Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 139 of 168
Found at i:40729416 original size:30 final size:31
Alignment explanation
Indices: 40729382--40729441 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
40729372 AAACCTTTTA
*
40729382 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
40729412 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
40729442 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:40740175 original size:18 final size:19
Alignment explanation
Indices: 40740152--40740201 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
40740142 TTAAAATTTA
40740152 TTTAATAATTTTATAT-AT
1 TTTAATAATTTTATATAAT
40740170 TTTAATAATATTT-TATAAT
1 TTTAATAAT-TTTATATAAT
40740189 TTT-ATAAATTTTA
1 TTTAAT-AATTTTA
40740202 AAGAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATAATTTTATATAAT
Found at i:40740181 original size:28 final size:28
Alignment explanation
Indices: 40740124--40740203 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
40740114 GGACTTAGAT
40740124 TTTAATTAATTTT-TAT-TTTTAAAATTTA
1 TTTAA-TAATTTTATATATTTTAAAA-TTA
40740152 TTTAATAATTTTATATATTTTAATAA-TA
1 TTTAATAATTTTATATATTTTAA-AATTA
* *
40740180 TTTTATAATTTTATAAATTTTAAA
1 TTTAATAATTTTATATATTTTAAA
40740204 GAAAAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
27 8 0.17
28 31 0.66
29 6 0.13
30 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTAATAATTTTATATATTTTAAAATTA
Found at i:40741518 original size:9 final size:8
Alignment explanation
Indices: 40741492--40741591 Score: 58
Period size: 8 Copynumber: 11.6 Consensus size: 8
40741482 TATTTTTTTT
40741492 AAATTTAA
1 AAATTTAA
40741500 AAATTTAA
1 AAATTTAA
40741508 AAATTTAA
1 AAATTTAA
* *
40741516 AAAATTAT
1 AAATTTAA
40741524 AAATCATTAA
1 AAAT--TTAA
* *
40741534 TATTATTAA
1 AAAT-TTAA
40741543 ATAA-TTATA
1 A-AATTTA-A
40741552 AAATTATAAA
1 AAATT-T-AA
*
40741562 AAAATTAA
1 AAATTTAA
* *
40741570 TATTTTAA
1 AAATTTAA
40741578 AAATTTTAA
1 AAA-TTTAA
40741587 AAATT
1 AAATT
40741592 AATTGAATAT
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
8 40 0.57
9 17 0.24
10 12 0.17
11 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
AAATTTAA
Found at i:40741543 original size:35 final size:35
Alignment explanation
Indices: 40741503--40741592 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 35
40741493 AATTTAAAAA
**
40741503 TTTAAAAATTTAAAAAATTAT-AAATCATTAATAT
1 TTTAAAAATTTAAAAAATTATAAAAAAATTAATAT
*
40741537 TATTAAATAA-TTATAAAATTATAAAAAAATTAATAT
1 T-TTAAA-AATTTAAAAAATTATAAAAAAATTAATAT
*
40741573 TTTAAAAATTTTAAAAATTA
1 TTTAAAAATTTAAAAAATTA
40741593 ATTGAATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
34 3 0.06
35 30 0.64
36 14 0.30
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
TTTAAAAATTTAAAAAATTATAAAAAAATTAATAT
Found at i:40741586 original size:17 final size:17
Alignment explanation
Indices: 40741530--40741586 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
40741520 TTATAAATCA
40741530 TTAATATTATTAAATAATT
1 TTAATATT-TTAAA-AATT
* * * **
40741549 ATAAAATTATAAAAAAA
1 TTAATATTTTAAAAATT
40741566 TTAATATTTTAAAAATT
1 TTAATATTTTAAAAATT
40741583 TTAA
1 TTAA
40741587 AAATTAATTG
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
17 18 0.64
18 4 0.14
19 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAATATTTTAAAAATT
Found at i:40751274 original size:18 final size:17
Alignment explanation
Indices: 40751248--40751283 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40751238 GTAAAGTAAT
40751248 AATACGATAATAAGAATA
1 AATACGATAATAA-AATA
*
40751266 AATATGATAATAAAATA
1 AATACGATAATAAAATA
40751283 A
1 A
40751284 CAATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (17 bp):
AATACGATAATAAAATA
Found at i:40751761 original size:19 final size:20
Alignment explanation
Indices: 40751715--40751761 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
40751705 CTATTACTCT
*
40751715 AAACAGAAA-AGAAAAGAAA
1 AAACATAAAGAGAAAAGAAA
*
40751734 AAAGATAAAGAGAAAA-AAA
1 AAACATAAAGAGAAAAGAAA
*
40751753 AAACCTAAA
1 AAACATAAA
40751762 AATCTAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.04
Consensus pattern (20 bp):
AAACATAAAGAGAAAAGAAA
Found at i:40755006 original size:18 final size:18
Alignment explanation
Indices: 40754985--40755021 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40754975 ATTTATATTT
40754985 TTTAAAAAATTATAAAAA
1 TTTAAAAAATTATAAAAA
*
40755003 TTTAAAAAATTCTAAAAA
1 TTTAAAAAATTATAAAAA
40755021 T
1 T
40755022 ATATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATTATAAAAA
Found at i:40755053 original size:8 final size:9
Alignment explanation
Indices: 40754985--40755050 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 9
40754975 ATTTATATTT
40754985 TTTAAAAAA
1 TTTAAAAAA
40754994 -TTATAAAAA
1 TTTA-AAAAA
40755003 TTTAAAAAA
1 TTTAAAAAA
40755012 TTCTAAAAATA
1 TT-TAAAAA-A
40755023 TATATAAATAAA
1 T-T-TAAA-AAA
*
40755035 GTT-AAAAA
1 TTTAAAAAA
40755043 TTTAAAAA
1 TTTAAAAA
40755051 TTTTCTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
8 8 0.17
9 18 0.38
10 10 0.21
11 3 0.06
12 6 0.13
13 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:40759585 original size:3 final size:3
Alignment explanation
Indices: 40759577--40759613 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
40759567 GAGGACATGG
*
40759577 GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
40759614 TGAATGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:40760688 original size:23 final size:22
Alignment explanation
Indices: 40760654--40760704 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
40760644 TCATGCAGAT
40760654 TTTTTTTATTAA-AACCATTTACA
1 TTTTTTTATTAATAACCA-TTA-A
* *
40760677 TTTTTTTGTTAATAATCATTAA
1 TTTTTTTATTAATAACCATTAA
40760699 TTTTTT
1 TTTTTT
40760705 ACATTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.28
23 14 0.56
24 4 0.16
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTTTATTAATAACCATTAA
Found at i:40760779 original size:6 final size:6
Alignment explanation
Indices: 40760768--40760798 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
40760758 TAAATTAATG
40760768 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
40760799 ATGTGTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:40761089 original size:16 final size:16
Alignment explanation
Indices: 40761068--40761098 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40761058 AAAATTAATA
40761068 AACAAAATTTAAAAAT
1 AACAAAATTTAAAAAT
40761084 AACAAAATTTAAAAA
1 AACAAAATTTAAAAA
40761099 AGTTGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AACAAAATTTAAAAAT
Found at i:40762222 original size:21 final size:21
Alignment explanation
Indices: 40762198--40762238 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40762188 TTTTCCCTCA
*
40762198 TTTTCTCTCCTTTTTCTTTTC
1 TTTTCTCTCATTTTTCTTTTC
* *
40762219 TTTTTTCTTATTTTTCTTTT
1 TTTTCTCTCATTTTTCTTTT
40762239 TCTGGACCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTCTCATTTTTCTTTTC
Found at i:40763307 original size:14 final size:14
Alignment explanation
Indices: 40763285--40763349 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
40763275 ACGAAAACGA
*
40763285 AAAAGAAAAATAAG
1 AAAATAAAAATAAG
**
40763299 AAAATAAAAA-GGG
1 AAAATAAAAATAAG
40763312 AAAATAAAAAATAA-
1 AAAAT-AAAAATAAG
40763326 AAAAT-AAAAT---
1 AAAATAAAAATAAG
40763336 AAAATAAAAATAAG
1 AAAATAAAAATAAG
40763350 GTACAAGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
10 5 0.12
11 5 0.12
12 5 0.12
13 6 0.15
14 19 0.47
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (14 bp):
AAAATAAAAATAAG
Found at i:40774223 original size:13 final size:13
Alignment explanation
Indices: 40774202--40774233 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40774192 AATATTAGTC
40774202 TTTTT-AACATAT
1 TTTTTAAACATAT
40774214 TTTTTAAACATAT
1 TTTTTAAACATAT
40774227 TTTTTAA
1 TTTTTAA
40774234 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTAAACATAT
Found at i:40774882 original size:18 final size:18
Alignment explanation
Indices: 40774832--40774883 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
40774822 ATATAGTTAC
40774832 TTTTAAAATAT-T-TA-A
1 TTTTAAAATATATATATA
* *
40774847 TTTTAAAATATCTTTATA
1 TTTTAAAATATATATATA
*
40774865 TTTTAATATATATATATA
1 TTTTAAAATATATATATA
40774883 T
1 T
40774884 ATAATTTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 11 0.35
16 1 0.03
17 2 0.06
18 17 0.55
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAAAATATATATATA
Found at i:40778301 original size:13 final size:13
Alignment explanation
Indices: 40778283--40778312 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40778273 CTGATTTATC
