Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold91
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: 1327174
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 48727 characters in sequence are not A, C, G, or T
File 7 of 8
Found at i:1065712 original size:13 final size:13
Alignment explanation
Indices: 1065694--1065718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1065684 CAATTCGTCA
1065694 TGTATCGATACAT
1 TGTATCGATACAT
1065707 TGTATCGATACA
1 TGTATCGATACA
1065719 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1065718 original size:33 final size:33
Alignment explanation
Indices: 1065674--1065738 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1065664 TCTAGGACAA
*
1065674 TGTATCAATACAAT-TCGTCATGTATCGATACAT
1 TGTATCAATACAATGT-GCCATGTATCGATACAT
*
1065707 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCAATACAATGTGCCATGTATCGATACA
1065739 AATAATGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCAATACAATGTGCCATGTATCGATACAT
Found at i:1065806 original size:13 final size:13
Alignment explanation
Indices: 1065788--1065815 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1065778 TACAATGCAT
1065788 AATGTATCGATAC
1 AATGTATCGATAC
1065801 AATGTATCGATAC
1 AATGTATCGATAC
1065814 AA
1 AA
1065816 AGCATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1065811 original size:33 final size:33
Alignment explanation
Indices: 1065769--1065834 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1065759 TGCCAGTTTC
*
1065769 ATGTATCGATACAATGCATAATGTATCGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
*
1065802 ATGTATCGATACAAAGCATAATGTATCTATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
1065835 TCTGGATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:1065826 original size:20 final size:20
Alignment explanation
Indices: 1065769--1065834 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
1065759 TGCCAGTTTC
*
1065769 ATGTATCGATACAATGCATA
1 ATGTATCGATACAAAGCATA
1065789 ATGTATCGAT----A-C--A
1 ATGTATCGATACAAAGCATA
1065802 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
*
1065822 ATGTATCTATACA
1 ATGTATCGATACA
1065835 TCTGGATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 11 0.30
15 1 0.03
17 1 0.03
18 1 0.03
20 23 0.62
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAAAGCATA
Found at i:1066195 original size:43 final size:43
Alignment explanation
Indices: 1066130--1066231 Score: 159
Period size: 43 Copynumber: 2.4 Consensus size: 43
1066120 ACACAATTCA
* *
1066130 TAATGTATCAATACATACATTTGAAATTTATAGCCGTTGTACT
1 TAATGTATCGATACATAAATTTGAAATTTATAGCCGTTGTACT
*
1066173 TAATGTATCGATACATAAATTTGAAATTTATAGCCGTTGTGCT
1 TAATGTATCGATACATAAATTTGAAATTTATAGCCGTTGTACT
* *
1066216 CAATGTATTGATACAT
1 TAATGTATCGATACAT
1066232 TTGACCATGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (43 bp):
TAATGTATCGATACATAAATTTGAAATTTATAGCCGTTGTACT
Found at i:1066323 original size:32 final size:33
Alignment explanation
Indices: 1066281--1066342 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
1066271 CAATTCATTG
1066281 TGTATGGATACCAAG-AACATGTATCGATACAA
1 TGTATGGATACCAAGCAACATGTATCGATACAA
* * * *
1066313 TGTATTGATACTAAGCAATATGTGTCGATA
1 TGTATGGATACCAAGCAACATGTATCGATA
1066343 TATATGACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 13 0.52
33 12 0.48
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (33 bp):
TGTATGGATACCAAGCAACATGTATCGATACAA
Found at i:1068216 original size:16 final size:16
Alignment explanation
Indices: 1068197--1068251 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1068187 ATTTATATTC
*
1068197 ATTTGAATTCAAAATT
1 ATTTGAATTAAAAATT
*
1068213 ATTTGAATTTAAAAATA
1 ATTTGAA-TTAAAAATT
** *
1068230 ATTAAAATTTAAAATT
1 ATTTGAATTAAAAATT
1068246 ATTTGA
1 ATTTGA
1068252 CTTATAATGA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 18 0.60
17 12 0.40
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (16 bp):
ATTTGAATTAAAAATT
Found at i:1068967 original size:2 final size:2
Alignment explanation
Indices: 1068962--1068987 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1068952 ACTATATGTA
1068962 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
1068988 TAAACCAAGT
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):
AT
Found at i:1069761 original size:27 final size:27
Alignment explanation
Indices: 1069705--1069770 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
1069695 AATATATTTT
* **
1069705 ATATATTTTATTTTAAACTACATTAGA
1 ATATATTTTATTTTAAAATACAAAAGA
*
1069732 ATATATTTTACTTTTAAAATA-AAAATA
1 ATATATTTTA-TTTTAAAATACAAAAGA
*
1069759 ATACA-TTTATTT
1 ATATATTTTATTT
1069771 GAATAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 3 0.09
26 4 0.12
27 17 0.52
28 9 0.27
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATATTTTATTTTAAAATACAAAAGA
Found at i:1070234 original size:18 final size:19
Alignment explanation
Indices: 1070202--1070257 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1070192 TTGTATTGAT
*
1070202 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1070221 TCATTGTA-CGATACATGG
1 ACATTGTATCGATACATGG
1070239 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1070258 AAACCGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.31
19 13 0.41
20 9 0.28
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1072128 original size:13 final size:13
Alignment explanation
Indices: 1072110--1072135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1072100 AATTTGATTA
1072110 TCCAAATTTAAAG
1 TCCAAATTTAAAG
1072123 TCCAAATTTAAAG
1 TCCAAATTTAAAG
1072136 AAGAAAAGTA
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TCCAAATTTAAAG
Found at i:1076661 original size:21 final size:22
Alignment explanation
Indices: 1076637--1076686 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1076627 ATCAAATCTT
* *
1076637 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1076658 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1076680 --TCAAAAT
1 CTTCAAAAT
1076687 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1078346 original size:22 final size:24
Alignment explanation
Indices: 1078304--1078348 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1078294 TTTTAACCGA
*
1078304 TTATCAAGGGGGAGAAATTTTTTT
1 TTATCAAGAGGGAGAAATTTTTTT
1078328 TTATCAA-AGGGA-AAATTTTTT
1 TTATCAAGAGGGAGAAATTTTTT
1078349 AACGAGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 7 0.35
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.42
Consensus pattern (24 bp):
TTATCAAGAGGGAGAAATTTTTTT
Found at i:1078939 original size:13 final size:13
Alignment explanation
Indices: 1078921--1078947 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1078911 GATACATTAC
1078921 TTGTATCGATACA
1 TTGTATCGATACA
1078934 TTGTATCGATACA
1 TTGTATCGATACA
1078947 T
1 T
1078948 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1078962 original size:32 final size:30
Alignment explanation
Indices: 1078905--1078966 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
1078895 CACACCCAGA
*
1078905 TGTATTGATACATTACTTGTATCGATACAT
1 TGTATCGATACATTACTTGTATCGATACAT
*
1078935 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACAT-TAC-TTGTATCGATACAT
1078967 GGACAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 12 0.43
31 2 0.07
32 14 0.50
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (30 bp):
TGTATCGATACATTACTTGTATCGATACAT
Found at i:1078977 original size:20 final size:19
Alignment explanation
Indices: 1078931--1078987 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1078921 TTGTATCGAT
*
1078931 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
1078950 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
1078969 ACAATTGTATTGATACATG
1 AC-ATTGTATCGATACATG
1078988 AAACTAGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1086759 original size:74 final size:76
Alignment explanation
Indices: 1086592--1086789 Score: 242
Period size: 74 Copynumber: 2.6 Consensus size: 76
1086582 AAATATAAAA
* * *
1086592 AATTCAAATATTAAATTTAAATTGGATATTGTCTTGATTT-AGTCTCATTAAATCTAAAATATCT
1 AATTCAAATTTTAAATTTAAATTGGATATTGTCTTGATTTAAATCTCAGTAAA--TAAAATATCT
* *
1086656 AGAATTTAAAATG
64 AAAATTCAAAATG
* * * * *
1086669 AATTCAAAATTTAAATTTAAATTTGATATTATCTTGATTTAAAT-TTAGTAAA-AAAATATTTAA
1 AATTCAAATTTTAAATTTAAATTGGATATTGTCTTGATTTAAATCTCAGTAAATAAAATATCTAA
1086732 AATTCAAAATG
66 AATTCAAAATG
* *
1086743 AATTCAAATTTTAAATTTAAGTTGGATATTGTATTGATTT-AATCTCA
1 AATTCAAATTTTAAATTTAAATTGGATATTGTCTTGATTTAAATCTCA
1086790 TGAATTATCA
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
73 3 0.03
74 56 0.54
77 42 0.41
78 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (76 bp):
AATTCAAATTTTAAATTTAAATTGGATATTGTCTTGATTTAAATCTCAGTAAATAAAATATCTAA
AATTCAAAATG
Found at i:1087254 original size:13 final size:13
Alignment explanation
Indices: 1087236--1087261 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1087226 TACACCAAGT
1087236 ATGTATCGATACA
1 ATGTATCGATACA
1087249 ATGTATCGATACA
1 ATGTATCGATACA
1087262 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1093452 original size:20 final size:20
Alignment explanation
Indices: 1093373--1093452 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1093363 AATGTCCAAA
*
1093373 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1093393 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1093418 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1093438 TTGTATCGATACATT
1 ATGTATCGATACATT
1093453 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1093456 original size:13 final size:13
Alignment explanation
Indices: 1093438--1093476 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1093428 ACATTTTTCT
1093438 TTGTATCGATACA
1 TTGTATCGATACA
1093451 TTGTATCGATACA
1 TTGTATCGATACA
*
1093464 CTGTATCGATACA
1 TTGTATCGATACA
1093477 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1093621 original size:21 final size:21
Alignment explanation
Indices: 1093597--1093643 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1093587 AAATCTTTTG
1093597 CAAAAT-ACTT-GTTTTTCACCT
1 CAAAATAACTTCGTTTTTCA--T
1093618 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1093638 CAAAAT
1 CAAAAT
1093644 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.40
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1093640 original size:20 final size:19
Alignment explanation
Indices: 1093599--1093641 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1093589 ATCTTTTGCA
1093599 AAATACTTGTTTTTCACCTC
1 AAATACTTGTTTTTCA-CTC
1093619 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1093639 AAA
1 AAA
1093642 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.42
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1095413 original size:31 final size:31
Alignment explanation
Indices: 1095378--1095442 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1095368 CAAATTCGTT
1095378 AAATTTATTTTGATTAAGGGAAAAATAAAAG
1 AAATTTATTTTGATTAAGGGAAAAATAAAAG
1095409 AAATTTATTTTGATTAAGGGAAAAATAAAAG
1 AAATTTATTTTGATTAAGGGAAAAATAAAAG
1095440 AAA
1 AAA
1095443 AATGTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (31 bp):
AAATTTATTTTGATTAAGGGAAAAATAAAAG
Found at i:1096068 original size:13 final size:13
Alignment explanation
Indices: 1096050--1096075 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1096040 TACACCAAGT
1096050 ATGTATCGATACA
1 ATGTATCGATACA
1096063 ATGTATCGATACA
1 ATGTATCGATACA
1096076 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1096073 original size:32 final size:33
