Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:2044213 original size:2 final size:2
Alignment explanation
Indices: 2044208--2044233 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2044198 AAAAAAAGTA
2044208 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
2044234 TAAAAAAATA
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:2044440 original size:30 final size:30
Alignment explanation
Indices: 2044392--2044459 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
2044382 ATCATTTTTT
*
2044392 TAATATTTTCGGTCATTTTTTAGCGCCTAG
1 TAATATTTTCGGTCATTTTTTAGCGCCTAA
* * *
2044422 TAATGTTTTCTGTTATTTTTTAGCGCCTAA
1 TAATATTTTCGGTCATTTTTTAGCGCCTAA
2044452 TAATATTT
1 TAATATTT
2044460 CTAATCATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51
Consensus pattern (30 bp):
TAATATTTTCGGTCATTTTTTAGCGCCTAA
Found at i:2044460 original size:29 final size:29
Alignment explanation
Indices: 2044392--2044472 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
2044382 ATCATTTTTT
* *
2044392 TAATATTTTCGGTCATTTTTTAGCGCCTAG
1 TAATA-TTTCTGTCATTTTTTAGCGCCTAA
* *
2044422 TAATGTTTTCTGTTATTTTTTAGCGCCTAA
1 TAAT-ATTTCTGTCATTTTTTAGCGCCTAA
*
2044452 TAATATTTCTAATCATTTTTT
1 TAATATTTCT-GTCATTTTTT
2044473 TGAAAATTCG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 5 0.12
30 37 0.88
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.53
Consensus pattern (29 bp):
TAATATTTCTGTCATTTTTTAGCGCCTAA
Found at i:2045499 original size:2 final size:2
Alignment explanation
Indices: 2045492--2045539 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
2045482 TTTGCACACC
* * *
2045492 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT 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
2045534 AT AT AT
1 AT AT AT
2045540 GTATGTATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2045526 original size:18 final size:18
Alignment explanation
Indices: 2045492--2045543 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
2045482 TTTGCACACC
*
2045492 ATATATATATATATATAT
1 ATATATATATATGTATAT
* *
2045510 ATATGTATGTATGTATAT
1 ATATATATATATGTATAT
2045528 ATATATATATATGTAT
1 ATATATATATATGTAT
2045544 GTATGTAGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
ATATATATATATGTATAT
Found at i:2045529 original size:22 final size:22
Alignment explanation
Indices: 2045501--2045547 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2045491 CATATATATA
*
2045501 TATATATATATATGTATGTATG
1 TATATATATATATATATGTATG
2045523 TATATATATATATATATGTATG
1 TATATATATATATATATGTATG
2045545 TAT
1 TAT
2045548 GTAGGAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (22 bp):
TATATATATATATATATGTATG
Found at i:2045533 original size:26 final size:26
Alignment explanation
Indices: 2045497--2045550 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2045487 ACACCATATA
2045497 TATATATATATATATATGTATGTATG
1 TATATATATATATATATGTATGTATG
2045523 TATATATATATATATATGTATGTATG
1 TATATATATATATATATGTATGTATG
2045549 TA
1 TA
2045551 GGAAGTGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (26 bp):
TATATATATATATATATGTATGTATG
Found at i:2045997 original size:14 final size:14
Alignment explanation
Indices: 2045987--2046019 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2045977 GTATTTAAGG
2045987 TTTAGGGTTTATAA
1 TTTAGGGTTTATAA
2046001 TTTAGGGTTT-TAA
1 TTTAGGGTTTATAA
*
2046014 GTTAGG
1 TTTAGG
2046020 AGTAGGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (14 bp):
TTTAGGGTTTATAA
Found at i:2049033 original size:20 final size:20
Alignment explanation
Indices: 2048987--2049030 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2048977 TTATGTTTTC
*
2048987 TTTTTAAATATATATATAAT
1 TTTTTAAATATAAATATAAT
*
2049007 TTTTTAATTATAAATA-AAT
1 TTTTTAAATATAAATATAAT
2049026 TTTTT
1 TTTTT
2049031 TAAAATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAAATATAAATATAAT
Found at i:2050623 original size:23 final size:23
Alignment explanation
Indices: 2050597--2050643 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2050587 TTGCGAATAT
2050597 TAAATGAACACTAAACAAACATA
1 TAAATGAACACTAAACAAACATA
2050620 TAAATGAACACTAAACAAACATA
1 TAAATGAACACTAAACAAACATA
2050643 T
1 T
2050644 TTTTGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.60, C:0.17, G:0.04, T:0.19
Consensus pattern (23 bp):
TAAATGAACACTAAACAAACATA
Found at i:2054224 original size:29 final size:28
Alignment explanation
Indices: 2054175--2054231 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
2054165 TTTTTATAAC
2054175 TCATTTCCATATTCTCTTCATTTCTTCCT
1 TCATTTCCATATTCTCTTCA-TTCTTCCT
* *
2054204 TCATTTTCATTTTCATC-TCATTCTTCCT
1 TCATTTCCATATTC-TCTTCATTCTTCCT
2054232 CTCTAAGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.32
29 15 0.60
30 2 0.08
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.56
Consensus pattern (28 bp):
TCATTTCCATATTCTCTTCATTCTTCCT
Found at i:2055210 original size:18 final size:18
Alignment explanation
Indices: 2055187--2055231 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2055177 GTGTAGAATT
* *
2055187 TGTCCCGAATGACTATTA
1 TGTCCCGAAAGACTACTA
2055205 TGTCCCGAAAGACTACTA
1 TGTCCCGAAAGACTACTA
2055223 TGTCCCGAA
1 TGTCCCGAA
2055232 GGACCACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (18 bp):
TGTCCCGAAAGACTACTA
Found at i:2055357 original size:21 final size:21
Alignment explanation
Indices: 2055319--2055358 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2055309 CCGAAGTACC
*
2055319 ACATATATATTCCAAAGGATT
1 ACATATATATCCCAAAGGATT
* *
2055340 ACATATATGTCCCGAAGGA
1 ACATATATATCCCAAAGGA
2055359 CCACGTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
ACATATATATCCCAAAGGATT
Found at i:2056249 original size:20 final size:20
Alignment explanation
Indices: 2056212--2056251 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2056202 ATGTTTCAAG
* *
2056212 GGTATCGATACCATCCTTAA
1 GGTACCGATACCACCCTTAA
*
2056232 GGTACCGATACTACCCTTAA
1 GGTACCGATACCACCCTTAA
2056252 ATATTGATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
GGTACCGATACCACCCTTAA
Found at i:2059317 original size:18 final size:18
Alignment explanation
Indices: 2059294--2059338 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2059284 GTGTAGAATT
* *
2059294 TGTCCCGAATGACTATTA
1 TGTCCCGAAAGACTACTA
2059312 TGTCCCGAAAGACTACTA
1 TGTCCCGAAAGACTACTA
2059330 TGTCCCGAA
1 TGTCCCGAA
2059339 GGACCACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (18 bp):
TGTCCCGAAAGACTACTA
Found at i:2059464 original size:21 final size:21
Alignment explanation
Indices: 2059426--2059465 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2059416 CCGAAGTACC
*
2059426 ACATATATATTCCAAAGGATT
1 ACATATATATCCCAAAGGATT
* *
2059447 ACATATATGTCCCGAAGGA
1 ACATATATATCCCAAAGGA
2059466 CCACGTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
ACATATATATCCCAAAGGATT
Found at i:2059679 original size:2 final size:2
Alignment explanation
Indices: 2059672--2059697 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2059662 TGTTCTTATC
2059672 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
2059698 CATGTAACAT
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:2060381 original size:20 final size:20
Alignment explanation
Indices: 2060335--2060412 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
2060325 GTTTCAAGGG
* * **
2060335 TATCGATACCATCCTTAAGG
1 TATCGATACTACCCTTAAAA
*
2060355 TACCGATACTACCCTTAAAA
1 TATCGATACTACCCTTAAAA
*
2060375 TATCGATAC--CTCTTTAACAA
1 TATCGATACTAC-CCTTAA-AA
2060395 GTATCGATACTACCCTTA
1 -TATCGATACTACCCTTA
2060413 CAAAATATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.02
19 5 0.11
20 25 0.56
21 9 0.20
22 4 0.09
23 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (20 bp):
TATCGATACTACCCTTAAAA
Found at i:2063439 original size:18 final size:18
