Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold69
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: 2104606
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 151874 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:1202453 original size:66 final size:65
Alignment explanation
Indices: 1202310--1202498 Score: 290
Period size: 66 Copynumber: 2.8 Consensus size: 65
1202300 TCATTTTTAT
*
1202310 CCATCATTCCATGCCTTCATTTTT-TATTCCATGCCCATCATTCTATGCCTTCATTTTTTTATTC
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATG---T--TTTTTTTATTC
1202374 CATGC
61 CATGC
* *
1202379 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATCCCATGTGTTTTTTTATTTCATG
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGT-TTTTTTTATTCCATG
1202444 C
65 C
1202445 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGTTTTTT
1 CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGTTTTTT
1202499 ATTTCTTGAT
Statistics
Matches: 114, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
65 5 0.04
66 63 0.55
67 1 0.01
69 24 0.21
70 21 0.18
ACGTcount: A:0.18, C:0.30, G:0.06, T:0.46
Consensus pattern (65 bp):
CCATCATTCCATGCCTTCATTTTTATATTCCATGCCCATCATTCCATGTTTTTTTTATTCCATGC
Found at i:1204347 original size:2 final size:2
Alignment explanation
Indices: 1204305--1204331 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1204295 TTTATTATTT
1204305 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1204332 TTGTTATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1204740 original size:34 final size:34
Alignment explanation
Indices: 1204696--1204854 Score: 291
Period size: 34 Copynumber: 4.7 Consensus size: 34
1204686 TACTCACCAC
* * *
1204696 ACATTACCTAACACACCTAATATTTTCACCAAAT
1 ACATCACCTAACACACCTAACATTCTCACCAAAT
1204730 ACATCACCTAACACACCTAACATTCTCACCAAAT
1 ACATCACCTAACACACCTAACATTCTCACCAAAT
1204764 ACATCACCTAACACACCTAACATTCTCACCAAAT
1 ACATCACCTAACACACCTAACATTCTCACCAAAT
1204798 ACATCACCTAACACACCTAACATTCTCACCAAAT
1 ACATCACCTAACACACCTAACATTCTCACCAAAT
1204832 ACATCACCTAACACACCTAACAT
1 ACATCACCTAACACACCTAACAT
1204855 GCTTCACCTA
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 122 1.00
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (34 bp):
ACATCACCTAACACACCTAACATTCTCACCAAAT
Found at i:1204772 original size:25 final size:25
Alignment explanation
Indices: 1204743--1204844 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
1204733 TCACCTAACA
1204743 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
*
1204768 CACCTAACA----CACCTAACATTC-T
1 CACCTAACATTCTCACC-AA-ATACAT
* *
1204790 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
1204811 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
1204836 CACCTAACA
1 CACCTAACA
1204845 CACCTAACAT
Statistics
Matches: 59, Mismatches: 5, Indels: 26
0.66 0.06 0.29
Matches are distributed among these distances:
20 1 0.02
21 11 0.19
22 15 0.25
23 7 0.12
24 3 0.05
25 22 0.37
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:1209617 original size:34 final size:34
Alignment explanation
Indices: 1209579--1209712 Score: 205
Period size: 34 Copynumber: 3.9 Consensus size: 34
1209569 AATATCTTAC
* * * * *
1209579 TCACCTAACACATTACCTAACACACTTAATATTT
1 TCACCAAATACATCACCTAACACACCTAACATTT
*
1209613 TCACCAAATACATCACCTAACACACCTAACATTA
1 TCACCAAATACATCACCTAACACACCTAACATTT
*
1209647 TCACCAAATACATCACCTAACACACCTAACATTC
1 TCACCAAATACATCACCTAACACACCTAACATTT
1209681 TCACCAAATACATCACCTAACACACCTAACAT
1 TCACCAAATACATCACCTAACACACCTAACAT
1209713 GCTTCACCTA
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 93 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (34 bp):
TCACCAAATACATCACCTAACACACCTAACATTT
Found at i:1210193 original size:75 final size:75
Alignment explanation
Indices: 1210063--1210208 Score: 172
Period size: 75 Copynumber: 1.9 Consensus size: 75
1210053 ACTTTTATAC
* * ** **
1210063 TAAGAAGTATTTTTTCCCTTTTTTCCATAATTGAATGCTTTAAGCAAAATTTTTAATCCATATTT
1 TAAGAAGTATTTTTTCCATTTTTTCCATAATTGAATGCTATAAAAAAAAAATTTAATCCATATTT
1210128 CTTTGACCTT
66 CTTTGACCTT
* *
1210138 TAAGAAGTA-TTTTTCCAATTTTTT-CATAACTT-AATGCTATAATAAAAAAAATTTAATCCCTG
1 TAAGAAGTATTTTTTCC-ATTTTTTCCATAA-TTGAATGCTATAA-AAAAAAAATTTAATCCATA
1210200 TTTCTTTGA
63 TTTCTTTGA
1210209 ATTTCAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
74 21 0.35
75 39 0.65
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (75 bp):
TAAGAAGTATTTTTTCCATTTTTTCCATAATTGAATGCTATAAAAAAAAAATTTAATCCATATTT
CTTTGACCTT
Found at i:1211519 original size:14 final size:14
Alignment explanation
Indices: 1211481--1211548 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
1211471 TACTTTTAAT
*
1211481 ATAAGTACTTTGGC
1 ATAAATACTTTGGC
* *
1211495 ACAACTACTTTGGC
1 ATAAATACTTTGGC
* *
1211509 ATAAATTCTTTTGGT
1 ATAAATAC-TTTGGC
* *
1211524 ATAAGTGCTTTGGC
1 ATAAATACTTTGGC
1211538 ATAAATACTTT
1 ATAAATACTTT
1211549 TGGTAGAGGT
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 31 0.74
15 11 0.26
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (14 bp):
ATAAATACTTTGGC
Found at i:1211521 original size:29 final size:29
Alignment explanation
Indices: 1211481--1211551 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
1211471 TACTTTTAAT
*
1211481 ATAAGTAC-TTTGGCACAACTACTTTGGC
1 ATAAATACTTTTGGCACAACTACTTTGGC
* * * * *
1211509 ATAAATTCTTTTGGTATAAGTGCTTTGGC
1 ATAAATACTTTTGGCACAACTACTTTGGC
1211538 ATAAATACTTTTGG
1 ATAAATACTTTTGG
1211552 TAGAGGTGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (29 bp):
ATAAATACTTTTGGCACAACTACTTTGGC
Found at i:1211552 original size:29 final size:29
Alignment explanation
Indices: 1211502--1211563 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
1211492 GGCACAACTA
* *
1211502 CTTTGGCATAAATTCTTTTGGTATAAGTG
1 CTTTGGCATAAATACTTTTGGTAGAAGTG
*
1211531 CTTTGGCATAAATACTTTTGGTAGAGGTG
1 CTTTGGCATAAATACTTTTGGTAGAAGTG
1211560 CTTT
1 CTTT
1211564 AGTACAGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (29 bp):
CTTTGGCATAAATACTTTTGGTAGAAGTG
Found at i:1212352 original size:32 final size:32
Alignment explanation
Indices: 1212311--1212376 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1212301 TCCAACAGCT
1212311 GAATTAAAAGAGAATCAACCAAGAAACATCAA
1 GAATTAAAAGAGAATCAACCAAGAAACATCAA
1212343 GAATTAAAAGAGAATCAACCAAGAAACATCAA
1 GAATTAAAAGAGAATCAACCAAGAAACATCAA
1212375 GA
1 GA
1212377 GATCAAAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.59, C:0.15, G:0.14, T:0.12
Consensus pattern (32 bp):
GAATTAAAAGAGAATCAACCAAGAAACATCAA
Found at i:1218179 original size:18 final size:20
Alignment explanation
Indices: 1218146--1218198 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 20
1218136 ATTAGATGAA
*
1218146 TTTGATGTTTAATTATA-TTG
1 TTTGATG-TGAATTATACTTG
1218166 TATT-AT-TGAATTATACTTG
1 T-TTGATGTGAATTATACTTG
1218185 TTTGATGTGAATTA
1 TTTGATGTGAATTA
1218199 GGGTCTATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 10 0.36
19 6 0.21
20 10 0.36
21 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (20 bp):
TTTGATGTGAATTATACTTG
Found at i:1218342 original size:13 final size:13
Alignment explanation
Indices: 1218324--1218367 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
1218314 ACAATATTCT
1218324 TTGTATCGATACA
1 TTGTATCGATACA
1218337 TTGTATCG----A
1 TTGTATCGATACA
1218346 -TGTATCGATACA
1 TTGTATCGATACA
1218358 TTGTATCGAT
1 TTGTATCGAT
1218368 GTATCGATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
8 7 0.27
9 1 0.04
12 1 0.04
13 17 0.65
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1218351 original size:21 final size:21
Alignment explanation
Indices: 1218325--1218378 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1218315 CAATATTCTT
1218325 TGTATCGATACATTGTATCGA
1 TGTATCGATACATTGTATCGA
1218346 TGTATCGATACATTGTATCGA
1 TGTATCGATACATTGTATCGA
1218367 TGTATCGATACA
1 TGTATCGATACA
1218379 AGGATTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (21 bp):
TGTATCGATACATTGTATCGA
Found at i:1218513 original size:21 final size:22
Alignment explanation
Indices: 1218487--1218536 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1218477 ATCAAATCTT
* *
1218487 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1218508 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1218530 --TCAAAAT
1 CTTCAAAAT
1218537 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1220694 original size:20 final size:20
Alignment explanation
Indices: 1220669--1220734 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1220659 CTACCATTGT
1220669 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
1220689 TTGTATCGAT--A---CA-A
1 TTGTATCGATACATGGCACA
1220703 -TGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
1220722 TTGTATCGATACA
1 TTGTATCGATACA
1220735 ACGTATCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
15 3 0.08
18 3 0.08
19 1 0.03
20 22 0.56
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
TTGTATCGATACATGGCACA
Found at i:1220708 original size:13 final size:13
Alignment explanation
Indices: 1220690--1220714 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1220680 CATGGCACAT
1220690 TGTATCGATACAA
1 TGTATCGATACAA
1220703 TGTATCGATACA
1 TGTATCGATACA
1220715 TGGCACATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1220712 original size:33 final size:33
Alignment explanation
Indices: 1220670--1220767 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1220660 TACCATTGTT
1220670 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATGGCACATTGTATCGATACAA
1220703 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATGGCACATTGTATCGATACAA
*
1220736 CGTATCGATACATGATG-A-ATTGTATCGATACA
1 TGTATCGATACATG--GCACATTGTATCGATACA
1220768 TTGCTTCAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
33 60 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATGGCACATTGTATCGATACAA
Found at i:1222704 original size:20 final size:20
Alignment explanation
Indices: 1222672--1222746 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1222662 TTTTACCCAG
*
1222672 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1222692 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1222712 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
*
1222732 ATGTATCAATACATT
1 ATGTATCGATACATT
1222747 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1224543 original size:61 final size:61
Alignment explanation
Indices: 1224472--1224593 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
1224462 TGAAATCAGC
* *
1224472 TTTCTGGAAAGGTATAGTTTGTAATTTTTTGATACCAAATGAATTTGGGGTGATTTTTCAA
1 TTTCTAGAAAGGTATAGTTTGTAATTTTTTGATACCAAATGAATTCGGGGTGATTTTTCAA
1224533 TTTCTAGAAAGGTATAGTTTGTAATTTTTTGATACCAAATGAATTCGGGGTGATTTTTCAA
1 TTTCTAGAAAGGTATAGTTTGTAATTTTTTGATACCAAATGAATTCGGGGTGATTTTTCAA
1224594 AGTTTGTCAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.43
Consensus pattern (61 bp):
TTTCTAGAAAGGTATAGTTTGTAATTTTTTGATACCAAATGAATTCGGGGTGATTTTTCAA
Found at i:1228140 original size:5 final size:5
Alignment explanation
Indices: 1228130--1228163 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1228120 TTATTATGTG
*
1228130 AAAAT AAAAT AAATTT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAA
1228164 TTTTAGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:1228150 original size:11 final size:11
Alignment explanation
Indices: 1228134--1228166 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1228124 TATGTGAAAA
1228134 TAAAATAAATT
1 TAAAATAAATT
*
1228145 TAAAATAAA-A
1 TAAAATAAATT
1228155 TAAAATAAATT
1 TAAAATAAATT
1228166 T
1 T
1228167 TAGTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:1229967 original size:56 final size:56
Alignment explanation
Indices: 1229880--1229988 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
1229870 GTAACAGTTA