Alignment explanation
Indices: 1096032--1096095 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1096022 TAGCCAAACT
* **
1096032 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1096064 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1096096 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1097885 original size:21 final size:21
Alignment explanation
Indices: 1097852--1097901 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1097842 TTGCAAGTTG
*
1097852 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1097874 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1097895 AAATAAA
1 AAATAAA
1097902 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1099719 original size:15 final size:15
Alignment explanation
Indices: 1099699--1099729 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1099689 TAAAAATGTC
*
1099699 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1099714 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1099729 C
1 C
1099730 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1101828 original size:13 final size:13
Alignment explanation
Indices: 1101810--1101835 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1101800 ACATTTTTCT
1101810 TTGTATCGATACA
1 TTGTATCGATACA
1101823 TTGTATCGATACA
1 TTGTATCGATACA
1101836 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1106410 original size:16 final size:17
Alignment explanation
Indices: 1106379--1106425 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1106369 TTAAGTTCGT
*
1106379 GTTATTTTATGTTTTAA
1 GTTATTTTAGGTTTTAA
*
1106396 GTTATTTT-GGTTTTAG
1 GTTATTTTAGGTTTTAA
*
1106412 GTCATTTTAGGTTT
1 GTTATTTTAGGTTT
1106426 GGGTTAATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.17, C:0.02, G:0.19, T:0.62
Consensus pattern (17 bp):
GTTATTTTAGGTTTTAA
Found at i:1107195 original size:35 final size:35
Alignment explanation
Indices: 1107150--1107224 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
1107140 TAATTACACT
1107150 TAAGT-CCCTTAGATTTAAACTATTTAAAAAATCC
1 TAAGTACCCTTAGATTTAAACTATTTAAAAAATCC
*
1107184 TAAGTACCCTTAGATTTAAACTATTTAAAATATCC
1 TAAGTACCCTTAGATTTAAACTATTTAAAAAATCC
1107219 TAAGTA
1 TAAGTA
1107225 ACTTTTACTC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 5 0.13
35 34 0.87
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (35 bp):
TAAGTACCCTTAGATTTAAACTATTTAAAAAATCC
Found at i:1108168 original size:25 final size:27
Alignment explanation
Indices: 1108133--1108194 Score: 96
Period size: 25 Copynumber: 2.4 Consensus size: 27
1108123 TTATAAATAA
1108133 GAAT-AAC-AATTATCATAAGGCTTAT
1 GAATAAACAAATTATCATAAGGCTTAT
1108158 GAA-AAA-AAATTATCATAAGGCTTAT
1 GAATAAACAAATTATCATAAGGCTTAT
1108183 GAATAAACAAAT
1 GAATAAACAAAT
1108195 ACCTCATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 26 0.79
26 3 0.09
27 4 0.12
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (27 bp):
GAATAAACAAATTATCATAAGGCTTAT
Found at i:1111472 original size:22 final size:20
Alignment explanation
Indices: 1111447--1111495 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1111437 AAATGCATCG
1111447 ATACATGTTTACAATTGTATCA
1 ATACAT-TTTAC-ATTGTATCA
* *
1111469 ATACATTTTTCATTGTATCG
1 ATACATTTTACATTGTATCA
1111489 ATACATT
1 ATACATT
1111496 CTGGGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 15 0.60
21 4 0.16
22 6 0.24
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (20 bp):
ATACATTTTACATTGTATCA
Found at i:1117620 original size:23 final size:24
Alignment explanation
Indices: 1117540--1117629 Score: 51
Period size: 23 Copynumber: 3.8 Consensus size: 24
1117530 TAAATATTTA
* * *
1117540 AAATTTATAT-TATATGAATTATA
1 AAATTGATATATATATAAATTATG
* * *
1117563 AAATTAGACATAAATACATAATT-TG
1 AAATT-GATATATATATA-AATTATG
**
1117588 AAATCAATAT-TATATAAATTATG
1 AAATTGATATATATATAAATTATG
* *
1117611 AAATTGATATGTTTATAAA
1 AAATTGATATATATATAAA
1117630 ATATTTTGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 9
0.68 0.20 0.13
Matches are distributed among these distances:
22 4 0.08
23 19 0.40
24 13 0.27
25 8 0.17
26 4 0.08
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (24 bp):
AAATTGATATATATATAAATTATG
Found at i:1123449 original size:55 final size:55
Alignment explanation
Indices: 1123258--1123449 Score: 210
Period size: 55 Copynumber: 3.5 Consensus size: 55
1123248 TGGCAAAAAT
* * *
1123258 AATGGAAATGAAAG-AGTTGAGCATAGTGCCACCACTACTCTGCATGGAAGATCC
1 AATGGAAATGAGAGTAGCTGAGCATAGTGCCACCACTACTCTGCATGGAAGAACC
* ** * * *
1123312 AATGAAAATGAGAGTAGCTGAGTGTAATGCCACCATTACTCTACAT-GATAGAACC
1 AATGGAAATGAGAGTAGCTGAGCATAGTGCCACCACTACTCTGCATGGA-AGAACC
* * * * * *
1123367 AATGGAAAT-AGGAATAGTTGGGAATAGTGCCACTACTACTCTGCATGGCAGAACC
1 AATGGAAATGA-GAGTAGCTGAGCATAGTGCCACCACTACTCTGCATGGAAGAACC
1123422 AATGGAAATGAGAGTAGCTGAGCATAGT
1 AATGGAAATGAGAGTAGCTGAGCATAGT
1123450 ACCTGGAGTT
Statistics
Matches: 109, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
54 15 0.14
55 92 0.84
56 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (55 bp):
AATGGAAATGAGAGTAGCTGAGCATAGTGCCACCACTACTCTGCATGGAAGAACC
Found at i:1126269 original size:2 final size:2
Alignment explanation
Indices: 1126262--1126291 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1126252 GAGATTGAAG
1126262 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
1126292 GTAAACAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1128465 original size:20 final size:20
Alignment explanation
Indices: 1128440--1128477 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1128430 TACTTCCAGT
1128440 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACATTTG
1128460 TTCATGTATCGATACATT
1 TTCATGTATCGATACATT
1128478 GTATCGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (20 bp):
TTCATGTATCGATACATTTG
Found at i:1128482 original size:13 final size:13
Alignment explanation
Indices: 1128464--1128488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1128454 CATTTGTTCA
1128464 TGTATCGATACAT
1 TGTATCGATACAT
1128477 TGTATCGATACA
1 TGTATCGATACA
1128489 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1137028 original size:33 final size:33
Alignment explanation
Indices: 1136985--1137049 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1136975 TTTGAGGTAA
* *
1136985 TGTATCGATACAATTCT-TCATGTATCGATACAT
1 TGTATCGATAC-ATTATGCCATGTATCGATACAT
*
1137018 TGTATGGATACATTATGCCATGTATCGATACA
1 TGTATCGATACATTATGCCATGTATCGATACA
1137050 AATAGTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATTATGCCATGTATCGATACAT
Found at i:1138850 original size:20 final size:21
Alignment explanation
Indices: 1138819--1138857 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1138809 AGGTCAAAAC
1138819 CCTAGAATGTATCGATACACA
1 CCTAGAATGTATCGATACACA
1138840 CCTAG-ATGTATCGATACA
1 CCTAGAATGTATCGATACA
1138858 TATTGCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (21 bp):
CCTAGAATGTATCGATACACA
Found at i:1138870 original size:20 final size:19
Alignment explanation
Indices: 1138847--1138918 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
1138837 ACACCTAGAT
1138847 GTATCGATACATATTGCTTA
1 GTATCGATACATATT-CTTA
* *
1138867 GTATCGATACATGTTCTTG
1 GTATCGATACATATTCTTA
* * *
1138886 GTATCAATAAATATTAAATTA
1 GTATCGATACATATT--CTTA
1138907 -TATCGATACATA
1 GTATCGATACATA
1138919 AAACTGGCAG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 15 0.37
20 24 0.59
21 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (19 bp):
GTATCGATACATATTCTTA
Found at i:1138970 original size:21 final size:20
Alignment explanation
Indices: 1138944--1138998 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1138934 AAAACTCACT
*
1138944 TTATATCGATACATACTTGAA
1 TTATATCGATACATA-GTGAA
* *
1138965 TTATATCGATACCTAGTGCA
1 TTATATCGATACATAGTGAA
*
1138985 TTGTATCGATACAT
1 TTATATCGATACAT
1138999 TGAACCCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (20 bp):
TTATATCGATACATAGTGAA
Found at i:1141626 original size:21 final size:21
Alignment explanation
Indices: 1141600--1141655 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
1141590 CTGCCAATTT
**
1141600 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
1141621 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
1141640 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1141656 GTATTGTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:1144957 original size:13 final size:13
Alignment explanation
Indices: 1144939--1144964 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1144929 CATTTTTTGG
1144939 TGTATCGATACAT
1 TGTATCGATACAT
1144952 TGTATCGATACAT
1 TGTATCGATACAT
1144965 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1144979 original size:32 final size:33
Alignment explanation
Indices: 1144919--1144982 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1144909 TACAAGCCAA
**
1144919 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
1144952 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
1144983 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:1147667 original size:53 final size:51
Alignment explanation
Indices: 1147554--1147671 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
1147544 AATTCTCCAC
* * *
1147554 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTAT
1147605 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAA-TTTCT-T
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAATTTTCTAT
1147656 CAAATCGGGGATACTC
1 --AATCGGGGATACTC
1147672 TAACCCCATT
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
51 32 0.53
52 5 0.08
53 23 0.38
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTAT
Found at i:1147757 original size:52 final size:51
Alignment explanation
Indices: 1147690--1147860 Score: 177
Period size: 52 Copynumber: 3.3 Consensus size: 51
1147680 TTATTTTCAA
*
1147690 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGGTTTTATT-CTAAAACACCAATTTTTTCACAATC
* * *
1147742 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTT--TAATC
1 GGGGATACTCCAACCCCGGTTTTATTCT-AAAACACCAATTTT--TTCACAATC
* * * * *
1147794 GGGGATACTCCATCTCCGATTTTATTTCCAAAAATACCAA-TTTTTCACAATC
1 GGGGATACTCCAACCCCGGTTTTA-TT-CTAAAACACCAATTTTTTCACAATC
*
1147846 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1147861 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
50 2 0.02
51 1 0.01
52 82 0.85
53 10 0.10
54 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTCTAAAACACCAATTTTTTCACAATC
Found at i:1147795 original size:132 final size:131
Alignment explanation
Indices: 1147558--1147803 Score: 327
Period size: 132 Copynumber: 1.9 Consensus size: 131
1147548 CTCCACAATC
* * * *
1147558 GGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTCTCAAAACACTAATTTTCTACAATCGGGGATACTCCAAC
*
1147623 TCCGATTTTATTTCCAAAAAACACCAATTTCTTCAAATCGGGGATACTCTAACCCCATTATTTTC
66 CCCGATTTTATTTCC-AAAAACACCAATTTCTTCAAATCGGGGATACTCTAACCCCATTATTTTC
1147688 AA
130 AA
* *
1147690 GGGGATACTCCAACCCCGGTTTTATTGCT-AAAACACTAATTTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATT-CTCAAAACACTAATTTTCT-ACAATCGGGGATACTCCA
* * * *
1147754 ACCCCGGTTTTATTTTC-AAAACGCCAATTTTCCTT-TAATCGGGGATACTC
64 ACCCCGATTTTATTTCCAAAAACACCAA-TTT-CTTCAAATCGGGGATACTC
1147804 CATCTCCGAT
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
131 9 0.09
132 55 0.56
133 35 0.35
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (131 bp):
GGGGATACTCCAACCCCGATTTTATTCTCAAAACACTAATTTTCTACAATCGGGGATACTCCAAC
CCCGATTTTATTTCCAAAAACACCAATTTCTTCAAATCGGGGATACTCTAACCCCATTATTTTCA
A
Found at i:1147880 original size:28 final size:28
