAAGTTTTTGTAATCTGTTCGTTCATGGACTTGAGACTTCCTAC
1 TTTATCTATTTAACTTA-TTAAAATTTTTTGTAATCTATTCGTTCATGGACTTGAGACTTCCTAC
*
1370379 AACTGGTATCAAAGCTTCCTTGTGTTTTCGTTGATTGCAAAAACATTTGATTCCGATGTTGTTCT
65 AACTGGTATCAAAGCTTCCTTGTGTTTTAGTTGATTGCAAAAACATTTGATTCCGATGTTGTTCT
1370444 TAATCCATTTACTTTTAGAAACTG
130 TAATCCATTTACTTTTAGAAACTG
* *
1370468 TTTATTTGTTTAACTTGATTAAAATTTTTTGTAATCTATTCGTTCATGGACTTGAGACTTCCTAC
1 TTTATCTATTTAACTT-ATTAAAATTTTTTGTAATCTATTCGTTCATGGACTTGAGACTTCCTAC
* *
1370533 AACTGGTATCAAAGCTTTCTTGTGTTTTAGTTG-TTACCGACTACAAAAACATTTGATTTCGATG
65 AACTGGTATCAAAGCTTCCTTGTGTTTTAGTTGATT---G----CAAAAACATTTGATTCCGATG
* **
1370597 TTGTTCTTGATCTGTTTACTTTT
123 TTGTTCTTAATCCATTTACTTTT
1370620 GTAAATTGTT
Statistics
Matches: 134, Mismatches: 10, Indels: 10
0.87 0.06 0.06
Matches are distributed among these distances:
153 2 0.01
154 90 0.67
155 1 0.01
156 1 0.01
160 40 0.30
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (153 bp):
TTTATCTATTTAACTTATTAAAATTTTTTGTAATCTATTCGTTCATGGACTTGAGACTTCCTACA
ACTGGTATCAAAGCTTCCTTGTGTTTTAGTTGATTGCAAAAACATTTGATTCCGATGTTGTTCTT
AATCCATTTACTTTTAGAAACTG
Found at i:1371395 original size:12 final size:12
Alignment explanation
Indices: 1371375--1371404 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1371365 ATGCATTAGA
*
1371375 TAATAATTTTCT
1 TAATTATTTTCT
1371387 TAATTATTTTCT
1 TAATTATTTTCT
1371399 TAATTA
1 TAATTA
1371405 AATTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATTATTTTCT
Found at i:1374627 original size:28 final size:28
Alignment explanation
Indices: 1374585--1374655 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
1374575 TTCTTTATTC
* * *
1374585 TTCTTTCTTAATTTCTTTTCCTTTGAAAT
1 TTCTTACTT-ATTTCGTTTCCTTTCAAAT
* *
1374614 TTCTTGCTTATTTCGTTTCCTTTCATAT
1 TTCTTACTTATTTCGTTTCCTTTCAAAT
*
1374642 TTCTTACTGATTTC
1 TTCTTACTTATTTC
1374656 ACTTCCTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 28 0.78
29 8 0.22
ACGTcount: A:0.14, C:0.20, G:0.06, T:0.61
Consensus pattern (28 bp):
TTCTTACTTATTTCGTTTCCTTTCAAAT
Found at i:1374661 original size:28 final size:28
Alignment explanation
Indices: 1374602--1374663 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
1374592 TTAATTTCTT
* * * **
1374602 TTCCTTTGAAATTTCTTGCTTATTTCGT
1 TTCCTTTCAAATTTCTTACTGATTTCAC
*
1374630 TTCCTTTCATATTTCTTACTGATTTCAC
1 TTCCTTTCAAATTTCTTACTGATTTCAC
1374658 TTCCTT
1 TTCCTT
1374664 GATCTTTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (28 bp):
TTCCTTTCAAATTTCTTACTGATTTCAC
Found at i:1380905 original size:12 final size:11
Alignment explanation
Indices: 1380883--1380958 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
1380873 AGAGAAAGAA
*
1380883 GAGAGAGGAGG
1 GAGATAGGAGG
1380894 GATGATAGGAGG
1 GA-GATAGGAGG
*
1380906 AGAGACAGGA--
1 -GAGATAGGAGG
*
1380916 GAGATAGTA--
1 GAGATAGGAGG
1380925 GAGATAGGAGG
1 GAGATAGGAGG
1380936 GATGATAGGAGG
1 GA-GATAGGAGG
1380948 AGAGATAGGAG
1 -GAGATAGGAG
1380959 AGATAATAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.07
12 31 0.57
13 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.49, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1380915 original size:24 final size:23
Alignment explanation
Indices: 1380882--1380974 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 23
1380872 AAGAGAAAGA
*
1380882 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATA-GAGG
* *
1380906 AGAGACAGGA--GA-GAT--AGT
1 AGAGATAGGAGGGATGATAGAGG
1380924 AGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATA-GAGG
* *
1380948 AGAGATAGGAGAGATAATAGA-G
1 AGAGATAGGAGGGATGATAGAGG
1380970 AGAGA
1 AGAGA
1380975 AGGGATGACA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
18 11 0.19
20 2 0.04
21 6 0.11
22 8 0.14
23 2 0.04
24 28 0.49
ACGTcount: A:0.43, C:0.01, G:0.45, T:0.11
Consensus pattern (23 bp):
AGAGATAGGAGGGATGATAGAGG
Found at i:1380917 original size:9 final size:9
Alignment explanation
Indices: 1380903--1380963 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
1380893 GGATGATAGG
*
1380903 AGGAGAGAC
1 AGGAGAGAT
1380912 AGGAGAGAT
1 AGGAGAGAT
*
1380921 AGTAGAGAT
1 AGGAGAGAT
*
1380930 AGGAGGGAT
1 AGGAGAGAT
* *
1380939 --GATAG-G
1 AGGAGAGAT
1380945 AGGAGAGAT
1 AGGAGAGAT
1380954 AGGAGAGAT
1 AGGAGAGAT
1380963 A
1 A
1380964 ATAGAGAGAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.43, C:0.02, G:0.44, T:0.11
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1380934 original size:42 final size:42
Alignment explanation
Indices: 1380873--1380991 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
1380863 TAGCCCTCAA
* *
1380873 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1380915 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
1380957 AGAGATAATAGAGAGAGAAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1380992 GAGAGAAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.44, C:0.02, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1380967 original size:12 final size:12
Alignment explanation
Indices: 1380927--1380974 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1380917 AGATAGTAGA
*
1380927 GATAGGAGGGAT
1 GATAGGAGAGAT
1380939 GATAGGAGGAGA-
1 GATAGGA-GAGAT
1380951 GATAGGAGAGAT
1 GATAGGAGAGAT
*
1380963 AATAGAGAGAGA
1 GATAG-GAGAGA
1380975 AGGGATGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 4 0.13
12 18 0.58
13 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:1385886 original size:15 final size:16
Alignment explanation
Indices: 1385859--1385888 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1385849 TTGTTATTTT
1385859 TTTCTGCTTCTTTCAA
1 TTTCTGCTTCTTTCAA
1385875 TTTCTG-TTCTTTCA
1 TTTCTGCTTCTTTCA
1385889 TCAATAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.23, G:0.07, T:0.60
Consensus pattern (16 bp):
TTTCTGCTTCTTTCAA
Found at i:1386378 original size:113 final size:113
Alignment explanation
Indices: 1386180--1386413 Score: 450
Period size: 113 Copynumber: 2.1 Consensus size: 113
1386170 AAACTAGGGG
1386180 AACATATATCAAGATATGGGTTCAATCTAGGGTTTCAAATAGTAGTCACGTCGTAAAATAGTAGC
1 AACATATATCAAGATATGGGTTCAATCTAGGGTTTCAAATAGTAGTCACGTCGTAAAATAGTAGC
*
1386245 TGCAATTTCTCAATAATGGCCACTTTTACCATGAAATCAATCATTATT
66 TGCAATTTCTCAATAATGGCCACTTTTACCATCAAATCAATCATTATT
1386293 AACATATATCAAGATATGGGTTCAATCTAGGGTTTCAAATAGTAGTCACGTCGTAAAATAGTAGC
1 AACATATATCAAGATATGGGTTCAATCTAGGGTTTCAAATAGTAGTCACGTCGTAAAATAGTAGC
1386358 TGCAATTTCTCAATAATGGCCACTTTTACCATCAAATCAATCATTATT
66 TGCAATTTCTCAATAATGGCCACTTTTACCATCAAATCAATCATTATT
*
1386406 GACATATA
1 AACATATA
1386414 AGTGACAGTT
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 119 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (113 bp):
AACATATATCAAGATATGGGTTCAATCTAGGGTTTCAAATAGTAGTCACGTCGTAAAATAGTAGC
TGCAATTTCTCAATAATGGCCACTTTTACCATCAAATCAATCATTATT
Found at i:1389670 original size:12 final size:11
Alignment explanation
Indices: 1389648--1389723 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1389638 AGAGAAAGAA
*
1389648 GAGAGAGGAGG
1 GAGATAGGAGG
1389659 GATGATAGGAGG
1 GA-GATAGGAGG
*
1389671 AGAGACAGGA--
1 -GAGATAGGAGG
*
1389681 GAGATAGTA--
1 GAGATAGGAGG
1389690 GAGATAGGAGG
1 GAGATAGGAGG
1389701 GATGATAGGAGG
1 GA-GATAGGAGG
*
1389713 AGAGACAGGAG
1 -GAGATAGGAG
1389724 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1389680 original size:24 final size:24
Alignment explanation
Indices: 1389647--1389732 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1389637 AAGAGAAAGA
*
1389647 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1389671 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1389689 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1389713 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1389733 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1389699 original size:42 final size:42
Alignment explanation
Indices: 1389638--1389756 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1389628 TAGCCCTCAA
* *
1389638 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1389680 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1389722 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1389757 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1399674 original size:12 final size:11
Alignment explanation
Indices: 1399652--1399727 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1399642 AGAGAAAGAA
*
1399652 GAGAGAGGAGG
1 GAGATAGGAGG
1399663 GATGATAGGAGG
1 GA-GATAGGAGG
*
1399675 AGAGACAGGA--
1 -GAGATAGGAGG
*
1399685 GAGATAGTA--
1 GAGATAGGAGG
1399694 GAGATAGGAGG
1 GAGATAGGAGG
1399705 GATGATAGGAGG
1 GA-GATAGGAGG
*
1399717 AGAGACAGGAG
1 -GAGATAGGAG
1399728 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1399684 original size:24 final size:24
Alignment explanation
Indices: 1399651--1399736 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1399641 AAGAGAAAGA
*
1399651 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1399675 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1399693 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1399717 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1399737 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1399703 original size:42 final size:42
Alignment explanation
Indices: 1399642--1399760 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1399632 TAGCCCTCAA
* *
1399642 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1399684 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1399726 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1399761 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1409218 original size:167 final size:166
Alignment explanation
Indices: 1408991--1409523 Score: 700
Period size: 167 Copynumber: 3.2 Consensus size: 166
1408981 AAATTCTTTT
* *
1408991 ATTTTCATTAGTTTTTGAATTTTTTCCTTAAAATTC-T-TTTTTTT-GAAATACA-GAGTTTTCT
1 ATTTTCATGAG-TTTTGAATTTTTTCCTTGAAATTCTTCTTTTTTTCGAAATA-AGGAGTTTTCT
* * * *
1409052 ACTCCGTGAATTTTTTTGAGGAGATTTTTCTTGGTTTTTAATTTTTAAGAGTCATCAAATATTAT
64 ACTCTGTGAATTTTTTCGAGG-GATTTTTCTTGGTTTTTAATTTTAAAAAGTCATCAAATATTAT
*
1409117 TATTTATCTCATATTAATTCAGTTTTAAAAAATAAATTC
