Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 4 of 362
Found at i:1318967 original size:20 final size:20
Alignment explanation
Indices: 1318924--1318967 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1318914 TTTTTGTCTT
* * *
1318924 AAATCCATAAAATCTTACTT
1 AAATCCATAAAACCTAACTA
*
1318944 AAATCGATAAAACCTAACTA
1 AAATCCATAAAACCTAACTA
1318964 AAAT
1 AAAT
1318968 AAAACCCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATCCATAAAACCTAACTA
Found at i:1328080 original size:38 final size:38
Alignment explanation
Indices: 1328029--1328106 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
1328019 CACCGGTGTC
* *
1328029 CTATGCATATTTGGACGTATGTACCGAGATATGACTCT
1 CTATGCATATTTGGACATATGTACCAAGATATGACTCT
* *
1328067 CTATGTATATTTGGCCATATGTACCAAGATATGACTCT
1 CTATGCATATTTGGACATATGTACCAAGATATGACTCT
1328105 CT
1 CT
1328107 GAGGACTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (38 bp):
CTATGCATATTTGGACATATGTACCAAGATATGACTCT
Found at i:1331631 original size:38 final size:38
Alignment explanation
Indices: 1331588--1331666 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
1331578 GAATCAAATT
* * *
1331588 AGACCGACCAGATTAAAAGTCAATCGACGTAATGGTCG
1 AGACCGACCAGATCAAAAATCAATCGACATAATGGTCG
* *
1331626 AGACCGACTAGATCAAAAATCAGTCGACATAATGGTCG
1 AGACCGACCAGATCAAAAATCAATCGACATAATGGTCG
1331664 AGA
1 AGA
1331667 GAAAGATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (38 bp):
AGACCGACCAGATCAAAAATCAATCGACATAATGGTCG
Found at i:1350056 original size:6 final size:6
Alignment explanation
Indices: 1350045--1350069 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1350035 GAAAGGAAAG
1350045 AGATGA AGATGA AGATGA AGATGA A
1 AGATGA AGATGA AGATGA AGATGA A
1350070 ACGACTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
AGATGA
Found at i:1358307 original size:21 final size:21
Alignment explanation
Indices: 1358283--1358326 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1358273 GAAATGAACA
1358283 TAGTTTTGGTCGTATAATGTT
1 TAGTTTTGGTCGTATAATGTT
1358304 TAGTTTTGGTCGTATAATGTT
1 TAGTTTTGGTCGTATAATGTT
1358325 TA
1 TA
1358327 TTGTTATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.05, G:0.23, T:0.52
Consensus pattern (21 bp):
TAGTTTTGGTCGTATAATGTT
Found at i:1363709 original size:3 final size:3
Alignment explanation
Indices: 1363701--1363726 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1363691 AGATTCAACG
1363701 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
1363727 ACCAAGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1372993 original size:16 final size:17
Alignment explanation
Indices: 1372972--1373009 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1372962 CATTTTAGTG
*
1372972 TTTATTTTTAT-ATTTA
1 TTTATTTATATAATTTA
*
1372988 TTTATTTATATAATTTT
1 TTTATTTATATAATTTA
1373005 TTTAT
1 TTTAT
1373010 ACTAGCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTATATAATTTA
Found at i:1374767 original size:22 final size:22
Alignment explanation
Indices: 1374736--1374794 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1374726 AAATTTTTAA
1374736 TAAATAAAAAATAA-AAAAATAT
1 TAAAT-AAAAATAATAAAAATAT
* *
1374758 TAAATTAAAATAATATAAATAT
1 TAAATAAAAATAATAAAAATAT
***
1374780 TTTTTAAAAATAATA
1 TAAATAAAAATAATA
1374795 TGGACGAGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATAAAAATAATAAAAATAT
Found at i:1377875 original size:21 final size:20
Alignment explanation
Indices: 1377842--1377880 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1377832 TTGTCATGTG
*
1377842 TTTTTTTATTAATTTATTTA
1 TTTTTTAATTAATTTATTTA
1377862 TTTTTTAATATAATTTATT
1 TTTTTTAAT-TAATTTATT
1377881 AACACTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTAATTAATTTATTTA
Found at i:1388891 original size:23 final size:22
Alignment explanation
Indices: 1388848--1388894 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1388838 TATTCTTTAG
* *
1388848 ATTTTACATATATATTTTTAAA
1 ATTTTACATATATAATCTTAAA
*
1388870 ATTTTACATGTTATAATCTTAAA
1 ATTTTACAT-ATATAATCTTAAA
1388893 AT
1 AT
1388895 ACCATGTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTTACATATATAATCTTAAA
Found at i:1397473 original size:13 final size:13
Alignment explanation
Indices: 1397451--1397488 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1397441 GGTTGGTACC
1397451 TAAT-TTCGATTT
1 TAATGTTCGATTT
1397463 TAATGTTCGATTT
1 TAATGTTCGATTT
*
1397476 TAATGTTCAATTT
1 TAATGTTCGATTT
1397489 GGAACTTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (13 bp):
TAATGTTCGATTT
Found at i:1397733 original size:31 final size:32
Alignment explanation
Indices: 1397684--1397748 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
1397674 TCAAATTGAA
* * *
1397684 AAAACTCAAAACTCAAATTTAATATT-AAATC
1 AAAACTAAAAACTCAAATTAAACATTAAAATC
1397715 AAAACTAAAATACT-AAATTAAACATTAAAATC
1 AAAACTAAAA-ACTCAAATTAAACATTAAAATC
1397747 AA
1 AA
1397749 CATAAATACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (32 bp):
AAAACTAAAAACTCAAATTAAACATTAAAATC
Found at i:1397734 original size:24 final size:24
Alignment explanation
Indices: 1397689--1397736 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1397679 TTGAAAAAAC
* *
1397689 TCAAAACTCAAATTTAATATTAAA
1 TCAAAACTAAAATCTAATATTAAA
1397713 TCAAAACTAAAATACTAA-ATTAAA
1 TCAAAACTAAAAT-CTAATATTAAA
1397737 CATTAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.29
Consensus pattern (24 bp):
TCAAAACTAAAATCTAATATTAAA
Found at i:1397792 original size:16 final size:16
Alignment explanation
Indices: 1397771--1397802 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1397761 ATCCTTATTA
1397771 AAATTATTTTTAATTT
1 AAATTATTTTTAATTT
1397787 AAATTATTTTTAATTT
1 AAATTATTTTTAATTT
1397803 GCATAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AAATTATTTTTAATTT
Found at i:1405406 original size:17 final size:19
Alignment explanation
Indices: 1405376--1405413 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
1405366 ATATATAATT
1405376 AAAAGATTATAAAAATAAA
1 AAAAGATTATAAAAATAAA
1405395 AAAAG-TTA-AAAAATAAA
1 AAAAGATTATAAAAATAAA
1405412 AA
1 AA
1405414 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 3 0.16
19 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAAGATTATAAAAATAAA
Found at i:1414991 original size:15 final size:15
Alignment explanation
Indices: 1414971--1415000 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1414961 AGATGAAGGA
1414971 GGTGAAACTTCTTCC
1 GGTGAAACTTCTTCC
1414986 GGTGAAACTTCTTCC
1 GGTGAAACTTCTTCC
1415001 TCAAGACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
GGTGAAACTTCTTCC
Found at i:1416888 original size:21 final size:22
Alignment explanation
Indices: 1416858--1416898 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1416848 ACACCAAGAA
*
1416858 AAAATCCAAATTCTAAAATATG
1 AAAATCCAAATACTAAAATATG
1416880 AAAA-CCAAATACTAAAATA
1 AAAATCCAAATACTAAAATA
1416899 CCCGGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAATCCAAATACTAAAATATG
Found at i:1422970 original size:82 final size:82
Alignment explanation
Indices: 1422833--1422999 Score: 334
Period size: 82 Copynumber: 2.0 Consensus size: 82
1422823 AATTTGTTTC
1422833 ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
1 ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
1422898 GTCAAGGTGATATTGTT
66 GTCAAGGTGATATTGTT
1422915 ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
1 ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
1422980 GTCAAGGTGATATTGTT
66 GTCAAGGTGATATTGTT
1422997 ATA
1 ATA
1423000 AACAAAAACC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (82 bp):
