Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 17
Found at i:2351160 original size:13 final size:12
Alignment explanation
Indices: 2351136--2351189 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
2351126 TTTTTGAATT
2351136 TTTTC-TTTTTC
1 TTTTCTTTTTTC
2351147 TTTTCTTTTCTTC
1 TTTTCTTTT-TTC
2351160 TTTTCTGATTTTTC
1 TTTTCT--TTTTTC
* *
2351174 TCTTCTTTTGTC
1 TTTTCTTTTTTC
2351186 TTTT
1 TTTT
2351190 TCTCTCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 5 0.14
12 11 0.31
13 9 0.25
14 8 0.22
15 3 0.08
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:2351160 original size:19 final size:18
Alignment explanation
Indices: 2351134--2351190 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
2351124 TCTTTTTGAA
2351134 TTTT-TTCTTTTTCTTTT
1 TTTTCTTCTTTTTCTTTT
2351151 CTTTTCTTC-TTTTCTGATTT
1 -TTTTCTTCTTTTTCT--TTT
*
2351171 TTCTCTTCTTTTGTCTTTT
1 TTTTCTTCTTTT-TCTTTT
2351190 T
1 T
2351191 CTCTCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 10 0.30
19 14 0.42
20 6 0.18
21 3 0.09
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTCTTCTTTTTCTTTT
Found at i:2359214 original size:16 final size:17
Alignment explanation
Indices: 2359193--2359229 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2359183 AACGTCTTTT
2359193 AAAACAATTTTAAGA-A
1 AAAACAATTTTAAGACA
*
2359209 AAAACATTTTTAAGACA
1 AAAACAATTTTAAGACA
2359226 AAAA
1 AAAA
2359230 TTGGTTTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAACAATTTTAAGACA
Found at i:2361324 original size:18 final size:18
Alignment explanation
Indices: 2361296--2361341 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2361286 ACCAGTCATA
* *
2361296 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCATTG
*
2361314 ACCGGACCCGACCCATTG
1 ACCCGACCCGACCCATTG
2361332 ACCCGACCCG
1 ACCCGACCCG
2361342 TTGACCGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.50, G:0.20, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:2361334 original size:13 final size:13
Alignment explanation
Indices: 2361318--2361347 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2361308 CCGTTGACCG
2361318 GACCCGACCCATT
1 GACCCGACCCATT
*
2361331 GACCCGACCCGTT
1 GACCCGACCCATT
2361344 GACC
1 GACC
2361348 GTTGACCGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:2362047 original size:36 final size:36
Alignment explanation
Indices: 2362007--2362079 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
2361997 AGTTCTGGAA
* *
2362007 TTAAGTGGTAAAAGAATCAGCCATGGAAATGTAGAT
1 TTAAGTGATAAAAGAATCAGACATGGAAATGTAGAT
* *
2362043 TTAAGTGATAAAAGAATCATACATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGACATGGAAATGTAGAT
2362079 T
1 T
2362080 ATAATTTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAGACATGGAAATGTAGAT
Found at i:2363889 original size:24 final size:25
Alignment explanation
Indices: 2363874--2363964 Score: 73
Period size: 24 Copynumber: 3.8 Consensus size: 25
2363864 ATTTCCTACT
*
2363874 TGAATTATGTTTTGATAT-ATGACC
1 TGAATTATGTTTTGATTTCATGACC
*
2363898 TGAATTATGTTTTGATTTC-TGATC
1 TGAATTATGTTTTGATTTCATGACC
* * * **
2363922 TGGATTCTGTTCTGATATT--TGTTC
1 TGAATTATGTTTTGAT-TTCATGACC
*
2363946 TGAATTCTGTTTTGATTTC
1 TGAATTATGTTTTGATTTC
2363965 TGATATCTCC
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.18, T:0.53
Consensus pattern (25 bp):
TGAATTATGTTTTGATTTCATGACC
Found at i:2365467 original size:3 final size:3
Alignment explanation
Indices: 2365459--2365484 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2365449 AATTAAAATT
2365459 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2365485 CAAAGACCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2365691 original size:43 final size:41
Alignment explanation
Indices: 2365641--2365733 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 41
2365631 ACACTACTCA
* * *
2365641 TACGTGATGAA-GAGTTCTGGTCATATAAGGGTGACACGGCTCC
1 TACGTGATGAAGGAGATATGGT--TA-AAGGATGACACGGCTCC
* *
2365684 TACGTGAT-AAGGAGATATGGTTAATGGATGACACGGTTCC
1 TACGTGATGAAGGAGATATGGTTAAAGGATGACACGGCTCC
2365724 TACGTGATGA
1 TACGTGATGA
2365734 TGACTGACCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
40 22 0.51
41 3 0.07
42 2 0.05
43 16 0.37
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (41 bp):
TACGTGATGAAGGAGATATGGTTAAAGGATGACACGGCTCC
Found at i:2365975 original size:130 final size:130
Alignment explanation
Indices: 2365782--2366021 Score: 340
Period size: 130 Copynumber: 1.8 Consensus size: 130
2365772 CTACACAATG
* * * *
2365782 AGGATGACTAGTTATCTAGGGGTGACACCGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGA
1 AGGATGACTAGTTATCTAGGGATGACACCGCTCCTACATAATGAGGAGGTATGGTCGGTGGATGA
* *
2365847 CACCGTTTCTACGTAATGAGGACGACGGACCATCTTTAGGGATAATAACACGGTTGCTATATGAT
66 CACCGTTCCTA-GTAATGAGGACGACAGACCATCTTTAGGGATAATAACACGGTTGCTATATGAT
2365912 A
130 A
* * **
2365913 AGGATGGCTAGTTATCTA-GGATGATATGGCTCCTACATAATGAGGAGGTATGGTCGAG-GGATG
1 AGGATGACTAGTTATCTAGGGATGACACCGCTCCTACATAATGAGGAGGTATGGTCG-GTGGATG
* *
2365976 ACACGGTTCCTAGTAATGAGGACGTCAGACCATCTTTAGGGATAAT
65 ACACCGTTCCTAGTAATGAGGACGACAGACCATCTTTAGGGATAAT
2366022 GGTTTCAAGA
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
129 32 0.33
130 46 0.48
131 18 0.19
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (130 bp):
AGGATGACTAGTTATCTAGGGATGACACCGCTCCTACATAATGAGGAGGTATGGTCGGTGGATGA
CACCGTTCCTAGTAATGAGGACGACAGACCATCTTTAGGGATAATAACACGGTTGCTATATGATA
Found at i:2366160 original size:66 final size:65
Alignment explanation
Indices: 2366023--2366216 Score: 201
Period size: 66 Copynumber: 2.9 Consensus size: 65
2366013 AGGGATAATG
** * * * * **
2366023 GTTTCAAGAGAAACCATCTCAAGAGAGACAAACTAGTTTCAAGGGAAACAGA-CTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGAGAAACA-ATCTCAAAGA-TGG
2366087 AT
64 AT
* * *
2366089 ATTTCAAGAGAAACTGTCTCAAGAGAGAAAAATTTTGTTTCAAGCGAAACAATCTCAAAGATGGG
1 GTTTCAAGAGAAACTGTCTCAAGAGAGAAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGATGGA
2366154 T
65 T
* * * * *
2366155 GTTTCAAGTGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGATAAACGATCTCAAAGAT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAATTTGTTTCAAGAGAAACAATCTCAAAGAT
2366217 TTTTCAAGAG
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
66 81 0.75
67 27 0.25
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGAAAAATTTGTTTCAAGAGAAACAATCTCAAAGATGGAT
Found at i:2370041 original size:24 final size:22
Alignment explanation
Indices: 2369980--2370041 Score: 54
Period size: 24 Copynumber: 2.6 Consensus size: 22
2369970 TTGTCATAAT
*
2369980 CATTTTTTTGAAAAACAATTAA
1 CATTTATTTGAAAAACAATTAA
*
2370002 -ATATTATTTAATAAAAACAATTATGA
1 CAT-TTATTT--GAAAAACAATTA--A
2370028 CATTTATTTGAAAA
1 CATTTATTTGAAAA
2370042 GTTTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
21 2 0.06
22 5 0.16
24 15 0.48
26 7 0.23
27 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.40
Consensus pattern (22 bp):
CATTTATTTGAAAAACAATTAA
Found at i:2370959 original size:30 final size:30
Alignment explanation
Indices: 2370893--2370976 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
2370883 ATCATATTTG
* * *
2370893 ATTTAAATGACCAAAATAGAAAAAATAGAA
1 ATTTAAAGGACTAAAATAGAAAAAACAGAA
* * * *
2370923 ACTTAAAGGACTAAAATAGCAAAACCATAA
1 ATTTAAAGGACTAAAATAGAAAAAACAGAA
2370953 ATTTAAAGGACTAAAATAAGAAAA
1 ATTTAAAGGACTAAAAT-AGAAAA
2370977 CAAATTGGAG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 39 0.89
31 5 0.11
ACGTcount: A:0.61, C:0.10, G:0.11, T:0.19
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGAAAAAACAGAA
Found at i:2374024 original size:29 final size:30
Alignment explanation
Indices: 2373963--2374029 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
2373953 CAACACTACA
* * *
2373963 CAACTTTTCAAAAATTATCAATTAGGTTCC
1 CAACTTTTCAAAAATTATAAAATAGGTCCC
2373993 CAACTTTTCAAAAATTATAAAAT-GGTCCC
1 CAACTTTTCAAAAATTATAAAATAGGTCCC
*
2374022 CAAATTTT
1 CAACTTTT
2374030 TATAAGGCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (30 bp):
CAACTTTTCAAAAATTATAAAATAGGTCCC
Found at i:2374744 original size:31 final size:31
Alignment explanation
Indices: 2374709--2374770 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2374699 ATAATTACCA
*
2374709 TCAAACCAAGACACCTCAACCTTATCATCTT
1 TCAAACAAAGACACCTCAACCTTATCATCTT
2374740 TCAAACAAAGACACCTCAACCTTATCATCTT
1 TCAAACAAAGACACCTCAACCTTATCATCTT
2374771 CCTTAAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.34, G:0.03, T:0.26
Consensus pattern (31 bp):
TCAAACAAAGACACCTCAACCTTATCATCTT
Found at i:2376579 original size:20 final size:20
Alignment explanation
Indices: 2376554--2376609 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2376544 ACCATAGGCA
*
2376554 AAGGTAGTATCAATATCATC
1 AAGGTAGTATCAATACCATC
*
2376574 AAGGTAGTATCGATACCATC
1 AAGGTAGTATCAATACCATC
*
2376594 AAGGTAGTATCGATAC
1 AAGGTAGTATCAATAC
2376610 TACCATGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (20 bp):
AAGGTAGTATCAATACCATC
Found at i:2376613 original size:23 final size:21
Alignment explanation
Indices: 2376554--2376620 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 21
2376544 ACCATAGGCA
*
2376554 AAGGTAGTATC-AATATCATC
1 AAGGTAGTATCGAATACCATC
2376574 AAGGTAGTATCG-ATACCATC
1 AAGGTAGTATCGAATACCATC
*
2376594 AAGGTAGTATCGATACTACCATG
1 AAGGTAGTATCGA-A-TACCATC
2376617 AAGG
1 AAGG
2376621 CTCAGATTCC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
20 30 0.73
22 1 0.02
23 10 0.24
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (21 bp):
AAGGTAGTATCGAATACCATC
Found at i:2380098 original size:19 final size:19
Alignment explanation
Indices: 2380074--2380110 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2380064 TAGAATGCAA
2380074 AAATGGTACTGATACCATG
1 AAATGGTACTGATACCATG
*
2380093 AAATGGTATTGATACCAT
1 AAATGGTACTGATACCAT
2380111 AGTGCAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (19 bp):
AAATGGTACTGATACCATG
Found at i:2385104 original size:6 final size:6
Alignment explanation
Indices: 2385095--2385176 Score: 73
Period size: 6 Copynumber: 14.2 Consensus size: 6
2385085 TACAATATAC
* *
2385095 ATATTT ATA--T ATATTT ATATAT ATATTT ATATTT ATA--T ACATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
* * * *
2385139 ATATTT ATATAT ATATAT ATATAT ATATAT ATAGTTT A
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATA-TTT A
