Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 78
Found at i:5576776 original size:9 final size:9
Alignment explanation
Indices: 5576753--5576794 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
5576743 GGATATAAGA
5576753 GATATATGT
1 GATATATGT
5576762 G-T-TATGT
1 GATATATGT
5576769 GATATATGT
1 GATATATGT
*
5576778 GTTATATGT
1 GATATATGT
5576787 GATATATG
1 GATATATG
5576795 GGAAAGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 6 0.21
8 2 0.07
9 21 0.72
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (9 bp):
GATATATGT
Found at i:5577005 original size:31 final size:32
Alignment explanation
Indices: 5576967--5577040 Score: 114
Period size: 31 Copynumber: 2.3 Consensus size: 32
5576957 GAGTGGAGGG
** *
5576967 TTACCTATGTTTTTCGGGACATATGGACA-GA
1 TTACCTATGTCATTCGAGACATATGGACAGGA
5576998 TTACCTATGTCATTCGAGACATATGGACAGGA
1 TTACCTATGTCATTCGAGACATATGGACAGGA
5577030 TTACCTATGTC
1 TTACCTATGTC
5577041 CTTCTGGACA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 26 0.67
32 13 0.33
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (32 bp):
TTACCTATGTCATTCGAGACATATGGACAGGA
Found at i:5577051 original size:32 final size:30
Alignment explanation
Indices: 5576967--5577052 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 30
5576957 GAGTGGAGGG
**
5576967 TTACCTATGTTTTTCGGGACATATGGACAGA
1 TTACCTATGTCATTC-GGACATATGGACAGA
5576998 TTACCTATGTCATTCGAGACATATGGACAGGA
1 TTACCTATGTCATTCG-GACATATGGACA-GA
*
5577030 TTACCTATGTCCTTCTGGACATA
1 TTACCTATGTCATTC-GGACATA
5577053 GATTTCATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 1 0.02
31 25 0.51
32 22 0.45
33 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (30 bp):
TTACCTATGTCATTCGGACATATGGACAGA
Found at i:5577808 original size:23 final size:22
Alignment explanation
Indices: 5577782--5577845 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
5577772 CAGCTCATAT
5577782 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
5577805 AATTGCACCGGAGTGTCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
5577828 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
5577846 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:5584635 original size:23 final size:22
Alignment explanation
Indices: 5584609--5584672 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
5584599 CAACTCATAT
5584609 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
5584632 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
5584655 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
5584673 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:5584813 original size:103 final size:103
Alignment explanation
Indices: 5584688--5585008 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
5584678 TAATGTCCAT
*
5584688 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
5584753 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
5584791 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
5584856 GACCTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
5584894 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
5584959 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
5584997 AAAGACCACATA
1 AAGGACCACATA
5585009 GACCCTCTAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:5585527 original size:19 final size:20
Alignment explanation
Indices: 5585490--5585527 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5585480 TTTTTTATTA
*
5585490 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
5585510 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
5585528 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:5585579 original size:21 final size:21
Alignment explanation
Indices: 5585555--5585597 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5585545 TCATATTCGT
*
5585555 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
5585576 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
5585597 T
1 T
5585598 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:5586478 original size:6 final size:6
Alignment explanation
Indices: 5586467--5587363 Score: 1551
Period size: 6 Copynumber: 152.5 Consensus size: 6
5586457 AACTCCATAA
* * *
5586467 GTATAT GTATAT GTACAT GTACAT GTATAT GTACAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
* * * *
5586515 GTACAT GTACAT GTACAT GTATAT GTATAT GTATAT ATATAT G--TAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5586561 GTATAT GTATAT G--TAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5586607 GTATAT G--TAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5586653 G--TAT GTATAT GTATAT GTATAT GTATAT G--TAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5586697 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5586745 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5586793 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
* * *
5586841 GTATAT GTATAT GTATAT ATATGT ATATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
* *
5586889 GTATA- -TATAT GTATAT GTACAT GTACAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
*
5586935 ATATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5586983 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5587031 GTATAT GTATAT GTATAT G--TAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5587077 GTATAT GTATAT GTATA- -TATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5587123 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5587171 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT G--TAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5587217 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5587265 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5587313 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
5587361 GTA
1 GTA
5587364 ATAAAGTGGT
Statistics
Matches: 857, Mismatches: 16, Indels: 36
0.94 0.02 0.04
Matches are distributed among these distances:
4 36 0.04
6 821 0.96
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (6 bp):
GTATAT
Found at i:5588277 original size:131 final size:131
Alignment explanation
Indices: 5587997--5588354 Score: 427
Period size: 131 Copynumber: 2.7 Consensus size: 131
5587987 GTTATGGTCG
* * * *
5587997 TCTAAGGGTGACACGACTCCTACGTGATGAGAAGATCTGGTCGGTGGATGACACGGTTCCTACGC
1 TCTAAGGGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGC
* * * * * *
5588062 GATGTGGA-CGACA-ACCATCTTCAGGAAGGGTGATAACACGGATCCTACACGATGAGGACGGCT
66 AATGAGGATGGA-AGACCATCTTTA-G--GGATGATAACACGGATCCTACACGATGAGGACGACT
*
5588125 GGTTA
127 GATTA
* * *
5588130 TCT-AGAGGTGACACGGCTCCTACATGATGTGGAGGTCTGGTCGATGGATGACACGGTTCCTATG
1 TCTAAG-GGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACG
* * * ** * *
5588194 TAATGAGGATGGTAGACCATCTTTAGGGATGATAACACGGTTCCTACGTGATGAGGATGATTGAT
65 CAATGAGGATGGAAGACCATCTTTAGGGATGATAACACGGATCCTACACGATGAGGACGACTGAT
5588259 TA
130 TA
*
5588261 TCTAAGGGTGACACGGCTCCTACATGATGAGGAGGACTGGTCGGTGGATGACACGGTTCCTACGC
1 TCTAAGGGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGC
*
5588326 AATGAGGATAGAATG-CCATCTTTAGGGAT
66 AATGAGGATGGAA-GACCATCTTTAGGGAT
5588355 AATATTTCAA
Statistics
Matches: 192, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
131 115 0.60
132 5 0.03
133 62 0.32
134 10 0.05
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (131 bp):
TCTAAGGGTGACACGGCTCCTACATGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGC
AATGAGGATGGAAGACCATCTTTAGGGATGATAACACGGATCCTACACGATGAGGACGACTGATT
A
Found at i:5588485 original size:67 final size:66
Alignment explanation
Indices: 5588359--5588583 Score: 283
Period size: 67 Copynumber: 3.4 Consensus size: 66
5588349 AGGGATAATA
* ** * * **
5588359 TTTCAAGGGAAACAAACTCAAAGATGATG-TTTGAAGAGAAAATGTCTCAAGAAAGACAAAATTT
1 TTTCAAGGGAAACATACTCAAAGATTTTGTTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
5588423 G
66 G
*
5588424 TTTCAAGGGAAACATACTCAAAGATTTTGTATTTTAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TTTCAAGGGAAACATACTCAAAGATTTTGT-TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
5588489 TG
65 TG
* * * *
5588491 TTTAAAGGGAAACAGACTCAAAGATTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATT
1 TTTCAAGGGAAACATACTCAAAGATTTTGT-TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
*
5588556 CG
65 TG
*
5588558 TTTCAAGGGAAACGAT-TTCAAAGATT
1 TTTCAAGGGAAAC-ATACTCAAAGATT
5588584 ATAAATTTTA
Statistics
Matches: 140, Mismatches: 17, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
65 26 0.19
67 113 0.81
68 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.27
Consensus pattern (66 bp):
TTTCAAGGGAAACATACTCAAAGATTTTGTTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
G
Found at i:5588503 original size:36 final size:35
Alignment explanation
Indices: 5588463--5588570 Score: 91
Period size: 36 Copynumber: 3.1 Consensus size: 35
5588453 TATTTTAAGA
*
5588463 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGG
1 GAAACTGTCTCAA-GGAGACAAAATTTGTTTCAAGG
* * ** *
5588499 GAAACAGACTCAA--AG---ATTTTATGTTTCAAGA
1 GAAACTGTCTCAAGGAGACAAAATT-TGTTTCAAGG
*
5588530 GAAACTGTCTCAAAGGAGACAAAATTCGTTTCAAGG
1 GAAACTGTCTC-AAGGAGACAAAATTTGTTTCAAGG
5588566 GAAAC
1 GAAAC
5588571 GATTTCAAAG
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
30 3 0.06
31 17 0.32
32 2 0.04
33 2 0.04
34 2 0.04
36 24 0.45
37 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (35 bp):
GAAACTGTCTCAAGGAGACAAAATTTGTTTCAAGG
Found at i:5588717 original size:35 final size:35
Alignment explanation
Indices: 5588629--5588720 Score: 103
Period size: 36 Copynumber: 2.6 Consensus size: 35
5588619 TATGTTTTAA
* * **
5588629 AGAAAAATGTTTCAAGCAAGATGAAATTTGTTTTG
1 AGAAAAATGTCTCAAGCGAGACAAAATTTGTTTTG
* * *
5588664 AGGGAAATTGTCTCAAGCGAGACAAAATTTGTTTTT
1 A-GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTG
*
5588700 AGAAAACTGTCTCAAGCGAGA
1 AGAAAAATGTCTCAAGCGAGA
5588721 AAATTTTTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 19 0.40
36 28 0.60
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (35 bp):
AGAAAAATGTCTCAAGCGAGACAAAATTTGTTTTG
Found at i:5589899 original size:20 final size:20
Alignment explanation
Indices: 5589871--5589931 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
5589861 CGTTGGGCTT
* *
5589871 GATATTACTGTAGCAATATC
1 GATACTACTGTAGCAGTATC
* *
5589891 GATACTACTATAGCAGTATT
1 GATACTACTGTAGCAGTATC
*
5589911 GATACTAATGTAGCAGTATC
1 GATACTACTGTAGCAGTATC
5589931 G
1 G
5589932 GTACCCATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (20 bp):
GATACTACTGTAGCAGTATC
Found at i:5590020 original size:19 final size:20
Alignment explanation
Indices: 5589977--5590026 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5589967 TACTTTTCAT
* * *
5589977 TACTGTTCACACAATATCGG
1 TACTATTCATACAATATCAG
5589997 TACTATTCATACAATA-CAG
1 TACTATTCATACAATATCAG
5590016 TACTATTCATA
1 TACTATTCATA
5590027 ATAAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAATATCAG
Found at i:5593375 original size:20 final size:20
Alignment explanation
Indices: 5593347--5593387 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5593337 CGTTGGGCTT
*
5593347 GATATTACTGTAGCAATATC
1 GATACTACTGTAGCAATATC
*
5593367 GATACTACTGTAGCAGTATC
1 GATACTACTGTAGCAATATC
5593387 G
1 G
5593388 GTAACCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (20 bp):
GATACTACTGTAGCAATATC