Alignment explanation
Indices: 1147848--1147916 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1147838 TCACAATCGA
*
1147848 GGATACTCCAACCTCGTTATTTCATC-A-G
1 GGATACTCCAACCTCGTTACTTC--CGAGG
1147876 GGATACTCCAACCTCGTTACTTCCGAGG
1 GGATACTCCAACCTCGTTACTTCCGAGG
1147904 GGATACTCCAACC
1 GGATACTCCAACC
1147917 CCGGCTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 36 0.95
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (28 bp):
GGATACTCCAACCTCGTTACTTCCGAGG
Found at i:1147881 original size:184 final size:184
Alignment explanation
Indices: 1147551--1147888 Score: 504
Period size: 184 Copynumber: 1.8 Consensus size: 184
1147541 CTCAATTCTC
* * *
1147551 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
* *
1147616 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAAATCGGGGATACTCTAACCCCAT
66 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAAATCGAGGATACTCCAACCCCAT
1147681 TATTTTCAAGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTT
131 TATTTTCAAGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTT
* * *
1147735 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGAT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGAT
* * *
1147800 ACTCCATCTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTC
65 ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCA-AATCGAGGATACTCCAACCCC
*
1147863 GTTA-TTTCATCA-GGGATACTCCAACC
129 ATTATTTTCA--AGGGGATACTCCAACC
1147889 TCGTTACTTC
Statistics
Matches: 138, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
183 9 0.07
184 93 0.67
185 36 0.26
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (184 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAAATCGAGGATACTCCAACCCCAT
TATTTTCAAGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTT
Found at i:1149636 original size:20 final size:22
Alignment explanation
Indices: 1149611--1149651 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
1149601 TTCTTTTCTT
1149611 TCCCCCTTAA-AA-ATAATTTC
1 TCCCCCTTAATAAGATAATTTC
1149631 TCCCCCTTAATAAGATAATTT
1 TCCCCCTTAATAAGATAATTT
1149652 TAACAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (22 bp):
TCCCCCTTAATAAGATAATTTC
Found at i:1151398 original size:21 final size:20
Alignment explanation
Indices: 1151352--1151398 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1151342 TTTGAAACTG
*
1151352 ATTTTGATGAAAAACGATGT
1 ATTTTGATGAAAAACGAAGT
*
1151372 AATTTGAAGTGAAAAAC-AAGT
1 ATTTTG-A-TGAAAAACGAAGT
1151393 ATTTTG
1 ATTTTG
1151399 CAAAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTTTGATGAAAAACGAAGT
Found at i:1151539 original size:13 final size:13
Alignment explanation
Indices: 1151521--1151559 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1151511 ATAATCCCCC
*
1151521 TGTATCGATACAG
1 TGTATCGATACAA
1151534 TGTATCGATACAA
1 TGTATCGATACAA
1151547 TGTATCGATACAA
1 TGTATCGATACAA
1151560 AGAAAGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1151571 original size:20 final size:20
Alignment explanation
Indices: 1151546--1151625 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 20
1151536 TATCGATACA
*
1151546 ATGTATCGATACAAAGAAAG
1 ATGTATCGATACATAGAAAG
*
1151566 ATGTATCGATACATTGAATTTTCCAG
1 ATGTATCGATACATAGAA------AG
*
1151592 ATGTATCGATACATAGAAAC
1 ATGTATCGATACATAGAAAG
1151612 ATGTATCGATACAT
1 ATGTATCGATACAT
1151626 TTTGGAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 31 0.62
26 19 0.38
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATAGAAAG
Found at i:1164204 original size:21 final size:20
Alignment explanation
Indices: 1164178--1164251 Score: 80
Period size: 19 Copynumber: 3.7 Consensus size: 20
1164168 CTGCCAATTT
**
1164178 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA-TTGAA
1164199 CATGTATCGATAC-ATTGAA
1 CATGTATCGATACAATTGAA
* *
1164218 CATGTATCGATACAA-GGCAG
1 CATGTATCGATACAATTG-AA
1164238 CATGTATCGATACA
1 CATGTATCGATACA
1164252 TCTGGGTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 17 0.36
20 17 0.36
21 13 0.28
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1170879 original size:13 final size:13
Alignment explanation
Indices: 1170861--1170886 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1170851 TACAGCAAGT
1170861 ATGTATCGATACA
1 ATGTATCGATACA
1170874 ATGTATCGATACA
1 ATGTATCGATACA
1170887 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1173140 original size:21 final size:21
Alignment explanation
Indices: 1173107--1173151 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1173097 TTGCAAGTTG
*
1173107 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1173129 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1173149 AAA
1 AAA
1173152 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1174975 original size:15 final size:15
Alignment explanation
Indices: 1174955--1174985 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1174945 TAAAAATGTC
*
1174955 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1174970 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1174985 C
1 C
1174986 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1176495 original size:30 final size:27
Alignment explanation
Indices: 1176385--1176495 Score: 143
Period size: 27 Copynumber: 4.0 Consensus size: 27
1176375 AGAATAGATT
1176385 AAGGGGGAGTAGTTGATAAATGTTTTA
1 AAGGGGGAGTAGTTGATAAATGTTTTA
* *
1176412 AAGGGGGAATAGTTG-TAAATGTTTTGTT
1 AAGGGGGAGTAGTTGATAAATG-TTT-TA
*
1176440 AAGGGGGAGTAGTTGATAAAAGTTTTA
1 AAGGGGGAGTAGTTGATAAATGTTTTA
1176467 AAGGGGGAGTAGTTGTTAATAAATGTTTT
1 AAGGGGGAGTAGTTG---ATAAATGTTTT
1176496 GTTGAGGGAG
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.08
27 33 0.46
28 18 0.25
29 5 0.07
30 10 0.14
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (27 bp):
AAGGGGGAGTAGTTGATAAATGTTTTA
Found at i:1176505 original size:30 final size:30
Alignment explanation
Indices: 1176386--1176505 Score: 72
Period size: 30 Copynumber: 4.2 Consensus size: 30
1176376 GAATAGATTA
* **
1176386 AGGG-GGAGTAGTTGATAAATG-TTT-TAA
1 AGGGAGGAGTAGTTAATAAATGTTTTGTTG
* * *
1176413 AGGG-GGAATAGTT-GTAAATGTTTTGTTA
1 AGGGAGGAGTAGTTAATAAATGTTTTGTTG
* * ***
1176441 AGGG-GGAGTAGTTGATAAAAGTTTTAAAG
1 AGGGAGGAGTAGTTAATAAATGTTTTGTTG
* * *
1176470 GGGGAGTAGTTGTTAATAAATGTTTTGTTG
1 AGGGAGGAGTAGTTAATAAATGTTTTGTTG
1176500 AGGGAG
1 AGGGAG
1176506 AGAAAAGTTG
Statistics
Matches: 70, Mismatches: 19, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
26 6 0.09
27 15 0.21
28 14 0.20
29 12 0.17
30 23 0.33
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.34
Consensus pattern (30 bp):
AGGGAGGAGTAGTTAATAAATGTTTTGTTG
Found at i:1177184 original size:20 final size:21
Alignment explanation
Indices: 1177154--1177192 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1177144 AGGTCAAAAC
1177154 CCTAGAATGTATCGATACACA
1 CCTAGAATGTATCGATACACA
1177175 CCTA-AATGTATCGATACA
1 CCTAGAATGTATCGATACA
1177193 TATTGCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (21 bp):
CCTAGAATGTATCGATACACA
Found at i:1177248 original size:20 final size:20
Alignment explanation
Indices: 1177182--1177236 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1177172 ACACCTAAAT
1177182 GTATCGATACATATTGCTTA
1 GTATCGATACATATTGCTTA
**
1177202 GTATCGATACATGCT-CTTA
1 GTATCGATACATATTGCTTA
1177221 GTATCGATACATATTG
1 GTATCGATACATATTG
1177237 AATTATATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
GTATCGATACATATTGCTTA
Found at i:1182475 original size:21 final size:20
Alignment explanation
Indices: 1182451--1182502 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1182441 TGCTAATGAA
*
1182451 ATGTATCGATACTTTCACAAG
1 ATGTATCGATACATT-ACAAG
* * *
1182472 ATGTATCGACACATTGCAAT
1 ATGTATCGATACATTACAAG
1182492 ATGTATCGATA
1 ATGTATCGATA
1182503 GAAATAAGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTACAAG
Found at i:1183600 original size:78 final size:77
Alignment explanation
Indices: 1183519--1183821 Score: 299
Period size: 78 Copynumber: 3.9 Consensus size: 77
1183509 TTCCTTGATA
* * * * *
1183519 AAAAATTTAATATTTTGGAGATAAAAACGGGGTCAAAGTA-CCCCTAG-AAATAACGGGGTTAGA
1 AAAAA-TTAATGTTTTGGAAATAAAAACGAGGT-AGAGTATCCCCTCGAAAATAACGGGGTTAGA
*
1183582 GTATCCCAATGGTG
64 GTATCCCAATTGTG
* * * * * *
1183596 AAAAATCAATGTTTTAGAAATAAAATCGAGGTGGAGTATCCCCTCGAAAATAACAGGATTAGAGT
1 AAAAATTAATGTTTTGGAAATAAAAACGAGGTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGT
* *
1183661 ATTTCCGATTGTG
66 A-TCCCAATTGTG
* * *
1183674 AAAAATTAATGTTTTGGAAAT-AAGACTAGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAG
1 AAAAATTAATGTTTTGGAAATAAAAACGAGG-TAGAGTATCCCCTCGAAAATAACGGGGTTAGAG
1183738 TATCCCCAATTGTG
65 TAT-CCCAATTGTG
** ** * * * *
1183752 AAAAATTGGTGTTTTGGAAATAAAATTGGGGTTGGAGTATCCCCTCG-AAATAACAGGGTTGGAG
1 AAAAATTAATGTTTTGGAAATAAAAACGAGG-TAGAGTATCCCCTCGAAAATAACGGGGTTAGAG
1183816 TATCCC
65 TATCCC
1183822 CTCGAAAATA
Statistics
Matches: 186, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
75 4 0.02
76 27 0.15
77 32 0.17
78 104 0.56
79 19 0.10
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (77 bp):
AAAAATTAATGTTTTGGAAATAAAAACGAGGTAGAGTATCCCCTCGAAAATAACGGGGTTAGAGT
ATCCCAATTGTG
Found at i:1183813 original size:27 final size:27
Alignment explanation
Indices: 1183780--1183876 Score: 167
Period size: 28 Copynumber: 3.5 Consensus size: 27
1183770 AATAAAATTG
1183780 GGGTTGGAGTATCCCCTCGAAATAACA
1 GGGTTGGAGTATCCCCTCGAAATAACA
1183807 GGGTTGGAGTATCCCCTCGAAAATAACA
1 GGGTTGGAGTATCCCCTCG-AAATAACA
*
1183835 GGATTGGAGTATCCCCTCAGAAATAACA
1 GGGTTGGAGTATCCCCTC-GAAATAACA
1183863 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
1183877 GTGATTGTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
27 19 0.29
28 46 0.70
29 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCTCGAAATAACA
Found at i:1183822 original size:78 final size:79
Alignment explanation
Indices: 1183566--1183822 Score: 324
Period size: 78 Copynumber: 3.3 Consensus size: 79
1183556 GTACCCCTAG
* * * * *
1183566 AAATAACGGGGTTAGAGTAT-CCCAATGGTGAAAAATCAATGTTTTAGAAATAAAATCGAGG-TG
1 AAATAACAGGGTTAGAGTATCCCCAATTGTGAAAAATTAATGTTTTGGAAATAAAATTGAGGTTG
1183629 GAGTATCCCCTCGA
66 GAGTATCCCCTCGA
* ** * * * *
1183643 AAATAACAGGATTAGAGTATTTCCGATTGTGAAAAATTAATGTTTTGGAAATAAGACT-AGGTTA
1 AAATAACAGGGTTAGAGTATCCCCAATTGTGAAAAATTAATGTTTTGGAAATAAAATTGAGGTTG
1183707 GAGTATCCCCTCGA
66 GAGTATCCCCTCGA
* * ** *
1183721 AAATAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATTGGGGTTG
1 AAATAACAGGGTTAGAGTATCCCCAATTGTGAAAAATTAATGTTTTGGAAATAAAATTGAGGTTG
1183786 GAGTATCCCCTCG-
66 GAGTATCCCCTCGA
*
1183799 AAATAACAGGGTTGGAGTATCCCC
1 AAATAACAGGGTTAGAGTATCCCC
1183823 TCGAAAATAA
Statistics
Matches: 153, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
77 21 0.14
78 115 0.75
79 17 0.11
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (79 bp):
AAATAACAGGGTTAGAGTATCCCCAATTGTGAAAAATTAATGTTTTGGAAATAAAATTGAGGTTG
GAGTATCCCCTCGA
Found at i:1186363 original size:20 final size:20
Alignment explanation
Indices: 1186334--1186389 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1186324 ATGTATCGTT
*
1186334 ACAATATATCGATACAATGA
1 ACAATGTATCGATACAATGA
* *
1186354 ACAATGTATCAATATAATGA
1 ACAATGTATCGATACAATGA
1186374 ACAATGTATCGATACA
1 ACAATGTATCGATACA
1186390 TCTGGGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1188452 original size:19 final size:19
Alignment explanation
Indices: 1188428--1188464 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1188418 GAAGGGGGTT
1188428 GGTAGGGGTAGGGGTGCTC
1 GGTAGGGGTAGGGGTGCTC