ATATACACCTTGTTCTAGTAGTAGAAAAATAACAGTAGCTGATGGTTCTGTGATCACAGTGGCCG
GTCAAGGTGATATTGTT
Found at i:1424269 original size:21 final size:21
Alignment explanation
Indices: 1424243--1424283 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1424233 TCCAGCAACC
*
1424243 AAACACTCTCATTCCAGCTCT
1 AAACACTCCCATTCCAGCTCT
*
1424264 AAACACTCCCATTCCGGCTC
1 AAACACTCCCATTCCAGCTC
1424284 CTGTCCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.41, G:0.07, T:0.24
Consensus pattern (21 bp):
AAACACTCCCATTCCAGCTCT
Found at i:1432769 original size:33 final size:33
Alignment explanation
Indices: 1432731--1432797 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1432721 TGGTCAAAGC
1432731 TAACGACACAATTTTCACACCATCATCAGATGT
1 TAACGACACAATTTTCACACCATCATCAGATGT
1432764 TAACGACACAATTTTCACACCATCATCAGATGT
1 TAACGACACAATTTTCACACCATCATCAGATGT
1432797 T
1 T
1432798 CTTAAAGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.28
Consensus pattern (33 bp):
TAACGACACAATTTTCACACCATCATCAGATGT
Found at i:1446895 original size:19 final size:20
Alignment explanation
Indices: 1446852--1446927 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
1446842 CCCTAAATTG
1446852 AGTTCGAATGATACTAAATTTCA
1 AGTTC-AATGAT--TAAATTTCA
1446875 AGTTCAATGATTAAA-TTCA
1 AGTTCAATGATTAAATTTCA
*
1446894 AG-T--AT-ACTAAATTTCA
1 AGTTCAATGATTAAATTTCA
*
1446910 AGTTTAATGATTAAATTT
1 AGTTCAATGATTAAATTT
1446928 AAATATATTG
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
15 5 0.11
16 8 0.17
17 1 0.02
18 1 0.02
19 8 0.17
20 12 0.26
22 6 0.13
23 5 0.11
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (20 bp):
AGTTCAATGATTAAATTTCA
Found at i:1446911 original size:16 final size:17
Alignment explanation
Indices: 1446862--1446912 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
1446852 AGTTCGAATG
1446862 ATACTAAATTTCAAGTTCA
1 ATACTAAATTTCAAG-T-A
*
1446881 ATGATTAAA-TTCAAGT-
1 AT-ACTAAATTTCAAGTA
1446897 ATACTAAATTTCAAGT
1 ATACTAAATTTCAAGT
1446913 TTAATGATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 5 0.18
16 9 0.32
18 1 0.04
19 8 0.29
20 5 0.18
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (17 bp):
ATACTAAATTTCAAGTA
Found at i:1449886 original size:27 final size:27
Alignment explanation
Indices: 1449855--1449909 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1449845 CTTCCAAGTG
1449855 TTGTTTATTCAAAACCAAACCCTCCAA
1 TTGTTTATTCAAAACCAAACCCTCCAA
*
1449882 TTGTTTATTCAAAGCCAAACCCTCCAA
1 TTGTTTATTCAAAACCAAACCCTCCAA
1449909 T
1 T
1449910 GGGTCGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (27 bp):
TTGTTTATTCAAAACCAAACCCTCCAA
Found at i:1452760 original size:24 final size:24
Alignment explanation
Indices: 1452724--1452787 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
1452714 TAAATTATTA
1452724 AATTTTTAT-AAAAAAATAAATAT
1 AATTTTTATAAAAAAAATAAATAT
1452747 AATTTTTATAAAAAAAATAAATAT
1 AATTTTTATAAAAAAAATAAATAT
1452771 AATTTTT-TAAAAAAAAT
1 AATTTTTATAAAAAAAAT
1452788 TAGTTTAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 19 0.47
24 21 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATTTTTATAAAAAAAATAAATAT
Found at i:1452796 original size:23 final size:23
Alignment explanation
Indices: 1452711--1452787 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 23
1452701 TCCAATAATT
*
1452711 AAATAAATTATTAAATTTTTATAAAA
1 AAATAAA-TA-TAATTTTTTA-AAAA
1452737 AAATAAATATAATTTTTATAAAAA
1 AAATAAATATAATTTTT-TAAAAA
1452761 AAATAAATATAATTTTTTAAAAA
1 AAATAAATATAATTTTTTAAAAA
1452784 AAAT
1 AAAT
1452788 TAGTTTAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
23 10 0.20
24 28 0.57
25 4 0.08
26 7 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATAAATATAATTTTTTAAAAA
Found at i:1454244 original size:19 final size:20
Alignment explanation
Indices: 1454209--1454254 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
1454199 AATTTTTATT
*
1454209 AAAAATATATAATACAT-AA
1 AAAAATATATAAAACATCAA
1454228 AAAAATACTA-AAAACATCAA
1 AAAAATA-TATAAAACATCAA
1454248 AATAAAT
1 AA-AAAT
1454255 GTTTCCTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.57
20 6 0.26
21 4 0.17
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAATATATAAAACATCAA
Found at i:1470654 original size:7 final size:7
Alignment explanation
Indices: 1470642--1470672 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1470632 ATTACCTAAT
1470642 AAAATAA
1 AAAATAA
1470649 AAAATAA
1 AAAATAA
1470656 AAAATAA
1 AAAATAA
*
1470663 AGAATAA
1 AAAATAA
1470670 AAA
1 AAA
1470673 CGCAAATTTT
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:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:1470814 original size:10 final size:9
Alignment explanation
Indices: 1470789--1470813 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1470779 TTTTAAAAGG
1470789 AAAAAAATT
1 AAAAAAATT
1470798 AAAAAAATT
1 AAAAAAATT
1470807 AAAAAAA
1 AAAAAAA
1470814 AAAGGAAAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAAAATT
Found at i:1479838 original size:8 final size:8
Alignment explanation
Indices: 1479825--1479849 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1479815 TTATGTTTAA
1479825 TATATTAT
1 TATATTAT
1479833 TATATTAT
1 TATATTAT
1479841 TATATTAT
1 TATATTAT
1479849 T
1 T
1479850 GTATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATTAT
Found at i:1481192 original size:15 final size:15
Alignment explanation
Indices: 1481172--1481228 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
1481162 CGATGAATTT
1481172 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
1481187 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
1481202 ATTGAATTTATATTG
1 ATTGAATTTATATTG
1481217 ATTGAA-TTATAT
1 ATTGAATTTATAT
1481229 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:1481648 original size:21 final size:21
Alignment explanation
Indices: 1481613--1481708 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1481603 AGGCACTTTA
1481613 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
1481636 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
1481657 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * * **
1481678 TGTGTCGTTTTAGGCACTTTA
1 TGTGTCGTATCAGGCACCTCG
1481699 TGTGTCGTAT
1 TGTGTCGTAT
1481709 ACTGATCAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 58 0.87
23 9 0.13
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:1481683 original size:42 final size:42
Alignment explanation
Indices: 1481600--1481708 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 42
1481590 GGCTTTATCG
* *
1481600 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTA--TCAGGCACCTCGTGTGTCGT
*
1481644 ATCAGGCACCTCGTGTGTCGTATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCGT
* * * *
1481686 TTTAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTCATGTGTCGTAT
1481709 ACTGATCAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 38 0.67
44 19 0.33
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.36
Consensus pattern (42 bp):
ATCAGGCACCTCATGTGTCGTATCAGGCACCTCGTGTGTCGT
Found at i:1484525 original size:18 final size:19
Alignment explanation
Indices: 1484497--1484537 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1484487 GATATAGGCC
1484497 CCTTTT-TTTTTT-CTTTT
1 CCTTTTCTTTTTTCCTTTT
1484514 -CTTTTCTTTTTTCCTTTT
1 CCTTTTCTTTTTTCCTTTT
1484532 CCTTTT
1 CCTTTT
1484538 TTCTTACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 5 0.24
19 5 0.24
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
CCTTTTCTTTTTTCCTTTT
Found at i:1485085 original size:29 final size:28
Alignment explanation
Indices: 1485052--1485122 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
