Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 19
Found at i:1174440 original size:30 final size:30
Alignment explanation
Indices: 1174382--1174440 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1174372 TAAAAAATTA
* * * *
1174382 AATATTTTAAATATCTATTTTGAGAAAAAG
1 AATATTTTAAAAAACTATTTTAACAAAAAG
1174412 AATATTTTAAAAAACTATTTTAACAAAAA
1 AATATTTTAAAAAACTATTTTAACAAAAA
1174441 TAATTCTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (30 bp):
AATATTTTAAAAAACTATTTTAACAAAAAG
Found at i:1177227 original size:8 final size:7
Alignment explanation
Indices: 1177201--1177225 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1177191 GAGTTTTTTT
1177201 AAAATTA
1 AAAATTA
1177208 AAAATTA
1 AAAATTA
1177215 AAAATTA
1 AAAATTA
1177222 AAAA
1 AAAA
1177226 ATATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTA
Found at i:1179822 original size:22 final size:23
Alignment explanation
Indices: 1179770--1179824 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
1179760 ATTTTTTAGA
** *
1179770 AAAATAT-AAATATTTTAAATTT
1 AAAATATAAAATATTAAAAAGTT
*
1179792 AAAACATAAAATATTAAAAAGTT
1 AAAATATAAAATATTAAAAAGTT
1179815 -AAATATAAAA
1 AAAATATAAAA
1179825 ATATCATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAATATAAAATATTAAAAAGTT
Found at i:1180918 original size:14 final size:14
Alignment explanation
Indices: 1180873--1180919 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1180863 AAGTTATGAA
* *
1180873 TTAATTTATATACT
1 TTAATTTATTTATT
*
1180887 TTAATTTAATTAATT
1 TTAATTT-ATTTATT
1180902 TTAATTTATTTATT
1 TTAATTTATTTATT
1180916 TTAA
1 TTAA
1180920 ATATTTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATTTATTTATT
Found at i:1185354 original size:16 final size:17
Alignment explanation
Indices: 1185333--1185365 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1185323 CATCACCCAA
*
1185333 TGATAT-TTTTTAGATT
1 TGATATATTTTCAGATT
1185349 TGATATATTTTCAGATT
1 TGATATATTTTCAGATT
1185366 CTTTCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (17 bp):
TGATATATTTTCAGATT
Found at i:1188945 original size:87 final size:87
Alignment explanation
Indices: 1188786--1188946 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
1188776 TTAAAATGCT
* *
1188786 CTAAAAAAATAATGAGAGCCAAAATAACTATTCGGTTAAATCTTAGGAGCATTTATGTTCTAAAA
1 CTAAAAAAATAATGAGAGCCAAAATAACTATTCAGTTAAATCTTACGAGCATTTATGTTCTAAAA
**
1188851 TGGAACGTTGGGAGCCAAAATA
66 TAAAACGTTGGGAGCCAAAATA
* * * *
1188873 CTAAAAAAATAAT-ATAGACCAAAATAATTATTCAGTTAAATGTTAACGA-CATTTTTGTTCTAA
1 CTAAAAAAATAATGAGAG-CCAAAATAACTATTCAGTTAAATCTT-ACGAGCATTTATGTTCTAA
1188936 AATAAAACGTT
64 AATAAAACGTT
1188947 AGAATCCAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 3 0.05
87 58 0.91
88 3 0.05
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (87 bp):
CTAAAAAAATAATGAGAGCCAAAATAACTATTCAGTTAAATCTTACGAGCATTTATGTTCTAAAA
TAAAACGTTGGGAGCCAAAATA
Found at i:1194625 original size:6 final size:7
Alignment explanation
Indices: 1194603--1194632 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1194593 GTCAAAGAAA
1194603 GTCAACG
1 GTCAACG
1194610 GTCAACG
1 GTCAACG
1194617 GTC-ACG
1 GTCAACG
1194623 GTCAACG
1 GTCAACG
1194630 GTC
1 GTC
1194633 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:1194625 original size:13 final size:13
Alignment explanation
Indices: 1194607--1194632 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1194597 AAGAAAGTCA
1194607 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1194620 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1194633 GGGTCGGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:1194659 original size:10 final size:10
Alignment explanation
Indices: 1194641--1194709 Score: 72
Period size: 9 Copynumber: 7.1 Consensus size: 10
1194631 TCGGGTCGGG
*
1194641 TCAATCCGGT
1 TCAAACCGGT
*
1194651 TCAGACCGG-
1 TCAAACCGGT
1194660 TCAAACCGGT
1 TCAAACCGGT
*
1194670 TCGAACCGG-
1 TCAAACCGGT
1194679 TCAAACCGGT
1 TCAAACCGGT
*
1194689 TCAAAACTGG-
1 TC-AAACCGGT
1194699 TCAAACCGGT
1 TCAAACCGGT
1194709 T
1 T
1194710 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.46
10 20 0.42
11 6 0.12
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1194661 original size:19 final size:20
Alignment explanation
Indices: 1194639--1194709 Score: 101
Period size: 19 Copynumber: 3.6 Consensus size: 20
1194629 GGTCGGGTCG
*
1194639 GGTCAATCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
1194658 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
1194677 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
1194697 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1194710 TTCCAGCAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 30 0.64
20 16 0.34
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:1201905 original size:13 final size:14
Alignment explanation
Indices: 1201887--1201915 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1201877 GTCAAAGAAA
1201887 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
1201900 GTCAACGGTCAACG
1 GTCAACGGTCAACG
1201914 GT
1 GT
1201916 GGGGCCGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.24, C:0.28, G:0.31, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:1201932 original size:7 final size:7
Alignment explanation
Indices: 1201887--1201915 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1201877 GTCAAAGAAA
1201887 GTCAACG
1 GTCAACG
1201894 GTC-ACG
1 GTCAACG
1201900 GTCAACG
1 GTCAACG
1201907 GTCAACG
1 GTCAACG
1201914 GT
1 GT
1201916 GGGGCCGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.24, C:0.28, G:0.31, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:1201963 original size:19 final size:19
Alignment explanation
Indices: 1201939--1202025 Score: 104
Period size: 19 Copynumber: 4.5 Consensus size: 19
1201929 GGTCGGGTTG
*
1201939 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
1201958 GATCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1201977 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
1201996 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
1202016 GGTCAAACCG
1 GGTCAAACCG
1202026 ACGTTTGGTA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 47 0.78
20 12 0.20
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1201995 original size:10 final size:10
Alignment explanation
Indices: 1201941--1202025 Score: 70
Period size: 9 Copynumber: 8.8 Consensus size: 10
1201931 TCGGGTTGGG
*
1201941 TCAACCCGGT
1 TCAAACCGGT
* *
1201951 TCAGACC-GA
1 TCAAACCGGT
*
1201960 TCAACCCGGT
1 TCAAACCGGT
*
1201970 TCAGACCGG-
1 TCAAACCGGT
1201979 TCAAACCGGT
1 TCAAACCGGT
*
1201989 TCGAACCGG-
1 TCAAACCGGT
1201998 TCAAACCGGT
1 TCAAACCGGT
*
1202008 TCAAAACTGG-
1 TC-AAACCGGT
1202018 TCAAACCG
1 TCAAACCG
1202026 ACGTTTGGTA
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
9 27 0.47
10 25 0.43
11 6 0.10
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.16
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1202817 original size:427 final size:426
Alignment explanation
Indices: 1202023--1202828 Score: 1542
Period size: 427 Copynumber: 1.9 Consensus size: 426
1202013 ACTGGTCAAA
1202023 CCGACGTTTGGTAGCGTTTCACTTCAATTAATTTGAAGGGTTTGTTCATCGCTTGATGAGAACAC
1 CCGACGTTTGGTAGCGTTTCACTTCAATTAATTTGAAGGGTTTGTTCATCGCTTGATGAGAACAC
1202088 AACGGTGGTTTCAATTTTACGATTGGACGTCGAACGGCGTCGGAATCGGGCTTGGAAGTAAGGGT
66 AACGGTGGTTTCAATTTTACGATTGGACGTCGAACGGCGTCGGAATCGGGCTTGGAAGTAAGGGT
1202153 ACGAGAGAAGGAAAATTGAGCAATTCTCAATTGTGTTTTCTGATTTACAATCAGAAACCACGCTT
131 ACGAGAGAAGGAAAATTGAGCAATTCTCAATTGTGTTTTCTGATTTACAATCAGAAACCACGCTT
1202218 AAATTATAAGCCTGCCGACACTCCTTGGAGGAATTCAGGGTTTGGTCCCTGAATTTCCTTCAACT
196 AAATTATAAGCCTGCCGACACTCCTTGGAGGAATTCAGGGTTTGGTCCCTGAATTTCCTTCAACT
*
1202283 TATAAAATGGCCTATAACTTTTCATAAATTTTAGTTCAGTCATTAAATTTCACCAATTTTCACAA
261 TATAAAATGGCCTATAACTTTTCATAAATTTTAGTCCAGTCATTAAATTTCACCAATTTTCACAA
1202348 TTAACGTCCAATTTCAATTAAATATTATTTTGTAAATATTCGGGTTGTTACATTCCCGGCGATAG
326 TTAACGTCCAATTTCAATTAAATATTATTTTGTAAATATTCGGGTTGTTACATTCCCGGCGATAG
1202413 AGCTAAAAAAAACGACGATGCTTTGACTGAAAATTC
391 AGCTAAAAAAAACGACGATGCTTTGACTGAAAATTC
*
1202449 CCGACGTTTGGTAGCGTTTCACTTCAATTAATTTGAAGGGTTTGTTCCTCGCTTGATGATGAACA
1 CCGACGTTTGGTAGCGTTTCACTTCAATTAATTTGAAGGGTTTGTTCATCGCTTGATGA-GAACA
1202514 CAACGGTGGTTTCAATTTTACGATTGGACGTCGAACGGCGTCGGAATCGGGCTTGGAAGTAAGGG
65 CAACGGTGGTTTCAATTTTACGATTGGACGTCGAACGGCGTCGGAATCGGGCTTGGAAGTAAGGG
1202579 TACGAGAGAAGGAAAATTGAGCAAATTCTCAATTGTGTTTTCTGATTTACAATCAGAAACCACGC
130 TACGAGAGAAGGAAAATTGAGC-AATTCTCAATTGTGTTTTCTGATTTACAATCAGAAACCACGC
* *
1202644 TTAAATTATAAGCCTGCTGACACTCCTTGGAGGTATTCAGGGTTTGGTCCCTGAATTTCCTTCAA
194 TTAAATTATAAGCCTGCCGACACTCCTTGGAGGAATTCAGGGTTTGGTCCCTGAATTTCCTTCAA
*
1202709 CTTATAAAATGGCCTATAAC-TTTCATAACTTTTAGTCCAGTCATTAAATTTCACCAATTTTCAC
259 CTTATAAAATGGCCTATAACTTTTCATAAATTTTAGTCCAGTCATTAAATTTCACCAATTTTCAC
1202773 AATTAACGTCCAATTTCAATTAAATATTATTTTGTAAATATTCGGGTTGTTACATT
324 AATTAACGTCCAATTTCAATTAAATATTATTTTGTAAATATTCGGGTTGTTACATT
1202829 ATTGGCACCA
Statistics
Matches: 373, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
426 58 0.16
427 190 0.51
428 125 0.34
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (426 bp):
CCGACGTTTGGTAGCGTTTCACTTCAATTAATTTGAAGGGTTTGTTCATCGCTTGATGAGAACAC
AACGGTGGTTTCAATTTTACGATTGGACGTCGAACGGCGTCGGAATCGGGCTTGGAAGTAAGGGT
ACGAGAGAAGGAAAATTGAGCAATTCTCAATTGTGTTTTCTGATTTACAATCAGAAACCACGCTT
AAATTATAAGCCTGCCGACACTCCTTGGAGGAATTCAGGGTTTGGTCCCTGAATTTCCTTCAACT
TATAAAATGGCCTATAACTTTTCATAAATTTTAGTCCAGTCATTAAATTTCACCAATTTTCACAA
TTAACGTCCAATTTCAATTAAATATTATTTTGTAAATATTCGGGTTGTTACATTCCCGGCGATAG