* * *
1229880 AAGGAACGTTATGTCCAAAAATCACCGAAGTAATAGCCAGGTTAAATTTATAATCT
1 AAGGAACATTATGTCCAAAAATCACCAAAGTAAGAGCCAGGTTAAATTTATAATCT
1229936 AAGGAACATTATGTCCAAAAATCACCAAAGTAAGAGCCAGGTTAAATTTATAA
1 AAGGAACATTATGTCCAAAAATCACCAAAGTAAGAGCCAGGTTAAATTTATAA
1229989 ACTTTCAAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (56 bp):
AAGGAACATTATGTCCAAAAATCACCAAAGTAAGAGCCAGGTTAAATTTATAATCT
Found at i:1233724 original size:23 final size:21
Alignment explanation
Indices: 1233700--1233766 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 21
1233690 TTGTAAAAAT
*
1233700 TTTAAAAATTTTTATATTAATA
1 TTTAAATATTTTTATATTAA-A
*
1233722 TTTATATA-TTTTATAATTAAA
1 TTTAAATATTTTTAT-ATTAAA
1233743 TTTAAATATTTTTTATTATTAAA
1 TTTAAATA-TTTTTA-TATTAAA
1233766 T
1 T
1233767 AATAATTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 14 0.37
22 11 0.29
23 12 0.32
24 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAAATATTTTTATATTAAA
Found at i:1235547 original size:28 final size:28
Alignment explanation
Indices: 1235516--1235572 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1235506 ATCTTCTTAC
1235516 TACATTGTTTTAATATTTTCGATCCAAT
1 TACATTGTTTTAATATTTTCGATCCAAT
1235544 TACATTGTTTTAATATTTTCGATCCAAT
1 TACATTGTTTTAATATTTTCGATCCAAT
1235572 T
1 T
1235573 GATAGTGATA
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:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (28 bp):
TACATTGTTTTAATATTTTCGATCCAAT
Found at i:1237125 original size:28 final size:27
Alignment explanation
Indices: 1237075--1237156 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
1237065 TGACACGAAC
* *
1237075 ATAATATATTAAAAACAAT-TAAAATAT
1 ATAAAATA-TAAAAATAATATAAAATAT
1237102 GATAAAATATAAAAATAATAT-AAATAT
1 -ATAAAATATAAAAATAATATAAAATAT
* * *
1237129 ATAAACATCTCAAAATTTATATAAAATA
1 ATAAA-ATAT-AAAAATAATATAAAATA
1237157 AATTATTAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 5 0.11
27 18 0.40
28 17 0.38
29 5 0.11
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (27 bp):
ATAAAATATAAAAATAATATAAAATAT
Found at i:1237126 original size:27 final size:26
Alignment explanation
Indices: 1237096--1237231 Score: 77
Period size: 27 Copynumber: 5.2 Consensus size: 26
1237086 AAAACAATTA
1237096 AAATATGATAAAATATAAAAATAATAT
1 AAATAT-ATAAAATATAAAAATAATAT
* * *
1237123 AAATATATAAACATCTCAAAAT-TTAT
1 AAATATATAAA-ATATAAAAATAATAT
* * *
1237149 ATAA-A-ATAAATTATTAACATAATA-
1 A-AATATATAAAATATAAAAATAATAT
* * * *
1237173 AAATTTATATAAATA-AATAATATTTT
1 AAATATATA-AAATATAAAAATAATAT
*
1237199 AAATATAATTATAATA-AAAAATAATAT
1 AAATAT-A-TAAAATATAAAAATAATAT
1237226 AAATAT
1 AAATAT
1237232 GATACTAATA
Statistics
Matches: 80, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
23 2 0.03
24 7 0.09
25 15 0.19
26 19 0.24
27 35 0.44
28 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (26 bp):
AAATATATAAAATATAAAAATAATAT
Found at i:1237188 original size:18 final size:18
Alignment explanation
Indices: 1237140--1237188 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1237130 TAAACATCTC
1237140 AAAATTTATAT-AA-AAT
1 AAAATTTATATAAATAAT
1237156 -AAA-TTAT-TAACATAAT
1 AAAATTTATATAA-ATAAT
1237172 AAAATTTATATAAATAA
1 AAAATTTATATAAATAA
1237189 ATAATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 1 0.04
14 5 0.19
15 4 0.15
16 3 0.11
17 3 0.11
18 8 0.30
19 3 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTTATATAAATAAT
Found at i:1237752 original size:19 final size:21
Alignment explanation
Indices: 1237703--1237755 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
1237693 ATTTATTATT
1237703 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
1237724 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
1237744 -AAATTTTAATAT
1 TAAATTTTAATAT
1237756 TTTATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 11 0.38
22 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1239121 original size:2 final size:2
Alignment explanation
Indices: 1239114--1239144 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1239104 GTATGCATGT
1239114 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1239145 CCTCTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1245576 original size:17 final size:18
Alignment explanation
Indices: 1245538--1245576 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1245528 ATTATTTGAA
1245538 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
*
1245556 AAATTCATTTTATAT-AT
1 AAATTAATTTTATATAAT
1245573 AAAT
1 AAAT
1245577 ATAGATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:1245631 original size:28 final size:28
Alignment explanation
Indices: 1245587--1245667 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
1245577 ATAGATTTCA
*
1245587 ATAAATAAATAATTAAATATATTAAATAC
1 ATAAATATATAA-TAAATATATTAAATAC
* *
1245616 A-AAATAGTATAATAAAAAT-TTAAATAT
1 ATAAATA-TATAATAAATATATTAAATAC
*
1245643 ATTAAATATATAAT-AATATAGTAAA
1 A-TAAATATATAATAAATATATTAAA
1245668 AATTTACTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 12 0.28
28 21 0.49
29 10 0.23
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (28 bp):
ATAAATATATAATAAATATATTAAATAC
Found at i:1245668 original size:36 final size:36
Alignment explanation
Indices: 1245586--1245673 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
1245576 TATAGATTTC
1245586 AATA-AATAAATAA-TTAAATATATTAAATACAAAAT
1 AATATAATAAA-AATTTAAATATATTAAATACAAAAT
* * *
1245621 AGTATAATAAAAATTTAAATATATTAAATATATAAT
1 AATATAATAAAAATTTAAATATATTAAATACAAAAT
*
1245657 AATATAGTAAAAATTTA
1 AATATAATAAAAATTTA
1245674 CTCAAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 5 0.11
36 41 0.89
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (36 bp):
AATATAATAAAAATTTAAATATATTAAATACAAAAT
Found at i:1245827 original size:16 final size:16
Alignment explanation
Indices: 1245808--1245866 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
1245798 CCAAATTCAC
1245808 ATAAACTTAAACCCAA
1 ATAAACTTAAACCCAA
* *
1245824 ATAAACTTAAATCTAA
1 ATAAACTTAAACCCAA
* *
1245840 ATAAACTAAAACTCAA
1 ATAAACTTAAACCCAA
*
1245856 A-AAACCTAAAC
1 ATAAACTTAAAC
1245867 ATACCCGAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
15 8 0.23
16 27 0.77
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.20
Consensus pattern (16 bp):
ATAAACTTAAACCCAA
Found at i:1245834 original size:22 final size:22
Alignment explanation
Indices: 1245783--1245834 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1245773 AATTTAAACC
*
1245783 AACTTAAACCCAAACCCAAATT
1 AACTTAAACCCAAACCCAAATA
* * **
1245805 CACATAAACTTAAACCCAAATA
1 AACTTAAACCCAAACCCAAATA
1245827 AACTTAAA
1 AACTTAAA
1245835 TCTAAATAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (22 bp):
AACTTAAACCCAAACCCAAATA
Found at i:1245840 original size:22 final size:21
Alignment explanation
Indices: 1245783--1245840 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
1245773 AATTTAAACC
* *
1245783 AACTTAAACCCAAACCCAAATT
1 AACTTAAA-CTAAACCCAAATA
* *
1245805 CACATAAACTTAAACCCAAATA
1 AACTTAAAC-TAAACCCAAATA
1245827 AACTTAAATCTAAA
1 AACTTAAA-CTAAA
1245841 TAAACTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (21 bp):
AACTTAAACTAAACCCAAATA
Found at i:1246193 original size:65 final size:64
Alignment explanation
Indices: 1246067--1246193 Score: 193
Period size: 65 Copynumber: 2.0 Consensus size: 64
1246057 ATATTTTTTT
* * *
1246067 ATTTAAATTTAAAAAATTTAATTAAATTATTTAAATATAAATTTAATTTAATTTGATTAAAAAA
1 ATTTAAACTTAAAAAATTTAATTAAATTATTTAAATATAAATTTAATTTAATTTAACTAAAAAA
*
1246131 ATTTAAAACTTAAAAAATTTAATTAATTTATTTAAAT-TCAAATTTAATTTAATTTAACTAAAA
1 ATTT-AAACTTAAAAAATTTAATTAAATTATTTAAATAT-AAATTTAATTTAATTTAACTAAAA
1246194 TTATATATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 5 0.09
65 52 0.91
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (64 bp):
ATTTAAACTTAAAAAATTTAATTAAATTATTTAAATATAAATTTAATTTAATTTAACTAAAAAA
Found at i:1246194 original size:21 final size:21
Alignment explanation
Indices: 1246153--1246195 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1246143 AAAAATTTAA
* *
1246153 TTAATTTATTTAAATTCAAAT
1 TTAATTTATTTAAACTAAAAT
1246174 TTAATTTAATTT-AACTAAAAT
1 TTAATTT-ATTTAAACTAAAAT
1246195 T
1 T
1246196 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATTTATTTAAACTAAAAT
Found at i:1247340 original size:11 final size:11
Alignment explanation
Indices: 1247324--1247348 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1247314 TATCTAGCAT
1247324 AATCTTATATA
1 AATCTTATATA
1247335 AATCTTATATA
1 AATCTTATATA
1247346 AAT
1 AAT
1247349 ATATAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATCTTATATA
Found at i:1249864 original size:13 final size:15
Alignment explanation
Indices: 1249845--1249883 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
1249835 ATTCAATTTG
1249845 TTCATTTCATTTTTC
1 TTCATTTCATTTTTC
1249860 -T-ATTT--TTTTTC
1 TTCATTTCATTTTTC
1249871 TTCATTTCATTTT
1 TTCATTTCATTTT
1249884 CATCTCCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 8
0.71 0.00 0.29
Matches are distributed among these distances:
11 6 0.30
12 1 0.05
13 8 0.40
14 1 0.05
15 4 0.20
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (15 bp):
TTCATTTCATTTTTC
Found at i:1251269 original size:77 final size:76
Alignment explanation
Indices: 1251040--1251270 Score: 179
Period size: 77 Copynumber: 3.0 Consensus size: 76
1251030 TCATTACATG
* * * *
1251040 ATATTATA--GAGTCCATTAAGGTTA-CTGATATACTTTTATATC-AAAGGTATACTTTAGGGGT
1 ATATTATATCGAGTTCATTAAGGTTATC-GAAATACTTTCATGTCGAAA-GTATACTTTAGGGGT
1251101 ATTTTAATAATTTT
64 ATTTT-ATAATTTT
** * * * * * *
1251115 ACCTTATGATCGAG-TCTTTAAGGATCATCGAAATA-TTTACATGTTGAATGTGTGCTTTAGGGG
1 ATATTAT-ATCGAGTTCATTAAGG-TTATCGAAATACTTT-CATGTCGAAAGTATACTTTAGGGG
*
1251178 TAGGTTTT-TCATTTT
63 TA--TTTTATAATTTT
* * * *
1251193 GTATTATATCGAGTTCATTAAGGTTATCGAGATACTTTCATGTCGAAAGTATTCTTTAAGGGTAT
1 ATATTATATCGAGTTCATTAAGGTTATCGAAATACTTTCATGTCGAAAGTATACTTTAGGGGTAT
1251258 TTTAGTAATTTT
66 TTTA-TAATTTT
1251270 A
1 A
1251271 CCTTAGAGTT
Statistics
Matches: 117, Mismatches: 26, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
75 9 0.08
76 1 0.01
77 52 0.44
78 48 0.41
79 3 0.03
80 4 0.03
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (76 bp):
ATATTATATCGAGTTCATTAAGGTTATCGAAATACTTTCATGTCGAAAGTATACTTTAGGGGTAT
TTTATAATTTT
Found at i:1251323 original size:155 final size:153
Alignment explanation
Indices: 1251041--1251465 Score: 409
Period size: 155 Copynumber: 2.8 Consensus size: 153
1251031 CATTACATGA
* * * * *
1251041 TATTATA-GAGTCCATTAAGGTTA-CTGATATACTTTTATATC-AAAGGTATACTTTAGGGGTAT
1 TATTATATGAGTTCATTAAGGTTATC-GAGATACTTTCATATCGAAA-GTATTCTTTAAGGGTAT
* * * * *
1251103 TTTAATAATTTTACCTTATGATCGAGT-CTTTAAGGATCA-TCGAAATA-TTTACATGTTGAATG
64 TTTAATAATTTTACCTTA-GATTGAGTCCTTTAA-GATCACTAG-GATACTTT-CATGCTGAAAG
* * * *
1251165 TGTGCTTTAGGGGTAGGTTTTTCATTTTG
125 TGTGCTTCAAGGGTAGGTTTGTCATTTCG
*
1251194 TATTATATCGAGTTCATTAAGGTTATCGAGATACTTTCATGTCGAAAGTATTCTTTAAGGGTATT
1 TATTATAT-GAGTTCATTAAGGTTATCGAGATACTTTCATATCGAAAGTATTCTTTAAGGGTATT
*
1251259 TTAGTAATTTTACCTTAGAGTTGAGTCCTTTAAGATCACTAGGATACTTTCATGCTGAAAGTGTG
65 TTAATAATTTTACCTTAGA-TTGAGTCCTTTAAGATCACTAGGATACTTTCATGCTGAAAGTGTG
*
1251324 CTTCAAGGTTAGGTTTGTCATTTCG
129 CTTCAAGGGTAGGTTTGTCATTTCG
* * * * * * **
1251349 TATCATATAGAGTT-TTTTAGATTATCGAGATACTTTCACATCGAAGGTATAT-TTTAGAGGACA
1 TATTATAT-GAGTTCATTAAGGTTATCGAGATACTTTCATATCGAAAGTAT-TCTTTA-AGGGTA
** * *
1251412 TTTTAATAATTTTGTCTTAGAATTGAGTCCATT-AGAGTCACCAGGATACTTTCA
63 TTTTAATAATTTTACCTTAG-ATTGAGTCCTTTAAGA-TCACTAGGATACTTTCA
1251466 CGTTGAAGGT
Statistics
Matches: 228, Mismatches: 32, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
153 7 0.03
154 39 0.17
155 166 0.73
156 16 0.07
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (153 bp):
