Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007921.1 Hibiscus syriacus cultivar Beakdansim tig00110325_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: 892961
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:273553 original size:2 final size:2
Alignment explanation
Indices: 273546--273571 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
273536 TAGTTTACCC
273546 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
273572 GGTAAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:278423 original size:30 final size:30
Alignment explanation
Indices: 278389--278458 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
278379 GCAAAACTCT
278389 CGAGATAATGTTATCGAAAAAATTATTTCA
1 CGAGATAATGTTATCGAAAAAATTATTTCA
278419 CGAGATAATGTTATCGAAAAAATTATTTCA
1 CGAGATAATGTTATCGAAAAAATTATTTCA
278449 CGAGATAATG
1 CGAGATAATG
278459 CACTCCCAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (30 bp):
CGAGATAATGTTATCGAAAAAATTATTTCA
Found at i:279242 original size:21 final size:21
Alignment explanation
Indices: 279212--279260 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
279202 ACAAAAATTT
279212 AGTTAATTAGTTTGTTAGTATAA
1 AGTT-ATTAGTTTGTTAGT-TAA
279235 A-TTATTAGTTTGTTAGTTAA
1 AGTTATTAGTTTGTTAGTTAA
279255 AGTTAT
1 AGTTAT
279261 ATTATATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 2 0.08
23 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTTAGTTAA
Found at i:279270 original size:28 final size:28
Alignment explanation
Indices: 279237--279290 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
279227 TAGTATAAAT
279237 TATTAGTTTGTTAGTTAAAGTTATATTA
1 TATTAGTTTGTTAGTTAAAGTTATATTA
*
279265 TATTAGTTTGTTAGTTTAAGTTATAT
1 TATTAGTTTGTTAGTTAAAGTTATAT
279291 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (28 bp):
TATTAGTTTGTTAGTTAAAGTTATATTA
Found at i:281537 original size:23 final size:23
Alignment explanation
Indices: 281510--281553 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
281500 AAATTAAAAT
*
281510 AATAATAAAATTGATTTAAATCA
1 AATAATAAAATTAATTTAAATCA
* *
281533 AATAATATAGTTAATTTAAAT
1 AATAATAAAATTAATTTAAAT
281554 AATAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AATAATAAAATTAATTTAAATCA
Found at i:281740 original size:19 final size:18
Alignment explanation
Indices: 281714--281767 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 18
281704 TTGTTCAATA
281714 ATTT-TAATCAAAATAAAT
1 ATTTATAAT-AAAATAAAT
281732 ATTTATAAT-AAAT--AT
1 ATTTATAATAAAATAAAT
*
281747 -TTTATATTAAAATAAAT
1 ATTTATAATAAAATAAAT
281764 ATTT
1 ATTT
281768 TGATTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 7 0.23
15 6 0.20
17 6 0.20
18 7 0.23
19 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTATAATAAAATAAAT
Found at i:281775 original size:18 final size:19
Alignment explanation
Indices: 281738--281778 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
281728 AAATATTTAT
*
281738 AATAAATATTTTATATTAA
1 AATAAATATTTTAGATTAA
281757 AATAAATATTTT-GATTAA
1 AATAAATATTTTAGATTAA
281775 AATA
1 AATA
281779 GAGAATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AATAAATATTTTAGATTAA
Found at i:282901 original size:30 final size:32
Alignment explanation
Indices: 282867--282938 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 32
282857 ATCCTTAAAC
282867 AACTAATAAAATATTCTTTTA-TATAAT-TAA
1 AACTAATAAAATATTCTTTTATTATAATATAA
* * *
282897 AACTAATAAACTATTTTTTTATTATAATATAC
1 AACTAATAAAATATTCTTTTATTATAATATAA
*
282929 TACTAATAAA
1 AACTAATAAA
282939 TAAACTTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 19 0.53
31 6 0.17
32 11 0.31
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (32 bp):
AACTAATAAAATATTCTTTTATTATAATATAA
Found at i:285058 original size:6 final size:6
Alignment explanation
Indices: 285047--285071 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
285037 CCGTCTCGTC
285047 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
285072 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:285199 original size:21 final size:21
Alignment explanation
Indices: 285152--285199 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
285142 CCACCAGTCG
* **
285152 TTGCGATTTTGGACTATCGCA
1 TTGCGAATTTGGAAAATCGCA
**
285173 ACGCGAATTTGGAAAATCGCA
1 TTGCGAATTTGGAAAATCGCA
285194 TTGCGA
1 TTGCGA
285200 TAGTCGATGT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (21 bp):
TTGCGAATTTGGAAAATCGCA
Found at i:286389 original size:19 final size:18
Alignment explanation
Indices: 286367--286436 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 18
286357 ATGTTATTAT
286367 ATATATATTTTTTAATTAA
1 ATATATATTTTTTAA-TAA
286386 ATATATATTTTTATTGAATAA
1 ATATATA-TTTT-TT-AATAA
*
286407 AAATA-ATATTTTTAATAA
1 ATATATAT-TTTTTAATAA
286425 ATATATTATTTT
1 ATATA-TATTTT
286437 GGGATATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 9 0.21
19 13 0.30
20 10 0.23
21 9 0.21
22 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
ATATATATTTTTTAATAA
Found at i:286391 original size:21 final size:20
Alignment explanation
Indices: 286365--286436 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
286355 TAATGTTATT
286365 ATATATATATTTTTTAATTAA
1 ATATATATATTTTTTAA-TAA
286386 ATATATAT-TTTTATTGAATAA
1 ATATATATATTTT-TT-AATAA
*
286407 AAATA-ATA-TTTTTAATAA
1 ATATATATATTTTTTAATAA
286425 ATATAT-TATTTT
1 ATATATATATTTT
286437 GGGATATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
18 11 0.25
19 5 0.11
20 9 0.20
21 17 0.39
22 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
ATATATATATTTTTTAATAA
Found at i:286427 original size:22 final size:23
Alignment explanation
Indices: 286384--286427 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
286374 TTTTTTAATT
* *
286384 AAATATATATTTTTATTGAATAA
1 AAATATATATTTTTAATAAATAA
286407 AAATA-ATATTTTTAATAAATA
1 AAATATATATTTTTAATAAATA
286428 TATTATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATATATTTTTAATAAATAA
Found at i:286443 original size:15 final size:13
Alignment explanation
Indices: 286427--286452 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
286417 TTTAATAAAT
286427 ATATTATTTTGGG
1 ATATTATTTTGGG
286440 ATATTATTTTGGG
1 ATATTATTTTGGG
286453 GACGAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
ATATTATTTTGGG
Found at i:288382 original size:31 final size:31
Alignment explanation
Indices: 288347--288451 Score: 129
Period size: 31 Copynumber: 3.4 Consensus size: 31
288337 TCTATGTGTT
288347 AAAAGTGATGATGTATTACATATTATATGTC
1 AAAAGTGATGATGTATTACATATTATATGTC
* *
288378 AAAAGTGATGATGTATTACATACTACATGTC
1 AAAAGTGATGATGTATTACATATTATATGTC
** ** *
288409 AAAAGTGATGACATAACACATGTTATATGTC
1 AAAAGTGATGATGTATTACATATTATATGTC
* *
288440 CAAAGCGATGAT
1 AAAAGTGATGAT
288452 ATAATGATGT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (31 bp):
AAAAGTGATGATGTATTACATATTATATGTC
Found at i:305896 original size:21 final size:21
Alignment explanation
Indices: 305855--305896 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
305845 TATATTAGTT
*
305855 TTTTTAGTAATTTAATTTTTA
1 TTTTTAGTAATTTAATATTTA
* *
305876 TTTTTAGTATTTTTATATTTA
1 TTTTTAGTAATTTAATATTTA
305897 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTAGTAATTTAATATTTA
Found at i:305911 original size:25 final size:26
Alignment explanation
Indices: 305873--305923 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
305863 AATTTAATTT
*
305873 TTATTTTTAGTATTTTTATA-TTTAA
1 TTATTTTTAGTATTTGTATAGTTTAA
305898 TTATTTTATA-TATTTGTATAGTTTAA
1 TTATTTT-TAGTATTTGTATAGTTTAA
305924 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (26 bp):
TTATTTTTAGTATTTGTATAGTTTAA
Found at i:310585 original size:15 final size:16
Alignment explanation
Indices: 310565--310596 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
310555 TGGCAGATCG
310565 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
310580 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
310596 A
1 A
310597 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:316173 original size:2 final size:2
Alignment explanation
Indices: 316166--316223 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
316156 ATTAACTTTC
316166 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
316208 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
316224 GTTGAAAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321358 original size:2 final size:2
Alignment explanation
Indices: 321351--321398 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
321341 TTCCGCAAAA
321351 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
321393 AT AT AT
1 AT AT AT
321399 CAAATCAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:330635 original size:19 final size:19
Alignment explanation
Indices: 330596--330652 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
330586 ACAATTAACC
* *
330596 GGTAGAATCGACTGAGAACT
1 GGTAAAATCGA-TGTGAACT
330616 GGTAAAATCGATGTGAACT
1 GGTAAAATCGATGTGAACT
* * *
330635 GGCAAAACCGGTGTGAAC
1 GGTAAAATCGATGTGAAC
330653 CTCCGGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 22 0.69
20 10 0.31
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (19 bp):
GGTAAAATCGATGTGAACT
Found at i:331056 original size:17 final size:16
Alignment explanation
Indices: 331030--331068 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
331020 GAATTAAATT
*
331030 AATTAGATATTATTTA
1 AATTAAATATTATTTA
331046 CAATTAAATATTATTTA
1 -AATTAAATATTATTTA
331063 AATTAA
1 AATTAA
331069 TTGTAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
AATTAAATATTATTTA
Found at i:338540 original size:69 final size:69
Alignment explanation
Indices: 338429--338564 Score: 272
Period size: 69 Copynumber: 2.0 Consensus size: 69
338419 GGCTCCTAAC
338429 GTGAGCGAGCCGACGAGCGAAGATGGTCTGGCACTCAGGCTTGATGCCTTTGCATAAACCGATGA
1 GTGAGCGAGCCGACGAGCGAAGATGGTCTGGCACTCAGGCTTGATGCCTTTGCATAAACCGATGA
338494 TGAT
66 TGAT
338498 GTGAGCGAGCCGACGAGCGAAGATGGTCTGGCACTCAGGCTTGATGCCTTTGCATAAACCGATGA
1 GTGAGCGAGCCGACGAGCGAAGATGGTCTGGCACTCAGGCTTGATGCCTTTGCATAAACCGATGA
338563 TG
66 TG
338565 CAGCGGTGCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.21
Consensus pattern (69 bp):
GTGAGCGAGCCGACGAGCGAAGATGGTCTGGCACTCAGGCTTGATGCCTTTGCATAAACCGATGA
TGAT
Found at i:342383 original size:35 final size:35
Alignment explanation
Indices: 342337--342406 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
342327 TACGAAGCTA
342337 ATTCACACGAGTCATCAGAAATACATACAGTTTTG
1 ATTCACACGAGTCATCAGAAATACATACAGTTTTG
342372 ATTCACACGAGTCATCAGAAATACATACAGTTTTG
1 ATTCACACGAGTCATCAGAAATACATACAGTTTTG
342407 GTTCCATGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (35 bp):
ATTCACACGAGTCATCAGAAATACATACAGTTTTG
Found at i:343261 original size:196 final size:196
Alignment explanation
Indices: 342883--343269 Score: 496
Period size: 196 Copynumber: 2.0 Consensus size: 196
342873 TCATTATATA
* **
342883 TTAGCAAATCAGGTTGTTTACTGTTAGAATACACTTCTAGTGATCAAAATTTGAAATCTTGAAAA
1 TTAGCAAATCAGGTTGTTTACTGGTAGAATACACTTCTAGTGATCAAAATTTGAAATAGTGAAAA
* * * * *
342948 TGCATAACCAAGAGATATAGTAGACCTATGCTATTCGAACTCTAAAGAACCTCGATATACATGAA
66 CGCATAACCAAGAGATATAGTAGACCTATGCTACTCGAACTCTAAAAAACCTCAAAATACATGAA
* * * *
343013 AAAACTTTGAAAAGACTAACCATACTTGTACCCGACACTCTCAGCCGAATCCAAATAACACCGAT
131 AAAACTTAGAAAAGACCAACCATACTCGTACCCAACACTCTCAGCCGAATCCAAATAACACCGAT
343078 G
196 G
* * * **
343079 TTAGCAAATCATGTTGTTTATTGGTAGAATGCTTTTCTAGTGATCAAAATTTGAAATAGT-AAAA
1 TTAGCAAATCAGGTTGTTTACTGGTAGAATACACTTCTAGTGATCAAAATTTGAAATAGTGAAAA
