Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold109
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: 1855911
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.34
Warning! 69956 characters in sequence are not A, C, G, or T
File 9 of 13
Found at i:1187431 original size:24 final size:24
Alignment explanation
Indices: 1187399--1187449 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1187389 TAAACTTGTC
*
1187399 AAGATTTAAATCTTATTTTTTCCT
1 AAGATTTAAATCTTATTTTTGCCT
1187423 AAGATTTAAATCTTATTTTTGCCT
1 AAGATTTAAATCTTATTTTTGCCT
1187447 AAG
1 AAG
1187450 TTATTGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (24 bp):
AAGATTTAAATCTTATTTTTGCCT
Found at i:1188427 original size:27 final size:27
Alignment explanation
Indices: 1188370--1188442 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
1188360 CTTCACAATC
1188370 GGGGATACTCCAACCCCGTTAATCATCA
1 GGGGATACTCCAACCCCGTTAATCA-CA
*
1188398 -GGGATACTCCAACCCCGTTATTTC-CGA
1 GGGGATACTCCAACCCCGTTA-ATCAC-A
*
1188425 GGGGACACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1188443 GCTTTATTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.25, C:0.36, G:0.21, T:0.19
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCACA
Found at i:1201025 original size:14 final size:13
Alignment explanation
Indices: 1201006--1201039 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1200996 CCTTCTCTTC
*
1201006 AAAAAAAAAGCAA
1 AAAAAAAAAACAA
1201019 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
1201032 AGAAAAAA
1 AAAAAAAA
1201040 GAGAGAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:1202172 original size:55 final size:55
Alignment explanation
Indices: 1202050--1203200 Score: 1160
Period size: 55 Copynumber: 19.9 Consensus size: 55
1202040 GATGCCTTTT
*
1202050 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC-GAGACGCCTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAG-GACG----C
1202109 TCTTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
1 -C-TTTTAAAGCCCACACAAGTTGGTGGCATCTTCC-AGTCCTCAAAGAGCAGGACGC
1202166 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTT-CCAGTCCTCAAAGAGCAGGACG------C
*
1202227 CTTTTAAAGCCCACACAACTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCC-AGTCCTCAAAGAGCAGGACGC
*
1202282 CTCTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTT-CCAGTCCTCAAAGAGCAGGACG------C
* * *
1202343 CTTTTAAAGCCCACATAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGTAGGATGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCC-AGTCCTCAAAGAGCAGGACGC
* *
1202398 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC
* * **
1202453 CTCTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAATCCTCAAAGAGCAGGATAC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCC-AGTCCTCAAAGAGCAGGACGC
1202508 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGCC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCC-AGTCCTCAAAGAGCAGGACG-C
* * *
1202564 TTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGC
1 --C-T-TTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC
* * *
1202624 CTTTTAAAGCCCACCCAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC
* * *
1202678 TTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAAAGCAGGACGCC
1 -----CTTTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACG-C
* * *
1202740 TTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCC
1 ----CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACG-C
* * * *
1202799 TTCTTCTTTCAAAGCCTACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGC
1 --C-T-TTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC
* * * *
1202859 CTTTTAAAGCCCACCCAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGATGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC
* *
1202913 TTTTTCTTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCC-CTAAAGAGCAGGACGCC
1 -----CTTTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTC-AAAGAGCAGGACG-C
* *
1202975 TTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCC
1 ----CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACG-C
* * * *
1203034 TTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAATCCTCAAAGAGCAGGACAC
1 --C-T-TTT-AAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC
* * * *
1203094 CTTTCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC
* * **
1203149 CTTTCAAAGCCCACACGAGTTGGTGGCA-CTTTTTAGTCCTCAAAGAGCAGGA
1 CTTTTAAAGCCCACACAAGTTGGTGGCATC-TTCCAGTCCTCAAAGAGCAGGA
1203201 TATACTTTAT
Statistics
Matches: 963, Mismatches: 73, Indels: 115
0.84 0.06 0.10
Matches are distributed among these distances:
54 46 0.05
55 381 0.40
56 18 0.02
57 10 0.01
58 6 0.01
59 58 0.06
60 160 0.17
61 277 0.29
62 7 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAGAGCAGGACGC
Found at i:1202185 original size:116 final size:115
Alignment explanation
Indices: 1202050--1203200 Score: 1416
Period size: 116 Copynumber: 10.0 Consensus size: 115
1202040 GATGCCTTTT
*
1202050 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGC-GAGACGCCTTCTCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAG-GACGCCTTCTCTTT
*
1202114 TTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
64 TCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
*
1202166 CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTT-TCAGTCCTCAAAGAGCAGGACGCCTTCT-CTTT
*
1202231 T-AAAGCCCACACAACTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
64 TCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
* *
1202282 CTCTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTT-TCAGTCCTCAAAGAGCAGGACGCCTTCT-CTTT
* * *
1202347 T-AAAGCCCACATAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGTAGGATGC
64 TCAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
* *
1202398 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGAC-AC--CTC--TT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACGCCTTCTCTTTT
* **
1202458 -AAAGCCCACACAAGTTGGTGGCACTTCCTAATCCTCAAAGAGCAGGATAC
65 CAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
*
1202508 CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCCTTCT-TCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCCTCAAAGAGCAGGACGCCTTCTCT-TT
* * *
1202572 TCAAAGCCCACACAAGTTGGTGGCATTTTCC-AATCCTCAAAGAGCAGGATGC
64 TCAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
* * * * *
1202624 CTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCTTTTC
* * *
1202689 AAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCCCAAAAAGCAGGACGCC
66 AAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG-C
* * *
1202740 TTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTCT-T
1 ----CTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCT
* * * *
1202804 CTTTCAAAGCCTACACAAGTTGGTGGCATTTTCC-AATCCTCAAAGAGCAGGATGC
62 -TTTCAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
* * * *
1202859 CTTTTAAAGCCCACCCAAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCTTTT
* *
1202923 CAAAGCCCACACAAGTTAGTGGCATTTTCC-AGTCC-CTAAAGAGCAGGACGCC
65 CAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTC-AAAGAGCAGGACG-C
* *
1202975 TTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCT-T
1 ----CTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCT
** * *
1203039 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTCAATCCTCAAAGAGCAGGACAC
62 -TTTCAAAGCCCACACAAGTTGGTGGCACTTCCT-AGTCCTCAAAGAGCAGGACGC
* *
1203094 CTTTCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG----C-C-TTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCTTTT
* **
1203153 CAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
65 CAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGA
1203201 TATACTTTAT
Statistics
Matches: 935, Mismatches: 64, Indels: 78
0.87 0.06 0.07
Matches are distributed among these distances:
109 1 0.00
110 140 0.15
111 6 0.01
112 2 0.00
113 4 0.00
114 1 0.00
115 199 0.21
116 368 0.39
117 10 0.01
118 2 0.00
119 7 0.01
120 194 0.21
121 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (115 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCTTTTC
AAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGC
Found at i:1202823 original size:235 final size:234
Alignment explanation
Indices: 1202019--1203200 Score: 1555
Period size: 235 Copynumber: 5.1 Consensus size: 234
1202009 CTCTTTCCGC
* * *
1202019 TTTCCAGTCCTCAAAGAGTAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
* *
1202084 AGTCCTCAAAGAGC-GAGACGCCTTC-TCTTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTA
65 AGTCCTCAAAGAGCAG-GACGCCTTCTTC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCC-A
* *
1202146 GTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAA
127 ATCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGTCCTCAAA
*
1202210 GAGCAGGACGCCTTCTCCTTTT-AAAGCCCACACAACTTGGTGGCA-
190 GAGCAGGACG-CTT-TCCTTTTCAAAGCCCACACAAGTTGGTGGCAT
*
1202255 CTTCCTAGTCCTCAAAGAGCAGGACGCC---TC--TTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TTTCC-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTT-C
* * * * *
1202315 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACATAAGTTGGTGGCA-CTTCCTAG
64 CAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC-AA
* **
1202379 TCCTCAAAGAGTAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGA
128 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGA
* *
1202444 GCAGGA--C--ACCTCTT-AAAGCCCACACAAGTTGGTGGCA-
192 GCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCAT
* * **
1202481 CTTCCTAATCCTCAAAGAGCAGGA-----TACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TTTCC-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1202541 TAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
65 -AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
*
1202606 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
129 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
* *
1202671 AGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAT
194 AGGACGC-TTTCCTTTTCAAAGCCCACACAAGTTGGTGGCAT
* * *
1202713 TTTCCAGTCCCCAAAAAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-C
1 TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
* *
1202777 AGTCCTCAAAGAGCAGGATGCCTTCTTCTTTCAAAGCCTACACAAGTTGGTGGCATTTTCCAATC
65 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
* *
1202842 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCA
130 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
* * *
1202907 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTAGTGGCAT
195 GGACGC-TTTCCTTTTCAAAGCCCACACAAGTTGGTGGCAT
*
1202948 TTTCCAGTCC-CTAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-
1 TTTCCAGTCCTC-AAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTC
*
1203011 CAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAAT
64 CAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
** * *
1203076 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAG
129 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAG
*
1203141 CAGGACG----CC-TTTCAAAGCCCACACGAGTTGGTGGCACT
193 CAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA-T
*
1203179 TTT-TAGTCCTCAAAGAGCAGGA
1 TTTCCAGTCCTCAAAGAGCAGGA
1203201 TATACTTTAT
Statistics
Matches: 866, Mismatches: 52, Indels: 62
0.88 0.05 0.06
Matches are distributed among these distances:
224 1 0.00
225 21 0.02
226 178 0.21
227 5 0.01
229 1 0.00
230 45 0.05
231 46 0.05
232 153 0.18
233 4 0.00
234 3 0.00
235 332 0.38
236 54 0.06
237 23 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (234 bp):
TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCA
GTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCC
TCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAG
GACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCAT
Found at i:1203100 original size:26 final size:26
Alignment explanation
Indices: 1203069--1203155 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
1203059 TGGTGGCATT
1203069 TTTCAATCCTCAAAGAGCAGGACACC
1 TTTCAATCCTCAAAGAGCAGGACACC
* * *
1203095 TTTCAAAGCC-CACACA-AGTTAGTGGCACC
1 TTTC-AATCCTCA-A-AGAG-CAG-GACACC
* *
1203124 TTTCAGTCCTCAAAGAGCAGGACGCC
1 TTTCAATCCTCAAAGAGCAGGACACC
1203150 TTTCAA
1 TTTCAA
1203156 AGCCCACACG
Statistics
Matches: 45, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
26 15 0.33
27 10 0.22
28 9 0.20
29 11 0.24
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (26 bp):
TTTCAATCCTCAAAGAGCAGGACACC
Found at i:1203270 original size:42 final size:42
Alignment explanation
Indices: 1203184--1203272 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
1203174 GCACTTTTTA
* * **
1203184 GTCCTCAAAGAGCAGGATATACTTTATTTTCCTCTTTCTTTT
1 GTCCTCAAAGAGCAGGACATACTTTATTTCCCTCTTTCCGTT
* * *
1203226 GTCCTCAGAGAGCAGGACGTA-TTTCATTTCCCTTTTTCCGTT
1 GTCCTCAAAGAGCAGGACATACTTT-ATTTCCCTCTTTCCGTT
1203268 GTCCT
1 GTCCT
1203273 TGGAAAATGG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACATACTTTATTTCCCTCTTTCCGTT
Found at i:1218327 original size:15 final size:15
Alignment explanation
Indices: 1218307--1218340 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1218297 CTTCTCTTCC
*
1218307 AAAAAAAAAGCAAA-
1 AAAAAAAAAACAAAG
1218321 AAAAAAAAAACAAAG
1 AAAAAAAAAACAAAG
1218336 AAAAA
1 AAAAA
1218341 GGAGAGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAG
Found at i:1219472 original size:55 final size:55
Alignment explanation
Indices: 1219320--1220499 Score: 1137
Period size: 55 Copynumber: 20.4 Consensus size: 55
1219310 TCCTTTCGCT
* * *
1219320 TTCCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCATACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACG-C----CTTTTAAAGCCCACACAAGTTGGTGGCATC
* *
1219380 TTCCAGTCCTCAAAGAGCGGGACACCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA-C
1 TTCCAGTCCTCAAAGAGCAGG--A-C-GC-C-TTTTAAAGCCCACACAAGTTGGTGGCATC
1219440 TTCCTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
1 TTCC-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
*
1219495 TTCCCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
1 TT-CCAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCATC
* *
1219556 TTCCTAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-C
1 TTCC-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
1219611 TTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
1 TT-CCAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCATC
*
1219672 TTCCTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCAT-
1 TTCC-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
** * *
1219727 TTTTAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-C
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* **
1219781 TTCCTAATCCTCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCA-C
1 TTCC-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* *
1219836 TTCCCAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATT
1 TT-CCAGTCCTCAAAGAGCAGGACG-C--C-T-TTT-AAAGCCCACACAAGTTGGTGGCATC
* * * * *
1219898 TTCCAATCCTCAAAGAGCAGGATGCCTTTTAAAGCCTACCCAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * *
1219953 TT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCTCACACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACGC-----CTTTT-AAAGCCCACACAAGTTGGTGGCATC
* * * *
1220013 TTCCAGTCCCCAAAGAGCAAGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACG-C----CTTTTAAAGCCCACACAAGTTGGTGGCATC
* *
1220073 TT-CAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGA---C-GC--CTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * *
1220133 TTCCAATCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * *
1220188 TT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTCGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACGC-----CTTTT-AAAGCCCACACAAGTTGGTGGCATC
* * *
1220248 TTCCAATCC-CTAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACC
1 TTCCAGTCCTC-AAAGAGCAGGACG-C----CTTTTAAAGCCCACACAAGTTGGTGGCATC
*
1220308 TT-CAGTCCTCAAAGAGCAGGACGTCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATT
1 TTCCAGTCCTCAAAGAGCAGGACG-C--C-T-TTT-AAAGCCCACACAAGTTGGTGGCATC
* * * *
1220368 TTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
* * * *
1220423 TTTCAGTCCTCAAAGAGCAGGACGTCTTTCAAAGCCCACACGAGTTGGTGGCA-C
1 TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
**
1220477 TTTTTAGTCCTCAAAGAGCAGGA
1 -TTCCAGTCCTCAAAGAGCAGGA
1220500 TACACTTTAT
Statistics
Matches: 975, Mismatches: 84, Indels: 127
0.82 0.07 0.11
Matches are distributed among these distances:
54 91 0.09
55 341 0.35
56 13 0.01
57 7 0.01
58 5 0.01
59 51 0.05
60 183 0.19
61 276 0.28
62 7 0.01
63 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
TTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATC
Found at i:1219533 original size:116 final size:115
Alignment explanation
Indices: 1219350--1220499 Score: 1412
Period size: 116 Copynumber: 10.0 Consensus size: 115
1219340 GATGCCTTTT
* ** * *
1219350 CTTTTAAAGCCCATACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGACACCTTC-TCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTCTTC-TT
*
1219414 TTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
64 TTAAAGCCCACACAAGTTGGTGGCATCTTCC-AATCCTCAAAGAGCAGGACGC
* *
1219466 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAAGACGCCTTCTCCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGTCCTCAAAGAGCAGGACGCCTTCTTCTT
* *
1219530 TTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACAC
64 TTAAAGCCCACACAAGTTGGTGGCATCTTCC-AATCCTCAAAGAGCAGGACGC
* *
1219582 CTCTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGTCCTCAAAGAGCAGGACGCCTTCTTCTT
* *
1219646 TTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGATGC
64 TTAAAGCCCACACAAGTTGGTGGCATCTTCC-AATCCTCAAAGAGCAGGACGC
** * *
1219698 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTAGTCCTCAAAGAGCAGGAC-AC--C-TC--TT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTT
**
1219757 AAAGCCCACACAAGTTGGTGGCA-CTTCCTAATCCTCAAAGAGCAGGATAC
66 AAAGCCCACACAAGTTGGTGGCATCTTCC-AATCCTCAAAGAGCAGGACGC
*
1219807 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGATGCCTTCTTCTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGTCCTCAAAGAGCAGGACGCCTTCTTCTT
* * *
1219871 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGC
64 TTAAAGCCCACACAAGTTGGTGGCATCTTCCAATCCTCAAAGAGCAGGACGC
* * * *
1219923 CTTTTAAAGCCTACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATG-CTTTTTCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTT
* * * * *
1219987 CAAAGCTCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAAGACGCC
66 -AAAGCCCACACAAGTTGGTGGCATCTTCCAATCCTCAAAGAGCAGGACG-C
* *
1220039 TTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTCTTC
1 ----CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTTC
* *
1220104 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGC
62 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAATCCTCAAAGAGCAGGACGC
* * *
1220158 CTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATG-CTTTTTCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTT
* *
1220222 CAAAGCCCACACAAGTCGGTGGCATTTTCCAATCC-CTAAAGAGCAGGACGCC
66 -AAAGCCCACACAAGTTGGTGGCATCTTCCAATCCTC-AAAGAGCAGGACG-C
* *
1220274 TTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTCAGTCCTCAAAGAGCAGGACGTCTTCTTC
1 ----CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTTC
* * *
1220339 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACAC
62 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCCAATCCTCAAAGAGCAGGACGC
*
1220393 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG------TCTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTT
* * ** *
1220452 CAAAGCCCACACGAGTTGGTGGCA-CTTTTTAGTCCTCAAAGAGCAGGA
65 TAAAGCCCACACAAGTTGGTGGCATC-TTCCAATCCTCAAAGAGCAGGA
1220500 TACACTTTAT
Statistics
Matches: 941, Mismatches: 62, Indels: 68
0.88 0.06 0.06
Matches are distributed among these distances:
108 2 0.00
109 78 0.08
110 65 0.07
111 2 0.00
112 1 0.00
113 1 0.00
114 23 0.02
115 210 0.22
116 338 0.36
117 10 0.01
119 2 0.00
120 189 0.20
121 20 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (115 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTT
AAAGCCCACACAAGTTGGTGGCATCTTCCAATCCTCAAAGAGCAGGACGC
Found at i:1220136 original size:235 final size:233
Alignment explanation
Indices: 1219319--1220499 Score: 1547
Period size: 235 Copynumber: 5.1 Consensus size: 233
1219309 CTCCTTTCGC
* * *
1219319 TTTCCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCATACAAGTTGGTGGCATTTTCC
1 TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
* * * *
1219384 AGTCCTCAAAGAGCGGGACACCTTC-TCTTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAG
65 AGTCCTCAAAGAGCAGGACGCCTTCTTC-TTTTAAAGCCCACACAAGTTGGTGGCATTTTCC-AA
*
1219447 TCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAG
128 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT--CAGTCCTCAAAG
* *
1219511 AGCAAGACGCCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCA-
191 AGCAGGA-G-CTT-TTCTTTTCAAAGCCCACACAAGTTGGTGGCAT
* *
1219555 CTTCCTAGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TTTCC-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTT-C
* * *
1219615 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAG
64 CAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC-AA
** *
1219679 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTAGTCCTCAAAGAG
128 TCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAG
** *
1219744 CAGGA-C--ACCTCTT-AAAGCCCACACAAGTTGGTGGCA-
193 CAGGAGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAT
* * **
1219780 CTTCCTAATCCTCAAAGAGCAGGA-----TACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
1 TTTCC-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTT-C
* *
1219840 CAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
64 CAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
* *
1219905 CCTCAAAGAGCAGGATGCCTTTTAAAGCCTACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
129 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC
*
1219970 AGGATGCTTTTTCTTTTCAAAGCTCACACAAGTTGGTGGCAT
194 AGGA-GC-TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAT
* * *
1220012 TTTCCAGTCCCCAAAGAGCAAGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-C
1 TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
*
1220076 AGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
65 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
*
1220141 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
130 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
*
1220206 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTCGGTGGCAT
195 GGA-GC-TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAT
* *
1220247 TTTCCAATCC-CTAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-
1 TTTCCAGTCCTC-AAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTC
* *
1220310 CAGTCCTCAAAGAGCAGGACGTCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
64 CAGTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAAT
** *
1220375 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAG
129 CCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAG
* *
1220440 CAGGA-C--GTC-TTTCAAAGCCCACACGAGTTGGTGGCACT
193 CAGGAGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-T
*
1220478 TTT-TAGTCCTCAAAGAGCAGGA
