Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold559.1
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: 936611
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 17223 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:651947 original size:124 final size:124
Alignment explanation
Indices: 651727--651971 Score: 454
Period size: 124 Copynumber: 2.0 Consensus size: 124
651717 TCTATCAAGC
* *
651727 AAAGCCTTAATGATTGAGAATAATCAAATTGATTGATGGTATATTGAATTATACACTTCAAATTT
1 AAAGCCTTAATGATTGAGAATAATCAAATTGATTGATGGTACATAGAATTATACACTTCAAATTT
*
651792 CCATCCTATATAAAATATTAATGCATAAAATATTAGTCTCAATGTTTTTTAAACCGTAT
66 CCATCCTATATAAAATATTAATGCATAAAATATTAATCTCAATGTTTTTTAAACCGTAT
651851 AAAGCCTTAATGATTGAGAATAATCAAATTGATTGATGGTACATAGAATTATACACTTCAAATTT
1 AAAGCCTTAATGATTGAGAATAATCAAATTGATTGATGGTACATAGAATTATACACTTCAAATTT
*
651916 CCATCCTATATAAAATATTAATGCATAAAATATTAATCTTAATGTTTTTTAAACCG
66 CCATCCTATATAAAATATTAATGCATAAAATATTAATCTCAATGTTTTTTAAACCG
651972 GATTGGTGGT
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 117 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (124 bp):
AAAGCCTTAATGATTGAGAATAATCAAATTGATTGATGGTACATAGAATTATACACTTCAAATTT
CCATCCTATATAAAATATTAATGCATAAAATATTAATCTCAATGTTTTTTAAACCGTAT
Found at i:652361 original size:2 final size:2
Alignment explanation
Indices: 652354--652397 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
652344 ACCAAACACG
652354 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
652396 TC
1 TC
652398 CCATAATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:657092 original size:38 final size:38
Alignment explanation
Indices: 657049--657125 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
657039 GTTTTTAGTT
657049 ATGGAATGATTAATTAGAATGGAGTGTTAATGGCACTA
1 ATGGAATGATTAATTAGAATGGAGTGTTAATGGCACTA
657087 ATGGAATGATTAATTAGAATGGAGTGTTAATGGCACTA
1 ATGGAATGATTAATTAGAATGGAGTGTTAATGGCACTA
657125 A
1 A
657126 CTTTATGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (38 bp):
ATGGAATGATTAATTAGAATGGAGTGTTAATGGCACTA
Found at i:657109 original size:18 final size:18
Alignment explanation
Indices: 657049--657109 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
657039 GTTTTTAGTT
657049 ATGGAATGATTAATTAGA
1 ATGGAATGATTAATTAGA
* * *
657067 ATGGAGTG-TTAATGGCACTA
1 ATGGAATGATTAAT--TA-GA
657087 ATGGAATGATTAATTAGA
1 ATGGAATGATTAATTAGA
657105 ATGGA
1 ATGGA
657110 GTGTTAATGG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 5 0.15
18 13 0.39
19 2 0.06
20 8 0.24
21 5 0.15
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.31
Consensus pattern (18 bp):
ATGGAATGATTAATTAGA
Found at i:660168 original size:25 final size:25
Alignment explanation
Indices: 660140--660204 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
660130 AGCTCCTCCA
* *
660140 AGCTAAATAAT-GGTAAGCTCATACG
1 AGCTAAAT-ATCGGTAAGCTAATAAG
*
660165 AGCTAAGTATCGGTAAGCTAATAAG
1 AGCTAAATATCGGTAAGCTAATAAG
*
660190 AGCTGAA-ATCGGTAA
1 AGCTAAATATCGGTAA
660205 CCCTAATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 10 0.29
25 24 0.71
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (25 bp):
AGCTAAATATCGGTAAGCTAATAAG
Found at i:668922 original size:22 final size:24
Alignment explanation
Indices: 668896--668939 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
668886 GAAAAATATT
668896 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
668918 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
668940 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:669084 original size:20 final size:20
Alignment explanation
Indices: 669061--669121 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
669051 AATTTGATAA
669061 ATTTACTAATCAAATGTTAG
1 ATTTACTAATCAAATGTTAG
* ** * *
669081 ATTT--T-ATTACTTGATAA
1 ATTTACTAATCAAATGTTAG
669098 ATTTACTAATCAAATGTTAG
1 ATTTACTAATCAAATGTTAG
669118 ATTT
1 ATTT
669122 TATTACAACA
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
17 11 0.39
18 1 0.04
19 1 0.04
20 15 0.54
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTTACTAATCAAATGTTAG
Found at i:669104 original size:37 final size:37
Alignment explanation
Indices: 669054--669127 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
669044 AATTAATAAT
669054 TTGATAAATTTACTAATCAAATGTTAGATTTTATTAC
1 TTGATAAATTTACTAATCAAATGTTAGATTTTATTAC
669091 TTGATAAATTTACTAATCAAATGTTAGATTTTATTAC
1 TTGATAAATTTACTAATCAAATGTTAGATTTTATTAC
669128 AACAATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (37 bp):
TTGATAAATTTACTAATCAAATGTTAGATTTTATTAC
Found at i:669182 original size:16 final size:16
Alignment explanation
Indices: 669161--669202 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
669151 AATAATTTGA
*
669161 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
669177 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
669193 TAGTTTTAAT
1 TAATTTTAAT
669203 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:669186 original size:22 final size:23
Alignment explanation
Indices: 669176--669237 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
669166 TTACTAACAA
* * *
669176 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
669198 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
669221 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
669238 CGGGTCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:671698 original size:15 final size:13
Alignment explanation
Indices: 671670--671709 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 13
671660 TTTGACATCA
671670 AACTTATCAATTC
1 AACTTATCAATTC
671683 AACTTAATCAAATTC
1 AACTT-ATC-AATTC
671698 AACCTTATCAAT
1 AA-CTTATCAAT
671710 CATACCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.21
14 6 0.25
15 10 0.42
16 3 0.12
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (13 bp):
AACTTATCAATTC
Found at i:673542 original size:20 final size:19
Alignment explanation
Indices: 673506--673549 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
673496 AGTTTAATAA
*
673506 TTAATAAACTTTAATTAAC
1 TTAATAAACCTTAATTAAC
*
673525 TTAATCAAACCTTGATTAAC
1 TTAAT-AAACCTTAATTAAC
673545 TTAAT
1 TTAAT
673550 TAATCAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (19 bp):
TTAATAAACCTTAATTAAC
Found at i:685540 original size:45 final size:46
Alignment explanation
Indices: 685450--685547 Score: 135
Period size: 49 Copynumber: 2.1 Consensus size: 46
685440 AAAAAACATA
* * *
685450 AAAATTTGTATAAATTATTAGAAATTAATTAAAAATCATAAAATTTTAT
1 AAAATTTATAAAAAGTATTAGAAATTAATT---AATCATAAAATTTTAT