Alignment explanation
Indices: 2063416--2063460 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2063406 GTATAGAATT
* *
2063416 TGTCCCGAATGACTATTA
1 TGTCCCGAAAGACTACTA
2063434 TGTCCCGAAAGACTACTA
1 TGTCCCGAAAGACTACTA
2063452 TGTCCCGAA
1 TGTCCCGAA
2063461 GGACCACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (18 bp):
TGTCCCGAAAGACTACTA
Found at i:2064477 original size:40 final size:40
Alignment explanation
Indices: 2064433--2064523 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
2064423 TATTTCAAGG
* *
2064433 GTATCGATACCATCCTTAAGGTACCGATACTACCCTTATA
1 GTATCGATACCATCCTTAAGGTACCAATACTACCCTTACA
2064473 GTATCGATACCATCCTTAAGGTACCAATACTACCCTTACA
1 GTATCGATACCATCCTTAAGGTACCAATACTACCCTTACA
2064513 GTATCGATACC
1 GTATCGATACC
2064524 TCTTCAACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (40 bp):
GTATCGATACCATCCTTAAGGTACCAATACTACCCTTACA
Found at i:2064522 original size:20 final size:20
Alignment explanation
Indices: 2064433--2064553 Score: 88
Period size: 20 Copynumber: 6.0 Consensus size: 20
2064423 TATTTCAAGG
* *
2064433 GTATCGATACCATCCTTA-A
1 GTATCGATACTACCCTTACA
* *
2064452 GGTACCGATACTACCCTTATA
1 -GTATCGATACTACCCTTACA
* *
2064473 GTATCGATACCATCCTTA-A
1 GTATCGATACTACCCTTACA
* *
2064492 GGTACCAATACTACCCTTACA
1 -GTATCGATACTACCCTTACA
*
2064513 GTATCGATAC--CTCTTCAACAA
1 GTATCGATACTACCCTT--AC-A
2064534 GTATCGATACTACCCTTACA
1 GTATCGATACTACCCTTACA
2064554 AAATACTCAT
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.05
19 1 0.01
20 55 0.70
21 15 0.19
23 4 0.05
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (20 bp):
GTATCGATACTACCCTTACA
Found at i:2067428 original size:19 final size:19
Alignment explanation
Indices: 2067378--2067428 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
2067368 GTTATTAATG
*
2067378 TTTTATTCATTTTTTTTAAA
1 TTTTATT-ATTATTTTTAAA
* *
2067398 TTTAACTCATTATTTTTAAA
1 TTTTA-TTATTATTTTTAAA
2067418 TTTTATTATTA
1 TTTTATTATTA
2067429 ATATAGATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.20
20 19 0.76
21 1 0.04
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATTATTATTTTTAAA
Found at i:2070368 original size:21 final size:21
Alignment explanation
Indices: 2070326--2070376 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2070316 CATAAAGTTT
*
2070326 GTTCACATTCACTGGTTCAAA
1 GTTCACATTCACTGATTCAAA
* *
2070347 GTTCACATTCACTTATTTAAA
1 GTTCACATTCACTGATTCAAA
*
2070368 GTTTACATT
1 GTTCACATT
2070377 TCTATAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:2070829 original size:54 final size:54
Alignment explanation
Indices: 2070758--2070900 Score: 153
Period size: 54 Copynumber: 2.6 Consensus size: 54
2070748 ACCACCCTTC
* *
2070758 AAGGGTATCGATGCCTCCTCATGGTACCGATACCGAA-ATAACATTCGATGTTAT
1 AAGGGTATCGATACCTCCTCAAGGTACCGATACC-AATATAACATTCGATGTTAT
* * * * ** *
2070812 AAGGGTATCAATACCTCCCCAAGGTACCGATGCCAATCTGGCATTCGATGTTTT
1 AAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGTTAT
* * *
2070866 AAGGGTATCGATACCATCCTTAAGTTATCGATACC
1 AAGGGTATCGATACC-TCCTCAAGGTACCGATACC
2070901 CATCCCTTAC
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
53 2 0.03
54 56 0.78
55 14 0.19
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (54 bp):
AAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGTTAT
Found at i:2070896 original size:20 final size:21
Alignment explanation
Indices: 2070864--2070923 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
2070854 ATTCGATGTT
2070864 TTAAGGGTATCGATACCAT-CC
1 TTAA-GGTATCGATACCATCCC
*
2070885 TTAAGTTATCGATACCCATCCC
1 TTAAGGTATCGATA-CCATCCC
*
2070907 TTACGGTATCGATACCA
1 TTAAGGTATCGATACCA
2070924 CTCTCAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.26
21 11 0.32
22 14 0.41
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (21 bp):
TTAAGGTATCGATACCATCCC
Found at i:2077044 original size:23 final size:23
Alignment explanation
Indices: 2077012--2077064 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
2077002 TCTCGAATAA
**
2077012 CCACATAGGTTTGCACTGAAGTG
1 CCACATAGGTTTGCACCAAAGTG
*
2077035 CTACATAGGTTTGCACCAAAGTG
1 CCACATAGGTTTGCACCAAAGTG
2077058 CCACATA
1 CCACATA
2077065 TTTGTCCCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (23 bp):
CCACATAGGTTTGCACCAAAGTG
Found at i:2077083 original size:21 final size:21
Alignment explanation
Indices: 2077058--2077107 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2077048 CACCAAAGTG
*
2077058 CCACATATTTGTCCC-GAATGA
1 CCACATAATTGTCCCAG-ATGA
*
2077079 GCACATAATTGTCCCAGATGA
1 CCACATAATTGTCCCAGATGA
2077100 CCACATAA
1 CCACATAA
2077108 AACCCTCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (21 bp):
CCACATAATTGTCCCAGATGA
Found at i:2077266 original size:21 final size:21
Alignment explanation
Indices: 2077240--2077290 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
2077230 AATAAAGTTT
*
2077240 GTTCACATTCACTGGTTCAAA
1 GTTCACATTCACTGATTCAAA
*
2077261 GTTCACATTCACTTATTCAAA
1 GTTCACATTCACTGATTCAAA
*
2077282 GTTTACATT
1 GTTCACATT
2077291 TCTATAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:2077746 original size:54 final size:54
Alignment explanation
Indices: 2077678--2077800 Score: 149
Period size: 54 Copynumber: 2.3 Consensus size: 54
2077668 ACCACCCTTC
* * *
2077678 AAGGGTATCAATACCTCCTCATGGTACCGATACCGAA-ATAACATTCGATGTTAT
1 AAGGGTATCGATACCTCCCCAAGGTACCGATACC-AATATAACATTCGATGTTAT
* * * * *
2077732 AAGGGTATCGATACCTCCCCAAGGTACTGGTACCAATCTGACATTCGATGTTTT
1 AAGGGTATCGATACCTCCCCAAGGTACCGATACCAATATAACATTCGATGTTAT
*
2077786 AAGGTTATCGATACC
1 AAGGGTATCGATACC
2077801 ATAATTAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 2 0.03
54 57 0.97
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (54 bp):
AAGGGTATCGATACCTCCCCAAGGTACCGATACCAATATAACATTCGATGTTAT
Found at i:2077823 original size:21 final size:22
Alignment explanation
Indices: 2077784--2077842 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2077774 ATTCGATGTT
2077784 TTAAGGTTATCGATA-CCAT-AA
1 TTAAGG-TATCGATACCCATCAA
**
2077805 TTAAGGTATCGATACCCATCCC
1 TTAAGGTATCGATACCCATCAA
*
2077827 TTACGGTATCGATACC
1 TTAAGGTATCGATACC
2077843 ACTCTCAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.24
21 10 0.30
22 15 0.45
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (22 bp):
TTAAGGTATCGATACCCATCAA
Found at i:2078873 original size:14 final size:16
Alignment explanation
Indices: 2078843--2078875 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2078833 AATTTCATTG
2078843 TTTGATAAATGATTTT
1 TTTGATAAATGATTTT
2078859 TTTGA-AAAT-ATTTT
1 TTTGATAAATGATTTT
2078873 TTT
1 TTT
2078876 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (16 bp):
TTTGATAAATGATTTT
Found at i:2078886 original size:20 final size:24
Alignment explanation
Indices: 2078858--2078916 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
2078848 TAAATGATTT
*
2078858 TTTTGAAAAT-ATTT-TTTT-A-A
1 TTTTAAAAATAATTTATTTTCATA
2078878 TTTTAAAAATAATTTATTTTCATA
1 TTTTAAAAATAATTTATTTTCATA
*
2078902 TATTTAAAAAAAATT
1 T-TTTAAAAATAATT
2078917 GAAAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 9 0.28
21 4 0.12
22 4 0.12
23 1 0.03
24 2 0.06
25 12 0.38
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTAAAAATAATTTATTTTCATA
Found at i:2079206 original size:26 final size:26
Alignment explanation
Indices: 2079177--2079229 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2079167 CCTAATTTAT
*
2079177 ATTAGTGGTACATTTCAATGCATGTC
1 ATTAGTGGTACATTTCAATGAATGTC
*
2079203 ATTAGTGGTGCATTTCAATGAATGTC
1 ATTAGTGGTACATTTCAATGAATGTC
2079229 A
1 A
2079230 CACATTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTAGTGGTACATTTCAATGAATGTC
Found at i:2079362 original size:2 final size:2
Alignment explanation