1 TTTCCAGTCCTCAAAGAGCAGGA
1220500 TACACTTTAT
Statistics
Matches: 864, Mismatches: 55, Indels: 58
0.88 0.06 0.06
Matches are distributed among these distances:
223 1 0.00
225 200 0.23
226 4 0.00
227 1 0.00
228 1 0.00
230 44 0.05
231 63 0.07
232 134 0.16
233 3 0.00
234 4 0.00
235 333 0.39
236 53 0.06
237 23 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (233 bp):
TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCA
GTCCTCAAAGAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAATCC
TCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAG
GAGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAT
Found at i:1220423 original size:29 final size:29
Alignment explanation
Indices: 1220338--1220427 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
1220328 ACGTCTTCTT
1220338 CTTTCAAAGCCCACACAAGTTGGTGGCA-
1 CTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * * **
1220366 TTTTCCAA-TCCTCA-AAG-AGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGG-CAC
1220393 CTTTCAAAGCCCACACAAGTTGGTGGCAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCAC
1220422 CTTTCA
1 CTTTCA
1220428 GTCCTCAAAG
Statistics
Matches: 43, Mismatches: 14, Indels: 9
0.65 0.21 0.14
Matches are distributed among these distances:
25 3 0.07
26 5 0.12
27 10 0.23
28 10 0.23
29 12 0.28
30 3 0.07
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (29 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:1221890 original size:16 final size:17
Alignment explanation
Indices: 1221858--1221891 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1221848 TAAAAAATTA
*
1221858 CTAAAATTATTTTCATG
1 CTAAAATTATATTCATG
1221875 CTAAAATT-TATTCATG
1 CTAAAATTATATTCATG
1221891 C
1 C
1221892 ATGGCTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (17 bp):
CTAAAATTATATTCATG
Found at i:1223693 original size:20 final size:20
Alignment explanation
Indices: 1223668--1223707 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1223658 TTAAGCACAG
1223668 TATATTTAAAAAAAGAATTC
1 TATATTTAAAAAAAGAATTC
*
1223688 TATATTTGAAAAAAGAATTC
1 TATATTTAAAAAAAGAATTC
1223708 CATTAAGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (20 bp):
TATATTTAAAAAAAGAATTC
Found at i:1224936 original size:21 final size:21
Alignment explanation
Indices: 1224910--1224984 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
1224900 AAATTATCCA
1224910 AATGTATCGATACATTTAAAG
1 AATGTATCGATACATTTAAAG
***
1224931 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTAAAG
*
1224952 AATGTATCGATACATTCTACA-
1 AATGTATCGATACATT-TAAAG
1224973 AATGTATCGATA
1 AATGTATCGATA
1224985 TAGGGTCCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 46 0.98
22 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTAAAG
Found at i:1225046 original size:19 final size:19
Alignment explanation
Indices: 1225022--1225089 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
1225012 AATTCAACAA
1225022 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1225041 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
1225056 --TGTATCGATACACAAGT
1 TTTGTATCGATACATAAGT
*
1225073 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1225090 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1225061 original size:13 final size:13
Alignment explanation
Indices: 1225043--1225067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1225033 ACATAAGTTT
1225043 TGTATCGATACAA
1 TGTATCGATACAA
1225056 TGTATCGATACA
1 TGTATCGATACA
1225068 CAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1225065 original size:32 final size:32
Alignment explanation
Indices: 1225024--1225086 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1225014 TTCAACAATT
* *
1225024 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACACAAGTATTGTATCGATACAA
1225056 TGTATCGATACACAAGTATTGTATCGATACA
1 TGTATCGATACACAAGTATTGTATCGATACA
1225087 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACACAAGTATTGTATCGATACAA
Found at i:1229477 original size:21 final size:21
Alignment explanation
Indices: 1229430--1229485 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1229420 TGCAAACAGT
*
1229430 AAATGTATCGATACATAAGTG
1 AAATGTATCGATACATAACTG
**
1229451 -AATGTATCGATACATGCCTG
1 AAATGTATCGATACATAACTG
1229471 AAATGTATCGATACA
1 AAATGTATCGATACA
1229486 AAACCACTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
AAATGTATCGATACATAACTG
Found at i:1232081 original size:24 final size:24
Alignment explanation
Indices: 1232049--1232099 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1232039 TAAACTTGTC
*
1232049 AAGATTTAAATCTTATTTTTTCCT
1 AAGATTTAAATCTTATTTTTGCCT
1232073 AAGATTTAAATCTTATTTTTGCCT
1 AAGATTTAAATCTTATTTTTGCCT
1232097 AAG
1 AAG
1232100 TTATTGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (24 bp):
AAGATTTAAATCTTATTTTTGCCT
Found at i:1232147 original size:26 final size:26
Alignment explanation
Indices: 1232111--1232160 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1232101 TATTGTCATC
1232111 GGGGATACTCCAACCCCATTTTTTGA
1 GGGGATACTCCAACCCCATTTTTTGA
*
1232137 GGGGATACTCCAACCCCGTTTTTT
1 GGGGATACTCCAACCCCATTTTTT
1232161 AATCAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (26 bp):
GGGGATACTCCAACCCCATTTTTTGA
Found at i:1233466 original size:11 final size:11
Alignment explanation
Indices: 1233450--1233479 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1233440 AGATAAGAAG
1233450 AAAAAAAACAA
1 AAAAAAAACAA
1233461 AAAAAAAACAA
1 AAAAAAAACAA
1233472 AAAAAAAA
1 AAAAAAAA
1233480 GCTCTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:1236938 original size:52 final size:52
Alignment explanation
Indices: 1236738--1236918 Score: 308
Period size: 52 Copynumber: 3.5 Consensus size: 52
1236728 CGAAATATGA
* * *
1236738 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
*
1236790 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATTGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
* *
1236842 AAATTTGCCTACATGTATCGATACATTTTATAGTGTATCGATACATCTTGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1236894 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1236919 AAGATCAGTG
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
Found at i:1236945 original size:13 final size:13
Alignment explanation
Indices: 1236927--1236951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1236917 CAAAGATCAG
1236927 TGTATCGATACAA
1 TGTATCGATACAA
1236940 TGTATCGATACA
1 TGTATCGATACA
1236952 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1237018 original size:19 final size:19
Alignment explanation
Indices: 1236994--1237090 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
1236984 TAGCTTACAT
1236994 TATATCGATACAACACTTA
1 TATATCGATACAACACTTA
1237013 TATATCGAT---ACA--T-
1 TATATCGATACAACACTTA
*
1237026 TGTATCGATACAACACTTA
1 TATATCGATACAACACTTA
*
1237045 TGTATCGAT---ACA--T-
1 TATATCGATACAACACTTA
1237058 TATATCGATACAACACTTTA
1 TATATCGATACAACAC-TTA
*
1237078 TGTATCGATACAA
1 TATATCGATACAA
1237091 ATCATTGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 25
0.69 0.03 0.28
Matches are distributed among these distances:
13 16 0.26
14 2 0.03
16 12 0.19
18 1 0.02
19 19 0.31
20 12 0.19
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (19 bp):
TATATCGATACAACACTTA
Found at i:1237032 original size:32 final size:32
Alignment explanation
Indices: 1236989--1237089 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
1236979 GGCAGTAGCT
*
1236989 TACATTATATCGATACAACACTTATATATCGA
1 TACATTATATCGATACAACACTTATGTATCGA
*
1237021 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTATATCGATACAACACTTATGTATCGA
1237053 TACATTATATCGATACAACACTTTATGTATCGA
1 TACATTATATCGATACAACAC-TTATGTATCGA
1237086 TACA
1 TACA
1237090 AATCATTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (32 bp):
TACATTATATCGATACAACACTTATGTATCGA
Found at i:1237168 original size:21 final size:21
Alignment explanation
Indices: 1237127--1237168 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1237117 GTTGGGACCT
*
1237127 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1237148 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1237169 AAATGTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1238095 original size:31 final size:31
Alignment explanation
Indices: 1238054--1238137 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 31
1238044 TTAAAGAAGA
1238054 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAA-GGT
1238086 TG-CACCAACTTGTGT--GCTTTTG-AAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
**
1238113 TGCCACTGAC-T-TGTGGGCTTTTGAA
1 TGCCACCAACTTGTGTGGGCTTTTGAA
1238138 GAGATACCAC
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 3 0.07
27 6 0.13
28 14 0.30
29 8 0.17
31 13 0.28
32 2 0.04
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.35
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
Found at i:1238155 original size:29 final size:29
Alignment explanation
Indices: 1238113--1238434 Score: 448
Period size: 29 Copynumber: 11.0 Consensus size: 29
1238103 TTTTGAAGGT
* *
1238113 TGCCACTGACTTGTGGGCTTTTGAAGAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* *
1238142 TACCACTGACTTGTGGGCTTTGGAAAAAGG
1 TGCCACTGACTTGTGGGCTTTGG-AAAAGA
* *
1238172 TTCCACTGGCTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* *
1238201 TACCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
* *
1238231 TGCCACTGACTTGTGGGCTTTTGAAAAGT
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* *
1238260 TACCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
* *
1238290 TGCCACTGACTTGTGGGTTTTGGAAAAAA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1238319 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1238348 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* *
1238377 TACCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
*
1238407 TGCCACTAACTTGTGGGCTTT-GAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1238435 AAAAGGTGCT
Statistics
Matches: 262, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
28 1 0.00
29 164 0.63
30 97 0.37
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGGAAAAGA
Found at i:1238202 original size:59 final size:59
Alignment explanation
Indices: 1238108--1238434 Score: 505
Period size: 59 Copynumber: 5.6 Consensus size: 59
1238098 TGTGCTTTTG
* *
1238108 AAGGTTGCCACTGACTTGTGGGCTTTTGAAGAGATACCACTGACTTGTGGGCTTTGGAAA
1 AAGG-TGCCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAA
* *
1238168 AAGGTTCCACTGGCTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAA
1 AAGGTGCCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAA
* * *
1238227 AGGGTGCCACTGACTTGTGGGCTTTTGAAAAGTTACCACTGACTTGTGGGCTTTGGAAA
1 AAGGTGCCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAA
* * * *
1238286 AGGGTGCCACTGACTTGTGGGTTTTGGAAAAAATGCCACTGACTTGTGGGCTTTGG-AA
1 AAGGTGCCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAA
*
1238344 AAGATGCCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAA
1 AAGGTGCCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAA
* *
1238403 AGGGTGCCACTAACTTGTGGGCTTT-GAAAAGA
1 AAGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
1238435 AAAAGGTGCT
Statistics
Matches: 244, Mismatches: 22, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
58 60 0.25
59 180 0.74
60 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (59 bp):
AAGGTGCCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAA
Found at i:1238207 original size:88 final size:88
Alignment explanation
Indices: 1238115--1238433 Score: 457
Period size: 88 Copynumber: 3.6 Consensus size: 88
1238105 TTGAAGGTTG
* * *
1238115 CCACTGACTTGTGGGCTTTTGAAGA-GATACCACTGACTTGTGGGCTTTGGAAAAAGGTTCCACT