TATTATATGAGTTCATTAAGGTTATCGAGATACTTTCATATCGAAAGTATTCTTTAAGGGTATTT
TAATAATTTTACCTTAGATTGAGTCCTTTAAGATCACTAGGATACTTTCATGCTGAAAGTGTGCT
TCAAGGGTAGGTTTGTCATTTCG
Found at i:1252270 original size:22 final size:22
Alignment explanation
Indices: 1252242--1252290 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1252232 ATGTATAGTG
1252242 ATGAACAGTAATGTATCAATAC
1 ATGAACAGTAATGTATCAATAC
* **
1252264 ATGAACAGTGATGTATTGATAC
1 ATGAACAGTAATGTATCAATAC
1252286 ATGAA
1 ATGAA
1252291 TAATGATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (22 bp):
ATGAACAGTAATGTATCAATAC
Found at i:1252350 original size:20 final size:20
Alignment explanation
Indices: 1252327--1252389 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1252317 GTTGGACTCA
1252327 ATGTATAGTAATAAACAGTG
1 ATGTATAGTAATAAACAGTG
*
1252347 ATGTATCGATATATAAACAGTG
1 ATGTATAG-TA-ATAAACAGTG
** * *
1252369 ATAAATAGTGATGAACAGTG
1 ATGTATAGTAATAAACAGTG
1252389 A
1 A
1252390 AAAATGAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 17 0.49
21 3 0.09
22 15 0.43
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (20 bp):
ATGTATAGTAATAAACAGTG
Found at i:1255626 original size:21 final size:20
Alignment explanation
Indices: 1255597--1255671 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 20
1255587 AACTCAGCAT
1255597 TTTCATTTTGCAACTCATTTCA
1 TTTC-TTTT-CAACTCATTTCA
1255619 TTTCTTTTCCAACTCA-TTCA
1 TTTCTTTT-CAACTCATTTCA
* * *
1255639 TTTTCTTCTTTAATTCATTTAA
1 -TTTCTT-TTCAACTCATTTCA
1255661 TTTCTTTTCAA
1 TTTCTTTTCAA
1255672 GAATATTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
20 8 0.18
21 28 0.62
22 9 0.20
ACGTcount: A:0.21, C:0.21, G:0.01, T:0.56
Consensus pattern (20 bp):
TTTCTTTTCAACTCATTTCA
Found at i:1256052 original size:17 final size:17
Alignment explanation
Indices: 1256030--1256064 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1256020 TTTTAGGAGG
1256030 TCTCTTTGCTTTGTTCA
1 TCTCTTTGCTTTGTTCA
1256047 TCTCTTTGCTTTGTTCA
1 TCTCTTTGCTTTGTTCA
1256064 T
1 T
1256065 TTTTAAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.11, T:0.60
Consensus pattern (17 bp):
TCTCTTTGCTTTGTTCA
Found at i:1257839 original size:73 final size:73
Alignment explanation
Indices: 1257720--1257868 Score: 226
Period size: 73 Copynumber: 2.0 Consensus size: 73
1257710 GATATACATT
* * *
1257720 TGAAATTATAACCGTTGGGCTTAATGCATAGTGATGAACAATGATGTATCGATACATGAACAGTG
1 TGAAATTATAACCATTGGGCTCAATGCATAGTGATGAACAATGATGTATCGATACATGAACAGTA
1257785 ATGAACAG
66 ATGAACAG
* * * *
1257793 TGAAATTATAGCCATTGGGCTCAATGTATAGTGATGAACAGTGATGTATCGATATATGAACAGTA
1 TGAAATTATAACCATTGGGCTCAATGCATAGTGATGAACAATGATGTATCGATACATGAACAGTA
*
1257858 ATGAATAG
66 ATGAACAG
1257866 TGA
1 TGA
1257869 TAAACAGTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (73 bp):
TGAAATTATAACCATTGGGCTCAATGCATAGTGATGAACAATGATGTATCGATACATGAACAGTA
ATGAACAG
Found at i:1260310 original size:20 final size:20
Alignment explanation
Indices: 1260271--1260311 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1260261 GTTTTGCTGG
* **
1260271 TGTTTGCTTGCTGTTTTTGC
1 TGTTTACTTGCTGTCATTGC
1260291 TGTTTACTTGCTGTCATTGC
1 TGTTTACTTGCTGTCATTGC
1260311 T
1 T
1260312 TACTGTTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.17, G:0.22, T:0.56
Consensus pattern (20 bp):
TGTTTACTTGCTGTCATTGC
Found at i:1260808 original size:80 final size:80
Alignment explanation
Indices: 1260675--1260931 Score: 291
Period size: 80 Copynumber: 3.2 Consensus size: 80
1260665 ATCATCAGCA
* * ** * * ** * *
1260675 TTTAATTTCATGCATGAATTGTATTATTTTTTAGCAGCTGTTATTTTTTTATTTTT-AGCAGCTG
1 TTTAATTTCATGCATGATTTATATCCTTTTTCAGCAACTACTACTTTCTTATTTTTCAGCAGCTG
* ** *
1260739 TTTCGTTTGCTTTTGT
66 TTT-ATCAGCATTTGT
* *
1260755 TTTAATTTCATGCATGATTTATATCCTTTTTCAGCAACTACTGCTTTCTTATTTTTCAGCAACTG
1 TTTAATTTCATGCATGATTTATATCCTTTTTCAGCAACTACTACTTTCTTATTTTTCAGCAGCTG
1260820 TTTATCAGCATTTGT
66 TTTATCAGCATTTGT
* * * * **
1260835 TTTAATTTCATGCATGATTTATATTCTTTTTCAGCAGCTATTACTTTTTTATTTTTCAATAGCTG
1 TTTAATTTCATGCATGATTTATATCCTTTTTCAGCAACTACTACTTTCTTATTTTTCAGCAGCTG
*
1260900 TTTATCAGCACTTGT
66 TTTATCAGCATTTGT
1260915 TTTAATTTCATGCATGA
1 TTTAATTTCATGCATGA
1260932 ATTGCCACTT
Statistics
Matches: 151, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
80 141 0.93
81 10 0.07
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (80 bp):
TTTAATTTCATGCATGATTTATATCCTTTTTCAGCAACTACTACTTTCTTATTTTTCAGCAGCTG
TTTATCAGCATTTGT
Found at i:1261111 original size:33 final size:33
Alignment explanation
Indices: 1261045--1261123 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
1261035 TTAATTCTTA
*
1261045 ATTTTTTTATTTTTTATATTATAGTCATTTTTT
1 ATTTTTTTATTTTTTATATTATAGTCATATTTT
1261078 ATTTTTTTATTTTTATATTATTATA-T-ATATTTT
1 ATTTTTTTATTTTT-TA-TATTATAGTCATATTTT
**
1261111 ATTTAATTATTTT
1 ATTTTTTTATTTT
1261124 GTATCAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 31 0.76
34 3 0.07
35 7 0.17
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (33 bp):
ATTTTTTTATTTTTTATATTATAGTCATATTTT
Found at i:1262477 original size:25 final size:25
Alignment explanation
Indices: 1262443--1262493 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1262433 ATGTTGCTTC
1262443 ACTTACATTGTAGTTAATAAAAAAA
1 ACTTACATTGTAGTTAATAAAAAAA
* * * *
1262468 ACTTGCATTGTATTTCATTAAAAAA
1 ACTTACATTGTAGTTAATAAAAAAA
1262493 A
1 A
1262494 TAACATTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (25 bp):
ACTTACATTGTAGTTAATAAAAAAA
Found at i:1265813 original size:92 final size:92
Alignment explanation
Indices: 1265715--1265912 Score: 247
Period size: 92 Copynumber: 2.2 Consensus size: 92
1265705 ACAGTGTGAG
* * *
1265715 ATTTACAATCAGTCAACTTTTCTCTT-TTTCTACTAAAAAGAATTC-GATTCTCAAATATAATAT
1 ATTTACAATCAATCAACTTTTCT-TTCTTTCTAC-AAAAAGAAATCTGATTCTCAAAAATAATAT
** * * * * *
1265778 ATGCATTAGTCTAATTCTTATAGTTTAAC
64 AAACATTAGCCTAATCCCTAGAGTCTAAC
* *
1265807 ATTTACAATCAATCAACTTTTCTTTCTTTCTACCAAAAGAAATCTGATTCTCAAAAATAATCTAA
1 ATTTACAATCAATCAACTTTTCTTTCTTTCTACAAAAAGAAATCTGATTCTCAAAAATAATATAA
*
1265872 ACATTAGCCTAATCCCTAGAGTCTGAC
66 ACATTAGCCTAATCCCTAGAGTCTAAC
1265899 ATTTACAATCAATC
1 ATTTACAATCAATC
1265913 TTTTAATACC
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
91 11 0.12
92 80 0.88
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (92 bp):
ATTTACAATCAATCAACTTTTCTTTCTTTCTACAAAAAGAAATCTGATTCTCAAAAATAATATAA
ACATTAGCCTAATCCCTAGAGTCTAAC
Found at i:1267297 original size:25 final size:23
Alignment explanation
Indices: 1267262--1267316 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
1267252 TTATGATTAA
*
1267262 TAATTTTAATTT-TAATTTTCTTT
1 TAATTTTAATTTCT-ATTTTATTT
1267285 TAATTTTGAAATTTCTATTTTATTT
1 TAATTTT--AATTTCTATTTTATTT
*
1267310 TATTTTT
1 TAATTTT
1267317 TAACTATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.26
25 19 0.70
26 1 0.04
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (23 bp):
TAATTTTAATTTCTATTTTATTT
Found at i:1267354 original size:24 final size:24
Alignment explanation
Indices: 1267322--1267369 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1267312 TTTTTTAACT
1267322 ATGGAAACTAGTGTAGTTGGTTTC
1 ATGGAAACTAGTGTAGTTGGTTTC
*
1267346 ATGGAAACTAGTTTAGTTGGTTTC
1 ATGGAAACTAGTGTAGTTGGTTTC
1267370 CAACTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (24 bp):
ATGGAAACTAGTGTAGTTGGTTTC
Found at i:1269201 original size:153 final size:154
Alignment explanation
Indices: 1268990--1269989 Score: 441
Period size: 153 Copynumber: 6.5 Consensus size: 154
1268980 CTAGAGACAT
* * * * * * * *** *
1268990 TTTGATAATTTTTCTAGAACCGAGTTTTAGGTAGTCATCGAGTTATTTTTATGCCAAAGGTATGC
1 TTTGGTAATTTTTTTAAAATCGAGTCTTAGGTAGTTATCAAGTCGCTTTTATGCCAAAGGTGTGC
* * * *
1269055 ATTTAGGATAGGTTCATCATTTTCTTATCGTTTTTGTGTCCTTTAAGATTACCACGAT-TCTTTC
66 GTTTAGGATAGGTTCATCATTTTCTTATCATTTTTGTGTCCTTTAAGATTAACAAGATAT-TTTC
* ** * *
1269119 ACGTCGAAGGTATACTTAGGGGTAC
130 ACGTCGAAAGTATACCCAAGGGCAC
* * * * *
1269144 TTTGGTAA-TTTTTTAAAATCGAGTTTTAGGTGGTTA-CTAGGTTGCTTTTATACCAAAGGTGTG
1 TTTGGTAATTTTTTTAAAATCGAGTCTTAGGTAGTTATC-AAGTCGCTTTTATGCCAAAGGTGTG
* * * * *
1269207 TGTTTAGGATAGGTTCATCCTTTTCTTATCATTTTCGTGTTCTTTAAGGTTAACAAGATATTTTC
65 CGTTTAGGATAGGTTCATCATTTTCTTATCATTTTTGTGTCCTTTAAGATTAACAAGATATTTTC
* * *
1269272 ACGTTGAAAGTATACCCAATGGCAT
130 ACGTCGAAAGTATACCCAAGGGCAC
*
1269297 TTTGGTAATTTTTTTAAAATCGTGTCTTAGGTAGTTATCAAGTCGCTTTTATGCCAAAGGTGTGC
1 TTTGGTAATTTTTTTAAAATCGAGTCTTAGGTAGTTATCAAGTCGCTTTTATGCCAAAGGTGTGC
* * * * * * * **
1269362 GTTTAAGATATGTTCATCATTTT-TTATTATTTTTGTATCTTTTAGGGTT-ATTAGTATACTTTT
66 GTTTAGGATAGGTTCATCATTTTCTTATCATTTTTGTGTCCTTTAAGATTAACAAG-ATA-TTTT
* * * *
1269425 -ATGTC-CAAGATATACCCTAAGAGCAT
129 CACGTCGAAAG-TATACCC-AAGGGCAC
* * * * * * * * *
1269451 TTTAGTAA-TTTCTTAGAATTGTGT-TGTAGATAGTCACCAAGTCGTTTTTATGCCAAA-GT-TG
1 TTTGGTAATTTTTTTAAAATCGAGTCT-TAGGTAGTTATCAAGTCGCTTTTATGCCAAAGGTGTG
* * * ** * * * * ** *
1269512 CCTTTAGGATTA-GTTCATTC-TTTACTTATCGTTTTCATATCTTTTAGGGTTTTCAGGATATTT
65 CGTTTAGGA-TAGGTTCA-TCATTTTCTTATCATTTTTGTGTCCTTTAAGATTAACAAGATATTT
* ** *
1269575 TCACGTCG-AAGATATATCTTAGAGGCAT
128 TCACGTCGAAAG-TATACCCAAG-GGCAC
* * * * * * * * * *
1269603 TTTGATAATTTTTCCTTGAACT-GAGTCTTGGGCAGTCA-CTAGGTCACTTTTATGTCAAAAGTG
1 TTTGGTAATTTTT--TTAAAATCGAGTCTTAGGTAGTTATC-AAGTCGCTTTTATGCCAAAGGTG
* * * * * * * *
1269666 TGTGTTTAGGATAGTTTCACCTTTTTCTTATCGTTTTTGTGTCCTTT-AGAGTTACCGAGATACT
63 TGCGTTTAGGATAGGTTCATCATTTTCTTATCATTTTTGTGTCCTTTAAGA-TTAACAAGATATT
* * * *
1269730 TTCATGTCAAAAGTATACCCTAAGAGTA-
127 TTCACGTCGAAAGTATACCC-AAGGGCAC
** * * * ** *
1269758 TCTTGGTAA-TTTCGT-AAA-CAGAGTCCTAGGTGGTCA-CTGGGTCGTTTTTATGCCAAA-G-G
1 T-TTGGTAATTTTTTTAAAATC-GAGTCTTAGGTAGTTATC-AAGTCGCTTTTATGCCAAAGGTG
** * * * * * * ** *
1269817 TG-GTTTAGGATA-GTTCATCATTTAATTATTATCTTCGTGTCTTTTAGGGTTGCCGAGATATTT
63 TGCGTTTAGGATAGGTTCATCATTTTCTTATCATTTTTGTGTCCTTTAAGATTAACAAGATATTT
* * ** * * *
1269880 TCACATCGAAGGTATACTTTAAGAGTAT
128 TCACGTCGAAAGTATAC-CCAAGGGCAC
* *** * * * ** * * *
1269908 TTTAGTAATTTTTTCTTTTATCGAGTCTAAGGTAGTCACCGGGTTGTTTTTATGCCAAAGGTGCG
1 TTTGGTAATTTTTT-TAAAATCGAGTCTTAGGTAGTTATCAAGTCGCTTTTATGCCAAAGGTGTG
1269973 CGTTTAGGATAGGTTCA
65 CGTTTAGGATAGGTTCA
1269990 CCCTTTTAGG
Statistics
Matches: 648, Mismatches: 155, Indels: 84
0.73 0.17 0.09
Matches are distributed among these distances:
149 61 0.09
150 15 0.02
151 27 0.04
152 97 0.15
153 232 0.36
154 119 0.18
155 26 0.04
156 66 0.10
157 5 0.01
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (154 bp):
TTTGGTAATTTTTTTAAAATCGAGTCTTAGGTAGTTATCAAGTCGCTTTTATGCCAAAGGTGTGC
GTTTAGGATAGGTTCATCATTTTCTTATCATTTTTGTGTCCTTTAAGATTAACAAGATATTTTCA
CGTCGAAAGTATACCCAAGGGCAC
Found at i:1270047 original size:156 final size:152
Alignment explanation
Indices: 1269481--1270380 Score: 479
Period size: 156 Copynumber: 5.8 Consensus size: 152
1269471 GTGTTGTAGA
** * * *
1269481 TAGTCACCAAGTCGTTTTTATGCCAAAGTTGCCTTTAGGATTA-GTTCAT-TCTTT-ACTTATCG
1 TAGTCACCGGGTCGTTTTTATGCCAAAGGTGCGTTTAGGA-TAGGTTCATCT-TTTAACTT-T-A
* * * * *
1269543 TTTTCATATCTTTTAGGGTTTTCAGGATATTTTCACGTCGAAGATATA-TCTT-AGAGGCATTTT
62 TTTTCATGTCTTTTAGGG-TTGCCGGATACTTTCACGTCGAAGGTATACT-TTAAGA-GCATTTT
* * * *
1269606 -GATAATTTTTCCTTGAACTGAGTCTTGGG
124 AG-TAATTTTTTCTTGAACTGAATCCTAGG
* ** ** * * * * * *
1269635 CAGTCACTAGGTCACTTTTATGTCAAAAGTGTGTGTTTAGGATAGTTTCACCTTTT-TCTTATCG
1 TAGTCACCGGGTCGTTTTTATG-CCAAAG-GTGCGTTTAGGATAGGTTCATCTTTTAACTT-T-A
** * * * * * * ** * * *
1269699 TTTTTGTGTCCTTTAGAGTTACCGAGATACTTTCATGTCAAAAGTATACCCTAAGAGTATCTTGG
62 TTTTCATGTCTTTTAGGGTTGCCG-GATACTTTCACGTCGAAGGTATACTTTAAGAGCATTTTAG
* * * *
1269764 TAA---TTTCGTAAACAGAGTCCTAGG
126 TAATTTTTTCTTGAACTGAATCCTAGG
* * * * *
1269788 TGGTCACTGGGTCGTTTTTATGCCAAAGGTG-GTTTAGGATA-GTTCATCATTTAATTATTATCT
1 TAGTCACCGGGTCGTTTTTATGCCAAAGGTGCGTTTAGGATAGGTTCATCTTTTAACT-TTATTT
