Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005637.1 Hibiscus syriacus cultivar Beakdansim tig00013142_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: 575832
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:302283 original size:60 final size:59
Alignment explanation
Indices: 302144--302284 Score: 167
Period size: 59 Copynumber: 2.4 Consensus size: 59
302134 AATGAAATTG
* * * * * * **
302144 CAAAACTTTAGGGATCAATTTAGAATAAGGGTCATAGTTTGGAATGAAATTGGAATGTT
1 CAAAAGTTTAAGGACCAATTTAGAATAAGGCTCATAGTTTGGAATAAAATTAGAATACT
* *
302203 CAAAAGTTTAAGGACTAATTTAGAATAAGTCTCATAGTTTAAGG-ATAAAATTAGAATACT
1 CAAAAGTTTAAGGACCAATTTAGAATAAGGCTCATAGTTT--GGAATAAAATTAGAATACT
302263 CAAAAGTTTAAGGACCAATTTA
1 CAAAAGTTTAAGGACCAATTTA
302285 AAATGAGAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 34 0.49
60 33 0.48
61 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (59 bp):
CAAAAGTTTAAGGACCAATTTAGAATAAGGCTCATAGTTTGGAATAAAATTAGAATACT
Found at i:302906 original size:24 final size:24
Alignment explanation
Indices: 302853--302909 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
302843 TAAATAGGAT
* *
302853 TTTGACATCCTTTATTATCATGAC
1 TTTGATATACTTTATTATCATGAC
302877 TTTGATATACTTTATTATCATGAC
1 TTTGATATACTTTATTATCATGAC
302901 TTTGATATA
1 TTTGATATA
302910 TATTAGGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (24 bp):
TTTGATATACTTTATTATCATGAC
Found at i:305798 original size:21 final size:22
Alignment explanation
Indices: 305774--305815 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
305764 TAGGGTGTTC
*
305774 AATGTTGAATTTTAA-TTATGG
1 AATGTCGAATTTTAAGTTATGG
*
305795 AATGTCGGATTTTAAGTTATG
1 AATGTCGAATTTTAAGTTATG
305816 CTGATGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (22 bp):
AATGTCGAATTTTAAGTTATGG
Found at i:309350 original size:14 final size:14
Alignment explanation
Indices: 309331--309414 Score: 53
Period size: 14 Copynumber: 5.8 Consensus size: 14
309321 TTCAATTATG
309331 AAATAAAAAAATTA
1 AAATAAAAAAATTA
309345 AAATAAAAAAGAATTA
1 AAAT-AAAAA-AATTA
* * * *
309361 ATAGAACAATATTA
1 AAATAAAAAAATTA
*
309375 AAAGAAAAAAA-TA
1 AAATAAAAAAATTA
* * *
309388 AATTTCAAAATATTA
1 AA-ATAAAAAAATTA
309403 AAACTAAAAAAA
1 AAA-TAAAAAAA
309415 ATGAATAAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
13 4 0.08
14 21 0.41
15 19 0.37
16 7 0.14
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (14 bp):
AAATAAAAAAATTA
Found at i:309468 original size:24 final size:27
Alignment explanation
Indices: 309420--309468 Score: 68
Period size: 24 Copynumber: 1.9 Consensus size: 27
309410 AAAAAATGAA
*
309420 TAAAACAAAATAAAAAAGATGTTAATT
1 TAAAACAAAATAAAAAAGATATTAATT
309447 TAAAA-AAAA-AAAAAA-ATATTAA
1 TAAAACAAAATAAAAAAGATATTAA
309469 ATAAGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 6 0.29
26 4 0.19
27 5 0.24
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (27 bp):
TAAAACAAAATAAAAAAGATATTAATT
Found at i:310210 original size:15 final size:15
Alignment explanation
Indices: 310190--310220 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
310180 ATTGAATCAT
*
310190 TGATTTGTTTTGTTG
1 TGATTTGTGTTGTTG
310205 TGATTTGTGTTGTTG
1 TGATTTGTGTTGTTG
310220 T
1 T
310221 TGCTGTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.29, T:0.65
Consensus pattern (15 bp):
TGATTTGTGTTGTTG
Found at i:310547 original size:9 final size:9
Alignment explanation
Indices: 310533--310557 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
310523 ATTTGGACCA
310533 AAATAAATT
1 AAATAAATT
310542 AAATAAATT
1 AAATAAATT
310551 AAATAAA
1 AAATAAA
310558 AAGGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAATAAATT
Found at i:310652 original size:37 final size:37
Alignment explanation
Indices: 310611--310812 Score: 237
Period size: 37 Copynumber: 5.4 Consensus size: 37
310601 ATAAAAATTT
* *
310611 TATATAATATATATTTTCAAAATATTTTCAAAAATTA
1 TATATTATATATATTTTCAAAATATTTTCAAAAACTA
* * *
310648 TATATTACATATATTTTCAAATTGTTTTCAAAAAACTA
1 TATATTATATATATTTTCAAAATATTTTC-AAAAACTA
* * *
310686 TATATTATATATATTTTCAAAATGTTTCCAGAAACTA
1 TATATTATATATATTTTCAAAATATTTTCAAAAACTA
*
310723 TATATTATATATATTTTCAAAATATTTT-TAAAACTA
1 TATATTATATATATTTTCAAAATATTTTCAAAAACTA
* ** *
310759 TATATTATATATGTTATGAAAAATTATTTTTC-GAAACTA
1 TATATTATATATATT-TTCAAAA-TA-TTTTCAAAAACTA
310798 TATATTATATATATT
1 TATATTATATATATT
310813 AATAAAACCC
Statistics
Matches: 142, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
36 20 0.14
37 63 0.44
38 35 0.25
39 24 0.17
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
TATATTATATATATTTTCAAAATATTTTCAAAAACTA
Found at i:310699 original size:75 final size:73
Alignment explanation
Indices: 310602--310770 Score: 221
Period size: 75 Copynumber: 2.3 Consensus size: 73
310592 ATATAATACA
* * * * *
310602 TAAAAATTTTATATAATATATATTTTCAAAATATTTTCAAAAATTATATATTACATATATTTTCA
1 TAAAAACTATATATTATATATATTTTCAAAATATTTCCAAAAACTATATATTACATATATTTTCA
* *
310667 AATTGTTT
66 AAATATTT
* * *
310675 TCAAAAAACTATATATTATATATATTTTCAAAATGTTTCCAGAAACTATATATTATATATATTTT
1 T--AAAAACTATATATTATATATATTTTCAAAATATTTCCAAAAACTATATATTACATATATTTT
310740 CAAAATATTT
64 CAAAATATTT
*
310750 TTAAAACTATATATTATATAT
1 TAAAAACTATATATTATATAT
310771 GTTATGAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
73 20 0.24
75 63 0.76
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (73 bp):
TAAAAACTATATATTATATATATTTTCAAAATATTTCCAAAAACTATATATTACATATATTTTCA
AAATATTT
Found at i:310795 original size:75 final size:74
Alignment explanation
Indices: 310611--310812 Score: 210
Period size: 75 Copynumber: 2.7 Consensus size: 74
310601 ATAAAAATTT
* ** * * * * * * *
310611 TATATAATATATATTTTCAAAATATTTTCAAAAATTATATATTACATATATTTTCAAATTGTTTT
1 TATATTATATATATTTGAAAAATGTTTCCAGAAACTATATATTATATATATTTTCAAAATATTTT
310676 CAAAAAACTA
66 -AAAAAACTA
**
310686 TATATTATATATATTTTCAAAATGTTTCCAGAAACTATATATTATATATATTTTCAAAATATTTT
1 TATATTATATATATTTGAAAAATGTTTCCAGAAACTATATATTATATATATTTTCAAAATATTTT
*
310751 -TAAAACTA
66 AAAAAACTA
* * *
310759 TATATTATATATGTTATGAAAAATTATTTTTC-GAAACTATATATTATATATATT
1 TATATTATATATATT-TGAAAAA-T-GTTTCCAGAAACTATATATTATATATATT
310813 AATAAAACCC
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
73 21 0.19
74 5 0.05
75 80 0.73
76 4 0.04
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (74 bp):
TATATTATATATATTTGAAAAATGTTTCCAGAAACTATATATTATATATATTTTCAAAATATTTT
AAAAAACTA
Found at i:312429 original size:35 final size:35
Alignment explanation
Indices: 312363--312429 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
312353 GAATGAAACG
*
312363 AAGTACTGAATGAAAGAAAATTGAATTCAAAATAA
1 AAGTACTGAATGAAAGAAAATTGAATCCAAAATAA
*
312398 AAGTACTGAATGAAAGAAAATTGAGTCCAAAA
1 AAGTACTGAATGAAAGAAAATTGAATCCAAAA
312430 GAAATGAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.21
Consensus pattern (35 bp):
AAGTACTGAATGAAAGAAAATTGAATCCAAAATAA
Found at i:319279 original size:23 final size:22
Alignment explanation
Indices: 319230--319310 Score: 92
Period size: 23 Copynumber: 3.7 Consensus size: 22
319220 GAACCTCCAT
* * *
319230 GGGGTATCGATTCCCCTAC-AG
1 GGGGAATCGGTTCCCCTTCAAG
319251 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCCTTC-AAG
*
319274 GGGGAATCGGTTCCACTTCAAG
1 GGGGAATCGGTTCCCCTTCAAG
* *
319296 GGGGTATCGATTCCC
1 GGGGAATCGGTTCCC
319311 TCTATACTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 16 0.31
22 15 0.29
23 20 0.39
ACGTcount: A:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAG
Found at i:328640 original size:305 final size:305
Alignment explanation
Indices: 328089--328698 Score: 1202
Period size: 305 Copynumber: 2.0 Consensus size: 305
328079 AATTTGAAAT
328089 CATTGAAAAATCATTTAAAAAGATAACCAGAAATTAATTCTGGCCTGACTCACTTACCTGTCCCT
1 CATTGAAAAATCATTTAAAAAGATAACCAGAAATTAATTCTGGCCTGACTCACTTACCTGTCCCT
328154 AGTGGAGTCGCCAAGCTGTCGTAGCCGTCTTTCGGGTTGGGCCCAAAATTGGGCTTTGACTTGAA
66 AGTGGAGTCGCCAAGCTGTCGTAGCCGTCTTTCGGGTTGGGCCCAAAATTGGGCTTTGACTTGAA
328219 TAAAACACGTTGGAGTCACCACCGATCATTTAATAAAAGGGTTGATCGGATACCTTAATCTATCA
131 TAAAACACGTTGGAGTCACCACCGATCATTTAATAAAAGGGTTGATCGGATACCTTAATCTATCA
328284 TCTTACCTGATTTGCGTTTTACCATAAATATATCGGATTCGGGAGTTAGTTACAGCCAAGGAATG
196 TCTTACCTGATTTGCGTTTTACCATAAATATATCGGATTCGGGAGTTAGTTACAGCCAAGGAATG
328349 ATTAGCACCCTTGAACTGTCCTTTCGATATCGTTTTAATTTATCG
261 ATTAGCACCCTTGAACTGTCCTTTCGATATCGTTTTAATTTATCG
328394 CATTGAAAAATCATTTAAAAAGATAACCAGAAATTAATTCTGGCCTGACTCACTTACCTGTCCCT
1 CATTGAAAAATCATTTAAAAAGATAACCAGAAATTAATTCTGGCCTGACTCACTTACCTGTCCCT
*
328459 AGTGGAGTTGCCAAGCTGTCGTAGCCGTCTTTCGGGTTGGGCCCAAAATTGGGCTTTGACTTGAA
66 AGTGGAGTCGCCAAGCTGTCGTAGCCGTCTTTCGGGTTGGGCCCAAAATTGGGCTTTGACTTGAA
328524 TAAAACACGTTGGAGTCACCACCGATCATTTAATAAAAGGGTTGATCGGATACCTTAATCTATCA
131 TAAAACACGTTGGAGTCACCACCGATCATTTAATAAAAGGGTTGATCGGATACCTTAATCTATCA
*
328589 TCTTACCTGATTTGCGTTTTACCATAAATATATCGGATTCGGGAGTTAGTTACAGTCAAGGAATG
196 TCTTACCTGATTTGCGTTTTACCATAAATATATCGGATTCGGGAGTTAGTTACAGCCAAGGAATG
328654 ATTAGCACCCTTGAACTGTCCTTTCGATATCGTTTTAATTTATCG
261 ATTAGCACCCTTGAACTGTCCTTTCGATATCGTTTTAATTTATCG
328699 GTTGTCTTAA
Statistics
Matches: 303, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 303 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (305 bp):
CATTGAAAAATCATTTAAAAAGATAACCAGAAATTAATTCTGGCCTGACTCACTTACCTGTCCCT
AGTGGAGTCGCCAAGCTGTCGTAGCCGTCTTTCGGGTTGGGCCCAAAATTGGGCTTTGACTTGAA
TAAAACACGTTGGAGTCACCACCGATCATTTAATAAAAGGGTTGATCGGATACCTTAATCTATCA
TCTTACCTGATTTGCGTTTTACCATAAATATATCGGATTCGGGAGTTAGTTACAGCCAAGGAATG