1 CCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACTTGTGGGCTTTGG-AAAAGGTTCCACT
*
1238179 GGCTTGTGGGCTTTGGAAAAGATA
65 GACTTGTGGGCTTTGGAAAAGATA
* *
1238203 CCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAA-GTTACCACT
1 CCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACTTGTGGGCTTTGGAAAAGGTT-CCACT
* *
1238267 GACTTGTGGGCTTTGGAAAAGGGTG
65 GACTTGTGGGCTTTGGAAAA-GATA
* * * *
1238292 CCACTGACTTGTGGGTTTTGGAAAA-AATGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
1 CCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACTTGTGGGCTTTGGAAAAGGTTCCACTG
1238356 ACTTGTGGGCTTTGGAAAAGATA
66 ACTTGTGGGCTTTGGAAAAGATA
* *
1238379 CCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTT-GAAAAG
1 CCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACTTGTGGGCTTTGGAAAAG
1238434 AAAAAGGTGC
Statistics
Matches: 206, Mismatches: 20, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
87 35 0.17
88 122 0.59
89 49 0.24
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (88 bp):
CCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACTTGTGGGCTTTGGAAAAGGTTCCACTG
ACTTGTGGGCTTTGGAAAAGATA
Found at i:1238483 original size:34 final size:34
Alignment explanation
Indices: 1238417--1238501 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
1238407 TGCCACTAAC
* * *
1238417 TTGTGGGCTTTGAAAA-GAAAAAGGTGCTACGGAG
1 TTGTGGGCTTT-AAAAGGGAAAAGATGCCACGGAG
1238451 TTGTGGGCTTTAAAAGGGAAAAGATGCCACGGAG
1 TTGTGGGCTTTAAAAGGGAAAAGATGCCACGGAG
*
1238485 TTATGGGC-TTAAAAGGG
1 TTGTGGGCTTTAAAAGGG
1238502 TGAGGAATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 13 0.28
34 33 0.72
ACGTcount: A:0.32, C:0.09, G:0.35, T:0.24
Consensus pattern (34 bp):
TTGTGGGCTTTAAAAGGGAAAAGATGCCACGGAG
Found at i:1239956 original size:1 final size:1
Alignment explanation
Indices: 1239952--1240039 Score: 59
Period size: 1 Copynumber: 88.0 Consensus size: 1
1239942 GTTGTTGTTG
* * * * * * * * *
1239952 TTTTTATTTTTTTTTCTTTGTTTTTTTGTTTTTGTTTTTTTTTTTGTTTTTTTCTTCTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * **
1240017 TTTGTTTATTTGGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTT
1240040 GTGGAGGACG
Statistics
Matches: 63, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:1239997 original size:26 final size:26
Alignment explanation
Indices: 1239937--1240019 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
1239927 ATCCGGACCC
* *
1239937 TTTTTGTTGTTGTTGTTTTTATTTTTTT
1 TTTTTGTT-TTTTTGTTTTT-CTTTTTT
*
1239965 TTCTTTGTTTTTTTGTTTTTGTTTTTT
1 TT-TTTGTTTTTTTGTTTTTCTTTTTT
* *
1239992 TTTTTGTTTTTTTCTTCTTCTTTTTT
1 TTTTTGTTTTTTTGTTTTTCTTTTTT
1240018 TT
1 TT
1240020 GTTTATTTGG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 23 0.47
27 8 0.16
28 12 0.24
29 6 0.12
ACGTcount: A:0.01, C:0.05, G:0.10, T:0.84
Consensus pattern (26 bp):
TTTTTGTTTTTTTGTTTTTCTTTTTT
Found at i:1240003 original size:41 final size:43
Alignment explanation
Indices: 1239952--1240041 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 43
1239942 GTTGTTGTTG
* *
1239952 TTTTTATTTTTTT-TTCTT-TGTTTTTTTG-TT-TTTGTTTTTT
1 TTTTTGTTTTTTTCTTCTTCT-TTTTTTTGTTTATTTGGTTTTT
1239992 TTTTTGTTTTTTTCTTCTTCTTTTTTTTGTTTATTTGGTTTTT
1 TTTTTGTTTTTTTCTTCTTCTTTTTTTTGTTTATTTGGTTTTT
1240035 TTTTTGT
1 TTTTTGT
1240042 GGAGGACGCC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
40 12 0.27
41 13 0.30
42 3 0.07
43 16 0.36
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.84
Consensus pattern (43 bp):
TTTTTGTTTTTTTCTTCTTCTTTTTTTTGTTTATTTGGTTTTT
Found at i:1240034 original size:44 final size:40
Alignment explanation
Indices: 1239937--1240039 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 40
1239927 ATCCGGACCC
1239937 TTTTTGTTGTTGTTGTTTTTATTTTTTTTTCTTTGTTTTTTTG
1 TTTTTGTT-TT-TT-TTTTTATTTTTTTTTCTTTGTTTTTTTG
*
1239980 TTTTTGTTTTTTTTTTTGTTTTTTTCTTCTTCT-TTTTTTTG
1 TTTTTGTTTTTTTTTTTATTTTTTT-TTCTT-TGTTTTTTTG
*
1240021 TTTATTTGGTTTTTTTTTT
1 -TT-TTTGTTTTTTTTTTT
1240040 GTGGAGGACG
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
40 12 0.22
41 15 0.28
42 5 0.09
43 22 0.41
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.83
Consensus pattern (40 bp):
TTTTTGTTTTTTTTTTTATTTTTTTTTCTTTGTTTTTTTG
Found at i:1240038 original size:23 final size:23
Alignment explanation
Indices: 1239959--1240039 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
1239949 TTGTTTTTAT
* *
1239959 TTTTTTTTCTTTGTTTTTTTGTTTTTG
1 TTTTTTTT-TTTG-TTTTTTG--CTTC
*
1239986 TTTTTTTTTTTGTTTTTTTCTTC
1 TTTTTTTTTTTGTTTTTTGCTTC
* *
1240009 TTCTTTTTTTTGTTTATTTGGTT-
1 TTTTTTTTTTTGTTT-TTTGCTTC
1240032 TTTTTTTT
1 TTTTTTTT
1240040 GTGGAGGACG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 23 0.50
24 5 0.11
25 6 0.13
26 4 0.09
27 8 0.17
ACGTcount: A:0.01, C:0.05, G:0.09, T:0.85
Consensus pattern (23 bp):
TTTTTTTTTTTGTTTTTTGCTTC
Found at i:1251800 original size:13 final size:13
Alignment explanation
Indices: 1251782--1251806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1251772 CAAAGATCAG
1251782 TGTATCGATACAA
1 TGTATCGATACAA
1251795 TGTATCGATACA
1 TGTATCGATACA
1251807 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1251877 original size:19 final size:18
Alignment explanation
Indices: 1251848--1251945 Score: 72
Period size: 13 Copynumber: 5.8 Consensus size: 18
1251838 GTAGCTTACA
*
1251848 TTGTATTGATACAACACT
1 TTGTATCGATACAACACT
1251866 TCTGTATCGAT---ACA--
1 T-TGTATCGATACAACACT
1251880 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
*
1251898 TATGTATCGAT---ATA--
1 T-TGTATCGATACAACACT
1251912 TTGTATCGATACAACACTT
1 TTGTATCGATACAACAC-T
1251931 TATGTATCGATACAA
1 T-TGTATCGATACAA
1251946 ATCGTTGAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 26
0.68 0.03 0.28
Matches are distributed among these distances:
13 18 0.29
14 2 0.03
16 10 0.16
18 2 0.03
19 18 0.29
20 13 0.21
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:1251885 original size:32 final size:32
Alignment explanation
Indices: 1251844--1251944 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
1251834 GGCAGTAGCT
* *
1251844 TACATTGTATTGATACAACACTTCTGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1251876 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
1251908 TATATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1251941 TACA
1 TACA
1251945 AATCGTTGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 50 0.78
33 14 0.22
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1252458 original size:88 final size:87
Alignment explanation
Indices: 1252291--1252470 Score: 279
Period size: 88 Copynumber: 2.1 Consensus size: 87
1252281 CTTGGTTGTT
* *
1252291 TTTGTTTTAAAGTTCACTAAAAAACCAACCTTTAATCAATAACTTCTTCTATATATTTTAAACTA
1 TTTGTTTTAAAGTTCACTAAAAAACCAACCTTTAATCAAAAACTTCTTCTATACATTTTAAACTA
* *
1252356 AGTTTTCTTGTTTTCTAGTTTG
66 AGTTTGCTTGTTTTCTAGCTTG
* * * *
1252378 TTTGTTTTAAATTTCACTAAAAAATCAACCTTTAATCATAAAACTTGTTTTATACATTTTAAACT
1 TTTGTTTTAAAGTTCACTAAAAAACCAACCTTTAATCA-AAAACTTCTTCTATACATTTTAAACT
1252443 AAGTTTGCTTGTTTTCTAGCTTG
65 AAGTTTGCTTGTTTTCTAGCTTG
1252466 TTTGT
1 TTTGT
1252471 ATCATGTCAT
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 36 0.43
88 48 0.57
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.48
Consensus pattern (87 bp):
TTTGTTTTAAAGTTCACTAAAAAACCAACCTTTAATCAAAAACTTCTTCTATACATTTTAAACTA
AGTTTGCTTGTTTTCTAGCTTG
Found at i:1252958 original size:58 final size:58
Alignment explanation
Indices: 1252857--1253078 Score: 229
Period size: 58 Copynumber: 3.8 Consensus size: 58
1252847 CCATGTGCAC
* * * * **
1252857 ATCTAAGGTCATTTTAGTAAATTTTATGCATTTTAAGGTCATTTAAGTTATTTTGCATA
1 ATCTAAGGTCATTTTAG-CAATTTCATGCATTTTAAGGCCATTTAGGTTATTTCACATA
* * *
1252916 ATCTAAGGCCATTTTAGCAATTTCATGCTTTTTAAGGCCATTTAGGTTATTTCATATA
1 ATCTAAGGTCATTTTAGCAATTTCATGCATTTTAAGGCCATTTAGGTTATTTCACATA
* * * *
1252974 ATCT-AGAGTCATCTTAGCAAACTTCAT-CATTTTAATGCCATTTAGGTTACTTCACATA
1 ATCTAAG-GTCATTTTAGC-AATTTCATGCATTTTAAGGCCATTTAGGTTATTTCACATA
* *
1253032 ATCTATGGTCA-TTTAGCAATTTCCAT-CATTTT-AGGACTATTTAGGTT
1 ATCTAAGGTCATTTTAGCAATTT-CATGCATTTTAAGG-CCATTTAGGTT
1253079 TGGTAGTTAT
Statistics
Matches: 137, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
56 6 0.04
57 26 0.19
58 81 0.59
59 24 0.18
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (58 bp):
ATCTAAGGTCATTTTAGCAATTTCATGCATTTTAAGGCCATTTAGGTTATTTCACATA
Found at i:1255983 original size:5 final size:5
Alignment explanation
Indices: 1255951--1255999 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
1255941 TATATTAAAT
* *
1255951 TATTA TGTTA -ATTA TATT- TAAATA TATTA TATTA TATT- TATTA TATTA
1 TATTA TATTA TATTA TATTA T-ATTA TATTA TATTA TATTA TATTA TATTA
1255999 T
1 T
1256000 CATATTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
4 8 0.22
5 27 0.75
6 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:1255986 original size:20 final size:20
Alignment explanation
Indices: 1255964--1256032 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1255954 TATGTTAATT
*
1255964 ATATTTAAATATATTATATT
1 ATATTTAAATATATTATATC
*
1255984 ATATTT-ATTATA-T-TATC
1 ATATTTAAATATATTATATC
1256001 ATATTTAAATAT-TTCATATC
1 ATATTTAAATATATT-ATATC
*
1256021 ATAGTTAAATAT
1 ATATTTAAATAT
1256033 GATTCTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.22
18 6 0.15
19 5 0.12
20 21 0.51
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (20 bp):
ATATTTAAATATATTATATC
Found at i:1255992 original size:24 final size:23
Alignment explanation
Indices: 1255939--1256005 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
1255929 TTAACTATGA
*
1255939 TATATATTAAATTATTATGTTAAT
1 TATAT-TTAAATTATTATATTAAT
1255963 TATATTTAAATATATTATATTATAT
1 TATATTTAAAT-TATTATATTA-AT
* *
1255988 T-TA-TTATATTATCATATT
1 TATATTTAAATTATTATATT
1256006 TAAATATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 8 0.21
23 11 0.29
24 16 0.42
25 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (23 bp):
TATATTTAAATTATTATATTAAT
Found at i:1255994 original size:14 final size:14
Alignment explanation
Indices: 1255951--1255999 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1255941 TATATTAAAT
* *
1255951 TATTATGTTAATTA
1 TATTATATTTATTA
* *
1255965 TATTTAAATATATTA
1 TA-TTATATTTATTA
1255980 TATTATATTTATTA
1 TATTATATTTATTA
1255994 TATTAT
1 TATTAT
1256000 CATATTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TATTATATTTATTA
Found at i:1256004 original size:29 final size:32
Alignment explanation
Indices: 1255940--1255997 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1255930 TAACTATGAT
1255940 ATATATTAAATTATTATGTTAATTATATTTAA
1 ATATATTAAATTATTATGTTAATTATATTTAA
*
1255972 ATATATTATATTA-TAT-TT-ATTATATT
1 ATATATTAAATTATTATGTTAATTATATT
1255998 ATCATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 2 0.08
31 3 0.12
32 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (32 bp):
ATATATTAAATTATTATGTTAATTATATTTAA
Found at i:1256005 original size:37 final size:37
Alignment explanation
Indices: 1255941--1256012 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1255931 AACTATGATA
* *
1255941 TATATTAAATTATTATGTTAATTATATTTAAATATAT
1 TATATTAAATTATTATATTAATCATATTTAAATATAT
*
1255978 TATATTATATTTATTATATT-ATCATATTTAAATAT
1 TATATTA-AATTATTATATTAATCATATTTAAATAT
1256013 TTCATATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 21 0.68
38 10 0.32
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (37 bp):
TATATTAAATTATTATATTAATCATATTTAAATATAT
Found at i:1257460 original size:18 final size:20
Alignment explanation
Indices: 1257428--1257467 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1257418 GACTCATAAG
1257428 AAAAAAAAAGCTTAAA-TAT
1 AAAAAAAAAGCTTAAATTAT