128 TATTTATCTCATATTAATTCATTTTTAAAAAATAAATTC
* *
1409156 ATTTTAATGAGTTTTGGATTTTTTCCTTGAAATTCTTCTTTTTTTCGAAATAAGGAGTTTTCTAC
1 ATTTTCATGAGTTTTGAATTTTTTCCTTGAAATTCTTCTTTTTTTCGAAATAAGGAGTTTTCTAC
* * *
1409221 TCTGTGAATTTTTTCGAGGTGATTTTTATTGGTTTTTAATTTTCAAAAGTCATAAAATATTATTA
66 TCTGTGAATTTTTTCGAGG-GATTTTTCTTGGTTTTTAATTTTAAAAAGTCATCAAATATTATTA
1409286 TTTATCTCATATTAATTCATTTTTAAAAAAATAAATTC
130 TTTATCTCATATTAATTCATTTTT-AAAAAATAAATTC
* * * * * * * * * *
1409324 ATTTTCATGAGTTCTAGATTTTTTTCCTTGAAATT-TCCCTTTGTCCAAAACATGGTGTTTTCTA
1 ATTTTCATGAGTT-TTGAATTTTTTCCTTGAAATTCTTCTTTTTTTCGAAATAAGGAGTTTTCTA
* ** *
1409388 CTCTGT-AATTTTTTCGAGGGAATTTTTCTTGGTTTTTAATTTTAAAAATTCATCAAATACCATC
65 CTCTGTGAATTTTTTCGAGGG-ATTTTTCTTGGTTTTTAATTTTAAAAAGTCATCAAATATTATT
*
1409452 ATTTATTTCATATTAATTCATTTTTAAAAAATAAATTC
129 ATTTATCTCATATTAATTCATTTTTAAAAAATAAATTC
*
1409490 ATTTTCATGAATTTTGAATTTTTCTCCTTGAAAT
1 ATTTTCATGAGTTTTGAATTTTT-TCCTTGAAAT
1409524 CCCCTTTATC
Statistics
Matches: 325, Mismatches: 35, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
164 22 0.07
165 18 0.06
166 44 0.14
167 171 0.53
168 52 0.16
169 18 0.06
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (166 bp):
ATTTTCATGAGTTTTGAATTTTTTCCTTGAAATTCTTCTTTTTTTCGAAATAAGGAGTTTTCTAC
TCTGTGAATTTTTTCGAGGGATTTTTCTTGGTTTTTAATTTTAAAAAGTCATCAAATATTATTAT
TTATCTCATATTAATTCATTTTTAAAAAATAAATTC
Found at i:1411309 original size:128 final size:127
Alignment explanation
Indices: 1411177--1411413 Score: 368
Period size: 129 Copynumber: 1.9 Consensus size: 127
1411167 TTTTTTAATC
* ** * * * *
1411177 TTTTATATTCTTATGGGTATCTGTAAGGGTATAAAAGATTTC-AAAAACTTTTTGTATCTTTTCG
1 TTTTATATTCCTATGGGTATCCATAAGGATATAAAAGATTTCAAAAAACTTTTCGTATATTTTCA
1411241 GGTATCCATTAAGGTACGAAATGATTTTTTCAAAACATAAATAAATATCAATTATTTTCAAGTT
66 GGTATCCATTAAGGTACGAAATGATTTTTT-AAAA-ATAAATAAATATCAATTATTTTCAAGTT
1411305 TTTTATATTCCTATGGGTATCCATAAGGATATAAAAGATTTCAAAAAACTTTTCGTATATTTTCA
1 TTTTATATTCCTATGGGTATCCATAAGGATATAAAAGATTTCAAAAAACTTTTCGTATATTTTCA
* *
1411370 GGTATCCATTAAGGTATGAAATGATTTTTTAAAAATAATTAAAT
66 GGTATCCATTAAGGTACGAAATGATTTTTTAAAAATAAATAAAT
1411414 TAACTCTCCT
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
127 9 0.09
128 42 0.42
129 48 0.48
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (127 bp):
TTTTATATTCCTATGGGTATCCATAAGGATATAAAAGATTTCAAAAAACTTTTCGTATATTTTCA
GGTATCCATTAAGGTACGAAATGATTTTTTAAAAATAAATAAATATCAATTATTTTCAAGTT
Found at i:1411561 original size:149 final size:149
Alignment explanation
Indices: 1411279--1411565 Score: 341
Period size: 149 Copynumber: 1.9 Consensus size: 149
1411269 TTCAAAACAT
*
1411279 AAATAAATATCAATTATTTTCAAGTTTTTTATATTCCTATGGGTATCCATAAGGATATAAAAGAT
1 AAATAAATATCAATCATTTTCAAGTTTTTTATATTCCTATGGGTATCCATAAGGATATAAAAGAT
* *
1411344 TTCAAAAAACTTTTCGTATATTTTCAGGTATCCATTAAGGTATGAAATGATTTTTTAAAAATAAT
66 TT-AAAAAACTTTTCGTATATTTTCAGGTATCCATCAAGGTACGAAATGATTTTTTAAAAATAAT
1411409 TAAATTAACTCTCCTCACTA
130 TAAATTAACTCTCCTCACTA
* * *** * *
1411429 AAATAAATATTAATCATTTTTAA-TTTTTTATATTCCTATGGGTATTTGTAGGGGTATTAAAAGA
1 AAATAAATATCAATCATTTTCAAGTTTTTTATATTCCTATGGGTATCCATAAGGATA-TAAAAGA
* * * * *
1411493 TTT-TAAAATTTTTTGTAT-TTTAGT-GGGTTTCCATCAAGGTACGAAATGATTTTTTTAAGAAA
65 TTTAAAAAACTTTTCGTATATTT--TCAGGTATCCATCAAGGTACGAAATGA-TTTTTTAA-AAA
*
1411555 -ATTTAAATTAA
126 TAATTAAATTAA
1411566 ATAGGGGAAA
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
147 3 0.03
148 33 0.28
149 47 0.41
150 33 0.28
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (149 bp):
AAATAAATATCAATCATTTTCAAGTTTTTTATATTCCTATGGGTATCCATAAGGATATAAAAGAT
TTAAAAAACTTTTCGTATATTTTCAGGTATCCATCAAGGTACGAAATGATTTTTTAAAAATAATT
AAATTAACTCTCCTCACTA
Found at i:1418083 original size:20 final size:21
Alignment explanation
Indices: 1418047--1418085 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1418037 TGGACACATT
1418047 AAAATGCATGAAACATGGCAC
1 AAAATGCATGAAACATGGCAC
1418068 AAAATGCATG-AACATGGC
1 AAAATGCATGAAACATGGC
1418086 TTGTTAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAATGCATGAAACATGGCAC
Found at i:1419112 original size:20 final size:20
Alignment explanation
Indices: 1419045--1419101 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1419035 AAAAACCCAA
* * *
1419045 AATGTATCGATACATTGAGT
1 AATGTATCAATACATTCAAT
*
1419065 AATGTATCAATACATTGCAAG
1 AATGTATCAATACATT-CAAT
*
1419086 CATGTATCAATACATT
1 AATGTATCAATACATT
1419102 TACTTATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
AATGTATCAATACATTCAAT
Found at i:1419922 original size:96 final size:97
Alignment explanation
Indices: 1419804--1420000 Score: 281
Period size: 96 Copynumber: 2.0 Consensus size: 97
1419794 TAGTGCAGGT
*
1419804 TTTTGGAAAGGTTTGAGTGCCACCAACTTGTGTGAGCTTATTAGGTCCT-CCAACTCATGCGAGC
1 TTTTGGAAAGGTTTGAGTGCCACCAACTTGTGTGAGCTTATTAAGTCCTACCAACTCATGCGAGC
1419868 TTTGAGAAATGATGCCACCTACTCT-TGTGGGC
66 TTTGAGAAATGATGCCACCTA-TCTGTGTGGGC
* * * ** * **
1419900 TTTTGGGAAGGTTTGAGTGCCACCAACTTGTGTGGGCTTTTTAAGTGTTACCAGCTTGTGCGAGC
1 TTTTGGAAAGGTTTGAGTGCCACCAACTTGTGTGAGCTTATTAAGTCCTACCAACTCATGCGAGC
*
1419965 TTTGAGAAATGATGCCACCTATTTGTGTGGGC
66 TTTGAGAAATGATGCCACCTATCTGTGTGGGC
1419997 TTTT
1 TTTT
1420001 CGGTGCCACC
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
96 45 0.51
97 44 0.49
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (97 bp):
TTTTGGAAAGGTTTGAGTGCCACCAACTTGTGTGAGCTTATTAAGTCCTACCAACTCATGCGAGC
TTTGAGAAATGATGCCACCTATCTGTGTGGGC
Found at i:1420425 original size:36 final size:36
Alignment explanation
Indices: 1420312--1420658 Score: 406
Period size: 36 Copynumber: 9.6 Consensus size: 36
1420302 GATTTAAAAA
* ** *
1420312 GGTTGCCACCAACTCATGTGGACTTTGAAAAATGTTT
1 GGTTGCCACCGACTTGTGTGGACTTTG-AAAAGGTTT
* *
1420349 GGTTGCCATCAACTTGTGTGGACTTTGAAAAAGGTTT
1 GGTTGCCACCGACTTGTGTGGACTTTG-AAAAGGTTT
* *
1420386 GGTTGCCACCGACTCGTGTGGACTTTGTAAAGGTTT
1 GGTTGCCACCGACTTGTGTGGACTTTGAAAAGGTTT
** * *
1420422 GGTTGCCACTAACTCGTGTGGACTTTGAAAAGTTTT
1 GGTTGCCACCGACTTGTGTGGACTTTGAAAAGGTTT
* ** *
1420458 GCTTGCCACTAACTTGTGTGGACTTTGAAAAAGTTT
1 GGTTGCCACCGACTTGTGTGGACTTTGAAAAGGTTT
* * *
1420494 GGTTGCCATCGACTCGTGTGGACTTTGTAAAGGTTT
1 GGTTGCCACCGACTTGTGTGGACTTTGAAAAGGTTT
* * *
1420530 GGTTGCCACTGACTCGTGTGGACTTTGAAAAGTTTT
1 GGTTGCCACCGACTTGTGTGGACTTTGAAAAGGTTT
*
1420566 GGTTGCCACTGACTTGTGTGGACTTTGAAAAGGTTT
1 GGTTGCCACCGACTTGTGTGGACTTTGAAAAGGTTT
* * *
1420602 GGTTGCCACTGACTTGTGTAGACTTTGGAAAAAGTTT
1 GGTTGCCACCGACTTGTGTGGACTTT-GAAAAGGTTT
* * *
1420639 GGTTACTACTGACTTGTGTG
1 GGTTGCCACCGACTTGTGTG
1420659 TTGCCACTAA
Statistics
Matches: 275, Mismatches: 34, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
36 192 0.70
37 83 0.30
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.35
Consensus pattern (36 bp):
GGTTGCCACCGACTTGTGTGGACTTTGAAAAGGTTT
Found at i:1420519 original size:108 final size:107
Alignment explanation
Indices: 1420312--1420642 Score: 493
Period size: 108 Copynumber: 3.0 Consensus size: 107
1420302 GATTTAAAAA
* * *
1420312 GGTTGCCACCAACTCATGTGGACTTTGAAAAATGTTTGGTTGCCA-TCAACTTGTGTGGACTTTG
1 GGTTGCCACTAACTCGTGTGGACTTTGAAAAGT-TTTGGTTGCCACT-AACTTGTGTGGACTTTG
1420376 AAAAAGGTTTGGTTGCCACCGACTCGTGTGGACTTTGTAAAGGTTT
64 AAAAA-GTTTGGTTGCCA-CGACTCGTGTGGACTTTGTAAAGGTTT
*
1420422 GGTTGCCACTAACTCGTGTGGACTTTGAAAAGTTTTGCTTGCCACTAACTTGTGTGGACTTTGAA
1 GGTTGCCACTAACTCGTGTGGACTTTGAAAAGTTTTGGTTGCCACTAACTTGTGTGGACTTTGAA
1420487 AAAGTTTGGTTGCCATCGACTCGTGTGGACTTTGTAAAGGTTT
66 AAAGTTTGGTTGCCA-CGACTCGTGTGGACTTTGTAAAGGTTT
* *
1420530 GGTTGCCACTGACTCGTGTGGACTTTGAAAAGTTTTGGTTGCCACTGACTTGTGTGGACTTTGAA
1 GGTTGCCACTAACTCGTGTGGACTTTGAAAAGTTTTGGTTGCCACTAACTTGTGTGGACTTTGAA
* * * * *
1420595 AAGGTTTGGTTGCCACTGACTTGTGTAGACTTTGGAAAAAGTTT
66 AAAGTTTGGTTGCCAC-GACTCGTGTGGACTTT-GTAAAGGTTT
1420639 GGTT
1 GGTT
1420643 ACTACTGACT
Statistics
Matches: 205, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
107 1 0.00
108 129 0.63
109 44 0.21
110 31 0.15
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.35
Consensus pattern (107 bp):
GGTTGCCACTAACTCGTGTGGACTTTGAAAAGTTTTGGTTGCCACTAACTTGTGTGGACTTTGAA
AAAGTTTGGTTGCCACGACTCGTGTGGACTTTGTAAAGGTTT
Found at i:1420687 original size:55 final size:54
Alignment explanation
Indices: 1420603--1420712 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 54
1420593 AAAAGGTTTG
* * *
1420603 GTTGCCACTGACTTGTGTAGACTTTGGAAAAAGTTTGGTTACTACTGACTTGTGT
1 GTTGCCACTAACTCGTGTAGACTTTGGAAAAAGTTTGGTTACCACT-ACTTGTGT
* * *
1420658 GTTGCCACTAACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCACTACTTGTGT
1 GTTGCCACTAACTCGTGTAGACTTTGGAAAAAGTTTGGTTACCACTACTTGTGT
1420712 G
1 G
1420713 AACTTTGGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
54 9 0.18
55 40 0.82
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.36
Consensus pattern (54 bp):
GTTGCCACTAACTCGTGTAGACTTTGGAAAAAGTTTGGTTACCACTACTTGTGT
Found at i:1420758 original size:128 final size:127
Alignment explanation
Indices: 1420531--1420770 Score: 367
Period size: 128 Copynumber: 1.9 Consensus size: 127
1420521 TAAAGGTTTG
* * *
1420531 GTTGCCACTGACTCGTGTGGACTTTGAAAAGTTTTGGTTGCCACTGACTTGTGTGGACTTTGAAA
1 GTTGCCACTAACTCGTGTGGACTTTGAAAAGGTTTGGTTGCCACTGACTTGTGTGAACTTTGAAA
* *
1420596 AGGTTTGGTTGCCACTGACTTGTGTAGACTTTGGAAAAAGTTTGGTTACTACTGACTTGTGT
66 AGGTTTGGTTGCCACTAACTCGTGTAGACTTTGGAAAAAGTTTGGTTACTACTGACTTGTGT
1420658 GTTGCCACTAACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCACT-ACTTGTGTGAACTTTGGA
1 GTTGCCACTAACTCGTGTGGACTTT-GAAAAGGTTTGGTTGCCACTGACTTGTGTGAACTTT-GA
* * *
1420722 AAAGGTTTTGTTGCTA-TCAACTCGTGTAGACTTTGGAAAAGGTTTGGTT
64 AAAGGTTTGGTTGCCACT-AACTCGTGTAGACTTTGGAAAAAGTTTGGTT
1420771 GCCACCGACT
Statistics
Matches: 102, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
127 39 0.38
128 63 0.62
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.37
Consensus pattern (127 bp):
GTTGCCACTAACTCGTGTGGACTTTGAAAAGGTTTGGTTGCCACTGACTTGTGTGAACTTTGAAA
AGGTTTGGTTGCCACTAACTCGTGTAGACTTTGGAAAAAGTTTGGTTACTACTGACTTGTGT
Found at i:1420764 original size:37 final size:37
Alignment explanation
Indices: 1420658--1420920 Score: 263
Period size: 37 Copynumber: 7.2 Consensus size: 37