*
1188447 GGTAGGGGTAGGGTTGCT
1 GGTAGGGGTAGGGGTGCT
1188465 TGGCAGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.08, G:0.57, T:0.24
Consensus pattern (19 bp):
GGTAGGGGTAGGGGTGCTC
Found at i:1188991 original size:15 final size:15
Alignment explanation
Indices: 1188967--1188998 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1188957 ACATTAAAAT
1188967 TGTATCAATACAATA
1 TGTATCAATACAATA
*
1188982 TGTATTAATACAATA
1 TGTATCAATACAATA
1188997 TG
1 TG
1188999 CATTGTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (15 bp):
TGTATCAATACAATA
Found at i:1189041 original size:48 final size:49
Alignment explanation
Indices: 1188989--1189089 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 49
1188979 ATATGTATTA
**
1188989 ATACAA-TATGCATTGTATTGATACAATCTAG-AAAACCCAAATGTATCG
1 ATACAAGT-TGCATTGTATCAATACAATCTAGAAAAACCCAAATGTATCG
* * *
1189037 ATACAAGTTGCATTGTATCAATACATTCTAGAAAAATCCATATGTATCG
1 ATACAAGTTGCATTGTATCAATACAATCTAGAAAAACCCAAATGTATCG
1189086 ATAC
1 ATAC
1189090 TTTGAATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 26 0.57
49 20 0.43
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (49 bp):
ATACAAGTTGCATTGTATCAATACAATCTAGAAAAACCCAAATGTATCG
Found at i:1193695 original size:20 final size:19
Alignment explanation
Indices: 1193670--1193719 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1193660 CAGTTTCATG
**
1193670 TATCGATACAATTGTCCATA
1 TATCGATACAA-TGAACATA
*
1193690 TATCGATACAATGAACATG
1 TATCGATACAATGAACATA
1193709 TATCGATACAA
1 TATCGATACAA
1193720 AGCATAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (19 bp):
TATCGATACAATGAACATA
Found at i:1196248 original size:18 final size:19
Alignment explanation
Indices: 1196225--1196260 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1196215 TAAAGAATAT
1196225 TGTATCGATACA-TCTGGG
1 TGTATCGATACATTCTGGG
1196243 TGTATCGATACATTCTGG
1 TGTATCGATACATTCTGG
1196261 AAAATTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTCTGGG
Found at i:1199066 original size:13 final size:13
Alignment explanation
Indices: 1199048--1199072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1199038 CATTTTATGG
1199048 TGTATCGATACAA
1 TGTATCGATACAA
1199061 TGTATCGATACA
1 TGTATCGATACA
1199073 TACTATGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1199088 original size:32 final size:33
Alignment explanation
Indices: 1199025--1199092 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1199015 CGTTACAAGC
* **
1199025 CAATGTATTGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1199058 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1199090 CAA
1 CAA
1199093 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1199171 original size:20 final size:21
Alignment explanation
Indices: 1199124--1199175 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1199114 GCCAATGACC
**
1199124 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
1199145 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
1199165 TGTATCGATAC
1 TGTATCGATAC
1199176 TGTGCAACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:1201055 original size:13 final size:13
Alignment explanation
Indices: 1201037--1201061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1201027 CAATTCAACA
1201037 TGTATCGATACAT
1 TGTATCGATACAT
1201050 TGTATCGATACA
1 TGTATCGATACA
1201062 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1201059 original size:33 final size:33
Alignment explanation
Indices: 1201017--1201081 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1201007 TTAGAAGCAA
1201017 TGTATCGATACAAT-T-CAACATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
1201050 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
1201082 AATAGTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:1201154 original size:19 final size:19
Alignment explanation
Indices: 1201111--1201165 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
1201101 TTGCCAATTT
**
1201111 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
1201131 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
1201150 ATGTATCGATACAATG
1 ATGTATCGATACAATG
1201166 TATCAATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:1202244 original size:13 final size:13
Alignment explanation
Indices: 1202226--1202253 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1202216 CGTTACAAGC
1202226 CAATGTATCGATA
1 CAATGTATCGATA
1202239 CAATGTATCGATA
1 CAATGTATCGATA
1202252 CA
1 CA
1202254 TATTGTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1203091 original size:20 final size:20
Alignment explanation
Indices: 1203066--1203185 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
1203056 AAATGCTTTC
1203066 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
1203086 TATCGATACATCTGGGTAAAAAGAGAATG
1 TATCGATACAT-T--G----AA-A-AATG
*
1203115 TATCGATACATTGAAGAATG
1 TATCGATACATTGAAAAATG
* * *
1203135 TATCGATACATTCATACATG
1 TATCGATACATTGAAAAATG
*
1203155 TATCGATATATTGAAAAATG
1 TATCGATACATTGAAAAATG
1203175 TATCGATACAT
1 TATCGATACAT
1203186 CTAGGTACTT
Statistics
Matches: 81, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
20 57 0.70
21 1 0.01
22 2 0.02
23 1 0.01
26 1 0.01
27 2 0.02
28 2 0.02
29 15 0.19
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
TATCGATACATTGAAAAATG
Found at i:1206228 original size:11 final size:10
Alignment explanation
Indices: 1206209--1206281 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
1206199 TGTACCAAAC
1206209 AAAAAAATAA
1 AAAAAAATAA
*
1206219 TAAAATAAT-A
1 -AAAAAAATAA
*
1206229 AAAAAAACAA
1 AAAAAAATAA
*
1206239 AAAAAAACAA
1 AAAAAAATAA
*
1206249 AAAAACCA-AA
1 AAAAA-AATAA
* *
1206259 AAACAAACAA
1 AAAAAAATAA
*
1206269 ACAAAAATAA
1 AAAAAAATAA
1206279 AAA
1 AAA
1206282 GGTCCAGATG
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
9 7 0.14
10 34 0.69
11 8 0.16
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1206240 original size:8 final size:8
Alignment explanation
Indices: 1206229--1206275 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
1206219 TAAAATAATA
1206229 AAAAAAAC
1 AAAAAAAC
1206237 AAAAAAAAAC
1 --AAAAAAAC
1206247 AAAAAAAC
1 AAAAAAAC
*
1206255 CAAAAAAC
1 AAAAAAAC
*
1206263 AAACAAAC
1 AAAAAAAC
1206271 AAAAA
1 AAAAA
1206276 TAAAAAGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 25 0.76
10 8 0.24
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1206242 original size:19 final size:19
Alignment explanation
Indices: 1206205--1206281 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
1206195 CCTTTGTACC
*
1206205 AAACAAAAAAATA-ATAAAA
1 AAACAAAAAAA-ACAAAAAA
* *
1206224 TAATAAAAAAAACAAAAAA
1 AAACAAAAAAAACAAAAAA
*
1206243 AAACAAAAAAACCAAAAAA
1 AAACAAAAAAAACAAAAAA
*
1206262 CAAACAAACAAAAATAAAAA
1 -AAACAAA-AAAAACAAAAA
1206282 GGTCCAGATG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
18 1 0.02
19 30 0.64
20 7 0.15
21 9 0.19
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.06
Consensus pattern (19 bp):
AAACAAAAAAAACAAAAAA
Found at i:1206260 original size:20 final size:19
Alignment explanation
Indices: 1206205--1206274 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
1206195 CCTTTGTACC
*
1206205 AAACAAAAAAATAATAAAATA
1 AAACAAAAAAACAA-AAAA-A
*
1206226 ATA-AAAAAAAC-AAAAAA
1 AAACAAAAAAACAAAAAAA
*
1206243 AAACAAAAAAACCAAAAAAC
1 AAACAAAAAAA-CAAAAAAA
1206263 AAACAAACAAAA
1 AAACAAA-AAAA
1206275 ATAAAAAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 3 0.07
18 11 0.27
19 2 0.05
20 19 0.46
21 6 0.15
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (19 bp):
AAACAAAAAAACAAAAAAA
Found at i:1207529 original size:28 final size:28
Alignment explanation
Indices: 1207494--1208485 Score: 929
Period size: 28 Copynumber: 34.5 Consensus size: 28
1207484 CGTTCATCTC
* * *
1207494 TTCAAAGCCCATAGGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1207522 TTTAAAGCCCACAAGTCAGTAGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** * *
1207549 CTTCAAAAAACCACAAGTAAGTAGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
1207579 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1207607 TCTCAAAGCCCACAAGTCAGTGGTATCCT
1 T-TCAAAGCCCACAAGTCAGTGGCATCCT
*
1207636 TTCAAAACCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1207664 TTTAAAGCCCACATGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1207692 TTCAAAGCCCACATGTCAGTGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1207720 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1207748 TTCAAAGCCCACAAGTCAGTGGCAT-AT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1207775 TTTAAAGCCCACAAGAT-AGTGGCATCCT
1 TTCAAAGCCCACAAG-TCAGTGGCATCCT
1207803 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1207831 TCTCAAAGCCCACAACTTAGTGGTATCCT
1 T-TCAAAGCCCACAAGTCAGTGGCATCCT
* *
1207860 TTCAAAACCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1207888 TTTAAAGCCCACATGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1207916 TTCAAAGCCCACATGTCAGTGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1207944 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1207972 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1208000 TTTAAAGCTCATAAGTCAGTGGCA-CCTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC--T
* *
1208029 TTCAAAGCCCACAAG-CTAGTGGTAACTCT
1 TTCAAAGCCCACAAGTC-AGTGGCATC-CT
* *
1208058 TTCAAAGCCCACAAGTCAGTGGTAACCCCT
1 TTCAAAGCCCACAAGTCAGTGG-CA-TCCT
* * *
1208088 TTCAAAGCCCATAAATCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1208116 TTCAAAGCCCACAAGTCAGTGGTA-CCATT
1 TTCAAAGCCCACAAGTCAGTGGCATCC--T
* * * ** *
1208145 TTCAAAGCCCAGAAGCCAGCGATAACTCTT
1 TTCAAAGCCCACAAGTCAGTG-GCA-TCCT
* * * ** *
1208175 TTCGAAGCCCACATGTAAGTGATAACTCTT
1 TTCAAAGCCCACAAGTCAGTG-GCA-TCCT
** *
1208205 TTCAAAGCCCACACAAGTTGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
* * *
1208237 TTCAAAGCCCACACAAATCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
* * *
1208269 TTCAAAGCCAACACAAATCGGTGGCACCCT
1 TTCAAAGCC--CACAAGTCAGTGGCATCCT
*
1208299 TCCAAAGCCCACAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
*
1208327 TTCAAAGCCCACAAGTAAGTGGCATACACT
1 TTCAAAGCCCACAAGTCAGTGGCAT-C-CT
** *
1208357 TTCAAAGCCCACAAGTTGGTGGCACCCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* *
1208386 TT-AAAGCCCACAAGTCGGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * ***
1208413 TTTAAAGCCCACAAGTCGGTGGTGCCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
1208441 TTCAAAGCCCACACAAGTCGGTGCCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
1208473 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1208486 CAAGTTAGTA
Statistics
Matches: 828, Mismatches: 101, Indels: 68
0.83 0.10 0.07
Matches are distributed among these distances:
27 37 0.04
28 454 0.55
29 140 0.17
30 110 0.13
31 10 0.01
32 77 0.09
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1209733 original size:50 final size:50
Alignment explanation
Indices: 1209657--1209753 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 50
1209647 AAAGTCACAT
*
1209657 TTTTACCCAGATGTATCGATATATTTTTCAATGT-TTCGATACATTCTCTC
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATT-GATACATTCTCTC
* *
1209707 TTTTACCTAGATGTATCGATACATTTTTTAATGTATTGATACATTCT
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATTGATACATTCT
1209754 TCAATGTATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 41 0.95
51 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.47
Consensus pattern (50 bp):
TTTTACCCAGATGTATCGATACATTTTTCAATGTATTGATACATTCTCTC
Found at i:1209742 original size:20 final size:20
