Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 4 of 160
Found at i:818470 original size:21 final size:21
Alignment explanation
Indices: 818445--818507 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
818435 TCCGAAATTA
818445 ATAAAATATTAATTTTATAAT
1 ATAAAATATTAATTTTATAAT
*
818466 ATAAAATATT-ATTTTTTAA-
1 ATAAAATATTAATTTTATAAT
*
818485 ATATAAATATATAATTATATAAT
1 ATA-AAATAT-TAATTTTATAAT
818508 TATATATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 14 0.40
21 11 0.31
22 7 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAAAATATTAATTTTATAAT
Found at i:818492 original size:20 final size:20
Alignment explanation
Indices: 818443--818507 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
818433 GATCCGAAAT
818443 TAATA-AAATATTAATTTTA
1 TAATATAAATATTAATTTTA
*
818462 TAATATAAAATATT-ATTTTT
1 TAATAT-AAATATTAATTTTA
*
818482 TAAATATAAATATATAATTATA
1 T-AATATAAATAT-TAATTTTA
818504 TAAT
1 TAAT
818508 TATATATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.13
20 12 0.32
21 16 0.42
22 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATAAATATTAATTTTA
Found at i:818511 original size:22 final size:21
Alignment explanation
Indices: 818443--818515 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 21
818433 GATCCGAAAT
818443 TAATA-AAATAT-TAATTTTA
1 TAATATAAATATATAATTTTA
* *
818462 TAATATAAA-ATATTATTTTT
1 TAATATAAATATATAATTTTA
*
818482 TAAATATAAATATATAATTATA
1 T-AATATAAATATATAATTTTA
*
818504 TAAT-TATATATA
1 TAATATAAATATA
818516 AATAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 7 0.16
20 17 0.39
21 11 0.25
22 9 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATAAATATATAATTTTA
Found at i:829779 original size:25 final size:25
Alignment explanation
Indices: 829753--829804 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
829743 TTAAATCTTT
829753 TTTTA-ATAAAAAAATTTAAC-AAA
1 TTTTATATAAAAAAATTTAACTAAA
* *
829776 TTTTATCTAAAAAAATTTATCTAAA
1 TTTTATATAAAAAAATTTAACTAAA
829801 TTTT
1 TTTT
829805 GTCCTAGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 13 0.52
25 7 0.28
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTATATAAAAAAATTTAACTAAA
Found at i:830522 original size:22 final size:20
Alignment explanation
Indices: 830482--830521 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
830472 AGGTTTTTCA
830482 TTTTTTTTAATTCTTAAAAT
1 TTTTTTTTAATTCTTAAAAT
830502 TTTTTTATCTAATT-TTAAAA
1 TTTTTT-T-TAATTCTTAAAA
830522 AAATTACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTTAATTCTTAAAAT
Found at i:838586 original size:15 final size:15
Alignment explanation
Indices: 838556--838599 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
838546 ACATAATATG
*
838556 ATAATATAATATAAAA
1 ATAATA-AAAATAAAA
838572 ATAATAAAAAT-AAA
1 ATAATAAAAATAAAA
838586 ATATATAAAAATAA
1 ATA-ATAAAAATAA
838600 TATAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 12 0.48
16 7 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAATAAAAATAAAA
Found at i:838596 original size:10 final size:11
Alignment explanation
Indices: 838536--838604 Score: 57
Period size: 11 Copynumber: 5.8 Consensus size: 11
838526 TATAAATTTG
*
838536 ATAATTTAAAA
1 ATAATATAAAA
*
838547 CATAATATGATAAT
1 -ATAATAT-A-AAA
838561 ATAATATAAAA
1 ATAATATAAAA
*
838572 ATAATAAAAATA
1 ATAATATAAA-A
*
838584 AAATATATAAAA
1 ATA-ATATAAAA
838596 ATAATATAA
1 ATAATATAA
838605 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
11 17 0.37
12 13 0.28
13 14 0.30
14 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:841340 original size:2 final size:2
Alignment explanation
Indices: 841333--841366 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
841323 CAGATAGATG
841333 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
841367 TATATATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:852842 original size:19 final size:19
Alignment explanation
Indices: 852818--852856 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
852808 TAGAGTGACC
*
852818 TAACCACTTTCCTGCATAT
1 TAACCACCTTCCTGCATAT
852837 TAACCACCTTCCTGCATAT
1 TAACCACCTTCCTGCATAT
852856 T
1 T
852857 TTTATGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (19 bp):
TAACCACCTTCCTGCATAT
Found at i:854888 original size:82 final size:84
Alignment explanation
Indices: 854788--854953 Score: 237
Period size: 84 Copynumber: 2.0 Consensus size: 84
854778 AAAGATGATG
* * *
854788 TTATAAACAAAATGAGGGAACTGA-CCC-AGAATTTGAAACATATAAGTAATCAAATTCATATTA
1 TTATAAACAAAATGAGGGAACTGACCCCGAAAATTTGAAACATATAAGCAATAAAATTCATATTA
*
854851 ATTACATTGTCAGCACATT
66 ATTACATTATCAGCACATT
* * **
854870 TTATAAACAGAATGAGGGAACTGACCCCGAAAATTTGAAACATTTAAGCAATAAAATTGGTATTA
1 TTATAAACAAAATGAGGGAACTGACCCCGAAAATTTGAAACATATAAGCAATAAAATTCATATTA
*
854935 CTTACATTATCAGCACATT
66 ATTACATTATCAGCACATT
854954 CAATGAGGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 23 0.32
83 3 0.04
84 47 0.64
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (84 bp):
TTATAAACAAAATGAGGGAACTGACCCCGAAAATTTGAAACATATAAGCAATAAAATTCATATTA
ATTACATTATCAGCACATT
Found at i:866184 original size:2 final size:2
Alignment explanation
Indices: 866177--866205 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
866167 ATCTAGATTT
866177 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
866206 TCATGCTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:868626 original size:8 final size:8
Alignment explanation
Indices: 868613--868640 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
868603 ATATCTCTCT
868613 TTGTCCCA
1 TTGTCCCA
868621 TTGTCCCA
1 TTGTCCCA
868629 TTGTCCCA
1 TTGTCCCA
868637 TTGT
1 TTGT
868641 TTCTGCTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.32, G:0.14, T:0.43
Consensus pattern (8 bp):
TTGTCCCA
Found at i:870078 original size:21 final size:21
Alignment explanation
Indices: 870054--870099 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
870044 CCGAATTTTT
870054 AATATAAACCTAGGTTAATAA
1 AATATAAACCTAGGTTAATAA
****
870075 AATATTTTTCTAGGTTAATAA
1 AATATAAACCTAGGTTAATAA
870096 AATA
1 AATA
870100 GCTAGGTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (21 bp):
AATATAAACCTAGGTTAATAA
Found at i:878514 original size:2 final size:2
Alignment explanation
Indices: 878507--878536 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
878497 ATTAAAGCCA
878507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
878537 TTTAAACTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:884355 original size:13 final size:12
Alignment explanation
Indices: 884337--884383 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
884327 ACATAAAAAC
884337 AAAAGAAAAATAG
1 AAAA-AAAAATAG
*
884350 AAAAGAGAAATAG
1 AAAA-AAAAATAG
884363 AGAAAAAAAA-AG
1 A-AAAAAAAATAG
884375 AAAAAAAAA
1 AAAAAAAAA
884384 GGGTGTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.26
12 3 0.10
13 17 0.55
14 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (12 bp):
AAAAAAAAATAG
Found at i:894170 original size:4 final size:4
Alignment explanation
Indices: 894163--894201 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
894153 TATATATATA
*
894163 TATG TATG TATG TTTG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
894202 TAGAATTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:925075 original size:9 final size:9
Alignment explanation
Indices: 925061--925086 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
925051 TCTGAAGAAA
925061 GTATGTCTG
1 GTATGTCTG
925070 GTATGTCTG
1 GTATGTCTG
925079 GTATGTCT
1 GTATGTCT
925087 ATGCCTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.46
Consensus pattern (9 bp):
GTATGTCTG
Found at i:929831 original size:13 final size:13
Alignment explanation
Indices: 929789--929838 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
929779 AAATAGTTGG
*
929789 TTTTGATTTTAAT
1 TTTTTATTTTAAT
*
929802 TTTTTATCTTAATT
1 TTTTTATTTTAA-T
*
929816 TTTTTATTTTGAT
1 TTTTTATTTTAAT
*
929829 TTTGTATTTT
1 TTTTTATTTT
929839 TCTTACATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:933314 original size:18 final size:19
Alignment explanation
Indices: 933287--933322 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
933277 TGACATCATA
*
933287 TATACTAAAA-TAACTAAT
1 TATACAAAAATTAACTAAT
933305 TATACAAAAATTAACTAA
1 TATACAAAAATTAACTAA