* *
343143 GCGCATAGCCAAGAGATATAGTAGA-CTGATGTTACTCGAACTCTAAACAAACCTCAAAATACAT
66 -CGCATAACCAAGAGATATAGTAGACCT-ATGCTACTCGAACTCTAAA-AAACCTCAAAATACAT
* * *
343207 GAAAAAAACTTAGAAACGACCAACCATCCTCGTATCCAACA-T-TC-GCCGGAATCCAAATAACA
128 G-AAAAAACTTAGAAAAGACCAACCATACTCGTACCCAACACTCTCAGCC-GAATCCAAATAACA
343269 C
191 C
343270 AAATTTAGAC
Statistics
Matches: 164, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
195 9 0.05
196 108 0.66
197 15 0.09
198 32 0.20
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (196 bp):
TTAGCAAATCAGGTTGTTTACTGGTAGAATACACTTCTAGTGATCAAAATTTGAAATAGTGAAAA
CGCATAACCAAGAGATATAGTAGACCTATGCTACTCGAACTCTAAAAAACCTCAAAATACATGAA
AAAACTTAGAAAAGACCAACCATACTCGTACCCAACACTCTCAGCCGAATCCAAATAACACCGAT
G
Found at i:348491 original size:21 final size:21
Alignment explanation
Indices: 348439--348491 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
348429 GTTTCCAGAT
348439 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* * *
348460 TCGTAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
348481 TCGCAATGCGA
1 TCGCAATGCGA
348492 TTTACATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:348547 original size:21 final size:21
Alignment explanation
Indices: 348500--348636 Score: 131
Period size: 21 Copynumber: 6.6 Consensus size: 21
348490 GATTTACATA
* * *
348500 TTCGCATTACGATAGTCCAAG
1 TTCGCGTTGCGATAGTCGAAG
348521 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
** *
348542 TTCGCGTTGCGATTTTTC-AAA
1 TTCGCGTTGCGA-TAGTCGAAG
348563 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * *
348582 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCGAAG
348605 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
348624 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
348637 TTATTCCAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
18 3 0.03
19 20 0.22
21 59 0.63
22 3 0.03
23 8 0.09
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:348618 original size:42 final size:42
Alignment explanation
Indices: 348525--348661 Score: 260
Period size: 42 Copynumber: 3.3 Consensus size: 42
348515 TCCAAGTTCG
348525 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTT-TT-CAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
348565 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
348607 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
348649 CGTTGCGATAGTC
1 CGTTGCGATAGTC
348662 CAAAATCGCA
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
40 32 0.34
41 2 0.02
42 61 0.64
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:348652 original size:21 final size:21
Alignment explanation
Indices: 348546--348657 Score: 92
Period size: 21 Copynumber: 5.4 Consensus size: 21
348536 TCGAAGTTCG
348546 CGTTGCGATTT-TT-CAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
348565 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
348584 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
* * *
348607 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
348626 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
348649 CGTTGCGAT
1 CGTTGCGAT
348658 AGTCCAAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
17 1 0.01
18 1 0.01
19 20 0.28
21 33 0.46
23 16 0.23
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:350336 original size:294 final size:294
Alignment explanation
Indices: 349921--351584 Score: 1858
Period size: 294 Copynumber: 5.6 Consensus size: 294
349911 TTCTTCTATA
* * ** * ** **
349921 TCGCATTCAAGTTCCGCTTCTGGCTCGGCCT-CACATTCTAGTTCATCTTCACAAGCCGGCTCTT
1 TCGCATTCAAGTTCAGCTTCTAGCTC-ATCTGCACATTCTAGTTCAGCTTCACATTCAAGCTCTT
* * * * * *
349985 TTCATCATTTTGGTTCTTTCAAAGGTTCTGGCTCTTCTGCAGATCCTAATGATTCTAAAGGTTCT
65 TTAATCATTCTGGTTCTTTTAAAGGTTCTGGCGCTTCTGCAGATTCTAATGATTCTAAAGGTTCC
* *
350050 GGCTCTGTTGCGACTTCTCAATCTTCATCCGGTTCTGGGACTTCTGGTTCCTCTACAAGTTCCGG
130 GGGTCTGTTGCGACTTCTCAAGCTTCATCCGGTTCTGGGACTTCTGGTTCCTCTACAAGTTCCGG
* * *
350115 TTCTTCTTCAACTTCTGGCAATTCTAAGGGTCCTGGAGAATCCTCACAATCTAATTCTGTAAATC
195 TTCTTCATCAACTTCTGGCAATTCTAAGGGTCCTGGAGAATCCTCACAATCCAATTCTGCAAATC
*
350180 AAGGTGGTGTTGCAGGTCAAGGTTCTGCATCTTTC
260 AAGGTGGTGTTGCGGGTCAAGGTTCTGCATCTTTC
* * * *
350215 TCGCATTCAAGTTCAGCTTCTAGCTCATCCT-CACGTTCTAG-TCTGGCTTCACACTCAAGCACT
1 TCGCATTCAAGTTCAGCTTCTAGCTCAT-CTGCACATTCTAGTTC-AGCTTCACATTCAAGCTCT
*
350278 TTTAATCATTCTGGTTCTTTTAAAGGTTCTAGCGCTTCTGCAGATTCTAATGATTCTAAAGGTTC
64 TTTAATCATTCTGGTTCTTTTAAAGGTTCTGGCGCTTCTGCAGATTCTAATGATTCTAAAGGTTC
* * *
350343 TGGGTCTGTTGCGACTTCTCAATCTTCATCCGGTTCTGGGACTTCTGGTTCCTCTACAAGTTTCG
129 CGGGTCTGTTGCGACTTCTCAAGCTTCATCCGGTTCTGGGACTTCTGGTTCCTCTACAAGTTCCG
* * * *
350408 GTTCTTCATCAACTTCTGGCAATTCTAAGGATCCTGGAGAATCTTCACAATCTAATTATGCAAAT
194 GTTCTTCATCAACTTCTGGCAATTCTAAGGGTCCTGGAGAATCCTCACAATCCAATTCTGCAAAT
350473 CAAGGTGGTGTTGCGGGTCAAGGTTCTGCATCTTTC
259 CAAGGTGGTGTTGCGGGTCAAGGTTCTGCATCTTTC
* * *
350509 TCGCATTCAAGTTCAGCTTCTAGCTCATCTACACGTTTTAGTTCAGCTTCACATTCAAGCTCTTT
1 TCGCATTCAAGTTCAGCTTCTAGCTCATCTGCACATTCTAGTTCAGCTTCACATTCAAGCTCTTT
* * * *
350574 TAATCATTCTGGTTCTGTTAAAGGTTCTGGTGCTTCTGTAGATTCTAATGATTCTAAAAGTTCCG
66 TAATCATTCTGGTTCTTTTAAAGGTTCTGGCGCTTCTGCAGATTCTAATGATTCTAAAGGTTCCG
* * * *
350639 GGTCTGTTGCGACTTCTCAAGCGTCATCCGGTTATGGGGCTTCTGGTTCCTCTACAAGTTCTGGT
131 GGTCTGTTGCGACTTCTCAAGCTTCATCCGGTTCTGGGACTTCTGGTTCCTCTACAAGTTCCGGT
* * * * *
350704 TCTTCATTAGCTTCTGGCAATTCTAAAGGTTCT-GATGAATCCTTACAATCCAATTCTGCAAATC
196 TCTTCATCAACTTCTGGCAATTCTAAGGGTCCTGGA-GAATCCTCACAATCCAATTCTGCAAATC
* *
350768 AAGGTGGTGTTACGGGTCATGGTTCTGCATCTTTC
260 AAGGTGGTGTTGCGGGTCAAGGTTCTGCATCTTTC
350803 TCGCATTCAAGTTCAGCTTCTAGCTCATCTGCACATTCTAGTTCAGCTTCACATTCAAGCTCTTT
1 TCGCATTCAAGTTCAGCTTCTAGCTCATCTGCACATTCTAGTTCAGCTTCACATTCAAGCTCTTT
*
350868 TAATCATTATGGTTCTTTTAAAGGTTCTGGCGCTTCTGCAGATTCTAATGATTCTAAAGGTTCCG
66 TAATCATTCTGGTTCTTTTAAAGGTTCTGGCGCTTCTGCAGATTCTAATGATTCTAAAGGTTCCG
* * * * * *
350933 GGTCTGTTGCGACTTCTCAAGCTTCATCCGATTCTGGGGCTTTTGGATCCTTTACAAGTTCTGGT
131 GGTCTGTTGCGACTTCTCAAGCTTCATCCGGTTCTGGGACTTCTGGTTCCTCTACAAGTTCCGGT
* * * * * * *
350998 TCTTCATCAGCTTCTGGCAATTCTAAGGGTTCTGAAAAATCTTCGCAATCCAATTCTACAAATCA
196 TCTTCATCAACTTCTGGCAATTCTAAGGGTCCTGGAGAATCCTCACAATCCAATTCTGCAAATCA
* *
351063 AGGTGGTGTTGCGGGTCATGGCTCTGCATCTTTC
261 AGGTGGTGTTGCGGGTCAAGGTTCTGCATCTTTC
351097 TCGCATTCAAGTTCAGCTTCTAGCTCATCTGCACATTCTAGTTCATCTTCTAGCTCATCTGCACA
1 TCGCATTCAAGTTCAGCTTCTAGCTCATCTGCACATTCTAG------TTC-AG--C-T-T-CACA
** * * * * *
351162 TTCTAGTTCAGCTTCACATTCAAACTCTTTTAATCATTCTGGTTCTTCTAACGGTTTTAGCGCTT
54 TTC-A----AGC-T--C-TTTTAA-TC--A------TTCTGGTTCTTTTAAAGGTTCTGGCGCTT
* * * * * * * *
351227 CTGCA-AATCTTAATGATTCTAAAGGCTT-TGGGCCTATTGCAAATTCTCAATCTTCATCTGGTT
101 CTGCAGATTC-TAATGATTCTAAAGG-TTCCGGGTCTGTTGCGACTTCTCAAGCTTCATCCGGTT
** *** * ** * * * * *
351290 CTGGGGTTTCTGG-T--TCTACGAA-TTTTAGTTCTTCATTAGGTGCTGGTAATTCAAAAGGTTC
164 CTGGGACTTCTGGTTCCTCTAC-AAGTTCCGGTTCTTCATCAACTTCTGGCAATTCTAAGGGTCC
* * * * * *
351351 TGGTGCATCCTCACAATCCAATTCTGTAAATCAAGGTGGTATTGCGGGT-AATGGCTCTACATCT
228 TGGAGAATCCTCACAATCCAATTCTGCAAATCAAGGTGGTGTTGCGGGTCAA-GGTTCTGCATCT
351415 TTC
292 TTC
* *
351418 TCGCATTCAAGTTCAGCTTCTAGTTCATCTTCACATTCTAGTTCAGCTTCACATTCAAGCTCTTT
1 TCGCATTCAAGTTCAGCTTCTAGCTCATCTGCACATTCTAGTTCAGCTTCACATTCAAGCTCTTT
* ** * ** * * *
351483 TAATAATT-TCGGTTCTTTTAAAGGCACCGGAACTTTTGTAGATTCTAATGATTCTAAAGGTTCT
66 TAATCATTCT-GGTTCTTTTAAAGGTTCTGGCGCTTCTGCAGATTCTAATGATTCTAAAGGTTCC
* * *
351547 GGGTCTATTGCAACTTCTCAATCTTCATCCGGTTCTGG
130 GGGTCTGTTGCGACTTCTCAAGCTTCATCCGGTTCTGG
351585 TTCTTTATCA
Statistics
Matches: 1190, Mismatches: 137, Indels: 89
0.84 0.10 0.06
Matches are distributed among these distances:
290 3 0.00
291 72 0.06
292 3 0.00
293 6 0.01
294 831 0.70
295 3 0.00
299 1 0.00
300 7 0.01
301 3 0.00
303 2 0.00
304 4 0.00
305 1 0.00
306 7 0.01
307 1 0.00
308 1 0.00
309 7 0.01
310 1 0.00
311 4 0.00
312 2 0.00
314 3 0.00
315 7 0.01
316 2 0.00
320 1 0.00
321 128 0.11
322 2 0.00
323 4 0.00
324 82 0.07
325 2 0.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (294 bp):
TCGCATTCAAGTTCAGCTTCTAGCTCATCTGCACATTCTAGTTCAGCTTCACATTCAAGCTCTTT
TAATCATTCTGGTTCTTTTAAAGGTTCTGGCGCTTCTGCAGATTCTAATGATTCTAAAGGTTCCG
GGTCTGTTGCGACTTCTCAAGCTTCATCCGGTTCTGGGACTTCTGGTTCCTCTACAAGTTCCGGT
TCTTCATCAACTTCTGGCAATTCTAAGGGTCCTGGAGAATCCTCACAATCCAATTCTGCAAATCA
AGGTGGTGTTGCGGGTCAAGGTTCTGCATCTTTC
Found at i:350843 original size:18 final size:18
Alignment explanation
Indices: 350820--350864 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
350810 CAAGTTCAGC
*
350820 TTCTAGCTCATCTGCACA
1 TTCTAGCTCAGCTGCACA
* *
350838 TTCTAGTTCAGCTTCACA
1 TTCTAGCTCAGCTGCACA
*
350856 TTCAAGCTC
1 TTCTAGCTC
350865 TTTTAATCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.36
Consensus pattern (18 bp):
TTCTAGCTCAGCTGCACA
Found at i:351134 original size:30 final size:30
Alignment explanation
Indices: 351100--351176 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
351090 ATCTTTCTCG
*
351100 CATTCAAGTTCAGCTTCTAGCTCATCTGCA
1 CATTCTAGTTCAGCTTCTAGCTCATCTGCA
*
351130 CATTCTAGTTCATCTTCTAGCTCATCTGCA
1 CATTCTAGTTCAGCTTCTAGCTCATCTGCA
351160 CATTCTAGTTCAGCTTC
1 CATTCTAGTTCAGCTTC
351177 ACATTCAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.38
Consensus pattern (30 bp):
CATTCTAGTTCAGCTTCTAGCTCATCTGCA
Found at i:351137 original size:18 final size:18
Alignment explanation
Indices: 351114--351182 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 18
351104 CAAGTTCAGC
351114 TTCTAGCTCATCTGCACA
1 TTCTAGCTCATCTGCACA
*
351132 TTCTAGTTCA--T---C-
1 TTCTAGCTCATCTGCACA
351144 TTCTAGCTCATCTGCACA
1 TTCTAGCTCATCTGCACA
* * *
351162 TTCTAGTTCAGCTTCACA
1 TTCTAGCTCATCTGCACA
351180 TTC
1 TTC
351183 AAACTCTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
12 9 0.22
13 1 0.03
14 1 0.03
16 1 0.03
17 1 0.03
18 27 0.68
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.39
Consensus pattern (18 bp):
TTCTAGCTCATCTGCACA
Found at i:351450 original size:18 final size:18
Alignment explanation
Indices: 351435--351473 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
351425 CAAGTTCAGC
*
351435 TTCTAGTTCATCTTCACA
1 TTCTAGTTCAGCTTCACA
351453 TTCTAGTTCAGCTTCACA
1 TTCTAGTTCAGCTTCACA
351471 TTC
1 TTC
351474 AAGCTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.28, G:0.08, T:0.44
Consensus pattern (18 bp):
TTCTAGTTCAGCTTCACA
Found at i:351783 original size:249 final size:249
Alignment explanation
Indices: 351349--351798 Score: 654
Period size: 249 Copynumber: 1.8 Consensus size: 249
351339 TTCAAAAGGT
* * * *
351349 TCTGGTGCATCCTCACAATCCAATTCTGTAAATCAAGGTGGTATTGCGGGTAATGGCTCTACATC
1 TCTGGTGAATCCTCACAATCCAATTCTGCAAATCAAGGTGGTATTGCGGATAATAGCTCTACATC
* *
351414 TTTCTCGCATTCAAGTTCAGCTTCTAGTTCATCTTCACATTCTAGTTCAGCTTCACATTCAAGCT
66 CTTCTCGCATTCAAGTTCAGCTTCTAGTTCATCGTCACATTCTAGTTCAGCTTCACATTCAAGCT
* * *
351479 CTTTTAATAATTTCGGTTCTTTTAAAGGCACCGGAACTTTTGTAGATTCTAATGATTCTAAAGGT
131 CTTTAAATAATTTCGGTTCTTTTAAAGGCACCGGAACTTTTGCAGATTATAATGATTCTAAAGGT
351544 TCTGGGTCTATTGCAACTTCTCAATCTTCATCCGGTTCTGGTTCTTTATCAGGA
196 TCTGGGTCTATTGCAACTTCTCAATCTTCATCCGGTTCTGGTTCTTTATCAGGA
* * *
351598 TCTGGTGAATCCTCACAATCCAATTCTGCAAATCAAGGTGGTGTTGCGGATCATAGCTCTGCATC
1 TCTGGTGAATCCTCACAATCCAATTCTGCAAATCAAGGTGGTATTGCGGATAATAGCTCTACATC
* * *
351663 CTTCTCTCATTCAAGTTCAGCTTCTAGCTT-ATCGTCACATTCTAGTTCAGCTTTACATTCCAGC
66 CTTCTCGCATTCAAGTTCAGCTTCTAG-TTCATCGTCACATTCTAGTTCAGCTTCACATTCAAGC
* ** * ** *
351727 TCTTTAAATCA-TTCTGGTTCTTTTAAAGGTTCTGGCTCTTCTT-CATATTATAATGATTCTAAA