ATTAGCACCCTTGAACTGTCCTTTCGATATCGTTTTAATTTATCG
Found at i:328894 original size:16 final size:16
Alignment explanation
Indices: 328870--328912 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
328860 AAAAAAATAA
328870 AAATAAAAATTAATA-TT
1 AAATAAAAA--AATATTT
328887 AAATAAAAAAATATTT
1 AAATAAAAAAATATTT
328903 AAATAAAAAA
1 AAATAAAAAA
328913 CGAATAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.16
16 12 0.48
17 9 0.36
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAAAAAAATATTT
Found at i:329840 original size:14 final size:15
Alignment explanation
Indices: 329821--329850 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
329811 ATTGAATCAT
329821 TGATTTGT-TTGTTG
1 TGATTTGTGTTGTTG
329835 TGATTTGTGTTGTTG
1 TGATTTGTGTTGTTG
329850 T
1 T
329851 TGCTGTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (15 bp):
TGATTTGTGTTGTTG
Found at i:330189 original size:5 final size:5
Alignment explanation
Indices: 330169--330235 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
330159 TTTGGACCAA
* * *
330169 AAAAT AAAAA ATAAAT AAAAT AAAAT AAAAT AAAAT ATAAT AATAT AATAA-
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT
* *
330220 ATAAT AAAAT ATAAT A
1 AAAAT AAAAT AAAAT A
330236 CATAAATATT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
4 2 0.04
5 43 0.86
6 5 0.10
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:330307 original size:39 final size:38
Alignment explanation
Indices: 330246--330620 Score: 153
Period size: 39 Copynumber: 9.3 Consensus size: 38
330236 CATAAATATT
* * *
330246 TATATAATATATA-TTTTAAAAATATTTTCTAAAATTA
1 TATATTATATATATTTTTTAAAATATTTTCTAAAACTA
*
330283 TATATTATATATATTTTTTCAAAATGTTTT-TAAAAAACTA
1 TATATTATATATATTTTTT-AAAATATTTTCT--AAAACTA
330323 TATATTATATATATTTCCTATATATCATATATATTTTCAAAATATTTTTAAAAACTA
1 TATATTATATATATTT--T-T-TA--A-A-ATATTTTC----------T-AAAACTA
* * ** **
330380 TATATAATATATA-GTTTTAAAA-ATAATCTAAAAAAA
1 TATATTATATATATTTTTTAAAATATTTTCTAAAACTA
* * * *
330416 TATATAATATATAGTTTTTGAAAACATTTT-GAAAA-TA
1 TATATTATATATA-TTTTTTAAAATATTTTCTAAAACTA
*
330453 TATATATAATATATATATTTTTAAAAGGT-TTTTCAAAAACTATA
1 TATAT-T-ATATATAT-TTTTTAAAA--TATTTTCTAAAAC--TA
* * *
330497 TATATTATATATATATTTTCAAAATGTTTTCAAAAACTA
1 TATATTATATATAT-TTTTTAAAATATTTTCTAAAACTA
* *
330536 TATA-T-TATAT-TTTTTTAGATTATTTT-TAAAACTA
1 TATATTATATATATTTTTTAAAATATTTTCTAAAACTA
* ***
330570 TATATTATATATGTTATGAAAAAATATTTT-TCAAAACTA
1 TATATTATATATATT-TTTTAAAATATTTTCT-AAAACTA
330609 TATATTATATAT
1 TATATTATATAT
330621 TATATATATA
Statistics
Matches: 265, Mismatches: 32, Indels: 80
0.70 0.08 0.21
Matches are distributed among these distances:
34 11 0.04
35 12 0.05
36 24 0.09
37 26 0.10
38 28 0.11
39 52 0.20
40 27 0.10
41 15 0.06
42 18 0.07
43 3 0.01
44 8 0.03
45 1 0.00
46 1 0.00
47 10 0.04
48 1 0.00
49 1 0.00
50 1 0.00
52 2 0.01
53 1 0.00
54 1 0.00
56 1 0.00
57 20 0.08
58 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (38 bp):
TATATTATATATATTTTTTAAAATATTTTCTAAAACTA
Found at i:330332 original size:38 final size:37
Alignment explanation
Indices: 330246--330338 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 37
330236 CATAAATATT
* *
330246 TATATAATATATATTTTAAAAATATTTTCTAAAATTA
1 TATATTATATATATTTTAAAAATATTTTCTAAAACTA
* *
330283 TATATTATATATATTTTTTCAAAATGTTTT-TAAAAAACTA
1 TATATTATATATA--TTTTAAAAATATTTTCT--AAAACTA
330323 TATATTATATATATTT
1 TATATTATATATATTT
330339 CCTATATATC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
37 12 0.25
38 4 0.08
39 13 0.27
40 19 0.40
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (37 bp):
TATATTATATATATTTTAAAAATATTTTCTAAAACTA
Found at i:330345 original size:20 final size:20
Alignment explanation
Indices: 330320--330358 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
330310 TTTTAAAAAA
*
330320 CTATATATTATATATATTTC
1 CTATATATCATATATATTTC
330340 CTATATATCATATATATTT
1 CTATATATCATATATATTT
330359 TCAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (20 bp):
CTATATATCATATATATTTC
Found at i:330353 original size:58 final size:57
Alignment explanation
Indices: 330283--330392 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 57
330273 TCTAAAATTA
* * *
330283 TATATTATATATATTTTTTCAAAATGTTTTTAAAAAACTATATATTATATATATTTCC
1 TATATTATATATATATTTTCAAAATATTTTT-AAAAACTATATATAATATATATTTCC
330341 TATA-TATCATATATATTTTCAAAATATTTTTAAAAACTATATATAATATATA
1 TATATTAT-ATATATATTTTCAAAATATTTTTAAAAACTATATATAATATATA
330393 GTTTTAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
57 23 0.48
58 25 0.52
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (57 bp):
TATATTATATATATATTTTCAAAATATTTTTAAAAACTATATATAATATATATTTCC
Found at i:330367 original size:20 final size:20
Alignment explanation
Indices: 330324--330367 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
330314 AAAAAACTAT
* * *
330324 ATATTATATATATTTCCTAT
1 ATATCATATATATTTCCAAA
*
330344 ATATCATATATATTTTCAAA
1 ATATCATATATATTTCCAAA
330364 ATAT
1 ATAT
330368 TTTTAAAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATCATATATATTTCCAAA
Found at i:330421 original size:95 final size:97
Alignment explanation
Indices: 330246--330428 Score: 237
Period size: 97 Copynumber: 1.9 Consensus size: 97
330236 CATAAATATT
* * * * **
330246 TATATAATATATATTTTAAAAATATTTTCTAAAATTATATATTATATATATTTTTTCAAAATGTT
1 TATATAATATATATTTTAAAAATATTTTCTAAAACTATATATAATATATATGTTTTAAAAATGAA
* * *
330311 TTTAAAAAACTATATATTATATATATTTCCTA
66 TCTAAAAAAATATATAATATATATATTTCCTA
* *
330343 TATATCATATATATTTTCAAAATATTTT-TAAAAACTATATATAATATATA-GTTTTAAAAAT-A
1 TATATAATATATATTTTAAAAATATTTTCT-AAAACTATATATAATATATATGTTTTAAAAATGA
330405 ATCTAAAAAAATATATAATATATA
65 ATCTAAAAAAATATATAATATATA
330429 GTTTTTGAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
95 20 0.27
96 10 0.14
97 44 0.59
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (97 bp):
TATATAATATATATTTTAAAAATATTTTCTAAAACTATATATAATATATATGTTTTAAAAATGAA
TCTAAAAAAATATATAATATATATATTTCCTA
Found at i:330426 original size:36 final size:38
Alignment explanation
Indices: 330342--330433 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 38
330332 TATATTTCCT
* * * * *
330342 ATATATCATATATA-TTTTCAAAATATTTTTAAAAACT
1 ATATATAATATATAGTTTTAAAAATATATCTAAAAACA
330379 ATATATAATATATAGTTTTAAAAATA-ATCTAAAAA-A
1 ATATATAATATATAGTTTTAAAAATATATCTAAAAACA
330415 ATATATAATATATAGTTTT
1 ATATATAATATATAGTTTT
330434 TGAAAACATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 19 0.39
37 20 0.41
38 10 0.20
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (38 bp):
ATATATAATATATAGTTTTAAAAATATATCTAAAAACA
Found at i:330507 original size:42 final size:41
Alignment explanation
Indices: 330341--330540 Score: 154
Period size: 39 Copynumber: 5.1 Consensus size: 41
330331 ATATATTTCC
** *
330341 TATAT-ATCATATATATTTTCAAAATATTTTTAAAAAC--TA
1 TATATAAT-ATATATATTTTCAAAAGGTTTTCAAAAACTATA
* * **
330380 TATATAATATATA-GTTTT-AAAA-ATAATCTAAAAA--A-A
1 TATATAATATATATATTTTCAAAAGGTTTTC-AAAAACTATA
* ** *
330416 TATATAATATATAGT-TTTTGAAAACATTTT-GAAAA-TATA
1 TATATAATATATA-TATTTTCAAAAGGTTTTCAAAAACTATA
*
330455 TATATAATATATATATTTTTAAAAGGTTTTTCAAAAACTATA
1 TATATAATATATATATTTTCAAAAGG-TTTTCAAAAACTATA
* *
330497 TATATTATATATATATTTTCAAAATGTTTTCAAAAACTATA
1 TATATAATATATATATTTTCAAAAGGTTTTCAAAAACTATA
330538 TAT
1 TAT
330541 TATATTTTTT
Statistics
Matches: 134, Mismatches: 14, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
36 17 0.13
37 17 0.13
38 10 0.07
39 35 0.26
40 6 0.04
41 22 0.16
42 27 0.20
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (41 bp):
TATATAATATATATATTTTCAAAAGGTTTTCAAAAACTATA
Found at i:331349 original size:22 final size:22
Alignment explanation
Indices: 331301--331365 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
331291 TATATGCCTG
*
331301 CAGTGCTAAGGCACTTTAGTAT
1 CAGTGCGAAGGCACTTTAGTAT
*
331323 CAGTGCGAATGCACTTTCA-TAT
1 CAGTGCGAAGGCACTTT-AGTAT
* *
331345 TAGTGTTG-AGGCACTTTAGTA
1 CAGTG-CGAAGGCACTTTAGTA
331366 CTAGTACTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (22 bp):
CAGTGCGAAGGCACTTTAGTAT
Found at i:334916 original size:22 final size:20
Alignment explanation
Indices: 334878--334917 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
334868 ATTTATTTGT
*
334878 TTTATTTTACATTTTAATGC
1 TTTATTTTAAATTTTAATGC
334898 TTTATATTTAAATTGTTAAT
1 TTTAT-TTTAAATT-TTAAT
334918 TTTAAACGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTATTTTAAATTTTAATGC
Found at i:335052 original size:24 final size:23
Alignment explanation
Indices: 335025--335084 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
335015 ATTTATTAAC
*
335025 TACTAACCGCTAACTTTGCTAATT
1 TACTAACCACTAACTTT-CTAATT
335049 TACTAA-CATCTAACTTTCTAATT
1 TACTAACCA-CTAACTTTCTAATT
335072 T-CTAACCACTAAC
1 TACTAACCACTAAC
335085 CGCTAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 9 0.27
23 10 0.30
24 14 0.42
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (23 bp):
TACTAACCACTAACTTTCTAATT
Found at i:335249 original size:29 final size:29
Alignment explanation
Indices: 335216--335281 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
335206 TTCAATTTCT
*
335216 TTTAATTTCTATCATTTACATTT-TTGCAC
1 TTTAATTTATATCATTTACATTTCTT-CAC
* * *
335245 TTTAATTTATGTTATTTACATTTCTTCCC
1 TTTAATTTATATCATTTACATTTCTTCAC
335274 TTTAATTT
1 TTTAATTT
335282 TTTTATTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 30 0.94
30 2 0.06
ACGTcount: A:0.23, C:0.15, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTAATTTATATCATTTACATTTCTTCAC