2385177 CGAAATACAA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
4 7 0.11
6 55 0.85
7 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (6 bp):
ATATTT
Found at i:2385108 original size:10 final size:10
Alignment explanation
Indices: 2385090--2385171 Score: 87
Period size: 10 Copynumber: 8.4 Consensus size: 10
2385080 CAATCTACAA
*
2385090 TATACATATT
1 TATATATATT
2385100 TATATATATT
1 TATATATATT
2385110 TATATATA--
1 TATATATATT
*
2385118 TATTTATATT
1 TATATATATT
*
2385128 TATATACATT
1 TATATATATT
* *
2385138 TATATTTATA
1 TATATATATT
*
2385148 TATATATATA
1 TATATATATT
*
2385158 TATATATATA
1 TATATATATT
2385168 TATA
1 TATA
2385172 GTTTACGAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
8 7 0.11
10 55 0.89
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (10 bp):
TATATATATT
Found at i:2385169 original size:16 final size:16
Alignment explanation
Indices: 2385089--2385171 Score: 94
Period size: 16 Copynumber: 5.2 Consensus size: 16
2385079 TCAATCTACA
* *
2385089 ATATACATATTTATAT
1 ATATATATATATATAT
*
2385105 ATATTTATATATATAT
1 ATATATATATATATAT
* * *
2385121 TTATATTTATATACAT
1 ATATATATATATATAT
* *
2385137 TTATATTTATATATAT
1 ATATATATATATATAT
2385153 ATATATATATATATAT
1 ATATATATATATATAT
2385169 ATA
1 ATA
2385172 GTTTACGAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATATATATATATAT
Found at i:2385416 original size:85 final size:85
Alignment explanation
Indices: 2385228--2385441 Score: 265
Period size: 85 Copynumber: 2.5 Consensus size: 85
2385218 AATGGCGTGT
* *
2385228 GCTTCAATGACACGCAATATAAGTCATACATGTGTGTCATAAATTTATGACACACAAATGTATGT
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
*
2385293 CAAGCAGATTTATGACGGGG
66 CAAGCAGATTTATGACAGGG
* * * *
2385313 GCTTCAATGATACGCAATGTAAGTTATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
*
2385378 C-ATCTTA-ATTTATGACAGGG
66 CAAGC--AGATTTATGACAGGG
* **
2385398 GCTTCAATGACACTCAATG-AACGTCATTA-ATGCACGTCATAAAT
1 GCTTCAATGACACGCAATGTAA-GTCA-TACATGCGTGTCATAAAT
2385442 GTGCGTCATA
Statistics
Matches: 112, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
84 4 0.04
85 105 0.94
86 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (85 bp):
GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTATGT
CAAGCAGATTTATGACAGGG
Found at i:2390123 original size:17 final size:17
Alignment explanation
Indices: 2390101--2390135 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2390091 AGAGACTATA
2390101 ATGAATAAATGAAAAAT
1 ATGAATAAATGAAAAAT
2390118 ATGAATAAATGAAAAAT
1 ATGAATAAATGAAAAAT
2390135 A
1 A
2390136 CAGTGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (17 bp):
ATGAATAAATGAAAAAT
Found at i:2391171 original size:25 final size:25
Alignment explanation
Indices: 2391125--2391178 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
2391115 ACTTTATTCA
2391125 TTTTATTTTCTTTAGTTTTTTTATT
1 TTTTATTTTCTTTAGTTTTTTTATT
*
2391150 TTTTATTATT-TTT-GTTTATTTTCTT
1 TTTTATT-TTCTTTAGTTT-TTTTATT
2391175 TTTT
1 TTTT
2391179 TACTAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 4 0.15
25 20 0.77
26 2 0.08
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTATTTTCTTTAGTTTTTTTATT
Found at i:2391918 original size:17 final size:18
Alignment explanation
Indices: 2391886--2391919 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2391876 ATTCATATAT
*
2391886 TTTATTCCTTCGTGTGAA
1 TTTATTCCTCCGTGTGAA
2391904 TTTATT-CTCCGTGTGA
1 TTTATTCCTCCGTGTGA
2391920 GCATATGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.50
Consensus pattern (18 bp):
TTTATTCCTCCGTGTGAA
Found at i:2393007 original size:14 final size:15
Alignment explanation
Indices: 2392981--2393011 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2392971 TACTTAAACA
2392981 TATTTTGCATTTTTT
1 TATTTTGCATTTTTT
2392996 TATTTT-CATTTTTT
1 TATTTTGCATTTTTT
2393010 TA
1 TA
2393012 CATTCGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (15 bp):
TATTTTGCATTTTTT
Found at i:2393943 original size:93 final size:95
Alignment explanation
Indices: 2393770--2393949 Score: 269
Period size: 95 Copynumber: 1.9 Consensus size: 95
2393760 AAATATATAT
*
2393770 AATAAAGCTTGAGTTATCCCTCTAAAGTAATTGGTTAAACGCCCCAGCTTTATGGATAAGATTCA
1 AATAAAGCTTGAGTTATCCATCTAAAGTAATTGGTTAAACGCCCCAGCTTTATGGATAAGATTCA
2393835 GCTAGCCTGATAAAGGTGATTACAATGTAC
66 GCTAGCCTGATAAAGGTGATTACAATGTAC
* * * *
2393865 AATAAAGCTTGAGTTGA-CCATCTAGA-TCAATTGGTTAAATG-CCCAGTTTTAT-GATAATATT
1 AATAAAGCTTGAGTT-ATCCATCTAAAGT-AATTGGTTAAACGCCCCAGCTTTATGGATAAGATT
2393926 CAGCTAGCCTGATAAAGGTGATTA
64 CAGCTAGCCTGATAAAGGTGATTA
2393950 TAATATCTAT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
93 32 0.41
94 11 0.14
95 34 0.44
96 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (95 bp):
AATAAAGCTTGAGTTATCCATCTAAAGTAATTGGTTAAACGCCCCAGCTTTATGGATAAGATTCA
GCTAGCCTGATAAAGGTGATTACAATGTAC
Found at i:2394020 original size:93 final size:91
Alignment explanation
Indices: 2393798--2394027 Score: 241
Period size: 93 Copynumber: 2.4 Consensus size: 91
2393788 CCTCTAAAGT
*
2393798 AATTGGTTAAACGCCCCAGCTTTATGGATAAGATTCAGCTAGCCTGATAAAGGTGATTACAATGT
1 AATTGGTTAAACGCCCCAGCTTTAT-G---AGATTCAGCTAGCCTGATAAAGGTGATTACAATAT
* * *
2393863 ACAATAAAGCTTGAGTTGACCATCTAGATC
62 ACAATAAAGATTAAATTGACCATCTAGATC
* * * *
2393893 AATTGGTTAAATG-CCCAGTTTTATGATAATATTCAGCTAGCCTGATAAAGGTGATTATAATAT-
1 AATTGGTTAAACGCCCCAGCTTTATG---AGATTCAGCTAGCCTGATAAAGGTGATTACAATATA
* * *
2393956 CTATACAATGATATTAAATTGTCCCTCTAGATC
63 CAATA-AA-G--ATTAAATTGACCATCTAGATC
2393989 AATTGGTTAAACGCCCCAGCTTTATG-GATTCAGCTAGCC
1 AATTGGTTAAACGCCCCAGCTTTATGAGATTCAGCTAGCC
2394028 AGACAATGGC
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
92 4 0.03
93 50 0.43
94 11 0.09
95 12 0.10
96 28 0.24
97 11 0.09
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (91 bp):
AATTGGTTAAACGCCCCAGCTTTATGAGATTCAGCTAGCCTGATAAAGGTGATTACAATATACAA
TAAAGATTAAATTGACCATCTAGATC
Found at i:2395388 original size:20 final size:20
Alignment explanation
Indices: 2395363--2395482 Score: 116
Period size: 20 Copynumber: 6.4 Consensus size: 20
2395353 TGAGATAGTT
2395363 TCTCTTGAAACAAATTTGTC
1 TCTCTTGAAACAAATTTGTC
2395383 TCTCTTGAAACAAATTTGTC
1 TCTCTTGAAACAAATTTGTC
* *
2395403 TCTCTTGAGAC--AGTT-TC
1 TCTCTTGAAACAAATTTGTC
*
2395420 -C-CTTGAAACAAATTTTATC
1 TCTCTTGAAACAAA-TTTGTC
*
2395439 TCTCTTGAGAC-AA--T-T-
1 TCTCTTGAAACAAATTTGTC
2395454 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAA-TTTGTC
2395475 TCTCTTGA
1 TCTCTTGA
2395483 GACAGTTTCC
Statistics
Matches: 82, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
15 17 0.21
16 4 0.05
17 4 0.05
18 5 0.06
19 3 0.04
20 34 0.41
21 15 0.18
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.41
Consensus pattern (20 bp):
TCTCTTGAAACAAATTTGTC
Found at i:2395408 original size:55 final size:57
Alignment explanation
Indices: 2395333--2395451 Score: 179
Period size: 55 Copynumber: 2.1 Consensus size: 57
2395323 AATTTACTCA
* * *
2395333 AAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA-TTTGTCTCTCTTG
1 AAACAAAG-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTG
2395390 AAACAAA-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTG
1 AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTG
*
2395446 AGACAA
1 AAACAA
2395452 TTTCTCTTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
55 33 0.58
56 17 0.30
57 7 0.12
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (57 bp):
AAACAAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTG
Found at i:2395448 original size:36 final size:36
Alignment explanation
Indices: 2395386--2395568 Score: 231
Period size: 36 Copynumber: 5.3 Consensus size: 36
2395376 ATTTGTCTCT
2395386 CTTGAAACAAA-TTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
* * *
2395421 CTTGAAACAAATTTTATCTCTCTTGAGACAATTTCT
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
2395457 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
* * *
2395493 CTTGAAACAAA------ATCT-TTGA-ATATGTTTTC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACA-GTTTCC
*
2395522 CTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
2395558 CTTGAAACAAA
1 CTTGAAACAAA
2395569 ATCTTTCAAT
Statistics
Matches: 124, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.02
29 19 0.15
30 3 0.02
35 14 0.11
36 84 0.68
37 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCC
Found at i:2395519 original size:29 final size:29
Alignment explanation
Indices: 2395487--2395595 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 29
2395477 TCTTGAGACA
2395487 GTTTCCCTTGAAACAAAATCTTTGAATAT
1 GTTTCCCTTGAAACAAAATCTTTGAATAT
* * * *
2395516 GTTTTCCTTAAAACAAATTTTGTCTCTCTTGAGACA-
1 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATAT
*
2395552 GTTTCCCTTGAAACAAAATCTTTCAATAT
1 GTTTCCCTTGAAACAAAATCTTTGAATAT
*
2395581 GTTTTCCTTGAAACA
1 GTTTCCCTTGAAACA
2395596 GATTTTGTCT
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
28 2 0.03
29 32 0.52
30 3 0.05
35 3 0.05
36 19 0.31
37 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (29 bp):
GTTTCCCTTGAAACAAAATCTTTGAATAT
Found at i:2395542 original size:65 final size:65
Alignment explanation
Indices: 2395386--2395621 Score: 307
Period size: 65 Copynumber: 3.5 Consensus size: 65
2395376 ATTTGTCTCT
*
2395386 CTTGAAACAAA-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGAC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA----A--TCT-TTGA-AT
*
2395450 A--ATTTC
58 ATGTTTTC
2395456 TCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT
1 -CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTT
2395521 C
65 C
* *
2395522 CTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTCAATATGTTTTC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTC
* * *
2395587 CTTGAAACAGATTTTGTCTCCCTTGAGACAATTTC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
2395622 TTTTGGAACT
Statistics
Matches: 154, Mismatches: 8, Indels: 12
0.89 0.05 0.07
Matches are distributed among these distances:
64 2 0.01
65 98 0.64
66 7 0.05
68 1 0.01
71 11 0.07
72 35 0.23
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.39
Consensus pattern (65 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTC
Found at i:2395650 original size:37 final size:36
Alignment explanation
Indices: 2395583--2395791 Score: 231
Period size: 36 Copynumber: 5.8 Consensus size: 36