130 TCTTTAAATAATTTC-GGTTCTTTTAAAGGCACCGGAACTT-TTGCAGATTATAATGATTCTAAA
351790 GGTTCTGGG
193 GGTTCTGGG
351799 GCTTTCGGTT
Statistics
Matches: 176, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
248 3 0.02
249 169 0.96
250 4 0.02
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (249 bp):
TCTGGTGAATCCTCACAATCCAATTCTGCAAATCAAGGTGGTATTGCGGATAATAGCTCTACATC
CTTCTCGCATTCAAGTTCAGCTTCTAGTTCATCGTCACATTCTAGTTCAGCTTCACATTCAAGCT
CTTTAAATAATTTCGGTTCTTTTAAAGGCACCGGAACTTTTGCAGATTATAATGATTCTAAAGGT
TCTGGGTCTATTGCAACTTCTCAATCTTCATCCGGTTCTGGTTCTTTATCAGGA
Found at i:352383 original size:267 final size:267
Alignment explanation
Indices: 352029--352511 Score: 657
Period size: 267 Copynumber: 1.8 Consensus size: 267
352019 GTTCTACCGA
* * * *
352029 GACTTTACAATCTTCATTAGGTTCTGGGGCTTCAAACTCCTCAACAAGTTCTGGTTCTTCATTAG
1 GACTTCACAATCTTCATTAGGTTCTGGAGCTTCAAACTCCTCAACAAGTTCTAGTTCTTCATCAG
* * * *
352094 GTTCTAGTGATTCCAAGGGTTCTGGATCATCCTCGCTTTCCAAATCTACAACTCAAGGTGGTGTT
66 ATTCTAGTGATTCCAAGGGTTCTGGATCATCCTCGCATTCCAAATCTACAACTCAAGGTAGTGCT
* * ** * *
352159 ACAAGTCATGGTTCTTCATCTTTCTCACATTCAAATTCAACTTCTGGATCATCCTTACATTCCAG
131 ACAAGTAATGGCTCTTCATCTTTCTCACATTCAAATTCAACCACTGGATCATCCTCACATACCAG
352224 TTC-TT-TCGCACATTCTGCTTCTTCTAAAGATTTTGGCTCTTCCGCAGATTCCAAGGATTCTGG
196 TTCATTCTCGCA-A-TCTGCTTCTTCTAAAGATTTTGGCTCTTCCGCAGATTCCAAGGATTCTGG
352287 TTCTACTAT
259 TTCTACTAT
* * ** *
352296 GACTTCACAATCTTTATTAGGTTCTGGAGCTTCAAATTCCTCTGCAAGTTCTAGTTCTTCGTCAG
1 GACTTCACAATCTTCATTAGGTTCTGGAGCTTCAAACTCCTCAACAAGTTCTAGTTCTTCATCAG
* * * ** * *
352361 ATTCTAGCT-ATTCCATGGGTTCTGGTTCATCCTTGCATTCCAGTTCTGCAACTCATGGTAGTGC
66 ATTCTAG-TGATTCCAAGGGTTCTGGATCATCCTCGCATTCCAAATCTACAACTCAAGGTAGTGC
* * *
352425 TACAAGTAATGGCTCTTCATCTTTTTCACATTCAAGTTCAGCCACTGGATCATCCTCACATACCA
130 TACAAGTAATGGCTCTTCATCTTTCTCACATTCAAATTCAACCACTGGATCATCCTCACATACCA
352490 GTTCATTCTCGCAATCTGCTTC
195 GTTCATTCTCGCAATCTGCTTC
352512 ATCTGAAGGT
Statistics
Matches: 184, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
267 175 0.95
268 4 0.02
269 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (267 bp):
GACTTCACAATCTTCATTAGGTTCTGGAGCTTCAAACTCCTCAACAAGTTCTAGTTCTTCATCAG
ATTCTAGTGATTCCAAGGGTTCTGGATCATCCTCGCATTCCAAATCTACAACTCAAGGTAGTGCT
ACAAGTAATGGCTCTTCATCTTTCTCACATTCAAATTCAACCACTGGATCATCCTCACATACCAG
TTCATTCTCGCAATCTGCTTCTTCTAAAGATTTTGGCTCTTCCGCAGATTCCAAGGATTCTGGTT
CTACTAT
Found at i:353673 original size:39 final size:39
Alignment explanation
Indices: 353632--353833 Score: 163
Period size: 39 Copynumber: 5.2 Consensus size: 39
353622 TTACATGACA
** * *
353632 GTTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCA
1 GTTCTTCTGCAACATCTAACCACTCTGCCGCACACACCG
* * *
353671 GTTCTTCTGCAACATCTAACCACTCTTCCGCAAACACTG
1 GTTCTTCTGCAACATCTAACCACTCTGCCGCACACACCG
* * * **
353710 GTTCTTTTGCGACATCTAACCACTCAGCCGCA-AGCATTG
1 GTTCTTCTGCAACATCTAACCACTCTGCCGCACA-CACCG
* * * * ** *
353749 GTTCTTCTGCAAAATCTACCCATTCCGCTACACACACTG
1 GTTCTTCTGCAACATCTAACCACTCTGCCGCACACACCG
* * ** * *
353788 GTTCTTTTGCAGCATCTAGTCACTTTGCCGCACAAACCG
1 GTTCTTCTGCAACATCTAACCACTCTGCCGCACACACCG
353827 GTTCTTC
1 GTTCTTC
353834 CACACACACC
Statistics
Matches: 127, Mismatches: 34, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
38 1 0.01
39 125 0.98
40 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.30
Consensus pattern (39 bp):
GTTCTTCTGCAACATCTAACCACTCTGCCGCACACACCG
Found at i:353697 original size:21 final size:21
Alignment explanation
Indices: 353634--353703 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
353624 ACATGACAGT
**
353634 TCTTCTGCAACATCTAGTCAC
1 TCTTCTGCAACATCTAACCAC
* *
353655 TCTGCTGC-ACA-C--ACCAGT
1 TCTTCTGCAACATCTAACCA-C
353673 TCTTCTGCAACATCTAACCAC
1 TCTTCTGCAACATCTAACCAC
*
353694 TCTTCCGCAA
1 TCTTCTGCAA
353704 ACACTGGTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
17 2 0.05
18 7 0.19
19 4 0.11
20 4 0.11
21 16 0.43
22 4 0.11
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (21 bp):
TCTTCTGCAACATCTAACCAC
Found at i:353714 original size:78 final size:78
Alignment explanation
Indices: 353632--353833 Score: 214
Period size: 78 Copynumber: 2.6 Consensus size: 78
353622 TTACATGACA
* * * * *
353632 GTTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAGTTCTTCTGCAACATCTAACCACTCT
1 GTTCTTTTGCAACATCTAGTCACTCTGCCGCACACACCGGTTCTTCTGCAAAATCT-ACC-C-AT
353697 TCCGC-A-A-ACACTG
63 TCCGCTACACACACTG
* ** * **
353710 GTTCTTTTGCGACATCTAACCACTCAGCCGCA-AGCATTGGTTCTTCTGCAAAATCTACCCATTC
1 GTTCTTTTGCAACATCTAGTCACTCTGCCGCACA-CACCGGTTCTTCTGCAAAATCTACCCATTC
353774 CGCTACACACACTG
65 CGCTACACACACTG
* * *
353788 GTTCTTTTGCAGCATCTAGTCACTTTGCCGCACAAACCGGTTCTTC
1 GTTCTTTTGCAACATCTAGTCACTCTGCCGCACACACCGGTTCTTC
353834 CACACACACC
Statistics
Matches: 99, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
75 6 0.06
76 2 0.02
77 5 0.05
78 85 0.86
79 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.30
Consensus pattern (78 bp):
GTTCTTTTGCAACATCTAGTCACTCTGCCGCACACACCGGTTCTTCTGCAAAATCTACCCATTCC
GCTACACACACTG
Found at i:353940 original size:78 final size:76
Alignment explanation
Indices: 353857--354073 Score: 199
Period size: 78 Copynumber: 2.8 Consensus size: 76
353847 TCTTCTACAT
* *
353857 CATCTAGCCATTCTGCATCACATGGCAGTTCTTTTGCAACATCTAGTCACTCTGCTGCACA-CAC
1 CATCTAGCCATTCTGCA-CACAT-GC-GTTCTTCTGCAACATCTAGTCACTCTGCAGCACAGCAC
353921 TAGTTCCTCTGCAA
63 TAGTTCCTCTGCAA
* * * * * *
353935 CATCTAGCCACTCTGCCGCACACA-CCGGTTCTTCTGCGACATCTAGCCACTCAGCCGCA-AGCA
1 CATCTAGCCA-T-T-CTGCACACATGC-GTTCTTCTGCAACATCTAGTCACTCTGCAGCACAGCA
* *
353998 CTGGTTCTTCTGCAA
62 CTAGTTCCTCTGCAA
* *
354013 AATCTAGCCATTCCGCTGCACACACTG-GTTCTTCTGCAACATCTAGTCACTTTGCAGCACA
1 CATCTAGCCATT---CTGCACACA-TGCGTTCTTCTGCAACATCTAGTCACTCTGCAGCACA
354074 AATTGGTTCT
Statistics
Matches: 112, Mismatches: 18, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
76 1 0.01
77 2 0.02
78 98 0.88
79 2 0.02
80 5 0.04
81 4 0.04
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.27
Consensus pattern (76 bp):
CATCTAGCCATTCTGCACACATGCGTTCTTCTGCAACATCTAGTCACTCTGCAGCACAGCACTAG
TTCCTCTGCAA
Found at i:353941 original size:18 final size:21
Alignment explanation
Indices: 353891--353950 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
353881 GCAGTTCTTT
353891 TGCAACATCTAGTCACTCTGC
1 TGCAACATCTAGTCACTCTGC
*
353912 TGCACACA-CTAGT-TC-CT-C
1 TGCA-ACATCTAGTCACTCTGC
*
353930 TGCAACATCTAGCCACTCTGC
1 TGCAACATCTAGTCACTCTGC
353951 CGCACACACC
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
17 3 0.10
18 9 0.29
19 3 0.10
20 3 0.10
21 10 0.32
22 3 0.10
ACGTcount: A:0.23, C:0.37, G:0.13, T:0.27
Consensus pattern (21 bp):
TGCAACATCTAGTCACTCTGC
Found at i:353988 original size:252 final size:252
Alignment explanation
Indices: 353542--354262 Score: 1093
Period size: 252 Copynumber: 2.9 Consensus size: 252
353532 CACACAAGTC
* * **
353542 CTGCAGCATCTAGTCACTTTGTCGCACAAACTGGTTCTACCACACATGCCGGATCTTCTACATCA
1 CTGCAGCATCTAGTCACTTTGCCGCACAAACTGGTTCTTCCACACACACCGGATCTTCTACATCA
* * *
353607 TCTAGTCATTCTGCATTACATGACAGTTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAG
66 TCTAGCCATTCTGCATCACATGGCAGTTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAG
* * * * * *
353672 TTCTTCTGCAACATCTAACCACTCTTCCGCAAACACTGGTTCTTTTGCGACATCTAACCACTCAG
131 TTCTTCTGCAACATCTAGCCACTCTGCCGCACACACCGGTTCTTCTGCGACATCTAGCCACTCAG
*
353737 CCGCAAGCATTGGTTCTTCTGCAAAATCTACCCATTCCGCTACACACACTGGTTCTT
196 CCGCAAGCACTGGTTCTTCTGCAAAATCTACCCATTCCGCTACACACACTGGTTCTT
* *
353794 TTGCAGCATCTAGTCACTTTGCCGCACAAACCGGTTCTTCCACACACACCGGATCTTCTACATCA
1 CTGCAGCATCTAGTCACTTTGCCGCACAAACTGGTTCTTCCACACACACCGGATCTTCTACATCA
* *
353859 TCTAGCCATTCTGCATCACATGGCAGTTCTTTTGCAACATCTAGTCACTCTGCTGCACACACTAG
66 TCTAGCCATTCTGCATCACATGGCAGTTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAG
*
353924 TTCCTCTGCAACATCTAGCCACTCTGCCGCACACACCGGTTCTTCTGCGACATCTAGCCACTCAG
131 TTCTTCTGCAACATCTAGCCACTCTGCCGCACACACCGGTTCTTCTGCGACATCTAGCCACTCAG
* *
353989 CCGCAAGCACTGGTTCTTCTGCAAAATCTAGCCATTCCGCTGCACACACTGGTTCTT
196 CCGCAAGCACTGGTTCTTCTGCAAAATCTACCCATTCCGCTACACACACTGGTTCTT
* * * *
354046 CTGCAACATCTAGTCACTTTGCAGCACAAATTGGTTCTTCCACACGCACCGGATCTTCTACATCA
1 CTGCAGCATCTAGTCACTTTGCCGCACAAACTGGTTCTTCCACACACACCGGATCTTCTACATCA
* * * * *
354111 TCTAGCCATTCTGCAGCACATAGTAGTTCTTCTGCAAGATCTAGTCACTCTGCTGCACACACCAA
66 TCTAGCCATTCTGCATCACATGGCAGTTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAG
* * * * * *
354176 TTCTTCTGTAACATCTAGTCATTCTGCTGCACACACCGGTTCTTCTGCAACATCTAGCCACTCTG
131 TTCTTCTGCAACATCTAGCCACTCTGCCGCACACACCGGTTCTTCTGCGACATCTAGCCACTCAG
*
354241 CCACACA-CACTGGTTCTTCTGC
196 CCGCA-AGCACTGGTTCTTCTGC
354263 GACATCTAGC
Statistics
Matches: 426, Mismatches: 42, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
252 425 1.00
253 1 0.00
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (252 bp):
CTGCAGCATCTAGTCACTTTGCCGCACAAACTGGTTCTTCCACACACACCGGATCTTCTACATCA
TCTAGCCATTCTGCATCACATGGCAGTTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAG
TTCTTCTGCAACATCTAGCCACTCTGCCGCACACACCGGTTCTTCTGCGACATCTAGCCACTCAG
CCGCAAGCACTGGTTCTTCTGCAAAATCTACCCATTCCGCTACACACACTGGTTCTT
Found at i:354081 original size:39 final size:39
Alignment explanation
Indices: 353884--354085 Score: 235
Period size: 39 Copynumber: 5.2 Consensus size: 39
353874 TCACATGGCA
* * * *
353884 GTTCTTTTGCAACATCTAGTCACTCTGCTGCACACACTA
1 GTTCTTCTGCAACATCTAGCCACTCTGCCGCACACACTG
* *
353923 GTTCCTCTGCAACATCTAGCCACTCTGCCGCACACACCG
1 GTTCTTCTGCAACATCTAGCCACTCTGCCGCACACACTG
* *
353962 GTTCTTCTGCGACATCTAGCCACTCAGCCGCA-AGCACTG
1 GTTCTTCTGCAACATCTAGCCACTCTGCCGCACA-CACTG
* * * *
354001 GTTCTTCTGCAAAATCTAGCCATTCCGCTGCACACACTG
1 GTTCTTCTGCAACATCTAGCCACTCTGCCGCACACACTG
* * * * *
354040 GTTCTTCTGCAACATCTAGTCACTTTGCAGCACAAATTG
1 GTTCTTCTGCAACATCTAGCCACTCTGCCGCACACACTG
354079 GTTCTTC
1 GTTCTTC
354086 CACACGCACC
Statistics
Matches: 138, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
38 1 0.01
39 136 0.99
40 1 0.01
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.29
Consensus pattern (39 bp):
GTTCTTCTGCAACATCTAGCCACTCTGCCGCACACACTG
Found at i:354153 original size:39 final size:39
Alignment explanation
Indices: 354099--354277 Score: 171
Period size: 39 Copynumber: 4.6 Consensus size: 39
354089 ACGCACCGGA
* * * * **
354099 TCTTCTACATCATCTAGCCATTCTGCAGCACATAGTAGT
1 TCTTCTGCAACATCTAGCCACTCTGCAGCACACACCAGT
* * * *
354138 TCTTCTGCAAGATCTAGTCACTCTGCTGCACACACCAAT
1 TCTTCTGCAACATCTAGCCACTCTGCAGCACACACCAGT
* * * * *
354177 TCTTCTGTAACATCTAGTCATTCTGCTGCACACACCGGT
1 TCTTCTGCAACATCTAGCCACTCTGCAGCACACACCAGT
**
354216 TCTTCTGCAACATCTAGCCACTCTGCCA-CACACACTGGT
1 TCTTCTGCAACATCTAGCCACTCTG-CAGCACACACCAGT
* *
354255 TCTTCTGCGACATCTAGCAACTC
1 TCTTCTGCAACATCTAGCCACTC
354278 AGCCGCAAGC
Statistics
Matches: 117, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 116 0.99
40 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.13, T:0.30
Consensus pattern (39 bp):
TCTTCTGCAACATCTAGCCACTCTGCAGCACACACCAGT
Found at i:354258 original size:78 final size:79
Alignment explanation
Indices: 354109--354376 Score: 231
Period size: 78 Copynumber: 3.4 Consensus size: 79
354099 TCTTCTACAT
* * * * * * *
354109 CATCTAG-CCATTCTGCAGCACATAGTAGTTCTTCTGCAAGATCTAGTCACTCTGCTGCACACAC
1 CATCTAGTCAATTCTGCTGCACACACTGGTTCTTCTGCAAAATCTAGCCACTCTGCTGCACACAC
***
354173 CAATTCTTCTGTAA
66 TGGTTCTTCTGTAA
* * **
354187 CATCTAGTC-ATTCTGCTGCACACACCGGTTCTTCTGCAACATCTAGCCACTCTGCCACACACAC