Found at i:335308 original size:14 final size:14
Alignment explanation
Indices: 335291--335323 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
335281 TTTTTATTCT
335291 AATTTCAACATTTA
1 AATTTCAACATTTA
335305 AATTTCAACATTTA
1 AATTTCAACATTTA
*
335319 CATTT
1 AATTT
335324 TAGTCATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTCAACATTTA
Found at i:337533 original size:17 final size:17
Alignment explanation
Indices: 337513--337574 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
337503 ATCTTATTTT
*
337513 TTTGTATTTTGTTTGCA
1 TTTGCATTTTGTTTGCA
* **
337530 TTTGCATTTTCTTAT-TT
1 TTTGCATTTTGTT-TGCA
*
337547 TTCTGTATTTTGTTTGCA
1 TT-TGCATTTTGTTTGCA
337565 TTTGCATTTT
1 TTTGCATTTT
337575 CACATCATAA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
17 21 0.64
18 12 0.36
ACGTcount: A:0.11, C:0.10, G:0.13, T:0.66
Consensus pattern (17 bp):
TTTGCATTTTGTTTGCA
Found at i:337543 original size:35 final size:35
Alignment explanation
Indices: 337495--337575 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 35
337485 AATAATTTCT
*
337495 TTTGC-TTTATCTTATTTTTTTGTATTTTGTTTGCA
1 TTTGCATTT-TCTTATTTTTCTGTATTTTGTTTGCA
337530 TTTGCATTTTCTTATTTTTCTGTATTTTGTTTGCA
1 TTTGCATTTTCTTATTTTTCTGTATTTTGTTTGCA
337565 TTTGCATTTTC
1 TTTGCATTTTC
337576 ACATCATAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 41 0.93
36 3 0.07
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (35 bp):
TTTGCATTTTCTTATTTTTCTGTATTTTGTTTGCA
Found at i:338709 original size:18 final size:18
Alignment explanation
Indices: 338682--338727 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
338672 GCTAAAATGA
*
338682 TATCGATACCGAAGTGGG
1 TATCGGTACCGAAGTGGG
338700 TATCGGTACCGAAGTGGG
1 TATCGGTACCGAAGTGGG
338718 TATCGGTACC
1 TATCGGTACC
338728 ATAGAAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.24
Consensus pattern (18 bp):
TATCGGTACCGAAGTGGG
Found at i:339343 original size:54 final size:54
Alignment explanation
Indices: 339116--339336 Score: 300
Period size: 54 Copynumber: 4.1 Consensus size: 54
339106 TTGCATTGTT
* * * *
339116 GTATCAGTACTATGTGTGCAACCCACATAATTCATAATGAGTTAGTCAATTACC
1 GTATCAGCACTATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACC
* * *
339170 GTATC-GACACTATGTGTGCAGCCCACAAAATTCATAATGAGCTTGTTAATTACC
1 GTATCAG-CACTATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACC
* * * *
339224 ATATCATCATTATGTGTGTAACCCACAAAATTCATAATGAGTTTGTGAATTACC
1 GTATCAGCACTATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACC
* * *
339278 GTATCAGCACTATGTGTGCAACTCACGAAATTCATAATGAGTTTGTGAATTACT
1 GTATCAGCACTATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACC
339332 GTATC
1 GTATC
339337 GACACTACAT
Statistics
Matches: 145, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 144 0.99
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (54 bp):
GTATCAGCACTATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACC
Found at i:344891 original size:13 final size:13
Alignment explanation
Indices: 344873--344897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
344863 TTGTTCTGTC
344873 TCAAATGAAAGAG
1 TCAAATGAAAGAG
344886 TCAAATGAAAGA
1 TCAAATGAAAGA
344898 ACAAGAGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (13 bp):
TCAAATGAAAGAG
Found at i:346118 original size:42 final size:42
Alignment explanation
Indices: 346040--346136 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
346030 AATTGGTAAG
* *
346040 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGAAAGATGATTAAA
* * * * *
346082 TCCTTCGGGTCATCTGTTAGTCTTTCGAGAAAGATGA-TAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGAAAGATGATTAAA
* *
346123 TCATTTGGGCCATC
1 TCCTTCGGGCCATC
346137 TATAAGACCT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 14 0.31
42 31 0.69
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCAAGAAAGATGATTAAA
Found at i:346361 original size:42 final size:41
Alignment explanation
Indices: 346297--346392 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
346287 AATTGGTAAG
* * * *
346297 TCCTTCGGGCCATCAATAAGTCTTTCGAGTATGATGATTAAA
1 TCCTTCGGGTCATCAACAAGTCTTTCGAGCAAGATGA-TAAA
* * *
346339 TCCTTCGGGTCATCTACCAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGTCATCAACAAGTCTTTCGAGCAAGATGATAAA
*
346380 TCATTCGGGTCAT
1 TCCTTCGGGTCAT
346393 TTAGAAGACC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 15 0.33
42 31 0.67
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGTCATCAACAAGTCTTTCGAGCAAGATGATAAA
Found at i:346432 original size:257 final size:259
Alignment explanation
Indices: 345910--346681 Score: 1145
Period size: 257 Copynumber: 3.0 Consensus size: 259
345900 TTGTTTTTAT
** * *
345910 ATAATTTGAAAAATGAGAAATCAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAGTT
1 ATAATTTGAAAAATGAGAAGGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
* *
345975 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTATTAAACTATTTCCAAAATTGGTAAG
66 TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAG
* *
346040 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATCTGTTAGTCT
131 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCT
* * * **
346105 TTCGAGAAAGATGATAAGTCATTTGGGCCATCTATAAGACCTTTGGGTAAGGTTCTTTCATATG
196 TTCGAGAAAGATGATAAGTCATTTGGGCCATCTATAAGACCTTTGGGAAAGATGCTTTCATACA
* * * * * *
346169 ATAATTTGAAAAATTAGAAGGCGATTCTC-AATTTTATCATTTAGTATTTTCAAAAAAT-AAAAT
1 ATAATTTGAAAAATGAGAAGGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
*
346232 TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTAACTAGTAAACTATTTCCAAAATTGGTAAG
66 TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAG
* * **
346297 TCCTTCGGGCCATCAATAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTCATCTACCAGTCT
131 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCT
* * * * * *
346362 TTCGAGCAAGATGATAAGTCATTCGGGTCATTTAGAAGACCTTTGGGCAAGATGCTTTCATACA
196 TTCGAGAAAGATGATAAGTCATTTGGGCCATCTATAAGACCTTTGGGAAAGATGCTTTCATACA
* * *
346426 ATAATTTGAAAAATGAGAAGGTGATTTTCAAAGTTTCTCATTTGGTATTTTGAGAAAATGAAATT
1 ATAATTTGAAAAATGAGAAGGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
*
346491 TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTTAG
66 TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAG
* ** *
346556 TCCTTCGAGAAATCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTCAGGTCATCTGTCAGTCT
131 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCT
* * * *
346620 TTCGAGAAAGATAATAAGTCCTTTGGGCCATCTATAACACCTTTGAGAAAGATGCTTTCATA
196 TTCGAGAAAGATGATAAGTCATTTGGGCCATCTATAAGACCTTTGGGAAAGATGCTTTCATA
346682 TGGTATTTTT
Statistics
Matches: 453, Mismatches: 58, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
257 204 0.45
258 120 0.26
259 129 0.28
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (259 bp):
ATAATTTGAAAAATGAGAAGGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATT
TTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAG
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCT
TTCGAGAAAGATGATAAGTCATTTGGGCCATCTATAAGACCTTTGGGAAAGATGCTTTCATACA
Found at i:346793 original size:14 final size:14
Alignment explanation
Indices: 346737--346875 Score: 66
Period size: 14 Copynumber: 9.1 Consensus size: 14
346727 TTAAATTTTT
*
346737 AAAAG-AAAAGAGA
1 AAAAGAAAAAGAAA
*
346750 AAAGGAAAAACTGAAA
1 AAAAGAAAAA--GAAA
*
346766 AATTAAGAAAAAGAAT
1 AA--AAGAAAAAGAAA
*
346782 AAAAGAATAAGAAA
1 AAAAGAAAAAGAAA
*
346796 AAAAGAACAGAGAAA
1 AAAAGAA-AAAGAAA
**
346811 ATGAGAAAAAAGAATGAA
1 AAAAG-AAAAAG-A--AA
*
346829 AAAAGAACGAAAAGGAA
1 AAAAG-A--AAAAGAAA
*
346846 AAAAG-AAGAGAAA
1 AAAAGAAAAAGAAA
346859 AAAGAGAAAAAGAAA
1 AAA-AGAAAAAGAAA
346874 AA
1 AA
346876 TGAAATGAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
13 13 0.14
14 23 0.24
15 20 0.21
16 13 0.14
17 7 0.07
18 14 0.15
20 5 0.05
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.05
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:346852 original size:28 final size:27
Alignment explanation
Indices: 346814--346925 Score: 93
Period size: 27 Copynumber: 4.0 Consensus size: 27
346804 AGAGAAAATG
346814 AGAAAAAAGAATGAAAAAAGAACGAAAA
1 AGAAAAAAGAATGAAAAAAGAA-GAAAA
* *
346842 GGAAAAAAGAAGAGAAAAAAG-AGAAAA
1 AGAAAAAAGAA-TGAAAAAAGAAGAAAA
* *
346869 AGAAAAATGAAATGAAAAATAGAAAAAAA
1 AGAAAAAAG-AATGAAAAA-AGAAGAAAA
* *
346898 TAGAGAGAAAAAAATGAAGAAAG-AGAAA
1 -AGA-A-AAAAGAATGAAAAAAGAAGAAA
346926 TTAAATAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
27 18 0.27
28 15 0.22
29 17 0.25
30 5 0.07
31 9 0.13
32 3 0.04
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (27 bp):
AGAAAAAAGAATGAAAAAAGAAGAAAA
Found at i:346858 original size:18 final size:17
Alignment explanation
Indices: 346826--346873 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
346816 AAAAAAGAAT
*
346826 GAAAAAAGAACGAAAAG
1 GAAAAAAGAAAGAAAAG
*
346843 GAAAAAAGAAGAGAAAAAA
1 GAAAAAAGAA-AG-AAAAG
346862 GAGAAAAAGAAA
1 GA-AAAAAGAAA
346874 AATGAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 10 0.38
18 1 0.04
19 7 0.27
20 8 0.31
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAGAAAAG
Found at i:347969 original size:175 final size:175
Alignment explanation
Indices: 347678--348036 Score: 664
Period size: 175 Copynumber: 2.1 Consensus size: 175
347668 CCACTTGAGC
*
347678 AGCTCCACGTGAAGCTTCAGTCACCAAATCATGGCCCCAACTACCAATGACTCTTCAATGTCTCC
1 AGCTCCATGTGAAGCTTCAGTCACCAAATCATGGCCCCAACTACCAATGACTCTTCAATGTCTCC