1485042 AAACCGTAAA
* *
1485052 AAAATATTAAAAACAGTAAAAAGTATTTT
1 AAAATATTAAAAACAGTAAAAAATA-ATT
**
1485081 AAAATATATAAAAATTGTAAAAAATAATT
1 AAAATAT-TAAAAACAGTAAAAAATAATT
*
1485110 AAATTATTAAAAA
1 AAAATATTAAAAA
1485123 AGCAAATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.17
29 15 0.42
30 15 0.42
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
AAAATATTAAAAACAGTAAAAAATAATT
Found at i:1485104 original size:20 final size:20
Alignment explanation
Indices: 1485081--1485253 Score: 65
Period size: 20 Copynumber: 8.9 Consensus size: 20
1485071 AAAGTATTTT
1485081 AAAATATATAAAAATTGTAA
1 AAAATATATAAAAATTGTAA
* * *
1485101 AAAATA-AT-TAAATTATTA
1 AAAATATATAAAAATTGTAA
** * * *
1485119 AAAA-A-GCAAATATTTTTA
1 AAAATATATAAAAATTGTAA
* * *
1485137 ACAATATTTTAAAATTGTAA
1 AAAATATATAAAAATTGTAA
*
1485157 AAAATAT-TAAAAATTATAA
1 AAAATATATAAAAATTGTAA
* **
1485176 AATAT-TAATTAAATTTTGTAA
1 AAAATAT-A-TAAAAATTGTAA
* *
1485197 AAATTAT-TAAAAATTGCAA
1 AAAATATATAAAAATTGTAA
* *
1485216 ATAAT-TATTAAAAGTTGTAA
1 AAAATATA-TAAAAATTGTAA
* * *
1485236 AAATTATTTCAAAATTGT
1 AAAATATATAAAAATTGT
1485254 GAACCAATAG
Statistics
Matches: 107, Mismatches: 36, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
17 1 0.01
18 23 0.21
19 29 0.27
20 40 0.37
21 13 0.12
22 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATATATAAAAATTGTAA
Found at i:1485188 original size:21 final size:19
Alignment explanation
Indices: 1485147--1485243 Score: 86
Period size: 19 Copynumber: 4.9 Consensus size: 19
1485137 ACAATATTTT
* *
1485147 AAAATTGTAAAAAATATTA
1 AAAATTATAAAAATTATTA
1485166 AAAATTATAAAATATTAATTA
1 AAAATTATAAAA-ATT-ATTA
** *
1485187 AATTTTGTAAAAATTATTA
1 AAAATTATAAAAATTATTA
**
1485206 AAAATTGCAAATAATTATTA
1 AAAATTATAAA-AATTATTA
* *
1485226 AAAGTTGTAAAAATTATT
1 AAAATTATAAAAATTATT
1485244 TCAAAATTGT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
19 30 0.46
20 22 0.34
21 13 0.20
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAATTATAAAAATTATTA
Found at i:1485209 original size:10 final size:10
Alignment explanation
Indices: 1485154--1485243 Score: 55
Period size: 10 Copynumber: 9.1 Consensus size: 10
1485144 TTTAAAATTG
*
1485154 TAAAAAATAT
1 TAAAAATTAT
1485164 TAAAAATTA-
1 TAAAAATTAT
1485173 T-AAAA-TAT
1 TAAAAATTAT
*
1485181 TAATTAAATTTT
1 TAA--AAATTAT
1485193 GTAAAAATTAT
1 -TAAAAATTAT
*
1485204 TAAAAATT-G
1 TAAAAATTAT
*
1485213 CAAATAATTAT
1 TAAA-AATTAT
* *
1485224 TAAAAGTT-G
1 TAAAAATTAT
1485233 TAAAAATTAT
1 TAAAAATTAT
1485243 T
1 T
1485244 TCAAAATTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 12 0.20
10 24 0.40
11 12 0.20
12 2 0.03
13 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:1485218 original size:39 final size:39
Alignment explanation
Indices: 1485145--1485252 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 39
1485135 TAACAATATT
* *
1485145 TTAAAA-TTGTAAAAAATATTAAAAATTATAAAAT-ATTAA
1 TTAAAAGTTGTAAAAATTATTAAAAATT-GAAAATAATT-A
** *
1485184 TTAAATTTTGTAAAAATTATTAAAAATTGCAAATAATTA
1 TTAAAAGTTGTAAAAATTATTAAAAATTGAAAATAATTA
*
1485223 TTAAAAGTTGTAAAAATTATTTCAAAATTG
1 TTAAAAGTTGTAAAAATTA-TTAAAAATTG
1485253 TGAACCAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
39 27 0.46
40 32 0.54
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (39 bp):
TTAAAAGTTGTAAAAATTATTAAAAATTGAAAATAATTA
Found at i:1491301 original size:25 final size:25
Alignment explanation
Indices: 1491268--1491319 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1491258 TGATAAACAT
*
1491268 ATTCAAATACTT-AAAAAAATTATAA
1 ATTCAAATAATTCAAAAAAA-TATAA
*
1491293 ATTCGAATAATTCAAAAAAATATAA
1 ATTCAAATAATTCAAAAAAATATAA
1491318 AT
1 AT
1491320 ATTTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
ATTCAAATAATTCAAAAAAATATAA
Found at i:1497904 original size:7 final size:7
Alignment explanation
Indices: 1497892--1497926 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1497882 TGCTTTACTG
1497892 CTCACCA
1 CTCACCA
1497899 CTCACCA
1 CTCACCA
1497906 CTCACCA
1 CTCACCA
1497913 CTCACCA
1 CTCACCA
1497920 CTCACCA
1 CTCACCA
1497927 TATATTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.57, G:0.00, T:0.14
Consensus pattern (7 bp):
CTCACCA
Found at i:1499433 original size:29 final size:29
Alignment explanation
Indices: 1499363--1499435 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
1499353 TACATTTTAT
1499363 TTTTTATTAAAAAAATAGATAAATTAATC
1 TTTTTATTAAAAAAATAGATAAATTAATC
* *
1499392 TTTGTATATTAAATATAA-A-ATAAATTGATC
1 TTT-T-TATTAAA-AAAATAGATAAATTAATC
1499422 ATTTTTATTAAAAA
1 -TTTTTATTAAAAA
1499436 TTTCATCCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 1 0.03
29 10 0.27
30 12 0.32
31 11 0.30
32 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (29 bp):
TTTTTATTAAAAAAATAGATAAATTAATC
Found at i:1502181 original size:15 final size:15
Alignment explanation
Indices: 1502161--1502194 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1502151 TTTGAACCAG
* *
1502161 ATTTTTTATATTTTT
1 ATTTTTTAAATATTT
1502176 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
1502191 ATTT
1 ATTT
1502195 AATCAAACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:1504059 original size:5 final size:5
Alignment explanation
Indices: 1504051--1504081 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1504041 ATTACATGAC
1504051 ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA A
1504082 ACTTAGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:1509620 original size:149 final size:149
Alignment explanation
Indices: 1509350--1509650 Score: 602
Period size: 149 Copynumber: 2.0 Consensus size: 149
1509340 ACAAGTCTGC
1509350 AGAATATTGGGAATATTAAAGTCGGAATATACTCGTCAGAAAAAAAAAATCTCAGTATTAAACTT
1 AGAATATTGGGAATATTAAAGTCGGAATATACTCGTCAGAAAAAAAAAATCTCAGTATTAAACTT
1509415 GCTTTGCTATTGTTTCGCTTTGAAGGAATATCTTCTCGATGCTAGCAACTCATTGGTTGAAATGG
66 GCTTTGCTATTGTTTCGCTTTGAAGGAATATCTTCTCGATGCTAGCAACTCATTGGTTGAAATGG
1509480 TTCATTCTTGTTAGCTAGG
131 TTCATTCTTGTTAGCTAGG
1509499 AGAATATTGGGAATATTAAAGTCGGAATATACTCGTCAGAAAAAAAAAATCTCAGTATTAAACTT
1 AGAATATTGGGAATATTAAAGTCGGAATATACTCGTCAGAAAAAAAAAATCTCAGTATTAAACTT
1509564 GCTTTGCTATTGTTTCGCTTTGAAGGAATATCTTCTCGATGCTAGCAACTCATTGGTTGAAATGG
66 GCTTTGCTATTGTTTCGCTTTGAAGGAATATCTTCTCGATGCTAGCAACTCATTGGTTGAAATGG
1509629 TTCATTCTTGTTAGCTAGG
131 TTCATTCTTGTTAGCTAGG
1509648 AGA
1 AGA
1509651 GGCTACTAAT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (149 bp):
AGAATATTGGGAATATTAAAGTCGGAATATACTCGTCAGAAAAAAAAAATCTCAGTATTAAACTT
GCTTTGCTATTGTTTCGCTTTGAAGGAATATCTTCTCGATGCTAGCAACTCATTGGTTGAAATGG
TTCATTCTTGTTAGCTAGG
Found at i:1513161 original size:18 final size:18
Alignment explanation
Indices: 1513138--1513175 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1513128 ACATCAATAT
1513138 TTTCTACATCAAACCCAG
1 TTTCTACATCAAACCCAG
*
1513156 TTTCTACATCGAACCCAG
1 TTTCTACATCAAACCCAG
1513174 TT
1 TT
1513176 CCAACCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.32
Consensus pattern (18 bp):
TTTCTACATCAAACCCAG
Found at i:1521047 original size:29 final size:29
Alignment explanation
Indices: 1520993--1521057 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
1520983 TGAATTTTAA
* * * *
1520993 TTTTAATATAATTTGGACTCATTTAATTT
1 TTTTAATATAATGTGGACTAAATTAATCT
1521022 TTTTAATA-ATATGTGGACTAAATTAATCT
1 TTTTAATATA-ATGTGGACTAAATTAATCT
*
1521051 ATTTAAT
1 TTTTAAT
1521058 TATCCAATCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (29 bp):
TTTTAATATAATGTGGACTAAATTAATCT
Found at i:1526121 original size:8 final size:8
Alignment explanation