Found at i:5593460 original size:20 final size:20
Alignment explanation
Indices: 5593432--5593501 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
5593422 TACTGTTCAT
* * *
5593432 TACTGTTCACACAGTATCGA
1 TACTATTCATACAGTATCAA
*
5593452 TACTATTCATATAGTATCAA
1 TACTATTCATACAGTATCAA
*
5593472 TATTATTCATACAGTA-CAA
1 TACTATTCATACAGTATCAA
5593491 TACTATTCATA
1 TACTATTCATA
5593502 AAAAAAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 13 0.30
20 30 0.70
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (20 bp):
TACTATTCATACAGTATCAA
Found at i:5594404 original size:10 final size:10
Alignment explanation
Indices: 5594380--5594422 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
5594370 TTCTTTGCTC
5594380 TTTTGTTTG-
1 TTTTGTTTGT
5594389 -TTTGTTTGT
1 TTTTGTTTGT
5594398 TTTTGTTTGT
1 TTTTGTTTGT
*
5594408 TTTTCTTTGCT
1 TTTTGTTTG-T
5594419 TTTT
1 TTTT
5594423 TCTCTGCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 8 0.27
10 17 0.57
11 5 0.17
ACGTcount: A:0.00, C:0.05, G:0.16, T:0.79
Consensus pattern (10 bp):
TTTTGTTTGT
Found at i:5598006 original size:21 final size:20
Alignment explanation
Indices: 5597980--5598039 Score: 88
Period size: 18 Copynumber: 3.0 Consensus size: 20
5597970 GTTCTTAAGG
5597980 AGTGGTCCTTCGGGACAAAT
1 AGTGGTCCTTCGGGACAAAT
*
5598000 CAGTGGTCATTCGGGAC--AT
1 -AGTGGTCCTTCGGGACAAAT
5598019 AGTGGTCCTTCGGGACAAAT
1 AGTGGTCCTTCGGGACAAAT
5598039 A
1 A
5598040 TACAGTGCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 15 0.43
19 2 0.06
20 3 0.09
21 15 0.43
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAAAT
Found at i:5598453 original size:21 final size:21
Alignment explanation
Indices: 5598429--5598468 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5598419 TAATTGAGGA
5598429 AAAAGG-TATATAAATAAGTAT
1 AAAAGGATAT-TAAATAAGTAT
*
5598450 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAAATAAGT
5598469 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAAATAAGTAT
Found at i:5601117 original size:65 final size:64
Alignment explanation
Indices: 5601003--5601153 Score: 189
Period size: 65 Copynumber: 2.3 Consensus size: 64
5600993 GCACTAAGAG
* * *
5601003 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT-GGTGCATCGA
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGG-TAAGTGCATCGA
* * * *
5601067 TGCATCAAATGCATTCGATATTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTAAGTGCATCG
1 TGCATCAAATGCATTCGAT-GTTTCA-AAATAGCCACAGTGCATCGATGCATGGTAAGTGCATCG
5601131 A
64 A
*
5601132 TGCATGAAATGCATTCGATGTT
1 TGCATCAAATGCATTCGATGTT
5601154 CAATTTAATT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
64 21 0.28
65 51 0.68
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGTAAGTGCATCGA
Found at i:5601192 original size:65 final size:63
Alignment explanation
Indices: 5601038--5601203 Score: 183
Period size: 65 Copynumber: 2.6 Consensus size: 63
5601028 AAATAGCCAG
* *
5601038 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATATTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGA-ATGTTCATAAAAT-CTC
* ** * **
5601103 AGTGCATCGGTGCATGGTAAGTGCATCGATGCATGAAATGCATTCG-ATGTTCAATTTAAT-TC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGAATGTTC-ATAAAATCTC
*
5601165 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
5601204 CTCTGAAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
62 3 0.04
63 5 0.06
64 20 0.24
65 56 0.67
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGAATGTTCATAAAATCTC
Found at i:5603899 original size:44 final size:44
Alignment explanation
Indices: 5603810--5603906 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
5603800 GCTCTTGTGC
* *
5603810 ATCGATGCACATTCAAGGGCGTGCATCGGTGCATCAGCTGATGT
1 ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
* *
5603854 ATCGATGCACATTCATAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTCA-AGGGCATGCATCGGTGCATCAGCTAA-TGT
5603898 ATCGATGCA
1 ATCGATGCA
5603907 TTAAGCACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 4 0.09
44 39 0.83
45 4 0.09
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
Found at i:5609825 original size:65 final size:65
Alignment explanation
Indices: 5609691--5609851 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
5609681 GTTCACTAAG
* * * * *
5609691 AGTGCATCTATGCATCAAGTGCATTCAATG-TTTCAAAATAGCCAGAGTGCATTGATGCATGGCA
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCA
* * * * *
5609755 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGC
5609819 A
65 A
*
5609820 AGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATCAAATGCATTCGATGTT
5609852 CAATTTAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 26 0.31
65 54 0.65
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCA
Found at i:5609889 original size:20 final size:20
Alignment explanation
Indices: 5609864--5609919 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
5609854 ATTTAATTCA
5609864 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
5609884 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
5609904 TGGTGCATCGGTGCAT
1 TGGTGCATCGATGCAT
5609920 CACTCTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:5609890 original size:65 final size:63
Alignment explanation
Indices: 5609692--5609900 Score: 178
Period size: 65 Copynumber: 3.2 Consensus size: 63
5609682 TTCACTAAGA
* * * * * *
5609692 GTGCATCTATGCATCAAGTGCATTCAATGTTTCA-AAATAGC-CAGAGTGCATTGATGCATGGCA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGG-A
5609755 -G
62 TG
* *
5609756 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGG-TA
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGAT-
*
5609820 A
63 G
**
5609821 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGGA-
5609884 TG
62 TG
5609886 GTGCATCGATGCATG
1 GTGCATCGATGCATG
5609901 GATTGGTGCA
Statistics
Matches: 122, Mismatches: 12, Indels: 21
0.79 0.08 0.14
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 46 0.38
65 64 0.52
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGATG
Found at i:5620543 original size:3 final size:3
Alignment explanation
Indices: 5620535--5620574 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5620525 CCTACAAATG
5620535 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5620575 GTTTTTAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5622222 original size:15 final size:15
Alignment explanation
Indices: 5622170--5622224 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
5622160 GTTGGACGGA
*
5622170 CGGATGTGGGGCGGG
1 CGGATGCGGGGCGGG
*
5622185 CGGATGCGAGGCGGG
1 CGGATGCGGGGCGGG
5622200 CGGA-----GGCGGG
1 CGGATGCGGGGCGGG
5622210 CGGATGCGGGGCGGG
1 CGGATGCGGGGCGGG
5622225 TGAGGTCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
10 10 0.30
15 23 0.70
ACGTcount: A:0.09, C:0.18, G:0.65, T:0.07
Consensus pattern (15 bp):
CGGATGCGGGGCGGG
Found at i:5622870 original size:197 final size:198
Alignment explanation
Indices: 5622605--5622965 Score: 548
Period size: 197 Copynumber: 1.8 Consensus size: 198
5622595 TTAGTGATGC
* * *
5622605 CTTTGCTGCTGATTCTGAAGTGAAAGGCATTGTTCTTTTCCATTTTAGGGTCCAAGGTTTCTGCA
1 CTTTGCTACTGATTCTGAACTGAAAGGCATTGTTCTTTTCCATTTTAGGATCCAAGGTTTCTGCA
* *
5622670 TCAGCTCATCCCGATCAGGGGTTGGACCCGGAAGAATCGAACGAGTCGAAGAGTTCATCGACAAT
66 TCAGCTCATCCCGATCAGGGGTTGGACCCGGAAGAATCGAACAAGTCGAAGAGTTCATCAACAAT
*
5622735 CTGTTGTGTAATGACGACC-ACGAATCCAATCCTCTGTCTTCATCTCTTCTTTTTCTACAACTTT
131 CTGTTGTGTAATGACG-CCGACGAATCCAAACCTCTGTCTTCATCTCTTCTTTTTCTACAACTTT
5622799 TGTT
195 TGTT
** *
5622803 CTTTGCTACTGATTGC-GAACTGAAAGGCATTGTT-TTTTCTTTTTTAGGATCCTAGGTTTCTGC
1 CTTTGCTACTGATT-CTGAACTGAAAGGCATTGTTCTTTTCCATTTTAGGATCCAAGGTTTCTGC
* ** * *
5622866 ATCAGCTCATCCCGATTAGGGGTTGGTGCCGGAAGAATCGCACAATTCGAAGAGTTCATCAACAA
65 ATCAGCTCATCCCGATCAGGGGTTGGACCCGGAAGAATCGAACAAGTCGAAGAGTTCATCAACAA
*
5622931 TCTGTTGTGTAATGGCGCCGACGAATCCAAACCTC
130 TCTGTTGTGTAATGACGCCGACGAATCCAAACCTC
5622966 CATCTCTTTT
Statistics
Matches: 146, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
196 2 0.01
197 113 0.77
198 30 0.21
199 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (198 bp):
CTTTGCTACTGATTCTGAACTGAAAGGCATTGTTCTTTTCCATTTTAGGATCCAAGGTTTCTGCA
TCAGCTCATCCCGATCAGGGGTTGGACCCGGAAGAATCGAACAAGTCGAAGAGTTCATCAACAAT
CTGTTGTGTAATGACGCCGACGAATCCAAACCTCTGTCTTCATCTCTTCTTTTTCTACAACTTTT
GTT
Found at i:5623250 original size:126 final size:126
Alignment explanation
Indices: 5623025--5623257 Score: 439
Period size: 126 Copynumber: 1.8 Consensus size: 126
5623015 TCGTGAAGTG
*
5623025 AAAGGCCTTGTTGTTTTCTTTTCTAGGGTTCTAGGTGTCTGCATCTCAGTTTGTCGTAAACTAAT
1 AAAGGCCTTGTTGTTTTCTTTTCTAGGGTTCTAGGTGTCTGCATCACAGTTTGTCGTAAACTAAT
*
5623090 CGCCGAAGATTTGGAACGCAGGTAGTCATATGAGCTCTTAGACGAGACGACTCCACCGCCA
66 CGCCGAAGATTTGGAACCCAGGTAGTCATATGAGCTCTTAGACGAGACGACTCCACCGCCA
*
5623151 AAAGGCCTTGTTGTTTTCTTTTCTAGGGTTCTAGGTGTCTGCGTCACAGTTTGTCGTAAACTAAT
1 AAAGGCCTTGTTGTTTTCTTTTCTAGGGTTCTAGGTGTCTGCATCACAGTTTGTCGTAAACTAAT
5623216 CGCCGAAGATTTGGAACCCAGGTAGTCATATGAGCTCTTAGA
66 CGCCGAAGATTTGGAACCCAGGTAGTCATATGAGCTCTTAGA
5623258 TGGGACTCCA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 104 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (126 bp):
AAAGGCCTTGTTGTTTTCTTTTCTAGGGTTCTAGGTGTCTGCATCACAGTTTGTCGTAAACTAAT
CGCCGAAGATTTGGAACCCAGGTAGTCATATGAGCTCTTAGACGAGACGACTCCACCGCCA
Found at i:5623482 original size:19 final size:19
Alignment explanation
Indices: 5623458--5623514 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
5623448 GAATTATATT
5623458 AAAATATTTAAAATTCTAA
1 AAAATATTTAAAATTCTAA
* *
5623477 AAAATA-TTACAAA-ACTCA
1 AAAATATTTA-AAATTCTAA
* *
5623495 AAATTATATAAAATTCTAA
1 AAAATATTTAAAATTCTAA
5623514 A
1 A
5623515 CAATGTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATATTTAAAATTCTAA
Found at i:5623857 original size:28 final size:28
Alignment explanation
Indices: 5623814--5623882 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
5623804 CATTAAACTA
*
5623814 TTAAAAAAATA-ATATTATTAAATGCAT
1 TTAAAAAGATATATATTATTAAATGCAT
**
5623841 TTAAAAAGATATATATTATTAAATGTGT
1 TTAAAAAGATATATATTATTAAATGCAT
*
5623869 TTAATAAGATATAT
1 TTAAAAAGATATAT
5623883 CTAACCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 10 0.27
28 27 0.73
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (28 bp):
TTAAAAAGATATATATTATTAAATGCAT
Found at i:5630625 original size:60 final size:58
Alignment explanation
Indices: 5630552--5630683 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 58
5630542 TATCAAGGGC
* * *
5630552 AAAG-TACACAAATAGTC-CCTCATCTATAGGATGATATTTTATTGAGTCCCTCGATTATTA
1 AAAGTTACA-AAATAGTCACC-CA-CTATAGGATGATACTTTATTGAGTCACT-GACTATTA
* * * *
5630612 AAAGTTACAAAATAGTCATCCGACTATAGGGTGTTCCTTTATTGAGTCACTGACTATTA
1 AAAGTTACAAAATAGTCA-CCCACTATAGGATGATACTTTATTGAGTCACTGACTATTA
5630671 AAAGTTACAAAAT
1 AAAGTTACAAAAT
5630684 GGCCACCGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 20 0.32
60 35 0.56
61 5 0.08
62 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (58 bp):
AAAGTTACAAAATAGTCACCCACTATAGGATGATACTTTATTGAGTCACTGACTATTA
Found at i:5634896 original size:123 final size:127
Alignment explanation
Indices: 5634634--5634900 Score: 409
Period size: 123 Copynumber: 2.1 Consensus size: 127
5634624 CTTGGTTCAC
5634634 CTTCTTCTTCTTCTTCGCCTTGACCCTCCTCTTCTTCATGTCGCCTCCTTTCTTCTTCTTCTTCT
