Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014333.1 Kokia drynarioides strain JFW-HI SEQ_129370, 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: 1084406
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 65 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:797171 original size:110 final size:108
Alignment explanation
Indices: 796922--797215 Score: 310
Period size: 109 Copynumber: 2.7 Consensus size: 108
796912 CAAGTCAAAT
* * * * * * *
796922 TGTGTTGCGTCTCACTTTGTTTGCTCCTCTACTAGCCAGGTTGGATTATATCCAA-TGAGACAAG
1 TGTGTTGC-TCTCACTTTATGTGCTCCTTTGCGAGCTAGGTTGGATTATATCCAACT-AGACAAA
* *
796986 GTTTATGATTTGCTCCATAGTGAGCATAGCTCTTATGCGAGCTAA
64 GATTCTGATTTGCTCCATAGTGAGCATAGCTCTTATGCGAGCTAA
* * *
797031 TGTGATTTG-TCTCA--TTATGCATGCTCCTTTGCGAGCTAGGTTAGATTGTATCCAACTAGTCA
1 TGTG--TTGCTCTCACTTTATG--TGCTCCTTTGCGAGCTAGGTTGGATTATATCCAACTAGACA
* * ** * *
797093 AAGCTTCTGATTTTCTCTTTAGTGAGCGTAGCTCCTTATGTGAGCTAA
62 AAGATTCTGATTTGCTCCATAGTGAGCATAGCT-CTTATGCGAGCTAA
*
797141 TGTGTTGCCTCTCACTTTATGTGCTCCTTTGCGAGCTAGGTTGGATTATATCCAACGAGACAAAG
1 TGTGTTG-CTCTCACTTTATGTGCTCCTTTGCGAGCTAGGTTGGATTATATCCAACTAGACAAAG
797206 ATTCTG-TTTG
65 ATTCTGATTTG
797216 ACGAATCAAC
Statistics
Matches: 152, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
107 3 0.02
108 3 0.02
109 70 0.46
110 68 0.45
111 3 0.02
112 5 0.03
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (108 bp):
TGTGTTGCTCTCACTTTATGTGCTCCTTTGCGAGCTAGGTTGGATTATATCCAACTAGACAAAGA
TTCTGATTTGCTCCATAGTGAGCATAGCTCTTATGCGAGCTAA
Found at i:798059 original size:22 final size:23
Alignment explanation
Indices: 798012--798059 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
798002 TATAATATTC
*
798012 AAACAATATTAAAAAAGACAGCA
1 AAACAATATTAAAAAAGACAGAA
*
798035 AAACAATATTAAAAAA-ACATAA
1 AAACAATATTAAAAAAGACAGAA
798057 AAA
1 AAA
798060 ATAACATCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.71, C:0.10, G:0.04, T:0.15
Consensus pattern (23 bp):
AAACAATATTAAAAAAGACAGAA
Found at i:798085 original size:12 final size:12
Alignment explanation
Indices: 798070--798145 Score: 66
Period size: 12 Copynumber: 6.4 Consensus size: 12
798060 ATAACATCCA
798070 AACAATAAAAAC
1 AACAATAAAAAC
*
798082 AACAATCAAAAC
1 AACAATAAAAAC
* *
798094 AACAGT-AAAGC
1 AACAATAAAAAC
* *
798105 AATAACAAAAAC
1 AACAATAAAAAC
798117 AACAA-AAATAAC
1 AACAATAAA-AAC
* *
798129 AAAAACAAAAAC
1 AACAATAAAAAC
798141 AACAA
1 AACAA
798146 AAGTAGTACC
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
11 10 0.20
12 38 0.75
13 3 0.06
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.07
Consensus pattern (12 bp):
AACAATAAAAAC
Found at i:798093 original size:21 final size:21
Alignment explanation
Indices: 798048--798095 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
798038 CAATATTAAA
*
798048 AAAAC-ATAAAAAATAACATC
1 AAAACAATAAAAAACAACATC
*
798068 CAAACAAT-AAAAACAACAATC
1 AAAACAATAAAAAACAAC-ATC
798089 AAAACAA
1 AAAACAA
798096 CAGTAAAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.71, C:0.19, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAACAATAAAAAACAACATC
Found at i:798137 original size:15 final size:15
Alignment explanation
Indices: 798089--798147 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
798079 AACAACAATC
*
798089 AAAACAACAGTAAAGCA
1 AAAACAACA--AAAACA
*
798106 ATAACAA-AAACAACA
1 AAAACAACAAA-AACA
*
798121 AAAATAACAAAAACA
1 AAAACAACAAAAACA
798136 AAAACAACAAAA
1 AAAACAACAAAA
798148 GTAGTACCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 2 0.06
15 23 0.66
16 4 0.11
17 6 0.17
ACGTcount: A:0.75, C:0.17, G:0.03, T:0.05
Consensus pattern (15 bp):
AAAACAACAAAAACA
Found at i:798147 original size:9 final size:9
Alignment explanation
Indices: 798108--798145 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
798098 GTAAAGCAAT
798108 AACAAAAAC
1 AACAAAAAC
*
798117 AACAAAAAT
1 AACAAAAAC
798126 AACAAAAAC
1 AACAAAAAC
798135 AA-AAACAAC
1 AACAAA-AAC
798144 AA
1 AA
798146 AAGTAGTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 3 0.12
9 23 0.88
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (9 bp):
AACAAAAAC
Found at i:802279 original size:37 final size:38
Alignment explanation
Indices: 802206--802302 Score: 153
Period size: 37 Copynumber: 2.6 Consensus size: 38
802196 GTCAGTAAAT
* *
802206 AATT-TTAAAATTATTAAATTTATTTTTTTGAAATATAA
1 AATTATTAAAATTATTATA-TTATTATTTTGAAATATAA
802244 AATTATTAAAATTATTATATTA-TATTTTGAAATATAA
1 AATTATTAAAATTATTATATTATTATTTTGAAATATAA
802281 AATTATTAAAATTATTATATTA
1 AATTATTAAAATTATTATATTA
802303 AAATATATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
37 36 0.64
38 7 0.12
39 13 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (38 bp):
AATTATTAAAATTATTATATTATTATTTTGAAATATAA
Found at i:802376 original size:21 final size:21
Alignment explanation
Indices: 802352--802391 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
802342 TCACTGTTTC
802352 TTCCATCAATCTCATTTTTTT
1 TTCCATCAATCTCATTTTTTT
* * *
802373 TTCCTTCCATCTGATTTTT
1 TTCCATCAATCTCATTTTT
802392 GAAGACAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.25, G:0.03, T:0.57
Consensus pattern (21 bp):
TTCCATCAATCTCATTTTTTT
Found at i:803547 original size:23 final size:22
Alignment explanation
Indices: 803521--803592 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 22
803511 CAAAACTCTT
*
803521 ACCCAAAATCCACAAATTCGACC
1 ACCCAAAATCC-CAAATTCGACA
*
803544 ACCCAAAATCCCCAAATTCAACA
1 ACCCAAAAT-CCCAAATTCGACA
*
803567 ACCTAAAATCTCCAAATTCGACA
1 ACCCAAAATC-CCAAATTCGACA
803590 ACC
1 ACC
803593 ATAAACAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.93
24 2 0.05
ACGTcount: A:0.44, C:0.38, G:0.03, T:0.15
Consensus pattern (22 bp):
ACCCAAAATCCCAAATTCGACA
Found at i:804085 original size:18 final size:17
Alignment explanation
Indices: 804049--804087 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
804039 TAAACTATTG
* *
804049 TTTTTTAATTTTAATTA
1 TTTTTTAATTTAAAATA
804066 TTTTTTAACTTTAAAATA
1 TTTTTTAA-TTTAAAATA
804084 TTTT
1 TTTT
804088 GTTGTGACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTAATTTAAAATA
Found at i:808609 original size:14 final size:14
Alignment explanation
Indices: 808575--808608 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
808565 TTGAGCAAAC
808575 CTTTCTTCTCTCTTT
1 CTTT-TTCTCTCTTT
808590 CTTTTTCTCTCTTT
1 CTTTTTCTCTCTTT
808604 -TTTTT
1 CTTTTT
808609 TAAGCATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 10 0.53
15 4 0.21
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
CTTTTTCTCTCTTT
Found at i:813652 original size:17 final size:18
Alignment explanation
Indices: 813632--813673 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
813622 ACTACAATGC
813632 AAATGTACTAACAAAT-A
1 AAATGTACTAACAAATAA
** *
813649 AAATGTTGTGACAAATAA
1 AAATGTACTAACAAATAA
813667 AAATGTA
1 AAATGTA
813674 ATGACCACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATGTACTAACAAATAA
Found at i:814118 original size:12 final size:12
Alignment explanation
Indices: 814080--814122 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
814070 TGTCGGGGCA
814080 TCTTCCTTCTCT
1 TCTTCCTTCTCT
*
814092 TCATTCTTCTCCTCT
1 TC-TTC--CTTCTCT
814107 TCTTCCTTCTCT
1 TCTTCCTTCTCT
814119 TCTT
1 TCTT
814123 TAGTGTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 12 0.46
13 3 0.12
14 3 0.12
15 8 0.31
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTTCCTTCTCT
Found at i:814131 original size:27 final size:28
Alignment explanation
Indices: 814080--814140 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
814070 TGTCGGGGCA
**
814080 TCTTCCTTCTCTTCATTCTTCTCC-TCT
1 TCTTCCTTCTCTTCATTAGTCTCCTTCT
* *
814107 TCTTCCTTCTCTTCTTTAGTGTCCTTCT
1 TCTTCCTTCTCTTCATTAGTCTCCTTCT
814135 T-TTCCT
1 TCTTCCT
814141 CAGGTTCCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.03, C:0.36, G:0.03, T:0.57
Consensus pattern (28 bp):
TCTTCCTTCTCTTCATTAGTCTCCTTCT
Found at i:829119 original size:17 final size:17
Alignment explanation
Indices: 829099--829135 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
829089 ACTACAATGC
829099 AAATGTACTAACAAATA
1 AAATGTACTAACAAATA
* *
829116 AAATGTAGTGACAAATA
1 AAATGTACTAACAAATA
829133 AAA
1 AAA
829136 AATGCAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (17 bp):
AAATGTACTAACAAATA
Found at i:830630 original size:16 final size:16
Alignment explanation
Indices: 830609--830641 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
830599 AATGAAATAC
830609 CTTATATTTTGTTTGG
1 CTTATATTTTGTTTGG
830625 CTTATATTTTGTTTGG
1 CTTATATTTTGTTTGG
830641 C
1 C
830642 CTAGGACAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.61
Consensus pattern (16 bp):
CTTATATTTTGTTTGG
Found at i:834847 original size:61 final size:61
Alignment explanation
Indices: 834780--834905 Score: 198
Period size: 61 Copynumber: 2.1 Consensus size: 61
834770 TAAAATAATC
* * *
834780 AATCAATGTCAATGCAATTAGAGTTAAACTTCAAATATTAAATGTTAGTGTACTGAAAATA
1 AATCAATGTCAACGCAATTAGAGTTAAACTTCAAATATTAAACGTCAGTGTACTGAAAATA
* * *
834841 AATCAATTTGAACGCAATTAGAGTTAAATTTCAAATATTAAACGTCAGTGTACTGAAAATA
1 AATCAATGTCAACGCAATTAGAGTTAAACTTCAAATATTAAACGTCAGTGTACTGAAAATA
834902 AATC
1 AATC
834906 CAATTGTGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (61 bp):
AATCAATGTCAACGCAATTAGAGTTAAACTTCAAATATTAAACGTCAGTGTACTGAAAATA
Found at i:862159 original size:7 final size:7
Alignment explanation
Indices: 862147--862211 Score: 130
Period size: 7 Copynumber: 9.3 Consensus size: 7
862137 TAGCAATATT
862147 TCTTTTC
1 TCTTTTC
862154 TCTTTTC
1 TCTTTTC
862161 TCTTTTC
1 TCTTTTC
862168 TCTTTTC
1 TCTTTTC
862175 TCTTTTC
1 TCTTTTC
862182 TCTTTTC
1 TCTTTTC
862189 TCTTTTC
1 TCTTTTC
862196 TCTTTTC
1 TCTTTTC
862203 TCTTTTC
1 TCTTTTC
862210 TC
1 TC
862212 ATTCAACATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