AGCTAAAAAAAACGACGATGCTTTGACTGAAAATTC
Found at i:1203144 original size:17 final size:18
Alignment explanation
Indices: 1203122--1203155 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1203112 AAAATGAAGT
1203122 AAAGAGAAGAAA-AAGGA
1 AAAGAGAAGAAACAAGGA
*
1203139 AAAGAGGAGAAACAAGG
1 AAAGAGAAGAAACAAGG
1203156 TAAGAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (18 bp):
AAAGAGAAGAAACAAGGA
Found at i:1204351 original size:25 final size:24
Alignment explanation
Indices: 1204314--1204378 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
1204304 TAATTAATAT
* *
1204314 TTTATTT-TTATTTTTATAAATTTA
1 TTTATTTATAATTTTTAT-AATTAA
*
1204338 TTTATTTATAATTTTTCCTAATTAA
1 TTTATTTATAATTTTT-ATAATTAA
*
1204363 TTTATATA-AATTTTTA
1 TTTATTTATAATTTTTA
1204379 ATTTAACAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
24 14 0.41
25 19 0.56
26 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTATTTATAATTTTTATAATTAA
Found at i:1205195 original size:20 final size:20
Alignment explanation
Indices: 1205170--1205207 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1205160 TTTGGTTCAC
*
1205170 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
1205190 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
1205208 GGAATATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:1205210 original size:18 final size:19
Alignment explanation
Indices: 1205170--1205213 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1205160 TTTGGTTCAC
*
1205170 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
1205190 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
1205208 GGAATA
1 GGAATA
1205214 TGATTACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:1205434 original size:36 final size:36
Alignment explanation
Indices: 1205360--1205434 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
1205350 ACAAGTTGGA
*
1205360 AAATATTTATATATTTTCTTTAAAAATTAAATTCAT
1 AAATATTTATATATTTTCTTTAAAAATTAAAATCAT
1205396 AAAT-TTTATATAATTTT-TTTACAAAATTGAAAAT-AT
1 AAATATTTATAT-ATTTTCTTTA-AAAATT-AAAATCAT
1205432 AAA
1 AAA
1205435 AAGGTTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
35 11 0.31
36 20 0.57
37 4 0.11
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
AAATATTTATATATTTTCTTTAAAAATTAAAATCAT
Found at i:1212041 original size:16 final size:16
Alignment explanation
Indices: 1212005--1212035 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1211995 TATAAATAGT
*
1212005 AAAATATTAAATATTA
1 AAAATATAAAATATTA
1212021 AAAATATAAAATATT
1 AAAATATAAAATATT
1212036 TCAAATTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATAAAATATTA
Found at i:1216031 original size:21 final size:22
Alignment explanation
Indices: 1216005--1216070 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
1215995 AGCGGAAAAT
*
1216005 GAAGCAAG-GGAAGCCGAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
*
1216026 GCAGC-AGCGGAAGCAGAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
* * *
1216047 GAAGC-AGTGGCAGCACAGAGA
1 GAAGCAAGCGGAAGCAGAGAGA
1216068 GAA
1 GAA
1216071 TCAACATATC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.41, C:0.17, G:0.41, T:0.02
Consensus pattern (22 bp):
GAAGCAAGCGGAAGCAGAGAGA
Found at i:1216511 original size:43 final size:43
Alignment explanation
Indices: 1216447--1216562 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
1216437 GCTTTTGTAT
* * *
1216447 TAAAAACGCCGCTAAACCTCAACGCCTATTAC-GACATTTTAGC
1 TAAAAACGCCGCTAAATCTCAACACATATTACGGA-ATTTTAGC
* * * *
1216490 TAAAAACGTCGCTAAATCTCAACACATATTGCGGAGTTTTCGC
1 TAAAAACGCCGCTAAATCTCAACACATATTACGGAATTTTAGC
*
1216533 TAAAAACGCCGCTAAATCTCAAGACATATT
1 TAAAAACGCCGCTAAATCTCAACACATATT
1216563 GCAGCGTTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 61 0.97
44 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (43 bp):
TAAAAACGCCGCTAAATCTCAACACATATTACGGAATTTTAGC
Found at i:1216582 original size:43 final size:43
Alignment explanation
Indices: 1216448--1216599 Score: 130
Period size: 43 Copynumber: 3.5 Consensus size: 43
1216438 CTTTTGTATT
* * * * * * *
1216448 AAAAACGCCGCTAAACCTCAACGCCTATTAC-GACATTTTAGCT
1 AAAAACGCCGCTAAATCTCAACACATATTGCAGA-GTTTTCGCA
* * *
1216491 AAAAACGTCGCTAAATCTCAACACATATTGCGGAGTTTTCGCT
1 AAAAACGCCGCTAAATCTCAACACATATTGCAGAGTTTTCGCA
* *
1216534 AAAAACGCCGCTAAATCTCAAGACATATTGCAGCGTTTGT-G-A
1 AAAAACGCCGCTAAATCTCAACACATATTGCAGAGTTT-TCGCA
* *
1216576 AGAAAACGCCACTAAATATCAACA
1 A-AAAACGCCGCTAAATCTCAACA
1216600 ACTTTGGCAG
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
42 1 0.01
43 87 0.96
44 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAATCTCAACACATATTGCAGAGTTTTCGCA
Found at i:1218321 original size:16 final size:16
Alignment explanation
Indices: 1218300--1218339 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1218290 ATGACATAAG
1218300 CTATGTGA-AAAATGAT
1 CTATGTGACAAAATG-T
*
1218316 CTATGTGACTAAATGT
1 CTATGTGACAAAATGT
1218332 CTATGTGA
1 CTATGTGA
1218340 TAAGCTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (16 bp):
CTATGTGACAAAATGT
Found at i:1218467 original size:23 final size:23
Alignment explanation
Indices: 1218441--1218529 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
1218431 TATGCGATCA
*
1218441 TTCGAGACAATTCTACGTGGTCC
1 TTCGGGACAATTCTACGTGGTCC
* *
1218464 TTCGGGACATTTCTACGCGGTCC
1 TTCGGGACAATTCTACGTGGTCC
* * * *
1218487 TTCGGGACAATACTATGTGTTCT
1 TTCGGGACAATTCTACGTGGTCC
* *
1218510 TTCGGGACATTTCTATGTGG
1 TTCGGGACAATTCTACGTGG
1218530 CACTTCGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (23 bp):
TTCGGGACAATTCTACGTGGTCC
Found at i:1218536 original size:23 final size:22
Alignment explanation
Indices: 1218441--1218587 Score: 96
Period size: 23 Copynumber: 6.2 Consensus size: 22
1218431 TATGCGATCA
* *
1218441 TTCGAGACAATTCTACGTGGTCC
1 TTCGGGACATTTCTACGTGG-CC
*
1218464 TTCGGGACATTTCTACGCGGTCC
1 TTCGGGACATTTCTACGTGG-CC
* * * * *
1218487 TTCGGGACAATACTATGTGTTCT
1 TTCGGGACATTTCTACGTG-GCC
*
1218510 TTCGGGACATTTCTATGTGGCAC
1 TTCGGGACATTTCTACGTGGC-C
* *
1218533 TTCGTTGTAAATTTCTACGTGGCAC
1 TTCG--GGACATTTCTACGTGGC-C
*
1218558 TTCGGTGCAAATTTCTACGTGGCAC
1 TTCGG-G-ACATTTCTACGTGGC-C
1218583 TTCGG
1 TTCGG
1218588 TGCAATTTGT
Statistics
Matches: 101, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.01
23 58 0.57
25 42 0.42
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (22 bp):
TTCGGGACATTTCTACGTGGCC
Found at i:1218554 original size:25 final size:25
Alignment explanation
Indices: 1218518--1218600 Score: 123
Period size: 25 Copynumber: 3.4 Consensus size: 25
1218508 CTTTCGGGAC
* * *
1218518 ATTTCTATGTGGCACTTCGTTGTAA
1 ATTTCTACGTGGCACTTCGGTGCAA
1218543 ATTTCTACGTGGCACTTCGGTGCAA
1 ATTTCTACGTGGCACTTCGGTGCAA
1218568 ATTTCTACGTGGCACTTCGGTGC-A
1 ATTTCTACGTGGCACTTCGGTGCAA
*
1218592 ATTTGTACG
1 ATTTCTACG
1218601 AGTTGTGGTG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
24 9 0.17
25 45 0.83
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (25 bp):
ATTTCTACGTGGCACTTCGGTGCAA
Found at i:1218775 original size:32 final size:32
Alignment explanation
Indices: 1218712--1218775 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1218702 GTGCATAATA
* * * * *
1218712 TTACATGTTCTTGTTTGGTGAAGTGTGTGATG
1 TTACAAGTTATTGTTTGGTGAAATATATGATG
*
1218744 TTACAAGTTATTGTTTTGTGAAATATATGATG
1 TTACAAGTTATTGTTTGGTGAAATATATGATG
1218776 CATTCTGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (32 bp):
TTACAAGTTATTGTTTGGTGAAATATATGATG
Found at i:1220731 original size:26 final size:28
Alignment explanation
Indices: 1220702--1220770 Score: 70
Period size: 31 Copynumber: 2.4 Consensus size: 28
1220692 GAATAATACC
1220702 ATATTTAATATATGTAT-TTC-AATAAA
1 ATATTTAATATATGTATATTCTAATAAA
* *
1220728 ATATCTAATGTAATATTTATATTCTAATAAA
1 ATATTTAA--T-ATATGTATATTCTAATAAA
*
1220759 ATGTTTAATATA
1 ATATTTAATATA
1220771 CTATTTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
26 7 0.21
28 4 0.12
29 8 0.24
30 3 0.09
31 12 0.35
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (28 bp):
ATATTTAATATATGTATATTCTAATAAA
Found at i:1228134 original size:45 final size:43
Alignment explanation
Indices: 1228058--1228325 Score: 156
Period size: 42 Copynumber: 6.3 Consensus size: 43
1228048 CTGTTCTTTC
*
1228058 AAACGCCGCTATATGT-T-ATGATTTATAGTGGCATTTTTGT-TAAAAA
1 AAACGCCGCTA-AT-TCTCATG-TTTTTAGTGGCATTTTTGTCT---AA
* * *
1228104 AAATGCCGCTACTTCTCATGTTTTTAGTGGCATTTTT-TCTAC
1 AAACGCCGCTAATTCTCATGTTTTTAGTGGCATTTTTGTCTAA
* * *
1228146 AAACGCCGCTAATTCTCTTGTTTTTAGTGGCGTTTTTG-CTAC
1 AAACGCCGCTAATTCTCATGTTTTTAGTGGCATTTTTGTCTAA
* * * * * * * *
1228188 AAATGACGCTAACTCTCTTGTCTTGAGTGGC-GTTTTGTCTAC
1 AAACGCCGCTAATTCTCATGTTTTTAGTGGCATTTTTGTCTAA
* ** * ** * *
1228230 AAAGGCCGCTAATTCTTTTGTCTTTAGTGGTGTTTTTTTCTAC
1 AAACGCCGCTAATTCTCATGTTTTTAGTGGCATTTTTGTCTAA
* * * * **
1228273 AAACGCCACT-ATTCTCTTGTCTTTAGTGGCGTTTTT-AATACA
1 AAACGCCGCTAATTCTCATGTTTTTAGTGGCATTTTTGTCTA-A
1228315 AAACGCCGCTA
1 AAACGCCGCTA
1228326 TATATTATGA
Statistics
Matches: 184, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
41 7 0.04
42 126 0.68
43 17 0.09
44 2 0.01
45 19 0.10
46 13 0.07
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (43 bp):
AAACGCCGCTAATTCTCATGTTTTTAGTGGCATTTTTGTCTAA
Found at i:1228168 original size:42 final size:42
Alignment explanation
Indices: 1228108--1228325 Score: 258
Period size: 42 Copynumber: 5.2 Consensus size: 42
1228098 TAAAAAAAAT
* * * *
1228108 GCCGCTACTTCTCATGTTTTTAGTGGCATTTTTTCTACAAAC
1 GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTTCTACAAAC
* * *
1228150 GCCGCTAATTCTCTTGTTTTTAGTGGCGTTTTTGCTACAAAT