1 CTTCTTCTTCTTCTTCGCCTTGACCCTCCTCTTCTTCATGTCGCCTCC--TCTTCTTCTTCTTCT
*
5634699 TCTTCCCTTGCCCTCCTTTGCCGCTCTTCTTCCTGTCTTCGGGCTTCCTCTTGCTCTCTACTTG
64 TCTTCCCTTGCCCTCCTTTGCCGCTCTTCTTCCCGTCTTCGGGCTTCCTCTTGCTCTCTACTTG
* ** * *
5634763 GTTCACCTTCTTCTTCGCCTTGACCTTTCTCTTCTTCATGTCGCCT-C-C-T-TTCTTCTTCTTC
1 CTTCTTCTTCTTCTTCGCCTTGACCCTCCTCTTCTTCATGTCGCCTCCTCTTCTTCTTCTTCTTC
* *
5634824 TTCCCTTGCCCTCCTTTGCCGCTCTTCTTCCCGTCTTCGGGCTTCCTTTTGCTCTCTCCTTG
66 TTCCCTTGCCCTCCTTTGCCGCTCTTCTTCCCGTCTTCGGGCTTCCTCTTGCTCTCTACTTG
5634886 CTTCTTCTTC-TCTTC
1 CTTCTTCTTCTTCTTC
5634901 TCCTCTCAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
122 5 0.04
123 78 0.61
124 1 0.01
125 1 0.01
128 1 0.01
129 41 0.32
ACGTcount: A:0.02, C:0.40, G:0.10, T:0.48
Consensus pattern (127 bp):
CTTCTTCTTCTTCTTCGCCTTGACCCTCCTCTTCTTCATGTCGCCTCCTCTTCTTCTTCTTCTTC
TTCCCTTGCCCTCCTTTGCCGCTCTTCTTCCCGTCTTCGGGCTTCCTCTTGCTCTCTACTTG
Found at i:5634916 original size:27 final size:27
Alignment explanation
Indices: 5634886--5634957 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
5634876 TCTCTCCTTG
*
5634886 CTTCTTCTTCTCTTCTCCTCTCAGCTT
1 CTTCTTCTTCTCTTCTCCTCTCAGCTC
* * * *
5634913 CTTCCTCTTCCCTTCTTCTTTCAGCTC
1 CTTCTTCTTCTCTTCTCCTCTCAGCTC
*
5634940 CCTCTTCTTCTCTT-TCCT
1 CTTCTTCTTCTCTTCTCCT
5634958 TAGCCTCTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 3 0.08
27 33 0.92
ACGTcount: A:0.03, C:0.43, G:0.03, T:0.51
Consensus pattern (27 bp):
CTTCTTCTTCTCTTCTCCTCTCAGCTC
Found at i:5635157 original size:54 final size:53
Alignment explanation
Indices: 5634910--5635445 Score: 373
Period size: 54 Copynumber: 9.7 Consensus size: 53
5634900 CTCCTCTCAG
* *
5634910 CTTCTTCCTCTTCCCTTCTTCTTTC-AG-CTCCCTCTTCTTCTCTT-TCCTT-AGCCT
1 CTTCTTCCTCTTCCCTTC-TCCTTCGAGCCT-CCTCTTC--C-CTTCTCCTTCGGCCT
* **
5634964 C-T-TT-CTCTTCCCTTCTGGCTTC-TTCCTCCTCTTCCCTTCTCCTTCGAGCCTCCT
1 CTTCTTCCTCTTCCCTTCT-CCTTCGAGCCTCCTCTTCCCTTCTCCTTCG-G---CCT
* * * **
5635018 CTTCCTCCTCTTTCCTTCTGGCTTC-TTCCTCCTCTTCCCTTCTCCTTCGAGCCT
1 CTTCTTCCTCTTCCCTTCT-CCTTCGAGCCTCCTCTTCCCTTCTCCTTCG-GCCT
* * * **
5635072 CTTCTTCCTCTTTCCTCCTGGCTTC-TTCCTCCTCTTCCCTTCTCCTTCGAGCCT
1 CTTCTTCCTCTTCCCTTCT-CCTTCGAGCCTCCTCTTCCCTTCTCCTTCG-GCCT
*
5635126 CTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCTT-TCCTCCTGGCTTCTT
1 CTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCC-CTTCTCCTTC-GGC--C-T
* * *
5635183 CTTCTTCTGCCTCTTCCCTTCT-CTTCCGAGCCTCCTCTTCCTTCTCTTTCCTCCTGGCTT
1 CTTC-T-T-CCTCTTCCCTTCTCCTT-CGAGCCTCCTCTTCC--CT-TCTCCTTC-GGCCT
* * *
5635243 CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTT-CCTCCTCCTTCCTGGCTT
1 CTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCCTTCTCCTT-C-GGCCT
* * * *
5635297 CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCTTCCTGGCTT
1 CTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTT-C-CCTTCTCCTT-C-GGCCT
* *
5635354 CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCC-T-GGCTT
1 CTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTT-C-CCTTC-TCCTTCGGCCT
* *
5635408 CTTCTTCCTCTTCCCTTCTCTTTCGAGTCTCCTCTTCC
1 CTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCC
5635446 TCCTTTTTCT
Statistics
Matches: 428, Mismatches: 24, Indels: 62
0.83 0.05 0.12
Matches are distributed among these distances:
48 3 0.01
49 6 0.01
50 1 0.00
51 22 0.05
52 5 0.01
53 10 0.02
54 180 0.42
55 5 0.01
56 3 0.01
57 135 0.32
58 6 0.01
59 5 0.01
60 33 0.08
61 3 0.01
62 1 0.00
63 10 0.02
ACGTcount: A:0.02, C:0.45, G:0.07, T:0.46
Consensus pattern (53 bp):
CTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCCTTCTCCTTCGGCCT
Found at i:5635169 original size:201 final size:200
Alignment explanation
Indices: 5634961--5635344 Score: 569
Period size: 201 Copynumber: 1.9 Consensus size: 200
5634951 CTTTCCTTAG
*
5634961 CCTCTTT-CTCTTCCCTTCTGGCTTCTTCCT-CCTCTTCCCTTCTCCTT-CGAGCCTCCTCTTCC
1 CCTCTTTCCTCCTCCCTTCT-GCTTCTT-CTGCCTCTTCCCTTCT-CTTCCGAGCCTCCTCTTCC
* * *
5635023 TCCTCTTTCCTTCTGGCTTCTTCCTCCTCTTCCCTTCTCCTTCGAGCCTCTTCTTCCTCTTTCC-
63 TCCTCTTTCCTCCTGGCTTCTTCCTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTC-CTCCT
* *
5635087 TCCTGGCTTCTTCCTCCTCTTCCCTTCTCCTTCGAGCCTCTTCTTCCTCTTCCCTTCTCCTTCGA
127 TCCTGGCTTCTTCCTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCCT-CCTTCTCCTTCGA
5635152 GCCTCCTCTT
191 GCCTCCTCTT
** * *
5635162 CCTCTTTCCTCCTGGCTTCTTCTTCTTCTGCCTCTTCCCTTCTCTTCCGAGCCTCCTCTTCCTTC
1 CCTCTTTCCTCCTCCCTTCTGCTTCTTCTGCCTCTTCCCTTCTCTTCCGAGCCTCCTCTTCCTCC
* *
5635227 TCTTTCCTCCTGGCTTCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCCT
66 TCTTTCCTCCTGGCTTCTTCCTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCCTCCTTCCT
* *
5635292 GGCTTCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCT
131 GGCTTCTTCCTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCCTCCTTCT
5635345 TCCTGGCTTC
Statistics
Matches: 165, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
200 14 0.08
201 142 0.86
202 9 0.05
ACGTcount: A:0.02, C:0.46, G:0.07, T:0.45
Consensus pattern (200 bp):
CCTCTTTCCTCCTCCCTTCTGCTTCTTCTGCCTCTTCCCTTCTCTTCCGAGCCTCCTCTTCCTCC
TCTTTCCTCCTGGCTTCTTCCTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCCTCCTTCCT
GGCTTCTTCCTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCCTCCTTCTCCTTCGAGCCTC
CTCTT
Found at i:5635174 original size:111 final size:106
Alignment explanation
Indices: 5634910--5635445 Score: 427
Period size: 111 Copynumber: 4.8 Consensus size: 106
5634900 CTCCTCTCAG
*
5634910 CTTCTTCCTCTTCCCTTCTTCTTTC-AG-CTCCCTCTTCTTCTCTT--TCCTTAGCCTC-T-TT-
1 CTTCTTCCTCTTCCCTTC-TCTTTCGAGCCT-CCTCTTC--CTCTTCCTCC-TGGCCTCTTCTTC
**
5634968 CTCTTCCCTTCTGGCTTC-TTCCTCCTCTTCCCTTCTCCTTC-GAGCCTCCT
61 CTCTTCCCTTCT--CTTCGAGCCTCCTCTTCCCTTCTCCTTCTG-G---CCT
* * **
5635018 CTTCCTCCTCTTTCCTTCTGGC-TTC-TTCCTCCTCTTCC-CTT-CTCCTTCGAGCCTCTTCTTC
1 CTTCTTCCTCTTCCCTTCT--CTTTCGAGCCTCCTCTTCCTCTTCCTCC-T-G-GCCTCTTCTTC
* * **
5635079 CTCTTTCCTCCTGGCTTC-TTCCTCCTCTTCCCTTCTCCTTC-GAGCCT
61 CTCTTCCCTTCT--CTTCGAGCCTCCTCTTCCCTTCTCCTTCTG-GCCT
*
5635126 CTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCTTTCCTCCTGGCTTCTTCTTCTTCT
1 CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTC-TTCCTCCTGGC--C-TCTTC-T-T
* * *
5635191 GCCTCTTCCCTTCTCTTCCGAGCCTCCTCTTCCTTCTCTTTCCTCCTGGCTT
60 -CCTCTTCCCTTCTCTT-CGAGCCTCCTCTTCC--CT-TCTCCTTCTGGCCT
* *
5635243 CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCCTGGCTTCTTCTTCCTCT
1 CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCTTCC-TCCTGGCCTCTTCTTCCTCT
* * *
5635308 TCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCTTCCTGGCTT
65 TCCCTTCTC-TTCGAGCCTCCTCTT-C-CCTTCTCCTT-CTGGCCT
* *
5635354 CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCTTCTTCTTCCTCT
1 CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCT-CTTCCTCCTGGCCTCTTCTTCCTCT
*
5635419 TCCCTTCTCTTTCGAGTCTCCTCTTCC
65 TCCCTTCTC-TTCGAGCCTCCTCTTCC
5635446 TCCTTTTTCT
Statistics
Matches: 368, Mismatches: 28, Indels: 63
0.80 0.06 0.14
Matches are distributed among these distances:
105 3 0.01
106 7 0.02
107 4 0.01
108 64 0.17
109 7 0.02
110 10 0.03
111 170 0.46
112 11 0.03
113 4 0.01
114 27 0.07
116 5 0.01
117 55 0.15
118 1 0.00
ACGTcount: A:0.02, C:0.45, G:0.07, T:0.46
Consensus pattern (106 bp):
CTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCTTCCTCCTGGCCTCTTCTTCCTCTT
CCCTTCTCTTCGAGCCTCCTCTTCCCTTCTCCTTCTGGCCT
Found at i:5635230 original size:33 final size:32
Alignment explanation
Indices: 5635192--5635290 Score: 88
Period size: 33 Copynumber: 3.2 Consensus size: 32
5635182 TCTTCTTCTG
5635192 CCTCTTCCCTTCTCTTCCGAGCCTCCTCTTCCT
1 CCTCTTCCCTTCTCTT-CGAGCCTCCTCTTCCT
* * *
5635225 TCTCTTTCC-TC-C-T-G-G-CT--TCTTCTT
1 CCTCTTCCCTTCTCTTCGAGCCTCCTCTTCCT
5635249 CCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCT
1 CCTCTTCCCTTCTC-TTCGAGCCTCCTCTTCCT
5635282 CCTCCTTCC
1 CCT-CTTCC
5635291 TGGCTTCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 19
0.67 0.08 0.25
Matches are distributed among these distances:
24 13 0.26
25 2 0.04
26 3 0.06
27 1 0.02
28 2 0.04
29 1 0.02
30 2 0.04
31 3 0.06
32 2 0.04
33 16 0.32
34 5 0.10
ACGTcount: A:0.02, C:0.48, G:0.06, T:0.43
Consensus pattern (32 bp):
CCTCTTCCCTTCTCTTCGAGCCTCCTCTTCCT
Found at i:5635386 original size:24 final size:24
Alignment explanation
Indices: 5635359--5635445 Score: 68
Period size: 24 Copynumber: 3.4 Consensus size: 24
5635349 GGCTTCTTCT
5635359 TCCTCTTCCCTTCTCTTTCGAGCC
1 TCCTCTTCCCTTCTCTTTCGAGCC
** *
5635383 TCCTCTTCCTCCTTCTTCCTGGCTTC-TTCT
1 TCCTCTT-C-CCTTC-T-CT---TTCGAGCC
*
5635413 TCCTCTTCCCTTCTCTTTCGAGTC
1 TCCTCTTCCCTTCTCTTTCGAGCC
5635437 TCCTCTTCC
1 TCCTCTTCC
5635446 TCCTTTTTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
23 3 0.06
24 16 0.33
25 1 0.02
26 7 0.15
27 2 0.04
28 7 0.15
29 1 0.02
30 8 0.17
31 3 0.06
ACGTcount: A:0.02, C:0.45, G:0.07, T:0.46
Consensus pattern (24 bp):
TCCTCTTCCCTTCTCTTTCGAGCC
Found at i:5635446 original size:54 final size:54
Alignment explanation
Indices: 5635125--5635483 Score: 483
Period size: 54 Copynumber: 6.5 Consensus size: 54
5635115 CCTTCGAGCC
* * *
5635125 TCTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCTTTCCTCCTGGCTTCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGG---CT
* *
5635182 TCTTCTTCTGCCTCTTCCCTTCTCTTCCGAGCCTCCTCTTCCTTCTCTTTCCTCCTGGCT
1 TCTTC-T-T-CCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCC-TC-C-TTCTTCCTGGCT
*
5635242 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCCTGGCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCT
5635296 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCTTCCTGGCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTC-T--TCCTCCTTCTTCCTGGCT
5635353 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCT
* * *
5635407 TCTTCTTCCTCTTCCCTTCTCTTTCGAGTCTCCTCTTCCTCCTT-TTTCT-TCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCT
5635459 TGGCTTCTTCCTCTT-CCTT-TCTTTC
1 T--CTTCTTCCTCTTCCCTTCTCTTTC
5635484 CCTTTCAATT
Statistics
Matches: 281, Mismatches: 10, Indels: 27
0.88 0.03 0.08
Matches are distributed among these distances:
52 9 0.03
53 8 0.03
54 118 0.42
55 2 0.01
56 3 0.01
57 88 0.31
58 2 0.01
59 2 0.01
60 37 0.13
61 2 0.01
63 10 0.04
ACGTcount: A:0.02, C:0.44, G:0.07, T:0.47
Consensus pattern (54 bp):
TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCT
Found at i:5635446 original size:111 final size:111
Alignment explanation
Indices: 5635125--5635468 Score: 535
Period size: 111 Copynumber: 3.0 Consensus size: 111
5635115 CCTTCGAGCC
* * *
5635125 TCTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCTCTTTCCTCCTGGCTTCTTCTTCTTC
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGG---CTTCTTC-T-
* * *
5635190 TGCCTCTTCCCTTCTCTTCCGAGCCTCCTCTTCCTTCTCTTTCCTCCTGGCT
61 T-CCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCTTTCTTCCTGGCT
*
5635242 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCCTGGCTTCTTCTTCCTC
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCTTCTTCTTCCTC
*
5635307 TTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCTTCCTGGCT
66 TTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCTTTCTTCCTGGCT
5635353 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCTTCTTCTTCCTC
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCTTCTTCTTCCTC
* * *