2395573 TTCAATATGT
* *
2395583 TTTC-CTTGAAACAGATTTTGTCTCCCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * * * *
2395618 TTTCTTTTGGAACTAAGTCTTGTCTCTCTTGAGACAT
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAA
* * *
2395655 TTTTTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* **
2395691 TTTCCCTCAAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAA
**
2395728 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACGG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * *
2395764 TTTCCCTTTAAACAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCTCT
2395792 ATACAGTTTC
Statistics
Matches: 143, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
35 4 0.03
36 80 0.56
37 59 0.41
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:2395714 original size:73 final size:72
Alignment explanation
Indices: 2395582--2395791 Score: 267
Period size: 73 Copynumber: 2.9 Consensus size: 72
2395572 TTTCAATATG
* * * * ** ** *
2395582 TTTTCCTTGAAACAGATTTTGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTCTTGTCTCTCT
1 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAGTTTTGTCTCTCT
*
2395647 TGAGACAT
65 TGAGACAA
* *
2395655 TTTTTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTCAAAACAAAGTTTTGTCTCTCT
1 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAGTTTTGTCTCTCT
2395720 TGAGACAA
65 TGAGACAA
* * *
2395728 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTTAAACAAGTTTTGTCTCTCT
1 TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAGTTTTGTCTCTCT
2395792 ATACAGTTTC
Statistics
Matches: 119, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 15 0.13
73 104 0.87
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (72 bp):
TTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAGTTTTGTCTCTCTT
GAGACAA
Found at i:2395916 original size:34 final size:33
Alignment explanation
Indices: 2395862--2396013 Score: 270
Period size: 33 Copynumber: 4.6 Consensus size: 33
2395852 TTTGGAGACA
2395862 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
2395895 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
*
2395928 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
2395961 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT-
1 GTTTCTCTTGAAACAC-AAAAAACCTTTG-AAATC
2395995 GTTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
2396014 GACCTTCGAG
Statistics
Matches: 116, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
33 84 0.72
34 28 0.24
35 4 0.03
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
Found at i:2396177 original size:82 final size:81
Alignment explanation
Indices: 2396010--2396247 Score: 311
Period size: 82 Copynumber: 3.0 Consensus size: 81
2396000 TCTTGAAACA
* * *
2396010 CAAAGACCTTCGAGTTCGACTACACTCAGCTTTGAGGGAACATCATTTGCAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGC
*
2396075 TAGAAGGGTTATCTAC
66 TAAAAGGGTTATCTAC
* * *
2396091 CAAAGACCTTTGAGTTCGACTACACTCAGCTTCGAGGGCACTATCATTTGTAGCATAGCTCAGGG
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCAC-ATCATTTGCAGCATAGCTCAAGG
*
2396156 CTAAAAGGGTTATCTGC
65 CTAAAAGGGTTATCTAC
* * * * **
2396173 CAAAGACCTTCGAGTTCGATTCCATTCAGC-TC-AAGGCACATCATTCACAGCATAGCTCAAGG-
1 CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGC
2396235 TAAGAAGGGTTAT
66 TAA-AAGGGTTAT
2396248 TTGTCAACGA
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
78 3 0.02
79 28 0.20
80 6 0.04
81 40 0.29
82 61 0.44
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (81 bp):
CAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGC
TAAAAGGGTTATCTAC
Found at i:2397481 original size:17 final size:16
Alignment explanation
Indices: 2397444--2397482 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2397434 TTAAATATTT
2397444 TTTTATTTTATTTCTA
1 TTTTATTTTATTTCTA
* *
2397460 GTTTATTCTTATTTTTA
1 TTTTATT-TTATTTCTA
2397477 TTTTAT
1 TTTTAT
2397483 ATTTTTAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTATTTTATTTCTA
Found at i:2397527 original size:9 final size:8
Alignment explanation
Indices: 2397515--2397579 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 8
2397505 TTTTTTTACG
2397515 TTATTCATT
1 TTATT-ATT
*
2397524 TTATTTTCT
1 TTATTAT-T
2397533 TTATTA-T
1 TTATTATT
2397540 TTATTATT
1 TTATTATT
2397548 TTATTTATT
1 TTA-TTATT
*
2397557 TTGTTTATT
1 TT-ATTATT
* *
2397566 TTCTTTTT
1 TTATTATT
2397574 TTATTA
1 TTATTA
2397580 ACTTTTAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.16
8 13 0.29
9 25 0.56
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:2397584 original size:13 final size:13
Alignment explanation
Indices: 2397522--2397585 Score: 53
Period size: 12 Copynumber: 5.1 Consensus size: 13
2397512 ACGTTATTCA
*
2397522 TTTTATTTTC-TT
1 TTTTATTTACTTT
* *
2397534 TATTATTTA-TTA
1 TTTTATTTACTTT
2397546 TTTTATTTA-TTT
1 TTTTATTTACTTT
*
2397558 TGTTTATTTTCTTT
1 T-TTTATTTACTTT
*
2397572 TTTTATTAACTTT
1 TTTTATTTACTTT
2397585 T
1 T
2397586 AATTATCTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 19 0.46
13 18 0.44
14 4 0.10
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTATTTACTTT
Found at i:2399723 original size:35 final size:35
Alignment explanation
Indices: 2399677--2399753 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
2399667 AACATAATCA
2399677 TCAATTATATTCTAAACCTCAAAGTCCAAAATACT
1 TCAATTATATTCTAAACCTCAAAGTCCAAAATACT
* * **
2399712 TCAATTATATTCTAAATCTCAAATTTTAAAATACT
1 TCAATTATATTCTAAACCTCAAAGTCCAAAATACT
*
2399747 TTAATTA
1 TCAATTA
2399754 CATGCCCAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.17, G:0.01, T:0.39
Consensus pattern (35 bp):
TCAATTATATTCTAAACCTCAAAGTCCAAAATACT
Found at i:2399978 original size:3 final size:3
Alignment explanation
Indices: 2399959--2400010 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
2399949 CTACATAAAC
2399959 ATT A-T ATT ATAT ATT ATT ATT ATT ATAT ATT ATT A-T ATT ATT ATAT
1 ATT ATT ATT AT-T ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT AT-T
2400005 ATT ATT
1 ATT ATT
2400011 TTGTCCGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.09
3 31 0.70
4 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2399978 original size:10 final size:10
Alignment explanation
Indices: 2399959--2400010 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
2399949 CTACATAAAC
2399959 ATTATATTATAT
1 ATTATA-TAT-T
2399971 ATTAT-TATT
1 ATTATATATT
2399980 ATTATATATT
1 ATTATATATT
2399990 A-T-TATATT
1 ATTATATATT
2399998 ATTATATATT
1 ATTATATATT
2400008 ATT
1 ATT
2400011 TTGTCCGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 17 0.46
12 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATATATT
Found at i:2400007 original size:18 final size:17
Alignment explanation
Indices: 2399963--2400011 Score: 82
Period size: 18 Copynumber: 2.9 Consensus size: 17
2399953 ATAAACATTA
2399963 TATTATATATTA-TTAT
1 TATTATATATTATTTAT
2399979 TATTATATATTATTATAT
1 TATTATATATTATT-TAT
2399997 TATTATATATTATTT
1 TATTATATATTATTT
2400012 TGTCCGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.39
17 2 0.06
18 17 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTATATATTATTTAT
Found at i:2400304 original size:23 final size:23
Alignment explanation
Indices: 2400278--2400325 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2400268 ATAAAGTACA
*
2400278 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2400301 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2400324 AT
1 AT
2400326 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2400837 original size:23 final size:23
Alignment explanation
Indices: 2400802--2400874 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2400792 ATACTTTACA
*
2400802 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2400825 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
2400848 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2400871 ATAT
1 ATAT
2400875 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2401326 original size:23 final size:23
Alignment explanation
Indices: 2401293--2401365 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2401283 ATACTTTACA
2401293 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
*
2401316 ATATAAACACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
** *
2401339 ATATAAGTGCTACCTATTACATC
1 ATATAAGCACTACCTATTACATT
2401362 ATAT
1 ATAT
2401366 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:2401749 original size:489 final size:491
Alignment explanation
Indices: 2400399--2402202 Score: 3240
Period size: 491 Copynumber: 3.7 Consensus size: 491
2400389 TTATAATATG
* *
2400399 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTTAAAGTTATATAATTTATG
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAAGATCGATACTTTTTTTTAAAGTTATGTAATTTATG
*
2400464 TTTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACTTACAATATTAATTTAATAATTTCATTTG
65 TTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTG
2400527 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
130 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
*
2400592 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATAT
195 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATAT
* *
2400657 ATACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCA
260 ATACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCA
* *
2400722 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATACGTATGAACACTTTTATAAAAAG
325 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAG
2400787 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
390 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
2400852 AAGTGCTACCTATTACATCATATTTTTACCTATTATA
455 AAGTGCTACCTATTACATCATATTTTTACCTATTATA
*
2400889 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATA-TTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTTAAAGTTATGTAATTTATGT
*
2400953 TTCAATTTTTTTGTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCACTTG
66 TTCAATTTTTTT-TAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTG
2401018 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
130 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAAT
*
2401083 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATAT
195 ATTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATAT
* * *