1 GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTTCTACAAAC
* * * * *
1228192 GACGCTAACTCTCTTGTCTTGAGTGGCGTTTTGTCTACAAAG
1 GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTTCTACAAAC
* *
1228234 GCCGCTAATTCTTTTGTCTTTAGTGGTGTTTTTTTCTACAAAC
1 GCCGCTAATTCTCTTGTCTTTAGTGGCG-TTTTTTCTACAAAC
* **
1228277 GCCACT-ATTCTCTTGTCTTTAGTGGCGTTTTTAATACAAAAC
1 GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTTCTAC-AAAC
1228319 GCCGCTA
1 GCCGCTA
1228326 TATATTATGA
Statistics
Matches: 148, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
41 8 0.05
42 123 0.83
43 17 0.11
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.42
Consensus pattern (42 bp):
GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTTCTACAAAC
Found at i:1231132 original size:82 final size:83
Alignment explanation
Indices: 1230940--1231367 Score: 350
Period size: 83 Copynumber: 5.2 Consensus size: 83
1230930 AAAAAATGAT
* * ** ** * * * *
1230940 GCTATAGTACTACTCTGTTGCGGTGTTT-TTTGAAAAAAAAACCACTATAAATAAACCCTATTAC
1 GCTAAAGTACTACTATGTTGCGACGTTTGTTT--AAAAAATGCCACTATAGATGAACTCTATTAT
* *
1231004 GACATTTGTATAAAAACTCC
64 GACGTTTGTATAAAAACGCC
* * *
1231024 ACTAAAGTACTACTCTGTTGCGACGTTTGTTTTAAAAATGCCACTATAGATGAACTCTATTATTG
1 GCTAAAGTACTACTATGTTGCGACGTTTGTTTAAAAAATGCCACTATAGATGAACTCTATTA-TG
*
1231089 -CGTTTGTA-CAAAACGCC
65 ACGTTTGTATAAAAACGCC
* * * *
1231106 GCTAAAGTAATACTTTGTTGCAACGTTTGTTGAAAAAATGCCACTATAGATGAAAC-CTATTATG
1 GCTAAAGTACTACTATGTTGCGACGTTTGTTTAAAAAATGCCACTATAGATG-AACTCTATTATG
*
1231170 ATGTTTGTATAAAAACGCC
65 ACGTTTGTATAAAAACGCC
* * * * * * **
1231189 GTTAAAATACTACTATGTTGCGGCGTTTGTTGAATAAA-GACACTATAGATGAACTCTATTGCGA
1 GCTAAAGTACTACTATGTTGCGACGTTTGTTTAAAAAATGCCACTATAGATGAACTCTATTATGA
* * *
1231253 TGTTTGTATAAAAAACACT
66 CGTTTGTAT-AAAAACGCC
* * * * * * *
1231272 GCTAAAATACTACTCTGTTGCG--GTATTTTTTGAAAAATACCACTATAGATGAACCCAATTAT-
1 GCTAAAGTACTACTATGTTGCGACGT-TTGTTTAAAAAATGCCACTATAGATGAACTCTATTATG
* * **
1231334 AGCATTTGTTTAAAAACATC
65 A-CGTTTGTATAAAAACGCC
1231354 GCTAAAGTACTACT
1 GCTAAAGTACTACT
1231368 CTATCACGGC
Statistics
Matches: 282, Mismatches: 52, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
81 7 0.02
82 123 0.44
83 124 0.44
84 25 0.09
85 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (83 bp):
GCTAAAGTACTACTATGTTGCGACGTTTGTTTAAAAAATGCCACTATAGATGAACTCTATTATGA
CGTTTGTATAAAAACGCC
Found at i:1231381 original size:165 final size:163
Alignment explanation
Indices: 1230947--1231369 Score: 433
Period size: 165 Copynumber: 2.6 Consensus size: 163
1230937 GATGCTATAG
* * * *
1230947 TACTACTCTGTTGCGGTGTTTTTTGAAAAAAAAACCACTATAAATAAACCCTATTACGACATTTG
1 TACTACTCTGTTGCGGTGTTTTTTG-AAAAAATACCACTATAGATGAACCCTATTATG-CATTTG
* * * *
1231012 TATAAAAACTCCACTAAAGTACTACTCTGTTGCGACGTTTGTTTTAAAAATGCCACTATAGATGA
64 TATAAAAACT-CGCTAAAGTACTACTCTGTTGCGGCGTTTGTTTGAAAAATGACACTATAGATGA
** * * *
1231077 ACTCTATTATTGCGTTTGTACAAAACGCCGCTAAAG
128 ACTCTATTAGCGCGTTTGTAAAAAACACCGCTAAAA
* * *** * * *
1231113 TAATACTTTGTTGCAACGTTTGTTGAAAAAATGCCACTATAGATGAAACCTATTATG-ATGTTTG
1 TACTACTCTGTTGCGGTGTTTTTTGAAAAAATACCACTATAGATGAACCCTATTATGCA--TTTG
* * * *
1231177 TATAAAAACGCCGTTAAAATACTACTATGTTGCGGCGTTTG-TTGAATAAA-GACACTATAGATG
64 TATAAAAAC-TCGCTAAAGTACTACTCTGTTGCGGCGTTTGTTTGAA-AAATGACACTATAGATG
* *
1231240 AACTCTATT-GCGATGTTTGTATAAAAAACACTGCTAAAA
127 AACTCTATTAGCG-CGTTTG--TAAAAAACACCGCTAAAA
* *
1231279 TACTACTCTGTTGCGGTATTTTTTG-AAAAATACCACTATAGATGAACCCAATTATAGCATTTGT
1 TACTACTCTGTTGCGGTGTTTTTTGAAAAAATACCACTATAGATGAACCCTATTAT-GCATTTGT
*
1231343 TTAAAAACATCGCTAAAGTACTACTCT
65 ATAAAAAC-TCGCTAAAGTACTACTCT
1231370 ATCACGGCGT
Statistics
Matches: 205, Mismatches: 43, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
163 2 0.01
164 30 0.15
165 120 0.59
166 52 0.25
167 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (163 bp):
TACTACTCTGTTGCGGTGTTTTTTGAAAAAATACCACTATAGATGAACCCTATTATGCATTTGTA
TAAAAACTCGCTAAAGTACTACTCTGTTGCGGCGTTTGTTTGAAAAATGACACTATAGATGAACT
CTATTAGCGCGTTTGTAAAAAACACCGCTAAAA
Found at i:1232804 original size:42 final size:43
Alignment explanation
Indices: 1232726--1232908 Score: 180
Period size: 42 Copynumber: 4.3 Consensus size: 43
1232716 TTGTGATTTA
* * *
1232726 TAGTGGCATTTTTGTTAAAAAATGCCGCTAATTCTCTTGGT-TT
1 TAGTGGCGTTTTTGCT-ACAAATGCCGCTAATTCTCTTGGTCTT
* * *
1232769 TAGTGGCGTTTTTGCTACAAATGACGCTAACTCTCTT-GCCTT
1 TAGTGGCGTTTTTGCTACAAATGCCGCTAATTCTCTTGGTCTT
* * *
1232811 TAGTGGCG-TTTTGTCTACAAAGGCTGCTAATTCT-TTTGTCTT
1 TAGTGGCGTTTTTG-CTACAAATGCCGCTAATTCTCTTGGTCTT
* *
1232853 TAGTGGTGTTTTTCTGCTACAAACGCCGCT-ATTCTCTT-GTCTT
1 TAGTGGCG-TTTT-TGCTACAAATGCCGCTAATTCTCTTGGTCTT
*
1232896 TAGTGGCATTTTT
1 TAGTGGCGTTTTT
1232909 AATACAAAAC
Statistics
Matches: 117, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
41 9 0.08
42 59 0.50
43 30 0.26
44 17 0.15
45 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.44
Consensus pattern (43 bp):
TAGTGGCGTTTTTGCTACAAATGCCGCTAATTCTCTTGGTCTT
Found at i:1232916 original size:85 final size:84
Alignment explanation
Indices: 1232726--1232916 Score: 201
Period size: 85 Copynumber: 2.2 Consensus size: 84
1232716 TTGTGATTTA
* * *
1232726 TAGTGGCATTTTTGT-TAAAAAATGCCGCTAATTCTCTTGGTTTTAGTGGCGTTTTTGCTACAAA
1 TAGTGGCA-TTTTGTAT-ACAAAGGCTGCTAATTCTCTTGGTTTTAGTGGCGTTTTTGCTACAAA
*
1232790 TGACGCTAACTCTCTTGCCTT
64 CGACGCTAACTCTCTTGCCTT
* * * *
1232811 TAGTGGCGTTTTGTCTACAAAGGCTGCTAATTCT-TTTGTCTTTAGTGGTGTTTTTCTGCTACAA
1 TAGTGGCATTTTGTATACAAAGGCTGCTAATTCTCTTGGT-TTTAGTGGCG-TTTT-TGCTACAA
* * *
1232875 ACGCCGCT-ATTCTCTTGTCTT
63 ACGACGCTAACTCTCTTGCCTT
1232896 TAGTGGCATTTT-TAATACAAA
1 TAGTGGCATTTTGT-ATACAAA
1232917 ACGCCGCTAT
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
83 4 0.04
84 31 0.35
85 40 0.45
86 14 0.16
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (84 bp):
TAGTGGCATTTTGTATACAAAGGCTGCTAATTCTCTTGGTTTTAGTGGCGTTTTTGCTACAAACG
ACGCTAACTCTCTTGCCTT
Found at i:1235609 original size:42 final size:41
Alignment explanation
Indices: 1235563--1235692 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 41
1235553 TATAAAAACT
*
1235563 CCACTAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATG
1 CCACTAAAGTA-TACTCTGTTGCAGCGTTTGTTGAAAAAATG
* * ** * * *
1235605 CCACTATAG-ATGAACTCTATTGTTGTGTTTG-T-ACAAAACG
1 CCACTAAAGTAT--ACTCTGTTGCAGCGTTTGTTGAAAAAATG
* *
1235645 CCGCTAAAGTAATACTCTGTTGCAACGTTTGTTGAAAAAATG
1 CCACTAAAGT-ATACTCTGTTGCAGCGTTTGTTGAAAAAATG
1235687 CCACTA
1 CCACTA
1235693 TAGATGAAAC
Statistics
Matches: 65, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
40 27 0.42
41 3 0.05
42 35 0.54
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (41 bp):
CCACTAAAGTATACTCTGTTGCAGCGTTTGTTGAAAAAATG
Found at i:1235663 original size:82 final size:84
Alignment explanation
Indices: 1235479--1235910 Score: 398
Period size: 83 Copynumber: 5.2 Consensus size: 84
1235469 AAAAAATGAT
* * * ** * * *
1235479 GCTATAGTACTACTCTGTTGCGGTGTTTTTTGGAAAAAAAACACCACTATAAATTAACCCTATT-
1 GCTAAAGTACTACTCTGTTGCGGCGTTTGTT-G--AAAAAATGCCACTATAGATGAACTCTATTG
* * *
1235543 ACGGCATTTGTATAAAAACTCC
63 ATGACATTTGTATAAAAACGCC
* *
1235565 ACTAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACTCTATTGTTG
1 GCTAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACTCTATTGATG
** *
1235630 -TGTTTGTA-CAAAACGCC
66 ACATTTGTATAAAAACGCC
* **
1235647 GCTAAAGTAATACTCTGTTGCAACGTTTGTTGAAAAAATGCCACTATAGATGAAAC-CTATT-AT
1 GCTAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATG-AACTCTATTGAT
1235710 GACATTTGTATAAAAACGCC
65 GACATTTGTATAAAAACGCC
* * * * *
1235730 GTTAAAGTACTACTATGTAGAGGCGTTTGTTGAAAAAA-GCCACTATAGATGAACTCTATTG-CG
1 GCTAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACTCTATTGATG
* *
1235793 ACATTTGTATAAAAACACT
66 ACATTTGTATAAAAACGCC
* * * ** * * *
1235812 GCTAAAATACTACACTGTTGTGGTATTTTTTTGAAAAACA--CCATTATAGATGAACCCTATT-A
1 GCTAAAGTACTACTCTGTTGCGG-CGTTTGTTGAAAAA-ATGCCACTATAGATGAACTCTATTGA
** * *
1235874 CAACATTTGTTTAAAAACACC
64 TGACATTTGTATAAAAACGCC
1235895 GCTAAAGTACTACTCT
1 GCTAAAGTACTACTCT
1235911 ATCACGGCGT
Statistics
Matches: 288, Mismatches: 49, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
81 5 0.02
82 119 0.41
83 134 0.47
84 2 0.01
85 1 0.00
86 27 0.09
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (84 bp):
GCTAAAGTACTACTCTGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACTCTATTGATG
ACATTTGTATAAAAACGCC
Found at i:1235862 original size:165 final size:164
Alignment explanation
Indices: 1235515--1235908 Score: 454
Period size: 165 Copynumber: 2.4 Consensus size: 164
1235505 TTTTTGGAAA
* * * * * *
1235515 AAAAACACCACTATAAATTAACCCTATTACGGCATTTGTATAAAAACTCCACTAAAGTACTACTC
1 AAAAACACCACTATAGATGAACCCTATTACGACATTTGTATAAAAACACCGCTAAAGTACTACTA
* * * ** * *
1235580 TGTTGCGGCGTTTGTTGAAAAAATGCCACTATAGATGAACTCTATTGTTGTGTTTGTACAAAACG
66 TGTAGAGGCGTTTGTTGAAAAAATGCCACTATAGATGAACTCTATTGTCGCATTTGTAAAAAACA
* *
1235645 CCGCTAAAGTAATACTCTGTTGCAACGTTTGTTG
131 CCGCTAAAATAATACACTGTTGCAACGTTTGTTG
* * * *
1235679 AAAAA-ATGCCACTATAGATGAAACCTATTATGACATTTGTATAAAAACGCCGTTAAAGTACTAC
1 AAAAACA--CCACTATAGATGAACCCTATTACGACATTTGTATAAAAACACCGCTAAAGTACTAC
1235743 TATGTAGAGGCGTTTGTTGAAAAAA-GCCACTATAGATGAACTCTATTG-CGACATTTGTATAAA
64 TATGTAGAGGCGTTTGTTGAAAAAATGCCACTATAGATGAACTCTATTGTCG-CATTTGTA-AAA
* * ** * *
1235806 AACACTGCTAAAATACTACACTGTTGTGGTA-TTTTTTTG
127 AACACCGCTAAAATAATACACTG-T-TGCAACGTTTGTTG
* * *
1235845 AAAAACACCATTATAGATGAACCCTATTACAACATTTGTTTAAAAACACCGCTAAAGTACTACT
1 AAAAACACCACTATAGATGAACCCTATTACGACATTTGTATAAAAACACCGCTAAAGTACTACT
1235909 CTATCACGGC
Statistics