* * * *
1269851 TCGTGTCTTTTAGGGTTGCCGAGATATTTTCACATCGAAGGTATACTTTAAGAGTATTTTAGTAA
65 TCATGTCTTTTAGGGTTGCCG-GATACTTTCACGTCGAAGGTATACTTTAAGAGCATTTTAGTAA
** *
1269916 TTTTTTCTTTTA-TCGAGT-CTAAGG
129 TTTTTTCTTGAACT-GAATCCT-AGG
* * **
1269940 TAGTCACCGGGTTGTTTTTATGCCAAAGGTGCGCGTTTAGGATAGGTTCACCCTTTTAGGTTTAT
1 TAGTCACCGGGTCGTTTTTATGCCAAAGGT--GCGTTTAGGATAGGTTCA-TCTTTTAACTTTAT
* * * * *
1270005 TTTAATGTCTTTTAGGGTTACTCGGATACTTTCACGTTGAAGGTATCCTTT-AGAGACATTTTTG
63 TTTCATGTCTTTTAGGGTTGC-CGGATACTTTCACGTCGAAGGTATACTTTAAGAG-CATTTTAG
* * *
1270069 TAATTATTGCTTGAACTGAATCCTGGG
126 TAATTTTTTCTTGAACTGAATCCTAGG
* * * * * ** * *
1270096 TAATCACCAGGTCATTTTTATGCCAAAGGTATGCTTTTATGATAGGTTCATCTTTTTCCATCATT
1 TAGTCACCGGGTCGTTTTTATGCCAAAGG--TGCGTTTAGGATAGGTTCATCTTTTAACTTTATT
* * * * *
1270161 TTCATGTCCTTTAAGGTTGCCAGGATACTTTCACGTCGAAGATATACTTTAAAAGCATTTTGGTA
64 TTCATGTCTTTTAGGGTTGCC-GGATACTTTCACGTCGAAGGTATACTTTAAGAGCATTTTAGTA
* * *
1270226 ATTTTTT-TT-AACCGAATCTTTGG
128 ATTTTTTCTTGAACTGAATCCTAGG
* * * * * * * * *
1270249 TAATCATCAGGTCGCTTTTTATGCAAAAAGTATACTTTTAAGATAGGTTCATCCTTTT-ACATTA
1 TAGTCACCGGGTCG-TTTTTATGC-CAAAG-GTGCGTTTAGGATAGGTTCAT-CTTTTAACTTTA
** * * * * ** *
1270313 TTTTTGTATCTTTTAGGGTTGCTAGGATATTTTCACATCGAATATATACCTT-AGAGGCATTTTA
62 TTTTCATGTCTTTTAGGGTTGC-CGGATACTTTCACGTCGAAGGTATACTTTAAGA-GCATTTTA
1270377 GTAA
125 GTAA
1270381 ATTTCTCTGA
Statistics
Matches: 579, Mismatches: 133, Indels: 68
0.74 0.17 0.09
Matches are distributed among these distances:
149 62 0.11
150 12 0.02
151 6 0.01
152 45 0.08
153 57 0.10
154 104 0.18
155 98 0.17
156 178 0.31
157 16 0.03
158 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (152 bp):
TAGTCACCGGGTCGTTTTTATGCCAAAGGTGCGTTTAGGATAGGTTCATCTTTTAACTTTATTTT
CATGTCTTTTAGGGTTGCCGGATACTTTCACGTCGAAGGTATACTTTAAGAGCATTTTAGTAATT
TTTTCTTGAACTGAATCCTAGG
Found at i:1270227 original size:155 final size:154
Alignment explanation
Indices: 1270028--1270391 Score: 381
Period size: 154 Copynumber: 2.4 Consensus size: 154
1270018 AGGGTTACTC
* * * * * *
1270028 GGATACTTTCACGTTGAAGGTATCCTTT-AGAGACATTTTTGTAATTATTGCTTGAACTGAATCC
1 GGATACTTTCACGTCGAAGATATACTTTAAAAG-CATTTTAGTAATT-TT-CTTGAACCGAATCC
* * * * * *
1270092 TGGGTAATCACCAGGTC-ATTTTTATGCCAAAGGTATGCTTTTATGATAGGTTCATCTTTTTCCA
63 TGGGTAATCACCAGGTCGATTTTTATGCAAAAAGTATACTTTTAAGATAGGTTCATCCTTTTACA
*
1270156 TCATTTTCATGTCCTTTAAGGTTGCCA
128 TCATTTTCATATCCTTTAAGGTTGCCA
* * * * *
1270183 GGATACTTTCACGTCGAAGATATACTTTAAAAGCATTTTGGTAATTTTTTTTAACCGAATCTTTG
1 GGATACTTTCACGTCGAAGATATACTTTAAAAGCATTTTAGTAATTTTCTTGAACCGAATCCTGG
* * *
1270248 GTAATCATCAGGTCGCTTTTTATGCAAAAAGTATACTTTTAAGATAGGTTCATCCTTTTACATTA
66 GTAATCACCAGGTCGATTTTTATGCAAAAAGTATACTTTTAAGATAGGTTCATCCTTTTACATCA
** * * *
1270313 TTTTTGTATCTTTTAGGGTTGCTA
131 TTTTCATATCCTTTAAGGTTGCCA
* * * * * * *
1270337 GGATATTTTCACATCGAATATATACCTTAGAGGCATTTTAGTAAATTTCTCTGAA
1 GGATACTTTCACGTCGAAGATATACTTTAAAAGCATTTTAGTAATTTTCT-TGAA
1270392 ATCGAGTCCT
Statistics
Matches: 171, Mismatches: 35, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
153 25 0.15
154 103 0.60
155 40 0.23
156 3 0.02
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.41
Consensus pattern (154 bp):
GGATACTTTCACGTCGAAGATATACTTTAAAAGCATTTTAGTAATTTTCTTGAACCGAATCCTGG
GTAATCACCAGGTCGATTTTTATGCAAAAAGTATACTTTTAAGATAGGTTCATCCTTTTACATCA
TTTTCATATCCTTTAAGGTTGCCA
Found at i:1272522 original size:84 final size:83
Alignment explanation
Indices: 1272374--1272533 Score: 207
Period size: 84 Copynumber: 1.9 Consensus size: 83
1272364 CAAAAAGAAT
* * * *
1272374 AAATTTTTTTAGGTAATTAAAAATACATTTTTCTAGTTCTTTTCTTCTCACCAAAGCCTTCC-TT
1 AAATTATTTTAGGTAATTAAAAACACATTTTTCTAGTTCTTTTCTTCCCACAAAAGCCTTCCTTT
1272438 TGTTTTAGTTCACTCTAAA
66 TG-TTTAGTTCACTCTAAA
* * * *
1272457 AAATTATTTTAGGTAATTAAAAGCACTTTTTTTCTAGTTCTTTTCTTCCCTCTAAAAGTC-TCCT
1 AAATTATTTTAGGTAATTAAAAACAC-ATTTTTCTAGTTCTTTTCTTCCCAC-AAAAGCCTTCCT
1272521 TTTGTTTAGTTCA
64 TTTGTTTAGTTCA
1272534 ACCTTCTTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
83 23 0.35
84 34 0.52
85 9 0.14
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.48
Consensus pattern (83 bp):
AAATTATTTTAGGTAATTAAAAACACATTTTTCTAGTTCTTTTCTTCCCACAAAAGCCTTCCTTT
TGTTTAGTTCACTCTAAA
Found at i:1272982 original size:23 final size:23
Alignment explanation
Indices: 1272956--1272999 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1272946 CTAAAACATG
1272956 AATTTAAAT-TTTAAATAAATTTA
1 AATTTAAATATTTAAA-AAATTTA
1272979 AATTTAAATATTTAAAAAATT
1 AATTTAAATATTTAAAAAATT
1273000 GCGATCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAAATATTTAAAAAATTTA
Found at i:1272986 original size:16 final size:17
Alignment explanation
Indices: 1272956--1272988 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1272946 CTAAAACATG
1272956 AATTTAAATTTTAAATA
1 AATTTAAATTTTAAATA
1272973 AATTTAAA-TTTAAATA
1 AATTTAAATTTTAAATA
1272989 TTTAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTTAAATA
Found at i:1274502 original size:2 final size:2
Alignment explanation
Indices: 1274495--1274525 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1274485 TATTATATTT
1274495 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1274526 TTCAGATCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1284173 original size:79 final size:77
Alignment explanation
Indices: 1284066--1284555 Score: 349
Period size: 79 Copynumber: 6.2 Consensus size: 77
1284056 AAGAGAAACG
* ** *
1284066 GGGTTGGAGTATTCCCTCAAAAATAACGGGATTAGAATATCCCCGATGGTGAAAAATCGATATTT
1 GGGTTGGAGTATCCCCTCGGAAATAACGGG-TT-GAGTATCCCCGATGGTGAAAAATCGATATTT
1284131 TAGAAATAAAATTA
64 TAGAAATAAAATTA
* * * * * ** *
1284145 GGGTTTGAGTATCTCTTTGGAAGTAACGGGGTTGCAGTATCCTTGATGGTGAAAAATCAATATTT
1 GGGTTGGAGTATCCCCTCGGAAATAAC-GGGTTG-AGTATCCCCGATGGTGAAAAATCGATATTT
* *
1284210 TGGAAATAAAATTG
64 TAGAAATAAAATTA
*
1284224 GGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATTGATATTT
1 GGGTTGGAGTATCCCCTCGGAAATAAC-GGGTT-GAGTATCCCCGATGGTGAAAAATCGATATTT
* * **
1284289 TAAAAATATAA-CC
64 TAGAAATAAAATTA
* * *** * ** * *
1284302 GGAGTTGAAATATCTTTTCGGAAATAATGGGGTTGGAGTATCCCCGATCATGGAAAATC-AGTGT
1 GG-GTTGGAGTATCCCCTCGGAAATAA-CGGGTT-GAGTATCCCCGATGGTGAAAAATCGA-TAT
* * *
1284366 TTTAAAAATATAA-TC
62 TTTAGAAATAAAATTA
* * * ** * * * * * *
1284381 GGGATTGAATTATCCCTTCAAAAATAACGAGGTTGGAGTATCTCCAATGGTAAAAAATTGGTGTT
1 GGG-TTGGAGTATCCCCTCGGAAATAACG-GGTT-GAGTATCCCCGATGGTGAAAAATCGATATT
*
1284446 TTAGAAATAAAACCT-
63 TTAGAAATAAAA-TTA
* * * * *
1284461 GAGTTGGAGTGTCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATAGTGGAAAATCGATATTT
1 GGGTTGGAGTATCCCCTCGGAAATAAC-GGGTT-GAGTATCCCCGATGGTGAAAAATCGATATTT
**
1284526 TAGAAATAAAATCG
64 TAGAAATAAAATTA
1284540 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
1284556 GATGATGGAA
Statistics
Matches: 321, Mismatches: 77, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
78 6 0.02
79 307 0.96
80 7 0.02
81 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (77 bp):
GGGTTGGAGTATCCCCTCGGAAATAACGGGTTGAGTATCCCCGATGGTGAAAAATCGATATTTTA
GAAATAAAATTA
Found at i:1284359 original size:158 final size:154
Alignment explanation
Indices: 1284064--1284555 Score: 518
Period size: 158 Copynumber: 3.1 Consensus size: 154
1284054 CGAAGAGAAA
* * * *
1284064 CGGGGTTGGAGTATTCCCTCAAAAATAACGGGATTAGAATATCCCCGATGGTGAAAAATCGATAT
1 CGGGGTTGGAGTATCCCCTCAAAAATAACGGG-TTGGAGTATCCCCGATGGTGAAAAATTGATAT
** * * **
1284129 TTTAGAAATAAAATTAGG-GTTTGAGTATCTCTTTGGAAGTAACGGGGTTGCAGTATCCTTGATG
65 TTTAGAAATAAAA-CCGGAG-TTGAGTATCT-TTTGGAAATAACGGGGTTGGAGTATCCCCGAT-
* * *
1284193 GTGAAAAATCAATATTTTGGAAATAAAAT
126 ATGGAAAATCAATATTTTAGAAATAAAAT
* **
1284222 TGGGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGGTGAAAAATTGATAT
1 CGGGGTTGGAGTATCCCCTCAAAAATAAC-GGGTTGGAGTATCCCCGATGGTGAAAAATTGATAT
* * * *
1284287 TTTAAAAATATAACCGGAGTTGAAATATCTTTTCGGAAATAATGGGGTTGGAGTATCCCCGATCA
65 TTTAGAAATAAAACCGGAGTTG-AGTATCTTTT-GGAAATAACGGGGTTGGAGTATCCCCGAT-A
* * * *
1284352 TGGAAAATCAGTGTTTTAAAAATATAAT
127 TGGAAAATCAATATTTTAGAAATAAAAT
* * * * * * * * *
1284380 CGGGATTGAATTATCCCTTCAAAAATAACGAGGTTGGAGTATCTCCAATGGTAAAAAATTGGTGT
1 CGGGGTTGGAGTATCCCCTCAAAAATAACG-GGTTGGAGTATCCCCGATGGTGAAAAATTGATAT
* * **
1284445 TTTAGAAATAAAACCTGAGTTGGAGTGTCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATAG
65 TTTAGAAATAAAACCGGAGTT-GAGTAT-CTTTTGGAAATAACGGGGTTGGAGTATCCCCGATA-
*
1284510 TGGAAAATCGATATTTTAGAAATAAAAT
127 TGGAAAATCAATATTTTAGAAATAAAAT
1284538 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1284556 GATGATGGAA
Statistics
Matches: 272, Mismatches: 54, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
157 10 0.04
158 255 0.94
159 7 0.03
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (154 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAACGGGTTGGAGTATCCCCGATGGTGAAAAATTGATATT
TTAGAAATAAAACCGGAGTTGAGTATCTTTTGGAAATAACGGGGTTGGAGTATCCCCGATATGGA
AAATCAATATTTTAGAAATAAAAT
Found at i:1284553 original size:51 final size:51
Alignment explanation
Indices: 1284487--1284587 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
1284477 TTGGAAATAA
*
1284487 CGGGGTTGGAGTATCCCCGAT-AGTGGAAAATCGATATTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATGA-TGGAAAATCGATATCTTAGAAATAAAAT
* *
1284538 CGGGGTTGGAGTATCCCCGATGATGGAAAATCGGTGTCTTAGAAATAAAA
1 CGGGGTTGGAGTATCCCCGATGATGGAAAATCGATATCTTAGAAATAAAA
1284588 CATCAATGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 45 0.98
52 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATGATGGAAAATCGATATCTTAGAAATAAAAT
Found at i:1286605 original size:21 final size:20
Alignment explanation
Indices: 1286557--1286611 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1286547 AAAAACCCAG
**
1286557 AATGTATCGATACAATGAAA
1 AATGTATCGATACAAACAAA
* *
1286577 AATATATCGATACAAACAGTA
1 AATGTATCGATACAAACA-AA
1286598 AATGTATCGATACA
1 AATGTATCGATACA
1286612 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAACAAA
Found at i:1286684 original size:20 final size:20
Alignment explanation
Indices: 1286639--1286712 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
1286629 AGGGTGGCTT
* *
1286639 TGTATCGATACATTTTAGTCA
1 TGTATCGATACA-TTTACTTA
*
1286660 TGTATCGATACATTCACTTA
1 TGTATCGATACATTTACTTA
* *
1286680 TGTATCGATATATTTACTATT
1 TGTATCGATACATTTACT-TA
1286701 TGTATCGATACA
1 TGTATCGATACA
1286713 AATTGTAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 21 0.47
21 24 0.53
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTACTTA
Found at i:1286799 original size:25 final size:21
Alignment explanation
Indices: 1286750--1286791 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1286740 GTTAGGACCT
1286750 TGTATCGATACATCAAAGGCA
1 TGTATCGATACATCAAAGGCA
1286771 TGTATCGATACATCAAAGGCA
1 TGTATCGATACATCAAAGGCA
1286792 AAAATGTAAC
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:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
TGTATCGATACATCAAAGGCA
Found at i:1287616 original size:58 final size:57
Alignment explanation
Indices: 1287499--1287687 Score: 159
Period size: 58 Copynumber: 3.3 Consensus size: 57
1287489 TCTTAAGGTA
* * * * *
1287499 CATGAAAATACATAAATGATCCTAATCATGAAAAATTACTAAGATGGCCCTAAACTG
1 CATGAAATTACATAAATGATCCTAATCATAAAAAATTACTAAAATGACCATAAACTG
*
1287556 CATGAAATTGCATAAAT-AGTCCTAAATCATAAAAAATTACTAAAAT-ACTCAT-AACTTG
1 CATGAAATTACATAAATGA-TCCT-AATCATAAAAAATTACTAAAATGAC-CATAAAC-TG
* ** * * * * * *
1287614 CATGAAATTACACAAATGATTCAAAATCATGAAAAATGACTAACATGAACTTAAAATG
1 CATGAAATTACATAAATGA-TCCTAATCATAAAAAATTACTAAAATGACCATAAACTG
* *
1287672 CATGAAACTGCATAAA
1 CATGAAATTACATAAA
1287688 GGTCCCTAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 13
0.76 0.14 0.09
Matches are distributed among these distances:
56 1 0.01
