Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 196 of 199
Found at i:57095275 original size:3 final size:3
Alignment explanation
Indices: 57095267--57095306 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
57095257 TAGTTACCAC
57095267 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
57095307 GCAAACAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:57101931 original size:111 final size:111
Alignment explanation
Indices: 57101696--57101941 Score: 327
Period size: 111 Copynumber: 2.2 Consensus size: 111
57101686 TCATCAAAGT
* * * *
57101696 CATGCAAACAGAATATAACCGAGTCATTCCGATCCGTCGATCTAGCCATTAATCTAACCCTAAAC
1 CATGGAAACAGAACATAACCAAGTCATTCCGATCCGTCAATCTAGCCATTAATCTAACCCTAAAC
* * *
57101761 TTTGAAATTTCTGGCGAAATTAAATAAGGCTCAAAAGTGTTAGAAG
66 TTTCAAATTTCTGGCGAAATTAAAGAAGGCTCAAAAGTGTAAGAAG
* * **
57101807 CATGGAAACAGAACATAACCAAGTCCTTCCGTTCCGTCAATCTAGCGGTTAATCTAACCCTAAAC
1 CATGGAAACAGAACATAACCAAGTCATTCCGATCCGTCAATCTAGCCATTAATCTAACCCTAAAC
* *
57101872 -TTCAAATTT-TCGAGTGAAA-TCAAGAAGGCTCAAAAGTGTAAGAAG
66 TTTCAAATTTCT-G-GCGAAATTAAAGAAGGCTCAAAAGTGTAAGAAG
57101917 CATGGAAACAAGAACATAACCAAGT
1 CATGGAAAC-AGAACATAACCAAGT
57101942 AAAACCAGAT
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
109 1 0.01
110 41 0.34
111 77 0.65
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (111 bp):
CATGGAAACAGAACATAACCAAGTCATTCCGATCCGTCAATCTAGCCATTAATCTAACCCTAAAC
TTTCAAATTTCTGGCGAAATTAAAGAAGGCTCAAAAGTGTAAGAAG
Found at i:57103764 original size:3 final size:3
Alignment explanation
Indices: 57103756--57103802 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
57103746 GAAAATGTTG
57103756 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
57103803 ATTCTTTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:57105244 original size:19 final size:20
Alignment explanation
Indices: 57105200--57105257 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
57105190 TTAATTACAA
* *
57105200 ATATTTAACTATTATATTATT
1 ATATTTAAATATAAT-TTATT
57105221 ATATTTAAATATAATTTA-T
1 ATATTTAAATATAATTTATT
*
57105240 ATATTCTAATTA-AATTTA
1 ATATT-TAAATATAATTTA
57105258 GTAAATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 12 0.36
20 8 0.24
21 13 0.39
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTTAAATATAATTTATT
Found at i:57105506 original size:13 final size:13
Alignment explanation
Indices: 57105488--57105548 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
57105478 CTCAAATTTT
*
57105488 TCAAAAGTACTTC
1 TCAAAAGCACTTC
*
57105501 TCAAAAGCACTTT
1 TCAAAAGCACTTC
* * * *
57105514 TCCACAGCATTTT
1 TCAAAAGCACTTC
*
57105527 TCAAAAGCACTTT
1 TCAAAAGCACTTC
57105540 TCAAAAGCA
1 TCAAAAGCA
57105549 ATGAAGAACT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.30
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:57105548 original size:26 final size:26
Alignment explanation
Indices: 57105485--57105548 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
57105475 ACACTCAAAT
*
57105485 TTTTCAAAAGTACTTCTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
* * * *
57105511 TTTTCCACAGCATTTTTCAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAGCAC
57105537 TTTTCAAAAGCA
1 TTTTCAAAAGCA
57105549 ATGAAGAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAGCAC
Found at i:57105833 original size:19 final size:21
Alignment explanation
Indices: 57105809--57105849 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
57105799 TCATATGTAC
57105809 TTTAT-GTTATTTT-TAATTT
1 TTTATGGTTATTTTATAATTT
*
57105828 TTTATGGTTTTTTTATAATTT
1 TTTATGGTTATTTTATAATTT
57105849 T
1 T
57105850 AAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTATGGTTATTTTATAATTT
Found at i:57106665 original size:29 final size:29
Alignment explanation
Indices: 57106632--57106698 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
57106622 ATAAGGACAT
* *
57106632 GATCAAATTAATCAT-TTTACTATTAAATA
1 GATCAAATTAATC-TCTATACTATTAAAAA
**
57106661 GATCATTTTAATCTCTATACTATTAAAAA
1 GATCAAATTAATCTCTATACTATTAAAAA
57106690 GAATCAAAT
1 G-ATCAAAT
57106699 AAGTTCAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.80
30 5 0.17
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (29 bp):
GATCAAATTAATCTCTATACTATTAAAAA
Found at i:57107070 original size:31 final size:31
Alignment explanation
Indices: 57107006--57107105 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
57106996 ACAAAGTTTA
* *
57107006 TCAAATGAA-AGCCAAA-C-TTTTCAAAGTGA
1 TCAAAT-AAGAGCCAAACCTTTTTAAAAGTGC
57107035 TCAAATAAGAGCCAAACCTTTTTAAAAGTGC
1 TCAAATAAGAGCCAAACCTTTTTAAAAGTGC
* * *
57107066 TCAAATAAGAGTCAAACCTTTTTGAAAGTAC
1 TCAAATAAGAGCCAAACCTTTTTAAAAGTGC
57107097 TCAAATAAG
1 TCAAATAAG
57107106 GGCTTCTCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
28 2 0.03
29 13 0.21
30 1 0.02
31 47 0.75
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (31 bp):
TCAAATAAGAGCCAAACCTTTTTAAAAGTGC
Found at i:57121217 original size:28 final size:28
Alignment explanation
Indices: 57121185--57121240 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
57121175 GTCCTTGCTA
57121185 AACGATAACTGTTAAAGTCATTAAGTTT
1 AACGATAACTGTTAAAGTCATTAAGTTT
* *
57121213 AACGATAATTGTTAAATTCATTAAGTTT
1 AACGATAACTGTTAAAGTCATTAAGTTT
57121241 TGCTATTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (28 bp):
AACGATAACTGTTAAAGTCATTAAGTTT
Found at i:57121878 original size:30 final size:30
Alignment explanation
Indices: 57121842--57121901 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
57121832 GTTATAATAG
57121842 GAACTCGTATTAACAAGCTGGATATTATCT
1 GAACTCGTATTAACAAGCTGGATATTATCT
57121872 GAACTCGTATTAACAAGCTGGATATTATCT
1 GAACTCGTATTAACAAGCTGGATATTATCT
57121902 TTCTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (30 bp):
GAACTCGTATTAACAAGCTGGATATTATCT
Found at i:57121897 original size:15 final size:15
Alignment explanation
Indices: 57121849--57121898 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
57121839 TAGGAACTCG
57121849 TATTAACAAGCTGGA
1 TATTAACAAGCTGGA
* *
57121864 TATTATCTGAA-CTCG-
1 TATTAAC--AAGCTGGA
57121879 TATTAACAAGCTGGA
1 TATTAACAAGCTGGA
57121894 TATTA
1 TATTA
57121899 TCTTTCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.07
14 3 0.11
15 17 0.63
16 3 0.11
17 2 0.07
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (15 bp):
TATTAACAAGCTGGA
Found at i:57131336 original size:33 final size:33
Alignment explanation
Indices: 57131294--57131357 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
57131284 TTTTCACTGG
57131294 GGTAGGATTGAAATATATAGTAAATACTAACGA
1 GGTAGGATTGAAATATATAGTAAATACTAACGA
**
57131327 GGTAGGATTGAGCTATATAGTAAATACTAAC
1 GGTAGGATTGAAATATATAGTAAATACTAAC
57131358 ACAGATAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (33 bp):
GGTAGGATTGAAATATATAGTAAATACTAACGA
Found at i:57142455 original size:21 final size:21
Alignment explanation
Indices: 57142430--57142474 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
57142420 CTTTTGTTTC
*
57142430 AATTATTGTTTTTTTAG-TGAA
1 AATTATTATTTTTTT-GTTGAA
57142451 AATTATTATTTTTTTGTTGAA
1 AATTATTATTTTTTTGTTGAA
57142472 AAT
1 AAT
57142475 AAAGAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (21 bp):
AATTATTATTTTTTTGTTGAA
Found at i:57144985 original size:42 final size:41
Alignment explanation
Indices: 57144899--57144995 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
57144889 TAATTCTTTT
* *
57144899 ATTA-AAATTATATATATCTTAATATTTTTTTAATATTTAC
1 ATTATAAATTATATATATCTTAATATTTTTTTAATATATAA
57144939 ATTATAATATTATATATCA-CTTTAGATATTTTTTT-AT-TATAA
1 ATTATAA-ATTATATAT-ATC-TTA-ATATTTTTTTAATATATAA
*
57144981 ATTATAAAATATATA
1 ATTATAAATTATATA
57144996 AAAGAATAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
40 4 0.08
41 9 0.18
42 20 0.41
43 6 0.12
44 10 0.20
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (41 bp):
ATTATAAATTATATATATCTTAATATTTTTTTAATATATAA
Found at i:57150604 original size:2 final size:2
Alignment explanation
Indices: 57150597--57150621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57150587 TCTCCCCGTG
57150597 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 T
57150622 GTGATCCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57150971 original size:86 final size:86
Alignment explanation
Indices: 57150876--57151038 Score: 254
Period size: 86 Copynumber: 1.9 Consensus size: 86
57150866 CTTAATTCAT
* *
57150876 TGTGATGTATGCATCCACAATCCCAATTTAAATCTTGAGTTTGGTAAGTTTTTATGTCAGCTTTA
1 TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
57150941 AGTAGAATTATCTTAACTAAC
66 AGTAGAATTATCTTAACTAAC
* ***
57150962 TGTGATGTATGCATCCGCAATTTTAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
1 TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
* *
57151027 GGTGGAATTATC
66 AGTAGAATTATC
57151039 AAGCATACAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (86 bp):
TGTGATGTATGCATCCACAATCCCAATTTAAATCTCGAGTTTGGTAAGCTTTTATGTCAGCTTTA
AGTAGAATTATCTTAACTAAC
Found at i:57154008 original size:30 final size:32
Alignment explanation
Indices: 57153965--57154035 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