*
40778283 TTTTTTTTTTCCT
1 TTTTTTTTTTCAT
40778296 TTTTTTTTTTCAT
1 TTTTTTTTTTCAT
40778309 TTTT
1 TTTT
40778313 GAGAATTATT
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:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTTCAT
Found at i:40779028 original size:31 final size:31
Alignment explanation
Indices: 40778978--40779039 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
40778968 TTAATCGTGG
* * *
40778978 GTGACTAAAATTATAAAAGTATATAATGACA
1 GTGAATAAAATGATAAAAGTATATAACGACA
*
40779009 GTGAATAAAATGATTAAAGTATATAACGACA
1 GTGAATAAAATGATAAAAGTATATAACGACA
40779040 TTACTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (31 bp):
GTGAATAAAATGATAAAAGTATATAACGACA
Found at i:40781251 original size:26 final size:25
Alignment explanation
Indices: 40781212--40781260 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
40781202 TTTATGATAC
40781212 ATATACATACGCATGGCTTTTATAAT
1 ATATACATACGCAT-GCTTTTATAAT
* * *
40781238 ATATATATAGGCATTCTTTTATA
1 ATATACATACGCATGCTTTTATA
40781261 CAGTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (25 bp):
ATATACATACGCATGCTTTTATAAT
Found at i:40785002 original size:30 final size:30
Alignment explanation
Indices: 40784957--40785021 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
40784947 ACTTATTTTA
40784957 TTGTTAATTTTGTTATTATCTTAGAGGCAT
1 TTGTTAATTTTGTTATTATCTTAGAGGCAT
*
40784987 TTGTT-ATTTTCGTTATTATTTTAGAGGCAT
1 TTGTTAATTTT-GTTATTATCTTAGAGGCAT
40785017 TTGTT
1 TTGTT
40785022 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATCTTAGAGGCAT
Found at i:40787765 original size:98 final size:98
Alignment explanation
Indices: 40787596--40787790 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
40787586 ATACAATAAA
*
40787596 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
40787661 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
40787694 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
40787759 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
40787791 CATGATTTTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:40789372 original size:19 final size:19
Alignment explanation
Indices: 40789348--40789460 Score: 172
Period size: 19 Copynumber: 5.8 Consensus size: 19
40789338 AATCATATAT
40789348 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
40789367 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
40789386 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
40789407 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
40789426 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
40789445 TCTAATATTGCATATC
1 TCTAAGATTGCATATC
40789461 CTCAAAAATT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 66 0.78
21 19 0.22
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40789413 original size:40 final size:38
Alignment explanation
Indices: 40789325--40789460 Score: 164
Period size: 40 Copynumber: 3.4 Consensus size: 38
40789315 AAATTAAATC
*
40789325 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
40789367 TCTAAGATTATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGC--ATATCATA
* *
40789407 TCTAAGATTGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
40789445 TCTAATATTGCATATC
1 TCTAAGATTACATATC
40789461 CTCAAAAATT
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
38 34 0.40
39 3 0.03
40 35 0.41
41 4 0.05
42 10 0.12
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:40789415 original size:59 final size:59
Alignment explanation
Indices: 40789348--40789459 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
40789338 AATCATATAT
*
40789348 TCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTGCATATATCATA
* * *
40789407 TCTAAGATTGCATATCATATCTAGGATTGCATATCATATCTAATATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTGCATAT
40789460 CCTCAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (59 bp):
TCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTGCATATATCATA
Found at i:40789455 original size:38 final size:38
Alignment explanation
Indices: 40789341--40789460 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 38
40789331 ATTACAAAAT
*
40789341 CATAT-AT-TCTAAGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
*
40789377 TATATCATATCTAAGATTGCATATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGC--ATATCATATCTAAGATTG
* *
40789417 CATATCATATCTAGGATTGCATATCATATCTAATATTG
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTG
40789455 CATATC
1 CATATC
40789461 CTCAAAAATT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
36 4 0.05
37 2 0.03
38 34 0.45
40 35 0.47
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGATTG
Found at i:40790290 original size:22 final size:22
Alignment explanation
Indices: 40790265--40790336 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
40790255 CAACTAAACC
40790265 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
40790287 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
40790309 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
40790331 CTCATG
1 CTCATG
40790337 TTTGAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:40798456 original size:15 final size:14
Alignment explanation
Indices: 40798426--40798462 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
40798416 TAAAAATTCT
*
40798426 TTAAAATTACAAAA
1 TTAAAATTAAAAAA
40798440 TTAAAATATAAAAAA
1 TTAAAAT-TAAAAAA
40798455 TTAAAATT
1 TTAAAATT
40798463 CAATGTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
TTAAAATTAAAAAA
Found at i:40803968 original size:2 final size:2
Alignment explanation
Indices: 40803961--40803991 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40803951 TTTATCCTAT
40803961 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
40803992 CCAGGTGGAA
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:40806764 original size:21 final size:20
Alignment explanation
Indices: 40806740--40806781 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40806730 AAAACTAGAA
40806740 AAAAAAAATCAAAATGTTTAT
1 AAAAAAAATCAAAAT-TTTAT
* *
40806761 AAAAAAATTCCAAATTTTAT
1 AAAAAAAATCAAAATTTTAT
40806781 A
1 A
40806782 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAAAAATCAAAATTTTAT
Found at i:40809722 original size:17 final size:17
Alignment explanation
Indices: 40809702--40809735 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40809692 ATTTTCACAC
*
40809702 TATAATGATTTTTTTAA
1 TATAATGATTATTTTAA
*
40809719 TATAATTATTATTTTAA
1 TATAATGATTATTTTAA
40809736 AAGAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATAATGATTATTTTAA
Found at i:40812353 original size:3 final size:3
Alignment explanation
Indices: 40812345--40812372 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40812335 GAGAAAAACG
40812345 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40812373 AAGTTGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40814401 original size:30 final size:30
Alignment explanation
Indices: 40814365--40814476 Score: 179
Period size: 30 Copynumber: 3.7 Consensus size: 30
40814355 AATATCTCGG
40814365 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
40814395 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* * *
40814425 TACCCAAATCTTTGACTTTCTATTATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTGA
* *
40814455 TACCCATATATTTGATTTTCCA
1 TACCCATATCTTTGACTTTCCA
40814477 TAAATATGGA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.45
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCCAATATTTGA
Found at i:40814408 original size:15 final size:15
Alignment explanation
Indices: 40814365--40814470 Score: 65
Period size: 15 Copynumber: 7.1 Consensus size: 15
40814355 AATATCTCGG
*
40814365 TACCCATATCTTTGA
1 TACCCATATATTTGA
**
40814380 CTTTCCA-ATATTTGA
1 -TACCCATATATTTGA
*
40814395 TACCCATATCTTTGA
1 TACCCATATATTTGA
**
40814410 CTTTCCA-ATATTTGA
1 -TACCCATATATTTGA
* *
40814425 TACCCAAATCTTTGA
1 TACCCATATATTTGA
** *
40814440 CTTTCTAT-TATTTGA
1 -TACCCATATATTTGA
40814455 TACCCATATATTTGA
1 TACCCATATATTTGA
40814470 T
1 T
40814471 TTTCCATAAA
Statistics
Matches: 65, Mismatches: 20, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
14 12 0.18
15 42 0.65
16 11 0.17
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
TACCCATATATTTGA
Found at i:40819097 original size:30 final size:30
Alignment explanation
Indices: 40819062--40819171 Score: 170
Period size: 30 Copynumber: 3.7 Consensus size: 30
40819052 AATATCTCGG
40819062 TACCCATATCTTTGACTTTTCAATATTTGA
1 TACCCATATCTTTGACTTTTCAATATTTGA
*
40819092 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTTCAATATTTGA
*
40819122 TACCCATATCTTTGAC-TTTCTATTATTTGA