Matches: 192, Mismatches: 31, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
163 2 0.01
164 34 0.18
165 140 0.73
166 12 0.06
167 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (164 bp):
AAAAACACCACTATAGATGAACCCTATTACGACATTTGTATAAAAACACCGCTAAAGTACTACTA
TGTAGAGGCGTTTGTTGAAAAAATGCCACTATAGATGAACTCTATTGTCGCATTTGTAAAAAACA
CCGCTAAAATAATACACTGTTGCAACGTTTGTTG
Found at i:1237493 original size:43 final size:43
Alignment explanation
Indices: 1237334--1237494 Score: 150
Period size: 42 Copynumber: 3.8 Consensus size: 43
1237324 CCACTAAAAC
* * * *
1237334 GCCGCTAATTCTCTTGTTTTTTGTGGCGTTTTT-GCTACAAAT
1 GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTATCTACAAAG
** * *
1237376 GATGCTAACTCTCTTATCTTTAGTGGCG-TTTTATCTACAAAG
1 GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTATCTACAAAG
* ** * *
1237418 GCCGCTAATTCTTTTGTCTTTAGTGGTTTTTTTTTGCTTC-AAG
1 GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTAT-CTACAAAG
*
1237461 CGCCG-TTATTCTCTTGTCTTTAGTGGCGTTTTTA
1 -GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTA
1237495 ATACAAAACG
Statistics
Matches: 93, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 4 0.04
42 50 0.54
43 32 0.34
44 7 0.08
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (43 bp):
GCCGCTAATTCTCTTGTCTTTAGTGGCGTTTTTATCTACAAAG
Found at i:1240315 original size:82 final size:82
Alignment explanation
Indices: 1240102--1240557 Score: 436
Period size: 82 Copynumber: 5.5 Consensus size: 82
1240092 TACCAAACTG
* * ** * * * * *
1240102 TTGCGGCGTTTGTAAAAAAAACGATGCTATAGTACTACTCTATTGTGGTGTTTTTTGAAAAAAAA
1 TTGCGACGTTTGT-ATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTGTT---AAAAAA
* * *
1240167 ACACCACTATAAATGAACCCTA
62 A-GCCACTATAGATGAACTCTA
* * * * * * *
1240189 TTACGGCATTTGTATAAAAACTCCACTAAAGTACTACTCTGTTGCGGCGTTTATTAAAAAAATGT
1 TTGCGACGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTGTTAAAAAAA-GC
1240254 CACTATAGATGAACTCTA
65 CACTATAGATGAACTCTA
* * * ** *
1240272 TTGTTG-CGTTTGTA-CAAAACGCCGCTAAAGTAATACTCTGTTGCAACGTTTGTTGAAAAAATG
1 TTG-CGACGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTGTT-AAAAAAAG
1240335 CCACTATAGATGAAAC-CTA
64 CCACTATAGATG-AACTCTA
* * * *
1240354 TTACGACGTTTGTATAAAAACGCCGTTAAAGTACTACTATGTTGCGGCGTTTGTTGAAAAAAGCC
1 TTGCGACGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTGTTAAAAAAAGCC
1240419 ACTATAGATGAACTCTA
66 ACTATAGATGAACTCTA
* * ** * *
1240436 TTGCGACGTTTGTATAAAAACGCTGCTAAAATACTACTCTGTTGCGGTATTTTTTGAAAAACA-C
1 TTGCGACGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTGTT-AAAAAAAGC
*
1240500 CACTATAGATGAACCCTA
65 CACTATAGATGAACTCTA
* *
1240518 TTGC-AGCGTTTGTTTAAAAACGTCGCTAAAGTACTACTCT
1 TTGCGA-CGTTTGTATAAAAACGCCGCTAAAGTACTACTCT
1240558 ATCACGGCGT
Statistics
Matches: 307, Mismatches: 54, Indels: 21
0.80 0.14 0.05
Matches are distributed among these distances:
81 5 0.02
82 178 0.58
83 80 0.26
84 1 0.00
86 32 0.10
87 11 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (82 bp):
TTGCGACGTTTGTATAAAAACGCCGCTAAAGTACTACTCTGTTGCGGCGTTTGTTAAAAAAAGCC
ACTATAGATGAACTCTA
Found at i:1240405 original size:41 final size:41
Alignment explanation
Indices: 1240360--1240482 Score: 101
Period size: 41 Copynumber: 3.0 Consensus size: 41
1240350 CCTATTACGA
1240360 CGTTTGTATAAAAACGCCGTTAAAGTACTACTATGTTGCGG
1 CGTTTGTATAAAAACGCCGTTAAAGTACTACTATGTTGCGG
* * * * *
1240401 CGTTTGT-TGAAAAAAGCCACTATAGATGAACT-CTA--TTGCGA
1 CGTTTGTAT-AAAAACGCC-GT-TA-AAGTACTACTATGTTGCGG
* * * *
1240442 CGTTTGTATAAAAACGCTGCTAAAATACTACTCTGTTGCGG
1 CGTTTGTATAAAAACGCCGTTAAAGTACTACTATGTTGCGG
1240483 TATTTTTTGA
Statistics
Matches: 60, Mismatches: 14, Indels: 16
0.67 0.16 0.18
Matches are distributed among these distances:
38 4 0.07
39 4 0.07
40 1 0.02
41 39 0.65
42 2 0.03
43 5 0.08
44 5 0.08
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (41 bp):
CGTTTGTATAAAAACGCCGTTAAAGTACTACTATGTTGCGG
Found at i:1240458 original size:165 final size:164
Alignment explanation
Indices: 1240163--1240555 Score: 497
Period size: 165 Copynumber: 2.4 Consensus size: 164
1240153 TTTTTGAAAA
* * * * * *
1240163 AAAAACACCACTATAAATGAACCCTATTACGGCATTTGTATAAAAACTCCACTAAAGTACTACTC
1 AAAAACACCACTATAGATGAACCCTATTACGACGTTTGTATAAAAACGCCGCTAAAGTACTACTA
* * *
1240228 TGTTGCGGCGTTTATTAAAAAAATGTCACTATAGATGAACTCTATTGTTGCGTTTGTACAAAACG
66 TGTTGCGGCGTTTATTAAAAAAATGCCACTATAGATGAACTCTATTGTCGCGTTTGTAAAAAACG
* *
1240293 CCGCTAAAGTAATACTCTGTTGCAACGTTTGTTG
131 CCGCTAAAATAATACTCTGTTGCAACATTTGTTG
* *
1240327 AAAAA-ATGCCACTATAGATGAAACCTATTACGACGTTTGTATAAAAACGCCGTTAAAGTACTAC
1 AAAAACA--CCACTATAGATGAACCCTATTACGACGTTTGTATAAAAACGCCGCTAAAGTACTAC
* *
1240391 TATGTTGCGGCGTTTGTTGAAAAAA-GCCACTATAGATGAACTCTATTG-CGACGTTTGTATAAA
64 TATGTTGCGGCGTTTATTAAAAAAATGCCACTATAGATGAACTCTATTGTCG-CGTTTGTA-AAA
* * *** *
1240454 AACGCTGCTAAAATACTACTCTGTTGCGGTATTTTTTG
127 AACGCCGCTAAAATAATACTCTGTTGCAACATTTGTTG
* * *
1240492 AAAAACACCACTATAGATGAACCCTATTGC-AGCGTTTGTTTAAAAACGTCGCTAAAGTACTACT
1 AAAAACACCACTATAGATGAACCCTATTACGA-CGTTTGTATAAAAACGCCGCTAAAGTACTACT
1240556 CTATCACGGC
Statistics
Matches: 197, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
163 3 0.02
164 85 0.43
165 108 0.55
166 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (164 bp):
AAAAACACCACTATAGATGAACCCTATTACGACGTTTGTATAAAAACGCCGCTAAAGTACTACTA
TGTTGCGGCGTTTATTAAAAAAATGCCACTATAGATGAACTCTATTGTCGCGTTTGTAAAAAACG
CCGCTAAAATAATACTCTGTTGCAACATTTGTTG
Found at i:1241634 original size:23 final size:22
Alignment explanation
Indices: 1241584--1241636 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 22
1241574 ACCTTATCTG
1241584 AATTAATCGATTAATAAATTAA
1 AATTAATCGATTAATAAATTAA
1241606 ATATTAAT-GATTATATTAAA-TATA
1 A-ATTAATCGATTA-A-TAAATTA-A
1241630 AATTAAT
1 AATTAAT
1241637 AATTCCTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 6 0.22
23 15 0.56
24 6 0.22
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (22 bp):
AATTAATCGATTAATAAATTAA
Found at i:1243051 original size:2 final size:2
Alignment explanation
Indices: 1243046--1243075 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1243036 TTAAAAAGGG
1243046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1243076 TCAACTGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1248690 original size:21 final size:21
Alignment explanation
Indices: 1248631--1248691 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1248621 ATAGTAAGTA
*
1248631 AAATAAATATAAAAAAATATAG
1 AAATAAA-ACAAAAAAATATAG
* *
1248653 AAA-AAGAAGAAAAAAATATAT
1 AAATAA-AACAAAAAAATATAG
*
1248674 AAATAAAACAAATAAATA
1 AAATAAAACAAAAAAATA
1248692 AAATAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (21 bp):
AAATAAAACAAAAAAATATAG
Found at i:1248692 original size:17 final size:16
Alignment explanation
Indices: 1248662--1248784 Score: 72
Period size: 18 Copynumber: 7.2 Consensus size: 16
1248652 GAAAAAGAAG
*
1248662 AAAAAAATATATAAAT
1 AAAAAAATAAATAAAT
1248678 AAAACAAATAAATAAA-
1 AAAA-AAATAAATAAAT
* *
1248694 ATAATAAT-AATAAAGT
1 AAAAAAATAAATAAA-T
*
1248710 AAAAATAATATATATATAT
1 AAAAA-AATA-A-ATAAAT
*
1248729 ATATAAAATAAA-AAAT
1 A-AAAAAATAAATAAAT
*
1248745 AAAAAATTGTAAATAAAT
1 AAAAAA--ATAAATAAAT
*
1248763 AAATAAATATAAATTAAT
1 AAA-AAA-ATAAATAAAT
1248781 AAAA
1 AAAA
1248785 CTGATAATAA
Statistics
Matches: 83, Mismatches: 12, Indels: 23
0.70 0.10 0.19
Matches are distributed among these distances:
14 6 0.07
15 7 0.08
16 14 0.17
17 19 0.23
18 20 0.24
19 10 0.12
20 7 0.08
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAAAATAAATAAAT
Found at i:1248707 original size:14 final size:14
Alignment explanation
Indices: 1248688--1248804 Score: 53
Period size: 14 Copynumber: 7.9 Consensus size: 14
1248678 AAAACAAATA
1248688 AATAAAATAATAAT
1 AATAAAATAATAAT
* *
1248702 AATAAAGTAAAAAT
1 AATAAAATAATAAT
*
1248716 AAT-ATAT-ATATAT
1 AATAAAATAATA-AT
*
1248729 ATATAAAATAAAAAAT
1 A-ATAAAAT-AATAAT
1248745 AA-AAAATTGTAAATAAAT
1 AATAAAA---T-AAT-AAT
*
1248763 AAATAAATATAA-ATT
1 -AATAAA-ATAATAAT
*
1248778 AATAAAACTGATAAT
1 AATAAAA-TAATAAT
1248793 AATAAAATAATA
1 AATAAAATAATA
1248805 TATATATATA
Statistics
Matches: 77, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
12 2 0.03
13 6 0.08
14 33 0.43
15 15 0.19
16 3 0.04
17 8 0.10
18 4 0.05
19 2 0.03
20 3 0.04
21 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (14 bp):
AATAAAATAATAAT
Found at i:1248734 original size:28 final size:25
Alignment explanation
Indices: 1248620--1248748 Score: 70
Period size: 25 Copynumber: 5.0 Consensus size: 25
1248610 AGTAAAGATA
* * *
1248620 AATAGTAAGTAAAATAAATATAAAAA
1 AATAATAA-TAAAATAAAAATAAAAT
*
1248646 AAT-ATAGA-AAAAGAAGAAA-AAAAT
1 AATAATA-ATAAAATAA-AAATAAAAT
*
1248670 ATATAAATAA-AACAA-ATAAATAAAAT
1 A-AT-AATAATAA-AATAAAAATAAAAT
* *
1248696 AATAATAATAAAGTAAAAATAATAT
1 AATAATAATAAAATAAAAATAAAAT
1248721 ATATATATATATAAAATAAAAAATAAAA
1 A-ATA-ATA-ATAAAAT-AAAAATAAAA
1248749 AATTGTAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
24 17 0.21
25 23 0.29
26 17 0.21
27 8 0.10
28 6 0.08
29 9 0.11
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (25 bp):
AATAATAATAAAATAAAAATAAAAT
Found at i:1248773 original size:42 final size:41
Alignment explanation
Indices: 1248672--1248773 Score: 96
Period size: 42 Copynumber: 2.4 Consensus size: 41
1248662 AAAAAAATAT
* * * *
1248672 ATAAATAAAACAAATAAATAAAATAATAATAATAAAGTAAAA
1 ATAAAT-AAATAAATATATAAAATAAAAATAAAAAAGTAAAA
* * * **
1248714 ATAATATATATATATATATAAAATAAAAAATAAAAAATTGTAA
1 ATAA-ATAAATAAATATATAAAAT-AAAAATAAAAAAGTAAAA
1248757 ATAAATAAATAAATATA
1 ATAAATAAATAAATATA
1248774 AATTAATAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 28 0.60