Indices: 2079357--2079394 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2079347 AAAAACCCTA
2079357 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
2079395 TAATTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2082464 original size:2 final size:2
Alignment explanation
Indices: 2082457--2082490 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2082447 GAATAATTTG
2082457 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
2082491 TACATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2083157 original size:27 final size:27
Alignment explanation
Indices: 2083126--2083177 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2083116 AAACTTAAGG
2083126 GCTTTGCAACTACCCCCAAGAAACTGA
1 GCTTTGCAACTACCCCCAAGAAACTGA
*
2083153 GCTTTGCAACTACTCCCAAGAAACT
1 GCTTTGCAACTACCCCCAAGAAACT
2083178 TTATCCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.21
Consensus pattern (27 bp):
GCTTTGCAACTACCCCCAAGAAACTGA
Found at i:2085034 original size:32 final size:32
Alignment explanation
Indices: 2084998--2085065 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
2084988 TGTCATGTCA
*
2084998 AAAAAATCCA-TTAAATGACACATATCACGTCT
1 AAAAAAT-CAGTTAAATGACACATATCACATCT
* *
2085030 -AAAAATCATGTTAAGTGACACATGTCACATCT
1 AAAAAATCA-GTTAAATGACACATATCACATCT
2085062 AAAA
1 AAAA
2085066 TTTTTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 2 0.07
31 6 0.20
32 19 0.63
33 3 0.10
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (32 bp):
AAAAAATCAGTTAAATGACACATATCACATCT
Found at i:2086832 original size:3 final size:3
Alignment explanation
Indices: 2086809--2086849 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
2086799 TTGTCCCGTT
* *
2086809 TTA TTA TAA TAA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2086850 ATAAATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2088482 original size:2 final size:2
Alignment explanation
Indices: 2088475--2088502 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2088465 TATATTAGTC
2088475 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
2088503 TTGTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2093821 original size:17 final size:18
Alignment explanation
Indices: 2093792--2093825 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2093782 TTACAATTAA
2093792 TCAACCACATCTTCTTCC
1 TCAACCACATCTTCTTCC
2093810 TCAACC-CATCTTCTTC
1 TCAACCACATCTTCTTC
2093826 TTCTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (18 bp):
TCAACCACATCTTCTTCC
Found at i:2094453 original size:18 final size:18
Alignment explanation
Indices: 2094420--2094465 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2094410 AAGAAAGAAA
*
2094420 GAAGAAG-AGATTGGGTT
1 GAAGAAGAAGATGGGGTT
*
2094437 GAGGAAGAAGATGGGGTT
1 GAAGAAGAAGATGGGGTT
2094455 GAAGAAGAAGA
1 GAAGAAGAAGA
2094466 ATAGTCGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.41, C:0.00, G:0.43, T:0.15
Consensus pattern (18 bp):
GAAGAAGAAGATGGGGTT
Found at i:2096802 original size:3 final size:3
Alignment explanation
Indices: 2096794--2096826 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2096784 TAATGCCATG
2096794 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
2096827 AACCCAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:2108867 original size:23 final size:23
Alignment explanation
Indices: 2108841--2108894 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
2108831 AAATGCACTG
2108841 AAGTGCCACGTAGAATTGCACCA
1 AAGTGCCACGTAGAATTGCACCA
*
2108864 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCA
2108887 AAGTGCCA
1 AAGTGCCA
2108895 TATAAAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCA
Found at i:2109421 original size:2 final size:2
Alignment explanation
Indices: 2109407--2109458 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
2109397 ACTCATAGTC
2109407 AT AT AT AGT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2109449 AT AT AT AT AT
1 AT AT AT AT AT
2109459 CATTTTACCT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2111923 original size:90 final size:90
Alignment explanation
Indices: 2111783--2111960 Score: 266
Period size: 90 Copynumber: 2.0 Consensus size: 90
2111773 TAATCCCGAA
* * * * * * *
2111783 TATTTAATTTCAACTAATTAAATATAGATTTAATTAATTTTAAATAATAAAATCCCTGATATAAT
1 TATTAAATTCCAACTAATTAAACATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAC
2111848 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
* *
2111873 TATTAAATTCCAATTAATTAAACATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAACTAATTAAACATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAC
*
2111938 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
2111961 GTGTGTTAGG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (90 bp):
TATTAAATTCCAACTAATTAAACATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:2112786 original size:16 final size:16
Alignment explanation
Indices: 2112765--2112805 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
2112755 CTTCACGTGA
2112765 AGAAGAAGAAGAAAGG
1 AGAAGAAGAAGAAAGG
*
2112781 AGAAGAAGAAGAAATG
1 AGAAGAAGAAGAAAGG
2112797 AGAAGAAGA
1 AGAAGAAGA
2112806 GAACTCTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (16 bp):
AGAAGAAGAAGAAAGG
Found at i:2113254 original size:17 final size:17
Alignment explanation
Indices: 2113232--2113265 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2113222 TTTCCTCTCT
2113232 TTCTATTCTGCATTTTC
1 TTCTATTCTGCATTTTC
2113249 TTCTATTCTGCATTTTC
1 TTCTATTCTGCATTTTC
2113266 CTTTGTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.59
Consensus pattern (17 bp):
TTCTATTCTGCATTTTC
Found at i:2115605 original size:23 final size:23
Alignment explanation
Indices: 2115587--2115647 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
2115577 CTCGTATAAA
2115587 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
2115610 TGCACCGAAGTTCCACATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
2115633 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
2115648 TATAAAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2116176 original size:14 final size:14
Alignment explanation
Indices: 2116153--2116183 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2116143 ATTCCAACTC
2116153 ATAGTAATATATAT
1 ATAGTAATATATAT
*
2116167 ATAGTTATATATAT
1 ATAGTAATATATAT
2116181 ATA
1 ATA
2116184 TATCATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (14 bp):
ATAGTAATATATAT
Found at i:2117383 original size:64 final size:63
Alignment explanation
Indices: 2117295--2117454 Score: 164
Period size: 64 Copynumber: 2.5 Consensus size: 63
2117285 CCCTTAACAT
* * *
2117295 GTGCATCGATGCACTACTCATGCATCGATACAC-AA-AGCACCTTCGATGTTT-TAATCTTAAGG
1 GTGCATCGATGCACTCCT-ATGCATCGATACACTAATAGCA--TTCGATATTTCCAATCTTAA-G
2117357 GG
62 GG
* * * * *
2117359 GTGTATCGATGCACTCCCTATGCATCGATGCACTAATTGCATTCGATATTTCCATTTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACTAATAGCATTCGATATTTCCAATCTTAAGGG
*
2117423 GTGCATCGATGCACTTCCTGTGCATCGATACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACA
2117455 TACTGAACAA
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
64 66 0.82
65 11 0.14
66 3 0.04
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACTAATAGCATTCGATATTTCCAATCTTAAGGG
Found at i:2123260 original size:5 final size:5
Alignment explanation
Indices: 2123232--2123272 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
2123222 CCAAAGTTTA
*
2123232 AAAAT -AAAT -AAAT -AAAT AAGAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
2123273 ATCCAAAGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 12 0.36
5 21 0.64
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:2129091 original size:32 final size:33
Alignment explanation
Indices: 2129049--2129162 Score: 126
Period size: 32 Copynumber: 3.5 Consensus size: 33