1 TACCCATATCTTTGACTTTTC-AATATTTGA
*
40819152 TACCCATATATTTGA-TTTTC
1 TACCCATATCTTTGACTTTTC
40819172 CATAAATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
29 3 0.04
30 71 0.96
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.47
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTTCAATATTTGA
Found at i:40819105 original size:15 final size:15
Alignment explanation
Indices: 40819084--40819167 Score: 73
Period size: 15 Copynumber: 5.6 Consensus size: 15
40819074 TGACTTTTCA
40819084 ATATTTGATACCCAT
1 ATATTTGATACCCAT
* **
40819099 ATCTTTGACTTTCCA-
1 ATATTTGA-TACCCAT
40819114 ATATTTGATACCCAT
1 ATATTTGATACCCAT
* ** *
40819129 ATCTTTGACTTTCTAT
1 ATATTTGA-TACCCAT
40819145 -TATTTGATACCCAT
1 ATATTTGATACCCAT
40819159 ATATTTGAT
1 ATATTTGAT
40819168 TTTCCATAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
14 8 0.16
15 35 0.69
16 8 0.16
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.46
Consensus pattern (15 bp):
ATATTTGATACCCAT
Found at i:40821765 original size:15 final size:16
Alignment explanation
Indices: 40821747--40821787 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
40821737 TTAAGGTGTT
*
40821747 ATTTTATAA-GTTGAA
1 ATTTTATAATGTTAAA
40821762 ATTTTA-AATGTTAAA
1 ATTTTATAATGTTAAA
40821777 ATTTATATAAT
1 ATTT-TATAAT
40821788 AAATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 15 0.68
16 2 0.09
17 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (16 bp):
ATTTTATAATGTTAAA
Found at i:40823140 original size:15 final size:13
Alignment explanation
Indices: 40823103--40823144 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 13
40823093 TACCATGTAT
40823103 AAATGTTAGAATTA
1 AAAT-TTAGAATTA
40823117 AAA-TTAGAATTA
1 AAATTTAGAATTA
40823129 CAAATTTTAGAATTA
1 -AAA-TTTAGAATTA
40823144 A
1 A
40823145 GACTAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.36
13 3 0.12
14 4 0.16
15 9 0.36
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (13 bp):
AAATTTAGAATTA
Found at i:40823579 original size:19 final size:19
Alignment explanation
Indices: 40823555--40823617 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
40823545 TTTTTTTTAT
40823555 AAAAATCGTAAAAAATATA
1 AAAAATCGTAAAAAATATA
* **
40823574 AAAAATTGTAAAATTTCAT-
1 AAAAATCGTAAAAAAT-ATA
*
40823593 AAAAATCATAAAAAAATTATA
1 AAAAATCGT-AAAAAA-TATA
40823614 AAAA
1 AAAA
40823618 TGCATTAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 20 0.61
20 8 0.24
21 5 0.15
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAATCGTAAAAAATATA
Found at i:40823628 original size:30 final size:28
Alignment explanation
Indices: 40823551--40823628 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 28
40823541 AGAATTTTTT
*
40823551 TTATAAAAAT-CGTAAAAAATATAAAAAA
1 TTATAAAAATGCAT-AAAAATATAAAAAA
* * *
40823579 TTGTAAAATTTCATAAAAATCATAAAAAAA
1 TTATAAAAATGCATAAAAAT-AT-AAAAAA
*
40823609 TTATAAAAATGCATTAAAAT
1 TTATAAAAATGCATAAAAAT
40823629 GCCCTTTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 14 0.35
29 4 0.10
30 22 0.55
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (28 bp):
TTATAAAAATGCATAAAAATATAAAAAA
Found at i:40847840 original size:14 final size:14
Alignment explanation
Indices: 40847821--40847848 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40847811 CTCAGTAACA
40847821 TTGATTGTTGATGC
1 TTGATTGTTGATGC
40847835 TTGATTGTTGATGC
1 TTGATTGTTGATGC
40847849 GTCAATCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.29, T:0.50
Consensus pattern (14 bp):
TTGATTGTTGATGC
Found at i:40858757 original size:51 final size:49
Alignment explanation
Indices: 40858627--40858819 Score: 217
Period size: 51 Copynumber: 3.8 Consensus size: 49
40858617 AGTTGCTAGG
* *
40858627 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-GATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAATAGAT-GA
* * * *
40858677 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAG-AT-GA
* * * *
40858728 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT--AGATGA
* *
40858779 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGA
40858820 GTATCATTTA
Statistics
Matches: 119, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
49 4 0.03
50 36 0.30
51 77 0.65
52 1 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGATGA
Found at i:40858850 original size:102 final size:100
Alignment explanation
Indices: 40858629--40858819 Score: 276
Period size: 101 Copynumber: 1.9 Consensus size: 100
40858619 TTGCTAGGTC
* * *
40858629 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTACTA
1 ACGTGTGTA-TACTATGTGCAGGCTACTACGTGTACCGGAATGAAAGATCACATGTGTAGTACTA
* *
40858694 TGTGCAGGCTACTATGCGTACCGAATAGCTTCGATC
65 TGTGCAGGCTACTATGCGAACCGAATAGCTTCGATA
*
40858730 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGAAAATGATCACATGTGTAGTAC
1 ACGTGTGTA-TACTATGTGCAGGCTACTACGTGTACCGGAATG-AAA-GATCACATGTGTAGTAC
*
40858794 TATGTGCAGGCTACTATGTGAACCGA
63 TATGTGCAGGCTACTATGCGAACCGA
40858820 GTATCATTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 3 0.04
101 40 0.49
102 39 0.48
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (100 bp):
ACGTGTGTATACTATGTGCAGGCTACTACGTGTACCGGAATGAAAGATCACATGTGTAGTACTAT
GTGCAGGCTACTATGCGAACCGAATAGCTTCGATA
Found at i:40861333 original size:17 final size:17
Alignment explanation
Indices: 40861311--40861345 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40861301 CACTTAATTT
*
40861311 ACATATATTACTGAAAC
1 ACATATATCACTGAAAC
*
40861328 ACATATATCACTGTAAC
1 ACATATATCACTGAAAC
40861345 A
1 A
40861346 TTTTCATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (17 bp):
ACATATATCACTGAAAC
Found at i:40864494 original size:21 final size:20
Alignment explanation
Indices: 40864472--40864547 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 20
40864462 TTTTGTTTAG
*
40864472 CTCTTTCGAGCTTCTGTTCAG
1 CTCTTT-GAGCTTCTGTTCAA
* *
40864493 CTCTTACGAGCTTATGTTCAA
1 CTCTT-TGAGCTTCTGTTCAA
40864514 CTCTTATGAGCTTCTGTTCAA
1 CTCTT-TGAGCTTCTGTTCAA
40864535 CT-TTTGAGCTTCT
1 CTCTTTGAGCTTCT
40864548 ATTGGCGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 9 0.18
20 2 0.04
21 38 0.78
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (20 bp):
CTCTTTGAGCTTCTGTTCAA
Found at i:40864796 original size:10 final size:8
Alignment explanation
Indices: 40864781--40864807 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40864771 TGATGGCACA
40864781 TGATATAT
1 TGATATAT
40864789 TGATATAT
1 TGATATAT
40864797 TGATATAT
1 TGATATAT
40864805 TGA
1 TGA
40864808 AATGGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (8 bp):
TGATATAT
Found at i:40867099 original size:19 final size:22
Alignment explanation
Indices: 40867072--40867117 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
40867062 AGATAATCTC
40867072 AAAACAACAATATT-TAAATAAA
1 AAAAC-ACAATATTATAAATAAA
40867094 AAAACACAATATTATAAATAAA
1 AAAACACAATATTATAAATAAA
40867116 AA
1 AA
40867118 CTCAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAACACAATATTATAAATAAA
Found at i:40867126 original size:22 final size:21
Alignment explanation
Indices: 40867072--40867126 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
40867062 AGATAATCTC
40867072 AAAACAACAATATTTAAATAAA
1 AAAACAA-AATATTTAAATAAA
*
40867094 AAAACACAATATTATAAATAAA
1 AAAACAAAATATT-TAAATAAA
**
40867116 AACTCAAAATA
1 AAAACAAAATA
40867127 ACATATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAACAAAATATTTAAATAAA
Found at i:40867471 original size:2 final size:2
Alignment explanation
Indices: 40867464--40867506 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
40867454 TTATAAGGTA
40867464 AT AT AT AT AT AT 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 AT AT AT AT AT AT
40867506 A
1 A
40867507 ATAATGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40874772 original size:18 final size:18
Alignment explanation
Indices: 40874726--40874772 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40874716 AATAAAGTAT
*
40874726 TATAAGCCCAATATATTT
1 TATAAGCCCAATATATTA
* *
40874744 TATAGGTCCAATATATTA
1 TATAAGCCCAATATATTA
*
40874762 TGTAAGCCCAA
1 TATAAGCCCAA
40874773 ACTAAATAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TATAAGCCCAATATATTA
Found at i:40885503 original size:6 final size:7
Alignment explanation
Indices: 40885485--40885509 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40885475 CTATCCCTTC
40885485 GTTTTTT
1 GTTTTTT
40885492 GTTTTTT
1 GTTTTTT
40885499 GTTTTTT
1 GTTTTTT
40885506 GTTT
1 GTTT
40885510 GTAAGGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (7 bp):
GTTTTTT
Found at i:40888238 original size:2 final size:2
Alignment explanation