2401148 ATACCGTAACATAAAAAATAAATCATTAAATACATATAATTACTAAATTGATATCTTAAAACTCA
260 ATACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCA
*
2401213 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAT
325 CTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAG
*
2401278 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACACTACCTATTACATTATAT
390 GATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATAT
2401343 AAGTGCTACCTATTACATCATATTTTTACCTATTATA
455 AAGTGCTACCTATTACATCATATTTTTACCTATTATA
*
2401380 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTTAAAGTTATGTAATTTATGT
2401444 TTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
*
2401508 ACACAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
2401573 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* * * * *
2401638 TATCATAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
261 TACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCAC
*
2401703 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
326 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGG
*
2401768 ATAGATACTTTACAACATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
391 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
*
2401833 AGCGCTACCTATTACATCATATTTTTACCTATTATA
456 AGTGCTACCTATTACATCATATTTTTACCTATTATA
2401869 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTTAAAGTTATGTAATTTATGT
*
2401934 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
66 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
* *
2401999 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
131 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
* * *
2402064 TTAACCAAAGATAGTAATAAATATGTAATATATATGCTTATTGATTTTAATTTAATAATAATATA
196 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* * *
2402129 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
261 TACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCAC
2402194 TCAAAAGAT
326 TCAAAAGAT
2402203 GTACATACCT
Statistics
Matches: 1271, Mismatches: 37, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
488 31 0.02
489 455 0.36
490 57 0.04
491 728 0.57
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (491 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTTTTTTAAAGTTATGTAATTTATGT
TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGC
ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
TACCGTAACATAAAAAATAAATCATTAGACACATATAATTACTAAATTAATATCTTAAAACTCAC
TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAAGG
ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
AGTGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:2401817 original size:23 final size:23
Alignment explanation
Indices: 2401791--2401854 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
2401781 AACATAAGCA
2401791 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
*
2401814 CTACCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAAACG
*
2401837 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
2401855 TTTTACCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:2404141 original size:200 final size:200
Alignment explanation
Indices: 2403817--2404580 Score: 1343
Period size: 200 Copynumber: 3.8 Consensus size: 200
2403807 AACATTAAAC
* * *
2403817 AGTGTCGATACA-TATTATATACCAATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* * *
2403881 AAAAATTACCTATTACATTATACTTATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
*
2403946 GGATTGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
2404011 TACAAA
195 TACAAA
2404017 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
2404082 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGTGG-TCGACACTTTTTATATAT
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATG-GGATCGACACTTTTTATATAT
*
2404146 AGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
2404211 TACAAA
195 TACAAA
*
2404217 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
2404282 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
2404347 GATCGACACTGTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
2404412 ACAAA
196 ACAAA
* * *
2404417 AGTGTTGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
2404482 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
2404547 GATCGACACTTTATGGTTGTACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
2404581 ATTGTAAATT
Statistics
Matches: 540, Mismatches: 21, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
199 2 0.00
200 532 0.99
201 6 0.01
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:2404716 original size:19 final size:19
Alignment explanation
Indices: 2404692--2404741 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
2404682 ATTATATTCA
2404692 TATACAAAATTATAAATCG
1 TATACAAAATTATAAATCG
*
2404711 TATACAAAATTATAAATCT
1 TATACAAAATTATAAATCG
2404730 TATACAAAATTA
1 TATACAAAATTA
2404742 ACCCTACATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:2406421 original size:33 final size:33
Alignment explanation
Indices: 2406384--2406449 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2406374 CATCTTAATA
*
2406384 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
2406417 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
2406450 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:2406546 original size:21 final size:21
Alignment explanation
Indices: 2406486--2406547 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
2406476 CTTATGCCTC
* * * *
2406486 TCAAGTGTATCTTCGACTATC
1 TCAAGTTTCTCTTCGACTCTA
2406507 TCAAGTTTCTCTTCGACTCTA
1 TCAAGTTTCTCTTCGACTCTA
2406528 TCAAGTTTCTCTTCGACTCT
1 TCAAGTTTCTCTTCGACTCT
2406548 TGATTGTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.42
Consensus pattern (21 bp):
TCAAGTTTCTCTTCGACTCTA
Found at i:2410485 original size:2 final size:2
Alignment explanation
Indices: 2410478--2410513 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2410468 CAATTTATTA
2410478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2410514 TTAGTTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2421462 original size:48 final size:48
Alignment explanation
Indices: 2421399--2421530 Score: 205
Period size: 46 Copynumber: 2.8 Consensus size: 48
2421389 TCAACTTCTC
* * **
2421399 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTTTA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
*
2421447 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
2421493 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
2421531 GCTGATTCAA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 43 0.57
48 33 0.43
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
Found at i:2421464 original size:112 final size:112
Alignment explanation
Indices: 2421266--2421488 Score: 367
Period size: 112 Copynumber: 2.0 Consensus size: 112
2421256 TTTGATCCCA
* *
2421266 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAATTGGAACATGTCTCTCTTC
1 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
*
2421331 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTCG
66 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT-CTTCG
* *
2421379 ATTCAATGGATCAACT-TCTCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
1 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
**
2421443 TTTAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTC
66 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTC
2421489 TCCAAGATTT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 4 0.04
112 83 0.81
113 16 0.16
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (112 bp):
ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCG
Found at i:2421687 original size:113 final size:113
Alignment explanation
Indices: 2421447--2421854 Score: 666
Period size: 113 Copynumber: 3.7 Consensus size: 113
2421437 CTCTTCTTTA
* * *
2421447 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* * *
2421510 CAGAGTAAGTGGAACAAGTCT--GCTGATTCAATGGATAAACTTCCCC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
*
2421556 AGATCTGATATTCCCTTCAGAGTAAGCAGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
2421621 TAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
*
2421669 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTTTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
2421734 CAGAGTAAGTGGAACAAGTCTACCCTGATTCAATGGATCAAC-TCCCTC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCC-C
*
2421782 AGATCTGATATTCCCTTCAGAGTAAGCGAAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
2421847 CAGA-AAAG
66 CAGAGAAAG
2421855 AAGCGGAACA
Statistics
Matches: 279, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
109 32 0.11
111 46 0.16
112 7 0.03
113 194 0.70
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (113 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
Found at i:2423928 original size:2 final size:2
Alignment explanation
Indices: 2423921--2423964 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2423911 CAATTTATTA
2423921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2423963 AT
1 AT
2423965 TTAGTTGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2425029 original size:17 final size:18
Alignment explanation
Indices: 2425007--2425049 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
2424997 ATATATCCGG
2425007 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
2425024 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
2425044 TATCAT
1 TATCAT
2425050 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:2425067 original size:20 final size:19
Alignment explanation
Indices: 2425012--2425058 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2425002 TCCGGTATCA
2425012 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
2425031 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2425052 TTTTACC
1 TTTTACC
2425059 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2425238 original size:20 final size:19
Alignment explanation
Indices: 2425193--2425239 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2425183 TCCGGTAACG
*
2425193 TTTTACCGGTTTTATTATT
1 TTTTACCGGTTTTATCATT
2425212 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2425233 TTTTACC
1 TTTTACC
2425240 TGGTATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2425283 original size:181 final size:182
Alignment explanation