43 19 0.40
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (41 bp):
ATAAATAAATAAATATATAAAATAAAAATAAAAAAGTAAAA
Found at i:1250031 original size:39 final size:35
Alignment explanation
Indices: 1249977--1250066 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 35
1249967 CGAGGGTTTG
*
1249977 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTGTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTT-T-T-T-T
* *
1250016 GTGTTTCAAGAGAAACAATTTCGAGGGTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
*
1250051 GCGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
1250067 TGTCTCAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 16 0.34
36 1 0.02
37 1 0.02
38 1 0.02
39 28 0.60
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (35 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
Found at i:1250101 original size:36 final size:36
Alignment explanation
Indices: 1250053--1250168 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 36
1250043 TTTTTTTTGC
* *
1250053 GTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATTT
1 GTTTCAAAAGAAACTGTCTCAAGAGGGATAAAATTT
* *
1250089 GTTTCAAAAGAAACTGTCTCAAGAGAGATAAAACTTA
1 GTTTCAAAAGAAACTGTCTCAAGAGGGATAAAA-TTT
*
1250126 G-TTCTAAAAGAAACTGTCTCAAG-GGAGATGAAATTT
1 GTTTC-AAAAGAAACTGTCTCAAGAGG-GATAAAATTT
1250162 GTTTCAA
1 GTTTCAA
1250169 GGAAAAGATA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
36 39 0.57
37 30 0.43
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
GTTTCAAAAGAAACTGTCTCAAGAGGGATAAAATTT
Found at i:1251487 original size:32 final size:32
Alignment explanation
Indices: 1251436--1251525 Score: 128
Period size: 32 Copynumber: 2.8 Consensus size: 32
1251426 ATTCCCAAAG
*
1251436 ATGCCCCAATATTCT-ATGTTGAATCTCAAAAA
1 ATGCCCCAAAATT-TGATGTTGAATCTCAAAAA
*
1251468 ATGCCCCAAAATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAAAATTTGATGTTGAATCTCAAAAA
**
1251500 ATGCCCCAGCATTTGATGTTGAATCT
1 ATGCCCCAAAATTTGATGTTGAATCT
1251526 TTAAGATGCC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 1 0.02
32 51 0.98
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (32 bp):
ATGCCCCAAAATTTGATGTTGAATCTCAAAAA
Found at i:1252601 original size:7 final size:7
Alignment explanation
Indices: 1252589--1252633 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
1252579 TTTTTCTTTA
1252589 TTTTTGC
1 TTTTTGC
1252596 TTTTTGC
1 TTTTTGC
1252603 TTTTT--
1 TTTTTGC
1252608 TGTTTT-C
1 T-TTTTGC
1252615 TTTTTGC
1 TTTTTGC
1252622 TTTTTGC
1 TTTTTGC
1252629 TTTTT
1 TTTTT
1252634 TTTGTTCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 1 0.03
6 8 0.23
7 26 0.74
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (7 bp):
TTTTTGC
Found at i:1252632 original size:19 final size:19
Alignment explanation
Indices: 1252572--1252626 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
1252562 CATATGCGTC
*
1252572 TTGTTTT-TTTTT-CTTTA
1 TTGTTTTCTTTTTGCTTTT
*
1252589 TT-TTTGCTTTTTGCTTTT
1 TTGTTTTCTTTTTGCTTTT
1252607 TTGTTTTCTTTTTGCTTTT
1 TTGTTTTCTTTTTGCTTTT
1252626 T
1 T
1252627 GCTTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 3 0.09
17 7 0.22
18 6 0.19
19 16 0.50
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (19 bp):
TTGTTTTCTTTTTGCTTTT
Found at i:1255733 original size:16 final size:15
Alignment explanation
Indices: 1255685--1255753 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 15
1255675 ATAAAAATGT
1255685 AAGAAATAAACAAATA
1 AAGAAA-AAACAAATA
*
1255701 AAGAAAATTA-AAATA
1 AAGAAAA-AACAAATA
1255716 AAGAAAAAACAAATTA
1 AAGAAAAAACAAA-TA
* * *
1255732 AATAAAAGATAAGATA
1 AAGAAAAAACAA-ATA
1255748 AAGAAA
1 AAGAAA
1255754 GCAAAGATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 1 0.02
15 16 0.37
16 25 0.58
17 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (15 bp):
AAGAAAAAACAAATA
Found at i:1255782 original size:4 final size:4
Alignment explanation
Indices: 1255775--1255911 Score: 67
Period size: 4 Copynumber: 35.8 Consensus size: 4
1255765 ATAGTAAGTA
* * * *
1255775 AAAT AAAT AAA- AAAT AAAT AAAA AAAG AAAA AAAT ATAT AAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * *
1255821 ATAAT -AAT AAA- AAGT -AA- AAAT AATAT ATAT ATAT ATAT ATAT ATAAT
1 A-AAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT A-AAT
* * * *
1255868 AAAT -AAT AAAT AAA- AAAT -ATT AAAT ATAT ATAT AAAT TAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1255912 ACTAATAATA
Statistics
Matches: 105, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
3 20 0.19
4 79 0.75
5 6 0.06
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:1255833 original size:33 final size:35
Alignment explanation
Indices: 1255785--1255849 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
1255775 AAATAAATAA
1255785 AAAATAAATAAAAAAAG-AAAAA-AATATATAAAT
1 AAAATAAATAAAAAAAGTAAAAATAATATATAAAT
1255818 AAAAT-AATAATAAAAAGTAAAAATAATATATA
1 AAAATAAATAA-AAAAAGTAAAAATAATATATA
1255850 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 5 0.17
33 11 0.38
34 5 0.17
35 8 0.28
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (35 bp):
AAAATAAATAAAAAAAGTAAAAATAATATATAAAT
Found at i:1255879 original size:85 final size:87
Alignment explanation
Indices: 1255780--1255944 Score: 223
Period size: 87 Copynumber: 1.9 Consensus size: 87
1255770 AAGTAAAATA
1255780 AATAAAAAATAAATAAAAAA-A-GAAAAAAATATATAAA-TAA-AATAA-TAATAAAAAGTAAAA
1 AATAAAAAATAAATAAAAAATATGAAAAAAATATATAAATTAATAA-AACTAATAAAAA--AAAA
1255840 ATAATATATATATATATATATATAT
63 ATAATATATATATATATATATATAT
* * * * *
1255865 AATAAATAATAAATAAAAAATATTAAATATATATATAAATTAATAAAACTAATAATAAAAAAATA
1 AATAAAAAATAAATAAAAAATATGAAAAAAATATATAAATTAATAAAACTAATAAAAAAAAAATA
1255930 ATATATATATATATA
66 ATATATATATATATA
1255945 ATCTAAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
85 19 0.27
86 1 0.01
87 35 0.50
88 5 0.07
89 10 0.14
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (87 bp):
AATAAAAAATAAATAAAAAATATGAAAAAAATATATAAATTAATAAAACTAATAAAAAAAAAATA
ATATATATATATATATATATAT
Found at i:1255881 original size:11 final size:11
Alignment explanation
Indices: 1255776--1255932 Score: 78
Period size: 11 Copynumber: 14.4 Consensus size: 11
1255766 TAGTAAGTAA
*
1255776 AATAAATAAAA
1 AATAAATAAAT
*
1255787 AATAAATAAAAA
1 AATAAAT-AAAT
* *
1255799 AAGAAAAAAAT
1 AATAAATAAAT
1255810 ATATAAATAAAAT
1 A-ATAAAT-AAAT
1255823 AAT-AATAAA-
1 AATAAATAAAT
1255832 AAGT-AA-AAAT
1 AA-TAAATAAAT
* *
1255842 AATATATATAT
1 AATAAATAAAT
* *
1255853 ATATATATATAT
1 A-ATAAATAAAT
1255865 AATAAAT-AAT
1 AATAAATAAAT
1255875 AAATAAA-AAAT
1 -AATAAATAAAT
* *
1255886 ATTAAATATAT
1 AATAAATAAAT
*
1255897 ATATAAATTAAT
1 A-ATAAATAAAT
*
1255909 AA-AACT-AAT
1 AATAAATAAAT
*
1255918 AATAAAAAAAT
1 AATAAATAAAT
1255929 AATA
1 AATA
1255933 TATATATATA
Statistics
Matches: 115, Mismatches: 17, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
9 11 0.10
10 21 0.18
11 44 0.38
12 34 0.30
13 5 0.04
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:1255930 original size:50 final size:47
Alignment explanation
Indices: 1255815--1255926 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 47
1255805 AAAATATATA
* * *
1255815 AATAAAATAATAATAAAAAGT-AAAAATAATATATATATATATATAT
1 AATAAAATAATAATAAAAAATAAAAAATAATAAATATATATATAAAT
* * *
1255861 -ATATAAT-A-AATAATAAATAAAAAATATTAAATATATATATAAATT
1 AATAAAATAATAATAAAAAATAAAAAATAATAAATATATATATAAA-T
1255906 AATAAAACTAATAATAAAAAA
1 AATAAAA-TAATAATAAAAAA
1255927 ATAATATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
43 8 0.15
44 22 0.42
45 7 0.13
46 5 0.10
47 1 0.02
48 1 0.02
49 8 0.15
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (47 bp):
AATAAAATAATAATAAAAAATAAAAAATAATAAATATATATATAAAT
Found at i:1258783 original size:9 final size:10
Alignment explanation
Indices: 1258771--1258808 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
1258761 AATTATTTAA
1258771 TTAT-TTTTT
1 TTATATTTTT
1258780 TTATATTTTT
1 TTATATTTTT
1258790 TTATATTTTT
1 TTATATTTTT
1258800 TTAT-TTTTT
1 TTATATTTTT
1258809 ATAATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTATATTTTT
Found at i:1258808 original size:8 final size:9
Alignment explanation
Indices: 1258771--1258811 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
1258761 AATTATTTAA
*
1258771 TTATTTTTT
1 TTATATTTT
1258780 TTATATTTTT
1 TTATA-TTTT
1258790 TTATATTTT
1 TTATATTTT
1258799 TT-TATTTT
1 TTATATTTT
1258807 TTATA
1 TTATA
1258812 ATTATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 8 0.28
9 12 0.41
10 9 0.31
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTATATTTT
Found at i:1259746 original size:13 final size:13
Alignment explanation
Indices: 1259730--1259755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1259720 GTGAATTTAT
1259730 AAAGAATAAAATA
1 AAAGAATAAAATA
1259743 AAAGAATAAAATA
1 AAAGAATAAAATA
1259756 TTAATCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAGAATAAAATA
Found at i:1261459 original size:11 final size:11
Alignment explanation
Indices: 1261443--1261484 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1261433 TTTAATTGAA
1261443 TTATTTATATT
1 TTATTTATATT
1261454 TTATTTATATT
1 TTATTTATATT
*
1261465 TTATATTAT-TA
1 TTAT-TTATATT
1261476 TTATTTATA
1 TTATTTATA
1261485 AATAGTCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTTATATT
Found at i:1261616 original size:11 final size:11
Alignment explanation
Indices: 1261596--1261663 Score: 63
Period size: 11 Copynumber: 6.5 Consensus size: 11
1261586 GGAGAGAATT
1261596 ATTA-TTAATA
1 ATTATTTAATA
1261606 ATTATTTAATA
1 ATTATTTAATA
* * * *
1261617 ATGATTGATTG
1 ATTATTTAATA
1261628 ATTA-TTAAT-