57153955 AGCTTAATAT
** **
57153965 TATTATATTAATAAAAAAATATTTTTA-AAAA
1 TATTATAAAAATAAAAAAATATTAATATAAAA
*
57153996 TATT-TAAAAATAATAAAATATTAATATAAAA
1 TATTATAAAAATAAAAAAATATTAATATAAAA
57154027 TATTATAAA
1 TATTATAAA
57154036 TTTCAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 17 0.52
31 12 0.36
32 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
TATTATAAAAATAAAAAAATATTAATATAAAA
Found at i:57154036 original size:22 final size:21
Alignment explanation
Indices: 57154002--57154044 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
57153992 AAAATATTTA
57154002 AAAATAATAAAATATT-AATAT
1 AAAATAATAAAAT-TTCAATAT
*
57154023 AAAATATTATAAATTTCAATAT
1 AAAATAATA-AAATTTCAATAT
57154045 TATTAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATAATAAAATTTCAATAT
Found at i:57154183 original size:15 final size:15
Alignment explanation
Indices: 57154163--57154219 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
57154153 ATTCAATATT
57154163 AATATTTTAATAATA
1 AATATTTTAATAATA
*
57154178 AATATTTATAACAATTATA
1 AATATTT-T---AATAATA
*
57154197 AATATATTAATAATA
1 AATATTTTAATAATA
*
57154212 AATGTTTT
1 AATATTTT
57154220 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 19 0.58
16 1 0.03
18 1 0.03
19 12 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:57157118 original size:13 final size:13
Alignment explanation
Indices: 57157096--57157125 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
57157086 TCATGGTTTG
*
57157096 AAGAAGAAGAAAA
1 AAGAAAAAGAAAA
57157109 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
57157122 AAGA
1 AAGA
57157126 GAATGAAAAT
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:57158357 original size:6 final size:6
Alignment explanation
Indices: 57158306--57158342 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
57158296 ACGAAGAAGA
57158306 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
57158343 GAATGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:57159989 original size:6 final size:6
Alignment explanation
Indices: 57159978--57160006 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
57159968 TTTATGAACA
57159978 ATATGT ATATGT ATATGT ATATGT ATATG
1 ATATGT ATATGT ATATGT ATATGT ATATG
57160007 ATTACAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
ATATGT
Found at i:57164008 original size:25 final size:25
Alignment explanation
Indices: 57163971--57164024 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
57163961 CCATTTTTTT
* * *
57163971 AATAAACACTAAAAATTTATTTTTAA
1 AATAAACAATAAAAA-GTATTTTAAA
57163997 AATAAA-AATAAAAAGTATTTTAAA
1 AATAAACAATAAAAAGTATTTTAAA
57164021 AATA
1 AATA
57164025 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.48
25 7 0.28
26 6 0.24
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AATAAACAATAAAAAGTATTTTAAA
Found at i:57164021 original size:11 final size:11
Alignment explanation
Indices: 57164005--57164035 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
57163995 AAAATAAAAA
57164005 TAAAAAGTATTT
1 TAAAAA-TATTT
57164017 TAAAAATATTT
1 TAAAAATATTT
57164028 TAAAAATA
1 TAAAAATA
57164036 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:57172160 original size:28 final size:28
Alignment explanation
Indices: 57172095--57172150 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
57172085 TTAGGAGCTG
57172095 GTGCATAATTCAGGGAAATAATCTACTA
1 GTGCATAATTCAGGGAAATAATCTACTA
57172123 GTGCATAATTCAGGGAAATAATCTACTA
1 GTGCATAATTCAGGGAAATAATCTACTA
57172151 AGGATGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (28 bp):
GTGCATAATTCAGGGAAATAATCTACTA
Found at i:57188732 original size:20 final size:20
Alignment explanation
Indices: 57188709--57188747 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57188699 CTGGTTTTCT
*
57188709 AATTTTTTAATGTATTTTTA
1 AATTTTTTAATGAATTTTTA
*
57188729 AATTTTTTTATGAATTTTT
1 AATTTTTTAATGAATTTTT
57188748 TTTTTCTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
AATTTTTTAATGAATTTTTA
Found at i:57190846 original size:16 final size:15
Alignment explanation
Indices: 57190820--57190874 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
57190810 ATTAAGATTT
*
57190820 TAAATTTAAAAAATA
1 TAAAATTAAAAAATA
57190835 TAGAAATT-AAAAATGA
1 TA-AAATTAAAAAAT-A
*
57190851 TAAATTTAAAAAATA
1 TAAAATTAAAAAATA
57190866 T-AAATTAAA
1 TAAAATTAAA
57190875 TACATAACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.21
15 14 0.41
16 13 0.38
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
TAAAATTAAAAAATA
Found at i:57198607 original size:31 final size:29
Alignment explanation
Indices: 57198569--57198646 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
57198559 CTAACGGCTT
* *
57198569 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
57198600 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
57198629 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
57198647 TGAGCCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:57198663 original size:31 final size:29
Alignment explanation
Indices: 57198594--57198667 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
57198584 ACAACGTGAT
**
57198594 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGCCA
*
57198623 AACATAAGTGACTAAAATGTAACATGAGCCA
1 AACATAAGTGACTAAAACGTAACAT--GCCA
*
57198654 AACAAAAGTGACTA
1 AACATAAGTGACTA
57198668 TTTTAGAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGCCA
Found at i:57229249 original size:12 final size:12
Alignment explanation
Indices: 57229232--57229265 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57229222 TAGTATTTAT
57229232 ATTAAATTATAA
1 ATTAAATTATAA
*
57229244 ATTAAAATATAA
1 ATTAAATTATAA
*
57229256 AATAAATTAT
1 ATTAAATTAT
57229266 CTATATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATTAAATTATAA
Found at i:57233463 original size:12 final size:13
Alignment explanation
Indices: 57233446--57233483 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
57233436 TAGCTTTTCC
57233446 TTTTTA-ATAATT
1 TTTTTATATAATT
*
57233458 TTTTTATATTTATT
1 TTTTTATA-TAATT
57233472 TTTTTATATAAT
1 TTTTTATATAAT
57233484 GTCTAGAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTATATAATT
Found at i:57245056 original size:2 final size:2
Alignment explanation
Indices: 57245049--57245080 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57245039 ATTTACACCT
57245049 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
57245081 ATGTTGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57249069 original size:2 final size:2
Alignment explanation
Indices: 57249062--57249089 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57249052 AAAGGTAATT
57249062 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
57249090 AAACAAAACT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57259464 original size:77 final size:77
Alignment explanation
Indices: 57259337--57259496 Score: 284
Period size: 77 Copynumber: 2.1 Consensus size: 77
57259327 TCCCCCAATT
*
57259337 TTTTACAACTTAGTTTCACGCCCCATGAAATAGCTTTACATGTCACATATCTGCGAACCAAAATC
1 TTTTACAACTTAGTTTCACGCCCCATGAAATAGCTTTACATGTCACATATCTACGAACCAAAATC
57259402 TAAACAATTTTC
66 TAAACAATTTTC
* * *
57259414 TTTTATAACTTAGTTTCAGGCCCCATGAAATAGCTTTACATGTCACATATCTACGAACTAAAATC
1 TTTTACAACTTAGTTTCACGCCCCATGAAATAGCTTTACATGTCACATATCTACGAACCAAAATC
57259479 TAAACAATTTTC
66 TAAACAATTTTC
57259491 TTTTAC
1 TTTTAC
57259497 GATCTTCGAC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.35
Consensus pattern (77 bp):
TTTTACAACTTAGTTTCACGCCCCATGAAATAGCTTTACATGTCACATATCTACGAACCAAAATC
TAAACAATTTTC
Found at i:57264430 original size:16 final size:16
Alignment explanation
Indices: 57264397--57264430 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57264387 TAATTCTCTG
**
57264397 TACAAGCTGCTTTTTT
1 TACAAGCTGCTTGGTT
57264413 TACAAGCTGCTTGGTT
1 TACAAGCTGCTTGGTT
57264429 TA
1 TA
57264431 ATGTTGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (16 bp):
TACAAGCTGCTTGGTT
Found at i:57276605 original size:26 final size:27
Alignment explanation
Indices: 57276563--57276613 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
57276553 AGGTCAAGAG
*
57276563 TCAAATTTAACTAAAAAA-GAATAAAGT
1 TCAAATTTAAC-AAAAAATAAATAAAGT
57276590 TCAAA-TTAACAAAAAATAAATAAA
1 TCAAATTTAACAAAAAATAAATAAA
57276614 AATAAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 11 0.50
27 5 0.23
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.24
Consensus pattern (27 bp):
TCAAATTTAACAAAAAATAAATAAAGT
Found at i:57284829 original size:13 final size:14
Alignment explanation
Indices: 57284802--57284830 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
57284792 ATTTCTTCAG
57284802 TTTTTTTTTCTCTT
1 TTTTTTTTTCTCTT
57284816 TTTTTTTTTC-CTT
1 TTTTTTTTTCTCTT
57284829 TT
1 TT
57284831 CGTTCAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTCTCTT
Found at i:57285231 original size:13 final size:13
Alignment explanation
Indices: 57285213--57285244 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
57285203 GCCTAATGTG
57285213 ATATGTGCTTTGA
1 ATATGTGCTTTGA
57285226 ATATGTGCTTTGA
1 ATATGTGCTTTGA