933323 CTAATACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (19 bp):
TATACAAAAATTAACTAAT
Found at i:937659 original size:26 final size:26
Alignment explanation
Indices: 937611--937660 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
937601 ACTCTATGAA
* * *
937611 TTCATTGAATCATTAATTCCTCAATC
1 TTCATTGAAACATTAACTACTCAATC
*
937637 TTCATTGAAACTTTAACTACTCAA
1 TTCATTGAAACATTAACTACTCAA
937661 AAAATTTATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (26 bp):
TTCATTGAAACATTAACTACTCAATC
Found at i:938712 original size:19 final size:19
Alignment explanation
Indices: 938688--938725 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
938678 AATCTTTAAA
938688 AAATCATCATCATCATTAT
1 AAATCATCATCATCATTAT
*
938707 AAATCATCATTATCATTAT
1 AAATCATCATCATCATTAT
938726 TTTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATCATCATCATCATTAT
Found at i:951118 original size:18 final size:18
Alignment explanation
Indices: 951085--951139 Score: 101
Period size: 18 Copynumber: 3.0 Consensus size: 18
951075 AAGGAAAGAA
951085 CTAAAAAATACAAAAATT
1 CTAAAAAATACAAAAATT
951103 CTTAAAAAATACAAAAATT
1 C-TAAAAAATACAAAAATT
951122 CTAAAAAATACAAAAATT
1 CTAAAAAATACAAAAATT
951140 ATTTTTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.50
19 18 0.50
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (18 bp):
CTAAAAAATACAAAAATT
Found at i:952999 original size:33 final size:32
Alignment explanation
Indices: 952962--953034 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
952952 AGTTATAATC
* * *
952962 ATAATCAAGTATTACATTCATATAATCAATTGA
1 ATAATCAAATATCACATTCATATAATC-ACTGA
*
952995 ATAATCAAATATCACATTCATATGATCACTGA
1 ATAATCAAATATCACATTCATATAATCACTGA
953027 ATAATCAA
1 ATAATCAA
953035 TTAACAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (32 bp):
ATAATCAAATATCACATTCATATAATCACTGA
Found at i:956224 original size:2 final size:2
Alignment explanation
Indices: 956217--956248 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
956207 CAGGTAAATT
*
956217 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
956249 CTTCTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:965348 original size:17 final size:17
Alignment explanation
Indices: 965326--965360 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
965316 GTAAATACAT
*
965326 AAAAATTTAATTTTTTA
1 AAAAATTTAATTTATTA
*
965343 AAAAATTTTATTTATTA
1 AAAAATTTAATTTATTA
965360 A
1 A
965361 TGAGATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAAATTTAATTTATTA
Found at i:969645 original size:21 final size:22
Alignment explanation
Indices: 969614--969666 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
969604 ATATATAATT
969614 ATATATTTATA-TTTAAAAAATA
1 ATAT-TTTATATTTTAAAAAATA
*
969636 ATGTTTTATATTTTAAAAAATA
1 ATATTTTATATTTTAAAAAATA
969658 ATATTTTAT
1 ATATTTTAT
969667 TAATTTCGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTTTATATTTTAAAAAATA
Found at i:974077 original size:3 final size:3
Alignment explanation
Indices: 974069--974183 Score: 97
Period size: 3 Copynumber: 41.3 Consensus size: 3
974059 GTTGGTGTAC
974069 TAT TAT TA- TAT TA- TAT TA- TAT TA- TAT TA- TAT TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
974110 TA- TAT TAT TAT CA- TAG TAT AAT GTAT TAA TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
* *
974153 TAT TAT TAT TAT TAT TAT TAC TAC TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
974184 GTTGTTGTAG
Statistics
Matches: 93, Mismatches: 8, Indels: 22
0.76 0.07 0.18
Matches are distributed among these distances:
2 19 0.20
3 72 0.77
4 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:974082 original size:5 final size:5
Alignment explanation
Indices: 974072--974170 Score: 103
Period size: 5 Copynumber: 19.2 Consensus size: 5
974062 GGTGTACTAT
*
974072 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TTATCA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA
* * *
974123 TAGTA TAATG TATTA -A-TA TATTA TTATTA TTATTA TTATTA TTATTA
1 TATTA TATTA TATTA TATTA TATTA -TATTA -TATTA -TATTA -TATTA
974170 T
1 T
974171 TACTACTATT
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
3 2 0.02
4 2 0.02
5 52 0.63
6 27 0.33
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:974092 original size:15 final size:16
Alignment explanation
Indices: 974069--974182 Score: 124
Period size: 18 Copynumber: 6.9 Consensus size: 16
974059 GTTGGTGTAC
974069 TATTATTATATTATAT
1 TATTATTATATTATAT
974085 TA-TATTATATTATAT
1 TATTATTATATTATAT
974100 TA-TATTATATTATAT
1 TATTATTATATTATAT
* *
974115 TATTATCATAGTATAAT
1 TATTATTATATTAT-AT
*
974132 GTATTAATATATTATTAT
1 -TATTATTATATTA-TAT
974150 TATTATTATTATTATTAT
1 TATTATTA-TATTA-TAT
*
974168 TATTACTACTATTAT
1 TATTATTA-TATTAT
974183 TGTTGTTGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
15 30 0.35
16 11 0.13
17 10 0.12
18 33 0.39
19 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (16 bp):
TATTATTATATTATAT
Found at i:975115 original size:5 final size:5
Alignment explanation
Indices: 975092--975134 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
975082 TTCCGTTTTC
*
975092 TATTT TCATTT TATTTT TAATT TATTT TATTT TATTT TATTT T
1 TATTT T-ATTT TA-TTT TATTT TATTT TATTT TATTT TATTT T
975135 TGTTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 24 0.71
6 10 0.29
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:975120 original size:16 final size:16
Alignment explanation
Indices: 975099--975149 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
975089 TTCTATTTTC
975099 ATTTTATTTTTAATTT
1 ATTTTATTTTTAATTT
*
975115 ATTTTA-TTTTATTTT
1 ATTTTATTTTTAATTT
*
975130 ATTTT-TGTTTTTATTT
1 ATTTTAT-TTTTAATTT
975146 ATTT
1 ATTT
975150 GCATTTAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
ATTTTATTTTTAATTT
Found at i:981397 original size:37 final size:37
Alignment explanation
Indices: 981356--981428 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
981346 CTTGGTTCGA
981356 TCCAGATCATCTT-TTTGA-TTCTTCAATCTCGGCTCAG
1 TCCAGATCATCTTCTTT-ACTT-TTCAATCTCGGCTCAG
* *
981393 TCCAGGTCATCTTCTTTACTTTTCAATCTTGGCTCA
1 TCCAGATCATCTTCTTTACTTTTCAATCTCGGCTCA
981429 ATCTAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 27 0.84
38 5 0.16
ACGTcount: A:0.18, C:0.27, G:0.12, T:0.42
Consensus pattern (37 bp):
TCCAGATCATCTTCTTTACTTTTCAATCTCGGCTCAG
Found at i:981707 original size:5 final size:5
Alignment explanation
Indices: 981697--981894 Score: 95
Period size: 5 Copynumber: 38.2 Consensus size: 5
981687 TGTGTACTAT
* * *
981697 TATTA TATTA TATTA TATTA TATTA TATTA TATTG TCA-TA TTATCA TAGTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA -TATTA TATTA
* * *
981748 TAGTG TATTA -A-TA TATTA TATAGTA TATTA TATTA TTACTA CTATTA
1 TATTA TATTA TATTA TATTA TAT--TA TATTA TATTA -TATTA -TATTA
* * * *
981795 T-TATA GTTTGTG TACTA TTATTA TATTA TATTA TATTA TATTG TCA-TA
1 TAT-TA -TAT-TA TATTA -TATTA TATTA TATTA TATTA TATTA T-ATTA
* * * *
981843 TTATCA TAGTA TAGTG TATTA -A-TA TATTA TATTA TATAGTA TATTA
1 -TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT--TA TATTA
981889 TATTA T
1 TATTA T
981895 TACTACTATT
Statistics
Matches: 149, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
3 4 0.03
4 5 0.03
5 108 0.72
6 20 0.13
7 12 0.08
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (5 bp):
TATTA
Found at i:981837 original size:106 final size:110
Alignment explanation
Indices: 981707--981908 Score: 367
Period size: 106 Copynumber: 1.9 Consensus size: 110
981697 TATTATATTA
981707 TATTATATTATATTATATTATATTGTCATATTATCATAGTATAGTGTA-T-TA-A-TATATTATA
1 TATTATATTATATTATATTATATTGTCATATTATCATAGTATAGTGTATTATATATTATATTATA
981768 TAGTATATTATATTATTACTACTATTATTATAGTTTGTGTACTAT
66 TAGTATATTATATTATTACTACTATTATTATAGTTTGTGTACTAT
981813 TATTATATTATATTATATTATATTGTCATATTATCATAGTATAGTGTATTAATATATTATATTAT
1 TATTATATTATATTATATTATATTGTCATATTATCATAGTATAGTGTATT-ATATATTATATTAT
981878 ATAGTATATTATATTATTACTACTATTATTA
65 ATAGTATATTATATTATTACTACTATTATTA
981909 CTTTTATTAT
Statistics
Matches: 91, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
106 48 0.53
107 1 0.01
109 2 0.02
110 1 0.01
111 39 0.43
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (110 bp):
TATTATATTATATTATATTATATTGTCATATTATCATAGTATAGTGTATTATATATTATATTATA
TAGTATATTATATTATTACTACTATTATTATAGTTTGTGTACTAT