1420648 TGACTTGTGT
1420658 GTTGCCA-CTAACTCGTGTGGACTTTGGAAAAGGTTTG
1 GTTGCCATC-AACTCGTGTGGACTTTGGAAAAGGTTTG
* * * *
1420695 GTTGCCA-CTACTTGTGTGAACTTTGGAAAAGGTTTT
1 GTTGCCATCAACTCGTGTGGACTTTGGAAAAGGTTTG
* *
1420731 GTTGCTATCAACTCGTGTAGACTTTGGAAAAGGTTTG
1 GTTGCCATCAACTCGTGTGGACTTTGGAAAAGGTTTG
* * *
1420768 GTTGCCACCGACTGGTGTGGACTTTGGAAAAGGTTTG
1 GTTGCCATCAACTCGTGTGGACTTTGGAAAAGGTTTG
* *
1420805 GTTGCCAAT-GACTCGTGTGGACTTTAGAAAAGGTTTG
1 GTTGCC-ATCAACTCGTGTGGACTTTGGAAAAGGTTTG
* * *
1420842 GTTGCCA-CTGACTTGTGTGG-CATTT-GAAAAAGTTTG
1 GTTGCCATC-AACTCGTGTGGAC-TTTGGAAAAGGTTTG
* * **
1420878 GTTGCCATCGAA-TTGTGTGG-TTTTGGAAAAGGTTAC
1 GTTGCCATC-AACTCGTGTGGACTTTGGAAAAGGTTTG
1420914 GTTGCCA
1 GTTGCCA
1420921 CCGACTTGCG
Statistics
Matches: 193, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
35 3 0.02
36 72 0.37
37 117 0.61
38 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.34
Consensus pattern (37 bp):
GTTGCCATCAACTCGTGTGGACTTTGGAAAAGGTTTG
Found at i:1420821 original size:74 final size:75
Alignment explanation
Indices: 1420658--1420950 Score: 336
Period size: 74 Copynumber: 4.0 Consensus size: 75
1420648 TGACTTGTGT
* * *
1420658 GTTGCCACT-AACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCA-CTACTTGTGTGAACTTTGG
1 GTTGCCAATCAACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCACCGACTTGTGTGGACTTTGG
*
1420721 AAAAGGTTTT
66 AAAAGGTTTG
* * *
1420731 GTTG-CTATCAACTCGTGTAGACTTTGGAAAAGGTTTGGTTGCCACCGACTGGTGTGGACTTTGG
1 GTTGCCAATCAACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCACCGACTTGTGTGGACTTTGG
1420795 AAAAGGTTTG
66 AAAAGGTTTG
* * *
1420805 GTTGCCAAT-GACTCGTGTGGACTTTAGAAAAGGTTTGGTTGCCACTGACTTGTGTGG-CATTT-
1 GTTGCCAATCAACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCACCGACTTGTGTGGAC-TTTG
*
1420867 GAAAAAGTTTG
65 GAAAAGGTTTG
* * ** * *
1420878 GTTGCC-ATCGAA-TTGTGTGG-TTTTGGAAAAGGTTACGTTGCCACCGACTTGCGTAGACTTTA
1 GTTGCCAATC-AACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCACCGACTTGTGTGGACTTT-
1420940 GGAAAA-GTTTG
64 GGAAAAGGTTTG
1420951 ACATGACTTT
Statistics
Matches: 188, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
72 36 0.19
73 68 0.36
74 81 0.43
75 3 0.02
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.34
Consensus pattern (75 bp):
GTTGCCAATCAACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCACCGACTTGTGTGGACTTTGG
AAAAGGTTTG
Found at i:1420871 original size:110 final size:110
Alignment explanation
Indices: 1420658--1420920 Score: 300
Period size: 110 Copynumber: 2.4 Consensus size: 110
1420648 TGACTTGTGT
** * * *
1420658 GTTGCCACTAACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCACTACTTGTGTGAACTTTGGAA
1 GTTGCCACCGACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCAATACTCGTGTGAACTTTAGAA
* * *
1420723 AAGGTTTTGTTGCTATCAACTCGTGTAGACTTTGGAAAAGGTTTG
66 AAGGTTTGGTTGCCATCAACTCGTGTAGACTTTGGAAAAAGTTTG
* *
1420768 GTTGCCACCGACTGGTGTGGACTTTGGAAAAGGTTTGGTTGCCAATGACTCGTGTGGACTTTAGA
1 GTTGCCACCGACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCAAT-ACTCGTGTGAACTTTAGA
* * *
1420833 AAAGGTTTGGTTGCCA-CTGACTTGTGT-GGCATTT-GAAAAAGTTTG
65 AAAGGTTTGGTTGCCATC-AACTCGTGTAGAC-TTTGGAAAAAGTTTG
* * * * **
1420878 GTTGCCATCGAATTGTGTGG-TTTTGGAAAAGGTTACGTTGCCA
1 GTTGCCACCGACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCA
1420921 CCGACTTGCG
Statistics
Matches: 131, Mismatches: 19, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
109 20 0.15
110 72 0.55
111 39 0.30
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.34
Consensus pattern (110 bp):
GTTGCCACCGACTCGTGTGGACTTTGGAAAAGGTTTGGTTGCCAATACTCGTGTGAACTTTAGAA
AAGGTTTGGTTGCCATCAACTCGTGTAGACTTTGGAAAAAGTTTG
Found at i:1421082 original size:23 final size:25
Alignment explanation
Indices: 1421051--1421096 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
1421041 CACTGGACTT
1421051 AAAGATTTTGACA-A-ATTTTGACA
1 AAAGATTTTGACAGAGATTTTGACA
*
1421074 AAAGTTTTTGACAGAGATTTTGA
1 AAAGATTTTGACAGAGATTTTGA
1421097 TGAATATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 1 0.05
25 7 0.35
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (25 bp):
AAAGATTTTGACAGAGATTTTGACA
Found at i:1422545 original size:17 final size:18
Alignment explanation
Indices: 1422509--1422554 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
1422499 TATTTATTTC
1422509 AATAAATA-ATATTCATCT
1 AATAAATATA-ATTCATCT
1422527 AATAAATATAATT-ATCT
1 AATAAATATAATTCATCT
*
1422544 AATAATTATAA
1 AATAAATATAA
1422555 AACTAGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.54
18 11 0.42
19 1 0.04
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATATAATTCATCT
Found at i:1427685 original size:18 final size:18
Alignment explanation
Indices: 1427662--1427698 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1427652 GGGAGGCTCC
1427662 TATAAATTTAATAATTTA
1 TATAAATTTAATAATTTA
1427680 TATAAATTTAATAATTTA
1 TATAAATTTAATAATTTA
1427698 T
1 T
1427699 GCAGTGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATAAATTTAATAATTTA
Found at i:1428107 original size:21 final size:20
Alignment explanation
Indices: 1428081--1428154 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 20
1428071 GCAAGGCAAG
1428081 AGCAAGAACATTAGACATTTT
1 AGCAAGAACATT-GACATTTT
*
1428102 AGCAAGAAAAACTACTTG-CAATTT
1 AGCAAG---AAC-A-TTGACATTTT
1428126 AGCAAGAACATTGGACATTTT
1 AGCAAGAACATT-GACATTTT
1428147 AGCAAGAA
1 AGCAAGAA
1428155 AAACTATGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 22 0.50
24 14 0.32
25 2 0.05
26 2 0.05
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (20 bp):
AGCAAGAACATTGACATTTT
Found at i:1432938 original size:30 final size:28
Alignment explanation
Indices: 1432904--1432966 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1432894 ATTTGGCAAC
1432904 TCAATTTAAGCG-ATTAATAGTTAATTAAAT
1 TCAATTTAAGCGAATT--TA-TTAATTAAAT
*
1432934 TCAATTTAAGTGAATTTATTAATTAAAT
1 TCAATTTAAGCGAATTTATTAATTAAAT
1432962 TCAAT
1 TCAAT
1432967 GATTTCGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 15 0.48
29 2 0.06
30 11 0.35
31 3 0.10
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (28 bp):
TCAATTTAAGCGAATTTATTAATTAAAT
Found at i:1433034 original size:3 final size:3
Alignment explanation
Indices: 1433028--1433071 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1433018 ATTATTTGCT
1433028 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1433072 TTGCTTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1433219 original size:16 final size:16
Alignment explanation
Indices: 1433198--1433230 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1433188 ATATTACATG
1433198 TTGTGATATGTATACC
1 TTGTGATATGTATACC
1433214 TTGTGATATGTATACC
1 TTGTGATATGTATACC
1433230 T
1 T
1433231 ACGTGATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (16 bp):
TTGTGATATGTATACC
Found at i:1440868 original size:164 final size:163
Alignment explanation
Indices: 1440635--1441168 Score: 583
Period size: 166 Copynumber: 3.2 Consensus size: 163
1440625 TTTGGGAAGA
* * * * * * *
1440635 TTTTCATTGGTTTAAAACTTTTAAAATTCATCAAATATTATTATTTAACTCATATTAAATCATTT
1 TTTTC-TTGGTTTAAAATTTTTAAAATTCATCAAATATCATCATATAATTCATATTAAATTAATT
*
1440700 TTGAAAAATTCATTTATTTTCATGAGTTTTCATTTATTTCTT-AAATTTTCCTATTTTTGAAATA
65 TTGAAAAATTCATTTATTTTCATGAGTTTTAATTT-TTTCTTAAAATTTTCCTATTTTTGAAATA
*
1440764 CGAAGTTTTTTACTCCATAAATATTTACGAGGGGAT
129 CGAAGTTTTTTACTCCATAAATGTTTACG-GGGGAT
* * *
1440800 TTTTCTTGGTTTATAATTTTTAAAATTCATAAAATATCATCATATAATTCACATTAAATTAATTT
1 TTTTCTTGGTTTAAAATTTTTAAAATTCATCAAATATCATCATATAATTCATATTAAATTAATTT
* * * * * *
1440865 TGAAAAATTCATTTATTTGCTTGACTTTTTAATTTTTTCCTTAAAATTCTCTTGTTTTTGAAATA
66 TGAAAAATTCATTTATTTTCATGA-GTTTTAATTTTTT-CTTAAAATTTTCCTATTTTTGAAATA
* * * * *
1440930 C-AGACTTCTTTACT-CGTAAACGTTTATGGGGGGCAT
129 CGA-AGTTTTTTACTCCATAAATGTTTA-CGGGGG-AT
* * * *
1440966 TTTTCTTGGTTTATAATTTTTAAAATTTATCAAATATCATCATCTAATTCATATTAAATTAGTTT
1 TTTTCTTGGTTTAAAATTTTTAAAATTCATCAAATATCATCATATAATTCATATTAAATTAATTT
* * * * *
1441031 TGAAAAAGTCCTTT-TATTTCATGAGTTTTGAATTGTTTCTTCAAAATTTTCCTATTTTTGCAAG
66 TGAAAAATTCATTTAT-TTTCATGAGTTTT-AATTTTTTCTT-AAAATTTTCCTATTTTTGAAAT
* *
1441095 ACGAAGTTTTTTACTCCATAAATGTTTTCGGGATGAT
128 ACGAAGTTTTTTACTCCATAAATGTTTACGGG-GGAT
** *
1441132 TTTTCTAAG-TTAAAATTTTTTAAAATTCATCTAATAT
1 TTTTCTTGGTTTAAAA-TTTTTAAAATTCATCAAATAT
1441169 TGTTATTAAA
Statistics
Matches: 305, Mismatches: 51, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
164 75 0.25
165 43 0.14
166 176 0.58
167 11 0.04
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (163 bp):
TTTTCTTGGTTTAAAATTTTTAAAATTCATCAAATATCATCATATAATTCATATTAAATTAATTT
TGAAAAATTCATTTATTTTCATGAGTTTTAATTTTTTCTTAAAATTTTCCTATTTTTGAAATACG
AAGTTTTTTACTCCATAAATGTTTACGGGGGAT
Found at i:1441419 original size:24 final size:24
Alignment explanation
Indices: 1441374--1441419 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1441364 ATCTTAATTT
* *
1441374 TTAATTTTTACAATCTATTTTTTA
1 TTAATTTTTACAATATAATTTTTA
* *
1441398 TTAATTTTTAGAGTATAATTTT
1 TTAATTTTTACAATATAATTTT
1441420 ACGAATAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
TTAATTTTTACAATATAATTTTTA
Found at i:1443728 original size:156 final size:154
Alignment explanation
Indices: 1443295--1443962 Score: 531
Period size: 156 Copynumber: 4.3 Consensus size: 154
1443285 AAGGTGCACC
* ** * * *
1443295 TTTAGAATAGGTTCAT-CTTTCTATAATAATTTTTAGGTCCTTTAAGGGTATCAAG-TAC-TTCT
1 TTTAGGATAGGTTCATCCCATCTATAAT-CTTTTTAAGTCCTTT-AGGTTATCAAGATACTTTC-
* * * * *
1443357 ATGTCGAAGGTAT-CCCCTAAGGGGTTTTCATAA-TTTTCTAGAACTGAGTCCTAGGTTGTCACT
63 ATGTCGAAGGTATACCCAT-AGGGGTTTTCATAATTTTTCTAGAACCGACTCCTAGGTTATCACC
* * *
1443420 AGG-TCTGCTTTTATGTC-AAAGGTGGGTC
127 AGGTTC-GATTTTATGCCGAAA-GTGGGTA
* * * *
1443448 TTTAGGATAGGTTTATCCCAGCTATAACCTTTTTAAGT-CTGCTAGGGTTATCGAA-ATACTTTC
1 TTTAGGATAGGTTCATCCCATCTATAATCTTTTTAAGTCCT-TTA-GGTTATC-AAGATACTTTC
** * * * * *
1443511 ATGTCGAAGGTATACCCATAAGGGTGTTTTTTTAATTTTTTTAGAATCAACTCTTAAGTTATCAC
63 ATGTCGAAGGTATACCCAT-AGGG-GTTTTCATAATTTTTCTAGAACCGACTCCTAGGTTATCAC
* *
1443576 CAGGTTCGGTTTTATGCCGAAAGTAGGTA
126 CAGGTTCGATTTTATGCCGAAAGTGGGTA
