Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 20 of 253
Found at i:5519867 original size:54 final size:54
Alignment explanation
Indices: 5519802--5520005 Score: 157
Period size: 54 Copynumber: 3.8 Consensus size: 54
5519792 CAATTGATCG
* *
5519802 GTTATCCAGTAATAGTCAATTATTTAGTAAAATCAGGTATTCAGTAACAA-CTAA
1 GTTATTCAGTAATAGTCAATTATTCAGTAAAATCAGGTATTCAGTAACAATC-AA
* * * **
5519856 GTTATTCAGTAACAGTC-ATTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 GTTATTCAGTAATAGTCAATT-ATTCAGT-AAAATCAGGTATTCAGTAACAATCAA
* * * * * *
5519911 -TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA-ATATCCAGTAACAGTCAA
1 GTTATTCAGTAATAGTCAATTATTCAGTAA-AATC-AGGTATTCAGTAACAATCAA
* * * * *
5519965 -TTATCCGGTAACAGTTAATTATTCAGTAATAATCAGTTATT
1 GTTATTCAGTAATAGTCAATTATTCAGTAA-AATCAGGTATT
5520006 TTATACCTTT
Statistics
Matches: 116, Mismatches: 27, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
53 5 0.04
54 87 0.75
55 23 0.20
56 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (54 bp):
GTTATTCAGTAATAGTCAATTATTCAGTAAAATCAGGTATTCAGTAACAATCAA
Found at i:5520399 original size:20 final size:22
Alignment explanation
Indices: 5520355--5520429 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 22
5520345 AATAGGGTAT
*
5520355 TTAATTCAT-TTTTCAGTTTTCAA
1 TTAATTCATATTTTCA--ATTCAA
5520378 TTAATTCATATTTT-AA-TCAA
1 TTAATTCATATTTTCAATTCAA
5520398 TTAACTAT-ATATTTTCAATTCAA
1 TTAA-T-TCATATTTTCAATTCAA
5520421 TATAATTCA
1 T-TAATTCA
5520430 ATTCACTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
20 8 0.18
21 8 0.18
22 4 0.09
23 17 0.39
24 7 0.16
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (22 bp):
TTAATTCATATTTTCAATTCAA
Found at i:5521860 original size:22 final size:22
Alignment explanation
Indices: 5521835--5521885 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5521825 TTTCATTCTG
*
5521835 TTTCTTTTCTATCTCTTTTTTT
1 TTTCTTTTCTATCTCTTTTGTT
* * *
5521857 TTTCATTTCTTTTTCTTTTGTT
1 TTTCTTTTCTATCTCTTTTGTT
*
5521879 TTACTTT
1 TTTCTTT
5521886 ATATATATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTCTTTTCTATCTCTTTTGTT
Found at i:5521867 original size:16 final size:16
Alignment explanation
Indices: 5521825--5521875 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
5521815 CTCTGTTTCG
* *
5521825 TTTCA-TTCTGTTTCT
1 TTTCATTTCTTTTTTT
*
5521840 TTTCTATCTCTTTTTTT
1 TTTC-ATTTCTTTTTTT
5521857 TTTCATTTCTTTTTCTT
1 TTTCATTTCTTTTT-TT
5521874 TT
1 TT
5521876 GTTTTACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.14
16 10 0.34
17 15 0.52
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTCATTTCTTTTTTT
Found at i:5527780 original size:18 final size:19
Alignment explanation
Indices: 5527731--5527780 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
5527721 TATAATATAA
5527731 TTATTTAATTAATAAATATC
1 TTATTTAA-TAATAAATATC
5527751 TT-TTATAAAATAATAAATAT-
1 TTATT-T--AATAATAAATATC
5527771 TTATTTAATA
1 TTATTTAATA
5527781 TCTAATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 4 0.15
19 2 0.08
20 6 0.23
21 12 0.46
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATTTAATAATAAATATC
Found at i:5528621 original size:23 final size:23
Alignment explanation
Indices: 5528595--5528655 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 23
5528585 AGGCACTTTA
5528595 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCGTATTTTAGGCACCTCG
* **
5528618 TGTGTCGTA--TCAACCACCTCG
1 TGTGTCGTATTTTAGGCACCTCG
5528639 TGTGTCG--TTTTAGGCAC
1 TGTGTCGTATTTTAGGCAC
5528656 TTTATGTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
21 21 0.70
23 9 0.30
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.36
Consensus pattern (23 bp):
TGTGTCGTATTTTAGGCACCTCG
Found at i:5528663 original size:21 final size:21
Alignment explanation
Indices: 5528585--5528664 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
5528575 TTTACTAATC
* *
5528585 AGGCACTTTATGTGTCGTATTTT
1 AGGCACCTCATGTGTCG--TTTT
* * *
5528608 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCATGTGTCGTTTT
** *
5528629 AACCACCTCGTGTGTCGTTTT
1 AGGCACCTCATGTGTCGTTTT
* *
5528650 AGGCACTTTATGTGT
1 AGGCACCTCATGTGT
5528665 TGTATTCTGA
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
21 29 0.67
23 14 0.33
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (21 bp):
AGGCACCTCATGTGTCGTTTT
Found at i:5531860 original size:31 final size:32
Alignment explanation
Indices: 5531790--5531861 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
5531780 TAAAAACCTT
* * * * *
5531790 TAAGTTCAAACTCTAATATGAAAGCAATTGTC
1 TAAGTTCATACCCAAATATGAAAACAATTGAC
5531822 TAA-TTCATACCCAAATATGAAAACAATT-AC
1 TAAGTTCATACCCAAATATGAAAACAATTGAC
5531852 TAAGTTCATA
1 TAAGTTCATA
5531862 AATTAATTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 4 0.12
31 27 0.79
32 3 0.09
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (32 bp):
TAAGTTCATACCCAAATATGAAAACAATTGAC
Found at i:5540536 original size:27 final size:27
Alignment explanation
Indices: 5540495--5540548 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5540485 ACCAAGGTTG
5540495 TGGTTCTTAAAAAATAGATCGTAGACT
1 TGGTTCTTAAAAAATAGATCGTAGACT
**
5540522 TGGTTCTTACGAAATAGATCGTAGACT
1 TGGTTCTTAAAAAATAGATCGTAGACT
5540549 ATCATCTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (27 bp):
TGGTTCTTAAAAAATAGATCGTAGACT
Found at i:5545156 original size:15 final size:15
Alignment explanation
Indices: 5545127--5545160 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5545117 GTGAATATCA
5545127 AAATTCATTTAATAT
1 AAATTCATTTAATAT
5545142 AAATT-ATTTATATAT
1 AAATTCATTTA-ATAT
5545157 AAAT
1 AAAT
5545161 ATAAAATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTCATTTAATAT
Found at i:5549756 original size:27 final size:27
Alignment explanation
Indices: 5549726--5549792 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
5549716 AGTCCGCTAA
* *
5549726 GACAGTAGACACGTGGTAATCTGTTAG
1 GACAGTAAACACGTGGTAATCTGTCAG
* *
5549753 GACAGTAAACATGTGGTAATTTGTCAG
1 GACAGTAAACACGTGGTAATCTGTCAG
5549780 GACAGTAAACACG
1 GACAGTAAACACG
5549793 GAATAGTCCG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (27 bp):
GACAGTAAACACGTGGTAATCTGTCAG
Found at i:5549865 original size:27 final size:27
Alignment explanation
Indices: 5549726--5549870 Score: 86
Period size: 27 Copynumber: 5.4 Consensus size: 27
5549716 AGTCCGCTAA
* * * * *
5549726 GACAGTAGACACGTGGTAATCTGTTAG
1 GACAGTAAACACGAGGTAGTTTGTCAG
* * *
5549753 GACAGTAAACATGTGGTAATTTGTCAG
1 GACAGTAAACACGAGGTAGTTTGTCAG
* **
5549780 GACAGTAAACACG-GAATAGTCCGTC-G
1 GACAGTAAACACGAG-GTAGTTTGTCAG
*
5549806 AGACAGTAAACAC-AGGGTAGCCCTTCG-CA-
1 -GACAGTAAACACGA-GGTAG---TTTGTCAG
5549835 -ACAGTAAACACGAGGTAGTTTGTCAG
1 GACAGTAAACACGAGGTAGTTTGTCAG
5549861 GACAGTAAAC
1 GACAGTAAAC
5549871 TCGGAGTAGT
Statistics
Matches: 94, Mismatches: 12, Indels: 24
0.72 0.09 0.18
Matches are distributed among these distances:
24 3 0.03
25 2 0.02
26 2 0.02
27 81 0.86
28 2 0.02
29 1 0.01
30 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (27 bp):
GACAGTAAACACGAGGTAGTTTGTCAG
Found at i:5552238 original size:46 final size:46
Alignment explanation
Indices: 5552136--5552366 Score: 311
Period size: 46 Copynumber: 4.9 Consensus size: 46
5552126 TTTGACATGA
* * *
5552136 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTCATTTTC-TGTCACGT
1 TGCCATAGTATCTTTCAACCATGGTCTTA--CA--CA-TTTCATATCACGT
*
5552186 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCATGT
1 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
* *
5552232 TGCCATAGTGTCTTTCAACTATGGTCTTACACATTTCATATCACGT
1 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
* * *
5552278 TGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATATCAGGT
1 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
* *
5552324 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCA
5552367 GAGAGCACAC
Statistics
Matches: 166, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
45 4 0.02
46 133 0.80
48 2 0.01
50 27 0.16
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (46 bp):
TGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
Found at i:5554425 original size:16 final size:16
Alignment explanation
Indices: 5554386--5554425 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
5554376 AATCTCAATT
*
5554386 TTTCTCTTTTTCCTTC
1 TTTCTTTTTTTCCTTC
5554402 TTTCCTTTTTTTCCTTC
1 TTT-CTTTTTTTCCTTC
5554419 TTTCTTT
1 TTTCTTT
5554426 CCCCTGCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCTTTTTTTCCTTC
Found at i:5554473 original size:15 final size:15
Alignment explanation
Indices: 5554451--5554489 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5554441 TCGTTTCATC
5554451 ATTTCTTTCTTTTTCT
1 ATTTCTTT-TTTTTCT
*
5554467 A-TTCTTTTTTTTTT
1 ATTTCTTTTTTTTCT
5554481 ATTTCTTTT
1 ATTTCTTTT
5554490 ACTTTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 13 0.62
16 1 0.05
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTCTTTTTTTTCT
Found at i:5554624 original size:18 final size:20
Alignment explanation
Indices: 5554590--5554629 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
5554580 TCTTTCTTTA
5554590 ATCTATTTATTATATAA-AT
1 ATCTATTTATTATATAATAT
5554609 ATCT-TTTATT-TAATAATAT
1 ATCTATTTATTAT-ATAATAT
5554628 AT
1 AT
5554630 AATTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
ATCTATTTATTATATAATAT
Found at i:5556991 original size:26 final size:27
Alignment explanation
Indices: 5556958--5557022 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
5556948 GTGAATATTG
* *
5556958 TATA-TATTTATATATAATATTATTTT
1 TATATTATTTATATATAACATTATTAT
*
5556984 TA-ATTATTGTAT-TTTAACATTATTAT
1 TATATTATT-TATATATAACATTATTAT
*
5557010 TATATTATATATA
1 TATATTATTTATA
5557023 CTTCTTCGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
25 1 0.03
26 22 0.71
27 8 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TATATTATTTATATATAACATTATTAT
Found at i:5569512 original size:69 final size:69
Alignment explanation
Indices: 5569392--5569565 Score: 201
Period size: 69 Copynumber: 2.5 Consensus size: 69
5569382 CTTTCCAAGG
**
5569392 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
5569455 T-TTAAA
65 TGTT--A
** * *
5569461 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
*
5569526 GTTT
66 GTTA
* ** *