1 ATTATTTAATA
1261637 ATTA-TTAATA
1 ATTATTTAATA
*
1261647 ATAATTTAATA
1 ATTATTTAATA
1261658 ATTATT
1 ATTATT
1261664 ATTAATCTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
9 9 0.20
10 10 0.22
11 27 0.59
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (11 bp):
ATTATTTAATA
Found at i:1261706 original size:65 final size:64
Alignment explanation
Indices: 1261633--1261780 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 64
1261623 GATTGATTAT
* * *
1261633 TAAT-ATTATTAATAATAATTTA-ATAATTATTATTAAT-CTAATGATTTGATATTTAATGATTT
1 TAATGATTATTAATAATAATTTATATAAATA-T-TTAATGATAATGATTTGATA-CTAATGATTT
1261695 AA
63 AA
* **
1261697 TAATGATTATTAATAATTATTTATTATAAATATTTAATGATTTTGATTTGATACTAATGATTTAA
1 TAATGATTATTAATAATAATTTA-TATAAATATTTAATGATAATGATTTGATACTAATGATTTAA
* *
1261762 TAATGATCACTAATAATAA
1 TAATGATTATTAATAATAA
1261781 AATTATAAGA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
64 4 0.06
65 49 0.69
66 12 0.17
67 6 0.08
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (64 bp):
TAATGATTATTAATAATAATTTATATAAATATTTAATGATAATGATTTGATACTAATGATTTAA
Found at i:1261805 original size:65 final size:66
Alignment explanation
Indices: 1261674--1261805 Score: 155
Period size: 65 Copynumber: 2.0 Consensus size: 66
1261664 ATTAATCTAA
* * * ** *
1261674 TGATTTGATATTTAATGATTTAATAATGATTATTAATAATTATTTATTATAAATATTTAATGATT
1 TGATTTGATATCTAATGATTTAATAATGATCACTAATAATTATAAATTATAAATATTTAATAATT
1261739 T
66 T
1261740 TGATTTGATA-CTAATGATTTAATAATGATCACTAATAA-TA-AAATTATAAGAT-TTGATAATA
1 TGATTTGATATCTAATGATTTAATAATGATCACTAATAATTATAAATTATAA-ATATT--TAATA
1261801 ATTT
63 ATTT
1261805 T
1 T
1261806 TAATAATGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
63 9 0.16
64 4 0.07
65 34 0.60
66 10 0.18
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (66 bp):
TGATTTGATATCTAATGATTTAATAATGATCACTAATAATTATAAATTATAAATATTTAATAATT
T
Found at i:1261810 original size:34 final size:33
Alignment explanation
Indices: 1261772--1261842 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
1261762 TAATGATCAC
*
1261772 TAATAAT-AAAATTATAAGATTTGATAATAATTTT
1 TAATAATGAAAACTATAA-ATTTGATAAT-ATTTT
** *
1261806 TAATAATGATTACTATTAATTTGATAATATTTT
1 TAATAATGAAAACTATAAATTTGATAATATTTT
1261839 TAAT
1 TAAT
1261843 TTTTTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 9 0.28
34 17 0.53
35 6 0.19
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (33 bp):
TAATAATGAAAACTATAAATTTGATAATATTTT
Found at i:1264600 original size:34 final size:34
Alignment explanation
Indices: 1264560--1264639 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 34
1264550 AATATGTTCG
* *
1264560 CGAACACTAGAA-GAACATGTCCACAAATGTTATA
1 CGAACACTA-AACAAACATGTCCACAAACGTTATA
* *
1264594 CGAACACTAAACAAACATGTTCACAAACGTTAAA
1 CGAACACTAAACAAACATGTCCACAAACGTTATA
* *
1264628 AGAACATTAAAC
1 CGAACACTAAAC
1264640 TAATGTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 2 0.05
34 37 0.95
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (34 bp):
CGAACACTAAACAAACATGTCCACAAACGTTATA
Found at i:1264633 original size:23 final size:23
Alignment explanation
Indices: 1264601--1264695 Score: 84
Period size: 23 Copynumber: 4.2 Consensus size: 23
1264591 ATACGAACAC
*
1264601 TAAACAAACATGTTCACAAACGT
1 TAAACGAACATGTTCACAAACGT
* ** * *
1264624 TAAAAGAACAT-TAAACTAATGT
1 TAAACGAACATGTTCACAAACGT
**
1264646 TAAACGAATGTGTTCACAAACGT
1 TAAACGAACATGTTCACAAACGT
* * *
1264669 TTAACGAAAATGTTCGCAAACGT
1 TAAACGAACATGTTCACAAACGT
1264692 TAAA
1 TAAA
1264696 TAAACGAACA
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
22 15 0.28
23 38 0.72
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (23 bp):
TAAACGAACATGTTCACAAACGT
Found at i:1264777 original size:30 final size:31
Alignment explanation
Indices: 1264743--1264807 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
1264733 ATTCGAACAC
*
1264743 AATATTAAA-A-ATTTAAACGAATACAAACCA
1 AATATTAAATATATTTAAA-AAATACAAACCA
*
1264773 AATA-TAAATATCTTTAAAAAATACAAACCA
1 AATATTAAATATATTTAAAAAATACAAACCA
1264803 AATAT
1 AATAT
1264808 AATTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 4 0.13
30 20 0.67
31 6 0.20
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (31 bp):
AATATTAAATATATTTAAAAAATACAAACCA
Found at i:1264876 original size:17 final size:17
Alignment explanation
Indices: 1264856--1264888 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1264846 TCATCTCCAA
*
1264856 CACTATCTCTATATTAC
1 CACTATCTCTACATTAC
1264873 CACTATCTCTACATTA
1 CACTATCTCTACATTA
1264889 AAACTAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (17 bp):
CACTATCTCTACATTAC
Found at i:1264894 original size:17 final size:17
Alignment explanation
Indices: 1264857--1264901 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1264847 CATCTCCAAC
* **
1264857 ACTATCTCTATATTACC
1 ACTATCTCTACATTAAA
1264874 ACTATCTCTACATTAAA
1 ACTATCTCTACATTAAA
*
1264891 ACTAACTCTAC
1 ACTATCTCTAC
1264902 TTTATTCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (17 bp):
ACTATCTCTACATTAAA
Found at i:1265058 original size:25 final size:25
Alignment explanation
Indices: 1265030--1265095 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1265020 CATAAAAGAT
*
1265030 AAAATAAAAGAAAATAAT-ATAATAA
1 AAAATAAAA-AAAATAATAAAAATAA
*
1265055 AAAA-ATAACAAAATAATAAAAATAA
1 AAAATA-AAAAAAATAATAAAAATAA
*
1265080 AAAATAACAAAAATAA
1 AAAATAAAAAAAATAA
1265096 CAACAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 9 0.26
25 24 0.71
26 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.17
Consensus pattern (25 bp):
AAAATAAAAAAAATAATAAAAATAA
Found at i:1265061 original size:16 final size:16
Alignment explanation
Indices: 1265030--1265108 Score: 72
Period size: 16 Copynumber: 4.9 Consensus size: 16
1265020 CATAAAAGAT
*
1265030 AAAATAAAAGAAAATAA
1 AAAATAACA-AAAATAA
*
1265047 TATAATAA-AAAAATAA
1 -AAAATAACAAAAATAA
*
1265063 CAAAATAATAAAAATAA
1 -AAAATAACAAAAATAA
1265080 AAAATAACAAAAAT-A
1 AAAATAACAAAAATAA
* *
1265095 ACAACAACAAAAAT
1 AAAATAACAAAAAT
1265109 TTGTAACGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
15 13 0.24
16 26 0.48
17 9 0.17
18 6 0.11
ACGTcount: A:0.77, C:0.06, G:0.01, T:0.15
Consensus pattern (16 bp):
AAAATAACAAAAATAA
Found at i:1265096 original size:9 final size:9
Alignment explanation
Indices: 1265050--1265098 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
1265040 AAAATAATAT
1265050 AATAA-AAA
1 AATAACAAA
1265058 AATAAC-AA
1 AATAACAAA
*
1265066 AATAATAAA
1 AATAACAAA
1265075 AAT-A-AAA
1 AATAACAAA
1265082 AATAACAAA
1 AATAACAAA
1265091 AATAACAA
1 AATAACAA
1265099 CAACAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 6 0.17
8 14 0.39
9 16 0.44
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (9 bp):
AATAACAAA
Found at i:1265108 original size:24 final size:24
Alignment explanation
Indices: 1265054--1265107 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
1265044 TAATATAATA
*
1265054 AAAAAATAACAAAATAATAAAAAT
1 AAAAAATAACAAAATAACAAAAAT
* *
1265078 AAAAAATAACAAAAATAACAACAAC
1 AAAAAATAAC-AAAATAACAAAAAT
1265103 AAAAA
1 AAAAA
1265108 TTTGTAACGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (24 bp):
AAAAAATAACAAAATAACAAAAAT
Found at i:1269368 original size:13 final size:13
Alignment explanation
Indices: 1269350--1269378 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1269340 GGGTAAGAAA
1269350 AATATTTTAAAAT
1 AATATTTTAAAAT
1269363 AATATTTTAAAAT
1 AATATTTTAAAAT
1269376 AAT
1 AAT
1269379 TTGAGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATATTTTAAAAT
Found at i:1280353 original size:22 final size:22
Alignment explanation
Indices: 1280328--1280371 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1280318 GGTGGAAAGG
1280328 AATCAATGAAATGGTTTTGTGT
1 AATCAATGAAATGGTTTTGTGT
*
1280350 AATCGATGAAATGGTTTTGTGT
1 AATCAATGAAATGGTTTTGTGT
1280372 GAGAGTGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.41
Consensus pattern (22 bp):
AATCAATGAAATGGTTTTGTGT
Found at i:1281040 original size:12 final size:12
Alignment explanation
Indices: 1281019--1281052 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1281009 TCGGTGCTAA
1281019 ATTTGGTTGTTT
1 ATTTGGTTGTTT
*
1281031 ATTTGCTTGTTT
1 ATTTGGTTGTTT
*
1281043 GTTTGGTTGT
1 ATTTGGTTGT
1281053 CTGGTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.03, G:0.26, T:0.65
Consensus pattern (12 bp):
ATTTGGTTGTTT
Found at i:1283389 original size:16 final size:17
Alignment explanation
Indices: 1283368--1283404 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1283358 TATTCATTCC
1283368 AGATTTCCATGACA-TT
1 AGATTTCCATGACATTT
*
1283384 AGATTTGCATGACATTT
1 AGATTTCCATGACATTT
1283401 AGAT
1 AGAT
1283405 AGAAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (17 bp):
AGATTTCCATGACATTT
Found at i:1287638 original size:2 final size:2
Alignment explanation
Indices: 1287631--1287662 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1287621 ACCATAAAAG
1287631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1287663 TATTTTCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1288521 original size:20 final size:20
Alignment explanation
Indices: 1288493--1288531 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1288483 CAAATACTAA
1288493 AAAAAATGTCAAAAAAATAG
1 AAAAAATGTCAAAAAAATAG
* *
1288513 AAAATATGTCATAAAAATA
1 AAAAAATGTCAAAAAAATA
1288532 TAATTATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (20 bp):
AAAAAATGTCAAAAAAATAG
Found at i:1288690 original size:2 final size:2
Alignment explanation
Indices: 1288683--1288766 Score: 152
Period size: 2 Copynumber: 42.5 Consensus size: 2