1443605 TTTAGGATAGGTTCATCCCATCTATAATCTTTTTAAGTCCTTTAGGTTATCAAGATACTTTCATG
1 TTTAGGATAGGTTCATCCCATCTATAATCTTTTTAAGTCCTTTAGGTTATCAAGATACTTTCATG
* * *
1443670 TCGAAGGTATATCCATAGGGGCATTTTCATAATTTTTCTAGAACCGACTCCTAGGTTATCATCGG
66 TCGAAGGTATACCCATAGGGG--TTTTCATAATTTTTCTAGAACCGACTCCTAGGTTATCACCAG
* *
1443735 GTTTGATTTTATGCCGAAGGTGGGTA
129 GTTCGATTTTATGCCGAAAGTGGGTA
* * * **
1443761 TTTAGGATAGGTTTATCCCATCTAT-ATCTTTTTTTAAGTCCTTTAGGGGTAT-TAGGCAC-TTC
1 TTTAGGATAGGTTCATCCCATCTATAATC--TTTTTAAGTCCTTTA-GGTTATCAAGATACTTTC
* * * * * ** ** * * *
1443823 TATGCCAAAGCTATCCCCAGAGAGCATTTTCATAA-TTTTCTAGAATTGAGTCCTAGGTTGTCAT
63 -ATGTCGAAGGTATACCCATAG-GGGTTTTCATAATTTTTCTAGAACCGACTCCTAGGTTATCAC
* *
1443887 C-GAG-TCCATTTTTATGCTG-AAGATGGGTA
126 CAG-GTTCGA-TTTTATGCCGAAAG-TGGGTA
* * * *
1443916 TTTAGGATAGGTTCCTCCCATCCATAATATTTTCTTAGTCCTTTAGG
1 TTTAGGATAGGTTCATCCCATCTATAATCTTTT-TAAGTCCTTTAGG
1443963 GTATTGGGTA
Statistics
Matches: 420, Mismatches: 70, Indels: 49
0.78 0.13 0.09
Matches are distributed among these distances:
152 3 0.01
153 29 0.07
154 37 0.09
155 95 0.23
156 134 0.32
157 109 0.26
158 13 0.03
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (154 bp):
TTTAGGATAGGTTCATCCCATCTATAATCTTTTTAAGTCCTTTAGGTTATCAAGATACTTTCATG
TCGAAGGTATACCCATAGGGGTTTTCATAATTTTTCTAGAACCGACTCCTAGGTTATCACCAGGT
TCGATTTTATGCCGAAAGTGGGTA
Found at i:1446263 original size:20 final size:19
Alignment explanation
Indices: 1446238--1446291 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
1446228 CTGCCAGTTT
*
1446238 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGTA
1446258 CATGTATCGATACAATGTA
1 CATGTATCGATACAATGTA
*
1446277 TATGTATCGATACAA
1 CATGTATCGATACAA
1446292 AGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGTA
Found at i:1446283 original size:19 final size:19
Alignment explanation
Indices: 1446239--1446308 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 19
1446229 TGCCAGTTTC
**
1446239 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGTAT
1446259 ATGTATCGATACAATGTAT
1 ATGTATCGATACAATGTAT
* *
1446278 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAATGTAT
1446297 AATGTATCGATA
1 -ATGTATCGATA
1446309 TATCTGGGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 20 0.44
20 25 0.56
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGTAT
Found at i:1446303 original size:20 final size:19
Alignment explanation
Indices: 1446259--1446308 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1446249 ACAATTGTCC
* *
1446259 ATGTATCGATACAATGTAT
1 ATGTATCGATACAAAGCAT
1446278 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAAAGCAT
1446297 AATGTATCGATA
1 -ATGTATCGATA
1446309 TATCTGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACAAAGCAT
Found at i:1446910 original size:22 final size:22
Alignment explanation
Indices: 1446885--1446926 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1446875 AGATAAACAT
*
1446885 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCACTTTATCAAAGC
1446907 ATTTCTCCCACTTTATCAAA
1 ATTTCTCCCACTTTATCAAA
1446927 AAAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTTCTCCCACTTTATCAAAGC
Found at i:1454850 original size:13 final size:13
Alignment explanation
Indices: 1454832--1454857 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1454822 CATTATGAAT
1454832 TGTATCGATACAA
1 TGTATCGATACAA
1454845 TGTATCGATACAA
1 TGTATCGATACAA
1454858 CATTCCATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1454944 original size:13 final size:13
Alignment explanation
Indices: 1454926--1454952 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1454916 TACAATGAAC
1454926 ATGTATCGATACA
1 ATGTATCGATACA
1454939 ATGTATCGATACA
1 ATGTATCGATACA
1454952 A
1 A
1454953 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1457483 original size:21 final size:21
Alignment explanation
Indices: 1457457--1457509 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1457447 CTTAGAAATA
1457457 TGTATTGATACTTCATGAACT
1 TGTATTGATACTTCATGAACT
*
1457478 TGTATTGACACTTCATGAACT
1 TGTATTGATACTTCATGAACT
1457499 TGTATTGATAC
1 TGTATTGATAC
1457510 ATAACCTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATTGATACTTCATGAACT
Found at i:1458934 original size:13 final size:13
Alignment explanation
Indices: 1458916--1458941 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1458906 CAATTTTTTG
1458916 TGTATCGATACAT
1 TGTATCGATACAT
1458929 TGTATCGATACAT
1 TGTATCGATACAT
1458942 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1459006 original size:21 final size:21
Alignment explanation
Indices: 1458980--1459096 Score: 139
Period size: 21 Copynumber: 5.7 Consensus size: 21
1458970 CTGCCAAGAA
*
1458980 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1459001 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1459021 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
1459042 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1459062 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1459083 ATGTATCGATACAT
1 ATGTATCGATACAT
1459097 TGCAACATGT
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 31 0.40
21 46 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1459026 original size:20 final size:20
Alignment explanation
Indices: 1459001--1459114 Score: 138
Period size: 20 Copynumber: 5.6 Consensus size: 20
1458991 CATCTTTTTT
1459001 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1459021 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1459042 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1459062 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1459083 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1459103 ATGTATCGATAC
1 ATGTATCGATAC
1459115 TTTGAGTTGT
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 44 0.58
21 32 0.42
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1459037 original size:41 final size:41
Alignment explanation
Indices: 1458980--1459114 Score: 261
Period size: 41 Copynumber: 3.3 Consensus size: 41
1458970 CTGCCAAGAA
*
1458980 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1459021 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1459062 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1459103 ATGTATCGATAC
1 ATGTATCGATAC
1459115 TTTGAGTTGT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1459748 original size:16 final size:16
Alignment explanation
Indices: 1459717--1459762 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
1459707 CTCTCCTTTG
1459717 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
1459735 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
1459751 TCTCCCCCTTAA
1 TCTCCCCCTTAA
1459763 TCAAGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
18 8 0.29
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:1461586 original size:13 final size:13
Alignment explanation
Indices: 1461568--1461606 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1461558 ATAATCACCC
*
1461568 TGTATCGATACAG
1 TGTATCGATACAA
1461581 TGTATCGATACAA
1 TGTATCGATACAA
1461594 TGTATCGATACAA
1 TGTATCGATACAA
1461607 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1461617 original size:20 final size:20
Alignment explanation
Indices: 1461592--1461670 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1461582 GTATCGATAC
1461592 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
1461612 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
1461637 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
1461656 ACATGTATCGATACA
1 A-ATGTATCGATACA
1461671 TTTTGGACAA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:1463704 original size:15 final size:15
Alignment explanation
Indices: 1463684--1463714 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1463674 ATTTCGTTTG
*
1463684 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1463699 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1463714 G
1 G
1463715 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1467795 original size:13 final size:13
Alignment explanation
Indices: 1467777--1467802 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1467767 CAATTTTTTG
1467777 TGTATCGATACAT
1 TGTATCGATACAT
1467790 TGTATCGATACAT
1 TGTATCGATACAT
1467803 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1467867 original size:21 final size:21
Alignment explanation
Indices: 1467841--1467957 Score: 139
Period size: 21 Copynumber: 5.7 Consensus size: 21
1467831 CTGCCAAGAA
*
1467841 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1467862 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1467882 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
1467903 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1467923 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1467944 ATGTATCGATACAT
1 ATGTATCGATACAT
1467958 TGCAACATGT
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 31 0.40
21 46 0.60
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1467887 original size:20 final size:20
Alignment explanation
Indices: 1467862--1467975 Score: 138
Period size: 20 Copynumber: 5.6 Consensus size: 20
1467852 CATCTTTTTT
1467862 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1467882 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1467903 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1467923 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1467944 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1467964 ATGTATCGATAC
1 ATGTATCGATAC
1467976 TTTGAGTTGT
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 44 0.58
21 32 0.42
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1467898 original size:41 final size:41
Alignment explanation
Indices: 1467841--1467975 Score: 261
Period size: 41 Copynumber: 3.3 Consensus size: 41
1467831 CTGCCAAGAA
*
1467841 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1467882 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1467923 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1467964 ATGTATCGATAC
1 ATGTATCGATAC
1467976 TTTGAGTTGT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1469188 original size:27 final size:26