5635418 TTCCCTTCTCTTTCGAGTCTCCTCTTCCTCCTTTTTCTTCTTGGCT
66 TTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCTTTCTTCCTGGCT
5635464 TCTTC
1 TCTTC
5635469 CTCTTCCTTT
Statistics
Matches: 214, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
111 157 0.73
112 1 0.00
113 1 0.00
114 7 0.03
117 48 0.22
ACGTcount: A:0.02, C:0.44, G:0.07, T:0.47
Consensus pattern (111 bp):
TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTCTTCCTGGCTTCTTCTTCCTC
TTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCTTTCTTCCTGGCT
Found at i:5635463 original size:57 final size:56
Alignment explanation
Indices: 5635125--5635468 Score: 484
Period size: 57 Copynumber: 6.1 Consensus size: 56
5635115 CCTTCGAGCC
* *
5635125 TCTTCTTCCTCTTCCCTTCTCCTTCGAGCCTCCTCTTCCT-C-TTTCCTCCTGGCTTCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTTTCTTCCTGG---CT
* * *
5635182 TCTTCTTCTGCCTCTTCCCTTCTCTTCCGAGCCTCCTCTTCCTTCTCTTTCCTCCTGGCT
1 TCTTC-T-T-CCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCT-TTTCTTCCTGGCT
*
5635242 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCC--TCCTTCCTGGCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTTTCTTCCTGGCT
*
5635296 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTCCTTCTTCCTGGCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCT-TTTCTTCCTGGCT
5635353 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCC--TTCTTCCTGGCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTTTCTTCCTGGCT
* *
5635407 TCTTCTTCCTCTTCCCTTCTCTTTCGAGTCTCCTCTTCCTCCTTTTTCTTCTTGGCT
1 TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCC-TTTTCTTCCTGGCT
5635464 TCTTC
1 TCTTC
5635469 CTCTTCCTTT
Statistics
Matches: 266, Mismatches: 9, Indels: 24
0.89 0.03 0.08
Matches are distributed among these distances:
54 105 0.39
57 107 0.40
58 2 0.01
59 2 0.01
60 38 0.14
61 1 0.00
63 11 0.04
ACGTcount: A:0.02, C:0.44, G:0.07, T:0.47
Consensus pattern (56 bp):
TCTTCTTCCTCTTCCCTTCTCTTTCGAGCCTCCTCTTCCTCCTTTTCTTCCTGGCT
Found at i:5645010 original size:133 final size:134
Alignment explanation
Indices: 5644709--5645265 Score: 527
Period size: 139 Copynumber: 4.0 Consensus size: 134
5644699 AAACAATCAT
* ** * * *
5644709 AATCGATCATAAATCCATCAGATGATGAATCTTTTAACTGTCAACTATGCTATTAATGGAAATTG
1 AATCGATCTTAAATCCATCAGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAG
* * * ***
5644774 CACTGAAGTCCACATTACATGTGGAACTAACAAAAAAATGTAGTTAGAATCAATCTCAAATCCAT
66 CACTGCAGTCCAAACTACATGT-G--C-AA-AGCTAAATGTAGTTAGAATCAATCTCAAATCCAT
*
5644839 GTGATGATG
126 CTGATGATG
* * *
5644848 AATCGACCTTAAATCCATCAGATGGTGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATTG
1 AATCGATCTTAAATCCATCAGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAG
* * * *
5644913 CACTGCAGTCCAGACCACATGTGC-AAGCTAAATGTAGTTAGAGTCGATCTCAAATCCATCTGAT
66 CACTGCAGTCCAAACTACATGTGCAAAGCTAAATGTAGTTAGAATCAATCTCAAATCCATCTGAT
5644977 GATG
131 GATG
* ** *
5644981 AATCGATTTTAAATCCATTGGATGATGAATCTTTTAACCGTCAAC---GCTATTAGTGAAAATAG
1 AATCGATCTTAAATCCATCAGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAG
* *
5645043 CACCATTCCAAAGTCCAAACTACACT-TGCAGTAACAGCTAAATGTAGTTAGAATCCATCTCAAA
66 CA-C--TGC--AGTCCAAACTACA-TGTGC---AA-AGCTAAATGTAGTTAGAATCAATCTCAAA
*
5645107 T-CATCTAATGATG
121 TCCATCTGATGATG
**
5645120 AATCGATCTTAAA-CCATTGGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAG
1 AATCGATCTTAAATCCATCAGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAG
* * * * *
5645184 CACCTTTTCAAAGTCCAAACTACACGTGTGGTAACAGCTAAATGTTGTTAGAATCGATCTTAAAT
66 CA-C--TGC--AGTCCAAACTACA--TGT-GCAA-AGCTAAATGTAGTTAGAATCAATCTCAAAT
5645249 CCAT-TGGATGATG
122 CCATCT-GATGATG
5645262 AATC
1 AATC
5645266 TTTTAACCAT
Statistics
Matches: 359, Mismatches: 40, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
130 18 0.05
131 1 0.00
133 78 0.22
134 1 0.00
135 14 0.04
136 2 0.01
138 31 0.09
139 100 0.28
140 28 0.08
141 70 0.19
142 14 0.04
143 1 0.00
144 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (134 bp):
AATCGATCTTAAATCCATCAGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAG
CACTGCAGTCCAAACTACATGTGCAAAGCTAAATGTAGTTAGAATCAATCTCAAATCCATCTGAT
GATG
Found at i:5645196 original size:141 final size:141
Alignment explanation
Indices: 5644809--5645265 Score: 577
Period size: 133 Copynumber: 3.3 Consensus size: 141
5644799 ACTAACAAAA
* * * ** *
5644809 AAATGTAGTTAGAATCAATCTCAAATCCATGTGATGATGAATCGACCTTAAATCCATCAGATGGT
1 AAATGTAGTTAGAATCGATCTCAAATCCATCTGATGATGAATCGATCTTAAATCCATTGGATGAT
* * * *
5644874 GAATCTTTTAACCATCAACTATGCTATTAGTGAAAATTGCA-C-TGC--AGTCCAGACCACA-TG
66 GAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAGCACCTTCCAAAGTCCAAACTACACT-
5644934 TGC---A-AGCT
130 TGCGTAACAGCT
* *
5644942 AAATGTAGTTAGAGTCGATCTCAAATCCATCTGATGATGAATCGATTTTAAATCCATTGGATGAT
1 AAATGTAGTTAGAATCGATCTCAAATCCATCTGATGATGAATCGATCTTAAATCCATTGGATGAT
*
5645007 GAATCTTTTAACCGTCAAC---GCTATTAGTGAAAATAGCACCATTCCAAAGTCCAAACTACACT
66 GAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAGCACC-TTCCAAAGTCCAAACTACACT
5645069 TGCAGTAACAGCT
130 TGC-GTAACAGCT
* *
5645082 AAATGTAGTTAGAATCCATCTCAAAT-CATCTAATGATGAATCGATCTTAAA-CCATTGGATGAT
1 AAATGTAGTTAGAATCGATCTCAAATCCATCTGATGATGAATCGATCTTAAATCCATTGGATGAT
*
5645145 GAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAGCACCTTTTCAAAGTCCAAACTACACG
66 GAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAGCACC-TTCCAAAGTCCAAACTACAC-
5645210 TGTG-GTAACAGCT
129 T-TGCGTAACAGCT
* *
5645223 AAATGTTGTTAGAATCGATCTTAAATCCAT-TGGATGATGAATC
1 AAATGTAGTTAGAATCGATCTCAAATCCATCT-GATGATGAATC
5645266 TTTTAACCAT
Statistics
Matches: 282, Mismatches: 24, Indels: 27
0.85 0.07 0.08
Matches are distributed among these distances:
130 18 0.06
131 1 0.00
133 77 0.27
135 14 0.05
136 1 0.00
138 30 0.11
139 24 0.09
140 28 0.10
141 73 0.26
142 14 0.05
143 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (141 bp):
AAATGTAGTTAGAATCGATCTCAAATCCATCTGATGATGAATCGATCTTAAATCCATTGGATGAT
GAATCTTTTAACCATCAACTATGCTATTAGTGAAAATAGCACCTTCCAAAGTCCAAACTACACTT
GCGTAACAGCT
Found at i:5645341 original size:116 final size:116
Alignment explanation
Indices: 5645119--5645403 Score: 436
Period size: 116 Copynumber: 2.5 Consensus size: 116
5645109 ATCTAATGAT
5645119 GAATCGATCTTAAA-CCATTGGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATA
1 GAATCGATCTTAAATCCATTGGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATA
* * * *
5645183 GCACCTTTTCAAAGTCCAAACTACACGTGTGGTAACAGCTAAATGTT-GTTA
66 GCACCATTCCAAAGTCCAAACTACACGTGCGGTAACAACTAAAT-TTAGTTA
*
5645234 GAATCGATCTTAAATCCATTGGATGATGAATCTTTTAACCATCAACTAGGCTATTAGTGAAAATA
1 GAATCGATCTTAAATCCATTGGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATA
5645299 GCACCATTCCAAAGTCCAAACTACACGTGCGGTAACAACTAAATTTAGTTA
66 GCACCATTCCAAAGTCCAAACTACACGTGCGGTAACAACTAAATTTAGTTA
* * *
5645350 -AAGTCGATCTCAAATCC-TCT-GATGATGAATCTTTTAAGCGTCAACTATGCTATT
1 GAA-TCGATCTTAAATCCAT-TGGATGATGAATCTTTTAACCATCAACTATGCTATT
5645404 GACAAAAATC
Statistics
Matches: 157, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
115 50 0.32
116 107 0.68
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (116 bp):
GAATCGATCTTAAATCCATTGGATGATGAATCTTTTAACCATCAACTATGCTATTAGTGAAAATA
GCACCATTCCAAAGTCCAAACTACACGTGCGGTAACAACTAAATTTAGTTA
Found at i:5646582 original size:6 final size:6
Alignment explanation
Indices: 5646573--5646613 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
5646563 GTGTGAAATC
5646573 AAACAG AAACAG AAACAG AAACAG AAACAG AAACAG AAACA
1 AAACAG AAACAG AAACAG AAACAG AAACAG AAACAG AAACA
5646614 ATAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.17, G:0.15, T:0.00
Consensus pattern (6 bp):
AAACAG
Found at i:5650416 original size:54 final size:54
Alignment explanation
Indices: 5650355--5650673 Score: 403
Period size: 54 Copynumber: 5.9 Consensus size: 54
5650345 AAAACCACAG
* *
5650355 AATTCATAATATGCTTATGAACGACTGTATCGACACTAAGTGTGCAACCCATAG-
1 AATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGCAACCCA-AGA
* * *
5650409 AATTCATAATATGTTTATGAACGACCGTATCAACACTAATTGTGCATTACGC-AG-
1 AATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGCA--ACCCAAGA
* * * *
5650463 AATTCATAATATATTTATGAATGACCGTATCGGCACTAAGTGTGCAAAACCCACGA
1 AATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGC--AACCCAAGA
* *
5650519 AATTCATAATATGTTTATGAACGACCTTATCGACACTAAGTGTGCAACCCACGA
1 AATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGCAACCCAAGA
* *
5650573 AATTCATAATATGTTTATGAATGACCGTATCGACACTAAGTGTGCAACACCACGA
1 AATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGCAAC-CCAAGA
* * *
5650628 AATTCATAATTTGTTTATGAAAGACCGTATC-AGCACTATGTGTGCA
1 AATTCATAATATGTTTATGAACGACCGTATCGA-CACTAAGTGTGCA
5650674 CCTCAAAGAA
Statistics
Matches: 236, Mismatches: 21, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
54 143 0.61
55 48 0.20
56 45 0.19
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (54 bp):
AATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGCAACCCAAGA
Found at i:5650563 original size:110 final size:107
Alignment explanation
Indices: 5650347--5650673 Score: 428
Period size: 110 Copynumber: 3.0 Consensus size: 107
5650337 ATGTGTACAA
* * * *
5650347 AACCACAGAATTCATAATATGCTTATGAACGACTGTATCGACACTAAGTGTGC--AACCCA-TAG
1 AACC-CAGAATTCATAATATGTTTATGAATGACCGTATCGACACTAAGTGTGCAAAACCCACGA-
*
5650409 AATTCATAATATGTTTATGAACGACCGTATCAACACTAATTGTGC
64 AATTCATAATATGTTTATGAACGACCGTATC-ACACTAAGTGTGC
* * *
5650454 ATTACGCAGAATTCATAATATATTTATGAATGACCGTATCGGCACTAAGTGTGCAAAACCCACGA
1 A--ACCCAGAATTCATAATATGTTTATGAATGACCGTATCGACACTAAGTGTGCAAAACCCACGA
*
5650519 AATTCATAATATGTTTATGAACGACCTTATCGACACTAAGTGTGC
64 AATTCATAATATGTTTATGAACGACCGTATC-ACACTAAGTGTGC
*
5650564 AACCCACGAAATTCATAATATGTTTATGAATGACCGTATCGACACTAAGTGTGCAACA-CCACGA
1 AACCCA-G-AATTCATAATATGTTTATGAATGACCGTATCGACACTAAGTGTGCAAAACCCACGA
* * *
5650628 AATTCATAATTTGTTTATGAAAGACCGTATCAGCACTATGTGTGC
64 AATTCATAATATGTTTATGAACGACCGTATCA-CACTAAGTGTGC
5650673 A
1 A
5650674 CCTCAAAGAA
Statistics
Matches: 194, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
107 1 0.01
108 48 0.25
109 49 0.25
110 95 0.49
111 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (107 bp):
AACCCAGAATTCATAATATGTTTATGAATGACCGTATCGACACTAAGTGTGCAAAACCCACGAAA
TTCATAATATGTTTATGAACGACCGTATCACACTAAGTGTGC
Found at i:5659502 original size:39 final size:39
Alignment explanation
Indices: 5659434--5659515 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
5659424 CGCTTCGGCT
** * *
5659434 AGGGTAAGTCCTTATTGCATGCTCATTTGCTTTGTGCAC
1 AGGGTAAGTCCTTACCGCAGGCTCATTTGCTTCGTGCAC
* * *
5659473 AGGGTAAGTCCTTACCGTAGGCTCCTTTGCTTCGTGCAT
1 AGGGTAAGTCCTTACCGCAGGCTCATTTGCTTCGTGCAC
5659512 AGGG
1 AGGG
5659516 AAAACCTTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (39 bp):
AGGGTAAGTCCTTACCGCAGGCTCATTTGCTTCGTGCAC
Found at i:5660714 original size:14 final size:14
Alignment explanation
Indices: 5660695--5660722 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5660685 GGTAAACTTG
5660695 CATGATGTAAGTGA
1 CATGATGTAAGTGA
5660709 CATGATGTAAGTGA
1 CATGATGTAAGTGA
5660723 TACAAATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (14 bp):
CATGATGTAAGTGA
Found at i:5662636 original size:21 final size:21
Alignment explanation
Indices: 5662595--5662661 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