Alignment explanation
Indices: 1209717--1209773 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1209707 TTTTACCTAG
* *
1209717 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTCTTCA
*
1209737 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
1209757 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1209774 ATCTTTTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1209770 original size:70 final size:72
Alignment explanation
Indices: 1209667--1209822 Score: 235
Period size: 72 Copynumber: 2.2 Consensus size: 72
1209657 TTTTACCCAG
* * * * *
1209667 ATGTATCGATATATTTTTCAATGTTTCGATACATTCTCTC-TTTTA-CCTAGATGTATCGATACA
1 ATGTATTGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCTAGATGTATCGATACA
*
1209730 TTTTTTA
66 TTTTTCA
*
1209737 ATGTATTGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCTAGATGTATTGATACA
1 ATGTATTGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCTAGATGTATCGATACA
1209802 TTTTTCA
66 TTTTTCA
1209809 ATGTATTGATACAT
1 ATGTATTGATACAT
1209823 CTAGTTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 35 0.45
71 5 0.06
72 37 0.48
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (72 bp):
ATGTATTGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCTAGATGTATCGATACA
TTTTTCA
Found at i:1210676 original size:20 final size:22
Alignment explanation
Indices: 1210636--1210683 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1210626 TAGCCGTTGA
*
1210636 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1210658 CCATGCA-TTTTTAAC-ATG-T
1 CCATGCATTTTTTAACTATGTT
1210677 CCA-GCAT
1 CCATGCAT
1210684 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 3 0.12
21 7 0.29
22 7 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1211049 original size:20 final size:19
Alignment explanation
Indices: 1211003--1211059 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1210993 TTGTATTGAT
*
1211003 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
1211022 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
1211041 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1211060 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1211116 original size:20 final size:19
Alignment explanation
Indices: 1211091--1211173 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
1211081 CCATTGTTTA
1211091 TATCGATACATGGCACATTG
1 TATCGATACATGGCA-ATTG
*
1211111 TATCGAT--A---CAA-TA
1 TATCGATACATGGCAATTG
1211124 TATCGATACATGATG-AATTG
1 TATCGATACATG--GCAATTG
1211144 TATCGATACATGGCACATTG
1 TATCGATACATGGCA-ATTG
1211164 TATCGATACA
1 TATCGATACA
1211174 ATATATCGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
13 8 0.16
14 1 0.02
15 3 0.06
18 2 0.04
19 3 0.06
20 34 0.67
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (19 bp):
TATCGATACATGGCAATTG
Found at i:1211126 original size:33 final size:32
Alignment explanation
Indices: 1211089--1211153 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1211079 TACCATTGTT
1211089 TATATCGATACATG-GCACATTGTATCGATACAA
1 TATATCGATACATGAG-A-ATTGTATCGATACAA
1211122 TATATCGATACATGATGAATTGTATCGATACA
1 TATATCGATACATGA-GAATTGTATCGATACA
1211154 TGGCACATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (32 bp):
TATATCGATACATGAGAATTGTATCGATACAA
Found at i:1211167 original size:53 final size:53
Alignment explanation
Indices: 1211091--1211207 Score: 234
Period size: 53 Copynumber: 2.2 Consensus size: 53
1211081 CCATTGTTTA
1211091 TATCGATACATGGCACATTGTATCGATACAATATATCGATACATGATGAATTG
1 TATCGATACATGGCACATTGTATCGATACAATATATCGATACATGATGAATTG
1211144 TATCGATACATGGCACATTGTATCGATACAATATATCGATACATGATGAATTG
1 TATCGATACATGGCACATTGTATCGATACAATATATCGATACATGATGAATTG
1211197 TATCGATACAT
1 TATCGATACAT
1211208 TGCTTCTAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 64 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (53 bp):
TATCGATACATGGCACATTGTATCGATACAATATATCGATACATGATGAATTG
Found at i:1211181 original size:33 final size:32
Alignment explanation
Indices: 1211144--1211206 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
1211134 TGATGAATTG
1211144 TATCGATACATG-GCACATTGTATCGATACAATA
1 TATCGATACATGAG-A-ATTGTATCGATACAATA
1211177 TATCGATACATGATGAATTGTATCGATACA
1 TATCGATACATGA-GAATTGTATCGATACA
1211207 TTGCTTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TATCGATACATGAGAATTGTATCGATACAATA
Found at i:1211202 original size:20 final size:20
Alignment explanation
Indices: 1211124--1211207 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
1211114 CGATACAATA
1211124 TATCGATACATGATGAATTG
1 TATCGATACATGATGAATTG
1211144 TATCGATACATG--GCACATTG
1 TATCGATACATGATG-A-ATTG
1211164 TATCGATACA--AT--A---
1 TATCGATACATGATGAATTG
1211177 TATCGATACATGATGAATTG
1 TATCGATACATGATGAATTG
1211197 TATCGATACAT
1 TATCGATACAT
1211208 TGCTTCTAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
13 10 0.19
15 2 0.04
16 1 0.02
17 1 0.02
18 1 0.02
19 1 0.02
20 37 0.70
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (20 bp):
TATCGATACATGATGAATTG
Found at i:1217522 original size:21 final size:21
Alignment explanation
Indices: 1217498--1217537 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1217488 TCAAATATTT
*
1217498 TTCAAAATTCTTCATTTTTAC
1 TTCAAAATACTTCATTTTTAC
1217519 TTCAAAATACTTCATTTTT
1 TTCAAAATACTTCATTTTT
1217538 CACCAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (21 bp):
TTCAAAATACTTCATTTTTAC
Found at i:1217544 original size:20 final size:20
Alignment explanation
Indices: 1217499--1217546 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1217489 CAAATATTTT
*
1217499 TCAAAATTCTTCATTTTTAC
1 TCAAAATACTTCATTTTTAC
1217519 TTCAAAATACTTCATTTTTCAC
1 -TCAAAATACTTCATTTTT-AC
1217541 -CAAAAT
1 TCAAAAT
1217547 TATCAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 17 0.68
22 2 0.08
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TCAAAATACTTCATTTTTAC
Found at i:1224556 original size:475 final size:474
Alignment explanation
Indices: 1223617--1224604 Score: 1018
Period size: 475 Copynumber: 2.1 Consensus size: 474
1223607 TGAGATGAAC
*
1223617 ATGGATTCTAGTAATGATCTTCTTTCATTTTATGATTAGACACTATAAACACATTCTCCTCATGA
1 ATGGATTCTAGTAATGATCTTCTATCATTTTATGATTAGACACTATAAACACATTCTCCTCATGA
* * * *
1223682 ATAAATGATATTGGTGATTTTCTATTGCATGGAAATCTTTTCTTTGCCCTATATTTCTTAAAATC
66 ACAAATGATACTGATGATTTTCTATTACATGGAAATCTTTTCTTTGCCCTATATTTCTTAAAATC
* * ** *
1223747 AAAGGTCATACCTTAAATAAGACAAGCATCAATTCTCGTAATTGTCTCCATTATTTTCAAGATTG
131 AAAGGTCATACCTTAAATAACACAAGCATCAACTCTCGTAACAGTCCCCATTATTTTCAAGATTG
* * * * * **
1223812 TGAACAAAAAAGACATTCCCTTCATTAGGATACTTGGCATTTATGCTTTAGTGTCGTAAGAAAAC
196 GGAACAAAAAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTAGTGTCACAAGAAAAC
* * **
1223877 CTTTTCTTTCCAACATTTTTCGTAGAATCAAAGTTTGTCTCTTAATTAAGACAAACATGAATAGT
261 CTTTTCTTTCCAACATTTTTCGTAGAATCAAAGTTCGTCTCTCAAAGAAGACAAACATGAATAGT
**** * * * * *
1223942 CATACTAATTCCCATTCTTTTTAGGATTAGGCATCTAAAACATAATTTTCTCATAAGGATACATG
326 CATACTAATTCCCATTCTACACACGATTAGGCACCTAAAACATAATTTCCTCACAACGATACATG
*** * * * **
1224007 ATATTGATGCTTTGGTTTTGCAAGAAAGGCTTTCTTCCCACCAATTTTTGTAAATGATAAGTTTG
391 ATATTGATGCTTTAACTTCGCAAAAAAGGCTTTCTTCCCACCAATTTTTGTAAA-GATAAGCTCA
*
1224072 TGCCTCAAATGAGACAAA-T
455 TGCCTCAAATAAGACAAAGT
* * * * *
1224091 ATGGATTCTAGTTATGATCTT-TAATCATTTTGTGATTAGGCACTATAAACATATTCTCCTCTTT
1 ATGGATTCTAGTAATGATCTTCT-ATCATTTTATGATTAGACACTATAAACACATTCTCCTC-AT
* * * * * *
1224155 AGGACAAATGATGCTGATGATTTTTTTTTACATTGAAATCTTTTCTTTGCCCTAT-TTTTTTAAA
64 -GAACAAATGATACTGATGATTTTCTATTACATGGAAATCTTTTCTTTGCCCTATATTTCTTAAA
* * * ** *
1224219 ATCAAAGTTCATCCCTTAAATAACATAAGCATTGACTCTCGTAACAGTCCCCATTCTTTTCAAGA
128 ATCAAAGGTCATACCTTAAATAACACAAGCATCAACTCTCGTAACAGTCCCCATTATTTTCAAGA
*
1224284 TTGGGAACCAAAAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTAGTGTCACAAGAA
193 TTGGGAACAAAAAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTAGTGTCACAAGAA
** * *
1224349 AAGTTTTTCTTTCC-ACTATTTTT-GATAGAATCAAAGTTCGT-TCCTCAAAGGAGACAACCATG
258 AACCTTTTCTTTCCAAC-ATTTTTCG-TAGAATCAAAGTTCGTCT-CTCAAAGAAGACAAACATG
** * * * * * *
1224411 GGTTGTCATAAC-CATTTCCA-TCTACACACGATTAGGCACCCT-AAATAT-GTTCTCCTCACCA
320 AATAGTCAT-ACTAATTCCCATTCTACACACGATTAGGCA-CCTAAAACATAATT-TCCTCACAA
** ** *
1224472 CGATACATGATATTGATGCTTTAACTTCGCAATAAAAGTTTTTCTT-TGACCTATTTTCCT-TAA
382 CGATACATGATATTGATGCTTTAACTTCGCAA-AAAAGGCTTTCTTCCCACCAATTTT--TGTAA
**
1224535 A-ATCAATGCTCATTTCTCAAATAAGACAAAGT
444 AGAT-AA-GCTCATGCCTCAAATAAGACAAAGT
*
1224567 -TGGATTCTAGTAAT-AGTC-TCTATTCATTTTAGGATTAG
1 ATGGATTCTAGTAATGA-TCTTCTA-TCATTTTATGATTAG
1224605 GAACCAAAAA
Statistics
Matches: 417, Mismatches: 79, Indels: 35
0.79 0.15 0.07
Matches are distributed among these distances:
473 5 0.01
474 122 0.29
475 241 0.58
476 49 0.12
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (474 bp):
ATGGATTCTAGTAATGATCTTCTATCATTTTATGATTAGACACTATAAACACATTCTCCTCATGA
ACAAATGATACTGATGATTTTCTATTACATGGAAATCTTTTCTTTGCCCTATATTTCTTAAAATC
AAAGGTCATACCTTAAATAACACAAGCATCAACTCTCGTAACAGTCCCCATTATTTTCAAGATTG
GGAACAAAAAACACATTCCCTTCATTAGGATACATGACATTGATGCTTTAGTGTCACAAGAAAAC
CTTTTCTTTCCAACATTTTTCGTAGAATCAAAGTTCGTCTCTCAAAGAAGACAAACATGAATAGT
CATACTAATTCCCATTCTACACACGATTAGGCACCTAAAACATAATTTCCTCACAACGATACATG
ATATTGATGCTTTAACTTCGCAAAAAAGGCTTTCTTCCCACCAATTTTTGTAAAGATAAGCTCAT
GCCTCAAATAAGACAAAGT
Found at i:1226265 original size:476 final size:475
Alignment explanation
Indices: 1224830--1226734 Score: 2151
Period size: 474 Copynumber: 4.0 Consensus size: 475
1224820 TTCTTCACCA
* * * *
1224830 TATTTTCCTTAAAATCAAAGTTCATCCCCTAAATAAGACAAGCATTGATTCACGTAACAGTCTCC
1 TATTTTCCTTAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGATTCTCATAACAGTCTCC
* * * ** *
1224895 ATT-TTTTCTAAGAGTAGGAACCAAAAACACATTCCCTTTTTTAGGATACATGACATTGATGCTT
66 ATTATTTTC-AGGATTAGGAACCTAAAACACATTCCCTTCATTAGGATACATGACATTGAGGCTT
* * *
1224959 TGGTGTCGCAAGAAAAGCTTTTCATTCCACCATTTTTGATAGAATCAAAGTTTGTCTCTTATATA
130 TGGTGTCGCAAGAAAAGCTTTTCTTTCCACCAATTTTGATAGAATCAAAGTTTGTCTCTTAAATA
* * * * * *
1225024 AGACAAACATGAAAAGTCATACTAATTCTCATTCTTTT-TAGATTAGGCACCATAAATATAGTAC
195 AAACAAACATGAATAGTCATACTAATCCCCATTCTTTTCTAGATTAGGCACCATAAACATAGTAT
* * ***
1225088 TATCATAAGGATGCACGATATTGATGCTTTGGTTTCCCAAGAAAAGCTTTCTTCCCTTTAATTTT
260 TATCATAAGGATGCACGATATTGATGCTTTGG-TTCTCAAGAAAGGCTTTCTTCCCACCAATTTT
* * * * *
1225153 TATAAAGTCTAAGTTCGT-GCCTCAAATAAGACAACCATGGATTCTAGTAATGATCTTCATTCAT
324 TGTAAAGTCTAAGTTCGTCTCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTT-TTTCAT
* * *
1225217 TTTGTGATTAGGCACTAT-AA-ACATTCTCCTCATCAGGATAATTGATATTGATGATTTTCTTTT
388 TTTGTGATTAGGCACTATAAACACATTCTCCTCATTAGGATAAATGATATTAATGATTTTCTTTT
* * *
1225280 GCGTGAAAATCTTTTCATTGCCCT
453 GCATGGAAATC-TTTCATTGGCCT
* * * * * * * *
1225304 T-TTCT-CATAGAATTAAAGTTCATCCCGTAAATAAGAAAATCATCAATTCTCATAACAGTCTCC
1 TATTTTCCTTAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGATTCTCATAACAGTCTCC
* *
1225367 ATTATTTTCAGGATTGGGAACCTAAAACACATTCCCTTCATTAGGATACATGACGTTGATGGCTT
66 ATTATTTTCAGGATTAGGAACCTAAAACACATTCCCTTCATTAGGATACATGACATTGA-GGCTT
* * * ** * *
1225432 TGGTGTCACCAA-AAAAGCTTTTTATTTCTA-CTGTTATTGATAAAATCAAAATTTGTCTCTTAA
130 TGGTGTC-GCAAGAAAAGC-TTTTCTTTCCACCAATT-TTGATAGAATCAAAGTTTGTCTCTTAA
* * * * * *
1225495 ATAAAACAAAC-TTAATACTCATACTAATCCCTATTCATTTCAAGATTACGCACCATAAACATAG
192 ATAAAACAAACATGAATAGTCATACTAATCCCCATTCTTTTCTAGATTAGGCACCATAAACATAG
* * * * * * *
1225559 TCTTCTCATAAGGA-GACATGATATTGGTGCATTGGTTTTGCAAGGAAGGCATTT-TT-CCACCA
257 TATTATCATAAGGATG-CACGATATTGATGCTTTGGTTCT-CAAGAAAGGC-TTTCTTCCCACCA