685499 AAAATTTATAAAAAGTATTAGAAATTAATT-ATCATAAAATTTTAT
1 AAAATTTATAAAAAGTATTAGAAATTAATTAATCATAAAATTTTAT
685544 AAAA
1 AAAA
685548 GTAAGGGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 19 0.41
49 27 0.59
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (46 bp):
AAAATTTATAAAAAGTATTAGAAATTAATTAATCATAAAATTTTAT
Found at i:688967 original size:11 final size:11
Alignment explanation
Indices: 688951--688981 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
688941 AAGTATGGGT
688951 AGGTATGGGAA
1 AGGTATGGGAA
*
688962 AGGTATGGGCA
1 AGGTATGGGAA
688973 AGGTATGGG
1 AGGTATGGG
688982 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:693059 original size:18 final size:18
Alignment explanation
Indices: 693036--693124 Score: 115
Period size: 18 Copynumber: 4.9 Consensus size: 18
693026 CCAACTACTG
*
693036 TATACGTGAACAGTACCA
1 TATACGTGAATAGTACCA
* *
693054 TATACGTGAATAGTGCCG
1 TATACGTGAATAGTACCA
*
693072 TATACGTGAATAGTACCG
1 TATACGTGAATAGTACCA
* **
693090 TATACATGAATAGTGTCA
1 TATACGTGAATAGTACCA
693108 TATACGTGAATAGTACC
1 TATACGTGAATAGTACC
693125 GTAAACGGTC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (18 bp):
TATACGTGAATAGTACCA
Found at i:693125 original size:36 final size:36
Alignment explanation
Indices: 693036--693127 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 36
693026 CCAACTACTG
* * * *
693036 TATACGTGAACAGTACCATATACGTGAATAGTGCCG
1 TATACGTGAATAGTACCGTATACATGAATAGTGCCA
*
693072 TATACGTGAATAGTACCGTATACATGAATAGTGTCA
1 TATACGTGAATAGTACCGTATACATGAATAGTGCCA
693108 TATACGTGAATAGTACCGTA
1 TATACGTGAATAGTACCGTA
693128 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACATGAATAGTGCCA
Found at i:693431 original size:11 final size:11
Alignment explanation
Indices: 693404--693446 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
693394 TGACCTTTCC
693404 AAGGTATGGG-
1 AAGGTATGGGA
*
693414 TAGGTATGGGA
1 AAGGTATGGGA
*
693425 AAGGTATGGGC
1 AAGGTATGGGA
693436 AAGGTATGGGA
1 AAGGTATGGGA
693447 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:693443 original size:22 final size:21
Alignment explanation
Indices: 693404--693446 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
693394 TGACCTTTCC
*
693404 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
693425 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
693447 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:700182 original size:23 final size:23
Alignment explanation
Indices: 700139--700182 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
700129 ATTTTCAAAA
* *
700139 TTCTTCTCTTATCTTTGTTCTTC
1 TTCTTCTCTAATATTTGTTCTTC
700162 TTCTTCTCTCAATATTT-TTCT
1 TTCTTCTCT-AATATTTGTTCT
700183 ATTCCAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.09, C:0.25, G:0.02, T:0.64
Consensus pattern (23 bp):
TTCTTCTCTAATATTTGTTCTTC
Found at i:705911 original size:210 final size:208
Alignment explanation
Indices: 705272--705941 Score: 855
Period size: 210 Copynumber: 3.2 Consensus size: 208
705262 TGAAAACTCG
* *
705272 CCAATTCCTTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCAAAATCTGGAATC
1 CCAATTCATTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAAT-
* * **
705337 CG-ACTTAAATTAGAACAAAGATATAGATCTAATTCTTTAAGATAAGTGGAGGTAGATAATCTGT
65 CGAACTTAAATTAGAACAAAGATATAGA-CTAATTCTTTGAGACAAG-GGAGGTAGATAATCCAT
*
705401 CTCCGATCTTGCTTATATTTTTACAACTGGAAATTTTAAGCTTTTCAAGAGATGAACATC-TTCT
128 CTCCGATCTTGCTTATATTTTTACAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTTC-
* *
705465 TGTTATGGGAAGAACTT
192 AGTTATCGGAAGAACTT
* * *
705482 CCAATTCGTTGTAGCTATTAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
1 CCAATTCATTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
* *
705547 AAACTTAAATTAGAACAAAGATATATA-TAATTCTTTGAGACAATGGGAGGTAGATAATCCATCT
66 GAACTTAAATTAGAACAAAGATATAGACTAATTCTTTGAGACAA-GGGAGGTAGATAATCCATCT
* *
705611 CCGATCTTGCTTATATTTTTACAACTGGAAATTCTAAGCTTTTCAATAGATGAACATCTTCCAGT
130 CCGATCTTGCTTATATTTTTACAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTTCAGT
*
705676 TATTGGAAGAACTT
195 TATCGGAAGAACTT
* * ** *
705690 CCAATTCATTGCACCTATTAATTGACAGGCTTTGAAGAGA-GAAAATTCCTTCCAAATTTGGAAT
1 CCAATTCATTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAA-TCCTTCCAAATCTGGAAT
* ** *
705754 CGAACTTAAATTAGGACAATTATATAGACCTAATTCTTTGAGACAAGCGCAGGTAGATAATCCAT
65 CGAACTTAAATTAGAACAAAGATATAGA-CTAATTCTTTGAGACAAG-GGAGGTAGATAATCCAT
* * *** * * *
705819 CTCCAATCTTGCTTA-ATTTTTCGCAACCAAAAATGCTAAGCTTTTCAAGAGATAAACACCTTTC
128 CTCCGATCTTGCTTATATTTTT-ACAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTTC
* * *
705883 AGGTAACGAAAGAACTT
192 AGTTATCGGAAGAACTT
* * * *
705900 CTAACTCATTGCAACTATCAATTGACAGGTTTTGAAGAGAGG
1 CCAATTCATTGCAGCTATCAATTGACAGATTTTGAAGAGAGG
705942 GGGTAAATAA
Statistics
Matches: 405, Mismatches: 46, Indels: 17
0.87 0.10 0.04
Matches are distributed among these distances:
207 5 0.01
208 177 0.44
209 11 0.03
210 211 0.52
211 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (208 bp):
CCAATTCATTGCAGCTATCAATTGACAGATTTTGAAGAGAGGAAAATCCTTCCAAATCTGGAATC
GAACTTAAATTAGAACAAAGATATAGACTAATTCTTTGAGACAAGGGAGGTAGATAATCCATCTC
CGATCTTGCTTATATTTTTACAACTGGAAATTCTAAGCTTTTCAAGAGATGAACATCTTTCAGTT
ATCGGAAGAACTT
Found at i:706246 original size:348 final size:347
Alignment explanation
Indices: 705645--706289 Score: 821
Period size: 348 Copynumber: 1.9 Consensus size: 347
705635 CTGGAAATTC
* * *
705645 TAAGCTTTTCAATAGATGAACATCTTCCAGTTATTGGAAGAACTTCCAATTCATTGCACCTATTA
1 TAAGCTTTTCAAGAGATGAACATCTTCCAGTTACTGGAAGAACTTCCAATTCATTACACCTATTA
** * * * *
705710 ATTGACAGGCTTTGAAGAGAGAAAATTCCTTCCAAATTTGGAATCGAACTTAAATTAGGACAATT
66 ATTGACAGAATTTGAAGAGAGAAAATTCCTTCCAAATCTGGAACCGAACTTAAATTAGAACAATG
* * * * * * **
705775 ATATAGACCTAATTCTTTGAGACAAGCGCAGGTAGATAATCCATCTCCAATCTTGCTTAATTTTT
131 ACATAGACATAATTATTTCAGACAAGCGCAGCTAAATAATCCATCTCCAATCTTGCTTAAACTTT
* ** *
705840 CGCAACCAAAAATGCTAAGCTTTTCAAGAGATAAACACCTTTCAGGTAACGAAAGAACTTCTAAC
196 CACAACCAAAAATAATAAGCTTTTCAAGAGATAAACACC-TTCAGGTAACGAAAGAACTTCCAAC
*
705905 TCATTGCAACTATCAATTGACAGGTTTTGAAGAGAGGGGGTAAATAATCCGTCTCCAATCTTGTT
260 TCATTGCAACTATCAATTGACAGATTTTGAAGAGAGGGGGTAAATAATCCGTCTCCAATCTTGTT
705970 TAATTTTTCGCAACAAAAAATGT
325 TAATTTTTCGCAACAAAAAATGT
* * *
705993 TAAGCTTTTCAAGAGATGAACATCTTCCTA-TTACTGGAAGAACTTTCAATTCCTTACAGCTATT
1 TAAGCTTTTCAAGAGATGAACATCTTCC-AGTTACTGGAAGAACTTCCAATTCATTACACCTATT
* * *
706057 AATTGATAGAATTTTAAGAGAGAAACATT-CTTCCAAGTCTGGAACCGAACTTAAATTAGAACAA