1288673 AAAGAAGAAG
*
1288683 GA GA GA GA G- GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1288724 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1288766 G
1 G
1288767 CATGTAGTTT
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1297741 original size:21 final size:21
Alignment explanation
Indices: 1297716--1297763 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1297706 TTTTTTTTTC
* *
1297716 ATATAATATATTTAAAT-TTA
1 ATATAAAATATATAAATATTA
1297736 ATTATAAAATATATAAATATTA
1 A-TATAAAATATATAAATATTA
1297758 ATATAA
1 ATATAA
1297764 GGTTATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATAAAATATATAAATATTA
Found at i:1297832 original size:2 final size:2
Alignment explanation
Indices: 1297825--1297857 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1297815 GGGCATTTTG
1297825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1297858 TGTTCTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1310485 original size:55 final size:55
Alignment explanation
Indices: 1310419--1310529 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
1310409 CAAAGCATTA
*
1310419 TATAAAATTGGGTTAATTACCCCATTCATACATGAATTATATCCGATTTTCAGTT
1 TATAAAATTGGGTTAATTACCCCATTCATACATGAACTATATCCGATTTTCAGTT
1310474 TATAAAATTGGGTTAATTACCCCATTCATACATGAACTATATCCGATTTTCAGTT
1 TATAAAATTGGGTTAATTACCCCATTCATACATGAACTATATCCGATTTTCAGTT
1310529 T
1 T
1310530 CATACATAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (55 bp):
TATAAAATTGGGTTAATTACCCCATTCATACATGAACTATATCCGATTTTCAGTT
Found at i:1317051 original size:32 final size:32
Alignment explanation
Indices: 1317012--1317077 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1317002 TAAAATAAAC
1317012 AAACCAAATCCTGTTTATTATATTCATTCTAT
1 AAACCAAATCCTGTTTATTATATTCATTCTAT
1317044 AAACCAAATCCTGTTTATTATATTCATTCTAT
1 AAACCAAATCCTGTTTATTATATTCATTCTAT
1317076 AA
1 AA
1317078 TTTAATTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (32 bp):
AAACCAAATCCTGTTTATTATATTCATTCTAT
Found at i:1317151 original size:18 final size:18
Alignment explanation
Indices: 1317130--1317165 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1317120 AGGATTCTTT
1317130 TTAGAAATAAGGAATAAA
1 TTAGAAATAAGGAATAAA
1317148 TTAGAAATAAGGAATAAA
1 TTAGAAATAAGGAATAAA
1317166 GAAATCATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (18 bp):
TTAGAAATAAGGAATAAA
Found at i:1317217 original size:21 final size:21
Alignment explanation
Indices: 1317177--1317215 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1317167 AAATCATGGA
1317177 TAAATCCAAGCGACTCTTTCT
1 TAAATCCAAGCGACTCTTTCT
1317198 TAAATCCAAGCGA-TCTTT
1 TAAATCCAAGCGACTCTTT
1317216 TCGTAGGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TAAATCCAAGCGACTCTTTCT
Found at i:1320848 original size:23 final size:23
Alignment explanation
Indices: 1320804--1320867 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1320794 CAGCTCATAT
*
1320804 AAATGCACCAAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * * *
1320827 AATTGCGCCTAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
1320850 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1320868 TATAAGATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1326308 original size:23 final size:23
Alignment explanation
Indices: 1326272--1326335 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1326262 CAGCTCATAT
*
1326272 AAATGCACCGAAGTGCCACGTAG
1 AAATACACCGAAGTGCCACGTAG
* * *
1326295 AATTACACCTAAGTGCCGCGTAG
1 AAATACACCGAAGTGCCACGTAG
*
1326318 AAATGCACCGAAGTGCCA
1 AAATACACCGAAGTGCCA
1326336 TATAAGATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACGTAG
Found at i:1329290 original size:13 final size:13
Alignment explanation
Indices: 1329273--1329313 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1329263 AGATCATCAT
1329273 CATATAACATATA
1 CATATAACATATA
*
1329286 TATATAACATATA
1 CATATAACATATA
*
1329299 CATATCACATA-A
1 CATATAACATATA
1329311 CAT
1 CAT
1329314 GTAATACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (13 bp):
CATATAACATATA
Found at i:1335893 original size:20 final size:20
Alignment explanation
Indices: 1335857--1335894 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1335847 ATCCTATTCC
**
1335857 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1335877 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1335895 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1336229 original size:16 final size:16
Alignment explanation
Indices: 1336210--1336260 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1336200 ATTATTATTC
1336210 TGTAATAAATTATATA
1 TGTAATAAATTATATA
* *
1336226 TGTAA-ATATTATTATTC
1 TGTAATAAATTA-TA-TA
1336243 TGTAATAAATTAATATA
1 TGTAATAAATT-ATATA
1336260 T
1 T
1336261 ATTATTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
15 5 0.19
16 7 0.26
17 8 0.30
18 6 0.22
19 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (16 bp):
TGTAATAAATTATATA
Found at i:1336231 original size:33 final size:34
Alignment explanation
Indices: 1336194--1336260 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
1336184 GATTTGAATG
1336194 GTAAATATTATTATTCTGTAATAAATT-ATATAT
1 GTAAATATTATTATTCTGTAATAAATTAATATAT
1336227 GTAAATATTATTATTCTGTAATAAATTAATATAT
1 GTAAATATTATTATTCTGTAATAAATTAATATAT
1336261 ATTATTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (34 bp):
GTAAATATTATTATTCTGTAATAAATTAATATAT
Found at i:1336254 original size:15 final size:15
Alignment explanation
Indices: 1336203--1336254 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
1336193 GGTAAATATT
1336203 ATTATTCTGTAATAA
1 ATTATTCTGTAATAA
* *
1336218 ATTATATATGTAAATATT
1 ATTAT-TCTGT-AATA-A
1336236 ATTATTCTGTAATAA
1 ATTATTCTGTAATAA
1336251 ATTA
1 ATTA
1336255 ATATATATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 9 0.30
16 8 0.27
17 8 0.27
18 5 0.17
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (15 bp):
ATTATTCTGTAATAA
Found at i:1337244 original size:17 final size:17
Alignment explanation
Indices: 1337207--1337240 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1337197 ATTCATTAAT
*
1337207 ATTTACGTGAATAGTGA
1 ATTTACGTGAATAGTAA
1337224 ATTTA-GTGAATAGTAA
1 ATTTACGTGAATAGTAA
1337240 A
1 A
1337241 ATTTTATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTAA
Found at i:1344138 original size:29 final size:29
Alignment explanation
Indices: 1344095--1344177 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
1344085 CTCACCTAAC
1344095 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
** *
1344125 TAAATGATGTAAGCAATGACATTTTTATT
1 TAAATGATGTAAGCAATGACATCATTACT
1344154 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1344178 ATTCAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:1348414 original size:29 final size:30
Alignment explanation
Indices: 1348371--1348458 Score: 126
Period size: 29 Copynumber: 2.9 Consensus size: 30
1348361 CTCACCTAAC
*
1348371 TAAATTGATGTAAGCAATAACATCA-TTACT
1 TAAA-TGATGTAAGCAATGACATCATTTACT
*
1348401 TAAATGATGTAAGCAATGACAT-ATTTATT
1 TAAATGATGTAAGCAATGACATCATTTACT
1348430 TAAATGATGTAAGCAATGACATCAATTTA
1 TAAATGATGTAAGCAATGACATC-ATTTA
1348459 GTTTGAGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
28 1 0.02
29 43 0.81
30 4 0.08
31 5 0.09
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (30 bp):
TAAATGATGTAAGCAATGACATCATTTACT
Found at i:1356145 original size:17 final size:17
Alignment explanation
Indices: 1356112--1356154 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1356102 TTTTTCTCCA
*
1356112 ATAAATTTAAAGGATAT
1 ATAAATTTAAAAGATAT
*
1356129 -TATAATTTAAAATATAT
1 ATA-AATTTAAAAGATAT
1356146 ATAAATTTA
1 ATAAATTTA
1356155 TTGATTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
ATAAATTTAAAAGATAT
Found at i:1358020 original size:18 final size:18
Alignment explanation
Indices: 1357977--1358039 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
1357967 TCACGGAATG
1357977 TAAGATTACCGACGGGAA
1 TAAGATTACCGACGGGAA
* * *
1357995 TAATATTACTGACTGGAA
1 TAAGATTACCGACGGGAA
* ** *
1358013 TAGGATTACCGGTGAGAA
1 TAAGATTACCGACGGGAA
1358031 TAAGATTAC
1 TAAGATTAC
1358040 TGAGAATGTT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (18 bp):
TAAGATTACCGACGGGAA
Found at i:1358929 original size:37 final size:36
Alignment explanation
Indices: 1358859--1358931 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
1358849 TGGAAAATAT
* *
1358859 TTATATATTTTCTTTAAAAATTTAAATTCATAAAAA
1 TTATATATTTTCTTTAAAAATTGAAAATCATAAAAA
*
1358895 TTATATAATTTTTTTTATAAAATTGAAAAT-ATAAAAA
1 TTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAAAA
1358932 GGTTTAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 6 0.19
37 16 0.50
38 10 0.31
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (36 bp):
TTATATATTTTCTTTAAAAATTGAAAATCATAAAAA
Found at i:1359819 original size:23 final size:23
Alignment explanation
Indices: 1359775--1359819 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1359765 AATTTGGTGC
* *
1359775 AAAATTTTAATATATATCTTTTA
1 AAAATATTAATATATATATTTTA
1359798 AAAATATTAAGTATATA-ATTTT
1 AAAATATTAA-TATATATATTTT
1359820 TTTCTCTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
AAAATATTAATATATATATTTTA
Found at i:1364902 original size:20 final size:20
Alignment explanation
Indices: 1364877--1364927 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1364867 ATATACCTTG
*
1364877 GTATCGATACTA-GCCTCTTA
1 GTATCGATACTACCCCT-TTA
*
1364897 GTATCGATACCACCCCTTTA
1 GTATCGATACTACCCCTTTA
1364917 GTATCGATACT
1 GTATCGATACT
1364928 CTCTTAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (20 bp):