57285239 ATATGT
1 ATATGT
57285245 TCAATGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (13 bp):
ATATGTGCTTTGA
Found at i:57291407 original size:17 final size:16
Alignment explanation
Indices: 57291375--57291417 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
57291365 AATTGATCCG
*
57291375 AATTTTATAATTTTTAA
1 AATTTT-TATTTTTTAA
*
57291392 TATATTTTATTTTTTAA
1 AAT-TTTTATTTTTTAA
57291409 AATTTTTAT
1 AATTTTTAT
57291418 AATTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.27
17 13 0.59
18 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTTTTATTTTTTAA
Found at i:57292571 original size:21 final size:21
Alignment explanation
Indices: 57292529--57292571 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
57292519 TATTTACATA
**
57292529 TTTTATAAATATTTAAATAAT
1 TTTTATAAATAAATAAATAAT
57292550 TTTTATCAAATAAATAAA-AAT
1 TTTTAT-AAATAAATAAATAAT
57292571 T
1 T
57292572 CAATGCTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTATAAATAAATAAATAAT
Found at i:57293060 original size:37 final size:37
Alignment explanation
Indices: 57293007--57293087 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
57292997 TAATCATATT
*
57293007 AAATTATGATACATTCATGATGATGTGATTAAAAATC
1 AAATTATGATACATTCATGATGATGTGATTAAAAAAC
*
57293044 AATTTATGATACATTCATGATGATGTGATTAAAAAAC
1 AAATTATGATACATTCATGATGATGTGATTAAAAAAC
57293081 AAATTAT
1 AAATTAT
57293088 AAATATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (37 bp):
AAATTATGATACATTCATGATGATGTGATTAAAAAAC
Found at i:57298839 original size:33 final size:33
Alignment explanation
Indices: 57298802--57298906 Score: 126
Period size: 33 Copynumber: 3.3 Consensus size: 33
57298792 CAGTTAGTAC
*
57298802 GGATGATGCTCCTTTAAGCAGGACAAGTAGCAG
1 GGATGATGCTCCTTTAAGCAGGCCAAGTAGCAG
* * * *
57298835 GGATG-TG-T-CTATAAGCCGGCCAACTAGTAG
1 GGATGATGCTCCTTTAAGCAGGCCAAGTAGCAG
* *
57298865 GGATGATGCCCCTTCAAGCAGGCCAAGTAGCAG
1 GGATGATGCTCCTTTAAGCAGGCCAAGTAGCAG
57298898 GGATGATGC
1 GGATGATGC
57298907 CCCTATAATC
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
30 22 0.38
31 3 0.05
32 2 0.03
33 31 0.53
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.20
Consensus pattern (33 bp):
GGATGATGCTCCTTTAAGCAGGCCAAGTAGCAG
Found at i:57298907 original size:33 final size:32
Alignment explanation
Indices: 57298802--57298919 Score: 116
Period size: 33 Copynumber: 3.7 Consensus size: 32
57298792 CAGTTAGTAC
* *
57298802 GGATGATGCTCCTTTAAGCAGGACAAGTAGCAG
1 GGATGATGC-CCCTTAAGCAGGCCAAGTAGCAG
* * * *
57298835 GGATG-TG--TCTATAAGCCGGCCAACTAGTAG
1 GGATGATGCCCCT-TAAGCAGGCCAAGTAGCAG
57298865 GGATGATGCCCCTTCAAGCAGGCCAAGTAGCAG
1 GGATGATGCCCCTT-AAGCAGGCCAAGTAGCAG
*
57298898 GGATGATGCCCCTATAATCAGG
1 GGATGATGCCCCT-TAAGCAGG
57298920 TTGGGTGTTG
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
29 1 0.01
30 20 0.29
31 2 0.03
32 3 0.04
33 41 0.60
34 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (32 bp):
GGATGATGCCCCTTAAGCAGGCCAAGTAGCAG
Found at i:57301621 original size:23 final size:24
Alignment explanation
Indices: 57301595--57301640 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
57301585 ACTAAAAATT
57301595 TATTTT-AAAAATAAAAAATAAAG
1 TATTTTAAAAAATAAAAAATAAAG
57301618 TATTTTAAAAAATAAAAAATAAA
1 TATTTTAAAAAATAAAAAATAAA
57301641 AATATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
TATTTTAAAAAATAAAAAATAAAG
Found at i:57301648 original size:24 final size:23
Alignment explanation
Indices: 57301595--57301648 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
57301585 ACTAAAAATT
* *
57301595 TATTTTAAAAATAAAAAATAAAG
1 TATTTAAAAAATAAAAAATAAAA
57301618 TATTTTAAAAAATAAAAAATAAAAA
1 TA-TTTAAAAAATAAAAAAT-AAAA
57301643 TATTTA
1 TATTTA
57301649 TTATATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 20 0.74
25 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TATTTAAAAAATAAAAAATAAAA
Found at i:57302528 original size:8 final size:8
Alignment explanation
Indices: 57302510--57302539 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
57302500 TACATTTAAA
57302510 TTTTAACTT
1 TTTTAA-TT
57302519 TTTTAATT
1 TTTTAATT
57302527 TTTTAATT
1 TTTTAATT
57302535 TTTTA
1 TTTTA
57302540 TTCTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTAATT
Found at i:57302546 original size:15 final size:17
Alignment explanation
Indices: 57302511--57302547 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
57302501 ACATTTAAAT
*
57302511 TTTAACTTTTTTAATTT
1 TTTAACTTTTTTAATTC
57302528 TTTAA-TTTTTT-ATTC
1 TTTAACTTTTTTAATTC
57302543 TTTAA
1 TTTAA
57302548 AATTGAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAACTTTTTTAATTC
Found at i:57306129 original size:24 final size:24
Alignment explanation
Indices: 57306088--57306141 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
57306078 GTGGAATTCA
* *
57306088 ATACATATGTAATCGGTGTCATGC
1 ATACATATATAATCGGTGTCATAC
57306112 ATACATATATAGAT-GGTGTCATAC
1 ATACATATATA-ATCGGTGTCATAC
57306136 ATACAT
1 ATACAT
57306142 GCTCTGAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (24 bp):
ATACATATATAATCGGTGTCATAC
Found at i:57306269 original size:20 final size:20
Alignment explanation
Indices: 57306244--57306310 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
57306234 GTGGAATTCA
57306244 ATACATACATAGATGGTGTC
1 ATACATACATAGATGGTGTC
*
57306264 ATACATACATAGA-GAGTTTC
1 ATACATACATAGATG-GTGTC
*
57306284 ATACATACATATATGGTGTC
1 ATACATACATAGATGGTGTC
57306304 ATACATA
1 ATACATA
57306311 TATTCATACA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
ATACATACATAGATGGTGTC
Found at i:57315888 original size:22 final size:21
Alignment explanation
Indices: 57315863--57315919 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
57315853 CTTGAAATGC
* *
57315863 ATTTTTTTAAATGTTTTATAAT
1 ATTTTTTTAAAT-TTTAAAAAT
*
57315885 ATTTTTATAAATTTTAAAAAT
1 ATTTTTTTAAATTTTAAAAAT
*
57315906 ATATTTTTGAAATT
1 AT-TTTTTTAAATT
57315920 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTTTTTTAAATTTTAAAAAT
Found at i:57315932 original size:35 final size:35
Alignment explanation
Indices: 57315885--57315953 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
57315875 GTTTTATAAT
*
57315885 ATTTTTATAAATTTTAAAAATATATTTTTGAAATTA
1 ATTTTTATAAATTTTAAAAAT-TATTTTTAAAATTA
*
57315921 ATTTTT-TAAATTTTAAATATTATTTTTAAAATT
1 ATTTTTATAAATTTTAAAAATTATTTTTAAAATT
57315954 TTAAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 12 0.39
35 13 0.42
36 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (35 bp):
ATTTTTATAAATTTTAAAAATTATTTTTAAAATTA
Found at i:57315938 original size:20 final size:21
Alignment explanation
Indices: 57315910--57315968 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
57315900 AAAAATATAT
*
57315910 TTTTGAAAT-TAATTTTTTAAA
1 TTTT-AAATATAATTTTTAAAA
*
57315931 TTTTAAATATTATTTTTAAAA
1 TTTTAAATATAATTTTTAAAA
57315952 TTTTAAATATATATTTT
1 TTTTAAATATA-ATTTT
57315969 AATAATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.73
22 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTAAATATAATTTTTAAAA
Found at i:57315945 original size:21 final size:22
Alignment explanation
Indices: 57315921--57315968 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
57315911 TTTGAAATTA
*
57315921 ATTTTTTAAATTTTAAATAT-T
1 ATTTTTAAAATTTTAAATATAT
57315942 ATTTTTAAAATTTTAAATATAT
1 ATTTTTAAAATTTTAAATATAT
57315964 ATTTT
1 ATTTT
57315969 AATAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTTAAAATTTTAAATATAT
Found at i:57316248 original size:12 final size:12
Alignment explanation
Indices: 57316233--57316316 Score: 57
Period size: 11 Copynumber: 7.8 Consensus size: 12
57316223 TAATATTTAA
57316233 AATTTTAAAAAT
1 AATTTTAAAAAT
57316245 AA-TTT--AAAT
1 AATTTTAAAAAT
57316254 --T-TTAAAAAT
1 AATTTTAAAAAT
57316263 AA-TTTAAAAAT
1 AATTTTAAAAAT
57316274 AATATTT-AAAAT
1 AAT-TTTAAAAAT
*
57316286 --TTTAAAAAAT
1 AATTTTAAAAAT
57316296 AA-TTT-AAAAT
1 AATTTTAAAAAT
57316306 AATATTTAAAA
1 AAT-TTTAAAA
57316317 TTTAAAAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 27
0.66 0.02 0.32
Matches are distributed among these distances:
7 2 0.04
9 10 0.18
10 13 0.23
11 15 0.27
12 10 0.18
13 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATTTTAAAAAT
Found at i:57316286 original size:20 final size:19
Alignment explanation
Indices: 57316263--57316338 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 19
57316253 TTTTAAAAAT
57316263 AATTTAAAAATAATATTTAA
1 AATTT-AAAATAATATTTAA
*
57316283 AATTTTAAA-AA-A--T--
1 AATTTAAAATAATATTTAA
57316296 AATTTAAAATAATATTTAA
1 AATTTAAAATAATATTTAA
57316315 AATTTAAAAATATATATTATAA
1 AATTT-AAAATA-ATATT-TAA
57316337 AA
1 AA
57316339 CATTTCAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
13 8 0.18
14 2 0.04
15 2 0.04
17 2 0.04
18 2 0.04
19 8 0.18
20 11 0.24
21 5 0.11
22 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTAAAATAATATTTAA
Found at i:57316291 original size:32 final size:32
Alignment explanation
Indices: 57316236--57316326 Score: 138
Period size: 32 Copynumber: 3.0 Consensus size: 32
57316226 TATTTAAAAT
57316236 TTTAAAAAT-A-ATTT-AAATTTTAAAAATAA