TCTTTTC
Found at i:864788 original size:21 final size:22
Alignment explanation
Indices: 864748--864788 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
864738 GAAAAAGGTT
*
864748 AAAAGAAACTTGTAGAGAAAAG
1 AAAAGAAACTCGTAGAGAAAAG
*
864770 AAAATAAACTCGT-GAGAAA
1 AAAAGAAACTCGTAGAGAAA
864789 GTAAGAGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.59, C:0.07, G:0.20, T:0.15
Consensus pattern (22 bp):
AAAAGAAACTCGTAGAGAAAAG
Found at i:876430 original size:40 final size:39
Alignment explanation
Indices: 876333--876442 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 39
876323 GACTTCTTCA
* * * *
876333 GGGGTTTGTTGCGACATAAACATGCTGTGTTACGACAAAG
1 GGGGTTTGTTG-TACATAGACATTCTATGTTACGACAAAG
* * *
876373 GGGGTTTGTCGTAACATAGACATTCTATGTTGCGACATAG
1 GGGGTTTGTTGT-ACATAGACATTCTATGTTACGACAAAG
876413 GGGGTTTGTTGATACATAGACATTCTATGT
1 GGGGTTTGTTG-TACATAGACATTCTATGT
876443 CGCTACAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 59 0.98
41 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (39 bp):
GGGGTTTGTTGTACATAGACATTCTATGTTACGACAAAG
Found at i:877680 original size:20 final size:20
Alignment explanation
Indices: 877651--877735 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
877641 AAATCTAGTT
* *
877651 AAAATTATTTTAAACATGTC
1 AAAATCATTTTAAACAAGTC
* *
877671 AAAATCA-TTTGAACTAAGTA
1 AAAATCATTTTAAAC-AAGTC
**
877691 AAAATCATTTT-AACACTTC
1 AAAATCATTTTAAACAAGTC
**
877710 AAAATGTTTTTCAAACAAGTC
1 AAAATCATTTT-AAACAAGTC
877731 AAAAT
1 AAAAT
877736 AGCTTCAGGC
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 17 0.34
20 19 0.38
21 14 0.28
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (20 bp):
AAAATCATTTTAAACAAGTC
Found at i:877806 original size:18 final size:18
Alignment explanation
Indices: 877775--877809 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
877765 TTTGGCTAAG
*
877775 TATCGATAATTCTTGAAA
1 TATCGATAACTCTTGAAA
*
877793 TATCGATACCTCTTGAA
1 TATCGATAACTCTTGAA
877810 GAATCGGGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (18 bp):
TATCGATAACTCTTGAAA
Found at i:889697 original size:21 final size:21
Alignment explanation
Indices: 889673--889712 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
889663 ATTCTTGTAG
*
889673 AATCTTGATATATATGTAACT
1 AATCATGATATATATGTAACT
889694 AATCATGATATATATGTAA
1 AATCATGATATATATGTAA
889713 AAACATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
AATCATGATATATATGTAACT
Found at i:889719 original size:19 final size:20
Alignment explanation
Indices: 889678--889719 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
889668 TGTAGAATCT
*
889678 TGATATATATGTAACTAATCA
1 TGATATATATGTAAC-AAACA
889699 TGATATATATGTAA-AAACA
1 TGATATATATGTAACAAACA
889718 TG
1 TG
889720 TTTTATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
21 14 0.70
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (20 bp):
TGATATATATGTAACAAACA
Found at i:890302 original size:22 final size:23
Alignment explanation
Indices: 890260--890302 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
890250 GTAAGTTTAA
* *
890260 AATAAATTTAATATAATATGTGT
1 AATAAACTAAATATAATATGTGT
890283 AATAAACTAAATA-AATATGT
1 AATAAACTAAATATAATATGT
890303 TATGAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (23 bp):
AATAAACTAAATATAATATGTGT
Found at i:892184 original size:19 final size:19
Alignment explanation
Indices: 892162--892206 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
892152 TTATATTAAG
892162 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
892181 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
892200 ATTTAAT
1 ATTTAAT
892207 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:893033 original size:15 final size:15
Alignment explanation
Indices: 893015--893065 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
893005 TCCTATTTTC
893015 TATTTCTTTTAATTT
1 TATTTCTTTTAATTT
*
893030 TATTTTCTTTTATTTT
1 TA-TTTCTTTTAATTT
* *
893046 TAATTCTGTTT-CTTT
1 TATTTCT-TTTAATTT
893061 TATTT
1 TATTT
893066 TTGCTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (15 bp):
TATTTCTTTTAATTT
Found at i:893035 original size:22 final size:22
Alignment explanation
Indices: 893008--893067 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
892998 TCGATTTTCC
893008 TATTTTCTATTT-CTTTTAATTT
1 TATTTTCT-TTTACTTTTAATTT
* *
893030 TATTTTCTTTTATTTTTAATTC
1 TATTTTCTTTTACTTTTAATTT
* *
893052 T-GTTTCTTTTATTTTT
1 TATTTTCTTTTACTTTT
893068 GCTTAAATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTT
Found at i:893038 original size:16 final size:16
Alignment explanation
Indices: 893017--893047 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
893007 CTATTTTCTA
893017 TTTCTTTTAATTTTAT
1 TTTCTTTTAATTTTAT
*
893033 TTTCTTTTATTTTTA
1 TTTCTTTTAATTTTA
893048 ATTCTGTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTAATTTTAT
Found at i:903132 original size:22 final size:22
Alignment explanation
Indices: 903107--903148 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
903097 TTTTTTATTG
*
903107 TTTTGGTTGCTGTTTTGGTGCT
1 TTTTGGTTACTGTTTTGGTGCT
**
903129 TTTTTTTTACTGTTTTGGTG
1 TTTTGGTTACTGTTTTGGTG
903149 TTGTTTTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.02, C:0.07, G:0.26, T:0.64
Consensus pattern (22 bp):
TTTTGGTTACTGTTTTGGTGCT
Found at i:903157 original size:20 final size:19
Alignment explanation
Indices: 903026--903162 Score: 99
Period size: 20 Copynumber: 7.1 Consensus size: 19
903016 TATATTGTTA
*
903026 TTTTGGTGCTTTTTTACTG
1 TTTTGGTGTTTTTTTACTG
*
903045 TTTTGGTTGTTGTTTTTTGCTG
1 TTTTGG-TG-T-TTTTTTACTG
*
903067 TTTTGATTGTTTTTTTACTG
1 TTTTG-GTGTTTTTTTACTG
*
903087 TTTTGGTGATTTTTTTATTG
1 TTTTGGTG-TTTTTTTACTG
*
903107 TTTT-G-G-----TTGCTG
1 TTTTGGTGTTTTTTTACTG
903119 TTTTGGTGCTTTTTTTTTACTG
1 TTTTGGTG---TTTTTTTACTG
903141 TTTTGGTGTTGTTTTTACTG
1 TTTTGGTGTT-TTTTTACTG
903161 TT
1 TT
903163 ATTTTTGCTA
Statistics
Matches: 93, Mismatches: 9, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
12 8 0.09
13 1 0.01
14 1 0.01
18 1 0.01
19 11 0.12
20 41 0.44
21 1 0.01
22 29 0.31
ACGTcount: A:0.05, C:0.06, G:0.22, T:0.67
Consensus pattern (19 bp):
TTTTGGTGTTTTTTTACTG
Found at i:903168 original size:34 final size:34
Alignment explanation
Indices: 903095--903182 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
903085 TGTTTTGGTG
* **
903095 ATTTTTTTATTGTTTTGGTTGCTGTTTTGGTGCTT
1 ATTTTTTTACTGTTTTGG-TGCTGTTTTACTGCTT
*
903130 -TTTTTTTACTGTTTTGGTGTTGTTTTTACTG-TT
1 ATTTTTTTACTGTTTTGGTGCTG-TTTTACTGCTT
*
903163 ATTTTTGCTACTGTTTTGGT
1 ATTTTT-TTACTGTTTTGGT
903183 TGTTTGGATG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 6 0.13
34 27 0.60
35 12 0.27
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.66
Consensus pattern (34 bp):
ATTTTTTTACTGTTTTGGTGCTGTTTTACTGCTT
Found at i:903171 original size:54 final size:51
Alignment explanation
Indices: 903057--903171 Score: 142
Period size: 54 Copynumber: 2.2 Consensus size: 51
903047 TTGGTTGTTG
*
903057 TTTTTTGCTGTTTTGATTGTTTTTTTACTGTTTTGGTGATTTTTTTATTGT
1 TTTTTTGCTGTTTTGATTGTTTTTTTACTGTTTTGGTGATTTTTTTACTGT
* * *
903108 TTTGGTTGCTGTTTTGGTGCTTTTTTTTTACTGTTTTGGTG-TTGTTTTTACTGT
1 TTT-TTTGCTGTTTTGAT--TGTTTTTTTACTGTTTTGGTGATT-TTTTTACTGT
903162 TATTTTTGCT
1 T-TTTTTGCT
903172 ACTGTTTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
51 3 0.06
52 12 0.22
53 2 0.04
54 35 0.65
55 2 0.04
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (51 bp):
TTTTTTGCTGTTTTGATTGTTTTTTTACTGTTTTGGTGATTTTTTTACTGT
Found at i:904453 original size:29 final size:29
Alignment explanation
Indices: 904430--904495 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
904420 TTTAATTTTT
904430 TGCCACGTTAGCATTATTTTTTAAATTGA
1 TGCCACGTTAGCATTATTTTTTAAATTGA
*
904459 TGTCACGTTAGCATTATTTTTTAAATTGA
1 TGCCACGTTAGCATTATTTTTTAAATTGA
904488 TGCCACGT
1 TGCCACGT
904496 CATTCGATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (29 bp):
TGCCACGTTAGCATTATTTTTTAAATTGA
Found at i:907414 original size:167 final size:167
Alignment explanation
Indices: 907138--907473 Score: 645
Period size: 167 Copynumber: 2.0 Consensus size: 167
907128 ATGCGATTAG
907138 TTTGGTAAGACAGTTTATGCATGACCCTCGTGAAGCTCATATGTAGGCAGTATTGCGAATTTTGT
1 TTTGGTAAGACAGTTTATGCATGACCCTCGTGAAGCTCATATGTAGGCAGTATTGCGAATTTTGT
907203 ACTATTTGAAGTCTGCACTAGACAAAGGTATTCTTTTCTCAAGATAGAAGTATTTACAGATGCAA
66 ACTATTTGAAGTCTGCACTAGACAAAGGTATTCTTTTCTCAAGATAGAAGTATTTACAGATGCAA
907268 ATTGGCCTGACTCTCTTGAGGGAGGAAATTTAGTCAC
131 ATTGGCCTGACTCTCTTGAGGGAGGAAATTTAGTCAC
*
907305 TTTGGTAAGACAGTTTATGCATGATCCTCGTGAAGCTCATATGTAGGCAGTATTGCGAATTTTGT
1 TTTGGTAAGACAGTTTATGCATGACCCTCGTGAAGCTCATATGTAGGCAGTATTGCGAATTTTGT
* *
907370 ACTATTTGAAGTCTGCACTGGACAAAGGTGTTCTTTTCTCAAGATAGAAGTATTTACAGATGCAA
66 ACTATTTGAAGTCTGCACTAGACAAAGGTATTCTTTTCTCAAGATAGAAGTATTTACAGATGCAA
907435 ATTGGCCTGACTCTCTTGAGGGAGGAAATTTAGTCAC
131 ATTGGCCTGACTCTCTTGAGGGAGGAAATTTAGTCAC
907472 TT
1 TT
907474 GGAGGAGTAA
Statistics
Matches: 166, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 166 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (167 bp):
TTTGGTAAGACAGTTTATGCATGACCCTCGTGAAGCTCATATGTAGGCAGTATTGCGAATTTTGT
ACTATTTGAAGTCTGCACTAGACAAAGGTATTCTTTTCTCAAGATAGAAGTATTTACAGATGCAA
ATTGGCCTGACTCTCTTGAGGGAGGAAATTTAGTCAC
Found at i:916245 original size:30 final size:27
Alignment explanation
Indices: 916218--916428 Score: 154
Period size: 30 Copynumber: 7.1 Consensus size: 27
916208 TTTTTTGATT
916218 CCCAAAGTTTTCAAAAATTCAAATTTGA
1 CCCAAA-TTTTCAAAAATTCAAATTTGA
* *
916246 CTCTAAAAATTTTTAAAAATTCAAAATTTG-
1 C-C--CAAATTTTCAAAAATTC-AAATTTGA
916276 CCCTTAAATTTTCTAAAAATTCAAATTTGA
1 CCC--AAATTTTC-AAAAATTCAAATTTGA
*
916306 CCCTCAAATTTTTCAAAAATTCAAATTTCAA
1 -CC-CAAA-TTTTCAAAAATTCAAATTT-GA
* *
916337 CCTTAAATTTTCCAAAAATTTAAATTTGA