57 23 0.22
58 75 0.71
59 6 0.06
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (57 bp):
CATGAAATTACATAAATGATCCTAATCATAAAAAATTACTAAAATGACCATAAACTG
Found at i:1289987 original size:20 final size:21
Alignment explanation
Indices: 1289945--1289997 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1289935 TTTAACAATT
1289945 TGTATCGATACAATAAGGCAA
1 TGTATCGATACAATAAGGCAA
*
1289966 TGTATCGATGC-ATAAGTG-AA
1 TGTATCGATACAATAAG-GCAA
*
1289986 TGTGTCGATACA
1 TGTATCGATACA
1289998 TGCTTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (21 bp):
TGTATCGATACAATAAGGCAA
Found at i:1291153 original size:28 final size:29
Alignment explanation
Indices: 1291085--1291155 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
1291075 GAAATAAAAT
1291085 CGGGGTTGGAGTAT-TCCCTCGGAAATAA
1 CGGGGTTGGAGTATCTCCCTCGGAAATAA
* * * *
1291113 CAGGATTGAAGTATCT-CCTTGGAAATAA
1 CGGGGTTGGAGTATCTCCCTCGGAAATAA
*
1291141 TGGGGTTGGAGTATC
1 CGGGGTTGGAGTATC
1291156 CCGATTATGA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (29 bp):
CGGGGTTGGAGTATCTCCCTCGGAAATAA
Found at i:1291207 original size:50 final size:51
Alignment explanation
Indices: 1291142--1291240 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
1291132 TGGAAATAAT
* *
1291142 GGGGTTGGAGTAT-CCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACC
1 GGGGTCGGAGTATCCCCGATTATAAAAAATTGGTGTTTTGAAAATAAAACC
* *
1291192 GGGGTCGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTGGAAATAAAA
1 GGGGTCGGAGTATCCCCGATTATAAAAAATTGGTGTTTTGAAAATAAAA
1291241 ACACGAATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 12 0.27
51 32 0.73
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (51 bp):
GGGGTCGGAGTATCCCCGATTATAAAAAATTGGTGTTTTGAAAATAAAACC
Found at i:1293682 original size:13 final size:13
Alignment explanation
Indices: 1293635--1293664 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1293625 GTAAACCCAA
*
1293635 AATGTATTGATAC
1 AATGTATCGATAC
1293648 AATGTATCGATAC
1 AATGTATCGATAC
1293661 AATG
1 AATG
1293665 AACAATGTAT
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:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1300557 original size:24 final size:24
Alignment explanation
Indices: 1300514--1300573 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 24
1300504 TCTGAAAAGG
1300514 AAAAAGATTTGGCCATATC-TTCTTT
1 AAAAA-ATTT-GCCATATCTTTCTTT
1300539 ACAAAAATTTGCCATATCTTTCTTT
1 A-AAAAATTTGCCATATCTTTCTTT
*
1300564 AAAAACTTTG
1 AAAAAATTTG
1300574 AAAGATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 16 0.50
25 12 0.38
26 4 0.12
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (24 bp):
AAAAAATTTGCCATATCTTTCTTT
Found at i:1300887 original size:22 final size:21
Alignment explanation
Indices: 1300856--1300900 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1300846 TATTTTTATT
1300856 TAAATTTAAT-TATAAAATATA
1 TAAATTTAATATA-AAAATATA
1300877 TAAATATTAATATAAAAATATA
1 TAAAT-TTAATATAAAAATATA
1300899 TA
1 TA
1300901 TTTTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.23
22 15 0.68
23 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATATAAAAATATA
Found at i:1303329 original size:13 final size:13
Alignment explanation
Indices: 1303307--1303339 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1303297 CGCAGACATC
*
1303307 AGCAAGAAGAAAA
1 AGCAAAAAGAAAA
1303320 AGCAAAAAGAAAA
1 AGCAAAAAGAAAA
1303333 AG-AAAAA
1 AGCAAAAA
1303340 TCAGGAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (13 bp):
AGCAAAAAGAAAA
Found at i:1303557 original size:20 final size:21
Alignment explanation
Indices: 1303527--1303568 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1303517 AAATTTTCGG
*
1303527 GATAGATTTTAAATTTTAAAA
1 GATAGATTTTAAATTTCAAAA
*
1303548 GATAGA-TTTAGATTTCAAAA
1 GATAGATTTTAAATTTCAAAA
1303568 G
1 G
1303569 TAGTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (21 bp):
GATAGATTTTAAATTTCAAAA
Found at i:1305693 original size:2 final size:2
Alignment explanation
Indices: 1305686--1305715 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1305676 CAGATGGTTC
1305686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1305716 TATGAATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1309332 original size:28 final size:28
Alignment explanation
Indices: 1309290--1309352 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1309280 AATCTATAAA
*
1309290 TAAAGTTATTCAGTCTCGTTACATGCAT
1 TAAAGTTATTCAGTCTCGTTACATACAT
* *
1309318 TAAAGTTATTTAGTCTCGTTATATACAT
1 TAAAGTTATTCAGTCTCGTTACATACAT
1309346 TAAAGTT
1 TAAAGTT
1309353 TATTATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (28 bp):
TAAAGTTATTCAGTCTCGTTACATACAT
Found at i:1311958 original size:17 final size:17
Alignment explanation
Indices: 1311936--1311989 Score: 74
Period size: 18 Copynumber: 3.2 Consensus size: 17
1311926 TTAAGCAACT
1311936 AGAAAAAAAAAGAAAAA
1 AGAAAAAAAAAGAAAAA
*
1311953 AGAAAAATAAAGAAAAAA
1 AGAAAAAAAAAG-AAAAA
*
1311971 AGAAAAGAAAA-AAAAA
1 AGAAAAAAAAAGAAAAA
1311987 AGA
1 AGA
1311990 GGAAGAAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.24
17 11 0.33
18 14 0.42
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAA
Found at i:1311971 original size:13 final size:12
Alignment explanation
Indices: 1311936--1311987 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 12
1311926 TTAAGCAACT
1311936 AGAAAAAAAAAGA
1 AGAAAAAAAAA-A
*
1311949 AAAAAGAAAAATAA
1 AGAAA-AAAAA-AA
1311963 AGAAAAAAAGAAA
1 AGAAAAAAA-AAA
1311976 AGAAAAAAAAAA
1 AGAAAAAAAAAA
1311988 GAGGAAGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
12 3 0.09
13 19 0.56
14 11 0.32
15 1 0.03
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.02
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:1311973 original size:25 final size:24
Alignment explanation
Indices: 1311940--1311989 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
1311930 GCAACTAGAA
1311940 AAAAAAAGAAAA-AAGAAAAATAAAG
1 AAAAAAAGAAAAGAA-AAAAA-AAAG
1311965 AAAAAAAGAAAAGAAAAAAAAAAG
1 AAAAAAAGAAAAGAAAAAAAAAAG
1311989 A
1 A
1311990 GGAAGAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 5 0.21
25 17 0.71
26 2 0.08
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (24 bp):
AAAAAAAGAAAAGAAAAAAAAAAG
Found at i:1311996 original size:30 final size:29
Alignment explanation
Indices: 1311938--1311996 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1311928 AAGCAACTAG
*
1311938 AAAAAAAAAGAAAAAAGAAAAATAAAGAA
1 AAAAAAAAAGAAAAAAGAAAAAGAAAGAA
*
1311967 AAAAAGAAAAGAAAAAA-AAAAGAGGAAGAA
1 AAAAA-AAAAGAAAAAAGAAAA-AGAAAGAA
1311997 GAGAGATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (29 bp):
AAAAAAAAAGAAAAAAGAAAAAGAAAGAA
Found at i:1312735 original size:59 final size:59
Alignment explanation
Indices: 1312639--1312758 Score: 156
Period size: 59 Copynumber: 2.0 Consensus size: 59
1312629 AAAAACCATC
*
1312639 TTCATGCATATTAGAATCCTTTTAGTAATGTTTATGTATTCT-AGAGTCATTTAGGTTAT
1 TTCATGCATATTAGAATCCTTTTAGCAATGTTTATGTATTCTAAG-GTCATTTAGGTTAT
* * *
1312698 TTCATGTATATTAAGGA-CCTTTTAGCAAT-TTTCATGTATTTTAAGGTCATTTAGGTTAT
1 TTCATGCATATT-AGAATCCTTTTAGCAATGTTT-ATGTATTCTAAGGTCATTTAGGTTAT
1312757 TT
1 TT
1312759 ACATAATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
58 3 0.06
59 46 0.85
60 5 0.09
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (59 bp):
TTCATGCATATTAGAATCCTTTTAGCAATGTTTATGTATTCTAAGGTCATTTAGGTTAT
Found at i:1312995 original size:78 final size:79
Alignment explanation
Indices: 1312884--1313284 Score: 284
Period size: 78 Copynumber: 5.1 Consensus size: 79
1312874 ATAATGTGTG
* * * * * *
1312884 TCCATAAAGGTCATTTAAGTAACT-GTACC-TAAAAATTGAGTATTTAGGATTATGTGGGAACTT
1 TCCATTAAGGTCATTTAGGTAA-TAGTACCTTAAAAATTGAATCTTTAGGGTCATGTGGGAACTT
*
1312947 TCATGTTGATACATA
65 TCATGTTAATACATA
* ** * *
1312962 TCAATTAAGGTCATTTAGGT-ATAGTACCTTAAAAA-CCAATCTCTAGGGTCATGTAGGAACTTT
1 TCCATTAAGGTCATTTAGGTAATAGTACCTTAAAAATTGAATCTTTAGGGTCATGTGGGAACTTT
*
1313025 CATGTTAATACATG
66 CATGTTAATACATA
* * * * * * *
1313039 TCCATTAAGATAATTTAGGTAATA-TGA-CTTTAACATAGAATCTTTAAGGTCATATGGGAACTT
1 TCCATTAAGGTCATTTAGGTAATAGT-ACCTTAAAAATTGAATCTTTAGGGTCATGTGGGAACTT
* *
1313102 TCTTGTTGATACATA
65 TCATGTTAATACATA
* * * * * * *
1313117 TCCCTTAGAGGTCATCTAGATAATAATACCTT-AAAACTGAGT-TTCTAGGGTCATGTGGGAATT
1 TCCATTA-AGGTCATTTAGGTAATAGTACCTTAAAAATTGAATCTT-TAGGGTCATGTGGGAACT
* *
1313180 TTCATGTTAATATATG
64 TTCATGTTAATACATA
* * * * * ** * *
1313196 TCTATTAAGGTCATTTCA-ATAATATTGCATT-AAAA-CCAAGTCTCTAGGGTCATATGGGAACT
1 TCCATTAAGGTCATTT-AGGTAATAGTACCTTAAAAATTGAA-TCTTTAGGGTCATGTGGGAACT
* *
1313258 TTCATGTTGATACATG
64 TTCATGTTAATACATA
*
1313274 TCTATTAAGGT
1 TCCATTAAGGT
1313285 TATATAAGTG
Statistics
Matches: 254, Mismatches: 57, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
76 1 0.00
77 63 0.25
78 132 0.52
79 54 0.21
80 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (79 bp):
TCCATTAAGGTCATTTAGGTAATAGTACCTTAAAAATTGAATCTTTAGGGTCATGTGGGAACTTT
CATGTTAATACATA
Found at i:1313197 original size:157 final size:155
Alignment explanation
Indices: 1312938--1313284 Score: 398
Period size: 157 Copynumber: 2.2 Consensus size: 155
1312928 TAGGATTATG
* * *
1312938 TGGGAACTTTCATGTTGATACATATCAATTAAGGTCATTTAGGTATAGTACCTTAAAAACCAATC
1 TGGGAACTTTCATGTTGATACATATCAATTAAGGTCATCTAGATATAATACCTTAAAAACCAATC
*
1313003 TCTAGGGTCATGTAGGAACTTTCATGTTAATACATGTCCATTAAGATAATTT-AGGTAATA-TGA
66 TCTAGGGTCATGTAGGAACTTTCATGTTAATACATGTCCATTAAGATAATTTCA-ATAATATTG-
* * *
1313066 CTTTAACATA-GAA-TCTTTAAGGTCATA
129 CATTAA-A-ACCAAGTCTCTAAGGTCATA
* ** *
1313093 TGGGAACTTTCTTGTTGATACATATCCCTTAGAGGTCATCTAGATAATAATACCTT-AAAACTGA
1 TGGGAACTTTCATGTTGATACATATCAATTA-AGGTCATCTAGAT-ATAATACCTTAAAAAC-CA
* * * * * * * *
1313157 GTTTCTAGGGTCATGTGGGAATTTTCATGTTAATATATGTCTATTAAGGTCATTTCAATAATATT
63 ATCTCTAGGGTCATGTAGGAACTTTCATGTTAATACATGTCCATTAAGATAATTTCAATAATATT
*
1313222 GCATTAAAACCAAGTCTCTAGGGTCATA
128 GCATTAAAACCAAGTCTCTAAGGTCATA
* *
1313250 TGGGAACTTTCATGTTGATACATGTCTATTAAGGT
1 TGGGAACTTTCATGTTGATACATATCAATTAAGGT
1313285 TATATAAGTG
Statistics
Matches: 161, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
155 29 0.18
156 23 0.14
157 106 0.66
158 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (155 bp):
TGGGAACTTTCATGTTGATACATATCAATTAAGGTCATCTAGATATAATACCTTAAAAACCAATC
TCTAGGGTCATGTAGGAACTTTCATGTTAATACATGTCCATTAAGATAATTTCAATAATATTGCA
TTAAAACCAAGTCTCTAAGGTCATA
Found at i:1313299 original size:78 final size:78
Alignment explanation
Indices: 1312935--1313368 Score: 360
Period size: 78 Copynumber: 5.6 Consensus size: 78
1312925 ATTTAGGATT
* * * * *
1312935 ATGTGGGAACTTTCATGTTGATACATATCAATTAAGGTCATTTAGGT-ATAGTACCTTAAAAACC
1 ATGTGGGAACTTTCATGTTGATACATGTCCATTAAGGTCATTTAAGTAATATTACATT-AAAACC
1312999 AA-TCTCTAGGGTC
65 AAGTCTCTAGGGTC
* * * * * * *
1313012 ATGTAGGAACTTTCATGTTAATACATGTCCATTAAGATAATTTAGGTAATATGACTTTAACATA-
1 ATGTGGGAACTTTCATGTTGATACATGTCCATTAAGGTCATTTAAGTAATATTACATTAA-A-AC
* * *
1313076 GAA-TCTTTAAGGTC
64 CAAGTCTCTAGGGTC
* * * * * * *
1313090 ATATGGGAACTTTCTTGTTGATACATATCCCTTAGAGGTCATCT-AGATAATAATACCTTAAAAC
1 ATGTGGGAACTTTCATGTTGATACATGTCCATTA-AGGTCATTTAAG-TAATATTACATTAAAAC
** *
1313154 TGAGTTTCTAGGGTC
64 CAAGTCTCTAGGGTC
* * * * *
1313169 ATGTGGGAATTTTCATGTTAATATATGTCTATTAAGGTCATTTCAA-TAATATTGCATTAAAACC
1 ATGTGGGAACTTTCATGTTGATACATGTCCATTAAGGTCATTT-AAGTAATATTACATTAAAACC
1313233 AAGTCTCTAGGGTC
65 AAGTCTCTAGGGTC
* * * * * * **
1313247 ATATGGGAACTTTCATGTTGATACATGTCTATTAAGGTTATATAAGTGATATTACATGAGTACCA
1 ATGTGGGAACTTTCATGTTGATACATGTCCATTAAGGTCATTTAAGTAATATTACATTAAAACCA
1313312 AGTCTCTAGGGTC
66 AGTCTCTAGGGTC
* * ** * *
1313325 TTGTGGGAAGTTTCATGCCGATGCATGTCC-TTTAGAGTCATTTA
1 ATGTGGGAACTTTCATGTTGATACATGTCCATTAAG-GTCATTTA
1313369 GGTTATCAGA
Statistics