347743 ATACACGCACGAGTTAGTAAGCACCAAGGTGGTCCCATGGCCTCTGCTCCAACACATGCCATTTA
66 ATACACGCACGAGTTAGTAAGCACCAAGGTGGTCCCATGGCCTCTGCTCCAACACATGCCATTTA
347808 TGCCCCATCAGCTCCGTGCCAACAACTACCCGGTTGCACAAAGTT
131 TGCCCCATCAGCTCCGTGCCAACAACTACCCGGTTGCACAAAGTT
* *
347853 AGCTCCATGTGAAGCTTCAGTCACCAAATCATGGCCCCAATTGCCAATGACTCTTCAATGTCTCC
1 AGCTCCATGTGAAGCTTCAGTCACCAAATCATGGCCCCAACTACCAATGACTCTTCAATGTCTCC
347918 ATACACGCACGAGTTAGTAAGCACCAAGGTGGTCCCATGGCCTCTGCTCCAACACATGCCATTTA
66 ATACACGCACGAGTTAGTAAGCACCAAGGTGGTCCCATGGCCTCTGCTCCAACACATGCCATTTA
* * *
347983 TGCCCCATCAGCTCCGTGCCAACAACTTCCCGGTTGTACCAAGTT
131 TGCCCCATCAGCTCCGTGCCAACAACTACCCGGTTGCACAAAGTT
348028 AGCTCCATG
1 AGCTCCATG
348037 GTATCCCTCC
Statistics
Matches: 178, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 178 1.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.23
Consensus pattern (175 bp):
AGCTCCATGTGAAGCTTCAGTCACCAAATCATGGCCCCAACTACCAATGACTCTTCAATGTCTCC
ATACACGCACGAGTTAGTAAGCACCAAGGTGGTCCCATGGCCTCTGCTCCAACACATGCCATTTA
TGCCCCATCAGCTCCGTGCCAACAACTACCCGGTTGCACAAAGTT
Found at i:349178 original size:16 final size:16
Alignment explanation
Indices: 349157--349187 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
349147 TGTTAATTGC
*
349157 TTTTAATTTTGTTCAT
1 TTTTAATTTTCTTCAT
349173 TTTTAATTTTCTTCA
1 TTTTAATTTTCTTCA
349188 ATTTGGTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTAATTTTCTTCAT
Found at i:352119 original size:54 final size:54
Alignment explanation
Indices: 352028--352829 Score: 884
Period size: 54 Copynumber: 14.8 Consensus size: 54
352018 CCATACGATC
* * *
352028 ATTCATTCCACATAAGAAGAATTCCGTGAAATGCAC-CTATAGTGCCGAAACGATT
1 ATTCA-TCCACATAGGATGAATTCCGTGAAATGCACACT-TAGTGCCGAAACGACT
* * * **
352083 ATTCATCCATATAGGATGAATTCTGTGAAATGCAC-CTTTAGTGCCAAAACGGTT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGCCGAAACGACT
* ** * ** *
352137 ATTCATCCACATAGGATGAAGTATGTGAAATACAC-CTTCAGTGCCGAAATAATT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT-AGTGCCGAAACGACT
* *
352191 ATTCATCCACATATGATGAATTCCGTGAAATGCACACTTAGTGCTGAAACGACT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGACT
* * *
352245 ATTTATCCACATAGAATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGCT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGACT
* * *
352299 ATTCATCCACATAGGATAAATTCCGTGAAAAGCACACTTAGTGCCGAAACGGCT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGACT
** *
352353 ATTCATTTACATA-GAGTGAATTCCGTGAAATGCACACTTAGTGCCGAAA-TAGCT
1 ATTCATCCACATAGGA-TGAATTCCGTGAAATGCACACTTAGTGCCGAAACGA-CT
* ** *
352407 ATTCATCCACATAGGATTAATTATGTGAAATGCAC-CTTTAGTGCCGAAAC-AGTT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGCCGAAACGA-CT
* ** *
352461 ATTCATCCACATATGATGAATTATGTGAAATGCACACTTAGTACCGAAACGACT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGACT
* * * *
352515 ATTTATCCACATAGAATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGCT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGACT
* * * * * * *
352569 ATTCATCCGCATAAGATAAATTTCGTCAAATACACACTTAGTGCCGAAACGGCT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGACT
* * * * * *
352623 ATTCATCTATATAGAATGAATTCCGTGAAATACACACTTAGTGCCGAAATGGCT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGACT
* * *
352677 ATTCATCCACATAGGATGAATTCTGTGAAATGCAC-CTTTAGTGCCGATACGGCT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGCCGAAACGACT
* * * ** * **
352731 TTTCATCTACATTGGATGAATTCTATGAAATGCAC-CTTTAGTGCTGAAATAACT
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGCCGAAACGACT
*
352785 ATTCATCCACATAGGATGAATTCCGTGAAATTCACACTTAGTGCC
1 ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCC
352830 TATTTGGTAA
Statistics
Matches: 638, Mismatches: 97, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
53 6 0.01
54 618 0.97
55 14 0.02
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
ATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGACT
Found at i:353352 original size:95 final size:94
Alignment explanation
Indices: 353187--353364 Score: 248
Period size: 95 Copynumber: 1.9 Consensus size: 94
353177 TAATACTTCT
* * * *
353187 ATACTATGGTATCGATACCCCCTCCGGTATTGATACCGATTTTAGGTTCAATGTTGCCTAGTATT
1 ATACTATGGTACCGATACCCCCTCCGGTATCGATACCGATTTTAGATTCAATGTTACCTAGTATT
* *
353252 GATACCCTTACCATGGTATCGATACTACC
66 AATACCCTTACAATGGTATCGATACTACC
** ** *
353281 ATACTATGGTACCGATACCCCCTTCCGGTATCGATACCGATTTTAGATTTGATGTTATTTGGTAT
1 ATACTATGGTACCGATACCCCC-TCCGGTATCGATACCGATTTTAGATTCAATGTTACCTAGTAT
353346 TAATACCCTTACAATGGTA
65 TAATACCCTTACAATGGTA
353365 CTATTCTATC
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
94 21 0.29
95 51 0.71
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (94 bp):
ATACTATGGTACCGATACCCCCTCCGGTATCGATACCGATTTTAGATTCAATGTTACCTAGTATT
AATACCCTTACAATGGTATCGATACTACC
Found at i:373331 original size:19 final size:20
Alignment explanation
Indices: 373289--373332 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
373279 ATTATGCTTT
* *
373289 AAATTAATGTTTTGGTGTTG
1 AAATTAAAGTTATGGTGTTG
373309 AAATTAAAGTTATGGTG-TG
1 AAATTAAAGTTATGGTGTTG
373328 AAATT
1 AAATT
373333 GGATTATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (20 bp):
AAATTAAAGTTATGGTGTTG
Found at i:377056 original size:14 final size:15
Alignment explanation
Indices: 377023--377060 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
377013 AAGGGATATA
377023 ACCATGCATGCCAAAC
1 ACCATGCATGCC-AAC
377039 ACCATGCATGCC-AC
1 ACCATGCATGCCAAC
377053 ACCATGCA
1 ACCATGCA
377061 AATCAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.45
16 12 0.55
ACGTcount: A:0.34, C:0.39, G:0.13, T:0.13
Consensus pattern (15 bp):
ACCATGCATGCCAAC
Found at i:377887 original size:18 final size:18
Alignment explanation
Indices: 377864--377908 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
377854 CTATACAAGT
377864 GTGACTATTCCAAGACTA
1 GTGACTATTCCAAGACTA
*
377882 GTGACTATTCCAAGGCTA
1 GTGACTATTCCAAGACTA
*
377900 GTGCCTATT
1 GTGACTATT
377909 ATAGATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (18 bp):
GTGACTATTCCAAGACTA
Found at i:385113 original size:22 final size:22
Alignment explanation
Indices: 385088--385163 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
385078 ATATGCCAAT
*
385088 AGTGCTAAGGCACTTTAATATC
1 AGTGCTAAGGCACTTTAGTATC
* * * *
385110 AGTGCGAATGCACTTTCGTATT
1 AGTGCTAAGGCACTTTAGTATC
* *
385132 AGTGCTGAGGCATTTTAGTA-C
1 AGTGCTAAGGCACTTTAGTATC
385153 TAGTGCTAAGG
1 -AGTGCTAAGG
385164 TATTTCCATT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (22 bp):
AGTGCTAAGGCACTTTAGTATC
Found at i:387140 original size:21 final size:20
Alignment explanation
Indices: 387082--387141 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
387072 TAGCACGAAA
* *
387082 CTAAATTACCTTGACAATGAT
1 CTAAAGTACCTTG-CATTGAT
*
387103 CTAAAGTTCCTTGGCATTGAT
1 CTAAAGTACCTT-GCATTGAT
387124 CTAAAGTACCTTAGCATT
1 CTAAAGTACCTT-GCATT
387142 AATTTATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (20 bp):
CTAAAGTACCTTGCATTGAT
Found at i:390787 original size:14 final size:14
Alignment explanation
Indices: 390768--390794 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
390758 AGTAATCAAT
390768 TTTAAAAATTCTTC
1 TTTAAAAATTCTTC
390782 TTTAAAAATTCTT
1 TTTAAAAATTCTT
390795 GATTATGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAAAAATTCTTC
Found at i:391481 original size:64 final size:65
Alignment explanation
Indices: 391324--391483 Score: 234
Period size: 65 Copynumber: 2.5 Consensus size: 65
391314 GAATAAATTG
* * * * *
391324 AACATCGAATGCATTTTATGCATCGATACACATACCATGCATTGATGCACTCAGGTTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTATTATCAA
*
391389 AACATCGAATGCATTTAATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTATT-TCA
1 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAGGCTATTATCA
391452 A
65 A
*
391453 AACATCGAATGCATTTTATGCATTGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
391484 CCTTAGTGCA
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 33 0.38
65 53 0.62
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTATTATCAA
Found at i:396178 original size:84 final size:83
Alignment explanation
Indices: 396090--396251 Score: 236
Period size: 84 Copynumber: 1.9 Consensus size: 83
396080 AATGCATTTT
* * * *
396090 ATGCATCGATGCACATA-CCATGCATCGATGCACTCAGGTTTTTATGAAAACATTGAATGCATTT
1 ATGCATCGATACACA-AGCCATGCATCGATGCACTCAGGCTATT-TCAAAACATTGAATGCATTT
396154 AATGCATCGATGCACAATCC
64 AATGCATCGATGCACAATCC
* * *
396174 ATGCATCGATACACAAGCCATGCATCGATGGACTCAGGCTATTTCAAAACATTGAATGCGTTTTA
1 ATGCATCGATACACAAGCCATGCATCGATGCACTCAGGCTATTTCAAAACATTGAATGCATTTAA
396239 TGCATCGATGCAC
66 TGCATCGATGCAC
396252 CCTTAGTGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
83 33 0.47
84 37 0.53
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (83 bp):
ATGCATCGATACACAAGCCATGCATCGATGCACTCAGGCTATTTCAAAACATTGAATGCATTTAA
TGCATCGATGCACAATCC
Found at i:396179 original size:19 final size:19
Alignment explanation
Indices: 396155--396203 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
396145 AATGCATTTA
*
396155 ATGCATCGATGCACAATCC
1 ATGCATCGATGCACAAGCC
*
396174 ATGCATCGATACACAAGCC
1 ATGCATCGATGCACAAGCC
396193 ATGCATCGATG
1 ATGCATCGATG
396204 GACTCAGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (19 bp):
ATGCATCGATGCACAAGCC
Found at i:404306 original size:20 final size:21
Alignment explanation
Indices: 404281--404322 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