1 CATCTAGTCAATTCTGCTGCACACACTGGTTCTTCTGCAAAATCTAGCCACTCTGCTGCACACAC
**
354251 TGGTTCTTCTGCGA
66 TGGTTCTTCTGTAA
* * * * * * * **
354265 CATCTAG-CAACTCAGCCGCA-AGCATTGGTTCTTCTGCAAAAACTAGCCATTCTGTTGCACGTA
1 CATCTAGTCAATTCTGCTGCACA-CACTGGTTCTTCTGCAAAATCTAGCCACTCTGCTGCACACA
*
354328 CTGGCTCTTCTGTAA
65 CTGGTTCTTCTGTAA
** *
354343 CATCTAGTCGCTT-TGCTGCACAAACTGGTTCTTC
1 CATCTAGTCAATTCTGCTGCACACACTGGTTCTTC
354377 CACAAAGGAC
Statistics
Matches: 148, Mismatches: 37, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
77 2 0.01
78 142 0.96
79 4 0.03
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (79 bp):
CATCTAGTCAATTCTGCTGCACACACTGGTTCTTCTGCAAAATCTAGCCACTCTGCTGCACACAC
TGGTTCTTCTGTAA
Found at i:354263 original size:291 final size:291
Alignment explanation
Indices: 353885--354827 Score: 1001
Period size: 291 Copynumber: 3.2 Consensus size: 291
353875 CACATGGCAG
* * *
353885 TTCTTTTGCAACATCTAGTCACTCTGCTGCACACACTAGTTCCTCTGCAACATCTAGCCACTCTG
1 TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGTTCTTCTGCAACATCTAGCCACTCTG
*
353950 CCGCACACACCGGTTCTTCTGCGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTGCAAAA
66 CCGCACACACTGGTTCTTCTGCGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTGCAAAA
* *
354015 TCTAGCCATTCCGCTGCACACACTGGTTCTTCTGCAACATCTAGTCACTTTGCAGCACAAATTGG
131 TCTAGCCATTCCGCTGCACACACTGGCTCTTCTGCAACATCTAGTCACTTTGCAGCACAAACTGG
* * *
354080 TTCTTCCAC-ACGCACCGGATCTTCTACATCATCTAGCCATTCTGCAGCACATAGTAGTTCTTCT
196 TTCTTCCACAAAGCA-CGGATCTTCTACATCATCTAGCCATTCTGCAGCACACAGCAGTTCTTCT
* *
354144 GCAAGATCTAGTCACTCTGCTGCACACACCAA
260 GCAACATCTAGTCACACTGCTGCACACACCAA
* * *
354176 TTCTTCTGTAACATCTAGTCATTCTGCTGCACACACCGGTTCTTCTGCAACATCTAGCCACTCTG
1 TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGTTCTTCTGCAACATCTAGCCACTCTG
* * *
354241 CCACACACACTGGTTCTTCTGCGACATCTAGCAACTCAGCCGCAAGCATTGGTTCTTCTGCAAAA
66 CCGCACACACTGGTTCTTCTGCGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTGCAAAA
* * * ** * * *
354306 ACTAGCCATTCTGTTGCACGTACTGGCTCTTCTGTAACATCTAGTCGCTTTGCTGCACAAACTGG
131 TCTAGCCATTCCGCTGCACACACTGGCTCTTCTGCAACATCTAGTCACTTTGCAGCACAAACTGG
* * * *
354371 TTCTTCCACAAAGGACGGATCTTCTACATCATCTAGTCATTCTGCATCACACGGCAGTTCTTCTG
196 TTCTTCCACAAAGCACGGATCTTCTACATCATCTAGCCATTCTGCAGCACACAGCAGTTCTTCTG
*
354436 CAACATCTAGTCACACTGCTGCACACACCAG
261 CAACATCTAGTCACACTGCTGCACACACCAA
* * * * * *
354467 TTCTTCTGCAACATCTAGCCACTCTGCCGCACACACTGGTTCTTCAGCGACATCTAGTCACTCAG
1 TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGTTCTTCTGCAACATCTAGCCACTCTG
* * * * * *
354532 CCGCA-AGCATTGGTTCTTCTGCAAAATCTAGTCATTTC-GCTGCACA-CACTGGTTCTTCTGCA
66 CCGCACA-CACTGGTTCTTCTGCGACATCTAGCCA-CTCAGCCGCA-AGCACTGGTTCTTCTGCA
* * * * * * * *
354594 ACATCTAGTCACTT-TGCCGCACAAACTGG-T-TT-TTCCACA-C-ACGTCGGATCTTCTGCATC
128 AAATCTAGCCA-TTCCGCTGCACACACTGGCTCTTCTGCAACATCTA-GTC--A-CTT-TGCAGC
* * ** * * * * * * * ** * * * *
354653 ATCTAGC-CATTCTGCAACACA-CGACAGTTCTTCTGCAACATCTAGTAACTCTGCTGTACACAC
187 A-CAAACTGGTTCTTCCACAAAGC-ACGGATCTTCTACATCATCTAGCCATTCTGCAGCACACAG
* ** *
354716 CAATTCTTCTGCAACATCTAGTCATTCTGCTGCACACACCAG
250 CAGTTCTTCTGCAACATCTAGTCACACTGCTGCACACACCAA
* * * * * *
354758 TTCTTCTGCGACATCTAGCCACTCTGCCGCACACACTGGTTCTTCTGCGACATCTAGTCACTCAG
1 TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGTTCTTCTGCAACATCTAGCCACTCTG
354823 CCGCA
66 CCGCA
354828 AGTATTGGTT
Statistics
Matches: 555, Mismatches: 85, Indels: 24
0.84 0.13 0.04
Matches are distributed among these distances:
286 1 0.00
287 4 0.01
288 4 0.01
289 2 0.00
290 5 0.01
291 528 0.95
292 11 0.02
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (291 bp):
TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGTTCTTCTGCAACATCTAGCCACTCTG
CCGCACACACTGGTTCTTCTGCGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTGCAAAA
TCTAGCCATTCCGCTGCACACACTGGCTCTTCTGCAACATCTAGTCACTTTGCAGCACAAACTGG
TTCTTCCACAAAGCACGGATCTTCTACATCATCTAGCCATTCTGCAGCACACAGCAGTTCTTCTG
CAACATCTAGTCACACTGCTGCACACACCAA
Found at i:354294 original size:213 final size:213
Alignment explanation
Indices: 353896--354298 Score: 506
Period size: 213 Copynumber: 1.9 Consensus size: 213
353886 TCTTTTGCAA
* *
353896 CATCTAGTCACTCTGCTGCACACACTAGTTCCTCTGCAACATCTAGCCACTCTGCCGCACACACC
1 CATCTAGCCACTCTGCAGCACACACTAGTTCCTCTGCAACATCTAGCCACTCTGCCGCACACACC
** * * *
353961 GGTTCTTCTGCGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTGCAAAATCTAGCCATTC
66 AATTCTTCTGCAACATCTAGCCACTCAGCCGCAAGCACCGGTTCTTCTGCAAAATCTAGCCACTC
** **
354026 CGCTGCACACACTGGTTCTTCTGCAACATCTAGTCACTTTGCAGCACAAATTGGTTCTTCCACAC
131 CGCCACACACACTGGTTCTTCTGCAACATCTAGTCACTCAGCAGCACAAATTGGTTCTTCCACAC
354091 GCACCGGATCTTCTACAT
196 GCACCGGATCTTCTACAT
* * * * * * *
354109 CATCTAGCCATTCTGCAGCACATAGTAGTTCTTCTGCAAGATCTAGTCACTCTGCTGCACACACC
1 CATCTAGCCACTCTGCAGCACACACTAGTTCCTCTGCAACATCTAGCCACTCTGCCGCACACACC
* * * * * *
354174 AATTCTTCTGTAACATCTAGTCATTCTGCTGCACA-CACCGGTTCTTCTGCAACATCTAGCCACT
66 AATTCTTCTGCAACATCTAGCCACTCAGCCGCA-AGCACCGGTTCTTCTGCAAAATCTAGCCACT
* * * *
354238 CTGCCACACACACTGGTTCTTCTGCGACATCTAG-CAACTCAGCCGCA-AGCATTGGTTCTTC
130 CCGCCACACACACTGGTTCTTCTGCAACATCTAGTC-ACTCAGCAGCACA-AATTGGTTCTTC
354299 TGCAAAAACT
Statistics
Matches: 159, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
212 2 0.01
213 156 0.98
214 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (213 bp):
CATCTAGCCACTCTGCAGCACACACTAGTTCCTCTGCAACATCTAGCCACTCTGCCGCACACACC
AATTCTTCTGCAACATCTAGCCACTCAGCCGCAAGCACCGGTTCTTCTGCAAAATCTAGCCACTC
CGCCACACACACTGGTTCTTCTGCAACATCTAGTCACTCAGCAGCACAAATTGGTTCTTCCACAC
GCACCGGATCTTCTACAT
Found at i:354311 original size:39 final size:39
Alignment explanation
Indices: 354205--354303 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
354195 CATTCTGCTG
* * *
354205 CACACACCGGTTCTTCTGCAACATCTAGCCACTCTGCCA
1 CACACACTGGTTCTTCTGCAACATCTAGCAACTCAGCCA
* *
354244 CACACACTGGTTCTTCTGCGACATCTAGCAACTCAGCCG
1 CACACACTGGTTCTTCTGCAACATCTAGCAACTCAGCCA
*
354283 CA-AGCATTGGTTCTTCTGCAA
1 CACA-CACTGGTTCTTCTGCAA
354304 AAACTAGCCA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
38 1 0.02
39 51 0.98
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.25
Consensus pattern (39 bp):
CACACACTGGTTCTTCTGCAACATCTAGCAACTCAGCCA
Found at i:354444 original size:39 final size:37
Alignment explanation
Indices: 354390--354616 Score: 147
Period size: 39 Copynumber: 5.9 Consensus size: 37
354380 AAAGGACGGA
* * * *
354390 TCTTCTACATCATCTAGTCATTCTGCATCACACGGCAGT
1 TCTTCTGCAACATCTAGTCACTCTGC--CACACAGCAGT
* *
354429 TCTTCTGCAACATCTAGTCACACTGCTGCACACACCAGT
1 TCTTCTGCAACATCTAGTCACTCTGC--CACACAGCAGT
* *
354468 TCTTCTGCAACATCTAGCCACTCTGCCGCACACA-CTGGT
1 TCTTCTGCAACATCTAGTCACTCTG-C-CACACAGC-AGT
* * * *
354507 TCTTCAGCGACATCTAGTCACTCAGCCGCA-AGCATTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCCACACAGCA---GT
* * *
354546 TCTTCTGCAAAATCTAGTCA-TTTCGCTGCACACA-CTGGT
1 TCTTCTGCAACATCTAGTCACTCT-GC--CACACAGC-AGT
* *
354585 TCTTCTGCAACATCTAGTCACTTTGCCGCACA
1 TCTTCTGCAACATCTAGTCACTCTGCCACACA
354617 AACTGGTTTT
Statistics
Matches: 150, Mismatches: 26, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
36 1 0.01
37 9 0.06
38 3 0.02
39 128 0.85
40 4 0.03
41 4 0.03
42 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (37 bp):
TCTTCTGCAACATCTAGTCACTCTGCCACACAGCAGT
Found at i:354484 original size:78 final size:75
Alignment explanation
Indices: 354390--354605 Score: 186
Period size: 78 Copynumber: 2.8 Consensus size: 75
354380 AAAGGACGGA
* * *
354390 TCTTCTACATCATCTAGTCATTCTGCATCACACGGCAGTTCTTCTGCAACATCTAGTCACACTGC
1 TCTTCTGCAACATCTAGTCATTCTGCA-CACAC-GC-GTTCTTCTGCAACATCTAGTCACACAGC
*
354455 TGCACA-CACCAGT
63 CGCA-AGCACCAGT
* * * * *
354468 TCTTCTGCAACATCTAGCCACTCTGCCGCACACACTG-GTTCTTCAGCGACATCTAGTCACTCAG
1 TCTTCTGCAACATCTAGTCA-T-T-CTGCACACAC-GCGTTCTTCTGCAACATCTAGTCACACAG
***
354532 CCGCAAGCATTGGT
62 CCGCAAGCACCAGT
*
354546 TCTTCTGCAAAATCTAGTCATTTCGCTGCACACACTG-GTTCTTCTGCAACATCTAGTCAC
1 TCTTCTGCAACATCTAGTCA-TT--CTGCACACAC-GCGTTCTTCTGCAACATCTAGTCAC
354606 TTTGCCGCAC
Statistics
Matches: 114, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
77 2 0.02
78 100 0.88
79 1 0.01
80 7 0.06
81 4 0.04
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (75 bp):
TCTTCTGCAACATCTAGTCATTCTGCACACACGCGTTCTTCTGCAACATCTAGTCACACAGCCGC
AAGCACCAGT
Found at i:354622 original size:39 final size:39
Alignment explanation
Indices: 354427--354624 Score: 238
Period size: 39 Copynumber: 5.1 Consensus size: 39
354417 TCACACGGCA
* * **
354427 GTTCTTCTGCAACATCTAGTCACACTGCTGCACACACCA
1 GTTCTTCTGCAACATCTAGTCACTCTGCCGCACACACTG
*
354466 GTTCTTCTGCAACATCTAGCCACTCTGCCGCACACACTG
1 GTTCTTCTGCAACATCTAGTCACTCTGCCGCACACACTG
* * * *
354505 GTTCTTCAGCGACATCTAGTCACTCAGCCGCA-AGCATTG
1 GTTCTTCTGCAACATCTAGTCACTCTGCCGCACA-CACTG
* * *
354544 GTTCTTCTGCAAAATCTAGTCA-TTTCGCTGCACACACTG
1 GTTCTTCTGCAACATCTAGTCACTCT-GCCGCACACACTG
* *
354583 GTTCTTCTGCAACATCTAGTCACTTTGCCGCACAAACTG
1 GTTCTTCTGCAACATCTAGTCACTCTGCCGCACACACTG
354622 GTT
1 GTT
354625 TTTCCACACA
Statistics
Matches: 135, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
38 2 0.01
39 129 0.96
40 4 0.03
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (39 bp):
GTTCTTCTGCAACATCTAGTCACTCTGCCGCACACACTG
Found at i:354648 original size:174 final size:174
Alignment explanation
Indices: 354468--354798 Score: 416
Period size: 174 Copynumber: 1.9 Consensus size: 174
354458 ACACACCAGT
** * * *
354468 TCTTCTGCAACATCTAGCCACTCTGCCGCACAC-ACTGGTTCTTCAGCGACATCTAGTCACTCAG
1 TCTTCTGCAACATCTAGCCACTCTGCAACACACGAC-AGTTCTTCAGCAACATCTAGTAACTCAG
**** **
354532 CCGCA-AGCATTGGTTCTTCTGCAAAATCTAGTCATT-TCGCTGCACACACTGGTTCTTCTGCAA
65 CCGCACA-CACCAATTCTTCTGCAAAATCTAGTCATTCT-GCTGCACACACCAGTTCTTCTGCAA
* *
354595 CATCTAGTCACTTTGCCGCACAAACTGGTTTTTCCACACACGTCGGA
128 CATCTAGCCACTCTGCCGCACAAACTGGTTTTTCCACACACGTCGGA
* * * *
354642 TCTTCTGCATCATCTAGCCATTCTGCAACACACGACAGTTCTTCTGCAACATCTAGTAACTCTGC
1 TCTTCTGCAACATCTAGCCACTCTGCAACACACGACAGTTCTTCAGCAACATCTAGTAACTCAGC
* * * *
354707 TGTACACACCAATTCTTCTGCAACATCTAGTCATTCTGCTGCACACACCAGTTCTTCTGCGACAT
66 CGCACACACCAATTCTTCTGCAAAATCTAGTCATTCTGCTGCACACACCAGTTCTTCTGCAACAT
*
354772 CTAGCCACTCTGCCGCACACACTGGTT
131 CTAGCCACTCTGCCGCACAAACTGGTT
354799 CTTCTGCGAC
Statistics
Matches: 132, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
174 128 0.97
175 4 0.03
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (174 bp):
TCTTCTGCAACATCTAGCCACTCTGCAACACACGACAGTTCTTCAGCAACATCTAGTAACTCAGC
CGCACACACCAATTCTTCTGCAAAATCTAGTCATTCTGCTGCACACACCAGTTCTTCTGCAACAT
CTAGCCACTCTGCCGCACAAACTGGTTTTTCCACACACGTCGGA
Found at i:354826 original size:39 final size:39
Alignment explanation
Indices: 354642--355662 Score: 271
Period size: 39 Copynumber: 26.4 Consensus size: 39
354632 ACACGTCGGA
* * * ** *
354642 TCTTCTGCATCATCTAGCCATTCTGCAACACACGAC-AGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACAC-ACTGGT
* * ***
354681 TCTTCTGCAACATCTAGTAACTCTGCTGTACACACCAAT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
* **
354720 TCTTCTGCAACATCTAGTCATTCTGCTGCACACACCAGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
* * *
354759 TCTTCTGCGACATCTAGCCACTCTGCCGCACACACTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
* * * * *
354798 TCTTCTGCGACATCTAGTCACTCAGCCGCA-AGTATTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACA-CACTGGT
* * * * * *
354837 TCTTATGCAAAATCTAGTCATTCCGTTGCACGCACTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