Matches: 280, Mismatches: 66, Indels: 21
0.76 0.18 0.06
Matches are distributed among these distances:
77 50 0.18
78 177 0.63
79 52 0.19
80 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36
Consensus pattern (78 bp):
ATGTGGGAACTTTCATGTTGATACATGTCCATTAAGGTCATTTAAGTAATATTACATTAAAACCA
AGTCTCTAGGGTC
Found at i:1314005 original size:99 final size:99
Alignment explanation
Indices: 1313834--1314032 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
1313824 AACTCTCAAA
1313834 CCCTTTTCATATAAATCTTTAGTTTTTAAGTAAACCTTAGAGTTTATTTTCGAGAGTTTCGTAAC
1 CCCTTTTCATATAAATCTTTAGTTTTTAAGTAAACCTTAGAGTTTATTTTCGAGAGTTTCGTAAC
1313899 CTTTAAAAGATAAACTTCGATAGGAGACCAACCT
66 CTTTAAAAGATAAACTTCGATAGGAGACCAACCT
1313933 CCCTTTTCATATAAATCTTTAGTTTTTAAGTAAACCTTAGAGTTTATTTTCGAGAGTTTCGTAAC
1 CCCTTTTCATATAAATCTTTAGTTTTTAAGTAAACCTTAGAGTTTATTTTCGAGAGTTTCGTAAC
1313998 CTTTAAAAGATAAACTTCGATAGGAGACCAACCT
66 CTTTAAAAGATAAACTTCGATAGGAGACCAACCT
1314032 C
1 C
1314033 ATCTAACCAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (99 bp):
CCCTTTTCATATAAATCTTTAGTTTTTAAGTAAACCTTAGAGTTTATTTTCGAGAGTTTCGTAAC
CTTTAAAAGATAAACTTCGATAGGAGACCAACCT
Found at i:1316921 original size:2 final size:2
Alignment explanation
Indices: 1316914--1316941 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1316904 AAACACGTTA
1316914 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
1316942 CCCTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1322677 original size:13 final size:13
Alignment explanation
Indices: 1322659--1322686 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1322649 ATACAAAGAT
1322659 CAATGTATCGATA
1 CAATGTATCGATA
1322672 CAATGTATCGATA
1 CAATGTATCGATA
1322685 CA
1 CA
1322687 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1336540 original size:28 final size:25
Alignment explanation
Indices: 1336495--1336559 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
1336485 AAAAAAAAGA
*
1336495 AAAAAAAAAGGAATAAAGGAAAGGAAG
1 AAAAAAAAA-GAA-AAGGGAAAGGAAG
1336522 --AAAAAAAGAAAAGGGAAAGGAAG
1 AAAAAAAAAGAAAAGGGAAAGGAAG
*
1336545 AAAAGAAAAGAAAAG
1 AAAAAAAAAGAAAAG
1336560 AAAAAGAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 12 0.35
24 3 0.09
25 19 0.56
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAGAAAAGGGAAAGGAAG
Found at i:1336541 original size:36 final size:35
Alignment explanation
Indices: 1336484--1336566 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
1336474 TTTATTATAA
* * *
1336484 AAAAAAAAAGAAAAAAAAAAGGAATAAAGGAAAGG
1 AAAAAAAAAGAAAAAAAAAAGGAAGAAAAGAAAAG
***
1336519 AAGAAAAAAAGAAAAGGGAAAGGAAGAAAAGAAAAG
1 AA-AAAAAAAGAAAAAAAAAAGGAAGAAAAGAAAAG
1336555 AAAAGAAAAAGA
1 AAAA-AAAAAGA
1336567 GTAAAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 4 0.10
36 36 0.90
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (35 bp):
AAAAAAAAAGAAAAAAAAAAGGAAGAAAAGAAAAG
Found at i:1336562 original size:23 final size:22
Alignment explanation
Indices: 1336509--1336559 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
1336499 AAAAAGGAAT
1336509 AAAGGAAAGGAAGAAAAAAAGA
1 AAAGGAAAGGAAGAAAAAAAGA
1336531 AAAGGGAAAGGAAGAAAAGAAAAGA
1 AAA-GGAAAGGAAG-AAA-AAAAGA
1336556 AAAG
1 AAAG
1336560 AAAAAGAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.12
23 10 0.38
24 4 0.15
25 9 0.35
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AAAGGAAAGGAAGAAAAAAAGA
Found at i:1340046 original size:19 final size:18
Alignment explanation
Indices: 1340016--1340060 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1340006 TTTTTTAAAA
1340016 AATTATTTTTATATTTT-T
1 AATTATTTTTAT-TTTTAT
1340034 AATTATATTTTATTTTTAT
1 AATTAT-TTTTATTTTTAT
1340053 AATT-TTTT
1 AATTATTTT
1340061 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 11 0.44
19 11 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
AATTATTTTTATTTTTAT
Found at i:1340881 original size:26 final size:25
Alignment explanation
Indices: 1340829--1340885 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1340819 TTTTAAAATT
1340829 AAAT-AAAAACAAAAAAAAACTTAA
1 AAATAAAAAACAAAAAAAAACTTAA
*
1340853 AAATAAAAAACTAAAAAAAA-TTAATA
1 AAATAAAAAACAAAAAAAAACTT-A-A
1340879 AAATAAA
1 AAATAAA
1340886 TTTCTTGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 6 0.21
25 15 0.52
26 8 0.28
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (25 bp):
AAATAAAAAACAAAAAAAAACTTAA
Found at i:1341134 original size:20 final size:20
Alignment explanation
Indices: 1341118--1341165 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 20
1341108 TTTAATATAT
1341118 AATTTAAAAATAAAATAAAA
1 AATTTAAAAATAAAATAAAA
1341138 AATTTAAAAATAATTAATAAAA
1 AATTTAAAAATAA--AATAAAA
1341160 TAATTT
1 -AATTT
1341166 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.52
22 7 0.28
23 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTTAAAAATAAAATAAAA
Found at i:1346225 original size:20 final size:20
Alignment explanation
Indices: 1346200--1346255 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1346190 TAAAAAACTC
*
1346200 AGAATGTATCGATACAATTA
1 AGAATGTATCGATACAATAA
*
1346220 AGAATGTATCAATACAATAA
1 AGAATGTATCGATACAATAA
*
1346240 AAAATGTATCGATACA
1 AGAATGTATCGATACA
1346256 TTTGCTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (20 bp):
AGAATGTATCGATACAATAA
Found at i:1350238 original size:2 final size:2
Alignment explanation
Indices: 1350231--1350277 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1350221 CATTAAGTTT
1350231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1350273 TA TA T
1 TA TA T
1350278 TTGCAGTCTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1351648 original size:2 final size:2
Alignment explanation
Indices: 1351641--1351686 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1351631 CAAATAAACC
1351641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1351683 TA TA
1 TA TA
1351687 GTTCTTGTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1352204 original size:20 final size:20
Alignment explanation
Indices: 1352162--1352210 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
1352152 GGAAAAAAAA
1352162 TTAAAAAGAAAGTAGATAGTT
1 TTAAAAAG-AAGTAGATAGTT
*
1352183 TTAAAAAG-AGTTGATAGATT
1 TTAAAAAGAAGTAGATAG-TT
1352203 TTAAAAAG
1 TTAAAAAG
1352211 TTACTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.31
20 10 0.38
21 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (20 bp):
TTAAAAAGAAGTAGATAGTT
Found at i:1352733 original size:2 final size:2
Alignment explanation
Indices: 1352726--1352762 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1352716 TAAATAGTGC
1352726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1352763 AAGCTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1353534 original size:68 final size:65
Alignment explanation
Indices: 1353462--1353606 Score: 157
Period size: 69 Copynumber: 2.1 Consensus size: 65
1353452 TTAAAAAAAA
*
1353462 AAAAAAAGAGTGGCCAAACATAAATATAC-CTTATTTTGAAATAATAATGCAAAATATTTCAAAA
1 AAAAAAAGAG-GGCC-AACATAAATAT-CTCTTATTTTCAAATAATAATGCAAAATA-TTCAAAA
1353526 AATT
62 AATT
* * **
1353530 AAAAAAATTTAAGGGCCAACATAAATATCTCTTATTTTCAAATAATAATGTAAGGTATTCAAAAA
1 AAAAAAA---GAGGGCCAACATAAATATCTCTTATTTTCAAATAATAATGCAAAATATTCAAAAA
*
1353595 CTT
63 ATT
*
1353598 TAAAAAAGA
1 AAAAAAAGA
1353607 AAAAAAAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
65 1 0.02
68 24 0.37
69 34 0.52
70 4 0.06
71 2 0.03
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (65 bp):
AAAAAAAGAGGGCCAACATAAATATCTCTTATTTTCAAATAATAATGCAAAATATTCAAAAAATT
Found at i:1356246 original size:166 final size:165
Alignment explanation
Indices: 1356032--1356440 Score: 486
Period size: 166 Copynumber: 2.5 Consensus size: 165
1356022 TAAAATTCAA
*
1356032 TATTATTTAATTCATATTAAACTT-GTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGAATTT
1 TATTATTTATTTCATATTAAA-TTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGAATTT
*** * * * **
1356096 TTTTCTTGAAATTTTTCTGT-TTTCAAAATACA-AAGTTTTCTACTTCGTATATCTTTTCGGGGA
65 TTTTCTTGAAATTCCCCT-TATCTCAAAA-A-AGAAGTTTTCTACTTCATAAAT-TTTTCAAGGA
* *
1356159 GATTTTTCTTGGTTTTTAATTTTT-AAATCCATCAAATGT
126 GATTTTTCTTAGTTTTTAATTTTTAAAATCCATCAAATAT
* * * * ** * *
1356198 TGTTATTTATTTTATGTTAAATTAGTTTTCAGAAATTTGTTTATTTTCATGAGTTTTTAAATTTT
1 TATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGAATTTT
* * *
1356263 TTTCCTTGAAATTCCCCTTAATCTGAAAAAAGAATTTTTCTGCTTCATAAATTTTTCAAGGAGAT
66 TTT-CTTGAAATTCCCCTT-ATCTCAAAAAAGAAGTTTTCTACTTCATAAATTTTTCAAGGAGAT
*
1356328 TTTTCTTAGTTTTTAATTTTTAAAATCTATCAAATAT
129 TTTTCTTAGTTTTTAATTTTTAAAATCCATCAAATAT
* *
1356365 TATTATTTATTTCATATTAAATTAGCTTTCAAAAATTCATTCATGTTCATGAGTTTTTG-ATTTT
1 TATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGAATTTT
1356429 TTTCTTTGAAAT
66 TTTC-TTGAAAT
1356441 CTCTTTTTTC
Statistics
Matches: 203, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
165 3 0.01
166 104 0.51
167 90 0.44
168 6 0.03
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (165 bp):
TATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGAATTTT
TTTCTTGAAATTCCCCTTATCTCAAAAAAGAAGTTTTCTACTTCATAAATTTTTCAAGGAGATTT
TTCTTAGTTTTTAATTTTTAAAATCCATCAAATAT
Found at i:1356515 original size:167 final size:163
Alignment explanation
Indices: 1355970--1356530 Score: 467
Period size: 166 Copynumber: 3.4 Consensus size: 163
1355960 TAAATTACGG
* * * *
1355970 AGTTTTCT-TCTCTGTAAGTTTTTTGAGAGGATTTGTCTTGGTTTTTAATTTTTAAAA--T-TC-
1 AGTTTTCTAT-TCTATAA-TTTTTCG-GAGGATTTTTCTTAGTTTTTAATTTTTAAAATCTATCA
*
1356030 -A-A-TATTATTTAATTCATATTAAACTT-GTTTTCAAAAATTCATTCATTTTCATGAGTTTTTG
63 AATATTATTATTTATTTCATATTAAA-TTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTG
*
1356091 AATTTTTTTCTTGAAAT-T-TTTCTGTTTTC--AAAATACAA
127 -ATTTTTTTCTTGAAATCTCTTT-T-TTCTCGAAAAAT-C-A
* * *
1356129 AGTTTTCTACTTCGTAT-ATCTTTTCGGGGAGATTTTTCTTGGTTTTTAATTTTT-AAATCCATC
1 AGTTTTCTA-TTC-TATAAT-TTTTCGGAG-GATTTTTCTTAGTTTTTAATTTTTAAAATCTATC
* * * * * ** *
1356192 AAATGTTGTTATTTATTTTATGTTAAATTAGTTTTCAGAAATTTGTTTATTTTCATGAGTTTTTA
62 AAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTT-
* * * ** **
1356257 AATTTTTTTCCTTGAAATTCCCCTTAATCT-GAAAAAAGA
126 GATTTTTTT-CTTGAAA-TCTCTTTTTTCTCGAAAAATCA
* *
1356296 ATTTTTCTGCTTC-ATAAATTTTTCAAGGA-GATTTTTCTTAGTTTTTAATTTTTAAAATCTATC
1 AGTTTTCT-ATTCTAT-AATTTTTC--GGAGGATTTTTCTTAGTTTTTAATTTTTAAAATCTATC
* *
1356359 AAATATTATTATTTATTTCATATTAAATTAGCTTTCAAAAATTCATTCATGTTCATGAGTTTTTG
62 AAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTG
1356424 ATTTTTTTCTTTGAAATCTCTTTTTTCTCGAAAAATCA
127 ATTTTTTTC-TTGAAATCTCTTTTTTCTCGAAAAATCA
* ** *
1356462 AGTTTTCTATTCTATGAATATTTTCGGTAGGACTTTTT-TTAGTGTAAAATTTTTAAAATGTATC
1 AGTTTTCTATTCTAT-AAT-TTTTCGG-AGGA-TTTTTCTTAGTTTTTAATTTTTAAAATCTATC
*
1356526 TAATA
62 AAATA
1356531 ATGTCATGGA
Statistics
Matches: 317, Mismatches: 52, Indels: 58
0.74 0.12 0.14
Matches are distributed among these distances:
159 14 0.04
160 31 0.10
161 3 0.01
162 2 0.01
164 1 0.00
165 18 0.06
166 117 0.37
167 115 0.36
168 10 0.03
169 4 0.01
170 2 0.01
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (163 bp):
AGTTTTCTATTCTATAATTTTTCGGAGGATTTTTCTTAGTTTTTAATTTTTAAAATCTATCAAAT
ATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTGATTT
TTTTCTTGAAATCTCTTTTTTCTCGAAAAATCA
Found at i:1357882 original size:20 final size:20
Alignment explanation
Indices: 1357845--1357892 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1357835 ACATTTTCAA
*
1357845 AAATAAATCAAAGTAAAATT
1 AAATAAATCAAAGTAAAAAT
1357865 AAATAAATCAAA-TAAAAAAT
1 AAATAAATCAAAGT-AAAAAT
*
1357885 GAATAAAT
1 AAATAAAT
1357893 ATTCTTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (20 bp):
AAATAAATCAAAGTAAAAAT
Found at i:1363625 original size:43 final size:43
Alignment explanation
Indices: 1363577--1363713 Score: 121