1 CC-CAAATTTT-CAAAAATTCAAATTTGA
* *
916366 CCCTTAAATTTTTCAAAAGTTCAAATTTAA
1 CCC--AAA-TTTTCAAAAATTCAAATTTGA
* *
916396 CCCTTAAAGTTTTTAAAAATTAAAATTTGA
1 CCC--AAA-TTTTCAAAAATTCAAATTTGA
916426 CCC
1 CCC
916429 CGTTTTAATG
Statistics
Matches: 150, Mismatches: 17, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.01
29 23 0.15
30 103 0.69
31 22 0.15
32 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (27 bp):
CCCAAATTTTCAAAAATTCAAATTTGA
Found at i:916296 original size:60 final size:58
Alignment explanation
Indices: 916225--916428 Score: 252
Period size: 60 Copynumber: 3.4 Consensus size: 58
916215 ATTCCCAAAG
*
916225 TTTTC-AAAAATTCAAATTTGACTCTAAAAATTTTT-AAAAATTCAAAATTTGCCCTTAAA
1 TTTTCTAAAAATTCAAATTTGACCCT-AAAATTTTTCAAAAATTC-AAATTT-CCCTTAAA
*
916284 TTTTCTAAAAATTCAAATTTGACCCTCAAATTTTTCAAAAATTCAAATTTCAACCTTAAA
1 TTTTCTAAAAATTCAAATTTGACCCTAAAATTTTTCAAAAATTCAAATTTC--CCTTAAA
* * * *
916344 TTTTCCAAAAATTTAAATTTGACCCTTAAATTTTTCAAAAGTTCAAATTTAACCCTTAAA
1 TTTTCTAAAAATTCAAATTTGACCCTAAAATTTTTCAAAAATTCAAATTT--CCCTTAAA
*
916404 GTTTT-TAAAAATTAAAATTTGACCC
1 -TTTTCTAAAAATTCAAATTTGACCC
916429 CGTTTTAATG
Statistics
Matches: 130, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
58 1 0.01
59 19 0.15
60 105 0.81
61 4 0.03
62 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (58 bp):
TTTTCTAAAAATTCAAATTTGACCCTAAAATTTTTCAAAAATTCAAATTTCCCTTAAA
Found at i:916305 original size:90 final size:88
Alignment explanation
Indices: 916218--916427 Score: 239
Period size: 90 Copynumber: 2.3 Consensus size: 88
916208 TTTTTTGATT
*
916218 CCCAAAGTTTTCAAAAATTCAAATTTGACTCTAAAAATTTT-TAAAAATTCAAAATTTG-CCCTT
1 CCCAAAGTTTTCAAAAATTCAAATTTGAC-CT-AAAATTTTCCAAAAATT-AAAATTTGACCCTT
*
916281 AAA-TTTTCTAAAAATTCAAATTTGAC
63 AAATTTTTC-AAAAATTCAAATTTGAA
* * * *
916307 CCTCAAATTTTTCAAAAATTCAAATTTCAACCTTAAATTTTCCAAAAATTTAAATTTGACCCTTA
1 CC-CAAAGTTTTCAAAAATTCAAATTT-GACCTAAAATTTTCCAAAAATTAAAATTTGACCCTTA
*
916372 AATTTTTCAAAAGTTCAAATTT-AA
64 AATTTTTCAAAAATTCAAATTTGAA
* *
916396 CCCTTAAAGTTTTTAAAAATTAAAATTTGACC
1 CCC--AAAGTTTTCAAAAATTCAAATTTGACC
916428 CCGTTTTAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
88 1 0.01
89 22 0.21
90 73 0.71
91 7 0.07
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (88 bp):
CCCAAAGTTTTCAAAAATTCAAATTTGACCTAAAATTTTCCAAAAATTAAAATTTGACCCTTAAA
TTTTTCAAAAATTCAAATTTGAA
Found at i:927249 original size:40 final size:39
Alignment explanation
Indices: 927205--927391 Score: 134
Period size: 40 Copynumber: 4.7 Consensus size: 39
927195 ACCAGAGTAT
* *
927205 AGATTGAAGACCATCCGATCTCCTACCTCGATCATGAGGC
1 AGATTGAAGACCATCCAATCTCTTACC-CGATCATGAGGC
* * *
927245 AGATTGAAAACCATCCAATCTCTTACCCTAACCA-GAGGGC
1 AGATTGAAGACCATCCAATCTCTTACCC-GATCATGA-GGC
* * * *
927285 AAATTGAAGACCATCCTATCTTTTACCCCGATCATG-GGAT
1 AGATTGAAGACCATCCAATCTCTTA-CCCGATCATGAGG-C
* * *
927325 AGATTGAAGA-AATCCAATCAT-TTACCCTAATCA-AAGGGC
1 AGATTGAAGACCATCCAATC-TCTTACCC-GATCATGA-GGC
*
927364 AGATTGAAGACTAT-CAGATCTCTTACCC
1 AGATTGAAGACCATCCA-ATCTCTTACCC
927392 CGACTGTGGA
Statistics
Matches: 116, Mismatches: 19, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
38 3 0.03
39 32 0.28
40 77 0.66
41 4 0.03
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (39 bp):
AGATTGAAGACCATCCAATCTCTTACCCGATCATGAGGC
Found at i:927317 original size:80 final size:78
Alignment explanation
Indices: 927180--927411 Score: 247
Period size: 79 Copynumber: 2.9 Consensus size: 78
927170 TTACAACCTT
*** * *
927180 CAATCTTTTACCCTAACCAGAGTATAGATTGAAGACCATCCGATCTCCTACCTCGATCATGAGG-
1 CAATC-TTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATG-GGA
927244 CAGATTGAA-AACCATC
64 CAGATTGAAGAA--ATC
* * * *
927260 CAATCTCTTACCCTAACCAGAGGGCAAATTGAAGACCATCCTATCTTTTACCCCGATCATGGGAT
1 CAATCT-TTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGAC
927325 AGATTGAAGAAATC
65 AGATTGAAGAAATC
* * * *
927339 CAATCATTTACCCTAATCAAAGGGCAGATTGAAGACTATCAGATCTCTTACCCCGA-C-TGTGGA
1 CAATC-TTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATG-GGA
927402 GCAGATTGAA
64 -CAGATTGAA
927412 ACAAGCCAAT
Statistics
Matches: 129, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
77 2 0.02
78 4 0.03
79 61 0.47
80 60 0.47
81 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (78 bp):
CAATCTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGGGACA
GATTGAAGAAATC
Found at i:927372 original size:79 final size:79
Alignment explanation
Indices: 927180--927394 Score: 238
Period size: 80 Copynumber: 2.7 Consensus size: 79
927170 TTACAACCTT
* * *** * *
927180 CAATCTTTTACCCTAACCAGAGTATAGATTGAAGACCATCCGATCTCCTACCTCGATCATGAGGC
1 CAATCTCTTACCCTAACCAAAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGAGGC
927245 AGATTGAAAACCATC
66 AGATTGAAAA-CATC
* * * *
927260 CAATCTCTTACCCTAACCAGAGGGCAAATTGAAGACCATCCTATCTTTTACCCCGATCATG-GGA
1 CAATCTCTTACCCTAACCAAAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGAGG-
*
927324 TAGATTGAAGAA-ATC
65 CAGATTGAA-AACATC
* * *
927339 CAATCAT-TTACCCTAATCAAAGGGCAGATTGAAGACTATCAGATCTCTTACCCCGA
1 CAATC-TCTTACCCTAACCAAAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGA
927395 CTGTGGAGCA
Statistics
Matches: 115, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
79 52 0.45
80 61 0.53
81 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (79 bp):
CAATCTCTTACCCTAACCAAAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGATCATGAGGC
AGATTGAAAACATC
Found at i:927885 original size:11 final size:12
Alignment explanation
Indices: 927861--927890 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
927851 CAATCCAAAT
927861 TTTATTATTTTA
1 TTTATTATTTTA
927873 TTTATTA-TTTA
1 TTTATTATTTTA
927884 TTTATTA
1 TTTATTA
927891 AATAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:929145 original size:60 final size:59
Alignment explanation
Indices: 929073--929340 Score: 321
Period size: 60 Copynumber: 4.5 Consensus size: 59
929063 TTTGATCCCC
* *
929073 AAAGTTTTCAAAAATTCAAATTTTACCCTCAAATTTTTCAAAAATTCAAAATTT-GCCCTT
1 AAAGTTTTCAAAAATTCAAATTTGACCC-CAAATTTTTCAAAAATTC-AAATTTAACCCTT
*
929133 AAA-TTTTCCAAAAATTCAAATTTGACCCCCAATTTTTCCAAAAATTCAAATTTAATCCC-T
1 AAAGTTTT-CAAAAATTCAAATTTGACCCCAAATTTTT-CAAAAATTCAAATTTAA-CCCTT
* * * * * *
929193 AAAGTTTTCAAAAAATCAAATCTGACCCTTAAATTTTCCTAAAATTCAAATTTCACCCTT
1 AAAGTTTTCAAAAATTCAAATTTGACCC-CAAATTTTTCAAAAATTCAAATTTAACCCTT
* *
929253 AAA--TTTCTAAAAATTCAAATTTAACCCCTAAATTTTTCAAAAGTTCAAATTTAACCCTT
1 AAAGTTTTC-AAAAATTCAAATTTGACCCC-AAATTTTTCAAAAATTCAAATTTAACCCTT
*
929312 AAAGTTTTCAAAAATTAAAATTTGACCCC
1 AAAGTTTTCAAAAATTCAAATTTGACCCC
929341 GTTTTAATGT
Statistics
Matches: 177, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
58 4 0.02
59 66 0.37
60 90 0.51
61 17 0.10
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (59 bp):
AAAGTTTTCAAAAATTCAAATTTGACCCCAAATTTTTCAAAAATTCAAATTTAACCCTT
Found at i:929301 original size:89 final size:88
Alignment explanation
Indices: 929078--929340 Score: 334
Period size: 89 Copynumber: 2.9 Consensus size: 88
929068 TCCCCAAAGT
*
929078 TTTCAAAAATTCAAATTTTACCCTCAAATTTTTCAAAAATTCAAAATTTG-CCCTTAAATTTTCC
1 TTTCAAAAATTCAAATTTAACCCT-AAATTTTTCAAAAATTC-AAATTTGACCCTTAAATTTTCC
*
929142 AAAAATTCAAATTTGACCCCCAATT
64 AAAAATTCAAATTTGACCCCCAATA
* * *
929167 TTTCCAAAAATTCAAATTTAATCCCTAAAGTTTTCAAAAAATCAAATCTGACCCTTAAATTTTCC
1 TTT-CAAAAATTCAAATTTAA-CCCTAAATTTTTCAAAAATTCAAATTTGACCCTTAAATTTTCC
* * **
929232 TAAAATTCAAATTTCACCCTTAA-A
64 AAAAATTCAAATTTGACCCCCAATA
* *
929256 TTTCTAAAAATTCAAATTTAACCCCTAAATTTTTCAAAAGTTCAAATTTAACCCTTAAAGTTTT-
1 TTTC-AAAAATTCAAATTTAA-CCCTAAATTTTTCAAAAATTCAAATTTGACCCTTAAA-TTTTC
*
929320 CAAAAATTAAAATTTGACCCC
63 CAAAAATTCAAATTTGACCCC
929341 GTTTTAATGT
Statistics
Matches: 150, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
88 1 0.01
89 77 0.51
90 68 0.45
91 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.36
Consensus pattern (88 bp):
TTTCAAAAATTCAAATTTAACCCTAAATTTTTCAAAAATTCAAATTTGACCCTTAAATTTTCCAA
AAATTCAAATTTGACCCCCAATA
Found at i:929333 original size:30 final size:29
Alignment explanation
Indices: 929077--929339 Score: 271
Period size: 30 Copynumber: 8.8 Consensus size: 29
929067 ATCCCCAAAG
* *
929077 TTTTCAAAAATTCAAATTTTACCCTCAAA
1 TTTTCAAAAATTCAAATTTAACCCTTAAA
*
929106 TTTTTCAAAAATTCAAAATTT-GCCCTTAAA
1 -TTTTCAAAAATTC-AAATTTAACCCTTAAA
* ** *
929136 TTTTCCAAAAATTCAAATTTGACCCCCAAT
1 TTTT-CAAAAATTCAAATTTAACCCTTAAA
929166 TTTTCCAAAAATTCAAATTTAATCCC-TAAA
1 TTTT-CAAAAATTCAAATTTAA-CCCTTAAA
* * *
929196 GTTTTCAAAAAATCAAATCTGACCCTTAAA
1 -TTTTCAAAAATTCAAATTTAACCCTTAAA
* *
929226 TTTTCCTAAAATTCAAATTTCACCCTTAAA
1 TTTT-CAAAAATTCAAATTTAACCCTTAAA
*
929256 -TTTCTAAAAATTCAAATTTAACCCCTAAA
1 TTTTC-AAAAATTCAAATTTAACCCTTAAA
*
929285 TTTTTCAAAAGTTCAAATTTAACCCTTAAA
1 -TTTTCAAAAATTCAAATTTAACCCTTAAA
* *
929315 GTTTTCAAAAATTAAAATTTGACCC
1 -TTTTCAAAAATTCAAATTTAACCC
929340 CGTTTTAATG
Statistics
Matches: 198, Mismatches: 25, Indels: 20
0.81 0.10 0.08
Matches are distributed among these distances:
28 1 0.01
29 41 0.21
30 139 0.70
31 17 0.09
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTCAAAAATTCAAATTTAACCCTTAAA
Found at i:929365 original size:119 final size:118
Alignment explanation
Indices: 929113--929339 Score: 300
Period size: 119 Copynumber: 1.9 Consensus size: 118
929103 AAATTTTTCA
* * *
929113 AAAATTCAAAATTT-GCCCTTAAATTTTCCAAAAATTCAAATTTGACCCCCAATTTTTCCAAAAA
1 AAAATTC-AAATTTCACCCTTAAATTTTCCAAAAATTCAAATTTAACCCCAAATTTTTCCAAAAA
* *
929177 TTCAAATTTAATCCCTAAAGTTTTCAAAAAATCAAATCTGACCCTTAAATTTTCCT
65 TTCAAATTTAATCCCTAAAGTTTTCAAAAAATAAAATCTGACCCTT--ATTATCCT
* *
929233 AAAATTCAAATTTCACCCTTAAA-TTTCTAAAAATTCAAATTTAACCCCTAAATTTTT-CAAAAG
1 AAAATTCAAATTTCACCCTTAAATTTTCCAAAAATTCAAATTTAACCCC-AAATTTTTCCAAAAA
* *
929296 TTCAAATTTAA-CCCTTAAAGTTTTCAAAAATTAAAATTTGACCC
65 TTCAAATTTAATCCC-TAAAGTTTTCAAAAAATAAAATCTGACCC