1 TTTAAAAATAATATTTAAAATTTTAAAAATAA
57316265 TTTAAAAATAATATTTAAAATTTTAAAAAATAA
1 TTTAAAAATAATATTTAAAATTTT-AAAAATAA
57316298 TTT-AAAATAATATTTAAAA-TTTAAAAATA
1 TTTAAAAATAATATTTAAAATTTTAAAAATA
57316327 TATATTATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
29 9 0.16
30 8 0.14
31 7 0.12
32 23 0.40
33 11 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTAAAAATAATATTTAAAATTTTAAAAATAA
Found at i:57316317 original size:12 final size:12
Alignment explanation
Indices: 57316258--57316317 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
57316248 TTAAATTTTA
*
57316258 AAAATAAT-TTA
1 AAAATAATATTT
57316269 AAAATAATATTT
1 AAAATAATATTT
57316281 --AA-AAT-TTT
1 AAAATAATATTT
57316289 AAAA-AATAATTT
1 AAAATAAT-ATTT
57316301 AAAATAATATTT
1 AAAATAATATTT
57316313 AAAAT
1 AAAAT
57316318 TTAAAAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 7 0.17
11 8 0.19
12 18 0.43
13 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATAATATTT
Found at i:57316396 original size:9 final size:8
Alignment explanation
Indices: 57316371--57316412 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
57316361 TTTTTTAATT
57316371 AAAAAT-A
1 AAAAATAA
57316378 AAAAATAA
1 AAAAATAA
57316386 AAAAATAA
1 AAAAATAA
*
57316394 AAAAAGGAA
1 AAAAA-TAA
*
57316403 AAATATAA
1 AAAAATAA
57316411 AA
1 AA
57316413 CTTAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
7 6 0.20
8 18 0.60
9 6 0.20
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:57316412 original size:23 final size:23
Alignment explanation
Indices: 57316370--57316431 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
57316360 GTTTTTTAAT
*
57316370 TAAAAATA-AAAAATAAAAAA-A
1 TAAAAAAAGAAAAATAAAAAACA
* *
57316391 TAAAAAAAGGAAAAATATAAAACT
1 TAAAAAAA-GAAAAATAAAAAACA
57316415 TAAAAAAAGAAAGAATA
1 TAAAAAAAGAAA-AATA
57316432 GGACAAAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 7 0.21
23 15 0.44
24 12 0.35
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (23 bp):
TAAAAAAAGAAAAATAAAAAACA
Found at i:57316418 original size:24 final size:22
Alignment explanation
Indices: 57316370--57316431 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
57316360 GTTTTTTAAT
*
57316370 TAAAAATA-AAAAATAAAAAAA
1 TAAAAAAAGAAAAATAAAAAAA
**
57316391 TAAAAAAAGGAAAAATATAAAACT
1 TAAAAAAA-GAAAAATA-AAAAAA
57316415 TAAAAAAAGAAAGAATA
1 TAAAAAAAGAAA-AATA
57316432 GGACAAAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 7 0.21
23 11 0.32
24 16 0.47
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (22 bp):
TAAAAAAAGAAAAATAAAAAAA
Found at i:57320908 original size:3 final size:3
Alignment explanation
Indices: 57320900--57320950 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
57320890 ACCCATTCCG
57320900 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
57320949 TT
1 TT
57320951 GTGTATTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:57327315 original size:21 final size:18
Alignment explanation
Indices: 57327264--57327303 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
57327254 CATTTTTATT
*
57327264 ATAAAAAATAAATTAGTA
1 ATAAAAATTAAATTAGTA
57327282 ATAAAAATTAAATTAGTA
1 ATAAAAATTAAATTAGTA
57327300 ATAA
1 ATAA
57327304 TTGAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAAAAATTAAATTAGTA
Found at i:57327687 original size:18 final size:17
Alignment explanation
Indices: 57327660--57327694 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57327650 ACTACATCCA
57327660 ATATACTTTTCATTCCT
1 ATATACTTTTCATTCCT
*
57327677 ATATCACTTTTCTTTCCT
1 ATAT-ACTTTTCATTCCT
57327695 TTTTTGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATACTTTTCATTCCT
Found at i:57331137 original size:14 final size:15
Alignment explanation
Indices: 57331118--57331146 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57331108 TTGTGCTAAC
57331118 AAATATG-ATGCTCA
1 AAATATGTATGCTCA
57331132 AAATATGTATGCTCA
1 AAATATGTATGCTCA
57331147 TTACCAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (15 bp):
AAATATGTATGCTCA
Found at i:57333810 original size:24 final size:23
Alignment explanation
Indices: 57333775--57333831 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
57333765 GTGGAATTCG
*
57333775 ATACATACATATGTA-ATCGGTGTC
1 ATACATACATATATAGAT-GGT-TC
*
57333799 ATTCATACATATATAGATGGTTC
1 ATACATACATATATAGATGGTTC
57333822 ATACATACAT
1 ATACATACAT
57333832 GCTCTGAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.38
24 16 0.55
25 2 0.07
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (23 bp):
ATACATACATATATAGATGGTTC
Found at i:57333961 original size:20 final size:20
Alignment explanation
Indices: 57333936--57333996 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
57333926 GTGGAATTCA
57333936 ATACATACATAGATGGTGTC
1 ATACATACATAGATGGTGTC
*
57333956 ATACATACATAGA-GAGTTTC
1 ATACATACATAGATG-GTGTC
*
57333976 ATACATACATATATGGTGTC
1 ATACATACATAGATGGTGTC
57333996 A
1 A
57333997 ACCTTACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.03
20 34 0.94
21 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (20 bp):
ATACATACATAGATGGTGTC
Found at i:57344695 original size:12 final size:12
Alignment explanation
Indices: 57344668--57344704 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
57344658 CCTATTCAAT
57344668 TCAATTAAATAAA
1 TCAATTAAA-AAA
57344681 TCAATTAAAAAA
1 TCAATTAAAAAA
57344693 TCAATTAAAAAA
1 TCAATTAAAAAA
57344705 ATTCATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (12 bp):
TCAATTAAAAAA
Found at i:57344705 original size:13 final size:13
Alignment explanation
Indices: 57344668--57344706 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
57344658 CCTATTCAAT
*
57344668 TCAATTAAATAAA
1 TCAATTAAAAAAA
57344681 TCAATT-AAAAAA
1 TCAATTAAAAAAA
57344693 TCAATTAAAAAAA
1 TCAATTAAAAAAA
57344706 T
1 T
57344707 TCATGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
TCAATTAAAAAAA
Found at i:57344715 original size:25 final size:25
Alignment explanation
Indices: 57344668--57344717 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
57344658 CCTATTCAAT
* *
57344668 TCAATTAAATAAATCAATTAAAAAA
1 TCAATTAAAAAAATCAATGAAAAAA
57344693 TCAATTAAAAAAATTC-ATGAAAAAA
1 TCAATTAAAAAAA-TCAATGAAAAAA
57344718 AAAAATCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (25 bp):
TCAATTAAAAAAATCAATGAAAAAA
Found at i:57349646 original size:2 final size:2
Alignment explanation
Indices: 57349639--57349664 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57349629 TACAGTTCTT
57349639 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
57349665 AACTTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57351541 original size:16 final size:16
Alignment explanation
Indices: 57351520--57351559 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
57351510 CGTTTGGTTC
* *
57351520 GGTGTATTGGATTAGA
1 GGTGTAATGGAATAGA
57351536 GGTGTAATGGAATAGA
1 GGTGTAATGGAATAGA
*
57351552 GATGTAAT
1 GGTGTAAT
57351560 AGCAAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (16 bp):
GGTGTAATGGAATAGA
Found at i:57360406 original size:19 final size:19
Alignment explanation
Indices: 57360384--57360438 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
57360374 TACAAATTTG
57360384 GAAGGTATTTTCAAATATA
1 GAAGGTATTTTCAAATATA
**
57360403 GAAGGTATAATCAAATATA
1 GAAGGTATTTTCAAATATA
57360422 GAAGGTATTTTCAAATA
1 GAAGGTATTTTCAAATA
57360439 ATTATACCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (19 bp):
GAAGGTATTTTCAAATATA
Found at i:57373310 original size:143 final size:142
Alignment explanation
Indices: 57373047--57373332 Score: 475
Period size: 143 Copynumber: 2.0 Consensus size: 142
57373037 AAGTGTCACG
* * * *
57373047 AAAAGCTTTCCTGACATAATTATGAATGGAGAAATGATTGAAAATGCCATAAGGAGTGGGGAGAT
1 AAAAACTTTCCTAACATAATTATGAATGGAGAAATGATTGAAAACGCCATAAGGAGTGAGGAGAT
* *
57373112 CGAGGCTGAAGAAAGTAACCGAAGGTCGGCTCCGAAGAAAAAGGAGAATGAGGTGAACAACATGA
66 CAAGGCTGAAGAAAGTAACCGAAGGTCGGCTCCGAAGAAAAAAGAGAATGAGGTGAACAACATGA
57373177 GCACCTATCAACA
131 GCACCTAT-AACA
*
57373190 AAAAACTTTCCTAACATAGTTATGAATGGAGAAATGATTGAAAACGCCATAAGGAGTGAGGAGA-
1 AAAAACTTTCCTAACATAATTATGAATGGAGAAATGATTGAAAACGCCATAAGGAGTGAGGAGAT
*
57373254 CTAAGGCTGGAGAAAGTAACCGAAGGTCGGCTCCGAAGAAAAAAGAGAATGAGGTGAACAACATG
66 C-AAGGCTGAAGAAAGTAACCGAAGGTCGGCTCCGAAGAAAAAAGAGAATGAGGTGAACAACATG
57373319 AGCACCTATAACA
130 AGCACCTATAACA
57373332 A
1 A
57373333 GGGTTACTCA
Statistics
Matches: 134, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
142 6 0.04
143 128 0.96
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.17
Consensus pattern (142 bp):
AAAAACTTTCCTAACATAATTATGAATGGAGAAATGATTGAAAACGCCATAAGGAGTGAGGAGAT
CAAGGCTGAAGAAAGTAACCGAAGGTCGGCTCCGAAGAAAAAAGAGAATGAGGTGAACAACATGA
GCACCTATAACA
Found at i:57377076 original size:19 final size:20
Alignment explanation
Indices: 57377052--57377104 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 20
57377042 ATTTAATACA
57377052 TTCTATATTTGAATAAG-CT
1 TTCTATATTTGAATAAGACT
57377071 TTCTATATTT-AAT-AGACT
1 TTCTATATTTGAATAAGACT
* *
57377089 TTCCATATTTGTATAA
1 TTCTATATTTGAATAA
57377105 ATTTAATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 14 0.48