* * * * * * ** * *
354876 TCTTCCGCAGCATATGGTCAATTTGCCACACAAAATGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
* * * *
354915 TCTTC--C-ACA-C-ACGCCAGATCTTCT--ACATCATCTAG-
1 TCTTCTGCAACATCTA-GTCA-CTCTGCTGCACA-CA-CTGGT
* * *
354950 CCATTCTGCATCACA-CGGTAGT---TCTTCTGCA-ACATCTAG-
1 TC-TTCTGCA--ACATC--TAGTCACTCTGCTGCACACA-CTGGT
* * * * *
354989 TCACTCTGCTACA-C-ACGCTAATTCTTCTG----C--TGGT
1 TC-TTCTGCAACATCTA-G-TCACTCTGCTGCACACACTGGT
* * * * *
355023 TCTTC-GACGACATCTAGCCACTCAGCCGCA-AGCATTGGT
1 TCTTCTG-CAACATCTAGTCACTCTGCTGCACA-CACTGGT
** * ** * *
355062 TCTTCTATAAAATCTAACCACTCCGCTGCACGCACTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
* *** * **
355101 TCATCTATGACATCTAGTCATTCAACTGCA-AGCACTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACA-CACTGGT
*** * * *
355140 TCTTCTATGACATCTAGCCACTCTGCCGCACATACTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
* * ** * * *
355179 TTTTTTGCGGCATCTAGCCACTCTGCCGCA-ACCACAGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACA-CACTGGT
* * *
355218 TCTTCTGCGACATCTAGCCACTCTGGCT-CACACACTAGT
1 TCTTCTGCAACATCTAGTCACTCT-GCTGCACACACTGGT
*** * * * *
355257 TCTTCTGTGGCATCCAGTCACTCCGCCGCACGCACTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
* * * *
355296 TCTTCTGTAACATCTAGCCACTCTAGC-GCACATATTGGT
1 TCTTCTGCAACATCTAGTCACTCT-GCTGCACACACTGGT
** * * *
355335 TCTTCTGCAATGTCTAGTCACCCT-ATCGCACACACTGAT
1 TCTTCTGCAACATCTAGTCACTCTGCT-GCACACACTGGT
* * * * * * *
355374 TCTTCTACGACATCTAGCCAATCTGCCT-TACGCACAGGT
1 TCTTCTGCAACATCTAGTCACTCTG-CTGCACACACTGGT
*** * *
355413 TCTTCTGCGGTATCTAG-CTACTCTGCTGCACGCACTGAT
1 TCTTCTGCAACATCTAGTC-ACTCTGCTGCACACACTGGT
* * * * * *
355452 TCTTTTGTGAA-ACCTAGTCACTCTGCTACACATATTGGT
1 TCTTCTG-CAACATCTAGTCACTCTGCTGCACACACTGGT
* * * ** *
355491 TCTTCTGCGACATCTAGCCA-TTTAGCCACAAACACTGGT
1 TCTTCTGCAACATCTAGTCACTCT-GCTGCACACACTGGT
* * * *
355530 TCTTCTACAACATCTAGCCACTCTGGC-GCAAACACTAGT
1 TCTTCTGCAACATCTAGTCACTCT-GCTGCACACACTGGT
* * *
355569 TCTTCTGCAGCATCTAGCCACTCTG-TCGCACACACTAGT
1 TCTTCTGCAACATCTAGTCACTCTGCT-GCACACACTGGT
**** * * *
355608 TCTTCTATGGCATCTAGTCATTCCGCTGCACGCACTGGT
1 TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
*
355647 TCTTCTGCGACATCTA
1 TCTTCTGCAACATCTA
355663 ACCTCTCTAT
Statistics
Matches: 733, Mismatches: 193, Indels: 112
0.71 0.19 0.11
Matches are distributed among these distances:
32 1 0.00
33 13 0.02
34 8 0.01
35 7 0.01
36 13 0.02
37 6 0.01
38 14 0.02
39 650 0.89
40 13 0.02
41 6 0.01
43 1 0.00
44 1 0.00
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (39 bp):
TCTTCTGCAACATCTAGTCACTCTGCTGCACACACTGGT
Found at i:354828 original size:291 final size:291
Alignment explanation
Indices: 354428--355018 Score: 934
Period size: 291 Copynumber: 2.0 Consensus size: 291
354418 CACACGGCAG
354428 TTCTTCTGCAACATCTAGTCACACTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
1 TTCTTCTGCAACATCTAGTCACACTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
*
354493 CCGCACACACTGGTTCTTCAGCGACATCTAGTCACTCAGCCGCAAGCATTGGTTCTTCTGCAAAA
66 CCGCACACACTGGTTCTTCAGCGACATCTAGTCACTCAGCCGCAAGCATTGGTTCTTATGCAAAA
* * * * * *
354558 TCTAGTCATTTCGCTGCACACACTGGTTCTTCTGCAACATCTAGTCACTTTGCCGCACAAACTGG
131 TCTAGTCATTCCGCTGCACACACTGGTTCTTCCGCAACATATAGTCAATTTGCCACACAAAATGG
* * * *
354623 TTTTTCCACACACGTCGGATCTTCTGCATCATCTAGCCATTCTGCAACACACGACAGTTCTTCTG
196 TTCTTCCACACACGCCAGATCTTCTACATCATCTAGCCATTCTGCAACACACGACAGTTCTTCTG
354688 CAACATCTAGTAACTCTGCTGTACACAC-C-AA
261 CAACATCTAGTAACTCTGC--TACACACGCTAA
** *
354719 TTCTTCTGCAACATCTAGTCATTCTGCTGCACACACCAGTTCTTCTGCGACATCTAGCCACTCTG
1 TTCTTCTGCAACATCTAGTCACACTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
* *
354784 CCGCACACACTGGTTCTTCTGCGACATCTAGTCACTCAGCCGCAAGTATTGGTTCTTATGCAAAA
66 CCGCACACACTGGTTCTTCAGCGACATCTAGTCACTCAGCCGCAAGCATTGGTTCTTATGCAAAA
* * * *
354849 TCTAGTCATTCCGTTGCACGCACTGGTTCTTCCGCAGCATATGGTCAATTTGCCACACAAAATGG
131 TCTAGTCATTCCGCTGCACACACTGGTTCTTCCGCAACATATAGTCAATTTGCCACACAAAATGG
* **
354914 TTCTTCCACACACGCCAGATCTTCTACATCATCTAGCCATTCTGCATCACACGGTAGTTCTTCTG
196 TTCTTCCACACACGCCAGATCTTCTACATCATCTAGCCATTCTGCAACACACGACAGTTCTTCTG
*
354979 CAACATCTAGTCACTCTGCTACACACGCTAA
261 CAACATCTAGTAACTCTGCTACACACGCTAA
355010 TTCTTCTGC
1 TTCTTCTGC
355019 TGGTTCTTCG
Statistics
Matches: 274, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
289 7 0.03
290 1 0.00
291 266 0.97
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.29
Consensus pattern (291 bp):
TTCTTCTGCAACATCTAGTCACACTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
CCGCACACACTGGTTCTTCAGCGACATCTAGTCACTCAGCCGCAAGCATTGGTTCTTATGCAAAA
TCTAGTCATTCCGCTGCACACACTGGTTCTTCCGCAACATATAGTCAATTTGCCACACAAAATGG
TTCTTCCACACACGCCAGATCTTCTACATCATCTAGCCATTCTGCAACACACGACAGTTCTTCTG
CAACATCTAGTAACTCTGCTACACACGCTAA
Found at i:354839 original size:252 final size:251
Alignment explanation
Indices: 354176--354856 Score: 925
Period size: 252 Copynumber: 2.7 Consensus size: 251
354166 CACACACCAA
* * *
354176 TTCTTCTGTAACATCTAGTCATTCTGCTGCACACACCGGTTCTTCTGCAACATCTAGCCACTCTG
1 TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
* *
354241 CCACACACACTGGTTCTTCTGCGACATCTAGCAACTCAGCCGCAAGCATTGGTTCTTCTGCAAAA
66 CCGCACACACTGGTTCTTCTGCGACATCTAGCCACTCAGCCGCAAGCATTGGTTCTTCTGCAAAA
* * * * * * * *
354306 ACTAGCCATTCTGTTGCACGTACTGGCTCTTCTGTAACATCTAGTCGCTTTGCTGCACAAACTGG
131 TCTAGTCATTC-GCTGCAAGTACTGGTTCTTCTGCAACATCTAGTCACTTTGCCGCACAAACTGG
* * * *
354371 TTCTTCCACAAAGGACGGATCTTCTACATCATCTAGTCATTCTGCATCACACGGCAG
195 TTCTTCCACAAACGACGGATCTTCTACATCATCTAGCCATTCTGCAACACACGACAG
*
354428 TTCTTCTGCAACATCTAGTCACACTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
1 TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
* *
354493 CCGCACACACTGGTTCTTCAGCGACATCTAGTCACTCAGCCGCAAGCATTGGTTCTTCTGCAAAA
66 CCGCACACACTGGTTCTTCTGCGACATCTAGCCACTCAGCCGCAAGCATTGGTTCTTCTGCAAAA
*
354558 TCTAGTCATTTCGCTGCACA-CACTGGTTCTTCTGCAACATCTAGTCACTTTGCCGCACAAACTG
131 TCTAGTCA-TTCGCTGCA-AGTACTGGTTCTTCTGCAACATCTAGTCACTTTGCCGCACAAACTG
* * * *
354622 GTTTTTCCACACACGTCGGATCTTCTGCATCATCTAGCCATTCTGCAACACACGACAG
194 GTTCTTCCACAAACGACGGATCTTCTACATCATCTAGCCATTCTGCAACACACGACAG
* * * * *
354680 TTCTTCTGCAACATCTAGTAACTCTGCTGTACACACCAATTCTTCTGCAACATCTAGTCATTCTG
1 TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
* ** * * * *
354745 CTGCACACACCAGTTCTTCTGCGACATCTAGCCACTCTGCCGCACA-CACTGGTTCTTCTGCGAC
66 CCGCACACACTGGTTCTTCTGCGACATCTAGCCACTCAGCCGCA-AGCATTGGTTCTTCTGCAAA
* * * * *
354809 ATCTAGTCACTCAGCCGCAAGTATTGGTTCTTATGCAAAATCTAGTCA
130 ATCTAGTCATTC-GCTGCAAGTACTGGTTCTTCTGCAACATCTAGTCA
354857 TTCCGTTGCA
Statistics
Matches: 378, Mismatches: 46, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
251 3 0.01
252 371 0.98
253 4 0.01
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (251 bp):
TTCTTCTGCAACATCTAGTCACTCTGCTGCACACACCAGTTCTTCTGCAACATCTAGCCACTCTG
CCGCACACACTGGTTCTTCTGCGACATCTAGCCACTCAGCCGCAAGCATTGGTTCTTCTGCAAAA
TCTAGTCATTCGCTGCAAGTACTGGTTCTTCTGCAACATCTAGTCACTTTGCCGCACAAACTGGT
TCTTCCACAAACGACGGATCTTCTACATCATCTAGCCATTCTGCAACACACGACAG
Found at i:355177 original size:78 final size:78
Alignment explanation
Indices: 355018--355662 Score: 386
Period size: 78 Copynumber: 8.3 Consensus size: 78
355008 AATTCTTCTG
* * * *
355018 CTGGTTCTTC-GACGACATCTAGCCACTCAGCCGCAAGCATTGGTTCTTCTATAAAATCTAACCA
1 CTGGTTCTTCTG-TGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTATAACATCTAGCCA
* * *
355082 CTCCGCTGCACGCA
65 CTCTGCCGCACACA
* * * * * * *
355096 CTGGTTCATCTATGACATCTAGTCATTCAACTGCAAGCACTGGTTCTTCTATGACATCTAGCCAC
1 CTGGTTCTTCTGTGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTATAACATCTAGCCAC
*
355161 TCTGCCGCACATA
66 TCTGCCGCACACA
* * * * * * * ***
355174 CTGGTTTTTTTGCGGCATCTAGCCACTCTGCCGCAACCACAGGTTCTTCTGCGACATCTAGCCAC
1 CTGGTTCTTCTGTGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTATAACATCTAGCCAC
* *
355239 TCTGGCTCACACA
66 TCTGCCGCACACA
* * * * * * *
355252 CTAGTTCTTCTGTGGCATCCAGTCACTCCGCCGCACGCACTGGTTCTTCTGTAACATCTAGCCAC
1 CTGGTTCTTCTGTGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTATAACATCTAGCCAC
*
355317 TCTAG-CGCACATA
66 TCT-GCCGCACACA
* ** ** * * * * **
355330 TTGGTTCTTCTGCAATGTCTAGTCACCCTA-TCGCACA-CACTGATTCTTCTACGACATCTAGCC
1 CTGGTTCTTCTGTGACATCTAGCCACTC-AGCCGCA-AGCACTGGTTCTTCTATAACATCTAGCC
* ** *
355393 AATCTGCCTTACGCA
64 ACTCTGCCGCACACA
* * ** * * * * * * * * *
355408 CAGGTTCTTCTGCGGTATCTAGCTACTCTGCTGCACGCACTGATTCTTTTGTGAA-ACCTAGTCA
1 CTGGTTCTTCTGTGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTAT-AACATCTAGCCA
** *
355472 CTCTGCTACACATA
65 CTCTGCCGCACACA
* * * * * * *
355486 TTGGTTCTTCTGCGACATCTAGCCATTTAGCCACAAACACTGGTTCTTCTACAACATCTAGCCAC
1 CTGGTTCTTCTGTGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTATAACATCTAGCCAC
* *
355551 TCTGGCGCAAACA
66 TCTGCCGCACACA
* * * * * ** *
355564 CTAGTTCTTCTG-CAGCATCTAGCCACTCTGTCGCACA-CACTAGTTCTTCTATGGCATCTAGTC
1 CTGGTTCTTCTGTGA-CATCTAGCCACTCAGCCGCA-AGCACTGGTTCTTCTATAACATCTAGCC
* * * *
355627 ATTCCGCTGCACGCA
64 ACTCTGCCGCACACA
*
355642 CTGGTTCTTCTGCGACATCTA
1 CTGGTTCTTCTGTGACATCTA
355663 ACCTCTCTAT
Statistics
Matches: 419, Mismatches: 136, Indels: 24
0.72 0.23 0.04
Matches are distributed among these distances:
77 4 0.01
78 411 0.98
79 4 0.01
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (78 bp):
CTGGTTCTTCTGTGACATCTAGCCACTCAGCCGCAAGCACTGGTTCTTCTATAACATCTAGCCAC
TCTGCCGCACACA
Found at i:355259 original size:117 final size:116
Alignment explanation
Indices: 355021--355662 Score: 377
Period size: 117 Copynumber: 5.5 Consensus size: 116
355011 TCTTCTGCTG
* * * * ** * *
355021 GTTCTTCGACGACATCTAGCCACTCAGCCGCA-AGCATTGGTTCTTCTATAAAATCTAACCACTC
1 GTTCTTCTATGACATCTAGCCACTCTGCCGCACA-CACTGGTTCTTCTGCAACATCTAGCCACTC
* * * * ** * * ** *
355085 CGCTGCACGCACTGGTTCATCTATGACATCTAGTCATTC-AACTGCA-AGCACTG
65 TGCCGCAC-CACAGGTTCTTCTGCGACATCTAGCCACTCTGGC-GCACA-CACTA
* * * **
355138 GTTCTTCTATGACATCTAGCCACTCTGCCGCACATACTGGTTTTTTTGCGGCATCTAGCCACTCT
1 GTTCTTCTATGACATCTAGCCACTCTGCCGCACACACTGGTTCTTCTGCAACATCTAGCCACTCT
*
355203 GCCGCAACCACAGGTTCTTCTGCGACATCTAGCCACTCTGGCTCACACACTA
66 GCCGC-ACCACAGGTTCTTCTGCGACATCTAGCCACTCTGGCGCACACACTA
* * * * * * *
355255 GTTCTTCTGTGGCATCCAGTCACTCCGCCGCACGCACTGGTTCTTCTGTAACATCTAGCCACTCT
1 GTTCTTCTATGACATCTAGCCACTCTGCCGCACACACTGGTTCTTCTGCAACATCTAGCCACTCT
* * ** * * **
355320 AG-CGCA-CATATTGGTTCTTCTGCAATGTCTAGTCACCCTATCGCACACACT-
66 -GCCGCACCACA--GGTTCTTCTGCGACATCTAGCCACTCTGGCGCACACACTA
* * ** * * *** *
355371 GATTCTTCTACGACATCTAGCCAATCTGCCTTACGCACAGGTTCTTCTGCGGTATCTAGCTACTC
1 G-TTCTTCTATGACATCTAGCCACTCTGCCGCACACACTGGTTCTTCTGCAACATCTAGCCACTC
* * * * * * * * * * * *
355436 TGCTGCACGCACTGATTCTTTTGTGAAACCTAGTCACTCT-GCTACACATATTG
65 TGCCGCAC-CACAGGTTCTTCTGCGACATCTAGCCACTCTGGC-GCACACACTA
** * * * *
355489 GTTCTTCTGCGACATCTAGCCA-TTTAGCCACAAACACTGGTTCTTCTACAACATCTAGCCACTC
1 GTTCTTCTATGACATCTAGCCACTCT-GCCGCACACACTGGTTCTTCTGCAACATCTAGCCACTC
* * *
355553 TGGCGCAAACACTA-GTTCTTCTGC-AGCATCTAGCCACTCTGTCGCACACACTA
65 TGCCGC-ACCAC-AGGTTCTTCTGCGA-CATCTAGCCACTCTGGCGCACACACTA
* * * * * * *
355606 GTTCTTCTATGGCATCTAGTCATTCCGCTGCACGCACTGGTTCTTCTGCGACATCTA
1 GTTCTTCTATGACATCTAGCCACTCTGCCGCACACACTGGTTCTTCTGCAACATCTA
355663 ACCTCTCTAT
Statistics
Matches: 391, Mismatches: 115, Indels: 38
0.72 0.21 0.07
Matches are distributed among these distances:
115 3 0.01
116 7 0.02
117 369 0.94
118 10 0.03
119 2 0.01
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (116 bp):