5569530 TAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
5569566 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 86 0.95
70 3 0.03
71 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTA
Found at i:5569777 original size:72 final size:73
Alignment explanation
Indices: 5569569--5570694 Score: 1329
Period size: 74 Copynumber: 15.2 Consensus size: 73
5569559 TAAGCCTTTT
* *
5569569 AATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
5569633 GTAATTTC
66 GTAATTTC
* * ** *
5569641 AATTTCTG-TTGTCAAAAAAATTAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTG
1 AATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
5569705 AGGTAATTTC
64 AGGTAATTTC
* *
5569715 AATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
5569779 GTAATTTC
66 GTAATTTC
***
5569787 AATTTCTGTTGTAAAAAAAATCAACTCATATTGCGAGA--TGAGTTGAGCCTCAGGACACGCTGA
1 AATTTCTGTT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
5569850 GGTAATTTC
65 GGTAATTTC
*
5569859 AATTTTTGTTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
5569923 GT-ATTTC
66 GTAATTTC
5569930 AATTTCTG--TTTCAAAAATCAACTCATATTGCGAGA--TGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
5569991 GTAATTTC
66 GTAATTTC
**
5569999 AATTTCTG---TT-AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
5570060 GTAATTTC
66 GTAATTTC
* *
5570068 AATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
5570132 GTAATTTC
66 GTAATTTC
* * **
5570140 AATTTCTG-TTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTG
1 AATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
5570204 AGGTATTTTC
64 AGGTAATTTC
* * *
5570214 AATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTG
1 AATTTCTGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
5570279 AGGTATTTTCAATTCCTGTTC
64 AGG-----T-AA----T-TTC
*
5570300 AATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
5570365 GTAATTTC
66 GTAATTTC
* * *
5570373 AATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGA
1 AATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
*
5570438 GGTATTTTC
65 GGTAATTTC
* ** * * *
5570447 AAATTCT-ACTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCT-TGGCTCACG-T
1 AATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCT
* *
5570509 GTTGAGTCACTTTC
63 G-AG-GT-AATTTC
** * *
5570523 AATTTCTGTTTTTATGTCTGTTTTCTAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGG
1 AATTTCTG--TTT-T-TC------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* *
5570588 GCACGCTGAGGTATTTTC
56 ACACGCTGAGGTAATTTC
* ** * * *
5570606 AATTACTGTTTGGCAAAAACCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAG
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
5570671 GTATTTTC
66 GTAATTTC
*
5570679 CATTTCTGTTTTTCAA
1 AATTTCTGTTTTTCAA
5570695 TTTATGTTTT
Statistics
Matches: 920, Mismatches: 84, Indels: 99
0.83 0.08 0.09
Matches are distributed among these distances:
67 23 0.03
68 30 0.03
69 58 0.06
70 44 0.05
71 21 0.02
72 208 0.23
73 77 0.08
74 253 0.28
75 60 0.07
76 11 0.01
78 2 0.00
79 3 0.00
80 2 0.00
81 6 0.01
83 12 0.01
84 51 0.06
85 40 0.04
86 19 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (73 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTAATTTC
Found at i:5570452 original size:159 final size:158
Alignment explanation
Indices: 5570137--5571185 Score: 528
Period size: 159 Copynumber: 6.3 Consensus size: 158
5570127 CTGAGGTAAT
* * **
5570137 TTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACAT
1 TTCAATTTATGTT-TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
5570202 TGAGGTATTTTCAATTTCTG-CTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
63 TGAGGTATTTTCAATTTCTGTTTTTTCAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
** **
5570266 TCAAGACACGTTGAGGTATTTTC-AATTCCTG
127 TCGGGACACGCCGAGGTATTTTCAAATTCCTG
5570297 TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 TTCAATTTATG--TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
*
5570362 GAGGTAATTTCAATTTCTGTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
64 GAGGTATTTTCAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
5570426 GGGGCACGCCGAGGTATTTTCAAATTCTACT-
129 GGGACACGCCGAGGTATTTTCAAATTC--CTG
* * *
5570457 TTC-A---A------AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCT-TGGCTCACG-TG
1 TTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTG
* * *** *
5570510 TTGAGTCACTTTCAATTTCTGTTTTTATGTCTGTTTTCTAAATCAACTCATATTGCAAGAGGTGA
65 -AG-GT-ATTTTCAATTTCTG-TTTT-T-TC-----AAAAAATCAACTCATATTGCGAGAGGTGA
* * *
5570575 GTTGAGCCTCGGGGCACGCTGAGGTATTTTC-AATTACTG
119 GTTGAGCCTCGGGACACGCCGAGGTATTTTCAAATTCCTG
* * * *
5570614 ------TT-TG--GCAAAAACCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGA
1 TTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
* * * * *
5570670 GGTATTTTCCATTTCTGTTTTTCAATTTATGTTTTCAAAAATCAATTCATATTGCTAGAGGTGAA
66 GGTATTTTCAATTTCTG-TTTT---TTCA-------AAAAATCAACTCATATTGCGAGAGGTGAG
* * * * *
5570735 TGGAGCCTCAGGTCATACGCCGAGGTATTTTCAATAGATGT-TTT
120 TTGAGCCTC-GG-GACACGCCGAGGTATTTTC-A-A-AT-TCCTG
** * ** *
5570779 TTCCAATTCCTGCTTCTCAAAAAAAAATTTTAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
1 TT-CAATTTATG-TT-TC----AAAAA--TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* * *
5570844 ACACGTTGAGGTATTTTCAAGTTCTG-CTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGA
57 ACACGCTGAGGTATTTTCAATTTCTGTTTTTTC---AAAAAATCAACTCATATTGCGAGAGGTGA
*** * * * * *
5570908 GTTGAGCCTCAGCTCTCACACTGAGGTATTTTCAATTTTTCGTTTT
119 GTTGAGCCTC-G-GGACACGCCGAGGTATTTTCAA--ATTC--CTG
* *
5570954 TTCAATTTATGCTTTTCAAATTCTACTTTTCCAAAATCAGCTCATATTGCAAGAGGTGAGTTGAG
1 TTCAATTTATG----T----TTC-A-------AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* * * * ** *
5571019 CCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT---AATTTCAACTCATATTACGAGAG
50 CCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAG
5571081 GTGAGTTGAGCCTCGGGACACACGCCGAGGTATTTTC-AATTAAGCCT-
115 GTGAGTTGAGCCTCGGG--ACACGCCGAGGTATTTTCAAATT---CCTG
** * * *
5571128 TTTGATTT-TCTTTCAAAAAAAAATCAACTCATATTGCGAAAAGTGAGTTGAGCCTCAG
1 TTCAATTTATGTTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
5571186 TTCACATGTT
Statistics
Matches: 692, Mismatches: 104, Indels: 185
0.71 0.11 0.19
Matches are distributed among these distances:
147 4 0.01
148 41 0.06
149 2 0.00
150 13 0.02
151 4 0.01
152 1 0.00
153 2 0.00
156 20 0.03
157 3 0.00
158 97 0.14
159 161 0.23
160 20 0.03
161 53 0.08
162 2 0.00
164 1 0.00
165 6 0.01
166 1 0.00
168 1 0.00
169 1 0.00
172 3 0.00
173 5 0.01
174 66 0.10
175 6 0.01
176 2 0.00
177 53 0.08
178 2 0.00
180 2 0.00
181 9 0.01
182 51 0.07
183 56 0.08
184 4 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (158 bp):
TTCAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
GGTATTTTCAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
GACACGCCGAGGTATTTTCAAATTCCTG
Found at i:5570555 original size:233 final size:230
Alignment explanation
Indices: 5569583--5570678 Score: 1172
Period size: 233 Copynumber: 4.9 Consensus size: 230
5569573 TTTGTTTTTC
* * * * * *
5569583 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTTTCAATTCCT
**** * * ** *
5569648 G-----T-TG-TCAAAAAAATTAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACATGCTGA
66 GTTATTTATGTTTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGA
* * *
5569706 GGTAATTTCAATTTTTGTTTT-TC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGG
131 GGTAATTTCAATTTCTGTTTTCACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* * * * *
5569769 ACACGCTGAGGTAATTTCAATTTCT-GTTGTAAAA
196 ACACGCTGAGGTATTTTCAAATTCTACTTTTCAAA
* * * *
5569803 AAAATCAACTCATATTGCG--AGATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA-----
1 AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTTTCAATTCCT
*
5569861 --T-TTT-TGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
66 GTTATTTATGTTTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGA
5569922 GGT-ATTTCAATTTCTG-TTT--CAAAAATCAACTCATATTGCGAGA--TGAGTTGAGCCTCAGG
131 GGTAATTTCAATTTCTGTTTTCACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* *
5569981 ACACGCTGAGGTAATTTC-AATT-T-CTGTT---A
196 ACACGCTGAGGTATTTTCAAATTCTACTTTTCAAA
* * * *
5570010 AAAATCAACTCATATTGCGAGAA-ATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA----
1 AAAATCAACTCATATTGCGA-AAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTTTCAATTCC
*
5570070 ---T-TTT-TGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTG
65 TGTTATTTATGTTTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTG
* * *
5570130 AGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAA
130 AGGTAATTTCAATTTCTGTTTTCACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
** * * *
5570195 GACACATTGAGGTATTTTCAATTTCTGCTTTTCAAG
195 GACACGCTGAGGTATTTTCAAATTCTACTTTTCAAA
* *
5570231 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTCCT
1 AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTTTCAATTCCT
*
5570296 GTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
66 GTT--ATTTATGTTTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGC
**
5570361 TGAGGTAATTTCAATTTCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
128 TGAGGTAATTTCAATTTCTGTTTTCACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * *
5570426 GGGGCACGCCGAGGTATTTTCAAATTCTAC-TTTCAAA
193 AGGACACGCTGAGGTATTTTCAAATTCTACTTTTCAAA
** *
5570463 AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCT-TGGCTCACGTGTTGA-GTCACTTTCAAT
1 AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAG-ACAC--GTTGAGGT-ACTTTCAAT
* * * *
5570526 TTCTGTT-TTTATGTCTGTTTTCTAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGC
62 TCCTGTTATTTATG--T-TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGAC
* * ** * *
5570590 ACGCTGAGGTATTTTCAATTACTG-TTTGGCAAAAACCAACTCATACTGCGAGAGGTGAGTTGAG
124 ACGCTGAGGTAATTTCAATTTCTGTTTTCACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
*
5570654 CCTCAGGACATGCTGAGGTATTTTC
189 CCTCAGGACACGCTGAGGTATTTTC
5570679 CATTTCTGTT
Statistics
Matches: 771, Mismatches: 65, Indels: 68
0.85 0.07 0.08
Matches are distributed among these distances:
207 20 0.03
209 100 0.13
210 17 0.02
211 5 0.01
212 34 0.04
213 24 0.03
214 24 0.03
215 45 0.06
216 52 0.07
217 1 0.00
218 42 0.05
220 19 0.02
221 53 0.07