5662585 ATGGTCCTCT
* *
5662595 GGGATAATTATATGGTC-CTTC
1 GGGATAAATATGTGG-CACTTC
5662616 GGGATAAATATGTGGCACTTC
1 GGGATAAATATGTGGCACTTC
*
5662637 GGTGCA-AACCTATGTGGCACTTC
1 GG-G-ATAA-ATATGTGGCACTTC
5662660 GG
1 GG
5662662 TGCAAACCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 1 0.03
21 19 0.49
22 3 0.08
23 16 0.41
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (21 bp):
GGGATAAATATGTGGCACTTC
Found at i:5662652 original size:23 final size:23
Alignment explanation
Indices: 5662624--5662699 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
5662614 TCGGGATAAA
5662624 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
5662647 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
* *
5662670 TATGTGGCATTTTGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
5662693 TATGTGG
1 TATGTGG
5662700 TCATTCAAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:5665315 original size:15 final size:15
Alignment explanation
Indices: 5665295--5665329 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5665285 ACCAATTTCA
5665295 ATGGCTCCTTATAGG
1 ATGGCTCCTTATAGG
*
5665310 ATGGCTCCTTATATG
1 ATGGCTCCTTATAGG
5665325 ATGGC
1 ATGGC
5665330 CCCTATGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (15 bp):
ATGGCTCCTTATAGG
Found at i:5666628 original size:16 final size:16
Alignment explanation
Indices: 5666609--5666643 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5666599 AGAGCGGATT
5666609 AAGGAATTACAAAAGA
1 AAGGAATTACAAAAGA
5666625 AAGGAATTACAAAAGA
1 AAGGAATTACAAAAGA
5666641 AAG
1 AAG
5666644 ATAATAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.63, C:0.06, G:0.20, T:0.11
Consensus pattern (16 bp):
AAGGAATTACAAAAGA
Found at i:5669000 original size:19 final size:21
Alignment explanation
Indices: 5668976--5669027 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
5668966 ATGCGAAATT
5668976 GGTATCGGTACCTTG-A-GGA
1 GGTATCGGTACCTTGCAGGGA
*
5668995 GGTATCGATACCCTTGCAGGGA
1 GGTATCGGTA-CCTTGCAGGGA
*
5669017 AGTATCGGTAC
1 GGTATCGGTAC
5669028 TGTAGGAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.33
20 5 0.19
21 2 0.07
22 11 0.41
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (21 bp):
GGTATCGGTACCTTGCAGGGA
Found at i:5669623 original size:23 final size:23
Alignment explanation
Indices: 5669593--5669680 Score: 130
Period size: 23 Copynumber: 3.9 Consensus size: 23
5669583 TCGGGACAAA
5669593 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
5669616 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
5669639 TATGTGGTC-CTTCGG-GACAAA--
1 TATGTGG-CACTTCGGTG-CAAACC
5669660 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCACTTCGGTGCAAA
5669681 TTACGAGCTG
Statistics
Matches: 61, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.02
21 17 0.28
22 2 0.03
23 40 0.66
24 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:5670749 original size:31 final size:31
Alignment explanation
Indices: 5670714--5670777 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
5670704 TACTACAAAC
* * *
5670714 TTGTTTAAACATAGTTTGTACTAAAATACCA
1 TTGTTTAAACATAGGTTATAATAAAATACCA
5670745 TTGTTTAAACATAGGTTATAATAAAATACCA
1 TTGTTTAAACATAGGTTATAATAAAATACCA
5670776 TT
1 TT
5670778 AACATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (31 bp):
TTGTTTAAACATAGGTTATAATAAAATACCA
Found at i:5671256 original size:26 final size:26
Alignment explanation
Indices: 5671220--5671271 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
5671210 GAAGTGTTAA
5671220 TACACATAAGGTCGTGCCCT-CCATAT
1 TACACATAAGGTCGTG-CCTACCATAT
5671246 TACACATAAGGTCGTGCCTACCATAT
1 TACACATAAGGTCGTGCCTACCATAT
5671272 GCATTAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (26 bp):
TACACATAAGGTCGTGCCTACCATAT
Found at i:5673439 original size:15 final size:15
Alignment explanation
Indices: 5673412--5673441 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5673402 ATAATTATAG
5673412 TATTTTTATTTTTTT
1 TATTTTTATTTTTTT
5673427 TATTGTTTATTTTTT
1 TATT-TTTATTTTTT
5673442 CGAACTAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TATTTTTATTTTTTT
Found at i:5675483 original size:16 final size:16
Alignment explanation
Indices: 5675462--5675495 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5675452 GGCTAAACCT
5675462 AGATGTCATGTGTGTG
1 AGATGTCATGTGTGTG
5675478 AGATGTCATGTGTGTG
1 AGATGTCATGTGTGTG
5675494 AG
1 AG
5675496 CACGATGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.38, T:0.35
Consensus pattern (16 bp):
AGATGTCATGTGTGTG
Found at i:5676046 original size:60 final size:60
Alignment explanation
Indices: 5675982--5676096 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
5675972 ACCATGATTG
* *
5675982 TCATTCTAAATTTGTCCTCAAACTTTTT-AACACTTCAATTTCATCCGCAAACTATTACAT
1 TCATTCTAAATTAGTCCCCAAACTTTTTGAACACTTCAATTTCATCC-CAAACTATTACAT
* *
5676042 TCATTCTAAATTAGTCCCCAAACTTTTTGAGCATTTCAATTTCATCCCAAACTAT
1 TCATTCTAAATTAGTCCCCAAACTTTTTGAACACTTCAATTTCATCCCAAACTAT
5676097 ATGTATATCC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 34 0.68
61 16 0.32
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCCCAAACTTTTTGAACACTTCAATTTCATCCCAAACTATTACAT
Found at i:5677160 original size:87 final size:87
Alignment explanation
Indices: 5677049--5677308 Score: 484
Period size: 87 Copynumber: 3.0 Consensus size: 87
5677039 AATAGTTGAG
* * *
5677049 AGAAGAAAGTTAAGGATTAATTACATTCAGCGGATTTGGGTGCCATAATTATCCATATCTACACA
1 AGAAGAAAATTAAGGATTAATTACATTCAGTGGATTTGGGTGCCATAATTATCCATATCTACATA
5677114 TGCTGTTCAGCTAATATCCTTT
66 TGCTGTTCAGCTAATATCCTTT
5677136 AGAAGAAAATTAAGGATTAATTACATTCAGTGGATTTGGGTGCCATAATTATCCATATCTACATA
1 AGAAGAAAATTAAGGATTAATTACATTCAGTGGATTTGGGTGCCATAATTATCCATATCTACATA
5677201 TGCTGTTCAGCTAATATCCTTT
66 TGCTGTTCAGCTAATATCCTTT
*
5677223 AGAAGAAAATTAAGGATTAATTACATTCAGTGGATTTGGGTGCCATAATTATCCATACCTACATA
1 AGAAGAAAATTAAGGATTAATTACATTCAGTGGATTTGGGTGCCATAATTATCCATATCTACATA
5677288 TGCTGTTCAGCTAATATCCTT
66 TGCTGTTCAGCTAATATCCTT
5677309 ACATATAAAG
Statistics
Matches: 169, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 169 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (87 bp):
AGAAGAAAATTAAGGATTAATTACATTCAGTGGATTTGGGTGCCATAATTATCCATATCTACATA
TGCTGTTCAGCTAATATCCTTT
Found at i:5681168 original size:30 final size:29
Alignment explanation
Indices: 5681111--5681168 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5681101 GTGACATACA
* *
5681111 AAAAAAAATCATATACACATATTTTAACT
1 AAAAAAAATCATAAACACATATATTAACT
5681140 AAAAAAAATCATAAAC-CATGCATATTAAC
1 AAAAAAAATCATAAACACAT--ATATTAAC
5681169 ATATTATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.60
30 7 0.28
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.26
Consensus pattern (29 bp):
AAAAAAAATCATAAACACATATATTAACT
Found at i:5682478 original size:24 final size:24
Alignment explanation
Indices: 5682449--5682494 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5682439 GGTCTCCTCT
*
5682449 TTTTCTCTGTTTTTTTTAGTTTTC
1 TTTTCTCTCTTTTTTTTAGTTTTC
* *
5682473 TTTTCTTTCTTTTTTTTCGTTT
1 TTTTCTCTCTTTTTTTTAGTTT
5682495 AAAATGTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTCTCTCTTTTTTTTAGTTTTC
Found at i:5683011 original size:55 final size:54
Alignment explanation
Indices: 5682971--5683378 Score: 428
Period size: 55 Copynumber: 7.6 Consensus size: 54
5682961 TGACGAGCAT
* * *
5682971 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCA-AAAACGGGTCC
* *
5683026 GCTCTCTATTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
* * *
5683081 GCTCTCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAGACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
*
5683136 GCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGTCC
* **
5683191 GCTCCCTA-TCCGTTCAGGGAGTATA-AGACTCG----ATCTTCAATAAACGTTTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-AAACGGGTCC
* * **
5683242 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
* * **
5683297 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCC
*
5683348 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC
5683379 AATCTTCAAC
Statistics
Matches: 317, Mismatches: 22, Indels: 31
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.00
51 89 0.28
52 3 0.01
54 4 0.01
55 217 0.68
56 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAACGGGTCC
Found at i:5683112 original size:110 final size:110
Alignment explanation
Indices: 5682971--5683393 Score: 475
Period size: 106 Copynumber: 4.0 Consensus size: 110
5682961 TGACGAGCAT
* * *
5682971 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTC-ATAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAAT-AAACGTGTCCGCTCCCTA
5683034 TTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
64 TTCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* * * *
5683081 GCTCTCTATTTCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATAGACGGGTCCGCTCCCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAACGTGTCCGCTCCCTAT
* * *
5683145 CCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCC
65 TCATTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCC
* *
5683191 GCTCCCTA-TCCGTTCAGGGAGTATAAGACTCG----ATCTTCAATAAACGTTTCCGCTCCCTAT
1 GCTCCCTATTCC-TTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCGCTCCCTAT
* * * **
5683251 TCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACAAACTTGTCC
65 TCATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* ** *
5683297 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCGCTCCCTATT
* *
5683358 CCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
66 CATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
5683394 AGTTTGCTTC
Statistics
Matches: 273, Mismatches: 30, Indels: 28
0.82 0.09 0.08
Matches are distributed among these distances:
102 15 0.05
105 1 0.00
106 131 0.48
107 3 0.01
109 4 0.01
110 113 0.41
111 6 0.02
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (110 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGTGTCCGCTCCCTATT
CATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
Found at i:5684768 original size:17 final size:17
Alignment explanation
Indices: 5684746--5684887 Score: 69
Period size: 17 Copynumber: 9.1 Consensus size: 17
5684736 CCTCCTTTTA
5684746 TTTCTCTTTTTTTCATT
1 TTTCTCTTTTTTTCATT
5684763 TTTCTC---TTTT--TT
1 TTTCTCTTTTTTTCATT
* *
5684775 TTTCTTTTTTTTTAATT
1 TTTCTCTTTTTTTCATT
* *
5684792 TTTAT-TTTTTCTCATT
1 TTTCTCTTTTTTTCATT
* * *
5684808 TTTTTCCTTTCTTC--T
1 TTTCTCTTTTTTTCATT
*
5684823 TTTCT-TCTTTTTC-TT
1 TTTCTCTTTTTTTCATT
*
5684838 TTTCTC-ATTTTT-ATT
1 TTTCTCTTTTTTTCATT
* * *
5684853 ATTATTTTTTTTTCATT
1 TTTCTCTTTTTTTCATT
5684870 TTTCAT-TTTTTTTC-TT
1 TTTC-TCTTTTTTTCATT
5684886 TT
1 TT
5684888 ATTTCTTCTT
Statistics
Matches: 94, Mismatches: 19, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
12 7 0.07
14 9 0.10
15 25 0.27
16 22 0.23
17 30 0.32
18 1 0.01
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTCTTTTTTTCATT
Found at i:5684785 original size:9 final size:9
Alignment explanation
Indices: 5684740--5684894 Score: 73
Period size: 10 Copynumber: 16.3 Consensus size: 9
5684730 TTGAACCCTC
*
5684740 CTTTTATTT
1 CTTTTTTTT
5684749 CTCTTTTTTT
1 CT-TTTTTTT
* *
5684759 CATTTTTCT
1 CTTTTTTTT
5684768 CTTTTTTTTT
1 C-TTTTTTTT
5684778 CTTTTTTTT
1 CTTTTTTTT
**
5684787 -TAATTTTT