Indices: 40888226--40888274 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
40888216 GATAGTTAAG
40888226 AT AT CAT AT AT AT 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 AT AT AT AT AT AT
40888269 AT AT AT
1 AT AT AT
40888275 GGGCAAAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40893181 original size:14 final size:15
Alignment explanation
Indices: 40893157--40893191 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40893147 TACTTTAATC
40893157 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
40893172 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
40893187 ATGGT
1 ATGGT
40893192 AATGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:40893514 original size:47 final size:47
Alignment explanation
Indices: 40893445--40893657 Score: 364
Period size: 47 Copynumber: 4.6 Consensus size: 47
40893435 AAGTAAATGA
*
40893445 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTTCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
40893492 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGT-C----ATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
40893534 ATGTATATGCTGTCAAATTTTGATGTACAAATGTAGTCCAATTATAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
*
40893581 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
40893628 ATGTATATGCTGTCAAATTTTGATGTACAA
1 ATGTATATGCTGTCAAATTTTGATGTACAA
40893658 TTATATATGT
Statistics
Matches: 158, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
42 40 0.25
43 1 0.01
46 1 0.01
47 116 0.73
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (47 bp):
ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATAT
Found at i:40893584 original size:25 final size:24
Alignment explanation
Indices: 40893556--40893632 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
40893546 TCAAATTTTG
40893556 ATGTACAAATGTAGTCCAATTATAT
1 ATGTACAAATGTAGTCCAATTAT-T
* *
40893581 ATGT--ATATGCT-GTCAAATT-TT
1 ATGTACAAATG-TAGTCCAATTATT
*
40893602 GATGTACAAATGCAGTCCAATTATTT
1 -ATGTACAAATGTAGTCCAATTA-TT
40893628 ATGTA
1 ATGTA
40893633 TATGCTGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
21 1 0.03
22 5 0.12
23 11 0.28
24 12 0.30
25 9 0.22
26 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (24 bp):
ATGTACAAATGTAGTCCAATTATT
Found at i:40893593 original size:89 final size:93
Alignment explanation
Indices: 40893445--40893732 Score: 374
Period size: 89 Copynumber: 3.2 Consensus size: 93
40893435 AAGTAAATGA
*
40893445 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTTCAATTATATATGTATATGCTGTCAAAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATGTATATGCTGTCAAAT
40893510 TTTGATGTACAAATGCAGT-C-A-TA-T
66 TTTGATGTACAAATGCAGTCCAATTATT
*
40893534 ATGTATATGCTGTCAAATTTTGATGTACAAATGTAGTCCAATTATATATGTATATGCTGTCAAAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATGTATATGCTGTCAAAT
40893599 TTTGATGTACAAATGCAGTCCAATTATTT
66 TTTGATGTACAAATGCAGTCCAATTA-TT
*
40893628 ATGTATATGCTGTCAAATTTTGATG------T--A---CAATTATATATGTATATGCTGTCAGAT
1 ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATGTATATGCTGTCAAAT
* *
40893682 TTTGATATATAAATGCAGTCCAAATT-TT
66 TTTGATGTACAAATGCAGTCC-AATTATT
* *
40893710 GTATATATGCTGTCCAAATTTTG
1 ATGTATATGCTGT-CAAATTTTG
40893733 GTGTGAAAAT
Statistics
Matches: 185, Mismatches: 7, Indels: 20
0.87 0.03 0.09
Matches are distributed among these distances:
82 13 0.07
83 54 0.29
84 4 0.02
86 1 0.01
88 1 0.01
89 82 0.44
90 1 0.01
91 1 0.01
92 2 0.01
94 26 0.14
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (93 bp):
ATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATGTATATGCTGTCAAAT
TTTGATGTACAAATGCAGTCCAATTATT
Found at i:40893659 original size:36 final size:36
Alignment explanation
Indices: 40893619--40893687 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
40893609 AAATGCAGTC
*
40893619 CAATTATTTATGTATATGCTGTCAAATTTTGATGTA
1 CAATTATATATGTATATGCTGTCAAATTTTGATGTA
*
40893655 CAATTATATATGTATATGCTGTCAGATTTTGAT
1 CAATTATATATGTATATGCTGTCAAATTTTGAT
40893688 ATATAAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.46
Consensus pattern (36 bp):
CAATTATATATGTATATGCTGTCAAATTTTGATGTA
Found at i:40893719 original size:22 final size:23
Alignment explanation
Indices: 40893667--40893732 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
40893657 ATTATATATG
*
40893667 TATATGCTGT-CAGATTTTGATA
1 TATATGCTGTCCAAATTTTGATA
*
40893689 TATAAATGCAGTCCAAATTTTG-TA
1 TAT--ATGCTGTCCAAATTTTGATA
40893713 TATATGCTGTCCAAATTTTG
1 TATATGCTGTCCAAATTTTG
40893733 GTGTGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 19 0.50
24 11 0.29
25 8 0.21
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (23 bp):
TATATGCTGTCCAAATTTTGATA
Found at i:40893728 original size:83 final size:83
Alignment explanation
Indices: 40893572--40893732 Score: 252
Period size: 83 Copynumber: 1.9 Consensus size: 83
40893562 AAATGTAGTC
* * *
40893572 CAATTATATATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTTATGTATATG
1 CAATTATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCCAAATATTTATATATATG
40893637 CTGTCAAATTTTGATGTA
66 CTGTCAAATTTTGATGTA
* * *
40893655 CAATTATATATGTATATGCTGTCAGATTTTGATATATAAATGCAGTCCAAAT-TTTGTATATATG
1 CAATTATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCCAAATATTTATATATATG
40893719 CTGTCCAAATTTTG
66 CTGT-CAAATTTTG
40893733 GTGTGAAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
82 14 0.20
83 57 0.80
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (83 bp):
CAATTATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCCAAATATTTATATATATG
CTGTCAAATTTTGATGTA
Found at i:40893768 original size:130 final size:133
Alignment explanation
Indices: 40893448--40893777 Score: 379
Period size: 130 Copynumber: 2.5 Consensus size: 133
40893438 TAAATGAATG
* * * *
40893448 TATATGCTGTCAAATTTTGATGTACAAATGCAGTTCAATTATATATGTATATGCTGTCAAATTTT
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATGTATATAAATGCTGTCAAATTTT
* *
40893513 GATGTACAAATGCAGTCATATATGTATATGCTGTCAAATTTTGATGTACAAATGTAGTCCAATTA
66 GATGTACAAAT---GTCATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCCAATTA
*
40893578 TATATG
128 TATATA
* * *
40893584 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATTTATGTATATGCTGTCAAATTTT
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATGTATATAAATGCTGTCAAATTTT
* *
40893649 GATGTAC-AAT-T-ATATATGTATATGCTGTCAGATTTTGATATATAAATGCAGTCCAAATT-T-
66 GATGTACAAATGTCATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCC-AATTATA
*
40893709 TGTA
130 TATA
* * *
40893713 TATATGCTGTCCAAATTTTGGTGTGA-AAATGCTA-TCTAGTT-TGGTATATAAATGCTGTTCAA
1 TATATGCTGT-CAAATTTTGATGT-ACAAATGC-AGTCCAATTAT-GTATATAAATGCTG-TCAA
40893775 ATT
61 ATT
40893778 GATGTATAAT
Statistics
Matches: 174, Mismatches: 14, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
129 13 0.07
130 74 0.43
131 14 0.08
135 3 0.02
136 70 0.40
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (133 bp):
TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATGTATATAAATGCTGTCAAATTTT
GATGTACAAATGTCATATATGTATATGCTGTCAAATTTTGATATACAAATGCAGTCCAATTATAT
ATA
Found at i:40894383 original size:33 final size:33
Alignment explanation
Indices: 40894346--40894413 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
40894336 GATTAATTTT
* *
40894346 ATATTTTATGTATCGTTATATTAAATTATTTAA
1 ATATTTCATATATCGTTATATTAAATTATTTAA
* *
40894379 ATATTTCATATCTCTTTATATTAAATTATTTAA
1 ATATTTCATATATCGTTATATTAAATTATTTAA
40894412 AT
1 AT
40894414 CTTATTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (33 bp):
ATATTTCATATATCGTTATATTAAATTATTTAA
Found at i:40894415 original size:24 final size:23
Alignment explanation
Indices: 40894371--40894415 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
40894361 TTATATTAAA
*
40894371 TTATTTAAATATTTCATATCTCT
1 TTATTTAAATATTTCAAATCTCT
40894394 TTATATTAAATTATTT-AAATCT
1 TTAT-TTAAA-TATTTCAAATCT
40894416 TATTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 10 0.53
25 5 0.26
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATTTAAATATTTCAAATCTCT
Found at i:40912327 original size:89 final size:90
Alignment explanation
Indices: 40912217--40913043 Score: 1163
Period size: 89 Copynumber: 9.3 Consensus size: 90
40912207 TATTGGTAGC
* * * * *
40912217 GAAGTGGATCGAATATA-CAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCAGAA-AAAGC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
* *
40912280 AGATCTTGTCTTCATGCACTGGCAT
66 AGATCTTGTCTTCATGTACTGGCGT
* *
40912305 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGAT-TGAAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
40912369 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
* * * * * * *