228 1 0.00
231 10 0.01
232 109 0.14
233 191 0.25
234 24 0.03
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (230 bp):
AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAAGACACGTTGAGGTACTTTCAATTCCT
GTTATTTATGTTTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGA
GGTAATTTCAATTTCTGTTTTCACAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
ACACGCTGAGGTATTTTCAAATTCTACTTTTCAAA
Found at i:5570672 original size:73 final size:73
Alignment explanation
Indices: 5570553--5570689 Score: 211
Period size: 73 Copynumber: 1.9 Consensus size: 73
5570543 TTTTCTAAAT
* * *
5570553 CAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTGTTTG
1 CAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTACTGTTTG
5570618 GCAAAAAC
66 GCAAAAAC
* * * *
5570626 CAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCCATTTCTGTTT
1 CAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTACTGTTT
5570690 TTCAATTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (73 bp):
CAACTCATACTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTACTGTTTG
GCAAAAAC
Found at i:5573125 original size:26 final size:27
Alignment explanation
Indices: 5573092--5573156 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 27
5573082 GTGAATATTG
* *
5573092 TATA-TATTTATATATAATATTATTTT
1 TATATTATTTATATATAACATTATTAT
*
5573118 TA-ATTATTGTAT-TTTAACATTATTAT
1 TATATTATT-TATATATAACATTATTAT
*
5573144 TATATTATATATA
1 TATATTATTTATA
5573157 CTTCTTCGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
25 1 0.03
26 22 0.71
27 8 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TATATTATTTATATATAACATTATTAT
Found at i:5576589 original size:47 final size:48
Alignment explanation
Indices: 5576467--5576644 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 48
5576457 TGTAACCCGC
* * *
5576467 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATT-ACAT
* *
5576513 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTACAT
* *
5576563 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTACAT
*
5576605 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
5576645 TCAACCATCC
Statistics
Matches: 111, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 5 0.05
43 2 0.02
44 3 0.03
45 29 0.26
46 33 0.30
47 29 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (48 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTACAT
Found at i:5576632 original size:92 final size:93
Alignment explanation
Indices: 5576474--5576644 Score: 299
Period size: 92 Copynumber: 1.8 Consensus size: 93
5576464 CGCCCATAAG
* * *
5576474 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
5576539 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
5576567 CGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
5576631 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
5576645 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 43 0.58
93 31 0.42
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:5582941 original size:25 final size:24
Alignment explanation
Indices: 5582907--5582963 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5582897 AAATTATTAA
*
5582907 AAATATAAAATGTATTATAAAGATT
1 AAATAAAAAATGTA-TATAAAGATT
* * *
5582932 AAATAAAAAATTTATATTAATATT
1 AAATAAAAAATGTATATAAAGATT
5582956 AAATAAAA
1 AAATAAAA
5582964 TAAAAACCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAAAAATGTATATAAAGATT
Found at i:5586000 original size:6 final size:6
Alignment explanation
Indices: 5585989--5586035 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
5585979 GTCTGTATAT
5585989 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACA
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACA
5586036 TATATATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (6 bp):
ATACAC
Found at i:5588043 original size:17 final size:17
Alignment explanation
Indices: 5588009--5588042 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
5587999 CTTCTCAATG
5588009 GTCAAGTTTCAATTTTT
1 GTCAAGTTTCAATTTTT
5588026 GTCACAGTTTCAATTTT
1 GTCA-AGTTTCAATTTT
5588043 GGTCCCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.50
Consensus pattern (17 bp):
GTCAAGTTTCAATTTTT
Found at i:5588955 original size:21 final size:21
Alignment explanation
Indices: 5588929--5588977 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5588919 TTTTAAAATT
* *
5588929 TAAAAATTATTAAATAAATCA
1 TAAAAATTATAAAAAAAATCA
* *
5588950 TGAAAATTATAAAAAAAATTA
1 TAAAAATTATAAAAAAAATCA
5588971 TAAAAAT
1 TAAAAAT
5588978 CTTAAATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAAAATTATAAAAAAAATCA
Found at i:5588969 original size:12 final size:12
Alignment explanation
Indices: 5588952--5588976 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5588942 ATAAATCATG
5588952 AAAATTATAAAA
1 AAAATTATAAAA
5588964 AAAATTATAAAA
1 AAAATTATAAAA
5588976 A
1 A
5588977 TCTTAAATTT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:5589147 original size:19 final size:18
Alignment explanation
Indices: 5589125--5589173 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
5589115 TTTTAAAATT
*
5589125 TTTTGAATTTTTTTTATAA
1 TTTT-AATTTTTTTAATAA
*
5589144 TTTTTATGTTTTTTAATAA
1 TTTTAAT-TTTTTTAATAA
5589163 TTTTAAATTTT
1 TTTT-AATTTT
5589174 AGAAGGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 21 0.84
20 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTAATTTTTTTAATAA
Found at i:5589166 original size:29 final size:29
Alignment explanation
Indices: 5589092--5589166 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
5589082 CAGTATTGTT
**
5589092 ATTTTTTAATGAAACTTTTATAATTTTAAA
1 ATTTTTTAAT-AATTTTTTATAATTTTAAA
* * *
5589122 ATTTTTTGAAT-TTTTTTTATAATTTTTAT
1 ATTTTTT-AATAATTTTTTATAATTTTAAA
*
5589151 GTTTTTTAATAATTTT
1 ATTTTTTAATAATTTT
5589167 AAATTTTAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
28 3 0.08
29 23 0.64
30 7 0.19
31 3 0.08
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (29 bp):
ATTTTTTAATAATTTTTTATAATTTTAAA
Found at i:5589173 original size:18 final size:19
Alignment explanation
Indices: 5589115--5589173 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
5589105 ACTTTTATAA
*
5589115 TTTTAA-AATTTTTTGAATTT
1 TTTTAATAA-TTTTT-AAATT
* **
5589135 TTTTTATAATTTTTATGTT
1 TTTTAATAATTTTTAAATT
5589154 TTTTAATAA-TTTTAAATT
1 TTTTAATAATTTTTAAATT
5589172 TT
1 TT
5589174 AGAAGGGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 9 0.28
19 11 0.34
20 10 0.31
21 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTAATAATTTTTAAATT
Found at i:5596367 original size:19 final size:17
Alignment explanation
Indices: 5596328--5596370 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
5596318 TTGTCACTAA
*
5596328 AATTTTATTTTAGATTG
1 AATTTTATTTTAAATTG
*
5596345 AATTTTATTATTTAAATTT
1 AATTTTA-T-TTTAAATTG
5596364 AATTTTA
1 AATTTTA
5596371 AAATATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 14 0.64
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
AATTTTATTTTAAATTG
Found at i:5596587 original size:24 final size:21
Alignment explanation
Indices: 5596553--5596598 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
5596543 TGATATTTTA
5596553 TAAATTAATTTATTGTTAAATATT
1 TAAATTAATTT-TT-TTAAA-ATT
*
5596577 TAAATTTATTTTTTTAAAATT
1 TAAATTAATTTTTTTAAAATT
5596598 T
1 T
5596599 TATTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 5 0.24
23 2 0.10
24 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TAAATTAATTTTTTTAAAATT
Found at i:5602123 original size:38 final size:39
Alignment explanation
Indices: 5602079--5602170 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 39
5602069 CGTTTTGAAT
5602079 AAAAACGCCAC-AAAGAGCGAGCATTAGCGGCGTTTCTA
1 AAAAACGCCACTAAAGAGCGAGCATTAGCGGCGTTTCTA
* * * *
5602117 AAAAACG-CAGCTAAAGATCGATCTTTAGCGGCGTTTTTA
1 AAAAACGCCA-CTAAAGAGCGAGCATTAGCGGCGTTTCTA
5602156 ATAAAAGCGCCACTA
1 A-AAAA-CGCCACTA
5602171 TAGGTTCACA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
37 2 0.04
38 8 0.18
39 24 0.53
40 4 0.09
41 5 0.11
42 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (39 bp):
AAAAACGCCACTAAAGAGCGAGCATTAGCGGCGTTTCTA
Found at i:5602359 original size:40 final size:39
Alignment explanation
Indices: 5602256--5602360 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 39
5602246 TCAATGGTAT
*
5602256 TAGCGGCGTTTG-TACAAAAACGCCGCTATAGATCAGTAC
1 TAGCGGCGTTTGTTA-AAAAACGCCGCTAAAGATCAGTAC
* *
5602295 TAGTGGCGTTT-TTAAAGAAGCGCCGCTAAAGGTATGCA-TA-
1 TAGCGGCGTTTGTTAAA-AAACGCCGCTAAA-G-AT-CAGTAC
5602335 TAGCGGCGTTTGTTAAAAAACGCCGC
1 TAGCGGCGTTTGTTAAAAAACGCCGC
5602361 AAAATTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
38 2 0.04
39 23 0.42
40 19 0.35
41 9 0.16
42 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (39 bp):
TAGCGGCGTTTGTTAAAAAACGCCGCTAAAGATCAGTAC
Found at i:5602914 original size:21 final size:22
Alignment explanation
Indices: 5602888--5602928 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5602878 GGTACTTTAC
5602888 GGTTTAGGGTATATG-GTTAAG
1 GGTTTAGGGTATATGAGTTAAG
*
5602909 GGTTTAGGGTTTATGAGTTA
1 GGTTTAGGGTATATGAGTTA
5602929 TTATTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (22 bp):
GGTTTAGGGTATATGAGTTAAG
Found at i:5603342 original size:287 final size:285
Alignment explanation
Indices: 5602785--5603345 Score: 611
Period size: 287 Copynumber: 2.0 Consensus size: 285
5602775 TGACTGATTG
* * * *
5602785 TTTTTTAATTTATATGTTGAATATTTTCTTATATAATTGTAAAAGAGATTGTATTAATTTTAAAA
1 TTTTTTAATTTATATATTAAATAATTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAA
* * *** * *
5602850 TATTGAATTAATTATCATTATAGTTTAGGGTACTTTACGGTTTAGGGTATATGGTTAAGGGTTTA
66 TATTAAATTAATCATCATTATAGTTTAGGGTACTTTACAAATCAAGGTATATGGTTAAGGGTTTA
* ** * *
5602915 GGGTTTATGAGTTATTATTTTAAGGTTTAGGGATTATGGGGTTTAAGGGCTATGGTTTAAGTGTC
131 GGGCTTATGAGTTACAACTTTAAGGTTTAGGAATTAT-GGGTTTAAGGGCTATGGTTTAAGTGTC
* * * ** * * * *
5602980 AGGGGTTAGGGGTTTAGAGTTTATGTTTTATTATTCAGGGTTTATGGATTATGGATTAGGGATTA
195 AGGGGTTAAGGGTTTAGAGGTTAGGGGTCAGTATTCAGGGTTTAAGGATTATGGA-TAAGGATTA
*
5603045 TGGGTTTAGGGTTTTGATTAATTAGTA
259 TAGGTTTAGGGTTTTGATTAATTAGTA
* *
5603072 TTTTTTAATTTATATATTAAATAATTTCTTATATAATTGTGAAAGAGATAGTGTTAATTTTAAAA
1 TTTTTTAATTTATATATTAAATAATTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAA
* *