65 AATTGACAGAATTTGAAGAGAGAAA-ATTCCTTCCAAATCTGGAACCGAACTTAAATTAGAACAA
* * * * * * *
706121 TGACATAGATATAATTATTTCAGACAAGTGGAGCTAAATAATTCGTCTTCGATCTTGCTTAAACT
129 TGACATAGACATAATTATTTCAGACAAGCGCAGCTAAATAATCCATCTCCAATCTTGCTTAAACT
* * * *
706186 TTCACAACCCAAAATAATAAGCTTTTCAAGAGATGAACAACC-TCCGGTTATA-GGAAGAACTTC
194 TTCACAACCAAAAATAATAAGCTTTTCAAGAGATAAAC-ACCTTCAGG-TA-ACGAAAGAACTTC
* * * *
706249 CAATTCCTTGTAGCTATCAATTGACAGATTTTGAAGAGAGG
256 CAACTCATTGCAACTATCAATTGACAGATTTTGAAGAGAGG
706290 AAAATCCTTC
Statistics
Matches: 249, Mismatches: 43, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
347 4 0.02
348 237 0.95
349 8 0.03
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (347 bp):
TAAGCTTTTCAAGAGATGAACATCTTCCAGTTACTGGAAGAACTTCCAATTCATTACACCTATTA
ATTGACAGAATTTGAAGAGAGAAAATTCCTTCCAAATCTGGAACCGAACTTAAATTAGAACAATG
ACATAGACATAATTATTTCAGACAAGCGCAGCTAAATAATCCATCTCCAATCTTGCTTAAACTTT
CACAACCAAAAATAATAAGCTTTTCAAGAGATAAACACCTTCAGGTAACGAAAGAACTTCCAACT
CATTGCAACTATCAATTGACAGATTTTGAAGAGAGGGGGTAAATAATCCGTCTCCAATCTTGTTT
AATTTTTCGCAACAAAAAATGT
Found at i:706387 original size:210 final size:210
Alignment explanation
Indices: 705993--706392 Score: 459
Period size: 210 Copynumber: 1.9 Consensus size: 210
705983 CAAAAAATGT
* * * * *
705993 TAAGCTTTTCAAGAGATGAACATCTTCCTATTACTGGAAGAACTTTCAATTCCTTACAGCTATTA
1 TAAGCTTTTCAAGAGATGAACAACCTCCGATTACTGGAAGAACTTCCAATTCCTTACAGCTATCA
* * * *
706058 ATTGATAGAATTTTAAGAGAGAAACATTCTTCCAAGTCTGGAACCGAACTTAAATTAGAACAATG
66 ATTGACAGAATTTTAAGAGAGAAACATCCTTCCAAATCTGGAACCGAACTTAAATTAGAACAATC
* * * * * **
706123 ACATAGATATAATTATTTCAGACAAGTGGAGCTAAATAATTCGTCTTCGATCTTGCTTAAACTTT
131 ACATAAATATAATTATTTAAGACAAATAGAGCTAAACAACCCGTCTTCGATCTTGCTTAAACTTT
706188 CACAACCCAAAATAA
196 CACAACCCAAAATAA
* **
706203 TAAGCTTTTCAAGAGATGAACAACCTCCGGTTA-TAGGAAGAACTTCCAATTCCTTGTAGCTATC
1 TAAGCTTTTCAAGAGATGAACAACCTCCGATTACT-GGAAGAACTTCCAATTCCTTACAGCTATC
*
706267 AATTGACAG-ATTTTGAAGAGAGGAAA-ATCCTTCCAAATCTGGAATCC-AACTTAAATTAGGAC
65 AATTGACAGAATTTT-AAGAGA-GAAACATCCTTCCAAATCTGGAA-CCGAACTTAAATTAGAAC
*** * * * * **
706329 AATCTTTTAAATCTAATTCTTTAAGATAAATAGAGGTTGACAACCCGTC-TCTGATCTTGCTTAA
127 AATCACATAAATATAATTATTTAAGACAAATAGAGCTAAACAACCCGTCTTC-GATCTTGCTTAA
706393 TGTTTTACAC
Statistics
Matches: 156, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
209 8 0.05
210 142 0.91
211 6 0.04
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (210 bp):
TAAGCTTTTCAAGAGATGAACAACCTCCGATTACTGGAAGAACTTCCAATTCCTTACAGCTATCA
ATTGACAGAATTTTAAGAGAGAAACATCCTTCCAAATCTGGAACCGAACTTAAATTAGAACAATC
ACATAAATATAATTATTTAAGACAAATAGAGCTAAACAACCCGTCTTCGATCTTGCTTAAACTTT
CACAACCCAAAATAA
Found at i:712238 original size:12 final size:12
Alignment explanation
Indices: 712221--712249 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
712211 TTTAAATAAA
712221 TTTATAATATTT
1 TTTATAATATTT
712233 TTTATAATATTT
1 TTTATAATATTT
712245 TTTAT
1 TTTAT
712250 TATAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATAATATTT
Found at i:712239 original size:20 final size:20
Alignment explanation
Indices: 712132--712233 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
712122 TAAATTTTCT
712132 TAAATTTT-ATGATTTTAAA
1 TAAATTTTAATGATTTTAAA
* * *
712151 TTAATTTCTAATAATTTT-TA
1 TAAATTT-TAATGATTTTAAA
**
712171 TAAATTTTAATTTTTTATAAA
1 TAAATTTTAATGATTT-TAAA
712192 TTAAAAAAATTTTAATGATTTTAAA
1 -T----AAATTTTAATGATTTTAAA
712217 TAAATTTATAAT-ATTTT
1 TAAATTT-TAATGATTTT
712234 TTATAATATT
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
19 13 0.20
20 20 0.31
21 12 0.19
22 1 0.02
24 1 0.02
25 4 0.06
26 13 0.20
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (20 bp):
TAAATTTTAATGATTTTAAA
Found at i:712297 original size:64 final size:64
Alignment explanation
Indices: 712133--712314 Score: 208
Period size: 66 Copynumber: 2.8 Consensus size: 64
712123 AAATTTTCTT
*
712133 AAATTTT-ATGATTTTAAATTAATTTCTAATAATTTTTATAAATTTTAATTTTTTATAAATTAAA
1 AAATTTTAATGATTTTAAATTAATTTCTAATAATTTTTATAAA-TTT-ATTTATTATAAATTAAA
712197 A
64 A
* * * * *
712198 AAATTTTAATGATTTTAAATAAATTTATAATATTTTTTATAATATTT-TTTATTATAAATTTATA
1 AAATTTTAATGATTTTAAATTAATTTCTAATAATTTTTATAA-ATTTATTTATTATAAATTAAAA
* ** * *
712262 AAGTTTT-ATTCTTTTTAATTAGTTTCTAATAATTTTTATAAAATTTATTTATT
1 AAATTTTAATGATTTTAAATTAATTTCTAATAATTTTTAT-AAATTTATTTATT
712315 TTTATGCTTT
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
63 29 0.29
64 28 0.28
65 7 0.07
66 34 0.34
67 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (64 bp):
AAATTTTAATGATTTTAAATTAATTTCTAATAATTTTTATAAATTTATTTATTATAAATTAAAA
Found at i:716645 original size:22 final size:23
Alignment explanation
Indices: 716598--716660 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
716588 ATGCAATCGT
* *
716598 AGATATGA-TATGTAATCCTAGA
1 AGATATGATTTTGTAATACTAGA
*
716620 AGATATGATTTTGTAATATTAG-
1 AGATATGATTTTGTAATACTAGA
*
716642 AGATTTGA-TTTGTAGATAC
1 AGATATGATTTTGTA-ATAC
716661 CTTTCGATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 6 0.18
22 18 0.53
23 10 0.29
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
AGATATGATTTTGTAATACTAGA
Found at i:727651 original size:191 final size:191
Alignment explanation
Indices: 727319--727683 Score: 525
Period size: 191 Copynumber: 1.9 Consensus size: 191
727309 TGAATTTTTG
* * * *
727319 TGGTTGTTTCCCCAGTGGTTCTTCTTTATCAAGCTTTCTATGATTTTTAAATGAGTTTAACCAGA
1 TGGTTGTTTCCCCACTGATTCTTATTCATCAAGCTTTCTATGATTTTTAAATGAGTTTAACCAGA
* *
727384 GTTATCTCACACTACTGCAGCAAATTTCTTCCTATATATTTTTGGGCTTATTTTTGTATGAGCAG
66 GTTATCACACACTACTGCAACAAATTTCTTCCTATATATTTTTGGGCTTATTTTTGTATGAGCAG
*** * *
727449 GCTTGTGGTT-GGATGTACATTTGTTACCTCTACATGTATGAATGAGTTTTTTTGGATTTC
131 GCCAATGGTTGGGATGTACACTTGCTACCTCTACATGTATGAATGAGTTTTTTTGGATTTC
* *
727509 TGGTTGTTTTCCTACTGATTCTTATTCATCAAGCTTTCTATGATTTTTAAATGAGTTTTAACCAG
1 TGGTTGTTTCCCCACTGATTCTTATTCATCAAGCTTTCTATGATTTTTAAATGAG-TTTAACCAG
* * *
727574 AGTTATCACACACTACTGCAACAAATTTCTTTCTATGTATTTTTGGGTTTATTTTTGTATGAGCA
65 AGTTATCACACACTACTGCAACAAATTTCTTCCTATATATTTTTGGGCTTATTTTTGTATGAGCA
* * * * *
727639 TGCCAATGGTTGGGGTGTACACTTGCTACCTGTGCATGTGTGAAT
130 GGCCAATGGTTGGGATGTACACTTGCTACCTCTACATGTATGAAT
727684 AAATTTTGTT
Statistics
Matches: 152, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
190 49 0.32
191 76 0.50
192 27 0.18
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (191 bp):
TGGTTGTTTCCCCACTGATTCTTATTCATCAAGCTTTCTATGATTTTTAAATGAGTTTAACCAGA
GTTATCACACACTACTGCAACAAATTTCTTCCTATATATTTTTGGGCTTATTTTTGTATGAGCAG
GCCAATGGTTGGGATGTACACTTGCTACCTCTACATGTATGAATGAGTTTTTTTGGATTTC