929340 CGTTTTAATG
Statistics
Matches: 96, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
118 3 0.03
119 71 0.74
120 22 0.23
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.35
Consensus pattern (118 bp):
AAAATTCAAATTTCACCCTTAAATTTTCCAAAAATTCAAATTTAACCCCAAATTTTTCCAAAAAT
TCAAATTTAATCCCTAAAGTTTTCAAAAAATAAAATCTGACCCTTATTATCCT
Found at i:931688 original size:23 final size:21
Alignment explanation
Indices: 931637--931688 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
931627 TTATCTAATT
* * *
931637 TATTTAAATATTTTTAAGATT
1 TATTTTAATATTTTGAAGATA
931658 TATTTTAATAGTTTTGAATGATA
1 TATTTTAATA-TTTTGAA-GATA
931681 TATTTTAA
1 TATTTTAA
931689 ACAACTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 6 0.23
23 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56
Consensus pattern (21 bp):
TATTTTAATATTTTGAAGATA
Found at i:932424 original size:20 final size:20
Alignment explanation
Indices: 932371--932427 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
932361 GGCCGTCGTT
*
932371 CCTTGCCACGTCAACACCGA
1 CCTTGCCACGTCAGCACCGA
*
932391 CCTTGCCACGTCAGCATCGA
1 CCTTGCCACGTCAGCACCGA
*
932411 CCTTGCCACATCAGCAC
1 CCTTGCCACGTCAGCAC
932428 ATGAGGACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.44, G:0.16, T:0.18
Consensus pattern (20 bp):
CCTTGCCACGTCAGCACCGA
Found at i:933427 original size:13 final size:12
Alignment explanation
Indices: 933386--933441 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
933376 GACTTACATT
*
933386 TTTTTAATTTAA
1 TTTTTAATTTTA
*
933398 TCCTTT-ATTATTA
1 T-TTTTAATT-TTA
933411 TTTTTAATTTATA
1 TTTTTAATTT-TA
*
933424 TTTTAAATTTTA
1 TTTTTAATTTTA
933436 TTTTTA
1 TTTTTA
933442 TGTCAATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 15 0.43
13 20 0.57
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAATTTTA
Found at i:938475 original size:5 final size:5
Alignment explanation
Indices: 938467--938561 Score: 63
Period size: 5 Copynumber: 18.8 Consensus size: 5
938457 AATAAGATAA
* ** * *
938467 AAAAG AAAAG AAAAG AATAG AATGG AAAAA AAAAG AAAA- AAGAG AAAA-
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
*
938515 AAGAA- AAAAG AAAA- AAGAGAA AAAAG AAAAG AAAAAG AAAAAG AAAA
1 AA-AAG AAAAG AAAAG AA-A-AG AAAAG AAAAG -AAAAG -AAAAG AAAA
938562 AGGAGTGGTC
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
4 9 0.12
5 50 0.68
6 13 0.18
7 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:938480 original size:23 final size:22
Alignment explanation
Indices: 938454--938550 Score: 99
Period size: 23 Copynumber: 4.2 Consensus size: 22
938444 AAATTTCACC
*
938454 AAAAATAAGATAAAAAAGAAAAG
1 AAAAA-AAGAGAAAAAAGAAAAG
*
938477 AAAAGAATAGAATGGAAAAA-AAAAG
1 AAAA-AA-AG-A-GAAAAAAGAAAAG
*
938502 -AAAAAAGAGAAAAAAGAAAAA
1 AAAAAAAGAGAAAAAAGAAAAG
938523 AGAAAAAAGAGAAAAAAGAAAAG
1 A-AAAAAAGAGAAAAAAGAAAAG
938546 AAAAA
1 AAAAA
938551 GAAAAAGAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.10
21 5 0.08
22 6 0.10
23 28 0.45
24 6 0.10
25 6 0.10
26 5 0.08
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAAAAGAGAAAAAAGAAAAG
Found at i:938507 original size:7 final size:7
Alignment explanation
Indices: 938495--938562 Score: 79
Period size: 7 Copynumber: 9.7 Consensus size: 7
938485 AGAATGGAAA
938495 AAAAAAG
1 AAAAAAG
938502 AAAAAAGAG
1 -AAAAA-AG
938511 AAAAAAG
1 AAAAAAG
938518 AAAAAAG
1 AAAAAAG
938525 AAAAAAG
1 AAAAAAG
938532 AGAAAAA-
1 A-AAAAAG
*
938539 AGAAAAG
1 AAAAAAG
938546 -AAAAAG
1 AAAAAAG
938552 -AAAAAG
1 AAAAAAG
938558 AAAAA
1 AAAAA
938563 GGAGTGGTCG
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
6 15 0.28
7 22 0.41
8 15 0.28
9 2 0.04
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:938507 original size:9 final size:9
Alignment explanation
Indices: 938454--938556 Score: 70
Period size: 9 Copynumber: 11.6 Consensus size: 9
938444 AAATTTCACC
*
938454 AAAAATAAG
1 AAAAAAAAG
*
938463 ATAAAAAAG
1 AAAAAAAAG
938472 AAAAGAAAAG
1 AAAA-AAAAG
* **
938482 AATAGAATGG
1 AA-AAAAAAG
938492 AAAAAAAA-
1 AAAAAAAAG
*
938500 AGAAAAAAG
1 AAAAAAAAG
*
938509 AGAAAAAAG
1 AAAAAAAAG
938518 --AAAAAAG
1 AAAAAAAAG
*
938525 AAAAAAGAG
1 AAAAAAAAG
938534 AAAAAAGAA-
1 AAAAAA-AAG
*
938543 AAGAAAAAG
1 AAAAAAAAG
938552 AAAAA
1 AAAAA
938557 GAAAAAGGAG
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
7 7 0.10
8 9 0.12
9 43 0.59
10 13 0.18
11 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.04
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:938514 original size:16 final size:15
Alignment explanation
Indices: 938494--938562 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 15
938484 TAGAATGGAA
938494 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
938509 AGAAAAAAGAAAAAAG
1 A-AAAAAAGAAAAAAG
938525 AAAAAAGAGAAAAAAG
1 AAAAAA-AGAAAAAAG
*
938541 AAAAGAAAAAGAAAAAG
1 AAAA-AAAGA-AAAAAG
938558 AAAAA
1 AAAAA
938563 GGAGTGGTCG
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
15 6 0.12
16 31 0.63
17 12 0.24
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:938561 original size:23 final size:22
Alignment explanation
Indices: 938466--938563 Score: 76
Period size: 23 Copynumber: 4.3 Consensus size: 22
938456 AAATAAGATA
*
938466 AAAAAGAAAAGAAAAGAATAGAATGG
1 AAAAAGAAAAGAAAA-AA-A-AA-AG
* *
938492 AAAAA-AAAAGAAAAAAGAGA-
1 AAAAAGAAAAGAAAAAAAAAAG
*
938512 AAAAAGAAAA-AAGAAAAAAGAG
1 AAAAAGAAAAGAA-AAAAAAAAG
938534 AAAAAAGAAAAGAAAAAGAAAAAG
1 -AAAAAGAAAAGAAAAA-AAAAAG
938558 AAAAAG
1 AAAAAG
938564 GAGTGGTCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.11
21 11 0.18
22 1 0.02
23 19 0.31
24 9 0.15
25 9 0.15
26 5 0.08
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAAAAAAAG
Found at i:939627 original size:50 final size:49
Alignment explanation
Indices: 939573--939806 Score: 138
Period size: 50 Copynumber: 4.7 Consensus size: 49
939563 TAGAGCAAGA
*
939573 TGAAGCTACAACACCAAATCCTACACCTTTGAAGTTGTAGTGGGTCAGAT
1 TGAAGCTACAACACCAAATCATACACC-TTGAAGTTGTAGTGGGTCAGAT
* * * * * * *
939623 TGAAGCTATAGA-AGCAAATCTTTATCTCCCT-AAGGTTGCAATGGAG-CAAGA-
1 TGAAGCTACA-ACACCAAATC-ATA-CACCTTGAA-GTTGTAGTGG-GTC-AGAT
* *
939674 TGAAGCTACAACATCAAATCATATACCCTTGAAGTTGTAGTGGGTCAGAT
1 TGAAGCTACAACACCAAATCATACA-CCTTGAAGTTGTAGTGGGTCAGAT
* ** * * * *
939724 TGAAGCTACAAAAGTAAATCTTATCTCCTTGAAGATGAAGTGAGG-CAGGA-
1 TGAAGCTACAACACCAAATCATA-CACCTTGAAGTTGTAGTG-GGTCA-GAT
* * *
939774 TAAAGTTACAACACCAAATCATATATCCTTGAA
1 TGAAGCTACAACACCAAATCATACA-CCTTGAA
939807 TTTATAGTTG
Statistics
Matches: 138, Mismatches: 31, Indels: 30
0.69 0.16 0.15
Matches are distributed among these distances:
49 4 0.03
50 92 0.67
51 35 0.25
52 7 0.05
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (49 bp):
TGAAGCTACAACACCAAATCATACACCTTGAAGTTGTAGTGGGTCAGAT
Found at i:939676 original size:101 final size:101
Alignment explanation
Indices: 939534--939806 Score: 327
Period size: 101 Copynumber: 2.7 Consensus size: 101
939524 AAATTACAGT
* * * *
939534 AGCAAATCTTTATCTCTCTAAAGTTGTAGTAGAGCAAGATGAAGCTACAACACCAAATCCTACAC
1 AGCAAATCTTTATCTCCCTAAAGTTGCAATAGAGCAAGATGAAGCTACAACACCAAATCATACAC
* * *
939599 CTTTGAAGTTGTAGTGGGTCAGATTGAAGCTATAGA
66 CCTTGAAGTTGTAGTGGGTCAGATTGAAGCTACAAA
* * * *
939635 AGCAAATCTTTATCTCCCTAAGGTTGCAATGGAGCAAGATGAAGCTACAACATCAAATCATATAC
1 AGCAAATCTTTATCTCCCTAAAGTTGCAATAGAGCAAGATGAAGCTACAACACCAAATCATACAC
939700 CCTTGAAGTTGTAGTGGGTCAGATTGAAGCTACAAA
66 CCTTGAAGTTGTAGTGGGTCAGATTGAAGCTACAAA
* * * * * * * *
939736 AGTAAATC-TTATCTCCTTGAAGATG-AAGT-GAGGCAGGATAAAGTTACAACACCAAATCATAT
1 AGCAAATCTTTATCTCCCTAAAGTTGCAA-TAGA-GCAAGATGAAGCTACAACACCAAATCATAC
*
939798 ATCCTTGAA
64 ACCCTTGAA
939807 TTTATAGTTG
Statistics
Matches: 149, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
99 4 0.03
100 48 0.32
101 97 0.65
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (101 bp):
AGCAAATCTTTATCTCCCTAAAGTTGCAATAGAGCAAGATGAAGCTACAACACCAAATCATACAC
CCTTGAAGTTGTAGTGGGTCAGATTGAAGCTACAAA
Found at i:940887 original size:43 final size:42
Alignment explanation
Indices: 940817--940936 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 42
940807 TTATCTTAGT
* *
940817 CATAAGTTCTTCCATTTACAAGTAATCTTATGCTCTAACCGAGA
1 CATAAGTT-TTCCATTTA-AAATAATCTTATGCTCTAACCAAGA
* *
940861 CATAAGTTTTCCATTTATAAACAATCTTATGCTCTAGCCAAGA
1 CATAAGTTTTCCATTTA-AAATAATCTTATGCTCTAACCAAGA
* *
940904 CATAAGTCTTCC-TTTAAACATAATCTCATGCTC
1 CATAAGTTTTCCATTTAAA-ATAATCTTATGCTC
940937 ATCCCGAGTC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.03
42 16 0.24
43 41 0.61
44 8 0.12
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (42 bp):
CATAAGTTTTCCATTTAAAATAATCTTATGCTCTAACCAAGA
Found at i:940954 original size:42 final size:42
Alignment explanation
Indices: 940901--941219 Score: 458
Period size: 42 Copynumber: 7.6 Consensus size: 42
940891 GCTCTAGCCA
*
940901 AGACATAAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
1 AGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
* * * * *
940943 AGTCACGAGTCTTCCTTTAAATATAATCTCATACTCATCCTG
1 AGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
* * *
940985 AGACATGAGTCTTCCTTTAAACCTAATCTCATGATCATCTCG
1 AGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
** **
941027 AGACATGAGTCTTCCTTTAAATGTAATCTCATGCTGTTCCCG
1 AGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
* *
941069 AGATATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCTG
1 AGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
*
941111 AGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
1 AGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
* *
941153 AGACATGAGTCTTCCTTTAAACATAATCTTATGCTCATCCTG
1 AGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
*
941195 AGACATGAGTCTTCCATTTATACAT
1 AGACATGAGTCTTCC-TTTAAACAT
941220 CAAGTGATTC
Statistics
Matches: 243, Mismatches: 33, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