Alignment explanation
Indices: 1469130--1469180 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1469120 TTTTCAAGTT
*
1469130 TTAATTTTTACAATTTAATCGTTTTTA
1 TTAATTTTTACAATATAATC-TTTTTA
*
1469157 TTAATTTTTACAGTATAAT-TTTTT
1 TTAATTTTTACAATATAATCTTTTT
1469181 GAATTAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
27 17 0.77
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (26 bp):
TTAATTTTTACAATATAATCTTTTTA
Found at i:1472897 original size:20 final size:20
Alignment explanation
Indices: 1472872--1472958 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
1472862 TTTACCTAGA
1472872 TGTATCGATACATTTTTCAT
1 TGTATCGATACATTTTTCAT
*
1472892 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTTTTCAT
1472912 TGTATCGAT--A-----CAT
1 TGTATCGATACATTTTTCAT
*
1472925 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTTTTCAT
1472945 TGTATCGATACATT
1 TGTATCGATACATT
1472959 CAGGCATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
13 12 0.21
15 1 0.02
18 1 0.02
20 44 0.76
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTTTCAT
Found at i:1472907 original size:13 final size:13
Alignment explanation
Indices: 1472889--1472938 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
1472879 ATACATTTTT
1472889 CATTGTATCGATA
1 CATTGTATCGATA
1472902 CATTGT-TC---A
1 CATTGTATCGATA
1472911 --TTGTATCGATA
1 CATTGTATCGATA
1472922 CATTGTATCGATA
1 CATTGTATCGATA
1472935 CATT
1 CATT
1472939 TTTCAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
7 4 0.13
8 2 0.06
9 1 0.03
11 1 0.03
12 2 0.06
13 21 0.68
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1472931 original size:33 final size:33
Alignment explanation
Indices: 1472889--1472958 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
1472879 ATACATTTTT
*
1472889 CATTGTATCGATACATTGTTCATTGTATCGATA
1 CATTGTATCGATACATTGTTCAATGTATCGATA
*
1472922 CATTGTATCGATACATTTTTCAATGTATCGATA
1 CATTGTATCGATACATTGTTCAATGTATCGATA
1472955 CATT
1 CATT
1472959 CAGGCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (33 bp):
CATTGTATCGATACATTGTTCAATGTATCGATA
Found at i:1475712 original size:51 final size:52
Alignment explanation
Indices: 1475596--1475712 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 52
1475586 ATTTCCAAAG
* *** * *
1475596 GGATACTCCAA-CCCTGACTTTATTTCTAAAATATTGATTTCTCATAATCGG
1 GGATACTCCAACCCCTGACTTTATTTCTAAAACACCAATTTCTCACAATCGA
* *
1475647 GGATACTCCAACCCCT-ATTTTATTTCTAAAACACCAATTTTTCACAATCGA
1 GGATACTCCAACCCCTGACTTTATTTCTAAAACACCAATTTCTCACAATCGA
1475698 GGATACTCCAACCCC
1 GGATACTCCAACCCC
1475713 GTTATTTTCG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.32
Consensus pattern (52 bp):
GGATACTCCAACCCCTGACTTTATTTCTAAAACACCAATTTCTCACAATCGA
Found at i:1475773 original size:130 final size:131
Alignment explanation
Indices: 1475252--1475799 Score: 736
Period size: 131 Copynumber: 4.2 Consensus size: 131
1475242 ATTTTTCATC
* * * *
1475252 TCGGGG-TACTCCAA-CCCTGGTTTTATTTCCAAAACATCAAT-TTTTCATAATCAGGGATACTC
1 TCGGGGATACTCCAACCCCT-ATTTTATTTCTAAAACACCAATCTTTTCACAATCAGGGATACTC
* * *
1475314 CAATCCCTTTATTTTCGAGGGGATACTCTAACCCCGGCTTTATTTCTAAAATATTGATTTATCAC
65 CAATCCCGTTATTTTCGAGGGGATACTCTAACCCCGACTTTATTTCTAAAATATTGATTTCTCAC
1475379 AA
130 AA
* * *
1475381 TCGGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATCAGAGATACTCT
1 TCGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATCTTTTCACAATCAGGGATACTCC
* *
1475446 AATCCCGTTATTTTCGAGGGAATACTCTAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACA
66 AATCCCGTTATTTTCGAGGGGATACTCTAACCCCGACTTTATTTCTAAAATATTGATTTCTCACA
1475511 A
131 A
1475512 TCGGGGATACTCCAA-CCCTAATTTTATTTCTAAAACACCAATCTTTTCACAATCAGGGATACTC
1 TCGGGGATACTCCAACCCCT-ATTTTATTTCTAAAACACCAATCTTTTCACAATCAGGGATACTC
* * * * * * * *
1475576 TAATCCTGTTATTTCCAAAGGGATACTCCAACCCTGACTTTATTTCTAAAATATTGATTTCTCAT
65 CAATCCCGTTATTTTCGAGGGGATACTCTAACCCCGACTTTATTTCTAAAATATTGATTTCTCAC
1475641 AA
130 AA
1475643 TCGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCAAT-TTTTCACAATC-GAGGATACTC
1 TCGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATCTTTTCACAATCAG-GGATACTC
* * **
1475706 CAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTATTT-TCAAAATACCGATTT-TCT
65 CAATCCCGTTATTTTCGAGGGGATACTCTAACCCCGACTTTATTTCT-AAAATATTGATTTCTC-
*
1475769 ATAA
128 ACAA
* *
1475773 TTGGGGATACTCCAGCCCC-ATTGTTAT
1 TCGGGGATACTCCAACCCCTATT-TTAT
1475800 CTCCAAAATA
Statistics
Matches: 376, Mismatches: 34, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
129 13 0.03
130 121 0.32
131 238 0.63
132 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (131 bp):
TCGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATCTTTTCACAATCAGGGATACTCC
AATCCCGTTATTTTCGAGGGGATACTCTAACCCCGACTTTATTTCTAAAATATTGATTTCTCACA
A
Found at i:1476919 original size:90 final size:91
Alignment explanation
Indices: 1476758--1476926 Score: 295
Period size: 90 Copynumber: 1.9 Consensus size: 91
1476748 CGTTGCGACA
* *
1476758 GATATATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAGAA
1 GATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAAAA
1476823 TCTATCGATACATTCATACATGTATC
66 TCTATCGATACATTCATACATGTATC
*
1476849 GATACATTAAAAAATGTATTGATACATCTGGGT-AAAAGACAGAATGTATCGATACATTGAAAAA
1 GATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAAAA
*
1476913 TGTATCGATACATT
66 TCTATCGATACATT
1476927 TGGGTAAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 43 0.58
91 31 0.42
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.30
Consensus pattern (91 bp):
GATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAAAA
TCTATCGATACATTCATACATGTATC
Found at i:1476938 original size:24 final size:20
Alignment explanation
Indices: 1476801--1476926 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
1476791 AAAAAGACAG
*
1476801 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * *
1476821 AATCTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
1476841 CATGTATCGATACATTAAAA
1 AATGTATCGATACATTGAAA
*
1476861 AATGTATTGATACATCTGGGTAAAAGACA
1 AATGTATCGATACAT-T--G----A-A-A
1476890 GAATGTATCGATACATTGAAA
1 -AATGTATCGATACATTGAAA
1476911 AATGTATCGATACATT
1 AATGTATCGATACATT
1476927 TGGGTAAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
20 61 0.73
21 2 0.02
22 1 0.01
23 1 0.01
27 2 0.02
28 1 0.01
29 2 0.02
30 14 0.17
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1480632 original size:73 final size:73
Alignment explanation
Indices: 1480493--1480669 Score: 180
Period size: 73 Copynumber: 2.4 Consensus size: 73
1480483 CTTTAGGATG
* *
1480493 GGTAAGAAAAAGAGTCTAGCTCTTTGTGGACTCAAGTAAACAGGTGCCACTAGTTTGTGCAAGCT
1 GGTAAGAAAAAGAGTCCAGCTCTTTGTGGACTCAAGTAAACAGGTGCCACTAGTTTATGCAAGCT
1480558 TTGTAGTT
66 TTGTAGTT
* * * * ***
1480566 GGTAAGAAAAAGTA-TCCAGCTTTTTGTGGACT-AAGGTAGATAGGTGCCATTAGTTTATGTGGG
1 GGTAAGAAAAAG-AGTCCAGCTCTTTGTGGACTCAA-GTAAACAGGTGCCACTAGTTTATGCAAG
* * *
1480629 CTTTATGGTA
64 CTTTGTAGTT
* * *
1480639 GGTAA-AAGAGGAGTCCAACTCTTTGTGGACT
1 GGTAAGAAAAAGAGTCCAGCTCTTTGTGGACT
1480670 TAGGTAAATT
Statistics
Matches: 85, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
71 1 0.01
72 22 0.26
73 61 0.72
74 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (73 bp):
GGTAAGAAAAAGAGTCCAGCTCTTTGTGGACTCAAGTAAACAGGTGCCACTAGTTTATGCAAGCT
TTGTAGTT
Found at i:1488639 original size:52 final size:52
Alignment explanation
Indices: 1488504--1488639 Score: 130
Period size: 52 Copynumber: 2.6 Consensus size: 52
1488494 GTTCTTAGAA
* * * * * * * * *
1488504 ATGACAAAGGTGCTAATATGTTGATCCAAGGCTAGCGATATTGGACTTAAAT
1 ATGATAAAAGTGCCAATATATTGATTCATGGCAAGCGAAATTGGACTTAAAG
* * *
1488556 ATGATAAAAGTGCCAATGTATTGATTTATGGCAAGCGAAATTGGTCTTAAAG
1 ATGATAAAAGTGCCAATATATTGATTCATGGCAAGCGAAATTGGACTTAAAG
* *
1488608 ATGATAAGAGTGCCAATATGCTT-ATTCATGGC
1 ATGATAAAAGTGCCAATAT-ATTGATTCATGGC
1488640 CAGTAACACT
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
52 65 0.97
53 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (52 bp):
ATGATAAAAGTGCCAATATATTGATTCATGGCAAGCGAAATTGGACTTAAAG
Found at i:1488694 original size:52 final size:52
Alignment explanation
Indices: 1488638--1488737 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
1488628 CTTATTCATG
* * *
1488638 GCCAGTAACACTGGTTTTAGAGATGACAAAGGTGCCAATGTGCTGATTGAAA
1 GCCAGCAACACTGGTCTTAGAAATGACAAAGGTGCCAATGTGCTGATTGAAA
*
1488690 GCCAGCAACATTGGTCTTAGAAATGACAAAGGTGCCAATGTGCTGATT
1 GCCAGCAACACTGGTCTTAGAAATGACAAAGGTGCCAATGTGCTGATT
1488738 TAAGGCTAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (52 bp):
GCCAGCAACACTGGTCTTAGAAATGACAAAGGTGCCAATGTGCTGATTGAAA
Found at i:1489418 original size:27 final size:27
Alignment explanation
Indices: 1489380--1489431 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1489370 AAAAGGATTA
*
1489380 GGTGGCACCAGCTCGTGTGGGCTTTTG
1 GGTGGCACCAGCTCGTGCGGGCTTTTG
*
1489407 GGTGTCACCAGCTCGTGCGGGCTTT
1 GGTGGCACCAGCTCGTGCGGGCTTT
1489432 GAAAAAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.08, C:0.25, G:0.38, T:0.29
Consensus pattern (27 bp):
GGTGGCACCAGCTCGTGCGGGCTTTTG
Found at i:1489592 original size:31 final size:31
Alignment explanation
Indices: 1489520--1489729 Score: 164
Period size: 31 Copynumber: 6.7 Consensus size: 31
1489510 TGTGCTACTG
* * *
1489520 ACTTGTGTGGAATTTAGAAAAGATGCCACCA
1 ACTTGTGTGGACTTTGGAAAGGATGCCACCA
* *
1489551 ACTTGGGTGGACTTTGGAAAGGATGCCACTA
1 ACTTGTGTGGACTTTGGAAAGGATGCCACCA
1489582 A-TTCGTGTGGACTTT--AACTATGG-TGCCACCA
1 ACTT-GTGTGGACTTTGGAA--A-GGATGCCACCA
* * *
1489613 ACTTGTGTGGA-TTTTGACAAGATTATGCCACTA
1 ACTTGTGTGGACTTTGGA-AAG--GATGCCACCA
* * *
1489646 ACTTGTATGGACTTTGGATAGGGTGCCACCA
1 ACTTGTGTGGACTTTGGAAAGGATGCCACCA
*
1489677 ACTCGTGTGGACTTT--AACTAGGATGCCACCA
1 ACTTGTGTGGACTTTGGAA--AGGATGCCACCA
* *
1489708 ACTCGTGTGGACTTTGAAAAGG
1 ACTTGTGTGGACTTTGGAAAGG
1489730 CTTGGTTGCC
Statistics
Matches: 144, Mismatches: 19, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
29 3 0.02
30 6 0.04
31 103 0.72
32 5 0.03
33 22 0.15
34 5 0.03
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (31 bp):
ACTTGTGTGGACTTTGGAAAGGATGCCACCA