Indices: 2424979--2425451 Score: 705
Period size: 181 Copynumber: 2.6 Consensus size: 182
2424969 CGTACTTACG
* *
2424979 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
2425044 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
2425109 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
2425160 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATTATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
2425225 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
2425290 AGGATTTAAAATTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * **
2425342 AAAGTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
2425407 TGTCATAGTTTTACCTATTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2425452 AATTTGGATC
Statistics
Matches: 262, Mismatches: 29, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
181 166 0.63
182 96 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:2427326 original size:148 final size:143
Alignment explanation
Indices: 2426999--2427295 Score: 364
Period size: 148 Copynumber: 2.0 Consensus size: 143
2426989 CCGACAATAC
* * ** * * *
2426999 TCAATTCAGTTTATAAAATAGTTGACTTGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCA
1 TCAAATCATTTTATAAAATAGTACAATCGAAATATTTTCGATTTGAGTTTATAAAATTTAAATCA
* *
2427064 AGTCGAATTGAATTTTGGAGTTTACGTTTAAATTTAATTATAAATATTTATCATATTATAATATT
66 AGTCGAATTGAATTTTCGAGTTTACGTTTAAATTTAATTATAAATATTTATAATATTATAATATT
2427129 ATTTGATTATAAT
131 ATTTGATTATAAT
** ** *
2427142 TCAGGTCATTTTATAAAATAGTTGACTCGAAATATTTTCGATTTGAGTTTATAAAATTTAAATCA
1 TCAAATCATTTTATAAAATAGTACAATCGAAATATTTTCGATTTGAGTTTATAAAATTTAAATCA
*
2427207 AGTCGAATTGAATTGAATTTTCGA-TATT-CTGTTTAAATTTAATTATAACTATTTATAATATTA
66 AGTC-----GAATTGAATTTTCGAGT-TTAC-GTTTAAATTTAATTATAAATATTTATAATATTA
*
2427270 TAATATTATTTGATTCTAAT
124 TAATATTATTTGATTATAAT
*
2427290 TTAAAT
1 TCAAAT
2427296 AGTTTTTTTA
Statistics
Matches: 135, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
143 64 0.47
147 2 0.01
148 69 0.51
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.46
Consensus pattern (143 bp):
TCAAATCATTTTATAAAATAGTACAATCGAAATATTTTCGATTTGAGTTTATAAAATTTAAATCA
AGTCGAATTGAATTTTCGAGTTTACGTTTAAATTTAATTATAAATATTTATAATATTATAATATT
ATTTGATTATAAT
Found at i:2427831 original size:35 final size:35
Alignment explanation
Indices: 2427792--2427862 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
2427782 GGGGTTGGGC
*
2427792 ATGTAATTAAAGTATTTTAAAATTTGAGGTTTAGA
1 ATGTAATTAAAGCATTTTAAAATTTGAGGTTTAGA
* * * *
2427827 ATGTAATTGATGCATTTTAGAATTTGGGGTTTAGA
1 ATGTAATTAAAGCATTTTAAAATTTGAGGTTTAGA
2427862 A
1 A
2427863 CATAGTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.42
Consensus pattern (35 bp):
ATGTAATTAAAGCATTTTAAAATTTGAGGTTTAGA
Found at i:2427872 original size:35 final size:35
Alignment explanation
Indices: 2427805--2427873 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
2427795 TAATTAAAGT
**
2427805 ATTTTAAAATTTGAGGTTTAGAATGTAATTGATGC
1 ATTTTAAAATTTGAGGTTTAGAACATAATTGATGC
* * *
2427840 ATTTTAGAATTTGGGGTTTAGAACATAGTTGATG
1 ATTTTAAAATTTGAGGTTTAGAACATAATTGATG
2427874 ATTATGTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (35 bp):
ATTTTAAAATTTGAGGTTTAGAACATAATTGATGC
Found at i:2430443 original size:7 final size:7
Alignment explanation
Indices: 2430431--2430649 Score: 119
Period size: 7 Copynumber: 32.3 Consensus size: 7
2430421 ATTAATAAAA
2430431 ATAATAT
1 ATAATAT
2430438 ATAATAAT
1 ATAAT-AT
2430446 ATAA-AT
1 ATAATAT
2430452 ATAA-AT
1 ATAATAT
*
2430458 ATTAATAG
1 A-TAATAT
2430466 ATAATA-
1 ATAATAT
2430472 AT-ATAT
1 ATAATAT
2430478 AT-ATACT
1 ATAATA-T
2430485 ATAATAT
1 ATAATAT
*
2430492 ATATAAAT
1 ATA-ATAT
2430500 ATAATAT
1 ATAATAT
**
2430507 ATAATGC
1 ATAATAT
2430514 ATAATA-
1 ATAATAT
*
2430520 AAAATAT
1 ATAATAT
2430527 AT-ATACT
1 ATAATA-T
* *
2430534 ATTATAC
1 ATAATAT
**
2430541 ATAACGT
1 ATAATAT
*
2430548 A-CA-AT
1 ATAATAT
2430553 ATAATAT
1 ATAATAT
2430560 ATAATAT
1 ATAATAT
2430567 ATAATAT
1 ATAATAT
2430574 AT-ATA-
1 ATAATAT
*
2430579 CTAATA-
1 ATAATAT
*
2430585 ATGAAAAT
1 AT-AATAT
2430593 AT-ATACT
1 ATAATA-T
2430600 ATAATACT
1 ATAATA-T
2430608 AT--TAT
1 ATAATAT
2430613 ATAATAT
1 ATAATAT
2430620 ATAATAT
1 ATAATAT
2430627 A-ACATAT
1 ATA-ATAT
**
2430634 ACCATAT
1 ATAATAT
2430641 ATAATAT
1 ATAATAT
2430648 AT
1 AT
2430650 TATAATATAT
Statistics
Matches: 168, Mismatches: 23, Indels: 42
0.72 0.10 0.18
Matches are distributed among these distances:
5 9 0.05
6 38 0.23
7 92 0.55
8 29 0.17
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:2430444 original size:16 final size:17
Alignment explanation
Indices: 2430423--2430659 Score: 83
Period size: 19 Copynumber: 13.1 Consensus size: 17
2430413 AAAAACACAT
2430423 TAATA-AAAATAATATA
1 TAATATAAAATAATATA
*
2430439 TAATAATATAAATATAAATA
1 TAAT-ATA-AAATA-ATATA
* *
2430459 TTAATAGATAATAATATA
1 -TAATATAAAATAATATA
**
2430477 T-ATATACTATAATATA
1 TAATATAAAATAATATA
*
2430493 T-ATA-AATATAATATA
1 TAATATAAAATAATATA
2430508 TAATGCATAATAA-AA-ATA
1 TAAT--ATAA-AATAATATA
** * *
2430526 T-ATATACTATTATACA
1 TAATATAAAATAATATA
* *
2430542 TAACGTACAATATAATATA
1 TAA--TATAAAATAATATA
*
2430561 TAATATATAATATATATA
1 TAATATAAAATA-ATATA
2430579 CTAATAATGAAAATATATACTA
1 -TAAT-AT-AAAATA-ATA-TA
*
2430601 TAATACTATTATATAATATA
1 TAATA-TA--AAATAATATA
2430621 TAATATAACATATACCATATA
1 TAATATAA-A-ATA--ATATA
**
2430642 TAATATATTATAATATA
1 TAATATAAAATAATATA
2430659 T
1 T
2430660 GCTATTTTAA
Statistics
Matches: 169, Mismatches: 25, Indels: 53
0.68 0.10 0.21
Matches are distributed among these distances:
14 1 0.01
15 15 0.09
16 25 0.15
17 18 0.11
18 15 0.09
19 38 0.22
20 18 0.11
21 33 0.20
22 6 0.04
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
TAATATAAAATAATATA
Found at i:2430474 original size:22 final size:20
Alignment explanation
Indices: 2430423--2430511 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 20
2430413 AAAAACACAT
2430423 TAATAA-AA-ATAATATATAA
1 TAATAATAATATAA-ATATAA
2430442 TAAT-ATAAATATAAATATTAA
1 TAATAAT-AATATAAATA-TAA
* *
2430463 TAGATAATAATATATATATAC
1 TA-ATAATAATATAAATATAA
2430484 T-ATAATATATATAAATATAA
1 TAATAATA-ATATAAATATAA
2430504 TATATAAT
1 TA-ATAAT
2430512 GCATAATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.02
19 10 0.18
20 16 0.28
21 12 0.21
22 16 0.28
23 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (20 bp):
TAATAATAATATAAATATAA
Found at i:2430479 original size:2 final size:2
Alignment explanation
Indices: 2430434--2430659 Score: 65
Period size: 2 Copynumber: 123.0 Consensus size: 2
2430424 AATAAAAATA
* * *
2430434 AT AT AT A- AT A- AT AT AA AT AT AA AT AT -T A- AT AG AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2430471 A- AT AT AT AT AT ACT AT A- AT AT AT AT AA AT AT A- AT AT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** * * * * * *
2430510 AT GC AT A- AT AA AA AT AT AT AT ACT AT -T AT AC AT A- AC GT AC
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
2430550 A- AT AT A- AT AT AT A- AT AT AT A- AT AT AT AT ACT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
2430587 GA- AA AT AT AT ACT AT A- AT ACT AT -T AT AT A- AT AT AT A- AT
1 -AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* *
2430625 AT A- AC AT AT ACC AT AT AT A- AT AT AT -T AT A- AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
2430660 GCTATTTTAA
Statistics
Matches: 166, Mismatches: 24, Indels: 68
0.64 0.09 0.26
Matches are distributed among these distances:
1 27 0.16
2 127 0.77
3 12 0.07
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.38
Consensus pattern (2 bp):
AT
Found at i:2430528 original size:22 final size:20
Alignment explanation
Indices: 2430408--2430628 Score: 69
Period size: 22 Copynumber: 10.2 Consensus size: 20
2430398 GTGCCTGGAG
* *
2430408 ATAATAAAAACACAT-TAAT
1 ATAATAAAAATATATATAAT
*
2430427 A-AA-AATAATATATAATAAT
1 ATAATAAAAATATAT-ATAAT
*
2430446 ATAAATATAAATAT-TAATAGAT
1 AT-AATAAAAATATAT-ATA-AT
* *
2430468 AATAATATATATATACTATAAT
1 -ATAATAAAAATATA-TATAAT
*
2430490 ATATATAAATATAATATATAAT
1 ATA-ATAAAAAT-ATATATAAT
2430512 GCATAATAAAAATATATATACTATT
1 --ATAATAAAAATATATATA--A-T
2430537 ATACATAACGTACAATATA-AT-AT
1 ATA-ATAA---A-AATATATATAAT
* *
2430560 ATAATATATAATATATATACT
1 ATAATA-AAAATATATATAAT
2430581 AATAATGAAAATATATACTATAAT
1 -ATAAT-AAAA-ATATA-TATAAT
* * *
2430605 ACTATTATATA-ATATATAAT
1 A-TAATAAAAATATATATAAT
2430625 ATAA
1 ATAA
2430629 CATATACCAT
Statistics
Matches: 157, Mismatches: 16, Indels: 58
0.68 0.07 0.25
Matches are distributed among these distances:
17 7 0.04
18 2 0.01
19 14 0.09
20 9 0.06
21 14 0.09
22 51 0.32
23 32 0.20
24 18 0.11
25 1 0.01
27 3 0.02
28 6 0.04
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAATAAAAATATATATAAT
Found at i:2430554 original size:53 final size:48
Alignment explanation
Indices: 2430423--2430572 Score: 159
Period size: 49 Copynumber: 3.1 Consensus size: 48
2430413 AAAAACACAT
2430423 TAATAAAA-ATA-ATA-TATAATA-ATATAAATATAA-ATATTAATAGA
1 TAATAAAATATATATACTATAATACATATAAATATAATATA-TAATAGA
* *
2430467 TAATAATATATATATACTATAATATATATAAATATAATATATAAT-GCA
1 TAATAAAATATATATACTATAATACATATAAATATAATATATAATAG-A
* *
2430515 TAATAAAAATATATATACTATTATACATAACGTACAATATAATATATAATATA
1 TAAT-AAAATATATATACTATAATACAT-A--TA-AATATAATATATAATAGA
2430568 TAATA
1 TAATA
2430573 TATATACTAA
Statistics
Matches: 89, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
44 7 0.08
45 3 0.03
46 3 0.03
47 8 0.09
48 21 0.24
49 23 0.26
50 1 0.01
52 3 0.03
53 20 0.22
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (48 bp):
TAATAAAATATATATACTATAATACATATAAATATAATATATAATAGA
Found at i:2431059 original size:16 final size:17
Alignment explanation
Indices: 2431037--2431080 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
2431027 TCTCTGACGT
2431037 TTCTTGATTCTTGCCAA
1 TTCTTGATTCTTGCCAA
*
2431054 -TCTTGATT-TT-CTAA
1 TTCTTGATTCTTGCCAA
2431068 TTCTTGATTCTTG
1 TTCTTGATTCTTG
2431081 ATTCTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (17 bp):
TTCTTGATTCTTGCCAA
Found at i:2431683 original size:23 final size:23
Alignment explanation
Indices: 2431657--2431701 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2431647 TGGACATTCC
*
2431657 TTTTTATTTTTTCTTCTTTTTTG
1 TTTTTATTTTTTCTTCTATTTTG
* *
2431680 TTTTTGTTTTTTTTTCTATTTT