Found at i:734337 original size:19 final size:19
Alignment explanation
Indices: 734310--734346 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
734300 TATTTTAAAG
*
734310 TTATTTAGGTAGATAAATT
1 TTATATAGGTAGATAAATT
734329 TTATATAGGTAGATAAAT
1 TTATATAGGTAGATAAAT
734347 CTTAGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (19 bp):
TTATATAGGTAGATAAATT
Found at i:738220 original size:18 final size:19
Alignment explanation
Indices: 738197--738232 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
738187 TATTTTAAAG
738197 TTATTTA-GTAAATAAATC
1 TTATTTAGGTAAATAAATC
*
738215 TTATTTAGGTAGATAAAT
1 TTATTTAGGTAAATAAAT
738233 ATTAGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAAATAAATC
Found at i:748223 original size:14 final size:14
Alignment explanation
Indices: 748204--748232 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
748194 GCGCACGGAA
748204 ACAACCGTACGCTG
1 ACAACCGTACGCTG
748218 ACAACCGTACGCTG
1 ACAACCGTACGCTG
748232 A
1 A
748233 GTATTTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.21, T:0.14
Consensus pattern (14 bp):
ACAACCGTACGCTG
Found at i:749718 original size:5 final size:5
Alignment explanation
Indices: 749697--749769 Score: 71
Period size: 5 Copynumber: 14.4 Consensus size: 5
749687 TTACTTTATT
749697 TAATA TATATAA TAATA TAATA TAATA TAATA TAAT- TAATA TATTATA
1 TAATA TA-AT-A TAATA TAATA TAATA TAATA TAATA TAATA TA--ATA
* *
749745 TTATA TTATA TAATA -AA-A TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
749770 CATAACACAA
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
3 1 0.02
4 8 0.14
5 39 0.66
6 4 0.07
7 7 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TAATA
Found at i:749744 original size:24 final size:23
Alignment explanation
Indices: 749693--749769 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 23
749683 CTATTTACTT
749693 TATT-TAATAT-ATATAATAATA
1 TATTATAATATAATATAATAATA
*
749714 TAATATAATATAATATAATTAATA
1 TATTATAATATAATATAA-TAATA
* *
749738 TATTATATTATATTATATAATAAAA
1 TATTATA--ATATAATATAATAATA
*
749763 TAATATA
1 TATTATA
749770 CATAACACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
21 3 0.07
22 6 0.13
23 6 0.13
24 11 0.24
25 10 0.22
26 10 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAATATAATATAATAATA
Found at i:749756 original size:36 final size:36
Alignment explanation
Indices: 749696--749764 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
749686 TTTACTTTAT
*
749696 TTAATATATATAATAATATAATATAATATAATATAA
1 TTAATATATATAATAATATAATATAATAAAATATAA
* *
749732 TTAATATAT-TATATTATATTATATAATAAAATA
1 TTAATATATATA-ATAATATAATATAATAAAATA
749765 ATATACATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
TTAATATATATAATAATATAATATAATAAAATATAA
Found at i:750875 original size:18 final size:17
Alignment explanation
Indices: 750842--750880 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
750832 TTTTATAAAT
750842 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
750860 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
750877 TGTG
1 TGTG
750881 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:755043 original size:40 final size:40
Alignment explanation
Indices: 754987--755545 Score: 580
Period size: 40 Copynumber: 13.9 Consensus size: 40
754977 GGAAATGAAG
* *
754987 ACGTGCTCCTGATTGTAC-TCGGGTACCCCTGAATGGACAT
1 ACGTGCTCCTGTTTGTACTTC-GGTACCCCTGAATGCACAT
* * *
755027 ACGTGCTCGTGTTTGTACTTCGGTACCCCTGAACGCATAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
* * * * * * *
755067 ATGTGCTCCTGCTGTTTGTATTTCGATACCCTTAAATGCAGAA
1 ACGTGCT-C--CTGTTTGTACTTCGGTACCCCTGAATGCACAT
* * *
755110 ACATGCTCCTGTTTGTACTTTGGTACCCTTGAATGCACAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
* * ***
755150 ACGTGCTCCTGTTTGTACTTCGGTACCCTTCAACATACAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
** * *
755190 ATTTTCTCCTATTTGTACTTCGGTACCCCTGAATGCACAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
* * *
755230 ACGTGCTCCTATTTGTACTTCGGTACCTCTGAATGCACAA
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
** * *
755270 ACGTGCTCCTGTTTGTACTTTAGTACCCCTGAATACATAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
** * *
755310 ACGTGCTCCTGTTTGTACTTCGGTACCTTTAAACGCACAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
* * *
755350 ACGTGCTCCTATTTATACTTTGGTACCCCTGAATGCACAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
* ** * *
755390 ACGTGCTCCTATTTGTACTTCAATACCCTTGAATGCACAG
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
* * *
755430 ACGTGCTCCTGTTTGTACTTTGATACCCCTAAATGCACAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
* * *
755470 ACATGCTCCTGTTTGTACTTCGGTACCCTTAAATGCACAT
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
* * * * * *
755510 ACGTACTCCTATTTGTAATTCAGTGCCTCTGAATGC
1 ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGC
755546 CTCAGAGTTG
Statistics
Matches: 426, Mismatches: 89, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
40 393 0.92
41 3 0.01
42 1 0.00
43 29 0.07
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (40 bp):
ACGTGCTCCTGTTTGTACTTCGGTACCCCTGAATGCACAT
Found at i:757625 original size:11 final size:12
Alignment explanation
Indices: 757609--757655 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
757599 CTTAATCACT
757609 TTAATATTAA-A
1 TTAATATTAAGA
757620 TTAATA-TAAGA
1 TTAATATTAAGA
757631 TT--TATTAAGA
1 TTAATATTAAGA
*
757641 TAAATATT-AGA
1 TTAATATTAAGA
757652 TTAA
1 TTAA
757656 GTTTAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
9 2 0.07
10 9 0.30
11 15 0.50
12 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (12 bp):
TTAATATTAAGA
Found at i:757652 original size:21 final size:20
Alignment explanation
Indices: 757613--757653 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
757603 ATCACTTTAA
*
757613 TATTAAATTAATATAAGATT
1 TATTAAATAAATATAAGATT
*
757633 TATTAAGATAAATATTAGATT
1 TATTAA-ATAAATATAAGATT
757654 AAGTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
TATTAAATAAATATAAGATT
Found at i:757684 original size:59 final size:59
Alignment explanation
Indices: 757613--757744 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 59
757603 ATCACTTTAA
* * *
757613 TATTAAATTAATATAA-GATTTAT-T-AAGATAAATATTAGA-TTAAGTTTAATATTAAATC
1 TATTAAAATAATATAACG-TTTATCTAAAGATAAACATTAAATTTAA-TTTAATATTAAA-C
757671 TTATTAAAATAATATAACGTTTATCTACAAGATAAACATTAAATTTAATTTAATATTAAAC
1 -TATTAAAATAATATAACGTTTATCTA-AAGATAAACATTAAATTTAATTTAATATTAAAC
757732 TATT-AAATAATAT