Indices: 1526110--1526139 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
1526100 CGTGTGAGTG
1526110 TGTCGGGC
1 TGTCGGGC
1526118 TGTCGGGC
1 TGTCGGGC
1526126 TGTCGGGC
1 TGTCGGGC
1526134 TGTCGG
1 TGTCGG
1526140 CACTGGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.50, T:0.27
Consensus pattern (8 bp):
TGTCGGGC
Found at i:1527047 original size:14 final size:15
Alignment explanation
Indices: 1527025--1527101 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1527015 CAATCAAACA
1527025 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
1527039 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
1527054 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
1527074 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
1527088 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
1527102 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:1527066 original size:20 final size:20
Alignment explanation
Indices: 1527041--1527080 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1527031 AATATTTTCC
*
1527041 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1527061 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1527081 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1527086 original size:34 final size:35
Alignment explanation
Indices: 1527029--1527095 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1527019 CAAACACCAG
*
1527029 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1527064 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1527096 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1528014 original size:7 final size:7
Alignment explanation
Indices: 1527978--1528002 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1527968 TTTAATTTCC
1527978 TTTTAAA
1 TTTTAAA
1527985 TTTTAAA
1 TTTTAAA
1527992 TTTTAAA
1 TTTTAAA
1527999 TTTT
1 TTTT
1528003 CATTTTATAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:1529859 original size:39 final size:39
Alignment explanation
Indices: 1529749--1529886 Score: 104
Period size: 39 Copynumber: 3.5 Consensus size: 39
1529739 GACCTCGAGT
* *
1529749 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT-
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCT--ATTC
** * **
1529790 CGATGAGGTACAGGGTACCAACT-TTACTTCGGCTATTC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTATTC
* *
1529828 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTATTC
* *
1529867 CGATGAGGCACTGAGTGTCA
1 CGATGAGACACTGGGTGTCA
1529887 TTTGGTGTGT
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
37 3 0.04
38 18 0.23
39 36 0.47
40 4 0.05
41 14 0.18
42 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTATTC
Found at i:1530009 original size:18 final size:18
Alignment explanation
Indices: 1529986--1530026 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1529976 AAAAAAAAAG
1529986 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
1530004 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
1530022 AGAAA
1 AGAAA
1530027 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:1530545 original size:20 final size:20
Alignment explanation
Indices: 1530522--1530559 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1530512 GTTATTAAAT
1530522 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
1530542 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
1530560 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:1531570 original size:31 final size:29
Alignment explanation
Indices: 1531529--1531597 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1531519 CAAGCCCGAA
1531529 TATATTATGTTAGAAAAAATAATTATACTAAT
1 TATATTATGTT--AAAAAATAATTATA-TAAT
* *
1531561 TATA-TATGTTAAATAATAATTTTATAAT
1 TATATTATGTTAAAAAATAATTATATAAT
1531589 TATAATTAT
1 TAT-ATTAT
1531598 ATTTATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 7 0.21
29 13 0.39
30 3 0.09
31 6 0.18
32 4 0.12
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (29 bp):
TATATTATGTTAAAAAATAATTATATAAT
Found at i:1531593 original size:6 final size:6
Alignment explanation
Indices: 1531581--1531617 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1531571 AAATAATAAT
* *
1531581 TTTATA ATTATA ATTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
1531618 CAAATCACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:1534736 original size:15 final size:15
Alignment explanation
Indices: 1534713--1534751 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
1534703 TATATTTACC
1534713 AAATAAATTTTC-AT
1 AAATAAATTTTCAAT
1534727 AAATTAAATTTTCAAT
1 AAA-TAAATTTTCAAT
1534743 AAATAAATT
1 AAATAAATT
1534752 ATTATTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.13
15 15 0.65
16 5 0.22
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATAAATTTTCAAT
Found at i:1539991 original size:15 final size:15
Alignment explanation
Indices: 1539971--1540018 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1539961 AAATTCAACA
1539971 ATTAATTATTAAAAT
1 ATTAATTATTAAAAT
* *
1539986 ATTAATTATAAAAAA
1 ATTAATTATTAAAAT
*
1540001 ATTAATATATTTAAAT
1 ATTAAT-TATTAAAAT
1540017 AT
1 AT
1540019 CATCTCAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTATTAAAAT
Found at i:1541336 original size:18 final size:18
Alignment explanation
Indices: 1541299--1541337 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1541289 TTCTAAATAT
* *
1541299 AATTAATTAATTAATTAA
1 AATTAATTAATCAATAAA
*
1541317 AATTAATTAATCGATAAA
1 AATTAATTAATCAATAAA
1541335 AAT
1 AAT
1541338 AGTAGCAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTAATTAATCAATAAA
Found at i:1545149 original size:174 final size:174
Alignment explanation
Indices: 1544859--1545206 Score: 696
Period size: 174 Copynumber: 2.0 Consensus size: 174
1544849 ATTAGTTGAA
1544859 AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
1 AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
1544924 TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
66 TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
1544989 CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
131 CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
1545033 AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
1 AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
1545098 TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
66 TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
1545163 CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
131 CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
1545207 CCCCAAAATT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (174 bp):
AAAATCTATTAAAACAGAAGTTGGTGTTGTGGGGCTTTAATTAGTGTCAAATTTCTCTAATTATT
TAATTAATCACAAATTTTTCTCTATCATTTGGATAGCACCTAGTCTTACTTAAAACTATATTTAT
CTGGGATTTTTTTTGAAAAGTTCTCACTCCAATGCTTCCCCCCC
Found at i:1545505 original size:22 final size:23
Alignment explanation
Indices: 1545463--1545508 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1545453 ATTATATTTC
1545463 AGTTCTATGGTTCAAAAAAATTA
1 AGTTCTATGGTTCAAAAAAATTA
1545486 AGTTCTATGGTTC-AAAAAATTA
1 AGTTCTATGGTTCAAAAAAATTA
1545508 A
1 A
1545509 ATGTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (23 bp):
AGTTCTATGGTTCAAAAAAATTA
Found at i:1549116 original size:24 final size:24
Alignment explanation
Indices: 1549084--1549131 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1549074 AACAATATAT
1549084 ATGTATGAAATCTATTCTAAATTC
1 ATGTATGAAATCTATTCTAAATTC
1549108 ATGTATGAAATCTATTCTAAATTC
1 ATGTATGAAATCTATTCTAAATTC
1549132 CCATAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (24 bp):
ATGTATGAAATCTATTCTAAATTC