Found at i:1489657 original size:95 final size:95
Alignment explanation
Indices: 1489542--1489724 Score: 269
Period size: 95 Copynumber: 1.9 Consensus size: 95
1489532 TTTAGAAAAG
* * *
1489542 ATGCCACCAACTTGGGTGGACTTTGGAAAGGATGCCACTAATTCGTGTGGACTTTAACTATGG-T
1 ATGCCACCAACTTGGATGGACTTTGGAAAGGATGCCACCAACTCGTGTGGACTTTAACTA-GGAT
* *
1489606 GCCACCAACTTGTGTGGATTTTGACAAGATT
65 GCCACCAACTCGTGTGGACTTTGACAAGATT
* * * *
1489637 ATGCCACTAACTTGTATGGACTTTGGATAGGGTGCCACCAACTCGTGTGGACTTTAACTAGGATG
1 ATGCCACCAACTTGGATGGACTTTGGAAAGGATGCCACCAACTCGTGTGGACTTTAACTAGGATG
1489702 CCACCAACTCGTGTGGACTTTGA
66 CCACCAACTCGTGTGGACTTTGA
1489725 AAAGGCTTGG
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 2 0.03
95 76 0.97
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (95 bp):
ATGCCACCAACTTGGATGGACTTTGGAAAGGATGCCACCAACTCGTGTGGACTTTAACTAGGATG
CCACCAACTCGTGTGGACTTTGACAAGATT
Found at i:1489660 original size:64 final size:62
Alignment explanation
Indices: 1489543--1489725 Score: 178
Period size: 64 Copynumber: 2.9 Consensus size: 62
1489533 TTAGAAAAGA
* * *
1489543 TGCCACCAACTTGGGTGGACTTTGGAAAGGATGCCACTAATTCGTGTGGACTTT-AACTATGG
1 TGCCACCAACTTGTGTGGACTTTGGAAAGGATGCCACTAATTCGTATGGACTTTGAA-TAGGG
* * *
1489605 TGCCACCAACTTGTGTGGA-TTTTGACAAGATTATGCCACTAACTT-GTATGGACTTTGGATAGG
1 TGCCACCAACTTGTGTGGACTTTGGA-AAG--GATGCCACTAA-TTCGTATGGACTTTGAATAGG
1489668 G
62 G
* * * *
1489669 TGCCACCAACTCGTGTGGACTTT--AACTAGGATGCCACCAACTCGTGTGGACTTTGAA
1 TGCCACCAACTTGTGTGGACTTTGGAA--AGGATGCCACTAATTCGTATGGACTTTGAA
1489726 AAGGCTTGGT
Statistics
Matches: 100, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
61 6 0.06
62 43 0.43
63 1 0.01
64 44 0.44
65 6 0.06
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (62 bp):
TGCCACCAACTTGTGTGGACTTTGGAAAGGATGCCACTAATTCGTATGGACTTTGAATAGGG
Found at i:1489753 original size:36 final size:36
Alignment explanation
Indices: 1489700--1489916 Score: 209
Period size: 36 Copynumber: 5.9 Consensus size: 36
1489690 TTAACTAGGA
* * *
1489700 TGCCACCAACTCGTGTGGACTTTGAAAAGGCTTGGT
1 TGCCACCGACTTGTGTGGACTTTGAAAAGGTTTGGT
* * * * *
1489736 TGCCAGCTACTTATGTGGACTTTGGAAAGGCTTGGT
1 TGCCACCGACTTGTGTGGACTTTGAAAAGGTTTGGT
* * * ***
1489772 TACCATCGATTTGTGTGGACTTTGACTGGGGTTTGGT
1 TGCCACCGACTTGTGTGGACTTTGA-AAAGGTTTGGT
* * *
1489809 TGCCACCGACTTGTGTAGACTTTGACTAGGGTTTGGT
1 TGCCACCGACTTGTGTGGACTTTGA-AAAGGTTTGGT
* ** * *
1489846 TACCACTAACTTGTGTGGACATTGGAAAGGTTTGGT
1 TGCCACCGACTTGTGTGGACTTTGAAAAGGTTTGGT
1489882 TGCCACCGACTTGTGTGGACTTTGAAAAAGGTTTG
1 TGCCACCGACTTGTGTGGACTTTG-AAAAGGTTTG
1489917 ACACAAGTGT
Statistics
Matches: 146, Mismatches: 33, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
36 79 0.54
37 67 0.46
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (36 bp):
TGCCACCGACTTGTGTGGACTTTGAAAAGGTTTGGT
Found at i:1489871 original size:110 final size:109
Alignment explanation
Indices: 1489700--1489906 Score: 272
Period size: 110 Copynumber: 1.9 Consensus size: 109
1489690 TTAACTAGGA
* * *
1489700 TGCCACCAACTCGTGTGGACTTTGAAAAGGCTTGGTTGCCAGCTACTTATGTGGACTTTGGAAAG
1 TGCCACCAACTCGTGTAGACTTTGAAAAGGCTTGGTTACCAGCTACTTATGTGGACATTGGAAAG
* *
1489765 GCTTGGTTACCATCGATTTGTGTGGACTTTGACTGGGGTTTGGT
66 GCTTGGTTACCACCGACTTGTGTGGACTTTGACTGGGGTTTGGT
* * * * * *
1489809 TGCCACCGACTTGTGTAGACTTTGACTAGGGTTTGGTTACCA-CTAACTTGTGTGGACATTGGAA
1 TGCCACCAACTCGTGTAGACTTTGA-AAAGGCTTGGTTACCAGCT-ACTTATGTGGACATTGGAA
* *
1489873 AGGTTTGGTTGCCACCGACTTGTGTGGACTTTGA
64 AGGCTTGGTTACCACCGACTTGTGTGGACTTTGA
1489907 AAAAGGTTTG
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
109 24 0.29
110 59 0.71
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (109 bp):
TGCCACCAACTCGTGTAGACTTTGAAAAGGCTTGGTTACCAGCTACTTATGTGGACATTGGAAAG
GCTTGGTTACCACCGACTTGTGTGGACTTTGACTGGGGTTTGGT
Found at i:1489915 original size:73 final size:72
Alignment explanation
Indices: 1489702--1489916 Score: 209
Period size: 73 Copynumber: 2.9 Consensus size: 72
1489692 AACTAGGATG
* * * * * * * *
1489702 CCACCAACTCGTGTGGACTTTGAAAAGGCTTGGTTGCCAGCTACTTATGTGGACTTTG-GAAAGG
1 CCACTAACTTGTGTGGAC-TTGGAAAGGTTTGGTTGCCACCGACTTGTGTGGACTTTGAAAAAGG
*
1489766 CTTGGTTA
65 TTTGGTTA
* * * ** * ** *
1489774 CCA-TCGATTTGTGTGGACTTTGACTGGGGTTTGGTTGCCACCGACTTGTGTAGACTTTGACTAG
1 CCACT-AACTTGTGTGGACTTGGA--AAGGTTTGGTTGCCACCGACTTGTGTGGACTTTGAAAAA
1489838 GGTTTGGTTA
63 GGTTTGGTTA
1489848 CCACTAACTTGTGTGGACATTGGAAAGGTTTGGTTGCCACCGACTTGTGTGGACTTTGAAAAAGG
1 CCACTAACTTGTGTGGAC-TTGGAAAGGTTTGGTTGCCACCGACTTGTGTGGACTTTGAAAAAGG
1489913 TTTG
65 TTTG
1489917 ACACAAGTGT
Statistics
Matches: 111, Mismatches: 26, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
71 3 0.03
72 13 0.12
73 66 0.59
74 24 0.22
75 5 0.05
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.33
Consensus pattern (72 bp):
CCACTAACTTGTGTGGACTTGGAAAGGTTTGGTTGCCACCGACTTGTGTGGACTTTGAAAAAGGT
TTGGTTA
Found at i:1490233 original size:26 final size:27
Alignment explanation
Indices: 1490186--1490242 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
1490176 CATGTTTTAT
* * *
1490186 TTGATAAAGATCTTTGA-TAAAAGTTC
1 TTGATAAAGATCTTTAACAAAAACTTC
1490212 TTGATAATAG-TCTTTAACAAAAACTTC
1 TTGATAA-AGATCTTTAACAAAAACTTC
1490239 TTGA
1 TTGA
1490243 CATGAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (27 bp):
TTGATAAAGATCTTTAACAAAAACTTC
Found at i:1492151 original size:13 final size:13
Alignment explanation
Indices: 1492133--1492158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1492123 CAATTTTTTG
1492133 TGTATCGATACAT
1 TGTATCGATACAT
1492146 TGTATCGATACAT
1 TGTATCGATACAT
1492159 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1492895 original size:21 final size:21
Alignment explanation
Indices: 1492854--1492897 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1492844 CTCTCCTTTA
* *
1492854 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1492875 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1492896 TC
1 TC
1492898 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1494711 original size:13 final size:13
Alignment explanation
Indices: 1494693--1494731 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1494683 ATAATCACCC
1494693 TGTATCGATACAA
1 TGTATCGATACAA
1494706 TGTATCGATACAA
1 TGTATCGATACAA
1494719 TGTATCGATACAA
1 TGTATCGATACAA
1494732 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1496828 original size:15 final size:15
Alignment explanation
Indices: 1496808--1496838 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1496798 ATTTCGTTTG
*
1496808 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1496823 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1496838 G
1 G
1496839 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1498671 original size:21 final size:21
Alignment explanation
Indices: 1498642--1498686 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1498632 AAGTTTTCAT
*
1498642 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1498662 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1498684 TTT
1 TTT
1498687 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1500921 original size:13 final size:13
Alignment explanation
Indices: 1500903--1500928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1500893 CAATTTTTTG
1500903 TGTATCGATACAT
1 TGTATCGATACAT
1500916 TGTATCGATACAT
1 TGTATCGATACAT
1500929 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1504057 original size:79 final size:77
Alignment explanation
Indices: 1503934--1504235 Score: 336
Period size: 79 Copynumber: 3.8 Consensus size: 77
1503924 CTCTAAATAC
* ** *
1503934 GGGGTTGGGGTAT-CCCAAGATGAAAAATTTAGCATTTTGGAAATAAGATGAAGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGGAAATAA-AAG-AGGTTGGAGTATC
1503998 CCCTCAGAATTGAT
64 CCCTCAGAATTGAT
* * *
1504012 GGGGTTGGAGTATCCCTAAGATGAAAATTTTAATATTTTGGAAATAAAAGCAGGATTGGAATATC
1 GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGGAAATAAAAG-AGG-TTGGAGTATC
* * *
1504077 CCCTCAGAAATAAC
64 CCCTCAGAATTGAT
* * ** *
1504091 AGAGTTGGAGTATCCCCAAGATGAAAAAAATAATATTATGGAAATAAAAGCGAGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGGAAATAAAA--GAGGTTGGAGTATC
* *
1504156 TCCTCAAAATTGAT
64 CCCTCAGAATTGAT
* * * *
1504170 GAGGTTGGAGTATCCCCAAGATGAAAATTTTAAAATTTTGGAAATAAAAATGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGGAAAT-AAAA-GAGGTTGGAGTATC
1504235 C
64 C
1504236 TCTCGAGATG
Statistics
Matches: 184, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
78 17 0.09
79 159 0.86
80 7 0.04
81 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (77 bp):
GGGGTTGGAGTATCCCCAAGATGAAAAATTTAATATTTTGGAAATAAAAGAGGTTGGAGTATCCC
CTCAGAATTGAT
Found at i:1504276 original size:52 final size:51
Alignment explanation
Indices: 1504172--1504289 Score: 175
Period size: 52 Copynumber: 2.3 Consensus size: 51
1504162 AAATTGATGA
1504172 GGTTGGAGTATCCCCAAGATGAAAATTTTAAAATTTTGGAAATAAAAATGG
1 GGTTGGAGTATCCCCAAGATGAAAATTTTAAAATTTTGGAAATAAAAATGG
* *
1504223 GGTTGGAGTATCCTCTCGAGATGAAAGTTTTAAAA-TTTGGAAATAAAAATGG
1 GGTTGGAGTATCC-C-CAAGATGAAAATTTTAAAATTTTGGAAATAAAAATGG
* *
1504275 GGTTTGACTATCCCC
1 GGTTGGAGTATCCCC
1504290 TTGGAATTGA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
50 1 0.02
51 14 0.23
52 29 0.48
53 17 0.28
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAAGATGAAAATTTTAAAATTTTGGAAATAAAAATGG
Found at i:1504348 original size:210 final size:209
Alignment explanation
Indices: 1504010--1504447 Score: 540
Period size: 210 Copynumber: 2.1 Consensus size: 209
1504000 CTCAGAATTG
* *
1504010 ATGGGGTTGGAGTATCCCTAAGATGAAAATTTTAATATTTTGGAAATAAAAGCAGGATTGGAATA
1 ATGGGGTTGGAGTATCCCTAAGATGAAAATTTTAATAATTTGGAAATAAAAACAGGATTGGAATA
1504075 TCCCCTCAGAAATAACAGAGTTGGAGTATCCCCAAGATGAAAAAAATAATATTATGGAAATAAAA
66 TCCCCTCAGAAATAACAGAGTTGGAGTATCCCCAAGATGAAAAAAATAATATTATGGAAATAAAA
* *
1504140 GCGAGGTTGGAGTAT-CTCCTCA-AAATTGATGAGGTTGGAGTATCCCCAAGATGAAAATTTTAA
131 GCGAGGTTGGAGTATCCT-CTCAGAAA-TAATGAGGTTGGAGTATCCCCAAGATAAAAATTTTAA
1504203 AATTTTGGAAATAAAA
194 AATTTTGGAAATAAAA
* * ** * * *
1504219 ATGGGGTTGGAGTATCCTCTCGAGATGAAAGTTTTAA-AATTTGGAAATAAAAATGGGGTTTGAC
1 ATGGGGTTGGAGTATCC-CT-AAGATGAAAATTTTAATAATTTGGAAATAAAAACAGGATTGGAA