*
1257447 AAAAAAAAA-TTTAAATTAT
1 AAAAAAAAAGCTTAAATTAT
1257466 AA
1 AA
1257468 TTCCAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAAAAAAGCTTAAATTAT
Found at i:1257660 original size:22 final size:22
Alignment explanation
Indices: 1257631--1257711 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
1257621 TGCGAGCTGA
1257631 AAAATAAATAAATAC-AAACCC
1 AAAATAAATAAATACAAAACCC
**
1257652 AAATATAAATTGATACAAAACCC
1 AAA-ATAAATAAATACAAAACCC
* * *
1257675 AAAATAAATAAATATAAAATCA
1 AAAATAAATAAATACAAAACCC
*
1257697 AAAATTAAAAAAATA
1 AAAA-TAAATAAATA
1257712 AAATTTCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.06
22 28 0.57
23 18 0.37
ACGTcount: A:0.68, C:0.11, G:0.01, T:0.20
Consensus pattern (22 bp):
AAAATAAATAAATACAAAACCC
Found at i:1257710 original size:23 final size:23
Alignment explanation
Indices: 1257675--1257724 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1257665 TACAAAACCC
*
1257675 AAAA-TAAATAAATATAAA-ATCA
1 AAAATTAAAAAAATA-AAATATCA
*
1257697 AAAATTAAAAAAATAAAATTTCA
1 AAAATTAAAAAAATAAAATATCA
1257720 AAAAT
1 AAAAT
1257725 AATTAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATTAAAAAAATAAAATATCA
Found at i:1257732 original size:22 final size:22
Alignment explanation
Indices: 1257630--1257733 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 22
1257620 TTGCGAGCTG
* **
1257630 AAAAATAAATAAATACAAACCC
1 AAAAATAAATAAATATAAAATC
* ** * *
1257652 AAATATAAATTGATACAAAACC
1 AAAAATAAATAAATATAAAATC
*
1257674 CAAAATAAATAAATATAAAATC
1 AAAAATAAATAAATATAAAATC
1257696 AAAAATTAAA-AAA-ATAAAATTTC
1 AAAAA-TAAATAAATATAAAA--TC
*
1257719 AAAAATAATTAAATA
1 AAAAATAAATAAATA
1257734 CAAGCCAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
21 6 0.09
22 44 0.68
23 14 0.22
24 1 0.02
ACGTcount: A:0.67, C:0.10, G:0.01, T:0.22
Consensus pattern (22 bp):
AAAAATAAATAAATATAAAATC
Found at i:1258119 original size:27 final size:27
Alignment explanation
Indices: 1258087--1258161 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
1258077 AACAAGTCAT
* *
1258087 TATTTTTGATAAACAAAAAGGAACCAC
1 TATTTTTGACAAACACAAAGGAACCAC
* *
1258114 TATTTTTTACACACACAAAGGAACCAC
1 TATTTTTGACAAACACAAAGGAACCAC
1258141 TATTTTTGACAAACACAAAGG
1 TATTTTTGACAAACACAAAGG
1258162 GTGGCTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (27 bp):
TATTTTTGACAAACACAAAGGAACCAC
Found at i:1260072 original size:21 final size:22
Alignment explanation
Indices: 1260034--1260079 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1260024 ATTTATTGAA
* **
1260034 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1260055 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1260077 ACT
1 ACT
1260080 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1262560 original size:33 final size:33
Alignment explanation
Indices: 1262523--1262589 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1262513 TTCAACGATT
1262523 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1262556 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1262589 T
1 T
1262590 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1262561 original size:13 final size:13
Alignment explanation
Indices: 1262543--1262567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1262533 CATAAAATGT
1262543 TGTATCGATACAA
1 TGTATCGATACAA
1262556 TGTATCGATACA
1 TGTATCGATACA
1262568 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1262648 original size:13 final size:13
Alignment explanation
Indices: 1262630--1262654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1262620 ATTACTCAAA
1262630 TGTATCGATACAT
1 TGTATCGATACAT
1262643 TGTATCGATACA
1 TGTATCGATACA
1262655 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1271020 original size:30 final size:30
Alignment explanation
Indices: 1270984--1271040 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
1270974 AAATACCTTT
1270984 TCAAAGTCCACGACTCAGTGGCATTTTGTC
1 TCAAAGTCCACGACTCAGTGGCATTTTGTC
1271014 TCAAAGTCCACGACTCAGTGGCATTTT
1 TCAAAGTCCACGACTCAGTGGCATTTT
1271041 TTCTTTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (30 bp):
TCAAAGTCCACGACTCAGTGGCATTTTGTC
Found at i:1271107 original size:34 final size:34
Alignment explanation
Indices: 1271044--1271638 Score: 623
Period size: 34 Copynumber: 17.9 Consensus size: 34
1271034 GCATTTTTTC
*
1271044 TTTAAAGCCCACAACTCCGTGGTA-C----TCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* *
1271073 TTTAAAGCCCACAACTTCGTGGCACCTTCTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
**
1271107 TCCAAAGCCCACAACTCCGTGGCA-C----TC--
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1271134 TTTAAAGCCCACAACTCCGTGGCACCTTTTTC-T
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
1271167 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTT
* *
1271204 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1271238 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCT-T
*
1271274 TTTCAAAGCCCACGACTCCGTGGCA-C----TC--
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
1271302 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* *
1271336 TTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTT
* * *
1271373 TTCAAAGCCCACAACTCTGTGGCACCTTTTTCTG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* *
1271407 TTTAAAGCCCACAACTCTGTGGCACCTTCTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* * *
1271441 TTCAAAGCCCACGACTCTGTGGCA-C----TCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
**
1271470 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTT
1271505 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTT
* *
1271542 TTCAAAGCCCACAACTCCGTGGCACTTTTTTC-T
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
1271575 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
* *
1271611 TTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTT
1271639 CTCCCTTCTC
Statistics
Matches: 490, Mismatches: 37, Indels: 73
0.82 0.06 0.12
Matches are distributed among these distances:
27 42 0.09
28 5 0.01
29 49 0.10
30 1 0.00
31 3 0.01
32 4 0.01
33 51 0.10
34 145 0.30
35 68 0.14
36 25 0.05
37 97 0.20
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
Found at i:1271143 original size:27 final size:27
Alignment explanation
Indices: 1271042--1271196 Score: 148
Period size: 29 Copynumber: 5.2 Consensus size: 27
1271032 TGGCATTTTT
*
1271042 TCTTTAAAGCCCACAACTCCGTGGTAC
1 TCTTTAAAGCCCACAACTCCGTGGCAC
*
1271069 TCTTTTTAAAGCCCACAACTTCGTGGCACCTTC
1 TC--TTTAAAGCCCACAACTCCGTGGCA----C
1271102 TTCTTTCCAAAGCCCACAACTCCGTGGCAC
1 -TCTTT--AAAGCCCACAACTCCGTGGCAC
1271132 TCTTTAAAGCCCACAACTCCGTGGCACC
1 TCTTTAAAGCCCACAACTCCGTGGCA-C
*
1271160 TTTTTCTTTTAAAGCCCACAACTCTGTGGCAC
1 ----TC-TTTAAAGCCCACAACTCCGTGGCAC
1271192 TCTTT
1 TCTTT
1271197 TTCCCTTTTC
Statistics
Matches: 109, Mismatches: 4, Indels: 30
0.76 0.03 0.21
Matches are distributed among these distances:
27 26 0.24
28 3 0.03
29 27 0.25
30 1 0.01
32 6 0.06
33 24 0.22
34 22 0.20
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (27 bp):
TCTTTAAAGCCCACAACTCCGTGGCAC
Found at i:1271268 original size:71 final size:69
Alignment explanation
Indices: 1271137--1271638 Score: 630
Period size: 71 Copynumber: 7.4 Consensus size: 69
1271127 GGCACTCTTT
*
1271137 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CC
1271202 TTTTC
65 TTTTC
1271207 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-
1271272 CTTTTC
64 CTTTTC
* *
1271278 AAAGCCCACGACTCCGTGGCA-C----TC-TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-CT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1271335 TTTC
66 TTTC
* *
1271339 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCTGTGGCAC-CTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTT-AAAGCCCACAACTCCGTGGCACTCTTTT
1271403 T-CTGTTT-
62 TCCT-TTTC
* * * *
1271410 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCTGTGGCACTC----T--
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCC
1271469 TTTT-
65 TTTTC
*
1271473 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-
1271538 CCTTTTC
63 CCTTTTC
*
1271545 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CC
1271610 TTTT-
65 TTTTC
* *
1271614 -AAGTCCACAACTCCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTT
1271639 CTCCCTTCTC
Statistics
Matches: 389, Mismatches: 19, Indels: 50
0.85 0.04 0.11
Matches are distributed among these distances:
61 25 0.06
63 30 0.08
64 53 0.14
65 5 0.01
66 2 0.01
67 1 0.00
68 50 0.13
69 2 0.01
70 80 0.21
71 116 0.30
72 25 0.06
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.32
Consensus pattern (69 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TTTC
Found at i:1271329 original size:98 final size:97
Alignment explanation
Indices: 1271207--1271599 Score: 453
Period size: 98 Copynumber: 3.9 Consensus size: 97
1271197 TTCCCTTTTC
*
1271207 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCT-TTTCAAAGCCCACAACTCCGTGGCA--CTTTTTC
*
1271271 TCTTTTCAAAGCCCACGACTCCGTGGCA-C-TCTTT
63 TCTTTT-AAAGCCCACAACTCCGTGGCACCTTCTTT
* *
1271305 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCA--CTTTTTCT
*
1271370 CTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTGTTT
64 CTTTT-AAAGCCCACAACTCCGTGGCACC---TTC--TTT
* * *
1271410 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCTGTGGCAC----TCT-T
1 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTCTCT
1271470 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
66 TTTAAAGCCCACAACTCCGTGGCAC-C---TT--CTTT
*
1271508 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTT-
1 AAAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTC
1271572 TCTTTTAAAGCCCACAACTCCGTGGCAC
63 TCTTTTAAAGCCCACAACTCCGTGGCAC
1271600 TCTTTTTCCC
Statistics
Matches: 263, Mismatches: 13, Indels: 31
0.86 0.04 0.10
Matches are distributed among these distances:
97 24 0.09
98 117 0.44
99 8 0.03
100 1 0.00
101 26 0.10
103 3 0.01
104 1 0.00
105 83 0.32
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.31
Consensus pattern (97 bp):
AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTCTCT
TTTAAAGCCCACAACTCCGTGGCACCTTCTTT
Found at i:1271398 original size:169 final size:165
Alignment explanation
Indices: 1271073--1271638 Score: 879
Period size: 169 Copynumber: 3.4 Consensus size: 165
1271063 TGGTACTCTT
* *
1271073 TTTAAAGCCCACAACTTCGTGGCACCTTCTTCTTTCCAAAGCCCACAACTCCGTGGCACTCTTTA
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTA
1271138 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCT
66 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCT
1271203 TTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
131 TTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
* *
1271238 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTCT
1 TTTAAAGCCCACAACTCCGTGGCAC-C-TTCT-TCTTTTCAAAGCCCACAACTCCGTGGCACTCT
*
1271303 TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTT
63 TTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCTGTGGCACTCTTTTT
*
1271368 CCCTTTTCAAAGCCCACAACTCTGTGGCACCTTTTTCTG
127 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
* * *
1271407 TTTAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCTGTGGCACTCTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTC--TT
* *
1271472 TAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
64 TAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
*
1271537 CCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCT-
127 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
* *
1271575 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT--AAGTCCACAACTCCGTGGCA-TCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT--CTTTTCAAAGCCCACAACTCCGTGGCACTCT