Found at i:1549187 original size:3 final size:3
Alignment explanation
Indices: 1549179--1549218 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1549169 ACTTGGGAAC
1549179 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1549219 CTACTACTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1554755 original size:15 final size:14
Alignment explanation
Indices: 1554716--1554763 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
1554706 AAATTTTTAA
1554716 AAATATTCAAAAAAT
1 AAAT-TTCAAAAAAT
*
1554731 AAGAATTCAAAAAAT
1 AA-ATTTCAAAAAAT
1554746 AAATTGTC-AAAAAT
1 AAATT-TCAAAAAAT
1554760 AAAT
1 AAAT
1554764 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 12 0.41
15 16 0.55
16 1 0.03
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (14 bp):
AAATTTCAAAAAAT
Found at i:1555079 original size:15 final size:16
Alignment explanation
Indices: 1555059--1555095 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1555049 ACGCGCTGCC
1555059 ATAAAAA-TAT-ATTA
1 ATAAAAATTATAATTA
1555073 TATAAAAATTATAATTA
1 -ATAAAAATTATAATTA
1555090 ATAAAA
1 ATAAAA
1555096 GGTTAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 9 0.45
17 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAAAATTATAATTA
Found at i:1557054 original size:3 final size:3
Alignment explanation
Indices: 1557041--1557077 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1557031 TATTCATTTA
*
1557041 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1557078 CCCATCAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1561242 original size:26 final size:25
Alignment explanation
Indices: 1561212--1561271 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
1561202 ATTGAAATGG
*
1561212 TTTATTTTATTGATAAAA-ATAATATA
1 TTTATTTTATT-ATAAAAGAT-ATAAA
*
1561238 TTTATTTGATTATAAAAGATATAAA
1 TTTATTTTATTATAAAAGATATAAA
1561263 TATTATTTT
1 T-TTATTTT
1561272 TAAATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (25 bp):
TTTATTTTATTATAAAAGATATAAA
Found at i:1566771 original size:120 final size:120
Alignment explanation
Indices: 1566614--1567244 Score: 1016
Period size: 120 Copynumber: 5.2 Consensus size: 120
1566604 TATATTTAGA
* * * * *
1566614 AAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 AAAA-TATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGT
*
1566679 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATT
* * * *
1566735 AAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTTAGT
1 AAAATATATTTAATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGT
* * *
1566799 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATT
1566855 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
* *
1566920 AATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAATTATATAGTTTAATT
66 AATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAATTATATATTTTAATT
*
1566975 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
*
1567040 AATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAATTATATATTTTAATT
66 AATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAATTATATATTTTAATT
1567095 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
1 AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
* *
1567160 AATTCATATAAGAATATTGATTATTAAGAATTTTATTATAAATTATATATTTTAATT
66 AATTCATATAAGAATATTTAATATTAAGAATTTTA-T-TAAATTATATATTTTAATT
1567217 AAAATATATTTAATAATAATTATGTTAA
1 AAAATATATTTAATAATAATTATGTTAA
1567245 AATATGATTA
Statistics
Matches: 485, Mismatches: 19, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
119 4 0.01
120 425 0.88
121 9 0.02
122 47 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (120 bp):
AAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTA
AATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATT
Found at i:1567097 original size:18 final size:17
Alignment explanation
Indices: 1567069--1567103 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1567059 ATTATTAAGA
*
1567069 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1567086 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1567104 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1567224 original size:18 final size:19
Alignment explanation
Indices: 1567189--1567225 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1567179 ATTATTAAGA
1567189 ATTTTATTATAAATTATAT
1 ATTTTATTATAAATTATAT
1567208 ATTTTAATTA-AAA-TATAT
1 ATTTT-ATTATAAATTATAT
1567226 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTATTATAAATTATAT
Found at i:1567482 original size:16 final size:16
Alignment explanation
Indices: 1567461--1567529 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
1567451 TATTAGCTAT
1567461 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1567477 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1567494 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1567510 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1567526 TACA
1 TACA
1567530 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1567503 original size:33 final size:32
Alignment explanation
Indices: 1567461--1567529 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
1567451 TATTAGCTAT
1567461 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
1567494 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
1567526 TACA
1 TACA
1567530 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:1570598 original size:13 final size:14
Alignment explanation
Indices: 1570580--1570608 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1570570 TAAGGGTTCC
1570580 TTAAAATTA-TTTT
1 TTAAAATTACTTTT
1570593 TTAAAATTACTTTT
1 TTAAAATTACTTTT
1570607 TT
1 TT
1570609 TATTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAAAATTACTTTT
Found at i:1587457 original size:3 final size:3
Alignment explanation
Indices: 1587449--1587502 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
1587439 TTGAGTTGTA
* *
1587449 TAT TAT TAT TACT T-T TAG AAT TTAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
1587495 TAT TAT TA
1 TAT TAT TA
1587503 CCATCTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 2 0.05
3 38 0.86
4 4 0.09
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1587992 original size:19 final size:18
Alignment explanation
Indices: 1587959--1587995 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1587949 TGTCCATTTA
1587959 ATAAAAATTAAAATTAAT
1 ATAAAAATTAAAATTAAT
*
1587977 ATAAAAACTTAGAATTAAT
1 ATAAAAA-TTAAAATTAAT
1587996 TATATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAAAAATTAAAATTAAT
Found at i:1596522 original size:23 final size:23
Alignment explanation
Indices: 1596491--1596537 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1596481 CTCCTATATA
1596491 TGCTCACTGAGTTCCTAATAATT
1 TGCTCACTGAGTTCCTAATAATT
* * *
1596514 TGCTTACTGATTTCGTAATAATT
1 TGCTCACTGAGTTCCTAATAATT
1596537 T
1 T
1596538 ACTTGCTCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (23 bp):
TGCTCACTGAGTTCCTAATAATT
Found at i:1596680 original size:2 final size:2
Alignment explanation
Indices: 1596673--1596706 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1596663 TCGAAAAGAA
1596673 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1596707 GATTTATTTC
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:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1598560 original size:24 final size:24
Alignment explanation
Indices: 1598528--1598576 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1598518 TAACTCTTTA
1598528 TAAAAAAA-TAATATTAATTTAAAT
1 TAAAAAAATTAA-ATTAATTTAAAT
*
1598552 TAAAAAAATTAAATTATTTTAAAT
1 TAAAAAAATTAAATTAATTTAAAT
1598576 T