1 CTTTTTTTT
* *
5684795 ATTTTTTCT
1 CTTTTTTTT
*
5684804 CATTTTTTTC
1 C-TTTTTTTT
5684814 CTTTCTTCTTTT
1 C-TT-TT-TTTT
*
5684826 CTTCTTTTT
1 CTTTTTTTT
*
5684835 C-TTTTTCT
1 CTTTTTTTT
*
5684843 CATTTTTATT
1 C-TTTTTTTT
*
5684853 ATTATTTTTT
1 CTT-TTTTTT
5684863 -TTTCATTTTT
1 CTTT--TTTTT
5684873 CATTTTTTTT
1 C-TTTTTTTT
*
5684883 CTTTTATTT
1 CTTTTTTTT
5684892 CTT
1 CTT
5684895 CTTCAAGCGA
Statistics
Matches: 110, Mismatches: 23, Indels: 26
0.69 0.14 0.16
Matches are distributed among these distances:
8 13 0.12
9 41 0.37
10 45 0.41
11 4 0.04
12 7 0.06
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.77
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:5684799 original size:24 final size:24
Alignment explanation
Indices: 5684772--5684880 Score: 85
Period size: 25 Copynumber: 4.2 Consensus size: 24
5684762 TTTTCTCTTT
*
5684772 TTTTTTCTTTTTTTTTAATTTTTA
1 TTTTTTCTTTTTTTTTCATTTTTA
* * *
5684796 TTTTTTCTCATTTTTTTCCTTTCTTC
1 TTTTTTCT-TTTTTTTTCATTT-TTA
5684822 TTTTCTTCTTTTTCTTTTTCTCATTTTTA
1 TTTT-TTC--TTT-TTTTT-TCATTTTTA
* *
5684851 -TTATTATTTTTTTTTCATTTTTCA
1 TTTTTTCTTTTTTTTTCATTTTT-A
5684875 TTTTTT
1 TTTTTT
5684881 TTCTTTTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
23 8 0.12
24 14 0.21
25 17 0.26
26 6 0.09
27 5 0.08
28 3 0.05
29 8 0.12
30 5 0.08
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTTCTTTTTTTTTCATTTTTA
Found at i:5684801 original size:29 final size:29
Alignment explanation
Indices: 5684741--5684801 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
5684731 TGAACCCTCC
* *
5684741 TTTTATTTCTCTTTTTTTCATTTTTCTCT
1 TTTTATTTCTCTTTTTTTAATTTTTATCT
* *
5684770 TTTTTTTTCTTTTTTTTTAATTTTTAT-T
1 TTTTATTTCTCTTTTTTTAATTTTTATCT
5684798 TTTT
1 TTTT
5684802 CTCATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTATTTCTCTTTTTTTAATTTTTATCT
Found at i:5704899 original size:18 final size:17
Alignment explanation
Indices: 5704872--5704971 Score: 66
Period size: 16 Copynumber: 5.8 Consensus size: 17
5704862 AAGAAGAAAT
5704872 AAAA-GAGAAAAAATGA
1 AAAATGAGAAAAAATGA
5704888 AAAAGTGAGAAAAAAT-A
1 AAAA-TGAGAAAAAATGA
* *
5704905 AAAATGATGGAAAAACGAAA
1 AAAATGA-GAAAAAATG--A
*
5704925 AAAATG-GAAAAGGGAAGGA
1 AAAATGAGAAAA---AATGA
*
5704944 AAAATGA-AAAAAAAGA
1 AAAATGAGAAAAAATGA
5704960 AAAATGA-AAAAA
1 AAAATGAGAAAAA
5704972 GAGAAATAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 20
0.73 0.05 0.21
Matches are distributed among these distances:
16 23 0.33
17 11 0.16
18 14 0.20
19 11 0.16
20 7 0.10
21 3 0.04
ACGTcount: A:0.71, C:0.01, G:0.20, T:0.08
Consensus pattern (17 bp):
AAAATGAGAAAAAATGA
Found at i:5704918 original size:17 final size:18
Alignment explanation
Indices: 5704876--5704926 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
5704866 AGAAATAAAA
5704876 GAGAAAAAATGAAAAAGT
1 GAGAAAAAATGAAAAAGT
5704894 GAGAAAAAAT-AAAAA-T
1 GAGAAAAAATGAAAAAGT
* *
5704910 GATGGAAAAACGAAAAA
1 GA-GAAAAAATGAAAAA
5704927 AATGGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 3 0.10
17 11 0.38
18 15 0.52
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.10
Consensus pattern (18 bp):
GAGAAAAAATGAAAAAGT
Found at i:5704935 original size:28 final size:27
Alignment explanation
Indices: 5704897--5704967 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
5704887 AAAAAGTGAG
*
5704897 AAAAAAT-AAAAATGATGGAAAAACGA
1 AAAAAATGAAAAATGAAGGAAAAACGA
** *
5704923 AAAAAATGGAAAAGGGAAGGAAAAATGA
1 AAAAAAT-GAAAAATGAAGGAAAAACGA
*
5704951 AAAAAAAGAAAAATGAA
1 AAAAAATGAAAAATGAA
5704968 AAAAGAGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 7 0.19
27 8 0.22
28 21 0.58
ACGTcount: A:0.70, C:0.01, G:0.20, T:0.08
Consensus pattern (27 bp):
AAAAAATGAAAAATGAAGGAAAAACGA
Found at i:5704963 original size:16 final size:16
Alignment explanation
Indices: 5704942--5704977 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5704932 AAAAGGGAAG
5704942 GAAAAATGAAAAAAAA
1 GAAAAATGAAAAAAAA
*
5704958 GAAAAATGAAAAAAGA
1 GAAAAATGAAAAAAAA
5704974 GAAA
1 GAAA
5704978 TAAAAGGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (16 bp):
GAAAAATGAAAAAAAA
Found at i:5706354 original size:51 final size:51
Alignment explanation
Indices: 5706293--5706698 Score: 731
Period size: 51 Copynumber: 7.9 Consensus size: 51
5706283 GAAGCAAATT
5706293 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
5706344 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGTGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5706395 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5706446 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5706497 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
5706548 AGTTCGTTGAAGATTAAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5706599 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* * *
5706650 AGTTTGTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAG
1 AGTTCGTTGAAGA----TTGAGTCCTATACTCTCTGAATGAATAGGGAG
5706699 AAGACACGTT
Statistics
Matches: 344, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
51 314 0.91
55 30 0.09
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (51 bp):
AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
Found at i:5712448 original size:7 final size:7
Alignment explanation
Indices: 5712432--5712491 Score: 59
Period size: 7 Copynumber: 8.1 Consensus size: 7
5712422 ATGGATTGCT
*
5712432 TCTTTTC
1 TCTTTCC
5712439 TCTTTCC
1 TCTTTCC
5712446 TCTTTCC
1 TCTTTCC
*
5712453 T-TGGATTACT
1 TCT---TT-CC
5712463 TCTTTCC
1 TCTTTCC
5712470 TCTTTCC
1 TCTTTCC
5712477 TCTTTCC
1 TCTTTCC
5712484 TCTTTCC
1 TCTTTCC
5712491 T
1 T
5712492 TGGATTACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
6 1 0.02
7 37 0.82
8 2 0.04
9 2 0.04
10 2 0.04
11 1 0.02
ACGTcount: A:0.03, C:0.35, G:0.03, T:0.58
Consensus pattern (7 bp):
TCTTTCC
Found at i:5712465 original size:31 final size:31
Alignment explanation
Indices: 5712423--5712484 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
5712413 AATACAAGGA
* *
5712423 TGGATTGCTTCTTTTCTCTTTCCTCTTTCCT
1 TGGATTACTTCTTTCCTCTTTCCTCTTTCCT
5712454 TGGATTACTTCTTTCCTCTTTCCTCTTTCCT
1 TGGATTACTTCTTTCCTCTTTCCTCTTTCCT
5712485 CTTTCCTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.05, C:0.31, G:0.08, T:0.56
Consensus pattern (31 bp):
TGGATTACTTCTTTCCTCTTTCCTCTTTCCT
Found at i:5716124 original size:31 final size:31
Alignment explanation
Indices: 5716089--5716148 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5716079 AATTTGGTGA
** *
5716089 ATTCAATATGTCCTTGTCACTAGGAACTCAC
1 ATTCAATATGTAATTCTCACTAGGAACTCAC
*
5716120 ATTCAATATGTAATTCTTACTAGGAACTC
1 ATTCAATATGTAATTCTCACTAGGAACTC
5716149 CCAAACTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (31 bp):
ATTCAATATGTAATTCTCACTAGGAACTCAC
Found at i:5716710 original size:18 final size:19
Alignment explanation
Indices: 5716687--5716728 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5716677 GTAATAAAAT
* *
5716687 ATTAAAATTA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
5716705 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
5716723 ATTAAA
1 ATTAAA
5716729 GTAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 13 0.65
19 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.10, T:0.26
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:5717359 original size:18 final size:17
Alignment explanation
Indices: 5717308--5717356 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
5717298 GAAAACAAAG
5717308 CTTGAAAAATAAAAGAA
1 CTTGAAAAATAAAAGAA
**
5717325 AATGAAAAATGAAAAGAA
1 CTTGAAAAAT-AAAAGAA
*
5717343 CTTGAAAAGTAAAA
1 CTTGAAAAATAAAA
5717357 AGAGAAAGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.65, C:0.04, G:0.14, T:0.16
Consensus pattern (17 bp):
CTTGAAAAATAAAAGAA
Found at i:5722268 original size:18 final size:19
Alignment explanation
Indices: 5722245--5722286 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5722235 GTAATAAAAT
*
5722245 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
5722263 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
5722281 ATTAAA
1 ATTAAA
5722287 GTAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:5728238 original size:184 final size:185
Alignment explanation
Indices: 5727979--5728352 Score: 599
Period size: 184 Copynumber: 2.0 Consensus size: 185
5727969 AAATTAAAAT
* *
5727979 AATTTTTAATTCAAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAGTT
1 AATTTTTAATTCAAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATT
5728044 TCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT-AGATCCTAAATTAT
66 TCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGA-ATCCTAAATTAT
* * *
5728108 TAATTGAGTTTTAAATGGTTTGGGCTTAGCCCATATGCTATATATAATATTTTTAA
130 TAATTGAGTTTTAAATGGTTTGGGCTGAACCCATATGCTATATATAATATATTTAA
* * *
5728164 TATTTTTAATT-AAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAGAATAAAAATT
1 AATTTTTAATTCAAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATT
* * * *
5728228 TTATATAATTTTTTTAATTAATTAATATTGATTTAGTTTTAAAAGTTATTGAATCTTAAATTATT
66 TCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGAATCCTAAATTATT
* *
5728293 AATTGGGTTTTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATATTTAA
131 AATTGAGTTTTAAATGGTTTGGGCTGAACCCATATGCTATATATAATATATTTAA
5728348 AATTT
1 AATTT
5728353 AATTTCGGTT
Statistics
Matches: 173, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
184 162 0.94
185 11 0.06
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.45
Consensus pattern (185 bp):
AATTTTTAATTCAAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATT
TCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGAATCCTAAATTATT
AATTGAGTTTTAAATGGTTTGGGCTGAACCCATATGCTATATATAATATATTTAA
Found at i:5730842 original size:20 final size:20
Alignment explanation
Indices: 5730819--5730944 Score: 175
Period size: 20 Copynumber: 6.3 Consensus size: 20
5730809 AAACTCCTAT
*
5730819 TTCGCAACCCAGAAGTCAAA
1 TTCGCAACACAGAAGTCAAA
*
5730839 TTCGCAACACATAAGTCAAA
1 TTCGCAACACAGAAGTCAAA
*
5730859 TTCGCAACCCCA-AAGTCAAA
1 TTCGCAA-CACAGAAGTCAAA
*
5730879 TTCACAACACAGAAGTCAAA
1 TTCGCAACACAGAAGTCAAA
*
5730899 TTCGCAACCCA-AAGTCAAA
1 TTCGCAACACAGAAGTCAAA
*
5730918 TTTGCAACACAGAAGTCAAA
1 TTCGCAACACAGAAGTCAAA
5730938 TTCGCAA
1 TTCGCAA
5730945 AGCACGTTTA
Statistics
Matches: 93, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 20 0.22
20 70 0.75
21 3 0.03
ACGTcount: A:0.43, C:0.28, G:0.12, T:0.17
Consensus pattern (20 bp):
TTCGCAACACAGAAGTCAAA
Found at i:5730926 original size:39 final size:39
Alignment explanation
Indices: 5730819--5730944 Score: 207
Period size: 40 Copynumber: 3.2 Consensus size: 39
5730809 AAACTCCTAT
*
5730819 TTCGCAACCCAGAAGTCAAATTCGCAACACATAAGTCAAA
1 TTCGCAACCCA-AAGTCAAATTCGCAACACAGAAGTCAAA
*
5730859 TTCGCAACCCCAAAGTCAAATTCACAACACAGAAGTCAAA
1 TTCGCAA-CCCAAAGTCAAATTCGCAACACAGAAGTCAAA
*
5730899 TTCGCAACCCAAAGTCAAATTTGCAACACAGAAGTCAAA
1 TTCGCAACCCAAAGTCAAATTCGCAACACAGAAGTCAAA
5730938 TTCGCAA
1 TTCGCAA
5730945 AGCACGTTTA
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 37 0.46
40 40 0.49
41 4 0.05
ACGTcount: A:0.43, C:0.28, G:0.12, T:0.17
Consensus pattern (39 bp):
TTCGCAACCCAAAGTCAAATTCGCAACACAGAAGTCAAA
Found at i:5731097 original size:22 final size:22
Alignment explanation