2129039 ATACTAGCAG
* *
2129049 TGTTGCATTCAAATAATGCACAACAGTA-TTAA
1 TGTTGTATTCAGATAATGCACAACAGTAGTTAA
* *
2129081 TGTTGTATTCAGATAATGAACAACAG-AGTTAC
1 TGTTGTATTCAGATAATGCACAACAGTAGTTAA
* *
2129113 TGTTGTATTCAGATAATGCATAACAGT-GTCAA
1 TGTTGTATTCAGATAATGCACAACAGTAGTTAA
** *
2129145 TGTCATATTTAGATAATG
1 TGTTGTATTCAGATAATG
2129163 TAAAGAAATT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
31 1 0.01
32 68 0.99
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTTGTATTCAGATAATGCACAACAGTAGTTAA
Found at i:2129678 original size:24 final size:24
Alignment explanation
Indices: 2129651--2129706 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
2129641 TAACTGTCAT
2129651 GTATGTTTATTTTGATACCATATA
1 GTATGTTTATTTTGATACCATATA
*
2129675 GTATGTTTATTTTGATACCTTATA
1 GTATGTTTATTTTGATACCATATA
2129699 GTATGTTT
1 GTATGTTT
2129707 TAAAATGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (24 bp):
GTATGTTTATTTTGATACCATATA
Found at i:2139287 original size:53 final size:54
Alignment explanation
Indices: 2139217--2139325 Score: 202
Period size: 53 Copynumber: 2.0 Consensus size: 54
2139207 AAGAAAAACA
*
2139217 AAACTTGTAGTAACAATTCAAGAATTTTTCTTTTAAGAATGCCA-AAAAAATGG
1 AAACTTGTAGTAACAATTCAAGAAATTTTCTTTTAAGAATGCCACAAAAAATGG
2139270 AAACTTGTAGTAACAATTCAAGAAATTTTCTTTTAAGAATGCCACAAAAAATGG
1 AAACTTGTAGTAACAATTCAAGAAATTTTCTTTTAAGAATGCCACAAAAAATGG
2139324 AA
1 AA
2139326 CATTATGTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 43 0.80
54 11 0.20
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (54 bp):
AAACTTGTAGTAACAATTCAAGAAATTTTCTTTTAAGAATGCCACAAAAAATGG
Found at i:2140999 original size:2 final size:2
Alignment explanation
Indices: 2140994--2141029 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2140984 CAAGTAGTTG
*
2140994 TA TA TA CA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2141030 GTTAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2155689 original size:22 final size:22
Alignment explanation
Indices: 2155657--2155701 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2155647 CAAAATTTAG
*
2155657 CGAAATTGAAATTAA-TCAGAAT
1 CGAAATCGAAATTAACTC-GAAT
2155679 CGAAATCGAAATTAACTCGAAT
1 CGAAATCGAAATTAACTCGAAT
2155701 C
1 C
2155702 AAAAGTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (22 bp):
CGAAATCGAAATTAACTCGAAT
Found at i:2157303 original size:24 final size:24
Alignment explanation
Indices: 2157271--2157318 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2157261 AAACTATAAG
*
2157271 GAACGTGTCACAAGAGCAGAGAAA
1 GAACATGTCACAAGAGCAGAGAAA
2157295 GAACATGTCACAAGAGCAGAGAAA
1 GAACATGTCACAAGAGCAGAGAAA
2157319 TTGTGTCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.27, T:0.08
Consensus pattern (24 bp):
GAACATGTCACAAGAGCAGAGAAA
Found at i:2157328 original size:22 final size:23
Alignment explanation
Indices: 2157271--2157339 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 23
2157261 AAACTATAAG
2157271 GAACGTGTCACAAGAGCAGAGAAA
1 GAACGTGTCACAAGAGCAGAG-AA
*
2157295 GAACATGTCACAAGAGCAGAGAA
1 GAACGTGTCACAAGAGCAGAGAA
**
2157318 -ATTGTGTCACAAG-GACAGAGAA
1 GAACGTGTCACAAGAG-CAGAGAA
2157340 TCTTATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 17 0.43
23 2 0.05
24 20 0.50
ACGTcount: A:0.45, C:0.16, G:0.28, T:0.12
Consensus pattern (23 bp):
GAACGTGTCACAAGAGCAGAGAA
Found at i:2171088 original size:23 final size:23
Alignment explanation
Indices: 2171038--2171102 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
2171028 AGATTAGATC
2171038 TGAGAATAAATGAGAG-TTGTTT
1 TGAGAATAAATGAGAGTTTGTTT
*
2171060 TGAGAATAAATGAGAGTTTTTTT
1 TGAGAATAAATGAGAGTTTGTTT
*
2171083 TTAGAATAAATGAGAGTTTG
1 TGAGAATAAATGAGAGTTTG
2171103 AATACACAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.37, C:0.00, G:0.25, T:0.38
Consensus pattern (23 bp):
TGAGAATAAATGAGAGTTTGTTT
Found at i:2178728 original size:60 final size:60
Alignment explanation
Indices: 2178662--2178775 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 60
2178652 GCTCAGAGAA
* *
2178662 AAGTTCATTATAATGTTTTCAATACAAATTTCATAAATCTTCAACTTAAGTACACATGCT
1 AAGTTCATTATAAAGTTTTCAATACAAAATTCATAAATCTTCAACTTAAGTACACATGCT
* *
2178722 AAGTTCATTATAAAGTTTTCAATGCAAAATTCCTAAATCTTCAACTTAAGTACA
1 AAGTTCATTATAAAGTTTTCAATACAAAATTCATAAATCTTCAACTTAAGTACA
2178776 TGTTACGTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (60 bp):
AAGTTCATTATAAAGTTTTCAATACAAAATTCATAAATCTTCAACTTAAGTACACATGCT
Found at i:2186282 original size:20 final size:20
Alignment explanation
Indices: 2186257--2186310 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2186247 GGCCATCCGA
2186257 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
2186277 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
2186297 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
2186311 CCGAGGTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.37, G:0.28, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:2186324 original size:10 final size:10
Alignment explanation
Indices: 2186257--2186310 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
2186247 GGCCATCCGA
2186257 CCGAGGCCAT
1 CCGAGGCCAT
*
2186267 CCGAAAG-CAT
1 CCG-AGGCCAT
2186277 CCGAGGCCAT
1 CCGAGGCCAT
2186287 CCGAGAG-CAT
1 CCGAG-GCCAT
2186297 CCGAGGCCAT
1 CCGAGGCCAT
2186307 CCGA
1 CCGA
2186311 CCGAGGTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 3 0.08
10 32 0.84
11 3 0.08
ACGTcount: A:0.26, C:0.37, G:0.28, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:2186394 original size:33 final size:33
Alignment explanation
Indices: 2186353--2186436 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
2186343 ACCGAATTCC
*
2186353 CTCGCTCGGTTGCCCTCGAATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGAATGCCCTCGCATAG
*
2186386 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGAATGCCCTCGCATAG
* * *
2186419 CTCGTTCGGATGGCCTCG
1 CTCGCTCGGTTGCCCTCG
2186437 GTCGGATGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.10, C:0.38, G:0.26, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGAATGCCCTCGCATAG
Found at i:2186409 original size:10 final size:10
Alignment explanation
Indices: 2186357--2186497 Score: 66
Period size: 10 Copynumber: 13.1 Consensus size: 10
2186347 AATTCCCTCG
*
2186357 CTCGGTTGCC
1 CTCGGATGCC
* *
2186367 CTCGAATTCC
1 CTCGGATGCC
*
2186377 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
2186389 GCTCGGTTGCC
1 -CTCGGATGCC
2186400 CTCGGATGCC
1 CTCGGATGCC
*
2186410 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
2186422 GTTCGGATGGCC
1 -CTCGGAT-GCC
**
2186434 TCGGTCGGATGAT
1 -C--TCGGATGCC
*
2186447 CTCGGATGCT
1 CTCGGATGCC
*
2186457 CTCGGATGGC
1 CTCGGATGCC
*
2186467 CTCGGATGCT
1 CTCGGATGCC
* *
2186477 TTCGGATGGC
1 CTCGGATGCC
2186487 CTCGGATGCC
1 CTCGGATGCC
2186497 C
1 C
2186498 AGCGTGTTGG
Statistics
Matches: 97, Mismatches: 26, Indels: 16
0.70 0.19 0.12
Matches are distributed among these distances:
10 68 0.70
11 4 0.04
12 6 0.06
13 13 0.13
14 6 0.06
ACGTcount: A:0.11, C:0.33, G:0.30, T:0.26
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:2186463 original size:20 final size:20
Alignment explanation
Indices: 2186447--2186495 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2186437 GTCGGATGAT
2186447 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
*
2186467 CTCGGATGCTTTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
2186487 CTCGGATGC
1 CTCGGATGC
2186496 CCAGCGTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.29, G:0.35, T:0.27
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:2186472 original size:30 final size:30
Alignment explanation
Indices: 2186438--2186494 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2186428 ATGGCCTCGG
2186438 TCGGATGATCTCGGAT-GCTCTCGGATGGCC