GTTCTTCTATGACATCTAGCCACTCTGCCGCACACACTGGTTCTTCTGCAACATCTAGCCACTCT
GCCGCACCACAGGTTCTTCTGCGACATCTAGCCACTCTGGCGCACACACTA
Found at i:355625 original size:156 final size:156
Alignment explanation
Indices: 355018--355671 Score: 534
Period size: 156 Copynumber: 4.2 Consensus size: 156
355008 AATTCTTCTG
* * * ** * *
355018 CTGGTTCTTC-GACGACATCTAGCCACTC-AGCCGCAAGCATTGGTTCTTCTATAAAATCTAACC
1 CTGGTTCTTCTG-CGACATCTAGCCACTCTAGCCACAAACACTGGTTCTTCTACGACATCTAGCC
* * * * ** * * * ** *
355081 ACTC-CGCTGCACGCACTGGTTCATCTATGACATCTAGTCATTCAACTGCAAGCACTGGTTCTTC
65 ACTCTGGCT-CACACACTAGTTCTTCTGCGGCATCTAGCCACTCTGC-GCACGCACTGGTTCTTC
*
355145 TATGACATCTAGCCACTCTGCCGCACATA
128 TATGACATCTAGCCACTCTGCTGCACATA
* * * * * * *
355174 CTGGTTTTTTTGCGGCATCTAGCCACTCT-GCCGCAACCACAGGTTCTTCTGCGACATCTAGCCA
1 CTGGTTCTTCTGCGACATCTAGCCACTCTAGCCACAAACACTGGTTCTTCTACGACATCTAGCCA
* * * * *
355238 CTCTGGCTCACACACTAGTTCTTCTGTGGCATCCAGTCACTCCGCCGCACGCACTGGTTCTTCTG
66 CTCTGGCTCACACACTAGTTCTTCTGCGGCATCTAGCCACTCTG-CGCACGCACTGGTTCTTCTA
*
355303 TAACATCTAGCCACTCTAGC-GCACATA
130 TGACATCTAGCCACTCT-GCTGCACATA
* * ** * * * *
355330 TTGGTTCTTCTGCAATGTCTAGTCACCCTATCGCAC--ACACTGATTCTTCTACGACATCTAGCC
1 CTGGTTCTTCTGCGACATCTAGCCACTCTAGC-CACAAACACTGGTTCTTCTACGACATCTAGCC
* * * * * * * *
355393 AATCTGCCTTACGCAC-AGGTTCTTCTGCGGTATCTAGCTACTCTGCTGCACGCACTGATTCTTT
65 ACTCTGGCTCACACACTA-GTTCTTCTGCGGCATCTAGCCACTCTGC-GCACGCACTGGTTCTTC
* * * * *
355457 TGTGAAACCTAGTCACTCTGCTACACATA
128 TATGACATCTAGCCACTCTGCTGCACATA
* * *
355486 TTGGTTCTTCTGCGACATCTAGCCA-TTTAGCCACAAACACTGGTTCTTCTACAACATCTAGCCA
1 CTGGTTCTTCTGCGACATCTAGCCACTCTAGCCACAAACACTGGTTCTTCTACGACATCTAGCCA
* * * * *
355550 CTCTGGCGCAAACACTAGTTCTTCTGCAGCATCTAGCCACTCTGTCGCACACACTAGTTCTTCTA
66 CTCTGGCTCACACACTAGTTCTTCTGCGGCATCTAGCCACTCTG-CGCACGCACTGGTTCTTCTA
* * * * **
355615 TGGCATCTAGTCATTCCGCTGCACGCA
130 TGACATCTAGCCACTCTGCTGCACATA
* *
355642 CTGGTTCTTCTGCGACATCTAACCTCTCTA
1 CTGGTTCTTCTGCGACATCTAGCCACTCTA
355672 TCGGAGATGC
Statistics
Matches: 392, Mismatches: 91, Indels: 29
0.77 0.18 0.06
Matches are distributed among these distances:
154 3 0.01
155 7 0.02
156 367 0.94
157 13 0.03
158 2 0.01
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (156 bp):
CTGGTTCTTCTGCGACATCTAGCCACTCTAGCCACAAACACTGGTTCTTCTACGACATCTAGCCA
CTCTGGCTCACACACTAGTTCTTCTGCGGCATCTAGCCACTCTGCGCACGCACTGGTTCTTCTAT
GACATCTAGCCACTCTGCTGCACATA
Found at i:355822 original size:39 final size:39
Alignment explanation
Indices: 355742--355840 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
355732 CACACATCAA
** *
355742 TTCTTCTACAACATCTAGCCACTCTGTCGCACGCACTGG
1 TTCTTCTATGACATCTAGCCACTCTGTCGCAAGCACTGG
* * *
355781 TTCTTCTATGACATCTGGCCACTCTGTTGCAAGTA-TCGG
1 TTCTTCTATGACATCTAGCCACTCTGTCGCAAGCACT-GG
* *
355820 TTCTTCTGTGACATCAAGCCA
1 TTCTTCTATGACATCTAGCCA
355841 GCCTATTGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 1 0.02
39 49 0.98
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.32
Consensus pattern (39 bp):
TTCTTCTATGACATCTAGCCACTCTGTCGCAAGCACTGG
Found at i:356043 original size:39 final size:40
Alignment explanation
Indices: 355997--356130 Score: 157
Period size: 39 Copynumber: 3.4 Consensus size: 40
355987 GCTCTTCTAA
*
355997 GACATCTAATCACTCTATCGCAAGCATTGGTTCTTCTGCG
1 GACATCTAATCACTCTGTCGCAAGCATTGGTTCTTCTGCG
* * * *
356037 GA-ATCTAGTCACTCTGGCACAAGCATTGGTTCTTCTG-T
1 GACATCTAATCACTCTGTCGCAAGCATTGGTTCTTCTGCG
* *
356075 GACATCTAATCACTCTGTCGTAAGCACTGGTTCTTCTGC-
1 GACATCTAATCACTCTGTCGCAAGCATTGGTTCTTCTGCG
* * *
356114 AACATCTAGTCATTCTG
1 GACATCTAATCACTCTG
356131 CTGCACACAC
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
38 2 0.03
39 75 0.95
40 2 0.03
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (40 bp):
GACATCTAATCACTCTGTCGCAAGCATTGGTTCTTCTGCG
Found at i:356149 original size:39 final size:39
Alignment explanation
Indices: 356106--356180 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
356096 AAGCACTGGT
* * *
356106 TCTTCTGCAACATCTAGTCATTCTGCTGCACACACTAGC
1 TCTTCTACAACATCTAGTCACTCTGCCGCACACACTAGC
** *
356145 TCTTCTACGGCATCTAGTCACTCTGCCGCTCACACT
1 TCTTCTACAACATCTAGTCACTCTGCCGCACACACT
356181 GATTCTTCTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.20, C:0.36, G:0.13, T:0.31
Consensus pattern (39 bp):
TCTTCTACAACATCTAGTCACTCTGCCGCACACACTAGC
Found at i:356149 original size:78 final size:78
Alignment explanation
Indices: 355970--356193 Score: 215
Period size: 78 Copynumber: 2.9 Consensus size: 78
355960 TTGCGACTGG
* * * *
355970 TTCTTCTGCACACAC-AGGCTCTTCTAAGACATCTAATCACTCTATCGCAAGCATTGGTTCTTCT
1 TTCTGCTGCACACACTA-GCTCTTCTAAGACATCTAATCACTCTGTCGTAAGCACTGGTTCTTCT
*
356034 GCGGAATCTAGTCA
65 GCGAAATCTAGTCA
* * * * **
356048 CTCTG--GCACAAGCATTGGTTCTTCTGTGACATCTAATCACTCTGTCGTAAGCACTGGTTCTTC
1 TTCTGCTGCAC-A-CACTAGCTCTTCTAAGACATCTAATCACTCTGTCGTAAGCACTGGTTCTTC
356111 TGC-AACATCTAGTCA
64 TGCGAA-ATCTAGTCA
* * * * * *
356126 TTCTGCTGCACACACTAGCTCTTCTACGGCATCTAGTCACTCTGCCGCTCA-CACTGATTCTTCT
1 TTCTGCTGCACACACTAGCTCTTCTAAGACATCTAATCACTCTGTCG-TAAGCACTGGTTCTTCT
356190 GCGA
65 GCGA
356194 TTTCTAATCA
Statistics
Matches: 116, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
76 4 0.03
77 2 0.02
78 102 0.88
79 4 0.03
80 4 0.03
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (78 bp):
TTCTGCTGCACACACTAGCTCTTCTAAGACATCTAATCACTCTGTCGTAAGCACTGGTTCTTCTG
CGAAATCTAGTCA
Found at i:377399 original size:19 final size:19
Alignment explanation
Indices: 377377--377413 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
377367 TTAATTCTTG
* *
377377 ATTTTTATATTAATTTTAA
1 ATTTTTAAAATAATTTTAA
377396 ATTTTTAAAATAATTTTA
1 ATTTTTAAAATAATTTTA
377414 TTGTGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTTAAAATAATTTTAA
Found at i:377593 original size:29 final size:29
Alignment explanation
Indices: 377555--377610 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
377545 GATTAAGAAA
*
377555 TTAAATTAATATTTTATATA-AATTTAAGG
1 TTAAAATAATA-TTTATATAGAATTTAAGG
377584 TTAAAATAATATTTATATAGAATTTAA
1 TTAAAATAATATTTATATAGAATTTAA
377611 AGATTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
TTAAAATAATATTTATATAGAATTTAAGG
Found at i:399768 original size:22 final size:22
Alignment explanation
Indices: 399737--399790 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
399727 ATGGAAAATG
399737 AAAAAAAAACAAAATTT-ATTA
1 AAAAAAAAACAAAATTTGATTA
* *
399758 CAAAAACAAACATAATTTGATTA
1 -AAAAAAAAACAAAATTTGATTA
399781 AAAAAGAAAA
1 AAAAA-AAAA
399791 GAAGACAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (22 bp):
AAAAAAAAACAAAATTTGATTA
Found at i:400101 original size:22 final size:23
Alignment explanation
Indices: 400070--400112 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
400060 ATGACAAAAA
*
400070 AAACAAAATTT-ATTACAAAATC
1 AAACAAAATTTGATTAAAAAATC
*
400092 AAACAGAATTTGATTAAAAAA
1 AAACAAAATTTGATTAAAAAA
400113 GAAAAGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (23 bp):
AAACAAAATTTGATTAAAAAATC
Found at i:400193 original size:326 final size:332
Alignment explanation
Indices: 399458--400471 Score: 1548
Period size: 343 Copynumber: 3.0 Consensus size: 332
399448 TCTTTTCTTA
** *
399458 AAAATAATGGGGGTGC--AAAAAAATTCCTCCATTTTTCTTTAACATATTATACTAAATTTCAC-
1 AAAATAATTAGGGTGCAAAAAAAAATTCTTCCATTTTTCTTTAACATATTATACTAAATTTCACT
*
399520 TTTTTTTT-TAAATAATGGGGATGCA-TTTAACTCCTAGGGGGCTTAGTGCATCCGCCCCTGATA
66 TTTTTTTTCTAAATAATGGGGATGCACTTAAAC-CC------GC-T--T-CA-CCGCCCCTGATA
*
399583 CACACCATTAACATTAACATAAAACATATATAACAATGATAACTTCTTGACAAACTGACTTTATC
119 CACACCATTACCATTAACATAAAACATATATAACAATGATAACTTCTTGACAAACTGACTTTATC
* *
399648 ATAATTCAATCACAAGTTATCTTCAATGATAACCAAATAAATTTTATCTGAATTTAGGAATACGA
184 ATAATTCAATCACAAGCTATCTTCAATGATAACCAAATAAATTTTATCTGAATTTAGAAATACGA
* *
399713 TGTTAAATTCAATCATGGAAAATGAAAAAAAAACAAAATTTATTACAAAAACAAACATAATTTGA
249 TGTTAAATTCAATCATGGAAAATGAAAAAAAAACAAAATTTATTACAAAATCAAACAGAATTTGA
399778 TTAAAAAAGAAAAGAAGAC
314 TTAAAAAAGAAAAGAAGAC
*
399797 AAAATAATTGGGGTGCAAAAAAAAATTCTTCCATTTTTCTTTAACATATTATACTAAATTTCACT
1 AAAATAATTAGGGTGCAAAAAAAAATTCTTCCATTTTTCTTTAACATATTATACTAAATTTCACT
399862 TTTTTTTT-TAAATAATGGGGATGCAC-TAAACCC-C-T-A-CGCCCCTGATACACACCATTACC
66 TTTTTTTTCTAAATAATGGGGATGCACTTAAACCCGCTTCACCGCCCCTGATACACACCATTACC
* * *
399921 ATTAACATAAAACATATATAACAATGATAACTTCTTGACAAACTGACGTTCTCATAATTAAATCA
131 ATTAACATAAAACATATATAACAATGATAACTTCTTGACAAACTGACTTTATCATAATTCAATCA
*
399986 CAAGCTATCTTCAATGATAACCAAATAAATTTTATCTGAATTTAGAAATACGATGTTAATTTCAA
196 CAAGCTATCTTCAATGATAACCAAATAAATTTTATCTGAATTTAGAAATACGATGTTAAATTCAA
400051 TCATGGAAAATGACAAAAAAAACAAAATTTATTACAAAATCAAACAGAATTTGATTAAAAAAGAA
261 TCATGGAAAATGA-AAAAAAAACAAAATTTATTACAAAATCAAACAGAATTTGATTAAAAAAGAA
400116 AAGAAGAC
325 AAGAAGAC
* *
400124 AAAATAATTAGGGTGCAAAGAAAAATTCTTCCATTTTTCTTTAACATATTATATTAAATTTCA-T
1 AAAATAATTAGGGTGCAAAAAAAAATTCTTCCATTTTTCTTTAACATATTATACTAAATTTCACT
*
400188 TTTTTTTTCTAAATAATGGGGATGCACTTAACCCCTAGGGAGCTTAGTGCATCCGCCCCTGATAC
66 TTTTTTTTCTAAATAATGGGGATGCACTTAAACCC------GC-T--T-CA-CCGCCCCTGATAC
* *
400253 ACACCATTACCATTAACATAAAACATATATAACAATTATAACTTCTCGACAAACTGACTTTATCA
120 ACACCATTACCATTAACATAAAACATATATAACAATGATAACTTCTTGACAAACTGACTTTATCA
400318 TAATTCAATCACAAGCTATCTTCAATGATAACCAAATAAATTTTATCTGAATTTAGAAATACGAT
185 TAATTCAATCACAAGCTATCTTCAATGATAACCAAATAAATTTTATCTGAATTTAGAAATACGAT
400383 GTTAAATTCAATCATGGAAAATGAAAAAAAAAACAAAATTTATTACAAAATCAAACAGAATTTGA
250 GTTAAATTCAATCATGGAAAATG-AAAAAAAAACAAAATTTATTACAAAATCAAACAGAATTTGA
400448 TTAAAAAAGAAAAGAAGAC
314 TTAAAAAAGAAAAGAAGAC
400467 AAAAT
1 AAAAT
400472 TATTTTTTTA
Statistics
Matches: 630, Mismatches: 22, Indels: 42
0.91 0.03 0.06
Matches are distributed among these distances:
326 168 0.27
327 135 0.21
328 7 0.01
330 1 0.00
334 1 0.00
335 1 0.00
339 16 0.03
341 48 0.08
342 29 0.05
343 223 0.35
344 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (332 bp):
AAAATAATTAGGGTGCAAAAAAAAATTCTTCCATTTTTCTTTAACATATTATACTAAATTTCACT
TTTTTTTTCTAAATAATGGGGATGCACTTAAACCCGCTTCACCGCCCCTGATACACACCATTACC
ATTAACATAAAACATATATAACAATGATAACTTCTTGACAAACTGACTTTATCATAATTCAATCA
CAAGCTATCTTCAATGATAACCAAATAAATTTTATCTGAATTTAGAAATACGATGTTAAATTCAA
TCATGGAAAATGAAAAAAAAACAAAATTTATTACAAAATCAAACAGAATTTGATTAAAAAAGAAA
AGAAGAC
Found at i:400438 original size:22 final size:23
Alignment explanation
Indices: 400413--400455 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
400403 ATGAAAAAAA
*
400413 AAACAAAATTT-ATTACAAAATC
1 AAACAAAATTTGATTAAAAAATC
*
400435 AAACAGAATTTGATTAAAAAA
1 AAACAAAATTTGATTAAAAAA
400456 GAAAAGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (23 bp):
AAACAAAATTTGATTAAAAAATC
Found at i:401074 original size:3 final size:3
Alignment explanation
Indices: 401066--401091 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
401056 TTATATTAAT
401066 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
401092 TACATACAAC
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:409155 original size:12 final size:12
Alignment explanation
Indices: 409140--409168 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
409130 CAACATCATC
409140 ATCAATATCAAT
1 ATCAATATCAAT
409152 ATCAATATCAAT
1 ATCAATATCAAT
409164 ATCAA
1 ATCAA
409169 GGGATACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (12 bp):
ATCAATATCAAT
Found at i:409155 original size:18 final size:18
Alignment explanation
Indices: 409128--409168 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
409118 ACACAGTAAC
409128 ATCAACATC-ATCATCAAT