Indices: 5731083--5731125 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5731073 GACGACATTT
5731083 GTCCCCATCTCCGACGAAATCC
1 GTCCCCATCTCCGACGAAATCC
5731105 GTCCCCATCTCC-AGCGAAATC
1 GTCCCCATCTCCGA-CGAAATC
5731126 TGTCTATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.23, C:0.44, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCC
Found at i:5731473 original size:20 final size:20
Alignment explanation
Indices: 5731450--5731540 Score: 137
Period size: 20 Copynumber: 4.5 Consensus size: 20
5731440 AAACTTAAAT
*
5731450 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
5731470 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
5731490 TCGCAACGCGAAAATAAAAA
1 TCGCAACGCGAAAATGAAAA
*
5731510 TCGCAACGCGGAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
5731530 TCGCAATGCGA
1 TCGCAACGCGA
5731541 TTTTAGTTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:5731593 original size:41 final size:39
Alignment explanation
Indices: 5731536--5731618 Score: 139
Period size: 41 Copynumber: 2.1 Consensus size: 39
5731526 AAAATCGCAA
5731536 TGCGATTTTAGTTTCGCGTTGCGATTTTCATGTTCGCGT
1 TGCGATTTTAGTTTCGCGTTGCGATTTTCATGTTCGCGT
*
5731575 TGCGATTTTCTAGTTTCGCGTTGCGATTTTCATTTTCGCGT
1 TGCGA-TTT-TAGTTTCGCGTTGCGATTTTCATGTTCGCGT
5731616 TGC
1 TGC
5731619 AAATTTAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 5 0.12
40 3 0.07
41 33 0.80
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (39 bp):
TGCGATTTTAGTTTCGCGTTGCGATTTTCATGTTCGCGT
Found at i:5731631 original size:20 final size:20
Alignment explanation
Indices: 5731536--5731618 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
5731526 AAAATCGCAA
5731536 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCAGTTTCGCGT
5731555 TGCGATTTTCA-TGTTCGCGT
1 TGCGATTTTCAGT-TTCGCGT
5731575 TGCGATTTTCTAGTTTCGCGT
1 TGCGATTTTC-AGTTTCGCGT
*
5731596 TGCGATTTTCATTTTCGCGT
1 TGCGATTTTCAGTTTCGCGT
5731616 TGC
1 TGC
5731619 AAATTTAAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
19 10 0.17
20 30 0.51
21 18 0.31
22 1 0.02
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (20 bp):
TGCGATTTTCAGTTTCGCGT
Found at i:5733777 original size:21 final size:21
Alignment explanation
Indices: 5733747--5733845 Score: 137
Period size: 21 Copynumber: 4.7 Consensus size: 21
5733737 GATGCACCTA
5733747 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
5733768 -CTATTGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
5733789 TCATCATTGAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
5733810 TCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
5733831 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
5733846 TCCCGCCCGC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:5733859 original size:42 final size:42
Alignment explanation
Indices: 5733747--5733865 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
5733737 GATGCACCTA
* * * **
5733747 TCATCGTTCAAGAGGCCCCTCCTATTGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCGCCCACCGTTCAAGAGGCCCCTC
* * * *
5733789 TCATCATTGAAGAGGCCCCTCTCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCGCCCACCGTTCAAGAGGCCCCTC
* * * *
5733831 TCATCGTTCAAGAGGTCCCGCCCGCCGTTTAAGAG
1 TCATCATTCAAGAGGCCCCGCCCACCGTTCAAGAG
5733866 CCCTATTCAC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.20, C:0.34, G:0.22, T:0.24
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCGCCCACCGTTCAAGAGGCCCCTC
Found at i:5735448 original size:20 final size:20
Alignment explanation
Indices: 5735423--5735478 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5735413 GTTGAAGGTA
* *
5735423 CAAATTCGCGTTGTGATAGT
1 CAAATTCGCGTTGCGAAAGT
***
5735443 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCGTTGCGAAAGT
5735463 CAAATTCGCGTTGCGA
1 CAAATTCGCGTTGCGA
5735479 TTTTCGGTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (20 bp):
CAAATTCGCGTTGCGAAAGT
Found at i:5735793 original size:18 final size:18
Alignment explanation
Indices: 5735770--5735805 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5735760 AAGCCGGTTG
*
5735770 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
5735788 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
5735806 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:5739078 original size:40 final size:40
Alignment explanation
Indices: 5739033--5739131 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
5739023 TTGCTAAATT
5739033 AAATTCGTGTTGCGAATTCGAAAATC-GAGTTGCAAATTTG
1 AAATTCGTGTTGCGAATTCGAAAATCAGA-TTGCAAATTTG
* * * *
5739073 AAATTC-AGTTGCGAATTTGAAATTCAGTATTGCGAATTTG
1 AAATTCGTGTTGCGAATTCGAAAATCAG-ATTGCAAATTTG
*
5739113 AAATTCAGTATTGCGAATT
1 AAATTC-GTGTTGCGAATT
5739132 TGACTTATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
39 16 0.33
40 23 0.47
41 1 0.02
42 9 0.18
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.35
Consensus pattern (40 bp):
AAATTCGTGTTGCGAATTCGAAAATCAGATTGCAAATTTG
Found at i:5739107 original size:21 final size:21
Alignment explanation
Indices: 5739033--5739134 Score: 124
Period size: 21 Copynumber: 5.0 Consensus size: 21
5739023 TTGCTAAATT
* *
5739033 AAATTC-GTGTTGCGAATTCG
1 AAATTCAGTATTGCGAATTTG
* *
5739053 AAAATC-G-AGTTGCAAATTTG
1 AAATTCAGTA-TTGCGAATTTG
5739073 AAATTCAG--TTGCGAATTTG
1 AAATTCAGTATTGCGAATTTG
5739092 AAATTCAGTATTGCGAATTTG
1 AAATTCAGTATTGCGAATTTG
5739113 AAATTCAGTATTGCGAATTTG
1 AAATTCAGTATTGCGAATTTG
5739134 A
1 A
5739135 CTTATGTGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
19 18 0.25
20 20 0.28
21 34 0.47
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (21 bp):
AAATTCAGTATTGCGAATTTG
Found at i:5739182 original size:20 final size:21
Alignment explanation
Indices: 5739142--5739182 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5739132 TGACTTATGT
*
5739142 GTTGCGATTTTCCAAATTCGC
1 GTTGCGATTTTACAAATTCGC
*
5739163 GTTGCGA-TTTACATATTCGC
1 GTTGCGATTTTACAAATTCGC
5739183 AACGCGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (21 bp):
GTTGCGATTTTACAAATTCGC
Found at i:5739203 original size:21 final size:21
Alignment explanation
Indices: 5739179--5739219 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5739169 ATTTACATAT
5739179 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAATTTGGAAAA
5739200 TCGCAACGCGAATTTGGAAA
1 TCGCAACGCGAATTTGGAAA
5739220 CTGGGTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAATTTGGAAAA
Found at i:5740506 original size:21 final size:21
Alignment explanation
Indices: 5740478--5740523 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5740468 AGAATGATAA
5740478 ATTT-GAAATTAAGGTTAGAG
1 ATTTAGAAATTAAGGTTAGAG
*
5740498 ATTTAGAAATTAGGGTTAGAG
1 ATTTAGAAATTAAGGTTAGAG
5740519 ATTTA
1 ATTTA
5740524 AGTTTGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (21 bp):
ATTTAGAAATTAAGGTTAGAG
Found at i:5745006 original size:18 final size:18
Alignment explanation
Indices: 5744967--5745002 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5744957 TTAAAAAGTA
*
5744967 TAATGATTTATTTAAAAT
1 TAATCATTTATTTAAAAT
5744985 TAATCATTTA-TTAAAAT
1 TAATCATTTATTTAAAAT
5745002 T
1 T
5745003 TAATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATCATTTATTTAAAAT
Found at i:5745701 original size:18 final size:18
Alignment explanation
Indices: 5745678--5745714 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5745668 TATTAAAATT
5745678 ATAATTAAATTTT-AATAA
1 ATAATT-AATTTTAAATAA
5745696 ATAATTAATTTTAAATAA
1 ATAATTAATTTTAAATAA
5745714 A
1 A
5745715 CCCTTATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATTAATTTTAAATAA
Found at i:5747140 original size:24 final size:25
Alignment explanation
Indices: 5747108--5747158 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
5747098 TTAATATCAT
*
5747108 TAAAAT-AAAAATAGTAATAAAACA
1 TAAAATAAAAAACAGTAATAAAACA
5747132 TAAAATAAAAAACAGTAATAAAACA
1 TAAAATAAAAAACAGTAATAAAACA
5747157 TA
1 TA
5747159 TTTATAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.20
Consensus pattern (25 bp):
TAAAATAAAAAACAGTAATAAAACA
Found at i:5747870 original size:201 final size:201
Alignment explanation
Indices: 5747523--5747893 Score: 492
Period size: 201 Copynumber: 1.8 Consensus size: 201
5747513 GAGTCATACG
* * **
5747523 AGCATACACATATAATGCACAAGTATTGTAGAACACAATATCAATGTGCCACTTTAAGGAATACA
1 AGCATACACATATAATACACAAGTATTGTAGAACACAACATCAATGTGCCACAATAAGGAATACA
* * * ** *
5747588 CCACACCATCATCACATAAGTGCAGGCACCACCATCACTTAGACGTTAGATTCGTGTCATGAAAT
66 CCACACCATCATCACATAAGTACAAGCACCACCACCACACAGACGTTAGATTCGTGTCATAAAAT
* * *
5747653 GTATTCTTGGTACTTTAGCACCACTGTCACACAGACGTCAAACTCGTGCTCAATATAATGCAGCT
131 GTATTCCTGATACTTTAGCAACACTGTCACACAGACGTCAAACTCGTGCTCAATATAATGCAGCT
5747718 GCTAGT
196 GCTAGT
* * * * *
5747724 AGCATACACATATAATACATAAGTGTTGTAGAACACAACGTCAATGTGCTAGAATAAGGAATACA
1 AGCATACACATATAATACACAAGTATTGTAGAACACAACATCAATGTGCCACAATAAGGAATACA
* * * * * *
5747789 TCGCACCATTATCACTTACA-TACAAGCACCACCACCACACAGATGTTAGATTTGTGTCATAAAA
66 CCACACCATCATCACATA-AGTACAAGCACCACCACCACACAGACGTTAGATTCGTGTCATAAAA
**
5747853 TGTATTCCTGATACTTTAGCAACACTGTCACTTAGACGTCA
130 TGTATTCCTGATACTTTAGCAACACTGTCACACAGACGTCA
5747894 GGTTACATGC
Statistics
Matches: 143, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
201 142 0.99
202 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (201 bp):
AGCATACACATATAATACACAAGTATTGTAGAACACAACATCAATGTGCCACAATAAGGAATACA
CCACACCATCATCACATAAGTACAAGCACCACCACCACACAGACGTTAGATTCGTGTCATAAAAT
GTATTCCTGATACTTTAGCAACACTGTCACACAGACGTCAAACTCGTGCTCAATATAATGCAGCT
GCTAGT
Found at i:5749856 original size:426 final size:426
Alignment explanation
Indices: 5749063--5749915 Score: 1643
Period size: 426 Copynumber: 2.0 Consensus size: 426
5749053 CATTATTCTT
5749063 GGGGTGATCTATTCATTTACGGGACCAAATTACATAATTTTTTAAAATTACACTTTGGTACCTAA
1 GGGGTGATCTATTCATTTACGGGACCAAATTACATAATTTTTTAAAATTACACTTTGGTACCTAA
*
5749128 ATTTTCCCAAGATTATACTATGGCCACTAAACTTTTAAAATTTTCATTTTGGTCACTATATGAAA
66 ATTTTCCCAAGATTATACAATGGCCACTAAACTTTTAAAATTTTCATTTTGGTCACTATATGAAA
5749193 TTTTGGGGTATTGCACTTTTCTTTGTTTTTATGGCACATTTGTTCGTATGATTTTATGGACAATT
131 TTTTGGGGTATTGCACTTTTCTTTGTTTTTATGGCACATTTGTTCGTATGATTTTATGGACAATT
*
5749258 CTGTTTATCATTATGATAGTTTAACTTTTCGTGTTGCATTCTTCACATCGCATCTCTTGATCAAG
196 CTGTTTATCATTATGATAGTTTAACTTTTCGTGTTGCATTCTTCACATAGCATCTCTTGATCAAG
*
5749323 AAAGGTCGATGATCTCGTACAGTTAGATCTCTTTTTGTGTCAGTTTGTCAATGCAATCAAAACTG
261 AAAGGTCGATGATCTCATACAGTTAGATCTCTTTTTGTGTCAGTTTGTCAATGCAATCAAAACTG
5749388 TTCATGGAGCTATTGTCATATTGATTCTCTTAATCTCCACACCTTCATCAATATTGCATCTAGGT
326 TTCATGGAGCTATTGTCATATTGATTCTCTTAATCTCCACACCTTCATCAATATTGCATCTAGGT
5749453 TTAAATAGAGACATTAAAATTATTGATAGTTAATAG
391 TTAAATAGAGACATTAAAATTATTGATAGTTAATAG
5749489 GGGGTGATCTATTCATTTACGGGACCAAATTACATAATTTTTTAAAATTACACTTTGGTACCTAA
1 GGGGTGATCTATTCATTTACGGGACCAAATTACATAATTTTTTAAAATTACACTTTGGTACCTAA
*
5749554 ATTTTCCCAAGTTTATACAATGGCCACTAAACTTTTAAAATTTTCATTTTGGTCACTATATGAAA
66 ATTTTCCCAAGATTATACAATGGCCACTAAACTTTTAAAATTTTCATTTTGGTCACTATATGAAA
*
5749619 TTTTGGGGTATTGCACTTTTCTTTGTTTTTATGGCATATTTGTTCGTATGATTTTATGGACAATT
131 TTTTGGGGTATTGCACTTTTCTTTGTTTTTATGGCACATTTGTTCGTATGATTTTATGGACAATT
*
5749684 CTGTTTATCATTATGATAGTTTGACTTTTCGTGTTGCATTCTTCACATAGCATCTCTTGATCAAG
196 CTGTTTATCATTATGATAGTTTAACTTTTCGTGTTGCATTCTTCACATAGCATCTCTTGATCAAG
*
5749749 AAAGGTCGATGATCTCATACAGTTAGATCTCTTTTTGTGTCAGTTTGTCAATGCAATCAAAATTG