1 TATTAAAATAATAT
757745 TATTTTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
59 29 0.45
60 6 0.09
61 1 0.02
62 25 0.38
63 4 0.06
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATATAACGTTTATCTAAAGATAAACATTAAATTTAATTTAATATTAAAC
Found at i:758269 original size:13 final size:13
Alignment explanation
Indices: 758253--758277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
758243 TTTTTCAAGA
758253 AAATTCTTTAATC
1 AAATTCTTTAATC
758266 AAATTCTTTAAT
1 AAATTCTTTAAT
758278 TGAACAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTCTTTAATC
Found at i:759381 original size:16 final size:16
Alignment explanation
Indices: 759360--759390 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
759350 CTATGCACGC
*
759360 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
759376 AAAATACAAAAGACA
1 AAAATACAAAAGACA
759391 TAATAGTTAA
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:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:777638 original size:31 final size:31
Alignment explanation
Indices: 777594--777655 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
777584 ATGCTACAAG
777594 TCTTTGTACTTTTTTGTATTTT-AAAATTTAA
1 TCTTTGTACTTTTTTG-ATTTTAAAAATTTAA
* *
777625 TCTTTTTATTTTTTTGATTTTAAAAATTTAA
1 TCTTTGTACTTTTTTGATTTTAAAAATTTAA
777656 GTACAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (31 bp):
TCTTTGTACTTTTTTGATTTTAAAAATTTAA
Found at i:779205 original size:12 final size:12
Alignment explanation
Indices: 779190--779219 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
779180 TTAATTTTAA
779190 ATTTTTATATAT
1 ATTTTTATATAT
779202 ATTTTTATATAT
1 ATTTTTATATAT
779214 -TTTTTA
1 ATTTTTA
779220 AAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTTATATAT
Found at i:779244 original size:20 final size:22
Alignment explanation
Indices: 779206--779249 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
779196 ATATATATTT
779206 TTATATATTTTTTAAAAAATAA
1 TTATATATTTTTTAAAAAATAA
*
779228 TTATA-ATTTTTTTAAAATATAA
1 TTATATA-TTTTTTAAAAAATAA
779250 ATTTTGGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATATATTTTTTAAAAAATAA
Found at i:783175 original size:19 final size:19
Alignment explanation
Indices: 783153--783190 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
783143 TGATTATTAC
783153 AAAATTAT-TAAGATTTCTT
1 AAAATTATCTAAG-TTTCTT
*
783172 AAAATTTTCTAAGTTTCTT
1 AAAATTATCTAAGTTTCTT
783191 TGAAAATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (19 bp):
AAAATTATCTAAGTTTCTT
Found at i:788607 original size:44 final size:44
Alignment explanation
Indices: 788557--788641 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
788547 ATTAAAACTT
*
788557 AATTAATACTATTGTTAATATATTTTCATTAAATTCCAATACCC
1 AATTAATACTATTGTTAATATACTTTCATTAAATTCCAATACCC
*
788601 AATTAATACTATTGTTAATATACTTTCATTAAATTCGAATA
1 AATTAATACTATTGTTAATATACTTTCATTAAATTCCAATA
788642 TGTGATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (44 bp):
AATTAATACTATTGTTAATATACTTTCATTAAATTCCAATACCC
Found at i:789758 original size:14 final size:14
Alignment explanation
Indices: 789739--789765 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
789729 AACACTAATG
789739 GTGTTAAAAAATTC
1 GTGTTAAAAAATTC
789753 GTGTTAAAAAATT
1 GTGTTAAAAAATT
789766 ATGCATTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.37
Consensus pattern (14 bp):
GTGTTAAAAAATTC
Found at i:792006 original size:5 final size:5
Alignment explanation
Indices: 791996--792042 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
791986 GAACAAATAT
* *
791996 ATTCG ATTCG ATTCG ATTCG AATTCC ATCTC- ACTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG ATTCG A
792043 GAAAACTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (5 bp):
ATTCG
Found at i:794549 original size:32 final size:32
Alignment explanation
Indices: 794487--794557 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
794477 ATTCAATAAT
** *
794487 TTAAATAAGAAATATTATTTTACACTAATTAC
1 TTAAATAAGAAATATTATTTTACAAAAATTAA
794519 TGTAAATAA-AAATATTATATTTA-AAAAATTAA
1 T-TAAATAAGAAATATTAT-TTTACAAAAATTAA
794551 TTAAATA
1 TTAAATA
794558 TTAAACAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 6 0.18
32 17 0.50
33 11 0.32
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (32 bp):
TTAAATAAGAAATATTATTTTACAAAAATTAA
Found at i:797105 original size:6 final size:6
Alignment explanation
Indices: 797094--797124 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
797084 TCATCTCAAA
797094 CACACC CACACC CACACC CACACC CACACC C
1 CACACC CACACC CACACC CACACC CACACC C
797125 CTACACACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (6 bp):
CACACC
Found at i:799388 original size:21 final size:21
Alignment explanation
Indices: 799358--799418 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
799348 TATCAATTTA
*
799358 AAAAAT-TATAAAACATAAA-
1 AAAAATATATAAAAAATAAAG
799377 AATAAATATATAAAAAATAAAG
1 AA-AAATATATAAAAAATAAAG
*
799399 AAAAATATAT-AATAATAAAG
1 AAAAATATATAAAAAATAAAG
799419 TACAAAAGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.35
21 20 0.54
22 2 0.05
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAAATATATAAAAAATAAAG
Found at i:803518 original size:16 final size:16
Alignment explanation
Indices: 803497--803530 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
803487 CCAATATCCA
* *
803497 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
803513 ATTATCACATTTACAC
1 ATTATCACATTTACAC
803529 AT
1 AT
803531 ATATATTCAT
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:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:809081 original size:29 final size:29
Alignment explanation
Indices: 808997--809107 Score: 89
Period size: 31 Copynumber: 3.7 Consensus size: 29
808987 GATTAAATCA
* *
808997 AAATTAAAGCTTCCA-GTATATAATTGAACC
1 AAATTAAAG-TT-CATGTATATAATTGCACT
* *
809027 ACAATTAGAATTTCATGTGTATAATTGCACT
1 A-AATTA-AAGTTCATGTATATAATTGCACT
* *
809058 AAATTAAAGTTCATGTATACAATTACACATT
1 AAATTAAAGTTCATGTATATAATTGCAC--T
* *
809089 AAATCAAAGTTTATGTATA
1 AAATTAAAGTTCATGTATA
809108 ATTTTGATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
29 18 0.27
30 8 0.12
31 38 0.58
32 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATATAATTGCACT
Found at i:814456 original size:98 final size:98
Alignment explanation
Indices: 814285--814481 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
814275 GTGCAATAAA
*
814285 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
814350 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