1 ATCAACATCAAT-ATCAAT
*
409146 ATCAATATCAATATCAAT
1 ATCAACATCAATATCAAT
409164 ATCAA
1 ATCAA
409169 GGGATACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (18 bp):
ATCAACATCAATATCAAT
Found at i:411426 original size:14 final size:14
Alignment explanation
Indices: 411407--411453 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
411397 CACATTATCA
411407 GATTTAGGTTTTAG
1 GATTTAGGTTTTAG
*
411421 GATTTATGTTTATA-
1 GATTTAGGTTT-TAG
*
411435 G-TTTAGGGTTTAG
1 GATTTAGGTTTTAG
411448 GATTTA
1 GATTTA
411454 TTACAAAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 15 0.56
15 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (14 bp):
GATTTAGGTTTTAG
Found at i:412057 original size:2 final size:2
Alignment explanation
Indices: 412050--412099 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
412040 TTTAAATTAA
* * * *
412050 AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
412090 AT AT AT AT AT
1 AT AT AT AT AT
412100 CGGCCCGATA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:412075 original size:17 final size:17
Alignment explanation
Indices: 412049--412098 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
412039 ATTTAAATTA
*
412049 AATATATATATATATAT
1 AATATTTATATATATAT
412066 AATATTTATATAT-T-T
1 AATATTTATATATATAT
*
412081 AAT-TTAAATATATATAT
1 AATATT-TATATATATAT
412098 A
1 A
412099 TCGGCCCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 2 0.07
15 10 0.36
16 2 0.07
17 14 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTATATATATAT
Found at i:412925 original size:4 final size:4
Alignment explanation
Indices: 412916--413003 Score: 158
Period size: 4 Copynumber: 22.0 Consensus size: 4
412906 AAAAGTACAC
412916 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
412964 CATA CATA CATA CATA CATA CATA TATT CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
413004 TATATATATA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 80 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:414514 original size:27 final size:28
Alignment explanation
Indices: 414476--414533 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
414466 GCTTAACTAA
*
414476 TCACGATGTTTAAAACACTAAAA-ACAC
1 TCACAATGTTTAAAACACTAAAACACAC
414503 TCACAATGTTTAAAACACTAAAACACAC
1 TCACAATGTTTAAAACACTAAAACACAC
414531 TCA
1 TCA
414534 TTGATTAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.22
Consensus pattern (28 bp):
TCACAATGTTTAAAACACTAAAACACAC
Found at i:414541 original size:26 final size:26
Alignment explanation
Indices: 414485--414541 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
414475 ATCACGATGT
*
414485 TTAAAACACTAAAAACACTCACAATGT
1 TTAAAACACTAAAAACACT-ACAATGA
*
414512 TTAAAACACTAAAACACACT-CATTGA
1 TTAAAACACTAAAA-ACACTACAATGA
414538 TTAA
1 TTAA
414542 GCAGTGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 8 0.30
27 14 0.52
28 5 0.19
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.25
Consensus pattern (26 bp):
TTAAAACACTAAAAACACTACAATGA
Found at i:433036 original size:21 final size:21
Alignment explanation
Indices: 433010--433049 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
433000 CTCCATCGTC
* *
433010 TTCTACCAGTCATCTATCATA
1 TTCTACCAATCATCGATCATA
433031 TTCTACCAATCATCGATCA
1 TTCTACCAATCATCGATCA
433050 GAGATCTACC
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:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (21 bp):
TTCTACCAATCATCGATCATA
Found at i:442318 original size:15 final size:15
Alignment explanation
Indices: 442298--442328 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
442288 TCAGTAATCA
442298 ACCCTATACTTTATT
1 ACCCTATACTTTATT
442313 ACCCTATACTTTATT
1 ACCCTATACTTTATT
442328 A
1 A
442329 TTACATCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (15 bp):
ACCCTATACTTTATT
Found at i:451771 original size:2 final size:2
Alignment explanation
Indices: 451764--451817 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
451754 GCAAGTATTT
451764 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
451806 TA TA TA TA TA TA
1 TA TA TA TA TA TA
451818 AACATATTCG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:454252 original size:21 final size:21
Alignment explanation
Indices: 454210--454252 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
454200 TTTCTGGGTT
* * *
454210 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
454231 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
454252 A
1 A
454253 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:454313 original size:66 final size:67
Alignment explanation
Indices: 454210--454381 Score: 231
Period size: 67 Copynumber: 2.6 Consensus size: 67
454200 TTTCTGGGTT
* * *
454210 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATG
454273 CTAG
64 CTAG
* * *
454277 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
*
454342 TG
66 AG
* *
454344 AGGGGAATCGATACCCCCAGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCC
454382 ATGAGAAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
65 2 0.02
66 22 0.23
67 70 0.74
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
AG
Found at i:454370 original size:20 final size:20
Alignment explanation
Indices: 454345--454382 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
454335 GATTGCTTGA
*
454345 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
454365 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
454383 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:454778 original size:30 final size:30
Alignment explanation
Indices: 454744--454802 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
454734 GTTATATGAG
* *
454744 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
454774 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
454803 ACTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:455044 original size:22 final size:23
Alignment explanation
Indices: 455016--455061 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
455006 TTATGGACAT
455016 AATTCTAC-GGGCACTTCGGTGC
1 AATTCTACGGGGCACTTCGGTGC
455038 AATTCTACGGGGCACTTCGGTGC
1 AATTCTACGGGGCACTTCGGTGC
455061 A
1 A
455062 TTTATACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
AATTCTACGGGGCACTTCGGTGC
Found at i:455069 original size:23 final size:23
Alignment explanation
Indices: 455016--455069 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
455006 TTATGGACAT
*
455016 AATTCTAC-GGGCACTTCGGTGC
1 AATTATACGGGGCACTTCGGTGC
*
455038 AATTCTACGGGGCACTTCGGTGC
1 AATTATACGGGGCACTTCGGTGC
*
455061 ATTTATACG
1 AATTATACG
455070 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
AATTATACGGGGCACTTCGGTGC
Found at i:461137 original size:21 final size:21
Alignment explanation
Indices: 461095--461137 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
461085 TTTCTGGGTT
* * *
461095 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
461116 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
461137 A
1 A
461138 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:461198 original size:66 final size:67
Alignment explanation
Indices: 461095--461267 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
461085 TTTCTGGGTT
* * * *
461095 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACG-AAATGAATTTCTAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATG
461158 CTAG
64 CTAG
* * *
461162 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
*
461227 TG
66 AG
* *
461229 AGGGGAATCGATACCCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA-GGGGGGAACCGATACCCCC
461268 ATGAGAAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 2 0.02
66 22 0.24
67 51 0.55
68 18 0.19
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
AG
Found at i:461685 original size:29 final size:30
Alignment explanation
Indices: 461634--461691 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
461624 GTTATATGAG
* *
461634 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
461664 CTATGTGAT-AAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
461692 ACTACGCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:461702 original size:29 final size:29
Alignment explanation
Indices: 461644--461702 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
461634 CTATGTGATA
* * * * *
461644 AAGGTATGTAAATGATATGTCTATGTGAT
1 AAGGTATGGAAATAATATGACTACGCGAT
461673 AAGGTATGGAAATAATATGACTACGCGAT
1 AAGGTATGGAAATAATATGACTACGCGAT
461702 A
1 A
461703 TGAACTACGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.31
Consensus pattern (29 bp):
AAGGTATGGAAATAATATGACTACGCGAT
Found at i:461931 original size:22 final size:23
Alignment explanation
Indices: 461903--461948 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
461893 TTATGGACAT
461903 AATTCTAC-GGGCACTTCGGTGC
1 AATTCTACGGGGCACTTCGGTGC
461925 AATTCTACGGGGCACTTCGGTGC
1 AATTCTACGGGGCACTTCGGTGC
461948 A
1 A
461949 TTTATACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
AATTCTACGGGGCACTTCGGTGC
Found at i:461956 original size:23 final size:23
Alignment explanation
Indices: 461903--461956 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
461893 TTATGGACAT
*
461903 AATTCTAC-GGGCACTTCGGTGC
1 AATTATACGGGGCACTTCGGTGC
*
461925 AATTCTACGGGGCACTTCGGTGC
1 AATTATACGGGGCACTTCGGTGC
*
461948 ATTTATACG
1 AATTATACG
461957 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
AATTATACGGGGCACTTCGGTGC
Found at i:463629 original size:21 final size:21
Alignment explanation
Indices: 463588--463631 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
463578 TTTTTTAGTG
*
463588 AGCTTAACGAGCAACGAATCA
1 AGCTTAACGAGAAACGAATCA
463609 AGCTTAACGAGAAAC-AGATCA
1 AGCTTAACGAGAAACGA-ATCA
463630 AG
1 AG
463632 TTGAGTAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (21 bp):
AGCTTAACGAGAAACGAATCA
Found at i:477822 original size:4 final size:4
Alignment explanation
Indices: 477815--478138 Score: 648
Period size: 4 Copynumber: 81.0 Consensus size: 4
477805 TTTATATATA
477815 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
477863 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
477911 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
477959 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
478007 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
478055 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
478103 TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
478139 AAGCAAAATA
Statistics
Matches: 320, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 320 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:481449 original size:5 final size:5
Alignment explanation
Indices: 481439--481466 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
481429 GTCAGCACAT
481439 GGTAG GGTAG GGTAG GGTAG GGTAG GGT
1 GGTAG GGTAG GGTAG GGTAG GGTAG GGT
481467 TACTTTAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.61, T:0.21
Consensus pattern (5 bp):
GGTAG
Found at i:486434 original size:14 final size:17
Alignment explanation
Indices: 486400--486436 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
486390 TCGTATTTAA
486400 TTCTTTTGCATTATGGT
1 TTCTTTTGCATTATGGT
486417 TTCTTTTG-ATT-T-GT
1 TTCTTTTGCATTATGGT
486431 TTCTTT
1 TTCTTT
486437 GTATAGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 3 0.15
17 8 0.40
ACGTcount: A:0.08, C:0.11, G:0.14, T:0.68
Consensus pattern (17 bp):
TTCTTTTGCATTATGGT
Found at i:499525 original size:12 final size:12
Alignment explanation