261 AAAGGTCGATGATCTCATACAGTTAGATCTCTTTTTGTGTCAGTTTGTCAATGCAATCAAAACTG
5749814 TTCATGGAGCTATTGTCATATTGATTCTCTTAATCTCCACACCTTCATCAATATTGCATCTAGGT
326 TTCATGGAGCTATTGTCATATTGATTCTCTTAATCTCCACACCTTCATCAATATTGCATCTAGGT
5749879 TTAAATAGAGACATTAAAATTATTGATAGTTAATAG
391 TTAAATAGAGACATTAAAATTATTGATAGTTAATAG
5749915 G
1 G
5749916 TTTTGCTGTA
Statistics
Matches: 420, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
426 420 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (426 bp):
GGGGTGATCTATTCATTTACGGGACCAAATTACATAATTTTTTAAAATTACACTTTGGTACCTAA
ATTTTCCCAAGATTATACAATGGCCACTAAACTTTTAAAATTTTCATTTTGGTCACTATATGAAA
TTTTGGGGTATTGCACTTTTCTTTGTTTTTATGGCACATTTGTTCGTATGATTTTATGGACAATT
CTGTTTATCATTATGATAGTTTAACTTTTCGTGTTGCATTCTTCACATAGCATCTCTTGATCAAG
AAAGGTCGATGATCTCATACAGTTAGATCTCTTTTTGTGTCAGTTTGTCAATGCAATCAAAACTG
TTCATGGAGCTATTGTCATATTGATTCTCTTAATCTCCACACCTTCATCAATATTGCATCTAGGT
TTAAATAGAGACATTAAAATTATTGATAGTTAATAG
Found at i:5749991 original size:35 final size:35
Alignment explanation
Indices: 5749913--5749992 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
5749903 GATAGTTAAT
*
5749913 AGGTTTTGCTGTAAGATAAACATGCATTCAAGAGA
1 AGGTTTTGGTGTAAGATAAACATGCATTCAAGAGA
*
5749948 AGGTTTTGGTGTAAGATAAACATGCATTCAATAGA
1 AGGTTTTGGTGTAAGATAAACATGCATTCAAGAGA
5749983 AGGTTTTGGT
1 AGGTTTTGGT
5749993 TTTATTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.33
Consensus pattern (35 bp):
AGGTTTTGGTGTAAGATAAACATGCATTCAAGAGA
Found at i:5759370 original size:21 final size:19
Alignment explanation
Indices: 5759348--5759386 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
5759338 AAAAAACCAT
5759348 TTTTA-ATAATAAAATAATTA
1 TTTTAGATAA-AAAA-AATTA
5759368 TTTTAGATAAAAAAAATTA
1 TTTTAGATAAAAAAAATTA
5759387 AGAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TTTTAGATAAAAAAAATTA
Found at i:5766087 original size:113 final size:113
Alignment explanation
Indices: 5765883--5766109 Score: 427
Period size: 113 Copynumber: 2.0 Consensus size: 113
5765873 TTCTTCTTTA
*
5765883 TAGCGCCGCTTATTTACTTGTTTCGTGTATCTCACTCGTTATTTTGAAATGTCTTGGCTAGAGTT
1 TAGCGCCGCTTATTTACTTGTTTCGTGTATCTCACTCGTTATTTTGAAATATCTTGGCTAGAGTT
* *
5765948 TGGCGGATCTTTGGATTTGGCGGCTGTGATTGATTTTGTTGACTCAGG
66 TGGCGGATCTTTGGATTTGACAGCTGTGATTGATTTTGTTGACTCAGG
5765996 TAGCGCCGCTTATTTACTTGTTTCGTGTATCTCACTCGTTATTTTGAAATATCTTGGCTAGAGTT
1 TAGCGCCGCTTATTTACTTGTTTCGTGTATCTCACTCGTTATTTTGAAATATCTTGGCTAGAGTT
5766061 TGGCGGATCTTTGGATTTGACAGCTGTGATTGATTTTGTTGACTCAGG
66 TGGCGGATCTTTGGATTTGACAGCTGTGATTGATTTTGTTGACTCAGG
5766109 T
1 T
5766110 CACGACTTGA
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.43
Consensus pattern (113 bp):
TAGCGCCGCTTATTTACTTGTTTCGTGTATCTCACTCGTTATTTTGAAATATCTTGGCTAGAGTT
TGGCGGATCTTTGGATTTGACAGCTGTGATTGATTTTGTTGACTCAGG
Found at i:5770525 original size:22 final size:22
Alignment explanation
Indices: 5770500--5770543 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5770490 CACAATTTTG
*
5770500 TTTTTTAAATATTAATCAATAA
1 TTTTTTAAATAGTAATCAATAA
**
5770522 TTTTTTTTATAGTAATCAATAA
1 TTTTTTAAATAGTAATCAATAA
5770544 AGTTTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTTTAAATAGTAATCAATAA
Found at i:5772397 original size:16 final size:16
Alignment explanation
Indices: 5772372--5772404 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5772362 TAATAAATAA
5772372 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
5772388 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
5772404 A
1 A
5772405 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:5775434 original size:2 final size:2
Alignment explanation
Indices: 5775427--5775534 Score: 139
Period size: 2 Copynumber: 54.0 Consensus size: 2
5775417 ACTTATATTC
* * ** *
5775427 AT AT AT AT AT AT AT AT AT AT AT AT A- AT TT CAT AT AC CC AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
5775469 AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5775511 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
5775535 TTACACATGA
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
1 2 0.02
2 90 0.96
3 2 0.02
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5775991 original size:55 final size:55
Alignment explanation
Indices: 5775902--5776581 Score: 1017
Period size: 55 Copynumber: 12.4 Consensus size: 55
5775892 GGAGAATAGC
* * * * *
5775902 ACTCGAAC-ATCTTCAAAAATCACGT-TAGCTCCCTAGTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCT-GCCCCCTATTTCTTCAGAGAGTATAAG
* *
5775956 ACTCGAACAATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
5776011 ACTCGAACAATCTTCAACAATCGCGTCTGCCCTCTATTTCTTCATAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
5776066 ACTCGAACAATCTTCAA-AGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACA-ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
5776121 ACTCGAACAATCTTCAACGATCGTGTCTCCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
5776176 ACTCGAACAATCTTCAACGATCGCGTCT-CCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
5776230 ACCCAAACAATTTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
5776285 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
5776340 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
5776395 ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * *
5776450 ACTCAAAGAATATTCAACGATCGCGTCTGCCCCATATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * ** **
5776505 ACTCGAATAATCTTCAATAATCTTGTCTGCTTCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
5776560 ACTCGATCAATTTTCAATAATC
1 ACTCGAACAATCTTCAACAATC
5776582 ATTGGGAAAC
Statistics
Matches: 577, Mismatches: 44, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
54 58 0.10
55 518 0.90
56 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:5777610 original size:14 final size:15
Alignment explanation
Indices: 5777591--5777628 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
5777581 TTTGTTTTTG
5777591 TTTTTTTTCTCTTC-
1 TTTTTTTTCTCTTCA
5777605 TTTTTTTT-TCTTCA
1 TTTTTTTTCTCTTCA
5777619 TTTGTTTTTC
1 TTT-TTTTTC
5777629 ATTTGCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.24
14 11 0.52
15 5 0.24
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTTTTCTCTTCA
Found at i:5777631 original size:11 final size:11
Alignment explanation
Indices: 5777615--5777658 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
5777605 TTTTTTTTTC
5777615 TTCATTTGTTT
1 TTCATTTGTTT
*
5777626 TTCATTTGCTT
1 TTCATTTGTTT
5777637 TTCATTTGTTT
1 TTCATTTGTTT
5777648 TTCATTT-TTT
1 TTCATTTGTTT
5777658 T
1 T
5777659 CCTTTTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.73
Consensus pattern (11 bp):
TTCATTTGTTT
Found at i:5777665 original size:17 final size:17
Alignment explanation
Indices: 5777645--5777704 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
5777635 TTTTCATTTG
5777645 TTTTTCATTTTTTTCCT
1 TTTTTCATTTTTTTCCT
*
5777662 TTTTTCCTTTTTTTCCT
1 TTTTTCATTTTTTTCCT
*
5777679 TTTTT-A---TTTTCAT
1 TTTTTCATTTTTTTCCT
5777692 TTTTTCATTTTTT
1 TTTTTCATTTTTT
5777705 CTTTTCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
17 24 0.67
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCATTTTTTTCCT
Found at i:5777666 original size:39 final size:38
Alignment explanation
Indices: 5777623--5777709 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
5777613 TCTTCATTTG
*
5777623 TTTTTCATTTGCTTTT-CATTTGT-TTTTCATTTTTTTCCT
1 TTTTTCATTT--TTTTCCATTTGTATTTTCA-TTTTTTCAT
* * *
5777662 TTTTTCCTTTTTTTCCTTTTTTATTTTCATTTTTTCAT
1 TTTTTCATTTTTTTCCATTTGTATTTTCATTTTTTCAT
5777700 TTTTTC-TTTT
1 TTTTTCATTTT
5777710 CATTTTTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
37 8 0.19
38 19 0.45
39 15 0.36
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (38 bp):
TTTTTCATTTTTTTCCATTTGTATTTTCATTTTTTCAT
Found at i:5777696 original size:8 final size:8
Alignment explanation
Indices: 5777645--5777725 Score: 59
Period size: 8 Copynumber: 10.6 Consensus size: 8
5777635 TTTTCATTTG
5777645 TTTTTCATT
1 TTTTTCA-T
*
5777654 TTTTTCCT
1 TTTTTCAT
*
5777662 TTTTTCCTT
1 TTTTT-CAT
*
5777671 TTTTTCCT
1 TTTTTCAT
5777679 TTTTT-A-
1 TTTTTCAT
5777685 -TTTTCAT
1 TTTTTCAT
5777692 TTTTTCAT
1 TTTTTCAT
5777700 TTTTTC--
1 TTTTTCAT
5777706 -TTTTCA-
1 TTTTTCAT
5777712 TTTTTCAT
1 TTTTTCAT
5777720 CTTTTT
1 -TTTTT
5777726 TTTCAGCTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
5 9 0.15
6 1 0.02
7 6 0.10
8 26 0.43
9 18 0.30
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:5777696 original size:21 final size:21
Alignment explanation
Indices: 5777670--5777766 Score: 85
Period size: 21 Copynumber: 4.6 Consensus size: 21
5777660 CTTTTTTCCT
*
5777670 TTTTTTCCTTTTTTATTTTCA
1 TTTTTTCATTTTTTATTTTCA
*
5777691 TTTTTTCATTTTTTCTTTTCA
1 TTTTTTCATTTTTTATTTTCA
*
5777712 -TTTTTCATCTTTT-TTTTCA
1 TTTTTTCATTTTTTATTTTCA
**
5777731 GCTTTTTTTTCAGCTTTT-TTTTCA
1 ----TTTTTTCATTTTTTATTTTCA
5777755 TTTTTT-ATTTTT
1 TTTTTTCATTTTT
5777767 CCTTGCTCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
19 10 0.15
20 18 0.28
21 19 0.29
24 18 0.28
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTTTCATTTTTTATTTTCA
Found at i:5777727 original size:12 final size:12
Alignment explanation
Indices: 5777712--5777754 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
5777702 TTTCTTTTCA
*
5777712 TTTTTCATCTTT
1 TTTTTCAGCTTT
5777724 TTTTTCAGCTTT
1 TTTTTCAGCTTT
5777736 TTTTTCAGCTTT
1 TTTTTCAGCTTT
5777748 TTTTTCA
1 TTTTTCA
5777755 TTTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTTCAGCTTT
Found at i:5777736 original size:20 final size:20
Alignment explanation
Indices: 5777693--5777736 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5777683 TATTTTCATT
* *
5777693 TTTTCATTTTTTCTTTTCAT
1 TTTTCATCTTTTCTTTTCAC
5777713 TTTTCATCTTTT-TTTTCAGC
1 TTTTCATCTTTTCTTTTCA-C
5777733 TTTT
1 TTTT
5777737 TTTTCAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTCATCTTTTCTTTTCAC
Found at i:5777760 original size:12 final size:12
Alignment explanation
Indices: 5777592--5777765 Score: 72
Period size: 12 Copynumber: 13.8 Consensus size: 12
5777582 TTGTTTTTGT
*
5777592 TTTTTTTCTCTTCT
1 TTTTTTT-T-TTCA
5777606 TTTTTTTTCTTCA
1 TTTTTTTT-TTCA
*
5777619 -TTTGTTTTTCA
1 TTTTTTTTTTCA
**
5777630 -TTTGCTTTTCA
1 TTTTTTTTTTCA
*
5777641 -TTTGTTTTTCA
1 TTTTTTTTTTCA
5777652 TTTTTTTCCTTT--
1 TTTTTTT--TTTCA
*
5777664 TTTCCTTTTTTTCC
1 TTT--TTTTTTTCA
5777678 TTTTTTATTTTCA
1 TTTTTT-TTTTCA
5777691 TTTTTTCATTTTTTC-
1 --TTTT--TTTTTTCA
*
5777706 TTTTCATTTTTCA
1 TTTT-TTTTTTCA
*
5777719 TCTTTTTTTTCA
1 TTTTTTTTTTCA
**
5777731 GCTTTTTTTTCA
1 TTTTTTTTTTCA
**
5777743 GCTTTTTTTTCA
1 TTTTTTTTTTCA
5777755 TTTTTTATTTT
1 TTTTTT-TTTT
5777766 TCCTTGCTCT
Statistics
Matches: 133, Mismatches: 13, Indels: 29
0.76 0.07 0.17
Matches are distributed among these distances:
11 24 0.18
12 60 0.45
13 21 0.16
14 17 0.13
15 4 0.03
16 5 0.04
17 2 0.02
ACGTcount: A:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:5780016 original size:18 final size:18
Alignment explanation
Indices: 5779995--5780038 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5779985 CTCATCCCTC
*
5779995 TTTGGCACTGGGACAATA
1 TTTGCCACTGGGACAATA
5780013 TTTGCCACTGGGACAATA
1 TTTGCCACTGGGACAATA
*
5780031 TTCGCCAC
1 TTTGCCAC
5780039 CCACTTAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (18 bp):
TTTGCCACTGGGACAATA
Done.