1 TTTTTATTTTTTCTTCTATTTT
2431702 CGATTTAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.04, C:0.07, G:0.04, T:0.84
Consensus pattern (23 bp):
TTTTTATTTTTTCTTCTATTTTG
Found at i:2440597 original size:31 final size:31
Alignment explanation
Indices: 2440562--2440623 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2440552 ATAATTACCA
*
2440562 TCAAACCACGACACCTCAACCTTATCATCTT
1 TCAAACCAAGACACCTCAACCTTATCATCTT
2440593 TCAAACCAAGACACCTCAACCTTATCATCTT
1 TCAAACCAAGACACCTCAACCTTATCATCTT
2440624 CCTTACGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (31 bp):
TCAAACCAAGACACCTCAACCTTATCATCTT
Found at i:2441767 original size:3 final size:3
Alignment explanation
Indices: 2441759--2441822 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
2441749 TTAAAATTTC
*
2441759 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
*
2441805 ATA ATA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA
2441823 CTCGGACAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2446790 original size:17 final size:18
Alignment explanation
Indices: 2446768--2446801 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2446758 AAATCACTTT
2446768 ATTTTA-TAAAAAAAGAA
1 ATTTTAGTAAAAAAAGAA
*
2446785 ATTTTAGTTAAAAAAGA
1 ATTTTAGTAAAAAAAGA
2446802 CTTGATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (18 bp):
ATTTTAGTAAAAAAAGAA
Found at i:2449256 original size:35 final size:35
Alignment explanation
Indices: 2449163--2449258 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
2449153 AACACATTCA
* * * * *
2449163 TCAATTATATTCTAAATCCCAAAGTCCAAAATGCT
1 TCAATTACATGCTAAACCCCAAATTCCAAAATACT
* *
2449198 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATGCTAAACCCCAAATTCCAAAATACT
*
2449233 TCAATTACATGCTCAACCCCAAATTC
1 TCAATTACATGCTAAACCCCAAATTC
2449259 ATGATTCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (35 bp):
TCAATTACATGCTAAACCCCAAATTCCAAAATACT
Found at i:2449608 original size:143 final size:144
Alignment explanation
Indices: 2449414--2449702 Score: 440
Period size: 148 Copynumber: 2.0 Consensus size: 144
2449404 AATACTCAAT
* * *
2449414 TCAGTTTATAAAATAGTTGACTTGAGATTTTTTCGATTTGAGTTTATAAAATTTAAATTAAGTC-
1 TCAGTTTATAAAATAGTTGACTCGAGATATTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCA
* *
2449478 GAATTGAATTTTCGAGTTTAC-GTTTAAATTTAATTATAAATATTTATCATATTATAATATTATT
66 GAATTGAATTTTCGAGATT-CTGTTTAAATTTAATTATAAATATTTATAATATTATAATATTATT
2449542 TGAATATAATTTAGG
130 TGAATATAATTTAGG
2449557 TCAGTTTATAAAATAGTTGACTCGTA-ATATTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TCAGTTTATAAAATAGTTGACTCG-AGATATTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
2449621 GAATTGAATTGAATTTTCGAGATTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATAT
65 --A--GAATTGAATTTTCGAGATTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATAT
* *
2449686 TATTTGATTCTAATTTA
126 TATTTGAATATAATTTA
2449703 AATAGTTTTT
Statistics
Matches: 132, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
143 59 0.45
144 1 0.01
147 1 0.01
148 71 0.54
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.47
Consensus pattern (144 bp):
TCAGTTTATAAAATAGTTGACTCGAGATATTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCA
GAATTGAATTTTCGAGATTCTGTTTAAATTTAATTATAAATATTTATAATATTATAATATTATTT
GAATATAATTTAGG
Found at i:2450733 original size:47 final size:47
Alignment explanation
Indices: 2450667--2450761 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
2450657 TATATCAAGA
2450667 AAAAATATTTTTAAAAGAATATGTTCCGAGAGAAACATTCTCAAAAG
1 AAAAATATTTTTAAAAGAATATGTTCCGAGAGAAACATTCTCAAAAG
** *
2450714 AAAAATATTTTTAAAAGAATATGTTTTGAGAGAAATATTCTCAAAAG
1 AAAAATATTTTTAAAAGAATATGTTCCGAGAGAAACATTCTCAAAAG
2450761 A
1 A
2450762 GGATGAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (47 bp):
AAAAATATTTTTAAAAGAATATGTTCCGAGAGAAACATTCTCAAAAG
Found at i:2452892 original size:7 final size:7
Alignment explanation
Indices: 2452880--2453048 Score: 105
Period size: 7 Copynumber: 25.3 Consensus size: 7
2452870 ATTAATAAAA
2452880 ATAATAT
1 ATAATAT
2452887 ATAATAAT
1 ATAAT-AT
2452895 ATAA-AT
1 ATAATAT
2452901 ATTAATAT
1 A-TAATAT
2452909 ATAATA-
1 ATAATAT
2452915 AT-ATAT
1 ATAATAT
2452921 ATAA-AT
1 ATAATAT
2452927 ATAATAT
1 ATAATAT
**
2452934 ATAATGC
1 ATAATAT
2452941 ATAATA-
1 ATAATAT
*
2452947 AAAATAT
1 ATAATAT
2452954 AT-ATACT
1 ATAATA-T
*
2452961 ATAATAC
1 ATAATAT
*
2452968 ATAACAT
1 ATAATAT
*
2452975 A-CA-AT
1 ATAATAT
2452980 ATAATAT
1 ATAATAT
2452987 ATAATAT
1 ATAATAT
2452994 AT-ATA-
1 ATAATAT
*
2452999 CTAATA-
1 ATAATAT
*
2453005 ATGAAAAT
1 AT-AATAT
2453013 AT-ATACT
1 ATAATA-T
2453020 ATAATACT
1 ATAATA-T
2453028 AT--TAT
1 ATAATAT
*
2453033 ATACTAT
1 ATAATAT
2453040 ATAATAT
1 ATAATAT
2453047 AT
1 AT
2453049 GAAATGACCA
Statistics
Matches: 129, Mismatches: 15, Indels: 36
0.72 0.08 0.20
Matches are distributed among these distances:
5 10 0.08
6 34 0.26
7 64 0.50
8 21 0.16
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:2452908 original size:12 final size:11
Alignment explanation
Indices: 2452874--2453004 Score: 79
Period size: 12 Copynumber: 11.1 Consensus size: 11
2452864 AAACACATTA
*
2452874 ATAAAAATAAT
1 ATAAATATAAT
*
2452885 ATATA-ATAAT
1 ATAAATATAAT
2452895 ATAAATATTAAT
1 ATAAATA-TAAT
2452907 ATATAATAATATAT
1 ATA-AAT-ATA-AT
2452921 ATAAATATAAT
1 ATAAATATAAT
2452932 ATATAATGCATAAT
1 ATA-AAT--ATAAT
*
2452946 AAAAATAT-AT
1 ATAAATATAAT
*
2452956 AT-ACTATAAT
1 ATAAATATAAT
*
2452966 ACATAACATACAAT
1 --ATAA-ATATAAT
2452980 ATAATATATAAT
1 ATAA-ATATAAT
*
2452992 ATATATACTAAT
1 ATAAATA-TAAT
2453004 A
1 A
2453005 ATGAAAATAT
Statistics
Matches: 96, Mismatches: 10, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
9 4 0.04
10 14 0.15
11 15 0.16
12 33 0.34
13 12 0.12
14 18 0.19
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.36
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:2452909 original size:22 final size:21
Alignment explanation
Indices: 2452874--2452998 Score: 88
Period size: 22 Copynumber: 6.1 Consensus size: 21
2452864 AAACACATTA
*
2452874 ATAAAAATAATATATAATAAT
1 ATAAATATAATATATAATAAT
2452895 ATAAATATTAATATATAATAAT
1 ATAAATA-TAATATATAATAAT
2452917 AT--ATATAA-ATATAAT-AT
1 ATAAATATAATATATAATAAT
*
2452934 AT-AATGCATAATA-AAAATATAT
1 ATAAAT--ATAATATATAATA-AT
* * *
2452956 AT-ACTATAATACATAA-CAT
1 ATAAATATAATATATAATAAT
*
2452975 A-CAATATAATATATAATATAT
1 ATAAATATAATATATAATA-AT
2452996 ATA
1 ATA
2452999 CTAATAATGA
Statistics
Matches: 83, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
17 4 0.05
18 9 0.11
19 18 0.22
20 17 0.20
21 13 0.16
22 22 0.27
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (21 bp):
ATAAATATAATATATAATAAT
Found at i:2454455 original size:44 final size:44
Alignment explanation
Indices: 2454400--2454486 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
2454390 TTTAGAGCGT
*
2454400 CCTTTTAGGTTTTCACGCTAAACACCCTTTTTTATGTAAAACTC
1 CCTTTTAGGTTTTCACGCTAAACACCCTTTTTTATGAAAAACTC
* ** * *
2454444 CCTTTTGGGTTTTCATTCTAAACACCTTTTTTTTTGAAAAACT
1 CCTTTTAGGTTTTCACGCTAAACACCCTTTTTTATGAAAAACT
2454487 TCAGCGAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (44 bp):
CCTTTTAGGTTTTCACGCTAAACACCCTTTTTTATGAAAAACTC
Found at i:2457951 original size:2 final size:2
Alignment explanation
Indices: 2457946--2457975 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2457936 CGTAGAAAAA
2457946 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
2457976 GAAAAAGAAG
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:2469232 original size:46 final size:46
Alignment explanation
Indices: 2469165--2469270 Score: 194
Period size: 46 Copynumber: 2.3 Consensus size: 46
2469155 TGCACTAAGG
2469165 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGGA
* *
2469211 GTGCATTGATGCATAAAATGCATTCGATGTTTCAAACAAGCTTGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGGA
2469257 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2469271 GGATTTGATG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGGA
Found at i:2469282 original size:41 final size:42
Alignment explanation
Indices: 2469181--2469284 Score: 129
Period size: 46 Copynumber: 2.4 Consensus size: 42
2469171 CGATGCATAA
*
2469181 AATGCATTCGATGTTTCAAACAAGCCTGGAGTGCATTGATGC
1 AATGCATTCGATGTTTCAAACAAGCCTGGAGTGCATCGATGC
*
2469223 ATAAAATGCATTCGATGTTTCAAACAAGCTTGGAGTGCATCGATGC
1 ----AATGCATTCGATGTTTCAAACAAGCCTGGAGTGCATCGATGC
* *
2469269 -ATGGATTTGATGTTTC
1 AATGCATTCGATGTTTC
2469285 CATAAAATTC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
41 14 0.26
46 40 0.74
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (42 bp):
AATGCATTCGATGTTTCAAACAAGCCTGGAGTGCATCGATGC
Found at i:2469987 original size:27 final size:27
Alignment explanation
Indices: 2469948--2470004 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
2469938 CTAAATGATA
* *
2469948 CAAAAATCTAATAAACCAA-TATAAGTT
1 CAAAAACCAAATAAA-CAATTATAAGTT
* *
2469975 CAAAAACCAAATATATAATTATAAGTT
1 CAAAAACCAAATAAACAATTATAAGTT
2470002 CAA
1 CAA
2470005 GCATTCAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (27 bp):
CAAAAACCAAATAAACAATTATAAGTT
Found at i:2472058 original size:44 final size:43
Alignment explanation
Indices: 2471970--2472082 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 43
2471960 CGATGGGTGT
*
2471970 ATCGATGCACTGC-TGAGTGCATCGATAAACATTCAAGGAGTGC
1 ATCGATGCACTGCAT-AGTGTATCGATAAACATTCAAGGAGTGC
* * * *
2472013 ATCGGTGCATCTTCATGGTGTATCGATACACATTCATAGGA-TGC
1 ATCGATGCA-CTGCATAGTGTATCGATAAACATTCA-AGGAGTGC
*
2472057 ATCGATGCACTGGATAGTGTATCGAT
1 ATCGATGCACTGCATAGTGTATCGAT
2472083 GCATTATGCA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
43 22 0.38
44 31 0.53
45 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
ATCGATGCACTGCATAGTGTATCGATAAACATTCAAGGAGTGC
Found at i:2472061 original size:23 final size:23
Alignment explanation
Indices: 2471987--2472062 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
2471977 CACTGCTGAG
*
2471987 TGCATCGATAAACATTCA-AGGA
1 TGCATCGATACACATTCATAGGA
* *
2472009 GTGCATCGGTGCATC-TTCAT-GG-
1 -TGCATCGATACA-CATTCATAGGA
*
2472031 TGTATCGATACACATTCATAGGA
1 TGCATCGATACACATTCATAGGA
2472054 TGCATCGAT
1 TGCATCGAT
2472063 GCACTGGATA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.02
21 14 0.34
22 2 0.05
23 23 0.56