** * * ** * *** * *
1504283 TATCCCCTTGGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGTAAATAA
64 TATCCCCTCAGAAATAACAGAGTTGGAGTATCCCCAAGATGAAAAAAATAATATTATGGAAATAA
* * * *
1504348 AAGCGGGGTTGGAGTATCCTTTCAGAAATAATGGGGTTGGAGTATCCCCGAGATAAAAATTTTAA
129 AAGCGAGGTTGGAGTATCCTCTCAGAAATAATGAGGTTGGAGTATCCCCAAGATAAAAATTTTAA
* *
1504413 TATTTTGTAAATAAAA
194 AATTTTGGAAATAAAA
* *
1504429 ATGAGGTTAGAGTATCCCT
1 ATGGGGTTGGAGTATCCCT
1504448 TCGGAATTGA
Statistics
Matches: 194, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
209 19 0.10
210 156 0.80
211 19 0.10
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (209 bp):
ATGGGGTTGGAGTATCCCTAAGATGAAAATTTTAATAATTTGGAAATAAAAACAGGATTGGAATA
TCCCCTCAGAAATAACAGAGTTGGAGTATCCCCAAGATGAAAAAAATAATATTATGGAAATAAAA
GCGAGGTTGGAGTATCCTCTCAGAAATAATGAGGTTGGAGTATCCCCAAGATAAAAATTTTAAAA
TTTTGGAAATAAAA
Found at i:1504366 original size:79 final size:80
Alignment explanation
Indices: 1504219--1504918 Score: 751
Period size: 79 Copynumber: 8.8 Consensus size: 80
1504209 GGAAATAAAA
* * * * *
1504219 ATGGGGTTGGAGTATCCTCTCGAGATGAAAGTTTTAA-AATTTGGAAATAAAAATGGGGTTTGAC
1 ATGGGGTTGGAGTATCC-C-CGAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAG
1504283 TATCCCCTT-GGAATTG
64 TATCCCCTTCGGAATTG
* * ***
1504299 ATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGTAAATAAAAGCGGGGTTGGAGTA
1 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTA
* * * *
1504364 T-CCTTTCAGAAATA
66 TCCCCTTCGGAATTG
* * *
1504378 ATGGGGTTGGAGTATCCCCGAGATAAAAATTTTAATATTTTGTAAATAAAAAT-GAGGTTAGAGT
1 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAATAG-GGTTGGAGT
1504442 AT-CCCTTCGGAATTG
65 ATCCCCTTCGGAATTG
1504457 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTA
1 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTA
*
1504522 TCCCC-TCGAAATTG
66 TCCCCTTCGGAATTG
* * * *
1504536 AGGGGGTTGGAGTATCCCCAAGATGAAAATTTTAAAATTTTGGAAATAAAAACT-GGGTTGGAAT
1 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAA-TAGGGTTGGAGT
* * *
1504600 AT-CCCTTCGAAAATA
65 ATCCCCTTCGGAATTG
** *** * *
1504615 ACAGGGTTGGAGTATCTTTGAGATGAAAATTTTAATATGTTGGAAATAAAAATAGGGTTGCAGTA
1 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTA
* *
1504680 T-TCCTTCAGAATTG
66 TCCCCTTCGGAATTG
* * * * *
1504694 AAGGGGTTGGAGTCTCCCCAAGATG-AAATTTTAAAATTTTGGAAATAAAAACT-GGGTTGGAAT
1 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAA-TAGGGTTGGAGT
* *
1504757 ATCCCC-TCGGAAATA
65 ATCCCCTTCGGAATTG
*** *** * * *
1504772 ACAAGGTTGGAGTATCTTTGAGATGAAAAATTTAATATTTTGGAAATAAAAATTGGGTTGCAGTA
1 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTA
*
1504837 T-CCCTTTGGAATTG
66 TCCCCTTCGGAATTG
* * * * **
1504851 AAGGGGTTGGAGTCTCCCCAAGATGAAAAATTTAATATTTTGGAAATAAAAGCAGGGTTGGAGTA
1 ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTA
1504916 TCC
66 TCC
1504919 TCGAGATGAA
Statistics
Matches: 518, Mismatches: 88, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
78 85 0.16
79 410 0.79
80 23 0.04
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (80 bp):
ATGGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTA
TCCCCTTCGGAATTG
Found at i:1504488 original size:289 final size:289
Alignment explanation
Indices: 1503994--1504530 Score: 799
Period size: 289 Copynumber: 1.9 Consensus size: 289
1503984 AAGGTTGGAG
*
1503994 TATCCCCTCAGAATTGATGGGGTTGGAGTATCCCTAAGATGAAAATTTTAATATTTTGGAAATAA
1 TATCCCCTCAGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAA
1504059 AAGCAGGATTGGAATATCCCCTCAGAAATAACAGAGTTGGAGTATCCCCAAGATGAAAAAAATAA
66 AAGCAGGATTGGAATATCCCCTCAGAAATAACAGAGTTGGAGTATCCCCAAGATGAAAAAAATAA
* *
1504124 TATTATGGAAATAAAAGCGAGGTTGGAGTATCTCCTCAAAATTGATGAGGTTGGAGTATCCCCAA
131 TATTATGGAAATAAAAACGAGGTTAGAGTATCTCCTCAAAATTGATGAGGTTGGAGTATCCCCAA
* *
1504189 GATGAAAATTTTAAAATTTTGGAAATAAAAATGGGGTTGGAGTATCCTCTCGAGATGAAAGTTTT
196 GATGAAAATTTTAAAATTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCGAGATGAAAGTTTT
1504254 AAAATTTGGAAATAAAAATGGGGTTTGAC
261 AAAATTTGGAAATAAAAATGGGGTTTGAC
** *
1504283 TATCCCCTTGGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGTAAATAA
1 TATCCCCTCAGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAA
* * * ** ** * * **
1504348 AAGCGGGGTTGGAGTATCCTTTCAGAAATAATGGGGTTGGAGTATCCCCGAGAT-AAAAATTTTA
66 AAGCAGGATTGGAATATCCCCTCAGAAATAACAGAGTTGGAGTATCCCCAAGATGAAAAA-AATA
* * * ** *
1504412 ATATTTTGTAAATAAAAATGAGGTTAGAGTATC-CCTTCGGAATTGATGGGGTTGGAGTATCCCC
130 ATATTATGGAAATAAAAACGAGGTTAGAGTATCTCC-TCAAAATTGATGAGGTTGGAGTATCCCC
* *
1504476 GAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCGA
194 AAGATGAAAATTTTAAAATTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCGA
1504531 AATTGAGGGG
Statistics
Matches: 219, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
288 7 0.03
289 212 0.97
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (289 bp):
TATCCCCTCAGAATTGATGGGGTTGGAGTATCCCCAAGATGAAAATTTTAATATTTTGGAAATAA
AAGCAGGATTGGAATATCCCCTCAGAAATAACAGAGTTGGAGTATCCCCAAGATGAAAAAAATAA
TATTATGGAAATAAAAACGAGGTTAGAGTATCTCCTCAAAATTGATGAGGTTGGAGTATCCCCAA
GATGAAAATTTTAAAATTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTCGAGATGAAAGTTTT
AAAATTTGGAAATAAAAATGGGGTTTGAC
Found at i:1504914 original size:51 final size:51
Alignment explanation
Indices: 1504854--1504952 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
1504844 GGAATTGAAG
* * *
1504854 GGGTTGGAGTCTCCCCAAGATGAAAAATTTAATA-TTTTGGAAATAAAAGCA
1 GGGTTGGAGTATCCCCAAGATGAAAAA-TCAATATTTTTGGAAAGAAAAGCA
* *
1504905 GGGTTGGAGTATCCTCGAGATGAAAAATCAATATTTTTGGAAAGAAAA
1 GGGTTGGAGTATCCCCAAGATGAAAAATCAATATTTTTGGAAAGAAAA
1504953 AATTTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 5 0.12
51 37 0.88
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.27
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCAAGATGAAAAATCAATATTTTTGGAAAGAAAAGCA
Found at i:1504989 original size:157 final size:155
Alignment explanation
Indices: 1504476--1504966 Score: 512
Period size: 157 Copynumber: 3.1 Consensus size: 155
1504466 GAGTATCCCC
* * * * * * * *
1504476 GAGATGAAAATTTTAATATTTTGGAAATAAAAATAGGGTTGGAGTATCCCCTC-GAAATTGAGGG
1 GAGAAGAAAAATTTAAAAATTTGGAAATAAAAATTGGGTTGCAGTATCCCTTCAG-AATTGAAGG
* *
1504540 GGTTGGAGTATCCCCAAGATGAAAATTTTAAAATTTTGGAAATAAAAACTGGGTTGGAATATCCC
65 GGTTGGAGTCTCCCCAAGATGAAAA-TTTAAAATTTTGGAAATAAAAACAGGGTTGGAATATCCC
* * * * *
1504605 TTCGAAAATAACAGGGTTGGAGTATCTTT
129 -TCGGAAATAACA-AGATGCAATATCTTT
* * * * *
1504634 GAGATG-AAAATTTTAATATGTTGGAAATAAAAATAGGGTTGCAGTATTCCTTCAGAATTGAAGG
1 GAGAAGAAAAATTTAAAAAT-TTGGAAATAAAAATTGGGTTGCAGTATCCCTTCAGAATTGAAGG
* *
1504698 GGTTGGAGTCTCCCCAAGATGAAATTTTAAAATTTTGGAAATAAAAACTGGGTTGGAATATCCCC
65 GGTTGGAGTCTCCCCAAGATGAAAATTTAAAATTTTGGAAATAAAAACAGGGTTGGAATAT-CCC
* * *
1504763 TCGGAAATAACAAGGTTGGAGTATCTTT
129 TCGGAAATAACAA-GATGCAATATCTTT
* * * **
1504791 GAGATGAAAAATTTAATATTTTGGAAATAAAAATTGGGTTGCAGTATCCCTTTGGAATTGAAGGG
1 GAGAAGAAAAATTTAAAAATTTGGAAATAAAAATTGGGTTGCAGTATCCCTTCAGAATTGAAGGG
* * *
1504856 GTTGGAGTCTCCCCAAGATGAAAAATTTAATATTTTGGAAATAAAAGCAGGGTTGGAGTAT-CCT
66 GTTGGAGTCTCCCCAAGATG-AAAATTTAAAATTTTGGAAATAAAAACAGGGTTGGAATATCCCT
* *
1504920 C-GAGATGAA-AA-AT-CAATATTTTT
130 CGGAAAT-AACAAGATGCAATATCTTT
1504943 G-GAAAGAAAAAATTTAAAAATTTG
1 GAG-AAG-AAAAATTTAAAAATTTG
1504967 ACAAAAATAC
Statistics
Matches: 290, Mismatches: 34, Indels: 23
0.84 0.10 0.07
Matches are distributed among these distances:
151 1 0.00
152 10 0.03
153 16 0.06
155 6 0.02
156 6 0.02
157 136 0.47
158 114 0.39
159 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (155 bp):
GAGAAGAAAAATTTAAAAATTTGGAAATAAAAATTGGGTTGCAGTATCCCTTCAGAATTGAAGGG
GTTGGAGTCTCCCCAAGATGAAAATTTAAAATTTTGGAAATAAAAACAGGGTTGGAATATCCCTC
GGAAATAACAAGATGCAATATCTTT
Found at i:1513705 original size:20 final size:19
Alignment explanation
Indices: 1513680--1513733 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1513670 GTTTGAAGCA
1513680 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATATC--C
*
1513700 ATGTATCGATATAATATGCC
1 ATGTATCGATACAATAT-CC
1513720 ATGTATCGATACAA
1 ATGTATCGATACAA
1513734 ACAGTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATATCC
Found at i:1513787 original size:20 final size:19
Alignment explanation
Indices: 1513762--1513815 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1513752 TTGCCAGTTT
***
1513762 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TAAA
*
1513782 CATGTATCAATACAATAAA
1 CATGTATCGATACAATAAA
1513801 CATGTATCGATACAA
1 CATGTATCGATACAA
1513816 AGTATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:1514772 original size:33 final size:33
Alignment explanation
Indices: 1514730--1514796 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1514720 AAGTGCACTA
* *
1514730 AAGTGCTCATCCATGCGCTGCGAGAGTGAAGTG
1 AAGTGCTCATCCATGCGCTACGAAAGTGAAGTG
* * *
1514763 AAGTGCTCATTCATGTGCTATGAAAGTGAAGTG
1 AAGTGCTCATCCATGCGCTACGAAAGTGAAGTG
1514796 A
1 A
1514797 TCAACTCTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (33 bp):
AAGTGCTCATCCATGCGCTACGAAAGTGAAGTG
Found at i:1520801 original size:3 final size:3
Alignment explanation
Indices: 1520793--1520825 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1520783 TCCGAGTCAA
*
1520793 CAT CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1520826 TGTCTTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
CAT
Found at i:1522557 original size:32 final size:33
Alignment explanation
Indices: 1522516--1522578 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
1522506 ACAATTGCGC
*
1522516 ATGTATCGATACAATG-A-ACATGTATCGATAAA
1 ATGTATCGATACAAAGCATA-ATGTATCGATAAA
1522548 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
1522579 CATACAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATAAA
Found at i:1528152 original size:168 final size:164
Alignment explanation
Indices: 1527941--1528290 Score: 379
Period size: 168 Copynumber: 2.1 Consensus size: 164
1527931 AATCATCATT
** **
1527941 TTAGTTTTGAAAATTTTATTTTTTATGAGCTTTTCATTTTTTTCCTT-AAGATTTCCTTATTTCC
1 TTAGTTTTGAAAATTTTATTTTTTATGAGCTTTTCATTTTTTTCCTTGAA-ATGCCCTTACGTCC
* * ** * *