* * * * *
1225621 ATTTTTGCAAAGTTTAAGTTCGTGCTTCAAATAAGACAAATGAGACAAACATGGAGTCTAATAAT
319 ATTTTTGTAAAGTCTAAGTTCGT-C-TC--CT----CAAATGAGACAAACATGGATTCTAGTAAT
* * *
1225686 GATCTTCTTTCATTTTATGATTAGGCACTATAAACACATTATCCTCATTAGGATAAATGATATTC
376 GATCTT-TTTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCATTAGGATAAATGATATTA
** *
1225751 ATGATTTTCTTTTGCATGGAAATCTTTTTTTTGCCT
440 ATGATTTTCTTTTGCATGGAAATCTTTCATTGGCCT
* *
1225787 TATTTTCCTTAAAATCAAAGTTCATCCCTTAAACAAGACAAGCATCGATTCTCATAACAGTCTTC
1 TATTTTCCTTAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGATTCTCATAACAGTCTCC
* * * * *
1225852 ATTATTTTTATGATTGGGAACCTAAAACACATTCCATTCATTAGGATACATCACATTGAGGCTTT
66 ATTATTTTCAGGATTAGGAACCTAAAACACATTCCCTTCATTAGGATACATGACATTGAGGCTTT
1225917 GGTGTCGCAAGAAAAGCTTTTCTTTCCACCAATTTTGATAGAATCAAAGTTTGTCTCTTAAATAA
131 GGTGTCGCAAGAAAAGCTTTTCTTTCCACCAATTTTGATAGAATCAAAGTTTGTCTCTTAAATAA
* * * * *
1225982 AACAAGCATGAATATTCATACTAATCCCCATTTTTTTCTGGATTAGGCACCATAAACATAGTAGT
196 AACAAACATGAATAGTCATACTAATCCCCATTCTTTTCTAGATTAGGCACCATAAACATAGTATT
* * * * *
1226047 ATTATAAGGATGCATGATATTGATGCTTTGGATTCTGAAGAAAGGCTTTCTCCCCACCAATCTTT
261 ATCATAAGGATGCACGATATTGATGCTTTGG-TTCTCAAGAAAGGCTTTCTTCCCACCAATTTTT
* * *
1226112 GTAAAGTCTAAGTTCGTC-CCTCAAATGAGCCAAACATGGATTCTAGCAATGACCTTTATTCATT
325 GTAAAGTCTAAGTTCGTCTCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTTT-TTCATT
1226176 TTGTGATTAGGCACTATAAACACATTCTCCTC-TCTAGGATAAATGATATTAATGATTTTCTTTT
389 TTGTGATTAGGCACTATAAACACATTCTCCTCAT-TAGGATAAATGATATTAATGATTTTCTTTT
*
1226240 GCATGGAAATCTTTCCTTGGCCT
453 GCATGGAAATCTTTCATTGGCCT
* * * *
1226263 TATTTTCCTTAAAATCAAAGTTTATCCCTTAAAAAAGATAAGCATCGATTCTCGTAACAGTCTCC
1 TATTTTCCTTAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGATTCTCATAACAGTCTCC
* * * * *
1226328 ATTATTTTCAGGATTAGGAACCTAAAATACAATCCTTTCATTAGGATAAATGACATTGATGCTTT
66 ATTATTTTCAGGATTAGGAACCTAAAACACATTCCCTTCATTAGGATACATGACATTGAGGCTTT
* * *
1226393 GGTGTCGCAAGAAAAGCTTTTCTTTCCATCAATTTTGATGGAATCAAAGTTTGTCTC-T-AAGAA
131 GGTGTCGCAAGAAAAGCTTTTCTTTCCACCAATTTTGATAGAATCAAAGTTTGTCTCTTAAATAA
* ** * * * * * *
1226456 AACAAGCATGAATAGTCATACTAATCCTTATTCTATTCTGGACTAAGC-CATATAAACATAGTCT
196 AACAAACATGAATAGTCATACTAATCCCCATTCTTTTCTAGATTAGGCAC-CATAAACATAGTAT
* * * * * * ** *
1226520 TCTAATAAGGATACACGATATTGATACTTTGGTTTTCCAAGAAAGGCTTTTTTTACTCCAATTTT
260 TATCATAAGGATGCACGATATTGATGCTTTGGTTCT-CAAGAAAGGCTTTCTTCCCACCAATTTT
* * * * * *
1226585 TGTAATGTCTAAGTTCG-CGCCTTAAAAGAGACAAACATGGATTCTAGTAATGAACTACTTTCAT
324 TGTAAAGTCTAAGTTCGTCTCCTCAAATGAGACAAACATGGATTCTAGTAATGATCT-TTTTCAT
*
1226649 TTT-TGGATTAGGCACCATAAACACATTCTCCTCATTAGGATAAATGATATTGACAAT-ATTTTT
388 TTTGT-GATTAGGCACTATAAACACATTCTCCTCATTAGGATAAATGATATT---AATGA-TTTT
* * *
1226712 TTTTTGCAAGCAAATCTTTCATT
448 CTTTTGCATGGAAATCTTTCATT
1226735 AGGATACATG
Statistics
Matches: 1209, Mismatches: 181, Indels: 79
0.82 0.12 0.05
Matches are distributed among these distances:
472 94 0.08
473 82 0.07
474 306 0.25
475 8 0.01
476 288 0.24
477 26 0.02
478 1 0.00
480 1 0.00
482 55 0.05
483 61 0.05
484 154 0.13
485 133 0.11
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (475 bp):
TATTTTCCTTAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGATTCTCATAACAGTCTCC
ATTATTTTCAGGATTAGGAACCTAAAACACATTCCCTTCATTAGGATACATGACATTGAGGCTTT
GGTGTCGCAAGAAAAGCTTTTCTTTCCACCAATTTTGATAGAATCAAAGTTTGTCTCTTAAATAA
AACAAACATGAATAGTCATACTAATCCCCATTCTTTTCTAGATTAGGCACCATAAACATAGTATT
ATCATAAGGATGCACGATATTGATGCTTTGGTTCTCAAGAAAGGCTTTCTTCCCACCAATTTTTG
TAAAGTCTAAGTTCGTCTCCTCAAATGAGACAAACATGGATTCTAGTAATGATCTTTTTCATTTT
GTGATTAGGCACTATAAACACATTCTCCTCATTAGGATAAATGATATTAATGATTTTCTTTTGCA
TGGAAATCTTTCATTGGCCT
Found at i:1227036 original size:365 final size:365
Alignment explanation
Indices: 1226362--1227065 Score: 1200
Period size: 365 Copynumber: 1.9 Consensus size: 365
1226352 AAATACAATC
1226362 CTTTCATTAGGATAAATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCATCAATT
1 CTTTCATTAGGATAAATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCATCAATT
*
1226427 TTGATGGAATCAAAGTTTGTCTCTAAGAAAACAAGCATGAATAGTCATACTAATCCTTATTCTAT
66 TTGATGGAATCAAAGTTTGTCTCTAAGAAAACAAACATGAATAGTCATACTAATCCTTATTCTAT
*
1226492 TCTGGACTAAGCCATATAAACATAGTCTTCTAATAAGGATACACGATATTGATACTTTGGTTTTC
131 TCTGGACTAAGCCATATAAACATAGTCTTCTAATAAGGATACACGATATTGATACTTTGGTTTCC
* * * *
1226557 CAAGAAAGGCTTTTTTTACTCCAATTTTTGTAATGTCTAAGTTCGCGCCTTAAAAGAGACAAACA
196 CAAGAAAGGCTTTCTTCACACCAATTTTTGTAATGTCTAAGTTCGCGCCTCAAAAGAGACAAACA
1226622 TGGATTCTAGTAATGAACTACTTTCATTTTTGGATTAGGCACCATAAACACATTCTCCTCATTAG
261 TGGATTCTAGTAATGAACTACTTTCATTTTTGGATTAGGCACCATAAACACATTCTCCTCATTAG
1226687 GATAAATGATATTGACAATATTTTTTTTTTGCAAGCAAAT
326 GATAAATGATATTGACAATATTTTTTTTTTGCAAGCAAAT
*
1226727 CTTTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCATCAATT
1 CTTTCATTAGGATAAATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCATCAATT
1226792 TTGATGGAATCAAAGTTTGTCTCTAAGAAAACAAACATGAATAGTCATACTAATCCTTATTCTAT
66 TTGATGGAATCAAAGTTTGTCTCTAAGAAAACAAACATGAATAGTCATACTAATCCTTATTCTAT
* * * *
1226857 TCTGGACTAAGCCGTATAAACATAGTCTTCTAATAAGGATACATGATATTGATTCTTTTGTTTCC
131 TCTGGACTAAGCCATATAAACATAGTCTTCTAATAAGGATACACGATATTGATACTTTGGTTTCC
* * *
1226922 CAAGAAAGGCTTTCTTCCCACCAATTTTTGTGAA-GTCTAAGTTTGTGCCTCAAATA-AGACAAA
196 CAAGAAAGGCTTTCTTCACACCAATTTTTGT-AATGTCTAAGTTCGCGCCTCAAA-AGAGACAAA
* *
1226985 CATGGATTCTAGTAAT-AATCTTCTTTCA-TTTTGTGATTAGGCACTATAAACACATTCTCCTCA
259 CATGGATTCTAGTAATGAA-CTACTTTCATTTTTG-GATTAGGCACCATAAACACATTCTCCTCA
1227048 TTAGGATAAATGATATTG
322 TTAGGATAAATGATATTG
1227066 GTGATTTTCT
Statistics
Matches: 319, Mismatches: 16, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
364 7 0.02
365 309 0.97
366 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (365 bp):
CTTTCATTAGGATAAATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCATCAATT
TTGATGGAATCAAAGTTTGTCTCTAAGAAAACAAACATGAATAGTCATACTAATCCTTATTCTAT
TCTGGACTAAGCCATATAAACATAGTCTTCTAATAAGGATACACGATATTGATACTTTGGTTTCC
CAAGAAAGGCTTTCTTCACACCAATTTTTGTAATGTCTAAGTTCGCGCCTCAAAAGAGACAAACA
TGGATTCTAGTAATGAACTACTTTCATTTTTGGATTAGGCACCATAAACACATTCTCCTCATTAG
GATAAATGATATTGACAATATTTTTTTTTTGCAAGCAAAT
Found at i:1228929 original size:476 final size:476
Alignment explanation
Indices: 1226729--1230227 Score: 4026
Period size: 476 Copynumber: 7.4 Consensus size: 476
1226719 AAGCAAATCT
* *
1226729 TTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCATCAATTTT
1 TTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCACCATTTTT
* * *
1226794 GATGGAATCAAAGTTTGTCTC-TAAGA-AA-ACAAACATGAATAGTCATACTAATCCTTATTCTA
66 GATAGAATCAAAGTTTGTCTCTTAA-ATAAGACAAACATGAATAGTCATACTAATCCCTATTCTT
* * * * * * *
1226856 TTCTGGACTAAGC-CGTATAAACATAGTCTTCTAATAAGGATACATGATATTGATTCTTTTGTTT
130 TTCTGGATTAGGCAC-CATAAACATAGTCTTCTCATAAGGATACATGATATTGGTGCTTTGGTTT
* * * * *
1226920 CCCAAGAAAGGC-TTTCTTCCCACCAATTTTTGTGAAGTCTAAGTTTGTGCCTCAAATAAGACAA
194 CACAAGAAAGGCATTT-TTCCCACCAATTTTTGTAAAGTCTAAGTTCGTACCTCAAATGAGACAA
* *
1226984 ACATGGATTCTAGTAATAATCTTCTTTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCAT
258 ACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCAT
* * * *
1227049 TAGGATAAATGATATTGGTGATTTTCTTTTGCATGGAAACCTTTTCTTTGCCCTGTTTTCTTTAA
323 TAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
* * ** * * *
1227114 AATCAAAGTTCATCCCATAAATAAAACAAGCATAAATTCTCACAACAGTCTCAATTATTTTCAGG
388 AATCAAAGTTCATCCCATAAATAAGACAAGCATCAATTCTCGTAAAAGTCTCCATTATTTTCAAG
**
1227179 ATTAAGAACCTAAAACACATTCCC
453 ATTGGGAACCTAAAACACATTCCC
* * * *
1227203 TTCATTAGGGTAGATGCCATTGATGCTTTGGTGTCACAA-AAAAGCTTTTCTTTCC-CCTATTTT
1 TTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCACC-ATTTT
* * * * * * *
1227266 TTATAAAATCATAGTTTGTCTCTTAAATAAGACAAATATGAATACTCATACTAATCCCCATTATT
65 TGATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCTATTCTT
* * * *
1227331 TT-TAGGATTAGGCACCATAGACATAGTCGTCGCAT---GATACATAATATTGGTGCTTTGGTTT
130 TTCT-GGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACATGATATTGGTGCTTTGGTTT
* * *
1227392 CACAAGAAAAGC-TTTTTCTCACCAATTTTTGTAAAGTCTAAGTTCATACCTCAAATGAGACAAA
194 CACAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCGTACCTCAAATGAGACAAA
* * * * * * * * **
1227456 CATGGATTTTAGTAATGATCTTCTTTCATTTTATGATTAGGCATTATGAACATAGTCTCCTTAAA
259 CATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCATT
** * * *
1227521 AGGATAAATTTTATTGATCATTTTTTTTTGCATGTAAATCTTTTCTTTGCCCTATTTTCCTTAAA
324 AGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAA
* * *** * *
1227586 TTCAACA-TTCATCCTAGGGATAAGACAGGCATCAATTCTCATAACAA-TCTCCATTATTTTCAA
389 ATCAA-AGTTCATCCCATAAATAAGACAAGCATCAATTCTCGTAA-AAGTCTCCATTATTTTCAA
* *
1227649 GATTGGGAACCAAAAACACATTCTCT
452 GATTGGGAACCTAAAACACATTC-CC
* *
1227675 TTTATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTTTTTCCA-CAGTTTT
1 TTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCACCA-TTTT
* * * *
1227739 TGATAGAATCTAAGTTTGCCTCTTAAATAGGACAAACATTAATAGTCATACTAATCCCTATTCTT
65 TGATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCTATTCTT
* *
1227804 TT-TGGGATTAGGCACCATAAACATAGTAC-TCTCATAAGGATACATGATTTTGATGCTTTGGTT
130 TTCT-GGATTAGGCACCATAAACATAGT-CTTCTCATAAGGATACATGATATTGGTGCTTTGGTT
* * * * * *
1227867 TCATAAGAAAGGCATTTTTCTCACTAATTTTTGTAGAGTCTAAGTTCGTGCCTCAAATAAGACAA
193 TCACAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCGTACCTCAAATGAGACAA
* * * *
1227932 ATATGGATTCTAGTACA-GATCTTCATTCATTTTGTGATTAGCCACTATAGACACAATCTCCTCA
258 ACATGGATTCTAGTA-ATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCA
* * * * * * * * *
1227996 TTAGGATATATGATACTAATGATTTTCTTTTGCATGTAAATCTGTTCTCTACCCTATTCTCTTTA
322 TTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTA
* * * * * ** *
1228061 AAATCAAAGTTCATCCCTTAAATAAGCCATGCGTCAATTCTCGTAACAGTCTCTGTTATTTTTAA
387 AAATCAAAGTTCATCCCATAAATAAGACAAGCATCAATTCTCGTAAAAGTCTCCATTATTTTCAA
* *
1228126 GATTGGGAACCTAAAACAAAGTCCC
452 GATTGGGAACCTAAAACACATTCCC
* * * * * * * *
1228151 CTCTTTAGGATACAAGATATTGATGCTTTGGTGTTGCAAGAAATGCTTTTATTTCCACCGTTTTT
1 TTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCACCATTTTT
* *
1228216 GATAGAATCAAAG--TGTCTCTTAAATAAGACAAACATGAATACTCATACTAATCCCCATTCTTT
66 GATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCTATTCTTT
* * * * * * *
1228279 TCAGGATTAAGTACCATAAACATAGTCTTCTCATAAAGATACATCATGTTGGAGCTTTGGTTTCA
131 TCTGGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACATGATATTGGTGCTTTGGTTTCA
* * * *
1228344 CAAGAAAGGCCTTTTTCCCACCAATTTTTGTAAATTCTAAGTTC-AAGCCTCAAATAAGACAAAC
196 CAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCGTA-CCTCAAATGAGACAAAC
* * *
1228408 ATGGATTCTAGTAATAATCTTCTTTCATTTTGTAATTAGGCACTATAAACACATTCTCCTCATTA
260 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCATTA
* *
1228473 GGATAAATGATATTGATGATTTTCTTTTGCATGGAAATATTTTCTTTGTCCTATTTTCCTTAAAA
325 GGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAA
* * * *
1228538 TCAAAGTTCATCCCATAAATAAGACAAGTATCGATCCTCGTAAAAGTCTCCATTATTTTCAGGAT
390 TCAAAGTTCATCCCATAAATAAGACAAGCATCAATTCTCGTAAAAGTCTCCATTATTTTCAAGAT
*
1228603 TGGGAACCTAAAATACATTCCC
455 TGGGAACCTAAAACACATTCCC
* * * * * ** *
1228625 TTTATTTGGATACATGACATTGATGATTTGGTGTTGCAAGAAATGCTTTTCTTTCCTTCGTTTTT
1 TTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCACCATTTTT
* * * * * * *
1228690 GAAAAAATCATAGTTTATCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCTTACTATTT
66 GATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCTATTCTTT
* * * *
1228755 TCTGGATTAGGCACCATAAACGTAATCTTCTCATAAAGATGCATGATATTGGTGCTTTGGTTTCA