814383 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
814448 CCTTTAAAATCTCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
814481 A
1 A
814482 TTATTTTTAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:814510 original size:21 final size:20
Alignment explanation
Indices: 814481--814531 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
814471 TATTTCCTTT
814481 ATTATTTTTAAAATTTGAAA
1 ATTATTTTTAAAATTTGAAA
*
814501 ATTATATTTTTAAATTTG--A
1 ATTAT-TTTTAAAATTTGAAA
814520 ATT-TTTTTAAAA
1 ATTATTTTTAAAA
814532 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 7 0.25
18 1 0.04
19 4 0.14
20 5 0.18
21 11 0.39
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
ATTATTTTTAAAATTTGAAA
Found at i:818903 original size:183 final size:183
Alignment explanation
Indices: 818595--818963 Score: 720
Period size: 183 Copynumber: 2.0 Consensus size: 183
818585 TTACTCCCAT
818595 TATATCGGAGGGACTTATCCTATATCGATCAACCATATCCTTCTACATAGATCGTGGTATATCCA
1 TATATCGGAGGGACTTATCCTATATCGATCAACCATATCCTTCTACATAGATCGTGGTATATCCA
818660 ACATCAGCCTTTATAGAACAACCAGTTACGGTGTACATTTGACTGTATCAAAAAATACAACTGAC
66 ACATCAGCCTTTATAGAACAACCAGTTACGGTGTACATTTGACTGTATCAAAAAATACAACTGAC
818725 GATGTTGGGATAATGATGATATCAAGTCTGAGGATCATATACATATTAATCAC
131 GATGTTGGGATAATGATGATATCAAGTCTGAGGATCATATACATATTAATCAC
818778 TATATCGGAGGGACTTATCCTATATCGATCAACCATATCCTTCTACATAGATCGTGGTATATCCA
1 TATATCGGAGGGACTTATCCTATATCGATCAACCATATCCTTCTACATAGATCGTGGTATATCCA
* *
818843 ACATCAGCCTTTATAGAACAACCAGTTTCGGTGTGCATTTGACTGTATCAAAAAATACAACTGAC
66 ACATCAGCCTTTATAGAACAACCAGTTACGGTGTACATTTGACTGTATCAAAAAATACAACTGAC
818908 GATGTTGGGATAATGATGATATCAAGTCTGAGGATCATATACATATTAATCAC
131 GATGTTGGGATAATGATGATATCAAGTCTGAGGATCATATACATATTAATCAC
818961 TAT
1 TAT
818964 GAGTAATGTT
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 184 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (183 bp):
TATATCGGAGGGACTTATCCTATATCGATCAACCATATCCTTCTACATAGATCGTGGTATATCCA
ACATCAGCCTTTATAGAACAACCAGTTACGGTGTACATTTGACTGTATCAAAAAATACAACTGAC
GATGTTGGGATAATGATGATATCAAGTCTGAGGATCATATACATATTAATCAC
Found at i:820031 original size:9 final size:9
Alignment explanation
Indices: 820017--820041 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
820007 GATAAAGTAA
820017 AATTAAATT
1 AATTAAATT
820026 AATTAAATT
1 AATTAAATT
820035 AATTAAA
1 AATTAAA
820042 AGTAATATAA
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:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:820501 original size:11 final size:11
Alignment explanation
Indices: 820430--820533 Score: 50
Period size: 12 Copynumber: 9.9 Consensus size: 11
820420 ATTCCAAAAA
*
820430 TAATATTATTT
1 TAATATTAATT
*
820441 TAATA--GATT
1 TAATATTAATT
820450 TAATATTTAATT
1 TAATA-TTAATT
820462 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
820474 TAATAGT-ATT
1 TAATATTAATT
820484 T--TATTAATT
1 TAATATTAATT
820493 TAATATTAA--
1 TAATATTAATT
820502 -AATGATT-ATCT
1 TAAT-ATTAAT-T
820513 TAATATTAAATT
1 TAATATT-AATT
820525 TAAT-TTAAT
1 TAATATTAAT
820534 GTTTATCTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 29
0.68 0.06 0.27
Matches are distributed among these distances:
8 7 0.10
9 14 0.19
10 5 0.07
11 21 0.29
12 24 0.33
13 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (11 bp):
TAATATTAATT
Found at i:820614 original size:12 final size:12
Alignment explanation
Indices: 820599--820639 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
820589 AACTAATATT
820599 TATTAAGATAAA
1 TATTAAGATAAA
820611 TATTAAGATAAA
1 TATTAAGATAAA
820623 TATT-AGATTAAA
1 TATTAAGA-TAAA
820635 T-TTAA
1 TATTAA
820640 TATTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (12 bp):
TATTAAGATAAA
Found at i:820784 original size:10 final size:10
Alignment explanation
Indices: 820766--820795 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
820756 TTCTCCGAAA
*
820766 AGATTATTTC
1 AGATAATTTC
820776 AGATAATTTC
1 AGATAATTTC
820786 AGATAATTTC
1 AGATAATTTC
820796 TAGACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (10 bp):
AGATAATTTC
Found at i:823189 original size:7 final size:7
Alignment explanation
Indices: 823177--823221 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
823167 TCCAAAATAA
823177 AATGTCC
1 AATGTCC
823184 AATGTCC
1 AATGTCC
823191 AATGTCC
1 AATGTCC
*
823198 AAAGTCC
1 AATGTCC
*
823205 AAAGTCC
1 AATGTCC
*
823212 AAAGTCC
1 AATGTCC
823219 AAT
1 AAT
823222 TTACAACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (7 bp):
AATGTCC
Found at i:823194 original size:14 final size:14
Alignment explanation
Indices: 823177--823221 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
823167 TCCAAAATAA
*
823177 AATGTCCAATGTCC
1 AATGTCCAAAGTCC
823191 AATGTCCAAAGTCC
1 AATGTCCAAAGTCC
*
823205 AAAGTCCAAAGTCC
1 AATGTCCAAAGTCC
823219 AAT
1 AAT
823222 TTACAACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (14 bp):
AATGTCCAAAGTCC
Found at i:833223 original size:21 final size:21
Alignment explanation
Indices: 833199--833240 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
833189 AAAAATTATA
833199 CTTAATTTAGAGATTCAAATC
1 CTTAATTTAGAGATTCAAATC
833220 CTTAATTTAGAGATTCAAATC
1 CTTAATTTAGAGATTCAAATC
833241 ACTTCGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
CTTAATTTAGAGATTCAAATC
Found at i:839605 original size:14 final size:15
Alignment explanation
Indices: 839579--839618 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
839569 TTAAGAATTT
*
839579 TATTAAATT-ATATA
1 TATTTAATTAATATA
839593 T-TTTAATTAATATA
1 TATTTAATTAATATA
839607 TATTTAA-TAATA
1 TATTTAATTAATA
839619 ATTATGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTAATATA
Found at i:839608 original size:18 final size:17
Alignment explanation
Indices: 839544--839611 Score: 67
Period size: 16 Copynumber: 4.2 Consensus size: 17
839534 GAAATTGAGA
839544 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
839561 A-TTTATT--ATTA-AGA
1 ATTTTATTAAATTATA-T
839575 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
839592 ATTTTAATT-AA-TATAT
1 ATTTT-ATTAAATTATAT
839608 ATTT
1 ATTT
839612 AATAATAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 6 0.14
16 15 0.35
17 12 0.28
18 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:839801 original size:39 final size:41
Alignment explanation
Indices: 839756--839861 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
839746 TTTCCTTATG
* *
839756 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAAAACAAGAATTAC
*