1 TCGGATGATCTCGGATGGC-CTCGGATGGCC
* *
2186468 TCGGATGCTTTCGGATGGCCTCGGATG
1 TCGGATGATCTCGGATGGCCTCGGATG
2186495 CCCAGCGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.12, C:0.25, G:0.35, T:0.28
Consensus pattern (30 bp):
TCGGATGATCTCGGATGGCCTCGGATGGCC
Found at i:2186600 original size:29 final size:29
Alignment explanation
Indices: 2186542--2186643 Score: 168
Period size: 29 Copynumber: 3.5 Consensus size: 29
2186532 CTGCATGGAT
* *
2186542 TGCATGGCGACCTACCTAGGTTGCTGGGCG
1 TGCATGGCGACCTA-GTAGGTCGCTGGGCG
*
2186572 TGCATGGCGACCTAGTAGGTCGTTGGGCG
1 TGCATGGCGACCTAGTAGGTCGCTGGGCG
2186601 TGCATGGCGACCTAGTAGGTCGCTGGGCG
1 TGCATGGCGACCTAGTAGGTCGCTGGGCG
2186630 TGCATGGCGACCTA
1 TGCATGGCGACCTA
2186644 TATGGGGACT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
29 54 0.79
30 14 0.21
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.23
Consensus pattern (29 bp):
TGCATGGCGACCTAGTAGGTCGCTGGGCG
Found at i:2189369 original size:25 final size:25
Alignment explanation
Indices: 2189341--2189393 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
2189331 AAACGGGGAT
*
2189341 GGGAAAAAATCGTTTATGTTAAACG
1 GGGAAAAAACCGTTTATGTTAAACG
2189366 GGG-AAAAACCGTTTATGTTAAACG
1 GGGAAAAAACCGTTTATGTTAAACG
2189390 GGGA
1 GGGA
2189394 CGGGGACGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.38, C:0.09, G:0.28, T:0.25
Consensus pattern (25 bp):
GGGAAAAAACCGTTTATGTTAAACG
Found at i:2206040 original size:16 final size:16
Alignment explanation
Indices: 2206019--2206049 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2206009 AAAAATAAAT
2206019 GAACATAAACGAACAC
1 GAACATAAACGAACAC
2206035 GAACATAAACGAACA
1 GAACATAAACGAACA
2206050 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:2206156 original size:16 final size:16
Alignment explanation
Indices: 2206137--2206167 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2206127 AAACGCGCAC
2206137 GAACACGAACATAAAT
1 GAACACGAACATAAAT
2206153 GAACACGAACATAAA
1 GAACACGAACATAAA
2206168 CGTTGGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (16 bp):
GAACACGAACATAAAT
Found at i:2206159 original size:22 final size:22
Alignment explanation
Indices: 2206119--2206163 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2206109 TAATAAATAA
**
2206119 ACGAACATAAACGCGCACGAAC
1 ACGAACATAAACGAACACGAAC
*
2206141 ACGAACATAAATGAACACGAAC
1 ACGAACATAAACGAACACGAAC
2206163 A
1 A
2206164 TAAACGTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.27, G:0.16, T:0.07
Consensus pattern (22 bp):
ACGAACATAAACGAACACGAAC
Found at i:2206414 original size:11 final size:11
Alignment explanation
Indices: 2206398--2206426 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2206388 TCGAGACTTG
2206398 AGCTCGATTCA
1 AGCTCGATTCA
2206409 AGCTCGATTCA
1 AGCTCGATTCA
2206420 AGCTCGA
1 AGCTCGA
2206427 CATTGCCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:2207250 original size:10 final size:10
Alignment explanation
Indices: 2207235--2207267 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
2207225 TAAATGAATA
*
2207235 AACATAAACG
1 AACATAACCG
2207245 AACATAACCG
1 AACATAACCG
2207255 AACATAACCG
1 AACATAACCG
2207265 AAC
1 AAC
2207268 GAACATAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.55, C:0.27, G:0.09, T:0.09
Consensus pattern (10 bp):
AACATAACCG
Found at i:2207268 original size:24 final size:24
Alignment explanation
Indices: 2207241--2207305 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
2207231 AATAAACATA
*
2207241 AACGAACATAACCGAACATAACCG
1 AACGAACATAACCGAACATAACAG
* *
2207265 AACGAACATAAACAAACATAACAG
1 AACGAACATAACCGAACATAACAG
2207289 AACGAACATAACCGAAC
1 AACGAACATAACCGAAC
2207306 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.55, C:0.26, G:0.11, T:0.08
Consensus pattern (24 bp):
AACGAACATAACCGAACATAACAG
Found at i:2207272 original size:14 final size:14
Alignment explanation
Indices: 2207253--2207306 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
2207243 CGAACATAAC
2207253 CGAACATAACCGAA
1 CGAACATAACCGAA
2207267 CGAACAT-A---AA
1 CGAACATAACCGAA
* *
2207277 CAAACATAACAGAA
1 CGAACATAACCGAA
2207291 CGAACATAACCGAA
1 CGAACATAACCGAA
2207305 CG
1 CG
2207307 TTCACGAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 23 0.70
ACGTcount: A:0.54, C:0.26, G:0.13, T:0.07
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:2207384 original size:40 final size:40
Alignment explanation
Indices: 2207338--2207439 Score: 204
Period size: 40 Copynumber: 2.5 Consensus size: 40
2207328 ACGAGACTTA
2207338 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
1 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
2207378 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
1 TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
2207418 TGTTCATGTTCGTTCATTTAAT
1 TGTTCATGTTCGTTCATTTAAT
2207440 AAATAAACGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (40 bp):
TGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCT
Found at i:2210911 original size:22 final size:22
Alignment explanation
Indices: 2210883--2210924 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2210873 CATAACGGAT
*
2210883 GTTATTACGGTCATTGTAGGAA
1 GTTATTACGATCATTGTAGGAA
2210905 GTTATTACGATCATTGTAGG
1 GTTATTACGATCATTGTAGG
2210925 TATCACAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (22 bp):
GTTATTACGATCATTGTAGGAA
Found at i:2214022 original size:15 final size:15
Alignment explanation
Indices: 2214004--2214041 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2213994 CCAAGAGGCA
2214004 CATGCGCATTGGACC
1 CATGCGCATTGGACC
* *
2214019 CATGCGTATTGGATC
1 CATGCGCATTGGACC
2214034 CATGCGCA
1 CATGCGCA
2214042 CTATTATGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (15 bp):
CATGCGCATTGGACC
Found at i:2218135 original size:26 final size:25
Alignment explanation
Indices: 2218106--2218176 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
2218096 AAAAGGAAAG
2218106 TAAAATACTAATAATAATATGTATATT
1 TAAAA-ACTAAT-ATAATATGTATATT
* *
2218133 AAAAAACT-ATATAATATATATATT
1 TAAAAACTAATATAATATGTATATT
2218157 TCAAAAAC-AATATAATATGT
1 T-AAAAACTAATATAATATGT
2218177 TTTCAAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
24 13 0.34
25 18 0.47
26 3 0.08
27 4 0.11
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.37
Consensus pattern (25 bp):
TAAAAACTAATATAATATGTATATT
Found at i:2218183 original size:22 final size:23
Alignment explanation
Indices: 2218119--2218183 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 23
2218109 AATACTAATA
* *
2218119 ATAATATGTATATTAAAAAACTAT
1 ATAATATGTAT-TTCAAAAACAAT
*
2218143 ATAATATATATATTTCAAAAACAAT
1 AT-A-ATATGTATTTCAAAAACAAT
2218168 ATAATATGT-TTTCAAA
1 ATAATATGTATTTCAAA
2218184 GATTATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 7 0.20
23 5 0.14
24 3 0.09
25 13 0.37
26 7 0.20
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (23 bp):
ATAATATGTATTTCAAAAACAAT
Found at i:2218245 original size:38 final size:37
Alignment explanation
Indices: 2218189--2218308 Score: 145
Period size: 38 Copynumber: 3.2 Consensus size: 37
2218179 TCAAAGATTA
* *
2218189 TATATATTATATACGTTTTCAAGAATCGTTTTTTAAAAAC
1 TATATATTATAT--GTTTTCAAAAATC-ATTTTTAAAAAC
*
2218229 TATATATTATATGTTTTCAAAAAACCATTTTTAAAAAC
1 TATATATTATATGTTTTC-AAAAATCATTTTTAAAAAC
* *
2218267 TATATATTATAT-ATTTCAAAAAT-ATTTTCAAAAAC
1 TATATATTATATGTTTTCAAAAATCATTTTTAAAAAC
2218302 TATATAT
1 TATATAT
2218309 ATCTTCAAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
35 18 0.25
36 5 0.07
37 4 0.05
38 29 0.40
39 5 0.07
40 12 0.16
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATATTATATGTTTTCAAAAATCATTTTTAAAAAC
Found at i:2218327 original size:2 final size:2
Alignment explanation
Indices: 2218322--2218410 Score: 139