Period size: 43 Copynumber: 3.3 Consensus size: 43
1363567 CATTGAGTAA
*
1363577 TGTATCAATACATTTCCTTGGTAGTAGCTTTGTAGCGATACAT
1 TGTATCGATACATTTCCTTGGTAGTAGCTTTGTAGCGATACAT
* * *
1363620 TGTATCGATACA--ACACTTATGTATCGATA-CATTG-A--G-TA-A-
1 TGTATCGATACATTTC-CTT-GGTA--G-TAGCTTTGTAGCGATACAT
*
1363659 TGTATCGATACATTTCCTTGGCAGTAGCTTTGTAGCGATACAT
1 TGTATCGATACATTTCCTTGGTAGTAGCTTTGTAGCGATACAT
1363702 TGTATCGATACA
1 TGTATCGATACA
1363714 ACACTTATGT
Statistics
Matches: 72, Mismatches: 8, Indels: 28
0.67 0.07 0.26
Matches are distributed among these distances:
36 2 0.03
37 5 0.07
38 1 0.01
39 14 0.19
40 5 0.07
41 6 0.08
42 5 0.07
43 26 0.36
44 1 0.01
45 5 0.07
46 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (43 bp):
TGTATCGATACATTTCCTTGGTAGTAGCTTTGTAGCGATACAT
Found at i:1363656 original size:82 final size:82
Alignment explanation
Indices: 1363556--1363735 Score: 333
Period size: 82 Copynumber: 2.2 Consensus size: 82
1363546 TATCGATACA
* *
1363556 ATGTATTGATACATTGAGTAATGTATCAATACATTTCCTTGGTAGTAGCTTTGTAGCGATACATT
1 ATGTATCGATACATTGAGTAATGTATCAATACATTTCCTTGGCAGTAGCTTTGTAGCGATACATT
1363621 GTATCGATACAACACTT
66 GTATCGATACAACACTT
*
1363638 ATGTATCGATACATTGAGTAATGTATCGATACATTTCCTTGGCAGTAGCTTTGTAGCGATACATT
1 ATGTATCGATACATTGAGTAATGTATCAATACATTTCCTTGGCAGTAGCTTTGTAGCGATACATT
1363703 GTATCGATACAACACTT
66 GTATCGATACAACACTT
1363720 ATGTATCGATACATTG
1 ATGTATCGATACATTG
1363736 TATCGATACA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 95 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (82 bp):
ATGTATCGATACATTGAGTAATGTATCAATACATTTCCTTGGCAGTAGCTTTGTAGCGATACATT
GTATCGATACAACACTT
Found at i:1363710 original size:13 final size:13
Alignment explanation
Indices: 1363688--1363777 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
1363678 GGCAGTAGCT
*
1363688 TTGTAGCGATACA
1 TTGTATCGATACA
1363701 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
1363717 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1363733 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
1363749 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1363765 TTGTATCGATACA
1 TTGTATCGATACA
1363778 ACACTTATGT
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 30 0.47
14 2 0.03
16 12 0.19
18 2 0.03
19 18 0.28
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1363726 original size:19 final size:19
Alignment explanation
Indices: 1363702--1363796 Score: 106
Period size: 19 Copynumber: 5.6 Consensus size: 19
1363692 AGCGATACAT
1363702 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1363721 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1363734 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1363753 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1363766 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1363785 TGTATCGATACA
1 TGTATCGATACA
1363797 GTTACTGTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 18 0.28
14 2 0.03
16 12 0.19
18 2 0.03
19 30 0.47
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1363735 original size:32 final size:32
Alignment explanation
Indices: 1363689--1363796 Score: 207
Period size: 32 Copynumber: 3.4 Consensus size: 32
1363679 GCAGTAGCTT
*
1363689 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1363721 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1363753 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1363785 TGTATCGATACA
1 TGTATCGATACA
1363797 GTTACTGTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 75 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:1364730 original size:48 final size:48
Alignment explanation
Indices: 1364562--1365698 Score: 733
Period size: 48 Copynumber: 24.7 Consensus size: 48
1364552 GAAGAATGCT
* * **
1364562 AATATGCTGATTCAAGGCCAACGACTTTGGGTTTCAAAGATGACGAAGATGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGATGA-G--G-TGCC
*
1364615 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-AGGTGCC
** *
1364664 AATGCGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGATGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * *
1364712 AATATACTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGGTTGAGGTGCT
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA----TGAGGTGCC
* * * * * * * *
1364764 GATGTGCTGATTGAAGGCCAACGACATCGGTCTTAAAGATAAAGATGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-GAGGTGCC
* * *
1364813 AATATGCTGATTCAAGGCCAGCGATACTGGGC-T-----T---GTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * * **
1364852 AATGTGCTGATTTAAGGCCAGCGACATTAGTCTTAAAGACAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* *
1364900 AATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T-A--TGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * * ** *
1364939 AATGTGCTGATTTAAGGCCAGCGACATTAGTCTTAAAGACAAGGTGTC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* *
1364987 AATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T-A--TGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * *
1365026 AATGTGCTGATTCAAGGCCAACGACATCGGACTT--A-A--AGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * ** *
1365069 AATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGGTGCG
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* *
1365117 AATATGCTGATTCAAGGCCAGCGATATTGGAC-TCAAGATGGAAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G---AGGTGCC
* * * *
1365168 AATATGTTGATTCAAGGCTAGCGATATTGGAC-T-----T---GTGCT
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * **
1365207 AATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
** * * *
1365255 AATATGCTGATTCAAGGCCAAAGATATTGGAC-TCAAGATAGAAAATGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G---AGGTGCC
* *
1365306 AATATGCTGATTCAAGGCCAACGATATTGGACTT--A-AT--GGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * *
1365349 AATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATGAAGATGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-AGGTGCC
* * *
1365398 AATGTGCTGATTCAAGGCCAGCGATATTGGGC-T-----T---GTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * **
1365437 AATATGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
*
1365485 AATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-GAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * *
1365528 AATATGCTGATTCAAGGCTAGCGACGTTGGTCTTAAAGATGAAGATGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-AGGTGCC
* * * *
1365577 AATGTGCTGATTCAAGGCCAGCGATACTGGGC-T-----T---GTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * * **
1365616 AATGTGTTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* *
1365664 AATATGCTGATTCAAGGCCAACGATATTGGACTTA
1 AATATGCTGATTCAAGGCCAGCGACATTGGACTTA
1365699 GAGGAAGATG
Statistics
Matches: 855, Mismatches: 147, Indels: 169
0.73 0.13 0.14
Matches are distributed among these distances:
39 184 0.22
40 6 0.01
41 3 0.00
43 108 0.13
44 1 0.00
45 2 0.00
46 5 0.01
47 13 0.02
48 241 0.28
49 139 0.16
50 2 0.00
51 74 0.09
52 47 0.05
53 30 0.04
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (48 bp):
AATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
Found at i:1364863 original size:39 final size:40
Alignment explanation
Indices: 1364809--1365092 Score: 153
Period size: 39 Copynumber: 6.7 Consensus size: 40
1364799 AAGATAAAGA
* *
1364809 TGCCAATATGCTGATTCAAGGCCAGCGATACT-GGGCTTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATACTAGGACTTG
* * **
1364848 TGCCAATGTGCTGATTTAAGGCCAGCGACATTAGTCTTAAAGACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCG--A-TA--C-T-AGGAC-TTG
* * * *
1364896 TGCCAATATGCTGATTCAAGGCCAGCGATA-TTGGGCTTA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATACTAGGACTTG
* * **
1364935 TGCCAATGTGCTGATTTAAGGCCAGCGACATTAGTCTTAAAGACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCG--A-TA--C-T-AGGAC-TTG
* * * * *
1364983 TGTCAATATGCTGATTCAAGGCCAGCGATA-TTGGGCTTA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATACTAGGACTTG
* * *
1365022 TGCCAATGTGCTGATTCAAGGCCAACGACA-TCGGACTTAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATACTAGGACTT----G
*
1365065 TGCCAATGTGCTGATTCAAGGCTAGCGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGA
1365093 CATTGGTCTT
Statistics
Matches: 183, Mismatches: 40, Indels: 40
0.70 0.15 0.15
Matches are distributed among these distances:
39 82 0.45
40 4 0.02
41 4 0.02
42 4 0.02
43 26 0.14
44 1 0.01
45 5 0.03
46 3 0.02
47 4 0.02
48 50 0.27
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (40 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGATACTAGGACTTG
Found at i:1365231 original size:268 final size:272
Alignment explanation
Indices: 1364848--1365696 Score: 806
Period size: 268 Copynumber: 3.1 Consensus size: 272
1364838 ACTGGGCTTG
* * * * * * *
1364848 TGCCAATGTGCTGATTTAAGGCCAGCGACATTAGTCTTAA-A--GACAAGGTGCCAATATGCTGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGAAAAGGTGCCAATATGCTGA
* *
1364910 TTCAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTTAAGGCCAGCGACATTAGTCTTAA
66 TTCAAGGCCAGCGATATTGGACTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAA
* ** * *
1364975 AGACAAGGTGTCAATATGCTGATTCAAGGCCAGCGATATTGGGCT-T-A-TGCCAATGTGCTGAT
131 AGACAAGGTGCCAATATGCTGATTCAAGGCCAAAGATATTGGACTATAAGTGCCAATATGCTGAT
1365037 TCAAGGCCAACGACATCGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCT
196 TCAAGGCCAACGACATCGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCT
*
1365102 TAAAGA-CAAGG
261 TAAAGATCAAGA
* *
1365113 TGCGAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGAAAAGGTGCCAATATGTTGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGAAAAGGTGCCAATATGCTGA
* * * * *
1365178 TTCAAGGCTAGCGATATTGGACTTGTGCTAATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAA
66 TTCAAGGCCAGCGATATTGGACTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAA
1365243 AGACAAGGTGCCAATATGCTGATTCAAGGCCAAAGATATTGGACTCAAGATAGAAAATGTGCCAA
131 AGACAAGGTGCCAATATGCTGATTCAAGGCCAAAGATATTGGACT----AT----AA-GTGCCAA
* * *
1365308 TATGCTGATTCAAGGCCAACGATATTGGACTTAATGGTGCCAATGTGCTGATTCAAGGCTAGCGA
187 TATGCTGATTCAAGGCCAACGACATCGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGA
*
1365373 CATTGGTCTTAAAGATGAAGA
252 CATTGGTCTTAAAGATCAAGA
* *
1365394 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCT-----T-------GTGCCAATATGCTGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGAAAAGGTGCCAATATGCTGA
* * * * *
1365447 TTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
66 TTCAAGGCCAGCGATATTGGACTT-------A--TGCCAATGTGCTGATTCAAGGCCAGCGACAT
* * * ** ** *
1365512 TGGACTT--AG---AGGTGCCAATATGCTGATTCAAGGCTAGCGACGTTGGTCTTAAAGATGAAG
122 TAGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAAAGATATTGGAC-T----AT-AAG
* * * * *
1365572 ATGCCAATGTGCTGATTCAAGGCCAGCGATA-CTGGGCTT----GTGCCAATGTGTTGATTCAAG
181 -TGCCAATATGCTGATTCAAGGCCAACGACATC-GGACTTAAAGGTGCCAATGTGCTGATTCAAG
*
1365632 G-TCAGCGACATTGGTCTTAAAGA-CAAGG
244 GCT-AGCGACATTGGTCTTAAAGATCAAGA
*
1365660 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
1365697 TAGAGGAAGA
Statistics
Matches: 497, Mismatches: 58, Indels: 57
0.81 0.09 0.09
Matches are distributed among these distances:
265 33 0.07
266 39 0.08
267 41 0.08
268 118 0.24
269 34 0.07
270 1 0.00
271 35 0.07
273 34 0.07
274 6 0.01
276 3 0.01
278 34 0.07
280 82 0.16
281 37 0.07
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (272 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGAAAAGGTGCCAATATGCTGA
TTCAAGGCCAGCGATATTGGACTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAA
AGACAAGGTGCCAATATGCTGATTCAAGGCCAAAGATATTGGACTATAAGTGCCAATATGCTGAT
TCAAGGCCAACGACATCGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCT
TAAAGATCAAGA
Found at i:1365244 original size:138 final size:135
Alignment explanation
Indices: 1365022--1365696 Score: 698