Found at i:981904 original size:17 final size:17
Alignment explanation
Indices: 981700--981906 Score: 95
Period size: 17 Copynumber: 11.5 Consensus size: 17
981690 GTACTATTAT
981700 TATATTATATTATAT--
1 TATATTATATTATATAC
**
981715 TATATTATATTATATTG
1 TATATTATATTATATAC
*
981732 TCATATTATCA-TAGTATAGTG
1 T-ATATTAT-ATTA-TATA--C
* *
981753 TATTAATATATTATATAG
1 TA-TATTATATTATATAC
981771 TATATTATATTATTACTAC
1 TATATTATATTA-TA-TAC
* *
981790 TATTATTATAGTTTGTGTAC
1 TA-TATTATA--TTATATAC
981810 TATTATTATATTATAT--
1 TA-TATTATATTATATAC
* *
981826 TATATTATATTGTCATAT
1 TATATTATATTAT-ATAC
*
981844 TATCATAGTATAGTGTAT-TAA
1 TAT-AT--TATA-T-TATATAC
*
981865 TATATTATATTATATAG
1 TATATTATATTATATAC
981882 TATATTATATTAT-TAC
1 TATATTATATTATATAC
981898 TACTATTAT
1 TA-TATTAT
981907 TACTTTTATT
Statistics
Matches: 155, Mismatches: 13, Indels: 46
0.72 0.06 0.21
Matches are distributed among these distances:
15 25 0.16
16 11 0.07
17 32 0.21
18 25 0.16
19 10 0.06
20 28 0.18
21 19 0.12
22 3 0.02
23 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (17 bp):
TATATTATATTATATAC
Found at i:981920 original size:106 final size:100
Alignment explanation
Indices: 981694--981924 Score: 329
Period size: 106 Copynumber: 2.2 Consensus size: 100
981684 GTTTGTGTAC
*
981694 TATTATTATATTA-TATTATATTATATTATATTATATTGTCATATTATCATAGTATAGTGTATTA
1 TATTATTTTATTATTATTATATTATATTATATTATATTGTCATATTATCATAGTATAGTGTATTA
981758 ATATATTATATAGTATATTATATTATTACTACTAT
66 ATATATTATATAGTATATTATATTATTACTACTAT
*
981793 TATTATAGTTTGTGTACTATTATTATATTATATTATATTATATTGTCATATTATCATAGTATAGT
1 TA-T-TA--TT-T-TATTATTATTATATTATATTATATTATATTGTCATATTATCATAGTATAGT
981858 GTATTAATATATTATATTATATAGTATATTATATTATTACTACTAT
60 GTA-T--TA-A-TATATTATATAGTATATTATATTATTACTACTAT
981904 TATTACTTTTATTATTATTAT
1 TATTA-TTTTATTATTATTAT
981925 TGTTGTTGTT
Statistics
Matches: 116, Mismatches: 4, Indels: 17
0.85 0.03 0.12
Matches are distributed among these distances:
99 2 0.02
100 1 0.01
101 2 0.02
103 2 0.02
105 4 0.03
106 59 0.51
107 2 0.02
108 2 0.02
109 4 0.03
110 2 0.02
111 36 0.31
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (100 bp):
TATTATTTTATTATTATTATATTATATTATATTATATTGTCATATTATCATAGTATAGTGTATTA
ATATATTATATAGTATATTATATTATTACTACTAT
Found at i:981963 original size:9 final size:9
Alignment explanation
Indices: 981951--981984 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
981941 GTTGTTACTA
981951 TTTTTTTAT
1 TTTTTTTAT
981960 TTTTTTTAT
1 TTTTTTTAT
981969 TTTTTTT-T
1 TTTTTTTAT
981977 CTTTTTTT
1 -TTTTTTT
981985 CGATGCTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 1 0.04
9 23 0.96
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:981966 original size:10 final size:10
Alignment explanation
Indices: 981951--981984 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
981941 GTTGTTACTA
981951 TTTTTTTA-T
1 TTTTTTTATT
981960 TTTTTTTATT
1 TTTTTTTATT
*
981970 TTTTTTTCTT
1 TTTTTTTATT
981980 TTTTT
1 TTTTT
981985 CGATGCTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.06, C:0.03, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:981971 original size:17 final size:17
Alignment explanation
Indices: 981949--981983 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
981939 TTGTTGTTAC
981949 TATTTTTTTATT-TTTTT
1 TATTTTTTT-TTCTTTTT
981966 TATTTTTTTTTCTTTTT
1 TATTTTTTTTTCTTTTT
981983 T
1 T
981984 TCGATGCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.89
Consensus pattern (17 bp):
TATTTTTTTTTCTTTTT
Found at i:982820 original size:19 final size:17
Alignment explanation
Indices: 982798--982863 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 17
982788 TTCTTTTTCC
982798 ATTTTCATTTTATTTTTT
1 ATTTT-ATTTTATTTTTT
982816 GATTTTA-TTTA--TTTT
1 -ATTTTATTTTATTTTTT
982831 ATTTTATTTTATTTTATT
1 ATTTTATTTTATTTT-TT
982849 AGTTTT-TGTTTATTT
1 A-TTTTAT-TTTATTT
982864 GCATTTAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
14 6 0.15
15 8 0.20
17 6 0.15
18 5 0.12
19 16 0.39
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.76
Consensus pattern (17 bp):
ATTTTATTTTATTTTTT
Found at i:982825 original size:5 final size:5
Alignment explanation
Indices: 982798--982848 Score: 63
Period size: 5 Copynumber: 10.6 Consensus size: 5
982788 TTCTTTTTCC
*
982798 ATTTT CATTTT A-TTT -TTTG ATTTT A-TTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT -ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
982846 ATT
1 ATT
982849 AGTTTTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
4 9 0.22
5 26 0.65
6 5 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:982855 original size:15 final size:15
Alignment explanation
Indices: 982798--982848 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
982788 TTCTTTTTCC
982798 ATTTTCATTTTATT-T
1 ATTTT-ATTTTATTGT
*
982813 -TTTGATTTTATT-T
1 ATTTTATTTTATTGT
*
982826 ATTTTATTTTATTTT
1 ATTTTATTTTATTGT
982841 ATTTTATT
1 ATTTTATT
982849 AGTTTTTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 9 0.28
14 14 0.44
15 9 0.28
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (15 bp):
ATTTTATTTTATTGT
Found at i:983369 original size:19 final size:20
Alignment explanation
Indices: 983334--983371 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
983324 ATCTAATGAA
983334 TTTTCTAAAAATAAATAATT
1 TTTTCTAAAAATAAATAATT
983354 TTTTCTAAAAAT-AATAAT
1 TTTTCTAAAAATAAATAAT
983372 AATAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTCTAAAAATAAATAATT
Found at i:991277 original size:17 final size:17
Alignment explanation
Indices: 991240--991292 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
991230 TTTTTATAAG
*
991240 ATTATTGTGATAATATA
1 ATTATTGAGATAATATA
* *
991257 ATTATTGAGATAATTTT
1 ATTATTGAGATAATATA
*
991274 ATTATTAAGATAATCATA
1 ATTATTGAGATAAT-ATA
991292 A
1 A
991293 CGTTCATGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (17 bp):
ATTATTGAGATAATATA
Found at i:991524 original size:40 final size:40
Alignment explanation
Indices: 991460--991537 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
991450 TTGTTTAAAG
* * *
991460 ATAATAATTTTTAAAATATTAATAAT-ATTTATTTATTTT
1 ATAATAATTATTAAAATATAAATAATAATATATTTATTTT
*
991499 ATAATAAATTATTAAATTATAAATAATAATATATTTATT
1 ATAAT-AATTATTAAAATATAAATAATAATATATTTATT
991538 AATAAGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 5 0.15
40 18 0.55
41 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
ATAATAATTATTAAAATATAAATAATAATATATTTATTTT
Found at i:991594 original size:19 final size:18
Alignment explanation
Indices: 991557--991595 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
991547 ATTTATTTTT
**
991557 ATAATATAAATTATTAAA
1 ATAATATAAATTAACAAA
991575 ATAATATCAAATTAACAAA
1 ATAATAT-AAATTAACAAA
991594 AT
1 AT
991596 GAAACCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATATAAATTAACAAA
Found at i:997148 original size:15 final size:15
Alignment explanation
Indices: 997128--997179 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
997118 TAAAAAATAA
997128 ATTTTAAATATTAAT
1 ATTTTAAATATTAAT
997143 ATTTTAAAT-TTAA-
1 ATTTTAAATATTAAT
997156 ATTTATTAAATATT-AT
1 A-TT-TTAAATATTAAT
997172 ATTTTAAA
1 ATTTTAAA
997180 AATAATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 11 0.33
15 18 0.55
16 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTAAATATTAAT
Found at i:997150 original size:22 final size:22
Alignment explanation
Indices: 997125--997179 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
997115 AAATAAAAAA
*
997125 TAAATTTTAAA-TATTAATATTT
1 TAAATTTTAAATTATTAA-ATAT
997147 TAAA-TTTAAATTTATTAAATAT
1 TAAATTTTAAA-TTATTAAATAT
*
997169 TATATTTTAAA
1 TAAATTTTAAA
997180 AATAATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 6 0.21
22 10 0.36
23 12 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATTTTAAATTATTAAATAT
Found at i:997464 original size:14 final size:14
Alignment explanation
Indices: 997445--997480 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
997435 GGTATGAATT
997445 AATTTGAATTATTA
1 AATTTGAATTATTA
*
997459 AATTTGTA-TATTA
1 AATTTGAATTATTA
997472 AATTTGAAT
1 AATTTGAAT
997481 CAAATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
AATTTGAATTATTA
Found at i:997559 original size:18 final size:18
Alignment explanation
Indices: 997536--997575 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