Period size: 2 Copynumber: 45.5 Consensus size: 2
2218312 TTCAAAAACA
*
2218322 AT AT AT AT AT A- AT AT AT AT AT AT AT A- AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2218362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2218403 CAT AT AT A
1 -AT AT AT A
2218411 CTAAATAAAG
Statistics
Matches: 81, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
1 3 0.04
2 76 0.94
3 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2218331 original size:21 final size:19
Alignment explanation
Indices: 2218288--2218329 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2218278 TATTTCAAAA
*
2218288 ATATTTTCAAAAACTATAT
1 ATATCTTCAAAAACTATAT
*
2218307 ATATCTTCAAAAACAATAT
1 ATATCTTCAAAAACTATAT
2218326 ATAT
1 ATAT
2218330 ATAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATCTTCAAAAACTATAT
Found at i:2219413 original size:201 final size:201
Alignment explanation
Indices: 2219059--2219471 Score: 560
Period size: 201 Copynumber: 2.1 Consensus size: 201
2219049 CGACTGAAGT
* * * * * *
2219059 TATGTTGTAAATTAGGCTGGAAGATAGTTCATTGTTGCTAAATCACAGCTAACCTAGGTCTTCTT
1 TATGTTGTGAATTAGGCTGGAAGATAATTCATTGTAGCTAAATCACAACCAACCTAGGCCTTCTT
* *
2219124 CTTGGCTTAAAGACCTCGGTTTAAAATTCAATCAGAAAATAGTTCCTCGCTTCTACCATGCGATT
66 CTTGGCTTAAAGACCTCGGTCTAAAATTCAATCAGAAAATAGTTCATCGCTTCTACCATGCGATT
* * * ** * *
2219189 GATAAGCCATCGAGTTGAATGGAATCGAACTCGAAAGTTTTCGTTGACTGATAGCCCTTCTTGCT
131 GATAAGCCATCGAGCTGAATGGAATCAAACTCGAAAGTTTTCATTGACAAATAACCCTTCTTGCC
2219254 TTGAGC
196 TTGAGC
* * * **
2219260 TATGCTGTGAATTAGGCTGGGAGATAATTCCTTGTAGCTAAATCGTAACCAACCTAGGCCTTCTT
1 TATGTTGTGAATTAGGCTGGAAGATAATTCATTGTAGCTAAATCACAACCAACCTAGGCCTTCTT
* * * *
2219325 CTTGGCTTAAAGACCTCGGTCTAAAATTTAGTTAGAAAGTAGTTCATCG-TTGCTACCATGC-AG
66 CTTGGCTTAAAGACCTCGGTCTAAAATTCAATCAGAAAATAGTTCATCGCTT-CTACCATGCGA-
* *
2219388 TTGATACGCCCTCGAGCTGAATGGAATCAAACTCGAAAGTTTTCATTGACAAATAACCCTTCTTG
129 TTGATAAGCCATCGAGCTGAATGGAATCAAACTCGAAAGTTTTCATTGACAAATAACCCTTCTTG
2219453 CCTTGAGC
194 CCTTGAGC
2219461 TATGTTGTGAA
1 TATGTTGTGAA
2219472 CGGTTCCTCT
Statistics
Matches: 183, Mismatches: 27, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
200 3 0.02
201 180 0.98
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (201 bp):
TATGTTGTGAATTAGGCTGGAAGATAATTCATTGTAGCTAAATCACAACCAACCTAGGCCTTCTT
CTTGGCTTAAAGACCTCGGTCTAAAATTCAATCAGAAAATAGTTCATCGCTTCTACCATGCGATT
GATAAGCCATCGAGCTGAATGGAATCAAACTCGAAAGTTTTCATTGACAAATAACCCTTCTTGCC
TTGAGC
Found at i:2219891 original size:23 final size:23
Alignment explanation
Indices: 2219865--2219919 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
2219855 TAAATTGAAT
*
2219865 CCATTCTGAATTATCTCTCGAAC
1 CCATTCTGAATTAGCTCTCGAAC
*
2219888 CCA-TCTGAATTGGCTCTCGAAC
1 CCATTCTGAATTAGCTCTCGAAC
2219910 CCGATT-TGAA
1 CC-ATTCTGAA
2219920 GTTGATTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 19 0.68
23 8 0.29
24 1 0.04
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (23 bp):
CCATTCTGAATTAGCTCTCGAAC
Found at i:2242784 original size:23 final size:23
Alignment explanation
Indices: 2242751--2242818 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
2242741 CATCTTTTAT
*
2242751 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
2242774 GGCACTTCGGTGCAATTCTATGT
1 GGCACTTCGGTGCATTTCTACGC
* *
2242797 GGCACTTTGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
2242819 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:2243099 original size:6 final size:6
Alignment explanation
Indices: 2243088--2243134 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
2243078 AATGTATTAC
* * *
2243088 ATGATA ATGATA TTGATA TTGATA ATGATA GA-GATC ATGATA ATGAT
1 ATGATA ATGATA ATGATA ATGATA ATGATA -ATGATA ATGATA ATGAT
2243135 GGTATATGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 1 0.03
6 33 0.94
7 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (6 bp):
ATGATA
Found at i:2243128 original size:18 final size:18
Alignment explanation
Indices: 2243087--2243134 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
2243077 AAATGTATTA
**
2243087 CATGATAATGATATTGAT
1 CATGATAATGATAGAGAT
2243105 -ATTGATAATGATAGAGAT
1 CA-TGATAATGATAGAGAT
2243123 CATGATAATGAT
1 CATGATAATGAT
2243135 GGTATATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:2243481 original size:16 final size:15
Alignment explanation
Indices: 2243460--2243489 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2243450 CGCATGCTTC
2243460 CCCTTTTTCTCTTTTT
1 CCCTTTTTCT-TTTTT
2243476 CCCTTTTTCTTTTT
1 CCCTTTTTCTTTTT
2243490 GTCCAAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
CCCTTTTTCTTTTTT
Found at i:2248570 original size:2 final size:2
Alignment explanation
Indices: 2248563--2248597 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2248553 TCATTCTACA
2248563 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
2248598 ATTTACGACA
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:2248765 original size:85 final size:85
Alignment explanation
Indices: 2248615--2248782 Score: 198
Period size: 85 Copynumber: 2.0 Consensus size: 85
2248605 ACATACAATC
* * * * *
2248615 ATGACACACGAATGTGTGTCATCTTTTCTAATGACGTGTGCTTCAATGACATGTAATGTAAGTCA
1 ATGACACACAAATGTGTGTCATCTTTTCTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCA
**
2248680 TAAATGCGTGCCATAAATTT
66 TAAATGCGCACCATAAATTT
* * *
2248700 ATGACACACAAATGTGTGTCGTCTTCATT-T-ATGACGGGGGCTTCAATGACGCGCAATG-AGCG
1 ATGACACACAAATGTGTGTCATCTT--TTCTAATGACGGGGGCTTCAATGACACGCAATGTA-AG
2248762 TCATAAATGCGCACCATAAAT
63 TCATAAATGCGCACCATAAAT
2248783 GAATGTCATA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 1 0.01
85 66 0.94
86 1 0.01
87 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (85 bp):
ATGACACACAAATGTGTGTCATCTTTTCTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCA
TAAATGCGCACCATAAATTT
Found at i:2248783 original size:26 final size:26
Alignment explanation
Indices: 2248754--2248821 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
2248744 AATGACGCGC
2248754 AATGAGCGTCATAAATGCGCACCATA
1 AATGAGCGTCATAAATGCGCACCATA
** * ***
2248780 AATGAATGTCATAAATGTGTGTCATA
1 AATGAGCGTCATAAATGCGCACCATA
*
2248806 AATGTGCGTCATAAAT
1 AATGAGCGTCATAAAT
2248822 TTATGACGCA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGCACCATA
Found at i:2248810 original size:13 final size:13
Alignment explanation
Indices: 2248776--2248821 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
2248766 AAATGCGCAC
**
2248776 CATAAATGAATGT
1 CATAAATGTGTGT
2248789 CATAAATGTGTGT
1 CATAAATGTGTGT
*
2248802 CATAAATGTGCGT
1 CATAAATGTGTGT
2248815 CATAAAT
1 CATAAAT
2248822 TTATGACGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (13 bp):
CATAAATGTGTGT
Found at i:2262051 original size:23 final size:23
Alignment explanation
Indices: 2262025--2262093 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
2262015 ACATCTTATA
* *
2262025 CGGCACTACAGTGCATTTCTACG
1 CGGCACTTCGGTGCATTTCTACG
* *
2262048 CGGCACTTCGGTGCAATTCTATG
1 CGGCACTTCGGTGCATTTCTACG
* *
2262071 TGGCACTTCGGTGCATTTATACG
1 CGGCACTTCGGTGCATTTCTACG
2262094 AACTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
CGGCACTTCGGTGCATTTCTACG
Found at i:2263177 original size:26 final size:28
Alignment explanation
Indices: 2263140--2263200 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2263130 TATATATAAA
* * *
2263140 ATAATATGTATT-TA-TTAAAAAACTAT
1 ATAATATATATTATATTTAAAAAACAAC
*
2263166 ATAATATATATTATATTTCAAAAACAAC
1 ATAATATATATTATATTTAAAAAACAAC
2263194 ATAATAT
1 ATAATAT
2263201 GTTTTCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 11 0.38
27 2 0.07
28 16 0.55
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (28 bp):
ATAATATATATTATATTTAAAAAACAAC
Found at i:2263262 original size:23 final size:23
Alignment explanation