1 T
1598577 GAGATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAAAAAATTAAATTAATTTAAAT
Found at i:1599476 original size:16 final size:15
Alignment explanation
Indices: 1599447--1599478 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1599437 GCTTTGGACT
1599447 TAAATATAATAGATA
1 TAAATATAATAGATA
1599462 TAAATATAGATAGATA
1 TAAATATA-ATAGATA
1599478 T
1 T
1599479 TTGTCATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (15 bp):
TAAATATAATAGATA
Found at i:1610704 original size:21 final size:20
Alignment explanation
Indices: 1610678--1610730 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
1610668 AAATATGTAA
1610678 TTATATAATAAAAAATAAATT
1 TTATATAATAAAAAAT-AATT
* **
1610699 TTATATATTTTAAAATAATT
1 TTATATAATAAAAAATAATT
1610719 TTA-ATTAATAAA
1 TTATA-TAATAAA
1610731 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 1 0.04
20 11 0.44
21 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATATAATAAAAAATAATT
Found at i:1610789 original size:89 final size:89
Alignment explanation
Indices: 1610628--1610797 Score: 236
Period size: 89 Copynumber: 1.9 Consensus size: 89
1610618 TAATTCATAT
*
1610628 TTTTAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAAAA
1 TTTTAATTAATAAATCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAAAA
1610693 TAAA-TTTTATATATTTTAAAATAA
66 TAAATTTTTA-ATATTTTAAAATAA
* * * * **
1610717 TTTTAATTAATAAATTTTTTATTTATATATA-AAAATAATAATTATGTAATTATGTAATGAAATT
1 TTTTAATTAATAAATCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAAT-AAAAA
*
1610781 ATATATTTTTAATATTT
65 ATAAATTTTTAATATTT
1610798 ATAATTATGT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
88 25 0.35
89 41 0.58
90 5 0.07
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (89 bp):
TTTTAATTAATAAATCTTTTATTTATATAAATAAAATAATAAATATGTAATTATATAATAAAAAA
TAAATTTTTAATATTTTAAAATAA
Found at i:1616672 original size:12 final size:12
Alignment explanation
Indices: 1616655--1616687 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1616645 TCGCCTGTCC
1616655 ATATTAATTTTT
1 ATATTAATTTTT
1616667 ATATT-ATTTTT
1 ATATTAATTTTT
1616678 ATA-TAATTTT
1 ATATTAATTTT
1616688 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1616842 original size:29 final size:30
Alignment explanation
Indices: 1616809--1616868 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1616799 CAATTTAACA
*
1616809 AGCAAATGCCTCT-AAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
* *
1616838 AGCAAATGTCTTTAAAATAATAAAAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
1616868 A
1 A
1616869 ACAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.27
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:1616927 original size:22 final size:22
Alignment explanation
Indices: 1616902--1616944 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1616892 TATCCAAATA
1616902 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
1616924 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
1616945 AATAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:1616948 original size:11 final size:11
Alignment explanation
Indices: 1616909--1616949 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1616899 ATAATAACAA
1616909 CAAAATAGTAG
1 CAAAATAGTAG
* *
1616920 CAACATAATAG
1 CAAAATAGTAG
*
1616931 TAAAATAGTAG
1 CAAAATAGTAG
1616942 CAAAATAG
1 CAAAATAG
1616950 GAAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:1618534 original size:43 final size:43
Alignment explanation
Indices: 1618486--1618597 Score: 206
Period size: 43 Copynumber: 2.6 Consensus size: 43
1618476 CCGGTATTAC
1618486 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
1618529 GCCTGCTAGGCATGAAGGCCCGAATACACATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1618572 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
1618598 TAATACCAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.29, C:0.32, G:0.27, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:1618637 original size:38 final size:38
Alignment explanation
Indices: 1618590--1618942 Score: 564
Period size: 38 Copynumber: 9.3 Consensus size: 38
1618580 GGCACGAAGG
* * * * *
1618590 CCCGAATATAATACCAGCACTAGGCCTGTGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1618628 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** * **
1618666 CCCGGATATTTTACCAGCACGAAGCCTGTAGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTG-CGGGATTTAA
1618705 GCCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1618744 CCCGGATATAATACCAGCA-GAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
1618781 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1618819 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
1618857 CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1618895 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1618933 CCCGGATATA
1 CCCGGATATA
1618943 CATCGAATAT
Statistics
Matches: 291, Mismatches: 21, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
37 36 0.12
38 215 0.74
39 14 0.05
40 26 0.09
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:1632776 original size:13 final size:13
Alignment explanation
Indices: 1632747--1632788 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1632737 GATTGTCCTA
1632747 TTAATTGATTTGA-
1 TTAATTGATTT-AT
*
1632760 TTAATTGATTTTT
1 TTAATTGATTTAT
1632773 TTAATTG-TTTAT
1 TTAATTGATTTAT
1632785 TTAA
1 TTAA
1632789 CGGTGAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TTAATTGATTTAT
Found at i:1633181 original size:20 final size:21
Alignment explanation
Indices: 1633145--1633191 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1633135 AATTTCAACA
1633145 TTAA-TAATAATTTTAAT-TT
1 TTAATTAATAATTTTAATATT
1633164 TTAATTAAT-ATTTCTAATATT
1 TTAATTAATAATTT-TAATATT
1633185 TT-ATTAA
1 TTAATTAA
1633192 AAATGGCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 8 0.32
20 13 0.52
21 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATTAATAATTTTAATATT
Found at i:1634506 original size:22 final size:22
Alignment explanation
Indices: 1634476--1634519 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1634466 TTTGGTATTT
1634476 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
1634498 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
1634520 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:1639029 original size:11 final size:11
Alignment explanation
Indices: 1639013--1639043 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1639003 GTATGCAATT
1639013 TTTTTTTTCAA
1 TTTTTTTTCAA
*
1639024 TTTTTTTTCAT
1 TTTTTTTTCAA
1639035 TTTTTTTTC
1 TTTTTTTTC
1639044 GAACTCCTTT
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:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:1639387 original size:22 final size:22
Alignment explanation
Indices: 1639357--1639400 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1639347 TTTGGTATTT
1639357 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
1639379 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
1639401 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:1644657 original size:27 final size:27
Alignment explanation
Indices: 1644605--1644658 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1644595 AAAGAAGTCG
**
1644605 GGTTCACAAAGTCGGGAGCATGGTGGT
1 GGTTCACAAAGTCGGGAGCAACGTGGT
1644632 GGTTCACAAAGTCGGGAGCAACGTGGT
1 GGTTCACAAAGTCGGGAGCAACGTGGT
1644659 TGATGGACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (27 bp):
GGTTCACAAAGTCGGGAGCAACGTGGT
Found at i:1647452 original size:30 final size:27
Alignment explanation