997526 AATCGAATTA
997536 TATATAATTTTT-AATTTT
1 TATAT-ATTTTTAAATTTT
997554 TATATATTTTTAAATTTT
1 TATATATTTTTAAATTTT
997572 TATA
1 TATA
997576 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATATTTTTAAATTTT
Found at i:997655 original size:31 final size:33
Alignment explanation
Indices: 997589--997657 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
997579 TAAAAATAAT
* *
997589 AATTTTATATCAAAATCTATTTAAATATATTAA
1 AATTTTATATCAAAATCAATATAAATATATTAA
* *
997622 AATTTTATATTAAAA-CAATATATATA-ATTAA
1 AATTTTATATCAAAATCAATATAAATATATTAA
997653 AATTT
1 AATTT
997658 AGAATATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 10 0.31
32 8 0.25
33 14 0.44
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (33 bp):
AATTTTATATCAAAATCAATATAAATATATTAA
Found at i:998116 original size:2 final size:2
Alignment explanation
Indices: 998109--998143 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
998099 TTGAACCCAA
*
998109 AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
998144 TAAACATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:1000508 original size:13 final size:15
Alignment explanation
Indices: 1000490--1000522 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1000480 CTTGATGTAC
1000490 ATTTTAA-ATTT-TA
1 ATTTTAATATTTATA
1000503 ATTTTAATATTTATA
1 ATTTTAATATTTATA
1000518 ATTTT
1 ATTTT
1000523 TATTTCTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 4 0.22
15 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTAATATTTATA
Found at i:1000614 original size:2 final size:2
Alignment explanation
Indices: 1000607--1000638 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1000597 GTAACTGGTT
1000607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1000639 AAAGAATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1001564 original size:2 final size:2
Alignment explanation
Indices: 1001557--1001583 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1001547 TTAAACCTTG
1001557 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1001584 TTGAAGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1007804 original size:16 final size:16
Alignment explanation
Indices: 1007785--1007827 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
1007775 AATCATTAAA
1007785 ATTATCATAAATCATC
1 ATTATCATAAATCATC
*
1007801 ATTATCAAACCAAATCATC
1 ATTATC--A-TAAATCATC
1007820 ATTATCAT
1 ATTATCAT
1007828 TCAAATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
16 6 0.27
17 1 0.05
18 1 0.05
19 14 0.64
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTATCATAAATCATC
Found at i:1022176 original size:7 final size:7
Alignment explanation
Indices: 1022166--1022196 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1022156 AAAAATAAAA
1022166 AAATTTT
1 AAATTTT
*
1022173 AAATATT
1 AAATTTT
1022180 AAATTTT
1 AAATTTT
1022187 AAATTTT
1 AAATTTT
1022194 AAA
1 AAA
1022197 ATTATTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
AAATTTT
Found at i:1022185 original size:14 final size:14
Alignment explanation
Indices: 1022166--1022210 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1022156 AAAAATAAAA
1022166 AAATTTTAAATATT
1 AAATTTTAAATATT
*
1022180 AAATTTTAAATTTT
1 AAATTTTAAATATT
*
1022194 AAAATTATTAGATATT
1 -AAATT-TTAAATATT
1022210 A
1 A
1022211 TTTTTTAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 13 0.50
15 6 0.23
16 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
AAATTTTAAATATT
Found at i:1023023 original size:64 final size:64
Alignment explanation
Indices: 1022941--1023060 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 64
1022931 AAAATTTAAG
* *
1022941 GGGATTATTAAAAGCGTTTTTTGC-TATAA-ACTTCTTGAATAATACCC-TCATAAAAAATGGAT
1 GGGATTATTAAAAGCGTTTTTTACAAATAACAC--CTTGAATAAT-CCCTTCATAAAAAATGGAT
1023003 AA
63 AA
*
1023005 GGGATTATTGAATA-CGTTTTTTACAAATAACACCTTGAATAATCCCTTCATAAAAA
1 GGGATTATT-AAAAGCGTTTTTTACAAATAACACCTTGAATAATCCCTTCATAAAAA
1023061 TAGAAGTGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
63 3 0.06
64 37 0.76
65 7 0.14
66 2 0.04
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (64 bp):
GGGATTATTAAAAGCGTTTTTTACAAATAACACCTTGAATAATCCCTTCATAAAAAATGGATAA
Found at i:1023346 original size:63 final size:61
Alignment explanation
Indices: 1022805--1023344 Score: 223
Period size: 62 Copynumber: 8.7 Consensus size: 61
1022795 TAATCTTTTC
* * * * * * * ** *
1022805 TAAAAAATTGAAA-TGATTATTGAATGCGTTTTTAGCAGAAAATACCTTGAATTATCCCCTAA
1 TAAAAAATT-AAAGGGATTATTGAAGGCGTTTTTTGTAAAAAATACCTTCAATAAT-ATCTTA
* * * * * * * * *
1022867 TAAAAAA-TGAAGGTAATTATTGAAGGTGTTTTCTATCAAAAATGCCTTCAATAATCTCATCA
1 TAAAAAATTAAAGG-GATTATTGAAGGCGTTTTTTGTAAAAAATACCTTCAATAATATC-TTA
* * * * * * * * * * *
1022929 TCAAAATTTAAGGGGATTATTAAAAGCGTTTTTTGCTATAAACT-TCTTGAATAATACCCTCA
1 TAAAAAATTAAAGGGATTATTGAAGGCGTTTTTTG-TAAAAAATACCTTCAATAATA-TCTTA
* ** ** * * * **
1022991 TAAAAAATGGATAAGGGATTATTGAATACGTTTTTTACAAATAACACCTTGAATAATCCCTTCA
1 TAAAAAAT-TA-AAGGGATTATTGAAGGCGTTTTTTGTAAAAAATACCTTCAATAATATCTT-A
* *** * ** * * **
1023055 T-AAAAA-TAGAAGTGATTATTGAAGATATTTTCTGCCAAATATTCCTTCAATAAT-TCTCC
1 TAAAAAATTA-AAGGGATTATTGAAGGCGTTTTTTGTAAAAAATACCTTCAATAATATCTTA
* * * *
1023114 TAAAAAATTAGATGAGATTATTGAAGGCGTTTTTTGTCAAAAATACCTTCAATAATATCCTTG
1 TAAAAAATTA-AAGGGATTATTGAAGGCGTTTTTTGTAAAAAATACCTTCAATAATAT-CTTA
* * * * * * * * * *
1023177 TCAAAATTTAAAGGGATTATTGAAGACATTTTTTATATACAACACATTGAATAATAATCTTA
1 TAAAAAATTAAAGGGATTATTGAAGGCGTTTTTTGTAAAAAATACCTTCAATAAT-ATCTTA
* * * * *
1023239 TAAAAAA-TAAAGGTGATTATTGAATGTGTTTTTTGTAAAAAAAATACCTTTAATAAT-TTTTT
1 TAAAAAATTAAAGG-GATTATTGAAGGCGTTTTTTGT--AAAAAATACCTTCAATAATATCTTA
*
1023301 TAAAAAATTAGAGGGAATTATTGAAGGCGTTTTTTAGTAAAAAA
1 TAAAAAATTAAAGGG-ATTATTGAAGGCGTTTTTT-GTAAAAAA
1023345 ATGTTTTAAA
Statistics
Matches: 349, Mismatches: 108, Indels: 42
0.70 0.22 0.08
Matches are distributed among these distances:
59 1 0.00
60 9 0.03
61 82 0.23
62 153 0.44
63 56 0.16
64 48 0.14
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (61 bp):
TAAAAAATTAAAGGGATTATTGAAGGCGTTTTTTGTAAAAAATACCTTCAATAATATCTTA
Found at i:1030717 original size:161 final size:158
Alignment explanation
Indices: 1030548--1031572 Score: 636
Period size: 160 Copynumber: 6.4 Consensus size: 158
1030538 TTTTGATGAT
* * * *
1030548 TTCAATACATGATATTAAACTTATCCAAATTATTAAACTTAGTTTCTATGATTGATATATATAAA
1 TTCAATACATGATATTAAACTTATCCAAATGATTGAACTTAGTTT-TATGATTGATATATGTGAA
* * *
1030613 AAAGTTATTGTTTACATCTACTTTGGACTTTTTGTGCCGTTAATAGGTAAAAATATAAATTTATC
65 AAAGTTATCGTTTACATCTA-TTTAGACTTTTTGTGCCGTTAAAAGG-AAAAATATAAATTTATC
1030678 ATTATTGTTCTATTTTAACAGTTTGAATAGC
128 ATTATTGTTCTATTTTAACAGTTTGAATAGC
* * * *** * * *
1030709 TCCAATACAAGATAATAAACTTATTGGAATGATTGAACCTAGTTTT-TGCAATTGATATGTGTAA
1 TTCAATACATGATATTAAACTTATCCAAATGATTGAACTTAGTTTTATG--ATTGATATATGTGA
* ** * * * * * *
1030773 AAAAGTTATCATTTATGTCTATTTAAAGCTTTTTGTGCTGTTAAGA-GACAAACATGCAA---AT
64 AAAAGTTATCGTTTACATCTATTTAGA-CTTTTTGTGCCGTTAAAAGGAAAAATAT-AAATTTAT
* * *
1030834 --TTGTTGTTCTATTTTAACAATTTGCATAGC
127 CATTATTGTTCTATTTTAACAGTTTGAATAGC
* * * * * * *
1030864 TTCAATACATGATATTAAACTTGTCGAAATAATTAAATTTAGTTTTCA-CATTTGATATGTGTGA
1 TTCAATACATGATATTAAACTTATCCAAATGATTGAACTTAGTTTT-ATGA-TTGATATATGTGA
* * * * * * *
1030928 AAAAGCTAACATTTACAT-TAGTGTAGGACTTTTTATGCCGTTAAAAGGCAAAATGCA-AAATTG
64 AAAAGTTATCGTTTACATCTA-TTTA-GACTTTTTGTGCCGTTAAAAGGAAAAAT--ATAAATTT
*
1030991 AT-ATTATTGTTCTATTTTAACAGTTT-AGATAAC
125 ATCATTATTGTTCTATTTTAACAGTTTGA-ATAGC
* * ** *
1031024 TTTAATACATGATAATAAACTTATCTGAATGATTGAACTT-GATTTCTATTG-TTGATATTTGTG
1 TTCAATACATGATATTAAACTTATCCAAATGATTGAACTTAG-TTT-TA-TGATTGATATATGTG
* * * * *
1031087 AAAAAGTTATCGTTTACGTTTATTTATGACTATTTCTGTCGTTAAAAGGAAAAAATATAAATTT-
63 AAAAAGTTATCGTTTACATCTATTTA-GACTTTTTGTGCCGTTAAAAGG-AAAAATATAAATTTA
* * *
1031151 GCTATTATTATTCTATTTTAACAGTTTGGAT-GC
126 TC-ATTATTGTTCTATTTTAACAGTTTGAATAGC
* * *** * * *
1031184 TTCAATACATAATATTAAACTTTTTTGAATAATTGAACTTGGTTTT-TGCTGTTGATATATGTGA
1 TTCAATACATGATATTAAACTTATCCAAATGATTGAACTTAGTTTTATG--ATTGATATATGTGA
* * * * * *
1031248 AAAAGTTGTTGTTTACCTCTATTTAAGA-TTTTTCGGGCCATTAAAAGGTAAAAATACAAATTTA
64 AAAAGTTATCGTTTACATCTATTT-AGACTTTTT-GTGCCGTTAAAAGG-AAAAATATAAATTTA
* * * * *
1031312 -CTGTTATTTTTCTATTTTAATAATTT-AGATAAC
126 TC-ATTATTGTTCTATTTTAACAGTTTGA-ATAGC