Period size: 138 Copynumber: 4.9 Consensus size: 135
1365012 ATTGGGCTTA
* * * *
1365022 TGCCAATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-GTGCCAATGTGCTGATTCAAGGC
*
1365087 TAGCGACATTGGTCTTAAAGACAAGGTGCGAATATGCTGATTCAAGGCCAGCGATATTGGACTCA
63 -AGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCA
1365152 AGATGGAAAAGG
127 AGAT-G--AAGG
* * *
1365164 TGCCAATATGTTGATTCAAGGCTAGCGATATTGGACTT-GTGCTAATGTGCTGATTCAAGGTCAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGG-CAG
**
1365228 CGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAAAGATATTGGACTCAAGA
65 CGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAGA
*
1365293 TAGAAAATG
130 T-G--AAGG
*
1365302 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAATGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A--GTGCCAATGTGCTGATTCAAGGC
* * * *
1365367 TAGCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCT-
63 -AGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTC
1365431 ----T----G
126 AAGATGAAGG
* * * *
1365433 TGCCAATATGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-------A-GTGCCAATGTGCTGATTC
* * * **
1365498 AAGGCCAGCGATATTGGACTT--AG---AGGTGCCAATATGCTGATTCAAGGCTAGCGACGTTGG
58 AAGG-CAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
* * *
1365558 TCTTAAAGATGAAGA
122 AC-TCAAGATGAAGG
* * * *
1365573 TGCCAATGTGCTGATTCAAGGCCAGCGATACTGGGCTT-GTGCCAATGTGTTGATTCAAGGTCAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGG-CAG
*
1365637 CGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACT
65 CGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
1365697 TAGAGGAAGA
Statistics
Matches: 453, Mismatches: 51, Indels: 65
0.80 0.09 0.11
Matches are distributed among these distances:
130 33 0.07
131 70 0.15
133 2 0.00
134 2 0.00
135 1 0.00
136 70 0.15
137 3 0.01
138 128 0.28
139 1 0.00
140 33 0.07
141 1 0.00
142 73 0.16
143 36 0.08
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (135 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGGCAGC
GACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTCAAGAT
GAAGG
Found at i:1365287 original size:87 final size:87
Alignment explanation
Indices: 1364765--1365284 Score: 591
Period size: 87 Copynumber: 5.9 Consensus size: 87
1364755 TGAGGTGCTG
* * * * *
1364765 ATGTGCTGATTGAAGGCCAACGACATCGGTCTTAAAGATAAAGATGCCAATATGCTGATTCAAGG
1 ATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATTCAAGG
*
1364830 CCAGCGATACTGGGCTTGTGCCA
65 CCAGCGATATTGGGCTTGTGCCA
* *
1364853 ATGTGCTGATTTAAGGCCAGCGACATTAGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGC
1 ATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGC
*
1364918 CAGCGATATTGGGCTTATGCCA
66 CAGCGATATTGGGCTTGTGCCA
* * *
1364940 ATGTGCTGATTTAAGGCCAGCGACATTAGTCTTAAAGACAAGGTGTCAATATGCTGATTCAAGGC
1 ATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGC
*
1365005 CAGCGATATTGGGCTTATGCCA
66 CAGCGATATTGGGCTTGTGCCA
* * * *
1365027 ATGTGCTGATTCAAGGCCAACGACATCGGACTT----A-AAGGTGCCAATGTGCTGATTCAAGGC
1 ATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGC
* * * *
1365087 TAGCGACATTGGTCTTAAAGACAAGGTGCGA
66 CAGCGATATTGGGCTT---------GTGCCA
* * * * * *
1365118 ATATGCTGATTCAAGGCCAGCGATATTGGACTCAAGATGGAAAAGGTGCCAATATGTTGATTCAA
1 ATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAA-A--GACAAGGTGCCAATATGCTGATTCAA
* * *
1365183 GGCTAGCGATATTGGACTTGTGCTA
63 GGCCAGCGATATTGGGCTTGTGCCA
*
1365208 ATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGC
1 ATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGC
**
1365273 CAAAGATATTGG
66 CAGCGATATTGG
1365285 ACTCAAGATA
Statistics
Matches: 374, Mismatches: 41, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
82 37 0.10
83 1 0.00
87 195 0.52
88 34 0.09
89 1 0.00
90 35 0.09
91 32 0.09
98 1 0.00
99 38 0.10
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (87 bp):
ATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGC
CAGCGATATTGGGCTTGTGCCA
Found at i:1365448 original size:39 final size:40
Alignment explanation
Indices: 1365394--1365650 Score: 176
Period size: 39 Copynumber: 6.0 Consensus size: 40
1365384 AAGATGAAGA
* *
1365394 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT-G
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAG
* *
1365433 TGCCAATATGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT-------A-G
* *
1365481 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT--A-G
* * *
1365524 TGCCAATATGCTGATTCAAGGCTAGCGACGTTGGTCTTAAAGATGAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGC-T-----T--AG
* * *
1365572 ATGCCAATGTGCTGATTCAAGGCCAGCGATACTGGGCTT-G
1 -TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAG
* * * *
1365612 TGCCAATGTGTTGATTCAAGGTCAGCGACATTGGTCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA
1365651 AAGACAAGGT
Statistics
Matches: 175, Mismatches: 26, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
39 67 0.38
40 1 0.01
43 36 0.21
44 1 0.01
48 38 0.22
49 32 0.18
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (40 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAG
Found at i:1365466 original size:88 final size:88
Alignment explanation
Indices: 1365249--1365697 Score: 548
Period size: 88 Copynumber: 5.0 Consensus size: 88
1365239 TTAAAGACAA
** * * * *
1365249 GGTGCCAATATGCTGATTCAAGGCCAAAGATATTGGAC-TCAAGATAGAAAATGTGCCAATATGC
1 GGTGCCAATATGCTGATTCAAGG-CAGCGACATTGGTCTTAAAGAT-GAAGA--TGCCAATATGC
*
1365313 TGATTCAAGGCCAACGATATTGGACTTAAT
62 TGATTCAAGGCCAGCGATATTGGAC-T--T
* *
1365343 GGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGA
1 GGTGCCAATATGCTGATTCAAGGC-AGCGACATTGGTCTTAAAGATGAAGATGCCAATATGCTGA
*
1365408 TTCAAGGCCAGCGATATTGGGCTT
65 TTCAAGGCCAGCGATATTGGACTT
* *
1365432 -GTGCCAATATGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGA
1 GGTGCCAATATGCTGATTCAAGG-CAGCGACATTGGTCTTAAAGATGAAGATGCCAATATGCTGA
1365495 TTCAAGGCCAGCGATATTGGACTT
65 TTCAAGGCCAGCGATATTGGACTT
* *
1365519 AGAGGTGCCAATATGCTGATTCAAGGCTAGCGACGTTGGTCTTAAAGATGAAGATGCCAATGTGC
1 ---GGTGCCAATATGCTGATTCAAGGC-AGCGACATTGGTCTTAAAGATGAAGATGCCAATATGC
* *
1365584 TGATTCAAGGCCAGCGATACTGGGCTT
62 TGATTCAAGGCCAGCGATATTGGACTT
* * * *
1365611 -GTGCCAATGTGTTGATTCAAGGTCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGA
1 GGTGCCAATATGCTGATTCAAGG-CAGCGACATTGGTCTTAAAGATGAAGATGCCAATATGCTGA
*
1365674 TTCAAGGCCAACGATATTGGACTT
65 TTCAAGGCCAGCGATATTGGACTT
1365698 AGAGGAAGAT
Statistics
Matches: 315, Mismatches: 30, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
87 76 0.24
88 80 0.25
89 3 0.01
90 1 0.00
91 42 0.13
92 71 0.23
93 1 0.00
94 35 0.11
95 6 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (88 bp):
GGTGCCAATATGCTGATTCAAGGCAGCGACATTGGTCTTAAAGATGAAGATGCCAATATGCTGAT
TCAAGGCCAGCGATATTGGACTT
Found at i:1365512 original size:179 final size:179
Alignment explanation
Indices: 1365250--1365702 Score: 737
Period size: 179 Copynumber: 2.5 Consensus size: 179
1365240 TAAAGACAAG
* ** * * * * *
1365250 GTGCCAATATGCTGATTCAAGGCCAAAGATATTGGACTCAAGATAGAAAATGTGCCAATATGCTG
1 GTGCCAATATGCTGATTCAAGGTCAGCGACATTGGTCT-TA-A-AGACAAGGTGCCAATATGCTG
*
1365315 ATTCAAGGCCAACGATATTGGACTTA-ATGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGG
63 ATTCAAGGCCAACGATATTGGACTTAGA-GGTGCCAATATGCTGATTCAAGGCTAGCGACATTGG
*
1365379 TCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
127 TCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGATACTGGGCTT
1365432 GTGCCAATATGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATATGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* *
1365497 CAAGGCCAGCGATATTGGACTTAGAGGTGCCAATATGCTGATTCAAGGCTAGCGACGTTGGTCTT
66 CAAGGCCAACGATATTGGACTTAGAGGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGTCTT
1365562 AAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGATACTGGGCTT
131 AAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGATACTGGGCTT
* *
1365611 GTGCCAATGTGTTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATATGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1365676 CAAGGCCAACGATATTGGACTTAGAGG
66 CAAGGCCAACGATATTGGACTTAGAGG
1365703 AAGATGCCAC
Statistics
Matches: 255, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
179 219 0.86
180 2 0.01
181 1 0.00
182 33 0.13
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (179 bp):
GTGCCAATATGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
CAAGGCCAACGATATTGGACTTAGAGGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGTCTT
AAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGATACTGGGCTT
Found at i:1365778 original size:28 final size:28
Alignment explanation
Indices: 1365715--1365875 Score: 164
Period size: 28 Copynumber: 5.6 Consensus size: 28
1365705 GATGCCACCA
**
1365715 ACTTGTGTGGGCTTTTGAAAGGGTTG-CACCA
1 ACTTGTGT--GCTTTTG-AA-GGTTGCCACTG
*
1365746 ACTTGTGTGCTTTTGAAGGTTGCCATTG
1 ACTTGTGTGCTTTTGAAGGTTGCCACTG
* **
1365774 ACTTGTGTGCTTTTAAAGGTTGTGACTG
1 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1365802 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGTGCTTTTGAAGGTTGCCACTG
* * *
1365830 ACTTGTGGGC-TTTGAAAGGGGTGCCACCG
1 ACTTGTGTGCTTTTG-AA-GGTTGCCACTG
*
1365859 ACTTGTGGGCTTTTGAA
1 ACTTGTGTGCTTTTGAA
1365876 AAGAGTGCCA
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.08
28 64 0.57
29 28 0.25
30 4 0.04
31 8 0.07
ACGTcount: A:0.17, C:0.16, G:0.31, T:0.37
Consensus pattern (28 bp):
ACTTGTGTGCTTTTGAAGGTTGCCACTG
Found at i:1365810 original size:56 final size:56
Alignment explanation
Indices: 1365720--1365875 Score: 206
Period size: 56 Copynumber: 2.8 Consensus size: 56
1365710 CACCAACTTG
* * *
1365720 TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGTGCTTTTGAAGGTTGCCATTGACT
1 TGTGGGC-TTTGAAAGGGGTGCACCGACTTGTGTGCTTTTGAAGGTTGCCACTGACT
* * * *
1365777 TGTGTGCTTTTAAAGGTTGTG-ACTGACTTGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGG-GGTGCACCGACTTGTGTGCTTTTGAAGGTTGCCACTGACT
*
1365833 TGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGCTTTTGAA
1 TGTGGGCTTTGAAAGGGGTG-CACCGACTTGTGTGCTTTTGAA
1365876 AAGAGTGCCA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
55 3 0.04
56 54 0.64
57 27 0.32
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.37
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGGGTGCACCGACTTGTGTGCTTTTGAAGGTTGCCACTGACT
Found at i:1365918 original size:34 final size:34
Alignment explanation
Indices: 1365874--1365972 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 34
1365864 TGGGCTTTTG
*
1365874 AAAAGAGTGCCACTA-ACTTATGGGCTTAAAAAGA
1 AAAAGAGTGCCAC-AGACTTATGGACTTAAAAAGA
* *
1365908 AAAAGGGTGCCACAGAGTTATGGACTTAAAAAGA
1 AAAAGAGTGCCACAGACTTATGGACTTAAAAAGA
* * * *
1365942 AAAAAAGTACCACGGAGC-TGTGGACTTAAAA
1 AAAAGAGTGCCACAGA-CTTATGGACTTAAAA
1365973 GGGTGCCTCG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 1 0.02
34 53 0.98
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.18
Consensus pattern (34 bp):
AAAAGAGTGCCACAGACTTATGGACTTAAAAAGA
Found at i:1365977 original size:61 final size:61
Alignment explanation
Indices: 1365908--1366060 Score: 225
Period size: 61 Copynumber: 2.5 Consensus size: 61
1365898 CTTAAAAAGA
*
1365908 AAAAGGGTGCCACAGAGTTATGGACTTAAAAAGAAAAAAAGTACCACGGAGCTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAAAGTACCACGGAGCTGTGGACTT
* * * * * * *
1365969 AAAAGGGTGCCTCGGAGCTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAAAGTACCACGGAGCTGTGGACTT
*
1366030 AAAAGGGTGCCACAGAGTCGTGGACTTAAAA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAA
1366061 GGGTGCCACA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 80 1.00
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.18
Consensus pattern (61 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAAAAAGTACCACGGAGCTGTGGACTT
Done.