Indices: 1647399--1647458 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 27
1647389 ATTTAACAAG
*
1647399 TAAATATTTTTAAAATAATAAAATTAA
1 TAAATATTTTTAAAATAACAAAATTAA
1647426 TAAATATTTTTTAAATAATAACAAAATTAA
1 TAAATA-TTTTT-AA-AATAACAAAATTAA
1647456 TAA
1 TAA
1647459 TAAAATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.21
28 5 0.17
29 2 0.07
30 16 0.55
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATATTTTTAAAATAACAAAATTAA
Found at i:1648039 original size:19 final size:19
Alignment explanation
Indices: 1648011--1648047 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1648001 CGTAAAATTT
* *
1648011 AAATACTATTAAATTAATA
1 AAATAATATTAAAATAATA
1648030 AAATAATATTAAAATAAT
1 AAATAATATTAAAATAAT
1648048 TATCAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATAATATTAAAATAATA
Found at i:1650027 original size:11 final size:11
Alignment explanation
Indices: 1650013--1650052 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1650003 TGTTTTCTCC
1650013 CTATTTTACTA
1 CTATTTTACTA
1650024 CTATTTTACTA
1 CTATTTTACTA
* * *
1650035 TTATGTTGCTA
1 CTATTTTACTA
1650046 CTATTTT
1 CTATTTT
1650053 GTTGTTATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (11 bp):
CTATTTTACTA
Found at i:1651399 original size:46 final size:46
Alignment explanation
Indices: 1651324--1651427 Score: 138
Period size: 46 Copynumber: 2.3 Consensus size: 46
1651314 TTATCTTTGA
* * * *
1651324 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTC-TTTTCTTGT
*
1651370 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCTTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCTTGT
*
1651416 CACGTTGCCATG
1 CATGTTGCCATG
1651428 TCATATCACG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
45 5 0.10
46 46 0.90
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCTTGT
Found at i:1651529 original size:110 final size:110
Alignment explanation
Indices: 1651329--1651536 Score: 319
Period size: 110 Copynumber: 1.9 Consensus size: 110
1651319 TTTGACATGA
* * * * *
1651329 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAAC
* * *
1651394 CATGGTCTTATTCTTTTCTTGTCACGTTGCCATGTCATATCACGT
66 CATGGTCTTATTCATTTCATATCACGTTGCCATGTCATATCACGT
*
1651439 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAA
1 TGCCATAGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAGGTTGCCATGGTATCTTTCAA
1651503 CCATGGTCTTATTCATTTCATATCACGTTGCCAT
65 CCATGGTCTTATTCATTTCATATCACGTTGCCAT
1651537 AGTATCTTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 4 0.05
110 84 0.95
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (110 bp):
TGCCATAGTATCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTATTCATTTCATATCACGTTGCCATGTCATATCACGT
Found at i:1651585 original size:92 final size:92
Alignment explanation
Indices: 1651428--1651803 Score: 680
Period size: 92 Copynumber: 4.1 Consensus size: 92
1651418 CGTTGCCATG
1651428 TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1651493 TATCTTTCAACCATGGTCTTATTCATT
66 TATCTTTCAACCATGGTCTTATTCATT
* *
1651520 TCATATCACGTTGCCATAGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCAATGG
1 TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1651585 TATCTTTCAACCATGGTCTTATTCATT
66 TATCTTTCAACCATGGTCTTATTCATT
* *
1651612 TCATATCACGTTGCCATGATATCTTTCAACTATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
*
1651677 TATCTTTCAACCATGGCCTTATTCATT
66 TATCTTTCAACCATGGTCTTATTCATT
1651704 TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
* **
1651769 TATCTTTCAACCATGATCTTAGACATT
66 TATCTTTCAACCATGGTCTTATTCATT
1651796 TCATATCA
1 TCATATCA
1651804 GAGAGCACAC
Statistics
Matches: 271, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 271 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (92 bp):
TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
TATCTTTCAACCATGGTCTTATTCATT
Found at i:1651804 original size:46 final size:46
Alignment explanation
Indices: 1651428--1651804 Score: 601
Period size: 46 Copynumber: 8.2 Consensus size: 46
1651418 CGTTGCCATG
*
1651428 TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
**
1651474 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* *
1651520 TCATATCACGTTGCCATAGTATCTTTCAACCATGGTCTTACACATT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* **
1651566 TCATATCAGGTTGCAATGGTATCTTTCAACCATGGTCTTATTCATT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* * *
1651612 TCATATCACGTTGCCATGATATCTTTCAACTATGGTCTTACACATT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* **
1651658 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGCCTTATTCATT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
*
1651704 TCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
* *
1651750 TCATATCAGGTTGCCATGGTATCTTTCAACCATGATCTTAGACATT
1 TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
1651796 TCATATCAG
1 TCATATCAG
1651805 AGAGCACACT
Statistics
Matches: 300, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 300 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
TCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
Found at i:1653971 original size:32 final size:31
Alignment explanation
Indices: 1653925--1654014 Score: 105
Period size: 30 Copynumber: 3.0 Consensus size: 31
1653915 TTTCTTTCTT
*
1653925 TATATA-CTAA-TAAAATAATAAAAAAATAA
1 TATATATCTAATTAAAATAATAATAAAATAA
* *
1653954 TAATATATCTTATTAAAATACTAATAAAATAA
1 T-ATATATCTAATTAAAATAATAATAAAATAA
* *
1653986 TATTTATCTAATT-AAATAATTATAAAATA
1 TATATATCTAATTAAAATAATAATAAAATA
1654015 TCAAAATATC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.02
30 19 0.37
31 13 0.25
32 18 0.35
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (31 bp):
TATATATCTAATTAAAATAATAATAAAATAA
Found at i:1657233 original size:7 final size:7
Alignment explanation
Indices: 1657221--1657246 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1657211 ATATAATTAA
1657221 ATTATTT
1 ATTATTT
1657228 ATTATTT
1 ATTATTT
1657235 ATTATTT
1 ATTATTT
1657242 ATTAT
1 ATTAT
1657247 ACAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTATTT
Found at i:1657425 original size:15 final size:16
Alignment explanation
Indices: 1657393--1657426 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1657383 AAAGACAAGA
1657393 ATTTTATTACAGTTCT
1 ATTTTATTACAGTTCT
*
1657409 ATTTTATTTCA-TTCT
1 ATTTTATTACAGTTCT
1657424 ATT
1 ATT
1657427 CAACCAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTTATTACAGTTCT
Found at i:1667773 original size:7 final size:7
Alignment explanation
Indices: 1667761--1667787 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1667751 AAATGAATTC
1667761 TAAAATA
1 TAAAATA
1667768 TAAAATA
1 TAAAATA
1667775 TAAAATA
1 TAAAATA
1667782 TAAAAT
1 TAAAAT
1667788 GAGTATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAAATA
Found at i:1669381 original size:3 final size:3
Alignment explanation
Indices: 1669373--1669403 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1669363 CAACATGCAT
1669373 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1669404 AGAAACCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1674634 original size:16 final size:17
Alignment explanation
Indices: 1674613--1674646 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1674603 TAAATTTTAA
*
1674613 TTTAATATATAA-TAGG
1 TTTAATACATAATTAGG
1674629 TTTAATACATAATTAGG
1 TTTAATACATAATTAGG
1674646 T
1 T
1674647 ACCTAAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTAATACATAATTAGG
Found at i:1682634 original size:86 final size:86
Alignment explanation
Indices: 1682535--1682711 Score: 223
Period size: 86 Copynumber: 2.1 Consensus size: 86