* * * * * * *
1031345 TTTAATACATGATATTAAATTTTTTCAAATGATTGAACTTAGTTCTCA-CAGTTGATAAATGTGA
1 TTCAATACATGATATTAAACTTATCCAAATGATTGAACTTAGTT-TTATGA-TTGATATATGTGA
* * * * * * * * * * *
1031409 AAAAGTTGTTGTTTACCTTTGTTTAAGATTTTTTTTTACCATTAAAAGGCAAAAATACAAAGTT-
64 AAAAGTTATCGTTTACATCTATTT-AGA-CTTTTTGTGCCGTTAAAAGG-AAAAATATAAATTTA
* * * * *
1031473 GCTGTTATTGTTCTGTTTTAACAGCTTGGATAGC
126 TC-ATTATTGTTCTATTTTAACAGTTTGAATAGC
* * * * * * * *
1031507 TTCAATATATGATATTAAATTTGTTCAAATGATTGAATTTGGTTTTCATAATTGATATGTGTGAA
1 TTCAATACATGATATTAAACTTATCCAAATGATTGAACTTAGTTTT-ATGATTGATATATGTGAA
1031572 A
65 A
1031573 GGCCAACATG
Statistics
Matches: 682, Mismatches: 137, Indels: 89
0.75 0.15 0.10
Matches are distributed among these distances:
154 3 0.00
155 107 0.16
156 7 0.01
157 4 0.01
158 1 0.00
159 17 0.02
160 241 0.35
161 193 0.28
162 103 0.15
163 6 0.01
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (158 bp):
TTCAATACATGATATTAAACTTATCCAAATGATTGAACTTAGTTTTATGATTGATATATGTGAAA
AAGTTATCGTTTACATCTATTTAGACTTTTTGTGCCGTTAAAAGGAAAAATATAAATTTATCATT
ATTGTTCTATTTTAACAGTTTGAATAGC
Found at i:1030971 original size:155 final size:156
Alignment explanation
Indices: 1030517--1031048 Score: 380
Period size: 155 Copynumber: 3.4 Consensus size: 156
1030507 CAATTTTGTA
* * * * * * *
1030517 ATTATTGTTTTGTTTTAATAGTTTTGAT-GATTTCAATACATGATATTAAACTTATCCAAATTAT
1 ATTATTGTTCTATTTTAACAG-TTTGATAG-CTTCAATACATGATAATAAACTTATCGAAATAAT
* ** * * * *** * **
1030581 TAAACTTAG-TTTCTATGATTGATATATATAAAAAAGTTATTGTTTACATCTACTTTGGA-CTTT
64 TAAACCTAGTTTTC-ACAATTGATATGTGTAAAAAAGCTAACATTTACATCTA-TGTAAAGCTTT
* * **
1030644 TTGTGCCGTTAATAGGTA-AAAATATAAATTTAT
127 TTATGCCGTTAA-AAG-ACAAAATGCAAA--TAT
* * * * *
1030677 CATTATTGTTCTATTTTAACAGTTTGAATAGCTCCAATACAAGATAATAAACTTATTGGAATGAT
1 -ATTATTGTTCTATTTTAACAGTTTG-ATAGCTTCAATACATGATAATAAACTTATCGAAATAAT
* ** * * ** *
1030742 TGAACCTAGTTTTTGCAATTGATATGTGTAAAAAAGTTATCATTTATGTCTATTTAAAGCTTTTT
64 TAAACCTAGTTTTCACAATTGATATGTGTAAAAAAGCTAACATTTACATCTATGTAAAGCTTTTT
* * *
1030807 GTGCTGTTAAGAGACAAACATGC-AA-AT
129 ATGCCGTTAAAAGACAAA-ATGCAAATAT
* * * *
1030834 -TTGTTGTTCTATTTTAACAATTTGCATAGCTTCAATACATGATATTAAACTTGTCGAAATAATT
1 ATTATTGTTCTATTTTAACAGTTTG-ATAGCTTCAATACATGATAATAAACTTATCGAAATAATT
** * * *
1030898 AAATTTAGTTTTCACATTTGATATGTGTGAAAAAGCTAACATTTACAT-TAGTGT-AGGACTTTT
65 AAACCTAGTTTTCACAATTGATATGTGTAAAAAAGCTAACATTTACATCTA-TGTAAAG-CTTTT
*
1030961 TATGCCGTTAAAAGGCAAAATGCAAAATTGAT
128 TATGCCGTTAAAAGACAAAATGC-AAA-T-AT
* *
1030993 ATTATTGTTCTATTTTAACAGTTTAGATAACTTTAATACATGATAATAAACTTATC
1 ATTATTGTTCTATTTTAACAGTTT-GATAGCTTCAATACATGATAATAAACTTATC
1031049 TGAATGATTG
Statistics
Matches: 293, Mismatches: 63, Indels: 31
0.76 0.16 0.08
Matches are distributed among these distances:
154 8 0.03
155 113 0.39
156 2 0.01
157 2 0.01
159 3 0.01
160 61 0.21
161 100 0.34
162 4 0.01
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (156 bp):
ATTATTGTTCTATTTTAACAGTTTGATAGCTTCAATACATGATAATAAACTTATCGAAATAATTA
AACCTAGTTTTCACAATTGATATGTGTAAAAAAGCTAACATTTACATCTATGTAAAGCTTTTTAT
GCCGTTAAAAGACAAAATGCAAATAT
Found at i:1031081 original size:160 final size:160
Alignment explanation
Indices: 1030397--1031525 Score: 610
Period size: 161 Copynumber: 7.0 Consensus size: 160
1030387 TAAGTTTATA
* * * * *
1030397 ATATTAAACTTAT-TCGAATTATTGAACTTGATTTTTATTGTTAATATATGT-ATTATAATTTA-
1 ATATTAAACTTATCT-GAATAATTGAACTTGATTTCTATTGTTGATATATGTGA--AAAAGTTAT
** *** * * * **
1030459 CAATTTATGTCTATTTTCAAGTTTTTATGTCGTTACAAGGTAAAAATGCAATTTTG-TAATTATT
63 C-ATTTACATCTATTTAGGACTTTTTATGCCGTTAAAAGGTAAAAATGCAAAATTGAT-ATTATT
* * * *
1030523 GTTTTGTTTTAATAGTTTTGAT-GATTTCAATACATG
126 GTTCTATTTTAACAG-TTTGATAG-CTTCAATACATG
** * * * * *
1030559 ATATTAAACTTATCCAAATTATTAAACTT-AGTTTCTA-TGATTGATATATATAAAAAAGTTATT
1 ATATTAAACTTATCTGAATAATTGAACTTGA-TTTCTATTG-TTGATATATGTGAAAAAGTTATC
* * * *
1030622 GTTTACATCTACTTT-GGACTTTTTGTGCCGTTAATAGGTAAAAAT--ATAAATTTATCATTATT
64 ATTTACATCTA-TTTAGGACTTTTTATGCCGTTAAAAGGTAAAAATGCA-AAATTGAT-ATTATT
* *
1030684 GTTCTATTTTAACAGTTTGAATAGCTCCAATACAAG
126 GTTCTATTTTAACAGTTTG-ATAGCTTCAATACATG
* * * * * *
1030720 ATAATAAACTTAT-TGGAATGATTGAACCT-AGTT-T-TTGCAATTGATATGTGTAAAAAAGTTA
1 ATATTAAACTTATCT-GAATAATTGAACTTGATTTCTATTG---TTGATATATGTGAAAAAGTTA
** * * * * ** * *
1030781 TCATTTATGTCTATTTA-AAGCTTTTTGTGCTGTTAAGAGACAAACATGC--AA---AT-TTGTT
62 TCATTTACATCTATTTAGGA-CTTTTTATGCCGTTAAAAGGTAAAAATGCAAAATTGATATTATT
*
1030839 GTTCTATTTTAACAATTTGCATAGCTTCAATACATG
126 GTTCTATTTTAACAGTTTG-ATAGCTTCAATACATG
* * * * * * * *
1030875 ATATTAAACTTGTC-GAAATAATTAAATTTAGTTTTC-ACAT-TTGATATGTGTGAAAAAGCTAA
1 ATATTAAACTTATCTG-AATAATTGAACTT-GATTTCTA-TTGTTGATATATGTGAAAAAGTTAT
* *
1030937 CATTTACAT-TAGTGTAGGACTTTTTATGCCGTTAAAAGG-CAAAATGCAAAATTGATATTATTG
63 CATTTACATCTA-TTTAGGACTTTTTATGCCGTTAAAAGGTAAAAATGCAAAATTGATATTATTG
* *
1031000 TTCTATTTTAACAGTTTAGATAACTTTAATACATG
127 TTCTATTTTAACAGTTT-GATAGCTTCAATACATG
* * * *
1031035 ATAATAAACTTATCTGAATGATTGAACTTGATTTCTATTGTTGATATTTGTGAAAAAGTTATCGT
1 ATATTAAACTTATCTGAATAATTGAACTTGATTTCTATTGTTGATATATGTGAAAAAGTTATCAT
* * * * * * * ** * * *
1031100 TTACGTTTATTTATGACTATTTCTGTCGTTAAAAGGAAAAAATATAAATTTGCTATTATTATTCT
66 TTACATCTATTTAGGACTTTTTATGCCGTTAAAAGGTAAAAATGCAAAATTGATATTATTGTTCT
*
1031165 ATTTTAACAGTTTGGAT-GCTTCAATACATA
131 ATTTTAACAGTTT-GATAGCTTCAATACATG
* * * * ** * **
1031195 ATATTAAACTTTTTTGAATAATTGAACTTGGTTTTTGCTGTTGATATATGTGAAAAAGTTGTTGT
1 ATATTAAACTTATCTGAATAATTGAACTTGATTTCTATTGTTGATATATGTGAAAAAGTTATCAT
* * ** * * * * *
1031260 TTACCTCTATTTAAGA-TTTTTCGGGCCATTAAAAGGTAAAAATAC-AAATTTACTGTTATTTTT
66 TTACATCTATTTAGGACTTTTT-ATGCCGTTAAAAGGTAAAAATGCAAAATTGA-TATTATTGTT
* * * *
1031323 CTATTTTAATAATTTAGATAACTTTAATACATG
129 CTATTTTAACAGTTT-GATAGCTTCAATACATG
* * * * * ** * * *
1031356 ATATTAAA-TTTTTTCAAATGATTGAACTT-AGTTCTCACAGTTGATAAATGTGAAAAAGTTGTT
1 ATATTAAACTTATCT-GAATAATTGAACTTGATTTCT-ATTGTTGATATATGTGAAAAAGTTATC
* * * * * * * * * * * * * *
1031419 GTTTACCTTTGTTTAAGATTTTTTTTTACCATTAAAAGGCAAAAATACAAAGTTGCTGTTATTGT
64 ATTTACATCTATTTAGGA-CTTTTTATGCCGTTAAAAGGTAAAAATGCAAAATTGATATTATTGT
* * *
1031484 TCTGTTTTAACAGCTTGGATAGCTTCAATATATG
128 TCTATTTTAACAG-TTTGATAGCTTCAATACATG
1031518 ATATTAAA
1 ATATTAAA
1031526 TTTGTTCAAA
Statistics
Matches: 756, Mismatches: 163, Indels: 96
0.74 0.16 0.09
Matches are distributed among these distances:
154 9 0.01
155 101 0.13
156 3 0.00
157 4 0.01
159 21 0.03
160 248 0.33
161 256 0.34
162 102 0.13
163 12 0.02
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (160 bp):
ATATTAAACTTATCTGAATAATTGAACTTGATTTCTATTGTTGATATATGTGAAAAAGTTATCAT
TTACATCTATTTAGGACTTTTTATGCCGTTAAAAGGTAAAAATGCAAAATTGATATTATTGTTCT
ATTTTAACAGTTTGATAGCTTCAATACATG
Found at i:1040038 original size:20 final size:20
Alignment explanation
Indices: 1040009--1040048 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1039999 AAATTTTATG
1040009 AAAAAATATTATAGAATATT
1 AAAAAATATTATAGAATATT
* * *
1040029 AAAAATTATTTTATAATATT
1 AAAAAATATTATAGAATATT
1040049 TTTAGTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAAAATATTATAGAATATT
Found at i:1042382 original size:23 final size:21
Alignment explanation
Indices: 1042351--1042393 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1042341 TTCTTTTTCT
1042351 TAATCTTTTTCTATTTTTCAGTA
1 TAATCTTTTT-T-TTTTTCAGTA
*
1042374 TAATTTTTTTTTTTTTCAGT
1 TAATCTTTTTTTTTTTCAGT
1042394 TTGAATAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 1 0.05
23 9 0.47
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (21 bp):
TAATCTTTTTTTTTTTCAGTA
Found at i:1055038 original size:16 final size:17
Alignment explanation
Indices: 1055017--1055052 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1055007 TTTTTTTTGT
1055017 TTTTAATTTAATC-TCC
1 TTTTAATTTAATCATCC
*
1055033 TTTTAATTTGATCATCC
1 TTTTAATTTAATCATCC
1055050 TTT
1 TTT
1055053 GAAATGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.22, C:0.17, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTAATTTAATCATCC
Found at i:1056002 original size:24 final size:26
Alignment explanation
Indices: 1055945--1056022 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
1055935 ATAAATAAAA
1055945 TTTTATTAA-ATAATTAAAT-TAT-TAT
1 TTTTATTAATATAA--AAATATATATAT
*
1055970 TTTAAATTAAT-TAAAAATA-ATATAT
1 TTT-TATTAATATAAAAATATATATAT