404271 CCATCATCTT
404281 AAAAATGGGTT-CAACTCAAA
1 AAAAATGGGTTGCAACTCAAA
*
404301 AAAAATGGGTTGCAACTTAAA
1 AAAAATGGGTTGCAACTCAAA
404322 A
1 A
404323 TGGGGTGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAAATGGGTTGCAACTCAAA
Found at i:404322 original size:18 final size:18
Alignment explanation
Indices: 404278--404377 Score: 71
Period size: 18 Copynumber: 5.4 Consensus size: 18
404268 AACCCATCAT
404278 CTTAAAAATGGGTT-CAA
1 CTTAAAAATGGGTTGCAA
*
404295 CTCAAAAAAAATGGGTTGCAA
1 CT---TAAAAATGGGTTGCAA
*
404316 CTT-AAAATGGGGTGCAA
1 CTTAAAAATGGGTTGCAA
* * *
404333 C-CAGAAAATAGATTGCAA
1 CTTA-AAAATGGGTTGCAA
* *
404351 CTTAAAAATAGGTTGTAA
1 CTTAAAAATGGGTTGCAA
404369 CTTTAAAAA
1 C-TTAAAAA
404378 AGAGTTTTGC
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
17 16 0.25
18 25 0.38
19 8 0.12
20 11 0.17
21 5 0.08
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (18 bp):
CTTAAAAATGGGTTGCAA
Found at i:407899 original size:17 final size:17
Alignment explanation
Indices: 407877--407916 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
407867 TGGCGTTGAA
*
407877 ATACAAAGAAGGAACGT
1 ATACAAAGAAAGAACGT
407894 ATACAAAGAAAGAACGT
1 ATACAAAGAAAGAACGT
407911 ATACAA
1 ATACAA
407917 CTGATCAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.12
Consensus pattern (17 bp):
ATACAAAGAAAGAACGT
Found at i:411679 original size:17 final size:18
Alignment explanation
Indices: 411653--411691 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
411643 GTACAACCAG
*
411653 AAAATAGGTTGTAAC-TT
1 AAAATAGGTTGCAACTTT
*
411670 AAAATGGGTTGCAACTTT
1 AAAATAGGTTGCAACTTT
411688 AAAA
1 AAAA
411692 AGGGGTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (18 bp):
AAAATAGGTTGCAACTTT
Found at i:415753 original size:24 final size:24
Alignment explanation
Indices: 415725--415797 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 24
415715 TACCATTTAA
415725 TACCATAAGCTCGTAAGCTTATTT
1 TACCATAAGCTCGTAAGCTTATTT
* *
415749 TACCAATAAACT--T-A-C-CA-TT
1 TACC-ATAAGCTCGTAAGCTTATTT
415768 TATCCATAAGCTCGTAAGCTTATTT
1 TA-CCATAAGCTCGTAAGCTTATTT
415793 TACCA
1 TACCA
415798 ATACACTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
19 10 0.27
20 3 0.08
21 2 0.05
22 2 0.05
23 2 0.05
24 8 0.22
25 10 0.27
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (24 bp):
TACCATAAGCTCGTAAGCTTATTT
Found at i:415780 original size:44 final size:44
Alignment explanation
Indices: 415714--415899 Score: 318
Period size: 44 Copynumber: 4.2 Consensus size: 44
415704 GTGCAATATT
*
415714 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATAAAC
1 TTACCATTT-AT-CCATAAGCTCGTAAGCTTATTTTACCAATACAC
415760 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
* *
415804 TTACCATTTATCCATAAGCTTGTAAGCTTATTTTACCAGTACAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
415848 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
*
415892 TTGCCATT
1 TTACCATT
415900 ATTCCCTAAC
Statistics
Matches: 134, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
44 123 0.92
45 2 0.01
46 9 0.07
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
Found at i:415931 original size:20 final size:20
Alignment explanation
Indices: 415906--415947 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
415896 CATTATTCCC
* *
415906 TAACCATATACCATAGACAA
1 TAACCATAAACAATAGACAA
415926 TAACCATAAACAATAGACAA
1 TAACCATAAACAATAGACAA
415946 TA
1 TA
415948 GCCCAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.19
Consensus pattern (20 bp):
TAACCATAAACAATAGACAA
Found at i:416748 original size:10 final size:9
Alignment explanation
Indices: 416734--416767 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
416724 CAAAACACGT
416734 AAAAAAATA
1 AAAAAAATA
*
416743 ATAAAAATA
1 AAAAAAATA
416752 AATAAAAATA
1 AA-AAAAATA
416762 AAAAAA
1 AAAAAA
416768 TGAATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAAATA
Found at i:416766 original size:18 final size:19
Alignment explanation
Indices: 416736--416776 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
416726 AAACACGTAA
416736 AAAAATAATAAAAATAAAT
1 AAAAATAATAAAAATAAAT
*
416755 AAAAATAA-AAAAATGAAT
1 AAAAATAATAAAAATAAAT
416773 AAAA
1 AAAA
416777 TGTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAATAATAAAAATAAAT
Found at i:416778 original size:9 final size:9
Alignment explanation
Indices: 416736--416776 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
416726 AAACACGTAA
416736 AAAAATAAT
1 AAAAATAAT
416745 AAAAATAAAT
1 AAAAAT-AAT
416755 AAAAATAA-
1 AAAAATAAT
416763 AAAAATGAAT
1 AAAAAT-AAT
416773 AAAA
1 AAAA
416777 TGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.21
9 10 0.34
10 13 0.45
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAAATAAT
Found at i:416839 original size:17 final size:17
Alignment explanation
Indices: 416819--416865 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
416809 ATATAATGGA
416819 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
* *
416836 GTAAAAGAAATTAAAAAT
1 GTAAAA-AAATAAAAAAG
416854 G-AATAAAAATAA
1 GTAA-AAAAATAA
416866 TGTGTACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:416981 original size:13 final size:13
Alignment explanation
Indices: 416963--416987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
416953 CATGATATTA
416963 AGAAAAAAATAAT
1 AGAAAAAAATAAT
416976 AGAAAAAAATAA
1 AGAAAAAAATAA
416988 AATAAAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:416991 original size:18 final size:18
Alignment explanation
Indices: 416968--417025 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
416958 TATTAAGAAA
*
416968 AAAATAATAGAAAAAAAT
1 AAAATAATATAAAAAAAT
* *
416986 AAAATAAAATAAAAATAT
1 AAAATAATATAAAAAAAT
* *
417004 AATATATATATAAATAAAT
1 AAAATA-ATATAAAAAAAT
417023 AAA
1 AAA
417026 TAGAAACAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATAATATAAAAAAAT
Found at i:417138 original size:8 final size:8
Alignment explanation
Indices: 417125--417159 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
417115 AGAAAAATTA
417125 ATACATAT
1 ATACATAT
417133 ATACATAT
1 ATACATAT
*
417141 ATATATAT
1 ATACATAT
*
417149 ATATATAT
1 ATACATAT
417157 ATA
1 ATA
417160 TAATGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (8 bp):
ATACATAT
Found at i:417142 original size:2 final size:2
Alignment explanation
Indices: 417129--417180 Score: 63
Period size: 2 Copynumber: 26.5 Consensus size: 2
417119 AAATTAATAC
*
417129 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
*
417170 AG AT AT AT AT A
1 AT AT AT AT AT A
417181 AAAAATAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (2 bp):
AT
Found at i:417196 original size:21 final size:22
Alignment explanation
Indices: 417143--417206 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
417133 ATACATATAT
* * * *
417143 ATATATATATATATATATAATG
1 ATATAGATATATATAAAAAATA
417165 ATATAAGATATATATAAAAAATA
1 ATAT-AGATATATATAAAAAATA
*
417188 ATATA-ATATAAATAAAAAA
1 ATATAGATATATATAAAAAA
417207 AGGAATATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.36
22 5 0.14
23 18 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (22 bp):
ATATAGATATATATAAAAAATA
Found at i:417234 original size:21 final size:21
Alignment explanation
Indices: 417196--417236 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
417186 TAATATAATA
*
417196 TAAATAAAAAAAGGAATATAG
1 TAAATAAAAAAAGAAATATAG
417217 TAAATAAATAAAA-AAATATA
1 TAAATAAA-AAAAGAAATATA
417237 ATTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (21 bp):
TAAATAAAAAAAGAAATATAG
Found at i:420082 original size:77 final size:77
Alignment explanation
Indices: 419963--420109 Score: 267
Period size: 77 Copynumber: 1.9 Consensus size: 77
419953 GATCGAGTCG
** *
419963 AGTCAAAATTTTTTGAGTTATTTGAGTTGACGAGTTGTATTTTACAATTCGAATTTAACTCAAAA
1 AGTCAAAAAATTTTGAGTTATTTGAGTTGACGAATTGTATTTTACAATTCGAATTTAACTCAAAA
420028 TTTTTCGAGTTT
66 TTTTTCGAGTTT
420040 AGTCAAAAAATTTTGAGTTATTTGAGTTGACGAATTGTATTTTACAATTCGAATTTAACTCAAAA
1 AGTCAAAAAATTTTGAGTTATTTGAGTTGACGAATTGTATTTTACAATTCGAATTTAACTCAAAA
420105 TTTTT
66 TTTTT
420110 TCAAGTCGAG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (77 bp):
AGTCAAAAAATTTTGAGTTATTTGAGTTGACGAATTGTATTTTACAATTCGAATTTAACTCAAAA
TTTTTCGAGTTT
Found at i:428818 original size:23 final size:23
Alignment explanation
Indices: 428785--428849 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
428775 CAGCTCATAT
428785 AAATGCACCGAAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
* **
428808 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCATGTAG
*
428831 AAATGCACCGTAGTGCCAT
1 AAATGCACCGAAGTGCCAT
428850 ATAAGATGTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:429540 original size:45 final size:46
Alignment explanation
Indices: 429471--429573 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 46
429461 CACCCCTTGA
* * * * *
429471 GGTATCGGTACCCTTACTGTATTCTGTTATT-TTTTCGTTCAAGAG
1 GGTATCAGTACCCTCACTATATTCTGTGATTCTTTTCATTCAAGAG
* *
429516 GGTATCAGTACTCTCACTATATTCTGTGATTCTTTTCATTTAAGAG
1 GGTATCAGTACCCTCACTATATTCTGTGATTCTTTTCATTCAAGAG
429562 GGTATCAGTACC
1 GGTATCAGTACC
429574 TGTTTAATGG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 26 0.53
46 23 0.47
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (46 bp):
GGTATCAGTACCCTCACTATATTCTGTGATTCTTTTCATTCAAGAG
Found at i:447664 original size:93 final size:93
Alignment explanation
Indices: 447521--447730 Score: 339
Period size: 93 Copynumber: 2.3 Consensus size: 93
447511 GAAAAAATAT