Indices: 2263234--2263289 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
2263224 CAAAAACCCA
*
2263234 TTTTAAAAAC-TATATTATATGTT
1 TTTTAAAAACATATATTATAT-AT
2263257 TTTTAAAAACTATATATTATATAT
1 TTTTAAAAAC-ATATATTATATAT
2263281 TTTTAAAAA
1 TTTTAAAAA
2263290 TATGTTCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 10 0.33
24 10 0.33
25 10 0.33
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTAAAAACATATATTATATAT
Found at i:2263510 original size:2 final size:2
Alignment explanation
Indices: 2263503--2263537 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2263493 ACCATGCTTC
2263503 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
2263538 ATTGTCAATC
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:2263915 original size:24 final size:26
Alignment explanation
Indices: 2263887--2263935 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
2263877 ATTATATATA
*
2263887 ATAATATGTA-GATATTT-AAAAACT
1 ATAATATATATGATATTTCAAAAACT
*
2263911 ATAATATATATTATATTTCAAAAAC
1 ATAATATATATGATATTTCAAAAAC
2263936 AACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 6 0.29
26 6 0.29
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (26 bp):
ATAATATATATGATATTTCAAAAACT
Found at i:2264087 original size:36 final size:36
Alignment explanation
Indices: 2264047--2264174 Score: 105
Period size: 38 Copynumber: 3.4 Consensus size: 36
2264037 TTTCAAAAAC
*
2264047 TATATG-TTTCAAAAAAAACCTTTTTAAAAACTATAT
1 TATATGTTTTC-AAAAAAACCTTTTCAAAAACTATAT
* **
2264083 TATATGTTTTCAAAAATATGTTTTCAAAAACTATATT
1 TATATGTTTTCAAAAAAACCTTTTCAAAAACTATA-T
* **** * *
2264120 ATATATATTTTCAAAAACTGTTTTTTAAAAATTATATAT
1 -TATATGTTTTCAAAAAAACCTTTTCAAAAA--CTATAT
2264159 TATATGTTTTCAAAAA
1 TATATGTTTTCAAAAA
2264175 CTATATTATA
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
36 26 0.35
37 5 0.07
38 39 0.52
39 1 0.01
40 4 0.05
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATGTTTTCAAAAAAACCTTTTCAAAAACTATAT
Found at i:2264103 original size:14 final size:14
Alignment explanation
Indices: 2264084--2264112 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2264074 AAACTATATT
2264084 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
2264098 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
2264112 A
1 A
2264113 CTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:2264134 original size:38 final size:37
Alignment explanation
Indices: 2264067--2264174 Score: 139
Period size: 38 Copynumber: 2.9 Consensus size: 37
2264057 AAAAAAAACC
2264067 TTTTTAAAAACTATAT-TATATGTTTTCAAAAATATG-
1 TTTTTAAAAACTATATATATATGTTTTCAAAAA-ATGT
* * *
2264103 TTTTCAAAAACTATATTATATATATTTTCAAAAACTGT
1 TTTTTAAAAACTATA-TATATATGTTTTCAAAAAATGT
*
2264141 TTTTTAAAAATTATATATTATATGTTTTCAAAAA
1 TTTTTAAAAACTATATA-TATATGTTTTCAAAAA
2264175 CTATATTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
36 14 0.23
37 5 0.08
38 43 0.69
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTTTAAAAACTATATATATATGTTTTCAAAAAATGT
Found at i:2264173 original size:24 final size:24
Alignment explanation
Indices: 2264141--2264199 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2264131 CAAAAACTGT
*
2264141 TTTTTAAAAATTATA-TATTATATG
1 TTTTTAAAAACTATATTA-TATATG
*
2264165 TTTTCAAAAACTATATTATATATG
1 TTTTTAAAAACTATATTATATATG
2264189 TTTTTAAAAAC
1 TTTTTAAAAAC
2264200 CATTTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (24 bp):
TTTTTAAAAACTATATTATATATG
Found at i:2264175 original size:62 final size:61
Alignment explanation
Indices: 2264098--2264235 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 61
2264088 GTTTTCAAAA
** * *
2264098 ATATGTTTTCAAAAACTATATTATATATATTTTCAAAAACTGTTTTTTAAAAATTATATATT
1 ATATGTTTTCAAAAACTATATTATATATATTTTCAAAAAC-CATTTTAAAAAACTATATATT
* *
2264160 ATATGTTTTCAAAAACTATATTATATATGTTTTTAAAAACCATTTTAAAAAACTATATATT
1 ATATGTTTTCAAAAACTATATTATATATATTTTCAAAAACCATTTTAAAAAACTATATATT
*
2264221 ATATGTTTTTAAAAA
1 ATATGTTTTCAAAAA
2264236 TATGTTTCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 31 0.45
62 38 0.55
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (61 bp):
ATATGTTTTCAAAAACTATATTATATATATTTTCAAAAACCATTTTAAAAAACTATATATT
Found at i:2264224 original size:37 final size:37
Alignment explanation
Indices: 2264165--2264262 Score: 119
Period size: 37 Copynumber: 2.6 Consensus size: 37
2264155 ATATTATATG
*
2264165 TTTTCAAAAACTATATTATATATGTTTTTAAAAACCA
1 TTTTAAAAAACTATATTATATATGTTTTTAAAAACCA
*
2264202 TTTTAAAAAACTATA-TATTATATGTTTTTAAAAA-TA
1 TTTTAAAAAACTATATTA-TATATGTTTTTAAAAACCA
* *
2264238 TGTTTCCAAAAACTATACTATATAT
1 T-TTT-AAAAAACTATATTATATAT
2264263 CTTCAAAAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.07
37 33 0.61
38 15 0.28
39 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTAAAAAACTATATTATATATGTTTTTAAAAACCA
Found at i:2264311 original size:12 final size:12
Alignment explanation
Indices: 2264296--2264320 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2264286 TATTTTTGAA
2264296 ATTATTATATAT
1 ATTATTATATAT
2264308 ATTATTATATAT
1 ATTATTATATAT
2264320 A
1 A
2264321 CTAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTATTATATAT
Found at i:2264456 original size:2 final size:2
Alignment explanation
Indices: 2264449--2264473 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2264439 ACCATGCTTC
2264449 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 A
2264474 ATTGTCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2271397 original size:186 final size:186
Alignment explanation
Indices: 2271083--2271454 Score: 696
Period size: 186 Copynumber: 2.0 Consensus size: 186
2271073 TTGGTTGAAC
2271083 ATTTAATTACCAATTAACCCACATCATGGCACCCACCACGCGTATATAATAAAGTTCATGAATAC
1 ATTTAATTACCAATTAACCCACATCATGGCACCCACCACGCGTATATAATAAAGTTCATGAATAC
2271148 AATTTATTTTTATCAATGTAAAGATGACGTCAAAAAATCATCTAGCCATAGTCACTACTTACAAA
66 AATTTATTTTTATCAATGTAAAGATGACGTCAAAAAATCATCTAGCCATAGTCACTACTTACAAA
2271213 ATTTGGCATTC-TTTGTCAAACCTGGAGGTTTCACCAAATCATCTAACAAGATATTT
131 ATTTGGCATTCTTTTGTCAAACCTGGAGGTTTCA-CAAATCATCTAACAAGATATTT
2271269 ATTTAATTACCATAATTAACCCACATCATGGCACCCACCACGCGTATATAATAAA-TTCATGAAT
1 ATTTAATTACC--AATTAACCCACATCATGGCACCCACCACGCGTATATAATAAAGTTCATGAAT
2271333 ACAATTTA-TTTTATCAATGTAAAGATGACGTCAAAAAATCATCTAGCCATAGTCACTACTTACA
64 ACAATTTATTTTTATCAATGTAAAGATGACGTCAAAAAATCATCTAGCCATAGTCACTACTTACA
2271397 AAATTTGGCATTCTTTTGTCAAACCTGGAGGTTTCACAAATCATCTAACAAGATATTT
129 AAATTTGGCATTCTTTTGTCAAACCTGGAGGTTTCACAAATCATCTAACAAGATATTT
2271455 TATATGAGAA
Statistics
Matches: 183, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
186 102 0.56
187 39 0.21
188 42 0.23
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.31
Consensus pattern (186 bp):
ATTTAATTACCAATTAACCCACATCATGGCACCCACCACGCGTATATAATAAAGTTCATGAATAC
AATTTATTTTTATCAATGTAAAGATGACGTCAAAAAATCATCTAGCCATAGTCACTACTTACAAA
ATTTGGCATTCTTTTGTCAAACCTGGAGGTTTCACAAATCATCTAACAAGATATTT
Found at i:2271670 original size:21 final size:20
Alignment explanation
Indices: 2271589--2271689 Score: 69
Period size: 21 Copynumber: 5.0 Consensus size: 20
2271579 TCGCAATCAG
2271589 TTTCCAAATCGCAACGCGAT
1 TTTCCAAATCGCAACGCGAT
** *
2271609 TCTTGAAAATCGCAATGCGAT
1 T-TTCCAAATCGCAACGCGAT
** * **
2271630 AGTACAAATTCGCATTGCGAT
1 TTTCCAAA-TCGCAACGCGAT
*
2271651 TTTCCAGAATCGCAACGCGAA
1 TTTCCA-AATCGCAACGCGAT
* *
2271672 TAT-GAAATCGCAACGCGA
1 TTTCCAAATCGCAACGCGA
2271690 ACATAAATCG
Statistics
Matches: 62, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.21
20 6 0.10
21 41 0.66
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
TTTCCAAATCGCAACGCGAT
Found at i:2271699 original size:18 final size:19
Alignment explanation
Indices: 2271658--2271706 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
2271648 GATTTTCCAG
*
2271658 AATCGCAACGCGAATATGA