5603137 TATTAAATTAATCATCTTTATAGTTTAGGGTTTACTGTTTACAAATCAAGGTATATGGTTTATGG
66 TATTAAATTAATCATCATTATAGTTTAGGG--TAC--TTTACAAATCAAGGTATATGG-TTAAGG
* *
5603202 TTTTAGGGCTTATGAGTTACAACTTTAAGGGTTT-GTGAATTAT-GGTTTAAGGGCT-GGTGTTT
126 GTTTAGGGCTTATGAGTTACAACTTTAA-GGTTTAG-GAATTATGGGTTTAAGGGCTATG-GTTT
*
5603264 AAG-GTTTAGGGGTTAAGGG-TTACG-GGTTAGGGGTCAGT-TT-AGGGTTTAAAGG-TTATGTG
188 AAGTG-TCAGGGGTTAAGGGTTTA-GAGGTTAGGGGTCAGTATTCAGGGTTT-AAGGATTATG-G
* *
5603323 -TAAGGTTTATAGTTTTAGGGTTT
249 ATAAGGATTATAGGTTTAGGGTTT
5603346 AGGGTTTTAG
Statistics
Matches: 227, Mismatches: 35, Indels: 24
0.79 0.12 0.08
Matches are distributed among these distances:
287 105 0.46
288 12 0.05
289 9 0.04
290 13 0.06
291 48 0.21
292 29 0.13
293 11 0.05
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.45
Consensus pattern (285 bp):
TTTTTTAATTTATATATTAAATAATTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAA
TATTAAATTAATCATCATTATAGTTTAGGGTACTTTACAAATCAAGGTATATGGTTAAGGGTTTA
GGGCTTATGAGTTACAACTTTAAGGTTTAGGAATTATGGGTTTAAGGGCTATGGTTTAAGTGTCA
GGGGTTAAGGGTTTAGAGGTTAGGGGTCAGTATTCAGGGTTTAAGGATTATGGATAAGGATTATA
GGTTTAGGGTTTTGATTAATTAGTA
Found at i:5603346 original size:7 final size:7
Alignment explanation
Indices: 5603336--5603396 Score: 79
Period size: 7 Copynumber: 8.7 Consensus size: 7
5603326 GGTTTATAGT
5603336 TTTAGGG
1 TTTAGGG
5603343 TTTAGGG
1 TTTAGGG
*
5603350 TTTTAGAG
1 -TTTAGGG
5603358 TTTAGGG
1 TTTAGGG
*
5603365 GTT-GGG
1 TTTAGGG
*
5603371 GTTAGGG
1 TTTAGGG
5603378 TTTAGGG
1 TTTAGGG
5603385 TTTAGGG
1 TTTAGGG
5603392 TTTAG
1 TTTAG
5603397 TGTTAATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.12
7 36 0.75
8 6 0.12
ACGTcount: A:0.15, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:5603676 original size:14 final size:14
Alignment explanation
Indices: 5603640--5603676 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
5603630 AAAAAAAATG
5603640 AAATTATTTAGATT
1 AAATTATTTAGATT
5603654 AAATT-TTTAGATT
1 AAATTATTTAGATT
5603667 AAATTATTTA
1 AAATTATTTA
5603677 AAAGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
AAATTATTTAGATT
Found at i:5607833 original size:13 final size:13
Alignment explanation
Indices: 5607815--5607849 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
5607805 TTACATAATA
*
5607815 CATAAATATGTAT
1 CATAAATATATAT
5607828 CATAAATATATAT
1 CATAAATATATAT
5607841 CATATAATA
1 CATA-AATA
5607850 ACTTACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (13 bp):
CATAAATATATAT
Found at i:5607859 original size:9 final size:9
Alignment explanation
Indices: 5607847--5608013 Score: 80
Period size: 9 Copynumber: 19.0 Consensus size: 9
5607837 ATATCATATA
5607847 ATAACTTAC
1 ATAACTTAC
*
5607856 ATAACTTAT
1 ATAACTTAC
*
5607865 ATACCTTAC
1 ATAACTTAC
*
5607874 A-AA-ATAC
1 ATAACTTAC
* *
5607881 ATAA-ATAT
1 ATAACTTAC
* *
5607889 ATATCATATC
1 ATAACTTA-C
5607899 ATAACTTAC
1 ATAACTTAC
*
5607908 ACAACTTAC
1 ATAACTTAC
5607917 ATAA--TAC
1 ATAACTTAC
* *
5607924 ATAA-ATAT
1 ATAACTTAC
* *
5607932 ATATCATATC
1 ATAACTTA-C
5607942 ATAACTTAC
1 ATAACTTAC
*
5607951 ATACCTTAC
1 ATAACTTAC
* *
5607960 ATAAATGTAT
1 ATAACT-TAC
* *
5607970 ATCA-TAAC
1 ATAACTTAC
5607978 ATAACTTAC
1 ATAACTTAC
5607987 ATAACTTAC
1 ATAACTTAC
5607996 A-AAGCTTAC
1 ATAA-CTTAC
*
5608005 TTAACTTAC
1 ATAACTTAC
5608014 GTAATACATA
Statistics
Matches: 121, Mismatches: 27, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
7 11 0.09
8 20 0.17
9 71 0.59
10 19 0.16
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:5607903 original size:43 final size:43
Alignment explanation
Indices: 5607855--5607965 Score: 177
Period size: 43 Copynumber: 2.6 Consensus size: 43
5607845 TAATAACTTA
*
5607855 CATAACTTATATACCTTACAAAATACATAAATATATATCATAT
1 CATAACTTACATACCTTACAAAATACATAAATATATATCATAT
* * *
5607898 CATAACTTACACAACTTACATAATACATAAATATATATCATAT
1 CATAACTTACATACCTTACAAAATACATAAATATATATCATAT
5607941 CATAACTTACATACCTTACATAAAT
1 CATAACTTACATACCTTACA-AAAT
5607966 GTATATCATA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
43 57 0.95
44 3 0.05
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (43 bp):
CATAACTTACATACCTTACAAAATACATAAATATATATCATAT
Found at i:5607903 original size:52 final size:49
Alignment explanation
Indices: 5607828--5607958 Score: 166
Period size: 43 Copynumber: 2.7 Consensus size: 49
5607818 AAATATGTAT
*
5607828 CATAAATATATATCATATAATAACTTACATAACTTATATACCTTACAAAATA
1 CATAAATATATATCATATCATAACTTACATAACTTA-A-A-CTTACAAAATA
*
5607880 CATAAATATATATCATATCATAACTTAC---AC---AACTTACATAATA
1 CATAAATATATATCATATCATAACTTACATAACTTAAACTTACAAAATA
*
5607923 CATAAATATATATCATATCATAACTTACATACCTTA
1 CATAAATATATATCATATCATAACTTACATAACTTA
5607959 CATAAATGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
43 38 0.54
44 1 0.01
45 1 0.01
46 1 0.01
49 2 0.03
52 27 0.39
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (49 bp):
CATAAATATATATCATATCATAACTTACATAACTTAAACTTACAAAATA
Found at i:5607919 original size:36 final size:36
Alignment explanation
Indices: 5607878--5607996 Score: 139
Period size: 36 Copynumber: 3.1 Consensus size: 36
5607868 CCTTACAAAA
*
5607878 TACATAAATATATATCATATCATAACTTACACAACTTACAT
1 TACATAAATATATATCATATCATAACTT--AC-A-TAAC-T
*
5607919 AATACATAAATATATATCATATCATAACTTACATACCT
1 --TACATAAATATATATCATATCATAACTTACATAACT
* *
5607957 TACATAAATGTATATCATAACATAACTTACATAACT
1 TACATAAATATATATCATATCATAACTTACATAACT
5607993 TACA
1 TACA
5607997 AAGCTTACTT
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
36 37 0.52
38 1 0.01
39 2 0.03
40 1 0.01
41 2 0.03
43 28 0.39
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (36 bp):
TACATAAATATATATCATATCATAACTTACATAACT
Found at i:5613133 original size:13 final size:14
Alignment explanation
Indices: 5613117--5613145 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5613107 TTCTAAATAT
5613117 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
5613130 TTATAATTGTTTAA
1 TTATAATTGTTTAA
5613144 TT
1 TT
5613146 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:5613578 original size:15 final size:16
Alignment explanation
Indices: 5613553--5613583 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5613543 GCAACAACTT
5613553 AGAGCGGAGGCAGCAG
1 AGAGCGGAGGCAGCAG
5613569 AGAG-GGAGGCAGCAG
1 AGAGCGGAGGCAGCAG
5613584 TAGCAGTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.16, G:0.52, T:0.00
Consensus pattern (16 bp):
AGAGCGGAGGCAGCAG
Found at i:5613609 original size:21 final size:21
Alignment explanation
Indices: 5613561--5613610 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5613551 TTAGAGCGGA
5613561 GGCAGCAGAGAGGGAGGCAGC
1 GGCAGCAGAGAGGGAGGCAGC
* * *
5613582 AGTAGCAGTGAGGGAGGCAGC
1 GGCAGCAGAGAGGGAGGCAGC
5613603 GGCAGCAG
1 GGCAGCAG
5613611 CGATGGCAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.18, G:0.50, T:0.04
Consensus pattern (21 bp):
GGCAGCAGAGAGGGAGGCAGC
Found at i:5614050 original size:43 final size:43
Alignment explanation
Indices: 5613988--5614094 Score: 162
Period size: 43 Copynumber: 2.5 Consensus size: 43
5613978 GGCTTTTAAT
5613988 GGCGCTTTTTT-ACAAACGCCGCTAAAAGCCATGACTTTTAGC
1 GGCGCTTTTTTAACAAACGCCGCTAAAAGCCATGACTTTTAGC
* * *
5614030 GGCTCTTTTTTAACAAACGCCGCTAAAAGTCATGGCTTTTAGC
1 GGCGCTTTTTTAACAAACGCCGCTAAAAGCCATGACTTTTAGC
*
5614073 GGCGCTTTTTTAAATAAACGCC
1 GGCGCTTTTTT-AACAAACGCC
5614095 ACCAATTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
42 10 0.17
43 39 0.67
44 9 0.16
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
GGCGCTTTTTTAACAAACGCCGCTAAAAGCCATGACTTTTAGC
Found at i:5618322 original size:30 final size:30
Alignment explanation
Indices: 5618287--5618345 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5618277 TATTTTATTG
5618287 TTAATTTGGTTATTATTTTA-ATGACATTTA
1 TTAATTTGGTTATTATTTTAGA-GACATTTA
*
5618317 TTAATTTTGTTATTATTTTAGAGACATTT
1 TTAATTTGGTTATTATTTTAGAGACATTT
5618346 GCTTGTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (30 bp):
TTAATTTGGTTATTATTTTAGAGACATTTA
Found at i:5618491 original size:12 final size:12
Alignment explanation
Indices: 5618470--5618503 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5618460 TATATTTTTT
*
5618470 AAAATTATATAA
1 AAAATAATATAA
5618482 AAAATAATATAA
1 AAAATAATATAA
*
5618494 AAATTAATAT
1 AAAATAATAT
5618504 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:5619374 original size:79 final size:79
Alignment explanation
Indices: 5619277--5619436 Score: 302
Period size: 79 Copynumber: 2.0 Consensus size: 79
5619267 ACTGGTCATG
5619277 CATCAATGTAATTATCCATCCAAAAGCCACGTCTCAACATATTAATTTCAAGACAGCAAAAGTTG
1 CATCAATGTAATTATCCATCCAAAAGCCACGTCTCAACATATTAATTTCAAGACAGCAAAAGTTG
5619342 GCCATACATCAACA
66 GCCATACATCAACA
*
5619356 CATCAATGTAATTATCCATCCAAAAGCCACGTCTCAATATATTAATTTCAAGACAGCAAAAGTTG
1 CATCAATGTAATTATCCATCCAAAAGCCACGTCTCAACATATTAATTTCAAGACAGCAAAAGTTG
*
5619421 GCCATGCATCAACA
66 GCCATACATCAACA
5619435 CA
1 CA
5619437 GTTGTCATTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (79 bp):
CATCAATGTAATTATCCATCCAAAAGCCACGTCTCAACATATTAATTTCAAGACAGCAAAAGTTG
GCCATACATCAACA
Found at i:5622848 original size:30 final size:31
Alignment explanation
Indices: 5622789--5622852 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
5622779 ACTTAACAAG
5622789 CAAATGCCTCTAAAATAATAAAAAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAAATTAA
* *
5622820 CAAATGCCTTTAAAATAAT-AACAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAAATTAA
5622850 CAA
1 CAA
5622853 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.23
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATAAAAAAAATTAA
Found at i:5625141 original size:10 final size:10
Alignment explanation
Indices: 5625114--5625163 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
5625104 TTAAATTCTA
5625114 AAAGATAAAT
1 AAAGATAAAT
*
5625124 ACAA-ATAATT
1 A-AAGATAAAT
*
5625134 AAAGATAATT
1 AAAGATAAAT
5625144 AAAGATAAAT
1 AAAGATAAAT
5625154 AAAGATAAAT
1 AAAGATAAAT
5625164 GCTAAAAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 2 0.06
10 32 0.89
11 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5625991 original size:23 final size:23
Alignment explanation
Indices: 5625961--5626006 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5625951 GAGGGATGAC
*
5625961 AGCGAAGCACTCTACCTCGGTTA