* * *
447521 TTTATTTGAAAATTATTAATCGAACCAAATTAACCGATTTTTTTCTTTAACATTAATCGAACCGA
1 TTTATTTGAAAATTATTAACCGAACAAAATTAACCGAATTTTTTCTTTAACATTAATCGAACCGA
*
447586 AATTATTGGACCGTTAATCGAATCGAAA
66 AATTATTGGACCGTTAATCGAATCAAAA
* *
447614 TTTATTTGAAAATTATTAACCGAACAAAATTAAGCGAATTTTTTCTTTAACATTAATCGAACTGA
1 TTTATTTGAAAATTATTAACCGAACAAAATTAACCGAATTTTTTCTTTAACATTAATCGAACCGA
*
447679 AATTATTTGACCGTTAATCGAATCAAAA
66 AATTATTGGACCGTTAATCGAATCAAAA
* *
447707 ATTATTTGAAAAATATTAACCGAA
1 TTTATTTGAAAATTATTAACCGAA
447731 TTTTTTTCTT
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 108 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (93 bp):
TTTATTTGAAAATTATTAACCGAACAAAATTAACCGAATTTTTTCTTTAACATTAATCGAACCGA
AATTATTGGACCGTTAATCGAATCAAAA
Found at i:447810 original size:66 final size:66
Alignment explanation
Indices: 447730--447902 Score: 215
Period size: 66 Copynumber: 2.6 Consensus size: 66
447720 TATTAACCGA
*
447730 ATTTTTTTCTTTAACCATTAATCGAACCATAATTTATTTGAAAATTATTAACCAAATAAAATAAA
1 ATTTTTTTCTTTAACCATTAATCGAA-CATAATTTATTTGAAAATTATTAACCAAACAAAATAAA
**
447795 TT
65 CC
* * * * *
447797 A-TTTTTTCTTTAACCGTTAATTGAATC-TAATTTTATTTGAAAATTATTAACCGAACCAAATCA
1 ATTTTTTTCTTTAACCATTAATCGAA-CATAA-TTTATTTGAAAATTATTAACCAAACAAAATAA
447860 ACC
64 ACC
* *
447863 ATTTTTTTCTTTAACCATTAATCGAACAAAAATTATTTGA
1 ATTTTTTTCTTTAACCATTAATCGAACATAATTTATTTGA
447903 CCGTTAATCG
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
65 3 0.03
66 62 0.69
67 25 0.28
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (66 bp):
ATTTTTTTCTTTAACCATTAATCGAACATAATTTATTTGAAAATTATTAACCAAACAAAATAAAC
C
Found at i:449417 original size:54 final size:54
Alignment explanation
Indices: 449359--449580 Score: 315
Period size: 54 Copynumber: 4.1 Consensus size: 54
449349 GAACTCGAAT
* *
449359 ATCTTCAATAATCGTGTCTGCTCCCTAGTCCTTCAGAGAGTATAAGACTCAAAC
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAAC
* * * * *
449413 ATCTTCAACAATCGTGTATGCTCGCTATTTCTTCATAGAGTATAAGACTCGAAC
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAAC
449467 AATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAG-GAGTATAAGACTCGAATA-
1 -ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC-AA-AC
* *
449522 ATCTTCAACAATCGTGTC-GCTCCCTATTCCTTAAGAGAGTATAAGACTCGAAC
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAAC
449575 ATCTTC
1 ATCTTC
449581 TTCAAAGGGT
Statistics
Matches: 149, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
52 1 0.01
53 23 0.15
54 91 0.61
55 33 0.22
56 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (54 bp):
ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAAC
Found at i:449734 original size:54 final size:54
Alignment explanation
Indices: 449558--450064 Score: 544
Period size: 54 Copynumber: 9.4 Consensus size: 54
449548 TTCCTTAAGA
*
449558 GAGTATA-AGACTCGAACATCTTCTTCAAA-GGGTTTGCTCCCTCCTTCTTTAGG
1 GAGTATAGA-ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
* * *
449611 GAGTATGGAACTCGAACATCTTTTTCAAACGGGTTCGCT-CCTCCTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
*
449664 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCATCCTTCTTTAGG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
* ** * *
449718 GAGTATAGAACTCGAACGATC-TCTACAAATAGGTTCGCTCCCTCTTTGTTTAGG
1 GAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
* * * * *
449772 GAGTATGGAACTCAAACATCTTCTTCAAATGGGTTCACTCACTCCTTCTTTAGG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
* ** * * * *
449826 GAGTATAGAACTCGAACGT-TCTCCGCAAACAGGTCCACTCCCT-CTATTTTTAGG
1 GAGTATAGAACTCGAACATCT-TCTTCAAACGGGTTCGCTCCCTCCT-TCTTTAGG
* * * * *
449880 GAGTATGGAACTCGATCATATTTTTCAAACGGGTTCGCTCCCTCTTTCTTTAGG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
* * ** ** *
449934 GAGTATAGAACTCAAATGATC-TCCACAAATAGGTTCGCTCCCTCTTTCTTTAGG
1 GAGTATAGAACTCGAA-CATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
* * *
449988 GAGTAT-GAAACTCGAACATCTTCTTCAAACGGGTTTGCTCACTCCGTCTTTAGG
1 GAGTATAG-AACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
* *
450042 GAGTATGGAACTTGAACAATCTT
1 GAGTATAGAACTCGAAC-ATCTT
450065 TTTTGCTTCA
Statistics
Matches: 376, Mismatches: 64, Indels: 26
0.81 0.14 0.06
Matches are distributed among these distances:
53 85 0.23
54 278 0.74
55 13 0.03
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (54 bp):
GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCTTCTTTAGG
Found at i:449818 original size:108 final size:108
Alignment explanation
Indices: 449567--450063 Score: 626
Period size: 108 Copynumber: 4.6 Consensus size: 108
449557 AGAGTATAAG
* * *
449567 ACTCGAACATCTTCTTCAAA-GGGTTTGCTCCCTCCTTCTTTAGGGAGTATGGAACTCGAAC-AT
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCACTCCTTCTTTAGGGAGTATAGAACTCGAACGAT
*** * * * *
449630 CTTTTTCAAACGGGTTCGCT-CCTCCTTCTTTAAGGAGTATAGA
66 C-TCCACAAACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
449673 ACTCGAACATCTTCTTCAAACGGGTTCGCTC-CATCCTTCTTTAGGGAGTATAGAACTCGAACGA
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCAC-TCCTTCTTTAGGGAGTATAGAACTCGAACGA
* * *
449737 TCTCTACAAATAGGTTCGCTCCCTCTTTGTTTAGGGAGTATGGA
65 TCTCCACAAACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * * *
449781 ACTCAAACATCTTCTTCAAATGGGTTCACTCACTCCTTCTTTAGGGAGTATAGAACTCGAACGTT
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCACTCCTTCTTTAGGGAGTATAGAACTCGAACGAT
* * *
449846 CTCCGCAAACAGGTCCACTCCCTCTATT-TTTAGGGAGTATGGA
66 CTCCACAAACAGGTTCGCTCCCTCT-TTCTTTAGGGAGTATGGA
* * * * * * *
449889 ACTCGATCATATTTTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAAATGAT
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCACTCCTTCTTTAGGGAGTATAGAACTCGAACGAT
* *
449954 CTCCACAAATAGGTTCGCTCCCTCTTTCTTTAGGGAGTATGAA
66 CTCCACAAACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * * * *
449997 ACTCGAACATCTTCTTCAAACGGGTTTGCTCACTCCGTCTTTAGGGAGTATGGAACTTGAACAAT
1 ACTCGAACATCTTCTTCAAACGGGTTCGCTCACTCCTTCTTTAGGGAGTATAGAACTCGAACGAT
450062 CT
66 CT
450064 TTTTTGCTTC
Statistics
Matches: 337, Mismatches: 47, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
106 21 0.06
107 53 0.16
108 260 0.77
109 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (108 bp):
ACTCGAACATCTTCTTCAAACGGGTTCGCTCACTCCTTCTTTAGGGAGTATAGAACTCGAACGAT
CTCCACAAACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
Found at i:450534 original size:74 final size:74
Alignment explanation
Indices: 450413--450588 Score: 264
Period size: 74 Copynumber: 2.4 Consensus size: 74
450403 TTACTCCAGC
* * * *
450413 ACTCTTCTGAGAAGGCTTAAAATGGA-TTGCTTCACTACTCTTCGGTGAAGGCTTAGAATAGATT
1 ACTCTTCGGTGAAGGCTTAAGATTGACTTGCTTCACTACTCTTCGGTGAAGGCTTAGAATAGATT
*
450477 TGCTTCACT
66 TGATTCACT
* * * *
450486 ACTCTTTGGTGAAGGCTTAAGATTGACTTGCTTCACTACTCTTTGGTGAAGGCTTAGGATTGATT
1 ACTCTTCGGTGAAGGCTTAAGATTGACTTGCTTCACTACTCTTCGGTGAAGGCTTAGAATAGATT
450551 TGATTCACT
66 TGATTCACT
450560 ACTCTTCGGTGAAGGCTTAAGATTGACTT
1 ACTCTTCGGTGAAGGCTTAAGATTGACTT
450589 TGATCCAATA
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 21 0.23
74 71 0.77
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (74 bp):
ACTCTTCGGTGAAGGCTTAAGATTGACTTGCTTCACTACTCTTCGGTGAAGGCTTAGAATAGATT
TGATTCACT
Found at i:450584 original size:37 final size:37
Alignment explanation
Indices: 450413--450590 Score: 234
Period size: 37 Copynumber: 4.8 Consensus size: 37
450403 TTACTCCAGC
* * * *
450413 ACTCTTCTGAGAAGGCTTAAAATGGA-TTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
*
450449 ACTCTTCGGTGAAGGCTT-AGAATAGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAG-ATTGATTTGCTTCACT
* *
450486 ACTCTTTGGTGAAGGCTTAAGATTGACTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
* * *
450523 ACTCTTTGGTGAAGGCTTAGGATTGATTTGATTCACT
1 ACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
450560 ACTCTTCGGTGAAGGCTTAAGATTGACTTTG
1 ACTCTTCGGTGAAGGCTTAAGATTGA-TTTG
450591 ATCCAATATC
Statistics
Matches: 126, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
35 1 0.01
36 20 0.16
37 99 0.79
38 6 0.05
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
Found at i:452035 original size:125 final size:125
Alignment explanation
Indices: 451853--452113 Score: 328
Period size: 125 Copynumber: 2.1 Consensus size: 125
451843 TTAGTGTTGA
* * *
451853 AACATCATCTTATTCTGGTACAAGCCCTCAAAATGACCCAACACCTCAAATTATAAGGCTTATTC
1 AACATTATCTTATACTGGTACAAGCCCTCAAAATGACCCAACACCTCAAATTATAAGGCTCATTC
* * *
451918 -CCAAAGCCTTCTTGGTCTGTATCTTGTCATCTCAACATGACGTGGGTTCAGTCATGCCCC
66 TCC-AAGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGACGTGGGTTCAGCCATGCCCC
* ** * * * * *
451978 TACATTATCTTATACTGGTACGTGCCTTTAAAAT-ATCCCACCACCTCAAGTTGTAAGGCTCATT
1 AACATTATCTTATACTGGTACAAGCCCTCAAAATGA-CCCAACACCTCAAATTATAAGGCTCATT
* * * *
452042 CTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGCCGTGCCCC
65 CTCCAAGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGACGTGGGTTCAGCCATGCCCC
452103 AACATTATCTT
1 AACATTATCTT
452114 CACTTGAATG
Statistics
Matches: 115, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
124 1 0.01
125 113 0.98
126 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (125 bp):
AACATTATCTTATACTGGTACAAGCCCTCAAAATGACCCAACACCTCAAATTATAAGGCTCATTC
TCCAAGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGACGTGGGTTCAGCCATGCCCC
Found at i:453092 original size:39 final size:40
Alignment explanation
Indices: 453049--453124 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
453039 TATTTAGATA
*