GTATCGATACTACCCCTTTA
Found at i:1365012 original size:64 final size:64
Alignment explanation
Indices: 1364937--1365074 Score: 240
Period size: 64 Copynumber: 2.2 Consensus size: 64
1364927 TCTCTTAAAG
* *
1364937 GTATCGATACCCTCTACTATTTCATCTTAAAAATAAATTAGAAGTATCAATACTCCTGTGGAAA
1 GTATCGATACCCTCTACTATTTCATCTTAAAAACAAATTAGAAGTATCAATACTCCCGTGGAAA
* *
1365001 GTATCGATACCCTCTACTATTTCATCTTGAAAACAAATTAGAAGTATCGATACTCCCGTGGAAA
1 GTATCGATACCCTCTACTATTTCATCTTAAAAACAAATTAGAAGTATCAATACTCCCGTGGAAA
1365065 GTATCGATAC
1 GTATCGATAC
1365075 TCAACCCTGG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (64 bp):
GTATCGATACCCTCTACTATTTCATCTTAAAAACAAATTAGAAGTATCAATACTCCCGTGGAAA
Found at i:1366913 original size:168 final size:166
Alignment explanation
Indices: 1366238--1366995 Score: 723
Period size: 168 Copynumber: 4.5 Consensus size: 166
1366228 ATCTCTACCG
* * * * *
1366238 TCATTTGTGCATATAATTGAGTAAAAAATGCAGAGAAAATTTGACAAAAAAGGAAGGCTCGTCCC
1 TCATCTGTGCATATAATTGACTGAAAAATGCAGAGAAAATATGACAAAAAAGGAAGGCTCATCCC
* * * *
1366303 ACAAAAAGCTCTTTCACCTTTTTTAAAGAATCATTGTCATGTCATAGTGTCTCATCCCATCAAAC
66 ACAAGAAGCT-TTTCACATTTTTCAAAGAATTA-TGTCATGTCATAGTGTCTCATCCCATCAAAC
* *
1366368 ATA-AGAGG-TTGATATGAATAGTTCCTCGATTGGGAACA
129 ATAGAG-GGATTGACATGAATAGTTCC-CGACTGGGAACA
* * * * *
1366406 TCATCTATGAATATAATTGACTGAAAAATGCAGAGAAAATCAT-ATAAAAAGGGGAAGGTTCATC
1 TCATCTGTGCATATAATTGACTGAAAAATGCAGAGAAAAT-ATGACAAAAA-AGGAAGGCTCATC
*
1366470 CCACAAGAAGTGCTTTT-ACATTTTTCAAAGAA-TA--TC-T-ACATAGTGTCTCATCCCATCAA
64 CCACAAGAA--GCTTTTCACATTTTTCAAAGAATTATGTCATGTCATAGTGTCTCATCCCATCAA
** * * * * **
1366529 ATGTA-AGGGGTTCACATGAATAGCTCTCGACTATGAACA
127 ACATAGAGGGATTGACATGAATAGTTCCCGACTGGGAACA
* * *
1366568 TCATCTATGCATATAATTGACTGAAAAATGCAGAGAAAATTTGAAAAAAAAAGGCAAGGCTCATC
1 TCATCTGTGCATATAATTGACTGAAAAATGCAGAGAAAATATG-ACAAAAAAGG-AAGGCTCATC
* * * * *
1366633 CCACAAGAAGCGCTTTCACATTTTTCAGAGAATTTCTGTTATTTCATAGTGTCTCATCCCATCAA
64 CCACAAGAAGC-TTTTCACATTTTTCAAAGAA-TTATGTCATGTCATAGTGTCTCATCCCATCAA
* * * *
1366698 ACATAG-GGGGTTGACTTGAATAGTTCACCAACTGAGAACA
127 ACATAGAGGGATTGACATGAATAGTTC-CCGACTGGGAACA
* ** * *
1366738 TCATCTGTGCATATAATTGATTGAAAAATATAGAGAAAATATGACAAAAAATAGAAGGCTCGTCC
1 TCATCTGTGCATATAATTGACTGAAAAATGCAGAGAAAATATGACAAAAAA-GGAAGGCTCATCC
* * * * *
1366803 CATAAGAAGCATTTTCACCTTTGTCAGAGAATTATGTCATGTCATACTGTCTCATCCCATCAAAC
65 CACAAGAAGC-TTTTCACATTTTTCAAAGAATTATGTCATGTCATAGTGTCTCATCCCATCAAAC
*** * * *
1366868 ATAGAATTATTGAC-TAAATAATTCCCTGATTGGGAACA
129 ATAGAGGGATTGACATGAATAGTTCCC-GACTGGGAACA
** ** *
1366906 TCATCTGTATATATAATTGACTGAAAAATATAGAGAAAATCTGACATAAAAAGGAAGGCTCATCC
1 TCATCTGTGCATATAATTGACTGAAAAATGCAGAGAAAATATGACA-AAAAAGGAAGGCTCATCC
*
1366971 CACAAGAAATG-ATTTCACATTTTTC
65 CACAAG-AA-GCTTTTCACATTTTTC
1366996 TATTCATTTT
Statistics
Matches: 487, Mismatches: 79, Indels: 48
0.79 0.13 0.08
Matches are distributed among these distances:
161 3 0.01
162 55 0.11
163 77 0.16
164 1 0.00
165 3 0.01
167 3 0.01
168 162 0.33
169 128 0.26
170 52 0.11
171 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (166 bp):
TCATCTGTGCATATAATTGACTGAAAAATGCAGAGAAAATATGACAAAAAAGGAAGGCTCATCCC
ACAAGAAGCTTTTCACATTTTTCAAAGAATTATGTCATGTCATAGTGTCTCATCCCATCAAACAT
AGAGGGATTGACATGAATAGTTCCCGACTGGGAACA
Found at i:1367755 original size:102 final size:102
Alignment explanation
Indices: 1367596--1367826 Score: 261
Period size: 102 Copynumber: 2.3 Consensus size: 102
1367586 AACATCATTT
* * *
1367596 CAAGTTCAAGGGGAAGGCATTCATCTACCAACTTCTTCGACCTCAACATGGTCATGCCATCGA-C
1 CAAGTTCAAGGGGAAGACATTCATCTACCAACTTCTTCGACCTCAACATCGACATGCC-TCGAGC
*
1367660 ACAACAATTTGTTCAAAACCCATATGACACTATTACTC
65 ACAACAATCTGTTCAAAACCCATATGACACTATTACTC
* * * * * * * **
1367698 CAAGTTCTATGGGAAGACATTCATTTACCAACTTTTTTGACCTCAATATCGAGATGCCTTTAGCA
1 CAAGTTCAAGGGGAAGACATTCATCTACCAACTTCTTCGACCTCAACATCGACATGCCTCGAGCA
* *
1367763 CAACAATCTGTTCAAAACCCATATGACATTA-TACCTT
66 CAACAATCTGTTCAAAACCCATATGACACTATTA-CTC
* *
1367800 CAAGTTTAAGTGGAATG-CATTCATCTA
1 CAAGTTCAAGGGGAA-GACATTCATCTA
1367827 TTAACTTGTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
101 4 0.04
102 101 0.95
103 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (102 bp):
CAAGTTCAAGGGGAAGACATTCATCTACCAACTTCTTCGACCTCAACATCGACATGCCTCGAGCA
CAACAATCTGTTCAAAACCCATATGACACTATTACTC
Found at i:1369605 original size:22 final size:20
Alignment explanation
Indices: 1369573--1369612 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1369563 ATGTCACAAC
1369573 CTCTTTAAGAGATTGAATCTAA
1 CTCTTTAAGAG-TT-AATCTAA
*
1369595 CTCTTTCAGAGTTAATCT
1 CTCTTTAAGAGTTAATCT
1369613 GCAAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
CTCTTTAAGAGTTAATCTAA
Found at i:1370352 original size:22 final size:24
Alignment explanation
Indices: 1370326--1370379 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
1370316 TTAATCTAAC
1370326 CCTAAACCA-TTTGAA-CAAAAAAT
1 CCTAAACCACTTT-AACCAAAAAAT
*
1370349 -CTAAACCACTTTAACCTAAAAAT
1 CCTAAACCACTTTAACCAAAAAAT
1370372 CCTAAACC
1 CCTAAACC
1370380 GCTCAACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.22
Consensus pattern (24 bp):
CCTAAACCACTTTAACCAAAAAAT
Found at i:1370387 original size:23 final size:23
Alignment explanation
Indices: 1370343--1370387 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1370333 CATTTGAACA
*
1370343 AAAAATCTAAACCACTTTAACCT
1 AAAAATCTAAACCACTTCAACCT
*
1370366 AAAAATCCTAAACCGC-TCAACC
1 AAAAAT-CTAAACCACTTCAACC
1370388 AACCCTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAAATCTAAACCACTTCAACCT
Found at i:1375628 original size:2 final size:2
Alignment explanation
Indices: 1375621--1375663 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1375611 ACCGGTGTTT
1375621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1375663 T
1 T
1375664 TGTCGGAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1386983 original size:30 final size:31
Alignment explanation
Indices: 1386926--1386994 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
1386916 TCGGGTCGGG
1386926 TATATATATTTAAATTAAATATATAAATATTA
1 TATATATATTTAAATTAAATATATAAAT-TTA
* * *
1386958 TATATATTTTTTAATTTAAT-T-TAAATTTA
1 TATATATATTTAAATTAAATATATAAATTTA
1386987 T-TA-ATATT
1 TATATATATT
1386995 ATATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 4 0.12
30 5 0.15
31 1 0.03
32 17 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TATATATATTTAAATTAAATATATAAATTTA
Found at i:1387019 original size:38 final size:38
Alignment explanation
Indices: 1386926--1387011 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
1386916 TCGGGTCGGG
* *
1386926 TATAT-AT-ATTTAAATTAAATATATAAATATTATATA
1 TATATAATAATTTAATTTAAATTTATAAATATTATATA
* ** *
1386962 TATTTTTTAATTTAATTTAAATTTATTAATATTATATA
1 TATATAATAATTTAATTTAAATTTATAAATATTATATA
1387000 TATATAATAATT
1 TATATAATAATT
1387012 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 4 0.10
37 1 0.03
38 35 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (38 bp):
TATATAATAATTTAATTTAAATTTATAAATATTATATA
Found at i:1388295 original size:15 final size:16
Alignment explanation
Indices: 1388263--1388296 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1388253 ATAAATATAG
1388263 AAAAATCTTAGTTAAA
1 AAAAATCTTAGTTAAA
1388279 AAAAATCTTAGTTAAA
1 AAAAATCTTAGTTAAA
1388295 AA
1 AA
1388297 TTATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAAATCTTAGTTAAA
Found at i:1392066 original size:29 final size:30
Alignment explanation
Indices: 1392024--1392094 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1392014 TTATAATTAA
1392024 AAATCAATGT-AATTA-CTAAATT-TTTAATT
1 AAATCAAT-TAAATTATC-AAATTATTTAATT
*
1392053 AAATCAATTAAATTATCCAATTATTTAATT
1 AAATCAATTAAATTATCAAATTATTTAATT
* *
1392083 GATTCAATTAAA
1 AAATCAATTAAA
1392095 CCACCTACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.03
29 17 0.47
30 18 0.50
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (30 bp):
AAATCAATTAAATTATCAAATTATTTAATT
Found at i:1392560 original size:16 final size:17
Alignment explanation
Indices: 1392523--1392566 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1392513 GATAAAATAA
* *
1392523 TTAAACAAATTATTCGT
1 TTAAATAAATTATTCAT
1392540 TTAAATAAATTATT-AT
1 TTAAATAAATTATTCAT
*
1392556 TTAAATTAATT
1 TTAAATAAATT
1392567 GTAAACTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (17 bp):
TTAAATAAATTATTCAT
Found at i:1392734 original size:29 final size:30
Alignment explanation
Indices: 1392669--1392763 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 30
1392659 AAATTTGTTC
* * *
1392669 GGTTCAGTTAATAATTTTCAAAAAAAATTT
1 GGTTCAATTAATAATTTTCAAATAAATTTT
*
1392699 GG-----TTAATAATTTTCAAATTAA-TTT
1 GGTTCAATTAATAATTTTCAAATAAATTTT
*
1392723 GGTTCGATTAATAATTTTCAAATAAATTTT
1 GGTTCAATTAATAATTTTCAAATAAATTTT
1392753 GGTTCAATTAA
1 GGTTCAATTAA
1392764 CCTAACCGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 5 0.09
25 17 0.31
29 18 0.33
30 15 0.27
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (30 bp):
GGTTCAATTAATAATTTTCAAATAAATTTT
Found at i:1392975 original size:29 final size:30
Alignment explanation
Indices: 1392913--1392986 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
1392903 AATATCGGTT
* *
1392913 AATTTT-GTTC-GTTTATAATTTTCAAATT
1 AATTTTGGTTCGGTTAATAATTTTCAAATA
1392941 AA-TTTGGTTCGGTTAATAATTTT-AAATA
1 AATTTTGGTTCGGTTAATAATTTTCAAATA
*
1392969 AATTTTGGTTCGATTAAT
1 AATTTTGGTTCGGTTAAT
1392987 CGAACAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 3 0.08
28 12 0.30
29 25 0.62
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.51
Consensus pattern (30 bp):
AATTTTGGTTCGGTTAATAATTTTCAAATA
Done.