42 235 0.97
43 8 0.03
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.34
Consensus pattern (42 bp):
AGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATCCCG
Found at i:942437 original size:42 final size:42
Alignment explanation
Indices: 942381--942643 Score: 282
Period size: 42 Copynumber: 6.5 Consensus size: 42
942371 TATACTCTAA
* * * * *
942381 CGAGTCATAAGTCTTCCTTTAATCGA-ATTTTTATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATC-ATAATCTCATTCTCATCT
942423 CGAGACATGAGTCTTCCTTTAATCATAATCTCA---T--TCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
942460 -----CATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
942497 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
* *
942539 AGAGACATGAGTCTTCCTTTAATCATAATCTCCTTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
* * * * *
942581 CAAGACATGAGTCTTTCATTT-ATACA-AATCCTCATGCTCAACC
1 CGAGACATGAGTC-TTCCTTTAAT-CATAAT-CTCATTCTCATCT
*
942624 CGAGACACGAGTCTTCCTTT
1 CGAGACATGAGTCTTCCTTT
942644 TTATACATCA
Statistics
Matches: 190, Mismatches: 17, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
32 28 0.15
35 1 0.01
37 6 0.03
39 1 0.01
41 1 0.01
42 125 0.66
43 28 0.15
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCT
Found at i:942465 original size:32 final size:32
Alignment explanation
Indices: 942428--942494 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
942418 CATCTCGAGA
942428 CATGAGTCTTCCTTTAATCATAATCTCATTCT
1 CATGAGTCTTCCTTTAATCATAATCTCATTCT
942460 CATGAGTCTTCCTTTAATCATAATCTCATTCT
1 CATGAGTCTTCCTTTAATCATAATCTCATTCT
942492 CAT
1 CAT
942495 CTCGAGACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.43
Consensus pattern (32 bp):
CATGAGTCTTCCTTTAATCATAATCTCATTCT
Found at i:942511 original size:74 final size:76
Alignment explanation
Indices: 942385--942595 Score: 266
Period size: 74 Copynumber: 2.7 Consensus size: 76
942375 CTCTAACGAG
* * * *
942385 TCATAAGTCTTCCTTTAATCGA-ATTTTTATTCTCATCTCGAGACATGAGTCTTCCTTTAATCAT
1 TCATGAGTCTTCCTTTAATC-ATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTTAATCAT
942449 AATCTCA-T-TC
65 AATCTCATTATC
942459 TCATGAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTTAATCATA
1 TCATGAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTTAATCATA
942524 ATCTCATTCTCATC
66 ATCTCA-T-T-ATC
* *
942538 TAGAGACATGAGTCTTCCTTTAATCATAATCTCCTTCTCATCTCAAGACATGAGTCTT
1 T-----CATGAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATGAGTCTT
942596 TCATTTATAC
Statistics
Matches: 120, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
73 1 0.01
74 65 0.54
77 1 0.01
79 3 0.03
84 50 0.42
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (76 bp):
TCATGAGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTTAATCATA
ATCTCATTATC
Found at i:945982 original size:20 final size:20
Alignment explanation
Indices: 945957--946011 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
945947 GATTGTCGTT
945957 CCTTGCCACGCCACCACTGG
1 CCTTGCCACGCCACCACTGG
* *
945977 CCTTGCCACGTCAGCACTGG
1 CCTTGCCACGCCACCACTGG
*
945997 CCTCGCCACGTCCAC
1 CCTTGCCACG-CCAC
946012 ATACGAGGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.15, C:0.49, G:0.20, T:0.16
Consensus pattern (20 bp):
CCTTGCCACGCCACCACTGG
Found at i:947090 original size:13 final size:12
Alignment explanation
Indices: 947074--947107 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
947064 TATGCACCCC
947074 TTTTATTTTATAT
1 TTTTATTTTAT-T
947087 TTTTATTTTATT
1 TTTTATTTTATT
947099 TATTTATTT
1 T-TTTATTT
947108 CATGCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:957595 original size:37 final size:39
Alignment explanation
Indices: 957510--957599 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 39
957500 TTAACCATAT
* *
957510 TCTCATTCTCATCTTGAGACATGAGTCTTCCTTAGTCAAAA
1 TCTCATTCTCATCTCGAGACATGAG--TTCCTTAATCAAAA
957551 TCTCATTCTCATCTCGAGACATGAG-T-CTTAATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTTCCTTAATCAAAA
957588 TCTCATTCTCAT
1 TCTCATTCTCAT
957600 TTTGAGTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
37 22 0.47
38 1 0.02
41 24 0.51
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.37
Consensus pattern (39 bp):
TCTCATTCTCATCTCGAGACATGAGTTCCTTAATCAAAA
Found at i:960383 original size:20 final size:19
Alignment explanation
Indices: 960358--960414 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
960348 GTGCCAGGCA
960358 GTGTGACAGGGCACACATCC
1 GTGTGACAGGG-ACACATCC
960378 GTGTGACTGAGGGACACATCC
1 GTGTGAC--AGGGACACATCC
*
960399 ATGTGACAGGGGACAC
1 GTGTGACA-GGGACAC
960415 GCCTGTGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.03
20 14 0.42
21 14 0.42
22 4 0.12
ACGTcount: A:0.26, C:0.25, G:0.33, T:0.16
Consensus pattern (19 bp):
GTGTGACAGGGACACATCC
Found at i:960687 original size:10 final size:11
Alignment explanation
Indices: 960659--960684 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
960649 CATGTGGTCT
960659 AAAAACCACCC
1 AAAAACCACCC
960670 AAAAACCACCC
1 AAAAACCACCC
960681 AAAA
1 AAAA
960685 CCATAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACCACCC
Found at i:962823 original size:15 final size:16
Alignment explanation
Indices: 962791--962824 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
962781 TTTTCATCTC
962791 ATTTACATTTACGTTA
1 ATTTACATTTACGTTA
*
962807 ATTTGCATTTA-GTTA
1 ATTTACATTTACGTTA
962822 ATT
1 ATT
962825 ACTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (16 bp):
ATTTACATTTACGTTA
Found at i:979356 original size:69 final size:70
Alignment explanation
Indices: 979276--979407 Score: 203
Period size: 69 Copynumber: 1.9 Consensus size: 70
979266 ACTTGAATAG
*
979276 GACAACACTTAATTCAACCAAATTGGTCGTAAAATTTTCAGCATTTGACAGCAT-GTAAAACCTC
1 GACAACACTTAATTCAACCAAATTGGTCGTAAAATTTTCAACATTTGACAGCATAGTAAAACCTC
979340 AACAA
66 AACAA
* * * * *
979345 GACAACGCTTAATTCAACCAAATTTGTCTTAAAATTTTCAACATTTGATAGCATATTAAAACC
1 GACAACACTTAATTCAACCAAATTGGTCGTAAAATTTTCAACATTTGACAGCATAGTAAAACC
979408 ACATTCGGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
69 49 0.88
70 7 0.12
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (70 bp):
GACAACACTTAATTCAACCAAATTGGTCGTAAAATTTTCAACATTTGACAGCATAGTAAAACCTC
AACAA
Found at i:980525 original size:43 final size:43
Alignment explanation
Indices: 980428--980888 Score: 419
Period size: 43 Copynumber: 10.7 Consensus size: 43
980418 CCAACCTAAT
* * * * * * **
980428 TATACTGGCACAAACATAATGCATCATTGGATATACAGAAGTATG
1 TATACTGGCAC--ACACAGTGCATCATCGGATAAACCGAAGAAAA
* *
980473 TATACTGGCACGA-ACAGTGCATCATCGGATTAATCGAAGAAAA
1 TATACTGGCAC-ACACAGTGCATCATCGGATAAACCGAAGAAAA
** * * *
980516 TATTTTGGCACATACAATGCATCATCGAATAAACCGAAGAAAA
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGAAAA
* * * * *
980559 TATACTGGCACACACAATGCATCATCAGAAAAAGC-AAAAAATA
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGAAA-A
* * * *
980602 TATACTAG--CACACAGTGCATAATCGGAGAAACCGAA-ACAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGA-AAA
* * **
980643 TATACTGGCACACATAGTGAATCATCGGATAAATTGAAGAAAA
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGAAAA
* * * * *
980686 TATATTGGCACACACAGTGCATGATCGGATAAATCGAAGCAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGAAAA
* * * *
980729 TATATTGGCACACTCAGTGCATCATTGGATAAACCGAAAAAAA
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGAAAA
* * ** * *
980772 TATAATGGCACATACAGTGCATCATTAGATAAACCGAAGCAAC
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGAAAA
*
980815 TATACTGGCACACACAGTGCATCATCGGATAAACCAAAGAAAA
1 TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGAAAA
** *
980858 TATACTAACACACATAGTGCATCATCGGATA
1 TATACTGGCACACACAGTGCATCATCGGATA
980889 TACTGAAGTA
Statistics
Matches: 338, Mismatches: 71, Indels: 16
0.80 0.17 0.04
Matches are distributed among these distances:
41 28 0.08
42 10 0.03
43 287 0.85
44 2 0.01
45 11 0.03
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.21
Consensus pattern (43 bp):
TATACTGGCACACACAGTGCATCATCGGATAAACCGAAGAAAA
Found at i:981348 original size:282 final size:283
Alignment explanation
Indices: 980843--981408 Score: 954
Period size: 282 Copynumber: 2.0 Consensus size: 283
980833 GCATCATCGG
* ** * * *
980843 ATAAACCAAAGAAAATATACTAACACACATAGTGCATCATCGGATATACTGAAGTATCTCCTATA
1 ATAAACCAAAGAAAATATACTAACACACACAGTGCATCATCAAAAATACCGAAGTATCTCCTACA
*
980908 CACTTAATACGAAATAAATTTCATTTCCATGTTAAAATTCAATCCACATTCTATCATCTCCATTT
66 CACTTAATACGAAATAAATTTCATTTCCATCTTAAAATTCAATCCACATTCTATCATCTCCATTT
* * *
980973 CACCATGAATTCATTATTAGAGTGCCATATATAACATTTTCTACCAAATTTAACACTAAGTACGA
131 CACCATGAATTCATTATTAAAGTACCATATATAACATTTTCAACCAAATTTAACACTAAGTACGA
981038 CTTATCAATTAAATCATCTTACTTTCTATTTTATTCTATTCAATACCCATAGTCATAATTCAATT
196 CTTATCAATTAAATCATCTTACTTTCTATTTTATTCTATTCAATACCCATAGTCATAATTCAATT
* *
981103 TATGCAATAATTATGAGTAATTT
261 TATACAATAATTATGACTAATTT
* * *
981126 ATAAACCAAAGAAAATATACTAGCACACACAGTGCATCAT-AAAAATACCGAAGTATCTCTTGCA
1 ATAAACCAAAGAAAATATACTAACACACACAGTGCATCATCAAAAATACCGAAGTATCTCCTACA
*
981190 CACTTAATATGAAATAAATTTCATTTCCATCTTAAAATTCAATCCACATTCTATCATCTCCATTT
66 CACTTAATACGAAATAAATTTCATTTCCATCTTAAAATTCAATCCACATTCTATCATCTCCATTT
981255 CACCATGAATTCATTATTAAAGTACCATATATAACATTTTCAACCAAATTTAACACTAAGTACGA
131 CACCATGAATTCATTATTAAAGTACCATATATAACATTTTCAACCAAATTTAACACTAAGTACGA
* * *
981320 CTTATCAATTAAATCATCTTACTTTCTATTTTATTCTATTTAGTACCCATTGTCATAATTCAATT
196 CTTATCAATTAAATCATCTTACTTTCTATTTTATTCTATTCAATACCCATAGTCATAATTCAATT
981385 TATACAATAATTATGACTAATTT
261 TATACAATAATTATGACTAATTT
981408 A
1 A
981409 ATTCATCATC
Statistics
Matches: 264, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
282 226 0.86
283 38 0.14
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.36
Consensus pattern (283 bp):
ATAAACCAAAGAAAATATACTAACACACACAGTGCATCATCAAAAATACCGAAGTATCTCCTACA