453049 AACTTGATT-TAATTTTCCATTT-TCTGGCTAGCTGAAACC
1 AACTTGATTGTAATTTTCC-TTTATCAGGCTAGCTGAAACC
*
453088 AACTTTATTGTAATTTTCCTTTATCAGGCTAGCTGAA
1 AACTTGATTGTAATTTTCCTTTATCAGGCTAGCTGAA
453125 GGATTCATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 11 0.33
40 22 0.67
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (40 bp):
AACTTGATTGTAATTTTCCTTTATCAGGCTAGCTGAAACC
Found at i:456217 original size:55 final size:55
Alignment explanation
Indices: 456137--456279 Score: 180
Period size: 55 Copynumber: 2.6 Consensus size: 55
456127 ACTTCAAACT
* * * * * * *
456137 TCATTCGTCGGATGTCTTTCTTCATGGATCGA-TCTTTAATTAGTTTCATATTTCA
1 TCATTCATCGGATGTCCTTCTTCATGAATC-ATTCTTCAATCAGGTTCAAATTTCA
*
456192 TCATTCATCGGATGTCCTTCTTCATGAATCATTCTTCAATCAGGTTCAAATTTCT
1 TCATTCATCGGATGTCCTTCTTCATGAATCATTCTTCAATCAGGTTCAAATTTCA
* *
456247 TCTTTCATCAGATGTCCTTCTTCATGAATCATT
1 TCATTCATCGGATGTCCTTCTTCATGAATCATT
456280 TAAATGCCTC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 1 0.01
55 76 0.99
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.45
Consensus pattern (55 bp):
TCATTCATCGGATGTCCTTCTTCATGAATCATTCTTCAATCAGGTTCAAATTTCA
Found at i:456439 original size:23 final size:22
Alignment explanation
Indices: 456399--456442 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
456389 TATAAATATG
*
456399 CAAATGCAATAAATCCAAAATA
1 CAAATGCAATAAAACCAAAATA
*
456421 CAAATGGACATAAAACCAAAAT
1 CAAATGCA-ATAAAACCAAAAT
456443 GGGTTAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.59, C:0.18, G:0.07, T:0.16
Consensus pattern (22 bp):
CAAATGCAATAAAACCAAAATA
Found at i:459941 original size:25 final size:25
Alignment explanation
Indices: 459910--459963 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
459900 TTAATTTATT
* *
459910 TAATTACTTATTAT-ATATATACTAA
1 TAATTACTTATAATAATAT-TAATAA
459935 TAATTACTTATAATAATATTAATAA
1 TAATTACTTATAATAATATTAATAA
459960 TAAT
1 TAAT
459964 AATAAACTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATTACTTATAATAATATTAATAA
Found at i:463351 original size:23 final size:18
Alignment explanation
Indices: 463299--463339 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
463289 CTTAAACTGT
463299 ACCAATTATTACAGATGA
1 ACCAATTATTACAGATGA
463317 ACCAATTATTACAGATGA
1 ACCAATTATTACAGATGA
463335 ACCAA
1 ACCAA
463340 CCCTTAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (18 bp):
ACCAATTATTACAGATGA
Found at i:465099 original size:534 final size:534
Alignment explanation
Indices: 464089--465099 Score: 1819
Period size: 534 Copynumber: 1.9 Consensus size: 534
464079 TTTTAAAAAC
464089 TCTTATTTTATGTTTTTTGACGTCCTAAGTCTGAATCGGAAGTCTGTTTCTCCAAATTCAAACTT
1 TCTTATTTTATGTTTTTTGACGTCCTAAGTCTGAATCGGAAGTCTGTTTCTCCAAATTCAAACTT
*
464154 GGTAAGTTGTTTTTCAATATTTCATCTGCCAATTCAATCAAATTTCCATGTTTAAGACATATTTC
66 GGTAAGTTGTTTTTCAATATTTCATCAGCCAATTCAATCAAATTTCCATGTTTAAGACATATTTC
* *
464219 TGATACAATTCATTTTTCATGTATATGAAATATTATGGGAAGTCGAATTTATGTTTGAGGGCATT
131 TGATACAATTCATTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATGTTTGAGGGAATT
*
464284 TGATTGGAGTTTAACAAATTGAACGATGTAGCTCGAGAATTGAGGTAATACGTTACTCCCCATTG
196 TGATTGCAGTTTAACAAATTGAACGATGTAGCTCGAGAATTGAGGTAATACGTTACTCCCCATTG
464349 CATGCAATATGGTATAAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGATTGTAATA
261 CATGCAATATGGTATAAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGATTGTAATA
*
464414 AATATGAATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAGACCCGAA
326 AATAAGAATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAGACCCGAA
*
464479 TGAATGATATTAAAAATTAAGATATTTGTATGAAATTCTAATCTCAGTTATTGTTTGAATAAACA
391 TGAATGATATTAAAAATTAAGAAATTTGTATGAAATTCTAATCTCAGTTATTGTTTGAATAAACA
464544 ATTAATCTTGAAACATTCATTTAACTTTATATTTGATCGTTGGTAACGATAAACGTTAACTTTCA
456 ATTAATCTTGAAACATTCATTTAACTTTATATTTGATCGTTGGTAACGATAAACGTTAACTTTCA
464609 TCTAAAAGTTAAAT
521 TCTAAAAGTTAAAT
* * **
464623 TCTTATTTTATG-TTTTTGACGTCCTGAGTTTGAATTTGAAGTCTGTTTCTCCAAATTCAAACTT
1 TCTTATTTTATGTTTTTTGACGTCCTAAGTCTGAATCGGAAGTCTGTTTCTCCAAATTCAAACTT
*
464687 GGTAAGTTGTTTTTCAATATTTCATCAGCTAATTCAATCAAATTTCCATGTTTAAGACATATTTC
66 GGTAAGTTGTTTTTCAATATTTCATCAGCCAATTCAATCAAATTTCCATGTTTAAGACATATTTC
* *
464752 TGATGCAATTCATTTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATTTTTGAGGGAAT
131 TGATACAATTCA-TTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATGTTTGAGGGAAT
*
464817 TTGATTGCAGTTTAACAAA-TGAAACGATGTAGCTCGAGAATTGAGGTAATACGTTATTCCCCAT
195 TTGATTGCAGTTTAACAAATTG-AACGATGTAGCTCGAGAATTGAGGTAATACGTTACTCCCCAT
*
464881 TGCATGCAATATGGTATGAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGATTGTAA
259 TGCATGCAATATGGTATAAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGATTGTAA
*
464946 TAAATAAGAATTATTCTAAACTCATACTAACATTGGTAAAATGATGATAAATCGATTGAGACCCG
324 TAAATAAGAATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAGACCCG
* *
465011 AATGAATGCTATTAAAATTTAAGAAATTTGTATGAAATTCTAATCTCAGTTATTGTTTGAATAAA
389 AATGAATGATATTAAAAATTAAGAAATTTGTATGAAATTCTAATCTCAGTTATTGTTTGAATAAA
*
465076 CAATTAATCTTGAAACGTTCATTT
454 CAATTAATCTTGAAACATTCATTT
465100 TGAGTTATCC
Statistics
Matches: 456, Mismatches: 19, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
533 124 0.27
534 332 0.73
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (534 bp):
TCTTATTTTATGTTTTTTGACGTCCTAAGTCTGAATCGGAAGTCTGTTTCTCCAAATTCAAACTT
GGTAAGTTGTTTTTCAATATTTCATCAGCCAATTCAATCAAATTTCCATGTTTAAGACATATTTC
TGATACAATTCATTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATGTTTGAGGGAATT
TGATTGCAGTTTAACAAATTGAACGATGTAGCTCGAGAATTGAGGTAATACGTTACTCCCCATTG
CATGCAATATGGTATAAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGATTGTAATA
AATAAGAATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAGACCCGAA
TGAATGATATTAAAAATTAAGAAATTTGTATGAAATTCTAATCTCAGTTATTGTTTGAATAAACA
ATTAATCTTGAAACATTCATTTAACTTTATATTTGATCGTTGGTAACGATAAACGTTAACTTTCA
TCTAAAAGTTAAAT
Found at i:477679 original size:22 final size:22
Alignment explanation
Indices: 477653--477695 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
477643 GTTATCGCAA
477653 CCCCAAACTTAAGCTATTGCAC
1 CCCCAAACTTAAGCTATTGCAC
477675 CCCCAAACTTAAGCTATTGCA
1 CCCCAAACTTAAGCTATTGCA
477696 TGTCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.35, G:0.09, T:0.23
Consensus pattern (22 bp):
CCCCAAACTTAAGCTATTGCAC
Found at i:487317 original size:40 final size:40
Alignment explanation
Indices: 487262--487343 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
487252 TACAGGTTTA
*
487262 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
487302 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
487342 TA
1 TA
487344 GCACTACGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATATG
Found at i:487537 original size:45 final size:45
Alignment explanation
Indices: 487448--487570 Score: 194
Period size: 45 Copynumber: 2.7 Consensus size: 45
487438 GTAACCATGC
*
487448 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
487492 AAATAAGCTTACGAGCTCATGGAATAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
487537 AAATAAGCTTACGAGCTTATGGTTAATAAATGGT
1 AAATAAGCTTACGAGCTTATGG--AATAAATGGT
487571 GAAATATTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
44 24 0.33
45 38 0.53
47 10 0.14
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:491552 original size:18 final size:18
Alignment explanation
Indices: 491531--491573 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
491521 TTTTGCCACA
491531 ACATCACCATTTGTTATC
1 ACATCACCATTTGTTATC
491549 ACATCACCATTTGTTATC
1 ACATCACCATTTGTTATC
491567 ACATCAC
1 ACATCAC
491574 ACCATCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (18 bp):
ACATCACCATTTGTTATC
Found at i:494683 original size:18 final size:18
Alignment explanation
Indices: 494662--494700 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
494652 GCCACAACAG
494662 CACCATTTGTTATCACAT
1 CACCATTTGTTATCACAT
494680 CACCATTTGTTATCACAT
1 CACCATTTGTTATCACAT
494698 CAC
1 CAC
494701 ACCATCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.31, G:0.05, T:0.36
Consensus pattern (18 bp):
CACCATTTGTTATCACAT
Found at i:499620 original size:20 final size:20
Alignment explanation
Indices: 499592--499637 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
499582 TTAGTTGACG
* *
499592 CTCGGGAAAAAATCAGGACA
1 CTCGAGAAAAAATCAAGACA
499612 CTCGAGAAAAAATCAAGACA
1 CTCGAGAAAAAATCAAGACA
499632 CTCGAG
1 CTCGAG
499638 TTCGTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (20 bp):
CTCGAGAAAAAATCAAGACA
Found at i:518740 original size:11 final size:12
Alignment explanation
Indices: 518720--518744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
518710 TTCGATGCTA
518720 TTTTGTTTTTTT
1 TTTTGTTTTTTT
518732 TTTTGTTTTTTT
1 TTTTGTTTTTTT
518744 T
1 T
518745 AAAAAGATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:535585 original size:29 final size:29
Alignment explanation
Indices: 535543--535614 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
535533 TATAAAAGCA
* *
535543 TGGTGTAC-TTCTTTGATTAATATCAAGTT
1 TGGT-TACTTTCTTTAATGAATATCAAGTT
535572 TGGTTACTTTCTTTAATGAATATCAAGTT
1 TGGTTACTTTCTTTAATGAATATCAAGTT
535601 TGGTTACTTTCTTT
1 TGGTTACTTTCTTT
535615 TACACTCTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.51
Consensus pattern (29 bp):
TGGTTACTTTCTTTAATGAATATCAAGTT
Found at i:536717 original size:47 final size:47
Alignment explanation
Indices: 536665--536754 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 47
536655 CTAAAATATA
*