1528005 AAAAAACTCAAA-TTTCTATTCCATAAAGGTTTTCGCTGCGGTTTTTCTT-GATTTGAAATTTTT
65 AAAAAACT-AAATTTTCTATTCCATAAAAGTTCTCGAAG-GGATTTTCTTCGATTTAAAATTTTT
1528068 A-ATATTCATCAAATATCATCACTTAATTCATAATAAA
128 AGA-ATTCATCAAATATCATCACTTAATTCATAATAAA
* *
1528105 TTAGTTTTGAAAAATTCATATATTTTTTCATGAGTTTTTCA-TTTTTTCTTTGAAATGCCCTTAC
1 TTAGTTTTG-AAAATT--T-TATTTTTT-ATGAGCTTTTCATTTTTTTCCTTGAAATGCCCTTAC
* *
1528169 GTCCAAAAAACTAAATTTTCTATTGCATAAAAGTTCTCGAAGGGATTTTCTTCGGTTTAAAATTT
61 GTCCAAAAAACTAAATTTTCTATTCCATAAAAGTTCTCGAAGGGATTTTCTTCGATTTAAAATTT
* ** * ** *
1528234 TTAGAATTCATCTAATATTGTCA-TTAAACTCCCATTAAA
126 TTAGAATTCATCAAATATCATCACTT-AATTCATAATAAA
1528273 TTAGTTTTGAAAATTTTA
1 TTAGTTTTGAAAATTTTA
1528291 ATTTATTTCA
Statistics
Matches: 155, Mismatches: 21, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
164 11 0.07
165 7 0.05
167 21 0.14
168 102 0.66
169 14 0.09
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (164 bp):
TTAGTTTTGAAAATTTTATTTTTTATGAGCTTTTCATTTTTTTCCTTGAAATGCCCTTACGTCCA
AAAAACTAAATTTTCTATTCCATAAAAGTTCTCGAAGGGATTTTCTTCGATTTAAAATTTTTAGA
ATTCATCAAATATCATCACTTAATTCATAATAAA
Found at i:1528806 original size:10 final size:10
Alignment explanation
Indices: 1528784--1528814 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1528774 TGGAGCAAAT
1528784 AAAGAAA-AA
1 AAAGAAAGAA
1528793 AAAGAAAGAA
1 AAAGAAAGAA
1528803 AAAGAAAGAA
1 AAAGAAAGAA
1528813 AA
1 AA
1528815 GATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:1528806 original size:19 final size:19
Alignment explanation
Indices: 1528784--1528830 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1528774 TGGAGCAAAT
1528784 AAAGAAAAAAAAGA-AAGAA
1 AAAGAAAAAAAAGATAA-AA
*
1528803 AAAGAAAGAAAAGATAAAA
1 AAAGAAAAAAAAGATAAAA
*
1528822 AAATAAAAA
1 AAAGAAAAA
1528831 TTAGTTAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAGAAAAAAAAGATAAAA
Found at i:1528824 original size:10 final size:9
Alignment explanation
Indices: 1528784--1528830 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
1528774 TGGAGCAAAT
1528784 AAAGAAAAA
1 AAAGAAAAA
1528793 AAAGAAAGAA
1 AAAGAAA-AA
*
1528803 AAAGAAAGA
1 AAAGAAAAA
1528812 AAAGATAAAA
1 AAAGA-AAAA
*
1528822 AAATAAAAA
1 AAAGAAAAA
1528831 TTAGTTAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:1529689 original size:17 final size:17
Alignment explanation
Indices: 1529669--1529705 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1529659 AAAATTTTTG
1529669 AAAATAAAA-AATAAAAT
1 AAAATAAAATAAT-AAAT
1529686 AAAATAAAATAATAAAT
1 AAAATAAAATAATAAAT
1529703 AAA
1 AAA
1529706 TATTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATAAAATAATAAAT
Found at i:1534487 original size:159 final size:161
Alignment explanation
Indices: 1534269--1534724 Score: 622
Period size: 159 Copynumber: 2.8 Consensus size: 161
1534259 CAAAACTCTT
* * * *
1534269 GAAAACGAATTAATTTTTTAAAAC-AGAATTAATAT-AATTAAATAATGATGTTTGATGAATTTT
1 GAAAATGAATGAATTTTTGAAAACTA-AATTAATATGAAATAAATAATGATGTTTGATGAATTTT
*
1534332 AAAAATTGAAAACCGAGAAAAATCCTCTCGAAAAAATTTACGGAGTAGAAAACATCGTATTTCGA
65 AAAAATTGAAAACCGAGAAAAATCC-CTCAAAAAAATTTACGGAGTAGAAAACATCGTATTTCGA
**
1534397 AAAAAGAA-AGTTTCAAGG-AA-AAAAATTCAG
129 AAAAAGAAGAGTTTCAAGGAAATAAAAAACCAG
* *
1534427 GAACATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATGTTGTTTGATGAATTTTA
1 GAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATGATGTTTGATGAATTTTA
*
1534492 AAAATTGAAAACTC-AGAAAAATCCCATCAAAAAAATTTACGGAGTAGAAAACATCGTATTTTGA
66 AAAATTGAAAAC-CGAGAAAAATCCC-TCAAAAAAATTTACGGAGTAGAAAACATCGTATTTCGA
* *
1534556 AAAAATAAGAGTTTCAAGGAAAAAATAAAAAACCAT
129 AAAAAGAAGAGTTTCAAGG---AAATAAAAAACCAG
*
1534592 GAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTA
1 GAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATGATGTTTGATGAATTTTA
* * * *
1534657 AAAATTGTAAACTGAGAAAAATCCC-CTAAAAAAATTTACAGAGTAGAAAACA-CAGTTTTTCGA
66 AAAATTGAAAACCGAGAAAAATCCCTC-AAAAAAATTTACGGAGTAGAAAACATC-GTATTTCGA
1534720 AAAAA
129 AAAAA
1534725 AGGGGAGTTT
Statistics
Matches: 265, Mismatches: 20, Indels: 20
0.87 0.07 0.07
Matches are distributed among these distances:
158 30 0.11
159 93 0.35
160 11 0.04
163 2 0.01
164 38 0.14
165 91 0.34
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.28
Consensus pattern (161 bp):
GAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATGATGTTTGATGAATTTTA
AAAATTGAAAACCGAGAAAAATCCCTCAAAAAAATTTACGGAGTAGAAAACATCGTATTTCGAAA
AAAGAAGAGTTTCAAGGAAATAAAAAACCAG
Found at i:1534735 original size:165 final size:165
Alignment explanation
Indices: 1534187--1534737 Score: 644
Period size: 165 Copynumber: 3.4 Consensus size: 165
1534177 AAACCAAGAC
* * * * * * * *
1534187 AAATCTCC-CAAAAATAATTTACGAAGAAG-AAACCTCGATTTCTCCAAAAAAGGAGAATTTCAA
1 AAATCCCCTCAAAAA-AATTTACGGAGTAGAAAACATCG-TTTTTCGAAAAAAAGAGAGTTTCAA
* ** * * * * * *
1534250 -CAAAAAATCCAAAACTCTTGAAAACGAATTAATTTTTTAAAACAGAATTAATAT-AATTAAATA
64 GGAAAAAATAAAAAAC-CATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATA
*
1534313 ATGATGTTTGATGAATTTTAAAAATTGAAAACCGAGAA
128 ATGATGTTTGATGAATTTTAAAAATTGAAAACTGAGAA
* * * *
1534351 AAATCCTCTCGAAAAAATTTACGGAGTAGAAAACATCGTATTTCG-AAAAAAGAAAGTTTCAAGG
1 AAATCCCCTCAAAAAAATTTACGGAGTAGAAAACATCGTTTTTCGAAAAAAAGAGAGTTTCAAGG
** * * *
1534415 ----AA-AAAAATTCAGGAACATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATAATG
66 AAAAAATAAAAAACCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATG
* *
1534475 TTGTTTGATGAATTTTAAAAATTGAAAACTCAGAA
131 ATGTTTGATGAATTTTAAAAATTGAAAACTGAGAA
*
1534510 AAATCCCATCAAAAAAATTTACGGAGTAGAAAACATCGTATTTT-GAAAAAATA-AGAGTTTCAA
1 AAATCCCCTCAAAAAAATTTACGGAGTAGAAAACATCGT-TTTTCGAAAAAA-AGAGAGTTTCAA
1534573 GGAAAAAATAAAAAACCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAA
64 GGAAAAAATAAAAAACCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAA
*
1534638 TGATGTTTGATGAATTTTAAAAATTGTAAACTGAGAA
129 TGATGTTTGATGAATTTTAAAAATTGAAAACTGAGAA
* *
1534675 AAATCCCCT-AAAAAAATTTACAGAGTAGAAAACA-CAGTTTTTCGAAAAAAAGGGGAGTTTCAA
1 AAATCCCCTCAAAAAAATTTACGGAGTAGAAAACATC-GTTTTTCGAAAAAAA-GAGAGTTTCAA
1534738 AATAAATTAA
Statistics
Matches: 326, Mismatches: 45, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
158 30 0.09
159 83 0.25
160 21 0.06
161 1 0.00
163 20 0.06
164 57 0.17
165 114 0.35
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.27
Consensus pattern (165 bp):
AAATCCCCTCAAAAAAATTTACGGAGTAGAAAACATCGTTTTTCGAAAAAAAGAGAGTTTCAAGG
AAAAAATAAAAAACCATGAAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAATG
ATGTTTGATGAATTTTAAAAATTGAAAACTGAGAA
Found at i:1534846 original size:124 final size:124
Alignment explanation
Indices: 1534618--1534861 Score: 343
Period size: 124 Copynumber: 2.0 Consensus size: 124
1534608 TTGAAAACTG
* *
1534618 AATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGTAAACTGAGAAAAATCCCC
1 AATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACAGAGAAAAATCCCC
*
1534683 TAAAAAAATTTACAGAGTAGAAAACACAGTTTTTCGAAAAAAAGGGGAGTTTCAAAATA
66 TAAAAAAATTTACAGAGTAGAAAACACAGTTTTTCGAAAAAAAGGAGAGTTTCAAAATA
*
1534742 AATTAATATGAAATAAATAATGATGTTTGATGAA-TTTAAAAATTGAAAACAGAGAAAAATCTCC
1 AATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACAGAGAAAAATCCCC
* ** * *
1534806 TCAGAAAAATTT-GTGAAGTAGAAAATATC-GTATTTT-GAAAAAAATGAGAGTTTCAA
66 T-AAAAAAATTTACAG-AGTAGAAAACA-CAGT-TTTTCGAAAAAAAGGAGAGTTTCAA
1534862 GGAAAAACCA
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
123 29 0.27
124 73 0.68
125 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (124 bp):
AATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTGAAAACAGAGAAAAATCCCC
TAAAAAAATTTACAGAGTAGAAAACACAGTTTTTCGAAAAAAAGGAGAGTTTCAAAATA
Found at i:1536793 original size:126 final size:126
Alignment explanation
Indices: 1536556--1536786 Score: 288
Period size: 126 Copynumber: 1.8 Consensus size: 126
1536546 GTCGATGGGC
** ** * *
1536556 AAATGAAAGATGAAGAAGTCTCCCAAGTCTAAGCCGACGGGTAGATAAAAGATGAAGAAGTCTTC
1 AAATGAAAGATGAAGAAGTCTCCCAAGAATAAGCCGACGGACAGACAAAAGATGAAGAAGTCTCC
*
1536621 CAGGTCTGAGTTGATGGGAAAACAATTGATGAAGAAGTCTCTCGAGTTCGAGCCAATAGGA
66 CAGGTCTGAGCTGATGGGAAAACAATTGATGAAGAAGTCTCTCGAGTTCGAGCCAATAGGA
* * * *
1536682 AAATGAAAGATGAAGAAGTTTCCCAGGAATAAGCCGATGGACAGACGAAAGATGAAGGAA-TCTC
1 AAATGAAAGATGAAGAAGTCTCCCAAGAATAAGCCGACGGACAGACAAAAGATGAA-GAAGTCTC
* **
1536746 CCAGGTGTGAGCCT-ATAGGG-AAATGATTGATGAAGAAGTCT
65 CCAGGTCTGAG-CTGAT-GGGAAAACAATTGATGAAGAAGTCT
1536787 TCCGAGTCTA
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
126 81 0.92
127 7 0.08
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (126 bp):
AAATGAAAGATGAAGAAGTCTCCCAAGAATAAGCCGACGGACAGACAAAAGATGAAGAAGTCTCC
CAGGTCTGAGCTGATGGGAAAACAATTGATGAAGAAGTCTCTCGAGTTCGAGCCAATAGGA
Found at i:1549457 original size:129 final size:131
Alignment explanation
Indices: 1549294--1549529 Score: 336
Period size: 130 Copynumber: 1.8 Consensus size: 131
1549284 TCAAAAAGTG
* *
1549294 TCATTTCGTACCTTAATGGATACCTGCAAAGATACGAAAAGTTTTTCAG-AATCTTTTATAC-CC
1 TCATTTCGTACCTTAATGGAAACC-GCAAAGATACAAAAAGTTTTT-AGAAATCTTTTATACTCC
** * *
1549357 TACGGATACCCATAGGAATATAAAAAATTTA-AAAATGATTAATATTTATTTATTTTTGAAAAAA
64 TACAAATACCCATAGAAATATAAAAAATTGAGAAAATGATTAATATTTATTTATTTTTGAAAAAA
1549421 AAA
129 AAA
* *
1549424 TCATTTCGTACCTTACTGGAAACC-CAAAAGATACAAAAAGTTTTTTGAAATCTTTTATACTCCT
1 TCATTTCGTACCTTAATGGAAACCGC-AAAGATACAAAAAGTTTTTAGAAATCTTTTATACTCCT
*
1549488 ACAAATACCCATAGAAATATAAAAGATTGAGAAAATGATTAA
65 ACAAATACCCATAGAAATATAAAAAATTGAGAAAATGATTAA
1549530 CAGTTGTTGC
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
128 2 0.02
129 30 0.32
130 50 0.54
131 11 0.12
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (131 bp):
TCATTTCGTACCTTAATGGAAACCGCAAAGATACAAAAAGTTTTTAGAAATCTTTTATACTCCTA
CAAATACCCATAGAAATATAAAAAATTGAGAAAATGATTAATATTTATTTATTTTTGAAAAAAAA
A
Found at i:1550413 original size:11 final size:12
Alignment explanation
Indices: 1550397--1550427 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1550387 GTTTTTACTA
1550397 TTTTTCTTTCT-
1 TTTTTCTTTCTC
1550408 TTTTTCTTTCTC
1 TTTTTCTTTCTC
1550420 TTTTTCTT
1 TTTTTCTT
1550428 CTCATTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTCTC
Done.