Indices: 499496--499533 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
499486 AATTATTAAC
499496 ATATTTAA-AAT
1 ATATTTAATAAT
*
499507 ATATTTATTAAT
1 ATATTTAATAAT
*
499519 ATTTTTAATAAT
1 ATATTTAATAAT
499531 ATA
1 ATA
499534 ATACAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:499525 original size:23 final size:23
Alignment explanation
Indices: 499478--499535 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
499468 CATTTTAATA
499478 AAAATATTAATTATTAACATATTT
1 AAAATA-TAATTATTAACATATTT
* * *
499502 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAACATATTT
499525 AATAATATAAT
1 AA-AATATAAT
499536 ACAATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAACATATTT
Found at i:499555 original size:17 final size:16
Alignment explanation
Indices: 499524--499561 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
499514 TTAATATTTT
499524 TAATAATATAATACAA
1 TAATAATATAATACAA
*
499540 TAATAATATTATTACAA
1 TAATAATA-TAATACAA
499557 TAATA
1 TAATA
499562 TACTCAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAATATAATACAA
Found at i:499584 original size:26 final size:26
Alignment explanation
Indices: 499545--499601 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
499535 TACAATAATA
*
499545 ATATTATTACAATA-AT-ATACTCAATT
1 ATATTATAACAATATATGATACT--ATT
*
499571 ATATTATAATAATATATGATACTATT
1 ATATTATAACAATATATGATACTATT
499597 ATATT
1 ATATT
499602 CTTATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 20 0.74
27 2 0.07
28 5 0.19
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (26 bp):
ATATTATAACAATATATGATACTATT
Found at i:499973 original size:23 final size:23
Alignment explanation
Indices: 499940--499983 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
499930 TATTCTAATA
*
499940 TTTTTATAAT-AATGATATTAAG
1 TTTTTATAATAAATAATATTAAG
499962 TTTTATATAATAAATAATATTA
1 TTTT-TATAATAAATAATATTA
499984 TTTATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
TTTTTATAATAAATAATATTAAG
Found at i:505957 original size:2 final size:2
Alignment explanation
Indices: 505947--505983 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
505937 TTTTTTTAAA
*
505947 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
505984 GTATGTATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:506529 original size:4 final size:4
Alignment explanation
Indices: 506520--506549 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
506510 TGGAGTTGAG
506520 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
506550 TGAGTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:518557 original size:2 final size:2
Alignment explanation
Indices: 518550--518584 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
518540 TGAAACGATG
518550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
518585 GTATTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:520243 original size:32 final size:30
Alignment explanation
Indices: 520176--520260 Score: 102
Period size: 32 Copynumber: 2.8 Consensus size: 30
520166 AGAGAGGGTG
*
520176 AAGCTTAGCAAAGCTTAGGAATATGATTGA
1 AAGCTTAGCAAAGCTTAGGAATATGAGTGA
* *
520206 AAGCTTAGAAAAGCTATGAGAGAATTTGAGT-A
1 AAGCTTAGCAAAGCT-T-AG-GAATATGAGTGA
520238 AAGCTTAGCAAAGCTTA-GAATAT
1 AAGCTTAGCAAAGCTTAGGAATAT
520261 TGAGGTTGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
28 5 0.11
30 15 0.32
31 2 0.04
32 17 0.36
33 8 0.17
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.26
Consensus pattern (30 bp):
AAGCTTAGCAAAGCTTAGGAATATGAGTGA
Found at i:523098 original size:21 final size:22
Alignment explanation
Indices: 523074--523116 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
523064 ACTCTAATTC
*
523074 TAAATTATAAATT-TTAACCCT
1 TAAATTATAAATTCTAAACCCT
*
523095 TAAATTTTAAATTCTAAACCCT
1 TAAATTATAAATTCTAAACCCT
523117 AGATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTATAAATTCTAAACCCT
Found at i:523471 original size:2 final size:2
Alignment explanation
Indices: 523464--523494 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
523454 ATGAATGCAC
523464 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
523495 GATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:523501 original size:2 final size:2
Alignment explanation
Indices: 523496--523522 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
523486 GAGAGAGAGG
523496 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
523523 CACTTGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:536629 original size:6 final size:6
Alignment explanation
Indices: 536615--536645 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
536605 CCGGCCACAG
*
536615 CTGAGT CTGACT CTGACT CTGACT CTGACT C
1 CTGACT CTGACT CTGACT CTGACT CTGACT C
536646 GGAGTTGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.32
Consensus pattern (6 bp):
CTGACT
Found at i:537172 original size:30 final size:31
Alignment explanation
Indices: 537093--537164 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 31
537083 TTATGGTGAC
537093 CATTTTATAATAATTTGATAAATTTAA-TAT
1 CATTTTATAATAATTTGATAAATTTAATTAT
** *
537123 TTTTTTGTAATAATTTGATAAATTTAATTAT
1 CATTTTATAATAATTTGATAAATTTAATTAT
537154 CATTTTATAAT
1 CATTTTATAAT
537165 GTATGATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 24 0.69
31 11 0.31
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (31 bp):
CATTTTATAATAATTTGATAAATTTAATTAT
Found at i:544015 original size:12 final size:11
Alignment explanation
Indices: 543986--544071 Score: 57
Period size: 12 Copynumber: 7.3 Consensus size: 11
543976 AGATATCAAA
*
543986 AATCAAAACAG
1 AATCAGAACAG
*
543997 AATTCAGATCAG
1 AA-TCAGAACAG
*
544009 ATATCAGAACAT
1 A-ATCAGAACAG
544021 AATCTA-AATCAG
1 AATC-AGAA-CAG
544033 AAATCAGAACAG
1 -AATCAGAACAG
* *
544045 AATTCATATCAG
1 AA-TCAGAACAG
544057 AAATCAGAACAG
1 -AATCAGAACAG
544069 AAT
1 AAT
544072 TCAAATTGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
11 12 0.21
12 37 0.64
13 9 0.16
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:544085 original size:48 final size:47
Alignment explanation
Indices: 543984--544088 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 47
543974 GGAGATATCA
* * *
543984 AAAATCAAAACAGAATTCAGATCAGATATCAGAACATAATCTAAATC
1 AAAATCAGAACAGAATTCAGATCAGAAATCAGAACAGAATCTAAATC
* *
544031 AGAAATCAGAACAGAATTCATATCAGAAATCAGAACAGAAT-TCAAATTG
1 A-AAATCAGAACAGAATTCAGATCAGAAATCAGAACAGAATCT-AAA-TC
544080 AAAATCAGA
1 AAAATCAGA
544089 TAAAACATTC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
47 2 0.04
48 46 0.92
49 2 0.04
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.20
Consensus pattern (47 bp):
AAAATCAGAACAGAATTCAGATCAGAAATCAGAACAGAATCTAAATC
Found at i:544088 original size:24 final size:24
Alignment explanation
Indices: 543980--544077 Score: 126
Period size: 24 Copynumber: 4.1 Consensus size: 24
543970 AAATGGAGAT
* * *
543980 ATCAAAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAA
* *
544004 ATCAGATATCAGAACATAA-TCTAA
1 ATCAGAAATCAGAACAGAATTC-AA
*
544028 ATCAGAAATCAGAACAGAATTCAT
1 ATCAGAAATCAGAACAGAATTCAA
544052 ATCAGAAATCAGAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
544076 AT
1 AT
544078 TGAAAATCAG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
23 2 0.03
24 59 0.94
25 2 0.03
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:547495 original size:2 final size:2
Alignment explanation
Indices: 547479--547524 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
547469 ATACTTCATT
*
547479 TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
547520 TA TA T
1 TA TA T
547525 GAGAGAATCA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:550673 original size:56 final size:56
Alignment explanation
Indices: 550587--550699 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
550577 AACCCGCAAA
550587 ACCTATTAATATATGTTACAAGAAAAGGGATGAATTGATCGATTGCAGTAAAGTCT
1 ACCTATTAATATATGTTACAAGAAAAGGGATGAATTGATCGATTGCAGTAAAGTCT
*
550643 ACCTATTAATATATGTTGCAAGAAAAGGGATGAATTGATCGATTGCAGTAAAGTCT
1 ACCTATTAATATATGTTACAAGAAAAGGGATGAATTGATCGATTGCAGTAAAGTCT
550699 A
1 A
550700 GTAGACTACG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (56 bp):
ACCTATTAATATATGTTACAAGAAAAGGGATGAATTGATCGATTGCAGTAAAGTCT
Found at i:551693 original size:23 final size:23
Alignment explanation
Indices: 551640--551723 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
551630 CGTGATCGTG
* *
551640 AACATATTTGTTTATATATTTATT
1 AACATATTCGTTTA-ATATTTACT
* **
551664 AATATATTCGTTTAACGTTTACT
1 AACATATTCGTTTAATATTTACT
* *
551687 AACATATTCATTTAATATTTACG
1 AACATATTCGTTTAATATTTACT
*
551710 AATATATTCGTTTA
1 AACATATTCGTTTA
551724 TATGATTCGA
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
23 36 0.75
24 12 0.25
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.50
Consensus pattern (23 bp):
AACATATTCGTTTAATATTTACT
Found at i:556189 original size:80 final size:80
Alignment explanation
Indices: 556052--556210 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
556042 GATGGATTGA
* * * *
556052 AGAAATCACATTTTTGTTAGTTTATATGAATTGCATTATTAAATTGTATATAGATGAGATAATAC
1 AGAAATCACATGTTTGTCAGTTTATATGAATTGCATGACTAAATTGTATATAGATGAGATAATAC
556117 GATTACATGATATAT
66 GATTACATGATATAT
* * *
556132 AGAAATCACATGTTTGTCAGTTTATATGAATTGCATGACTACATTGTATATATATGAGATAGTAC
1 AGAAATCACATGTTTGTCAGTTTATATGAATTGCATGACTAAATTGTATATAGATGAGATAATAC
556197 GATTACATGATATA
66 GATTACATGATATA
556211 CATACTTCGA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (80 bp):
AGAAATCACATGTTTGTCAGTTTATATGAATTGCATGACTAAATTGTATATAGATGAGATAATAC
GATTACATGATATAT
Found at i:568118 original size:153 final size:153
Alignment explanation
Indices: 567840--568127 Score: 522
Period size: 153 Copynumber: 1.9 Consensus size: 153
567830 TATTTTGATT
* *
567840 TTAATTGAAACAGTACCGTGTTAGCATTGTCATGTCATTCCGAACCTAGCGCGTACTTTATTATA
1 TTAATTGAAACAGTACCATGTTAGCATTGTCATATCATTCCGAACCTAGCGCGTACTTTATTATA
*
567905 AACCACGTGGGTTGGAGGCCCACATCTTTTAAGTGCGTATTACGGCTCCCTGCTATTCTATTTTG
66 AACCACGTGGGTTGGAGGCCCACATCTTTTAAGTGCGTATTACAGCTCCCTGCTATTCTATTTTG
567970 ATTTTAATTATATCGTGTAAATA
131 ATTTTAATTATATCGTGTAAATA
* * *
567993 TTAATTGTAACAGTACCATGTTAGCATTGTCATATCATTCCGATCCTAGTGCGTACTTTATTATA
1 TTAATTGAAACAGTACCATGTTAGCATTGTCATATCATTCCGAACCTAGCGCGTACTTTATTATA
568058 AACCACGTGGGTTGGAGGCCCACATCTTTTAAGTGCGTATTACAGCTCCCTGCTATTCTATTTTG
66 AACCACGTGGGTTGGAGGCCCACATCTTTTAAGTGCGTATTACAGCTCCCTGCTATTCTATTTTG
568123 ATTTT
131 ATTTT
568128 TTTCCAGTTT
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
153 129 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (153 bp):
TTAATTGAAACAGTACCATGTTAGCATTGTCATATCATTCCGAACCTAGCGCGTACTTTATTATA
AACCACGTGGGTTGGAGGCCCACATCTTTTAAGTGCGTATTACAGCTCCCTGCTATTCTATTTTG
ATTTTAATTATATCGTGTAAATA
Found at i:571458 original size:25 final size:25
Alignment explanation
Indices: 571430--571477 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
571420 TTAGTGGAAA
571430 AAAATATTATCAATAA-AA-AATATCT
1 AAAATA-TAT-AATAATAATAATATCT
571455 AAAATATATAATAATAATAATAT
1 AAAATATATAATAATAATAATAT
571478 ATAATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 5 0.24
25 11 0.52
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATATATAATAATAATAATATCT
Found at i:579856 original size:2 final size:2
Alignment explanation
Indices: 579844--579885 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
579834 TCATAACAGC
579844 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
579885 T
1 T
579886 TATCGTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.