1 AGCGAAGCACCCTACCTCGGTTA
5625984 AGCGAAGCACCCTACCTCGGTTA
1 AGCGAAGCACCCTACCTCGGTTA
5626007 CTTAGTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.20
Consensus pattern (23 bp):
AGCGAAGCACCCTACCTCGGTTA
Found at i:5632100 original size:20 final size:22
Alignment explanation
Indices: 5632071--5632120 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
5632061 ATTTATTAAT
5632071 ATAA-AAAATAAAGT-AAT-AA
1 ATAATAAAATAAAGTAAATGAA
5632090 ATAATAAAATAAAGTAAAATGAA
1 ATAATAAAATAAAGT-AAATGAA
5632113 ATAATAAA
1 ATAATAAA
5632121 TAATAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.15
20 10 0.37
22 3 0.11
23 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (22 bp):
ATAATAAAATAAAGTAAATGAA
Found at i:5632129 original size:15 final size:15
Alignment explanation
Indices: 5632071--5632129 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
5632061 ATTTATTAAT
* *
5632071 ATAAAAAATAAAGTA
1 ATAAATAATAAAATA
5632086 ATAAATAATAAAATA
1 ATAAATAATAAAATA
*
5632101 A-AGTAA-AATGAAATA
1 ATA--AATAATAAAATA
5632116 ATAAATAATAAAAT
1 ATAAATAATAAAAT
5632130 TAAAATTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 3 0.08
15 30 0.83
16 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAAATAATAAAATA
Found at i:5632150 original size:17 final size:16
Alignment explanation
Indices: 5632125--5632159 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5632115 AATAAATAAT
*
5632125 AAAATTAAAATTAGAAA
1 AAAAATAAAATTA-AAA
5632142 AAAAATAAAATTAAAA
1 AAAAATAAAATTAAAA
5632158 AA
1 AA
5632160 TTTGGGTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAAATAAAATTAAAA
Found at i:5635182 original size:24 final size:25
Alignment explanation
Indices: 5635155--5635206 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5635145 ACCTAGCCTC
*
5635155 TTTTAAT-AACTAGGGCACAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
* *
5635179 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
5635204 TTT
1 TTT
5635207 CGGTAAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTAGGGCAAAGCCCT
Found at i:5635196 original size:25 final size:25
Alignment explanation
Indices: 5635162--5635231 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
5635152 CTCTTTTAAT
* * *
5635162 AACTAGGGCACAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
5635187 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
5635212 AACTGGGGCATAGCCATTTT
1 AACTGGGGCAAAGCCCTTTT
5635232 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:5635464 original size:27 final size:27
Alignment explanation
Indices: 5635434--5635602 Score: 232
Period size: 27 Copynumber: 6.3 Consensus size: 27
5635424 GGGGTAAAAT
* *
5635434 GGTAATT-TAACCCCACAAGGGTATCTC
1 GGTAATTCT-ACCCTACAAGGGTATTTC
5635461 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
5635488 GGTAATTCTACCTTACAAAGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
5635515 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
5635542 GATAATTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
5635569 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
5635596 AGTAATT
1 GGTAATT
5635603 TCACAATCGA
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
27 125 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:5635643 original size:27 final size:27
Alignment explanation
Indices: 5635607--5635832 Score: 310
Period size: 27 Copynumber: 8.4 Consensus size: 27
5635597 GTAATTTCAC
* *
5635607 AATCGAGGGTAAAACTGCAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
5635634 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
5635661 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
5635688 AATCGAGGG-AAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
5635714 AATCGAGGATAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
*
5635741 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATA
* *
5635768 AATCGAGGGTAAAATGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATA
** * *
5635795 AATTTAGGGTAAAACGGTAATTTTTTA
1 AATCGAGGGTAAAACGGTAATTCTATA
5635822 AATCGAGGGTA
1 AATCGAGGGTA
5635833 CTTTGGTAAT
Statistics
Matches: 172, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 23 0.13
27 149 0.87
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTATA
Found at i:5635670 original size:80 final size:80
Alignment explanation
Indices: 5635595--5635832 Score: 270
Period size: 80 Copynumber: 3.0 Consensus size: 80
5635585 AAGGGTATTT
* *
5635595 CAGTAATTTCACAATCGAGGGTAAAACTGCAATTCTATAAATCGAGGGTAAAACGATAATTCTGT
1 CAGTAATTTCACAATCGAGGGTAAAACTGTAATTCTATAAATCGAGGGTAAAACGATAATTCTAT
5635660 AAATCGAGGGTAAAA
66 AAATCGAGGGTAAAA
* * * *
5635675 CAGTAA-TTCTATAAATCGAGGG-AAAACGGTAATTCTGTAAATCGAGGATAAAAC-AGTAATTC
1 CAGTAATTTC-A-CAATCGAGGGTAAAACTGTAATTCTATAAATCGAGGGTAAAACGA-TAATTC
5635737 TATAAATCGAGGGTAAAA
63 TATAAATCGAGGGTAAAA
* * ** * *
5635755 CGGTAATTCTGTA-AATCGAGGGTAAAA-TGATAATTCTATAAATTTAGGGTAAAACGGTAATTT
1 CAGTAATT-T-CACAATCGAGGGTAAAACTG-TAATTCTATAAATCGAGGGTAAAACGATAATTC
*
5635818 TTTAAATCGAGGGTA
63 TATAAATCGAGGGTA
5635833 CTTTGGTAAT
Statistics
Matches: 133, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
79 4 0.03
80 73 0.55
81 54 0.41
82 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.28
Consensus pattern (80 bp):
CAGTAATTTCACAATCGAGGGTAAAACTGTAATTCTATAAATCGAGGGTAAAACGATAATTCTAT
AAATCGAGGGTAAAA
Found at i:5635680 original size:107 final size:107
Alignment explanation
Indices: 5635595--5635816 Score: 279
Period size: 107 Copynumber: 2.1 Consensus size: 107
5635585 AAGGGTATTT
* *
5635595 CAGTAATT-T-CACAATCGAGGGTAAAACTGCAATTCTATAAATCGAGGGTAAAACGATAATTCT
1 CAGTAATTCTGCA-AATCGAGGATAAAACAGCAATTCTATAAATCGAGGGTAAAACGATAATTCT
* *
5635658 GTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGAAAA
65 GTAAATCGAGGGTAAAACAGTAATTCTACAAATCAAGGGAAAA
* * * *
5635701 CGGTAATTCTGTAAATCGAGGATAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTG
1 CAGTAATTCTGCAAATCGAGGATAAAACAGCAATTCTATAAATCGAGGGTAAAACGATAATTCTG
* * **
5635766 TAAATCGAGGGTAAAA-TGATAATTCTATAAATTTAGGGTAAAA
66 TAAATCGAGGGTAAAACAG-TAATTCTACAAATCAAGGG-AAAA
*
5635809 CGGTAATT
1 CAGTAATT
5635817 TTTTAAATCG
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
106 8 0.08
107 82 0.80
108 13 0.13
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (107 bp):
CAGTAATTCTGCAAATCGAGGATAAAACAGCAATTCTATAAATCGAGGGTAAAACGATAATTCTG
TAAATCGAGGGTAAAACAGTAATTCTACAAATCAAGGGAAAA
Found at i:5635843 original size:54 final size:54
Alignment explanation
Indices: 5635607--5635832 Score: 348
Period size: 54 Copynumber: 4.2 Consensus size: 54
5635597 GTAATTTCAC
* * *
5635607 AATCGAGGGTAAAACTGCAATTCTATAAATCGAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
5635661 AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGG-AAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
*
5635714 AATCGAGGATAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
* ** * *
5635768 AATCGAGGGTAAAA-TGATAATTCTATAAATTTAGGGTAAAACGGTAATTTTTTA
1 AATCGAGGGTAAAACAG-TAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
5635822 AATCGAGGGTA
1 AATCGAGGGTA
5635833 CTTTGGTAAT
Statistics
Matches: 160, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
53 52 0.32
54 108 0.68
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (54 bp):
AATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTA
Found at i:5638206 original size:24 final size:25
Alignment explanation
Indices: 5638173--5638230 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
5638163 CTGGAGAACT
*
5638173 AGCCTCTTTTAAT-AACTAGGGCAA
1 AGCCTTTTTTAATAAACTAGGGCAA
*
5638197 AGCCTTTTTTGATAAACTAGGGCAA
1 AGCCTTTTTTAATAAACTAGGGCAA
5638222 AGTCCTTTT
1 AG-CCTTTT
5638231 CGGTAAACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 11 0.37
25 13 0.43
26 6 0.20
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (25 bp):
AGCCTTTTTTAATAAACTAGGGCAA
Found at i:5638237 original size:25 final size:24
Alignment explanation
Indices: 5638186--5638255 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
5638176 CTCTTTTAAT
*
5638186 AACTAGGGCAAAGCCTTTTTTGATA
1 AACTAGGGCAAAGCC-TTTTCGATA
*
5638211 AACTAGGGCAAAGTCCTTTTCGGTA
1 AACTAGGGCAAAG-CCTTTTCGATA
* *
5638236 AACTGGGGCATAGCCCTTTT
1 AACTAGGGCAAAG-CCTTTT
5638256 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 37 0.95
26 2 0.05
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (24 bp):
AACTAGGGCAAAGCCTTTTCGATA
Found at i:5638506 original size:27 final size:27
Alignment explanation
Indices: 5638458--5638626 Score: 185
Period size: 27 Copynumber: 6.3 Consensus size: 27
5638448 GGGGTAAAAT
* * *
5638458 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
5638485 GGTAATTTTACCCTCCAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
5638512 GGTAATTCTAGCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
5638539 GGTAATTCTACCATACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
5638566 GGTAATTCTACCCTACAAGGCTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
5638593 AGTAATTCTACCTTTCATGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
5638620 AGTAATT
1 GGTAATT
5638627 TCACAATTGA
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:5638667 original size:27 final size:27
Alignment explanation
Indices: 5638635--5638857 Score: 306
Period size: 27 Copynumber: 8.3 Consensus size: 27
5638625 TTTCACAATT
*
5638635 GAGGGTAAAACGATAATTCTGTAAATC
1 GAGGGTAAAACGATAATTCTATAAATC
5638662 GAGGGTAAAACGATAATTCTATAAATC
1 GAGGGTAAAACGATAATTCTATAAATC
**
5638689 GAGGGTAAAAAAATAATTCTATAAATC
1 GAGGGTAAAACGATAATTCTATAAATC
* *
5638716 GAAGGTAAAACGGTAATTCTATAAATC
1 GAGGGTAAAACGATAATTCTATAAATC
*
5638743 GAGGGTAAAAC-AGTAATTCTATAAATT
1 GAGGGTAAAACGA-TAATTCTATAAATC
* * *
5638770 GAAGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAACGATAATTCTATAAATC
*
5638797 GAGGGTAAAATGATAATTCTATAAATC
1 GAGGGTAAAACGATAATTCTATAAATC
* *
5638824 GAGGGTAAAAC-AGTAATTTTGTAAATC
1 GAGGGTAAAACGA-TAATTCTATAAATC
5638851 GAGGGTA
1 GAGGGTA
5638858 CTTTGGTAAT
Statistics
Matches: 172, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 171 0.99
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (27 bp):
GAGGGTAAAACGATAATTCTATAAATC
Found at i:5638880 original size:81 final size:80
Alignment explanation