**
1055995 TTTTATTAATATATTAATATATATAT
1 TTTTATTAATATAAAAATATATATAT
1056021 TT
1 TT
1056023 ATAAAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
24 12 0.28
25 15 0.35
26 16 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTATTAATATAAAAATATATATAT
Found at i:1056034 original size:24 final size:22
Alignment explanation
Indices: 1055982--1056034 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
1055972 TAAATTAATT
*
1055982 AAAAA-TAATATATTTTTATTA
1 AAAAATTAATATATTTTTATAA
* *
1056003 ATATATTAATATATATATTTATAA
1 AAAAATTAATATAT-T-TTTATAA
1056027 AAAAATTA
1 AAAAATTA
1056035 TCTAAATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 3 0.12
22 8 0.33
23 1 0.04
24 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAATTAATATATTTTTATAA
Found at i:1056210 original size:13 final size:14
Alignment explanation
Indices: 1056186--1056215 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1056176 TAGAGATAAT
1056186 ATAAAAATTAAAAA
1 ATAAAAATTAAAAA
1056200 ATAAAAA-TAAAAA
1 ATAAAAATTAAAAA
1056213 ATA
1 ATA
1056216 CTCTATCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAAAAATTAAAAA
Found at i:1067686 original size:3 final size:3
Alignment explanation
Indices: 1067680--1067706 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1067670 TTCTTCTCCT
1067680 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1067707 GTGTCACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1081730 original size:2 final size:2
Alignment explanation
Indices: 1081725--1081755 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1081715 TGCAGACTTT
*
1081725 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1081756 CTTTTGGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1083156 original size:12 final size:13
Alignment explanation
Indices: 1083131--1083159 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1083121 ATTAAGACGA
1083131 TAATTTTGTAAAT
1 TAATTTTGTAAAT
1083144 TAATTTT-TAAAT
1 TAATTTTGTAAAT
1083156 TAAT
1 TAAT
1083160 CAATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
TAATTTTGTAAAT
Found at i:1087273 original size:87 final size:87
Alignment explanation
Indices: 1087126--1087298 Score: 265
Period size: 87 Copynumber: 2.0 Consensus size: 87
1087116 GCAGGAAAGT
* * * *
1087126 CAACCTTCAAAGTATATTGAAGAAGACACTCATAACCTAACGGAGCATGACACTGGGGATGCACC
1 CAACCTTCAAAGAATATTGAAGAAGACACTCAAAACCTAACGGAGCATAACACTGAGGATGCACC
1087191 AAATGCAGTTCAAAGCAGAGAA
66 AAATGCAGTTCAAAGCAGAGAA
* * *
1087213 CAACCTTCAAAGAATATTGAAGAAGATACTCAAAACTTAACTGAGCATAACACTGAGGATGCACC
1 CAACCTTCAAAGAATATTGAAGAAGACACTCAAAACCTAACGGAGCATAACACTGAGGATGCACC
* *
1087278 GAATGCAGTTCAAAGTAGAGA
66 AAATGCAGTTCAAAGCAGAGA
1087299 CGACTTGAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (87 bp):
CAACCTTCAAAGAATATTGAAGAAGACACTCAAAACCTAACGGAGCATAACACTGAGGATGCACC
AAATGCAGTTCAAAGCAGAGAA
Found at i:1093322 original size:15 final size:16
Alignment explanation
Indices: 1093295--1093324 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1093285 TTTCTTTCTA
1093295 TTACTTAATAAGTTGT
1 TTACTTAATAAGTTGT
1093311 TTACTT-ATAAGTTG
1 TTACTTAATAAGTTG
1093325 CCCTTCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (16 bp):
TTACTTAATAAGTTGT
Found at i:1095046 original size:28 final size:29
Alignment explanation
Indices: 1095015--1095083 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
1095005 ATACCGTAAG
*
1095015 TAAAAATAATTATAAAAATAAAA-A-TATA
1 TAAAAATAATTAAAAAAATAAAATATTA-A
*
1095043 TAAAATTAA-TAAAAAAATAAAATATTAA
1 TAAAAATAATTAAAAAAATAAAATATTAA
*
1095071 TAAAAATGATTAA
1 TAAAAATAATTAA
1095084 TTATTTGATC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 12 0.35
28 17 0.50
29 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (29 bp):
TAAAAATAATTAAAAAAATAAAATATTAA
Found at i:1095053 original size:19 final size:19
Alignment explanation
Indices: 1095031--1095077 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1095021 TAATTATAAA
1095031 AATAAAAATATATAAA-ATT
1 AATAAAAATATA-AAATATT
*
1095050 AATAAAAAAATAAAATATT
1 AATAAAAATATAAAATATT
1095069 AATAAAAAT
1 AATAAAAAT
1095078 GATTAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAAAAATATAAAATATT
Found at i:1095189 original size:7 final size:7
Alignment explanation
Indices: 1095172--1095205 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1095162 ATAAATAATA
1095172 ATTATTAT
1 ATTATT-T
1095180 ATTATTT
1 ATTATTT
*
1095187 ATTAGTT
1 ATTATTT
1095194 ATTATTT
1 ATTATTT
1095201 ATTAT
1 ATTAT
1095206 ATTTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (7 bp):
ATTATTT
Found at i:1096128 original size:2 final size:2
Alignment explanation
Indices: 1096121--1096147 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1096111 ACTAACTAAT
1096121 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1096148 CCCGGAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1112225 original size:31 final size:32
Alignment explanation
Indices: 1112189--1112248 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1112179 AAAAATCTTT
*
1112189 GTTGATTTTCT-ACCTTTTGTAGATTCACTTA
1 GTTGATTTTCTAACCTTTTATAGATTCACTTA
1112220 GTTGATTTTCTAACCTTTTATAGATTCAC
1 GTTGATTTTCTAACCTTTTATAGATTCAC
1112249 CGTCACCTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.50
Consensus pattern (32 bp):
GTTGATTTTCTAACCTTTTATAGATTCACTTA
Found at i:1119275 original size:15 final size:16
Alignment explanation
Indices: 1119251--1119288 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1119241 ATGATATCTC
1119251 AATTTAAAAA-TATAA
1 AATTTAAAAATTATAA
* *
1119266 AATTTTAAAATTATTA
1 AATTTAAAAATTATAA
1119282 AATTTAA
1 AATTTAA
1119289 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAAAAATTATAA
Found at i:1119433 original size:24 final size:25
Alignment explanation
Indices: 1119395--1119450 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
1119385 TTGTTCATCT
1119395 TATTTTTTGAGATATCTCAAAA-TTA
1 TATTTTTTGAGATAT-TCAAAAGTTA
* * *
1119420 TATTTTTTTA-ATATTTAAAAGTTT
1 TATTTTTTGAGATATTCAAAAGTTA
1119444 TATTTTT
1 TATTTTT
1119451 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.19
24 13 0.48
25 9 0.33
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (25 bp):
TATTTTTTGAGATATTCAAAAGTTA
Found at i:1119468 original size:24 final size:23
Alignment explanation
Indices: 1119413--1119469 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
1119403 GAGATATCTC
*
1119413 AAAATTATATTTTTTTAATATTT
1 AAAATTATTTTTTTTTAATATTT
* *
1119436 AAAAGT-TTTATTTTT-ATATTTT
1 AAAATTATTTTTTTTTAATA-TTT
1119458 AAAATTATTTTT
1 AAAATTATTTTT
1119470 ATGATTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 3 0.11
22 15 0.56
23 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
AAAATTATTTTTTTTTAATATTT
Found at i:1119903 original size:7 final size:7
Alignment explanation
Indices: 1119893--1119917 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1119883 TATTAAATAT
1119893 ATATAAA
1 ATATAAA
1119900 ATATAAA
1 ATATAAA
1119907 ATATAAA
1 ATATAAA
1119914 ATAT
1 ATAT
1119918 TTATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATATAAA
Found at i:1121664 original size:16 final size:16
Alignment explanation
Indices: 1121645--1121677 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1121635 ATTTAATTTA
1121645 TATTT-AAATAAATTAT
1 TATTTCAAA-AAATTAT
1121661 TATTTCAAAAAATTAT
1 TATTTCAAAAAATTAT
1121677 T
1 T
1121678 TATGTTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTCAAAAAATTAT
Found at i:1121759 original size:26 final size:28
Alignment explanation
Indices: 1121730--1121793 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
1121720 TTTAAAAATA
*
1121730 AATTAAAAATTAATTATTT-TTT-ATGT
1 AATTAAAAATCAATTATTTATTTAATGT
* *
1121756 AATTTAAAATCAATTTTTTATTTGAATGT
1 AATTAAAAATCAATTATTTATTT-AATGT
1121785 AA-TAAAAAT
1 AATTAAAAAT
1121794 ATAAAAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 16 0.52
27 3 0.10
28 6 0.19
29 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (28 bp):
AATTAAAAATCAATTATTTATTTAATGT
Found at i:1126418 original size:11 final size:11
Alignment explanation
Indices: 1126404--1126446 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1126394 TTTAAAACTC
1126404 ATTTATTTATT
1 ATTTATTTATT
*
1126415 ATTTATTTGTT
1 ATTTATTTATT
* *
1126426 ATTTGTTTACT
1 ATTTATTTATT