1 AATCGCAACGCGAACATGA
2271677 AATCGCAACGCGAACAT-A
1 AATCGCAACGCGAACATGA
2271695 AATCGCAACGCG
1 AATCGCAACGCG
2271707 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAACATGA
Found at i:2271721 original size:20 final size:20
Alignment explanation
Indices: 2271658--2271883 Score: 228
Period size: 20 Copynumber: 11.4 Consensus size: 20
2271648 GATTTTCCAG
* **
2271658 AATCGCAACGCGAATATG-A
1 AATCGCAACGCGTATCCGTA
* *
2271677 AATCGCAACGCG-A-ACATA
1 AATCGCAACGCGTATCCGTA
2271695 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2271715 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2271735 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2271755 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2271775 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2271795 AATCGCAACG-ATAGTCCGTA
1 AATCGCAACGCGTA-TCCGTA
* * *
2271815 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2271835 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2271855 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2271875 AATCACAAC
1 AATCGCAAC
2271884 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
17 1 0.01
18 14 0.08
19 15 0.09
20 144 0.82
21 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2275053 original size:20 final size:19
Alignment explanation
Indices: 2275003--2275183 Score: 196
Period size: 19 Copynumber: 10.2 Consensus size: 19
2274993 GCAACGAGAG
2275003 AATCGCAATGC-AAATGAA
1 AATCGCAATGCGAAATGAA
*
2275021 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2275035 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2275055 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2275074 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2275088 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2275108 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2275127 AATCGCAAT--G--A-GAG
1 AATCGCAATGCGAAATGAA
2275141 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
2275161 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2275180 AATC
1 AATC
2275184 ACATTGCGAT
Statistics
Matches: 139, Mismatches: 6, Indels: 35
0.77 0.03 0.19
Matches are distributed among these distances:
14 33 0.24
15 2 0.01
16 3 0.02
17 5 0.04
18 7 0.05
19 47 0.34
20 42 0.30
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2275092 original size:53 final size:53
Alignment explanation
Indices: 2275003--2275183 Score: 312
Period size: 53 Copynumber: 3.4 Consensus size: 53
2274993 GCAACGAGAG
* *
2275003 AATCGCAATGC-AAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
2275055 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
2275108 AATCGCAATGCGAAATGAAAATCGCAATGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
2275161 AATCGCAATGCGAAATGAAAATC
1 AATCGCAATGCGAAATGAAAATC
2275184 ACATTGCGAT
Statistics
Matches: 124, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
52 11 0.09
53 112 0.90
54 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:2275165 original size:34 final size:33
Alignment explanation
Indices: 2275102--2275176 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 33
2275092 GCAATGCGGA
2275102 AATGA-AAATCGCAATGC-GAAATGAAAATCGC
1 AATGAGAAATCGCAATGCGGAAATGAAAATCGC
2275133 AATGAGAGAATCGCAATGCGGAAATGAAAATCGC
1 AATGAGA-AATCGCAATGCGGAAATGAAAATCGC
*
2275167 AATGCGAAAT
1 AATGAGAAAT
2275177 GAAAATCACA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
31 5 0.12
32 1 0.03
33 14 0.35
34 20 0.50
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.16
Consensus pattern (33 bp):
AATGAGAAATCGCAATGCGGAAATGAAAATCGC
Found at i:2275226 original size:53 final size:52
Alignment explanation
Indices: 2275163--2275278 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
2275153 GAAATGAAAA
*
2275163 TCGCAATGCGAAATGAAAATCACATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCACATTGCGATTCTCTCGTTGCGATTTTCATT
** ** ** *
2275215 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCACATTGCGATTCTCTCGTTGCGATTTTCATT
2275268 TCGCATTGCGA
1 TCGCATTGCGA
2275279 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCACATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2275293 original size:53 final size:53
Alignment explanation
Indices: 2275185--2275299 Score: 214
Period size: 53 Copynumber: 2.2 Consensus size: 53
2275175 ATGAAAATCA
2275185 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
2275238 CATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCG
1 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT-CG
2275291 CATTGCGAT
1 CATTGCGAT
2275300 AGTCATTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 19 0.31
53 42 0.69
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (53 bp):
CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
Found at i:2275307 original size:20 final size:19
Alignment explanation
Indices: 2275201--2275299 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
2275191 GATTCTCTCG
2275201 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2275221 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2275240 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2275254 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2275273 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2275293 TTGCGAT
1 TTGCGAT
2275300 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 25 0.35
20 26 0.37
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2275425 original size:14 final size:14
Alignment explanation
Indices: 2275406--2275442 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2275396 CATCAATTAC
2275406 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2275420 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2275434 ACAAATCAA
1 ACAAATCAA
2275443 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2277404 original size:19 final size:19
Alignment explanation
Indices: 2277352--2277523 Score: 125
Period size: 19 Copynumber: 9.6 Consensus size: 19
2277342 TAGTTTACTT
* *
2277352 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
2277372 TCGCAAACGCGAAATGAGAA
1 TCGC-AACGCGAAATGAAAA
* **
2277392 TCGCAACGAGAAA-CCAAA
1 TCGCAACGCGAAATGAAAA
**
2277410 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
2277429 TCGCAACGCGAACTGAAAA
1 TCGCAACGCGAAATGAAAA
*
2277448 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2277462 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
2277480 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
2277494 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2277513 TCGCAATGCGA
1 TCGCAACGCGA
2277524 TTTTGGTTTC
Statistics
Matches: 122, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
13 1 0.01
14 17 0.14
16 9 0.07
17 4 0.03
18 23 0.19
19 48 0.39
20 12 0.10
21 8 0.07
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2277465 original size:14 final size:14
Alignment explanation
Indices: 2277446--2277501 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
2277436 GCGAACTGAA
*
2277446 AATCGCAACGACAG
1 AATCGCAACGAAAG
2277460 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
2277477 AAATCGCAACGAGAG
1 -AATCGCAACGAAAG
2277492 AATCGCAACG
1 AATCGCAACG
2277502 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 8 0.22
17 1 0.03
18 8 0.22
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2277486 original size:32 final size:33
Alignment explanation
Indices: 2277427--2277518 Score: 150
Period size: 32 Copynumber: 2.8 Consensus size: 33
2277417 GCGAAACCAA
*
2277427 AATCGCAACGCGAACTGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
2277460 AATCGCAATGCGAAATG-AAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
2277492 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2277519 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Done.