Indices: 5638621--5638882 Score: 296
Period size: 81 Copynumber: 3.2 Consensus size: 80
5638611 GGGTATTTCA
* * *
5638621 GTAATTTCACAATTGAGGGTAAAACGATAATTCTGTAAATCGAGGGTAAAAC-GATAATTCTATA
1 GTAATTTTACAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAG-TAATTCTATA
*
5638685 AATCGAGGGTAAAAAA
65 AATCGAGGGTAAAAAG
* * *
5638701 ATAATTCTATA-AATCGAAGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTAT
1 GTAATT-T-TACAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAGTAATTCTAT
* * *
5638765 AAATTGAAGGTAAAACG
64 AAATCGAGGGTAAAAAG
* * *
5638782 GTAATTCTGTA-AATCGAGGGTAAAATGATAATTCTATAAATCGAGGGTAAAACAGTAATTTTGT
1 GTAATT-T-TACAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAGTAATTCTAT
****
5638846 AAATCGAGGGTACTTTG
64 AAATCGAGGGTAAAAAG
5638863 GTAATTTTACAAGTCGAGGG
1 GTAATTTTACAA-TCGAGGG
5638883 CAGTTCAATA
Statistics
Matches: 154, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
79 2 0.01
80 8 0.05
81 142 0.92
82 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.29
Consensus pattern (80 bp):
GTAATTTTACAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAACAGTAATTCTATAA
ATCGAGGGTAAAAAG
Found at i:5644524 original size:16 final size:16
Alignment explanation
Indices: 5644505--5644573 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
5644495 TTTTACATAT
*
5644505 AAAATATAATAAAATA
1 AAAATATAATAAAAGA
5644521 AAAATA-AA-AAACAGA
1 AAAATATAATAAA-AGA
*
5644536 ATAAATATATATAAAATA
1 A-AAATATA-ATAAAAGA
5644554 AAATATATAATAAAAGA
1 AAA-ATATAATAAAAGA
5644571 AAA
1 AAA
5644574 CTTTTTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
14 3 0.07
15 5 0.11
16 11 0.25
17 13 0.30
18 9 0.20
19 3 0.07
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAATATAATAAAAGA
Found at i:5644895 original size:11 final size:11
Alignment explanation
Indices: 5644863--5644896 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5644853 ATGTTAGATT
5644863 TAAATTAAAAA
1 TAAATTAAAAA
5644874 TAAA-TAAAAA
1 TAAATTAAAAA
*
5644884 TAAATTATAAA
1 TAAATTAAAAA
5644895 TA
1 TA
5644897 TTAAAATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAATTAAAAA
Found at i:5646490 original size:86 final size:86
Alignment explanation
Indices: 5646394--5646670 Score: 228
Period size: 86 Copynumber: 3.2 Consensus size: 86
5646384 ATACCAAATC
5646394 ATCTTGGATCTGCTTTAGTAAAATCATCTGAAGGTTAGATCTGCTATGTATCTGTTATCCGTCAA
1 ATCTTGGATCTGCTTTAGTAAAATCATCTGAAGGTTAGATCTGCTATGTATCTGTTATCCGTCAA
5646459 AATGGAGATACCAAATCTGTT
66 AATGGAGATACCAAATCTGTT
* * * * * * * *
5646480 ATCTTGGATCTGCTTTGGTGTGAGAA-CATCCGAAAGTCAAATCTGCTATGTCT-TCGATTTGTT
1 ATCTTGGATCTGCTTT--AGT-AAAATCATCTGAAGGTTAGATCTGCTATGTATCT-G--TT-AT
**
5646543 CCTTGT-AAACA-CAAGGATACCAAATC----
59 CC--GTCAAA-ATGGA-GATACCAAATCTGTT
* * *** *
5646569 ATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGTTAGATTTGCTATGTATCTGCGCTCCGTCGA
1 ATCTTGGATCTGCTTTAGTAAAATCATCTGAAGGTTAGATCTGCTATGTATCTGTTATCCGTCAA
* *
5646634 AATGGAGATTCCAGATCTGTT
66 AATGGAGATACCAAATCTGTT
*
5646655 ATCTTGGACCTGCTTT
1 ATCTTGGATCTGCTTT
5646671 TGTGTGAGAA
Statistics
Matches: 143, Mismatches: 29, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
82 12 0.08
83 3 0.02
84 3 0.02
86 33 0.23
87 25 0.17
88 26 0.18
89 18 0.13
90 2 0.01
91 3 0.02
92 4 0.03
93 14 0.10
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (86 bp):
ATCTTGGATCTGCTTTAGTAAAATCATCTGAAGGTTAGATCTGCTATGTATCTGTTATCCGTCAA
AATGGAGATACCAAATCTGTT
Found at i:5646582 original size:89 final size:88
Alignment explanation
Indices: 5646353--5646758 Score: 245
Period size: 88 Copynumber: 4.6 Consensus size: 88
5646343 AAATCCGCGG
* * * *
5646353 TGTCTTCGATTTGCTCCTTGTGAACACAAGGATACCAAATCATCTTGGATCTGCTTT-AGT-AAA
1 TGTCTTCGATTTGTTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTTTGTGTGAGA
* * * *
5646416 ATCATCTGAAGGTTAGATCTGCTA
66 A-CATCCGAAAGTCAAATCTGCTA
* * **
5646440 TGT-ATC--TGTT-ATCC--GTCAAA-A-TGGAGATACCAAATCTGTTATCTTGGATCTGCTTTG
1 TGTCTTCGAT-TTGTTCCTTGT-AAACACAAG-GATACCAAATC----ATCTTGGATCTGCTTT-
5646497 GTGTGAGAACATCCGAAAGTCAAATCTGCTA
58 GTGTGAGAACATCCGAAAGTCAAATCTGCTA
** *
5646528 TGTCTTCGATTTGTTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGC-TTCAGT-AAA
1 TGTCTTCGATTTGTTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTTTGTGTGAGA
* * * * *
5646591 ATCATCTGAAGGTTAGATTTGCTA
66 A-CATCCGAAAGTCAAATCTGCTA
* ** * * *** * * *
5646615 TGT-ATC--TGCGCTCCGTCG-AAA-TGGA-GATTCCAGATCTGTTATCTTGGACCTGCTTTTGT
1 TGTCTTCGATTTGTTCC-TTGTAAACACAAGGATACCAAATC----ATCTTGGATCTGC-TTTGT
5646674 GTGAGAACATCCGAAAGTCAAATCTGCTA
60 GTGAGAACATCCGAAAGTCAAATCTGCTA
* *
5646703 TGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTT
1 TGTCTTCGATTTGTTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTT
5646759 CAATATAAAC
Statistics
Matches: 232, Mismatches: 54, Indels: 65
0.66 0.15 0.19
Matches are distributed among these distances:
81 1 0.00
82 23 0.10
83 3 0.01
84 12 0.05
85 4 0.02
86 35 0.15
87 25 0.11
88 51 0.22
89 35 0.15
90 4 0.02
91 12 0.05
92 4 0.02
93 22 0.09
94 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (88 bp):
TGTCTTCGATTTGTTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTTTGTGTGAGA
ACATCCGAAAGTCAAATCTGCTA
Found at i:5646654 original size:175 final size:175
Alignment explanation
Indices: 5646353--5646895 Score: 872
Period size: 175 Copynumber: 3.1 Consensus size: 175
5646343 AAATCCGCGG
* *
5646353 TGTCTTCGATTTGCTCCTTGTGAACACAAGGATACCAAATCATCTTGGATCTGCTTTAGTAAAAT
1 TGTCTTCGATTTGCTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTTCAGTAAAAT
* * * * *
5646418 CATCTGAAGGTTAGATCTGCTATGTATCTGTTATCCGTCAAAATGGAGATACCAAATCTGTTATC
66 CATCTGAAGGTTAGATTTGCTATGTATCTGCTCTCCGTCGAAATGGAGATACCAGATCTGTTATC
5646483 TTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTA
131 TTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTA
*
5646528 TGTCTTCGATTTGTTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTTCAGTAAAAT
1 TGTCTTCGATTTGCTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTTCAGTAAAAT
* *
5646593 CATCTGAAGGTTAGATTTGCTATGTATCTGCGCTCCGTCGAAATGGAGATTCCAGATCTGTTATC
66 CATCTGAAGGTTAGATTTGCTATGTATCTGCTCTCCGTCGAAATGGAGATACCAGATCTGTTATC
* *
5646658 TTGGACCTGCTTTTGTGTGAGAACATCCGAAAGTCAAATCTGCTA
131 TTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTA
* * * *
5646703 TGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAATATAAA
1 TGTCTTCGATTTGCTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTTCAGTA-AAA
* * * *
5646768 -CATCTGAAGGTTAGATTTTCTATATGTCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTAT
65 TCATCTGAAGGTTAGATTTGCTATGTATCTGCTCTCCGTCGAAATGGAGATACCAGATCTGTTAT
*
5646832 CTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAGATCTGCTA
130 CTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTA
*
5646878 TGTCTTCAATTTGCTCCT
1 TGTCTTCGATTTGCTCCT
5646896 CGTCGAAGAT
Statistics
Matches: 342, Mismatches: 25, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
175 339 0.99
176 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (175 bp):
TGTCTTCGATTTGCTCCTTGTAAACACAAGGATACCAAATCATCTTGGATCTGCTTCAGTAAAAT
CATCTGAAGGTTAGATTTGCTATGTATCTGCTCTCCGTCGAAATGGAGATACCAGATCTGTTATC
TTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTA
Found at i:5654946 original size:15 final size:15
Alignment explanation
Indices: 5654904--5654953 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
5654894 ATAACTTTGA
* *
5654904 ATGCAAACG-ATGTG
1 ATGCAAATGCATGAG
5654918 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
5654933 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
5654947 ATGCAAA
1 ATGCAAA
5654954 AGGACATCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 10 0.32
15 11 0.35
16 6 0.19
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:5654952 original size:14 final size:16
Alignment explanation
Indices: 5654917--5654953 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5654907 CAAACGATGT
5654917 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
5654932 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
5654947 -ATGCAAA
1 GATGCAAA
5654954 AGGACATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:5658853 original size:12 final size:12
Alignment explanation
Indices: 5658836--5658876 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
5658826 AATAAATATA
5658836 ATGAAATGTAAT
1 ATGAAATGTAAT
*
5658848 ATGAAATAT-A-
1 ATGAAATGTAAT
5658858 ATGAAATGTAAT
1 ATGAAATGTAAT
5658870 ATGAAAT
1 ATGAAAT
5658877 ATGTATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 8 0.32
11 2 0.08
12 15 0.60
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.32
Consensus pattern (12 bp):
ATGAAATGTAAT
Found at i:5658856 original size:22 final size:22
Alignment explanation
Indices: 5658829--5658878 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
5658819 AAACTTAAAT
5658829 AAATATAATGAAATGTAATATG
1 AAATATAATGAAATGTAATATG
5658851 AAATATAATGAAATGTAATATG
1 AAATATAATGAAATGTAATATG
5658873 AAATAT
1 AAATAT
5658879 GTATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (22 bp):
AAATATAATGAAATGTAATATG
Found at i:5658933 original size:6 final size:6
Alignment explanation
Indices: 5658922--5658954 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5658912 AAAATATAAT
*
5658922 AAAATA AAAATA AAAA-A GAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
5658955 ACAGAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:5658945 original size:17 final size:17
Alignment explanation
Indices: 5658923--5658955 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5658913 AAATATAATA
5658923 AAATAAAAATAAAAAAG
1 AAATAAAAATAAAAAAG
5658940 AAATAAAAATAAAAAA
1 AAATAAAAATAAAAAA
5658956 CAGAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (17 bp):
AAATAAAAATAAAAAAG
Found at i:5658954 original size:18 final size:18
Alignment explanation
Indices: 5658923--5658964 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5658913 AAATATAATA
5658923 AAATAAAAATAAAAA-AG
1 AAATAAAAATAAAAACAG
5658940 AAATAAAAATAAAAAACAG
1 AAATAAAAAT-AAAAACAG
5658959 -AATAAA
1 AAATAAA
5658965 TATATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
18 11 0.48
19 2 0.09
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (18 bp):
AAATAAAAATAAAAACAG
Found at i:5658980 original size:18 final size:17