19 12 0.41
20 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (20 bp):
TTCTATATTTGAATAAGACT
Found at i:57377324 original size:19 final size:19
Alignment explanation
Indices: 57377256--57377325 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
57377246 TATGGAAGGT
*
57377256 ATACCTTCCATATTAG-AA
1 ATACCTTCCATATTTGAAA
*
57377274 AT--CTTCCATATTTGATA
1 ATACCTTCCATATTTGAAA
57377291 ATACC-TCCTATATTTGAAA
1 ATACCTTCC-ATATTTGAAA
*
57377310 ATACCTTCCAAATTTG
1 ATACCTTCCATATTTG
57377326 TATTAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 11 0.26
17 3 0.07
18 5 0.12
19 21 0.49
20 3 0.07
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (19 bp):
ATACCTTCCATATTTGAAA
Found at i:57381333 original size:17 final size:18
Alignment explanation
Indices: 57381311--57381354 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
57381301 CAAGTAGCTC
*
57381311 AAAATGATCCAAATC-TG
1 AAAATGATCCAAAACTTG
57381328 AAAATGA-CCAAAACTTG
1 AAAATGATCCAAAACTTG
57381345 -AAATGATCCA
1 AAAATGATCCA
57381355 TAACCATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.20
Consensus pattern (18 bp):
AAAATGATCCAAAACTTG
Found at i:57386348 original size:21 final size:22
Alignment explanation
Indices: 57386324--57386382 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
57386314 TTTTACTATA
*
57386324 TTAAAAATAAATTTT-TATTTT
1 TTAAAAATAAATTTTATAATTT
* *
57386345 TTAATAATTATATTTTATAATTT
1 TTAA-AAATAAATTTTATAATTT
57386368 TTAAATAATTAAATT
1 TTAAA-AA-TAAATT
57386383 AATTTTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 4 0.14
22 10 0.34
23 10 0.34
24 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAAAATAAATTTTATAATTT
Found at i:57387038 original size:10 final size:11
Alignment explanation
Indices: 57387025--57387053 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
57387015 ATCAGGTCAG
57387025 ATCAAATC-AA
1 ATCAAATCAAA
57387035 ATCAAATCAAA
1 ATCAAATCAAA
57387046 ATCAAATC
1 ATCAAATC
57387054 TCATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (11 bp):
ATCAAATCAAA
Found at i:57387357 original size:65 final size:65
Alignment explanation
Indices: 57387213--57387342 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
57387203 TTAATTCTTG
* *
57387213 TATAATATGATATATGTTCAAGGTTTACCTCTCCCAATAATATCGTTTCGAAATTTAAATTGTTA
1 TATAATATAATATATGTTCAAGGTTTACCTCTCCCAATAATATCGTTCCGAAATTTAAATTGTTA
* * *
57387278 TATAATATAATATATGTTCGAGGTTTACCTCTCCCAATAATGTTGTTCCGAAATTTAAATTGTTA
1 TATAATATAATATATGTTCAAGGTTTACCTCTCCCAATAATATCGTTCCGAAATTTAAATTGTTA
57387343 ATCTTTTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (65 bp):
TATAATATAATATATGTTCAAGGTTTACCTCTCCCAATAATATCGTTCCGAAATTTAAATTGTTA
Found at i:57392231 original size:397 final size:398
Alignment explanation
Indices: 57390611--57393321 Score: 4771
Period size: 398 Copynumber: 6.8 Consensus size: 398
57390601 ATAAAAAACA
* * * * * * * *
57390611 GCTTTTGAAAAGTTTGATAGTATTTACTATTGCCGTCAAAAAGTACTTTTGAAAATGATAAAGTG
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAAT-ATAAAATG
* * * * *** ** * * * *
57390676 TTAATTTTAAACACGGTGTTGTAAAGTGAAAGATTTGTTGGGGGGTAAAAAAAGGTAACTTCGTT
65 TCAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAA-GTAACTTTGTT
*
57390741 G-AAAGTACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAA
129 GAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAA
*
57390805 AAAGCTGATTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAAT
194 AAAGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAAT
57390870 TTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAA
259 TTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAA
* * * *
57390935 ATTTTTAACCTTCAACTTTTGGAAAAATGTTTTTCAATGAACTTACCTTTTTATCTCCCATTAAA
324 ATTTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAA
57391000 TCTTTCATAT
389 TCTTTCATAT
* * * *
57391010 GCTTTTGAAAAGTTTGATAATGTTTACTATTACTGTTAAAAAGTACTTTTGAGAAGATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATATAAAATGT
*
57391075 CAATTTTAGACATGATGCCAGAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
*
57391140 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCTTAGTTTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
57391205 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
57391270 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
57391335 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
326 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
57391400 TTTCATAT
391 TTTCATAT
* * * * * ** *
57391408 GCTTTTAAAAAGTTTGATAATGTTTATCATTGCCGTTAAAAAGTATTTTTGAGAAGATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATATAAAATGT
* ** *
57391473 TAATTTTAGACATGATGTTATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTCGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
* *
57391538 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCTTAGATTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
57391603 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
57391668 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
*
57391733 TTTTAGCCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
326 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
57391798 TTTCATAT
391 TTTCATAT
*
57391806 GCTTTTGAAAAGTTTGATAATATTTACCATTACTGTCAAAAAGTGCTTTTGAGAATATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATATAAAATGT
*
57391871 CAATTTTAGACATGATGCCAGAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
57391936 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
*
57392001 AGCTGATTGCTTACCAAATTTTTGTTGTTTACTGCTTT-CAGCCTCAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
57392065 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
* *
57392130 TTTTAACCTTCAGCTTTTGGAAAAATGTTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
326 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
57392195 TTTCATAT
391 TTTCATAT
* *
57392203 GCTTTTGAAAAGTTTGATAATGTTTACCATTACGGTCAAAAAGTGCATTTGAGAATATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATATAAAATGT
57392268 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
57392333 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
57392398 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
*
57392463 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTATGATTCTAACCCAAGCCAAAAT
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
*
57392528 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACATTTTTATCTCCCATTAAATC
326 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
57392593 TTTCATAT
391 TTTCATAT
* *
57392601 GCTTTTGAAAAGTTTGATAATGTTTACCATTACGGTCAAAAAGTGCATTTGAGAATATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATATAAAATGT
57392666 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
57392731 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
57392796 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
*
57392861 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTAATTCTAACCCAAGCCAAAA-
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
57392925 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
326 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
57392990 TTTCATAT
391 TTTCATAT
* *
57392998 GCTTTTGAAAAGTTTGATAATGTTTACCATTGCTGTCAAAAAGTGCTTTTGAAAATATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATATAAAATGT
57393063 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
*
57393128 AAAATACTTTTCCAAAATTTTTAGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
* *
57393193 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCAAGCCTTAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
* * *
57393258 GGTAAACAAAGAGCTCTTCAAACCAAACCATGATTTTAAATTGTGATTCTAACCCAAGCCAAAA
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAA
57393322 AGCCAAAATT
Statistics
Matches: 2225, Mismatches: 85, Indels: 6
0.96 0.04 0.00
Matches are distributed among these distances:
397 785 0.35
398 1391 0.63
399 49 0.02
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (398 bp):
GCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATATAAAATGT
CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
TTTCATAT
Found at i:57392471 original size:795 final size:796
Alignment explanation
Indices: 57390611--57393321 Score: 4807
Period size: 795 Copynumber: 3.4 Consensus size: 796
57390601 ATAAAAAACA
* * * *
57390611 GCTTTTGAAAAGTTTGATAGTATTTACTATTGCCGTCAAAAAGTACTTTTGAAAATGATAAAGTG
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTGCCGTCAAAAAGTACTTTTGAAAAT-ATAAAATG
* * * * *** ** * * *
57390676 TTAATTTTAAACACGGTGTTGTAAAGTGAAAGATTTGTTGGGGGGTAAAAAAAGGTAACTTCGTT
65 TCAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAA-GTAACTTCGTT
*
57390741 G-AAAGTACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAA
129 GAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAA
*
57390805 AAAGCTGATTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAAT
194 AAAGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAAT
57390870 TTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAA
259 TTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAA
* * * *
57390935 ATTTTTAACCTTCAACTTTTGGAAAAATGTTTTTCAATGAACTTACCTTTTTATCTCCCATTAAA
324 ATTTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAA
* * *
57391000 TCTTTCATATGCTTTTGAAAAGTTTGATAATGTTTACTATTACTGTTAAAAAGTACTTTTGAGAA
389 TCTTTCATATGCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAA
*
57391065 GATAAAATGTCAATTTTAGACATGATGCCAGAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTA
454 TATAAAATGTCAATTTTAGACATGATGCCAGAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTA
*
57391130 ACTTTGTTGAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCTTAGTTTAAAATCATGTT
519 ACTTTGTTGAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTT
57391195 CGGTTTAAAAAGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAA
584 CGGTTTAAAAAGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAA
57391260 CAAAAAATTTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCC
649 CAAAAAATTTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCC
57391325 AAGCCAAAATTTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTC
714 AAGCCAAAATTTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTC
57391390 CCATTAAATCTTTCATAT
779 CCATTAAATCTTTCATAT
* * * * * *
57391408 GCTTTTAAAAAGTTTGATAATGTTTATCATTGCCGTTAAAAAGTATTTTTGAGAAGATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTGCCGTCAAAAAGTACTTTTGAAAATATAAAATGT
* **
57391473 TAATTTTAGACATGATGTTATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTCGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTCGTTGA
* *
57391538 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCTTAGATTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
57391603 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
57391668 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
*
57391733 TTTTAGCCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
326 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
*
57391798 TTTCATATGCTTTTGAAAAGTTTGATAATATTTACCATTACTGTCAAAAAGTGCTTTTGAGAATA
391 TTTCATATGCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATA
57391863 TAAAATGTCAATTTTAGACATGATGCCAGAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAAC
456 TAAAATGTCAATTTTAGACATGATGCCAGAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAAC
57391928 TTTGTTGAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCG
521 TTTGTTGAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCG
*
57391993 GTTTAAAAAGCTGATTGCTTACCAAATTTTTGTTGTTTACTGCTTT-CAGCCTCAATAGTAAACA
586 GTTTAAAAAGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACA
57392057 AAAAATTTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAA
651 AAAAATTTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAA
* *
57392122 GCCAAAATTTTTAACCTTCAGCTTTTGGAAAAATGTTTTTCAATAAACTTACCTTTTTATCTCCC
716 GCCAAAATTTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCC
57392187 ATTAAATCTTTCATAT
781 ATTAAATCTTTCATAT
* * * * *
57392203 GCTTTTGAAAAGTTTGATAATGTTTACCATTACGGTCAAAAAGTGCATTTGAGAATATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTGCCGTCAAAAAGTACTTTTGAAAATATAAAATGT
*
57392268 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTCGTTGA
57392333 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
57392398 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
*
57392463 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTATGATTCTAACCCAAGCCAAAAT
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
*
57392528 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACATTTTTATCTCCCATTAAATC
326 TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
* *
57392593 TTTCATATGCTTTTGAAAAGTTTGATAATGTTTACCATTACGGTCAAAAAGTGCATTTGAGAATA
391 TTTCATATGCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATA
*
57392658 TAAAATGTCAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAAC
456 TAAAATGTCAATTTTAGACATGATGCCAGAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAAC
57392723 TTTGTTGAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCG
521 TTTGTTGAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCG
57392788 GTTTAAAAAGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACA
586 GTTTAAAAAGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACA
*
57392853 AAAAATTTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTAATTCTAACCCAA
651 AAAAATTTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAA
57392918 GCCAAAA-TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCC
716 GCCAAAATTTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCC
57392982 ATTAAATCTTTCATAT
781 ATTAAATCTTTCATAT
* *
57392998 GCTTTTGAAAAGTTTGATAATGTTTACCATTGCTGTCAAAAAGTGCTTTTGAAAATATAAAATGT
1 GCTTTTGAAAAGTTTGATAATGTTTACCATTGCCGTCAAAAAGTACTTTTGAAAATATAAAATGT
*
57393063 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTTGTTGA
66 CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTCGTTGA
*
57393128 AAAATACTTTTCCAAAATTTTTAGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
131 AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
* *
57393193 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCAAGCCTTAATAGTAAACAAAAAATTT
196 AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
* * *
57393258 GGTAAACAAAGAGCTCTTCAAACCAAACCATGATTTTAAATTGTGATTCTAACCCAAGCCAAAA
261 GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAA
57393322 AGCCAAAATT
Statistics
Matches: 1838, Mismatches: 74, Indels: 6
0.96 0.04 0.00
Matches are distributed among these distances:
795 1166 0.63
796 625 0.34
797 47 0.03
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (796 bp):
GCTTTTGAAAAGTTTGATAATGTTTACCATTGCCGTCAAAAAGTACTTTTGAAAATATAAAATGT
CAATTTTAGACATGATGCCATAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAACTTCGTTGA
AAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCGGTTTAAAA
AGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACAAAAAATTT
GGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAAGCCAAAAT
TTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCCATTAAATC
TTTCATATGCTTTTGAAAAGTTTGATAATGTTTACCATTACTGTCAAAAAGTGCTTTTGAGAATA
TAAAATGTCAATTTTAGACATGATGCCAGAAAGTGAAAGATTTAATGGGAGATGAAAAAAGTAAC
TTTGTTGAAAAATACTTTTCCAAAATTTTTGGCTTGGTTAAAATCCTAGTTTAAAATCATGTTCG
GTTTAAAAAGCTGCTTGCTTACCAAATTTTTGTTGTTTACTGCTTTCCAGCCTCAATAGTAAACA
AAAAATTTGGTAAACAAAGAGCTCTTCAACCCAAACTATGATTTCAAATTGTGATTCTAACCCAA
GCCAAAATTTTTAACCTTCAGCTCTTGGAAAAATGCTTTTCAATAAACTTACCTTTTTATCTCCC
ATTAAATCTTTCATAT
Found at i:57393583 original size:28 final size:28
Alignment explanation
Indices: 57393551--57393604 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
57393541 TTAGCCCTAG
57393551 ACAACTATGCATAGTATTAGTATCTCGC
1 ACAACTATGCATAGTATTAGTATCTCGC
* *
57393579 ACAACTATGTATGGTATTAGTATCTC
1 ACAACTATGCATAGTATTAGTATCTC
57393605 ACAACCATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (28 bp):
ACAACTATGCATAGTATTAGTATCTCGC
Found at i:57399491 original size:11 final size:11
Alignment explanation
Indices: 57399475--57399499 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57399465 GAAATGTGCC
57399475 TTTACATCACA
1 TTTACATCACA
57399486 TTTACATCACA
1 TTTACATCACA
57399497 TTT
1 TTT
57399500 GATCAGTAAC
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:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTACATCACA
Found at i:57407762 original size:14 final size:14
Alignment explanation
Indices: 57407745--57407815 Score: 65
Period size: 14 Copynumber: 4.8 Consensus size: 14
57407735 TAGTAAAACA
57407745 AAAGTAAAAA-AAAG
1 AAAG-AAAAAGAAAG
*
57407759 AAAGAAAAAGAGAG
1 AAAGAAAAAGAAAG
57407773 AAAGCAAAAATGAAACAG
1 AAAG-AAAAA-G-AA-AG
57407791 AAAGAAAGAAGAAA-
1 AAAGAAA-AAGAAAG
57407805 AAAGAAAAAGA
1 AAAGAAAAAGA
57407816 CGAACAGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
13 9 0.18
14 18 0.37
15 6 0.12
16 3 0.06
17 5 0.10
18 8 0.16
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAGAAAG
Found at i:57410793 original size:24 final size:23
Alignment explanation
Indices: 57410762--57410808 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
57410752 TATTCACACA
57410762 TATTCTTA-CTTAATTTCAAATGT
1 TATTCTTACCTTAATTT-AAATGT
*
57410785 TATTACTTACCTTACTTTAAATGT
1 TATT-CTTACCTTAATTTAAATGT
57410809 CCCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGT
Found at i:57425634 original size:11 final size:12
Alignment explanation
Indices: 57425621--57425655 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
57425611 AATTTACTTC
57425621 AAAAATAAAACA
1 AAAAATAAAACA
*
57425633 AAAAATAAAAAA
1 AAAAATAAAACA
57425645 TAAAAATAAAA
1 -AAAAATAAAA
57425656 ACATTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAAATAAAACA
Found at i:57434294 original size:31 final size:31
Alignment explanation
Indices: 57434256--57434318 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
57434246 TAAGCCCGTA
57434256 ATATAGGGTTAAATCTTCTAAAAGAAAGTAC
1 ATATAGGGTTAAATCTTCTAAAAGAAAGTAC
57434287 ATATAGGGTTAAATCTTCTAAAAGAAAGTAC
1 ATATAGGGTTAAATCTTCTAAAAGAAAGTAC
57434318 A
1 A
57434319 AGTATTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (31 bp):