839796 C-ATTACGCCTCTATTCCATTCCATTCAACCAAAAAGAAGAATTAC
1 CTATTACGCCTC---T--ATTCCATTCAACCAAAAACAAGAATTAC
839841 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
839862 ACACTTCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 9 0.16
40 1 0.02
41 8 0.14
42 1 0.02
43 1 0.02
44 22 0.39
45 4 0.07
46 10 0.18
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAAAACAAGAATTAC
Found at i:839836 original size:44 final size:46
Alignment explanation
Indices: 839769--839861 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
839759 TTACACCTCT
*
839769 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAAAACAAGAATTACCTATTACGCCTCTATTCC
*
839813 ATTCCATTCAACCAAAAAGAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAAAACAAGAATTACCTATTACGCCTCTATTCC
839859 ATT
1 ATT
839862 ACACTTCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 22 0.49
45 4 0.09
46 19 0.42
ACGTcount: A:0.37, C:0.30, G:0.05, T:0.28
Consensus pattern (46 bp):
ATTCCATTCAACCAAAAACAAGAATTACCTATTACGCCTCTATTCC
Found at i:850706 original size:30 final size:30
Alignment explanation
Indices: 850670--850728 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
850660 ATGTGAGCTA
850670 AAGCAAATGGCAAATAACAATGCCCATGGT
1 AAGCAAATGGCAAATAACAATGCCCATGGT
*
850700 AAGCAAATGGCAAATAACAATGCCTATGG
1 AAGCAAATGGCAAATAACAATGCCCATGG
850729 CAAATGACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (30 bp):
AAGCAAATGGCAAATAACAATGCCCATGGT
Found at i:853532 original size:2 final size:2
Alignment explanation
Indices: 853527--853553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
853517 AATATATATG
853527 AC AC AC 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 A
853554 TTTCCTTACC
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:862719 original size:50 final size:50
Alignment explanation
Indices: 862645--862761 Score: 162
Period size: 50 Copynumber: 2.3 Consensus size: 50
862635 TGAAGGCTAC
* ** * * *
862645 GTGAAGACTACTAAATGAATCGTAAAACTTGATCATGTGTATAGTACTAT
1 GTGAAGGCTACTACGTGAACCGTAAAAATTGATCACGTGTATAGTACTAT
* *
862695 GTGAAGGCTATTACGTGAACCGTAAAAATTGATCACGTGTGTAGTACTAT
1 GTGAAGGCTACTACGTGAACCGTAAAAATTGATCACGTGTATAGTACTAT
862745 GTGAAGGCTACTACGTG
1 GTGAAGGCTACTACGTG
862762 TATCGAATGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (50 bp):
GTGAAGGCTACTACGTGAACCGTAAAAATTGATCACGTGTATAGTACTAT
Found at i:865343 original size:24 final size:24
Alignment explanation
Indices: 865311--865361 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
865301 ATTAGAATCT
865311 TTACTTGTTT-CTTTACTTACTCAC
1 TTACTTGTTTAC-TTACTTACTCAC
* *
865335 TTACTTGTTTACTTACTTGCTTAC
1 TTACTTGTTTACTTACTTACTCAC
865359 TTA
1 TTA
865362 AATAACTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.55
Consensus pattern (24 bp):
TTACTTGTTTACTTACTTACTCAC
Found at i:865348 original size:12 final size:12
Alignment explanation
Indices: 865323--865361 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
865313 ACTTGTTTCT
* *
865323 TTACTTACTCAC
1 TTACTTGCTTAC
*
865335 TTACTTGTTTAC
1 TTACTTGCTTAC
865347 TTACTTGCTTAC
1 TTACTTGCTTAC
865359 TTA
1 TTA
865362 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:865557 original size:50 final size:50
Alignment explanation
Indices: 865482--865724 Score: 288
Period size: 50 Copynumber: 4.7 Consensus size: 50
865472 TTTTCTGTAC
* * * **
865482 TGCCAATGCCATATCTCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
865532 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
865582 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
865632 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATTTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
**
865688 TGTGAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
865725 TCTTATTCCC
Statistics
Matches: 167, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
50 130 0.78
53 2 0.01
56 35 0.21
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:868364 original size:7 final size:7
Alignment explanation
Indices: 868346--868381 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
868336 TAAAAATAAG
868346 TTTTCT-
1 TTTTCTC
868352 TTTTCTC
1 TTTTCTC
868359 TTTTCTC
1 TTTTCTC
868366 TTTTCTC
1 TTTTCTC
868373 TTTGTCTC
1 TTT-TCTC
868381 T
1 T
868382 CGTTTTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 17 0.61
8 5 0.18
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (7 bp):
TTTTCTC
Found at i:872197 original size:153 final size:153
Alignment explanation
Indices: 871913--872866 Score: 1320
Period size: 153 Copynumber: 6.2 Consensus size: 153
871903 TTTAGTGTGT
* * *
871913 TTTTATTGAAAGTAATAAAATCCGGTAAAAAAATACGAACAAAAGGCCGAAATAA-GAGTTTTTT
1 TTTT-TTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCAAAATAATG-GTTTTTT
* * *
871977 TTAAATTTATTT-AAAAACAAACTAAATGAATACATTTCAAACATAATATACTGAAATAATGTAA
64 TTAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
*
872041 AATAATAAAATTAGAAAATATTATA
129 AATAATAAAATTAGAAAATAATATA
* * * *
872066 TTTTTT-AAAGTAATAAAATTCGGGAAAAAAATACAAACAAAGGGTCAAAATAATGGTTTTTTAC
1 TTTTTTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCAAAATAATGGTTTTTT-T
* *
872130 TAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAA
65 TAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
872195 ATAATAAAATTAGAAAATAATATA
130 ATAATAAAATTAGAAAATAATATA
* *
872219 TTTTTATTGAAAGTAATAAAATCTGGGAAAAAAATACGAACAAAGGGCCGAAACAAGAAT--TTT
1 -TTTT-TTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCC--AA-AATAATGGTTT
* * * *
872282 TTTTTAAAAATTTATTTTAAAAACACACTAAATGAATACATTTGAAACATAATGTACTTAAACAA
61 TTTTT--AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAA
872347 TGTAAAATAATAAAATTAGAAAATAATATA
124 TGTAAAATAATAAAATTAGAAAATAATATA
* *
872377 TTTTTT-AAAGTAATAAAATCCGAGGAAAAAAATACGAACAAAGGG-GAAAATAATAGTTTTTTT
1 TTTTTTGAAAGTAATAAAATCCG-GGAAAAAAATACGAACAAAGGGCCAAAATAATGGTTTTTTT
* * *
872440 AAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAA
65 TAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAA
872505 ATAATAAAA-TAGGAAAATAATATA
130 ATAATAAAATTA-GAAAATAATATA
* *
872529 TTTTTATTGAAAGTAATAAAATCC-GG-AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
1 -TTTT-TTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCAAAATAATGGTTTTTT
* **
872592 TTAAATATAAATAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
64 TTAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
* *
872657 AATAATAAAATTAGAAAGTAGTATA
129 AATAATAAAATTAGAAAATAATATA
* * * *
872682 TTTTTTAAAAGTAATAAAATCCGAGGAAAAAAATACGAACAAATGGCTAAAATAAGGGTTTTTTT