536665 GAAATAATATTTCCAATCTTTATCTATCATTCTTTAAAATTTTTATG
1 GAAATAATATTTCCAATCTTTATCTATCATTCTTCAAAATTTTTATG
536712 GAAATAATATTTCCAATCTTTATCTATCATTCTTCAAAATTTT
1 GAAATAATATTTCCAATCTTTATCTATCATTCTTCAAAATTTT
536755 GTGAAATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.48
Consensus pattern (47 bp):
GAAATAATATTTCCAATCTTTATCTATCATTCTTCAAAATTTTTATG
Found at i:543274 original size:29 final size:30
Alignment explanation
Indices: 543241--543304 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
543231 TCTCTTAAAA
* **
543241 AAATTCGAGGACTAAA-TTGAATTTTGATT
1 AAATTCGAGGAATAAAGTAAAATTTTGATT
* *
543270 AAATTTGGGGAATAAAGTAAAATTTTGATT
1 AAATTCGAGGAATAAAGTAAAATTTTGATT
543300 AAATT
1 AAATT
543305 TGGATCCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (30 bp):
AAATTCGAGGAATAAAGTAAAATTTTGATT
Found at i:543805 original size:13 final size:13
Alignment explanation
Indices: 543787--543811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
543777 ATAGCTCGAT
543787 CTGACCCGACCCG
1 CTGACCCGACCCG
543800 CTGACCCGACCC
1 CTGACCCGACCC
543812 AACATGATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.56, G:0.20, T:0.08
Consensus pattern (13 bp):
CTGACCCGACCCG
Found at i:544578 original size:39 final size:39
Alignment explanation
Indices: 544523--544658 Score: 184
Period size: 39 Copynumber: 3.5 Consensus size: 39
544513 CTCTCTTCAT
* * * *
544523 AGGCTCATCAGTTTTGTGATCAGGGTAAGTCCTTACCGC
1 AGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGC
*
544562 AGGCTCCTCAGCTTTGTGCTCAAGGTAAGTCCTTACTGC
1 AGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGC
** *
544601 AGGCTCCTTGGCTTTGTGCTCAGGGTAAGTCCTTATTGC
1 AGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGC
544640 AGGCTCCTCTA-CTTTGTGC
1 AGGCTCCTC-AGCTTTGTGC
544659 ACATGATAAG
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.33
Consensus pattern (39 bp):
AGGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTGC
Found at i:544683 original size:78 final size:78
Alignment explanation
Indices: 544535--544686 Score: 189
Period size: 78 Copynumber: 1.9 Consensus size: 78
544525 GCTCATCAGT
* * ** **
544535 TTTGTGATCAGGGTAAGTCCTTACCGCAGGCTCCTCAGCTTTGTGCTCAAGGTAAGTCCTTACTG
1 TTTGTGATCAGGGTAAGTCCTTACCGCAGGCTCCTCAGCTTTGTGCACAAGATAAGAACTTACCA
544600 CAGGCTCCTTGGC
66 CAGGCTCCTTGGC
* ** *
544613 TTTGTGCTCAGGGTAAGTCCTTATTGCAGGCTCCTCTA-CTTTGTGCACATGATAAGAACTTACC
1 TTTGTGATCAGGGTAAGTCCTTACCGCAGGCTCCTC-AGCTTTGTGCACAAGATAAGAACTTACC
*
544677 ATAGGCTCCT
65 ACAGGCTCCT
544687 CTACTTTGTG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
78 61 0.98
79 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (78 bp):
TTTGTGATCAGGGTAAGTCCTTACCGCAGGCTCCTCAGCTTTGTGCACAAGATAAGAACTTACCA
CAGGCTCCTTGGC
Found at i:551706 original size:15 final size:15
Alignment explanation
Indices: 551686--551716 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
551676 GCACATTAAA
551686 ATTAGACATCATTTC
1 ATTAGACATCATTTC
*
551701 ATTAGAGATCATTTC
1 ATTAGACATCATTTC
551716 A
1 A
551717 CAAAATGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (15 bp):
ATTAGACATCATTTC
Found at i:557949 original size:39 final size:39
Alignment explanation
Indices: 557853--557993 Score: 167
Period size: 39 Copynumber: 3.6 Consensus size: 39
557843 GGCTCCTCAA
* ** * * *
557853 CTTTGTGCTCATGGTAAGAACTTACCGTAGGCTCCTAGG
1 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTTGG
557892 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTTGG
1 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTTGG
* * *
557931 CTTTGTGCTCAGGGTAAGTCCTTACTACAGGTTCCTCT-A
1 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCT-TGG
* *
557970 CTTTGTGCACAGGGTAAGCCCTTA
1 CTTTGTGCTCAGGGTAAGTCCTTA
557994 TTGGGTGTAC
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 89 0.99
40 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (39 bp):
CTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTTGG
Found at i:559242 original size:59 final size:59
Alignment explanation
Indices: 559151--559622 Score: 714
Period size: 59 Copynumber: 8.0 Consensus size: 59
559141 CTATTTTTTT
* * *
559151 ATCTAACTTG-ATTAGTGGCACCTTTATGCCAAATGCACATTTAGGCATTTAACCTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * *
559209 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATACACAGTTAGGCATTTAACTTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * * *
559268 ATCTAACTTGAATTATTGGCTCCTTTCTACCAAATGCATAGTTAGGCATTTAACCTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* *
559327 ATCTAAATTGCATTATT-GCACCTTTCTGCCAAATTCACAGTTAGGCATTTAACCTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * ** *
559385 ATCTAACTTGCATTATTGACACCTTTCTGCCAAATACACAGTTATACATTTAACATTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* * * *
559444 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCATAGTTAGGCATTGAACTTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
*
559503 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGTATTTAACCTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
* *
559562 ATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAATTAGGCATTTAACCTTTC
1 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
559621 AT
1 AT
559623 TTTAGAGAAA
Statistics
Matches: 372, Mismatches: 40, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
58 63 0.17
59 309 0.83
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (59 bp):
ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTC
Found at i:559462 original size:176 final size:176
Alignment explanation
Indices: 559151--559622 Score: 748
Period size: 176 Copynumber: 2.7 Consensus size: 176
559141 CTATTTTTTT
* * *
559151 ATCTAACTTG-ATTAGTGGCACCTTTATGCCAAATGCACATTTAGGCATTTAACCTTTCATCTAA
1 ATCTAACTTGCATTA-TTGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTCATCTAA
*
559215 CTTGCATTATTGGCACCTTTCTTCCAAATACACAGTTAGGCATTTAACTTTTCATCTAACTTGAA
65 CTTGCATTATTGGCACCTTTCTTCCAAATACACAGTTAGGCATTTAACATTTCATCTAACTTGAA
* *
559280 TTATTGGCTCCTTTCTACCAAATGCATAGTTAGGCATTTAACCTTTC
130 TTATTGGCACCTTTCTACCAAATGCATAGTTAGGCATTGAACCTTTC
* *
559327 ATCTAAATTGCATTATTGCACCTTTCTGCCAAATTCACAGTTAGGCATTTAACCTTTCATCTAAC
1 ATCTAACTTGCATTATTGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTCATCTAAC
* * ** *
559392 TTGCATTATTGACACCTTTCTGCCAAATACACAGTTATACATTTAACATTTCATCTAACTTGCAT
66 TTGCATTATTGGCACCTTTCTTCCAAATACACAGTTAGGCATTTAACATTTCATCTAACTTGAAT
* *
559457 TATTGGCACCTTTCTTCCAAATGCATAGTTAGGCATTGAACTTTTC
131 TATTGGCACCTTTCTACCAAATGCATAGTTAGGCATTGAACCTTTC
*
559503 ATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGTATTTAACCTTTCATCTAA
1 ATCTAACTTGCATTATT-GCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTCATCTAA
* * *
559568 CTTGCATTATTGGCACCTTTCTTCCAAATGCACAATTAGGCATTTAACCTTTCAT
65 CTTGCATTATTGGCACCTTTCTTCCAAATACACAGTTAGGCATTTAACATTTCAT
559623 TTTAGAGAAA
Statistics
Matches: 269, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
176 172 0.64
177 97 0.36
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (176 bp):
ATCTAACTTGCATTATTGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACCTTTCATCTAAC
TTGCATTATTGGCACCTTTCTTCCAAATACACAGTTAGGCATTTAACATTTCATCTAACTTGAAT
TATTGGCACCTTTCTACCAAATGCATAGTTAGGCATTGAACCTTTC
Found at i:559529 original size:27 final size:27
Alignment explanation
Indices: 559440--559529 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 27
559430 ACATTTAACA
559440 TTTCATCTAACTTGCATTATTGGCACC
1 TTTCATCTAACTTGCATTATTGGCACC
* * * *
559467 TTTCTTCCAA-ATGCA-TAGTTAGGCATTGAACT
1 TTTCATCTAACTTGCATTA-TT-GGC-----ACC
559499 TTTCATCTAACTTGCATTATTGGCACC
1 TTTCATCTAACTTGCATTATTGGCACC
559526 TTTC
1 TTTC
559530 TGCCAAATGC
Statistics
Matches: 46, Mismatches: 8, Indels: 18
0.64 0.11 0.25
Matches are distributed among these distances:
25 2 0.04
26 6 0.13
27 17 0.37
32 13 0.28
33 6 0.13
34 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (27 bp):
TTTCATCTAACTTGCATTATTGGCACC
Found at i:566224 original size:59 final size:59
Alignment explanation
Indices: 566132--566491 Score: 576
Period size: 59 Copynumber: 6.1 Consensus size: 59
566122 ATACATTGTT
* * *
566132 TTTCATCCAACTTGCATTAATGGCACTTTTCTGCCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * *
566191 TTTCATCTAACTTGCATTATTGGAACCTTTCTGCCAAATGCACATTTAGGAATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * *
566250 TTTCATCTAACTTGCATTATTGGAACCTTTCTTCCAAATGCACAGTTAGACATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* * * *
566309 TTTCATCTAACTTGTACTATTGGCACCTTTCTGCCAAATGCACAATTAGACATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
* *
566368 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCATAATTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
*
566427 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCTTTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
566486 TTTCAT
1 TTTCAT
566492 TTTAGAGAAA
Statistics
Matches: 279, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 279 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (59 bp):
TTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAACC
Found at i:573874 original size:17 final size:19
Alignment explanation
Indices: 573846--573894 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
573836 TATTTTGAAA
573846 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
573864 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
573883 CACCGATGCACT
1 CATCGATGCACT
573895 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Done.