ATATAGGGTTAAATCTTCTAAAAGAAAGTAC
Found at i:57443797 original size:4 final size:4
Alignment explanation
Indices: 57443788--57443830 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
57443778 CAATTCAAGA
57443788 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
57443831 AGGAAAACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:57444015 original size:4 final size:4
Alignment explanation
Indices: 57444006--57444033 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
57443996 AATTCAAGAC
57444006 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
57444034 TAAAGGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:57446452 original size:3 final size:3
Alignment explanation
Indices: 57446444--57446481 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
57446434 CATCATGTGC
57446444 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
57446482 AATTTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:57447428 original size:10 final size:11
Alignment explanation
Indices: 57447411--57447436 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
57447401 GAAGAGAATG
57447411 GAAAAAAAAAA
1 GAAAAAAAAAA
57447422 GAAAAAAAAAA
1 GAAAAAAAAAA
57447433 GAAA
1 GAAA
57447437 GAAAGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:57449373 original size:21 final size:21
Alignment explanation
Indices: 57449312--57449376 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
57449302 TTTTTTGAAT
*
57449312 TTTCTATATATTTAATTATTTC
1 TTTCTATAT-TTTTATTATTTC
* *
57449334 --TC-ATATTTTT-TAAAATTC
1 TTTCTATATTTTTAT-TATTTC
57449352 TTTCTATATTTTTATTATTTC
1 TTTCTATATTTTTATTATTTC
57449373 TTTC
1 TTTC
57449377 CATTTTTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 11
0.67 0.10 0.22
Matches are distributed among these distances:
17 1 0.03
18 7 0.21
19 4 0.12
20 4 0.12
21 16 0.48
22 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTCTATATTTTTATTATTTC
Found at i:57449611 original size:19 final size:19
Alignment explanation
Indices: 57449587--57449624 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
57449577 CTTTAATTAC
57449587 TAAATTAAAAAATAAATAT
1 TAAATTAAAAAATAAATAT
* *
57449606 TAAATTGAAAAATGAATAT
1 TAAATTAAAAAATAAATAT
57449625 AATTCGAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAATTAAAAAATAAATAT
Found at i:57469531 original size:18 final size:21
Alignment explanation
Indices: 57469503--57469545 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
57469493 TCACGTAAAT
57469503 AAATAATTT-AAAATT-ATAA
1 AAATAATTTAAAAATTCATAA
57469522 AAAT-ATTTAAAAATTCATAA
1 AAATAATTTAAAAATTCATAA
57469542 AAAT
1 AAAT
57469546 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.18
19 10 0.45
20 8 0.36
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAATTTAAAAATTCATAA
Found at i:57469542 original size:10 final size:9
Alignment explanation
Indices: 57469512--57469554 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
57469502 TAAATAATTT
57469512 AAAATTATA
1 AAAATTATA
*
57469521 AAAATATTTA
1 AAAAT-TATA
57469531 AAAATTCATA
1 AAAATT-ATA
*
57469541 AAAATTAAA
1 AAAATTATA
57469550 AAAAT
1 AAAAT
57469555 AAGGCAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:57469552 original size:19 final size:19
Alignment explanation
Indices: 57469512--57469554 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
57469502 TAAATAATTT
**
57469512 AAAATTATAAAAATATTTA
1 AAAATTATAAAAATATAAA
57469531 AAAATTCATAAAAAT-TAAA
1 AAAATT-ATAAAAATATAAA
57469550 AAAAT
1 AAAAT
57469555 AAGGCAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATTATAAAAATATAAA
Found at i:57469841 original size:30 final size:32
Alignment explanation
Indices: 57469773--57469858 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 32
57469763 GTCGGAAATT
* * *
57469773 TAATTAAAATTTTTTAAAACTTT-TAAGGAGCT
1 TAATTAAAATTTTTAAAAATTTTGTAA-GAGCA
57469805 TAATTAAAATTTTTAAAAATTTTGTAA-A-CA
1 TAATTAAAATTTTTAAAAATTTTGTAAGAGCA
* *
57469835 TAATTAAAAATTTTAAAATTTTTG
1 TAATTAAAATTTTTAAAAATTTTG
57469859 AAGGACCTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 23 0.48
31 1 0.02
32 21 0.44
33 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (32 bp):
TAATTAAAATTTTTAAAAATTTTGTAAGAGCA
Found at i:57470127 original size:17 final size:17
Alignment explanation
Indices: 57470107--57470140 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57470097 TATATTTATT
* *
57470107 TTTTAAATTTTTTTTAA
1 TTTTAAAATATTTTTAA
57470124 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
57470141 AATACTTTTT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:57470127 original size:18 final size:19
Alignment explanation
Indices: 57470101--57470138 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
57470091 AATAAATATA
* *
57470101 TTTATTTTTTAAAT-TTTT
1 TTTAATTTTAAAATATTTT
57470119 TTTAATTTTAAAATATTTT
1 TTTAATTTTAAAATATTTT
57470138 T
1 T
57470139 AAAATACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTAATTTTAAAATATTTT
Found at i:57470160 original size:32 final size:29
Alignment explanation
Indices: 57470103--57470165 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
57470093 TAAATATATT
*
57470103 TATTTTTTAAATTTTTTTTAATTTTAAAA
1 TATTTTTAAAATTTTTTTTAATTTTAAAA
57470132 TATTTTTAAAATACTTTTTTTAATTTTTAAAA
1 TATTTTTAAAAT--TTTTTTTAA-TTTTAAAA
57470164 TA
1 TA
57470166 AATTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.37
31 9 0.30
32 10 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTTTTAAAATTTTTTTTAATTTTAAAA
Found at i:57470171 original size:22 final size:22
Alignment explanation
Indices: 57470132--57470190 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
57470122 AATTTTAAAA
*
57470132 TATTTTTAAAAT-ACTTTTT-T
1 TATTTTTAAAATAAATTTTTAT
57470152 TAATTTTTAAAATAAATTTTTAT
1 T-ATTTTTAAAATAAATTTTTAT
57470175 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
57470191 AGGCCGGGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.32
22 14 0.41
23 8 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTTTTAAAATAAATTTTTAT
Found at i:57471492 original size:4 final size:4
Alignment explanation
Indices: 57471483--57471507 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57471473 GGAAAAGCTG
57471483 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
57471508 GCCACTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:57481125 original size:4 final size:4
Alignment explanation
Indices: 57481118--57481228 Score: 80
Period size: 4 Copynumber: 26.2 Consensus size: 4
57481108 TTATGCATGC
* * *
57481118 ATGT ATGT AGGGT ATGT AATGT ATGGC ATGGT ATGT A-GTT TTGT ATGT
1 ATGT ATGT A-TGT ATGT -ATGT AT-GT AT-GT ATGT ATG-T ATGT ATGT
* * * *
57481166 ATGT ATGT ATGT ATGT ATGC ATGC ATGT ATGT GTGT ATGT AGGGT ATGTT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT ATG-T
*
57481216 ATGT ACGT ATGT A
1 ATGT ATGT ATGT A
57481229 AATAAGGTAA
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
3 1 0.01
4 63 0.73
5 22 0.26
ACGTcount: A:0.23, C:0.04, G:0.30, T:0.43
Consensus pattern (4 bp):
ATGT
Found at i:57485838 original size:33 final size:32
Alignment explanation
Indices: 57485763--57485841 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
57485753 GCAATATTTA
* * * *
57485763 AATGTAAGATCATAGCTGGGCTATGGCATTTT
1 AATGTAAGACCATAACTGGGCTATGGCACTTG
* *
57485795 AATGAAAAGACCATAACTGGGTTATGGCACCTTG
1 AATG-TAAGACCATAACTGGGCTATGGCA-CTTG
57485829 AATGTAAGACCAT
1 AATGTAAGACCAT
57485842 GGTTGGACCA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 4 0.11
33 28 0.74
34 6 0.16
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (32 bp):
AATGTAAGACCATAACTGGGCTATGGCACTTG
Found at i:57485912 original size:107 final size:101
Alignment explanation
Indices: 57485732--57485951 Score: 280
Period size: 107 Copynumber: 2.1 Consensus size: 101
57485722 AATTGATGGA
* * *
57485732 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGATCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTACGGCATTCTAA
* **
57485797 TGAAAAGACCATAACTGGGTTATGGCACCT-TGAATG
66 TGAAAAGACCATAACTGAGTTATGGCA-CTACAAATG
*
57485833 TAAGACCATGGTTGGACCATGGCAGTATATATATACATGTGTAAGACCATAGCTGGGCTACGGCA
1 TAAGACCATGGTTGGACCATGGCA--ATAT-T-TA-A-ATGTAAGACCATAGCTGGGCTACGGCA
* * *
57485898 TTCTGATGATAAGACCATAACTGAGTTATTGCACTACAAATG
60 TTCTAATGAAAAGACCATAACTGAGTTATGGCACTACAAATG
57485940 TAAGACCATGGT
1 TAAGACCATGGT
57485952 AGGGCAGGGC
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
101 24 0.24
103 4 0.04
104 1 0.01
105 2 0.02
106 3 0.03
107 68 0.67
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAGACCATAGCTGGGCTACGGCATTCTAA
TGAAAAGACCATAACTGAGTTATGGCACTACAAATG
Found at i:57487789 original size:11 final size:12
Alignment explanation
Indices: 57487788--57487867 Score: 67
Period size: 11 Copynumber: 6.5 Consensus size: 12
57487778 TTTTAAAAAA
57487788 TTAAAAAAGTATT
1 TTAAAAAA-TATT
57487801 TT-AAAAATATT
1 TTAAAAAATATT
57487812 TT-AAAAATATT
1 TTAAAAAATATT
* **
57487823 TTAAAATTAAAAAAA
1 TT-AAA--AAATATT
57487838 TTAAAAAAGTATT
1 TTAAAAAA-TATT
57487851 TT-AAAAATATT
1 TTAAAAAATATT
57487862 TTAAAA
1 TTAAAA