CACTTAATACGAAATAAATTTCATTTCCATCTTAAAATTCAATCCACATTCTATCATCTCCATTT
CACCATGAATTCATTATTAAAGTACCATATATAACATTTTCAACCAAATTTAACACTAAGTACGA
CTTATCAATTAAATCATCTTACTTTCTATTTTATTCTATTCAATACCCATAGTCATAATTCAATT
TATACAATAATTATGACTAATTT
Found at i:996386 original size:23 final size:23
Alignment explanation
Indices: 996356--996404 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
996346 TAGCACTAGG
**
996356 TTTTTACACACCATTTTTTAGAC
1 TTTTTACACACCATTTCCTAGAC
996379 TTTTTACACACCATTTCCTAGAC
1 TTTTTACACACCATTTCCTAGAC
996402 TTT
1 TTT
996405 ACTTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTTTACACACCATTTCCTAGAC
Found at i:997002 original size:14 final size:16
Alignment explanation
Indices: 996973--997005 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
996963 ACAACTCAAC
996973 TTTTACTCTATTTTAT
1 TTTTACTCTATTTTAT
996989 TTTTA-TCT-TTTTAT
1 TTTTACTCTATTTTAT
997003 TTT
1 TTT
997006 CATGCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 3 0.18
16 5 0.29
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTACTCTATTTTAT
Found at i:1001412 original size:13 final size:13
Alignment explanation
Indices: 1001394--1001419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1001384 AGAAAAATAG
1001394 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
1001407 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
1001420 TGAGTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:1002760 original size:17 final size:17
Alignment explanation
Indices: 1002724--1002762 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1002714 CCAAGGGACT
* *
1002724 AGACATAGGGAACTCAA
1 AGACTTAGGGAACCCAA
*
1002741 AGACTTAGGGAACCCGA
1 AGACTTAGGGAACCCAA
1002758 AGACT
1 AGACT
1002763 AACTACTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.13
Consensus pattern (17 bp):
AGACTTAGGGAACCCAA
Found at i:1004134 original size:93 final size:95
Alignment explanation
Indices: 1003935--1004136 Score: 318
Period size: 95 Copynumber: 2.1 Consensus size: 95
1003925 TTATAATTAT
* * * *
1003935 TAATTATAATGATTTTGTTAAATATTAAAACAAGGAAGTTAATATCCTTTTGGAAATGATATATA
1 TAATTATAATTATTTCGTTAAATATTAAAACAAGGAAGTTAATATCCTTTTAGAAATGAGATATA
* *
1004000 ATGTTTTAATAAACCTTCCATAATTTAACG
66 ATGTTTTAATAAACCTTCAATAATTTAACA
* *
1004030 TAATTATAATTATTTCGTTAAATATTAAAACATGGAAGTTAATATTCTTTTAGAAA-G-GATATA
1 TAATTATAATTATTTCGTTAAATATTAAAACAAGGAAGTTAATATCCTTTTAGAAATGAGATATA
1004093 ATGTTTTAATAAACCTTCAATAATTTAACA
66 ATGTTTTAATAAACCTTCAATAATTTAACA
1004123 TAATTATAATTATT
1 TAATTATAATTATT
1004137 AGTTATAATA
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
93 47 0.47
94 1 0.01
95 51 0.52
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (95 bp):
TAATTATAATTATTTCGTTAAATATTAAAACAAGGAAGTTAATATCCTTTTAGAAATGAGATATA
ATGTTTTAATAAACCTTCAATAATTTAACA
Found at i:1004157 original size:106 final size:108
Alignment explanation
Indices: 1004033--1004226 Score: 277
Period size: 107 Copynumber: 1.8 Consensus size: 108
1004023 TTTAACGTAA
* * * *
1004033 TTATAATTATTTCGTTAAATATT-AAAACATGGAAGTTAATAT-TCTTTTAGAAAGGATATAATG
1 TTATAATAATTTCCTTAAATATTAAAAACATGAAAGTTAATATCT-TTTTAGAAAAGATATAATG
*
1004096 TTTTAATAAACCTTCAATA-ATTTAACATAATTATAATTATTAG
65 ATTTAATAAACCTTCAATATATTTAACATAATTATAATTATTAG
* *
1004139 TTATAATAATTTCCTTAAATATTAAAAACATGAAAGTTAATATCTTTTTGGAAAATATATAATGA
1 TTATAATAATTTCCTTAAATATTAAAAACATGAAAGTTAATATCTTTTTAGAAAAGATATAATGA
* *
1004204 TTTAATAAATCTTCCATATATTT
66 TTTAATAAACCTTCAATATATTT
1004227 CTTTAAAGGA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
106 21 0.28
107 50 0.66
108 5 0.07
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (108 bp):
TTATAATAATTTCCTTAAATATTAAAAACATGAAAGTTAATATCTTTTTAGAAAAGATATAATGA
TTTAATAAACCTTCAATATATTTAACATAATTATAATTATTAG
Found at i:1004299 original size:123 final size:123
Alignment explanation
Indices: 1004156--1004526 Score: 487
Period size: 123 Copynumber: 3.0 Consensus size: 123
1004146 AATTTCCTTA
* * *
1004156 AATATTAAAAACATGAAAGTTAATATCTTTTTGGAAAATATATAATGATTTAATAAATCTTCCAT
1 AATATTAAAAAGATGGAAGTTAATATCTTTTTGGAAAATATATAATGTTTTAATAAATCTTCCAT
1004221 ATATTTCTTTAAAGGAATATTTTCATTTTAATATGAGATATTATATAAAAGGAAATTG
66 ATATTTCTTTAAAGGAATATTTTCATTTTAATATGAGATATTATATAAAAGGAAATTG
*
1004279 AATATTAAAAAGATGGAAGTTAATAT-TCTTTT-GAAAATAATATAATGTTTTAATAAACCTTCC
1 AATATTAAAAAGATGGAAGTTAATATCT-TTTTGGAAAAT-ATATAATGTTTTAATAAATCTTCC
* * *
1004342 ATATATTTCTTTAAAGGAATATTTCCATTTTAATATGAGATATTATATATAAGGAAGTTG
64 ATATATTTCTTTAAAGGAATATTTTCATTTTAATATGAGATATTATATAAAAGGAAATTG
* * * * ** *
1004402 AATATTAAAAACG-TAGAAGTTAACATCCTTTTGGGAAGGATATAATGTTTTAATAAATCTTTCA
1 AATATTAAAAA-GATGGAAGTTAATATCTTTTTGGAAAATATATAATGTTTTAATAAATCTTCCA
* * * * *
1004466 TATATTTCTCTAAAGATATATATTTTCAATTTAATATGGGATATTAAAAATAAAAGGAAAT
65 TATATTTCTTTAAAG-GA-ATATTTTCATTTTAATATGAGATATT--ATATAAAAGGAAAT
1004527 ATAGCAGAAT
Statistics
Matches: 216, Mismatches: 23, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
122 7 0.03
123 170 0.79
124 5 0.02
125 23 0.11
127 11 0.05
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (123 bp):
AATATTAAAAAGATGGAAGTTAATATCTTTTTGGAAAATATATAATGTTTTAATAAATCTTCCAT
ATATTTCTTTAAAGGAATATTTTCATTTTAATATGAGATATTATATAAAAGGAAATTG
Found at i:1010841 original size:18 final size:19
Alignment explanation
Indices: 1010810--1010847 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1010800 TCTATCAGAA
**
1010810 CAAATGCAGTCAC-ATAGT
1 CAAATGCAACCACAATAGT
1010828 CAAATGCAACCACAATAGT
1 CAAATGCAACCACAATAGT
1010847 C
1 C
1010848 TGTGCTACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.18
Consensus pattern (19 bp):
CAAATGCAACCACAATAGT
Found at i:1018268 original size:16 final size:16
Alignment explanation
Indices: 1018235--1018268 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1018225 TTCATGCCTA
*
1018235 TAAATTGTCGGCGTAT
1 TAAATTGTCGGCGAAT
*
1018251 TAAATTGTCGGTGAAT
1 TAAATTGTCGGCGAAT
1018267 TA
1 TA
1018269 TTCTATCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (16 bp):
TAAATTGTCGGCGAAT
Found at i:1020998 original size:81 final size:81
Alignment explanation
Indices: 1020908--1021057 Score: 282
Period size: 81 Copynumber: 1.9 Consensus size: 81
1020898 ATAAGCCTTA
*
1020908 ACACCACTTAAACTATAATAATTATTCACCTCTTAGACATATTTATTCGATATCAAAAACTATTT
1 ACACCACTTAAACTATAATAATTAATCACCTCTTAGACATATTTATTCGATATCAAAAACTATTT
1020973 TTAACCGTCATTATTT
66 TTAACCGTCATTATTT
*
1020989 ACACCACTTAAACTATAATAATTAATCACCTCTTAGACATATTTATTTGATATCAAAAACTATTT
1 ACACCACTTAAACTATAATAATTAATCACCTCTTAGACATATTTATTCGATATCAAAAACTATTT
1021054 TTAA
66 TTAA
1021058 TAGTGAGTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (81 bp):
ACACCACTTAAACTATAATAATTAATCACCTCTTAGACATATTTATTCGATATCAAAAACTATTT
TTAACCGTCATTATTT
Found at i:1021259 original size:59 final size:55
Alignment explanation
Indices: 1021109--1021259 Score: 144
Period size: 56 Copynumber: 2.6 Consensus size: 55
1021099 ATTTATACAT
* * * *
1021109 CCTTATTGATAGCCTAATTCCAATAATAAATAACAATGGACAGCAACGATTAAACAC
1 CCTT-TTGACAGCTTAATTCCAATAATAAATAACAATGAACAGCAAC-ACTAAACAC
* *
1021166 CCTTTTGACAGCTTAA-TCCTAATAATAAAGAACAATGAATAGCAA-ACTAAACAC
1 CCTTTTGACAGCTTAATTCC-AATAATAAATAACAATGAACAGCAACACTAAACAC
* *
1021220 CCATTTTTTACAGTTTGATGATTCCAATAATAAATAACAA
1 CC--TTTTGACAGCTT-A--ATTCCAATAATAAATAACAA
1021260 ATGACAGTAC
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
54 10 0.13
55 3 0.04
56 42 0.54
57 5 0.06
59 15 0.19
60 3 0.04
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (55 bp):
CCTTTTGACAGCTTAATTCCAATAATAAATAACAATGAACAGCAACACTAAACAC
Found at i:1027763 original size:19 final size:18
Alignment explanation
Indices: 1027741--1027783 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1027731 ATCACAAGGG
*
1027741 AAAATCACATAGTTTTAGA
1 AAAATC-CATACTTTTAGA
* *
1027760 AAAATCGATACTTTTGGA
1 AAAATCCATACTTTTAGA
1027778 AAAATC
1 AAAATC
1027784 GTAGATTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (18 bp):
AAAATCCATACTTTTAGA
Found at i:1034047 original size:17 final size:18
Alignment explanation
Indices: 1034012--1034050 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
1034002 ATAATCACTT
1034012 TAATATTAATTTATTAAA
1 TAATATTAATTTATTAAA
1034030 TAATATT-ATTT-TTGAAA
1 TAATATTAATTTATT-AAA
1034047 TAAT
1 TAAT
1034051 TAATTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.10
17 11 0.55
18 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TAATATTAATTTATTAAA
Found at i:1037133 original size:176 final size:176
Alignment explanation
Indices: 1036830--1037192 Score: 618
Period size: 176 Copynumber: 2.1 Consensus size: 176
1036820 TAGTAACAGA
1036830 TTAACAAAATAGCAGTTGAAGAGCAGCTGAGAAATCAACTTTAAATACTTGTGTAAACAACAGAT
1 TTAA-AAAATAGCAGTTGAAGAGCAGCTGAGAAATCAACTTTAAATACTTGTGTAAACAACAGAT
* * * *
1036895 GAAAGGAATGAATGAATTTCTGGAACAATGAAAATATATAGATTTTTTCATATTCTTTTTGACTT
65 GAAAGGAATGAATGAATTTCTAGAACAATGAAAATATATAGATTTTTTCATACTCATTTTGACCT
* *
1036960 AATTTTATGCAAATTCTGAGTAATTAATGTCAAAAAATATAATTTAT
130 AATTTCATACAAATTCTGAGTAATTAATGTCAAAAAATATAATTTAT
* * *
1037007 TTAAAAAATAGCAGTTGAAGAGCAGTTTAGAAATCAACTTTAAATACTTGTGTAAACAACATATG
1 TTAAAAAATAGCAGTTGAAGAGCAGCTGAGAAATCAACTTTAAATACTTGTGTAAACAACAGATG
1037072 AAAGGAATGAATGAATTTCTAGAACAATGAAAATATATAGATTTTTTCATACTCATTTTGACCTA
66 AAAGGAATGAATGAATTTCTAGAACAATGAAAATATATAGATTTTTTCATACTCATTTTGACCTA
*
1037137 ATTTCATACAAATTCTGAGTAATTAATGTCGAAAAATATAATTTAT
131 ATTTCATACAAATTCTGAGTAATTAATGTCAAAAAATATAATTTAT
*
1037183 TTATAAAATA
1 TTAAAAAATA
1037193 ATTAATTCAT
Statistics
Matches: 175, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
176 171 0.98
177 4 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (176 bp):
TTAAAAAATAGCAGTTGAAGAGCAGCTGAGAAATCAACTTTAAATACTTGTGTAAACAACAGATG
AAAGGAATGAATGAATTTCTAGAACAATGAAAATATATAGATTTTTTCATACTCATTTTGACCTA