Alignment explanation
Indices: 5658908--5658990 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 17
5658898 AATATTTTAC
*
5658908 ATATAAAATATAATAAA
1 ATATAAAATAAAATAAA
*
5658925 ATA-AAAATAAAAAAGAA
1 ATATAAAATAAAATA-AA
5658942 ATA-AAAATAAAA-AACA
1 ATATAAAATAAAATAA-A
5658958 GA-ATAAATATATATAATAAA
1 -ATATAAA-ATA-A-AATAAA
*
5658978 ATATATAATAAAA
1 ATATAAAATAAAA
5658991 GATTTTTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
15 1 0.02
16 12 0.22
17 23 0.43
18 4 0.07
19 5 0.09
20 7 0.13
21 2 0.04
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (17 bp):
ATATAAAATAAAATAAA
Found at i:5658981 original size:12 final size:12
Alignment explanation
Indices: 5658959--5658990 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
5658949 TAAAAAACAG
5658959 AATAAATATATAT
1 AATAAA-ATATAT
5658972 AATAAAATATAT
1 AATAAAATATAT
5658984 AATAAAA
1 AATAAAA
5658991 GATTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAAATATAT
Found at i:5660772 original size:38 final size:38
Alignment explanation
Indices: 5660721--5660797 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
5660711 TTTATTAGTT
* *
5660721 TTTTCATCTATCCCTATGAATACACTTGTATTTGTAAA
1 TTTTCATCGATCCCTATGAATACACTTGTATTCGTAAA
5660759 TTTTCATCGATCCCTATGAATACACTTGTATTCGTAAA
1 TTTTCATCGATCCCTATGAATACACTTGTATTCGTAAA
5660797 T
1 T
5660798 ACACATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (38 bp):
TTTTCATCGATCCCTATGAATACACTTGTATTCGTAAA
Found at i:5671122 original size:12 final size:12
Alignment explanation
Indices: 5671105--5671130 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5671095 TATAATTTGC
5671105 AAAACACCATTA
1 AAAACACCATTA
5671117 AAAACACCATTA
1 AAAACACCATTA
5671129 AA
1 AA
5671131 TATATTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACACCATTA
Found at i:5678617 original size:34 final size:31
Alignment explanation
Indices: 5678546--5678609 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
5678536 ATTTATTTTC
5678546 TTGTTAATTTTATTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTTATTATTTTAAAGACAT
*
5678577 TTGTTAATTTTA-TTATTATTTTAGAGACAT
1 TTGTTAATTTTATTTATTATTTTAAAGACAT
5678607 TTG
1 TTG
5678610 ATTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (31 bp):
TTGTTAATTTTATTTATTATTTTAAAGACAT
Found at i:5679302 original size:47 final size:47
Alignment explanation
Indices: 5679233--5679327 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
5679223 TGTGATTGTG
5679233 AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAAACTAATAGT
1 AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAAACTAATAGT
*
5679280 AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAGACTAATAGT
1 AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAAACTAATAGT
5679327 A
1 A
5679328 GCATATGAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.29
Consensus pattern (47 bp):
AATGAAAAGTGTTGAATGAGTATGCTATGAGTGCATAAACTAATAGT
Found at i:5681548 original size:17 final size:18
Alignment explanation
Indices: 5681526--5681559 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5681516 AATCTGGACA
5681526 TGTGGG-CCACACGGGCG
1 TGTGGGTCCACACGGGCG
*
5681543 TGTGGGTCTACACGGGC
1 TGTGGGTCCACACGGGC
5681560 AGACCACATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.18
Consensus pattern (18 bp):
TGTGGGTCCACACGGGCG
Found at i:5686608 original size:11 final size:11
Alignment explanation
Indices: 5686592--5686631 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
5686582 CTCAATCAAT
5686592 AACAAAAAAAA
1 AACAAAAAAAA
5686603 AAC-AAAAAAA
1 AACAAAAAAAA
*
5686613 AACGAAAACAAA
1 AAC-AAAAAAAA
5686625 AACAAAA
1 AACAAAA
5686632 TTTTTTATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 10 0.38
11 7 0.27
12 9 0.35
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAAAAA
Found at i:5686609 original size:6 final size:6
Alignment explanation
Indices: 5686592--5686631 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
5686582 CTCAATCAAT
*
5686592 AACAAA AA-AAA AAC-AA AA-AAA AACGAA AACAAA AACAAA A
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA A
5686632 TTTTTTATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
5 13 0.45
6 16 0.55
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:5691582 original size:44 final size:44
Alignment explanation
Indices: 5691519--5691679 Score: 241
Period size: 44 Copynumber: 3.5 Consensus size: 44
5691509 CTTGAGTACT
5691519 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
5691563 TCTGATCAGTGACAAGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAA--G-----TGATAAGTGGTAGCTTTAGCTACACTTA
* *
5691614 TCTGATCAATGACAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
5691658 TCTGATCAGTGACAAGTGATAA
1 TCTGATCAGTGACAAGTGATAA
5691680 ATGTGATTAG
Statistics
Matches: 107, Mismatches: 3, Indels: 14
0.86 0.02 0.11
Matches are distributed among these distances:
44 63 0.59
46 1 0.01
49 1 0.01
51 42 0.39
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:5691602 original size:51 final size:51
Alignment explanation
Indices: 5691526--5691682 Score: 229
Period size: 51 Copynumber: 3.2 Consensus size: 51
5691516 ACTTCTGATC
* *
5691526 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
5691577 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA
1 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
5691628 A--G-----TGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
5691672 AGTGATAAATG
1 AGTGATAAATG
5691683 TGATTAGTGG
Statistics
Matches: 94, Mismatches: 5, Indels: 14
0.83 0.04 0.12
Matches are distributed among these distances:
44 41 0.44
46 1 0.01
49 1 0.01
51 51 0.54
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (51 bp):
AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:5704349 original size:21 final size:21
Alignment explanation
Indices: 5704325--5704368 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5704315 TTATCTTTTA
5704325 TTTGGACTTTATTTTGGAGTT
1 TTTGGACTTTATTTTGGAGTT
5704346 TTTGGACTTTATTTTGGAGTT
1 TTTGGACTTTATTTTGGAGTT
5704367 TT
1 TT
5704369 CGCATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.05, G:0.23, T:0.59
Consensus pattern (21 bp):
TTTGGACTTTATTTTGGAGTT
Found at i:5704835 original size:18 final size:18
Alignment explanation
Indices: 5704790--5704829 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5704780 AGGATCTGAT
5704790 TATGCATCTGAATATGTA
1 TATGCATCTGAATATGTA
* *
5704808 TCTGCATCTGGATATGTA
1 TATGCATCTGAATATGTA
5704826 TATG
1 TATG
5704830 ATTCTGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (18 bp):
TATGCATCTGAATATGTA
Found at i:5708182 original size:22 final size:23
Alignment explanation
Indices: 5708140--5708182 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5708130 TTCTTTTATA
*
5708140 TATAACAATATACTTTTATATTC
1 TATAACAATATACTTTAATATTC
*
5708163 TATAA-AATATAGTTTAATAT
1 TATAACAATATACTTTAATAT
5708183 GCAATAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TATAACAATATACTTTAATATTC
Found at i:5708189 original size:22 final size:23
Alignment explanation
Indices: 5708141--5708189 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
5708131 TCTTTTATAT
* * *
5708141 ATAACAATATACTTTTATATTCT
1 ATAACAATATACTTTAATATGCA
*
5708164 ATAA-AATATAGTTTAATATGCA
1 ATAACAATATACTTTAATATGCA
5708186 ATAA
1 ATAA
5708190 TCTTACTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (23 bp):
ATAACAATATACTTTAATATGCA
Found at i:5713440 original size:46 final size:46
Alignment explanation
Indices: 5713378--5713643 Score: 334
Period size: 46 Copynumber: 6.0 Consensus size: 46
5713368 TTTGACGTGA
* * * * * *
5713378 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
5713424 TGTCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5713470 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5713516 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
5713562 TGTCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5713600 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5713644 AGAGCACACT
Statistics
Matches: 194, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
38 32 0.16
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 148 0.76
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:5713608 original size:38 final size:38
Alignment explanation
Indices: 5713557--5713632 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
5713547 CATTTCATAT
*
5713557 CAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5713595 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5713633 TTTCATATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:5715519 original size:17 final size:17
Alignment explanation
Indices: 5715497--5715531 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5715487 ATACTTACCT
5715497 TGTTCTATTGATACTAA
1 TGTTCTATTGATACTAA
5715514 TGTTCTATTGATACTAA
1 TGTTCTATTGATACTAA
5715531 T
1 T
5715532 CTTTAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TGTTCTATTGATACTAA
Found at i:5719348 original size:28 final size:27
Alignment explanation
Indices: 5719302--5719355 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
5719292 TCGACGACCG
*
5719302 ATAAAAAAATAAAAGAGAAACAAGAAAA
1 ATAAAAAAATAAAAAAGAAA-AAGAAAA
5719330 ATAAAAAAA-AAGAAAAGAAAAAGAAA
1 ATAAAAAAATAA-AAAAGAAAAAGAAA
5719356 TTGAGGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (27 bp):
ATAAAAAAATAAAAAAGAAAAAGAAAA
Found at i:5719350 original size:11 final size:11
Alignment explanation
Indices: 5719323--5719355 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5719313 AAAGAGAAAC
*
5719323 AAGAAAAATAA
1 AAGAAAAAGAA
5719334 AA-AAAAAGAA
1 AAGAAAAAGAA
5719344 AAGAAAAAGAA
1 AAGAAAAAGAA
5719355 A
1 A
5719356 TTGAGGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:5722830 original size:29 final size:29
Alignment explanation
Indices: 5722755--5722867 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 29
5722745 TACATACATG
* * *
5722755 CATATAGCCCACTAGGCTCAATCTCAT--T
1 CATATGGCCCACTACGCCCAAT-TCATACT
* *
5722783 CATATGGCCTATCT-GGCCCAATTCATACT
1 CATATGGCCCA-CTACGCCCAATTCATACT
* * *
5722812 CTTATGGCCCACTACGCCCAATTCACATT
1 CATATGGCCCACTACGCCCAATTCATACT
* * *
5722841 CATATGGCCCATTAGGCCCAAATCATA
1 CATATGGCCCACTACGCCCAATTCATA
5722868 GTATACTCAT