40912394 GAAGTAGATCAAAGGTAACAGATCTTGCCTCCCCATACTGGTGGTGGAGTAGAT-TGAAGAAAAG
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAA-
* *
40912458 CAGATCTTCTTTTCATGTACTGGCGT
65 CAGATCTTGTCTTCATGTACTGGCGT
* * * *
40912484 GAAGTAGATCAAAGATACCAGATCTTATCTCCCCATACTGGTGGTGGAGTAGATC-GAAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
40912548 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
* * *
40912573 GAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCA-AAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
*
40912637 AGATCTTGTCTTCATGTACTGGTGT
66 AGATCTTGTCTTCATGTACTGGCGT
* * * *
40912662 GAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGAGAAGCAGATCA-AAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
*
40912726 AGATCTTGTCTTCATGTACCGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
* * * * *
40912751 GAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATGCTGGTGGCGAAGCAAATCA-AAGAAAAC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
40912815 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
* * * * * *
40912840 GAAGTAGATCAAAGATAGCAGATCTTATCTTCCCATACTGGTGGTGAAGTAGATAATAA-AAAGC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
40912904 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
*
40912929 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC-GAAGAAAGC
1 GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
40912993 AGATCTTGTCTTCATGTACTGGCGT
66 AGATCTTGTCTTCATGTACTGGCGT
*
40913018 GAAGTAGATCGAAGATTA-CAGATCTT
1 GAAGTAGATCAAAGA-TACCAGATCTT
40913044 ATCTCCCTAA
Statistics
Matches: 675, Mismatches: 56, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
88 19 0.03
89 570 0.84
90 86 0.13
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (90 bp):
GAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAGAAGAAAAC
AGATCTTGTCTTCATGTACTGGCGT
Found at i:40918655 original size:21 final size:22
Alignment explanation
Indices: 40918629--40918672 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
40918619 CAGAAATGTT
40918629 ATAAACTAAAAGA-AAT-ATAGA
1 ATAAAC-AAAAGAGAATAATAGA
*
40918650 ATAAACAAGAGAGAATAATAGA
1 ATAAACAAAAGAGAATAATAGA
40918672 A
1 A
40918673 AAATGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.16
Consensus pattern (22 bp):
ATAAACAAAAGAGAATAATAGA
Found at i:40920392 original size:86 final size:86
Alignment explanation
Indices: 40920244--40920420 Score: 309
Period size: 86 Copynumber: 2.1 Consensus size: 86
40920234 AAATACATTG
*
40920244 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAATCTAGGCT
1 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
*
40920309 ACAGTGATAACAAATTTAACT
66 ACAGTGATAACAAACTTAACT
* *
40920330 AACTAAAGTTAGAAATGTCATTACAACCAAAGTATAGAGATTGAAAGTGTATATAAACCTAGGCT
1 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
*
40920395 ACAGTGATAACTAACTTAACT
66 ACAGTGATAACAAACTTAACT
40920416 AACTA
1 AACTA
40920421 TAAGAACACC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (86 bp):
AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
ACAGTGATAACAAACTTAACT
Found at i:40921266 original size:21 final size:22
Alignment explanation
Indices: 40921206--40921266 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
40921196 ATTTGATAAC
40921206 TTTTA-AAGAATTT-TAATATGT
1 TTTTATAA-AATTTATAATATGT
*
40921227 TTTTATAAAATTTAAAATATG-
1 TTTTATAAAATTTATAATATGT
* *
40921248 TTTTATTAATTTTATAATA
1 TTTTATAAAATTTATAATA
40921267 ATTTATTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 26 0.76
22 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTATAAAATTTATAATATGT
Found at i:40921303 original size:19 final size:19
Alignment explanation
Indices: 40921281--40921332 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
40921271 ATTAGAATTA
40921281 TATATATTTTTAT-ATTTTT
1 TATAT-TTTTTATGATTTTT
*
40921300 TATATTTTTTCTGATTTTT
1 TATATTTTTTATGATTTTT
*
40921319 TAATCTTTTTTATG
1 T-ATATTTTTTATG
40921333 GAAAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 12 0.43
20 10 0.36
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (19 bp):
TATATTTTTTATGATTTTT
Found at i:40921316 original size:10 final size:9
Alignment explanation
Indices: 40921281--40921331 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
40921271 ATTAGAATTA
40921281 TATATATTTT
1 TATAT-TTTT
40921291 TATATTTTT
1 TATATTTTT
40921300 TATATTTTT
1 TATATTTTT
*
40921309 TCTGATTTTT
1 TAT-ATTTTT
*
40921319 TAATCTTTTT
1 T-ATATTTTT
40921329 TAT
1 TAT
40921332 GGAAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 17 0.47
10 18 0.50
11 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (9 bp):
TATATTTTT
Found at i:40934354 original size:8 final size:8
Alignment explanation
Indices: 40934341--40934370 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
40934331 AATTTTCACC
40934341 AAAAAAGA
1 AAAAAAGA
40934349 AAAAAAGA
1 AAAAAAGA
40934357 AAAAAA-A
1 AAAAAAGA
40934364 AAAAAAG
1 AAAAAAG
40934371 GGAAATTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:40934361 original size:15 final size:15
Alignment explanation
Indices: 40934341--40934370 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40934331 AATTTTCACC
*
40934341 AAAAAAGAAAAAAAG
1 AAAAAAAAAAAAAAG
40934356 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
40934371 GGAAATTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:40946410 original size:15 final size:15
Alignment explanation
Indices: 40946390--40946424 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40946380 CCCTTTTTGT
* *
40946390 AAAAATTAAAAATTA
1 AAAAATAAAAAAATA
40946405 AAAAATAAAAAAATA
1 AAAAATAAAAAAATA
40946420 AAAAA
1 AAAAA
40946425 GGTGCAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:40947023 original size:26 final size:26
Alignment explanation
Indices: 40946987--40947040 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
40946977 GACCTAAGTA
40946987 TACACATTAATCTCTGCATTACTTCT
1 TACACATTAATCTCTGCATTACTTCT
40947013 TACACATTAATCTCTGCATTACTTCT
1 TACACATTAATCTCTGCATTACTTCT
40947039 TA
1 TA
40947041 AGAAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43
Consensus pattern (26 bp):
TACACATTAATCTCTGCATTACTTCT
Found at i:40951501 original size:3 final size:3
Alignment explanation
Indices: 40951493--40951517 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40951483 CTTGTTTTTC
40951493 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
40951518 CTAGGGAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40952010 original size:16 final size:15
Alignment explanation
Indices: 40951970--40952015 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
40951960 AAAATTAAAC
40951970 CAAA-TTAAAATTT-
1 CAAATTTAAAATTTA
* *
40951983 CATATATAAAATTATA
1 CAAATTTAAAATT-TA
40951999 CAAATTTAAAATTTA
1 CAAATTTAAAATTTA
40952014 CA
1 CA
40952016 TGTTAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.12
14 7 0.27
15 5 0.19
16 11 0.42
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (15 bp):
CAAATTTAAAATTTA
Found at i:40955500 original size:41 final size:41
Alignment explanation
Indices: 40955455--40955629 Score: 207
Period size: 41 Copynumber: 4.3 Consensus size: 41
40955445 TAGCAGATGT
*
40955455 AGTGCCGGTGAAT-T-AATTCAGACTT-TAAGTCTAGCAGGCTA
1 AGTGCCGGTG-ATCTGAA-TCAG-CTTATAAGCCTAGCAGGCTA
* *
40955496 AGTGCCGGTGATCTGAACCAGGTTATGAA-CCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCAGCTTAT-AAGCCTAGCAGGCTA
* * *
40955537 TGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCAGCTTATAAGCCTAGCAGGCTA
*
40955578 CGTGCCGGTGATCTGAATCAGGC-TATAAGCCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCA-GCTTATAAGCCTAGCAGGCTA
40955619 AGTGCCGGTGA
1 AGTGCCGGTGA
40955630 ATATGTTAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
40 6 0.05
41 108 0.91
42 5 0.04
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (41 bp):
AGTGCCGGTGATCTGAATCAGCTTATAAGCCTAGCAGGCTA
Found at i:40959791 original size:25 final size:26
Alignment explanation
Indices: 40959732--40959805 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
40959722 GCTCATTAGA
*
40959732 CCATATAATCAGGAAGCTATCTCTCGAG
1 CCATATAA-CAGGAAGCT-TATCTCGAG
* *
40959760 CTATATAACAGGAAGCTTATGT-GAG
1 CCATATAACAGGAAGCTTATCTCGAG
**
40959785 CCATATAATGGGAAGCTTATC
1 CCATATAACAGGAAGCTTATC
40959806 CAGGCTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 20 0.51
26 3 0.08
27 9 0.23
28 7 0.18
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (26 bp):
CCATATAACAGGAAGCTTATCTCGAG
Found at i:40959924 original size:25 final size:24
Alignment explanation
Indices: 40959896--40959947 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
40959886 ATTAATCGAT
* *