1271637 TT
63 TT
1271639 CTCCCTTCTC
Statistics
Matches: 371, Mismatches: 19, Indels: 21
0.90 0.05 0.05
Matches are distributed among these distances:
165 24 0.06
166 34 0.09
167 6 0.02
168 116 0.31
169 182 0.49
170 4 0.01
171 5 0.01
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (165 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTA
AAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCT
TTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTG
Found at i:1271596 original size:70 final size:70
Alignment explanation
Indices: 1271469--1271638 Score: 281
Period size: 70 Copynumber: 2.4 Consensus size: 70
1271459 GTGGCACTCT
1271469 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTT
1 TTTTAAAGCCCACAACTCCGTGGCACT-TTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTT
1271534 TTTCCC
65 TTTCCC
*
1271540 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 TTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTT
1271604 TTTCCC
65 TTTCCC
*
1271610 TTTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCA-CTTT
1271639 CTCCCTTCTC
Statistics
Matches: 95, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
68 19 0.20
69 4 0.04
70 40 0.42
71 9 0.09
72 23 0.24
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (70 bp):
TTTTAAAGCCCACAACTCCGTGGCACTTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTT
TTCCC
Found at i:1271654 original size:105 final size:102
Alignment explanation
Indices: 1271016--1271659 Score: 650
Period size: 105 Copynumber: 6.4 Consensus size: 102
1271006 ATTTTGTCTC
* * * * * *
1271016 AAAGTCCACGACTCAGTGGCA-TTTTTTC-TTT-AAAGCCCACAACTCCGTGGTAC---TCT-TT
1 AAAGCCCACAACTCCGTGGCACTTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTT
* *
1271074 TTAAAGCCCACAACTTCGTGGCAC-CTTCTT--CTTT
66 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
*
1271108 CCAAAGCCCACAACTCCGTGGCA----C-TC-TTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
1 --AAAGCCCACAACTCCGTGGCACTTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
*
1271166 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
64 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC-TTT
1271206 CAAAGCCCACAACTCCGTGGCACCTTT-TTCTGTTT-AAAGCCCACAACTCCGTGGCACTCTTTT
1 -AAAGCCCACAACTCCGTGGCA-CTTTCTTCT-TTTCAAAGCCCACAACTCCGTGGCA--CTTTT
*
1271269 TCTCTTTTCAAAGCCCACGACTCCGTGGCA--C----T--CTTT
61 T-TCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
* *
1271305 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACTTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACT-TTTTT--
* **
1271370 CTTTTCAAAGCCCACAACTCTGTGGCAC-CTTTTTCTGTTT
63 CTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
* * * * *
1271410 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCTGTGGCAC---TCT-TT
1 AAAGCCCACAACTCCGTGGCACTTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTT
1271471 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
66 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
*
1271508 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTT
1 AAAGCCCACAACTCCGTGGCACT-TTCTT--CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTT
1271573 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
63 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
* * * *
1271613 TAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCTCTAAAGCCCACA
1 AAAGCCCACAACTCCGTGGCA-CTTTCT-TCTTTTC-AAAGCCCACA
1271660 CAAGTCGGTG
Statistics
Matches: 473, Mismatches: 34, Indels: 75
0.81 0.06 0.13
Matches are distributed among these distances:
90 26 0.05
93 2 0.00
94 42 0.09
95 5 0.01
96 3 0.01
97 54 0.11
98 108 0.23
99 8 0.02
100 1 0.00
101 28 0.06
102 3 0.01
103 1 0.00
104 31 0.07
105 128 0.27
106 8 0.02
107 6 0.01
108 19 0.04
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (102 bp):
AAAGCCCACAACTCCGTGGCACTTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTT
TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
Found at i:1271720 original size:33 final size:33
Alignment explanation
Indices: 1271641--1271747 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
1271631 GCATCTTTCT
1271641 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGC-AA
*
1271675 CCCTTCTCTAAAGCCCACACAAGTTGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
1271708 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1271741 CCCTTCT
1 CCCTTCT
1271748 AAGCCCAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
33 39 0.57
34 30 0.43
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.21
Consensus pattern (33 bp):
CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:1271805 original size:49 final size:49
Alignment explanation
Indices: 1271747--1272968 Score: 1264
Period size: 49 Copynumber: 24.7 Consensus size: 49
1271737 GCAACCCTTC
* * * *
1271747 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1271796 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1271845 TAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1271894 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1271943 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1271992 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1272041 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1272090 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* * *
1272142 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CC----T-TCATCTT
* * * * * * * * *
1272197 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-CT-TCA-TCTT
* * * ** * ** * ** * *
1272250 CTCA-TCATCATTTTAAGTCCAATATCGCTGGCCT-TG-A-ATCAGCATATTGGCATCTTCATCT
1 -TAAGTC--CAATGT-AG--C--TGGC-CTTGAATCAGCACATTGGC--A---CCTTC---ATCT
1272311 T
49 T
* *
1272312 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1272361 TAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * **
1272404 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATATTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1272453 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1272502 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
*
1272554 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1272603 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
1272652 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1272701 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
1272750 GAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
1272793 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1272842 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
1272885 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--CTT-CATCTT
*
1272937 TAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
1272969 GTTGACATCC
Statistics
Matches: 980, Mismatches: 140, Indels: 103
0.80 0.11 0.08
Matches are distributed among these distances:
43 115 0.12
45 2 0.00
47 2 0.00
49 636 0.65
50 3 0.00
51 4 0.00
52 122 0.12
53 6 0.01
54 7 0.01
55 48 0.05
56 3 0.00
57 5 0.01
58 4 0.00
59 3 0.00
60 9 0.01
61 5 0.01
62 5 0.01
63 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:1272028 original size:147 final size:147
Alignment explanation
Indices: 1271747--1272968 Score: 1436
Period size: 147 Copynumber: 8.2 Consensus size: 147
1271737 GCAACCCTTC
* * * * *
1271747 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* * * * * *
1271812 GGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATTAGCAT
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
1271877 ATTGGCACCTTTATCTT
131 ATTGGCACCTTTATCTT
* * *
1271894 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* *
1271959 GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
* * *
1272024 ATTGGCACCTTCACCAT
131 ATTGGCACCTTTATCTT
*
1272041 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* *
1272106 GGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAG
66 GGCCTTGAATCAGCACATTGGCACC--TT-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
* *
1272171 CACGTTGACATCCTTTTTCTCATCTT
128 CACATTGGCA-CC---TT-T-ATCTT
* * * * * * *
1272197 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG---------CAC----CT--TCATC--T
* * *
1272262 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGC
49 TTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
*
1272327 TGGCCTTGACTCAGCACATTGGCACCTTTATCTT
114 TGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1272361 TAAGTCCAATGTAGCTGGCCTTAAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* ** *
1272420 GGCCTTGAATCAGCATATTGGCATATTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
*
1272485 ATTGGCACCTTCATCTT
131 ATTGGCACCTTTATCTT
* * *
1272502 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTTTAAGTCCAATATA
* * *
1272567 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
63 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
* * *
1272632 CATATTGGCATCTTCATCTT
128 CACATTGGCACCTTTATCTT
* *
1272652 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* * * *
1272717 GGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
1272782 ATTGGCA-C-----CTT
131 ATTGGCACCTTTATCTT
* * * * *
1272793 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* *
1272858 GGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
*
1272917 ATTGGCACATTTTCCATCTT
131 ATTGGCAC-CTTT--ATCTT
*
1272937 TAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
1272969 GTTGACATCC
Statistics
Matches: 935, Mismatches: 96, Indels: 91
0.83 0.09 0.08
Matches are distributed among these distances:
135 38 0.04
137 1 0.00
141 217 0.23
143 1 0.00
144 31 0.03
145 1 0.00
146 1 0.00
147 300 0.32
148 3 0.00
149 2 0.00
150 169 0.18
151 2 0.00
154 2 0.00
155 2 0.00
156 32 0.03
164 34 0.04
165 4 0.00
166 2 0.00
169 4 0.00
170 41 0.04
171 7 0.01
173 41 0.04
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (147 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
ATTGGCACCTTTATCTT
Found at i:1272991 original size:389 final size:384
Alignment explanation
Indices: 1272252--1273034 Score: 1210
Period size: 389 Copynumber: 2.0 Consensus size: 384
1272242 TCACTTTTCT
* * * *
1272252 CATCATCATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
1 CATCTTCATTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * *
1272317 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCT
66 CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTGAAGTCCAATGTAGCTGGCCT
1272382 TAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATATT
131 TAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATATT
*
1272447 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
196 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--CA-CTTTAAGTCCAAT
*
1272512 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTG
257 ATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTG
* * * * *
1272577 ACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
322 AATCAGCACATTGACACCTTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGG
* *
1272640 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
1 CATCTTCAT-TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAG
* * *
1272705 TCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCTGGCC
65 TCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTGAAGTCCAATGTAGCTGGCC
* * *
1272770 TTGACTCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCT
130 TTAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATAT
1272835 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-CTTTAAGTCCAATATA
195 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCACTTTAAGTCCAATATA
*
1272898 GCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAAT
260 GCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAAT
* * *