24 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (23 bp):
TGCATCGATACACATTCATAGGA
Found at i:2482273 original size:2 final size:2
Alignment explanation
Indices: 2482268--2482292 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2482258 ATGATATATA
2482268 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2482293 TATGCTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2485988 original size:20 final size:20
Alignment explanation
Indices: 2485963--2486061 Score: 110
Period size: 20 Copynumber: 4.8 Consensus size: 20
2485953 TCAAAATGGA
2485963 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
2485983 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
* *
2486003 GTGCATTGATACACTAGTGGCA-G
1 GTGCATGGATGCACTA----CATG
* *
2486026 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTACA-TG
2486047 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2486062 TTGACACCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.03
20 34 0.50
21 16 0.24
23 14 0.21
24 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:2486306 original size:21 final size:21
Alignment explanation
Indices: 2486282--2486321 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2486272 ATGTTTAATG
2486282 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
2486303 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
2486322 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:2489273 original size:20 final size:20
Alignment explanation
Indices: 2489248--2489326 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
2489238 TCAAAATGGA
2489248 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
* **
2489268 GTGCATCGATGCACTAGTGGTAG
1 GTGCATGGATGCACTA--CAT-G
* * *
2489291 GTGCATTGATGCACTGCAGGG
1 GTGCATGGATGCACTACA-TG
2489312 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2489327 TTGACACCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 15 0.33
21 15 0.33
22 1 0.02
23 15 0.33
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:2502123 original size:2 final size:2
Alignment explanation
Indices: 2502116--2502167 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2502106 TGTCAATCTA
2502116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2502158 AT AT AT AT AT
1 AT AT AT AT AT
2502168 GTATGACATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2502346 original size:13 final size:13
Alignment explanation
Indices: 2502330--2502363 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2502320 GCAATGAGCA
2502330 TCATAAATGCGCG
1 TCATAAATGCGCG
*
2502343 TCATAAATGTGCG
1 TCATAAATGCGCG
2502356 TCATAAAT
1 TCATAAAT
2502364 TTATGACGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:2503733 original size:33 final size:33
Alignment explanation
Indices: 2503681--2503758 Score: 76
Period size: 33 Copynumber: 2.4 Consensus size: 33
2503671 TAATAAAAAC
2503681 ATATTAATA-AA-AGTAATATA-A-AATAATATT
1 ATATTAATATAATAGTAATATATACAATAAT-TT
*
2503711 AATATTAATATAATA-TATATATATACTATAATTT
1 -ATATTAATATAATAGTA-ATATATACAATAATTT
*
2503745 ATATAAATATAATA
1 ATATTAATATAATA
2503759 CATAATGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 9 0.22
32 4 0.10
33 19 0.47
34 3 0.08
35 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (33 bp):
ATATTAATATAATAGTAATATATACAATAATTT
Found at i:2504876 original size:31 final size:31
Alignment explanation
Indices: 2504838--2504926 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 31
2504828 ATTAAGAGTA
* *
2504838 TATGGTCCCTAATGTTATCGATTCATTCGAT
1 TATGGTCCCTAACGTTATCGATCCATTCGAT
* *
2504869 TATGGTCCCTAACATTATCAATCCATTCGAT
1 TATGGTCCCTAACGTTATCGATCCATTCGAT
*
2504900 TATGGTTCCTAACGTTATCGATCCATT
1 TATGGTCCCTAACGTTATCGATCCATT
2504927 TAATTTTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (31 bp):
TATGGTCCCTAACGTTATCGATCCATTCGAT
Found at i:2506194 original size:29 final size:28
Alignment explanation
Indices: 2506129--2506194 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
2506119 AAGCCTTAGA
* * * *
2506129 AAAATTGGGGACAATTTCGTAAGTTTTG
1 AAAATTGAGGACAAATTCGTAAATTTGG
*
2506157 AAAAGTTGAGGATAAATTCGTAAATTCTGG
1 AAAA-TTGAGGACAAATTCGTAAATT-TGG
2506187 AAAATTGA
1 AAAATTGA
2506195 TGGGTTGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.13
29 21 0.68
30 6 0.19
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (28 bp):
AAAATTGAGGACAAATTCGTAAATTTGG
Found at i:2507226 original size:13 final size:14
Alignment explanation
Indices: 2507208--2507249 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2507198 GGCTATTATC
2507208 TATTGTTTATGGT-
1 TATTGTTTATGGTA
*
2507221 TATTGTCTATGGTA
1 TATTGTTTATGGTA
*
2507235 CATTG-TTATGGTA
1 TATTGTTTATGGTA
2507248 TA
1 TA
2507250 ATGGCAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.52
Consensus pattern (14 bp):
TATTGTTTATGGTA
Found at i:2507312 original size:44 final size:44
Alignment explanation
Indices: 2507240--2507382 Score: 184
Period size: 44 Copynumber: 3.3 Consensus size: 44
2507230 TGGTACATTG
* *
2507240 TTATGG-TATAATGGCAAATATATTGGTAAAATAAGCTTATGAGC
1 TTATGGATA-AATTGCAAGTATATTGGTAAAATAAGCTTATGAGC
* * * *
2507284 TTATGGAT-TATTGGTAAGTATAATGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATT-GCAAGTATATTGGTAAAATAAGCTTATGAGC
*
2507328 TTATGGATAAATTGCAAGTACATTGGTAAAATAAGCTTATGAGC
1 TTATGGATAAATTGCAAGTATATTGGTAAAATAAGCTTATGAGC
2507372 TTATGG-TAAAT
1 TTATGGATAAAT
2507383 AAATGGTAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
43 7 0.08
44 74 0.87
45 4 0.05
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (44 bp):
TTATGGATAAATTGCAAGTATATTGGTAAAATAAGCTTATGAGC
Found at i:2507749 original size:12 final size:12
Alignment explanation
Indices: 2507732--2507758 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2507722 AATTTTTGAA
2507732 AGTTACTGTAGC
1 AGTTACTGTAGC
2507744 AGTTACTGTAGC
1 AGTTACTGTAGC
2507756 AGT
1 AGT
2507759 ATTGTTCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (12 bp):
AGTTACTGTAGC
Found at i:2515348 original size:126 final size:122
Alignment explanation
Indices: 2515127--2515350 Score: 322
Period size: 126 Copynumber: 1.8 Consensus size: 122
2515117 TTGAGTACGA
* *
2515127 TGGTTATCGATCGATTTTGTTTAATGCATTATTGCATTTTTGTACCAATAATTTGTGTACTATGG
1 TGGTTATCGATCGATTTTGCTTAATGCATTATTGCATTTTTGCACCAATAATTTGTGTACTATGG
2515192 CACTATGTGTGCAATGATGGTGTTCATAATGAGCACTTGTTAATACCTTGAATAAGG
66 CACTATGTGTGCAATGATGGTGTTCATAATGAGCACTTGTTAATACCTTGAATAAGG
* ** * * *
2515249 TGGTTATCGATCGATTTTGCTTAATGCATTTGTTGCATTTTTCGCATTAGTACCTTTGTGTACTT
1 TGGTTATCGATCGATTTTGCTTAATGCA-TTATTGCATTTTT-GCACCAATA-ATTTGTGTACTA
* *
2515314 TCGGCATTATGTGTGCATTGATGGTGTTCATAATGAG
63 T-GGCACTATGTGTGCAATGATGGTGTTCATAATGAG
2515351 TTTGTGAATT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
122 27 0.31
123 12 0.14
124 5 0.06
125 11 0.12
126 33 0.38
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (122 bp):
TGGTTATCGATCGATTTTGCTTAATGCATTATTGCATTTTTGCACCAATAATTTGTGTACTATGG
CACTATGTGTGCAATGATGGTGTTCATAATGAGCACTTGTTAATACCTTGAATAAGG
Found at i:2519277 original size:168 final size:170
Alignment explanation
Indices: 2518999--2519336 Score: 662
Period size: 168 Copynumber: 2.0 Consensus size: 170
2518989 ATAAAATAAT
2518999 AAATTAGAGGAATTCAAAATATAGTATTTCAACTTCTAATTCAAATCCGATATCAGGTAGTAACA
1 AAATTAGAGGAATTCAAAATATAGTATTTCAACTTCTAATTCAAATCCGATATCAGGTAGTAACA
2519064 AGCTACATATAATAAATAAAGCTGCCTAATTTAAAATCCCATTTAAAATACCTTTTAAAGCATGG
66 AGCTACATATAATAAATAAAGCTGCCTAATTTAAAATCCCATTTAAAATACCTTTTAAAGCATGG
2519129 TTTAGTATCAT-A-ATATGTTTATACTAAATTATATTTAA
131 TTTAGTATCATAATATATGTTTATACTAAATTATATTTAA
2519167 AAATTAGAGGAATTCAAAATATAGTATTTCAACTTCTAATTCAAATCCGATATCAGGTAGTAACA
1 AAATTAGAGGAATTCAAAATATAGTATTTCAACTTCTAATTCAAATCCGATATCAGGTAGTAACA
2519232 AGCTACATATAATAAATAAAGCTGCCTAATTTAAAATCCCATTTAAAATACCTTTTAAAGCATGG
66 AGCTACATATAATAAATAAAGCTGCCTAATTTAAAATCCCATTTAAAATACCTTTTAAAGCATGG
2519297 TTTAGTATCATAATATATGTTTATACTAAATTATATTTAA
131 TTTAGTATCATAATATATGTTTATACTAAATTATATTTAA
2519337 CACTAACCAT
Statistics
Matches: 168, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
168 141 0.84
169 1 0.01
170 26 0.15
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (170 bp):
AAATTAGAGGAATTCAAAATATAGTATTTCAACTTCTAATTCAAATCCGATATCAGGTAGTAACA
AGCTACATATAATAAATAAAGCTGCCTAATTTAAAATCCCATTTAAAATACCTTTTAAAGCATGG
TTTAGTATCATAATATATGTTTATACTAAATTATATTTAA
Found at i:2519854 original size:10 final size:10
Alignment explanation
Indices: 2519839--2519867 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2519829 GCCATTGATC
2519839 AACAACAAGA
1 AACAACAAGA
2519849 AACAACAAGA
1 AACAACAAGA
2519859 AACAACAAG
1 AACAACAAG
2519868 CAACTAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.69, C:0.21, G:0.10, T:0.00
Consensus pattern (10 bp):
AACAACAAGA
Found at i:2525483 original size:21 final size:21
Alignment explanation
Indices: 2525409--2525490 Score: 76
Period size: 23 Copynumber: 3.9 Consensus size: 21
2525399 TATTTGGCAG
* *
2525409 AGGGAATCGATACCCCC-ATA
1 AGGGAACCGATACCCCCTGTA
* *
2525429 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATACCCCCTGT-A
*
2525451 ATGGGAACCGATTCCCCCTGTA
1 A-GGGAACCGATACCCCCTGTA
* *
2525473 GGGGAATCGATACCCCCT
1 AGGGAACCGATACCCCCT
2525491 TGGGGTTCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.29
21 16 0.31
22 3 0.06
23 18 0.35
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.20
Consensus pattern (21 bp):
AGGGAACCGATACCCCCTGTA
Found at i:2529454 original size:27 final size:26
Alignment explanation
Indices: 2529416--2529467 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
2529406 CCACCATCAA
*
2529416 CACTATGTATCCTTTAGTACTGACCCG
1 CACTAGGTATCCTTTAGTAC-GACCCG
2529443 CACTAGGTATCCTTTAGTACGACCC
1 CACTAGGTATCCTTTAGTACGACCC
2529468 AATATGCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (26 bp):
CACTAGGTATCCTTTAGTACGACCCG
Found at i:2529641 original size:22 final size:22
Alignment explanation
Indices: 2529616--2529660 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2529606 CCGCAATAAC
*
2529616 ATTCATAATAAATATAATATAT
1 ATTCATAATAAAAATAATATAT
* *
2529638 ATTCATGATAAAAATCATATAT
1 ATTCATAATAAAAATAATATAT
2529660 A
1 A
2529661 ATAACCTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTCATAATAAAAATAATATAT
Found at i:2533207 original size:22 final size:22
Alignment explanation