1 TTTTTTGAAAGTAATAAAATCCG-GGAAAAAAATACGAACAAAGGGCCAAAATAATGG-TTTTTT
* *
872747 TTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATGTAA
64 TTAAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAA
* *
872812 AATAAT-AAATTAAAAAATAGTATA
129 AATAATAAAATTAGAAAATAATATA
*
872836 TTTTTT-AAAGTAATAAAATCCGGAAAAAAAA
1 TTTTTTGAAAGTAATAAAATCCGGGAAAAAAA
872867 AACAAATGGC
Statistics
Matches: 718, Mismatches: 59, Indels: 49
0.87 0.07 0.06
Matches are distributed among these distances:
151 67 0.09
152 129 0.18
153 193 0.27
154 65 0.09
155 104 0.14
156 61 0.08
157 10 0.01
158 84 0.12
159 5 0.01
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (153 bp):
TTTTTTGAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCAAAATAATGGTTTTTTTT
AAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
TAATAAAATTAGAAAATAATATA
Found at i:873024 original size:14 final size:14
Alignment explanation
Indices: 872974--873028 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
872964 ATAAATAAAC
872974 TTTTTTGTA-TATT
1 TTTTTTGTATTATT
* *
872987 ATTTTAGTATT-TT
1 TTTTTTGTATTATT
*
873000 TTTATT-T-TTATT
1 TTTTTTGTATTATT
873012 TTTTTTGTATTATT
1 TTTTTTGTATTATT
873026 TTT
1 TTT
873029 GTAAAATACC
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
11 2 0.06
12 8 0.25
13 13 0.41
14 9 0.28
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (14 bp):
TTTTTTGTATTATT
Found at i:880175 original size:21 final size:21
Alignment explanation
Indices: 880151--880205 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
880141 AGGTAAGAAA
* *
880151 ATAAAAATATATAAAATTATC
1 ATAAAAATAAATAAAATGATC
*
880172 ATAAAAATAAATAATATGATC
1 ATAAAAATAAATAAAATGATC
*
880193 ATAAATATAAATA
1 ATAAAAATAAATA
880206 TTATTTATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAAAAATAAATAAAATGATC
Found at i:881950 original size:16 final size:15
Alignment explanation
Indices: 881919--881958 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
881909 TTATTTATTA
881919 AATTAA-TTTAAATT
1 AATTAATTTTAAATT
881933 AATTAATTTTACAATT
1 AATTAATTTTA-AATT
*
881949 AAATAATTTT
1 AATTAATTTT
881959 CTCAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 13 0.57
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTAATTTTAAATT
Found at i:884131 original size:13 final size:13
Alignment explanation
Indices: 884109--884138 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
884099 GCATATCTTT
884109 TATTGCATTTTAA
1 TATTGCATTTTAA
*
884122 TATTGTATTTTAA
1 TATTGCATTTTAA
884135 TATT
1 TATT
884139 TCATATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (13 bp):
TATTGCATTTTAA
Found at i:895082 original size:28 final size:28
Alignment explanation
Indices: 895042--895098 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
895032 AACTTGTATG
895042 TGTGTAAATATGTATTAGTTGAATAAGT
1 TGTGTAAATATGTATTAGTTGAATAAGT
895070 TGTGTAAATATGTATTAGTTGAATAAGT
1 TGTGTAAATATGTATTAGTTGAATAAGT
895098 T
1 T
895099 TAAAATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (28 bp):
TGTGTAAATATGTATTAGTTGAATAAGT
Found at i:896513 original size:31 final size:30
Alignment explanation
Indices: 896461--896599 Score: 109
Period size: 31 Copynumber: 4.5 Consensus size: 30
896451 ATGAATATTG
* * *
896461 ATATACCAAGCAATTAGGCAATGTATAACC
1 ATATACAAATCAATTTGGCAATGTATAACC
* *
896491 ATATACAAATCAAGTTTGGCAATATATAATC
1 ATATACAAATCAA-TTTGGCAATGTATAACC
* * **
896522 ATATACAAATCAAATTCGGC-ATCCTATATTC
1 ATATACAAATC-AATTTGGCAAT-GTATAACC
* * *
896553 ATAAACAATTCAATTTCGACAATGTATAACC
1 ATATACAAATCAATTT-GGCAATGTATAACC
* *
896584 ATGTACAAATTAATTT
1 ATATACAAATCAATTT
896600 CAGCAGTATT
Statistics
Matches: 85, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
30 17 0.20
31 64 0.75
32 4 0.05
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (30 bp):
ATATACAAATCAATTTGGCAATGTATAACC
Found at i:900560 original size:19 final size:19
Alignment explanation
Indices: 900536--900572 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
900526 AAATTCTATC
*
900536 TATTTTGGTTTATTTGAAG
1 TATTTTGGTTTATATGAAG
900555 TATTTTGGTTTATATGAA
1 TATTTTGGTTTATATGAA
900573 ATGAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (19 bp):
TATTTTGGTTTATATGAAG
Found at i:901956 original size:17 final size:17
Alignment explanation
Indices: 901931--901970 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
901921 TATTCTCTCA
*
901931 TCTTGTGTCTTATATTT
1 TCTTTTGTCTTATATTT
* *
901948 TCTTTTGTCTTTTGTTT
1 TCTTTTGTCTTATATTT
901965 TCTTTT
1 TCTTTT
901971 TACTATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.10, T:0.72
Consensus pattern (17 bp):
TCTTTTGTCTTATATTT
Found at i:903971 original size:24 final size:23
Alignment explanation
Indices: 903928--903972 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
903918 ATTTAATTTT
*
903928 AAAAAGTTTAATGATTAAATAAA
1 AAAAAGTTTAATGATAAAATAAA
903951 AAAAAGTTTAATGATCAAAATA
1 AAAAAGTTTAATGAT-AAAATA
903973 GAACGAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAAAGTTTAATGATAAAATAAA
Found at i:914730 original size:27 final size:26
Alignment explanation
Indices: 914692--914746 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
914682 ATAATGTGAG
*
914692 AAAATTCTGGCCTAGTTTGTAGGGAA
1 AAAATTCTGGCCTAGTTGGTAGGGAA
*
914718 NAAAATTGTGGCCTAGTTGGTAGGGAA
1 -AAAATTCTGGCCTAGTTGGTAGGGAA
914745 AA
1 AA
914747 TGCACATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.27
Consensus pattern (26 bp):
AAAATTCTGGCCTAGTTGGTAGGGAA
Found at i:932952 original size:52 final size:52
Alignment explanation
Indices: 932874--932978 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
932864 TGCTTGTACT
932874 GGTCAAACGCGAGGAAACAATGACGATTGAATACGGGGGGTTAACTCATCAC
1 GGTCAAACGCGAGGAAACAATGACGATTGAATACGGGGGGTTAACTCATCAC
*
932926 GGTCAAACGCGAGTAAACAATGACGATTGAATACGGGGGGTTAACTCATCAC
1 GGTCAAACGCGAGGAAACAATGACGATTGAATACGGGGGGTTAACTCATCAC
932978 G
1 G
932979 CTTGTGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (52 bp):
GGTCAAACGCGAGGAAACAATGACGATTGAATACGGGGGGTTAACTCATCAC
Found at i:934085 original size:41 final size:41
Alignment explanation
Indices: 934028--934108 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
934018 AATATTTTAG
*
934028 GGAGCAAGACCTAAAACTTAAGTCAGCAATACATGCCTTTT
1 GGAGCAAGACATAAAACTTAAGTCAGCAATACATGCCTTTT
934069 GGAGCAAGACATAAAACTTAAGTCAGCAATACATGCCTTT
1 GGAGCAAGACATAAAACTTAAGTCAGCAATACATGCCTTT
934109 ATTTTAGAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
GGAGCAAGACATAAAACTTAAGTCAGCAATACATGCCTTTT
Done.