131 TCTGGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACATGATATTGGTGCTTTGGTTTCA
* * ** * * *
1228820 CAAGAGAGGCTTTTTTCCCATAAATATTTGTAAAGTCTAAGTTCGTACCTGAAATGAGCCAAACA
196 CAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCGTACCTCAAATGAGACAAACA
* * *
1228885 TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAAGCACTATAAACATATTCTCCTTAGTT-
261 TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCA-TTA
* * * * * * * *
1228949 GGATAAATAATATTGATGATTTTCTTTTGGATGAAAATATTTTCTCTGCCCTGTTTTCTTTGAAA
325 GGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAA
* * *
1229014 TCAAAGTTCATCCCATAAATAAGACAAGCATCGATTCTTGTAACCAA-TCTCCATTATTTTTAAG
390 TCAAAGTTCATCCCATAAATAAGACAAGCATCAATTCTCGTAA--AAGTCTCCATTATTTTCAAG
* *
1229078 ATTGGGAAACTAAAACGCATTCCC
453 ATTGGGAACCTAAAACACATTCCC
* * * * * * * *
1229102 CTCATTAGGTTACTTGACATTGATGCCTTAGG-GCCCCAAGAAAAGCTTTTATTTCCACC-GTTT
1 TTCATTAGGATACATGACATTGATG-CTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCACCATTTT
* * * * * *
1229165 TGATAGAATCAAAGTTTGTCTTTTAAGTAAGACAAACATGAATACTCATACTAATCCTTATTATG
65 TGATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCTATTCTT
* * * * * *
1229230 TTATGGATTAGGTACCATAAAC-TCAGTCTTCTTATAAGGATACACGATATTAGTTCTTTGGTTT
130 TTCTGGATTAGGCACCATAAACAT-AGTCTTCTCATAAGGATACATGATATTGGTGCTTTGGTTT
*** * * *
1229294 TGTAAGAAAGGCATTTTTCCCACCAATTTTTGAAAAGTATAAGTTC-TAACCACAAATGAGACAA
194 CACAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCGT-ACCTCAAATGAGACAA
* * * *
1229358 ACATGGATTCTAGTAATGATCTTTATTCATTTTGCGATTAGGCACCATAAACACATTCTCCTGAT
258 ACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCAT
* * * * * * *
1229423 TAGGATAAATGATACTGATGTTTTTCTTTTGCATGAAAATATTTTCTTTACCTTATTTTCCTTCA
323 TAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
** * * *
1229488 AATCAAAGTTCATCCTTTAAATAAGACATGCATCGATTCTCGTAATAGTCTCCATT-TTTTCCAA
388 AATCAAAGTTCATCCCATAAATAAGACAAGCATCAATTCTCGTAAAAGTCTCCATTATTTT-CAA
* *
1229552 AATTGGGAACCAAAAACACATTCCC
452 GATTGGGAACCTAAAACACATTCCC
* * * * *
1229577 TTCATTAGGATACATGACGTTGATGCTTTGGTAAT-GCAAGAAAAGCTTTTCATTCTACCACTTT
1 TTCATTAGGATACATGACATTGATGCTTTGGT-GTCGCAAGAAAAGCTTTTCTTTCCACCATTTT
* * * * *
1229641 TGATACAATGAAGGTTTGCCTCTTAAATAGGACAAACATGAATAGTCATACTAATCCCTATTCTT
65 TGATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCTATTCTT
* * *** * *
1229706 TT-TGAGATTAGGCACCATAAACATAGTCTTCTCTTTAGGATACGCAATATTGATGTTTTGGTTT
130 TTCTG-GATTAGGCACCATAAACATAGTCTTCTCATAAGGATACATGATATTGGTGCTTTGGTTT
** **
1229770 TGCAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCGTGTCTCAAATGAGACAAA
194 CACAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCGTACCTCAAATGAGACAAA
* * * * * *
1229835 CATGGATTCTAGTAACGATCTTTATTCATTTTGTGATTAAGCACTATAAACATATTCTCCTTAGT
259 CATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCATT
* **
1229900 AAGATAAATGATATTGAT-AGTTTTCTTTTGCACAGAAATCTTTTCTTTGCCCTATTTTCCTTAA
324 AGGATAAATGATATTGATGA-TTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
* * * * * *
1229964 TATCAAAGTTCATCCCTTAAAAAAGACAAGCATCAGTTCTC-AAAATAG-CTACCATTATTCTCA
388 AATCAAAGTTCATCCCATAAATAAGACAAGCATCAATTCTCGTAAA-AGTCT-CCATTATTTTCA
* * ** *
1230027 GGATTGGAAATGTAAAACGCATTCCC
451 AGATTGGGAACCTAAAACACATTCCC
* * * *
1230053 TTCATTAGGATACATGACATTGTTGCTTTGGTGTCACAGGAAAAGCTTCTCTTTCCACCATTTTT
1 TTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCACCATTTTT
*
1230118 GATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACTTGAATAGTCATACTAATCCCCT-TTCTT
66 GATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAAT-CCCTATTCTT
* *
1230182 TTCAGGA-TATGGCACCATAAACATAGTCTTCTCACAAGGATACATG
130 TTCTGGATTA-GGCACCATAAACATAGTCTTCTCATAAGGATACATG
1230228 TAGACACCTC
Statistics
Matches: 2541, Mismatches: 433, Indels: 100
0.83 0.14 0.03
Matches are distributed among these distances:
471 221 0.09
472 74 0.03
473 145 0.06
474 453 0.18
475 137 0.05
476 1199 0.47
477 305 0.12
478 7 0.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (476 bp):
TTCATTAGGATACATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTCTTTCCACCATTTTT
GATAGAATCAAAGTTTGTCTCTTAAATAAGACAAACATGAATAGTCATACTAATCCCTATTCTTT
TCTGGATTAGGCACCATAAACATAGTCTTCTCATAAGGATACATGATATTGGTGCTTTGGTTTCA
CAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGTTCGTACCTCAAATGAGACAAACA
TGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACTATAAACACATTCTCCTCATTAG
GATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAAT
CAAAGTTCATCCCATAAATAAGACAAGCATCAATTCTCGTAAAAGTCTCCATTATTTTCAAGATT
GGGAACCTAAAACACATTCCC
Found at i:1230486 original size:20 final size:21
Alignment explanation
Indices: 1230461--1230517 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
1230451 TTTTCACAAT
*
1230461 TTGTATCGATGCATTGT-TCA
1 TTGTATCGATACATTGTCTCA
*
1230481 TTGTATCGATACGTT-TCTCA
1 TTGTATCGATACATTGTCTCA
1230501 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
1230518 ATCGATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.46
Consensus pattern (21 bp):
TTGTATCGATACATTGTCTCA
Found at i:1230517 original size:13 final size:13
Alignment explanation
Indices: 1230499--1230528 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1230489 ATACGTTTCT
1230499 CATTGTATCGATA
1 CATTGTATCGATA
1230512 CATTGTATCGATA
1 CATTGTATCGATA
1230525 CATT
1 CATT
1230529 TTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1230596 original size:20 final size:20
Alignment explanation
Indices: 1230544--1230617 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
1230534 TTTACCTAGA
*
1230544 TGTATCGATACAATT-TGCAT
1 TGTATCGATAC-ATTGTACAT
1230564 TGTATCGATACATTGCT-CAT
1 TGTATCGATACATTG-TACAT
* *
1230584 TGTATCGATACATTGTAAAA
1 TGTATCGATACATTGTACAT
1230604 TGTATCGATACATT
1 TGTATCGATACATT
1230618 CAAGCATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.08
20 44 0.90
21 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTGTACAT
Found at i:1232989 original size:30 final size:28
Alignment explanation
Indices: 1232955--1233010 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
1232945 CAAAATATAA
1232955 ATTTTTCATCGGGGATACTCCAACCCTGTT
1 ATTTTTCA--GGGGATACTCCAACCCTGTT
*
1232985 ATTTTTGAGGGGATACTCCAACCCTG
1 ATTTTTCAGGGGATACTCCAACCCTG
1233011 GTTTTATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 18 0.72
30 7 0.28
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (28 bp):
ATTTTTCAGGGGATACTCCAACCCTGTT
Found at i:1233057 original size:51 final size:51
Alignment explanation
Indices: 1232992--1233122 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 51
1232982 GTTATTTTTG
* * *
1232992 AGGGGATACTCCAACCCTGGTTTTATTTCTAAAATACTAATTTTCCACAAT
1 AGGGCATACTCCAACCCTGATTTTATTTCCAAAATACTAATTTTCCACAAT
* * * *
1233043 CGTGCATACTCCAACTCTGATTTTATTTCCAAAATACTAATTTTTCACAAT
1 AGGGCATACTCCAACCCTGATTTTATTTCCAAAATACTAATTTTCCACAAT
* *
1233094 AGGGGATACTCTAACCC---TTTTATTTCCAA
1 AGGGCATACTCCAACCCTGATTTTATTTCCAA
1233123 GGGGATACTT
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 12 0.18
51 56 0.82
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.37
Consensus pattern (51 bp):
AGGGCATACTCCAACCCTGATTTTATTTCCAAAATACTAATTTTCCACAAT
Found at i:1233131 original size:79 final size:79
Alignment explanation
Indices: 1233048--1233307 Score: 258
Period size: 79 Copynumber: 3.3 Consensus size: 79
1233038 ACAATCGTGC
* * * *
1233048 ATACTCCAACTCTGATTTTATTTCCAAAATACTAATTTTTCACAATAGGGGATACTCTAACCCTT
1 ATACTCCAACCCCGATTTTATTTCCAAAATACTAATTTTTCACAATAGGGGATACTCCAACCCTG
* *
1233113 TTATTTCCAAGGGG
66 TTATTTTCGAGGGG
* *** * * * * *
1233127 ATACTTCAACCCCGGCCTTATTT-CTAAAT-CATCGATTTTTCACAATCGAGAATACTCCAACCC
1 ATACTCCAACCCCGATTTTATTTCCAAAATAC-T-AATTTTTCACAATAGGGGATACTCCAACCC
* *
1233190 CGTTATTTTTGAGGGG
64 TGTTATTTTCGAGGGG
* * * * *
1233206 ATACTCCAACCTCGATTTCATTTTCAAAATACCAATTTTT-ATAATTA-GGGATACTCCAACCCT
1 ATACTCCAACCCCGATTTTATTTCCAAAATACTAATTTTTCACAA-TAGGGGATACTCCAACCCT
1233269 GTTATTTTCGAGGGG
65 GTTATTTTCGAGGGG
*
1233284 ATACTTCAACCCCGATTTTATTTC
1 ATACTCCAACCCCGATTTTATTTC
1233308 TGGAACACCA
Statistics
Matches: 140, Mismatches: 36, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
77 1 0.01
78 56 0.40
79 77 0.55
80 5 0.04
81 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (79 bp):
ATACTCCAACCCCGATTTTATTTCCAAAATACTAATTTTTCACAATAGGGGATACTCCAACCCTG
TTATTTTCGAGGGG
Found at i:1233165 original size:130 final size:127
Alignment explanation
Indices: 1232940--1233187 Score: 295
Period size: 130 Copynumber: 1.9 Consensus size: 127
1232930 TCCCGGTTTC
* ***
1232940 ATTTCCAAAATATAAATTTTTCATCGGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCCA
1 ATTTCCAAAATATAAATTTTTCATAGGGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCA
* ** * *
1233005 ACCCTGGTTTTATTTCTAAAATACTAATTTTCCACAATCGTGCATACTCCAACTCTGATTTT
66 ACCCCGGCCTTATTTCTAAAATACTAATTTTCCACAATCGAGAATACTCCAACTCTGATTTT
* *
1233067 ATTTCCAAAATACT-AATTTTTCACAATAGGGGATACTCTAACCCTTTTATTTCCAAGGGGATAC
1 ATTTCCAAAATA-TAAATTTTT--C-ATAGGGGATACTCCAACCCTGTTATTTCCAAGGGGATAC
* * *
1233131 TTCAACCCCGGCCTTATTTCT-AAAT-CATCGATTTTTCACAATCGAGAATACTCCAAC
62 TCCAACCCCGGCCTTATTTCTAAAATAC-T-AATTTTCCACAATCGAGAATACTCCAAC
1233188 CCCGTTATTT
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
127 19 0.19
128 2 0.02
129 6 0.06
130 74 0.73
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (127 bp):
ATTTCCAAAATATAAATTTTTCATAGGGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCA
ACCCCGGCCTTATTTCTAAAATACTAATTTTCCACAATCGAGAATACTCCAACTCTGATTTT
Found at i:1233282 original size:78 final size:79
Alignment explanation
Indices: 1233048--1233341 Score: 242
Period size: 78 Copynumber: 3.7 Consensus size: 79
1233038 ACAATCGTGC
* * * * *
1233048 ATACTCCAA-CTCTGATTTTATTTCCAAAATACTAATTTTTCACAATAGGGGATACTCTAACCCT
1 ATACTCCAACCCCGGATTTTATTTTCAAAATACCAATTTTTCACAATA-GGGATACTCCAACCCT
* * *
1233112 TTTATTTCCAAGGGG
65 GTTATTTTCGAGGGG
* ** * * * * *
1233127 ATACTTCAACCCCGG-CCTTA-TTTCTAAATCATCGATTTTTCACAATCGAGAATACTCCAACCC
1 ATACTCCAACCCCGGATTTTATTTTCAAAAT-ACCAATTTTTCACAATAG-GGATACTCCAACCC
* *
1233190 CGTTATTTTTGAGGGG
64 TGTTATTTTCGAGGGG
* * *
1233206 ATACTCCAACCTC-GATTTCATTTTCAAAATACCAATTTTT-ATAATTAGGGATACTCCAACCCT
1 ATACTCCAACCCCGGATTTTATTTTCAAAATACCAATTTTTCACAA-TAGGGATACTCCAACCCT
1233269 GTTATTTTCGAGGGG
65 GTTATTTTCGAGGGG
* ** * * * *
1233284 ATACTTCAACCCC-GATTTTA-TTTCTGGAACACCAATTTTCCATAATCGGGATACTCCA
1 ATACTCCAACCCCGGATTTTATTTTC-AAAATACCAATTTTTCACAATAGGGATACTCCA
1233342 GCCCCGTTGT
Statistics
Matches: 168, Mismatches: 39, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
77 4 0.02
78 79 0.47
79 74 0.44
80 11 0.07
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (79 bp):
ATACTCCAACCCCGGATTTTATTTTCAAAATACCAATTTTTCACAATAGGGATACTCCAACCCTG
TTATTTTCGAGGGG
Found at i:1235758 original size:476 final size:472
Alignment explanation
Indices: 1234325--1235939 Score: 1965
Period size: 476 Copynumber: 3.4 Consensus size: 472
1234315 AACAATACAC
* * * * * *
1234325 GATAATGATGCTTTGGTTTCGCAATAAAGGGTTTCTTCCTACCAATTTTTGTAAAATCTAAGTTC
1 GATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTTTTCCCACCAATTTTTGTAAAGTCTAAGTTC
*
1234390 GTGA-CTCAAATGAGACAAACATGGATTCTAGTAATGA-CCTTCATTCATTTTGTGATCACGCAC
66 GT-ATCTCAAATGAGACAAACATGGATTCTAGTAATGATCC-TCATTCATTTTGTGATTACGCAC
* *
1234453 TACAAACACATTCTCCTCAGTAGGATAAATGATATTGACGATTTTCTTTTGCATGGAAATCTTTT
129 TATAAACACATTCTCCTCAGTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTT
* *
1234518 CTTTACCCTATTTTCCATAAAATTAAAATTCATCCCTTAAATAAGACAAGCATCGATTCTTGTAA
194 CTTTACCCTATTTTCCATAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGATTCTTGTAA
* * *
1234583 CAATCTCCATTATTTTC-GGCATTGGGAAACTAAAACACATTCCCATCATTAGGATACATGACAT
259 TAGTCTCCATTATTTTCAGG-ATT-GGAAACTAAAACACATTCCCTTCATTAGGATACATGACAT
** * * *
1234647 TGATGCCTTAAG-GTCCTAAGAAAAGCTTTTATTTCCACCGTTTTTTATAGAATCAAAGTTTGTC
322 TGATG-CTTTGGTGTAC-AAGAAAAGCTTTTCTTTCCACCGTTTTTTATACAATCAAAGTTTGTC
* * * *
1234711 TCTTAAGTAAGACAAACATGAATAGTCATACCAATCCCCATTATTTTAAGGATTAGGAACCATAA
385 TCTTAAATAAGACAAACATGAATAGTCATACTAATCCCCATTTTTTTAAGG-TTAGGCACCATAA
** *
1234776 AGTTAGTCTTCTCATAAGGATACAC
449 ACATAGTCTTCTCATAAGGAT-CAT
* * * * * * *
1234801 GATATTGGTGCTTTGGTTTTGTAAGAAAGGCTTTTTTCTCTCCAACTTTTGTAAAGTATAAGTTT
1 GATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTTTTCCCACCAATTTTTGTAAAGTCTAAG-TT
** * * * *
1234866 CG-GCCACAAATGAGACAAACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCGCT
65 CGTATCTCAAATGAGACAAACATGGATTCTAGTAATGATCCTCATTCATTTTGTGATTACGCACT
* * * * * * *
1234930 ATAAACACATTCTCCTCATTAGGATAAATGATATAGATGTTTTTCTTTTGCTTGAAAATATTTTA
130 ATAAACACATTCTCCTCAGTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTC
* * * * *
1234995 TTTACCCTA-TTTCCTTAAAATCAAAGTTCATCTCATAAATAAGACATGCATCGATTCTCGTAAT
195 TTTACCCTATTTTCCATAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGATTCTTGTAAT
* * * * *
1235059 AGTTTCCATT-TTTTCCAAGATTGGGAACTAAAAACACATTCCCTTCATTAGGATACTTGATATT
260 AGTCTCCATTATTTT-CAGGATTGGAAACT-AAAACACATTCCCTTCATTAGGATACATGACATT
* * * * *
1235123 GATGCTTTGGTGATACAAGAAAAGCTTTTCATTCCACCATGTTTGATACAATCAAAGTTTGCCTC
323 GATGCTTTGGTG-TACAAGAAAAGCTTTTCTTTCCACCGTTTTTTATACAATCAAAGTTTGTCTC
* * ** *
1235188 TTAAATAGGACAAACATGCATAGTCATACTAATCCCCATTCTTTTCGAGATTAGGCACCATAAAC
387 TTAAATAAGACAAACATGAATAGTCATACTAATCCCCATT-TTTTTAAGGTTAGGCACCATAAAC
* ** *
1235253 ACAGTCTTCTTTTTAGGAT-AT
451 ATAGTCTTCTCATAAGGATCAT
* *
1235274 GCGATATTGATGTTTTGGTTTCGCAAGAAAGGCATTTTTCCCACCAATTTTTGTAAAGTCTAAGT
1 --GATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTTTTCCCACCAATTTTTGTAAAGTCTAAGT
* * * * * *
1235339 TCGTATCTCAAATGGGACAAACATTGATTCTAGTAACGATCCTCATTCATTTTGTCATTAAGCAA
64 TCGTATCTCAAATGAGACAAACATGGATTCTAGTAATGATCCTCATTCATTTTGTGATTACGCAC
* *
1235404 TATAAACATATTCTCCTTAGTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTT
129 TATAAACACATTCTCCTCAGTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTT
* * * * **
1235469 CTTTGCCCTATTTTTCATAAAGTCAAAGTTCATCCCTTAAAAAAGACAAGCATC-AGTTCTTAAA
194 CTTTACCCTATTTTCCATAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGA-TTCTTGTA
* * *
1235533 ATAGTCTCCATTATTTTCAGGATTAGAAACCTAATACGCATTCCCTTCATTAGGATACATGACAT
258 ATAGTCTCCATTATTTTCAGGATTGGAAA-CTAAAACACATTCCCTTCATTAGGATACATGACAT
* * ** * * *
1235598 TGTTGCTTTGGTGTTGCAAGAAAAGCTTTTCTTTCCTTCGTTTTTTAAATAATCATAGTTTGTCT
322 TGATGCTTTGGTG-TACAAGAAAAGCTTTTCTTTCCACCGTTTTTTATACAATCAAAGTTTGTCT
* * *
1235663 CTTAAATAAGACAAACATGAATAGTCATACTAATCCCTACTTTTTTTTAGGTTAGGCACCATAAT
386 CTTAAATAAGACAAACATGAATAGTCATACTAATCCCCA-TTTTTTTAAGGTTAGGCACCATAAA
1235728 CATAGTCTTCTCATAAGGATGCAT
450 CATAGTCTTCTCATAAGGAT-CAT
** * * * * *
1235752 GATATTGGCGCTTTCGTTTCACAAGAGAGGCTTTTTTCCCACAAATTTTTGTCAAGTCTAAGTTC
1 GATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTTTTCCCACCAATTTTTGTAAAGTCTAAGTTC
* * *
1235817 GT-TCCTCAAATGAGACAAACATGGATTCTAGTAATGAT-TTCATTTATTTTGTGATTACGCATT
66 GTAT-CTCAAATGAGACAAACATGGATTCTAGTAATGATCCTCATTCATTTTGTGATTACGCACT
* *
1235880 GTAAACACATTCTCCTCAGTAGGATAAATGATATTGATGATTTTCTTTTGCATGTAAATC
130 ATAAACACATTCTCCTCAGTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATC
1235940 AAAGTTTATC
Statistics
Matches: 957, Mismatches: 162, Indels: 41
0.82 0.14 0.04
Matches are distributed among these distances:
473 1 0.00
474 18 0.02
475 446 0.47
476 477 0.50
477 13 0.01
478 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (472 bp):
GATATTGATGCTTTGGTTTCGCAAGAAAGGCTTTTTTCCCACCAATTTTTGTAAAGTCTAAGTTC
GTATCTCAAATGAGACAAACATGGATTCTAGTAATGATCCTCATTCATTTTGTGATTACGCACTA
TAAACACATTCTCCTCAGTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTCT
TTACCCTATTTTCCATAAAATCAAAGTTCATCCCTTAAATAAGACAAGCATCGATTCTTGTAATA
GTCTCCATTATTTTCAGGATTGGAAACTAAAACACATTCCCTTCATTAGGATACATGACATTGAT
GCTTTGGTGTACAAGAAAAGCTTTTCTTTCCACCGTTTTTTATACAATCAAAGTTTGTCTCTTAA
ATAAGACAAACATGAATAGTCATACTAATCCCCATTTTTTTAAGGTTAGGCACCATAAACATAGT
CTTCTCATAAGGATCAT
Found at i:1236362 original size:241 final size:242
Alignment explanation
Indices: 1235935--1236460 Score: 804
Period size: 241 Copynumber: 2.2 Consensus size: 242
1235925 TTTTGCATGT
* * **
1235935 AAATCAAAGTTTATCCCTTAAATAGGACAAGCATCGATTCTCGTAACAATCTTTATCCTTATGCT
1 AAATCAAAGTTTATCCCTTAAATAAGACAAGCATCGATTCTCATAACAATCCCTATCCTTATGCT
* * *
1236000 TCCCACCACTTTTTGTAATGTCTAAGTTCGTGCCTCAAATGAGACAAACATGGATTGTAGTAATC
66 TCCCACCAATTTTTGTAATGTCTAAGTTCATGCCTCAAATGAGACAAACATGGATTCTAGTAATC
* * *
1236065 ATTTACATTTATTTAGTGATTAAGCACTATAAACACATTCTCCTCAGTAGGATAAATGATATTGA
131 ATTTACATTCATTTAGTGATTAAGCACTATAAACACATTCTCCTCAGCAAGATAAATGATATTGA
1236130 TGATTTTCTTTTGCAT-GAAAATCTTTTCTTTACCCTATTTTCCTTA
196 TGATTTTCTTTTGCATGGAAAATCTTTTCTTTACCCTATTTTCCTTA
1236176 AAATCAAAGTTTATCCCTTAAATAAGACAAGCATCGATTCTCATAACAATCCCTATCCTTATGCT
1 AAATCAAAGTTTATCCCTTAAATAAGACAAGCATCGATTCTCATAACAATCCCTATCCTTATGCT
* * *
1236241 TCCCACCAATTTTTGTAATGTCTAAGTTTATGCCTTAAATGAGACAAACATGGATTCTAGTAATG
66 TCCCACCAATTTTTGTAATGTCTAAGTTCATGCCTCAAATGAGACAAACATGGATTCTAGTAATC
* * *
1236306 ATCTT-CATTCATTTTGTGATTATGCACTATAAACACATTCTCCTCAGCAAGATAAATGATATTT
131 AT-TTACATTCATTTAGTGATTAAGCACTATAAACACATTCTCCTCAGCAAGATAAATGATATTG
* * * * * *
1236370 ATGTTTTTCTTTTGCATGGAAATTTTTTTGTTTGCCCTATTTTTCTTA
195 ATGATTTTCTTTTGCATGGAAAATCTTTTCTTTACCCTATTTTCCTTA
* * *
1236418 AAATCAAAGTTTACCCCTTATATAAGACAAGCATCAATTCTCA
1 AAATCAAAGTTTATCCCTTAAATAAGACAAGCATCGATTCTCA
1236461 AAATACTATC
Statistics
Matches: 258, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
241 191 0.74
242 67 0.26
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (242 bp):
AAATCAAAGTTTATCCCTTAAATAAGACAAGCATCGATTCTCATAACAATCCCTATCCTTATGCT
TCCCACCAATTTTTGTAATGTCTAAGTTCATGCCTCAAATGAGACAAACATGGATTCTAGTAATC
ATTTACATTCATTTAGTGATTAAGCACTATAAACACATTCTCCTCAGCAAGATAAATGATATTGA
TGATTTTCTTTTGCATGGAAAATCTTTTCTTTACCCTATTTTCCTTA
Found at i:1238794 original size:158 final size:158
Alignment explanation
Indices: 1238606--1238938 Score: 367
Period size: 158 Copynumber: 2.1 Consensus size: 158
1238596 GTTACAAGAG
* * * *
1238606 ATTGATGCTTTGGGGTT-GCAAGAAATGCTTTTTTTTCCATC-GCTTTTGATAGAA-TCAAAG-T
1 ATTGATGCTTT-GGTTTCGCAAGAAATGC-TTTTTTGCCACCAACTTTTG-TA-AAGTCAAAGCT
* * * *
1238667 -TTACCTCATCAAT-AGGACAAACATGAATAGTCCTACTAAT-CCCATTCTTCTC-CGGATTAGG
62 CGTACCTCA--AATGA-GACAAACATGAATAGTCATACTAATGCCCATTCTTCTCAAGAATT-GG
*
1238728 CACCCTAAACATAGTATTCTCATAAGGATACACGAT
123 CACCATAAACATAGTATTCTCATAAGGATACACGAT
* * * *
1238764 GTTGATGCTTTGGTTTCGCAAGAAATGCTTTTTTGCCACCAATTTTTGTAAAGTCTAAGCTCGTG
1 ATTGATGCTTTGGTTTCGCAAGAAATGCTTTTTTGCCACCAACTTTTGTAAAGTCAAAGCTCGTA
* * *
1238829 CCTCAAATGAGACAAACATGAATAGTCATACTAATGCCTATTTTTTTCAAGAATTGGCACCATAA
66 CCTCAAATGAGACAAACATGAATAGTCATACTAATGCCCATTCTTCTCAAGAATTGGCACCATAA
* *
1238894 ACATAGTATTCTCATAAGGATATATGAT
131 ACATAGTATTCTCATAAGGATACACGAT
*
1238922 ATTGGTGCTTTGGTTTC
1 ATTGATGCTTTGGTTTC
1238939 AAGGCTTTTT
Statistics
Matches: 147, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
156 2 0.01
157 48 0.33
158 87 0.59
159 10 0.07
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (158 bp):
ATTGATGCTTTGGTTTCGCAAGAAATGCTTTTTTGCCACCAACTTTTGTAAAGTCAAAGCTCGTA
CCTCAAATGAGACAAACATGAATAGTCATACTAATGCCCATTCTTCTCAAGAATTGGCACCATAA
ACATAGTATTCTCATAAGGATACACGAT
Found at i:1240351 original size:13 final size:13
Alignment explanation
Indices: 1240333--1240358 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1240323 ACATTTTGGG
1240333 ATGTATCGATACA
1 ATGTATCGATACA
1240346 ATGTATCGATACA
1 ATGTATCGATACA
1240359 TAATGTGTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1240353 original size:33 final size:32
Alignment explanation
Indices: 1240311--1240378 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1240301 CGTTACAAGC
**
1240311 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATAATGGG-TGTATCGATA
*
1240344 CAATGTATCGATACATAATGTGTGTATCGATA
1 CAATGTATCGATACATAATGGGTGTATCGATA
1240376 CAA
1 CAA
1240379 ATTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (32 bp):
CAATGTATCGATACATAATGGGTGTATCGATA
Found at i:1240461 original size:20 final size:21
Alignment explanation
Indices: 1240411--1240463 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1240401 GCCAATGACC
**
1240411 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
* *
1240432 AGTATTGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
1240452 TGTATCGATACA
1 TGTATCGATACA
1240464 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:1240469 original size:13 final size:13
Alignment explanation
Indices: 1240451--1240475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1240441 ACATTTGGTC
1240451 ATGTATCGATACA
1 ATGTATCGATACA
1240464 ATGTATCGATAC
1 ATGTATCGATAC
1240476 TGTGCAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1247977 original size:124 final size:124
Alignment explanation
Indices: 1247756--1248009 Score: 481
Period size: 124 Copynumber: 2.0 Consensus size: 124
1247746 TAGCCAATGA
1247756 GTTTGGACCATGTGGCTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAGATGGGTT
1 GTTTGGACCATGTGGCTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAGATGGGTT
*
1247821 TTGACATGTGGCAATTGATATTTAACATGAATCCTGACCACTTATGATGCAAAAAACTC
66 TTGACATATGGCAATTGATATTTAACATGAATCCTGACCACTTATGATGCAAAAAACTC
* *
1247880 TTTTGGACCTTGTGGCTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAGATGGGTT
1 GTTTGGACCATGTGGCTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAGATGGGTT
1247945 TTGACATATGGCAATTGATATTTAACATGAATCCTGACCACTTATGATGCAAAAAACTC
66 TTGACATATGGCAATTGATATTTAACATGAATCCTGACCACTTATGATGCAAAAAACTC
1248004 GTTTGG
1 GTTTGG
1248010 CAAAGGAAGA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 126 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (124 bp):
GTTTGGACCATGTGGCTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAGATGGGTT
TTGACATATGGCAATTGATATTTAACATGAATCCTGACCACTTATGATGCAAAAAACTC
Found at i:1248139 original size:13 final size:13
Alignment explanation
Indices: 1248121--1248146 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1248111 ACAAAGATCC
1248121 ATGTATCGATACA
1 ATGTATCGATACA
1248134 ATGTATCGATACA
1 ATGTATCGATACA
1248147 TTGAGCAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1248146 original size:33 final size:33
Alignment explanation
Indices: 1248104--1248166 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1248094 TTCCCAGATA
* *
1248104 TATCGATACAAAGATCCATGTATCGATACAATG
1 TATCGATACAAAGAGCAATGTATCGATACAATG
**
1248137 TATCGATACATTGAGCAATGTATCGATACA
1 TATCGATACAAAGAGCAATGTATCGATACA
1248167 TTTCCTTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (33 bp):
TATCGATACAAAGAGCAATGTATCGATACAATG
Found at i:1248231 original size:32 final size:32
Alignment explanation
Indices: 1248185--1248260 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
1248175 GCAGTAGCTT
* * *
1248185 TGTAGCGATACATTGTATCGATTCAACAGTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
1248217 TGTATCGATACATTGTATCTATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1248249 TGTATCGATACA
1 TGTATCGATACA
1248261 ATTACTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Done.