1272963 CAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTG
325 CAGCACATTGACA-CC----T-TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTG
1273028 G
384 G
1273029 CATCTT
1 CATCTT
1273035 TATCACTTTT
Statistics
Matches: 361, Mismatches: 27, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
383 89 0.25
384 2 0.01
385 1 0.00
388 9 0.02
389 260 0.72
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (384 bp):
CATCTTCATTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
CCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTGAAGTCCAATGTAGCTGGCCT
TAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATATT
CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCACTTTAAGTCCAATATAG
CTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATC
AGCACATTGACACCTTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGG
Found at i:1273939 original size:33 final size:33
Alignment explanation
Indices: 1273902--1273968 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1273892 TTCAACGATT
1273902 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1273935 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1273968 T
1 T
1273969 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1273940 original size:13 final size:13
Alignment explanation
Indices: 1273922--1273946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1273912 CATAAAATGT
1273922 TGTATCGATACAA
1 TGTATCGATACAA
1273935 TGTATCGATACA
1 TGTATCGATACA
1273947 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1274027 original size:13 final size:13
Alignment explanation
Indices: 1274009--1274033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1273999 ATTACTCAAA
1274009 TGTATCGATACAT
1 TGTATCGATACAT
1274022 TGTATCGATACA
1 TGTATCGATACA
1274034 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1274097 original size:51 final size:52
Alignment explanation
Indices: 1274042--1274161 Score: 208
Period size: 52 Copynumber: 2.3 Consensus size: 52
1274032 CACTGATCTT
*
1274042 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
1274093 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1274145 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1274162 ATAAATTTTC
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
51 19 0.29
52 44 0.67
53 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:1278229 original size:41 final size:41
Alignment explanation
Indices: 1278166--1278247 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
1278156 TTTTTGTAAA
*
1278166 CCTTTTTTCATGATATTACCTTTCAAGTCGAAAA-CTTATT
1 CCTTTTTTCATGATATTACCTTTCAAGTCAAAAATCTTATT
* *
1278206 CCTTTTTTCAGTGATTTTGCCTTTCAAGTCAAAAATCTTATT
1 CCTTTTTTCA-TGATATTACCTTTCAAGTCAAAAATCTTATT
1278248 ATTTTTCATG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 10 0.27
41 21 0.57
42 6 0.16
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (41 bp):
CCTTTTTTCATGATATTACCTTTCAAGTCAAAAATCTTATT
Found at i:1278253 original size:41 final size:40
Alignment explanation
Indices: 1278168--1278258 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 40
1278158 TTTGTAAACC
* *
1278168 TTTTTTCATGATATTACCTTTCAAGTCGAAAACTTATTCC
1 TTTTTTCATGATATTACCTTTCAAGTCAAAAACTTATTCA
* *
1278208 TTTTTTCAGTGATTTTGCCTTTCAAGTCAAAAATCTTATT-A
1 TTTTTTCA-TGATATTACCTTTCAAGTCAAAAA-CTTATTCA
1278249 -TTTTTCATGA
1 TTTTTTCATGA
1278259 ATTCGATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 3 0.07
40 15 0.33
41 21 0.47
42 6 0.13
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.48
Consensus pattern (40 bp):
TTTTTTCATGATATTACCTTTCAAGTCAAAAACTTATTCA
Found at i:1282617 original size:11 final size:11
Alignment explanation
Indices: 1282593--1282644 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1282583 AATCATTAAG
1282593 TTAAATACATAT
1 TTAAATA-ATAT
1282605 TTAAATAATAT
1 TTAAATAATAT
**
1282616 TTTTA-AATAT
1 TTAAATAATAT
**
1282626 TTAAATCTTAT
1 TTAAATAATAT
1282637 TTAAATAA
1 TTAAATAA
1282645 ATTAACCTAT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
10 8 0.26
11 16 0.52
12 7 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATAATAT
Found at i:1282793 original size:19 final size:19
Alignment explanation
Indices: 1282764--1282809 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1282754 TTTTTCATTC
1282764 AAAATTTTATAT-AAAAAAT
1 AAAA-TTTATATCAAAAAAT
*
1282783 AATAATTTATATCAAACAAT
1 AA-AATTTATATCAAAAAAT
1282803 AAAATTT
1 AAAATTT
1282810 CAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTTATATCAAAAAAT
Found at i:1286069 original size:11 final size:12
Alignment explanation
Indices: 1286042--1286074 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1286032 GAATATAATT
1286042 ATATAATATAAA
1 ATATAATATAAA
1286054 A-ATAAT-TAAA
1 ATATAATATAAA
1286064 ATATAATATAA
1 ATATAATATAA
1286075 TATAGAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.26
11 10 0.53
12 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:1286074 original size:35 final size:35
Alignment explanation
Indices: 1286033--1286116 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
1286023 ATAATTTTAG
1286033 AATATAATTATATAATATAAAAATA-ATTAAAATAT
1 AATATAATTATATAATATAAAAATATATTAAAA-AT
* **
1286068 AATATAA-TATAGAAATATATTAATATATTAAAAAT
1 AATATAATTATA-TAATATAAAAATATATTAAAAAT
*
1286103 TATATAATTATATA
1 AATATAATTATATA
1286117 TTTTTTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
34 4 0.10
35 26 0.63
36 11 0.27
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (35 bp):
AATATAATTATATAATATAAAAATATATTAAAAAT
Found at i:1286076 original size:19 final size:20
Alignment explanation
Indices: 1286036--1286110 Score: 51
Period size: 19 Copynumber: 4.1 Consensus size: 20
1286026 ATTTTAGAAT
*
1286036 ATAATTATATAATATAA-A-A
1 ATAATTAGA-AATATAATATA
1286055 ATAATTA-AAATATAATATA
1 ATAATTAGAAATATAATATA
1286074 AT-A-TAGAAATAT-AT-TA
1 ATAATTAGAAATATAATATA
*
1286090 ATATATTA-AAA-ATTATATA
1 ATA-ATTAGAAATATAATATA
1286109 AT
1 AT
1286111 TATATATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
16 4 0.08
17 13 0.27
18 15 0.31
19 16 0.33
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
ATAATTAGAAATATAATATA
Found at i:1286076 original size:27 final size:28
Alignment explanation
Indices: 1286042--1286095 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
1286032 GAATATAATT
1286042 ATATAATATAAAAATA-ATTAAAATATA
1 ATATAATATAAAAATATATTAAAATATA
* *
1286069 ATATAATATAGAAATATATTAATATAT
1 ATATAATATAAAAATATATTAAAATAT
1286096 TAAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (28 bp):
ATATAATATAAAAATATATTAAAATATA
Found at i:1286333 original size:2 final size:2
Alignment explanation
Indices: 1286328--1286359 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1286318 CTCTGCTCTT
*
1286328 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1286360 ATTACCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1286588 original size:23 final size:22
Alignment explanation
Indices: 1286534--1286594 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
1286524 ATTATATGAT
*
1286534 ATAAATATTATATTAAAAAAATA
1 ATAAATATAATA-TAAAAAAATA
* *
1286557 ATATGATATAATATAAAAAATTA
1 ATA-AATATAATATAAAAAAATA
*
1286580 GATAAATATATTATA
1 -ATAAATATAATATA
1286595 TTTTATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 21 0.68
24 10 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (22 bp):
ATAAATATAATATAAAAAAATA
Found at i:1287103 original size:16 final size:18
Alignment explanation
Indices: 1287082--1287114 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1287072 GGTTTGAAAA
1287082 TTTTTAA-TTT-TTTTAC
1 TTTTTAAGTTTATTTTAC
1287098 TTTTTAAGTTTATTTTA
1 TTTTTAAGTTTATTTTA
1287115 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTTAAGTTTATTTTAC
Found at i:1288596 original size:23 final size:22
Alignment explanation
Indices: 1288551--1288616 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
1288541 ATTTTTTATT
1288551 TAAATTTAATAATAAAAATATA
1 TAAATTTAATAATAAAAATATA
1288573 TAAATATTAAT-ATAAAAATA-A
1 TAAAT-TTAATAATAAAAATATA
**
1288594 TATTTTTAGATAATAAAACATAT
1 TAAATTTA-ATAATAAAA-ATAT
1288617 CTACAAGTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 3 0.08
21 6 0.16
22 20 0.54
23 8 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATTTAATAATAAAAATATA
Found at i:1293253 original size:11 final size:12
Alignment explanation
Indices: 1293215--1293258 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
1293205 AATTAAATAA
1293215 AAATAATATATT
1 AAATAATATATT
*
1293227 AAATAAATATTTTT
1 AAAT-AATA-TATT
1293241 AAATAATA-ATT
1 AAATAATATATT
1293252 AAATAAT
1 AAATAAT
1293259 TTTATATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 4 0.14
13 8 0.29
14 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAATAATATATT
Found at i:1293741 original size:21 final size:20
Alignment explanation
Indices: 1293712--1293750 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1293702 TATATAAATA
1293712 TATTATTAAAAAATAATTATT
1 TATTATTAAAAAA-AATTATT
* *
1293733 TATTTTTAAATAAAATTA
1 TATTATTAAAAAAAATTA
1293751 ATTTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTATTAAAAAAAATTATT
Found at i:1293785 original size:18 final size:18
Alignment explanation
Indices: 1293722--1293787 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 18
1293712 TATTATTAAA
* *
1293722 AAATAATTATTTATTTTT
1 AAATAATTAATTATATTT
*
1293740 AAATAAAATTAATTTTAAATTAT
1 AAAT--AATTAA--TTATATT-T
1293763 AAAATAATTAATTATATTT
1 -AAATAATTAATTATATTT
1293782 AAATAA
1 AAATAA
1293788 AAATAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
18 10 0.26
19 1 0.03
20 11 0.29
22 11 0.29
23 1 0.03
24 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATTAATTATATTT
Found at i:1293883 original size:26 final size:27
Alignment explanation
Indices: 1293854--1293914 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
1293844 GTGATATGTG
*
1293854 TTTTTAATAA-AATATAATATAATATA
1 TTTTTAATAATAATATAATAAAATATA
1293880 -TTTTAA-AATTAATATAATAAAATATA
1 TTTTTAATAA-TAATATAATAAAATATA
1293906 TTTATTAAT
1 TTT-TTAAT
1293915 TTTTTAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 2 0.07
25 6 0.21
26 15 0.52
27 2 0.07
28 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTTTAATAATAATATAATAAAATATA
Found at i:1294376 original size:2 final size:2
Alignment explanation
Indices: 1294371--1294396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1294361 AATTTTTTTA
1294371 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1294397 TTGTGACGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1295417 original size:26 final size:25
Alignment explanation
Indices: 1295345--1295438 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 25
1295335 ATCGATTGAT
1295345 ATAATATTTTAATTTTTTTATTTTTTA
1 ATAAT-TTTTAATTTTTTTA-TTTTTA
* * *
1295372 A-AATTTCTTTCACTTATTTATTTTTA
1 ATAA-TT-TTTAATTTTTTTATTTTTA
* *
1295398 ACTAATTTTTAATTTTTTTAGTCTTA
1 A-TAATTTTTAATTTTTTTATTTTTA
*
1295424 ATCATTTTT-ATTTTT
1 ATAATTTTTAATTTTT
1295439 ATAATTTCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
24 6 0.11
25 7 0.13
26 25 0.46
27 14 0.26
28 2 0.04
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (25 bp):
ATAATTTTTAATTTTTTTATTTTTA
Found at i:1297501 original size:11 final size:12
Alignment explanation
Indices: 1297474--1297506 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
1297464 GATAATTTCG
1297474 AATATAATATAT
1 AATATAATATAT
1297486 AATATAATAT-T
1 AATATAATATAT
1297497 AATATAATAT
1 AATATAATAT
1297507 GTTTAGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATAATATAT
Found at i:1297582 original size:20 final size:18
Alignment explanation
Indices: 1297537--1297582 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