57487868 TTTTAAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
11 23 0.42
12 16 0.29
13 7 0.13
14 3 0.05
15 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:57487801 original size:22 final size:20
Alignment explanation
Indices: 57487773--57487918 Score: 85
Period size: 21 Copynumber: 7.3 Consensus size: 20
57487763 TTTTTATTTT
57487773 AAAAT-TTTTAAAAAATTAA
1 AAAATATTTTAAAAAATTAA
*
57487792 AAAAGTATTTTAAAAATATTTTA
1 AAAA-TATTTTAAAAA-A-TTAA
57487815 AAAATATTTT--AAAATTAA
1 AAAATATTTTAAAAAATTAA
* *
57487833 AAAA-A-TTAAAAAAGTATTTTA
1 AAAATATTTTAAAAA--A-TTAA
**
57487854 AAAATATTTTAAAATTTTAA
1 AAAATATTTTAAAAAATTAA
* *
57487874 AAAA-A-ATAAAAAAGTATGTAA
1 AAAATATTTTAAAAA--AT-TAA
57487895 AAAATATTTT--AAAATTAA
1 AAAATATTTTAAAAAATTAA
57487913 AAAATA
1 AAAATA
57487919 AATATATTTA
Statistics
Matches: 97, Mismatches: 14, Indels: 33
0.67 0.10 0.23
Matches are distributed among these distances:
16 2 0.02
17 1 0.01
18 24 0.25
19 8 0.08
20 13 0.13
21 26 0.27
22 9 0.09
23 14 0.14
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATATTTTAAAAAATTAA
Found at i:57487829 original size:41 final size:39
Alignment explanation
Indices: 57487767--57487916 Score: 180
Period size: 41 Copynumber: 3.7 Consensus size: 39
57487757 GGCCCATTTT
*
57487767 TATTTT-AAAAT-TTTTAAAAAATTAAAAAAGTATTTTAAAAA-
1 TATTTTAAAAATATTTT--AAAATTAAAAAA--A-TTAAAAAAG
57487808 TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
*
57487847 TATTTTAAAAATATTTTAAAATTTTAAAAAAAATAAAAAAG
1 TATTTTAAAAATATTTTAAAA--TTAAAAAAATTAAAAAAG
* *
57487888 TATGTAAAAAATATTTTAAAATTAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAA
57487917 TAAATATATT
Statistics
Matches: 100, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
38 7 0.07
39 30 0.30
41 54 0.54
42 5 0.05
43 4 0.04
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (39 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAG
Found at i:57487843 original size:50 final size:50
Alignment explanation
Indices: 57487767--57487908 Score: 176
Period size: 50 Copynumber: 3.0 Consensus size: 50
57487757 GGCCCATTTT
*
57487767 TATTTTAAAATTTTTAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAAA
1 TATTTTAAAA--TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAAA
57487819 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATTTT--AAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAAA
* *
57487867 -ATTTT---A--AAAAAAA-TAAAAAAGTATGTAAAAAATATTTTAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
57487909 TTAAAAAATA
Statistics
Matches: 85, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
41 23 0.27
42 7 0.08
43 2 0.02
44 1 0.01
47 5 0.06
48 3 0.04
50 34 0.40
52 10 0.12
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (50 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAAA
Found at i:57487878 original size:11 final size:11
Alignment explanation
Indices: 57487773--57487908 Score: 57
Period size: 11 Copynumber: 13.1 Consensus size: 11
57487763 TTTTTATTTT
*
57487773 AAAATTTTTAA
1 AAAATTTTAAA
57487784 AAAA--TTAAA
1 AAAATTTTAAA
57487793 AAAGTATTTTAAA
1 AAA--ATTTTAAA
*
57487806 AATATTTTAAA
1 AAAATTTTAAA
*
57487817 AATATTTT---
1 AAAATTTTAAA
57487825 AAAA--TTAAA
1 AAAATTTTAAA
57487834 AAAA--TTAAA
1 AAAATTTTAAA
57487843 AAAGTATTTTAAA
1 AAA--ATTTTAAA
*
57487856 AATATTTT---
1 AAAATTTTAAA
57487864 AAAATTTTAAA
1 AAAATTTTAAA
*
57487875 AAAA--ATAAA
1 AAAATTTTAAA
* *
57487884 AAAGTATGTAAA
1 AAAAT-TTTAAA
57487896 AAATATTTTAAA
1 AAA-ATTTTAAA
57487908 A
1 A
57487909 TTAAAAAATA
Statistics
Matches: 97, Mismatches: 10, Indels: 35
0.68 0.07 0.25
Matches are distributed among these distances:
6 2 0.02
8 10 0.10
9 26 0.27
11 31 0.32
12 13 0.13
13 15 0.15
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAATTTTAAA
Found at i:57489458 original size:19 final size:20
Alignment explanation
Indices: 57489423--57489460 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
57489413 AAAACTAGTA
*
57489423 ACCAAATTTAACTAAAAATG
1 ACCAAATTTAACAAAAAATG
57489443 ACCAAA-TTAACAAAAAAT
1 ACCAAATTTAACAAAAAAT
57489461 ATAAACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.21
Consensus pattern (20 bp):
ACCAAATTTAACAAAAAATG
Found at i:57491312 original size:27 final size:25
Alignment explanation
Indices: 57491274--57491324 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
57491264 ATTCTTATAA
57491274 TTTAATTAATTAATTTTAGTCTTTTT
1 TTTAATTAATTAATTTTAGT-TTTTT
*
57491300 TTTAACTTGATTAATTTTAGTTTTT
1 TTTAA-TTAATTAATTTTAGTTTTT
57491325 ATACTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (25 bp):
TTTAATTAATTAATTTTAGTTTTTT
Found at i:57497706 original size:3 final size:3
Alignment explanation
Indices: 57497698--57497744 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
57497688 ATAATTTAAA
* *
57497698 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TTT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
57497745 AATTTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:57501597 original size:241 final size:238
Alignment explanation
Indices: 57501104--57501730 Score: 816
Period size: 241 Copynumber: 2.6 Consensus size: 238
57501094 CACCCATGTC
* *
57501104 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCACCAAATACATGATTTTTTTTTAAAGAA
1 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACAT--TTTTTTTTAAAAGAA
* * * * *
57501169 AAATGGAACATACCTGTGTCCTAAATAGACTTACATCTGCCACTTACGCTC-AGGTCCGATTAAC
64 AAATGGAACAAACCTGTGTCCTAAATAGACTTATATCTGACACTCACACTCGA-GTCCGATTAAC
* * *
57501233 AAAAAAGTACTAACATG---C-AACTATATGAAAGAATGGTTGCAATTACAAGCTCCAACTCATC
128 AAAAAAGTACTAGCATGTAACTAACTATATGAAAGAACGGTTGCAATTACAAGCTACAACTCATC
57501294 ATTTCAATTGAAGTACTCATGTCAGATACAACACATATTCATGCAA
193 ATTTCAATTGAAGTACTCATGTCAGATACAACACATATTCATGCAA
* * * * *
57501340 AGGAACAAGAGTATAGGAATATGATCTTTCAAAGACCTCCAAATACATTTTCTTTTTAAAAGGAA
1 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACATTTT-TTTTTAAAA-GAA
* * *
57501405 AAATGGAGCAAACCTGTGTCCTAAATAGGCTTATATTTGACACTCACACTCGAGTCCGATTAACA
64 AAATGGAACAAACCTGTGTCCTAAATAGACTTATATCTGACACTCACACTCGAGTCCGATTAACA
* ** * *
57501470 GAAAAAGTACTAGCATGTAACTAACTATATGAAAGAACGGTTGCAATTACTAGCTATGACTCGTT
129 -AAAAAGTACTAGCATGTAACTAACTATATGAAAGAACGGTTGCAATTACAAGCTACAACTCATC
* * * * *
57501535 GTTTCAATTTAAGTACTCGTGTCTGATACGACACATATTCATGCAA
193 ATTTCAATTGAAGTACTCATGTCAGATACAACACATATTCATGCAA
* *
57501581 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACA-TTTTTTTTAATAGTAAA
1 GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACATTTTTTTTTAAAAGAAAA
* * * * * * *
57501645 ATGGAACAAAACCCGTGTTCTAAAAAGCCTTATATCTAACATTCACACTCGAGTCTGATTAACAA
66 ATGGAAC-AAACCTGTGTCCTAAATAGACTTATATCTGACACTCACACTCGAGTCCGATTAACAA
57501710 AAAAGTACTAGCATGTAACTA
130 AAAAGTACTAGCATGTAACTA
57501731 TATGAAAGAA
Statistics
Matches: 338, Mismatches: 44, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
234 3 0.01
235 8 0.02
236 100 0.30
237 16 0.05
238 32 0.09
239 56 0.17
240 4 0.01
241 119 0.35
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (238 bp):
GGGTATAAGGGTATAGGAACATGATCTTTCAAAGACCTCCAAATACATTTTTTTTTAAAAGAAAA
ATGGAACAAACCTGTGTCCTAAATAGACTTATATCTGACACTCACACTCGAGTCCGATTAACAAA
AAAGTACTAGCATGTAACTAACTATATGAAAGAACGGTTGCAATTACAAGCTACAACTCATCATT
TCAATTGAAGTACTCATGTCAGATACAACACATATTCATGCAA
Found at i:57509557 original size:22 final size:23
Alignment explanation
Indices: 57509538--57509581 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
57509528 AGCCTTTACA
57509538 CTTTTA-TTTTTAAAAATTTAAT
1 CTTTTACTTTTTAAAAATTTAAT
*
57509560 CTTTTACTTTTTAAAATTTTAA
1 CTTTTACTTTTTAAAAATTTAA
57509582 ATTTCAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (23 bp):
CTTTTACTTTTTAAAAATTTAAT
Found at i:57510108 original size:12 final size:12
Alignment explanation
Indices: 57510091--57510120 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
57510081 CGTTGAATTT
57510091 ATCATCATCGGA
1 ATCATCATCGGA
*
57510103 ATCATCATCGTA
1 ATCATCATCGGA
57510115 ATCATC
1 ATCATC
57510121 TTTTGACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (12 bp):
ATCATCATCGGA
Found at i:57515855 original size:12 final size:12
Alignment explanation
Indices: 57515838--57515862 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57515828 TTCATGACAT
57515838 AATATGTTATAA
1 AATATGTTATAA
57515850 AATATGTTATAA
1 AATATGTTATAA
57515862 A
1 A
57515863 TTAAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATATGTTATAA
Found at i:57517090 original size:4 final size:4
Alignment explanation
Indices: 57517083--57517110 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
57517073 AAAACGTATA
57517083 CATG CATG CATG CATG CATG CATG CATG
1 CATG CATG CATG CATG CATG CATG CATG
57517111 TATGTATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (4 bp):
CATG
Found at i:57517115 original size:4 final size:4
Alignment explanation
Indices: 57517108--57517145 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
57517098 GCATGCATGC
57517108 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
57517146 TTCTAAGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Done.