ATTTCATACAAATTCTGAGTAATTAATGTCAAAAAATATAATTTAT
Found at i:1039596 original size:23 final size:23
Alignment explanation
Indices: 1039570--1039685 Score: 135
Period size: 23 Copynumber: 5.0 Consensus size: 23
1039560 ACAGTAGCAC
* *
1039570 GCTCTCCGATTAGCACTGTGTGT
1 GCTCTCCGTTTAGCACTTTGTGT
1039593 GCTCTCCGTTTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACTTTGTGT
* ** *
1039616 GCTCTCCGTTTAACACGCCT-CGT
1 GCTCTCCGTTTAGCAC-TTTGTGT
*
1039639 GCTCTTCGTTTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACTTTGTGT
* *
1039662 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCCGTTTAGCACTTTGTGT
1039685 G
1 G
1039686 TTCAGTATTT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 1 0.01
23 75 0.97
24 1 0.01
ACGTcount: A:0.11, C:0.27, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCCGTTTAGCACTTTGTGT
Found at i:1057109 original size:71 final size:71
Alignment explanation
Indices: 1057032--1057275 Score: 216
Period size: 71 Copynumber: 3.4 Consensus size: 71
1057022 ATTGAGATTT
*
1057032 TTTTTAATTTTAAATT-TAAA-TAAAGTTTTTCATATGAATTTAATGTTTTTTTATTTTTCGAAT
1 TTTTTAATATT-AATTATAAATTAAA-TTTTTCATATGAATTTAATGTTTTTTTATTTTTCGAAT
1057095 TTTGATAA
64 TTTGATAA
* * * ** **
1057103 TTTTTAATATTAATTATAAATTAAATTTTAT-AAAT-TATATTAAT-TATTATCAAGAGTTT-GA
1 TTTTTAATATTAATTATAAATTAAATTTT-TCATATGAAT-TTAATGT-TTTTTTA-TTTTTCGA
** **
1057164 ATTGAGATTT
62 ATTTTGATAA
*
1057174 TTTTTAATTTTAAATT-TAAA-TAAAGTTTTTCATATGAATTTAATGTTTTTTTTTATTTTTCGA
1 TTTTTAATATT-AATTATAAATTAAA-TTTTTCATATGAATTTAATG--TTTTTTTATTTTTCGA
*
1057237 ACTTTGATAA
62 ATTTTGATAA
1057247 TTTTTAATATTAATTATAAATTAAATTTT
1 TTTTTAATATTAATTATAAATTAAATTTT
1057276 ATAAATTATA
Statistics
Matches: 131, Mismatches: 26, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
70 12 0.09
71 64 0.49
72 21 0.16
73 29 0.22
74 5 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (71 bp):
TTTTTAATATTAATTATAAATTAAATTTTTCATATGAATTTAATGTTTTTTTATTTTTCGAATTT
TGATAA
Found at i:1057143 original size:142 final size:143
Alignment explanation
Indices: 1056980--1057305 Score: 609
Period size: 142 Copynumber: 2.3 Consensus size: 143
1056970 AATTCTTAAT
*
1056980 ATTAAATTTTATAATTTATATTAATTATTATCAAGAGTTTGAATTGAGATTTTTTTTAATTTTAA
1 ATTAAATTTTATAAATTATATTAATTATTATCAAGAGTTTGAATTGAGATTTTTTTTAATTTTAA
*
1057045 ATTTAAATAAAGTTTTTCATATGAATTTAATG-TTTTTTTATTTTTCGAATTTTGATAATTTTTA
66 ATTTAAATAAAGTTTTTCATATGAATTTAATGTTTTTTTTATTTTTCGAACTTTGATAATTTTTA
1057109 ATATTAATTATAA
131 ATATTAATTATAA
1057122 ATTAAATTTTATAAATTATATTAATTATTATCAAGAGTTTGAATTGAGATTTTTTTTAATTTTAA
1 ATTAAATTTTATAAATTATATTAATTATTATCAAGAGTTTGAATTGAGATTTTTTTTAATTTTAA
1057187 ATTTAAATAAAGTTTTTCATATGAATTTAATGTTTTTTTTTATTTTTCGAACTTTGATAATTTTT
66 ATTTAAATAAAGTTTTTCATATGAATTTAATG-TTTTTTTTATTTTTCGAACTTTGATAATTTTT
1057252 AATATTAATTATAA
130 AATATTAATTATAA
*
1057266 ATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTT
1 ATTAAATTTTATAAATTATATTAATTATTATCAAGAGTTT
1057306 TCATTTAAAT
Statistics
Matches: 179, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
142 96 0.54
144 83 0.46
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.54
Consensus pattern (143 bp):
ATTAAATTTTATAAATTATATTAATTATTATCAAGAGTTTGAATTGAGATTTTTTTTAATTTTAA
ATTTAAATAAAGTTTTTCATATGAATTTAATGTTTTTTTTATTTTTCGAACTTTGATAATTTTTA
ATATTAATTATAA
Found at i:1057320 original size:97 final size:97
Alignment explanation
Indices: 1057211--1057402 Score: 278
Period size: 97 Copynumber: 2.0 Consensus size: 97
1057201 TTTCATATGA
* * *
1057211 ATTTAATGTTTTTTTTTATTTTTCGAA-CTTTGATAATTTTTAATATTAATTATAAATTAAATTT
1 ATTTAA-GTTTTTTCTTATTTTTCAAAGCTTTGATAATTCTTAATATTAATTATAAATTAAATTT
*
1057275 TATAAATTATATTAATTATTATCAAAAGTTTTC
65 TATAAATTATATTAATTATTAACAAAAGTTTTC
* * *
1057308 ATTTAAATTTTTTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAATTATCAATTAAATTTT
1 ATTTAAGTTTTTTCTTATTTTTCAAAGCTTTGATAATTCTTAATATTAATTATAAATTAAATTTT
* * *
1057373 ATAATTTTTATTAATTATTAACAAGAGTTT
66 ATAAATTATATTAATTATTAACAAAAGTTT
1057403 GAATTGAGAT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 17 0.20
97 67 0.80
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (97 bp):
ATTTAAGTTTTTTCTTATTTTTCAAAGCTTTGATAATTCTTAATATTAATTATAAATTAAATTTT
ATAAATTATATTAATTATTAACAAAAGTTTTC
Found at i:1057539 original size:239 final size:240
Alignment explanation
Indices: 1057069--1057667 Score: 1032
Period size: 239 Copynumber: 2.5 Consensus size: 240
1057059 TTTCATATGA
* * *
1057069 ATTT-AATGTTTTT-TTATTTTTCGAA-TTTTGATAATTTTTAATATTAATTATAAATTAAATTT
1 ATTTAAAT-TTTTTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAATTATCAATTAAATTT
* * *
1057131 TATAAATTATATTAATTATTATCAAGAGTTTGAATTGAGATTTTTTTTAATTTTAAATTTAAATA
65 TATAATTTTTATTAATTATTAACAAGAGTTTGAATTGAGA-TTTTTTTAATTTTAAATTTAAATA
*
1057196 AAGTTTTTCATATGAATTTAATGTTTTTTTTTATTTTTCGAACTTTGATAATTTTTAATATTAAT
129 AAGTTTTTCATATGAATTTAATGTTTATTTTTATTTTTCGAACTTTGATAATTTTTAATATTAAT
1057261 TATAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTTTC
194 TATAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTTTC
1057308 ATTTAAATTTTTTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAATTATCAATTAAATTTT
1 ATTTAAATTTTTTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAATTATCAATTAAATTTT
1057373 ATAATTTTTATTAATTATTAACAAGAGTTTGAATTGAGATTTTTTTAATTTTAAATTTAAATAAA
66 ATAATTTTTATTAATTATTAACAAGAGTTTGAATTGAGATTTTTTTAATTTTAAATTTAAATAAA
*
1057438 GTTTTTCATATGAATTTAATG-TTATTTTTATTTTTCGAATTTTGATAATTTTTAATATTAATTA
131 GTTTTTCATATGAATTTAATGTTTATTTTTATTTTTCGAACTTTGATAATTTTTAATATTAATTA
1057502 TAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTTTC
196 TAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTTTC
*
1057547 ATTTAAATGTTTTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAATTATCAATTAAATTTT
1 ATTTAAATTTTTTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAATTATCAATTAAATTTT
*
1057612 ATAATTTTTATTAATTATTAACAAGAGTTTGAGATT-AGATTTTGTT-A-TTTAAATTT
66 ATAATTTTTATTAATTATTAACAAGAGTTTGA-ATTGAGATTTTTTTAATTTTAAATTT
1057668 TTATTTTCCC
Statistics
Matches: 346, Mismatches: 10, Indels: 10
0.95 0.03 0.03
Matches are distributed among these distances:
237 9 0.03
238 1 0.00
239 200 0.58
240 64 0.18
241 72 0.21
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (240 bp):
ATTTAAATTTTTTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAATTATCAATTAAATTTT
ATAATTTTTATTAATTATTAACAAGAGTTTGAATTGAGATTTTTTTAATTTTAAATTTAAATAAA
GTTTTTCATATGAATTTAATGTTTATTTTTATTTTTCGAACTTTGATAATTTTTAATATTAATTA
TAAATTAAATTTTATAAATTATATTAATTATTATCAAAAGTTTTC
Found at i:1057590 original size:97 final size:97
Alignment explanation
Indices: 1057451--1057748 Score: 325
Period size: 97 Copynumber: 3.0 Consensus size: 97
1057441 TTTCATATGA
* *
1057451 ATTT-AATGTTATTTTTATTTTTCGAATTTTGATAATTTTTAATATTAATTATAAATTAAATTTT
1 ATTTAAATGTTATTTTTATTTTTCAAATTTTGATAATTCTTAATATTAATTATAAATTAAATTTT
*
1057515 ATAAATTATATTAATTATTATCAAAAGTTTTC
66 ATAATTTATATTAATTATTATCAAAAGTTTTC
* *
1057547 ATTTAAATGTT-TTCTTATTTTTCAAAGTTTTGATAATTCTTAATATTAATTATCAATTAAATTT
1 ATTTAAATGTTATTTTTATTTTTCAAA-TTTTGATAATTCTTAATATTAATTATAAATTAAATTT
* * * *
1057611 TATAATTTTTATTAATTATTAACAAGAG-TTTG
65 TATAATTTATATTAATTATTATCAAAAGTTTTC
* * *
1057643 AGATTAGATTTTGTTATTTAAATTTTTATTTTCCCAAATTTTGATAA-TCTTTAATATTAATTAT
1 A-TTTA-A--ATG----TT--ATTTTTATTTT-TCAAATTTTGATAATTC-TTAATATTAATTAT
* *
1057707 AAATTAAATTTTATAATTTACATTAATTATTATCCAAAGTTT
54 AAATTAAATTTTATAATTTATATTAATTATTATCAAAAGTTT
1057749 GAATTAGGAT
Statistics
Matches: 167, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
96 21 0.13
97 68 0.41
98 1 0.01
100 2 0.01
104 2 0.01
106 2 0.01
107 65 0.39
108 6 0.04
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (97 bp):
ATTTAAATGTTATTTTTATTTTTCAAATTTTGATAATTCTTAATATTAATTATAAATTAAATTTT
ATAATTTATATTAATTATTATCAAAAGTTTTC
Found at i:1057690 original size:107 final size:107
Alignment explanation
Indices: 1057561--1057760 Score: 291
Period size: 107 Copynumber: 1.9 Consensus size: 107
1057551 AAATGTTTTC
* * **
1057561 TTATTTTTCAAAGTTTTGATAAT-TCTTAATATTAATTATCAATTAAATTTTATAATTTTTATTA
1 TTATTTTCCAAAGTTTTGATAATCT-TTAATATTAATTATAAATTAAATTTTATAATTTACATTA
1057625 ATTATTA-ACAAGAGTTTGAGATTA-GATTTTGTTATTTAAATTT
65 ATTATTATACAA-AGTTTGA-ATTAGGATTTTGTTATTTAAATTT
1057668 TTATTTTCCCAAA-TTTTGATAATCTTTAATATTAATTATAAATTAAATTTTATAATTTACATTA
1 TTATTTT-CCAAAGTTTTGATAATCTTTAATATTAATTATAAATTAAATTTTATAATTTACATTA
*
1057732 ATTATTATCCAAAGTTTGAATTAGGATTT
65 ATTATTATACAAAGTTTGAATTAGGATTT
1057761 GTTTTAAATA
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
106 4 0.05
107 72 0.86
108 8 0.10
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.52
Consensus pattern (107 bp):
TTATTTTCCAAAGTTTTGATAATCTTTAATATTAATTATAAATTAAATTTTATAATTTACATTAA
TTATTATACAAAGTTTGAATTAGGATTTTGTTATTTAAATTT
Found at i:1058681 original size:22 final size:22
Alignment explanation
Indices: 1058647--1058693 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1058637 TTGTGAACAA
* *
1058647 ATTAATTATATTGATGGTATAG
1 ATTAATTACATTGATGATATAG
* *
1058669 ATTAGTTACATTGTTGATATAG
1 ATTAATTACATTGATGATATAG
1058691 ATT
1 ATT
1058694 GAACAAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (22 bp):
ATTAATTACATTGATGATATAG
Found at i:1058878 original size:23 final size:23
Alignment explanation
Indices: 1058821--1058871 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1058811 TTTAAATTCA
*
1058821 ACGGTATAGATTGAGTTACATTT
1 ACGGTATAGATTGAGTTACATTG
*
1058844 ATGGTATAGATTGAGTTACATTG
1 ACGGTATAGATTGAGTTACATTG
1058867 ACGGT
1 ACGGT
1058872 TAAGATTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.37
Consensus pattern (23 bp):
ACGGTATAGATTGAGTTACATTG
Found at i:1058967 original size:32 final size:32
Alignment explanation
Indices: 1058926--1058989 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1058916 ACTCTATACA