1297527 TGTATGGTGT
1297537 TTATATTTAAAATTTTAA
1 TTATATTTAAAATTTTAA
*
1297555 -TGTATTTAATAATTTTATA
1 TTATATTTAA-AATTTTA-A
1297574 TTATATTTA
1 TTATATTTA
1297583 TATTTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.35
18 7 0.30
19 1 0.04
20 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATATTTAAAATTTTAA
Found at i:1297889 original size:2 final size:2
Alignment explanation
Indices: 1297882--1297908 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1297872 TTCCATCATA
1297882 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1297909 GTTTTACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1298819 original size:29 final size:27
Alignment explanation
Indices: 1298765--1298834 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 27
1298755 ATTTAATAAA
* **
1298765 ATAAAAATATTTTATTTAAATTTAATT
1 ATAAAAATATTTTATTAAAAAATAATT
1298792 ATAAAATATATTATTATTAAAAAATAATT
1 ATAAAA-ATATT-TTATTAAAAAATAATT
* * *
1298821 TTTAATATATTTTA
1 ATAAAAATATTTTA
1298835 AATAATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 9 0.26
28 10 0.29
29 16 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
ATAAAAATATTTTATTAAAAAATAATT
Found at i:1300638 original size:2 final size:2
Alignment explanation
Indices: 1300631--1300659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1300621 CAATTATTAG
1300631 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1300660 AGATATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1301469 original size:15 final size:15
Alignment explanation
Indices: 1301444--1301512 Score: 59
Period size: 15 Copynumber: 4.3 Consensus size: 15
1301434 TATTCCATAA
*
1301444 AAAAAAATATAATAT
1 AAAATAATATAATAT
*
1301459 AATATAATATAATA-
1 AAAATAATATAATAT
1301473 AAAATAATATAAATATAT
1 AAAATAATAT--A-ATAT
*
1301491 CAAAATTTATATAATAT
1 -AAAA-TAATATAATAT
1301508 AAAAT
1 AAAAT
1301513 TTTAATTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 9 0.20
15 13 0.30
16 5 0.11
17 7 0.16
18 1 0.02
19 4 0.09
20 5 0.11
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAATATAATAT
Found at i:1301481 original size:19 final size:20
Alignment explanation
Indices: 1301457--1301509 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1301447 AAAATATAAT
1301457 ATAATATAATATAAT-AAAA
1 ATAATATAATATAATCAAAA
1301476 ATAATATAA-ATATATCAAAA
1 ATAATATAATATA-ATCAAAA
* *
1301496 TTTATATAATATAA
1 ATAATATAATATAA
1301510 AATTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 11 0.38
20 12 0.41
21 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATATAATATAATCAAAA
Found at i:1301509 original size:5 final size:5
Alignment explanation
Indices: 1301449--1301489 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
1301439 CATAAAAAAA
*
1301449 AATAT AATAT AATAT AATAT AATA- AAAAT AATAT AAATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT A
1301490 TCAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.09
5 24 0.75
6 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:1301550 original size:33 final size:31
Alignment explanation
Indices: 1301482--1301556 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
1301472 AAAAATAATA
* *
1301482 TAAATATATCAAAATTTATATAATATAAAATTT
1 TAAATAT-T-AAAATTTATAAAATATAAAACTT
*
1301515 TAATTATTAAAATTTATAAAATATATAATACTT
1 TAAATATTAAAATTTATAAAATATA-AA-ACTT
1301548 TAAATATTA
1 TAAATATTA
1301557 TTATTATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 16 0.44
32 3 0.08
33 17 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAATATTAAAATTTATAAAATATAAAACTT
Found at i:1302001 original size:21 final size:21
Alignment explanation
Indices: 1301975--1302019 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1301965 TCTTCAATGG
1301975 TTTAATTTGTATTT-ATTAATT
1 TTTAA-TTGTATTTAATTAATT
*
1301996 TTTAATTGTTTTTAAATTAATT
1 TTTAATTGTATTT-AATTAATT
1302018 TT
1 TT
1302020 ATTTTTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTAATTGTATTTAATTAATT
Found at i:1303095 original size:15 final size:15
Alignment explanation
Indices: 1303075--1303119 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
1303065 ATTACTTTTT
1303075 TAACAATCACATTCC
1 TAACAATCACATTCC
* *
1303090 TAACAATCATATTCT
1 TAACAATCACATTCC
*
1303105 TAAAAATCACATTCC
1 TAACAATCACATTCC
1303120 ATTGAAATCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (15 bp):
TAACAATCACATTCC
Found at i:1305369 original size:21 final size:22
Alignment explanation
Indices: 1305328--1305369 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1305318 TGATCAAACT
1305328 TAAATATTAAACTCAATTGACC
1 TAAATATTAAACTCAATTGACC
*
1305350 TAAATATTAAAC-CTATTGAC
1 TAAATATTAAACTCAATTGAC
1305370 ACCCGAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (22 bp):
TAAATATTAAACTCAATTGACC
Found at i:1306867 original size:13 final size:13
Alignment explanation
Indices: 1306836--1306886 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 13
1306826 ATAGAGATGA
*
1306836 AAAATTA-TTTCT
1 AAAATTATTTTTT
1306848 AATAATTATTTTTT
1 AA-AATTATTTTTT
1306862 AAAATTATATTTTTT
1 AAAA-T-TATTTTTT
1306877 AAAATT-TTTT
1 AAAATTATTTT
1306887 AACATGATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 6 0.18
13 8 0.24
14 8 0.24
15 12 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:1306874 original size:15 final size:15
Alignment explanation
Indices: 1306854--1306882 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1306844 TTCTAATAAT
1306854 TATTTTTTAAAATTA
1 TATTTTTTAAAATTA
1306869 TATTTTTTAAAATT
1 TATTTTTTAAAATT
1306883 TTTTAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTTTAAAATTA
Found at i:1308868 original size:18 final size:17
Alignment explanation
Indices: 1308828--1308868 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1308818 TTAAATTTAA
1308828 ATAGTTTTTAAGAAGTG
1 ATAGTTTTTAAGAAGTG
*
1308845 AGAGTTTTTAAGAAGTCG
1 ATAGTTTTTAAGAAGT-G
1308863 ATAGTT
1 ATAGTT
1308869 GAGAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.39
Consensus pattern (17 bp):
ATAGTTTTTAAGAAGTG
Found at i:1309059 original size:2 final size:2
Alignment explanation
Indices: 1309052--1309080 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1309042 TTACTCACAT
1309052 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1309081 ATCTTCAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1309577 original size:2 final size:2
Alignment explanation
Indices: 1309570--1309600 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1309560 CTTGAAAATG
*
1309570 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1309601 ATACAAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1312121 original size:2 final size:2
Alignment explanation
Indices: 1312114--1312170 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
1312104 TGTAGTCTAA
* * *
1312114 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1312156 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1312171 ATAGTTGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1315948 original size:2 final size:2
Alignment explanation
Indices: 1315943--1315981 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1315933 TCAAATATGC
1315943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1315982 GGTCTTTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1319279 original size:23 final size:24
Alignment explanation
Indices: 1319253--1319297 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1319243 ATAAATTAAA
*
1319253 TTAAAAAT-TTAAATTTAATTTAT
1 TTAAAAATATAAAATTTAATTTAT
1319276 TTAAAAATATAAAATTTAATTT
1 TTAAAAATATAAAATTTAATTT
1319298 TGATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAAAAATATAAAATTTAATTTAT
Found at i:1319537 original size:17 final size:17
Alignment explanation
Indices: 1319523--1319556 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
1319513 AAATTAAAAT
1319523 TAAATAAATAATAAATAC
1 TAAAT-AATAATAAATAC
1319541 TAAATAATAATAAATA
1 TAAATAATAATAAATA
1319557 AATTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATAATAATAAATAC
Found at i:1320634 original size:14 final size:13
Alignment explanation
Indices: 1320610--1320673 Score: 58
Period size: 14 Copynumber: 4.7 Consensus size: 13
1320600 TTTTTAATAG
1320610 ATTTAAATATTTAA
1 ATTT-AATATTTAA
*
1320624 TATTTAATATTATTA
1 -ATTTAATATT-TAA
1320639 ATTTAA-ATTTAA
1 ATTTAATATTTAA
* *
1320651 ATAATAATATATAA
1 AT-TTAATATTTAA
1320665 ATTTAATAT
1 ATTTAATAT
1320674 AAATAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.10
13 12 0.29
14 19 0.46
15 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTAATATTTAA
Found at i:1320650 original size:20 final size:20
Alignment explanation
Indices: 1320618--1320679 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1320608 AGATTTAAAT
*
1320618 ATTTAATATTTAATATTATTA
1 ATTTAA-ATTTAATATTAATA
1320639 ATTTAAATTTAA-A-TAATA
1 ATTTAAATTTAATATTAATA
*
1320657 ATATATAAATTTAATATAAATA
1 AT-T-TAAATTTAATATTAATA
1320679 A
1 A
1320680 AAAATTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 6 0.17
19 2 0.06
20 15 0.43
21 7 0.20
22 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAAATTTAATATTAATA
Found at i:1320769 original size:26 final size:24
Alignment explanation
Indices: 1320723--1320778 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 24
1320713 GTGTATAATA
1320723 AATAAATTTAAATTTTAAAATACTT
1 AATAAATTTAAATTTTAAAATA-TT
*
1320748 ACATAAACTTTAAA-TTTCAAATATT
1 A-ATAAA-TTTAAATTTTAAAATATT
1320773 AATAAA
1 AATAAA
1320779 AATATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.18
25 4 0.14
26 13 0.46
27 6 0.21
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAAATTTAAATTTTAAAATATT
Found at i:1322490 original size:17 final size:16
Alignment explanation
Indices: 1322428--1322490 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
1322418 CGTATATAAT
*
1322428 TTTTAATATAAATATAA
1 TTTTAATA-AAATATTA
1322445 TTTTAAT--AAT-TTA
1 TTTTAATAAAATATTA
*
1322458 TATTATATAAATATATGTA
1 TTTTA-ATAAA-ATAT-TA
1322477 TTTTAATAAAATAT
1 TTTTAATAAAATAT
1322491 CTTTAATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 6 0.16
14 5 0.14
16 1 0.03
17 13 0.35
18 6 0.16
19 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TTTTAATAAAATATTA
Found at i:1323415 original size:19 final size:19
Alignment explanation
Indices: 1323393--1323429 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1323383 TGATTTCATG
* *
1323393 TTAATAATCTTTTAAATAC
1 TTAATAATATCTTAAATAC
1323412 TTAATAATATCTTAAATA
1 TTAATAATATCTTAAATA
1323430 AATTAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATAATATCTTAAATAC
Found at i:1323452 original size:16 final size:17
Alignment explanation
Indices: 1323431--1323473 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1323421 TCTTAAATAA
*
1323431 ATTAATAAAAT-ATTTT
1 ATTAATAAAATAATATT
*
1323447 ATTAATTAAATAATATT
1 ATTAATAAAATAATATT
1323464 A-TAATAAAAT
1 ATTAATAAAAT
1323474 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAATAAAATAATATT
Found at i:1324086 original size:35 final size:34
Alignment explanation
Indices: 1324037--1324159 Score: 120
Period size: 35 Copynumber: 3.4 Consensus size: 34
1324027 AAATTAAAAA
* *
1324037 ATATGTATAATAAATAATTAAAAATTATTAAATT
1 ATATTTATATTAAATAATTAAAAATTATTAAATT
*
1324071 AATATTTATATTAAATAATTAAATATATATTAAAATT
1 -ATATTTATATTAAATAATTAAAAAT-TATT-AAATT
* **
1324108 ATGTTTATGGTAAATAATAACTAAAAATTATTTAAATT
1 ATATTTATATTAAATAAT---TAAAAATTA-TTAAATT
*
1324146 ATATTTAAATTAAA
1 ATATTTATATTAAA
1324160 AAATAAATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
35 22 0.31
36 19 0.27
37 5 0.07
38 17 0.24
39 8 0.11
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (34 bp):
ATATTTATATTAAATAATTAAAAATTATTAAATT
Done.