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.06
28 18 0.26
29 46 0.68
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (29 bp):
CATATGGCCCACTACGCCCAATTCATACT
Found at i:5722964 original size:18 final size:19
Alignment explanation
Indices: 5722941--5722978 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5722931 ATGGGCCCGA
5722941 TAGCCCA-TCAGGCCCATT
1 TAGCCCATTCAGGCCCATT
*
5722959 TAGCCCATTCCGGCCCATT
1 TAGCCCATTCAGGCCCATT
5722978 T
1 T
5722979 GGCCAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.39, G:0.16, T:0.26
Consensus pattern (19 bp):
TAGCCCATTCAGGCCCATT
Found at i:5722987 original size:19 final size:19
Alignment explanation
Indices: 5722951--5722987 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5722941 TAGCCCATCA
*
5722951 GGCCCATTTAGCCCATTCC
1 GGCCCATTTAGCCAATTCC
*
5722970 GGCCCATTTGGCCAATTC
1 GGCCCATTTAGCCAATTC
5722988 TCAACCCAAG
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:0.16, C:0.38, G:0.19, T:0.27
Consensus pattern (19 bp):
GGCCCATTTAGCCAATTCC
Found at i:5723126 original size:16 final size:16
Alignment explanation
Indices: 5723085--5723127 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
5723075 GTAGCCCAAC
5723085 TTTCGGCTTTTCGACA
1 TTTCGGCTTTTCGACA
** **
5723101 TTTCTACTTTTCGGTA
1 TTTCGGCTTTTCGACA
5723117 TTTCGGCTTTT
1 TTTCGGCTTTT
5723128 GCCGTTCCAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.09, C:0.21, G:0.16, T:0.53
Consensus pattern (16 bp):
TTTCGGCTTTTCGACA
Found at i:5724379 original size:16 final size:16
Alignment explanation
Indices: 5724355--5724386 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5724345 AAGTTCGGGA
5724355 TTTCAGGATTTTTGGG
1 TTTCAGGATTTTTGGG
*
5724371 TTTCGGGATTTTTGGG
1 TTTCAGGATTTTTGGG
5724387 GGCGTTACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (16 bp):
TTTCAGGATTTTTGGG
Found at i:5726115 original size:17 final size:19
Alignment explanation
Indices: 5726093--5726133 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5726083 CATAAAGATA
5726093 AAACT-AAATAAAAACTG-
1 AAACTAAAATAAAAACTGT
*
5726110 AAACTAAAATAAAATCTGT
1 AAACTAAAATAAAAACTGT
5726129 AAACT
1 AAACT
5726134 CTAGGTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 11 0.52
19 5 0.24
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (19 bp):
AAACTAAAATAAAAACTGT
Found at i:5728252 original size:31 final size:31
Alignment explanation
Indices: 5728211--5728286 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
5728201 CCCCAAAATT
5728211 CACACGCCCGTGTGACATACC-CGTGTGGGCC
1 CACACGCCCGTGTGACATACCTC-TGTGGGCC
* *
5728242 CACACACCCGTGTGACATGCCTCTGTGGGCC
1 CACACGCCCGTGTGACATACCTCTGTGGGCC
*
5728273 CACACGCTCGTGTG
1 CACACGCCCGTGTG
5728287 GCACACACGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.16, C:0.38, G:0.28, T:0.18
Consensus pattern (31 bp):
CACACGCCCGTGTGACATACCTCTGTGGGCC
Found at i:5734765 original size:32 final size:33
Alignment explanation
Indices: 5734693--5734766 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
5734683 AAGGGTGGTA
* * * *
5734693 TTGAAAAGGAAAGGTATACTTTGTGTATACCAC
1 TTGAAAAGGAAAAGTACACTATATGTATACCAC
* *
5734726 TTAAAAAGGAAAAGTACACTATATGTGTA-CAC
1 TTGAAAAGGAAAAGTACACTATATGTATACCAC
5734758 TTGAAAAGG
1 TTGAAAAGG
5734767 TTATGTGCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 11 0.32
33 23 0.68
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (33 bp):
TTGAAAAGGAAAAGTACACTATATGTATACCAC
Found at i:5734819 original size:33 final size:33
Alignment explanation
Indices: 5734750--5734830 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
5734740 TACACTATAT
** * **
5734750 GTGTA-CACTTGAAAAGGTTATGTGCACTTCGT
1 GTGTACCACTTGAAAAGGGAATGTGCACCTCAA
5734782 GTGTACCACTTGAAAAGGGAATGTGCACCTCAA
1 GTGTACCACTTGAAAAGGGAATGTGCACCTCAA
* *
5734815 GTGTACAACTAGAAAA
1 GTGTACCACTTGAAAA
5734831 AGACAGGTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 5 0.12
33 36 0.88
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (33 bp):
GTGTACCACTTGAAAAGGGAATGTGCACCTCAA
Found at i:5737129 original size:14 final size:15
Alignment explanation
Indices: 5737110--5737146 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5737100 ATGGAATTTT
*
5737110 ATTAAAAATTA-AGA
1 ATTAAAAATTAGAAA
5737124 ATTAAAAA-TAGAAA
1 ATTAAAAATTAGAAA
5737138 ATTAAAAAT
1 ATTAAAAAT
5737147 GGAGGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (15 bp):
ATTAAAAATTAGAAA
Found at i:5737416 original size:17 final size:18
Alignment explanation
Indices: 5737391--5737426 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5737381 AAAATCACCC
5737391 TAATATAATTT-ATTTTT
1 TAATATAATTTAATTTTT
*
5737408 TAATTTAATTTAATTTTT
1 TAATATAATTTAATTTTT
5737426 T
1 T
5737427 TTAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATATAATTTAATTTTT
Found at i:5741606 original size:25 final size:25
Alignment explanation
Indices: 5741567--5741694 Score: 82
Period size: 25 Copynumber: 5.0 Consensus size: 25
5741557 GAAATAGATA
* *
5741567 TAAAAAAAATGTACATAATATAGTG
1 TAAAAAATATATACATAATATAGTG
*
5741592 TAAAAAATATATACATAATATAAT-
1 TAAAAAATATATACATAATATAGTG
*
5741616 T--AAAATATATACATAAGATAACATGTAGG
1 TAAAAAATATATACAT-A-AT-ATA-GT--G
* * *
5741645 AAAAAATATATATAAATAATATAGTA
1 TAAAAA-ATATATACATAATATAGTG
* * *
5741671 TTAAAGATATATACATAAAATAGT
1 TAAAAAATATATACATAATATAGT
5741695 ATAATATATA
Statistics
Matches: 79, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
22 13 0.16
23 1 0.01
24 3 0.04
25 39 0.49
26 4 0.05
28 2 0.03
29 2 0.03
30 2 0.03
31 4 0.05
32 9 0.11
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (25 bp):
TAAAAAATATATACATAATATAGTG
Found at i:5741623 original size:22 final size:22
Alignment explanation
Indices: 5741595--5741636 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5741585 TATAGTGTAA
*
5741595 AAAATATATACATAATATAATT
1 AAAATATATACATAAGATAATT
5741617 AAAATATATACATAAGATAA
1 AAAATATATACATAAGATAA
5741637 CATGTAGGAA
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:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATATATACATAAGATAATT
Found at i:5741705 original size:25 final size:25
Alignment explanation
Indices: 5741648--5741706 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
5741638 ATGTAGGAAA
*
5741648 AAATATATATAAATAATATAGTATT
1 AAATATATATAAATAAAATAGTATT
* *
5741673 AAAGATATATACATAAAATAGTA-T
1 AAATATATATAAATAAAATAGTATT
5741697 -AATATATATA
1 AAATATATATA
5741707 CGTAATGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 9 0.30
24 1 0.03
25 20 0.67
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (25 bp):
AAATATATATAAATAAAATAGTATT
Found at i:5741775 original size:26 final size:27
Alignment explanation
Indices: 5741736--5741786 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
5741726 TATACCTAAT
5741736 ATATTAAAAGAATAT-ATATATAATATA
1 ATATTAAAAGAATATAATA-ATAATATA
5741763 ATATTAAAA-AATATAATAATAATA
1 ATATTAAAAGAATATAATAATAATA
5741787 AAAAAGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATATTAAAAGAATATAATAATAATATA
Found at i:5744268 original size:387 final size:387
Alignment explanation
Indices: 5743551--5744321 Score: 1283
Period size: 387 Copynumber: 2.0 Consensus size: 387
5743541 CGTGTCAATA
* * *
5743551 AGTCCTTGAACTCTCCTTTTAAAGGCTAGGCAATTCTCCGTGGAATGCCCTTGGTTCCACGCGTA
1 AGTCCTTGAACTCTCCTCTTAAAGGCTAGGCAATTCTCCGTAGAATGCCCTTGGTTCAACGCGTA
*
5743616 GTATGCACAATTAGCGTTTGGATCGTACCACTTTGGGTATGGAGGTTTAAGGGGTGCCATGTAAT
66 GTATGCACAACTAGCGTTTGGATCGTACCACTTTGGGTATGGAGGTTTAAGGGGTGCCATGTAAT
* * * *
5743681 GGGGAGAAATTAGCTGTTTCTCCAAAAGTTTTGGGTATAATTCCCCATACGACATAGGGATAGGA
131 GGGGAGAAATCAGCTGTTTCTCCAAAAATTTTGGGTACAATTCCCCATACGACACAGGGATAGGA
* * *
5743746 GTAAATTGTGGTCTCTCGAGATTAGGCCTTACTGGTCTTGGTTCGTTTTTGGGCTGGCTTTGAGC
196 GTAAATTATGGTCTCTCGAGATTAAGCCTTACTGGTCTTGGTTCGTTTCTGGGCTGGCTTTGAGC
* *
5743811 GAGTATCGTATTTTGTGGGAATGTGGTGACGGGTCTTTGGTTGTTCGTGGCGTATACGGGGTAAG
261 GAGTACCGTATTTTGTGGGAATGTGGTGACGGATCTTTGGTTGTTCGTGGCGTATACGGGGTAAG
* *
5743876 AAGGAGGTGGTGCTTGGTAGTAAGGGGTTTGAGGGGGATAATAGAAATTTGGAGATGGAATG
326 AAGGAGGTGGTGCTTGATAGTAAGGGGTTTGAAGGGGATAATAGAAATTTGGAGATGGAATG
* * *
5743938 AGTCCTTGAACTCTCCTCTTAAAGGCTAGGTAATTTTTCGTAGAATG-CCTCTGGTTCAACGCGT
1 AGTCCTTGAACTCTCCTCTTAAAGGCTAGGCAATTCTCCGTAGAATGCCCT-TGGTTCAACGCGT
*
5744002 GGTATGCACAACTAGCGTTTGGATCGTACCACTTTGGGTATGGAGGTTTAAGGGGTGCCATGTAA
65 AGTATGCACAACTAGCGTTTGGATCGTACCACTTTGGGTATGGAGGTTTAAGGGGTGCCATGTAA
*
5744067 TGGGGAGAAATCAGTTGTTTCTCCAAAAATTTTGGGTACAATTCCCCATACGACACAGGGATAGG
130 TGGGGAGAAATCAGCTGTTTCTCCAAAAATTTTGGGTACAATTCCCCATACGACACAGGGATAGG
*
5744132 AGTAAATTATGGTCTCTCGGGATTAAGCCTTACTGGTCTTGGTTCGTTTCTGGGCTGGCTTTGAG
195 AGTAAATTATGGTCTCTCGAGATTAAGCCTTACTGGTCTTGGTTCGTTTCTGGGCTGGCTTTGAG
* * * * *
5744197 CGGGTACCGTGTTTTGTGGGAATGTGGTGACGGATTTTTGGTTGTTCGTGGCGTATATGGGGTAG
260 CGAGTACCGTATTTTGTGGGAATGTGGTGACGGATCTTTGGTTGTTCGTGGCGTATACGGGGTAA
*
5744262 GAAGGAGGTGGTGCTTGATAGTAAGGGGTTTGAAGGGGATAATAGAAATTTGGAGGTGGA
325 GAAGGAGGTGGTGCTTGATAGTAAGGGGTTTGAAGGGGATAATAGAAATTTGGAGATGGA
5744322 TAACTTCGAG
Statistics
Matches: 356, Mismatches: 27, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
386 3 0.01
387 353 0.99
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (387 bp):
AGTCCTTGAACTCTCCTCTTAAAGGCTAGGCAATTCTCCGTAGAATGCCCTTGGTTCAACGCGTA
GTATGCACAACTAGCGTTTGGATCGTACCACTTTGGGTATGGAGGTTTAAGGGGTGCCATGTAAT
GGGGAGAAATCAGCTGTTTCTCCAAAAATTTTGGGTACAATTCCCCATACGACACAGGGATAGGA
GTAAATTATGGTCTCTCGAGATTAAGCCTTACTGGTCTTGGTTCGTTTCTGGGCTGGCTTTGAGC
GAGTACCGTATTTTGTGGGAATGTGGTGACGGATCTTTGGTTGTTCGTGGCGTATACGGGGTAAG
AAGGAGGTGGTGCTTGATAGTAAGGGGTTTGAAGGGGATAATAGAAATTTGGAGATGGAATG
Found at i:5745094 original size:58 final size:58
Alignment explanation
Indices: 5745004--5745120 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
5744994 GAAGGCTTCA
5745004 GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
1 GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
*
5745062 GTGCCTTTTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
1 GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
5745120 G
1 G
5745121 ATTATCTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.14, C:0.30, G:0.15, T:0.42
Consensus pattern (58 bp):
GTGCCTTCTATTGCCTTGAGTCTTTCTTCCAAACTCCTATACTTCTCTTGAGCCTCGT
Done.