*
1126437 ATTTGTTTAT
1 ATTTATTTAT
1126447 AATAGTATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:1126540 original size:15 final size:15
Alignment explanation
Indices: 1126522--1126567 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1126512 TTTGTATTCG
1126522 TTTAAAATTTATTTA
1 TTTAAAATTTATTTA
1126537 TTT-AAATTTATTTGA
1 TTTAAAATTTATTT-A
* *
1126552 -TTATAATTTTTTTA
1 TTTAAAATTTATTTA
1126566 TT
1 TT
1126568 ATTTATGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTAAAATTTATTTA
Found at i:1126596 original size:26 final size:26
Alignment explanation
Indices: 1126528--1126614 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
1126518 TTCGTTTAAA
* * *
1126528 ATTTATTTATTTAAATTTATTTGATTAT
1 ATTTATTTATATATATTTA--TGATCAT
1126556 AATTT-TTT-TAT-TATTTATGATCAT
1 -ATTTATTTATATATATTTATGATCAT
1126580 ATTTATTTATATATATTTAT-ATACAT
1 ATTTATTTATATATATTTATGAT-CAT
*
1126606 ATTCATTTA
1 ATTTATTTA
1126615 ATGTTTACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 4 0.08
24 9 0.18
25 5 0.10
26 23 0.46
27 2 0.04
28 3 0.06
29 4 0.08
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTATTTATATATATTTATGATCAT
Found at i:1151629 original size:21 final size:22
Alignment explanation
Indices: 1151586--1151630 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1151576 TGATATTGGT
**
1151586 GGTTTATCCTTTGATGATTCAA
1 GGTTTATCCTTTGATGAGCCAA
1151608 GGTTT-TCCTTTGATGAGCCAA
1 GGTTTATCCTTTGATGAGCCAA
1151629 GG
1 GG
1151631 GCTTCTTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (22 bp):
GGTTTATCCTTTGATGAGCCAA
Found at i:1152274 original size:84 final size:84
Alignment explanation
Indices: 1152150--1152362 Score: 216
Period size: 84 Copynumber: 2.5 Consensus size: 84
1152140 TGATGGGAGG
* * * * *
1152150 CTAGCAGAGTCGTTGCAGAAGCTT-AGGAGGGTGGCAAATGGAGATGAAGATAGAGGTATTA-GA
1 CTAGCAGAGTCATTGCTGAA-ATTGAGGAGGGTGGCAAATGGAGATGAAGATAAAAGTA-TACGA
1152213 GGAAATGTAGG-TGAAGGAACA
64 GGAAATGT-GGCTGAAGGAACA
* * * * *
1152234 CTGGCGGAGTCATTGCTGAAATTGAGGAGGTTGGCTAATGGAGATGAAGGTAAAAGTATACGAGG
1 CTAGCAGAGTCATTGCTGAAATTGAGGAGGGTGGCAAATGGAGATGAAGATAAAAGTATACGAGG
*
1152299 AAATGTGGCTGATGGAACA
66 AAATGTGGCTGAAGGAACA
* ** * * * *
1152318 CTAGCAGAGTCTTTGCACAAGTTAAGAAGGGTGGCCAATGGAGAT
1 CTAGCAGAGTCATTGCTGAAATTGAGGAGGGTGGCAAATGGAGAT
1152363 TCAAATGGGA
Statistics
Matches: 105, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
83 6 0.06
84 99 0.94
ACGTcount: A:0.33, C:0.10, G:0.35, T:0.21
Consensus pattern (84 bp):
CTAGCAGAGTCATTGCTGAAATTGAGGAGGGTGGCAAATGGAGATGAAGATAAAAGTATACGAGG
AAATGTGGCTGAAGGAACA
Found at i:1158783 original size:9 final size:9
Alignment explanation
Indices: 1158765--1158795 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1158755 CCATATGAGT
1158765 ATACGTTTA
1 ATACGTTTA
*
1158774 ATATGTTTA
1 ATACGTTTA
1158783 ATACGTTTA
1 ATACGTTTA
1158792 ATAC
1 ATAC
1158796 ATCTTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (9 bp):
ATACGTTTA
Found at i:1159285 original size:29 final size:29
Alignment explanation
Indices: 1159240--1159321 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
1159230 TTGTGTTCTT
*
1159240 GTATATAT-TCGTGTTAGTCGTATCTATTC
1 GTATATATCT-GTATTAGTCGTATCTATTC
* * * *
1159269 GTGTATATCTGTATTAGTCATGTTTATTC
1 GTATATATCTGTATTAGTCGTATCTATTC
* *
1159298 GTATATATTTGTATTATTCGTATC
1 GTATATATCTGTATTAGTCGTATC
1159322 GTGTTTAAAC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 40 0.98
30 1 0.02
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.51
Consensus pattern (29 bp):
GTATATATCTGTATTAGTCGTATCTATTC
Found at i:1165433 original size:13 final size:13
Alignment explanation
Indices: 1165415--1165457 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1165405 AAGATTATCG
1165415 AATTTTATAAAAA
1 AATTTTATAAAAA
* *
1165428 AATTTTGTAACAA
1 AATTTTATAAAAA
* *
1165441 AATTTAAAAAAAA
1 AATTTTATAAAAA
1165454 AATT
1 AATT
1165458 ATGAAGTTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
AATTTTATAAAAA
Found at i:1190365 original size:15 final size:17
Alignment explanation
Indices: 1190345--1190376 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1190335 AATATTATGT
1190345 TTTATTT-T-TAAAAAA
1 TTTATTTATATAAAAAA
1190360 TTTATTTATATAAAAAA
1 TTTATTTATATAAAAAA
1190377 ATAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTATTTATATAAAAAA
Found at i:1190403 original size:18 final size:18
Alignment explanation
Indices: 1190354--1190416 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 18
1190344 TTTTATTTTT
*
1190354 AAAAAATT-TATTTATATA
1 AAAAAATTATATTAAT-TA
*
1190372 AAAAAA-TA-A-AAATTA
1 AAAAAATTATATTAATTA
*
1190387 AAAAAATTATATTAATTT
1 AAAAAATTATATTAATTA
*
1190405 AAAAATTTATAT
1 AAAAAATTATAT
1190417 GCATGTTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 8 0.22
16 4 0.11
17 3 0.08
18 21 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAAATTATATTAATTA
Found at i:1209208 original size:8 final size:8
Alignment explanation
Indices: 1209161--1209212 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
1209151 ATATCTAATG
*
1209161 TAAATAAA
1 TAAATATA
*
1209169 TAAATAAA
1 TAAATATA
1209177 TAAATAATA
1 TAAAT-ATA
*
1209186 TATATATA
1 TAAATATA
*
1209194 TATATATA
1 TAAATATA
1209202 TAAATAT-
1 TAAATATA
1209209 TAAA
1 TAAA
1209213 AGAAGAATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
7 4 0.10
8 30 0.75
9 6 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAATATA
Found at i:1209208 original size:12 final size:12
Alignment explanation
Indices: 1209164--1209208 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1209154 TCTAATGTAA
* *
1209164 ATAAATAAATAA
1 ATAAATATATAT
1209176 ATAAATAATATAT
1 ATAAAT-ATATAT
*
1209189 ATATATATATAT
1 ATAAATATATAT
1209201 ATAAATAT
1 ATAAATAT
1209209 TAAAAGAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:1217409 original size:14 final size:15
Alignment explanation
Indices: 1217390--1217418 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1217380 AAAATTATCA
1217390 AAATTTTA-AATTTT
1 AAATTTTATAATTTT
1217404 AAATTTTATAATTTT
1 AAATTTTATAATTTT
1217419 TATATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAATTTTATAATTTT
Found at i:1221106 original size:24 final size:24
Alignment explanation
Indices: 1221074--1221123 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1221064 GGCAATTAGA
1221074 TGTCAGCACAAGCTGAAGATAGCT
1 TGTCAGCACAAGCTGAAGATAGCT
1221098 TGTCAGCACAAGCTGAAGATAGCT
1 TGTCAGCACAAGCTGAAGATAGCT
1221122 TG
1 TG
1221124 ATGCTGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (24 bp):
TGTCAGCACAAGCTGAAGATAGCT
Found at i:1224289 original size:30 final size:30
Alignment explanation
Indices: 1224253--1224316 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1224243 TCAAATATTG
* *
1224253 AATATTTTATTGAATTTAATTAAATTTTTA
1 AATATTTTATTGAATTTAATTAAAATTGTA
**
1224283 AATA-TTTATTTTATTTAATTAAAATTGTA
1 AATATTTTATTGAATTTAATTAAAATTGTA
1224312 AATAT
1 AATAT
1224317 CTATTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
AATATTTTATTGAATTTAATTAAAATTGTA
Found at i:1224322 original size:29 final size:30
Alignment explanation
Indices: 1224266--1224332 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
1224256 ATTTTATTGA
* * *
1224266 ATTTAATTAAATTTTTAAATATTTA-TTTT
1 ATTTAATTAAAATTGTAAATATCTATTTTT
1224295 ATTTAATTAAAATTGTAAATATCTATTTTT
1 ATTTAATTAAAATTGTAAATATCTATTTTT
*
1224325 ATTCAATT
1 ATTTAATT
1224333 TAATTCTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (30 bp):
ATTTAATTAAAATTGTAAATATCTATTTTT
Found at i:1230609 original size:75 final size:75
Alignment explanation
Indices: 1230515--1230666 Score: 234
Period size: 75 Copynumber: 2.0 Consensus size: 75
1230505 ACCGCATACT
* * *
1230515 TTGAGTCAAGGGCTAAATTTGTAATTTGAAAATGA-TTCTATTCTCACTTCTTTATATTCTTTCA
1 TTGAGCCAAGGGCTAAATTTGTAATTTGAAAAT-ACTTCTATTCTCACTGCTTTATATTCCTTCA
1230579 GAGGAAAAAAC
65 GAGGAAAAAAC
* * *
1230590 TTGAGCCAAGGGCTAAATTTGTAATTTGGAAATACTTCTTTTCTCTCTGCTTTATATTCCTTCAG
1 TTGAGCCAAGGGCTAAATTTGTAATTTGAAAATACTTCTATTCTCACTGCTTTATATTCCTTCAG
1230655 AGGAAAAAAC
66 AGGAAAAAAC
1230665 TT
1 TT
1230667 AGTTCAAGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
74 1 0.01
75 69 0.99
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (75 bp):
TTGAGCCAAGGGCTAAATTTGTAATTTGAAAATACTTCTATTCTCACTGCTTTATATTCCTTCAG