40959896 AAGTTCTAGATAGTCATATATCGGG
1 AAGTTCAAGAGAGTCA-ATATCGGG
* *
40959921 AAGTTGAAGCGAGTCAATATCGGG
1 AAGTTCAAGAGAGTCAATATCGGG
40959945 AAG
1 AAG
40959948 CTCCGGAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.25
Consensus pattern (24 bp):
AAGTTCAAGAGAGTCAATATCGGG
Found at i:40973221 original size:19 final size:21
Alignment explanation
Indices: 40973170--40973222 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
40973160 TTTAGTGGAA
*
40973170 TCAAGTGAAATGAAATTTGAGT
1 TCAAGTCAAAT-AAATTTGAGT
*
40973192 T-AAGTCGAATAAATTT-A-T
1 TCAAGTCAAATAAATTTGAGT
40973210 TCAAGTCAAATAA
1 TCAAGTCAAATAA
40973223 TTTCTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 6 0.22
21 7 0.26
22 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (21 bp):
TCAAGTCAAATAAATTTGAGT
Found at i:40978334 original size:17 final size:17
Alignment explanation
Indices: 40978303--40978335 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40978293 GAACTTTATA
40978303 AAATATAAAAGATATTG
1 AAATATAAAAGATATTG
40978320 AAATGATAAAA-ATATT
1 AAAT-ATAAAAGATATT
40978336 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
AAATATAAAAGATATTG
Found at i:40978354 original size:9 final size:9
Alignment explanation
Indices: 40978302--40978407 Score: 63
Period size: 9 Copynumber: 11.4 Consensus size: 9
40978292 AGAACTTTAT
40978302 AAAATATAA
1 AAAATATAA
* *
40978311 AAGATAT-T
1 AAAATATAA
*
40978319 GAAATGATAA
1 AAAAT-ATAA
* *
40978329 AAATATTTTA
1 AAA-ATATAA
40978339 AAAATATAA
1 AAAATATAA
*
40978348 TAAATATAA
1 AAAATATAA
* *
40978357 TAACTATAA
1 AAAATATAA
40978366 AAAATCATAA
1 AAAAT-ATAA
40978376 AAAACTAT-A
1 AAAA-TATAA
*
40978385 AAAATATTTA
1 AAAATA-TAA
*
40978395 AAAATGTAA
1 AAAATATAA
40978404 AAAA
1 AAAA
40978408 AAATGAAATA
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
8 5 0.07
9 43 0.58
10 23 0.31
11 3 0.04
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (9 bp):
AAAATATAA
Found at i:40979802 original size:29 final size:29
Alignment explanation
Indices: 40979742--40979802 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
40979732 AATATTTTTT
* * *
40979742 AATTAATAACTCTTTTATTTATACAAATA
1 AATTAATAAATCTTTTAATTATACAAAAA
*
40979771 AATTAATAAAT-TTTTAATTATATAATAAA
1 AATTAATAAATCTTTTAATTATACAA-AAA
40979800 AAT
1 AAT
40979803 ATATTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (29 bp):
AATTAATAAATCTTTTAATTATACAAAAA
Found at i:40979818 original size:27 final size:29
Alignment explanation
Indices: 40979757--40979818 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 29
40979747 ATAACTCTTT
40979757 TATTTATACAAATAAATTAATAAATTTTTA
1 TATTTATACAAATAAA-TAATAAATTTTTA
* *
40979787 -A-TTATA-TAATAAA-AATATATTTTTA
1 TATTTATACAAATAAATAATAAATTTTTA
40979812 TATTTAT
1 TATTTAT
40979819 TATTATGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
25 11 0.39
26 1 0.04
27 10 0.36
28 5 0.18
29 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
TATTTATACAAATAAATAATAAATTTTTA
Found at i:40979844 original size:103 final size:102
Alignment explanation
Indices: 40979634--40979838 Score: 292
Period size: 103 Copynumber: 2.0 Consensus size: 102
40979624 TTAATTCATC
*
40979634 TTTTTAATTAATAACTCTTTTACTTATATAAATAAAATAATAAACATGTAATTATAAAATAAAAA
1 TTTTTAATTAATAACTCTTTTACTTATACAAATAAAATAATAAACATGTAATTATAAAATAAAAA
40979699 TATATATTTTTATGTATATACTATTATGTTAAAAATAT
66 TATATATTTTTATGTATATA-TATTATGTTAAAAATAT
* * ** * *
40979737 TTTTTAATTAATAACTCTTTTATTTATACAAATAAATTAATAAATTTTTAATTATATAATAAAAA
1 TTTTTAATTAATAACTCTTTTACTTATACAAATAAAATAATAAACATGTAATTATAAAATAAAAA
*
40979802 TATAT-TTTTATAT-T-TAT-TATTATGTTAAATATAT
66 TATATATTTT-TATGTATATATATTATGTTAAAAATAT
40979836 TTT
1 TTT
40979839 ATTTTTTTAA
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
99 19 0.20
101 3 0.03
102 5 0.05
103 66 0.71
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (102 bp):
TTTTTAATTAATAACTCTTTTACTTATACAAATAAAATAATAAACATGTAATTATAAAATAAAAA
TATATATTTTTATGTATATATATTATGTTAAAAATAT
Found at i:40980205 original size:72 final size:73
Alignment explanation
Indices: 40980129--40980289 Score: 202
Period size: 72 Copynumber: 2.2 Consensus size: 73
40980119 TATATTTATT
* * * * * *
40980129 AAAAATAATGATATTTGAAATAATTAATTGATTTTCTAATATTATAATTTATCATACTCACAATG
1 AAAAATAATGATATTTGAAATAATTAATTGATTTTATAATATTAAAAATCACCATACCCACAATG
40980194 TAGGT-GA
66 TAGGTGGA
** * *
40980201 AAAAATAATGATATTAAAAATAATTATTTGATTTTATAATATTAAAAATCACCATACCCGCAATG
1 AAAAATAATGATATTTGAAATAATTAATTGATTTTATAATATTAAAAATCACCATACCCACAATG
40980266 TAGGTGGA
66 TAGGTGGA
*
40980274 GAAAATAA--ATATTTGA
1 AAAAATAATGATATTTGA
40980290 CATATAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
71 6 0.08
72 60 0.80
73 9 0.12
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (73 bp):
AAAAATAATGATATTTGAAATAATTAATTGATTTTATAATATTAAAAATCACCATACCCACAATG
TAGGTGGA
Found at i:40980515 original size:97 final size:98
Alignment explanation
Indices: 40980359--40980551 Score: 253
Period size: 97 Copynumber: 2.0 Consensus size: 98
40980349 AAATATATTT
* * *
40980359 AACATAATGATAAATATAAAAAATATATTATATCATATACTTACATATTTATTAATTTATTTATA
1 AACATAATGATAAATATAAAAAATATATTATATCATATAATTACACAATTATTAATTTATTTATA
*
40980424 TAAATAAAGGAGTTATTAATTAAAAAAATTATA
66 TAAATAAAAGAGTTATTAATTAAAAAAATTATA
* * * * * * *
40980457 AACATAATGATATATATAATATATAT-TTTTATTATATAATTACACAATTATTATTTTATTTTTA
1 AACATAATGATAAATATAAAAAATATATTATATCATATAATTACACAATTATTAATTTATTTATA
* * *
40980521 TAAATAAAATATTTATTAATTAAAAATATTA
66 TAAATAAAAGAGTTATTAATTAAAAAAATTA
40980552 ATTAAAAAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
97 58 0.72
98 23 0.28
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (98 bp):
AACATAATGATAAATATAAAAAATATATTATATCATATAATTACACAATTATTAATTTATTTATA
TAAATAAAAGAGTTATTAATTAAAAAAATTATA
Found at i:40980562 original size:14 final size:13
Alignment explanation
Indices: 40980534--40980559 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40980524 ATAAAATATT
40980534 TATTAATTAAAAA
1 TATTAATTAAAAA
40980547 TATTAATTAAAAA
1 TATTAATTAAAAA
40980560 ATAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:40986781 original size:3 final size:3
Alignment explanation
Indices: 40986773--40986804 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40986763 TATACGTAGT
40986773 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40986805 TAATTGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40997989 original size:28 final size:28
Alignment explanation
Indices: 40997949--40998004 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
40997939 TTTTGTTGGT
*
40997949 TAAGGGCTCAAAATTTTGAGTAAAAAAA
1 TAAGGGCTCAAAATTTTCAGTAAAAAAA
* * *
40997977 TAAGGGTTGAAAATTTTCATTAAAAAAA
1 TAAGGGCTCAAAATTTTCAGTAAAAAAA
40998005 ATACAGATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (28 bp):
TAAGGGCTCAAAATTTTCAGTAAAAAAA
Found at i:41002675 original size:51 final size:51
Alignment explanation
Indices: 41002524--41002681 Score: 158
Period size: 51 Copynumber: 3.1 Consensus size: 51
41002514 TCTCCTCTAG
* * *
41002524 CTTGCCTACAAGATGGA-TTTGCCTCTAAGGATATCATA-CTTTTTAGATTCA
1 CTTGCCTACAAGAT-GACTTTGCCTCCAAGGATATCATACCTTCTAAG-TTCA
* ** * * **
41002575 CTTGCCTACAAAACAACTTTGCCTCCAAGGCTATCATACTTTCCCAGTTCA
1 CTTGCCTACAAGATGACTTTGCCTCCAAGGATATCATACCTTCTAAGTTCA
* * * *
41002626 CTTGCCTACAAGATGACTTTACCTCCACGGTTATCATACCTTCTAAGTTCG
1 CTTGCCTACAAGATGACTTTGCCTCCAAGGATATCATACCTTCTAAGTTCA
41002677 CTTGC
1 CTTGC
41002682 TTTCAATGAA
Statistics
Matches: 86, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
50 1 0.01
51 81 0.94
52 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (51 bp):
CTTGCCTACAAGATGACTTTGCCTCCAAGGATATCATACCTTCTAAGTTCA
Found at i:41004945 original size:7 final size:7
Alignment explanation
Indices: 41004933--41004957 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41004923 TGTAGTCGTA
41004933 AATGGTC
1 AATGGTC
41004940 AATGGTC
1 AATGGTC
41004947 AATGGTC
1 AATGGTC
41004954 AATG
1 AATG
41004958 CTTCAGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (7 bp):
AATGGTC
Found at i:41008191 original size:12 final size:12
Alignment explanation
Indices: 41008176--41008205 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
41008166 GCGCTTGGCA
41008176 AGGATAGGCAAT
1 AGGATAGGCAAT
41008188 AGGATAGGCAAT
1 AGGATAGGCAAT
41008200 AGGATA
1 AGGATA
41008206 CTATGGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.33, T:0.17
Consensus pattern (12 bp):
AGGATAGGCAAT
Found at i:41013174 original size:22 final size:20
Alignment explanation
Indices: 41013138--41013196 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
41013128 GGCCCGGCCC
41013138 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