Indices: 2533182--2533226 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2533172 TCGAAATAAC
*
2533182 ATTCATGATAAATATAATATAT
1 ATTCATGATAAAAATAATATAT
*
2533204 ATTCATGATAAAAATCATATAT
1 ATTCATGATAAAAATAATATAT
2533226 A
1 A
2533227 ATAACCTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (22 bp):
ATTCATGATAAAAATAATATAT
Found at i:2537128 original size:30 final size:30
Alignment explanation
Indices: 2537094--2537311 Score: 142
Period size: 30 Copynumber: 7.3 Consensus size: 30
2537084 TAAAGGACCT
* *
2537094 AAATAGCAAAAACATAAACTTAAAGGGATA
1 AAATAGCAAAAATAGAAACTTAAAGGGATA
* * *
2537124 AAATAGTAAAAATA-AAAATTTAAGGGACTA
1 AAATAGCAAAAATAGAAACTTAAAGGGA-TA
* * *
2537154 AAATAGAAAAAATAGAAATTTCAA-GGACTA
1 AAATAGCAAAAATAGAAACTTAAAGGGA-TA
* * * * *
2537184 AAATGGTAAAATTAGAAACTTAAAGAGCTA
1 AAATAGCAAAAATAGAAACTTAAAGGGATA
* * *
2537214 AAATAGTAAAAATAGAAAC-TAAA-GGCTCT
1 AAATAGCAAAAATAGAAACTTAAAGGGAT-A
* * * * *
2537243 AAATAGGAAATACAGACATTTAAA-GGACTA
1 AAATAGCAAAAATAGAAACTTAAAGGGA-TA
* * *
2537273 AAATAACAAAAATAAAAACTT-AAGGGACA
1 AAATAGCAAAAATAGAAACTTAAAGGGATA
2537302 AAATAGCAAA
1 AAATAGCAAA
2537312 TAATTATAAT
Statistics
Matches: 147, Mismatches: 34, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
28 3 0.02
29 41 0.28
30 94 0.64
31 9 0.06
ACGTcount: A:0.59, C:0.08, G:0.14, T:0.19
Consensus pattern (30 bp):
AAATAGCAAAAATAGAAACTTAAAGGGATA
Found at i:2537158 original size:60 final size:60
Alignment explanation
Indices: 2537081--2537307 Score: 194
Period size: 60 Copynumber: 3.8 Consensus size: 60
2537071 ATTGTATTCG
* * *
2537081 ATTTAAAGGACCT-AAATAGCAAAAACATAAACTTAAAGGGATAAAATAGTAAAAATAAAA
1 ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAA-GGATAAAATAGTAAAAATAGAA
* * * * * *
2537141 ATTTAAGGGA-CTAAAATAGAAAAAATAGAAATTTCAAGGACTAAAATGGTAAAATTAGAA
1 ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAAGGA-TAAAATAGTAAAAATAGAA
* * * * * * * * *
2537201 ACTTAAA-GAGCTAAAATAGTAAAAATAGAAAC-TAAAGGCTCTAAATAGGAAATACAGAC
1 ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAAGGAT-AAAATAGTAAAAATAGAA
* * * *
2537260 ATTTAAAGGA-CTAAAATAACAAAAATAAAAACTTAAGGGACAAAATAG
1 ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAAGGATAAAATAG
2537308 CAAATAATTA
Statistics
Matches: 131, Mismatches: 30, Indels: 13
0.75 0.17 0.07
Matches are distributed among these distances:
58 1 0.01
59 54 0.41
60 76 0.58
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.20
Consensus pattern (60 bp):
ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAAGGATAAAATAGTAAAAATAGAA
Found at i:2537285 original size:90 final size:90
Alignment explanation
Indices: 2537081--2537295 Score: 236
Period size: 90 Copynumber: 2.4 Consensus size: 90
2537071 ATTGTATTCG
* * * * *
2537081 ATTTAAAGGACCT-AAATAGCAAAAACATAAACTTAAAGGGATAAAATAGTAAAAATAAAAATTT
1 ATTTAAAGGA-CTAAAATAGCAAAAATAAAAACTTAAAGAGATAAAATAGTAAAAATAAAAACTA
* *
2537145 AAGGGACTAAAATAGAAAAAATAGAA
65 AAGGCACTAAAATAGAAAAAACAGAA
* * * * * * *
2537171 ATTTCAAGGACTAAAATGGTAAAATTAGAAACTTAAAGAGCTAAAATAGTAAAAATAGAAACTAA
1 ATTTAAAGGACTAAAATAGCAAAAATAAAAACTTAAAGAGATAAAATAGTAAAAATAAAAACTAA
* * * *
2537236 AGGCTCT-AAATAGGAAATACAGAC
66 AGGCACTAAAATAGAAAAAACAGAA
*
2537260 ATTTAAAGGACTAAAATAACAAAAATAAAAACTTAA
1 ATTTAAAGGACTAAAATAGCAAAAATAAAAACTTAA
2537296 GGGACAAAAT
Statistics
Matches: 101, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
89 45 0.45
90 56 0.55
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (90 bp):
ATTTAAAGGACTAAAATAGCAAAAATAAAAACTTAAAGAGATAAAATAGTAAAAATAAAAACTAA
AGGCACTAAAATAGAAAAAACAGAA
Found at i:2538393 original size:131 final size:131
Alignment explanation
Indices: 2538163--2538476 Score: 378
Period size: 131 Copynumber: 2.4 Consensus size: 131
2538153 TCTAGTCGAT
* * * * * * *
2538163 GGATGACACAGTTCCTACGCGATGAGGATGGCAGACCATATTTAGAGAGGGTGATAAAAAT-GTT
1 GGATGACACGGTTCCTACGTGATAAGGAAGGCAGACCATCTTT--A-AGGATGAT-AACATGGTT
** * *
2538227 CCTATATGACGAGGATGGTAGGTTATCTAGGGGTGACACGACTCCTATGCAATGAGAAGGTATGG
62 CCTACGTGATGAGGATGGTAGGTTATCTAAGGGTGACACGACTCCTATGCAATGAGAAGGTATGG
2538292 TCGGG
127 TCGGG
* *
2538297 GGATGACACGGTTCCTACGTGATAAGGAAGGCAGTCTATCTTTAAGGATGATAACATGGTTCCTA
1 GGATGACACGGTTCCTACGTGATAAGGAAGGCAGACCATCTTTAAGGATGATAACATGGTTCCTA
* * ** * * *
2538362 CGTGATGAGGATGGTTGGTTATCTAAGGGTGACACGGCTCCTATGTGATGAGGAGGTCTGGTCTG
66 CGTGATGAGGATGGTAGGTTATCTAAGGGTGACACGACTCCTATGCAATGAGAAGGTATGGTCGG
2538427 G
131 G
* * *
2538428 GGATGACACGGTTCCTACGTGATGAGGATGGCAGACCATCTTTAGGGAT
1 GGATGACACGGTTCCTACGTGATAAGGAAGGCAGACCATCTTTAAGGAT
2538477 AATGTCTCAA
Statistics
Matches: 154, Mismatches: 25, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
130 4 0.03
131 113 0.73
132 1 0.01
134 36 0.23
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (131 bp):
GGATGACACGGTTCCTACGTGATAAGGAAGGCAGACCATCTTTAAGGATGATAACATGGTTCCTA
CGTGATGAGGATGGTAGGTTATCTAAGGGTGACACGACTCCTATGCAATGAGAAGGTATGGTCGG
G
Found at i:2538450 original size:40 final size:41
Alignment explanation
Indices: 2538354--2538458 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 41
2538344 ATGATAACAT
2538354 GGTTCCTACGTGATGAGGATGGTTGGTTATCTAAGGGTGACAC
1 GGTTCCTACGTGATGAGGATGGTTGG-T-TCTAAGGGTGACAC
* * *
2538397 GGCTCCTATGTGATGAGGA-GGTCTGG-TCT-GGGGATGACAC
1 GGTTCCTACGTGATGAGGATGGT-TGGTTCTAAGGG-TGACAC
2538437 GGTTCCTACGTGATGAGGATGG
1 GGTTCCTACGTGATGAGGATGG
2538459 CAGACCATCT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
39 3 0.06
40 26 0.48
41 2 0.04
42 3 0.06
43 20 0.37
ACGTcount: A:0.19, C:0.15, G:0.38, T:0.28
Consensus pattern (41 bp):
GGTTCCTACGTGATGAGGATGGTTGGTTCTAAGGGTGACAC
Found at i:2538584 original size:35 final size:35
Alignment explanation
Indices: 2538517--2538584 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
2538507 ACAAAATTCG
* *
2538517 TTTCAAGGGAAACGATCTCAAAGATGTTTGTTTTA
1 TTTCAAGGGAAACGATCCCAAAGATGTGTGTTTTA
2538552 TTTCAAGGGAAACAGA-CCCAAAGATAG-GTGTTT
1 TTTCAAGGGAAAC-GATCCCAAAGAT-GTGTGTTT
2538585 CAAGAGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 26 0.90
36 3 0.10
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (35 bp):
TTTCAAGGGAAACGATCCCAAAGATGTGTGTTTTA
Found at i:2538672 original size:63 final size:61
Alignment explanation
Indices: 2538582--2538738 Score: 185
Period size: 63 Copynumber: 2.6 Consensus size: 61
2538572 AAGATAGGTG
* ** * *
2538582 TTTCAAGAGAAACAATCTCAAGGGAGACAAAACTTGTTTCAAGAAAAACATACTCAAAGATTT
1 TTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAAAAACAGACTCAAAGA--T
* *
2538645 TTTCAAGAAAAACTGTCTCAAGAGAGACAAAACATTGTTTTAAGAGAAACAGACTCAAAGAT
1 TTTCAAGAAAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGAAAAACAGACTCAAAGAT
* *
2538707 CTT--A-AAAAATTGTCTCAAGAGAGACAAAACTT
1 TTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTT
2538739 TATTTTAAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
58 2 0.02
59 25 0.30
60 1 0.01
62 3 0.04
63 29 0.35
64 24 0.29
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (61 bp):
TTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAAAAACAGACTCAAAGAT
Found at i:2538732 original size:59 final size:61
Alignment explanation
Indices: 2538597--2538815 Score: 196
Period size: 59 Copynumber: 3.5 Consensus size: 61
2538587 AGAGAAACAA
* * * * *
2538597 TCTCAAGGGAGACAAAACTTGTTTCAAGAAAAACATACTCAAAGATTTTTTCAAGAAAAACTG
1 TCTCAAGAGAGACAAAACTTGTTTTAAGAGAAACAGACTCAAAGA-TTCTT-AAGAAAAACTG
*
2538660 TCTCAAGAGAGACAAAACATTGTTTTAAGAGAAACAGACTCAAAGA-TCTT-A-AAAAATTG
1 TCTCAAGAGAGACAAAAC-TTGTTTTAAGAGAAACAGACTCAAAGATTCTTAAGAAAAACTG
* * * * * *
2538719 TCTCAAGAGAGACAAAACTTTATTTTAAGAGAAATA-ATTTCAAAGTTTGTCTTAAGAAAGACTA
1 TCTCAAGAGAGACAAAAC-TTGTTTTAAGAGAAACAGA-CTCAAAG-AT-TCTTAAGAAAAACTG
** *
2538783 TCTCAAGTA-AGACAAAGTTTGTTTTGAGAGAAA
1 TCTCAAG-AGAGACAAAACTTGTTTTAAGAGAAA
2538816 TTGTCTTAAC
Statistics
Matches: 130, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
58 1 0.01
59 46 0.35
60 1 0.01
62 7 0.05
63 31 0.24
64 43 0.33
65 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (61 bp):
TCTCAAGAGAGACAAAACTTGTTTTAAGAGAAACAGACTCAAAGATTCTTAAGAAAAACTG
Found at i:2539060 original size:32 final size:33
Alignment explanation
Indices: 2539005--2539069 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
2538995 TCACTTCAAG
*
2539005 ATGTTGAATCTCCTAAAGATGCCCCAACGTTCA
1 ATGTTGAATCTCCTAAAGATGCCCCAACATTCA
2539038 ATGTTGAATCTCC-AAAGATGCCCCAACATTCA
1 ATGTTGAATCTCCTAAAGATGCCCCAACATTCA
2539070 TCATTTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (33 bp):
ATGTTGAATCTCCTAAAGATGCCCCAACATTCA
Found at i:2540739 original size:19 final size:19
Alignment explanation
Indices: 2540715--2540768 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2540705 CTTCTTGTCC
*
2540715 TCTTTTTTCTTTGTTTTTT
1 TCTTTTTTCTTTGTTTCTT
* *
2540734 TCTTTTCTCTTT-TTCCTT
1 TCTTTTTTCTTTGTTTCTT
*
2540752 T-GTTTTTCTTTGTTTCT
1 TCTTTTTTCTTTGTTTCT
2540769 CTTTGCCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 8 0.29
18 9 0.32
19 11 0.39
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (19 bp):
TCTTTTTTCTTTGTTTCTT
Found at i:2540746 original size:13 final size:12
Alignment explanation
Indices: 2540717--2540803 Score: 54
Period size: 12 Copynumber: 6.7 Consensus size: 12
2540707 TCTTGTCCTC
2540717 TTTTTTCTTTGT
1 TTTTTTCTTTGT
2540729 TTTTTTCTTT-T
1 TTTTTTCTTTGT
2540740 CTCTTTTTCCTTTG-
1 -T-TTTTT-CTTTGT
2540754 -TTTTTCTTTGT
1 TTTTTTCTTTGT
2540765 TTCTCTTTGCCCTTTGTT
1 TT-T-TTT---CTTTG-T
*
2540783 GTTTTTTCTTTTT
1 -TTTTTTCTTTGT
2540796 TTTTTTCT
1 TTTTTTCT
2540804 CTCTTTGTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 26
0.69 0.01 0.30
Matches are distributed among these distances:
10 5 0.08
11 6 0.10
12 20 0.33
13 7 0.11
14 11 0.18
17 8 0.13
18 2 0.03
19 2 0.03
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTCTTTGT
Found at i:2540747 original size:27 final size:27
Alignment explanation
Indices: 2540714--2540782 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
2540704 GCTTCTTGTC
*
2540714 CTCTTTTTTCTTTGTTTTT-TTCT-TTT
1 CTCTTTTTCCTTTGTTTTTCTT-TGTTT
2540740 CTCTTTTTCCTTTGTTTTTCTTTGTTT
1 CTCTTTTTCCTTTGTTTTTCTTTGTTT
**
2540767 CTCTTTGCCCTTTGTT
1 CTCTTTTTCCTTTGTT
2540783 GTTTTTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.72
Consensus pattern (27 bp):
CTCTTTTTCCTTTGTTTTTCTTTGTTT
Done.