1682525 CTGTCGTAGA
* *
1682535 AAAGTGGT-TAAAAAACATATAAGAGGTACATAAATTATTGTTTTTATGCAA-ATTTTTATTTTA
1 AAAGT-GTCTAAAAAACATATAAAAGGTACATAAATTATTGCTTTTATGCAATA-TTTTATTTTA
* * *
1682598 CATTCTTCTACATGATTAATTAT
64 AATTCTTCCACACGATTAATTAT
* * * * * *
1682621 GAAGTGTCTAAAAATCGTATAAAAGGTGCGTGAATTATTGCTTTTATGCAATATTTTATTTTAAA
1 AAAGTGTCTAAAAAACATATAAAAGGTACATAAATTATTGCTTTTATGCAATATTTTATTTTAAA
1682686 TTCTTCCACACGATTAATTAT
66 TTCTTCCACACGATTAATTAT
1682707 AAAGT
1 AAAGT
1682712 TTATAAGTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
85 2 0.03
86 74 0.96
87 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (86 bp):
AAAGTGTCTAAAAAACATATAAAAGGTACATAAATTATTGCTTTTATGCAATATTTTATTTTAAA
TTCTTCCACACGATTAATTAT
Found at i:1683610 original size:20 final size:20
Alignment explanation
Indices: 1683585--1683628 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1683575 AATTTAGAAT
* * *
1683585 TTTAATATTATTTATTTTAA
1 TTTAATATAATTAATTTCAA
1683605 TTTAATATAATTAATTTCAA
1 TTTAATATAATTAATTTCAA
1683625 TTTA
1 TTTA
1683629 TCAGTTTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATATAATTAATTTCAA
Found at i:1684104 original size:37 final size:37
Alignment explanation
Indices: 1684063--1684136 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1684053 ATTTACCTAA
1684063 GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
1 GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
1684100 GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
1 GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
1684137 AAAAATTAGG
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:0.14, G:0.16, T:0.32
Consensus pattern (37 bp):
GCCCAAAGGTTAACATGATATTTTAAAAGATTTGTAC
Found at i:1684675 original size:14 final size:14
Alignment explanation
Indices: 1684649--1684687 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1684639 ATATATGTTT
1684649 AAAAATT-ATATAA
1 AAAAATTAATATAA
1684662 AAATAA-TAATATAA
1 AAA-AATTAATATAA
1684676 AAAAATTAATAT
1 AAAAATTAATAT
1684688 GGGCAGGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATTAATATAA
Found at i:1690525 original size:22 final size:22
Alignment explanation
Indices: 1690483--1690524 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1690473 TTTTTAATTC
1690483 ATTAAACCTTTTCAAAATTTTA
1 ATTAAACCTTTTCAAAATTTTA
* *
1690505 ATTAAAGC-TTTCAGAATTTT
1 ATTAAACCTTTTCAAAATTTT
1690525 TTGAAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTAAACCTTTTCAAAATTTTA
Found at i:1692895 original size:30 final size:30
Alignment explanation
Indices: 1692859--1692959 Score: 91
Period size: 30 Copynumber: 3.5 Consensus size: 30
1692849 TTTGATTTTG
1692859 TTATTATAATTTATACAACAAATGTTTACA
1 TTATTATAATTTATACAACAAATGTTTACA
* ** **** *
1692889 TTATTATTATTTATTTATTTGAT-TTT--G
1 TTATTATAATTTATACAACAAATGTTTACA
*
1692916 TTATTATAAATTATACAACAAATGTTTACA
1 TTATTATAATTTATACAACAAATGTTTACA
*
1692946 TTATTATTATTTAT
1 TTATTATAATTTAT
1692960 TTATTTTTAG
Statistics
Matches: 49, Mismatches: 19, Indels: 6
0.66 0.26 0.08
Matches are distributed among these distances:
27 15 0.31
28 3 0.06
29 3 0.06
30 28 0.57
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (30 bp):
TTATTATAATTTATACAACAAATGTTTACA
Found at i:1692930 original size:57 final size:57
Alignment explanation
Indices: 1692839--1692965 Score: 245
Period size: 57 Copynumber: 2.2 Consensus size: 57
1692829 AGGTAATTTA
*
1692839 TATTTATTTATTTGATTTTGTTATTATAATTTATACAACAAATGTTTACATTATTAT
1 TATTTATTTATTTGATTTTGTTATTATAAATTATACAACAAATGTTTACATTATTAT
1692896 TATTTATTTATTTGATTTTGTTATTATAAATTATACAACAAATGTTTACATTATTAT
1 TATTTATTTATTTGATTTTGTTATTATAAATTATACAACAAATGTTTACATTATTAT
1692953 TATTTATTTATTT
1 TATTTATTTATTT
1692966 TTAGAATTTT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
57 69 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (57 bp):
TATTTATTTATTTGATTTTGTTATTATAAATTATACAACAAATGTTTACATTATTAT
Found at i:1702643 original size:3 final size:3
Alignment explanation
Indices: 1702572--1702631 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
1702562 TGCTATTACC
* * * *
1702572 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATA ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1702620 ATT ATA ATT ATT
1 ATT ATT ATT ATT
1702632 TATCGTTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1702806 original size:12 final size:12
Alignment explanation
Indices: 1702789--1702889 Score: 68
Period size: 12 Copynumber: 8.3 Consensus size: 12
1702779 CTCTCTGTAT
1702789 TTACTTATATTA
1 TTACTTATATTA
1702801 TTACTTATATTA
1 TTACTTATATTA
* *
1702813 TCA-TCACTATTA
1 TTACTTA-TATTA
*
1702825 TCA-TTATGATTTA
1 TTACTTAT-A-TTA
1702838 TTACTT-TATTA
1 TTACTTATATTA
*
1702849 TTA-TCATTATTA
1 TTACTTA-TATTA
1702861 TTACTAATATATTA
1 TTACT--TATATTA
*
1702875 TTA-TTATATTT
1 TTACTTATATTA
1702886 TTAC
1 TTAC
1702890 CCATTATTCT
Statistics
Matches: 72, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
10 1 0.01
11 18 0.25
12 34 0.47
13 8 0.11
14 10 0.14
15 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.01, T:0.56
Consensus pattern (12 bp):
TTACTTATATTA
Found at i:1702851 original size:3 final size:3
Alignment explanation
Indices: 1702796--1702881 Score: 52
Period size: 3 Copynumber: 29.0 Consensus size: 3
1702786 TATTTACTTA
* * * * * *
1702796 TAT TAT TACT TA- TAT TAT CAT CAC TAT TAT CAT TAT GATT TAT TAC
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * *
1702842 T-T TAT TAT TAT CAT TAT TAT TAC TAA TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1702882 ATTTTTACCC
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
2 5 0.08
3 54 0.84
4 5 0.08
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:1705252 original size:29 final size:29
Alignment explanation
Indices: 1705219--1705288 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1705209 GCATAAAAAT
*
1705219 AAAAATGATATTCACAATAAAAAAATAATA
1 AAAAATAATATTC-CAATAAAAAAATAATA
* *
1705249 AAAAATAATATTCTAATAAAATAATAA-A
1 AAAAATAATATTCCAATAAAAAAATAATA
* *
1705277 AGAAATAGTATT
1 AAAAATAATATT
1705289 TATAGTAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 11 0.31
29 12 0.34
30 12 0.34
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (29 bp):
AAAAATAATATTCCAATAAAAAAATAATA
Found at i:1705618 original size:3 final size:3
Alignment explanation
Indices: 1705610--1705666 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
1705600 AAGAAAAGCT
* *
1705610 ATA ATA ATA ATA GTA ATT ATA ATA A-A AGTA ATA ATA ATA A-A TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA -ATA
*
1705655 ATA ATA GTA ATA
1 ATA ATA ATA ATA
1705667 TTAGTGATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1705633 original size:15 final size:15
Alignment explanation
Indices: 1705610--1705660 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
1705600 AAGAAAAGCT
*
1705610 ATAATAATAATAGTA
1 ATAATAATAAAAGTA
*
1705625 ATTATAATAAAAGTA
1 ATAATAATAAAAGTA
1705640 ATAATAATAAATA-TA
1 ATAATAATAAA-AGTA
1705655 ATAATA
1 ATAATA
1705661 GTAATATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 31 0.97
16 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
ATAATAATAAAAGTA
Found at i:1705641 original size:24 final size:24
Alignment explanation
Indices: 1705614--1705671 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1705604 AAAGCTATAA
*
1705614 TAATAATAGTAATTATAATAAAAG
1 TAATAATAGTAAATATAATAAAAG
* *
1705638 TAATAATAATAAATATAATAATAG
1 TAATAATAGTAAATATAATAAAAG
*
1705662 TAATATTAGT
1 TAATAATAGT
1705672 GATAAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (24 bp):
TAATAATAGTAAATATAATAAAAG
Done.