41013160 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
41013181 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
41013197 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:41013187 original size:21 final size:21
Alignment explanation
Indices: 41013163--41013235 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
41013153 ACCAAAAATT
41013163 TATTTTAAAAATTAAAAAAAG
1 TATTTTAAAAATTAAAAAAAG
***
41013184 TATTTTAAAAA-TATTTTAAA-
1 TATTTTAAAAATTA-AAAAAAG
*
41013204 -ATTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATTAAAAAAAG
41013224 TATTTTAAAAAT
1 TATTTTAAAAAT
41013236 ATTTTAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
19 12 0.30
20 4 0.10
21 24 0.60
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
TATTTTAAAAATTAAAAAAAG
Found at i:41013222 original size:40 final size:40
Alignment explanation
Indices: 41013164--41013256 Score: 177
Period size: 40 Copynumber: 2.3 Consensus size: 40
41013154 CCAAAAATTT
41013164 ATTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
*
41013204 ATTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
41013244 ATTTTAAAAATTA
1 ATTTTAAAAATTA
41013257 TTTTAAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (40 bp):
ATTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
Found at i:41013255 original size:9 final size:9
Alignment explanation
Indices: 41013185--41013255 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
41013175 TAAAAAAAGT
41013185 ATTTTAAAA
1 ATTTTAAAA
*
41013194 ATATTTTAAA
1 AT-TTTAAAA
*
41013204 ATTTAAAAA
1 ATTTTAAAA
**
41013213 ATTAAAAAAA
1 ATT-TTAAAA
41013223 GTATTTTAAAA
1 --ATTTTAAAA
*
41013234 ATATTTTAAA
1 AT-TTTAAAA
41013244 ATTTTAAAA
1 ATTTTAAAA
41013253 ATT
1 ATT
41013256 ATTTTAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
9 21 0.43
10 21 0.43
11 4 0.08
12 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:41015307 original size:24 final size:22
Alignment explanation
Indices: 41015266--41015314 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
41015256 ATTCATTCAT
41015266 TATTTTTTTTGTATTTTTTAAA
1 TATTTTTTTTGTATTTTTTAAA
* *
41015288 TATTTTTATTTTTATATTTTTTAA
1 TATTTTT-TTTGTAT-TTTTTAAA
41015312 TAT
1 TAT
41015315 ATATAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 6 0.26
24 10 0.43
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTTTTTTTGTATTTTTTAAA
Found at i:41022161 original size:29 final size:30
Alignment explanation
Indices: 41022122--41022180 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
41022112 TTAGTCGTAA
* *
41022122 TGTGTATTTTTATAAAT-AAATTTTGATTT
1 TGTGTAATTTTATAAATGAAATTTTAATTT
* *
41022151 TGTGTAATTTTTTACATGAAATTTTAATTT
1 TGTGTAATTTTATAAATGAAATTTTAATTT
41022181 AATTTAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (30 bp):
TGTGTAATTTTATAAATGAAATTTTAATTT
Found at i:41022161 original size:30 final size:29
Alignment explanation
Indices: 41022122--41022180 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
41022112 TTAGTCGTAA
*
41022122 TGTGTATTTTTATAAAT-AAATTTTGATTT
1 TGTGTATTTTT-TAAATGAAATTTTAATTT
*
41022151 TGTGTAATTTTTTACATGAAATTTTAATTT
1 TGTGT-ATTTTTTAAATGAAATTTTAATTT
41022181 AATTTAATTC
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:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (29 bp):
TGTGTATTTTTTAAATGAAATTTTAATTT
Found at i:41022555 original size:19 final size:19
Alignment explanation
Indices: 41022531--41022567 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
41022521 TTGTCACTAA
41022531 CTAATAATCTAGAGTAATC
1 CTAATAATCTAGAGTAATC
41022550 CTAATAATCTAGAGTAAT
1 CTAATAATCTAGAGTAAT
41022568 ACTTTTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (19 bp):
CTAATAATCTAGAGTAATC
Found at i:41022588 original size:3 final size:3
Alignment explanation
Indices: 41022580--41022613 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
41022570 TTTTTCACTT
41022580 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41022614 CTCTCTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41025874 original size:5 final size:5
Alignment explanation
Indices: 41025864--41025891 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41025854 TAACCTTGGA
41025864 CTAGG CTAGG CTAGG CTAGG CTAGG CTA
1 CTAGG CTAGG CTAGG CTAGG CTAGG CTA
41025892 CGCTGAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (5 bp):
CTAGG
Found at i:41029537 original size:13 final size:14
Alignment explanation
Indices: 41029516--41029552 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
41029506 TCCAAGTTAG
41029516 ATAAAATAATTAAA
1 ATAAAATAATTAAA
*
41029530 AT-AAATAACTAAA
1 ATAAAATAATTAAA
41029543 ATAAAATAAT
1 ATAAAATAAT
41029553 AAATCAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:41035490 original size:27 final size:26
Alignment explanation
Indices: 41035451--41035507 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
41035441 AAATCCTAAA
* * *
41035451 TTTTCTTTGTTTCCTTCCCT-TTTTCT
1 TTTTCTTTCTTT-CTCCCCTGTTTTCG
41035477 TTTTCTTTCCTTTCTCCCCTGTTTTCG
1 TTTTCTTT-CTTTCTCCCCTGTTTTCG
41035504 TTTT
1 TTTT
41035508 GCTATTCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.00, C:0.28, G:0.05, T:0.67
Consensus pattern (26 bp):
TTTTCTTTCTTTCTCCCCTGTTTTCG
Found at i:41039523 original size:33 final size:33
Alignment explanation
Indices: 41039476--41039549 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
41039466 ATAATATCAT
* *
41039476 ATAATATCCTATTAGGAATTAAATTGTTAACAG
1 ATAATATCCTATTAGGAATTAAATTGCTAACAC
* *
41039509 ATAATAT-CTCATTAGGAATTAATTTGCTAAGAC
1 ATAATATCCT-ATTAGGAATTAAATTGCTAACAC
41039542 ATAATATC
1 ATAATATC
41039550 ACATAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (33 bp):
ATAATATCCTATTAGGAATTAAATTGCTAACAC
Found at i:41047678 original size:29 final size:30
Alignment explanation
Indices: 41047646--41047703 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
41047636 GAATTGTTTG
41047646 GATA-CAAGTTAAAG-AGAAGGGCTTATTTA
1 GATACCAA-TTAAAGTAGAAGGGCTTATTTA
**
41047675 GATACCAATTAAAGTTTAAGGGCTTATTT
1 GATACCAATTAAAGTAGAAGGGCTTATTT
41047704 GGGTGTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (30 bp):
GATACCAATTAAAGTAGAAGGGCTTATTTA
Found at i:41068954 original size:17 final size:17
Alignment explanation
Indices: 41068932--41068970 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
41068922 CAAGCTCAAA
41068932 CAAAGACGCAAACTCAT
1 CAAAGACGCAAACTCAT
* *
41068949 CAAAGATGCAAGCTCAT
1 CAAAGACGCAAACTCAT
41068966 CAAAG
1 CAAAG
41068971 TGCGAGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (17 bp):
CAAAGACGCAAACTCAT
Found at i:41070322 original size:19 final size:20
Alignment explanation
Indices: 41070298--41070338 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
41070288 AGTTTTTCTT
41070298 TAATTTATAATAATT-TTTA
1 TAATTTATAATAATTATTTA
* *
41070317 TAATTTTTAATTATTATTTA
1 TAATTTATAATAATTATTTA
41070337 TA
1 TA
41070339 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATTTATAATAATTATTTA
Found at i:41070526 original size:8 final size:9
Alignment explanation
Indices: 41070493--41070580 Score: 54
Period size: 10 Copynumber: 9.0 Consensus size: 9
41070483 AGTTGGTTTA
41070493 TATAATTTT
1 TATAATTTT
41070502 CTATAAGTTTT
1 -TATAA-TTTT
41070513 TATAATTTTT
1 TATAA-TTTT
41070523 TAATAATGTTT
1 T-ATAAT-TTT
*
41070534 CTATAATTTC
1 -TATAATTTT
*
41070544 TACAATATTT
1 TATAAT-TTT
*
41070554 TCATAA-TAT
1 T-ATAATTTT
41070563 T-TAATATTT
1 TATAAT-TTT
41070572 TATAATTTT
1 TATAATTTT
41070581 CTAAAGTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
7 3 0.05
9 14 0.23
10 25 0.40
11 19 0.31
12 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (9 bp):
TATAATTTT
Found at i:41070592 original size:20 final size:19
Alignment explanation
Indices: 41070493--41070592 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 19
41070483 AGTTGGTTTA
41070493 TATAATTTTCTATAAGT-TTT
1 TATAATTTTCTA-AA-TATTT
* *
41070513 TATAATTTTTTAATAATGTTT
1 TATAATTTTCT-A-AATATTT
41070534 CTATAA-TTTCTACAATATTT
1 -TATAATTTTCTA-AATATTT
*
41070554 TCATAATATT-T-AATATTT
1 T-ATAATTTTCTAAATATTT
41070572 TATAATTTTCTAAAGTATTT
1 TATAATTTTCTAAA-TATTT
41070592 T
1 T
41070593 TTATAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
17 7 0.11
18 9 0.14
19 3 0.05
20 29 0.44
21 13 0.20
22 5 0.08
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (19 bp):
TATAATTTTCTAAATATTT
Found at i:41070966 original size:12 final size:12
Alignment explanation
Indices: 41070949--41070974 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41070939 CAAAACAGAC
41070949 TTTTAGCGGCGT
1 TTTTAGCGGCGT
41070961 TTTTAGCGGCGT
1 TTTTAGCGGCGT
41070973 TT