1058926 CCTTTATCCTTTAGGATTTACATTAACTACCC
1 CCTTTATCCTTTAGGATTTACATTAACTACCC
1058958 CCTTTATCCTTTAGGATTTACATTAACTACCC
1 CCTTTATCCTTTAGGATTTACATTAACTACCC
1058990 TGTTAACTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (32 bp):
CCTTTATCCTTTAGGATTTACATTAACTACCC
Found at i:1061061 original size:53 final size:53
Alignment explanation
Indices: 1060989--1061096 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1060979 ACCCAGACCG
1060989 TGTAACTCACTGTTTCTAGTTCACAACACAAAATATCCACATGATCCAGAACA
1 TGTAACTCACTGTTTCTAGTTCACAACACAAAATATCCACATGATCCAGAACA
1061042 TGTAACTCACTGTTTCTAGTTCACAACACAAAATATCCACATGATCCAGAACA
1 TGTAACTCACTGTTTCTAGTTCACAACACAAAATATCCACATGATCCAGAACA
1061095 TG
1 TG
1061097 CCCATGTGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.27
Consensus pattern (53 bp):
TGTAACTCACTGTTTCTAGTTCACAACACAAAATATCCACATGATCCAGAACA
Found at i:1062912 original size:33 final size:33
Alignment explanation
Indices: 1062848--1062912 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
1062838 TGGCAATGAT
* * *
1062848 CTGATGTCGACCATTGATGACCCATTGTCAGGC
1 CTGATGTCGACCATTGAAGACCCACTATCAGGC
* *
1062881 CTGATGTCGGCCATTGAAGCCCCACTATCAGG
1 CTGATGTCGACCATTGAAGACCCACTATCAGG
1062913 TGCTTTTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.25
Consensus pattern (33 bp):
CTGATGTCGACCATTGAAGACCCACTATCAGGC
Found at i:1069925 original size:31 final size:31
Alignment explanation
Indices: 1069822--1069956 Score: 118
Period size: 31 Copynumber: 4.5 Consensus size: 31
1069812 TAAAATAACG
* * *
1069822 TTTGATACTTGAACTTAACACTTTTTTTTAA
1 TTTGGTACTTAAACTTAACACTTTTTTCTAA
* *
1069853 TTTGGTACCTAAACTT-----TTTTTATCCAA
1 TTTGGTACTTAAACTTAACACTTTTT-TCTAA
**
1069880 TTTGGTACACAAACTTAACACTTTTTTCTAA
1 TTTGGTACTTAAACTTAACACTTTTTTCTAA
* * *
1069911 TTTGCTACTTAAACTTGACACTTTTTTTTTAA
1 TTTGGTACTTAAACTTAACAC-TTTTTTCTAA
*
1069943 GTTGGTACTTAAAC
1 TTTGGTACTTAAAC
1069957 CTTTTGGGGT
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
26 5 0.06
27 17 0.21
31 34 0.41
32 26 0.32
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.47
Consensus pattern (31 bp):
TTTGGTACTTAAACTTAACACTTTTTTCTAA
Found at i:1069986 original size:91 final size:89
Alignment explanation
Indices: 1069822--1070014 Score: 224
Period size: 91 Copynumber: 2.1 Consensus size: 89
1069812 TAAAATAACG
* * ***
1069822 TTTGATACTTGAACTTAACACTTTTTTTTAATTTGGTACCTAAACTTTTTTTATCCAATTTGGTA
1 TTTGATACTTAAACTTAACACTTTTTTTTAAGTTGGTACCTAAACTTTTGGGATCCAATTTGGTA
1069887 CACAAACTTAACACTTTTTTCTAA
66 CACAAACTTAACACTTTTTTCTAA
* * * * *
1069911 TTTGCTACTTAAACTTGACACTTTTTTTTTAAGTTGGTACTTAAACCTTTTGGGGTCTAATTTGG
1 TTTGATACTTAAACTTAACAC-TTTTTTTTAAGTTGGTACCTAAA-CTTTTGGGATCCAATTTGG
*** * *
1069976 TACTTGAACTTGACTCTTTTTTCTAA
64 TACACAAACTTAACACTTTTTTCTAA
*
1070002 TTTGATACATAAA
1 TTTGATACTTAAA
1070015 TTTTTTTAAT
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
89 18 0.21
90 21 0.25
91 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (89 bp):
TTTGATACTTAAACTTAACACTTTTTTTTAAGTTGGTACCTAAACTTTTGGGATCCAATTTGGTA
CACAAACTTAACACTTTTTTCTAA
Found at i:1070300 original size:34 final size:30
Alignment explanation
Indices: 1070240--1070317 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 30
1070230 ATTTAGATAA
1070240 TAAATTAAAAAAAATATCAAATTCAAATAC
1 TAAATTAAAAAAAATATCAAATTCAAATAC
* *
1070270 TAAATTAAATAAAA-AT--AATTTAAATA-
1 TAAATTAAAAAAAATATCAAATTCAAATAC
1070296 TCAAATT-AAAAAAATATCAAAT
1 T-AAATTAAAAAAAATATCAAAT
1070318 ATTATATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
26 7 0.17
27 16 0.39
29 5 0.12
30 13 0.32
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.29
Consensus pattern (30 bp):
TAAATTAAAAAAAATATCAAATTCAAATAC
Found at i:1074800 original size:15 final size:15
Alignment explanation
Indices: 1074780--1074885 Score: 50
Period size: 15 Copynumber: 7.5 Consensus size: 15
1074770 AAATATGATT
1074780 TAAAAGAGTTTTAAA
1 TAAAAGAGTTTTAAA
*
1074795 TAAAAGA----TAAT
1 TAAAAGAGTTTTAAA
* *
1074806 TAAATAGAATTTTAAG
1 TAAA-AGAGTTTTAAA
*
1074822 TAAAAGAGTTTTAGA
1 TAAAAGAGTTTTAAA
*
1074837 TAAATA-A----TAAT
1 TAAA-AGAGTTTTAAA
* * *
1074848 TAAAATAGAATTTAAT
1 TAAAAGAG-TTTTAAA
1074864 TAAAAGAGTTTTAAA
1 TAAAAGAGTTTTAAA
1074879 TAAAAGA
1 TAAAAGA
1074886 TAATTTATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
10 1 0.01
11 14 0.20
12 3 0.04
15 32 0.46
16 19 0.28
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (15 bp):
TAAAAGAGTTTTAAA
Found at i:1074833 original size:42 final size:42
Alignment explanation
Indices: 1074780--1074890 Score: 172
Period size: 42 Copynumber: 2.6 Consensus size: 42
1074770 AAATATGATT
1074780 TAAAAGAGTTTTAAATAAAAGATAATT-AAATAGAATTTTAAG
1 TAAAAGAGTTTTAAATAAAAGATAATTAAAATAGAA-TTTAAG
* *
1074822 TAAAAGAGTTTTAGATAAATA-ATAATTAAAATAGAATTTAAT
1 TAAAAGAGTTTTAAATAAA-AGATAATTAAAATAGAATTTAAG
1074864 TAAAAGAGTTTTAAATAAAAGATAATT
1 TAAAAGAGTTTTAAATAAAAGATAATT
1074891 TATCAGAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
41 1 0.02
42 53 0.84
43 9 0.14
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (42 bp):
TAAAAGAGTTTTAAATAAAAGATAATTAAAATAGAATTTAAG
Found at i:1077184 original size:15 final size:16
Alignment explanation
Indices: 1077152--1077189 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1077142 TCAAGATAGA
*
1077152 ATTTTGAATTCATTTG
1 ATTTTGAATTCATATG
1077168 ATTTTGAA-TCATATG
1 ATTTTGAATTCATATG
1077183 ATATTTG
1 AT-TTTG
1077190 TAAATCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (16 bp):
ATTTTGAATTCATATG
Found at i:1083785 original size:24 final size:24
Alignment explanation
Indices: 1083720--1084364 Score: 398
Period size: 24 Copynumber: 26.9 Consensus size: 24
1083710 GCATTTACTG
* *
1083720 TCGTCAGCTTGCACACGTTTATAG-
1 TCGTCAGCTTGCATACGTTTA-CGC
* ** *
1083744 TCGCCAGCTTATATACATTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* * * * *
1083768 TCGTCAACTTGCACACATTTAAGG
1 TCGTCAGCTTGCATACGTTTACGC
* * ** *
1083792 TCATCAACTTATATAC-TTTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* * *
1083815 TCGTCAGCTTGCACACATTTACGA
1 TCGTCAGCTTGCATACGTTTACGC
* *
1083839 TCGTCAACATAT-C-TACATTTACGC
1 TCGTCAGC-T-TGCATACGTTTACGC
* * **
1083863 TCGTCAGCTTGCACACATTTACAT
1 TCGTCAGCTTGCATACGTTTACGC
** *
1083887 TCGTCAGCTTAAATACATTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* ** *
1083911 TCATCAGCTTATATATGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* *
1083935 TCGTCAACTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
** *
1083959 TCGTCAGCTTATATATGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* *
1083983 TCGTCAACTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
**
1084007 TCGTCAGCTTATATACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* * * *
1084031 TCGTTAGCTTGCACACGTTTATGG
1 TCGTCAGCTTGCATACGTTTACGC
**
1084055 TCGTCAGCTTATATACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* * *
1084079 TCGTCAGCTTGCTTATGTTTACAC
1 TCGTCAGCTTGCATACGTTTACGC
* **
1084103 TTGTCAGCTTATATACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
** *
1084127 TCGTCAATTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
** *
1084151 TCGTCAATTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* ** * *
1084175 TCATCAGCTTATATATGTTTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* * * *
1084199 TCGTCAACTTGCACACATTTACAC
1 TCGTCAGCTTGCATACGTTTACGC
* ** * *
1084223 TCGTCAGCATATATACATTTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* ** * *
1084247 TCGTCAACTTATATATGTTTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* * * * *
1084271 TCATCAGCTTGCACATGATTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* ** * *
1084295 TTGTCAGCTTATATATGTTTACAC
1 TCGTCAGCTTGCATACGTTTACGC
* *
1084319 TCATCAGCTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* **
1084343 TCGTCAGCCTATATACGTTTAC
1 TCGTCAGCTTGCATACGTTTAC
1084365 CTTAATTAAC
Statistics
Matches: 470, Mismatches: 145, Indels: 12
0.75 0.23 0.02
Matches are distributed among these distances:
22 1 0.00
23 19 0.04
24 447 0.95
25 2 0.00
26 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (24 bp):
TCGTCAGCTTGCATACGTTTACGC
Found at i:1083932 original size:48 final size:48
Alignment explanation
Indices: 1083856--1084364 Score: 478
Period size: 48 Copynumber: 10.6 Consensus size: 48
1083846 CATATCTACA
** * * ** ** * *
1083856 TTTACGCTCGTCAGCTTGCACACATTTACATTCGTCAGCTTAAATACA
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * *
1083904 TTTACGCTCATCAGCTTATATATGTTTACGCTCGTCAACTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* *
1083952 TTTACGCTCGTCAGCTTATATATGTTTACGCTCGTCAACTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
*
1084000 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * ** *
1084048 TTTATGGTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCTTATG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * **
1084096 TTTACACTTGTCAGCTTATATACGTTTACGCTCGTCAATTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
** ** * * ** * *
1084144 TTTACGCTCGTCAATTTGCACACGTTTACGCTCATCAGCTTATATATG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * ** * * * * ** * *
1084192 TTTATGCTCGTCAACTTGCACACATTTACACTCGTCAGCATATATACA
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * * * * *
1084240 TTTATGCTCGTCAACTTATATATGTTTATGCTCATCAGCTTGCACATG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * * * * *
1084288 ATTATGCTTGTCAGCTTATATATGTTTACACTCATCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
*
1084336 TTTACGCTCGTCAGCCTATATACGTTTAC
1 TTTACGCTCGTCAGCTTATATACGTTTAC
1084365 CTTAATTAAC
Statistics
Matches: 382, Mismatches: 79, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 382 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (48 bp):
TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
Done.