AGGAAAAAAC
Found at i:1235175 original size:9 final size:9
Alignment explanation
Indices: 1235161--1235185 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1235151 AACATAAGTA
1235161 AACAATAGT
1 AACAATAGT
1235170 AACAATAGT
1 AACAATAGT
1235179 AACAATA
1 AACAATA
1235186 CTTATAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (9 bp):
AACAATAGT
Found at i:1237926 original size:3 final size:3
Alignment explanation
Indices: 1237918--1237950 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1237908 TTCTAGTATT
1237918 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1237951 CTATTAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1246778 original size:18 final size:18
Alignment explanation
Indices: 1246757--1246801 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1246747 GGCTGGGGCA
1246757 GAGGCTGAGGCTGAGACT
1 GAGGCTGAGGCTGAGACT
* * *
1246775 GAGGCTGAAGCTGTGCCT
1 GAGGCTGAGGCTGAGACT
*
1246793 CAGGCTGAG
1 GAGGCTGAG
1246802 CTTGAGGAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.42, T:0.18
Consensus pattern (18 bp):
GAGGCTGAGGCTGAGACT
Found at i:1246781 original size:30 final size:30
Alignment explanation
Indices: 1246724--1246781 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1246714 GGCTGGCTTT
* *
1246724 GCAGAGGATGTGGCTGCAGCTGGGGCTGGG
1 GCAGAGGATGAGGCTGCAGCTGAGGCTGGG
*
1246754 GCAGAGGCTGAGGCTG-AGACTGAGGCTG
1 GCAGAGGATGAGGCTGCAG-CTGAGGCTG
1246782 AAGCTGTGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.16
Consensus pattern (30 bp):
GCAGAGGATGAGGCTGCAGCTGAGGCTGGG
Found at i:1258132 original size:2 final size:2
Alignment explanation
Indices: 1258125--1258150 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1258115 AACCAGTTAA
1258125 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1258151 TTAATGCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1261264 original size:20 final size:20
Alignment explanation
Indices: 1261241--1261278 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1261231 CAATTAATTT
*
1261241 TAAATTAAATTATTTAAAAC
1 TAAATTAAATTAATTAAAAC
1261261 TAAATTAAATTAATTAAA
1 TAAATTAAATTAATTAAA
1261279 TTAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATTAAATTAATTAAAAC
Found at i:1261277 original size:4 final size:5
Alignment explanation
Indices: 1261240--1261286 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
1261230 TCAATTAATT
* *
1261240 TTAAA TTAAA TT-AT TTAAAA CTAAA TTAAA TT-AA TTAAA TTAAA TTA
1 TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TTAAA TTA
1261287 TTTTAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 7 0.20
5 26 0.74
6 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:1261987 original size:23 final size:23
Alignment explanation
Indices: 1261961--1262004 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1261951 AATATCGATT
1261961 TTTAAGTTT-TAAAATTAATAAGA
1 TTTAA-TTTATAAAATTAATAAGA
*
1261984 TTTAATTTATTAAATTAATAA
1 TTTAATTTATAAAATTAATAA
1262005 TTTTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
TTTAATTTATAAAATTAATAAGA
Found at i:1262891 original size:22 final size:21
Alignment explanation
Indices: 1262835--1262891 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
1262825 TTGAAATTTT
* *
1262835 TTTTTATTTTAAATATTTATA
1 TTTTTATTTTTATTATTTATA
**
1262856 TATTTT-TTCATATTATTTAATA
1 T-TTTTATTTTTATTATTT-ATA
1262878 TTTTTATTTTTATT
1 TTTTTATTTTTATT
1262892 TTTTCTATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTATTTTTATTATTTATA
Found at i:1280918 original size:2 final size:2
Alignment explanation
Indices: 1280911--1280941 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1280901 CACGATCGCT
*
1280911 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1280942 TTATTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1284068 original size:14 final size:15
Alignment explanation
Indices: 1284039--1284125 Score: 59
Period size: 15 Copynumber: 5.3 Consensus size: 15
1284029 ATTTTATAAT
1284039 TTTTTTAAAAATTTA
1 TTTTTTAAAAATTTA
*
1284054 TTTTTTAAATATTATA
1 TTTTTTAAAAATT-TA
* *
1284070 TAATTTATTGAAAA-TAA
1 T--TTT-TTAAAAATTTA
1284087 TTTTTTTAAAAATTATAA
1 -TTTTTTAAAAATT-T-A
1284105 TACTTTTTAAAAATTTA
1 T--TTTTTAAAAATTTA
1284122 TTTT
1 TTTT
1284126 GTTGGGAATC
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
15 21 0.38
16 7 0.12
17 4 0.07
18 7 0.12
19 17 0.30
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (15 bp):
TTTTTTAAAAATTTA
Found at i:1284125 original size:35 final size:35
Alignment explanation
Indices: 1284032--1284125 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 35
1284022 TCAATAAATT
* *
1284032 TTATAAT-TTTTTTAAAAATTTA-TTTTTTAAATA
1 TTATAATAATTTTTAAAAATTTATTTTTTTAAAAA
* *
1284065 TTAT-ATAATTTATTGAAAA-TAATTTTTTTAAAAA
1 TTATAATAATTT-TTAAAAATTTATTTTTTTAAAAA
*
1284099 TTATAATACTTTTTAAAAATTTATTTT
1 TTATAATAATTTTTAAAAATTTATTTT
1284126 GTTGGGAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
32 2 0.04
33 9 0.18
34 26 0.53
35 12 0.24
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (35 bp):
TTATAATAATTTTTAAAAATTTATTTTTTTAAAAA
Found at i:1298243 original size:3 final size:3
Alignment explanation
Indices: 1298235--1298267 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1298225 TTGTGGGTAA
1298235 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1298268 TTGTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1300576 original size:29 final size:30
Alignment explanation
Indices: 1300520--1300576 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1300510 TAATAATTTT
* * *
1300520 AAAAATTTTAAATGGTAGATTTTTTTTAAA
1 AAAAATTTTAAATGGAAGAATTTCTTTAAA
*
1300550 AAAAATTTTAGAT-GAAGAATTTCTTTA
1 AAAAATTTTAAATGGAAGAATTTCTTTA
1300577 GATTTGATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 11 0.48
30 12 0.52
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (30 bp):
AAAAATTTTAAATGGAAGAATTTCTTTAAA
Found at i:1300661 original size:7 final size:7
Alignment explanation
Indices: 1300641--1300683 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
1300631 TATTTTTTTT
*
1300641 AAATGAA
1 AAATTAA
*
1300648 AATTTAA
1 AAATTAA
1300655 AAATTAA
1 AAATTAA
1300662 AAATTAA
1 AAATTAA
*
1300669 AAA-TAT
1 AAATTAA
1300675 AAATTAA
1 AAATTAA
1300682 AA
1 AA
1300684 TTTTCGGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:1302156 original size:24 final size:26
Alignment explanation
Indices: 1302128--1302190 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 26
1302118 ATATTTAATT
* *
1302128 TATTATTAATATATAAAAT-TTA-TA
1 TATTATTAATAAATAAAATAATATTA
1302152 TATTATTAATAAATAAAATAATATTA
1 TATTATTAATAAATAAAATAATATTA
*
1302178 TTTTATTAATAAA
1 TATTATTAATAAA
1302191 ATTAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 18 0.53
25 2 0.06
26 14 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTATTAATAAATAAAATAATATTA
Found at i:1302209 original size:26 final size:26
Alignment explanation
Indices: 1302128--1302209 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 26
1302118 ATATTTAATT
* *
1302128 TATTATTAATATATAAAAT-TTAT-A
1 TATTATTAATAAATAAAATAATATGA
*
1302152 TATTATTAATAAATAAAATAATATTA
1 TATTATTAATAAATAAAATAATATGA
* * *
1302178 TTTTATTAATAAAATTAATTAA-ATGA
1 TATTATTAAT-AAATAAAATAATATGA
1302204 TATTAT
1 TATTAT
1302210 CTTATTAATG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 18 0.38
25 3 0.06
26 18 0.38
27 9 0.19
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (26 bp):
TATTATTAATAAATAAAATAATATGA
Found at i:1305039 original size:85 final size:85
Alignment explanation
Indices: 1304944--1305102 Score: 259
Period size: 85 Copynumber: 1.9 Consensus size: 85
1304934 TCATAAAATA
1304944 ATAATATTAATAATAATGAAATCAGCAATAA-TTTAACTT-CAAATAATCAAGATTCCACTAATT
1 ATAATATTAATAATAATGAAATCAGCAA-AAGTTTAA-TTGCAAATAATCAAGATTCCACTAATT
*
1305007 ATGTTTAAAGCACTTTTTATTG
64 ATGATTAAAGCACTTTTTATTG
* *
1305029 ATAATATTAATAATAATGGAATTAGCAAAAGTTTAATTGCAAATAATCAAGATTCCACTAATTAT
1 ATAATATTAATAATAATGAAATCAGCAAAAGTTTAATTGCAAATAATCAAGATTCCACTAATTAT
1305094 GATTAAAGC
66 GATTAAAGC
1305103 GTTAGTTATT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
84 4 0.06
85 65 0.94
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (85 bp):
ATAATATTAATAATAATGAAATCAGCAAAAGTTTAATTGCAAATAATCAAGATTCCACTAATTAT
GATTAAAGCACTTTTTATTG
Done.