1 TT
41070975 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:41071364 original size:114 final size:114
Alignment explanation
Indices: 41071043--41071478 Score: 598
Period size: 114 Copynumber: 3.9 Consensus size: 114
41071033 AAAATAAGCA
* * * ** * * *
41071043 TTAGCGGTGTTTTTGAGAAAGCGCTGCAAAAAA-CCTAAGCGAAACGAC-ATCGTTTCCCGAGCT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCT-GTTTTCTGAGCT
* * *
41071106 TTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCAGGGAT
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * *
41071156 TTAACGACGTTTTTGGAAAAGCGCTGC-AAAAATCCTAAGCCC-A--ACGC-GTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCTGTTTTCTGAGCTT
*
41071216 TTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
41071265 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCTGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCTGTTTTCTGAGCTT
* * * *
41071330 TCGGCGATTTAACGGTGTTTTTAAGAACGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * *
41071379 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGTCCAACGGCGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCTGTTTTCTGAGCTT
41071444 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
41071479 AAGAAAACCT
Statistics
Matches: 285, Mismatches: 31, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
109 79 0.28
110 17 0.06
111 1 0.00
112 6 0.02
113 33 0.12
114 149 0.52
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGACGCTGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:41071392 original size:223 final size:225
Alignment explanation
Indices: 41071043--41071478 Score: 612
Period size: 223 Copynumber: 1.9 Consensus size: 225
41071033 AAAATAAGCA
* * *
41071043 TTAGCGGTGTTTTTGAGAAAGCGCTGCAAAAAACCTAAGCGAAACGACATCGTTTCCCGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAACGACATCGTTTCCCGAGCTTT
* *
41071108 CAGGGATTTAGCGGCGTTTTTAAGAAAGCGTCGCTAATGCTCAGGGATTTAACGACGTTTTTGGA
66 CAGGGATTTAACGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAACGACGTTTTTGGA
* * *
41071173 AAAGCGCTGC-AAAAATCCTAAGCCCAA-CG-CGTTTTCTGAGCTTTTGGGGATTTAGCGGCGTT
131 AAAGCGCCGCAAAAAAACCTAAGCCCAAGCGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTT
41071235 TTTAAGAAAGCGCCGCTAATGCTCAGGGCT
196 TTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * * *
41071265 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAATCCTAAGCCCAACGAC-GCTGTTTTCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAA-CCTAAGCCAAACGACATC-GTTTCCCGAGCT
* * * * *
41071329 TTC-GGCGATTTAACGGTGTTTTTAAGAACGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT
64 TTCAGG-GATTTAACGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAACGACGTTTTT
* *
41071393 GGGAAAGCGCCGCAAAAAAACCTAAGTCCAACGGCGCCGTTTTCTGAGCTTTCGGGGATTTAGCG
128 GGAAAAGCGCCGCAAAAAAACCTAAGCCCAA--GCGCCGTTTTCTGAGCTTTCGGGGATTTAGCG
41071458 GCGTTTTTAAGAAAGCGCCGC
191 GCGTTTTTAAGAAAGCGCCGC
41071479 AAGAAAACCT
Statistics
Matches: 186, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
222 33 0.18
223 88 0.47
224 15 0.08
227 2 0.01
228 48 0.26
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (225 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAACGACATCGTTTCCCGAGCTTT
CAGGGATTTAACGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGATTTAACGACGTTTTTGGA
AAAGCGCCGCAAAAAAACCTAAGCCCAAGCGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTT
TTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:41071497 original size:73 final size:73
Alignment explanation
Indices: 41071378--41071557 Score: 290
Period size: 73 Copynumber: 2.5 Consensus size: 73
41071368 TGCTCAGGGC
* * *
41071378 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGTCCAACGGCGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
41071443 TTCGGGGA
66 TTCGGGGA
* *
41071451 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAGAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
41071516 TTCGGGGA
66 TTCGGGGA
*
41071524 TTTAGCGGCG-TTTTGAGAAAAGCGCCGCTAAAAA
1 TTTAGCGGCGTTTTTGAG-AAAGCGCCGCAAAAAA
41071558 TAATTTATCT
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 6 0.06
73 92 0.94
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGA
Found at i:41072091 original size:15 final size:15
Alignment explanation
Indices: 41072071--41072117 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
41072061 TGTTTTAATG
*
41072071 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
41072086 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
41072100 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
41072114 TTTA
1 TTTA
41072118 AGGGTTGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:41072153 original size:15 final size:14
Alignment explanation
Indices: 41072129--41072198 Score: 72
Period size: 15 Copynumber: 4.9 Consensus size: 14
41072119 GGGTTGAGAT
41072129 TTAAGGTTTAGGGG
1 TTAAGGTTTAGGGG
41072143 TTAAGGGTTTAGGGG
1 TTAA-GGTTTAGGGG
*
41072158 TT-AGATGTTAGGGG
1 TTAAGGT-TTAGGGG
*
41072172 TTAAGAG-TTAGGGAT
1 TTAAG-GTTTAGGG-G
41072187 TTAAGGTTTAGG
1 TTAAGGTTTAGG
41072199 AATTCAGGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.04
14 21 0.45
15 24 0.51
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (14 bp):
TTAAGGTTTAGGGG
Found at i:41072720 original size:134 final size:133
Alignment explanation
Indices: 41072563--41072812 Score: 378
Period size: 134 Copynumber: 1.9 Consensus size: 133
41072553 ATTTTATAAA
* *
41072563 AAATCAATTTATAAAAACAAAAAAAAATT-TTAGCATAGCAAAACGGCGTCATTTTGTTCAAAAT
1 AAATCAATTTATAAAAAC-AAAAAAAATTATTAGAATAGCAAAACGGCATCATTTTGTTCAAAAT
* *
41072627 GAAAAAAATTTTGCGGCGTTTTTCATAAAAACGCCGCAAAAGATAAGCAATAAAAAACGCCGCAA
65 GAAAAAAA-TTTGCGGCGTTTGTCATAAAAACGCCGCAAAAGATAAGAAATAAAAAACGCCGCAA
41072692 AAAAT
129 AAAAT
* ** *
41072697 AAATCAATTTATTAAAAA-TAAAAATTTTAGTTAGAATAGCAAAACGGCATCGTTTTGTTCAAAA
1 AAATCAATTTA-TAAAAACAAAAAAAATTA-TTAGAATAGCAAAACGGCATCATTTTGTTCAAAA
41072761 TGAAAAAAATTTGCGGCGTTTGTCATAAAAACGCCGCAAAAGATAAGAAATA
64 TGAAAAAAATTTGCGGCGTTTGTCATAAAAACGCCGCAAAAGATAAGAAATA
41072813 GCATAAAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
133 7 0.07
134 52 0.50
135 46 0.44
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (133 bp):
AAATCAATTTATAAAAACAAAAAAAATTATTAGAATAGCAAAACGGCATCATTTTGTTCAAAATG
AAAAAAATTTGCGGCGTTTGTCATAAAAACGCCGCAAAAGATAAGAAATAAAAAACGCCGCAAAA
AAT
Found at i:41072831 original size:32 final size:31
Alignment explanation
Indices: 41072787--41072868 Score: 139
Period size: 32 Copynumber: 2.6 Consensus size: 31
41072777 CGTTTGTCAT
41072787 AAAAACGCCGCAAAAGATAAGAAATAGCATA
1 AAAAACGCCGCAAAAGATAAGAAATAGCATA
*
41072818 AAAAACCGCCGCAAAAGATAAGCAATAGCATA
1 AAAAA-CGCCGCAAAAGATAAGAAATAGCATA
41072850 AAAAACGCCGCAAAA-ATAA
1 AAAAACGCCGCAAAAGATAA
41072869 ATCAATTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
30 4 0.08
31 15 0.31
32 30 0.61
ACGTcount: A:0.57, C:0.20, G:0.15, T:0.09
Consensus pattern (31 bp):
AAAAACGCCGCAAAAGATAAGAAATAGCATA
Found at i:41073104 original size:108 final size:106
Alignment explanation
Indices: 41072847--41073140 Score: 370
Period size: 108 Copynumber: 2.8 Consensus size: 106
41072837 AAGCAATAGC
* * *
41072847 ATAAAAAACGCCGCAAAAATAAATCAATTTATAAAAAATAAAATAAAAAATTTTTAGCATAGCAA
1 ATAAAAAACGCCGCAAAAATAAATCAATTTAT--TAAA-AAAATAAAAAAATTTTAGAATAGCAA
* * * *
41072912 AACGGTGTCATTTTGTTC----AAAATGAAATAGCGGCGTTTTT
63 AACGGCGTCGTTTTGTTCAAAAAAAATGAAATAGCAGCATTTTT
*
41072952 AT---AAACGCCGCAAAAAATAAATCAATTTA-TAAAAAAATAAAAAAATTTTAGAATAGCAAGA
1 ATAAAAAACGCCGC-AAAAATAAATCAATTTATTAAAAAAATAAAAAAATTTTAGAATAGCAAAA
*
41073013 CGGCGTCGTTTTGTTCAAAAAAAAATTAGAATAGCAGCATTTTT
65 CGGCGTCGTTTTGTTC-AAAAAAAATGA-AATAGCAGCATTTTT
**
41073057 ATAAAAAACGCCGCAAAAATAAATCAATTTATTAAAAAAATAAAAAAAAATTAGAATAGCAAAAC
1 ATAAAAAACGCCGCAAAAATAAATCAATTTATTAAAAAAATAAAAAAATTTTAGAATAGCAAAAC
*
41073122 GACGTCGTTTTGTTCAAAA
66 GGCGTCGTTTTGTTCAAAA
41073141 TGAAAAAATT
Statistics
Matches: 165, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
99 39 0.24
100 3 0.02
102 9 0.05
103 17 0.10
104 6 0.04
105 17 0.10
107 21 0.13
108 53 0.32
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.26
Consensus pattern (106 bp):
ATAAAAAACGCCGCAAAAATAAATCAATTTATTAAAAAAATAAAAAAATTTTAGAATAGCAAAAC
GGCGTCGTTTTGTTCAAAAAAAATGAAATAGCAGCATTTTT
Found at i:41076594 original size:18 final size:17
Alignment explanation
Indices: 41076571--41076603 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41076561 GTTTATTTTA
41076571 AATTTTTTGTACATATT
1 AATTTTTTGTACATATT
41076588 AATTTTTTGTACATAT
1 AATTTTTTGTACATAT
41076604 AAAGTAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
AATTTTTTGTACATATT
Done.